/*
 *  Copyright 2013-2021 by the individuals mentioned in the source code history
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 *   Unless required by applicable law or agreed to in writing, software
 *   distributed under the License is distributed on an "AS IS" BASIS,
 *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 */

#include <algorithm>
#include <stdarg.h>
#include <limits>
#include <random>
#include <fstream>
#include <forward_list>
#include <map>

#include "glue.h"
#include "Compute.h"
#include "omxState.h"
#include "omxExportBackendState.h"
#include "omxRFitFunction.h"
#include "matrix.h"
#include "omxState.h"
#include "omxData.h"
#include <Eigen/Cholesky>
#include <Eigen/QR>
#include <Eigen/CholmodSupport>
#include <Eigen/Dense>
#include <RcppEigenWrap.h>
#include "finiteDifferences.h"
#include "autoTune.h"
#include "minicsv.h"
#include "LoadDataAPI.h"
#include "EnableWarnings.h"

void pda(const double *ar, int rows, int cols);

static const char *statusCodeLabels[] = { // see ComputeInform type
		"OK", "OK/green",
		"infeasible linear constraint",
		"infeasible non-linear constraint",
		"iteration limit/blue",
		"not convex/red",
		"nonzero gradient/red",
		"bad deriv",
		"?",
		"internal error",
		"infeasible start"
};

SEXP allocInformVector(int size)
{
	return makeFactor(Rf_allocVector(INTSXP, size),
			  OMX_STATIC_ARRAY_SIZE(statusCodeLabels), statusCodeLabels);
}

void FitContext::calcNumFree()
{
  std::vector<bool> &po = profiledOutZ;
  u_numFree = numParam - std::count(po.begin(), po.end(), true);
  freeToIndexMap.clear();
  freeToParamMap.resize(u_numFree);
  for (int fx=0, px=0; px < numParam; ++px) {
    if (po[px]) continue;
    freeToIndexMap.emplace(varGroup->vars[px]->name, fx);
    freeToParamMap[fx++] = px;
  }

  // ???? TODO
	// for (int cx=0; cx < int(childList.size()); ++cx) {
	// 	childList[cx]->prepConstraints();
	// }
}

void FitContext::queue(HessianBlock *hb)
{
	if (hb->vars.size() == 0) {
		delete hb;
		return;
	}

	// std::cout << "queue " << allBlocks.size() << " var map: ";
	// for (int vm=0; vm < (int) hb->vars.size(); ++vm) {
	// 	std::cout << vm << ":" << hb->vars[vm] << ",";
	// }
	// std::cout << "\n" << hb->mat << "\n";

	if (OMX_DEBUG) {
		std::vector<int>::iterator it = std::unique(hb->vars.begin(), hb->vars.end());
		if (std::distance(hb->vars.end(),it) != 0) {
			mxThrow("HessianBlock var mapping is not 1-to-1");
		}
		int prev = hb->vars[0];
		for (int vx=1; vx < int(hb->vars.size()); vx++) {
			if (prev > hb->vars[vx]) {
				mxThrow("hb->vars must be sorted");
			}
			prev = hb->vars[vx];
		}
	}

	minBlockSize = std::max(int(hb->vars.size()), minBlockSize);
	allBlocks.push_back(hb);
}

void FitContext::analyzeHessianBlock(HessianBlock *hb)
{
	for (size_t vx=0; vx < hb->vars.size(); ++vx) {
		HessianBlock *hb2 = blockByVar[ hb->vars[vx] ];
		if (!hb2) continue;

		for (size_t vx2=0; vx2 < hb2->vars.size(); ++vx2) {
			blockByVar[ hb2->vars[vx2] ] = NULL;
		}
		estNonZero -= hb2->estNonZero();

		if (hb->vars.size() < hb2->vars.size()) std::swap(hb, hb2);

		// std::cout << "hb: ";
		// for (int i : hb->vars) std::cout << i << ' ';
		// std::cout << "\nhb2: ";
		// for (int i : hb2->vars) std::cout << i << ' ';
		// std::cout << "\n";
		bool inc = std::includes(hb->vars.begin(), hb->vars.end(), hb2->vars.begin(), hb2->vars.end());
		//std::cout << "includes " << inc << "\n";
		if (inc) {
			hb->subBlocks.push_back(hb2);
		} else {
			HessianBlock *par2 = new HessianBlock;
			mergeBlocks.push_back(par2);
			par2->merge = true;
			par2->vars = hb->vars;
			par2->vars.insert(par2->vars.end(), hb2->vars.begin(), hb2->vars.end());
			std::inplace_merge(par2->vars.begin(), par2->vars.begin() + hb->vars.size(), par2->vars.end());
			int nsize = std::unique(par2->vars.begin(), par2->vars.end()) - par2->vars.begin();
			par2->vars.resize(nsize);
			par2->mat.resize(nsize, nsize);
			par2->mat.triangularView<Eigen::Upper>().setZero();
			par2->subBlocks.push_back(hb);
			par2->subBlocks.push_back(hb2);
			analyzeHessianBlock(par2);
			return;
		}
	}

	for (size_t vx=0; vx < hb->vars.size(); ++vx) {
		blockByVar[ hb->vars[vx] ] = hb;
	}
	estNonZero += hb->estNonZero();
	maxBlockSize = std::max(int(hb->vars.size()), maxBlockSize);
	//mxLog("queue maxBlocksize %d sparse %f", maxBlockSize, estNonZero / double(numParam * numParam));
}

void FitContext::analyzeHessian()
{
	// If we knew the minBlockSize was large then we wouldn't even
	// try to build merge blocks.
	// If maxBlockSize is greater than some threshold then we should
	// also give up.

	if (blockByVar.size()) return;

	blockByVar.assign(numParam, NULL);

	for (size_t bx=0; bx < allBlocks.size(); ++bx) {
		analyzeHessianBlock(allBlocks[bx]);
	}
}

void FitContext::negateHessian()
{
	// this assumes that we haven't processed the blocks yet, need to check TODO
	for (size_t bx=0; bx < allBlocks.size(); ++bx) {
		allBlocks[bx]->mat *= -1.0;
	}
}

void FitContext::refreshDenseHess()
{
	if (haveDenseHess) return;

	int numFree = getNumFree();
	hess.resize(numFree, numFree);

	hess.triangularView<Eigen::Upper>().setZero();

	// if allBlocks.size() == 0 then what? TODO
	for (size_t bx=0; bx < allBlocks.size(); ++bx) {
		HessianBlock *hb = allBlocks[bx];

		std::vector<int> &map = hb->vars;
		size_t bsize = map.size();

		for (size_t v1=0; v1 < bsize; ++v1) {
			for (size_t v2=0; v2 <= v1; ++v2) {
				hess(map[v2], map[v1]) += hb->mat(v2, v1);
			}
		}
	}

	haveDenseHess = true;
}

void FitContext::copyDenseHess(double *dest)
{
	refreshDenseHess();
	int np = hess.rows();
	for (int v1=0; v1 < np; ++v1) {
		for (int v2=0; v2 <= v1; ++v2) {
			double coef = hess.selfadjointView<Eigen::Upper>()(v2,v1);
			if (v1==v2) {
				dest[v1 * np + v2] = coef;
			} else {
				dest[v1 * np + v2] = coef;
				dest[v2 * np + v1] = coef;
			}
		}
	}
}

double *FitContext::getDenseHessUninitialized()
{
	int numFree = getNumFree();
	hess.resize(numFree, numFree);

	// Assume the caller is going to fill it out
	haveDenseHess = true;
	haveDenseIHess = false;
	return hess.data();
}

struct allFiniteHelper {
	typedef double Scalar;
	typedef Eigen::DenseIndex  Index;
	bool finite;
	void init(const Scalar& value, Index i, Index j) {
		finite = true;
		if (i <= j) finite = std::isfinite(value);
	};
	void operator() (const Scalar& value, Index i, Index j) {
		if (i <= j) finite &= std::isfinite(value);
	};
};

static void InvertSymmetricNR(Eigen::MatrixXd &hess, Eigen::MatrixXd &ihess)
{
	ihess = hess;
	ThinMatrix ihessMat(ihess.data(), ihess.rows(), ihess.cols());

	if (!InvertSymmetricPosDef(ihessMat, 'U')) return;

	int numParams = hess.rows();
	allFiniteHelper afh;
	hess.visit(afh);
	if (!afh.finite) {
		ihess = Eigen::MatrixXd::Zero(numParams, numParams);
		return;
	}

	Eigen::Map< Eigen::MatrixXd > EihessMat(ihess.data(), ihess.rows(), ihess.cols());
	ForceInvertSymmetricPosDef(EihessMat);
}

void FitContext::refreshDenseIHess()
{
	if (haveDenseIHess) return;

	refreshDenseHess();

	ihess = hess;
	ThinMatrix ihessMat(ihess.data(), ihess.rows(), ihess.cols());
	InvertSymmetricIndef(ihessMat, 'U');

	haveDenseIHess = true;
}

void FitContext::refreshSparseHess()
{
	if (haveSparseHess) return;

	sparseHess.resize(numParam, numParam);
	sparseHess.setZero();

	// need to sort allBlocks for performance TODO
	for (size_t bx=0; bx < allBlocks.size(); ++bx) {
		HessianBlock *hb = allBlocks[bx];

		std::vector<int> &map = hb->vars;
		size_t bsize = map.size();

		for (size_t v1=0; v1 < bsize; ++v1) {
			for (size_t v2=0; v2 <= v1; ++v2) {
				sparseHess.coeffRef(map[v2], map[v1]) += hb->mat(v2, v1);
			}
		}
	}

	haveSparseHess = true;
}

static double norm1(const Eigen::SparseMatrix<double> &mat)
{
	// norm_1, maximum column sum
	double maxCol = 0;
	for (int k=0; k < mat.outerSize(); ++k) {
		double col = 0;
		for (Eigen::SparseMatrix<double>::InnerIterator it(mat,k); it; ++it) {
			col += fabs(it.value());
		}
		maxCol = std::max(maxCol, col);
	}
	return maxCol;
}

static double frobeniusNorm(const Eigen::SparseMatrix<double> &mat)
{
	double total=0;
	for (int k=0; k < mat.outerSize(); ++k) {
		for (Eigen::SparseMatrix<double>::InnerIterator it(mat,k); it; ++it) {
			total += it.value() * it.value();
		}
	}
	return total / mat.nonZeros();
}

static bool soleymani2013(const Eigen::SparseMatrix<double> &mat, Eigen::SparseMatrix<double> &imat)
{
       imat.setIdentity();
       imat /= frobeniusNorm(mat);

       Eigen::SparseMatrix<double> I1(mat.rows(), mat.cols());
       I1.setIdentity();
       Eigen::SparseMatrix<double> I7(mat.rows(), mat.cols());
       I7 = I1 * 7;
       Eigen::SparseMatrix<double> I21(mat.rows(), mat.cols());
       I21 = I1 * 21;
       Eigen::SparseMatrix<double> I35(mat.rows(), mat.cols());
       I35 = I1 * 35;

       double maxCol;
       int iter = 0;
       Eigen::SparseMatrix<double> AV = mat.selfadjointView<Eigen::Upper>() * imat;
       while (++iter < 100) {
               // try prune() on the multiplications TODO
               // try selfadjointView TODO
               Eigen::SparseMatrix<double> rpart =
                       (AV * (AV * (AV * (AV * (AV * (AV - I7) + I21) -I35) + I35) -I21) + I7);

               Eigen::SparseMatrix<double> prev = imat;
               imat = prev * rpart;
               AV = mat.selfadjointView<Eigen::Upper>() * imat;

               Eigen::SparseMatrix<double> diff = I1 - AV;
               maxCol = norm1(diff);
               if (maxCol < 1e-6) {
                       break;
               }
       }
       //mxLog("soleymani2013 invert in %d iter, maxCol %.2g", iter, maxCol);
       return false;
}

SEXP sparseInvert_wrapper(SEXP Rmat)
{
	ProtectAutoBalanceDoodad mpi;

	SEXP matrixDims;
	Rf_protect(matrixDims = Rf_getAttrib(Rmat, R_DimSymbol));
	int *dimList = INTEGER(matrixDims);
	int rows = dimList[0];
	int cols = dimList[1];
	if (rows != cols) mxThrow("Must be square");

	double *matData = REAL(Rmat);

	Eigen::SparseMatrix<double> mat(rows,cols);
	for (int cx=0; cx < cols; ++cx) {
		for (int rx=0; rx < rows; ++rx) {
			double val = matData[cx * rows + rx];
			if (val == 0) continue;
			mat.coeffRef(rx, cx) = val;
		}
	}

	Eigen::SparseMatrix<double> imat(rows,cols);
	if (soleymani2013(mat, imat)) mxThrow("Invert failed");

	SEXP ret;
	Rf_protect(ret = Rf_allocMatrix(REALSXP, rows, cols));
	double *retData = REAL(ret);
	for (int cx=0; cx < cols; ++cx) {
		for (int rx=0; rx < rows; ++rx) {
			retData[cx * rows + rx] = imat.coeff(rx, cx);
		}
	}

	return ret;
}

void FitContext::testMerge()
{
	const int UseId = 2;

	analyzeHessian();

	//std::cout << "block count " << allBlocks.size() << std::endl;

	sparseHess.resize(numParam, numParam);
	sparseHess.setZero();

	for (int vx=0; vx < numParam; ++vx) {
		HessianBlock *hb = blockByVar[vx];
		hb->addSubBlocks();
	}

	for (int vx=0; vx < numParam; ++vx) {
		HessianBlock *hb = blockByVar[vx];
		if (hb->useId == UseId) continue;
		hb->useId = UseId;

		// std::cout << "add block " << vx << "\nvar map: ";
		// for (int vm=0; vm < (int) hb->vars.size(); ++vm) {
		// 	std::cout << vm << ":" << hb->vars[vm] << ",";
		// }
		// std::cout << "\n" << hb->mmat << "\n";

		size_t size = hb->mmat.rows();
		for (size_t col=0; col < size; ++col) {
			for (size_t row=0; row <= col; ++row) {
				int vr = hb->vars[row];
				int vc = hb->vars[col];
				sparseHess.coeffRef(vr,vc) = hb->mmat(row,col);
			}
		}
	}

	refreshDenseHess();
	Eigen::MatrixXd dense = sparseHess;
	Eigen::MatrixXd diff = (dense - hess).selfadjointView<Eigen::Upper>();
	// std::cout << "difference\n" << diff << std::endl;
	// std::cout << "sparse\n" << dense << std::endl;
	// std::cout << "dense\n" << hess << std::endl;
	double bad = diff.cwiseAbs().maxCoeff();
	if (bad > .0001) mxThrow("Hess: dense sparse mismatch %f", bad);
}

bool FitContext::refreshSparseIHess()
{
	if (haveSparseIHess) return true;

	const int AcceptableDenseInvertSize = 100;
	const bool checkResult = OMX_DEBUG;

	//testMerge();

	sparseIHess.resize(numParam, numParam);
	sparseIHess.setZero();

	// sparseness by size simulation
	//mxLog("minBlockSize %d maxBlocksize %d sparse %f", maxBlockSize, estNonZero / double(numParam * numParam));

	if (minBlockSize < AcceptableDenseInvertSize) {
		analyzeHessian();
	}
	if (maxBlockSize < std::min(int(numParam), AcceptableDenseInvertSize)) {
		const int UseId = 1;
		for (int vx=0; vx < numParam; ++vx) {
			HessianBlock *hb = blockByVar[vx];
			if (!hb) mxThrow("Attempting to invert Hessian, "
					  "but no Hessian information for '%s'", varGroup->vars[vx]->name);
			if (hb->useId == UseId) continue;
			hb->useId = UseId;

			hb->addSubBlocks();
			size_t size = hb->mmat.rows();

			InvertSymmetricNR(hb->mmat, hb->imat);

			for (size_t col=0; col < size; ++col) {
				for (size_t row=0; row <= col; ++row) {
					int vr = hb->vars[row];
					int vc = hb->vars[col];
					sparseIHess.coeffRef(vr,vc) = hb->imat(row,col);
				}
			}
		}
	} else {
		return false;

		// Needs more work TODO
		// if (estNonZero / double(numParam * numParam) < .2)
		refreshSparseHess();
		if (soleymani2013(sparseHess, sparseIHess)) {
			sparseIHess.setZero();  // NR will try steepest descent
		}
	}

	if (checkResult) {
		refreshDenseHess();
		InvertSymmetricNR(hess, ihess);
		ihess.triangularView<Eigen::Lower>() = ihess.transpose().triangularView<Eigen::Lower>();
		Eigen::MatrixXd denseI = sparseIHess;
		denseI.triangularView<Eigen::Lower>() = denseI.transpose().triangularView<Eigen::Lower>();
		Eigen::MatrixXd resid = ihess - denseI;
		double bad = resid.cwiseAbs().maxCoeff();
		if (bad > .01) {
			// std::cout << "dense\n" << ihess << std::endl;
			// std::cout << "sparse\n" << denseI << std::endl;
			mxThrow("IHess: dense sparse mismatch %f", bad);
		}

		if (0) {
			int nonZero = 0;
			for (int cx=0; cx < numParam; ++cx) {
				for (int rx=0; rx <= cx; ++rx) {
					if (hess(rx,cx) != 0) {
						if (rx == cx) nonZero += 1;
						else nonZero += 2;
					}
				}
			}
			mxLog("done %f maxBlocksize %d est sparse %f actual sparse %f", bad, maxBlockSize,
			      estNonZero / double(numParam * numParam),
			      nonZero / double(numParam * numParam));
		}
	}

        haveSparseIHess = true;
	return true;
}

Eigen::VectorXd FitContext::ihessGradProd()
{
	for (int px=0; px < int(gradZ.size()); ++px) {
		if (std::isfinite(gradZ[px])) continue;
		mxLog("FitContext::ihessGradProd grad[%d/%s] missing",
		      px, varGroup->vars[freeToParamMap[px]]->name);
	}
	if (refreshSparseIHess()) {
		return sparseIHess.selfadjointView<Eigen::Upper>() * gradZ;
	} else {
		refreshDenseHess();
		InvertSymmetricNR(hess, ihess);
		return ihess.selfadjointView<Eigen::Upper>() * gradZ;
	}
}

Eigen::VectorXd FitContext::ihessDiag()
{
	refreshDenseIHess();
	return ihess.diagonal();
}

double *FitContext::getDenseIHessUninitialized()
{
	int numFree = getNumFree();
	ihess.resize(numFree, numFree);

	// Assume the caller is going to fill it out
	haveDenseIHess = true;
	haveDenseHess = false;
	return ihess.data();
}

void FitContext::copyDenseIHess(double *dest)
{
	refreshDenseIHess();

	int np = ihess.rows();
	for (int v1=0; v1 < np; ++v1) {
		for (int v2=0; v2 <= v1; ++v2) {
			double coef = ihess.selfadjointView<Eigen::Upper>()(v2,v1);
			if (v1==v2) {
				dest[v1 * np + v2] = coef;
			} else {
				dest[v1 * np + v2] = coef;
				dest[v2 * np + v1] = coef;
			}
		}
	}
}

double *FitContext::getDenseHessianish()
{
	if (haveDenseHess) return hess.data();
	if (haveDenseIHess) return ihess.data();
	return NULL;
}

int FitContext::getDenseHessianishSize()
{
	if (haveDenseHess) return hess.rows();
	if (haveDenseIHess) return ihess.rows();
	return 0;
}

HessianBlock *HessianBlock::clone()
{
	HessianBlock *hb = new HessianBlock;
	hb->vars = vars;
	hb->mat.resize(vars.size(), vars.size());
	return hb;
}

void HessianBlock::addSubBlocks()
{
	if (mmat.rows()) return;

	mmat = mat;

	std::vector<int> vmap; // we could localize the vars map instead of computing the mapping each time TODO

	for (size_t bx=0; bx < subBlocks.size(); ++bx) {
		HessianBlock *sb = subBlocks[bx];
		sb->addSubBlocks();
	}

	//std::cout << "initial " << id << "\n" << mmat << std::endl;

	for (size_t bx=0; bx < subBlocks.size(); ++bx) {
		HessianBlock *sb = subBlocks[bx];

		//std::cout << "subblock " << sb->id << "\n" << sb->mmat << std::endl;

		size_t numVars = sb->vars.size();
		vmap.resize(numVars);
		for (size_t vx=0; vx < numVars; ++vx) {
			// std::set has special method for this TODO
			int px = std::lower_bound(vars.begin(), vars.end(), sb->vars[vx]) - vars.begin();
			vmap[vx] = px;
		}

		for (size_t v1=0; v1 < numVars; ++v1) {
			for (size_t v2=0; v2 <= v1; ++v2) {
				mmat(vmap[v2], vmap[v1]) += sb->mmat(v2, v1);
			}
		}
	}

	//std::cout << "result " << id << "\n" << mmat << std::endl;
}

int HessianBlock::estNonZero() const
{
	if (!merge) {
		return int(vars.size() * vars.size());
	} else {
		int total = 0;
		for (size_t bx=0; bx < subBlocks.size(); ++bx) {
			HessianBlock *sb = subBlocks[bx];
			total += sb->estNonZero();
		}
		return std::min(total, int(vars.size() * vars.size()));
	}
}

void FitContext::init()
{
	numParam = varGroup->vars.size();
  u_numFree = -1;
	wanted = 0;
	mac = parent? parent->mac : 0;
	fit = parent? parent->fit : NA_REAL;
	previousReportFit = nan("uninit");
	fitUnits = parent? parent->fitUnits : FIT_UNITS_UNINITIALIZED;
	skippedRows = 0;
	est.resize(numParam);
	infoDefinite = NA_LOGICAL;
	infoCondNum = NA_REAL;
	infoA = NULL;
	infoB = NULL;
	inform = INFORM_UNINITIALIZED;
	iterations = 0;
	ciobj = 0;
	openmpUser = false;
	ordinalRelativeError = 0;
	computeCount = 0;
  permitParallel = false;

	hess.resize(numParam, numParam);  // TODO why needed? should be numFree, WRONG DIMENSION
	ihess.resize(numParam, numParam);  // TODO why needed?

	clearHessian();
}

void FitContext::clearHessian()
{
	for (size_t bx=0; bx < mergeBlocks.size(); ++bx) {
		delete mergeBlocks[bx];
	}
	for (size_t bx=0; bx < allBlocks.size(); ++bx) {
		delete allBlocks[bx];
	}

	allBlocks.clear();
	mergeBlocks.clear();
	blockByVar.clear();
	haveSparseHess = false;
	haveSparseIHess = false;
	haveDenseHess = false;
	haveDenseIHess = false;
	estNonZero = 0;
	minBlockSize = 0;
	maxBlockSize = 0;
}

bool FitContext::hasActiveBoxConstraint(int skip) const
{
  const int verbose = 0;
	double eps = sqrt(std::numeric_limits<double>::epsilon());

  for (int vx=0; vx < getNumFree(); ++vx) {
    if (vx == skip) continue;
		bool active=false;
    int px = freeToParamMap[vx];
		if (est[px] <= varGroup->vars[px]->lbound + eps) {
			if (verbose >= 2)
				mxLog("Param %s at lbound %f", varGroup->vars[px]->name, est[px]);
			active=true;
		}
		if (est[px] >= varGroup->vars[px]->ubound - eps) {
			if (verbose >= 2)
				mxLog("Param %s at ubound %f", varGroup->vars[px]->name, est[px]);
			active=true;
		}
    if (active) return true;
  }
  return false;
}

void FitContext::calcStderrs()
{
	int numFree = getNumFree();
	stderrs.resize(numFree);
	if (vcov.rows() != numFree || vcov.cols() != numFree) {
		mxThrow("FitContext::calcStderrs vcov size wrong %d vs %d",
          vcov.rows(), numFree);
	}
	const double scale = fabs(Global->llScale);

	if(constraintJacobian.rows()){
		Eigen::MatrixXd hesstmp(numFree, numFree);
		if(fitUnits == FIT_UNITS_MINUS2LL){
			copyDenseHess(hesstmp.data());
			hesstmp = hesstmp/scale;
		}
		else{ //WLS case--'hesstmp' is actually not a Hessian matrix, but the inverse of the WLS sampling-covariance matrix.
			Eigen::LLT< Eigen::MatrixXd > cholVcov;
			cholVcov.compute(vcov.selfadjointView<Eigen::Lower>());
			if(cholVcov.info() != Eigen::Success){
				Eigen::FullPivLU< Eigen::MatrixXd > luVcov(vcov.selfadjointView<Eigen::Lower>());
				if(luVcov.isInvertible()){
					hesstmp = luVcov.inverse();
				}
				else{ //This is supposed to never happen with WLS...
					Rf_warning(
						"constraint-adjusted standard errors could not be calculated because the sampling covariance matrix was uninvertible");
					return;
				}
			}
			else{
				hesstmp = cholVcov.solve(Eigen::MatrixXd::Identity( vcov.rows(), vcov.cols() ));
			}
		}
		Eigen::FullPivHouseholderQR<Eigen::MatrixXd> qrj(constraintJacobian.transpose());
		Eigen::MatrixXd Q = qrj.matrixQ();
		Eigen::MatrixXd U = Q.block(0, qrj.rank(), Q.rows(), Q.cols()-qrj.rank());
		if(U.rows()==0 || U.cols()==0){
			Rf_warning(
				"standard errors could not be calculated because no basis could be found for the nullspace of the constraint Jacobian");
			return;
		}
		if(OMX_DEBUG){mxPrintMat("basis",U);}
		Eigen::MatrixXd centr = U.transpose() * hesstmp * U;
		//centr should be symmetric, will almost always be invertible, may sometimes not be PD:
		Eigen::LLT< Eigen::MatrixXd > cholCentr;
		//Ff center is PD, we'd rather calculate its inverse via its Cholesky factorization:
		cholCentr.compute(centr.selfadjointView<Eigen::Lower>());
		if(cholCentr.info() != Eigen::Success){ //<--Will be true if centr is not PD.
			Eigen::FullPivLU< Eigen::MatrixXd > luCentr(centr.selfadjointView<Eigen::Lower>());
			if(luCentr.isInvertible()){
				centr = luCentr.inverse();
			}
			else{
				Rf_warning(
					"constraint-adjusted standard errors could not be calculated because the coefficient matrix of the quadratic form was uninvertible");
				return;
			}
		}
		else{
			centr = cholCentr.solve(Eigen::MatrixXd::Identity( centr.rows(), centr.cols() ));
		}
		vcov = U * centr * U.transpose();
	}

	for(int i = 0; i < numFree; i++) {
		double got = vcov(i,i);
		if (got <= 0) {
			stderrs[i] = NA_REAL;
			continue;
		}
		stderrs[i] = sqrt(got);
	}
}

FitContext::FitContext(omxState *u_state)
{
	parent = NULL;
	varGroup = Global->findVarGroup(FREEVARGROUP_ALL);
	init();
	profiledOutZ.assign(numParam, false);

	auto &startingValues = Global->startingValues;
	state = u_state;
	if (numParam) {
		if (int(startingValues.size()) != numParam) {
			mxThrow("Got %d starting values for %d parameters",
				int(startingValues.size()), int(numParam));
		}
    est = startingValues;
	}
	//equality.resize(state->numEqC);
	//inequality.resize(state->numIneqC);
}

FitContext::FitContext(FitContext *u_parent, FreeVarGroup *u_varGroup)
{
	this->parent = u_parent;
	this->varGroup = u_varGroup;
	init();

	state = parent->state;
	FreeVarGroup *src = parent->varGroup;
	FreeVarGroup *dest = varGroup;
	size_t dvars = varGroup->vars.size();
	if (dvars == 0) return;
	mapToParent.resize(dvars);
	profiledOutZ.resize(numParam);

	size_t d1 = 0;
	for (size_t s1=0; s1 < src->vars.size(); ++s1) {
		if (src->vars[s1] != dest->vars[d1]) continue;
		mapToParent[d1] = s1;
		est[d1] = parent->est[s1];
		profiledOutZ[d1] = parent->profiledOutZ[s1];
		if (++d1 == dvars) break;
	}
	if (d1 != dvars) mxThrow("Parent free parameter group (id=%d) is not a superset of %d",
			       src->id[0], dest->id[0]);


	wanted = parent->wanted;
	infoDefinite = parent->infoDefinite;
	infoCondNum = parent->infoCondNum;
	iterations = parent->iterations;
	if (parent->ciobj) ciobj = parent->ciobj->clone();
}

void FitContext::updateParent()
{
	FreeVarGroup *src = varGroup;
	FreeVarGroup *dest = parent->varGroup;
	size_t svars = varGroup->vars.size();

	parent->wanted |= wanted;
	parent->fit = fit;
	parent->fitUnits = fitUnits;
	parent->skippedRows = skippedRows;
	parent->mac = mac;
	parent->infoDefinite = infoDefinite;
	parent->infoCondNum = infoCondNum;
	parent->iterations = iterations;
	parent->recordOrdinalRelativeError(getOrdinalRelativeError());

	// rewrite using mapToParent TODO

	if (svars > 0) {
		for (size_t d1=0, s1 = 0; d1 < dest->vars.size(); ++d1) {
			if (dest->vars[d1] != src->vars[s1]) continue;
			parent->est[d1] = est[s1];
			if (++s1 == svars) break;
		}
	}

	// pda(est, 1, svars);
	// pda(parent->est, 1, dvars);
}

int FitContext::getGlobalComputeCount()
{
	FitContext *fc = this;
	if (fc->parent && fc->parent->childList.size()) {
		// Kids for multithreading only appear as leaves of tree
		fc = fc->parent;
	}
	int cc = fc->getLocalComputeCount();
	while (fc->parent) {
		fc = fc->parent;
		cc += fc->getLocalComputeCount();
	}
	return cc;
}

int FitContext::getLocalComputeCount()
{
	int cc = computeCount;
	for (size_t cx=0; cx < childList.size(); ++cx) {
		cc += childList[cx]->getLocalComputeCount();
	}
	return cc;
}

void FitContext::updateParentAndFree()
{
	updateParent();
	delete this;
}

void FitContext::log(int what)
{
	std::string buf;
	if (what & FF_COMPUTE_MAXABSCHANGE) buf += string_snprintf("MAC: %.5f\n", mac);
	if (what & FF_COMPUTE_FIT) buf += string_snprintf("fit: %.5f (scale %f)\n", fit, Global->llScale);
	if (what & FF_COMPUTE_ESTIMATE) {
    int count = numParam;
		buf += string_snprintf("est %d: c(", (int) count);
		for (int vx=0; vx < count; ++vx) {
			buf += string_snprintf("%.16f", est[vx]);
			if (vx < count - 1) buf += ", ";
		}
		buf += ")\n";
	}
	if (what & FF_COMPUTE_GRADIENT) {
    int count = getNumFree();
		buf += string_snprintf("gradient %d: c(", (int) count);
		for (int vx=0; vx < count; ++vx) {
      buf += string_snprintf("%.5f", gradZ[vx]);
			if (vx < count - 1) buf += ", ";
		}
		buf += ")\n";
	}
	if (what & FF_COMPUTE_HESSIAN) {
    int count = getNumFree();
		refreshDenseHess();
		buf += string_snprintf("hessian %d x %d: c(\n", (int) count, (int) count);
		for (int v1=0; v1 < count; ++v1) {
			for (int v2=0; v2 < count; ++v2) {
				double coef;
				if (v1 > v2) {
					coef = hess.selfadjointView<Eigen::Upper>()(v2,v1);
				} else {
					coef = hess.selfadjointView<Eigen::Upper>()(v1,v2);
				}
				buf += string_snprintf("%.5f", coef);
				if (v1 < count - 1 || v2 < count - 1) buf += ", ";
			}
			buf += "\n";
		}
		buf += ")\n";
	}
	mxLogBig(buf);
}

std::string FitContext::asProgressReport()
{
	std::string str;
	if (!std::isfinite(previousReportFit) || !std::isfinite(fit)) {
		str = string_snprintf("evaluations %d fit %.6g", getGlobalComputeCount(), fit);
	} else {
		str = string_snprintf("evaluations %d fit %.6g change %.4g",
													getGlobalComputeCount(), fit, fit - previousReportFit);
	}
	previousReportFit = fit;
	return str;
}

void FitContext::resetIterationError()
{
	IterationError.clear();
}

void FitContext::resetOrdinalRelativeError()
{
	if (childList.size()) {
		for (size_t cx=0; cx < childList.size(); ++cx) {
			childList[cx]->resetOrdinalRelativeError();
		}
	}
	if (OMX_DEBUG && ordinalRelativeError > .01) {
		mxLog("reset ordinalRelativeError %g back to zero", ordinalRelativeError);
	}
	ordinalRelativeError = 0;
}

void FitContext::recordIterationError(const char* msg, ...)
{
	// Can avoid overhead of setting error if one is already set TODO
	va_list ap;
	va_start(ap, msg);
	string_vsnprintf(msg, ap, IterationError);
	va_end(ap);
}

std::string FitContext::getIterationError()
{
	if (childList.size()) {
		size_t tlen = 0;
		for (size_t cx=0; cx < childList.size(); ++cx) {
			tlen += childList[cx]->IterationError.size();
		}
		// Fit function may not have used parallel processing
		if (tlen == 0) return IterationError;

		std::string result;
		for (size_t cx=0; cx < childList.size(); ++cx) {
			auto &str = childList[cx]->IterationError;
			if (!str.size()) continue;
			result += string_snprintf("%d: %s\n", int(cx), str.c_str());
		}
		return result;
	} else {
		return IterationError;
	}
}

static void u_fixSymmetry(const char *name, double *mat, size_t numParam, bool force)
{
	for (size_t h1=1; h1 < numParam; h1++) {
		for (size_t h2=0; h2 < h1; h2++) {
			if (!force && mat[h2 * numParam + h1] != 0) {
				omxRaiseErrorf("%s is not upper triangular", name);
				break;
			}
			mat[h2 * numParam + h1] = mat[h1 * numParam + h2];
		}
	}
}

void FitContext::ensureParamWithinBox(bool nudge)
{
	if (OMX_DEBUG) mxLog("FitContext::ensureParamWithinBox(nudge=%d)", nudge);
	for (size_t px = 0; px < varGroup->vars.size(); ++px) {
		omxFreeVar *fv = varGroup->vars[px];
		if (nudge && !profiledOutZ[px] && est[px] == 0.0) {
			est[px] += 0.1;
		}
		if (fv->lbound > est[px]) {
			est[px] = fv->lbound + 1.0e-6;
		}
		if (fv->ubound < est[px]) {
			est[px] = fv->ubound - 1.0e-6;
		}
        }
}

void FitContext::copyParamToModel()
{
	copyParamToModelClean();
	varGroup->markDirty(state);
}

void copyParamToModelInternal(FreeVarGroup *varGroup, omxState *os, double *at)
{
	size_t numParam = varGroup->vars.size();

	for(size_t k = 0; k < numParam; k++) {
		omxFreeVar* freeVar = varGroup->vars[k];
		freeVar->copyToState(os, at[k]);
	}
}

void FitContext::copyParamToModelClean()
{
	if(numParam == 0) return;

	copyParamToModelInternal(varGroup, state, est.data());

	if (RFitFunction) {  // special hack
    omxRFitFunction* rFitFunction = (omxRFitFunction*)RFitFunction;

    ProtectedSEXP estimate(Rf_allocVector(REALSXP, getNumFree()));
    double *eptr = REAL(estimate);
    copyEstToOptimizer(eptr);

    ProtectedSEXP theCall(Rf_allocVector(LANGSXP, 4));

		// imxUpdateModelValues does not handle parameters with equality
		// constraints. This is a bug.
    SETCAR(theCall, Rf_install("imxUpdateModelValues"));
    SETCADR(theCall, rFitFunction->model);
    SETCADDR(theCall, rFitFunction->flatModel);
    SETCADDDR(theCall, estimate);

    rFitFunction->model = Rf_eval(theCall, R_GlobalEnv);

    Rf_setAttrib(rFitFunction->rObj, Rf_install("model"), rFitFunction->model);

    omxMarkDirty(RFitFunction->matrix);
  }

	if (childList.size() == 0 || !openmpUser) return;

	for(size_t i = 0; i < childList.size(); i++) {
		childList[i]->est = est;
		childList[i]->copyParamToModel();
	}
}

bool FitContext::isUnconstrained()
{
	omxState *st = state;
  return st->conListX.size() == 0;
}

omxMatrix *FitContext::lookupDuplicate(omxMatrix* element)
{
	if (element == NULL) return NULL;
	return state->lookupDuplicate(element);
}

// Rethink this whole design TODO
// If we compute things blockwise then most of this can go away?
void FitContext::preInfo()
{
	size_t npsq = numParam * numParam;

	if (!infoA) infoA = new double[npsq];
	if (!infoB) infoB = new double[npsq];

	switch (infoMethod) {
	case INFO_METHOD_SANDWICH:
	case INFO_METHOD_MEAT:
		OMXZERO(infoA, npsq);
		OMXZERO(infoB, npsq);
		break;
	case INFO_METHOD_BREAD:
		OMXZERO(infoA, npsq);
		break;
	case INFO_METHOD_HESSIAN:
		clearHessian();
		break;
	default:
		mxThrow("Unknown information matrix estimation method %d", infoMethod);
	}
}

void FitContext::postInfo()
{
	switch (infoMethod) {
	case INFO_METHOD_SANDWICH:{
		// move into FCDeriv TODO
		std::vector<double> work(numParam * numParam);
		ThinMatrix amat(infoA, numParam, numParam);
		InvertSymmetricIndef(amat, 'U');
		u_fixSymmetry("InfoB", infoB, numParam, false);
		ThinMatrix bmat(infoB, numParam, numParam);
		ThinMatrix wmat(work.data(), numParam, numParam);
		ThinMatrix hmat(getDenseIHessUninitialized(), numParam, numParam);
		SymMatrixMultiply('L', amat, bmat, wmat);
		SymMatrixMultiply('R', amat, wmat, hmat);
		wanted |= FF_COMPUTE_IHESSIAN;
		break;}
	case INFO_METHOD_MEAT:{
		memcpy(getDenseHessUninitialized(), infoB, sizeof(double) * numParam * numParam); // avoid copy TODO
		wanted |= FF_COMPUTE_HESSIAN;
		break;}
	case INFO_METHOD_BREAD:{
		memcpy(getDenseHessUninitialized(), infoA, sizeof(double) * numParam * numParam); // avoid copy TODO
		wanted |= FF_COMPUTE_HESSIAN;
		break;}
	case INFO_METHOD_HESSIAN:
		if (Global->llScale > 0) negateHessian();
		wanted |= FF_COMPUTE_HESSIAN;
		break;
	default:
		mxThrow("Unknown information matrix estimation method %d", infoMethod);
	}
}

bool FitContext::isClone() const
{
	return state->isClone();
}

struct ParallelInvalidator : StateInvalidator {
  typedef StateInvalidator super;
  ParallelInvalidator(omxState &u_st) : super(u_st) {}
	virtual void doExpectation() override {}
  virtual void doData() override {}
  virtual void doMatrix() override {}
};

void FitContext::createChildren(omxMatrix *alg, bool u_permitParallel)
{
	if (childList.size()) {
		diagParallel(OMX_DEBUG, "FitContext::createChildren: ignored, childList already populated");
    return;
  }

  openmpUser = false;
	if (Global->numThreads <= 1) {
		diagParallel(OMX_DEBUG, "FitContext::createChildren: max threads set to 1");
    u_permitParallel = false;
	}

  diagParallel(OMX_DEBUG, "FitContext::createChildren(%s, %d)",
               alg? alg->name() : "NULL", u_permitParallel);

  ParallelInvalidator pi(*state);
  pi();

  permitParallel = u_permitParallel;
  if (alg) omxAlgebraPreeval(alg, this);

	if (Global->numThreads <= 1)  return;

  createChildren1();

  if (alg) {
    for (auto kid : childList) omxAlgebraPreeval(alg, kid);
  }
  if (!u_permitParallel) {
    if (openmpUser) OOPS;
  }
}

void FitContext::createChildren1()
{
	for(size_t j = 0; j < state->expectationList.size(); j++) {
		if (!state->expectationList[j]->canDuplicate) {
			diagParallel(OMX_DEBUG, "FitContext::createChildren: %s cannot be duplicated",
				     state->expectationList[j]->name);
			return;
		}
	}
	for(size_t j = 0; j < state->algebraList.size(); j++) {
		omxFitFunction *ff = state->algebraList[j]->fitFunction;
		if (!ff) continue;
		if (!ff->canDuplicate) {
			diagParallel(OMX_DEBUG, "FitContext::createChildren: %s cannot be duplicated",
				     state->algebraList[j]->name());
			return;
		}
		if (ff->openmpUser) {
			diagParallel(OMX_DEBUG, "FitContext::createChildren: %s is an OpenMP user",
				     state->algebraList[j]->name());
      openmpUser = true;
		}
	}

	diagParallel(OMX_DEBUG, "FitContext::createChildren: create %d FitContext for parallel processing; OpenMP user=%d",
		     Global->numThreads, openmpUser);

	int numThreads = Global->numThreads;

	childList.reserve(numThreads);

	for(int ii = 0; ii < numThreads; ii++) {
		FitContext *kid = new FitContext(this, varGroup);
		kid->state = new omxState(state, openmpUser);
		kid->state->initialRecalc(kid);
    kid->calcNumFree();
		childList.push_back(kid);
	}

	if (OMX_DEBUG) mxLog("FitContext::createChildren: done creating %d omxState", Global->numThreads);
}

void FitContext::destroyChildren()
{
	if (0 == childList.size()) return;
	IterationError = getIterationError();
	for (int cx=0; cx < int(childList.size()); ++cx) {
		recordOrdinalRelativeError(childList[cx]->getOrdinalRelativeError());
		delete childList[cx];
	}
	childList.clear();
}

FitContext::~FitContext()
{
  //mxLog("destroy FitContext %p", this);

	destroyChildren();

	if (parent) {
		parent->computeCount += computeCount;
		computeCount = 0;

		if (parent->state != state) delete state;
	}

	clearHessian();
	if (infoA) delete [] infoA;
	if (infoB) delete [] infoB;
}

omxFitFunction *FitContext::RFitFunction = NULL;

void FitContext::setRFitFunction(omxFitFunction *rff)
{
	if (rff) {
		Global->numThreads = 1;
		if (RFitFunction) {
			mxThrow("You can only create 1 MxRFitFunction per independent model");
		}
	}
	RFitFunction = rff;
}

void FitContext::withoutCIobjective(std::function<void()> fn)
{
  if (!ciobj) OOPS;
  if (disabledCiobj) OOPS;
  toggleCIObjective();
  fn();
  toggleCIObjective();
}

void FitContext::toggleCIObjective()
{
  std::swap(ciobj, disabledCiobj);
  for (auto kid : childList) kid->toggleCIObjective();
}

void CIobjective::evalFit(omxFitFunction *ff, int want, FitContext *fc)
{
  fc->withoutCIobjective([&](){ ComputeFit("CI", ff->matrix, FF_COMPUTE_FIT, fc); });
}

void CIobjective::checkSolution(FitContext *fc)
{
	if (fc->getInform() > INFORM_UNCONVERGED_OPTIMUM) return;

	if (getDiag() != DIAG_SUCCESS) {
		fc->setInform(INFORM_NONLINEAR_CONSTRAINTS_INFEASIBLE);
	}
}

void CIobjective::setGrad(FitContext *fc)
{
  if (CI->varIndex >= 0 && !constrained) {
    fc->gradZ.setZero();
    fc->gradZ[ CI->varIndex ] = lowerBound? 1 : -1;
  } else {
    fc->gradZ.setConstant(NA_REAL);
  }
}

class EMAccel {
protected:
	FitContext *fc;
	int numParam;
	std::vector<double> prevAdj1;
	std::vector<double> prevAdj2;
	int verbose;

public:
	EMAccel(FitContext *u_fc, int u_verbose) : fc(u_fc), verbose(u_verbose) {
		numParam = fc->getNumFree();
		prevAdj1.assign(numParam, 0);
		prevAdj2.resize(numParam);
		dir.resize(numParam);
	};
	virtual ~EMAccel() {};
	template <typename T> void recordTrajectory(std::vector<T> &prevEst) {
		prevAdj2 = prevAdj1;
		for (int px=0; px < numParam; ++px) {
			prevAdj1[px] = fc->est[px] - prevEst[px];
		}
	}

	Eigen::VectorXd dir;
	virtual bool calcDirection(bool major) = 0;
	virtual void recalibrate() = 0;
	virtual bool retry() { return false; };
};

class Ramsay1975 : public EMAccel {
	// Ramsay, J. O. (1975). Solving Implicit Equations in
	// Psychometric Data Analysis.  Psychometrika, 40(3), 337-360.

	double minCaution;
	double highWatermark;
	bool goingWild;
	void restart(bool myFault);  // no longer in use

public:
	double maxCaution;
	double caution;

	Ramsay1975(FitContext *fc, int verbose, double minCaution);
	virtual void recalibrate() override;
	virtual bool calcDirection(bool major) override;
};

Ramsay1975::Ramsay1975(FitContext *u_fc, int u_verbose, double u_minCaution) :
	EMAccel(u_fc, u_verbose), minCaution(u_minCaution)
{
	maxCaution = 0.0;
	caution = 0;
	highWatermark = std::max(0.5, caution);  // arbitrary guess

	if (verbose >= 2) {
		mxLog("Ramsay: %d parameters, caution %f, min caution %f",
		      numParam, caution, minCaution);
	}
}

bool Ramsay1975::calcDirection(bool major)
{
	for (int vx=0; vx < numParam; ++vx) {
		const double prevEst = fc->est[vx] - prevAdj1[vx];
		dir[vx] = ((1 - caution) * fc->est[vx] + caution * prevEst) - fc->est[vx];
	}
	return true;
}

void Ramsay1975::recalibrate()
{
	if (numParam == 0) return;

	double normPrevAdj2 = 0;
	double normAdjDiff = 0;
	std::vector<double> adjDiff(numParam);

	// The choice of norm is also arbitrary. Other norms might work better.
	for (int px=0; px < numParam; ++px) {
		adjDiff[px] = prevAdj1[px] - prevAdj2[px];
		normPrevAdj2 += prevAdj2[px] * prevAdj2[px];
	}

	for (int px=0; px < numParam; ++px) {
		normAdjDiff += adjDiff[px] * adjDiff[px];
	}
	if (normAdjDiff == 0) {
		return;
	}

	double ratio = sqrt(normPrevAdj2 / normAdjDiff);
	//if (verbose >= 3) mxLog("Ramsay[%d]: sqrt(%.5f/%.5f) = %.5f",
	// flavor, normPrevAdj2, normAdjDiff, ratio);

	double newCaution = 1 - (1-caution) * ratio;
	if (newCaution > .95) newCaution = .95;  // arbitrary guess
	if (newCaution < 0) newCaution /= 2;     // don't get overconfident
	if (newCaution < minCaution) newCaution = minCaution;
	if (newCaution < caution) {
		caution = newCaution/3 + 2*caution/3;  // don't speed up too fast, arbitrary ratio
	} else {
		caution = newCaution;
	}
	maxCaution = std::max(maxCaution, caution);
	goingWild = false;
	if (caution < highWatermark || (normPrevAdj2 < 1e-3 && normAdjDiff < 1e-3)) {
		if (verbose >= 3) mxLog("Ramsay: %.2f caution", caution);
	} else {
		if (verbose >= 3) {
			mxLog("Ramsay: caution %.2f > %.2f, extreme oscillation, restart recommended",
			      caution, highWatermark);
		}
		goingWild = true;
	}
	highWatermark += .02; // arbitrary guess
}

void Ramsay1975::restart(bool myFault)
{
	prevAdj1.assign(numParam, 0);
	prevAdj2.assign(numParam, 0);
	myFault |= goingWild;
	if (myFault) {
		highWatermark = 1 - (1 - highWatermark) * .5; // arbitrary guess
		caution = std::max(caution, highWatermark);   // arbitrary guess
		maxCaution = std::max(maxCaution, caution);
		highWatermark = caution;
	}
	if (numParam && verbose >= 3) {
		mxLog("Ramsay: restart%s with %.2f caution %.2f highWatermark",
		      myFault? " (my fault)":"", caution, highWatermark);
	}
}

class Varadhan2008 : public EMAccel {
	bool retried;
	double maxAlpha;
	double alpha;
	Eigen::Map< Eigen::VectorXd > rr;
	Eigen::VectorXd vv;

public:
	Varadhan2008(FitContext *u_fc, int u_verbose) :
		EMAccel(u_fc, u_verbose), rr(&prevAdj2[0], numParam), vv(numParam)
	{
		alpha = 0;
		maxAlpha = 0;
		retried = false;
	};
	virtual void recalibrate() override;
	virtual bool retry() override;
	virtual bool calcDirection(bool major) override;
};

bool Varadhan2008::calcDirection(bool major)
{
	if (!major) return false;
	if (verbose >= 3) mxLog("Varadhan: alpha = %.2f", alpha);

	for (int vx=0; vx < numParam; ++vx) {
		double adj2 = prevAdj1[vx] + prevAdj2[vx];
		double t0 = fc->est[vx] - adj2;
		dir[vx] = (t0 + 2 * alpha * rr[vx] + alpha * alpha * vv[vx]) - fc->est[vx];
	}
	return true;
}

void Varadhan2008::recalibrate()
{
	if (numParam == 0) return;

	memcpy(vv.data(), &prevAdj1[0], sizeof(double) * numParam);
	vv -= rr;

	if (maxAlpha && !retried && alpha > 0) maxAlpha = alpha*2;
	double newAlpha = rr.norm() / vv.norm();
	alpha = newAlpha - 0.5;     // slightly more conservative seems to help
	if (!std::isfinite(alpha) || alpha < 1) alpha = 1;
	if (maxAlpha && alpha > maxAlpha) alpha = maxAlpha;

	retried = false;
}

bool Varadhan2008::retry()
{
	retried = true;
	if (alpha == 1) return false;

	alpha = alpha / 4;
	if (alpha < 1.5) alpha = 1;
	maxAlpha = alpha;
	return true;
}

omxCompute::omxCompute()
{
	varGroup = NULL;
}

void omxCompute::collectResultsHelper(FitContext *fc, std::vector< omxCompute* > &clist,
				      LocalComputeResult *lcr, MxRList *out)
{
	for (std::vector< omxCompute* >::iterator it = clist.begin(); it != clist.end(); ++it) {
		omxCompute *c1 = *it;
		c1->collectResults(fc, lcr, out);
	}
}

void omxCompute::collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out)
{
	MxRList *slots = new MxRList();
        reportResults(fc, slots, out);
	if (slots->size()) {
		lcr->push_back(std::make_pair(computeId, slots));
	} else {
		delete slots;
	}
}

omxCompute::~omxCompute()
{}

void omxCompute::initFromFrontend(omxState *globalState, SEXP rObj)
{
	ProtectedSEXP Rid(R_do_slot(rObj, Rf_install("id")));
	if (Rf_length(Rid) != 1) mxThrow("MxCompute has no ID");
	computeId = INTEGER(Rid)[0];

	ProtectedSEXP Rpersist(R_do_slot(rObj, Rf_install(".persist")));
	dotPersist = Rf_asLogical(Rpersist);

	varGroup = Global->findVarGroup(computeId);

	if (!varGroup) {
		ProtectedSEXP Rfreeset(R_do_slot(rObj, Rf_install("freeSet")));
		if (Rf_length(Rfreeset) == 0) {
			varGroup = Global->findVarGroup(FREEVARGROUP_NONE);
		} else if (strcmp(CHAR(STRING_ELT(Rfreeset, 0)), ".")==0) {
			varGroup = Global->findVarGroup(FREEVARGROUP_ALL);
		} else {
			Rf_warning("MxCompute ID %d references matrix '%s' in its freeSet "
				"but this matrix contains no free parameters",
				computeId, CHAR(STRING_ELT(Rfreeset, 0)));
			varGroup = Global->findVarGroup(FREEVARGROUP_NONE);
		}
	}
	if (OMX_DEBUG) {
		mxLog("MxCompute id %d assigned to var group %d", computeId, varGroup->id[0]);
	}
}

void omxCompute::complainNoFreeParam()
{
	if (Global->ComputePersist) {
		omxRaiseErrorf("%s: model has no free parameters; "
			       "You may want to reset your model's "
			       "compute plan with model$compute <- mxComputeDefault() "
			       "and try again", name);
	} else {
		// should never happen, see MxRun.R
		omxRaiseErrorf("%s: model has no free parameters", name);
	}
}

class EnterVarGroup {
	bool narrowed;
 public:
	FitContext *narrow;
	EnterVarGroup(FitContext *fc, FreeVarGroup *varGroup) {
		narrow = fc;
		narrowed = fc->varGroup != varGroup;
		if (narrowed) narrow = new FitContext(fc, varGroup);
	}
	~EnterVarGroup() {
		if (narrowed) narrow->updateParentAndFree();
	}
};

void omxCompute::compute(FitContext *fc)
{
	EnterVarGroup evg(fc, varGroup);
	computeWithVarGroup(evg.narrow);
}

struct LeaveComputeWithVarGroup {
	FitContext *fc;
	bool toResetInform;
	ComputeInform origInform;
	const char *name;

	LeaveComputeWithVarGroup(FitContext *u_fc, struct omxCompute *compute) : fc(u_fc), name(compute->name) {
		origInform = fc->getInform();
		toResetInform = compute->accumulateInform();
		if (toResetInform) fc->setInform(INFORM_UNINITIALIZED);
		if (Global->debugProtectStack) {
			mxLog("enter %s: protect depth %d", name, Global->mpi->getDepth());
		}
	};
	~LeaveComputeWithVarGroup() {
    fc->numericalGradTool.reset();
		fc->destroyChildren();
		if (toResetInform) fc->setInform(std::max(origInform, fc->getInform()));
		Global->checkpointMessage(fc, "%s", name);
		if (Global->debugProtectStack) {
			mxLog("exit %s: protect depth %d", name, Global->mpi->getDepth());
		}

	}
};

void omxCompute::computeWithVarGroup(FitContext *fc)
{
	LeaveComputeWithVarGroup lcwvg(fc, this);
	computeImpl(fc);
}

class ComputeContainer : public omxCompute {
	typedef omxCompute super;
protected:
	std::vector< omxCompute* > clist;
public:
	virtual void collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out) override;
};

void ComputeContainer::collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out)
{
	super::collectResults(fc, lcr, out);
	collectResultsHelper(fc, clist, lcr, out);
}

class omxComputeSequence : public ComputeContainer {
	typedef ComputeContainer super;
	bool independent;

 public:
	virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
	virtual ~omxComputeSequence();
};

class omxComputeIterate : public ComputeContainer {
	typedef ComputeContainer super;
	int maxIter;
	double maxDuration;
	double tolerance;
	int iterations;
	int verbose;

 public:
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
	virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
	virtual ~omxComputeIterate();
};

class ComputeLoop : public ComputeContainer {
	typedef ComputeContainer super;
	int verbose;
	int indicesLength;
	int *indices;
	int maxIter;
	double maxDuration;
	int iterations;
	int startFrom;

 public:
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
	virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
	virtual ~ComputeLoop();
};

class omxComputeOnce : public omxCompute {
	typedef omxCompute super;
	std::vector< omxMatrix* > algebras;
	std::vector< omxExpectation* > expectations;
	std::vector< const char* > predict;
	const char *how;
	int verbose;
	bool mac;
	bool starting;
	bool fit;
	bool gradient;
	bool hessian;
	bool ihessian;
	bool infoMat;
	enum ComputeInfoMethod infoMethod;
	bool hgprod;
	bool isBestFit; // for backward compatibility

 public:
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeEM : public omxCompute {
	typedef omxCompute super;
  std::unique_ptr<omxCompute> estep;
  std::unique_ptr<omxCompute> mstep;
	omxMatrix *fit3;   // rename to observedFit
	int EMcycles;
	int maxIter;
	int mstepIter;
	int totalMstepIter;
	double tolerance;
	double semTolerance;
	int verbose;
	Eigen::VectorXd lbound;
	Eigen::VectorXd ubound;
	const char *accelName;
	bool useRamsay;
	bool useVaradhan;
  std::unique_ptr<EMAccel> accel;
	enum EMInfoMethod {
		EMInfoNone,
		EMInfoMengRubinFamily,
		EMInfoOakes
	} information;
	std::vector< omxMatrix * > infoFitFunction;
	enum ComputeInfoMethod infoMethod;
	enum SEMMethod { ClassicSEM, TianSEM, GridSEM, AgileSEM } semMethod;
	double *semMethodData;
	int semMethodLen;
	bool semDebug;
	bool semFixSymmetry;
	bool semForcePD;
	int agileMaxIter;
	SEXP rateMatrix; //debug
	SEXP inputInfoMatrix; //debug
	SEXP outputInfoMatrix; //debug
	SEXP origEigenvalues; //debug
	double noiseTarget;
	double noiseTolerance;
	std::vector<double*> estHistory;
	Eigen::MatrixXd probeOffset;
	std::vector<double> diffWork;
	std::vector<int> paramProbeCount;
	Eigen::VectorXd optimum;
	double bestFit;
 	static const double MIDDLE_START;
	static const double MIDDLE_END;
	size_t maxHistLen;
	int semProbeCount;

	void observedFit(FitContext *fc);
	template <typename T1>
	void accelLineSearch(bool major, FitContext *fc, Eigen::MatrixBase<T1> &preAccel);
	template <typename T>
	bool probeEM(FitContext *fc, int vx, double offset, Eigen::MatrixBase<T> &rijWork);

	template <typename T>
	void recordDiff(FitContext *fc, int v1, Eigen::MatrixBase<T> &rijWork,
			double *stdDiff, bool *mengOK);
	void MengRubinFamily(FitContext *fc);

	void Oakes(FitContext *fc);

 public:
	template <typename T1, typename T2>
	void dEstep(FitContext *fc, Eigen::MatrixBase<T1> &x, Eigen::MatrixBase<T2> &result);

        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
	virtual void collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
	virtual ~ComputeEM();
};

const double ComputeEM::MIDDLE_START = 0.105360515657826281366; // -log(.9) constexpr
const double ComputeEM::MIDDLE_END = 0.001000500333583534363566; // -log(.999) constexpr

struct ComputeSetOriginalStarts : public omxCompute {
	virtual bool accumulateInform() override { return false; };
        virtual void computeImpl(FitContext *fc) override;
};

class ComputeStandardError : public omxCompute {
	typedef omxCompute super;
	omxMatrix *fitMat;
	std::vector<omxExpectation *> exList;
	std::vector<int> numStats;
	bool wlsStats;
	double x2;
	int df;
	double x2m, x2mv;
	double madj, mvadj, dstar;

	struct visitEx {
		ComputeStandardError &top;
		visitEx(ComputeStandardError *cse) : top(*cse) {};
		void operator()(omxMatrix *mat) const
		{
			if (!mat->fitFunction) {
				omxRaiseErrorf("%s: Cannot compute SEs when '%s' included in fit",
					 top.name, mat->name());
				return;
			}
			omxExpectation *e1 = mat->fitFunction->expectation;
			if (!e1) return;
			if (!e1->data) {
				omxRaiseErrorf("%s: expectation '%s' does not have data",
					 top.name, e1->name);
				return;
			}
			omxData *d1 = e1->data;
			d1->visitObsStats([this, d1](obsSummaryStats &o1) {
					if (o1.asymCov) return;
					mxThrow("%s: terribly sorry, master, but '%s' does not "
						"include the asymptotic covariance matrix hence "
						"standard errors cannot be computed",
						top.name, d1->name);
				});
			top.exList.push_back(e1);
		}
	};

 public:
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

struct ParJacobianSense {
	FitContext *fc;
	std::vector<omxExpectation *> *exList;
	std::vector<omxMatrix *> *alList;
	int numOf;
	std::vector<int> numStats;
	int maxNumStats;
	int totalNumStats;
  int numFree;
	int defvar_row;
	Eigen::ArrayXd ref;
	Eigen::MatrixXd result;

	// default defvar_row to 1 or 0? TODO
	ParJacobianSense() : exList(0), alList(0), defvar_row(1) {};

	void attach(std::vector<omxExpectation *> *u_exList, std::vector<omxMatrix *> *u_alList) {
		if (u_exList && u_alList) mxThrow("u_exList && u_alList");
		exList = u_exList;
		alList = u_alList;
		numOf = exList? exList->size() : alList->size();
		numStats.reserve(numOf);
		maxNumStats = 0;
		totalNumStats = 0;
		for (int ex=0; ex < numOf; ++ex) {
			int nss = exList? (*exList)[ex]->numSummaryStats() : (*alList)[ex]->size();
			numStats.push_back(nss);
			totalNumStats += nss;
			maxNumStats = std::max(nss, maxNumStats);
		}
	};

	void measureRef(FitContext *u_fc) {
		using Eigen::Map;
		using Eigen::VectorXd;
		fc = u_fc;
		numFree = fc->getNumFree();
		result.resize(totalNumStats, numFree);
		ref.resize(totalNumStats);
    VectorXd point(numFree);
    fc->copyEstToOptimizer(point);
		(*this)(point.data(), -1, ref);
	}

	template <typename T1>
	void operator()(double *myPars, int thrId, Eigen::ArrayBase<T1> &result1) const {
    FitContext *fc2 = thrId >= 0? fc->childList[thrId] : fc;
    Eigen::Map< Eigen::VectorXd > Est(myPars, numFree);
    fc2->setEstFromOptimizer(Est);
    omxState *st = fc2->state;
		Eigen::VectorXd tmp(maxNumStats);
		for (int ex=0, offset=0; ex < numOf; offset += numStats[ex++]) {
			if (exList) {
				st->lookupDuplicate((*exList)[ex])->asVector(fc2, defvar_row, tmp);
				result1.block(offset, 0, numStats[ex], 1) =
					tmp.array().segment(0, numStats[ex]);
			} else {
				omxMatrix *mat = st->lookupDuplicate((*alList)[ex]);
				omxRecompute(mat, fc2);
				EigenVectorAdaptor vec(mat);
				if (numStats[ex] != vec.size()) {
					mxThrow("Algebra '%s' changed size during Jacobian", mat->name());
				}
				result1.block(offset, 0, numStats[ex], 1) = vec;
			}
		}
	}
};

class ComputeJacobian : public omxCompute {
	typedef omxCompute super;
	std::vector<omxExpectation *> exList;
	std::vector<omxMatrix *> alList;
	omxData *data;
	ParJacobianSense sense;

 public:
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeHessianQuality : public omxCompute {
	typedef omxCompute super;
	int verbose;
 public:
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeReportDeriv : public omxCompute {
	typedef omxCompute super;
 public:
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeCheckpoint : public omxCompute {
	typedef omxCompute super;

	struct snap {
		int evaluations;
		int iterations;
		time_t timestamp;
		std::vector<int> computeLoopIndex;
		Eigen::VectorXd est;
		double fit;
		FitStatisticUnits fitUnits;
		int inform;
		Eigen::VectorXd stderrs;
		Eigen::VectorXd gradient;
		Eigen::VectorXd vcov;
		Eigen::VectorXd algebraEnt;
    Eigen::VectorXd sampleSize;
		std::vector< std::string > extra;
	};

	const char *path;
	std::ofstream ofs;
	bool toReturn;
	std::vector<omxMatrix*> algebras;
	int numAlgebraEnt;
	bool wroteHeader;
	std::vector<std::string> colnames;
	std::forward_list<snap> snaps;
	int numSnaps;
	int numParam;
	bool inclPar, inclLoop, inclFit, inclCounters, inclStatus;
	bool inclSEs;
	bool inclGradient;
	bool inclVcov;
	bool inclVcovWLS;
  std::set<std::string> vcovFilterSet;
  std::map<std::string, std::vector<bool> > exoVcovFilter;
  std::vector<bool> vcovFilter;
  int vcovEntries;
  bool inclSampleSize;
	bool badSEWarning;
	bool firstTime;
	size_t numExtraCols;

 public:
	virtual bool accumulateInform() override { return false; };
        virtual void initFromFrontend(omxState *, SEXP rObj) override;
        virtual void computeImpl(FitContext *fc) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeReportExpectation : public omxCompute {
	typedef omxCompute super;
 public:
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeBootstrap : public omxCompute {
	typedef omxCompute super;

	struct context {
		omxData *data;
		std::vector<int> origCumSum;
		std::vector<int> resample;
	};
	std::vector< context > contexts;
  std::unique_ptr<omxCompute> plan;
	int verbose;
	int numReplications;
	int seed;
	//std::vector<double> quantile;
	bool parallel;
	int only;

	int previousNumParam;
	SEXP previousData;
	SEXP rawOutput;
	MxRList onlyWeight;

 public:
	virtual bool accumulateInform() override { return false; };
	virtual void initFromFrontend(omxState *, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
	virtual void collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out) override;
	virtual void reportResults(FitContext *fc, MxRList *, MxRList *result) override;
};

class ComputeGenerateData : public omxCompute {
	typedef omxCompute super;
	std::vector< omxExpectation* > expectations;
	MxRList simData;

 public:
	virtual void initFromFrontend(omxState *globalState, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
        virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *out) override;
};

class ComputeLoadData : public omxCompute {
	typedef omxCompute super;

	static std::vector< std::unique_ptr<LoadDataProviderBase2> > Providers;
	std::unique_ptr<LoadDataProviderBase2> provider;

	omxData *data;
	bool useOriginalData;

	struct ColumnInvalidator : StateInvalidator {
		typedef StateInvalidator super;
		omxData *data;
		const std::vector< int > &columns;
		ColumnInvalidator(omxState &u_st, omxData *u_data,
				  const std::vector< int > &u_columns) :
			super(u_st), data(u_data), columns(u_columns) {};
		virtual void doData() override { data->invalidateColumnsCache(columns); };
	};

 public:
	static void loadedHook();
	static void addProvider(std::unique_ptr<LoadDataProviderBase2> ldp)
  { Providers.emplace_back(std::move(ldp)); }
	virtual void initFromFrontend(omxState *globalState, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
	virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *) override;
};

std::vector<std::unique_ptr<LoadDataProviderBase2> > ComputeLoadData::Providers;

void ComputeLoadDataLoadedHook()
{ ComputeLoadData::loadedHook(); }

class ComputeLoadMatrix : public omxCompute {
	typedef omxCompute super;

	enum LoadMethod {
		LoadCSV,
		LoadDataFrame
	} loadMethod;

	std::vector< omxMatrix* > mat;
	std::vector< mini::csv::ifstream* > streams;
	std::vector<bool> hasRowNames;
	bool useOriginalData;
	// origData is not really needed until it is possible to seek backwards
	std::vector<Eigen::MatrixXd> origData;
	int line;
	Rcpp::DataFrame observed;

	void loadFromCSV(FitContext *fc, int index);
	void loadDataFrame(FitContext *fc, int index);

 public:
	virtual ~ComputeLoadMatrix();
	virtual void initFromFrontend(omxState *globalState, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
};

class ComputeLoadContext : public omxCompute {
	typedef omxCompute super;

	int verbose;
	int loadCounter;
	char sep;
	bool header;
	std::vector<const char *> colnames;
	std::string path;
	std::unique_ptr< mini::csv::ifstream > st;
	int cpIndex;
	int numColumns;
	int *columnPtr;
	int maxColumn;
	int curLine;

	void reopen();

 public:
	virtual void initFromFrontend(omxState *globalState, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
	virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *) override;
};

class ComputeTryCatch : public omxCompute {
	typedef omxCompute super;
	std::unique_ptr< omxCompute > plan;
	int cpIndex;

public:
	virtual void initFromFrontend(omxState *, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
	virtual void collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out) override;
};

class ComputePenaltySearch : public omxCompute {
	typedef omxCompute super;

	int verbose;
	std::vector< omxMatrix* > fitfunction;
	std::unique_ptr< omxCompute > plan;
  double ebicGamma;
  DataFrame result;

 public:
	virtual void initFromFrontend(omxState *globalState, SEXP rObj) override;
	virtual void computeImpl(FitContext *fc) override;
	virtual void reportResults(FitContext *fc, MxRList *slots, MxRList *) override;
};

void ComputePenaltySearch::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

  S4 obj(rObj);

	PushLoopIndex pli(name);

  verbose = Rf_asInteger(obj.slot("verbose"));
  IntegerVector ffv = obj.slot("fitfunction");
  if (ffv.size() != 1) mxThrow("%s: can add the regularization penalty to "
                               "exactly one fit function (not %d of them)", ffv.size());
	for (int wx=0; wx < ffv.size(); ++wx) {
    omxMatrix *mat = globalState->algebraList[ ffv[wx] ];
    if (!mat->isFitFunction()) mxThrow("%s: %s is not a fit function", name, mat->name());
    fitfunction.push_back(mat);
  }
  if (fitfunction.size() != 1) mxThrow("%s: a fitfunction is required", name);

  const char *approach = obj.slot("approach");
  if (!strEQ(approach, "EBIC"))
    mxThrow("%s: approach '%s' not implemented", name, approach);

  ebicGamma = Rf_asReal(obj.slot("ebicGamma"));

  S4 Rplan = obj.slot("plan");
	plan = std::unique_ptr< omxCompute >(omxNewCompute(globalState, Rplan.attr("class")));
	plan->initFromFrontend(globalState, Rplan);
}

void ComputePenaltySearch::computeImpl(FitContext *fc)
{
  auto &fvg = *Global->findVarGroup(FREEVARGROUP_ALL);
  if (int(fvg.vars.size()) != fc->numParam)
    mxThrow("%s: FitContext narrowed to %d parameters", name, fc->numParam);
  auto &pg = Global->penaltyGrid;

  int gridSize = 1;
  for (auto it = pg.cbegin(); it != pg.cend(); ++it) {
    NumericVector g1(it->second);
    gridSize *= g1.size();
  }
  if (verbose >= 1) mxLog("%s: grid size %d", name, gridSize);

  CharacterVector rnames;
  rnames.push_back("EBIC");
  result.push_back(NumericVector(gridSize));
  rnames.push_back("EP");
  result.push_back(IntegerVector(gridSize));
  rnames.push_back("fit");
  result.push_back(NumericVector(gridSize));
  rnames.push_back("objective");
  result.push_back(NumericVector(gridSize));
  rnames.push_back("statusCode");
  result.push_back(allocInformVector(gridSize));
  int resultParamOffset = result.size();
  for (int px=0; px < fc->numParam; ++px) {
    rnames.push_back(fvg.vars[px]->name);
    result.push_back(NumericVector(gridSize));
  }
  result.attr("names") = rnames;

  double bestEBIC = NA_REAL;
  int bestGridIndex = -1;
  for (int gx=0; gx < gridSize; ++gx) {
		PushLoopIndex pli(name, gx, gridSize);
    int abscissa = gx;
    for (auto it = pg.cbegin(); it != pg.cend(); ++it) {
      NumericVector g1(it->second);
      fc->est[it->first] = g1[abscissa % g1.size()];
      //mxLog("%s: [%d] %s = %f", name, gx, fvg.vars[it->first]->name, fc->est[it->first]);
      abscissa /= g1.size();
    }
    plan->compute(fc);
    int zero = 0;
    for (auto &a1 : fc->state->algebraList) {
      if (!a1->isPenalty()) continue;
      zero += a1->penalty->countNumZero(fc);
    }
    int EP = fc->getNumFree() - zero; //estimatedParameters
    int observedStats = 0;
    fitfunction[0]->fitFunction->traverse([&observedStats](omxMatrix *f1){
      auto ff = f1->fitFunction;
      if (ff->expectation) observedStats += ff->expectation->numObservedStats();
    });
    int DF = observedStats - EP;

    // how to extend support to multiple groups? TODO
    auto ex = fitfunction[0]->fitFunction->expectation;
    if (!ex) mxThrow("%s: fitfunction '%s' does not have an expectation", fitfunction[0]->name());
    int np = ex->numManifestVars();
    int nfac = ex->numLatentVars();
    if (nfac < 1) nfac = 1;
    double cvDF = ((np*np+1)/2. + np - EP)/DF;
    if (!ex->data) mxThrow("%s: expectation '%s' has no associated data", ex->name);
    if (fitfunction[0]->fitFunction->units != FIT_UNITS_MINUS2LL) {
      mxThrow("%s: fit function '%s' must be -2ll units (not %s)",
              name, fitfunction[0]->name(), fitUnitsToName(fitfunction[0]->fitFunction->units));
    }
    double ll = fitfunction[0]->data[0];
    double N = omxDataNumObs(ex->data);
    double EBIC;
    if (strEQ(ex->data->getType(), "raw")) {
      EBIC = ll * cvDF + (log(N) * EP + 2*EP * ebicGamma * log(np+nfac));
    } else {
      EBIC = ll +         log(N) * EP + 2*EP * ebicGamma * log(np+nfac);
    }
    if (bestGridIndex == -1 || EBIC < bestEBIC) {
      bestGridIndex = gx;
      bestEBIC = EBIC;
    }
    {NumericVector v = result[0]; v[gx] = EBIC;}
    {IntegerVector v = result[1]; v[gx] = EP;}
    {NumericVector v = result[2]; v[gx] = ll;}
    {NumericVector v = result[3]; v[gx] = fc->getFit();}
    {IntegerVector v = result[4]; v[gx] = fc->wrapInform();}
    for (int px=0; px < fc->numParam; ++px) {
      NumericVector vec = result[resultParamOffset+px];
      vec[gx] = fc->est[px];
    }
    std::string detail = std::to_string(gx+1) + "/" + std::to_string(gridSize);
    Global->reportProgress1(name, detail);
  }

  if (verbose >= 1) mxLog("-> best[%d] %f", bestGridIndex, bestEBIC);

  for (int px=0; px < fc->numParam; ++px) {
    NumericVector vec = result[resultParamOffset+px];
    fc->est[px] = vec[bestGridIndex];
  }
  fc->wanted &= ~FF_COMPUTE_FIT;  // discard garbage
  // auxillary information like per-row likelihoods need a refresh
  ComputeFit(name, fitfunction[0], FF_COMPUTE_FIT, fc);
}

void ComputePenaltySearch::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	MxRList output;
	output.add("detail", result);
	slots->add("output", output.asR());
}

static class omxCompute *newComputeSequence()
{ return new omxComputeSequence(); }

static class omxCompute *newComputeIterate()
{ return new omxComputeIterate(); }

static class omxCompute *newComputeLoop()
{ return new ComputeLoop(); }

static class omxCompute *newComputeOnce()
{ return new omxComputeOnce(); }

static class omxCompute *newComputeEM()
{ return new ComputeEM(); }

static class omxCompute *newComputeHessianQuality()
{ return new ComputeHessianQuality(); }

static class omxCompute *newComputeReportDeriv()
{ return new ComputeReportDeriv(); }

static class omxCompute *newComputeReportExpectation()
{ return new ComputeReportExpectation(); }

static class omxCompute *newComputeBootstrap()
{ return new ComputeBootstrap(); }

static class omxCompute *newComputeGenerateData()
{ return new ComputeGenerateData(); }

static class omxCompute *newComputeLoadMatrix()
{ return new ComputeLoadMatrix(); }

static class omxCompute *newComputeCheckpoint()
{ return new ComputeCheckpoint(); }

struct omxComputeTableEntry {
        char name[32];
        omxCompute *(*ctor)();
};

static const struct omxComputeTableEntry omxComputeTable[] = {
        {"MxComputeNumericDeriv", &newComputeNumericDeriv},
        {"MxComputeGradientDescent", &newComputeGradientDescent},
	{"MxComputeSequence", &newComputeSequence },
	{"MxComputeIterate", &newComputeIterate },
	{"MxComputeLoop", &newComputeLoop },
	{"MxComputeOnce", &newComputeOnce },
        {"MxComputeNewtonRaphson", &newComputeNewtonRaphson},
        {"MxComputeEM", &newComputeEM },
	{"MxComputeStandardError",
	 []()->omxCompute* { return new ComputeStandardError; }},
	{"MxComputeHessianQuality", &newComputeHessianQuality},
	{"MxComputeReportDeriv", &newComputeReportDeriv},
	{"MxComputeConfidenceInterval", &newComputeConfidenceInterval},
	{"MxComputeReportExpectation", &newComputeReportExpectation},
	{"MxComputeTryHard", &newComputeTryHard},
	{"MxComputeNelderMead", &newComputeNelderMead},
	{"MxComputeBootstrap", &newComputeBootstrap},
	{"MxComputeGenerateData", &newComputeGenerateData},
	{"MxComputeLoadData",
	 []()->omxCompute* { return new ComputeLoadData; }},
	{"MxComputeLoadMatrix", &newComputeLoadMatrix},
	{"MxComputeCheckpoint", newComputeCheckpoint},
	{"MxComputeSimAnnealing", &newComputeGenSA},
	{"MxComputeJacobian",
	 []()->omxCompute* { return new ComputeJacobian; }},
	{"MxComputeSetOriginalStarts",
	 []()->omxCompute* { return new ComputeSetOriginalStarts; }},
	{"MxComputeTryCatch",
	 []()->omxCompute* { return new ComputeTryCatch; }},
	{"MxComputeLoadContext",
	 []()->omxCompute* { return new ComputeLoadContext; }},
	{"MxComputePenaltySearch",
	 []()->omxCompute* { return new ComputePenaltySearch; }}
};

omxCompute *omxNewCompute(omxState* os, const char *type)
{
        omxCompute *got = NULL;

        for (size_t fx=0; fx < OMX_STATIC_ARRAY_SIZE(omxComputeTable); fx++) {
                const struct omxComputeTableEntry *entry = omxComputeTable + fx;
                if(strcmp(type, entry->name) == 0) {
                        got = entry->ctor();
			got->name = entry->name;
                        break;
                }
        }

        if (!got) mxThrow("Compute plan step '%s' is not implemented", type);

        return got;
}

void omxComputeSequence::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	SEXP slotValue;
	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("independent")));
	independent = Rf_asLogical(slotValue);
	}

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("steps")));

	for (int cx = 0; cx < Rf_length(slotValue); cx++) {
		SEXP step = VECTOR_ELT(slotValue, cx);
		SEXP s4class;
		const char *s4name;
		{
			ScopedProtect p1(s4class, STRING_ELT(Rf_getAttrib(step, R_ClassSymbol), 0));
			s4name = CHAR(s4class);
		}
		omxCompute *compute = omxNewCompute(globalState, s4name);
		clist.push_back(compute);
		compute->initFromFrontend(globalState, step);
		if (isErrorRaised()) break;
	}

	if (independent) {
		bool fail = false;
		for (int c1 = 1; c1 < (int) clist.size(); ++c1) {
			for (int c2 = 0; c2 < c1; ++c2) {
				if (clist[c1]->varGroup->isDisjoint(clist[c2]->varGroup)) continue;
				omxRaiseErrorf("mxComputeSequence(independent=TRUE) but steps "
					       "%d and %d contain some of the same "
					       "free parameters", 1+c1, 1+c2);
				fail = true;
				break;
			}
			if (fail) break;
		}
	}
}

void omxComputeSequence::computeImpl(FitContext *fc)
{
	for (size_t cx=0; cx < clist.size(); ++cx) {
		clist[cx]->compute(fc);
		if (isErrorRaised()) break;
	}
}

omxComputeSequence::~omxComputeSequence()
{
	for (size_t cx=0; cx < clist.size(); ++cx) {
		delete clist[cx];
	}
}

void ComputeTryCatch::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	auto &cp = Global->checkpointColnames;
	cpIndex = cp.size();
	std::string errCol(string_snprintf("catch%d", int(Global->computeLoopIndex.size())));
	cp.push_back(errCol);

	SEXP slotValue;
	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("plan")));
	SEXP s4class;
	Rf_protect(s4class = STRING_ELT(Rf_getAttrib(slotValue, R_ClassSymbol), 0));
	plan = std::unique_ptr< omxCompute >(omxNewCompute(globalState, CHAR(s4class)));
	plan->initFromFrontend(globalState, slotValue);
}

void ComputeTryCatch::computeImpl(FitContext *fc)
{
	auto &cv = Global->checkpointValues;
	cv[cpIndex] = "";
	try {
		plan->compute(fc);
	} catch( std::exception &ex ) {
		cv[cpIndex] = ex.what();
	} catch(...) {
		cv[cpIndex] = "c++ exception (unknown reason)";
	}
	if (isErrorRaisedIgnTime()) {
		cv[cpIndex] = Global->getBads();
		Global->bads.clear();
	}
	Global->throwOnUserInterrupted();
}

void ComputeTryCatch::collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out)
{
	super::collectResults(fc, lcr, out);
	std::vector< omxCompute* > clist(1);
	clist[0] = plan.get();
	collectResultsHelper(fc, clist, lcr, out);
}

void omxComputeIterate::initFromFrontend(omxState *globalState, SEXP rObj)
{
	SEXP slotValue;

	super::initFromFrontend(globalState, rObj);

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("maxIter")));
	maxIter = INTEGER(slotValue)[0];
	}

	{
		ProtectedSEXP RmaxDur(R_do_slot(rObj, Rf_install("maxDuration")));
		maxDuration = Rf_asReal(RmaxDur);
	}

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("tolerance")));
	tolerance = REAL(slotValue)[0];
	if (std::isfinite(tolerance) && tolerance <= 0) mxThrow("tolerance must be positive");
	}

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("steps")));

	for (int cx = 0; cx < Rf_length(slotValue); cx++) {
		SEXP step = VECTOR_ELT(slotValue, cx);
		SEXP s4class;
		const char *s4name;
		{
			ScopedProtect p1(s4class, STRING_ELT(Rf_getAttrib(step, R_ClassSymbol), 0));
			s4name = CHAR(s4class);
		}
		omxCompute *compute = omxNewCompute(globalState, s4name);
		if (isErrorRaised()) break;
		clist.push_back(compute);
		compute->initFromFrontend(globalState, step);
	}

	{
		ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("verbose")));
		verbose = Rf_asInteger(slotValue);
	}
	iterations = 0;
}

void omxComputeIterate::computeImpl(FitContext *fc)
{
	double prevFit = 0;
	double mac = tolerance * 10;
	time_t startTime = time(0);
	while (1) {
		++iterations;
		++fc->iterations;
		for (size_t cx=0; cx < clist.size(); ++cx) {
			clist[cx]->compute(fc);
			if (isErrorRaised()) break;
		}
		if (fc->wanted & FF_COMPUTE_MAXABSCHANGE) {
			if (fc->mac < 0) {
				Rf_warning("MAC estimated at %.4f; something is wrong", fc->mac);
				break;
			} else {
				mac = fc->mac;
				if (verbose) mxLog("ComputeIterate: mac %.9g", mac);
			}
		}
		if (fc->wanted & FF_COMPUTE_FIT) {
			if (fc->getFit() == 0) {
				Rf_warning("Fit estimated at 0; something is wrong");
				break;
			}
			if (prevFit != 0) {
				double change = (prevFit - fc->getFit()) / fc->getFit();
				if (verbose) mxLog("ComputeIterate: fit %.9g rel change %.9g", fc->getFit(), change);
				mac = fabs(change);
			} else {
				if (verbose) mxLog("ComputeIterate: initial fit %.9g", fc->getFit());
			}
			prevFit = fc->getFit();
		}
		if (std::isfinite(tolerance)) {
			if (!(fc->wanted & (FF_COMPUTE_MAXABSCHANGE | FF_COMPUTE_FIT))) {
				omxRaiseErrorf("ComputeIterate: neither MAC nor fit available");
			}
			if (mac < tolerance) break;
		}
		if (std::isfinite(maxDuration) && time(0) - startTime > maxDuration) break;
		if (isErrorRaised() || iterations >= maxIter) break;
	}
}

void omxComputeIterate::reportResults(FitContext *fc, MxRList *slots, MxRList *out)
{
	MxRList output;
	output.add("iterations", Rf_ScalarInteger(iterations));
	slots->add("output", output.asR());
}

omxComputeIterate::~omxComputeIterate()
{
	for (size_t cx=0; cx < clist.size(); ++cx) {
		delete clist[cx];
	}
}

void ComputeLoop::initFromFrontend(omxState *globalState, SEXP rObj)
{
	SEXP slotValue;

	super::initFromFrontend(globalState, rObj);

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("maxIter")));
	maxIter = INTEGER(slotValue)[0];
	}

	{
		ProtectedSEXP RstartFrom(R_do_slot(rObj, Rf_install("startFrom")));
		startFrom = Rf_asInteger(RstartFrom);
		ProtectedSEXP Rverbose(R_do_slot(rObj, Rf_install("verbose")));
		verbose = Rf_asInteger(Rverbose);
		ProtectedSEXP Rindices(R_do_slot(rObj, Rf_install("indices")));
		indicesLength = Rf_length(Rindices);
		indices = INTEGER(Rindices);
		ProtectedSEXP RmaxDur(R_do_slot(rObj, Rf_install("maxDuration")));
		maxDuration = Rf_asReal(RmaxDur);
	}

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("steps")));

	PushLoopIndex pli(name);

	for (int cx = 0; cx < Rf_length(slotValue); cx++) {
		SEXP step = VECTOR_ELT(slotValue, cx);
		SEXP s4class;
		const char *s4name;
		{
			ScopedProtect p1(s4class, STRING_ELT(Rf_getAttrib(step, R_ClassSymbol), 0));
			s4name = CHAR(s4class);
		}
		omxCompute *compute = omxNewCompute(globalState, s4name);
		if (isErrorRaised()) break;
		clist.push_back(compute);
		compute->initFromFrontend(globalState, step);
	}

	iterations = 0;
}

void ComputeLoop::computeImpl(FitContext *fc)
{
	bool hasIndices = indicesLength != 0;
	bool hasMaxIter = maxIter != NA_INTEGER;
	time_t startTime = time(0);
	int lastIndex = indicesLength;
	if (hasMaxIter) lastIndex = std::min(lastIndex, maxIter);
	while (1) {
		PushLoopIndex pli(name, hasIndices? indices[iterations] : startFrom+iterations,
											iterations, lastIndex);
		++iterations;
		++fc->iterations;
		for (size_t cx=0; cx < clist.size(); ++cx) {
			clist[cx]->compute(fc);
			if (isErrorRaised()) {
				if (verbose) mxLog("%s: error raised at step %d", name, int(cx));
				break;
			}
		}
		if (std::isfinite(maxDuration) && time(0) - startTime > maxDuration) {
			if (verbose) mxLog("%s: maximum duration", name);
			break;
		}
		if (hasMaxIter && iterations >= maxIter) {
			if (verbose) mxLog("%s: maximum iterations", name);
			break;
		}
		if (hasIndices && iterations >= indicesLength) {
			if (verbose) mxLog("%s: completed todo list", name);
			break;
		}
		if (isErrorRaised()) {
			if (verbose) mxLog("%s: error raised", name);
			break;
		}
		if (!hasMaxIter) {
			auto &clm = Global->computeLoopMax;
			int m1 = clm[clm.size() - 1];
			if (m1) {
				// filled in by sub compute plan
				maxIter = m1;
				hasMaxIter = true;
			}
		}
	}
}

void ComputeLoop::reportResults(FitContext *fc, MxRList *slots, MxRList *out)
{
	MxRList output;
	output.add("iterations", Rf_ScalarInteger(iterations));
	slots->add("output", output.asR());
}

ComputeLoop::~ComputeLoop()
{
	for (size_t cx=0; cx < clist.size(); ++cx) {
		delete clist[cx];
	}
}

void ComputeEM::initFromFrontend(omxState *globalState, SEXP rObj)
{
	SEXP slotValue;
	SEXP s4class;

	super::initFromFrontend(globalState, rObj);

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("estep")));
	Rf_protect(s4class = STRING_ELT(Rf_getAttrib(slotValue, R_ClassSymbol), 0));
	estep = std::unique_ptr<omxCompute>(omxNewCompute(globalState, CHAR(s4class)));
	estep->initFromFrontend(globalState, slotValue);

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("mstep")));
	Rf_protect(s4class = STRING_ELT(Rf_getAttrib(slotValue, R_ClassSymbol), 0));
	mstep = std::unique_ptr<omxCompute>(omxNewCompute(globalState, CHAR(s4class)));
	mstep->initFromFrontend(globalState, slotValue);

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("observedFit")));
	fit3 = globalState->algebraList[ INTEGER(slotValue)[0] ];
	if (fit3->fitFunction) {
		omxCompleteFitFunction(fit3);
	}

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("maxIter")));
	maxIter = INTEGER(slotValue)[0];
	if (maxIter < 0) mxThrow("maxIter must be non-negative");
	}

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("tolerance")));
	tolerance = REAL(slotValue)[0];
	if (tolerance <= 0) mxThrow("tolerance must be positive");
	}

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("verbose")));
	verbose = Rf_asInteger(slotValue);
	}

	useRamsay = false;
	useVaradhan = false;
	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("accel")));
	accelName = CHAR(STRING_ELT(slotValue, 0));
	if (strEQ(accelName, "ramsay1975")) {
		useRamsay = true;
	} else if (strEQ(accelName, "varadhan2008")) {
		useVaradhan = true;
	} else if (STRING_ELT(slotValue, 0) == NA_STRING || strEQ(accelName, "")) {
		accelName = "none";
	} else {
		Rf_warning("%s: unknown acceleration method %s ignored", name, accelName);
		accelName = "none";
	}

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("information")));
	const char *infoName = CHAR(STRING_ELT(slotValue, 0));
	information = EMInfoNone;
	if (STRING_ELT(slotValue, 0) == NA_STRING) {
		// ok
	} else if (strEQ(infoName, "mr1991")) {
		information = EMInfoMengRubinFamily;
	} else if (strEQ(infoName, "oakes1999")) {
		information = EMInfoOakes;
	} else {
		Rf_warning("%s: unknown information method %s ignored", name, infoName);
	}

	if (information == EMInfoOakes) {
		infoMethod = INFO_METHOD_HESSIAN;

		SEXP infoArgs, argNames;
		Rf_protect(infoArgs = R_do_slot(rObj, Rf_install("infoArgs")));
		Rf_protect(argNames = Rf_getAttrib(infoArgs, R_NamesSymbol));

		for (int ax=0; ax < Rf_length(infoArgs); ++ax) {
			const char *key = R_CHAR(STRING_ELT(argNames, ax));
			slotValue = VECTOR_ELT(infoArgs, ax);
			if (strEQ(key, "fitfunction")) {
				for (int fx=0; fx < Rf_length(slotValue); ++fx) {
					omxMatrix *ff = globalState->algebraList[INTEGER(slotValue)[fx]];
					if (!ff->fitFunction) mxThrow("infoArgs$fitfunction is %s, not a fitfunction", ff->name());
					infoFitFunction.push_back(ff);
				}
			} else if (strEQ(key, "inputInfo")) {
				infoMethod = stringToInfoMethod(CHAR(slotValue));
			} else {
				mxLog("%s: unknown key %s", name, key);
			}
		}
	}

	if (information == EMInfoMengRubinFamily) {
		// TODO remove SEM prefix everywhere
		infoMethod = INFO_METHOD_HESSIAN;
		semMethod = AgileSEM;
		agileMaxIter = 1;
		semDebug = false;
		semFixSymmetry = true;
		semForcePD = false;
		noiseTarget = exp(-5.2); //constexpr
		noiseTolerance = exp(2.0); //constexpr

		// Meng & Rubin set this parameter in terms of the absolute tolerance
		// instead of the relative tolerance. semTolerance is used to compare
		// parameter estimates, not log-likelihood, so we cannot provide a
		// sane default based on the tolerance.
		semTolerance = 0.01; // sqrt(1e-4)

		SEXP infoArgs, argNames;
		Rf_protect(infoArgs = R_do_slot(rObj, Rf_install("infoArgs")));
		Rf_protect(argNames = Rf_getAttrib(infoArgs, R_NamesSymbol));

		for (int ax=0; ax < Rf_length(infoArgs); ++ax) {
			const char *key = R_CHAR(STRING_ELT(argNames, ax));
			slotValue = VECTOR_ELT(infoArgs, ax);
			if (strEQ(key, "fitfunction")) {
        // Why do we allow more than one here? How is this
        // different from a multigroup fit function?
				for (int fx=0; fx < Rf_length(slotValue); ++fx) {
					omxMatrix *ff = globalState->algebraList[INTEGER(slotValue)[fx]];
					if (!ff->fitFunction) mxThrow("infoArgs$fitfunction is %s, not a fitfunction", ff->name());
					infoFitFunction.push_back(ff);
				}
			} else if (strEQ(key, "inputInfo")) {
				infoMethod = stringToInfoMethod(CHAR(slotValue));
			} else if (strEQ(key, "semMethod")) {
				semMethodLen = Rf_length(slotValue);
				if (semMethodLen == 0) {
					semMethod = AgileSEM;
					semMethodData = NULL;
				} else if (Rf_isReal(slotValue)) {
					semMethodData = REAL(slotValue);
					semMethod = GridSEM;
				} else if (Rf_isString(slotValue)) {
					const char *methodName = CHAR(Rf_asChar(slotValue));
					if (strEQ(methodName, "mr")) {
						semMethod = ClassicSEM;
					} else if (strEQ(methodName, "tian")) {
						semMethod = TianSEM;
					} else if (strEQ(methodName, "agile")) {
						semMethod = AgileSEM;
					} else {
						mxThrow("Unknown SEM method '%s'", methodName);
					}
				}
			} else if (strEQ(key, "agileMaxIter")) {
				agileMaxIter = INTEGER(slotValue)[0];
			} else if (strEQ(key, "semDebug")) {
				semDebug = Rf_asLogical(slotValue);
			} else if (strEQ(key, "semFixSymmetry")) {
				semFixSymmetry = Rf_asLogical(slotValue);
			} else if (strEQ(key, "semForcePD")) {
				semForcePD = Rf_asLogical(slotValue);
			} else if (strEQ(key, "semTolerance")) {
				semTolerance = Rf_asReal(slotValue);
				if (semTolerance <= 0) mxThrow("semTolerance must be positive");
			} else if (strEQ(key, "noiseTarget")) {
				noiseTarget = REAL(slotValue)[0];
				if (noiseTarget <= 0) mxThrow("noiseTarget must be positive");
			} else if (strEQ(key, "noiseTolerance")) {
				noiseTolerance = REAL(slotValue)[0];
				if (noiseTolerance < 1) mxThrow("noiseTolerance must be >=1");
			} else {
				mxLog("%s: unknown key %s", name, key);
			}
		}
		if (!semFixSymmetry && semForcePD) {
			Rf_warning("%s: semFixSymmetry must be enabled for semForcePD", name);
			semForcePD = false;
		}
	}

	if (information != EMInfoNone && infoFitFunction.size() == 0) {
		omxRaiseErrorf("%s: at least one fitfunction is required to estimate the information matrix. "
			       "Add something like infoArgs=list(fitfunction='fitfunction')", name);
	}

	inputInfoMatrix = NULL;
	outputInfoMatrix = NULL;
	rateMatrix = NULL;
	origEigenvalues = NULL;
}

template <typename T>
bool ComputeEM::probeEM(FitContext *fc, int vx, double offset, Eigen::MatrixBase<T> &rijWork)
{
	bool failed = false;
	probeOffset(paramProbeCount[vx], vx) = offset;

  Eigen::VectorXd loc = optimum;
  loc[vx] += offset;
  fc->setEstFromOptimizer(loc);

	if (verbose >= 3) mxLog("ComputeEM: probe %d of %s offset %.6f",
				1+paramProbeCount[vx], fc->varGroup->vars[vx]->name, offset);

	estep->compute(fc);
	fc->wanted &= ~FF_COMPUTE_HESSIAN;  // discard garbage
	int informSave = fc->getInform();  // not sure if we want to hide inform here TODO
	mstep->compute(fc);
	if (fc->getInform() > INFORM_UNCONVERGED_OPTIMUM) {
		if (verbose >= 3) mxLog("ComputeEM: probe failed with code %d", fc->getInform());
		failed = true;
	}
	fc->setInform(informSave);

  fc->copyEstToOptimizer(loc);
	rijWork.col(paramProbeCount[vx]) = (loc - optimum) / offset;

	paramProbeCount[vx] += 1;
	++semProbeCount;
	return failed;
}

template <typename T>
void ComputeEM::recordDiff(FitContext *fc, int v1, Eigen::MatrixBase<T> &rijWork,
			   double *stdDiff, bool *mengOK)
{
	const int h1 = paramProbeCount[v1]-2;
	const int h2 = h1+1;

	Eigen::ArrayXd diff = (rijWork.col(h1) - rijWork.col(h2)).array().abs();
	*mengOK = (diff < semTolerance).all();

	double dist = fabs(probeOffset(h1, v1) - probeOffset(h2, v1));
	if (dist < tolerance/4) mxThrow("SEM: invalid probe offset distance %.9f", dist);
	*stdDiff = diff.sum() / (diff.size() * dist);
	diffWork[v1 * maxHistLen + h1] = *stdDiff;
	if (verbose >= 2) mxLog("ComputeEM: (%f,%f) mengOK %d diff %f stdDiff %f",
				probeOffset(h1, v1), probeOffset(h2, v1),
				*mengOK, diff.sum() / diff.size(), *stdDiff);
}

void ComputeEM::observedFit(FitContext *fc)
{
	ComputeFit("EM", fit3, FF_COMPUTE_FIT, fc);
	if (verbose >= 4) mxLog("ComputeEM[%d]: observed fit = %f", EMcycles, fc->getFit());

	if (!(fc->wanted & FF_COMPUTE_FIT)) {
		omxRaiseErrorf("ComputeEM: fit not available");
	}
	if (fc->getFit() == 0) {
		omxRaiseErrorf("Fit estimated at 0; something is wrong");
	}
}

template <typename T1>
void ComputeEM::accelLineSearch(bool major, FitContext *fc, Eigen::MatrixBase<T1> &preAccel)
{
	if (!accel->calcDirection(major)) {
		observedFit(fc);
		return;
	}
	if (verbose >= 4) mxPrintMat("accelDir", accel->dir);
	double speed = 1.0;
	int retry = 3;
	while (--retry) {
    Eigen::VectorXd pVec((accel->dir * speed + preAccel).cwiseMax(lbound).cwiseMin(ubound));
    fc->setEstFromOptimizer(pVec);
		observedFit(fc);
		if (std::isfinite(fc->getFit())) return;
		speed *= .3;
		if (verbose >= 3) mxLog("%s: fit NaN; reduce accel speed to %f", name, speed);
	}
	// give up
  fc->setEstFromOptimizer(preAccel);
	observedFit(fc);
}

void ComputeEM::computeImpl(FitContext *fc)
{
	const double Scale = fabs(Global->llScale);
	double prevFit = 0;
	double mac = tolerance * 10;
	bool converged = false;
  // Can't omxAlgebraPreeval because fit function is unknown here
  fc->calcNumFree();
	const int freeVars = fc->getNumFree();
	bool in_middle = false;
	maxHistLen = 0;
	EMcycles = 0;
	semProbeCount = 0;
	lbound.resize(0);

	if (verbose >= 1) mxLog("ComputeEM: Welcome, tolerance=%g accel=%s info=%d",
				tolerance, accelName, information);

	if (useRamsay) accel = std::make_unique<Ramsay1975>(fc, verbose, -1.25);
	if (useVaradhan) accel = std::make_unique<Varadhan2008>(fc, verbose);

	int mstepInform = INFORM_UNINITIALIZED;
	std::vector<double> prevEst(fc->getNumFree());
	while (EMcycles < maxIter) {
		++ EMcycles;
    fc->copyEstToOptimizer(prevEst);
		if (verbose >= 4) mxLog("ComputeEM[%d]: E-step", EMcycles);
		estep->compute(fc);
		fc->wanted &= ~FF_COMPUTE_DERIV;

		{
			if (verbose >= 4) mxLog("ComputeEM[%d]: M-step", EMcycles);
			FitContext *fc1 = new FitContext(fc, mstep->varGroup);
			int startIter = fc1->iterations;
			mstep->compute(fc1);
			fc1->wanted &= ~FF_COMPUTE_HESSIAN;  // discard garbage
			mstepIter = fc1->iterations - startIter;
			totalMstepIter += mstepIter;
			mstepInform = fc1->getInform();
			fc1->updateParentAndFree();
		}

		if (accel) {
			if (!lbound.size()) {
				// bounds might have changed
				lbound.resize(freeVars);
				ubound.resize(freeVars);
				for(int px = 0; px < int(freeVars); px++) {
					lbound[px] = varGroup->vars[px]->lbound;
					ubound[px] = varGroup->vars[px]->ubound;
				}
				if (verbose >= 3) {
					mxPrintMat("lbound", lbound);
					mxPrintMat("ubound", ubound);
				}
			}

			Eigen::VectorXd preAccel(fc->getNumFree());
      fc->copyEstToOptimizer(preAccel);
			accel->recordTrajectory(prevEst);

			if (EMcycles > 3 && (EMcycles + 1) % 3 == 0) {
				accel->recalibrate();
				accelLineSearch(true, fc, preAccel);
				while (prevFit < fc->getFit()) {
					if (!accel->retry()) break;
					accelLineSearch(true, fc, preAccel);
				}
			} else {
				accelLineSearch(false, fc, preAccel);
			}
		} else {
			observedFit(fc);
		}

		if (!std::isfinite(fc->getFit())) {
			omxRaiseErrorf("%s: fit not finite in iteration %d", name, EMcycles);
		}

		double change = 0;
		if (prevFit != 0) {
			if (verbose >= 5) {
				for (int px=0; px < freeVars; ++px) {
					omxFreeVar *fv = fc->varGroup->vars[px];
					mxLog("%d~%s %.4f -> %.4f",
					      px, fv->name, prevEst[px], fc->est[px]);
				}
			}

			change = (prevFit - fc->getFit()) / fc->getFit();
			if (verbose >= 2) mxLog("ComputeEM[%d]: msteps %d fit %.9g rel change %.9g",
                              EMcycles, mstepIter, fc->getFit(), change);
			mac = fabs(change);

			// For Tian, in_middle depends on the absolute (not relative) change in LL!
			const double absMac = fabs(prevFit - fc->getFit());
			if (absMac < MIDDLE_START * Scale) in_middle = true;
			if (absMac < MIDDLE_END * Scale) in_middle = false;
		} else {
			if (verbose >= 2) mxLog("ComputeEM: msteps %d initial fit %.9g",
                              mstepIter, fc->getFit());
		}

		prevFit = fc->getFit();
		converged = mac < tolerance;
		++fc->iterations;
		if (isErrorRaised() || converged) break;

		if (semMethod == ClassicSEM || ((semMethod == TianSEM || semMethod == AgileSEM) && in_middle)) {
			double *estCopy = new double[freeVars];
      fc->copyEstToOptimizer(estCopy);
			estHistory.push_back(estCopy);
		}
	}

	int wanted = FF_COMPUTE_FIT | FF_COMPUTE_BESTFIT | FF_COMPUTE_ESTIMATE;
	fc->wanted = wanted;
	fc->setInform(converged? mstepInform : INFORM_ITERATION_LIMIT);
	bestFit = fc->getFit();
	if (verbose >= 1) mxLog("ComputeEM: cycles %d/%d total mstep %d fit %f inform %d",
				EMcycles, maxIter, totalMstepIter, bestFit, fc->getInform());

	if (!converged || fc->skippedRows || information == EMInfoNone) return;

	optimum.resize(freeVars);
  fc->copyEstToOptimizer(optimum);

	if (information == EMInfoMengRubinFamily) {
		MengRubinFamily(fc);
	} else if (information == EMInfoOakes) {
		Oakes(fc);
	} else {
		mxThrow("Unknown information method %d", information);
	}

	fc->setFit(bestFit);
  fc->setEstFromOptimizer(optimum);
}

struct estep_jacobian_functional {
	ComputeEM *em;
	FitContext *fc;

	estep_jacobian_functional(ComputeEM *u_em, FitContext *u_fc) : em(u_em), fc(u_fc) {};

	template <typename T1, typename T2>
	void operator()(Eigen::MatrixBase<T1> &x, Eigen::MatrixBase<T2> &result) const {
		em->dEstep(fc, x, result);
	}
};

template <typename T1, typename T2>
void ComputeEM::dEstep(FitContext *fc, Eigen::MatrixBase<T1> &x, Eigen::MatrixBase<T2> &result)
{
  fc->setEstFromOptimizer(x);

	for (size_t fx=0; fx < infoFitFunction.size(); ++fx) {
    ComputeFit("EM", infoFitFunction[fx], FF_COMPUTE_PREOPTIMIZE, fc);
	}

  fc->setEstFromOptimizerClean(optimum);

	fc->gradZ = Eigen::VectorXd::Zero(fc->getNumFree());
	for (size_t fx=0; fx < infoFitFunction.size(); ++fx) {
    ComputeFit("EM", infoFitFunction[fx], FF_COMPUTE_GRADIENT, fc);
	}
	result = fc->gradZ;
	reportProgress(fc);
}

void ComputeEM::Oakes(FitContext *fc)
{
	if (verbose >= 1) mxLog("ComputeEM: Oakes1999 method=simple");

	int wanted = fc->wanted;
	const int freeVars = (int) fc->varGroup->vars.size();

	estep->compute(fc);
	fc->wanted &= ~FF_COMPUTE_HESSIAN;  // discard garbage

	fc->initGrad();
	for (size_t fx=0; fx < infoFitFunction.size(); ++fx) {
    ComputeFit("EM", infoFitFunction[fx], FF_COMPUTE_PREOPTIMIZE, fc);
    ComputeFit("EM", infoFitFunction[fx], FF_COMPUTE_GRADIENT, fc);
	}

	Eigen::VectorXd optimumCopy = optimum;  // will be modified
	Eigen::VectorXd refGrad(freeVars);
	refGrad = fc->gradZ;
	//mxPrintMat("refGrad", refGrad);

	Eigen::MatrixXd jacobian(freeVars, freeVars);
	estep_jacobian_functional ejf(this, fc);
	fd_jacobian<false>(GradientAlgorithm_Forward, 1, 1e-5, ejf, refGrad, optimumCopy, jacobian);

	fc->infoMethod = infoMethod;
	fc->preInfo();
	for (size_t fx=0; fx < infoFitFunction.size(); ++fx) {
    ComputeFit("EM", infoFitFunction[fx], FF_COMPUTE_INFO, fc);
	}
	fc->postInfo();

	fc->refreshDenseHess();
	double *hess = fc->getDenseHessUninitialized();
	Eigen::Map< Eigen::MatrixXd > hessMat(hess, freeVars, freeVars);
	hessMat += (jacobian + jacobian.transpose()) * 0.5;  //only need upper triangle TODO

	fc->wanted = wanted | FF_COMPUTE_HESSIAN;
}

void ComputeEM::MengRubinFamily(FitContext *fc)
{
	const int freeVars = (int) fc->varGroup->vars.size();

	if (verbose >= 1) mxLog("ComputeEM: MengRubinFamily tolerance=%f semMethod=%d, semTolerance=%f ideal noise=[%f,%f]",
				tolerance, semMethod, semTolerance,
				noiseTarget/noiseTolerance, noiseTarget*noiseTolerance);

	if (semMethod == AgileSEM) {
		maxHistLen = 2 + agileMaxIter * 2;
	} else if (semMethod == ClassicSEM || semMethod == TianSEM) {
		maxHistLen = estHistory.size();
	} else {
		maxHistLen = semMethodLen;
	}

	probeOffset.resize(maxHistLen, freeVars);
	diffWork.resize(maxHistLen * freeVars);
	paramProbeCount.assign(freeVars, 0);
	Eigen::MatrixXd rij(freeVars, freeVars);

	int semConverged=0;
	for (int v1=0; v1 < freeVars; ++v1) {
		Eigen::MatrixXd rijWork(freeVars, maxHistLen);
		int pick = 0;
		bool paramConverged = false;
		if (semMethod == AgileSEM) {
			double offset1 = .001;
			const double stepSize = offset1 * .01;

			if (probeEM(fc, v1, offset1, rijWork)) break;
			double offset2 = offset1 + stepSize;
			if (probeEM(fc, v1, offset2, rijWork)) break;
			double diff;
			bool mengOK;
			recordDiff(fc, v1, rijWork, &diff, &mengOK);
			double midOffset = (offset1 + offset2) / 2;

			paramConverged = true;
			int iter = 0;
			std::vector<double> coefHist(agileMaxIter);
			while (++iter <= agileMaxIter &&
			       !(noiseTarget/noiseTolerance < diff && diff < noiseTarget*noiseTolerance)) {
				coefHist[iter-1] = diff * midOffset * midOffset;
				double coef = 0;
				for (int cx=0; cx < iter; ++cx) coef += coefHist[cx];
				coef /= iter;
				if (verbose >= 4) mxLog("ComputeEM: agile iter[%d] coef=%.6g", iter, coef);
				offset1 = sqrt(coef/noiseTarget);
				if (probeEM(fc, v1, offset1, rijWork)) {
					paramConverged = false;
					break;
				}
				if (iter < agileMaxIter || semDebug) {
					offset2 = offset1 + stepSize;
					if (probeEM(fc, v1, offset2, rijWork)) {
						paramConverged = false;
						break;
					}
					midOffset = (offset1 + offset2) / 2;
					recordDiff(fc, v1, rijWork, &diff, &mengOK);
				}
				pick += 2;
			}
		} else if (semMethod == ClassicSEM || semMethod == TianSEM) {
			if (!estHistory.size()) {
				if (verbose >= 1) mxLog("ComputeEM: no history available;"
							" Classic or Tian SEM require convergence history");
				return;
			}
			for (size_t hx=0; hx < estHistory.size(); ++hx) {
				double popt = optimum[v1];
				double offset1 = estHistory[hx][v1] - popt;
				if (paramProbeCount[v1] && fabs(probeOffset(paramProbeCount[v1]-1, v1) -
							     offset1) < tolerance) continue;
				if (fabs(offset1) < tolerance) continue;
				if (probeEM(fc, v1, offset1, rijWork)) break;
				if (hx == 0) continue;
				pick = hx;
				double diff;
				bool mengOK;
				recordDiff(fc, v1, rijWork, &diff, &mengOK);
				if (mengOK) {
					paramConverged = true;
					break;
				}
			}
		} else {
			for (int hx=0; hx < semMethodLen; ++hx) {
				probeEM(fc, v1, semMethodData[hx], rijWork); // ignore errors
				if (hx == 0) continue;
				double diff;
				bool mengOK;
				recordDiff(fc, v1, rijWork, &diff, &mengOK);
			}
			paramConverged = true;
		}

		const char *pname = fc->varGroup->vars[v1]->name;
		if (paramConverged) {
			++semConverged;
			rij.col(v1) = rijWork.col(pick);
			if (verbose >= 2) mxLog("ComputeEM: %s converged in %d probes",
						pname, paramProbeCount[v1]);
		} else {
			if (verbose >= 2) mxLog("ComputeEM: %s failed to converge after %d probes",
						pname, paramProbeCount[v1]);
			break;
		}
	}

	if (verbose >= 1) {
		if (semConverged == freeVars) {
			mxLog("ComputeEM: %d probes used to estimate Hessian", semProbeCount);
		} else {
			mxLog("ComputeEM: %d probes used for SEM but failed to converge", semProbeCount);
		}
	}
	if (semConverged < freeVars) return;

	if (semDebug) {
		Rf_protect(rateMatrix = Rf_allocMatrix(REALSXP, freeVars, freeVars));
		memcpy(REAL(rateMatrix), rij.data(), sizeof(double) * freeVars * freeVars);
	}

	rij = Eigen::MatrixXd::Identity(freeVars, freeVars) - rij;

	//mxLog("rij symm");
	//pda(rij.data(), freeVars, freeVars);

	estep->compute(fc);
	fc->wanted &= ~FF_COMPUTE_HESSIAN;  // discard garbage

	int wanted = fc->wanted;
	fc->wanted = 0;
	fc->infoMethod = infoMethod;
	fc->preInfo();
	for (size_t fx=0; fx < infoFitFunction.size(); ++fx) {
    ComputeFit("EM", infoFitFunction[fx], FF_COMPUTE_INFO, fc);
	}
	fc->postInfo();

	Rf_protect(inputInfoMatrix = Rf_allocMatrix(REALSXP, freeVars, freeVars));
	double *hess = REAL(inputInfoMatrix);
	fc->copyDenseHess(hess);

	ThinMatrix rijMat(rij.data(), freeVars, freeVars);
	ThinMatrix hessMat(hess, freeVars, freeVars);
	std::vector<double> infoBuf(freeVars * freeVars);
	ThinMatrix infoMat(infoBuf.data(), freeVars, freeVars);

	SymMatrixMultiply('L', hessMat, rijMat, infoMat);  // result not symmetric!

	if (semDebug) {
		// ihess is always symmetric, this could be asymmetric
		Rf_protect(outputInfoMatrix = Rf_allocMatrix(REALSXP, freeVars, freeVars));
		memcpy(REAL(outputInfoMatrix), infoBuf.data(), sizeof(double) * freeVars * freeVars);
	}

	double *ihess = fc->getDenseIHessUninitialized();
	int singular;
	if (semFixSymmetry) {
		MeanSymmetric(infoMat);
		singular = InvertSymmetricIndef(infoMat, 'U');
		memcpy(ihess, infoBuf.data(), sizeof(double) * freeVars * freeVars);
	} else {
		ThinMatrix ihessMat(ihess, freeVars, freeVars);
		singular = MatrixSolve(infoMat, ihessMat, true);
	}
	if (singular) {
		if (verbose >= 1) mxLog("ComputeEM: SEM Hessian is singular %d", singular);
		return;
	}

	if (semForcePD) {
		double *oev = NULL;
		if (semDebug) {
			Rf_protect(origEigenvalues = Rf_allocVector(REALSXP, freeVars));
			oev = REAL(origEigenvalues);
		}
		Eigen::Map< Eigen::MatrixXd > mat(ihess, freeVars, freeVars);
		ForceInvertSymmetricPosDef(mat, oev, &fc->infoCondNum);
	}

	fc->wanted = wanted | FF_COMPUTE_IHESSIAN;
	//pda(fc->ihess, freeVars, freeVars);
}

void ComputeEM::collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out)
{
	super::collectResults(fc, lcr, out);

	std::vector< omxCompute* > clist(1);
	clist[0] = mstep.get();

	collectResultsHelper(fc, clist, lcr, out);
}

void ComputeEM::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	size_t numFree = fc->varGroup->vars.size();
	if (!numFree) return;

	MxRList out;
	out.add("EMcycles", Rf_ScalarInteger(EMcycles));
	out.add("totalMstep", Rf_ScalarInteger(totalMstepIter));
	out.add("semProbeCount", Rf_ScalarInteger(semProbeCount));
	slots->add("output", out.asR());

	if (semDebug) {
		const int freeVars = (int) fc->varGroup->vars.size();
		MxRList dbg;

		if (probeOffset.size()) {
			SEXP Rpo;
			Rf_protect(Rpo = Rf_allocMatrix(REALSXP, maxHistLen, freeVars));
			memcpy(REAL(Rpo), probeOffset.data(), sizeof(double) * maxHistLen * freeVars);
			dbg.add("probeOffset", Rpo);
		}

		if (diffWork.size()) {
			SEXP Rdiff;
			Rf_protect(Rdiff = Rf_allocMatrix(REALSXP, maxHistLen, freeVars));
			memcpy(REAL(Rdiff), diffWork.data(), sizeof(double) * maxHistLen * freeVars);
			dbg.add("semDiff", Rdiff);
		}

		if (paramProbeCount.size()) {
			SEXP Rphl;
			Rf_protect(Rphl = Rf_allocVector(INTSXP, freeVars));
			memcpy(INTEGER(Rphl), paramProbeCount.data(), sizeof(int) * freeVars);
			dbg.add("paramHistLen", Rphl);
		}

		if (inputInfoMatrix) dbg.add("inputInfo", inputInfoMatrix);
		if (outputInfoMatrix) dbg.add("outputInfo", outputInfoMatrix);
		if (rateMatrix) dbg.add("rateMatrix", rateMatrix);
		if (origEigenvalues) dbg.add("origEigenvalues", origEigenvalues);

		slots->add("debug", dbg.asR());
	}
}

ComputeEM::~ComputeEM()
{
	for (size_t hx=0; hx < estHistory.size(); ++hx) {
		delete [] estHistory[hx];
	}
	estHistory.clear();
}

enum ComputeInfoMethod omxCompute::stringToInfoMethod(const char *iMethod)
{
	enum ComputeInfoMethod infoMethod = INFO_METHOD_DEFAULT; // to avoid gcc warning
	if (strcmp(iMethod, "sandwich")==0) {
		infoMethod = INFO_METHOD_SANDWICH;
	} else if (strcmp(iMethod, "meat")==0) {
		infoMethod = INFO_METHOD_MEAT;
	} else if (strcmp(iMethod, "bread")==0) {
		infoMethod = INFO_METHOD_BREAD;
	} else if (strcmp(iMethod, "hessian")==0) {
		infoMethod = INFO_METHOD_HESSIAN;
	} else {
		mxThrow("Unknown information matrix estimation method '%s'", iMethod);
	}
	return infoMethod;
}

void omxComputeOnce::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	SEXP slotValue;
	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("from")));
	for (int wx=0; wx < Rf_length(slotValue); ++wx) {
		if (isErrorRaised()) return;
		int objNum = INTEGER(slotValue)[wx];
		if (objNum >= 0) {
			omxMatrix *algebra = globalState->algebraList[objNum];
			if (algebra->fitFunction) {
				omxCompleteFitFunction(algebra);
			}
			algebras.push_back(algebra);
		} else {
			omxExpectation *expectation = globalState->expectationList[~objNum];
			omxCompleteExpectation(expectation);
			expectations.push_back(expectation);
		}
	}
	if (algebras.size() && expectations.size()) {
		mxThrow("MxComputeOnce cannot evaluate expectations and fitfunctions at the same time");
	}

	{ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("verbose")));
	verbose = Rf_asInteger(slotValue);
	}

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("what")));
	int whatLen = Rf_length(slotValue);
	if (algebras.size()) {
		if (whatLen == 0) {
			fit = true;
		}
		for (int wx=0; wx < whatLen; ++wx) {
			SEXP elem;
			Rf_protect(elem = STRING_ELT(slotValue, wx));
			const char *what = CHAR(elem);
			if      (strcmp(what, "maxAbsChange")==0) mac = true;
			else if (strcmp(what, "set-starting-values")==0) starting = true;
			else if (strcmp(what, "fit")         ==0) fit = true;
			else if (strcmp(what, "gradient")    ==0) gradient = true;
			else if (strcmp(what, "hessian")     ==0) hessian = true;
			else if (strcmp(what, "information") ==0) infoMat = true;
			else if (strcmp(what, "ihessian")    ==0) ihessian = true;
			else omxRaiseErrorf("mxComputeOnce: don't know how to compute %s", what);
		}

		if (hessian && infoMat) mxThrow("Cannot compute the Hessian and Fisher Information matrix simultaneously");
	} else {
		for (int wx=0; wx < whatLen; ++wx) {
			SEXP elem;
			ScopedProtect p1(elem, STRING_ELT(slotValue, wx));
			predict.push_back(CHAR(elem));
		}
	}

	{ ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install(".is.bestfit")));
	isBestFit = Rf_asLogical(slotValue);
	}

	bool howConflict = false;
	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("how")));
	if (Rf_length(slotValue) > 1) {
		omxRaiseErrorf("mxComputeOnce: more than one method specified");
	} else if (Rf_length(slotValue) == 1) {
		SEXP elem;
		Rf_protect(elem = STRING_ELT(slotValue, 0));
		if (algebras.size()) {
			const char *iMethod = CHAR(elem);
			if (infoMat) {
				infoMethod = stringToInfoMethod(iMethod);
				if (infoMethod == INFO_METHOD_MEAT && gradient && whatLen == 2) {
					//OK
				} else if (whatLen > 1) {
					howConflict = true;
				}
			} else {
				omxRaiseErrorf("mxComputeOnce: unknown method %s requested", iMethod);
			}
		} else {
			how = CHAR(elem);
			if (whatLen > 1) howConflict = true;
		}
	}
	if (howConflict) {
		omxRaiseErrorf("mxComputeOnce: when how is specified, you can only compute one thing at a time");
	}

	for (int ax=0; ax < (int) algebras.size(); ++ax) {
		omxFitFunction *ff = algebras[ax]->fitFunction;
		if (gradient && !ff) {
			mxThrow("Gradient requested but not available");
		}
		if ((hessian || ihessian || hgprod) && (!ff || !ff->hessianAvailable)) {
			// add a separate flag for hgprod TODO
			mxThrow("Hessian requested but not available");
		}
		// add check for information TODO
	}
}

void omxComputeOnce::computeImpl(FitContext *fc)
{
  fc->calcNumFree();

	if (algebras.size()) {
		int want = 0;
		if (starting) {
			want |= FF_COMPUTE_STARTING;
		}
		if (mac) {
			want |= FF_COMPUTE_MAXABSCHANGE;
			fc->mac = 0;
		}
		if (fit) {
			want |= FF_COMPUTE_FIT;
			if (isBestFit) want |= FF_COMPUTE_BESTFIT;
			fc->setFit(0);
		}
		if (gradient) {
			want |= FF_COMPUTE_GRADIENT;
		}
		if (hessian) {
			want |= FF_COMPUTE_HESSIAN;
			fc->clearHessian();
		}
		if (infoMat) {
			want |= FF_COMPUTE_INFO;
			fc->infoMethod = infoMethod;
			fc->initGrad(); // remove? TODO
			fc->clearHessian();
			fc->preInfo();
		}
		if (ihessian) {
			want |= FF_COMPUTE_IHESSIAN;
			fc->clearHessian();
		}
		if (!want) return;

    fc->createChildren();

		for (size_t wx=0; wx < algebras.size(); ++wx) {
			omxMatrix *algebra = algebras[wx];
			if (algebra->fitFunction) {
				omxAlgebraPreeval(algebra, fc);

				ComputeFit("Once", algebra, want, fc);
				if (infoMat) {
					fc->postInfo();
				}
			} else {
				omxMarkDirty(algebra);
				omxRecompute(algebra, fc);
			}
		}
	} else if (expectations.size()) {
		if (predict.size() > 1) mxThrow("Not implemented");
		const char *pr1 = "nothing"; // better to default to 0 ?
		if (predict.size()) pr1 = predict[0];
		for (size_t wx=0; wx < expectations.size(); ++wx) {
			omxExpectation *expectation = expectations[wx];
			omxExpectationCompute(fc, expectation, pr1, how);
		}
	}
}

void omxComputeOnce::reportResults(FitContext *fc, MxRList *slots, MxRList *out)
{
	for (size_t ax=0; ax < algebras.size(); ++ax) {
		omxFitFunction *ff = algebras[ax]->fitFunction;
		if (!ff) continue;
		omxPopulateFitFunction(algebras[ax], out);
	}
}

void ComputeJacobian::initFromFrontend(omxState *state, SEXP rObj)
{
	super::initFromFrontend(state, rObj);

	ProtectedSEXP Rof(R_do_slot(rObj, Rf_install("of")));
	int numOf = Rf_length(Rof);
	if (!numOf) mxThrow("%s: must provide at least one expectation", name);
	exList.reserve(numOf);
	for (int ex=0; ex < numOf; ++ex) {
		int objNum = INTEGER(Rof)[ex];
		if (objNum < 0) {
			omxExpectation *e1 = state->expectationList[~objNum];
			omxCompleteExpectation(e1);
			exList.push_back(e1);
		} else {
			omxMatrix *algebra = state->algebraList[objNum];
			if (algebra->fitFunction) {
				omxCompleteFitFunction(algebra);
			}
			alList.push_back(algebra);
		}
	}

	if (exList.size()) {
		sense.attach(&exList, 0);
	} else {
		sense.attach(0, &alList);
	}

	data = 0;
	ProtectedSEXP Rdata(R_do_slot(rObj, Rf_install("data")));
	int objNum = Rf_asInteger(Rdata);
	if (objNum != NA_INTEGER) data = state->dataList[objNum];

	ProtectedSEXP Rdefvar_row(R_do_slot(rObj, Rf_install("defvar.row")));
	sense.defvar_row = Rf_asInteger(Rdefvar_row);
}

void ComputeJacobian::computeImpl(FitContext *fc)
{
  fc->calcNumFree();  // can't omxAlgebraPreeval because no fitmat
	int numFree = fc->getNumFree();
	if (sense.defvar_row != NA_INTEGER) {
		data->loadDefVars(fc->state, sense.defvar_row - 1);
	}

  sense.measureRef(fc);
  fc->createChildren();
  AutoTune<JacobianGadget> jg(name);
  jg.setWork(std::unique_ptr<JacobianGadget>(new JacobianGadget(numFree)));
  jg.work().setAlgoOptions(GradientAlgorithm_Forward, 2, 1e-4);
  jg(sense, sense.ref, [&fc](){ return fc->getCurrentFree(); }, false, sense.result);
  fc->destroyChildren();
}

void ComputeJacobian::reportResults(FitContext *fc, MxRList *slots, MxRList *out)
{
	MxRList output;
	output.add("jacobian", Rcpp::wrap(sense.result));
	slots->add("output", output.asR());
}

void FitContext::resetToOriginalStarts()
{
	setInform(INFORM_UNINITIALIZED);
	auto &startingValues = Global->startingValues;
	auto &vars = varGroup->vars;
	for (int vx=0; vx < int(vars.size()); ++vx) {
    if (profiledOutZ[vx]) continue;
		auto *fv = vars[vx];
		est[vx] = startingValues[fv->id];
	}
	fit = NA_REAL;
	mac = NA_REAL;
	fitUnits = FIT_UNITS_UNINITIALIZED;
	skippedRows = 0;
	vcov.resize(0,0);
	stderrs.resize(0);
	clearHessian();
	resetIterationError();
}

void ComputeSetOriginalStarts::computeImpl(FitContext *fc)
{
	fc->resetToOriginalStarts();
}

void ComputeStandardError::initFromFrontend(omxState *state, SEXP rObj)
{
	super::initFromFrontend(state, rObj);

	wlsStats = false;
	fitMat = omxNewMatrixFromSlot(rObj, state, "fitfunction");
}

template <typename T1> bool isULS(const Eigen::MatrixBase<T1> &acov)
{
	for (int cx=0; cx < acov.cols(); ++cx) {
		for (int rx=cx; rx < acov.rows(); ++rx) {
			if (acov(rx,cx) == 0.0) continue;
			if (cx == rx && acov(rx,cx) == 1.0) continue;
			return false;
		}
	}
	return true;
}

void ComputeStandardError::computeImpl(FitContext *fc)
{
	if (fc->fitUnits == FIT_UNITS_UNINITIALIZED) return;
	int numFree = fc->getNumFree();
	if (fc->fitUnits == FIT_UNITS_MINUS2LL) {
		if (!fc->vcov.size()) {
			fc->vcov.resize(numFree, numFree);
			const double Scale = fabs(Global->llScale);
			fc->refreshDenseIHess();
			//fc->ihess is not actually the inverted Hessian,
			//but there's a method for constructing the inverted Hessian from it:
			fc->copyDenseIHess(fc->vcov.data());
			fc->vcov = Scale * fc->vcov;
		}
		fc->calcStderrs();
		return;
	}

	if (!(fc->fitUnits == FIT_UNITS_SQUARED_RESIDUAL ||
	      fc->fitUnits == FIT_UNITS_SQUARED_RESIDUAL_CHISQ)) return;
	if (!fitMat) return;

	exList.clear();
	std::function<void(omxMatrix*)> ve = visitEx(this);
	fitMat->fitFunction->traverse(ve);

	double totalWeight = 0;
	int numOrdinal = 0;
	int totalStats = 0;
	numStats.reserve(exList.size());
	for (auto &e1 : exList) {
		e1->data->visitObsStats([&](obsSummaryStats &o1){
				numOrdinal += o1.numOrdinal;
				totalWeight += o1.totalWeight;
				int sz = o1.asymCov->rows;
				numStats.push_back(sz);
				totalStats += sz;
			});
	}

	Eigen::VectorXd obStats(totalStats);
	Eigen::VectorXd exStats(totalStats);
	Eigen::MatrixXd Vmat(totalStats,totalStats);
	Eigen::MatrixXd Wmat(totalStats,totalStats);
	Vmat.setZero();
	Wmat.setZero();
	for (int ex=0, sx=0, offset=0; ex < int(exList.size()); ++ex) {
		omxData *d1 = exList[ex]->data;

		d1->visitObsStats([&](obsSummaryStats &o1){
				int sz = numStats[sx];

				// filter out missing variables TODO
				Eigen::VectorXd vec1(sz);
				exList[ex]->asVector(fc, 0, vec1);
				exStats.segment(offset, sz) = vec1;
				if (o1.thresholdMat) {
					EigenMatrixAdaptor oTh(o1.thresholdMat);
          auto &oThresh = o1.thresholdCols;
					normalToStdVector(o1.covMat, o1.meansMat, o1.slopeMat,
                            [&oThresh, &oTh](int r,int c)->double{ return oTh(r, oThresh[c].column); },
														oThresh, vec1);
				} else {
					normalToStdVector(o1.covMat, o1.meansMat, o1.slopeMat,
														[](int r,int c)->double{ return 0; },
														o1.thresholdCols, vec1);
				}
				obStats.segment(offset, sz) = vec1;

				if (o1.useWeight) {
					EigenMatrixAdaptor uw(o1.useWeight);
					Vmat.block(offset,offset,sz,sz) = uw;
				} else {
					Vmat.block(offset,offset,sz,sz).setIdentity();
				}

				EigenMatrixAdaptor ac(o1.asymCov);
				Wmat.block(offset,offset,sz,sz) = ac;
				offset += sz;
				sx += 1;
			});
	}

	ParJacobianSense sense;
	sense.attach(&exList, 0);
	sense.measureRef(fc);
  fc->createChildren(fitMat, false);
  AutoTune<JacobianGadget> jg(name);
  jg.setWork(std::unique_ptr<JacobianGadget>(new JacobianGadget(numFree)));
  jg.work().setAlgoOptions(GradientAlgorithm_Central, 4, 1e-4);
  jg(sense, sense.ref, [&fc](){ return fc->getCurrentFree(); }, false, sense.result);
  fc->destroyChildren();

	Eigen::FullPivHouseholderQR<Eigen::MatrixXd> qr1(sense.result);
	Eigen::MatrixXd q1 = qr1.matrixQ();
	Eigen::MatrixXd jacOC = q1.block(0, qr1.rank(), q1.rows(), q1.cols() - qr1.rank());
	if (jacOC.cols()) {
		Eigen::MatrixXd zqb = jacOC.transpose() * Wmat * jacOC;
		MoorePenroseInverseSq(zqb);

		Eigen::VectorXd diff = obStats - exStats;
		x2 = diff.transpose() * jacOC * zqb * jacOC.transpose() * diff;
		Eigen::FullPivHouseholderQR<Eigen::MatrixXd> qr2(jacOC);
		df = qr2.rank();
	} else {
		x2 = 0;
		df = 0;
	}

	Eigen::MatrixXd dvd = sense.result.transpose() * Vmat * sense.result;
	if (InvertSymmetricIndef(dvd, 'L') > 0) return;

	fc->vcov = dvd.selfadjointView<Eigen::Lower>() * sense.result.transpose() *
		Vmat * Wmat * Vmat * sense.result * dvd.selfadjointView<Eigen::Lower>();
	fc->calcStderrs();

	Eigen::MatrixXd Umat = Vmat - Vmat * sense.result * dvd.selfadjointView<Eigen::Lower>() *
		sense.result.transpose() * Vmat;
	Eigen::MatrixXd UW = Umat * Wmat;
	Eigen::MatrixXd UW2 = UW * UW; // unclear if this should be UW^2 i.e. elementwise power
	double trUW = UW.diagonal().array().sum();
	madj = trUW / df;
	x2m = fc->getFit() / madj;
	dstar = (trUW * trUW) / UW2.diagonal().array().sum();
	mvadj = (trUW*trUW) / dstar;
	x2mv = fc->getFit() / mvadj;
	// N.B. x2mv is off by a factor of N where N is the total number of rows in all data sets for the ULS case.
	if (isULS(Vmat)) x2mv /= totalWeight;
	wlsStats = true;
}

void ComputeStandardError::reportResults(FitContext *fc, MxRList *slots, MxRList *out)
{
	int numFree = fc->getNumFree();
	SEXP parNames=0, dimnames=0;

	if (fc->vcov.size() || fc->stderrs.size()) {
		if (numFree != fc->stderrs.size()) OOPS;

		parNames = Rf_allocVector(STRSXP, numFree);
		Rf_protect(parNames);
		for (int vx=0, px=0; vx < int(fc->numParam); ++vx) {
			if (fc->profiledOutZ[vx]) continue;
			SET_STRING_ELT(parNames, px++, Rf_mkChar(varGroup->vars[vx]->name));
		}

		dimnames = Rf_allocVector(VECSXP, 2);
		Rf_protect(dimnames);
		SET_VECTOR_ELT(dimnames, 0, parNames);
	}

	if (fc->vcov.size()) {
		SEXP Vcov;
		Rf_protect(Vcov = Rf_allocMatrix(REALSXP, fc->vcov.rows(), fc->vcov.cols()));
		memcpy(REAL(Vcov), fc->vcov.data(), sizeof(double) * fc->vcov.rows() * fc->vcov.cols());
		Rf_setAttrib(Vcov, R_DimNamesSymbol, dimnames);
		out->add("vcov", Vcov);
	}

	if (fc->stderrs.size()) {
		SEXP stdErrors;
		Rf_protect(stdErrors = Rf_allocMatrix(REALSXP, numFree, 1));
		memcpy(REAL(stdErrors), fc->stderrs.data(), sizeof(double) * numFree);
		Rf_setAttrib(stdErrors, R_DimNamesSymbol, dimnames);
		out->add("standardErrors", stdErrors);
	}

	if (wlsStats) {
		out->add("chi", Rf_ScalarReal(x2));
		out->add("chiDoF", Rf_ScalarInteger(df));
		out->add("chiM", Rf_ScalarReal(x2m));
		out->add("chiMV", Rf_ScalarReal(x2mv));
		out->add("chiMadjust", Rf_ScalarReal(madj));
		out->add("chiMVadjust", Rf_ScalarReal(mvadj));
		out->add("chiDoFstar", Rf_ScalarReal(dstar));
	}
}

void ComputeHessianQuality::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	SEXP slotValue;

	ScopedProtect p1(slotValue, R_do_slot(rObj, Rf_install("verbose")));
	verbose = Rf_asInteger(slotValue);
}

bool FitContext::isGradientTooLarge()
{
		double gradNorm = 0.0;
		double feasibilityTolerance = Global->feasibilityTolerance;
    int numFree = getNumFree();
		for (int gx=0; gx < numFree; ++gx) {
      omxFreeVar &fv = *varGroup->vars[ freeToParamMap[gx] ];
			if ((gradZ[gx] > 0 && fabs(est[gx] - fv.lbound) < feasibilityTolerance) ||
			    (gradZ[gx] < 0 && fabs(est[gx] - fv.ubound) < feasibilityTolerance)) continue;
			double g1 = gradZ[gx];
			gradNorm += g1 * g1;
		}
		gradNorm = sqrt(gradNorm);
    return gradNorm > Global->getGradientThreshold(fit);
}

bool FitContext::isEffectivelyUnconstrained()
{
  if (isUnconstrained()) return true;

	/*
	 * If there are equality MxConstraints, then the quality of the generically calculated Hessian will not be informative;
	 * we must rely upon the optimizer's status code.
	 * (Completely boneheaded equality MxConstraints, like constraining a free parameter equal to itself, are assumed to be the user's problem.)
	 * The quality of the generically calculated Hessian is likewise uninformative if there are active inequality MxConstraints.
	 * But, if there are no equalities, and all of the inequalities are inactive, then we might as well proceed (corner case as that may be):
	*/
  ConstraintVec EqC(this, "eq",
                    [](const omxConstraint &con){ return con.opCode == omxConstraint::EQUALITY; });
  if (EqC.getCount()) {
    if (EqC.verbose >= 1) mxLog("isEffectivelyUnconstrained: equality constraint active");
    return false;
  }

  ConstraintVec IneqC(this, "ineq",
                      [](const omxConstraint &con){ return con.opCode != omxConstraint::EQUALITY; });
  Eigen::ArrayXd ineq(IneqC.getCount());
  IneqC.eval(this, ineq.data());
  if (ineq.sum() != 0.0) {
    if (IneqC.verbose >= 1) mxLog("isEffectivelyUnconstrained: inequality "
                                  "constraint active (%f)", ineq.sum());
    return false;
  }

  return true;
}

void ComputeHessianQuality::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	if (!(fc->wanted & (FF_COMPUTE_HESSIAN | FF_COMPUTE_IHESSIAN))) return;

  if (!fc->isEffectivelyUnconstrained()) return;

	// See Luenberger & Ye (2008) Second Order Test (p. 190) and Condition Number (p. 239)

	if (fc->infoDefinite != NA_LOGICAL || !doubleEQ(fc->infoCondNum, NA_REAL)) {
		if (verbose >= 1) {
			mxLog("%s: information matrix already determined to be non positive definite; skipping", name);
		}
		return; // already set elsewhere
	}

	int numParams = fc->getDenseHessianishSize();
	if (numParams == 0) return;

	fc->infoDefinite = false;
	double *hessMem = fc->getDenseHessianish();
	if (!hessMem) {
		if (verbose >= 1) {
			mxLog("%s: information matrix not available; skipping", name);
		}
		return;
	}
	Eigen::Map< Eigen::MatrixXd > hess(hessMem, numParams, numParams);
	hess.triangularView<Eigen::Lower>() = hess.transpose().triangularView<Eigen::Lower>();
	Eigen::LDLT< Eigen::MatrixXd > cholH(hess);
	if (cholH.info() != Eigen::Success || !(cholH.vectorD().array() > 0.0).all()) {
		if (verbose >= 1) {
			mxLog("%s: Cholesky decomposition failed", name);
		}
		return;
	}

	Eigen::MatrixXd ihess(numParams, numParams);
	ihess.setIdentity();
	ihess = cholH.solve(ihess);

	// see LAPACK's dtrcon
	double cn = ihess.colwise().sum().maxCoeff() * hess.colwise().sum().maxCoeff();
	if (!std::isfinite(cn)) {
		if (verbose >= 1) {
			mxLog("%s: result is not finite", name);
		}
		return;
	}

	if (cn < 1.0) cn = 1/cn;

	fc->infoDefinite = true;
	fc->infoCondNum = cn;
}

void ComputeReportDeriv::reportResults(FitContext *fc, MxRList *, MxRList *result)
{
	if( fc->state->conListX.size() ){
		/* After the call to the backend,
		 * frontend function nameGenericConstraintOutput(), in R/MxRunHelperFunctions.R, uses 'constraintNames',
		 * 'constraintRows', and 'constraintCols' to populate the dimnames of 'constraintFunctionValues' and
		 * 'constraintJacobian'.
		 */
		SEXP cv, cjac;
    fc->state->reportConstraints(*result);
		if( fc->constraintFunVals.size() ){
			Rf_protect(cv = Rf_allocVector( REALSXP, fc->constraintFunVals.size() ));
			memcpy( REAL(cv), fc->constraintFunVals.data(), sizeof(double) * fc->constraintFunVals.size() );
			result->add("constraintFunctionValues", cv);
		}
		if( fc->constraintJacobian.rows() ){
			Rf_protect(cjac = Rf_allocMatrix( REALSXP, fc->constraintJacobian.rows(), fc->constraintJacobian.cols() ));
			memcpy( REAL(cjac), fc->constraintJacobian.data(), sizeof(double) * fc->constraintJacobian.rows() * fc->constraintJacobian.cols() );
			result->add("constraintJacobian", cjac);
		}
	}

	if (!(fc->wanted & (FF_COMPUTE_GRADIENT|FF_COMPUTE_HESSIAN|FF_COMPUTE_IHESSIAN))) return;

	int numFree = fc->getNumFree();

	SEXP parNames = Rf_allocVector(STRSXP, numFree);
	Rf_protect(parNames);
	for (int vx=0, px=0; vx < int(fc->numParam); ++vx) {
		if (fc->profiledOutZ[vx]) continue;
		SET_STRING_ELT(parNames, px++, Rf_mkChar(varGroup->vars[vx]->name));
	}

	if (fc->wanted & FF_COMPUTE_GRADIENT) {
		SEXP Rgradient = Rf_allocVector(REALSXP, numFree);
		result->add("gradient", Rgradient);
		double *gp = REAL(Rgradient);
		fc->copyGradToOptimizer(gp);
		Rf_setAttrib(Rgradient, R_NamesSymbol, parNames);
	}

	if (fc->wanted & (FF_COMPUTE_HESSIAN | FF_COMPUTE_IHESSIAN)) {
		SEXP dimnames = Rf_allocVector(VECSXP, 2);
		Rf_protect(dimnames);
		for (int dx=0; dx < 2; ++dx) SET_VECTOR_ELT(dimnames, dx, parNames);

		if (numFree != fc->hess.rows()) {
			if (OMX_DEBUG) mxLog("free %d hessian %d", numFree, fc->hess.rows());
			return;
		}
		if (fc->wanted & FF_COMPUTE_HESSIAN) {
			SEXP Rhessian;
			Rhessian = Rf_allocMatrix(REALSXP, numFree, numFree);
			result->add("hessian", Rhessian);
			fc->copyDenseHess(REAL(Rhessian));
			Rf_setAttrib(Rhessian, R_DimNamesSymbol, dimnames);
		}
		if (numFree != fc->ihess.rows()) {
			if (OMX_DEBUG) mxLog("free %d ihessian %d", numFree, fc->ihess.rows());
			return;
		}
		if (fc->wanted & FF_COMPUTE_IHESSIAN) {
			SEXP Rihessian;
			Rihessian = Rf_allocMatrix(REALSXP, numFree, numFree);
			result->add("ihessian", Rihessian);
			fc->copyDenseIHess(REAL(Rihessian));
			Rf_setAttrib(Rihessian, R_DimNamesSymbol, dimnames);
		}
	}
}

void ComputeReportExpectation::reportResults(FitContext *fc, MxRList *, MxRList *result)
{
	std::vector< omxExpectation* > &expectationList = fc->state->expectationList;

	SEXP expectations;
	Rf_protect(expectations = Rf_allocVector(VECSXP, expectationList.size()));

	for(size_t index = 0; index < expectationList.size(); index++) {
		if(OMX_DEBUG) { mxLog("Final Calculation of Expectation %d.", (int) index); }
		omxExpectation *curExpectation = expectationList[index];
		omxExpectationCompute(fc, curExpectation);
		SEXP rExpect;
		Rf_protect(rExpect = Rf_allocVector(LGLSXP, 1)); // placeholder to attach attributes
		if(OMX_DEBUG) { mxLog("Expectation %d has attribute population.", (int) index); }
		curExpectation->populateAttr(rExpect);
		SET_VECTOR_ELT(expectations, index, rExpect);
	}

	result->add("expectations", expectations);
}

void ComputeBootstrap::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	SEXP slotValue;
	SEXP s4class;

	Rf_protect(slotValue = R_do_slot(rObj, Rf_install("plan")));
	Rf_protect(s4class = STRING_ELT(Rf_getAttrib(slotValue, R_ClassSymbol), 0));
	plan = std::unique_ptr<omxCompute>(omxNewCompute(globalState, CHAR(s4class)));
	plan->initFromFrontend(globalState, slotValue);

	ProtectedSEXP Rdata(R_do_slot(rObj, Rf_install("data")));
	for (int wx=0; wx < Rf_length(Rdata); ++wx) {
		if (isErrorRaised()) return;
		int objNum = INTEGER(Rdata)[wx];
		context ctx;
		ctx.data = globalState->dataList[objNum];
		int numRows = ctx.data->numRawRows();
		if (!numRows) {
			mxThrow("%s: data '%s' of type '%s' cannot have row weights",
				 name, ctx.data->name, ctx.data->getType());
		}
		int *origRowFreq = ctx.data->getFreqColumn();
		ctx.origCumSum.resize(numRows);
		ctx.resample.resize(ctx.origCumSum.size());
		if (origRowFreq) {
			std::partial_sum(origRowFreq, origRowFreq + ctx.origCumSum.size(),
					 ctx.origCumSum.begin());
		} else {
			for (int rx=0; rx < numRows; ++rx) ctx.origCumSum[rx] = 1+rx;
		}
		contexts.push_back(ctx);
	}

	ProtectedSEXP Rverbose(R_do_slot(rObj, Rf_install("verbose")));
	verbose = Rf_asInteger(Rverbose);

	ProtectedSEXP Rrepl(R_do_slot(rObj, Rf_install("replications")));
	numReplications = Rf_asInteger(Rrepl);

	ProtectedSEXP Rparallel(R_do_slot(rObj, Rf_install("parallel")));
	parallel = Rf_asLogical(Rparallel);

	ProtectedSEXP Ronly(R_do_slot(rObj, Rf_install("only")));
	only = Rf_asInteger(Ronly);
	if (only != NA_INTEGER) {
		numReplications = 1;
	}

	previousNumParam = -1;
	previousData = 0;

	ProtectedSEXP Routput(R_do_slot(rObj, Rf_install("output")));
	ProtectedSEXP RoutputNames(Rf_getAttrib(Routput, R_NamesSymbol));
	for (int ax=0; ax < Rf_length(Routput); ++ax) {
		const char *key = R_CHAR(STRING_ELT(RoutputNames, ax));
		SEXP val = VECTOR_ELT(Routput, ax);
		if (strEQ(key, "raw")) {
			previousData = val;
		} else if (strEQ(key, "numParam")) {
			previousNumParam = Rf_asInteger(val);
		}
	}
}

void ComputeBootstrap::computeImpl(FitContext *fc)
{
	if (verbose >= 1) mxLog("%s: %d replications seed=%d parallel=%d",
				name, numReplications, seed, int(parallel));

	int numCols = fc->numParam + 3;
	Rf_protect(rawOutput = Rf_allocVector(VECSXP, numCols));
	SEXP colNames;
	{
		ProtectedSEXP colNamesP(Rf_allocVector(STRSXP, numCols));
		Rf_setAttrib(rawOutput, R_NamesSymbol, colNamesP);
		colNames = colNamesP;
	}

	SET_STRING_ELT(colNames, 0, Rf_mkChar("seed"));
	SET_VECTOR_ELT(rawOutput, 0, Rf_allocVector(INTSXP, numReplications));
	SET_STRING_ELT(colNames, 1, Rf_mkChar("fit"));
	SET_VECTOR_ELT(rawOutput, 1, Rf_allocVector(REALSXP, numReplications));
	for (int px=0; px < int(fc->numParam); ++px) {
		SET_STRING_ELT(colNames, 2+px, Rf_mkChar(varGroup->vars[px]->name));
		SET_VECTOR_ELT(rawOutput, 2+px, Rf_allocVector(REALSXP, numReplications));
	}
	SET_STRING_ELT(colNames, 2+fc->numParam, Rf_mkChar("statusCode"));
	SET_VECTOR_ELT(rawOutput, 2+fc->numParam, allocInformVector(numReplications));
	markAsDataFrame(rawOutput, numReplications);

	if (previousData && (previousNumParam != int(fc->numParam) ||
			     Rf_length(previousData) != Rf_length(rawOutput))) {
		if (verbose >= 1) mxLog("%s: discarded mismatching previous data (%d/%d %d/%d)",
					name, previousNumParam, int(fc->numParam),
					Rf_length(previousData), Rf_length(rawOutput));
		previousData = 0;
	}

	for (int repl=0; repl < numReplications; ++repl) {
		INTEGER(VECTOR_ELT(rawOutput, 0))[repl] = NA_INTEGER;
		for (int cx=0; cx <= int(fc->numParam); ++cx) {
			REAL(VECTOR_ELT(rawOutput, 1 + cx))[repl] = NA_REAL;
		}
		INTEGER(VECTOR_ELT(rawOutput, 2 + fc->numParam))[repl] = NA_INTEGER;
	}
	if (only == NA_INTEGER && previousData) {
		int toCopy = std::min(Rf_length(VECTOR_ELT(previousData, 0)),
				      numReplications);
		if (verbose >= 1) mxLog("%s: copying %d rows from previous run", name, toCopy);
		memcpy(INTEGER(VECTOR_ELT(rawOutput, 0)),
		       INTEGER(VECTOR_ELT(previousData, 0)),
		       toCopy * sizeof(int));
		for (int cx=0; cx <= int(fc->numParam); ++cx) {
			memcpy(REAL(VECTOR_ELT(rawOutput, 1+cx)),
			       REAL(VECTOR_ELT(previousData, 1+cx)),
			       toCopy * sizeof(double));
		}
		memcpy(INTEGER(VECTOR_ELT(rawOutput, 2 + fc->numParam)),
		       INTEGER(VECTOR_ELT(previousData, 2 + fc->numParam)),
		       toCopy * sizeof(int));
	}

	// implement parallel TODO

	auto *seedVec = INTEGER(VECTOR_ELT(rawOutput, 0));
	if (only == NA_INTEGER || !previousData) {
		BorrowRNGState grs;
		for (int repl=0; repl < numReplications; ++repl) {
			if (seedVec[repl] != NA_INTEGER) continue;
			int seed1 = unif_rand() * std::numeric_limits<int>::max();
			if (seed1 == NA_INTEGER) seed1 = 0; // maybe impossible
			seedVec[repl] = seed1;
		}
	} else {
		if (only <= Rf_length(VECTOR_ELT(previousData, 0))) {
			if (verbose >= 1) mxLog("%s: using only=%d", name, only);
			seedVec[0] = INTEGER(VECTOR_ELT(previousData, 0))[only - 1];
		} else {
			mxThrow("%s: only=%d but previous data has just %d replications",
				 name, only, Rf_length(VECTOR_ELT(previousData, 0)));
		}
	}

	for (int repl=0; repl < numReplications && !isErrorRaised(); ++repl) {
		std::mt19937 generator(seedVec[repl]);
		if (INTEGER(VECTOR_ELT(rawOutput, 2 + fc->numParam))[repl] != NA_INTEGER) continue;
		if (verbose >= 2) mxLog("%s: replication %d", name, repl);
		fc->state->invalidateCache();
		for (auto &ctx : contexts) {
			ctx.resample.assign(ctx.origCumSum.size(), 0);
			int last = ctx.origCumSum.size() - 1;
			int total = ctx.origCumSum[last];
			std::uniform_int_distribution<int> dist(1, total);
			for (int sx=0; sx < total; ++sx) {
				int pick = dist(generator);
				auto rowPick = std::lower_bound(ctx.origCumSum.begin(), ctx.origCumSum.end(), pick);
				int row = rowPick - ctx.origCumSum.begin();
				ctx.resample[row] += 1;
			}
			ctx.data->setFreqColumn(ctx.resample.data());
			if (only != NA_INTEGER) {
				onlyWeight.add(ctx.data->name, Rcpp::wrap(ctx.resample));
			}
		}
		fc->state->connectToData();
		fc->resetToOriginalStarts();
		plan->compute(fc);
		if (only == NA_INTEGER) {
			fc->wanted &= ~FF_COMPUTE_DERIV;  // discard garbage
		}
		REAL(VECTOR_ELT(rawOutput, 1))[repl] = fc->getFit();
		for (int px=0; px < int(fc->numParam); ++px) {
			REAL(VECTOR_ELT(rawOutput, 2 + px))[repl] = fc->est[px];
		}
		INTEGER(VECTOR_ELT(rawOutput, 2 + fc->numParam))[repl] = fc->wrapInform();
		reportProgress(fc);
	}

	for (auto &ctx : contexts) {
		ctx.data->setFreqColumn(ctx.data->getOriginalFreqColumn());
	}

	if (only == NA_INTEGER) {
		fc->resetToOriginalStarts();
		fc->copyParamToModel();
		fc->wanted &= ~FF_COMPUTE_FIT;  // discard garbage
	}
}

void ComputeBootstrap::collectResults(FitContext *fc, LocalComputeResult *lcr, MxRList *out)
{
	super::collectResults(fc, lcr, out);
	std::vector< omxCompute* > clist(1);
	clist[0] = plan.get();
	collectResultsHelper(fc, clist, lcr, out);
}

void ComputeBootstrap::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	MxRList output;
	output.add("numParam", Rcpp::wrap(int(fc->numParam)));
	output.add("raw", rawOutput);
	if (only != NA_INTEGER) {
		output.add("frequency", onlyWeight.asR());
	}
	slots->add("output", output.asR());
}

void ComputeGenerateData::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	ProtectedSEXP Rexp(R_do_slot(rObj, Rf_install("expectation")));
	for (int wx=0; wx < Rf_length(Rexp); ++wx) {
		if (isErrorRaised()) return;
		int objNum = INTEGER(Rexp)[wx];
		omxExpectation *expectation = globalState->expectationList[objNum];
		expectations.push_back(expectation);
	}
}

void ComputeGenerateData::computeImpl(FitContext *fc)
{
	if (simData.size()) mxThrow("Cannot generate data more than once");

	BorrowRNGState grs;

	for (auto ex : expectations) {
		ex->generateData(fc, simData);
	}
}

void ComputeGenerateData::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	slots->add("output", simData.asR());
}

class LoadDataCSVProvider : public LoadDataProvider<LoadDataCSVProvider> {
	std::unique_ptr< mini::csv::ifstream > icsv;
	int cpIndex;
	bool byrow;

	virtual const char *getName() override { return "csv"; };
	virtual void init(SEXP rObj) override {
		ProtectedSEXP Rbyrow(R_do_slot(rObj, Rf_install("byrow")));
		byrow = Rf_asLogical(Rbyrow);
    if (verbose) mxLog("%s: byrow=%d", name, byrow);
		ProtectedSEXP Rcs(R_do_slot(rObj, Rf_install("cacheSize")));

		if (!byrow) stripeSize = std::max(Rf_asInteger(Rcs), 1);
		requireFile(rObj);
	}
	virtual void addCheckpointColumns(std::vector< std::string > &cp) override
	{
		if (rowNames == 0 || !byrow) return;
		cpIndex = cp.size();
		auto &rc = *rawCols;
		for (int cx=0; cx < int(columns.size()); ++cx) {
			std::string c1 = fileName + ":" + rc[ columns[cx] ].name;
			cp.push_back(c1);
		}
	}
	void loadByCol(int index);
	void loadByRow(int index);
	virtual void loadRowImpl(int index) override
	{
		if (!byrow) {
			loadByCol(index);
		} else {
			loadByRow(index);
		}
	}
	void mxScanInt(mini::csv::ifstream &st, ColumnData &rc, int *out);
};

void LoadDataCSVProvider::mxScanInt(mini::csv::ifstream &st, ColumnData &rc, int *out)
{
	const std::string &rn = st.get_delimited_str();
	if (isNA(rn)) {
		*out = NA_INTEGER;
		return;
	}
	if (rc.levelNames.size()) {
		bool found = false; // maybe use a map for better performance?
		for (int lx=0; lx < int(rc.levelNames.size()); ++lx) {
			if (rn == rc.levelNames[lx]) {
				found = true;
				*out = 1+lx;
				break;
			}
		}
		if (!found) mxThrow("%s: factor level '%s' unrecognized in column '%s'",
				    name, rn.c_str(), rc.name);
	} else {
		std::istringstream is(rn);
		is >> *out;
	}
}

void LoadDataCSVProvider::loadByCol(int index)
{
  //if (verbose >= 2) mxLog("%s::loadByCol(%d)", name, index);
	if (stripeStart == -1 ||
	    index < stripeStart || index >= stripeEnd) {
		bool backward = index < stripeStart;
		stripeStart = std::max(0, index - backward * (stripeSize - 1));

		loadCounter += 1;
		mini::csv::ifstream st(filePath);
		st.set_delimiter(' ', "##");
		for (int rx=0; rx < skipRows; ++rx) st.skip_line();
		int stripeAvail = stripeSize;
		for (int rx=0,dr=0; rx < srcRows; ++rx) {
			bool gotLine = false;
			try {
				gotLine = st.read_line();
			} catch (...) {
				// ignore
			}
			if (!gotLine) {
				mxThrow("%s: ran out of data for '%s' (need %d rows but only found %d)",
					 name, dataName, srcRows, 1+rx);
			}
			if (skipRow(rx)) continue;
			int toSkip = stripeStart * columns.size() + skipCols;
			for (int jx=0; jx < toSkip; ++jx) {
				std::string rn;
				st >> rn;
			}
			for (int sx=0,dx=0; sx < stripeAvail; ++sx) {
				auto &rc = *rawCols;
				try {
					for (int cx=0; cx < int(columns.size()); ++cx) {
						if (colTypes[cx] == COLUMNDATA_NUMERIC) {
							st >> stripeData[dx].realData[dr];
						} else {
							mxScanInt(st, rc[ columns[cx] ],
								  &stripeData[dx].intData[dr]);
						}
						dx += 1;
					}
				} catch (...) {
					// assume we tried to read off the end of the line
					stripeAvail = sx;
				}
			}
			dr += 1;
		}
		stripeEnd = stripeStart + stripeAvail;
		if (verbose >= 2) {
			mxLog("%s: loaded stripes [%d,%d) of %d columns each",
			      name, stripeStart, stripeEnd, int(columns.size()));
		}
	}

	if (index < stripeStart || index >= stripeEnd) {
		mxThrow("%s: no data available for %d", name, index);
	}

	int offset = (index - stripeStart) * columns.size();
	auto &rc = *rawCols;
	for (int cx=0; cx < int(columns.size()); ++cx) {
		rc[ columns[cx] ].setBorrow(stripeData[offset + cx]);
	}
}

void LoadDataCSVProvider::loadByRow(int index)
{
	auto &rc = *rawCols;
	if (!icsv || index < curRecord) {
    if (verbose >= 2) mxLog("%s: reconnecting to %s", name, filePath.c_str());
		icsv = std::unique_ptr< mini::csv::ifstream >(new mini::csv::ifstream(filePath));
		icsv->set_delimiter(' ', "##");
		for (int rx=0; rx < skipRows; ++rx) {
			if (1+rx == colNames) {
				// TODO
			}
			icsv->skip_line();
		}
		curRecord = 0;
		loadCounter += 1;
	}

	while (index > curRecord) {
		icsv->skip_line();
		curRecord += 1;
	}
	for (int cx=0; cx < int(columns.size()); ++cx) {
		if (!icsv->read_line()) {
			mxThrow("%s: ran out of data for '%s' at record %d",
				name, dataName, 1+index);
		}
		for (int sx=0; sx < skipCols; ++sx) {
			std::string rn;
			*icsv >> rn;
			if (checkpoint && 1+sx == rowNames) {
				auto &cv = *checkpointValues;
				cv[cpIndex + cx] = rn;
			}
		}
		if (colTypes[cx] == COLUMNDATA_NUMERIC) {
			for (int rx=0, dr=0; rx < srcRows; ++rx) {
				const std::string& str = icsv->get_delimited_str();
        if (!str.size()) mxThrow("%s: cannot find column %d (row %d in file)", name, dr, rx);
				if (skipRow(rx)) continue;
				if (isNA(str)) {
					stripeData[cx].realData[dr] = NA_REAL;
				} else {
					std::istringstream is(str);
					is >> stripeData[cx].realData[dr];
          if (verbose >= 3 && dr < 20) {
            mxLog("%s >> %d %f", str.c_str(), dr, stripeData[cx].realData[dr]);
          }
				}
				dr += 1;
			}
		} else {
			for (int rx=0,dr=0; rx < srcRows; ++rx) {
				if (skipRow(rx)) {
					icsv->get_delimited_str();
					continue;
				}
				mxScanInt(*icsv, rc[ columns[cx] ],
					  &stripeData[cx].intData[dr]);
				dr += 1;
			}
		}
	}
	curRecord += 1;
	for (int cx=0; cx < int(columns.size()); ++cx) {
    if (verbose >= 2) {
      std::string buf;
      if (colTypes[cx] == COLUMNDATA_NUMERIC) {
        for (int rx=0; rx < std::min(12, srcRows); ++rx) {
          auto val = stripeData[cx].realData[rx];
          if (std::isfinite(val)) {
            buf += string_snprintf("%f ", stripeData[cx].realData[rx]);
          } else { buf += "NA "; }
        }
      } else {
        for (int rx=0; rx < std::min(12, srcRows); ++rx)
          buf += string_snprintf("%d ", stripeData[cx].intData[rx]);
      }
      mxLog("%s: replace column %d with %s", name, columns[cx], buf.c_str());
    }
		rc[ columns[cx] ].setBorrow(stripeData[cx]);
	}
}

class LoadDataDFProvider : public LoadDataProvider<LoadDataDFProvider> {
	bool byrow;
	Rcpp::DataFrame observed;

	virtual const char *getName() override { return "data.frame"; };
	virtual int getNumVariants() override {
		return (observed.nrows() / srcRows) * (observed.ncol() / columns.size());
	}
	virtual void init(SEXP rObj) override {
		ProtectedSEXP Rbyrow(R_do_slot(rObj, Rf_install("byrow")));
		byrow = Rf_asLogical(Rbyrow);
		if (byrow) mxThrow("byrow=TRUE not implemented for data.frame data");

		ProtectedSEXP Robs(R_do_slot(rObj, Rf_install("observed")));
		observed = Robs;
		if (int(observed.size()) < int(colTypes.size())) {
			mxThrow("%s: provided observed data only has %d columns but %d requested",
				name, int(observed.size()), int(colTypes.size()));
		}
		if (observed.nrows() % srcRows != 0) {
			mxThrow("%s: original data has %d rows, "
					 "does not divide the number of observed rows %d evenly (remainder %d)",
					 name, srcRows, observed.nrows(), observed.nrows() % srcRows);
		}
		if (observed.ncol() % columns.size() != 0) {
			mxThrow("%s: original data has %d columns, "
					 "does not divide the number of observed columns %d evenly (remainder %d)",
					 name, int(columns.size()), observed.ncol(), observed.ncol() % columns.size());
		}
		if (observed.nrows() != srcRows && observed.ncol() != int(columns.size())) {
			mxThrow("%s: additional data must be in rows or columns, but not both");
		}
		CharacterVector obNames = observed.attr("names");
		for (int cx=0; cx < int(colTypes.size()); ++cx) {
			if (colTypes[cx] == COLUMNDATA_NUMERIC) {
				// OK
			} else {
				IntegerVector vec = observed[cx];
				if (vec.hasAttribute("levels")) {
					CharacterVector lev = vec.attr("levels");
					auto &rc = (*rawCols)[ columns[cx] ];
					if (int(rc.levelNames.size()) != int(lev.size())) {
						mxThrow("%s: observed column %d (%s) has a different number"
								 "of factor levels %d compare to the original data %d",
								 name, 1+cx, as<const char *>(obNames[cx]),
								 int(lev.size()), int(rc.levelNames.size()));
					}
				}
			}
		}
	}
	virtual void loadRowImpl(int index) override
	{
		auto &rc = *rawCols;
		if (observed.nrows() != srcRows) {
			int rowBase = index * srcRows;
			if (observed.nrows() < rowBase + srcRows) {
				mxThrow("%s: index %d requested but observed data only has %d sets of rows",
						 name, index, observed.nrows() / srcRows);
			}
			for (int cx=0; cx < int(columns.size()); ++cx) {
				RObject vec = observed[cx];
				if (colTypes[cx] == COLUMNDATA_NUMERIC) {
					NumericVector avec(vec);
					for (int rx=0,dr=0; rx < srcRows; ++rx) {
						if (skipRow(rx)) continue;
						stripeData[cx].realData[dr] = avec[rowBase + rx];
						dr += 1;
					}
				} else {
					IntegerVector ivec(vec);
					for (int rx=0,dr=0; rx < srcRows; ++rx) {
						if (skipRow(rx)) continue;
						stripeData[cx].intData[dr] = ivec[rowBase + rx];
						dr += 1;
					}
				}
				rc[ columns[cx] ].setBorrow(stripeData[cx]);
			}
		} else {
			int colBase = index * columns.size();
			if (observed.ncol() < int(colBase + columns.size())) {
				mxThrow("%s: index %d requested but observed data only has %d sets of columns",
						 name, index, observed.ncol() / columns.size());
			}
			for (int cx=0; cx < int(columns.size()); ++cx) {
				RObject vec = observed[colBase + cx];
				if (colTypes[cx] == COLUMNDATA_NUMERIC) {
					NumericVector avec(vec);
					rc[ columns[cx] ].setBorrow(avec.begin());
				} else {
					IntegerVector ivec(vec);
					rc[ columns[cx] ].setBorrow(ivec.begin());
				}
			}
		}
	}
};

void LoadDataProviderBase2::commonInit(SEXP rObj, const char *u_name,
                                       const char *u_dataName, int u_rows,
                                       std::vector<ColumnData> &u_rawCols,
                                       ColMapType &u_rawColMap,
                                       std::vector< std::string > &u_checkpointValues,
                                       bool useOriginalData)
{
	name = u_name;
	dataName = u_dataName;
	destRows = u_rows;
	srcRows = u_rows;
	rawCols = &u_rawCols;
	rawColMap = &u_rawColMap;
	checkpointValues = &u_checkpointValues;

	curRecord = -1;
	loadCounter = 0;
	stripeSize = 1;
	stripeStart = -1;
	stripeEnd = -1;

	ProtectedSEXP Rverbose(R_do_slot(rObj, Rf_install("verbose")));
	verbose = Rf_asInteger(Rverbose);

	rowNames = NA_INTEGER;
	colNames = NA_INTEGER;
	ProtectedSEXP Rrownames(R_do_slot(rObj, Rf_install("row.names")));
	if (Rf_length(Rrownames)) rowNames = Rf_asInteger(Rrownames);
	ProtectedSEXP Rcolnames(R_do_slot(rObj, Rf_install("col.names")));
	if (Rf_length(Rcolnames)) colNames = Rf_asInteger(Rcolnames);

	ProtectedSEXP Rskiprows(R_do_slot(rObj, Rf_install("skip.rows")));
	skipRows = Rf_asInteger(Rskiprows);
	ProtectedSEXP Rskipcols(R_do_slot(rObj, Rf_install("skip.cols")));
	skipCols = Rf_asInteger(Rskipcols);

	ProtectedSEXP RnaStr(R_do_slot(rObj, Rf_install("na.strings")));
	for (int x1=0; x1 < Rf_length(RnaStr); ++x1) {
		naStrings.push_back(R_CHAR(STRING_ELT(RnaStr, x1)));
	}

	ProtectedSEXP Rcol(R_do_slot(rObj, Rf_install("column")));
	for (int cx=0; cx < Rf_length(Rcol); ++cx) {
		auto cn = R_CHAR(STRING_ELT(Rcol, cx));
		auto &rcm = *rawColMap;
		auto rci = rcm.find(cn);
		if (rci == rcm.end()) {
			omxRaiseErrorf("%s: column '%s' not found in '%s'",
				       name, cn, dataName);
			continue;
		}
		columns.push_back(rci->second);
		auto &rc = u_rawCols[rci->second];
		colTypes.push_back(rc.type);
		if (useOriginalData) origData.emplace_back(rc.steal());
	}

	ProtectedSEXP Rcheckpoint(R_do_slot(rObj, Rf_install("checkpointMetadata")));
	checkpoint = Rf_asLogical(Rcheckpoint);

	ProtectedSEXP RrowFilter(R_do_slot(rObj, Rf_install("rowFilter")));
	rowFilter = 0;
	if (Rf_length(RrowFilter)) {
		rowFilter = INTEGER(RrowFilter);
		srcRows = Rf_length(RrowFilter);
		int numSkip = std::accumulate(rowFilter, rowFilter + srcRows, 0);
		if (destRows != srcRows - numSkip) {
			mxThrow("rowFilter skips %d rows but %d-%d does not match the number of "
							"rows of observed data %d", numSkip, srcRows, numSkip, destRows);
		}
	}
}

void ComputeLoadData::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	ProtectedSEXP RoriginalData(R_do_slot(rObj, Rf_install("originalDataIsIndexOne")));
	useOriginalData = Rf_asLogical(RoriginalData);

	ProtectedSEXP Rmethod(R_do_slot(rObj, Rf_install("method")));
	const char *methodName = R_CHAR(STRING_ELT(Rmethod, 0));

  data = 0;
	ProtectedSEXP Rdata(R_do_slot(rObj, Rf_install("dest")));
	if (Rf_length(Rdata) > 1)
		mxThrow("%s: can only handle 1 destination MxData", name);
  int objNum = Rf_asInteger(Rdata);
  if (objNum != -1) {
    data = globalState->dataList[objNum];
  }

	for (auto &pr : Providers) {
		if (strEQ(methodName, pr->getName())) {
			provider = pr->clone();
      if (data) {
        auto &rd = data->getUnfilteredRawData();
        provider->commonInit(rObj, name, data->name, rd.rows, rd.rawCols,
                             data->rawColMap, Global->checkpointValues, useOriginalData);
      } else {
        int rows = 0;
        std::vector<ColumnData> rawCols;
        ColMapType rawColMap;
        provider->commonInit(rObj, name, 0, rows, rawCols,
                             rawColMap, Global->checkpointValues, useOriginalData);
      }
			provider->init(rObj);
			break;
		}
	}
	if (!provider) {
		std::string avail;
		for (auto &pr : Providers) {
			avail += " ";
			avail += pr->getName();
		}
		mxThrow("%s: unknown provider '%s'; available providers are:%s",
						name, methodName, avail.c_str());
	}

	if (provider->wantCheckpoint()) {
		auto &cp = Global->checkpointColnames;
		provider->addCheckpointColumns(cp);
	}
}

void ComputeLoadData::computeImpl(FitContext *fc)
{
	std::vector<int> &clc = Global->computeLoopIndex;
  int index = 0;
	if (clc.size()) index = clc[clc.size()-1] - 1;  // innermost loop index

	if (data) data->setModified();
	if (useOriginalData && index == 0) {
		provider->loadOrigRow();
	} else {
		index -= useOriginalData; // 0 == the first record
		provider->loadRow(index);
    if (clc.size()) {
      auto &clm = Global->computeLoopMax;
      auto &max = clm.at(clm.size()-1);
      if (max == 0) max = provider->getNumVariants();
    }
	}

  if (data) {
    auto &columns = provider->getColumns();
    ColumnInvalidator ci(*fc->state, data, columns);
    ci();
    data->evalAlgebras(fc);
    fc->state->connectToData();
  }
}

void ComputeLoadData::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	MxRList dbg;
	dbg.add("loadCounter", Rf_ScalarInteger(provider->getLoadCounter()));
	slots->add("debug", dbg.asR());

	MxRList output;
	output.add("rowsAvailable", Rcpp::wrap(provider->getNumVariants()));
	slots->add("output", output.asR());
}

void ComputeLoadData::loadedHook()
{
	Providers.clear();
	Providers.push_back(std::make_unique<LoadDataCSVProvider>());
	Providers.push_back(std::make_unique<LoadDataDFProvider>());
}

unsigned int DJBHash(const char *str, std::size_t len)
{
   unsigned int hash = 5381;

   for(std::size_t i = 0; i < len; i++) {
     hash = ((hash << 5) + hash) + str[i];
   }

   return hash;
}

void AddLoadDataProvider(double version, unsigned int otherHash,
                         std::unique_ptr<LoadDataProviderBase2> ldp)
{
  std::size_t sz2[] = {
               sizeof(dataPtr),
               sizeof(LoadDataProviderBase2),
               sizeof(ColumnData)
  };
  auto apiHash = DJBHash((char*)sz2, sizeof(sz2));
	if (version == OPENMX_LOAD_DATA_API_VERSION) {
		if (otherHash != apiHash) {
			mxThrow("Cannot add mxComputeLoadData provider, version matches "
							"but OpenMx is compiled with different compiler options (%u != %u)",
							otherHash, apiHash);
		}
	} else {
		mxThrow("Cannot add mxComputeLoadData provider, version mismatch");
	}
	ComputeLoadData::addProvider(std::move(ldp));
}

void ComputeLoadContext::reopen()
{
	loadCounter += 1;
	try {
		st = std::unique_ptr<mini::csv::ifstream>(new mini::csv::ifstream(path));
	} catch (...) {
		mxThrow("%s: failed to open '%s'", name, path.c_str());
	}
	st->set_delimiter(sep, "##");
}

void ComputeLoadContext::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	loadCounter = 0;

	ProtectedSEXP Rverbose(R_do_slot(rObj, Rf_install("verbose")));
	verbose = Rf_asInteger(Rverbose);
	ProtectedSEXP Rheader(R_do_slot(rObj, Rf_install("header")));
	header = Rf_asInteger(Rheader);
	ProtectedSEXP Rcolnames(R_do_slot(rObj, Rf_install("col.names")));
	for (int cx=0; cx < Rf_length(Rcolnames); ++cx) {
		colnames.push_back(R_CHAR(STRING_ELT(Rcolnames, cx)));
	}

	ProtectedSEXP Rcol(R_do_slot(rObj, Rf_install("column")));
	numColumns = Rf_length(Rcol);
	columnPtr = INTEGER(Rcol);
	if (numColumns == 0) return;

	ProtectedSEXP Rsep(R_do_slot(rObj, Rf_install("sep")));
	const char *sepStr = R_CHAR(STRING_ELT(Rsep, 0));
	if (strlen(sepStr) != 1) mxThrow("%s: sep must be a single character, not '%s'", name, sepStr);
	sep = sepStr[0];

	auto &cp = Global->checkpointColnames;
	cpIndex = cp.size();
	Eigen::Map< Eigen::ArrayXi > col(columnPtr, numColumns);
	if (col.minCoeff() < 1) mxThrow("%s: the first column is 1, not %d",
				   name, col.minCoeff());
	maxColumn = col.maxCoeff();
	//mxLog("%s: len %d max %d", name, numColumns, maxColumn);

	ProtectedSEXP Rpath(R_do_slot(rObj, Rf_install("path")));
	path = R_CHAR(STRING_ELT(Rpath, 0));
	reopen();
	if (header) {
		if (!st->read_line()) mxThrow("%s: cannot read header of '%s'", name, path.c_str());
	}
	if (colnames.size()) {
		for (int cx=0; cx < numColumns; ++cx) cp.push_back(colnames[cx]);
	} else if (header) {
		int xx=0;
		for (int cx=0; cx < maxColumn; ++cx) {
			std::string c1;
			*st >> c1;
			if (cx == col[xx]-1) {
				if (verbose) mxLog("cx %d xx %d %s", cx, xx, c1.c_str());
				cp.push_back(c1);
				if (++xx == numColumns) break;
			}
		}
		if (xx != numColumns) mxThrow("%s: columns must be ordered from first to last", name);
	} else {
		for (int cx=0; cx < numColumns; ++cx) {
			std::string c1 = string_snprintf(":%d", col[cx]);
			cp.push_back(path + c1);
		}
	}
	curLine = 0;
}

void ComputeLoadContext::computeImpl(FitContext *fc)
{
	if (numColumns == 0) return;

	std::vector<int> &clc = Global->computeLoopIndex;
	if (clc.size() == 0) mxThrow("%s: must be used within a loop", name);
	int index = clc[clc.size()-1] - 1;  // innermost loop index

	if (index < curLine) {
		reopen();
		st->skip_line(); // header
		curLine = 0;
	}
	while (index > curLine) {
		st->skip_line();
		curLine += 1;
	}

	bool fail = false; // not sure how failure is reported
	try {
		fail = !st->read_line();
	} catch (...) {
		fail = true;
	}
	if (fail) mxThrow("%s: '%s' ran out of data at record %d",
			  name, path.c_str(), 1+index);

	Eigen::Map< Eigen::ArrayXi > col(columnPtr, numColumns);
	auto &cv = Global->checkpointValues;

	for (int cx=0, xx=0; cx < maxColumn; ++cx) {
		std::string c1;
		*st >> c1;
		if (cx == col[xx]-1) {
			cv[cpIndex + xx] = c1;
			if (++xx == numColumns) break;
		}
	}
	curLine += 1;
}

void ComputeLoadContext::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	MxRList dbg;
	dbg.add("loadCounter", Rf_ScalarInteger(loadCounter));
	slots->add("debug", dbg.asR());
}

void ComputeLoadMatrix::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);

	ProtectedSEXP RoriginalData(R_do_slot(rObj, Rf_install("originalDataIsIndexOne")));
	useOriginalData = Rf_asLogical(RoriginalData);

	ProtectedSEXP Rdata(R_do_slot(rObj, Rf_install("dest")));
	ProtectedSEXP Rpath(R_do_slot(rObj, Rf_install("path")));
	hasRowNames.resize(Rf_length(Rdata));
	if (useOriginalData) origData.resize(Rf_length(Rdata));
	ProtectedSEXP Rrownames(R_do_slot(rObj, Rf_install("row.names")));
	ProtectedSEXP Rcolnames(R_do_slot(rObj, Rf_install("col.names")));

	ProtectedSEXP Rmethod(R_do_slot(rObj, Rf_install("method")));
	const char *methodName = R_CHAR(STRING_ELT(Rmethod, 0));
	if (strEQ(methodName, "csv")) {
		loadMethod = LoadCSV;
		if (Rf_length(Rpath) != Rf_length(Rdata)) {
			mxThrow("%s: %d matrices to load but only %d paths",
				name, Rf_length(Rdata), Rf_length(Rpath));
		}
	} else if (strEQ(methodName, "data.frame")) {
		loadMethod = LoadDataFrame;
	} else {
		mxThrow("%s: unknown method '%s'", name, methodName);
	}

	int numElem = 0;
	for (int wx=0; wx < Rf_length(Rdata); ++wx) {
		if (isErrorRaised()) return;
		int objNum = ~INTEGER(Rdata)[wx];
		omxMatrix *m1 = globalState->matrixList[objNum];
		if (m1->hasPopulateSubstitutions()) {
			omxRaiseErrorf("%s: matrix '%s' has populate substitutions",
				       name, m1->name());
		}
		numElem += m1->numNonConstElements();
		EigenMatrixAdaptor Em1(m1);
		if (useOriginalData) origData[wx] = Em1;
		mat.push_back(m1);

		if (loadMethod != LoadDataFrame) {
			const char *p1 = R_CHAR(STRING_ELT(Rpath, wx));
			// convert to std::string to work around mini::csv constructor bug
			// https://github.com/shaovoon/minicsv/issues/8
			streams.push_back(new mini::csv::ifstream(std::string(p1)));
			mini::csv::ifstream &st = *streams[wx];
			st.set_delimiter(' ', "##");
			if (INTEGER(Rcolnames)[wx % Rf_length(Rcolnames)]) {
				st.skip_line();
			}
		}

		hasRowNames[wx] = INTEGER(Rrownames)[wx % Rf_length(Rrownames)];
		//mxLog("ld %s %s", d1->name, p1);
	}
	line = 1;

	if (loadMethod == LoadDataFrame) {
		ProtectedSEXP Robs(R_do_slot(rObj, Rf_install("observed")));
		observed = Robs;
		if (int(observed.size()) < numElem) {
			mxThrow("%s: provided observed data only has %d columns but %d requested",
				name, int(observed.size()), numElem);
		}
		Rcpp::CharacterVector obNames = observed.attr("names");
		for (int cx=0; cx < numElem; ++cx) {
			if (Rcpp::is<Rcpp::NumericVector>(observed[cx])) continue;

			mxThrow("%s: observed column %d (%s) is not type 'numeric'",
				name, 1+cx, Rcpp::as<const char *>(obNames[cx]));
		}
	}

}

ComputeLoadMatrix::~ComputeLoadMatrix()
{
	for (auto st : streams) delete st;
	streams.clear();
}

void ComputeLoadMatrix::computeImpl(FitContext *fc)
{
	std::vector<int> &clc = Global->computeLoopIndex;
	if (clc.size() == 0) mxThrow("%s: must be used within a loop", name);
	int index = clc[clc.size()-1];  // innermost loop index
	if (useOriginalData && index == 1) {
		for (int dx=0; dx < int(mat.size()); ++dx) {
			EigenMatrixAdaptor Em(mat[dx]);
			Em.derived() = origData[dx];
		}
		return;
	} else {
		index -= useOriginalData; // 1 == the first record
		switch (loadMethod) {
		case LoadCSV:
			loadFromCSV(fc, index);
			break;
		case LoadDataFrame:
			loadDataFrame(fc, index);
			break;
		default:
			mxThrow("%s: unknown load method %d", name, loadMethod);
		}
	}

	fc->state->invalidateCache();
	fc->state->connectToData();
	fc->state->omxInitialMatrixAlgebraCompute(fc);
	if (isErrorRaised()) mxThrow("%s", Global->getBads()); // ?still necessary?
}

struct clmStream {
	Rcpp::DataFrame &observed;
	const int row;
	int curCol;
	clmStream(Rcpp::DataFrame &u_ob, int u_row) : observed(u_ob), row(u_row) { curCol = 0; };

	void operator >> (double& val)
	{
		auto vec = observed[curCol];
		val = REAL(vec)[row];
		curCol += 1;
	}
};

void ComputeLoadMatrix::loadDataFrame(FitContext *fc, int index)
{
	if (observed.nrows() < index) {
		mxThrow("%s: index %d requested but observed data only has %d rows",
			name, index, observed.nrows());
	}

	clmStream st(observed, index - 1);
	for (int dx=0; dx < int(mat.size()); ++dx) {
		mat[dx]->loadFromStream(st);
	}
}

void ComputeLoadMatrix::loadFromCSV(FitContext *fc, int index)
{
	if (line > index) {
		mxThrow("%s: at line %d, cannot seek backwards to line %d",
			 name, line, index);
	}
	while (line < index) {
		for (int dx=0; dx < int(mat.size()); ++dx) {
			mini::csv::ifstream &st = *streams[dx];
			st.skip_line();
		}
		line += 1;
	}
	for (int dx=0; dx < int(mat.size()); ++dx) {
		mini::csv::ifstream &st = *streams[dx];
		if (!st.read_line()) {
			mxThrow("%s: ran out of data for matrix '%s'",
				 name, mat[dx]->name());
		}
		if (hasRowNames[dx]) {
			std::string rn;
			st >> rn;  // discard it
		}
		mat[dx]->loadFromStream(st);
	}
	line += 1;
}

void ComputeCheckpoint::initFromFrontend(omxState *globalState, SEXP rObj)
{
	super::initFromFrontend(globalState, rObj);
	badSEWarning = false;

	ProtectedSEXP Rappend(R_do_slot(rObj, Rf_install("append")));
	bool append = Rf_asLogical(Rappend);

	ProtectedSEXP Rheader(R_do_slot(rObj, Rf_install("header")));
	wroteHeader = !Rf_asLogical(Rheader);

	firstTime = true;
	numExtraCols = 0;

	path = 0;
	ProtectedSEXP Rpath(R_do_slot(rObj, Rf_install("path")));
	if (Rf_length(Rpath) == 1) {
		path = R_CHAR(STRING_ELT(Rpath, 0));
		ofs.open(path, append? std::ofstream::app : std::ofstream::trunc);
		if (!ofs.is_open()) {
			mxThrow("Failed to open '%s' for writing", path);
		}
	}

	ProtectedSEXP RtoReturn(R_do_slot(rObj, Rf_install("toReturn")));
	toReturn = Rf_asLogical(RtoReturn);

	ProtectedSEXP Rpar(R_do_slot(rObj, Rf_install("parameters")));
	inclPar = Rf_asLogical(Rpar);

	ProtectedSEXP RloopInd(R_do_slot(rObj, Rf_install("loopIndices")));
	inclLoop = Rf_asLogical(RloopInd);

	ProtectedSEXP Rfit(R_do_slot(rObj, Rf_install("fit")));
	inclFit = Rf_asLogical(Rfit);

	ProtectedSEXP Rcounters(R_do_slot(rObj, Rf_install("counters")));
	inclCounters = Rf_asLogical(Rcounters);

	ProtectedSEXP Rstatus(R_do_slot(rObj, Rf_install("status")));
	inclStatus = Rf_asLogical(Rstatus);

	ProtectedSEXP Rse(R_do_slot(rObj, Rf_install("standardErrors")));
	inclSEs = Rf_asLogical(Rse);

	ProtectedSEXP Rgradient(R_do_slot(rObj, Rf_install("gradient")));
	inclGradient = Rf_asLogical(Rgradient);

	ProtectedSEXP Rvcov(R_do_slot(rObj, Rf_install("vcov")));
	inclVcov = Rf_asLogical(Rvcov);

  inclVcovWLS = false;
  if (R_has_slot(rObj, Rf_install("vcovWLS"))) {
    ProtectedSEXP Rv(R_do_slot(rObj, Rf_install("vcovWLS")));
    inclVcovWLS = Rf_asLogical(Rv);
    inclVcov |= inclVcovWLS;
  }

  inclSampleSize = false;
  if (R_has_slot(rObj, Rf_install("sampleSize"))) {
    ProtectedSEXP Rss(R_do_slot(rObj, Rf_install("sampleSize")));
    inclSampleSize = Rf_asLogical(Rss);
  }

  auto &vg = *Global->findVarGroup(FREEVARGROUP_ALL);
  numParam = vg.vars.size();

  if (inclVcov) {
    S4 ro(rObj);
    vcovFilter.assign(numParam, true);
    bool filter = false;
    if (ro.hasSlot("useVcovFilter")) filter = ro.slot("useVcovFilter");
    if (filter) {
      vcovFilter.assign(numParam, false);
      if (ro.slot("vcovFilter") != R_NilValue) {
        CharacterVector vcf = ro.slot("vcovFilter");
        for (int fx=0; fx < vcf.size(); ++fx) {
          String pstr = vcf[fx];
          auto pname = pstr.get_cstring();
          vcovFilterSet.insert(pname);
          int vx = vg.lookupVar(pname);
          if (vx >= 0) vcovFilter[vx] = true;
        }
      }
    }
  }

	ProtectedSEXP Rwhat(R_do_slot(rObj, Rf_install("what")));
	for (int wx=0; wx < Rf_length(Rwhat); ++wx) {
		if (isErrorRaised()) return;
		int objNum = INTEGER(Rwhat)[wx];
		omxMatrix *algebra = globalState->algebraList[objNum];
		if (algebra->fitFunction) {
			omxCompleteFitFunction(algebra);
		}
		algebras.push_back(algebra);
	}

	if (inclCounters) {
		colnames.push_back("OpenMxEvals");
		colnames.push_back("iterations");
	}
	colnames.push_back("timestamp");
	if (inclLoop) {
		auto &clc = Global->computeLoopContext;
		for (int lx=0; lx < int(clc.size()); ++lx) {
			colnames.push_back(string_snprintf("%s%d", clc[lx], 1+lx));
		}
	}

	std::vector< omxFreeVar* > &vars = Global->findVarGroup(FREEVARGROUP_ALL)->vars;

	if (inclPar) {
		for(int j = 0; j < numParam; j++) {
			colnames.push_back(vars[j]->name);
		}
	}

	if (inclFit) {
		colnames.push_back("objective");
		colnames.push_back("fitUnits");
	}
	if (inclStatus) colnames.push_back("statusCode");
	if (inclSEs) {
		for(int j = 0; j < numParam; j++) {
			std::string c1 = vars[j]->name;
			c1 += "SE";
			colnames.push_back(c1);
		}
	}
	if (inclGradient) {
		for (auto v1 : vars) {
			std::string c1 = v1->name;
			c1 += "Grad";
			colnames.push_back(c1);
		}
	}
	if (inclVcov) {
    vcovEntries = 0;
		for (int cx=0; cx < numParam; ++cx) {
			for (int rx=cx; rx < numParam; ++rx) {
        if (cx != rx && (!vcovFilter[cx] || !vcovFilter[rx])) continue;
				std::string c1 = "V";
				c1 += vars[rx]->name;
				c1 += ":";
				c1 += vars[cx]->name;
				colnames.push_back(c1);
        vcovEntries += 1;
			}
		}
	}

	numAlgebraEnt = 0;
	for (auto &mat : algebras) {
		for (int cx=0; cx < mat->cols; ++cx) {
			for (int rx=0; rx < mat->rows; ++rx) {
				colnames.push_back(string_snprintf("%s[%d,%d]", mat->name(), 1+rx, 1+cx));
			}
		}
		numAlgebraEnt += mat->cols * mat->rows;
	}

  if (inclSampleSize) {
    for (auto dat : globalState->dataList) {
      std::string str = dat->name;
      str += ".nrow";
      colnames.push_back(str);
    }
  }

	// TODO: confidence intervals, hessian, constraint algebras
	// what does Eric Schmidt include in per-voxel output?
	// remove old checkpoint code?
	numSnaps = 0;
}

void ComputeCheckpoint::computeImpl(FitContext *fc)
{
	// if ((timePerCheckpoint && timePerCheckpoint <= now - lastCheckpoint) ||
	//     (iterPerCheckpoint && iterPerCheckpoint <= fc->iterations - lastIterations) ||
	//     (evalsPerCheckpoint && evalsPerCheckpoint <= curEval - lastEvaluation)) {

	if (firstTime) {
    if (inclVcovWLS) {
      for (auto dat : fc->state->dataList) {
        if (!dat->hasVcov()) continue;
        auto &o1 = dat->getSingleObsSummaryStats();
        for (int vx=0; vx < int(o1.perVar.size()); ++vx) {
          std::string scope = dat->name;
          scope += ".";
          scope += o1.dc[vx];
          int numPred = o1.numPredictors(vx);
          auto iter = exoVcovFilter.emplace(std::make_pair(scope, std::vector<bool>{}));
          auto &mask = iter.first->second;
          mask.assign(numPred, vcovFilterSet.empty());
          for (int cx=0; cx < numPred; ++cx) {
            std::string key = scope + "." + dat->getExoPredictorName(vx, cx);
            if (vcovFilterSet.find(key) == vcovFilterSet.end()) continue;
            mask[cx] = true;
          }

          for (int cx=0; cx < numPred; ++cx) {
            for (int rx=cx; rx < numPred; ++rx) {
              if (cx != rx && (!mask[cx] || !mask[rx])) continue;
              std::string c1 = scope + ".V";
              c1 += dat->getExoPredictorName(vx, rx);
              c1 += ":";
              c1 += dat->getExoPredictorName(vx, cx);
              colnames.push_back(c1);
              vcovEntries += 1;
            }
          }
        }
      }
    }

		auto &xcn = Global->checkpointColnames;
		numExtraCols = xcn.size();
		colnames.insert(colnames.end(), xcn.begin(), xcn.end());
		firstTime = false;
	}

	snap s1;
	s1.evaluations = fc->getGlobalComputeCount();
	s1.iterations = fc->iterations;
	s1.timestamp = time(0);
	if (inclLoop) s1.computeLoopIndex = Global->computeLoopIndex;
	if (inclPar) {
		s1.est = fc->est;
	}
	s1.fit = fc->getFit();
	s1.fitUnits = fc->fitUnits;
	s1.inform = fc->wrapInform();
	if (inclSEs) {
		if (fc->stderrs.size() && fc->stderrs.size() != int(fc->numParam)) {
			if (!badSEWarning) {
				Rf_warning("%s: there are %d standard errors but %d parameters",
					   name, fc->stderrs.size(), int(fc->numParam));
				badSEWarning = true;
			}
		}
		s1.stderrs = fc->stderrs;
	}
	if (inclGradient) s1.gradient = fc->gradZ;
	if (inclVcov) {
		s1.vcov.resize(vcovEntries);
		int lx=0;
    for (int cx=0; cx < numParam; ++cx) {
      for (int rx=cx; rx < numParam; ++rx) {
        if (cx != rx && (!vcovFilter[cx] || !vcovFilter[rx])) continue;
        s1.vcov[lx++] = fc->vcov.rows() == numParam? fc->vcov(rx, cx) : NA_REAL;
      }
    }
    if (inclVcovWLS) {
      for (auto dat : fc->state->dataList) {
        if (!dat->hasVcov()) continue;
        auto &o1 = dat->getSingleObsSummaryStats();
        for (int vx=0; vx < int(o1.perVar.size()); ++vx) {
          std::string scope = dat->name;
          scope += ".";
          scope += o1.dc[vx];
          auto &mask = exoVcovFilter[scope];
          auto &pv = o1.perVar[vx];
          int numPred = o1.numPredictors(vx);
          for (int cx=0; cx < numPred; ++cx) {
            for (int rx=cx; rx < numPred; ++rx) {
              if (cx != rx && (!mask[cx] || !mask[rx])) continue;
              s1.vcov[lx++] = pv.vcov(rx, cx);
            }
          }
        }
      }
    }
	}
	s1.algebraEnt.resize(numAlgebraEnt);

	{int xx=0;
	for (auto &mat : algebras) {
		for (int cx=0; cx < mat->cols; ++cx) {
			for (int rx=0; rx < mat->rows; ++rx) {
				EigenMatrixAdaptor eM(mat);
				s1.algebraEnt[xx] = eM(rx, cx);
				xx += 1;
			}
		}
	}}

  auto &dataList = fc->state->dataList;
  s1.sampleSize.resize(dataList.size());
  for (int dx=0; dx < int(dataList.size()); ++dx) {
    s1.sampleSize[dx] = dataList[dx]->nrows();
  }

	s1.extra = Global->checkpointValues;

	if (ofs.is_open()) {
		const int digits = std::numeric_limits<double>::digits10 + 1;
		if (!wroteHeader) {
			bool first = true;
			for (auto &cn : colnames) {
				if (first) { first=false; }
				else       { ofs << '\t'; }
				ofs << cn;
			}
			ofs << std::endl;
			wroteHeader = true;
		}

		bool first = true;
		if (inclCounters) {
			if (first) { first=false; }
			else       { ofs << '\t'; }
			ofs << s1.evaluations;
			ofs << '\t' << s1.iterations;
		}
		if (1) {
			if (first) { first=false; }
			else       { ofs << '\t'; }
			const int timeBufSize = 32;
			char timeBuf[timeBufSize];
			struct tm *nowTime = localtime(&s1.timestamp);
			strftime(timeBuf, timeBufSize, "%b %d %Y %I:%M:%S %p", nowTime);
			ofs << timeBuf;
		}
		if (inclLoop) {
			auto &clc = s1.computeLoopIndex;
			for (int lx=0; lx < int(clc.size()); ++lx) {
				ofs << '\t' << clc[lx];
			}
		}
		if (inclPar) {
			for (int x1=0; x1 < int(s1.est.size()); ++x1) {
				ofs << '\t' << std::setprecision(digits) << s1.est[x1];
			}
		}
		if (inclFit) {
			ofs << '\t' << std::setprecision(digits) << s1.fit;
			ofs << '\t' << fitUnitsToName(s1.fitUnits);
		}
		if (inclStatus) {
			if (s1.inform == NA_INTEGER) {
				ofs << '\t' << "NA";
			} else {
				ofs << '\t' << statusCodeLabels[s1.inform - 1];
			}
		}
		if (inclSEs) {
			if (s1.stderrs.size()) {
				for (int x1=0; x1 < int(s1.est.size()); ++x1) {
					ofs << '\t' << std::setprecision(digits) << s1.stderrs[x1];
				}
			} else {
				for (int x1=0; x1 < int(s1.est.size()); ++x1) {
					ofs << '\t' << NA_REAL;
				}
			}
		}
		if (inclGradient) {
			if (s1.gradient.size()) {
				for (int x1=0; x1 < int(s1.est.size()); ++x1) {
					ofs << '\t' << std::setprecision(digits) << s1.gradient[x1];
				}
			} else {
				for (int x1=0; x1 < int(s1.est.size()); ++x1) {
					ofs << '\t' << NA_REAL;
				}
			}
		}
		if (inclVcov) {
			int numVcov = vcovEntries;
			if (s1.vcov.size()) {
				for (int x1=0; x1 < numVcov; ++x1) {
					ofs << '\t' << std::setprecision(digits) << s1.vcov[x1];
				}
			} else {
				for (int x1=0; x1 < numVcov; ++x1) {
					ofs << '\t' << NA_REAL;
				}
			}
		}
		for (int x1=0; x1 < int(s1.algebraEnt.size()); ++x1) {
			ofs << '\t' << std::setprecision(digits) << s1.algebraEnt[x1];
		}
		if (inclSampleSize) {
      for (int dx=0; dx < s1.sampleSize.size(); ++dx) {
        ofs << '\t' << s1.sampleSize[dx];
      }
    }
		for (auto &x1 : s1.extra) ofs << '\t' << x1;
		ofs << std::endl;
		ofs.flush();
	}

	if (toReturn) {
		snaps.push_front(s1);
		numSnaps += 1;
	}
}

void ComputeCheckpoint::reportResults(FitContext *fc, MxRList *slots, MxRList *)
{
	const bool debug = false;
	if (ofs.is_open()) {
		ofs.close();
	}
	if (!toReturn) return;

	snaps.reverse();

	SEXP log;
	Rf_protect(log = Rf_allocVector(VECSXP, colnames.size()));
	int curCol=0;
	if (inclCounters) {
		{
			SEXP col = Rf_allocVector(INTSXP, numSnaps);
			if (debug) mxLog("log[%d] = %s (evaluations)", curCol, colnames[curCol].c_str());
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = INTEGER(col);
			int sx=0;
			for (auto &s1 : snaps) v[sx++] = s1.evaluations;
		}
		{
			SEXP col = Rf_allocVector(INTSXP, numSnaps);
			if (debug) mxLog("log[%d] = %s (iterations)", curCol, colnames[curCol].c_str());
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = INTEGER(col);
			int sx=0;
			for (auto &s1 : snaps) v[sx++] = s1.iterations;
		}
	}
	{
		SEXP POSIXct;
		Rf_protect(POSIXct = Rf_allocVector(STRSXP, 2));
		SET_STRING_ELT(POSIXct, 0, Rf_mkChar("POSIXct"));
		SET_STRING_ELT(POSIXct, 1, Rf_mkChar("POSIXt"));
		SEXP col = Rf_allocVector(REALSXP, numSnaps);
		Rf_setAttrib(col, R_ClassSymbol, POSIXct);
		if (debug) mxLog("log[%d] = %s (timestamp)", curCol, colnames[curCol].c_str());
		SET_VECTOR_ELT(log, curCol++, col);
		auto *v = REAL(col);
		int sx=0;
		for (auto &s1 : snaps) v[sx++] = s1.timestamp;
	}
	if (inclLoop) {
		auto &clc = snaps.front().computeLoopIndex;
		for (int lx=0; lx < int(clc.size()); ++lx) {
			SEXP col = Rf_allocVector(INTSXP, numSnaps);
			if (debug) mxLog("log[%d] = %s (loop index %d)", curCol, colnames[curCol].c_str(), lx);
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = INTEGER(col);
			int sx=0;
			for (auto &s1 : snaps) v[sx++] = s1.computeLoopIndex[lx];
		}
	}
	if (inclPar) {
		auto numEst = int(snaps.front().est.size());
		for (int x1=0; x1 < numEst; ++x1) {
			SEXP col = Rf_allocVector(REALSXP, numSnaps);
			if (debug) mxLog("log[%d] = %s (parameter %d/%d)", curCol, colnames[curCol].c_str(),
			      x1, numEst);
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = REAL(col);
			int sx=0;
			for (auto &s1 : snaps) v[sx++] = s1.est[x1];
		}
	}
	if (inclFit) {
		SEXP col1 = Rf_allocVector(REALSXP, numSnaps);
		if (debug) mxLog("log[%d] = %s (fit)", curCol, colnames[curCol].c_str());
		SET_VECTOR_ELT(log, curCol++, col1);
		SEXP col2 = makeFitUnitsFactor(Rf_allocVector(INTSXP, numSnaps));
		SET_VECTOR_ELT(log, curCol++, col2);
		auto *v = REAL(col1);
		auto *vu = INTEGER(col2);
		int sx=0;
		for (auto &s1 : snaps) {
			v[sx] = s1.fit;
			if (s1.fitUnits == FIT_UNITS_UNINITIALIZED) {
				vu[sx] = NA_INTEGER;
			} else {
				vu[sx] = s1.fitUnits;
			}
			sx += 1;
		}
	}
	if (inclStatus) {
		SEXP col = allocInformVector(numSnaps);
		if (debug) mxLog("log[%d] = %s (inform)", curCol, colnames[curCol].c_str());
		SET_VECTOR_ELT(log, curCol++, col);
		auto *v = INTEGER(col);
		int sx=0;
		for (auto &s1 : snaps) v[sx++] = s1.inform;
	}
	if (inclSEs) {
		auto numEst = int(snaps.front().est.size());
		for (int x1=0; x1 < numEst; ++x1) {
			SEXP col = Rf_allocVector(REALSXP, numSnaps);
			if (debug) mxLog("log[%d] = %s (SE %d/%d)", curCol, colnames[curCol].c_str(), x1, numEst);
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = REAL(col);
			int sx=0;
			for (auto &s1 : snaps) {
				if (s1.stderrs.size()) {
					v[sx++] = s1.stderrs[x1];
				} else {
					v[sx++] = NA_REAL;
				}
			}
		}
	}
	if (inclGradient) {
		auto numEst = int(snaps.front().est.size());
		for (int x1=0; x1 < numEst; ++x1) {
			SEXP col = Rf_allocVector(REALSXP, numSnaps);
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = REAL(col);
			int sx=0;
			for (auto &s1 : snaps) {
				v[sx++] = s1.gradient.size()? s1.gradient[x1] : NA_REAL;
			}
		}
	}
	if (inclVcov) {
		int numVcov = vcovEntries;
		for (int x1=0; x1 < numVcov; ++x1) {
			SEXP col = Rf_allocVector(REALSXP, numSnaps);
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = REAL(col);
			int sx=0;
			for (auto &s1 : snaps) {
				v[sx++] = s1.vcov.size()? s1.vcov[x1] : NA_REAL;
			}
		}
	}
	for (int x1=0; x1 < numAlgebraEnt; ++x1) {
		SEXP col = Rf_allocVector(REALSXP, numSnaps);
		if (debug) mxLog("log[%d] = %s (alge %d/%d)", curCol, colnames[curCol].c_str(), x1, numAlgebraEnt);
		SET_VECTOR_ELT(log, curCol++, col);
		auto *v = REAL(col);
		int sx=0;
		for (auto &s1 : snaps) v[sx++] = s1.algebraEnt[x1];
	}
	if (inclSampleSize) {
		auto numSS = int(snaps.front().sampleSize.size());
		for (int x1=0; x1 < numSS; ++x1) {
			SEXP col = Rf_allocVector(REALSXP, numSnaps);
			if (debug) mxLog("log[%d] = %s (parameter %d/%d)", curCol, colnames[curCol].c_str(),
			      x1, numSS);
			SET_VECTOR_ELT(log, curCol++, col);
			auto *v = REAL(col);
			int sx=0;
			for (auto &s1 : snaps) v[sx++] = s1.sampleSize[x1];
		}
	}
	auto &xcn = Global->checkpointColnames;
	if (xcn.size() != numExtraCols) {
		mxThrow("%s: xcn.size() != numExtraCols; %d != %d",
			name, int(xcn.size()), int(numExtraCols));
	}
	for (int x1=0; x1 < int(xcn.size()); ++x1) {
		SEXP col = Rf_allocVector(STRSXP, numSnaps);
		if (debug) mxLog("log[%d] = %s (extra %d/%d)", curCol, colnames[curCol].c_str(), x1, int(xcn.size()));
		SET_VECTOR_ELT(log, curCol++, col);
		int sx=0;
		for (auto &s1 : snaps) SET_STRING_ELT(col, sx++, Rf_mkChar(s1.extra[x1].c_str()));
	}

	markAsDataFrame(log, numSnaps);
	SEXP logCols;
	Rf_protect(logCols = Rf_allocVector(STRSXP, colnames.size()));
	Rf_setAttrib(log, R_NamesSymbol, logCols);
	for (int cx=0; cx < int(colnames.size()); ++cx) {
		SET_STRING_ELT(logCols, cx, Rf_mkChar(colnames[cx].c_str()));
	}

	slots->add("log", log);
}
