Sun, 18 Mar 2018

Package spuRs updated to version 2.0.1 with previous version 2.0.0 dated 2014-07-24

Title: Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R"
Description: Provides functions and datasets from Jones, O.D., R. Maillardet, and A.P. Robinson. 2014. An Introduction to Scientific Programming and Simulation, Using R. 2nd Ed. Chapman And Hall/CRC.
Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Maintainer: Andrew Robinson <apro@unimelb.edu.au>

Diff between spuRs versions 2.0.0 dated 2014-07-24 and 2.0.1 dated 2018-03-18

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Package Brobdingnag updated to version 1.2-5 with previous version 1.2-4 dated 2013-12-05

Title: Very Large Numbers in R
Description: Handles very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. The package includes a vignette that gives a step-by-step introduction to using S4 methods.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package XRJulia updated to version 0.7.7 with previous version 0.7.6 dated 2017-10-20

Title: Structured Interface to Julia
Description: A Julia interface structured according to the general form described in package 'XR' and in the book "Extending R".
Author: John M. Chambers
Maintainer: John Chambers <jmc@r-project.org>

Diff between XRJulia versions 0.7.6 dated 2017-10-20 and 0.7.7 dated 2018-03-18

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Package XR updated to version 0.7.2 with previous version 0.7.1 dated 2017-10-24

Title: A Structure for Interfaces from R
Description: Support for interfaces from R to other languages, built around a class for evaluators and a combination of functions, classes and methods for communication. Will be used through a specific language interface package. Described in the book "Extending R".
Author: John M. Chambers
Maintainer: John Chambers <jmc@r-project.org>

Diff between XR versions 0.7.1 dated 2017-10-24 and 0.7.2 dated 2018-03-18

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Package QuantTools updated to version 0.5.7 with previous version 0.5.6 dated 2017-09-19

Title: Enhanced Quantitative Trading Modelling
Description: Download and organize historical market data from multiple sources like Yahoo (<https://finance.yahoo.com>), Google (<https://www.google.com/finance>), Finam (<https://www.finam.ru/profile/moex-akcii/sberbank/export/>), MOEX (<https://www.moex.com/en/derivatives/contracts.aspx>) and IQFeed (<https://www.iqfeed.net/symbolguide/index.cfm?symbolguide=lookup>). Code your trading algorithms in modern C++11 with powerful event driven tick processing API including trading costs and exchange communication latency and transform detailed data seamlessly into R. In just few lines of code you will be able to visualize every step of your trading model from tick data to multi dimensional heat maps.
Author: Stanislav Kovalevsky
Maintainer: Stanislav Kovalevsky <so.kovalevsky@gmail.com>

Diff between QuantTools versions 0.5.6 dated 2017-09-19 and 0.5.7 dated 2018-03-18

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Package msme updated to version 0.5.3 with previous version 0.5.1 dated 2014-07-21

Title: Functions and Datasets for "Methods of Statistical Model Estimation"
Description: Functions and datasets from Hilbe, J.M., and Robinson, A.P. 2013. Methods of Statistical Model Estimation. Chapman & Hall / CRC.
Author: Joseph Hilbe and Andrew Robinson
Maintainer: Andrew Robinson <apro@unimelb.edu.au>

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New package bcgam with initial version 1.0
Package: bcgam
Title: Bayesian Constrained Generalised Linear Models
Version: 1.0
Authors@R: c( person("Cristian", "Oliva-Aviles", email = "coliva@colostate.edu", role = c("aut", "cre")), person("Mary C.", "Meyer", email="meyer@stat.colostate.edu", role="aut"))
Description: Fits generalised partial linear regression models using a Bayesian approach, where shape and smoothness constraints are imposed on nonparametrically modelled predictors through shape-restricted splines, and no constraints are imposed on optional parametrically modelled covariates. See Meyer et al. (2011) <doi/10.1080/10485252.2011.597852> for more details. IMPORTANT: before installing 'bcgam', you need to install 'Rtools' (Windows) or 'Xcode' (Mac OS X). These are required for the correct installation of 'nimble' (<https://r-nimble.org/download>).
Depends: R (>= 3.2.2), nimble (>= 0.6-9)
Imports: stats, graphics, igraph, coda
SystemRequirements: Rtools (>= 3.3) for Windows, Xcode (>= 9.0) for Mac OS X
Suggests: testthat
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-03-17 17:38:44 UTC; boliche
Author: Cristian Oliva-Aviles [aut, cre], Mary C. Meyer [aut]
Maintainer: Cristian Oliva-Aviles <coliva@colostate.edu>
Repository: CRAN
Date/Publication: 2018-03-18 22:06:50 UTC

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Package smatr updated to version 3.4-8 with previous version 3.4-3 dated 2014-01-06

Title: (Standardised) Major Axis Estimation and Testing Routines
Description: Methods for fitting bivariate lines in allometry using the major axis (MA) or standardised major axis (SMA), and for making inferences about such lines. The available methods of inference include confidence intervals and one-sample tests for slope and elevation, testing for a common slope or elevation amongst several allometric lines, constructing a confidence interval for a common slope or elevation, and testing for no shift along a common axis, amongst several samples. See Warton et al. 2012 <doi:10.1111/j.2041-210X.2011.00153.x> for methods description.
Author: David Warton <David.Warton@unsw.edu.au>, Remko Duursma, Daniel Falster and Sara Taskinen.
Maintainer: Remko Duursma <remkoduursma@gmail.com>

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Package sentometrics updated to version 0.3 with previous version 0.2 dated 2017-11-13

Title: An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2017) <https://ssrn.com/abstract=3067734>.
Author: David Ardia [aut], Keven Bluteau [aut], Samuel Borms [aut, cre], Kris Boudt [aut]
Maintainer: Samuel Borms <samuel.borms@unine.ch>

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Package pgmm updated to version 1.2.2 with previous version 1.2.1 dated 2018-03-15

Title: Parsimonious Gaussian Mixture Models
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.
Author: Paul D. McNicholas [aut, cre], Aisha ElSherbiny [aut], K. Raju Jampani [ctb], Aaron F. McDaid [aut], T. Brendan Murphy [aut], Larry Banks [ctb]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>

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Package longclust updated to version 1.2.2 with previous version 1.2.1 dated 2018-03-14

Title: Model-Based Clustering and Classification for Longitudinal Data
Description: Clustering or classification of longitudinal data based on a mixture of multivariate t or Gaussian distributions with a Cholesky-decomposed covariance structure.
Author: Paul D. McNicholas [aut, cre], K. Raju Jampani [aut] (May to Dec 2012), Sanjeena Subedi [aut]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>

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Package LearnBayes updated to version 2.15.1 with previous version 2.15 dated 2014-05-29

Title: Functions for Learning Bayesian Inference
Description: A collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.
Author: Jim Albert
Maintainer: Jim Albert <albert@bgsu.edu>

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Package implyr updated to version 0.2.3 with previous version 0.2.2 dated 2018-02-11

Title: R Interface for Apache Impala
Description: 'SQL' back-end to 'dplyr' for Apache Impala, the massively parallel processing query engine for Apache 'Hadoop'. Impala enables low-latency 'SQL' queries on data stored in the 'Hadoop' Distributed File System '(HDFS)', Apache 'HBase', Apache 'Kudu', and Amazon Simple Storage Service '(S3)'. See <https://impala.apache.org> for more information about Impala.
Author: Ian Cook [aut, cre], Cloudera [cph]
Maintainer: Ian Cook <ian@cloudera.com>

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Package DHARMa updated to version 0.1.6 with previous version 0.1.5 dated 2017-03-12

Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted generalized linear mixed models. Currently supported are generalized linear mixed models from 'lme4' (classes 'lmerMod', 'glmerMod'), generalized additive models ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Alternatively, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (Theoretical Ecology, University of Regensburg, Regensburg, Germany)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

Diff between DHARMa versions 0.1.5 dated 2017-03-12 and 0.1.6 dated 2018-03-18

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 DHARMa-0.1.6/DHARMa/NAMESPACE                                                                            |    1 
 DHARMa-0.1.6/DHARMa/NEWS                                                                                 |   24 
 DHARMa-0.1.6/DHARMa/R/DHARMa.R                                                                           |   10 
 DHARMa-0.1.6/DHARMa/R/benchmarkPvalues.R                                                                 |   14 
 DHARMa-0.1.6/DHARMa/R/createData.R                                                                       |    2 
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 DHARMa-0.1.6/DHARMa/R/random.R                                                                           |only
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 DHARMa-0.1.6/DHARMa/README.md                                                                            |    6 
 DHARMa-0.1.6/DHARMa/inst/doc/DHARMa.R                                                                    |   13 
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 DHARMa-0.1.6/DHARMa/man/plot.DHARMa.Rd                                                                   |    3 
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 DHARMa-0.1.6/DHARMa/man/print.DHARMa.Rd                                                                  |    2 
 DHARMa-0.1.6/DHARMa/man/simulateResiduals.Rd                                                             |    4 
 DHARMa-0.1.6/DHARMa/man/testOverdispersion.Rd                                                            |    2 
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 DHARMa-0.1.6/DHARMa/man/testSimulatedResiduals.Rd                                                        |    2 
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 DHARMa-0.1.6/DHARMa/man/testTemporalAutocorrelation.Rd                                                   |   16 
 DHARMa-0.1.6/DHARMa/man/testUniformity.Rd                                                                |    6 
 DHARMa-0.1.6/DHARMa/man/testZeroInflation.Rd                                                             |    2 
 DHARMa-0.1.6/DHARMa/tests/testthat/testModelTypes.R                                                      |    7 
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 DHARMa-0.1.6/DHARMa/vignettes/DHARMa.Rmd                                                                 |   59 +
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Package RcppSMC updated to version 0.2.1 with previous version 0.2.0 dated 2017-08-28

Title: Rcpp Bindings for Sequential Monte Carlo
Description: R access to the Sequential Monte Carlo Template Classes by Johansen <doi:10.18637/jss.v030.i06> is provided. At present, four additional examples have been added, and the first example from the JSS paper has been extended. Further integration and extensions are planned.
Author: Dirk Eddelbuettel, Adam M. Johansen and Leah F. South
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppSMC versions 0.2.0 dated 2017-08-28 and 0.2.1 dated 2018-03-18

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Permanent link

Package expands updated to version 2.1.1 with previous version 2.1.0 dated 2018-02-24

Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (<http://www.ncbi.nlm.nih.gov/pubmed/24177718>). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 2.1 include: (i) new parameter ploidy in runExPANdS.R allows specification of non-diploid background ploidies (e.g. for near-triploid cell lines); (ii) parallel computing option is available. Further documentation and FAQ available at <http://dna-discovery.stanford.edu/software/expands>.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>

Diff between expands versions 2.1.0 dated 2018-02-24 and 2.1.1 dated 2018-03-18

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Package g2f updated to version 0.2 with previous version 0.1 dated 2016-10-08

Title: Find and Fill Gaps in Metabolic Networks
Description: For a given metabolic network, this package finds the gaps (metabolites not produced or not consumed in any other reaction), and fills it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database <http://www.genome.jp/kegg/> is available.
Author: Daniel Osorio [aut, cre], Kelly Botero [aut], Janneth Gonzalez [aut, ths], Andres Pinzon [aut]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>

Diff between g2f versions 0.1 dated 2016-10-08 and 0.2 dated 2018-03-18

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Package Peptides updated to version 2.3 with previous version 2.2 dated 2017-06-05

Title: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre], Paola Rondon-Villarreal [aut, ths], Rodrigo Torres [aut, ths], J. Sebastian Paez [ctb]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>

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Package sGMRFmix updated to version 0.2.0 with previous version 0.1.3 dated 2018-02-28

Title: Sparse Gaussian Markov Random Field Mixtures for Anomaly Detection
Description: An implementation of sparse Gaussian Markov random field mixtures presented by Ide et al. (2016) <doi:10.1109/ICDM.2016.0119>. It provides a novel anomaly detection method for multivariate noisy sensor data. It can automatically handle multiple operational modes. And it can also compute variable-wise anomaly scores.
Author: Koji Makiyama [cre, aut]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>

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Package RankAggreg updated to version 0.6.4 with previous version 0.6.3 dated 2018-03-13

Title: Weighted Rank Aggregation
Description: Performs aggregation of ordered lists based on the ranks using several different algorithms: Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm (for small problems).
Author: Vasyl Pihur <vpihur@gmail.com>, Somnath Datta <somnath.datta@louisville.edu>, Susmita Datta <susmita.datta@louisville.edu>
Maintainer: Vasyl Pihur <vpihur@gmail.com>

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Package Rgretl updated to version 0.2.2 with previous version 0.2.1 dated 2018-03-06

Title: Interface to 'gretlcli'
Description: An interface to 'GNU gretl': running 'gretl' scripts from, estimating econometric models with backward passing of model results, opening 'gretl' data files (.gdt). 'gretl' can be downloaded from <http://gretl.sourceforge.net>. This package could make life on introductory/intermediate econometrics courses much easier: full battery of the required regression diagnostics, including White's heteroskedasticity test, restricted ols estimation, advanced weak instrument test after iv estimation, very convenient dealing with lagged variables in models, standard case treatment in unit root tests, vector auto- regressions, and vector error correction models. Datasets for 8 popular econometrics textbooks can be installed into 'gretl' from its server. All datasets can be easily imported using this package.
Author: Oleh Komashko
Maintainer: Oleh Komashko <oleg_komashko@ukr.net>

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Package denstrip updated to version 1.5.4 with previous version 1.5.3 dated 2014-02-20

Title: Density Strips and Other Methods for Compactly Illustrating Distributions
Description: Graphical methods for compactly illustrating probability distributions, including density strips, density regions, sectioned density plots and varying width strips.
Author: Christopher Jackson
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>

Diff between denstrip versions 1.5.3 dated 2014-02-20 and 1.5.4 dated 2018-03-18

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Package WaveletComp updated to version 1.1 with previous version 1.0 dated 2014-12-16

Title: Computational Wavelet Analysis
Description: Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.
Author: Angi Roesch <angi@angi-stat.com> and Harald Schmidbauer <harald@hs-stat.com>
Maintainer: Angi Roesch <angi@angi-stat.com>

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Package Rgb updated to version 1.6.1 with previous version 1.5.1 dated 2017-04-21

Title: The R Genome Browser
Description: Classes and methods to efficiently handle (slice, annotate, draw ...) genomic features (such as genes or transcripts), and an interactive interface to browse them.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal <maressyl@gmail.com>

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Package OpenMx updated to version 2.9.6 with previous version 2.8.3 dated 2017-11-06

Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications as things that can be generated and manipulated programmatically. Structural equation models may be specified with reticular action model matrices or paths, linear structural relations matrices or paths, or directly in matrix algebra. Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential equations, state space, and many others. MacOS users can download the most up-to-date package binaries from <http://openmx.ssri.psu.edu>. See Neale, Hunter, Pritikin, Zahery, Brick, Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut], Michael C. Neale [aut], Hermine H. Maes [aut], Michael J. Wilde [ctb], Michael Spiegel [aut], Timothy R. Brick [aut], Ryne Estabrook [aut], Timothy C. Bates [aut], Paras Mehta [ctb], Timo von Oertzen [ctb], Ross J. Gore [aut], Michael D. Hunter [aut], Daniel C. Hackett [ctb], Julian Karch [ctb], Andreas M. Brandmaier [ctb], Joshua N. Pritikin [aut, cre], Mahsa Zahery [aut], Robert M. Kirkpatrick [aut], Yang Wang [ctb], Charles Driver [ctb], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Association for Computing Machinery [cph], Dieter Kraft [cph], Stefan Wilhelm [cph], Manjunath B G [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between OpenMx versions 2.8.3 dated 2017-11-06 and 2.9.6 dated 2018-03-18

 OpenMx-2.8.3/OpenMx/inst/models/passing/excludeVar.R                                                  |only
 OpenMx-2.8.3/OpenMx/src/omxFIMLSingleIteration.cpp                                                    |only
 OpenMx-2.9.6/OpenMx/DESCRIPTION                                                                       |   16 
 OpenMx-2.9.6/OpenMx/MD5                                                                               | 1128 +++++-----
 OpenMx-2.9.6/OpenMx/NAMESPACE                                                                         |    1 
 OpenMx-2.9.6/OpenMx/NEWS                                                                              |   17 
 OpenMx-2.9.6/OpenMx/R/0ClassUnion.R                                                                   |    2 
 OpenMx-2.9.6/OpenMx/R/DefinitionVars.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/DiagMatrix.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/FullMatrix.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/IdenMatrix.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/LowerMatrix.R                                                                   |    2 
 OpenMx-2.9.6/OpenMx/R/MxAlgebra.R                                                                     |    2 
 OpenMx-2.9.6/OpenMx/R/MxAlgebraConvert.R                                                              |    2 
 OpenMx-2.9.6/OpenMx/R/MxAlgebraFunctions.R                                                            |    2 
 OpenMx-2.9.6/OpenMx/R/MxAlgebraObjective.R                                                            |    2 
 OpenMx-2.9.6/OpenMx/R/MxAlgebraTransform.R                                                            |    2 
 OpenMx-2.9.6/OpenMx/R/MxApply.R                                                                       |    2 
 OpenMx-2.9.6/OpenMx/R/MxAutoStart.R                                                                   |    2 
 OpenMx-2.9.6/OpenMx/R/MxBounds.R                                                                      |    2 
 OpenMx-2.9.6/OpenMx/R/MxCommunication.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxCompare.R                                                                     |  377 +++
 OpenMx-2.9.6/OpenMx/R/MxCompute.R                                                                     |   40 
 OpenMx-2.9.6/OpenMx/R/MxConstraint.R                                                                  |    2 
 OpenMx-2.9.6/OpenMx/R/MxCycleDetection.R                                                              |    2 
 OpenMx-2.9.6/OpenMx/R/MxData.R                                                                        |   41 
 OpenMx-2.9.6/OpenMx/R/MxDataWLS.R                                                                     |   14 
 OpenMx-2.9.6/OpenMx/R/MxDeparse.R                                                                     |    2 
 OpenMx-2.9.6/OpenMx/R/MxDependencies.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/MxDetectCores.R                                                                 |    2 
 OpenMx-2.9.6/OpenMx/R/MxDiff.R                                                                        |    2 
 OpenMx-2.9.6/OpenMx/R/MxErrorHandling.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxEval.R                                                                        |   21 
 OpenMx-2.9.6/OpenMx/R/MxExpectation.R                                                                 |    2 
 OpenMx-2.9.6/OpenMx/R/MxExpectationGREML.R                                                            |   84 
 OpenMx-2.9.6/OpenMx/R/MxExpectationLISREL.R                                                           |    9 
 OpenMx-2.9.6/OpenMx/R/MxExpectationMixture.R                                                          |   58 
 OpenMx-2.9.6/OpenMx/R/MxExpectationNormal.R                                                           |   48 
 OpenMx-2.9.6/OpenMx/R/MxExpectationRAM.R                                                              |   21 
 OpenMx-2.9.6/OpenMx/R/MxExpectationStateSpace.R                                                       |    7 
 OpenMx-2.9.6/OpenMx/R/MxFIMLObjective.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxFactorScores.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunction.R                                                                 |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunctionAlgebra.R                                                          |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunctionGREML.R                                                            |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunctionML.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunctionR.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunctionRow.R                                                              |    2 
 OpenMx-2.9.6/OpenMx/R/MxFitFunctionWLS.R                                                              |   20 
 OpenMx-2.9.6/OpenMx/R/MxFlatModel.R                                                                   |    7 
 OpenMx-2.9.6/OpenMx/R/MxFlatSearchReplace.R                                                           |    2 
 OpenMx-2.9.6/OpenMx/R/MxGraph.R                                                                       |    2 
 OpenMx-2.9.6/OpenMx/R/MxGraphviz.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/MxInterval.R                                                                    |    4 
 OpenMx-2.9.6/OpenMx/R/MxLISRELModel.R                                                                 |    2 
 OpenMx-2.9.6/OpenMx/R/MxLISRELObjective.R                                                             |    2 
 OpenMx-2.9.6/OpenMx/R/MxMI.R                                                                          |    2 
 OpenMx-2.9.6/OpenMx/R/MxMLObjective.R                                                                 |    2 
 OpenMx-2.9.6/OpenMx/R/MxMatrix.R                                                                      |    2 
 OpenMx-2.9.6/OpenMx/R/MxMatrixFunctions.R                                                             |    2 
 OpenMx-2.9.6/OpenMx/R/MxModel.R                                                                       |   40 
 OpenMx-2.9.6/OpenMx/R/MxModelDisplay.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/MxModelFunctions.R                                                              |    2 
 OpenMx-2.9.6/OpenMx/R/MxModelParameters.R                                                             |    2 
 OpenMx-2.9.6/OpenMx/R/MxMultiModel.R                                                                  |    6 
 OpenMx-2.9.6/OpenMx/R/MxNamespace.R                                                                   |    2 
 OpenMx-2.9.6/OpenMx/R/MxObjectiveMetaData.R                                                           |    2 
 OpenMx-2.9.6/OpenMx/R/MxOptions.R                                                                     |    4 
 OpenMx-2.9.6/OpenMx/R/MxPath.R                                                                        |   70 
 OpenMx-2.9.6/OpenMx/R/MxRAMMetaData.R                                                                 |    2 
 OpenMx-2.9.6/OpenMx/R/MxRAMModel.R                                                                    |   19 
 OpenMx-2.9.6/OpenMx/R/MxRAMObjective.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/MxRAMtoML.R                                                                     |    2 
 OpenMx-2.9.6/OpenMx/R/MxRObjective.R                                                                  |    2 
 OpenMx-2.9.6/OpenMx/R/MxRename.R                                                                      |    2 
 OpenMx-2.9.6/OpenMx/R/MxReservedNames.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxRestore.R                                                                     |    2 
 OpenMx-2.9.6/OpenMx/R/MxRetro.R                                                                       |only
 OpenMx-2.9.6/OpenMx/R/MxRobustSE.R                                                                    |   42 
 OpenMx-2.9.6/OpenMx/R/MxRowObjective.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/R/MxRun.R                                                                         |   29 
 OpenMx-2.9.6/OpenMx/R/MxRunHelperFunctions.R                                                          |    6 
 OpenMx-2.9.6/OpenMx/R/MxSE.R                                                                          |    2 
 OpenMx-2.9.6/OpenMx/R/MxSaturatedModel.R                                                              |    2 
 OpenMx-2.9.6/OpenMx/R/MxSearchReplace.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxSquareBracket.R                                                               |    2 
 OpenMx-2.9.6/OpenMx/R/MxSummary.R                                                                     |   37 
 OpenMx-2.9.6/OpenMx/R/MxSwift.R                                                                       |    2 
 OpenMx-2.9.6/OpenMx/R/MxThreshold.R                                                                   |   32 
 OpenMx-2.9.6/OpenMx/R/MxTryHard.R                                                                     |    2 
 OpenMx-2.9.6/OpenMx/R/MxTypes.R                                                                       |    2 
 OpenMx-2.9.6/OpenMx/R/MxUnitTesting.R                                                                 |    5 
 OpenMx-2.9.6/OpenMx/R/MxUntitled.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/MxVersion.R                                                                     |    2 
 OpenMx-2.9.6/OpenMx/R/OriginalMx.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/StandMatrix.R                                                                   |    2 
 OpenMx-2.9.6/OpenMx/R/SymmMatrix.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/UnitMatrix.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/ZeroMatrix.R                                                                    |    2 
 OpenMx-2.9.6/OpenMx/R/omxBrownie.R                                                                    |   54 
 OpenMx-2.9.6/OpenMx/R/omxConstrainThresholds.R                                                        |    2 
 OpenMx-2.9.6/OpenMx/R/omxGetNPSOL.R                                                                   |    2 
 OpenMx-2.9.6/OpenMx/R/zzz.R                                                                           |    4 
 OpenMx-2.9.6/OpenMx/README.md                                                                         |   14 
 OpenMx-2.9.6/OpenMx/configure                                                                         |   37 
 OpenMx-2.9.6/OpenMx/data/twinData.rda                                                                 |binary
 OpenMx-2.9.6/OpenMx/demo/AlternativeApproaches.R                                                      |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateCorrelation.R                                                       |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateHeterogeneity_MatrixRaw.R                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateHeterogeneity_PathRaw.R                                             |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated.R                                                         |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated_MatrixCov.R                                               |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated_MatrixCovCholesky.R                                       |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated_MatrixRaw.R                                               |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated_MatrixRawCholesky.R                                       |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated_PathCov.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/BivariateSaturated_PathRaw.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/DefinitionMeans_MatrixRaw.R                                                  |    2 
 OpenMx-2.9.6/OpenMx/demo/DefinitionMeans_PathRaw.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/demo/GrowthMixtureModel_MatrixRaw.R                                               |    2 
 OpenMx-2.9.6/OpenMx/demo/GrowthMixtureModel_PathRaw.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/LISRELJointFactorModel.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/LatentGrowthCurveModel_MatrixRaw.R                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/LatentGrowthCurveModel_PathRaw.R                                             |    2 
 OpenMx-2.9.6/OpenMx/demo/LatentGrowthCurveModel_PathRaw_ModelRec.R                                    |    2 
 OpenMx-2.9.6/OpenMx/demo/LatentGrowthCurveModel_PathRaw_ObjectAdd.R                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/MatrixAlgebra.R                                                              |    2 
 OpenMx-2.9.6/OpenMx/demo/MultipleRegression_MatrixCov.R                                               |    2 
 OpenMx-2.9.6/OpenMx/demo/MultipleRegression_MatrixRaw.R                                               |    2 
 OpenMx-2.9.6/OpenMx/demo/MultipleRegression_PathCov.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/MultipleRegression_PathRaw.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/MultivariateRegression_MatrixCov.R                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/MultivariateRegression_MatrixRaw.R                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/MultivariateRegression_PathCov.R                                             |    2 
 OpenMx-2.9.6/OpenMx/demo/MultivariateRegression_PathRaw.R                                             |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorJoint_MatrixRawRAM.R                                                |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorJoint_PathRaw.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorMatrixDemo.R                                                        |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorModel_LikelihoodVector.R                                            |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorModel_MatrixCov.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorModel_MatrixRaw.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorModel_PathCov.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorModel_PathRaw.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorOrdinal01_MatrixRaw.R                                               |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorOrdinal_MatrixRaw.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorOrdinal_MatrixRawRAM.R                                              |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorOrdinal_PathRaw.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/OneFactorPathDemo.R                                                          |    2 
 OpenMx-2.9.6/OpenMx/demo/OneLocusLikelihood.R                                                         |    2 
 OpenMx-2.9.6/OpenMx/demo/RObjectiveLISRELFactorRegression.R                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/RowObjectiveFIMLBivariateSaturated.R                                         |    2 
 OpenMx-2.9.6/OpenMx/demo/RowObjectiveSimpleExamples.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/SimpleCheckpoint.R                                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/SimpleRegression_MatrixCov.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/SimpleRegression_MatrixRaw.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/demo/SimpleRegression_PathCov.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/SimpleRegression_PathRaw.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/TwoFactorModel_MatrixCov.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/TwoFactorModel_MatrixRaw.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/demo/TwoFactorModel_PathCov.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/TwoFactorModel_PathRaw.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/TwoLocusLikelihood.R                                                         |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateSaturated.R                                                        |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateSaturated_MatrixCov.R                                              |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateSaturated_MatrixRaw.R                                              |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateSaturated_PathCov.R                                                |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateSaturated_PathRaw.R                                                |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateTwinAnalysis.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateTwinAnalysis_MatrixRaw.R                                           |    2 
 OpenMx-2.9.6/OpenMx/demo/UnivariateTwinAnalysis_PathRaw.R                                             |    2 
 OpenMx-2.9.6/OpenMx/demo/mxThreshold.R                                                                |    2 
 OpenMx-2.9.6/OpenMx/demo/omxConstrainMLThresholds.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/CITATION                                                                     |   19 
 OpenMx-2.9.6/OpenMx/inst/models/failing/SimpleConfidenceIntervals.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/180209--defvars.R                                             |only
 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWith2LevelModerator-a.R                        |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/nightly/AnalyticGradientTest.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/FactorScores.R                                                |    6 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/GREML_monophenotype_1GRM.R                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/GREML_monophenotype_1GRM_GradDesc.R                           |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/GrowthMixtureModelRandomStarts.R                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/InvalidComparisonDetection.R                                  |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/JointMissingTest.R                                            |only
 OpenMx-2.9.6/OpenMx/inst/models/nightly/JointWLS.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/ModelIdentification.R                                         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/ModificationIndexCheck.R                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/MultigroupRobustSE_test.R                                     |   34 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/MultilevelStateSpaceEx5.R                                     |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/NelderMeadUnitTesting.R                                       |    4 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/OneFactorOrdinal01_MatrixRaw.R                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/OneFactorOrdinal_MatrixRaw.R                                  |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_100days.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_100days_cov.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_100days_cov_baseline.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_100days_raw.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_100days_raw_baseline.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_test1L2M.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/PPML_test1L3M.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/Power1.R                                                      |only
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 OpenMx-2.9.6/OpenMx/inst/models/nightly/RAM-3Factor-24Indicators-covdata-a.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RAM-3Factor-24Indicators-megadata-a.R                         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RAM-3Factor-24Indicators-rawdata-a.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RAM-3Factor-48Indicators-covdata-a.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RAM-3Factor-48Indicators-rawdata-a.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RAM-3Factor-96Indicators-covdata-a.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitions.R         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitionsAllFixed.R |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/StateSpaceContinuous.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/fm-example2-8.R                                               |    8 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/ifa-bifactor.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/startsTestMissing.R                                           |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/startsTestNoMissing.R                                         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/thresholdModel1Factor3Variate.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/thresholdModel1Factor5Variate.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/thresholdModel1Factor5VariateWLS.R                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/thresholdModel1Factor8Variate.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/nightly/univACErSEM.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/ACEDuplicateMatrices.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/ACELRTCI20160808.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Acemix.R                                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Acemix2.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/AlgebraComputePassing.R                                       |    6 
 OpenMx-2.9.6/OpenMx/inst/models/passing/AlgebraDeriv.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/AlgebraErrorDetection.R                                       |    6 
 OpenMx-2.9.6/OpenMx/inst/models/passing/AlgebraTransformations.R                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/AnalyticConstraintJacobians--Eq_and_Ineq.R                    |    4 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/AnalyticConstraintJacobians--PowellBenchmark.R                |   25 
 OpenMx-2.9.6/OpenMx/inst/models/passing/AugmentedGREMLfitfunction.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_MatrixCov.R                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_MatrixRaw.R                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_PathCov.R                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_PathRaw.R                                      |   13 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_Transpose_MatrixCov.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_Transpose_MatrixRaw.R                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_Tree_Matrix.R                                  |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Autoregressive_Tree_Path.R                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/BivRegRawTestSE.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/BivRegStdTestSE.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/BogusDefinitionVariables.R                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/BootstrapParallel.R                                           |    4 
 OpenMx-2.9.6/OpenMx/inst/models/passing/BukinN2_regressiontest.R                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/CIduplicates.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/CheckpointingEveryIteration.R                                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/ConfidenceIntervalsDefVar.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/ConstantSubstitution.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/ContinuousOnlyWLSTest.R                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/DataErrorDetection.R                                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/DataFrame.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/DefinitionMeans.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/DefinitionMeansPath.R                                         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/DefinitionTest2.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/FIMLLikelihoodFrontend.R                                      |    4 
 OpenMx-2.9.6/OpenMx/inst/models/passing/FitMultigroup.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/FourAAAA.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GREML--151123missingDataRegressionTest.R                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GREML--minimal_test_model.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GREML--polyphenotype.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GREML--testStarterFunctionWithMissingData.R                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GREML_Error_Detection.R                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GREML_intercept_check.R                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GeneralizedEstimatingEquations.R                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/GraphvizTest.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IgnoreFixedConfidenceIntervals.R                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/InitializationErrorDetection.R                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-BivariateRaw.R                                       |   10 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-BivariateStd.R                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-MultiRegRaw.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-MultiRegStd.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-MultivariateRegRaw.R                                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-OneFactorCov.R                                       |   19 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-OneFactorRaw.R                                       |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-UnivariateRaw.R                                      |   23 
 OpenMx-2.9.6/OpenMx/inst/models/passing/IntroSEM-UnivariateStd.R                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/InvalidCovarianceMLObjective.R                                |    4 
 OpenMx-2.9.6/OpenMx/inst/models/passing/JointFIMLRegressionTest.R                                     |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/JointFIMLTest.R                                               |    7 
 OpenMx-2.9.6/OpenMx/inst/models/passing/LAD--CheckCode6.R                                             |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/LCAlazarsfeld.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/LGC_MatrixCov.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/LGC_PathCov.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/LISRELExoEndoOnly.R                                           |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/LISRELFactorRegression_Matrix.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/LisrelTypeCheck.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/MLErrorConditions.R                                           |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/MatrixErrorDetection.R                                        |    4 
 OpenMx-2.9.6/OpenMx/inst/models/passing/ModelIndexErrorChecking.R                                     |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/MultiRegStdTestSE.R                                           |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/MultipleRegression_MatrixRawReverse.R                         |    2 
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 OpenMx-2.9.6/OpenMx/inst/models/passing/MxBoundsTesting.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/MxEvalDefinitionVar.R                                         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/MxPath.R                                                      |only
 OpenMx-2.9.6/OpenMx/inst/models/passing/MxTryHardTest.R                                               |    7 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NamesReferencesErrorDetection.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NelderMead--bothConstraintTypes.R                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NelderMeadErrorTesting.R                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NelderMeadTest--eqConstraint.R                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NelderMeadTest--ineqConstraints.R                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NelderMeadTest.R                                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/NormalML.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/OneFactorModel_PathCovReverse.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/OrdinalPathTest.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/OrdinalTest.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/OrdinalTestAlgebra.R                                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/RAM-FIML-defvars.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/RAMInverseTest.R                                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/RAMObjectiveErrors.R                                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/RemoveEntriesTest.R                                           |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SanityTest.R                                                  |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SaturatedWLSTest.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Simple--CheckCode6.R                                          |    3 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleAlgebraCIs.R                                            |    6 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleConfidenceIntervals.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleConstraint.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleCovariance.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleMLAlgebraCIs.R                                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleMix.R                                                   |   19 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SimpleRObjective.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/StandardErrorsSimple.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/StateSpaceAlg.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/StateSpaceErrorCheck.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/StateSpaceInputs.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/StateSpaceMissingData.R                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/StateSpaceOsc.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SubStateSpaceOsc.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Substitutions.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SummaryCheck.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/SummaryFitStatistics.R                                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/TestRowObjective.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/TestRowObjectiveExistenceVector.R                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/TestUseOptimizer.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/Tiny_GREML_model_for_full_debug_logging.R                     |   10 
 OpenMx-2.9.6/OpenMx/inst/models/passing/TwinAnalysisLikelihoodVector.R                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/TwinAnalysis_Multivariate_Matrix_Raw.R                        |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/UnivHetModTwinAnalysis_MatrixRawOrdNIQmfFv3.R                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/UnivariateRandomInterceptWide.R                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/UselessConstraint.R                                           |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/WLS+CI.R                                                      |only
 OpenMx-2.9.6/OpenMx/inst/models/passing/WarmStartTest.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/automaticStarts.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/bivCorM.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/bivLognormDemo.R                                              |    8 
 OpenMx-2.9.6/OpenMx/inst/models/passing/checkStandardizedLoadingsEtcetera.R                           |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/check_models_can_be_rerun.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/cycle.R                                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/defvaralgebra.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/derivFilter.R                                                 |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/dmvnorm.R                                                     |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/jointFactorWls.R                                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxLog.R                                                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxSE_test.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxSave.R                                                      |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxVersion.R                                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxmanual31-a.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxmanual61-a.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/mxmanual61-b.R                                                |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/nonlinearDefinitionTest.R                                     |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/omxMnor.R                                                     |   18 
 OpenMx-2.9.6/OpenMx/inst/models/passing/oneLocusLikelihood.R                                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/rfitfunc.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/rowAlgTest140708.R                                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/simplestCI.R                                                  |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/startingValues.R                                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/startingValues2.R                                             |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/stdizedRAMpaths--UserProvidedCov.R                            |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/testAllint.R                                                  |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/testNumericDerivWithConstraintWarning.R                       |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/test_mxBootstrapStdizeRAMpaths.R                              |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/test_thresh_kept_in_order.R                                   |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/twoLocusLikelihood.R                                          |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/univACEP.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/univACE_drop_helper.R                                         |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/univSatM.R                                                    |    2 
 OpenMx-2.9.6/OpenMx/inst/models/passing/vectorEqualsT.R                                               |    2 
 OpenMx-2.9.6/OpenMx/inst/tools/updateCopyright.sh                                                     |   18 
 OpenMx-2.9.6/OpenMx/man/MxAlgebra-class.Rd                                                            |    2 
 OpenMx-2.9.6/OpenMx/man/MxBounds-class.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/MxCI-class.Rd                                                                 |    2 
 OpenMx-2.9.6/OpenMx/man/MxConstraint-class.Rd                                                         |    2 
 OpenMx-2.9.6/OpenMx/man/MxData-class.Rd                                                               |    2 
 OpenMx-2.9.6/OpenMx/man/MxMatrix-class.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/MxModel-class.Rd                                                              |    2 
 OpenMx-2.9.6/OpenMx/man/Named-entity.Rd                                                               |    2 
 OpenMx-2.9.6/OpenMx/man/OpenMx.Rd                                                                     |    2 
 OpenMx-2.9.6/OpenMx/man/cvectorize.Rd                                                                 |    2 
 OpenMx-2.9.6/OpenMx/man/diag2vec.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/eigenvec.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/imxFlattenModel.Rd                                                            |    4 
 OpenMx-2.9.6/OpenMx/man/imxRobustSE.Rd                                                                |   16 
 OpenMx-2.9.6/OpenMx/man/imxWlsChiSquare.Rd                                                            |    2 
 OpenMx-2.9.6/OpenMx/man/imxWlsStandardErrors.Rd                                                       |    2 
 OpenMx-2.9.6/OpenMx/man/mxAlgebra.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/mxAlgebraObjective.Rd                                                         |    2 
 OpenMx-2.9.6/OpenMx/man/mxBootstrap.Rd                                                                |    5 
 OpenMx-2.9.6/OpenMx/man/mxBootstrapEval.Rd                                                            |    4 
 OpenMx-2.9.6/OpenMx/man/mxBootstrapStdizeRAMpaths.Rd                                                  |    7 
 OpenMx-2.9.6/OpenMx/man/mxBounds.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/mxCI.Rd                                                                       |    2 
 OpenMx-2.9.6/OpenMx/man/mxCheckIdentification.Rd                                                      |    2 
 OpenMx-2.9.6/OpenMx/man/mxCompare.Rd                                                                  |    3 
 OpenMx-2.9.6/OpenMx/man/mxComputeConfidenceInterval.Rd                                                |    3 
 OpenMx-2.9.6/OpenMx/man/mxComputeGradientDescent.Rd                                                   |   29 
 OpenMx-2.9.6/OpenMx/man/mxConstraint.Rd                                                               |    8 
 OpenMx-2.9.6/OpenMx/man/mxData.Rd                                                                     |   18 
 OpenMx-2.9.6/OpenMx/man/mxDataWLS.Rd                                                                  |   10 
 OpenMx-2.9.6/OpenMx/man/mxEval.Rd                                                                     |    2 
 OpenMx-2.9.6/OpenMx/man/mxEvaluateOnGrid.Rd                                                           |    2 
 OpenMx-2.9.6/OpenMx/man/mxExpectationLISREL.Rd                                                        |    2 
 OpenMx-2.9.6/OpenMx/man/mxExpectationNormal.Rd                                                        |    2 
 OpenMx-2.9.6/OpenMx/man/mxExpectationRAM.Rd                                                           |    2 
 OpenMx-2.9.6/OpenMx/man/mxExpectationStateSpace.Rd                                                    |    2 
 OpenMx-2.9.6/OpenMx/man/mxExpectationStateSpaceContinuousTime.Rd                                      |    2 
 OpenMx-2.9.6/OpenMx/man/mxFIMLObjective.Rd                                                            |    2 
 OpenMx-2.9.6/OpenMx/man/mxFactor.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/mxFactorScores.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/mxFitFunctionAlgebra.Rd                                                       |    2 
 OpenMx-2.9.6/OpenMx/man/mxFitFunctionML.Rd                                                            |    2 
 OpenMx-2.9.6/OpenMx/man/mxFitFunctionMultigroup.Rd                                                    |    2 
 OpenMx-2.9.6/OpenMx/man/mxFitFunctionR.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/mxFitFunctionRow.Rd                                                           |    2 
 OpenMx-2.9.6/OpenMx/man/mxFitFunctionWLS.Rd                                                           |    2 
 OpenMx-2.9.6/OpenMx/man/mxGenerateData.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/mxGetExpected.Rd                                                              |    4 
 OpenMx-2.9.6/OpenMx/man/mxKalmanScores.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/mxLISRELObjective.Rd                                                          |    2 
 OpenMx-2.9.6/OpenMx/man/mxMI.Rd                                                                       |    2 
 OpenMx-2.9.6/OpenMx/man/mxMLObjective.Rd                                                              |    2 
 OpenMx-2.9.6/OpenMx/man/mxMatrix.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/mxModel.Rd                                                                    |    2 
 OpenMx-2.9.6/OpenMx/man/mxOption.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/mxPath.Rd                                                                     |    2 
 OpenMx-2.9.6/OpenMx/man/mxPower.Rd                                                                    |only
 OpenMx-2.9.6/OpenMx/man/mxRAMObjective.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/mxRObjective.Rd                                                               |    2 
 OpenMx-2.9.6/OpenMx/man/mxRename.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/mxRestore.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/mxRetro.Rd                                                                    |only
 OpenMx-2.9.6/OpenMx/man/mxRowObjective.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/mxRun.Rd                                                                      |    5 
 OpenMx-2.9.6/OpenMx/man/mxSave.Rd                                                                     |    2 
 OpenMx-2.9.6/OpenMx/man/mxThreshold.Rd                                                                |    2 
 OpenMx-2.9.6/OpenMx/man/mxTryHard.Rd                                                                  |    1 
 OpenMx-2.9.6/OpenMx/man/mxTypes.Rd                                                                    |    2 
 OpenMx-2.9.6/OpenMx/man/mxVersion.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/myFADataRaw.Rd                                                                |    2 
 OpenMx-2.9.6/OpenMx/man/omxAllInt.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/omxApply.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/omxAssignFirstParameters.Rd                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/omxBrownie.Rd                                                                 |   17 
 OpenMx-2.9.6/OpenMx/man/omxCheckEquals.Rd                                                             |    2 
 OpenMx-2.9.6/OpenMx/man/omxCheckIdentical.Rd                                                          |    2 
 OpenMx-2.9.6/OpenMx/man/omxCheckSetEquals.Rd                                                          |    2 
 OpenMx-2.9.6/OpenMx/man/omxCheckTrue.Rd                                                               |    2 
 OpenMx-2.9.6/OpenMx/man/omxCheckWithinPercentError.Rd                                                 |    2 
 OpenMx-2.9.6/OpenMx/man/omxGetParameters.Rd                                                           |    2 
 OpenMx-2.9.6/OpenMx/man/omxGraphviz.Rd                                                                |    2 
 OpenMx-2.9.6/OpenMx/man/omxLapply.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/omxLocateParameters.Rd                                                        |    2 
 OpenMx-2.9.6/OpenMx/man/omxLogical.Rd                                                                 |    2 
 OpenMx-2.9.6/OpenMx/man/omxMatrixOperations.Rd                                                        |    2 
 OpenMx-2.9.6/OpenMx/man/omxMnor.Rd                                                                    |    2 
 OpenMx-2.9.6/OpenMx/man/omxModelDeleteData.Rd                                                         |only
 OpenMx-2.9.6/OpenMx/man/omxParallelCI.Rd                                                              |    2 
 OpenMx-2.9.6/OpenMx/man/omxRMSEA.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/omxSapply.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/omxSaturatedModel.Rd                                                          |    2 
 OpenMx-2.9.6/OpenMx/man/omxSelectRowsAndCols.Rd                                                       |    2 
 OpenMx-2.9.6/OpenMx/man/omxSetParameters.Rd                                                           |    2 
 OpenMx-2.9.6/OpenMx/man/rvectorize.Rd                                                                 |    2 
 OpenMx-2.9.6/OpenMx/man/summary.MxModel.Rd                                                            |    6 
 OpenMx-2.9.6/OpenMx/man/tr.Rd                                                                         |    2 
 OpenMx-2.9.6/OpenMx/man/twinData.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/vec2diag.Rd                                                                   |    2 
 OpenMx-2.9.6/OpenMx/man/vech.Rd                                                                       |    2 
 OpenMx-2.9.6/OpenMx/man/vech2full.Rd                                                                  |    2 
 OpenMx-2.9.6/OpenMx/man/vechs.Rd                                                                      |    2 
 OpenMx-2.9.6/OpenMx/man/vechs2full.Rd                                                                 |    2 
 OpenMx-2.9.6/OpenMx/src/AlgebraFunctions.h                                                            |  133 +
 OpenMx-2.9.6/OpenMx/src/Compute.cpp                                                                   |   54 
 OpenMx-2.9.6/OpenMx/src/Compute.h                                                                     |   59 
 OpenMx-2.9.6/OpenMx/src/ComputeGD.cpp                                                                 |  120 -
 OpenMx-2.9.6/OpenMx/src/ComputeNM.cpp                                                                 |   86 
 OpenMx-2.9.6/OpenMx/src/ComputeNM.h                                                                   |    2 
 OpenMx-2.9.6/OpenMx/src/Makevars.in                                                                   |    2 
 OpenMx-2.9.6/OpenMx/src/MarkovExpectation.cpp                                                         |    2 
 OpenMx-2.9.6/OpenMx/src/MarkovFF.cpp                                                                  |    2 
 OpenMx-2.9.6/OpenMx/src/algebraOp.h                                                                   |    4 
 OpenMx-2.9.6/OpenMx/src/ba81quad.cpp                                                                  |   40 
 OpenMx-2.9.6/OpenMx/src/ba81quad.h                                                                    |   10 
 OpenMx-2.9.6/OpenMx/src/fitMultigroup.cpp                                                             |   11 
 OpenMx-2.9.6/OpenMx/src/glue.cpp                                                                      |    3 
 OpenMx-2.9.6/OpenMx/src/glue.h                                                                        |   21 
 OpenMx-2.9.6/OpenMx/src/nloptcpp.cpp                                                                  |    4 
 OpenMx-2.9.6/OpenMx/src/omxAlgebra.cpp                                                                |   64 
 OpenMx-2.9.6/OpenMx/src/omxAlgebra.h                                                                  |    5 
 OpenMx-2.9.6/OpenMx/src/omxAlgebraFitFunction.cpp                                                     |   25 
 OpenMx-2.9.6/OpenMx/src/omxCsolnp.h                                                                   |    2 
 OpenMx-2.9.6/OpenMx/src/omxData.cpp                                                                   |   62 
 OpenMx-2.9.6/OpenMx/src/omxData.h                                                                     |   21 
 OpenMx-2.9.6/OpenMx/src/omxDefines.h                                                                  |   26 
 OpenMx-2.9.6/OpenMx/src/omxExpectation.cpp                                                            |   72 
 OpenMx-2.9.6/OpenMx/src/omxExpectation.h                                                              |    4 
 OpenMx-2.9.6/OpenMx/src/omxExpectationBA81.cpp                                                        |   37 
 OpenMx-2.9.6/OpenMx/src/omxExpectationBA81.h                                                          |    2 
 OpenMx-2.9.6/OpenMx/src/omxExportBackendState.cpp                                                     |    2 
 OpenMx-2.9.6/OpenMx/src/omxFIMLFitFunction.cpp                                                        |  239 --
 OpenMx-2.9.6/OpenMx/src/omxFIMLFitFunction.h                                                          |   80 
 OpenMx-2.9.6/OpenMx/src/omxFitFunction.cpp                                                            |   14 
 OpenMx-2.9.6/OpenMx/src/omxFitFunction.h                                                              |    3 
 OpenMx-2.9.6/OpenMx/src/omxFitFunctionBA81.cpp                                                        |   10 
 OpenMx-2.9.6/OpenMx/src/omxGREMLExpectation.cpp                                                       |   12 
 OpenMx-2.9.6/OpenMx/src/omxGREMLExpectation.h                                                         |    2 
 OpenMx-2.9.6/OpenMx/src/omxGREMLfitfunction.cpp                                                       |    2 
 OpenMx-2.9.6/OpenMx/src/omxHessianCalculation.cpp                                                     |   32 
 OpenMx-2.9.6/OpenMx/src/omxImportFrontendState.cpp                                                    |   13 
 OpenMx-2.9.6/OpenMx/src/omxLISRELExpectation.cpp                                                      |    5 
 OpenMx-2.9.6/OpenMx/src/omxLISRELExpectation.h                                                        |    2 
 OpenMx-2.9.6/OpenMx/src/omxMLFitFunction.cpp                                                          |   10 
 OpenMx-2.9.6/OpenMx/src/omxMatrix.cpp                                                                 |   87 
 OpenMx-2.9.6/OpenMx/src/omxMatrix.h                                                                   |   16 
 OpenMx-2.9.6/OpenMx/src/omxNPSOLSpecific.cpp                                                          |    2 
 OpenMx-2.9.6/OpenMx/src/omxNPSOLSpecific.h                                                            |    2 
 OpenMx-2.9.6/OpenMx/src/omxNormalExpectation.cpp                                                      |    5 
 OpenMx-2.9.6/OpenMx/src/omxRAMExpectation.cpp                                                         |    9 
 OpenMx-2.9.6/OpenMx/src/omxRFitFunction.cpp                                                           |   28 
 OpenMx-2.9.6/OpenMx/src/omxRFitFunction.h                                                             |    4 
 OpenMx-2.9.6/OpenMx/src/omxRowFitFunction.cpp                                                         |    2 
 OpenMx-2.9.6/OpenMx/src/omxRowFitFunction.h                                                           |    2 
 OpenMx-2.9.6/OpenMx/src/omxSadmvnWrapper.h                                                            |   28 
 OpenMx-2.9.6/OpenMx/src/omxState.cpp                                                                  |    3 
 OpenMx-2.9.6/OpenMx/src/omxState.h                                                                    |    7 
 OpenMx-2.9.6/OpenMx/src/omxStateSpaceExpectation.cpp                                                  |    2 
 OpenMx-2.9.6/OpenMx/src/omxSymbolTable.cpp                                                            |  188 -
 OpenMx-2.9.6/OpenMx/src/omxSymbolTable.h                                                              |    3 
 OpenMx-2.9.6/OpenMx/src/omxWLSFitFunction.cpp                                                         |   21 
 OpenMx-2.9.6/OpenMx/src/slsqp.c                                                                       |    2 
 OpenMx-2.9.6/OpenMx/src/ssMLFit.cpp                                                                   |    9 
 OpenMx-2.9.6/OpenMx/src/subnp.cpp                                                                     |  649 ++++-
 571 files changed, 3654 insertions(+), 2303 deletions(-)

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Package rts updated to version 1.0-45 with previous version 1.0-38 dated 2017-08-14

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between rts versions 1.0-38 dated 2017-08-14 and 1.0-45 dated 2018-03-18

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Package hierNet updated to version 1.7 with previous version 1.6 dated 2014-04-29

Title: A Lasso for Hierarchical Interactions
Description: Fits sparse interaction models for continuous and binary responses subject to the strong (or weak) hierarchy restriction that an interaction between two variables only be included if both (or at least one of) the variables is included as a main effect. For more details, see Bien, J., Taylor, J., Tibshirani, R., (2013) "A Lasso for Hierarchical Interactions." Annals of Statistics. 41(3). 1111-1141.
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien <jbien@usc.edu>

Diff between hierNet versions 1.6 dated 2014-04-29 and 1.7 dated 2018-03-18

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Package GGIR updated to version 1.5-18 with previous version 1.5-17 dated 2018-02-19

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in van Hees and colleagues (2014) <doi: 10.1152/japplphysiol.00421.2014> and (2015) <doi: 10.1371/journal.pone.0142533>. The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <http://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com/product/ax3>. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb], Jairo H Migueles [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>

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Package lcyanalysis updated to version 1.0.1 with previous version 1.0.0 dated 2017-11-03

Title: Stock Data Analysis Functions
Description: Analysis of stock data ups and downs trend, the stock technical analysis indicators function have trend line, reversal pattern and market trend.
Author: Chun-Yu Liu [aut,cph], Shu-Nung Yao [rev,ths]
Maintainer: Chun-Yu Liu <john401528@gmail.com>

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Package icaOcularCorrection (with last version 3.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-07-12 3.0.0
2013-06-25 2.2.4
2013-06-12 2.1
2011-11-03 1.3
2010-11-15 1.2
2010-11-13 1.1
2010-11-05 1.0

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Package rquery updated to version 0.4.1 with previous version 0.4.0 dated 2018-03-10

Title: Relational Query Generator for Data Manipulation at Scale
Description: A 'SQL' query generator based on Edgar F. Codd's relational algebra and experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as `Spark` and databases. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible modeling step, and convenience methods for applying query trees to in-memory 'data.frame's.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package DLMtool updated to version 5.1 with previous version 5.0.2 dated 2017-11-25

Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management procedures for data-limited fisheries (see Carruthers et al (2014) <doi:10.1016/j.fishres.2013.12.014>).
Author: Tom Carruthers [aut, cre], Adrian Hordyk [aut]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>

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 403 files changed, 4314 insertions(+), 2827 deletions(-)

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