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
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 14 ++++++++++++++ data/kew.rda |binary data/treeg.rda |binary data/trees.rda |binary data/ufc.plots.rda |binary data/ufc.rda |binary inst/resources/scripts/newton_gamma.r | 2 +- man/kew.Rd | 9 +++++---- 10 files changed, 36 insertions(+), 21 deletions(-)
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>
Diff between Brobdingnag versions 1.2-4 dated 2013-12-05 and 1.2-5 dated 2018-03-18
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 6 ++++++ build/vignette.rds |binary inst/doc/brob.pdf |binary inst/doc/brobpaper.pdf |binary man/brob.Rd | 11 +++++++++++ 7 files changed, 28 insertions(+), 11 deletions(-)
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
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/RJuliaConnect.R | 24 +++++++++++++++--------- man/XRjulia-package.Rd | 5 ++--- man/findJulia.Rd | 4 +++- man/functions.Rd | 18 +++++++++++------- 6 files changed, 42 insertions(+), 31 deletions(-)
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
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Interface.R | 24 ++++++++++++++++-------- man/evaluatorActions.Rd | 4 ++-- 4 files changed, 25 insertions(+), 17 deletions(-)
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
DESCRIPTION | 6 MD5 | 93 ++++++----- NEWS.md | 18 ++ R/bw.R | 50 +++--- R/doc_BBands.R | 18 +- R/doc_Crossover.R | 14 - R/doc_Ema.R | 12 - R/doc_Order.R | 46 ++--- R/doc_Processor.R | 256 ++++++++++++++++----------------- R/doc_RollPercentRank.R | 10 - R/doc_RollRange.R | 18 +- R/doc_RollSd.R | 10 - R/doc_RollVolumeProfile.R | 12 - R/doc_Rsi.R | 12 - R/doc_Sma.R | 12 - R/doc_Stochastic.R | 18 +- R/get_market_data.R | 134 +++++++++++++++-- R/iqfeed.R | 16 +- R/na_locf.R | 7 R/plot_dts.R | 43 ++++- R/round_POSIXct.R | 1 R/settings.R | 5 R/store_market_data.R | 58 +++++++ inst/include/Alarm.h | 2 inst/include/BackTest/Candle.h | 12 + inst/include/BackTest/Order.h | 48 ++++-- inst/include/BackTest/Processor.h | 39 +++-- inst/include/BackTest/ProcessorMulti.h |only inst/include/Indicators/Crossover.h | 7 inst/include/Indicators/RollLinReg.h | 4 inst/include/ListBuilder.h | 16 -- inst/include/Utils.h | 12 + man/cpp_BBands.Rd | 18 +- man/cpp_Crossover.Rd | 14 - man/cpp_Ema.Rd | 12 - man/cpp_Order.Rd | 44 ++--- man/cpp_Processor.Rd | 254 ++++++++++++++++---------------- man/cpp_RollPercentRank.Rd | 10 - man/cpp_RollRange.Rd | 18 +- man/cpp_RollSd.Rd | 10 - man/cpp_RollVolumeProfile.Rd | 12 - man/cpp_Rsi.Rd | 12 - man/cpp_Sma.Rd | 12 - man/cpp_Stochastic.Rd | 18 +- man/get_market_data.Rd | 61 +++++++ man/plot_dts.Rd | 12 - man/settings.Rd | 2 src/run_tests.cpp | 1 48 files changed, 930 insertions(+), 589 deletions(-)
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>
Diff between msme versions 0.5.1 dated 2014-07-21 and 0.5.3 dated 2018-03-18
ChangeLog | 2 DESCRIPTION | 14 +++--- MD5 | 28 ++++++------ NAMESPACE | 14 ++++++ NEWS | 7 ++- R/ml_glm_2.R | 23 ++++++++-- R/nbinomial1.R | 126 +++++++------------------------------------------------ data/doll.rda |binary data/heart.rda |binary data/medpar.rda |binary data/rwm5yr.rda |binary data/titanic.rda |binary data/ufc.rda |binary man/ml_glm2.Rd | 9 +++ man/nbinomial.Rd | 3 - 15 files changed, 89 insertions(+), 137 deletions(-)
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>
Diff between smatr versions 3.4-3 dated 2014-01-06 and 3.4-8 dated 2018-03-18
smatr-3.4-3/smatr/data/leaflife.RData |only smatr-3.4-3/smatr/data/leafmeas.RData |only smatr-3.4-8/smatr/DESCRIPTION | 27 +++-- smatr-3.4-8/smatr/MD5 | 25 ++-- smatr-3.4-8/smatr/NAMESPACE | 12 ++ smatr-3.4-8/smatr/R/fitted.sma.R | 4 smatr-3.4-8/smatr/R/lr.b.com.R | 11 -- smatr-3.4-8/smatr/R/plot.sma.R | 37 +++---- smatr-3.4-8/smatr/R/slope.com.R | 171 ++++++++++++++-------------------- smatr-3.4-8/smatr/R/slope.test.R | 5 smatr-3.4-8/smatr/R/sma.R | 66 +++++++------ smatr-3.4-8/smatr/README.md |only smatr-3.4-8/smatr/data/leaflife.rda |only smatr-3.4-8/smatr/data/leafmeas.rda |only smatr-3.4-8/smatr/man/plot.sma.Rd | 5 smatr-3.4-8/smatr/man/sma.Rd | 7 - 16 files changed, 195 insertions(+), 175 deletions(-)
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>
Diff between sentometrics versions 0.2 dated 2017-11-13 and 0.3 dated 2018-03-18
sentometrics-0.2/sentometrics/NEWS |only sentometrics-0.3/sentometrics/DESCRIPTION | 15 sentometrics-0.3/sentometrics/MD5 | 69 +- sentometrics-0.3/sentometrics/NAMESPACE | 4 sentometrics-0.3/sentometrics/NEWS.md |only sentometrics-0.3/sentometrics/R/attribution.R | 3 sentometrics-0.3/sentometrics/R/sentocorpus.R | 122 ++-- sentometrics-0.3/sentometrics/R/sentomeasures.R | 407 ++++++++++---- sentometrics-0.3/sentometrics/R/sentometrics.R | 36 - sentometrics-0.3/sentometrics/R/sentomodel.R | 53 - sentometrics-0.3/sentometrics/R/utils.R | 66 +- sentometrics-0.3/sentometrics/README.md | 18 sentometrics-0.3/sentometrics/data/lexicons.rda |binary sentometrics-0.3/sentometrics/data/valence.rda |binary sentometrics-0.3/sentometrics/inst/CITATION | 30 - sentometrics-0.3/sentometrics/man/add_features.Rd | 39 + sentometrics-0.3/sentometrics/man/compute_sentiment.Rd | 24 sentometrics-0.3/sentometrics/man/ctr_agg.Rd | 4 sentometrics-0.3/sentometrics/man/ctr_merge.Rd | 2 sentometrics-0.3/sentometrics/man/diff.sentomeasures.Rd |only sentometrics-0.3/sentometrics/man/extract_peakdocs.Rd |only sentometrics-0.3/sentometrics/man/fill_measures.Rd | 2 sentometrics-0.3/sentometrics/man/get_hows.Rd | 6 sentometrics-0.3/sentometrics/man/lexicons.Rd | 18 sentometrics-0.3/sentometrics/man/merge_measures.Rd | 2 sentometrics-0.3/sentometrics/man/perform_agg.Rd | 5 sentometrics-0.3/sentometrics/man/plot.sentomeasures.Rd | 4 sentometrics-0.3/sentometrics/man/plot.sentomodeliter.Rd | 3 sentometrics-0.3/sentometrics/man/select_measures.Rd | 32 - sentometrics-0.3/sentometrics/man/sento_corpus.Rd | 38 - sentometrics-0.3/sentometrics/man/sento_measures.Rd | 7 sentometrics-0.3/sentometrics/man/sento_model.Rd | 40 - sentometrics-0.3/sentometrics/man/sentometrics-package.Rd | 13 sentometrics-0.3/sentometrics/man/setup_lexicons.Rd | 28 sentometrics-0.3/sentometrics/man/subset_measures.Rd |only sentometrics-0.3/sentometrics/man/to_global.Rd | 39 - sentometrics-0.3/sentometrics/man/valence.Rd | 5 sentometrics-0.3/sentometrics/src/compute_df.cpp | 2 38 files changed, 734 insertions(+), 402 deletions(-)
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>
Diff between pgmm versions 1.2.1 dated 2018-03-15 and 1.2.2 dated 2018-03-18
ChangeLog | 6 +++++- DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/pgmmEM.R | 8 ++++---- man/pgmm.Rd | 4 ++-- 5 files changed, 20 insertions(+), 16 deletions(-)
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>
Diff between longclust versions 1.2.1 dated 2018-03-14 and 1.2.2 dated 2018-03-18
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/longclust-package.Rd | 4 ++-- src/t_chol.c | 4 ++-- 5 files changed, 16 insertions(+), 12 deletions(-)
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>
Diff between LearnBayes versions 2.15 dated 2014-05-29 and 2.15.1 dated 2018-03-18
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 11 +++++++++++ build/vignette.rds |binary inst/doc/BayesFactors.pdf |binary inst/doc/BinomialInference.pdf |binary inst/doc/DiscreteBayes.pdf |binary inst/doc/MCMCintro.pdf |binary inst/doc/MultilevelModeling.pdf |binary 9 files changed, 24 insertions(+), 13 deletions(-)
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>
Diff between implyr versions 0.2.2 dated 2018-02-11 and 0.2.3 dated 2018-03-18
DESCRIPTION | 12 ++-- MD5 | 16 +++-- NAMESPACE | 13 ++++ NEWS.md | 8 ++ R/db-impala.R | 54 ++++++++++++++++++ R/src_impala.R | 17 +++++ R/tbl_impala.R | 120 ++++++++++++++++++++++++++++++++++++++++++ man/impala_unnest.Rd |only tests/testthat/test-complex.R |only tests/testthat/test-data.R | 2 10 files changed, 224 insertions(+), 18 deletions(-)
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
DHARMa-0.1.5/DHARMa/man/if-predictor-is-a-factor-a-boxplot-will-be-plotted-instead-of-a-scatter-plot..Rd |only DHARMa-0.1.6/DHARMa/DESCRIPTION | 15 DHARMa-0.1.6/DHARMa/MD5 | 66 - 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 DHARMa-0.1.6/DHARMa/R/plotResiduals.R | 124 ++- DHARMa-0.1.6/DHARMa/R/random.R |only DHARMa-0.1.6/DHARMa/R/simulateResiduals.R | 19 DHARMa-0.1.6/DHARMa/R/testsParametric.R | 4 DHARMa-0.1.6/DHARMa/R/testsResiduals.R | 54 - DHARMa-0.1.6/DHARMa/README.md | 6 DHARMa-0.1.6/DHARMa/inst/doc/DHARMa.R | 13 DHARMa-0.1.6/DHARMa/inst/doc/DHARMa.Rmd | 59 + DHARMa-0.1.6/DHARMa/inst/doc/DHARMa.html | 413 +++++----- DHARMa-0.1.6/DHARMa/inst/examples/createDharmaHelp.R |only DHARMa-0.1.6/DHARMa/inst/examples/plotsHelp.R |only DHARMa-0.1.6/DHARMa/inst/examples/testSpatialAutocorrelationHelp.R |only DHARMa-0.1.6/DHARMa/inst/examples/testTemporalAutocorrelationHelp.R |only DHARMa-0.1.6/DHARMa/man/createDHARMa.Rd | 82 + DHARMa-0.1.6/DHARMa/man/plot.DHARMa.Rd | 3 DHARMa-0.1.6/DHARMa/man/plotQQunif.Rd |only DHARMa-0.1.6/DHARMa/man/plotResiduals.Rd |only DHARMa-0.1.6/DHARMa/man/plotSimulatedResiduals.Rd | 55 + 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 DHARMa-0.1.6/DHARMa/man/testOverdispersionParametric.Rd | 2 DHARMa-0.1.6/DHARMa/man/testPDistribution.Rd |only DHARMa-0.1.6/DHARMa/man/testSimulatedResiduals.Rd | 2 DHARMa-0.1.6/DHARMa/man/testSpatialAutocorrelation.Rd | 34 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 DHARMa-0.1.6/DHARMa/tests/testthat/testPlots.R |only DHARMa-0.1.6/DHARMa/vignettes/DHARMa.Rmd | 59 + 39 files changed, 757 insertions(+), 343 deletions(-)
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
RcppSMC-0.2.0/RcppSMC/src/helper.cpp |only RcppSMC-0.2.0/RcppSMC/src/history.cpp |only RcppSMC-0.2.0/RcppSMC/src/smc-exception.cpp |only RcppSMC-0.2.0/RcppSMC/src/staticModelAdapt.cpp |only RcppSMC-0.2.1/RcppSMC/ChangeLog | 67 ++++++ RcppSMC-0.2.1/RcppSMC/DESCRIPTION | 15 - RcppSMC-0.2.1/RcppSMC/MD5 | 40 +-- RcppSMC-0.2.1/RcppSMC/R/RcppExports.R | 8 RcppSMC-0.2.1/RcppSMC/R/plugin.R |only RcppSMC-0.2.1/RcppSMC/README.md | 4 RcppSMC-0.2.1/RcppSMC/inst/NEWS.Rd | 21 + RcppSMC-0.2.1/RcppSMC/inst/include/RcppSMC.h |only RcppSMC-0.2.1/RcppSMC/inst/include/history.h | 32 ++ RcppSMC-0.2.1/RcppSMC/inst/include/population.h | 10 RcppSMC-0.2.1/RcppSMC/inst/include/sampler.h | 195 ++++++++++++------ RcppSMC-0.2.1/RcppSMC/inst/include/smc-exception.h | 35 ++- RcppSMC-0.2.1/RcppSMC/inst/include/staticModelAdapt.h | 93 ++++++++ RcppSMC-0.2.1/RcppSMC/src/LinReg.cpp | 14 - RcppSMC-0.2.1/RcppSMC/src/LinReg_LA.cpp | 2 RcppSMC-0.2.1/RcppSMC/src/LinReg_LA_adapt.cpp | 64 ++--- RcppSMC-0.2.1/RcppSMC/src/RcppExports.cpp | 25 +- RcppSMC-0.2.1/RcppSMC/src/nonLinPMMH.cpp | 6 RcppSMC-0.2.1/RcppSMC/src/pflineart.cpp | 2 RcppSMC-0.2.1/RcppSMC/src/pfnonlinbs.cpp | 12 - 24 files changed, 475 insertions(+), 170 deletions(-)
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
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 12 ++++++++++-- R/Utils.R | 6 ++++++ R/buildPhylo.R | 2 +- R/runExPANdS.R | 6 ------ inst/doc/expands.pdf |binary 7 files changed, 26 insertions(+), 18 deletions(-)
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
DESCRIPTION | 18 +++++++++++++----- MD5 | 8 ++++---- R/gapFill.R | 25 +++++++++++++++++-------- R/getReference.R | 9 ++++++--- man/getReference.Rd | 5 ++++- 5 files changed, 44 insertions(+), 21 deletions(-)
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>
Diff between Peptides versions 2.2 dated 2017-06-05 and 2.3 dated 2018-03-18
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/stScales.R | 4 ++-- R/sysdata.rda |binary R/tScales.R | 4 ++-- data/AAdata.RData |binary man/stScales.Rd | 4 ++-- man/tScales.Rd | 4 ++-- 9 files changed, 27 insertions(+), 22 deletions(-)
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>
Diff between sGMRFmix versions 0.1.3 dated 2018-02-28 and 0.2.0 dated 2018-03-18
DESCRIPTION | 6 +- MD5 | 23 ++++---- NAMESPACE | 2 NEWS.md |only R/compute_anomaly_score.R | 6 +- R/plot.R | 42 +++++++++++----- R/sGMRFmix.R | 31 +++++++----- R/sparseGaussMix.R | 20 +++++-- build/vignette.rds |binary inst/doc/sGMRFmix.html | 105 ++++++++++++++++++++--------------------- man/plot_multivariate_data.Rd | 11 +++- man/sGMRFmix.Rd | 14 +++-- tests/testthat/test-sGMRFmix.R | 5 + 13 files changed, 156 insertions(+), 109 deletions(-)
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>
Diff between RankAggreg versions 0.6.3 dated 2018-03-13 and 0.6.4 dated 2018-03-18
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/RankAggreg.R | 10 +++++++--- inst/doc/RankAggreg.pdf |binary 5 files changed, 19 insertions(+), 11 deletions(-)
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>
Diff between Rgretl versions 0.2.1 dated 2018-03-06 and 0.2.2 dated 2018-03-18
Rgretl-0.2.1/Rgretl/man/get_grwd.Rd |only Rgretl-0.2.2/Rgretl/DESCRIPTION | 10 +++++----- Rgretl-0.2.2/Rgretl/MD5 | 11 +++++------ Rgretl-0.2.2/Rgretl/NEWS | 2 +- Rgretl-0.2.2/Rgretl/R/rgretl.R | 27 --------------------------- Rgretl-0.2.2/Rgretl/build/partial.rdb |binary Rgretl-0.2.2/Rgretl/man/Rgretl-package.Rd | 6 +++--- 7 files changed, 14 insertions(+), 42 deletions(-)
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
ChangeLog | 4 ++++ DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 28 +++++++++++++++++++++++++++- inst/NEWS | 6 ++++++ man/bpstrip.Rd | 3 +-- man/densregion.Rd | 1 - man/densregion.normal.Rd | 4 +++- man/densregion.survfit.Rd | 5 ++++- man/denstrip-package.Rd | 1 - man/denstrip.Rd | 13 +++++-------- man/denstrip.legend.Rd | 8 ++++++++ man/vwstrip.Rd | 3 +-- 13 files changed, 78 insertions(+), 36 deletions(-)
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>
Diff between WaveletComp versions 1.0 dated 2014-12-16 and 1.1 dated 2018-03-18
DESCRIPTION | 15 MD5 | 100 ++--- NAMESPACE | 8 NEWS.md |only R/ARIMA.R | 2 R/SurrogateData.R | 4 R/analyze.coherency.R | 33 + R/analyze.wavelet.R | 29 + R/arrow.R | 2 R/periodic_series.R | 18 R/reconstruct.R | 414 ++++++++++++++++++--- R/wc.R | 10 R/wc.angle.R | 9 R/wc.avg.R | 293 +++++++++++++-- R/wc.image.R | 484 ++++++++++++++++++++++--- R/wc.phasediff.image.R | 473 +++++++++++++++++++++--- R/wc.sel.phases.R | 414 +++++++++++++++++++-- R/wt.R | 4 R/wt.avg.R | 268 ++++++++++++- R/wt.image.R | 467 +++++++++++++++++++++--- R/wt.phase.image.R | 481 +++++++++++++++++++++--- R/wt.sel.phases.R | 452 ++++++++++++++++++++--- build |only data/USelection2016.Instagram.rda |only data/weather.radiation.Mannheim.rda |only man/AR.Rd | 21 - man/ARIMA.Rd | 54 +- man/COI.Rd | 24 - man/FXtrade.transactions.Rd | 13 man/FourierRand.Rd | 8 man/SurrogateData.Rd | 83 ++-- man/USelection2016.Instagram.Rd |only man/WaveletCoherency.Rd | 125 ++++-- man/WaveletComp-package.Rd | 83 +++- man/WaveletTransform.Rd | 51 ++ man/analyze.coherency.Rd | 462 +++++++++++++++-------- man/analyze.wavelet.Rd | 297 ++++++++++----- man/arrow.Rd | 22 - man/marriages.Turkey.Rd | 11 man/periodic.series.Rd | 46 +- man/reconstruct.Rd | 362 +++++++++++++----- man/ridge.Rd | 19 man/wc.Rd | 222 +++++++---- man/wc.angle.Rd | 71 ++- man/wc.avg.Rd | 357 ++++++++++++++---- man/wc.image.Rd | 696 ++++++++++++++++++++++++------------ man/wc.phasediff.image.Rd | 393 ++++++++++++++------ man/wc.sel.phases.Rd | 361 ++++++++++++++---- man/weather.radiation.Mannheim.Rd |only man/wt.Rd | 147 ++++--- man/wt.avg.Rd | 286 ++++++++++++-- man/wt.image.Rd | 534 ++++++++++++++++++++------- man/wt.phase.image.Rd | 352 +++++++++++++----- man/wt.sel.phases.Rd | 290 +++++++++++---- 54 files changed, 7282 insertions(+), 2088 deletions(-)
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>
Diff between Rgb versions 1.5.1 dated 2017-04-21 and 1.6.1 dated 2018-03-18
DESCRIPTION | 8 +- MD5 | 34 ++++----- R/1_drawable-class.R | 12 +++ R/2_drawable.list-class.R | 36 +++++++++ R/3_track.bam-class.R | 1 R/5_track.CNV-class.R | 2 R/browsePlot.R | 65 +++++++++++++---- R/draw.bg.R | 26 +++++- R/draw.boxes.R | 4 - R/segMerge.R | 4 - R/segOverlap.R | 4 - R/tk.browse.R | 171 ++++++++++++++++++++++++++++++++++------------ R/track.table.GTF.R | 5 + inst/NEWS.Rd | 18 ++++ inst/doc/Howto.pdf |binary man/Annotation.Rd | 8 +- man/draw.bg.Rd | 26 +++++- man/tk.browse.Rd | 14 ++- 18 files changed, 331 insertions(+), 107 deletions(-)
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 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWith2LevelModerator-b.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWith2LevelModerator-c.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWith2LevelModeratorAndMissing-a.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWith2LevelModeratorAndMissing-b.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWith2LevelModeratorAndMissing-c.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWithContinuousModerator-a.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWithContinuousModerator-b.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWithContinuousModerator-c.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWithContinuousModerator-d.R | 2 OpenMx-2.9.6/OpenMx/inst/models/nightly/3LatentMultiRegWithContinuousModerator-e.R | 2 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 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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(-)
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
DESCRIPTION | 13 +-- MD5 | 8 +- R/AAAClasses.R | 1 R/ModisDownload.R | 72 +++++++++++++-------- R/period.R | 177 ++++++++++++++++++++++++++++++++---------------------- 5 files changed, 160 insertions(+), 111 deletions(-)
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
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NAMESPACE | 18 ++++++++++-------- R/funcs.R | 14 +++++++------- man/hierNet.Rd | 2 +- man/hierNet.varimp.Rd | 4 ++-- man/predict.hierNet.Rd | 4 ++-- man/predict.hierNet.logistic.Rd | 4 ++-- man/predict.hierNet.path.Rd | 4 ++-- src/hierNet_init.c |only 10 files changed, 39 insertions(+), 36 deletions(-)
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>
Diff between GGIR versions 1.5-17 dated 2018-02-19 and 1.5-18 dated 2018-03-18
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 2 R/g.getmeta.R | 2 R/g.getstarttime.R | 18 R/g.part2.R | 3 R/g.part3.R | 10 R/g.part4.R | 697 ++++++++++++++---------------- R/g.part5.R | 24 - R/g.plot5.R | 2 R/g.report.part4.R | 59 +- R/g.shell.GGIR.R | 23 R/g.sib.det.R | 50 +- R/is_this_a_dst_night.R |only inst/NEWS.Rd | 17 man/GGIR-package.Rd | 4 man/g.part3.Rd | 8 man/g.part4.Rd | 5 man/is_this_a_dst_night.Rd |only tests/testthat/test_chainof5parts.R | 14 tests/testthat/test_ggetbout.R |only tests/testthat/test_is_this_a_dst_night.R |only 22 files changed, 517 insertions(+), 467 deletions(-)
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>
Diff between lcyanalysis versions 1.0.0 dated 2017-11-03 and 1.0.1 dated 2018-03-18
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/bearpower.R | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++++----- R/bullpower.R | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++--- 4 files changed, 145 insertions(+), 16 deletions(-)
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
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>
Diff between rquery versions 0.4.0 dated 2018-03-10 and 0.4.1 dated 2018-03-18
rquery-0.4.0/rquery/man/materialize_node.Rd |only rquery-0.4.1/rquery/DESCRIPTION | 14 rquery-0.4.1/rquery/MD5 | 147 ++++--- rquery-0.4.1/rquery/NAMESPACE | 13 rquery-0.4.1/rquery/NEWS.md | 10 rquery-0.4.1/rquery/R/dbi_ops.R |only rquery-0.4.1/rquery/R/ex_data_frame.R | 105 +++-- rquery-0.4.1/rquery/R/extend.R | 59 +-- rquery-0.4.1/rquery/R/if_else_block.R | 75 ++-- rquery-0.4.1/rquery/R/materialize.R | 241 +++++-------- rquery-0.4.1/rquery/R/natural_join.R | 24 - rquery-0.4.1/rquery/R/non_sql_node.R | 36 - rquery-0.4.1/rquery/R/order_by.R | 27 - rquery-0.4.1/rquery/R/partition_assignments.R | 1 rquery-0.4.1/rquery/R/project.R | 96 ++--- rquery-0.4.1/rquery/R/quantile.R |only rquery-0.4.1/rquery/R/relop.R | 68 +++ rquery-0.4.1/rquery/R/rename.R | 28 - rquery-0.4.1/rquery/R/rsummary.R | 132 ++++--- rquery-0.4.1/rquery/R/select_columns.R | 28 - rquery-0.4.1/rquery/R/select_rows.R | 43 +- rquery-0.4.1/rquery/R/sql_expr_set.R |only rquery-0.4.1/rquery/R/sql_node.R | 90 ++-- rquery-0.4.1/rquery/R/table_source.R | 152 +------- rquery-0.4.1/rquery/R/theta_join.R | 48 +- rquery-0.4.1/rquery/R/work_with_NULLs.R | 162 ++++---- rquery-0.4.1/rquery/README.md | 84 ++++ rquery-0.4.1/rquery/build/vignette.rds |binary rquery-0.4.1/rquery/inst/doc/AssigmentPartitioner.R | 15 rquery-0.4.1/rquery/inst/doc/AssigmentPartitioner.Rmd | 17 rquery-0.4.1/rquery/inst/doc/AssigmentPartitioner.html | 6 rquery-0.4.1/rquery/inst/doc/QueryGeneration.R | 9 rquery-0.4.1/rquery/inst/doc/QueryGeneration.Rmd | 10 rquery-0.4.1/rquery/inst/doc/QueryGeneration.html | 4 rquery-0.4.1/rquery/inst/doc/rquery_intro.R | 63 ++- rquery-0.4.1/rquery/inst/doc/rquery_intro.Rmd | 81 ++-- rquery-0.4.1/rquery/inst/doc/rquery_intro.html | 54 ++ rquery-0.4.1/rquery/man/column_names.Rd | 15 rquery-0.4.1/rquery/man/columns_used.Rd | 15 rquery-0.4.1/rquery/man/count_null_cols.Rd | 40 +- rquery-0.4.1/rquery/man/dbi_colnames.Rd |only rquery-0.4.1/rquery/man/dbi_copy_to.Rd | 18 rquery-0.4.1/rquery/man/dbi_nrow.Rd |only rquery-0.4.1/rquery/man/dbi_remove_table.Rd |only rquery-0.4.1/rquery/man/dbi_table.Rd | 36 + rquery-0.4.1/rquery/man/execute.Rd | 44 +- rquery-0.4.1/rquery/man/extend_nse.Rd | 20 - rquery-0.4.1/rquery/man/extend_se.Rd | 30 - rquery-0.4.1/rquery/man/if_else_block.Rd | 75 ++-- rquery-0.4.1/rquery/man/mark_null_cols.Rd | 40 +- rquery-0.4.1/rquery/man/materialize.Rd | 26 - rquery-0.4.1/rquery/man/natural_join.Rd | 24 - rquery-0.4.1/rquery/man/non_sql_node.Rd | 10 rquery-0.4.1/rquery/man/orderby.Rd | 20 - rquery-0.4.1/rquery/man/project_nse.Rd | 44 +- rquery-0.4.1/rquery/man/project_se.Rd | 44 +- rquery-0.4.1/rquery/man/quantile_cols.Rd |only rquery-0.4.1/rquery/man/quantile_node.Rd |only rquery-0.4.1/rquery/man/rename_columns.Rd | 20 - rquery-0.4.1/rquery/man/replace_null_cols.Rd | 70 +-- rquery-0.4.1/rquery/man/rquery_apply_to_data_frame.Rd | 40 -- rquery-0.4.1/rquery/man/rsummary.Rd | 37 + rquery-0.4.1/rquery/man/rsummary_node.Rd | 57 +-- rquery-0.4.1/rquery/man/select_columns.Rd | 20 - rquery-0.4.1/rquery/man/select_rows_nse.Rd | 22 - rquery-0.4.1/rquery/man/select_rows_se.Rd | 21 - rquery-0.4.1/rquery/man/sql_expr_set.Rd |only rquery-0.4.1/rquery/man/sql_node.Rd | 90 ++-- rquery-0.4.1/rquery/man/table_source.Rd | 28 - rquery-0.4.1/rquery/man/tables_used.Rd | 20 - rquery-0.4.1/rquery/man/theta_join_nse.Rd | 24 - rquery-0.4.1/rquery/man/theta_join_se.Rd | 24 - rquery-0.4.1/rquery/man/to_sql.Rd | 15 rquery-0.4.1/rquery/man/wrapr_function.relop.Rd | 38 +- rquery-0.4.1/rquery/tests/testthat/test_extend_partition.R | 47 +- rquery-0.4.1/rquery/tests/testthat/test_translation.R | 134 +++---- rquery-0.4.1/rquery/tools |only rquery-0.4.1/rquery/vignettes/AssigmentPartitioner.Rmd | 17 rquery-0.4.1/rquery/vignettes/QueryGeneration.Rmd | 10 rquery-0.4.1/rquery/vignettes/rquery_intro.Rmd | 81 ++-- 80 files changed, 1809 insertions(+), 1449 deletions(-)
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>
Diff between DLMtool versions 5.0.2 dated 2017-11-25 and 5.1 dated 2018-03-18
DLMtool-5.0.2/DLMtool/R/ChooseEffort.r |only DLMtool-5.0.2/DLMtool/R/ChooseMort.R |only DLMtool-5.0.2/DLMtool/R/ChooseSelect.r |only DLMtool-5.0.2/DLMtool/R/DLMextra.R |only DLMtool-5.0.2/DLMtool/R/DataObj.r |only DLMtool-5.0.2/DLMtool/R/DefinePMClasses.R |only DLMtool-5.0.2/DLMtool/R/Input.r |only DLMtool-5.0.2/DLMtool/R/LBSPR_MPs.r |only DLMtool-5.0.2/DLMtool/R/MSEObj.r |only DLMtool-5.0.2/DLMtool/R/MSEplotting.R |only DLMtool-5.0.2/DLMtool/R/MiscFuns.r |only DLMtool-5.0.2/DLMtool/R/MiscInt.r |only DLMtool-5.0.2/DLMtool/R/OMinit_doc.R |only DLMtool-5.0.2/DLMtool/R/OMinit_doc_plots.R |only DLMtool-5.0.2/DLMtool/R/Output.r |only DLMtool-5.0.2/DLMtool/R/Replace.r |only DLMtool-5.0.2/DLMtool/R/SampleCpars.R |only DLMtool-5.0.2/DLMtool/R/SampleFleetPars.r |only DLMtool-5.0.2/DLMtool/R/SampleImpPars.R |only DLMtool-5.0.2/DLMtool/R/SampleObsPars.R |only DLMtool-5.0.2/DLMtool/R/SampleSteepness.R |only DLMtool-5.0.2/DLMtool/R/SampleStockPars.R |only DLMtool-5.0.2/DLMtool/R/Selectivity_Functions.R |only DLMtool-5.0.2/DLMtool/R/SubOM.r |only DLMtool-5.0.2/DLMtool/R/XLloadfuns.r |only DLMtool-5.0.2/DLMtool/R/cpars.R |only DLMtool-5.0.2/DLMtool/R/plotFleet.r |only DLMtool-5.0.2/DLMtool/R/plotOM.R |only DLMtool-5.0.2/DLMtool/R/plotObsImp.R |only DLMtool-5.0.2/DLMtool/R/plotSelect.R |only DLMtool-5.0.2/DLMtool/R/plotStock.r |only DLMtool-5.0.2/DLMtool/R/runInMP.R |only DLMtool-5.0.2/DLMtool/R/runMSErobust.r |only DLMtool-5.0.2/DLMtool/R/testing.R |only DLMtool-5.0.2/DLMtool/R/userguide.R |only DLMtool-5.0.2/DLMtool/data/Generic_fleet.RData |only DLMtool-5.0.2/DLMtool/data/Generic_obs.RData |only DLMtool-5.0.2/DLMtool/man/CalcInput.Rd |only DLMtool-5.0.2/DLMtool/man/CalcOutput.Rd |only DLMtool-5.0.2/DLMtool/man/CheckConverg.Rd |only DLMtool-5.0.2/DLMtool/man/ChkDatNA.Rd |only DLMtool-5.0.2/DLMtool/man/DBSRA_ML.Rd |only DLMtool-5.0.2/DLMtool/man/DD_R.Rd |only DLMtool-5.0.2/DLMtool/man/InputRec-class.Rd |only DLMtool-5.0.2/DLMtool/man/Jplot.Rd |only DLMtool-5.0.2/DLMtool/man/LBSPR.Rd |only DLMtool-5.0.2/DLMtool/man/LBSPR_ItEff.Rd |only DLMtool-5.0.2/DLMtool/man/LBSPR_ItSel.Rd |only DLMtool-5.0.2/DLMtool/man/LBSPR_ItTAC.Rd |only DLMtool-5.0.2/DLMtool/man/MPclass.Rd |only DLMtool-5.0.2/DLMtool/man/OM_xl.Rd |only DLMtool-5.0.2/DLMtool/man/Sam.Rd |only DLMtool-5.0.2/DLMtool/man/Splot.Rd |only DLMtool-5.0.2/DLMtool/man/boxplot.MSE.Rd |only DLMtool-5.0.2/DLMtool/man/doprojPI_cpp.Rd |only DLMtool-5.0.2/DLMtool/man/genLenComp.Rd |only DLMtool-5.0.2/DLMtool/man/getFMSY3.Rd |only DLMtool-5.0.2/DLMtool/man/movfit.Rd |only DLMtool-5.0.2/DLMtool/man/optQ_cpp.Rd |only DLMtool-5.0.2/DLMtool/man/plot-Data.Rd |only DLMtool-5.0.2/DLMtool/man/plot-MSE.Rd |only DLMtool-5.0.2/DLMtool/man/popdyn.Rd |only DLMtool-5.0.2/DLMtool/man/popdynOneTS.Rd |only DLMtool-5.0.2/DLMtool/man/projOpt_cpp.Rd |only DLMtool-5.0.2/DLMtool/src/doprojPI_cpp.cpp |only DLMtool-5.0.2/DLMtool/src/optQ_cpp.cpp |only DLMtool-5.0.2/DLMtool/src/projOpt_cpp.cpp |only DLMtool-5.0.2/DLMtool/tests/manual/runtests.r |only DLMtool-5.0.2/DLMtool/tests/manual/test-Data.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-Imp.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-MPs.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-builtin.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-discard.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-overnight.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-perfectOM.R |only DLMtool-5.0.2/DLMtool/tests/manual/test-plotting.R |only DLMtool-5.0.2/DLMtool/tests/testthat |only DLMtool-5.0.2/DLMtool/tests/testthat.R |only DLMtool-5.1/DLMtool/DESCRIPTION | 14 DLMtool-5.1/DLMtool/MD5 | 703 +++--- DLMtool-5.1/DLMtool/NAMESPACE | 66 DLMtool-5.1/DLMtool/NEWS.md | 43 DLMtool-5.1/DLMtool/R/Blow_funcs.R | 301 +- DLMtool-5.1/DLMtool/R/DFO.R | 5 DLMtool-5.1/DLMtool/R/Data_Functions.R |only DLMtool-5.1/DLMtool/R/Data_Plotting.R |only DLMtool-5.1/DLMtool/R/DefineClasses.r | 710 ++++-- DLMtool-5.1/DLMtool/R/Fease_Functions.R |only DLMtool-5.1/DLMtool/R/MPs_Input.R |only DLMtool-5.1/DLMtool/R/MPs_Mixed.R |only DLMtool-5.1/DLMtool/R/MPs_Output.R |only DLMtool-5.1/DLMtool/R/MPs_Reference.R |only DLMtool-5.1/DLMtool/R/MPs_SupportingFunctions.R |only DLMtool-5.1/DLMtool/R/MSE_Plotting.R |only DLMtool-5.1/DLMtool/R/MSE_functions.R |only DLMtool-5.1/DLMtool/R/Misc_Exported.R |only DLMtool-5.1/DLMtool/R/Misc_Internal.R |only DLMtool-5.1/DLMtool/R/OM_Plotting.R |only DLMtool-5.1/DLMtool/R/OM_functions.R |only DLMtool-5.1/DLMtool/R/OM_init_doc.R |only DLMtool-5.1/DLMtool/R/RcppExports.R | 429 +-- DLMtool-5.1/DLMtool/R/Roxy_DataObjects.r | 112 DLMtool-5.1/DLMtool/R/SS2DLM.R | 72 DLMtool-5.1/DLMtool/R/SampleOM.R |only DLMtool-5.1/DLMtool/R/Sketch_Functions.R |only DLMtool-5.1/DLMtool/R/StochasticSRA.R | 17 DLMtool-5.1/DLMtool/R/iSCAM2DLM.R | 2 DLMtool-5.1/DLMtool/R/popdyn.R | 1918 +++++++++++------ DLMtool-5.1/DLMtool/R/runMSE.r | 1166 ++++++---- DLMtool-5.1/DLMtool/data/Albacore.RData |binary DLMtool-5.1/DLMtool/data/Atlantic_mackerel.RData |binary DLMtool-5.1/DLMtool/data/Blue_shark.RData |binary DLMtool-5.1/DLMtool/data/Bluefin_tuna.RData |binary DLMtool-5.1/DLMtool/data/Bluefin_tuna_WAtl.RData |binary DLMtool-5.1/DLMtool/data/Butterfish.RData |binary DLMtool-5.1/DLMtool/data/China_rockfish.RData |binary DLMtool-5.1/DLMtool/data/Cobia.RData |binary DLMtool-5.1/DLMtool/data/DataDescription.RData |binary DLMtool-5.1/DLMtool/data/DecE_Dom.RData |binary DLMtool-5.1/DLMtool/data/DecE_HDom.RData |binary DLMtool-5.1/DLMtool/data/DecE_NDom.RData |binary DLMtool-5.1/DLMtool/data/Example_datafile.RData |binary DLMtool-5.1/DLMtool/data/Feasibility.RData |binary DLMtool-5.1/DLMtool/data/Feasibility2.RData |binary DLMtool-5.1/DLMtool/data/FlatE_Dom.RData |binary DLMtool-5.1/DLMtool/data/FlatE_HDom.RData |binary DLMtool-5.1/DLMtool/data/FlatE_NDom.RData |binary DLMtool-5.1/DLMtool/data/FleetDescription.RData |binary DLMtool-5.1/DLMtool/data/Generic_DecE.RData |binary DLMtool-5.1/DLMtool/data/Generic_FlatE.RData |binary DLMtool-5.1/DLMtool/data/Generic_Fleet.RData |only DLMtool-5.1/DLMtool/data/Generic_IncE.RData |binary DLMtool-5.1/DLMtool/data/Generic_Obs.RData |only DLMtool-5.1/DLMtool/data/Gulf_blue_tilefish.RData |binary DLMtool-5.1/DLMtool/data/Herring.RData |binary DLMtool-5.1/DLMtool/data/ImpDescription.RData |binary DLMtool-5.1/DLMtool/data/Imprecise_Biased.RData |binary DLMtool-5.1/DLMtool/data/Imprecise_Unbiased.RData |binary DLMtool-5.1/DLMtool/data/IncE_HDom.RData |binary DLMtool-5.1/DLMtool/data/IncE_NDom.RData |binary DLMtool-5.1/DLMtool/data/Low_Effort_Non_Target.RData |binary DLMtool-5.1/DLMtool/data/Mackerel.RData |binary DLMtool-5.1/DLMtool/data/OMDescription.RData |binary DLMtool-5.1/DLMtool/data/ObsDescription.RData |binary DLMtool-5.1/DLMtool/data/Overages.RData |binary DLMtool-5.1/DLMtool/data/Perfect_Imp.RData |binary DLMtool-5.1/DLMtool/data/Perfect_Info.RData |binary DLMtool-5.1/DLMtool/data/Porgy.RData |binary DLMtool-5.1/DLMtool/data/Precise_Biased.RData |binary DLMtool-5.1/DLMtool/data/Precise_Unbiased.RData |binary DLMtool-5.1/DLMtool/data/Red_snapper.RData |binary DLMtool-5.1/DLMtool/data/Rockfish.RData |binary DLMtool-5.1/DLMtool/data/SimulatedData.RData |only DLMtool-5.1/DLMtool/data/Simulation_1.RData |binary DLMtool-5.1/DLMtool/data/Snapper.RData |binary DLMtool-5.1/DLMtool/data/Sole.RData |binary DLMtool-5.1/DLMtool/data/StockDescription.RData |binary DLMtool-5.1/DLMtool/data/Target_All_Fish.RData |binary DLMtool-5.1/DLMtool/data/Targeting_Small_Fish.RData |binary DLMtool-5.1/DLMtool/data/Toothfish.RData |binary DLMtool-5.1/DLMtool/data/ourReefFish.RData |binary DLMtool-5.1/DLMtool/data/testOM.RData |binary DLMtool-5.1/DLMtool/inst/Data.csv |only DLMtool-5.1/DLMtool/inst/Data.xlsx |only DLMtool-5.1/DLMtool/inst/OM.rmd |only DLMtool-5.1/DLMtool/inst/OM.xlsx |only DLMtool-5.1/DLMtool/man/AvC.Rd | 2 DLMtool-5.1/DLMtool/man/AvC_MLL.Rd |only DLMtool-5.1/DLMtool/man/BK.Rd | 2 DLMtool-5.1/DLMtool/man/BK_CC.Rd | 2 DLMtool-5.1/DLMtool/man/BK_ML.Rd | 2 DLMtool-5.1/DLMtool/man/BlankSelPlot.Rd | 2 DLMtool-5.1/DLMtool/man/Blow_opt.Rd | 25 DLMtool-5.1/DLMtool/man/CC1.Rd | 4 DLMtool-5.1/DLMtool/man/CC4.Rd | 4 DLMtool-5.1/DLMtool/man/CSRA.Rd | 2 DLMtool-5.1/DLMtool/man/CSRAfunc.Rd | 6 DLMtool-5.1/DLMtool/man/Can.Rd | 13 DLMtool-5.1/DLMtool/man/Cant.Rd | 9 DLMtool-5.1/DLMtool/man/ChkObj.Rd | 2 DLMtool-5.1/DLMtool/man/ChooseEffort.Rd | 2 DLMtool-5.1/DLMtool/man/ChooseM.Rd | 2 DLMtool-5.1/DLMtool/man/ChooseSelect.Rd | 2 DLMtool-5.1/DLMtool/man/CompSRA.Rd | 2 DLMtool-5.1/DLMtool/man/CompSRA4010.Rd | 2 DLMtool-5.1/DLMtool/man/Converge.Rd | 49 DLMtool-5.1/DLMtool/man/Cplot.Rd | 4 DLMtool-5.1/DLMtool/man/DAAC.Rd | 2 DLMtool-5.1/DLMtool/man/DBSRA.Rd | 2 DLMtool-5.1/DLMtool/man/DBSRA4010.Rd | 2 DLMtool-5.1/DLMtool/man/DBSRA_40.Rd | 2 DLMtool-5.1/DLMtool/man/DCAC.Rd | 2 DLMtool-5.1/DLMtool/man/DCAC4010.Rd | 2 DLMtool-5.1/DLMtool/man/DCAC_40.Rd | 2 DLMtool-5.1/DLMtool/man/DCAC_ML.Rd | 2 DLMtool-5.1/DLMtool/man/DD.Rd | 9 DLMtool-5.1/DLMtool/man/DD4010.Rd | 8 DLMtool-5.1/DLMtool/man/DDe.Rd | 9 DLMtool-5.1/DLMtool/man/DDe75.Rd | 9 DLMtool-5.1/DLMtool/man/DDes.Rd | 11 DLMtool-5.1/DLMtool/man/DLMDataDir.Rd | 8 DLMtool-5.1/DLMtool/man/DLMextra.Rd | 2 DLMtool-5.1/DLMtool/man/DOM.Rd | 4 DLMtool-5.1/DLMtool/man/DTe40.Rd | 2 DLMtool-5.1/DLMtool/man/DTe50.Rd | 2 DLMtool-5.1/DLMtool/man/Data-class.Rd | 24 DLMtool-5.1/DLMtool/man/DataDescription.Rd | 2 DLMtool-5.1/DLMtool/man/DataInit.Rd |only DLMtool-5.1/DLMtool/man/Data_xl.Rd | 2 DLMtool-5.1/DLMtool/man/DepF.Rd | 2 DLMtool-5.1/DLMtool/man/DynF.Rd | 2 DLMtool-5.1/DLMtool/man/EtargetLopt.Rd | 2 DLMtool-5.1/DLMtool/man/FMSYref.Rd | 4 DLMtool-5.1/DLMtool/man/FMSYref50.Rd | 2 DLMtool-5.1/DLMtool/man/FMSYref75.Rd | 2 DLMtool-5.1/DLMtool/man/Fadapt.Rd | 2 DLMtool-5.1/DLMtool/man/Fdem.Rd | 2 DLMtool-5.1/DLMtool/man/Fdem_CC.Rd | 2 DLMtool-5.1/DLMtool/man/Fdem_ML.Rd | 2 DLMtool-5.1/DLMtool/man/Fease.Rd | 4 DLMtool-5.1/DLMtool/man/Fease_xl.Rd | 2 DLMtool-5.1/DLMtool/man/Fleet-class.Rd | 16 DLMtool-5.1/DLMtool/man/FleetDescription.Rd | 2 DLMtool-5.1/DLMtool/man/ForceCor.Rd | 2 DLMtool-5.1/DLMtool/man/Fratio.Rd | 2 DLMtool-5.1/DLMtool/man/Fratio4010.Rd | 2 DLMtool-5.1/DLMtool/man/Fratio_CC.Rd | 2 DLMtool-5.1/DLMtool/man/Fratio_ML.Rd | 2 DLMtool-5.1/DLMtool/man/GB_CC.Rd | 2 DLMtool-5.1/DLMtool/man/GB_slope.Rd | 2 DLMtool-5.1/DLMtool/man/GB_target.Rd | 2 DLMtool-5.1/DLMtool/man/Gcontrol.Rd | 2 DLMtool-5.1/DLMtool/man/HDAAC.Rd | 2 DLMtool-5.1/DLMtool/man/ICI.Rd | 2 DLMtool-5.1/DLMtool/man/ICI2.Rd | 2 DLMtool-5.1/DLMtool/man/IT10.Rd | 2 DLMtool-5.1/DLMtool/man/IT5.Rd | 2 DLMtool-5.1/DLMtool/man/ITM.Rd | 2 DLMtool-5.1/DLMtool/man/ITe10.Rd | 2 DLMtool-5.1/DLMtool/man/ITe5.Rd | 2 DLMtool-5.1/DLMtool/man/Imp-class.Rd | 2 DLMtool-5.1/DLMtool/man/ImpDescription.Rd | 2 DLMtool-5.1/DLMtool/man/Input.Rd | 2 DLMtool-5.1/DLMtool/man/Iratio.Rd | 2 DLMtool-5.1/DLMtool/man/Islope1.Rd | 2 DLMtool-5.1/DLMtool/man/Islope4.Rd | 2 DLMtool-5.1/DLMtool/man/Itarget1.Rd | 2 DLMtool-5.1/DLMtool/man/Itarget1_MPA.Rd |only DLMtool-5.1/DLMtool/man/Itarget4.Rd | 2 DLMtool-5.1/DLMtool/man/ItargetE1.Rd | 2 DLMtool-5.1/DLMtool/man/ItargetE4.Rd | 2 DLMtool-5.1/DLMtool/man/Kplot.Rd | 6 DLMtool-5.1/DLMtool/man/L2A.Rd | 4 DLMtool-5.1/DLMtool/man/L95target.Rd | 2 DLMtool-5.1/DLMtool/man/LinInterp.Rd | 2 DLMtool-5.1/DLMtool/man/Lratio_BHI.Rd | 2 DLMtool-5.1/DLMtool/man/Lratio_BHI2.Rd | 2 DLMtool-5.1/DLMtool/man/LstepCC1.Rd | 2 DLMtool-5.1/DLMtool/man/LstepCC4.Rd | 2 DLMtool-5.1/DLMtool/man/LstepCE1.Rd | 2 DLMtool-5.1/DLMtool/man/LstepCE2.Rd | 2 DLMtool-5.1/DLMtool/man/Ltarget1.Rd | 2 DLMtool-5.1/DLMtool/man/Ltarget4.Rd | 2 DLMtool-5.1/DLMtool/man/LtargetE1.Rd | 2 DLMtool-5.1/DLMtool/man/LtargetE4.Rd | 2 DLMtool-5.1/DLMtool/man/MCD.Rd | 2 DLMtool-5.1/DLMtool/man/MCD4010.Rd | 2 DLMtool-5.1/DLMtool/man/ML2D.Rd | 4 DLMtool-5.1/DLMtool/man/MPStats.Rd | 6 DLMtool-5.1/DLMtool/man/MPtype.Rd |only DLMtool-5.1/DLMtool/man/MRnoreal.Rd | 2 DLMtool-5.1/DLMtool/man/MRreal.Rd | 6 DLMtool-5.1/DLMtool/man/MSE-class.Rd | 2 DLMtool-5.1/DLMtool/man/NAor0.Rd | 2 DLMtool-5.1/DLMtool/man/NFref.Rd | 2 DLMtool-5.1/DLMtool/man/NOAA_plot.Rd | 4 DLMtool-5.1/DLMtool/man/Needed.Rd | 9 DLMtool-5.1/DLMtool/man/OM-class.Rd | 43 DLMtool-5.1/DLMtool/man/OMDescription.Rd | 2 DLMtool-5.1/DLMtool/man/OMdoc.Rd | 11 DLMtool-5.1/DLMtool/man/OMexample.Rd | 7 DLMtool-5.1/DLMtool/man/OMinit.Rd | 7 DLMtool-5.1/DLMtool/man/OneRep.Rd | 2 DLMtool-5.1/DLMtool/man/PMobj-class.Rd | 2 DLMtool-5.1/DLMtool/man/PWhisker.Rd | 2 DLMtool-5.1/DLMtool/man/Pplot.Rd | 10 DLMtool-5.1/DLMtool/man/Pplot2.Rd | 2 DLMtool-5.1/DLMtool/man/Range.Rd | 5 DLMtool-5.1/DLMtool/man/Rcontrol.Rd | 2 DLMtool-5.1/DLMtool/man/Rcontrol2.Rd | 2 DLMtool-5.1/DLMtool/man/Rec-class.Rd |only DLMtool-5.1/DLMtool/man/Replace.Rd | 6 DLMtool-5.1/DLMtool/man/Required.Rd | 14 DLMtool-5.1/DLMtool/man/SBT1.Rd | 2 DLMtool-5.1/DLMtool/man/SBT2.Rd | 2 DLMtool-5.1/DLMtool/man/SPMSY.Rd | 2 DLMtool-5.1/DLMtool/man/SPSRA.Rd | 2 DLMtool-5.1/DLMtool/man/SPSRA_ML.Rd | 2 DLMtool-5.1/DLMtool/man/SPmod.Rd | 2 DLMtool-5.1/DLMtool/man/SPslope.Rd | 6 DLMtool-5.1/DLMtool/man/SampleCpars.Rd | 2 DLMtool-5.1/DLMtool/man/SampleFleetPars.Rd | 2 DLMtool-5.1/DLMtool/man/SampleImpPars.Rd | 2 DLMtool-5.1/DLMtool/man/SampleObsPars.Rd | 2 DLMtool-5.1/DLMtool/man/SampleStockPars.Rd | 2 DLMtool-5.1/DLMtool/man/Sense.Rd | 2 DLMtool-5.1/DLMtool/man/SimulatedData.Rd |only DLMtool-5.1/DLMtool/man/SketchFun.Rd | 2 DLMtool-5.1/DLMtool/man/Stock-class.Rd | 2 DLMtool-5.1/DLMtool/man/StockDescription.Rd | 2 DLMtool-5.1/DLMtool/man/Sub.Rd | 4 DLMtool-5.1/DLMtool/man/SubOM.Rd | 2 DLMtool-5.1/DLMtool/man/TAC.Rd | 2 DLMtool-5.1/DLMtool/man/TACfilter.Rd | 2 DLMtool-5.1/DLMtool/man/Tplot.Rd | 4 DLMtool-5.1/DLMtool/man/Tplot2.Rd | 4 DLMtool-5.1/DLMtool/man/Tplot3.Rd | 2 DLMtool-5.1/DLMtool/man/TradePlot.Rd | 10 DLMtool-5.1/DLMtool/man/VOI.Rd | 6 DLMtool-5.1/DLMtool/man/VOI2.Rd | 4 DLMtool-5.1/DLMtool/man/VOIplot.Rd | 9 DLMtool-5.1/DLMtool/man/XL2Data.Rd |only DLMtool-5.1/DLMtool/man/XL2OM.Rd | 2 DLMtool-5.1/DLMtool/man/YPR.Rd | 2 DLMtool-5.1/DLMtool/man/YPR_CC.Rd | 2 DLMtool-5.1/DLMtool/man/YPR_ML.Rd | 2 DLMtool-5.1/DLMtool/man/alphaconv.Rd | 2 DLMtool-5.1/DLMtool/man/applyMP.Rd |only DLMtool-5.1/DLMtool/man/avail.Rd | 10 DLMtool-5.1/DLMtool/man/barplot.MSE.Rd | 2 DLMtool-5.1/DLMtool/man/betaconv.Rd | 2 DLMtool-5.1/DLMtool/man/boxplot.Data.Rd | 2 DLMtool-5.1/DLMtool/man/calcMean.Rd | 2 DLMtool-5.1/DLMtool/man/calcProb.Rd | 2 DLMtool-5.1/DLMtool/man/checkMSE.Rd | 2 DLMtool-5.1/DLMtool/man/condmet.Rd | 2 DLMtool-5.1/DLMtool/man/curE.Rd | 2 DLMtool-5.1/DLMtool/man/curE75.Rd | 2 DLMtool-5.1/DLMtool/man/cv.Rd | 2 DLMtool-5.1/DLMtool/man/derive_beta_par.Rd | 2 DLMtool-5.1/DLMtool/man/dnormal.Rd | 2 DLMtool-5.1/DLMtool/man/getAFC.Rd | 4 DLMtool-5.1/DLMtool/man/getBlow.Rd | 25 DLMtool-5.1/DLMtool/man/getEffhist.Rd | 2 DLMtool-5.1/DLMtool/man/getFref3.Rd | 8 DLMtool-5.1/DLMtool/man/getclass.Rd | 4 DLMtool-5.1/DLMtool/man/getmov2.Rd | 2 DLMtool-5.1/DLMtool/man/getq3.Rd | 10 DLMtool-5.1/DLMtool/man/getsel.Rd | 2 DLMtool-5.1/DLMtool/man/gettempvar.Rd | 2 DLMtool-5.1/DLMtool/man/hist2.Rd | 2 DLMtool-5.1/DLMtool/man/joinMSE.Rd | 2 DLMtool-5.1/DLMtool/man/makePerf.Rd | 2 DLMtool-5.1/DLMtool/man/makeTransparent.Rd | 2 DLMtool-5.1/DLMtool/man/matlenlim.Rd | 4 DLMtool-5.1/DLMtool/man/matlenlim2.Rd | 2 DLMtool-5.1/DLMtool/man/mconv.Rd | 2 DLMtool-5.1/DLMtool/man/minlenLopt1.Rd | 2 DLMtool-5.1/DLMtool/man/optCPU.Rd |only DLMtool-5.1/DLMtool/man/optMSY.Rd | 6 DLMtool-5.1/DLMtool/man/optQ.Rd | 4 DLMtool-5.1/DLMtool/man/plot-Fleet.Rd | 2 DLMtool-5.1/DLMtool/man/plot-Imp.Rd | 2 DLMtool-5.1/DLMtool/man/plot-OM.Rd | 2 DLMtool-5.1/DLMtool/man/plot-Obs.Rd | 2 DLMtool-5.1/DLMtool/man/plot.Data.Rd |only DLMtool-5.1/DLMtool/man/plot.MSE.Rd |only DLMtool-5.1/DLMtool/man/plotFun.Rd | 4 DLMtool-5.1/DLMtool/man/plotM.Rd | 2 DLMtool-5.1/DLMtool/man/plotMPA.Rd |only DLMtool-5.1/DLMtool/man/plotOFL.Rd | 4 DLMtool-5.1/DLMtool/man/plotSelect.Rd | 2 DLMtool-5.1/DLMtool/man/plotStock.Rd | 2 DLMtool-5.1/DLMtool/man/popdynCPP.Rd | 4 DLMtool-5.1/DLMtool/man/replic8.Rd | 2 DLMtool-5.1/DLMtool/man/runInMP.Rd | 2 DLMtool-5.1/DLMtool/man/runMP.Rd |only DLMtool-5.1/DLMtool/man/runMSE.Rd | 46 DLMtool-5.1/DLMtool/man/runMSEnomsg.Rd | 2 DLMtool-5.1/DLMtool/man/runMSErobust.Rd | 28 DLMtool-5.1/DLMtool/man/sample_steepness2.Rd | 2 DLMtool-5.1/DLMtool/man/sampy.Rd | 2 DLMtool-5.1/DLMtool/man/sdconv.Rd | 2 DLMtool-5.1/DLMtool/man/setup.Rd | 6 DLMtool-5.1/DLMtool/man/show-MSE.Rd | 2 DLMtool-5.1/DLMtool/man/show-Rec.Rd |only DLMtool-5.1/DLMtool/man/simYears.Rd | 8 DLMtool-5.1/DLMtool/man/slotlim.Rd | 4 DLMtool-5.1/DLMtool/man/summary-MSE.Rd | 2 DLMtool-5.1/DLMtool/man/tdlnorm.Rd | 2 DLMtool-5.1/DLMtool/man/trlnorm.Rd | 2 DLMtool-5.1/DLMtool/man/updateMSE.Rd | 2 DLMtool-5.1/DLMtool/man/userguide.Rd | 2 DLMtool-5.1/DLMtool/man/validcpars.Rd | 2 DLMtool-5.1/DLMtool/man/wormplot.Rd | 4 DLMtool-5.1/DLMtool/man/writeCSV.Rd | 2 DLMtool-5.1/DLMtool/src/RcppExports.cpp | 157 - DLMtool-5.1/DLMtool/src/genLenComp.cpp | 400 ++- DLMtool-5.1/DLMtool/src/popddynCPP.cpp | 122 - DLMtool-5.1/DLMtool/tests/manual/old_stuff_delete_soon |only DLMtool-5.1/DLMtool/tests/manual/run-tests-code.R |only DLMtool-5.1/DLMtool/tests/manual/run-tests-thorough.R |only DLMtool-5.1/DLMtool/tests/manual/test-code |only 403 files changed, 4314 insertions(+), 2827 deletions(-)