Title: Environment for Assessing Recommender Systems
Description: Provides implementations of several popular recommendation systems. They can process standard recommendation datasets (user/item matrix) as input and generate rating predictions and recommendation lists. Standard algorithm implementations included in this package are: Global/Item/User-Average baselines, Item-Based KNN, FunkSVD, BPR and weighted ALS. They can be assessed according to the standard offline evaluation methodology for recommender systems using measures such as MAE, RMSE, Precision, Recall, AUC, NDCG, RankScore and coverage measures. The package is intended for rapid prototyping of recommendation algorithms and education purposes.
Author: Ludovik Çoba [aut, cre, cph],
Markus Zanker [ctb]
Maintainer: Ludovik Çoba <lcoba@unishk.edu.al>
Diff between rrecsys versions 0.9.2 dated 2016-04-04 and 0.9.5 dated 2016-05-31
rrecsys-0.9.2/rrecsys/R/getnDCG.R |only rrecsys-0.9.2/rrecsys/R/getrankscore.R |only rrecsys-0.9.5/rrecsys/DESCRIPTION | 8 +++--- rrecsys-0.9.5/rrecsys/MD5 | 34 ++++++++++++++------------- rrecsys-0.9.5/rrecsys/NAMESPACE | 3 +- rrecsys-0.9.5/rrecsys/R/AAA_registry.R | 5 ---- rrecsys-0.9.5/rrecsys/R/ALG_BPR.R | 2 - rrecsys-0.9.5/rrecsys/R/ALG_IB_kNN.R | 12 ++++++--- rrecsys-0.9.5/rrecsys/R/ALG_average.R | 2 - rrecsys-0.9.5/rrecsys/R/ALG_funkSVD.R | 4 ++- rrecsys-0.9.5/rrecsys/R/evalPred.R | 35 +++++++++++++++------------- rrecsys-0.9.5/rrecsys/R/evalRec.R | 14 ++++------- rrecsys-0.9.5/rrecsys/R/getAUC.R | 10 ++++---- rrecsys-0.9.5/rrecsys/R/nDCG.R |only rrecsys-0.9.5/rrecsys/R/prediction.R | 1 rrecsys-0.9.5/rrecsys/R/rankScore.R |only rrecsys-0.9.5/rrecsys/R/recommend.R | 7 ----- rrecsys-0.9.5/rrecsys/data/mlLatest100k.rda |binary rrecsys-0.9.5/rrecsys/man/mlLatest100k.Rd | 2 - rrecsys-0.9.5/rrecsys/man/nDCG.Rd |only rrecsys-0.9.5/rrecsys/man/rankScore.Rd |only 21 files changed, 68 insertions(+), 71 deletions(-)
Title: Data Manipulation with Parallelism and Shared Memory Matrices
Description: Provides a new form of data frame backed by shared memory matrices
and a way to manipulate them. Upon creation these data frames are shared across
multiple local nodes to allow for simple parallel processing.
Author: Jim Blundell [aut, cre, cph]
Maintainer: Jim Blundell <jeblundell@doctors.org.uk>
Diff between multiplyr versions 0.1.0 dated 2016-05-18 and 0.1.1 dated 2016-05-31
multiplyr-0.1.0/multiplyr/inst/doc/basics.pdf |only multiplyr-0.1.0/multiplyr/man/clsna.Rd |only multiplyr-0.1.0/multiplyr/man/dots2names.Rd |only multiplyr-0.1.0/multiplyr/tests/testthat/barrnumleft.desc |only multiplyr-0.1.0/multiplyr/tests/testthat/barrsense.desc |only multiplyr-0.1.0/multiplyr/vignettes/basics.html |only multiplyr-0.1.1/multiplyr/DESCRIPTION | 23 multiplyr-0.1.1/multiplyr/MD5 | 144 ++- multiplyr-0.1.1/multiplyr/NAMESPACE | 33 multiplyr-0.1.1/multiplyr/NEWS.md | 14 multiplyr-0.1.1/multiplyr/R/class.R | 501 ++++++------ multiplyr-0.1.1/multiplyr/R/internal.R | 248 +++++- multiplyr-0.1.1/multiplyr/R/multiplyr.R | 34 multiplyr-0.1.1/multiplyr/R/nse.R | 29 multiplyr-0.1.1/multiplyr/R/ops.R | 576 +++++++------- multiplyr-0.1.1/multiplyr/R/util.R | 213 +++++ multiplyr-0.1.1/multiplyr/README.md | 44 - multiplyr-0.1.1/multiplyr/build/vignette.rds |binary multiplyr-0.1.1/multiplyr/inst/doc/basics.Rmd | 16 multiplyr-0.1.1/multiplyr/inst/doc/basics.html |only multiplyr-0.1.1/multiplyr/man/Multiplyr-class.Rd | 84 +- multiplyr-0.1.1/multiplyr/man/Multiplyr-methods.Rd | 2 multiplyr-0.1.1/multiplyr/man/NA_class_.Rd |only multiplyr-0.1.1/multiplyr/man/add_rownames.Rd |only multiplyr-0.1.1/multiplyr/man/arrange.Rd | 10 multiplyr-0.1.1/multiplyr/man/between.Rd |only multiplyr-0.1.1/multiplyr/man/bm_morder.Rd |only multiplyr-0.1.1/multiplyr/man/bm_mpermute.Rd |only multiplyr-0.1.1/multiplyr/man/cumall.Rd |only multiplyr-0.1.1/multiplyr/man/cumany.Rd |only multiplyr-0.1.1/multiplyr/man/cummean.Rd |only multiplyr-0.1.1/multiplyr/man/define.Rd | 10 multiplyr-0.1.1/multiplyr/man/desc.Rd |only multiplyr-0.1.1/multiplyr/man/distinct.Rd | 7 multiplyr-0.1.1/multiplyr/man/distribute.Rd | 11 multiplyr-0.1.1/multiplyr/man/dotscapture.Rd |only multiplyr-0.1.1/multiplyr/man/dotscombine.Rd |only multiplyr-0.1.1/multiplyr/man/dotseval.Rd |only multiplyr-0.1.1/multiplyr/man/dotsname.Rd |only multiplyr-0.1.1/multiplyr/man/dotsname1.Rd |only multiplyr-0.1.1/multiplyr/man/filter.Rd | 7 multiplyr-0.1.1/multiplyr/man/first.Rd |only multiplyr-0.1.1/multiplyr/man/group_by.Rd | 7 multiplyr-0.1.1/multiplyr/man/group_sizes.Rd | 2 multiplyr-0.1.1/multiplyr/man/lag.Rd |only multiplyr-0.1.1/multiplyr/man/last.Rd |only multiplyr-0.1.1/multiplyr/man/lead.Rd |only multiplyr-0.1.1/multiplyr/man/multiplyr.Rd | 19 multiplyr-0.1.1/multiplyr/man/mutate.Rd | 11 multiplyr-0.1.1/multiplyr/man/n.Rd |only multiplyr-0.1.1/multiplyr/man/n_distinct.Rd |only multiplyr-0.1.1/multiplyr/man/n_groups.Rd |only multiplyr-0.1.1/multiplyr/man/nonunique.Rd |only multiplyr-0.1.1/multiplyr/man/nsa.Rd | 8 multiplyr-0.1.1/multiplyr/man/nth.Rd |only multiplyr-0.1.1/multiplyr/man/p.Rd | 2 multiplyr-0.1.1/multiplyr/man/partition_even.Rd | 4 multiplyr-0.1.1/multiplyr/man/partition_group.Rd | 4 multiplyr-0.1.1/multiplyr/man/reduce.Rd | 9 multiplyr-0.1.1/multiplyr/man/regroup.Rd | 2 multiplyr-0.1.1/multiplyr/man/rename.Rd | 10 multiplyr-0.1.1/multiplyr/man/select.Rd | 10 multiplyr-0.1.1/multiplyr/man/shutdown.Rd | 7 multiplyr-0.1.1/multiplyr/man/slice.Rd | 8 multiplyr-0.1.1/multiplyr/man/sm_desc_comp.Rd |only multiplyr-0.1.1/multiplyr/man/sm_desc_group.Rd |only multiplyr-0.1.1/multiplyr/man/sm_desc_subset.Rd |only multiplyr-0.1.1/multiplyr/man/sm_desc_update.Rd | 2 multiplyr-0.1.1/multiplyr/man/summarise.Rd | 9 multiplyr-0.1.1/multiplyr/man/test_transition.Rd | 2 multiplyr-0.1.1/multiplyr/man/transmute.Rd | 9 multiplyr-0.1.1/multiplyr/man/undefine.Rd | 9 multiplyr-0.1.1/multiplyr/man/ungroup.Rd | 2 multiplyr-0.1.1/multiplyr/man/within_group.Rd | 8 multiplyr-0.1.1/multiplyr/man/within_node.Rd | 8 multiplyr-0.1.1/multiplyr/tests/testthat.R | 3 multiplyr-0.1.1/multiplyr/tests/testthat/test-arrange.R | 30 multiplyr-0.1.1/multiplyr/tests/testthat/test-bm.R |only multiplyr-0.1.1/multiplyr/tests/testthat/test-class.R | 70 - multiplyr-0.1.1/multiplyr/tests/testthat/test-compact.R | 3 multiplyr-0.1.1/multiplyr/tests/testthat/test-filter.R | 5 multiplyr-0.1.1/multiplyr/tests/testthat/test-groups.R | 90 +- multiplyr-0.1.1/multiplyr/tests/testthat/test-mutate.R | 3 multiplyr-0.1.1/multiplyr/tests/testthat/test-nsa.R | 11 multiplyr-0.1.1/multiplyr/tests/testthat/test-partition.R | 34 multiplyr-0.1.1/multiplyr/tests/testthat/test-subset.R | 3 multiplyr-0.1.1/multiplyr/tests/testthat/test-summarise.R | 3 multiplyr-0.1.1/multiplyr/tests/testthat/test-utils.R | 84 ++ multiplyr-0.1.1/multiplyr/tests/testthat/test-within.R | 3 multiplyr-0.1.1/multiplyr/vignettes/basics.Rmd | 16 90 files changed, 1689 insertions(+), 827 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description:
Contains some auxiliary functions for multiple
imputation which complements existing functionality
in R.
In addition to some utility functions, main features
include plausible value imputation, multilevel
imputation functions, imputation using partial least
squares (PLS) for high dimensional predictors, nested
multiple imputation, and two-way imputation.
Author:
Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 1.7-8 dated 2016-02-18 and 1.8-0 dated 2016-05-31
miceadds-1.7-8/miceadds/R/fast.groupmean.R |only miceadds-1.7-8/miceadds/R/ma.wtd.statNA.R |only miceadds-1.7-8/miceadds/man/fast.groupmean.Rd |only miceadds-1.8-0/miceadds/DESCRIPTION | 21 - miceadds-1.8-0/miceadds/MD5 | 127 ++++--- miceadds-1.8-0/miceadds/NAMESPACE | 24 + miceadds-1.8-0/miceadds/R/GroupMean.R |only miceadds-1.8-0/miceadds/R/NMIcombine.R | 12 miceadds-1.8-0/miceadds/R/NMIwaldtest.R | 15 miceadds-1.8-0/miceadds/R/cor2fisher.R |only miceadds-1.8-0/miceadds/R/covTest.R |only miceadds-1.8-0/miceadds/R/cppfunction.R | 1 miceadds-1.8-0/miceadds/R/datalist2mids.R | 3 miceadds-1.8-0/miceadds/R/datlist_create.R | 38 -- miceadds-1.8-0/miceadds/R/fisher2cor.R |only miceadds-1.8-0/miceadds/R/ma.wtd.aux.data.R |only miceadds-1.8-0/miceadds/R/ma.wtd.corNA.R |only miceadds-1.8-0/miceadds/R/ma.wtd.covNA.R |only miceadds-1.8-0/miceadds/R/ma.wtd.curtosisNA.R |only miceadds-1.8-0/miceadds/R/ma.wtd.meanNA.R |only miceadds-1.8-0/miceadds/R/ma.wtd.quantileNA.R |only miceadds-1.8-0/miceadds/R/ma.wtd.sdNA.R |only miceadds-1.8-0/miceadds/R/ma.wtd.skewnessNA.R |only miceadds-1.8-0/miceadds/R/mice.impute.2l.binary.R |only miceadds-1.8-0/miceadds/R/mice.impute.2l.plausible.values.R | 3 miceadds-1.8-0/miceadds/R/mice.impute.2l.pls.R | 5 miceadds-1.8-0/miceadds/R/mice.impute.grouped.R | 7 miceadds-1.8-0/miceadds/R/micombine.F.R | 3 miceadds-1.8-0/miceadds/R/micombine.chisquare.R | 13 miceadds-1.8-0/miceadds/R/micombine.cor.R | 162 ++++++---- miceadds-1.8-0/miceadds/R/micombine.cov.R |only miceadds-1.8-0/miceadds/R/nested.datlist_create.R |only miceadds-1.8-0/miceadds/R/pool.mi.R | 7 miceadds-1.8-0/miceadds/R/scale_datlist.R | 3 miceadds-1.8-0/miceadds/R/scan0.R | 10 miceadds-1.8-0/miceadds/R/sub.micombine.cor.R |only miceadds-1.8-0/miceadds/R/sub.micombine.cov.R |only miceadds-1.8-0/miceadds/R/subset_datlist.R | 9 miceadds-1.8-0/miceadds/R/subset_nested.datlist.R | 12 miceadds-1.8-0/miceadds/R/vector2matrix.R |only miceadds-1.8-0/miceadds/R/write.datlist.R | 13 miceadds-1.8-0/miceadds/R/write.mice.imputation.R | 2 miceadds-1.8-0/miceadds/data/data.allison.gssexp.rda |binary miceadds-1.8-0/miceadds/data/data.allison.hip.rda |binary miceadds-1.8-0/miceadds/data/data.allison.usnews.rda |binary miceadds-1.8-0/miceadds/data/data.enders.depression.rda |binary miceadds-1.8-0/miceadds/data/data.enders.eatingattitudes.rda |binary miceadds-1.8-0/miceadds/data/data.enders.employee.rda |binary miceadds-1.8-0/miceadds/data/data.graham.ex3.rda |binary miceadds-1.8-0/miceadds/data/data.graham.ex6.rda |binary miceadds-1.8-0/miceadds/data/data.graham.ex8a.rda |binary miceadds-1.8-0/miceadds/data/data.graham.ex8b.rda |binary miceadds-1.8-0/miceadds/data/data.graham.ex8c.rda |binary miceadds-1.8-0/miceadds/data/data.internet.rda |binary miceadds-1.8-0/miceadds/data/data.largescale.rda |binary miceadds-1.8-0/miceadds/data/data.ma01.rda |binary miceadds-1.8-0/miceadds/data/data.ma02.rda |binary miceadds-1.8-0/miceadds/data/data.ma03.rda |binary miceadds-1.8-0/miceadds/data/data.ma04.rda |binary miceadds-1.8-0/miceadds/data/data.ma05.rda |binary miceadds-1.8-0/miceadds/data/data.ma06.rda |binary miceadds-1.8-0/miceadds/data/data.smallscale.rda |binary miceadds-1.8-0/miceadds/inst/NEWS | 57 +++ miceadds-1.8-0/miceadds/man/GroupMean.Rd |only miceadds-1.8-0/miceadds/man/ma.wtd.statNA.Rd | 93 +++++ miceadds-1.8-0/miceadds/man/mice.impute.2l.binary.Rd |only miceadds-1.8-0/miceadds/man/mice.impute.2l.plausible.values.Rd | 4 miceadds-1.8-0/miceadds/man/mice.impute.2lonly.pmm2.Rd | 4 miceadds-1.8-0/miceadds/man/miceadds-package.Rd | 2 miceadds-1.8-0/miceadds/man/micombine.chisquare.Rd | 2 miceadds-1.8-0/miceadds/man/micombine.cor.Rd | 61 +++ miceadds-1.8-0/miceadds/man/round2.Rd | 15 miceadds-1.8-0/miceadds/man/subset_datlist.Rd | 7 miceadds-1.8-0/miceadds/man/sumpreserving.rounding.Rd | 18 - miceadds-1.8-0/miceadds/man/systime.Rd | 16 miceadds-1.8-0/miceadds/man/write.datlist.Rd | 7 76 files changed, 524 insertions(+), 252 deletions(-)
Title: Data from the Book "Multivariate Statistical Modelling Based on
Generalized Linear Models", First Edition, by Ludwig Fahrmeir
and Gerhard Tutz
Description: Data and functions for the book "Multivariate Statistical
Modelling Based on Generalized Linear Models", first edition, by
Ludwig Fahrmeir and Gerhard Tutz. Useful when using the book.
Author: compiled by Kjetil B Halvorsen
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between Fahrmeir versions 2015.6.25 dated 2015-06-26 and 2016.5.31 dated 2016-05-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ man/Regensburg.Rd | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Useful Functions for Box, Hunter and Hunter II
Description: Functions and data sets reproducing some examples in
Box, Hunter and Hunter II. Useful for statistical design
of experiments, especially factorial experiments.
Author: Ernesto Barrios
Maintainer: Kjetil B.Halvorsen <kjetil1001@gmail.com>
Diff between BHH2 versions 2015.06.25 dated 2015-06-26 and 2016.05.31 dated 2016-05-31
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 4 ++++ NEWS | 3 +++ build/vignette.rds |binary data/corrosion.data.rda |binary data/heads.data.rda |binary data/penicillin.data.rda |binary data/poison.data.rda |binary data/shoes.data.rda |binary data/tab03B1.rda |binary data/tab03B2.rda |binary data/tomato.data.rda |binary data/woolen.data.rda |binary inst/doc/BHH2.pdf |binary 15 files changed, 25 insertions(+), 18 deletions(-)
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: The focus of the dnet is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.0.8 dated 2016-04-01 and 1.0.9 dated 2016-05-31
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/dDAGgeneSim.r | 4 ++-- R/dNetPipeline.r | 53 +++++++++++++++++++++++++++++++++++++++++------------ R/dRWR.r | 2 +- R/visDAG.r | 31 ++++++++++++++++++------------- R/visNet.r | 20 ++++++++++++++++---- man/dRWR.Rd | 2 +- man/visDAG.Rd | 7 +++++-- 9 files changed, 96 insertions(+), 47 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal maximum likelihood estimation of uni- and
multidimensional item response models (Rasch, 2PL, 3PL,
Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models)
and joint maximum likelihood estimation for models
from the Rasch family.
Latent regression models and plausible value imputation are
also supported.
Author:
Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 1.99-6 dated 2016-04-15 and 1.995-0 dated 2016-05-31
DESCRIPTION | 8 - MD5 | 18 +-- R/msq.itemfit.R | 21 ++- R/tam.fit.R | 14 +- inst/NEWS | 40 ++++++- man/IRTLikelihood.ctt.Rd | 4 man/TAM-package.Rd | 2 man/msq.itemfit.Rd | 5 man/tam.mml.Rd | 2 src/msq_itemfit.cpp | 257 +++++++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 337 insertions(+), 34 deletions(-)
Title: Multiplicative Competitive Interaction (MCI) Model
Description: The Multiplicative Competitive Interaction (MCI) Model by Nakanishi & Cooper (1974) <DOI:10.2307/3151146> is an econometric model for analyzing market shares and/or market areas. The functions in this package include fitting the MCI model, the log-centering transformation of MCI datasets and tools for data preparation.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between MCI versions 1.0.1 dated 2016-04-24 and 1.0.2 dated 2016-05-31
DESCRIPTION | 8 ++-- MD5 | 38 ++++++++++--------- NAMESPACE | 3 + R/ijmatrix.create.R | 92 ++++++++++++++++++++++++++++------------------ R/ijmatrix.shares.R | 53 +++++++++++++++----------- R/mci.fit.R | 38 +++++++++++-------- R/mci.transmat.R | 44 ++++++++++++++-------- R/mci.transvar.R | 95 +++++++++++++++++++++++++---------------------- R/var.asdummy.R | 44 +++++++++++++--------- R/var.check.R | 98 +++++++++++++++++++++++++++++++------------------ R/var.correct.R | 23 +++++++---- R/var.zetas.R |only man/ce.Rd | 2 - man/ijmatrix.create.Rd | 4 +- man/ijmatrix.shares.Rd | 4 +- man/mci.fit.Rd | 4 +- man/mci.transmat.Rd | 6 +-- man/mci.transvar.Rd | 8 ++-- man/var.check.Rd | 4 +- man/var.correct.Rd | 6 +-- man/var.zetas.Rd |only 21 files changed, 340 insertions(+), 234 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 4.8-0 dated 2016-03-10 and 4.991-1 dated 2016-05-31
DESCRIPTION | 10 +- MD5 | 51 ++++++---- NAMESPACE | 1 R/gdina.R | 197 +++++++++++++----------------------------- R/gdina.dif.R | 3 R/gdina.dif_aux.R | 10 +- R/gdina_mstep_item_ml.R |only R/gdina_mstep_item_ml_rrum.R |only R/gdina_mstep_item_ml_rrum2.R |only R/gdina_mstep_item_uls.R |only R/logpars2rrumpars.R |only R/numerical_Hessian.R | 19 ++-- R/print.summary.din.R | 6 - R/rrumpars2logpars.R |only R/summary.din.R | 4 R/summary.gdina.R | 10 +- data/data.cdm03.rda |only inst/NEWS | 23 ++++ man/CDM-package.Rd | 62 +++++++------ man/IRT.repDesign.Rd | 2 man/data.cdm.Rd | 56 ++++++++++- man/din.Rd | 2 man/din.deterministic.Rd | 2 man/din.validate.qmatrix.Rd | 2 man/gdina.Rd | 28 ++++- man/gdina.dif.Rd | 2 man/gdm.Rd | 6 - man/itemfit.sx2.Rd | 2 man/numerical_Hessian.Rd | 17 ++- man/slca.Rd | 8 - 30 files changed, 282 insertions(+), 241 deletions(-)
Title: Item Response Models for Multiple Ratings
Description:
Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program.
Author:
Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.4-0 dated 2016-03-07 and 0.5-0 dated 2016-05-31
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- data/data.immer09.rda |only data/data.immer10.rda |only inst/NEWS | 13 +++++++++++++ man/data.immer.Rd | 23 +++++++++++++++++++---- man/immer-package.Rd | 2 +- man/immer_HRM.Rd | 2 +- man/immer_cml.Rd | 2 +- man/lc2_agreement.Rd | 4 ++-- man/simulate_HRM.Rd | 2 +- 11 files changed, 52 insertions(+), 22 deletions(-)
Title: Data Supporting the 'VGAM' Package
Description: Data sets to accompany the VGAM package and
the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
<DOI:10.1007/978-1-4939-2818-7>.
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology).
Author: Thomas Yee [aut, cre, cph],
James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAMdata versions 1.0-0 dated 2015-10-29 and 1.0-2 dated 2016-05-31
DESCRIPTION | 15 +++++----- MD5 | 75 +++++++++++++++++++++++++++------------------------ NAMESPACE | 2 - NEWS | 23 ++++++++++++++- R/family.fishing.R | 3 +- data/bb.de.rda |binary data/bd.us.rda |binary data/belcap.rda |binary data/crashf.au.rda |binary data/crime.us.rda |binary data/datalist | 4 ++ data/ecb06it.rda |only data/ecb14it.rda |only data/exam1.rda |binary data/fibre15.rda |binary data/fibre1dot5.rda |binary data/gala.rda |binary data/hued.rda |binary data/huie.rda |binary data/huse.rda |binary data/oly12.rda |binary data/pirates1.rda |only data/pirates2.rda |only data/prison.us.rda |binary data/profs.nz.rda |binary data/rainfall.rda |binary data/rugby.rda |binary data/rugby.ties.rda |binary data/students.tw.rda |binary data/trapO.rda |binary data/tube10.rda |binary data/ugss.rda |binary data/vtinpat.rda |binary data/wffc.indiv.rda |binary data/wffc.nc.rda |binary data/wffc.rda |binary data/wffc.teams.rda |binary data/xs.nz.rda |binary man/ecbit.Rd |only man/oly12.Rd | 7 ++-- man/pirates1.Rd |only man/pirates2.Rd |only 42 files changed, 82 insertions(+), 47 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov <valentin.todorov@chello.at>,
Andreas Ruckstuhl <andreas.ruckstuhl@zhaw.ch>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Tobias Verbeke <tobias.verbeke@openanalytics.eu>,
Manuel Koller <mkoller@ispm.unibe.ch>,
Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.92-5 dated 2015-07-22 and 0.92-6 dated 2016-05-31
ChangeLog | 3 DESCRIPTION | 10 - MD5 | 108 +++++++++---------- NAMESPACE | 5 R/adjoutlyingness.R | 9 - R/classPC.R | 2 R/lmrob.MM.R | 29 +++-- R/lmrob.R | 13 +- TODO | 5 build/vignette.rds |binary inst/NEWS.Rd | 19 +++ inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.R | 163 ++++++++++++++--------------- inst/doc/lmrob_simulation.Rnw | 155 +++++++++++++-------------- inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary man/adjOutlyingness.Rd | 6 - man/classPC.Rd | 5 man/nlrob-algos.Rd | 2 man/nlrob.Rd | 15 +- man/summary.lmrob.Rd | 12 +- src/mc.c | 2 src/wgt_himed.c | 3 tests/NAcoef.R | 22 ++- tests/NAcoef.Rout.save | 30 +++-- vignettes/lmrob_simulation.Rnw | 155 +++++++++++++-------------- vignettes/plot-fig-AdB2-1.pdf |binary vignettes/plot-fig-Mscale-all.pdf |binary vignettes/plot-fig-Mscale.pdf |binary vignettes/plot-fig-cpr.pdf |binary vignettes/plot-fig-efficiency-all.pdf |binary vignettes/plot-fig-efficiency.pdf |binary vignettes/plot-fig-emp-level.pdf |binary vignettes/plot-fig-example-design.pdf |binary vignettes/plot-fig-lqq-level.pdf |binary vignettes/plot-fig-max-asymptotic-bias.pdf |binary vignettes/plot-fig-meanscale.pdf |binary vignettes/plot-fig-power-1-0_2.pdf |binary vignettes/plot-fig-power-1-0_4.pdf |binary vignettes/plot-fig-power-1-0_6.pdf |binary vignettes/plot-fig-power-1-0_8.pdf |binary vignettes/plot-fig-power-1-1.pdf |binary vignettes/plot-fig-psi-functions.pdf |binary vignettes/plot-fig-qscale-all.pdf |binary vignettes/plot-fig-qscale.pdf |binary vignettes/plot-fig-sdAdB2-1.pdf |binary vignettes/plot-fig-sdscale-1.pdf |binary vignettes/plot-fig-sdscale-all.pdf |binary vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary 55 files changed, 418 insertions(+), 355 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a platform for the implementation of new inference methods.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 1.4.1.1 dated 2016-03-28 and 1.5 dated 2016-05-31
DESCRIPTION | 10 MD5 | 174 ++++- NAMESPACE | 200 +++--- R/example.R | 78 +- R/generics.R | 2 R/initstate_pomp.R | 9 R/mif.R | 316 +++++++-- R/mif2.R | 79 +- R/mif2_methods.R | 368 +++++------ R/mif_methods.R | 40 - R/pfilter.R | 765 ++++++++++------------- R/pmcmc.R | 2 R/pomp.R | 197 +++++- build/partial.rdb |binary data/LondonYorke.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary demo/gompertz.R | 6 demo/logistic.R | 86 +- demo/rw2.R | 2 demo/sir.R | 9 inst/NEWS | 1352 +----------------------------------------- inst/NEWS.Rd | 953 ----------------------------- inst/examples/bbs.R | 5 inst/examples/blowflies.R | 2 inst/examples/dacca.R | 2 inst/examples/euler.sir.R | 5 inst/examples/gillespie.sir.R | 5 inst/examples/gompertz.R | 5 inst/examples/ou2.R | 5 inst/examples/ricker.R | 5 inst/examples/rw2.R | 2 man/blowflies.Rd | 4 man/example.Rd | 7 man/lowlevel.Rd | 9 man/mif.Rd | 35 - man/mif2.Rd | 2 man/pfilter.Rd | 21 man/pmcmc.Rd | 2 man/pomp.Rd | 102 ++- src/initstate.c | 28 src/mif2.c | 7 src/pfilter.c | 75 -- src/pomp_internal.h | 3 src/resample.c |only src/simulate.c | 51 - tests |only 47 files changed, 1566 insertions(+), 3464 deletions(-)
Title: Trend Classification Algorithm
Description: This algorithm classifies the trends into linear, quadratic, cubic, concealed and no-trend types. The "concealed trends" are those trends that possess quadratic or cubic forms, but the net change from the start of the time period to the end of the time period hasn't been significant. The "no-trend" category includes simple linear trends with statistically in-significant slope coefficient.
Author: Sadegh Jamali, Hristo Tomov
Maintainer: Hristo Tomov <tomov.hristo@gmail.com>
Diff between PolyTrend versions 1.1 dated 2016-05-12 and 1.2 dated 2016-05-31
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- R/plot.PolyTrend.R | 10 ++++++++-- data/ex.d.rda |binary data/ex.e.rda |binary man/PolyTrend.Rd | 51 ++++++++++++++++++++++----------------------------- man/ex.a.Rd | 2 +- man/ex.b.Rd | 2 +- man/ex.c.Rd | 4 ++-- man/ex.d.Rd | 8 ++++---- man/ex.e.Rd | 8 ++++---- man/ex.f.Rd | 2 +- man/ex.g.Rd | 4 ++-- man/ex.h.Rd | 4 ++-- man/ex.k.Rd | 2 +- man/ex.m.Rd | 2 +- man/ex.n.Rd | 2 +- 17 files changed, 71 insertions(+), 72 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb],
Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.10 dated 2016-04-12 and 0.2.11 dated 2016-05-31
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 19 ++++++++++++++++++- R/forceNetwork.R | 8 ++++++-- R/sankeyNetwork.R | 11 +++++++++-- R/simpleNetwork.R | 9 ++++++--- R/utils.R | 24 +++++++++++++++++++++++- README.md | 2 +- inst/htmlwidgets/diagonalNetwork.js | 8 +++++++- inst/htmlwidgets/lib/sankey.js | 10 ++++++++++ inst/htmlwidgets/radialNetwork.js | 10 ++++++++-- inst/htmlwidgets/sankeyNetwork.js | 13 ++++++++++--- man/sankeyNetwork.Rd | 6 +++++- 13 files changed, 119 insertions(+), 33 deletions(-)
Title: Multi-Level Vector Autoregression
Description: Compute estimates of the multivariate vector autoregression model as
introduced by Bringmann et al. (2013) which can be extended through treatment effects,
covariates and pre- and post-assessment effects.
Author: Sacha Epskamp, Marie K. Deserno and Laura F. Bringmann
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between mlVAR versions 0.1.0 dated 2015-06-10 and 0.3.0 dated 2016-05-31
mlVAR-0.1.0/mlVAR/man/plotMethod.Rd |only mlVAR-0.1.0/mlVAR/man/printsummary.Rd |only mlVAR-0.3.0/mlVAR/DESCRIPTION | 12 mlVAR-0.3.0/mlVAR/MD5 | 44 +- mlVAR-0.3.0/mlVAR/NAMESPACE | 34 + mlVAR-0.3.0/mlVAR/NEWS |only mlVAR-0.3.0/mlVAR/R/Bayes_mlVAR.R |only mlVAR-0.3.0/mlVAR/R/JAGSmodels.R |only mlVAR-0.3.0/mlVAR/R/NodeWise.R |only mlVAR-0.3.0/mlVAR/R/S3Methods.R | 554 ++++++++++++++++++++++++++++--- mlVAR-0.3.0/mlVAR/R/S3Methods0.R |only mlVAR-0.3.0/mlVAR/R/effects.R | 98 ++++- mlVAR-0.3.0/mlVAR/R/leastSquares_mlVAR.R |only mlVAR-0.3.0/mlVAR/R/lmer_murmur.R |only mlVAR-0.3.0/mlVAR/R/mlVAR.R | 400 +++++++++++++--------- mlVAR-0.3.0/mlVAR/R/mlVAR0.R |only mlVAR-0.3.0/mlVAR/R/mlVARcompare.R |only mlVAR-0.3.0/mlVAR/R/mlVARmodel.R |only mlVAR-0.3.0/mlVAR/R/modelMatrix.R |only mlVAR-0.3.0/mlVAR/R/movingWindow.R |only mlVAR-0.3.0/mlVAR/R/simulateVAR.R | 89 ++++ mlVAR-0.3.0/mlVAR/R/stepWise.R |only mlVAR-0.3.0/mlVAR/inst/COPYRIGHTS | 2 mlVAR-0.3.0/mlVAR/man/fixedEffects.Rd | 11 mlVAR-0.3.0/mlVAR/man/getNet.Rd |only mlVAR-0.3.0/mlVAR/man/mlVAR.Rd | 192 +++++----- mlVAR-0.3.0/mlVAR/man/mlVAR0.Rd |only mlVAR-0.3.0/mlVAR/man/mlVARcompare.Rd |only mlVAR-0.3.0/mlVAR/man/mlVARsim.Rd |only mlVAR-0.3.0/mlVAR/man/mlVARsim0.Rd |only mlVAR-0.3.0/mlVAR/man/plot.mlVAR.Rd |only mlVAR-0.3.0/mlVAR/man/plotMethod0.Rd |only mlVAR-0.3.0/mlVAR/man/printsummary0.Rd |only mlVAR-0.3.0/mlVAR/man/simulateVAR.Rd | 13 mlVAR-0.3.0/mlVAR/man/summary.mlVAR.Rd |only 35 files changed, 1116 insertions(+), 333 deletions(-)
Title: Mandallaz' Model-Assisted Small Area Estimators
Description: An S4 implementation of the unbiased extension of the model-
assisted synthetic-regression estimator proposed by
Mandallaz (2013) <DOI:10.1139/cjfr-2012-0381>,
Mandallaz et al. (2013) <DOI:10.1139/cjfr-2013-0181> and
Mandallaz (2014) <DOI:10.1139/cjfr-2013-0449>.
It yields smaller variances than the standard bias correction,
the generalised regression estimator.
Author: Andreas Dominik Cullmann [aut, cre],
Daniel Mandallaz [ctb],
Alexander Francis Massey [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_masae@arcor.de>
Diff between maSAE versions 0.1-4 dated 2016-02-26 and 0.1-5 dated 2016-05-31
DESCRIPTION | 17 ++++---- MD5 | 14 +++---- README.md | 2 - build/vignette.rds |binary inst/doc/maSAE.R | 101 ++++++++++++++++++++++++---------------------------- inst/doc/maSAE.Rnw | 85 ++++++++++++++++++++----------------------- inst/doc/maSAE.pdf |binary vignettes/maSAE.Rnw | 85 ++++++++++++++++++++----------------------- 8 files changed, 144 insertions(+), 160 deletions(-)
Title: Multiple Class Area under ROC Curve
Description: An S4 implementation of Eq. (3) and Eq. (7) by David J. Hand and
Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
Author: Andreas Dominik Cullmann [aut, cre],
Edgar Kublin [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_handtill2001@arcor.de>
Diff between HandTill2001 versions 0.2-11 dated 2016-02-24 and 0.2-12 dated 2016-05-31
DESCRIPTION | 21 ++---- MD5 | 12 +-- build/vignette.rds |binary inst/doc/consensus_auc.R | 154 +++++++++++++++++++------------------------- inst/doc/consensus_auc.Rnw | 128 ++++++++++++++++-------------------- inst/doc/consensus_auc.pdf |binary vignettes/consensus_auc.Rnw | 128 ++++++++++++++++-------------------- 7 files changed, 196 insertions(+), 247 deletions(-)
Title: Functions to Calculate Relatedness on Diploid Genetic Data
Description: Functions to calculate pairwise relatedness on diploid genetic datasets. Different estimators for relatedness can be combined with information on geographical distances. Information on heterozygosity, allele- and genotype diversity as well as genetic F-statistics are provided for each population.
Author: Philipp Kraemer [aut, cre],
Gabriele Gerlach [aut]
Maintainer: Philipp Kraemer <Philipp.Kraemer@uni-oldenburg.de>
Diff between Demerelate versions 0.8-1 dated 2013-12-17 and 0.9 dated 2016-05-31
Demerelate-0.8-1/Demerelate/R/emp.calc.R |only Demerelate-0.8-1/Demerelate/R/queller.R |only Demerelate-0.8-1/Demerelate/man/demereldist.Rd |only Demerelate-0.8-1/Demerelate/man/demerelpop.Rd |only Demerelate-0.8-1/Demerelate/man/demerelref.Rd |only Demerelate-0.8-1/Demerelate/man/emp.calc.Rd |only Demerelate-0.8-1/Demerelate/man/queller.Rd |only Demerelate-0.9/Demerelate/DESCRIPTION | 18 - Demerelate-0.9/Demerelate/MD5 | 83 +++--- Demerelate-0.9/Demerelate/NAMESPACE | 10 Demerelate-0.9/Demerelate/R/Bxy.R |only Demerelate-0.9/Demerelate/R/Demerelate.R | 78 +++-- Demerelate-0.9/Demerelate/R/Emp.calc.R |only Demerelate-0.9/Demerelate/R/Fis.calc.R | 44 +-- Demerelate-0.9/Demerelate/R/Li.R |only Demerelate-0.9/Demerelate/R/Lin.reg.distance.R | 44 ++- Demerelate-0.9/Demerelate/R/Loci.test.R | 138 ++++++++-- Demerelate-0.9/Demerelate/R/Mxy.R |only Demerelate-0.9/Demerelate/R/Sxy.R |only Demerelate-0.9/Demerelate/R/allele.sharing.R | 149 +++------- Demerelate-0.9/Demerelate/R/glm.prep.R | 2 Demerelate-0.9/Demerelate/R/loiselle.R |only Demerelate-0.9/Demerelate/R/loiselle.w.R |only Demerelate-0.9/Demerelate/R/lxy.R |only Demerelate-0.9/Demerelate/R/lxy.w.R |only Demerelate-0.9/Demerelate/R/morans.R |only Demerelate-0.9/Demerelate/R/morans.fin.R |only Demerelate-0.9/Demerelate/R/morans.fin.w.R |only Demerelate-0.9/Demerelate/R/morans.w.R |only Demerelate-0.9/Demerelate/R/random.pairs.R | 5 Demerelate-0.9/Demerelate/R/relate.calc.R | 228 ++++++++++++++-- Demerelate-0.9/Demerelate/R/ritland.R |only Demerelate-0.9/Demerelate/R/ritland.w.R |only Demerelate-0.9/Demerelate/R/rxy.R |only Demerelate-0.9/Demerelate/R/stat.pops.R | 276 ++++++++++++++------ Demerelate-0.9/Demerelate/R/wang.R |only Demerelate-0.9/Demerelate/R/wang.compose.R |only Demerelate-0.9/Demerelate/R/wang.fin.R |only Demerelate-0.9/Demerelate/R/wang.fin.w.R |only Demerelate-0.9/Demerelate/R/wang.w.R |only Demerelate-0.9/Demerelate/man/Demerelate-package.Rd | 73 +++-- Demerelate-0.9/Demerelate/man/Demerelate.Rd | 52 ++- Demerelate-0.9/Demerelate/man/Emp.calc.Rd |only Demerelate-0.9/Demerelate/man/Example.Data.Rd |only Demerelate-0.9/Demerelate/man/F.stat.Rd | 4 Demerelate-0.9/Demerelate/man/Fis.Rd | 4 Demerelate-0.9/Demerelate/man/Fis.calc.Rd | 16 - Demerelate-0.9/Demerelate/man/Lin.reg.distance.Rd | 10 Demerelate-0.9/Demerelate/man/Loci.test.Rd | 39 ++ Demerelate-0.9/Demerelate/man/Similarity.Index.Rd |only Demerelate-0.9/Demerelate/man/allele.sharing.Rd | 40 +- Demerelate-0.9/Demerelate/man/geo.dist.Rd | 6 Demerelate-0.9/Demerelate/man/glm.prep.Rd | 2 Demerelate-0.9/Demerelate/man/input.txt.Rd | 2 Demerelate-0.9/Demerelate/man/offspring.Rd | 4 Demerelate-0.9/Demerelate/man/relate.calc.Rd | 9 Demerelate-0.9/Demerelate/man/stat.pops.Rd | 9 Demerelate-0.9/Demerelate/man/weir.Rd | 2 58 files changed, 901 insertions(+), 446 deletions(-)
Title: Summaries and Population Structure Analyses of Genetic Data
Description: A toolkit for analyzing stratified population genetic data.
Author: Eric Archer [aut, cre],
Paula Adams [aut],
Brita Schneiders [aut]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between strataG versions 1.0.3 dated 2016-04-04 and 1.0.5 dated 2016-05-31
strataG-1.0.3/strataG/R/arlequin.R |only strataG-1.0.3/strataG/R/gtypes2df.R |only strataG-1.0.3/strataG/R/internals.R |only strataG-1.0.3/strataG/R/jmodeltest.R |only strataG-1.0.3/strataG/R/parseLocusNames.R |only strataG-1.0.3/strataG/man/arlequin.Rd |only strataG-1.0.3/strataG/man/exptdNumAlleles.Rd |only strataG-1.0.3/strataG/man/gtypes2df.Rd |only strataG-1.0.3/strataG/man/jmodeltest.Rd |only strataG-1.0.3/strataG/man/parseLocusNames.Rd |only strataG-1.0.5/strataG/DESCRIPTION | 42 +- strataG-1.0.5/strataG/MD5 | 265 +++++++-------- strataG-1.0.5/strataG/NAMESPACE | 17 strataG-1.0.5/strataG/R/LDgenepop.R | 12 strataG-1.0.5/strataG/R/alleleFreqFormat.R | 9 strataG-1.0.5/strataG/R/alleleFreqs.R | 8 strataG-1.0.5/strataG/R/alleleSplit.R | 84 +++- strataG-1.0.5/strataG/R/allelicRichness.R | 2 strataG-1.0.5/strataG/R/as.data.frame.gtypes.R |only strataG-1.0.5/strataG/R/as.matrix.gtypes.R | 86 +++- strataG-1.0.5/strataG/R/as.multidna.R | 13 strataG-1.0.5/strataG/R/baseFreqs.R | 13 strataG-1.0.5/strataG/R/createConsensus.R | 6 strataG-1.0.5/strataG/R/df2gtypes.R | 14 strataG-1.0.5/strataG/R/dupGenotypes.R | 13 strataG-1.0.5/strataG/R/evanno.R | 15 strataG-1.0.5/strataG/R/expectedNumAlleles.R | 13 strataG-1.0.5/strataG/R/fasta.R | 11 strataG-1.0.5/strataG/R/fastsimcoal.R | 43 ++ strataG-1.0.5/strataG/R/fastsimcoal.input.R | 14 strataG-1.0.5/strataG/R/fixedDifferences.R | 13 strataG-1.0.5/strataG/R/freq2GenData.R | 13 strataG-1.0.5/strataG/R/fstToNm.R | 7 strataG-1.0.5/strataG/R/gelato.R | 33 - strataG-1.0.5/strataG/R/genepop.R | 35 + strataG-1.0.5/strataG/R/gtypes.accessors.R | 77 ++-- strataG-1.0.5/strataG/R/gtypes.class.R | 2 strataG-1.0.5/strataG/R/gtypes2genind.R | 47 +- strataG-1.0.5/strataG/R/gtypes2loci.R | 24 - strataG-1.0.5/strataG/R/gtypes2phyDat.R |only strataG-1.0.5/strataG/R/haplotypeLikelihoods.R | 3 strataG-1.0.5/strataG/R/heterozygosity.R | 12 strataG-1.0.5/strataG/R/hweTest.R | 4 strataG-1.0.5/strataG/R/idRows.R | 53 +-- strataG-1.0.5/strataG/R/initialize.gtypes.R | 4 strataG-1.0.5/strataG/R/is.gtypes.R |only strataG-1.0.5/strataG/R/jackHWE.R | 32 - strataG-1.0.5/strataG/R/labelHaplotypes.R | 65 +-- strataG-1.0.5/strataG/R/mRatio.R | 2 strataG-1.0.5/strataG/R/mafft.R | 6 strataG-1.0.5/strataG/R/mega.R | 31 - strataG-1.0.5/strataG/R/nucleotideDiversity.R | 14 strataG-1.0.5/strataG/R/numAlleles.R | 2 strataG-1.0.5/strataG/R/numGensEq.R | 9 strataG-1.0.5/strataG/R/popStructStat.R | 2 strataG-1.0.5/strataG/R/popStructTest.R | 28 - strataG-1.0.5/strataG/R/privateAlleles.R | 5 strataG-1.0.5/strataG/R/propUniqueAlleles.R | 11 strataG-1.0.5/strataG/R/qaqc.R | 14 strataG-1.0.5/strataG/R/readGenData.R | 4 strataG-1.0.5/strataG/R/sequence2gtypes.R | 4 strataG-1.0.5/strataG/R/sharedLoci.R | 24 - strataG-1.0.5/strataG/R/simGammaHaps.R | 2 strataG-1.0.5/strataG/R/strataG-internal.R |only strataG-1.0.5/strataG/R/strataSplit.R | 7 strataG-1.0.5/strataG/R/stratify.R | 19 - strataG-1.0.5/strataG/R/structure.R | 33 + strataG-1.0.5/strataG/R/summarizeLoci.R | 18 - strataG-1.0.5/strataG/R/summary.gtypes.R | 46 +- strataG-1.0.5/strataG/R/tajimasD.R | 5 strataG-1.0.5/strataG/R/theta.R | 5 strataG-1.0.5/strataG/R/trimNs.R | 22 + strataG-1.0.5/strataG/R/validIupacCodes.R | 3 strataG-1.0.5/strataG/R/variableSites.R | 7 strataG-1.0.5/strataG/R/wrightFst.R | 7 strataG-1.0.5/strataG/R/write.arlequin.R |only strataG-1.0.5/strataG/R/write.gtypes.R | 58 ++- strataG-1.0.5/strataG/README.md | 10 strataG-1.0.5/strataG/build/vignette.rds |binary strataG-1.0.5/strataG/inst/doc/external.programs.html | 4 strataG-1.0.5/strataG/inst/doc/gtypes.html | 78 ++-- strataG-1.0.5/strataG/inst/doc/population.structure.html | 34 - strataG-1.0.5/strataG/inst/doc/qaqc.html | 74 ++-- strataG-1.0.5/strataG/inst/doc/sequences.html | 54 +-- strataG-1.0.5/strataG/inst/doc/summaries.html | 4 strataG-1.0.5/strataG/inst/extdata |only strataG-1.0.5/strataG/man/LDgenepop.Rd | 14 strataG-1.0.5/strataG/man/alleleFreqFormat.Rd | 8 strataG-1.0.5/strataG/man/alleleFreqs.Rd | 7 strataG-1.0.5/strataG/man/alleleSplit.Rd | 36 +- strataG-1.0.5/strataG/man/as.data.frame.gtypes.Rd |only strataG-1.0.5/strataG/man/as.matrix-gtypes-method.Rd | 31 + strataG-1.0.5/strataG/man/as.multidna.Rd | 15 strataG-1.0.5/strataG/man/baseFreqs.Rd | 13 strataG-1.0.5/strataG/man/df2gtypes.Rd | 4 strataG-1.0.5/strataG/man/dupGenotypes.Rd | 8 strataG-1.0.5/strataG/man/evanno.Rd | 15 strataG-1.0.5/strataG/man/expectedNumAlleles.Rd |only strataG-1.0.5/strataG/man/fasta.Rd | 8 strataG-1.0.5/strataG/man/fastsimcoal.Rd | 36 ++ strataG-1.0.5/strataG/man/fixedDifferences.Rd | 14 strataG-1.0.5/strataG/man/freq2GenData.Rd | 8 strataG-1.0.5/strataG/man/fstToNm.Rd | 9 strataG-1.0.5/strataG/man/gelato.Rd | 9 strataG-1.0.5/strataG/man/genepop.Rd | 33 + strataG-1.0.5/strataG/man/gtypes.accessors.Rd | 46 +- strataG-1.0.5/strataG/man/gtypes2genind.Rd | 17 strataG-1.0.5/strataG/man/gtypes2loci.Rd | 17 strataG-1.0.5/strataG/man/gtypes2phyDat.Rd |only strataG-1.0.5/strataG/man/heterozygosity.Rd | 3 strataG-1.0.5/strataG/man/hweTest.Rd | 5 strataG-1.0.5/strataG/man/idRows.Rd | 31 + strataG-1.0.5/strataG/man/initialize-gtypes-method.Rd | 2 strataG-1.0.5/strataG/man/is.gtypes.Rd |only strataG-1.0.5/strataG/man/jackHWE.Rd | 18 - strataG-1.0.5/strataG/man/labelHaplotypes.Rd | 37 +- strataG-1.0.5/strataG/man/mafft.Rd | 8 strataG-1.0.5/strataG/man/mega.Rd | 17 strataG-1.0.5/strataG/man/nucleotideDiversity.Rd | 5 strataG-1.0.5/strataG/man/numAlleles.Rd | 2 strataG-1.0.5/strataG/man/numGensEq.Rd | 11 strataG-1.0.5/strataG/man/popStructTest.Rd | 26 - strataG-1.0.5/strataG/man/privateAlleles.Rd | 6 strataG-1.0.5/strataG/man/propUniqueAlleles.Rd | 12 strataG-1.0.5/strataG/man/qaqc.Rd | 14 strataG-1.0.5/strataG/man/sequence2gtypes.Rd | 4 strataG-1.0.5/strataG/man/sharedLoci.Rd | 5 strataG-1.0.5/strataG/man/strataG-internal.Rd |only strataG-1.0.5/strataG/man/strataSplit.Rd | 8 strataG-1.0.5/strataG/man/stratify.Rd | 20 - strataG-1.0.5/strataG/man/structure.Rd | 26 - strataG-1.0.5/strataG/man/summarizeLoci.Rd | 18 - strataG-1.0.5/strataG/man/summary-gtypes-method.Rd | 24 - strataG-1.0.5/strataG/man/tajimasD.Rd | 6 strataG-1.0.5/strataG/man/theta.Rd | 6 strataG-1.0.5/strataG/man/trimNs.Rd | 15 strataG-1.0.5/strataG/man/validIupacCodes.Rd | 3 strataG-1.0.5/strataG/man/variableSites.Rd | 7 strataG-1.0.5/strataG/man/wrightFst.Rd | 9 strataG-1.0.5/strataG/man/write.arlequin.Rd |only strataG-1.0.5/strataG/man/write.gtypes.Rd | 29 + strataG-1.0.5/strataG/vignettes/external.programs.Rmd | 2 strataG-1.0.5/strataG/vignettes/gtypes.Rmd | 20 + strataG-1.0.5/strataG/vignettes/msats.csv |only strataG-1.0.5/strataG/vignettes/summaries.Rmd | 2 145 files changed, 1614 insertions(+), 885 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 2.0 dated 2016-03-03 and 2.0.1 dated 2016-05-31
rfPermute-2.0.1/rfPermute/DESCRIPTION | 18 +++-- rfPermute-2.0.1/rfPermute/MD5 | 20 +++--- rfPermute-2.0.1/rfPermute/NAMESPACE | 18 ++++- rfPermute-2.0.1/rfPermute/R/impHeatmap.R |only rfPermute-2.0.1/rfPermute/R/plot.rfPermute.R | 3 rfPermute-2.0.1/rfPermute/R/proximity.plot.r | 78 ++++++++++++++++-------- rfPermute-2.0.1/rfPermute/R/rfPermute.R | 5 - rfPermute-2.0.1/rfPermute/R/rfPermute.default.R | 12 ++- rfPermute-2.0.1/rfPermute/README.md |only rfPermute-2.0.1/rfPermute/man/impHeatmap.Rd |only rfPermute-2.0.1/rfPermute/man/proximity.plot.Rd | 25 +++++-- rfPermute-2.0.1/rfPermute/man/rfPermute.Rd | 5 - rfPermute-2.0/rfPermute/NEWS.md |only 13 files changed, 123 insertions(+), 61 deletions(-)
Title: Efficient Iterator for Permutations and Combinations
Description: A collection of iterators for generating permutations and combinations with or
without replacement; with distinct items or non-distinct items (multiset).
The generated sequences are in lexicographical order (dictionary order). The
algorithms to generate permutations and combinations are memory efficient. These
iterative algorithms enable users to process all sequences without putting all
results in the memory at the same time. The algorithms are written in C/C++ for
faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.2.9-1 dated 2016-04-20 and 0.3.0 dated 2016-05-31
DESCRIPTION | 15 +++--- MD5 | 34 +++++++------- NAMESPACE | 2 R/combination.R | 16 +++--- R/iterator.R | 38 ++++++++++------ R/permutation.R | 20 ++++---- R/utilities.R | 87 ++++++++++++++++++++++++++++---------- README.md | 2 man/getlength.Rd | 10 +++- man/iterpc.Rd | 2 man/multichoose.Rd | 7 +-- man/nc_multiset.Rd | 6 +- man/np_multiset.Rd | 6 +- src/combination.cpp | 6 +- src/mbcomb/Makefile | 5 -- src/permutation.cpp | 6 +- tests/testthat/test-combination.R | 36 +++++++-------- tests/testthat/test-permutation.R | 35 ++++++++------- 18 files changed, 200 insertions(+), 133 deletions(-)