Title: Submit R Calculations to a 'SLURM' Cluster
Description: Functions that simplify submitting R scripts to a 'SLURM' cluster
workload manager, in part by automating the division of embarrassingly parallel
calculations across cluster nodes.
Author: Philippe Marchand [aut],
Mike Smorul [ctb],
Ian Carroll [ctb, cre]
Maintainer: Ian Carroll <icarroll@sesync.org>
Diff between rslurm versions 0.3.2 dated 2017-04-07 and 0.3.3 dated 2017-04-09
rslurm-0.3.2/rslurm/NEWS.md |only rslurm-0.3.2/rslurm/inst/doc/overview.R |only rslurm-0.3.2/rslurm/inst/doc/overview.Rmd |only rslurm-0.3.2/rslurm/inst/doc/overview.html |only rslurm-0.3.2/rslurm/vignettes/overview.Rmd |only rslurm-0.3.3/rslurm/DESCRIPTION | 12 ++-- rslurm-0.3.3/rslurm/MD5 | 20 +++---- rslurm-0.3.3/rslurm/R/rslurm.R | 14 +---- rslurm-0.3.3/rslurm/README.md | 73 +++++++++++++++++++++++++++-- rslurm-0.3.3/rslurm/build/vignette.rds |binary rslurm-0.3.3/rslurm/inst/NEWS.Rd |only rslurm-0.3.3/rslurm/inst/doc/rslurm.R |only rslurm-0.3.3/rslurm/inst/doc/rslurm.Rmd |only rslurm-0.3.3/rslurm/inst/doc/rslurm.html |only rslurm-0.3.3/rslurm/man/rslurm-package.Rd | 37 +++++++++++++- rslurm-0.3.3/rslurm/vignettes/rslurm.Rmd |only 16 files changed, 122 insertions(+), 34 deletions(-)
Title: Estimate Procedure in Case of First Order Autocorrelation
Description: Solve first order autocorrelation problems using an iterative method. This procedure estimates both autocorrelation and beta coefficients recursively until we reach the convergence (8th decimal). The residuals are computed after estimating Beta using EGLS approach and Rho is estimated using the previous residuals.
Author: Stefano Spada [aut, cre],
Matteo Quartagno [ctb],
Marco Tamburini [ctb],
David Robinson [ctb]
Maintainer: Stefano Spada <lostefanospada@gmail.com>
Diff between orcutt versions 2.0 dated 2017-01-28 and 2.1 dated 2017-04-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/cochrane.orcutt.R | 12 +++++++----- data/icecream.rda |binary man/orcutt-package.Rd | 4 ++-- 5 files changed, 17 insertions(+), 15 deletions(-)
Title: Miscellaneous Esoteric Statistical Scripts
Description: A mixed collection of useful and semi-useful diverse
statistical functions, some of which may even be referenced in
The R Primer book.
Author: Claus Thorn Ekstrøm <claus@rprimer.dk>
Maintainer: Claus Ekstrøm <claus@rprimer.dk>
Diff between MESS versions 0.4-3 dated 2016-06-21 and 0.4-15 dated 2017-04-09
MESS-0.4-15/MESS/DESCRIPTION | 19 +-- MESS-0.4-15/MESS/MD5 | 171 ++++++++++++++++------------- MESS-0.4-15/MESS/NAMESPACE | 18 ++- MESS-0.4-15/MESS/R/MESS-package.R | 18 +-- MESS-0.4-15/MESS/R/RcppExports.R | 55 ++++++++- MESS-0.4-15/MESS/R/adaptive.weights.R | 7 - MESS-0.4-15/MESS/R/categorize.R |only MESS-0.4-15/MESS/R/drop1.geeglm.R | 161 ++++++++++++++++----------- MESS-0.4-15/MESS/R/expand.R |only MESS-0.4-15/MESS/R/fac2num.R | 10 - MESS-0.4-15/MESS/R/power.binom.test.R | 122 ++++---------------- MESS-0.4-15/MESS/R/power.mcnemar.test.R | 64 +++++----- MESS-0.4-15/MESS/R/power.t.test.R | 6 - MESS-0.4-15/MESS/R/prepost.R |only MESS-0.4-15/MESS/R/qic.R | 11 + MESS-0.4-15/MESS/R/residualplot.R | 6 - MESS-0.4-15/MESS/R/round_percent.R |only MESS-0.4-15/MESS/R/screener.R |only MESS-0.4-15/MESS/R/wallyplot.R | 5 MESS-0.4-15/MESS/R/writexml.R | 2 MESS-0.4-15/MESS/README.md |only MESS-0.4-15/MESS/build |only MESS-0.4-15/MESS/data/superroot2.rda |binary MESS-0.4-15/MESS/inst |only MESS-0.4-15/MESS/man/MESS.Rd | 10 - MESS-0.4-15/MESS/man/QIC.Rd | 22 ++- MESS-0.4-15/MESS/man/adaptive.weights.Rd | 12 +- MESS-0.4-15/MESS/man/age.Rd | 7 - MESS-0.4-15/MESS/man/auc.Rd | 7 - MESS-0.4-15/MESS/man/bdstat.Rd | 6 - MESS-0.4-15/MESS/man/bees.Rd | 1 MESS-0.4-15/MESS/man/categorize.Rd |only MESS-0.4-15/MESS/man/clotting.Rd | 1 MESS-0.4-15/MESS/man/cmd.Rd | 7 - MESS-0.4-15/MESS/man/col.alpha.Rd | 7 - MESS-0.4-15/MESS/man/col.shade.Rd | 7 - MESS-0.4-15/MESS/man/col.tint.Rd | 7 - MESS-0.4-15/MESS/man/common.shared.Rd | 9 - MESS-0.4-15/MESS/man/drop1.geeglm.Rd | 9 - MESS-0.4-15/MESS/man/drop1.geem.Rd |only MESS-0.4-15/MESS/man/earthquakes.Rd | 3 MESS-0.4-15/MESS/man/expand_table.Rd |only MESS-0.4-15/MESS/man/extended.shared.Rd | 9 - MESS-0.4-15/MESS/man/fac2num.Rd | 11 - MESS-0.4-15/MESS/man/feature.test.Rd | 9 - MESS-0.4-15/MESS/man/filldown.Rd | 1 MESS-0.4-15/MESS/man/geekin.Rd | 7 - MESS-0.4-15/MESS/man/gkgamma.Rd | 7 - MESS-0.4-15/MESS/man/greenland.Rd | 1 MESS-0.4-15/MESS/man/happiness.Rd | 1 MESS-0.4-15/MESS/man/ht.Rd | 1 MESS-0.4-15/MESS/man/icecreamads.Rd | 1 MESS-0.4-15/MESS/man/kwdata.Rd | 1 MESS-0.4-15/MESS/man/lifeexpect.Rd | 3 MESS-0.4-15/MESS/man/lower.tri.vector.Rd | 7 - MESS-0.4-15/MESS/man/matched.Rd | 1 MESS-0.4-15/MESS/man/mfastLmCpp.Rd |only MESS-0.4-15/MESS/man/nh4.Rd | 1 MESS-0.4-15/MESS/man/onemargintest.Rd |only MESS-0.4-15/MESS/man/ordered.clusters.Rd | 7 - MESS-0.4-15/MESS/man/panel.hist.Rd | 7 - MESS-0.4-15/MESS/man/panel.r2.Rd | 7 - MESS-0.4-15/MESS/man/picea.Rd | 1 MESS-0.4-15/MESS/man/power_binom_test.Rd |only MESS-0.4-15/MESS/man/power_mcnemar_test.Rd |only MESS-0.4-15/MESS/man/power_t_test.Rd |only MESS-0.4-15/MESS/man/prepost.test.Rd |only MESS-0.4-15/MESS/man/qdiag.Rd | 1 MESS-0.4-15/MESS/man/qpcr.Rd | 1 MESS-0.4-15/MESS/man/quadform.Rd | 1 MESS-0.4-15/MESS/man/rainman.Rd | 1 MESS-0.4-15/MESS/man/repmat.Rd | 8 + MESS-0.4-15/MESS/man/residualplot.Rd | 17 +- MESS-0.4-15/MESS/man/rmvt.pedigree.Rd | 7 - MESS-0.4-15/MESS/man/rmvtnorm.pedigree.Rd | 7 - MESS-0.4-15/MESS/man/rootonorm.Rd | 9 - MESS-0.4-15/MESS/man/round_percent.Rd |only MESS-0.4-15/MESS/man/scorefct.Rd | 1 MESS-0.4-15/MESS/man/screen_variables.Rd |only MESS-0.4-15/MESS/man/segregate.genes.Rd | 7 - MESS-0.4-15/MESS/man/sinv.Rd | 1 MESS-0.4-15/MESS/man/smokehealth.Rd | 1 MESS-0.4-15/MESS/man/soccer.Rd | 1 MESS-0.4-15/MESS/man/superroot2.Rd | 1 MESS-0.4-15/MESS/man/tracemp.Rd | 7 + MESS-0.4-15/MESS/man/wallyplot.Rd | 16 +- MESS-0.4-15/MESS/man/write.xml.Rd | 3 MESS-0.4-15/MESS/src/MESS_init.c |only MESS-0.4-15/MESS/src/RcppExports.cpp | 78 +++++++------ MESS-0.4-15/MESS/src/mfastLm.cpp | 23 +++ MESS-0.4-15/MESS/src/onemargin.cpp |only MESS-0.4-15/MESS/src/repmat.cpp | 6 + MESS-0.4-15/MESS/src/trace.cpp | 5 MESS-0.4-15/MESS/vignettes |only MESS-0.4-3/MESS/man/mfastLm_cpp.Rd |only MESS-0.4-3/MESS/man/power.binom.test.Rd |only MESS-0.4-3/MESS/man/power.mcnemar.test.Rd |only MESS-0.4-3/MESS/man/power.t.test.Rd |only 98 files changed, 558 insertions(+), 517 deletions(-)
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. Alternating optimization is
an iterative process where the genetic score weights, the environmental score weights,
and the main model parameters are estimated in turn assuming the other parameters to
be constant. This approach has greatly enhanced predictive power over traditional GxE
models which include only a single genetic variant and a single environmental
exposure. Gene x gene interactions (GxG) and environment x environment interactions
(ExE) can be incorporated into the genetic and environmental scores. Any standard
model formula can be used, it doesn't have to be a two-way interaction model.
Although this approach was made for GxE modelling, the genetic score doesn't need to
contain genetic variables and the environmental score doesn't need to contain
environmental variables, therefore this approach is highly flexible.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.0.2 dated 2017-04-02 and 1.0.3 dated 2017-04-09
DESCRIPTION | 8 +- MD5 | 22 ++--- R/LEGIT.R | 183 ++++++++++++++++++++++++++++++++++--------------- inst/doc/LEGIT.Rmd | 1 inst/doc/LEGIT.html | 41 +++++++--- man/LEGIT.Rd | 2 man/LEGIT_cv.Rd | 11 ++ man/backward_step.Rd | 7 + man/forward_step.Rd | 6 - man/predict.LEGIT.Rd | 2 man/stepwise_search.Rd | 10 +- vignettes/LEGIT.Rmd | 1 12 files changed, 197 insertions(+), 97 deletions(-)
Title: Tables with Labels and Some Useful Functions from Spreadsheets
and 'SPSS' Statistics
Description: Package provides tabulation functions with support of 'SPSS'-style labels,
multiple / nested banners, weights and multiple-response variables.
Additionally it offers useful functions for data processing in the social /
marketing research surveys - popular data transformation functions from 'SPSS' Statistics
('RECODE', 'COUNT', 'COMPUTE', 'DO IF', etc.) and 'Excel' ('COUNTIF', 'VLOOKUP', etc.).
Proper methods for labelled variables add value labels support to base R and other packages.
Package aimed to help people to move data processing from 'Excel'/'SPSS' to R.
Author: Gregory Demin
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.5.5 dated 2016-10-18 and 0.7.1 dated 2017-04-09
expss-0.5.5/expss/R/f.R |only expss-0.5.5/expss/R/utils.R |only expss-0.5.5/expss/inst/doc/UsageExamples.R |only expss-0.5.5/expss/inst/doc/UsageExamples.Rmd |only expss-0.5.5/expss/inst/doc/UsageExamples.html |only expss-0.5.5/expss/man/category.Rd |only expss-0.5.5/expss/man/compute.Rd |only expss-0.5.5/expss/man/dichotomy.Rd |only expss-0.5.5/expss/man/f.Rd |only expss-0.5.5/expss/man/merge.simple_table.Rd |only expss-0.5.5/expss/man/vars_range.Rd |only expss-0.5.5/expss/tests/testthat/rds/elem_fre1.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre10.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre11.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre12.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre13.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre14.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre15.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre16.rds |only expss-0.5.5/expss/tests/testthat/rds/elem_fre17.rds |only 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|only expss-0.7.1/expss/R/add_rows.R | 75 expss-0.7.1/expss/R/apply_labels.R |only expss-0.7.1/expss/R/category.R | 173 +- expss-0.7.1/expss/R/common_table_utils.R |only expss-0.7.1/expss/R/count_if.R | 138 - expss-0.7.1/expss/R/criteria_functions.R | 194 +- expss-0.7.1/expss/R/cro.R |only expss-0.7.1/expss/R/cro_fun.R |only expss-0.7.1/expss/R/custom_tables.R |only expss-0.7.1/expss/R/deprecated.R |only expss-0.7.1/expss/R/dichotomy.R | 425 ++--- expss-0.7.1/expss/R/do_repeat.R |only expss-0.7.1/expss/R/drop_empty.R |only expss-0.7.1/expss/R/dtfrm.R | 4 expss-0.7.1/expss/R/expss.R | 49 expss-0.7.1/expss/R/expss_options.R |only expss-0.7.1/expss/R/fctr.R |only expss-0.7.1/expss/R/fre.R | 629 +------ expss-0.7.1/expss/R/grouping.R |only expss-0.7.1/expss/R/html_datatable.R |only expss-0.7.1/expss/R/html_table.R |only expss-0.7.1/expss/R/if_na.R | 4 expss-0.7.1/expss/R/if_val.R | 276 ++- expss-0.7.1/expss/R/info.R | 4 expss-0.7.1/expss/R/keep.R | 206 +- expss-0.7.1/expss/R/labels.R | 234 +- expss-0.7.1/expss/R/match.R | 10 expss-0.7.1/expss/R/merge.R | 134 + expss-0.7.1/expss/R/modify.R | 211 +- expss-0.7.1/expss/R/mrset.R |only expss-0.7.1/expss/R/na_if.R | 10 expss-0.7.1/expss/R/names2labels.R | 61 expss-0.7.1/expss/R/nest.R |only expss-0.7.1/expss/R/product_test.R | 2 expss-0.7.1/expss/R/prop.R | 2 expss-0.7.1/expss/R/qc.R | 54 expss-0.7.1/expss/R/read_spss.R | 6 expss-0.7.1/expss/R/ref.R | 26 expss-0.7.1/expss/R/selectors.R | 232 +- expss-0.7.1/expss/R/sort.R | 12 expss-0.7.1/expss/R/split_labels.R |only expss-0.7.1/expss/R/sum.R | 30 expss-0.7.1/expss/R/tab_sort.R |only expss-0.7.1/expss/R/values2labels.R | 9 expss-0.7.1/expss/R/vec_ops.R | 163 + expss-0.7.1/expss/R/vlookup.R | 7 expss-0.7.1/expss/R/weighted_stats.R |only expss-0.7.1/expss/R/where.R | 129 + expss-0.7.1/expss/R/window_fun.R |only expss-0.7.1/expss/R/write_labels.R | 203 +- expss-0.7.1/expss/R/zzz_experimental.R | 258 +-- expss-0.7.1/expss/build/vignette.rds |binary 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expss-0.7.1/expss/man/fre.Rd | 137 - expss-0.7.1/expss/man/htmlTable.etable.Rd |only expss-0.7.1/expss/man/if_na.Rd | 7 expss-0.7.1/expss/man/if_val.Rd | 107 - expss-0.7.1/expss/man/info.Rd | 3 expss-0.7.1/expss/man/keep.Rd | 46 expss-0.7.1/expss/man/match_row.Rd | 17 expss-0.7.1/expss/man/merge.etable.Rd |only expss-0.7.1/expss/man/modify.Rd | 83 - expss-0.7.1/expss/man/mrset.Rd |only expss-0.7.1/expss/man/na_if.Rd | 12 expss-0.7.1/expss/man/names2labels.Rd | 9 expss-0.7.1/expss/man/nest.Rd |only expss-0.7.1/expss/man/product_test.Rd | 3 expss-0.7.1/expss/man/prop.Rd | 3 expss-0.7.1/expss/man/qc.Rd | 1 expss-0.7.1/expss/man/read_spss.Rd | 4 expss-0.7.1/expss/man/ref.Rd | 27 expss-0.7.1/expss/man/sort_asc.Rd | 9 expss-0.7.1/expss/man/split_labels.Rd |only expss-0.7.1/expss/man/sum_row.Rd | 44 expss-0.7.1/expss/man/tab_sort_asc.Rd |only expss-0.7.1/expss/man/tables.Rd |only expss-0.7.1/expss/man/unlab.Rd | 1 expss-0.7.1/expss/man/val_lab.Rd | 55 expss-0.7.1/expss/man/values2labels.Rd | 5 expss-0.7.1/expss/man/var_lab.Rd | 27 expss-0.7.1/expss/man/vars.Rd |only expss-0.7.1/expss/man/vectors.Rd | 71 expss-0.7.1/expss/man/vlookup.Rd | 6 expss-0.7.1/expss/man/w_mean.Rd |only expss-0.7.1/expss/man/where.Rd | 44 expss-0.7.1/expss/man/window_fun.Rd |only expss-0.7.1/expss/man/write_labels.Rd | 67 expss-0.7.1/expss/tests/testthat/rds/add_rows10.rds |binary expss-0.7.1/expss/tests/testthat/rds/add_rows10e.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows11.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows11e.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows12.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows12e.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows7.rds |binary expss-0.7.1/expss/tests/testthat/rds/add_rows7e.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows7ee.rds |only expss-0.7.1/expss/tests/testthat/rds/add_rows8.rds |binary expss-0.7.1/expss/tests/testthat/rds/add_rows8e.rds |only 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expss-0.7.1/expss/tests/testthat/rds/cro_mean3.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_mean4.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_mean5.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_mean6.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_mean8.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_mean_out.txt | 12 expss-0.7.1/expss/tests/testthat/rds/cro_median1.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_median2.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_median6.rds |only expss-0.7.1/expss/tests/testthat/rds/cro_median8.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_methods_2.rds |only expss-0.7.1/expss/tests/testthat/rds/cro_methods_3.rds |only expss-0.7.1/expss/tests/testthat/rds/cro_mult_by_mult.rds |only expss-0.7.1/expss/tests/testthat/rds/cro_real1.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_real1w.rds |binary expss-0.7.1/expss/tests/testthat/rds/cro_real2.rds |binary 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expss-0.7.1/expss/tests/testthat/rds/table_summary_df2.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df3.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df4.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df5.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df5a.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df5b.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df5bb.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df5c.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df6.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df7.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df8.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df9.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df_dates1.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df_dates2.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df_dates3.rds |only expss-0.7.1/expss/tests/testthat/rds/table_summary_df_dates4.rds |only expss-0.7.1/expss/tests/testthat/test_add_rows.R | 32 expss-0.7.1/expss/tests/testthat/test_apply_labels.R |only expss-0.7.1/expss/tests/testthat/test_by_groups.R |only expss-0.7.1/expss/tests/testthat/test_category.R | 86 - expss-0.7.1/expss/tests/testthat/test_count_if.R | 19 expss-0.7.1/expss/tests/testthat/test_criteria_functions.R | 21 expss-0.7.1/expss/tests/testthat/test_cro_extended.R |only expss-0.7.1/expss/tests/testthat/test_cro_fun_df_extended.R |only expss-0.7.1/expss/tests/testthat/test_cro_fun_extended.R |only expss-0.7.1/expss/tests/testthat/test_custom_tables.R |only expss-0.7.1/expss/tests/testthat/test_dichotomy.R | 299 ++- expss-0.7.1/expss/tests/testthat/test_do_repeat.R |only expss-0.7.1/expss/tests/testthat/test_drop_empty.R |only expss-0.7.1/expss/tests/testthat/test_drop_unused_labels.R |only expss-0.7.1/expss/tests/testthat/test_experimental.R | 37 expss-0.7.1/expss/tests/testthat/test_fctr.R |only expss-0.7.1/expss/tests/testthat/test_fre.R | 742 ++++++--- expss-0.7.1/expss/tests/testthat/test_htmlTable.R |only expss-0.7.1/expss/tests/testthat/test_html_datatable.R |only expss-0.7.1/expss/tests/testthat/test_if_val.R | 354 +++- expss-0.7.1/expss/tests/testthat/test_if_val_with_na.R | 2 expss-0.7.1/expss/tests/testthat/test_info.R | 15 expss-0.7.1/expss/tests/testthat/test_keep.R | 143 + expss-0.7.1/expss/tests/testthat/test_labels.R | 97 + expss-0.7.1/expss/tests/testthat/test_mean_if.R | 33 expss-0.7.1/expss/tests/testthat/test_merge.R | 200 ++ expss-0.7.1/expss/tests/testthat/test_methods.R | 289 +++ expss-0.7.1/expss/tests/testthat/test_modify.R | 160 + expss-0.7.1/expss/tests/testthat/test_mrset.R |only expss-0.7.1/expss/tests/testthat/test_na_if.R | 6 expss-0.7.1/expss/tests/testthat/test_names2labels.R | 24 expss-0.7.1/expss/tests/testthat/test_nest.R |only expss-0.7.1/expss/tests/testthat/test_selectors.R | 144 - expss-0.7.1/expss/tests/testthat/test_sort.R | 2 expss-0.7.1/expss/tests/testthat/test_split_labels.R |only expss-0.7.1/expss/tests/testthat/test_subst.R | 8 expss-0.7.1/expss/tests/testthat/test_sum.R | 7 expss-0.7.1/expss/tests/testthat/test_sum_if.R | 10 expss-0.7.1/expss/tests/testthat/test_tab_sort.R |only expss-0.7.1/expss/tests/testthat/test_utils.R |only expss-0.7.1/expss/tests/testthat/test_values2labels.R | 12 expss-0.7.1/expss/tests/testthat/test_vec_ops.R | 31 expss-0.7.1/expss/tests/testthat/test_weighted_stats.R |only expss-0.7.1/expss/tests/testthat/test_where.R | 146 + expss-0.7.1/expss/tests/testthat/test_window_fun.R |only expss-0.7.1/expss/tests/testthat/test_write_labels.R | 90 - expss-0.7.1/expss/vignettes/TablesWithLabelsInR.Rmd |only 624 files changed, 6232 insertions(+), 3360 deletions(-)
Title: An R Package Skeleton Generator
Description: A tool for bootstrapping new packages with useful defaults,
including a test suite outline that passes checks and helpers for running
tests, checking test coverage, building vignettes, and more. Package
skeletons it creates are set up for pushing your package to
'GitHub' and using other hosted services for building and test automation.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between skeletor versions 1.0.2 dated 2017-01-01 and 1.0.4 dated 2017-04-09
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/configure.R | 4 ++-- R/skeletor.R | 8 ++++---- inst/pkg/DESCRIPTION | 4 +++- inst/pkg/README.md | 2 +- inst/pkg/travis.yml | 2 -- man/configure.Rd | 3 +-- man/skeletor.Rd | 3 +-- tests/testthat/test-skeletor-conf.R | 4 ++++ 11 files changed, 38 insertions(+), 30 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R.
The package controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 1.5 dated 2017-01-31 and 1.6 dated 2017-04-09
DESCRIPTION | 8 +-- MD5 | 68 ++++++++++++++------------- NAMESPACE | 6 ++ R/SimDesign.R | 6 ++ R/SimFunctions.R | 7 ++ R/SimShiny.R | 4 - R/functions.R | 35 ++++++++------ R/generate.R |only R/runSimulation.R | 107 ++++++++++++++++++++++++++++--------------- R/summary_functions.R | 9 ++- build/vignette.rds |binary man/Analyse.Rd | 11 ++-- man/Attach.Rd | 1 man/BF_sim.Rd | 7 +- man/BF_sim_alternative.Rd | 7 +- man/ECR.Rd | 1 man/EDR.Rd | 1 man/Generate.Rd | 12 +++- man/MAE.Rd | 1 man/RD.Rd | 1 man/RE.Rd | 1 man/RMSE.Rd | 1 man/SimAnova.Rd | 1 man/SimClean.Rd | 1 man/SimDesign.Rd | 13 +++-- man/SimFunctions.Rd | 8 ++- man/SimResults.Rd | 1 man/SimShiny.Rd | 5 -- man/Summarise.Rd | 4 - man/add_missing.Rd | 1 man/aggregate_simulations.Rd | 1 man/bias.Rd | 1 man/rHeadrick.Rd |only man/rValeMaurelli.Rd |only man/rmgh.Rd |only man/runSimulation.Rd | 106 +++++++++++++++++++++++------------------- tests/tests/test-SimDesign.R | 1 37 files changed, 254 insertions(+), 183 deletions(-)
Title: Displays User Feedback Next to Shiny Inputs
Description: Easily display user feedback next to Shiny inputs. The feedback message is displayed when the feedback condition evaluates to TRUE.
Author: Andy Merlino [aut, cre]
Maintainer: Andy Merlino <merlinoa88@gmail.com>
Diff between shinyFeedback versions 0.0.2 dated 2016-12-20 and 0.0.3 dated 2017-04-09
DESCRIPTION | 10 +- MD5 | 32 ++++----- NEWS.md | 7 +- R/feedback-wrappers.R | 9 -- R/feedback.R | 22 ++++-- README.md | 33 ++++++--- build/vignette.rds |binary inst/doc/shinyFeedback-intro.R | 36 ++++++++++ inst/doc/shinyFeedback-intro.Rmd | 75 +++++++++++++++++---- inst/doc/shinyFeedback-intro.html | 69 +++++++++++++++----- inst/srcjs/checkFeedback.js | 131 +++++++++++++++++++++++++------------- man/feedback.Rd | 1 man/feedbackDanger.Rd | 3 man/feedbackSuccess.Rd | 3 man/feedbackWarning.Rd | 3 man/useShinyFeedback.Rd | 1 vignettes/shinyFeedback-intro.Rmd | 75 +++++++++++++++++---- 17 files changed, 370 insertions(+), 140 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with
the 'qdap' package that may be useful outside of the context of
discourse analysis. Tools include
removal/extraction/replacement of abbreviations, dates, dollar
amounts, email addresses, hash tags, numbers, percentages,
citations, person tags, phone numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapRegex versions 0.6.0 dated 2015-12-13 and 0.7.2 dated 2017-04-09
qdapRegex-0.6.0/qdapRegex/inst/qdapRegex_logo |only qdapRegex-0.7.2/qdapRegex/DESCRIPTION | 25 - qdapRegex-0.7.2/qdapRegex/MD5 | 153 ++++--- qdapRegex-0.7.2/qdapRegex/NAMESPACE | 4 qdapRegex-0.7.2/qdapRegex/NEWS | 27 + qdapRegex-0.7.2/qdapRegex/R/explain.R | 82 +--- qdapRegex-0.7.2/qdapRegex/R/grab.R | 1 qdapRegex-0.7.2/qdapRegex/R/qdapRegex-package.R | 8 qdapRegex-0.7.2/qdapRegex/R/rm_.R | 17 qdapRegex-0.7.2/qdapRegex/R/rm_citation.R | 87 ++++ qdapRegex-0.7.2/qdapRegex/R/rm_dollar.R | 2 qdapRegex-0.7.2/qdapRegex/R/rm_non_ascii.R | 8 qdapRegex-0.7.2/qdapRegex/R/utils.R | 9 qdapRegex-0.7.2/qdapRegex/README.md | 49 +- qdapRegex-0.7.2/qdapRegex/data/regex_cheat.rda |binary qdapRegex-0.7.2/qdapRegex/data/regex_supplement.rda |binary qdapRegex-0.7.2/qdapRegex/data/regex_usa.rda |binary qdapRegex-0.7.2/qdapRegex/inst/CITATION | 8 qdapRegex-0.7.2/qdapRegex/man/S.Rd | 7 qdapRegex-0.7.2/qdapRegex/man/bind.Rd | 27 - qdapRegex-0.7.2/qdapRegex/man/bind_or.Rd | 19 qdapRegex-0.7.2/qdapRegex/man/c.extracted.Rd | 3 qdapRegex-0.7.2/qdapRegex/man/case.Rd | 13 qdapRegex-0.7.2/qdapRegex/man/cheat.Rd | 11 qdapRegex-0.7.2/qdapRegex/man/escape.Rd | 17 qdapRegex-0.7.2/qdapRegex/man/explain.Rd | 45 +- qdapRegex-0.7.2/qdapRegex/man/grab.Rd | 11 qdapRegex-0.7.2/qdapRegex/man/group.Rd | 19 qdapRegex-0.7.2/qdapRegex/man/group_or.Rd | 17 qdapRegex-0.7.2/qdapRegex/man/is.regex.Rd | 11 qdapRegex-0.7.2/qdapRegex/man/pastex.Rd | 45 +- qdapRegex-0.7.2/qdapRegex/man/print.explain.Rd | 3 qdapRegex-0.7.2/qdapRegex/man/print.extracted.Rd | 3 qdapRegex-0.7.2/qdapRegex/man/print.regexr.Rd | 3 qdapRegex-0.7.2/qdapRegex/man/qdapRegex.Rd | 25 - qdapRegex-0.7.2/qdapRegex/man/regex_cheat.Rd | 9 qdapRegex-0.7.2/qdapRegex/man/regex_supplement.Rd | 168 -------- qdapRegex-0.7.2/qdapRegex/man/regex_usa.Rd | 10 qdapRegex-0.7.2/qdapRegex/man/rm_.Rd | 31 - qdapRegex-0.7.2/qdapRegex/man/rm_abbreviation.Rd | 110 +---- qdapRegex-0.7.2/qdapRegex/man/rm_between.Rd | 132 ++---- qdapRegex-0.7.2/qdapRegex/man/rm_bracket.Rd | 154 ++------ qdapRegex-0.7.2/qdapRegex/man/rm_caps.Rd | 110 +---- qdapRegex-0.7.2/qdapRegex/man/rm_caps_phrase.Rd | 110 +---- qdapRegex-0.7.2/qdapRegex/man/rm_citation.Rd | 141 ++----- qdapRegex-0.7.2/qdapRegex/man/rm_citation_tex.Rd | 113 +---- qdapRegex-0.7.2/qdapRegex/man/rm_city_state.Rd | 113 +---- qdapRegex-0.7.2/qdapRegex/man/rm_city_state_zip.Rd | 112 +---- qdapRegex-0.7.2/qdapRegex/man/rm_date.Rd | 122 +----- qdapRegex-0.7.2/qdapRegex/man/rm_default.Rd | 102 +---- qdapRegex-0.7.2/qdapRegex/man/rm_dollar.Rd | 113 +---- qdapRegex-0.7.2/qdapRegex/man/rm_email.Rd | 120 +----- qdapRegex-0.7.2/qdapRegex/man/rm_emoticon.Rd | 106 +---- qdapRegex-0.7.2/qdapRegex/man/rm_endmark.Rd | 118 +----- qdapRegex-0.7.2/qdapRegex/man/rm_hash.Rd | 118 +----- qdapRegex-0.7.2/qdapRegex/man/rm_nchar_words.Rd | 124 +----- qdapRegex-0.7.2/qdapRegex/man/rm_non_ascii.Rd | 127 +----- qdapRegex-0.7.2/qdapRegex/man/rm_non_words.Rd | 110 +---- qdapRegex-0.7.2/qdapRegex/man/rm_number.Rd | 115 +---- qdapRegex-0.7.2/qdapRegex/man/rm_percent.Rd | 108 +---- qdapRegex-0.7.2/qdapRegex/man/rm_phone.Rd | 118 +----- qdapRegex-0.7.2/qdapRegex/man/rm_postal_code.Rd | 106 +---- qdapRegex-0.7.2/qdapRegex/man/rm_repeated_characters.Rd | 113 +---- qdapRegex-0.7.2/qdapRegex/man/rm_repeated_phrases.Rd | 111 +---- qdapRegex-0.7.2/qdapRegex/man/rm_repeated_words.Rd | 105 +---- qdapRegex-0.7.2/qdapRegex/man/rm_tag.Rd | 126 +----- qdapRegex-0.7.2/qdapRegex/man/rm_time.Rd | 231 +++--------- qdapRegex-0.7.2/qdapRegex/man/rm_title_name.Rd | 110 +---- qdapRegex-0.7.2/qdapRegex/man/rm_url.Rd | 123 +----- qdapRegex-0.7.2/qdapRegex/man/rm_white.Rd | 137 ++----- qdapRegex-0.7.2/qdapRegex/man/rm_zip.Rd | 134 ++---- qdapRegex-0.7.2/qdapRegex/man/validate.Rd | 30 - qdapRegex-0.7.2/qdapRegex/tests/testthat/test-S.R | 5 qdapRegex-0.7.2/qdapRegex/tests/testthat/test-as_count.R |only qdapRegex-0.7.2/qdapRegex/tests/testthat/test-c.extracted.R |only qdapRegex-0.7.2/qdapRegex/tests/testthat/test-pastex.R | 2 qdapRegex-0.7.2/qdapRegex/tests/testthat/test-rm_.R | 21 + qdapRegex-0.7.2/qdapRegex/tools |only 78 files changed, 1657 insertions(+), 3270 deletions(-)
Title: Tools for Grid-Based Survey Sampling Design
Description: Multi-stage cluster surveys of households are commonly performed by
governments and programmes to monitor population-level demographic, social,
economic, and health outcomes. Generally, communities are sampled from
subpopulations (strata) in a first stage, and then households are listed and
sampled in a second stage. In this typical two-stage design, sampled communities
are the Primary Sampling Units (PSUs) and households are the Secondary Sampling
Units (SSUs). Census data typically serve as the sample frame from which PSUs
are selected. However, if census data are outdated inaccurate, or too
geographically course, gridded population data (such as <http://www.worldpop.org.uk>)
can be used as a sample frame instead. GridSample generates PSUs from gridded
population data according to user-specified complex survey design characteristics
and household sample size. In gridded population sampling, like census sampling,
PSUs are selected within each stratum using a serpentine sampling method, and can
be oversampled in urban or rural areas to ensure a minimum sample size in each of
these important sub-domains. Furthermore, because grid cells are uniform in size
and shape, gridded population sampling allows for samples to be representative of
both the population and of space, which is not possible with a census sample frame.
Author: Dana R. Thomson (University of Southampton), Nick W. Ruktanonchai
(University of Southampton), Forrest R. Stevens (University of Louisville),
Marcia Castro (Harvard University), Andrew J. Tatem (University of Southampton)
Maintainer: Nick Ruktanonchai <nrukt00@gmail.com>
Diff between gridsample versions 0.1.3 dated 2016-11-30 and 0.2.0 dated 2017-04-09
gridsample-0.1.3/gridsample/R/gs_mode.R |only gridsample-0.1.3/gridsample/R/gs_rasterize.R |only gridsample-0.1.3/gridsample/R/gs_sample.R |only gridsample-0.1.3/gridsample/R/gs_zonal_raster.R |only gridsample-0.2.0/gridsample/DESCRIPTION | 51 ++++----- gridsample-0.2.0/gridsample/LICENSE | 4 gridsample-0.2.0/gridsample/MD5 | 31 +++-- gridsample-0.2.0/gridsample/NAMESPACE | 1 gridsample-0.2.0/gridsample/NEWS |only gridsample-0.2.0/gridsample/R/data.R |only gridsample-0.2.0/gridsample/R/gs_mode.r |only gridsample-0.2.0/gridsample/R/gs_rasterize.r |only gridsample-0.2.0/gridsample/R/gs_sample.r |only gridsample-0.2.0/gridsample/R/gs_zonal_raster.r |only gridsample-0.2.0/gridsample/README.md |only gridsample-0.2.0/gridsample/build |only gridsample-0.2.0/gridsample/data |only gridsample-0.2.0/gridsample/inst |only gridsample-0.2.0/gridsample/man/RWAshp.Rd |only gridsample-0.2.0/gridsample/man/gs_mode.Rd | 41 +++---- gridsample-0.2.0/gridsample/man/gs_rasterize.Rd | 67 ++++++------ gridsample-0.2.0/gridsample/man/gs_sample.Rd | 115 ++++++++++++--------- gridsample-0.2.0/gridsample/man/gs_zonal_raster.Rd | 3 gridsample-0.2.0/gridsample/vignettes |only 24 files changed, 174 insertions(+), 139 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure (Zhao and Shojaie, 2016 <doi:10.1111/biom.12418>) to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>
Diff between Grace versions 0.5.2 dated 2017-03-12 and 0.5.3 dated 2017-04-09
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- R/grace.R | 19 +++++++++++-------- R/grace.test.R | 11 +++++++---- R/graceI.test.R | 5 +++-- man/grace.Rd | 5 ++++- man/grace.test.Rd | 11 +++++++---- man/graceI.test.Rd | 5 ++++- 8 files changed, 49 insertions(+), 32 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 2.0 include: (i) copy-neutral LOH are now modelled; (ii) more robust calculation of cell frequency probabilities from kernel density estimates instead of Gaussian mixtures. 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 1.7.2 dated 2016-04-04 and 2.0.0 dated 2017-04-09
expands-1.7.2/expands/java/Common.java |only expands-1.7.2/expands/java/ExPANdS.java |only expands-2.0.0/expands/DESCRIPTION | 15 expands-2.0.0/expands/MD5 | 77 +- expands-2.0.0/expands/NAMESPACE | 4 expands-2.0.0/expands/NEWS.md |only expands-2.0.0/expands/R/assignMutations.R | 322 +--------- expands-2.0.0/expands/R/assignQuantityToMutation.R | 6 expands-2.0.0/expands/R/assignQuantityToSP.R | 131 +--- expands-2.0.0/expands/R/buildMultiSamplePhylo.R | 15 expands-2.0.0/expands/R/buildPhylo.R | 99 ++- expands-2.0.0/expands/R/cellfrequency_pdf.R | 129 ---- expands-2.0.0/expands/R/clusterCellFrequencies.R | 17 expands-2.0.0/expands/R/computeCellFrequencyDistributions.R | 102 +-- expands-2.0.0/expands/R/plotSPs.R | 33 - expands-2.0.0/expands/R/readSNVandCBS.R |only expands-2.0.0/expands/R/runExPANdS.R | 246 ++----- expands-2.0.0/expands/build/vignette.rds |binary expands-2.0.0/expands/inst/doc/expands.R | 26 expands-2.0.0/expands/inst/doc/expands.Rnw | 44 - expands-2.0.0/expands/inst/doc/expands.pdf |binary expands-2.0.0/expands/inst/java/expands.jar |binary expands-2.0.0/expands/java/lib |only expands-2.0.0/expands/java/src |only expands-2.0.0/expands/java/uml |only expands-2.0.0/expands/man/assignMutations.Rd | 26 expands-2.0.0/expands/man/assignQuantityToMutation.Rd | 2 expands-2.0.0/expands/man/assignQuantityToSP.Rd | 26 expands-2.0.0/expands/man/buildMultiSamplePhylo.Rd | 14 expands-2.0.0/expands/man/buildPhylo.Rd | 4 expands-2.0.0/expands/man/cellfrequency_pdf.Rd | 47 - expands-2.0.0/expands/man/clusterCellFrequencies.Rd | 2 expands-2.0.0/expands/man/computeCellFrequencyDistributions.Rd | 4 expands-2.0.0/expands/man/plotSPs.Rd | 12 expands-2.0.0/expands/man/runExPANdS.Rd | 30 expands-2.0.0/expands/vignettes/ID_MRD_001_metKidney.sps | 137 ++-- expands-2.0.0/expands/vignettes/ID_MRD_001_metLung.sps | 247 +++---- expands-2.0.0/expands/vignettes/ID_MRD_001_primPancreas.sps | 311 ++++----- expands-2.0.0/expands/vignettes/expands.Rnw | 44 - 39 files changed, 876 insertions(+), 1296 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according to the Kemeny's axiomatic approach.
Rankings can or cannot contain ties, rankings can be both complete or incomplete.
The package contains both branch-and-bound algorithms and heuristic solutions recently proposed.
The package also provide some useful utilities for deal with preference rankings.
Essential references:
Emond, E.J., and Mason, D.W. (2002) <doi:10.1002/mcda.313>;
D'Ambrosio, A., Amodio, S., and Iorio, C. (2015) <doi:10.1285/i20705948v8n2p198>;
Amodio, S., D'Ambrosio, A., and Siciliano R. (2016) <doi:10.1016/j.ejor.2015.08.048>;
D'Ambrosio, A., Mazzeo, G., Iorio, C., and Siciliano, R. (2017) <doi:10.1016/j.cor.2017.01.017>.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio
<sonia.amodio@unina.it>, Giulio Mazzeo <giuliomazzeo@gmail.com>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 1.0.2 dated 2015-09-29 and 2.0.0 dated 2017-04-09
ConsRank-1.0.2/ConsRank/R/ALL.r |only ConsRank-2.0.0/ConsRank/DESCRIPTION | 26 ++++-- ConsRank-2.0.0/ConsRank/MD5 | 86 +++++++++++++++------ ConsRank-2.0.0/ConsRank/NAMESPACE | 42 +++++++++- ConsRank-2.0.0/ConsRank/R/BBFULL.R |only ConsRank-2.0.0/ConsRank/R/BBconsensus.R |only ConsRank-2.0.0/ConsRank/R/BBconsensus2.R |only ConsRank-2.0.0/ConsRank/R/DECOR.R |only ConsRank-2.0.0/ConsRank/R/DECORcore.R |only ConsRank-2.0.0/ConsRank/R/EMCons.R |only ConsRank-2.0.0/ConsRank/R/FASTDECOR.R |only ConsRank-2.0.0/ConsRank/R/FASTcons.R |only ConsRank-2.0.0/ConsRank/R/Penalty.R |only ConsRank-2.0.0/ConsRank/R/PenaltyBB2.R |only ConsRank-2.0.0/ConsRank/R/QuickCons.R |only ConsRank-2.0.0/ConsRank/R/ReorderingBB.R |only ConsRank-2.0.0/ConsRank/R/Tau_X.R |only ConsRank-2.0.0/ConsRank/R/branches.R |only ConsRank-2.0.0/ConsRank/R/childclosint.R |only ConsRank-2.0.0/ConsRank/R/childtie.R |only ConsRank-2.0.0/ConsRank/R/combincost.R |only ConsRank-2.0.0/ConsRank/R/combinpmatr.R |only ConsRank-2.0.0/ConsRank/R/crossover.R |only ConsRank-2.0.0/ConsRank/R/findbranches.R |only ConsRank-2.0.0/ConsRank/R/findconsensusBB.R |only ConsRank-2.0.0/ConsRank/R/kemenyd.R |only ConsRank-2.0.0/ConsRank/R/kemenydesign.R |only ConsRank-2.0.0/ConsRank/R/labels.R |only ConsRank-2.0.0/ConsRank/R/mutaterand1.R |only ConsRank-2.0.0/ConsRank/R/polyplot.R |only ConsRank-2.0.0/ConsRank/R/reordering.R |only ConsRank-2.0.0/ConsRank/R/scorematrix.R |only ConsRank-2.0.0/ConsRank/R/tabulaterows.R |only ConsRank-2.0.0/ConsRank/man/BBFULL.Rd | 71 +++++++---------- ConsRank-2.0.0/ConsRank/man/BBconsensus.Rd | 52 +++++-------- ConsRank-2.0.0/ConsRank/man/BBconsensus2.Rd | 60 ++++++--------- ConsRank-2.0.0/ConsRank/man/ConsRank-package.Rd | 29 ++++--- ConsRank-2.0.0/ConsRank/man/DECOR.Rd |only ConsRank-2.0.0/ConsRank/man/DECORcore.Rd |only ConsRank-2.0.0/ConsRank/man/EMCons.Rd | 77 ++++++++----------- ConsRank-2.0.0/ConsRank/man/FASTDECOR.Rd |only ConsRank-2.0.0/ConsRank/man/FASTcons.Rd | 95 ++++++++++-------------- ConsRank-2.0.0/ConsRank/man/Penalty.Rd | 32 +++----- ConsRank-2.0.0/ConsRank/man/PenaltyBB2.Rd | 32 +++----- ConsRank-2.0.0/ConsRank/man/QuickCons.Rd | 75 +++++++----------- ConsRank-2.0.0/ConsRank/man/ReorderingBB.Rd | 27 ++---- ConsRank-2.0.0/ConsRank/man/Tau_X.Rd | 56 +++++--------- ConsRank-2.0.0/ConsRank/man/branches.Rd | 62 +++++---------- ConsRank-2.0.0/ConsRank/man/childclosint.Rd |only ConsRank-2.0.0/ConsRank/man/childtie.Rd |only ConsRank-2.0.0/ConsRank/man/combincost.Rd |only ConsRank-2.0.0/ConsRank/man/combinpmatr.Rd | 53 ++++--------- ConsRank-2.0.0/ConsRank/man/crossover.Rd |only ConsRank-2.0.0/ConsRank/man/findbranches.Rd | 43 +++------- ConsRank-2.0.0/ConsRank/man/findconsensusBB.Rd | 28 ++----- ConsRank-2.0.0/ConsRank/man/kemenyd.Rd | 59 +++++--------- ConsRank-2.0.0/ConsRank/man/kemenydesign.Rd | 26 ++---- ConsRank-2.0.0/ConsRank/man/labels.Rd | 49 ++++-------- ConsRank-2.0.0/ConsRank/man/mutaterand1.Rd |only ConsRank-2.0.0/ConsRank/man/polyplot.Rd | 67 +++++++--------- ConsRank-2.0.0/ConsRank/man/reordering.Rd | 27 ++---- ConsRank-2.0.0/ConsRank/man/scorematrix.Rd | 43 ++++------ ConsRank-2.0.0/ConsRank/man/tabulaterows.Rd | 49 +++++------- 63 files changed, 550 insertions(+), 716 deletions(-)
Title: Simple R Cache
Description: Simple result caching in R based on R.cache. The global environment is not
considered when caching results simplifying moving files between multiple instances
of R. Relies on more base functions than R.cache (e.g. cached results are saved using
saveRDS() and readRDS()).
Author: Augustin Luna, Vinodh Rajapakse
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between simpleRCache versions 0.2.2 dated 2016-03-01 and 0.3.2 dated 2017-04-09
DESCRIPTION | 20 +++++++++++--------- MD5 | 17 +++++++++++------ R/memoizedCall.R | 26 +++++++++++++++++++------- build |only inst |only man/addMemoization.Rd | 1 - man/memoizedCall.Rd | 5 ++++- man/setCacheRootPath.Rd | 1 - vignettes/usingSimpleRCache.Rmd | 4 ++++ 9 files changed, 49 insertions(+), 25 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.1 dated 2017-04-06 and 1.4.2 dated 2017-04-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- tests/testthat/testthat.get.R | 1 + tests/testthat/testthat.misc.R | 1 + 4 files changed, 8 insertions(+), 6 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 2.1-2 dated 2016-12-18 and 2.1-3 dated 2017-04-09
DESCRIPTION | 8 +- MD5 | 40 +++++----- R/DAS-scale.R | 6 - R/fromLme4.R | 5 + R/psiFunc2.R | 22 ++--- R/rlmer.R | 12 +-- build/vignette.rds |binary inst/doc/rlmer.pdf |binary inst/include/robustlmm.h | 41 +--------- man/chgDefaults.Rd | 4 - man/other.Rd | 4 - man/plot-methods.Rd | 4 - man/psi2propII.Rd | 4 - src/Integration.cpp | 160 ++++++++++++++++++++++++++++------------ src/Integration.h | 96 +++++++++++++++++++++++- src/PsiFunction.cpp | 30 ++++--- src/PsiFunction.h | 71 ++++++++++++++++- src/globals.h | 5 - src/misc.h |only src/robustlmm_init.cpp |only tests/compare-methods.Rout.save | 18 ++-- vignettes/jss.dtx |only vignettes/jsslogo.pdf |only 23 files changed, 368 insertions(+), 162 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <ari@lamsteinconsulting.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>
Diff between choroplethr versions 3.5.3 dated 2017-01-10 and 3.6.0 dated 2017-04-09
DESCRIPTION | 13 +++-- MD5 | 91 +++++++++++++++++++++------------------- NAMESPACE | 10 ++++ NEWS | 7 +++ R/acs.R | 54 +++++++++++++++++++++++ R/get_county_demographics.R | 2 R/get_state_demograhpics.R | 2 R/get_tract_demographics.R |only R/tracts.R |only R/utils.R |only README.md | 2 man/Admin1Choropleth.Rd | 1 man/Admin1RegionChoropleth.Rd | 1 man/Choropleth.Rd | 1 man/CountryChoropleth.Rd | 1 man/CountyChoropleth.Rd | 1 man/CountyZoomChoropleth.Rd | 1 man/StateChoropleth.Rd | 1 man/TractChoropleth.Rd |only man/USAChoropleth.Rd | 1 man/admin1_choropleth.Rd | 1 man/admin1_region_choropleth.Rd | 1 man/calculate_percent_change.Rd |only man/choroplethr.Rd | 1 man/choroplethr_acs.Rd | 1 man/choroplethr_animate.Rd | 1 man/choroplethr_wdi.Rd | 1 man/continental_us_states.Rd | 1 man/country_choropleth.Rd | 1 man/county_choropleth.Rd | 1 man/county_choropleth_acs.Rd | 1 man/county_zoom_choropleth.Rd | 1 man/df_county_demographics.Rd | 1 man/df_japan_census.Rd | 1 man/df_pop_country.Rd | 1 man/df_pop_county.Rd | 1 man/df_pop_state.Rd | 1 man/df_president.Rd | 7 +-- man/df_president_ts.Rd | 1 man/df_state_demographics.Rd | 1 man/double_map.Rd |only man/get_acs_data.Rd | 1 man/get_acs_df.Rd | 1 man/get_county_demographics.Rd | 3 - man/get_state_demographics.Rd | 3 - man/get_tract_demographics.Rd |only man/get_tract_map.Rd |only man/state_choropleth.Rd | 1 man/state_choropleth_acs.Rd | 1 man/tract_choropleth.Rd |only man/zip_map.Rd | 1 51 files changed, 135 insertions(+), 90 deletions(-)
Title: Estimation and Inference of Two-Way pAUC, pAUC and pODC
Description: Tools for estimating and inferring two-way partial area under receiver operating characteristic curves (two-way pAUC), partial area under receiver operating characteristic curves (pAUC), and partial area under ordinal dominance curves (pODC). Methods includes Mann-Whitney statistic and Jackknife, etc.
Author: Hanfang Yang, Kun Lu, Xiang Lyu, Feifang Hu, Yichuan Zhao
Maintainer: Xiang Lyu <lyu17@purdue.edu>
Diff between tpAUC versions 2.0.1 dated 2017-01-13 and 2.1.1 dated 2017-04-09
DESCRIPTION | 10 +++--- MD5 | 42 ++++++++++++++-------------- R/podc.R | 15 ++++------ R/podc.ci.R | 12 ++++---- R/podc.est.R | 32 +++++---------------- R/proc.R | 17 +++++------ R/proc.ci.R | 12 ++++---- R/proc.est.R | 31 +++++---------------- R/tpAUC-package.r | 6 ++-- R/tproc.est.R | 27 +++--------------- inst/doc/tpAUCguide.R | 14 ++++----- inst/doc/tpAUCguide.Rmd | 50 +++++++++++++++++----------------- inst/doc/tpAUCguide.html | 69 ++++++++++++++++++++--------------------------- man/podc.Rd | 14 ++++----- man/podc.ci.Rd | 8 ++--- man/podc.est.Rd | 16 ++++------ man/proc.Rd | 16 ++++------ man/proc.ci.Rd | 8 ++--- man/proc.est.Rd | 16 ++++------ man/tpAUC.Rd | 6 ++-- man/tproc.est.Rd | 11 ++----- vignettes/tpAUCguide.Rmd | 50 +++++++++++++++++----------------- 22 files changed, 206 insertions(+), 276 deletions(-)
Title: Annotation of Metabolites from Liquid Chromatography-Mass
Spectrometry Data
Description: Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS) data from .mzXML files, providing an inclusion list of metabolites/fragments (Only the ion mass). The function returns the identification and quantification of the peaks presented in the sample, as well as the non-identified metabolites/fragments.
Author: Manuel David Peris Diaz
Maintainer: Manuel David Peris Diaz <madape@alumni.uv.es>
Diff between MetaboList versions 1.0 dated 2016-12-28 and 1.1 dated 2017-04-09
DESCRIPTION | 6 - MD5 | 6 - R/annotation.R | 319 +++++++++++++++++++++++++++++++++--------------------- man/annotation.rd | 17 +- 4 files changed, 212 insertions(+), 136 deletions(-)