Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 1.5.4 dated 2016-09-15 and 1.5.5 dated 2016-12-03
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/BAT.R | 39 ++++++++++++++++++++------------------- data/arrabida.rda |binary data/geres.rda |binary data/guadiana.rda |binary man/alpha.Rd | 2 +- man/beta.Rd | 2 +- man/sim.spatial.Rd | 8 ++++---- 9 files changed, 40 insertions(+), 39 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), Mahalanobis distance are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis and John Burkardt
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.7 dated 2016-12-01 and 1.7.1 dated 2016-12-03
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 7 +++---- R/diri.nr2.R | 4 ++-- man/Rfast-package.Rd | 6 +++--- src/diri_nr_type2.cpp | 40 ++++++++++++++++++++-------------------- src/mn.cpp | 19 +++++++++++++++++++ src/mn.h | 4 ++++ src/rowMaxs.cpp | 4 ++-- src/rowMins.cpp | 4 ++-- 10 files changed, 68 insertions(+), 46 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models in R.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.1.0 dated 2016-10-06 and 0.2.0 dated 2016-12-03
DESCRIPTION | 17 -- MD5 | 25 +- NEWS.md | 8 R/data.R |only R/partial.R | 108 +++++++----- R/plotPartial.R | 357 +++++++++++++++++++++++------------------- R/utils.R | 72 ++++++++ README.md | 187 +++++++++++++++++----- data |only man/boston.Rd |only man/partial.Rd | 66 ++++++- man/pima.Rd |only man/plotPartial.Rd | 5 tests/testthat/test-partial.R | 53 ++++-- tests/testthat/test-utils.R | 213 ++++++++++++++++++++----- 15 files changed, 779 insertions(+), 332 deletions(-)
Title: Text Extraction and Rendering of PDF Documents
Description: Utilities based on libpoppler for extracting text,
fonts, attachments and metadata from a pdf file. Also implements
rendering of PDF to bitmaps on supported platforms.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between pdftools versions 0.5 dated 2016-08-28 and 1.0 dated 2016-12-03
DESCRIPTION | 10 ++++---- MD5 | 18 +++++++-------- NEWS | 3 ++ R/RcppExports.R | 2 - R/render.R | 4 +-- configure | 13 +++++++++- man/pdf_render_page.Rd | 4 +-- man/pdftools.Rd | 6 ++--- src/RcppExports.cpp | 58 ++++++++++++++++++++++++------------------------- src/bindings.cpp | 10 +++++++- 10 files changed, 74 insertions(+), 54 deletions(-)
Title: Oxycline Index from Matrix Echograms
Description: Tools for oxycline depth calculation from echogram matrices.
Author: Wencheng Lau-Medrano [aut, cre],
Ricardo Oliveros-Ramos [ctb]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between oXim versions 1.0.1 dated 2016-08-17 and 1.1.0 dated 2016-12-03
oXim-1.0.1/oXim/NEWS.md |only oXim-1.0.1/oXim/R/RcppExports.R |only oXim-1.0.1/oXim/src |only oXim-1.1.0/oXim/DESCRIPTION | 18 oXim-1.1.0/oXim/MD5 | 92 - oXim-1.1.0/oXim/NAMESPACE | 50 oXim-1.1.0/oXim/R/auxiliar.R | 266 +- oXim-1.1.0/oXim/R/echoData-class.R | 283 +-- oXim-1.1.0/oXim/R/oXim-internal.R |only oXim-1.1.0/oXim/R/oXim-main.R | 486 ++--- oXim-1.1.0/oXim/R/oxyclineData-class.R | 403 ++-- oXim-1.1.0/oXim/R/oxyclineData-internal.R | 904 +++------- oXim-1.1.0/oXim/build/vignette.rds |binary oXim-1.1.0/oXim/data/defaultFilterSettings.RData |binary oXim-1.1.0/oXim/demo/00Index | 13 oXim-1.1.0/oXim/demo/calculate_oxycline_limits.R | 34 oXim-1.1.0/oXim/demo/create_filter_configuration.R |only oXim-1.1.0/oXim/demo/methods_echoData.R | 47 oXim-1.1.0/oXim/demo/methods_oxyclineData.R | 53 oXim-1.1.0/oXim/demo/read_echoData.R | 26 oXim-1.1.0/oXim/inst/doc/vignette.R | 54 oXim-1.1.0/oXim/inst/doc/vignette.Rmd | 198 +- oXim-1.1.0/oXim/inst/doc/vignette.html | 360 +-- oXim-1.1.0/oXim/man/colPalette.Rd | 34 oXim-1.1.0/oXim/man/createFilterSetting.Rd | 99 - oXim-1.1.0/oXim/man/defaultFilterSettings.Rd | 30 oXim-1.1.0/oXim/man/echogramPlot.Rd | 66 oXim-1.1.0/oXim/man/echogramPlot.echoData.Rd |only oXim-1.1.0/oXim/man/echogramPlot.oxyclineData.Rd |only oXim-1.1.0/oXim/man/getOxyrange.Rd | 68 oXim-1.1.0/oXim/man/oXim-package.Rd | 39 oXim-1.1.0/oXim/man/plot.echoData.Rd | 36 oXim-1.1.0/oXim/man/plot.oxyclineData.Rd | 52 oXim-1.1.0/oXim/man/print.echoData.Rd | 34 oXim-1.1.0/oXim/man/print.oxyclineData.Rd | 34 oXim-1.1.0/oXim/man/print.summary.echoData.Rd | 34 oXim-1.1.0/oXim/man/print.summary.oxyclineData.Rd | 34 oXim-1.1.0/oXim/man/readEchograms.Rd | 90 oXim-1.1.0/oXim/man/summary.echoData.Rd | 34 oXim-1.1.0/oXim/man/summary.oxyclineData.Rd | 34 oXim-1.1.0/oXim/vignettes/vignette.Rmd | 198 +- oXim-1.1.0/oXim/vignettes/vignette_cache/html/__packages | 4 oXim-1.1.0/oXim/vignettes/vignette_cache/html/unnamed-chunk-3_ccf9ce7567b0d833c5dd0791c366e4a2.RData |binary oXim-1.1.0/oXim/vignettes/vignette_cache/html/unnamed-chunk-3_ccf9ce7567b0d833c5dd0791c366e4a2.rdb |binary oXim-1.1.0/oXim/vignettes/vignette_cache/html/unnamed-chunk-3_ccf9ce7567b0d833c5dd0791c366e4a2.rdx |binary oXim-1.1.0/oXim/vignettes/vignette_cache/html/unnamed-chunk-7_9f403fae10ff7304bad716657a27b4e7.RData |binary oXim-1.1.0/oXim/vignettes/vignette_cache/html/unnamed-chunk-7_9f403fae10ff7304bad716657a27b4e7.rdb |binary oXim-1.1.0/oXim/vignettes/vignette_cache/html/unnamed-chunk-7_9f403fae10ff7304bad716657a27b4e7.rdx |binary oXim-1.1.0/oXim/vignettes/vignette_files/figure-html/unnamed-chunk-10-1.png |binary oXim-1.1.0/oXim/vignettes/vignette_files/figure-html/unnamed-chunk-6-1.png |binary 50 files changed, 2080 insertions(+), 2127 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths, cre],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between lmerTest versions 2.0-32 dated 2016-06-22 and 2.0-33 dated 2016-12-03
DESCRIPTION | 18 ++++++------- MD5 | 27 ++++++++++---------- NAMESPACE | 8 ++++-- NEWS | 5 +++ R/generalFunctions.R | 21 ++++++++++++--- R/satterth.R | 2 - man/difflsmeans.Rd | 10 +------ man/lsmeans.Rd | 10 +++---- man/lsmeansLT.Rd |only tests/Examples/lmerTest-Ex.Rout.save | 46 ++++++++++++++++++++++++++++------- tests/lmerMod.R | 2 - tests/summary.R | 3 +- tests/testANCOVA.R | 4 +-- tests/testContrasts.R | 2 - tests/updateData.R | 4 +-- 15 files changed, 105 insertions(+), 57 deletions(-)
Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Description: A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
Author: Ken Kellner <contact@kenkellner.com>
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between jagsUI versions 1.4.2 dated 2016-02-22 and 1.4.4 dated 2016-12-03
DESCRIPTION | 12 ++++---- MD5 | 40 ++++++++++++++------------- NAMESPACE | 12 ++++---- NEWS | 8 +++++ R/View.R |only R/autojags.R | 2 - R/geninits.R | 6 ++-- R/getdim.R | 18 +++++++++--- R/jags.R | 2 - R/jagsbasic.R | 2 - R/runparallel.R | 4 ++ R/traceplot.R | 77 +++++++++++++++++++++++------------------------------ R/update.R | 2 - R/updatebasic.R | 7 ++-- man/View.Rd |only man/autojags.Rd | 6 ++-- man/jags.Rd | 6 ++-- man/jagsbasic.Rd | 6 ++-- man/ppcheck.Rd | 2 - man/traceplot.Rd | 10 ++++-- man/update.Rd | 6 ++-- man/whiskerplot.Rd | 2 - 22 files changed, 124 insertions(+), 106 deletions(-)
Title: Testing 'DBI' Back Ends
Description: A helper that tests 'DBI' back ends for conformity
to the interface.
Author: Kirill Müller [aut, cre],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between DBItest versions 1.3 dated 2016-07-07 and 1.4 dated 2016-12-03
DESCRIPTION | 46 - MD5 | 116 ++ NAMESPACE | 4 NEWS.md | 32 R/DBItest.R | 6 R/context.R | 21 R/expectations.R | 9 R/import-dbi.R | 6 R/run.R | 2 R/s4.R |only R/spec-.R |only R/spec-compliance-methods.R |only R/spec-compliance-read-only.R |only R/spec-compliance.R |only R/spec-connection-connect.R |only R/spec-connection-data-type.R |only R/spec-connection-get-info.R |only R/spec-connection.R |only R/spec-driver-class.R |only R/spec-driver-constructor.R |only R/spec-driver-data-type.R |only R/spec-driver-get-info.R |only R/spec-driver.R |only R/spec-getting-started.R |only R/spec-meta-bind-.R |only R/spec-meta-bind-multi-row.R |only R/spec-meta-bind.R |only R/spec-meta-column-info.R |only R/spec-meta-get-info-result.R |only R/spec-meta-get-row-count.R |only R/spec-meta-get-rows-affected.R |only R/spec-meta-get-statement.R |only R/spec-meta-is-valid-connection.R |only R/spec-meta-is-valid-result.R |only R/spec-meta.R |only R/spec-result-create-table-with-data-type.R |only R/spec-result-fetch.R |only R/spec-result-get-query.R |only R/spec-result-roundtrip.R |only R/spec-result-send-query.R |only R/spec-result.R |only R/spec-sql-list-fields.R |only R/spec-sql-list-tables.R |only R/spec-sql-quote-identifier.R |only R/spec-sql-quote-string.R |only R/spec-sql-read-write-roundtrip.R |only R/spec-sql-read-write-table.R |only R/spec-sql.R |only R/spec-stress-connection.R |only R/spec-stress-driver.R |only R/spec-stress.R |only R/spec-transaction-begin-commit.R |only R/spec-transaction-begin-rollback.R |only R/spec-transaction-with-transaction.R |only R/spec-transaction.R |only R/spec.R |only R/test-all.R | 10 R/test-compliance.R | 106 -- R/test-connection.R | 149 --- R/test-driver.R | 137 --- R/test-getting-started.R | 52 - R/test-meta.R | 974 ------------------------ R/test-result.R | 1095 ---------------------------- R/test-sql.R | 600 --------------- R/test-stress.R |only R/test-transaction.R |only R/tweaks.R | 33 R/utils.R | 50 + build/vignette.rds |binary inst/doc/test.html | 4 man/DBIspec-wip.Rd |only man/DBIspec.Rd |only man/DBItest-package.Rd | 13 man/context.Rd | 15 man/make_placeholder_fun.Rd |only man/test_all.Rd | 30 man/test_compliance.Rd | 17 man/test_connection.Rd | 34 man/test_driver.Rd | 37 man/test_getting_started.Rd | 20 man/test_meta.Rd | 254 ------ man/test_result.Rd | 232 ----- man/test_sql.Rd | 107 -- man/test_stress.Rd |only man/test_transaction.Rd |only man/tweaks.Rd | 7 86 files changed, 346 insertions(+), 3872 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, a fast friendly file reader and parallel file writer. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.9.8 dated 2016-11-25 and 1.10.0 dated 2016-12-03
DESCRIPTION | 24 MD5 | 64 +- NEWS.md | 37 + R/data.table.R | 24 R/fread.R | 22 R/onAttach.R | 5 R/test.data.table.R | 17 inst/doc/datatable-faq.R | 37 - inst/doc/datatable-faq.Rmd | 241 +++----- inst/doc/datatable-faq.html | 330 ++++-------- inst/doc/datatable-intro.html | 8 inst/doc/datatable-keys-fast-subset.html | 10 inst/doc/datatable-reference-semantics.html | 4 inst/doc/datatable-reshape.html | 4 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 22 inst/tests/tests.Rraw | 149 ++++- man/IDateTime.Rd | 60 +- man/J.Rd | 5 man/duplicated.Rd | 27 man/foverlaps.Rd | 188 +++--- man/fwrite.Rd | 2 man/split.Rd | 5 src/dogroups.c | 23 src/fmelt.c | 34 - src/fread.c | 31 - src/fwrite.c | 8 src/gsumm.c | 103 +-- src/init.c | 19 src/rbindlist.c | 42 - src/subset.c | 31 - src/transpose.c | 11 src/uniqlist.c | 94 +-- vignettes/datatable-faq.Rmd | 241 +++----- 33 files changed, 912 insertions(+), 1010 deletions(-)