Title: Detection of Structural Changes in Climate and Environment Time
Series
Description: Tools for automatic model selection and diagnostics for Climate and Environmental data. In particular the envcpt() function does automatic model selection between a variety of trend, changepoint and autocorrelation models. The envcpt() function should be your first port of call.
Author: Rebecca Killick [aut, cre],
Claudie Beaulieu [aut],
Simon Taylor [aut],
Harjit Hullait [aut]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between EnvCpt versions 1.0 dated 2018-01-18 and 1.1 dated 2018-09-11
DESCRIPTION | 12 - MD5 | 21 +- NAMESPACE | 8 - NEWS | 14 + R/diagnostics.R | 328 ++++++++++++++++++++++++++++++++--------- R/envcpt.R | 191 ++++++++++++++--------- man/AIC.Rd | 46 +++-- man/AICweights.Rd |only man/envcpt-package.Rd | 40 +++-- man/envcpt.Rd | 47 ++++- man/plot.envcpt.Rd | 38 +++- tests/testthat/test-examples.R | 41 +++-- 12 files changed, 550 insertions(+), 236 deletions(-)
Title: Pathway and Gene-Level Association Test
Description: Pathway and gene level association test using raw data or summary statistics.
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang, R Core Team
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Diff between ARTP2 versions 0.9.32 dated 2017-05-24 and 0.9.44 dated 2018-09-11
DESCRIPTION | 14 +++-- MD5 | 96 +++++++++++++++++++++++------------------ NAMESPACE | 5 +- NEWS.md | 6 ++ R/align.ambig.meta.R |only R/align.ambig.snps.R |only R/align.ambig.study.R |only R/align.reference.R | 22 +++++---- R/ambig.check.data.R |only R/ambig.snps.R |only R/expand_pathway.R |only R/filter.ambig.snps.R |only R/generate.normal.statistics.R | 12 +++-- R/load.pathway.definition.R | 3 - R/load.reference.allele.R | 92 ++++++++++++++++++++++++--------------- R/load.reference.geno.R | 55 ++++++++++++----------- R/load.summary.files.R | 15 +++++- R/load.summary.statistics.R | 19 ++++++-- R/makeVector.R |only R/meta.R | 9 ++- R/options.default.R | 2 R/options.setup.R | 8 +++ R/parseDelimVec.R |only R/rawData.dataframe.setup.R | 4 - R/rawData.genofiles.setup.R | 7 ++ R/rawData.plinkfiles.setup.R | 3 + R/read.bed.R | 38 +++++++++++----- R/recover.stat.R | 2 R/reference.type.R | 4 + R/reformat.reference.path.R | 6 +- R/reformat.snps.R |only R/removeWhiteSpace.R |only R/split.pathway.R | 3 + R/summaryData.setup.R | 25 +++++++++- R/tester.R |only R/update.setup.R | 4 + R/validate.reference.R | 23 ++++++++- README.md | 2 data/data.rda |binary data/geno.rda |binary data/pathway.rda |binary data/ref.does.rda |only data/ref.geno.rda |binary data/subj.id.rda |binary inst/extdata/chr1.bim | 2 inst/extdata/pathway.txt.gz |binary inst/extdata/study1.txt.gz |binary inst/extdata/study2.txt.gz |binary man/ARTP2-package.Rd | 8 +-- man/meta.Rd | 11 ++-- man/options.Rd | 31 ++++++++----- man/rARTP.Rd | 20 ++++++-- man/read.bed.Rd | 6 +- man/ref.does.Rd |only man/sARTP.Rd | 42 +++++++++++++---- man/warm.start.Rd | 7 +- 56 files changed, 410 insertions(+), 196 deletions(-)
Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a
correlation matrix using 'ggplot2'. It provides a solution for reordering the
correlation matrix and displays the significance level on the plot. It also
includes a function for computing a matrix of correlation p-values.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggcorrplot versions 0.1.1 dated 2016-01-12 and 0.1.2 dated 2018-09-11
DESCRIPTION | 12 ++-- MD5 | 17 ++++- R/ggcorrplot.R | 156 +++++++++++++++++++++++++++++++++--------------------- README.md | 99 ++++++++++++---------------------- man/ggcorrplot.Rd | 57 ++++++++++++------- tools |only 6 files changed, 190 insertions(+), 151 deletions(-)
Title: A Tool for Processing Steem Data
Description: Steem is a blockchain-based social media platform (see <https://en.wikipedia.org/wiki/Steemit>). The Steem social activity data are saved in the Steem blockchain, the SteemDB database, the SteemSQL database, and so on. 'steemr' is an R package that downloads the Steem data from the SteemDB and SteemSQL servers, re-organizes the data in a user-friendly way, and visualizes the data for further analysis.
Author: Peng Zhao <pzhao@pzhao.net>
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between steemr versions 0.0.4 dated 2018-06-19 and 0.0.5 dated 2018-09-11
DESCRIPTION | 11 +++++------ MD5 | 6 +++--- R/steemr.R | 3 ++- man/follower.Rd | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Forecasting Long-Term Growth of the U.S. Stock Market
Description: A long-term forecast model called "Jubilee-Tectonic model" is implemented to forecast future returns of the U.S. stock market, Treasury yield, and gold price. The five-factor model can forecast the 10-year and 20-year future equity returns with high R-squared above 80 percent. It is based on linear growth and mean reversion characteristics in the U.S. stock market. In addition, this model enhances the CAPE model by introducing the hypothesis that there are fault lines in the historical CAPE, which can be calibrated and corrected through statistical learning.
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Diff between jubilee versions 0.2.4 dated 2018-09-03 and 0.2.5 dated 2018-09-11
DESCRIPTION | 12 - MD5 | 45 ++-- NEWS.md | 5 build/vignette.rds |binary inst/doc/jubilee-manual.pdf |only inst/doc/jubilee-tutorial.ltx | 307 ++++++++++++++-------------- inst/doc/jubilee-tutorial.pdf |binary inst/extdata/BAA.csv | 3 inst/extdata/GOLDAMGBD228NLBM.csv | 2 inst/extdata/TB3MS.csv | 1 inst/extdata/UNRATE.csv | 1 inst/extdata/ie_data.xls |binary vignettes/jubilee-tutorial.ltx | 307 ++++++++++++++-------------- vignettes/z-jubi-tut-20y-smr-GSI-plot-1.pdf |binary vignettes/z-jubi-tut-20y-smr-YS-plot-1.pdf |binary vignettes/z-jubi-tut-20y-smr-raw-plot-1.pdf |binary vignettes/z-jubi-tut-demo-Yt-1.pdf |binary vignettes/z-jubi-tut-forecast-10y-X-1.pdf |binary vignettes/z-jubi-tut-forecast-10y-rtn-1.pdf |binary vignettes/z-jubi-tut-forecast-20y-X-1.pdf |binary vignettes/z-jubi-tut-forecast-20y-rtn-1.pdf |binary vignettes/z-jubi-tut-inflation-1.pdf |binary vignettes/z-jubi-tut-unrate-1.pdf |binary vignettes/z-jubi-tut-unrate-yoy-1.pdf |binary 24 files changed, 350 insertions(+), 333 deletions(-)
Title: A Fast Solver for Henderson Mixed Model Equation via Row
Operations
Description: Consider the linear mixed model with normal random effects. A typical method to solve Henderson's Mixed Model Equations (HMME) is recursive estimation of the fixed effects and random effects. We provide a fast, stable, and scalable solver to the HMME without computing matrix inverse. See Kim (2017) <arXiv:1710.09663> for more details.
Author: Jiwoong Kim [aut],
Kisung You [aut, cre]
Maintainer: Kisung You <kyou@nd.edu>
Diff between HMMEsolver versions 0.1.0 dated 2017-12-05 and 0.1.1 dated 2018-09-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary src/Makevars | 4 ++-- src/Makevars.win | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 0.5.0 dated 2018-01-03 and 0.6.0 dated 2018-09-11
DESCRIPTION | 20 MD5 | 146 ++++-- NAMESPACE | 12 R/bart_par4.R |only R/cra_exp.R |only R/cra_linear.R |only R/igt_orl.R |only R/peer_ocu.R | 738 ++++++++++++++++---------------- R/prl_ewa.R | 231 +++++----- R/prl_fictitious.R | 229 +++++---- R/prl_fictitious_multipleB.R | 212 ++++----- R/prl_fictitious_rp.R | 233 +++++----- R/prl_fictitious_rp_woa.R |only R/prl_fictitious_woa.R |only R/prl_rp.R | 232 +++++----- R/prl_rp_multipleB.R | 239 +++++----- R/pst_gainloss_Q.R |only R/rdt_happiness.R |only R/ts_par4.R |only R/ts_par6.R |only R/ts_par7.R |only R/wcs_sql.R |only inst/NEWS | 12 inst/extdata/bart_exampleData.txt |only inst/extdata/cra_exampleData.txt |only inst/extdata/pst_exampleData.txt |only inst/extdata/rdt_exampleData.txt |only inst/extdata/ts_exampleData.txt |only inst/extdata/wcs_answersheet.txt |only inst/extdata/wcs_exampleData.txt |only inst/plotting/plot_functions.R | 193 ++++++-- inst/stan/bandit2arm_delta.stan | 94 +--- inst/stan/bandit4arm_4par.stan | 108 ++-- inst/stan/bandit4arm_lapse.stan | 116 ++--- inst/stan/bart_par4.stan |only inst/stan/choiceRT_ddm.stan | 55 +- inst/stan/choiceRT_ddm_single.stan | 20 inst/stan/choiceRT_lba.stan | 210 ++++----- inst/stan/choiceRT_lba_single.stan | 196 ++++---- inst/stan/cra_linear.stan |only inst/stan/dd_cs.stan | 88 +-- inst/stan/dd_cs_single.stan | 32 - inst/stan/dd_exp.stan | 82 +-- inst/stan/dd_hyperbolic.stan | 82 +-- inst/stan/dd_hyperbolic_single.stan | 26 - inst/stan/gng_m1.stan | 122 ++--- inst/stan/gng_m1_reg.stan | 136 +++-- inst/stan/gng_m2.stan | 138 +++-- inst/stan/gng_m2_reg.stan | 154 +++--- inst/stan/gng_m3.stan | 160 +++--- inst/stan/gng_m3_reg.stan | 180 ++++--- inst/stan/gng_m4.stan | 194 ++++---- inst/stan/gng_m4_reg.stan | 214 ++++----- inst/stan/igt_orl.stan |only inst/stan/igt_pvl_decay.stan | 118 ++--- inst/stan/igt_pvl_delta.stan | 110 ++-- inst/stan/igt_vpp.stan | 119 ++--- inst/stan/peer_ocu.stan | 103 ++-- inst/stan/prl_ewa.stan | 174 ++++--- inst/stan/prl_fictitious.stan | 163 ++++--- inst/stan/prl_fictitious_multipleB.stan | 169 ++++--- inst/stan/prl_fictitious_rp.stan | 185 ++++---- inst/stan/prl_fictitious_rp_woa.stan |only inst/stan/prl_fictitious_woa.stan |only inst/stan/prl_rp.stan | 145 +++--- inst/stan/prl_rp_multipleB.stan | 163 ++++--- inst/stan/pst_gainloss_Q.stan |only inst/stan/ra_noLA.stan | 82 +-- inst/stan/ra_noRA.stan | 82 +-- inst/stan/ra_prospect.stan | 88 +-- inst/stan/rdt_happiness.stan |only inst/stan/ts_par4.stan |only inst/stan/ts_par6.stan |only inst/stan/ts_par7.stan |only inst/stan/ug_bayes.stan | 126 ++--- inst/stan/ug_delta.stan | 108 ++-- inst/stan/wcs_sql.stan |only man/bart_par4.Rd |only man/cra_exp.Rd |only man/cra_linear.Rd |only man/igt_orl.Rd |only man/prl_ewa.Rd | 48 +- man/prl_fictitious.Rd | 48 +- man/prl_fictitious_multipleB.Rd | 38 - man/prl_fictitious_rp.Rd | 50 +- man/prl_fictitious_rp_woa.Rd |only man/prl_fictitious_woa.Rd |only man/prl_rp.Rd | 48 +- man/prl_rp_multipleB.Rd | 48 +- man/pst_gainloss_Q.Rd |only man/rdt_happiness.Rd |only man/ts_par4.Rd |only man/ts_par6.Rd |only man/ts_par7.Rd |only man/wcs_sql.Rd |only 95 files changed, 3804 insertions(+), 3315 deletions(-)
Title: Sequential Pairwise Online Rating Techniques
Description: Calculates ratings for two-player or
multi-player challenges. Methods included in package such as are able to
estimate ratings (players strengths) and their evolution in time, also able to
predict output of challenge. Algorithms are based on Bayesian Approximation
Method, and they don't involve any matrix inversions nor likelihood estimation.
Parameters are updated sequentially, and computation doesn't require any
additional RAM to make estimation feasible. Additionally, base of the package
is written in C++ what makes sport computation even faster. Methods used in the
package refers to Mark E. Glickman (1999) <http://www.glicko.net/research/glicko.pdf>;
Mark E. Glickman (2001) <doi:10.1080/02664760120059219>;
Ruby C. Weng, Chih-Jen Lin (2011) <http://jmlr.csail.mit.edu/papers/volume12/weng11a/weng11a.pdf>;
W. Penny, Stephen J. Roberts (1999) <doi:10.1109/IJCNN.1999.832603>.
Author: Dawid Kałędkowski [aut, cre]
Maintainer: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
Diff between sport versions 0.1.0 dated 2018-09-03 and 0.1.1 dated 2018-09-11
sport-0.1.0/sport/README.md |only sport-0.1.0/sport/inst/doc/sport_package_vignette.R |only sport-0.1.0/sport/inst/doc/sport_package_vignette.Rmd |only sport-0.1.0/sport/inst/doc/sport_package_vignette.html |only sport-0.1.0/sport/vignettes/sport_package_vignette.Rmd |only sport-0.1.1/sport/DESCRIPTION | 8 - sport-0.1.1/sport/MD5 | 27 ++-- sport-0.1.1/sport/R/RcppExports.R | 2 sport-0.1.1/sport/build/vignette.rds |binary sport-0.1.1/sport/inst/doc/sport_in_R.R |only sport-0.1.1/sport/inst/doc/sport_in_R.Rmd |only sport-0.1.1/sport/inst/doc/sport_in_R.html |only sport-0.1.1/sport/src/RcppExports.cpp | 1 sport-0.1.1/sport/src/bbt.cpp | 12 +- sport-0.1.1/sport/src/dbl.cpp | 6 - sport-0.1.1/sport/src/glicko.cpp | 67 +++++------ sport-0.1.1/sport/src/glicko.h | 97 +++++------------ sport-0.1.1/sport/tests/testthat/test_glicko2_run.R | 7 - sport-0.1.1/sport/vignettes/sport_in_R.Rmd |only 19 files changed, 96 insertions(+), 131 deletions(-)
Title: Bayesian Framework for Computational Modeling
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>),
the present package aim to provide a framework for conducting Bayesian
analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the
Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>).
The initial version include several modules for conducting Bayesian
equivalents of chi-squared tests, analysis of variance (ANOVA),
multiple (hierarchical) regression, softmax regression, and for fitting data
(e.g., structural equation modeling).
Author: Øystein Olav Skaar [aut, cre]
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>
Diff between bfw versions 0.1.0 dated 2018-06-20 and 0.2.0 dated 2018-09-11
bfw-0.1.0/bfw/inst/extdata/models/stats_metric2.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_metric2_robust.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_metric3.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_metric3_robust.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_metric4.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_metric4_robust.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_nominal2.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_nominal3.txt |only bfw-0.1.0/bfw/inst/extdata/models/stats_nominal4.txt |only bfw-0.1.0/bfw/vignettes/ProjectAllData-Mean-StagesOfCheese-Plot01-1528465133.png |only bfw-0.1.0/bfw/vignettes/ProjectAllData-Mean-StagesOfCheese-Plot01-1528466639.png |only bfw-0.1.0/bfw/vignettes/ProjectAllData-Mean-StagesOfCheese-Plot01-1528467502.png |only bfw-0.1.0/bfw/vignettes/fit_latent_data.md |only bfw-0.1.0/bfw/vignettes/fit_observed_data.md |only bfw-0.1.0/bfw/vignettes/metric.md |only bfw-0.1.0/bfw/vignettes/plot_data.md |only bfw-0.1.0/bfw/vignettes/regression.md |only bfw-0.2.0/bfw/DESCRIPTION | 18 bfw-0.2.0/bfw/LICENSE | 4 bfw-0.2.0/bfw/MD5 | 156 bfw-0.2.0/bfw/NAMESPACE | 4 bfw-0.2.0/bfw/NEWS.md | 107 bfw-0.2.0/bfw/R/basic_functions.R | 1908 +++++----- bfw-0.2.0/bfw/R/data_cats.R | 22 bfw-0.2.0/bfw/R/mcmc.R | 829 ++-- bfw-0.2.0/bfw/R/mcmc_diag.R | 324 - bfw-0.2.0/bfw/R/mcmc_misc.R | 897 ++-- bfw-0.2.0/bfw/R/mcmc_summary.R | 124 bfw-0.2.0/bfw/R/plotdata.R | 1011 ++--- bfw-0.2.0/bfw/R/settings.R | 605 +-- bfw-0.2.0/bfw/R/stats_bernoulli.R | 248 - bfw-0.2.0/bfw/R/stats_covariate.R | 407 +- bfw-0.2.0/bfw/R/stats_fit.R | 466 +- bfw-0.2.0/bfw/R/stats_kappa.R | 204 - bfw-0.2.0/bfw/R/stats_mean.R | 318 - bfw-0.2.0/bfw/R/stats_metric.R | 400 +- bfw-0.2.0/bfw/R/stats_nominal.R | 526 +- bfw-0.2.0/bfw/R/stats_regression.R | 184 bfw-0.2.0/bfw/R/stats_softmax.R | 264 - bfw-0.2.0/bfw/README.md | 154 bfw-0.2.0/bfw/build/vignette.rds |binary bfw-0.2.0/bfw/inst/doc/fit_latent_data.html | 578 --- bfw-0.2.0/bfw/inst/doc/fit_latent_data.md |only bfw-0.2.0/bfw/inst/doc/fit_observed_data.html | 936 +--- bfw-0.2.0/bfw/inst/doc/fit_observed_data.md |only bfw-0.2.0/bfw/inst/doc/metric.R | 234 - bfw-0.2.0/bfw/inst/doc/metric.Rmd | 241 - bfw-0.2.0/bfw/inst/doc/metric.html | 620 --- bfw-0.2.0/bfw/inst/doc/metric.md |only bfw-0.2.0/bfw/inst/doc/plot_data.Rmd | 6 bfw-0.2.0/bfw/inst/doc/plot_data.html | 452 -- bfw-0.2.0/bfw/inst/doc/plot_data.md |only bfw-0.2.0/bfw/inst/doc/regression.html | 484 -- bfw-0.2.0/bfw/inst/doc/regression.md |only bfw-0.2.0/bfw/inst/extdata/data/Cats.R | 176 bfw-0.2.0/bfw/inst/extdata/data/ProjectAllData-Mean-StagesOfCheese-Plot01-1528465133.png |only bfw-0.2.0/bfw/inst/extdata/data/ProjectAllData-Mean-StagesOfCheese-Plot01-1528466639.png |only bfw-0.2.0/bfw/inst/extdata/data/ProjectAllData-Mean-StagesOfCheese-Plot01-1528467502.png |only bfw-0.2.0/bfw/inst/extdata/models/stats_bernoulli.txt | 10 bfw-0.2.0/bfw/inst/extdata/models/stats_covariate.txt | 74 bfw-0.2.0/bfw/inst/extdata/models/stats_covariate_robust.txt | 78 bfw-0.2.0/bfw/inst/extdata/models/stats_fit_cfa.txt |only bfw-0.2.0/bfw/inst/extdata/models/stats_fit_latent.txt | 80 bfw-0.2.0/bfw/inst/extdata/models/stats_fit_latent_robust.txt | 84 bfw-0.2.0/bfw/inst/extdata/models/stats_fit_observed.txt | 141 bfw-0.2.0/bfw/inst/extdata/models/stats_fit_observed_robust.txt | 149 bfw-0.2.0/bfw/inst/extdata/models/stats_kappa.txt | 30 bfw-0.2.0/bfw/inst/extdata/models/stats_mean.txt | 24 bfw-0.2.0/bfw/inst/extdata/models/stats_mean_robust.txt | 28 bfw-0.2.0/bfw/inst/extdata/models/stats_metric.txt | 45 bfw-0.2.0/bfw/inst/extdata/models/stats_metric_robust.txt | 53 bfw-0.2.0/bfw/inst/extdata/models/stats_nominal.txt | 45 bfw-0.2.0/bfw/inst/extdata/models/stats_regression.txt | 88 bfw-0.2.0/bfw/inst/extdata/models/stats_regression_robust.txt | 92 bfw-0.2.0/bfw/inst/extdata/models/stats_softmax.txt | 74 bfw-0.2.0/bfw/inst/extdata/models/stats_softmax_robust.txt | 82 bfw-0.2.0/bfw/man/DiagMCMC.Rd | 42 bfw-0.2.0/bfw/man/ETA.Rd |only bfw-0.2.0/bfw/man/FileName.Rd | 4 bfw-0.2.0/bfw/man/FlattenList.Rd | 3 bfw-0.2.0/bfw/man/ParsePlot.Rd | 34 bfw-0.2.0/bfw/man/PlotData.Rd | 11 bfw-0.2.0/bfw/man/RunContrasts.Rd | 3 bfw-0.2.0/bfw/man/RunMCMC.Rd | 13 bfw-0.2.0/bfw/man/StatsCovariate.Rd | 9 bfw-0.2.0/bfw/man/StatsFit.Rd | 6 bfw-0.2.0/bfw/man/StatsMetric.Rd | 6 bfw-0.2.0/bfw/man/StatsNominal.Rd | 4 bfw-0.2.0/bfw/man/TidyCode.Rd |only bfw-0.2.0/bfw/man/TrimSplit.Rd | 4 bfw-0.2.0/bfw/man/bfw.Rd | 45 bfw-0.2.0/bfw/vignettes/metric.Rmd | 241 - bfw-0.2.0/bfw/vignettes/plot_data.Rmd | 6 93 files changed, 6693 insertions(+), 7822 deletions(-)
Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage
temporal-context data in a data-centric format, which is built on top of
the 'tibble'. The 'tsibble' aims at easily manipulating and analysing temporal
data, including counting and filling time gaps, aggregate over calendar periods,
performing rolling window calculations, and etc.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>),
Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>),
Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>),
Mitchell O'Hara-Wild [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between tsibble versions 0.5.1 dated 2018-08-20 and 0.5.2 dated 2018-09-11
DESCRIPTION | 8 ++-- MD5 | 74 ++++++++++++++++++++-------------------- NAMESPACE | 16 +------- NEWS.md | 19 ++++++++++ R/as-tsibble.R | 52 +++++++++++++++++----------- R/dplyr-verbs.R | 4 +- R/fill-na.R | 8 ++-- R/format.R | 5 ++ R/holiday.R | 22 +++++------ R/index-by.R | 12 ++++-- R/parse-key.R | 9 ++-- R/period.R | 6 --- R/reexports.R | 12 +----- R/slide.R | 17 ++++----- R/split-by.R | 11 +++-- R/stretch.R | 8 ++-- R/tidyr-verbs.R | 18 +++++---- R/tile.R | 6 +-- R/ts2tsibble.R | 2 - R/utils.R | 20 ++++++++++ R/zzz.R | 8 ++++ README.md | 2 - inst/doc/intro-tsibble.html | 10 ++--- inst/doc/window.html | 10 ++--- man/as-tibble.Rd | 7 --- man/as-tsibble.Rd | 4 +- man/index-by.Rd | 2 - man/is-tsibble.Rd | 2 - man/reexports.Rd | 6 +-- man/slide.Rd | 3 - man/slide2.Rd | 4 +- man/stretch2.Rd | 2 - tests/testthat/test-dplyr.R | 18 +++------ tests/testthat/test-index-fun.R | 1 tests/testthat/test-indexby.R | 1 tests/testthat/test-split.R | 8 ++-- tests/testthat/test-tidyr.R | 20 +++++----- tests/testthat/test-tsibble.R | 11 ++++- 38 files changed, 242 insertions(+), 206 deletions(-)
Title: An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Description: A suite of tools to allow you to download all
publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from
the 'Malaria Atlas Project' <https://map.ox.ac.uk/> servers as well as utility functions for plotting
the downloaded data.
Author: Daniel Pfeffer [aut] (<https://orcid.org/0000-0002-2204-3488>),
Tim Lucas [aut, cre] (<https://orcid.org/0000-0003-4694-8107>),
Daniel May [aut] (<https://orcid.org/0000-0003-0005-2452>),
Suzanne Keddie [aut] (<https://orcid.org/0000-0003-1254-7794>),
Jen Rozier [aut] (<https://orcid.org/0000-0002-2610-7557>),
Harry Gibson [aut] (<https://orcid.org/0000-0001-6779-3250>),
Nick Golding [ctb],
David Smith [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>
Diff between malariaAtlas versions 0.0.1 dated 2018-04-10 and 0.0.2 dated 2018-09-11
DESCRIPTION | 19 - MD5 | 115 ++++-- NAMESPACE | 10 R/autoplot.MAPshp.R | 6 R/autoplot.pr.points.R | 11 R/autoplot.vector.points.R |only R/convertPrevalence.R | 17 R/extractRaster.R | 24 - R/getPR.R | 81 +++- R/getRaster.R | 40 ++ R/getShp.R | 182 ++++++---- R/getVecOcc.R |only R/isAvailable.R | 153 +------- R/isAvailable_pr.R |only R/isAvailable_vec.R |only R/listData.R | 20 - R/listPoints.R | 73 ++-- R/listRaster.R | 32 + R/listShp.R | 49 +- R/listSpecies.R |only R/malariaAtlas.R | 2 README.md | 546 +++++++++++++++++++------------ build/vignette.rds |binary inst/doc/overview.R | 40 ++ inst/doc/overview.Rmd | 61 +++ inst/doc/overview.html | 204 +++++++++-- man/as.pr.points.Rd |only man/as.vectorpoints.Rd |only man/autoplot.MAPshp.Rd | 4 man/autoplot.vector.points.Rd |only man/convertPrevalence.Rd | 6 man/extractRaster.Rd | 20 - man/figures/unnamed-chunk-10-1.png |binary man/figures/unnamed-chunk-11-1.png |only man/figures/unnamed-chunk-12-1.png |only man/figures/unnamed-chunk-13-1.png |binary man/figures/unnamed-chunk-14-1.png |binary man/figures/unnamed-chunk-15-1.png |only man/figures/unnamed-chunk-16-1.png |binary man/figures/unnamed-chunk-17-1.png |binary man/figures/unnamed-chunk-19-1.png |only man/figures/unnamed-chunk-20-1.png |only man/figures/unnamed-chunk-21-1.png |only man/figures/unnamed-chunk-22-1.png |only man/figures/unnamed-chunk-23-1.png |only man/figures/unnamed-chunk-24-1.png |only man/figures/unnamed-chunk-25-1.png |only man/figures/unnamed-chunk-26-1.png |only man/figures/unnamed-chunk-27-1.png |only man/figures/unnamed-chunk-28-1.png |only man/figures/unnamed-chunk-9-1.png |binary man/getPR.Rd | 8 man/getRaster.Rd | 4 man/getShp.Rd | 29 + man/getVecOcc.Rd |only man/isAvailable.Rd | 36 -- man/isAvailable_pr.Rd |only man/isAvailable_vec.Rd |only man/listData.Rd | 9 man/listPoints.Rd | 11 man/listShp.Rd | 4 man/listSpecies.Rd |only tests/testthat/test_as.class.R |only tests/testthat/test_autoplot.MAPraster.R | 46 +- tests/testthat/test_extractRaster.R |only tests/testthat/test_getPR.R | 75 +++- tests/testthat/test_getRaster.R | 67 +++ tests/testthat/test_getShp.R | 63 +-- tests/testthat/test_getVecOcc.R |only tests/testthat/test_isAvailable.R | 67 ++- tests/testthat/test_listData.R | 158 +++++++- tests/testthat/test_plots.R |only vignettes/overview.Rmd | 61 +++ 73 files changed, 1612 insertions(+), 741 deletions(-)
Title: Kriging-Based Inversion for Deterministic and Noisy Computer
Experiments
Description: Criteria and algorithms for sequentially estimating level sets of a multivariate numerical function, possibly observed with noise.
Author: Clement Chevalier, Victor Picheny, David Ginsbourger and Dario Azzimonti
Maintainer: Clement Chevalier <clement.chevalier@unine.ch>
Diff between KrigInv versions 1.3.1 dated 2014-12-22 and 1.4.1 dated 2018-09-11
KrigInv-1.3.1/KrigInv/R/camelback2.R |only KrigInv-1.3.1/KrigInv/R/computeAuxVariables_noChol.R |only KrigInv-1.3.1/KrigInv/R/computeAuxVariables_update.R |only KrigInv-1.3.1/KrigInv/R/fun_test2d_ranjan.R |only KrigInv-1.3.1/KrigInv/R/fundet.R |only KrigInv-1.3.1/KrigInv/R/jn_optim.R |only KrigInv-1.3.1/KrigInv/R/lili2D.R |only KrigInv-1.3.1/KrigInv/R/max_sur.R |only KrigInv-1.3.1/KrigInv/R/max_timse.R |only KrigInv-1.3.1/KrigInv/R/predict_update_km.R |only KrigInv-1.3.1/KrigInv/R/sur_optim.R |only KrigInv-1.3.1/KrigInv/R/timse_optim.R |only KrigInv-1.3.1/KrigInv/R/update_km.R |only KrigInv-1.3.1/KrigInv/man/camelback2.Rd |only KrigInv-1.3.1/KrigInv/man/computeAuxVariables_noChol.Rd |only KrigInv-1.3.1/KrigInv/man/computeAuxVariables_update.Rd |only KrigInv-1.3.1/KrigInv/man/fun_test2d_ranjan.Rd |only KrigInv-1.3.1/KrigInv/man/fundet.Rd |only KrigInv-1.3.1/KrigInv/man/jn_optim.Rd |only KrigInv-1.3.1/KrigInv/man/lili2D.Rd |only KrigInv-1.3.1/KrigInv/man/max_sur.Rd |only KrigInv-1.3.1/KrigInv/man/max_timse.Rd |only KrigInv-1.3.1/KrigInv/man/predict_update_km.Rd |only KrigInv-1.3.1/KrigInv/man/sur_optim.Rd |only KrigInv-1.3.1/KrigInv/man/timse_optim.Rd |only KrigInv-1.3.1/KrigInv/man/update_km.Rd |only KrigInv-1.4.1/KrigInv/DESCRIPTION | 23 KrigInv-1.4.1/KrigInv/MD5 | 144 ++-- KrigInv-1.4.1/KrigInv/NAMESPACE | 93 +-- KrigInv-1.4.1/KrigInv/R/EGI.R | 102 +-- KrigInv-1.4.1/KrigInv/R/EGIparallel.R | 214 +++++-- KrigInv-1.4.1/KrigInv/R/bichon_optim.R | 46 - KrigInv-1.4.1/KrigInv/R/computeQuickKrigcov.R | 6 KrigInv-1.4.1/KrigInv/R/computeRealVolumeConstant.R | 232 ++++---- KrigInv-1.4.1/KrigInv/R/excursion_probability.R |only KrigInv-1.4.1/KrigInv/R/integration_design.R | 35 - KrigInv-1.4.1/KrigInv/R/jn_optim_parallel.R |only KrigInv-1.4.1/KrigInv/R/jn_optim_parallel2.R |only KrigInv-1.4.1/KrigInv/R/max_futureVol_parallel.R |only KrigInv-1.4.1/KrigInv/R/max_infill_criterion.R | 163 ++--- KrigInv-1.4.1/KrigInv/R/max_sur_parallel.R | 86 +- KrigInv-1.4.1/KrigInv/R/max_timse_parallel.R | 13 KrigInv-1.4.1/KrigInv/R/max_vorob_parallel.R | 356 ++++++------ KrigInv-1.4.1/KrigInv/R/print_uncertainty_1d.R | 212 ++++--- KrigInv-1.4.1/KrigInv/R/print_uncertainty_2d.R | 213 ++++--- KrigInv-1.4.1/KrigInv/R/print_uncertainty_nd.R | 279 +++++---- KrigInv-1.4.1/KrigInv/R/ranjan_optim.R | 44 - KrigInv-1.4.1/KrigInv/R/sur_optim_parallel.R | 58 +- KrigInv-1.4.1/KrigInv/R/sur_optim_parallel2.R | 8 KrigInv-1.4.1/KrigInv/R/timse_optim_parallel.R | 112 +-- KrigInv-1.4.1/KrigInv/R/timse_optim_parallel2.R | 30 - KrigInv-1.4.1/KrigInv/R/tmse_optim.R | 13 KrigInv-1.4.1/KrigInv/R/tsee_optim.R | 46 - KrigInv-1.4.1/KrigInv/R/vorobVol_optim_parallel.R |only KrigInv-1.4.1/KrigInv/R/vorobVol_optim_parallel2.R |only KrigInv-1.4.1/KrigInv/R/vorob_optim_parallel.R | 145 ++--- KrigInv-1.4.1/KrigInv/R/vorob_optim_parallel2.R | 30 - KrigInv-1.4.1/KrigInv/man/EGI.Rd | 463 +++++++++------- KrigInv-1.4.1/KrigInv/man/EGIparallel.Rd | 449 +++++++++------ KrigInv-1.4.1/KrigInv/man/KrigInv-package.Rd | 56 - KrigInv-1.4.1/KrigInv/man/bichon_optim.Rd | 31 - KrigInv-1.4.1/KrigInv/man/computeQuickKrigcov.Rd | 184 +++--- KrigInv-1.4.1/KrigInv/man/computeRealVolumeConstant.Rd | 147 ++--- KrigInv-1.4.1/KrigInv/man/excursion_probability.Rd |only KrigInv-1.4.1/KrigInv/man/integration_design.Rd | 228 +++---- KrigInv-1.4.1/KrigInv/man/jn_optim_parallel.Rd |only KrigInv-1.4.1/KrigInv/man/jn_optim_parallel2.Rd |only KrigInv-1.4.1/KrigInv/man/max_futureVol_parallel.Rd |only KrigInv-1.4.1/KrigInv/man/max_infill_criterion.Rd | 200 +++--- KrigInv-1.4.1/KrigInv/man/max_sur_parallel.Rd | 231 ++++--- KrigInv-1.4.1/KrigInv/man/max_timse_parallel.Rd | 251 ++++---- KrigInv-1.4.1/KrigInv/man/max_vorob_parallel.Rd | 236 ++++---- KrigInv-1.4.1/KrigInv/man/precomputeUpdateData.Rd | 164 ++--- KrigInv-1.4.1/KrigInv/man/predict_nobias_km.Rd | 252 ++++---- KrigInv-1.4.1/KrigInv/man/predict_update_km_parallel.Rd | 237 ++++---- KrigInv-1.4.1/KrigInv/man/print_uncertainty.Rd | 149 ++--- KrigInv-1.4.1/KrigInv/man/print_uncertainty_1d.Rd | 306 +++++----- KrigInv-1.4.1/KrigInv/man/print_uncertainty_2d.Rd | 352 +++++------- KrigInv-1.4.1/KrigInv/man/print_uncertainty_nd.Rd | 245 ++++---- KrigInv-1.4.1/KrigInv/man/ranjan_optim.Rd | 22 KrigInv-1.4.1/KrigInv/man/sur_optim_parallel.Rd | 196 +++--- KrigInv-1.4.1/KrigInv/man/sur_optim_parallel2.Rd | 251 ++++---- KrigInv-1.4.1/KrigInv/man/timse_optim_parallel.Rd | 215 +++---- KrigInv-1.4.1/KrigInv/man/timse_optim_parallel2.Rd | 279 ++++----- KrigInv-1.4.1/KrigInv/man/tmse_optim.Rd | 24 KrigInv-1.4.1/KrigInv/man/tsee_optim.Rd | 159 ++--- KrigInv-1.4.1/KrigInv/man/vorobVol_optim_parallel.Rd |only KrigInv-1.4.1/KrigInv/man/vorobVol_optim_parallel2.Rd |only KrigInv-1.4.1/KrigInv/man/vorob_optim_parallel.Rd | 207 +++---- KrigInv-1.4.1/KrigInv/man/vorob_optim_parallel2.Rd | 255 ++++---- KrigInv-1.4.1/KrigInv/man/vorob_threshold.Rd | 130 ++-- KrigInv-1.4.1/KrigInv/tests |only 92 files changed, 4503 insertions(+), 4119 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and predictions of
any machine learning model.
Implemented methods are:
Feature importance described by Fisher et al. (2018) <arXiv:1801.01489>,
accumulated local effects plots described by Apley (2018) <arXiv:1612.08468>,
partial dependence plots described by Friedman (2001) <http://www.jstor.org/stable/2699986>,
individual conditional expectation ('ice') plots described by Goldstein et al. (2013) <doi:10.1080/10618600.2014.907095>,
local models (variant of 'lime') described by Ribeiro et. al (2016) <arXiv:1602.04938>,
the Shapley Value described by Strumbelj et. al (2014) <doi:10.1007/s10115-013-0679-x>,
feature interactions described by Friedman et. al <doi:10.1214/07-AOAS148> and
tree surrogate models.
Author: Christoph Molnar [aut, cre]
Maintainer: Christoph Molnar <christoph.molnar@gmail.com>
Diff between iml versions 0.6.0 dated 2018-08-17 and 0.7.0 dated 2018-09-11
iml-0.6.0/iml/R/Partial.R |only iml-0.6.0/iml/man/plot.Partial.Rd |only iml-0.6.0/iml/tests/testthat/test-Partial.R |only iml-0.7.0/iml/DESCRIPTION | 16 +- iml-0.7.0/iml/MD5 | 75 ++++++----- iml-0.7.0/iml/NAMESPACE | 5 iml-0.7.0/iml/NEWS.md | 8 + iml-0.7.0/iml/R/FeatureEffect-ale.R |only iml-0.7.0/iml/R/FeatureEffect.R |only iml-0.7.0/iml/R/FeatureImp.R | 11 + iml-0.7.0/iml/R/Interaction.R | 2 iml-0.7.0/iml/R/InterpretationMethod.R | 2 iml-0.7.0/iml/R/LocalModel.R | 11 + iml-0.7.0/iml/R/MarginalGenerator.R | 3 iml-0.7.0/iml/R/TreeSurrogate.R | 3 iml-0.7.0/iml/R/utils.R | 140 +++++++++++++++++++--- iml-0.7.0/iml/inst/CITATION |only iml-0.7.0/iml/inst/doc/intro.R | 12 - iml-0.7.0/iml/inst/doc/intro.Rmd | 24 +-- iml-0.7.0/iml/inst/doc/intro.html | 76 +++++------ iml-0.7.0/iml/inst/doc/parallel.R | 4 iml-0.7.0/iml/inst/doc/parallel.Rmd | 6 iml-0.7.0/iml/inst/doc/parallel.html | 20 +-- iml-0.7.0/iml/man/FeatureEffect.Rd |only iml-0.7.0/iml/man/Interaction.Rd | 3 iml-0.7.0/iml/man/LocalModel.Rd | 7 - iml-0.7.0/iml/man/Partial.Rd | 137 --------------------- iml-0.7.0/iml/man/TreeSurrogate.Rd | 3 iml-0.7.0/iml/man/calculate.ale.cat.Rd |only iml-0.7.0/iml/man/calculate.ale.num.Rd |only iml-0.7.0/iml/man/calculate.ale.num.cat.Rd |only iml-0.7.0/iml/man/calculate.ale.num.num.Rd |only iml-0.7.0/iml/man/impute_cells.Rd |only iml-0.7.0/iml/man/order_levels.Rd |only iml-0.7.0/iml/man/plot.FeatureEffect.Rd |only iml-0.7.0/iml/tests/testthat/Rplots.pdf |binary iml-0.7.0/iml/tests/testthat/helper-predictor.R | 10 + iml-0.7.0/iml/tests/testthat/test-FeatureEffect.R |only iml-0.7.0/iml/tests/testthat/test-FeatureImp.R | 15 ++ iml-0.7.0/iml/tests/testthat/test-Interaction.R | 1 iml-0.7.0/iml/tests/testthat/test-LocalModel.R | 1 iml-0.7.0/iml/tests/testthat/test-Shapley.R | 1 iml-0.7.0/iml/tests/testthat/test-TreeSurrogate.R | 1 iml-0.7.0/iml/tests/testthat/test-utils.R | 67 ++++++++-- iml-0.7.0/iml/vignettes/intro.Rmd | 24 +-- iml-0.7.0/iml/vignettes/parallel.Rmd | 6 46 files changed, 388 insertions(+), 306 deletions(-)
Title: Omics Data Integration Using Kernel Methods
Description: Kernel-based methods are powerful methods for integrating
heterogeneous types of data. mixKernel aims at providing methods to combine
kernel for unsupervised exploratory analysis. Different solutions are
provided to compute a meta-kernel, in a consensus way or in a way that
best preserves the original topology of the data. mixKernel also integrates
kernel PCA to visualize similarities between samples in a non linear space
and from the multiple source point of view. Functions to assess and display
important variables are also provided in the package.
Author: Jerome Mariette [aut, cre],
Nathalie Villa-Vialaneix [aut]
Maintainer: Jerome Mariette <jerome.mariette@inra.fr>
Diff between mixKernel versions 0.1 dated 2017-05-17 and 0.2 dated 2018-09-11
DESCRIPTION | 15 ++- MD5 | 26 +++--- NAMESPACE | 8 + NEWS | 8 + R/cim.kernel.R | 10 +- R/combine.kernels.R | 21 +++- R/kernel.pca.R | 3 R/kernel.pca.permute.R | 60 ++++++++++---- R/kernels.R | 160 +++++++++++++++++++++++++++++++++++--- R/plot.kernel.pca.R | 6 - R/zzz.R | 13 +-- inst/doc/mixKernelUsersGuide.Rmd | 131 +++++++++---------------------- inst/doc/mixKernelUsersGuide.html | 125 +++++++++++++---------------- man/compute.kernel.Rd | 35 +++++--- 14 files changed, 383 insertions(+), 238 deletions(-)
Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing, spherical texture mapping, lambertian reflectance, and ambient occlusion to produce hillshades of elevation matrices. Includes water detection and layering functions, programmable color palette generation, several built-in textures, 2D and 3D plotting options, and the ability to export 3D maps to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayshader versions 0.4.7 dated 2018-08-31 and 0.5.1 dated 2018-09-11
rayshader-0.4.7/rayshader/R/write_png.R |only rayshader-0.4.7/rayshader/man/write_png.Rd |only rayshader-0.5.1/rayshader/DESCRIPTION | 16 +++---- rayshader-0.5.1/rayshader/MD5 | 34 ++++++++-------- rayshader-0.5.1/rayshader/NAMESPACE | 3 - rayshader-0.5.1/rayshader/NEWS |only rayshader-0.5.1/rayshader/R/make_base.R | 20 ++++----- rayshader-0.5.1/rayshader/R/make_lines.R | 33 ++++++++++++--- rayshader-0.5.1/rayshader/R/make_shadow.R | 4 - rayshader-0.5.1/rayshader/R/make_water.R | 16 +++---- rayshader-0.5.1/rayshader/R/make_waterlines.R | 8 +-- rayshader-0.5.1/rayshader/R/plot_3d.R | 36 ++++++++++------- rayshader-0.5.1/rayshader/R/plot_map.R | 6 ++ rayshader-0.5.1/rayshader/R/save_3dprint.R |only rayshader-0.5.1/rayshader/R/save_png.R |only rayshader-0.5.1/rayshader/README.md | 7 +-- rayshader-0.5.1/rayshader/man/figures/raylogosmall.png |only rayshader-0.5.1/rayshader/man/make_lines.Rd | 4 + rayshader-0.5.1/rayshader/man/save_3dprint.Rd |only rayshader-0.5.1/rayshader/man/save_png.Rd |only rayshader-0.5.1/rayshader/src/calculate_normal.cpp | 4 - rayshader-0.5.1/rayshader/src/lambshade.cpp | 4 - 22 files changed, 119 insertions(+), 76 deletions(-)
Title: A Toolbox for Writing Pretty Papers and Reports
Description: A toolbox for writing 'knitr', 'Sweave' or other 'LaTeX'- or 'markdown'-based
reports and to prettify the output of various estimated models.
Author: Benjamin Hofner, with contributions by many others (see inst/CONTRIBUTIONS)
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between papeR versions 1.0-2 dated 2017-02-16 and 1.0-3 dated 2018-09-11
ChangeLog | 37 ++++++++++++++++++++++++++++- DESCRIPTION | 8 +++--- MD5 | 19 +++++++------- R/summarize.R | 6 ++-- build/vignette.rds |binary inst/NEWS.Rd | 10 +++++++ inst/doc/papeR_introduction.html | 8 +++--- inst/doc/papeR_with_latex.pdf |binary man/papeR-package.Rd | 4 +-- tests/testthat/test-toLatex.R | 3 -- vignettes/papeR_with_latex-concordance.tex |only 11 files changed, 70 insertions(+), 25 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <bart.kranstauber@ieu.uzh.ch>
Diff between move versions 3.0.2 dated 2017-11-07 and 3.1.0 dated 2018-09-11
move-3.0.2/move/tests/testthat/Rplots.pdf |only move-3.1.0/move/ChangeLog | 4 move-3.1.0/move/DESCRIPTION | 11 move-3.1.0/move/MD5 | 62 ++-- move-3.1.0/move/NAMESPACE | 4 move-3.1.0/move/R/WebImport.R | 30 +- move-3.1.0/move/R/move.R | 10 move-3.1.0/move/R/print.R | 3 move-3.1.0/move/R/split.R | 6 move-3.1.0/move/R/subset.R | 6 move-3.1.0/move/R/thinTrack.R |only move-3.1.0/move/build/vignette.rds |binary move-3.1.0/move/inst/doc/browseMovebank.pdf |binary move-3.1.0/move/inst/doc/move.pdf |binary move-3.1.0/move/man/UDStack.Rd | 6 move-3.1.0/move/man/angle.Rd | 10 move-3.1.0/move/man/brownian.bridge.dyn.Rd | 4 move-3.1.0/move/man/corridor.Rd | 16 - move-3.1.0/move/man/distance.Rd | 10 move-3.1.0/move/man/getMovebankData.Rd | 1 move-3.1.0/move/man/getMovebankNonLocationData.Rd | 2 move-3.1.0/move/man/getMovebankSensorAttributes.Rd | 2 move-3.1.0/move/man/hrBootstrap.Rd | 6 move-3.1.0/move/man/interpolateTime.Rd | 6 move-3.1.0/move/man/move.Rd | 2 move-3.1.0/move/man/seglength.Rd | 8 move-3.1.0/move/man/speed.Rd | 10 move-3.1.0/move/man/thinTrack.Rd |only move-3.1.0/move/man/timeLag.Rd | 10 move-3.1.0/move/man/turnAngleGc.Rd | 10 move-3.1.0/move/tests/testthat/test.getDataRepositoryData.R | 74 +++-- move-3.1.0/move/tests/testthat/test.license.R |only move-3.1.0/move/tests/testthat/test.subSet.R | 172 +++++------- move-3.1.0/move/tests/testthat/test.web.R | 17 + 34 files changed, 296 insertions(+), 206 deletions(-)
Title: Latent Markov Models with and without Covariates
Description: Fit certain versions of the Latent Markov model for longitudinal categorical data.
Author: Francesco Bartolucci, Silvia Pandolfi - University of Perugia (IT)
Maintainer: Francesco Bartolucci <bart@stat.unipg.it>
Diff between LMest versions 2.4.2 dated 2018-03-11 and 2.4.3 dated 2018-09-11
DESCRIPTION | 10 ++++----- MD5 | 38 ++++++++++++++++++++++++++++++------ NAMESPACE | 12 +++++++---- R/bootstrap_lm_basic.R | 6 ++--- R/bootstrap_lm_basic_cont.R |only R/bootstrap_lm_cov_latent_cont.R |only R/complk_cont.R |only R/draw_lm_basic_cont.R |only R/draw_lm_cov_latent_cont.R |only R/est_lm_basic_cont.R |only R/est_lm_cov_latent_cont.R |only R/lk_comp_latent_cont.R |only R/print.LMbasiccont.R |only R/print.LMlatentcont.R |only R/prob_post_cov_cont.R |only R/search.model.LM.R | 13 +++++++++++- R/summary.LMbasiccont.R |only R/summary.LMlatentcont.R |only man/LMest-package.Rd | 4 +-- man/bootstrap_lm_basic_cont.Rd |only man/bootstrap_lm_cov_latent_cont.Rd |only man/complk_cont.Rd |only man/draw_lm_basic_cont.Rd |only man/draw_lm_cov_latent_cont.Rd |only man/est_lm_basic_cont.Rd |only man/est_lm_cov_latent_cont.Rd |only man/lk_comp_latent_cont.Rd |only man/print.LMbasiccont.Rd |only man/print.LMlatentcont.Rd |only man/prob_post_cov_cont.Rd |only man/search.model.LM.Rd | 8 +++---- man/summary.LMbasiccont.Rd |only man/summary.LMlatentcont.Rd |only 33 files changed, 66 insertions(+), 25 deletions(-)
Title: A Time Series Toolbox for Official Statistics
Description: Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.
Author: Matthias Bannert [aut, cre],
Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>
Diff between tstools versions 0.3.7 dated 2018-07-16 and 0.3.8 dated 2018-09-11
DESCRIPTION | 8 - MD5 | 39 +++-- NAMESPACE | 1 R/add_legend.R | 35 +++-- R/low_level_bar_plots.R | 182 ++++++++++----------------- R/low_level_line_plots.R | 44 +++--- R/read_swissdata.R | 7 - R/read_ts.R | 10 - R/themes.R | 26 +++ R/tsplot.R | 252 +++++++++++++++++++++++++++++--------- R/utils.R | 15 ++ inst/doc/tstools.R | 24 +++ inst/doc/tstools.Rmd | 68 ++++++++++ inst/doc/tstools.html | 287 +++++++++++++++++++++++++------------------- man/compute_decimal_time.Rd | 2 man/get_date_vector.Rd |only man/init_tsplot_theme.Rd | 84 +++++++----- man/read_swissdata.Rd | 5 man/read_ts.Rd | 5 man/tsplot.Rd | 10 - vignettes/tstools.Rmd | 68 ++++++++++ 21 files changed, 770 insertions(+), 402 deletions(-)
Title: Sensitivity Analysis for Comparative Methods
Description: An implementation of sensitivity analysis for phylogenetic comparative
methods. The package is an umbrella of statistical and graphical methods that
estimate and report different types of uncertainty in PCM:
(i) Species Sampling uncertainty (sample size; influential species and clades).
(ii) Phylogenetic uncertainty (different topologies and/or branch lengths).
(iii) Data uncertainty (intraspecific variation and measurement error).
Author: Gustavo Paterno [cre, aut],
Gijsbert Werner [aut],
Caterina Penone [aut],
Pablo Martinez [ctb]
Maintainer: Gustavo Paterno <paternogbc@gmail.com>
Diff between sensiPhy versions 0.8.2 dated 2018-06-12 and 0.8.3 dated 2018-09-11
DESCRIPTION | 8 +++---- MD5 | 44 ++++++++++++++++++++-------------------- NEWS.md | 6 +++++ R/clade_physig.R | 2 + R/influ_physig.R | 2 + R/intra_phyglm.R | 2 - R/intra_physig.R | 2 + R/samp_physig.R | 2 + R/tree_influ_phyglm.R | 10 --------- R/tree_influ_phylm.R | 3 -- R/tree_intra_phylm.R | 2 - R/tree_phyglm.R | 2 - R/tree_phylm.R | 4 +-- R/tree_physig.R | 4 +-- R/tree_samp_phylm.R | 2 - inst/doc/sensiPhy_vignette.html | 4 +-- man/clade_physig.Rd | 2 + man/influ_physig.Rd | 2 + man/intra_physig.Rd | 2 + man/samp_physig.Rd | 2 + man/tree_influ_phyglm.Rd | 9 -------- man/tree_influ_phylm.Rd | 3 -- man/tree_physig.Rd | 2 + 23 files changed, 62 insertions(+), 59 deletions(-)
Title: Get Data from the 'KOF Datenservice' API
Description: Read Swiss time series data from the 'KOF Datenservice' API, <https://datenservice.kof.ethz.ch>. The API provides macroeconomic survey data, business cycle and further macro economic time series about Switzerland. The package itself is a set of wrappers around the 'KOF Datenservice' API. The 'kofdata' package is able to consume public information as well as data that requires an API token.
Author: Matthias Bannert [aut, cre],
Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>
Diff between kofdata versions 0.1.3.1 dated 2018-06-18 and 0.1.3.2 dated 2018-09-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 1 - tests/testthat/test_get_metadata.R | 10 +++++----- 4 files changed, 12 insertions(+), 13 deletions(-)
Title: Air Pollution Removal by Dry Deposition on Trees
Description: The model estimates air pollution removal by dry deposition on trees. It also estimates or uses hourly values for aerodynamic resistance, boundary layer resistance, canopy resistance, stomatal resistance, cuticular resistance, mesophyll resistance, soil resistance, friction velocity and deposition velocity. It also allows plotting graphical results for a specific time period. The pollutants are nitrogen dioxide, ozone, sulphur dioxide, carbon monoxide and particulate matter. Baldocchi D (1994) <doi:10.1093/treephys/14.7-8-9.1069>. Farquhar GD, von Caemmerer S, Berry JA (1980) Planta 149: 78-90. Hirabayashi S, Kroll CN, Nowak DJ (2015) i-Tree Eco Dry Deposition Model. Nowak DJ, Crane DE, Stevens JC (2006) <doi:10.1016/j.ufug.2006.01.007>. US EPA (1999) PCRAMMET User's Guide. EPA-454/B-96-001. Weiss A, Norman JM (1985) Agricultural and Forest Meteorology 34: 205—213.
Author: Silvestre Garcia de Jalon
Maintainer: Silvestre Garcia de Jalon <s.garciadejalon@gmail.com>
Diff between TreeDep versions 0.1.1 dated 2018-05-30 and 0.1.2 dated 2018-09-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Daylight.R | 4 ++-- R/TreeDep_plot.R | 3 ++- man/Daylight.Rd | 6 +++--- man/TreeDep_plot.Rd | 7 +++++-- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Pretty Print R Code in the Terminal
Description: Replace the standard print method for functions with one that
performs syntax highlighting, using ANSI colors, if the terminal
supports them.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between prettycode versions 1.0.1 dated 2017-12-12 and 1.0.2 dated 2018-09-11
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 9 +++++++++ R/print.R | 44 +++++++++++++++++++++++++++++++++++++++----- inst/README.markdown | 4 ++-- man/prettycode.Rd | 5 +++-- man/print.function.Rd | 7 +++++-- tests/testthat/test-print.R | 11 +++++++++++ 9 files changed, 82 insertions(+), 23 deletions(-)
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau Guillerme and Smith (2017) <doi:10.1101/209775>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph],
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 0.1.2 dated 2018-03-19 and 0.2.0 dated 2018-09-11
DESCRIPTION | 19 MD5 | 111 +- NAMESPACE | 26 NEWS.md | 26 R/Bootstrap.R | 7 R/Fitch.R | 9 R/Jackknife.R |only R/RandomTreeScore.R | 4 R/Ratchet.R | 84 +- R/SPR.R | 1 R/Support.R |only R/TBR.R | 99 ++ R/TreeSearch.R | 39 R/ape_interface.R |only R/data.R | 8 R/helper_functions.R | 18 R/mpl_morphyex.R | 16 R/mpl_prepare_data.R | 36 R/parse_files.R | 100 ++ R/phylo.R | 13 R/tree_display.R | 61 + R/tree_rearrangement.R | 81 + build/partial.rdb |binary build/vignette.rds |binary data/brewer.R | 27 inst/apa-old-doi-prefix.csl | 1440 +++++++++++++++++------------------ inst/doc/getting-started.html | 4 inst/doc/inapplicable.R | 46 - inst/doc/inapplicable.Rmd | 59 + inst/doc/inapplicable.html | 105 +- inst/doc/load-data.Rmd | 16 inst/doc/load-data.html | 12 inst/doc/profile-scores.html | 4 inst/doc/profile.html | 22 inst/tests/Fleas_nex.nex |only inst/tests/Fleas_nex.txt |only inst/tests/benchmark_timing.R | 27 inst/tests/hyolith_benchmark.R |only man/ApeTime.Rd |only man/DescendantEdges.Rd | 11 man/ICSteps.Rd | 4 man/MorphyBootstrap.Rd | 25 man/NNI.Rd | 5 man/NewickTree.Rd |only man/Ratchet.Rd | 115 ++ man/ReadCharacters.Rd | 8 man/ReadTntTree.Rd | 58 + man/RearrangeEdges.Rd | 6 man/RootTree.Rd |only man/SPR.Rd | 2 man/SortTree.Rd |only man/SplitFrequency.Rd |only man/SuccessiveApproximations.Rd | 3 man/SupportColour.Rd |only man/TBR.Rd | 27 man/TreeSearch.Rd | 27 man/UniqueExceptHits.Rd |only man/brewer.Rd | 10 tests/testthat/test-ape-interface.R |only tests/testthat/test-ape-tree.nex |only tests/testthat/test-mpl-search.R | 61 + tests/testthat/test-tree-rearrange.R | 29 vignettes/inapplicable.Rmd | 59 + vignettes/load-data.Rmd | 16 64 files changed, 1886 insertions(+), 1100 deletions(-)
Title: Perform the Complete Processing of a Set of Proton Nuclear
Magnetic Resonance Spectra
Description: Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free induction decay (raw data) and based on a processing sequence (macro-command file). An additional file specifies all the spectra to be considered by associating their sample code as well as the levels of experimental factors to which they belong. More detail can be found in Jacob et al. (2017) <doi:10.1007/s11306-017-1178-y>.
Author: Daniel Jacob [cre, aut] (<https://orcid.org/0000-0002-6687-7169>),
Catherine Deborde [ctb],
Marie Lefebvre [ctb]
Maintainer: Daniel Jacob <daniel.jacob@inra.fr>
Diff between Rnmr1D versions 1.2.0 dated 2018-08-14 and 1.2.1 dated 2018-09-11
DESCRIPTION | 10 +++--- MD5 | 28 +++++++++--------- R/RcppExports.R | 4 ++ R/Rnmr.R | 13 +++++++- R/RnmrTools.R | 28 +++++++++++++++--- R/StatTools.R | 15 +++++++-- R/doProcessing.R | 6 +++ build/partial.rdb |binary inst/doc/Rnmr1D.html | 78 +++++++++++++++++++++++++-------------------------- man/Spec1rProcpar.Rd | 2 - man/doProcessing.Rd | 4 ++ man/plotLoadings.Rd | 4 +- man/plotScores.Rd | 8 ++++- src/RcppExports.cpp | 13 ++++++++ src/libCspec.cpp | 44 +++++++++++++++++++++++----- 15 files changed, 177 insertions(+), 80 deletions(-)
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.1.0 dated 2017-09-08 and 1.2.1 dated 2018-09-11
DESCRIPTION | 15 MD5 | 105 ++-- NAMESPACE | 4 NEWS.md | 22 R/E_step.R | 81 +++ R/M_step.R | 12 R/estimateEM.R | 439 ++++++++++++++---- R/generic_functions.R | 44 + R/init_EM.R | 645 +++++++++++++-------------- R/plot_functions.R | 84 +++ build/vignette.rds |binary inst/CITATION | 4 inst/doc/monkeys.R |only inst/doc/monkeys.Rmd |only inst/doc/monkeys.html |only inst/doc/tutorial.R | 3 inst/doc/tutorial.Rmd | 9 inst/doc/tutorial.html | 44 + man/PhyloEM.Rd | 59 +- man/check.selection.strength.Rd | 4 man/check_dimensions.Rd | 4 man/check_range_alpha.Rd |only man/compute_E.simple.Rd | 3 man/compute_expectations.scOU.Rd | 4 man/compute_gauss_lasso.Rd | 4 man/compute_log_likelihood.simple.Rd | 8 man/compute_mahalanobis_distance.simple.Rd | 5 man/compute_tree_correlations_matrix.scOU.Rd | 4 man/compute_variance_covariance.OU.Rd | 3 man/compute_variance_covariance.OU.nonsym.Rd |only man/compute_variance_covariance.scOU.Rd | 3 man/estimateEM.Rd | 41 - man/extract.enumerate_parsimony.Rd | 4 man/extract.equivalent_shifts.Rd | 4 man/extract.variance_covariance.Rd | 5 man/find_grid_alpha.Rd | 10 man/find_rotation.Rd |only man/get_criterion.Rd |only man/imputed_traits.Rd | 8 man/init.EM.lasso.Rd | 11 man/init.alpha.gamma.estimation.Rd | 4 man/merge_rotations.Rd |only man/model_selection.Rd | 4 man/params_BM.Rd | 4 man/params_OU.Rd | 11 man/params_process.PhyloEM.Rd | 4 man/plot.PhyloEM.Rd | 15 man/plot.enumerate_parsimony.Rd | 3 man/plot.equivalent_shifts.Rd | 7 man/plot.params_process.Rd | 11 man/plot_criterion.Rd |only man/sample_shifts_edges.Rd | 3 man/simul_process.Rd | 4 man/simulate_internal.Rd | 4 man/update.enumerate_parsimony.Rd | 4 man/wrapper_E_step.Rd | 4 tests/testthat/test-utilities-rotations.R |only vignettes/monkeys.Rmd |only vignettes/tutorial.Rmd | 9 59 files changed, 1180 insertions(+), 606 deletions(-)
More information about PhylogeneticEM at CRAN
Permanent link
Title: Acquisition and Processing of MODIS Products
Description: Download and processing functionalities for the Moderate Resolution
Imaging Spectroradiometer (MODIS). The package provides automated access to the
global online data archives LP DAAC (<https://lpdaac.usgs.gov/>), LAADS
(<https://ladsweb.modaps.eosdis.nasa.gov/>) and NSIDC (<https://nsidc.org/>)
as well as processing capabilities such as file conversion, mosaicking,
subsetting and time series filtering.
Author: Matteo Mattiuzzi [aut],
Jan Verbesselt [ctb],
Tomislav Hengl [ctb],
Anja Klisch [ctb],
Forrest Stevens [ctb],
Steven Mosher [ctb],
Bradley Evans [ctb],
Agustin Lobo [ctb],
Koen Hufkens [ctb],
Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between MODIS versions 1.1.2 dated 2018-01-25 and 1.1.3 dated 2018-09-11
MODIS-1.1.2/MODIS/R/addCollection.R |only MODIS-1.1.2/MODIS/R/addProduct.R |only MODIS-1.1.2/MODIS/R/addServer.R |only MODIS-1.1.2/MODIS/inst/external/EPSGinfo.RData |only MODIS-1.1.2/MODIS/inst/external/LAADS_ftp.txt |only MODIS-1.1.2/MODIS/inst/external/LPDAAC_ftp.txt |only MODIS-1.1.2/MODIS/inst/external/sdunl.hdf |only MODIS-1.1.2/MODIS/man/addCollection.Rd |only MODIS-1.1.2/MODIS/man/addProduct.Rd |only MODIS-1.1.2/MODIS/man/addServer.Rd |only MODIS-1.1.2/MODIS/man/lpdaacLogin.Rd |only MODIS-1.1.3/MODIS/DESCRIPTION | 27 MODIS-1.1.3/MODIS/MD5 | 124 +-- MODIS-1.1.3/MODIS/NAMESPACE | 9 MODIS-1.1.3/MODIS/NEWS | 23 MODIS-1.1.3/MODIS/R/EarthdataLogin.R |only MODIS-1.1.3/MODIS/R/MODIS-deprecated.R |only MODIS-1.1.3/MODIS/R/MODIS-package.R | 10 MODIS-1.1.3/MODIS/R/MODIS_QC.R | 231 +++--- MODIS-1.1.3/MODIS/R/MODISoptions.R | 31 MODIS-1.1.3/MODIS/R/arcStats.R | 3 MODIS-1.1.3/MODIS/R/checkIntegrity.R | 3 MODIS-1.1.3/MODIS/R/delHdf.R | 14 MODIS-1.1.3/MODIS/R/detectBitInfo.R | 6 MODIS-1.1.3/MODIS/R/doOptions.R | 17 MODIS-1.1.3/MODIS/R/gdalControls.R | 4 MODIS-1.1.3/MODIS/R/genString.R | 9 MODIS-1.1.3/MODIS/R/getCollection.R | 42 - MODIS-1.1.3/MODIS/R/getHdf.R | 79 +- MODIS-1.1.3/MODIS/R/getPart.R | 3 MODIS-1.1.3/MODIS/R/getProduct.R | 7 MODIS-1.1.3/MODIS/R/getStruc.R | 32 MODIS-1.1.3/MODIS/R/getTile.R | 117 ++- MODIS-1.1.3/MODIS/R/lpdaacLogin.R | 42 - MODIS-1.1.3/MODIS/R/makeWeights.R | 26 MODIS-1.1.3/MODIS/R/minorFuns.R | 328 ++++++--- MODIS-1.1.3/MODIS/R/orgTime.R | 2 MODIS-1.1.3/MODIS/R/runGdal.R | 358 ++++++++-- MODIS-1.1.3/MODIS/R/runMrt.R | 2 MODIS-1.1.3/MODIS/R/transDate.R | 2 MODIS-1.1.3/MODIS/R/whittaker.R | 2 MODIS-1.1.3/MODIS/R/zz_lazyload.R | 12 MODIS-1.1.3/MODIS/R/zzz.R | 3 MODIS-1.1.3/MODIS/README.md | 12 MODIS-1.1.3/MODIS/inst/external/MODIS_FTPinfo.RData |binary MODIS-1.1.3/MODIS/inst/external/MODIS_Products.RData |binary MODIS-1.1.3/MODIS/inst/external/collections.RData |binary MODIS-1.1.3/MODIS/inst/external/modis_sinusoidal_grid_world.dbf |only MODIS-1.1.3/MODIS/inst/external/modis_sinusoidal_grid_world.prj |only MODIS-1.1.3/MODIS/inst/external/modis_sinusoidal_grid_world.shp |only MODIS-1.1.3/MODIS/inst/external/modis_sinusoidal_grid_world.shx |only MODIS-1.1.3/MODIS/inst/external/modland_products.xlsx |binary MODIS-1.1.3/MODIS/inst/external/modsnow_products.xlsx |only MODIS-1.1.3/MODIS/inst/external/tiletable.txt | 4 MODIS-1.1.3/MODIS/inst/gdal |only MODIS-1.1.3/MODIS/man/EarthdataLogin.Rd |only MODIS-1.1.3/MODIS/man/MODIS-deprecated.Rd |only MODIS-1.1.3/MODIS/man/MODIS-package.Rd | 2 MODIS-1.1.3/MODIS/man/MODISoptions.Rd | 17 MODIS-1.1.3/MODIS/man/arcStats.Rd | 3 MODIS-1.1.3/MODIS/man/delHdf.Rd | 16 MODIS-1.1.3/MODIS/man/detectBitInfo.Rd | 6 MODIS-1.1.3/MODIS/man/getCollection.Rd | 14 MODIS-1.1.3/MODIS/man/getHdf.Rd | 31 MODIS-1.1.3/MODIS/man/getTile.Rd | 29 MODIS-1.1.3/MODIS/man/lpdaacLogin-deprecated.Rd |only MODIS-1.1.3/MODIS/man/makeWeights.Rd | 5 MODIS-1.1.3/MODIS/man/minorFuns.Rd | 4 MODIS-1.1.3/MODIS/man/orgTime.Rd | 6 MODIS-1.1.3/MODIS/man/runGdal.Rd | 32 MODIS-1.1.3/MODIS/man/runMrt.Rd | 2 MODIS-1.1.3/MODIS/man/transDate.Rd | 2 MODIS-1.1.3/MODIS/tests/testthat/test-genString.R | 2 MODIS-1.1.3/MODIS/tests/testthat/test-skipDuplicateProducts.R | 8 74 files changed, 1151 insertions(+), 612 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management
procedures for data-limited fisheries
(see Carruthers et al (2014) <doi:10.1016/j.fishres.2013.12.014>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
M. Bryan [ctb],
HF. Geremont [ctb],
C. Grandin [ctb],
W. Harford [ctb],
Q. Huynh [ctb],
C. Walters [ctb]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 5.2.2 dated 2018-08-17 and 5.2.3 dated 2018-09-11
DLMtool-5.2.2/DLMtool/data/Generic_fleet.RData |only DLMtool-5.2.2/DLMtool/data/Generic_obs.RData |only DLMtool-5.2.3/DLMtool/DESCRIPTION | 15 - DLMtool-5.2.3/DLMtool/MD5 | 224 ++++++++-------- DLMtool-5.2.3/DLMtool/NAMESPACE | 6 DLMtool-5.2.3/DLMtool/NEWS.md | 16 + DLMtool-5.2.3/DLMtool/R/Data_Functions.R | 39 ++ DLMtool-5.2.3/DLMtool/R/DefineClasses.r | 22 + DLMtool-5.2.3/DLMtool/R/MPs_Input.R | 16 + DLMtool-5.2.3/DLMtool/R/MSE_functions.R | 1 DLMtool-5.2.3/DLMtool/R/Misc_Exported.R | 13 DLMtool-5.2.3/DLMtool/R/Misc_Internal.R | 4 DLMtool-5.2.3/DLMtool/R/OM_Plotting.R | 78 ++++- DLMtool-5.2.3/DLMtool/R/SampleOM.R | 50 ++- DLMtool-5.2.3/DLMtool/R/Sketch_Functions.R | 14 - DLMtool-5.2.3/DLMtool/R/StochasticSRA.R | 2 DLMtool-5.2.3/DLMtool/R/aaImportFrom.R | 3 DLMtool-5.2.3/DLMtool/R/data2OMfunctions.r |only DLMtool-5.2.3/DLMtool/R/popdyn.R | 177 +++++++----- DLMtool-5.2.3/DLMtool/R/runMSE.r | 100 ++++--- DLMtool-5.2.3/DLMtool/R/sysdata.rda |binary DLMtool-5.2.3/DLMtool/data/Generic_Fleet.RData |only DLMtool-5.2.3/DLMtool/data/Generic_Obs.RData |only DLMtool-5.2.3/DLMtool/data/datalist | 4 DLMtool-5.2.3/DLMtool/man/AvC.Rd | 3 DLMtool-5.2.3/DLMtool/man/AvC_MLL.Rd | 3 DLMtool-5.2.3/DLMtool/man/BK.Rd | 2 DLMtool-5.2.3/DLMtool/man/CC1.Rd | 3 DLMtool-5.2.3/DLMtool/man/CSRAfunc.Rd | 4 DLMtool-5.2.3/DLMtool/man/CompSRA.Rd | 2 DLMtool-5.2.3/DLMtool/man/Converge.Rd | 6 DLMtool-5.2.3/DLMtool/man/DBSRA.Rd | 2 DLMtool-5.2.3/DLMtool/man/DCAC.Rd | 17 - DLMtool-5.2.3/DLMtool/man/DD.Rd | 3 DLMtool-5.2.3/DLMtool/man/DD_R.Rd | 4 DLMtool-5.2.3/DLMtool/man/DDe.Rd | 5 DLMtool-5.2.3/DLMtool/man/DFO_quant.Rd | 4 DLMtool-5.2.3/DLMtool/man/DFO_tab_formatted.Rd | 4 DLMtool-5.2.3/DLMtool/man/DTe40.Rd | 2 DLMtool-5.2.3/DLMtool/man/DynF.Rd | 3 DLMtool-5.2.3/DLMtool/man/EtargetLopt.Rd | 7 DLMtool-5.2.3/DLMtool/man/Fadapt.Rd | 4 DLMtool-5.2.3/DLMtool/man/Fdem.Rd | 2 DLMtool-5.2.3/DLMtool/man/Fease.Rd | 5 DLMtool-5.2.3/DLMtool/man/Fratio.Rd | 3 DLMtool-5.2.3/DLMtool/man/GB_CC.Rd | 3 DLMtool-5.2.3/DLMtool/man/GB_slope.Rd | 3 DLMtool-5.2.3/DLMtool/man/GB_target.Rd | 3 DLMtool-5.2.3/DLMtool/man/Gcontrol.Rd | 3 DLMtool-5.2.3/DLMtool/man/Growth2OM.Rd |only DLMtool-5.2.3/DLMtool/man/ICI.Rd | 3 DLMtool-5.2.3/DLMtool/man/IT5.Rd | 2 DLMtool-5.2.3/DLMtool/man/ITM.Rd | 4 DLMtool-5.2.3/DLMtool/man/ITe5.Rd | 4 DLMtool-5.2.3/DLMtool/man/Iratio.Rd | 3 DLMtool-5.2.3/DLMtool/man/Islope1.Rd | 19 - DLMtool-5.2.3/DLMtool/man/Itarget1.Rd | 3 DLMtool-5.2.3/DLMtool/man/Itarget1_MPA.Rd | 3 DLMtool-5.2.3/DLMtool/man/ItargetE1.Rd | 15 - DLMtool-5.2.3/DLMtool/man/Kplot.Rd | 4 DLMtool-5.2.3/DLMtool/man/LBSPR.Rd | 4 DLMtool-5.2.3/DLMtool/man/LBSPRgen.Rd | 4 DLMtool-5.2.3/DLMtool/man/LH2OM.Rd | 9 DLMtool-5.2.3/DLMtool/man/LSRA_MCMC_sim.Rd | 6 DLMtool-5.2.3/DLMtool/man/LSRA_opt.Rd | 4 DLMtool-5.2.3/DLMtool/man/LSRA_opt_cpp.Rd | 4 DLMtool-5.2.3/DLMtool/man/LW2OM.Rd |only DLMtool-5.2.3/DLMtool/man/Lratio_BHI.Rd | 3 DLMtool-5.2.3/DLMtool/man/LstepCC1.Rd | 2 DLMtool-5.2.3/DLMtool/man/LstepCE1.Rd | 10 DLMtool-5.2.3/DLMtool/man/Ltarget1.Rd | 3 DLMtool-5.2.3/DLMtool/man/LtargetE1.Rd | 3 DLMtool-5.2.3/DLMtool/man/MCD.Rd | 2 DLMtool-5.2.3/DLMtool/man/MPStats.Rd | 4 DLMtool-5.2.3/DLMtool/man/MRreal.Rd | 2 DLMtool-5.2.3/DLMtool/man/MSE-class.Rd | 2 DLMtool-5.2.3/DLMtool/man/OMdoc.Rd | 7 DLMtool-5.2.3/DLMtool/man/Pplot2.Rd | 14 - DLMtool-5.2.3/DLMtool/man/Rcontrol.Rd | 5 DLMtool-5.2.3/DLMtool/man/SBT1.Rd | 7 DLMtool-5.2.3/DLMtool/man/SPMSY.Rd | 3 DLMtool-5.2.3/DLMtool/man/SPSRA.Rd | 3 DLMtool-5.2.3/DLMtool/man/SPmod.Rd | 7 DLMtool-5.2.3/DLMtool/man/SPslope.Rd | 3 DLMtool-5.2.3/DLMtool/man/SRAsim.Rd | 5 DLMtool-5.2.3/DLMtool/man/SampleFleetPars.Rd | 4 DLMtool-5.2.3/DLMtool/man/SampleStockPars.Rd | 4 DLMtool-5.2.3/DLMtool/man/SimulatedData.Rd | 1 DLMtool-5.2.3/DLMtool/man/StochasticSRA.Rd | 8 DLMtool-5.2.3/DLMtool/man/StochasticSRAcpp.Rd | 6 DLMtool-5.2.3/DLMtool/man/VOI2.Rd | 3 DLMtool-5.2.3/DLMtool/man/VOIplot.Rd | 6 DLMtool-5.2.3/DLMtool/man/YPR.Rd | 2 DLMtool-5.2.3/DLMtool/man/cheatsheets.Rd |only DLMtool-5.2.3/DLMtool/man/compplot.Rd | 3 DLMtool-5.2.3/DLMtool/man/curE.Rd | 2 DLMtool-5.2.3/DLMtool/man/getBlow.Rd | 6 DLMtool-5.2.3/DLMtool/man/getFref3.Rd | 8 DLMtool-5.2.3/DLMtool/man/getq3.Rd | 6 DLMtool-5.2.3/DLMtool/man/join_plots.Rd | 4 DLMtool-5.2.3/DLMtool/man/matlenlim.Rd | 2 DLMtool-5.2.3/DLMtool/man/optCPU.Rd | 3 DLMtool-5.2.3/DLMtool/man/optMSY.Rd | 4 DLMtool-5.2.3/DLMtool/man/optQ.Rd | 6 DLMtool-5.2.3/DLMtool/man/plot-Imp.Rd | 3 DLMtool-5.2.3/DLMtool/man/plot-OM.Rd | 6 DLMtool-5.2.3/DLMtool/man/plot-Obs.Rd | 3 DLMtool-5.2.3/DLMtool/man/plotMPA.Rd | 4 DLMtool-5.2.3/DLMtool/man/plotStock.Rd | 4 DLMtool-5.2.3/DLMtool/man/popdynCPP.Rd | 6 DLMtool-5.2.3/DLMtool/man/popdynOneTScpp.Rd | 4 DLMtool-5.2.3/DLMtool/man/runCOSEWIC.Rd | 16 - DLMtool-5.2.3/DLMtool/man/runMSE.Rd | 20 - DLMtool-5.2.3/DLMtool/man/simYears.Rd | 6 DLMtool-5.2.3/DLMtool/man/writeCSV.Rd | 4 DLMtool-5.2.3/DLMtool/src/popddynCPP.cpp | 9 DLMtool-5.2.3/DLMtool/tests/manual/run-tests-thorough.R | 2 117 files changed, 737 insertions(+), 488 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-22 0.2.3
Title: 'zoo' Objects with Column Attributes
Description: Tools for manipulating multivariate time series data by extending
'zoo' class.
Author: Ran-Ran He [aut, cre]
Maintainer: Ran-Ran He <heranran2006@163.com>
Diff between zoocat versions 0.2.0 dated 2016-11-10 and 0.2.0.1 dated 2018-09-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 1 + data/tropSST.rda |binary 4 files changed, 7 insertions(+), 6 deletions(-)
Title: Yet Another Canonical Correlation Analysis Package
Description: Provides an alternative canonical correlation/redundancy
analysis function, with associated print, plot, and summary methods.
A method for generating helio plots is also included.
Author: Carter T. Butts <buttsc@uci.edu>
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between yacca versions 1.1 dated 2009-01-09 and 1.1.1 dated 2018-09-11
DESCRIPTION | 13 +++++++++---- MD5 |only NAMESPACE |only R/zzz.R | 34 +++++++++++++++++----------------- 4 files changed, 26 insertions(+), 21 deletions(-)
Title: Username, Full Name, Email Address, 'GitHub' Username of the
Current User
Description: Look up the username and full name of the current user,
the current user's email address and 'GitHub' username,
using various sources of system and configuration information.
Author: Gábor Csárdi [aut, cre],
Maëlle Salmon [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between whoami versions 1.1.2 dated 2017-10-20 and 1.2.0 dated 2018-09-11
DESCRIPTION | 20 +++- MD5 | 21 ++--- R/whoami.R | 159 ++++++++++++++++++++++++++++++-------- inst/NEWS.md | 14 +++ inst/README.md | 6 - man/email_address.Rd | 1 man/fullname.Rd | 1 man/gh_username.Rd | 15 ++- man/username.Rd | 1 man/whoami.Rd | 23 +++++ tests/testthat/test-gh-username.R | 13 +++ tests/testthat/test-memoize.R |only 12 files changed, 222 insertions(+), 52 deletions(-)
Title: Time Machine
Description: Implements the Time Machine, a simulation approach for stochastic
trees.
Author: Gianluca Campanella [aut, cre],
Marc Chadeau-Hyam [aut],
Maria De Iorio [ctb],
Ajay Jasra [ctb]
Maintainer: Gianluca Campanella <gianluca@campanella.org>
Diff between TimeMachine versions 1.2 dated 2014-01-13 and 1.2.1 dated 2018-09-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 11 +++++++++++ README.md | 2 +- data/pdm.rda |binary 5 files changed, 19 insertions(+), 8 deletions(-)
Title: Partial Least Squares Regression for Cox Models and Related
Techniques
Description: Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>),
Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>)
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Diff between plsRcox versions 1.7.3 dated 2018-06-02 and 1.7.3.1 dated 2018-09-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/plsRcox.R | 2 +- data/Xmicro.censure_compl_imp.RData |binary data/micro.censure.RData |binary 6 files changed, 12 insertions(+), 10 deletions(-)
Title: Sample Size Calculations for Longitudinal Data
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue <mdonohue@usc.edu>
Diff between longpower versions 1.0-16 dated 2016-07-25 and 1.0-16.1 dated 2018-09-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 5 +++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.63 dated 2018-02-27 and 1.64-1 dated 2018-09-11
WGCNA-1.63/WGCNA/man/WGCNA-package.Rd |only WGCNA-1.64-1/WGCNA/Changelog | 51 + WGCNA-1.64-1/WGCNA/DESCRIPTION | 12 WGCNA-1.64-1/WGCNA/MD5 | 34 WGCNA-1.64-1/WGCNA/R/Functions-fromSimilarity.R | 4 WGCNA-1.64-1/WGCNA/R/Functions.R | 535 ++++++++++++--- WGCNA-1.64-1/WGCNA/R/GOenrichmentAnalysis.R | 20 WGCNA-1.64-1/WGCNA/R/branchSplit.R | 5 WGCNA-1.64-1/WGCNA/R/corFunctions.R | 2 WGCNA-1.64-1/WGCNA/R/multiData.R | 7 WGCNA-1.64-1/WGCNA/R/standardScreeningBinaryTrait.R | 2 WGCNA-1.64-1/WGCNA/man/bicor.Rd | 5 WGCNA-1.64-1/WGCNA/man/binarizeCategoricalColumns.Rd |only WGCNA-1.64-1/WGCNA/man/binarizeCategoricalVariable.Rd |only WGCNA-1.64-1/WGCNA/man/convertNumericColumnsToNumeric.Rd |only WGCNA-1.64-1/WGCNA/man/cor.Rd | 8 WGCNA-1.64-1/WGCNA/man/factorizeNonNumericColumns.Rd |only WGCNA-1.64-1/WGCNA/man/labeledHeatmap.Rd | 6 WGCNA-1.64-1/WGCNA/man/pickSoftThreshold.Rd | 8 WGCNA-1.64-1/WGCNA/man/signifNumeric.Rd |only WGCNA-1.64-1/WGCNA/src/networkFunctions.c | 13 21 files changed, 594 insertions(+), 118 deletions(-)
Title: Robust Gaussian Stochastic Process Emulation
Description: Robust parameter estimation and prediction of Gaussian stochastic process emulators. It allows for robust parameter estimation and prediction using Gaussian stochastic process emulator. See the reference: Mengyang Gu, Xiaojing Wang and Jim Berger (2017) <arXiv:1708.04738>.
Author: Mengyang Gu [aut, cre],
Jesus Palomo [aut],
James Berger [aut]
Maintainer: Mengyang Gu <mgu6@jhu.edu>
Diff between RobustGaSP versions 0.5.5 dated 2018-03-27 and 0.5.6 dated 2018-09-11
RobustGaSP-0.5.5/RobustGaSP/R/Plot.R |only RobustGaSP-0.5.5/RobustGaSP/R/Sample.R |only RobustGaSP-0.5.5/RobustGaSP/man/detpep10curv.Rd |only RobustGaSP-0.5.5/RobustGaSP/man/fried.Rd |only RobustGaSP-0.5.5/RobustGaSP/man/hig02.Rd |only RobustGaSP-0.5.5/RobustGaSP/man/limetal02non.Rd |only RobustGaSP-0.5.6/RobustGaSP/CHANGELOG | 8 RobustGaSP-0.5.6/RobustGaSP/DESCRIPTION | 13 RobustGaSP-0.5.6/RobustGaSP/MD5 | 57 +-- RobustGaSP-0.5.6/RobustGaSP/NAMESPACE | 29 + RobustGaSP-0.5.6/RobustGaSP/R/functions.R | 249 ++-------------- RobustGaSP-0.5.6/RobustGaSP/R/onAtUn.R | 4 RobustGaSP-0.5.6/RobustGaSP/R/plot.rgasp.R |only RobustGaSP-0.5.6/RobustGaSP/R/predict.R | 7 RobustGaSP-0.5.6/RobustGaSP/R/rgasp.R | 4 RobustGaSP-0.5.6/RobustGaSP/R/simulate.R |only RobustGaSP-0.5.6/RobustGaSP/R/structure.R | 49 ++- RobustGaSP-0.5.6/RobustGaSP/build/partial.rdb |binary RobustGaSP-0.5.6/RobustGaSP/inst/extdata/example.r | 20 - RobustGaSP-0.5.6/RobustGaSP/man/RobustGaSP-package.Rd | 12 RobustGaSP-0.5.6/RobustGaSP/man/Sample.rgasp.Rd | 6 RobustGaSP-0.5.6/RobustGaSP/man/as.S3prediction.Rd | 4 RobustGaSP-0.5.6/RobustGaSP/man/as.S4prediction.Rd | 4 RobustGaSP-0.5.6/RobustGaSP/man/borehole.Rd | 20 - RobustGaSP-0.5.6/RobustGaSP/man/dettepepel.3.data.Rd |only RobustGaSP-0.5.6/RobustGaSP/man/friedman.5.data.Rd |only RobustGaSP-0.5.6/RobustGaSP/man/higdon.1.data.Rd |only RobustGaSP-0.5.6/RobustGaSP/man/leave_one_out_rgasp.Rd | 4 RobustGaSP-0.5.6/RobustGaSP/man/limetal.2.data.Rd |only RobustGaSP-0.5.6/RobustGaSP/man/log_approx_ref_prior.Rd | 11 RobustGaSP-0.5.6/RobustGaSP/man/plot.rgasp.Rd | 21 - RobustGaSP-0.5.6/RobustGaSP/man/predict.rgasp.Rd | 10 RobustGaSP-0.5.6/RobustGaSP/man/rgasp.Rd | 36 +- RobustGaSP-0.5.6/RobustGaSP/man/show.rgasp.Rd | 4 RobustGaSP-0.5.6/RobustGaSP/man/simulate.rgasp.Rd |only RobustGaSP-0.5.6/RobustGaSP/src/functions.cpp | 5 36 files changed, 238 insertions(+), 339 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp'
for solving problems in combinatorics and computational mathematics.
There are combination/permutation functions that are both flexible as
well as efficient with respect to speed and memory. Constraint
parameters allow for generation of all combinations/permutations of a
vector meeting specific criteria (e.g. finding all combinations such
that the sum is less than a bound). Capable of generating specific
combinations/permutations (e.g. retrieve only the nth lexicographical
result) which sets up nicely for parallelization as well as random
sampling. Gmp support permits exploration where the total number of
results is large (e.g. comboSample(10000, 500, n = 4)). Additionally,
there are several highly efficient number theoretic functions that
are useful for problems common in computational mathematics. Some of
these functions make use of the fast integer division library
'libdivide' by <http://ridiculousfish.com>. The primeSieve function
is based on the segmented sieve of Eratosthenes implementation by
Kim Walisch. It is capable of generating all primes less than a
billion in just over 1 second. It can also quickly generate prime
numbers over a range (e.g. primeSieve(10^13, 10^13+10^9)). Finally,
there is a prime counting function that implements a simple variations
of Legendre's formula based on the algorithm by Kim Walisch.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.0.3 dated 2018-06-30 and 2.1.0 dated 2018-09-11
RcppAlgos-2.0.3/RcppAlgos/NEWS |only RcppAlgos-2.0.3/RcppAlgos/src/ConstraintsUtils.cpp |only RcppAlgos-2.1.0/RcppAlgos/DESCRIPTION | 61 RcppAlgos-2.1.0/RcppAlgos/MD5 | 57 RcppAlgos-2.1.0/RcppAlgos/NAMESPACE | 3 RcppAlgos-2.1.0/RcppAlgos/R/Combinatorics.R | 80 RcppAlgos-2.1.0/RcppAlgos/R/RcppExports.R | 8 RcppAlgos-2.1.0/RcppAlgos/README.md | 279 +- RcppAlgos-2.1.0/RcppAlgos/inst/NEWS.Rd |only RcppAlgos-2.1.0/RcppAlgos/inst/include/CleanConvert.h |only RcppAlgos-2.1.0/RcppAlgos/inst/include/CombPermUtils.h | 18 RcppAlgos-2.1.0/RcppAlgos/inst/include/Combinations.h | 269 +- RcppAlgos-2.1.0/RcppAlgos/inst/include/ComboResults.h |only RcppAlgos-2.1.0/RcppAlgos/inst/include/ConstraintsUtils.h | 158 + RcppAlgos-2.1.0/RcppAlgos/inst/include/CountGmp.h |only RcppAlgos-2.1.0/RcppAlgos/inst/include/NthResult.h | 11 RcppAlgos-2.1.0/RcppAlgos/inst/include/Permutations.h | 364 +-- RcppAlgos-2.1.0/RcppAlgos/inst/include/PermuteResults.h |only RcppAlgos-2.1.0/RcppAlgos/inst/include/importExportMPZ.h |only RcppAlgos-2.1.0/RcppAlgos/man/RcppAlgos-package.Rd | 6 RcppAlgos-2.1.0/RcppAlgos/man/combinatoricsCount.Rd | 9 RcppAlgos-2.1.0/RcppAlgos/man/combinatoricsGeneral.Rd | 136 - RcppAlgos-2.1.0/RcppAlgos/man/combinatoricsSample.Rd | 81 RcppAlgos-2.1.0/RcppAlgos/src/CombPermUtils.cpp | 104 RcppAlgos-2.1.0/RcppAlgos/src/Combinatorics.cpp | 1127 ++++++---- RcppAlgos-2.1.0/RcppAlgos/src/CountGmp.cpp |only RcppAlgos-2.1.0/RcppAlgos/src/Makevars | 1 RcppAlgos-2.1.0/RcppAlgos/src/NthResult.cpp | 269 ++ RcppAlgos-2.1.0/RcppAlgos/src/RcppExports.cpp | 30 RcppAlgos-2.1.0/RcppAlgos/src/SampleContainer.cpp | 569 ++++- RcppAlgos-2.1.0/RcppAlgos/src/importExportMPZ.cpp |only RcppAlgos-2.1.0/RcppAlgos/tests/testthat/testComboGeneral.R | 226 +- RcppAlgos-2.1.0/RcppAlgos/tests/testthat/testParallel.R |only RcppAlgos-2.1.0/RcppAlgos/tests/testthat/testPermuteGeneral.R | 235 +- RcppAlgos-2.1.0/RcppAlgos/tests/testthat/testSample.R | 222 + 35 files changed, 2976 insertions(+), 1347 deletions(-)
Title: Incremental Calculation of Dynamic Time Warping
Description: The Dynamic Time Warping (DTW) distance for time series allows non-linear alignments of time series to match similar patterns in time series of different lengths and or different speeds. Beside the traditional implementation of the DTW algorithm, the specialities of this package are, (1) the incremental calculation, which is specifically useful for life data streams due to computationally efficiency, (2) the vector based implementation of the traditional DTW algorithm which is faster because no matrices are allocated and is especially useful for computing distance matrices of pairwise DTW distances for many time series and (3) the combination of incremental and vector-based calculation. C++ in the heart. For details about DTW see the original paper "Dynamic programming algorithm optimization for spoken word recognition" by Sakoe and Chiba (1978) <DOI:10.1109/TASSP.1978.1163055>.
Author: Maximilian Leodolter
Maintainer: Maximilian Leodolter <maximilian.leodolter@gmail.com>
Diff between IncDTW versions 1.0.3 dated 2018-05-14 and 1.0.4 dated 2018-09-11
IncDTW-1.0.3/IncDTW/R/Rfunctions.R |only IncDTW-1.0.4/IncDTW/DESCRIPTION | 18 IncDTW-1.0.4/IncDTW/MD5 | 73 IncDTW-1.0.4/IncDTW/NAMESPACE | 34 IncDTW-1.0.4/IncDTW/R/DBA.R |only IncDTW-1.0.4/IncDTW/R/RcppExports.R | 100 - IncDTW-1.0.4/IncDTW/R/data_preparation.R |only IncDTW-1.0.4/IncDTW/R/dtw.R |only IncDTW-1.0.4/IncDTW/R/dtw_plot.R |only IncDTW-1.0.4/IncDTW/R/idtw.R |only IncDTW-1.0.4/IncDTW/R/notes.R |only IncDTW-1.0.4/IncDTW/build/vignette.rds |binary IncDTW-1.0.4/IncDTW/data |only IncDTW-1.0.4/IncDTW/inst/doc/Incremental_Dynamic_Time_Warping.R | 185 - IncDTW-1.0.4/IncDTW/inst/doc/Incremental_Dynamic_Time_Warping.Rmd | 266 +- IncDTW-1.0.4/IncDTW/inst/doc/Incremental_Dynamic_Time_Warping.html | 320 +-- IncDTW-1.0.4/IncDTW/inst/doc/Runtime_Comparison.R |only IncDTW-1.0.4/IncDTW/inst/doc/Runtime_Comparison.Rmd |only IncDTW-1.0.4/IncDTW/inst/doc/Runtime_Comparison.html |only IncDTW-1.0.4/IncDTW/man/DBA.Rd |only IncDTW-1.0.4/IncDTW/man/IncDTW-package.Rd | 24 IncDTW-1.0.4/IncDTW/man/dec_dm.Rd | 4 IncDTW-1.0.4/IncDTW/man/drink_glass.Rd |only IncDTW-1.0.4/IncDTW/man/dtw.Rd | 66 IncDTW-1.0.4/IncDTW/man/dtw2vec.Rd | 19 IncDTW-1.0.4/IncDTW/man/dtw_dismat.Rd |only IncDTW-1.0.4/IncDTW/man/dtw_partial.Rd |only IncDTW-1.0.4/IncDTW/man/idtw.Rd | 29 IncDTW-1.0.4/IncDTW/man/idtw2vec.Rd | 31 IncDTW-1.0.4/IncDTW/man/norm.Rd |only IncDTW-1.0.4/IncDTW/man/plot_dba.Rd |only IncDTW-1.0.4/IncDTW/man/plot_idtw.Rd | 36 IncDTW-1.0.4/IncDTW/src/GCM.cpp | 577 ++++-- IncDTW-1.0.4/IncDTW/src/IncDTW.h |only IncDTW-1.0.4/IncDTW/src/Makevars |only IncDTW-1.0.4/IncDTW/src/Makevars.win |only IncDTW-1.0.4/IncDTW/src/RcppExports.cpp | 327 ++- IncDTW-1.0.4/IncDTW/src/dtw2vec.cpp | 959 ++++++++-- IncDTW-1.0.4/IncDTW/src/dtw_dismat.cpp |only IncDTW-1.0.4/IncDTW/src/dtw_disvec.cpp |only IncDTW-1.0.4/IncDTW/src/help_functions.cpp |only IncDTW-1.0.4/IncDTW/src/init.c | 86 IncDTW-1.0.4/IncDTW/tests |only IncDTW-1.0.4/IncDTW/vignettes/Incremental_Dynamic_Time_Warping.Rmd | 266 +- IncDTW-1.0.4/IncDTW/vignettes/Runtime_Comparison.Rmd |only 45 files changed, 2407 insertions(+), 1013 deletions(-)
Title: Bivariate Probability Distributions
Description: Provides alternatives to persp() for plotting bivariate functions, including both step and continuous functions. Also, provides convenience functions for constructing and plotting bivariate probability distributions. Currently, only normal distributions are supported but other probability distributions are likely to be added in the near future.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between bivariate versions 0.1.5 dated 2018-08-16 and 0.1.6 dated 2018-09-11
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/doc/bivariate.Rnw | 4 ++-- inst/doc/bivariate.pdf |binary vignettes/bivariate.Rnw | 4 ++-- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Knowledge Space Theory Input/Output
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstIO' package
provides basic functionalities to read and write KST data from/to
files to be used together with the 'kst', 'kstMatrix', 'pks' or
'DAKS' packages.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstIO versions 0.1-0 dated 2018-01-04 and 0.2-0 dated 2018-09-11
Changelog | 7 DESCRIPTION | 13 - MD5 | 22 +- R/read_kbase.R | 3 R/read_kdata.R | 1 R/read_kspace.R | 1 R/read_kstructure.R | 1 build/vignette.rds |binary inst/doc/kstIO.R | 2 inst/doc/kstIO.Rnw | 479 ++++++++++++++++++++++++++-------------------------- inst/doc/kstIO.pdf |binary vignettes/kstIO.Rnw | 479 ++++++++++++++++++++++++++-------------------------- 12 files changed, 510 insertions(+), 498 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.8.0 dated 2018-01-17 and 2.9.0 dated 2018-09-11
datarobot-2.8.0/datarobot/man/ReformatListOfModels.Rd |only datarobot-2.9.0/datarobot/DESCRIPTION | 6 datarobot-2.9.0/datarobot/MD5 | 146 - datarobot-2.9.0/datarobot/NAMESPACE | 12 datarobot-2.9.0/datarobot/NEWS | 28 datarobot-2.9.0/datarobot/R/Blenders.R | 39 datarobot-2.9.0/datarobot/R/ConnectToDataRobot.R | 23 datarobot-2.9.0/datarobot/R/Enums.R | 46 datarobot-2.9.0/datarobot/R/GetModelJobs.R | 3 datarobot-2.9.0/datarobot/R/GetPredictions.R | 9 datarobot-2.9.0/datarobot/R/GetProject.R | 16 datarobot-2.9.0/datarobot/R/GetProjectList.R | 19 datarobot-2.9.0/datarobot/R/ModelDeployment.R |only datarobot-2.9.0/datarobot/R/Models.R | 172 - datarobot-2.9.0/datarobot/R/Partitions.R | 50 datarobot-2.9.0/datarobot/R/PrimeModels.R | 1 datarobot-2.9.0/datarobot/R/ReasonCodes.R | 19 datarobot-2.9.0/datarobot/R/RequestSampleSizeUpdate.R | 22 datarobot-2.9.0/datarobot/R/ServerData.R |only datarobot-2.9.0/datarobot/R/StartAutopilot.R | 21 datarobot-2.9.0/datarobot/R/TrainingPredictions.R | 12 datarobot-2.9.0/datarobot/R/WaitForAsyncReturn.R | 2 datarobot-2.9.0/datarobot/build/vignette.rds |binary datarobot-2.9.0/datarobot/inst/doc/AdvancedVignette.html | 1388 ++++++++-- datarobot-2.9.0/datarobot/inst/doc/ComparingSubsets.html | 578 ++-- datarobot-2.9.0/datarobot/inst/doc/DatetimePartitionedProjects.html | 372 +- datarobot-2.9.0/datarobot/inst/doc/IntroductionToDataRobot.Rmd | 3 datarobot-2.9.0/datarobot/inst/doc/IntroductionToDataRobot.html | 458 ++- datarobot-2.9.0/datarobot/inst/doc/ModelDeployments.R |only datarobot-2.9.0/datarobot/inst/doc/ModelDeployments.Rmd |only datarobot-2.9.0/datarobot/inst/doc/ModelDeployments.html |only datarobot-2.9.0/datarobot/inst/doc/Multiclass.html | 683 ++-- datarobot-2.9.0/datarobot/inst/doc/PartialDependence.html | 635 ++-- datarobot-2.9.0/datarobot/inst/doc/RatingTables.html | 740 +++-- datarobot-2.9.0/datarobot/inst/doc/ReasonCodeVignette.html | 968 ++++-- datarobot-2.9.0/datarobot/inst/doc/TimeSeries.Rmd | 1 datarobot-2.9.0/datarobot/inst/doc/TimeSeries.html | 295 +- datarobot-2.9.0/datarobot/inst/doc/TrainingPredictions.R | 2 datarobot-2.9.0/datarobot/inst/doc/TrainingPredictions.Rmd | 2 datarobot-2.9.0/datarobot/inst/doc/TrainingPredictions.html | 368 +- datarobot-2.9.0/datarobot/inst/doc/VariableImportance.html | 603 ++-- datarobot-2.9.0/datarobot/man/BlendMethods.Rd | 2 datarobot-2.9.0/datarobot/man/CleanServerData.Rd |only datarobot-2.9.0/datarobot/man/CreateDatetimePartitionSpecification.Rd | 27 datarobot-2.9.0/datarobot/man/DeleteReasonCodes.Rd | 2 datarobot-2.9.0/datarobot/man/DifferencingMethod.Rd |only datarobot-2.9.0/datarobot/man/DownloadReasonCodes.Rd | 2 datarobot-2.9.0/datarobot/man/GenerateDatetimePartition.Rd | 3 datarobot-2.9.0/datarobot/man/GetAllReasonCodesRowsAsDataFrame.Rd | 2 datarobot-2.9.0/datarobot/man/GetBlenderModelFromJobId.Rd | 4 datarobot-2.9.0/datarobot/man/GetDatetimeModelObject.Rd | 8 datarobot-2.9.0/datarobot/man/GetFrozenModel.Rd | 11 datarobot-2.9.0/datarobot/man/GetModel.Rd | 11 datarobot-2.9.0/datarobot/man/GetModelDeployment.Rd |only datarobot-2.9.0/datarobot/man/GetModelDeploymentActionLog.Rd |only datarobot-2.9.0/datarobot/man/GetModelDeploymentServiceStatistics.Rd |only datarobot-2.9.0/datarobot/man/GetModelJob.Rd | 2 datarobot-2.9.0/datarobot/man/GetProject.Rd | 13 datarobot-2.9.0/datarobot/man/GetProjectList.Rd | 15 datarobot-2.9.0/datarobot/man/GetReasonCodesMetadata.Rd | 2 datarobot-2.9.0/datarobot/man/GetReasonCodesRows.Rd | 2 datarobot-2.9.0/datarobot/man/GetServerDataInRows.Rd |only datarobot-2.9.0/datarobot/man/ListModelDeployments.Rd |only datarobot-2.9.0/datarobot/man/ModelDeploymentStatus.Rd |only datarobot-2.9.0/datarobot/man/PeriodicityMaxTimeStep.Rd |only datarobot-2.9.0/datarobot/man/PeriodicityTimeUnits.Rd |only datarobot-2.9.0/datarobot/man/RequestFrozenModel.Rd | 15 datarobot-2.9.0/datarobot/man/RequestModelDeployment.Rd |only datarobot-2.9.0/datarobot/man/RequestNewModel.Rd | 15 datarobot-2.9.0/datarobot/man/RequestSampleSizeUpdate.Rd | 12 datarobot-2.9.0/datarobot/man/SetTarget.Rd | 13 datarobot-2.9.0/datarobot/man/TreatAsExponential.Rd |only datarobot-2.9.0/datarobot/man/UpdateModelDeployment.Rd |only datarobot-2.9.0/datarobot/man/datarobot-package.Rd | 2 datarobot-2.9.0/datarobot/man/summary.dataRobotModelDeploymentsList.Rd |only datarobot-2.9.0/datarobot/tests/testthat/test-StartAutopilot.R | 36 datarobot-2.9.0/datarobot/vignettes/IntroductionToDataRobot.Rmd | 3 datarobot-2.9.0/datarobot/vignettes/ModelDeployments.Rmd |only datarobot-2.9.0/datarobot/vignettes/TimeSeries.Rmd | 1 datarobot-2.9.0/datarobot/vignettes/TrainingPredictions.Rmd | 2 datarobot-2.9.0/datarobot/vignettes/actionLog.rds |only datarobot-2.9.0/datarobot/vignettes/getModelDeployment.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeployments.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsLimit2.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsLimit2OrderByLabel.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsOffset2.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsQuery.rds |only datarobot-2.9.0/datarobot/vignettes/serverHealth.rds |only datarobot-2.9.0/datarobot/vignettes/updatedModelDeployment.rds |only 89 files changed, 5418 insertions(+), 2529 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Thomas Jones [aut, cre],
William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 2.1.2 dated 2018-04-29 and 2.1.3 dated 2018-09-11
DESCRIPTION | 17 - MD5 | 69 ++--- R/CalcPhiPrime.R | 3 R/CorrectS.R | 3 R/DepluralizeDtm.R | 4 R/Files2Vec.R | 4 R/FitLdaModel.R | 10 R/FormatRawLdaOutput.R | 4 R/GetPhiPrime.R | 8 R/textmineR-deprecated.R | 9 R/zzz.R |only README.md | 2 build/vignette.rds |binary inst/doc/a_start_here.R | 2 inst/doc/a_start_here.Rmd | 2 inst/doc/a_start_here.html | 8 inst/doc/b_document_clustering.R | 2 inst/doc/b_document_clustering.Rmd | 2 inst/doc/b_document_clustering.html | 4 inst/doc/c_topic_modeling.R | 42 +-- inst/doc/c_topic_modeling.Rmd | 42 +-- inst/doc/c_topic_modeling.html | 480 ++++++++++++++++++------------------ inst/doc/d_text_embeddings.R | 4 inst/doc/d_text_embeddings.Rmd | 4 inst/doc/d_text_embeddings.html | 216 ++++++++-------- inst/doc/e_doc_summarization.R | 4 inst/doc/e_doc_summarization.Rmd | 4 inst/doc/e_doc_summarization.html | 18 - man/FormatRawLdaOutput.Rd | 3 man/Vec2Dtm.Rd | 4 man/textmineR-deprecated.Rd | 9 vignettes/a_start_here.Rmd | 2 vignettes/b_document_clustering.Rmd | 2 vignettes/c_topic_modeling.Rmd | 42 +-- vignettes/d_text_embeddings.Rmd | 4 vignettes/e_doc_summarization.Rmd | 4 36 files changed, 550 insertions(+), 487 deletions(-)
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions, such as information
value, variable filter, optimal woe binning, scorecard scaling and
performance evaluation etc.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.1.8 dated 2018-06-12 and 0.1.9 dated 2018-09-11
scorecard-0.1.8/scorecard/R/splitdf.R |only scorecard-0.1.9/scorecard/DESCRIPTION | 33 ++++--- scorecard-0.1.9/scorecard/LICENSE | 4 scorecard-0.1.9/scorecard/MD5 | 46 +++++----- scorecard-0.1.9/scorecard/NEWS.md | 10 ++ scorecard-0.1.9/scorecard/R/condition_fun.R | 14 +++ scorecard-0.1.9/scorecard/R/germancredit.R | 13 +-- scorecard-0.1.9/scorecard/R/info_value.R | 15 +++ scorecard-0.1.9/scorecard/R/perf.R | 8 - scorecard-0.1.9/scorecard/R/scorecard.R | 9 +- scorecard-0.1.9/scorecard/R/split_df.R |only scorecard-0.1.9/scorecard/R/var_filter.R | 26 ++++-- scorecard-0.1.9/scorecard/R/woebin.R | 109 ++++++++++++++------------ scorecard-0.1.9/scorecard/README.md | 68 +++------------- scorecard-0.1.9/scorecard/build/vignette.rds |binary scorecard-0.1.9/scorecard/inst/doc/demo.Rmd | 4 scorecard-0.1.9/scorecard/inst/doc/demo.html | 8 - scorecard-0.1.9/scorecard/man/germancredit.Rd | 13 +-- scorecard-0.1.9/scorecard/man/iv.Rd | 15 +++ scorecard-0.1.9/scorecard/man/split_df.Rd | 17 +++- scorecard-0.1.9/scorecard/man/var_filter.Rd | 7 + scorecard-0.1.9/scorecard/man/woebin.Rd | 16 ++- scorecard-0.1.9/scorecard/man/woebin_plot.Rd | 5 - scorecard-0.1.9/scorecard/man/woebin_ply.Rd | 1 scorecard-0.1.9/scorecard/vignettes/demo.Rmd | 4 25 files changed, 257 insertions(+), 188 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.5-0 dated 2018-08-22 and 2.5-1 dated 2018-09-11
Rcmdr-2.5-0/Rcmdr/inst/etc/Thumbs.db |only Rcmdr-2.5-0/Rcmdr/vignettes/Thumbs.db |only Rcmdr-2.5-1/Rcmdr/DESCRIPTION | 10 Rcmdr-2.5-1/Rcmdr/MD5 | 26 Rcmdr-2.5-1/Rcmdr/NEWS | 6 Rcmdr-2.5-1/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary Rcmdr-2.5-1/Rcmdr/inst/po/eu/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.5-1/Rcmdr/inst/po/fr/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.5-1/Rcmdr/inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.5-1/Rcmdr/man/Rcmdr-package.Rd | 4 Rcmdr-2.5-1/Rcmdr/po/R-Rcmdr.pot | 7 Rcmdr-2.5-1/Rcmdr/po/R-eu.po | 330 ++++++---- Rcmdr-2.5-1/Rcmdr/po/R-fr.po | 135 +++- Rcmdr-2.5-1/Rcmdr/po/R-id.po | 76 +- Rcmdr-2.5-1/Rcmdr/po/R-ja.po | 104 +++ 15 files changed, 509 insertions(+), 189 deletions(-)
Title: PHATE - Potential of Heat-Diffusion for Affinity-Based
Transition Embedding
Description: PHATE is a tool for visualizing high dimensional single-cell data
with natural progressions or trajectories. PHATE uses a novel conceptual framework
for learning and visualizing the manifold inherent to biological systems in which
smooth transitions mark the progressions of cells from one state to another.
To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic
stem cells, human embryonic stem cells, and bone marrow samples, check out our preprint on bioRxiv
at <http://biorxiv.org/content/early/2017/03/24/120378>.
Author: Krishnan Srinivasan [aut],
Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>
Diff between phateR versions 0.2.8 dated 2018-07-03 and 0.2.9 dated 2018-09-11
DESCRIPTION | 10 ++++---- MD5 | 27 ++++++++++++++-------- R/phate.R | 11 ++++----- R/utils.R | 35 ++++++++++++++++++++++------- README.md | 18 ++++++++++---- inst/examples |only man/figures/README-adjust-parameters-1.png |binary man/figures/README-ggplot-1.png |binary man/figures/README-plot-results-1.png |binary man/install.phate.Rd | 7 +---- man/phate.Rd | 22 +++++++++--------- man/summary.Rd | 2 - 12 files changed, 83 insertions(+), 49 deletions(-)
Title: Hotelling's T^2 Test and Variants
Description: A set of R functions which implements Hotelling's T^2 test and some variants of it. Functions are also included for Aitchison's additive log ratio and centred log ratio transformations.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between Hotelling versions 1.0-4 dated 2017-07-17 and 1.0-5 dated 2018-09-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + R/hotelling.test.r | 3 ++- man/hotelling.test.Rd | 2 -- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Large-Scale Social Network Analysis
Description: We present an implementation of the algorithms required to simulate large-scale social networks and retrieve their most relevant metrics.
Author: Nazrul Shaikh [aut, cre],
Xu Dong [aut],
Luis Castro [aut],
Christian Llano [ctb]
Maintainer: Nazrul Shaikh <networkgroupr@gmail.com>
Diff between fastnet versions 0.1.5 dated 2018-07-05 and 0.1.6 dated 2018-09-11
fastnet-0.1.5/fastnet/R/from.csc.R |only fastnet-0.1.5/fastnet/R/from.csr.R |only fastnet-0.1.5/fastnet/man/from.csc.Rd |only fastnet-0.1.5/fastnet/man/from.csr.Rd |only fastnet-0.1.6/fastnet/DESCRIPTION | 10 +++++----- fastnet-0.1.6/fastnet/MD5 | 10 +++------- fastnet-0.1.6/fastnet/NAMESPACE | 2 -- fastnet-0.1.6/fastnet/NEWS.md | 4 ++++ 8 files changed, 12 insertions(+), 14 deletions(-)
Title: Resistance Relationship Networks using Graphical LASSO
Description: Novel methods are needed to analyze the large amounts of antimicrobial resistance (AMR) data generated by AMR surveillance programs. This package is used to estimate resistance relationship networks, or 'Rnets', from empirical antimicrobial susceptibility data. These networks can be used to study relationships between antimicrobial resistances (typically measured using MICs) and genes in populations. The 'GitHub' for this package is available at <https://GitHub.com/EpidemiologyDVM/Rnets>. Bug reports and features requests should be directed to the same 'GitHub' site. The methods used in 'Rnets' are available in the following publications: An overview of the method in WJ Love, et al., "Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012" (2016) <doi:10.1371/journal.pcbi.1005160>; The graphical LASSO for sparsity in J Friedman, T Hastie, R Tibshirani "Sparse inverse covariance estimation with the graphical lasso" (2007) <doi:10.1093/biostatistics/kxm045>; L1 penalty selection in H Liu, K Roeder, L Wasserman "Stability Approach to Regularization Selection (StARS) for High Dimensional Graphical Models" (2010) <arXiv:1006.3316>; Modularity for graphs with negative edge weights in S Gomez, P Jensen, A Arenas. "Analysis of community structure in networks of correlated data" (2009) <doi:10.1103/PhysRevE.80.016114>.
Author: William Love [aut, cre]
Maintainer: William Love <wjlove@ncsu.edu>
Diff between Rnets versions 0.9.8 dated 2017-12-12 and 1.0.2 dated 2018-09-11
Rnets-0.9.8/Rnets/R/Rnet_classes.R |only Rnets-0.9.8/Rnets/man/Sq2L.Rd |only Rnets-0.9.8/Rnets/man/plot-Rnet.basic.Rd |only Rnets-0.9.8/Rnets/man/plot-rnetStrata.Rd |only Rnets-0.9.8/Rnets/man/rnetMultiStrata.Rd |only Rnets-0.9.8/Rnets/man/signedModularity-igraph.Rd |only Rnets-0.9.8/Rnets/man/signedModularity-matrix.Rd |only Rnets-0.9.8/Rnets/man/signedModularity-rnetBasic.Rd |only Rnets-0.9.8/Rnets/man/signedModularity-rnetMultiStrata.Rd |only Rnets-0.9.8/Rnets/man/signedModularity.Rd |only Rnets-1.0.2/Rnets/DESCRIPTION | 14 Rnets-1.0.2/Rnets/MD5 | 92 +- Rnets-1.0.2/Rnets/NAMESPACE | 9 Rnets-1.0.2/Rnets/NEWS.md | 7 Rnets-1.0.2/Rnets/R/Assign_Emetadata.R | 135 ++-- Rnets-1.0.2/Rnets/R/Assign_Vmetadata.R | 151 ++-- Rnets-1.0.2/Rnets/R/Clean_Sigma.R | 13 Rnets-1.0.2/Rnets/R/GenR.R | 66 - Rnets-1.0.2/Rnets/R/Gomez_modularity_v6_1.R | 48 - Rnets-1.0.2/Rnets/R/L1_selection.R | 110 +-- Rnets-1.0.2/Rnets/R/Rnet.R | 148 ++-- Rnets-1.0.2/Rnets/R/Rnet_heatmap.r | 131 +-- Rnets-1.0.2/Rnets/R/Sq2L.R | 14 Rnets-1.0.2/Rnets/R/classes.R |only Rnets-1.0.2/Rnets/R/methods-plot.R | 188 +++-- Rnets-1.0.2/Rnets/R/methods-print.R | 25 Rnets-1.0.2/Rnets/R/methods-summary.R | 110 +++ Rnets-1.0.2/Rnets/build/vignette.rds |binary Rnets-1.0.2/Rnets/data/EC_COORDS.rda |binary Rnets-1.0.2/Rnets/data/E_ATTRS.rda |binary Rnets-1.0.2/Rnets/data/NARMS_EC_DATA.rda |binary Rnets-1.0.2/Rnets/data/V_ATTRS.rda |binary Rnets-1.0.2/Rnets/inst/doc/Rnets-vignette.R | 101 ++- Rnets-1.0.2/Rnets/inst/doc/Rnets-vignette.Rmd | 283 +++++++- Rnets-1.0.2/Rnets/inst/doc/Rnets-vignette.html | 431 +++++++++++-- Rnets-1.0.2/Rnets/man/Assign_Emetadata.Rd | 40 - Rnets-1.0.2/Rnets/man/Assign_Vmetadata.Rd | 38 - Rnets-1.0.2/Rnets/man/Clean_Sigma.Rd | 11 Rnets-1.0.2/Rnets/man/L1Selection.Rd | 28 Rnets-1.0.2/Rnets/man/Rnet.Rd | 62 - Rnets-1.0.2/Rnets/man/Rnet_Heatmap.Rd | 60 - Rnets-1.0.2/Rnets/man/Sq2Long.Rd |only Rnets-1.0.2/Rnets/man/dot-Gen_R.Rd | 6 Rnets-1.0.2/Rnets/man/image.edge_heatmap.Rd |only Rnets-1.0.2/Rnets/man/plot-RnetBasic.Rd |only Rnets-1.0.2/Rnets/man/print.Rd | 7 Rnets-1.0.2/Rnets/man/rnetBasic.Rd | 12 Rnets-1.0.2/Rnets/man/rnetInput.Rd | 14 Rnets-1.0.2/Rnets/man/rnetStrata.Rd | 12 Rnets-1.0.2/Rnets/man/rnetSubset.Rd |only Rnets-1.0.2/Rnets/man/signed_modularity-igraph.Rd |only Rnets-1.0.2/Rnets/man/signed_modularity-matrix.Rd |only Rnets-1.0.2/Rnets/man/signed_modularity-rnetBasic.Rd |only Rnets-1.0.2/Rnets/man/signed_modularity-rnetMultiStrata.Rd |only Rnets-1.0.2/Rnets/man/signed_modularity.Rd |only Rnets-1.0.2/Rnets/man/summary-L1selection.Rd |only Rnets-1.0.2/Rnets/man/summary-rnetSubset.Rd |only Rnets-1.0.2/Rnets/vignettes/Rnets-vignette.Rmd | 283 +++++++- 58 files changed, 1875 insertions(+), 774 deletions(-)
Title: Modeling and Map Production using Random Forest and Related
Stochastic Models
Description: Creates sophisticated models of training data and validates the models with an independent test set, cross validation, or Out Of Bag (OOB) predictions on the training data. Create graphs and tables of the model validation results. Applies these models to GIS .img files of predictors to create detailed prediction surfaces. Handles large predictor files for map making, by reading in the .img files in chunks, and output to the .txt file the prediction for each data chunk, before reading the next chunk of data.
Author: Elizabeth Freeman, Tracey Frescino
Maintainer: Elizabeth Freeman <eafreeman@fs.fed.us>
Diff between ModelMap versions 3.3.5 dated 2016-07-03 and 3.4.0.1 dated 2018-09-11
DESCRIPTION | 16 - MD5 | 60 ++-- NAMESPACE | 2 R/internal.R | 558 ++++++++++++++++-------------------------- R/model.build.R | 110 ++++---- R/model.diagnostics.R | 99 ++++--- R/model.importance.plot.R | 126 ++++----- R/model.interaction.plot.R | 53 ++- R/model.mapmake.R | 67 ++--- build/vignette.rds |binary inst/CHANGELOG | 19 + inst/CITATION | 4 inst/doc/ExploreModelMap.R | 1 inst/doc/ExploreModelMap.Rnw | 6 inst/doc/ExploreModelMap.pdf |binary inst/doc/VModelMap.R | 345 ------------------------- inst/doc/VModelMap.Rnw | 455 +--------------------------------- inst/doc/VModelMap.pdf |binary inst/doc/Vquantile.R | 1 inst/doc/Vquantile.Rnw | 4 inst/doc/Vquantile.pdf |binary man/ModelMap-package.Rd | 10 man/get.test.Rd | 2 man/model.build.Rd | 49 --- man/model.diagnostics.Rd | 16 - man/model.importance.plot.Rd | 43 --- man/model.interaction.plot.Rd | 2 man/model.mapmake.Rd | 15 - vignettes/ExploreModelMap.Rnw | 6 vignettes/VModelMap.Rnw | 455 +--------------------------------- vignettes/Vquantile.Rnw | 4 31 files changed, 607 insertions(+), 1921 deletions(-)
Title: Fast Algorithms for Best Subset Selection
Description: Highly optimized toolkit for (approximately) solving L0-regularized learning problems.
The algorithms are based on coordinate descent and local combinatorial search.
For more details, check the paper by Hazimeh and Mazumder (2018) <arXiv:1803.01454>;
the link is provided in the URL field below.
Author: Hussein Hazimeh, Rahul Mazumder
Maintainer: Hussein Hazimeh <hazimeh@mit.edu>
Diff between L0Learn versions 1.0.2 dated 2018-07-02 and 1.0.7 dated 2018-09-11
DESCRIPTION | 8 MD5 | 56 - NAMESPACE | 2 R/RcppExports.R | 8 R/coef.R | 45 R/cvfit.R | 35 R/fit.R | 34 R/predict.R | 22 build/vignette.rds |binary cleanup | 2 configure | 419 +++++++- configure.ac | 131 ++ inst/doc/L0Learn-vignette.Rmd | 9 inst/doc/L0Learn-vignette.html | 1950 +++++++++++++++++++++++++++++++++-------- man/L0Learn.cvfit.Rd | 5 man/L0Learn.fit.Rd | 4 man/coef.L0Learn.Rd | 13 man/predict.L0Learn.Rd | 11 src/CDL012Swaps.cpp | 10 src/CrossValidation.cpp | 3 src/Grid.cpp | 2 src/Makevars.in | 2 src/Makevars.win | 4 src/Normalize.cpp | 13 src/RInterface.cpp | 3 src/RcppExports.cpp | 18 src/include/GridParams.h | 1 src/include/Normalize.h | 2 vignettes/L0Learn-vignette.Rmd | 9 29 files changed, 2294 insertions(+), 527 deletions(-)
Title: Access EPA 'ECHO' Data
Description: An R interface to United States Environmental
Protection Agency (EPA) Environmental Compliance
History Online ('ECHO') Application Program Interface
(API). 'ECHO' provides information about EPA permitted
facilities, discharges, and other reporting info
associated with permitted entities. Data are obtained
from <https://echo.epa.gov/>.
Author: Michael Schramm [aut, cre]
Maintainer: Michael Schramm <michael.schramm@ag.tamu.edu>
Diff between echor versions 0.1.0 dated 2018-04-23 and 0.1.1 dated 2018-09-11
echor-0.1.0/echor/tests/testthat/ofmpub.epa.gov |only echor-0.1.0/echor/tests/testthat/test-echoAirGetFacilityInfo.R |only echor-0.1.0/echor/tests/testthat/test-echoGetCAAPR.R |only echor-0.1.0/echor/tests/testthat/test-echoGetEffluent.R |only echor-0.1.0/echor/tests/testthat/test-echoWaterGetFacilityInfo.R |only echor-0.1.0/echor/tests/testthat/test-echoWaterGetParams.R |only echor-0.1.0/echor/vignettes/data |only echor-0.1.1/echor/DESCRIPTION | 14 echor-0.1.1/echor/MD5 | 70 echor-0.1.1/echor/NAMESPACE | 22 echor-0.1.1/echor/NEWS.md | 13 echor-0.1.1/echor/R/air.R | 164 echor-0.1.1/echor/R/echoGetFacilities.R |only echor-0.1.1/echor/R/echoGetReports.R |only echor-0.1.1/echor/R/sdw.R |only echor-0.1.1/echor/R/utils.R | 139 echor-0.1.1/echor/R/water.R | 176 - echor-0.1.1/echor/README.md | 130 echor-0.1.1/echor/build/vignette.rds |binary echor-0.1.1/echor/inst/doc/introduction.R | 20 echor-0.1.1/echor/inst/doc/introduction.Rmd | 76 echor-0.1.1/echor/inst/doc/introduction.html | 1745 +--------- echor-0.1.1/echor/man/echoAirGetMeta.Rd |only echor-0.1.1/echor/man/echoGetFacilities.Rd |only echor-0.1.1/echor/man/echoGetReports.Rd |only echor-0.1.1/echor/man/echoSDWGetMeta.Rd |only echor-0.1.1/echor/man/echoSDWGetSystems.Rd |only echor-0.1.1/echor/man/echoWaterGetMeta.Rd |only echor-0.1.1/echor/man/figures/README-example2-1.png |binary echor-0.1.1/echor/man/figures/README-example3-1.png |only echor-0.1.1/echor/man/figures/README-unnamed-chunk-2-1.png |binary echor-0.1.1/echor/man/figures/README-unnamed-chunk-3-1.png |only echor-0.1.1/echor/tests/testthat.R | 3 echor-0.1.1/echor/tests/testthat/test-expected_errors.R |only echor-0.1.1/echor/tests/testthat/test-expected_objects.R |only echor-0.1.1/echor/vignettes/introduction |only echor-0.1.1/echor/vignettes/introduction.Rmd | 76 37 files changed, 961 insertions(+), 1687 deletions(-)
Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable
way to store tables from databases. This package provides convenient
functions for exporting tables from relational database connections
into compressed text files and streaming those text files back into
a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Richard FitzJohn [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between arkdb versions 0.0.1 dated 2018-08-20 and 0.0.3 dated 2018-09-11
DESCRIPTION | 10 ++--- MD5 | 14 +++---- NAMESPACE | 1 NEWS.md | 12 +++++- R/assert.R | 31 +++++++++++++++-- README.md | 35 ++++++++++--------- inst/doc/arkdb.html | 78 ++++++++++++++++++++++---------------------- tests/testthat/test-arkdb.R | 20 ++++++++++- 8 files changed, 124 insertions(+), 77 deletions(-)