Title: Linking Geographic Information Systems, Remote Sensing and Other
Command Line Tools
Description: Functions to simplify the linking of open source GIS and remote sensing related command line interfaces.
Author: Chris Reudenbach [cre, aut],
Tim Appelhans [ctb]
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>
Diff between link2GI versions 0.4-0 dated 2019-11-22 and 0.4.1 dated 2019-12-17
DESCRIPTION | 16 - MD5 | 72 ++++--- NAMESPACE | 5 NEWS | 10 - NEWS.md | 10 - R/grass7Control.R | 3 R/link2GI-package.R | 18 - R/link2giKarim.R | 189 ++++++++++++++++++ R/linkGRASS.R | 2 R/linkOTB.R | 22 +- R/linkSAGA.R | 8 R/parseOTB.R | 44 ++-- README.md | 80 ++++---- build/vignette.rds |binary data/rgb.rda |binary inst/doc/link2GI1.R | 303 ------------------------------ inst/doc/link2GI1.Rmd | 458 ---------------------------------------------- inst/doc/link2GI1.html | 410 ----------------------------------------- inst/doc/link2GI2.R |only inst/doc/link2GI2.Rmd |only inst/doc/link2GI2.html |only inst/doc/link2GI3.R |only inst/doc/link2GI3.Rmd |only inst/doc/link2GI3.html |only inst/doc/link2GI4.R |only inst/doc/link2GI4.Rmd |only inst/doc/link2GI4.html |only inst/doc/link2GI5.Rmd |only inst/doc/link2GI5.html |only man/gvec2sf.Rd |only man/link2GI.Rd | 14 - man/linkAll.Rd |only man/linkGRASS7.Rd | 2 man/linkSAGA.Rd | 8 man/parseOTBAlgorithms.Rd | 2 man/parseOTBFunction.Rd | 6 man/rgb.Rd | 4 man/runOTB.Rd | 6 man/setenvGRASSw.Rd | 2 man/setenvOTB.Rd | 4 man/sf2gvec.Rd |only vignettes/link2GI1.Rmd | 458 ---------------------------------------------- vignettes/link2GI2.Rmd |only vignettes/link2GI3.Rmd |only vignettes/link2GI4.Rmd |only vignettes/link2GI5.Rmd |only 46 files changed, 402 insertions(+), 1754 deletions(-)
Title: Integrative Survival Modeling
Description: Contains implementations of
integrative survival analysis routines, including
regular Cox cure rate model proposed by
Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531>
via an EM algorithm proposed by
Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>,
regularized Cox cure rate model with elastic net penalty following
Masud et al. (2018) <doi:10.1177/0962280216677748>, and
Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>, and
weighted concordance index for cure models proposed by
Asano and Hirakawa (2017) <doi:10.1080/10543406.2017.1293082>.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>),
Kun Chen [ctb] (<https://orcid.org/0000-0003-3579-5467>),
Jun Yan [ctb] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between intsurv versions 0.2.0 dated 2019-08-03 and 0.2.1 dated 2019-12-17
intsurv-0.2.0/intsurv/src/assessment.h |only intsurv-0.2.0/intsurv/src/coxph_cure.h |only intsurv-0.2.0/intsurv/src/coxph_cure_uncer.h |only intsurv-0.2.0/intsurv/src/coxph_reg.h |only intsurv-0.2.0/intsurv/src/logistic_reg.h |only intsurv-0.2.0/intsurv/src/nonparametric.h |only intsurv-0.2.0/intsurv/src/splines.h |only intsurv-0.2.0/intsurv/src/utils.h |only intsurv-0.2.1/intsurv/DESCRIPTION | 12 +- intsurv-0.2.1/intsurv/MD5 | 80 +++++++++--------- intsurv-0.2.1/intsurv/NEWS.md | 15 +++ intsurv-0.2.1/intsurv/R/assessment.R | 8 - intsurv-0.2.1/intsurv/R/cox_cure.R | 21 ++-- intsurv-0.2.1/intsurv/R/cox_cure_net.R | 31 +++--- intsurv-0.2.1/intsurv/R/misc.R | 2 intsurv-0.2.1/intsurv/R/prep_model.R | 35 +++++-- intsurv-0.2.1/intsurv/README.md | 18 ++-- intsurv-0.2.1/intsurv/inst/CITATION | 2 intsurv-0.2.1/intsurv/inst/examples/cox_cure.R | 6 - intsurv-0.2.1/intsurv/inst/examples/cox_cure_net.R | 7 - intsurv-0.2.1/intsurv/inst/include |only intsurv-0.2.1/intsurv/inst/tinytest |only intsurv-0.2.1/intsurv/man/cIndex.Rd | 8 - intsurv-0.2.1/intsurv/man/coef-iCoxph-method.Rd | 1 intsurv-0.2.1/intsurv/man/coef.cox_cure_net.Rd | 6 - intsurv-0.2.1/intsurv/man/cox_cure.Rd | 14 +-- intsurv-0.2.1/intsurv/man/cox_cure_net.Rd | 19 ++-- intsurv-0.2.1/intsurv/man/show-method.Rd | 1 intsurv-0.2.1/intsurv/man/summary-iCoxph-method.Rd | 1 intsurv-0.2.1/intsurv/src/Makevars | 2 intsurv-0.2.1/intsurv/src/Makevars.win | 2 intsurv-0.2.1/intsurv/src/RcppExports.cpp | 1 intsurv-0.2.1/intsurv/src/assessment_export.cpp | 10 -- intsurv-0.2.1/intsurv/src/coxph_cure_export.cpp | 27 ++---- intsurv-0.2.1/intsurv/src/coxph_cure_uncer_export.cpp | 29 +++--- intsurv-0.2.1/intsurv/src/coxph_reg_export.cpp | 13 -- intsurv-0.2.1/intsurv/src/logistic_reg_export.cpp | 13 +- intsurv-0.2.1/intsurv/src/nonparametric_export.cpp | 11 -- intsurv-0.2.1/intsurv/src/utils_export.cpp | 4 intsurv-0.2.1/intsurv/tests |only 40 files changed, 211 insertions(+), 188 deletions(-)
Title: Estimate Growth Rates from Experimental Data
Description: A collection of methods to determine growth rates from
experimental data, in particular from batch experiments and
plate reader trials.
Author: Thomas Petzoldt [aut, cre] (<https://orcid.org/0000-0002-4951-6468>)
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between growthrates versions 0.7.2 dated 2018-06-18 and 0.8.1 dated 2019-12-17
growthrates-0.7.2/growthrates/data/antibiotic.txt.gz |only growthrates-0.7.2/growthrates/data/bactgrowth.txt.gz |only growthrates-0.8.1/growthrates/DESCRIPTION | 26 growthrates-0.8.1/growthrates/MD5 | 111 + growthrates-0.8.1/growthrates/NAMESPACE | 2 growthrates-0.8.1/growthrates/R/aab_growthmodel-constructor.R | 6 growthrates-0.8.1/growthrates/R/all_growthmodels.R | 4 growthrates-0.8.1/growthrates/R/cost.R | 7 growthrates-0.8.1/growthrates/R/fit_growthmodel.R | 2 growthrates-0.8.1/growthrates/R/grow_baranyi.R | 5 growthrates-0.8.1/growthrates/R/grow_exponential.R | 5 growthrates-0.8.1/growthrates/R/grow_genlogistic.R | 9 growthrates-0.8.1/growthrates/R/grow_gompertz.R | 7 growthrates-0.8.1/growthrates/R/grow_gompertz2.R |only growthrates-0.8.1/growthrates/R/grow_huang.R | 5 growthrates-0.8.1/growthrates/R/grow_logistic.R | 5 growthrates-0.8.1/growthrates/R/grow_richards.R | 5 growthrates-0.8.1/growthrates/R/grow_twostep.R | 8 growthrates-0.8.1/growthrates/R/predict.R | 83 + growthrates-0.8.1/growthrates/README.md |only growthrates-0.8.1/growthrates/build/partial.rdb |binary growthrates-0.8.1/growthrates/build/vignette.rds |binary growthrates-0.8.1/growthrates/data/antibiotic.txt |only growthrates-0.8.1/growthrates/data/bactgrowth.txt |only growthrates-0.8.1/growthrates/inst/doc/Introduction.R | 40 growthrates-0.8.1/growthrates/inst/doc/Introduction.Rmd | 8 growthrates-0.8.1/growthrates/inst/doc/Introduction.html | 558 +++++++-- growthrates-0.8.1/growthrates/inst/doc/User_models.R | 28 growthrates-0.8.1/growthrates/inst/doc/User_models.Rmd | 18 growthrates-0.8.1/growthrates/inst/doc/User_models.html | 566 +++++++--- growthrates-0.8.1/growthrates/inst/doc/examples/example_logistic_saturation.R |only growthrates-0.8.1/growthrates/inst/doc/examples/example_spline.R | 4 growthrates-0.8.1/growthrates/inst/doc/examples/example_user_defined_growthmodel.R | 3 growthrates-0.8.1/growthrates/inst/doc/examples/example_user_defined_ode_compiled.R | 5 growthrates-0.8.1/growthrates/inst/doc/examples/example_user_defined_ode_model.R | 2 growthrates-0.8.1/growthrates/inst/doc/examples/startvalue_heuristics.R | 2 growthrates-0.8.1/growthrates/inst/doc/examples/test_cOde.R |only growthrates-0.8.1/growthrates/man/all_easylinear.Rd | 1 growthrates-0.8.1/growthrates/man/all_growthmodels.Rd | 5 growthrates-0.8.1/growthrates/man/all_splines.Rd | 1 growthrates-0.8.1/growthrates/man/cost.Rd | 4 growthrates-0.8.1/growthrates/man/fit_easylinear.Rd | 1 growthrates-0.8.1/growthrates/man/fit_growthmodel.Rd | 1 growthrates-0.8.1/growthrates/man/fit_spline.Rd | 1 growthrates-0.8.1/growthrates/man/grow_baranyi.Rd | 5 growthrates-0.8.1/growthrates/man/grow_exponential.Rd | 5 growthrates-0.8.1/growthrates/man/grow_genlogistic.Rd | 6 growthrates-0.8.1/growthrates/man/grow_gompertz.Rd | 11 growthrates-0.8.1/growthrates/man/grow_gompertz2.Rd |only growthrates-0.8.1/growthrates/man/grow_huang.Rd | 5 growthrates-0.8.1/growthrates/man/grow_logistic.Rd | 5 growthrates-0.8.1/growthrates/man/grow_richards.Rd | 5 growthrates-0.8.1/growthrates/man/grow_twostep.Rd | 7 growthrates-0.8.1/growthrates/man/growthmodel-constructor.Rd | 8 growthrates-0.8.1/growthrates/man/growthrates-classes.Rd | 16 growthrates-0.8.1/growthrates/man/multisplit.Rd | 3 growthrates-0.8.1/growthrates/man/plot.Rd | 4 growthrates-0.8.1/growthrates/man/predict.Rd | 38 growthrates-0.8.1/growthrates/src/twostep.c | 6 growthrates-0.8.1/growthrates/vignettes/Introduction.Rmd | 8 growthrates-0.8.1/growthrates/vignettes/User_models.Rmd | 18 61 files changed, 1152 insertions(+), 536 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.93 dated 2019-11-20 and 1.95 dated 2019-12-17
DESCRIPTION | 10 ++--- MD5 | 84 ++++++++++++++++++++++++------------------------ NAMESPACE | 1 R/faMB.R |only R/faMain.R | 27 ++++++++++++--- R/faScores.R | 24 +++++++++++++ R/faStandardize.R | 4 +- R/faX.R | 8 ++++ inst/CITATION | 4 +- inst/news/index.html | 15 ++++++-- man/BiFAD.Rd | 13 ++++--- man/Box26.Rd | 1 man/GenerateBoxData.Rd | 1 man/Ledermann.Rd | 1 man/RnpdMAP.Rd | 8 ++-- man/SLi.Rd | 1 man/SchmidLeiman.Rd | 1 man/bigen.Rd | 10 ++--- man/eigGen.Rd | 2 - man/faAlign.Rd | 17 +++++---- man/faEKC.Rd | 1 man/faMB.Rd |only man/faMain.Rd | 1 man/faScores.Rd | 1 man/faSort.Rd | 25 +++++++------- man/faStandardize.Rd | 1 man/faX.Rd | 1 man/fals.Rd | 1 man/fapa.Rd | 1 man/fareg.Rd | 5 +- man/fungibleExtrema.Rd | 6 +-- man/fungibleL.Rd | 10 ++--- man/fungibleR.Rd | 36 ++++++++++---------- man/gen4PMData.Rd | 2 - man/itemDescriptives.Rd | 10 ++--- man/normF.Rd | 6 +-- man/orderFactors.Rd | 1 man/print.faMain.Rd | 1 man/promaxQ.Rd | 1 man/rarc.Rd | 4 +- man/smoothBY.Rd | 4 +- man/smoothLG.Rd | 16 ++++----- man/summary.faMain.Rd | 1 man/tetcorQuasi.Rd | 8 ++-- 44 files changed, 225 insertions(+), 150 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-18 1.1
2015-03-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-12 0.9-3
2018-06-15 0.9-2
2018-02-08 0.9-1
2018-01-16 0.9-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-16 0.1.0
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.4 dated 2019-12-17 and 0.4.1 dated 2019-12-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ build/partial.rdb |binary src/10_ordinal_covPrepare.cpp | 9 ++++++--- 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming with
palettes spread over many packages with many different API's. This packages
aims to collect all color palettes across the R ecosystem under the same
package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between paletteer versions 0.2.1 dated 2019-02-13 and 1.0.0 dated 2019-12-17
paletteer-0.2.1/paletteer/tests/testthat/test-continuous-ggplot2-scales.R |only paletteer-0.2.1/paletteer/tests/testthat/test-discrete-ggplot2-scales.R |only paletteer-0.2.1/paletteer/tests/testthat/test-paletteer_c-wrappers.R |only paletteer-1.0.0/paletteer/DESCRIPTION | 12 paletteer-1.0.0/paletteer/LICENSE.note | 136 +++++++ paletteer-1.0.0/paletteer/MD5 | 133 +++++-- paletteer-1.0.0/paletteer/NAMESPACE | 8 paletteer-1.0.0/paletteer/NEWS.md | 26 + paletteer-1.0.0/paletteer/R/completeme.R |only paletteer-1.0.0/paletteer/R/data.R | 46 +- paletteer-1.0.0/paletteer/R/ggplot2_scales_continuous.R | 21 - paletteer-1.0.0/paletteer/R/ggplot2_scales_discrete.R | 32 - paletteer-1.0.0/paletteer/R/paletteer.R |only paletteer-1.0.0/paletteer/R/paletteer_c.R | 30 - paletteer-1.0.0/paletteer/R/paletteer_c_wrappers.R | 12 paletteer-1.0.0/paletteer/R/paletteer_d.R | 31 - paletteer-1.0.0/paletteer/R/paletteer_dynamic.R | 28 - paletteer-1.0.0/paletteer/R/sysdata.rda |only paletteer-1.0.0/paletteer/README.md | 178 +++++----- paletteer-1.0.0/paletteer/data/paletteer_packages.rda |only paletteer-1.0.0/paletteer/data/palettes_c_names.rda |binary paletteer-1.0.0/paletteer/data/palettes_d.rda |binary paletteer-1.0.0/paletteer/data/palettes_d_names.rda |binary paletteer-1.0.0/paletteer/inst/AUTHORS | 2 paletteer-1.0.0/paletteer/man/figures/README-unnamed-chunk-2-1.png |binary paletteer-1.0.0/paletteer/man/figures/README-unnamed-chunk-3-1.png |binary paletteer-1.0.0/paletteer/man/figures/README-unnamed-chunk-4-1.png |binary paletteer-1.0.0/paletteer/man/figures/README-unnamed-chunk-6-1.png |only paletteer-1.0.0/paletteer/man/figures/logo.png |binary paletteer-1.0.0/paletteer/man/figures/paletteer-demo.gif |only paletteer-1.0.0/paletteer/man/ggplot2-scales-continuous.Rd | 17 paletteer-1.0.0/paletteer/man/ggplot2-scales-discrete.Rd | 20 - paletteer-1.0.0/paletteer/man/paletteer-package.Rd | 18 - paletteer-1.0.0/paletteer/man/paletteer_c.Rd | 15 paletteer-1.0.0/paletteer/man/paletteer_d.Rd | 18 - paletteer-1.0.0/paletteer/man/paletteer_dynamic.Rd | 15 paletteer-1.0.0/paletteer/man/paletteer_packages.Rd |only paletteer-1.0.0/paletteer/man/palettes_c_names.Rd | 4 paletteer-1.0.0/paletteer/man/palettes_d.Rd | 15 paletteer-1.0.0/paletteer/man/palettes_d_names.Rd | 15 paletteer-1.0.0/paletteer/tests/figs |only paletteer-1.0.0/paletteer/tests/testthat/Rplots.pdf |only paletteer-1.0.0/paletteer/tests/testthat/test-completeme.R |only paletteer-1.0.0/paletteer/tests/testthat/test-ggplot2_scales_continuous.R |only paletteer-1.0.0/paletteer/tests/testthat/test-ggplot2_scales_discrete.R |only paletteer-1.0.0/paletteer/tests/testthat/test-paletteer_c.R | 24 - paletteer-1.0.0/paletteer/tests/testthat/test-paletteer_c_wrappers.R |only paletteer-1.0.0/paletteer/tests/testthat/test-paletteer_d.R | 35 - paletteer-1.0.0/paletteer/tests/testthat/test-paletteer_dynamic.R | 28 - paletteer-1.0.0/paletteer/tests/testthat/test-vdiffr_palette_check.R |only 50 files changed, 573 insertions(+), 346 deletions(-)
Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.4.3 dated 2018-11-22 and 1.5.0 dated 2019-12-17
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Title: Multivariate Extreme Value Distributions
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes [Dombry, Engelke and Oesting (2016) <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] (<https://orcid.org/0000-0002-9135-014X>),
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut],
Scott D. Grimshaw [aut],
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb],
Raphael Huser [aut]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 1.12 dated 2019-06-24 and 1.13 dated 2019-12-17
DESCRIPTION | 12 +- MD5 | 138 ++++++++++++------------ NAMESPACE | 21 +++ NEWS | 12 ++ R/bivpot.R | 2 R/extcoef.R | 2 R/gp.R | 9 - R/mle.R | 194 ++++++++++++++++++++++++++++++++++ R/penultimate.R | 29 +++-- R/profile.R | 6 - R/rmev.R | 7 + R/specdens.R | 3 R/threshold.R | 6 - R/univdist.R | 252 ++++++++++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/mev-vignette.Rnw | 2 inst/doc/mev-vignette.pdf |binary man/NC.diag.Rd | 11 + man/W.diag.Rd | 20 ++- man/angmeas.Rd | 14 +- man/angmeasdir.Rd | 14 +- man/chibar.Rd | 3 man/clikmgp.Rd | 16 ++ man/confint.eprof.Rd | 10 + man/egp-function.Rd | 10 + man/egp.fit.Rd | 3 man/egp.fitrange.Rd | 11 + man/egp2.fit.Rd | 15 ++ man/emplik.Rd | 11 + man/expme.Rd | 8 + man/ext.index.Rd | 9 + man/extcoef.Rd | 17 ++- man/extgp-functions.Rd | 54 ++++++--- man/fit.egp.Rd | 14 +- man/fit.extgp.Rd | 15 ++ man/fit.gev.Rd | 3 man/fit.gpd.Rd | 11 + man/fit.pp.Rd | 2 man/fit.rlarg.Rd | 3 man/gev.bcor.Rd | 3 man/gev.mle.Rd | 9 + man/gev.pll.Rd | 15 ++ man/gev.tem.Rd | 14 +- man/gevN.infomat.Rd | 11 + man/gp.fit.Rd | 9 + man/gpd.bcor.Rd | 3 man/gpd.ll.Rd | 2 man/gpd.mle.Rd | 10 + man/gpd.pll.Rd | 19 ++- man/gpd.tem.Rd | 16 ++ man/lambdadep.Rd | 3 man/likmgp.Rd | 14 ++ man/maxstabtest.Rd | 10 + man/pp.Rd | 28 ----- man/pp.infomat.Rd |only man/pp.ll.Rd |only man/pp.score.Rd |only man/rgparp.Rd | 23 +++- man/rlarg.Rd | 13 -- man/rlarg.infomat.Rd |only man/rlarg.ll.Rd | 9 + man/rlarg.score.Rd | 9 + man/rmev.Rd | 23 +++- man/rmevspec.Rd | 16 ++ man/rparp.Rd | 19 ++- man/rparpcs.Rd | 11 + man/smith.penult.Rd | 5 man/smith.penult.fn.Rd | 20 ++- man/taildep.Rd | 19 ++- man/tstab.gpd.Rd | 10 + src/sampling.cpp | 9 - vignettes/mev-vignette.Rnw | 2 72 files changed, 939 insertions(+), 384 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. Users can collect open-access avian recordings or enter their own data into a workflow that facilitates spectrographic visualization and measurement of acoustic parameters. 'warbleR' makes use of the basic sound analysis tools from the package 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, detect signals automatically, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre]
(<https://orcid.org/0000-0003-3594-619X>),
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.1.18 dated 2019-11-04 and 1.1.19 dated 2019-12-17
DESCRIPTION | 10 - MD5 | 204 +++++++++++++++++------------------ NAMESPACE | 2 NEWS.md | 17 ++ R/autodetec.R | 2 R/catalog.R | 2 R/checksels.R | 8 - R/checkwavs.R | 7 - R/compare.methods.R | 4 R/coor.test.R | 2 R/cut_sels.R | 2 R/dfts.R | 4 R/ffts.R | 2 R/fixwavs.R | 4 R/frange.R | 2 R/inflections.R | 2 R/lspec.R | 2 R/lspec2pdf.R | 27 ++++ R/mfcc_stats.R | 4 R/mp32wav.R | 8 - R/multi_DTW.R | 2 R/ovlp_sels.R | 2 R/querxc.R | 4 R/read_wave.R | 2 R/rename_waves_est.R |only R/resample_est.R | 2 R/selection_table.R | 7 - R/seltailor.R | 2 R/sig2noise.R | 5 R/snrspecs.R | 2 R/sp.en.ts.R | 2 R/specan.R | 4 R/specreator.R | 61 +++++++--- R/trackfreqs.R | 6 - R/try_na.R | 2 R/warbleR-package.R | 2 R/wpd_features.R | 3 R/xcorr.R | 26 ++-- build/vignette.rds |binary data/lbh_selec_table.rda |binary data/new_function_names.rda |binary data/selec.table.rda |binary data/sim.coor.sing.rda |binary data/sim_coor_sing.rda |binary inst/doc/Intro_to_warbleR.Rmd | 1 inst/doc/Intro_to_warbleR.html | 38 +++--- inst/doc/warbleR_workflow_01.Rmd | 1 inst/doc/warbleR_workflow_01.html | 14 +- inst/doc/warbleR_workflow_02.Rmd | 1 inst/doc/warbleR_workflow_02.html | 16 +- inst/doc/warbleR_workflow_03.Rmd | 1 inst/doc/warbleR_workflow_03.html | 20 ++- man/auto_detec.Rd | 39 +++++- man/check_sels.Rd | 10 + man/color.spectro.Rd | 17 +- man/color_spectro.Rd | 34 ++++- man/compare_methods.Rd | 34 ++++- man/coor_graph.Rd | 13 +- man/coor_test.Rd | 15 ++ man/dfDTW.Rd | 17 +- man/df_DTW.Rd | 33 ++++- man/df_ts.Rd | 31 ++++- man/dfts.Rd | 17 +- man/ffDTW.Rd | 17 +- man/ff_DTW.Rd | 23 +++ man/ff_ts.Rd | 22 +++ man/ffts.Rd | 17 +- man/filter_sels.Rd | 12 +- man/fix_wavs.Rd | 11 + man/freq_range.Rd | 34 ++++- man/freq_range_detec.Rd | 21 ++- man/full_spec.Rd | 28 +++- man/full_spec2pdf.Rd | 9 + man/inflections.Rd | 2 man/make.selection.table.Rd | 16 ++ man/manual_loc.Rd | 24 +++- man/move.imgs.Rd | 5 man/move_imgs.Rd | 14 +- man/multi_DTW.Rd | 17 +- man/open_wd.Rd | 5 man/phylo_spectro.Rd | 17 +- man/quer_xc.Rd | 11 + man/rename_waves_est.Rd |only man/resample_est.Rd | 5 man/se_ts.Rd | 23 +++ man/sel_tailor.Rd | 34 ++++- man/snr_specs.Rd | 32 ++++- man/snrspecs.Rd | 17 +- man/sp.en.ts.Rd | 17 +- man/spec_an.Rd | 21 ++- man/specreator.Rd | 29 +++- man/spectrograms.Rd | 41 +++++-- man/split_wavs.Rd | 5 man/sub-.extended_selection_table.Rd | 3 man/track_freqs.Rd | 63 ++++++++-- man/trackfreqs.Rd | 17 +- man/warbleR.Rd | 1 man/wpd_features.Rd | 1 man/x_corr.Rd | 19 ++- man/xc_maps.Rd | 3 vignettes/Intro_to_warbleR.Rmd | 1 vignettes/warbleR_workflow_01.Rmd | 1 vignettes/warbleR_workflow_02.Rmd | 1 vignettes/warbleR_workflow_03.Rmd | 1 104 files changed, 1002 insertions(+), 439 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling tools for
developing cellular automata, dynamic raster models, and agent based models
in 'SpaDES'.
Included are various methods for spatial spreading, spatial agents, GIS
operations, random map generation, and others.
See '?SpaDES.tools' for an categorized overview of these additional tools.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>),
Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>),
Yong Luo [ctb],
Steve Cumming [ctb],
Jean Marchal [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES.tools versions 0.3.3 dated 2019-11-25 and 0.3.4 dated 2019-12-17
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 12 ++++++++++++ tests/testthat/test-spread2.R | 32 +++++++++++++++++--------------- 4 files changed, 37 insertions(+), 23 deletions(-)
Title: Database Interface and 'MariaDB' Driver
Description: Implements a 'DBI'-compliant interface to 'MariaDB'
(<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>)
databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RMariaDB versions 1.0.7 dated 2019-12-02 and 1.0.8 dated 2019-12-17
DESCRIPTION | 61 ++++++++++++------ MD5 | 78 ++++++++++++----------- NEWS.md | 6 + R/MariaDBDriver.R | 16 ++++ R/connect.R | 8 +- R/quote.R | 24 +++++-- R/table.R | 7 -- README.md | 19 ++++- configure | 5 - man/MariaDBDriver-class.Rd | 3 man/RMariaDB-package.Rd | 9 +- man/dbConnect-MariaDBDriver-method.Rd | 28 ++++++-- man/dbDataType.Rd | 1 man/mariadb-quoting.Rd | 1 man/mariadb-tables.Rd | 48 +++++++++----- man/mariadbHasDefault.Rd | 2 man/query.Rd | 7 -- man/result-meta.Rd | 1 man/transactions.Rd | 3 src/DbConnection.cpp | 21 ++++-- src/DbConnection.h | 1 src/DbResult.cpp | 113 +++++++++++++++------------------- src/DbResult.h | 43 ++++++------ src/DbResultImpl.h |only src/DbResultImplDecl.h |only src/Makevars.in | 2 src/Makevars.win | 14 +++- src/MariaBinding.cpp | 10 ++- src/MariaBinding.h | 3 src/MariaResult.cpp |only src/MariaResult.h |only src/MariaResultPrep.cpp | 23 +++--- src/MariaResultPrep.h | 11 ++- src/MariaResultSimple.cpp | 15 +--- src/MariaResultSimple.h | 8 +- src/MariaRow.h | 3 src/pch.h | 4 + src/result.cpp | 3 tests/testthat/helper-DBItest.R | 10 ++- tests/testthat/test-DBItest.R | 17 ----- tests/testthat/test-dbWriteTable.R | 7 +- tools/winlibs.R | 5 - 42 files changed, 372 insertions(+), 268 deletions(-)
Title: Estimate Kinship and FST under Arbitrary Population Structure
Description: Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>),
John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between popkin versions 1.2.2 dated 2019-05-13 and 1.3.0 dated 2019-12-17
popkin-1.2.2/popkin/R/get_mem_lim_m.R |only popkin-1.2.2/popkin/R/popkin-deprecated.R |only popkin-1.2.2/popkin/man/inbrDiag-deprecated.Rd |only popkin-1.2.2/popkin/man/neff-deprecated.Rd |only popkin-1.2.2/popkin/man/plotPopkin-deprecated.Rd |only popkin-1.2.2/popkin/man/popkin-deprecated.Rd |only popkin-1.2.2/popkin/man/rescalePopkin-deprecated.Rd |only popkin-1.2.2/popkin/man/weightsSubpops-deprecated.Rd |only popkin-1.3.0/popkin/DESCRIPTION | 8 popkin-1.3.0/popkin/MD5 | 57 - popkin-1.3.0/popkin/NAMESPACE | 5 popkin-1.3.0/popkin/NEWS.md | 106 ++ popkin-1.3.0/popkin/R/get_A.R | 91 + popkin-1.3.0/popkin/R/get_mem_lim.R | 6 popkin-1.3.0/popkin/R/inbr_diag.R | 39 popkin-1.3.0/popkin/R/n_eff.R | 55 - popkin-1.3.0/popkin/R/plot_popkin.R | 915 ++++++++++++------- popkin-1.3.0/popkin/R/popkin.R | 36 popkin-1.3.0/popkin/R/rescale_popkin.R | 27 popkin-1.3.0/popkin/R/solve_m_mem_lim.R |only popkin-1.3.0/popkin/R/weights_subpops.R | 25 popkin-1.3.0/popkin/README.md |only popkin-1.3.0/popkin/build/vignette.rds |binary popkin-1.3.0/popkin/inst/doc/popkin.R | 198 ++-- popkin-1.3.0/popkin/inst/doc/popkin.Rmd | 167 ++- popkin-1.3.0/popkin/inst/doc/popkin.html | 221 ++-- popkin-1.3.0/popkin/man/figures |only popkin-1.3.0/popkin/man/inbr_diag.Rd | 7 popkin-1.3.0/popkin/man/n_eff.Rd | 13 popkin-1.3.0/popkin/man/plot_popkin.Rd | 143 ++ popkin-1.3.0/popkin/man/popkin-package.Rd | 4 popkin-1.3.0/popkin/man/popkin.Rd | 22 popkin-1.3.0/popkin/tests/testthat/test_popkin.R | 140 ++ popkin-1.3.0/popkin/tests/testthat/test_popkin_fn.R | 2 popkin-1.3.0/popkin/vignettes/popkin.Rmd | 167 ++- 35 files changed, 1577 insertions(+), 877 deletions(-)
Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and
'broom.mixed' package-related data analysis workflows. In particular,
the generic functions tidy(), glance(), and augment() choose
appropriate S3 methods from these two packages depending on which
package exports the needed method. Additionally, 'grouped_' and
'boot_' variants of the generics provides a convenient way to execute
functions across a combination of grouping variable(s) in a dataframe
or bootstrap them.
Author: Indrajeet Patil [aut, cre, ctb]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 0.0.6 dated 2019-10-26 and 1.0.0 dated 2019-12-17
broomExtra-0.0.6/broomExtra/R/boot_generics.R |only broomExtra-0.0.6/broomExtra/man/boot_augment.Rd |only broomExtra-0.0.6/broomExtra/man/boot_glance.Rd |only broomExtra-0.0.6/broomExtra/man/boot_tidy.Rd |only broomExtra-0.0.6/broomExtra/man/figures |only broomExtra-0.0.6/broomExtra/tests/testthat/test-boot_generics.R |only broomExtra-1.0.0/broomExtra/DESCRIPTION | 13 broomExtra-1.0.0/broomExtra/MD5 | 48 broomExtra-1.0.0/broomExtra/NAMESPACE | 20 broomExtra-1.0.0/broomExtra/NEWS.md | 4 broomExtra-1.0.0/broomExtra/R/generics.R | 6 broomExtra-1.0.0/broomExtra/R/grouped_generics.R | 6 broomExtra-1.0.0/broomExtra/README.md | 328 +----- broomExtra-1.0.0/broomExtra/build/broomExtra.pdf |binary broomExtra-1.0.0/broomExtra/inst/doc/available_methods.R | 6 broomExtra-1.0.0/broomExtra/inst/doc/available_methods.html | 481 +++++----- broomExtra-1.0.0/broomExtra/inst/doc/tests_and_coverage.R | 2 broomExtra-1.0.0/broomExtra/inst/doc/tests_and_coverage.Rmd | 29 broomExtra-1.0.0/broomExtra/inst/doc/tests_and_coverage.html | 117 +- broomExtra-1.0.0/broomExtra/man/augment.Rd | 4 broomExtra-1.0.0/broomExtra/man/glance.Rd | 4 broomExtra-1.0.0/broomExtra/man/grouped_augment.Rd | 8 broomExtra-1.0.0/broomExtra/man/grouped_glance.Rd | 8 broomExtra-1.0.0/broomExtra/man/grouped_tidy.Rd | 8 broomExtra-1.0.0/broomExtra/man/tidy.Rd | 4 broomExtra-1.0.0/broomExtra/tests/README.md | 31 broomExtra-1.0.0/broomExtra/vignettes/tests_and_coverage.Rmd | 29 27 files changed, 479 insertions(+), 677 deletions(-)
Title: Estimation of Multinormal Mixture Distribution
Description: Fit multivariate mixture of normal distribution using
covariance structure.
Author: Charles-Edouard Giguere
Maintainer: Charles-Edouard Giguere <ce.giguere@gmail.com>
Diff between mmeln versions 1.3 dated 2018-05-16 and 1.4 dated 2019-12-17
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/mutil.R | 4 ++-- build/partial.rdb |binary 5 files changed, 12 insertions(+), 10 deletions(-)
Title: Genetics Input/Output Functions
Description: Implements readers and writers for file formats associated with genetics data. Reading and writing plink BED/BIM/FAM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles plink and eigenstrat tables (FAM, BIM, IND, and SNP files). There are also "make" functions for FAM and BIM tables with default values to go with simulated genotype data.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between genio versions 1.0.10 dated 2019-05-28 and 1.0.12 dated 2019-12-17
DESCRIPTION | 8 - MD5 | 51 ++++--- NAMESPACE | 2 NEWS.md | 16 ++ R/read_bed.R | 3 R/read_phen.R |only R/write_bim.R | 2 R/write_fam.R | 2 R/write_ind.R | 2 R/write_phen.R |only R/write_plink.R | 16 +- R/write_snp.R | 2 R/write_tab_generic.R | 4 README.md | 2 build/vignette.rds |binary inst/doc/genio.R | 42 ++--- inst/doc/genio.html | 307 +++++++++++++++++++++---------------------- inst/extdata/sample.phen |only inst/extdata/sample2.phen.gz |only man/figures |only man/genio.Rd | 2 man/read_bed.Rd | 10 + man/read_phen.Rd |only man/write_bim.Rd | 2 man/write_fam.Rd | 2 man/write_ind.Rd | 2 man/write_phen.Rd |only man/write_plink.Rd | 7 man/write_snp.Rd | 2 tests/testthat/test-genio.R | 130 +++++++++++++++++- 30 files changed, 395 insertions(+), 221 deletions(-)
Title: Variance Function Program
Description: Variance function estimation for models proposed by W. Sadler in his variance function program
('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is
to fit multiple variance functions to a data set and consequently assess which function reflects
the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship
is of great importance when individual test-results are used for defining follow-up treatment of patients.
Author: Andre Schuetzenmeister [cre, aut],
Florian Dufey [aut],
Andrea Geistanger [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VFP versions 1.1 dated 2019-11-06 and 1.2 dated 2019-12-17
DESCRIPTION | 24 MD5 | 53 NAMESPACE | 5 R/vfp.R | 7092 ++++++++++++++++++++++--------------------- build |only inst/ChangLog.txt | 7 inst/UnitTests/runit.tests.R | 38 inst/doc |only man/VFP-Package.Rd | 4 man/addGrid.Rd | 3 man/deriveCx.Rd | 17 man/fit.vfp.Rd | 6 man/getMat.VCA.Rd | 11 man/plot.VFP.Rd | 4 man/precisionPlot.Rd |only man/t.coef.Rd | 4 vignettes |only 17 files changed, 3836 insertions(+), 3432 deletions(-)
Title: Retrieve Genomic and Clinical Data from TCGA
Description: The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see <http://www.cbioportal.org/> for more information). 'TCGAretriever' is easy to use (get all the TCGA data you need with a few lines of code), enforces reliable data download (via 'httr'), and is suitable for downloading large volumes of data.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between TCGAretriever versions 1.3 dated 2016-07-30 and 1.5 dated 2019-12-17
TCGAretriever-1.3/TCGAretriever/R/TCGAretriever-internal.R |only TCGAretriever-1.3/TCGAretriever/R/basic_tcga_query.R |only TCGAretriever-1.3/TCGAretriever/R/expand_cases.R |only TCGAretriever-1.3/TCGAretriever/R/fetch_all_tcgadata.R |only TCGAretriever-1.3/TCGAretriever/R/get_cancer_studies.R |only TCGAretriever-1.3/TCGAretriever/R/get_cancer_types.R |only TCGAretriever-1.3/TCGAretriever/R/get_case_lists.R |only TCGAretriever-1.3/TCGAretriever/R/get_clinical_data.R |only TCGAretriever-1.3/TCGAretriever/R/get_ext_mutation.R |only TCGAretriever-1.3/TCGAretriever/R/get_genetic_profiles.R |only TCGAretriever-1.3/TCGAretriever/R/get_profile_data.R |only TCGAretriever-1.3/TCGAretriever/R/get_protein_data.R |only TCGAretriever-1.3/TCGAretriever/R/get_protein_info.R |only TCGAretriever-1.3/TCGAretriever/R/make_groups.R |only TCGAretriever-1.3/TCGAretriever/R/trim_rnaseq_tcgadata.R |only TCGAretriever-1.3/TCGAretriever/man/trim_rnaseq_tcgadata.Rd |only TCGAretriever-1.5/TCGAretriever/DESCRIPTION | 20 ++-- TCGAretriever-1.5/TCGAretriever/MD5 | 54 ++++------- TCGAretriever-1.5/TCGAretriever/NAMESPACE | 20 +++- TCGAretriever-1.5/TCGAretriever/R/TCGAretr_scr.R |only TCGAretriever-1.5/TCGAretriever/build |only TCGAretriever-1.5/TCGAretriever/inst |only TCGAretriever-1.5/TCGAretriever/man/TCGAretriever-package.Rd | 40 ++++++-- TCGAretriever-1.5/TCGAretriever/man/basic_tcga_query.Rd | 27 +++-- TCGAretriever-1.5/TCGAretriever/man/expand_cases.Rd | 28 +++-- TCGAretriever-1.5/TCGAretriever/man/fetch_all_tcgadata.Rd | 49 ++++++--- TCGAretriever-1.5/TCGAretriever/man/get_cancer_studies.Rd | 26 +++-- TCGAretriever-1.5/TCGAretriever/man/get_cancer_types.Rd | 29 +++-- TCGAretriever-1.5/TCGAretriever/man/get_case_lists.Rd | 37 ++++--- TCGAretriever-1.5/TCGAretriever/man/get_clinical_data.Rd | 46 +++++---- TCGAretriever-1.5/TCGAretriever/man/get_ext_mutation.Rd | 43 +++++--- TCGAretriever-1.5/TCGAretriever/man/get_genetic_profiles.Rd | 32 +++--- TCGAretriever-1.5/TCGAretriever/man/get_profile_data.Rd | 39 ++++--- TCGAretriever-1.5/TCGAretriever/man/get_protein_data.Rd | 34 ++++-- TCGAretriever-1.5/TCGAretriever/man/get_protein_info.Rd | 48 ++++++--- TCGAretriever-1.5/TCGAretriever/man/make_groups.Rd | 52 +++++----- TCGAretriever-1.5/TCGAretriever/vignettes |only 37 files changed, 376 insertions(+), 248 deletions(-)
Title: Estimate Percentiles from an Ordered Categorical Variable
Description: An implementation of two functions that estimate values for percentiles from an ordered categorical variable as described by Reardon (2011, isbn:978-0-87154-372-1). One function estimates percentile differences from two percentiles while the other returns the values for every percentile from 1 to 100.
Author: Jorge Cimentada [aut, cre] (<https://orcid.org/0000-0001-5594-1156>)
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>
Diff between perccalc versions 1.0.4 dated 2019-12-09 and 1.0.5 dated 2019-12-17
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/utils.R | 2 +- inst/doc/perc_calculator_example.html | 4 ++-- inst/doc/perc_warning_example.html | 4 ++-- inst/doc/pisa_example.html | 4 ++-- 7 files changed, 21 insertions(+), 17 deletions(-)
Title: Optimos Prime Helps Calculate Autoecological Data for Biological
Species
Description: Calculates autoecological data (optima and tolerance ranges) of a biological species
given an environmental matrix. The package calculates by weighted averaging, using the number of occurrences to adjust the
tolerance assigned to each taxon to estimate optima and tolerance range in cases where taxa
have unequal occurrences. See the detailed methodology by Birks et al. (1990) <doi:10.1098/rstb.1990.0062>, and a
case example by Potapova and Charles (2003) <doi:10.1046/j.1365-2427.2003.01080.x>.
Author: María Belén Sathicq [aut],
María Mercedes Nicolosi Gelis [aut],
Joaquín Cochero [cre]
Maintainer: Joaquín Cochero <jcochero@ilpla.edu.ar>
Diff between optimos.prime versions 0.1.0 dated 2019-02-18 and 0.1.1 dated 2019-12-17
optimos.prime-0.1.0/optimos.prime/man/enviromental_df.Rd |only optimos.prime-0.1.1/optimos.prime/DESCRIPTION | 6 +- optimos.prime-0.1.1/optimos.prime/MD5 | 30 +++++----- optimos.prime-0.1.1/optimos.prime/R/data.R | 6 +- optimos.prime-0.1.1/optimos.prime/R/op_calculate.R | 18 +++--- optimos.prime-0.1.1/optimos.prime/R/op_lists.R | 16 ++--- optimos.prime-0.1.1/optimos.prime/R/op_plot.R | 2 optimos.prime-0.1.1/optimos.prime/R/optimos.prime.R | 4 + optimos.prime-0.1.1/optimos.prime/data/environmental_data.RData |binary optimos.prime-0.1.1/optimos.prime/data/species_data.RData |binary optimos.prime-0.1.1/optimos.prime/man/environmental_data_example_2.Rd | 2 optimos.prime-0.1.1/optimos.prime/man/environmental_df.Rd |only optimos.prime-0.1.1/optimos.prime/man/op_calculate.Rd | 16 ++--- optimos.prime-0.1.1/optimos.prime/man/op_lists.Rd | 14 ++-- optimos.prime-0.1.1/optimos.prime/man/op_plot.Rd | 10 +-- optimos.prime-0.1.1/optimos.prime/man/optimos.prime.Rd | 3 - optimos.prime-0.1.1/optimos.prime/man/species_data_example_2.Rd | 2 17 files changed, 66 insertions(+), 63 deletions(-)
Title: Bucky's Archive for Data Analysis in the Social Sciences
Description: Provides functions for various statistical techniques commonly used in the social sciences, including functions to compute clustered robust standard errors, combine results across multiply-imputed data sets, and simplify the addition of robust and clustered robust standard errors.
Author: Alexander Tahk [aut, cre]
Maintainer: Alexander Tahk <tahk@alum.mit.edu>
Diff between bucky versions 1.0.5 dated 2018-10-29 and 1.0.6 dated 2019-12-17
bucky-1.0.5/bucky/NEWS |only bucky-1.0.6/bucky/DESCRIPTION | 10 +++++----- bucky-1.0.6/bucky/MD5 | 18 +++++++++--------- bucky-1.0.6/bucky/NEWS.md |only bucky-1.0.6/bucky/R/clustered-robust.R | 18 ++++++++++++++++-- bucky-1.0.6/bucky/R/mult-imp.R | 8 ++++---- bucky-1.0.6/bucky/build/partial.rdb |binary bucky-1.0.6/bucky/man/bucky-package.Rd | 2 +- bucky-1.0.6/bucky/man/mi.eval.Rd | 16 +++++++++++----- bucky-1.0.6/bucky/man/robustify.Rd | 12 +++++++++--- bucky-1.0.6/bucky/man/vcovCR.Rd | 2 +- 11 files changed, 56 insertions(+), 30 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.1.2 dated 2019-05-06 and 1.1.3 dated 2019-12-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/04-reaper.R | 4 ++-- build/vignette.rds |binary data/savedSims.rda |binary inst/doc/Thresher.pdf |binary tests/04-reap.Rout.save | 8 ++++---- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from <https://www.bls.gov/>. The U.S. Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between blscrapeR versions 3.1.6 dated 2019-01-29 and 3.2.0 dated 2019-12-17
DESCRIPTION | 10 +++--- MD5 | 50 +++++++++++++++--------------- NEWS.md | 9 +++++ R/data.R | 25 +++++++++++++-- R/inflation.R | 14 ++++++-- build/vignette.rds |binary data/datalist | 1 data/naics.rda |only data/series_ids.rda |binary inst/doc/Employment_and_Unemployment.R | 12 +++---- inst/doc/Employment_and_Unemployment.html | 36 ++++++++++++--------- inst/doc/Inflation_and_Prices.R | 8 ++-- inst/doc/Inflation_and_Prices.html | 24 +++++++++----- inst/doc/Mapping_BLS_Data.R | 10 +++--- inst/doc/Mapping_BLS_Data.html | 40 +++++++++++++----------- inst/doc/Pay_and_Benefits.R | 10 +++--- inst/doc/Pay_and_Benefits.html | 30 ++++++++++-------- inst/doc/QCEW_API.R | 10 +++--- inst/doc/QCEW_API.html | 24 +++++++++----- man/bls_api.Rd | 13 ++++++- man/bls_map_county.Rd | 12 +++++-- man/bls_map_state.Rd | 9 ++++- man/map_bls.Rd | 13 ++++++- man/naics.Rd |only man/niacs.Rd | 4 +- man/qcew_api.Rd | 3 - man/series_ids.Rd | 4 +- 27 files changed, 231 insertions(+), 140 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analyzing function interfaces.
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between vctrs versions 0.2.0 dated 2019-07-05 and 0.2.1 dated 2019-12-17
DESCRIPTION | 6 MD5 | 28 - NEWS.md | 5 build/vctrs.pdf |binary build/vignette.rds |binary inst/doc/s3-vector.R | 138 ++--- inst/doc/s3-vector.html | 1185 ++++++++++++++++++++++---------------------- inst/doc/stability.R | 58 +- inst/doc/stability.html | 415 +++++++-------- inst/doc/type-size.R | 66 +- inst/doc/type-size.html | 549 ++++++++++---------- src/bind.c | 4 src/utils.c | 2 src/utils.h | 10 tests/testthat/test-slice.R | 6 15 files changed, 1246 insertions(+), 1226 deletions(-)
Title: Estimation and Prediction for Remote Effects Spatial Process
Models
Description: Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <doi:10.1002/env.2523>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>. This material is based upon work supported by the National Science Foundation under grant number AGS 1419558. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
Author: Joshua Hewitt
Maintainer: Joshua Hewitt <joshua.hewitt@duke.edu>
Diff between telefit versions 1.0.1 dated 2019-02-18 and 1.0.2 dated 2019-12-17
DESCRIPTION | 12 - MD5 | 51 ++--- NAMESPACE | 1 NEWS.md | 16 + R/extractRegion.R | 85 +++++--- R/extractStData.R | 60 ++++-- R/plot.stData.R | 6 inst |only man/coef.stPredict.Rd | 3 man/extractRegion.Rd | 15 + man/extractStData.Rd | 33 ++- man/mergeCovmat.Rd | 12 + man/plot.stData.Rd | 34 ++- man/plot.stFit.Rd | 26 ++ man/plot.stPredict.Rd | 19 + man/plot.teleCor.Rd | 12 + man/stFit.Rd | 24 +- man/stLL.Rd | 22 +- man/stPredict.Rd | 26 ++ man/svcFit.Rd | 16 + man/svcPredict.Rd | 12 + man/teleCor.Rd | 9 man/telefit.Rd | 1 src/RcppExports.cpp | 3 src/stpmod.cpp | 495 ++++++++++++++++++++++++-------------------------- src/svcMod.cpp | 198 ++++++++++---------- src/svcPredict.cpp | 54 ++--- 27 files changed, 738 insertions(+), 507 deletions(-)
Title: Analyzing Multiple Omics Data with an Offset Approach
Description: Fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block.
Author: Simon Klau, Roman Hornung, Alina Bauer
Maintainer: Simon Klau <simonklau@ibe.med.uni-muenchen.de>
Diff between prioritylasso versions 0.2.2 dated 2019-06-05 and 0.2.3 dated 2019-12-17
DESCRIPTION | 8 - MD5 | 20 +-- NAMESPACE | 18 +- build/vignette.rds |binary inst/doc/prioritylasso_vignette.R | 40 +++--- inst/doc/prioritylasso_vignette.html | 147 +++++++++++----------- man/cvm_prioritylasso.Rd | 178 +++++++++++++------------- man/pl_data.Rd | 80 ++++++------ man/predict.prioritylasso.Rd | 82 ++++++------ man/prioritylasso.Rd | 232 +++++++++++++++++------------------ tests/testthat/test-predict.R | 214 ++++++++++++++++---------------- 11 files changed, 514 insertions(+), 505 deletions(-)
Title: A Replacement and Extension of the 'optim' Function
Description: Provides a test of replacement and extension of the optim()
function to unify and streamline optimization capabilities in R
for smooth, possibly box constrained functions of several or
many parameters. This version has a reduced set of methods and is
intended to be on CRAN.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <nashjc@uottawa.ca>
Diff between optimr versions 2016-8.16 dated 2016-08-16 and 2019-12.16 dated 2019-12-17
optimr-2016-8.16/optimr/inst/developmentnotes |only optimr-2016-8.16/optimr/inst/doc/voptimr.pdf |only optimr-2019-12.16/optimr/DESCRIPTION | 12 optimr-2019-12.16/optimr/MD5 | 25 - optimr-2019-12.16/optimr/NEWS | 9 optimr-2019-12.16/optimr/R/opm.R | 4 optimr-2019-12.16/optimr/R/optimr.R | 12 optimr-2019-12.16/optimr/build/vignette.rds |binary optimr-2019-12.16/optimr/inst/CITATION | 4 optimr-2019-12.16/optimr/inst/doc/voptimr.R | 6 optimr-2019-12.16/optimr/inst/doc/voptimr.html |only optimr-2019-12.16/optimr/man/opm.Rd | 18 optimr-2019-12.16/optimr/man/optimr.Rd | 588 ++++++++++++------------- optimr-2019-12.16/optimr/tests/bdstest0.R | 6 optimr-2019-12.16/optimr/tests/scbdtest0.R | 4 15 files changed, 345 insertions(+), 343 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>),
Grant McDermott [ctb],
Karl Dunkle Werner [ctb],
Matthieu Stigler [ctb],
Daniel Lüdecke [ctb]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.8-4 dated 2019-12-11 and 2.8-5 dated 2019-12-17
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- inst/NEWS.Rd | 7 +++++++ inst/doc/biascorrection.pdf |binary inst/doc/identification.R | 4 ++-- inst/doc/identification.Rnw | 33 +++++++++++++++++++++------------ inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary vignettes/identification.Rnw | 33 +++++++++++++++++++++------------ 10 files changed, 65 insertions(+), 40 deletions(-)
Title: Simulation and Analysis Tools for Clinical Dose Response
Modeling
Description: Bayesian and ML Emax model fitting, graphics and simulation for clinical dose
response. The summary data from the dose response meta-analyses in
Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and
Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229>
Wu, Banerjee, Jin, Menon, Martin, and Heatherington(2017) <doi:10.1177/0962280216684528>
are included
in the package. The prior distributions for the Bayesian analyses default to
the posterior predictive distributions derived from these references.
Author: Neal Thomas [aut, cre] (<https://orcid.org/0000-0002-1915-8487>),
Jing Wu [aut]
Maintainer: Neal Thomas <snthomas99@gmail.com>
Diff between clinDR versions 1.9 dated 2019-01-04 and 2.2.1 dated 2019-12-17
clinDR-1.9/clinDR/data/examples14.rda |only clinDR-1.9/clinDR/data/examples16.rda |only clinDR-1.9/clinDR/man/examples14.Rd |only clinDR-1.9/clinDR/man/examples16.Rd |only clinDR-2.2.1/clinDR/DESCRIPTION | 14 clinDR-2.2.1/clinDR/MD5 | 182 +- clinDR-2.2.1/clinDR/NAMESPACE | 5 clinDR-2.2.1/clinDR/R/SeEmax.R | 2 clinDR-2.2.1/clinDR/R/checkMonoEmax.R | 2 clinDR-2.2.1/clinDR/R/compileStanModels.R | 8 clinDR-2.2.1/clinDR/R/emaxfun.R | 16 clinDR-2.2.1/clinDR/R/emaxsim.R | 6 clinDR-2.2.1/clinDR/R/emaxsimB.R | 46 clinDR-2.2.1/clinDR/R/emaxsolve.R |only clinDR-2.2.1/clinDR/R/fitEmax.R | 101 - clinDR-2.2.1/clinDR/R/fitEmaxB.R | 688 +++++++--- clinDR-2.2.1/clinDR/R/generic.R | 34 clinDR-2.2.1/clinDR/R/plot.emaxsimB.R | 2 clinDR-2.2.1/clinDR/R/plot.emaxsimobj.R | 22 clinDR-2.2.1/clinDR/R/plot.fitEmax.R | 47 clinDR-2.2.1/clinDR/R/plot.plotB.R | 110 - clinDR-2.2.1/clinDR/R/plotB.R | 16 clinDR-2.2.1/clinDR/R/plotD.R | 4 clinDR-2.2.1/clinDR/R/predict.fitEmax.R | 26 clinDR-2.2.1/clinDR/R/predict.fitEmaxB.R | 8 clinDR-2.2.1/clinDR/R/print.emaxsimB.R | 3 clinDR-2.2.1/clinDR/R/selEstan.R | 12 clinDR-2.2.1/clinDR/R/showStanModels.R | 4 clinDR-2.2.1/clinDR/R/summary.emaxsim.R | 20 clinDR-2.2.1/clinDR/R/summary.emaxsimB.R | 31 clinDR-2.2.1/clinDR/R/targetCI.R | 2 clinDR-2.2.1/clinDR/R/targetD.R | 4 clinDR-2.2.1/clinDR/data/metaData.rda |only clinDR-2.2.1/clinDR/inst/NEWS | 37 clinDR-2.2.1/clinDR/inst/models/basemodel.stan | 12 clinDR-2.2.1/clinDR/inst/models/mrmodel.stan |only clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.densityplot_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.densityplot_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmax_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmax_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotB_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotB_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotD_new.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotD_old.pdf |binary clinDR-2.2.1/clinDR/inst/tests/extraGraphics/test.densityplots.R | 44 clinDR-2.2.1/clinDR/inst/tests/extraGraphics/test.plot.fitEmax.R | 4 clinDR-2.2.1/clinDR/inst/tests/extraGraphics/test.plotB.R | 70 - clinDR-2.2.1/clinDR/inst/tests/extraGraphics/test.plotD.R | 9 clinDR-2.2.1/clinDR/inst/tests/runIndvidualTests.R | 21 clinDR-2.2.1/clinDR/inst/tests/runIndvidualTests2.R |only clinDR-2.2.1/clinDR/inst/tests/test.checkMonoEmax.R | 61 clinDR-2.2.1/clinDR/inst/tests/test.checkMonoEmaxlocalParm.R |only clinDR-2.2.1/clinDR/inst/tests/test.emaxfun.R | 62 clinDR-2.2.1/clinDR/inst/tests/test.emaxsim.R | 7 clinDR-2.2.1/clinDR/inst/tests/test.emaxsimB.R | 22 clinDR-2.2.1/clinDR/inst/tests/test.emaxsimBlocalParm.R |only clinDR-2.2.1/clinDR/inst/tests/test.fitEmax.R | 98 + clinDR-2.2.1/clinDR/inst/tests/test.fitEmaxB.R | 41 clinDR-2.2.1/clinDR/inst/tests/test.fitEmaxBlocalParm.R |only clinDR-2.2.1/clinDR/man/BrextractB.Rd | 5 clinDR-2.2.1/clinDR/man/DRDensityPlot.Rd | 14 clinDR-2.2.1/clinDR/man/FixedMean.Rd | 27 clinDR-2.2.1/clinDR/man/checkMonoEmax.Rd | 29 clinDR-2.2.1/clinDR/man/clinDR-package.Rd | 4 clinDR-2.2.1/clinDR/man/coef.Rd | 9 clinDR-2.2.1/clinDR/man/compileStanModels.Rd | 2 clinDR-2.2.1/clinDR/man/emaxPrior.control.Rd |only clinDR-2.2.1/clinDR/man/emaxsimB.Rd | 44 clinDR-2.2.1/clinDR/man/emaxsolve.Rd |only clinDR-2.2.1/clinDR/man/fitEmax.Rd | 2 clinDR-2.2.1/clinDR/man/fitEmaxB.Rd | 30 clinDR-2.2.1/clinDR/man/mcmc.control.Rd | 6 clinDR-2.2.1/clinDR/man/metaData.Rd |only clinDR-2.2.1/clinDR/man/nllogis.Rd | 12 clinDR-2.2.1/clinDR/man/plot.emaxsimB.Rd | 5 clinDR-2.2.1/clinDR/man/plot.emaxsimBobj.Rd | 31 clinDR-2.2.1/clinDR/man/plot.emaxsimobj.Rd | 4 clinDR-2.2.1/clinDR/man/plot.fitEmax.Rd | 7 clinDR-2.2.1/clinDR/man/plot.fitEmaxB.Rd | 28 clinDR-2.2.1/clinDR/man/plot.plotB.Rd | 44 clinDR-2.2.1/clinDR/man/plotB.Rd | 46 clinDR-2.2.1/clinDR/man/plotBdensity.Rd | 22 clinDR-2.2.1/clinDR/man/plotD.Rd | 9 clinDR-2.2.1/clinDR/man/predict.emaxsimB.Rd | 5 clinDR-2.2.1/clinDR/man/predict.emaxsimBobj.Rd | 5 clinDR-2.2.1/clinDR/man/predict.fitEmaxB.Rd | 20 clinDR-2.2.1/clinDR/man/print.emaxsimB.Rd | 5 clinDR-2.2.1/clinDR/man/prior.control.Rd | 4 clinDR-2.2.1/clinDR/man/selEstan.Rd | 10 clinDR-2.2.1/clinDR/man/showStanModels.Rd | 9 clinDR-2.2.1/clinDR/man/startEmax.Rd | 7 clinDR-2.2.1/clinDR/man/summary.emaxsimB.Rd | 5 clinDR-2.2.1/clinDR/man/summary.emaxsimBobj.Rd | 5 99 files changed, 1524 insertions(+), 834 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photos, tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station including GIS export) and can visualise species activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 1.2 dated 2019-12-05 and 1.2.1 dated 2019-12-17
DESCRIPTION | 14 MD5 | 44 +- NAMESPACE | 1 NEWS | 19 R/onAttach.R | 4 R/recordTable.R | 101 ++--- R/recordTableIndividual.R | 45 +- R/spatialDetectionHistory.R | 2 R/variousOtherHelperFunctions.R | 103 +++-- build/vignette.rds |binary data/camtrapsMultiSeason.rda |only data/recordTableIndividualSampleMultiSeason.rda |only data/recordTableSampleMultiSeason.rda |only inst/doc/DataExploration.html | 14 inst/doc/DataExtraction.R | 112 ++--- inst/doc/DataExtraction.Rmd | 114 ++--- inst/doc/DataExtraction.html | 463 ++++++++++++++++++------ inst/doc/ImageOrganisation.html | 56 +- inst/doc/SpeciesIndividualIdentification.html | 88 ++-- man/camtrapR-package.Rd | 3 man/camtrapsMultiSeason.Rd |only man/detectionHistory.Rd | 34 + man/recordTableIndividualSampleMultiSeason.Rd |only man/recordTableSampleMultiSeason.Rd |only man/spatialDetectionHistory.Rd | 44 ++ vignettes/DataExtraction.Rmd | 114 ++--- 26 files changed, 851 insertions(+), 524 deletions(-)
Title: Modeling Framework for Cellular Communities in their
Environments
Description: Can be used for simulation of organisms living in
communities (Bauer and Zimmermann (2017) <doi:10.1371/journal.pcbi.1005544>).
Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.
Author: Eugen Bauer [aut],
Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
Diff between BacArena versions 1.8 dated 2019-02-15 and 1.8.1 dated 2019-12-17
DESCRIPTION | 17 +-- MD5 | 192 ++++++++++++++++++------------------- NAMESPACE | 1 NEWS | 15 ++ R/Arena.R | 69 ++++++++++--- R/Organism.R | 159 +++++++++++++++++++++--------- R/Stuff.R | 26 ++++- R/data.R | 2 R/matlab.R |only README.md | 7 + build/vignette.rds |binary data/colpal.rda |binary data/sihumi_test.rda |binary inst/doc/BacArena-Introduction.pdf |binary man/Arena-class.Rd | 2 man/Arena-constructor.Rd | 3 man/BacArena.Rd | 1 man/HeatMapFeeding.Rd | 1 man/Human-constructor.Rd | 8 + man/NemptyHood.Rd | 7 - man/Organism-constructor.Rd | 27 ++++- man/Organism.Rd | 4 man/Substance-constructor.Rd | 17 ++- man/addDefaultMed.Rd | 1 man/addEssentialMed.Rd | 4 man/addEval.Rd | 1 man/addOrg.Rd | 33 +++++- man/addSubs.Rd | 43 ++++++-- man/cellgrowth.Rd | 1 man/changeDiff.Rd | 1 man/changeFobj.Rd | 1 man/changeOrg.Rd | 1 man/changeSub.Rd | 1 man/checkCorr.Rd | 1 man/checkPhen.Rd | 1 man/checkPhen_par.Rd | 1 man/chemotaxis.Rd | 1 man/colpal3.Rd | 2 man/constrain.Rd | 4 man/consume.Rd | 4 man/createGradient.Rd | 23 +++- man/dat2mat.Rd | 1 man/diffuse.Rd | 1 man/diffusePDE.Rd | 4 man/diffuseR.Rd | 1 man/diffuse_par.Rd | 1 man/emptyHood.Rd | 7 - man/evalArena.Rd | 25 +++- man/extractMed.Rd | 7 - man/findFeeding.Rd | 23 +++- man/findFeeding2.Rd | 7 - man/findFeeding3.Rd | 4 man/findInArena.Rd | 4 man/findRxnFlux.Rd | 7 - man/flushSubs.Rd | 1 man/fluxVarSim.Rd | 1 man/getArena.Rd | 1 man/getCorrM.Rd | 4 man/getPhenoMat.Rd | 1 man/getPhenotype.Rd | 4 man/getSubHist.Rd | 1 man/getSublb.Rd | 1 man/getVarSubs.Rd | 19 ++- man/growExp.Rd | 1 man/growLin.Rd | 1 man/growth.Rd | 1 man/growth_par.Rd | 1 man/lysis.Rd | 1 man/minePheno.Rd | 4 man/move.Rd | 1 man/optimizeLP.Rd | 27 +++-- man/plotAbundance.Rd | 9 + man/plotCurves.Rd | 21 +++- man/plotCurves2.Rd | 33 ++++-- man/plotGrowthCurve.Rd | 9 + man/plotInterNum.Rd | 3 man/plotPhenCurve.Rd | 14 ++ man/plotReaActivity.Rd | 8 + man/plotShadowCost.Rd | 23 +++- man/plotSpecActivity.Rd | 13 ++ man/plotSubCurve.Rd | 13 +- man/plotSubDist.Rd | 1 man/plotSubDist2.Rd | 1 man/plotSubUsage.Rd | 3 man/plotTotFlux.Rd | 1 man/readMATmod.Rd |only man/redEval.Rd | 1 man/rmSubs.Rd | 1 man/selPheno.Rd | 1 man/setKinetics.Rd | 1 man/simBac.Rd | 27 ++++- man/simBac_par.Rd | 27 ++++- man/simEnv.Rd | 39 +++++-- man/simEnv_par.Rd | 35 +++++- man/simHum.Rd | 28 ++++- man/statPheno.Rd | 4 man/stirEnv.Rd | 1 man/unit_conversion.Rd | 1 98 files changed, 770 insertions(+), 392 deletions(-)
Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following
Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package.
The primary objective of this package is to perform a variance component analysis (VCA)
according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement
Procedures" (2014). There are plotting methods for visualization of an experimental design,
plotting random effects and residuals. For ANOVA type estimation two methods for computing
ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of
variance components can be derived, which is used in estimating confidence intervals. Linear
hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific
values of covariables and with custom weighting schemes for factor variables. See ?VCA for a
more comprehensive description of the features.
Author: Andre Schuetzenmeister [aut, cre], Florian Dufey [aut]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.4.1 dated 2019-11-14 and 1.4.2 dated 2019-12-17
VCA-1.4.1/VCA/inst/doc/How_to_work_with_package_VCA.pdf |only VCA-1.4.2/VCA/DESCRIPTION | 11 ++-- VCA-1.4.2/VCA/MD5 | 40 ++++++++++++---- VCA-1.4.2/VCA/R/anova.R | 6 +- VCA-1.4.2/VCA/R/plot.R | 2 VCA-1.4.2/VCA/R/vca.R | 11 ++-- VCA-1.4.2/VCA/build |only VCA-1.4.2/VCA/inst/ChangeLog.txt | 8 +++ VCA-1.4.2/VCA/inst/UnitTests/runit.anovaVCA.R | 7 ++ VCA-1.4.2/VCA/inst/UnitTests/runit.misc.R | 25 ++++++++++ VCA-1.4.2/VCA/inst/doc/VCA_package_vignette.R |only VCA-1.4.2/VCA/inst/doc/VCA_package_vignette.Rmd |only VCA-1.4.2/VCA/inst/doc/VCA_package_vignette.html |only VCA-1.4.2/VCA/man/VCA-Package.Rd | 4 - VCA-1.4.2/VCA/vignettes |only 15 files changed, 89 insertions(+), 25 deletions(-)
Title: Trim an Object
Description: A lightweight toolkit to reduce the size of a list object. The
object is minimized by recursively removing elements from the object
one-by-one. The process is constrained by a reference function call
specified by the user, where the target object is given as an argument.
The procedure will not allow elements to be removed from the object, that
will cause results from the function call to diverge from the function
call with the original object.
Author: Lars Kjeldgaard [aut, cre]
Maintainer: Lars Kjeldgaard <lars_kjeldgaard@hotmail.com>
Diff between trimmer versions 0.7.6 dated 2019-12-17 and 0.7.7 dated 2019-12-17
DESCRIPTION | 6 - MD5 | 6 - R/support_functions.R | 4 inst/doc/trimmer.html | 205 +++++++++++++++++++++++--------------------------- 4 files changed, 106 insertions(+), 115 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016) <doi:10.18608/jla.2016.33.3>.
Author: Cody L Marquart [aut, cre] (<https://orcid.org/0000-0002-3387-6792>),
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rENA versions 0.2.0.0 dated 2019-10-07 and 0.2.0.1 dated 2019-12-17
rENA-0.2.0.0/rENA/R/rdata.to.set.R |only rENA-0.2.0.0/rENA/R/update.data.R |only rENA-0.2.0.0/rENA/R/xlsx.to.s3csv.R |only rENA-0.2.0.1/rENA/DESCRIPTION | 12 rENA-0.2.0.1/rENA/MD5 | 69 rENA-0.2.0.1/rENA/NAMESPACE | 1 rENA-0.2.0.1/rENA/NEWS.md | 4 rENA-0.2.0.1/rENA/R/RcppExports.R | 10 rENA-0.2.0.1/rENA/R/ena.R | 2 rENA-0.2.0.1/rENA/R/ena.generate.R |only rENA-0.2.0.1/rENA/R/ena.make.set.R | 2 rENA-0.2.0.1/rENA/R/ena.plot.subtraction.R | 12 rENA-0.2.0.1/rENA/R/ena.plot.trajectory.R | 6 rENA-0.2.0.1/rENA/R/ena.plotter.R | 12 rENA-0.2.0.1/rENA/R/ena.rotate.by.mean.R | 2 rENA-0.2.0.1/rENA/R/ena.set.creator.R | 10 rENA-0.2.0.1/rENA/R/zzz.R | 2 rENA-0.2.0.1/rENA/README.md | 12 rENA-0.2.0.1/rENA/inst/doc/getting-started.R | 12 rENA-0.2.0.1/rENA/inst/doc/getting-started.Rmd | 14 rENA-0.2.0.1/rENA/inst/doc/getting-started.html | 2508 +++++++++++++-- rENA-0.2.0.1/rENA/inst/doc/means-rotation.R | 2 rENA-0.2.0.1/rENA/inst/doc/means-rotation.Rmd | 4 rENA-0.2.0.1/rENA/inst/doc/means-rotation.html | 2234 ++++++++++++- rENA-0.2.0.1/rENA/inst/include/rENA_RcppExports.h | 21 rENA-0.2.0.1/rENA/inst/scripts |only rENA-0.2.0.1/rENA/man/ENARotationSet.Rd | 2 rENA-0.2.0.1/rENA/man/ENAdata.Rd | 2 rENA-0.2.0.1/rENA/man/ENAplot.Rd | 2 rENA-0.2.0.1/rENA/man/ENAset.Rd | 2 rENA-0.2.0.1/rENA/man/ena.make.set.Rd | 2 rENA-0.2.0.1/rENA/man/vector_to_ut.Rd |only rENA-0.2.0.1/rENA/src/Makevars | 1 rENA-0.2.0.1/rENA/src/RcppExports.cpp | 37 rENA-0.2.0.1/rENA/src/ena.cpp | 32 rENA-0.2.0.1/rENA/tests/testthat/test-ena_wrapper.R |only rENA-0.2.0.1/rENA/tests/testthat/test-table_subsetting.R |only rENA-0.2.0.1/rENA/vignettes/getting-started.Rmd | 14 rENA-0.2.0.1/rENA/vignettes/means-rotation.Rmd | 4 39 files changed, 4648 insertions(+), 401 deletions(-)
Title: Estimation in Nonprobability Sampling
Description: Different inference procedures are proposed in the literature to correct for selection bias that might be introduced with non-random selection mechanisms. A class of methods to correct for selection bias is to apply a statistical model to predict the units not in the sample (super-population modeling). Other studies use calibration or Statistical Matching (statistically match nonprobability and probability samples). To date, the more relevant methods are weighting by Propensity Score Adjustment (PSA).
The Propensity Score Adjustment method was originally developed to construct weights by estimating response probabilities and using them in Horvitz–Thompson type estimators. This method is usually used by combining a non-probability sample with a reference sample to construct propensity models for the non-probability sample. Calibration can be used in a posterior way to adding information of auxiliary variables.
Propensity scores in PSA are usually estimated using logistic regression models. Machine learning classification algorithms can be used as alternatives for logistic regression as a technique to estimate propensities.
The package 'NonProbEst' implements some of these methods and thus provides a wide options to work with data coming from a non-probabilistic sample.
Author: Luis Castro Martín <luiscastro193@gmail.com>, Ramón Ferri García <rferri@ugr.es> and María del Mar Rueda <mrueda@ugr.es>
Maintainer: Luis Castro Martín <luiscastro193@gmail.com>
Diff between NonProbEst versions 0.2.2 dated 2019-11-29 and 0.2.3 dated 2019-12-17
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- R/NonProbEst.R | 44 ++++++++++++++++++++++++++++++++++++++++++++ man/model_calibrated.Rd |only 4 files changed, 51 insertions(+), 6 deletions(-)
Title: Time Series Analysis 'OpenBudgets.eu'
Description: Estimate and return the needed parameters for visualizations designed for 'OpenBudgets.eu' <http://openbudgets.eu/> time series data. Calculate time series model and forecast parameters in budget time series data of municipalities across Europe, according to the 'OpenBudgets.eu' data model. There are functions for measuring deterministic and stochastic trend of the input time series data with 'ACF', 'PACF', 'Phillips Perron' test, 'Augmented Dickey Fuller (ADF)' test, 'Kwiatkowski-Phillips-Schmidt-Shin (KPSS)' test, 'Mann Kendall' test for monotonic trend and 'Cox and Stuart' trend test, decomposing with local regression models or 'stl' decomposition, fitting the appropriate 'arima' model and provide forecasts for the input 'OpenBudgets.eu' time series fiscal data. Also, can be used generally to extract visualization parameters convert them to 'JSON' format and use them as input in a different graphical interface.
Author: Kleanthis Koupidis [aut, cre],
Charalampos Bratsas [aut]
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>
Diff between TimeSeries.OBeu versions 1.2.3 dated 2019-01-20 and 1.2.4 dated 2019-12-17
DESCRIPTION | 14 MD5 | 48 - NAMESPACE | 2 README.md | 552 ++++++++++++---------- build/vignette.rds |binary inst/doc/TimeSeries.OBeuOpenCPU.R | 4 inst/doc/TimeSeries.OBeuOpenCPU.html | 337 +++++++++++-- inst/doc/TimeSeriesOBeu.R | 8 inst/doc/TimeSeriesOBeu.Rmd | 2 inst/doc/TimeSeriesOBeu.html | 849 ++++++++++++++++++++++------------- man/Athens_approved_ts.Rd | 34 - man/Athens_draft_ts.Rd | 34 - man/Athens_executed_ts.Rd | 34 - man/Athens_reserved_ts.Rd | 34 - man/Athens_revised_ts.Rd | 34 - man/open_spending.ts.Rd | 76 +-- man/ts.acf.Rd | 120 ++-- man/ts.analysis.Rd | 246 +++++----- man/ts.forecast.Rd | 110 ++-- man/ts.non.seas.decomp.Rd | 130 ++--- man/ts.non.seas.model.Rd | 118 ++-- man/ts.seasonal.decomp.Rd | 128 ++--- man/ts.seasonal.model.Rd | 120 ++-- man/ts.stationary.test.Rd | 108 ++-- vignettes/TimeSeriesOBeu.Rmd | 2 25 files changed, 1840 insertions(+), 1304 deletions(-)
More information about TimeSeries.OBeu at CRAN
Permanent link
Title: Obtaining Open Data from Instituto Canario De Estadistica
(ISTAC) API
Description: You can access to open data published in Instituto Canario De Estadistica (ISTAC) APIs at <https://www.gobiernodecanarias.org/istac/api/>.
Author: Alberto Gonzalez [aut, cre]
Maintainer: Alberto Gonzalez <jgonyanp@gobiernodecanarias.org>
Diff between istacr versions 0.1.0 dated 2019-05-03 and 0.1.1 dated 2019-12-17
DESCRIPTION | 8 +- MD5 | 14 ++--- R/indicators_indicators.R | 2 R/statistical_resources_cubes.R | 28 +++++----- R/structural_resources_category.R | 2 man/get_datasets_agency_resource_version.Rd | 3 - man/get_indicators_code_data.Rd | 2 man/get_structuralresources_category_schemes_agency_resource_version_categories.Rd | 2 8 files changed, 33 insertions(+), 28 deletions(-)
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] (Hash table implementation in src/pfhash.h),
R Core Team [cph] (Used/adapted several code snippets from R sources,
see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.7 dated 2019-03-15 and 0.2.8 dated 2019-12-17
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/alike.html | 49 +++++++++++++++++++++++++++++++++++++------------ inst/doc/vetr.html | 39 ++++++++++++++++++++++++++++++++------- src/alike.h | 36 ++++++++++++++++++------------------ src/init.c | 25 +++++++++++++++++++++++++ src/validate.h | 14 +++++++------- tests/valgrind/run.R | 3 ++- 10 files changed, 138 insertions(+), 57 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.0.0 dated 2019-12-10 and 1.0.1 dated 2019-12-17
DESCRIPTION | 8 +-- MD5 | 74 +++++++++++++++---------------- NEWS.md | 5 ++ R/utils.R | 3 - inst/doc/SDMtune.html | 2 tests/testthat/test-ANN-class.R | 1 tests/testthat/test-BRT-class.R | 1 tests/testthat/test-RF-class.R | 1 tests/testthat/test-aicc.R | 1 tests/testthat/test-auc.R | 1 tests/testthat/test-chart-utils.R | 2 tests/testthat/test-clamp.R | 2 tests/testthat/test-confMatrix.R | 1 tests/testthat/test-doJk.R | 1 tests/testthat/test-gridSearch.R | 1 tests/testthat/test-modelReport.R | 1 tests/testthat/test-optimizeModel.R | 1 tests/testthat/test-plotPA.R | 2 tests/testthat/test-plotROC.R | 2 tests/testthat/test-plotResponse.R | 1 tests/testthat/test-predict-ANN.R | 1 tests/testthat/test-predict-BRT.R | 1 tests/testthat/test-predict-RF.R | 1 tests/testthat/test-predict-SDMmodel.R | 1 tests/testthat/test-predict-SDMmodelCV.R | 1 tests/testthat/test-prepareSWD.R | 1 tests/testthat/test-randomSearch.R | 1 tests/testthat/test-reduceVar.R | 1 tests/testthat/test-train.R | 1 tests/testthat/test-trainANN.R | 1 tests/testthat/test-trainBRT.R | 1 tests/testthat/test-trainMaxent.R | 1 tests/testthat/test-trainMaxnet.R | 1 tests/testthat/test-trainRF.R | 1 tests/testthat/test-tss.R | 1 tests/testthat/test-utils.R | 7 ++ tests/testthat/test-varImp.R | 1 tests/testthat/test-varSel.R | 1 38 files changed, 83 insertions(+), 52 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija 2019
<doi:10.1101/576827> for more details.
Author: Christoph Hafemeister [aut, cre]
(<https://orcid.org/0000-0001-6365-8254>)
Maintainer: Christoph Hafemeister <chafemeister@nygenome.org>
Diff between sctransform versions 0.2.0 dated 2019-04-12 and 0.2.1 dated 2019-12-17
DESCRIPTION | 12 ++--- MD5 | 41 +++++++++-------- NAMESPACE | 2 NEWS.md |only R/RcppExports.R | 8 ++- R/denoise.R | 8 ++- R/generate.R |only R/plotting.R | 21 +++++++- R/utils.R | 96 ++++++++++++++++++++++++++++++++++------ R/vst.R | 14 +++-- man/correct.Rd | 2 man/correct_counts.Rd | 2 man/generate.Rd |only man/get_model_var.Rd |only man/get_residual_var.Rd | 3 + man/get_residuals.Rd | 3 + man/plot_model_pars.Rd | 4 + man/smooth_via_pca.Rd | 2 man/vst.Rd | 10 ++-- src/RcppExports.cpp | 22 +++++++-- src/utils.cpp | 13 +++++ tests/testthat/test_denoising.R | 1 tests/testthat/test_generate.R |only tests/testthat/test_vst.R | 1 24 files changed, 207 insertions(+), 58 deletions(-)
Title: Statistical Tools for Quantitative Genetic Analyses
Description: Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.
Author: Peter Soerensen [aut, cre],
Palle Duun Rohde [aut],
Izel Fourie Soerensen [aut]
Maintainer: Peter Soerensen <peter.sorensen@r-qgg.org>
Diff between qgg versions 1.0.0 dated 2019-12-13 and 1.0.1 dated 2019-12-17
DESCRIPTION | 8 +- MD5 | 14 ++--- R/compute_genotype_matrix.R | 8 +- man/gprep.Rd | 8 +- src/Makevars | 3 - src/bedfuncs.f90 | 52 +++++++++---------- src/bigreml.f90 | 120 +++++++++++++++++++++++++++++++++++++++++++- src/qgg_init.c | 4 - 8 files changed, 168 insertions(+), 49 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.3.3 dated 2019-07-06 and 0.4 dated 2019-12-17
DESCRIPTION | 14 - MD5 | 162 ++++++++------- NAMESPACE | 9 NEWS | 16 + R/00_steps_to_implement_model.R | 3 R/01_classes.R | 21 +- R/03_modelformation_fixTau.R |only R/03_modelformation_formModelMatrices.R | 8 R/03_modelformation_generateParameterTable.R | 23 +- R/03_modelformation_impliedcovstructures.R | 66 ++++++ R/03_modelformation_matrixSetup_SD.R |only R/03_modelformation_matrixSetup_delta.R | 2 R/03_modelformation_matrixSetup_mu.R | 6 R/03_modelformation_matrixSetup_omega.R | 2 R/03_modelformation_matrixSetup_rho.R |only R/03_modelformation_matrixSetup_tau.R |only R/03_modelformation_samplestats_norawts.R | 227 +++++++++++++++++----- R/04_generalFit_fitfunction.R | 4 R/04_generalFit_gradient.R | 6 R/04_generalfit_FisherInformation.R | 15 + R/04_generalfit_VCOV.R |only R/04_generalfit_impliedModel.R | 3 R/04_generalfit_prepareModel.R | 3 R/05_MLestimator_expected_hessian_Gauss.R | 26 ++ R/05_MLestimator_gradient_Gauss.R | 32 ++- R/06_ULS_expectedHessian.R | 14 - R/06_ULS_fitfunction.R | 53 ++++- R/06_ULS_gradient.R | 47 ++++ R/06_weightsMatrix.R | 22 +- R/07_FIMLestimator_expected_hessian_Gauss.R | 35 ++- R/07_FIMLestimator_gradient_Gauss.R | 35 ++- R/09_modelmodifivation_emergencystart.R | 78 ++++++- R/14_varcov_derivatives.R | 120 +++++++++-- R/14_varcov_implied.R | 6 R/14_varcov_prepare.R | 10 R/15_lvm_derivatives.R | 24 +- R/15_lvm_identify.R | 16 - R/15_lvm_implied.R | 2 R/15_lvm_prepare.R | 2 R/16_var1_derivatives.R | 2 R/18_dlvm1_derivatives.R | 9 R/18_dlvm1_identify.R | 2 R/18_dlvm1_implied.R | 2 R/19_tsdlvm1_identify.R | 8 R/19_tsdlvm1_implied.R | 2 R/20_meta_varcov_derivatives.R |only R/20_meta_varcov_implied.R |only R/20_meta_varcov_prepare.R |only R/RcppExports.R | 52 +++++ R/a_models_bifactor.R | 4 R/a_models_corr.R |only R/a_models_dlvm1.R | 8 R/a_models_latentgrowth.R | 2 R/a_models_lvm.R | 18 - R/a_models_meta_varcov.R |only R/a_models_tsdlvm1.R | 8 R/a_models_varcov.R | 276 +++++++++++++++++++++------ R/b_modelexpansions_addMIs.R | 9 R/b_modelexpansions_addSEs.R | 13 - R/b_modelexpansions_identify.R | 2 R/c_runmodel.R | 16 + R/d_stepup.R | 55 ++++- R/e_modelmodifications_freepar.R | 23 +- R/e_modelmodifications_prune.R | 43 +++- R/f_conveneince_usecpp.R | 7 R/f_convenience_printMethod.R | 3 R/h_modelsearch.R |only build/partial.rdb |binary man/MIs.Rd | 2 man/dlvm1_family.Rd | 4 man/fit.Rd | 2 man/fixpar_freepar.Rd | 5 man/getVCOV.Rd |only man/getmatrix.Rd | 2 man/lvm_family.Rd | 28 +- man/modelsearch.Rd |only man/parameters.Rd | 2 man/prune.Rd | 2 man/psychonetrics-class.Rd | 1 man/runmodel.Rd | 2 man/stepup.Rd | 22 +- man/tsdlvm1_family.Rd | 4 man/varcov_family.Rd | 40 +++ src/06_WLS_Wmat.cpp | 34 ++- src/07_FIMLestimator_jacobian_gauss.cpp | 59 +---- src/10_ordinal_covPrepare.cpp |only src/10_ordinal_cppFuns.cpp |only src/10_ordinal_cppFuns.h |only src/Makevars | 1 src/RcppExports.cpp | 197 +++++++++++++++++++ 90 files changed, 1600 insertions(+), 483 deletions(-)
Title: Solar Radiation
Description: Functions to compute insolation on complex terrain.
Author: Javier G. Corripio
Maintainer: Javier G. Corripio <jgc@meteoexploration.com>
Diff between insol versions 1.2 dated 2019-01-16 and 1.2.1 dated 2019-12-17
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/cgrad.R | 2 +- R/doshade.R | 2 +- man/aspect.Rd | 1 - man/cgrad.Rd | 1 - man/doshade.Rd | 1 - man/hillshading.Rd | 1 - man/insolation.Rd | 1 - man/slope.Rd | 1 - 10 files changed, 16 insertions(+), 22 deletions(-)
Title: Cluster Analysis 'OpenBudgets.eu'
Description: Estimate and return the needed parameters for visualisations designed for 'OpenBudgets' <http://openbudgets.eu/> data. Calculate cluster analysis measures in Budget data of municipalities across Europe, according to the 'OpenBudgets' data model. It involves a set of techniques and algorithms used to find and divide the data into groups of similar observations. Also, can be used generally to extract visualisation parameters convert them to 'JSON' format and use them as input in a different graphical interface.
Author: Kleanthis Koupidis [aut, cre],
Charalampos Bratsas [aut],
Jaroslav Kuchar [ctb]
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>
Diff between Cluster.OBeu versions 1.2.2 dated 2019-01-20 and 1.2.3 dated 2019-12-17
DESCRIPTION | 11 - MD5 | 42 ++-- NAMESPACE | 2 NEWS.md | 5 R/cl.summary.R | 8 README.md | 55 +++-- build/vignette.rds |binary inst/doc/Cluster.OBeuOpenCPU.R | 4 inst/doc/Cluster.OBeuOpenCPU.html | 319 ++++++++++++++++++++++++++++---- inst/doc/ClusterOBeu.R | 6 inst/doc/ClusterOBeu.Rmd | 2 inst/doc/ClusterOBeu.html | 375 +++++++++++++++++++++++++++++++------- man/city_data.Rd | 32 +-- man/cl.analysis.Rd | 114 +++++------ man/cl.features.Rd | 82 ++++---- man/cl.plot.Rd | 54 ++--- man/cl.summary.Rd | 56 ++--- man/convex.hulls.Rd | 38 +-- man/ellipses.Rd | 38 +-- man/nums.Rd | 44 ++-- man/open_spending.cl.Rd | 84 ++++---- vignettes/ClusterOBeu.Rmd | 2 22 files changed, 929 insertions(+), 444 deletions(-)
Title: Encode Categorical Features
Description: Functions for dummy encoding, frequency encoding,
label encoding, leave-one-out encoding, mean encoding, median
encoding, and one-hot encoding.
Author: Bernie Gray [aut, cre] (<https://orcid.org/0000-0001-9190-6032>),
Mark Roepke [ctb]
Maintainer: Bernie Gray <bfgray3@gmail.com>
Diff between cattonum versions 0.0.2 dated 2018-05-01 and 0.0.3 dated 2019-12-17
cattonum-0.0.2/cattonum/R/mean-median.R |only cattonum-0.0.3/cattonum/DESCRIPTION | 50 cattonum-0.0.3/cattonum/LICENSE | 4 cattonum-0.0.3/cattonum/MD5 | 85 cattonum-0.0.3/cattonum/NAMESPACE | 37 cattonum-0.0.3/cattonum/NEWS.md | 49 cattonum-0.0.3/cattonum/R/RcppExports.R |only cattonum-0.0.3/cattonum/R/aggregate.R |only cattonum-0.0.3/cattonum/R/cattonum-methods.R |only cattonum-0.0.3/cattonum/R/cattonum.R | 25 cattonum-0.0.3/cattonum/R/constructors.R |only cattonum-0.0.3/cattonum/R/dummy-onehot.R | 270 +- cattonum-0.0.3/cattonum/R/freq.R | 105 - cattonum-0.0.3/cattonum/R/label.R | 299 +-- cattonum-0.0.3/cattonum/R/loo.R | 141 - cattonum-0.0.3/cattonum/R/utils.R | 179 - cattonum-0.0.3/cattonum/README.md | 164 - cattonum-0.0.3/cattonum/build/vignette.rds |binary cattonum-0.0.3/cattonum/inst/doc/introduction.R | 150 - cattonum-0.0.3/cattonum/inst/doc/introduction.Rmd | 232 +- cattonum-0.0.3/cattonum/inst/doc/introduction.html | 917 +++++----- cattonum-0.0.3/cattonum/man/catto_aggregate.Rd |only cattonum-0.0.3/cattonum/man/catto_dummy.Rd | 60 cattonum-0.0.3/cattonum/man/catto_freq.Rd | 60 cattonum-0.0.3/cattonum/man/catto_label.Rd | 103 - cattonum-0.0.3/cattonum/man/catto_loo.Rd | 64 cattonum-0.0.3/cattonum/man/catto_mean.Rd | 64 cattonum-0.0.3/cattonum/man/catto_median.Rd | 65 cattonum-0.0.3/cattonum/man/catto_onehot.Rd | 60 cattonum-0.0.3/cattonum/man/cattonum.Rd | 24 cattonum-0.0.3/cattonum/man/cattonum_df.Rd |only cattonum-0.0.3/cattonum/man/cattonum_df2.Rd |only cattonum-0.0.3/cattonum/src |only cattonum-0.0.3/cattonum/tests/testthat.R | 8 cattonum-0.0.3/cattonum/tests/testthat/helpers.R | 236 +- cattonum-0.0.3/cattonum/tests/testthat/test-aggregate.R |only cattonum-0.0.3/cattonum/tests/testthat/test-cattonum-methods.R |only cattonum-0.0.3/cattonum/tests/testthat/test-conditions.R |only cattonum-0.0.3/cattonum/tests/testthat/test-constructors.R |only cattonum-0.0.3/cattonum/tests/testthat/test-dummy.R | 214 +- cattonum-0.0.3/cattonum/tests/testthat/test-freq.R | 177 - cattonum-0.0.3/cattonum/tests/testthat/test-label.R | 259 +- cattonum-0.0.3/cattonum/tests/testthat/test-lintfree.R |only cattonum-0.0.3/cattonum/tests/testthat/test-loo.R | 166 - cattonum-0.0.3/cattonum/tests/testthat/test-mean.R | 197 +- cattonum-0.0.3/cattonum/tests/testthat/test-median.R | 168 - cattonum-0.0.3/cattonum/tests/testthat/test-onehot.R | 139 - cattonum-0.0.3/cattonum/tests/testthat/test-print-cattonum-df.txt |only cattonum-0.0.3/cattonum/tests/testthat/test-print-cattonum-df2.txt |only cattonum-0.0.3/cattonum/tests/testthat/test-summary-cattonum-df.txt |only cattonum-0.0.3/cattonum/tests/testthat/test-summary-cattonum-df2.txt |only cattonum-0.0.3/cattonum/vignettes/introduction.Rmd | 232 +- 52 files changed, 2490 insertions(+), 2513 deletions(-)
Title: Standardize Plant Names According to World Flora Online
Taxonomic Backbone
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between WorldFlora versions 1.0 dated 2019-12-13 and 1.1 dated 2019-12-17
DESCRIPTION | 12 ++-- MD5 | 15 ++--- NAMESPACE | 2 R/WFO.match.R | 136 +++++++++++++++++++++++++++++++++++++++------- R/WFO.url.R |only data/WFO.example.RData |binary inst/ChangeLog | 32 ++++++++++ inst/etc/WFO.example.xlsx |binary man/WFO.match.Rd | 85 +++++++++++++++++++++++----- 9 files changed, 235 insertions(+), 47 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between reticulate versions 1.13 dated 2019-07-24 and 1.14 dated 2019-12-17
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Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre],
Lavinia Baumstark [aut],
Stephen Wirth [aut],
Anastasis Giannousakis [aut],
Renato Rodrigues [aut],
Benjamin Leon Bodirsky [aut],
Ulrich Kreidenweis [aut]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 1.64.4 dated 2019-12-16 and 1.64.5 dated 2019-12-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/doc/madrat.html | 4 ++-- man/getISOlist.Rd | 4 ++-- man/toolConvertMapping.Rd | 2 +- man/toolGetMapping.Rd | 2 +- man/toolSubtypeSelect.Rd | 8 ++------ tests/testthat/test-toolAggregate.R | 2 +- 8 files changed, 20 insertions(+), 24 deletions(-)
Title: Disaggregation Modelling
Description: Fits disaggregation regression models using 'TMB' ('Template Model
Builder'). When the response data are aggregated to polygon level but
the predictor variables are at a higher resolution, these models can be
useful. Regression models with spatial random fields. A useful reference for disaggregation modelling is
Lucas et al. (2019) <doi:10.1101/548719>.
Author: Anita Nandi [aut, cre] (<https://orcid.org/0000-0002-5087-2494>),
Tim Lucas [aut] (<https://orcid.org/0000-0003-4694-8107>),
Rohan Arambepola [aut],
Andre Python [aut] (<https://orcid.org/0000-0001-8094-7226>)
Maintainer: Anita Nandi <anita.k.nandi@gmail.com>
Diff between disaggregation versions 0.1.1 dated 2019-12-09 and 0.1.2 dated 2019-12-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/disaggregation.html | 4 ++-- tests/testthat/test-fit-model.R | 10 ++++++++-- tests/testthat/test-plotting.R | 10 ++++++++-- tests/testthat/test-predict-model.R | 11 ++++++++--- 6 files changed, 34 insertions(+), 17 deletions(-)
More information about disaggregation at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-26 1.6.2
2014-09-19 1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-27 0.9.4
2014-01-02 0.9.2
2013-10-05 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-15 1.5.11
2019-02-28 1.5.10
2018-11-12 1.5.9
2018-09-24 1.5.8
2018-06-03 1.5.7
2018-05-13 1.5.4
2018-05-06 1.5.3
2018-04-03 1.4.2
Title: Trim an Object
Description: A lightweight toolkit to reduce the size of a list object. The
object is minimized by recursively removing elements from the object
one-by-one. The process is constrained by a reference function call
specified by the user, where the target object is given as an argument.
The procedure will not allow elements to be removed from the object, that
will cause results from the function call to diverge from the function
call with the original object.
Author: Lars Kjeldgaard [aut, cre]
Maintainer: Lars Kjeldgaard <lars_kjeldgaard@hotmail.com>
Diff between trimmer versions 0.7.5 dated 2019-12-15 and 0.7.6 dated 2019-12-17
DESCRIPTION | 6 - MD5 | 6 - R/support_functions.R | 14 --- inst/doc/trimmer.html | 209 ++++++++++++++++++++++++++------------------------ 4 files changed, 117 insertions(+), 118 deletions(-)
Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions. Methods developed in
Roberts et al (2014) <doi:10.1111/ajps.12103> and
Roberts et al (2016) <doi:10.1080/01621459.2016.1141684>. Vignette
is Roberts et al (2019) <doi:10.18637/jss.v091.i02>.
Author: Margaret Roberts [aut],
Brandon Stewart [aut, cre],
Dustin Tingley [aut],
Kenneth Benoit [ctb]
Maintainer: Brandon Stewart <bms4@princeton.edu>
Diff between stm versions 1.3.4 dated 2019-10-30 and 1.3.5 dated 2019-12-17
DESCRIPTION | 6 ++--- MD5 | 43 ++++++++++++++++++------------------- R/STMestep.R | 2 - R/STMlncpp.R | 2 - R/cloud.R | 2 - R/findThoughts.R | 2 - R/findTopic.R | 4 +-- R/fitNewDocuments.R | 4 +-- R/labelTopics.R | 6 ++--- R/makeDesignMatrix.R | 6 ++--- R/prepDocuments.R | 2 - R/produce_cmatrix.R | 2 - R/readCorpus.R | 4 +-- R/s.R | 2 - R/spectral.R | 4 +-- R/stm.R | 4 +-- R/thetaPosterior.R | 6 ++--- inst/NEWS.Rd | 5 ++++ inst/doc/stmVignette.pdf |binary tests/testthat/Rplots.pdf |only tests/testthat/test-quanteda-stm.R | 4 +-- tests/testthat/test-stm-options.R | 10 ++++---- tests/testthat/test-visualize.R | 2 - 23 files changed, 64 insertions(+), 58 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.0.2 dated 2019-11-11 and 4.1.0 dated 2019-12-17
secr-4.0.2/secr/R/sighting.chat.R |only secr-4.0.2/secr/src/pdot.cpp |only secr-4.0.2/secr/src/polygon.cpp |only secr-4.1.0/secr/DESCRIPTION | 14 secr-4.1.0/secr/MD5 | 137 - secr-4.1.0/secr/NAMESPACE | 4 secr-4.1.0/secr/NEWS | 29 secr-4.1.0/secr/R/AIC.R | 41 secr-4.1.0/secr/R/LLsurface.secr.R | 7 secr-4.1.0/secr/R/LRtest.R | 7 secr-4.1.0/secr/R/RcppExports.R | 44 secr-4.1.0/secr/R/autoini.R | 31 secr-4.1.0/secr/R/esa.R | 33 secr-4.1.0/secr/R/fastsecrloglik.R | 20 secr-4.1.0/secr/R/fxi.R | 69 secr-4.1.0/secr/R/generalsecrloglik.R | 118 - secr-4.1.0/secr/R/loglikhelperfn.R | 32 secr-4.1.0/secr/R/make.mask.R | 3 secr-4.1.0/secr/R/methods.R | 3 secr-4.1.0/secr/R/pdot.R | 44 secr-4.1.0/secr/R/reduce.R | 8 secr-4.1.0/secr/R/regionN.R | 74 secr-4.1.0/secr/R/score.test.R | 4 secr-4.1.0/secr/R/secr.design.MS.R | 93 - secr-4.1.0/secr/R/secr.fit.R | 2146 +++++++++++++-------------- secr-4.1.0/secr/R/sim.capthist.R | 8 secr-4.1.0/secr/R/sim.secr.R | 8 secr-4.1.0/secr/R/suggest.buffer.R | 28 secr-4.1.0/secr/R/utility.R | 7 secr-4.1.0/secr/R/verify.R | 3 secr-4.1.0/secr/data/OVpossum.RData |binary secr-4.1.0/secr/data/deermouse.RData |binary secr-4.1.0/secr/data/hornedlizard.RData |binary secr-4.1.0/secr/data/housemouse.RData |binary secr-4.1.0/secr/data/ovenbird.RData |binary secr-4.1.0/secr/data/ovensong.RData |binary secr-4.1.0/secr/data/possum.RData |binary secr-4.1.0/secr/data/secrdemo.RData |binary secr-4.1.0/secr/data/skink.RData |binary secr-4.1.0/secr/data/stoatDNA.RData |binary secr-4.1.0/secr/inst/doc/secr-datainput.pdf |binary secr-4.1.0/secr/inst/doc/secr-overview.Rmd | 24 secr-4.1.0/secr/inst/doc/secr-overview.pdf |binary secr-4.1.0/secr/man/AIC.secr.Rd | 16 secr-4.1.0/secr/man/AICcompatible.Rd |only secr-4.1.0/secr/man/LLsurface.Rd | 12 secr-4.1.0/secr/man/LRtest.Rd | 17 secr-4.1.0/secr/man/autoini.Rd | 9 secr-4.1.0/secr/man/details.Rd | 2 secr-4.1.0/secr/man/score.test.Rd | 8 secr-4.1.0/secr/man/secr-package.Rd | 4 secr-4.1.0/secr/man/secr.design.MS.Rd | 7 secr-4.1.0/secr/man/secr.fit.Rd | 1 secr-4.1.0/secr/man/sim.capthist.Rd | 18 secr-4.1.0/secr/man/suggest.buffer.Rd | 4 secr-4.1.0/secr/src/RcppExports.cpp | 165 +- secr-4.1.0/secr/src/apdot.cpp |only secr-4.1.0/secr/src/autoini.cpp | 119 - secr-4.1.0/secr/src/detectfn.cpp | 59 secr-4.1.0/secr/src/makegk.cpp | 10 secr-4.1.0/secr/src/makegkpoly.cpp | 235 -- secr-4.1.0/secr/src/poly.h |only secr-4.1.0/secr/src/polygonN.cpp |only secr-4.1.0/secr/src/prwifastproximity.cpp | 63 secr-4.1.0/secr/src/prwipolygon.cpp | 45 secr-4.1.0/secr/src/prwisignal.cpp | 18 secr-4.1.0/secr/src/prwisimple.cpp | 47 secr-4.1.0/secr/src/secr.h | 115 - secr-4.1.0/secr/src/sightingexpectedmusk.cpp | 47 secr-4.1.0/secr/src/simsecr.cpp | 34 secr-4.1.0/secr/src/trapping.cpp | 37 secr-4.1.0/secr/src/utils.cpp | 217 +- secr-4.1.0/secr/vignettes/secr-overview.Rmd | 24 73 files changed, 2293 insertions(+), 2079 deletions(-)
Title: Toolkit for Corpus Analysis
Description: Library for corpus analysis using the Corpus Workbench as an
efficient back end for indexing and querying large corpora. The package offers
functionality to flexibly create partitions and to carry out basic statistical
operations (count, co-occurrences etc.). The original full text of documents
can be reconstructed and inspected at any time. Beyond that, the package is
intended to serve as an interface to packages implementing advanced statistical
procedures. Respective data structures (document term matrices, term co-
occurrence matrices etc.) can be created based on the indexed corpora.
Author: Andreas Blaette [aut, cre] (<https://orcid.org/0000-0001-8970-8010>),
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between polmineR versions 0.7.11 dated 2019-01-08 and 0.8.0 dated 2019-12-17
polmineR-0.7.11/polmineR/R/CQI.R |only polmineR-0.7.11/polmineR/R/Labels.R |only polmineR-0.7.11/polmineR/R/browse.R |only polmineR-0.7.11/polmineR/R/cqpserver.R |only polmineR-0.7.11/polmineR/R/label.R |only polmineR-0.7.11/polmineR/R/t_test.R |only polmineR-0.7.11/polmineR/R/tempcorpus.R |only polmineR-0.7.11/polmineR/README.md |only polmineR-0.7.11/polmineR/configure |only polmineR-0.7.11/polmineR/inst/Rscript |only polmineR-0.7.11/polmineR/inst/graffle |only polmineR-0.7.11/polmineR/inst/init |only polmineR-0.7.11/polmineR/inst/sh |only polmineR-0.7.11/polmineR/man/CQI.Rd |only polmineR-0.7.11/polmineR/man/Corpus-class.Rd |only polmineR-0.7.11/polmineR/man/Labels-class.Rd |only polmineR-0.7.11/polmineR/man/browse.Rd |only polmineR-0.7.11/polmineR/man/corpus-method.Rd |only polmineR-0.7.11/polmineR/man/corpus_class.Rd |only polmineR-0.7.11/polmineR/man/label_method.Rd |only polmineR-0.7.11/polmineR/man/tempcorpus.Rd |only polmineR-0.7.11/polmineR/man/tempcorpus_class.Rd |only polmineR-0.7.11/polmineR/tools |only polmineR-0.8.0/polmineR/DESCRIPTION | 50 polmineR-0.8.0/polmineR/MD5 | 320 +-- polmineR-0.8.0/polmineR/NAMESPACE | 36 polmineR-0.8.0/polmineR/NEWS.md | 627 +++++-- polmineR-0.8.0/polmineR/R/S4classes.R | 596 +++++-- polmineR-0.8.0/polmineR/R/TermDocumentMatrix.R | 296 ++- polmineR-0.8.0/polmineR/R/annotations.R |only polmineR-0.8.0/polmineR/R/as.VCorpus.R | 32 polmineR-0.8.0/polmineR/R/as.markdown.R | 39 polmineR-0.8.0/polmineR/R/as.speeches.R | 184 ++ polmineR-0.8.0/polmineR/R/bundle.R | 29 polmineR-0.8.0/polmineR/R/coerce.R |only polmineR-0.8.0/polmineR/R/context.R | 328 ++- polmineR-0.8.0/polmineR/R/cooccurrences.R | 130 + polmineR-0.8.0/polmineR/R/corpus.R | 676 ++++---- polmineR-0.8.0/polmineR/R/count.R | 276 ++- polmineR-0.8.0/polmineR/R/cpos.R | 189 +- polmineR-0.8.0/polmineR/R/decode.R | 326 ++- polmineR-0.8.0/polmineR/R/dispersion.R | 156 + polmineR-0.8.0/polmineR/R/encoding.R | 26 polmineR-0.8.0/polmineR/R/enrich.R | 176 +- polmineR-0.8.0/polmineR/R/features.R | 44 polmineR-0.8.0/polmineR/R/format.R | 60 polmineR-0.8.0/polmineR/R/highlight.R | 35 polmineR-0.8.0/polmineR/R/hits.R | 211 +- polmineR-0.8.0/polmineR/R/html.R | 180 +- polmineR-0.8.0/polmineR/R/info.R |only polmineR-0.8.0/polmineR/R/kwic.R | 412 +++- polmineR-0.8.0/polmineR/R/mail.R | 54 polmineR-0.8.0/polmineR/R/make_region_matrix.R |only polmineR-0.8.0/polmineR/R/ngrams.R | 21 polmineR-0.8.0/polmineR/R/opencpu.R |only polmineR-0.8.0/polmineR/R/p_attributes.R | 42 polmineR-0.8.0/polmineR/R/partition.R | 374 +--- polmineR-0.8.0/polmineR/R/partition_bundle.R | 50 polmineR-0.8.0/polmineR/R/polmineR.R | 53 polmineR-0.8.0/polmineR/R/read.R | 54 polmineR-0.8.0/polmineR/R/regions.R | 62 polmineR-0.8.0/polmineR/R/registry.R | 54 polmineR-0.8.0/polmineR/R/renamed.R | 190 ++ polmineR-0.8.0/polmineR/R/s_attributes.R | 247 ++ polmineR-0.8.0/polmineR/R/size.R | 79 polmineR-0.8.0/polmineR/R/split.R |only polmineR-0.8.0/polmineR/R/stats.R | 117 + polmineR-0.8.0/polmineR/R/store.R | 2 polmineR-0.8.0/polmineR/R/templates.R | 11 polmineR-0.8.0/polmineR/R/terms.R | 33 polmineR-0.8.0/polmineR/R/textstat.R | 26 polmineR-0.8.0/polmineR/R/token_stream.R | 186 +- polmineR-0.8.0/polmineR/R/tooltips.R | 18 polmineR-0.8.0/polmineR/R/trim.R | 18 polmineR-0.8.0/polmineR/R/type.R | 11 polmineR-0.8.0/polmineR/R/use.R | 39 polmineR-0.8.0/polmineR/R/utils.R | 47 polmineR-0.8.0/polmineR/R/view.R | 16 polmineR-0.8.0/polmineR/R/weigh.R | 9 polmineR-0.8.0/polmineR/R/zzz.R | 74 polmineR-0.8.0/polmineR/build/vignette.rds |binary polmineR-0.8.0/polmineR/inst/CITATION | 6 polmineR-0.8.0/polmineR/inst/doc/OpenCPU.R |only polmineR-0.8.0/polmineR/inst/doc/OpenCPU.Rmd |only polmineR-0.8.0/polmineR/inst/doc/OpenCPU.html |only polmineR-0.8.0/polmineR/inst/doc/vignette.R | 2 polmineR-0.8.0/polmineR/inst/doc/vignette.Rmd | 7 polmineR-0.8.0/polmineR/inst/doc/vignette.html | 842 +++++----- polmineR-0.8.0/polmineR/inst/extdata/cwb/indexed_corpora/germaparlmini/info.md |only polmineR-0.8.0/polmineR/inst/extdata/cwb/registry/germaparlmini | 4 polmineR-0.8.0/polmineR/inst/extdata/cwb/registry/reuters | 4 polmineR-0.8.0/polmineR/inst/fulltext |only polmineR-0.8.0/polmineR/inst/shiny/global.R | 3 polmineR-0.8.0/polmineR/inst/shiny/modules/cooccurrences.R | 60 polmineR-0.8.0/polmineR/inst/shiny/modules/count.R | 64 polmineR-0.8.0/polmineR/inst/shiny/modules/dispersion.R | 89 - polmineR-0.8.0/polmineR/inst/shiny/modules/features.R | 40 polmineR-0.8.0/polmineR/inst/shiny/modules/kwic.R | 80 polmineR-0.8.0/polmineR/inst/shiny/modules/partition.R | 65 polmineR-0.8.0/polmineR/inst/shiny/modules/settings.R | 1 polmineR-0.8.0/polmineR/inst/shiny/ui.R | 2 polmineR-0.8.0/polmineR/man/all_cooccurrences.Rd | 10 polmineR-0.8.0/polmineR/man/annotations.Rd |only polmineR-0.8.0/polmineR/man/as.DocumentTermMatrix.Rd | 89 - polmineR-0.8.0/polmineR/man/as.VCorpus.Rd | 16 polmineR-0.8.0/polmineR/man/as.markdown.Rd | 10 polmineR-0.8.0/polmineR/man/as.speeches.Rd | 46 polmineR-0.8.0/polmineR/man/bundle.Rd | 26 polmineR-0.8.0/polmineR/man/chisquare-method.Rd | 4 polmineR-0.8.0/polmineR/man/context-class.Rd | 4 polmineR-0.8.0/polmineR/man/context-method.Rd | 37 polmineR-0.8.0/polmineR/man/cooccurrences.Rd | 39 polmineR-0.8.0/polmineR/man/corpus-class.Rd |only polmineR-0.8.0/polmineR/man/corpus_methods.Rd |only polmineR-0.8.0/polmineR/man/count-method.Rd | 31 polmineR-0.8.0/polmineR/man/count_class.Rd | 41 polmineR-0.8.0/polmineR/man/cpos-method.Rd | 71 polmineR-0.8.0/polmineR/man/decode.Rd | 112 - polmineR-0.8.0/polmineR/man/dispersion-method.Rd | 59 polmineR-0.8.0/polmineR/man/encoding.Rd | 6 polmineR-0.8.0/polmineR/man/features-class.Rd | 1 polmineR-0.8.0/polmineR/man/features.Rd | 12 polmineR-0.8.0/polmineR/man/get_token_stream-method.Rd | 113 + polmineR-0.8.0/polmineR/man/get_type.Rd | 6 polmineR-0.8.0/polmineR/man/highlight.Rd | 21 polmineR-0.8.0/polmineR/man/hits.Rd | 76 polmineR-0.8.0/polmineR/man/html-method.Rd | 90 - polmineR-0.8.0/polmineR/man/kwic-class.Rd | 171 +- polmineR-0.8.0/polmineR/man/kwic.Rd | 93 - polmineR-0.8.0/polmineR/man/ll.Rd | 15 polmineR-0.8.0/polmineR/man/mail-method.Rd | 18 polmineR-0.8.0/polmineR/man/ngrams.Rd | 22 polmineR-0.8.0/polmineR/man/ocpu_exec.Rd |only polmineR-0.8.0/polmineR/man/p_attributes.Rd | 12 polmineR-0.8.0/polmineR/man/partition.Rd | 20 polmineR-0.8.0/polmineR/man/partition_bundle-class.Rd | 11 polmineR-0.8.0/polmineR/man/partition_bundle-method.Rd | 4 polmineR-0.8.0/polmineR/man/partition_class.Rd | 82 polmineR-0.8.0/polmineR/man/partition_to_string.Rd |only polmineR-0.8.0/polmineR/man/pmi.Rd | 23 polmineR-0.8.0/polmineR/man/polmineR-defunct.Rd |only polmineR-0.8.0/polmineR/man/polmineR-generics.Rd |only polmineR-0.8.0/polmineR/man/polmineR-package.Rd | 8 polmineR-0.8.0/polmineR/man/read-method.Rd | 14 polmineR-0.8.0/polmineR/man/reexports.Rd |only polmineR-0.8.0/polmineR/man/regions_class.Rd | 2 polmineR-0.8.0/polmineR/man/registry.Rd | 24 polmineR-0.8.0/polmineR/man/registry_reset.Rd | 2 polmineR-0.8.0/polmineR/man/renamed.Rd | 12 polmineR-0.8.0/polmineR/man/s_attributes-method.Rd | 99 - polmineR-0.8.0/polmineR/man/size-method.Rd | 34 polmineR-0.8.0/polmineR/man/slice.Rd | 8 polmineR-0.8.0/polmineR/man/subcorpus-class.Rd | 93 - polmineR-0.8.0/polmineR/man/subcorpus_bundle.Rd |only polmineR-0.8.0/polmineR/man/subset.Rd |only polmineR-0.8.0/polmineR/man/t_test.Rd | 68 polmineR-0.8.0/polmineR/man/templates.Rd | 3 polmineR-0.8.0/polmineR/man/terms.Rd | 6 polmineR-0.8.0/polmineR/man/textstat-class.Rd | 27 polmineR-0.8.0/polmineR/man/tooltips.Rd | 10 polmineR-0.8.0/polmineR/man/weigh-method.Rd | 2 polmineR-0.8.0/polmineR/tests/testthat/test_as.DocumentTermMatrix.R | 33 polmineR-0.8.0/polmineR/tests/testthat/test_as.markdown.R |only polmineR-0.8.0/polmineR/tests/testthat/test_as.regions.R |only polmineR-0.8.0/polmineR/tests/testthat/test_as.speeches.R |only polmineR-0.8.0/polmineR/tests/testthat/test_cooccurrences.R | 49 polmineR-0.8.0/polmineR/tests/testthat/test_count.R | 18 polmineR-0.8.0/polmineR/tests/testthat/test_cpos.R | 27 polmineR-0.8.0/polmineR/tests/testthat/test_decode.R | 25 polmineR-0.8.0/polmineR/tests/testthat/test_dispersion.R |only polmineR-0.8.0/polmineR/tests/testthat/test_enrich.R |only polmineR-0.8.0/polmineR/tests/testthat/test_get_template.R |only polmineR-0.8.0/polmineR/tests/testthat/test_get_token_stream.R |only polmineR-0.8.0/polmineR/tests/testthat/test_get_type.R | 1 polmineR-0.8.0/polmineR/tests/testthat/test_hits.R |only polmineR-0.8.0/polmineR/tests/testthat/test_kwic.R | 80 polmineR-0.8.0/polmineR/tests/testthat/test_ngrams.R |only polmineR-0.8.0/polmineR/tests/testthat/test_p_attributes.R |only polmineR-0.8.0/polmineR/tests/testthat/test_partition_bundle.R | 24 polmineR-0.8.0/polmineR/tests/testthat/test_s_attributes.R | 27 polmineR-0.8.0/polmineR/tests/testthat/test_size.R | 21 polmineR-0.8.0/polmineR/tests/testthat/test_split.R |only polmineR-0.8.0/polmineR/tests/testthat/test_subcorpus.R |only polmineR-0.8.0/polmineR/tests/testthat/test_subcorpus_bundle.R |only polmineR-0.8.0/polmineR/tests/testthat/test_summary.R |only polmineR-0.8.0/polmineR/tests/testthat/test_terms.R | 17 polmineR-0.8.0/polmineR/vignettes/OpenCPU.Rmd |only polmineR-0.8.0/polmineR/vignettes/vignette.Rmd | 7 188 files changed, 7247 insertions(+), 3475 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution,
provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities,
densities and density quantiles for four different types of the distribution,
the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
and Loots 2009) and FM5 - see documentation for details.
It provides the density function, distribution function, and Quantile-Quantile
plots.
It implements a variety of estimation methods for the distribution,
including diagnostic plots.
Estimation methods include the starship (all 4 types),
method of L-Moments for the GPD and FKML types, and a
number of methods for only the FKML type.
These include maximum likelihood, maximum product of spacings,
Titterington's method, Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>,
Benjamin Dean <Benjamin.Dean@uon.edu.au>, Sigbert Klinke, Paul van Staden
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.6 dated 2019-09-02 and 2.6.1 dated 2019-12-17
Changelog | 7 ++++++- DESCRIPTION | 29 ++++++++++++++++++----------- MD5 | 12 ++++++------ NEWS | 5 +++++ R/CheckParameters.R | 10 ++++++++-- R/fit.gpd.R | 14 +++++++------- man/fit.gpd.Rd | 11 ++++++++--- 7 files changed, 58 insertions(+), 30 deletions(-)
Title: Tools to create, modify and manage 'CWB' Corpora
Description: The 'Corpus Workbench' ('CWB', <http://cwb.sourceforge.net/>) offers a classic and mature
approach for working with large, linguistically and structurally annotated corpora. The 'CWB'
is memory efficient and its design makes running queries fast (Evert and Hardie 2011,
<http://www.stefan-evert.de/PUB/EvertHardie2011.pdf>). The 'cwbtools' package offers
pure R tools to create indexed corpus files as well as high-level wrappers for the original C
implementation of CWB as exposed by the 'RcppCWB' package
<https://CRAN.R-project.org/package=RcppCWB>. Additional functionality to add and
modify annotations of corpora from within R makes working with CWB indexed corpora
much more flexible and convenient. The 'cwbtools' package in combination with the R packages
'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR'
(<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure
to support the combination of quantitative and qualitative approaches for working
with textual data.
Author: Andreas Blaette [aut, cre],
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between cwbtools versions 0.1.1 dated 2019-12-09 and 0.1.2 dated 2019-12-17
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 13 +++++++++++++ inst/doc/europarl.R | 2 ++ inst/doc/europarl.Rmd | 3 +++ inst/doc/europarl.html | 10 ++++++---- inst/doc/vignette.R | 3 ++- inst/doc/vignette.Rmd | 3 ++- inst/doc/vignette.html | 13 +++++++------ vignettes/europarl.Rmd | 3 +++ vignettes/vignette.Rmd | 3 ++- 11 files changed, 54 insertions(+), 27 deletions(-)
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided. As of release 1.72.0-1, the following Boost libraries are
included: 'algorithm' 'align' 'any' 'atomic' 'bimap' 'bind'
'circular_buffer' 'compute' 'concept' 'config' 'container'
'date_time' 'detail' 'dynamic_bitset' 'exception' 'flyweight'
'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl'
'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator'
'math' 'move' 'mp11' 'mpl' 'multiprcecision' 'numeric' 'pending'
'phoenix' 'polygon' 'preprocessor' 'propery_tree' 'random' 'range'
'scope_exit' 'smart_ptr' 'sort' 'spirit' 'tuple' 'type_traits'
'typeof' 'unordered' 'utility' 'uuid'.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.72.0-1 dated 2019-12-16 and 1.72.0-2 dated 2019-12-17
BH-1.72.0-1/BH/inst/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54_cl.hpp |only BH-1.72.0-2/BH/ChangeLog | 11 ++++ BH-1.72.0-2/BH/DESCRIPTION | 26 +++++----- BH-1.72.0-2/BH/MD5 | 10 +-- BH-1.72.0-2/BH/build/partial.rdb |binary BH-1.72.0-2/BH/inst/NEWS.Rd | 11 ++++ BH-1.72.0-2/BH/inst/include/boost/numeric/odeint/stepper/runge_kutta_cash_karp54_classic.hpp |only 7 files changed, 41 insertions(+), 17 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Alex Lewin [aut],
Manuela Zucknick [ctb],
Waldir Leoncio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 1.0-3 dated 2019-12-07 and 1.0-4 dated 2019-12-17
BayesSUR-1.0-3/BayesSUR/R/example_GDSC_targets.R |only BayesSUR-1.0-3/BayesSUR/data/example_GDSC_targets.rda |only BayesSUR-1.0-3/BayesSUR/man/example_GDSC_targets.Rd |only BayesSUR-1.0-4/BayesSUR/DESCRIPTION | 10 BayesSUR-1.0-4/BayesSUR/MD5 | 33 +- BayesSUR-1.0-4/BayesSUR/R/BayesSUR.R | 9 BayesSUR-1.0-4/BayesSUR/R/RcppExports.R | 4 BayesSUR-1.0-4/BayesSUR/R/plotEstimator.R | 20 - BayesSUR-1.0-4/BayesSUR/R/plotMCMCdiag.R | 27 +- BayesSUR-1.0-4/BayesSUR/R/targetGene.R |only BayesSUR-1.0-4/BayesSUR/data/datalist | 2 BayesSUR-1.0-4/BayesSUR/data/targetGene.rda |only BayesSUR-1.0-4/BayesSUR/inst/doc/BayesSUR.pdf |binary BayesSUR-1.0-4/BayesSUR/man/BayesSUR.Rd | 7 BayesSUR-1.0-4/BayesSUR/man/plotMCMCdiag.Rd | 2 BayesSUR-1.0-4/BayesSUR/man/targetGene.Rd | 201 +++++++++++++++++- BayesSUR-1.0-4/BayesSUR/src/BayesSUR.cpp | 4 BayesSUR-1.0-4/BayesSUR/src/RcppExports.cpp | 9 BayesSUR-1.0-4/BayesSUR/src/drive.cpp | 7 BayesSUR-1.0-4/BayesSUR/src/drive.h | 2 20 files changed, 273 insertions(+), 64 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 1.10.0 dated 2019-09-10 and 2.0.0 dated 2019-12-17
rfacebookstat-1.10.0/rfacebookstat/R/fbGetLongTimeToken.R |only rfacebookstat-1.10.0/rfacebookstat/R/fbGetProjects.R |only rfacebookstat-1.10.0/rfacebookstat/R/fbGetToken.R |only rfacebookstat-1.10.0/rfacebookstat/man/fbGetProjects.Rd |only rfacebookstat-2.0.0/rfacebookstat/DESCRIPTION | 14 rfacebookstat-2.0.0/rfacebookstat/MD5 | 103 +-- rfacebookstat-2.0.0/rfacebookstat/NAMESPACE | 26 rfacebookstat-2.0.0/rfacebookstat/NEWS.md | 45 + rfacebookstat-2.0.0/rfacebookstat/R/authorization.R |only rfacebookstat-2.0.0/rfacebookstat/R/fbActions.R | 294 ++-------- rfacebookstat-2.0.0/rfacebookstat/R/fbDeleteAdAccountUsers.R | 19 rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdAccountUsers.R | 50 + rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdAccountUsersPermissions.R | 44 + rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdAccounts.R | 166 +++-- rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdAccountsConversions.R |only rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdCreative.R | 179 ++++-- rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdSets.R | 107 +++ rfacebookstat-2.0.0/rfacebookstat/R/fbGetAdVideos.R |only rfacebookstat-2.0.0/rfacebookstat/R/fbGetAds.R | 174 ++++- rfacebookstat-2.0.0/rfacebookstat/R/fbGetApps.R | 107 +++ rfacebookstat-2.0.0/rfacebookstat/R/fbGetBusinessManagers.R | 114 ++- rfacebookstat-2.0.0/rfacebookstat/R/fbGetBusinessUserAdAccounts.R | 95 ++- rfacebookstat-2.0.0/rfacebookstat/R/fbGetCampaigns.R | 117 +++ rfacebookstat-2.0.0/rfacebookstat/R/fbGetCatalogs.R | 39 + rfacebookstat-2.0.0/rfacebookstat/R/fbGetMarketingStat.R | 171 ++++- rfacebookstat-2.0.0/rfacebookstat/R/fbGetPages.R | 105 +++ rfacebookstat-2.0.0/rfacebookstat/R/fbGetUserAdAccounts.R |only rfacebookstat-2.0.0/rfacebookstat/R/fbParsers.R |only rfacebookstat-2.0.0/rfacebookstat/R/fbUpdateAdAccountUsers.R | 19 rfacebookstat-2.0.0/rfacebookstat/R/sysdata.rda |only rfacebookstat-2.0.0/rfacebookstat/R/zzz.R | 76 ++ rfacebookstat-2.0.0/rfacebookstat/README.md | 74 +- rfacebookstat-2.0.0/rfacebookstat/build/partial.rdb |binary rfacebookstat-2.0.0/rfacebookstat/build/vignette.rds |binary rfacebookstat-2.0.0/rfacebookstat/inst/doc/rfacebookstat-authorization.R |only rfacebookstat-2.0.0/rfacebookstat/inst/doc/rfacebookstat-authorization.Rmd |only rfacebookstat-2.0.0/rfacebookstat/inst/doc/rfacebookstat-authorization.html |only rfacebookstat-2.0.0/rfacebookstat/inst/doc/rfacebookstat-get-statistics.R | 32 - rfacebookstat-2.0.0/rfacebookstat/inst/doc/rfacebookstat-get-statistics.Rmd | 96 ++- rfacebookstat-2.0.0/rfacebookstat/inst/doc/rfacebookstat-get-statistics.html | 292 +++++---- rfacebookstat-2.0.0/rfacebookstat/man/fbAuth.Rd |only rfacebookstat-2.0.0/rfacebookstat/man/fbDeleteAdAccountUsers.Rd | 12 rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdAccountUsers.Rd | 4 rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdAccountUsersPermissions.Rd | 4 rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdAccounts.Rd | 8 rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdAccountsConversions.Rd |only rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdCreative.Rd | 4 rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdSets.Rd | 4 rfacebookstat-2.0.0/rfacebookstat/man/fbGetAdVideos.Rd |only rfacebookstat-2.0.0/rfacebookstat/man/fbGetAds.Rd | 8 rfacebookstat-2.0.0/rfacebookstat/man/fbGetApps.Rd | 16 rfacebookstat-2.0.0/rfacebookstat/man/fbGetBusinessManagers.Rd | 4 rfacebookstat-2.0.0/rfacebookstat/man/fbGetBusinessUserAdAccounts.Rd | 10 rfacebookstat-2.0.0/rfacebookstat/man/fbGetCampaigns.Rd | 8 rfacebookstat-2.0.0/rfacebookstat/man/fbGetCatalogs.Rd | 4 rfacebookstat-2.0.0/rfacebookstat/man/fbGetMarketingStat.Rd | 35 + rfacebookstat-2.0.0/rfacebookstat/man/fbGetPages.Rd | 17 rfacebookstat-2.0.0/rfacebookstat/man/fbGetSettings.Rd |only rfacebookstat-2.0.0/rfacebookstat/man/fbGetUserAdAccounts.Rd |only rfacebookstat-2.0.0/rfacebookstat/man/fbUpdateAdAccountUsers.Rd | 12 rfacebookstat-2.0.0/rfacebookstat/vignettes/rfacebookstat-authorization.Rmd |only rfacebookstat-2.0.0/rfacebookstat/vignettes/rfacebookstat-get-statistics.Rmd | 96 ++- 62 files changed, 1951 insertions(+), 853 deletions(-)
Title: Environmental Seismology Toolbox
Description: Environmental seismology is a scientific field that studies the
seismic signals, emitted by Earth surface processes. This package
provides all relevant functions to read/write seismic data files, prepare,
analyse and visualise seismic data, and generate reports of the processing
history.
Author: Michael Dietze [cre, aut, trl],
Christoph Burow [ctb],
Sophie Lagarde [ctb, trl]
Maintainer: Michael Dietze <mdietze@gfz-potsdam.de>
Diff between eseis versions 0.4.0 dated 2018-06-14 and 0.5.0 dated 2019-12-17
DESCRIPTION | 18 +- MD5 | 186 +++++++++++++++++------------ NAMESPACE | 24 +++ NEWS | 19 ++- R/aux_commondt.R |only R/aux_eseisobspy.R |only R/aux_fixmseed.R | 2 R/aux_getFDSNdata.R | 2 R/aux_getFDSNstation.R | 2 R/aux_getIRISdata.R | 2 R/aux_getevent.R | 251 +++++++++++++++++++++++++++++----------- R/aux_gettemperature.R | 2 R/aux_hvanalysis.R | 6 R/aux_initiateeseis.R | 7 - R/aux_obspyeseis.R |only R/aux_organisecubefiles.R | 32 ++--- R/aux_psdpanels.R | 4 R/aux_psdsummary.R | 4 R/aux_stationinfofile.R | 2 R/eseis-package.R | 8 - R/fmi_inversion.R |only R/fmi_parameters.R |only R/fmi_spectra.R |only R/gui_models.R |only R/list_logger.R | 32 ++++- R/methods_eseis.R |only R/model_bedload.R |only R/model_turbulence.R | 6 R/plot_components.R | 12 - R/plot_signal.R | 16 ++ R/plot_spectrogram.R | 58 ++++----- R/plot_spectrum.R | 6 R/read_mseed.R | 24 ++- R/read_sac.R | 52 +++++--- R/signal_aggregate.R | 67 ++-------- R/signal_clip.R | 4 R/signal_cut.R |only R/signal_deconvolve.R | 41 ++++-- R/signal_demean.R | 4 R/signal_detrend.R | 4 R/signal_envelope.R | 7 - R/signal_filter.R | 120 +++++++++++++++++-- R/signal_hilbert.R | 7 - R/signal_hvratio.R | 11 + R/signal_integrate.R | 6 R/signal_motion.R | 12 - R/signal_pad.R | 4 R/signal_rotate.R | 2 R/signal_sign.R |only R/signal_snr.R | 4 R/signal_spectrogram.R | 71 +++++++---- R/signal_spectrum.R | 13 +- R/signal_stalta.R | 6 R/signal_sum.R | 4 R/signal_taper.R | 4 R/signal_whiten.R |only R/spatial_amplitude.R |only R/spatial_convert.R | 7 - R/spatial_crop.R |only R/spatial_migrate.R | 191 +++++++++++++++--------------- R/spatial_pmax.R |only R/write_mseed.R |only R/write_report.R | 2 R/write_sac.R | 71 +++++++++-- R/zzz.R |only data/rockfall.rda |binary inst/shiny |only man/aux_commondt.Rd |only man/aux_eseisobspy.Rd |only man/aux_getFDSNdata.Rd | 12 + man/aux_getFDSNstation.Rd | 2 man/aux_getIRISdata.Rd | 10 + man/aux_getIRISstation.Rd | 10 + man/aux_getevent.Rd | 17 ++ man/aux_hvanalysis.Rd | 14 +- man/aux_obspyeseis.Rd |only man/aux_organisecentaurfiles.Rd | 15 +- man/aux_organisecubefiles.Rd | 17 ++ man/aux_psdpanels.Rd | 19 ++- man/aux_psdsummary.Rd | 18 ++ man/aux_stationinfofile.Rd | 26 +++- man/earthquake.Rd | 1 man/eseis.Rd | 6 man/fmi_inversion.Rd |only man/fmi_parameters.Rd |only man/fmi_spectra.Rd |only man/gui_models.Rd |only man/model_bedload.Rd |only man/model_turbulence.Rd | 20 ++- man/plot_components.Rd | 8 - man/plot_signal.Rd | 14 ++ man/plot_spectrogram.Rd | 8 - man/read_mseed.Rd | 17 ++ man/read_sac.Rd | 24 +++ man/rockfall.Rd | 2 man/signal_aggregate.Rd | 10 + man/signal_cut.Rd |only man/signal_deconvolve.Rd | 24 +++ man/signal_filter.Rd | 36 +++++ man/signal_motion.Rd | 2 man/signal_sign.Rd |only man/signal_spectrogram.Rd | 28 +++- man/signal_whiten.Rd |only man/spatial_amplitude.Rd |only man/spatial_crop.Rd |only man/spatial_distance.Rd | 11 + man/spatial_migrate.Rd | 15 +- man/spatial_pmax.Rd |only man/write_mseed.Rd |only man/write_sac.Rd | 16 ++ 110 files changed, 1249 insertions(+), 592 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized ML estimators for the
precision matrix as well as supporting functions to employ these estimators
in a graphical modeling setting.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 2.2.1 dated 2019-03-19 and 2.2.2 dated 2019-12-17
DESCRIPTION | 6 MD5 | 16 NAMESPACE | 1 R/rags2ridges.R | 29 - R/rags2ridgesVariants.r | 882 ++++++++++++++++++++++++------------------------ inst/NEWS.Rd | 8 man/GGMpathStats.Rd | 2 man/Ugraph.Rd | 2 man/edgeHeat.Rd | 2 9 files changed, 481 insertions(+), 467 deletions(-)
Title: Useful Shortcuts to Interact with 'RStudio' Scripts
Description: Integrates clipboard copied data in R Studio, loads and installs libraries within a R script and returns all valid arguments of a selected function.
Author: José Carlos Del Valle <jcval94@gmail.com>
Maintainer: José Carlos Del Valle <jcval94@gmail.com>
Diff between shortcuts versions 1.3.0 dated 2019-12-02 and 1.4.0 dated 2019-12-17
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ NAMESPACE | 3 +++ R/clear.code.R | 4 ++-- R/copypaste.R | 2 +- R/r.args.R | 1 - R/read.all.R |only inst/rstudio/addins.dcf | 5 +++++ man/read.all.Rd |only 9 files changed, 22 insertions(+), 13 deletions(-)
Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance
measures for asset or portfolio returns using methods as described in
Chen and Martin (2019) <https://ssrn.com/abstract=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPESE versions 1.0 dated 2019-11-06 and 1.0.1 dated 2019-12-17
DESCRIPTION | 8 +++--- MD5 | 60 ++++++++++++++++++++++----------------------- R/ES_SE.R | 4 +++ R/ESratio_SE.R | 8 +++++- R/EstimatorES.R | 18 ++++++++++++- R/EstimatorSE_utils.R | 5 +++ R/GLM_EN.R | 24 ++++++++++++++---- R/LPM_SE.R | 6 +++- R/Mean_SE.R | 4 +++ R/OmegaRatio_SE.R | 4 +++ R/Rachev_SE.R | 4 +++ R/SemiSD_SE.R | 4 +++ R/SharpeRatio_SE.R | 4 +++ R/SortinoRatio_SE.R | 4 +++ R/StdDev_SE.R | 7 ++++- R/VaR_SE.R | 4 +++ R/VaRratio_SE.R | 4 +++ inst/doc/RPESEVignette.pdf |binary man/ES.SE.Rd | 8 +++++- man/ESratio.SE.Rd | 5 +++ man/EstimatorSE.Rd | 9 +++++- man/LPM.SE.Rd | 7 ++++- man/Mean.SE.Rd | 8 +++++- man/OmegaRatio.SE.Rd | 5 +++ man/RachevRatio.SE.Rd | 8 +++++- man/SemiSD.SE.Rd | 8 +++++- man/SharpeRatio.SE.Rd | 5 +++ man/SortinoRatio.SE.Rd | 8 +++++- man/StdDev.SE.Rd | 8 +++++- man/VaR.SE.Rd | 5 +++ man/VaRratio.SE.Rd | 5 +++ 31 files changed, 209 insertions(+), 52 deletions(-)
Title: Interface to the Fish Tree of Life API
Description: An interface to the Fish Tree of Life API to download taxonomies,
phylogenies, fossil calibrations, and diversification rate information for
ray-finned fishes.
Author: Jonathan Chang [aut, cre] (<https://orcid.org/0000-0002-3811-1254>),
Michael E Alfaro [ctb],
Daniel L Rabosky [ctb],
Stephen A Smith [ctb]
Maintainer: Jonathan Chang <jonathan.chang@ucla.edu>
Diff between fishtree versions 0.3.1 dated 2019-05-31 and 0.3.2 dated 2019-12-17
DESCRIPTION | 12 - MD5 | 42 ++-- NAMESPACE | 1 NEWS.md | 18 + R/functions.R | 18 + R/utils.R | 14 - README.md | 19 + build/vignette.rds |binary inst/CITATION | 45 +++- inst/doc/community-analysis.R | 16 - inst/doc/community-analysis.Rmd | 2 inst/doc/community-analysis.html | 197 ++++++++++-------- inst/doc/comparative-analysis.R | 34 +-- inst/doc/comparative-analysis.html | 366 +++++++++++++++++++---------------- man/fishtree-package.Rd | 2 man/fishtree_complete_phylogeny.Rd | 13 - man/fishtree_phylogeny.Rd | 7 man/fishtree_tip_rates.Rd | 5 tests/testthat/test-sampling.R | 11 - vignettes/community-analysis.Rmd | 2 vignettes/comparative-analysis_cache |only 21 files changed, 492 insertions(+), 332 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.0.4-4 dated 2019-08-29 and 2.0.4-6 dated 2019-12-17
CHANGELOG | 10 +++ DESCRIPTION | 8 +- MD5 | 18 ++--- R/runjags.summaries.R | 2 R/template.jags.R | 18 ++--- R/utilities.invisible.R | 6 - build/vignette.rds |binary inst/doc/UserGuide.pdf |binary inst/doc/quickjags.R | 44 +++++++------- inst/doc/quickjags.html | 148 ++++++++++++++++++++++-------------------------- 10 files changed, 128 insertions(+), 126 deletions(-)
Title: Provides R-Language Code to Examine Quantitative Risk Management
Concepts
Description: Provides functions/methods to accompany the book
Quantitative Risk Management: Concepts, Techniques and Tools by
Alexander J. McNeil, Rudiger Frey, and Paul Embrechts.
Author: Bernhard Pfaff [aut, cre],
Marius Hofert [ctb],
Alexander McNeil [aut] (S-Plus original (QRMlib)),
Scott Ulmann [trl] (First R port as package QRMlib)
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between QRM versions 0.4-13 dated 2016-03-18 and 0.4-16 dated 2019-12-17
DESCRIPTION | 19 - MD5 | 80 +++--- R/GEV.R | 2 R/GIG.R | 19 - R/Gauss.R | 6 R/NH.R | 35 +- R/PointProcess.R | 595 +++++++++++++++++++++++------------------------ R/Student.R | 28 +- data/DJ.RData |binary data/DJ.df.RData |binary data/FXGBP.RData |binary data/FXGBP.df.RData |binary data/cac40.RData |binary data/cac40.df.RData |binary data/danish.RData |binary data/danish.df.RData |binary data/dji.RData |binary data/dji.df.RData |binary data/ftse100.RData |binary data/ftse100.df.RData |binary data/hsi.RData |binary data/hsi.df.RData |binary data/nasdaq.RData |binary data/nasdaq.df.RData |binary data/nikkei.RData |binary data/nikkei.df.RData |binary data/smi.RData |binary data/smi.df.RData |binary data/sp500.RData |binary data/sp500.df.RData |binary data/spdata.RData |binary data/spdata.df.RData |binary data/spdata.raw.RData |binary data/spdata.raw.df.RData |binary data/xdax.RData |binary data/xdax.df.RData |binary man/Gauss.Rd | 1 man/NH.Rd | 1 man/PointProcess.Rd | 1 man/QRM-package.Rd | 2 man/game.Rd | 1 41 files changed, 397 insertions(+), 393 deletions(-)
Title: Statistical Inference and Sure Independence Screening via Ball
Statistics
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence <doi:10.1214/17-AOS1579>, ball covariance <doi:10.1080/01621459.2018.1543600>, and ball correlation <doi:10.1080/01621459.2018.1462709>, are developed to analyze complex data in metric spaces, e.g, shape, directional, compositional and symmetric positive definite matrix data. The ball divergence and ball covariance based distribution-free tests are implemented to detecting distribution difference and association in metric spaces <arXiv:1811.03750>. Furthermore, several generic non-parametric feature selection procedures based on ball correlation, BCor-SIS and all of its variants, are implemented to tackle the challenge in the context of ultra high dimensional data.
Author: Xueqin Wang, Wenliang Pan, Heping Zhang, Hongtu Zhu, Yuan Tian, Weinan Xiao, Chengfeng Liu, Ruihuang Liu, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between Ball versions 1.3.8 dated 2019-05-31 and 1.3.9 dated 2019-12-17
Ball-1.3.8/Ball/src/utilize_R.h |only Ball-1.3.8/Ball/tests/testthat/test_bd_gwas.R |only Ball-1.3.9/Ball/DESCRIPTION | 8 Ball-1.3.9/Ball/MD5 | 66 +++--- Ball-1.3.9/Ball/NAMESPACE | 1 Ball-1.3.9/Ball/NEWS.md | 6 Ball-1.3.9/Ball/R/bcorsis.R | 100 ++++++--- Ball-1.3.9/Ball/R/bcov.R | 96 +++++---- Ball-1.3.9/Ball/R/bd.R | 68 ++++-- Ball-1.3.9/Ball/R/data.R | 1 Ball-1.3.9/Ball/R/utilize.R | 72 ++++++ Ball-1.3.9/Ball/R/wrap_c.R | 153 ++++++++++++-- Ball-1.3.9/Ball/inst/doc/Ball.R | 12 - Ball-1.3.9/Ball/inst/doc/Ball.Rmd | 12 - Ball-1.3.9/Ball/inst/doc/Ball.html | 54 ++--- Ball-1.3.9/Ball/man/bcorsis.Rd | 54 +++-- Ball-1.3.9/Ball/man/bcov.test.Rd | 29 ++ Ball-1.3.9/Ball/man/bd.Rd | 2 Ball-1.3.9/Ball/man/bd.test.Rd | 28 ++ Ball-1.3.9/Ball/src/BD.c | 82 +++++-- Ball-1.3.9/Ball/src/BI.c | 1 Ball-1.3.9/Ball/src/Makevars | 1 Ball-1.3.9/Ball/src/Makevars.win | 1 Ball-1.3.9/Ball/src/ball_init.c | 12 - Ball-1.3.9/Ball/src/bcor.c | 271 ++++++++++++++++++++++++-- Ball-1.3.9/Ball/src/bcor.h | 2 Ball-1.3.9/Ball/src/bdd_matrix.c |only Ball-1.3.9/Ball/src/bdd_matrix.h |only Ball-1.3.9/Ball/src/kbd.c | 4 Ball-1.3.9/Ball/src/surv.c | 206 ++++--------------- Ball-1.3.9/Ball/src/surv.h | 3 Ball-1.3.9/Ball/src/utilities.c | 37 ++- Ball-1.3.9/Ball/src/utilities.h | 2 Ball-1.3.9/Ball/tests/testthat/test_bcorsis.R | 26 ++ Ball-1.3.9/Ball/tests/testthat/test_bd.R | 20 - Ball-1.3.9/Ball/vignettes/Ball.Rmd | 12 - 36 files changed, 980 insertions(+), 462 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-12 0.0.8
2019-05-02 0.0.7
2019-03-23 0.0.6
2019-02-24 0.0.5
2019-02-13 0.0.4
2019-02-12 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-12 0.0.12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-29 1.0.7
2019-03-16 1.0.6
2019-01-11 1.0.5
2018-12-08 1.0.4
2018-08-19 1.0.2.1
2018-08-19 1.0.3
2018-04-09 1.0.2
2017-11-12 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-23 1.3.0
2016-10-05 1.2.0
2015-11-26 1.1.1
2015-05-17 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-20 0.4.0
2017-11-26 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-06 0.1.0
Title: Tools to Support Evidence Synthesis
Description: Researchers commonly need to summarize scientific information, a process known as 'evidence synthesis'. The first stage of a synthesis process (such as a systematic review or meta-analysis) is to download a list of references from academic search engines such as 'Web of Knowledge' or 'Scopus'. The traditional approach to systematic review is then to sort these data manually, first by locating and removing duplicated entries, and then screening to remove irrelevant content by viewing titles and abstracts (in that order). 'revtools' provides interfaces for each of these tasks. An alternative approach, however, is to draw on tools from machine learning to visualise patterns in the corpus. In this case, you can use 'revtools' to render ordinations of text drawn from article titles, keywords and abstracts, and interactively select or exclude individual references, words or topics.
Author: Martin J. Westgate [aut, cre]
Maintainer: Martin J. Westgate <martinjwestgate@gmail.com>
Diff between revtools versions 0.4.0 dated 2019-07-15 and 0.4.1 dated 2019-12-17
DESCRIPTION | 10 - MD5 | 74 +++++---- NAMESPACE | 5 R/add_line_breaks.R |only R/bibliography-methods.R | 4 R/find_duplicates.R | 77 +++++++--- R/format_citation.R | 267 +++++++++++++++++++----------------- R/import_shiny.R | 1 R/make_dtm.R | 200 +++++++++++++++++++++----- R/merge_columns.R | 15 +- R/plotly_functions.R | 2 R/read_bibliography.R | 265 ++++++++++++++++++----------------- R/revtools_csv.R | 8 - R/run_topic_model.R | 14 - R/screen_abstracts.R | 236 ++++++++++++++++++++++++------- R/screen_abstracts_infrastructure.R | 110 ++++++++++---- R/screen_abstracts_ui.R | 32 ++-- R/screen_duplicates.R | 15 +- R/screen_duplicates_ui.R | 2 R/screen_titles.R | 193 +++++++++++++------------- R/screen_titles_infrastructure.R | 43 +++-- R/screen_titles_ui.R | 4 R/screen_topics.R | 73 +++++---- R/screen_topics_infrastructure.R | 34 ++-- R/screen_topics_ui.R | 17 ++ R/tag_lookup.R | 92 ++++++++++++ R/write_bibliography.R | 17 +- inst/CITATION | 16 +- man/add_line_breaks.Rd |only man/find_duplicates.Rd | 16 +- man/format_citation.Rd | 6 man/make_dtm.Rd | 26 ++- man/revtools.Rd | 6 man/revwords.Rd | 4 man/run_topic_model.Rd | 5 man/screen_abstracts.Rd | 2 man/screen_duplicates.Rd | 3 man/screen_topics.Rd | 3 man/screen_topics_progress-class.Rd | 4 39 files changed, 1212 insertions(+), 689 deletions(-)
Title: Hierarchical Modeling and Frequency Method Checking on
Overdispersed Gaussian, Poisson, and Binomial Data
Description: We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly <josephkelly@post.harvard.edu>
Diff between Rgbp versions 1.1.3 dated 2018-05-17 and 1.1.4 dated 2019-12-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/gr.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: A Unified Framework for Input-Output Operations in R
Description: One function to read files. One function to write files. One
function to direct plots to screen or file. Automatic file format inference
and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih <djh.shih@gmail.com>
Diff between io versions 0.3.0 dated 2018-01-15 and 0.3.2 dated 2019-12-17
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/csv.R | 4 ++-- R/gct.R | 1 + R/hdf5.R | 44 ++++++++++++++++++++++++++++++++++++++++++-- R/vector.R | 6 +++--- man/io.Rd | 1 - man/qdraw.Rd | 16 +++++++++++++--- 8 files changed, 74 insertions(+), 24 deletions(-)
Title: Goodness-of-Fit Tests for Functional Data
Description: Implementation of several goodness-of-fit tests for functional
data. Currently, mostly related with the functional linear model with
functional/scalar response and functional/scalar predictor. The package
allows for the replication of the data applications considered in
García-Portugués, Álvarez-Liébana, Álvarez-Pérez and González-Manteiga
(2019) <arXiv:1909.07686>.
Author: Eduardo García-Portugués [aut, cre],
Javier Álvarez-Liébana [aut],
Gonzalo Álvarez-Pérez [ctb],
Manuel Febrero-Bande [ctb]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>
Diff between goffda versions 0.0.5 dated 2019-10-01 and 0.0.6 dated 2019-12-17
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ man/flm_test.Rd | 12 ++++++------ man/quadrature.Rd | 6 ++---- 5 files changed, 21 insertions(+), 19 deletions(-)
Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and
'geospatial' data from the British Columbia Data Catalogue
(<https://catalogue.data.gov.bc.ca/>). Search catalogue data records
based on keywords, data licence, sector, data format, and B.C.
government organization. View metadata directly in R, download many
data formats, and query 'geospatial' data available via the B.C.
government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] (<https://orcid.org/0000-0002-7840-692X>),
Sam Albers [aut, ctb] (<https://orcid.org/0000-0002-9270-7884>),
Stephanie Hazlitt [aut, ctb],
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>
Diff between bcdata versions 0.1.1 dated 2019-11-05 and 0.1.2 dated 2019-12-17
bcdata-0.1.1/bcdata/inst/doc/bcdata.R |only bcdata-0.1.2/bcdata/DESCRIPTION | 44 - bcdata-0.1.2/bcdata/MD5 | 82 + bcdata-0.1.2/bcdata/NAMESPACE | 11 bcdata-0.1.2/bcdata/NEWS.md | 23 bcdata-0.1.2/bcdata/R/bcdata-package.R | 1 bcdata-0.1.2/bcdata/R/bcdc-web-services.R | 10 bcdata-0.1.2/bcdata/R/bcdc_search.R | 49 + bcdata-0.1.2/bcdata/R/cql-geom-predicates.R | 35 bcdata-0.1.2/bcdata/R/cql-translator.R | 51 - bcdata-0.1.2/bcdata/R/get_data.R | 2 bcdata-0.1.2/bcdata/R/utils-classes.R | 70 + bcdata-0.1.2/bcdata/R/utils-is.R | 2 bcdata-0.1.2/bcdata/R/utils-mutate.R |only bcdata-0.1.2/bcdata/R/utils.R | 5 bcdata-0.1.2/bcdata/README.md | 21 bcdata-0.1.2/bcdata/build/vignette.rds |binary bcdata-0.1.2/bcdata/inst/doc/bcdata.Rmd | 313 ++++++- bcdata-0.1.2/bcdata/inst/doc/bcdata.html | 437 ++++------ bcdata-0.1.2/bcdata/inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd |only bcdata-0.1.2/bcdata/inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.html |only bcdata-0.1.2/bcdata/man/bcdata-package.Rd | 22 bcdata-0.1.2/bcdata/man/bcdc_browse.Rd | 9 bcdata-0.1.2/bcdata/man/bcdc_options.Rd | 2 bcdata-0.1.2/bcdata/man/bcdc_query_geodata.Rd | 8 bcdata-0.1.2/bcdata/man/bcdc_search.Rd | 13 bcdata-0.1.2/bcdata/man/bcdc_search_facets.Rd | 8 bcdata-0.1.2/bcdata/man/bcdc_tidy_resources.Rd |only bcdata-0.1.2/bcdata/man/cql_geom_predicates.Rd | 24 bcdata-0.1.2/bcdata/man/mutate.Rd |only bcdata-0.1.2/bcdata/man/mutate.bcdc_promise.Rd |only bcdata-0.1.2/bcdata/tests/testthat/test-cql-string.R | 16 bcdata-0.1.2/bcdata/tests/testthat/test-edge-cases.R |only bcdata-0.1.2/bcdata/tests/testthat/test-geom-operators.R | 56 + bcdata-0.1.2/bcdata/tests/testthat/test-get_record.R | 24 bcdata-0.1.2/bcdata/tests/testthat/test-print-methods.R | 2 bcdata-0.1.2/bcdata/tests/testthat/test-query-geodata-filter.R | 33 bcdata-0.1.2/bcdata/tests/testthat/test-query-geodata-mutate.R |only bcdata-0.1.2/bcdata/tests/testthat/test-query-geodata-select.R | 23 bcdata-0.1.2/bcdata/tests/testthat/test-search.R |only bcdata-0.1.2/bcdata/tests/testthat/test-utils.R | 9 bcdata-0.1.2/bcdata/vignettes/bcdata.Rmd | 313 ++++++- bcdata-0.1.2/bcdata/vignettes/bcdata.Rmd.orig |only bcdata-0.1.2/bcdata/vignettes/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd |only bcdata-0.1.2/bcdata/vignettes/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd.orig |only bcdata-0.1.2/bcdata/vignettes/precompile.R |only bcdata-0.1.2/bcdata/vignettes/vignette-fig-air_zones-1.png |only bcdata-0.1.2/bcdata/vignettes/vignette-fig-bbox-1.png |only bcdata-0.1.2/bcdata/vignettes/vignette-fig-district_parks-1.png |only bcdata-0.1.2/bcdata/vignettes/vignette-fig-districts-1.png |only bcdata-0.1.2/bcdata/vignettes/vignette-fig-dp_join-1.png |only bcdata-0.1.2/bcdata/vignettes/vignette-fig-regional_districts-1.png |only 52 files changed, 1247 insertions(+), 471 deletions(-)
Title: Command-Line Argument Parser
Description: Cross-platform command-line argument parser written purely in R
with no external dependencies. It is useful with the Rscript
front-end and facilitates turning an R script into an executable script.
Author: David J. H. Shih
Maintainer: David J. H. Shih <djh.shih@gmail.com>
Diff between argparser versions 0.4 dated 2016-04-04 and 0.6 dated 2019-12-17
DESCRIPTION | 10 - MD5 | 33 +++--- NAMESPACE | 1 R/argparser.R | 263 +++++++++++++++++++++++++++++++++++++++--------- R/include.R |only README.md | 23 ++-- demo/00Index | 1 demo/sum.R | 10 + demo/sum2.R |only man/add.argument.Rd | 12 +- man/add_argument.Rd | 16 ++ man/arg.parser.Rd | 1 man/arg_parser.Rd | 10 + man/argparser.Rd | 2 man/include.Rd |only man/parse.args.Rd | 1 man/parse_args.Rd | 1 man/print.arg.parser.Rd | 1 man/show_arg_labels.Rd |only man/spaces.Rd |only 20 files changed, 294 insertions(+), 91 deletions(-)
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>
Diff between CB2 versions 1.2.2 dated 2019-12-03 and 1.3.0 dated 2019-12-17
CB2-1.2.2/CB2/inst/extdata/Shifrut_et_al_2018_Cell.csv |only CB2-1.3.0/CB2/DESCRIPTION | 12 CB2-1.3.0/CB2/MD5 | 49 ++- CB2-1.3.0/CB2/NAMESPACE | 6 CB2-1.3.0/CB2/R/RcppExports.R | 6 CB2-1.3.0/CB2/R/helpers.R | 48 +++ CB2-1.3.0/CB2/R/utils.R | 24 + CB2-1.3.0/CB2/README.md | 10 CB2-1.3.0/CB2/build/vignette.rds |binary CB2-1.3.0/CB2/inst/doc/cb2-input-handling.R |only CB2-1.3.0/CB2/inst/doc/cb2-input-handling.Rmd |only CB2-1.3.0/CB2/inst/doc/cb2-input-handling.html |only CB2-1.3.0/CB2/inst/doc/cb2-tutorial.R | 38 +-- CB2-1.3.0/CB2/inst/doc/cb2-tutorial.Rmd | 2 CB2-1.3.0/CB2/inst/doc/cb2-tutorial.html | 212 ++++++++--------- CB2-1.3.0/CB2/inst/extdata/toydata/gzipped |only CB2-1.3.0/CB2/man/plot_count_distribution.Rd | 4 CB2-1.3.0/CB2/man/quant.Rd | 4 CB2-1.3.0/CB2/man/run_sgrna_quant.Rd | 8 CB2-1.3.0/CB2/src/AdaptiveHash.h | 164 +++++++------ CB2-1.3.0/CB2/src/CB2.cpp | 12 CB2-1.3.0/CB2/src/RcppExports.cpp | 8 CB2-1.3.0/CB2/tests/testthat/test.toydata.R | 42 ++- CB2-1.3.0/CB2/vignettes/cb2-count-matrix.R |only CB2-1.3.0/CB2/vignettes/cb2-input-handling.Rmd |only CB2-1.3.0/CB2/vignettes/cb2-tutorial.Rmd | 2 CB2-1.3.0/CB2/vignettes/references.bib |only 27 files changed, 376 insertions(+), 275 deletions(-)