Title: Helper Functions for Regression Analysis
Description: A set of functions used to automate commonly used methods in
regression analysis. This includes plotting interactions, and calculating
simple slopes, standardized coefficients, regions of significance
(Johnson & Neyman, 1936; cf. Spiller et al., 2012), etc. See the reghelper
documentation for more information, documentation, and examples.
Author: Jeffrey Hughes [aut, cre]
Maintainer: Jeffrey Hughes <jeff.hughes@gmail.com>
Diff between reghelper versions 0.3.6 dated 2020-04-16 and 1.0.0 dated 2020-09-07
DESCRIPTION | 15 +++-- MD5 | 22 ++++---- NAMESPACE | 2 NEWS.md | 128 ++++++++++++++++++++++++++++++++++----------------- R/beta.R | 79 ------------------------------- R/helper_functions.R | 107 ------------------------------------------ R/sig_regions.R | 2 R/simple_slopes.R | 88 ++++++++++++++++++----------------- README.md | 81 +++++++++++++++----------------- man/beta.Rd | 10 --- man/sig_regions.Rd | 2 man/simple_slopes.Rd | 3 - 12 files changed, 194 insertions(+), 345 deletions(-)
Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques.
Intrinsic dimension estimation methods for exploratory analysis are also provided.
For more details on the package, see the paper by You (2020) <arXiv:2005.11107>.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>),
Changhee Suh [ctb]
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between Rdimtools versions 1.0.3 dated 2020-05-22 and 1.0.4 dated 2020-09-07
Rdimtools-1.0.3/Rdimtools/R/linear_CSCORE.R |only Rdimtools-1.0.3/Rdimtools/R/linear_CSCOREG.R |only Rdimtools-1.0.3/Rdimtools/R/linear_DISR.R |only Rdimtools-1.0.3/Rdimtools/R/linear_FSCORE.R |only Rdimtools-1.0.3/Rdimtools/R/linear_LSCORE.R |only Rdimtools-1.0.3/Rdimtools/R/linear_LSDF.R |only Rdimtools-1.0.3/Rdimtools/R/linear_LSLS.R |only Rdimtools-1.0.3/Rdimtools/R/linear_LSPE.R |only Rdimtools-1.0.3/Rdimtools/R/linear_MCFS.R |only Rdimtools-1.0.3/Rdimtools/R/linear_NRSR.R |only Rdimtools-1.0.3/Rdimtools/R/linear_RSR.R |only Rdimtools-1.0.3/Rdimtools/R/linear_SPECS.R |only Rdimtools-1.0.3/Rdimtools/R/linear_SPECU.R |only Rdimtools-1.0.3/Rdimtools/R/linear_SPUFS.R |only Rdimtools-1.0.3/Rdimtools/R/linear_UDFS.R |only Rdimtools-1.0.3/Rdimtools/R/ver2_linear_ENET.R |only Rdimtools-1.0.3/Rdimtools/R/ver2_linear_LASSO.R |only Rdimtools-1.0.3/Rdimtools/man/linear_CSCORE.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_CSCOREG.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_DISR.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_ENET.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_FSCORE.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_LASSO.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_LSCORE.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_LSDF.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_LSLS.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_LSPE.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_MCFS.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_NRSR.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_RSR.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_SPECS.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_SPECU.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_SPUFS.Rd |only Rdimtools-1.0.3/Rdimtools/man/linear_UDFS.Rd |only Rdimtools-1.0.4/Rdimtools/DESCRIPTION | 19 - Rdimtools-1.0.4/Rdimtools/MD5 | 119 +++++---- Rdimtools-1.0.4/Rdimtools/NAMESPACE | 9 Rdimtools-1.0.4/Rdimtools/NEWS.md | 7 Rdimtools-1.0.4/Rdimtools/R/RcppExports.R | 4 Rdimtools-1.0.4/Rdimtools/R/Rdimtools-package.R | 5 Rdimtools-1.0.4/Rdimtools/R/feature_CSCORE.R |only Rdimtools-1.0.4/Rdimtools/R/feature_CSCOREG.R |only Rdimtools-1.0.4/Rdimtools/R/feature_DISR.R |only Rdimtools-1.0.4/Rdimtools/R/feature_FSCORE.R |only Rdimtools-1.0.4/Rdimtools/R/feature_LSCORE.R |only Rdimtools-1.0.4/Rdimtools/R/feature_LSDF.R |only Rdimtools-1.0.4/Rdimtools/R/feature_LSLS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_LSPE.R |only Rdimtools-1.0.4/Rdimtools/R/feature_MCFS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_MIFS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_NRSR.R |only Rdimtools-1.0.4/Rdimtools/R/feature_PROCRUSTES.R |only Rdimtools-1.0.4/Rdimtools/R/feature_RSR.R |only Rdimtools-1.0.4/Rdimtools/R/feature_SPECS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_SPECU.R |only Rdimtools-1.0.4/Rdimtools/R/feature_SPUFS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_UDFS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_UGFS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_UWDFS.R |only Rdimtools-1.0.4/Rdimtools/R/feature_WDFS.R |only Rdimtools-1.0.4/Rdimtools/R/nonlinear_FASTMAP.R | 8 Rdimtools-1.0.4/Rdimtools/R/ver2_feature_ENET.R |only Rdimtools-1.0.4/Rdimtools/R/ver2_feature_LASSO.R |only Rdimtools-1.0.4/Rdimtools/README.md | 29 +- Rdimtools-1.0.4/Rdimtools/build/partial.rdb |binary Rdimtools-1.0.4/Rdimtools/build/vignette.rds |binary Rdimtools-1.0.4/Rdimtools/inst/REFERENCES.bib | 51 +++ Rdimtools-1.0.4/Rdimtools/inst/doc/quick-start.R | 5 Rdimtools-1.0.4/Rdimtools/inst/doc/quick-start.Rmd | 19 + Rdimtools-1.0.4/Rdimtools/man/feature_CSCORE.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_CSCOREG.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_DISR.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_ENET.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_FSCORE.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_LASSO.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_LSCORE.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_LSDF.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_LSLS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_LSPE.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_MCFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_MIFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_NRSR.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_PROCRUSTES.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_RSR.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_SPECS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_SPECU.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_SPUFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_UDFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_UGFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_UWDFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/feature_WDFS.Rd |only Rdimtools-1.0.4/Rdimtools/man/figures/README-unnamed-chunk-2-1.png |binary Rdimtools-1.0.4/Rdimtools/man/figures/README-unnamed-chunk-3-1.png |only Rdimtools-1.0.4/Rdimtools/man/nonlinear_FastMap.Rd | 4 Rdimtools-1.0.4/Rdimtools/man/package-Rdimtools.Rd | 2 Rdimtools-1.0.4/Rdimtools/src/RcppExports.cpp | 12 Rdimtools-1.0.4/Rdimtools/src/ver2_computation.cpp | 43 +++ Rdimtools-1.0.4/Rdimtools/src/ver2_computation.h | 2 Rdimtools-1.0.4/Rdimtools/vignettes/quick-start.Rmd | 19 + Rdimtools-1.0.4/Rdimtools/vignettes/quick-start.html | 130 +++++----- 100 files changed, 333 insertions(+), 154 deletions(-)
Title: Miscellaneous Tools for the 'R4Epis' Project
Description: Contains tools for formatting inline code, renaming redundant
columns, aggregating age categories, and calculating proportions with
confidence intervals. This is part of the 'R4Epis' project
<https://r4epis.netlify.com>.
Author: Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>),
Dirk Schumacher [aut],
Alex Spina [ctb],
Kate Doyle [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between epikit versions 0.1.1 dated 2020-04-13 and 0.1.2 dated 2020-09-07
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- NEWS.md | 7 +++++++ R/age-categories.R | 4 ++-- R/cfr.R | 5 +++-- R/find_breaks.R | 2 +- R/inline_fun.R | 5 +++-- R/unite_ci.R | 2 +- README.md | 18 +++++++++++------- build/vignette.rds |binary inst/doc/intro.html | 36 ++++++++++++++++++++---------------- man/attack_rate.Rd | 2 +- man/find_breaks.Rd | 2 +- man/fmt_ci.Rd | 5 +++-- tests/testthat/test-proportion.R | 27 +++++++++++++++++++++++++++ 15 files changed, 100 insertions(+), 55 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.4.3 dated 2020-03-28 and 3.4.4 dated 2020-09-07
callr-3.4.3/callr/inst/doc |only callr-3.4.4/callr/DESCRIPTION | 8 - callr-3.4.4/callr/MD5 | 64 +++++++-------- callr-3.4.4/callr/NEWS.md | 6 + callr-3.4.4/callr/R/hook.R | 12 ++ callr-3.4.4/callr/R/r-session.R | 85 +++++++++++++++------ callr-3.4.4/callr/README.md | 4 callr-3.4.4/callr/man/callr.Rd | 4 callr-3.4.4/callr/man/convert_and_check_my_args.Rd | 4 callr-3.4.4/callr/man/default_repos.Rd | 4 callr-3.4.4/callr/man/get_result.Rd | 4 callr-3.4.4/callr/man/new_callr_error.Rd | 4 callr-3.4.4/callr/man/r.Rd | 6 - callr-3.4.4/callr/man/r_bg.Rd | 4 callr-3.4.4/callr/man/r_copycat.Rd | 4 callr-3.4.4/callr/man/r_process.Rd | 8 - callr-3.4.4/callr/man/r_process_options.Rd | 4 callr-3.4.4/callr/man/r_session.Rd | 56 +++++++++---- callr-3.4.4/callr/man/r_session_debug.Rd | 4 callr-3.4.4/callr/man/r_session_options.Rd | 4 callr-3.4.4/callr/man/r_vanilla.Rd | 4 callr-3.4.4/callr/man/rcmd.Rd | 4 callr-3.4.4/callr/man/rcmd_bg.Rd | 4 callr-3.4.4/callr/man/rcmd_copycat.Rd | 4 callr-3.4.4/callr/man/rcmd_process.Rd | 7 - callr-3.4.4/callr/man/rcmd_process_options.Rd | 4 callr-3.4.4/callr/man/rcmd_safe.Rd | 4 callr-3.4.4/callr/man/reexports.Rd | 9 -- callr-3.4.4/callr/man/rscript.Rd | 4 callr-3.4.4/callr/man/rscript_process.Rd | 7 - callr-3.4.4/callr/man/rscript_process_options.Rd | 4 callr-3.4.4/callr/tests/testthat/test-libpath.R | 19 ++++ callr-3.4.4/callr/tests/testthat/test-r-session.R | 16 +++ 33 files changed, 205 insertions(+), 174 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available.
Author: Maximilian Boeck [aut, cre] (<https://orcid.org/0000-0001-6024-8305>),
Martin Feldkircher [aut] (<https://orcid.org/0000-0002-5511-9215>),
Florian Huber [aut] (<https://orcid.org/0000-0002-2896-7921>),
Christopher Sims [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@wu.ac.at>
Diff between BGVAR versions 2.1.0 dated 2020-09-07 and 2.1.1 dated 2020-09-07
BGVAR-2.1.0/BGVAR/man/coef.bgvar.Rd |only BGVAR-2.1.0/BGVAR/man/fitted.bgvar.Rd |only BGVAR-2.1.0/BGVAR/man/logLik.bgvar.Rd |only BGVAR-2.1.0/BGVAR/man/lps.bgvar.pred.Rd |only BGVAR-2.1.0/BGVAR/man/residuals.bgvar.Rd |only BGVAR-2.1.0/BGVAR/man/rmse.bgvar.predict.Rd |only BGVAR-2.1.0/BGVAR/man/summary.bgvar.Rd |only BGVAR-2.1.0/BGVAR/man/vcov.bgvar.Rd |only BGVAR-2.1.1/BGVAR/DESCRIPTION | 6 +++--- BGVAR-2.1.1/BGVAR/MD5 | 26 +++++++++++++------------- BGVAR-2.1.1/BGVAR/NAMESPACE | 2 ++ BGVAR-2.1.1/BGVAR/R/bgvar.R | 20 ++++++++++---------- BGVAR-2.1.1/BGVAR/R/predict.R | 20 ++++++++++++++++---- BGVAR-2.1.1/BGVAR/man/bgvar.Rd | 4 ++-- BGVAR-2.1.1/BGVAR/man/coef.Rd |only BGVAR-2.1.1/BGVAR/man/fitted.Rd |only BGVAR-2.1.1/BGVAR/man/logLik.Rd |only BGVAR-2.1.1/BGVAR/man/lps.Rd |only BGVAR-2.1.1/BGVAR/man/residuals.Rd |only BGVAR-2.1.1/BGVAR/man/rmse.Rd |only BGVAR-2.1.1/BGVAR/man/summary.Rd |only BGVAR-2.1.1/BGVAR/man/vcov.Rd |only 22 files changed, 46 insertions(+), 32 deletions(-)
Title: A Driver Discovery Tool for Cancer Whole Genomes
Description: A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data. The method is part of the following publication: Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Molecular Cell (2020) <doi:10.1016/j.molcel.2019.12.027>.
Author: Juri Reimand [aut, cre],
Helen Zhu [aut]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
Diff between ActiveDriverWGS versions 1.0.1 dated 2019-03-22 and 1.1.0 dated 2020-09-07
DESCRIPTION | 27 - MD5 | 66 ++- NAMESPACE | 1 NEWS.md |only R/ADWGS_test.R | 490 ++++++++++++++++++---------- R/ActiveDriverWGS.R | 399 ++++++++++++++--------- R/cancer_gene_sites-data.R | 6 R/cancer_genes-data.R | 2 R/cll-data.R | 2 R/format_muts.R | 196 ++++++----- R/prepare_elements.R | 73 +++- README.md | 96 ++++- build/vignette.rds |binary data/cancer_gene_sites.RData |binary inst/doc/ActiveDriverWGSR.R | 32 + inst/doc/ActiveDriverWGSR.Rmd | 73 ++-- inst/doc/ActiveDriverWGSR.html | 568 +++++++++++++++++++++++---------- inst/extdata/chr17.PTM_sites.bed |only inst/extdata/mini.ptm.bed |only inst/extdata/ptm_chrom_error.bed |only inst/extdata/ptm_column_error.bed |only inst/extdata/ptm_id_error.bed |only inst/extdata/ptm_str_coords_error.bed |only man/ADWGS_test.Rd | 25 - man/ActiveDriverWGS.Rd | 29 + man/cancer_gene_sites.Rd | 12 man/cancer_genes.Rd | 8 man/cll_mutations.Rd | 8 man/dot-get_3n_context_of_mutations.Rd | 4 man/format_muts.Rd | 8 man/prepare_elements_from_BED4.Rd |only tests/testthat.R | 4 tests/testthat/test_ADWGS_test.R | 7 tests/testthat/test_ActiveDriverWGS.R | 3 tests/testthat/test_format_muts.R | 36 -- tests/testthat/test_input_format.R | 27 + tests/testthat/test_prepare_elements.R | 57 +++ vignettes/ActiveDriverWGSR.Rmd | 73 ++-- 38 files changed, 1581 insertions(+), 751 deletions(-)
More information about ActiveDriverWGS at CRAN
Permanent link
Title: A Framework for Various Types of Mortality / Life Tables
Description: Classes to implement and plot cohort life tables
for actuarial calculations. In particular, birth-year dependent mortality
tables using a yearly trend to extrapolate from a base year are implemented,
as well as period life table, cohort life tables using an age shift, and
merged life tables.
Author: Reinhold Kainhofer [aut, cre]
Maintainer: Reinhold Kainhofer <reinhold@kainhofer.com>
Diff between MortalityTables versions 2.0 dated 2020-08-26 and 2.0.1 dated 2020-09-07
DESCRIPTION | 12 + MD5 | 16 +- R/mortalityTables.list.R | 24 ++- R/mortalityTables.load.R | 66 +++++----- inst/doc/using-the-mortalityTables-package.Rmd | 74 +++++------ inst/doc/using-the-mortalityTables-package.html | 157 ++++++++---------------- man/MortalityTables-package.Rd | 1 man/mortalityTables.load.Rd | 6 vignettes/using-the-mortalityTables-package.Rmd | 74 +++++------ 9 files changed, 204 insertions(+), 226 deletions(-)
More information about MortalityTables at CRAN
Permanent link
Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between GJRM versions 0.2-2 dated 2020-02-07 and 0.2-3 dated 2020-09-07
GJRM-0.2-2/GJRM/R/gamlss.r |only GJRM-0.2-3/GJRM/ChangeLog | 7 GJRM-0.2-3/GJRM/DESCRIPTION | 8 GJRM-0.2-3/GJRM/MD5 | 338 ++++----- GJRM-0.2-3/GJRM/NAMESPACE | 12 GJRM-0.2-3/GJRM/R/AT.r | 34 GJRM-0.2-3/GJRM/R/BCDF.r | 4 GJRM-0.2-3/GJRM/R/BiCDF.r | 4 GJRM-0.2-3/GJRM/R/CopulaCLM.r | 13 GJRM-0.2-3/GJRM/R/Dpens.R | 2 GJRM-0.2-3/GJRM/R/Dpens2.R | 5 GJRM-0.2-3/GJRM/R/H.tri.r | 30 GJRM-0.2-3/GJRM/R/H.triESS.r | 28 GJRM-0.2-3/GJRM/R/H.triSS.r | 26 GJRM-0.2-3/GJRM/R/LM.bpm.r | 7 GJRM-0.2-3/GJRM/R/OR.r | 14 GJRM-0.2-3/GJRM/R/PE.r | 22 GJRM-0.2-3/GJRM/R/PosDefCor.R | 1 GJRM-0.2-3/GJRM/R/RR.r | 14 GJRM-0.2-3/GJRM/R/Reg2Copost.r | 1 GJRM-0.2-3/GJRM/R/SemiParBIV.fit.post.r | 14 GJRM-0.2-3/GJRM/R/SemiParBIV.r | 71 + GJRM-0.2-3/GJRM/R/SemiParTRIV.fit.post.r | 4 GJRM-0.2-3/GJRM/R/SemiParTRIV.r | 13 GJRM-0.2-3/GJRM/R/Tweedie.Functions.R |only GJRM-0.2-3/GJRM/R/Xdpred.r | 48 + GJRM-0.2-3/GJRM/R/ass.dp.r | 3 GJRM-0.2-3/GJRM/R/ass.ms.r | 5 GJRM-0.2-3/GJRM/R/bCopulaCLMgHsCont.R | 28 GJRM-0.2-3/GJRM/R/bcont.R | 29 GJRM-0.2-3/GJRM/R/bcont23.R | 25 GJRM-0.2-3/GJRM/R/bcont23twoParC.R | 21 GJRM-0.2-3/GJRM/R/bcont3.R | 19 GJRM-0.2-3/GJRM/R/bcont32.R | 25 GJRM-0.2-3/GJRM/R/bcont32twoParC.R | 20 GJRM-0.2-3/GJRM/R/bcont3twoParC.R | 19 GJRM-0.2-3/GJRM/R/bcontROB.R | 23 GJRM-0.2-3/GJRM/R/bcontSurv.R | 28 GJRM-0.2-3/GJRM/R/bcontSurvG.R | 23 GJRM-0.2-3/GJRM/R/bcontSurvGDep.R | 23 GJRM-0.2-3/GJRM/R/bcontSurvGDepA.R |only GJRM-0.2-3/GJRM/R/bcontSurvGcont2Surv.R | 21 GJRM-0.2-3/GJRM/R/bcontSurvGuniv.R | 11 GJRM-0.2-3/GJRM/R/bcontSurvGunivI.R | 32 GJRM-0.2-3/GJRM/R/bcontSurvGunivI_ExcessHazard.R |only GJRM-0.2-3/GJRM/R/bcontSurvGunivInform.r | 14 GJRM-0.2-3/GJRM/R/bcontSurvGunivL.R | 14 GJRM-0.2-3/GJRM/R/bcontSurvGunivL_ExcessHazard.R |only GJRM-0.2-3/GJRM/R/bcontSurvGunivMIXED.R | 33 GJRM-0.2-3/GJRM/R/bcontSurvGunivMIXED_ExcessHazard.R |only GJRM-0.2-3/GJRM/R/bcontSurvGunivMIXED_LeftTruncation.R |only GJRM-0.2-3/GJRM/R/bcontSurvGuniv_ExcessHazard.R |only GJRM-0.2-3/GJRM/R/bconttwoParC.R | 18 GJRM-0.2-3/GJRM/R/bcorrec.R | 52 - GJRM-0.2-3/GJRM/R/bcorrec2.R | 13 GJRM-0.2-3/GJRM/R/bcorrecDiscr.R | 31 GJRM-0.2-3/GJRM/R/bcorrecFuncs.R | 152 ++-- GJRM-0.2-3/GJRM/R/bdiscrcont.R | 41 - GJRM-0.2-3/GJRM/R/bdiscrcont12.R | 41 - GJRM-0.2-3/GJRM/R/bdiscrcont13.R | 30 GJRM-0.2-3/GJRM/R/bdiscrcont23.R | 29 GJRM-0.2-3/GJRM/R/bdiscrdiscr.R | 48 - GJRM-0.2-3/GJRM/R/bdiscrdiscr11.R | 48 - GJRM-0.2-3/GJRM/R/bdiscrdiscr12.R | 49 - GJRM-0.2-3/GJRM/R/bprobgHs.r | 38 - GJRM-0.2-3/GJRM/R/bprobgHsCont.r | 26 GJRM-0.2-3/GJRM/R/bprobgHsCont3.r | 20 GJRM-0.2-3/GJRM/R/bprobgHsCont3SS.r | 17 GJRM-0.2-3/GJRM/R/bprobgHsCont3binTW.r |only GJRM-0.2-3/GJRM/R/bprobgHsContSS.r | 19 GJRM-0.2-3/GJRM/R/bprobgHsContUniv.r | 17 GJRM-0.2-3/GJRM/R/bprobgHsContUniv3.r | 12 GJRM-0.2-3/GJRM/R/bprobgHsContUnivBIN.r | 11 GJRM-0.2-3/GJRM/R/bprobgHsDiscr1.r | 40 - GJRM-0.2-3/GJRM/R/bprobgHsDiscr1SS.r | 27 GJRM-0.2-3/GJRM/R/bprobgHsDiscr2.r | 40 - GJRM-0.2-3/GJRM/R/bprobgHsDiscr2SS.r | 27 GJRM-0.2-3/GJRM/R/bprobgHsFixTheta.r | 31 GJRM-0.2-3/GJRM/R/bprobgHsPO.r | 20 GJRM-0.2-3/GJRM/R/bprobgHsPO0.r | 17 GJRM-0.2-3/GJRM/R/bprobgHsSS.r | 31 GJRM-0.2-3/GJRM/R/bprobgHstwoParC.r | 31 GJRM-0.2-3/GJRM/R/conv.check.r | 22 GJRM-0.2-3/GJRM/R/copgHs.r | 93 -- GJRM-0.2-3/GJRM/R/copgHs2.r | 26 GJRM-0.2-3/GJRM/R/copgHs3.r | 21 GJRM-0.2-3/GJRM/R/copgHsAT.r | 35 GJRM-0.2-3/GJRM/R/copgHsCond.r | 10 GJRM-0.2-3/GJRM/R/copgHsCont.r | 138 +-- GJRM-0.2-3/GJRM/R/copulaReg.fit.post.r | 4 GJRM-0.2-3/GJRM/R/copulaSampleSel.fit.post.r | 4 GJRM-0.2-3/GJRM/R/copulaSampleSel.r | 13 GJRM-0.2-3/GJRM/R/cv.inform.r | 8 GJRM-0.2-3/GJRM/R/distrHs.r | 216 +++-- GJRM-0.2-3/GJRM/R/distrHsAT.r | 53 - GJRM-0.2-3/GJRM/R/distrHsAT1.r | 23 GJRM-0.2-3/GJRM/R/distrHsATDiscr.r | 40 - GJRM-0.2-3/GJRM/R/distrHsATDiscr2.r | 27 GJRM-0.2-3/GJRM/R/distrHsDiscr.r | 118 +-- GJRM-0.2-3/GJRM/R/dof.tr.R | 3 GJRM-0.2-3/GJRM/R/edf.loop.r | 18 GJRM-0.2-3/GJRM/R/enu.tr.R | 32 GJRM-0.2-3/GJRM/R/eta.tr.R | 32 GJRM-0.2-3/GJRM/R/func.OPT.r | 15 GJRM-0.2-3/GJRM/R/g.tri.r | 48 - GJRM-0.2-3/GJRM/R/g.triESS.r | 46 - GJRM-0.2-3/GJRM/R/g.triSS.r | 40 - GJRM-0.2-3/GJRM/R/gamlss.R |only GJRM-0.2-3/GJRM/R/gamlss.fit.post.r | 2 GJRM-0.2-3/GJRM/R/ggmtrust.R | 6 GJRM-0.2-3/GJRM/R/gjrm.r | 106 +- GJRM-0.2-3/GJRM/R/hazsurv.plot.r | 621 +++++++++++------ GJRM-0.2-3/GJRM/R/imputeCounter.r | 64 - GJRM-0.2-3/GJRM/R/imputeSS.r | 44 - GJRM-0.2-3/GJRM/R/int.postcheck.R | 39 - GJRM-0.2-3/GJRM/R/jc.probs.r | 19 GJRM-0.2-3/GJRM/R/jc.probs1.r | 276 +++---- GJRM-0.2-3/GJRM/R/jc.probs2.r | 116 +-- GJRM-0.2-3/GJRM/R/jc.probs3.r | 52 - GJRM-0.2-3/GJRM/R/jc.probs4.r | 68 - GJRM-0.2-3/GJRM/R/jc.probs5.r | 80 +- GJRM-0.2-3/GJRM/R/jc.probs6.r | 90 +- GJRM-0.2-3/GJRM/R/jc.probs7.r | 72 - GJRM-0.2-3/GJRM/R/lmc.R | 155 +++- GJRM-0.2-3/GJRM/R/logLik.lmc.r |only GJRM-0.2-3/GJRM/R/mm.r | 9 GJRM-0.2-3/GJRM/R/mmf.r | 9 GJRM-0.2-3/GJRM/R/numch.r | 44 - GJRM-0.2-3/GJRM/R/numgh.r | 57 - GJRM-0.2-3/GJRM/R/overall.svG.R | 14 GJRM-0.2-3/GJRM/R/pen.r | 1 GJRM-0.2-3/GJRM/R/plot.SemiParBIV.r | 24 GJRM-0.2-3/GJRM/R/post.check.R | 37 - GJRM-0.2-3/GJRM/R/postVb.r | 12 GJRM-0.2-3/GJRM/R/pream.wm.r | 16 GJRM-0.2-3/GJRM/R/pred.gp.r | 23 GJRM-0.2-3/GJRM/R/predict.CopulaCLM.r | 2 GJRM-0.2-3/GJRM/R/prev.r | 23 GJRM-0.2-3/GJRM/R/print.summary.gamlss.r | 2 GJRM-0.2-3/GJRM/R/probm.R | 28 GJRM-0.2-3/GJRM/R/probmS.R | 18 GJRM-0.2-3/GJRM/R/r.resp.R | 17 GJRM-0.2-3/GJRM/R/rIC.R | 37 - GJRM-0.2-3/GJRM/R/rMVN.r | 2 GJRM-0.2-3/GJRM/R/regH.r | 2 GJRM-0.2-3/GJRM/R/resp.check.R | 19 GJRM-0.2-3/GJRM/R/rob.const.R | 8 GJRM-0.2-3/GJRM/R/rob.int.R | 24 GJRM-0.2-3/GJRM/R/sim.resp.R | 12 GJRM-0.2-3/GJRM/R/startsn.r | 2 GJRM-0.2-3/GJRM/R/summary.SemiParBIV.r | 20 GJRM-0.2-3/GJRM/R/summary.SemiParTRIV.r | 3 GJRM-0.2-3/GJRM/R/summary.copulaSampleSel.r | 1 GJRM-0.2-3/GJRM/R/summary.gamlss.r | 1 GJRM-0.2-3/GJRM/R/summary.gjrm.r | 1 GJRM-0.2-3/GJRM/R/survExcInd.r |only GJRM-0.2-3/GJRM/R/susu.r | 18 GJRM-0.2-3/GJRM/R/susutsn.r | 18 GJRM-0.2-3/GJRM/R/teta.tr.R | 17 GJRM-0.2-3/GJRM/R/triprobgHs.R | 53 - GJRM-0.2-3/GJRM/R/triprobgHsESS.R | 35 GJRM-0.2-3/GJRM/R/triprobgHsSS.R | 30 GJRM-0.2-3/GJRM/R/working.comp.r | 21 GJRM-0.2-3/GJRM/man/GJRM-package.Rd | 17 GJRM-0.2-3/GJRM/man/bprobgHsCont.Rd | 1 GJRM-0.2-3/GJRM/man/bprobgHsContUniv.Rd | 5 GJRM-0.2-3/GJRM/man/eta.tr.Rd | 3 GJRM-0.2-3/GJRM/man/gamlss.Rd | 163 +++- GJRM-0.2-3/GJRM/man/gjrm.Rd | 33 GJRM-0.2-3/GJRM/man/hazsurv.plot.Rd | 28 GJRM-0.2-3/GJRM/man/jc.probs.Rd | 10 GJRM-0.2-3/GJRM/man/lmc.Rd | 55 + GJRM-0.2-3/GJRM/man/logLik.SemiParBIV.Rd | 1 GJRM-0.2-3/GJRM/man/resp.check.Rd | 6 GJRM-0.2-3/GJRM/man/rob.int.Rd | 1 GJRM-0.2-3/GJRM/man/summary.gamlss.Rd | 16 176 files changed, 3359 insertions(+), 2647 deletions(-)
Title: Identification, Tuning, Visualisation and Analysis of Labour
Market Areas
Description: Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.
Author: Daniela Ichim, Luisa Franconi, Michele D'Alo', Guido van den Heuvel
Maintainer: Luisa Franconi <franconi@istat.it>
Diff between LabourMarketAreas versions 3.2.4 dated 2020-03-03 and 3.2.5 dated 2020-09-07
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- data/shpBrindisi.rda |binary data/shpSardinia.rda |binary man/LabourMarketAreas-package.Rd | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
More information about LabourMarketAreas at CRAN
Permanent link
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell [aut, cre],
Ken Aho [ctb],
Andreas Alfons [ctb],
Nanina Anderegg [ctb],
Tomas Aragon [ctb],
Chandima Arachchige [ctb],
Antti Arppe [ctb],
Adrian Baddeley [ctb],
Kamil Barton [ctb],
Ben Bolker [ctb],
Hans W. Borchers [ctb],
Frederico Caeiro [ctb],
Stephane Champely [ctb],
Daniel Chessel [ctb],
Leanne Chhay [ctb],
Clint Cummins [ctb],
Michael Dewey [ctb],
Harold C. Doran [ctb],
Stephane Dray [ctb],
Charles Dupont [ctb],
Dirk Eddelbuettel [ctb],
Claus Ekstrom [ctb],
Martin Elff [ctb],
Jeff Enos [ctb],
Richard W. Farebrother [ctb],
John Fox [ctb],
Romain Francois [ctb],
Michael Friendly [ctb],
Tal Galili [ctb],
Matthias Gamer [ctb],
Joseph L. Gastwirth [ctb],
Vilmantas Gegzna [ctb],
Yulia R. Gel [ctb],
Juergen Gross [ctb],
Gabor Grothendieck [ctb],
Frank E. Harrell Jr [ctb],
Richard Heiberger [ctb],
Michael Hoehle [ctb],
Christian W. Hoffmann [ctb],
Soeren Hojsgaard [ctb],
Torsten Hothorn [ctb],
Markus Huerzeler [ctb],
Wallace W. Hui [ctb],
Pete Hurd [ctb],
Rob J. Hyndman [ctb],
Christopher Jackson [ctb],
Matthias Kohl [ctb],
Mikko Korpela [ctb],
Max Kuhn [ctb],
Detlew Labes [ctb],
Friederich Leisch [ctb],
Jim Lemon [ctb],
Dong Li [ctb],
Martin Maechler [ctb],
Arni Magnusson [ctb],
Ben Mainwaring [ctb],
Daniel Malter [ctb],
George Marsaglia [ctb],
John Marsaglia [ctb],
Alina Matei [ctb],
David Meyer [ctb],
Weiwen Miao [ctb],
Giovanni Millo [ctb],
Yongyi Min [ctb],
David Mitchell [ctb],
Franziska Mueller [ctb],
Markus Naepflin [ctb],
Daniel Navarro [ctb],
Henric Nilsson [ctb],
Klaus Nordhausen [ctb],
Derek Ogle [ctb],
Hong Ooi [ctb],
Nick Parsons [ctb],
Sandrine Pavoine [ctb],
Tony Plate [ctb],
Luke Prendergast [ctb],
Roland Rapold [ctb],
William Revelle [ctb],
Tyler Rinker [ctb],
Brian D. Ripley [ctb],
Caroline Rodriguez [ctb],
Nathan Russell [ctb],
Nick Sabbe [ctb],
Venkatraman E. Seshan [ctb],
Michael Smithson [ctb],
Greg Snow [ctb],
Karline Soetaert [ctb],
Werner A. Stahel [ctb],
Alec Stephenson [ctb],
Mark Stevenson [ctb],
Ralf Stubner [ctb],
Matthias Templ [ctb],
Duncan Temple Lang [ctb],
Terry Therneau [ctb],
Yves Tille [ctb],
Luis Torgo [ctb],
Adrian Trapletti [ctb],
Joshua Ulrich [ctb],
Kevin Ushey [ctb],
Jeremy VanDerWal [ctb],
Bill Venables [ctb],
John Verzani [ctb],
Pablo J. Villacorta Iglesias [ctb],
Gregory R. Warnes [ctb],
Stefan Wellek [ctb],
Hadley Wickham [ctb],
Rand R. Wilcox [ctb],
Peter Wolf [ctb],
Daniel Wollschlaeger [ctb],
Joseph Wood [ctb],
Ying Wu [ctb],
Thomas Yee [ctb],
Achim Zeileis [ctb]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.37 dated 2020-07-10 and 0.99.38 dated 2020-09-07
DESCRIPTION | 34 ++-- MD5 | 86 +++++----- NAMESPACE | 10 - NEWS | 41 ++++- R/Desc.R | 6 R/DescTools.r | 253 ++++++++++++++++++++----------- R/StatsAndCIs.r | 362 ++++++++++++++++++++++++++++++++++++++++----- README.md | 8 man/AddMonths.Rd | 2 man/AndersonDarlingTest.Rd | 2 man/BarnardTest.Rd | 6 man/BinomCIn.Rd |only man/BinomDiffCI.Rd | 22 ++ man/BubbleLegend.Rd | 2 man/ColorLegend.Rd | 9 - man/Conf.Rd | 2 man/CutQ.Rd | 6 man/Desc.Rd | 2 man/DigitSum.Rd | 2 man/DoCall.Rd | 4 man/Fibonacci.Rd | 2 man/Format.Rd | 24 +- man/Gini.Rd | 2 man/Large.Rd | 4 man/MADCI.Rd |only man/MAE.Rd | 2 man/Median.Rd | 2 man/MultinomCI.Rd | 2 man/ORToRelRisk.Rd | 55 +++++- man/PlotArea.Rd | 2 man/PlotCorr.Rd | 2 man/PlotWeb.Rd | 2 man/PoissonCI.Rd | 2 man/QuantileCI.Rd |only man/RevCode.Rd |only man/SiegelTukeyTest.Rd | 2 man/StrTrunc.Rd | 2 man/TOne.Rd | 42 +++-- man/ToWrd.Rd | 2 man/Unwhich.Rd | 2 man/WrdFont.Rd | 6 man/XLGetRange.Rd | 2 man/XLView.Rd | 4 man/d.countries.Rd | 4 man/d.periodic.Rd | 2 man/paste.Rd | 2 46 files changed, 745 insertions(+), 285 deletions(-)
Title: Critical Line Algorithm in Pure R
Description: Implements 'Markowitz' Critical Line Algorithm ('CLA') for classical
mean-variance portfolio optimization, see Markowitz (1952) <doi:10.2307/2975974>.
Care has been taken for correctness in light of previous buggy implementations.
Author: Yanhao Shi <syhelena@163.com>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between CLA versions 0.95-1 dated 2019-05-11 and 0.96-0 dated 2020-09-07
DESCRIPTION | 16 ++--- MD5 | 20 +++---- NAMESPACE | 2 R/CLA.R | 79 +++++++++++++++++++++++----- TODO | 6 +- build/partial.rdb |binary inst/NEWS.Rd | 20 +++++-- inst/xtraR/platform-sessionInfo.R | 25 ++++++--- man/CLA.Rd | 26 +++++++++ man/muS.10ex.Rd | 4 - tests/SP500-ex.R | 104 ++++++++++++++++++++++++++++++++------ 11 files changed, 237 insertions(+), 65 deletions(-)
Title: ROC Curve Inference with and without Covariates
Description: Estimates the pooled (unadjusted) Receiver Operating Characteristic (ROC) curve, the covariate-adjusted ROC (AROC) curve, and the covariate-specific/conditional ROC (cROC) curve by different methods, both Bayesian and frequentist. Also, it provides functions to obtain ROC-based optimal cutpoints utilizing several criteria. Based on Erkanli, A. et al. (2006) <doi:10.1002/sim.2496>; Faraggi, D. (2003) <doi:10.1111/1467-9884.00350>; Gu, J. et al. (2008) <doi:10.1002/sim.3366>; Inacio de Carvalho, V. et al. (2013) <doi:10.1214/13-BA825>; Inacio de Carvalho, V., and Rodriguez-Alvarez, M.X. (2018) <arXiv:1806.00473>; Janes, H., and Pepe, M.S. (2009) <doi:10.1093/biomet/asp002>; Pepe, M.S. (1998) <http://www.jstor.org/stable/2534001?seq=1>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1016/j.csda.2010.07.018>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1007/s11222-010-9184-1>. Please see Rodriguez-Alvarez, M.X. and Inacio, V. (20208) <arXiv:2003.13111> for more details.
Author: Maria Xose Rodriguez-Alvarez [aut, cre]
(<https://orcid.org/0000-0002-1329-9238>),
Vanda Inacio [aut] (<https://orcid.org/0000-0001-8084-1616>)
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between ROCnReg versions 1.0-2 dated 2020-07-05 and 1.0-3 dated 2020-09-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 +++++- R/get_vars_formula.R | 6 +++--- build/partial.rdb |binary man/AROC.sp.Rd | 2 +- man/ROCnReg-package.Rd | 4 ++-- man/cROC.sp.Rd | 4 ++-- 8 files changed, 24 insertions(+), 20 deletions(-)
Title: Combine Parameter Estimates via Parametric Bootstrap
Description: Propagate uncertainty from several estimates when combining these estimates via a function.
This is done by using the parametric bootstrap to simulate values from the distribution of each estimate to build up an empirical distribution of the combined parameter.
Finally either the percentile method is used or the highest density interval is chosen to derive a confidence interval for the combined parameter with the desired coverage.
References: Davison and Hinkley (1997,ISBN:0-521-57471-4) for the parametric bootstrap and percentile method, Gelman et al. (2014,ISBN:978-1-4398-4095-5) for the highest density interval, Stockdale et al. (2020)<doi:10.1016/j.jhep.2020.04.008> for an example of combining conditional prevalences.
Author: Marc Henrion [aut, cre] (<https://orcid.org/0000-0003-1242-839X>)
Maintainer: Marc Henrion <mhenrion@mlw.mw>
Diff between bootComb versions 0.2.0 dated 2020-08-20 and 1.0.0 dated 2020-09-07
bootComb-0.2.0/bootComb/man/simScen1.Rd |only bootComb-0.2.0/bootComb/man/simScen2.Rd |only bootComb-0.2.0/bootComb/man/ssPoisPar.Rd |only bootComb-1.0.0/bootComb/DESCRIPTION | 8 bootComb-1.0.0/bootComb/MD5 | 53 ++-- bootComb-1.0.0/bootComb/NAMESPACE | 12 bootComb-1.0.0/bootComb/NEWS.md | 32 +- bootComb-1.0.0/bootComb/R/adjustPrevalence.R | 11 bootComb-1.0.0/bootComb/R/bootComb.R | 19 - bootComb-1.0.0/bootComb/R/fitDistributionsToCIs.R | 179 +++++++++++++- bootComb-1.0.0/bootComb/R/internalFunctions.R | 218 +++++++++++++++--- bootComb-1.0.0/bootComb/R/simulations.R | 51 ++-- bootComb-1.0.0/bootComb/README.md | 17 - bootComb-1.0.0/bootComb/man/adjPrevSensSpec.Rd | 2 bootComb-1.0.0/bootComb/man/bootComb.Rd | 12 bootComb-1.0.0/bootComb/man/getBetaFromCI.Rd | 10 bootComb-1.0.0/bootComb/man/getExpFromCI.Rd |only bootComb-1.0.0/bootComb/man/getGammaFromCI.Rd |only bootComb-1.0.0/bootComb/man/getNegBinFromCI.Rd |only bootComb-1.0.0/bootComb/man/getNormFromCI.Rd | 10 bootComb-1.0.0/bootComb/man/getPoisFromCI.Rd | 12 bootComb-1.0.0/bootComb/man/identifyBetaPars.Rd | 10 bootComb-1.0.0/bootComb/man/identifyExpPars.Rd |only bootComb-1.0.0/bootComb/man/identifyGammaPars.Rd |only bootComb-1.0.0/bootComb/man/identifyNegBinPars.Rd |only bootComb-1.0.0/bootComb/man/identifyNormPars.Rd | 8 bootComb-1.0.0/bootComb/man/identifyPoisPars.Rd | 10 bootComb-1.0.0/bootComb/man/simScenPrevSensSpec.Rd |only bootComb-1.0.0/bootComb/man/simScenProductTwoPrevs.Rd |only bootComb-1.0.0/bootComb/man/ssBetaPars.Rd | 6 bootComb-1.0.0/bootComb/man/ssExpPars.Rd |only bootComb-1.0.0/bootComb/man/ssGammaPars.Rd |only bootComb-1.0.0/bootComb/man/ssNegBinPars.Rd |only bootComb-1.0.0/bootComb/man/ssNormPars.Rd | 6 bootComb-1.0.0/bootComb/man/ssPoisPars.Rd |only 35 files changed, 514 insertions(+), 172 deletions(-)
Title: Valence Aware Dictionary and sEntiment Reasoner (VADER)
Description: A lexicon and rule-based sentiment analysis tool that is specifically
attuned to sentiments expressed in social media, and works well on texts from other
domains. Hutto & Gilbert (2014) <https://www.aaai.org/ocs/index.php/ICWSM/ICWSM14/paper/view/8109/8122>.
Author: Katherine Roehrick [aut, cre]
Maintainer: Katherine Roehrick <kr.gitcode@gmail.com>
Diff between vader versions 0.2.0 dated 2020-09-04 and 0.2.1 dated 2020-09-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 9 ++++++++- R/globals.R | 2 +- R/vader_df.R | 19 +++++++++++++++++-- R/vader_main_call.R | 32 +++++++++++++++++++++----------- R/vader_sentiment_vector.R | 10 ++++------ man/get_vader.Rd | 6 +++++- man/vader_df.Rd | 10 +++------- 9 files changed, 70 insertions(+), 40 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package.
'pkgdown' converts your documentation, vignettes, 'README', and more to
'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pkgdown versions 1.5.1 dated 2020-04-09 and 1.6.0 dated 2020-09-07
pkgdown-1.5.1/pkgdown/R/highlight.r |only pkgdown-1.5.1/pkgdown/R/link-article-index.R |only pkgdown-1.5.1/pkgdown/R/link-href.R |only pkgdown-1.5.1/pkgdown/R/link-packages.R |only pkgdown-1.5.1/pkgdown/R/link-topic-index.R |only pkgdown-1.5.1/pkgdown/R/metadata.R |only pkgdown-1.5.1/pkgdown/R/replay-html.r |only pkgdown-1.5.1/pkgdown/man/reexports.Rd |only pkgdown-1.5.1/pkgdown/tests/testthat/test-highlight.R |only pkgdown-1.5.1/pkgdown/tests/testthat/test-link-href.R |only pkgdown-1.5.1/pkgdown/tests/testthat/test-link-packages.R |only pkgdown-1.5.1/pkgdown/tests/testthat/test-metadata.R |only pkgdown-1.5.1/pkgdown/tests/testthat/test-replay-html.R |only pkgdown-1.6.0/pkgdown/DESCRIPTION | 19 pkgdown-1.6.0/pkgdown/MD5 | 186 +++---- pkgdown-1.6.0/pkgdown/NAMESPACE | 18 pkgdown-1.6.0/pkgdown/NEWS.md | 78 +++ pkgdown-1.6.0/pkgdown/R/autolink_html.R | 39 - pkgdown-1.6.0/pkgdown/R/build-articles.R | 49 + pkgdown-1.6.0/pkgdown/R/build-favicons.R | 16 pkgdown-1.6.0/pkgdown/R/build-home-index.R | 9 pkgdown-1.6.0/pkgdown/R/build-home.R | 18 pkgdown-1.6.0/pkgdown/R/build-news.R | 24 pkgdown-1.6.0/pkgdown/R/build-reference.R | 34 - pkgdown-1.6.0/pkgdown/R/build.r | 79 ++- pkgdown-1.6.0/pkgdown/R/context.R | 99 +-- pkgdown-1.6.0/pkgdown/R/deploy-site.R | 14 pkgdown-1.6.0/pkgdown/R/figure.R | 29 - pkgdown-1.6.0/pkgdown/R/html-build.R | 8 pkgdown-1.6.0/pkgdown/R/html-tweak.R | 74 -- pkgdown-1.6.0/pkgdown/R/init.R | 9 pkgdown-1.6.0/pkgdown/R/markdown.R | 9 pkgdown-1.6.0/pkgdown/R/package.r | 28 - pkgdown-1.6.0/pkgdown/R/pkgdown.R | 12 pkgdown-1.6.0/pkgdown/R/rd-data.R | 4 pkgdown-1.6.0/pkgdown/R/rd-example.R | 87 ++- pkgdown-1.6.0/pkgdown/R/rd-html.R | 156 +++--- pkgdown-1.6.0/pkgdown/R/repo.R | 9 pkgdown-1.6.0/pkgdown/R/rmarkdown.R | 8 pkgdown-1.6.0/pkgdown/R/test.R | 30 - pkgdown-1.6.0/pkgdown/R/usage.R | 5 pkgdown-1.6.0/pkgdown/R/utils.r | 52 -- pkgdown-1.6.0/pkgdown/README.md | 6 pkgdown-1.6.0/pkgdown/build/pkgdown.pdf |only pkgdown-1.6.0/pkgdown/build/vignette.rds |binary pkgdown-1.6.0/pkgdown/inst/assets/pkgdown.css | 4 pkgdown-1.6.0/pkgdown/inst/doc/linking.Rmd | 6 pkgdown-1.6.0/pkgdown/inst/doc/linking.html | 46 + pkgdown-1.6.0/pkgdown/inst/doc/metadata.Rmd | 4 pkgdown-1.6.0/pkgdown/inst/doc/metadata.html | 48 + pkgdown-1.6.0/pkgdown/inst/doc/pkgdown.Rmd | 2 pkgdown-1.6.0/pkgdown/inst/doc/pkgdown.html | 48 + pkgdown-1.6.0/pkgdown/inst/doc/search.html | 46 + pkgdown-1.6.0/pkgdown/man/autolink_html.Rd | 26 - pkgdown-1.6.0/pkgdown/man/build_articles.Rd | 35 - pkgdown-1.6.0/pkgdown/man/build_home.Rd | 22 pkgdown-1.6.0/pkgdown/man/build_news.Rd | 2 pkgdown-1.6.0/pkgdown/man/build_reference.Rd | 5 pkgdown-1.6.0/pkgdown/man/build_site.Rd | 72 +- pkgdown-1.6.0/pkgdown/man/deploy_site_github.Rd | 7 pkgdown-1.6.0/pkgdown/man/deploy_to_branch.Rd | 3 pkgdown-1.6.0/pkgdown/man/index.Rd | 1 pkgdown-1.6.0/pkgdown/man/test-crayon.Rd | 1 pkgdown-1.6.0/pkgdown/man/test-dont.Rd | 13 pkgdown-1.6.0/pkgdown/man/test-figures.Rd | 4 pkgdown-1.6.0/pkgdown/man/test-links.Rd | 1 pkgdown-1.6.0/pkgdown/man/test-lists.Rd | 1 pkgdown-1.6.0/pkgdown/man/test-output-styles.Rd | 1 pkgdown-1.6.0/pkgdown/man/test-params.Rd | 1 pkgdown-1.6.0/pkgdown/man/test-sexpr-title.Rd |only pkgdown-1.6.0/pkgdown/man/test-verbatim.Rd | 3 pkgdown-1.6.0/pkgdown/tests/testthat/assets/open-graph-customized/vignettes/open-graph.Rmd | 2 pkgdown-1.6.0/pkgdown/tests/testthat/assets/open-graph/vignettes/open-graph.Rmd | 2 pkgdown-1.6.0/pkgdown/tests/testthat/assets/reference-fail |only pkgdown-1.6.0/pkgdown/tests/testthat/assets/reference/NAMESPACE | 1 pkgdown-1.6.0/pkgdown/tests/testthat/assets/reference/R/funs.R | 6 pkgdown-1.6.0/pkgdown/tests/testthat/assets/reference/man/help.Rd |only pkgdown-1.6.0/pkgdown/tests/testthat/assets/version-formatting/docs/404.html | 2 pkgdown-1.6.0/pkgdown/tests/testthat/assets/version-formatting/docs/index.html | 2 pkgdown-1.6.0/pkgdown/tests/testthat/assets/version-formatting/docs/pkgdown.css | 4 pkgdown-1.6.0/pkgdown/tests/testthat/assets/version-formatting/docs/pkgdown.yml | 6 pkgdown-1.6.0/pkgdown/tests/testthat/assets/vignette-with-img.Rmd | 2 pkgdown-1.6.0/pkgdown/tests/testthat/test-build-home-index.R | 1 pkgdown-1.6.0/pkgdown/tests/testthat/test-build-news.R | 11 pkgdown-1.6.0/pkgdown/tests/testthat/test-build-reference-index.R | 4 pkgdown-1.6.0/pkgdown/tests/testthat/test-build-reference-index.txt | 5 pkgdown-1.6.0/pkgdown/tests/testthat/test-build-reference.R |only pkgdown-1.6.0/pkgdown/tests/testthat/test-html-tweak.R | 18 pkgdown-1.6.0/pkgdown/tests/testthat/test-markdown.R | 9 pkgdown-1.6.0/pkgdown/tests/testthat/test-package.r |only pkgdown-1.6.0/pkgdown/tests/testthat/test-rd-example-out.txt |only pkgdown-1.6.0/pkgdown/tests/testthat/test-rd-example.R | 28 + pkgdown-1.6.0/pkgdown/tests/testthat/test-rd-html-error.txt |only pkgdown-1.6.0/pkgdown/tests/testthat/test-rd-html.R | 255 +++++----- pkgdown-1.6.0/pkgdown/tests/testthat/test-rd-html.txt |only pkgdown-1.6.0/pkgdown/tests/testthat/test-repo.R | 11 pkgdown-1.6.0/pkgdown/tests/testthat/test-rmarkdown.R | 4 pkgdown-1.6.0/pkgdown/tests/testthat/test-rmarkown-error.txt | 6 pkgdown-1.6.0/pkgdown/tests/testthat/test-utils.R | 16 pkgdown-1.6.0/pkgdown/vignettes/linking.Rmd | 6 pkgdown-1.6.0/pkgdown/vignettes/metadata.Rmd | 4 pkgdown-1.6.0/pkgdown/vignettes/pkgdown.Rmd | 2 pkgdown-1.6.0/pkgdown/vignettes/test/jss.Rmd | 2 103 files changed, 1148 insertions(+), 871 deletions(-)
Title: Multiple Correspondence Analysis Variants
Description: Provides two variants of multiple correspondence analysis (ca):
multiple ca and ordered multiple ca via orthogonal polynomials of Emerson.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unicampania.it>
Diff between MCAvariants versions 2.2 dated 2019-01-21 and 2.5 dated 2020-09-07
MCAvariants-2.2/MCAvariants/data/alligator.dat.rda |only MCAvariants-2.2/MCAvariants/data/satisfaction.rda |only MCAvariants-2.5/MCAvariants/DESCRIPTION | 11 ++- MCAvariants-2.5/MCAvariants/MD5 | 16 +++-- MCAvariants-2.5/MCAvariants/NAMESPACE | 7 +- MCAvariants-2.5/MCAvariants/R/MCAvariants.R | 5 + MCAvariants-2.5/MCAvariants/R/caplot3d.R |only MCAvariants-2.5/MCAvariants/R/plot.MCAvariants.R | 59 ++++++++++++++------ MCAvariants-2.5/MCAvariants/data/alligator.dat.R |only MCAvariants-2.5/MCAvariants/data/satisfaction.R |only MCAvariants-2.5/MCAvariants/man/caplot3d.Rd |only MCAvariants-2.5/MCAvariants/man/plot.MCAvariants.Rd | 21 +++++-- 12 files changed, 80 insertions(+), 39 deletions(-)
Title: Inspection, Comparison and Visualisation of Data Frames
Description: A collection of utilities for columnwise summary, comparison and visualisation of data frames. Functions report missingness, categorical levels, numeric distribution, correlation, column types and memory usage.
Author: Alastair Rushworth [aut, cre],
David Wilkins [ctb]
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>
Diff between inspectdf versions 0.0.8 dated 2020-06-25 and 0.0.9 dated 2020-09-07
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 6 +++++- R/n_in.R | 5 +++-- R/plot_cat.R | 6 +++--- R/plot_imb.R | 4 +--- 6 files changed, 23 insertions(+), 20 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions. This package implements the
following distributions: Bernoulli, beta-binomial, beta-negative
binomial, beta prime, Bhattacharjee, Birnbaum-Saunders,
bivariate normal, bivariate Poisson, categorical, Dirichlet,
Dirichlet-multinomial, discrete gamma, discrete Laplace,
discrete normal, discrete uniform, discrete Weibull, Frechet,
gamma-Poisson, generalized extreme value, Gompertz,
generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t,
Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy,
Laplace, location-scale t, logarithmic, Lomax, multivariate
hypergeometric, multinomial, negative hypergeometric,
non-standard beta, normal mixture, Poisson mixture, Pareto,
power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam,
slash, triangular, truncated binomial, truncated normal,
truncated Poisson, Tukey lambda, Wald, zero-inflated binomial,
zero-inflated negative binomial, zero-inflated Poisson.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Diff between extraDistr versions 1.8.11 dated 2019-06-10 and 1.9.1 dated 2020-09-07
DESCRIPTION | 10 MD5 | 164 NEWS.md | 4 R/RcppExports.R | 4 R/truncated-normal-distribution.R | 4 inst |only man/BetaBinom.Rd | 3 man/BetaNegBinom.Rd | 3 man/BetaPrime.Rd | 6 man/Bhattacharjee.Rd | 3 man/BirnbaumSaunders.Rd | 6 man/BivNormal.Rd | 12 man/DiscreteGamma.Rd | 3 man/Frechet.Rd | 6 man/GEV.Rd | 6 man/GPD.Rd | 6 man/GammaPoiss.Rd | 3 man/Huber.Rd | 6 man/NSBeta.Rd | 7 man/Triangular.Rd | 6 man/TruncBinom.Rd | 6 man/TruncNormal.Rd | 28 man/TruncPoisson.Rd | 6 man/extraDistr.Rd | 1 src/RcppExports.cpp | 5722 +++++++++++++++++-- src/bernoulli-distribution.cpp | 1 src/beta-binomial-distribution.cpp | 1 src/beta-negative-binomial-distribution.cpp | 1 src/beta-prime-distribution.cpp | 1 src/bhattacharjee-distribution.cpp | 1 src/birnbaum-saunders-distribution.cpp | 1 src/bivariate-normal-distribution.cpp | 1 src/bivariate-poisson-distribution.cpp | 1 src/categorical-distribution-lp.cpp | 1 src/categorical-distribution.cpp | 1 src/dirichlet-distribution.cpp | 1 src/dirichlet-multinomial-distribution.cpp | 1 src/discrete-gamma-distribution.cpp | 1 src/discrete-laplace-distribution.cpp | 1 src/discrete-normal-distribution.cpp | 1 src/discrete-uniform-distribution.cpp | 1 src/discrete-weibull-distribution.cpp | 1 src/frechet-distribution.cpp | 1 src/gamma-poisson-distribution.cpp | 1 src/gev-distribution.cpp | 1 src/gompertz-distribution.cpp | 1 src/gpd-distribution.cpp | 1 src/gumbel-distribution.cpp | 1 src/half-cauchy-distribution.cpp | 1 src/half-normal-distribution.cpp | 1 src/half-t-distribution.cpp | 1 src/huber-distribution.cpp | 1 src/inverse-gamma-distribution.cpp | 1 src/kumaraswamy-distribution.cpp | 1 src/laplace-distribution.cpp | 1 src/location-scale-t-distribution.cpp | 1 src/logarithmic-series-distribution.cpp | 1 src/lomax-distribution.cpp | 1 src/mixture-of-normal-distributions.cpp | 1 src/mixture-of-poisson-distributions.cpp | 1 src/multinomial-distribution.cpp | 1 src/multivariate-hypergeometric-distribution.cpp | 1 src/negative-hypergeometric-distribution.cpp | 1 src/non-standart-beta-distribution.cpp | 1 src/pareto-distribution.cpp | 1 src/power-distribution.cpp | 1 src/proportion-distribution.cpp | 1 src/rademacher-distribution.cpp | 1 src/rayleigh-distribution.cpp | 1 src/shared.cpp | 1 src/shifted-gompertz-distribution.cpp | 1 src/skellam-distribution.cpp | 1 src/slash-distribution.cpp | 1 src/triangular-distribution.cpp | 1 src/truncated-binomial-distribution.cpp | 1 src/truncated-normal-distribution.cpp | 1 src/truncated-poisson-distribution.cpp | 1 src/tuckey-lambda-distribution.cpp | 1 src/wald-distribution.cpp | 1 src/zero-inflated-binomial-distribution.cpp | 1 src/zero-inflated-negative-binomial-distribution.cpp | 1 src/zero-inflated-poisson-distribution.cpp | 1 tests/testthat.R | 3 83 files changed, 5384 insertions(+), 701 deletions(-)
Title: Retrieve Data from the Census APIs
Description: A wrapper for the U.S. Census Bureau APIs that returns data frames of
Census data and metadata. Available datasets include the
Decennial Census, American Community Survey, Small Area Health Insurance Estimates,
Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
Author: Hannah Recht [aut, cre]
Maintainer: Hannah Recht <censusapi.rstats@gmail.com>
Diff between censusapi versions 0.6.0 dated 2019-04-13 and 0.7.0 dated 2020-09-07
censusapi-0.6.0/censusapi/inst/doc/example-masterlist.R |only censusapi-0.6.0/censusapi/inst/doc/example-masterlist.Rmd |only censusapi-0.6.0/censusapi/inst/doc/example-masterlist.html |only censusapi-0.6.0/censusapi/vignettes/example-masterlist.Rmd |only censusapi-0.7.0/censusapi/DESCRIPTION | 12 censusapi-0.7.0/censusapi/MD5 | 34 censusapi-0.7.0/censusapi/NEWS.md | 17 censusapi-0.7.0/censusapi/R/datasets.R | 1 censusapi-0.7.0/censusapi/R/getcensus_functions.R | 75 censusapi-0.7.0/censusapi/README.md | 4 censusapi-0.7.0/censusapi/build/vignette.rds |binary censusapi-0.7.0/censusapi/inst/doc/getting-started.R | 129 - censusapi-0.7.0/censusapi/inst/doc/getting-started.Rmd | 98 - censusapi-0.7.0/censusapi/inst/doc/getting-started.html | 999 ++++++++----- censusapi-0.7.0/censusapi/man/fips.Rd | 5 censusapi-0.7.0/censusapi/man/getCensus.Rd | 40 censusapi-0.7.0/censusapi/man/getFunction.Rd | 26 censusapi-0.7.0/censusapi/man/listCensusMetadata.Rd | 3 censusapi-0.7.0/censusapi/man/makeVarlist.Rd | 3 censusapi-0.7.0/censusapi/vignettes/getting-started.Rmd | 98 - 20 files changed, 979 insertions(+), 565 deletions(-)
Title: Create Area-Proportional Venn Diagrams from Biological Lists
Description: Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen et al. (2008) <doi:10.1186/1471-2164-9-488>.
Author: Tim Hulsen [aut, cre] (<https://orcid.org/0000-0002-0208-8443>)
Maintainer: Tim Hulsen <thulsen@gmail.com>
Diff between BioVenn versions 1.0.0 dated 2020-09-01 and 1.0.1 dated 2020-09-07
DESCRIPTION | 6 MD5 | 6 R/draw.venn.R | 1447 +++++++++++++++++++++++++++---------------------------- man/draw.venn.Rd | 28 - 4 files changed, 743 insertions(+), 744 deletions(-)
Title: Bayesian Treed Gaussian Process Models
Description: Bayesian nonstationary, semiparametric nonlinear regression
and design by treed Gaussian processes (GPs) with jumps to the limiting
linear model (LLM). Special cases also implemented include Bayesian
linear models, CART, treed linear models, stationary separable and
isotropic GPs, and GP single-index models. Provides 1-d and 2-d plotting functions
(with projection and slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided, including ALM,
ALC, and expected improvement. The latter supports derivative-free
optimization of noisy black-box functions.
Author: Robert B. Gramacy <rbg@vt.edu> and Matt A. Taddy <mataddy@amazon.com>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between tgp versions 2.4-14 dated 2016-02-07 and 2.4-16 dated 2020-09-07
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Title: 'FomanticUI' Support for Shiny
Description: Creating a great user interface for your Shiny apps
can be a hassle, especially if you want to work purely in R
and don't want to use, for instance HTML templates. This
package adds support for a powerful UI library 'FomanticUI' -
<https://fomantic-ui.com/> (before: Semantic). It also supports
universal UI input binding that works with various DOM elements.
Author: Filip Stachura [aut],
Dominik Krzeminski [cre],
Krystian Igras [aut],
Adam Forys [aut],
Paweł Przytuła [aut],
Jakub Chojna [aut],
Olga Mierzwa-Sulima [aut],
Ashley Baldry [ctb],
Jakub Chojna [ctb],
Olga Mierzwa-Sulima [ctb],
Pedro Manuel Coutinho da Silva [ctb],
Paweł Przytuła [ctb],
Kamil Żyła [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Dominik Krzeminski <dominik@appsilon.com>
Diff between shiny.semantic versions 0.3.0 dated 2020-03-13 and 0.4.0 dated 2020-09-07
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More information about shiny.semantic at CRAN
Permanent link
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 2.0.6 dated 2019-12-12 and 3.0.0 dated 2020-09-07
rpact-2.0.6/rpact/R/f_simulation_means.R |only rpact-2.0.6/rpact/R/f_simulation_rates.R |only rpact-2.0.6/rpact/R/f_simulation_survival.R |only rpact-2.0.6/rpact/inst/tests/testthat/test-f_simulation_means.R |only rpact-2.0.6/rpact/inst/tests/testthat/test-f_simulation_rates.R |only rpact-2.0.6/rpact/inst/tests/testthat/test-f_simulation_survival.R |only rpact-2.0.6/rpact/inst/tests/testthat/test_generic_functions.R |only rpact-2.0.6/rpact/man/TrialDesignPlanSurvival_summary.Rd |only rpact-2.0.6/rpact/src/rpact.c |only rpact-2.0.6/rpact/tests/testthat/test-f_simulation_means.R |only rpact-2.0.6/rpact/tests/testthat/test-f_simulation_rates.R |only rpact-2.0.6/rpact/tests/testthat/test-f_simulation_survival.R |only rpact-2.0.6/rpact/tests/testthat/test_generic_functions.R |only rpact-3.0.0/rpact/DESCRIPTION | 28 rpact-3.0.0/rpact/MD5 | 514 +- rpact-3.0.0/rpact/NAMESPACE | 195 - rpact-3.0.0/rpact/NEWS.md | 60 rpact-3.0.0/rpact/R/RcppExports.R | 4 rpact-3.0.0/rpact/R/class_analysis_dataset.R | 1105 ++++- rpact-3.0.0/rpact/R/class_analysis_results.R | 1405 ++++++- rpact-3.0.0/rpact/R/class_analysis_stage_results.R | 419 +- rpact-3.0.0/rpact/R/class_core_parameter_set.R | 429 +- rpact-3.0.0/rpact/R/class_core_plot_settings.R | 47 rpact-3.0.0/rpact/R/class_design.R | 356 + rpact-3.0.0/rpact/R/class_design_plan.R | 422 +- rpact-3.0.0/rpact/R/class_design_power_and_asn.R | 60 rpact-3.0.0/rpact/R/class_design_set.R | 288 + rpact-3.0.0/rpact/R/class_event_probabilities.R | 328 + rpact-3.0.0/rpact/R/class_simulation_results.R | 1641 ++++++-- rpact-3.0.0/rpact/R/class_summary.R | 1850 ++++++++-- rpact-3.0.0/rpact/R/class_time.R | 878 ++-- rpact-3.0.0/rpact/R/f_analysis_base.R | 1307 ++++--- rpact-3.0.0/rpact/R/f_analysis_base_means.R | 1215 +++--- rpact-3.0.0/rpact/R/f_analysis_base_rates.R | 1095 +++-- rpact-3.0.0/rpact/R/f_analysis_base_survival.R | 908 ++-- rpact-3.0.0/rpact/R/f_analysis_multiarm.R |only rpact-3.0.0/rpact/R/f_analysis_multiarm_means.R |only rpact-3.0.0/rpact/R/f_analysis_multiarm_rates.R |only rpact-3.0.0/rpact/R/f_analysis_multiarm_survival.R |only rpact-3.0.0/rpact/R/f_core_assertions.R | 988 ++++- rpact-3.0.0/rpact/R/f_core_constants.R | 610 ++- rpact-3.0.0/rpact/R/f_core_output_formats.R | 877 ++++ rpact-3.0.0/rpact/R/f_core_plot.R | 509 ++ rpact-3.0.0/rpact/R/f_core_utilities.R | 693 +-- rpact-3.0.0/rpact/R/f_design_fisher_combination_test.R | 142 rpact-3.0.0/rpact/R/f_design_group_sequential.R | 495 +- rpact-3.0.0/rpact/R/f_design_sample_size_calculator.R | 1650 +++----- rpact-3.0.0/rpact/R/f_design_utilities.R | 515 ++ rpact-3.0.0/rpact/R/f_simulation_base_means.R |only rpact-3.0.0/rpact/R/f_simulation_base_rates.R |only rpact-3.0.0/rpact/R/f_simulation_base_survival.R |only rpact-3.0.0/rpact/R/f_simulation_multiarm.R |only rpact-3.0.0/rpact/R/f_simulation_multiarm_means.R |only rpact-3.0.0/rpact/R/f_simulation_multiarm_rates.R |only rpact-3.0.0/rpact/R/f_simulation_multiarm_survival.R |only rpact-3.0.0/rpact/R/parameter_descriptions.R |only rpact-3.0.0/rpact/R/pkgname.R | 31 rpact-3.0.0/rpact/inst/extdata |only rpact-3.0.0/rpact/inst/tests/testthat/helper-class_analysis_dataset.R | 37 rpact-3.0.0/rpact/inst/tests/testthat/helper-f_analysis.R | 49 rpact-3.0.0/rpact/inst/tests/testthat/helper-f_analysis_means.R | 45 rpact-3.0.0/rpact/inst/tests/testthat/helper-f_analysis_rates.R | 47 rpact-3.0.0/rpact/inst/tests/testthat/helper-f_analysis_survival.R | 47 rpact-3.0.0/rpact/inst/tests/testthat/helper-f_core_assertions.R | 37 rpact-3.0.0/rpact/inst/tests/testthat/helper-f_core_utilities.R | 102 rpact-3.0.0/rpact/inst/tests/testthat/test-class_analysis_dataset.R | 999 ++++- rpact-3.0.0/rpact/inst/tests/testthat/test-class_summary.R | 301 + rpact-3.0.0/rpact/inst/tests/testthat/test-class_time.R | 1048 +++-- rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_base_means.R | 1237 +++--- rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_base_rates.R | 1679 +++------ rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_base_survival.R | 437 -- rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_input_validation.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_multiarm_means.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_multiarm_rates.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_analysis_multiarm_survival.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_core_assertions.R | 135 rpact-3.0.0/rpact/inst/tests/testthat/test-f_core_output_formats.R | 97 rpact-3.0.0/rpact/inst/tests/testthat/test-f_core_plot.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_core_utilities.R | 173 rpact-3.0.0/rpact/inst/tests/testthat/test-f_design_fisher_combination_test.R | 111 rpact-3.0.0/rpact/inst/tests/testthat/test-f_design_group_sequential_design.R | 168 rpact-3.0.0/rpact/inst/tests/testthat/test-f_design_power_calculator.R | 574 ++- rpact-3.0.0/rpact/inst/tests/testthat/test-f_design_sample_size_calculator.R | 1676 +++++---- rpact-3.0.0/rpact/inst/tests/testthat/test-f_design_utilities.R | 81 rpact-3.0.0/rpact/inst/tests/testthat/test-f_simulation_base_means.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_simulation_base_rates.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_simulation_base_survival.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_simulation_multiarm_means.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_simulation_multiarm_rates.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-f_simulation_multiarm_survival.R |only rpact-3.0.0/rpact/inst/tests/testthat/test-generic_functions.R |only rpact-3.0.0/rpact/man/AccrualTime.Rd | 26 rpact-3.0.0/rpact/man/AnalysisResultsConditionalDunnett.Rd |only rpact-3.0.0/rpact/man/AnalysisResultsFisher.Rd | 28 rpact-3.0.0/rpact/man/AnalysisResultsGroupSequential.Rd | 2 rpact-3.0.0/rpact/man/AnalysisResultsInverseNormal.Rd | 2 rpact-3.0.0/rpact/man/AnalysisResultsMultiArm.Rd |only rpact-3.0.0/rpact/man/AnalysisResultsMultiArmFisher.Rd |only rpact-3.0.0/rpact/man/AnalysisResultsMultiArmGroupSequential.Rd |only rpact-3.0.0/rpact/man/AnalysisResultsMultiArmInverseNormal.Rd |only rpact-3.0.0/rpact/man/AnalysisResults_as.data.frame.Rd | 8 rpact-3.0.0/rpact/man/AnalysisResults_names.Rd | 11 rpact-3.0.0/rpact/man/AnalysisResults_summary.Rd |only rpact-3.0.0/rpact/man/ClosedCombinationTestResults.Rd |only rpact-3.0.0/rpact/man/ConditionalPowerResults.Rd |only rpact-3.0.0/rpact/man/DatasetMeans.Rd | 2 rpact-3.0.0/rpact/man/DatasetRates.Rd | 14 rpact-3.0.0/rpact/man/DatasetSurvival.Rd | 16 rpact-3.0.0/rpact/man/EventProbabilities.Rd | 26 rpact-3.0.0/rpact/man/FieldSet.Rd | 26 rpact-3.0.0/rpact/man/FieldSet_names.Rd | 12 rpact-3.0.0/rpact/man/FieldSet_print.Rd | 10 rpact-3.0.0/rpact/man/FrameSet_as.matrix.Rd | 20 rpact-3.0.0/rpact/man/NumberOfSubjects.Rd | 26 rpact-3.0.0/rpact/man/ParameterSet.Rd | 26 rpact-3.0.0/rpact/man/ParameterSet_as.data.frame.Rd | 17 rpact-3.0.0/rpact/man/ParameterSet_print.Rd | 5 rpact-3.0.0/rpact/man/ParameterSet_summary.Rd | 47 rpact-3.0.0/rpact/man/PiecewiseSurvivalTime.Rd | 26 rpact-3.0.0/rpact/man/PowerAndAverageSampleNumberResult.Rd | 28 rpact-3.0.0/rpact/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd | 27 rpact-3.0.0/rpact/man/SimulationResults.Rd | 9 rpact-3.0.0/rpact/man/SimulationResultsMeans.Rd | 26 rpact-3.0.0/rpact/man/SimulationResultsMultiArmMeans.Rd |only rpact-3.0.0/rpact/man/SimulationResultsMultiArmRates.Rd |only rpact-3.0.0/rpact/man/SimulationResultsMultiArmSurvival.Rd |only rpact-3.0.0/rpact/man/SimulationResultsRates.Rd | 26 rpact-3.0.0/rpact/man/SimulationResultsSurvival.Rd | 26 rpact-3.0.0/rpact/man/SimulationResults_names.Rd |only rpact-3.0.0/rpact/man/StageResultsMeans.Rd | 2 rpact-3.0.0/rpact/man/StageResultsRates.Rd | 2 rpact-3.0.0/rpact/man/StageResultsSurvival.Rd | 2 rpact-3.0.0/rpact/man/StageResults_as.data.frame.Rd | 17 rpact-3.0.0/rpact/man/StageResults_names.Rd | 12 rpact-3.0.0/rpact/man/SummaryFactory.Rd |only rpact-3.0.0/rpact/man/TrialDesign.Rd | 36 rpact-3.0.0/rpact/man/TrialDesignCharacteristics_as.data.frame.Rd | 24 rpact-3.0.0/rpact/man/TrialDesignConditionalDunnett.Rd | 29 rpact-3.0.0/rpact/man/TrialDesignFisher.Rd | 6 rpact-3.0.0/rpact/man/TrialDesignPlan.Rd | 36 rpact-3.0.0/rpact/man/TrialDesignPlanMeans.Rd | 28 rpact-3.0.0/rpact/man/TrialDesignPlanRates.Rd | 28 rpact-3.0.0/rpact/man/TrialDesignPlanSurvival.Rd | 28 rpact-3.0.0/rpact/man/TrialDesignPlan_as.data.frame.Rd | 23 rpact-3.0.0/rpact/man/TrialDesignSet.Rd | 2 rpact-3.0.0/rpact/man/TrialDesignSet_as.data.frame.Rd | 29 rpact-3.0.0/rpact/man/TrialDesignSet_length.Rd | 14 rpact-3.0.0/rpact/man/TrialDesignSet_names.Rd | 17 rpact-3.0.0/rpact/man/TrialDesign_as.data.frame.Rd | 24 rpact-3.0.0/rpact/man/Trial_Design_Set_summary.Rd |only rpact-3.0.0/rpact/man/getAccrualTime.Rd | 331 - rpact-3.0.0/rpact/man/getAnalysisResults.Rd | 223 - rpact-3.0.0/rpact/man/getAvailablePlotTypes.Rd | 25 rpact-3.0.0/rpact/man/getClosedCombinationTestResults.Rd |only rpact-3.0.0/rpact/man/getClosedConditionalDunnettTestResults.Rd |only rpact-3.0.0/rpact/man/getConditionalPower.Rd | 107 rpact-3.0.0/rpact/man/getConditionalRejectionProbabilities.Rd | 50 rpact-3.0.0/rpact/man/getData.Rd | 55 rpact-3.0.0/rpact/man/getDataset.Rd | 145 rpact-3.0.0/rpact/man/getDesignCharacteristics.Rd | 38 rpact-3.0.0/rpact/man/getDesignConditionalDunnett.Rd |only rpact-3.0.0/rpact/man/getDesignFisher.Rd | 107 rpact-3.0.0/rpact/man/getDesignGroupSequential.Rd | 115 rpact-3.0.0/rpact/man/getDesignInverseNormal.Rd | 118 rpact-3.0.0/rpact/man/getDesignSet.Rd | 53 rpact-3.0.0/rpact/man/getEventProbabilities.Rd | 90 rpact-3.0.0/rpact/man/getFinalConfidenceInterval.Rd | 115 rpact-3.0.0/rpact/man/getFinalPValue.Rd | 40 rpact-3.0.0/rpact/man/getLambdaStepFunction.Rd |only rpact-3.0.0/rpact/man/getLogLevel.Rd | 17 rpact-3.0.0/rpact/man/getNumberOfSubjects.Rd | 52 rpact-3.0.0/rpact/man/getOutputFormat.Rd |only rpact-3.0.0/rpact/man/getPiecewiseSurvivalTime.Rd | 101 rpact-3.0.0/rpact/man/getPowerAndAverageSampleNumber.Rd | 43 rpact-3.0.0/rpact/man/getPowerMeans.Rd | 123 rpact-3.0.0/rpact/man/getPowerRates.Rd | 100 rpact-3.0.0/rpact/man/getPowerSurvival.Rd | 220 - rpact-3.0.0/rpact/man/getRawData.Rd | 52 rpact-3.0.0/rpact/man/getRepeatedConfidenceIntervals.Rd | 75 rpact-3.0.0/rpact/man/getRepeatedPValues.Rd | 54 rpact-3.0.0/rpact/man/getSampleSizeMeans.Rd | 94 rpact-3.0.0/rpact/man/getSampleSizeRates.Rd | 90 rpact-3.0.0/rpact/man/getSampleSizeSurvival.Rd | 218 - rpact-3.0.0/rpact/man/getSimulationMeans.Rd | 196 - rpact-3.0.0/rpact/man/getSimulationMultiArmMeans.Rd |only rpact-3.0.0/rpact/man/getSimulationMultiArmRates.Rd |only rpact-3.0.0/rpact/man/getSimulationMultiArmSurvival.Rd |only rpact-3.0.0/rpact/man/getSimulationRates.Rd | 180 rpact-3.0.0/rpact/man/getSimulationSurvival.Rd | 262 - rpact-3.0.0/rpact/man/getStageResults.Rd | 104 rpact-3.0.0/rpact/man/getTestActions.Rd | 35 rpact-3.0.0/rpact/man/param_accrualIntensity.Rd |only rpact-3.0.0/rpact/man/param_accrualTime.Rd |only rpact-3.0.0/rpact/man/param_activeArms.Rd |only rpact-3.0.0/rpact/man/param_adaptations.Rd |only rpact-3.0.0/rpact/man/param_allocationRatioPlanned.Rd |only rpact-3.0.0/rpact/man/param_allocationRatioPlanned_sampleSize.Rd |only rpact-3.0.0/rpact/man/param_alpha.Rd |only rpact-3.0.0/rpact/man/param_alternative.Rd |only rpact-3.0.0/rpact/man/param_beta.Rd |only rpact-3.0.0/rpact/man/param_bindingFutility.Rd |only rpact-3.0.0/rpact/man/param_calcEventsFunction.Rd |only rpact-3.0.0/rpact/man/param_calcSubjectsFunction.Rd |only rpact-3.0.0/rpact/man/param_conditionalPower.Rd |only rpact-3.0.0/rpact/man/param_conditionalPowerSimulation.Rd |only rpact-3.0.0/rpact/man/param_dataInput.Rd |only rpact-3.0.0/rpact/man/param_design.Rd |only rpact-3.0.0/rpact/man/param_design_with_default.Rd |only rpact-3.0.0/rpact/man/param_digits.Rd |only rpact-3.0.0/rpact/man/param_directionUpper.Rd |only rpact-3.0.0/rpact/man/param_dropoutRate1.Rd |only rpact-3.0.0/rpact/man/param_dropoutRate2.Rd |only rpact-3.0.0/rpact/man/param_dropoutTime.Rd |only rpact-3.0.0/rpact/man/param_effectMatrix.Rd |only rpact-3.0.0/rpact/man/param_effectMeasure.Rd |only rpact-3.0.0/rpact/man/param_epsilonValue.Rd |only rpact-3.0.0/rpact/man/param_eventTime.Rd |only rpact-3.0.0/rpact/man/param_gED50.Rd |only rpact-3.0.0/rpact/man/param_grid.Rd |only rpact-3.0.0/rpact/man/param_groups.Rd |only rpact-3.0.0/rpact/man/param_hazardRatio.Rd |only rpact-3.0.0/rpact/man/param_includeAllParameters.Rd |only rpact-3.0.0/rpact/man/param_informationRates.Rd |only rpact-3.0.0/rpact/man/param_intersectionTest.Rd |only rpact-3.0.0/rpact/man/param_kMax.Rd |only rpact-3.0.0/rpact/man/param_kappa.Rd |only rpact-3.0.0/rpact/man/param_lambda1.Rd |only rpact-3.0.0/rpact/man/param_lambda2.Rd |only rpact-3.0.0/rpact/man/param_legendPosition.Rd |only rpact-3.0.0/rpact/man/param_maxNumberOfEventsPerStage.Rd |only rpact-3.0.0/rpact/man/param_maxNumberOfIterations.Rd |only rpact-3.0.0/rpact/man/param_maxNumberOfSubjects.Rd |only rpact-3.0.0/rpact/man/param_maxNumberOfSubjectsPerStage.Rd |only rpact-3.0.0/rpact/man/param_maxNumberOfSubjects_survival.Rd |only rpact-3.0.0/rpact/man/param_median1.Rd |only rpact-3.0.0/rpact/man/param_median2.Rd |only rpact-3.0.0/rpact/man/param_minNumberOfEventsPerStage.Rd |only rpact-3.0.0/rpact/man/param_minNumberOfSubjectsPerStage.Rd |only rpact-3.0.0/rpact/man/param_nMax.Rd |only rpact-3.0.0/rpact/man/param_nPlanned.Rd |only rpact-3.0.0/rpact/man/param_niceColumnNamesEnabled.Rd |only rpact-3.0.0/rpact/man/param_normalApproximation.Rd |only rpact-3.0.0/rpact/man/param_palette.Rd |only rpact-3.0.0/rpact/man/param_pi1_rates.Rd |only rpact-3.0.0/rpact/man/param_pi1_survival.Rd |only rpact-3.0.0/rpact/man/param_pi2_rates.Rd |only rpact-3.0.0/rpact/man/param_pi2_survival.Rd |only rpact-3.0.0/rpact/man/param_piecewiseSurvivalTime.Rd |only rpact-3.0.0/rpact/man/param_plannedEvents.Rd |only rpact-3.0.0/rpact/man/param_plannedSubjects.Rd |only rpact-3.0.0/rpact/man/param_plotPointsEnabled.Rd |only rpact-3.0.0/rpact/man/param_rValue.Rd |only rpact-3.0.0/rpact/man/param_seed.Rd |only rpact-3.0.0/rpact/man/param_selectArmsFunction.Rd |only rpact-3.0.0/rpact/man/param_showSource.Rd |only rpact-3.0.0/rpact/man/param_showStatistics.Rd |only rpact-3.0.0/rpact/man/param_sided.Rd |only rpact-3.0.0/rpact/man/param_slope.Rd |only rpact-3.0.0/rpact/man/param_stDev.Rd |only rpact-3.0.0/rpact/man/param_stDevH1.Rd |only rpact-3.0.0/rpact/man/param_stDevSimulation.Rd |only rpact-3.0.0/rpact/man/param_stage.Rd |only rpact-3.0.0/rpact/man/param_stageResults.Rd |only rpact-3.0.0/rpact/man/param_successCriterion.Rd |only rpact-3.0.0/rpact/man/param_theta.Rd |only rpact-3.0.0/rpact/man/param_thetaH0.Rd |only rpact-3.0.0/rpact/man/param_thetaH1.Rd |only rpact-3.0.0/rpact/man/param_three_dots.Rd |only rpact-3.0.0/rpact/man/param_three_dots_plot.Rd |only rpact-3.0.0/rpact/man/param_threshold.Rd |only rpact-3.0.0/rpact/man/param_tolerance.Rd |only rpact-3.0.0/rpact/man/param_typeOfComputation.Rd |only rpact-3.0.0/rpact/man/param_typeOfDesign.Rd |only rpact-3.0.0/rpact/man/param_typeOfSelection.Rd |only rpact-3.0.0/rpact/man/param_typeOfShape.Rd |only rpact-3.0.0/rpact/man/param_userAlphaSpending.Rd |only rpact-3.0.0/rpact/man/param_varianceOption.Rd |only rpact-3.0.0/rpact/man/plot.AnalysisResults.Rd | 82 rpact-3.0.0/rpact/man/plot.Dataset.Rd | 28 rpact-3.0.0/rpact/man/plot.EventProbabilities.Rd |only rpact-3.0.0/rpact/man/plot.NumberOfSubjects.Rd |only rpact-3.0.0/rpact/man/plot.ParameterSet.Rd |only rpact-3.0.0/rpact/man/plot.SimulationResults.Rd | 68 rpact-3.0.0/rpact/man/plot.StageResults.Rd | 46 rpact-3.0.0/rpact/man/plot.TrialDesign.Rd | 49 rpact-3.0.0/rpact/man/plot.TrialDesignPlan.Rd | 43 rpact-3.0.0/rpact/man/plot.TrialDesignSet.Rd | 36 rpact-3.0.0/rpact/man/printCitation.Rd | 1 rpact-3.0.0/rpact/man/readDataset.Rd | 39 rpact-3.0.0/rpact/man/readDatasets.Rd | 10 rpact-3.0.0/rpact/man/resetLogLevel.Rd | 13 rpact-3.0.0/rpact/man/roxygen |only rpact-3.0.0/rpact/man/rpact.Rd | 8 rpact-3.0.0/rpact/man/setLogLevel.Rd | 19 rpact-3.0.0/rpact/man/setOutputFormat.Rd |only rpact-3.0.0/rpact/man/sub-TrialDesignSet-method.Rd | 9 rpact-3.0.0/rpact/man/testPackage.Rd | 10 rpact-3.0.0/rpact/man/utilitiesForPiecewiseExponentialDistribution.Rd | 28 rpact-3.0.0/rpact/man/utilitiesForSurvivalTrials.Rd | 30 rpact-3.0.0/rpact/man/writeDataset.Rd | 12 rpact-3.0.0/rpact/man/writeDatasets.Rd | 19 rpact-3.0.0/rpact/src/RcppExports.cpp | 17 rpact-3.0.0/rpact/src/f_design_group_sequential.c |only rpact-3.0.0/rpact/src/f_design_group_sequential_wrapper.cpp |only rpact-3.0.0/rpact/src/f_simulation_survival.cpp | 36 rpact-3.0.0/rpact/tests/testthat/helper-class_analysis_dataset.R | 37 rpact-3.0.0/rpact/tests/testthat/helper-f_analysis.R | 49 rpact-3.0.0/rpact/tests/testthat/helper-f_analysis_means.R | 45 rpact-3.0.0/rpact/tests/testthat/helper-f_analysis_rates.R | 47 rpact-3.0.0/rpact/tests/testthat/helper-f_analysis_survival.R | 47 rpact-3.0.0/rpact/tests/testthat/helper-f_core_assertions.R | 37 rpact-3.0.0/rpact/tests/testthat/helper-f_core_utilities.R | 102 rpact-3.0.0/rpact/tests/testthat/test-class_analysis_dataset.R | 999 ++++- rpact-3.0.0/rpact/tests/testthat/test-class_summary.R | 301 + rpact-3.0.0/rpact/tests/testthat/test-class_time.R | 1048 +++-- rpact-3.0.0/rpact/tests/testthat/test-f_analysis_base_means.R | 1237 +++--- rpact-3.0.0/rpact/tests/testthat/test-f_analysis_base_rates.R | 1679 +++------ rpact-3.0.0/rpact/tests/testthat/test-f_analysis_base_survival.R | 437 -- rpact-3.0.0/rpact/tests/testthat/test-f_analysis_input_validation.R |only rpact-3.0.0/rpact/tests/testthat/test-f_analysis_multiarm_means.R |only rpact-3.0.0/rpact/tests/testthat/test-f_analysis_multiarm_rates.R |only rpact-3.0.0/rpact/tests/testthat/test-f_analysis_multiarm_survival.R |only rpact-3.0.0/rpact/tests/testthat/test-f_core_assertions.R | 135 rpact-3.0.0/rpact/tests/testthat/test-f_core_output_formats.R | 97 rpact-3.0.0/rpact/tests/testthat/test-f_core_plot.R |only rpact-3.0.0/rpact/tests/testthat/test-f_core_utilities.R | 173 rpact-3.0.0/rpact/tests/testthat/test-f_design_fisher_combination_test.R | 111 rpact-3.0.0/rpact/tests/testthat/test-f_design_group_sequential_design.R | 168 rpact-3.0.0/rpact/tests/testthat/test-f_design_power_calculator.R | 574 ++- rpact-3.0.0/rpact/tests/testthat/test-f_design_sample_size_calculator.R | 1676 +++++---- rpact-3.0.0/rpact/tests/testthat/test-f_design_utilities.R | 81 rpact-3.0.0/rpact/tests/testthat/test-f_simulation_base_means.R |only rpact-3.0.0/rpact/tests/testthat/test-f_simulation_base_rates.R |only rpact-3.0.0/rpact/tests/testthat/test-f_simulation_base_survival.R |only rpact-3.0.0/rpact/tests/testthat/test-f_simulation_multiarm_means.R |only rpact-3.0.0/rpact/tests/testthat/test-f_simulation_multiarm_rates.R |only rpact-3.0.0/rpact/tests/testthat/test-f_simulation_multiarm_survival.R |only rpact-3.0.0/rpact/tests/testthat/test-generic_functions.R |only 338 files changed, 27612 insertions(+), 16694 deletions(-)
Title: Create Mini Map for Web Pages
Description: Quickly and easily add a mini map to your 'rmarkdown' html documents.
Author: Wei Su [aut, cre],
Lars Jung [aut, cph] (pagemap library in htmlwidgets/lib,
https://github.com/lrsjng/pagemap)
Maintainer: Wei Su <swsoyee@gmail.com>
Diff between pagemap versions 0.1.0 dated 2020-09-04 and 0.1.1 dated 2020-09-07
DESCRIPTION | 8 +++--- MD5 | 18 +++++++------- R/pagemap.R | 61 +++++++++++++++++++++++++++++++++++++++++++------- README.md | 35 ++++++++++++++++++++++------ inst/doc/pagemap.R | 29 ++++++++++++++++++----- inst/doc/pagemap.Rmd | 39 +++++++++++++++++++++++++------ inst/doc/pagemap.html | 35 ++++++++++++++++++---------- man/pagemap-shiny.Rd | 24 ++++++++++++++++++- man/pagemap.Rd | 26 ++++++++++++++++++--- vignettes/pagemap.Rmd | 39 +++++++++++++++++++++++++------ 10 files changed, 246 insertions(+), 68 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R.
The package focuses on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
When working with 'PowerPoint' presentations, slides can be added or removed; shapes inside
slides can also be added or removed. When working with 'Word' documents, a cursor can be
used to help insert or delete content at a specific location in the document. The package
does not require any installation of Microsoft products to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Frank Hangler [ctb] (function body_replace_all_text),
Liz Sander [ctb] (several documentation fixes),
Anton Victorson [ctb] (fixes xml structures),
Jon Calder [ctb] (update vignettes),
John Harrold [ctb] (fuction annotate_base),
John Muschelli [ctb] (google doc compatibility)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.3.13 dated 2020-08-29 and 0.3.14 dated 2020-09-07
officer-0.3.13/officer/R/deprecated.R |only officer-0.3.13/officer/man/ph_empty.Rd |only officer-0.3.13/officer/man/ph_with_gg_at.Rd |only officer-0.3.13/officer/man/ph_with_img_at.Rd |only officer-0.3.13/officer/man/ph_with_text.Rd |only officer-0.3.14/officer/DESCRIPTION | 9 +-- officer-0.3.14/officer/MD5 | 34 +++++-------- officer-0.3.14/officer/NAMESPACE | 11 ---- officer-0.3.14/officer/NEWS | 11 ++++ officer-0.3.14/officer/R/defunct.R | 64 +++++++------------------ officer-0.3.14/officer/R/docx_add.R | 24 ++++----- officer-0.3.14/officer/R/ooxml_block_objects.R | 35 ++++++++----- officer-0.3.14/officer/R/ooxml_run_objects.R | 32 ++++++++++++ officer-0.3.14/officer/R/pack_folder.R | 7 ++ officer-0.3.14/officer/README.md | 25 ++++----- officer-0.3.14/officer/man/block_list.Rd | 7 +- officer-0.3.14/officer/man/body_add_gg.Rd | 17 +----- officer-0.3.14/officer/man/body_add_img.Rd | 16 +----- officer-0.3.14/officer/man/figures/logo.png |only officer-0.3.14/officer/man/fpar.Rd | 22 ++++---- officer-0.3.14/officer/man/officer-defunct.Rd | 58 +++++++--------------- 21 files changed, 179 insertions(+), 193 deletions(-)
Title: Gliding Box Lacunarity and Other Metrics for 2D Random Closed
Sets
Description: Functions for estimating the gliding box lacunarity (GBL),
covariance, and pair-correlation of a random closed set (RACS) in 2D
from a binary coverage map (e.g. presence-absence land cover maps).
Contains a number of newly-developed covariance-based estimators of
GBL (Hingee et al., 2019) <doi:10.1007/s13253-019-00351-9> and
balanced estimators, proposed by Picka (2000)
<http://www.jstor.org/stable/1428408>, for covariance, centred
covariance, and pair-correlation. Also contains methods for
estimating contagion-like properties of RACS and simulating 2D Boolean
models. Binary coverage maps are usually represented as raster images
with pixel values of TRUE, FALSE or NA, with NA representing
unobserved pixels. A demo for extracting such a binary map from a
geospatial data format is provided. Binary maps may also be
represented using polygonal sets as the foreground, however for most
computations such maps are converted into raster images. The package
is based on research conducted during the author's PhD studies.
Author: Kassel Liam Hingee
Maintainer: Kassel Liam Hingee <kassel.hingee@gmail.com>
Diff between lacunaritycovariance versions 1.0-13 dated 2020-01-31 and 1.1-0 dated 2020-09-07
DESCRIPTION | 28 +-- MD5 | 96 +++++------ NAMESPACE | 97 +++++------ NEWS | 5 R/ccvc.R | 10 - R/contagpixelgrid.R | 2 R/cppicka.R | 2 R/gbl.R | 11 - R/gblc.R | 20 +- R/gblcc.R | 14 - R/gblemp.R | 2 R/gblg.R | 24 +- R/innerprodim.R | 92 +++++++++- R/pcln.R | 8 R/racscovariance.R | 10 - R/rbdd.R | 2 R/secondorderprops.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/estimate_RACS_properties.R | 3 inst/doc/estimate_RACS_properties.Rnw | 3 inst/doc/estimate_RACS_properties.pdf |binary man/cencovariance.Rd | 213 +++++++++++++------------ man/contagdiscstate.Rd | 168 +++++++++---------- man/contagpixelgrid.Rd | 130 +++++++-------- man/coverageprob.Rd | 100 +++++------ man/cppicka.Rd | 108 ++++++------ man/gbl.Rd | 196 ++++++++++++----------- man/gblc.Rd | 169 ++++++++++---------- man/gblcc.Rd | 160 ++++++++++-------- man/gblemp.Rd | 120 +++++++------- man/gblg.Rd | 133 +++++++-------- man/innerprod.im.Rd | 98 ++++++----- man/isbinarymap.Rd | 60 +++---- man/lacunaritycovariance-package.Rd | 2 man/paircorr.Rd | 220 +++++++++++++------------- man/placegrainsfromlib.Rd | 211 +++++++++++++------------ man/plugincvc.Rd | 96 +++++------ man/racscovariance.Rd | 278 +++++++++++++++++---------------- man/rbdd.Rd | 200 +++++++++++------------ man/rbdr.Rd | 134 +++++++-------- man/rblnd.Rd | 88 +++++----- man/rbpto.Rd | 183 ++++++++++----------- man/secondorderprops.Rd | 108 ++++++------ man/summary.imlist.Rd | 72 ++++---- tests/testthat/test-gbl.R | 60 ++++++- tests/testthat/test-innerprod.R | 4 tests/testthat/test-xiinputs.R | 10 - vignettes/estimate_RACS_properties.Rnw | 3 49 files changed, 1989 insertions(+), 1766 deletions(-)
More information about lacunaritycovariance at CRAN
Permanent link
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Specialization of method ggplot(): accept and convert on the fly
time series data. Geom: "table", "plot" and "grob" add insets to plots
using native data coordinates, while "table_npc", "plot_npc" and "grob_npc"
do the same using "npc" coordinates through new aesthetics "npcx" and "npcy".
Statistics: locate and tag peaks and valleys; count observations in different
quadrants of a plot; select observations based on 2D density; label with the
equation of a polynomial fitted with lm() or other types of models; labels
with P-value, R^2 or adjusted R^2 or information criteria for fitted models;
label with ANOVA table for fitted models; label with summary for fitted
models. Model fit classes for which suitable methods are provided by package
'broom' are supported. Scales and stats to build volcano and quadrant plots
based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.3.5 dated 2020-06-01 and 0.3.6 dated 2020-09-07
DESCRIPTION | 26 MD5 | 48 NAMESPACE | 3 NEWS | 11 R/annotate.r |only R/geom-quadrant-lines.R | 7 R/geom-table.R | 24 R/ggpmisc.R | 2 R/scale-continuous-logFC.r | 4 R/stat-apply.R | 132 +- R/stat-fit-broom.R | 2 R/stat-poly-eq.R | 90 + README.md | 8 build/vignette.rds |binary inst/doc/user-guide.R | 209 ++- inst/doc/user-guide.Rmd | 574 ++++++--- inst/doc/user-guide.html | 1820 ++++++++++++++++--------------- man/annotate.Rd |only man/figures/README-readme-05-1.png |binary man/figures/README-readme-06-1.png |binary man/figures/README-unnamed-chunk-1-1.png |binary man/ggpmisc-package.Rd | 2 man/stat_apply.Rd | 58 man/stat_poly_eq.Rd | 11 man/symmetric_limits.Rd | 4 vignettes/user-guide.Rmd | 574 ++++++--- 26 files changed, 2170 insertions(+), 1439 deletions(-)
Title: A Generalized Multiclass Support Vector Machine
Description: The GenSVM classifier is a generalized multiclass support vector
machine (SVM). This classifier aims to find decision boundaries that
separate the classes with as wide a margin as possible. In GenSVM, the
loss function is very flexible in the way that misclassifications are
penalized. This allows the user to tune the classifier to the dataset
at hand and potentially obtain higher classification accuracy than
alternative multiclass SVMs. Moreover, this flexibility means that
GenSVM has a number of other multiclass SVMs as special cases. One of
the other advantages of GenSVM is that it is trained in the primal
space, allowing the use of warm starts during optimization. This
means that for common tasks such as cross validation or repeated model
fitting, GenSVM can be trained very quickly. Based on: G.J.J. van den
Burg and P.J.F. Groenen (2018) <https://www.jmlr.org/papers/v17/14-526.html>.
Author: Gertjan van den Burg [aut, cre],
Patrick Groenen [ctb]
Maintainer: Gertjan van den Burg <gertjanvandenburg@gmail.com>
Diff between gensvm versions 0.1.3 dated 2019-12-02 and 0.1.4 dated 2020-09-07
DESCRIPTION | 14 +++--- MD5 | 88 ++++++++++++++++++++--------------------- NEWS.md | 4 + R/coef.gensvm.R | 2 R/coef.gensvm.grid.R | 2 R/fitted.gensvm.R | 2 R/fitted.gensvm.grid.R | 2 R/gensvm-package.R | 2 R/gensvm.R | 2 R/gensvm.accuracy.R | 2 R/gensvm.grid.R | 10 ++-- R/gensvm.maxabs.scale.R | 2 R/gensvm.refit.R | 2 R/gensvm.train.test.split.R | 5 -- R/plot.gensvm.R | 2 R/plot.gensvm.grid.R | 2 R/predict.gensvm.R | 6 -- R/predict.gensvm.grid.R | 5 -- R/print.gensvm.R | 2 R/print.gensvm.grid.R | 2 README.md | 4 - inst/CITATION | 2 man/coef.gensvm.Rd | 2 man/coef.gensvm.grid.Rd | 2 man/fitted.gensvm.Rd | 2 man/fitted.gensvm.grid.Rd | 2 man/gensvm-package.Rd | 2 man/gensvm.Rd | 24 ++++++++--- man/gensvm.accuracy.Rd | 2 man/gensvm.generate.cv.idx.Rd | 2 man/gensvm.grid.Rd | 14 +++++- man/gensvm.load.full.grid.Rd | 2 man/gensvm.load.small.grid.Rd | 2 man/gensvm.load.tiny.grid.Rd | 2 man/gensvm.maxabs.scale.Rd | 2 man/gensvm.refit.Rd | 24 ++++++++--- man/gensvm.train.test.split.Rd | 14 ++++-- man/gensvm.validate.params.Rd | 12 ++++- man/plot.gensvm.Rd | 17 ++++++- man/plot.gensvm.grid.Rd | 2 man/predict.gensvm.Rd | 2 man/predict.gensvm.grid.Rd | 2 man/print.gensvm.Rd | 2 man/print.gensvm.grid.Rd | 2 src/Makevars | 3 - 45 files changed, 181 insertions(+), 123 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available.
Author: Maximilian Boeck [aut, cre] (<https://orcid.org/0000-0001-6024-8305>),
Martin Feldkircher [aut] (<https://orcid.org/0000-0002-5511-9215>),
Florian Huber [aut] (<https://orcid.org/0000-0002-2896-7921>),
Christopher Sims [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@wu.ac.at>
Diff between BGVAR versions 2.0.1 dated 2020-06-24 and 2.1.0 dated 2020-09-07
BGVAR-2.0.1/BGVAR/R/BGVAR.R |only BGVAR-2.0.1/BGVAR/R/bgvar_main.R |only BGVAR-2.0.1/BGVAR/R/fevd.decomp.R |only BGVAR-2.0.1/BGVAR/R/hd.decomp.R |only BGVAR-2.0.1/BGVAR/R/irf_main.R |only BGVAR-2.0.1/BGVAR/R/predict.bgvar.R |only BGVAR-2.0.1/BGVAR/man/AIC.bgvar.Rd |only BGVAR-2.0.1/BGVAR/man/BIC.bgvar.Rd |only BGVAR-2.0.1/BGVAR/man/IRF.Rd |only BGVAR-2.0.1/BGVAR/man/IRF.cf.Rd |only BGVAR-2.0.1/BGVAR/man/cond.pred.Rd |only BGVAR-2.0.1/BGVAR/man/fevd.decomp.Rd |only BGVAR-2.0.1/BGVAR/man/gfevd.decomp.Rd |only BGVAR-2.0.1/BGVAR/man/hd.decomp.Rd |only BGVAR-2.0.1/BGVAR/man/plot.bgvar.Rd |only BGVAR-2.0.1/BGVAR/man/plot.bgvar.fevd.Rd |only BGVAR-2.0.1/BGVAR/man/plot.bgvar.irf.Rd |only BGVAR-2.0.1/BGVAR/man/plot.bgvar.pred.Rd |only BGVAR-2.0.1/BGVAR/man/plot.bgvar.resid.Rd |only BGVAR-2.0.1/BGVAR/man/predict.bgvar.Rd |only BGVAR-2.0.1/BGVAR/man/print.bgvar.CD.Rd |only BGVAR-2.0.1/BGVAR/man/print.bgvar.Rd |only BGVAR-2.0.1/BGVAR/man/print.bgvar.lps.Rd |only BGVAR-2.0.1/BGVAR/man/print.bgvar.rmse.Rd |only BGVAR-2.1.0/BGVAR/DESCRIPTION | 12 BGVAR-2.1.0/BGVAR/MD5 | 105 - BGVAR-2.1.0/BGVAR/NAMESPACE | 29 BGVAR-2.1.0/BGVAR/NEWS | 20 BGVAR-2.1.0/BGVAR/R/RcppExports.R | 12 BGVAR-2.1.0/BGVAR/R/bgvar-package.R |only BGVAR-2.1.0/BGVAR/R/bgvar.R |only BGVAR-2.1.0/BGVAR/R/fevd.R |only BGVAR-2.1.0/BGVAR/R/hd.R |only BGVAR-2.1.0/BGVAR/R/helpers.R | 188 -- BGVAR-2.1.0/BGVAR/R/irf.R |only BGVAR-2.1.0/BGVAR/R/plot.R |only BGVAR-2.1.0/BGVAR/R/predict.R |only BGVAR-2.1.0/BGVAR/R/utils.R | 74 BGVAR-2.1.0/BGVAR/README.md | 10 BGVAR-2.1.0/BGVAR/build/vignette.rds |binary BGVAR-2.1.0/BGVAR/inst/doc/examples.R | 92 BGVAR-2.1.0/BGVAR/inst/doc/examples.Rmd | 118 - BGVAR-2.1.0/BGVAR/inst/doc/examples.html | 1037 +++++------ BGVAR-2.1.0/BGVAR/man/DIC.Rd | 4 BGVAR-2.1.0/BGVAR/man/avg.pair.cc.Rd | 6 BGVAR-2.1.0/BGVAR/man/bgvar.Rd | 40 BGVAR-2.1.0/BGVAR/man/coef.bgvar.Rd | 4 BGVAR-2.1.0/BGVAR/man/cond.predict.Rd |only BGVAR-2.1.0/BGVAR/man/conv.diag.Rd | 2 BGVAR-2.1.0/BGVAR/man/eerData.Rd | 2 BGVAR-2.1.0/BGVAR/man/eerDataspf.Rd | 2 BGVAR-2.1.0/BGVAR/man/fevd.Rd |only BGVAR-2.1.0/BGVAR/man/fitted.bgvar.Rd | 4 BGVAR-2.1.0/BGVAR/man/gfevd.Rd |only BGVAR-2.1.0/BGVAR/man/hd.Rd |only BGVAR-2.1.0/BGVAR/man/irf.Rd |only BGVAR-2.1.0/BGVAR/man/irfcf.Rd |only BGVAR-2.1.0/BGVAR/man/logLik.bgvar.Rd | 4 BGVAR-2.1.0/BGVAR/man/lps.bgvar.pred.Rd | 10 BGVAR-2.1.0/BGVAR/man/monthlyData.Rd | 2 BGVAR-2.1.0/BGVAR/man/pesaranData.Rd | 2 BGVAR-2.1.0/BGVAR/man/plot.Rd |only BGVAR-2.1.0/BGVAR/man/predict.Rd |only BGVAR-2.1.0/BGVAR/man/resid.corr.test.Rd | 5 BGVAR-2.1.0/BGVAR/man/residuals.bgvar.Rd | 8 BGVAR-2.1.0/BGVAR/man/rmse.bgvar.predict.Rd | 10 BGVAR-2.1.0/BGVAR/man/summary.bgvar.Rd | 8 BGVAR-2.1.0/BGVAR/man/vcov.bgvar.Rd | 4 BGVAR-2.1.0/BGVAR/src/BVAR_linear.cpp | 36 BGVAR-2.1.0/BGVAR/src/RcppExports.cpp | 26 BGVAR-2.1.0/BGVAR/src/gvar_stacking.cpp | 28 BGVAR-2.1.0/BGVAR/vignettes/examples.Rmd | 118 - BGVAR-2.1.0/BGVAR/vignettes/fullbib.bib | 2600 ++-------------------------- 73 files changed, 1132 insertions(+), 3490 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded. From 'GEOS' 3.8.0, repair of geometries may also be attempted using 'gMakeValid()', which may, however, return a collection of geometries of different types.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.5-3 dated 2020-05-08 and 0.5-5 dated 2020-09-07
ChangeLog | 20 ++++++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 33 +++++++++++++++---------------- NAMESPACE | 3 +- R/rgeos_topology.R | 10 +++++++++ configure | 19 +++++++++-------- configure.ac | 1 inst/ChangeLog | 20 ++++++++++++++++++ inst/SVN_VERSION | 2 - man/labelpt.Rd | 2 - man/misc-gDistance.Rd | 2 - man/topo-unary-gCoverageUnion.Rd |only man/topo-unary-gDelaunayTriangulation.Rd | 2 - man/topo-unary-gSimplify.Rd | 2 - man/wkt-functions.Rd | 6 ++--- src/init.c | 3 ++ src/rgeos.h | 4 +++ src/rgeos_topology.c | 9 ++++++++ 18 files changed, 108 insertions(+), 38 deletions(-)
Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.1.2 dated 2020-09-01 and 1.1.3 dated 2020-09-07
DESCRIPTION | 8 - MD5 | 20 ++-- NEWS.md | 5 + R/RcppExports.R | 38 ++++----- inst/doc/proc_approx.Rmd | 4 inst/doc/proc_approx.html | 42 +++++----- inst/doc/proc_exact.html | 18 ++-- inst/include/PoissonBinomial_RcppExports.h | 78 +++++++++---------- src/PoissonBinomial.cpp | 118 ++++++++++++++++++----------- src/RcppExports.cpp | 64 +++++++-------- vignettes/proc_approx.Rmd | 4 11 files changed, 218 insertions(+), 181 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Variable Importance via Oscillations
Description: Provides an easy to calculate local variable importance measure based on Ceteris Paribus profile
and global variable importance measure based on Partial Dependence Profiles.
Author: Anna Kozak [aut, cre],
Przemyslaw Biecek [aut, ths]
Maintainer: Anna Kozak <anna1993kozak@gmail.com>
Diff between vivo versions 0.2.0 dated 2020-07-02 and 0.2.1 dated 2020-09-07
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/calculate_weight.R | 4 ++-- R/global_variable_importance.R | 21 +++++++++++++++++---- R/local_variable_importance.R | 2 +- inst/doc/vignette_apartments_global.html | 14 +++++++------- inst/doc/vignette_apartments_local.html | 20 ++++++++++---------- man/calculate_weight.Rd | 4 ++-- man/global_variable_importance.Rd | 2 +- man/local_variable_importance.Rd | 2 +- tests/testthat/objects_for_tests.R | 12 ++++++------ 12 files changed, 68 insertions(+), 50 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 3.2.0 dated 2020-07-16 and 3.2.1 dated 2020-09-07
DESCRIPTION | 23 - MD5 | 85 +++--- NAMESPACE | 29 +- NEWS.md | 42 ++- R/RcppExports.R | 12 R/clustering.R | 28 +- R/data.R | 4 R/differential_expression.R | 6 R/dimensional_reduction.R | 276 ++++++++++++++------- R/generics.R | 64 +++++ R/integration.R | 31 +- R/objects.R | 348 +++++++++++++++++++++++++-- R/preprocessing.R | 41 ++- R/tree.R | 14 - R/utilities.R | 217 ++++++++++++++--- R/visualization.R | 404 +++++++++++++++++++++++++++----- README.md | 2 man/AddModuleScore.Rd | 33 +- man/Cells.Rd | 3 man/ColorDimSplit.Rd | 6 man/DimPlot.Rd | 14 + man/Distances.Rd |only man/FastRowScale.Rd |only man/FindNeighbors.Rd | 6 man/Index.Rd |only man/Indices.Rd |only man/LoadAnnoyIndex.Rd |only man/MULTIseqDemux.Rd | 2 man/Neighbor-class.Rd |only man/Neighbors.Rd |only man/PlotClusterTree.Rd | 3 man/RenameCells.Rd | 5 man/RidgePlot.Rd | 10 man/RowMergeSparseMatrices.Rd | 2 man/RunUMAP.Rd | 26 +- man/SaveAnnoyIndex.Rd |only man/TopNeighbors.Rd |only man/UpdateSymbolList.Rd | 2 man/VlnPlot.Rd | 13 - man/as.Graph.Rd | 6 man/as.Neighbor.Rd |only man/cc.genes.Rd | 2 man/cc.genes.updated.2019.Rd | 2 src/RcppExports.cpp | 45 ++- src/data_manipulation.cpp | 139 ++++++++--- src/data_manipulation.h | 3 src/valid_pointer.c |only tests/testthat/test_data_manipulation.R | 26 +- tests/testthat/test_objects.R | 74 +++++ 49 files changed, 1644 insertions(+), 404 deletions(-)
Title: R Commander Plug-in for Case 1 (Object Case) Best-Worst Scaling
Description: Adds menu items to the R Commander for implementing case 1 (object case) best-worst scaling (BWS1) from designing choice sets to measuring preferences for items. BWS1 is a question-based survey method that constructs various combinations of items (choice sets) using the experimental designs, asks respondents to select the best and worst items in each choice set, and then measures preferences for the items by analyzing the responses. For details on BWS1, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.BWS1 versions 0.1-2 dated 2020-06-19 and 0.1-3 dated 2020-09-07
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS |only R/RcmdrPlugin.BWS1.R | 10 ++++++---- man/RcmdrPlugin.BWS1-package.Rd | 16 ++++++++++++---- 5 files changed, 26 insertions(+), 15 deletions(-)
More information about RcmdrPlugin.BWS1 at CRAN
Permanent link
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: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between prioritylasso versions 0.2.3 dated 2019-12-17 and 0.2.4 dated 2020-09-07
prioritylasso-0.2.3/prioritylasso/data/datalist |only prioritylasso-0.2.4/prioritylasso/DESCRIPTION | 11 prioritylasso-0.2.4/prioritylasso/MD5 | 21 prioritylasso-0.2.4/prioritylasso/R/predict.prioritylasso.R | 6 prioritylasso-0.2.4/prioritylasso/R/prioritylasso.R | 2 prioritylasso-0.2.4/prioritylasso/build/vignette.rds |binary prioritylasso-0.2.4/prioritylasso/inst/doc/prioritylasso_vignette.R | 258 +- prioritylasso-0.2.4/prioritylasso/inst/doc/prioritylasso_vignette.html | 1209 +++++----- prioritylasso-0.2.4/prioritylasso/man/cvm_prioritylasso.Rd | 21 prioritylasso-0.2.4/prioritylasso/man/pl_data.Rd | 6 prioritylasso-0.2.4/prioritylasso/man/predict.prioritylasso.Rd | 9 prioritylasso-0.2.4/prioritylasso/man/prioritylasso.Rd | 21 12 files changed, 798 insertions(+), 766 deletions(-)
Title: Interpretive Clustering for Repertory Grids
Description: Shiny UI to identify cliques of related constructs in repertory grid data.
See Burr, King, & Heckmann (2020) <doi:10.1080/14780887.2020.1794088> for a description
of the interpretive clustering (IC) method.
Author: Mark Heckmann [aut, cre, cph] (<https://orcid.org/0000-0002-0736-7417>),
Viv Burr [aut],
Nigel King [aut]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between OpenRepGrid.ic versions 0.3.0 dated 2020-07-30 and 0.3.1 dated 2020-09-07
DESCRIPTION | 32 +++++++++++++++------- MD5 | 24 ++++++++--------- R/02-calculate.R | 8 ++++- R/OpenRepGrid.ic.R | 2 - inst/examples/01-process-excel-file.R | 6 ++-- inst/shiny/server.R | 2 - inst/shiny/ui.R | 48 +++++++++++++++++++++------------- man/OpenRepGrid.ic.Rd | 8 ++--- man/dt_default.Rd | 32 +++++++++++----------- man/emptify_object.Rd | 28 +++++++++---------- man/fnum.Rd | 22 +++++++-------- man/make-names.Rd | 34 ++++++++++++------------ man/network_graph_images.Rd | 6 +++- 13 files changed, 142 insertions(+), 110 deletions(-)
More information about OpenRepGrid.ic at CRAN
Permanent link
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.9.1 dated 2020-08-26 and 0.9.5 dated 2020-09-07
insight-0.9.1/insight/tests/testthat/test-panelr.R |only insight-0.9.5/insight/DESCRIPTION | 14 insight-0.9.5/insight/MD5 | 33 - insight-0.9.5/insight/NAMESPACE | 1 insight-0.9.5/insight/NEWS.md | 11 insight-0.9.5/insight/R/find_formula.R | 18 insight-0.9.5/insight/R/get_data.R | 6 insight-0.9.5/insight/R/is_model.R | 1 insight-0.9.5/insight/R/is_model_supported.R | 1 insight-0.9.5/insight/R/n_obs.R | 7 insight-0.9.5/insight/R/utils_get_data.R | 95 ++++ insight-0.9.5/insight/R/utils_model_info.R | 2 insight-0.9.5/insight/build/partial.rdb |binary insight-0.9.5/insight/man/get_data.Rd | 4 insight-0.9.5/insight/tests/testthat/test-BayesFactorBF.R | 317 +++++++------- insight-0.9.5/insight/tests/testthat/test-crch.R | 2 insight-0.9.5/insight/tests/testthat/test-iv_robust.R | 1 insight-0.9.5/insight/tests/testthat/test-ivreg.R | 2 18 files changed, 309 insertions(+), 206 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-40 dated 2020-03-03 and 3.1-42 dated 2020-09-07
HH-3.1-40/HH/R/arima.diag.hh.s |only HH-3.1-40/HH/R/guiRemove.s |only HH-3.1-40/HH/R/intxplot.s |only HH-3.1-40/HH/R/orthogonal.s |only HH-3.1-40/HH/R/panel.pairs.hh.s |only HH-3.1-40/HH/R/panel.rug.h2.s |only HH-3.1-40/HH/R/print.multicomp.hh.s |only HH-3.1-40/HH/R/residual.plots.s |only HH-3.1-40/HH/R/stripbak.s |only HH-3.1-40/HH/R/sufficient.s |only HH-3.1-40/HH/R/trellis.device.hh.r |only HH-3.1-40/HH/R/trellis.device.hh.s |only HH-3.1-42/HH/DESCRIPTION | 8 - HH-3.1-42/HH/MD5 | 135 ++++++++++++++---------------- HH-3.1-42/HH/NEWS | 71 ++++++++++++++- HH-3.1-42/HH/R/arima.diag.hh.R |only HH-3.1-42/HH/R/as.likert.R | 4 HH-3.1-42/HH/R/as.matrix.listOfMatrices.R | 12 ++ HH-3.1-42/HH/R/col.hh.R | 70 +++++++++------ HH-3.1-42/HH/R/guiRemove.R |only HH-3.1-42/HH/R/hov.R | 12 -- HH-3.1-42/HH/R/hovBF.R | 2 HH-3.1-42/HH/R/interaction2wt.R | 46 ---------- HH-3.1-42/HH/R/intxplot.R |only HH-3.1-42/HH/R/ladder.R | 25 +---- HH-3.1-42/HH/R/likert.R | 64 +++++++------- HH-3.1-42/HH/R/likertMosaic.R | 11 ++ HH-3.1-42/HH/R/orthogonal.R |only HH-3.1-42/HH/R/panel.pairs.hh.R |only HH-3.1-42/HH/R/panel.rug.h2.R |only HH-3.1-42/HH/R/plot.hov.R | 51 ++--------- HH-3.1-42/HH/R/print.multicomp.hh.R |only HH-3.1-42/HH/R/residual.plots.R |only HH-3.1-42/HH/R/stripbak.R |only HH-3.1-42/HH/R/sufficient.R |only HH-3.1-42/HH/R/trellis.device.hh.R |only HH-3.1-42/HH/R/xysplom.R | 17 --- HH-3.1-42/HH/build/partial.rdb |binary HH-3.1-42/HH/demo/likert-paper.r | 27 +++++- HH-3.1-42/HH/inst/CITATION | 12 +- HH-3.1-42/HH/man/HH.package.Rd | 13 +- HH-3.1-42/HH/man/HHscriptnames.Rd | 15 +-- HH-3.1-42/HH/man/NormalAndT.Rd | 2 HH-3.1-42/HH/man/NormalAndTplot.Rd | 2 HH-3.1-42/HH/man/X.residuals.Rd | 11 +- HH-3.1-42/HH/man/ancova-class.Rd | 11 +- HH-3.1-42/HH/man/ancova.Rd | 11 +- HH-3.1-42/HH/man/ancovaplot.Rd | 11 +- HH-3.1-42/HH/man/arma.loop.Rd | 8 + HH-3.1-42/HH/man/as.likert.Rd | 2 HH-3.1-42/HH/man/as.multicomp.Rd | 12 +- HH-3.1-42/HH/man/cp.Rd | 11 +- HH-3.1-42/HH/man/datasets.Rd | 16 +-- HH-3.1-42/HH/man/hov.Rd | 13 +- HH-3.1-42/HH/man/hovBF.Rd | 2 HH-3.1-42/HH/man/interaction2wt.Rd | 16 +-- HH-3.1-42/HH/man/intxplot.Rd | 2 HH-3.1-42/HH/man/ladder.Rd | 35 +++---- HH-3.1-42/HH/man/likert.Rd | 4 HH-3.1-42/HH/man/likertMosaic.Rd | 4 HH-3.1-42/HH/man/lm.case.Rd | 11 +- HH-3.1-42/HH/man/mmc.Rd | 10 +- HH-3.1-42/HH/man/mmc.mean.Rd | 10 +- HH-3.1-42/HH/man/multicomp.order.Rd | 10 +- HH-3.1-42/HH/man/multicomp.reverse.Rd | 10 +- HH-3.1-42/HH/man/odds.ratio.Rd | 11 +- HH-3.1-42/HH/man/orthog.complete.Rd | 11 +- HH-3.1-42/HH/man/panel.cartesian.Rd | 11 +- HH-3.1-42/HH/man/panel.interaction2wt.Rd | 11 +- HH-3.1-42/HH/man/plot.hov.Rd | 15 +-- HH-3.1-42/HH/man/plot.mmc.multicomp.Rd | 10 +- HH-3.1-42/HH/man/plot.multicomp.Rd | 10 +- HH-3.1-42/HH/man/positioned-class.Rd | 11 +- HH-3.1-42/HH/man/regr1.plot.Rd | 11 +- HH-3.1-42/HH/man/regr2.plot.Rd | 11 +- HH-3.1-42/HH/man/resid.squares.Rd | 11 +- HH-3.1-42/HH/man/residual.plots.Rd | 11 +- HH-3.1-42/HH/man/tsdiagplot.Rd | 8 + HH-3.1-42/HH/man/vif.Rd | 11 +- HH-3.1-42/HH/man/xysplom.Rd | 13 +- 80 files changed, 508 insertions(+), 477 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Many conventional clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the the mirrored density plot (MD-plot) of clusterability are implemented. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>),
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.2.3 dated 2020-06-26 and 1.2.4 dated 2020-09-07
FCPS-1.2.3/FCPS/data/datalist |only FCPS-1.2.4/FCPS/DESCRIPTION | 14 FCPS-1.2.4/FCPS/MD5 | 35 - FCPS-1.2.4/FCPS/R/ClusterCount.R | 14 FCPS-1.2.4/FCPS/R/GenieClustering.R | 2 FCPS-1.2.4/FCPS/R/HierarchicalClusterDists.R | 2 FCPS-1.2.4/FCPS/R/MinimalEnergyClustering.R | 2 FCPS-1.2.4/FCPS/R/MinimaxLinkageClustering.R | 2 FCPS-1.2.4/FCPS/R/internalMDSestimate.R | 2 FCPS-1.2.4/FCPS/R/kmeansDist.R | 2 FCPS-1.2.4/FCPS/build/partial.rdb |binary FCPS-1.2.4/FCPS/build/vignette.rds |binary FCPS-1.2.4/FCPS/inst/doc/FCPS.html | 274 +++++++------- FCPS-1.2.4/FCPS/man/APclustering.Rd | 2 FCPS-1.2.4/FCPS/man/AutomaticProjectionBasedClustering.Rd | 11 FCPS-1.2.4/FCPS/man/ClusterCount.Rd | 60 +-- FCPS-1.2.4/FCPS/man/ClusterabilityMDplot.Rd | 4 FCPS-1.2.4/FCPS/man/DatabionicSwarmClustering.Rd | 7 FCPS-1.2.4/FCPS/man/HierarchicalClustering.Rd | 9 19 files changed, 239 insertions(+), 203 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.24.0 dated 2020-09-02 and 0.26.0 dated 2020-09-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-modelsummary.R | 13 +++++++------ 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Extension for 'DALEX' Package
Description: Provides wrapper of various machine learning models.
In applied machine learning, there
is a strong belief that we need to strike a balance
between interpretability and accuracy.
However, in field of the interpretable machine learning,
there are more and more new ideas for explaining black-box models,
that are implemented in 'R'.
'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models
including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library.
Important part of the package is Champion-Challenger analysis and innovative approach
to model performance across subsets of test data presented in Funnel Plot.
Third branch of 'DALEXtra' package is aspect importance analysis
that provides instance-level explanations for the groups of explanatory variables.
Author: Szymon Maksymiuk [aut, cre] (<https://orcid.org/0000-0002-3120-1601>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>),
Anna Kozak [ctb],
Hubert Baniecki [ctb]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between DALEXtra versions 1.3.2 dated 2020-07-28 and 2.0 dated 2020-09-07
DALEXtra-1.3.2/DALEXtra/R/aspect_importance.R |only DALEXtra-1.3.2/DALEXtra/man/aspect_importance.Rd |only DALEXtra-1.3.2/DALEXtra/man/aspect_importance_single.Rd |only DALEXtra-1.3.2/DALEXtra/man/get_sample.Rd |only DALEXtra-1.3.2/DALEXtra/man/group_variables.Rd |only DALEXtra-1.3.2/DALEXtra/man/plot.aspect_importance.Rd |only DALEXtra-1.3.2/DALEXtra/man/plot_aspects_importance_grouping.Rd |only DALEXtra-1.3.2/DALEXtra/man/plot_group_variables.Rd |only DALEXtra-1.3.2/DALEXtra/man/triplot.Rd |only DALEXtra-1.3.2/DALEXtra/tests/testthat/test_aspect_importance.R |only DALEXtra-2.0/DALEXtra/DESCRIPTION | 17 +--- DALEXtra-2.0/DALEXtra/MD5 | 41 ++++------ DALEXtra-2.0/DALEXtra/NAMESPACE | 39 ++------- DALEXtra-2.0/DALEXtra/NEWS.md | 6 + DALEXtra-2.0/DALEXtra/R/explain_mlr3.R | 2 DALEXtra-2.0/DALEXtra/R/explain_tidymodels.R |only DALEXtra-2.0/DALEXtra/R/model_info.R | 21 +++++ DALEXtra-2.0/DALEXtra/R/predict_surrogate.R |only DALEXtra-2.0/DALEXtra/R/yhat.R | 29 +++++++ DALEXtra-2.0/DALEXtra/inst/CITATION |only DALEXtra-2.0/DALEXtra/man/explain_mlr3.Rd | 2 DALEXtra-2.0/DALEXtra/man/explain_tidymodels.Rd |only DALEXtra-2.0/DALEXtra/man/figures/unnamed-chunk-5-1.png |binary DALEXtra-2.0/DALEXtra/man/figures/unnamed-chunk-8-2.png |binary DALEXtra-2.0/DALEXtra/man/figures/unnamed-chunk-8-3.png |binary DALEXtra-2.0/DALEXtra/man/figures/unnamed-chunk-8-4.png |binary DALEXtra-2.0/DALEXtra/man/model_info.Rd | 4 DALEXtra-2.0/DALEXtra/man/predict_surrogate.Rd |only DALEXtra-2.0/DALEXtra/man/yhat.Rd | 4 29 files changed, 102 insertions(+), 63 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 8.400 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.2.14.1.1 dated 2020-08-27 and 0.2.14.2.1 dated 2020-09-07
ChangeLog | 7 +++ DESCRIPTION | 6 +-- MD5 | 12 +++--- NEWS.md | 6 +++ inst/doc/using-rcppensmallen.html | 20 +++++----- inst/include/ensmallen_bits/ens_version.hpp | 2 - inst/include/ensmallen_bits/problems/fonseca_fleming_function.hpp | 20 ++++++---- 7 files changed, 45 insertions(+), 28 deletions(-)
Title: Helps Grade Assignment Submissions that are R Scripts
Description: After being given the location of your students' submissions and a test file, the function runs each .R file, and evaluates the results from all the given tests. Results are neatly returned in a data frame that has a row for each student, and a column for each test.
Author: Taylor Brown [aut, cre]
Maintainer: Taylor Brown <trb5me@virginia.edu>
Diff between gradeR versions 1.0.8 dated 2020-09-03 and 1.0.9 dated 2020-09-07
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 6 + R/grade.r | 124 +++++++++++++++-------------- build/vignette.rds |binary inst/doc/gradeR.html | 16 --- inst/doc/using_gradeR_with_Gradescope.html | 16 --- 7 files changed, 83 insertions(+), 99 deletions(-)
Title: Dynamic Models for Survival Data
Description: Time-varying coefficient models for interval censored and
right censored survival data including
1) Bayesian Cox model with time-independent, time-varying or
dynamic coefficients for right censored and interval censored data studied by
Sinha et al. (1999) <doi:10.1111/j.0006-341X.1999.00585.x> and
Wang et al. (2013) <doi:10.1007/s10985-013-9246-8>,
2) Spline based time-varying coefficient Cox model for right censored data
proposed by Perperoglou et al. (2006) <doi:10.1016/j.cmpb.2005.11.006>, and
3) Transformation model with time-varying coefficients for right censored data
using estimating equations proposed by
Peng and Huang (2007) <doi:10.1093/biomet/asm058>.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>),
Ming-Hui Chen [aut],
Xiaojing Wang [aut],
Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between dynsurv versions 0.4-1 dated 2020-08-28 and 0.4-2 dated 2020-09-07
ChangeLog | 8 +++++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/CITATION | 2 +- inst/examples/ex-bayesCox.R | 4 ++++ man/bayesCox.Rd | 4 ++++ 6 files changed, 25 insertions(+), 11 deletions(-)
Title: A Cheminformatics Modeling Laboratory for Fitting and Assessing
Machine Learning Models
Description: Contains a set of methods for fitting models and methods for
validating the resulting models. The statistical methodologies comprise
a comprehensive collection of approaches whose validity and utility have
been accepted by experts in the Cheminformatics field. As promising new
methodologies emerge from the statistical and data-mining communities, they
will be incorporated into the laboratory. These methods are aimed at discovering
quantitative structure-activity relationships (QSARs). However, the user can
directly input their own choices of descriptors and responses, so the capability
for comparing models is effectively unlimited.
Author: Jacqueline Hughes-Oliver [aut],
Jeremy Ash [aut, cre],
Atina Brooks [aut]
Maintainer: Jeremy Ash <jrash@ncsu.edu>
Diff between chemmodlab versions 1.0.0 dated 2017-04-21 and 1.1.0 dated 2020-09-07
DESCRIPTION | 31 ++-- MD5 | 29 ++- NAMESPACE | 36 ++-- NEWS.md |only R/applicability_domain.R |only R/model_assess.R | 12 + R/model_train.R | 332 ++++++++++++++++++++++++++++++++++++--------- R/performance_measures.R | 10 + R/read_in_data.R | 53 ++++--- R/set_model_params.R | 2 man/ApplicabilityDomain.Rd |only man/CombineSplits.Rd | 8 - man/MakeModelDefaults.Rd | 9 - man/ModelTrain.Rd | 68 +++++++-- man/aid364.Rd | 7 man/chemmodlab.Rd | 21 ++ man/plot.chemmodlab.Rd | 18 +- 17 files changed, 467 insertions(+), 169 deletions(-)
Title: Miscellaneous Tools
Description: Functions for performing quick observations or evaluations of data, including a variety of ways to list objects by size, class, etc. In addition, functions which mimic Unix shell commands, including 'head', 'tail' ,'pushd' ,and 'popd'. The functions 'seqle' and 'reverse.seqle' mimic the base 'rle' but can search for linear sequences. The function 'splatnd' allows the user to generate zero-argument commands without the need for 'makeActiveBinding' .
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>
Diff between cgwtools versions 3.0.1 dated 2019-02-12 and 3.2 dated 2020-09-07
cgwtools-3.0.1/cgwtools/R/lsdim.R |only cgwtools-3.0.1/cgwtools/man/lsdim.Rd |only cgwtools-3.2/cgwtools/ChangeLog | 1 cgwtools-3.2/cgwtools/DESCRIPTION | 8 +-- cgwtools-3.2/cgwtools/MD5 | 27 ++++++++--- cgwtools-3.2/cgwtools/NAMESPACE | 1 cgwtools-3.2/cgwtools/R/binit.R |only cgwtools-3.2/cgwtools/R/dim.R |only cgwtools-3.2/cgwtools/R/dirdir.R |only cgwtools-3.2/cgwtools/R/lssize.R | 77 ++++++++++++++++++--------------- cgwtools-3.2/cgwtools/R/minmaxcolrow.r |only cgwtools-3.2/cgwtools/R/segSegInt.r |only cgwtools-3.2/cgwtools/R/seqfinders.R |only cgwtools-3.2/cgwtools/man/binit.Rd |only cgwtools-3.2/cgwtools/man/dim.Rd |only cgwtools-3.2/cgwtools/man/dirdir.Rd |only cgwtools-3.2/cgwtools/man/findpat.Rd |only cgwtools-3.2/cgwtools/man/lsdata.Rd | 9 ++- cgwtools-3.2/cgwtools/man/minrow.Rd |only cgwtools-3.2/cgwtools/man/polyInt.Rd |only cgwtools-3.2/cgwtools/man/resave.Rd | 13 +++-- cgwtools-3.2/cgwtools/man/segSegInt.Rd |only 22 files changed, 79 insertions(+), 57 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-13 0.1.0
2019-12-08 0.0.3
2019-11-11 0.0.2
2019-10-06 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-12 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-06 1.0.4
2019-11-28 1.0.3
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] (<https://orcid.org/0000-0002-6608-0619>),
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.2.1 dated 2020-09-01 and 1.2.2 dated 2020-09-07
DESCRIPTION | 8 MD5 | 18 NEWS | 20 R/nifti.R | 14 inst/doxygen/html/a00002_source.html | 1097 +++++++++++++++++----------------- inst/include/RNifti/NiftiImage_impl.h | 50 - inst/include/niftilib/nifti2_image.h | 2 man/niftiHeader.Rd | 8 src/main.cpp | 30 tests/testthat/test-05-nifti.R | 6 10 files changed, 668 insertions(+), 585 deletions(-)
Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis
are included in this package. In particular, it computes standard errors for
parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>
Diff between EFAutilities versions 2.0.0 dated 2019-02-06 and 2.1.0 dated 2020-09-07
EFAutilities-2.0.0/EFAutilities/R/BootJack20161129_c.R |only EFAutilities-2.0.0/EFAutilities/R/ModelTest20181231_c.R |only EFAutilities-2.0.0/EFAutilities/R/MultRandRotation20190126_2_c.R |only EFAutilities-2.0.0/EFAutilities/R/PolycorGamma20161107_c.R |only EFAutilities-2.0.0/EFAutilities/R/efa20190119_c.R |only EFAutilities-2.0.0/EFAutilities/R/efaMR20190129_c.R |only EFAutilities-2.0.0/EFAutilities/R/oblqSE20181210_c.R |only EFAutilities-2.0.0/EFAutilities/R/orthSE20181210_c.R |only EFAutilities-2.0.0/EFAutilities/R/ssem20190120_c.R |only EFAutilities-2.0.0/EFAutilities/R/ssemSE20181212_c.R |only EFAutilities-2.1.0/EFAutilities/DESCRIPTION | 17 EFAutilities-2.1.0/EFAutilities/MD5 | 60 EFAutilities-2.1.0/EFAutilities/NAMESPACE | 7 EFAutilities-2.1.0/EFAutilities/NEWS.md | 3 EFAutilities-2.1.0/EFAutilities/R/BootJack20200816_c.R |only EFAutilities-2.1.0/EFAutilities/R/CompareSolutions20190124_c.R | 2 EFAutilities-2.1.0/EFAutilities/R/EFAModelDerivatives20161125_c.R | 2 EFAutilities-2.1.0/EFAutilities/R/ESEMpstQ20180816_c.R | 1 EFAutilities-2.1.0/EFAutilities/R/ModelTest20200827_c.R |only EFAutilities-2.1.0/EFAutilities/R/MultRandRotation20190126_c.r |only EFAutilities-2.1.0/EFAutilities/R/OblqDerivatives20181211_c.R | 4 EFAutilities-2.1.0/EFAutilities/R/efa20200828_c.R |only EFAutilities-2.1.0/EFAutilities/R/efaMR20200816_c.R |only EFAutilities-2.1.0/EFAutilities/R/oblqSE20200513._cR.R |only EFAutilities-2.1.0/EFAutilities/R/orthSE20200513_c.R |only EFAutilities-2.1.0/EFAutilities/R/polyACMf_c.R |only EFAutilities-2.1.0/EFAutilities/R/ssem20200709_c.R |only EFAutilities-2.1.0/EFAutilities/R/ssemSE20200513_c.R |only EFAutilities-2.1.0/EFAutilities/README.md | 2 EFAutilities-2.1.0/EFAutilities/build/vignette.rds |binary EFAutilities-2.1.0/EFAutilities/inst/doc/EFAutilities-vignette.R | 56 EFAutilities-2.1.0/EFAutilities/inst/doc/EFAutilities-vignette.Rmd | 55 EFAutilities-2.1.0/EFAutilities/inst/doc/EFAutilities-vignette.html |15876 +++++++++- EFAutilities-2.1.0/EFAutilities/man/BFI228.rd | 16 EFAutilities-2.1.0/EFAutilities/man/CPAI537.rd | 12 EFAutilities-2.1.0/EFAutilities/man/PolychoricRM.Rd |only EFAutilities-2.1.0/EFAutilities/man/efa.Rd | 87 EFAutilities-2.1.0/EFAutilities/man/efaMR.Rd | 2 EFAutilities-2.1.0/EFAutilities/man/ssem.Rd | 78 EFAutilities-2.1.0/EFAutilities/src |only EFAutilities-2.1.0/EFAutilities/vignettes/EFAutilities-vignette.Rmd | 55 41 files changed, 15945 insertions(+), 390 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph] (author of bundled libyajl)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between jsonlite versions 1.7.0 dated 2020-06-25 and 1.7.1 dated 2020-09-07
DESCRIPTION | 33 ++++++++++------------ MD5 | 46 ++++++++++++++++---------------- NEWS | 7 ++++ R/asJSON.ITime.R |only R/asJSON.character.R | 4 ++ R/asJSON.sf.R | 11 ++++--- R/fromJSON.R | 1 R/pack.R | 4 +- R/rbind_pages.R | 2 - R/read_json.R | 1 R/stream.R | 6 +++- R/unbox.R | 4 +- inst/doc/json-aaquickstart.html | 12 ++++---- inst/doc/json-apis.html | 2 - inst/doc/json-mapping.pdf |binary inst/doc/json-paging.Rmd | 2 - inst/doc/json-paging.html | 4 +- man/fromJSON.Rd | 3 ++ man/read_json.Rd | 3 ++ man/stream_in.Rd | 8 ++++- man/unbox.Rd | 4 +- tests/testthat/test-serializeJSON-S4.R | 15 +++------- tests/testthat/test-toJSON-sf.R | 4 +- tests/testthat/test_rbind_pages-names.R |only vignettes/json-paging.Rmd | 2 - 25 files changed, 101 insertions(+), 77 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in Gjessing, HK and Lie, RT (2006) <doi:10.1111/j.1529-8817.2005.00218.x>.
Author: Hakon K. Gjessing [aut, cre],
Miriam Gjerdevik [ctb] (functions 'lineByLine', 'cbindFiles',
'rbindFiles', 'snpPower', 'snpSampleSize', 'hapSim', 'hapRun',
'hapPower', 'hapPowerAsymp', and 'hapRelEff'),
Julia Romanowska [ctb] (<https://orcid.org/0000-0001-6733-1953>, new
data format, parallelisation, new documentation),
Oivind Skare [ctb] (TDT tests)
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 7.2.2 dated 2020-01-07 and 7.2.3 dated 2020-09-07
DESCRIPTION | 22 MD5 | 62 NAMESPACE | 3 R/f.data.R | 6 R/f.get.gen.data.cols.R | 2 R/genDataGetPart.R | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/A_Haplin_intro_installation.R | 24 inst/doc/A_Haplin_intro_installation.html | 577 ++++-- inst/doc/B_Reading_data.R | 158 - inst/doc/B_Reading_data.html | 1159 ++++++++----- inst/doc/C_Running_Haplin.R | 202 +- inst/doc/C_Running_Haplin.html | 2556 ++++++++++++++++-------------- inst/doc/D_Running_Haplin_on_cluster.R | 66 inst/doc/D_Running_Haplin_on_cluster.html | 623 +++++-- inst/doc/E_hapRelEff.R | 74 inst/doc/E_hapRelEff.html | 667 +++++-- man/create.missingness.matrix.Rd | 6 man/f.convert.matrix.ff.Rd | 9 man/genDataGetPart.Rd | 17 man/genDataPreprocess.Rd | 13 man/genDataRead.Rd | 20 man/getChildren.Rd | 8 man/getDyads.Rd | 8 man/getFathers.Rd | 8 man/getFullTriads.Rd | 8 man/getMothers.Rd | 8 man/plot.haplinSlide.Rd | 17 man/plot.haplinStrat.Rd | 17 man/plotPValues.Rd | 11 man/showGen.Rd | 3 32 files changed, 3790 insertions(+), 2568 deletions(-)
Title: Latent Class Analysis with Group Variable
Description: Fits latent class analysis (LCA) including group variable and covariates.
The group variable can be handled either by multilevel LCA described in Vermunt (2003) <DOI:10.1111/j.0081-1750.2003.t01-1-00131.x> or standard LCA at each level of group variable.
The covariates can be incorporated in the form of logistic regression (Bandeen-Roche et al. (1997) <DOI:10.1080/01621459.1997.10473658>).
Author: Youngsun Kim [aut, cre],
Hwan Chung [aut]
Maintainer: Youngsun Kim <kim0sun@korea.ac.kr>
Diff between glca versions 0.1.1 dated 2020-05-30 and 1.0.0 dated 2020-09-07
glca-0.1.1/glca/data/brfss.rda |only glca-0.1.1/glca/data/gss.rda |only glca-0.1.1/glca/data/nhanes.rda |only glca-0.1.1/glca/man/brfss.Rd |only glca-0.1.1/glca/man/gss.Rd |only glca-0.1.1/glca/man/nhanes.Rd |only glca-1.0.0/glca/DESCRIPTION | 24 +- glca-1.0.0/glca/MD5 | 68 +++--- glca-1.0.0/glca/NAMESPACE | 3 glca-1.0.0/glca/R/RcppExports.R | 12 - glca-1.0.0/glca/R/coef.glca.R | 195 +++++++++++++---- glca-1.0.0/glca/R/dataset.r | 194 ++++------------- glca-1.0.0/glca/R/glca.R | 75 +++--- glca-1.0.0/glca/R/glca.gof.R | 392 +++++++++++++----------------------- glca-1.0.0/glca/R/glca_em.R | 125 ++++++----- glca-1.0.0/glca/R/glca_em_test.R | 135 +++++++----- glca-1.0.0/glca/R/glca_encode.R | 223 +++++++++++--------- glca-1.0.0/glca/R/glca_gnr.R | 61 ++--- glca-1.0.0/glca/R/glca_init.R | 44 ++-- glca-1.0.0/glca/R/glca_init_test.R | 2 glca-1.0.0/glca/R/glca_output.R | 195 ++++++++--------- glca-1.0.0/glca/R/glca_score.R | 153 +++++++------- glca-1.0.0/glca/R/package.R | 6 glca-1.0.0/glca/R/plot.glca.R | 87 ++++--- glca-1.0.0/glca/R/print.glca.R | 54 +++- glca-1.0.0/glca/R/print.glca.gof.R | 46 +--- glca-1.0.0/glca/R/summary.glca.R | 132 ++++++++---- glca-1.0.0/glca/build/partial.rdb |binary glca-1.0.0/glca/data/gss08.rda |only glca-1.0.0/glca/data/nyts18.rda |only glca-1.0.0/glca/man/coef.glca.Rd | 11 - glca-1.0.0/glca/man/glca-package.Rd | 4 glca-1.0.0/glca/man/glca.Rd | 64 +++-- glca-1.0.0/glca/man/glca.gof.Rd | 64 +++-- glca-1.0.0/glca/man/gss08.Rd |only glca-1.0.0/glca/man/nyts18.Rd |only glca-1.0.0/glca/man/plot.glca.Rd | 22 +- glca-1.0.0/glca/man/summary.glca.Rd | 3 glca-1.0.0/glca/src/RcppExports.cpp | 36 ++- glca-1.0.0/glca/src/glca.cpp | 195 ++++++++++++++--- 40 files changed, 1409 insertions(+), 1216 deletions(-)
Title: Factor-Adjusted Robust Multiple Testing
Description: Performs robust multiple testing for means in the presence of known and unknown latent factors presented in Fan et al.(2019) "FarmTest: Factor-Adjusted Robust Multiple Testing With Approximate False Discovery Control" <doi:10.1080/01621459.2018.1527700>.
Implements a series of adaptive Huber methods combined with fast data-drive tuning schemes proposed in Ke et al.(2019) "User-Friendly Covariance Estimation for Heavy-Tailed Distributions" <doi:10.1214/19-STS711> to estimate model parameters and construct test statistics that are robust against heavy-tailed and/or asymmetric error distributions.
Extensions to two-sample simultaneous mean comparison problems are also included.
As by-products, this package contains functions that compute adaptive Huber mean, covariance and regression estimators that are of independent interest.
Author: Xiaoou Pan [aut, cre],
Yuan Ke [aut],
Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>
Diff between FarmTest versions 2.1.0 dated 2020-04-28 and 2.2.0 dated 2020-09-07
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ R/FarmTest-package.R | 4 +- R/FarmTest.R | 18 ++++++++--- R/RcppExports.R | 16 ++++++++-- README.md | 2 - man/FarmTest-package.Rd | 4 +- man/huber.mean.Rd | 2 - man/huber.reg.Rd | 8 +++-- src/FarmTest.cpp | 75 ++++++++++++++++++++++++++++++++++++++++++++---- src/RcppExports.cpp | 60 ++++++++++++++++++++++++++++++++++---- 11 files changed, 176 insertions(+), 43 deletions(-)