Title: Eigenvectors from Eigenvalues Sparse Principal Component
Analysis (EESPCA)
Description: Contains logic for computing sparse principal components via the EESPCA method,
which is based on an approximation of the eigenvector/eigenvalue identity.
Includes logic to support execution of the TPower and rifle sparse PCA methods,
as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle
via cross-validation to minimize the out-of-sample reconstruction error.
H. Robert Frost (2021) <arXiv:2006.01924>.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between EESPCA versions 0.4.0 dated 2021-10-06 and 0.5.0 dated 2021-10-13
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NAMESPACE | 2 +- R/EESPCA.R | 30 ++++++++++++++++++++++++------ inst/doc/EESPCA_Example.pdf |binary man/ComputeResidualMatrix.Rd | 8 +++++--- man/EESPCA-package.Rd | 3 ++- man/Reconstruct.Rd |only man/ReconstructionError.Rd | 8 +++++--- 9 files changed, 48 insertions(+), 24 deletions(-)
Title: Colorblind-Friendly Color Maps for R
Description: Color maps designed to improve graph readability for readers with
common forms of color blindness and/or color vision deficiency. The color
maps are also perceptually-uniform, both in regular form and also when
converted to black-and-white for printing. This package also contains
'ggplot2' bindings for discrete and continuous color and fill scales. A lean
version of the package called 'viridisLite' that does not include the
'ggplot2' bindings can be found at
<https://cran.r-project.org/package=viridisLite>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph],
Marco Sciaini [ctb, cph],
Antônio Pedro Camargo [ctb, cph],
Cédric Scherer [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.6.1 dated 2021-05-11 and 0.6.2 dated 2021-10-13
DESCRIPTION | 12 ++--- MD5 | 14 +++--- NEWS.md | 16 ++++++ build/vignette.rds |binary inst/doc/intro-to-viridis.R | 14 ++---- inst/doc/intro-to-viridis.Rmd | 16 +++--- inst/doc/intro-to-viridis.html | 95 +++++++++++++++++++++-------------------- vignettes/intro-to-viridis.Rmd | 16 +++--- 8 files changed, 96 insertions(+), 87 deletions(-)
Title: Truncated Positive Normal Model and Extensions
Description: Provide data generation and estimation tools for the truncated positive normal
model discussed in Gomez, Olmos, Varela and Bolfarine (2018) <doi:10.1007/s11766-018-3354-x>, the
slash truncated positive normal distribution and the bimodal truncated positive normal
distribution.
Author: Diego Gallardo [aut, cre],
Hector J. Gomez [aut],
Yolanda M. Gomez [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between tpn versions 1.0 dated 2021-07-19 and 1.1 dated 2021-10-13
DESCRIPTION | 21 ++++++++++++--------- INDEX | 2 ++ MD5 | 15 +++++++++++---- NAMESPACE | 7 ++++--- NEWS.md |only R/dbtpn.R |only R/est.btpn.R |only R/est.tpn.R | 2 +- R/pbtpn.R |only R/rbtpn.R |only man/btpn.Rd |only man/est.btpn.Rd |only 12 files changed, 30 insertions(+), 17 deletions(-)
Title: Power Calculations for SNP Studies with Censored Outcomes
Description: Conduct asymptotic and empirical power and sample size calculations for Single-Nucleotide Polymorphism (SNP) association studies with right censored time to event outcomes.
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Alexander Sibley <dcibioinformatics@duke.edu>
Diff between survSNP versions 0.24 dated 2016-06-29 and 0.25 dated 2021-10-13
DESCRIPTION | 11 +++++------ MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 6 +++--- NEWS | 6 ++++++ build/vignette.rds |binary configure | 24 +++++++++++++----------- configure.ac | 5 +++-- inst/CITATION | 4 ++-- inst/doc/survSNP.R | 26 +++++++++++++------------- inst/doc/survSNP.pdf |binary man/asypow.Rd | 2 +- man/censbnd.Rd | 2 +- man/hwe.Rd | 2 +- man/sim.snp.expsurv.power.Rd | 2 +- man/sim.snp.expsurv.sctest.Rd | 2 +- man/surv.exp.gt.model.Rd | 2 +- man/survSNP-package.Rd | 2 +- man/survSNP.power.table.Rd | 2 +- src/init.c |only 19 files changed, 71 insertions(+), 62 deletions(-)
Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Statistical methods for analyzing case-control point data. Methods include the ratio of kernel densities, the difference in K Functions, the spatial scan statistic, and q nearest neighbors of cases.
Author: Joshua French [aut, cre] (<https://orcid.org/0000-0002-9708-3353>)
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smacpod versions 2.2.2 dated 2021-09-14 and 2.3 dated 2021-10-13
DESCRIPTION | 14 +-- MD5 | 64 +++++++++------ NAMESPACE | 8 + NEWS | 4 R/Kdest.R | 60 +++++++------- R/extract.clusters.R |only R/kd.R | 8 - R/kdest-print.R | 8 + R/kdest-summary.R |only R/kdplus.test.R | 48 ++++++++++- R/logrr.R | 186 +++++++++++++++++++++++---------------------- R/logrr.test.R | 48 +++++++++-- R/logrrenv-print.R |only R/plot.kdenv.R | 21 ++--- R/plot.spscan.R | 35 +++++++- R/print.spscan.R |only R/qnn.test.R | 5 - R/spdensity.R | 1 R/spscan.test.R | 105 ++++++++++++++----------- R/summary.spscan.R |only build |only inst |only man/clusters.Rd |only man/kd.Rd | 9 +- man/kdest.Rd | 65 +++++++++------ man/kdplus.test.Rd | 9 +- man/logrr.Rd | 186 ++++++++++++++++++++++----------------------- man/plot.kdenv.Rd | 21 ++--- man/plot.spscan.Rd | 13 ++- man/print.kdenv_summary.Rd |only man/print.kdplus_test.Rd |only man/print.logrr_test.Rd |only man/print.logrrenv.Rd |only man/print.spscan.Rd |only man/qnn.test.Rd | 9 +- man/spscan.test.Rd | 98 +++++++++++++---------- man/summary.kdenv.Rd |only man/summary.spscan.Rd |only tests/test-all.R | 5 - vignettes |only 40 files changed, 617 insertions(+), 413 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2021,
<doi:10.31234/osf.io/kvsp7>; Maier, Bartoš & Wagenmakers, in press,
<doi:10.31234/osf.io/u4cns>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: František Bartoš [aut, cre] (<https://orcid.org/0000-0002-0018-5573>),
Maximilian Maier [aut] (<https://orcid.org/0000-0002-9873-6096>),
Eric-Jan Wagenmakers [ths] (<https://orcid.org/0000-0003-1596-1034>),
Joris Goosen [ctb],
Matthew Denwood [cph] (Original copyright holder of some modified code
where indicated.),
Martyn Plummer [cph] (Original copyright holder of some modified code
where indicated.)
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between RoBMA versions 2.0.0 dated 2021-07-08 and 2.1.0 dated 2021-10-13
DESCRIPTION | 11 MD5 | 88 NAMESPACE | 9 NEWS.md | 13 R/RoBMA-package.R | 26 R/check-input-and-settings.R | 31 R/diagnostics.R | 4 R/fit-and-marglik.R | 5 R/main.R | 24 R/plots.R | 233 +- R/summary.R | 56 R/transformations-tools.R |only R/transformations.R | 229 -- R/zzz.R | 16 README.md | 7 build/partial.rdb |binary configure | 2967 ++++++++++++++------------ configure.ac | 9 inst/doc/CustomEnsembles.html | 12 inst/doc/ReproducingBMA.html | 12 man/RoBMA-package.Rd | 19 man/RoBMA.Rd | 20 man/RoBMA_control.Rd | 6 man/check_setup.Rd | 2 man/effect_sizes.Rd | 50 man/figures/README-fig_forest-1.png |binary man/figures/README-fig_mu-1.png |binary man/figures/README-fig_mu_chain-1.png |binary man/figures/README-fig_mu_ind-1.png |binary man/figures/README-fig_tau-1.png |binary man/forest.Rd | 2 man/interpret.Rd |only man/plot.RoBMA.Rd | 5 man/plot_models.Rd | 7 src/RoBMA.cc | 6 src/transformations/d.cc | 13 src/transformations/d.h | 9 src/transformations/logOR.cc | 13 src/transformations/logOR.h | 9 src/transformations/r.cc | 34 src/transformations/r.h | 28 src/transformations/transformations_common.cc | 20 src/transformations/transformations_common.h | 6 src/transformations/z.cc | 11 src/transformations/z.h | 9 tests/testthat/test-0-CRAN.R | 2 46 files changed, 2305 insertions(+), 1718 deletions(-)
Title: Specify (Pre)Registrations and Export Them Human- And
Machine-Readably
Description: Preregistrations, or more generally, registrations, enable
explicit timestamped and (often but not necessarily publicly) frozen
documentation of plans and expectations as well as decisions and
justifications. In research, preregistrations are commonly used to
clearly document plans and facilitate justifications of deviations from
those plans, as well as decreasing the effects of publication bias by
enabling identification of research that was conducted but not published.
Like reporting guidelines, (pre)registration forms often have specific
structures that facilitate systematic reporting of important items. The
'preregr' package facilitates specifying (pre)registrations in R and
exporting them to a human-readable format (using R Markdown partials or
exporting to an 'HTML' file) as well as human-readable embedded data
(using 'JSON'), as well as importing such exported (pre)registration
specifications from such embedded 'JSON'.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
Diff between preregr versions 0.1.3 dated 2021-09-30 and 0.1.9 dated 2021-10-13
preregr-0.1.3/preregr/inst/extdata/preregr-spec-OSFprereg-form.xlsx |only preregr-0.1.3/preregr/inst/extdata/preregr-spec-incl-sysrev-reg-form.xlsx |only preregr-0.1.3/preregr/inst/extdata/preregr-spec-incl-sysrev-reg.yml |only preregr-0.1.3/preregr/inst/extdata/preregr-spec-preregQE-form.xlsx |only preregr-0.1.3/preregr/inst/extdata/preregr-spec-prp-quant-form.xlsx |only preregr-0.1.3/preregr/inst/extdata/preregr-spec-quali.xlsx |only preregr-0.1.9/preregr/DESCRIPTION | 14 preregr-0.1.9/preregr/MD5 | 167 +- preregr-0.1.9/preregr/NAMESPACE | 2 preregr-0.1.9/preregr/R/form_add.R | 10 preregr-0.1.9/preregr/R/form_fromSpreadsheet.R | 21 preregr-0.1.9/preregr/R/form_show.R | 5 preregr-0.1.9/preregr/R/form_to_html.R | 27 preregr-0.1.9/preregr/R/form_to_rmd_template.R | 38 preregr-0.1.9/preregr/R/forms.R |only preregr-0.1.9/preregr/R/forms_that_are_included.R | 100 + preregr-0.1.9/preregr/R/import_from_html.R | 20 preregr-0.1.9/preregr/R/opts.R | 2 preregr-0.1.9/preregr/R/prereg_justify.R | 26 preregr-0.1.9/preregr/R/prereg_knit_item_content.R | 21 preregr-0.1.9/preregr/R/prereg_next_item.R | 43 preregr-0.1.9/preregr/R/prereg_show_item_completion.R | 20 preregr-0.1.9/preregr/R/prereg_show_item_content.R | 19 preregr-0.1.9/preregr/R/prereg_spec_to_html.R | 42 preregr-0.1.9/preregr/R/prereg_spec_to_json.R | 17 preregr-0.1.9/preregr/R/prereg_spec_to_pdf.R |only preregr-0.1.9/preregr/R/prereg_spec_to_yaml.R | 17 preregr-0.1.9/preregr/R/prereg_specify.R | 13 preregr-0.1.9/preregr/R/preregr-package.R |only preregr-0.1.9/preregr/R/validate_value.R | 17 preregr-0.1.9/preregr/R/yaml_to_prereg_spec.R | 4 preregr-0.1.9/preregr/README.md | 15 preregr-0.1.9/preregr/build/partial.rdb |binary preregr-0.1.9/preregr/build/vignette.rds |binary preregr-0.1.9/preregr/data/examplePrereg_1.rda |only preregr-0.1.9/preregr/data/form_OSFprereg_v1.rda |binary preregr-0.1.9/preregr/data/form_generalPurpose_v1.rda |only preregr-0.1.9/preregr/data/form_inclSysRev_v0_92.rda |binary preregr-0.1.9/preregr/data/form_preregQE_v0_93.rda |binary preregr-0.1.9/preregr/data/form_prpQuant_v1.rda |binary preregr-0.1.9/preregr/inst/doc/creating_form_from_spreadsheet.html | 272 ---- preregr-0.1.9/preregr/inst/doc/creating_prereg_form.html | 514 ++----- preregr-0.1.9/preregr/inst/doc/form_OSFprereg_v1.Rmd | 4 preregr-0.1.9/preregr/inst/doc/form_OSFprereg_v1.html | 266 ---- preregr-0.1.9/preregr/inst/doc/form_generalPurpose_v1.R |only preregr-0.1.9/preregr/inst/doc/form_generalPurpose_v1.Rmd |only preregr-0.1.9/preregr/inst/doc/form_generalPurpose_v1.html |only preregr-0.1.9/preregr/inst/doc/form_inclSysRev_v0_92.Rmd | 4 preregr-0.1.9/preregr/inst/doc/form_inclSysRev_v0_92.html | 306 +--- preregr-0.1.9/preregr/inst/doc/form_preregQE_v0_93.Rmd | 4 preregr-0.1.9/preregr/inst/doc/form_preregQE_v0_93.html | 308 +--- preregr-0.1.9/preregr/inst/doc/form_prpQuant_v1.Rmd | 4 preregr-0.1.9/preregr/inst/doc/form_prpQuant_v1.html | 270 ---- preregr-0.1.9/preregr/inst/doc/importing_form_from_url.html | 358 +---- preregr-0.1.9/preregr/inst/doc/importing_pregistration_from_url.html | 282 ---- preregr-0.1.9/preregr/inst/doc/rmd_template_from_form.R | 12 preregr-0.1.9/preregr/inst/doc/rmd_template_from_form.Rmd | 19 preregr-0.1.9/preregr/inst/doc/rmd_template_from_form.html | 384 +---- preregr-0.1.9/preregr/inst/doc/specifying_prereg_content.html | 644 +++------- preregr-0.1.9/preregr/inst/extdata/preregr-form_OSFprereg_v1.xlsx |only preregr-0.1.9/preregr/inst/extdata/preregr-form_generalPurpose_v1.xlsx |only preregr-0.1.9/preregr/inst/extdata/preregr-form_inclSysRev_v0_92.xlsx |only preregr-0.1.9/preregr/inst/extdata/preregr-form_preregQE_v0_93.xlsx |only preregr-0.1.9/preregr/inst/extdata/preregr-form_prpQuant_v1.xlsx |only preregr-0.1.9/preregr/inst/extdata/preregr-spec-example1.yml |only preregr-0.1.9/preregr/inst/extdata/preregr-spec-generalPurpose-form.xlsx |only preregr-0.1.9/preregr/inst/templates |only preregr-0.1.9/preregr/man/examplePrereg_1.Rd |only preregr-0.1.9/preregr/man/export_to_yaml_or_json.Rd | 32 preregr-0.1.9/preregr/man/figures |only preregr-0.1.9/preregr/man/form_OSFprereg_v1.Rd | 68 - preregr-0.1.9/preregr/man/form_add.Rd | 8 preregr-0.1.9/preregr/man/form_generalPurpose_v1.Rd |only preregr-0.1.9/preregr/man/form_preregQE_v0_93.Rd | 52 preregr-0.1.9/preregr/man/form_show.Rd | 3 preregr-0.1.9/preregr/man/form_to_html.Rd | 12 preregr-0.1.9/preregr/man/forms.Rd |only preregr-0.1.9/preregr/man/import_from_html.Rd | 26 preregr-0.1.9/preregr/man/import_yaml_or_json.Rd | 4 preregr-0.1.9/preregr/man/prereg_initialize.Rd | 60 preregr-0.1.9/preregr/man/prereg_justify.Rd | 24 preregr-0.1.9/preregr/man/prereg_knit_item_content.Rd | 21 preregr-0.1.9/preregr/man/prereg_next_item.Rd | 38 preregr-0.1.9/preregr/man/prereg_show_item_completion.Rd | 20 preregr-0.1.9/preregr/man/prereg_show_item_content.Rd | 20 preregr-0.1.9/preregr/man/prereg_spec_to_html.Rd | 28 preregr-0.1.9/preregr/man/prereg_spec_to_pdf.Rd |only preregr-0.1.9/preregr/man/prereg_specify.Rd | 12 preregr-0.1.9/preregr/man/preregr-package.Rd |only preregr-0.1.9/preregr/man/read_spreadsheet.Rd | 130 +- preregr-0.1.9/preregr/man/rmd_templates.Rd | 172 +- preregr-0.1.9/preregr/man/validate_value.Rd | 12 preregr-0.1.9/preregr/tests/testthat/test-preregr.R | 484 ++++--- preregr-0.1.9/preregr/vignettes/form_OSFprereg_v1.Rmd | 4 preregr-0.1.9/preregr/vignettes/form_generalPurpose_v1.Rmd |only preregr-0.1.9/preregr/vignettes/form_inclSysRev_v0_92.Rmd | 4 preregr-0.1.9/preregr/vignettes/form_preregQE_v0_93.Rmd | 4 preregr-0.1.9/preregr/vignettes/form_prpQuant_v1.Rmd | 4 preregr-0.1.9/preregr/vignettes/rmd_template_from_form.Rmd | 19 99 files changed, 2123 insertions(+), 3449 deletions(-)
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package
and then attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between pkgload versions 1.2.2 dated 2021-09-11 and 1.2.3 dated 2021-10-13
DESCRIPTION | 6 +- MD5 | 18 ++++---- NEWS.md | 8 +++ R/load-dll.r | 2 R/load.r | 18 ++++++++ R/namespace-env.r | 14 ++---- R/utils.R | 4 + README.md | 2 tests/testthat/test-load.r | 51 +++++++++++++++++++++++-- tests/testthat/testDllRcpp/src/RcppExports.cpp | 5 ++ 10 files changed, 103 insertions(+), 25 deletions(-)
Title: Expanded Replacement and Extension of the 'optim' Function
Description: Provides a replacement and extension of the optim()
function to call to several function minimization codes in R in a single
statement. These methods handle smooth, possibly box constrained functions
of several or many parameters. Note that function 'optimr()' was prepared to
simplify the incorporation of minimization codes going forward. Also implements some
utility codes and some extra solvers, including safeguarded Newton methods.
Many methods previously separate are now included here.
This is the version for CRAN.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <nashjc@uottawa.ca>
Diff between optimx versions 2021-6.12 dated 2021-06-13 and 2021-10.12 dated 2021-10-13
optimx-2021-10.12/optimx/DESCRIPTION | 12 - optimx-2021-10.12/optimx/MD5 | 67 +++--- optimx-2021-10.12/optimx/NEWS | 11 - optimx-2021-10.12/optimx/R/Rvmminb.R | 2 optimx-2021-10.12/optimx/R/ctrldefault.R | 1 optimx-2021-10.12/optimx/R/optimr.R | 78 +++---- optimx-2021-10.12/optimx/R/optimx-package.R | 41 +++ optimx-2021-10.12/optimx/R/optimx.check.R | 3 optimx-2021-10.12/optimx/R/scalechk.R | 90 ++++---- optimx-2021-10.12/optimx/R/tnbc.R | 2 optimx-2021-10.12/optimx/build/vignette.rds |binary optimx-2021-10.12/optimx/inst/CITATION | 2 optimx-2021-10.12/optimx/inst/doc/Extend-optimx-code.R |only optimx-2021-10.12/optimx/inst/doc/Extend-optimx.pdf |binary optimx-2021-10.12/optimx/inst/doc/Rvmmin-code.R |only optimx-2021-10.12/optimx/inst/doc/Rvmmin.html | 5 optimx-2021-10.12/optimx/inst/doc/SNewton-code.R |only optimx-2021-10.12/optimx/inst/doc/SNewton.R | 1 optimx-2021-10.12/optimx/inst/doc/SNewton.Rmd | 1 optimx-2021-10.12/optimx/inst/doc/SNewton.html |only optimx-2021-10.12/optimx/man/Rcgmin.Rd | 2 optimx-2021-10.12/optimx/man/Rvmminb.Rd | 5 optimx-2021-10.12/optimx/man/gHgen.Rd | 2 optimx-2021-10.12/optimx/man/gHgenb.Rd | 2 optimx-2021-10.12/optimx/man/kktchk.Rd | 3 optimx-2021-10.12/optimx/man/opm.Rd | 8 optimx-2021-10.12/optimx/man/optchk.Rd | 4 optimx-2021-10.12/optimx/man/optimr.Rd | 5 optimx-2021-10.12/optimx/man/optimx.Rd | 8 optimx-2021-10.12/optimx/man/tn.Rd | 2 optimx-2021-10.12/optimx/man/tnbc.Rd | 2 optimx-2021-10.12/optimx/vignettes/Extend-optimx.bib | 178 ++++++++-------- optimx-2021-10.12/optimx/vignettes/Rvmmin.bib | 179 ++++++++--------- optimx-2021-10.12/optimx/vignettes/SNewton.Rmd | 1 optimx-2021-6.12/optimx/inst/doc/SNewton.pdf |only optimx-2021-6.12/optimx/po |only optimx-2021-6.12/optimx/vignettes/SNewton.html |only 37 files changed, 367 insertions(+), 350 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] (<https://orcid.org/0000-0003-0071-1745>),
Cory Merow [aut] (<https://orcid.org/0000-0003-0561-053X>),
Brian Maitner [aut] (<https://orcid.org/0000-0002-2118-9880>),
Jamie M. Kass [aut] (<https://orcid.org/0000-0002-9432-895X>),
Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>),
Robert P. Guralnick [aut] (<https://orcid.org/0000-0001-6682-1504>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.4.9 dated 2021-07-23 and 0.5.0 dated 2021-10-13
DESCRIPTION | 10 +- MD5 | 48 ++++++----- NEWS.md | 9 ++ R/GBIFLoginManager.R | 22 +++-- R/gbifRetriever.R | 22 ++++- R/getBIENpoints.R | 26 +++++- R/getGBIFpoints.R | 76 ++++++++++++++--- R/occCitation.R | 37 +++++--- R/occCite_plotting.R | 11 ++ R/occSum.R | 12 +- R/prevGBIFdownload.R | 18 +++- R/studyTaxonList.R | 10 +- R/taxonRectification.R | 10 ++ inst/doc/Advanced.R | 4 inst/doc/Advanced.Rmd | 4 inst/doc/Advanced.html | 132 ++++++++++++++++--------------- inst/doc/Simple.html | 18 ++-- man/figures/logo.png |only man/figures/occHex.ai |only man/figures/occHex.png |only man/getBIENpoints.Rd | 4 man/getGBIFpoints.Rd | 4 tests/testthat/test-occCitePrint.R |only tests/testthat/test-occSum.R | 22 ++++- tests/testthat/test-studyTaxonList.R | 8 + tests/testthat/test-taxonRectification.R | 8 + vignettes/Advanced.Rmd | 4 27 files changed, 352 insertions(+), 167 deletions(-)
Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre],
Gautier Stoll [ctb],
Guido Kroemer [ldr],
Jean-Pierre Marolleau [ldr],
Loïc Garçon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>
Diff between IFC versions 0.1.1 dated 2020-12-18 and 0.1.2 dated 2021-10-13
IFC-0.1.1/IFC/man/cpp_num_to_string.Rd |only IFC-0.1.1/IFC/man/scale_trans.Rd |only IFC-0.1.2/IFC/DESCRIPTION | 10 IFC-0.1.2/IFC/MD5 | 257 +++-- IFC-0.1.2/IFC/NAMESPACE | 8 IFC-0.1.2/IFC/R/DisplayGallery.R | 72 - IFC-0.1.2/IFC/R/ExportToDAF.R | 10 IFC-0.1.2/IFC/R/ExportToGallery.R | 91 +- IFC-0.1.2/IFC/R/ExportToNumpy.R | 88 +- IFC-0.1.2/IFC/R/ExportToReport.R | 664 ++++++++++----- IFC-0.1.2/IFC/R/ExportToXIF.R | 222 ++--- IFC-0.1.2/IFC/R/ExtractFromDAF.R | 93 +- IFC-0.1.2/IFC/R/ExtractFromXIF.R | 71 - IFC-0.1.2/IFC/R/ExtractImages_toBase64.R | 66 - IFC-0.1.2/IFC/R/ExtractImages_toFile.R | 64 - IFC-0.1.2/IFC/R/ExtractImages_toMatrix.R | 66 - IFC-0.1.2/IFC/R/ExtractMasks_toMatrix.R | 66 - IFC-0.1.2/IFC/R/RcppExports.R | 139 ++- IFC-0.1.2/IFC/R/XIFtoTIFF.R |only IFC-0.1.2/IFC/R/addText.R | 6 IFC-0.1.2/IFC/R/applyGatingStrategy.R |only IFC-0.1.2/IFC/R/autoplot.R | 59 - IFC-0.1.2/IFC/R/buildGraph.R | 83 + IFC-0.1.2/IFC/R/buildPopulation.R | 78 - IFC-0.1.2/IFC/R/buildRegion.R | 48 - IFC-0.1.2/IFC/R/checkObj.R |only IFC-0.1.2/IFC/R/data_add_regions.R | 198 ++-- IFC-0.1.2/IFC/R/data_rm_features.R | 17 IFC-0.1.2/IFC/R/data_rm_pops.R | 18 IFC-0.1.2/IFC/R/data_rm_regions.R | 12 IFC-0.1.2/IFC/R/data_to_DAF.R | 106 +- IFC-0.1.2/IFC/R/fcs.R |only IFC-0.1.2/IFC/R/gatingML.R |only IFC-0.1.2/IFC/R/getASSIST.R |only IFC-0.1.2/IFC/R/getAborted.R | 458 +++++----- IFC-0.1.2/IFC/R/getIFD.R | 292 +++--- IFC-0.1.2/IFC/R/getImagesValues.R | 337 ++++--- IFC-0.1.2/IFC/R/getInfo.R | 37 IFC-0.1.2/IFC/R/getOffsets.R | 228 ++--- IFC-0.1.2/IFC/R/graphs_utils.R | 368 ++++---- IFC-0.1.2/IFC/R/mergeXIF.R | 768 ++++++----------- IFC-0.1.2/IFC/R/objectExtract.R | 29 IFC-0.1.2/IFC/R/objectParam.R | 584 +++++++------ IFC-0.1.2/IFC/R/paletteIFC.R | 20 IFC-0.1.2/IFC/R/plotGraph.R | 237 +++-- IFC-0.1.2/IFC/R/popsCompute.R | 16 IFC-0.1.2/IFC/R/popsCopy.R | 4 IFC-0.1.2/IFC/R/popsGetSiblings.R | 34 IFC-0.1.2/IFC/R/popsRetrieveGraph.R | 39 IFC-0.1.2/IFC/R/popsWithin.R | 60 - IFC-0.1.2/IFC/R/progress_utils.R | 364 ++++---- IFC-0.1.2/IFC/R/readGatingStrategy.R |only IFC-0.1.2/IFC/R/readIFC.R | 112 +- IFC-0.1.2/IFC/R/redefine_utils.R |only IFC-0.1.2/IFC/R/stats.R |only IFC-0.1.2/IFC/R/strings_utils.R | 250 ++++- IFC-0.1.2/IFC/R/subsetOffsets.R | 178 ++-- IFC-0.1.2/IFC/R/subsetXIF.R | 921 +++++++++------------ IFC-0.1.2/IFC/R/tiff_utils.R | 167 +++ IFC-0.1.2/IFC/R/toBIN_features.R | 14 IFC-0.1.2/IFC/R/toBIN_images.R | 59 - IFC-0.1.2/IFC/R/toXML2_graphs.R | 26 IFC-0.1.2/IFC/R/toXML2_pops.R | 228 ++--- IFC-0.1.2/IFC/R/toXML2_regions.R | 107 +- IFC-0.1.2/IFC/R/trans_utils.R |only IFC-0.1.2/IFC/R/writeGatingStrategy.R |only IFC-0.1.2/IFC/inst/CITATION | 6 IFC-0.1.2/IFC/inst/include/align.hpp |only IFC-0.1.2/IFC/inst/include/decomp.hpp | 503 +++++++++-- IFC-0.1.2/IFC/inst/include/extract.hpp | 57 - IFC-0.1.2/IFC/inst/include/gate.hpp | 14 IFC-0.1.2/IFC/inst/include/resize.hpp | 2 IFC-0.1.2/IFC/inst/include/tiff.hpp | 443 ++++++++-- IFC-0.1.2/IFC/inst/include/trans.hpp | 78 - IFC-0.1.2/IFC/inst/include/utils.hpp | 18 IFC-0.1.2/IFC/man/BatchReport.Rd |only IFC-0.1.2/IFC/man/CreateGraphReport.Rd |only IFC-0.1.2/IFC/man/DisplayReport.Rd |only IFC-0.1.2/IFC/man/ExportToDAF.Rd | 4 IFC-0.1.2/IFC/man/ExportToFCS.Rd |only IFC-0.1.2/IFC/man/ExportToReport.Rd | 10 IFC-0.1.2/IFC/man/ExportToXIF.Rd | 4 IFC-0.1.2/IFC/man/ExtractFromDAF.Rd | 2 IFC-0.1.2/IFC/man/ExtractFromFCS.Rd |only IFC-0.1.2/IFC/man/IFC-package.Rd | 4 IFC-0.1.2/IFC/man/XIFtoTIFF.Rd |only IFC-0.1.2/IFC/man/adjustGraph.Rd | 4 IFC-0.1.2/IFC/man/applyGatingStrategy.Rd |only IFC-0.1.2/IFC/man/applyTrans.Rd |only IFC-0.1.2/IFC/man/autoplot.Rd | 8 IFC-0.1.2/IFC/man/base_axis_constr.Rd | 8 IFC-0.1.2/IFC/man/buildGraph.Rd | 23 IFC-0.1.2/IFC/man/buildMask.Rd |only IFC-0.1.2/IFC/man/buildPopulation.Rd | 20 IFC-0.1.2/IFC/man/buildRegion.Rd | 4 IFC-0.1.2/IFC/man/buildStats.Rd |only IFC-0.1.2/IFC/man/checkObj.Rd |only IFC-0.1.2/IFC/man/cpp_align.Rd |only IFC-0.1.2/IFC/man/cpp_extract.Rd | 4 IFC-0.1.2/IFC/man/cpp_fastTAGS.Rd |only IFC-0.1.2/IFC/man/cpp_int64_to_uint64.Rd |only IFC-0.1.2/IFC/man/cpp_rawdecomp.Rd |only IFC-0.1.2/IFC/man/cpp_transform.Rd | 4 IFC-0.1.2/IFC/man/cpp_uint32_to_raw.Rd |only IFC-0.1.2/IFC/man/cpp_uint64_to_int64.Rd |only IFC-0.1.2/IFC/man/data_rm_features.Rd | 6 IFC-0.1.2/IFC/man/data_rm_pops.Rd | 6 IFC-0.1.2/IFC/man/data_rm_regions.Rd | 6 IFC-0.1.2/IFC/man/data_to_DAF.Rd | 6 IFC-0.1.2/IFC/man/densCols.Rd | 2 IFC-0.1.2/IFC/man/extractStats.Rd |only IFC-0.1.2/IFC/man/feature_namer.Rd |only IFC-0.1.2/IFC/man/fromXML2_gating.Rd |only IFC-0.1.2/IFC/man/getASSIST.Rd |only IFC-0.1.2/IFC/man/getAborted.Rd | 3 IFC-0.1.2/IFC/man/getInfo.Rd | 3 IFC-0.1.2/IFC/man/getOffsets.Rd | 1 IFC-0.1.2/IFC/man/inv_colConv.Rd |only IFC-0.1.2/IFC/man/inv_smoothAsinh.Rd |only IFC-0.1.2/IFC/man/map_color.Rd |only IFC-0.1.2/IFC/man/map_style.Rd |only IFC-0.1.2/IFC/man/mergeXIF.Rd | 4 IFC-0.1.2/IFC/man/myScales.Rd | 4 IFC-0.1.2/IFC/man/next_bool.Rd |only IFC-0.1.2/IFC/man/num_to_string.Rd | 4 IFC-0.1.2/IFC/man/objectParam.Rd | 5 IFC-0.1.2/IFC/man/parseTrans.Rd |only IFC-0.1.2/IFC/man/plotGraph.Rd | 6 IFC-0.1.2/IFC/man/popsCompute.Rd | 9 IFC-0.1.2/IFC/man/popsCopy.Rd | 4 IFC-0.1.2/IFC/man/random_name.Rd |only IFC-0.1.2/IFC/man/readFCS.Rd |only IFC-0.1.2/IFC/man/readGatingML.Rd |only IFC-0.1.2/IFC/man/readGatingStrategy.Rd |only IFC-0.1.2/IFC/man/readIFC.Rd | 8 IFC-0.1.2/IFC/man/redefine_features_def.Rd |only IFC-0.1.2/IFC/man/redefine_features_def_feat.Rd |only IFC-0.1.2/IFC/man/redefine_features_def_msk_img.Rd |only IFC-0.1.2/IFC/man/redefine_masks.Rd |only IFC-0.1.2/IFC/man/redefine_masks_image.Rd |only IFC-0.1.2/IFC/man/redefine_masks_mask.Rd |only IFC-0.1.2/IFC/man/redefine_obj.Rd |only IFC-0.1.2/IFC/man/smoothAsinh.Rd |only IFC-0.1.2/IFC/man/specialr.Rd | 4 IFC-0.1.2/IFC/man/splitn.Rd | 9 IFC-0.1.2/IFC/man/statsCompute.Rd |only IFC-0.1.2/IFC/man/subsetOffsets.Rd | 2 IFC-0.1.2/IFC/man/subsetXIF.Rd | 4 IFC-0.1.2/IFC/man/switch_channel.Rd |only IFC-0.1.2/IFC/man/testXIF.Rd |only IFC-0.1.2/IFC/man/toCapFirstOnly.Rd |only IFC-0.1.2/IFC/man/toXML2_boolpop_gs.Rd |only IFC-0.1.2/IFC/man/toXML2_graphpop_gs.Rd |only IFC-0.1.2/IFC/man/toXML2_graphs_gs.Rd |only IFC-0.1.2/IFC/man/toXML2_spillover_gs.Rd |only IFC-0.1.2/IFC/man/toXML2_stats.Rd |only IFC-0.1.2/IFC/man/tryReportFileCreation.Rd |only IFC-0.1.2/IFC/man/usedefault_obj.Rd |only IFC-0.1.2/IFC/man/validate_bool.Rd |only IFC-0.1.2/IFC/man/writeGatingStrategy.Rd |only IFC-0.1.2/IFC/man/writeIFD.Rd |only IFC-0.1.2/IFC/src/RcppExports.cpp | 118 ++ IFC-0.1.2/IFC/src/ifc.cpp | 159 +++ 163 files changed, 5918 insertions(+), 4224 deletions(-)
Title: Access the 'Geographic Name Resolution Service'
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Author: Brad Boyle [aut],
Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between GNRS versions 0.3.3 dated 2021-10-08 and 0.3.4 dated 2021-10-13
DESCRIPTION | 8 +- MD5 | 78 ++++++++++++++++++----------- NEWS | 11 ++++ R/gnrs.R | 2 R/gnrs_acknowledgements.R | 2 R/gnrs_citations.R | 2 R/gnrs_data_dictionary.R | 2 R/gnrs_get_counties.R | 2 R/gnrs_get_countries.R | 2 R/gnrs_get_states.R | 2 R/gnrs_metadata.R | 2 R/gnrs_sources.R | 2 R/gnrs_super_simple.R | 2 R/gnrs_version.R | 2 inst/doc/GNRS.Rmd | 2 inst/doc/GNRS.html | 6 +- tests/fixtures |only tests/testthat/setup-gnrs.R | 10 +++ tests/testthat/test-gnrs.R | 28 +++++----- tests/testthat/test-gnrs_data_dictionary.R | 10 ++- tests/testthat/test-gnrs_error_handling.R | 69 ++++++++++++++++++------- tests/testthat/test-gnrs_get_counties.R | 37 +++++++------ tests/testthat/test-gnrs_get_countries.R | 9 +-- tests/testthat/test-gnrs_get_states.R | 21 ++++--- tests/testthat/test-gnrs_metadata.R | 7 +- tests/testthat/test-gnrs_super_simple.R | 59 ++++++++++----------- tests/testthat/test-gnrs_template.R | 9 ++- tests/testthat/test-gnrs_version.R | 8 +- vignettes/GNRS.Rmd | 2 29 files changed, 244 insertions(+), 152 deletions(-)
Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut],
Charles Karney [ctb] (GeographicLib),
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geosphere versions 1.5-10 dated 2019-05-26 and 1.5-14 dated 2021-10-13
DESCRIPTION | 11 MD5 | 82 +++---- R/antipodal.R | 12 - R/areaPolygon.R | 4 R/distHaversine.R | 43 +++ build/partial.rdb |only build/vignette.rds |binary inst/doc/geosphere.R | 1 inst/doc/geosphere.pdf |binary man/antipode.Rd | 2 man/area.Rd | 2 man/bearing.Rd | 2 man/bearingRhumb.Rd | 4 man/destPoint.Rd | 2 man/destPointRhumb.Rd | 6 man/dist2gc.Rd | 4 man/dist2line.Rd | 2 man/distCosine.Rd | 2 man/distGeo.Rd | 4 man/distHaversine.Rd | 4 man/distMeeus.Rd | 2 man/distRhumb.Rd | 2 man/distVincentyEllipsoid.Rd | 6 man/distVincentySphere.Rd | 2 man/distm.Rd | 2 man/finalDirection.Rd | 2 man/gcIntersect.Rd | 2 man/gcIntersectBearing.Rd | 4 man/gcLat.Rd | 2 man/gcLon.Rd | 2 man/gcMaxLat.Rd | 4 man/geodesic.Rd | 4 man/geosphere-package.Rd | 10 man/greatCircle.Rd | 2 man/greatCircleBearing.Rd | 2 man/horizon.Rd | 2 man/intermediate.Rd | 2 man/lengthLine.Rd | 2 man/perimeter.Rd | 2 man/randomCoordinates.Rd | 5 src/geodesic.c | 503 +++++++++++++++++++++---------------------- src/geodesic.h | 239 +++++++++++--------- src/pointInPolygon.cpp |only 43 files changed, 525 insertions(+), 465 deletions(-)
Title: Clonality Estimates in Tumor
Description: Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>; Romanel et al. (2015) <doi:10.1126/scitranslmed.aac9511>.
Author: Davide Prandi [aut],
Alessandro Romanel [ctb],
Tarcisio Fedrizzi [ctb],
Yari Ciani [cre]
Maintainer: Yari Ciani <yari.ciani@unitn.it>
Diff between CLONETv2 versions 2.1.0 dated 2019-05-20 and 2.2.1 dated 2021-10-13
DESCRIPTION | 23 ++++---- MD5 | 22 ++++---- NAMESPACE | 1 NEWS.md | 9 +++ R/CLONETv2_basic_functions.R | 3 - R/CLONETv2_compute_admixture.R | 21 +++++++ R/CLONETv2_compute_allele_specific_scna_table.R | 3 - R/CLONETv2_compute_ploidy.R | 64 +++++++++++++++++------- R/CLONETv2_compute_scna_clonality_table.R | 3 - man/CLONETv2-package.Rd | 16 +++++- man/compute_dna_admixture.Rd | 6 +- man/compute_ploidy.Rd | 5 + 12 files changed, 126 insertions(+), 50 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and direct
extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR',
'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma'
and 'xz'.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Ondrej Holy [cph] (archive_write_add_filter implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between archive versions 1.1.0 dated 2021-08-04 and 1.1.1 dated 2021-10-13
DESCRIPTION | 14 ++++++------ MD5 | 24 ++++++++++---------- NAMESPACE | 2 - NEWS.md | 8 ++++++ R/archive_extract.R | 6 ++--- R/cpp11.R | 2 - R/utils.R | 6 ++--- README.md | 6 ++--- build/archive.pdf |binary man/archive_extract.Rd | 2 - src/archive_extract.cpp | 51 ++++++++++++++++++++++++++++++++++++++------ src/archive_write_files.cpp | 21 ++++++++++++++++++ src/cpp11.cpp | 8 +++--- 13 files changed, 109 insertions(+), 41 deletions(-)
Title: File-System Toolbox for RAVE Project
Description: Includes multiple cross-platform read/write interfaces for
'RAVE' project. 'RAVE' stands for "R analysis and visualization of human
intracranial electroencephalography data". The whole project aims at
providing powerful free-source package that analyze brain recordings from
patients with electrodes placed on the cortical surface or inserted into
the brain. 'raveio' as part of this project provides tools to read/write
neurophysiology data from/to 'RAVE' file structure, as well as several
popular formats including 'EDF(+)', 'Matlab', 'BIDS-iEEG', and 'HDF5',
etc. Documentation and examples about 'RAVE' project are provided at
<https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("raveio")' for
details.
Author: Zhengjia Wang [aut, cre],
Beauchamp lab [cph, fnd]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between raveio versions 0.0.4 dated 2021-08-05 and 0.0.5 dated 2021-10-13
DESCRIPTION | 24 MD5 | 81 +- NAMESPACE | 29 NEWS.md | 10 R/aaa.R | 7 R/class-electrode-abstract.R |only R/class-electrode-lfp.R |only R/class-preprocess.R | 3 R/class-project.R | 7 R/class-subject.R | 11 R/hdf5.R | 1220 +++++++----------------------------------- R/hdf5r.R |only R/matlab.R | 16 R/pipeline-docs.R |only R/pipeline-install.R |only R/pipeline-knitr.R |only R/pipeline-tools.R |only R/rave-import.R | 2 R/tensor.R | 50 - R/threeBrain-instance.R |only R/zzz.R | 175 +++++- README.md | 11 build/partial.rdb |binary inst/CITATION | 8 inst/WORDLIST | 2 inst/rave-pipelines |only man/LFP_electrode.Rd |only man/LazyH5.Rd | 30 - man/RAVEAbstarctElectrode.Rd |only man/RAVEPreprocessSettings.Rd | 6 man/RAVEProject.Rd | 2 man/RAVESubject.Rd | 8 man/Tensor.Rd | 4 man/configure_knitr.Rd |only man/h5_names.Rd | 2 man/h5_valid.Rd | 18 man/load_h5.Rd | 9 man/rave-pipeline.Rd |only man/rave_brain.Rd |only man/read_mat.Rd | 4 man/save_h5.Rd | 7 41 files changed, 582 insertions(+), 1164 deletions(-)
Title: Concentration-Response Modeling of HTS or Transcriptomics Data
Description: Performs the basic concentration response curve fitting used
in the 'tcpl' package. It is a substitute for the original tcplFit() function
(and sub-functions) and allows a wider variety of concentration-response models.
All of the models included in the 'BMDExpress' package are now part of this package,
and the output includes a calculation of the bmd (Benchmark Dose or concentration)
value.
Author: Thomas Sheffield [aut],
Richard Judson [ctb],
Jason Brown [ctb, cre],
Sarah E. Davidson [ctb]
Maintainer: Jason Brown <brown.jason@epa.gov>
Diff between tcplfit2 versions 0.1.2 dated 2021-10-01 and 0.1.3 dated 2021-10-13
tcplfit2-0.1.2/tcplfit2/vignettes/tcplfit2-vignette.docx |only tcplfit2-0.1.3/tcplfit2/DESCRIPTION | 6 tcplfit2-0.1.3/tcplfit2/MD5 | 15 - tcplfit2-0.1.3/tcplfit2/NEWS.md | 5 tcplfit2-0.1.3/tcplfit2/build/partial.rdb |binary tcplfit2-0.1.3/tcplfit2/inst/doc/tcplfit2-vignette.R | 96 ++++++++++ tcplfit2-0.1.3/tcplfit2/inst/doc/tcplfit2-vignette.Rmd | 60 +++++- tcplfit2-0.1.3/tcplfit2/inst/doc/tcplfit2-vignette.html | 133 +++++++++------ tcplfit2-0.1.3/tcplfit2/vignettes/tcplfit2-vignette.Rmd | 60 +++++- 9 files changed, 300 insertions(+), 75 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.9.0 dated 2021-01-15 and 1.9.2 dated 2021-10-13
DESCRIPTION | 10 - MD5 | 48 +++---- R/jonckheere.test.R | 8 + R/manyOneUTest.R | 2 R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary data/Pentosan.rda |binary data/algae.rda |binary data/qPCR.rda |binary data/reviewers.rda |binary data/trout.rda |binary demo/trout.R | 8 - inst/NEWS.Rd | 19 +++ inst/doc/QuickReferenceGuide.html | 239 +++----------------------------------- man/bwsTrendTest.Rd | 10 + man/chackoTest.Rd | 10 + man/cuzickTest.Rd | 11 + man/flignerWolfeTest.Rd | 11 + man/johnsonTest.Rd | 11 + man/jonckheereTest.Rd | 10 + man/leTest.Rd | 11 + man/shanTest.Rd | 10 + man/spearmanTest.Rd | 11 + man/stepDownTrendTest.Rd | 11 + 25 files changed, 189 insertions(+), 251 deletions(-)
Title: Various Tools and Data for Quantitative Peace Science
Description: These are useful tools and data sets for the study of quantitative
peace science. The goal for this package is to include tools and data sets
for doing original research that mimics well what a user would have to previously
get from a software package that may not be well-sourced or well-supported.
Those software bundles were useful the extent to which they encourage replications
of long-standing analyses by starting the data-generating process from scratch. However,
a lot of the functionality can be done relatively quickly and more transparently
in the R programming language.
Author: Steve Miller [aut, cre] (<https://orcid.org/0000-0003-4072-6263>)
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between peacesciencer versions 0.5.0 dated 2021-06-21 and 0.6.0 dated 2021-10-13
peacesciencer-0.5.0/peacesciencer/data/capitals.rda |only peacesciencer-0.5.0/peacesciencer/data/cow_trade_ndy.rda |only peacesciencer-0.5.0/peacesciencer/man/capitals.Rd |only peacesciencer-0.5.0/peacesciencer/man/cow_trade_ndy.Rd |only peacesciencer-0.6.0/peacesciencer/DESCRIPTION | 12 peacesciencer-0.6.0/peacesciencer/MD5 | 126 +++-- peacesciencer-0.6.0/peacesciencer/NAMESPACE | 2 peacesciencer-0.6.0/peacesciencer/NEWS.md | 18 peacesciencer-0.6.0/peacesciencer/R/add_archigos.R | 8 peacesciencer-0.6.0/peacesciencer/R/add_atop_alliance.R | 2 peacesciencer-0.6.0/peacesciencer/R/add_capital_distance.R | 236 +++++++--- peacesciencer-0.6.0/peacesciencer/R/add_cow_majors.R | 2 peacesciencer-0.6.0/peacesciencer/R/add_cow_mids.R | 2 peacesciencer-0.6.0/peacesciencer/R/add_cow_trade.R | 29 - peacesciencer-0.6.0/peacesciencer/R/add_gml_mids.R | 3 peacesciencer-0.6.0/peacesciencer/R/add_igos.R | 2 peacesciencer-0.6.0/peacesciencer/R/add_minimum_distance.R | 5 peacesciencer-0.6.0/peacesciencer/R/add_peace_years.R | 29 + peacesciencer-0.6.0/peacesciencer/R/create_dyadyears.R | 16 peacesciencer-0.6.0/peacesciencer/R/create_leaderyears.R |only peacesciencer-0.6.0/peacesciencer/R/create_statedays.R | 10 peacesciencer-0.6.0/peacesciencer/R/create_stateyears.R | 10 peacesciencer-0.6.0/peacesciencer/R/data.R | 203 +++++--- peacesciencer-0.6.0/peacesciencer/R/download_extdata.R |only peacesciencer-0.6.0/peacesciencer/R/helpymchelperson.R |only peacesciencer-0.6.0/peacesciencer/R/show_duplicates.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_duration.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_fatality.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_hostility.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_jds.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_onsets.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_reciprocation.R |only peacesciencer-0.6.0/peacesciencer/R/whittle_conflicts_startmonth.R |only peacesciencer-0.6.0/peacesciencer/R/zzz.R | 21 peacesciencer-0.6.0/peacesciencer/README.md | 214 +-------- peacesciencer-0.6.0/peacesciencer/build/partial.rdb |binary peacesciencer-0.6.0/peacesciencer/data/archigos.rda |binary peacesciencer-0.6.0/peacesciencer/data/cow_capitals.rda |only peacesciencer-0.6.0/peacesciencer/data/cow_gw_years.rda |binary peacesciencer-0.6.0/peacesciencer/data/cow_mid_dirdisps.rda |binary peacesciencer-0.6.0/peacesciencer/data/cow_mindist.rda |binary peacesciencer-0.6.0/peacesciencer/data/cow_war_intra.rda |binary peacesciencer-0.6.0/peacesciencer/data/creg.rda |binary peacesciencer-0.6.0/peacesciencer/data/gml_dirdisp.rda |binary peacesciencer-0.6.0/peacesciencer/data/gml_mid_ddydisps.rda |binary peacesciencer-0.6.0/peacesciencer/data/gml_mid_disps.rda |only peacesciencer-0.6.0/peacesciencer/data/gw_capitals.rda |only peacesciencer-0.6.0/peacesciencer/data/gw_cow_years.rda |binary peacesciencer-0.6.0/peacesciencer/data/gw_mindist.rda |binary peacesciencer-0.6.0/peacesciencer/data/ps_bib.rda |binary peacesciencer-0.6.0/peacesciencer/inst/extdata |only peacesciencer-0.6.0/peacesciencer/man/add_capital_distance.Rd | 7 peacesciencer-0.6.0/peacesciencer/man/add_cow_trade.Rd | 7 peacesciencer-0.6.0/peacesciencer/man/add_gml_mids.Rd | 2 peacesciencer-0.6.0/peacesciencer/man/add_igos.Rd | 2 peacesciencer-0.6.0/peacesciencer/man/add_minimum_distance.Rd | 5 peacesciencer-0.6.0/peacesciencer/man/add_peace_years.Rd | 29 + peacesciencer-0.6.0/peacesciencer/man/archigos.Rd | 18 peacesciencer-0.6.0/peacesciencer/man/cow_capitals.Rd |only peacesciencer-0.6.0/peacesciencer/man/cow_mid_disps.Rd | 2 peacesciencer-0.6.0/peacesciencer/man/cow_mindist.Rd | 22 peacesciencer-0.6.0/peacesciencer/man/cow_war_intra.Rd | 3 peacesciencer-0.6.0/peacesciencer/man/create_leaderyears.Rd |only peacesciencer-0.6.0/peacesciencer/man/creg.Rd | 1 peacesciencer-0.6.0/peacesciencer/man/download_extdata.Rd |only peacesciencer-0.6.0/peacesciencer/man/gml_dirdisp.Rd | 2 peacesciencer-0.6.0/peacesciencer/man/gml_mid_ddydisps.Rd | 6 peacesciencer-0.6.0/peacesciencer/man/gml_mid_disps.Rd |only peacesciencer-0.6.0/peacesciencer/man/gw_capitals.Rd |only peacesciencer-0.6.0/peacesciencer/man/gw_mindist.Rd | 23 peacesciencer-0.6.0/peacesciencer/man/ps_bib.Rd | 5 peacesciencer-0.6.0/peacesciencer/man/show_duplicates.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_duration.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_fatality.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_hostility.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_jds.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_onsets.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_reciprocation.Rd |only peacesciencer-0.6.0/peacesciencer/man/whittle_conflicts_startmonth.Rd |only peacesciencer-0.6.0/peacesciencer/tests/testthat/test_nodamnduplicates.R | 4 80 files changed, 638 insertions(+), 450 deletions(-)
Title: Functions for Analyzing and Plotting Estuary Monitoring Data
Description: Tools for performing routine analysis and plotting tasks with environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System <http://cdmo.baruch.sc.edu/>. This package builds
on the functionality of the SWMPr package <https://cran.r-project.org/package=SWMPr>,
which is used to retrieve and organize the data. The combined set of tools
address common challenges associated with continuous time series data
for environmental decision making, and are intended for use in annual reporting activities.
References:
Beck, Marcus W. (2016) <ISSN 2073-4859><https://journal.r-project.org/archive/2016-1/beck.pdf>
Rudis, Bob (2014) <https://rud.is/b/2014/11/16/moving-the-earth-well-alaska-hawaii-with-r/>.
United States Environmental Protection Agency (2015) <https://cfpub.epa.gov/si/si_public_record_Report.cfm?Lab=OWOW&dirEntryId=327030>.
United States Environmental Protection Agency (2012) <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.646.1973&rep=rep1&type=pdf>.
Author: Julie Padilla [aut, ctb],
Marcus Beck [ctb],
Kimberly Cressman [ctb],
Dave Eslinger [cre, ctb],
Bob Rudis [ctb]
Maintainer: Dave Eslinger <dave.eslinger@noaa.gov>
Diff between SWMPrExtension versions 2.0.0 dated 2021-10-01 and 2.1.0 dated 2021-10-13
DESCRIPTION | 14 +- MD5 | 82 ++++++++-------- NAMESPACE | 12 -- NEWS.md | 6 + R/base_map.R |only R/res_custom_map.R | 139 +++++++++++++++++++--------- R/res_custom_sk_map.R | 157 +++++++++++++++++++++----------- R/res_local_map.R | 130 +++++++++++++++++--------- R/res_sk_map.R | 112 ++++++++++++++-------- man/annual_range.Rd | 166 +++++++++++++++++----------------- man/assign_season.Rd | 146 ++++++++++++++--------------- man/base_map.Rd |only man/counties_4269.Rd | 44 ++++----- man/create_sk_flextable_list.Rd | 130 +++++++++++++------------- man/create_sk_national_ft_reserves.Rd | 76 +++++++-------- man/ft_col_names.Rd | 48 ++++----- man/generate_results_table.Rd | 56 +++++------ man/generate_station_table.Rd | 52 +++++----- man/geographic_unique_stations.Rd | 62 ++++++------ man/get_reserve.Rd | 48 ++++----- man/get_shp_name.Rd | 48 ++++----- man/get_site_code.Rd | 48 ++++----- man/get_site_coordinates.Rd | 52 +++++----- man/get_sites.Rd | 70 +++++++------- man/import_local_nut.Rd | 84 ++++++++--------- man/raw_boxplot.Rd | 152 +++++++++++++++---------------- man/remove_inf_and_nan.Rd | 48 ++++----- man/res_custom_map.Rd | 52 +++++++--- man/res_custom_sk_map.Rd | 59 ++++++++---- man/res_local_map.Rd | 57 ++++++++--- man/res_sk_map.Rd | 29 +++-- man/sampling_stations_backup.Rd | 44 ++++----- man/set_date_break_labs.Rd | 54 +++++------ man/set_date_breaks.Rd | 54 +++++------ man/set_date_breaks_minor.Rd | 54 +++++------ man/sk_seasonal.Rd | 130 +++++++++++++------------- man/sk_tidy.Rd | 64 ++++++------- man/std_param_check.Rd | 66 ++++++------- man/summarise_handoff_files.Rd | 56 +++++------ man/title_labeler.Rd | 56 +++++------ man/update_sampling_stations.Rd | 92 +++++++++--------- man/y_count_labeler.Rd | 86 ++++++++--------- man/y_labeler.Rd | 64 ++++++------- 43 files changed, 1627 insertions(+), 1372 deletions(-)
More information about SWMPrExtension at CRAN
Permanent link
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.0 dated 2021-04-02 and 4.0.1 dated 2021-10-13
DESCRIPTION | 8 - MD5 | 89 +++++++------- NAMESPACE | 223 ++++++++++++++++++------------------- NEWS.md | 18 ++ R/bilat.symmetry.r | 6 R/compare.CR.R | 43 ++++--- R/compare.pls.r | 7 - R/coords.subset.r | 3 R/estimate.missing.r | 6 R/geomorph.support.code.r | 4 R/geomorph.utils.r | 29 ++++ R/gm.prcomp.R | 8 - R/gpagen.r | 4 R/gridPar.r | 2 R/integration.test.r | 7 - R/modularity.test.r | 4 R/morphol.disparity.r | 63 +++++++++- R/phylo.integration.r | 6 R/phylo.modularity.r | 3 R/procD.lm.r | 9 + R/readland.nts.r | 24 ++- R/readmulti.nts.r | 2 R/rotate.coords.R | 6 R/shape.predictor.r | 5 R/two.b.pls.r | 6 build/vignette.rds |binary inst/CITATION | 2 inst/doc/geomorph.PCA.html | 5 inst/doc/geomorph.assistance.html | 7 - inst/doc/geomorph.digitize3D.html | 5 inst/doc/geomorph.functions.html | 4 man/bilat.symmetry.Rd | 6 man/compare.CR.Rd | 4 man/compare.pls.Rd | 2 man/estimate.missing.Rd | 4 man/gm.prcomp.Rd | 8 - man/gridPar.Rd | 2 man/modularity.test.Rd | 3 man/morphol.disparity.Rd | 57 ++++++++- man/na.omit.geomorph.data.frame.Rd |only man/phylo.integration.Rd | 1 man/phylo.modularity.Rd | 1 man/procD.lm.Rd | 2 man/readland.nts.Rd | 6 man/readmulti.nts.Rd | 2 man/rotate.coords.Rd | 2 46 files changed, 450 insertions(+), 258 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.1.8 dated 2021-09-06 and 0.1.9 dated 2021-10-13
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS.md | 10 ++++++++++ R/aaa.R | 1 + R/shiny-compoundInput2.R | 12 +++++++----- build/vignette.rds |binary configure | 1 + configure.ac | 6 ++++-- inst/doc/r_expr_addons.html | 6 +++--- inst/doc/utility_functions.html | 2 +- man/compoundInput2.Rd | 7 +++---- src/utils.cpp | 6 ++++++ 13 files changed, 55 insertions(+), 33 deletions(-)
Title: 3D Brain Visualization
Description: A fast, interactive cross-platform, and easy to share
'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or
'AFNI/SUMA' surfaces. The viewer widget can be either standalone or
embedded into 'R-shiny' applications. The standalone version only require
a web browser with 'WebGL2' support (for example, 'Chrome'). It can be
inserted into any websites; see <https://dipterix.org/project/threebrain/>).
as an example. The 'R-shiny' support allows the 3D viewer to be dynamically
generated from reactive user inputs. This feature has been fully adopted by
'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to
analyze 'iEEG/eCoG' data. Documentation about 'threeBrain' is provided
by <https://dipterix.org/threeBrain/> and several vignettes included
in this package. To cite the package, please check our 'NeuroImage' paper
by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>),
or see 'citation("threeBrain")' for details.
Author: Zhengjia Wang [aut, cre, cph],
John Magnotti [aut],
Xiang Zhang [ctb, res],
Brian Metzger [res],
Elizabeth Nesbitt [res],
Meng Li [ths],
Michael Beauchamp [aut, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between threeBrain versions 0.2.1 dated 2021-08-03 and 0.2.3 dated 2021-10-13
DESCRIPTION | 21 MD5 | 36 NAMESPACE | 3 NEWS.md | 27 R/class_brain.R | 6 R/class_proxy.R | 35 R/ext_media.R |only R/fs_lut.R |only R/shiny-localization.R |only R/threejs_brain.R | 64 build |only inst/doc |only inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/main.js | 6754 +++++++++++------- inst/palettes/FSColorLUT.json |only man/freesurfer_lut.Rd |only man/localization_module.Rd |only man/threejs_brain.Rd | 3 man/video_content.Rd |only vignettes |only 19 files changed, 4295 insertions(+), 2654 deletions(-)
Title: Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2021,
<doi:10.1021/acs.analchem.1c00123>). Supported features include reading
spectral data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay
smoothing of spectral intensities with smooth_intens(), correcting
background noise with subtr_bg() in accordance with Zhao et al. (2007)
<doi:10.1366/000370207782597003>, and identifying spectra using an onboard
reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>).
Analyzed spectra can be shared with the Open Specy community. A Shiny app is
available via run_app() or online at
<https://wincowger.shinyapps.io/OpenSpecy/>.
Author: Win Cowger [cre, aut] (<https://orcid.org/0000-0001-9226-3104>),
Zacharias Steinmetz [aut] (<https://orcid.org/0000-0001-6675-5033>),
Andrew Gray [ctb] (<https://orcid.org/0000-0003-2252-7367>),
Hannah Hapich [ctb] (<https://orcid.org/0000-0003-0000-6632>),
Jennifer Lynch [ctb, dtc] (<https://orcid.org/0000-0003-3572-8782>),
Hannah De Frond [ctb, dtc] (<https://orcid.org/0000-0003-1199-0727>),
Keenan Munno [ctb, dtc] (<https://orcid.org/0000-0003-2916-5944>),
Chelsea Rochman [ctb, dtc] (<https://orcid.org/0000-0002-7624-711X>),
Sebastian Primpke [ctb, dtc] (<https://orcid.org/0000-0001-7633-8524>),
Orestis Herodotou [ctb, dtc]
Maintainer: Win Cowger <wincowger@gmail.com>
Diff between OpenSpecy versions 0.9.2 dated 2021-05-20 and 0.9.3 dated 2021-10-13
DESCRIPTION | 10 +- MD5 | 28 +++--- NEWS.md | 14 +++ R/OpenSpecy-package.R | 3 R/read_spec.R | 5 + README.md | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/sop.Rmd | 2 inst/doc/sop.html | 12 +- inst/shiny/server.R | 76 +++++++++++++---- inst/shiny/ui.R | 173 +++++++++++++++++++++++++-------------- man/OpenSpecy-package.Rd | 15 --- tests/testthat/test-manage_lib.R | 8 + vignettes/sop.Rmd | 2 15 files changed, 235 insertions(+), 119 deletions(-)
Title: The Expectation-Maximization Approach to Bayesian Variable
Selection
Description: An efficient expectation-maximization algorithm for fitting Bayesian spike-and-slab regularization paths for linear regression. Rockova and George (2014) <doi:10.1080/01621459.2013.869223>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gm2918@columbia.edu>
Diff between EMVS versions 1.1 dated 2019-12-13 and 1.2.1 dated 2021-10-13
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 11 ++++++++++- build/vignette.rds |binary inst/doc/EMVS_vignette.Rnw | 10 ++++------ inst/doc/EMVS_vignette.pdf |binary man/EMVS.Rd | 9 +++------ man/EMVSbest.Rd | 9 ++------- man/EMVSplot.Rd | 8 ++------ man/EMVSsummary.Rd | 9 ++------- src/functions.cpp | 6 +++--- vignettes/EMVS_vignette.Rnw | 10 ++++------ 12 files changed, 45 insertions(+), 57 deletions(-)
Title: 'R Markdown' Format for Scientific and Technical Writing
Description: Scientific and technical article format for the web. 'Distill' articles
feature attractive, reader-friendly typography, flexible layout options
for visualizations, and full support for footnotes and citations.
Author: JJ Allaire [aut, cre] (<https://orcid.org/0000-0003-0174-9868>),
Rich Iannone [aut],
Alison Presmanes Hill [aut] (<https://orcid.org/0000-0002-8082-1890>),
Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Google LLC [ctb, cph] (https://distill.pub/guide/),
Nick Williams [ctb, cph] (https://wicky.nillia.ms/headroom.js/),
Denis Demchenko [ctb, cph] (https://github.com/lancedikson/bowser),
The Polymer Authors [ctb, cph]
(https://www.webcomponents.org/polyfills/),
Gábor Csárdi [ctb, cph] (whoami),
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between distill versions 1.2 dated 2021-01-13 and 1.3 dated 2021-10-13
DESCRIPTION | 16 ++-- MD5 | 36 +++++----- NEWS.md | 21 ++++- R/appendices.R | 2 R/collections.R | 17 +--- R/create.R | 7 + R/distill_article.R | 7 - R/import.R | 5 - R/metadata.R | 10 ++ R/navigation.R | 6 - R/rstudio.R | 5 + R/sitemap.R | 4 - R/utils.R | 15 +--- inst/rmarkdown/templates/distill_article/resources/arrow.theme | 4 - inst/rmarkdown/templates/distill_article/resources/default.html | 27 +++++++ inst/rmarkdown/templates/distill_article/resources/distill.html | 5 + inst/rmarkdown/templates/distill_article/resources/listing.html | 5 - man/distill_article.Rd | 3 man/import_post.Rd | 5 - 19 files changed, 126 insertions(+), 74 deletions(-)
Title: Regression Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.
Author: Oldemar Rodriguez R. [aut, cre],
Andres Navarro D. [ctb, prg],
Diego Jimenez A. [ctb, prg],
Ariel Arroyo S. [ctb, prg]
Maintainer: Oldemar Rodriguez R. <oldemar.rodriguez@ucr.ac.cr>
Diff between regressoR versions 2.0.0 dated 2021-09-23 and 2.0.1 dated 2021-10-13
DESCRIPTION | 8 ++--- MD5 | 47 +++++++++++++++++------------------ R/Utilities.R | 11 -------- R/app_ui.R | 19 +++++++------- R/general_plots.R | 3 -- R/mod_KNN.R | 13 +++++---- R/mod_Predictive_Power.R | 6 +--- R/mod_SVM.R | 13 +++++---- R/mod_boosting.R | 15 +++++------ R/mod_correlacion.R | 12 ++++---- R/mod_dimension_reduction.R | 19 +++++++------- R/mod_dispersion.R | 5 +-- R/mod_distribuciones.R | 11 ++++---- R/mod_information_page.R | 2 - R/mod_linear_regression.R | 15 +++++------ R/mod_neural_networks.R | 15 +++++------ R/mod_new_data_predictions.R | 21 ++++++--------- R/mod_normal.R | 6 +--- R/mod_penalized_Regression.R | 18 ++++++------- R/mod_random_forests.R | 15 +++++------ R/mod_regression_trees.R | 13 +++++---- R/regressoR.R | 2 - R/utils_outputs.R | 6 ++-- inst/app/www/input_binding_colour.js |only inst/app/www/script_regressor.js | 6 ++-- 25 files changed, 146 insertions(+), 155 deletions(-)
Title: Generate QRcodes with R
Description: Create QRcode in R.
Author: Victor Teh [aut] (Original author),
Thierry Onkelinx [aut, cre] (Author of the reimplemented functions,
<https://orcid.org/0000-0001-8804-4216>)
Maintainer: Thierry Onkelinx <thierry.onkelinx@inbo.be>
Diff between qrcode versions 0.1.3 dated 2021-07-02 and 0.1.4 dated 2021-10-13
DESCRIPTION | 34 ++++------ MD5 | 89 ++++++++++++++++++-------- NAMESPACE | 26 +++++++ NEWS.md | 5 + R/DataStringBinary.R | 3 R/ECgenerator.R | 3 R/bits.R |only R/formatPolyGen.R | 3 R/generate_svg.R | 41 ++++++------ R/plot.R |only R/polynomialGenerator.R | 3 R/print.R |only R/qrFillUpMatrix.R | 3 R/qrInitMatrix.R | 3 R/qrInterleave.R | 23 ++++-- R/qrMask.R | 3 R/qrVersionInfo.R | 3 R/qr_code.R |only R/qr_encode.R |only R/qr_error.R |only R/qr_matrix.R |only R/qr_mode.R |only R/qr_version.R |only R/qrcode_gen.R | 34 ++++++++-- R/validate_qr.R |only R/versionPolyGen.R | 3 README.md | 110 +++++++++++++++++++++++++++------ inst |only man/DataStringBinary.Rd | 17 +++++ man/ECgenerator.Rd | 17 +++++ man/as.character.bits.Rd |only man/bits.Rd |only man/bits2int.Rd |only man/c.bits.Rd |only man/figures/example-1.png |only man/figures/qr.svg |only man/formatPolyGen.Rd | 17 +++++ man/generate_svg.Rd | 39 +++++++---- man/plot.qr_code.Rd |only man/polynomialGenerator.Rd | 17 +++++ man/print.bits.Rd |only man/print.qr_code.Rd |only man/qrFillUpMatrix.Rd | 17 +++++ man/qrInitMatrix.Rd | 17 +++++ man/qrInterleave.Rd | 17 +++++ man/qrMask.Rd | 17 +++++ man/qrVersionInfo.Rd | 17 +++++ man/qr_code.Rd |only man/qr_encode.Rd |only man/qr_error.Rd |only man/qr_matrix.Rd |only man/qr_mode.Rd |only man/qr_version.Rd |only man/qrcode_gen.Rd | 17 +++++ man/versionPolyGen.Rd | 17 +++++ tests/testthat/test_a_format_string.R |only tests/testthat/test_a_format_version.R |only tests/testthat/test_a_galois.R |only tests/testthat/test_a_qr_mode.R |only tests/testthat/test_b_qr_version.R |only tests/testthat/test_c_qr_encode.R |only tests/testthat/test_d_qr_code.R |only 62 files changed, 502 insertions(+), 113 deletions(-)
Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut],
Samuel Bosch [aut],
Ward Appeltans [ctb],
OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Diff between robis versions 2.8.1 dated 2021-09-30 and 2.8.2 dated 2021-10-13
DESCRIPTION | 10 ++-- MD5 | 12 ++--- NEWS.md | 4 + inst/doc/getting-started.R | 3 + inst/doc/getting-started.Rmd | 3 + inst/doc/getting-started.html | 90 +++++++++++++++++++++--------------------- vignettes/getting-started.Rmd | 3 + 7 files changed, 69 insertions(+), 56 deletions(-)
Title: Finding Optimal Microsampling Designs for Non-Compartmental
Pharmacokinetic Analysis
Description: Find optimal microsampling designs for non-compartmental pharacokinetic analysis using a general simulation methodology:
Algorithm III of Barnett, Helen, Helena Geys, Tom Jacobs, and Thomas Jaki. (2017) "Optimal Designs for Non-Compartmental
Analysis of Pharmacokinetic Studies. (currently unpublished)"
This methodology consist of (1) specifying a pharmacokinetic model
including variability among animals; (2) generating possible sampling times; (3)
evaluating performance of each time point choice on simulated data; (4)
generating possible schemes given a time point choice and additional constraints
and finally (5) evaluating scheme performance on simulated data. The default
settings differ from the article of Barnett and others, in the default pharmacokinetic model used and
the parameterization of variability among animals. Details can be found in the package vignette. A 'shiny'
web application is included, which guides users from model parametrization to
optimal microsampling scheme.
Author: Adriaan Blommaert [aut, cre],
Daan Seynaeve [ctb],
Helen Barnett [ctb],
Helena Geys [ctb],
Tom Jacobs [ctb],
Fetene Tekle [ctb],
Thomas Jaki [ctb]
Maintainer: Adriaan Blommaert <adriaan.blommaert@openanalytics.eu>
Diff between microsamplingDesign versions 1.0.7 dated 2020-04-05 and 1.0.8 dated 2021-10-13
DESCRIPTION | 8 MD5 | 4 inst/doc/microsamplingDesign.pdf | 734 +++++++++++++++++++-------------------- 3 files changed, 375 insertions(+), 371 deletions(-)
More information about microsamplingDesign at CRAN
Permanent link
Title: Likelihood Analyses for Common Statistical Tests
Description: A collection of functions that calculate the log likelihood
(support) for a range of statistical tests. Where possible the likelihood
function and likelihood interval for the observed data are displayed. The
evidential approach used here is based on the book "Likelihood" by A.W.F.
Edwards (1992, ISBN-13 : 978-0801844430), "Statistical Evidence" by R.
Royall (1997, ISBN-13 : 978-0412044113), S.N. Goodman & R. Royall
(2011) <doi:10.2105/AJPH.78.12.1568>, "Understanding
Psychology as a Science" by Z. Dienes (2008, ISBN-13 : 978-0230542310),
S. Glover & P. Dixon <https://link.springer.com/article/10.3758/BF03196706>
and others. This package accompanies "Evidence-Based Statistics" by
P. Cahusac (2020, ISBN-13 : 978-1119549802).
Author: Peter Cahusac [aut, cre] (<https://orcid.org/0000-0003-4976-2834>)
Maintainer: Peter Cahusac <peteqsac@gmail.com>
Diff between likelihoodR versions 1.0.4 dated 2021-05-03 and 1.0.5 dated 2021-10-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/L_OR.R | 39 +++++++++++++++++++++++++-------------- R/L_RR.R | 11 ++++++----- 4 files changed, 37 insertions(+), 25 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast
cumulative residuals, excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling. PLS for the
additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy
Silver and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 2.0.0 dated 2021-05-20 and 2.0.1 dated 2021-10-13
DESCRIPTION | 10 +++--- MD5 | 12 +++---- R/event.split.r | 22 +++++++------- man/event.split.Rd | 8 +---- man/res.mean.Rd | 3 - src/matrix.c | 46 +++++++++++++++--------------- src/matrix.h | 80 ++++++++++++++++++++++++++++------------------------- 7 files changed, 92 insertions(+), 89 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.3.5 dated 2021-06-09 and 0.3.6 dated 2021-10-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ README.md | 5 ++--- build/vignette.rds |binary inst/doc/c_interface.html | 40 ++++++++++++++++++++-------------------- man/shape_text.Rd | 2 +- src/string_shape.cpp | 12 ++++++------ 8 files changed, 46 insertions(+), 40 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 1.0.2 dated 2021-05-11 and 1.0.3 dated 2021-10-13
DESCRIPTION | 6 MD5 | 20 +- NEWS.md | 7 README.md | 17 -- build/vignette.rds |binary configure | 16 + inst/doc/c_interface.html | 375 ++++++++++----------------------------------- inst/include/systemfonts.h | 4 src/font_matching.cpp | 2 src/font_matching.h | 3 src/ft_cache.cpp | 11 + 11 files changed, 145 insertions(+), 316 deletions(-)
Title: Linear, Quadratic, and Rational Optimization
Description: Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'. Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp'.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Diff between optiSolve versions 0.1.2 dated 2020-03-10 and 1.0 dated 2021-10-13
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/cop.R | 17 +++++++++++------ R/simplify.R | 1 - R/solvecop.R | 2 +- build/partial.rdb |binary data/myQ.rda |binary data/myQ1.rda |binary data/myQ2.rda |binary data/phenotype.rda |binary man/lbcon.Rd | 2 +- man/ubcon.Rd | 2 +- 12 files changed, 30 insertions(+), 26 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between rjags versions 4-11 dated 2021-09-24 and 4-12 dated 2021-10-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/windows/zzz.R | 20 ++++++++++++++------ 3 files changed, 20 insertions(+), 12 deletions(-)
Title: Hypothesis Tests for Association Between Subgroups in Two Data
Views
Description: Tests for association between subgroups in two multivariate data views, two network data views, or a multivariate data view and a network data view. (Reference 1: Gao, L.L., Bien, J., and Witten, D. (2020) "Are Clusterings of Multiple Data Views Independent?", <doi:10.1093/biostatistics/kxz001> and Reference 2: Gao, L.L., Witten, D., Bien, J. (2021) Testing for Association in Multi-View Network Data, <doi:10.1111/biom.13464>.)
Author: Lucy L. Gao [aut, cre]
Maintainer: Lucy L. Gao <lucy.gao@uwaterloo.ca>
Diff between multiviewtest versions 2.0.0 dated 2019-08-27 and 2.0.1 dated 2021-10-13
DESCRIPTION | 15 +++++++-------- MD5 | 30 +++++++++++++++--------------- NEWS.md | 7 +++---- R/optimize_over_Pi.R | 4 ++-- R/test_indep_clust.R | 4 ++-- R/test_indep_clust_subset.R | 8 ++++---- R/test_indep_com.R | 14 +++++++++----- R/test_indep_com_clust.R | 12 ++++++++---- README.md | 2 +- man/multiviewtest-package.Rd | 2 +- man/optimize_over_Pi.Rd | 15 +++++++++++---- man/pl_est_com.Rd | 3 +-- man/test_indep_clust.Rd | 15 ++++++++++++--- man/test_indep_clust_subset.Rd | 17 ++++++++++++++--- man/test_indep_com.Rd | 11 +++++++++-- man/test_indep_com_clust.Rd | 14 +++++++++++--- 16 files changed, 110 insertions(+), 63 deletions(-)
Title: GSL Nonlinear Least-Squares Fitting
Description: An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquadt algorithm with and without geodesic acceleration, and several variants of Powell's dogleg algorithm. Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.0.1 dated 2021-10-11 and 1.0.2 dated 2021-10-13
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS.md | 4 ++++ configure | 18 +++++++++--------- configure.ac | 2 +- src/Makevars.ucrt |only 6 files changed, 23 insertions(+), 18 deletions(-)
Title: Predict Gender from Names Using Historical Data
Description: Infers state-recorded gender categories from first names and dates of birth using historical
datasets. By using these datasets instead of lists of male and female names,
this package is able to more accurately infer the gender of a name, and it
is able to report the probability that a name was male or female. GUIDELINES:
This method must be used cautiously and responsibly. Please be sure to see the
guidelines and warnings about usage in the 'README' or the package documentation.
See Blevins and Mullen (2015) <http://www.digitalhumanities.org/dhq/vol/9/3/000223/000223.html>.
Author: Lincoln Mullen [aut, cre] (<https://orcid.org/0000-0001-5103-6917>),
Cameron Blevins [ctb],
Ben Schmidt [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between gender versions 0.5.4 dated 2020-05-15 and 0.6.0 dated 2021-10-13
gender-0.5.4/gender/R/gender_df.R |only gender-0.5.4/gender/man/gender_df.Rd |only gender-0.5.4/gender/tests/testthat/test-gender_df.R |only gender-0.6.0/gender/DESCRIPTION | 25 - gender-0.6.0/gender/MD5 | 33 - gender-0.6.0/gender/NAMESPACE | 1 gender-0.6.0/gender/NEWS.md | 5 gender-0.6.0/gender/R/gender-package.r | 7 gender-0.6.0/gender/R/gender.R | 2 gender-0.6.0/gender/R/install-genderdata-package.R | 12 gender-0.6.0/gender/README.md | 59 +-- gender-0.6.0/gender/build/vignette.rds |binary gender-0.6.0/gender/inst/CITATION | 2 gender-0.6.0/gender/inst/doc/predicting-gender.R | 15 gender-0.6.0/gender/inst/doc/predicting-gender.Rmd | 39 -- gender-0.6.0/gender/inst/doc/predicting-gender.html | 349 +++----------------- gender-0.6.0/gender/man/gender.Rd | 2 gender-0.6.0/gender/tests/testthat/test-ssa.r | 2 gender-0.6.0/gender/vignettes/predicting-gender.Rmd | 39 -- 19 files changed, 137 insertions(+), 455 deletions(-)
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changed in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 2.3.1 dated 2021-01-06 and 2.3.2 dated 2021-10-13
DESCRIPTION | 8 ++-- MD5 | 8 ++-- NEWS.md | 4 ++ R/fnsComparison.R | 7 +++- tests/testthat/test-fnsComparison.R | 60 +++++++++++++++++++++++++++++++++--- 5 files changed, 72 insertions(+), 15 deletions(-)
Title: Aligned Rank Transform
Description: The aligned rank transform for nonparametric
factorial ANOVAs as described by Wobbrock,
Findlater, Gergle, and Higgins (2011) <doi:10.1145/1978942.1978963>.
Also supports aligned rank transform contrasts as described
by Elkin, Kay, Higgins, and Wobbrock (2021)
<doi:10.1145/3472749.3474784>.
Author: Matthew Kay [aut, cre],
Lisa A. Elkin [aut],
James J. Higgins [aut],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between ARTool versions 0.11.0 dated 2021-02-24 and 0.11.1 dated 2021-10-13
DESCRIPTION | 23 +- MD5 | 49 ++--- NEWS.md | 8 R/anova.art.R | 4 R/art.R | 14 - R/art.con.R | 10 - R/art.con.internal.R | 4 R/artlm.con.R | 6 R/data.R | 12 - README.md | 32 +-- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 10 - inst/doc/art-contrasts.R | 5 inst/doc/art-contrasts.Rmd | 11 - inst/doc/art-contrasts.html | 352 ++++++++++++++++++++-------------------- inst/doc/art-effect-size.html | 17 + man/ElkinAB.Rd | 6 man/ElkinABC.Rd | 6 man/anova.art.Rd | 4 man/art.Rd | 10 - man/art.con.Rd | 10 - man/artlm.con.Rd | 6 man/summary.art.Rd | 4 tests/testthat/test.artlm.con.R | 8 vignettes/art-contrasts.Rmd | 11 - 26 files changed, 340 insertions(+), 282 deletions(-)
Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, it consists of several functions to perform various tasks, including
simulating or analyzing data, computing the significance thresholds and visualizing the
QTL mapping results. The single-QTL or multiple-QTL method that allows a host of
statistical models to be fitted and compared is applied to analyze the data for the
estimation of QTL parameters. The models include the linear regression, permutation test,
normal mixture model and truncated normal mixture model. The Gaussian stochastic process
is implemented to compute the significance thresholds for QTL detection onto a genetic
linkage map in the experimental populations. Two types of data, the complete genotyping
or selective genotyping data, from various experimental populations, including backcross,
F2, recombinant inbred (RI) populations, advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotpot detection, the statistical methods
can be developed based on either using the individual-level data or using the summarized
data. We have proposed a statistical framework that can handle both the individual-level
data and summarized QTL data for QTL hotspots detection. Our statistical framework can
overcome the underestimation of threshold arising from ignoring the correlation structure
among traits, and also identify the different types of hotspots with very low
computational cost during the detection process. Here, we attempt to provide the R codes
of our QTL mapping and hotspot detection methods for general use in genes, genomics and
genetics studies. The QTL mapping methods for the complete and selective genotyping
designs are based on the multiple interval mapping (MIM) model proposed by Kao, C.-H. ,
Z.-B. Zeng and R. D. Teasdale (1999) <doi:10.1534/genetics.103.021642> and H.-I Lee,
H.-A. Ho and C.-H. Kao (2014) <doi:10.1534/genetics.114.168385>, respectively. The QTL
hotspot detection analysis is based on the method by Wu, P.-Y., M.-.H. Yang, and C.-H.
Kao (2021) .
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 1.0.0 dated 2021-09-02 and 1.1.0 dated 2021-10-13
DESCRIPTION | 6 +++--- MD5 | 38 +++++++++++++++++++------------------- R/EM.MIM.R | 12 ++++++++---- R/EM.MIM2.R | 32 +++++++++++++++++++++++--------- R/IM.search.R | 10 +++++----- R/IM.search2.R | 10 +++++----- R/MIM.points.R | 2 +- R/MIM.points2.R | 3 ++- R/MIM.search.R | 2 +- R/MIM.search2.R | 3 ++- R/Q.make.R | 9 +++++++++ inst/extdata/exampledata.RDATA |binary man/EM.MIM.Rd | 4 +++- man/EM.MIM2.Rd | 4 ++++ man/IM.search.Rd | 2 +- man/IM.search2.Rd | 2 +- man/MIM.points.Rd | 2 +- man/MIM.points2.Rd | 3 ++- man/MIM.search.Rd | 2 +- man/MIM.search2.Rd | 3 ++- 20 files changed, 93 insertions(+), 56 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-10 0.1.1
Title: Tools for Case 1 Best-Worst Scaling
Description: Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. For details on best-worst scaling, see Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS versions 0.4-3 dated 2021-01-28 and 0.4-4 dated 2021-10-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 6 ++++++ R/bws.count.R | 30 +++++++++++++++++++++++++++--- R/bws.dataset.R | 29 ++++++++++++++++++++--------- man/bws.count.Rd | 5 ++++- 7 files changed, 68 insertions(+), 23 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.7.0 dated 2021-09-17 and 0.7.1 dated 2021-10-13
robustHD-0.7.0/robustHD/inst/tests |only robustHD-0.7.1/robustHD/DESCRIPTION | 10 robustHD-0.7.1/robustHD/MD5 | 117 +- robustHD-0.7.1/robustHD/NEWS | 9 robustHD-0.7.1/robustHD/R/AIC.R | 324 +++---- robustHD-0.7.1/robustHD/R/accessors.R | 404 ++++----- robustHD-0.7.1/robustHD/R/coef.R | 252 +++--- robustHD-0.7.1/robustHD/R/corHuber.R | 278 +++--- robustHD-0.7.1/robustHD/R/fastLasso.R | 100 +- robustHD-0.7.1/robustHD/R/fitted.R | 202 ++-- robustHD-0.7.1/robustHD/R/grouplars.R | 648 +++++++-------- robustHD-0.7.1/robustHD/R/grplars.R | 750 ++++++++--------- robustHD-0.7.1/robustHD/R/initialSubsets.R | 100 +- robustHD-0.7.1/robustHD/R/lambda0.R | 222 ++--- robustHD-0.7.1/robustHD/R/perry.R | 314 +++---- robustHD-0.7.1/robustHD/R/predict.R | 468 +++++------ robustHD-0.7.1/robustHD/R/print.R | 374 ++++---- robustHD-0.7.1/robustHD/R/regFun.R | 114 +- robustHD-0.7.1/robustHD/R/residuals.R | 342 ++++---- robustHD-0.7.1/robustHD/R/rlars.R | 696 ++++++++-------- robustHD-0.7.1/robustHD/R/seqModel.R | 212 ++--- robustHD-0.7.1/robustHD/R/setupCoefPlot.R | 570 ++++++------- robustHD-0.7.1/robustHD/R/setupCritPlot.R | 468 +++++------ robustHD-0.7.1/robustHD/R/setupDiagnosticPlot.R | 918 +++++++++++----------- robustHD-0.7.1/robustHD/R/sparseLTS.R | 19 robustHD-0.7.1/robustHD/R/standardize.R | 260 +++--- robustHD-0.7.1/robustHD/R/test.R | 62 - robustHD-0.7.1/robustHD/R/tsBlocks.R | 180 ++-- robustHD-0.7.1/robustHD/R/tslars.R | 644 +++++++-------- robustHD-0.7.1/robustHD/R/tslarsP.R | 608 +++++++------- robustHD-0.7.1/robustHD/R/utils.R | 508 ++++++------ robustHD-0.7.1/robustHD/R/weights.R | 116 +- robustHD-0.7.1/robustHD/R/winsorize.R | 384 ++++----- robustHD-0.7.1/robustHD/build/partial.rdb |binary robustHD-0.7.1/robustHD/man/AIC.seqModel.Rd | 216 ++--- robustHD-0.7.1/robustHD/man/TopGear.Rd | 152 +-- robustHD-0.7.1/robustHD/man/coef.seqModel.Rd | 230 ++--- robustHD-0.7.1/robustHD/man/corHuber.Rd | 226 ++--- robustHD-0.7.1/robustHD/man/fitted.seqModel.Rd | 222 ++--- robustHD-0.7.1/robustHD/man/getScale.Rd | 138 +-- robustHD-0.7.1/robustHD/man/grplars.Rd | 542 ++++++------ robustHD-0.7.1/robustHD/man/lambda0.Rd | 224 ++--- robustHD-0.7.1/robustHD/man/nci60.Rd | 111 +- robustHD-0.7.1/robustHD/man/partialOrder.Rd | 84 +- robustHD-0.7.1/robustHD/man/perry.seqModel.Rd | 286 +++--- robustHD-0.7.1/robustHD/man/plot.seqModel.Rd | 190 ++-- robustHD-0.7.1/robustHD/man/predict.seqModel.Rd | 242 ++--- robustHD-0.7.1/robustHD/man/residuals.seqModel.Rd | 230 ++--- robustHD-0.7.1/robustHD/man/rlars.Rd | 474 +++++------ robustHD-0.7.1/robustHD/man/robustHD-package.Rd | 44 - robustHD-0.7.1/robustHD/man/sparseLTS.Rd | 585 +++++++------- robustHD-0.7.1/robustHD/man/standardize.Rd | 152 +-- robustHD-0.7.1/robustHD/man/tsBlocks.Rd | 82 - robustHD-0.7.1/robustHD/man/tslars.Rd | 402 ++++----- robustHD-0.7.1/robustHD/man/tslarsP.Rd | 456 +++++----- robustHD-0.7.1/robustHD/man/weights.sparseLTS.Rd | 172 ++-- robustHD-0.7.1/robustHD/man/winsorize.Rd | 250 ++--- robustHD-0.7.1/robustHD/tests |only 58 files changed, 8204 insertions(+), 8179 deletions(-)
More information about pvcurveanalysis at CRAN
Permanent link
More information about KingCountyHouses at CRAN
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Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation and initialization of the hidden hybrid Markov/semi-Markov model, introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>.
Author: Morteza Amini [aut, cre, cph],
Afarin Bayat [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>
Diff between hhsmm versions 0.1.3 dated 2021-09-13 and 0.2.0 dated 2021-10-13
DESCRIPTION | 10 +++++----- MD5 | 31 ++++++++++++++++++------------- NAMESPACE | 4 ++++ R/cov-miss-mix-wt.R |only R/cov-mix-wt.R | 20 ++++++++++++++------ R/densComputeMiss.R |only R/hhsmmfit.R | 20 ++++++++++++++++---- R/initial-cluster.R | 20 ++++++++++++++++++-- R/initialize-model.R | 20 +++++++++++++++++--- R/mstep-missing-mix-mvnorm.R |only R/plot-hhsmm-data.R | 9 +++++++++ R/predict-hhsmm.R | 35 +++++++++++++++++------------------ man/cov.miss.mix.wt.Rd |only man/cov.mix.wt.Rd | 20 ++++++++++++++------ man/hhsmmfit.Rd | 2 +- man/initial_cluster.Rd | 5 ++++- man/initialize_model.Rd | 8 ++++++-- man/miss_mixmvnorm_mstep.Rd |only man/predict.hhsmm.Rd | 3 ++- 19 files changed, 145 insertions(+), 62 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 4.7-0 dated 2021-09-02 and 4.8 dated 2021-10-13
DESCRIPTION | 14 +++---- MD5 | 18 ++++----- NEWS | 5 ++ R/HelpersMG-package.R | 4 +- R/flexit.R | 61 +++++++++++++++++++++++++++------ R/format_ncdf.R | 85 ++++++++++++++++++++++++++++++++++------------- R/sysdata.rda |binary man/HelpersMG-package.Rd | 4 +- man/flexit.Rd | 18 ++++++++- man/format_ncdf.Rd | 6 ++- 10 files changed, 156 insertions(+), 59 deletions(-)
Title: Text Processing for Small or Big Data Files
Description: It offers functions for splitting, parsing, tokenizing and creating a vocabulary for big text data files. Moreover, it includes functions for building a document-term matrix and extracting information from those (term-associations, most frequent terms). It also embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. Lastly, it includes functions for Word Vector Representations (i.e. 'GloVe', 'fasttext') and incorporates functions for the calculation of (pairwise) text document dissimilarities. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between textTinyR versions 1.1.4 dated 2021-05-05 and 1.1.5 dated 2021-10-13
DESCRIPTION | 8 MD5 | 22 NEWS.md | 5 README.md | 18 build/vignette.rds |binary inst/doc/functionality_of_textTinyR_package.Rmd | 2 inst/doc/functionality_of_textTinyR_package.html | 2056 ++++++++++------------- inst/doc/word_vectors_doc2vec.Rmd | 10 inst/doc/word_vectors_doc2vec.html | 768 +++----- src/RcppExports.cpp | 5 vignettes/functionality_of_textTinyR_package.Rmd | 2 vignettes/word_vectors_doc2vec.Rmd | 10 12 files changed, 1285 insertions(+), 1621 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-14 2.1.1
2019-08-02 2.0.0
2019-01-21 1.1.0
2017-12-14 1.0.1
2017-11-20 1.0.0
2017-08-16 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-28 0.4.8
2019-03-18 0.4.7
2019-02-14 0.4.6
2018-05-16 0.4.5
2017-11-14 0.4.4
2017-09-05 0.4.3
2017-08-10 0.4.2
2016-11-08 0.4.1
2016-09-23 0.4.0
2016-04-25 0.3.1
2016-03-31 0.3.0
2015-09-29 0.2.1
Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled
time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007)
<doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints
where significance of an effect begins and ends, and the results can be plotted in various
types of heatmap for reporting. Mixed-effects models are supported using an implementation of
the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between permutes versions 2.1.1 dated 2021-09-14 and 2.2 dated 2021-10-13
DESCRIPTION | 10 +-- MD5 | 24 +++---- NAMESPACE | 26 ++++---- R/buildmer.R | 19 +++-- R/discoverability.R | 26 ++++---- inst/doc/buildmer.pdf |binary inst/doc/permutes.pdf |binary man/perm.glm.Rd | 2 man/perm.glmer.Rd | 6 + man/perm.lm.Rd | 14 ++-- man/perm.lmer.Rd | 6 + man/permu.test.Rd | 162 +++++++++++++++++++++++++------------------------- man/plot.permutes.Rd | 62 +++++++++---------- 13 files changed, 184 insertions(+), 173 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-07 4.0
2017-05-25 3.1
2016-01-11 3.0
2015-06-26 2.4
2015-05-09 2.3
2015-04-10 2.2
2015-03-11 2.1
2015-01-11 2.0
2014-10-14 1.2
2014-07-17 1.1
2014-01-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-04 2.0
2019-02-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-03 1.2.3
2021-07-16 1.2.2
2021-06-24 1.2.1
2021-06-14 1.2.0
2021-05-28 1.1.0
2021-05-18 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-04 0.3.4
2018-12-12 0.3.3
2018-04-30 0.3.2
2018-04-05 0.3.1
2018-03-13 0.3.0
Title: Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header
Files
Description: Provided within are two high quality and fast PPRNGs that may be
used in an 'OpenMP' parallel environment. In addition, there is a generator
for one dimensional low-discrepancy sequence. The objective of this library
to consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and
'vandercorput' (C++11-only) engines on CRAN by enabling others to link to the
header files inside of 'sitmo' instead of including a copy of each engine
within their individual package. Lastly, the package contains example
implementations using the 'sitmo' package and three accompanying vignette that
provide additional information.
Author: James Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Thijs van den Berg [aut, cph],
Ralf Stubner [ctb]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between sitmo versions 2.0.1 dated 2019-01-07 and 2.0.2 dated 2021-10-13
sitmo-2.0.1/sitmo/inst/doc/big_crush_test.R |only sitmo-2.0.2/sitmo/DESCRIPTION | 9 sitmo-2.0.2/sitmo/MD5 | 31 sitmo-2.0.2/sitmo/NEWS.md | 11 sitmo-2.0.2/sitmo/README.md | 25 sitmo-2.0.2/sitmo/build/vignette.rds |binary sitmo-2.0.2/sitmo/inst/doc/big_crush_test.Rmd | 4 sitmo-2.0.2/sitmo/inst/doc/big_crush_test.html | 7806 ++++++++--------- sitmo-2.0.2/sitmo/inst/doc/sitmo_internals.R | 535 + sitmo-2.0.2/sitmo/inst/doc/sitmo_internals.Rmd | 4 sitmo-2.0.2/sitmo/inst/doc/sitmo_internals.html | 829 - sitmo-2.0.2/sitmo/inst/doc/uniform_rng_with_sitmo.R | 6 sitmo-2.0.2/sitmo/inst/doc/uniform_rng_with_sitmo.html | 430 sitmo-2.0.2/sitmo/man/sitmo-package.Rd | 2 sitmo-2.0.2/sitmo/src/RcppExports.cpp | 5 sitmo-2.0.2/sitmo/vignettes/big_crush_test.Rmd | 4 sitmo-2.0.2/sitmo/vignettes/sitmo_internals.Rmd | 4 17 files changed, 4893 insertions(+), 4812 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <DOI:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>;
- rankograms and ranking by SUCRA;
- contribution matrix as described in Papakonstantinou et al. (2018) <DOI:10.12688/f1000research.14770.3> and Davies et al. (2021) <arXiv:2107.02886>.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Annabel Davies [aut] (<https://orcid.org/0000-0003-2320-7701>),
Theodoros Papakonstantinou [aut]
(<https://orcid.org/0000-0002-6630-6817>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 1.5-0 dated 2021-06-29 and 2.0-0 dated 2021-10-13
netmeta-1.5-0/netmeta/R/upgradenetmeta.R |only netmeta-1.5-0/netmeta/man/print.netmeta.Rd |only netmeta-2.0-0/netmeta/DESCRIPTION | 22 netmeta-2.0-0/netmeta/MD5 | 259 ++-- netmeta-2.0-0/netmeta/NAMESPACE | 55 - netmeta-2.0-0/netmeta/NEWS.md | 197 +++ netmeta-2.0-0/netmeta/R/Baker2009.R |only netmeta-2.0-0/netmeta/R/Dogliotti2014.R |only netmeta-2.0-0/netmeta/R/Linde2015.R | 13 netmeta-2.0-0/netmeta/R/Linde2016.R | 10 netmeta-2.0-0/netmeta/R/Senn2013.R | 10 netmeta-2.0-0/netmeta/R/Stowe2010.R |only netmeta-2.0-0/netmeta/R/as.data.frame.netconnection.R | 3 netmeta-2.0-0/netmeta/R/as.data.frame.netmeta.R | 5 netmeta-2.0-0/netmeta/R/bySummary.R | 5 netmeta-2.0-0/netmeta/R/chkmultiarm.R | 161 +-- netmeta-2.0-0/netmeta/R/compsplit.R | 13 netmeta-2.0-0/netmeta/R/contribution.matrix.R |only netmeta-2.0-0/netmeta/R/createB.R | 96 + netmeta-2.0-0/netmeta/R/createC.R | 191 ++- netmeta-2.0-0/netmeta/R/decomp.design.R | 47 netmeta-2.0-0/netmeta/R/decomp.tau.R | 11 netmeta-2.0-0/netmeta/R/dietaryfat.R | 4 netmeta-2.0-0/netmeta/R/discomb.R | 171 ++- netmeta-2.0-0/netmeta/R/forest.netbind.R | 38 netmeta-2.0-0/netmeta/R/forest.netcomb.R | 66 - netmeta-2.0-0/netmeta/R/forest.netcomparison.R |only netmeta-2.0-0/netmeta/R/forest.netcomplex.R |only netmeta-2.0-0/netmeta/R/forest.netmeta.R | 80 - netmeta-2.0-0/netmeta/R/forest.netsplit.R | 170 ++- netmeta-2.0-0/netmeta/R/formatCC.R | 29 netmeta-2.0-0/netmeta/R/formatComp.R | 28 netmeta-2.0-0/netmeta/R/funnel.netmeta.R | 41 netmeta-2.0-0/netmeta/R/hasse.R | 45 netmeta-2.0-0/netmeta/R/hatmatrix.R |only netmeta-2.0-0/netmeta/R/is.installed.package.R |only netmeta-2.0-0/netmeta/R/lowertri.R | 6 netmeta-2.0-0/netmeta/R/meta-aux.R |only netmeta-2.0-0/netmeta/R/meta-chk.R |only netmeta-2.0-0/netmeta/R/meta-format.R |only netmeta-2.0-0/netmeta/R/meta-het.R |only netmeta-2.0-0/netmeta/R/meta-is.R |only netmeta-2.0-0/netmeta/R/meta-set.R |only netmeta-2.0-0/netmeta/R/meta-xlab.R |only netmeta-2.0-0/netmeta/R/netbind.R | 101 + netmeta-2.0-0/netmeta/R/netcomb.R | 161 ++- netmeta-2.0-0/netmeta/R/netcomparison.R |only netmeta-2.0-0/netmeta/R/netcomplex.R |only netmeta-2.0-0/netmeta/R/netconnection.R | 45 netmeta-2.0-0/netmeta/R/netcontrib.R | 432 ++++---- netmeta-2.0-0/netmeta/R/netdistance.R | 2 netmeta-2.0-0/netmeta/R/netgraph-internal.R | 2 netmeta-2.0-0/netmeta/R/netgraph.discomb.R | 3 netmeta-2.0-0/netmeta/R/netgraph.netcomb.R | 5 netmeta-2.0-0/netmeta/R/netgraph.netconnection.R | 3 netmeta-2.0-0/netmeta/R/netgraph.netimpact.R | 16 netmeta-2.0-0/netmeta/R/netgraph.netmeta.R | 96 + netmeta-2.0-0/netmeta/R/netheat.R | 78 - netmeta-2.0-0/netmeta/R/netimpact.R | 15 netmeta-2.0-0/netmeta/R/netleague.R | 121 +- netmeta-2.0-0/netmeta/R/netmatrix.R | 8 netmeta-2.0-0/netmeta/R/netmeasures.R | 58 - netmeta-2.0-0/netmeta/R/netmeta-internal.R | 42 netmeta-2.0-0/netmeta/R/netmeta-package.R | 46 netmeta-2.0-0/netmeta/R/netmeta.R | 231 ++-- netmeta-2.0-0/netmeta/R/netmetabin.R | 222 ++-- netmeta-2.0-0/netmeta/R/netpairwise.R |only netmeta-2.0-0/netmeta/R/netposet.R | 103 + netmeta-2.0-0/netmeta/R/netrank.R | 149 ++ netmeta-2.0-0/netmeta/R/netsplit.R | 723 +++++++------ netmeta-2.0-0/netmeta/R/nma.additive.R | 47 netmeta-2.0-0/netmeta/R/nma.krahn.R | 11 netmeta-2.0-0/netmeta/R/nma.ruecker.R | 59 - netmeta-2.0-0/netmeta/R/pairwise.R | 187 ++- netmeta-2.0-0/netmeta/R/plot.netposet.R | 53 netmeta-2.0-0/netmeta/R/plot.netrank.R | 169 +-- netmeta-2.0-0/netmeta/R/plot.rankogram.R | 132 +- netmeta-2.0-0/netmeta/R/print.decomp.design.R | 78 + netmeta-2.0-0/netmeta/R/print.netbind.R | 62 - netmeta-2.0-0/netmeta/R/print.netcomb.R | 378 +++++-- netmeta-2.0-0/netmeta/R/print.netimpact.R | 83 + netmeta-2.0-0/netmeta/R/print.netmeta.R | 962 ++++++++++++------ netmeta-2.0-0/netmeta/R/print.summary.netcomb.R |only netmeta-2.0-0/netmeta/R/print.summary.netmeta.R |only netmeta-2.0-0/netmeta/R/rankogram.R | 280 +++-- netmeta-2.0-0/netmeta/R/setref.R | 55 - netmeta-2.0-0/netmeta/R/setseq.R | 3 netmeta-2.0-0/netmeta/R/stress.R | 2 netmeta-2.0-0/netmeta/R/summary.netcomb.R | 305 ----- netmeta-2.0-0/netmeta/R/summary.netmeta.R | 800 -------------- netmeta-2.0-0/netmeta/R/tau.within.R | 10 netmeta-2.0-0/netmeta/R/treats.R | 87 + netmeta-2.0-0/netmeta/R/updateversion.R |only netmeta-2.0-0/netmeta/R/uppertri.R | 3 netmeta-2.0-0/netmeta/data/Baker2009.rda |only netmeta-2.0-0/netmeta/data/Dogliotti2014.rda |only netmeta-2.0-0/netmeta/data/Stowe2010.rda |only netmeta-2.0-0/netmeta/man/Baker2009.Rd |only netmeta-2.0-0/netmeta/man/Dogliotti2014.Rd |only netmeta-2.0-0/netmeta/man/Linde2015.Rd | 11 netmeta-2.0-0/netmeta/man/Linde2016.Rd | 10 netmeta-2.0-0/netmeta/man/Senn2013.Rd | 10 netmeta-2.0-0/netmeta/man/Stowe2010.Rd |only netmeta-2.0-0/netmeta/man/decomp.design.Rd | 23 netmeta-2.0-0/netmeta/man/dietaryfat.Rd | 4 netmeta-2.0-0/netmeta/man/discomb.Rd | 91 + netmeta-2.0-0/netmeta/man/forest.netbind.Rd | 7 netmeta-2.0-0/netmeta/man/forest.netcomb.Rd | 12 netmeta-2.0-0/netmeta/man/forest.netcomparison.Rd |only netmeta-2.0-0/netmeta/man/forest.netcomplex.Rd |only netmeta-2.0-0/netmeta/man/forest.netmeta.Rd | 12 netmeta-2.0-0/netmeta/man/forest.netsplit.Rd | 29 netmeta-2.0-0/netmeta/man/funnel.netmeta.Rd | 6 netmeta-2.0-0/netmeta/man/hasse.Rd | 6 netmeta-2.0-0/netmeta/man/hatmatrix.Rd |only netmeta-2.0-0/netmeta/man/netbind.Rd | 29 netmeta-2.0-0/netmeta/man/netcomb.Rd | 92 + netmeta-2.0-0/netmeta/man/netcomparison.Rd |only netmeta-2.0-0/netmeta/man/netcomplex.Rd |only netmeta-2.0-0/netmeta/man/netconnection.Rd | 16 netmeta-2.0-0/netmeta/man/netcontrib.Rd | 141 ++ netmeta-2.0-0/netmeta/man/netgraph.netcomb.Rd | 2 netmeta-2.0-0/netmeta/man/netgraph.netimpact.Rd | 7 netmeta-2.0-0/netmeta/man/netheat.Rd | 12 netmeta-2.0-0/netmeta/man/netimpact.Rd | 7 netmeta-2.0-0/netmeta/man/netleague.Rd | 39 netmeta-2.0-0/netmeta/man/netmatrix.Rd | 2 netmeta-2.0-0/netmeta/man/netmeasures.Rd | 17 netmeta-2.0-0/netmeta/man/netmeta-package.Rd | 43 netmeta-2.0-0/netmeta/man/netmeta.Rd | 178 ++- netmeta-2.0-0/netmeta/man/netmetabin.Rd | 61 - 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Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates for group means and standard deviations and their differences and effect sizes. It implements the method of Kruschke (2013) Bayesian estimation supersedes the t test. Journal of Experimental Psychology: General, 142(2):573-603 <doi: 10.1037/a0029146>.
Author: John Kruschke [aut],
Mike Meredith [aut, cre]
Maintainer: Mike Meredith <mike@mmeredith.net>
Diff between BEST versions 0.5.3 dated 2021-05-17 and 0.5.4 dated 2021-10-13
DESCRIPTION | 17 ++++++++----- MD5 | 41 ++++++++++++++++---------------- NEWS | 46 ++++++++++++++++++++++++------------ R/plot.BEST.R | 7 ++++- R/plotAll.R | 60 ++++++++++++++++++++++++++++-------------------- R/plotAreaInROPE.R | 9 ++++--- R/plotDataPPC.R | 15 ++++++------ R/plotPost.R | 12 +++++---- R/plotPostPred.R | 5 ++-- R/postPriorOverlap.R | 12 ++++----- inst/WORDLIST |only inst/doc/BEST.pdf |binary man/BEST-package.Rd | 4 +-- man/BESTpower.Rd | 4 +-- man/makeData.Rd | 4 +-- man/pairs.BEST.Rd | 2 - man/plot.BEST.Rd | 16 ++++++++++++ man/plotAll.Rd | 16 ++++++++++++ man/plotAreaInROPE.Rd | 5 +++- man/plotPost.Rd | 23 ++++++++++++++++-- man/plotPostPred.Rd | 11 +++++++- man/postPriorOverlap.Rd | 12 ++++++++- 22 files changed, 213 insertions(+), 108 deletions(-)