Title: Ask Yes-No Questions
Description: Asks Yes-No questions with variable or custom responses.
Author: Ayla Pearson [cre] ,
Joe Thorley [aut, cph] ,
Hadley Wickham [aut, cph]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between yesno versions 0.1.2 dated 2020-07-10 and 0.1.3 dated 2024-07-26
DESCRIPTION | 34 ++++++++++++++----------- LICENSE |only MD5 | 14 +++++----- NEWS.md | 10 +++++++ README.md | 58 ++++++++++++++++++++----------------------- man/figures |only tests/testthat.R | 8 +++++ tests/testthat/test-yesno.R | 2 - tests/testthat/test-yesno2.R | 2 - 9 files changed, 74 insertions(+), 54 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parameteric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.1.0 dated 2024-05-04 and 1.2.0 dated 2024-07-26
WeightIt-1.1.0/WeightIt/R/mlogit_weightit.R |only WeightIt-1.1.0/WeightIt/build/WeightIt.pdf |only WeightIt-1.2.0/WeightIt/DESCRIPTION | 24 WeightIt-1.2.0/WeightIt/MD5 | 115 - WeightIt-1.2.0/WeightIt/NAMESPACE | 38 WeightIt-1.2.0/WeightIt/NEWS.md | 80 WeightIt-1.2.0/WeightIt/R/SHARED.R | 114 - WeightIt-1.2.0/WeightIt/R/calibrate.R | 9 WeightIt-1.2.0/WeightIt/R/chk-utilities.R | 18 WeightIt-1.2.0/WeightIt/R/dist_functions.R | 10 WeightIt-1.2.0/WeightIt/R/functions_for_processing.R | 354 ++- WeightIt-1.2.0/WeightIt/R/get_w_from_ps.R | 245 +- WeightIt-1.2.0/WeightIt/R/glm_weightit-methods.R |only WeightIt-1.2.0/WeightIt/R/glm_weightit.R | 1058 +++------- WeightIt-1.2.0/WeightIt/R/make_full_rank.R | 2 WeightIt-1.2.0/WeightIt/R/multinom_weightit.R |only WeightIt-1.2.0/WeightIt/R/ordinal_weightit.R |only WeightIt-1.2.0/WeightIt/R/plot.weightit.R |only WeightIt-1.2.0/WeightIt/R/predict.glm_weightit.R |only WeightIt-1.2.0/WeightIt/R/sbps.R | 94 WeightIt-1.2.0/WeightIt/R/summary.weightit.R | 68 WeightIt-1.2.0/WeightIt/R/weightit.R | 44 WeightIt-1.2.0/WeightIt/R/weightit.fit.R | 16 WeightIt-1.2.0/WeightIt/R/weightit2bart.R | 17 WeightIt-1.2.0/WeightIt/R/weightit2cbps.R | 769 ++----- WeightIt-1.2.0/WeightIt/R/weightit2ebal.R | 32 WeightIt-1.2.0/WeightIt/R/weightit2energy.R | 103 WeightIt-1.2.0/WeightIt/R/weightit2gbm.R | 393 ++- WeightIt-1.2.0/WeightIt/R/weightit2glm.R | 171 - WeightIt-1.2.0/WeightIt/R/weightit2ipt.R | 88 WeightIt-1.2.0/WeightIt/R/weightit2npcbps.R | 3 WeightIt-1.2.0/WeightIt/R/weightit2ps.R | 4 WeightIt-1.2.0/WeightIt/R/weightit2super.R | 50 WeightIt-1.2.0/WeightIt/R/weightit2user.R | 9 WeightIt-1.2.0/WeightIt/R/weightitMSM.R | 93 WeightIt-1.2.0/WeightIt/build/stage23.rdb |binary WeightIt-1.2.0/WeightIt/build/vignette.rds |binary WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.R | 3 WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.Rmd | 3 WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.html | 46 WeightIt-1.2.0/WeightIt/inst/doc/estimating-effects.Rmd | 20 WeightIt-1.2.0/WeightIt/inst/doc/estimating-effects.html | 397 +-- WeightIt-1.2.0/WeightIt/inst/doc/installing-packages.html | 6 WeightIt-1.2.0/WeightIt/man/WeightIt-package.Rd | 2 WeightIt-1.2.0/WeightIt/man/get_w_from_ps.Rd | 87 WeightIt-1.2.0/WeightIt/man/glm_weightit-methods.Rd |only WeightIt-1.2.0/WeightIt/man/glm_weightit.Rd | 101 WeightIt-1.2.0/WeightIt/man/method_bart.Rd | 15 WeightIt-1.2.0/WeightIt/man/method_ebal.Rd | 2 WeightIt-1.2.0/WeightIt/man/method_energy.Rd | 14 WeightIt-1.2.0/WeightIt/man/method_gbm.Rd | 48 WeightIt-1.2.0/WeightIt/man/method_glm.Rd | 22 WeightIt-1.2.0/WeightIt/man/method_ipt.Rd | 2 WeightIt-1.2.0/WeightIt/man/method_npcbps.Rd | 3 WeightIt-1.2.0/WeightIt/man/method_super.Rd | 22 WeightIt-1.2.0/WeightIt/man/method_user.Rd | 9 WeightIt-1.2.0/WeightIt/man/plot.weightit.Rd |only WeightIt-1.2.0/WeightIt/man/predict.glm_weightit.Rd |only WeightIt-1.2.0/WeightIt/tests/testthat/test-get_w_from_ps.R |only WeightIt-1.2.0/WeightIt/tests/testthat/test-glm_weightit.R | 71 WeightIt-1.2.0/WeightIt/tests/testthat/test-method_glm.R | 63 WeightIt-1.2.0/WeightIt/tests/testthat/test-multinom_weightit.R |only WeightIt-1.2.0/WeightIt/tests/testthat/test-ordinal_weightit.R |only WeightIt-1.2.0/WeightIt/vignettes/WeightIt.Rmd | 3 WeightIt-1.2.0/WeightIt/vignettes/estimating-effects.Rmd | 20 65 files changed, 2627 insertions(+), 2353 deletions(-)
Title: Single Sample Directional Gene Set Analysis
Description: A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed.
Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.
Author: Xingpeng Li [aut, cre],
Qi Qian [aut]
Maintainer: Xingpeng Li <xingpeng.li@pfizer.com>
Diff between ssdGSA versions 0.1.0 dated 2024-07-22 and 0.1.1 dated 2024-07-26
DESCRIPTION | 15 ++++++++------- MD5 | 2 +- 2 files changed, 9 insertions(+), 8 deletions(-)
Title: Repeated Measures Correlation
Description: Compute the repeated measures correlation, a statistical technique
for determining the overall within-individual relationship among paired measures
assessed on two or more occasions, first introduced by Bland and Altman (1995).
Includes functions for diagnostics, p-value, effect size with confidence
interval including optional bootstrapping, as well as graphing. Also includes
several example datasets. For more details, see the web documentation
<https://lmarusich.github.io/rmcorr/index.html> and the
original paper: Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash [aut] ,
Laura R. Marusich [aut, cre]
Maintainer: Laura R. Marusich <lmarusich@gmail.com>
Diff between rmcorr versions 0.6.0 dated 2023-08-09 and 0.7.0 dated 2024-07-26
rmcorr-0.6.0/rmcorr/tests/HCAPHS.csv |only rmcorr-0.7.0/rmcorr/DESCRIPTION | 15 - rmcorr-0.7.0/rmcorr/MD5 | 81 +++-- rmcorr-0.7.0/rmcorr/NAMESPACE | 1 rmcorr-0.7.0/rmcorr/NEWS.md | 11 rmcorr-0.7.0/rmcorr/R/data.R | 4 rmcorr-0.7.0/rmcorr/R/geom_rmc.R |only rmcorr-0.7.0/rmcorr/R/plot.rmc.R | 33 -- rmcorr-0.7.0/rmcorr/R/rmcorr-package.R | 4 rmcorr-0.7.0/rmcorr/R/rmcorr.R | 2 rmcorr-0.7.0/rmcorr/README.md | 4 rmcorr-0.7.0/rmcorr/build/partial.rdb |binary rmcorr-0.7.0/rmcorr/build/vignette.rds |binary rmcorr-0.7.0/rmcorr/inst/doc/CI_fix.R | 2 rmcorr-0.7.0/rmcorr/inst/doc/CI_fix.html | 6 rmcorr-0.7.0/rmcorr/inst/doc/FAQ_and_limitations.R | 2 rmcorr-0.7.0/rmcorr/inst/doc/FAQ_and_limitations.Rmd | 2 rmcorr-0.7.0/rmcorr/inst/doc/FAQ_and_limitations.html | 11 rmcorr-0.7.0/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.R | 22 - rmcorr-0.7.0/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.html | 8 rmcorr-0.7.0/rmcorr/inst/doc/compcor.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/compcor.html | 9 rmcorr-0.7.0/rmcorr/inst/doc/estimates_w_NaN.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/estimates_w_NaN.html | 48 +-- rmcorr-0.7.0/rmcorr/inst/doc/model_diag.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/model_diag.html | 11 rmcorr-0.7.0/rmcorr/inst/doc/overfitting.R |only rmcorr-0.7.0/rmcorr/inst/doc/overfitting.Rmd |only rmcorr-0.7.0/rmcorr/inst/doc/overfitting.html |only rmcorr-0.7.0/rmcorr/inst/doc/repro_bootstrapping.R | 2 rmcorr-0.7.0/rmcorr/inst/doc/repro_bootstrapping.html | 6 rmcorr-0.7.0/rmcorr/inst/doc/rmcorr_mat.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/rmcorr_mat.html | 9 rmcorr-0.7.0/rmcorr/man/HCAHPS2022.Rd | 4 rmcorr-0.7.0/rmcorr/man/geom_rmc.Rd |only rmcorr-0.7.0/rmcorr/man/plot.rmc.Rd | 38 -- rmcorr-0.7.0/rmcorr/man/rmcorr-package.Rd | 22 + rmcorr-0.7.0/rmcorr/man/rmcorr.Rd | 2 rmcorr-0.7.0/rmcorr/tests/testthat/Rplots.pdf |binary rmcorr-0.7.0/rmcorr/tests/testthat/_snaps/geom_rmc |only rmcorr-0.7.0/rmcorr/tests/testthat/_snaps/rmcorr.md | 42 +- rmcorr-0.7.0/rmcorr/tests/testthat/test-geom_rmc.R |only rmcorr-0.7.0/rmcorr/vignettes/FAQ_and_limitations.Rmd | 2 rmcorr-0.7.0/rmcorr/vignettes/overfitting.Rmd |only rmcorr-0.7.0/rmcorr/vignettes/references.bib | 149 ++++++++++ 45 files changed, 357 insertions(+), 211 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.0 dated 2024-07-24 and 1.2.1 dated 2024-07-26
DESCRIPTION | 11 +++-- MD5 | 16 ++++---- NEWS.md | 4 ++ R/import_methods.R | 2 - R/sysdata.rda |binary README.md | 2 - inst/doc/labelled.html | 4 +- inst/doc/rio.html | 70 +++++++++++++++++------------------ tests/testthat/test_format_parquet.R | 2 - 9 files changed, 58 insertions(+), 53 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.3 dated 2024-07-09 and 3.6.4 dated 2024-07-26
DESCRIPTION | 6 MD5 | 90 ++--- NEWS.md | 23 + R/gsDesign.R | 4 R/gsMethods.R | 17 R/gsSurv.R | 2 build/vignette.rds |binary inst/doc/ConditionalErrorSpending.Rmd | 4 inst/doc/ConditionalErrorSpending.html | 427 +++++++++++++----------- inst/doc/ConditionalPowerPlot.Rmd | 4 inst/doc/ConditionalPowerPlot.html | 6 inst/doc/GentleIntroductionToGSD.Rmd | 6 inst/doc/GentleIntroductionToGSD.html | 8 inst/doc/PoissonMixtureModel.Rmd | 32 - inst/doc/PoissonMixtureModel.html | 170 +++++---- inst/doc/SpendingFunctionOverview.Rmd | 6 inst/doc/SpendingFunctionOverview.html | 12 inst/doc/SurvivalOverview.Rmd | 12 inst/doc/SurvivalOverview.html | 12 inst/doc/VaccineEfficacy.Rmd | 32 - inst/doc/VaccineEfficacy.html | 568 +++++++++++++++++---------------- inst/doc/binomialSPRTExample.Rmd | 12 inst/doc/binomialSPRTExample.html | 250 +++++++------- inst/doc/gsDesignPackageOverview.Rmd | 6 inst/doc/gsDesignPackageOverview.html | 12 inst/doc/gsSurvBasicExamples.Rmd | 30 - inst/doc/gsSurvBasicExamples.html | 463 ++++++++++++++------------ inst/doc/nNormal.Rmd | 24 - inst/doc/nNormal.html | 44 +- inst/doc/toInteger.Rmd | 14 inst/doc/toInteger.html | 30 - man/gsDesign.Rd | 6 man/nSurv.Rd | 4 vignettes/ConditionalErrorSpending.Rmd | 4 vignettes/ConditionalPowerPlot.Rmd | 4 vignettes/GentleIntroductionToGSD.Rmd | 6 vignettes/PoissonMixtureModel.Rmd | 32 - vignettes/SpendingFunctionOverview.Rmd | 6 vignettes/SurvivalOverview.Rmd | 12 vignettes/VaccineEfficacy.Rmd | 32 - vignettes/binomialSPRTExample.Rmd | 12 vignettes/gsDesign.bib | 9 vignettes/gsDesignPackageOverview.Rmd | 6 vignettes/gsSurvBasicExamples.Rmd | 30 - vignettes/nNormal.Rmd | 24 - vignettes/toInteger.Rmd | 14 46 files changed, 1331 insertions(+), 1196 deletions(-)
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are:
flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>),
fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>),
rubber band based cartogram (Dougenik et al. (1985)
<doi:10.1111/j.0033-0124.1985.00075.x>).
Author: Pierre-Andre Cornillon [aut, cre],
Florent Demoraes [aut],
Flow-Based-Cartograms [cph]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between cartogramR versions 1.0-10 dated 2023-12-07 and 1.1-0 dated 2024-07-26
cartogramR-1.0-10/cartogramR/man/geom_cartogramR.Rd |only cartogramR-1.1-0/cartogramR/DESCRIPTION | 10 - cartogramR-1.1-0/cartogramR/MD5 | 54 ++++--- cartogramR-1.1-0/cartogramR/NAMESPACE | 1 cartogramR-1.1-0/cartogramR/R/as.sf.cartogramR.R | 12 - cartogramR-1.1-0/cartogramR/R/as.sfc.cartogramR.R | 2 cartogramR-1.1-0/cartogramR/R/cartogramR-deprecated.R |only cartogramR-1.1-0/cartogramR/R/cartogramR.R | 52 ++++--- cartogramR-1.1-0/cartogramR/R/cartogramR_options.R | 6 cartogramR-1.1-0/cartogramR/R/from_coord_polygon.R | 6 cartogramR-1.1-0/cartogramR/R/geom_cartogramR.R | 68 ---------- cartogramR-1.1-0/cartogramR/R/make_layer.R | 18 +- cartogramR-1.1-0/cartogramR/R/plot.cartogramR.R | 2 cartogramR-1.1-0/cartogramR/R/print.cartogramR.R | 8 - cartogramR-1.1-0/cartogramR/R/print.summary.cartogramR.R | 8 - cartogramR-1.1-0/cartogramR/R/residuals.cartogramR.R | 41 +++--- cartogramR-1.1-0/cartogramR/R/summary.cartogramR.R | 12 + cartogramR-1.1-0/cartogramR/R/to_coord_polygon.R | 6 cartogramR-1.1-0/cartogramR/R/warp_features.R |only cartogramR-1.1-0/cartogramR/man/cartogramR-deprecated.Rd |only cartogramR-1.1-0/cartogramR/man/cartogramR.Rd | 19 +- cartogramR-1.1-0/cartogramR/man/cartogramR_options.Rd | 35 +---- cartogramR-1.1-0/cartogramR/man/france_rivers.Rd | 2 cartogramR-1.1-0/cartogramR/man/geom_cartogramR-deprecated.Rd |only cartogramR-1.1-0/cartogramR/man/grid_analysis.Rd | 2 cartogramR-1.1-0/cartogramR/man/make_layer.Rd | 4 cartogramR-1.1-0/cartogramR/man/plot.dbv.cartogramR.Rd | 3 cartogramR-1.1-0/cartogramR/man/residuals.cartogramR.Rd | 10 - cartogramR-1.1-0/cartogramR/man/summary.cartogramR.Rd | 7 - cartogramR-1.1-0/cartogramR/man/summary.gridanalysis.cartogramR.Rd | 3 cartogramR-1.1-0/cartogramR/man/warp_features.Rd |only 31 files changed, 169 insertions(+), 222 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
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Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph parameter estimation,
model selection based on the Graph Information Criterion, statistical tests to discriminate two or more populations of graphs,
correlation between graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>, Fujita et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>, Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Grover E. Castro Guzman [aut],
Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 1.0.2 dated 2024-07-03 and 1.0.3 dated 2024-07-26
DESCRIPTION | 10 - MD5 | 70 ++++---- NAMESPACE | 3 R/GIC.R | 88 +++++----- R/anogva.R | 94 +++++------ R/graph.acf.R | 13 - R/graph.cem.R | 190 +++++++++++----------- R/graph.cor.test.R | 44 ++--- R/graph.dist.R | 97 +++++------ R/graph.entropy.R | 35 ++-- R/graph.hclust.R | 43 ++--- R/graph.kmeans.R | 154 +++++++++--------- R/graph.model.selection.R | 85 ++++------ R/graph.models.R | 265 +++++++++++++++---------------- R/graph.mult.scaling.R | 60 +++---- R/graph.param.estimator.R | 205 ++++++++++++------------ R/graph.spectral.density.R | 355 +++++++++++++++++++++--------------------- R/graph.takahashi.test.R | 100 ++++++----- R/plot.statGraph.R |only R/print.statGraph.R | 84 +++++---- R/sp.anogva.R | 108 ++++++------ R/summary.statGraph.R |only R/utils.R | 210 ++++++++++++------------ man/GIC.Rd | 30 +-- man/anogva.Rd | 6 man/graph.cem.Rd | 12 - man/graph.cor.test.Rd | 6 man/graph.dist.Rd | 6 man/graph.entropy.Rd | 2 man/graph.hclust.Rd | 22 +- man/graph.kmeans.Rd | 12 - man/graph.model.selection.Rd | 16 - man/graph.mult.scaling.Rd | 10 - man/graph.param.estimator.Rd | 32 +-- man/graph.spectral.density.Rd | 8 man/graph.takahashi.test.Rd | 18 +- man/sp.anogva.Rd | 10 - 37 files changed, 1271 insertions(+), 1232 deletions(-)
Title: A Shiny App for Design of Experiments in Life Sciences
Description: A shiny design of experiments (DOE) app that aids in the creation of traditional,
un-replicated, augmented and partially-replicated designs applied to agriculture,
plant breeding, forestry, animal and biological sciences.
Author: Didier Murillo [cre, aut],
Salvador Gezan [aut],
Ana Heilman [ctb],
Thomas Walk [ctb],
Johan Aparicio [ctb],
Matthew Seefeldt [ctb],
Jean-Marc Montpetit [ctb],
Richard Horsley [ctb],
North Dakota State University [cph]
Maintainer: Didier Murillo <didier.murilloflorez@ndsu.edu>
Diff between FielDHub versions 1.4.0 dated 2024-07-09 and 1.4.2 dated 2024-07-26
FielDHub-1.4.0/FielDHub/inst/doc/optimized_arrangement.R |only FielDHub-1.4.0/FielDHub/inst/doc/optimized_arrangement.Rmd |only FielDHub-1.4.0/FielDHub/inst/doc/optimized_arrangement.html |only FielDHub-1.4.0/FielDHub/inst/doc/sparse_allocation.R |only FielDHub-1.4.0/FielDHub/inst/doc/sparse_allocation.Rmd |only FielDHub-1.4.0/FielDHub/inst/doc/sparse_allocation.html |only FielDHub-1.4.0/FielDHub/vignettes/optimized_arrangement.Rmd |only FielDHub-1.4.0/FielDHub/vignettes/sparse_allocation.Rmd |only FielDHub-1.4.2/FielDHub/DESCRIPTION | 6 FielDHub-1.4.2/FielDHub/MD5 | 53 +- FielDHub-1.4.2/FielDHub/R/app_ui.R | 4 FielDHub-1.4.2/FielDHub/R/fct_incomplete_blocks.R | 9 FielDHub-1.4.2/FielDHub/R/fct_row_column.R | 227 ++++++++---- FielDHub-1.4.2/FielDHub/R/globals.R | 5 FielDHub-1.4.2/FielDHub/R/mod_RowCol.R | 22 + FielDHub-1.4.2/FielDHub/R/utils_S3_methods.R | 28 - FielDHub-1.4.2/FielDHub/R/utils_plot_latinSQ.R | 2 FielDHub-1.4.2/FielDHub/R/utils_row_col_optimization.R |only FielDHub-1.4.2/FielDHub/build/vignette.rds |binary FielDHub-1.4.2/FielDHub/inst/WORDLIST | 6 FielDHub-1.4.2/FielDHub/inst/doc/RCBD_augmented.html | 6 FielDHub-1.4.2/FielDHub/inst/doc/alpha_lattice.html | 46 +- FielDHub-1.4.2/FielDHub/inst/doc/diagonal_arrangement.html | 9 FielDHub-1.4.2/FielDHub/inst/doc/full_factorial.html | 4 FielDHub-1.4.2/FielDHub/inst/doc/multi_location_prep.html | 73 +-- FielDHub-1.4.2/FielDHub/inst/doc/partially_replicated.html | 7 FielDHub-1.4.2/FielDHub/inst/doc/rcbd.html | 4 FielDHub-1.4.2/FielDHub/inst/doc/row_column.Rmd | 24 + FielDHub-1.4.2/FielDHub/inst/doc/row_column.html | 81 ++-- FielDHub-1.4.2/FielDHub/inst/doc/split_plot.html | 4 FielDHub-1.4.2/FielDHub/man/row_column.Rd | 76 ++-- FielDHub-1.4.2/FielDHub/vignettes/row_column.Rmd | 24 + 32 files changed, 469 insertions(+), 251 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include:
CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt).
FishPar(): Calculates length-based indicators (LBIs) proposed by Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> such as the percentage of mature fish (Pmat), percentage of optimal length fish (Popt), percentage of mega spawners (Pmega), and the sum of these as Pobj. This function also estimates confidence intervals for different lengths, visualizes length frequency distributions, a [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.4 dated 2024-07-09 and 0.1.5 dated 2024-07-26
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/FishPar.R | 3 ++- inst/doc/Introduction.html | 20 ++++++++++---------- 4 files changed, 20 insertions(+), 19 deletions(-)
More information about SampleSizeDiagnostics at CRAN
Permanent link
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.4-2 dated 2024-02-02 and 4.5 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 9 ++++++++- src/emf+.h | 33 +++++++++++++++++++++++++-------- 4 files changed, 40 insertions(+), 16 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.1.1 dated 2024-06-17 and 0.1.2 dated 2024-07-26
DESCRIPTION | 8 MD5 | 46 R/summariseTemporalSymmetry.R | 232 +- inst/doc/a02_Generate_a_sequence_cohort_set.R | 22 inst/doc/a02_Generate_a_sequence_cohort_set.Rmd | 23 inst/doc/a02_Generate_a_sequence_cohort_set.html | 104 - inst/doc/a03_Summarise_sequence_ratios.R | 22 inst/doc/a03_Summarise_sequence_ratios.Rmd | 263 +- inst/doc/a03_Summarise_sequence_ratios.html | 11 inst/doc/a04_Visualise_sequence_ratios.R | 22 inst/doc/a04_Visualise_sequence_ratios.Rmd | 23 inst/doc/a04_Visualise_sequence_ratios.html | 457 ++--- inst/doc/a05_Summarise_temporal_symmetry.R | 22 inst/doc/a05_Summarise_temporal_symmetry.Rmd | 23 inst/doc/a05_Summarise_temporal_symmetry.html | 31 inst/doc/a06_Visualise_temporal_symmetry.R | 22 inst/doc/a06_Visualise_temporal_symmetry.Rmd | 269 +-- inst/doc/a06_Visualise_temporal_symmetry.html | 9 tests/testthat/test-generateSequenceCohortSet.R | 2024 +++++++++++------------ vignettes/a02_Generate_a_sequence_cohort_set.Rmd | 23 vignettes/a03_Summarise_sequence_ratios.Rmd | 263 +- vignettes/a04_Visualise_sequence_ratios.Rmd | 23 vignettes/a05_Summarise_temporal_symmetry.Rmd | 23 vignettes/a06_Visualise_temporal_symmetry.Rmd | 269 +-- 24 files changed, 2235 insertions(+), 1999 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Streamline Population Genomic and Genetic Analyses
Description: Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.
Author: Keaka Farleigh [aut, cph, cre]
,
Mason Murphy [aut, cph, ctb] ,
Christopher Blair [aut, cph, ctb]
,
Tereza Jezkova [aut, cph, ctb]
Maintainer: Keaka Farleigh <keakafarleigh@gmail.com>
Diff between PopGenHelpR versions 1.3.0 dated 2024-05-09 and 1.3.1 dated 2024-07-26
PopGenHelpR-1.3.0/PopGenHelpR/R/Dif_stats.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Dif_stats_Map.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Div_Stats.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Div_Stats_Map.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Plot_ancestry.R |only PopGenHelpR-1.3.0/PopGenHelpR/man/Dif_Stats_Map.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Dif_stats.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Div_Stats_Map.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Div_stats.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Plot_ancestry.Rd |only PopGenHelpR-1.3.1/PopGenHelpR/DESCRIPTION | 11 PopGenHelpR-1.3.1/PopGenHelpR/MD5 | 28 -- PopGenHelpR-1.3.1/PopGenHelpR/NAMESPACE | 5 PopGenHelpR-1.3.1/PopGenHelpR/NEWS.md | 82 +++--- PopGenHelpR-1.3.1/PopGenHelpR/R/data.R | 241 ++++++++---------- PopGenHelpR-1.3.1/PopGenHelpR/man/Fst_dat.Rd | 6 PopGenHelpR-1.3.1/PopGenHelpR/man/Het_dat.Rd | 6 PopGenHelpR-1.3.1/PopGenHelpR/man/HornedLizard_Pop.Rd | 5 PopGenHelpR-1.3.1/PopGenHelpR/man/HornedLizard_VCF.Rd | 5 PopGenHelpR-1.3.1/PopGenHelpR/man/Q_dat.Rd | 5 20 files changed, 186 insertions(+), 208 deletions(-)
Title: Power in a Group Sequential Design
Description: Tools for the evaluation of interim analysis plans for sequentially
monitored trials on a survival endpoint; tools to construct efficacy and
futility boundaries, for deriving power of a sequential design at a specified
alternative, template for evaluating the performance of candidate plans at a
set of time varying alternatives. See Izmirlian, G. (2014) <doi:10.4310/SII.2014.v7.n1.a4>.
Author: Grant Izmirlian <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between PwrGSD versions 2.3.6 dated 2021-12-10 and 2.3.7 dated 2024-07-26
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/PwrGSD.R | 20 ++++++++++++-------- build/vignette.rds |binary inst/CITATION |only inst/doc/GrpSeqBnds-vignette.pdf |binary inst/doc/PwrGSD-vignette.pdf |binary inst/doc/cpd-PwrGSD-vignette.pdf |binary man/Ch0C-plot.cpd.PwrGSD.Rd | 2 +- man/Ch17-CRRtoRR.Rd | 6 +++--- src/SimPwrGSD.c | 2 -- 11 files changed, 29 insertions(+), 26 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny graphical user interface) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/>
and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical
Software, <doi:10.18637/ [...truncated...]
Author: Ross Ihaka [aut],
Paul Murrell [aut] ,
Kurt Hornik [aut] ,
Jason C. Fisher [aut] ,
Reto Stauffer [aut] ,
Claus O. Wilke [aut] ,
Claire D. McWhite [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 2.1-0 dated 2023-01-23 and 2.1-1 dated 2024-07-26
colorspace-2.1-0/colorspace/inst/hclwizard/html/python-example.html |only colorspace-2.1-1/colorspace/DESCRIPTION | 10 colorspace-2.1-1/colorspace/MD5 | 55 ++-- colorspace-2.1-1/colorspace/NAMESPACE | 1 colorspace-2.1-1/colorspace/NEWS.md | 31 ++ colorspace-2.1-1/colorspace/R/adjust_hcl.R | 10 colorspace-2.1-1/colorspace/R/adjust_transparency.R | 16 - colorspace-2.1-1/colorspace/R/cvd_image.R | 57 ++-- colorspace-2.1-1/colorspace/R/desaturate.R | 117 ++++++---- colorspace-2.1-1/colorspace/R/divergingx_hcl.R | 2 colorspace-2.1-1/colorspace/R/hcl_palettes.R | 4 colorspace-2.1-1/colorspace/R/hclplot.R | 66 +++-- colorspace-2.1-1/colorspace/R/lighten.R | 7 colorspace-2.1-1/colorspace/R/simulate_cvd.R | 13 - colorspace-2.1-1/colorspace/build/partial.rdb |binary colorspace-2.1-1/colorspace/build/vignette.rds |binary colorspace-2.1-1/colorspace/inst/CITATION | 80 +++--- colorspace-2.1-1/colorspace/inst/doc/colorspace.Rmd | 5 colorspace-2.1-1/colorspace/inst/doc/colorspace.html | 34 +- colorspace-2.1-1/colorspace/inst/doc/hcl-colors.pdf |binary colorspace-2.1-1/colorspace/inst/hclcolorpicker/server.R | 8 colorspace-2.1-1/colorspace/inst/hclwizard/html/python.html | 18 - colorspace-2.1-1/colorspace/inst/hclwizard/server.R | 114 ++++++++- colorspace-2.1-1/colorspace/inst/hclwizard/ui.R | 3 colorspace-2.1-1/colorspace/man/cvd_image.Rd | 11 colorspace-2.1-1/colorspace/man/desaturate.Rd | 19 - colorspace-2.1-1/colorspace/man/hcl_palettes.Rd | 2 colorspace-2.1-1/colorspace/vignettes/color.bib | 4 colorspace-2.1-1/colorspace/vignettes/colorspace.Rmd | 5 29 files changed, 433 insertions(+), 259 deletions(-)
Title: A Configurable 'shiny' Portal for Sharing Analysis of Molecular
Expression Data
Description: Enables deploying configuration file-based 'shiny' apps with minimal programming for interactive exploration and analysis showcase of molecular expression data. For exploration, supports visualization of correlations between rows of an expression matrix and a table of observations, such as clinical measures, and comparison of changes in expression over time. For showcase, enables visualizing the results of differential expression from package such as 'limma', co-expression modules from 'WGCNA' and lower dimensional projections.
Author: Rafael Henkin [cre, aut, cph]
Maintainer: Rafael Henkin <r.henkin@qmul.ac.uk>
Diff between shinyExprPortal versions 1.1.0 dated 2024-02-06 and 1.2.0 dated 2024-07-26
DESCRIPTION | 8 - MD5 | 42 +++++----- NEWS.md | 6 + R/app_config.R | 2 R/app_server.R | 2 R/create_example.R | 4 R/create_mod_template.R | 6 - R/mod_compareTrajGroups.R | 6 - R/mod_geneModulesHeatmap.R | 23 +++-- R/mod_geneModulesHeatmap_utils.R | 3 R/mod_geneProjectionOverlay.R | 3 R/mod_multiMeasureCorr.R | 6 - R/mod_singleGeneCorr.R | 9 +- R/mod_singleMeasureCorr.R | 3 build/vignette.rds |binary inst/doc/config.html | 80 +++++++++---------- inst/doc/customization.html | 4 inst/doc/dataprep.html | 142 +++++++++++++++++----------------- inst/doc/shinyExprPortal.Rmd | 6 - inst/doc/shinyExprPortal.html | 159 +++++++++++++++++++-------------------- man/create_module_template.Rd | 5 - vignettes/shinyExprPortal.Rmd | 6 - 22 files changed, 279 insertions(+), 246 deletions(-)
More information about shinyExprPortal at CRAN
Permanent link
Title: Analysis of Chronological Patterns from Archaeological Count
Data
Description: A toolkit for absolute and relative dating and analysis of
chronological patterns. This package includes functions for
chronological modeling and dating of archaeological assemblages from
count data. It provides methods for matrix seriation. It also allows
to compute time point estimates and density estimates of the
occupation and duration of an archaeological site.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kairos versions 2.1.0 dated 2024-02-26 and 2.1.1 dated 2024-07-26
DESCRIPTION | 20 ++++++------- MD5 | 56 +++++++++++++++++++------------------- NEWS.md | 4 ++ R/AllClasses.R | 2 - R/AllGenerics.R | 55 +++++++++++++++++++++---------------- R/kairos-package.R | 4 +- R/mcd.R | 21 ++++++++++++-- README.md | 36 ++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/event.html | 14 ++++----- inst/doc/seriation.html | 6 ---- man/AoristicSum-class.Rd | 2 - man/aoristic.Rd | 4 +- man/data.frame.Rd | 4 +- man/event.Rd | 4 +- man/figures/README-aoristic-2.png |binary man/fit.Rd | 4 +- man/kairos-package.Rd | 4 +- man/mcd.Rd | 4 +- man/model.Rd | 5 ++- man/plot_aoristic.Rd | 6 ++-- man/plot_event.Rd | 4 +- man/plot_fit.Rd | 4 +- man/plot_mcd.Rd | 4 +- man/plot_time.Rd | 4 +- man/predict_event.Rd | 5 ++- man/resample_mcd.Rd | 4 +- man/series.Rd | 5 ++- 29 files changed, 152 insertions(+), 133 deletions(-)
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<https://pyyaml.org/wiki/LibYAML>) for R.
Author: Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb],
Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb],
Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb],
Michael Quinn [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between yaml versions 2.3.9 dated 2024-07-05 and 2.3.10 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/verbatim_logical.Rd | 12 ++++++------ src/dumper.c | 1 + src/implicit.c | 1 + 5 files changed, 16 insertions(+), 14 deletions(-)
Title: R-Language Based Calculus Operations for Teaching
Description: Software to support the introductory *MOSAIC Calculus*
textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>),
one of many data- and modeling-oriented educational resources developed by
Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and
numerical differentiation and integration, as well as support for
applied linear algebra (for data science), and differential equations/dynamics.
Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc.
The software is suitable for general use, but intended mainly for teaching calculus.
Author: Daniel T. Kaplan <kaplan@macalester.edu>, Randall Pruim <rpruim@calvin.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Daniel Kaplan <kaplan@macalester.edu>
Diff between mosaicCalc versions 0.6.1 dated 2024-03-16 and 0.6.4 dated 2024-07-26
DESCRIPTION | 21 +++++++++++---------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 5 +---- NEWS.md | 11 +++++++++++ R/Calculus.R | 4 ++-- R/Integrate.R | 13 ++++++++++--- R/Zeros.R | 2 +- R/argM.R | 2 +- R/interactive_plot.R | 4 +++- R/makeODE.R | 10 +++++++--- R/numD.R | 2 +- R/symbolicD.R | 2 +- R/traj_plot_3D.R | 4 ++++ inst/doc/Calculus_with_R.html | 8 ++++---- inst/doc/Instructors.html | 13 +++++++------ inst/doc/quick-reference.html | 4 ++-- man/makeODE.Rd | 4 +++- man/symbolicD.Rd | 2 +- 18 files changed, 87 insertions(+), 58 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-17 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-18 1.1.31
2024-01-23 1.1.30
2023-09-05 1.1.29
2022-12-09 1.1.28
2022-02-23 1.1.27
2021-03-09 1.1.26
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-21 1.0.13
2021-03-09 1.0.12
Title: Regression Models with Break-Points / Change-Points Estimation
(with Possibly Random Effects)
Description: Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects. Multiple breakpoints for the same variable are allowed.
The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Estimation of piecewise-constant relationships and changepoints (mean-shift models) is
discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 2.1-0 dated 2024-05-14 and 2.1-1 dated 2024-07-26
DESCRIPTION | 13 +++++------ MD5 | 50 ++++++++++++++++++++++----------------------- NEWS | 6 +++++ R/intercept.r | 10 +++++---- R/plot.segmented.lme.r | 16 ++++++++++---- R/seg.Ar.fit.boot.r | 7 ++++-- R/seg.def.fit.boot.r | 5 +++- R/seg.glm.fit.boot.r | 7 +++++- R/seg.lm.fit.boot.r | 7 +++++- R/seg.num.fit.boot.r | 7 +++--- R/segConstr.glm.fit.boot.r | 8 ++++--- R/segConstr.lm.fit.boot.r | 8 ++++--- R/segmented.lme.r | 2 + R/segreg.r | 18 ++++++++++++++++ R/selgmented.R | 1 R/slope.R | 2 + R/step.glm.fit.boot.r | 25 ++++++++++++++++++---- R/step.lm.fit.boot.r | 7 +++++- R/step.num.fit.boot.r | 6 ++++- R/step.ts.fit.boot.r | 8 +++++-- R/stepreg.r | 14 ++++++++++++ man/seg.control.Rd | 4 +-- man/segmented-package.Rd | 4 +-- man/segmented.Rd | 10 ++++----- man/segreg.Rd | 4 +-- man/selgmented.Rd | 2 - 26 files changed, 176 insertions(+), 75 deletions(-)
Title: Bayesian Deming Regression for Method Comparison
Description: Regression methods to quantify the relation
between two measurement methods are provided by this package. The
focus is on a Bayesian Deming regressions family. With a Bayesian
method the Deming regression can be run in a traditional fashion or
can be run in a robust way just decreasing the degree of freedom
d.f. of the sampling distribution. With d.f. = 1 an extremely robust
Cauchy distribution can be sampled. Moreover, models for dealing
with heteroscedastic data are also provided. For reference see
G. Pioda (2024) <https://piodag.github.io/bd1/>.
Author: Giorgio Pioda [aut, cre]
Maintainer: Giorgio Pioda <gfwp@ticino.com>
Diff between rstanbdp versions 0.0.2 dated 2024-02-23 and 0.0.3 dated 2024-07-26
DESCRIPTION | 6 MD5 | 43 +++--- NAMESPACE | 1 NEWS.md | 15 ++ R/bdpCalcResponse.R | 18 +- R/bdpExtract.R | 9 + R/bdpPlot.R | 26 ++- R/bdpPlotResiduals.R | 23 ++- R/bdpSummary.R |only R/bdpreg.R | 18 +- R/plotBoxEllipses.R | 31 ++-- R/stanmodels.R | 3 inst/stan/bdpreg_exphettrunc.stan |only inst/stan/bdpreg_linhet.stan | 5 inst/stan/bdpreg_linhettrunc.stan | 5 man/bdpPlot.Rd | 4 man/bdpPlotBE.Rd | 4 man/bdpPlotResiduals.Rd | 8 - man/bdpSummary.Rd |only man/bdpreg.Rd | 5 src/RcppExports.cpp | 2 src/stanExports_bdpreg_exphettrunc.cc |only src/stanExports_bdpreg_exphettrunc.h |only src/stanExports_bdpreg_linhet.h | 219 ++++++++++++++++-------------- src/stanExports_bdpreg_linhettrunc.h | 243 ++++++++++++++++++---------------- 25 files changed, 397 insertions(+), 291 deletions(-)
Title: Multivariate Statistical Methods
Description: Algorithms to build set partitions and commutator matrices and their use in the
construction of multivariate d-Hermite polynomials; estimation and derivation of theoretical vector moments and vector
cumulants of multivariate distributions; conversion formulae for multivariate moments and cumulants. Applications to
estimation and derivation of multivariate measures of skewness and kurtosis; estimation and derivation of asymptotic
covariances for d-variate Hermite polynomials, multivariate moments and cumulants and measures of skewness and kurtosis.
The formulae implemented are discussed in Terdik (2021, ISBN:9783030813925), "Multivariate Statistical Methods".
Author: Gyorgy Terdik [aut],
Emanuele Taufer [aut, cre]
Maintainer: Emanuele Taufer <emanuele.taufer@unitn.it>
Diff between MultiStatM versions 1.2.1 dated 2024-01-31 and 2.0.0 dated 2024-07-26
MultiStatM-1.2.1/MultiStatM/man/Esti_EVSK.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Gram_Charlier.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Hermite_Poly_HN_Multi.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_MRSz.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_Mardia.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_Total.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_Variance_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_MMom_MCum.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Skew_MRSz.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Skew_Mardia.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Skew_Variance_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Variance_Skew_Kurt.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Coeff.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_CoeffMulti.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_N_Cov_X1_X2.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Nth.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_HN.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_HN_Multi.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_NH_Inv.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_NH_Multi_Inv.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_2Perm.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_DiagramsClosedNoLoops.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_Indecomposable.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_Pairs.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_Type_All.Rd |only MultiStatM-1.2.1/MultiStatM/man/Permutation_Inverse.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Cum2Mom.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Cum2MomMulti.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Mom2Cum.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Mom2CumMulti.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Stand_Multi.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_CFUSN_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_CFUSN_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_CFUSSD_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_SkewNorm_EVSK_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_SkewNorm_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_SkewNorm_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_UniAbs_EVSK_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Uni_EVSK_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Uni_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Uni_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_ZabsM_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Zabs_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Kmn.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Kperm.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Mixing.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Moment.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Elimination.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Qplication.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Symmetry.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_UnivMomCum.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Kmn.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Kperm.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Mixing.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Moment.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Elimination.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Qplication.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Symmetry.Rd |only MultiStatM-2.0.0/MultiStatM/DESCRIPTION | 8 MultiStatM-2.0.0/MultiStatM/MD5 | 123 - MultiStatM-2.0.0/MultiStatM/NEWS.md | 20 MultiStatM-2.0.0/MultiStatM/R/CallFcts.R |only MultiStatM-2.0.0/MultiStatM/R/Commutators.R | 354 --- MultiStatM-2.0.0/MultiStatM/R/Distributions.R | 221 - MultiStatM-2.0.0/MultiStatM/R/Estimation.r | 272 -- MultiStatM-2.0.0/MultiStatM/R/Hermite.r | 154 - MultiStatM-2.0.0/MultiStatM/R/MomCums.r | 120 - MultiStatM-2.0.0/MultiStatM/R/Partitions.r | 96 MultiStatM-2.0.0/MultiStatM/R/SupportFun.r | 78 MultiStatM-2.0.0/MultiStatM/inst/doc/Overview.R | 73 MultiStatM-2.0.0/MultiStatM/inst/doc/Overview.Rmd | 567 ++--- MultiStatM-2.0.0/MultiStatM/inst/doc/Overview.html | 1111 +++++----- MultiStatM-2.0.0/MultiStatM/man/CommutatorIndx.Rd |only MultiStatM-2.0.0/MultiStatM/man/CommutatorMatr.Rd |only MultiStatM-2.0.0/MultiStatM/man/Cum2Mom.Rd |only MultiStatM-2.0.0/MultiStatM/man/EVSKSkewNorm.Rd |only MultiStatM-2.0.0/MultiStatM/man/EVSKUniS.Rd |only MultiStatM-2.0.0/MultiStatM/man/EliminIndx.Rd |only MultiStatM-2.0.0/MultiStatM/man/EliminMatr.Rd |only MultiStatM-2.0.0/MultiStatM/man/HermiteCoeff.Rd |only MultiStatM-2.0.0/MultiStatM/man/HermiteCov12.Rd |only MultiStatM-2.0.0/MultiStatM/man/HermiteN.Rd |only MultiStatM-2.0.0/MultiStatM/man/HermiteN2X.Rd |only MultiStatM-2.0.0/MultiStatM/man/MVStandardize.Rd |only MultiStatM-2.0.0/MultiStatM/man/Mom2Cum.Rd |only MultiStatM-2.0.0/MultiStatM/man/MomCumCFUSN.Rd |only MultiStatM-2.0.0/MultiStatM/man/MomCumSkewNorm.Rd |only MultiStatM-2.0.0/MultiStatM/man/MomCumUniS.Rd |only MultiStatM-2.0.0/MultiStatM/man/MomCumZabs.Rd |only MultiStatM-2.0.0/MultiStatM/man/PartitionTypeAll.Rd |only MultiStatM-2.0.0/MultiStatM/man/Partitions.Rd |only MultiStatM-2.0.0/MultiStatM/man/PermutationInv.Rd |only MultiStatM-2.0.0/MultiStatM/man/QplicIndx.Rd |only MultiStatM-2.0.0/MultiStatM/man/QplicMatr.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleEVSK.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleGC.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleHermiteN.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleKurt.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleMomCum.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleSkew.Rd |only MultiStatM-2.0.0/MultiStatM/man/SampleVarianceSkewKurt.Rd |only MultiStatM-2.0.0/MultiStatM/man/SymIndx.Rd |only MultiStatM-2.0.0/MultiStatM/man/SymMatr.Rd |only MultiStatM-2.0.0/MultiStatM/man/UnivMomCum.Rd |only MultiStatM-2.0.0/MultiStatM/man/VarianceKurt.Rd |only MultiStatM-2.0.0/MultiStatM/man/VarianceSkew.Rd |only MultiStatM-2.0.0/MultiStatM/man/rCFUSN.Rd |only MultiStatM-2.0.0/MultiStatM/man/rCFUSSD.Rd |only MultiStatM-2.0.0/MultiStatM/man/rSkewNorm.Rd |only MultiStatM-2.0.0/MultiStatM/man/rUniS.Rd |only MultiStatM-2.0.0/MultiStatM/vignettes/Overview.Rmd | 567 ++--- 111 files changed, 1595 insertions(+), 2169 deletions(-)
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions. Methodology described in Murphy (2019)
<doi:10.1016/j.envsoft.2019.03.027>.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 2.0.11 dated 2024-02-23 and 2.0.12 dated 2024-07-26
DESCRIPTION | 8 MD5 | 18 NEWS | 27 NEWS.md | 27 R/gamTestSeason.r | 14 R/imputeCensored.R | 10 build/vignette.rds |binary inst/doc/Detrending_Flow_and_Salinity_Data.html | 14 inst/doc/Processing_Censored_Data.html | 8 inst/extdata/baytrends_install.nb.html | 6276 ++++++++++++------------ 10 files changed, 3226 insertions(+), 3176 deletions(-)
Title: Archaeological Time Series
Description: A toolkit for archaeological time series. This package
provides a system of classes and methods to represent and work with
archaeological time series. Dates are represented as "rata die" and
can be converted to (virtually) any calendar defined by Reingold and
Dershowitz (2018) <doi:10.1017/9781107415058>. This packages offers a
simple API that can be used by other specialized packages.
Author: Nicolas Frerebeau [aut, cre] ,
Joe Roe [aut] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between aion versions 1.0.2 dated 2023-10-26 and 1.0.4 dated 2024-07-26
DESCRIPTION | 22 MD5 | 74 +- NEWS.md | 6 R/AllGenerics.R | 2 R/aion-internal.R | 10 R/aion-package.R | 2 README.md | 71 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 19 inst/doc/aion.R | 30 - inst/doc/aion.Rmd | 44 + inst/doc/aion.html | 879 ++++++++++++----------------------- inst/doc/bibliography.Rmd | 10 inst/doc/bibliography.html | 341 ++----------- inst/doc/extending.R | 2 inst/doc/extending.Rmd | 14 inst/doc/extending.html | 751 +++++++++-------------------- man/aion-package.Rd | 3 man/arithmetic.Rd | 2 man/as_date.Rd | 2 man/as_decimal.Rd | 2 man/as_fixed.Rd | 2 man/as_year.Rd | 2 man/convert.Rd | 2 man/figures/README-time-series-1.png |binary man/fixed_gregorian.Rd | 2 man/fixed_julian.Rd | 2 man/format.Rd | 2 man/gregorian.Rd | 2 man/is.Rd | 2 man/julian.Rd | 2 man/plot.Rd | 2 man/pretty.Rd | 2 man/subset.Rd | 6 vignettes/aion.Rmd | 44 + vignettes/bibliography.Rmd | 10 vignettes/extending.Rmd | 14 38 files changed, 872 insertions(+), 1510 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-22 1.2.3
2024-05-17 1.2.1
2024-04-15 1.1.5
2024-02-06 1.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-09 1.1.0
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.11.0.1 dated 2024-02-14 and 1.12.0 dated 2024-07-26
DESCRIPTION | 13 MD5 | 89 - NAMESPACE | 1 R/corColumnOrder.R | 23 R/extractTestingResults.R | 8 R/getUPS1acc.R | 8 R/matrixNAneighbourImpute.R | 2 R/readAlphaPeptFile.R | 62 R/readDiaNNFile.R | 51 R/readDiaNNPeptides.R | 48 R/readFasta2.R | 51 R/readFragpipeFile.R | 55 R/readIonbotPeptides.R |only R/readMassChroQFile.R | 54 R/readMaxQuantFile.R | 66 R/readMaxQuantPeptides.R | 120 + R/readProlineFile.R | 83 - R/readProteomeDiscovererFile.R | 417 +++-- R/readProteomeDiscovererPeptides.R | 95 - R/readSampleMetaData.R | 460 +++-- R/readSdrf.R | 51 R/readWombatNormFile.R | 50 R/shortSoftwName.R | 4 build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 6 inst/doc/wrProteoVignette1.Rmd | 24 inst/doc/wrProteoVignette1.html | 1546 +++++++----------- inst/doc/wrProteoVignetteUPS1.R | 68 inst/doc/wrProteoVignetteUPS1.Rmd | 151 + inst/doc/wrProteoVignetteUPS1.html | 2939 +++++++++++++++--------------------- inst/extdata/tinyIonbotFile1.tsv.gz |only man/corColumnOrder.Rd | 19 man/extractTestingResults.Rd | 8 man/getUPS1acc.Rd | 8 man/readAlphaPeptFile.Rd | 10 man/readFasta2.Rd | 20 man/readFragpipeFile.Rd | 6 man/readIonbotPeptides.Rd |only man/readMassChroQFile.Rd | 6 man/readMaxQuantFile.Rd | 6 man/readMaxQuantPeptides.Rd | 14 man/readProlineFile.Rd | 8 man/readProteomeDiscovererFile.Rd | 6 man/readSampleMetaData.Rd | 22 man/readSdrf.Rd | 4 vignettes/wrProteoVignette1.Rmd | 24 vignettes/wrProteoVignetteUPS1.Rmd | 151 + 47 files changed, 3537 insertions(+), 3320 deletions(-)
Title: Accesses Weather Data from the Iowa Environment Mesonet
Description: Allows to get weather data from Automated Surface Observing
System (ASOS) stations (airports) in the whole world thanks to the
Iowa Environment Mesonet website.
Author: Maelle Salmon [aut, cre] ,
Brooke Anderson [rev] ,
CHAI Project [fnd] ,
rOpenSci [fnd] ,
Daryl Herzmann [ctb]
Maintainer: Maelle Salmon <maelle.salmon@yahoo.se>
Diff between riem versions 0.3.1 dated 2024-04-04 and 0.3.2 dated 2024-07-26
riem-0.3.1/riem/tests/testthat/fixtures/networks-error |only riem-0.3.2/riem/DESCRIPTION | 8 riem-0.3.2/riem/MD5 | 18 riem-0.3.2/riem/NEWS.md | 4 riem-0.3.2/riem/tests/testthat/fixtures/networks/mesonet.agron.iastate.edu/api/1/networks.json.json | 2716 ++++++---- riem-0.3.2/riem/tests/testthat/fixtures/stations/mesonet.agron.iastate.edu/api/1/network/IN__ASOS.json.json | 1905 +++++-- riem-0.3.2/riem/tests/testthat/fixtures/stations/mesonet.agron.iastate.edu/api/1/networks.json.json | 2716 ++++++---- riem-0.3.2/riem/tests/testthat/fixtures/warnings |only riem-0.3.2/riem/tests/testthat/helper-riem.R | 6 riem-0.3.2/riem/tests/testthat/setup.R | 1 riem-0.3.2/riem/tests/testthat/test-measures.R | 2 11 files changed, 4914 insertions(+), 2462 deletions(-)
Title: National Library of Norway Quantitative Text Data API Tools
Description: Tools for accessing data from National Library of Norway's dhlab (digital humanities laboratory).
Provides wrappers for accessing our API services at <https://api.nb.no/dhlab/>.
To learn more about dhlab, visit out site <https://www.nb.no/dh-lab/>.
Author: Ingerid Dale [aut, cre],
Lars Johnsen [aut, cph],
Lars Tungland [aut],
Andre Kasen [aut]
Maintainer: Ingerid Dale <ingerid.dale@nb.no>
Diff between dhlabR versions 1.0.2 dated 2023-06-09 and 1.0.6 dated 2024-07-26
DESCRIPTION | 22 +++++++++++++--------- MD5 | 32 +++++++++++++++++--------------- NEWS.md | 9 +++++++++ R/api_tools.R |only R/get_collocations.R | 7 ++++++- R/get_concordance.R | 9 +++++++-- R/get_dispersion.R | 8 +++++++- R/get_document_corpus.R | 8 +++++++- R/get_document_frequencies.R | 7 ++++++- R/get_metadata.R | 7 ++++++- R/get_ngram_from_book.R | 9 +++++++-- R/get_ngram_from_newspapers.R | 9 +++++++-- R/get_reference_words.R | 7 ++++++- R/get_urn_frequencies.R | 7 ++++++- R/ngram.R | 3 ++- man/get_concordance.Rd | 2 +- tests/testthat/test-api_tools.R |only tests/testthat/test-ngram.R | 2 +- 18 files changed, 108 insertions(+), 40 deletions(-)
Title: Pre-Processing XY Data from Experimental Methods
Description: A lightweight, dependency-free toolbox for pre-processing XY
data from experimental methods (i.e. any signal that can be measured
along a continuous variable). This package provides methods for
baseline estimation and correction, smoothing, normalization,
integration and peaks detection. Baseline correction methods includes
polynomial fitting as described in Lieber and Mahadevan-Jansen (2003)
<doi:10.1366/000370203322554518>, Rolling Ball algorithm after Kneen
and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>, SNIP algorithm
after Ryan et al. (1988) <doi:10.1016/0168-583X(88)90063-8>, 4S Peak
Filling after Liland (2015) <doi:10.1016/j.mex.2015.02.009> and more.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between alkahest versions 1.1.1 dated 2023-06-13 and 1.2.0 dated 2024-07-26
alkahest-1.1.1/alkahest/inst/doc/bibliography.R |only alkahest-1.1.1/alkahest/inst/doc/bibliography.Rmd |only alkahest-1.1.1/alkahest/inst/doc/bibliography.html |only alkahest-1.1.1/alkahest/vignettes/bibliography.Rmd |only alkahest-1.2.0/alkahest/DESCRIPTION | 19 - alkahest-1.2.0/alkahest/MD5 | 99 +++--- alkahest-1.2.0/alkahest/NAMESPACE | 2 alkahest-1.2.0/alkahest/NEWS.md | 6 alkahest-1.2.0/alkahest/R/AllGenerics.R | 65 ++++ alkahest-1.2.0/alkahest/R/alkahest-internal.R | 30 +- alkahest-1.2.0/alkahest/R/alkahest-package.R | 2 alkahest-1.2.0/alkahest/R/baseline.R | 67 ++++ alkahest-1.2.0/alkahest/R/data.R | 14 alkahest-1.2.0/alkahest/R/integrate.R | 4 alkahest-1.2.0/alkahest/R/peaks.R | 3 alkahest-1.2.0/alkahest/R/replace.R | 4 alkahest-1.2.0/alkahest/R/resample.R | 5 alkahest-1.2.0/alkahest/R/rescale.R | 40 ++ alkahest-1.2.0/alkahest/R/signal.R | 21 + alkahest-1.2.0/alkahest/R/smooth.R | 18 - alkahest-1.2.0/alkahest/R/xrd.R | 9 alkahest-1.2.0/alkahest/README.md | 149 ++++++++-- alkahest-1.2.0/alkahest/build/partial.rdb |binary alkahest-1.2.0/alkahest/build/vignette.rds |binary alkahest-1.2.0/alkahest/data/Raman.rda |only alkahest-1.2.0/alkahest/inst/CITATION | 2 alkahest-1.2.0/alkahest/inst/doc/baseline.R |only alkahest-1.2.0/alkahest/inst/doc/baseline.Rmd |only alkahest-1.2.0/alkahest/inst/doc/baseline.html |only alkahest-1.2.0/alkahest/inst/doc/smoothing.R |only alkahest-1.2.0/alkahest/inst/doc/smoothing.Rmd |only alkahest-1.2.0/alkahest/inst/doc/smoothing.html |only alkahest-1.2.0/alkahest/inst/examples/ex-baseline-asls.R |only alkahest-1.2.0/alkahest/inst/examples/ex-normalize.R |only alkahest-1.2.0/alkahest/inst/tinytest/_snaps/baseline_asls.rds |only alkahest-1.2.0/alkahest/inst/tinytest/test_baseline.R | 8 alkahest-1.2.0/alkahest/inst/tinytest/test_helpers.R | 4 alkahest-1.2.0/alkahest/inst/tinytest/test_rescale.R | 6 alkahest-1.2.0/alkahest/man/BEGe.Rd | 1 alkahest-1.2.0/alkahest/man/LaBr.Rd | 1 alkahest-1.2.0/alkahest/man/Raman.Rd |only alkahest-1.2.0/alkahest/man/XRD.Rd | 3 alkahest-1.2.0/alkahest/man/alkahest-package.Rd | 3 alkahest-1.2.0/alkahest/man/baseline_asls.Rd |only alkahest-1.2.0/alkahest/man/baseline_linear.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_peakfilling.Rd | 6 alkahest-1.2.0/alkahest/man/baseline_polynomial.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_rollingball.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_rubberband.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_snip.Rd | 1 alkahest-1.2.0/alkahest/man/replace_threshold.Rd | 4 alkahest-1.2.0/alkahest/man/rescale_area.Rd | 1 alkahest-1.2.0/alkahest/man/rescale_range.Rd | 1 alkahest-1.2.0/alkahest/man/rescale_snv.Rd |only alkahest-1.2.0/alkahest/man/rescale_total.Rd | 1 alkahest-1.2.0/alkahest/man/rescale_transform.Rd | 1 alkahest-1.2.0/alkahest/man/signal_correct.Rd | 21 + alkahest-1.2.0/alkahest/vignettes/baseline.Rmd |only alkahest-1.2.0/alkahest/vignettes/bibliography.bib | 38 ++ alkahest-1.2.0/alkahest/vignettes/smoothing.Rmd |only 60 files changed, 542 insertions(+), 121 deletions(-)
Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] ,
Kaio Dias [aut, cph] ,
Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>
Diff between ProbBreed versions 1.0.4.0 dated 2024-07-17 and 1.0.4.1 dated 2024-07-26
DESCRIPTION | 19 MD5 | 98 + NAMESPACE | 6 NEWS.md | 17 R/ProbBreed-package.R | 31 R/bayes_met.R | 2273 ------------------------------ R/extr_outs.R | 14 R/prob_sup.R | 6 R/stanmodels.R |only README.md | 513 +++--- build/partial.rdb |binary configure |only configure.win |only inst/include |only inst/stan |only man/ProbBreed-package.Rd | 20 man/bayes_met.Rd | 4 man/extr_outs.Rd | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/plot.extr.Rd | 12 man/plot.probsup.Rd | 4 man/prob_sup.Rd | 2 src |only 27 files changed, 472 insertions(+), 2549 deletions(-)
Title: ICESat-2 Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begu [...truncated...]
Author: Lampros Mouselimis [aut, cre] ,
OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between IceSat2R versions 1.0.4 dated 2022-11-17 and 1.0.5 dated 2024-07-26
DESCRIPTION | 14 MD5 | 59 +-- NAMESPACE | 2 NEWS.md | 12 R/API_utils.R | 64 +++ R/IceSat2R.R | 2 R/get_Atlas_data.R | 289 ++++++++++++++++-- R/get_Tracks_data.R | 4 R/mission_orbits.R | 49 ++- README.md | 19 - build/vignette.rds |binary data/RGT_cycle_14.rda |binary data/datalist | 2 data/ne_10m_glaciated_areas.rda |binary inst/data_files/technical_specs_urls.csv | 9 inst/doc/IceSat-2_Atlas_products_PDF.R | 34 +- inst/doc/IceSat-2_Atlas_products_PDF.pdf |binary inst/doc/IceSat-2_Mission_Orbits_PDF.R | 10 inst/doc/IceSat-2_Mission_Orbits_PDF.pdf |binary inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.R | 29 + inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.Rmd | 27 + inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.pdf |binary man/IceSat2R.Rd | 2 man/download_file.Rd |only man/getTracks.Rd | 2 man/get_atlas_data.Rd | 218 +++++++++++++ man/get_level3a_data.Rd | 6 man/vsi_nominal_orbits_wkt.Rd | 4 tests/testthat/setup.R | 6 tests/testthat/test-get_Atlas_data.R | 2 vignettes/IceSat-2_Virtual_File_System_Orbits_PDF.Rmd | 27 + 31 files changed, 747 insertions(+), 145 deletions(-)
Title: Estimation of the Weights Attached to the Two-Way Fixed Effects
Regressions
Description: Estimates the weights and measure of robustness to treatment effect heterogeneity attached to two-way fixed effects regressions.
Clément de Chaisemartin, Xavier D'Haultfœuille (2020) <DOI: 10.1257/aer.20181169>.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Shuo Zhang [aut],
Clement de Chaisemartin [aut],
Grant McDermott [ctb]
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Diff between TwoWayFEWeights versions 2.0.3 dated 2024-04-25 and 2.0.4 dated 2024-07-26
DESCRIPTION | 15 +++++++++------ MD5 | 3 ++- NEWS.md |only 3 files changed, 11 insertions(+), 7 deletions(-)
More information about TwoWayFEWeights at CRAN
Permanent link
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between nser versions 1.5.2 dated 2024-05-02 and 1.5.3 dated 2024-07-26
DESCRIPTION | 12 ++++++------ MD5 | 27 ++++++++++++++++----------- NAMESPACE | 4 ++++ R/bhav.R | 37 +++++++++++++++++++++---------------- R/bhav1.R |only R/bhavpr.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/bhav.Rmd | 15 ++++++--------- inst/doc/bhav.html | 17 ++++++++--------- inst/doc/bhav1.Rmd |only inst/doc/bhav1.html |only man/bhav.Rd | 8 ++++---- man/bhav1.Rd |only man/bhavpr.Rd | 2 +- vignettes/bhav.Rmd | 15 ++++++--------- vignettes/bhav1.Rmd |only 17 files changed, 74 insertions(+), 67 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.0.2 dated 2024-07-07 and 5.0.4 dated 2024-07-26
ChangeLog | 5 ++--- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/ETSmodel.R | 1 - R/TETScomponents.R | 10 ++++++++-- R/TETSmodel.R | 4 +--- R/TETSvalidate.R | 15 +++++++++++---- 7 files changed, 32 insertions(+), 23 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.7.0 dated 2023-10-25 and 2.8.0 dated 2024-07-26
DESCRIPTION | 25 MD5 | 186 +- NAMESPACE | 381 ++--- NEWS.md | 445 +++-- R/Information.R | 10 R/Islands.R |only R/MSTSegments.R | 6 R/Plot3.R | 2 R/RcppExports.R | 32 R/Reduce.R |only R/TreeDist-package.R | 4 R/VisualizeMatching.R | 8 R/cluster_stats.R | 14 R/kmeanspp.R | 6 R/lap.R | 5 R/median.R | 8 R/parallel.R | 2 R/plot.R | 28 R/spectral_clustering.R | 6 R/tree_distance.R | 30 R/tree_distance_info.R | 728 +++++---- R/tree_distance_kendall-colijn.R | 64 R/tree_distance_mast.R | 16 R/tree_distance_msi.R | 2 R/tree_distance_nni.R | 6 R/tree_distance_nye.R | 428 ++--- R/tree_distance_path.R | 64 R/tree_distance_rf.R | 322 ++-- R/tree_distance_spr.R | 172 +- R/tree_distance_utilities.R | 84 - R/tree_information.R | 2 R/trustworthiness.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 54 inst/WORDLIST | 2 inst/doc/Generalized-RF.R | 26 inst/doc/Generalized-RF.Rmd | 11 inst/doc/Generalized-RF.html | 67 inst/doc/Robinson-Foulds.R | 43 inst/doc/Robinson-Foulds.Rmd | 27 inst/doc/Robinson-Foulds.html | 5 inst/doc/Using-TreeDist.R | 2 inst/doc/Using-TreeDist.html | 8 inst/doc/compare-treesets.html | 1081 ++++++++++++++ inst/doc/different-leaves.html | 2 inst/doc/information.html | 43 inst/doc/landscapes.html | 31 inst/doc/tree-islands.R |only inst/doc/tree-islands.Rmd |only inst/doc/tree-islands.html |only inst/doc/treespace.R | 29 inst/doc/treespace.Rmd | 41 inst/doc/treespace.html | 239 +-- inst/doc/using-distances.R | 12 inst/doc/using-distances.html | 7 inst/treespace/app.R | 18 man/CalculateTreeDistance.Rd | 3 man/Islands.Rd |only man/JaccardRobinsonFoulds.Rd | 3 man/KMeansPP.Rd | 110 - man/KendallColijn.Rd | 5 man/LAPJV.Rd | 4 man/MSTSegments.Rd | 1 man/MapTrees.Rd | 1 man/MappingQuality.Rd | 1 man/MatchingSplitDistance.Rd | 3 man/NormalizeInfo.Rd | 75 - man/NyeSimilarity.Rd | 3 man/PathDist.Rd | 13 man/ReduceTrees.Rd |only man/Robinson-Foulds.Rd | 27 man/SPRDist.Rd | 61 man/SpectralEigens.Rd | 1 man/StartParallel.Rd | 2 man/TreeDist-package.Rd | 4 man/TreeDistance.Rd | 40 man/cluster-statistics.Rd | 1 man/median.multiPhylo.Rd | 1 src/RcppExports.cpp | 105 + src/day_1985.cpp | 2 src/lap.cpp | 16 src/path_vector.cpp |only src/reduce_tree.cpp |only src/reduce_tree.h |only src/spr.cpp |only tests/benchmark/benchmark.R | 12 tests/testthat/test-Islands.R |only tests/testthat/test-MSTSegments.R | 2 tests/testthat/test-Reduce.R |only tests/testthat/test-different-tips.R | 3 tests/testthat/test-information.R | 21 tests/testthat/test-tree_distance.R | 1947 +++++++++++++------------- tests/testthat/test-tree_distance_kc.R | 13 tests/testthat/test-tree_distance_path.R | 40 tests/testthat/test-tree_distance_spr.R | 213 ++ tests/testthat/test-tree_distance_utilities.R | 4 vignettes/Generalized-RF.Rmd | 11 vignettes/Robinson-Foulds.Rmd | 27 vignettes/tree-islands.Rmd |only vignettes/treespace.Rmd | 41 101 files changed, 4838 insertions(+), 2814 deletions(-)
Title: Game of 'tetRys'
Description: A game inspired by 'Tetris'. Opens a plot window device and starts a game of 'tetRys' in it. Steer the tetrominos with the arrow keys, press Pause to pause and Esc to end the game.
Author: Carsten Croonenbroeck [aut, cre]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Diff between tetRys versions 1.0 dated 2024-07-21 and 1.1 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ R/tetRys.R | 21 ++++++++++++++------- 4 files changed, 28 insertions(+), 14 deletions(-)
Title: Client for 'AcademyOcean API'
Description: Provide function for work with 'AcademyOcean API'
<https://academyocean.com/api>.
Author: Alexey Seleznev [aut, cre] ,
Netpeak [cph],
AcademyOcean [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between racademyocean versions 0.3.2 dated 2023-02-09 and 0.3.3 dated 2024-07-26
DESCRIPTION | 6 +- MD5 | 6 +- NEWS.md | 8 +++ R/utils.R | 134 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 81 insertions(+), 73 deletions(-)
Title: Identifying Infection with Machine Intelligence
Description: A novel machine learning method for plant viruses diagnostic using
genome sequencing data. This package includes three different machine
learning models, random forest, XGBoost, and elastic net, to train and
predict mapped genome samples. Mappability profile and unreliable regions
are introduced to the algorithm, and users can build a mappability profile
from scratch with functions included in the package. Plotting mapped sample
coverage information is provided.
Author: Haochen Ning [aut],
Ian Boyes [aut],
Ibrahim Numanagic [aut] ,
Michael Rott [aut],
Li Xing [aut] ,
Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Diff between iimi versions 1.1.0 dated 2024-07-18 and 1.1.1 dated 2024-07-26
DESCRIPTION | 6 MD5 | 10 - inst/doc/package_vignette.R | 54 ++++--- inst/doc/package_vignette.Rmd | 155 ++++++++++++-------- inst/doc/package_vignette.html | 304 ++++++++++++++++++++++------------------- vignettes/package_vignette.Rmd | 155 ++++++++++++-------- 6 files changed, 394 insertions(+), 290 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.4.1 dated 2024-04-28 and 1.4.2 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/glmm.gei.R | 6 +++--- inst/doc/MAGEE.Rnw | 9 +++++++-- inst/doc/MAGEE.pdf |binary man/MAGEE-package.Rd | 4 ++-- man/glmm.gei.Rd | 9 ++++++--- vignettes/MAGEE.Rnw | 9 +++++++-- 8 files changed, 36 insertions(+), 23 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Michael Dumelle [aut, cre] ,
Jay M. Ver Hoef [aut],
Erin Peterson [aut],
Alan Pearse [ctb],
Dan Isaak [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between SSN2 versions 0.1.1 dated 2024-01-15 and 0.2.0 dated 2024-07-26
SSN2-0.1.1/SSN2/R/create_netgeometry.R |only SSN2-0.1.1/SSN2/R/names.SSN.R |only SSN2-0.1.1/SSN2/R/ssn_get_netgeometry.R |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/distance/Knapp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.shx |only SSN2-0.1.1/SSN2/man/names.SSN.Rd |only SSN2-0.2.0/SSN2/DESCRIPTION | 12 SSN2-0.2.0/SSN2/MD5 | 247 +- SSN2-0.2.0/SSN2/NAMESPACE | 8 SSN2-0.2.0/SSN2/NEWS.md | 68 SSN2-0.2.0/SSN2/R/SSN2.R | 44 SSN2-0.2.0/SSN2/R/SSN_to_SSN2.R | 269 +- SSN2-0.2.0/SSN2/R/Torgegram.R | 344 +-- SSN2-0.2.0/SSN2/R/amongSitesDistMat.R | 17 SSN2-0.2.0/SSN2/R/anova.R | 18 SSN2-0.2.0/SSN2/R/checks.R | 58 SSN2-0.2.0/SSN2/R/cov_betahat_adjust.R | 29 SSN2-0.2.0/SSN2/R/cov_initial_search.R | 359 +-- SSN2-0.2.0/SSN2/R/cov_initial_search_glm.R | 375 ++- SSN2-0.2.0/SSN2/R/cov_matrix.R | 619 +++--- SSN2-0.2.0/SSN2/R/cov_vector.R | 536 ++--- SSN2-0.2.0/SSN2/R/createBinaryID.R | 127 - 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Title: Discrete Global Grids
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut],
Kevin Sahr [aut, cph],
Gerald Evenden [cph],
Angus Johnson [cph],
Frank Warmerdam [cph],
Even Rouault [cph],
Lian Song [ctb],
Sebastian Krantz [ctb, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between dggridR versions 3.0.0 dated 2023-01-18 and 3.1.0 dated 2024-07-26
DESCRIPTION | 33 ++-- MD5 | 44 ++--- NAMESPACE | 22 +- NEWS | 14 + R/cwrapper.R | 140 +++++++++--------- R/dggridR.R | 152 ++++++++++++-------- R/zzz.R | 7 README.md | 4 build/vignette.rds |binary inst/doc/dggridR.R | 41 ++--- inst/doc/dggridR.Rmd | 19 +- inst/doc/dggridR.html | 375 +++++++++++++++++++++++++------------------------- man/dgcellstogrid.Rd | 4 man/dgearthgrid.Rd | 6 man/dgrectgrid.Rd | 7 man/dgshptogrid.Rd | 11 - src/DgBoundedRF.h | 8 - src/DgDmdIDGG.cpp | 3 src/DgHexIDGG.cpp | 4 src/DgParamList.h | 4 src/DgTriIDGG.cpp | 3 src/shputils.c | 4 vignettes/dggridR.Rmd | 19 +- 23 files changed, 490 insertions(+), 434 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-25 0.3.2
2023-03-22 0.3.1
2023-02-20 0.3
2022-09-08 0.2.2
2022-05-26 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-12 0.5.1
2022-12-08 0.4.3
2022-05-24 0.4.2
2018-08-06 0.4
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.1.4 dated 2024-01-28 and 0.1.5 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++++--- NAMESPACE | 1 + NEWS.md | 4 ++++ R/yulab-msg.R |only R/yulab-utils-package.R |only man/yulab.utils-package.Rd |only man/yulab_msg.Rd |only 8 files changed, 16 insertions(+), 7 deletions(-)
Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks.
'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>.
This package offers an R interface to work with it.
It is designed to be distributed and efficient with the following advantages:
1. Faster training speed and higher efficiency.
2. Lower memory usage.
3. Better accuracy.
4. Parallel learning supported.
5. Capable of handling large-scale data.
In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions.
Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple m [...truncated...]
Author: Yu Shi [aut],
Guolin Ke [aut],
Damien Soukhavong [aut],
James Lamb [aut, cre],
Qi Meng [aut],
Thomas Finley [aut],
Taifeng Wang [aut],
Wei Chen [aut],
Weidong Ma [aut],
Qiwei Ye [aut],
Tie-Yan Liu [aut],
Nikita Titov [aut],
Yachen Yan [ctb],
Microsof [...truncated...]
Maintainer: James Lamb <jaylamb20@gmail.com>
Diff between lightgbm versions 4.4.0 dated 2024-06-15 and 4.5.0 dated 2024-07-26
DESCRIPTION | 10 - MD5 | 52 ++++----- R/lgb.Booster.R | 40 ++++++ R/lgb.Dataset.R | 9 + README.md | 2 configure | 18 +-- configure.ac | 2 inst/doc/basic_walkthrough.html | 3 man/lgb.Dataset.Rd | 8 + src/boosting/gbdt.cpp | 18 +-- src/boosting/gbdt.h | 2 src/c_api.cpp | 12 -- src/include/LightGBM/arrow.h | 2 src/include/LightGBM/boosting.h | 2 src/include/LightGBM/config.h | 19 +-- src/include/LightGBM/utils/log.h | 7 + src/io/config.cpp | 21 +++ src/io/dataset_loader.cpp | 4 src/io/dense_bin.hpp | 2 src/io/file_io.cpp | 129 ---------------------- src/io/metadata.cpp | 2 src/io/multi_val_dense_bin.hpp | 2 src/io/multi_val_sparse_bin.hpp | 3 src/io/sparse_bin.hpp | 2 src/lightgbm_R.cpp | 219 +++++++++++++++++++++----------------- src/lightgbm_R.h | 28 ++++ tests/testthat/test_lgb.Booster.R | 168 +++++++++++++++++++++++++++++ 27 files changed, 473 insertions(+), 313 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.4.1 dated 2024-02-13 and 1.5.1 dated 2024-07-26
DESCRIPTION | 12 +-- MD5 | 117 +++++++++++++++++++++++++++----------- NAMESPACE | 6 + NEWS.md | 43 +++++++++++++ R/Aaaa.R | 4 - R/class_ev.R | 16 ++++- R/class_evd.R | 4 + R/class_mrgmod.R | 1 R/data_set.R | 60 ++++++++++++------- R/events.R | 27 +++++--- R/mrgindata.R | 89 ++++++++++++++++++---------- R/mrgsolve.R | 10 ++- R/mwrite.R |only R/print.R | 5 - R/utils.R | 3 inst/WORDLIST | 3 inst/base/modelheader.h | 4 + inst/base/mrgsolv.h | 4 - inst/base/mrgsolve-evtools.h | 15 ++++ inst/include/datarecord.h | 16 +++-- inst/include/odeproblem.h | 7 -- inst/maintenance |only man/as_data_set.Rd | 38 ++++++++---- man/mread_yaml.Rd |only man/mwrite_cpp.Rd |only man/mwrite_yaml.Rd |only man/omega.Rd | 2 man/sigma.Rd | 2 man/valid_data_set.Rd | 37 +++++++----- man/valid_idata_set.Rd | 23 +++++-- src/dataobject.cpp | 4 - src/datarecord.cpp | 41 +++++++++++-- src/devtran.cpp | 29 ++++----- src/mrgsolve.cpp | 4 - src/odeproblem.cpp | 8 ++ tests/testthat/test-as_data_set.R | 94 ++++++++++++++++++++++++++++++ tests/testthat/test-carry_out.R | 30 +++++++++ tests/testthat/test-data_set.R | 4 - tests/testthat/test-mrgindata.R | 24 +++---- tests/testthat/test-mwrite.R |only 40 files changed, 582 insertions(+), 204 deletions(-)