Title: Reconstruct Paleoclimate and Paleoecology with Leaf Physiognomy
Description: Use leaf physiognomic methods to reconstruct mean annual
temperature (MAT), mean annual precipitation (MAP), and leaf dry mass
per area (Ma), along with other useful quantitative leaf traits. Methods
in this package described in Lowe et al. (in review).
Author: Matthew J. Butrim [aut, cre, cph],
Alexander J. Lowe [aut],
Andrew G. Flynn [aut],
Aly Baumgartner [aut],
Daniel J. Peppe [aut],
Dana L. Royer [aut]
Maintainer: Matthew J. Butrim <mbutrim@uwyo.edu>
Diff between dilp versions 1.0.0 dated 2024-03-11 and 1.1.0 dated 2024-04-05
DESCRIPTION | 6 MD5 | 21 +- NAMESPACE | 1 NEWS.md | 11 - R/data.R | 345 ++++++++++++++++------------------ R/dilp_functions.R | 123 ++++++++---- R/lma_functions.R | 486 ++++++++++++++++++++++++------------------------ R/utils.R | 146 ++++++++------ README.md | 2 inst/doc/dilp.html | 49 ++-- man/dilp.Rd | 8 man/view_regressions.Rd |only 12 files changed, 637 insertions(+), 561 deletions(-)
Title: Geographical Risk Analysis Based on Habitat Connectivity
Description: The geohabnet package is designed to perform a geographically or spatially explicit risk analysis of habitat connectivity. Xing et al (2021) <doi:10.1093/biosci/biaa067> proposed the concept of cropland connectivity as a risk factor for plant pathogen or pest invasions. As the functions in geohabnet were initially developed thinking on cropland connectivity, users are recommended to first be familiar with the concept by looking at the Xing et al paper. In a nutshell, a habitat connectivity analysis combines information from maps of host density, estimates the relative likelihood of pathogen movement between habitat locations in the area of interest, and applies network analysis to calculate the connectivity of habitat locations.
The functions of geohabnet are built to conduct a habitat connectivity analysis relying on geographic parameters (spatial resolution and spatial extent), dispersal parameters (in two commonly used dispersal kernels: inverse power law and negative exponent [...truncated...]
Author: Krishna Keshav [aut, cre],
Aaron Plex [aut] ,
Garrett Lab [ctb] ,
Karen Garrett [aut] ,
University of Florida [cph, fnd]
Maintainer: Krishna Keshav <kkeshav@ufl.edu>
Diff between geohabnet versions 2.1.0 dated 2024-03-28 and 2.1.1 dated 2024-04-05
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geohabnet-2.1.1/geohabnet/R/scales.R | 162 geohabnet-2.1.1/geohabnet/R/sean.R | 1468 +++---- geohabnet-2.1.1/geohabnet/R/show.R | 110 geohabnet-2.1.1/geohabnet/R/spam_crop.R | 152 geohabnet-2.1.1/geohabnet/R/strings.R | 94 geohabnet-2.1.1/geohabnet/R/utils-pipe.R | 28 geohabnet-2.1.1/geohabnet/README.md | 180 geohabnet-2.1.1/geohabnet/build/partial.rdb |binary geohabnet-2.1.1/geohabnet/build/vignette.rds |binary geohabnet-2.1.1/geohabnet/inst/ZeroRaster.tif |only geohabnet-2.1.1/geohabnet/inst/defaultParams.yaml | 68 geohabnet-2.1.1/geohabnet/inst/doc/LinkWeightsAnalysis.R | 38 geohabnet-2.1.1/geohabnet/inst/doc/LinkWeightsAnalysis.Rmd | 102 geohabnet-2.1.1/geohabnet/inst/doc/LinkWeightsAnalysis.html | 894 ++-- geohabnet-2.1.1/geohabnet/inst/doc/analysis.R | 314 - geohabnet-2.1.1/geohabnet/inst/doc/analysis.Rmd | 878 ++-- geohabnet-2.1.1/geohabnet/inst/doc/analysis.html | 2180 +++++------ geohabnet-2.1.1/geohabnet/inst/map_grey_background.tif |only geohabnet-2.1.1/geohabnet/inst/parameters.yaml | 68 geohabnet-2.1.1/geohabnet/man/Dispersal-kernels.Rd | 138 geohabnet-2.1.1/geohabnet/man/GeoModel-class.Rd | 34 geohabnet-2.1.1/geohabnet/man/GeoNetwork-class.Rd | 86 geohabnet-2.1.1/geohabnet/man/GeoRasters-class.Rd | 44 geohabnet-2.1.1/geohabnet/man/GlobalRast-class.Rd | 40 geohabnet-2.1.1/geohabnet/man/Gmap-class.Rd | 82 geohabnet-2.1.1/geohabnet/man/RiskMap-class.Rd | 42 geohabnet-2.1.1/geohabnet/man/STR_BETWEENNESS.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_CLOSENESS_CENTRALITY.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_DEGREE.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_DISTANCE_MATRIX.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_EAST.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_EIGEN_VECTOR_CENTRALITY.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_NEAREST_NEIGHBORS_SUM.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_NODE_STRENGTH.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_PAGE_RANK.Rd | 32 geohabnet-2.1.1/geohabnet/man/STR_WEST.Rd | 32 geohabnet-2.1.1/geohabnet/man/connectivity.Rd | 160 geohabnet-2.1.1/geohabnet/man/cropharvest_rast.Rd | 50 geohabnet-2.1.1/geohabnet/man/crops_rast.Rd | 56 geohabnet-2.1.1/geohabnet/man/dist_methods.Rd | 47 geohabnet-2.1.1/geohabnet/man/dot-indices.Rd | 34 geohabnet-2.1.1/geohabnet/man/geohabnet-package.Rd | 80 geohabnet-2.1.1/geohabnet/man/geoscale_param.Rd | 36 geohabnet-2.1.1/geohabnet/man/get_parameters.Rd | 66 geohabnet-2.1.1/geohabnet/man/get_rasters.Rd | 58 geohabnet-2.1.1/geohabnet/man/global_scales.Rd | 46 geohabnet-2.1.1/geohabnet/man/gplot.Rd | 50 geohabnet-2.1.1/geohabnet/man/hci_diff.Rd | 70 geohabnet-2.1.1/geohabnet/man/hci_mean.Rd | 92 geohabnet-2.1.1/geohabnet/man/hci_variance.Rd | 90 geohabnet-2.1.1/geohabnet/man/host_density-set.Rd | 32 geohabnet-2.1.1/geohabnet/man/load_parameters.Rd | 46 geohabnet-2.1.1/geohabnet/man/mapspam.Rd | 26 geohabnet-2.1.1/geohabnet/man/monfreda.Rd | 26 geohabnet-2.1.1/geohabnet/man/nn_sum.Rd | 130 geohabnet-2.1.1/geohabnet/man/pipe.Rd | 40 geohabnet-2.1.1/geohabnet/man/reset_params.Rd | 38 geohabnet-2.1.1/geohabnet/man/reso.Rd | 30 geohabnet-2.1.1/geohabnet/man/risk_indices.Rd | 54 geohabnet-2.1.1/geohabnet/man/sa_onrasters.Rd | 186 geohabnet-2.1.1/geohabnet/man/scales.Rd | 32 geohabnet-2.1.1/geohabnet/man/sean.Rd | 304 - geohabnet-2.1.1/geohabnet/man/search_crop.Rd | 73 geohabnet-2.1.1/geohabnet/man/sensitivity_analysis.Rd | 148 geohabnet-2.1.1/geohabnet/man/set_global_scales.Rd | 50 geohabnet-2.1.1/geohabnet/man/set_parameters.Rd | 52 geohabnet-2.1.1/geohabnet/man/setmaps-Gmap-method.Rd | 46 geohabnet-2.1.1/geohabnet/man/sp_rast.Rd | 74 geohabnet-2.1.1/geohabnet/man/supported_metrics.Rd | 46 geohabnet-2.1.1/geohabnet/man/supported_sources.Rd | 50 geohabnet-2.1.1/geohabnet/man/tiff_torast.Rd | 54 geohabnet-2.1.1/geohabnet/tests/testthat.R | 24 geohabnet-2.1.1/geohabnet/tests/testthat/params.yaml | 68 geohabnet-2.1.1/geohabnet/tests/testthat/test-functional.R | 28 geohabnet-2.1.1/geohabnet/tests/testthat/test-get_rasters.R | 10 geohabnet-2.1.1/geohabnet/tests/testthat/test-parameters.R | 82 geohabnet-2.1.1/geohabnet/tests/testthat/test-utilities.R | 14 geohabnet-2.1.1/geohabnet/vignettes/LinkWeightsAnalysis.Rmd | 102 geohabnet-2.1.1/geohabnet/vignettes/analysis.Rmd | 878 ++-- geohabnet-2.1.1/geohabnet/vignettes/references.bib | 262 - 205 files changed, 7729 insertions(+), 7920 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.2.0 dated 2024-01-09 and 3.2.1 dated 2024-04-05
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 3 +++ R/labkey.defaults.R | 5 +++++ man/Rlabkey-package.Rd | 6 +++--- man/labkey.getQueries.Rd | 2 +- man/labkey.getSchemas.Rd | 2 +- man/lsProjects.Rd | 2 +- man/makeFilter.Rd | 2 +- man/saveResults.Rd | 2 +- 10 files changed, 29 insertions(+), 21 deletions(-)
Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the
Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve
page text, information about users or the history of pages, and elements of
the category tree.
Author: Os Keyes [aut, cre], Brock Tilbert [ctb], Clemens Schmid [aut]
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between WikipediR versions 1.7.0 dated 2024-03-28 and 1.7.1 dated 2024-04-05
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/categories.R | 6 ++++-- R/content.R | 10 ++++++++-- R/metadata.R | 9 ++++++++- R/user_info.R | 6 ++++-- man/categories_in_page.Rd | 3 ++- man/page_backlinks.Rd | 2 ++ man/page_content.Rd | 2 ++ man/page_external_links.Rd | 2 ++ man/page_info.Rd | 3 ++- man/page_links.Rd | 2 ++ man/pages_in_category.Rd | 3 ++- man/random_page.Rd | 2 ++ man/revision_content.Rd | 3 ++- man/revision_diff.Rd | 3 ++- man/user_contributions.Rd | 4 ++-- man/user_information.Rd | 2 ++ 18 files changed, 69 insertions(+), 35 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 [Dias et al. (2022) <doi:10.1007/s00122-022-04041-y>]. 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 1.0.3.1 dated 2023-11-29 and 1.0.3.2 dated 2024-04-05
DESCRIPTION | 8 +-- MD5 | 11 ++-- NEWS.md | 10 +-- R/soy.R | 60 +++++++++++------------ README.md | 140 ++++++++++++++++++++++++++++-------------------------- build/partial.rdb |binary inst |only 7 files changed, 119 insertions(+), 110 deletions(-)
Title: Dynamic Data Explorer: Visualize and Forecast with 'TimeVizPro'
Description: Unleash the power of time-series data visualization with ease using our package. Designed with simplicity
in mind, it offers three key features through the 'shiny' package output. The first tab shows time- series
charts with forecasts, allowing users to visualize trends and changes effortlessly. The second one displays
Averages per country presented in tables with accompanying sparklines, providing a quick and attractive
overview of the data. The last tab presents A customizable world map colored based on user-defined
variables for any chosen number of countries, offering an advanced visual approach to understanding
geographical data distributions. This package operates with just a few simple arguments, enabling users
to conduct sophisticated analyses without the need for complex programming skills. Transform your
time-series data analysis experience with our user-friendly tool.
Author: Hossein Hassani [aut],
Fernando Cantu Bazaldua [aut],
Leila Marvian Mashhad [aut, cre]
Maintainer: Leila Marvian Mashhad <Leila.marveian@gmail.com>
Diff between TimeVizPro versions 1.0 dated 2024-04-03 and 1.0.1 dated 2024-04-05
DESCRIPTION | 22 +++++++++++----------- MD5 | 4 ++-- man/TimeVizPro.Rd | 2 +- 3 files changed, 14 insertions(+), 14 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor) or analysis of variance (for cases where more than two levels or factors exist) to calculate the fold change or relative expression. The functions also provide standard deviations and confidence limits for means and apply statistical mean comparisons. To facilitate using 'rtpcr', different datasets have been employed in the examples and the outputs ar [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 1.0.0 dated 2024-04-02 and 1.0.1 dated 2024-04-05
rtpcr-1.0.0/rtpcr/R/oneFACTORfcplot.r |only rtpcr-1.0.0/rtpcr/README.md |only rtpcr-1.0.0/rtpcr/man/oneFACTORfcplot.Rd |only rtpcr-1.0.1/rtpcr/COPYING |only rtpcr-1.0.1/rtpcr/DESCRIPTION | 8 rtpcr-1.0.1/rtpcr/MD5 | 42 +- rtpcr-1.0.1/rtpcr/NAMESPACE | 2 rtpcr-1.0.1/rtpcr/R/meanTech.r | 2 rtpcr-1.0.1/rtpcr/R/oneFACTORplot.r | 9 rtpcr-1.0.1/rtpcr/R/qpcrANCOVA.r |only rtpcr-1.0.1/rtpcr/R/qpcrANOVA.r | 47 -- rtpcr-1.0.1/rtpcr/R/qpcrTTEST.r | 2 rtpcr-1.0.1/rtpcr/R/qpcrTTESTplot.r | 5 rtpcr-1.0.1/rtpcr/R/threeFACTORplot.r | 10 rtpcr-1.0.1/rtpcr/R/twoFACTORplot.r | 75 ++- rtpcr-1.0.1/rtpcr/inst/doc/vignette.R | 165 +++++--- rtpcr-1.0.1/rtpcr/inst/doc/vignette.Rmd | 243 ++++++++--- rtpcr-1.0.1/rtpcr/inst/doc/vignette.html | 635 +++++++++++++++++-------------- rtpcr-1.0.1/rtpcr/man/qpcrANCOVA.Rd |only rtpcr-1.0.1/rtpcr/man/qpcrANOVA.Rd | 11 rtpcr-1.0.1/rtpcr/man/qpcrTTEST.Rd | 2 rtpcr-1.0.1/rtpcr/man/qpcrTTESTplot.Rd | 2 rtpcr-1.0.1/rtpcr/man/threeFACTORplot.Rd | 2 rtpcr-1.0.1/rtpcr/man/twoFACTORplot.Rd | 16 rtpcr-1.0.1/rtpcr/vignettes/vignette.Rmd | 243 ++++++++--- 25 files changed, 958 insertions(+), 563 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.8.1.0 dated 2024-03-03 and 0.12.8.2.0 dated 2024-04-05
ChangeLog | 22 +++++++++ DESCRIPTION | 8 +-- MD5 | 32 ++++++------- README.md | 5 -- configure | 18 +++---- configure.ac | 2 inst/NEWS.Rd | 12 ++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/Mat_meat.hpp | 56 +++++++---------------- inst/include/armadillo_bits/SpMat_bones.hpp | 2 inst/include/armadillo_bits/SpMat_meat.hpp | 39 ++++------------ inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/def_fftw3.hpp | 29 +++++++---- inst/include/armadillo_bits/translate_fftw3.hpp | 12 ++-- inst/include/armadillo_bits/wall_clock_bones.hpp | 4 - inst/include/armadillo_bits/wall_clock_meat.hpp | 20 +++----- 17 files changed, 134 insertions(+), 129 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among several built-in similarity/distance measures, computation of correlation,
cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.3.4 dated 2023-10-25 and 0.4.0 dated 2024-04-05
proxyC-0.3.4/proxyC/src/Makevars |only proxyC-0.3.4/proxyC/src/armadillo.h |only proxyC-0.4.0/proxyC/DESCRIPTION | 15 proxyC-0.4.0/proxyC/MD5 | 65 - proxyC-0.4.0/proxyC/NAMESPACE | 25 proxyC-0.4.0/proxyC/NEWS.md | 224 ++-- proxyC-0.4.0/proxyC/R/RcppExports.R | 46 proxyC-0.4.0/proxyC/R/proxy.R | 570 ++++++----- proxyC-0.4.0/proxyC/README.md | 250 ++--- proxyC-0.4.0/proxyC/build/vignette.rds |binary proxyC-0.4.0/proxyC/cleanup |only proxyC-0.4.0/proxyC/configure |only proxyC-0.4.0/proxyC/configure.ac |only proxyC-0.4.0/proxyC/inst/doc/measures.R | 6 proxyC-0.4.0/proxyC/inst/doc/measures.Rmd | 394 ++++---- proxyC-0.4.0/proxyC/inst/doc/measures.html | 914 +++++++++---------- proxyC-0.4.0/proxyC/inst/libtbb.R |only proxyC-0.4.0/proxyC/man/colSds.Rd | 48 proxyC-0.4.0/proxyC/man/colZeros.Rd | 44 proxyC-0.4.0/proxyC/man/images/unnamed-chunk-4-1.png |binary proxyC-0.4.0/proxyC/man/images/unnamed-chunk-5-1.png |binary proxyC-0.4.0/proxyC/man/images/unnamed-chunk-6-1.png |binary proxyC-0.4.0/proxyC/man/images/unnamed-chunk-7-1.png |binary proxyC-0.4.0/proxyC/man/images/unnamed-chunk-8-1.png |only proxyC-0.4.0/proxyC/man/simil.Rd | 256 ++--- proxyC-0.4.0/proxyC/src/Makevars.in |only proxyC-0.4.0/proxyC/src/Makevars.win | 6 proxyC-0.4.0/proxyC/src/RcppExports.cpp | 58 - proxyC-0.4.0/proxyC/src/linear.cpp | 127 +- proxyC-0.4.0/proxyC/src/pair.cpp | 243 ++--- proxyC-0.4.0/proxyC/src/proxyc.h | 31 proxyC-0.4.0/proxyC/src/utility.cpp |only proxyC-0.4.0/proxyC/tests/testthat.R | 6 proxyC-0.4.0/proxyC/tests/testthat/function.R | 312 +++--- proxyC-0.4.0/proxyC/tests/testthat/test-dist.R | 646 ++++++------- proxyC-0.4.0/proxyC/tests/testthat/test-proxy.R | 407 ++++---- proxyC-0.4.0/proxyC/tests/testthat/test-simil.R | 570 +++++------ proxyC-0.4.0/proxyC/vignettes/measures.Rmd | 394 ++++---- 38 files changed, 2883 insertions(+), 2774 deletions(-)
Title: Rolling and Expanding Statistics
Description: Fast and efficient computation of rolling and expanding statistics for time-series data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between roll versions 1.1.6 dated 2020-07-13 and 1.1.7 dated 2024-04-05
roll-1.1.6/roll/src/roll_mat.h |only roll-1.1.6/roll/src/roll_vec.h |only roll-1.1.7/roll/DESCRIPTION | 16 roll-1.1.7/roll/MD5 | 40 - roll-1.1.7/roll/NAMESPACE | 2 roll-1.1.7/roll/NEWS.md | 26 roll-1.1.7/roll/R/RcppExports.R | 4 roll-1.1.7/roll/R/roll.R | 53 + roll-1.1.7/roll/README.md | 6 roll-1.1.7/roll/build/partial.rdb |binary roll-1.1.7/roll/inst |only roll-1.1.7/roll/man/roll-package.Rd | 20 roll-1.1.7/roll/man/roll_crossprod.Rd |only roll-1.1.7/roll/src/Makevars | 4 roll-1.1.7/roll/src/Makevars.win | 4 roll-1.1.7/roll/src/RcppExports.cpp | 26 roll-1.1.7/roll/src/init.c | 26 roll-1.1.7/roll/src/roll.cpp | 976 ++++++++++++++++++--------- roll-1.1.7/roll/tests/testthat/helper-data.R | 10 roll-1.1.7/roll/tests/testthat/helper-zoo.R | 118 ++- roll-1.1.7/roll/tests/testthat/test-roll.R | 11 roll-1.1.7/roll/tests/testthat/test-zoo.R | 269 +++---- 22 files changed, 1077 insertions(+), 534 deletions(-)
Title: CFO-Type Designs in Phase I Clinical Trials
Description: In phase I clinical trials, the primary objective is to ascertain the maximum tolerated dose (MTD) corresponding to a specified target toxicity rate. The 'CFO' package facilitates the implementation of dose-finding trials by utilizing calibration-free odds type (CFO-type) designs. Specifically, it encompasses the calibration-free odds (CFO) (Jin and Yin (2022) <doi:10.1177/09622802221079353>), two-dimensional CFO (2dCFO) (Wang et al. (2023) <doi:10.3389/fonc.2023.1294258>), time-to-event CFO (TITE-CFO) (Jin and Yin (2023) <doi:10.1002/pst.2304>), fractional CFO (fCFO), accumulative CFO (aCFO), TITE-aCFO, and f-aCFO designs. The ‘CFO' package accommodates diverse CFO-type designs, allowing users to tailor the approach based on factors such as dose information inclusion, handling of late-onset toxicity, and the nature of the target drug (single-drug or drug-combination). The functionalities embedded in 'CFO' package include the determination of the dose level for the ne [...truncated...]
Author: Jialu Fang [aut, cre],
Wenliang Wang [aut],
Guosheng Yin [aut]
Maintainer: Jialu Fang <u3008682@connect.hku.hk>
Diff between CFO versions 1.1.0 dated 2024-03-05 and 1.1.1 dated 2024-04-05
DESCRIPTION | 7 +++---- MD5 | 4 ++-- R/plot.cfo.R | 30 +++++++++++++++++++++--------- 3 files changed, 26 insertions(+), 15 deletions(-)
Title: Adaptive Rejection Sampling
Description: Adaptive Rejection Sampling, Original version.
Author: Paulino Perez Rodriguez <perpdgo@colpos.mx> original C++ code
from Arnost Komarek based on ars.f written by P. Wild and W. R.
Gilks
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between ars versions 0.6 dated 2018-08-23 and 0.7 dated 2024-04-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 6 ++++-- R/ars.R | 19 +++++++++++++------ man/ars.Rd | 4 ++-- 5 files changed, 27 insertions(+), 18 deletions(-)
Title: Spatio-Temporal Point Pattern Methods, Model Fitting,
Diagnostics, Simulation, Local Tests
Description: Toolbox for different kinds of spatio-temporal analyses to be performed on observed point patterns, following the growing stream of literature on point process theory. This R package implements functions to perform different kinds of analyses on point processes, proposed in the papers (Siino, Adelfio, and Mateu 2018<doi:10.1007/s00477-018-1579-0>; Siino et al. 2018<doi:10.1002/env.2463>; Adelfio et al. 2020<doi:10.1007/s00477-019-01748-1>; D’Angelo, Adelfio, and Mateu 2021<doi:10.1016/j.spasta.2021.100534>; D’Angelo, Adelfio, and Mateu 2022<doi:10.1007/s00362-022-01338-4>; D’Angelo, Adelfio, and Mateu 2023<doi:10.1016/j.csda.2022.107679>). The main topics include modeling, statistical inference, and simulation issues on spatio-temporal point processes on Euclidean space and linear networks.
Author: Nicoletta D'Angelo [aut, cre] ,
Giada Adelfio [aut]
Maintainer: Nicoletta D'Angelo <nicoletta.dangelo@unipa.it>
Diff between stopp versions 0.2.0 dated 2024-03-19 and 0.2.1 dated 2024-04-05
stopp-0.2.0/stopp/R/display.R |only stopp-0.2.0/stopp/R/localplot.locstppm.R |only stopp-0.2.0/stopp/R/localplot.stlgcppm.R |only stopp-0.2.0/stopp/R/localsummary.locstppm.R |only stopp-0.2.0/stopp/R/localsummary.stlgcppm.R |only stopp-0.2.0/stopp/man/display.Rd |only stopp-0.2.0/stopp/man/localplot.locstppm.Rd |only stopp-0.2.0/stopp/man/localplot.stlgcppm.Rd |only stopp-0.2.0/stopp/man/localsummary.locstppm.Rd |only stopp-0.2.0/stopp/man/localsummary.stlgcppm.Rd |only stopp-0.2.1/stopp/DESCRIPTION | 8 stopp-0.2.1/stopp/MD5 | 68 +- stopp-0.2.1/stopp/NAMESPACE | 29 - stopp-0.2.1/stopp/R/globaldiag.R | 12 stopp-0.2.1/stopp/R/infl.R | 32 + stopp-0.2.1/stopp/R/internals.R | 619 +++++++++++++++++++++++++ stopp-0.2.1/stopp/R/localSTLKinhom.R | 6 stopp-0.2.1/stopp/R/localSTLginhom.R | 15 stopp-0.2.1/stopp/R/localdiag.R | 8 stopp-0.2.1/stopp/R/localplot.R |only stopp-0.2.1/stopp/R/localsummary.R |only stopp-0.2.1/stopp/R/plot.lista.R |only stopp-0.2.1/stopp/R/plot.stlgcppm.R | 4 stopp-0.2.1/stopp/R/print.lista.R |only stopp-0.2.1/stopp/R/print.sepstlppm.R |only stopp-0.2.1/stopp/R/print.sepstppm.R |only stopp-0.2.1/stopp/R/print.stlgcppm.R | 6 stopp-0.2.1/stopp/R/stlgcppm.R | 51 +- stopp-0.2.1/stopp/R/summary.lista.R |only stopp-0.2.1/stopp/R/summary.localdiag.R | 2 stopp-0.2.1/stopp/R/summary.localtest.R | 5 stopp-0.2.1/stopp/R/summary.sepstlppm.R |only stopp-0.2.1/stopp/R/summary.sepstppm.R |only stopp-0.2.1/stopp/R/summary.stlgcppm.R | 8 stopp-0.2.1/stopp/man/localSTLKinhom.Rd | 4 stopp-0.2.1/stopp/man/localSTLginhom.Rd | 4 stopp-0.2.1/stopp/man/localplot.Rd |only stopp-0.2.1/stopp/man/localsummary.Rd |only stopp-0.2.1/stopp/man/plot.lista.Rd |only stopp-0.2.1/stopp/man/plot.stlgcppm.Rd | 4 stopp-0.2.1/stopp/man/print.lista.Rd |only stopp-0.2.1/stopp/man/print.sepstlppm.Rd |only stopp-0.2.1/stopp/man/print.sepstppm.Rd |only stopp-0.2.1/stopp/man/print.stlgcppm.Rd | 6 stopp-0.2.1/stopp/man/stlgcppm.Rd | 6 stopp-0.2.1/stopp/man/summary.lista.Rd |only stopp-0.2.1/stopp/man/summary.sepstlppm.Rd |only stopp-0.2.1/stopp/man/summary.sepstppm.Rd |only stopp-0.2.1/stopp/man/summary.stlgcppm.Rd | 6 49 files changed, 801 insertions(+), 102 deletions(-)
Title: Semantic UI Support for Shiny
Description: Creating a great user interface for your Shiny apps can be a
hassle, especially if you want to work purely in R and don't want to
use, for instance HTML templates. This package adds support for a
powerful UI library Fomantic UI - <https://fomantic-ui.com/> (before
Semantic). It also supports universal UI input binding that works with
various DOM elements.
Author: Filip Stachura [aut],
Dominik Krzeminski [aut],
Krystian Igras [aut],
Adam Forys [aut],
Pawel Przytula [aut],
Jakub Chojna [aut],
Olga Mierzwa-Sulima [aut],
Jakub Nowicki [aut, cre],
Tymoteusz Makowski [aut],
Ashley Baldry [ctb],
Pedro Manuel Coutinh [...truncated...]
Maintainer: Jakub Nowicki <opensource+kuba@appsilon.com>
Diff between shiny.semantic versions 0.5.0 dated 2024-01-17 and 0.5.1 dated 2024-04-05
shiny.semantic-0.5.0/shiny.semantic/man/shiny.semantic.Rd |only shiny.semantic-0.5.1/shiny.semantic/DESCRIPTION | 15 shiny.semantic-0.5.1/shiny.semantic/MD5 | 37 - shiny.semantic-0.5.1/shiny.semantic/NEWS.md | 12 shiny.semantic-0.5.1/shiny.semantic/R/checkbox.R | 4 shiny.semantic-0.5.1/shiny.semantic/R/dropdown.R | 63 +-- shiny.semantic-0.5.1/shiny.semantic/R/shiny.R | 32 - shiny.semantic-0.5.1/shiny.semantic/R/shiny.semantic-package.R |only shiny.semantic-0.5.1/shiny.semantic/R/tables.R | 17 shiny.semantic-0.5.1/shiny.semantic/inst/doc/basics.html | 6 shiny.semantic-0.5.1/shiny.semantic/inst/doc/fomantic_js.html | 4 shiny.semantic-0.5.1/shiny.semantic/inst/doc/intro.html | 6 shiny.semantic-0.5.1/shiny.semantic/inst/doc/semantic_integration.html | 2 shiny.semantic-0.5.1/shiny.semantic/inst/www/shiny-semantic-DT.css | 3 shiny.semantic-0.5.1/shiny.semantic/inst/www/shiny-semantic-dropdown.js | 19 shiny.semantic-0.5.1/shiny.semantic/inst/www/shiny-semantic-slider.js | 4 shiny.semantic-0.5.1/shiny.semantic/man/semantic_DT.Rd | 11 shiny.semantic-0.5.1/shiny.semantic/man/shiny.semantic-package.Rd |only shiny.semantic-0.5.1/shiny.semantic/man/update_dropdown_input.Rd | 48 +- shiny.semantic-0.5.1/shiny.semantic/tests/testthat/setup-disable-crashpad.R |only shiny.semantic-0.5.1/shiny.semantic/tests/testthat/test_dropdown.R | 207 ++++++++++ shiny.semantic-0.5.1/shiny.semantic/tests/testthat/test_multiple_checkbox.R |only 22 files changed, 359 insertions(+), 131 deletions(-)
More information about shiny.semantic at CRAN
Permanent link
Title: Translate Models from System Dynamics Software into 'R'
Description: The goal of 'readsdr' is to bridge the design capabilities from
specialised System Dynamics software with the powerful numerical tools
offered by 'R' libraries. The package accomplishes this goal by parsing
'XMILE' files ('Vensim' and 'Stella') models into 'R' objects to construct
networks (graph theory); 'ODE' functions for 'Stan'; and inputs to simulate
via 'deSolve' as described in Duggan (2016) <doi:10.1007/978-3-319-34043-2>.
Author: Jair Andrade [aut, cre]
Maintainer: Jair Andrade <jair.albert.andrade@gmail.com>
Diff between readsdr versions 0.2.0 dated 2021-01-08 and 0.3.0 dated 2024-04-05
readsdr-0.2.0/readsdr/man/stan_data.Rd |only readsdr-0.2.0/readsdr/man/stan_transformed_data.Rd |only readsdr-0.3.0/readsdr/DESCRIPTION | 14 readsdr-0.3.0/readsdr/MD5 | 178 +++- readsdr-0.3.0/readsdr/NAMESPACE | 19 readsdr-0.3.0/readsdr/NEWS.md | 48 + readsdr-0.3.0/readsdr/R/SBC.R |only readsdr-0.3.0/readsdr/R/Vensim_workarounds.R |only readsdr-0.3.0/readsdr/R/arrange_variables.R | 21 readsdr-0.3.0/readsdr/R/arrays.R |only readsdr-0.3.0/readsdr/R/data.R |only readsdr-0.3.0/readsdr/R/delay.R |only readsdr-0.3.0/readsdr/R/extract_variables.R | 12 readsdr-0.3.0/readsdr/R/fun_gen_utils.R |only readsdr-0.3.0/readsdr/R/generate_deSolve_components.R | 30 readsdr-0.3.0/readsdr/R/impact_inputs.R |only readsdr-0.3.0/readsdr/R/interpreters.R |only readsdr-0.3.0/readsdr/R/loglik_fun.R |only readsdr-0.3.0/readsdr/R/output_utils.R |only readsdr-0.3.0/readsdr/R/par_trans.R |only readsdr-0.3.0/readsdr/R/posterior_fun.R |only readsdr-0.3.0/readsdr/R/prior_checks.R |only readsdr-0.3.0/readsdr/R/priors.R |only readsdr-0.3.0/readsdr/R/read_xmile.R | 69 - readsdr-0.3.0/readsdr/R/regex_patterns.R |only readsdr-0.3.0/readsdr/R/sd_bayes.R |only readsdr-0.3.0/readsdr/R/simulator_measurements.R |only readsdr-0.3.0/readsdr/R/simulator_utils.R |only readsdr-0.3.0/readsdr/R/simulators.R | 208 ++-- readsdr-0.3.0/readsdr/R/stan_data.R |only readsdr-0.3.0/readsdr/R/stan_gc.R |only readsdr-0.3.0/readsdr/R/stan_model.R |only readsdr-0.3.0/readsdr/R/stan_ode_function.R | 14 readsdr-0.3.0/readsdr/R/stan_params.R |only readsdr-0.3.0/readsdr/R/stan_postprocessing.R |only readsdr-0.3.0/readsdr/R/stan_trans_params.R |only readsdr-0.3.0/readsdr/R/stan_utils.R | 383 +++++--- readsdr-0.3.0/readsdr/R/stat_funs.R | 23 readsdr-0.3.0/readsdr/R/translate_smooth.R | 2 readsdr-0.3.0/readsdr/R/utils.R | 46 + readsdr-0.3.0/readsdr/R/var_consts_xmile.R | 236 ++++- readsdr-0.3.0/readsdr/R/what_if_from_time.R |only readsdr-0.3.0/readsdr/R/xmile_graph_funs.R | 24 readsdr-0.3.0/readsdr/R/xmile_helpers.R | 84 + readsdr-0.3.0/readsdr/R/xml_model_components.R | 168 ++- readsdr-0.3.0/readsdr/README.md | 128 +- readsdr-0.3.0/readsdr/build/vignette.rds |binary readsdr-0.3.0/readsdr/data |only readsdr-0.3.0/readsdr/inst/doc/Introduction_to_readsdr.R | 2 readsdr-0.3.0/readsdr/inst/doc/Introduction_to_readsdr.Rmd | 11 readsdr-0.3.0/readsdr/inst/doc/Introduction_to_readsdr.html | 427 +++++----- readsdr-0.3.0/readsdr/inst/models/LV.stmx |only readsdr-0.3.0/readsdr/inst/models/SEIR.stmx |only readsdr-0.3.0/readsdr/inst/models/SEIR_age.isdb |only readsdr-0.3.0/readsdr/inst/models/SEIR_age.stmx |only readsdr-0.3.0/readsdr/inst/models/SEIR_alt.stmx |only readsdr-0.3.0/readsdr/inst/models/SEIR_iota.stmx |only readsdr-0.3.0/readsdr/inst/models/SEjIkR.stmx |only readsdr-0.3.0/readsdr/man/Maryland.Rd |only readsdr-0.3.0/readsdr/man/expit.Rd |only readsdr-0.3.0/readsdr/man/extract_timeseries_stock.Rd | 2 readsdr-0.3.0/readsdr/man/extract_timeseries_var.Rd | 2 readsdr-0.3.0/readsdr/man/inv.Rd |only readsdr-0.3.0/readsdr/man/logit.Rd |only readsdr-0.3.0/readsdr/man/read_xmile.Rd | 9 readsdr-0.3.0/readsdr/man/reexports.Rd | 5 readsdr-0.3.0/readsdr/man/sd_Bayes.Rd |only readsdr-0.3.0/readsdr/man/sd_data_generator_fun.Rd |only readsdr-0.3.0/readsdr/man/sd_fixed_delay.Rd |only readsdr-0.3.0/readsdr/man/sd_impact_inputs.Rd |only readsdr-0.3.0/readsdr/man/sd_interpret_estimates.Rd |only readsdr-0.3.0/readsdr/man/sd_loglik_fun.Rd |only readsdr-0.3.0/readsdr/man/sd_measurements.Rd |only readsdr-0.3.0/readsdr/man/sd_net_change.Rd |only readsdr-0.3.0/readsdr/man/sd_posterior_fun.Rd |only readsdr-0.3.0/readsdr/man/sd_prior.Rd |only readsdr-0.3.0/readsdr/man/sd_prior_checks.Rd |only readsdr-0.3.0/readsdr/man/sd_sensitivity_run.Rd | 29 readsdr-0.3.0/readsdr/man/sd_simulate.Rd | 10 readsdr-0.3.0/readsdr/man/sd_what_if_from_time.Rd |only readsdr-0.3.0/readsdr/man/stan_ode_function.Rd | 5 readsdr-0.3.0/readsdr/tests/testthat/2d_pop.xmile |only readsdr-0.3.0/readsdr/tests/testthat/SEIR_C_meas.stan |only readsdr-0.3.0/readsdr/tests/testthat/SEIR_nbinom.stan |only readsdr-0.3.0/readsdr/tests/testthat/SEIR_nbinom_data_param.stan |only readsdr-0.3.0/readsdr/tests/testthat/SEIR_normal.stan |only readsdr-0.3.0/readsdr/tests/testthat/SEjIkR.xmile |only readsdr-0.3.0/readsdr/tests/testthat/SEjIkR.xmile.2 |only readsdr-0.3.0/readsdr/tests/testthat/SEjIkR_converted.mdl |only readsdr-0.3.0/readsdr/tests/testthat/test-SBC.R |only readsdr-0.3.0/readsdr/tests/testthat/test-Vensim_workarounds.R |only readsdr-0.3.0/readsdr/tests/testthat/test-arrange_variables.R | 8 readsdr-0.3.0/readsdr/tests/testthat/test-arrays.R |only readsdr-0.3.0/readsdr/tests/testthat/test-delay.R |only readsdr-0.3.0/readsdr/tests/testthat/test-extract_variables.R | 26 readsdr-0.3.0/readsdr/tests/testthat/test-generate_deSolve_components.R | 49 + readsdr-0.3.0/readsdr/tests/testthat/test-if_else_builtins.R | 7 readsdr-0.3.0/readsdr/tests/testthat/test-impact_inputs.R |only readsdr-0.3.0/readsdr/tests/testthat/test-interpreters.R |only readsdr-0.3.0/readsdr/tests/testthat/test-loglik_fun.R |only readsdr-0.3.0/readsdr/tests/testthat/test-output_utils.R |only readsdr-0.3.0/readsdr/tests/testthat/test-posterior_fun.R |only readsdr-0.3.0/readsdr/tests/testthat/test-prior_checks.R |only readsdr-0.3.0/readsdr/tests/testthat/test-priors.R |only readsdr-0.3.0/readsdr/tests/testthat/test-read_xmile.R | 54 - readsdr-0.3.0/readsdr/tests/testthat/test-sd_bayes.R |only readsdr-0.3.0/readsdr/tests/testthat/test-simulator_measurements.R |only readsdr-0.3.0/readsdr/tests/testthat/test-simulator_utils.R |only readsdr-0.3.0/readsdr/tests/testthat/test-simulators.R | 69 + readsdr-0.3.0/readsdr/tests/testthat/test-stan_data.R |only readsdr-0.3.0/readsdr/tests/testthat/test-stan_gc.R |only readsdr-0.3.0/readsdr/tests/testthat/test-stan_model.R |only readsdr-0.3.0/readsdr/tests/testthat/test-stan_ode_function.R | 6 readsdr-0.3.0/readsdr/tests/testthat/test-stan_params.R |only readsdr-0.3.0/readsdr/tests/testthat/test-stan_postprocessing.R |only readsdr-0.3.0/readsdr/tests/testthat/test-stan_trans_params.R |only readsdr-0.3.0/readsdr/tests/testthat/test-stan_utils.R | 126 +- readsdr-0.3.0/readsdr/tests/testthat/test-stat_funs.R | 9 readsdr-0.3.0/readsdr/tests/testthat/test-summaries.R | 6 readsdr-0.3.0/readsdr/tests/testthat/test-translate_SMOOTH.R | 4 readsdr-0.3.0/readsdr/tests/testthat/test-var_consts_xmile.R | 206 ++++ readsdr-0.3.0/readsdr/tests/testthat/test-what_if_from_time.R |only readsdr-0.3.0/readsdr/tests/testthat/test-xmile_graph_funs.R | 36 readsdr-0.3.0/readsdr/tests/testthat/test-xmile_helpers.R | 141 +++ readsdr-0.3.0/readsdr/tests/testthat/test-xml_model_components.R | 292 ++++++ readsdr-0.3.0/readsdr/tests/testthat/test_models |only readsdr-0.3.0/readsdr/tests/testthat/test_stan_files |only readsdr-0.3.0/readsdr/vignettes/Introduction_to_readsdr.Rmd | 11 128 files changed, 2344 insertions(+), 915 deletions(-)
Title: Abstractions for Promise-Based Asynchronous Programming
Description: Provides fundamental abstractions for doing asynchronous
programming in R using promises. Asynchronous programming is useful
for allowing a single R process to orchestrate multiple tasks in the
background while also attending to something else. Semantics are
similar to 'JavaScript' promises, but with a syntax that is idiomatic
R.
Author: Joe Cheng [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Joe Cheng <joe@posit.co>
Diff between promises versions 1.2.1 dated 2023-08-10 and 1.3.0 dated 2024-04-05
DESCRIPTION | 8 MD5 | 36 +- NAMESPACE | 3 NEWS.md | 5 R/promise.R | 22 + build/vignette.rds |binary inst/doc/promises_02_intro.html | 96 +++--- inst/doc/promises_03_overview.html | 232 ++++++++-------- inst/doc/promises_04_futures.Rmd | 7 inst/doc/promises_04_futures.html | 38 +- inst/doc/promises_05_future_promise.R | 4 inst/doc/promises_05_future_promise.html | 32 +- inst/doc/promises_06_shiny.Rmd | 10 inst/doc/promises_06_shiny.html | 344 ++++++++++++------------ inst/doc/promises_07_combining.html | 168 +++++------ inst/doc/promises_08_casestudy.html | 444 +++++++++++++++---------------- man/is.promise.Rd | 5 vignettes/promises_04_futures.Rmd | 7 vignettes/promises_06_shiny.Rmd | 10 19 files changed, 765 insertions(+), 706 deletions(-)
Title: Raw, Central and Standardized Moments of Parametric
Distributions
Description: To calculate the raw, central and standardized moments
from distribution parameters. To solve the distribution
parameters based on user-provided mean, standard deviation,
skewness and kurtosis. Normal, skew-normal, skew-t and Tukey
g-&-h distributions are supported, for now.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between param2moment versions 0.1.0 dated 2024-03-19 and 0.1.1 dated 2024-04-05
param2moment-0.1.0/param2moment/R/batchParam.R |only param2moment-0.1.0/param2moment/R/moment_GH.R |only param2moment-0.1.0/param2moment/R/moment_norm.R |only param2moment-0.1.0/param2moment/R/moment_sn.R |only param2moment-0.1.0/param2moment/R/moment_st.R |only param2moment-0.1.0/param2moment/man/param_GH.Rd |only param2moment-0.1.0/param2moment/man/param_sn.Rd |only param2moment-0.1.0/param2moment/man/param_st.Rd |only param2moment-0.1.1/param2moment/DESCRIPTION | 30 ++++++------ param2moment-0.1.1/param2moment/MD5 | 33 +++++++------- param2moment-0.1.1/param2moment/NAMESPACE | 13 ++--- param2moment-0.1.1/param2moment/R/TukeyGH.R |only param2moment-0.1.1/param2moment/R/moment.R | 2 param2moment-0.1.1/param2moment/R/moment2param.R |only param2moment-0.1.1/param2moment/R/norm.R |only param2moment-0.1.1/param2moment/R/sn.R |only param2moment-0.1.1/param2moment/R/st.R |only param2moment-0.1.1/param2moment/man/moment2GH.Rd |only param2moment-0.1.1/param2moment/man/moment2param.Rd |only param2moment-0.1.1/param2moment/man/moment2sn.Rd |only param2moment-0.1.1/param2moment/man/moment2st.Rd |only param2moment-0.1.1/param2moment/man/moment_GH.Rd | 16 +++++- param2moment-0.1.1/param2moment/man/moment_norm.Rd | 10 ++-- param2moment-0.1.1/param2moment/man/moment_sn.Rd | 12 +++-- param2moment-0.1.1/param2moment/man/moment_st.Rd | 18 +++++-- param2moment-0.1.1/param2moment/man/show-moment-method.Rd | 2 26 files changed, 81 insertions(+), 55 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library implementing 'Scalability Protocols', a reliable,
high-performance standard for common communications patterns including
publish/subscribe, request/reply and service discovery, over in-process,
IPC, TCP, WebSocket and secure TLS transports. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing, with intuitive 'aio' objects which resolve
automatically upon completion of asynchronous operations, and
synchronisation primitives allowing R to wait upon events signalled by
concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 0.13.2 dated 2024-03-01 and 0.13.5.1 dated 2024-04-05
nanonext-0.13.2/nanonext/man/sha256.Rd |only nanonext-0.13.5.1/nanonext/DESCRIPTION | 6 nanonext-0.13.5.1/nanonext/MD5 | 61 +++---- nanonext-0.13.5.1/nanonext/NAMESPACE | 5 nanonext-0.13.5.1/nanonext/NEWS.md | 11 + nanonext-0.13.5.1/nanonext/R/context.R | 17 +- nanonext-0.13.5.1/nanonext/R/messenger.R | 24 ++- nanonext-0.13.5.1/nanonext/R/nanonext-package.R | 5 nanonext-0.13.5.1/nanonext/R/socket.R | 6 nanonext-0.13.5.1/nanonext/R/tls.R | 83 ---------- nanonext-0.13.5.1/nanonext/R/utils.R | 24 ++- nanonext-0.13.5.1/nanonext/README.md | 24 +-- nanonext-0.13.5.1/nanonext/build/vignette.rds |binary nanonext-0.13.5.1/nanonext/inst/doc/nanonext.Rmd | 65 ++------ nanonext-0.13.5.1/nanonext/inst/doc/nanonext.html | 46 +---- nanonext-0.13.5.1/nanonext/man/base64enc.Rd | 3 nanonext-0.13.5.1/nanonext/man/messenger.Rd | 10 - nanonext-0.13.5.1/nanonext/man/nanonext-package.Rd | 4 nanonext-0.13.5.1/nanonext/man/next_config.Rd | 22 ++ nanonext-0.13.5.1/nanonext/man/reply.Rd | 6 nanonext-0.13.5.1/nanonext/man/request.Rd | 9 - nanonext-0.13.5.1/nanonext/man/socket.Rd | 6 nanonext-0.13.5.1/nanonext/src/Makevars.win | 4 nanonext-0.13.5.1/nanonext/src/aio.c | 4 nanonext-0.13.5.1/nanonext/src/core.c | 135 ++++++++++++----- nanonext-0.13.5.1/nanonext/src/init.c | 15 + nanonext-0.13.5.1/nanonext/src/nanonext.h | 10 - nanonext-0.13.5.1/nanonext/src/protocol.c | 4 nanonext-0.13.5.1/nanonext/src/tls.c | 122 --------------- nanonext-0.13.5.1/nanonext/tests/tests.R | 20 -- nanonext-0.13.5.1/nanonext/vignettes/nanonext.Rmd | 65 ++------ nanonext-0.13.5.1/nanonext/vignettes/nanonext.Rmd.orig | 44 +---- 32 files changed, 340 insertions(+), 520 deletions(-)
Title: Bivariate Copula Functions Based on Regular Grid
Description: Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.
Author: Rogelio Salinas Gutierrez [aut, cre, cph]
,
Angelica Hernandez Quintero [aut, cph]
,
Pedro Abraham Montoya Calzada [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rsalinas@correo.uaa.mx>
Diff between GRIDCOPULA versions 1.0.0 dated 2022-09-13 and 1.0.1 dated 2024-04-05
GRIDCOPULA-1.0.0/GRIDCOPULA/R/contour_color_grid.R |only GRIDCOPULA-1.0.0/GRIDCOPULA/R/normal_color_contour_grid.R |only GRIDCOPULA-1.0.0/GRIDCOPULA/R/normal_contour_grid.R |only GRIDCOPULA-1.0.0/GRIDCOPULA/R/rho_integrand_grid.R |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/calculate.ls.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/calculate.ml.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/cdf.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/contour_color_grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/count.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/equalities.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/ll.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/mi.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/normal.color.contour.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/normal.contour.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/normal.multiplication.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/objective.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/pdf.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/r.cond.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/rho.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/rho.integrand.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/tau.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/tau.integrand.grid.Rd |only GRIDCOPULA-1.0.0/GRIDCOPULA/man/validate.density.Rd |only GRIDCOPULA-1.0.1/GRIDCOPULA/DESCRIPTION | 27 + GRIDCOPULA-1.0.1/GRIDCOPULA/MD5 | 78 ++--- GRIDCOPULA-1.0.1/GRIDCOPULA/NAMESPACE | 14 GRIDCOPULA-1.0.1/GRIDCOPULA/R/aic_grid.R | 4 GRIDCOPULA-1.0.1/GRIDCOPULA/R/blomqvist_grid.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/calculate_ls.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/calculate_ml.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/cdf_grid.R | 53 ++- GRIDCOPULA-1.0.1/GRIDCOPULA/R/contour_grid.R | 145 +++++++++- GRIDCOPULA-1.0.1/GRIDCOPULA/R/count_grid.R | 28 + GRIDCOPULA-1.0.1/GRIDCOPULA/R/estimate_gridCopula.R | 157 +++++------ GRIDCOPULA-1.0.1/GRIDCOPULA/R/gini_grid.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/kernel_multiplication.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/measures_grid.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/normal_multiplication.R | 8 GRIDCOPULA-1.0.1/GRIDCOPULA/R/pdf_grid.R | 33 +- GRIDCOPULA-1.0.1/GRIDCOPULA/R/rho_grid.R | 23 - GRIDCOPULA-1.0.1/GRIDCOPULA/R/schweizer_grid.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/tailL_grid.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/R/tailU_grid.R |only GRIDCOPULA-1.0.1/GRIDCOPULA/README.md |only GRIDCOPULA-1.0.1/GRIDCOPULA/man/aic.grid.Rd | 11 GRIDCOPULA-1.0.1/GRIDCOPULA/man/bic.grid.Rd | 12 GRIDCOPULA-1.0.1/GRIDCOPULA/man/contour_grid.Rd | 102 ++++--- GRIDCOPULA-1.0.1/GRIDCOPULA/man/contour_image_grid.Rd | 9 GRIDCOPULA-1.0.1/GRIDCOPULA/man/d.grid.Rd | 75 ++--- GRIDCOPULA-1.0.1/GRIDCOPULA/man/data.grid.Rd | 6 GRIDCOPULA-1.0.1/GRIDCOPULA/man/estimate.gridCopula.Rd | 44 +-- GRIDCOPULA-1.0.1/GRIDCOPULA/man/image_color_grid.Rd | 4 GRIDCOPULA-1.0.1/GRIDCOPULA/man/measures.grid.Rd |only GRIDCOPULA-1.0.1/GRIDCOPULA/man/mosaic.grid.Rd | 4 GRIDCOPULA-1.0.1/GRIDCOPULA/man/p.grid.Rd | 75 ++--- GRIDCOPULA-1.0.1/GRIDCOPULA/man/perspective.grid.Rd | 9 GRIDCOPULA-1.0.1/GRIDCOPULA/man/r.grid.Rd | 17 - 57 files changed, 563 insertions(+), 375 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.5.1 dated 2023-11-21 and 0.6.0 dated 2024-04-05
DESCRIPTION | 8 - MD5 | 54 ++++--- NAMESPACE | 5 NEWS.md | 13 + R/geom_stripped_rows.R | 21 --- R/gglikert.R | 116 ++++++++++++++-- R/ggstats-package.R | 2 R/hex_bw.R |only R/label_number_abs.R | 3 R/round_any.R |only inst/WORDLIST | 3 inst/doc/ggcoef_model.R | 5 inst/doc/ggcoef_model.Rmd | 5 inst/doc/ggcoef_model.html | 205 +++++++++++++++++++++++++++--- inst/doc/gglikert.html | 54 +++---- inst/doc/stat_cross.html | 4 inst/doc/stat_prop.html | 16 +- inst/doc/stat_weighted_mean.html | 8 - man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/gglikert.Rd | 40 ++++- man/hex_bw.Rd |only man/label_number_abs.Rd | 3 man/round_any.Rd |only tests/testthat/test-ggcoef_model.R | 1 tests/testthat/test-gglikert.R | 31 ++++ vignettes/ggcoef_model.Rmd | 5 30 files changed, 464 insertions(+), 138 deletions(-)
Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components:
horizontal versions of 'Stats' and 'Geoms', and vertical versions
of 'Positions'. This package is now superseded by 'ggplot2' itself
which now has full native support for horizontal layouts. It
remains available for backward compatibility.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between ggstance versions 0.3.6 dated 2022-11-15 and 0.3.7 dated 2024-04-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/stat-boxploth.R | 3 +++ tests/testthat.R | 4 +--- 5 files changed, 17 insertions(+), 11 deletions(-)
Title: Miscellaneous Functions for the Analysis of Educational
Assessments
Description: Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive
analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep',
'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN').
The function for defining (weighted) contrasts in weighted effect coding refers to
te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>.
Functions for weighted statistics refer to
Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Author: Sebastian Weirich [aut, cre],
Martin Hecht [aut],
Karoline Sachse [aut],
Benjamin Becker [aut],
Nicole Mahler [aut],
Edna Grewers [ctb]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatTools versions 0.7.5 dated 2023-11-23 and 0.7.6 dated 2024-04-05
DESCRIPTION | 14 - MD5 | 72 +++--- NAMESPACE | 2 NEWS.md | 7 R/asNumericIfPossible.R | 194 ++++++++--------- R/catch_asNumericIfPossible.R | 33 +- R/contr.wec.weighted.r | 1 R/descr.r | 2 R/existsBackgroundVariables.r | 8 R/facToChar.r | 2 R/makeDataFrame.r | 4 R/makeTria.r | 16 - R/mergeAttr.r | 3 R/multiseq.r | 1 R/operator.r |only R/print_and_capture.r | 2 R/rbind_common.r | 12 + R/readMultisep.R | 25 +- R/recodeLookup.r | 2 R/remove_funs.R | 96 ++++---- R/seq2.R | 20 - R/tablePattern.r | 3 R/tableUnlist.r | 5 R/whereAre.r | 41 +-- R/wtdTable.r | 3 R/wtdVar.r | 2 man/makeTria.rd | 10 man/operator.Rd |only man/rbind_fill_vector.rd |only man/readMultisep.Rd | 5 man/removePattern.Rd | 14 - tests/testthat/test_asNumericIfPossible.R | 331 +++++++++++++++--------------- tests/testthat/test_insert.col.R | 2 tests/testthat/test_makeDataFrame.R | 6 tests/testthat/test_readMultisep.R |only tests/testthat/test_recodeLookup.R | 2 tests/testthat/test_remove_funs.R | 23 +- tests/testthat/test_seq2.R | 36 ++- tests/testthat/test_tableUnlist.R | 2 39 files changed, 565 insertions(+), 436 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.1.2 dated 2024-03-05 and 1.1.3 dated 2024-04-05
DESCRIPTION | 6 +- MD5 | 12 ++-- NEWS.md | 5 + R/file_functions.R | 88 ++++++++++++++++++++++++++++------- R/syspath.R | 65 +++++++++++++++++++++---- man/source.all.Rd | 17 +++++- tests/testthat/test-file_functions.R | 33 ++++++++++++- 7 files changed, 185 insertions(+), 41 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.14.0 dated 2023-08-07 and 1.15.0 dated 2024-04-05
DESCRIPTION | 18 - MD5 | 94 +++---- NAMESPACE | 4 NEWS.md | 19 + R/custom_tidiers.R | 23 + R/helpers.R | 15 + R/marginal_tidiers.R | 1 R/model_get_coefficients_type.R | 6 R/model_get_model_matrix.R | 9 R/model_get_terms.R | 15 + R/model_get_weights.R | 10 R/select_helpers.R | 2 R/tidy_disambiguate_terms.R | 6 R/tidy_identify_variables.R | 2 R/tidy_plus_plus.R | 12 README.md | 139 +++++----- build/vignette.rds |binary data/supported_models.rda |binary inst/WORDLIST | 1 inst/doc/tidy.R | 10 inst/doc/tidy.html | 394 +++++++++++++++---------------- man/model_compute_terms_contributions.Rd | 6 man/model_get_assign.Rd | 6 man/model_get_coefficients_type.Rd | 9 man/model_get_contrasts.Rd | 6 man/model_get_model.Rd | 4 man/model_get_model_frame.Rd | 6 man/model_get_model_matrix.Rd | 14 - man/model_get_n.Rd | 4 man/model_get_nlevels.Rd | 4 man/model_get_offset.Rd | 6 man/model_get_pairwise_contrasts.Rd | 6 man/model_get_response.Rd | 4 man/model_get_response_variable.Rd | 4 man/model_get_terms.Rd | 8 man/model_get_weights.Rd | 14 - man/model_get_xlevels.Rd | 6 man/model_identify_variables.Rd | 6 man/model_list_contrasts.Rd | 6 man/model_list_higher_order_variables.Rd | 6 man/model_list_terms_levels.Rd | 6 man/model_list_variables.Rd | 6 man/select_helpers.Rd | 2 man/supported_models.Rd | 6 man/tidy_plus_plus.Rd | 11 tests/testthat/test-identify_variables.R | 9 tests/testthat/test-marginal_tidiers.R | 8 tests/testthat/test-tidy_plus_plus.R | 74 +++++ 48 files changed, 627 insertions(+), 400 deletions(-)
Title: Bayesian Quantile Elastic Net for Genetic Study
Description: As heavy-tailed error distribution and outliers in the response variable widely exist, models which are robust to data contamination are highly demanded. Here, we develop a novel robust Bayesian variable selection method with elastic net penalty for quantile regression in genetic analysis. In particular, the spike-and-slab priors have been incorporated to impose sparsity. An efficient Gibbs sampler has been developed to facilitate computation.The core modules of the package have been developed in 'C++' and R.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu@ksu.edu>
Diff between Bayenet versions 0.1 dated 2023-05-24 and 0.2 dated 2024-04-05
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/Bayenet-package.R | 4 ++-- R/Bayenet.R | 8 ++++---- build/partial.rdb |binary man/Bayenet-package.Rd | 5 +++-- man/Bayenet.Rd | 8 ++++---- 7 files changed, 24 insertions(+), 23 deletions(-)
Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).
Author: Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen
Maintainer: Van-Dung Pham <dvp0001@auburn.edu>
Diff between PINSPlus versions 2.0.6 dated 2021-12-14 and 2.0.7 dated 2024-04-05
DESCRIPTION | 12 - MD5 | 18 - build/vignette.rds |binary inst/doc/PINSPlus.R | 50 ++-- inst/doc/PINSPlus.html | 504 +++++++++++++++++-------------------------------- man/AML2004.Rd | 2 man/KIRC.Rd | 4 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 5 10 files changed, 232 insertions(+), 365 deletions(-)
Title: Kinship Analysis with Linked Markers
Description: A 'shiny' application for forensic kinship testing, based on
the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R)
software 'Familias' and 'FamLink', but offers several unique features,
including visualisations and automated report generation. The
calculation of likelihood ratios supports pairs of linked markers, and
all common mutation models.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between KLINK versions 0.7.2 dated 2023-11-09 and 0.7.3 dated 2024-04-05
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 15 +++++++++++++++ R/plotPed.R | 6 ++---- R/prettyTable.R | 6 ++++-- R/utils.R | 15 --------------- R/writeResult.R | 12 ++++++++++-- data/LINKAGEMAP.rda |binary data/paternity.rda |binary inst/shiny/app.R | 30 ++++++++++++++++++++++++------ 10 files changed, 69 insertions(+), 43 deletions(-)
More information about BayesianMCPMod at CRAN
Permanent link
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.4.0 dated 2024-03-25 and 0.5.0 dated 2024-04-05
DESCRIPTION | 6 MD5 | 47 ++-- NAMESPACE | 4 NEWS.md | 27 ++ R/cpp11.R | 56 +++- R/extras.R | 9 R/factors.R | 10 R/nas.R | 7 R/overview.R | 113 ++++----- R/scalars.R |only R/sequences.R | 6 R/sset.R | 175 +++++++++++++-- R/utils.R | 56 ++++ README.md | 155 +++++++------ man/count_val.Rd |only man/is_na.Rd | 3 man/sset.Rd | 29 ++ src/attrs.cpp |only src/cheapr_cpp.h | 7 src/cpp11.cpp | 108 +++++++-- src/nas.cpp | 431 +++++++++++++++++++++++++------------- src/sequences.cpp | 2 src/sset.cpp |only src/utils.cpp | 194 ++++++----------- src/which.cpp | 171 +++++++++++++-- tests/testthat/_snaps/overview.md | 368 ++++++++++++++++---------------- tests/testthat/test-sset.R |only 27 files changed, 1282 insertions(+), 702 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-09 0.1.0
Title: Use Data from the Czech Public Finance Database
Description: Get programmatic access to data from the Czech public
budgeting and accounting database, Státní pokladna
<https://monitor.statnipokladna.cz/>.
Author: Petr Bouchal [aut, cre]
Maintainer: Petr Bouchal <pbouchal@gmail.com>
Diff between statnipokladna versions 0.7.2 dated 2022-12-12 and 0.7.3 dated 2024-04-05
DESCRIPTION | 8 - MD5 | 34 ++++---- NEWS.md | 5 + R/codelists.R | 6 - R/tables.R | 14 ++- README.md | 28 +++--- build/vignette.rds |binary inst/doc/data-issues-cz.R | 2 inst/doc/how-the-data-works-cz.R | 2 inst/doc/how-the-data-works.R | 2 inst/doc/statnipokladna.R | 2 inst/doc/workflow.html | 159 ++++++++++++++++++++------------------- man/sp_get_codelist_file.Rd | 2 man/sp_get_codelist_url.Rd | 2 man/sp_get_table_file.Rd | 2 man/sp_load_codelist.Rd | 2 man/sp_load_table.Rd | 2 tests/testthat/test-tables.R | 4 18 files changed, 150 insertions(+), 126 deletions(-)
More information about statnipokladna at CRAN
Permanent link
Title: Monte Carlo Data Simulation Package
Description: Monte Carlo simulation allows testing different conditions given to the correct structural equation models. This package runs Monte Carlo simulations under different conditions (such as sample size or normality of data). Within the package data sets can be simulated and run based on the given model.
First, continuous and normal data sets are generated based on the given model. Later Fleishman's power method (1978) <DOI:10.1007/BF02293811> is used to add non-normality if exists.
When data generation is completed (or when generated data sets are given) model test can also be run.
Please cite as "Orçan, F. (2021). MonteCarloSEM: An R Package to Simulate Data for SEM. International Journal of Assessment Tools in Education, 8 (3), 704-713."
Author: Fatih Orcan [aut, cre]
Maintainer: Fatih Orcan <fatihorcan84@gmail.com>
Diff between MonteCarloSEM versions 0.0.7 dated 2024-03-29 and 0.0.8 dated 2024-04-05
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/run.sem.sim.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Visualization of Clonal Expansion for Single Cell Immune
Profiles
Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Author: Qile Yang [cre, aut, cph]
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Diff between APackOfTheClones versions 1.0.0 dated 2024-01-13 and 1.1.0 dated 2024-04-05
APackOfTheClones-1.0.0/APackOfTheClones/R/aes_string.R |only APackOfTheClones-1.0.0/APackOfTheClones/R/parameter_estimators.R |only APackOfTheClones-1.0.0/APackOfTheClones/src/CircleNode.h |only APackOfTheClones-1.0.0/APackOfTheClones/src/IndexMapper.h |only APackOfTheClones-1.0.0/APackOfTheClones/src/ProgressBar.h |only APackOfTheClones-1.0.0/APackOfTheClones/tests/testthat/_snaps/AdjustAPOTC |only APackOfTheClones-1.0.0/APackOfTheClones/tests/testthat/_snaps/plot_API |only APackOfTheClones-1.0.0/APackOfTheClones/tests/testthat/testdata/deprecated_functions |only APackOfTheClones-1.1.0/APackOfTheClones/DESCRIPTION | 12 APackOfTheClones-1.1.0/APackOfTheClones/MD5 | 161 +- APackOfTheClones-1.1.0/APackOfTheClones/NAMESPACE | 9 APackOfTheClones-1.1.0/APackOfTheClones/R/APOTCPlot.R | 201 ++ APackOfTheClones-1.1.0/APackOfTheClones/R/APackOfTheClones-package.R | 2 APackOfTheClones-1.1.0/APackOfTheClones/R/AdjustAPOTC.R | 200 +- APackOfTheClones-1.1.0/APackOfTheClones/R/ApotcClonalNetwork.R |only APackOfTheClones-1.1.0/APackOfTheClones/R/ApotcData.R | 73 - APackOfTheClones-1.1.0/APackOfTheClones/R/ApotcIndexing.R | 78 - APackOfTheClones-1.1.0/APackOfTheClones/R/Main_algo.R | 9 APackOfTheClones-1.1.0/APackOfTheClones/R/RcppExports.R | 20 APackOfTheClones-1.1.0/APackOfTheClones/R/Repulsion.R | 102 - APackOfTheClones-1.1.0/APackOfTheClones/R/RunAPOTC.R | 125 - APackOfTheClones-1.1.0/APackOfTheClones/R/clusters.R | 94 - APackOfTheClones-1.1.0/APackOfTheClones/R/colors.R | 37 APackOfTheClones-1.1.0/APackOfTheClones/R/data.R | 15 APackOfTheClones-1.1.0/APackOfTheClones/R/deprecated_functions.R | 186 -- APackOfTheClones-1.1.0/APackOfTheClones/R/get_clone_sizes.R | 270 ++- APackOfTheClones-1.1.0/APackOfTheClones/R/ggplot2_functions.R |only APackOfTheClones-1.1.0/APackOfTheClones/R/insert_legend.R | 329 +++- APackOfTheClones-1.1.0/APackOfTheClones/R/plot_API.R | 107 - APackOfTheClones-1.1.0/APackOfTheClones/R/showCloneHighlight.R |only APackOfTheClones-1.1.0/APackOfTheClones/R/typecheck.R |only APackOfTheClones-1.1.0/APackOfTheClones/R/utils.R | 414 +++-- APackOfTheClones-1.1.0/APackOfTheClones/R/vizAPOTC.R | 32 APackOfTheClones-1.1.0/APackOfTheClones/R/zzz.R | 6 APackOfTheClones-1.1.0/APackOfTheClones/build/vignette.rds |binary APackOfTheClones-1.1.0/APackOfTheClones/inst/WORDLIST | 21 APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-install.R |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-install.Rmd |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-install.html |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.R | 104 + APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.Rmd | 126 + APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.html | 263 +++ APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-shared.R |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-shared.Rmd |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-shared.html |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-utils.R |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-utils.Rmd |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones-utils.html |only APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones.R | 49 APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones.Rmd | 103 - APackOfTheClones-1.1.0/APackOfTheClones/inst/doc/APackOfTheClones.html | 240 ++- APackOfTheClones-1.1.0/APackOfTheClones/man/APOTCPlot.Rd | 52 APackOfTheClones-1.1.0/APackOfTheClones/man/AdjustAPOTC.Rd | 35 APackOfTheClones-1.1.0/APackOfTheClones/man/combined_pbmc.Rd | 5 APackOfTheClones-1.1.0/APackOfTheClones/man/countCloneSizes.Rd | 31 APackOfTheClones-1.1.0/APackOfTheClones/man/count_clone_sizes.Rd | 42 APackOfTheClones-1.1.0/APackOfTheClones/man/getSharedClones.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/man/integrate_tcr.Rd | 46 APackOfTheClones-1.1.0/APackOfTheClones/man/mergeCloneSizes.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/man/mini_clonotype_data.Rd | 2 APackOfTheClones-1.1.0/APackOfTheClones/man/mini_seurat_obj.Rd | 2 APackOfTheClones-1.1.0/APackOfTheClones/man/overlayLegend.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/man/removeLegend.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/man/showCloneHighlight.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/man/vizAPOTC.Rd | 56 APackOfTheClones-1.1.0/APackOfTheClones/src/APOTCPlotHelpers.cpp |only APackOfTheClones-1.1.0/APackOfTheClones/src/AdjustAPOTCHelpers.cpp |only APackOfTheClones-1.1.0/APackOfTheClones/src/Circle.h |only APackOfTheClones-1.1.0/APackOfTheClones/src/CirclePacker.h | 121 - APackOfTheClones-1.1.0/APackOfTheClones/src/CloneLinkHelpers.cpp |only APackOfTheClones-1.1.0/APackOfTheClones/src/ClusterList.h |only APackOfTheClones-1.1.0/APackOfTheClones/src/RcppExports.cpp | 69 APackOfTheClones-1.1.0/APackOfTheClones/src/dataConversion.h |only APackOfTheClones-1.1.0/APackOfTheClones/src/exportedMathUtils.cpp |only APackOfTheClones-1.1.0/APackOfTheClones/src/math.h |only APackOfTheClones-1.1.0/APackOfTheClones/src/repulsion.cpp | 3 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/_snaps/ApotcClonalNetwork |only APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/_snaps/noscript-defaultApotcPlot/default-apotcplot.svg | 703 ---------- APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/_snaps/vizAPOTC/sample19.svg | 243 --- APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-AdjustAPOTC.R | 133 + APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-ApotcClonalNetwork.R |only APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-ApotcData.R | 33 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-clusters.R | 6 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-colors.R | 32 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-deprecated_functions.R | 52 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-get_clone_sizes.R | 40 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-insert_legend.R | 22 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-noscript-defaultApotcPlot.R | 48 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-plot_API.R | 13 APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-showCloneHighlight.R |only APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-typecheck.R |only APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/test-utils.R | 80 - APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/testdata/ApotcClonalNetwork |only APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/testdata/combined_pbmc/expected_clusterlists.rds |binary APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/testdata/get_clone_sizes/raw_strict_clone_sizes.rds |binary APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/testdata/showCloneHighlight |only APackOfTheClones-1.1.0/APackOfTheClones/vignettes/APackOfTheClones-install.Rmd |only APackOfTheClones-1.1.0/APackOfTheClones/vignettes/APackOfTheClones-runs.Rmd | 126 + APackOfTheClones-1.1.0/APackOfTheClones/vignettes/APackOfTheClones-shared.Rmd |only APackOfTheClones-1.1.0/APackOfTheClones/vignettes/APackOfTheClones-utils.Rmd |only APackOfTheClones-1.1.0/APackOfTheClones/vignettes/APackOfTheClones.Rmd | 103 - APackOfTheClones-1.1.0/APackOfTheClones/vignettes/archive/v0-main.Rmd | 39 102 files changed, 3108 insertions(+), 2417 deletions(-)
More information about APackOfTheClones at CRAN
Permanent link
Title: Tests for Variance Homogeneity
Description: Performs 20 omnibus tests for testing the composite hypothesis of variance homogeneity.
Author: Gozde Cosar [aut],
Osman Dag [aut, cre]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between vartest versions 1.0 dated 2024-03-23 and 1.1 dated 2024-04-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/g.test.R | 4 ++-- R/hartley.test.R | 2 +- man/bartletts.test.Rd | 2 +- man/cochrans.test.Rd | 2 +- man/g.test.Rd | 2 +- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: Shorten Function Names of Functions in Another Package and
Create an Index to Make Them Accessible
Description: When creating a package, authors may sometimes struggle with coming up with easy and straightforward function names, and at the same time hoping that other packages do not already have the same function names. In trying to meet this goal, sometimes, function names are not descriptive enough and may confuse the potential users. The purpose of this package is to serve as a package function short form generator and also provide shorthand names for other functions. Having this package will entice authors to create long function names without the fear of users not wanting to use their packages because of the long names. In a way, everyone wins - the authors can use long descriptive function names, and the users can use this package to make short functions names while still using the package in question.
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2shortcode versions 0.1 dated 2020-06-25 and 0.2 dated 2024-04-05
r2shortcode-0.1/r2shortcode/R/aaa.R |only r2shortcode-0.2/r2shortcode/DESCRIPTION | 17 r2shortcode-0.2/r2shortcode/MD5 | 46 - r2shortcode-0.2/r2shortcode/R/discardShortcodes.R | 2 r2shortcode-0.2/r2shortcode/R/indexPkg.R | 5 r2shortcode-0.2/r2shortcode/R/r2shortcode-package.R |only r2shortcode-0.2/r2shortcode/README.md |only r2shortcode-0.2/r2shortcode/build/vignette.rds |binary r2shortcode-0.2/r2shortcode/inst/doc/simple_samples.R | 10 r2shortcode-0.2/r2shortcode/inst/doc/simple_samples.Rmd | 2 r2shortcode-0.2/r2shortcode/inst/doc/simple_samples.html | 395 ++++++++++++--- r2shortcode-0.2/r2shortcode/man/chooseShortName.Rd | 74 +- r2shortcode-0.2/r2shortcode/man/clearStoredNames.Rd | 50 - r2shortcode-0.2/r2shortcode/man/discardShortcodes.Rd | 66 +- r2shortcode-0.2/r2shortcode/man/hasSpecialCharacters.Rd | 48 - r2shortcode-0.2/r2shortcode/man/hasUpperCase.Rd | 50 - r2shortcode-0.2/r2shortcode/man/help.Rd | 56 +- r2shortcode-0.2/r2shortcode/man/index.Rd | 51 - r2shortcode-0.2/r2shortcode/man/isUpperCase.Rd | 50 - r2shortcode-0.2/r2shortcode/man/nameAlreadyExists.Rd | 44 - r2shortcode-0.2/r2shortcode/man/r2shortcode-package.Rd |only r2shortcode-0.2/r2shortcode/man/searchNameSaveName.Rd | 56 +- r2shortcode-0.2/r2shortcode/man/shortenPkg.Rd | 60 +- r2shortcode-0.2/r2shortcode/man/storeChosenName.Rd | 44 - r2shortcode-0.2/r2shortcode/man/whatis.Rd | 56 +- r2shortcode-0.2/r2shortcode/vignettes/simple_samples.Rmd | 2 26 files changed, 725 insertions(+), 459 deletions(-)
Title: Drug Response Modeling and Biomarker Discovery
Description: Allows for building drug response models using screening data between bulk RNA-Seq and a drug response metric and two additional tools for biomarker discovery that have been developed by the Huang Laboratory at University of Minnesota.
There are 3 main functions within this package.
(1) calcPhenotype is used to build drug response models on RNA-Seq data and impute them on any other RNA-Seq dataset given to the model.
(2) GLDS is used to calculate the general level of drug sensitivity, which can improve biomarker discovery.
(3) IDWAS can take the results from calcPhenotype and link the imputed response back to available genomic (mutation and CNV alterations) to identify biomarkers.
Each of these functions comes from a paper from the Huang research laboratory. Below gives the relevant paper for each function.
calcPhenotype - Geeleher et al, Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines.
GLDS - Geeleher et al, Can [...truncated...]
Author: Danielle Maeser [aut] ,
Robert Gruener [aut, cre]
Maintainer: Robert Gruener <rgruener@umn.edu>
Diff between oncoPredict versions 0.2 dated 2021-09-24 and 1.2 dated 2024-04-05
oncoPredict-0.2/oncoPredict/vignettes/maf.txt |only oncoPredict-1.2/oncoPredict/DESCRIPTION | 63 oncoPredict-1.2/oncoPredict/MD5 | 79 oncoPredict-1.2/oncoPredict/NAMESPACE | 3 oncoPredict-1.2/oncoPredict/R/CALCPHENOTYPE.R | 273 oncoPredict-1.2/oncoPredict/R/GLDS.R | 2 oncoPredict-1.2/oncoPredict/R/IDWAS.R | 171 oncoPredict-1.2/oncoPredict/README.md | 3 oncoPredict-1.2/oncoPredict/build/vignette.rds |binary oncoPredict-1.2/oncoPredict/inst/doc/calcPhenotype.R | 6 oncoPredict-1.2/oncoPredict/inst/doc/calcPhenotype.Rmd | 4 oncoPredict-1.2/oncoPredict/inst/doc/calcPhenotype.html | 2821 - oncoPredict-1.2/oncoPredict/inst/doc/cnv.R | 20 oncoPredict-1.2/oncoPredict/inst/doc/cnv.Rmd | 18 oncoPredict-1.2/oncoPredict/inst/doc/cnv.html | 297 oncoPredict-1.2/oncoPredict/inst/doc/glds.R | 5 oncoPredict-1.2/oncoPredict/inst/doc/glds.Rmd | 3 oncoPredict-1.2/oncoPredict/inst/doc/glds.html | 670 oncoPredict-1.2/oncoPredict/inst/doc/mut.R | 30 oncoPredict-1.2/oncoPredict/inst/doc/mut.Rmd | 47 oncoPredict-1.2/oncoPredict/inst/doc/mut.html | 251 oncoPredict-1.2/oncoPredict/man/calcPhenotype.Rd | 41 oncoPredict-1.2/oncoPredict/man/completeMatrix.Rd | 5 oncoPredict-1.2/oncoPredict/man/doVariableSelection.Rd | 11 oncoPredict-1.2/oncoPredict/man/glds.Rd | 16 oncoPredict-1.2/oncoPredict/man/homogenizeData.Rd | 10 oncoPredict-1.2/oncoPredict/man/idwas.Rd | 5 oncoPredict-1.2/oncoPredict/man/map_cnv.Rd | 5 oncoPredict-1.2/oncoPredict/man/summarizeGenesByMean.Rd | 7 oncoPredict-1.2/oncoPredict/vignettes/Cell_Lines_Details.csv | 2006 oncoPredict-1.2/oncoPredict/vignettes/DrugPredictions.txt | 396 oncoPredict-1.2/oncoPredict/vignettes/calcPhenotype.Rmd | 4 oncoPredict-1.2/oncoPredict/vignettes/cnv.Rmd | 18 oncoPredict-1.2/oncoPredict/vignettes/cnv.txt |24002 +++++----- oncoPredict-1.2/oncoPredict/vignettes/complete_matrix_output_GDSCv2.txt | 202 oncoPredict-1.2/oncoPredict/vignettes/gdscv2_drugs.txt | 398 oncoPredict-1.2/oncoPredict/vignettes/glds.Rmd | 3 oncoPredict-1.2/oncoPredict/vignettes/markerMat.txt | 1802 oncoPredict-1.2/oncoPredict/vignettes/mut.Rmd | 47 oncoPredict-1.2/oncoPredict/vignettes/prostate_test_data.txt | 2002 oncoPredict-1.2/oncoPredict/vignettes/screened_compunds_rel_8.2.csv | 1038 41 files changed, 18258 insertions(+), 18526 deletions(-)
Title: A Data Interface Between 'GAMS' and R
Description: Read, analyze, modify, and write 'GAMS' (General Algebraic
Modeling System) data. The main focus of 'gamstransfer' is the
highly efficient transfer of data with 'GAMS' <https://www.gams.com/>,
while keeping these operations as simple as possible for the user. The
transfer of data usually takes place via an intermediate GDX (GAMS Data
Exchange) file. Additionally, 'gamstransfer' provides utility
functions to get an overview of 'GAMS' data and to check its validity.
Author: Atharv Bhosekar [aut, cre],
GAMS Development Corp. [cph, fnd],
GAMS Software GmbH [cph, fnd]
Maintainer: Atharv Bhosekar <abhosekar@gams.com>
Diff between gamstransfer versions 3.0.1 dated 2024-03-28 and 3.0.2 dated 2024-04-05
DESCRIPTION | 8 +++--- MD5 | 38 ++++++++++++++--------------- NEWS.md | 4 +++ man/gamstransfer-package.Rd | 2 - src/gdx/src/gdlib/gmsobj.cpp | 3 ++ src/gdx/src/gdlib/gmsobj.h | 3 -- src/utilities.hpp | 8 ++---- tests/testthat/data.gdx |binary tests/testthat/empty.gdx |binary tests/testthat/foo.lst | 2 - tests/testthat/gt.gdx |binary tests/testthat/out.gdx |binary tests/testthat/partial_equation.gdx |binary tests/testthat/partial_parameter.gdx |binary tests/testthat/partial_scalar.gdx |binary tests/testthat/partial_scalar_equation.gdx |binary tests/testthat/partial_scalar_variable.gdx |binary tests/testthat/partial_set.gdx |binary tests/testthat/partial_variable.gdx |binary tests/testthat/partial_write.gdx |binary 20 files changed, 35 insertions(+), 33 deletions(-)
Title: Value Added in Exports and Other Input-Output Table Analysis
Tools
Description: Analysis of trade in value added with international
input-output tables. Includes commands for easy data extraction,
matrix manipulation, decomposition of value added in gross exports and
calculation of value added indicators, with full geographical and
sector customization. Decomposition methods include Borin and Mancini
(2023) <doi:10.1080/09535314.2022.2153221>, Miroudot and Ye (2021)
<doi:10.1080/09535314.2020.1730308>, Wang et al. (2013)
<https://econpapers.repec.org/paper/nbrnberwo/19677.htm> and Koopman
et al. (2014) <doi:10.1257/aer.104.2.459>.
Author: Enrique Feas [aut, cre]
Maintainer: Enrique Feas <efeas@runbox.com>
Diff between exvatools versions 0.7.0 dated 2024-03-21 and 0.8.0 dated 2024-04-05
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md | 11 ++++++++++- R/extract_figaro.R | 2 +- R/extract_mrio.R |only R/get_geo_codes.R | 8 +++++--- R/get_sec_codes.R | 6 ++++-- R/info_geosec.R | 18 ++++++++++++++---- R/make_wio.R | 25 +++++++++++++++++++------ R/sysdata.rda |binary inst/WORDLIST | 2 ++ inst/doc/exvatools.Rmd | 5 +++-- inst/doc/exvatools.html | 40 ++++++++++++++++++++++++---------------- man/make_wio.Rd | 19 +++++++++++++------ vignettes/exvatools.Rmd | 5 +++-- 15 files changed, 115 insertions(+), 59 deletions(-)
Title: Effect Size Targeted Bayesian Two-Sample t-Tests via Markov
Chain Monte Carlo in Gaussian Mixture Models
Description: Provides an Markov-Chain-Monte-Carlo algorithm for Bayesian t-tests on the effect size. The underlying Gibbs sampler is based on a two-component Gaussian mixture and approximates the posterior distributions of the effect size, the difference of means and difference of standard deviations. A posterior analysis of the effect size via the region of practical equivalence is provided, too. For more details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between bayest versions 1.4 dated 2020-05-30 and 1.5 dated 2024-04-05
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/bayest.R | 104 ++++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/bayes.t.test.Rd | 2 - 5 files changed, 65 insertions(+), 57 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.11.5 dated 2023-10-03 and 0.11.6 dated 2024-04-05
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS | 3 +++ R/03_modelformation_samplestats_norawts.R | 10 +++++----- build/partial.rdb |binary 5 files changed, 18 insertions(+), 15 deletions(-)
Title: Processing Hemispherical Canopy Images
Description: Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Author: Francesco Chianucci [aut, cre]
,
Martin Macek [aut]
Maintainer: Francesco Chianucci <fchianucci@gmail.com>
Diff between hemispheR versions 1.1.3 dated 2024-01-08 and 1.1.4 dated 2024-04-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: Tools to Calibrate and Work with NEON Atmospheric Isotope Data
Description: Functions for downloading,
calibrating, and analyzing atmospheric isotope data bundled
into the eddy covariance data products of the National Ecological
Observatory Network (NEON) <https://www.neonscience.org>.
Calibration tools are provided for carbon and water isotope products.
Carbon isotope calibration details are found in Fiorella et al. (2021)
<doi:10.1029/2020JG005862>, and the readme
file at <https://github.com/lanl/NEONiso>. Tools for calibrating water
isotope products have been added as of 0.6.0, but have known deficiencies
and should be considered very experimental currently.
Author: Rich Fiorella [aut, cre]
Maintainer: Rich Fiorella <rfiorella@lanl.gov>
Diff between NEONiso versions 0.6.4 dated 2023-09-20 and 0.7.0 dated 2024-04-05
NEONiso-0.6.4/NEONiso/R/calibrate_carbon_bymonth.R |only NEONiso-0.6.4/NEONiso/R/calibrate_standards_carbon.R |only NEONiso-0.6.4/NEONiso/R/calibrate_standards_water.R |only NEONiso-0.6.4/NEONiso/R/calibrate_water_linreg_bymonth.R |only NEONiso-0.6.4/NEONiso/man/calibrate_carbon_bymonth.Rd |only NEONiso-0.6.4/NEONiso/man/calibrate_carbon_reference_data.Rd |only NEONiso-0.6.4/NEONiso/man/calibrate_standards_carbon.Rd |only NEONiso-0.6.4/NEONiso/man/calibrate_standards_water.Rd |only NEONiso-0.6.4/NEONiso/man/calibrate_water_linreg_bymonth.Rd |only NEONiso-0.6.4/NEONiso/man/calibrate_water_reference_data.Rd |only NEONiso-0.6.4/NEONiso/man/extract_carbon_calibration_data.Rd |only NEONiso-0.6.4/NEONiso/man/restructure_ambient_data.Rd |only NEONiso-0.6.4/NEONiso/man/restructure_ambient_data2.Rd |only NEONiso-0.6.4/NEONiso/man/terrestrial_relocatable_sites.Rd |only NEONiso-0.6.4/NEONiso/man/write_carbon_reference_data.Rd |only NEONiso-0.6.4/NEONiso/man/write_water_reference_data.Rd |only NEONiso-0.7.0/NEONiso/DESCRIPTION | 12 NEONiso-0.7.0/NEONiso/MD5 | 125 - NEONiso-0.7.0/NEONiso/NAMESPACE | 7 NEONiso-0.7.0/NEONiso/NEWS.md | 9 NEONiso-0.7.0/NEONiso/R/calibrate_ambient_carbon_Bowling2003.R | 16 NEONiso-0.7.0/NEONiso/R/calibrate_ambient_carbon_linreg.R | 3 NEONiso-0.7.0/NEONiso/R/calibrate_ambient_water_isotopes.R | 69 - NEONiso-0.7.0/NEONiso/R/calibrate_carbon.R | 91 - NEONiso-0.7.0/NEONiso/R/calibrate_water.R | 248 --- NEONiso-0.7.0/NEONiso/R/excised.R |only NEONiso-0.7.0/NEONiso/R/isotope_conversions.R | 16 NEONiso-0.7.0/NEONiso/R/output_functions.R | 503 +------ NEONiso-0.7.0/NEONiso/R/quality_control.R | 32 NEONiso-0.7.0/NEONiso/R/reference_data_extraction.R | 156 -- NEONiso-0.7.0/NEONiso/R/reference_data_regression.R | 457 +++--- NEONiso-0.7.0/NEONiso/R/reference_data_selection.R | 4 NEONiso-0.7.0/NEONiso/R/restructure_data.R | 682 ++++------ NEONiso-0.7.0/NEONiso/R/standard_corrections.R | 65 NEONiso-0.7.0/NEONiso/R/sysdata.rda |binary NEONiso-0.7.0/NEONiso/R/utility_functions.R | 57 NEONiso-0.7.0/NEONiso/build/partial.rdb |binary NEONiso-0.7.0/NEONiso/build/vignette.rds |binary NEONiso-0.7.0/NEONiso/inst/doc/example_workflow.R | 32 NEONiso-0.7.0/NEONiso/inst/doc/example_workflow.Rmd | 26 NEONiso-0.7.0/NEONiso/inst/doc/example_workflow.html | 24 NEONiso-0.7.0/NEONiso/inst/doc/reference_corrections.R | 4 NEONiso-0.7.0/NEONiso/inst/extdata/NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.packed.h5 |binary NEONiso-0.7.0/NEONiso/man/calculate_12CO2.Rd | 6 NEONiso-0.7.0/NEONiso/man/calculate_13CO2.Rd | 6 NEONiso-0.7.0/NEONiso/man/calibrate_ambient_carbon_linreg.Rd | 4 NEONiso-0.7.0/NEONiso/man/calibrate_ambient_water_linreg.Rd | 12 NEONiso-0.7.0/NEONiso/man/calibrate_carbon.Rd | 19 NEONiso-0.7.0/NEONiso/man/calibrate_water.Rd | 24 NEONiso-0.7.0/NEONiso/man/copy_qfqm_group.Rd | 2 NEONiso-0.7.0/NEONiso/man/copy_ucrt_group.Rd | 2 NEONiso-0.7.0/NEONiso/man/correct_carbon_ref_output.Rd | 4 NEONiso-0.7.0/NEONiso/man/extract_carbon_cal_data.Rd |only NEONiso-0.7.0/NEONiso/man/extract_water_calibration_data.Rd | 22 NEONiso-0.7.0/NEONiso/man/fit_water_regression.Rd | 24 NEONiso-0.7.0/NEONiso/man/ingest_data.Rd | 6 NEONiso-0.7.0/NEONiso/man/manage_local_EC_archive.Rd | 6 NEONiso-0.7.0/NEONiso/man/restructure_variables.Rd |only NEONiso-0.7.0/NEONiso/man/restructure_water_variables.Rd | 4 NEONiso-0.7.0/NEONiso/man/terrestrial_gradient_sites.Rd |only NEONiso-0.7.0/NEONiso/man/write_carbon_ambient_data.Rd | 4 NEONiso-0.7.0/NEONiso/man/write_carbon_calibration_data.Rd | 6 NEONiso-0.7.0/NEONiso/man/write_qfqm.Rd | 2 NEONiso-0.7.0/NEONiso/man/write_ucrt.Rd | 2 NEONiso-0.7.0/NEONiso/man/write_water_ambient_data.Rd |only NEONiso-0.7.0/NEONiso/man/write_water_calibration_data.Rd | 4 NEONiso-0.7.0/NEONiso/tests/testthat/test-data_extraction.R | 66 NEONiso-0.7.0/NEONiso/tests/testthat/test-data_ingestion.R | 48 NEONiso-0.7.0/NEONiso/tests/testthat/test-data_regression.R | 218 +-- NEONiso-0.7.0/NEONiso/tests/testthat/test-high_level_functions.R | 92 - NEONiso-0.7.0/NEONiso/tests/testthat/test-output_values.R | 92 - NEONiso-0.7.0/NEONiso/tests/testthat/test-standard_corrections.R | 18 NEONiso-0.7.0/NEONiso/tests/testthat/test-utility_functions.R | 11 NEONiso-0.7.0/NEONiso/vignettes/example_workflow.Rmd | 26 74 files changed, 1364 insertions(+), 2004 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-14 2.0-2
2015-09-24 0.1-5
2015-06-23 0.1-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-16 0.2.0
2019-01-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-06-29 0.0.9
2023-05-01 0.0.8
2023-02-24 0.0.7