Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.7-47 dated 2020-06-01 and 0.7-70 dated 2020-09-19
DESCRIPTION | 18 +- MD5 | 87 ++++++----- NAMESPACE | 83 ++++++----- R/ancThresh.R | 109 ++++++++++---- R/branching.diffusion.R | 4 R/brownie.lite.R | 34 ++-- R/contMap.R | 5 R/ctt.R | 7 R/drop.tip.simmap.R | 26 +++ R/fastAnc.R | 4 R/fitHRM.R |only R/fitMk.R | 135 ++++++++++++++---- R/fitPagel.R | 16 +- R/fitmultiMk.R | 4 R/fitpolyMk.R | 331 +++++++++++++++++++++++++++++++++++++++------ R/ltt.R | 8 - R/make.simmap.R | 4 R/phenogram.R | 69 ++++++--- R/phyl.pca.R | 9 - R/phylo.heatmap.R | 17 +- R/phylo.to.map.R | 23 ++- R/phylomorphospace.R | 6 R/phylosig.R | 25 ++- R/plotBranchbyTrait.R | 164 ++++++++++++++++++++++ R/plotTree.datamatrix.R | 18 +- R/rateshift.R | 70 ++++++--- R/rerootingMethod.R | 25 ++- R/simBMphylo.R | 6 R/threshBayes.R | 47 ++++-- R/utilities.R | 17 +- data/datalist | 4 data/flatworm.data.rda |only data/flatworm.tree.rda |only data/mammal.data.rda |binary data/mammal.tree.rda |binary data/vertebrate.data.rda |only data/vertebrate.tree.rda |only man/anoletree.Rd | 20 ++ man/as.Qmatrix.Rd | 4 man/drop.tip.contMap.Rd | 6 man/drop.tip.multiPhylo.Rd |only man/edge.widthMap.Rd |only man/fitMk.Rd | 45 +++++- man/phylomorphospace.Rd | 2 man/phytools-package.Rd | 2 man/plotTree.Rd | 6 man/plotTree.wBars.Rd | 15 ++ man/strahlerNumber.Rd | 2 48 files changed, 1137 insertions(+), 340 deletions(-)
Title: Power Analysis for Meta-Analysis
Description: A simple and effective tool for computing and visualizing statistical power for meta-analysis,
including power analysis of main effects, test of homogeneity, subgroup analysis, and categorical moderator analysis.
Author: Jason Griffin [aut, cre]
Maintainer: Jason Griffin <jasongriffin138@gmail.com>
Diff between metapower versions 0.1.0 dated 2020-04-07 and 0.2.0 dated 2020-09-19
metapower-0.1.0/metapower/R/homogen_power_plot.R |only metapower-0.1.0/metapower/R/power_plot.R |only metapower-0.1.0/metapower/R/print.modpower.R |only metapower-0.1.0/metapower/man/figures/logo.png |only metapower-0.1.0/metapower/man/figures/meta_logo.png |only metapower-0.1.0/metapower/man/homogen_power_plot.Rd |only metapower-0.1.0/metapower/man/power_plot.Rd |only metapower-0.2.0/metapower/DESCRIPTION | 18 metapower-0.2.0/metapower/MD5 | 95 ++- metapower-0.2.0/metapower/NAMESPACE | 25 metapower-0.2.0/metapower/NEWS.md | 17 metapower-0.2.0/metapower/R/CDF.R |only metapower-0.2.0/metapower/R/compute_homogen_power.R |only metapower-0.2.0/metapower/R/compute_homogen_range.R | 33 - metapower-0.2.0/metapower/R/compute_mod_power.R | 68 -- metapower-0.2.0/metapower/R/compute_mod_range.R |only metapower-0.2.0/metapower/R/compute_power.R | 50 + metapower-0.2.0/metapower/R/compute_power_range.R | 43 - metapower-0.2.0/metapower/R/compute_subgroup_power.R |only metapower-0.2.0/metapower/R/compute_subgroup_range.R |only metapower-0.2.0/metapower/R/compute_variance.R | 5 metapower-0.2.0/metapower/R/func.R |only metapower-0.2.0/metapower/R/homogen_power.R | 154 ++++-- metapower-0.2.0/metapower/R/homogen_power_integrity.R |only metapower-0.2.0/metapower/R/mod_power.R | 254 ++++------ metapower-0.2.0/metapower/R/mod_power_integrity.R |only metapower-0.2.0/metapower/R/mpower.R | 133 +++-- metapower-0.2.0/metapower/R/mpower_integrity.R | 75 +- metapower-0.2.0/metapower/R/plot_homogen_power.R |only metapower-0.2.0/metapower/R/plot_mod_power.R |only metapower-0.2.0/metapower/R/plot_mpower.R |only metapower-0.2.0/metapower/R/plot_subgroup_power.R |only metapower-0.2.0/metapower/R/print.homogen_power.R |only metapower-0.2.0/metapower/R/print.mod_power.R |only metapower-0.2.0/metapower/R/print.mpower.R | 28 - metapower-0.2.0/metapower/R/print.subgroup_power.R |only metapower-0.2.0/metapower/R/subgroup_power.R |only metapower-0.2.0/metapower/R/subgroup_power_integrity.R |only metapower-0.2.0/metapower/R/summary.homogen_power.R |only metapower-0.2.0/metapower/R/summary.mod_power.R |only metapower-0.2.0/metapower/R/summary.mpower.R |only metapower-0.2.0/metapower/R/summary.subgroup_power.R |only metapower-0.2.0/metapower/README.md | 134 +++-- metapower-0.2.0/metapower/build/vignette.rds |binary metapower-0.2.0/metapower/inst/CITATION | 6 metapower-0.2.0/metapower/inst/doc/Using-metapower.R | 12 metapower-0.2.0/metapower/inst/doc/Using-metapower.Rmd | 41 - metapower-0.2.0/metapower/inst/doc/Using-metapower.html | 226 ++++---- metapower-0.2.0/metapower/inst/metapower.bib | 13 metapower-0.2.0/metapower/inst/shiny_metapower |only metapower-0.2.0/metapower/man/figures/README-unnamed-chunk-3-1.png |binary metapower-0.2.0/metapower/man/figures/metapower_sticker.png |binary metapower-0.2.0/metapower/man/homogen_power.Rd |only metapower-0.2.0/metapower/man/mod_power.Rd | 50 - metapower-0.2.0/metapower/man/mpower.Rd | 30 - metapower-0.2.0/metapower/man/plot_homogen_power.Rd |only metapower-0.2.0/metapower/man/plot_mod_power.Rd |only metapower-0.2.0/metapower/man/plot_mpower.Rd |only metapower-0.2.0/metapower/man/plot_subgroup_power.Rd |only metapower-0.2.0/metapower/man/subgroup_power.Rd |only metapower-0.2.0/metapower/tests/testthat.R | 3 metapower-0.2.0/metapower/tests/testthat/test-input-output.R | 30 + metapower-0.2.0/metapower/tests/testthat/test-published-calc.R | 61 +- metapower-0.2.0/metapower/vignettes/Using-metapower.Rmd | 41 - 64 files changed, 917 insertions(+), 728 deletions(-)
Title: Computational Methods for Economic Complexity
Description: A wrapper of different methods from Linear Algebra for the equations
introduced in The Atlas of Economic Complexity and related literature. This
package provides standard matrix and graph output that can be used seamlessly
with other packages.
Author: Mauricio Vargas [aut, cre, cph]
(<https://orcid.org/0000-0003-1017-7574>),
Carlo Bottai [ctb] (improved the eigenvalues calculation),
Diego Kozlowski [ctb] (provided initial RCA function used up to v0.2.4),
Nico Pintar [rev] (suggested improvements to special cases in
eigenvalues calculation),
The World Bank [dtc] (World GDP per capita dataset),
Open Trade Statistics [dtc] (World Trade dataset)
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between economiccomplexity versions 1.0 dated 2020-02-20 and 1.1 dated 2020-09-19
economiccomplexity-1.0/economiccomplexity/inst/doc/basic-usage.R |only economiccomplexity-1.0/economiccomplexity/inst/doc/basic-usage.Rmd |only economiccomplexity-1.0/economiccomplexity/inst/doc/basic-usage.html |only economiccomplexity-1.0/economiccomplexity/vignettes/basic-usage.Rmd |only economiccomplexity-1.1/economiccomplexity/DESCRIPTION | 16 +++++----- economiccomplexity-1.1/economiccomplexity/MD5 | 14 ++++---- economiccomplexity-1.1/economiccomplexity/build/partial.rdb |binary economiccomplexity-1.1/economiccomplexity/build/vignette.rds |binary economiccomplexity-1.1/economiccomplexity/inst/doc/economiccomplexity.R |only economiccomplexity-1.1/economiccomplexity/inst/doc/economiccomplexity.Rmd |only economiccomplexity-1.1/economiccomplexity/inst/doc/economiccomplexity.html |only economiccomplexity-1.1/economiccomplexity/vignettes/economiccomplexity.Rmd |only 12 files changed, 15 insertions(+), 15 deletions(-)
More information about economiccomplexity at CRAN
Permanent link
Title: Calculates Disproportionate Impact When Binary Success Data are
Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index.
California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>.
California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/Files/DII/guidelines-for-measuring-disproportionate-impact-in-equity-plans-tfa-ada.pdf>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Diff between DisImpact versions 0.0.13 dated 2020-08-25 and 0.0.14 dated 2020-09-19
DESCRIPTION | 6 MD5 | 22 NEWS | 3 R/80_percent_index.R | 9 R/di_iterate.R | 12 R/percentage_point_gap.R | 9 R/proportionality_index.R | 12 inst/doc/Scaling-DI-Calculations.html | 255 +++++++-- inst/doc/Tutorial.html | 955 +++++++++++++++++++++------------- man/di_80_index.Rd | 6 man/di_ppg.Rd | 6 man/di_prop_index.Rd | 6 12 files changed, 866 insertions(+), 435 deletions(-)
Title: Fisher's z-Tests Concerning Difference of Correlations
Description: Computations of Fisher's z-tests concerning differences between correlations. diffcor.one() could be used to test for differences regarding an expected value, e.g., in construct validation. diffcor.two() may be useful in replication studies, to test if the original study and the replication study differed in terms of effects. diffcor.dep() can be applied to check if the correlation between one construct with another one (r12) is significantly different/higher/smaller than the correlation of one of the constructs with a third construct (r13), given the correlation of the constructs that are compared (r23). The outputs for all the three functions provide the test statistic in z-units as well as p-values. For diffcor.one() and diffcor.two(), the effect size Cohens q is additionally printed. It is a descriptive index to evaluate differences of independent correlations. Cohen (1988) suggested q = |.10|, |.30| and |.50| as small, moderate, and large differences.
Author: Christian Blötner
Maintainer: Christian Blötner <c.bloetner@gmail.com>
Diff between diffcor versions 0.3.0 dated 2020-08-24 and 0.4.0 dated 2020-09-19
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/source_code_diffcor.R | 22 +++++++++++----------- man/diffcor.Rd | 2 +- 4 files changed, 20 insertions(+), 20 deletions(-)
Title: Busca CEPs Brasileiros
Description: Retorna detalhes de dados de CEPs brasileiros, bairros, logradouros
e tal. (Returns info of Brazilian postal codes, city names, addresses
and so on.)
Author: Robert Myles McDonnell [aut, cre],
Eduardo Oliveira [ctb],
Rodrigo Giannotti [ctb]
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between cepR versions 0.1.1 dated 2020-06-02 and 0.1.2 dated 2020-09-19
DESCRIPTION | 25 +++++++--- MD5 | 12 ++-- NAMESPACE | 4 + NEWS.md | 5 ++ R/busca_multi.R |only R/parse_api.R | 21 +++++--- README.md | 130 ++++++++++++++++++++++++++++------------------------- man/busca_multi.Rd |only 8 files changed, 117 insertions(+), 80 deletions(-)
Title: Mediation Analysis with Missing Data Using Bootstrap
Description: Four methods for mediation analysis with missing data: Listwise deletion, Pairwise deletion, Multiple imputation, and Two Stage Maximum Likelihood algorithm. For MI and TS-ML, auxiliary variables can be included. Bootstrap confidence intervals for mediation effects are obtained. The robust method is also implemented for TS-ML. Since version 1.4, bmem adds the capability to conduct power analysis for mediation models. Details about the methods used can be found in these articles. Zhang and Wang (2003) <doi:10.1007/s11336-012-9301-5>. Zhang (2014) <doi:10.3758/s13428-013-0424-0>.
Author: Zhiyong Zhang and Lijuan Wang
Maintainer: Zhiyong Zhang <zhiyongzhang@nd.edu>
Diff between bmem versions 1.7 dated 2020-04-21 and 1.8 dated 2020-09-19
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 3 ++- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based
Null Model Analysis
Description: To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as 'iCAMP' (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model (Sloan et al 2006) <doi:10.1111/j.1462-2920.2005.00956.x> and quantifying assembly processes based on entire-community null models (Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche difference and phylogenetic distance calculation, phylogenetic signal test within phylogenetic groups, midpoint root of big trees, etc.
Author: Daliang Ning
Maintainer: Daliang Ning <ningdaliang@ou.edu>
Diff between iCAMP versions 1.2.8 dated 2020-09-09 and 1.2.9 dated 2020-09-19
DESCRIPTION | 11 ++++++----- MD5 | 40 ++++++++++++++++++++-------------------- inst/CITATION | 5 ++--- man/NRI.p.Rd | 2 +- man/NTI.p.Rd | 2 +- man/RC.bin.bigc.Rd | 2 +- man/RC.pc.Rd | 2 +- man/bNRI.bin.big.Rd | 2 +- man/bNRIn.p.Rd | 2 +- man/bNTI.bin.big.Rd | 2 +- man/bNTIn.p.Rd | 2 +- man/change.sigindex.Rd | 2 +- man/dniche.Rd | 2 +- man/iCAMP-package.Rd | 9 +++++---- man/icamp.big.Rd | 2 +- man/icamp.bins.Rd | 2 +- man/icamp.boot.Rd | 2 +- man/icamp.out.Rd | 2 +- man/ps.bin.Rd | 2 +- man/qp.bin.js.Rd | 2 +- man/taxa.binphy.big.Rd | 2 +- 21 files changed, 50 insertions(+), 49 deletions(-)
Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis
are included in this package. In particular, it computes standard errors for
parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>
Diff between EFAutilities versions 2.1.0 dated 2020-09-07 and 2.1.1 dated 2020-09-19
EFAutilities-2.1.0/EFAutilities/R/efa20200828_c.R |only EFAutilities-2.1.0/EFAutilities/R/polyACMf_c.R |only EFAutilities-2.1.0/EFAutilities/R/ssem20200709_c.R |only EFAutilities-2.1.0/EFAutilities/man/PolychoricRM.Rd |only EFAutilities-2.1.0/EFAutilities/src |only EFAutilities-2.1.1/EFAutilities/DESCRIPTION | 12 EFAutilities-2.1.1/EFAutilities/MD5 | 32 EFAutilities-2.1.1/EFAutilities/NAMESPACE | 5 EFAutilities-2.1.1/EFAutilities/NEWS.md | 4 EFAutilities-2.1.1/EFAutilities/R/BootJack20200816_c.R | 430 EFAutilities-2.1.1/EFAutilities/R/PolycorGamma20161107_c.R |only EFAutilities-2.1.1/EFAutilities/R/efa20200909.R |only EFAutilities-2.1.1/EFAutilities/R/efaMR20200816_c.R | 348 EFAutilities-2.1.1/EFAutilities/R/ssem20200909.R |only EFAutilities-2.1.1/EFAutilities/build/vignette.rds |binary EFAutilities-2.1.1/EFAutilities/inst/doc/EFAutilities-vignette.R | 16 EFAutilities-2.1.1/EFAutilities/inst/doc/EFAutilities-vignette.Rmd | 478 EFAutilities-2.1.1/EFAutilities/inst/doc/EFAutilities-vignette.html |15268 ---------- EFAutilities-2.1.1/EFAutilities/man/efa.Rd | 4 EFAutilities-2.1.1/EFAutilities/vignettes/EFAutilities-vignette.Rmd | 478 20 files changed, 967 insertions(+), 16108 deletions(-)
Title: 'sf'-Compatible Interface to 'Google Maps' APIs
Description: Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds; (4) map images using the 'Maps Static' API, returned as 'stars' objects.
Author: Michael Dorman [aut, cre],
Tom Buckley [ctb],
Alex Dannenberg [ctb],
Mihir Bhaskar [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between mapsapi versions 0.4.6 dated 2020-06-15 and 0.4.7 dated 2020-09-19
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 6 +++++- R/mp_directions.R | 2 +- R/mp_geocode.R | 2 +- R/mp_get_bounds.R | 2 +- R/mp_get_points.R | 5 +++-- R/mp_map.R | 2 +- R/mp_matrix.R | 2 +- build/vignette.rds |binary inst/doc/intro.Rmd | 8 ++++---- inst/doc/intro.html | 30 +++++++++++++++--------------- man/mp_directions.Rd | 2 +- man/mp_geocode.Rd | 2 +- man/mp_get_points.Rd | 3 ++- man/mp_map.Rd | 2 +- man/mp_matrix.Rd | 2 +- vignettes/intro.Rmd | 8 ++++---- 18 files changed, 62 insertions(+), 56 deletions(-)
Title: Compositional Data Analysis in Practice
Description: Univariate and multivariate methods for compositional data
analysis, based on logratios. The package implements the approach in the
book Compositional Data Analysis in Practice by Michael Greenacre (2018),
where accent is given to simple pairwise logratios. Selection can be made
of logratios that account for a maximum percentage of logratio variance.
Various multivariate analyses of logratios are included in the package.
Author: Michael Greenacre
Maintainer: Michael Greenacre <michael.greenacre@upf.edu>
Diff between easyCODA versions 0.31.1 dated 2019-03-10 and 0.34.3 dated 2020-09-19
DESCRIPTION | 14 - MD5 | 54 +++-- R/ACLUST.r |only R/CIplot_biv.r |only R/CLOSE.r |only R/LR.r | 4 R/PCA.r | 154 ++++++++------- R/PLOT.CA.r | 30 +-- R/PLOT.LRA.r | 23 +- R/PLOT.PCA.r | 32 ++- R/PLOT.RDA.r | 27 +- R/RDA.r | 30 +-- R/SLR.r | 66 +++--- R/STEP.r | 535 ++++++++++++++++++++++++++++++------------------------ R/VAR.r |only R/WARD.r |only R/invSLR.r |only build/partial.rdb |binary data/cups.RData |binary data/fish.RData |binary data/time.RData |binary data/veg.rda |binary man/ACLUST.Rd |only man/CA.Rd | 2 man/CIplot_biv.Rd |only man/CLOSE.Rd |only man/PCA.Rd | 5 man/PLOT.CA.Rd | 2 man/PLOT.LRA.Rd | 19 + man/PLOT.PCA.Rd | 20 +- man/PLOT.RDA.Rd | 10 - man/VAR.Rd |only man/WARD.Rd |only man/invSLR.Rd |only 34 files changed, 579 insertions(+), 448 deletions(-)
Title: A Simple XML Tree Parser and Generator
Description: Provides a simple XML tree parser/generator. It includes
functions to read XML files into R objects, get information out of
and into nodes, and write R objects back to XML code. It's not as
powerful as the 'XML' package and doesn't aim to be, but for simple
XML handling it could be useful. It was originally developed for
the R GUI and IDE 'RKWard' <https://rkward.kde.org>, to make plugin
development easier.
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between XiMpLe versions 0.10-2 dated 2017-12-12 and 0.10-3 dated 2020-09-19
ChangeLog | 8 DESCRIPTION | 32 ++- MD5 | 49 ++--- R/01_method_01_pasteXML.R | 22 +- R/01_method_05_XMLgenerators.R | 2 R/XiMpLe-internal.R | 11 - R/XiMpLe-package.R | 25 +- README.md | 21 +- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/NEWS.Rd | 14 + inst/doc/XiMpLe_vignette.R | 2 inst/doc/XiMpLe_vignette.Rmd | 2 inst/doc/XiMpLe_vignette.html | 382 +++++++++++++++++++++++++++++++++-------- man/XMLGetters-methods.Rd | 5 man/XMLNode.Rd | 10 - man/XMLTree.Rd | 3 man/XMLValidity.Rd | 10 - man/XMLgenerators.Rd | 34 ++- man/XiMpLe-package.Rd | 29 +-- man/node.Rd | 43 +++- man/pasteXML-methods.Rd | 24 +- man/pasteXMLTag.Rd | 15 + man/validXML.Rd | 26 ++ vignettes/XiMpLe_vignette.Rmd | 2 26 files changed, 568 insertions(+), 211 deletions(-)
Title: Bibtex Parser
Description: Utility to parse a bibtex file.
Author: Romain Francois [aut, cre],
Kurt Hornik [ctb],
Michael Koohafkan [ctb],
Mathew W. McLean [ctb]
Maintainer: ORPHANED
Diff between bibtex versions 0.4.2.2 dated 2020-01-02 and 0.4.2.3 dated 2020-09-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/grammar/bibparse.y | 2 +- inst/include/bibtex.h | 2 ++ man/read.bib.Rd | 2 +- src/bibparse.c | 2 +- 6 files changed, 14 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-05 2.1.6
2019-03-27 2.1.5
2018-11-15 2.1.2
Title: Get and Show Personal 'Google Scholar' Profile
Description: Provides functions to get personal 'Google Scholar'
profile data from web API and show it in table or figure format.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between tinyscholar versions 0.1.0 dated 2020-09-02 and 0.1.1 dated 2020-09-19
DESCRIPTION | 8 - MD5 | 16 +- NEWS.md | 4 R/scholar_search.R | 17 ++ inst/doc/tinyscholar.R | 13 +- inst/doc/tinyscholar.Rmd | 11 + inst/doc/tinyscholar.html | 268 ++++++++++++++++++++++++---------------------- man/scholar_search.Rd | 4 vignettes/tinyscholar.Rmd | 11 + 9 files changed, 207 insertions(+), 145 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.2.7 dated 2020-07-31 and 0.2.8 dated 2020-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 ++ NEWS.md | 10 ++++++++-- R/ropenblas.R | 32 ++++++++++++++++++-------------- README.md | 43 ++++++++++++++++++++++++++----------------- man/rnews.Rd | 8 ++++---- 7 files changed, 68 insertions(+), 47 deletions(-)
Title: Collaborative Filtering by Reference Classes
Description: The collaborative Filtering methodology has been widely used in recommendation systems, which
uses similarities between users or items to make recommendations. A class called CF was implemented,
where it is structured by matrices and composed of recommendation and database manipulation functions.
See Aggarwal (2016) <doi:10.1007/978-3-319-29659-3> for an overview.
Author: Thiago Lima, Jessica Kubrusly
Maintainer: Thiago Lima <thiagoaugusto@id.uff.br>
Diff between CFilt versions 0.1.0 dated 2020-06-19 and 0.2.0 dated 2020-09-19
DESCRIPTION | 6 MD5 | 10 R/CF.R | 856 +++++++++++++++++++++++++++++++++++++++++++++++++------ R/CFbuilder.R | 156 +++++++--- man/CF-class.Rd | 93 +++-- man/CFbuilder.Rd | 8 6 files changed, 961 insertions(+), 168 deletions(-)
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>),
Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>),
Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Diff between HEMDAG versions 2.6.1 dated 2020-03-03 and 2.7.3 dated 2020-09-19
HEMDAG-2.6.1/HEMDAG/R/GPAV.R |only HEMDAG-2.6.1/HEMDAG/R/HTD.R |only HEMDAG-2.6.1/HEMDAG/R/TPR-DAG.R |only HEMDAG-2.6.1/HEMDAG/R/heuristic.methods.R |only HEMDAG-2.6.1/HEMDAG/inst/HEMDAG_2.6.1.pdf |only HEMDAG-2.6.1/HEMDAG/man/AUPRC.Rd |only HEMDAG-2.6.1/HEMDAG/man/AUROC.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.GPAV.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.GPAV.holdout.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.HTD.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.HTD.holdout.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.flat.scores.normalization.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.full.annotation.matrix.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.heuristic.methods.Rd |only HEMDAG-2.6.1/HEMDAG/man/Do.heuristic.methods.holdout.Rd |only HEMDAG-2.6.1/HEMDAG/man/FMM.Rd |only HEMDAG-2.6.1/HEMDAG/man/GPAV.Rd |only HEMDAG-2.6.1/HEMDAG/man/GPAV.over.examples.Rd |only HEMDAG-2.6.1/HEMDAG/man/GPAV.parallel.Rd |only HEMDAG-2.6.1/HEMDAG/man/HTD-DAG.Rd |only HEMDAG-2.6.1/HEMDAG/man/Heuristic-Methods.Rd |only HEMDAG-2.6.1/HEMDAG/man/Multilabel.F.measure.Rd |only HEMDAG-2.6.1/HEMDAG/man/PXR.Rd |only HEMDAG-2.6.1/HEMDAG/man/TPR-DAG-cross-validation.Rd |only HEMDAG-2.6.1/HEMDAG/man/TPR-DAG-holdout.Rd |only HEMDAG-2.6.1/HEMDAG/man/TPR-DAG-variants.Rd |only HEMDAG-2.6.1/HEMDAG/man/ancestors.Rd |only HEMDAG-2.6.1/HEMDAG/man/check.DAG.integrity.Rd |only HEMDAG-2.6.1/HEMDAG/man/children.Rd |only HEMDAG-2.6.1/HEMDAG/man/descendants.Rd |only HEMDAG-2.6.1/HEMDAG/man/do.edges.from.HPO.obo.Rd |only HEMDAG-2.6.1/HEMDAG/man/do.subgraph.Rd |only HEMDAG-2.6.1/HEMDAG/man/do.submatrix.Rd |only HEMDAG-2.6.1/HEMDAG/man/do.unstratified.cv.data.Rd |only HEMDAG-2.6.1/HEMDAG/man/parents.Rd |only HEMDAG-2.6.1/HEMDAG/src/GPAV.cpp |only HEMDAG-2.7.3/HEMDAG/DESCRIPTION | 12 HEMDAG-2.7.3/HEMDAG/MD5 | 156 +- HEMDAG-2.7.3/HEMDAG/NAMESPACE | 70 - HEMDAG-2.7.3/HEMDAG/NEWS.md | 261 ++-- HEMDAG-2.7.3/HEMDAG/R/annotation.utility.R | 176 -- HEMDAG-2.7.3/HEMDAG/R/gpav.R |only HEMDAG-2.7.3/HEMDAG/R/graph.utility.R | 591 +++++---- HEMDAG-2.7.3/HEMDAG/R/htd.dag.R |only HEMDAG-2.7.3/HEMDAG/R/norm.fun.R | 85 - HEMDAG-2.7.3/HEMDAG/R/obozinski.methods.R |only HEMDAG-2.7.3/HEMDAG/R/perf.meas.R | 703 +++++------ HEMDAG-2.7.3/HEMDAG/R/pkg.attach.R | 2 HEMDAG-2.7.3/HEMDAG/R/pkg.import.R | 8 HEMDAG-2.7.3/HEMDAG/R/tpr.dag.R |only HEMDAG-2.7.3/HEMDAG/inst/HEMDAG_2.7.3.pdf |only HEMDAG-2.7.3/HEMDAG/inst/extdata/edges.txt.gz |binary HEMDAG-2.7.3/HEMDAG/inst/extdata/scores.list.txt.gz |only HEMDAG-2.7.3/HEMDAG/inst/extdata/scores.tupla.txt.gz |only HEMDAG-2.7.3/HEMDAG/man/HEMDAG-package.Rd | 22 HEMDAG-2.7.3/HEMDAG/man/adj.upper.tri.Rd | 18 HEMDAG-2.7.3/HEMDAG/man/auprc.Rd |only HEMDAG-2.7.3/HEMDAG/man/auroc.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.ancestors.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.children.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.consistent.graph.Rd | 8 HEMDAG-2.7.3/HEMDAG/man/build.descendants.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.edges.from.hpo.obo.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.parents.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.scores.matrix.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.subgraph.Rd |only HEMDAG-2.7.3/HEMDAG/man/build.submatrix.Rd |only HEMDAG-2.7.3/HEMDAG/man/check.annotation.matrix.integrity.Rd | 13 HEMDAG-2.7.3/HEMDAG/man/check.dag.integrity.Rd |only HEMDAG-2.7.3/HEMDAG/man/compute.flipped.graph.Rd | 4 HEMDAG-2.7.3/HEMDAG/man/constraints.matrix.Rd | 11 HEMDAG-2.7.3/HEMDAG/man/create.stratified.fold.df.Rd | 6 HEMDAG-2.7.3/HEMDAG/man/distances.from.leaves.Rd | 4 HEMDAG-2.7.3/HEMDAG/man/example.datasets.Rd | 20 HEMDAG-2.7.3/HEMDAG/man/find.best.f.Rd | 24 HEMDAG-2.7.3/HEMDAG/man/find.leaves.Rd | 4 HEMDAG-2.7.3/HEMDAG/man/fmax.Rd |only HEMDAG-2.7.3/HEMDAG/man/full.annotation.matrix.Rd | 16 HEMDAG-2.7.3/HEMDAG/man/gpav.Rd |only HEMDAG-2.7.3/HEMDAG/man/gpav.holdout.Rd |only HEMDAG-2.7.3/HEMDAG/man/gpav.over.examples.Rd |only HEMDAG-2.7.3/HEMDAG/man/gpav.parallel.Rd |only HEMDAG-2.7.3/HEMDAG/man/gpav.vanilla.Rd |only HEMDAG-2.7.3/HEMDAG/man/graph.levels.Rd | 12 HEMDAG-2.7.3/HEMDAG/man/hierarchical.checkers.Rd | 20 HEMDAG-2.7.3/HEMDAG/man/htd.Rd |only HEMDAG-2.7.3/HEMDAG/man/htd.holdout.Rd |only HEMDAG-2.7.3/HEMDAG/man/htd.vanilla.Rd |only HEMDAG-2.7.3/HEMDAG/man/lexicographical.topological.sort.Rd | 11 HEMDAG-2.7.3/HEMDAG/man/multilabel.F.measure.Rd |only HEMDAG-2.7.3/HEMDAG/man/normalize.max.Rd | 10 HEMDAG-2.7.3/HEMDAG/man/obozinski.heuristic.methods.Rd |only HEMDAG-2.7.3/HEMDAG/man/obozinski.holdout.Rd |only HEMDAG-2.7.3/HEMDAG/man/obozinski.methods.Rd |only HEMDAG-2.7.3/HEMDAG/man/pxr.Rd |only HEMDAG-2.7.3/HEMDAG/man/read.graph.Rd | 9 HEMDAG-2.7.3/HEMDAG/man/read.undirected.graph.Rd | 8 HEMDAG-2.7.3/HEMDAG/man/root.node.Rd | 2 HEMDAG-2.7.3/HEMDAG/man/scores.normalization.Rd | 20 HEMDAG-2.7.3/HEMDAG/man/specific.annotation.list.Rd | 10 HEMDAG-2.7.3/HEMDAG/man/specific.annotation.matrix.Rd | 15 HEMDAG-2.7.3/HEMDAG/man/stratified.cross.validation.Rd | 36 HEMDAG-2.7.3/HEMDAG/man/tpr.dag.Rd |only HEMDAG-2.7.3/HEMDAG/man/tpr.dag.cv.Rd |only HEMDAG-2.7.3/HEMDAG/man/tpr.dag.holdout.Rd |only HEMDAG-2.7.3/HEMDAG/man/transitive.closure.annotations.Rd | 14 HEMDAG-2.7.3/HEMDAG/man/tupla.matrix.Rd | 26 HEMDAG-2.7.3/HEMDAG/man/unstratified.cv.data.Rd |only HEMDAG-2.7.3/HEMDAG/man/weighted.adjacency.matrix.Rd | 13 HEMDAG-2.7.3/HEMDAG/man/write.graph.Rd | 9 HEMDAG-2.7.3/HEMDAG/src/gpav.cpp |only HEMDAG-2.7.3/HEMDAG/tests |only 112 files changed, 1212 insertions(+), 1217 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models and non-informative right-censoring may be considered. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value distribution as important special case.
Author: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com> and G. Paula and L. Vanegas
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.1.6 dated 2020-04-25 and 0.1.7 dated 2020-09-19
sglg-0.1.6/sglg/R/code_example_sglg.R |only sglg-0.1.7/sglg/DESCRIPTION | 12 +-- sglg-0.1.7/sglg/MD5 | 51 +++++++------- sglg-0.1.7/sglg/NAMESPACE | 2 sglg-0.1.7/sglg/R/bootglg.R |only sglg-0.1.7/sglg/R/envelope.sglg.R | 10 +- sglg-0.1.7/sglg/R/glg.R | 26 ++++--- sglg-0.1.7/sglg/R/kmpar.R | 3 sglg-0.1.7/sglg/R/lss.R | 22 +++--- sglg-0.1.7/sglg/R/plot.npc.R | 35 ++++++--- sglg-0.1.7/sglg/R/quantile_residuals.R | 1 sglg-0.1.7/sglg/R/rglg.R | 14 +-- sglg-0.1.7/sglg/R/sglg2.R | 14 +-- sglg-0.1.7/sglg/R/shape.R | 1 sglg-0.1.7/sglg/R/ssurvglg.R | 105 +++++++++++++++++------------ sglg-0.1.7/sglg/R/summary.sglg.R | 41 +++++------ sglg-0.1.7/sglg/R/survglg.R | 12 +-- sglg-0.1.7/sglg/man/bootglg.Rd |only sglg-0.1.7/sglg/man/glg.Rd | 5 - sglg-0.1.7/sglg/man/lss.Rd | 6 - sglg-0.1.7/sglg/man/plotnpc.Rd | 13 --- sglg-0.1.7/sglg/man/plotsurv.sglg.Rd | 2 sglg-0.1.7/sglg/man/rglg.Rd | 6 - sglg-0.1.7/sglg/man/sglg.Rd | 3 sglg-0.1.7/sglg/man/shape.Rd | 1 sglg-0.1.7/sglg/man/ssurvglg.Rd | 13 ++- sglg-0.1.7/sglg/man/survglg.Rd | 3 sglg-0.1.7/sglg/tests/testthat/test_sglg.R | 4 - 28 files changed, 221 insertions(+), 184 deletions(-)
Title: Tools for Data Splitting
Description: Fast, lightweight toolkit for data splitting. Data
sets can be partitioned into disjoint groups (e.g. into training,
validation, and test) or into (repeated) k-folds for subsequent
cross-validation. Besides basic splits, the package supports
stratified, grouped as well as blocked splitting. Furthermore,
cross-validation folds for time series data can be created. See e.g.
Hastie et al. (2001) <doi:10.1007/978-0-387-84858-7> for the basic
background on data partitioning and cross-validation.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between splitTools versions 0.2.1 dated 2020-04-18 and 0.3.0 dated 2020-09-19
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++++--------- NAMESPACE | 16 ++++++++-------- NEWS.md | 10 ++++++++++ R/partition.R | 41 +++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/splitTools.Rmd | 2 +- inst/doc/splitTools.html | 20 ++++++++++++++++++-- man/partition.Rd | 2 +- tests |only vignettes/splitTools.Rmd | 2 +- 11 files changed, 99 insertions(+), 28 deletions(-)
Title: Create Tables for Reporting Clinical Trials
Description: Create Tables for Reporting Clinical Trials.
Calculates descriptive statistics and hypothesis tests,
arranges the results in a table ready for reporting with LaTeX, HTML or Word.
Author: Armin Ströbel [aut, cre] (<https://orcid.org/0000-0002-6873-5332>),
Alan Haynes [aut] (<https://orcid.org/0000-0003-1374-081X>)
Maintainer: Armin Ströbel <arminstroebel@web.de>
Diff between atable versions 0.1.8 dated 2020-08-13 and 0.1.9 dated 2020-09-19
DESCRIPTION | 6 ++-- MD5 | 26 +++++++++++++------- R/atable.R | 18 ++++++++------ R/atable_options.R | 10 +++++++ R/helper.R | 54 +++++++++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/atable_usage.pdf |binary inst/doc/extending.R |only inst/doc/extending.Rnw |only inst/doc/extending.pdf |only inst/doc/modifying.R |only inst/doc/modifying.Rnw |only inst/doc/modifying.pdf |only man/atable.Rd | 7 ++++- man/atable_options.Rd | 3 ++ tests/testthat/test_atable.R | 17 +++++++++++++ vignettes/extending.Rnw |only vignettes/modifying.Rnw |only 18 files changed, 98 insertions(+), 43 deletions(-)
Title: Code Examples to Accompany the Book "R for Dummies"
Description: Contains all the code examples in the book "R for Dummies" (2nd
edition) by Andrie de Vries and Joris Meys. You can view the table of
contents as well as the sample code for each chapter.
Author: Andrie de Vries [aut, cre],
Joris Meys [aut]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between rfordummies versions 0.1.4 dated 2019-03-19 and 0.1.5 dated 2020-09-19
DESCRIPTION | 14 +++++------ MD5 | 54 +++++++++++++++++++++++---------------------- NEWS.md | 5 ++++ R/rfordummies-package.r | 4 +-- inst/WORDLIST |only man/ch01.Rd | 30 ++++++++++++++++--------- man/ch02.Rd | 30 ++++++++++++++++--------- man/ch03.Rd | 30 ++++++++++++++++--------- man/ch04.Rd | 30 ++++++++++++++++--------- man/ch05.Rd | 30 ++++++++++++++++--------- man/ch06.Rd | 30 ++++++++++++++++--------- man/ch07.Rd | 30 ++++++++++++++++--------- man/ch08.Rd | 36 +++++++++++++++++++----------- man/ch09.Rd | 30 ++++++++++++++++--------- man/ch10.Rd | 30 ++++++++++++++++--------- man/ch11.Rd | 30 ++++++++++++++++--------- man/ch12.Rd | 36 +++++++++++++++++++----------- man/ch13.Rd | 30 ++++++++++++++++--------- man/ch14.Rd | 30 ++++++++++++++++--------- man/ch15.Rd | 30 ++++++++++++++++--------- man/ch16.Rd | 30 ++++++++++++++++--------- man/ch17.Rd | 30 ++++++++++++++++--------- man/ch18.Rd | 30 ++++++++++++++++--------- man/ch19.Rd | 30 ++++++++++++++++--------- man/ch20.Rd | 30 ++++++++++++++++--------- man/elements.Rd | 6 +++-- man/rfordummies.Rd | 3 -- tests/spelling.R |only tests/testthat/test_1_ch.R | 4 +-- 29 files changed, 455 insertions(+), 247 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include a) Tsagris M.T., Preston S. and Wood A.T.A. (2011) A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis. b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534. c) Tsagris M. (2015). A novel, divergence based, regression for compositional data. Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. d) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Statistics, 6(2):47--57. e) Tsagris M., Preston S. and Wood A.T.A. (2016). Improved supervised classification for compositional data using the alpha-transformation. Journal of Classification, 33(2):243--261. <doi:10.1007/s00357-016-9207-5>. f) Tsagris M., Preston S. and Wood A.T.A. (2017). Nonparametric hypothesis testing for equality of means on the simplex. Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554> g) Tsagris M. and Stewart C. (2018). A Dirichlet regression model for compositional data with zeros. Lobachevskii Journal of Mathematics, 39(3): 398--412. <doi:10.1134/S1995080218030198>. h) Alenazi A. (2019). Regression for compositional data with compositional data as predictor variables with or without zero values. Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>. i) Tsagris M. and Stewart C. (2020). A folded model for compositional data analysis. Australian and New Zealand Journal of Statistics, 62(2):249--277. <doi:10.1111/anzs.12289>. j) Tsagris M., Alenazi A. and Stewart C. (2020). The alpha-k-NN regression for compositional data. <arXiv:2002.05137>. We further include functions for percentages (or proportions).
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 3.9 dated 2020-07-05 and 4.1 dated 2020-09-19
DESCRIPTION | 14 +++---- MD5 | 76 ++++++++++++++++++++++++------------------- NAMESPACE | 5 +- R/alfa.R | 2 - R/comp.knn.R | 8 ++-- R/cv.comp.reg.R | 2 - R/cv.tflr.R |only R/es.R |only R/esov.R |only R/esova.R |only R/green.R |only R/kl.compreg.R | 42 +++++++++++++++++++---- R/kl.compreg2.R | 17 +++++---- R/klcompreg.boot.R | 5 ++ R/tflr.R |only man/Compositional-package.Rd | 4 +- man/a.est.Rd | 2 - man/aknnreg.tune.Rd | 4 +- man/alfa.Rd | 2 - man/alfa.pcr.Rd | 4 +- man/alfa.profile.Rd | 9 ++--- man/alfa.rda.Rd | 2 - man/alfa.reg.Rd | 4 +- man/alfa.ridge.Rd | 4 +- man/alfa.tune.Rd | 2 - man/alfadist.Rd | 8 ++-- man/alfainv.Rd | 4 +- man/alfapcr.tune.Rd | 4 +- man/alfareg.tune.Rd | 4 +- man/alfaridge.plot.Rd | 2 - man/alfaridge.tune.Rd | 2 - man/alpha.mle.Rd | 2 - man/comp.knn.Rd | 2 - man/compknn.tune.Rd | 2 - man/cv.comp.reg.Rd | 2 - man/cv.tflr.Rd |only man/esov.Rd |only man/green.Rd |only man/helm.Rd | 2 - man/kl.alfapcr.Rd | 2 - man/kl.compreg.Rd | 9 ++--- man/kl.compreg2.Rd | 18 ++++++---- man/klalfapcr.tune.Rd | 2 - man/tflr.Rd |only 44 files changed, 162 insertions(+), 111 deletions(-)
Title: Standardize Plant Names According to World Flora Online
Taxonomic Backbone
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between WorldFlora versions 1.6 dated 2020-05-07 and 1.7 dated 2020-09-19
DESCRIPTION | 8 +++---- MD5 | 13 ++++++------ R/WFO.match.R | 10 +++++++++ R/WFO.remember.R | 2 - R/zzz.R | 5 +++- inst/CITATION |only inst/ChangeLog | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/WFO.match.Rd | 6 ++--- 8 files changed, 84 insertions(+), 16 deletions(-)
Title: Import and Handling for 'WhatsApp' Chat Logs
Description: A straightforward, easy-to-use and robust parsing package which aims to
digest history files from the popular messenger service 'WhatsApp' in all locales
and from all devices.
Author: Johannes Gruber [aut, cre]
Maintainer: Johannes Gruber <j.gruber.1@research.gla.ac.uk>
Diff between rwhatsapp versions 0.2.2 dated 2020-03-18 and 0.2.3 dated 2020-09-19
DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 3 NEWS.md | 6 R/emoji_lookup.R |only R/rwhatsapp.R | 68 +--- build/vignette.rds |binary data/emojis.rda |binary inst/CITATION | 2 inst/WORDLIST | 4 inst/doc/Text_Analysis_using_WhatsApp_data.html | 354 ++++++++++++------------ man/emojis.Rd | 16 - man/lookup_emoji.Rd |only tests/testthat/test-rwhatsapp.R | 20 + 14 files changed, 256 insertions(+), 249 deletions(-)
Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering. Clustering by
merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of the
separation of groupings. Cluster validation statistics
for distance based clustering including corrected Rand index.
Standardisation of cluster validation statistics by random clusterings and
comparison between many clustering methods and numbers of clusters based on
this.
Cluster-wise cluster stability assessment. Methods for estimation of
the number of clusters: Calinski-Harabasz, Tibshirani and Walther's
prediction strength, Fang and Wang's bootstrap stability.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Variable-wise statistics for cluster
interpretation. DBSCAN clustering. Interface functions for many
clustering methods implemented in R, including estimating the number of
clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
mixtures. For an overview see package?fpc.
Author: Christian Hennig <christian.hennig@unibo.it>
Maintainer: Christian Hennig <christian.hennig@unibo.it>
Diff between fpc versions 2.2-7 dated 2020-06-26 and 2.2-8 dated 2020-09-19
DESCRIPTION | 10 - MD5 | 36 ++--- R/clusterboot.R | 269 +++++++++++++++++++++++--------------- R/cquality20.R | 180 ------------------------- man/cgrestandard.Rd | 14 + man/clustatsum.Rd | 20 +- man/clusterbenchstats.Rd | 15 +- man/cqcluster.stats.Rd | 39 +++-- man/fpc-package.Rd | 21 +- man/kmeansCBI.Rd | 36 ++--- man/plot.valstat.Rd | 17 +- man/randomclustersim.Rd | 12 - man/stupidkaven.Rd | 7 man/stupidkcentroids.Rd | 17 +- man/stupidkfn.Rd | 7 man/stupidknn.Rd | 19 +- man/valstat.object.Rd | 26 +-- tests/Examples/fpc-Ex.Rout.save | 11 - tests/fpctests_notallin.Rout.save | 8 - 19 files changed, 340 insertions(+), 424 deletions(-)