Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson <gary.nelson@mass.gov>
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>
Diff between fishmethods versions 1.11-1 dated 2019-12-13 and 1.11-2 dated 2021-07-16
DESCRIPTION | 8 MD5 | 20 +- R/agesurv.R | 465 ++++++++++++++++++++++++++--------------------------- R/agesurvcl.R | 2 R/grotag.R | 4 R/growth.R | 2 man/agesurv.Rd | 10 - man/astrocalc4r.Rd | 9 - man/bheq.Rd | 3 man/grotag.Rd | 9 - man/nshrimp.Rd | 2 11 files changed, 269 insertions(+), 265 deletions(-)
Title: Utilities to Extract and Process 'YAML' Fragments
Description: Provides a number of functions to facilitate
extracting information in 'YAML' fragments from one or
multiple files, optionally structuring the information
in a 'data.tree'. 'YAML' (recursive acronym for "YAML ain't
Markup Language") is a convention for specifying structured
data in a format that is both machine- and human-readable.
'YAML' therefore lends itself well for embedding (meta)data
in plain text files, such as Markdown files. This principle
is implemented in 'yum' with minimal dependencies (i.e. only
the 'yaml' packages, and the 'data.tree' package can be
used to enable additional functionality).
Author: Gjalt-Jorn Peters [aut, cre]
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between yum versions 0.0.1 dated 2019-03-13 and 0.1.0 dated 2021-07-16
DESCRIPTION | 11 +++----- MD5 | 26 ++++++++++--------- NAMESPACE | 1 R/find_yaml_fragment_indices.R |only README.md | 52 +++++++++++++++++++++++++------------- man/build_tree.Rd | 13 +++++++-- man/delete_yaml_fragments.Rd | 9 +++++- man/extract_yaml_dir.Rd | 14 +++++++--- man/extract_yaml_fragments.Rd | 12 ++++++-- man/find_yaml_fragment_indices.Rd |only man/load_and_simplify.Rd | 39 +++++++++++++++++++--------- man/load_yaml_dir.Rd | 17 ++++++++---- man/load_yaml_fragments.Rd | 19 +++++++++---- man/load_yaml_list.Rd | 14 +++++++--- man/vecTxt.Rd | 13 +++++++-- 15 files changed, 163 insertions(+), 77 deletions(-)
Title: A Model Object Framework for Regression Analysis
Description: A utility library to facilitate the generalization of statistical methods built on a regression framework. Package developers can use 'modelObj' methods to initiate a regression analysis without concern for the details of the regression model and the method to be used to obtain parameter estimates. The specifics of the regression step are left to the user to define when calling the function. The user of a function developed within the 'modelObj' framework creates as input a 'modelObj' that contains the model and the R methods to be used to obtain parameter estimates and to obtain predictions. In this way, a user can easily go from linear to non-linear models within the same package.
Author: Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between modelObj versions 4.0 dated 2019-02-26 and 4.1 dated 2021-07-16
modelObj-4.0/modelObj/R/A01_methodObj.R |only modelObj-4.0/modelObj/R/A02_methodObjPredict.R |only modelObj-4.0/modelObj/R/A03_methodObjSolver.R |only modelObj-4.0/modelObj/R/A04_methodObjSolverFormula.R |only modelObj-4.0/modelObj/R/A05_methodObjSolverXY.R |only modelObj-4.0/modelObj/R/A06_modelObj.R |only modelObj-4.0/modelObj/R/A07_modelObjFormula.R |only modelObj-4.0/modelObj/R/A08_modelObjXY.R |only modelObj-4.0/modelObj/R/A09_modelObjFit.R |only modelObj-4.0/modelObj/man/internal-fit.Rd |only modelObj-4.0/modelObj/man/internal-predict.Rd |only modelObj-4.0/modelObj/man/method.Rd |only modelObj-4.0/modelObj/man/methodArgs.Rd |only modelObj-4.0/modelObj/man/methodObj-class.Rd |only modelObj-4.0/modelObj/man/methodObjPredict-class.Rd |only modelObj-4.0/modelObj/man/methodObjSolver-class.Rd |only modelObj-4.0/modelObj/man/methodObjSolverFormula-class.Rd |only modelObj-4.0/modelObj/man/methodObjSolverXY-class.Rd |only modelObj-4.0/modelObj/man/modelObj-internal-api.Rd |only modelObj-4.0/modelObj/man/modelObjFit.Rd |only modelObj-4.0/modelObj/man/newMethodObj.Rd |only modelObj-4.0/modelObj/man/newMethodObjPredict.Rd |only modelObj-4.0/modelObj/man/newMethodObjSolver.Rd |only modelObj-4.0/modelObj/man/newMethodObjSolverFormula.Rd |only modelObj-4.0/modelObj/man/newMethodObjSolverXY.Rd |only modelObj-4.0/modelObj/man/warnMsg.Rd |only modelObj-4.1/modelObj/DESCRIPTION | 18 ++- modelObj-4.1/modelObj/MD5 | 70 +++++--------- modelObj-4.1/modelObj/NAMESPACE | 6 - modelObj-4.1/modelObj/R/buildModelObj.R | 2 modelObj-4.1/modelObj/R/methodObj.R |only modelObj-4.1/modelObj/R/methodObjPredict.R |only modelObj-4.1/modelObj/R/methodObjSolver.R |only modelObj-4.1/modelObj/R/methodObjSolverFormula.R |only modelObj-4.1/modelObj/R/methodObjSolverXY.R |only modelObj-4.1/modelObj/R/modelObj.R |only modelObj-4.1/modelObj/R/modelObjFit.R |only modelObj-4.1/modelObj/R/modelObjFormula.R |only modelObj-4.1/modelObj/R/modelObjXY.R |only modelObj-4.1/modelObj/R/warnMsg.R | 30 ++---- modelObj-4.1/modelObj/build/vignette.rds |binary modelObj-4.1/modelObj/inst/doc/modelObj.R | 1 modelObj-4.1/modelObj/inst/doc/modelObj.pdf |binary modelObj-4.1/modelObj/man/buildModelObj.Rd | 9 + modelObj-4.1/modelObj/man/fit.Rd | 5 - modelObj-4.1/modelObj/man/fitObject.Rd | 8 + modelObj-4.1/modelObj/man/model.Rd | 9 + modelObj-4.1/modelObj/man/modelObj.Rd | 3 modelObj-4.1/modelObj/man/modelObjFit-class.Rd |only modelObj-4.1/modelObj/man/predict.Rd | 5 - modelObj-4.1/modelObj/man/predictor.Rd | 8 + modelObj-4.1/modelObj/man/predictorArgs.Rd | 12 ++ modelObj-4.1/modelObj/man/solver.Rd | 9 + modelObj-4.1/modelObj/man/solverArgs.Rd | 15 ++- 54 files changed, 117 insertions(+), 93 deletions(-)
Title: Bayesian Non-Parametric Dependent Models for Time-Indexed
Functional Data
Description: Estimates a collection of time-indexed functions under
either of Gaussian process (GP) or intrinsic Gaussian Markov
random field (iGMRF) prior formulations where a Dirichlet process
mixture allows sub-groupings of the functions to share the same
covariance or precision parameters. The GP and iGMRF formulations
both support any number of additive covariance or precision terms,
respectively, expressing either or both of multiple trend and
seasonality.
Author: Terrance Savitsky
Maintainer: Terrance Savitsky <tds151@gmail.com>
Diff between growfunctions versions 0.14 dated 2018-03-31 and 0.15 dated 2021-07-16
DESCRIPTION | 13 ++++------ MD5 | 46 +++++++++++++++++++------------------- NAMESPACE | 1 NEWS | 4 +++ R/cps.R | 1 build/partial.rdb |binary man/cluster_plot.Rd | 20 ++++++++++++---- man/cps.Rd | 7 ++--- man/fit_compare.Rd | 13 ++++++++-- man/gen_informative_sample.Rd | 22 ++++++++++++++---- man/gmrfdpPost.Rd | 27 +++++++++++++++++++--- man/gmrfdpcountPost.Rd | 30 ++++++++++++++++++++++-- man/gmrfdpgrow.Rd | 29 +++++++++++++++++++++-- man/gpBFixPost.Rd | 26 +++++++++++++++++++-- man/gpFixPost.Rd | 26 +++++++++++++++++++-- man/gpPost.Rd | 25 ++++++++++++++++++-- man/gpdpPost.Rd | 29 +++++++++++++++++++++-- man/gpdpbPost.Rd | 30 ++++++++++++++++++++++-- man/gpdpgrow.Rd | 32 +++++++++++++++++++++++--- man/growfunctions-package.Rd | 2 - man/informative_plot.Rd | 12 +++++++-- man/plot_cluster.Rd | 13 +++++++++- man/predict_functions.gpdpgrow.Rd | 10 ++++++-- man/predict_plot.Rd | 15 +++++++++--- 24 files changed, 345 insertions(+), 88 deletions(-)
Title: Beta Regression on a Bayesian Model
Description: Applies the Beta regression model in the Bayesian statistical view with the possibility of adding a spatial effect in the parameters, the Beta regression is used when the response variable is a proportion variable, that is, it only accepts values between 0 and 1.
The package 'bayesbr' uses 'rstan' package to build the Bayesian statistical models. The main function of the package receives as a parameter a form informing the independent variable and the co-variables of the model to be made, as output it returns a list with the results of the model. For more details see Ferrari and Cribari-Neto (2004) <doi:10.1080/0266476042000214501> and Hoffman and Gelman (2014) <arXiv:1111.4246>.
Author: Joao Melo [aut, cre],
Vinicius Mayrink [aut]
Maintainer: Joao Melo <pjoao266@gmail.com>
Diff between bayesbr versions 0.0.0.1 dated 2020-06-26 and 0.0.1.0 dated 2021-07-16
DESCRIPTION | 17 + MD5 | 96 +++++++--- NAMESPACE | 1 R/BIC_bayesbr.R | 3 R/ImpreciseTask.R | 1 R/ReadingSkills.R | 4 R/bayesbr-package.R | 2 R/bayesbr.R | 228 ++++++++++++++++++++++-- R/bayesbr_app.R |only R/bodyfat.R | 2 R/print.bayesbr.R | 12 + R/summary.bayesbr.R | 13 + R/summary_delta.R |only R/summary_tau_delta.R |only R/summary_tau_xi.R |only R/summary_xi.R |only R/utils.R |only R/values.R | 55 +++++ README.md | 9 build/partial.rdb |binary build/vignette.rds |only inst/doc |only inst/shiny |only inst/stan/bayesbr.stan | 40 +++- man/BIC_bayesbr.Rd | 2 man/ImpreciseTask.Rd | 1 man/ReadingSkills.Rd | 4 man/bayesbr-package.Rd | 2 man/bayesbr.Rd | 28 ++ man/bayesbr_app.Rd |only man/bodyfat.Rd | 2 man/figures |only man/summary_delta.Rd |only man/summary_tau_delta.Rd |only man/summary_tau_xi.Rd |only man/summary_xi.Rd |only man/values.Rd | 11 - src/Makevars | 10 - src/Makevars.win | 11 - src/stanExports_bayesbr.h | 430 ++++++++++++++++++++++++++++++++++++++-------- vignettes |only 41 files changed, 822 insertions(+), 162 deletions(-)
Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Outlier detection method that flags suspicious values within observations,
constrasting them against the normal values in a user-readable format, potentially
describing conditions within the data that make a given outlier more rare.
Full procedure is described in Cortes (2020) <arXiv:2001.00636>.
Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between outliertree versions 1.7.2 dated 2021-05-17 and 1.7.3 dated 2021-07-16
DESCRIPTION | 7 MD5 | 14 - inst/doc/Introducing_OutlierTree.html | 4 src/Rwrapper.cpp | 52 +++++++ src/clusters.cpp | 8 + src/fit_model.cpp | 243 +++++++++++++++++++--------------- src/outlier_tree.h | 5 src/predict.cpp | 31 ++++ 8 files changed, 245 insertions(+), 119 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.5.0 dated 2020-12-03 and 2.5.7 dated 2021-07-16
DESCRIPTION | 8 MD5 | 112 NAMESPACE | 4 R/DataSimians.R | 2 R/PGLS_fossil.R | 27 R/RRphylo.R | 51 R/StableTraitsR.R | 4 R/auxilliary.functions.R | 122 R/conv.map.R | 174 - R/distNodes.R | 2 R/evo.dir.R | 2 R/fix.poly.R | 4 R/makeL1.R | 2 R/overfitRR.R | 222 - R/plotRates.R | 30 R/random.evolvability.test.R | 6 R/rate.map.R |only R/retrieve.angles.R | 74 R/scaleTree.R | 10 R/search.conv.R | 57 R/search.shift.R | 40 R/search.trend.R | 71 R/tree.merger.R | 64 build/vignette.rds |binary data/DataSimians.rda |binary inst/CITATION | 38 inst/doc/RRphylo.html | 844 +---- inst/doc/Tree-Manipulation.Rmd | 2 inst/doc/Tree-Manipulation.html | 916 +---- inst/doc/overfitRR.R | 40 inst/doc/overfitRR.Rmd | 53 inst/doc/overfitRR.html | 479 -- inst/doc/search.conv.R | 21 inst/doc/search.conv.Rmd | 25 inst/doc/search.conv.html | 6406 ---------------------------------------- inst/doc/search.shift.R | 4 inst/doc/search.shift.Rmd | 10 inst/doc/search.shift.html | 532 --- inst/doc/search.trend.R | 87 inst/doc/search.trend.Rmd | 91 inst/doc/search.trend.html | 670 ---- inst/doc/swapONE.html | 280 - man/DataSimians.Rd | 2 man/PGLS_fossil.Rd | 19 man/fix.poly.Rd | 2 man/overfitRR.Rd | 116 man/plotRates.Rd | 11 man/rate.map.Rd |only man/retrieve.angles.Rd | 63 man/search.conv.Rd | 22 man/search.shift.Rd | 23 man/search.trend.Rd | 37 man/tree.merger.Rd | 20 vignettes/Tree-Manipulation.Rmd | 2 vignettes/overfitRR.Rmd | 53 vignettes/search.conv.Rmd | 25 vignettes/search.shift.Rmd | 10 vignettes/search.trend.Rmd | 91 58 files changed, 1908 insertions(+), 10174 deletions(-)
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors. See Coombes and colleagues
(2019) <doi:10.18637/jss.v090.c01>.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.2.6 dated 2020-11-11 and 1.3.1 dated 2021-07-16
Polychrome-1.2.6/Polychrome/inst/extData/barf.R |only Polychrome-1.2.6/Polychrome/inst/extData/juju.R |only Polychrome-1.2.6/Polychrome/inst/extData/tracker.Rda |only Polychrome-1.2.6/Polychrome/inst/extData/tracker.csv |only Polychrome-1.3.1/Polychrome/DESCRIPTION | 8 - Polychrome-1.3.1/Polychrome/MD5 | 39 +++--- Polychrome-1.3.1/Polychrome/NAMESPACE | 4 Polychrome-1.3.1/Polychrome/NEWS | 9 + Polychrome-1.3.1/Polychrome/R/07-memberPlot.R |only Polychrome-1.3.1/Polychrome/build/vignette.rds |binary Polychrome-1.3.1/Polychrome/data/Dark24.rda |binary Polychrome-1.3.1/Polychrome/data/Light24.rda |binary Polychrome-1.3.1/Polychrome/data/alphabet.rda |binary Polychrome-1.3.1/Polychrome/data/colorsafe.rda |binary Polychrome-1.3.1/Polychrome/data/glasbey.rda |binary Polychrome-1.3.1/Polychrome/data/iscc.rda |binary Polychrome-1.3.1/Polychrome/data/palette36.rda |binary Polychrome-1.3.1/Polychrome/data/sky-colors.rda |binary Polychrome-1.3.1/Polychrome/inst/doc/color-deficits.html | 79 +------------ Polychrome-1.3.1/Polychrome/inst/doc/creatingPalettes.html | 77 +----------- Polychrome-1.3.1/Polychrome/inst/doc/polychrome.html | 73 +----------- Polychrome-1.3.1/Polychrome/inst/doc/testgg.html | 73 +----------- Polychrome-1.3.1/Polychrome/man/memberPlot.Rd |only Polychrome-1.3.1/Polychrome/tests/test-07-member.R |only 24 files changed, 76 insertions(+), 286 deletions(-)
Title: Multi-Omic Integration via Sparse Singular Value Decomposition
Description: High dimensionality, noise and heterogeneity among
samples and features challenge the omic integration task. Here we
present an omic integration method based on sparse singular value
decomposition (SVD) to deal with these limitations, by: a. obtaining
the main axes of variation of the combined omics, b. imposing sparsity
constraints at both subjects (rows) and features (columns) levels
using Elastic Net type of shrinkage, and c. allowing both linear and
non-linear projections (via t-Stochastic Neighbor Embedding) of the
omic data to detect clusters in very convoluted data
(Gonzalez-Reymundez & Vazquez, 2020) <doi:10.1038/s41598-020-65119-5>.
Author: Agustin Gonzalez-Reymundez [aut, cre, cph],
Alexander Grueneberg [aut],
Ana Vazquez [ctb, ths]
Maintainer: Agustin Gonzalez-Reymundez <agugonrey@gmail.com>
Diff between MOSS versions 0.1.0 dated 2021-01-19 and 0.2.0 dated 2021-07-16
MOSS-0.1.0/MOSS/inst/MOSS_0.1.0.pdf |only MOSS-0.2.0/MOSS/DESCRIPTION | 26 MOSS-0.2.0/MOSS/MD5 | 79 +- MOSS-0.2.0/MOSS/NAMESPACE | 27 MOSS-0.2.0/MOSS/NEWS.md |only MOSS-0.2.0/MOSS/R/BHI.R | 96 +- MOSS-0.2.0/MOSS/R/aest_f.R | 64 - MOSS-0.2.0/MOSS/R/cov_adj.R |only MOSS-0.2.0/MOSS/R/dbscan_BHI.R | 136 +-- MOSS-0.2.0/MOSS/R/dbscan_SH.R | 90 +- MOSS-0.2.0/MOSS/R/metdat.R | 48 - MOSS-0.2.0/MOSS/R/moss.R | 331 ++++++-- MOSS-0.2.0/MOSS/R/moss_heatmap.R |only MOSS-0.2.0/MOSS/R/moss_jumpstart.R | 8 MOSS-0.2.0/MOSS/R/moss_select.R |only MOSS-0.2.0/MOSS/R/moss_signatures.R |only MOSS-0.2.0/MOSS/R/pca2tsne.R | 59 + MOSS-0.2.0/MOSS/R/prepro_na.R | 39 - MOSS-0.2.0/MOSS/R/simulate_data.R | 212 ++--- MOSS-0.2.0/MOSS/R/ssvdEN_sol_path.R | 45 - MOSS-0.2.0/MOSS/R/ssvdEN_sol_path_par.R |only MOSS-0.2.0/MOSS/R/tsne2clus.R | 686 +++++++++--------- MOSS-0.2.0/MOSS/README.md | 16 MOSS-0.2.0/MOSS/build/vignette.rds |binary MOSS-0.2.0/MOSS/inst/MOSS_working_example.pdf |binary MOSS-0.2.0/MOSS/inst/WORDLIST | 9 MOSS-0.2.0/MOSS/inst/doc/MOSS_working_example.R | 16 MOSS-0.2.0/MOSS/inst/doc/MOSS_working_example.Rmd | 16 MOSS-0.2.0/MOSS/inst/doc/MOSS_working_example.pdf |binary MOSS-0.2.0/MOSS/man/cov_adj.Rd |only MOSS-0.2.0/MOSS/man/moss.Rd | 60 + MOSS-0.2.0/MOSS/man/moss_heatmap.Rd |only MOSS-0.2.0/MOSS/man/moss_select.Rd |only MOSS-0.2.0/MOSS/man/moss_signatures.Rd |only MOSS-0.2.0/MOSS/man/pca2tsne.Rd | 13 MOSS-0.2.0/MOSS/man/prepro_na.Rd | 10 MOSS-0.2.0/MOSS/man/ssvdEN_sol_path.Rd | 11 MOSS-0.2.0/MOSS/man/ssvdEN_sol_path_par.Rd |only MOSS-0.2.0/MOSS/tests/spelling.R |only MOSS-0.2.0/MOSS/tests/testthat.R | 8 MOSS-0.2.0/MOSS/tests/testthat/test_aest_f.R | 46 - MOSS-0.2.0/MOSS/tests/testthat/test_metdat.R | 18 MOSS-0.2.0/MOSS/tests/testthat/test_moss.R | 274 +++---- MOSS-0.2.0/MOSS/tests/testthat/test_rrr.R | 82 +- MOSS-0.2.0/MOSS/tests/testthat/test_ssvdEN.R | 112 +- MOSS-0.2.0/MOSS/tests/testthat/test_ssvdEN_sol_path.R | 34 MOSS-0.2.0/MOSS/vignettes/MOSS_working_example.Rmd | 16 47 files changed, 1484 insertions(+), 1203 deletions(-)
Title: Multivariate and Functional Spatial Scan Statistics
Description: Allows to detect spatial clusters of abnormal values on multivariate or functional data. Martin KULLDORFF and Lan HUANG and Kevin KONTY (2009) <doi:10.1186/1476-072X-8-58>, Inkyung JUNG and Ho Jin CHO (2015) <doi:10.1186/s12942-015-0024-6>, Lionel CUCALA and Michael GENIN and Caroline LANIER and Florent OCCELLI (2017) <doi:10.1016/j.spasta.2017.06.001>, Lionel CUCALA and Michael GENIN and Florent OCCELLI and Julien SOULA (2019) <doi:10.1016/j.spasta.2018.10.002>, Zaineb SMIDA and Lionel CUCALA and Ali GANNOUN (2020) <https://hal.archives-ouvertes.fr/hal-02908496>, Camille FREVENT and Mohamed-Salem AHMED and Matthieu MARBAC and Michael GENIN (2021) <arXiv:2011.03482>, Camille FREVENT and Mohamed-Salem AHMED and Sophie DABO-NIANG and Michael GENIN (2021) <arXiv:2103.14401>.
Author: Camille FREVENT [aut, cre, cph],
Mohamed-Salem AHMED [aut],
Julien SOULA [aut],
Zaineb SMIDA [aut],
Lionel CUCALA [aut],
Sophie DABO-NIANG [aut],
Michaël GENIN [aut]
Maintainer: Camille FREVENT <camille.frevent@univ-lille.fr>
Diff between HDSpatialScan versions 1.0.1 dated 2021-05-27 and 1.0.2 dated 2021-07-16
HDSpatialScan-1.0.1/HDSpatialScan/R/plot_summary.R |only HDSpatialScan-1.0.1/HDSpatialScan/man/plot_curves_clusters.Rd |only HDSpatialScan-1.0.1/HDSpatialScan/man/plot_summary.Rd |only HDSpatialScan-1.0.1/HDSpatialScan/man/plot_summary_chart.Rd |only HDSpatialScan-1.0.1/HDSpatialScan/man/plot_summary_curves.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/DESCRIPTION | 15 HDSpatialScan-1.0.2/HDSpatialScan/MD5 | 101 HDSpatialScan-1.0.2/HDSpatialScan/NAMESPACE | 33 HDSpatialScan-1.0.2/HDSpatialScan/R/HDSpatialScan_Classes.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/HDSpatialScan_plot.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/HDSpatialScan_plotCurves.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/HDSpatialScan_plotSummary.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/HDSpatialScan_print.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/HDSpatialScan_summary.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/InitScan.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/SpatialScan.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/clusters.R | 32 HDSpatialScan-1.0.2/HDSpatialScan/R/dfree.R | 4 HDSpatialScan-1.0.2/HDSpatialScan/R/documentation_page.R | 5 HDSpatialScan-1.0.2/HDSpatialScan/R/finalizing_scan_procedure.R |only HDSpatialScan-1.0.2/HDSpatialScan/R/gaussian_multi.R | 8 HDSpatialScan-1.0.2/HDSpatialScan/R/permutations.R | 2 HDSpatialScan-1.0.2/HDSpatialScan/R/plot_map.R | 121 HDSpatialScan-1.0.2/HDSpatialScan/R/pointwise_dfree.R | 10 HDSpatialScan-1.0.2/HDSpatialScan/R/pointwise_wmw_uni.R | 2 HDSpatialScan-1.0.2/HDSpatialScan/R/posteriori_filtering.R | 174 HDSpatialScan-1.0.2/HDSpatialScan/R/scan_fonc.R | 1799 +--------- HDSpatialScan-1.0.2/HDSpatialScan/R/scan_multi.R | 416 -- HDSpatialScan-1.0.2/HDSpatialScan/R/scan_uni.R | 368 -- HDSpatialScan-1.0.2/HDSpatialScan/R/wmw_fonc.R | 2 HDSpatialScan-1.0.2/HDSpatialScan/R/wmw_multi.R | 4 HDSpatialScan-1.0.2/HDSpatialScan/R/wmw_uni.R | 2 HDSpatialScan-1.0.2/HDSpatialScan/data/map_sites.rda |binary HDSpatialScan-1.0.2/HDSpatialScan/man/DFFSS.Rd | 71 HDSpatialScan-1.0.2/HDSpatialScan/man/FinScan.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/HDSpatialScan-package.Rd | 4 HDSpatialScan-1.0.2/HDSpatialScan/man/InitScan.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/MDFFSS.Rd | 73 HDSpatialScan-1.0.2/HDSpatialScan/man/MG.Rd | 71 HDSpatialScan-1.0.2/HDSpatialScan/man/MNP.Rd | 70 HDSpatialScan-1.0.2/HDSpatialScan/man/MPFSS.Rd | 90 HDSpatialScan-1.0.2/HDSpatialScan/man/MRBFSS.Rd | 73 HDSpatialScan-1.0.2/HDSpatialScan/man/NPFSS.Rd | 72 HDSpatialScan-1.0.2/HDSpatialScan/man/PFSS.Rd | 71 HDSpatialScan-1.0.2/HDSpatialScan/man/ResScanOutput.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/ResScanOutputMulti.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/ResScanOutputMultiFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/ResScanOutputUni.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/ResScanOutputUniFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/SpatialScan.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/UG.Rd | 71 HDSpatialScan-1.0.2/HDSpatialScan/man/UNP.Rd | 70 HDSpatialScan-1.0.2/HDSpatialScan/man/URBFSS.Rd | 71 HDSpatialScan-1.0.2/HDSpatialScan/man/plot.ResScanOutput.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotCurves.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotCurves.ResScanOutputMultiFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotCurves.ResScanOutputUniFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotSummary.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotSummary.ResScanOutputMulti.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotSummary.ResScanOutputMultiFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plotSummary.ResScanOutputUniFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/plot_map.Rd | 29 HDSpatialScan-1.0.2/HDSpatialScan/man/plot_map2.Rd | 28 HDSpatialScan-1.0.2/HDSpatialScan/man/plot_schema.Rd | 28 HDSpatialScan-1.0.2/HDSpatialScan/man/print.ResScanOutput.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/summary.ResScanOutputMulti.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/summary.ResScanOutputMultiFunct.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/summary.ResScanOutputUni.Rd |only HDSpatialScan-1.0.2/HDSpatialScan/man/summary.ResScanOutputUniFunct.Rd |only 69 files changed, 836 insertions(+), 3154 deletions(-)
Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.3.13 dated 2020-11-11 and 3.4.0 dated 2021-07-16
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 9 ++++++++- R/cd01-distance.R | 16 ++++++++++++++-- build/vignette.rds |binary inst/doc/maha-test.pdf |binary inst/doc/oompa-cd.pdf |binary man/cd01-0-distanceMatrix.Rd | 3 ++- tests/test01-distance.R | 1 + tests/test01-distance.Rout.save | 12 +++++++++--- 10 files changed, 47 insertions(+), 20 deletions(-)
More information about ClassDiscovery at CRAN
Permanent link
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'.
Armadillo requires a C++11 compiler.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.10.5.0.0 dated 2021-05-23 and 0.10.6.0.0 dated 2021-07-16
ChangeLog | 289 ++++++++----- DESCRIPTION | 8 MD5 | 96 ++-- R/RcppArmadillo.package.skeleton.R | 4 R/SciPy2R.R | 4 R/fastLm.R | 4 README.md | 3 build/partial.rdb |binary configure | 18 configure.ac | 5 inst/NEWS.Rd | 22 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 1 inst/include/armadillo_bits/Col_bones.hpp | 5 inst/include/armadillo_bits/Col_meat.hpp | 53 ++ inst/include/armadillo_bits/Cube_bones.hpp | 12 inst/include/armadillo_bits/Cube_meat.hpp | 71 +++ inst/include/armadillo_bits/Mat_bones.hpp | 12 inst/include/armadillo_bits/Mat_meat.hpp | 129 ++++-- inst/include/armadillo_bits/Row_bones.hpp | 5 inst/include/armadillo_bits/Row_meat.hpp | 53 ++ inst/include/armadillo_bits/SpMat_bones.hpp | 1 inst/include/armadillo_bits/SpMat_meat.hpp | 107 ++++- inst/include/armadillo_bits/arma_config.hpp | 2 inst/include/armadillo_bits/arma_forward.hpp | 33 - inst/include/armadillo_bits/arma_rng.hpp | 10 inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/arrayops_meat.hpp | 42 + inst/include/armadillo_bits/auxlib_bones.hpp | 3 inst/include/armadillo_bits/auxlib_meat.hpp | 55 ++ inst/include/armadillo_bits/compiler_setup.hpp | 5 inst/include/armadillo_bits/csv_name.hpp | 3 inst/include/armadillo_bits/def_lapack.hpp | 24 + inst/include/armadillo_bits/diskio_bones.hpp | 24 - inst/include/armadillo_bits/diskio_meat.hpp | 402 ++++++++++++------- inst/include/armadillo_bits/field_bones.hpp | 35 - inst/include/armadillo_bits/field_meat.hpp | 66 +++ inst/include/armadillo_bits/fill.hpp |only inst/include/armadillo_bits/fn_chol.hpp | 75 +++ inst/include/armadillo_bits/fn_spsolve.hpp | 2 inst/include/armadillo_bits/memory.hpp | 12 inst/include/armadillo_bits/spop_normalise_bones.hpp | 2 inst/include/armadillo_bits/spop_normalise_meat.hpp | 200 ++------- inst/include/armadillo_bits/subview_bones.hpp | 26 - inst/include/armadillo_bits/subview_meat.hpp | 13 inst/include/armadillo_bits/translate_lapack.hpp | 22 + inst/tinytest/test_fastLm.R | 9 inst/tinytest/test_misc.R |only man/RcppArmadillo-package.Rd | 2 50 files changed, 1360 insertions(+), 613 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre],
Julian Müller [ctb]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between netrankr versions 0.3.0 dated 2020-09-09 and 1.0.0 dated 2021-07-16
netrankr-0.3.0/netrankr/R/florentine_m.R |only netrankr-1.0.0/netrankr/DESCRIPTION | 12 netrankr-1.0.0/netrankr/MD5 | 141 +- netrankr-1.0.0/netrankr/NAMESPACE | 15 netrankr-1.0.0/netrankr/NEWS.md | 10 netrankr-1.0.0/netrankr/R/aggregate.index.R | 14 netrankr-1.0.0/netrankr/R/approximate.ranks.R | 4 netrankr-1.0.0/netrankr/R/check.preservation.R | 12 netrankr-1.0.0/netrankr/R/data.R |only netrankr-1.0.0/netrankr/R/get.rankings.R | 11 netrankr-1.0.0/netrankr/R/hyperbolic.index.R | 8 netrankr-1.0.0/netrankr/R/indirect.relations.R | 12 netrankr-1.0.0/netrankr/R/mcmc.rank.R | 10 netrankr-1.0.0/netrankr/R/neighborhood.inclusion.R | 27 netrankr-1.0.0/netrankr/R/plot.rank.intervals.R | 89 - netrankr-1.0.0/netrankr/R/positional.dominance.R | 11 netrankr-1.0.0/netrankr/R/rank.analysis.R | 55 - netrankr-1.0.0/netrankr/R/rank.interval.R | 21 netrankr-1.0.0/netrankr/R/threshold.graph.R | 4 netrankr-1.0.0/netrankr/R/utils.R |only netrankr-1.0.0/netrankr/README.md | 107 +- netrankr-1.0.0/netrankr/build/vignette.rds |binary netrankr-1.0.0/netrankr/data/dbces11.rda |only netrankr-1.0.0/netrankr/inst/doc/benchmarks.html | 235 ---- netrankr-1.0.0/netrankr/inst/doc/centrality_indices.R | 6 netrankr-1.0.0/netrankr/inst/doc/centrality_indices.Rmd | 6 netrankr-1.0.0/netrankr/inst/doc/centrality_indices.html | 384 ++------ netrankr-1.0.0/netrankr/inst/doc/indirect_relations.R | 6 netrankr-1.0.0/netrankr/inst/doc/indirect_relations.Rmd | 6 netrankr-1.0.0/netrankr/inst/doc/indirect_relations.html | 296 +----- netrankr-1.0.0/netrankr/inst/doc/neighborhood_inclusion.R | 6 netrankr-1.0.0/netrankr/inst/doc/neighborhood_inclusion.Rmd | 8 netrankr-1.0.0/netrankr/inst/doc/neighborhood_inclusion.html | 376 +------ netrankr-1.0.0/netrankr/inst/doc/partial_centrality.R | 15 netrankr-1.0.0/netrankr/inst/doc/partial_centrality.Rmd | 26 netrankr-1.0.0/netrankr/inst/doc/partial_centrality.html | 343 +------ netrankr-1.0.0/netrankr/inst/doc/positional_dominance.R | 17 netrankr-1.0.0/netrankr/inst/doc/positional_dominance.Rmd | 20 netrankr-1.0.0/netrankr/inst/doc/positional_dominance.html | 300 +----- netrankr-1.0.0/netrankr/inst/doc/probabilistic_cent.R | 10 netrankr-1.0.0/netrankr/inst/doc/probabilistic_cent.Rmd | 23 netrankr-1.0.0/netrankr/inst/doc/probabilistic_cent.html | 382 ++------ netrankr-1.0.0/netrankr/inst/doc/threshold_graph.R | 5 netrankr-1.0.0/netrankr/inst/doc/threshold_graph.Rmd | 5 netrankr-1.0.0/netrankr/inst/doc/threshold_graph.html | 326 +----- netrankr-1.0.0/netrankr/inst/doc/use_case.R | 21 netrankr-1.0.0/netrankr/inst/doc/use_case.Rmd | 26 netrankr-1.0.0/netrankr/inst/doc/use_case.html | 476 ++-------- netrankr-1.0.0/netrankr/man/aggregate_positions.Rd | 14 netrankr-1.0.0/netrankr/man/approx_rank_relative.Rd | 2 netrankr-1.0.0/netrankr/man/dbces11.Rd |only netrankr-1.0.0/netrankr/man/figures/README-partial-1.png |binary netrankr-1.0.0/netrankr/man/florentine_m.Rd | 2 netrankr-1.0.0/netrankr/man/hyperbolic_index.Rd | 8 netrankr-1.0.0/netrankr/man/indirect_relations.Rd | 12 netrankr-1.0.0/netrankr/man/is_preserved.Rd | 12 netrankr-1.0.0/netrankr/man/neighborhood_inclusion.Rd | 18 netrankr-1.0.0/netrankr/man/plot.netrankr_full.Rd |only netrankr-1.0.0/netrankr/man/plot.netrankr_interval.Rd |only netrankr-1.0.0/netrankr/man/plot.netrankr_mcmc.Rd |only netrankr-1.0.0/netrankr/man/plot_rank_intervals.Rd | 27 netrankr-1.0.0/netrankr/man/positional_dominance.Rd | 11 netrankr-1.0.0/netrankr/man/print.netrankr_full.Rd |only netrankr-1.0.0/netrankr/man/print.netrankr_interval.Rd |only netrankr-1.0.0/netrankr/man/print.netrankr_mcmc.Rd |only netrankr-1.0.0/netrankr/man/rank_intervals.Rd | 5 netrankr-1.0.0/netrankr/man/threshold_graph.Rd | 4 netrankr-1.0.0/netrankr/tests/testthat/test_approximations.R | 2 netrankr-1.0.0/netrankr/tests/testthat/test_exact_rank_prob.R | 2 netrankr-1.0.0/netrankr/vignettes/centrality_indices.Rmd | 6 netrankr-1.0.0/netrankr/vignettes/indirect_relations.Rmd | 6 netrankr-1.0.0/netrankr/vignettes/neighborhood_inclusion.Rmd | 8 netrankr-1.0.0/netrankr/vignettes/partial_centrality.Rmd | 26 netrankr-1.0.0/netrankr/vignettes/positional_dominance.Rmd | 20 netrankr-1.0.0/netrankr/vignettes/probabilistic_cent.Rmd | 23 netrankr-1.0.0/netrankr/vignettes/threshold_graph.Rmd | 5 netrankr-1.0.0/netrankr/vignettes/use_case.Rmd | 26 77 files changed, 1168 insertions(+), 2958 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut],
Michela Pasetto [aut, cre],
Open Analytics [cph]
Maintainer: Michela Pasetto <michela.pasetto@openanalytics.eu>
Diff between clinUtils versions 0.0.2 dated 2021-07-14 and 0.0.3 dated 2021-07-16
DESCRIPTION | 11 MD5 | 14 inst/doc/clinUtils-vignette.R | 5 inst/doc/clinUtils-vignette.Rmd | 6 inst/doc/clinUtils-vignette.html | 73 - tests/testthat/test_getClinDT.R | 1415 +++++++++++++++---------------- tests/testthat/test_knitPrintListPlots.R | 125 +- vignettes/clinUtils-vignette.Rmd | 6 8 files changed, 840 insertions(+), 815 deletions(-)
Title: Flexible Phenotype Simulation from Different Genetic and Noise
Models
Description: Simulation is a critical part of method development and assessment
in quantitative genetics. 'PhenotypeSimulator' allows for the flexible
simulation of phenotypes under different models, including genetic variant
and infinitesimal genetic effects (reflecting population structure) as well
as non-genetic covariate effects, observational noise and additional
correlation effects. The different phenotype components are combined into a
final phenotype while controlling for the proportion of variance explained
by each of the components. For each effect component, the number of
variables, their distribution and the design of their effect across traits
can be customised. For the simulation of the genetic effects, external
genotype data from a number of standard software ('plink', 'hapgen2'/
'impute2', 'genome', 'bimbam', simple text files) can be imported. The final
simulated phenotypes and its components can be automatically saved into .rds
or .csv files. In addition, they can be saved in formats compatible with
commonly used genetic association software ('gemma', 'bimbam', 'plink',
'snptest', 'LiMMBo').
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>),
Konrad Rudolph [ctb] (<https://orcid.org/0000-0002-9866-7051>)
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>
Diff between PhenotypeSimulator versions 0.3.3 dated 2019-05-15 and 0.3.4 dated 2021-07-16
PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Sample-scripts-external-genotype-simulation.R |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Sample-scripts-external-genotype-simulation.Rmd |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Sample-scripts-external-genotype-simulation.pdf |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/tests/testthat/test-components.r |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/vignettes/Sample-scripts-external-genotype-simulation.Rmd |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/DESCRIPTION | 17 PhenotypeSimulator-0.3.4/PhenotypeSimulator/MD5 | 93 +-- PhenotypeSimulator-0.3.4/PhenotypeSimulator/NEWS.md | 15 PhenotypeSimulator-0.3.4/PhenotypeSimulator/R/PhenotypeSimulator.R | 1 PhenotypeSimulator-0.3.4/PhenotypeSimulator/R/commandlineFunctions.R | 1 PhenotypeSimulator-0.3.4/PhenotypeSimulator/R/genotypeFunctions.R | 58 +- PhenotypeSimulator-0.3.4/PhenotypeSimulator/R/outputFunctions.R | 54 +- PhenotypeSimulator-0.3.4/PhenotypeSimulator/README.md | 69 ++ PhenotypeSimulator-0.3.4/PhenotypeSimulator/build/vignette.rds |binary PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/CITATION | 1 PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/PhenotypeSimulator.R | 40 - PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/PhenotypeSimulator.pdf |binary PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/Simulation-and-LinearModel.R | 44 - PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/Simulation-and-LinearModel.Rmd | 252 +++++++--- PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/Simulation-and-LinearModel.pdf |binary PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/SimulationBasedOnExampleData.R | 30 - PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/SimulationBasedOnExampleData.Rmd | 18 PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/SimulationBasedOnExampleData.pdf |binary PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/sample-scripts-external-genotype-simulation.R |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/sample-scripts-external-genotype-simulation.Rmd |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/doc/sample-scripts-external-genotype-simulation.pdf |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/inst/extdata/vignettes/gwas_results_gemma_qqplot.png |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/PhenotypeSimulator.Rd | 4 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/correlatedBgEffects.Rd | 14 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/geneticBgEffects.Rd | 13 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/geneticFixedEffects.Rd | 21 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/getCausalSNPs.Rd | 22 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/getKinship.Rd | 14 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/noiseBgEffects.Rd | 15 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/noiseFixedEffects.Rd | 31 - PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/readStandardGenotypes.Rd | 44 + PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/runSimulation.Rd | 92 ++- PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/savePheno.Rd | 11 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/setModel.Rd | 29 - PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/simulateDist.Rd | 10 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/simulateGenotypes.Rd | 10 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/simulatePhenotypes.Rd | 28 - PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/standardiseGenotypes.Rd | 11 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/testNumerics.Rd | 3 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/transformNonlinear.Rd | 13 PhenotypeSimulator-0.3.4/PhenotypeSimulator/man/writeStandardOutput.Rd | 81 +-- PhenotypeSimulator-0.3.4/PhenotypeSimulator/tests/testthat/test-components.R |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/tests/testthat/test-genotype.r | 228 +++++---- PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/Simulation-and-LinearModel.Rmd | 252 +++++++--- PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/SimulationBasedOnExampleData.Rmd | 18 PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/cor_pheno-min.png |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/cor_simulated-min.png |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/gwas_results_gemma_qqplot.png |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/sample-scripts-external-genotype-simulation.Rmd |only PhenotypeSimulator-0.3.4/PhenotypeSimulator/vignettes/wallthickness-min.png |only 55 files changed, 1125 insertions(+), 532 deletions(-)
More information about PhenotypeSimulator at CRAN
Permanent link
Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary
data. See Abrams and colleagues, 2021, <doi:10.1093/bioinformatics/btab037>.
Author: Kevin R. Coombes, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 1.0.0 dated 2021-02-12 and 1.1.1 dated 2021-07-16
DESCRIPTION | 12 ++-- MD5 | 37 +++++++------ NAMESPACE | 4 + NEWS | 31 ++++++++++ R/02-binaryMatrix.R | 1 R/04-vis.R | 29 ++++++++-- R/06-som-umap.R |only build/vignette.rds |binary data/CML1000.rda |binary data/CML500.rda |binary data/fakedata.rda |binary data/lgfFeatures.rda |binary inst/doc/mercVis.html | 128 +++++++++++++-------------------------------- inst/doc/mercator.html | 77 +++------------------------ inst/doc/umap-som.R |only inst/doc/umap-som.Rmd |only inst/doc/umap-som.html |only man/Mercator-class.Rd | 24 +++++--- man/binaryMatrix.Rd | 2 tests/test-04vis.R | 26 +++++++-- tests/test-04vis.Rout.save | 32 ++++++++--- vignettes/umap-som.Rmd |only 22 files changed, 194 insertions(+), 209 deletions(-)
Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. medRxiv (2020) <doi:10.1101/2020.12.10.20225243>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre],
Piotr Dworzynski [aut],
Leila Arras [ctb],
Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>
Diff between CoOL versions 1.0.2 dated 2021-06-30 and 1.0.3 dated 2021-07-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/CoOL_functions.R | 7 ++++--- man/CoOL_2_train_neural_network.Rd | 4 ++-- src/RcppExports.cpp | 5 +++++ 5 files changed, 19 insertions(+), 13 deletions(-)
Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between set6 versions 0.2.1 dated 2021-02-17 and 0.2.2 dated 2021-07-16
DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- NEWS.md | 5 ++++- R/Set_Logicals.R | 2 +- build/vignette.rds |binary inst/doc/set6.html | 23 ++++++++++++++++++++--- 6 files changed, 35 insertions(+), 16 deletions(-)
Title: Ensemble Algorithms for Time Series Forecasting with Modeltime
Description: A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging,
weighted averaging, and stacking. These techniques are popular methods
to improve forecast accuracy and stability. Refer to papers such as
"Machine-Learning Models for Sales Time Series Forecasting" Pavlyshenko, B.M. (2019) <doi:10.3390>.
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime.ensemble versions 0.4.1 dated 2021-05-31 and 0.4.2 dated 2021-07-16
DESCRIPTION | 20 LICENSE | 4 MD5 | 77 - NAMESPACE | 122 - NEWS.md | 90 - R/00_global_variables.R | 10 R/00_imports.R | 12 R/dev-model_descriptions.R | 166 +- R/ensemble_average.R | 208 +-- R/ensemble_model_spec.R | 810 ++++++------- R/ensemble_weighted.R | 268 ++-- R/modeltime_calibrate.R | 26 R/modeltime_forecast.R | 1106 +++++++++--------- R/modeltime_recursive.R | 66 - R/modeltime_refit.R | 398 +++--- R/tibble-type_sum.R | 16 R/utils-pipe.R | 22 R/utils-tidy-eval.R | 94 - README.md | 396 +++--- build/vignette.rds |binary inst/doc/getting-started-with-modeltime-ensemble.R | 240 +-- inst/doc/getting-started-with-modeltime-ensemble.Rmd | 498 ++++---- inst/doc/getting-started-with-modeltime-ensemble.html | 783 ++++++------ inst/doc/recursive-ensembles.R | 344 ++--- inst/doc/recursive-ensembles.Rmd | 644 +++++----- inst/doc/recursive-ensembles.html | 916 +++++++------- man/ensemble_average.Rd | 124 +- man/ensemble_model_spec.Rd | 302 ++-- man/ensemble_weighted.Rd | 126 +- man/pipe.Rd | 24 man/tidyeval.Rd | 102 - tests/testthat.R | 38 tests/testthat/test-conf_by_id.R |only tests/testthat/test-ensemble_average.R | 382 +++--- tests/testthat/test-ensemble_model_spec.R | 586 ++++----- tests/testthat/test-ensemble_weighted.R | 234 +-- tests/testthat/test-panel-data.R | 466 +++---- tests/testthat/test-recursive.R | 466 +++---- vignettes/getting-started-with-modeltime-ensemble.Rmd | 498 ++++---- vignettes/recursive-ensembles.Rmd | 644 +++++----- 40 files changed, 5668 insertions(+), 5660 deletions(-)
More information about modeltime.ensemble at CRAN
Permanent link
Title: Multivariate Elastic Net Regression
Description: Implements high-dimensional multivariate regression by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement. If required, install MRCE or remMap from GitHub (<https://github.com/cran/MRCE>, <https://github.com/cran/remMap>).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between joinet versions 0.0.8 dated 2021-07-16 and 0.0.9 dated 2021-07-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>),
Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>),
Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>),
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.0.1 dated 2021-06-23 and 1.1.0 dated 2021-07-16
UCSCXenaShiny-1.0.1/UCSCXenaShiny/LICENSE |only UCSCXenaShiny-1.0.1/UCSCXenaShiny/inst/extdata/ccle_drug_response_extend.rda |only UCSCXenaShiny-1.1.0/UCSCXenaShiny/DESCRIPTION | 8 UCSCXenaShiny-1.1.0/UCSCXenaShiny/MD5 | 287 UCSCXenaShiny-1.1.0/UCSCXenaShiny/NAMESPACE | 150 UCSCXenaShiny-1.1.0/UCSCXenaShiny/NEWS.md | 28 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/GeomSplitViolin.R | 110 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/analyze_gene_drug_response.R | 905 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/ccle.R | 288 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/data.R | 244 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/ezcor.R | 870 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/get_pancan_value.R | 758 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/get_pcawg_value.R | 254 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/globalVariables.R | 34 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/load_data.R | 134 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/ope_pancan_value.R | 122 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/query_custom_value.R |only UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/query_toil_value_df.R | 122 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/query_value.R | 392 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/run.R | 48 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/tcga_surv.R | 412 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/utils-pipe.R | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/utils.R | 116 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/vis_analyze_gene_drug_response.R | 224 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/vis_ccle_value.R | 332 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/vis_identifier.R | 736 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/vis_pancan_value.R | 2537 - UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/vis_pcawg_value.R | 928 UCSCXenaShiny-1.1.0/UCSCXenaShiny/R/xenashiny.R | 18 UCSCXenaShiny-1.1.0/UCSCXenaShiny/README.md | 380 UCSCXenaShiny-1.1.0/UCSCXenaShiny/build/vignette.rds |binary UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/doc/api.R | 108 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/doc/api.Rmd | 254 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/doc/api.html | 886 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/modules_apps/app.R | 38 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/modules_apps/simple_module_from_rstudio.R | 66 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/modules_apps/xx_modules.R | 98 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/App.R | 656 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R | 124 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/home-pancan-search.R | 178 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-gene-drug-respose-df.R | 355 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-gene-drug-target.R | 359 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-genecor.R | 513 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-search.R | 329 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-file-upload.R | 238 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-group-comparison.R | 1492 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-matrix-correlation.R | 748 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-scatter-correlation.R | 752 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-surv-analysis.R | 1413 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-anatomy.R | 343 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-genecor.R | 496 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-immune.R | 358 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-radar.R | 402 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-search-cancer.R | 384 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-search.R | 385 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-til.R | 381 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-unicox.R | 355 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-genecor.R | 579 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-search.R | 430 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 692 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-unicox.R | 390 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/modules/modules-survival-analysis.R | 792 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/server/general-analysis.R | 298 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/server/global.R | 32 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/server/home.R | 170 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/server/modules.R | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/server/repository.R | 832 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/citation.md | 58 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/terms.md | 324 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/usage.md | 324 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/chooser.R | 94 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/developers.R | 244 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/footer.R | 32 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/general-analysis.R | 155 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/global.R | 22 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/help.R | 64 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/home.R | 284 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis.R | 156 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/ui/repository.R | 238 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/bootstrap4.css | 704 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/chooser-binding.js | 168 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-grid.css | 4098 +- UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-grid.min.css | 12 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-reboot.css | 658 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-reboot.min.css | 14 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap.css |17948 +++++----- UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap.min.css | 12 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.bundle.js |12656 +++---- UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.bundle.min.js | 12 UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.js | 7788 ++-- UCSCXenaShiny-1.1.0/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.min.js | 12 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/TCGA.organ.Rd | 30 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/UCSCXenaShiny.Rd | 18 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/analyze_gene_drug_response_asso.Rd | 74 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/analyze_gene_drug_response_diff.Rd | 130 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/app_run.Rd | 43 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/available_hosts.Rd | 34 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/ccle_absolute.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/ccle_info.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/ezcor.Rd | 98 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/ezcor_batch.Rd | 104 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/ezcor_partial_cor.Rd | 98 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/get_pancan_value.Rd | 298 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/keep_cat_cols.Rd | 44 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/load_data.Rd | 82 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/pcawg_info.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/pcawg_purity.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/pipe.Rd | 24 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/query_molecule_value.Rd | 76 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/query_pancan_value.Rd | 120 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/query_toil_value_df.Rd | 68 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_clinical.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_genome_instability.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_gtex.Rd | 30 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_purity.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_subtypes.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_surv.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_surv_analysis.Rd | 154 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/tcga_tmb.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/toil_info.Rd | 36 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_ccle_gene_cor.Rd | 108 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_ccle_tpm.Rd | 44 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_TIL_cor.Rd | 71 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_cor.Rd | 84 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_cor_cancer.Rd | 96 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_drug_response_asso.Rd | 52 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_drug_response_diff.Rd | 70 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_immune_cor.Rd | 69 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_msi_cor.Rd | 59 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_stemness_cor.Rd | 63 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_gene_tmb_cor.Rd | 59 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_identifier_cor.Rd | 136 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_identifier_grp_comparison.Rd | 212 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_identifier_grp_surv.Rd | 144 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_identifier_multi_cor.Rd | 149 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_pancan_anatomy.Rd | 62 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_pcawg_dist.Rd | 102 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_pcawg_gene_cor.Rd | 120 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_pcawg_unicox_tree.Rd | 74 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_toil_TvsN.Rd | 110 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_toil_TvsN_cancer.Rd | 92 UCSCXenaShiny-1.1.0/UCSCXenaShiny/man/vis_unicox_tree.Rd | 74 UCSCXenaShiny-1.1.0/UCSCXenaShiny/tests/testthat.R | 8 UCSCXenaShiny-1.1.0/UCSCXenaShiny/tests/testthat/test-run_app.R | 2 UCSCXenaShiny-1.1.0/UCSCXenaShiny/tests/testthat/test-vis_pancan_value.R | 10 UCSCXenaShiny-1.1.0/UCSCXenaShiny/vignettes/api.Rmd | 254 146 files changed, 38584 insertions(+), 38173 deletions(-)
Title: A 'Bootstrap 4' Version of 'shinydashboard'
Description: Make 'Bootstrap 4' Shiny dashboards. Use the full power
of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4'
<https://github.com/ColorlibHQ/AdminLTE>.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] (AdminLTE3 theme for Bootstrap 4),
Winston Chang [ctb, cph] (Utils functions from shinydashboard),
Thomas Park [ctb, cph] (Bootswatch Sketchy theme CSS)
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between bs4Dash versions 2.0.0 dated 2021-05-26 and 2.0.1 dated 2021-07-16
bs4Dash-2.0.0/bs4Dash/inst/bs4Dash-2.0.0 |only bs4Dash-2.0.1/bs4Dash/DESCRIPTION | 11 ++- bs4Dash-2.0.1/bs4Dash/MD5 | 56 ++++++++++++------- bs4Dash-2.0.1/bs4Dash/NAMESPACE | 1 bs4Dash-2.0.1/bs4Dash/NEWS.md | 11 +++ bs4Dash-2.0.1/bs4Dash/R/bs4Dash-package.r |only bs4Dash-2.0.1/bs4Dash/R/cards.R | 35 ++++++----- bs4Dash-2.0.1/bs4Dash/R/dashboardPage.R | 6 +- bs4Dash-2.0.1/bs4Dash/R/dashboardSidebar.R | 3 - bs4Dash-2.0.1/bs4Dash/R/deps.R | 16 +++-- bs4Dash-2.0.1/bs4Dash/R/render-functions.R | 2 bs4Dash-2.0.1/bs4Dash/build/bs4Dash.pdf |binary bs4Dash-2.0.1/bs4Dash/inst/bs4Dash-2.0.1 |only bs4Dash-2.0.1/bs4Dash/inst/doc/bs4Dash.html | 48 +++++++++++++--- bs4Dash-2.0.1/bs4Dash/inst/doc/css-preloader.html | 50 +++++++++++++--- bs4Dash-2.0.1/bs4Dash/inst/doc/extra-elements.html | 50 +++++++++++++--- bs4Dash-2.0.1/bs4Dash/inst/doc/improved-boxes.html | 50 +++++++++++++--- bs4Dash-2.0.1/bs4Dash/inst/doc/more-skins.html | 50 +++++++++++++--- bs4Dash-2.0.1/bs4Dash/inst/doc/step-by-step.html | 50 +++++++++++++--- bs4Dash-2.0.1/bs4Dash/inst/examples/vignettes-demos |only bs4Dash-2.0.1/bs4Dash/man/bs4Dash.Rd |only bs4Dash-2.0.1/bs4Dash/tests/testthat/test-bs4Cards.R | 16 ++--- 22 files changed, 335 insertions(+), 120 deletions(-)
Title: Add More 'AdminLTE2' Components to 'shinydashboard'
Description: Extend 'shinydashboard' with 'AdminLTE2' components.
'AdminLTE2' is a free 'Bootstrap 3' dashboard template available
at <https://adminlte.io>. Customize boxes, add timelines and a lot more.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] (AdminLTE2 theme for Bootstrap 3),
Guang Yang [ctb, cph] (ygdashboard original template),
Winston Chang [ctb, cph] (Functions from shinydashboard),
Victor Perrier [ctb] (improved the shinydashboardPlusGallery)
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between shinydashboardPlus versions 2.0.1 dated 2021-04-26 and 2.0.2 dated 2021-07-16
shinydashboardPlus-2.0.1/shinydashboardPlus/inst/shinydashboardPlus-2.0.0 |only shinydashboardPlus-2.0.2/shinydashboardPlus/DESCRIPTION | 6 shinydashboardPlus-2.0.2/shinydashboardPlus/MD5 | 63 ++++++---- shinydashboardPlus-2.0.2/shinydashboardPlus/NAMESPACE | 1 shinydashboardPlus-2.0.2/shinydashboardPlus/NEWS.md | 6 shinydashboardPlus-2.0.2/shinydashboardPlus/R/deps.R | 14 +- shinydashboardPlus-2.0.2/shinydashboardPlus/R/shinydashboardPlus-package.r |only shinydashboardPlus-2.0.2/shinydashboardPlus/build/shinydashboardPlus.pdf |binary shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/box-elements.html | 4 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/controlbar.html | 4 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/css-preloader.html | 4 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/enhanced-header.html | 4 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/improved-boxes.html | 4 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/more-skins.html | 4 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/doc/shinydashboardPlus.html | 2 shinydashboardPlus-2.0.2/shinydashboardPlus/inst/shinydashboardPlus-2.0.2 |only shinydashboardPlus-2.0.2/shinydashboardPlus/inst/vignettes-demos |only shinydashboardPlus-2.0.2/shinydashboardPlus/man/shinydashboardPlus.Rd |only 18 files changed, 71 insertions(+), 45 deletions(-)
More information about shinydashboardPlus at CRAN
Permanent link
Title: Core Functionality of the 'spatstat' Family
Description: Functionality for data analysis and modelling of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Chiara Fend [ctb],
Julian Gilbey [ctb],
Yongtao Guan [ctb],
Ute Hahn [ctb],
Kassel Hingee [ctb],
Abdollah Jalilian [ctb],
Marie-Colette van Lieshout [ctb],
Greg McSwiggan [ctb],
Tuomas Rajala [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb],
Hangsheng Wang [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.core versions 2.2-0 dated 2021-06-17 and 2.3-0 dated 2021-07-16
spatstat.core-2.2-0/spatstat.core/src/areadiff.c |only spatstat.core-2.3-0/spatstat.core/DESCRIPTION | 17 spatstat.core-2.3-0/spatstat.core/MD5 | 107 - spatstat.core-2.3-0/spatstat.core/NAMESPACE | 78 + spatstat.core-2.3-0/spatstat.core/NEWS | 105 + spatstat.core-2.3-0/spatstat.core/R/auc.R | 20 spatstat.core-2.3-0/spatstat.core/R/clusterfunctions.R | 33 spatstat.core-2.3-0/spatstat.core/R/clusterinfo.R | 108 + spatstat.core-2.3-0/spatstat.core/R/detPPF-class.R | 16 spatstat.core-2.3-0/spatstat.core/R/detpointprocfamilyfun.R | 29 spatstat.core-2.3-0/spatstat.core/R/dppm.R | 25 spatstat.core-2.3-0/spatstat.core/R/envelope.R | 71 + spatstat.core-2.3-0/spatstat.core/R/evalcovarslrm.R |only spatstat.core-2.3-0/spatstat.core/R/kppm.R | 613 +++++----- spatstat.core-2.3-0/spatstat.core/R/markcorr.R | 15 spatstat.core-2.3-0/spatstat.core/R/mincontrast.R | 113 - spatstat.core-2.3-0/spatstat.core/R/objsurf.R | 65 - spatstat.core-2.3-0/spatstat.core/R/pairs.im.R | 21 spatstat.core-2.3-0/spatstat.core/R/ppmclass.R | 4 spatstat.core-2.3-0/spatstat.core/R/quadrattest.R | 36 spatstat.core-2.3-0/spatstat.core/R/response.R |only spatstat.core-2.3-0/spatstat.core/R/rhohat.R | 28 spatstat.core-2.3-0/spatstat.core/R/rhohat.slrm.R |only spatstat.core-2.3-0/spatstat.core/R/slrm.R | 239 +++ spatstat.core-2.3-0/spatstat.core/R/summary.dppm.R | 10 spatstat.core-2.3-0/spatstat.core/R/summary.kppm.R | 11 spatstat.core-2.3-0/spatstat.core/R/sysdata.rda |binary spatstat.core-2.3-0/spatstat.core/R/transect.R | 92 - spatstat.core-2.3-0/spatstat.core/inst/doc/packagesizes.txt | 1 spatstat.core-2.3-0/spatstat.core/man/WindowOnly.Rd | 5 spatstat.core-2.3-0/spatstat.core/man/as.owin.Rd | 6 spatstat.core-2.3-0/spatstat.core/man/auc.Rd | 11 spatstat.core-2.3-0/spatstat.core/man/cov.im.Rd |only spatstat.core-2.3-0/spatstat.core/man/densityVoronoi.Rd | 2 spatstat.core-2.3-0/spatstat.core/man/domain.Rd | 3 spatstat.core-2.3-0/spatstat.core/man/dppm.Rd | 132 +- spatstat.core-2.3-0/spatstat.core/man/emend.slrm.Rd |only spatstat.core-2.3-0/spatstat.core/man/envelope.Rd | 19 spatstat.core-2.3-0/spatstat.core/man/intensity.slrm.Rd |only spatstat.core-2.3-0/spatstat.core/man/kppm.Rd | 119 + spatstat.core-2.3-0/spatstat.core/man/leverage.ppm.Rd | 1 spatstat.core-2.3-0/spatstat.core/man/leverage.slrm.Rd |only spatstat.core-2.3-0/spatstat.core/man/methods.objsurf.Rd | 25 spatstat.core-2.3-0/spatstat.core/man/methods.slrm.Rd | 16 spatstat.core-2.3-0/spatstat.core/man/model.frame.ppm.Rd | 10 spatstat.core-2.3-0/spatstat.core/man/objsurf.Rd | 3 spatstat.core-2.3-0/spatstat.core/man/pairs.im.Rd | 2 spatstat.core-2.3-0/spatstat.core/man/parameters.Rd | 3 spatstat.core-2.3-0/spatstat.core/man/plot.profilepl.Rd | 6 spatstat.core-2.3-0/spatstat.core/man/pseudoR2.Rd | 12 spatstat.core-2.3-0/spatstat.core/man/quadrat.test.Rd | 14 spatstat.core-2.3-0/spatstat.core/man/residuals.slrm.Rd |only spatstat.core-2.3-0/spatstat.core/man/response.Rd |only spatstat.core-2.3-0/spatstat.core/man/rhohat.Rd | 17 spatstat.core-2.3-0/spatstat.core/man/roc.Rd | 10 spatstat.core-2.3-0/spatstat.core/man/simulate.dppm.Rd | 13 spatstat.core-2.3-0/spatstat.core/man/spatstat.core-internal.Rd | 27 spatstat.core-2.3-0/spatstat.core/man/transect.im.Rd | 34 spatstat.core-2.3-0/spatstat.core/man/valid.slrm.Rd |only spatstat.core-2.3-0/spatstat.core/tests/testsK.R | 31 60 files changed, 1724 insertions(+), 654 deletions(-)
Title: Deep Learning Prediction of Effectors
Description: A tool that contains trained deep learning models
for predicting effector proteins. 'deepredeff' has been trained to
identify effector proteins using a set of known experimentally
validated effectors from either bacteria, fungi, or oomycetes.
Documentation is available via several vignettes, and the paper by
Kristianingsih and MacLean (2020) <doi:10.1101/2020.07.08.193250>.
Author: Ruth Kristianingsih [aut, cre, cph]
(<https://orcid.org/0000-0003-1873-6203>)
Maintainer: Ruth Kristianingsih <ruth.kristianingsih30@gmail.com>
Diff between deepredeff versions 0.1.0 dated 2020-10-23 and 0.1.1 dated 2021-07-16
DESCRIPTION | 7 MD5 | 16 +- NEWS.md | 9 + R/install.R | 8 + README.md | 44 +++--- build/vignette.rds |binary inst/doc/overview.html | 324 ++++++++++------------------------------------ inst/doc/predict.html | 307 ++++++++----------------------------------- man/install_tensorflow.Rd | 5 9 files changed, 191 insertions(+), 529 deletions(-)
Title: Data Import, Cleaning, and Conversions for Swimming Results
Description: The goal for of the 'SwimmeR' package is to provide means of acquiring, and then analyzing, data from swimming (and diving) competitions. To that end 'SwimmeR' allows results to be read in from .html sources, like 'Hy-Tek' real time results pages, '.pdf' files, 'ISL' results, and (on a development basis) '.hy3' files. Once read in, 'SwimmeR' can convert swimming times (performances) between the computationally useful format of seconds reported to the '100ths' place (e.g. 95.37), and the conventional reporting format (1:35.37) used in the swimming community. 'SwimmeR' can also score meets in a variety of formats with user defined point values, convert times between courses ('LCM', 'SCM', 'SCY') and draw single elimination brackets, as well as providing a suite of tools for working cleaning swimming data. This is a developmental package, not yet mature.
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>),
Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>
Diff between SwimmeR versions 0.10.0 dated 2021-06-02 and 0.11.0 dated 2021-07-16
SwimmeR-0.10.0/SwimmeR/R/swim_parse.R |only SwimmeR-0.10.0/SwimmeR/inst/extdata/2020_NI_Champs_Qualifier_UNAC.hy3 |only SwimmeR-0.10.0/SwimmeR/inst/extdata/DoubleColumnPDF.PNG |only SwimmeR-0.10.0/SwimmeR/inst/extdata/HSEmpireMeet.png |only SwimmeR-0.10.0/SwimmeR/inst/extdata/Texas-Florida-Indiana_image.png |only SwimmeR-0.10.0/SwimmeR/inst/extdata/df_standard.rds |only SwimmeR-0.11.0/SwimmeR/DESCRIPTION | 6 SwimmeR-0.11.0/SwimmeR/MD5 | 61 + SwimmeR-0.11.0/SwimmeR/NAMESPACE | 5 SwimmeR-0.11.0/SwimmeR/NEWS.md | 37 + SwimmeR-0.11.0/SwimmeR/R/Swim_Parse.R |only SwimmeR-0.11.0/SwimmeR/R/format_age.R | 12 SwimmeR-0.11.0/SwimmeR/R/format_results.R | 9 SwimmeR-0.11.0/SwimmeR/R/globals.R | 6 SwimmeR-0.11.0/SwimmeR/R/read_results.R | 31 SwimmeR-0.11.0/SwimmeR/R/splits_rename_omega.R |only SwimmeR-0.11.0/SwimmeR/R/splits_to_cumulative.R |only SwimmeR-0.11.0/SwimmeR/R/splits_to_lap.R |only SwimmeR-0.11.0/SwimmeR/R/swim_parse_omega.R |only SwimmeR-0.11.0/SwimmeR/README.md | 5 SwimmeR-0.11.0/SwimmeR/inst/doc/SwimmeR.R | 33 SwimmeR-0.11.0/SwimmeR/inst/doc/SwimmeR.Rmd | 52 + SwimmeR-0.11.0/SwimmeR/inst/doc/SwimmeR.html | 355 +++++----- SwimmeR-0.11.0/SwimmeR/inst/extdata/Omega_OT_100Br_Swimoff_2021.pdf |only SwimmeR-0.11.0/SwimmeR/inst/extdata/Omega_OT_400IM_Prelims_2021.pdf |only SwimmeR-0.11.0/SwimmeR/inst/extdata/Omega_OT_400m_Finals_2021.pdf |only SwimmeR-0.11.0/SwimmeR/inst/extdata/Omega_Wave1_1500_Finals_2021.pdf |only SwimmeR-0.11.0/SwimmeR/inst/extdata/Omega_Wave1_200fly_Finals_2021.pdf |only SwimmeR-0.11.0/SwimmeR/man/Swim_Parse.Rd | 2 SwimmeR-0.11.0/SwimmeR/man/age_format_helper.Rd | 2 SwimmeR-0.11.0/SwimmeR/man/read_results_flag.Rd |only SwimmeR-0.11.0/SwimmeR/man/splits_rename_omega.Rd |only SwimmeR-0.11.0/SwimmeR/man/splits_to_cumulative.Rd |only SwimmeR-0.11.0/SwimmeR/man/splits_to_cumulative_helper_recalc.Rd |only SwimmeR-0.11.0/SwimmeR/man/splits_to_lap.Rd |only SwimmeR-0.11.0/SwimmeR/man/splits_to_lap_helper_recalc.Rd |only SwimmeR-0.11.0/SwimmeR/man/swim_parse_omega.Rd |only SwimmeR-0.11.0/SwimmeR/tests/testthat/test-age_format.R | 6 SwimmeR-0.11.0/SwimmeR/tests/testthat/test-format_splits.R |only SwimmeR-0.11.0/SwimmeR/tests/testthat/test-hy3_parse.R | 9 SwimmeR-0.11.0/SwimmeR/tests/testthat/test-omega.R |only SwimmeR-0.11.0/SwimmeR/tests/testthat/test-read_results.R | 15 SwimmeR-0.11.0/SwimmeR/tests/testthat/test-swim_parse.R | 9 SwimmeR-0.11.0/SwimmeR/vignettes/SwimmeR.Rmd | 52 + 44 files changed, 506 insertions(+), 201 deletions(-)
Title: Character String Processing Facilities
Description: A multitude of character string/text/natural language
processing tools: pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation, sorting, padding,
wrapping, Unicode normalisation, date-time formatting and parsing,
and many more. They are fast, consistent, convenient, and -
thanks to 'ICU' (International Components for Unicode) -
portable across all locales and platforms.
Author: Marek Gagolewski [aut, cre, cph] (<https://orcid.org/0000-0003-0637-6028>),
Bartek Tartanus [ctb],
and others (stringi source code);
IBM, Unicode, Inc. and others (ICU4C source code, Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.7.2 dated 2021-07-14 and 1.7.3 dated 2021-07-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 +++++++- src/icu55/unicode/ucol.h | 4 ++-- src/icu55/unicode/uidna.h | 4 ++-- 5 files changed, 19 insertions(+), 13 deletions(-)
More information about ReplicationSuccess at CRAN
Permanent link
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation,
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 0.2.5 dated 2021-06-06 and 1.0.0 dated 2021-07-16
DESCRIPTION | 9 - MD5 | 32 +++-- NAMESPACE | 4 R/CNV.R |only R/Merge_methylation.R | 152 ++++++++++++++----------- R/SNP.R |only R/TCGA_id_conversion.R | 22 ++- R/ann_merge.r | 14 -- README.md | 200 +++++++++++++++++++++++++++------ inst/doc/GeoTcgaData.R | 99 ++++++++++++---- inst/doc/GeoTcgaData.Rmd | 150 +++++++++++++++++++----- inst/doc/GeoTcgaData.html | 247 ++++++++++++++++++++++++++++++----------- inst/extdata/build_hgnc_file.R | 6 man/Merge_methy_tcga.Rd | 2 man/diff_CNV.Rd |only man/diff_SNP.Rd |only man/diff_SNP_tcga.Rd |only man/id_conversion.Rd | 4 man/methyDiff.Rd |only vignettes/GeoTcgaData.Rmd | 150 +++++++++++++++++++----- 20 files changed, 806 insertions(+), 285 deletions(-)
Title: Power Analysis to Detect Spatial Relative Risk Clusters
Description: Calculate the statistical power to detect clusters using kernel-based
spatial relative risk functions that are estimated using the 'sparr' package.
Details about the 'sparr' package methods can be found in the tutorial: Davies
et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation
can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More
information about relative risk functions using kernel density estimation can
be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] (<https://orcid.org/0000-0001-9477-8582>),
Derek W. Brown [aut, cph] (<https://orcid.org/0000-0001-8393-1713>),
Mitchell J. Machiela [ctb] (<https://orcid.org/0000-0001-6538-9705>),
Timothy A. Myers [ctb],
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@nih.gov>
Diff between sparrpowR versions 0.2.2 dated 2021-06-28 and 0.2.3 dated 2021-07-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 12 ++++++++---- R/jitter_power.R | 7 ++++--- R/package.R | 2 +- R/spatial_power.R | 7 ++++--- build/partial.rdb |binary build/vignette.rds |binary tests/testthat/test-jitter_power.R | 18 ++++++++++++++---- tests/testthat/test-test-spatial_power.R | 14 ++++++++++++-- 11 files changed, 58 insertions(+), 31 deletions(-)
Title: Several Examined and Concealed States-Dependent Speciation and
Extinction
Description: Simultaneously infers state-dependent diversification across
two or more states of a single or multiple traits while accounting for the
role of a possible concealed trait. See Herrera-Alsina et al. 2019
Systematic Biology 68: 317-328 <DOI:10.1093/sysbio/syy057>.
Author: Leonel Herrera Alsina [aut],
Paul van Els [aut],
Rampal S. Etienne [cre, aut] (<https://orcid.org/0000-0003-2142-7612>)
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between secsse versions 2.1.5 dated 2021-05-25 and 2.1.7 dated 2021-07-16
DESCRIPTION | 8 MD5 | 26 - R/secsse_utils.R | 2 build/vignette.rds |binary inst/doc/Using_secsse.html | 620 ++++++++++++-------------------------- man/cla_id_paramPos.Rd | 50 +-- man/event_times.Rd | 40 +- man/example_phy_GeoSSE.Rd | 34 +- man/id_paramPos.Rd | 50 +-- man/phylo_Vign.Rd | 22 - man/prepare_full_lambdas.Rd | 42 +- man/q_doubletrans.Rd | 74 ++-- man/traitinfo.Rd | 22 - src/secsse_loglik_rhs_FORTRAN.f95 | 4 14 files changed, 384 insertions(+), 610 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 2.0.1 dated 2020-10-26 and 2.0.2 dated 2021-07-16
DESCRIPTION | 10 - MD5 | 72 ++++++------- NEWS.md | 14 ++ R/Appenders.R | 4 R/Args.R | 2 R/Cluster.R | 2 R/Layouts.R | 6 - R/Loggers.R | 4 R/Logging.R | 19 +++ R/ParallelLogger.R | 2 R/ShinyApps.R | 2 README.md | 6 - build/vignette.rds |binary inst/doc/Logging.R | 163 +++++++++++++++++------------- inst/doc/Logging.Rmd | 78 +++++++++----- inst/doc/Logging.pdf |binary inst/doc/Parallel.pdf |binary inst/shinyApps/LogViewer/global.R | 38 +------ inst/shinyApps/LogViewer/server.R | 204 ++++++++++++++++++++++++++++++++++++-- inst/shinyApps/LogViewer/ui.R | 17 ++- man/ParallelLogger-package.Rd | 2 man/addDefaultConsoleLogger.Rd | 50 ++++----- man/addDefaultEmailLogger.Rd | 2 man/convertSettingsToJson.Rd | 42 +++---- man/createConsoleAppender.Rd | 56 +++++----- man/launchLogViewer.Rd | 66 ++++++------ man/layoutTimestamp.Rd | 54 +++++----- man/logFatal.Rd | 40 +++---- man/logInfo.Rd | 58 +++++----- man/logTrace.Rd | 58 +++++----- man/logWarn.Rd | 40 +++---- man/matchInList.Rd | 90 ++++++++-------- man/registerLogger.Rd | 58 +++++----- man/saveSettingsToJson.Rd | 40 +++---- man/selectFromList.Rd | 76 +++++++------- tests/testthat.R | 1 vignettes/Logging.Rmd | 78 +++++++++----- 37 files changed, 864 insertions(+), 590 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 0.6.1 dated 2021-06-13 and 0.7.0 dated 2021-07-16
modeltime-0.6.1/modeltime/vignettes/model_fit.rds |only modeltime-0.6.1/modeltime/vignettes/refit_tbl.rds |only modeltime-0.6.1/modeltime/vignettes/temp |only modeltime-0.7.0/modeltime/DESCRIPTION | 10 modeltime-0.7.0/modeltime/MD5 | 58 ++-- modeltime-0.7.0/modeltime/NAMESPACE | 10 modeltime-0.7.0/modeltime/NEWS.md | 24 + modeltime-0.7.0/modeltime/R/00_global_variables.R | 3 modeltime-0.7.0/modeltime/R/dials-temporal_hierarchy_params.R |only modeltime-0.7.0/modeltime/R/modeltime-accuracy.R | 15 + modeltime-0.7.0/modeltime/R/modeltime-calibrate.R | 77 ++++-- modeltime-0.7.0/modeltime/R/modeltime-fit-workflowset.R | 20 + modeltime-0.7.0/modeltime/R/modeltime-forecast.R | 126 +++++++++- modeltime-0.7.0/modeltime/R/modeltime-refit.R | 9 modeltime-0.7.0/modeltime/R/parsnip-exp_smoothing.R | 13 - modeltime-0.7.0/modeltime/R/parsnip-temporal_hierarchy.R |only modeltime-0.7.0/modeltime/R/parsnip-temporal_hierarchy_data.R |only modeltime-0.7.0/modeltime/R/yardstick-metric-sets.R | 15 + modeltime-0.7.0/modeltime/R/zzz.R | 3 modeltime-0.7.0/modeltime/README.md | 15 + modeltime-0.7.0/modeltime/inst/doc/getting-started-with-modeltime.Rmd | 8 modeltime-0.7.0/modeltime/inst/doc/getting-started-with-modeltime.html | 80 +++--- modeltime-0.7.0/modeltime/man/exp_smoothing.Rd | 13 - modeltime-0.7.0/modeltime/man/modeltime_accuracy.Rd | 10 modeltime-0.7.0/modeltime/man/modeltime_calibrate.Rd | 20 + modeltime-0.7.0/modeltime/man/modeltime_forecast.Rd | 8 modeltime-0.7.0/modeltime/man/temporal_hier_fit_impl.Rd |only modeltime-0.7.0/modeltime/man/temporal_hier_predict_impl.Rd |only modeltime-0.7.0/modeltime/man/temporal_hierarchy.Rd |only modeltime-0.7.0/modeltime/man/temporal_hierarchy_params.Rd |only modeltime-0.7.0/modeltime/tests/testthat.R | 1 modeltime-0.7.0/modeltime/tests/testthat/test-algo-temporal_hierarchy.R |only modeltime-0.7.0/modeltime/tests/testthat/test-fit_workflowsets.R |only modeltime-0.7.0/modeltime/vignettes/getting-started-with-modeltime.Rmd | 8 modeltime-0.7.0/modeltime/vignettes/modeltime_roadmap.jpg |only 35 files changed, 431 insertions(+), 115 deletions(-)
Title: Simulated Predicted Probabilities for Multinomial Logit Models
Description: Functions to easily return simulated predicted probabilities and
first differences for multinomial logit models. It takes a specified
scenario and a multinomial model to predict probabilities with a set of
coefficients, drawn from a simulated sampling distribution. The simulated
predictions allow for meaningful plots with means and confidence intervals.
The methodological approach is based on the principles laid out by King,
Tomz, and Wittenberg (2000) <doi:10.2307/2669316> and Hanmer and Ozan Kalkan
(2016) <doi:10.1111/j.1540-5907.2012.00602.x>.
Author: Manuel Neumann [aut, cre] (<https://orcid.org/0000-0002-7953-3939>)
Maintainer: Manuel Neumann <manuel.neumann@mzes.uni-mannheim.de>
Diff between MNLpred versions 0.0.7 dated 2021-07-12 and 0.0.8 dated 2021-07-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/CITATION | 4 ++-- inst/doc/OVA_Predictions_For_MNL.html | 34 +++++++++++++++++----------------- tests/testthat/test_inputvariants.R | 11 ++++++----- 6 files changed, 37 insertions(+), 32 deletions(-)
More information about mlr3tuningspaces at CRAN
Permanent link
Title: Multivariate Elastic Net Regression
Description: Implements high-dimensional multivariate regression by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement. If required, install MRCE or remMap from GitHub (<https://github.com/cran/MRCE>, <https://github.com/cran/remMap>).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between joinet versions 0.0.7 dated 2021-03-09 and 0.0.8 dated 2021-07-16
.Rinstignore |only DESCRIPTION | 7 MD5 | 38 NEWS.md | 4 R/functions.R | 2579 ++++++++++++++++++++++++++------------------------ README.md | 2 build/vignette.rds |binary inst/doc/article.Rmd | 2 inst/doc/article.html | 311 +----- inst/doc/joinet.R | 140 +- inst/doc/joinet.Rmd | 2 inst/doc/joinet.html | 634 ++++-------- inst/doc/script.R | 985 +++++++++---------- inst/doc/script.Rmd | 1039 ++++++++++---------- inst/doc/script.html | 1407 ++++++++++++--------------- man/cv.joinet.Rd | 7 man/joinet.Rd | 55 - tests/testthat/test.R | 221 ++-- vignettes/article.Rmd | 2 vignettes/joinet.Rmd | 2 vignettes/script.Rmd | 1039 ++++++++++---------- 21 files changed, 4103 insertions(+), 4373 deletions(-)
Title: Australian Tax Policy Analysis
Description: Utilities to cost and evaluate Australian tax policy, including fast
projections of personal income tax collections, high-performance tax and
transfer calculators, and an interface to common indices from the Australian
Bureau of Statistics. Written to support Grattan Institute's Australian
Perspectives program, and related projects. Access to the Australian Taxation
Office's sample files of personal income tax returns is assumed.
Author: Hugh Parsonage [aut, cre],
Tim Cameron [aut],
Brendan Coates [aut],
Matthew Katzen [aut],
William Young [aut],
Ittima Cherastidtham [dtc],
W. Karsten [ctb],
M. Enrique Garcia [ctb],
Matt Cowgill [aut]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattan versions 1.9.0.4 dated 2021-01-29 and 1.9.0.9 dated 2021-07-16
grattan-1.9.0.4/grattan/R/anyWhich.R |only grattan-1.9.0.4/grattan/build |only grattan-1.9.0.4/grattan/inst/doc |only grattan-1.9.0.4/grattan/man/AnyWhich.Rd |only grattan-1.9.0.4/grattan/man/anyGeq.Rd |only grattan-1.9.0.4/grattan/man/pmax3.Rd |only grattan-1.9.0.4/grattan/man/pmaxC.Rd |only grattan-1.9.0.4/grattan/man/pmaxV.Rd |only grattan-1.9.0.4/grattan/man/pminC.Rd |only grattan-1.9.0.4/grattan/man/pminV.Rd |only grattan-1.9.0.4/grattan/man/validate_per.Rd |only grattan-1.9.0.4/grattan/src/AnyWhich.cpp |only grattan-1.9.0.4/grattan/src/Makevars.win |only grattan-1.9.0.4/grattan/src/anyOutside.cpp |only grattan-1.9.0.4/grattan/src/pmax3.cpp |only grattan-1.9.0.4/grattan/src/pmaxC.cpp |only grattan-1.9.0.4/grattan/src/pmaxV.cpp |only grattan-1.9.0.4/grattan/src/pminC.cpp |only grattan-1.9.0.4/grattan/src/pminV.cpp |only grattan-1.9.0.4/grattan/tests/testthat/test_AnyWhich.R |only grattan-1.9.0.4/grattan/tests/testthat/test_append_custom_series.R |only grattan-1.9.0.4/grattan/tests/testthat/test_income_tax_cpp.R |only grattan-1.9.0.4/grattan/tests/testthat/test_model_income_tax.R |only grattan-1.9.0.4/grattan/tests/testthat/test_pmax_friends.R |only grattan-1.9.0.4/grattan/tests/testthat/test_project.R |only grattan-1.9.0.4/grattan/tests/testthat/test_sapto.R |only grattan-1.9.0.4/grattan/tests/testthat/test_unemployment_benefit.R |only grattan-1.9.0.4/grattan/tests/testthat/test_weighted_ntile.R |only grattan-1.9.0.4/grattan/vignettes |only grattan-1.9.0.9/grattan/DESCRIPTION | 16 grattan-1.9.0.9/grattan/MD5 | 246 - grattan-1.9.0.9/grattan/NAMESPACE | 12 grattan-1.9.0.9/grattan/NEWS.md | 17 grattan-1.9.0.9/grattan/R/LITO.R | 4 grattan-1.9.0.9/grattan/R/RcppExports.R | 273 + grattan-1.9.0.9/grattan/R/age_pension.R | 2 grattan-1.9.0.9/grattan/R/age_pension_age.R | 2 grattan-1.9.0.9/grattan/R/carer_payment.R | 8 grattan-1.9.0.9/grattan/R/child_care_subsidy.R | 384 +- grattan-1.9.0.9/grattan/R/cpi_inflator.R | 2 grattan-1.9.0.9/grattan/R/cpi_inflator_quarters.R | 4 grattan-1.9.0.9/grattan/R/disability_pension.R | 2 grattan-1.9.0.9/grattan/R/family_tax_benefit.R | 6 grattan-1.9.0.9/grattan/R/grattan-package.R | 15 grattan-1.9.0.9/grattan/R/income_tax.R | 559 ++- grattan-1.9.0.9/grattan/R/kakwani.R |only grattan-1.9.0.9/grattan/R/lf_inflator.R | 593 +-- grattan-1.9.0.9/grattan/R/medicare_levy.R | 155 grattan-1.9.0.9/grattan/R/model_child_care_subsidy.R | 362 - grattan-1.9.0.9/grattan/R/model_income_tax.R | 1831 +++++----- grattan-1.9.0.9/grattan/R/model_income_tax2122.R |only grattan-1.9.0.9/grattan/R/new_medicare_levy.R | 12 grattan-1.9.0.9/grattan/R/newstart_allowance.R | 10 grattan-1.9.0.9/grattan/R/pmaxC.R |only grattan-1.9.0.9/grattan/R/rename_sf2alife.R |only grattan-1.9.0.9/grattan/R/rent_assistance.R | 2 grattan-1.9.0.9/grattan/R/residential_property_prices.R | 2 grattan-1.9.0.9/grattan/R/sapto.R | 50 grattan-1.9.0.9/grattan/R/student_repayment.R | 4 grattan-1.9.0.9/grattan/R/sysdata.rda |binary grattan-1.9.0.9/grattan/R/utils.R | 4 grattan-1.9.0.9/grattan/R/validate_date.R | 241 - grattan-1.9.0.9/grattan/R/validate_per.R | 122 grattan-1.9.0.9/grattan/R/wage_inflator.R | 2 grattan-1.9.0.9/grattan/R/youth_allowance.R | 27 grattan-1.9.0.9/grattan/R/zzz.R | 5 grattan-1.9.0.9/grattan/man/age_pension_age.Rd | 58 grattan-1.9.0.9/grattan/man/carer_payment.Rd | 182 grattan-1.9.0.9/grattan/man/child_care_subsidy.Rd | 200 - grattan-1.9.0.9/grattan/man/cpi_inflator.Rd | 2 grattan-1.9.0.9/grattan/man/cpi_inflator_quarters.Rd | 4 grattan-1.9.0.9/grattan/man/energy_supplement.Rd | 124 grattan-1.9.0.9/grattan/man/income_tax.Rd | 2 grattan-1.9.0.9/grattan/man/lf_inflator.Rd | 7 grattan-1.9.0.9/grattan/man/medicare_levy.Rd | 64 grattan-1.9.0.9/grattan/man/model_child_care_subsidy.Rd | 110 grattan-1.9.0.9/grattan/man/model_income_tax.Rd | 2 grattan-1.9.0.9/grattan/man/newstart_allowance.Rd | 174 grattan-1.9.0.9/grattan/man/reexports.Rd | 9 grattan-1.9.0.9/grattan/man/rent_assistance.Rd | 164 grattan-1.9.0.9/grattan/man/residential_property_prices.Rd | 2 grattan-1.9.0.9/grattan/man/sapto.Rd | 7 grattan-1.9.0.9/grattan/man/student_repayment.Rd | 92 grattan-1.9.0.9/grattan/man/validate_date.Rd | 5 grattan-1.9.0.9/grattan/man/wage_inflator.Rd | 2 grattan-1.9.0.9/grattan/man/youth_allowance.Rd | 206 - grattan-1.9.0.9/grattan/src/IncomeTax.cpp | 1 grattan-1.9.0.9/grattan/src/Medicare.h |only grattan-1.9.0.9/grattan/src/Offset.cpp | 70 grattan-1.9.0.9/grattan/src/Offset.h |only grattan-1.9.0.9/grattan/src/Person.h |only grattan-1.9.0.9/grattan/src/RcppExports.cpp | 642 ++- grattan-1.9.0.9/grattan/src/Sapto.cpp |only grattan-1.9.0.9/grattan/src/Sapto.h |only grattan-1.9.0.9/grattan/src/constants.cpp |only grattan-1.9.0.9/grattan/src/do_income_tax.cpp |only grattan-1.9.0.9/grattan/src/do_lito.cpp |only grattan-1.9.0.9/grattan/src/grattan.h | 57 grattan-1.9.0.9/grattan/src/grattanMedicareLevy.h |only grattan-1.9.0.9/grattan/src/medicare_levies.cpp |only grattan-1.9.0.9/grattan/src/sapto_rcpp_singleton.cpp | 1 grattan-1.9.0.9/grattan/src/yrs |only grattan-1.9.0.9/grattan/tests/testthat/test-decode_age_range.R |only grattan-1.9.0.9/grattan/tests/testthat/test-income_tax2.R |only grattan-1.9.0.9/grattan/tests/testthat/test_aus_pop_qtr.R | 169 grattan-1.9.0.9/grattan/tests/testthat/test_cpi.R | 41 grattan-1.9.0.9/grattan/tests/testthat/test_incometax_dotsATO.R | 60 grattan-1.9.0.9/grattan/tests/testthat/test_incometax_dotsATO_sfa.R | 20 grattan-1.9.0.9/grattan/tests/testthat/test_incometax_single.R | 204 - grattan-1.9.0.9/grattan/tests/testthat/test_lf_inflator.R | 9 grattan-1.9.0.9/grattan/tests/testthat/test_medicare_levy.R | 89 grattan-1.9.0.9/grattan/tests/testthat/test_modelCJ.R |only grattan-1.9.0.9/grattan/tests/testthat/test_rent_assistance.R | 6 grattan-1.9.0.9/grattan/tests/testthat/test_super_vars.R | 5 grattan-1.9.0.9/grattan/tests/testthat/test_total_receipts.R | 11 grattan-1.9.0.9/grattan/tests/testthat/test_utils.R | 3 grattan-1.9.0.9/grattan/tests/testthat/test_wage_inflator.R | 21 117 files changed, 4498 insertions(+), 3301 deletions(-)
Title: Generalized Linear Mixed Model Association Tests
Description: Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
Author: Han Chen, Matthew P. Conomos, Duy T. Pham
Maintainer: Han Chen <Han.Chen.2@uth.tmc.edu>
Diff between GMMAT versions 1.3.1 dated 2020-09-23 and 1.3.2 dated 2021-07-16
DESCRIPTION | 8 +-- MD5 | 20 ++++----- R/SMMAT.R | 85 +++++++++++++++++++++++++++------------ R/glmm.score.R | 40 +++++++++++++----- inst/COPYRIGHTS | 2 inst/doc/GMMAT.Rnw | 15 +++++- inst/doc/GMMAT.pdf |binary man/SMMAT.Rd | 4 - man/glmm.score.Rd | 2 src/fitglmm.cpp | 112 ++++++++++++++++++---------------------------------- vignettes/GMMAT.Rnw | 15 +++++- 11 files changed, 170 insertions(+), 133 deletions(-)
Title: Environmental Interpolation using Spatial Kernel Density
Estimation
Description: Estimates an ecological niche using occurrence data, covariates, and kernel
density-based estimation methods. For a single species with presence and absence data,
the 'envi' package uses the spatial relative risk function that is estimated using the
'sparr' package. Details about the 'sparr' package methods can be found in the tutorial:
Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can
be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about
relative risk functions using kernel density estimation can be found in J. F. Bithell
(1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] (<https://orcid.org/0000-0001-9477-8582>),
Lance A. Waller [ctb, ths] (<https://orcid.org/0000-0001-5002-8886>),
Emory University [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between envi versions 0.1.8 dated 2021-03-15 and 0.1.9 dated 2021-07-16
DESCRIPTION | 9 +++----- MD5 | 20 ++++++++--------- NAMESPACE | 1 NEWS.md | 5 ++++ R/lrren.R | 7 +++--- R/package.R | 2 - R/perlrren.R | 7 +++--- build/partial.rdb |binary build/vignette.rds |binary tests/testthat/test-lrren.R | 46 ++++++++++++++++++++++++----------------- tests/testthat/test-perlrren.R | 16 ++++++++++---- 11 files changed, 69 insertions(+), 44 deletions(-)
Title: Data Operator
Description: Flexibly convert data between long and wide format using just two
functions: reshape_toLong() and reshape_toWide().
Author: Jing Zhang, Zhi Jin
Maintainer: Jing Zhang<zj391120@163.com>
Diff between do versions 1.8.0.0 dated 2021-05-28 and 1.9.0.0 dated 2021-07-16
do-1.8.0.0/do/R/as.data.frame.rules.R |only do-1.8.0.0/do/R/common.R |only do-1.8.0.0/do/man/as.data.frame.rules.Rd |only do-1.8.0.0/do/man/common.Rd |only do-1.8.0.0/do/man/detach2.Rd |only do-1.9.0.0/do/DESCRIPTION | 8 do-1.9.0.0/do/MD5 | 76 ++++- do-1.9.0.0/do/NAMESPACE | 38 ++ do-1.9.0.0/do/R/Replace.R | 36 +- do-1.9.0.0/do/R/Replace0.R | 11 do-1.9.0.0/do/R/as.data.frame.R |only do-1.9.0.0/do/R/attr_herf.R |only do-1.9.0.0/do/R/cnOS.R |only do-1.9.0.0/do/R/col_split.R | 6 do-1.9.0.0/do/R/compare.R |only do-1.9.0.0/do/R/deparse0.R |only do-1.9.0.0/do/R/detach_rm_all.R | 2 do-1.9.0.0/do/R/exec.R |only do-1.9.0.0/do/R/file.name.R |only do-1.9.0.0/do/R/fmt.R |only do-1.9.0.0/do/R/give_names.R |only do-1.9.0.0/do/R/is.dir.R |only do-1.9.0.0/do/R/left_equal.R |only do-1.9.0.0/do/R/legal.R |only do-1.9.0.0/do/R/load_extdata.R |only do-1.9.0.0/do/R/mid.R | 2 do-1.9.0.0/do/R/model.data.R | 88 ++---- do-1.9.0.0/do/R/package_all.R |only do-1.9.0.0/do/R/read_R.R |only do-1.9.0.0/do/R/rm_nchar.R |only do-1.9.0.0/do/R/select.R |only do-1.9.0.0/do/R/seq_range.R |only do-1.9.0.0/do/R/show_function.R |only do-1.9.0.0/do/R/table_NA.R |only do-1.9.0.0/do/R/write_xlsx.R |only do-1.9.0.0/do/build/vignette.rds |binary do-1.9.0.0/do/inst/doc/version-update.html | 412 +++++++---------------------- do-1.9.0.0/do/man/Replace.Rd | 4 do-1.9.0.0/do/man/Replace0.Rd | 10 do-1.9.0.0/do/man/as.data.frame.Rd |only do-1.9.0.0/do/man/attr_herf.Rd |only do-1.9.0.0/do/man/cnOS.Rd |only do-1.9.0.0/do/man/col_split.Rd | 4 do-1.9.0.0/do/man/compare.Rd |only do-1.9.0.0/do/man/deparse0.Rd |only do-1.9.0.0/do/man/exec.Rd |only do-1.9.0.0/do/man/file.name.Rd |only do-1.9.0.0/do/man/fmt.Rd |only do-1.9.0.0/do/man/give_names.Rd |only do-1.9.0.0/do/man/is.dir.Rd |only do-1.9.0.0/do/man/left_equal.Rd |only do-1.9.0.0/do/man/legal.Rd |only do-1.9.0.0/do/man/load_extdata.Rd |only do-1.9.0.0/do/man/mid.Rd | 2 do-1.9.0.0/do/man/pakcage_all.Rd |only do-1.9.0.0/do/man/right_equal.Rd |only do-1.9.0.0/do/man/rm_nchar.Rd |only do-1.9.0.0/do/man/select.Rd |only do-1.9.0.0/do/man/seq_range.Rd |only do-1.9.0.0/do/man/show_function.Rd |only do-1.9.0.0/do/man/table_NA.Rd |only do-1.9.0.0/do/man/unlibray.Rd |only do-1.9.0.0/do/man/write_xlsx.Rd |only 63 files changed, 281 insertions(+), 418 deletions(-)
Title: Co-Clustering Adjusted Rand Index and Bikm1 Procedure for
Contingency and Binary Data-Sets
Description: Co-clustering of the rows and columns of a contingency or binary matrix, or double binary matrices and model selection for the number of row and column clusters. Three models are considered: the Poisson latent block model for contingency matrix, the binary latent block model for binary matrix and a new model we develop: the multiple latent block model for double binary matrices. A new procedure named bikm1 is implemented to investigate more efficiently the grid of numbers of clusters. Then, the studied model selection criteria are the integrated completed likelihood (ICL) and the Bayesian integrated likelihood (BIC). Finally, the co-clustering adjusted Rand index (CARI) to measure agreement between co-clustering partitions is implemented. Robert Valerie, Vasseur Yann, Brault Vincent (2021) <doi:10.1007/s00357-020-09379-w>.
Author: Valerie Robert [aut, cre]
Maintainer: Valerie Robert <valerie.robert.math@gmail.com>
Diff between bikm1 versions 1.0.0 dated 2020-01-28 and 1.1.0 dated 2021-07-16
DESCRIPTION | 13 MD5 | 37 +- NAMESPACE | 6 NEWS.md | 4 R/BIKM1_LBM_Binary-class.R | 11 R/BIKM1_LBM_Poisson-class.R | 2 R/bikm1-package.R | 3 R/bikm1_LBM_Poisson_functions.R | 532 +++++++++++++++++++++++++++++++---- R/bikm1_MLBM_Binary_functions.R | 319 +++++++++++++++++--- man/ARI-proc.Rd | 2 man/BinBlocRnd_MLBM-proc.Rd | 2 man/CARI-proc.Rd | 4 man/CE_LBM-proc.Rd | 16 - man/CE_simple-proc.Rd | 15 man/CoNMI-proc.Rd |only man/ENMI-proc.Rd |only man/MI_simple-proc.Rd |only man/NCE_LBM-proc.Rd |only man/NCE_simple-proc.Rd |only man/bikm1-package.Rd | 2 man/plot-BIKM1_LBM_Binary-method.Rd | 10 man/plot-BIKM1_LBM_Poisson-method.Rd | 2 22 files changed, 812 insertions(+), 168 deletions(-)
Title: TERN AusPlots Analysis Package
Description: Extraction, preparation, visualisation and analysis of TERN AusPlots ecosystem monitoring data. Direct access to plot-based data on vegetation and soils across Australia, including physical sample barcode numbers. Simple function calls extract the data and merge them into species occurrence matrices for downstream analysis, or calculate things like basal area and fractional cover. TERN AusPlots is a national field plot-based ecosystem surveillance monitoring method and dataset for Australia. The data have been collected across a national network of plots and transects by the Terrestrial Ecosystem Research Network (TERN - <https://www.tern.org.au>), an Australian Government NCRIS-enabled project, and its Ecosystem Surveillance platform (<https://www.tern.org.au/tern-observatory/tern-ecosystem-surveillance/>).
Author: Greg Guerin [aut, cre],
Tom Saleeba [aut],
Samantha Munroe [aut],
Bernardo Blanco-Martin [aut],
Irene Martín-Forés [aut],
Andrew Tokmakoff [aut]
Maintainer: Greg Guerin <ggueri01@gmail.com>
Diff between ausplotsR versions 1.2.5 dated 2021-07-15 and 1.2.6 dated 2021-07-16
DESCRIPTION | 10 - MD5 | 12 - NAMESPACE | 1 R/ausplots_queries.r | 10 - inst/doc/start_guide.R | 86 ++++++++++++++ inst/doc/start_guide.html | 280 +++++++++++++++++++++++++++++++++++++++++++++- man/ausplotsR-package.Rd | 4 7 files changed, 377 insertions(+), 26 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and direct
extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR',
'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma'
and 'xz'.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Ondrej Holy [cph] (archive_write_add_filter implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between archive versions 1.0.1 dated 2021-07-09 and 1.0.2 dated 2021-07-16
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ build/archive.pdf |binary src/archive.cpp | 3 +++ src/archive_extract.cpp | 2 ++ src/archive_read.cpp | 4 +++- src/archive_write.cpp | 5 +++++ src/archive_write_direct.cpp | 3 +++ src/r_archive.cpp | 2 +- src/r_archive.h | 29 +++++++++++++++++++++++++++-- tests/testthat/test-archive.R | 2 ++ tests/testthat/test-archive_extract.R | 10 +++++++++- tests/testthat/test-archive_read.R | 1 + tests/testthat/test-archive_write.R | 32 ++++++++++++++++++++++++++++++++ 15 files changed, 109 insertions(+), 22 deletions(-)
Title: Cell Type Identification and Discovery from Single Cell Gene
Expression Data
Description: An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.
Author: Mathew Chamberlain [aut, cre],
Virginia Savova [aut],
Richa Hanamsagar [aut],
Frank Nestle [aut],
Emanuele de Rinaldis [aut],
Sanofi US [fnd]
Maintainer: Mathew Chamberlain <chamberlainphd@gmail.com>
Diff between SignacX versions 2.2.2 dated 2021-06-24 and 2.2.3 dated 2021-07-16
DESCRIPTION | 8 ++--- MD5 | 26 +++++++++---------- NEWS.md | 12 ++++++++ R/MASC.R | 3 +- README.md | 8 ++--- inst/doc/Crabeating_vignette.html | 4 +- inst/doc/SignacFast-Seurat_AMP_RA.html | 4 +- inst/doc/signac-SPRING_Learning.html | 4 +- inst/doc/signac-Seurat_AMP.html | 4 +- inst/doc/signac-Seurat_AMP_RA.html | 4 +- inst/doc/signac-Seurat_CITE-seq.html | 4 +- inst/doc/signac-Seurat_pbmcs.html | 4 +- man/MASC.Rd | 3 +- vignettes/fls/tutorial_times_Crabeating_vignette.csv | 8 ++--- 14 files changed, 55 insertions(+), 41 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures
with quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 2.7.0 dated 2021-01-26 and 2.8.0 dated 2021-07-16
qgcomp-2.7.0/qgcomp/R/utility.R |only qgcomp-2.8.0/qgcomp/DESCRIPTION | 8 qgcomp-2.8.0/qgcomp/MD5 | 67 +- qgcomp-2.8.0/qgcomp/NAMESPACE | 2 qgcomp-2.8.0/qgcomp/NEWS.md | 10 qgcomp-2.8.0/qgcomp/R/base.R | 732 ++++++++-------------- qgcomp-2.8.0/qgcomp/R/base_bounds.R | 215 +++--- qgcomp-2.8.0/qgcomp/R/base_generics.R | 8 qgcomp-2.8.0/qgcomp/R/base_hurdle.R | 73 -- qgcomp-2.8.0/qgcomp/R/base_samplesplits.R | 18 qgcomp-2.8.0/qgcomp/R/base_simhelpers.R |only qgcomp-2.8.0/qgcomp/R/base_surv.R | 57 - qgcomp-2.8.0/qgcomp/R/base_utility.R |only qgcomp-2.8.0/qgcomp/R/base_zi.R | 52 - qgcomp-2.8.0/qgcomp/README.md | 2 qgcomp-2.8.0/qgcomp/inst/doc/qgcomp-vignette.R | 21 qgcomp-2.8.0/qgcomp/inst/doc/qgcomp-vignette.Rmd | 73 ++ qgcomp-2.8.0/qgcomp/inst/doc/qgcomp-vignette.html | 117 +++ qgcomp-2.8.0/qgcomp/inst/fig/fighex_social.png |only qgcomp-2.8.0/qgcomp/man/checknames.Rd | 2 qgcomp-2.8.0/qgcomp/man/msm.fit.Rd | 5 qgcomp-2.8.0/qgcomp/man/pointwisebound.boot.Rd | 1 qgcomp-2.8.0/qgcomp/man/pointwisebound.noboot.Rd | 25 qgcomp-2.8.0/qgcomp/man/qgcomp.Rd | 6 qgcomp-2.8.0/qgcomp/man/qgcomp.boot.Rd | 70 +- qgcomp-2.8.0/qgcomp/man/qgcomp.cox.boot.Rd | 3 qgcomp-2.8.0/qgcomp/man/qgcomp.hurdle.boot.Rd | 3 qgcomp-2.8.0/qgcomp/man/qgcomp.noboot.Rd | 6 qgcomp-2.8.0/qgcomp/man/qgcomp.partials.Rd | 18 qgcomp-2.8.0/qgcomp/man/qgcomp.zi.boot.Rd | 3 qgcomp-2.8.0/qgcomp/man/quantize.Rd | 6 qgcomp-2.8.0/qgcomp/man/se_comb.Rd | 2 qgcomp-2.8.0/qgcomp/man/simdata_quantized.Rd |only qgcomp-2.8.0/qgcomp/man/vc_comb.Rd | 4 qgcomp-2.8.0/qgcomp/tests/test_basics.R | 5 qgcomp-2.8.0/qgcomp/tests/test_bayesqgcomp.R | 4 qgcomp-2.8.0/qgcomp/vignettes/qgcomp-vignette.Rmd | 73 ++ 37 files changed, 891 insertions(+), 800 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Produce pdf, rtf, text report files.
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between ncar versions 0.4.3 dated 2021-06-10 and 0.4.4 dated 2021-07-16
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/pdfNCA.R | 28 +++++++++++++++------------- R/rtfNCA.R | 4 ++-- R/txtNCA.R | 4 ++-- inst/NEWS.Rd | 5 +++++ inst/doc/ncar-manual.pdf |binary man/pdfNCA.Rd | 4 +++- man/rtfNCA.Rd | 4 +++- man/txtNCA.Rd | 4 +++- 10 files changed, 47 insertions(+), 34 deletions(-)
Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), Anova of aligned ranks (Wobbrock, JO, Findlater, L., Gergle, D., Higgins , JJ (2011), <doi: 10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi: 10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Author: Gabriel Danilo Shimizu [aut, cre]
(<https://orcid.org/0000-0001-8524-508X>),
Rodrigo Yudi Palhaci Marubayashi [aut, ctb]
(<https://orcid.org/0000-0003-2778-8654>),
Leandro Simoes Azeredo Goncalves [aut, ctb]
(<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>
Diff between AgroR versions 1.2.1 dated 2021-06-24 and 1.2.2 dated 2021-07-16
DESCRIPTION | 8 +-- MD5 | 20 ++++--- NAMESPACE | 1 NEWS.md | 9 +++ R/DBCglm_function.R | 2 R/FAT2DICart_function.R | 7 +- R/auxiliar_function.R | 109 +++++++++++++++++++++++++++++++++++++++--- R/barplot_positive_function.R | 5 + R/pca_function.R |only man/DBC.glm.Rd | 2 man/PCA_function.Rd |only man/barplot_positive.Rd | 3 + 12 files changed, 139 insertions(+), 27 deletions(-)