Title: Convenience Functions for Psychology
Description: Make your workflow faster and easier. Easily customizable
plots (via 'ggplot2'), nice APA tables (following the style of the
*American Psychological Association*) exportable to Word (via
'flextable'), easily run statistical tests or check assumptions, and
automatize various other tasks.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between rempsyc versions 0.0.9 dated 2022-09-26 and 0.1.0 dated 2022-11-01
rempsyc-0.0.9/rempsyc/R/cormatrix_excel2.R |only rempsyc-0.0.9/rempsyc/R/lmsupport_modeleffectsizes.R |only rempsyc-0.0.9/rempsyc/man/cormatrix_excel2.Rd |only rempsyc-0.0.9/rempsyc/man/lmSupport_modelEffectSizes.Rd |only rempsyc-0.1.0/rempsyc/DESCRIPTION | 22 rempsyc-0.1.0/rempsyc/MD5 | 170 rempsyc-0.1.0/rempsyc/NAMESPACE | 46 rempsyc-0.1.0/rempsyc/NEWS.md | 52 rempsyc-0.1.0/rempsyc/R/cormatrix_excel.R | 437 + rempsyc-0.1.0/rempsyc/R/cormatrix_excel_deprecated.R |only rempsyc-0.1.0/rempsyc/R/find_mad.R | 2 rempsyc-0.1.0/rempsyc/R/global_variables.R | 2 rempsyc-0.1.0/rempsyc/R/nice_assumptions.R | 3 rempsyc-0.1.0/rempsyc/R/nice_contrasts.R | 31 rempsyc-0.1.0/rempsyc/R/nice_density.R | 52 rempsyc-0.1.0/rempsyc/R/nice_lm.R | 2 rempsyc-0.1.0/rempsyc/R/nice_lm_slopes.R | 11 rempsyc-0.1.0/rempsyc/R/nice_mod.R | 2 rempsyc-0.1.0/rempsyc/R/nice_na.R | 5 rempsyc-0.1.0/rempsyc/R/nice_normality.R | 10 rempsyc-0.1.0/rempsyc/R/nice_qq.R | 31 rempsyc-0.1.0/rempsyc/R/nice_scatter.R | 84 rempsyc-0.1.0/rempsyc/R/nice_slopes.R | 19 rempsyc-0.1.0/rempsyc/R/nice_t_test.R | 3 rempsyc-0.1.0/rempsyc/R/nice_table.R | 156 rempsyc-0.1.0/rempsyc/R/nice_var.R | 2 rempsyc-0.1.0/rempsyc/R/nice_varplot.R | 16 rempsyc-0.1.0/rempsyc/R/nice_violin.R | 88 rempsyc-0.1.0/rempsyc/R/overlap_circle.R | 7 rempsyc-0.1.0/rempsyc/R/rcompanion_groupwisemean.R | 34 rempsyc-0.1.0/rempsyc/R/reexports.R | 8 rempsyc-0.1.0/rempsyc/R/sr2.R |only rempsyc-0.1.0/rempsyc/R/utils.R | 31 rempsyc-0.1.0/rempsyc/R/zzz.R | 3 rempsyc-0.1.0/rempsyc/README.md | 211 rempsyc-0.1.0/rempsyc/inst/doc/assumptions.R | 6 rempsyc-0.1.0/rempsyc/inst/doc/assumptions.Rmd | 20 rempsyc-0.1.0/rempsyc/inst/doc/assumptions.html | 1034 ++-- rempsyc-0.1.0/rempsyc/inst/doc/circles.R | 6 rempsyc-0.1.0/rempsyc/inst/doc/circles.Rmd | 18 rempsyc-0.1.0/rempsyc/inst/doc/circles.html | 636 +- rempsyc-0.1.0/rempsyc/inst/doc/contrasts.R | 8 rempsyc-0.1.0/rempsyc/inst/doc/contrasts.Rmd | 13 rempsyc-0.1.0/rempsyc/inst/doc/contrasts.html | 1064 ++-- rempsyc-0.1.0/rempsyc/inst/doc/moderation.Rmd | 4 rempsyc-0.1.0/rempsyc/inst/doc/moderation.html | 1377 ++++-- rempsyc-0.1.0/rempsyc/inst/doc/randomize.R | 24 rempsyc-0.1.0/rempsyc/inst/doc/randomize.Rmd | 52 rempsyc-0.1.0/rempsyc/inst/doc/randomize.html | 844 ++- rempsyc-0.1.0/rempsyc/inst/doc/scatter.R | 42 rempsyc-0.1.0/rempsyc/inst/doc/scatter.Rmd | 48 rempsyc-0.1.0/rempsyc/inst/doc/scatter.html | 1189 ++--- rempsyc-0.1.0/rempsyc/inst/doc/t-test.R | 3 rempsyc-0.1.0/rempsyc/inst/doc/t-test.Rmd | 7 rempsyc-0.1.0/rempsyc/inst/doc/t-test.html | 1260 ++++- rempsyc-0.1.0/rempsyc/inst/doc/table.R | 38 rempsyc-0.1.0/rempsyc/inst/doc/table.Rmd | 51 rempsyc-0.1.0/rempsyc/inst/doc/table.html | 2293 ++++++++-- rempsyc-0.1.0/rempsyc/inst/doc/violin.R | 58 rempsyc-0.1.0/rempsyc/inst/doc/violin.Rmd | 85 rempsyc-0.1.0/rempsyc/inst/doc/violin.html | 1047 ++-- rempsyc-0.1.0/rempsyc/man/cormatrix_excel.Rd | 36 rempsyc-0.1.0/rempsyc/man/cormatrix_excel_deprecated.Rd |only rempsyc-0.1.0/rempsyc/man/figures/README-nice_contrasts-1.png |binary rempsyc-0.1.0/rempsyc/man/figures/README-nice_mod-1.png |binary rempsyc-0.1.0/rempsyc/man/figures/README-nice_slopes-1.png |binary rempsyc-0.1.0/rempsyc/man/figures/README-nice_t_test-1.png |binary rempsyc-0.1.0/rempsyc/man/figures/README-nice_violin-1.png |binary rempsyc-0.1.0/rempsyc/man/nice_density.Rd | 6 rempsyc-0.1.0/rempsyc/man/nice_lm_slopes.Rd | 5 rempsyc-0.1.0/rempsyc/man/nice_normality.Rd | 7 rempsyc-0.1.0/rempsyc/man/nice_scatter.Rd | 6 rempsyc-0.1.0/rempsyc/man/nice_slopes.Rd | 7 rempsyc-0.1.0/rempsyc/man/nice_table.Rd | 7 rempsyc-0.1.0/rempsyc/man/nice_varplot.Rd | 2 rempsyc-0.1.0/rempsyc/man/nice_violin.Rd | 21 rempsyc-0.1.0/rempsyc/man/overlap_circle.Rd | 4 rempsyc-0.1.0/rempsyc/man/rcompanion_groupwiseMean.Rd | 15 rempsyc-0.1.0/rempsyc/man/reexports.Rd | 4 rempsyc-0.1.0/rempsyc/man/sr2.Rd |only rempsyc-0.1.0/rempsyc/tests/testthat/niceviolinplothere.tiff |binary rempsyc-0.1.0/rempsyc/vignettes/assumptions.Rmd | 20 rempsyc-0.1.0/rempsyc/vignettes/circles.Rmd | 18 rempsyc-0.1.0/rempsyc/vignettes/contrasts.Rmd | 13 rempsyc-0.1.0/rempsyc/vignettes/moderation.Rmd | 4 rempsyc-0.1.0/rempsyc/vignettes/randomize.Rmd | 52 rempsyc-0.1.0/rempsyc/vignettes/scatter.Rmd | 48 rempsyc-0.1.0/rempsyc/vignettes/t-test.Rmd | 7 rempsyc-0.1.0/rempsyc/vignettes/table.Rmd | 51 rempsyc-0.1.0/rempsyc/vignettes/violin.Rmd | 85 90 files changed, 9028 insertions(+), 4157 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Damir Pulatov [cre, aut],
Michel Lang [aut]
Maintainer: Damir Pulatov <damirpolat@protonmail.com>
Diff between mlr3cluster versions 0.1.4 dated 2022-08-14 and 0.1.5 dated 2022-11-01
DESCRIPTION | 24 ++++++++++++------------ MD5 | 19 +++++++++++-------- NAMESPACE | 1 + NEWS.md | 5 ++++- R/LearnerClustDBSCAN.R | 2 +- R/LearnerClustFarthestFirst.R | 10 +++++++++- R/LearnerClustMclust.R |only R/zzz.R | 1 + man/mlr_learners_clust.FF.Rd | 4 +++- man/mlr_learners_clust.mclust.Rd |only tests/testthat/helper_expectations.R | 1 + tests/testthat/test_mlr_learners_clust_mclust.R |only 12 files changed, 43 insertions(+), 24 deletions(-)
Title: Implementation of Cluster-Polarization Coefficient
Description: Implements cluster-polarization coefficient for measuring distributional
polarization in single or multiple dimensions, as well as associated functions.
Contains support for hierarchical clustering, k-means, partitioning around medoids,
density-based spatial clustering with noise, and manually imposed cluster membership.
Author: Isaac Mehlhaff <isaac.mehlhaff@gmail.com>
Maintainer: Isaac Mehlhaff <isaac.mehlhaff@gmail.com>
Diff between CPC versions 2.2.1 dated 2022-06-01 and 2.3.0 dated 2022-11-01
DESCRIPTION | 8 +++--- MD5 | 20 +++++++++------- NAMESPACE | 7 +++-- NEWS.md | 10 +++++++- R/CPC.R | 62 +++++++++++++++++++++++++-------------------------- R/CPCdata.frame.R | 4 +-- R/SS.R | 4 +-- R/diff_multidim.R |only README.md | 2 - man/CPCdata.frame.Rd | 2 - man/SS.Rd | 2 - man/diff_multidim.Rd |only 12 files changed, 66 insertions(+), 55 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Zeke Marshall [ctb] ,
Thomas Etherington [ctb]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 2.0.0 dated 2022-09-21 and 2.0.1 dated 2022-11-01
shar-2.0.0/shar/R/onLoad.R |only shar-2.0.0/shar/inst/Hesselbarth_2021_Journal_of_Open_Source_Software_6_68.pdf |only shar-2.0.1/shar/DESCRIPTION | 17 ++++------ shar-2.0.1/shar/MD5 | 12 ++----- shar-2.0.1/shar/NEWS.md | 6 +++ shar-2.0.1/shar/inst/doc/get_started.html | 4 +- shar-2.0.1/shar/man/figures/README-plot-random_pattern-1.png |binary shar-2.0.1/shar/man/shar.Rd | 2 - 8 files changed, 22 insertions(+), 19 deletions(-)
Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <mail@roland-pfister.net>
Diff between schoRsch versions 1.9.1 dated 2020-12-15 and 1.10 dated 2022-11-01
DESCRIPTION | 12 ++++++------ MD5 | 6 ++++-- R/clear_all_but.R |only man/clear_all_but.Rd |only man/schoRsch.Rd | 30 ++++++++++++++++-------------- 5 files changed, 26 insertions(+), 22 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Melissa Hallow [aut],
Wenping Wang [aut],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Cleve Moler [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Gilber [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.0.10 dated 2022-10-20 and 2.0.11 dated 2022-11-01
rxode2-2.0.10/rxode2/src/rxode2parse.c |only rxode2-2.0.11/rxode2/DESCRIPTION | 12 rxode2-2.0.11/rxode2/MD5 | 42 - rxode2-2.0.11/rxode2/NEWS.md | 8 rxode2-2.0.11/rxode2/R/RcppExports.R | 2 rxode2-2.0.11/rxode2/R/err.R | 4 rxode2-2.0.11/rxode2/R/rxode-options.R | 21 rxode2-2.0.11/rxode2/R/rxode2_md5.R | 2 rxode2-2.0.11/rxode2/R/symengine.R | 630 ---------------------- rxode2-2.0.11/rxode2/R/utils.R | 8 rxode2-2.0.11/rxode2/inst/doc/rxode2-syntax.html | 373 ++++++------- rxode2-2.0.11/rxode2/inst/include/rxode2.h | 5 rxode2-2.0.11/rxode2/inst/tools/workaround.R | 11 rxode2-2.0.11/rxode2/man/rxIndLin_.Rd | 2 rxode2-2.0.11/rxode2/man/rxode2.Rd | 37 - rxode2-2.0.11/rxode2/src/Makevars.in | 4 rxode2-2.0.11/rxode2/src/call_dvode.c | 2 rxode2-2.0.11/rxode2/src/expm.cpp | 2 rxode2-2.0.11/rxode2/src/par_solve.cpp | 86 +-- rxode2-2.0.11/rxode2/src/rxData.cpp | 5 rxode2-2.0.11/rxode2/src/rxode2parse.cpp |only rxode2-2.0.11/rxode2/src/sbuf.c | 2 rxode2-2.0.11/rxode2/tests/testthat/test-ui-bad.R | 14 23 files changed, 323 insertions(+), 949 deletions(-)
Title: Optimized Automated Gaussian Mixture Assessment
Description: Necessary functions for optimized automated evaluation of the number and parameters of Gaussian mixtures in one-dimensional data. Various methods are available for parameter estimation and for determining the number of modes in the mixture. A detailed description of the methods ca ben found in Lotsch, J., Malkusch, S. and A. Ultsch. (2022) <doi:10.1016/j.imu.2022.101113>.
Author: Jorn Lotsch [aut,cre] ,
Sebastian Malkusch [aut] ,
Martin Maechler [ctb],
Peter Rousseeuw [ctb],
Anja Struyf [ctb],
Mia Hubert [ctb],
Kurt Hornik [ctb]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between opGMMassessment versions 0.3.2 dated 2022-05-27 and 0.3.3 dated 2022-11-01
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- inst |only man/opGMMassessment.Rd | 5 +++-- 4 files changed, 10 insertions(+), 8 deletions(-)
More information about opGMMassessment at CRAN
Permanent link
Title: Clustering and Prediction using Multi-Task Gaussian Processes
with Common Mean
Description: An implementation for the multi-task Gaussian processes with common
mean framework. Two main algorithms, called 'Magma' and 'MagmaClust',
are available to perform predictions for supervised learning problems, in
particular for time series or any functional/continuous data applications.
The corresponding articles has been respectively proposed by Arthur Leroy,
Pierre Latouche, Benjamin Guedj and Servane Gey (2022)
<doi:10.1007/s10994-022-06172-1>, and Arthur Leroy, Pierre Latouche,
Benjamin Guedj and Servane Gey (2020) <arXiv:2011.07866>.
Theses approaches leverage the learning of cluster-specific mean processes,
which are common across similar tasks, to provide enhanced prediction
performances (even far from data) at a linear computational cost (in
the number of tasks). 'MagmaClust' is a generalisation of 'Magma'
where the tasks are simultaneously clustered into groups, each being
associated to a specific mean process. User-oriented functions in the
package are decomposed [...truncated...]
Author: Arthur Leroy [aut, cre] ,
Pierre Latouche [aut],
Pierre Pathe [ctb],
Alexia Grenouilla [ctb],
Hugo Lelievre [ctb]
Maintainer: Arthur Leroy <arthur.leroy.pro@gmail.com>
Diff between MagmaClustR versions 1.0.1 dated 2022-08-29 and 1.1.0 dated 2022-11-01
MagmaClustR-1.0.1/MagmaClustR/tests/testthat/test-gradients-elbo-MagmaClust.R |only MagmaClustR-1.1.0/MagmaClustR/DESCRIPTION | 23 MagmaClustR-1.1.0/MagmaClustR/MD5 | 72 MagmaClustR-1.1.0/MagmaClustR/NAMESPACE | 3 MagmaClustR-1.1.0/MagmaClustR/NEWS.md | 56 MagmaClustR-1.1.0/MagmaClustR/R/data.R |only MagmaClustR-1.1.0/MagmaClustR/R/elbos.R | 60 MagmaClustR-1.1.0/MagmaClustR/R/em-magma.R | 43 MagmaClustR-1.1.0/MagmaClustR/R/gradients-elbos.R | 458 - MagmaClustR-1.1.0/MagmaClustR/R/gradients-likelihoods.R | 42 MagmaClustR-1.1.0/MagmaClustR/R/initialisation.R |only MagmaClustR-1.1.0/MagmaClustR/R/kernel-to-matrices.R | 80 MagmaClustR-1.1.0/MagmaClustR/R/kernels.R | 790 +- MagmaClustR-1.1.0/MagmaClustR/R/likelihoods.R | 715 + MagmaClustR-1.1.0/MagmaClustR/R/package-MagmaClustR.R | 120 MagmaClustR-1.1.0/MagmaClustR/R/plot-functions.R | 1994 ++--- MagmaClustR-1.1.0/MagmaClustR/R/prediction.R | 778 +- MagmaClustR-1.1.0/MagmaClustR/R/simulate-data.R | 389 - MagmaClustR-1.1.0/MagmaClustR/R/training.R | 3609 +++++----- MagmaClustR-1.1.0/MagmaClustR/R/utils-pipe.R | 28 MagmaClustR-1.1.0/MagmaClustR/R/vem-magmaclust.R | 36 MagmaClustR-1.1.0/MagmaClustR/README.md | 144 MagmaClustR-1.1.0/MagmaClustR/data |only MagmaClustR-1.1.0/MagmaClustR/man/expand_grid_inputs.Rd |only MagmaClustR-1.1.0/MagmaClustR/man/figures/README-display_Magma-1.png |binary MagmaClustR-1.1.0/MagmaClustR/man/figures/README-display_MagmaClust-1.png |binary MagmaClustR-1.1.0/MagmaClustR/man/figures/README-gif_Magma-1.gif |binary MagmaClustR-1.1.0/MagmaClustR/man/figures/README-train_and_predict_Magma-1.png |binary MagmaClustR-1.1.0/MagmaClustR/man/figures/README-train_and_predict_Magma_in_2-D-1.png |binary MagmaClustR-1.1.0/MagmaClustR/man/ini_kmeans.Rd | 6 MagmaClustR-1.1.0/MagmaClustR/man/ini_mixture.Rd | 2 MagmaClustR-1.1.0/MagmaClustR/man/pred_gp.Rd | 2 MagmaClustR-1.1.0/MagmaClustR/man/regularize_data.Rd |only MagmaClustR-1.1.0/MagmaClustR/man/simu_db.Rd | 22 MagmaClustR-1.1.0/MagmaClustR/man/simu_indiv_se.Rd | 9 MagmaClustR-1.1.0/MagmaClustR/man/swimmers.Rd |only MagmaClustR-1.1.0/MagmaClustR/man/weight.Rd |only MagmaClustR-1.1.0/MagmaClustR/tests/testthat/test-gradients-logL.R | 246 MagmaClustR-1.1.0/MagmaClustR/tests/testthat/test-kern_to_cov.R | 330 MagmaClustR-1.1.0/MagmaClustR/tests/testthat/test-kern_to_inv.R | 109 MagmaClustR-1.1.0/MagmaClustR/tests/testthat/test-test-general-execution-magma.R |only 41 files changed, 5424 insertions(+), 4742 deletions(-)
Title: Locally Stationary Two-Dimensional Wavelet Process Estimation
Scheme
Description: Estimates two-dimensional local wavelet spectra.
Author: Idris Eckley [aut, cre],
Guy Nason [aut],
Sarah Taylor [ctb],
Matthew Nunes [ctb]
Maintainer: Idris Eckley <i.eckley@lancaster.ac.uk>
Diff between LS2W versions 1.3.5 dated 2022-06-13 and 1.3.6 dated 2022-11-01
DESCRIPTION | 8 MD5 | 16 R/specplot.R | 2 src/extra.c | 25 src/extra.h |only src/functionsIE.c | 3716 +++++++++++++++++++++++++----------------------------- src/functionsIE.h |only src/phij.c | 169 -- src/phij.h |only src/testit.c | 138 -- src/testit.h |only 11 files changed, 1883 insertions(+), 2191 deletions(-)
Title: United Formula Annotation (UFA) for HRMS Data Processing
Description: A pipeline to annotate peaklists from the IDSL.IPA package with molecular formula of a prioritized chemical space using an isotopic profile matching approach. The IDSL.UFA pipeline only requires MS1 for formula annotation.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFA versions 1.6 dated 2022-10-04 and 1.7 dated 2022-11-01
IDSL.UFA-1.6/IDSL.UFA/R/UFA_logRecorder.R |only IDSL.UFA-1.6/IDSL.UFA/man/UFA_logRecorder.Rd |only IDSL.UFA-1.7/IDSL.UFA/DESCRIPTION | 11 IDSL.UFA-1.7/IDSL.UFA/MD5 | 36 -- IDSL.UFA-1.7/IDSL.UFA/NAMESPACE | 16 IDSL.UFA-1.7/IDSL.UFA/R/UFA_enumerated_chemical_space.R | 70 ++-- IDSL.UFA-1.7/IDSL.UFA/R/UFA_profile_visualizer.R | 174 +++++----- IDSL.UFA-1.7/IDSL.UFA/R/UFA_profile_visualizer_xlsxAnalyzer.R | 7 IDSL.UFA-1.7/IDSL.UFA/R/UFA_score_coefficient_corrector.R | 2 IDSL.UFA-1.7/IDSL.UFA/R/UFA_score_coefficient_workflow.R | 34 - IDSL.UFA-1.7/IDSL.UFA/R/UFA_workflow.R | 117 +++--- IDSL.UFA-1.7/IDSL.UFA/R/aligned_molecular_formula_annotator.R | 90 +++-- IDSL.UFA-1.7/IDSL.UFA/R/global.R | 2 IDSL.UFA-1.7/IDSL.UFA/R/isotopic_profile_molecular_formula_feeder.R | 40 +- IDSL.UFA-1.7/IDSL.UFA/R/molecular_formulas_source_IPDB.R | 36 +- IDSL.UFA-1.7/IDSL.UFA/R/score_coefficient_evaluation.R | 18 - IDSL.UFA-1.7/IDSL.UFA/R/score_coefficients_optimization.R | 16 IDSL.UFA-1.7/IDSL.UFA/R/zero_score_function.R | 22 - IDSL.UFA-1.7/IDSL.UFA/build/partial.rdb |binary IDSL.UFA-1.7/IDSL.UFA/inst/extdata/UFA_parameters.xlsx |binary 20 files changed, 375 insertions(+), 316 deletions(-)
Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract signals of organic compounds. The package performs ion pairing, peak detection, alignment, RT correction, gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs).
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.IPA versions 2.4 dated 2022-10-01 and 2.5 dated 2022-11-01
IDSL.IPA-2.4/IDSL.IPA/R/EIC_plotter.R |only IDSL.IPA-2.4/IDSL.IPA/R/IPA_Workflow.R |only IDSL.IPA-2.4/IDSL.IPA/R/asymmetry_factor.R |only IDSL.IPA-2.4/IDSL.IPA/R/baseline_developer.R |only IDSL.IPA-2.4/IDSL.IPA/R/chromatography_analysis.R |only IDSL.IPA-2.4/IDSL.IPA/R/der_5points_stencil.R |only IDSL.IPA-2.4/IDSL.IPA/R/derivative_skewness.R |only IDSL.IPA-2.4/IDSL.IPA/R/fronting_tailing_resolver.R |only IDSL.IPA-2.4/IDSL.IPA/R/gaussianity_measurement.R |only IDSL.IPA-2.4/IDSL.IPA/R/mz_clustering_xic.R |only IDSL.IPA-2.4/IDSL.IPA/R/peak_Xcol2.R |only IDSL.IPA-2.4/IDSL.IPA/R/peak_area.R |only IDSL.IPA-2.4/IDSL.IPA/R/peak_detection.R |only IDSL.IPA-2.4/IDSL.IPA/R/peak_property_table_correlation.R |only IDSL.IPA-2.4/IDSL.IPA/R/peak_sharpness.R |only IDSL.IPA-2.4/IDSL.IPA/R/peak_width.R |only IDSL.IPA-2.4/IDSL.IPA/R/pseudomoments_symmetry.R |only IDSL.IPA-2.4/IDSL.IPA/R/snr_rms.R |only IDSL.IPA-2.4/IDSL.IPA/R/snr_signal2baseline.R |only IDSL.IPA-2.4/IDSL.IPA/R/snr_xcms.R |only IDSL.IPA-2.4/IDSL.IPA/R/spectraList_filtering.R |only IDSL.IPA-2.4/IDSL.IPA/R/usp_tailing_factor.R |only IDSL.IPA-2.4/IDSL.IPA/R/xlsxAnalyzer_EIC.R |only IDSL.IPA-2.4/IDSL.IPA/inst/extdata/EIC_legend.png |only IDSL.IPA-2.4/IDSL.IPA/man/EIC_plotter.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/IPA_Workflow.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/asymmetry_factor.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/baseline_developer.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/chromatography_analysis.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/der_5points_stencil.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/derivative_skewness.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/fronting_tailing_resolver.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/gaussianity_measurement.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/mz_clustering_xic.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/peak_Xcol2.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/peak_area.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/peak_detection.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/peak_property_table_correlation.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/peak_sharpness.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/peak_width.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/pseudomoments_symmetry.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/snr_rms.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/snr_signal2baseline.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/snr_xcms.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/spectraList_filtering.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/usp_tailing_factor.Rd |only IDSL.IPA-2.4/IDSL.IPA/man/xlsxAnalyzer_EIC.Rd |only IDSL.IPA-2.5/IDSL.IPA/DESCRIPTION | 11 IDSL.IPA-2.5/IDSL.IPA/MD5 | 167 ++-- IDSL.IPA-2.5/IDSL.IPA/NAMESPACE | 15 IDSL.IPA-2.5/IDSL.IPA/R/IPA_CompoundsAnnotation.R | 251 +++--- IDSL.IPA-2.5/IDSL.IPA/R/IPA_GapFiller.R | 278 +------ IDSL.IPA-2.5/IDSL.IPA/R/IPA_IonPairing.R | 26 IDSL.IPA-2.5/IDSL.IPA/R/IPA_MSdeconvoluter.R | 6 IDSL.IPA-2.5/IDSL.IPA/R/IPA_PeakAlignment.R | 99 +- IDSL.IPA-2.5/IDSL.IPA/R/IPA_PeakAnalyzer.R | 240 ++++-- IDSL.IPA-2.5/IDSL.IPA/R/IPA_PeaklistAnnotation.R | 330 +------- IDSL.IPA-2.5/IDSL.IPA/R/IPA_TargetedAnalysis.R | 429 +++++------ IDSL.IPA-2.5/IDSL.IPA/R/IPA_baselineDeveloper.R |only IDSL.IPA-2.5/IDSL.IPA/R/IPA_logRecorder.R | 8 IDSL.IPA-2.5/IDSL.IPA/R/IPA_targeted_xlsxAnalyzer.R |only IDSL.IPA-2.5/IDSL.IPA/R/IPA_workflow.R |only IDSL.IPA-2.5/IDSL.IPA/R/IPA_xlsxAnalyzer.R | 19 IDSL.IPA-2.5/IDSL.IPA/R/MZclusteringRAWxic.R |only IDSL.IPA-2.5/IDSL.IPA/R/SNRbaseline.R |only IDSL.IPA-2.5/IDSL.IPA/R/SNRrms.R |only IDSL.IPA-2.5/IDSL.IPA/R/SNRxcms.R |only IDSL.IPA-2.5/IDSL.IPA/R/USPtailingFactor.R |only IDSL.IPA-2.5/IDSL.IPA/R/XIC.R | 12 IDSL.IPA-2.5/IDSL.IPA/R/asymmetryFactor.R |only IDSL.IPA-2.5/IDSL.IPA/R/chromatographicPeakDetector.R |only IDSL.IPA-2.5/IDSL.IPA/R/chromatographyPeakAnalysis.R |only IDSL.IPA-2.5/IDSL.IPA/R/derivative5pointsStencil.R |only IDSL.IPA-2.5/IDSL.IPA/R/derivativeSkewnessCalculator.R |only IDSL.IPA-2.5/IDSL.IPA/R/gapFillingCore.R |only IDSL.IPA-2.5/IDSL.IPA/R/gaussianityMeasurement.R |only IDSL.IPA-2.5/IDSL.IPA/R/global.R | 2 IDSL.IPA-2.5/IDSL.IPA/R/mzRTindexer.R | 10 IDSL.IPA-2.5/IDSL.IPA/R/peakAreaCalculator.R |only IDSL.IPA-2.5/IDSL.IPA/R/peakFrontingTailingResolver.R |only IDSL.IPA-2.5/IDSL.IPA/R/peakPropertyTableCorrelation.R |only IDSL.IPA-2.5/IDSL.IPA/R/peakSharpness.R |only IDSL.IPA-2.5/IDSL.IPA/R/peakWidthCalculator.R |only IDSL.IPA-2.5/IDSL.IPA/R/peakXcolFiller.R |only IDSL.IPA-2.5/IDSL.IPA/R/peak_alignment.R | 156 ++-- IDSL.IPA-2.5/IDSL.IPA/R/plot_mz_eic.R | 27 IDSL.IPA-2.5/IDSL.IPA/R/plot_simple_tic.R | 18 IDSL.IPA-2.5/IDSL.IPA/R/primary_peak_analyzer.R | 47 - IDSL.IPA-2.5/IDSL.IPA/R/pseudomomentsSymmetry.R |only IDSL.IPA-2.5/IDSL.IPA/R/recursive_mass_correction.R | 93 +- IDSL.IPA-2.5/IDSL.IPA/R/reference_peaks_detector.R | 31 IDSL.IPA-2.5/IDSL.IPA/R/sample_rt_corrector.R | 90 +- IDSL.IPA-2.5/IDSL.IPA/R/spectraListRoundingFiltering.R |only IDSL.IPA-2.5/IDSL.IPA/build/partial.rdb |binary IDSL.IPA-2.5/IDSL.IPA/inst/CITATION | 1 IDSL.IPA-2.5/IDSL.IPA/inst/extdata/IPA_parameters.xlsx |binary IDSL.IPA-2.5/IDSL.IPA/man/IPA_IonPairing.Rd | 16 IDSL.IPA-2.5/IDSL.IPA/man/IPA_MSdeconvoluter.Rd | 8 IDSL.IPA-2.5/IDSL.IPA/man/IPA_PeakAnalyzer.Rd | 2 IDSL.IPA-2.5/IDSL.IPA/man/IPA_TargetedAnalysis.Rd | 21 IDSL.IPA-2.5/IDSL.IPA/man/IPA_baselineDeveloper.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/IPA_targeted_xlsxAnalyzer.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/IPA_workflow.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/MZclusteringRAWxic.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/SNRbaseline.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/SNRrms.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/SNRxcms.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/USPtailingFactor.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/XIC.Rd | 10 IDSL.IPA-2.5/IDSL.IPA/man/asymmetryFactor.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/chromatographicPeakDetector.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/chromatographyPeakAnalysis.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/derivative5pointsStencil.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/derivativeSkewnessCalculator.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/gapFillingCore.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/gaussianityMeasurement.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/mzRTindexer.Rd | 4 IDSL.IPA-2.5/IDSL.IPA/man/peakAreaCalculator.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/peakFrontingTailingResolver.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/peakPropertyTableCorrelation.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/peakSharpness.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/peakWidthCalculator.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/peakXcolFiller.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/peak_alignment.Rd | 16 IDSL.IPA-2.5/IDSL.IPA/man/plot_mz_eic.Rd | 10 IDSL.IPA-2.5/IDSL.IPA/man/primary_peak_analyzer.Rd | 44 - IDSL.IPA-2.5/IDSL.IPA/man/pseudomomentsSymmetry.Rd |only IDSL.IPA-2.5/IDSL.IPA/man/recursive_mass_correction.Rd | 39 - IDSL.IPA-2.5/IDSL.IPA/man/reference_peaks_detector.Rd | 19 IDSL.IPA-2.5/IDSL.IPA/man/sample_rt_corrector.Rd | 18 IDSL.IPA-2.5/IDSL.IPA/man/spectraListRoundingFiltering.Rd |only 131 files changed, 1140 insertions(+), 1433 deletions(-)
Title: Flexible Parametric Cure Models
Description: Flexible parametric mixture and non-mixture cure models for time-to-event data.
Author: Jordan Amdahl [aut, cre]
Maintainer: Jordan Amdahl <jrdnmdhl@gmail.com>
Diff between flexsurvcure versions 1.3.0 dated 2022-06-17 and 1.3.1 dated 2022-11-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/flexsurvcure.R | 2 +- R/mixture.r | 10 +++------- R/nonmixture.R | 10 ++++++++-- inst/doc/flexsurvcure.html | 22 +++++++++++----------- 7 files changed, 38 insertions(+), 32 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stephane Dray <stephane.dray@univ-lyon1.fr>, Anne-Beatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sebastien Ollier, D [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-19 dated 2022-04-19 and 1.7-20 dated 2022-11-01
ChangeLog | 67 ++++++++++++++++++++++++++++++++++++ DESCRIPTION | 6 +-- MD5 | 92 +++++++++++++++++++++++++------------------------- R/area.plot.R | 2 - R/kdisteuclid.R | 2 - R/procuste.R | 6 +-- R/procuste.randtest.R | 24 ------------- R/s.label.R | 2 - R/s.logo.R | 2 - R/s.value.R | 2 - R/supdist.R | 2 - build/partial.rdb |binary data/mafragh.rda |binary man/atlas.Rd | 2 - man/atya.Rd | 2 - man/avijons.Rd | 2 - man/bca.Rd | 2 - man/bca.coinertia.Rd | 2 - man/buech.Rd | 2 - man/butterfly.Rd | 2 - man/bwca.dpcoa.Rd | 2 - man/capitales.Rd | 2 - man/chickenk.Rd | 2 - man/elec88.Rd | 2 - man/ggtortoises.Rd | 2 - man/irishdata.Rd | 2 - man/julliot.Rd | 2 - man/jv73.Rd | 2 - man/kcponds.Rd | 2 - man/mafragh.Rd | 2 - man/multispati.Rd | 2 - man/pcw.Rd | 2 - man/randboot.Rd | 2 - man/randtest.Rd | 5 ++ man/sarcelles.Rd | 2 - man/supdist.Rd | 2 - man/suprow.pta.Rd | 2 - man/t3012.Rd | 2 - man/tintoodiel.Rd | 2 - man/vegtf.Rd | 2 - man/wca.Rd | 2 - man/wca.coinertia.Rd | 2 - man/zealand.Rd | 2 - src/divsub.c | 20 +++++----- src/fourthcorner.c | 16 +++++--- src/phylog.c | 42 +++++++++++----------- src/testamova.c | 2 - 47 files changed, 202 insertions(+), 148 deletions(-)
Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
A modern take on the 'Tufte' design for pdf and html vignettes,
building on the 'tufte' package with additional contributions
from the 'knitr' and 'ggtufte' package, and also acknowledging
the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel and Jonathan Gilligan
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.1.3 dated 2020-07-18 and 0.1.4 dated 2022-11-01
ChangeLog | 51 +++++++ DESCRIPTION | 11 - MD5 | 32 ++-- R/html.R | 15 ++ README.md | 25 ++- build/vignette.rds |binary inst/NEWS.Rd | 13 + inst/doc/tintHtmlIntro.Rmd | 4 inst/doc/tintHtmlIntro.html | 70 ++++++++-- inst/doc/tintPdfIntro.Rmd | 4 inst/doc/tintPdfIntro.pdf |binary inst/rmarkdown/templates/tintHtml/resources/tint.css | 9 + inst/rmarkdown/templates/tintPdf/resources/tintPdf-template.tex | 1 man/tintHtml.Rd | 4 tests/simple.R | 4 vignettes/tintHtmlIntro.Rmd | 4 vignettes/tintPdfIntro.Rmd | 4 17 files changed, 194 insertions(+), 57 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R,
the 'targets' package brings together function-oriented programming and
'Make'-like declarative workflows.
It analyzes the dependency relationships among the tasks of a workflow,
skips steps that are already up to date, runs the necessary
computation with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between targets versions 0.13.5 dated 2022-09-26 and 0.14.0 dated 2022-11-01
DESCRIPTION | 6 MD5 | 189 ++++++++++++++------------ NAMESPACE | 10 + NEWS.md | 19 ++ R/class_aws.R | 36 +--- R/class_build.R | 8 - R/class_builder.R | 17 +- R/class_cue.R | 25 ++- R/class_feather.R | 11 + R/class_gcp.R | 27 +-- R/class_options.R | 35 +++- R/class_parquet.R | 11 + R/class_pattern.R | 10 - R/class_runtime.R | 58 +++++++ R/class_store_custom.R | 17 +- R/class_store_file.R | 2 R/class_url.R | 4 R/tar_cue.R | 13 + R/tar_debug_instructions.R |only R/tar_engine_knitr.R | 7 R/tar_format.R | 72 +++++++++ R/tar_invalidate.R | 2 R/tar_load_globals.R | 1 R/tar_make_clustermq.R | 32 ++-- R/tar_option_get.R | 3 R/tar_option_set.R | 26 +++ R/tar_path.R | 18 +- R/tar_path_script.R |only R/tar_path_script_support.R |only R/tar_path_store.R |only R/tar_path_target.R |only R/tar_resources.R | 7 R/tar_resources_clustermq.R | 6 R/tar_store.R | 20 +- R/tar_target.R | 15 -- R/tar_target_raw.R | 13 + R/utils_aws.R | 47 +----- R/utils_callr.R | 2 R/utils_cli.R | 6 R/utils_digest.R | 6 R/utils_gcp.R | 77 ++++------ inst/pipelines/_targets_r.R | 4 inst/templates/clustermq/slurm.tmpl | 4 inst/templates/github_actions.yaml | 4 man/tar_active.Rd | 4 man/tar_call.Rd | 4 man/tar_cancel.Rd | 4 man/tar_cue.Rd | 9 + man/tar_debug_instructions.Rd |only man/tar_definition.Rd | 4 man/tar_envir.Rd | 4 man/tar_format.Rd | 72 +++++++++ man/tar_group.Rd | 4 man/tar_invalidate.Rd | 2 man/tar_make_clustermq.Rd | 32 ++-- man/tar_name.Rd | 4 man/tar_option_set.Rd | 41 ++++- man/tar_path.Rd | 21 ++ man/tar_path_script.Rd |only man/tar_path_script_support.Rd |only man/tar_path_store.Rd |only man/tar_path_target.Rd |only man/tar_resources.Rd | 7 man/tar_resources_clustermq.Rd | 8 + man/tar_seed.Rd | 4 man/tar_source.Rd | 4 man/tar_store.Rd | 17 +- man/tar_target.Rd | 15 -- man/tar_target_raw.Rd | 7 tests/aws/test-class_aws_qs.R | 2 tests/aws/test-delete.R | 1 tests/aws/test-utils_aws.R | 8 - tests/gcp/test-class_gcp_parquet.R | 2 tests/gcp/test-class_gcp_qs.R | 2 tests/gcp/test-delete.R | 1 tests/gcp/test-utils_gcp.R | 1 tests/testthat/helper-gcp.R | 2 tests/testthat/helper-utils.R | 12 + tests/testthat/test-class_build.R | 33 ++++ tests/testthat/test-class_builder.R | 11 - tests/testthat/test-class_cue.R | 48 ++++++ tests/testthat/test-class_feather.R | 13 + tests/testthat/test-class_options.R | 32 +++- tests/testthat/test-class_parquet.R | 13 + tests/testthat/test-class_runtime.R | 43 +++++ tests/testthat/test-class_store_custom.R | 38 +++++ tests/testthat/test-class_store_file.R | 13 + tests/testthat/test-class_target.R | 18 ++ tests/testthat/test-class_torch.R | 8 - tests/testthat/test-class_url.R | 7 tests/testthat/test-tar_debug_instructions.R |only tests/testthat/test-tar_make.R | 23 ++- tests/testthat/test-tar_option_set.R | 14 + tests/testthat/test-tar_path.R | 43 +++-- tests/testthat/test-tar_path_script.R |only tests/testthat/test-tar_path_script_support.R |only tests/testthat/test-tar_path_store.R |only tests/testthat/test-tar_path_target.R |only tests/testthat/test-tar_sitrep.R | 16 +- tests/testthat/test-tar_store.R | 9 - tests/testthat/test-tar_target.R | 14 + tests/testthat/test-tar_workspace.R | 2 tests/testthat/test-utils_digest.R | 30 ++++ 103 files changed, 1179 insertions(+), 417 deletions(-)
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species
Description: Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly' and 'polyqtlR' packages.
Author: Cristiane Taniguti [aut, cre],
Gabriel de Siqueira Gesteira [aut],
Jeekin Lau [ctb],
Guilherme da Silva Pereira [ctb],
David Byrne [ctb],
Zhao-Bang Zeng [ctb],
Oscar Riera-Lizarazu [ctb],
Marcelo Mollinari [aut]
Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
Diff between viewpoly versions 0.3.1 dated 2022-10-10 and 0.3.2 dated 2022-11-01
viewpoly-0.3.1/viewpoly/tests/testthat/test-MAPpoly.R |only viewpoly-0.3.1/viewpoly/tests/testthat/test-QTLpoly.R |only viewpoly-0.3.1/viewpoly/tests/testthat/test-diaQTL.R |only viewpoly-0.3.1/viewpoly/tests/testthat/test-polymapR.R |only viewpoly-0.3.1/viewpoly/tests/testthat/test-polyqtlR.R |only viewpoly-0.3.2/viewpoly/DESCRIPTION | 6 +++--- viewpoly-0.3.2/viewpoly/MD5 | 11 +++-------- viewpoly-0.3.2/viewpoly/NEWS.md | 4 ++++ viewpoly-0.3.2/viewpoly/build/partial.rdb |binary 9 files changed, 10 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-06 0.1-5
2019-03-18 0.1-4
2013-07-24 0.1-3
2012-06-03 0.1-2
2009-05-04 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-08 0.2.1
2021-06-14 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-02 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-01 0.1.1
Title: Determine Thermal Vegetation Periods
Description: Collection of common methods to determine growing season length in
a simple manner. Start and end dates of the vegetation periods are calculated
solely based on daily mean temperatures and the day of the year.
Author: Robert Nuske [aut, cre] ,
Nordwestdeutsche Forstliche Versuchsanstalt [cph, fnd]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between vegperiod versions 0.3.1 dated 2021-02-02 and 0.4.0 dated 2022-11-01
DESCRIPTION | 24 ++-- MD5 | 30 +++-- NEWS.md | 8 + R/read_dwd.R | 4 R/veg_ends.R | 164 ++++++++++++++++++----------- R/veg_starts.R | 169 +++++++++++++++++++++++------- R/vegperiod.R | 127 ++++++++++++---------- README.md | 13 +- build/partial.rdb |binary inst/tinytest/test_veg_vegperiod.R | 6 - man/method_ETCCDI.Rd |only man/method_LWF-BROOK90.Rd |only man/method_Menzel.Rd |only man/method_NuskeAlbert.Rd |only man/method_Ribes.Rd |only man/method_vonWilpert.Rd |only man/read.DWDdata.Rd | 2 man/read.DWDstations.Rd | 2 man/vegperiod.Rd | 208 +++++++++++++++++++------------------ 19 files changed, 470 insertions(+), 287 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes
(simple sequential inhibition, Matern inhibition models, Matern cluster process,
Neyman-Scott cluster processes, log-Gaussian Cox processes, product shot noise cluster processes)
and simulation of Gibbs point processes (Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler). Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
Kasper Klitgaard Berthelsen [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 2.2-0 dated 2022-03-30 and 3.0-0 dated 2022-11-01
DESCRIPTION | 36 ++-- MD5 | 148 ++++++++++---------- NEWS | 30 ++++ R/clusterfunctions.R | 12 - R/clusterinfo.R | 6 R/rLGCP.R | 16 +- R/rPSNCP.R | 11 + R/rPerfect.R | 32 +--- R/random.R | 67 ++++----- R/randomNS.R | 27 +++ R/randommk.R | 291 +++++++++++++++++++++------------------- R/randomonlines.R | 14 + R/randompp3.R | 14 + R/randomppx.R | 13 + R/rmh.default.R | 7 R/rmhmodel.R | 8 - inst/doc/packagesizes.txt | 2 man/Window.rmhmodel.Rd | 4 man/as.owin.rmhmodel.Rd | 2 man/clusterfield.Rd | 9 - man/clusterkernel.Rd | 5 man/clusterradius.Rd | 2 man/default.expand.Rd | 14 - man/default.rmhcontrol.Rd | 4 man/domain.rmhmodel.Rd | 5 man/macros/defns.Rd | 25 +++ man/quadratresample.Rd | 6 man/rCauchy.Rd | 8 - man/rDGS.Rd | 2 man/rDiggleGratton.Rd | 2 man/rHardcore.Rd | 2 man/rLGCP.Rd | 6 man/rMatClust.Rd | 6 man/rNeymanScott.Rd | 2 man/rPSNCP.Rd | 8 - man/rPenttinen.Rd | 2 man/rStraussHard.Rd | 4 man/rThomas.Rd | 6 man/rVarGamma.Rd | 12 - man/rags.Rd | 2 man/ragsAreaInter.Rd | 8 - man/ragsMultiHard.Rd | 2 man/rcell.Rd | 4 man/reach.Rd | 16 +- man/rmh.Rd | 4 man/rmh.default.Rd | 9 - man/rmhmodel.Rd | 26 +-- man/rmhmodel.default.Rd | 6 man/rmhmodel.list.Rd | 18 +- man/rpoint.Rd | 11 + man/rshift.splitppp.Rd | 1 man/runifpoint.Rd | 7 man/spatstat.random-internal.Rd | 4 man/spatstat.random-package.Rd | 6 src/areaint.c | 14 - src/badgey.c | 18 -- src/dgs.c | 12 - src/diggra.c | 12 - src/dist2.c | 38 +++-- src/fiksel.c | 12 - src/getcif.c | 9 - src/geyer.c | 18 -- src/hardcore.c | 12 - src/lennard.c | 12 - src/lookup.c | 12 - src/multihard.c | 12 - src/penttinen.c | 12 - src/sftcr.c | 12 - src/straush.c | 12 - src/straushm.c | 12 - src/strauss.c | 12 - src/straussm.c | 12 - src/triplets.c | 12 - tests/RMH.R | 6 tests/Random.R | 6 75 files changed, 625 insertions(+), 646 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: A Versatile Cutting Tool
Description: A tool for cutting data into intervals. Allows singleton intervals.
Always includes the whole range of data by default. Flexible labelling.
Convenience functions for cutting by quantiles etc. Handles dates, times, units
and other vectors.
Author: David Hugh-Jones [aut, cre],
Daniel Possenriede [ctb]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between santoku versions 0.8.0 dated 2022-06-08 and 0.9.0 dated 2022-11-01
DESCRIPTION | 9 MD5 | 79 +-- NAMESPACE | 3 NEWS.md | 70 +++ R/breaks-impl.R | 186 +++++++- R/breaks.R | 145 ++---- R/chop.R | 292 +++++++++---- R/labels-impl.R | 33 + R/labels.R | 144 +++++- R/tab.R | 127 ++++-- README.md | 57 +- build/vignette.rds |binary inst/doc/santoku.R | 62 ++ inst/doc/santoku.Rmd | 153 ++++++- inst/doc/santoku.html | 738 ++++++++++++++++++++++------------- inst/doc/whats-new-in-0-9-0.R |only inst/doc/whats-new-in-0-9-0.Rmd |only inst/doc/whats-new-in-0-9-0.html |only man/brk_default.Rd | 2 man/brk_manual.Rd | 2 man/chop.Rd | 116 +++-- man/chop_equally.Rd | 12 man/chop_evenly.Rd | 3 man/chop_fn.Rd |only man/chop_mean_sd.Rd | 7 man/chop_n.Rd | 10 man/chop_proportions.Rd | 13 man/chop_quantiles.Rd | 23 - man/chop_width.Rd | 3 man/fillet.Rd | 17 man/lbl_dash.Rd | 4 man/lbl_endpoints.Rd | 12 man/lbl_glue.Rd | 4 man/lbl_intervals.Rd | 4 man/lbl_manual.Rd | 13 man/lbl_midpoints.Rd | 4 tests/testthat/test-breaks.R | 29 + tests/testthat/test-chop.R | 187 +++++++- tests/testthat/test-labels.R | 53 +- tests/testthat/test-tab.R | 4 tests/testthat/test-zzz-systematic.R | 133 ++++-- vignettes/santoku.Rmd | 153 ++++++- vignettes/whats-new-in-0-9-0.Rmd |only 43 files changed, 2092 insertions(+), 814 deletions(-)
Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix?
How much ram is your current R session using? How much ram do you even have?
Learn the scintillating answer to these and many more such questions with
the 'memuse' package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [ctb] ,
Wei-Chen Chen [ctb] ,
Dan Burgess [ctb]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between memuse versions 4.2-1 dated 2021-10-20 and 4.2-2 dated 2022-11-01
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/00-classes.r | 2 +- R/howmany.r | 2 +- README.md | 2 +- inst/doc/memuse-guide.Rnw | 8 ++++++-- inst/doc/memuse-guide.pdf |binary src/meminfo/src/getpid.c | 2 +- src/meminfo/src/meminfo.h | 2 +- src/memuse_native.c | 8 ++++---- src/wrappers.c | 8 ++++---- 12 files changed, 37 insertions(+), 29 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models <arXiv:2201.13095>.
Author: Sandra Siegfried [aut, cre] ,
Luisa Barbanti [aut] ,
Torsten Hothorn [aut]
Maintainer: Sandra Siegfried <sandra.siegfried@uzh.ch>
Diff between cotram versions 0.4-1 dated 2022-07-14 and 0.4-2 dated 2022-11-01
cotram-0.4-1/cotram/tests/Examples |only cotram-0.4-1/cotram/tests/mcotram-Ex.Rout.save |only cotram-0.4-2/cotram/DESCRIPTION | 12 - cotram-0.4-2/cotram/MD5 | 16 -- cotram-0.4-2/cotram/NAMESPACE | 2 cotram-0.4-2/cotram/R/mcotram.R | 121 +++++---------- cotram-0.4-2/cotram/demo/aquabirds.R | 19 +- cotram-0.4-2/cotram/inst/NEWS.Rd | 6 cotram-0.4-2/cotram/inst/doc/cotram.pdf |binary cotram-0.4-2/cotram/tests/mcotram-Ex.R | 191 +++++++++++++++++-------- 10 files changed, 208 insertions(+), 159 deletions(-)
More information about sarp.snowprofile.pyface at CRAN
Permanent link
Title: Proteomics Data Analysis and Modeling Tools
Description: A comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from 'MaxQuant' can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) <doi:10.1021/acs.jproteome.5b00981>), differential expression analysis (Ritchie et. al. (2015) <doi:10.1093/nar/gkv007>), and machine learning-based modeling (Kuhn (2008) <doi:10.18637/jss.v028.i05>).
Author: Chathurani Ranathunge [aut, cre, cph]
Maintainer: Chathurani Ranathunge <caranathunge86@gmail.com>
Diff between promor versions 0.1.0 dated 2022-07-20 and 0.1.1 dated 2022-11-01
DESCRIPTION | 6 - MD5 | 43 +++---- NEWS.md | 15 ++ R/createDF.R | 4 R/findDE.R | 24 ++-- R/handleNA.R | 14 +- R/handleTechReps.R | 4 R/modelPlots.R | 8 - R/normalize.R | 2 README.md | 27 +++- inst/CITATION |only inst/doc/intro_to_promor.html | 12 +- man/corr_plot.Rd | 4 man/feature_plot.Rd | 2 man/find_dep.Rd | 8 + man/heatmap_de.Rd | 6 - man/heatmap_na.Rd | 250 +++++++++++++++++++++--------------------- man/impute_plot.Rd | 2 man/norm_plot.Rd | 2 man/performance_plot.Rd | 2 man/roc_plot.Rd | 2 man/varimp_plot.Rd | 2 man/volcano_plot.Rd | 2 23 files changed, 246 insertions(+), 195 deletions(-)
Title: Power and Sample Size Calculations for Clinical Trials
Description: Efficient simulation-based power and sample size calculations are supported for a
broad class of late-stage clinical trials. The following modules are included in
the package:
Adaptive designs with data-driven sample size or event count re-estimation,
Adaptive designs with data-driven treatment selection,
Adaptive designs with data-driven population selection,
Optimal selection of a futility stopping rule,
Event prediction in event-driven trials,
Adaptive trials with response-adaptive randomization (experimental module),
Traditional trials with multiple objectives (experimental module).
Traditional trials with cluster-randomized designs (experimental module).
Author: Alex Dmitrienko [aut, cre]
Maintainer: Alex Dmitrienko <admitrienko@mediana.us>
Diff between MedianaDesigner versions 0.9 dated 2022-10-28 and 0.10 dated 2022-11-01
CHANGELOG | 3 ++- DESCRIPTION | 31 ++++++++++++++++--------------- MD5 | 6 +++--- R/ClustRand.r | 6 +++--- 4 files changed, 24 insertions(+), 22 deletions(-)
More information about MedianaDesigner at CRAN
Permanent link
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
minimal assertion functions with a focus on informative error messaging for
both missing and incorrect function arguments as well as other functions for
visualising colour palettes, quoting user input and working with age
intervals.
Author: Tim Taylor [aut, cre, cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 0.2.0 dated 2022-10-26 and 0.2.1 dated 2022-11-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ src/ageutils.c | 8 ++++---- 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Single Cell mRNA Soup eXterminator
Description: Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.
Author: Matthew Daniel Young
Maintainer: Matthew Daniel Young <my4@sanger.ac.uk>
Diff between SoupX versions 1.6.1 dated 2022-05-26 and 1.6.2 dated 2022-11-01
DESCRIPTION | 8 +- MD5 | 12 +-- R/adjustCounts.R | 12 ++- R/load10X.R | 15 ++- R/quickMarkers.R | 3 R/utils.R | 3 inst/doc/pbmcTutorial.html | 179 ++++++++++++++++++++++----------------------- 7 files changed, 122 insertions(+), 110 deletions(-)
Title: Interface the 'xts' API via 'Rcpp'
Description: Access to some of the C level functions of the 'xts' package.
In its current state, the package is mostly a proof-of-concept to support
adding useful functions, and does not yet add any of its own.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppXts versions 0.0.5 dated 2022-08-05 and 0.0.6 dated 2022-11-01
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/NEWS.Rd | 7 +++++++ src/init.c | 2 +- 5 files changed, 22 insertions(+), 9 deletions(-)
Title: Evaluating Multinomial Order Restrictions with Bridge Sampling
Description: Evaluate hypotheses concerning the distribution of multinomial
proportions using bridge sampling. The bridge sampling routine is able to
compute Bayes factors for hypotheses that entail inequality constraints,
equality constraints, free parameters, and mixtures of all three. These
hypotheses are tested against the encompassing hypothesis, that all parameters
vary freely or against the null hypothesis that all category proportions are equal.
For more information see Sarafoglou et al. (2020) <doi:10.31234/osf.io/bux7p>.
Author: Alexandra Sarafoglou [aut, cre]
,
Frederik Aust [aut] ,
Julia M. Haaf [aut] ,
Joris Goosen [aut],
Quentin F. Gronau [aut],
Maarten Marsman [aut]
Maintainer: Alexandra Sarafoglou <alexandra.sarafoglou@gmail.com>
Diff between multibridge versions 1.1.0 dated 2021-02-23 and 1.2.0 dated 2022-11-01
DESCRIPTION | 12 MD5 | 72 +- NAMESPACE | 1 NEWS.md | 8 R/bmult_S3methods.R | 23 R/bmult_binomBfInformed.R | 38 - R/bmult_compute_logml.R |only R/bmult_equalities_mult.R | 8 R/bmult_inequalities_binom.R | 7 R/bmult_inequalities_mult.R | 7 R/bmult_multBfInformed.R | 32 - R/data_journals.R | 2 R/data_lifestresses.R | 2 R/data_peas.R | 2 README.md | 13 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 18 inst/REFERENCES.bib | 312 +++++++++- inst/doc/MemoryOfLifestresses.html | 204 ++++-- inst/doc/MendelianLawsOfInheritance.html | 214 ++++-- inst/doc/PrevalenceOfStatisticalReportingErrors.html | 228 ++++--- man/bayes_factor.bmult.Rd | 5 man/binom_bf_equality.Rd | 18 man/binom_bf_informed.Rd | 2 man/figures/README-unnamed-chunk-4-1.png |binary man/mult_bf_equality.Rd | 18 man/plot.summary.bmult.Rd | 5 man/summary.bmult.Rd | 5 man/summary.bmult_bridge.Rd | 2 src/Makevars | 7 src/Makevars.win |only src/RcppExports.cpp | 5 src/truncatedSamplingSubiteration.cpp | 2 tests/testthat/testthat-S3methods.R | 591 ++++++++++++++----- tests/testthat/testthat-bayesfactors_binom.R | 151 ++++ tests/testthat/testthat-bayesfactors_equalities.R | 42 - tests/testthat/testthat-bayesfactors_mult.R | 545 +++++++++++++---- 38 files changed, 1988 insertions(+), 613 deletions(-)
Title: Tools to Deal with Interval-Valued Responses in Questionnaires
Description: A user-friendly toolbox for doing the statistical analysis of
interval-valued responses in questionnaires measuring intrinsically
imprecise human attributes or features (attitudes, perceptions, opinions,
feelings, etc.). In particular, this package provides S4 classes, methods,
and functions in order to compute basic arithmetic and statistical operations
with interval-valued data; prepare customized plots; associate each
interval-valued response to its equivalent Likert-type and visual analogue
scales answers through the minimum theta-distance and the mid-point criteria;
analyze the reliability of respondents' answers from the internal consistency
point of view by means of Cronbach's alpha coefficient; and simulate
interval-valued responses in this type of questionnaires. The package also
incorporates some real-life data that can be used to illustrate its working
with several non-trivial reproducible examples. The methodology used in this
package is based in many theoretical and applie [...truncated...]
Author: Jose Garcia-Garcia [aut, cre] ,
Maria Asuncion Lubiano [ctb]
Maintainer: Jose Garcia-Garcia <garciagarjose@uniovi.es>
Diff between IntervalQuestionStat versions 0.1.0 dated 2022-07-04 and 0.2.0 dated 2022-11-01
IntervalQuestionStat-0.1.0/IntervalQuestionStat/R/methods-ivd2likert.R |only IntervalQuestionStat-0.1.0/IntervalQuestionStat/R/methods-ivd2vas.R |only IntervalQuestionStat-0.1.0/IntervalQuestionStat/man/ivd2likert-methods.Rd |only IntervalQuestionStat-0.1.0/IntervalQuestionStat/man/ivd2vas-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/DESCRIPTION | 60 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/MD5 | 173 ++- IntervalQuestionStat-0.2.0/IntervalQuestionStat/NAMESPACE | 23 IntervalQuestionStat-0.2.0/IntervalQuestionStat/NEWS.md |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/IntervalData.R | 66 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/IntervalList.R | 102 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/IntervalMatrix.R | 107 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/IntervalQuestionStat-package.R | 121 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/class-IntervalData.R | 70 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/class-IntervalList.R | 50 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/class-IntervalMatrix.R | 52 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/class-virtual-IntervalDataOrIntervalList.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/class-virtual-IntervalListOrIntervalMatrix.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/cronbach.R | 168 ++- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/lackinfo.R | 75 + IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-apply.R | 70 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-arithmetic.R | 459 ++++++++-- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-as.IntervalData.R | 34 IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-as.IntervalList.R | 23 IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-c.R | 79 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-cbind.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-cov.R | 85 + IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-dim.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-distance.R | 52 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-extract.R | 227 ++++ IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-ivs2likert.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-ivs2vas.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-length.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-mean.R | 48 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-mid.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-ncol.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-nrow.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-plot.R | 190 ++-- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-rbind.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-show.R | 58 + IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-spr.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-sum.R | 48 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/methods-var.R | 68 + IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/simulIVS.R | 212 +++- IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/utils-is_single_positive_integer.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/utils-is_single_positive_real_number.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/utils-is_single_proportion.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/R/utils-is_single_real_number.R |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/README.md |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/build |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/data/lackinfo.rda |binary IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalData-class.Rd | 41 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalData.Rd | 42 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalDataOrIntervalList-class.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalList-class.Rd | 28 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalList.Rd | 63 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalListOrIntervalMatrix-class.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalMatrix-class.Rd | 24 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalMatrix.Rd | 61 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/IntervalQuestionStat-package.Rd | 110 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/apply-methods.Rd | 46 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/arithmetic-methods.Rd | 231 +++-- IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/as.IntervalData.Rd | 37 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/as.IntervalList.Rd | 31 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/c-methods.Rd | 25 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/cbind-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/cov-methods.Rd | 72 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/cronbach.Rd | 137 ++ IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/dim-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/distance-methods.Rd | 50 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/extract-methods.Rd | 98 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/figures |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/ivs2likert-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/ivs2vas-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/lackinfo.Rd | 73 + IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/length-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/mean-methods.Rd | 44 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/mid-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/ncol-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/nrow-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/plot-methods.Rd | 105 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/rbind-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/show-methods.Rd | 43 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/simulIVS.Rd | 98 +- IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/spr-methods.Rd |only IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/sum-methods.Rd | 39 IntervalQuestionStat-0.2.0/IntervalQuestionStat/man/var-methods.Rd | 60 - IntervalQuestionStat-0.2.0/IntervalQuestionStat/tests |only 87 files changed, 2912 insertions(+), 1366 deletions(-)
More information about IntervalQuestionStat at CRAN
Permanent link
Title: Conditional Random Fields for Labelling Sequential Data in
Natural Language Processing
Description: Wraps the 'CRFsuite' library <https://github.com/chokkan/crfsuite> allowing users
to fit a Conditional Random Field model and to apply it on existing data.
The focus of the implementation is in the area of Natural Language Processing where this R package allows you to easily build and apply models
for named entity recognition, text chunking, part of speech tagging, intent recognition or classification of any category you have in mind. Next to training, a small web application
is included in the package to allow you to easily construct training data.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Naoaki Okazaki [aut, ctb, cph] ,
libLBFGS library , Constant Quark Database software
),
Bob Jenkins [aut, ctb] ),
Jorge Nocedal [aut, ctb, cph] ),
Jesse Long [aut, ctb, cph] )
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between crfsuite versions 0.4 dated 2021-11-12 and 0.4.1 dated 2022-11-01
DESCRIPTION | 8 - MD5 | 28 +++--- NEWS.md | 4 build/vignette.rds |binary inst/doc/crfsuite-nlp.R | 2 inst/doc/crfsuite-nlp.Rmd | 2 inst/doc/crfsuite-nlp.html | 174 ++++++++++++++++++++++++++++++---------- src/crf/src/crf1d_encode.c | 2 src/crf/src/crf1d_feature.c | 2 src/crf/src/crfsuite_internal.h | 2 src/crf/src/params.c | 2 src/crf/src/params.h | 2 src/crf/src/quark.c | 2 src/crf/src/quark.h | 2 vignettes/crfsuite-nlp.Rmd | 2 15 files changed, 165 insertions(+), 69 deletions(-)
Title: Use Browser Cookies with 'shiny'
Description: Browser cookies are name-value pairs that are saved in a user's
browser by a website. Cookies allow websites to persist information about
the user and their use of the website. Here we provide tools for working
with cookies in 'shiny' apps, in part by wrapping the 'js-cookie' JavaScript
library <https://github.com/js-cookie/js-cookie>.
Author: Jon Harmon [aut, cre, cph] ,
Klaus Hartl [cph] ,
Fagner Brack [cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between cookies versions 0.1.0 dated 2022-11-01 and 0.1.1 dated 2022-11-01
DESCRIPTION | 6 - MD5 | 6 - NEWS.md | 4 tests/testthat/test-onload.R | 222 +++++++++++++++++++++---------------------- 4 files changed, 121 insertions(+), 117 deletions(-)
Title: Bayesian Network Meta-Analysis with Missing Participants
Description: A comprehensive suite of functions to perform and visualise
pairwise and network meta-analysis with aggregate binary or continuous
missing participant outcome data. The package covers core Bayesian one-stage
models implemented in a systematic review with multiple interventions,
including fixed-effect and random-effects network meta-analysis,
meta-regression, evaluation of the consistency assumption via the
node-splitting approach and the unrelated mean effects model, and
sensitivity analysis. Missing participant outcome data are addressed in all
models of the package. The package also offers a rich, user-friendly
visualisation toolkit that aids in appraising and interpreting the results
thoroughly and preparing the manuscript for journal submission.
The visualisation tools comprise the network plot, forest plots, panel of
diagnostic plots, heatmaps on the extent of missing participant outcome data
in the network, league heatmaps on estimation and prediction, rankograms,
Bland-Altman pl [...truncated...]
Author: Loukia Spineli [aut, cre],
Chrysostomos Kalyvas [ctb],
Katerina Papadimitropoulou [ctb]
Maintainer: Loukia Spineli <Spineli.Loukia@mh-hannover.de>
Diff between rnmamod versions 0.2.0 dated 2022-04-06 and 0.3.0 dated 2022-11-01
DESCRIPTION | 17 - MD5 | 105 ++++---- NAMESPACE | 8 NEWS.md | 33 ++ R/UME.plot_function.R | 11 R/balloon.plot.mod_function.R | 10 R/baseline.model_function.R |only R/describe.network_function.R | 51 ++-- R/forestplot.metareg_function.R | 314 +++++++++++++++++++++----- R/forestplot_function.R | 27 +- R/globals.R | 17 + R/heatmap.missing.network_function.R | 36 ++- R/heatmap.robustness_function.R | 24 +- R/improved.UME_function.R | 33 ++ R/league.table.absolute.user_function.R |only R/league.table.absolute_function.R | 105 ++++++-- R/mcmc.diagnostics_function.R | 143 +++++++---- R/metareg.plot_function.R | 30 +- R/network.plot_function.R | 2 R/nodesplit.plot_function.R | 37 +-- R/prepare.UME_function.R | 14 - R/prepare.model_function.R | 90 +++---- R/prepare.nodesplit_function.R | 4 R/quality.transitivity_function.R |only R/rnmamod.R.R | 22 + R/robustness.index.user_function.R |only R/robustness.index_function.R | 17 - R/run.UME_function.R | 44 ++- R/run.metareg_function.R | 58 +++- R/run.model_function.R | 119 ++++++--- R/run.nodesplit_function.R | 10 R/run.sensitivity_function.R | 25 +- R/run.series.meta_function.R | 186 +++++++++------ R/series.meta.plot_function.R | 19 + R/unrelated.effects.plot_function.R.R | 167 +++++++++---- build/partial.rdb |only build/vignette.rds |binary inst/doc/network_description.html | 342 +++++++++++++++++++++++++--- inst/doc/perform_network_metaanalysis.html | 348 ++++++++++++++++++++++++++--- inst/extdata/res_baker.rds |binary inst/extdata/res_liu.rds |binary inst/extdata/res_taylor.rds |binary man/balloon_plot.Rd | 4 man/baseline_model.Rd |only man/forestplot.Rd | 7 man/forestplot_metareg.Rd | 68 ++++- man/heatmap_robustness.Rd | 18 - man/league_table_absolute.Rd | 8 man/league_table_absolute_user.Rd |only man/mcmc_diagnostics.Rd | 8 man/metareg_plot.Rd | 10 man/netplot.Rd | 2 man/rnmamod-package.Rd | 22 + man/robustness_index.Rd | 17 - man/robustness_index_user.Rd |only man/run_metareg.Rd | 3 man/run_model.Rd | 57 +++- man/trans_quality.Rd |only 58 files changed, 2004 insertions(+), 688 deletions(-)
Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between jagshelper versions 0.1.8 dated 2022-10-21 and 0.1.9 dated 2022-11-01
DESCRIPTION | 8 +- MD5 | 28 ++++--- NAMESPACE | 5 + NEWS.md | 4 + R/jagshelper1.R | 139 ++++++++++++++++++++++++++++++++++++-- README.md | 3 inst/doc/jagshelper-vignette.R | 3 inst/doc/jagshelper-vignette.Rmd | 11 +++ inst/doc/jagshelper-vignette.html | 86 +++++++++++++---------- man/cor_jags.Rd |only man/jags_df.Rd | 7 + man/jagshelper-package.Rd | 4 - man/plotcor_jags.Rd |only man/pull_post.Rd | 2 tests/testthat/test_jagshelper.R | 11 +++ vignettes/jagshelper-vignette.Rmd | 11 +++ 16 files changed, 259 insertions(+), 63 deletions(-)
Title: Show Pride on 'ggplot2' Plots
Description: Provides multiple palettes based on pride flags with tailored themes.
Author: Laura Bakala [cre, aut, cph]
Maintainer: Laura Bakala <erdaradun.gaztea@gmail.com>
Diff between gglgbtq versions 0.1.0 dated 2022-08-16 and 0.1.1 dated 2022-11-01
DESCRIPTION | 19 ++++++++++------- MD5 | 41 +++++++++++++++++++++++--------------- NAMESPACE | 30 +++++++++++++-------------- NEWS.md | 7 ++++++ R/summary.R | 36 ++++++++++++++++----------------- R/themes.R | 33 ++++++++++++++++++++++++++++-- R/utils.R | 22 ++++++++++---------- R/zzz.R | 30 +++++++++++++-------------- R/zzz_data.R | 28 +++++++++++++++++++++++--- build |only inst/doc |only man/palette_lgbtq.Rd | 10 +++++++-- man/roxygen/templates/name.R | 4 +-- man/show_pride.Rd | 36 ++++++++++++++++----------------- man/theme_lgbtq.Rd | 10 +++++++-- tests/testthat.R | 8 +++---- tests/testthat/test-palettes.R | 44 ++++++++++++++++++++--------------------- tests/testthat/test-summary.R | 16 +++++++------- tests/testthat/test-themes.R | 12 +++++------ vignettes |only 20 files changed, 234 insertions(+), 152 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-18 0.1.1
2022-09-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-08 1.0.1
2022-02-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-14 0.1.2
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 1.2-0 dated 2022-10-15 and 1.3-0 dated 2022-11-01
DESCRIPTION | 8 +- MD5 | 10 +-- R/roger_interface.R | 94 +++++++++++++++++++-------------- inst/NEWS.Rd | 31 ++++++++++- man/roger-interface.Rd | 41 +++++++------- tests/interface-tests.R | 135 +++++++++++++++++++++--------------------------- 6 files changed, 174 insertions(+), 145 deletions(-)