Title: Managing Larger Data on a GitHub Repository
Description: Because larger (> 50 MB) data files cannot easily be committed to git,
a different approach is required to manage data associated with an analysis in a
GitHub repository. This package provides a simple work-around by allowing larger
(up to 2 GB) data files to piggyback on a repository as assets attached to individual
GitHub releases. These files are not handled by git in any way, but instead are
uploaded, downloaded, or edited directly by calls through the GitHub API. These
data files can be versioned manually by creating different releases. This approach
works equally well with public or private repositories. Data can be uploaded
and downloaded programmatically from scripts. No authentication is required to
download data from public repositories.
Author: Carl Boettiger [aut, cre, cph]
,
Tan Ho [aut] ,
Mark Padgham [ctb] ,
Jeffrey O Hanson [ctb] ,
Kevin Kuo [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between piggyback versions 0.1.3 dated 2022-05-19 and 0.1.4 dated 2022-07-19
piggyback-0.1.3/piggyback/R/pb_new_release.R |only piggyback-0.1.3/piggyback/man/pb_new_release.Rd |only piggyback-0.1.3/piggyback/tests/testthat/test-errors.R |only piggyback-0.1.3/piggyback/tests/testthat/test-gh.R |only piggyback-0.1.3/piggyback/tests/testthat/test-on-cran.R |only piggyback-0.1.3/piggyback/tests/testthat/test-timestamps.R |only piggyback-0.1.3/piggyback/tests/testthat/test-with-auth.R |only piggyback-0.1.3/piggyback/tests/testthat/test-without-auth.R |only piggyback-0.1.3/piggyback/tests/testthat/test-zzz-teardown.R |only piggyback-0.1.4/piggyback/DESCRIPTION | 23 ++-- piggyback-0.1.4/piggyback/MD5 | 59 +++++------ piggyback-0.1.4/piggyback/NAMESPACE | 2 piggyback-0.1.4/piggyback/NEWS.md | 13 ++ piggyback-0.1.4/piggyback/R/pb_delete.R | 2 piggyback-0.1.4/piggyback/R/pb_download.R | 21 ++- piggyback-0.1.4/piggyback/R/pb_info.R | 27 ++--- piggyback-0.1.4/piggyback/R/pb_release_create.R |only piggyback-0.1.4/piggyback/R/pb_release_delete.R |only piggyback-0.1.4/piggyback/R/pb_upload.R | 41 ++++--- piggyback-0.1.4/piggyback/R/utils.R | 48 -------- piggyback-0.1.4/piggyback/build/vignette.rds |binary piggyback-0.1.4/piggyback/inst/doc/alternatives.html | 4 piggyback-0.1.4/piggyback/inst/doc/intro.Rmd | 2 piggyback-0.1.4/piggyback/inst/doc/intro.html | 8 - piggyback-0.1.4/piggyback/inst/iris_upload.tsv.gz |only piggyback-0.1.4/piggyback/inst/mtcars_upload.tsv.gz |only piggyback-0.1.4/piggyback/man/pb_delete.Rd | 3 piggyback-0.1.4/piggyback/man/pb_download.Rd | 7 - piggyback-0.1.4/piggyback/man/pb_download_url.Rd | 3 piggyback-0.1.4/piggyback/man/pb_list.Rd | 3 piggyback-0.1.4/piggyback/man/pb_release_create.Rd |only piggyback-0.1.4/piggyback/man/pb_release_delete.Rd |only piggyback-0.1.4/piggyback/man/pb_upload.Rd | 7 - piggyback-0.1.4/piggyback/man/piggyback-package.Rd | 6 - piggyback-0.1.4/piggyback/tests/testthat.R | 1 piggyback-0.1.4/piggyback/tests/testthat/test-pb_download.R |only piggyback-0.1.4/piggyback/tests/testthat/test-pb_info.R |only piggyback-0.1.4/piggyback/tests/testthat/test-utils.R |only piggyback-0.1.4/piggyback/tests/testthat/test-with_auth.R |only piggyback-0.1.4/piggyback/vignettes/intro.Rmd | 2 40 files changed, 134 insertions(+), 148 deletions(-)
Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser.
Enables embedding a JB2 genome browser in a Shiny app or R Markdown
document. The browser can also be launched from an interactive R console.
The browser can be loaded with a variety of common genomics data types,
and can be used with a custom theme.
Author: Elliot Hershberg [aut, cre] ,
the JBrowse 2 Team [aut]
Maintainer: Elliot Hershberg <eahershberg@gmail.com>
Diff between JBrowseR versions 0.9.0 dated 2021-10-17 and 0.9.1 dated 2022-07-19
DESCRIPTION | 6 MD5 | 19 +- NAMESPACE | 1 NEWS.md | 5 R/text-index.R |only inst/doc/JBrowseR.html | 267 +++++++++++++++++++++++++++++-- inst/doc/creating-urls.html | 240 +++++++++++++++++++++++++++- inst/doc/custom-browser-tutorial.html | 287 +++++++++++++++++++++++++++++++--- inst/doc/json-tutorial.html | 244 +++++++++++++++++++++++++++- inst/htmlwidgets/JBrowseR.js | 187 ++++++++++++---------- man/text_index.Rd |only tests/testthat/test-text-index.R |only 12 files changed, 1093 insertions(+), 163 deletions(-)
Title: Semi-Parametric Dimension Reduction Models Using Orthogonality
Constrained Optimization
Description: Utilize an orthogonality constrained optimization algorithm of
Wen & Yin (2013) <DOI:10.1007/s10107-012-0584-1> to solve a variety of
dimension reduction problems in the semiparametric framework, such as
Ma & Zhu (2012) <DOI:10.1080/01621459.2011.646925>, Ma & Zhu (2013)
<DOI:10.1214/12-AOS1072>, Sun, Zhu, Wang & Zeng (2019) <arXiv:1704.05046>
and Zhou, Zhu & Zeng (2021) <arXiv:1802.06156>. It also serves as a general
purpose optimization solver for problems with orthogonality constraints.
Parallel computing for approximating the gradient is enabled
through 'OpenMP'.
Author: Ruilin Zhao [aut, cph],
Ruoqing Zhu [aut, cre, cph] ,
Jiyang Zhang [aut, cph],
Wenzhuo Zhou [aut, cph],
Peng Xu [aut, cph],
James Joseph Balamuta [ctb]
Maintainer: Ruoqing Zhu <teazrq@gmail.com>
Diff between orthoDr versions 0.6.4 dated 2019-09-05 and 0.6.5 dated 2022-07-19
orthoDr-0.6.4/orthoDr/man/param_check.Rd |only orthoDr-0.6.4/orthoDr/man/predict_orthoDr_pdose.Rd |only orthoDr-0.6.4/orthoDr/man/predict_orthoDr_reg.Rd |only orthoDr-0.6.4/orthoDr/man/predict_orthoDr_surv.Rd |only orthoDr-0.6.4/orthoDr/man/print.Rd |only orthoDr-0.6.5/orthoDr/DESCRIPTION | 51 ++- orthoDr-0.6.5/orthoDr/MD5 | 126 ++++----- orthoDr-0.6.5/orthoDr/NAMESPACE | 54 ++- orthoDr-0.6.5/orthoDr/R/CP_SIR.r | 121 +++++--- orthoDr-0.6.5/orthoDr/R/RcppExports.R | 93 ++++-- orthoDr-0.6.5/orthoDr/R/dist_cross.r | 31 +- orthoDr-0.6.5/orthoDr/R/distance.r | 112 ++++---- orthoDr-0.6.5/orthoDr/R/hMave.r | 270 ++++++++++--------- orthoDr-0.6.5/orthoDr/R/kernel_weight.r | 35 +- orthoDr-0.6.5/orthoDr/R/orthoDr-package.R |only orthoDr-0.6.5/orthoDr/R/orthoDr_pdose.r | 211 ++++++++------- orthoDr-0.6.5/orthoDr/R/orthoDr_reg.r | 239 +++++++++-------- orthoDr-0.6.5/orthoDr/R/orthoDr_surv.r | 214 ++++++++------- orthoDr-0.6.5/orthoDr/R/ortho_optim.r | 271 ++++++++++--------- orthoDr-0.6.5/orthoDr/R/pSAVE.r | 97 +++---- orthoDr-0.6.5/orthoDr/R/param_check.r | 91 +++--- orthoDr-0.6.5/orthoDr/R/predict.r | 289 +++++++++++---------- orthoDr-0.6.5/orthoDr/R/print.r | 59 ++-- orthoDr-0.6.5/orthoDr/R/silverman.r | 20 - orthoDr-0.6.5/orthoDr/R/skcm.r | 52 ++- orthoDr-0.6.5/orthoDr/R/view_dr_surv.r | 143 +++++----- orthoDr-0.6.5/orthoDr/README.md |only orthoDr-0.6.5/orthoDr/build |only orthoDr-0.6.5/orthoDr/inst/CITATION | 78 ++++- orthoDr-0.6.5/orthoDr/man/CP_SIR.Rd | 38 +- orthoDr-0.6.5/orthoDr/man/dist_cross.Rd | 16 - orthoDr-0.6.5/orthoDr/man/distance.Rd | 31 +- orthoDr-0.6.5/orthoDr/man/gen_solver.Rd | 29 +- orthoDr-0.6.5/orthoDr/man/hMave.Rd | 31 +- orthoDr-0.6.5/orthoDr/man/kernel_weight.Rd | 20 - orthoDr-0.6.5/orthoDr/man/local_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/orthoDr-package.Rd |only orthoDr-0.6.5/orthoDr/man/orthoDr_pdose.Rd | 105 ++++--- orthoDr-0.6.5/orthoDr/man/orthoDr_reg.Rd | 78 +++-- orthoDr-0.6.5/orthoDr/man/orthoDr_surv.Rd | 96 ++++-- orthoDr-0.6.5/orthoDr/man/ortho_optim.Rd | 62 +++- orthoDr-0.6.5/orthoDr/man/pSAVE.Rd | 18 - orthoDr-0.6.5/orthoDr/man/pdose_direct_solver.Rd | 29 +- orthoDr-0.6.5/orthoDr/man/pdose_semi_solver.Rd | 29 +- orthoDr-0.6.5/orthoDr/man/phd_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/predict.orthoDr.Rd | 77 +++-- orthoDr-0.6.5/orthoDr/man/print.orthoDr.Rd |only orthoDr-0.6.5/orthoDr/man/save_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/seff_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/silverman.Rd | 4 orthoDr-0.6.5/orthoDr/man/sir_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/skcm.clinical.Rd | 22 + orthoDr-0.6.5/orthoDr/man/skcm.melgene.Rd | 16 - orthoDr-0.6.5/orthoDr/man/surv_dm_solver.Rd | 28 +- orthoDr-0.6.5/orthoDr/man/surv_dn_solver.Rd | 28 +- orthoDr-0.6.5/orthoDr/man/surv_forward_solver.Rd | 25 + orthoDr-0.6.5/orthoDr/man/view_dr_surv.Rd | 51 ++- orthoDr-0.6.5/orthoDr/src/RcppExports.cpp | 5 orthoDr-0.6.5/orthoDr/src/gen_solver.cpp | 12 orthoDr-0.6.5/orthoDr/src/pdose_direct_solver.cpp | 7 orthoDr-0.6.5/orthoDr/src/pdose_semi_solver.cpp | 7 orthoDr-0.6.5/orthoDr/src/reg_local_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_phd_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_save_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_seff_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_sir_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/surv_dm_solver.cpp | 11 orthoDr-0.6.5/orthoDr/src/surv_dn_solver.cpp | 9 orthoDr-0.6.5/orthoDr/src/surv_forward_solver.cpp | 8 69 files changed, 2204 insertions(+), 1520 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamas Nepusz <ntamas@gmail.com>
Diff between igraph versions 1.3.3 dated 2022-07-14 and 1.3.4 dated 2022-07-19
DESCRIPTION | 6 - MD5 | 27 ++--- NEWS.md | 22 ++++ R/games.R | 43 ++++---- R/layout.R | 60 +++++++++--- inst/NEWS.md | 22 ++++ man/layout_nicely.Rd | 14 ++ man/layout_with_fr.Rd | 2 man/layout_with_kk.Rd | 5 - man/sample_bipartite.Rd | 20 ++-- man/sample_pref.Rd | 4 src/core/connectivity/components.c | 6 + src/core/games/preference.c | 58 ++++++----- src/rinterface.c | 178 +++++++++++++++++++++++------------- tests/testthat/test_layout_nicely.R |only 15 files changed, 317 insertions(+), 150 deletions(-)
Title: Delete or Merge Regressors Algorithms for Linear and Logistic
Model Selection and High-Dimensional Data
Description: Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Aleksandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <https://projecteuclid.org/euclid.ejs/1440507392>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>. Piotr Pokarowski, Wojciech Rejchel, Agnieszka Sołtys, Michał Frej and Jan Mielniczuk, 2022. Improving Lasso for model selection and prediction. Scandinavian Journal of Statistics, 49(2): 831–863. <doi:10.1111/sjos.12546>.
Author: Agnieszka Prochenka-Soltys [aut] ,
Piotr Pokarowski [aut],
Szymon Nowakowski [aut, cre]
Maintainer: Szymon Nowakowski <s.nowakowski@mimuw.edu.pl>
Diff between DMRnet versions 0.2.0 dated 2018-03-24 and 0.3.1 dated 2022-07-19
DMRnet-0.2.0/DMRnet/R/DMRnet-package.r |only DMRnet-0.2.0/DMRnet/R/cvfolds.R |only DMRnet-0.3.1/DMRnet/DESCRIPTION | 26 ++- DMRnet-0.3.1/DMRnet/MD5 | 128 ++++++++++------- DMRnet-0.3.1/DMRnet/NEWS.md |only DMRnet-0.3.1/DMRnet/R/DMR.R | 34 ++-- DMRnet-0.3.1/DMRnet/R/DMR4glm.R | 67 ++++++--- DMRnet-0.3.1/DMRnet/R/DMR4glm_help.R | 15 +- DMRnet-0.3.1/DMRnet/R/DMR4lm.R | 125 ++++++++++------- DMRnet-0.3.1/DMRnet/R/DMR4lm_help.R | 12 + DMRnet-0.3.1/DMRnet/R/DMRnet-package.R |only DMRnet-0.3.1/DMRnet/R/DMRnet.R | 99 +++++++++---- DMRnet-0.3.1/DMRnet/R/DMRnet4glm.R | 53 +++++-- DMRnet-0.3.1/DMRnet/R/DMRnet4glm_help.R | 4 DMRnet-0.3.1/DMRnet/R/DMRnet4lm.R | 93 ++++++++---- DMRnet-0.3.1/DMRnet/R/DMRnet4lm_help.R | 5 DMRnet-0.3.1/DMRnet/R/SOSnet4glm.R | 16 +- DMRnet-0.3.1/DMRnet/R/SOSnet4glm_help.R | 4 DMRnet-0.3.1/DMRnet/R/SOSnet4lm.R | 64 +++++--- DMRnet-0.3.1/DMRnet/R/SOSnet4lm_help.R | 55 +++++-- DMRnet-0.3.1/DMRnet/R/clusters_4glm_help.R |only DMRnet-0.3.1/DMRnet/R/clusters_4lm_help.R |only DMRnet-0.3.1/DMRnet/R/coef.DMR.R | 8 - DMRnet-0.3.1/DMRnet/R/coef.cv.DMR.R | 24 ++- DMRnet-0.3.1/DMRnet/R/coef.gic.DMR.R | 8 - DMRnet-0.3.1/DMRnet/R/cv.DMR.R | 85 ++--------- DMRnet-0.3.1/DMRnet/R/cv.DMRnet.R | 131 ++++++++---------- DMRnet-0.3.1/DMRnet/R/cv_GIC_indexed.R |only DMRnet-0.3.1/DMRnet/R/cv_MD_indexed.R |only DMRnet-0.3.1/DMRnet/R/cv_compute_model.R |only DMRnet-0.3.1/DMRnet/R/cv_indexation.mode_distribute.R |only DMRnet-0.3.1/DMRnet/R/gic.DMR.R | 14 - DMRnet-0.3.1/DMRnet/R/glamer_4glm.R |only DMRnet-0.3.1/DMRnet/R/glamer_4glm_help.R |only DMRnet-0.3.1/DMRnet/R/glamer_4lm.R |only DMRnet-0.3.1/DMRnet/R/glamer_4lm_help.R |only DMRnet-0.3.1/DMRnet/R/glamer_stats.R |only DMRnet-0.3.1/DMRnet/R/miete.R | 4 DMRnet-0.3.1/DMRnet/R/part2beta_glm_help.R | 35 ++-- DMRnet-0.3.1/DMRnet/R/part2beta_help.R | 91 +++++++----- DMRnet-0.3.1/DMRnet/R/plot.DMR.R | 10 - DMRnet-0.3.1/DMRnet/R/plot.cv.DMR.R | 9 - DMRnet-0.3.1/DMRnet/R/plot.gic.DMR.R | 8 - DMRnet-0.3.1/DMRnet/R/predict.DMR.R | 67 +++++++-- DMRnet-0.3.1/DMRnet/R/predict.cv.DMR.R | 29 ++- DMRnet-0.3.1/DMRnet/R/predict.gic.DMR.R | 16 +- DMRnet-0.3.1/DMRnet/R/print.DMR.R | 6 DMRnet-0.3.1/DMRnet/R/promoter.R | 2 DMRnet-0.3.1/DMRnet/R/release_questions.R |only DMRnet-0.3.1/DMRnet/R/t_stats.R | 2 DMRnet-0.3.1/DMRnet/R/w_stats.R | 5 DMRnet-0.3.1/DMRnet/README.md |only DMRnet-0.3.1/DMRnet/build |only DMRnet-0.3.1/DMRnet/inst |only DMRnet-0.3.1/DMRnet/man/DMR.Rd | 38 +++-- DMRnet-0.3.1/DMRnet/man/DMRnet-package.Rd | 40 +++-- DMRnet-0.3.1/DMRnet/man/DMRnet.Rd | 95 +++++++++---- DMRnet-0.3.1/DMRnet/man/coef.DMR.Rd | 5 DMRnet-0.3.1/DMRnet/man/coef.cv.DMR.Rd | 11 - DMRnet-0.3.1/DMRnet/man/coef.gic.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/cv.DMR.Rd | 37 +++-- DMRnet-0.3.1/DMRnet/man/cv.DMRnet.Rd | 44 +++--- DMRnet-0.3.1/DMRnet/man/gic.DMR.Rd | 15 -- DMRnet-0.3.1/DMRnet/man/miete.Rd | 11 - DMRnet-0.3.1/DMRnet/man/plot.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/plot.cv.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/plot.gic.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/predict.DMR.Rd | 22 ++- DMRnet-0.3.1/DMRnet/man/predict.cv.DMR.Rd | 22 ++- DMRnet-0.3.1/DMRnet/man/predict.gic.DMR.Rd | 15 +- DMRnet-0.3.1/DMRnet/man/print.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/promoter.Rd | 9 - DMRnet-0.3.1/DMRnet/vignettes |only 73 files changed, 1065 insertions(+), 688 deletions(-)
Title: SPAtial Resolution-SEnsitive Models of Outbreak Dynamics
Description: Implementation of spatially-explicit, stochastic disease models with customizable time windows that describe how parameter values fluctuate during outbreaks (e.g., in response to public health or conservation interventions).
Author: Joseph Mihaljevic [aut, cre] ,
Toby Hocking [ctb] ,
Seth Borkovec [ctb] ,
Saikanth Ratnavale [ctb]
Maintainer: Joseph Mihaljevic <Joseph.Mihaljevic@nau.edu>
Diff between SPARSEMODr versions 1.1.0 dated 2021-07-01 and 1.2.0 dated 2022-07-19
SPARSEMODr-1.1.0/SPARSEMODr/man/Time-varying-R0.Rd |only SPARSEMODr-1.1.0/SPARSEMODr/man/figures |only SPARSEMODr-1.2.0/SPARSEMODr/DESCRIPTION | 7 SPARSEMODr-1.2.0/SPARSEMODr/MD5 | 78 SPARSEMODr-1.2.0/SPARSEMODr/NEWS | 12 SPARSEMODr-1.2.0/SPARSEMODr/R/model_interface.R | 8 SPARSEMODr-1.2.0/SPARSEMODr/R/time_windows.R | 74 SPARSEMODr-1.2.0/SPARSEMODr/README.md | 171 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model-vary-hosp.R | 130 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model-vary-hosp.Rmd | 134 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model-vary-hosp.html | 937 +++++----- SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model.R | 109 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model.Rmd | 127 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model.html | 801 ++++---- SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/key-features.R | 59 SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/key-features.Rmd | 87 SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/key-features.html | 201 +- SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/seir-model.R | 107 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/seir-model.Rmd | 125 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/seir-model.html | 625 +++--- SPARSEMODr-1.2.0/SPARSEMODr/man/Movement.Rd | 4 SPARSEMODr-1.2.0/SPARSEMODr/man/SPARSEMOD-package.Rd | 2 SPARSEMODr-1.2.0/SPARSEMODr/man/model_interface.Rd | 47 SPARSEMODr-1.2.0/SPARSEMODr/man/model_parallel.Rd | 47 SPARSEMODr-1.2.0/SPARSEMODr/man/seir_control.Rd | 3 SPARSEMODr-1.2.0/SPARSEMODr/man/time_windows.Rd | 59 SPARSEMODr-1.2.0/SPARSEMODr/src/RcppExports.cpp | 5 SPARSEMODr-1.2.0/SPARSEMODr/src/covid19_model.cpp | 251 +- SPARSEMODr-1.2.0/SPARSEMODr/src/covid19_model.h | 14 SPARSEMODr-1.2.0/SPARSEMODr/src/general_model.h | 4 SPARSEMODr-1.2.0/SPARSEMODr/src/interface.cpp | 30 SPARSEMODr-1.2.0/SPARSEMODr/src/seir_model.cpp | 230 +- SPARSEMODr-1.2.0/SPARSEMODr/src/seir_model.h | 14 SPARSEMODr-1.2.0/SPARSEMODr/src/time_window_utils.cpp | 22 SPARSEMODr-1.2.0/SPARSEMODr/src/time_window_utils.h | 52 SPARSEMODr-1.2.0/SPARSEMODr/tests/testthat/test-model.R | 14 SPARSEMODr-1.2.0/SPARSEMODr/vignettes/covid-19-model-vary-hosp.Rmd | 134 - SPARSEMODr-1.2.0/SPARSEMODr/vignettes/covid-19-model.Rmd | 127 - SPARSEMODr-1.2.0/SPARSEMODr/vignettes/key-features.Rmd | 87 SPARSEMODr-1.2.0/SPARSEMODr/vignettes/seir-model.Rmd | 125 - 40 files changed, 2556 insertions(+), 2507 deletions(-)
Title: Functions for Web Development
Description: Organizational framework for web development in R including functions to
serve static and dynamic content via HTTP methods, includes the html5 package to
create HTML pages, and offers other utility functions for common tasks related
to web development.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between webdeveloper versions 1.0.1 dated 2022-07-06 and 1.0.2 dated 2022-07-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/webdeveloper.R | 23 +++++++++++------------ 3 files changed, 16 insertions(+), 17 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Gruen <dominic.gruen@gmail.com>
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.2.3 dated 2021-04-08 and 0.2.4 dated 2022-07-19
DESCRIPTION | 10 +- MD5 | 16 +-- R/VarID_functions.R | 2 build/vignette.rds |binary data/cc_genes.RData |binary data/intestinalData.RData |binary data/intestinalDataSmall.RData |binary inst/doc/RaceID.html | 194 +++++++++++++++++++---------------------- src/RcppExports.cpp | 5 + 9 files changed, 111 insertions(+), 116 deletions(-)
Title: Create HTML Content with Bootstrap 5 Classes and Layouts
Description: Functions are pre-configured to utilize Bootstrap 5 classes and
HTML structures to create Bootstrap-styled HTML quickly and easily. Includes
functions for creating common Bootstrap elements such as containers, rows, cols,
navbars, etc. Intended to be used with the html5 package. Learn more at
<https://getbootstrap.com/>.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between bsTools versions 1.0.0 dated 2022-06-22 and 1.0.2 dated 2022-07-19
DESCRIPTION | 6 ++-- MD5 | 8 +++--- R/bsTools2.R | 68 +++++++++++++++++++++++++++++++++++-------------------- man/bs_card.Rd | 17 ++++++++++++- man/bs_navbar.Rd | 3 ++ 5 files changed, 70 insertions(+), 32 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.2.0 dated 2022-06-08 and 1.2.1 dated 2022-07-19
DESCRIPTION | 8 LICENSE | 4 MD5 | 296 ++++---- NEWS.md | 19 R/00_global_variables.R | 18 R/autoplot-combined-dist.R | 558 +++++++-------- R/autoplot-four-graphs.R | 176 ++-- R/autoplot-multi-dist.R | 724 ++++++++++---------- R/autoplot-randomwalk.R | 374 +++++----- R/combine-multi-single-dist-tbl.R | 239 +++--- R/combine-tidy-distributions-tbl.R | 2 R/empirical-tidy-bootstrap.R | 190 ++--- R/empirical-tidy.R | 278 +++---- R/est-param-beta.R | 318 ++++---- R/est-param-binomial.R | 336 ++++----- R/est-param-cauchy.R | 194 ++--- R/est-param-exponential.R | 208 ++--- R/est-param-gamma.R | 250 +++--- R/est-param-geometric.R | 238 +++--- R/est-param-hypergeometric.R | 436 ++++++------ R/est-param-logistic.R | 272 +++---- R/est-param-lognormal.R | 228 +++--- R/est-param-negative-binomial.R | 296 ++++---- R/est-param-normal.R | 228 +++--- R/est-param-pareto.R | 240 +++--- R/est-param-poisson.R | 214 ++--- R/est-param-uniform.R | 218 +++--- R/est-param-weibull.R | 202 ++--- R/palette-color-blind.R | 80 +- R/random-tidy-beta.R | 252 +++--- R/random-tidy-binomial.R | 256 +++---- R/random-tidy-burr-inverse.R | 2 R/random-tidy-burr.R | 2 R/random-tidy-cauchy.R | 248 +++--- R/random-tidy-chisquare.R | 248 +++--- R/random-tidy-exponential-inverse.R | 2 R/random-tidy-exponential.R | 234 +++--- R/random-tidy-f.R | 252 +++--- R/random-tidy-gamma-inverse.R | 2 R/random-tidy-gamma.R | 258 +++---- R/random-tidy-general-beta.R | 2 R/random-tidy-general-pareto.R | 2 R/random-tidy-geom.R | 236 +++--- R/random-tidy-hypergeometric.R | 254 +++---- R/random-tidy-logistic.R | 240 +++--- R/random-tidy-lognormal.R | 248 +++--- R/random-tidy-mixture.R | 298 ++++---- R/random-tidy-negative-binomial.R | 2 R/random-tidy-normal-inverse.R | 266 +++---- R/random-tidy-normal.R | 254 +++---- R/random-tidy-paralogistic.R | 268 +++---- R/random-tidy-pareto-inverse.R | 2 R/random-tidy-pareto-single-param.R | 2 R/random-tidy-pareto.R | 2 R/random-tidy-poisson.R | 240 +++--- R/random-tidy-t.R | 250 +++--- R/random-tidy-uniform.R | 242 +++--- R/random-tidy-weibull-inverse.R | 2 R/random-tidy-weibull.R | 248 +++--- R/random-tidy-zero-truc-poisson.R | 2 R/random-tidy-zero-trunc-geometric.R | 2 R/random-tidy-zero-truncated-binomial.R | 2 R/random-zero-trunc-negative-binomial.R | 2 R/stats-beta-tbl.R | 170 ++-- R/stats-binomial-tbl.R | 174 ++-- R/stats-cauchy-tbl.R | 170 ++-- R/stats-chisquare-tbl.R | 180 ++-- R/stats-confidence-intervals.R | 130 +-- R/stats-exponential-tbl.R | 172 ++-- R/stats-f-tbl.R | 208 ++--- R/stats-gamma-tbl.R | 168 ++-- R/stats-geometric-tbl.R | 176 ++-- R/stats-hypergeometric-tbl.R | 196 ++--- R/stats-logistic-tbl.R | 172 ++-- R/stats-lognormal-tbl.R | 174 ++-- R/stats-negative-binomial-tbl.R | 174 ++-- R/stats-normal-tbl.R | 170 ++-- R/stats-pareto-tbl.R | 172 ++-- R/stats-poisson-tbl.R | 170 ++-- R/stats-t-tbl.R | 170 ++-- R/stats-uniform-tbl.R | 176 ++-- R/stats-weibull-tbl.R | 194 ++--- R/tidy-random-walk.R | 19 R/tidy_distribution_summary_tbl.R | 164 ++-- R/util-distribution-comparison.R | 500 +++++++------ R/utils-pipe.R | 28 R/utils-tidy-eval.R | 214 ++--- README.md | 25 build/vignette.rds |binary inst/doc/getting-started.Rmd | 122 +-- inst/doc/getting-started.html | 43 - man/bootstrap_unnest_tbl.Rd | 80 +- man/ci_hi.Rd | 76 +- man/ci_lo.Rd | 76 +- man/color_blind.Rd | 22 man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/pipe.Rd | 40 - man/td_scale_color_colorblind.Rd | 32 man/td_scale_fill_colorblind.Rd | 32 man/tidy_bootstrap.Rd | 108 +- man/tidy_burr.Rd | 2 man/tidy_distribution_comparison.Rd | 124 +-- man/tidy_four_autoplot.Rd | 168 ++-- man/tidy_generalized_beta.Rd | 2 man/tidy_generalized_pareto.Rd | 2 man/tidy_inverse_burr.Rd | 2 man/tidy_inverse_exponential.Rd | 2 man/tidy_inverse_gamma.Rd | 2 man/tidy_inverse_pareto.Rd | 2 man/tidy_inverse_weibull.Rd | 2 man/tidy_mixture_density.Rd | 128 +-- man/tidy_negative_binomial.Rd | 2 man/tidy_pareto.Rd | 2 man/tidy_pareto1.Rd | 2 man/tidy_t.Rd | 170 ++-- man/tidy_zero_truncated_binomial.Rd | 2 man/tidy_zero_truncated_geometric.Rd | 2 man/tidy_zero_truncated_negative_binomial.Rd | 2 man/tidy_zero_truncated_poisson.Rd | 2 man/tidyeval.Rd | 196 ++--- man/util_beta_stats_tbl.Rd | 120 +-- man/util_binomial_stats_tbl.Rd | 126 +-- man/util_cauchy_param_estimate.Rd | 136 +-- man/util_cauchy_stats_tbl.Rd | 118 +-- man/util_chisquare_stats_tbl.Rd | 116 +-- man/util_exponential_stats_tbl.Rd | 120 +-- man/util_f_stats_tbl.Rd | 116 +-- man/util_gamma_stats_tbl.Rd | 120 +-- man/util_geometric_stats_tbl.Rd | 120 +-- man/util_hypergeometric_stats_tbl.Rd | 118 +-- man/util_logistic_stats_tbl.Rd | 120 +-- man/util_lognormal_stats_tbl.Rd | 118 +-- man/util_negative_binomial_stats_tbl.Rd | 112 +-- man/util_normal_stats_tbl.Rd | 120 +-- man/util_pareto_stats_tbl.Rd | 124 +-- man/util_poisson_stats_tbl.Rd | 120 +-- man/util_t_stats_tbl.Rd | 116 +-- man/util_uniform_param_estimate.Rd | 136 +-- man/util_uniform_stats_tbl.Rd | 118 +-- man/util_weibull_param_estimate.Rd | 138 +-- man/util_weibull_stats_tbl.Rd | 120 +-- vignettes/getting-started.Rmd | 122 +-- 149 files changed, 10083 insertions(+), 9970 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1> and for a tutorial on some of the main functions available here, see Gilleland (2022) <doi: 10.5065/4px3-5a05>.
Author: Eric Gilleland [aut, cre],
Kim Elmore [ctb],
Caren Marzban [ctb],
Matt Pocernich [ctb],
Gregor Skok [ctb]
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.9 dated 2022-01-27 and 1.0 dated 2022-07-19
DESCRIPTION | 12 ++++++------ MD5 | 43 ++++++++++++++++++++++--------------------- NAMESPACE | 1 + R/FeatureTable.R | 2 +- R/Features.R | 10 +++++----- R/G2IL.R | 2 ++ R/Gbeta.R | 2 ++ R/GbetaIL.R | 2 ++ R/Hoods2d.R | 6 +++--- R/LocMeasures.R | 2 +- R/MergeForce.R | 2 +- R/Vgrams.R | 6 +++--- R/binarizer.R | 22 +++++++++++----------- R/compositer.R | 2 +- R/deltamm.R | 8 ++++---- R/functionals.R | 2 +- R/gmm.R | 2 +- R/interester.R | 2 +- R/minboundmatch.R | 2 +- R/spct.R | 4 ++-- R/warper.R | 2 +- inst |only man/hoods2d.Rd | 2 +- 23 files changed, 73 insertions(+), 65 deletions(-)
Title: Extract Muscle Synergies from Electromyography
Description: Provides a framework to factorise electromyography (EMG) data.
Tools are provided for raw data pre-processing, non negative matrix factorisation,
classification of factorised data and plotting of obtained outcomes.
In particular, reading from ASCII files is supported, along with wide-used
filtering approaches to process EMG data. All steps include one or more sensible
defaults that aim at simplifying the workflow. Yet, all functions are largely
tunable at need. Example data sets are included.
Author: Alessandro Santuz [aut, cre]
Maintainer: Alessandro Santuz <alessandro.santuz@gmail.com>
Diff between musclesyneRgies versions 1.1.3 dated 2022-02-10 and 1.2.5 dated 2022-07-19
DESCRIPTION | 12 - MD5 | 77 +++++---- NEWS.md | 171 +++++++++++++++++++++ R/HFD.R | 18 ++ R/Hurst.R | 28 +++ R/classify_kmeans.R | 57 +++---- R/filtEMG.R | 10 - R/normEMG.R | 14 - R/plot_classified_syns.R | 6 R/plot_rawEMG.R | 4 R/rawdata.R | 63 +++++-- R/sMLE.R | 6 R/subsetEMG.R | 28 ++- R/synsNMF.R | 48 ++++-- README.md | 76 ++++++--- build/partial.rdb |binary build/vignette.rds |binary data/RAW_DATA.RData |binary inst/CITATION |only inst/doc/analysis.R | 2 inst/doc/analysis.Rmd | 2 inst/doc/analysis.html | 209 +++++++++++++++++++++++++- inst/doc/plots.html | 223 +++++++++++++++++++++++++++- inst/doc/pro_tips.html | 214 ++++++++++++++++++++++++++- inst/doc/workflow.html | 268 ++++++++++++++++++++++++++++++---- man/HFD.Rd | 14 + man/Hurst.Rd | 26 +++ man/classify_kmeans.Rd | 11 + man/filtEMG.Rd | 2 man/normEMG.Rd | 2 man/rawdata.Rd | 15 + tests/testthat/test-EMG.R | 15 + tests/testthat/test-HFD.R | 5 tests/testthat/test-Hurst.R | 5 tests/testthat/test-classify_kmeans.R |only tests/testthat/test-filtEMG.R |only tests/testthat/test-normEMG.R |only tests/testthat/test-plots.R | 17 +- tests/testthat/test-sMLE.R | 4 tests/testthat/test-subsetEMG.R |only tests/testthat/test-synsNMF.R | 7 vignettes/analysis.Rmd | 2 42 files changed, 1428 insertions(+), 233 deletions(-)
More information about musclesyneRgies at CRAN
Permanent link
Title: Create R Markdown from Lists
Description: Programmatically create R Markdown documents from lists.
Author: Michael J. Kane [aut, cph, cre]
Maintainer: Michael J. Kane <michael.kane@yale.edu>
Diff between listdown versions 0.4.1 dated 2020-12-07 and 0.5.2 dated 2022-07-19
listdown-0.4.1/listdown/tests/testthat.R |only listdown-0.4.1/listdown/tests/testthat/make-reference.r |only listdown-0.5.2/listdown/DESCRIPTION | 15 listdown-0.5.2/listdown/MD5 | 109 - listdown-0.5.2/listdown/NAMESPACE | 25 listdown-0.5.2/listdown/NEWS.md | 10 listdown-0.5.2/listdown/R/build-site.r |only listdown-0.5.2/listdown/R/cc-dendro.r | 9 listdown-0.5.2/listdown/R/chunk-options.r | 6 listdown-0.5.2/listdown/R/chunk-writer.r | 100 listdown-0.5.2/listdown/R/class-and-tag.r |only listdown-0.5.2/listdown/R/depth-first-pres-list-visitor.r | 1 listdown-0.5.2/listdown/R/headers.r | 2 listdown-0.5.2/listdown/R/ld-write-file.r | 54 listdown-0.5.2/listdown/build/vignette.rds |binary listdown-0.5.2/listdown/inst/CITATION |only listdown-0.5.2/listdown/inst/doc/listdown.html | 1029 ++++++---- listdown-0.5.2/listdown/inst/doc/listdown.rmd | 2 listdown-0.5.2/listdown/man/class_and_tag.Rd |only listdown-0.5.2/listdown/man/ld_build_html_site.Rd |only listdown-0.5.2/listdown/man/ld_bundle_doc.Rd |only listdown-0.5.2/listdown/man/ld_create_doc.Rd |only listdown-0.5.2/listdown/man/ld_make_chunks.Rd | 4 listdown-0.5.2/listdown/man/ld_site_yaml.Rd |only listdown-0.5.2/listdown/man/listdown.Rd | 22 listdown-0.5.2/listdown/tests/testthat.r |only listdown-0.5.2/listdown/tests/testthat/reference-data/as-yml.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/cc-dendro.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/cc-list.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-decorator-option-1.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-1.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-2.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-3.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-4.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/ld-cc-list-2-output.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/listdown-page-bundle-after-creation.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/listdown-page-bundle.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/option-check.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/option-chunk-check.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/site_yaml.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/test-make-chunks-1.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-make-chunks-2.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-no-package.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-print-ld.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-print-with-decorator.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-rmarkdown-header.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-setup-expr.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-workflowr-header.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test_list.rds |binary listdown-0.5.2/listdown/tests/testthat/reference.r |only listdown-0.5.2/listdown/tests/testthat/test-add-chunk-elem-option.r | 67 listdown-0.5.2/listdown/tests/testthat/test-add-chunk-option.r | 40 listdown-0.5.2/listdown/tests/testthat/test-as-yml.r | 32 listdown-0.5.2/listdown/tests/testthat/test-cc-dendro.r | 42 listdown-0.5.2/listdown/tests/testthat/test-chunk-opts.r | 7 listdown-0.5.2/listdown/tests/testthat/test-create-doc.r |only listdown-0.5.2/listdown/tests/testthat/test-create-html-site.r |only listdown-0.5.2/listdown/tests/testthat/test-headers.r | 28 listdown-0.5.2/listdown/tests/testthat/test-list.r | 9 listdown-0.5.2/listdown/tests/testthat/test-make-chunks.r | 20 listdown-0.5.2/listdown/tests/testthat/test-no-package.r | 13 listdown-0.5.2/listdown/tests/testthat/test-setup-expr.r | 18 listdown-0.5.2/listdown/tests/testthat/test-site-yaml.r |only listdown-0.5.2/listdown/tests/testthat/test-write-file.r | 74 listdown-0.5.2/listdown/vignettes/listdown.rmd | 2 65 files changed, 1034 insertions(+), 706 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.0 dated 2022-05-31 and 1.0.0-2 dated 2022-07-19
DESCRIPTION | 6 +- MD5 | 26 +++++----- NEWS.md | 4 + R/CompareIsoGrowth_class.R | 5 - R/GlobalGrowthComparison_class.R | 5 - inst/doc/v02_growth_fitting.R | 5 + inst/doc/v02_growth_fitting.Rmd | 5 + inst/doc/v02_growth_fitting.html | 49 +++++++++---------- inst/doc/v03_growth_uncertainty.html | 12 ++-- inst/doc/v04_model_comparison.R | 10 ++- inst/doc/v04_model_comparison.Rmd | 10 ++- inst/doc/v04_model_comparison.html | 90 +++++++++++++++++------------------ vignettes/v02_growth_fitting.Rmd | 5 + vignettes/v04_model_comparison.Rmd | 10 ++- 14 files changed, 122 insertions(+), 120 deletions(-)
Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative time
series hospital data. Some of these include average length of stay, and
readmission rates. The aim is to provide a simple and consistent verb
framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ts versions 0.2.0 dated 2022-06-09 and 0.2.1 dated 2022-07-19
DESCRIPTION | 8 MD5 | 280 ++++---- NAMESPACE | 10 NEWS.md | 18 R/00_global_variables.R | 6 R/arima-string.R | 120 +-- R/augment-ts-acceleration.R | 164 ++-- R/augment-ts-velocity.R | 158 ++-- R/boilerplate-autoarima-xgboost.R | 514 +++++++------- R/boilerplate-autoarima.R | 496 +++++++------- R/boilerplate-croston.R | 514 +++++++------- R/boilerplate-exp-smoothing.R | 522 +++++++-------- R/boilerplate-glmnet.R | 510 +++++++------- R/boilerplate-lm.R | 340 ++++----- R/boilerplate-mars.R | 502 +++++++------- R/boilerplate-misc-functions.R | 70 +- R/boilerplate-nnetar.R | 514 +++++++------- R/boilerplate-prophet-reg.R | 516 +++++++------- R/boilerplate-prophet-xgboost.R | 528 +++++++-------- R/boilerplate-smooth-es.R | 530 +++++++-------- R/boilerplate-svm-poly.R | 518 +++++++------- R/boilerplate-svm-rbf.R | 516 +++++++------- R/boilerplate-theta.R | 320 ++++----- R/boilerplate-xgboost.R | 504 +++++++------- R/calibrate-plot-list.R | 264 +++---- R/diagnostic_plots.R | 622 +++++++++--------- R/helper-model-extraction.R | 172 ++-- R/internal-event-backward.R |only R/internal-event-both.R |only R/internal-event-forward.R |only R/pallette-color-blind.R | 154 ++-- R/simulate-ts-arima.R | 416 ++++++------ R/stats-confidence-intervals.R |only R/step-ts-acceleration.R | 376 +++++----- R/step-ts-velocity.R | 376 +++++----- R/tidy-fft.R | 564 ++++++++-------- R/time-helpers.R |only R/ts-auto-recipe.R | 366 +++++----- R/ts-calendar-heatmap-plt.R | 248 +++---- R/ts-compare-data.R | 226 +++--- R/ts-event-analysis-plot.R |only R/ts-event-analysis-tbl.R |only R/ts-feature-cluster-plt.R | 350 +++++----- R/ts-feature-cluster-tbl.R | 382 +++++------ R/ts-info-tbl.R | 290 ++++---- R/ts-lag-correlation.R |only R/ts-ma-plt.R | 598 ++++++++--------- R/ts-model-compare.R | 496 +++++++------- R/ts-model-rank.R | 216 +++--- R/ts-model-tuner.R | 8 R/ts-qq-plot.R | 260 +++---- R/ts-skedactiy-plot.R | 262 +++---- R/ts-sma-plot.R | 270 +++---- R/ts-splits-plot.R | 142 ++-- R/ts-to-tbl.R | 122 +-- R/ts-tune-spec-template.R | 29 R/ts-vva-plot.R | 208 +++--- R/ts_fcst_sim.R | 548 +++++++-------- R/ts_random_walk.R | 162 ++-- R/vec-ts-acceleration.R | 114 +-- R/vec-ts-velocity.R | 114 +-- R/wfs-arima-boost.R | 362 +++++----- R/wfs-arima-reg.R | 214 +++--- R/wfs-ets-reg.R | 384 +++++------ R/wfs-linear-reg.R | 244 +++---- R/wfs-mars-reg.R | 268 +++---- R/wfs-nnetar-reg.R | 264 +++---- R/wfs-prophet-reg.R | 434 ++++++------ R/wfs-svm-poly-reg.R | 268 +++---- R/wfs-svm-rbf.R | 254 +++---- R/zzz.R | 258 +++---- README.md | 16 build/vignette.rds |binary inst/doc/getting-started.Rmd | 222 +++--- inst/doc/getting-started.html | 26 inst/doc/using-tidy-fft.Rmd | 574 ++++++++-------- inst/doc/using-tidy-fft.html | 16 man/arima_string.Rd | 36 - man/assign_value.Rd | 24 man/calibrate_and_plot.Rd | 206 +++-- man/chr_assign.Rd | 24 man/ci_hi.Rd |only man/ci_lo.Rd |only man/color_blind.Rd | 50 - man/figures/README-ts_random_walk_ggplot_layers-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/get_recipe_call.Rd | 24 man/internal_ts_backward_event_tbl.Rd |only man/internal_ts_both_event_tbl.Rd |only man/internal_ts_forward_event_tbl.Rd |only man/model_extraction_helper.Rd | 8 man/required_pkgs.healthyR.ts.Rd | 50 - man/step_ts_acceleration.Rd | 202 ++--- man/step_ts_velocity.Rd | 202 ++--- man/tidy_fft.Rd | 206 ++--- man/ts_acceleration_augment.Rd | 108 +-- man/ts_acceleration_vec.Rd | 106 +-- man/ts_arima_simulator.Rd | 176 ++--- man/ts_auto_arima.Rd | 248 +++---- man/ts_auto_arima_xgboost.Rd | 248 +++---- man/ts_auto_croston.Rd | 266 +++---- man/ts_auto_exp_smoothing.Rd | 264 +++---- man/ts_auto_glmnet.Rd | 246 +++---- man/ts_auto_lm.Rd | 220 +++--- man/ts_auto_mars.Rd | 246 +++---- man/ts_auto_nnetar.Rd | 246 +++---- man/ts_auto_prophet_boost.Rd | 254 +++---- man/ts_auto_prophet_reg.Rd | 252 +++---- man/ts_auto_recipe.Rd | 196 ++--- man/ts_auto_smooth_es.Rd | 264 +++---- man/ts_auto_svm_poly.Rd | 256 +++---- man/ts_auto_svm_rbf.Rd | 256 +++---- man/ts_auto_theta.Rd | 208 +++--- man/ts_auto_xgboost.Rd | 242 +++---- man/ts_compare_data.Rd | 5 man/ts_event_analysis_plot.Rd |only man/ts_feature_cluster.Rd | 224 +++--- man/ts_feature_cluster_plot.Rd | 208 +++--- man/ts_forecast_simulator.Rd | 176 ++--- man/ts_get_date_columns.Rd |only man/ts_info_tbl.Rd | 128 +-- man/ts_is_date_class.Rd |only man/ts_lag_correlation.Rd |only man/ts_ma_plot.Rd | 158 ++-- man/ts_model_auto_tune.Rd | 403 ++++++----- man/ts_model_compare.Rd | 260 +++---- man/ts_model_rank_tbl.Rd | 196 ++--- man/ts_model_spec_tune_template.Rd | 138 ++- man/ts_qq_plot.Rd | 205 +++-- man/ts_scale_color_colorblind.Rd | 52 - man/ts_scale_fill_colorblind.Rd | 52 - man/ts_scedacity_scatter_plot.Rd | 213 +++--- man/ts_sma_plot.Rd | 118 +-- man/ts_splits_plot.Rd | 118 +-- man/ts_time_event_analysis_tbl.Rd |only man/ts_to_tbl.Rd | 96 +- man/ts_velocity_augment.Rd | 108 +-- man/ts_velocity_vec.Rd | 106 +-- man/ts_vva_plot.Rd | 100 +- man/ts_wfs_arima_boost.Rd | 266 +++---- man/ts_wfs_auto_arima.Rd | 172 ++-- man/ts_wfs_ets_reg.Rd | 258 +++---- man/ts_wfs_lin_reg.Rd | 174 ++--- man/ts_wfs_mars.Rd | 208 +++--- man/ts_wfs_nnetar_reg.Rd | 220 +++--- man/ts_wfs_prophet_reg.Rd | 310 ++++---- man/ts_wfs_svm_poly.Rd | 214 +++--- man/ts_wfs_svm_rbf.Rd | 208 +++--- vignettes/getting-started.Rmd | 222 +++--- vignettes/using-tidy-fft.Rmd | 574 ++++++++-------- 150 files changed, 15878 insertions(+), 15683 deletions(-)
Title: Visualizations of Distributions and Uncertainty
Description: Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for
visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as
frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as
bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include
but are not limited to: points with multiple uncertainty intervals,
eye plots (Spiegelhalter D., 1999) <https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>,
density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>,
quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>,
complementary cumulative distribution function
barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>,
and fit curves with multiple uncertainty ribbons.
Author: Matthew Kay [aut, cre],
Brenton M. Wiernik [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between ggdist versions 3.1.1 dated 2022-02-27 and 3.2.0 dated 2022-07-19
DESCRIPTION | 21 MD5 | 173 - NAMESPACE | 34 NEWS.md | 63 R/abstract_stat_slabinterval.R | 231 + R/binning_methods.R | 4 R/cut_cdf_qi.R | 30 R/distributions.R | 90 R/geom_dotsinterval.R | 49 R/geom_slabinterval.R | 162 - R/guide_rampbar.R |only R/point_interval.R | 12 R/rd_slabinterval.R | 32 R/scale_.R | 10 R/scale_colour_ramp.R | 8 R/scale_thickness.R |only R/stat_dotsinterval.R | 45 R/stat_slabinterval.R | 284 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/dotsinterval.R | 20 inst/doc/dotsinterval.Rmd | 33 inst/doc/dotsinterval.html | 868 ++++- inst/doc/freq-uncertainty-vis.Rmd | 6 inst/doc/freq-uncertainty-vis.html | 356 ++ inst/doc/lineribbon.R | 30 inst/doc/lineribbon.Rmd | 85 inst/doc/lineribbon.html | 839 ++++- inst/doc/slabinterval.R | 99 inst/doc/slabinterval.Rmd | 167 - inst/doc/slabinterval.html | 1447 +++++++--- man/RankCorr.Rd | 6 man/cut_cdf_qi.Rd | 32 man/geom_dotsinterval.Rd | 20 man/geom_interval.Rd | 4 man/geom_pointinterval.Rd | 4 man/geom_slab.Rd | 4 man/guide_rampbar.Rd |only man/lkjcorr_marginal.Rd | 8 man/scale_colour_ramp.Rd | 9 man/scale_thickness.Rd |only man/scales.Rd | 23 man/stat_ccdfinterval.Rd | 21 man/stat_cdfinterval.Rd | 21 man/stat_eye.Rd | 19 man/stat_gradientinterval.Rd | 21 man/stat_halfeye.Rd | 15 man/stat_histinterval.Rd | 19 man/stat_interval.Rd | 14 man/stat_lineribbon.Rd | 14 man/stat_pointinterval.Rd | 14 man/stat_ribbon.Rd | 14 man/stat_slab.Rd | 19 man/stat_slabinterval.Rd | 15 man/student_t.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/test.geom_dotsinterval/bin-dot-order-kept.svg |only tests/testthat/_snaps/test.geom_dotsinterval/bin-dot-order.svg |only tests/testthat/_snaps/test.geom_dotsinterval/max-binwidth.svg | 74 tests/testthat/_snaps/test.geom_dotsinterval/min-binwidth.svg | 74 tests/testthat/_snaps/test.geom_dotsinterval/swarm-both.svg | 10 tests/testthat/_snaps/test.geom_dotsinterval/swarm-bottom.svg | 14 tests/testthat/_snaps/test.geom_dotsinterval/swarm-dot-order.svg | 124 tests/testthat/_snaps/test.geom_dotsinterval/varying-scale-side-just.svg | 10 tests/testthat/_snaps/test.geom_dotsinterval/varying-side-and-just.svg | 12 tests/testthat/_snaps/test.geom_dotsinterval/varying-side.svg | 18 tests/testthat/_snaps/test.geom_dotsinterval/weave-both.svg | 8 tests/testthat/_snaps/test.geom_dotsinterval/weave-bottom.svg | 10 tests/testthat/_snaps/test.geom_dotsinterval/weave-dot-order.svg | 124 tests/testthat/_snaps/test.geom_dotsinterval/weave-top.svg | 6 tests/testthat/_snaps/test.geom_slabinterval/slabinterval-with-nas-in-thickness.svg |only tests/testthat/_snaps/test.guide_rampbar |only tests/testthat/_snaps/test.scale_colour_ramp/fill-ramp-with-slab-and-nas.svg | 81 tests/testthat/_snaps/test.scale_thickness |only tests/testthat/_snaps/test.stat_dist_slabinterval/fill-type-gradient-with-two-groups-h.svg | 8 tests/testthat/_snaps/test.stat_dist_slabinterval/fill-type-gradient-with-two-groups.svg | 8 tests/testthat/_snaps/test.stat_dist_slabinterval/halfeye-multiple-dists-per-group.svg |only tests/testthat/_snaps/test.stat_sample_slabinterval/fill-type-gradient-with-two-groups-h.svg | 8 tests/testthat/_snaps/test.stat_sample_slabinterval/fill-type-gradient-with-two-groups.svg | 8 tests/testthat/test.distributions.R | 10 tests/testthat/test.geom_dotsinterval.R | 35 tests/testthat/test.geom_slabinterval.R | 20 tests/testthat/test.guide_rampbar.R |only tests/testthat/test.point_interval.R | 63 tests/testthat/test.scale_colour_ramp.R | 9 tests/testthat/test.scale_thickness.R |only tests/testthat/test.stat_dist_slabinterval.R | 100 tests/testthat/test.stat_sample_slabinterval.R | 28 vignettes/dotsinterval.Rmd | 33 vignettes/freq-uncertainty-vis.Rmd | 6 vignettes/lineribbon.Rmd | 85 vignettes/slabinterval.Rmd | 167 - 92 files changed, 4901 insertions(+), 1774 deletions(-)
Title: Reference Interval Estimation using Real-World Data
Description: Indirect method for the estimation of reference intervals using Real-World Data ('RWD'). It takes routine measurements
of diagnostic tests, containing pathological and non-pathological samples as input and uses sophisticated
statistical methods to derive a model describing the distribution of the non-pathological samples. This distribution can then be
used to derive reference intervals.
Furthermore, the package offers functions for printing and plotting the results of the algorithm. See ?refineR for a more comprehensive description of the features.
Version 1.0 of the algorithm is described in detail in Ammer T., Schuetzenmeister A., Prokosch H.-U., Rauh M., Rank C.M., Zierk J. "refineR: A Novel Algorithm for Reference Interval Estimation from Real-World Data". Scientific Reports (2021) <doi:10.1038/s41598-021-95301-2>.
Author: Tatjana Ammer [aut, cre],
Christopher M Rank [aut],
Andre Schuetzenmeister [aut]
Maintainer: Tatjana Ammer <tatjana.ammer@roche.com>
Diff between refineR versions 1.5.0 dated 2022-06-03 and 1.5.1 dated 2022-07-19
refineR-1.5.0/refineR/build/partial.rdb |only refineR-1.5.0/refineR/inst/ChangeLog.txt |only refineR-1.5.1/refineR/DESCRIPTION | 10 +++-- refineR-1.5.1/refineR/MD5 | 28 ++++++++------ refineR-1.5.1/refineR/NEWS.md | 14 +++++-- refineR-1.5.1/refineR/R/algoInvHist.R | 52 +++++++++++++-------------- refineR-1.5.1/refineR/R/plot.R | 6 +-- refineR-1.5.1/refineR/R/utils.R | 34 ++++++++++++++--- refineR-1.5.1/refineR/build/vignette.rds |only refineR-1.5.1/refineR/inst/doc |only refineR-1.5.1/refineR/man/getRI.Rd | 4 +- refineR-1.5.1/refineR/man/plot.RWDRI.Rd | 6 +-- refineR-1.5.1/refineR/man/print.RWDRI.Rd | 4 +- refineR-1.5.1/refineR/man/refineR-Package.Rd | 7 +-- refineR-1.5.1/refineR/vignettes |only 15 files changed, 100 insertions(+), 65 deletions(-)
Title: 'Coroutines' for R
Description: Provides 'coroutines' for R, a family of functions that can
be suspended and resumed later on. This includes 'async' functions
(which await) and generators (which yield). 'Async' functions are
based on the concurrency framework of the 'promises' package.
Generators are based on a dependency free iteration protocol defined
in 'coro' and are compatible with iterators from the 'reticulate'
package.
Author: Lionel Henry [aut, cre],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between coro versions 1.0.2 dated 2021-12-03 and 1.0.3 dated 2022-07-19
DESCRIPTION | 39 ++++++++++++++++++++------------------- MD5 | 19 ++++++++++--------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/aaa.R | 4 ---- R/coro-package.R |only R/iterator.R | 16 +++++++--------- inst/doc/generator.html | 5 +++-- man/coro-package.Rd | 4 ++-- man/iterator.Rd | 34 +++++++++++++++++++++++++--------- tests/testthat/test-iterator.R | 17 +++++++++++++++++ 11 files changed, 92 insertions(+), 54 deletions(-)
Title: Easy to Make (Lazy) Tables
Description: Constructs tables of counts and proportions out of data sets with possibility to insert tables to Excel, Word, HTML, and PDF documents. Transforms tables to data suitable for modelling. Features Gibbs sampling based log-linear (NB2) and power analyses (original by Oleksandr Ocheredko <doi:10.35566/isdsa2019c5>) for tabulated data.
Author: Ocheredko Oleksandr
Maintainer: Ocheredko Oleksandr <Ocheredko@yahoo.com>
Diff between ltable versions 2.0.1 dated 2021-11-22 and 2.0.2 dated 2022-07-19
ltable-2.0.1/ltable/R/PowerPoisson.R |only ltable-2.0.1/ltable/R/Print.R |only ltable-2.0.1/ltable/R/RcppExports.R |only ltable-2.0.1/ltable/cleanup |only ltable-2.0.1/ltable/configure |only ltable-2.0.1/ltable/configure.ac |only ltable-2.0.1/ltable/inst/INSTALL.Rd |only ltable-2.0.1/ltable/man/powerpoisson.Rd |only ltable-2.0.1/ltable/src |only ltable-2.0.2/ltable/DESCRIPTION | 21 ++++------- ltable-2.0.2/ltable/MD5 | 40 ++++++++------------- ltable-2.0.2/ltable/NAMESPACE | 10 ++--- ltable-2.0.2/ltable/R/MCLogLin.R |only ltable-2.0.2/ltable/R/MCPower.R |only ltable-2.0.2/ltable/R/PrintPower.R |only ltable-2.0.2/ltable/inst/Doc/ltable.pdf |binary ltable-2.0.2/ltable/inst/NEWS.Rd | 8 ++-- ltable-2.0.2/ltable/man/MCLogLin.Rd |only ltable-2.0.2/ltable/man/MCPower.Rd |only ltable-2.0.2/ltable/man/ltable-package.Rd | 10 +++-- ltable-2.0.2/ltable/man/plot,powerClass-method.Rd | 6 ++- ltable-2.0.2/ltable/man/powerClass-class.Rd | 8 ++-- ltable-2.0.2/ltable/man/print,powerClass-method.Rd | 11 +++-- ltable-2.0.2/ltable/man/tableToData.Rd | 15 ++++--- ltable-2.0.2/ltable/man/table_f.Rd | 2 - ltable-2.0.2/ltable/man/z[,powerClass-method.Rd | 28 +++++++------- ltable-2.0.2/ltable/man/z[_-,powerClass-method.Rd | 23 ------------ 27 files changed, 83 insertions(+), 99 deletions(-)
Title: 2d, 2.5d, and 3d Delaunay Tessellations
Description: Construction and visualization of 2d Delaunay triangulations,
possibly constrained, 2.5d (i.e. elevated) Delaunay triangulations,
and 3d Delaunay triangulations.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between delaunay versions 1.0.0 dated 2022-07-06 and 1.1.0 dated 2022-07-19
delaunay-1.0.0/delaunay/src/Makevars |only delaunay-1.1.0/delaunay/DESCRIPTION | 9 ++++----- delaunay-1.1.0/delaunay/MD5 | 10 ++++++---- delaunay-1.1.0/delaunay/NEWS.md | 5 +++++ delaunay-1.1.0/delaunay/README.md | 1 + delaunay-1.1.0/delaunay/cleanup |only delaunay-1.1.0/delaunay/configure |only delaunay-1.1.0/delaunay/src/Makevars.in |only 8 files changed, 16 insertions(+), 9 deletions(-)
Title: Rmetrics - Chronological and Calendar Objects
Description: The 'timeDate' class fulfils the conventions of the ISO 8601
standard as well as of the ANSI C and POSIX standards. Beyond
these standards it provides the "Financial Center" concept
which allows to handle data records collected in different time
zones and mix them up to have always the proper time stamps with
respect to your personal financial center, or alternatively to the GMT
reference time. It can thus also handle time stamps from historical
data records from the same time zone, even if the financial
centers changed day light saving times at different calendar
dates.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Joe W. Byers [ctb],
Georgi N. Boshnakov [cre, ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 3043.102 dated 2018-02-21 and 4021.104 dated 2022-07-19
ChangeLog | 12 +++++++ DESCRIPTION | 37 +++++++++++++++-------- MD5 | 36 ++++++++++++---------- NAMESPACE | 5 +-- NEWS.md |only R/calendar-firstDay.R | 35 +++++++++++++--------- R/calendar-onOrAfter.R | 58 ++++++++++++++++++------------------- R/holiday-Dates.R | 13 ++++++++ R/holiday-NYSE.R | 2 + R/holiday-TSX.R | 1 inst/_pkgdown.yml |only man/calendar-Easter.Rd | 3 + man/calendar-dayOfWeek.Rd | 13 -------- man/calendar-dayOfYear.Rd | 14 -------- man/calendar-endpoints.Rd | 4 +- man/holiday-Dates.Rd | 2 + man/holiday-Listing.Rd | 2 - man/options-RmetricsOptions.Rd | 2 - man/timeDate-DaylightSavingTime.Rd | 4 +- man/timeDate-whichFormat.Rd | 2 - 20 files changed, 137 insertions(+), 108 deletions(-)
Title: The Online Regularized K-Means Clustering Algorithm
Description: Algorithm of online regularized k-means to deal with online multi(single) view data.
The philosophy of the package is described in Guo G. (2020)
<doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] ,
Miao Yu [aut],
Haoyue Song [aut],
Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between ORKM versions 0.3.0.0 dated 2022-06-10 and 0.4.0.0 dated 2022-07-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ORKMeans.R | 3 +-- 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Clean the R Console and Environment
Description: Small package to clean the R console and the R environment
with the call of just one function.
Author: Jonathan M. Mang [aut, cre] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between cleaR versions 0.0.3 dated 2022-06-27 and 0.0.4 dated 2022-07-19
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- R/clear.R | 2 +- 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Description: Functions to preprocess spectroscopic data
and conduct (representative) sample selection/calibration sampling.
Author: Antoine Stevens [aut, cre] ,
Leonardo Ramirez-Lopez [aut, cre] ,
Guillaume Hans [ctb]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between prospectr versions 0.2.4 dated 2022-04-03 and 0.2.5 dated 2022-07-19
prospectr-0.2.4/prospectr/NEWS |only prospectr-0.2.5/prospectr/DESCRIPTION | 10 +-- prospectr-0.2.5/prospectr/MD5 | 32 +++++----- prospectr-0.2.5/prospectr/NEWS.md |only prospectr-0.2.5/prospectr/R/AAA.R | 2 prospectr-0.2.5/prospectr/R/baseline.R | 20 +++--- prospectr-0.2.5/prospectr/R/cochranTest.R | 2 prospectr-0.2.5/prospectr/R/e2m.R | 18 +++--- prospectr-0.2.5/prospectr/R/kenstone.R | 4 - prospectr-0.2.5/prospectr/R/msc.R | 8 +- prospectr-0.2.5/prospectr/R/spliceCorrection.R | 7 ++ prospectr-0.2.5/prospectr/README.md | 7 +- prospectr-0.2.5/prospectr/build/prospectr.pdf |binary prospectr-0.2.5/prospectr/build/vignette.rds |binary prospectr-0.2.5/prospectr/inst/doc/prospectr.html | 28 ++------- prospectr-0.2.5/prospectr/man/spliceCorrection.Rd | 2 prospectr-0.2.5/prospectr/tests/testthat/test-kenStone.R | 45 ++++++++++++--- prospectr-0.2.5/prospectr/tests/testthat/test-msc.R | 2 18 files changed, 105 insertions(+), 82 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data:
tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation;
forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping:
co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>);
extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful
for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>);
model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre]
,
Pascal Obstetar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 4.0.2 dated 2022-07-18 and 4.0.3 dated 2022-07-19
DESCRIPTION | 10 ++--- MD5 | 8 ++-- R/aba.R | 6 ++- R/tree_detection.R | 91 ++++++++++++++++++++++++++----------------------- man/tree_extraction.Rd | 13 +++++-- 5 files changed, 74 insertions(+), 54 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-25 0.1.6
2021-11-30 0.1.5
2021-10-15 0.1.4
2021-06-24 0.1.3
2021-05-04 0.1.2
2021-04-22 0.1.1
2020-12-16 0.1.0
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. hhh4() estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
twinSIR() models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by H<f6>hle (2009)
<doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Saban<e [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.20.0 dated 2022-02-16 and 1.20.1 dated 2022-07-19
DESCRIPTION | 8 +- MD5 | 80 ++++++++++---------- NEWS.md | 12 +++ R/LRCUSUM.runlength.R | 5 - R/boda.R | 75 ++++++++----------- R/earsC.R | 4 - R/ks.plot.unif.R | 49 +++--------- R/nowcast.R | 9 +- R/twinstim_siaf.R | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.Rnw | 4 - inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.Rnw | 8 +- inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.pdf |binary inst/doc/twinstim.pdf |binary man/LRCUSUM.runlength.Rd | 6 - man/boda.Rd | 12 +-- man/categoricalCUSUM.Rd | 2 man/checkResidualProcess.Rd | 2 man/ks.plot.unif.Rd | 13 +-- man/m1.Rd | 4 - man/measles.weser.Rd | 13 +-- man/nowcast.Rd | 2 man/pairedbinCUSUM.Rd | 2 man/permutationTest.Rd | 4 - man/stsBP-class.Rd | 6 - man/stsNC-class.Rd | 6 - man/stsplot_spacetime.Rd | 26 +++--- man/twinSIR.Rd | 6 - src/init.c | 8 +- src/ks.c | 81 ++++++++++++--------- tests/testthat/test-hhh4_NA.R | 4 + vignettes/hhh4_spacetime.Rnw | 4 - vignettes/monitoringCounts-cache/boda.RData |binary vignettes/monitoringCounts-cache/boda.covars.RData |binary vignettes/monitoringCounts.Rnw | 8 +- 41 files changed, 230 insertions(+), 239 deletions(-)
Title: Interface to the 'PredictIt' API
Description: Wrapper to retrieve market data, explore available markets, and plot historical price data from the 'PredictIt' public API (<https://www.predictit.org/api/marketdata/all/>).
The package comes with a demo 'shiny' application for illustrating example use cases.
License to use data made available via the API is for non-commercial use and 'PredictIt' is the sole source of such data.
Author: Daniel Kovtun [cre, aut]
Maintainer: Daniel Kovtun <quantumfusetrader@gmail.com>
Diff between rpredictit versions 0.0.2 dated 2020-03-18 and 0.1.0 dated 2022-07-19
DESCRIPTION | 13 MD5 | 22 NEWS.md | 5 R/market_data.R | 16 README.md | 9 build/vignette.rds |binary inst/doc/rpredictit-vignette.R | 4 inst/doc/rpredictit-vignette.Rmd | 9 inst/doc/rpredictit-vignette.html | 1981 ++++++++++++++++++++++++++++++++++++-- man/format_market_data.Rd | 2 man/markets_table.Rd | 2 vignettes/rpredictit-vignette.Rmd | 9 12 files changed, 1937 insertions(+), 135 deletions(-)
Title: 'RStudio' Addins to Prettify 'JavaScript', 'C++', 'Python', and
More
Description: Provides 'RStudio' addins to prettify 'HTML', 'CSS', 'SCSS',
'JavaScript', 'JSX', 'Markdown', 'C(++)', 'LaTeX', 'Python', 'Julia',
'XML', 'Java', 'JSON', 'Ruby', and to reindent 'C(++)', 'Fortran',
'Java', 'Julia', 'Python', 'SAS', 'Scala', 'Shell', 'SQL' and
"TypeScript". Two kinds of addins are provided: 'Prettify' and
'Indent'. The 'Indent' addins only reindent the code, while the
'Prettify' addins also modify the code, e.g. trailing semi-colons are
added to 'JavaScript' code when they are missing.
Author: Stephane Laurent [aut, cre],
James Long and contributors [cph] ,
Zeb Zhao [cph] ,
Marijn Haverbeke [cph] ,
George Leslie-Waksman and other contributors [cph] ,
Austin Cheney [cph] ,
John Schlinkert [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between prettifyAddins versions 2.4.0 dated 2022-01-25 and 2.5.0 dated 2022-07-19
DESCRIPTION | 73 ++++++++++------------- LICENSE.note | 27 ++++++++ MD5 | 18 +++-- NAMESPACE | 1 NEWS.md | 7 ++ R/addins.R | 4 - R/prettifyJULIA.R | 151 ++++++++++++++++++++++++------------------------ R/prettify_V8.R | 75 +++++++++++++++++++++++ inst/libraries |only inst/rstudio/addins.dcf | 5 + man/wordWrap.Rd |only 11 files changed, 237 insertions(+), 124 deletions(-)
More information about prettifyAddins at CRAN
Permanent link
Title: Jacobi Theta Functions and Related Functions
Description: Evaluation of the Jacobi theta functions and related
functions: Weierstrass elliptic function, Weierstrass sigma function,
Weierstrass zeta function, Klein j-function, Dedekind eta function,
lambda modular function, Jacobi elliptic functions, Neville theta
functions, and Eisenstein series. Complex values of the variable are
supported.
Author: Stephane Laurent [aut, cre],
Mikael Fremling [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between jacobi versions 1.0.0 dated 2022-06-22 and 2.0.0 dated 2022-07-19
jacobi-1.0.0/jacobi/R/jtheta1primeprimeprime0.R |only jacobi-1.0.0/jacobi/R/p-weierstrass.R |only jacobi-1.0.0/jacobi/R/sigmaw.R |only jacobi-1.0.0/jacobi/man/En.Rd |only jacobi-1.0.0/jacobi/man/sigmaw.Rd |only jacobi-1.0.0/jacobi/tests/testthat/test-pweierstrass.R |only jacobi-1.0.0/jacobi/tests/testthat/test-sigmaw.R |only jacobi-2.0.0/jacobi/DESCRIPTION | 17 jacobi-2.0.0/jacobi/MD5 | 81 - jacobi-2.0.0/jacobi/NAMESPACE | 13 jacobi-2.0.0/jacobi/NEWS.md | 13 jacobi-2.0.0/jacobi/R/CostaMesh.R |only jacobi-2.0.0/jacobi/R/RcppExports.R | 108 +- jacobi-2.0.0/jacobi/R/agm.R | 2 jacobi-2.0.0/jacobi/R/am.R |only jacobi-2.0.0/jacobi/R/eisenstein.R | 16 jacobi-2.0.0/jacobi/R/eta-dedekind.R | 2 jacobi-2.0.0/jacobi/R/internal.R | 40 jacobi-2.0.0/jacobi/R/jellip.R | 4 jacobi-2.0.0/jacobi/R/jtheta.R | 119 +- jacobi-2.0.0/jacobi/R/jtheta1derivatives.R |only jacobi-2.0.0/jacobi/R/klein-j.R | 67 - jacobi-2.0.0/jacobi/R/lambda.R | 44 jacobi-2.0.0/jacobi/R/theta-neville.R | 54 - jacobi-2.0.0/jacobi/R/weierstrassStuff.R |only jacobi-2.0.0/jacobi/R/wp.R |only jacobi-2.0.0/jacobi/R/wpinv.R |only jacobi-2.0.0/jacobi/R/wsigma.R |only jacobi-2.0.0/jacobi/R/wzeta.R |only jacobi-2.0.0/jacobi/README.md | 28 jacobi-2.0.0/jacobi/man/CostaMesh.Rd |only jacobi-2.0.0/jacobi/man/EisensteinE.Rd |only jacobi-2.0.0/jacobi/man/am.Rd |only jacobi-2.0.0/jacobi/man/jellip.Rd | 4 jacobi-2.0.0/jacobi/man/jtheta1.Rd | 6 jacobi-2.0.0/jacobi/man/jtheta2.Rd | 6 jacobi-2.0.0/jacobi/man/jtheta3.Rd | 6 jacobi-2.0.0/jacobi/man/jtheta4.Rd | 6 jacobi-2.0.0/jacobi/man/kleinj.Rd | 27 jacobi-2.0.0/jacobi/man/lambda.Rd | 16 jacobi-2.0.0/jacobi/man/neville.Rd | 4 jacobi-2.0.0/jacobi/man/wp.Rd | 21 jacobi-2.0.0/jacobi/man/wpinv.Rd |only jacobi-2.0.0/jacobi/man/wsigma.Rd |only jacobi-2.0.0/jacobi/man/wzeta.Rd |only jacobi-2.0.0/jacobi/src/RcppExports.cpp | 336 ++++++ jacobi-2.0.0/jacobi/src/altjtheta.cpp |only jacobi-2.0.0/jacobi/src/jacobi.cpp | 850 ++++++++++++++++- jacobi-2.0.0/jacobi/src/jacobi_types.h | 14 jacobi-2.0.0/jacobi/tests/testthat/test-am.R |only jacobi-2.0.0/jacobi/tests/testthat/test-kleinj.R | 31 jacobi-2.0.0/jacobi/tests/testthat/test-wp.R |only jacobi-2.0.0/jacobi/tests/testthat/test-wpinv.R |only jacobi-2.0.0/jacobi/tests/testthat/test-wsigma.R |only jacobi-2.0.0/jacobi/tests/testthat/test-wzeta.R |only 55 files changed, 1697 insertions(+), 238 deletions(-)
Title: Tools for Stable Isotope Geochemistry
Description: This toolbox makes working with oxygen,
carbon, and clumped isotope data reproducible and straightforward.
Use it to quickly calculate isotope fractionation factors,
and apply paleothermometry equations.
Author: David Bajnai [aut, cre] ,
Julian Toedter [ctb]
Maintainer: David Bajnai <david.bajnai@uni-goettingen.de>
Diff between isogeochem versions 1.0.9 dated 2021-11-07 and 1.1.0 dated 2022-07-19
isogeochem-1.0.9/isogeochem/tests/testthat/Rplots.pdf |only isogeochem-1.1.0/isogeochem/DESCRIPTION | 14 isogeochem-1.1.0/isogeochem/MD5 | 55 +-- isogeochem-1.1.0/isogeochem/NAMESPACE | 1 isogeochem-1.1.0/isogeochem/NEWS.md | 89 ++--- isogeochem-1.1.0/isogeochem/R/a18.R | 23 + isogeochem-1.1.0/isogeochem/R/a18_c_H2O.R | 46 +- isogeochem-1.1.0/isogeochem/R/clumped.R | 2 isogeochem-1.1.0/isogeochem/R/d17O.R | 86 +++- isogeochem-1.1.0/isogeochem/R/data.R | 32 + isogeochem-1.1.0/isogeochem/R/quartz.R |only isogeochem-1.1.0/isogeochem/R/utils.R | 4 isogeochem-1.1.0/isogeochem/README.md | 90 +++-- isogeochem-1.1.0/isogeochem/build/partial.rdb |binary isogeochem-1.1.0/isogeochem/build/vignette.rds |binary isogeochem-1.1.0/isogeochem/data/meteoric_water.rda |only isogeochem-1.1.0/isogeochem/inst/WORDLIST | 264 ++++++++------- isogeochem-1.1.0/isogeochem/inst/doc/devils_hole.html | 238 ++++++++++++- isogeochem-1.1.0/isogeochem/inst/doc/kim_oneil_1997.html | 224 ++++++++++++ isogeochem-1.1.0/isogeochem/man/D47.Rd | 2 isogeochem-1.1.0/isogeochem/man/GTS2020.Rd | 3 isogeochem-1.1.0/isogeochem/man/LR04.Rd | 3 isogeochem-1.1.0/isogeochem/man/a18_CO2acid_c.Rd | 16 isogeochem-1.1.0/isogeochem/man/a18_c_H2O.Rd | 21 - isogeochem-1.1.0/isogeochem/man/d17O_c.Rd | 31 + isogeochem-1.1.0/isogeochem/man/d17O_qz.Rd |only isogeochem-1.1.0/isogeochem/man/devilshole.Rd | 3 isogeochem-1.1.0/isogeochem/man/meteoric_water.Rd |only isogeochem-1.1.0/isogeochem/man/mix_d17O.Rd | 27 + isogeochem-1.1.0/isogeochem/tests/testthat/test_a18.R | 22 - isogeochem-1.1.0/isogeochem/tests/testthat/test_d17O.R | 25 + 31 files changed, 993 insertions(+), 328 deletions(-)
Title: Simulation of Fossil and Taxonomy Data
Description: Simulating taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.3.0 dated 2022-04-19 and 2.3.1 dated 2022-07-19
DESCRIPTION | 8 MD5 | 50 - NEWS.md | 89 +- R/plot.fossils.R | 2 R/plot.taxonomy.R | 2 R/sim.fbd.R | 382 ++++----- R/sim.fossils.R | 30 R/sim.taxonomy.R | 48 - build/vignette.rds |binary inst/doc/SAtree.R | 42 - inst/doc/SAtree.html | 754 ++++++++++++------- inst/doc/fossils.R | 582 +++++++------- inst/doc/fossils.html | 1609 +++++++++++++++++++++++++---------------- inst/doc/intro.R | 62 - inst/doc/intro.html | 726 ++++++++++++------ inst/doc/paleotree.R | 44 - inst/doc/paleotree.html | 869 +++++++++++----------- inst/doc/simfbd.R | 48 - inst/doc/simfbd.html | 735 ++++++++++++------ inst/doc/taxonomy.R | 112 +- inst/doc/taxonomy.html | 978 ++++++++++++++++-------- man/sim.fbd.age.Rd | 17 man/sim.fbd.rateshift.taxa.Rd | 4 man/sim.fbd.taxa.Rd | 10 man/sim.fossils.environment.Rd | 7 man/sim.trait.values.Rd | 4 26 files changed, 4275 insertions(+), 2939 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.4.3 dated 2022-07-18 and 1.4.4 dated 2022-07-19
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NAMESPACE | 6 ++++++ NEWS.md | 2 +- R/aaa.R | 11 +++++++++++ inst/app/radiant.R | 2 +- inst/app/tools/data/manage_ui.R | 2 +- man/reexports.Rd | 7 +++++++ 8 files changed, 41 insertions(+), 16 deletions(-)
Title: Ternary Plots for Trinomial Regression Models
Description: An implementation of the ternary plot for interpreting regression
coefficients of trinomial regression models, as proposed in Santi, Dickson
and Espa (2019) <doi:10.1080/00031305.2018.1442368>. Ternary plots can be
drawn using either 'ggtern' package (based on 'ggplot2') or 'Ternary'
package (based on standard graphics). The package and its features are
illustrated in Santi, Dickson, Espa and Giuliani (2022)
<doi:10.18637/jss.v103.c01>.
Author: Flavio Santi [cre, aut] ,
Maria Michela Dickson [aut] ,
Giuseppe Espa [aut] ,
Diego Giuliani [aut]
Maintainer: Flavio Santi <flavio.santi@univr.it>
Diff between plot3logit versions 3.1.2 dated 2022-04-15 and 3.1.3 dated 2022-07-19
DESCRIPTION | 12 MD5 | 42 +-- NEWS.md | 11 R/conf_region.R | 3 R/data.R | 9 R/field3logit.R | 5 R/ggtern.R | 3 R/plot3logit-package.R | 3 README.md | 46 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 +-- inst/REFERENCES.bib | 11 inst/doc/plot3logit-overview.Rmd | 2 inst/doc/plot3logit-overview.html | 474 ++++++++++++++++++++++++++++++++------ man/USvote2016.Rd | 8 man/add_confregions.Rd | 3 man/autoplot.Hfield3logit.Rd | 10 man/field3logit.Rd | 5 man/gg3logit.Rd | 3 man/plot3logit-package.Rd | 3 vignettes/plot3logit-overview.Rmd | 2 22 files changed, 547 insertions(+), 146 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.5.3 dated 2022-05-27 and 0.5.4 dated 2022-07-19
DESCRIPTION | 6 MD5 | 28 +- NEWS.md | 4 R/downloading_tools.R | 552 ++++++++++++++++++++--------------------- R/get_oaproc.R | 2 R/index_nhdplus.R | 43 ++- build/vignette.rds |binary inst/doc/US_data.html | 487 ++++++++++++++++++++++++++++-------- inst/doc/advanced_network.html | 447 +++++++++++++++++++++++++++++---- inst/doc/indexing.html | 364 ++++++++++++++++++++++++--- inst/doc/nhdplusTools.html | 239 ++++++++++++++++- inst/doc/nhdplushr.html | 325 +++++++++++++++++++++--- inst/doc/plot_nhdplus.html | 304 ++++++++++++++++++++-- man/get_elev_along_path.Rd | 2 tests/testthat/test_index.R | 12 15 files changed, 2255 insertions(+), 560 deletions(-)
Title: Fast Covariance Estimation for Multivariate Sparse Functional
Data
Description: Multivariate functional principal component analysis via fast covariance estimation for
multivariate sparse functional data or longitudinal data proposed by Li, Xiao, and Luo (2020) <doi: 10.1002/sta4.245>.
Author: Cai Li [aut,cre] and Luo Xiao [aut]
Maintainer: Cai Li <cai.li.stats@gmail.com>
Diff between mfaces versions 0.1-3 dated 2021-04-30 and 0.1-4 dated 2022-07-19
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/face.sparse.inner.R | 6 ++++-- R/mface.sparse.R | 20 ++++++++++++++++---- R/predict.face.sparse.inner.R | 4 ++-- R/predict.mface.sparse.R | 6 +++--- build/partial.rdb |binary man/mface.sparse.Rd | 11 ++++++++--- man/mfaces-package.Rd | 6 +++--- man/predict.mface.sparse.Rd | 2 +- 10 files changed, 52 insertions(+), 33 deletions(-)
Title: Differential Expression Enrichment Tool
Description: RNA sequencing (RNA-seq) followed by differential gene expression analyses is a fundamental approach for making biological discoveries. Ongoing large-scale efforts to systematically process and normalize publicly available gene expression data facilitate rapid reanalyses of specific studies and the development of new methods for querying it. While there are several powerful tools for querying systematically processed publicly available RNA-seq data at the individual sample level, there are fewer options for querying differentially expressed gene (DEG) lists generated from these experiments. Here, we present the Differential Expression Enrichment Tool (DEET), which allows users to interact with 3162 consistently processed DEG lists curated from 142 RNA-seq datasets obtained from recount2 database, which contains data from consortiums (GTex, TCGA) and individual labs (SRA). To establish DEET we integrated systematically processed human RNA-seq data from recount2 with reported and predicted metadata from multiple sources and developed a CRAN R package and Shiny App where users can compare their genes, p-values, and coefficients against the DEG lists within DEET. Here we present DEET and demonstrate how it can facilitate hypothesis generation and provide biological insight from user-defined differential gene expression results. Reference: Sokolowski,D.J., Ahn J., Erdman,L., Hou,H., Ellis,K., Wang L., Goldenberg,A., and Wilson,M.D. (2022) Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. (In Preparation).
Author: Dustin Sokolowski [aut, cre],
Jedid Ahn [aut],
Lauren Erdman [aut],
Kai Ellis [aut],
Huayun Hou [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between DEET versions 1.0.2 dated 2022-06-27 and 1.0.5 dated 2022-07-19
DESCRIPTION | 13 +- MD5 | 34 ++--- NAMESPACE | 88 +++++++------- R/DEET_data_download.R | 6 R/DEET_enrich.R | 43 ++++++- data/DEET_example_data.rda |binary data/example_DEET_enrich_input.rda |binary inst/doc/DEET_vignette.html | 4 man/DEET_data_download.Rd | 142 +++++++++++------------ man/DEET_enrich.Rd | 120 +++++++++---------- man/DEET_enrichment_plot.Rd | 152 ++++++++++++------------- man/DEET_example_data.Rd | 66 +++++----- man/DEET_feature_extract.Rd | 108 ++++++++--------- man/DEET_feature_extract_example_matrix.Rd | 42 +++--- man/DEET_feature_extract_example_response.Rd | 42 +++--- man/DEET_plot_correlation.Rd | 72 +++++------ man/example_DEET_enrich_input.Rd | 44 +++---- man/proccess_and_plot_DEET_enrich.Rd | 164 +++++++++++++-------------- 18 files changed, 590 insertions(+), 550 deletions(-)
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.9.12 dated 2022-03-07 and 0.10.0 dated 2022-07-19
DESCRIPTION | 10 - MD5 | 92 ++++----- NAMESPACE | 2 NEWS | 8 R/bootstrap.R | 66 ++---- R/cfd.R | 196 +++++++++---------- R/cfda-package.R | 33 ++- R/dataPlot.R | 43 ++-- R/datasets.R | 63 +++++- R/encoding.R | 27 +- R/estimation.R | 2 R/fmca.print.R | 11 - R/plotEncoding.R | 11 - R/predict.R | 3 R/pretreatment.R | 197 +++++++++++++++++-- R/stat.R | 21 +- build/vignette.rds |binary data/flours.rda |only inst/doc/cfda.html | 370 ++++++++++++++++++++++++++++++++----- man/biofam2.Rd | 22 +- man/boxplot.timeSpent.Rd | 16 + man/care.Rd | 6 man/cfda-package.Rd | 33 ++- man/compute_duration.Rd | 13 + man/compute_number_jumps.Rd | 13 + man/compute_optimal_encoding.Rd | 28 ++ man/compute_time_spent.Rd | 13 + man/convertToCfd.Rd |only man/cut_data.Rd | 30 ++- man/estimate_pt.Rd | 13 + man/flours.Rd |only man/get_encoding.Rd | 11 + man/get_state.Rd | 1 man/hist.duration.Rd | 16 + man/hist.njump.Rd | 16 + man/matrixToCfd.Rd |only man/plot.fmca.Rd | 10 - man/plot.pt.Rd | 16 + man/plotComponent.Rd | 11 + man/plotData.Rd | 20 +- man/plotEigenvalues.Rd | 11 + man/predict.fmca.Rd | 10 - man/print.fmca.Rd | 16 + man/remove_duplicated_states.Rd | 15 + man/statetable.Rd | 14 + man/summary.fmca.Rd | 16 + man/summary_cfd.Rd | 17 + tests/testthat/test.pretreatment.R | 250 +++++++++++++++++++++++-- tests/testthat/test.stat.R | 32 +++ 49 files changed, 1435 insertions(+), 389 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <brandonedwards3@cmail.carleton.ca>
Diff between bbsBayes versions 2.5.0 dated 2022-07-11 and 2.5.1 dated 2022-07-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/fetch-bbs-data.R | 3 +-- README.md | 4 ++-- 4 files changed, 10 insertions(+), 11 deletions(-)
Title: TV Show Themes and Color Palettes for 'ggplot2' Graphics
Description: Contains various 'ggplot2' themes and color palettes based on TV shows
such as 'Game of Thrones', 'Brooklyn Nine-Nine', 'Avatar: The Last Airbender',
'Spongebob Squarepants', and more.
Author: Ryo Nakagawara [aut, cre]
Maintainer: Ryo Nakagawara <ryonakagawara@gmail.com>
Diff between tvthemes versions 1.3.0 dated 2022-03-16 and 1.3.1 dated 2022-07-19
tvthemes-1.3.0/tvthemes/inst/fonts/ChelseaMarket |only tvthemes-1.3.0/tvthemes/inst/fonts/Cinzel |only tvthemes-1.3.0/tvthemes/inst/fonts/GravitationFalls/readme.txt |only tvthemes-1.3.0/tvthemes/inst/fonts/Roboto-Condensed |only tvthemes-1.3.0/tvthemes/inst/fonts/Titillium-Web |only tvthemes-1.3.0/tvthemes/man/import_chelseaMarket.Rd |only tvthemes-1.3.0/tvthemes/man/import_cinzel.Rd |only tvthemes-1.3.0/tvthemes/man/import_robotoCondensed.Rd |only tvthemes-1.3.0/tvthemes/man/import_roboto_condensed.Rd |only tvthemes-1.3.0/tvthemes/man/import_titilliumWeb.Rd |only tvthemes-1.3.0/tvthemes/man/import_titillium_web.Rd |only tvthemes-1.3.0/tvthemes/tests/spelling.R |only tvthemes-1.3.1/tvthemes/DESCRIPTION | 13 tvthemes-1.3.1/tvthemes/MD5 | 166 - tvthemes-1.3.1/tvthemes/NAMESPACE | 6 tvthemes-1.3.1/tvthemes/NEWS.md | 7 tvthemes-1.3.1/tvthemes/R/import_fonts.r | 139 - tvthemes-1.3.1/tvthemes/R/palette_hilda.R | 2 tvthemes-1.3.1/tvthemes/README.md | 6 tvthemes-1.3.1/tvthemes/inst/doc/examples.html | 997 +++++----- tvthemes-1.3.1/tvthemes/inst/doc/fonts-and-colors.R | 4 tvthemes-1.3.1/tvthemes/inst/doc/fonts-and-colors.Rmd | 6 tvthemes-1.3.1/tvthemes/inst/doc/fonts-and-colors.html | 119 - tvthemes-1.3.1/tvthemes/inst/doc/tvthemes-1_0_0.html | 132 - tvthemes-1.3.1/tvthemes/man/attackOnTitan_pal.Rd | 220 +- tvthemes-1.3.1/tvthemes/man/avatarTLA_pal.Rd | 226 +- tvthemes-1.3.1/tvthemes/man/avatar_pal.Rd | 264 +- tvthemes-1.3.1/tvthemes/man/bigHero6_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/brooklyn99_pal.Rd | 280 +- tvthemes-1.3.1/tvthemes/man/figures/README-b99header-1.png |binary tvthemes-1.3.1/tvthemes/man/figures/airnomads_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/attackontitan.png |binary tvthemes-1.3.1/tvthemes/man/figures/b99regpal_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/bighero6.png |binary tvthemes-1.3.1/tvthemes/man/figures/bobspog.bg.png |binary tvthemes-1.3.1/tvthemes/man/figures/crystalgems.png |binary tvthemes-1.3.1/tvthemes/man/figures/earthkingdom_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/firenation_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/gravityfalls.png |binary tvthemes-1.3.1/tvthemes/man/figures/hilda.png |binary tvthemes-1.3.1/tvthemes/man/figures/kimpossible.png |binary tvthemes-1.3.1/tvthemes/man/figures/lastairbender.png |binary tvthemes-1.3.1/tvthemes/man/figures/parksandrec_both.png |binary tvthemes-1.3.1/tvthemes/man/figures/rickmorty_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/simpsons_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/sponge_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/stevenuniverse.png |binary tvthemes-1.3.1/tvthemes/man/figures/watertribe_plot.png |binary tvthemes-1.3.1/tvthemes/man/gravityFalls_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/hilda_pal.Rd | 237 +- tvthemes-1.3.1/tvthemes/man/import_avatar.Rd | 32 tvthemes-1.3.1/tvthemes/man/import_gravitationFalls.Rd | 38 tvthemes-1.3.1/tvthemes/man/import_rickAndMorty.Rd | 34 tvthemes-1.3.1/tvthemes/man/import_simpsons.Rd | 38 tvthemes-1.3.1/tvthemes/man/import_spongeBob.Rd | 30 tvthemes-1.3.1/tvthemes/man/import_theLastAirbender.Rd | 32 tvthemes-1.3.1/tvthemes/man/kimPossible_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/paintBikiniBottom.Rd | 74 tvthemes-1.3.1/tvthemes/man/parksAndRec_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/rickAndMorty_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/simpsons_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/spongeBob_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/sponge_images.Rd | 30 tvthemes-1.3.1/tvthemes/man/stevenUniverse_pal.Rd | 264 +- tvthemes-1.3.1/tvthemes/man/theme_avatar.Rd | 164 - tvthemes-1.3.1/tvthemes/man/theme_brooklyn99.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_hildaDay.Rd | 160 - tvthemes-1.3.1/tvthemes/man/theme_hildaDusk.Rd | 160 - tvthemes-1.3.1/tvthemes/man/theme_hildaNight.Rd | 160 - tvthemes-1.3.1/tvthemes/man/theme_parksAndRec.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_parksAndRecLight.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_parksAndRec_light.Rd | 156 - tvthemes-1.3.1/tvthemes/man/theme_rickAndMorty.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_simpsons.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_spongeBob.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_theLastAirbender.Rd | 146 - tvthemes-1.3.1/tvthemes/man/tvthemes.Rd | 80 tvthemes-1.3.1/tvthemes/man/westeros_pal.Rd | 276 +- tvthemes-1.3.1/tvthemes/tests/testthat/test-fonts.R | 12 tvthemes-1.3.1/tvthemes/vignettes/fonts-and-colors.Rmd | 6 80 files changed, 3594 insertions(+), 3668 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-21 0.7
2021-05-18 0.6
2018-11-29 0.5.2
2018-04-16 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-10 1.2.3
2021-12-10 1.2.2
2021-10-11 1.2.1