Title: Model Distillation and Interpretability Methods for Machine
Learning Models
Description: Provides several methods for model distillation and interpretability
for general black box machine learning models and treatment effect estimation
methods. For details on the algorithms implemented, see <https://forestry-labs.github.io/distillML/index.html>
Brian Cho, Theo F. Saarinen, Jasjeet S. Sekhon, Simon Walter.
Author: Brian Cho [aut],
Theo Saarinen [aut, cre],
Jasjeet Sekhon [aut],
Simon Walter [aut]
Maintainer: Theo Saarinen <theo_s@berkeley.edu>
Diff between distillML versions 0.1.0.9 dated 2022-07-07 and 0.1.0.13 dated 2023-03-24
DESCRIPTION | 12 +- MD5 | 30 +++--- R/interpret.R | 21 +--- R/plotter.R | 10 +- R/predictor.R | 15 +-- R/surrogate.R | 15 +-- man/Interpreter.Rd | 25 ++--- man/Predictor.Rd | 27 ++--- man/Surrogate.Rd | 27 ++--- tests/testthat/test-ale_plots.R | 17 +-- tests/testthat/test-distill_feats.R | 49 ++++------ tests/testthat/test-interpreter.R | 31 ++---- tests/testthat/test-localSurrogate.R | 27 ++--- tests/testthat/test-plotter.R | 158 ++++++++++++++++++++--------------- tests/testthat/test-predictor.R | 33 +------ tests/testthat/test-surrogate.R | 22 +--- 16 files changed, 236 insertions(+), 283 deletions(-)
Title: Random Forests, Linear Trees, and Gradient Boosting for
Inference and Interpretability
Description: Provides fast implementations of Honest Random Forests,
Gradient Boosting, and Linear Random Forests, with an emphasis on inference
and interpretability. Additionally contains methods for variable
importance, out-of-bag prediction, regression monotonicity, and
several methods for missing data imputation. Soren R. Kunzel,
Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon (2019) <arXiv:1906.06463>.
Author: Soeren Kuenzel [aut],
Theo Saarinen [aut, cre],
Simon Walter [aut],
Sam Antonyan [aut],
Edward Liu [aut],
Allen Tang [aut],
Jasjeet Sekhon [aut]
Maintainer: Theo Saarinen <theo_s@berkeley.edu>
Diff between Rforestry versions 0.9.0.152 dated 2022-12-21 and 0.10.0 dated 2023-03-24
Rforestry-0.10.0/Rforestry/DESCRIPTION | 15 Rforestry-0.10.0/Rforestry/MD5 | 83 Rforestry-0.10.0/Rforestry/NAMESPACE | 13 Rforestry-0.10.0/Rforestry/R/RcppExports.R | 16 Rforestry-0.10.0/Rforestry/R/backwards_compatible.R | 9 Rforestry-0.10.0/Rforestry/R/compute_rf_lp.R | 11 Rforestry-0.10.0/Rforestry/R/forestry.R | 940 ++------- Rforestry-0.10.0/Rforestry/R/plottree.R | 2 Rforestry-0.10.0/Rforestry/man/forestry.Rd | 32 Rforestry-0.10.0/Rforestry/man/getVI-forestry.Rd | 17 Rforestry-0.10.0/Rforestry/man/plot-forestry.Rd | 3 Rforestry-0.10.0/Rforestry/man/training_data_checker-forestry.Rd | 39 Rforestry-0.10.0/Rforestry/src/Makevars | 2 Rforestry-0.10.0/Rforestry/src/Makevars.win | 2 Rforestry-0.10.0/Rforestry/src/RFNode.cpp | 275 +- Rforestry-0.10.0/Rforestry/src/RFNode.h | 27 Rforestry-0.10.0/Rforestry/src/RcppExports.cpp | 50 Rforestry-0.10.0/Rforestry/src/dataFrame.cpp |only Rforestry-0.10.0/Rforestry/src/dataFrame.h |only Rforestry-0.10.0/Rforestry/src/forestry.cpp | 239 -- Rforestry-0.10.0/Rforestry/src/forestry.h | 32 Rforestry-0.10.0/Rforestry/src/forestryTree.cpp | 737 ++----- Rforestry-0.10.0/Rforestry/src/forestryTree.h | 59 Rforestry-0.10.0/Rforestry/src/rcpp_cppBuildInterface.cpp | 187 - Rforestry-0.10.0/Rforestry/src/sampling.h | 2 Rforestry-0.10.0/Rforestry/src/treeSplitting.cpp | 951 ---------- Rforestry-0.10.0/Rforestry/src/treeSplitting.h | 178 - Rforestry-0.10.0/Rforestry/src/utils.cpp | 78 Rforestry-0.10.0/Rforestry/src/utils.h | 53 Rforestry-0.10.0/Rforestry/tests/testthat/test-advancedCustomSampling.R |only Rforestry-0.10.0/Rforestry/tests/testthat/test-alternateVI.R |only Rforestry-0.10.0/Rforestry/tests/testthat/test-backward_compatibility.R | 25 Rforestry-0.10.0/Rforestry/tests/testthat/test-customSample.R |only Rforestry-0.10.0/Rforestry/tests/testthat/test-forestry_VariableImportance.R | 10 Rforestry-0.10.0/Rforestry/tests/testthat/test-terminalNodes.R | 4 Rforestry-0.9.0.152/Rforestry/R/adaptive_forestry.R |only Rforestry-0.9.0.152/Rforestry/README.md |only Rforestry-0.9.0.152/Rforestry/man/adaptiveForestry-forestry.Rd |only Rforestry-0.9.0.152/Rforestry/man/autoforestry-forestry.Rd |only Rforestry-0.9.0.152/Rforestry/man/autohonestRF.Rd |only Rforestry-0.9.0.152/Rforestry/man/correctedPredict-forestry.Rd |only Rforestry-0.9.0.152/Rforestry/man/getCI-forestry.Rd |only Rforestry-0.9.0.152/Rforestry/man/getSplitProps-forestry.Rd |only Rforestry-0.9.0.152/Rforestry/man/predict-adaptiveForestry.Rd |only Rforestry-0.9.0.152/Rforestry/src/DataFrame.cpp |only Rforestry-0.9.0.152/Rforestry/src/DataFrame.h |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-adaptiveRF.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-autoforestry.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-bootstrapPredictionIntervals.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-conformalIntervals.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-correctedPredict.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-localConformal.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-splitProps.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-symmetry.R |only Rforestry-0.9.0.152/Rforestry/tests/testthat/test-symmetry_multiple.R |only 55 files changed, 943 insertions(+), 3148 deletions(-)
Title: Summarises Package & Function Usage
Description: Consistent with 'knitr' syntax highlighting, 'usedthese' adds a
summary table of R package & function usage to a Quarto document and
enables aggregation of usage across a Quarto website. Learn more about
'usedthese' at <https://cgoo4.github.io/usedthese/>.
Author: Carl Goodwin [aut, cre]
Maintainer: Carl Goodwin <carl.goodwin@quantumjitter.com>
Diff between usedthese versions 0.3.1 dated 2023-02-24 and 0.3.2 dated 2023-03-24
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/used_there.R | 8 ++++++-- inst/doc/multipage.html | 28 ++++++++++++++-------------- tests/testthat/test-used_there.R | 7 +++++++ 6 files changed, 44 insertions(+), 28 deletions(-)
Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using
a headless browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre],
Gabor Csardi [aut],
Hadley Wickham [aut],
RStudio [cph, fnd],
Mango Solutions [cph, ccp]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinytest versions 1.5.2 dated 2023-03-22 and 1.5.3 dated 2023-03-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/on-load.R | 12 +++++++++++- 4 files changed, 21 insertions(+), 7 deletions(-)
Title: Growth Charts via Smooth Regression Quantiles with Automatic
Smoothness Estimation and Additive Terms
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms, including varying coefficients, via B-splines with L1-norm difference penalties.
The smoothing parameters are estimated as part of the model fitting, see Muggeo and others (2021) <doi:10.1177/1471082X20929802>. Monotonicity and concavity
constraints on the fitted curves are allowed, see Muggeo and others (2013) <doi:10.1007/s10651-012-0232-1> and also <doi:10.13140/RG.2.2.12924.85122> for some code examples.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between quantregGrowth versions 1.4-0 dated 2021-11-10 and 1.5-0 dated 2023-03-24
DESCRIPTION | 8 MD5 | 36 +-- NEWS | 10 R/AIC.gcrq.R | 28 +- R/gcrq.r | 21 + R/logLik.gcrq.R | 8 R/ncross.rq.fitXB.r | 2 R/plot.gcrq.R | 14 - R/predict.gcrq.R | 13 - build/vignette.rds |binary inst/CITATION | 44 +-- inst/doc/quantregGrowth.Rmd | 2 inst/doc/quantregGrowth.html | 477 ++++++++++++++++++++++++++++++++++-------- man/gcrq.Rd | 17 + man/logLik.gcrq.Rd | 12 - man/plot.gcrq.Rd | 9 man/ps.Rd | 8 man/quantregGrowth-package.Rd | 4 vignettes/quantregGrowth.Rmd | 2 19 files changed, 542 insertions(+), 173 deletions(-)
More information about quantregGrowth at CRAN
Permanent link
Title: Principal Tensor Analysis on k Modes
Description: A multiway method to decompose a tensor (array) of any order, as a generalisation of SVD also supporting non-identity metrics and penalisations. 2-way SVD with these extensions is also available. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these extensions.
Author: Didier G. Leibovici <doi:10.18637/jss.v034.i10>
Maintainer: Didier G. Leibovici <GeotRYcs@gmail.com>
Diff between PTAk versions 1.4-0 dated 2021-10-06 and 2.0.0 dated 2023-03-24
PTAk-1.4-0/PTAk/demo |only PTAk-2.0.0/PTAk/DESCRIPTION | 8 ++-- PTAk-2.0.0/PTAk/MD5 | 32 +++++++---------- PTAk-2.0.0/PTAk/R/PTAk.R | 57 ++++++++++++++++---------------- PTAk-2.0.0/PTAk/build/partial.rdb |binary PTAk-2.0.0/PTAk/data/Zone_climTUN.RData |binary PTAk-2.0.0/PTAk/data/crimerate.RData |binary PTAk-2.0.0/PTAk/data/timage12.RData |binary PTAk-2.0.0/PTAk/inst/CITATION | 21 ++++++----- PTAk-2.0.0/PTAk/inst/doc/PTAklogo.jpg |only PTAk-2.0.0/PTAk/inst/doc/PTAklogo.pdf |only PTAk-2.0.0/PTAk/inst/doc/index.html | 10 ++--- PTAk-2.0.0/PTAk/man/APSOLU3.Rd | 2 - PTAk-2.0.0/PTAk/man/CauRuimet.Rd | 2 - PTAk-2.0.0/PTAk/man/SVDgen.Rd | 8 ++-- PTAk-2.0.0/PTAk/man/plot.PTAk.Rd | 2 - 16 files changed, 70 insertions(+), 72 deletions(-)
Title: Track your Data Pipelines
Description: Track and
document 'dplyr' data pipelines. As you filter, mutate, and join your
way through a data set, 'dtrackr' seamlessly keeps track of your data
flow and makes publication ready documentation of a data pipeline simple.
Author: Robert Challen [aut, cre]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>
Diff between dtrackr versions 0.2.4 dated 2022-07-05 and 0.4.0 dated 2023-03-24
dtrackr-0.2.4/dtrackr/R/data.R |only dtrackr-0.2.4/dtrackr/data |only dtrackr-0.2.4/dtrackr/man/ILPD.Rd |only dtrackr-0.2.4/dtrackr/man/add_count.Rd |only dtrackr-0.2.4/dtrackr/man/landscape.Rd |only dtrackr-0.2.4/dtrackr/vignettes/joss/figure1-ilpd-consort.pdf |only dtrackr-0.2.4/dtrackr/vignettes/joss/paper.bib |only dtrackr-0.4.0/dtrackr/DESCRIPTION | 22 dtrackr-0.4.0/dtrackr/MD5 | 296 - dtrackr-0.4.0/dtrackr/NAMESPACE | 47 dtrackr-0.4.0/dtrackr/NEWS.md | 118 dtrackr-0.4.0/dtrackr/R/dot.R | 175 dtrackr-0.4.0/dtrackr/R/dtrackr.R | 1732 ++++++--- dtrackr-0.4.0/dtrackr/R/experimental |only dtrackr-0.4.0/dtrackr/README.md | 131 dtrackr-0.4.0/dtrackr/build/vignette.rds |binary dtrackr-0.4.0/dtrackr/inst/CITATION |only dtrackr-0.4.0/dtrackr/inst/doc/consort-example.R | 123 dtrackr-0.4.0/dtrackr/inst/doc/consort-example.Rmd | 161 dtrackr-0.4.0/dtrackr/inst/doc/consort-example.html | 920 ++-- dtrackr-0.4.0/dtrackr/inst/doc/dtrackr-options.R | 33 dtrackr-0.4.0/dtrackr/inst/doc/dtrackr-options.Rmd | 83 dtrackr-0.4.0/dtrackr/inst/doc/dtrackr-options.html | 1294 +++--- dtrackr-0.4.0/dtrackr/inst/doc/dtrackr.R | 12 dtrackr-0.4.0/dtrackr/inst/doc/dtrackr.Rmd | 165 dtrackr-0.4.0/dtrackr/inst/doc/dtrackr.html | 1920 ++++------ dtrackr-0.4.0/dtrackr/inst/doc/joining-pipelines.R | 15 dtrackr-0.4.0/dtrackr/inst/doc/joining-pipelines.Rmd | 35 dtrackr-0.4.0/dtrackr/inst/doc/joining-pipelines.html | 251 - dtrackr-0.4.0/dtrackr/inst/examples |only dtrackr-0.4.0/dtrackr/inst/lib/viz_licence.md |only dtrackr-0.4.0/dtrackr/man/add_count.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/add_tally.Rd | 102 dtrackr-0.4.0/dtrackr/man/anti_join.trackr_df.Rd | 76 dtrackr-0.4.0/dtrackr/man/arrange.trackr_df.Rd | 81 dtrackr-0.4.0/dtrackr/man/bind_cols.Rd |only dtrackr-0.4.0/dtrackr/man/bind_rows.Rd | 97 dtrackr-0.4.0/dtrackr/man/capture_exclusions.Rd | 15 dtrackr-0.4.0/dtrackr/man/comment.Rd | 43 dtrackr-0.4.0/dtrackr/man/count_subgroup.Rd | 75 dtrackr-0.4.0/dtrackr/man/distinct.trackr_df.Rd | 46 dtrackr-0.4.0/dtrackr/man/dot2svg.Rd | 8 dtrackr-0.4.0/dtrackr/man/exclude_all.Rd | 107 dtrackr-0.4.0/dtrackr/man/excluded.Rd | 9 dtrackr-0.4.0/dtrackr/man/figures |only dtrackr-0.4.0/dtrackr/man/filter.trackr_df.Rd | 71 dtrackr-0.4.0/dtrackr/man/flowchart.Rd | 78 dtrackr-0.4.0/dtrackr/man/full_join.trackr_df.Rd | 83 dtrackr-0.4.0/dtrackr/man/group_by.trackr_df.Rd | 76 dtrackr-0.4.0/dtrackr/man/group_modify.trackr_df.Rd | 47 dtrackr-0.4.0/dtrackr/man/history.Rd | 11 dtrackr-0.4.0/dtrackr/man/include_any.Rd | 104 dtrackr-0.4.0/dtrackr/man/inner_join.trackr_df.Rd | 78 dtrackr-0.4.0/dtrackr/man/intersect.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/left_join.trackr_df.Rd | 83 dtrackr-0.4.0/dtrackr/man/mutate.trackr_df.Rd | 70 dtrackr-0.4.0/dtrackr/man/nest_join.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/p_add_count.Rd | 104 dtrackr-0.4.0/dtrackr/man/p_add_tally.Rd | 101 dtrackr-0.4.0/dtrackr/man/p_anti_join.Rd | 102 dtrackr-0.4.0/dtrackr/man/p_arrange.Rd | 81 dtrackr-0.4.0/dtrackr/man/p_bind_cols.Rd |only dtrackr-0.4.0/dtrackr/man/p_bind_rows.Rd | 97 dtrackr-0.4.0/dtrackr/man/p_capture_exclusions.Rd | 15 dtrackr-0.4.0/dtrackr/man/p_clear.Rd | 7 dtrackr-0.4.0/dtrackr/man/p_comment.Rd | 43 dtrackr-0.4.0/dtrackr/man/p_copy.Rd | 13 dtrackr-0.4.0/dtrackr/man/p_count_if.Rd | 9 dtrackr-0.4.0/dtrackr/man/p_count_subgroup.Rd | 75 dtrackr-0.4.0/dtrackr/man/p_distinct.Rd | 49 dtrackr-0.4.0/dtrackr/man/p_exclude_all.Rd | 107 dtrackr-0.4.0/dtrackr/man/p_excluded.Rd | 9 dtrackr-0.4.0/dtrackr/man/p_filter.Rd | 73 dtrackr-0.4.0/dtrackr/man/p_flowchart.Rd | 78 dtrackr-0.4.0/dtrackr/man/p_full_join.Rd | 117 dtrackr-0.4.0/dtrackr/man/p_get.Rd | 11 dtrackr-0.4.0/dtrackr/man/p_get_as_dot.Rd | 24 dtrackr-0.4.0/dtrackr/man/p_group_by.Rd | 66 dtrackr-0.4.0/dtrackr/man/p_group_modify.Rd | 58 dtrackr-0.4.0/dtrackr/man/p_include_any.Rd | 104 dtrackr-0.4.0/dtrackr/man/p_inner_join.Rd | 112 dtrackr-0.4.0/dtrackr/man/p_intersect.Rd |only dtrackr-0.4.0/dtrackr/man/p_left_join.Rd | 117 dtrackr-0.4.0/dtrackr/man/p_mutate.Rd | 74 dtrackr-0.4.0/dtrackr/man/p_nest_join.Rd |only dtrackr-0.4.0/dtrackr/man/p_pause.Rd | 18 dtrackr-0.4.0/dtrackr/man/p_pivot_longer.Rd | 128 dtrackr-0.4.0/dtrackr/man/p_pivot_wider.Rd | 125 dtrackr-0.4.0/dtrackr/man/p_relocate.Rd | 85 dtrackr-0.4.0/dtrackr/man/p_rename.Rd | 74 dtrackr-0.4.0/dtrackr/man/p_rename_with.Rd | 77 dtrackr-0.4.0/dtrackr/man/p_resume.Rd | 30 dtrackr-0.4.0/dtrackr/man/p_right_join.Rd | 117 dtrackr-0.4.0/dtrackr/man/p_select.Rd | 74 dtrackr-0.4.0/dtrackr/man/p_semi_join.Rd | 100 dtrackr-0.4.0/dtrackr/man/p_set.Rd | 9 dtrackr-0.4.0/dtrackr/man/p_setdiff.Rd |only dtrackr-0.4.0/dtrackr/man/p_slice.Rd |only dtrackr-0.4.0/dtrackr/man/p_slice_head.Rd |only dtrackr-0.4.0/dtrackr/man/p_slice_max.Rd |only dtrackr-0.4.0/dtrackr/man/p_slice_min.Rd |only dtrackr-0.4.0/dtrackr/man/p_slice_sample.Rd |only dtrackr-0.4.0/dtrackr/man/p_slice_tail.Rd |only dtrackr-0.4.0/dtrackr/man/p_status.Rd | 59 dtrackr-0.4.0/dtrackr/man/p_summarise.Rd | 89 dtrackr-0.4.0/dtrackr/man/p_tagged.Rd | 1 dtrackr-0.4.0/dtrackr/man/p_track.Rd | 30 dtrackr-0.4.0/dtrackr/man/p_transmute.Rd | 77 dtrackr-0.4.0/dtrackr/man/p_ungroup.Rd | 41 dtrackr-0.4.0/dtrackr/man/p_union.Rd |only dtrackr-0.4.0/dtrackr/man/p_union_all.Rd |only dtrackr-0.4.0/dtrackr/man/p_untrack.Rd | 5 dtrackr-0.4.0/dtrackr/man/pause.Rd | 18 dtrackr-0.4.0/dtrackr/man/pivot_longer.trackr_df.Rd | 158 dtrackr-0.4.0/dtrackr/man/pivot_wider.trackr_df.Rd | 97 dtrackr-0.4.0/dtrackr/man/plot.trackr_graph.Rd | 13 dtrackr-0.4.0/dtrackr/man/print.trackr_graph.Rd | 1 dtrackr-0.4.0/dtrackr/man/relocate.trackr_df.Rd | 91 dtrackr-0.4.0/dtrackr/man/rename.trackr_df.Rd | 70 dtrackr-0.4.0/dtrackr/man/rename_with.trackr_df.Rd | 70 dtrackr-0.4.0/dtrackr/man/resume.Rd | 30 dtrackr-0.4.0/dtrackr/man/right_join.trackr_df.Rd | 83 dtrackr-0.4.0/dtrackr/man/save_dot.Rd | 59 dtrackr-0.4.0/dtrackr/man/select.trackr_df.Rd | 70 dtrackr-0.4.0/dtrackr/man/semi_join.trackr_df.Rd | 74 dtrackr-0.4.0/dtrackr/man/setdiff.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/slice.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/slice_head.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/slice_max.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/slice_min.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/slice_sample.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/slice_tail.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/status.Rd | 59 dtrackr-0.4.0/dtrackr/man/std_size.Rd | 17 dtrackr-0.4.0/dtrackr/man/summarise.trackr_df.Rd | 69 dtrackr-0.4.0/dtrackr/man/tagged.Rd | 1 dtrackr-0.4.0/dtrackr/man/track.Rd | 30 dtrackr-0.4.0/dtrackr/man/transmute.trackr_df.Rd | 73 dtrackr-0.4.0/dtrackr/man/ungroup.trackr_df.Rd | 42 dtrackr-0.4.0/dtrackr/man/union.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/union_all.trackr_df.Rd |only dtrackr-0.4.0/dtrackr/man/untrack.Rd | 5 dtrackr-0.4.0/dtrackr/tests/testthat.R | 2 dtrackr-0.4.0/dtrackr/tests/testthat/test-examples.R |only dtrackr-0.4.0/dtrackr/tests/testthat/test-github-issues.R |only dtrackr-0.4.0/dtrackr/tests/testthat/test-group_by.R | 5 dtrackr-0.4.0/dtrackr/tests/testthat/test-p_comment.R | 2 dtrackr-0.4.0/dtrackr/tests/testthat/test-p_exclude.R | 1 dtrackr-0.4.0/dtrackr/tests/testthat/test-p_group_modify.R | 2 dtrackr-0.4.0/dtrackr/tests/testthat/test-p_include.R | 2 dtrackr-0.4.0/dtrackr/tests/testthat/test-p_others.R | 2 dtrackr-0.4.0/dtrackr/tests/testthat/test-p_status.R | 15 dtrackr-0.4.0/dtrackr/tests/testthat/test-rsvg-scaling.R |only dtrackr-0.4.0/dtrackr/vignettes/consort-example.Rmd | 161 dtrackr-0.4.0/dtrackr/vignettes/dtrackr-options.Rmd | 83 dtrackr-0.4.0/dtrackr/vignettes/dtrackr.Rmd | 165 dtrackr-0.4.0/dtrackr/vignettes/dtrackr.bib | 114 dtrackr-0.4.0/dtrackr/vignettes/joining-pipelines.Rmd | 35 dtrackr-0.4.0/dtrackr/vignettes/joss/figure1-consort.pdf |only dtrackr-0.4.0/dtrackr/vignettes/joss/paper.md | 126 160 files changed, 7995 insertions(+), 5528 deletions(-)
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are two alternative ways to use this package. The first is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' runs in parallelizes with the 'future' framework. The other alternative is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 0.12.2 dated 2022-04-26 and 1.0.0 dated 2023-03-24
doFuture-0.12.2/doFuture/NEWS |only doFuture-0.12.2/doFuture/inst/doc/doFuture.html |only doFuture-0.12.2/doFuture/inst/doc/doFuture.md.rsp |only doFuture-0.12.2/doFuture/tests/cluster-missing-doFuture-pkg.R |only doFuture-0.12.2/doFuture/tests/doRNG,dopar.R |only doFuture-0.12.2/doFuture/tests/doRNG,dorng.R |only doFuture-0.12.2/doFuture/tests/foreach,errors.R |only doFuture-0.12.2/doFuture/tests/foreach,globals.R |only doFuture-0.12.2/doFuture/tests/foreach,nested_colon.R |only doFuture-0.12.2/doFuture/tests/foreach,nested_dopar.R |only doFuture-0.12.2/doFuture/tests/foreach.R |only doFuture-0.12.2/doFuture/tests/options.R |only doFuture-0.12.2/doFuture/vignettes/doFuture.md.rsp |only doFuture-1.0.0/doFuture/DESCRIPTION | 18 doFuture-1.0.0/doFuture/MD5 | 74 +- doFuture-1.0.0/doFuture/NAMESPACE | 3 doFuture-1.0.0/doFuture/NEWS.md |only doFuture-1.0.0/doFuture/R/000.import.R | 4 doFuture-1.0.0/doFuture/R/doFuture-package.R | 196 ++----- doFuture-1.0.0/doFuture/R/doFuture.R | 31 - doFuture-1.0.0/doFuture/R/dofuture_OP.R |only doFuture-1.0.0/doFuture/R/registerDoFuture.R | 156 +++++- doFuture-1.0.0/doFuture/R/withDoRNG.R |only doFuture-1.0.0/doFuture/build/vignette.rds |binary doFuture-1.0.0/doFuture/inst/CITATION | 8 doFuture-1.0.0/doFuture/inst/WORDLIST | 14 doFuture-1.0.0/doFuture/inst/doc/doFuture-1-overview.html |only doFuture-1.0.0/doFuture/inst/doc/doFuture-1-overview.md.rsp |only doFuture-1.0.0/doFuture/inst/doc/doFuture-2-dopar.html |only doFuture-1.0.0/doFuture/inst/doc/doFuture-2-dopar.md.rsp |only doFuture-1.0.0/doFuture/inst/doc/doFuture-3-dofuture.html |only doFuture-1.0.0/doFuture/inst/doc/doFuture-3-dofuture.md.rsp |only doFuture-1.0.0/doFuture/man/doFuture.Rd | 250 ++-------- doFuture-1.0.0/doFuture/man/grapes-dofuture-grapes.Rd |only doFuture-1.0.0/doFuture/man/registerDoFuture.Rd | 222 ++++++++ doFuture-1.0.0/doFuture/man/withDoRNG.Rd |only doFuture-1.0.0/doFuture/tests/foreach_dofuture,cluster-missing-doFuture-pkg.R |only doFuture-1.0.0/doFuture/tests/foreach_dofuture,errors.R |only doFuture-1.0.0/doFuture/tests/foreach_dofuture,globals.R |only doFuture-1.0.0/doFuture/tests/foreach_dofuture,nested_colon.R |only doFuture-1.0.0/doFuture/tests/foreach_dofuture,nested_dofuture.R |only doFuture-1.0.0/doFuture/tests/foreach_dofuture,rng.R |only doFuture-1.0.0/doFuture/tests/foreach_dofuture.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,cluster-missing-doFuture-pkg.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,doRNG,dopar.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,doRNG,dorng.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,errors.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,globals.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,nested_colon.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,nested_dopar.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar,options-for-export.R |only doFuture-1.0.0/doFuture/tests/foreach_dopar.R |only doFuture-1.0.0/doFuture/tests/incl/end.R | 2 doFuture-1.0.0/doFuture/tests/incl/start,load-only.R | 4 doFuture-1.0.0/doFuture/tests/registerDoFuture.R | 1 doFuture-1.0.0/doFuture/tests/times.R | 1 doFuture-1.0.0/doFuture/tests/withDoRNG.R |only doFuture-1.0.0/doFuture/vignettes/doFuture-1-overview.md.rsp |only doFuture-1.0.0/doFuture/vignettes/doFuture-2-dopar.md.rsp |only doFuture-1.0.0/doFuture/vignettes/doFuture-3-dofuture.md.rsp |only 60 files changed, 582 insertions(+), 402 deletions(-)
Title: Infer Geographic Origin from Isotopic Data
Description: Routines for re-scaling isotope maps using known-origin tissue isotope data, assigning origin of unknown samples, and summarizing and assessing assignment results. Methods are adapted from Wunder (2010, in ISBN:9789048133536) and Vander Zanden, H. B. et al. (2014) <doi:10.1111/2041-210X.12229> as described in Ma, C. et al. (2020) <doi:10.1111/2041-210X.13426>.
Author: Chao Ma, Gabe Bowen
Maintainer: Gabe Bowen <gabe.bowen@utah.edu>
Diff between assignR versions 2.2.1 dated 2022-07-11 and 2.2.2 dated 2023-03-24
assignR-2.2.1/assignR/tests/testthat/temp |only assignR-2.2.2/assignR/DESCRIPTION | 6 assignR-2.2.2/assignR/MD5 | 20 - assignR-2.2.2/assignR/NEWS.md | 3 assignR-2.2.2/assignR/R/getIsoscapes.R | 31 +- assignR-2.2.2/assignR/build/partial.rdb |binary assignR-2.2.2/assignR/build/vignette.rds |binary assignR-2.2.2/assignR/inst/CITATION | 10 assignR-2.2.2/assignR/inst/doc/assignR.html | 166 +++++++-------- assignR-2.2.2/assignR/tests/testthat/test_getIsoscapes.R | 4 assignR-2.2.2/assignR/tests/testthat/test_processing.R | 5 11 files changed, 130 insertions(+), 115 deletions(-)
Title: 'NetCDF' Geometry and Time Series
Description: Tools to create time series and geometry 'NetCDF' files.
Author: David Blodgett [aut, cre],
Luke Winslow [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between ncdfgeom versions 1.1.4 dated 2022-11-08 and 1.1.5 dated 2023-03-24
DESCRIPTION | 11 +++++------ MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/0_ncdfgeom.R | 2 +- README.md | 11 +++++++---- build/vignette.rds |binary inst/CITATION | 32 ++++++++++++++++---------------- inst/doc/geometry.html | 7 ++++--- inst/doc/ncdfgeom.R | 2 +- inst/doc/ncdfgeom.Rmd | 6 +++--- inst/doc/ncdfgeom.html | 42 ++++++++++++++++++++---------------------- vignettes/ncdfgeom.Rmd | 6 +++--- 12 files changed, 75 insertions(+), 70 deletions(-)
Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest'
algorithm used to impute mixed-type data sets by chaining random
forests, introduced by Stekhoven, D.J. and Buehlmann, P. (2012)
<doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the
lightning fast random jungle package 'ranger'. Between the iterative
model fitting, we offer the option of using predictive mean matching.
This firstly avoids imputation with values not already present in the
original data (like a value 0.3334 in 0-1 coded variable). Secondly,
predictive mean matching tries to raise the variance in the resulting
conditional distributions to a realistic level. This would allow e.g.
to do multiple imputation when repeating the call to missRanger(). A
formula interface allows to control which variables should be imputed
by which.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between missRanger versions 2.1.3 dated 2021-03-30 and 2.2.0 dated 2023-03-24
missRanger-2.1.3/missRanger/inst/doc/censored_variables.R |only missRanger-2.1.3/missRanger/inst/doc/censored_variables.Rmd |only missRanger-2.1.3/missRanger/inst/doc/censored_variables.html |only missRanger-2.1.3/missRanger/vignettes/censored_variables.Rmd |only missRanger-2.2.0/missRanger/DESCRIPTION | 21 missRanger-2.2.0/missRanger/MD5 | 65 missRanger-2.2.0/missRanger/NAMESPACE | 30 missRanger-2.2.0/missRanger/NEWS.md | 31 missRanger-2.2.0/missRanger/R/generateNA.R | 4 missRanger-2.2.0/missRanger/R/imputeUnivariate.R | 6 missRanger-2.2.0/missRanger/R/missRanger.R | 186 +- missRanger-2.2.0/missRanger/R/pmm.R | 15 missRanger-2.2.0/missRanger/README.md | 60 missRanger-2.2.0/missRanger/build/vignette.rds |binary missRanger-2.2.0/missRanger/inst/doc/missRanger.R | 66 missRanger-2.2.0/missRanger/inst/doc/missRanger.Rmd | 124 - missRanger-2.2.0/missRanger/inst/doc/missRanger.html | 908 ++++++---- missRanger-2.2.0/missRanger/inst/doc/multiple_imputation.R | 21 missRanger-2.2.0/missRanger/inst/doc/multiple_imputation.Rmd | 36 missRanger-2.2.0/missRanger/inst/doc/multiple_imputation.html | 462 +++-- missRanger-2.2.0/missRanger/inst/doc/working_with_censoring.R |only missRanger-2.2.0/missRanger/inst/doc/working_with_censoring.Rmd |only missRanger-2.2.0/missRanger/inst/doc/working_with_censoring.html |only missRanger-2.2.0/missRanger/man/convert.Rd | 44 missRanger-2.2.0/missRanger/man/figures |only missRanger-2.2.0/missRanger/man/generateNA.Rd | 64 missRanger-2.2.0/missRanger/man/imputeUnivariate.Rd | 60 missRanger-2.2.0/missRanger/man/missRanger.Rd | 209 +- missRanger-2.2.0/missRanger/man/pmm.Rd | 71 missRanger-2.2.0/missRanger/man/revert.Rd | 44 missRanger-2.2.0/missRanger/man/typeof2.Rd | 42 missRanger-2.2.0/missRanger/tests/testthat/test-generateNA.R | 17 missRanger-2.2.0/missRanger/tests/testthat/test-imputeUnivariate.R | 12 missRanger-2.2.0/missRanger/tests/testthat/test-missRanger.R | 143 + missRanger-2.2.0/missRanger/tests/testthat/test-pmm.R | 49 missRanger-2.2.0/missRanger/vignettes/missRanger.Rmd | 124 - missRanger-2.2.0/missRanger/vignettes/multiple_imputation.Rmd | 36 missRanger-2.2.0/missRanger/vignettes/working_with_censoring.Rmd |only 38 files changed, 1768 insertions(+), 1182 deletions(-)
Title: R Interface to RNG with Multiple Streams
Description: Provides an interface to the C implementation of the
random number generator with multiple independent streams
developed by L'Ecuyer et al (2002). The main purpose of this
package is to enable the use of this random number generator in
parallel R applications.
Author: Hana Sevcikova [aut, cre],
Tony Rossini [aut],
Pierre L'Ecuyer [cph]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between rlecuyer versions 0.3-5 dated 2019-11-21 and 0.3-7 dated 2023-03-24
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 4 ++-- R/rlecuyer.R | 3 +-- man/CreateStream.Rd | 12 ++++++++++-- man/CurrentStream.Rd | 6 +++--- man/SetPackageSeed.Rd | 33 +++++++++++++++++++++++++++++---- man/WriteState.Rd | 1 + man/init.Rd |only man/internal.Rd | 31 +++++++------------------------ man/rlecuyer-package.Rd |only src/RngWrap.c | 8 ++++---- src/zzz.c | 6 +++--- 14 files changed, 81 insertions(+), 59 deletions(-)
Title: Agent Based Model Simulation Framework
Description: A high-performance, flexible and extensible framework to
develop continuous-time agent based models. Its high performance
allows it to simulate millions of agents efficiently. Agents are
defined by their states (arbitrary R lists). The events are handled in
chronological order. This avoids the multi-event interaction problem
in a time step of discrete-time simulations, and gives precise
outcomes. The states are modified by provided or user-defined events.
The framework provides a flexible and customizable implementation of
state transitions (either spontaneous or caused by agent
interactions), making the framework suitable to apply to epidemiology
and ecology, e.g., to model life history stages, competition and
cooperation, and disease and information spread. The agent
interactions are flexible and extensible. The framework provides
random mixing and network interactions, and supports multi-level
mixing patterns. It can be easily extended to other interactions such
as inter- and intra [...truncated...]
Author: Junling Ma [aut, cre]
Maintainer: Junling Ma <junlingm@uvic.ca>
Diff between ABM versions 0.2 dated 2023-03-10 and 0.3 dated 2023-03-24
DESCRIPTION | 6 +- MD5 | 71 +++++++++++++++++--------------- NAMESPACE | 4 + NEWS.md |only R/ABM.R | 6 +- R/Agent.R | 79 ++++++++++++++++++++++++++++++++--- R/Contact.R | 2 R/Event.R | 4 - R/Population.R | 78 +++++++++++++++++++++++++++++------ R/RcppExports.R | 12 ++++- R/Simulation.R | 2 README.md | 11 ++++ inst/include/Agent.h | 58 ++++++++++++-------------- inst/include/Contact.h | 29 +++++++++++++ inst/include/Event.h | 74 +++++++++++++++++++++++++++++++-- inst/include/Network.h | 7 +++ inst/include/Population.h | 36 ++++++++++++++-- man/ABM.Rd | 4 + man/Agent.Rd | 49 ++++++++++++++++++++-- man/Contact.Rd | 2 man/Event.Rd | 2 man/Population.Rd | 32 +++++++++++++- man/Simulation.Rd | 5 +- man/addAgent.Rd |only man/getAgent.Rd |only man/getID.Rd | 8 +-- man/leave.Rd |only man/newAgent.Rd | 6 ++ man/newEvent.Rd | 2 man/setDeathTime.Rd |only man/setState.Rd | 2 man/setStates.Rd | 2 src/Agent.cpp | 102 ++++++++++++++++++---------------------------- src/Contact.cpp | 30 +++++++++++-- src/Event.cpp | 69 +++++++++++++++++++++++++++++++ src/Network.cpp | 49 +++++++++++++++++++--- src/Population.cpp | 39 +++++++++++++++-- src/RcppExports.cpp | 34 +++++++++++++-- src/Transition.cpp | 8 ++- 39 files changed, 724 insertions(+), 200 deletions(-)
Title: Import Data from Our World in Data
Description: Search and download the data used in over 3,000 Our World in Data charts.
Author: Piers York
Maintainer: Piers York <piersyork@gmail.com>
Diff between owidR versions 1.4.0 dated 2022-09-25 and 1.4.1 dated 2023-03-24
DESCRIPTION | 8 - MD5 | 10 - NEWS.md | 3 R/owid.R | 6 - build/vignette.rds |binary inst/doc/example-analysis.html | 236 +++++++++++++++++++++-------------------- 6 files changed, 140 insertions(+), 123 deletions(-)
Title: Leader Clustering Algorithm
Description: The leader clustering algorithm provides
a means for clustering a set of data points. Unlike many other clustering
algorithms it does not require the user to specify the number of clusters,
but instead requires the approximate radius of a cluster as its primary
tuning parameter. The package provides a fast implementation of this
algorithm in n-dimensions using Lp-distances (with special cases for p=1,2,
and infinity) as well as for spatial data using the Haversine
formula, which takes latitude/longitude pairs as inputs and clusters
based on great circle distances.
Author: Taylor B. Arnold
Maintainer: Taylor B. Arnold <tarnold2@richmond.edu>
Diff between leaderCluster versions 1.3 dated 2022-08-17 and 1.5 dated 2023-03-24
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- R/leaderCluster.R | 2 +- src/init.c | 2 +- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12>, Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between tclust versions 1.5-2 dated 2022-10-24 and 1.5-4 dated 2023-03-24
tclust-1.5-2/tclust/build |only tclust-1.5-4/tclust/ChangeLog | 12 tclust-1.5-4/tclust/DESCRIPTION | 10 tclust-1.5-4/tclust/MD5 | 23 - tclust-1.5-4/tclust/R/tclust.R | 5 tclust-1.5-4/tclust/README.md |only tclust-1.5-4/tclust/inst/CITATION | 33 - tclust-1.5-4/tclust/inst/work |only tclust-1.5-4/tclust/src/R_package.cpp | 4 tclust-1.5-4/tclust/src/clust.cpp | 579 +--------------------------------- tclust-1.5-4/tclust/src/clust.h | 114 ------ tclust-1.5-4/tclust/src/tclust.cpp | 15 tclust-1.5-4/tclust/src/tkmeans.cpp | 5 13 files changed, 90 insertions(+), 710 deletions(-)
Title: Variable Selection Oriented LASSO Bagging Algorithm
Description: A wrapped LASSO approach by integrating an ensemble learning strategy to help select efficient, stable, and high confidential variables from omics-based data. Using a bagging strategy in combination of a parametric method or inflection point search method for cut-off threshold determination. This package can integrate and vote variables generated from multiple LASSO models to determine the optimal candidates. Luo H, Zhao Q, et al (2020) <doi:10.1126/scitranslmed.aax7533> for more details.
Author: Jiaqi Liang [aut],
Chaoye Wang [aut, cre]
Maintainer: Chaoye Wang <wangcy1@sysucc.org.cn>
Diff between VSOLassoBag versions 0.99.0 dated 2022-11-25 and 0.99.1 dated 2023-03-24
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/lassoBagAddGPD.R | 93 +++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/VSOLassoBag.Rmd | 5 -- inst/doc/VSOLassoBag.html | 110 ++++++++++++++++++++++------------------------ man/VSOLassoBag.Rd | 5 +- vignettes/VSOLassoBag.Rmd | 5 -- 8 files changed, 126 insertions(+), 114 deletions(-)
Title: An Interface to the GUDHI Library for Topological Data Analysis
Description: Provides an interface to the GUDHI library which is a generic open
source C++ library, with a Python interface, for topological data analysis
(TDA) and higher dimensional geometry understanding. The library offers
state-of-the-art data structures and algorithms to construct simplicial
complexes and compute persistent homology.
Author: Aymeric Stamm [aut, cre] ,
GUDHI Editorial Board [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between rgudhi versions 0.1.0 dated 2023-01-19 and 0.2.0 dated 2023-03-24
rgudhi-0.1.0/rgudhi/man/plot.Rd |only rgudhi-0.2.0/rgudhi/DESCRIPTION | 12 - rgudhi-0.2.0/rgudhi/MD5 | 28 +- rgudhi-0.2.0/rgudhi/NAMESPACE | 3 rgudhi-0.2.0/rgudhi/NEWS.md | 13 + rgudhi-0.2.0/rgudhi/R/persistence-diagram.R | 97 +++++----- rgudhi-0.2.0/rgudhi/R/persistence_diagram_sample.R |only rgudhi-0.2.0/rgudhi/R/sklearn-cluster.R | 6 rgudhi-0.2.0/rgudhi/build/partial.rdb |binary rgudhi-0.2.0/rgudhi/man/Birch.Rd | 2 rgudhi-0.2.0/rgudhi/man/BisectingKMeans.Rd | 2 rgudhi-0.2.0/rgudhi/man/OPTICS.Rd | 2 rgudhi-0.2.0/rgudhi/man/autoplot.persistence_diagram.Rd |only rgudhi-0.2.0/rgudhi/man/mean.persistence_diagram_sample.Rd |only rgudhi-0.2.0/rgudhi/man/persistence_diagram_sample.Rd |only rgudhi-0.2.0/rgudhi/man/plot.persistence_diagram.Rd |only rgudhi-0.2.0/rgudhi/tests/testthat/_snaps/representation-vector-methods.md | 24 +- rgudhi-0.2.0/rgudhi/tests/testthat/_snaps/simplex-tree.md | 4 18 files changed, 115 insertions(+), 78 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Shawn Garbett [cre, ctb] ,
Benjamin Nutter [ctb, aut],
Stephen Lane [ctb],
Will Beasley [ctb],
Jeffrey Horner [aut],
Will Gray [ctb],
Jeremy Stephens [ctb],
Marcus Lehr [ctb]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.4.0 dated 2023-03-01 and 2.5.0 dated 2023-03-24
DESCRIPTION | 12 MD5 | 181 ++++++++------ NAMESPACE | 38 +- NEWS | 34 ++ R/allocationTable.R | 54 ++-- R/apiCall.R | 2 R/checkbox_suffixes.R | 37 +- R/constants.R |only R/deleteArms.R | 16 - R/deleteFiles.R | 28 -- R/deleteRecords.R | 45 +-- R/deprecated_recapProjectInfo.R | 65 ++--- R/exportArms.R | 95 ++++--- R/exportBundle.R | 24 - R/exportEvents.R | 32 +- R/exportFieldNames.R | 133 +++++----- R/exportFiles.R | 40 +-- R/exportInstruments.R | 21 - R/exportLogging.R |only R/exportMappings.R | 32 +- R/exportMetaData.R | 91 ++++--- R/exportNextRecordName.R | 18 - R/exportPDF.R | 37 +- R/exportProjectInformation.R | 21 - R/exportRecords.R | 72 ++--- R/exportRecords_offline.R | 26 +- R/exportReports.R | 56 ++-- R/exportSurveyParticipants.R | 19 - R/exportUsers.R | 238 ++++++++++++------ R/exportVersion.R | 15 - R/fieldChoiceMapping.R |only R/fieldToVar.R | 321 +++++++++++++++---------- R/genericApiCall.R | 14 - R/importArms.R | 21 - R/importFiles.R | 41 +-- R/importRecords.R | 73 +++-- R/makeApiCall.R |only R/missingSummary.R |only R/parseBranchingLogic.R | 3 R/redcapAPI-pkg.R | 2 R/redcapConnection.R | 191 ++++++++++++-- R/validateImport_methods.R | 162 +++++++++--- R/vectorToApiBodyList.R |only R/zzz.R | 5 README.md | 10 inst/extdata/data.csv | 26 +- inst/extdata/metadata.csv | 15 + inst/extdata/missingSummarTesting |only man/allocationTable.Rd | 21 - man/apiCall.Rd | 2 man/checkbox_suffixes.Rd | 4 man/constants.Rd |only man/deleteArms.Rd | 3 man/deleteFiles.Rd | 5 man/deleteRecords.Rd | 9 man/deprecated_redcapProjectInfo.Rd | 15 - man/exportArms.Rd | 37 +- man/exportBundle.Rd | 15 - man/exportEvents.Rd | 8 man/exportFieldNames.Rd | 28 +- man/exportFiles.Rd | 14 - man/exportInstruments.Rd | 5 man/exportLogging.Rd |only man/exportMappings.Rd | 13 - man/exportMetaData.Rd | 25 + man/exportNextRecordName.Rd | 5 man/exportPdf.Rd | 12 man/exportProjectInformation.Rd | 5 man/exportRecords.Rd | 29 -- man/exportReports.Rd | 17 - man/exportSurveyParticipants.Rd | 3 man/exportUsers.Rd | 27 +- man/exportVersion.Rd | 5 man/fieldChoiceMapping.Rd |only man/fieldToVar.Rd | 8 man/genericApiCall.Rd | 10 man/importArms.Rd | 3 man/importFiles.Rd | 13 - man/importRecords.Rd | 36 +- man/makeApiCall.Rd |only man/missingSummary.Rd |only man/redcapAPI.Rd | 2 man/redcapConnection.Rd | 48 ++- man/vectorToApiBodyList.Rd |only tests/testthat/helper-REDCapQACredentials.R | 11 tests/testthat/test-checkbox_suffixes.R |only tests/testthat/test-deleteRecords.R |only tests/testthat/test-exportArms.R | 63 ++++ tests/testthat/test-exportEvents.R |only tests/testthat/test-exportFieldNames.R |only tests/testthat/test-exportInstruments.R |only tests/testthat/test-exportLogging.R |only tests/testthat/test-exportMappings.R |only tests/testthat/test-exportMetaData.R |only tests/testthat/test-exportNextRecordName.R |only tests/testthat/test-exportProjectInformation.R |only tests/testthat/test-exportRecords.R | 231 +++++++++++++++++ tests/testthat/test-exportReports.R |only tests/testthat/test-exportUsers.R |only tests/testthat/test-exportVersion.R |only tests/testthat/test-fieldChoiceMapping.R |only tests/testthat/test-fieldToVar-mChoice.R |only tests/testthat/test-missingSummary.R |only tests/testthat/test-parseBranchingLogic.R |only tests/testthat/test-redcapConnection.R | 142 +++++++++++ tests/testthat/test-validateImport_methods.R |only tests/testthat/test-vectorToApiBodyList.R |only 107 files changed, 2009 insertions(+), 1231 deletions(-)
Title: Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Description: Bayesian nonparametric density estimation modeling mixtures by a Ferguson-Klass type algorithm for posterior normalized random measures.
Author: Julyan Arbel [ctb],
Ernesto Barrios [aut],
Guillaume Kon Kam King [aut, cre],
Antonio Lijoi [aut],
Luis E. Nieto-Barajas [aut],
Igor Pruenster [aut]
Maintainer: Guillaume Kon Kam King <guillaume.konkamking.work@gmail.com>
Diff between BNPdensity versions 2021.5.4 dated 2021-05-13 and 2023.3.8 dated 2023-03-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/multMixNRMI.R | 7 ++++--- man/as.mcmc.multNRMI.Rd | 6 ++++-- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Simple Engine for Generating Reports using R
Description: Runs R-code present in a pandoc markdown file and
includes the resulting output in the resulting markdown file. This
file can then be converted into any of the output formats
supported by pandoc. The package can also be used as an engine
for writing package vignettes.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between simplermarkdown versions 0.0.4 dated 2022-01-03 and 0.0.6 dated 2023-03-24
DESCRIPTION | 8 MD5 | 60 +++--- NAMESPACE | 5 NEWS | 36 +++ R/capture_output.R |only R/filter_pandoc_json_tree.R | 16 + R/format_eval.R |only R/get_block.R | 2 R/get_extensions.R |only R/markdown_block.R | 15 + R/md_figure.R | 24 +- R/mdweave.R | 10 - R/output_fun.R | 72 +++++-- R/raw_block.R | 2 R/run_and_capture.R |only build/vignette.rds |binary inst/doc/intro.html | 326 +++++++++++++++++++++------------ inst/doc/intro.md | 51 +---- inst/examples/example1.md | 26 ++ inst/examples/iris_copypaste.md |only inst/examples_output/example1.R | 11 + inst/examples_output/example1.md | 30 ++- inst/examples_output/figures/test.pdf |binary inst/examples_output/iris.md | 23 -- inst/examples_output/iris_copypaste.md |only man/format.Rd |only man/get_extensions.Rd |only man/markdown_block.Rd | 3 man/md_figure.Rd | 18 + man/mdweave.Rd | 7 man/output_fun.Rd | 63 ++++++ man/raw_block.Rd | 2 man/run_and_capture.Rd |only tests/test_mdweave.R | 39 +++ tests/test_run_and_capture.R |only vignettes/intro.md | 51 +---- 36 files changed, 623 insertions(+), 277 deletions(-)
More information about simplermarkdown at CRAN
Permanent link
Title: Tools and Data for Quantitative Peace Science Research
Description: These are useful tools and data sets for the study of quantitative
peace science. The goal for this package is to include tools and data sets
for doing original research that mimics well what a user would have to previously
get from a software package that may not be well-sourced or well-supported.
Those software bundles were useful the extent to which they encourage replications
of long-standing analyses by starting the data-generating process from scratch. However,
a lot of the functionality can be done relatively quickly and more transparently
in the R programming language.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between peacesciencer versions 1.0.0 dated 2022-03-25 and 1.1.0 dated 2023-03-24
peacesciencer-1.0.0/peacesciencer/tests |only peacesciencer-1.1.0/peacesciencer/DESCRIPTION | 10 peacesciencer-1.1.0/peacesciencer/MD5 | 146 ++++---- peacesciencer-1.1.0/peacesciencer/NAMESPACE | 2 peacesciencer-1.1.0/peacesciencer/NEWS.md | 12 peacesciencer-1.1.0/peacesciencer/R/add_cow_alliance.R | 2 peacesciencer-1.1.0/peacesciencer/R/add_cow_majors.R | 2 peacesciencer-1.1.0/peacesciencer/R/add_peace_years.R | 2 peacesciencer-1.1.0/peacesciencer/R/add_ucdp_acd.R | 7 peacesciencer-1.1.0/peacesciencer/R/data.R | 110 +++++- peacesciencer-1.1.0/peacesciencer/R/download_extdata.R | 128 +++++++ peacesciencer-1.1.0/peacesciencer/R/zzz.R | 3 peacesciencer-1.1.0/peacesciencer/README.md | 174 ++++------ peacesciencer-1.1.0/peacesciencer/build/partial.rdb |binary peacesciencer-1.1.0/peacesciencer/data/LEAD.rda |binary peacesciencer-1.1.0/peacesciencer/data/archigos.rda |binary peacesciencer-1.1.0/peacesciencer/data/atop_alliance.rda |binary peacesciencer-1.1.0/peacesciencer/data/ccode_democracy.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_alliance.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_capitals.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_contdir.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_ddy.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_gw_years.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_igo_ndy.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_igo_sy.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_majors.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_mid_ddydisps.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_mid_dirdisps.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_mid_disps.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_mindist.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_nmc.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_sdp_gdp.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_states.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_trade_sy.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_war_inter.rda |binary peacesciencer-1.1.0/peacesciencer/data/cow_war_intra.rda |binary peacesciencer-1.1.0/peacesciencer/data/creg.rda |binary peacesciencer-1.1.0/peacesciencer/data/false_cow_dyads.rda |binary peacesciencer-1.1.0/peacesciencer/data/false_gw_dyads.rda |binary peacesciencer-1.1.0/peacesciencer/data/gml_dirdisp.rda |binary peacesciencer-1.1.0/peacesciencer/data/gml_mid_ddlydisps.rda |binary peacesciencer-1.1.0/peacesciencer/data/gml_mid_ddydisps.rda |binary peacesciencer-1.1.0/peacesciencer/data/gml_mid_dirleaderdisps.rda |binary peacesciencer-1.1.0/peacesciencer/data/gml_mid_disps.rda |binary peacesciencer-1.1.0/peacesciencer/data/gml_part.rda |binary peacesciencer-1.1.0/peacesciencer/data/grh_arms_races.rda |binary peacesciencer-1.1.0/peacesciencer/data/gw_capitals.rda |binary peacesciencer-1.1.0/peacesciencer/data/gw_cow_years.rda |binary peacesciencer-1.1.0/peacesciencer/data/gw_ddy.rda |binary peacesciencer-1.1.0/peacesciencer/data/gw_mindist.rda |binary peacesciencer-1.1.0/peacesciencer/data/gw_sdp_gdp.rda |binary peacesciencer-1.1.0/peacesciencer/data/gw_states.rda |binary peacesciencer-1.1.0/peacesciencer/data/gwcode_democracy.rda |binary peacesciencer-1.1.0/peacesciencer/data/hief.rda |binary peacesciencer-1.1.0/peacesciencer/data/leader_codes.rda |binary peacesciencer-1.1.0/peacesciencer/data/lwuf.rda |binary peacesciencer-1.1.0/peacesciencer/data/maoz_powers.rda |binary peacesciencer-1.1.0/peacesciencer/data/ps_bib.rda |binary peacesciencer-1.1.0/peacesciencer/data/ps_data_version.rda |binary peacesciencer-1.1.0/peacesciencer/data/rugged.rda |binary peacesciencer-1.1.0/peacesciencer/data/td_rivalries.rda |binary peacesciencer-1.1.0/peacesciencer/data/tss_rivalries.rda |only peacesciencer-1.1.0/peacesciencer/data/ucdp_acd.rda |binary peacesciencer-1.1.0/peacesciencer/data/ucdp_onsets.rda |binary peacesciencer-1.1.0/peacesciencer/inst/CITATION | 27 - peacesciencer-1.1.0/peacesciencer/man/add_cow_majors.Rd | 2 peacesciencer-1.1.0/peacesciencer/man/add_peace_years.Rd | 2 peacesciencer-1.1.0/peacesciencer/man/add_ucdp_acd.Rd | 7 peacesciencer-1.1.0/peacesciencer/man/cow_ddy.Rd | 6 peacesciencer-1.1.0/peacesciencer/man/cow_majors.Rd | 2 peacesciencer-1.1.0/peacesciencer/man/cow_mindist.Rd | 14 peacesciencer-1.1.0/peacesciencer/man/cow_states.Rd | 2 peacesciencer-1.1.0/peacesciencer/man/download_extdata.Rd | 89 +++++ peacesciencer-1.1.0/peacesciencer/man/gw_ddy.Rd | 6 peacesciencer-1.1.0/peacesciencer/man/tss_rivalries.Rd |only 75 files changed, 528 insertions(+), 227 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>
Diff between marmap versions 1.0.9 dated 2023-01-09 and 1.0.10 dated 2023-03-24
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 1 - R/fortify.bathy.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary man/autoplot.bathy.Rd | 22 +++++++++++----------- man/fortify.bathy.Rd | 9 ++++++--- man/marmap.Rd | 4 ++-- 18 files changed, 42 insertions(+), 40 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.1.7 dated 2023-03-19 and 9.1.8 dated 2023-03-24
rswipl-9.1.7/rswipl/src/swipl-devel/packages/yaml |only rswipl-9.1.7/rswipl/src/swipl-devel/src/pl-sys.h |only rswipl-9.1.8/rswipl/DESCRIPTION | 8 rswipl-9.1.8/rswipl/MD5 | 157 +-- rswipl-9.1.8/rswipl/NEWS.md | 8 rswipl-9.1.8/rswipl/src/swipl-devel/CMAKE.md | 10 rswipl-9.1.8/rswipl/src/swipl-devel/CMakeLists.txt | 3 rswipl-9.1.8/rswipl/src/swipl-devel/VERSION | 2 rswipl-9.1.8/rswipl/src/swipl-devel/boot/engines.pl | 4 rswipl-9.1.8/rswipl/src/swipl-devel/cmake/Config.cmake | 4 rswipl-9.1.8/rswipl/src/swipl-devel/cmake/Install.cmake | 17 rswipl-9.1.8/rswipl/src/swipl-devel/cmake/PackageSelection.cmake | 9 rswipl-9.1.8/rswipl/src/swipl-devel/library/prolog_profile.pl | 24 rswipl-9.1.8/rswipl/src/swipl-devel/library/prolog_stack.pl | 1 rswipl-9.1.8/rswipl/src/swipl-devel/library/sort.pl | 9 rswipl-9.1.8/rswipl/src/swipl-devel/packages/clib/process.c | 12 rswipl-9.1.8/rswipl/src/swipl-devel/packages/clib/test_udp_sockets.pl | 3 rswipl-9.1.8/rswipl/src/swipl-devel/packages/clib/uri.c | 17 rswipl-9.1.8/rswipl/src/swipl-devel/packages/clib/uri.pl | 133 ++ rswipl-9.1.8/rswipl/src/swipl-devel/packages/cmake/PrologPackage.cmake | 3 rswipl-9.1.8/rswipl/src/swipl-devel/packages/http/html_write.pl | 3 rswipl-9.1.8/rswipl/src/swipl-devel/packages/http/http_unix_daemon.pl | 133 +- rswipl-9.1.8/rswipl/src/swipl-devel/packages/http/json.pl | 53 - rswipl-9.1.8/rswipl/src/swipl-devel/packages/http/test_json.pl | 4 rswipl-9.1.8/rswipl/src/swipl-devel/packages/sgml/test_sgml.pl | 32 rswipl-9.1.8/rswipl/src/swipl-devel/packages/ssl/CMakeLists.txt | 2 rswipl-9.1.8/rswipl/src/swipl-devel/packages/ssl/crypt_blowfish.c |only rswipl-9.1.8/rswipl/src/swipl-devel/packages/ssl/crypt_blowfish.h |only rswipl-9.1.8/rswipl/src/swipl-devel/packages/ssl/crypto.pl | 52 - rswipl-9.1.8/rswipl/src/swipl-devel/packages/ssl/crypto4pl.c | 27 rswipl-9.1.8/rswipl/src/swipl-devel/packages/ssl/test_ssl.pl | 12 rswipl-9.1.8/rswipl/src/swipl-devel/src/ATOMS | 1 rswipl-9.1.8/rswipl/src/swipl-devel/src/SWI-Prolog.h | 10 rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/files/test_pipe.pl | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/save/input/unicode.pl |only rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/save/test_qlf.pl |only rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/save/test_saved_states.pl | 4 rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/thread/test_engines.pl | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/thread/test_libthread.pl | 35 rswipl-9.1.8/rswipl/src/swipl-devel/src/Tests/transaction/test_transaction_deadlock.pl | 4 rswipl-9.1.8/rswipl/src/swipl-devel/src/config.h.cmake | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/mkvmi.c | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/os/SWI-Stream.h | 32 rswipl-9.1.8/rswipl/src/swipl-devel/src/os/pl-cstack.c | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/os/pl-prologflag.c | 5 rswipl-9.1.8/rswipl/src/swipl-devel/src/os/windows/uxnt.c | 79 + rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-alloc.c | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-alloc.h | 37 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-atom.c | 43 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-builtin.h | 7 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-event.c | 8 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-ext.c | 9 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-fli.c | 28 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-gc.c | 10 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-global.h | 59 - rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-incl.h | 11 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-index.c | 20 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-init.c | 4 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-mutex.h | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-nt.c | 5 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-pro.c | 6 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-proc.c | 14 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-prof.c | 73 + rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-prof.h | 9 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-rec.c | 6 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-sys.c | 64 - rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-thread.c | 446 ++++++--- rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-thread.h | 202 ++-- rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-trace.c | 8 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-vmi.h | 2 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-wam.c | 14 rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-wic.c | 473 ++++++---- rswipl-9.1.8/rswipl/src/swipl-devel/src/pl-wic.h | 8 73 files changed, 1611 insertions(+), 881 deletions(-)
Title: 'REDCap' Data Management
Description: Access and manage 'REDCap' data. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to programmatic access data and project meta data (such as the data dictionary) from the web. This package allows us to read 'REDCap' data, exported or using an API connection, identify missing or extreme values, identify missing 'REDCap' events in each observation, do a follow-up of the queries initially identified and it also facilitates the process of data management.
Author: Joao Carmezim [aut, cre],
Judith Penafiel [aut],
Pau Satorra [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <ubidi@idibell.cat>
Diff between REDCapDM versions 0.4.0 dated 2023-03-03 and 0.5.0 dated 2023-03-24
REDCapDM-0.4.0/REDCapDM/man/dic_checkboxes.Rd |only REDCapDM-0.4.0/REDCapDM/man/transform_name.Rd |only REDCapDM-0.5.0/REDCapDM/DESCRIPTION | 8 REDCapDM-0.5.0/REDCapDM/MD5 | 68 - REDCapDM-0.5.0/REDCapDM/NAMESPACE | 1 REDCapDM-0.5.0/REDCapDM/NEWS.md | 18 REDCapDM-0.5.0/REDCapDM/R/REDCapDM.R | 17 REDCapDM-0.5.0/REDCapDM/R/check_queries.R | 94 + REDCapDM-0.5.0/REDCapDM/R/covican.R | 2 REDCapDM-0.5.0/REDCapDM/R/rd_event.R | 270 +++-- REDCapDM-0.5.0/REDCapDM/R/rd_export.R |only REDCapDM-0.5.0/REDCapDM/R/rd_insert_na.R | 6 REDCapDM-0.5.0/REDCapDM/R/rd_query.R | 962 +++++++++----------- REDCapDM-0.5.0/REDCapDM/R/rd_rlogic.R | 32 REDCapDM-0.5.0/REDCapDM/R/rd_transform.R | 150 +-- REDCapDM-0.5.0/REDCapDM/R/redcap_data.R | 104 +- REDCapDM-0.5.0/REDCapDM/R/utils-transform.R | 301 ++---- REDCapDM-0.5.0/REDCapDM/data/covican.rda |binary REDCapDM-0.5.0/REDCapDM/inst/doc/REDCapDM.R | 23 REDCapDM-0.5.0/REDCapDM/inst/doc/REDCapDM.Rmd | 62 - REDCapDM-0.5.0/REDCapDM/inst/doc/REDCapDM.html | 509 +++++----- REDCapDM-0.5.0/REDCapDM/man/REDCapDM.Rd | 18 REDCapDM-0.5.0/REDCapDM/man/check_queries.Rd | 11 REDCapDM-0.5.0/REDCapDM/man/covican.Rd | 2 REDCapDM-0.5.0/REDCapDM/man/fill_data.Rd | 2 REDCapDM-0.5.0/REDCapDM/man/rd_event.Rd | 28 REDCapDM-0.5.0/REDCapDM/man/rd_export.Rd |only REDCapDM-0.5.0/REDCapDM/man/rd_insert_na.Rd | 4 REDCapDM-0.5.0/REDCapDM/man/rd_query.Rd | 40 REDCapDM-0.5.0/REDCapDM/man/rd_rlogic.Rd | 2 REDCapDM-0.5.0/REDCapDM/man/rd_transform.Rd | 23 REDCapDM-0.5.0/REDCapDM/man/recalculate.Rd | 4 REDCapDM-0.5.0/REDCapDM/man/redcap_data.Rd | 14 REDCapDM-0.5.0/REDCapDM/man/split_event.Rd | 2 REDCapDM-0.5.0/REDCapDM/man/split_form.Rd | 2 REDCapDM-0.5.0/REDCapDM/man/transform_checkboxes.Rd | 12 REDCapDM-0.5.0/REDCapDM/vignettes/REDCapDM.Rmd | 62 - 37 files changed, 1531 insertions(+), 1322 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data
analysis, drake rebuilds intermediate data objects when their
dependencies change, and it skips work when the results are already up
to date. Not every execution starts from scratch, there is native
support for parallel and distributed computing, and completed projects
have tangible evidence that they are reproducible. Extensive
documentation, from beginner-friendly tutorials to practical examples
and more, is available at the reference website
<https://docs.ropensci.org/drake/> and the online manual
<https://books.ropensci.org/drake/>.
Author: William Michael Landau [aut, cre]
,
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Mueller [ctb],
Ben Bond-Lamberty [ctb] ,
Tristan Mahr [ctb] ,
Miles McBain [ctb] ,
Noam Ross [ctb] ,
Ellis Hughes [ctb],
Matthew Mark Strasiotto [ctb],
Ben Marwick [...truncated...]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 7.13.4 dated 2022-08-19 and 7.13.5 dated 2023-03-24
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/cache.R | 2 +- R/create_drake_spec.R | 2 +- R/deprecated.R | 6 +++--- R/hash_tables.R | 4 ++-- R/make.R | 5 ++++- R/manage_memory.R | 29 +++++++++++++++++++++++------ R/vis_drake_graph.R | 4 ++-- inst/CITATION | 4 ++-- man/render_drake_graph.Rd | 2 +- man/vis_drake_graph.Rd | 2 +- 13 files changed, 60 insertions(+), 36 deletions(-)
Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects. This is demonstrated in Monnahan & Kristensen (2018) <DOI:10.1371/journal.pone.0197954>.
Author: Kasper Kristensen
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between tmbstan versions 1.0.4 dated 2022-03-21 and 1.0.7 dated 2023-03-24
tmbstan-1.0.4/tmbstan/inst/model.hpp |only tmbstan-1.0.4/tmbstan/src/include/model.hpp |only tmbstan-1.0.7/tmbstan/DESCRIPTION | 10 +++++----- tmbstan-1.0.7/tmbstan/MD5 | 16 ++++++++++------ tmbstan-1.0.7/tmbstan/NEWS |only tmbstan-1.0.7/tmbstan/R/tmbstan.R | 6 +++--- tmbstan-1.0.7/tmbstan/configure |only tmbstan-1.0.7/tmbstan/configure.win |only tmbstan-1.0.7/tmbstan/inst/model.stan |only tmbstan-1.0.7/tmbstan/inst/model226.stan |only tmbstan-1.0.7/tmbstan/man/tmbstan.Rd | 12 +++++++++--- tmbstan-1.0.7/tmbstan/src/Makevars | 1 - tmbstan-1.0.7/tmbstan/tools |only 13 files changed, 27 insertions(+), 18 deletions(-)
Title: Piece-Wise Exponential Additive Mixed Modeling Tools for
Survival Analysis
Description: The Piece-wise exponential (Additive Mixed) Model
(PAMM; Bender and others (2018) <doi: 10.1177/1471082X17748083>) is a
powerful model class for the analysis of survival (or time-to-event) data,
based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2019)), as well as support for left-truncated, competing risks and recurrent events data.
pammtools provides tidy workflow for survival analysis with PAMMs,
including data simulation, transformation and other functions for data
preprocessing and model post-processing as well as visualization.
Author: Andreas Bender [aut, cre] ,
Fabian Scheipl [aut] ,
Philipp Kopper [aut] ,
Lukas Burk [ctb]
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>
Diff between pammtools versions 0.5.8 dated 2022-01-08 and 0.5.91 dated 2023-03-24
DESCRIPTION | 8 +++--- MD5 | 24 +++++++++--------- NEWS.md | 3 ++ R/convenience-plots.R | 18 ++++++------- R/ggplot-extensions.R | 58 +++++++++++++++++++++++++++++++++++++------- R/lag-lead-utils.R | 4 +-- R/predict.R | 3 +- R/viz-elra.R | 30 +++++++++++----------- README.md | 4 +-- inst/CITATION | 24 ++++++++++++------ man/geom_hazard.Rd | 20 +++++++++------ man/geom_stepribbon.Rd | 29 +++++++++++++++------- man/predictSurvProb.pamm.Rd | 4 ++- 13 files changed, 151 insertions(+), 78 deletions(-)
Title: Weighted Metrics, Scoring Functions and Performance Measures for
Machine Learning
Description: Provides weighted versions of several metrics, scoring
functions and performance measures used in machine learning, including
average unit deviances of the Bernoulli, Tweedie, Poisson, and Gamma
distributions, see Jorgensen B. (1997, ISBN: 978-0412997112). The
package also contains a weighted version of generalized R-squared, see
e.g. Cohen, J. et al. (2002, ISBN: 978-0805822236). Furthermore,
'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph],
Christian Lorentzen [ctb, rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between MetricsWeighted versions 0.5.4 dated 2022-01-23 and 0.5.5 dated 2023-03-24
DESCRIPTION | 16 MD5 | 20 NEWS.md | 12 README.md | 34 + build/vignette.rds |binary inst/doc/MetricsWeighted.R | 88 +--- inst/doc/MetricsWeighted.Rmd | 134 +++--- inst/doc/MetricsWeighted.html | 864 +++++++++++++++++++++++++++--------------- man/figures |only tests/testthat/test-plots.R |only tests/testthat/test-stats.R | 79 +++ vignettes/MetricsWeighted.Rmd | 134 +++--- 12 files changed, 869 insertions(+), 512 deletions(-)
More information about MetricsWeighted at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-04 0.1
Title: Temporal Trend Analysis Graphical Interface
Description: This interface was created to develop a standard procedure
to analyse temporal trend in the framework of the OSPAR convention.
The analysis process run through 4 successive steps : 1) manipulate your data, 2)
select the parameters you want to analyse, 3) build your regulated
time series, 4) perform diagnosis and analysis and 5) read the results.
Statistical analysis call other package function such as Kendall tests
or cusum() function.
Author: David DEVREKER [aut, cre],
Alain LEFEBVRE [aut]
Maintainer: David DEVREKER <David.Devreker@ifremer.fr>
Diff between TTAinterfaceTrendAnalysis versions 1.5.8 dated 2021-10-06 and 1.5.9 dated 2023-03-24
DESCRIPTION | 11 +- MD5 | 22 ++--- NAMESPACE | 1 NEWS | 8 + R/FULLoption.r | 61 +++++++++---- R/TTAinterface.R | 179 ++++++++++++++++++++++++++++++++-------- R/fixdata.R | 191 +++++++++++++++++++++++++++++++++---------- R/selectdirectory.R | 193 +++++++++++++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/TTAVignette.pdf |binary man/FULLoption.Rd | 6 + man/TTAinterface-package.Rd | 2 12 files changed, 512 insertions(+), 162 deletions(-)
More information about TTAinterfaceTrendAnalysis at CRAN
Permanent link
Title: Download and Parse Public Data Released by B3 Exchange
Description: Download and parse public files released by B3 and convert them
into useful formats and data structures common to data analysis
practitioners.
Author: Wilson Freitas [aut, cre],
Marcelo Perlin [aut]
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Diff between rb3 versions 0.0.8 dated 2023-03-05 and 0.0.9 dated 2023-03-24
rb3-0.0.8/rb3/tests/fixtures/OpcoesAcoesEmAberto.yml |only rb3-0.0.9/rb3/DESCRIPTION | 6 rb3-0.0.9/rb3/MD5 | 55 rb3-0.0.9/rb3/NAMESPACE | 1 rb3-0.0.9/rb3/NEWS.md | 6 rb3-0.0.9/rb3/R/download-data.R | 8 rb3-0.0.9/rb3/R/downloaders.R | 34 rb3-0.0.9/rb3/R/rb3-package.R | 2 rb3-0.0.9/rb3/R/scraper-futures.R | 4 rb3-0.0.9/rb3/R/zzz.R | 1 rb3-0.0.9/rb3/inst/doc/B3-Indexes.html | 614 rb3-0.0.9/rb3/inst/doc/Fetching-historical-future-rates.R | 24 rb3-0.0.9/rb3/inst/doc/Fetching-historical-future-rates.Rmd | 15 rb3-0.0.9/rb3/inst/doc/Fetching-historical-future-rates.html | 567 rb3-0.0.9/rb3/inst/doc/Fetching-historical-yield-curve.R | 60 rb3-0.0.9/rb3/inst/doc/Fetching-historical-yield-curve.Rmd | 54 rb3-0.0.9/rb3/inst/doc/Fetching-historical-yield-curve.html | 495 rb3-0.0.9/rb3/inst/extdata/templates/AjustesDiarios.yaml | 1 rb3-0.0.9/rb3/inst/extdata/templates/COTAHIST_DAILY.yaml | 1 rb3-0.0.9/rb3/inst/extdata/templates/COTAHIST_MONTHLY.yaml | 1 rb3-0.0.9/rb3/inst/extdata/templates/COTAHIST_YEARLY.yaml | 1 rb3-0.0.9/rb3/inst/extdata/templates/TaxasReferenciais.yaml | 1 rb3-0.0.9/rb3/tests/fixtures/NegociosBTB.yml |44032 ++--------- rb3-0.0.9/rb3/tests/fixtures/NegociosBalcao.yml | 8 rb3-0.0.9/rb3/tests/testthat/test-downloaders.R | 4 rb3-0.0.9/rb3/vignettes/Fetching-historical-future-rates.Rmd | 15 rb3-0.0.9/rb3/vignettes/Fetching-historical-yield-curve.Rmd | 54 rb3-0.0.9/rb3/vignettes/futures_mget-20210101_20220427.rda |only rb3-0.0.9/rb3/vignettes/yc_ipca_mget.rda |only rb3-0.0.9/rb3/vignettes/yc_mget.rda |only rb3-0.0.9/rb3/vignettes/yc_usd_mget.rda |only 31 files changed, 12886 insertions(+), 33178 deletions(-)
Title: Functions for Generating PostgreSQL Statements/Scripts
Description: Create PostgreSQL statements/scripts from R, optionally executing the SQL statements.
Common SQL operations are included, although not every configurable option is available at this time.
SQL output is intended to be compliant with PostgreSQL syntax specifications. PostgreSQL documentation is available here
<https://www.postgresql.org/docs/current/index.html>.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between pgTools versions 1.0.1 dated 2022-09-15 and 1.0.2 dated 2023-03-24
DESCRIPTION | 10 ++++++---- MD5 | 4 ++-- R/pgTools.R | 2 ++ 3 files changed, 10 insertions(+), 6 deletions(-)
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 2.1.0 dated 2023-02-21 and 2.2.0 dated 2023-03-24
DESCRIPTION | 8 ++++---- MD5 | 33 ++++++++++++++++++--------------- NAMESPACE | 2 ++ NEWS.md | 13 +++++++++++++ R/RcppExports.R | 8 ++++++++ R/jtheta1derivatives.R | 5 +++-- R/weierstrassStuff.R | 33 ++++++++++++++++++++++++++++++++- R/wp.R | 4 ++-- R/wpinv.R | 2 +- R/wsigma.R | 2 +- R/wzeta.R | 2 +- man/ellipticInvariants.Rd |only man/halfPeriods.Rd |only src/RcppExports.cpp | 26 ++++++++++++++++++++++++++ src/altjtheta.cpp | 34 ++++++++++++++++++++-------------- src/jacobi.cpp | 16 ++++++++-------- tests/testthat/test-eisenstein.R |only tests/testthat/test-jtheta.R | 12 ++++++++++++ tests/testthat/test-wzeta.R | 6 +++--- 19 files changed, 154 insertions(+), 52 deletions(-)
Title: Joint Models of Survival and Multivariate Longitudinal Data
Description: Fit joint models of survival and multivariate longitudinal data. The longitudinal
data is specified by generalised linear mixed models. The joint models are fit via maximum
likelihood using an approximate expectation maximisation algorithm.
Bernhardt (2015) <doi:10.1016/j.csda.2014.11.011>.
Author: James Murray [aut, cre]
Maintainer: James Murray <j.murray7@ncl.ac.uk>
Diff between gmvjoint versions 0.2.0 dated 2023-03-13 and 0.2.1 dated 2023-03-24
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- R/EMUpdate.R | 2 +- R/dynPred-draws.R | 4 ++-- R/fitted.R | 4 ++-- R/inits.R | 9 +++++---- R/joint.R | 6 +----- R/loglik.R | 6 +----- R/misc.R | 21 +++++++++++++++++++++ R/survmod.R | 7 ++++--- README.md | 1 + build/partial.rdb |binary man/anova.joint.Rd | 6 +----- man/residuals.joint.Rd | 4 ++-- src/funs.cpp | 1 + 16 files changed, 63 insertions(+), 50 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut],
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [ [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 2.8-2 dated 2022-10-06 and 2.9-0 dated 2023-03-24
DESCRIPTION | 17 MD5 | 193 ++++--- NAMESPACE | 3 R/GGIR.R | 220 +++++---- R/applyExtFunction.R | 2 R/check_myfun.R | 30 - R/check_params.R | 80 ++- R/correctOlderMilestoneData.R |only R/createConfigFile.R | 27 - R/create_test_acc_csv.R | 82 ++- R/extract_params.R | 26 - R/g.analyse.perday.R | 97 ++- R/g.analyse.perfile.R | 26 - R/g.calibrate.R | 11 R/g.conv.actlog.R | 28 - R/g.dotorcomma.R | 14 R/g.getbout.R | 284 +++-------- R/g.getmeta.R | 6 R/g.impute.R | 12 R/g.imputeTimegaps.R | 59 +- R/g.inspectfile.R | 191 ++----- R/g.loadlog.R | 17 R/g.part1.R | 111 ++-- R/g.part2.R | 69 +- R/g.part3.R | 22 R/g.part4.R | 67 +- R/g.part4_extractid.R | 99 ++-- R/g.part5.R | 101 ++-- R/g.part5.addsib.R | 27 - R/g.part5.classifyNaps.R | 13 R/g.part5.handle_lux_extremes.R | 5 R/g.part5.wakesleepwindows.R | 84 +-- R/g.plot5.R | 143 +++-- R/g.readaccfile.R | 45 - R/g.report.part2.R | 11 R/g.report.part4.R | 43 + R/g.report.part5.R | 34 - R/g.sibreport.R | 18 R/g.weardec.R | 160 +++--- R/getfolderstructure.R | 26 - R/identify_level.R | 30 - R/iso8601chartime2POSIX.R | 4 R/load_params.R | 15 R/read.myacc.csv.R | 94 +++ R/zzz.R | 2 build/GGIR.pdf |binary build/vignette.rds |binary inst/CITATION | 3 inst/NEWS.Rd | 72 ++ inst/doc/CutPoints.Rmd | 49 +- inst/doc/CutPoints.html | 315 +++++++----- inst/doc/ExternalFunction.Rmd | 4 inst/doc/ExternalFunction.pdf |binary inst/doc/GGIR.R | 74 +-- inst/doc/GGIR.Rmd | 583 ++++++++++++------------ inst/doc/GGIR.html | 448 +++++++++--------- inst/doc/GGIRParameters.Rmd | 3 inst/doc/GGIRParameters.html | 324 ++++++------- inst/doc/TutorialDaySegmentAnalyses.Rmd | 3 inst/doc/TutorialDaySegmentAnalyses.html | 173 +++---- inst/doc/readmyacccsv.Rmd | 7 inst/doc/readmyacccsv.html | 186 +++---- man/GGIR-package.Rd | 4 man/GGIR.Rd | 157 +++--- man/correctOlderMilestoneData.Rd |only man/createConfigFile.Rd | 7 man/g.conv.actlog.Rd | 12 man/g.getbout.Rd | 47 - man/g.loadlog.Rd | 8 man/g.part1.Rd | 5 man/g.part2.Rd | 6 man/g.part3.Rd | 8 man/g.part4.Rd | 5 man/g.part4_extradctid.Rd | 6 man/g.part5.Rd | 5 man/g.report.part2.Rd | 13 man/g.report.part4.Rd | 90 +-- man/g.report.part5.Rd | 51 +- man/g.weardec.Rd | 47 + man/read.myacc.csv.Rd | 10 tests/testthat/test_chainof5parts.R | 111 ++-- tests/testthat/test_correctOlderMilestoneData.R |only tests/testthat/test_g.impute.R | 2 tests/testthat/test_g_conv_actlog.R | 10 tests/testthat/test_ggetbout.R | 146 ++---- tests/testthat/test_gloadlog.R | 6 tests/testthat/test_greadaccfile.R | 6 tests/testthat/test_gweardec.R |only tests/testthat/test_identify_levels.R | 32 - tests/testthat/test_load_check_params.R | 8 tests/testthat/test_part1_with_allmetrics.R | 7 tests/testthat/test_part5_fixmissingnight.R | 4 tests/testthat/test_read.myacc.csv.R | 416 ++++++++++------- tests/testthat/test_recordingEndSleepHour.R |only vignettes/CutPoints.Rmd | 49 +- vignettes/ExternalFunction.Rmd | 4 vignettes/GGIR.Rmd | 583 ++++++++++++------------ vignettes/GGIRParameters.Rmd | 3 vignettes/TutorialDaySegmentAnalyses.Rmd | 3 vignettes/readmyacccsv.Rmd | 7 100 files changed, 3649 insertions(+), 3121 deletions(-)
Title: Bayesian Multinomial Logistic Normal Regression
Description: Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation
and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for
scalability. 'fido' replaces the previous package 'stray'.
Author: Justin Silverman [aut],
Kim Roche [ctb],
Michelle Nixon [ctb, cre]
Maintainer: Michelle Nixon
<pistner@psu.edu>
Diff between fido versions 1.0.3 dated 2022-08-23 and 1.0.4 dated 2023-03-24
DESCRIPTION | 8 MD5 | 184 ++++++++--------- NEWS.md | 6 inst/CITATION | 10 inst/doc/introduction-to-fido.html | 145 ++++++-------- inst/doc/mitigating-pcrbias.html | 111 +++++----- inst/doc/non-linear-models.html | 139 ++++++------- inst/doc/orthus.html | 141 ++++++------- inst/doc/picking_priors.html | 14 - man/access_dims.Rd | 116 +++++------ man/alr.Rd | 38 +-- man/alrInv.Rd | 38 +-- man/alrInv_array.Rd | 42 ++-- man/alr_array.Rd | 42 ++-- man/as.list.Rd | 38 +-- man/as.list.orthusfit.Rd | 38 +-- man/as.list.pibblefit.Rd | 38 +-- man/as.orthusfit.Rd | 34 +-- man/as.pibblefit.Rd | 34 +-- man/basset_fit.Rd | 130 ++++++------ man/check_dims.Rd | 50 ++-- man/clr_array.Rd | 38 +-- man/coef.Rd | 50 ++-- man/coef.orthusfit.Rd | 56 ++--- man/coef.pibblefit.Rd | 56 ++--- man/conjugateLinearModel.Rd | 96 ++++----- man/convert_orthus_covariance.Rd | 104 +++++----- man/create_default_ilr_base.Rd | 34 +-- man/fido_package.Rd | 24 +- man/fido_transforms.Rd | 134 ++++++------ man/gather_array.Rd | 60 ++--- man/kernels.Rd | 80 +++---- man/lambda_to_iqlr.Rd | 110 +++++----- man/lmvgamma.Rd | 44 ++-- man/lmvgamma_deriv.Rd | 44 ++-- man/loglikMaltipooCollapsed.Rd | 104 +++++----- man/loglikPibbleCollapsed.Rd | 164 +++++++-------- man/mallard.Rd | 50 ++-- man/mallard_family.Rd | 50 ++-- man/maltipoo_fit.Rd | 162 +++++++-------- man/maltipoofit.Rd | 204 +++++++++---------- man/metadata.Rd | 36 +-- man/miniclo.Rd | 42 ++-- man/miniclo_array.Rd | 46 ++-- man/mongrel-deprecated.Rd | 104 +++++----- man/name.Rd | 38 +-- man/name.orthusfit.Rd | 40 +-- man/name.pibblefit.Rd | 38 +-- man/name_dims.Rd | 136 ++++++------- man/optimPibbleCollapsed.Rd | 330 ++++++++++++++++---------------- man/orthus_fit.Rd | 194 +++++++++--------- man/orthus_lr_transforms.Rd | 98 ++++----- man/orthus_sim.Rd | 76 +++---- man/orthus_tidy_samples.Rd | 60 ++--- man/orthusfit.Rd | 198 +++++++++---------- man/pcrbias_mock.Rd | 42 ++-- man/pibble_fit.Rd | 212 ++++++++++---------- man/pibble_sim.Rd | 58 ++--- man/pibble_tidy_samples.Rd | 60 ++--- man/pibblefit.Rd | 180 ++++++++--------- man/plot.pibblefit.Rd | 74 +++---- man/ppc.Rd | 38 +-- man/ppc.pibblefit.Rd | 72 +++--- man/ppc_summary.Rd | 50 ++-- man/predict.Rd | 50 ++-- man/predict.bassetfit.Rd | 106 +++++----- man/predict.pibblefit.Rd | 118 +++++------ man/print.Rd | 50 ++-- man/print.orthusfit.Rd | 58 ++--- man/print.pibblefit.Rd | 60 ++--- man/random_pibble_init.Rd | 54 ++--- man/refit.Rd | 38 +-- man/req.Rd | 38 +-- man/req.maltipoofit.Rd | 38 +-- man/req.orthusfit.Rd | 38 +-- man/req.pibblefit.Rd | 38 +-- man/sample_prior.Rd | 42 ++-- man/sample_prior.pibblefit.Rd | 104 +++++----- man/store_coord.Rd | 56 ++--- man/summarise_posterior.Rd | 66 +++--- man/summary.Rd | 38 +-- man/summary.orthusfit.Rd | 76 +++---- man/summary.pibblefit.Rd | 76 +++---- man/uncollapsePibble.Rd | 196 +++++++++---------- man/verify.Rd | 38 +-- man/verify.bassetfit.Rd | 38 +-- man/verify.maltipoofit.Rd | 38 +-- man/verify.orthusfit.Rd | 38 +-- man/verify.pibblefit.Rd | 38 +-- src/Makevars.in | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-numCores.R | 1 tests/testthat/test-orthus-transforms.R | 1 93 files changed, 3406 insertions(+), 3410 deletions(-)
Title: Interface to Chromosome Counts Database API
Description: A programmatic interface to the Chromosome Counts Database
(<http://ccdb.tau.ac.il/>), Rice et al. (2014) <doi:10.1111/nph.13191>.
This package is part of the 'ROpenSci' suite (<https://ropensci.org>).
Author: Matthew Pennell [aut] ,
Paula Andrea Martinez [aut] ,
Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between chromer versions 0.2 dated 2022-10-27 and 0.4 dated 2023-03-24
DESCRIPTION | 17 +++++++------ MD5 | 11 ++++----- NEWS.md | 16 +++++++++++-- R/ccdb_down.R |only README.md | 10 ++++---- tests/testthat/test-data-summary.R | 24 ++++++++++--------- tests/testthat/test-rank-query.R | 45 ++++++++++++++++++++----------------- 7 files changed, 73 insertions(+), 50 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-31 2.0.1
2019-02-08 2.0
2018-08-14 1.0
Title: Time Series Forecasting Using GRNN
Description: A general regression neural network (GRNN) is a variant of a
Radial Basis Function Network characterized by a fast single-pass learning.
'tsfgrnn' allows you to forecast time series using a GRNN model Francisco
Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Francisco
Martinez et al. (2022) <doi:10.1016/j.neucom.2021.12.028>. When the forecasting
horizon is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. You can consult and plot how the
prediction was done. It is also possible to assess the forecasting accuracy
of the model using rolling origin evaluation.
Author: Maria Pilar Frias-Bustamante [aut],
Ana Maria Martinez-Rodriguez [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfgrnn versions 1.0.2 dated 2022-05-30 and 1.0.4 dated 2023-03-24
DESCRIPTION | 8 +- MD5 | 23 ++++--- NEWS.md | 18 ++++-- R/plotting.R | 35 +++++++++--- README.md | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/tsfgrnn.html | 124 ++++++++++++++++++++++--------------------- man/autoplot.grnnForecast.Rd | 20 ++++-- man/grnn_examples.Rd | 2 man/grnn_forecasting.Rd | 14 ++-- man/grnn_weights.Rd | 2 man/rolling_origin.Rd | 14 ++-- 13 files changed, 152 insertions(+), 110 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 5.0.0-10 dated 2021-05-17 and 6.5.0-3 dated 2023-03-24
r2sundials-5.0.0-10/r2sundials/src/lib/nvector/serial/fnvector_serial.c |only r2sundials-5.0.0-10/r2sundials/src/lib/nvector/serial/fnvector_serial.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/band/fsunlinsol_band.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/band/fsunlinsol_band.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/dense/fsunlinsol_dense.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/dense/fsunlinsol_dense.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/lapackband/fsunlinsol_lapackband.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/lapackband/fsunlinsol_lapackband.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/lapackdense/fsunlinsol_lapackdense.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/lapackdense/fsunlinsol_lapackdense.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/pcg/fsunlinsol_pcg.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/pcg/fsunlinsol_pcg.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/spbcgs/fsunlinsol_spbcgs.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/spbcgs/fsunlinsol_spbcgs.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/spfgmr/fsunlinsol_spfgmr.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/spfgmr/fsunlinsol_spfgmr.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/spgmr/fsunlinsol_spgmr.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/spgmr/fsunlinsol_spgmr.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/sptfqmr/fsunlinsol_sptfqmr.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunlinsol/sptfqmr/fsunlinsol_sptfqmr.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunmatrix/band/fsunmatrix_band.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunmatrix/band/fsunmatrix_band.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunmatrix/dense/fsunmatrix_dense.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunmatrix/dense/fsunmatrix_dense.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunmatrix/sparse/fsunmatrix_sparse.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunmatrix/sparse/fsunmatrix_sparse.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunnonlinsol/fixedpoint/fsunnonlinsol_fixedpoint.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunnonlinsol/fixedpoint/fsunnonlinsol_fixedpoint.h |only r2sundials-5.0.0-10/r2sundials/src/lib/sunnonlinsol/newton/fsunnonlinsol_newton.c |only r2sundials-5.0.0-10/r2sundials/src/lib/sunnonlinsol/newton/fsunnonlinsol_newton.h |only r2sundials-6.5.0-3/r2sundials/DESCRIPTION | 18 r2sundials-6.5.0-3/r2sundials/MD5 | 325 - r2sundials-6.5.0-3/r2sundials/NEWS | 12 r2sundials-6.5.0-3/r2sundials/R/RcppExports.R | 21 r2sundials-6.5.0-3/r2sundials/build/partial.rdb |binary r2sundials-6.5.0-3/r2sundials/inst/CITATION | 4 r2sundials-6.5.0-3/r2sundials/inst/COPYRIGHTS | 4 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes.h | 122 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_bandpre.h | 2 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_bbdpre.h | 2 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_diag.h | 2 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_direct.h | 12 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_ls.h | 28 r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_proj.h |only r2sundials-6.5.0-3/r2sundials/inst/include/cvodes/cvodes_spils.h | 22 r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_cuda.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_hip.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_kokkos.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_manyvector.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_mpimanyvector.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_mpiplusx.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_openmp.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_openmpdev.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_parallel.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_parhyp.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_petsc.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_pthreads.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_raja.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_serial.h | 43 r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_sycl.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/nvector_trilinos.h |only r2sundials-6.5.0-3/r2sundials/inst/include/nvector/trilinos |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_band.h | 191 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_base.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_config.h | 249 - r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_config.in | 226 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_context.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_context.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_context_impl.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_convertibleto.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_cuda.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_cuda_policies.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_debug.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_dense.h | 332 - r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_direct.h | 305 - r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_export.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_futils.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_hashmap.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_hip.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_hip_policies.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_iterative.h | 355 + r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_iterative_impl.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_lapack.h | 233 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_lapack_defs.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_linearsolver.h | 146 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_linearsolver.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_logger.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_logger_impl.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_math.h | 144 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_matrix.h | 78 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_matrix.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_memory.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_mpi_types.h | 6 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_nonlinearsolver.h | 111 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_nonlinearsolver.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_nvector.h | 220 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_nvector.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_nvector_senswrapper.h | 4 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_profiler.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_sycl.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_sycl_policies.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_types.h | 90 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_utils.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_version.h | 2 r2sundials-6.5.0-3/r2sundials/inst/include/sundials/sundials_xbraid.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_band.h | 9 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_cusolversp_batchqr.h | 30 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_dense.h | 9 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_ginkgo.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_klu.h | 13 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_lapackband.h | 27 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_lapackdense.h | 27 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_magmadense.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_onemkldense.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_pcg.h | 35 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_spbcgs.h | 40 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_spfgmr.h | 41 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_spgmr.h | 43 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_sptfqmr.h | 36 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_superludist.h | 36 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol/sunlinsol_superlumt.h | 13 r2sundials-6.5.0-3/r2sundials/inst/include/sunlinsol_rmumps.h | 3 r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_band.h | 22 r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_cusparse.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_dense.h | 14 r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_ginkgo.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp |only r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_magmadense.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_onemkldense.h |only r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_slunrloc.h | 4 r2sundials-6.5.0-3/r2sundials/inst/include/sunmatrix/sunmatrix_sparse.h | 20 r2sundials-6.5.0-3/r2sundials/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h | 75 r2sundials-6.5.0-3/r2sundials/inst/include/sunnonlinsol/sunnonlinsol_newton.h | 24 r2sundials-6.5.0-3/r2sundials/inst/include/sunnonlinsol/sunnonlinsol_petscsnes.h | 6 r2sundials-6.5.0-3/r2sundials/inst/unitTests/runit.r2cvodes.R | 23 r2sundials-6.5.0-3/r2sundials/man/r2cvodes.Rd | 21 r2sundials-6.5.0-3/r2sundials/src/Makevars | 6 r2sundials-6.5.0-3/r2sundials/src/RcppExports.cpp | 5 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/LICENSE | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodea.c | 120 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodea_io.c | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes.c | 2432 +++++----- r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_bandpre.c | 8 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_bandpre_impl.h | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_bbdpre.c | 12 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_bbdpre_impl.h | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_diag.c | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_diag_impl.h | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_direct.c | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_impl.h | 421 + r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_io.c | 919 +++ r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_ls.c | 464 + r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_ls_impl.h | 27 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_nls.c | 86 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_nls_sim.c | 58 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_nls_stg.c | 8 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_nls_stg1.c | 2 r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_proj.c |only r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_proj_impl.h |only r2sundials-6.5.0-3/r2sundials/src/lib/cvodes/cvodes_spils.c | 2 r2sundials-6.5.0-3/r2sundials/src/lib/nvector/hip |only r2sundials-6.5.0-3/r2sundials/src/lib/nvector/serial/nvector_serial.c | 153 r2sundials-6.5.0-3/r2sundials/src/lib/readme.txt | 27 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_band.c | 148 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_context.c |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_context_impl.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_cuda.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_cuda_kernels.cuh |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_debug.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_dense.c | 169 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_direct.c | 150 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_futils.c |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_hashmap.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_hip.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_hip_kernels.hip.hpp |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_iterative.c | 405 + r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_iterative_impl.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_lapack_defs.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_linearsolver.c | 97 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_logger.c |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_logger_impl.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_math.c | 148 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_matrix.c | 83 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_memory.c |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_nonlinearsolver.c | 40 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_nvector.c | 562 +- r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_nvector_senswrapper.c | 90 r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_profiler.c |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_reductions.hpp |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_sycl.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_utils.h |only r2sundials-6.5.0-3/r2sundials/src/lib/sundials/sundials_version.c | 34 r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/band/sunlinsol_band.c | 23 r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/cusolversp/sunlinsol_cusolversp_batchqr.cu | 289 - r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/dense/sunlinsol_dense.c | 22 r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/lapackband/sunlinsol_lapackband.c | 42 r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/lapackdense/sunlinsol_lapackdense.c | 42 r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/magmadense |only r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/onemkldense |only r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/pcg/sunlinsol_pcg.c | 234 r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/spbcgs/sunlinsol_spbcgs.c | 289 - r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/spfgmr/sunlinsol_spfgmr.c | 258 - r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/spgmr/sunlinsol_spgmr.c | 266 - r2sundials-6.5.0-3/r2sundials/src/lib/sunlinsol/sptfqmr/sunlinsol_sptfqmr.c | 372 + r2sundials-6.5.0-3/r2sundials/src/lib/sunmatrix/band/sunmatrix_band.c | 58 r2sundials-6.5.0-3/r2sundials/src/lib/sunmatrix/cusparse |only r2sundials-6.5.0-3/r2sundials/src/lib/sunmatrix/dense/sunmatrix_dense.c | 195 r2sundials-6.5.0-3/r2sundials/src/lib/sunmatrix/magmadense |only r2sundials-6.5.0-3/r2sundials/src/lib/sunmatrix/onemkldense |only r2sundials-6.5.0-3/r2sundials/src/lib/sunmatrix/sparse/sunmatrix_sparse.c | 126 r2sundials-6.5.0-3/r2sundials/src/lib/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c | 152 r2sundials-6.5.0-3/r2sundials/src/lib/sunnonlinsol/newton/sunnonlinsol_newton.c | 105 r2sundials-6.5.0-3/r2sundials/src/r2sundials.cpp | 43 r2sundials-6.5.0-3/r2sundials/src/sunlinsol_rmumps.cpp | 61 215 files changed, 9011 insertions(+), 4136 deletions(-)
Title: Facilitation of Data Preparation and Plotting Procedures for RDA
and PCA Analyses
Description: Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects.
Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects.
Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
Method note : for the RDA output synthesis, several functions of the package 'RVAideMemoire', developed by Maxime Hervé, are exploited.
Author: Gregoire Bianchetti [aut, cre]
Maintainer: Gregoire Bianchetti <auguste.blam@gmail.com>
Diff between GABB versions 0.2.0 dated 2023-03-02 and 0.3.1 dated 2023-03-24
DESCRIPTION | 10 MD5 | 6 R/PCA_RDA_graphics.R | 887 ++++++++++++++++++++++++++++++++++++++++-------- man/PCA_RDA_graphics.Rd | 71 +++ 4 files changed, 825 insertions(+), 149 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.37 dated 2023-01-31 and 0.38 dated 2023-03-24
DESCRIPTION | 8 - LICENSE | 2 MD5 | 190 ++++++++++++++++---------------- NAMESPACE | 3 NEWS.md | 14 ++ R/api.R | 20 +-- R/base64.R | 34 ++--- R/cache.R | 242 +++++++++++++++++++++++++++++------------- R/command.R | 74 ++++++------ R/cran.R | 8 - R/data-structure.R | 36 +++--- R/encoding.R | 14 +- R/github.R | 16 +- R/image.R | 46 +++---- R/io.R | 122 ++++++++++----------- R/json.R | 8 - R/markdown.R | 14 +- R/os.R | 4 R/packages.R | 85 +++++++------- R/paths.R | 145 +++++++++++++------------ R/revcheck.R | 84 +++++++------- R/session.R | 28 ++-- R/string.R | 50 ++++---- R/utils.R | 67 +++++------ R/yaml.R |only build/vignette.rds |binary inst/doc/xfun.html | 188 ++++++++++++++++---------------- man/Rscript.Rd | 2 man/Rscript_call.Rd | 6 - man/attr.Rd | 5 man/base64_encode.Rd | 2 man/base64_uri.Rd | 12 +- man/base_pkgs.Rd | 2 man/bg_process.Rd | 34 ++--- man/broken_packages.Rd | 7 - man/bump_version.Rd | 2 man/cache_rds.Rd | 125 ++++++++++----------- man/crandalf_check.Rd | 2 man/dir_create.Rd | 6 - man/dir_exists.Rd | 6 - man/do_once.Rd | 2 man/download_cache.Rd |only man/download_file.Rd | 18 +-- man/embed_file.Rd | 14 +- man/exit_call.Rd | 4 man/file_ext.Rd | 6 - man/file_string.Rd | 4 man/format_bytes.Rd | 2 man/from_root.Rd | 6 - man/github_releases.Rd | 2 man/grep_sub.Rd | 5 man/gsub_file.Rd | 6 - man/install_github.Rd | 14 +- man/isFALSE.Rd | 6 - man/is_abs_path.Rd | 4 man/is_ascii.Rd | 2 man/is_blank.Rd | 6 - man/is_sub_path.Rd | 6 - man/magic_path.Rd | 3 man/mark_dirs.Rd | 6 - man/msg_cat.Rd | 12 +- man/native_encode.Rd | 10 - man/news2md.Rd | 6 - man/normalize_path.Rd | 2 man/parse_only.Rd | 2 man/pkg_attach.Rd | 25 ++-- man/proc_kill.Rd | 2 man/process_file.Rd | 6 - man/proj_root.Rd | 16 +- man/prose_index.Rd | 2 man/protect_math.Rd | 4 man/raw_string.Rd | 4 man/read_bin.Rd | 4 man/read_utf8.Rd | 4 man/relative_path.Rd | 3 man/rename_seq.Rd | 11 - man/rest_api.Rd | 21 +-- man/rev_check.Rd | 57 ++++----- man/same_path.Rd | 2 man/session_info.Rd | 4 man/set_envvar.Rd | 2 man/shrink_images.Rd | 6 - man/split_lines.Rd | 11 - man/split_source.Rd | 2 man/strict_list.Rd | 16 +- man/submit_cran.Rd | 4 man/system3.Rd | 2 man/tinify.Rd | 10 - man/tojson.Rd | 2 man/tree.Rd | 6 - man/try_error.Rd | 2 man/upload_ftp.Rd | 4 man/url_accessible.Rd | 2 man/url_filename.Rd | 9 + man/valid_syntax.Rd | 2 man/yaml_body.Rd |only man/yaml_load.Rd |only tests/test-cran/test-string.R | 4 98 files changed, 1104 insertions(+), 1006 deletions(-)
Title: Time Series Analysis with State Space Model
Description: Functions for statistical analysis, modeling and simulation of time
series with state space model, based on the methodology in Kitagawa
(2020, ISBN: 978-0-367-18733-0).
Author: The Institute of Statistical Mathematics, based on the program by
Genshiro Kitagawa
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>
Diff between TSSS versions 1.3.1 dated 2021-01-06 and 1.3.4 dated 2023-03-24
TSSS-1.3.1/TSSS/src/TSSS_f.h |only TSSS-1.3.1/TSSS/src/arfit.c |only TSSS-1.3.1/TSSS/src/arma.c |only TSSS-1.3.1/TSSS/src/armaft.c |only TSSS-1.3.1/TSSS/src/armaft2.c |only TSSS-1.3.1/TSSS/src/arsp.c |only TSSS-1.3.1/TSSS/src/boxcox.c |only TSSS-1.3.1/TSSS/src/crscor.c |only TSSS-1.3.1/TSSS/src/densty.c |only TSSS-1.3.1/TSSS/src/fftper.c |only TSSS-1.3.1/TSSS/src/klinfo.c |only TSSS-1.3.1/TSSS/src/lsar1.c |only TSSS-1.3.1/TSSS/src/lsar2.c |only TSSS-1.3.1/TSSS/src/lsqr.c |only TSSS-1.3.1/TSSS/src/marfit.c |only TSSS-1.3.1/TSSS/src/marlsq.c |only TSSS-1.3.1/TSSS/src/marspc.c |only TSSS-1.3.1/TSSS/src/ngsim.c |only TSSS-1.3.1/TSSS/src/ngsmth.c |only TSSS-1.3.1/TSSS/src/particle_smoother.c |only TSSS-1.3.1/TSSS/src/particle_smoother_nonlinear.c |only TSSS-1.3.1/TSSS/src/period.c |only TSSS-1.3.1/TSSS/src/polreg.c |only TSSS-1.3.1/TSSS/src/season.c |only TSSS-1.3.1/TSSS/src/simssm.c |only TSSS-1.3.1/TSSS/src/smooth.c |only TSSS-1.3.1/TSSS/src/trend.c |only TSSS-1.3.1/TSSS/src/tvar.c |only TSSS-1.3.1/TSSS/src/tvspc.c |only TSSS-1.3.1/TSSS/src/tvvar.c |only TSSS-1.3.1/TSSS/src/unicor.c |only TSSS-1.3.4/TSSS/DESCRIPTION | 8 TSSS-1.3.4/TSSS/MD5 | 196 +++++-------- TSSS-1.3.4/TSSS/NAMESPACE | 44 +-- TSSS-1.3.4/TSSS/NEWS.md |only TSSS-1.3.4/TSSS/R/arfit.R | 53 ++- TSSS-1.3.4/TSSS/R/armachar.R | 78 +++-- TSSS-1.3.4/TSSS/R/armafit.R | 97 ++++-- TSSS-1.3.4/TSSS/R/boxcox.R | 26 - TSSS-1.3.4/TSSS/R/crscor.R | 27 - TSSS-1.3.4/TSSS/R/klinfo.R | 24 - TSSS-1.3.4/TSSS/R/lsar.R | 160 ++++++----- TSSS-1.3.4/TSSS/R/lsqr.R | 33 +- TSSS-1.3.4/TSSS/R/marfit.R | 47 +-- TSSS-1.3.4/TSSS/R/marspc.R | 23 + TSSS-1.3.4/TSSS/R/ngsmth.R | 46 +-- TSSS-1.3.4/TSSS/R/pdfunc.R | 15 - TSSS-1.3.4/TSSS/R/period.R | 59 ++-- TSSS-1.3.4/TSSS/R/pfilter.R | 50 +-- TSSS-1.3.4/TSSS/R/polreg.R | 25 - TSSS-1.3.4/TSSS/R/season.R | 300 ++++++++++++--------- TSSS-1.3.4/TSSS/R/simulate.R | 74 ++--- TSSS-1.3.4/TSSS/R/trend.R | 71 +++- TSSS-1.3.4/TSSS/R/tsmooth.R | 35 +- TSSS-1.3.4/TSSS/R/tvvar.R | 94 +++--- TSSS-1.3.4/TSSS/R/unicor.R | 19 - TSSS-1.3.4/TSSS/data/BLSALLFOOD.rda |binary TSSS-1.3.4/TSSS/data/HAKUSAN.rda |binary TSSS-1.3.4/TSSS/data/Haibara.rda |binary TSSS-1.3.4/TSSS/data/MYE1F.rda |binary TSSS-1.3.4/TSSS/data/NLmodel.rda |binary TSSS-1.3.4/TSSS/data/Nikkei225.rda |binary TSSS-1.3.4/TSSS/data/PfilterSample.rda |binary TSSS-1.3.4/TSSS/data/Rainfall.rda |binary TSSS-1.3.4/TSSS/data/Sunspot.rda |binary TSSS-1.3.4/TSSS/data/Temperature.rda |binary TSSS-1.3.4/TSSS/data/WHARD.rda |binary TSSS-1.3.4/TSSS/man/HAKUSAN.Rd | 30 ++ TSSS-1.3.4/TSSS/man/Haibara.Rd | 29 ++ TSSS-1.3.4/TSSS/man/Rainfall.Rd | 2 TSSS-1.3.4/TSSS/man/TSSS-package.Rd | 12 TSSS-1.3.4/TSSS/man/Temperature.Rd | 2 TSSS-1.3.4/TSSS/man/boxcox.Rd | 2 TSSS-1.3.4/TSSS/man/crscor.Rd | 2 TSSS-1.3.4/TSSS/man/klinfo.Rd | 2 TSSS-1.3.4/TSSS/man/lsqr.Rd | 3 TSSS-1.3.4/TSSS/man/ngsmth.Rd | 7 TSSS-1.3.4/TSSS/man/pfilter.Rd | 2 TSSS-1.3.4/TSSS/man/pfilterNL.Rd | 4 TSSS-1.3.4/TSSS/man/season.Rd | 13 TSSS-1.3.4/TSSS/man/simssm.Rd | 2 TSSS-1.3.4/TSSS/man/trend.Rd | 1 TSSS-1.3.4/TSSS/src/TSSS-win.def |only TSSS-1.3.4/TSSS/src/TSSS.h | 41 +- TSSS-1.3.4/TSSS/src/arfitf.f | 25 - TSSS-1.3.4/TSSS/src/armaf.f | 32 +- TSSS-1.3.4/TSSS/src/armafit2f.f | 83 ++++- TSSS-1.3.4/TSSS/src/armaftf.f | 125 +++++--- TSSS-1.3.4/TSSS/src/boxcoxf.f | 26 - TSSS-1.3.4/TSSS/src/comsub.f | 221 ++++++--------- TSSS-1.3.4/TSSS/src/crscorf.f | 10 TSSS-1.3.4/TSSS/src/denstyf.f | 28 + TSSS-1.3.4/TSSS/src/fftperf.f | 44 +-- TSSS-1.3.4/TSSS/src/init.c | 127 ++++---- TSSS-1.3.4/TSSS/src/klinfof.f | 24 - TSSS-1.3.4/TSSS/src/lsar1f.f | 53 ++- TSSS-1.3.4/TSSS/src/lsar2f.f | 32 +- TSSS-1.3.4/TSSS/src/lsqrf.f | 98 +++++- TSSS-1.3.4/TSSS/src/marfitf.f | 34 +- TSSS-1.3.4/TSSS/src/marlsqf.f | 62 ++-- TSSS-1.3.4/TSSS/src/marspcf.f | 40 +- TSSS-1.3.4/TSSS/src/ngsimf.f | 66 ++-- TSSS-1.3.4/TSSS/src/ngsmthf.f | 152 +++++----- TSSS-1.3.4/TSSS/src/particle_smoother_nonlinearf.f | 25 + TSSS-1.3.4/TSSS/src/particle_smootherf.f | 56 ++- TSSS-1.3.4/TSSS/src/periodf.f | 21 - TSSS-1.3.4/TSSS/src/polregf.f | 65 +++- TSSS-1.3.4/TSSS/src/regF77.h |only TSSS-1.3.4/TSSS/src/seasonf.f | 177 +++++++----- TSSS-1.3.4/TSSS/src/simssmf.f | 33 +- TSSS-1.3.4/TSSS/src/smoothf.f | 33 +- TSSS-1.3.4/TSSS/src/trendf.f | 25 - TSSS-1.3.4/TSSS/src/tvarf.f | 54 +-- TSSS-1.3.4/TSSS/src/tvspcf.f | 17 - TSSS-1.3.4/TSSS/src/tvvarf.f | 51 +-- TSSS-1.3.4/TSSS/src/unicorf.f | 6 116 files changed, 2072 insertions(+), 1531 deletions(-)
Title: Statistical Modelling in Action with R
Description: Datasets and functions for the book "Modélisation statistique par la pratique avec R", F. Bertrand, E. Claeys and M. Maumy-Bertrand (2019, ISBN:9782100793525, Dunod, Paris). The first chapter of the book is dedicated to an introduction to the R statistical software. The second chapter deals with correlation analysis: Pearson, Spearman and Kendall simple, multiple and partial correlation coefficients. New wrapper functions for permutation tests or bootstrap of matrices of correlation are provided with the package. The third chapter is dedicated to data exploration with factorial analyses (PCA, CA, MCA, MDA) and clustering. The fourth chapter is dedicated to regression analysis: fitting and model diagnostics are detailed. The exercises focus on covariance analysis, logistic regression, Poisson regression, two-way analysis of variance for fixed or random factors. Various example datasets are shipped with the package: for instance on pokemon, world of warcraft, house tasks or food nutritio [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Emmanuelle Claeys [aut],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between ModStatR versions 1.3.2 dated 2022-11-28 and 1.3.3 dated 2023-03-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/CITATION | 17 +++++++++-------- 3 files changed, 15 insertions(+), 14 deletions(-)
Title: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry
Data)
Description: A tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>.
Author: Sadjad Fakouri-Baygi [aut] ,
Dinesh Barupal [cre, aut]
Maintainer: Dinesh Barupal <dinesh.barupal@mssm.edu>
Diff between IDSL.MXP versions 1.9 dated 2023-02-01 and 2.0 dated 2023-03-24
DESCRIPTION | 17 ++++++++--------- MD5 | 2 +- 2 files changed, 9 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-09 0.12.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-22 1.0.2
2021-05-11 1.0.1