Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling
techniques or better understand data generating processes. The user
specifies a set of relationships between covariates, and generates
data based on these specifications. The final data sets can represent
data from randomized control trials, repeated measure (longitudinal)
designs, and cluster randomized trials. Missingness can be generated
using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre] (<https://orcid.org/0000-0002-0292-8780>),
Jacob Wujciak-Jens [aut] (<https://orcid.org/0000-0002-7281-3989>)
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>
Diff between simstudy versions 0.2.0 dated 2020-10-06 and 0.2.1 dated 2020-10-07
DESCRIPTION | 12 - MD5 | 13 + NEWS.md | 15 -- R/asserts.R | 6 R/zzz.R |only README.md | 24 +-- inst/doc/clustered.html | 40 ++--- inst/doc/correlated.html | 328 +++++++++++++++++++++++------------------------ 8 files changed, 218 insertions(+), 220 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between RaceID versions 0.2.1 dated 2020-08-10 and 0.2.2 dated 2020-10-07
RaceID-0.2.1/RaceID/data/datalist |only RaceID-0.2.2/RaceID/DESCRIPTION | 18 +- RaceID-0.2.2/RaceID/MD5 | 40 ++--- RaceID-0.2.2/RaceID/NAMESPACE | 1 RaceID-0.2.2/RaceID/R/RcppExports.R | 8 + RaceID-0.2.2/RaceID/R/VarID_functions.R | 142 +++++++++++---------- RaceID-0.2.2/RaceID/R/intestinalData.R | 2 RaceID-0.2.2/RaceID/R/intestinalDataSmall.R | 2 RaceID-0.2.2/RaceID/build/vignette.rds |binary RaceID-0.2.2/RaceID/data/intestinalData.RData |binary RaceID-0.2.2/RaceID/data/intestinalDataSmall.RData |binary RaceID-0.2.2/RaceID/inst/doc/RaceID.R | 4 RaceID-0.2.2/RaceID/inst/doc/RaceID.Rmd | 4 RaceID-0.2.2/RaceID/inst/doc/RaceID.html | 96 +++++++------- RaceID-0.2.2/RaceID/man/compMean.Rd |only RaceID-0.2.2/RaceID/man/compNoise.Rd | 4 RaceID-0.2.2/RaceID/man/intestinalData.Rd | 6 RaceID-0.2.2/RaceID/man/intestinalDataSmall.Rd | 6 RaceID-0.2.2/RaceID/man/maxNoisyGenes.Rd | 2 RaceID-0.2.2/RaceID/src/RcppExports.cpp | 30 ++++ RaceID-0.2.2/RaceID/src/VarID.cpp | 32 ++++ RaceID-0.2.2/RaceID/vignettes/RaceID.Rmd | 4 22 files changed, 243 insertions(+), 158 deletions(-)
Title: Permutation Testing Network Module Preservation Across Datasets
Description: Functions for assessing the replication/preservation of a network
module's topology across datasets through permutation testing; Ritchie et al.
(2015) <doi: 10.1016/j.cels.2016.06.012>.
Author: Scott Ritchie [aut, cre]
Maintainer: Scott Ritchie <sritchie73@gmail.com>
Diff between NetRep versions 1.2.1 dated 2018-06-12 and 1.2.4 dated 2020-10-07
NetRep-1.2.1/NetRep/R/example-data.R |only NetRep-1.2.1/NetRep/README.md |only NetRep-1.2.4/NetRep/ChangeLog | 26 NetRep-1.2.4/NetRep/DESCRIPTION | 16 NetRep-1.2.4/NetRep/MD5 | 66 NetRep-1.2.4/NetRep/R/RcppExports.R | 70 NetRep-1.2.4/NetRep/R/disk-matrix-class.R | 2 NetRep-1.2.4/NetRep/R/multi-machine.R | 4 NetRep-1.2.4/NetRep/build/vignette.rds |binary NetRep-1.2.4/NetRep/inst/doc/NetRep.R | 590 +- NetRep-1.2.4/NetRep/inst/doc/NetRep.html | 2299 +++++----- NetRep-1.2.4/NetRep/man/NetRep.Rd | 1 NetRep-1.2.4/NetRep/man/example-data.Rd | 64 NetRep-1.2.4/NetRep/man/modulePreservation.Rd | 22 NetRep-1.2.4/NetRep/man/networkProperties.Rd | 15 NetRep-1.2.4/NetRep/man/nodeOrder.Rd | 19 NetRep-1.2.4/NetRep/man/permutationTest.Rd | 9 NetRep-1.2.4/NetRep/man/plotModule.Rd | 61 NetRep-1.2.4/NetRep/man/plotTopology.Rd | 279 - NetRep-1.2.4/NetRep/man/sampleOrder.Rd | 16 NetRep-1.2.4/NetRep/src/NetRep_types.h | 1 NetRep-1.2.4/NetRep/src/checkFinite.cpp | 1 NetRep-1.2.4/NetRep/src/netStats.h | 1 NetRep-1.2.4/NetRep/src/scale.h | 1 NetRep-1.2.4/NetRep/src/thread-utils.cpp | 1 NetRep-1.2.4/NetRep/src/utils.h | 1 NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/correlation_heatmap-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/disk_matrix_dry_run-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/disk_matrix_plot-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/dry_run-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/dry_run_customised-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/mean_degree-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/mean_degree_customised-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/modules_in_discovery-1.jpeg |binary NetRep-1.2.4/NetRep/vignettes/NetRep_files/figure-html/modules_in_test-1.jpeg |binary 35 files changed, 2087 insertions(+), 1478 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' with support for SSH and
HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors
and data-frames) for their arguments and return values. User credentials are
shared with command line 'git' through the git-credential store and ssh keys
stored on disk or ssh-agent. On Linux, a somewhat recent version of 'libgit2'
is required; we provide a 'PPA' for older Ubuntu 'LTS' versions.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Jennifer Bryan [ctb] (<https://orcid.org/0000-0002-6983-2759>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 0.3 dated 2019-10-29 and 1.0.0 dated 2020-10-07
gert-0.3/gert/man/branch.Rd |only gert-0.3/gert/man/commit.Rd |only gert-0.3/gert/man/fetch.Rd |only gert-0.3/gert/man/git_checkout_pull_request.Rd |only gert-0.3/gert/man/remotes.Rd |only gert-0.3/gert/man/repository.Rd |only gert-0.3/gert/man/signature.Rd |only gert-0.3/gert/man/stash.Rd |only gert-0.3/gert/man/tag.Rd |only gert-1.0.0/gert/DESCRIPTION | 49 +++-- gert-1.0.0/gert/MD5 | 108 ++++++----- gert-1.0.0/gert/NAMESPACE | 61 +++++- gert-1.0.0/gert/NEWS | 11 + gert-1.0.0/gert/R/archive.R |only gert-1.0.0/gert/R/branch.R | 91 ++++++--- gert-1.0.0/gert/R/commit.R | 171 ++++++++++++----- gert-1.0.0/gert/R/config.R | 149 +++++++++++++-- gert-1.0.0/gert/R/diff.R |only gert-1.0.0/gert/R/errors.R |only gert-1.0.0/gert/R/fetch.R | 158 ++++++++++++---- gert-1.0.0/gert/R/init.R | 73 ++++++- gert-1.0.0/gert/R/merge.R |only gert-1.0.0/gert/R/open.R |only gert-1.0.0/gert/R/pr.R | 45 +++- gert-1.0.0/gert/R/rebase.R |only gert-1.0.0/gert/R/remotes.R | 93 +++++++-- gert-1.0.0/gert/R/repository.R | 83 ++++---- gert-1.0.0/gert/R/signature.R | 77 ++++++- gert-1.0.0/gert/R/stash.R | 13 - gert-1.0.0/gert/R/tag.R | 13 - gert-1.0.0/gert/build |only gert-1.0.0/gert/cleanup |only gert-1.0.0/gert/configure | 16 - gert-1.0.0/gert/inst |only gert-1.0.0/gert/man/git_archive.Rd |only gert-1.0.0/gert/man/git_branch.Rd |only gert-1.0.0/gert/man/git_commit.Rd |only gert-1.0.0/gert/man/git_config.Rd | 78 ++++++- gert-1.0.0/gert/man/git_diff.Rd |only gert-1.0.0/gert/man/git_fetch.Rd |only gert-1.0.0/gert/man/git_merge.Rd |only gert-1.0.0/gert/man/git_open.Rd |only gert-1.0.0/gert/man/git_rebase.Rd |only gert-1.0.0/gert/man/git_remote.Rd |only gert-1.0.0/gert/man/git_repo.Rd |only gert-1.0.0/gert/man/git_signature.Rd |only gert-1.0.0/gert/man/git_stash.Rd |only gert-1.0.0/gert/man/git_tag.Rd |only gert-1.0.0/gert/man/github.Rd |only gert-1.0.0/gert/man/libgit2_config.Rd |only gert-1.0.0/gert/man/user_is_configured.Rd |only gert-1.0.0/gert/src/Makevars.in | 2 gert-1.0.0/gert/src/Makevars.win | 6 gert-1.0.0/gert/src/branch.c | 175 ++++++++++++++--- gert-1.0.0/gert/src/clone.c | 93 ++++++++- gert-1.0.0/gert/src/commit.c | 244 +++++++++++++++++++------ gert-1.0.0/gert/src/conflicts.c |only gert-1.0.0/gert/src/files.c | 24 +- gert-1.0.0/gert/src/init.c | 79 ++++++-- gert-1.0.0/gert/src/merge.c | 147 +++++++++++---- gert-1.0.0/gert/src/rebase.c |only gert-1.0.0/gert/src/tag.c | 5 gert-1.0.0/gert/src/utils.c | 75 +++++++ gert-1.0.0/gert/src/utils.h | 10 + gert-1.0.0/gert/src/version.c | 30 ++- gert-1.0.0/gert/tests/spelling.R |only gert-1.0.0/gert/tests/testthat/test-auth.R | 27 ++ gert-1.0.0/gert/tests/testthat/test-clone.R | 10 - gert-1.0.0/gert/tests/testthat/test-commit.R | 131 ++++++++++--- gert-1.0.0/gert/tests/testthat/test-config.R |only gert-1.0.0/gert/tests/testthat/test-merge.R |only gert-1.0.0/gert/tests/testthat/test-open.R |only gert-1.0.0/gert/tests/testthat/test-rebase.R |only gert-1.0.0/gert/tests/testthat/test-remotes.R |only gert-1.0.0/gert/vignettes |only 75 files changed, 1823 insertions(+), 524 deletions(-)
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.1.2 dated 2020-09-29 and 0.1.3 dated 2020-10-07
DESCRIPTION | 6 - MD5 | 36 +++---- NEWS.md | 12 ++ R/pop_data.R | 2 R/print.R | 8 - R/sort.R | 6 + R/table.R | 18 ++- R/table_bindings.R | 4 README.md | 20 +--- inst/doc/Tplyr.html | 163 ++++++++++++++++++++++++++++++----- inst/doc/desc.html | 102 +++++++++++++++++++++ inst/doc/options.html | 63 +++++++++++++ inst/doc/table.html | 62 ++++++++++++- tests/testthat/table_built_print.txt | 4 tests/testthat/table_built_str.txt | 3 tests/testthat/table_print.txt | 4 tests/testthat/table_str.txt | 3 tests/testthat/test-pop_data.R | 12 ++ tests/testthat/test-sort.R | 20 ++++ 19 files changed, 463 insertions(+), 85 deletions(-)
Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with
'mlr3', e.g. Grid Search, Random Search, or Simulated Annealing.
Various termination criteria can be set and combined. The class
'AutoTuner' provides a convenient way to perform nested resampling in
combination with 'mlr3'.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Daniel Schalk [aut] (<https://orcid.org/0000-0003-0950-1947>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.3.0 dated 2020-09-08 and 0.4.0 dated 2020-10-07
mlr3tuning-0.3.0/mlr3tuning/man/mlr_terminators.Rd |only mlr3tuning-0.3.0/mlr3tuning/man/trm.Rd |only mlr3tuning-0.3.0/mlr3tuning/man/trms.Rd |only mlr3tuning-0.4.0/mlr3tuning/DESCRIPTION | 12 - mlr3tuning-0.4.0/mlr3tuning/MD5 | 57 ++++---- mlr3tuning-0.4.0/mlr3tuning/NAMESPACE | 2 mlr3tuning-0.4.0/mlr3tuning/NEWS.md | 9 + mlr3tuning-0.4.0/mlr3tuning/R/ArchiveTuning.R | 8 - mlr3tuning-0.4.0/mlr3tuning/R/AutoTuner.R | 45 ++++-- mlr3tuning-0.4.0/mlr3tuning/R/TunerGenSA.R | 4 mlr3tuning-0.4.0/mlr3tuning/R/TunerNLoptr.R | 2 mlr3tuning-0.4.0/mlr3tuning/R/TunerRandomSearch.R | 2 mlr3tuning-0.4.0/mlr3tuning/R/TuningInstanceMulticrit.R | 2 mlr3tuning-0.4.0/mlr3tuning/R/TuningInstanceSingleCrit.R | 2 mlr3tuning-0.4.0/mlr3tuning/R/bibentries.R |only mlr3tuning-0.4.0/mlr3tuning/R/reexport.R | 25 --- mlr3tuning-0.4.0/mlr3tuning/README.md | 5 mlr3tuning-0.4.0/mlr3tuning/build/partial.rdb |binary mlr3tuning-0.4.0/mlr3tuning/man/ArchiveTuning.Rd | 2 mlr3tuning-0.4.0/mlr3tuning/man/AutoTuner.Rd | 39 ++++-- mlr3tuning-0.4.0/mlr3tuning/man/ObjectiveTuning.Rd | 2 mlr3tuning-0.4.0/mlr3tuning/man/TuningInstanceMultiCrit.Rd | 2 mlr3tuning-0.4.0/mlr3tuning/man/TuningInstanceSingleCrit.Rd | 2 mlr3tuning-0.4.0/mlr3tuning/man/mlr_tuners_gensa.Rd | 11 + mlr3tuning-0.4.0/mlr3tuning/man/mlr_tuners_nloptr.Rd | 4 mlr3tuning-0.4.0/mlr3tuning/man/mlr_tuners_random_search.Rd | 5 mlr3tuning-0.4.0/mlr3tuning/man/reexports.Rd |only mlr3tuning-0.4.0/mlr3tuning/tests/testthat/helper.R | 10 - mlr3tuning-0.4.0/mlr3tuning/tests/testthat/test_AutoTuner.R | 65 +++++++++- mlr3tuning-0.4.0/mlr3tuning/tests/testthat/test_Tuner.R | 4 mlr3tuning-0.4.0/mlr3tuning/tests/testthat/test_TuningInstanceMultiCrit.R | 23 ++- mlr3tuning-0.4.0/mlr3tuning/tests/testthat/test_TuningInstanceSingleCrit.R | 20 ++- 32 files changed, 242 insertions(+), 122 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre],
Benjamin Hugh Zachariae [aut]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.0.2 dated 2020-05-28 and 1.1.0 dated 2020-10-07
DESCRIPTION | 22 MD5 | 177 ++-- NAMESPACE | 10 NEWS.md | 25 R/baseline.R | 108 +- R/baseline_binomial.R | 1 R/baseline_gaussian.R | 3 R/baseline_multinomial.R | 4 R/baseline_wrappers.R | 135 +-- R/choosing_metrics_functions.R | 6 R/combine_predictors.R | 6 R/confusion_matrix.R | 51 - R/cross_validate.R | 33 R/cross_validate_fn.R | 91 +- R/data_documentation.R | 16 R/evaluate.R | 102 +- R/evaluate_predictions_binomial.R | 37 R/evaluate_predictions_gaussian.R | 10 R/evaluate_predictions_multinomial.R | 63 + R/evaluate_residuals.R | 24 R/extract_probabilities_of.R |only R/get_nested_model_coefficients.R | 2 R/helpers.R | 43 + R/most_challenging.R | 22 R/multiclass_probability_tibble.R | 8 R/package_info.R | 2 R/plot_confusion_matrix.R | 25 R/plot_metric_density.R | 14 R/plot_probabilities.R |only R/plot_probabilities_ecdf.R |only R/preprocess_functions.R | 4 R/process_info.R |only R/reconstruct_formulas.R | 6 R/select_definitions.R | 6 R/select_metrics.R | 8 R/set_info_cols.R | 11 R/set_metrics.R | 20 R/simplify_formula.R | 2 R/summarize_metrics.R | 4 R/update_hyperparameters.R | 8 R/validate.R | 28 R/validate_fn.R | 38 R/validate_list.R | 1 README.md | 262 +++--- build/cvms.pdf |binary inst/doc/available_metrics.html | 13 inst/doc/creating_a_confusion_matrix.html | 104 ++ inst/doc/cross_validating_custom_functions.html | 168 +++- inst/doc/evaluate_by_id.html | 167 +++- man/baseline.Rd | 106 +- man/baseline_binomial.Rd | 35 man/baseline_gaussian.Rd | 51 - man/baseline_multinomial.Rd | 49 - man/binomial_metrics.Rd | 2 man/combine_predictors.Rd | 4 man/compatible.formula.terms.Rd | 4 man/confusion_matrix.Rd | 45 - man/cross_validate.Rd | 33 man/cross_validate_fn.Rd | 95 +- man/cvms.Rd | 2 man/evaluate.Rd | 85 +- man/evaluate_residuals.Rd | 24 man/font.Rd | 4 man/gaussian_metrics.Rd | 2 man/most_challenging.Rd | 20 man/multiclass_probability_tibble.Rd | 8 man/multinomial_metrics.Rd | 2 man/musicians.Rd | 2 man/participant.scores.Rd | 2 man/plot_confusion_matrix.Rd | 23 man/plot_metric_density.Rd | 18 man/plot_probabilities.Rd |only man/plot_probabilities_ecdf.Rd |only man/precomputed.formulas.Rd | 2 man/predicted.musicians.Rd | 4 man/preprocess_functions.Rd | 4 man/process_info_binomial.Rd |only man/reconstruct_formulas.Rd | 6 man/select_definitions.Rd | 6 man/select_metrics.Rd | 8 man/simplify_formula.Rd | 2 man/summarize_metrics.Rd | 4 man/update_hyperparameters.Rd | 8 man/validate.Rd | 34 man/validate_fn.Rd | 92 +- man/wines.Rd | 2 tests/testthat/test_baseline.R | 451 +++++++++-- tests/testthat/test_cross_validate.R | 406 ++++------ tests/testthat/test_cross_validate_fn.R | 324 +++----- tests/testthat/test_evaluate.R | 942 ++++++++++++++++++++---- tests/testthat/test_plotting_functions.R | 36 tests/testthat/test_validate.R | 201 ++--- tests/testthat/test_validate_fn.R | 484 +++++------- 93 files changed, 3507 insertions(+), 2015 deletions(-)
Title: Multiple Heat Maps for Projected Coordinates
Description: Functions for displaying multiple images or scatterplots with a color
scale, i.e., heat maps, possibly with projected coordinates. The
package relies on the base graphics system, so graphics are
rendered rapidly.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between autoimage versions 2.1.12 dated 2020-07-20 and 2.2.1 dated 2020-10-07
DESCRIPTION | 16 MD5 | 160 +++---- NEWS | 4 R/auto_setup_functions_internal.R | 4 R/blank.plot.R | 40 - R/capoly.R | 52 +- R/copoly.R | 48 +- R/ggautoimage.R | 572 ++++++++++++++-------------- R/heat_ppoints.R | 8 R/legend.scale.R | 212 +++++----- R/narccap.R | 8 R/parrows.R | 98 ++-- R/ppoints.R | 74 +-- R/ppolygon.R | 164 ++++---- R/preamble.R | 14 R/psegments.R | 120 ++--- R/ptext.R | 200 ++++----- R/reset.par.R | 170 ++++---- R/rotate.R | 102 ++-- build/vignette.rds |binary inst/doc/autoimage.R | 5 inst/doc/autoimage.Rmd | 15 inst/doc/autoimage.html | 65 +-- inst/doc/autopoints.R | 2 inst/doc/autopoints.Rmd | 2 inst/doc/autopoints.html | 26 - inst/doc/ggplot2-comparison.R | 39 - inst/doc/ggplot2-comparison.Rmd | 69 +-- inst/doc/ggplot2-comparison.html | 139 +++--- man/autoimage.Rd | 464 +++++++++++----------- man/autolayout.Rd | 202 ++++----- man/autolegend.Rd | 196 ++++----- man/automar.Rd | 60 +- man/autopoints.Rd | 454 +++++++++++----------- man/autosize.Rd | 54 +- man/canada.Rd | 72 +-- man/copoly.Rd | 68 +-- man/ggautoimage.Rd | 264 ++++++------ man/heat_ppoints.Rd | 380 +++++++++--------- man/inarccap.Rd | 50 +- man/legend.scale.Rd | 172 ++++---- man/narccap.Rd | 106 ++--- man/parrows.Rd | 94 ++-- man/paxes.Rd | 138 +++--- man/pimage.Rd | 494 ++++++++++++------------ man/plines.Rd | 104 ++--- man/ppoints.Rd | 98 ++-- man/ppolygon.Rd | 94 ++-- man/psegments.Rd | 116 ++--- man/ptext.Rd | 130 +++--- man/reset.par.Rd | 46 +- man/rotate.Rd | 60 +- tests/test-all.R | 8 tests/testthat/test-MBA-interp.R | 56 +- tests/testthat/test-arg.check.autoimage.R | 44 +- tests/testthat/test-arg.check.autolayout.R | 104 ++--- tests/testthat/test-arg.check.ggautoimage.R | 120 ++--- tests/testthat/test-arg.check.paxes.R | 42 +- tests/testthat/test-arg.check.plines.R | 40 - tests/testthat/test-arg.check.ppolygon.R | 28 - tests/testthat/test-arg.check.ptext.R | 40 - tests/testthat/test-autoimage.R | 2 tests/testthat/test-autolayout.R | 90 ++-- tests/testthat/test-parrows.R | 56 +- tests/testthat/test-paxes.R | 28 - tests/testthat/test-pimage.R | 262 ++++++------ tests/testthat/test-pimage.xyz.setup.R | 84 ++-- tests/testthat/test-plines.R | 30 - tests/testthat/test-ppoints.R | 40 - tests/testthat/test-ppolygon.R | 30 - tests/testthat/test-psegments.R | 54 +- tests/testthat/test-ptext.R | 28 - tests/testthat/test-rotate.R | 58 +- tools/README/unnamed-chunk-2-1.png |binary tools/README/unnamed-chunk-2-2.png |binary tools/README/unnamed-chunk-3-1.png |binary tools/README/unnamed-chunk-4-1.png |binary tools/README/unnamed-chunk-5-1.png |binary vignettes/autoimage.Rmd | 15 vignettes/autopoints.Rmd | 2 vignettes/ggplot2-comparison.Rmd | 69 +-- 81 files changed, 3831 insertions(+), 3843 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.7-0 dated 2020-08-28 and 2.7-1 dated 2020-10-07
DESCRIPTION | 8 - MD5 | 18 +- NEWS | 8 + R/data-menu.R | 10 - R/statistics-means-menu.R | 8 - inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/pl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/pt_BR/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 4 po/R-pl.po | 269 +++++++++++++++++++++++++++++++++-- 10 files changed, 293 insertions(+), 32 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-13 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-15 3.5-0
2020-04-07 3.4-0
2020-01-29 3.3-3
2020-01-07 3.3-2
2019-12-11 3.3-1
2019-12-03 3.3-0
2019-11-01 3.2-0
2019-05-24 3.1-1
2019-04-25 3.0-0
2019-04-08 2.3-0
2019-02-22 2.2-0
2019-01-08 2.1-0
2018-12-07 2.0-0
2018-08-03 1.6-2
2018-06-28 1.6-1
2018-05-15 1.6-0
2018-04-27 1.5-3
2018-03-20 1.5-1
2018-01-25 1.5-0
2017-12-05 1.4-1
2017-10-30 1.4-0
2017-06-03 1.3-2
Title: Genome Interval Arithmetic
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R,
enabling interactive analysis and visualization of genome-scale data.
Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.
Author: Jay Hesselberth [aut, cre] (<https://orcid.org/0000-0002-6299-179X>),
Kent Riemondy [aut] (<https://orcid.org/0000-0003-0750-1273>),
RNA Bioscience Initiative [fnd]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between valr versions 0.6.1 dated 2020-05-08 and 0.6.2 dated 2020-10-07
DESCRIPTION | 21 + MD5 | 100 ++++----- NAMESPACE | 1 NEWS.md | 6 R/bed_absdist.r | 2 R/bed_closest.r | 2 R/bed_cluster.r | 2 R/bed_coverage.R | 2 R/bed_fisher.r | 2 R/bed_flank.r | 2 R/bed_intersect.r | 2 R/bed_jaccard.r | 2 R/bed_map.r | 2 R/bed_merge.r | 2 R/bed_projection.r | 2 R/bed_random.r | 4 R/bed_reldist.r | 2 R/bed_shift.r | 2 R/bed_shuffle.r | 4 R/bed_slop.r | 2 R/bed_sort.r | 2 R/bed_subtract.r | 2 R/bed_window.r | 2 R/db.r | 41 +++ R/valr-package.r | 1 README.md | 85 +++---- build/vignette.rds |binary inst/doc/valr.Rmd | 21 - inst/doc/valr.html | 536 ++++++++++++++++++++++++++++---------------------- man/bed_absdist.Rd | 2 man/bed_closest.Rd | 2 man/bed_cluster.Rd | 2 man/bed_coverage.Rd | 2 man/bed_fisher.Rd | 2 man/bed_flank.Rd | 2 man/bed_intersect.Rd | 2 man/bed_jaccard.Rd | 2 man/bed_map.Rd | 2 man/bed_merge.Rd | 2 man/bed_projection.Rd | 2 man/bed_random.Rd | 2 man/bed_reldist.Rd | 2 man/bed_shift.Rd | 2 man/bed_shuffle.Rd | 2 man/bed_slop.Rd | 2 man/bed_sort.Rd | 2 man/bed_subtract.Rd | 2 man/bed_window.Rd | 2 man/db.Rd | 7 man/read_bed.Rd | 4 vignettes/valr.Rmd | 21 - 51 files changed, 505 insertions(+), 419 deletions(-)
Title: Interface to the 'Pleiades' 'Archeological' Database
Description: Provides a set of functions for interacting with the
'Pleiades' (<https://pleiades.stoa.org/>) 'API', including
getting status data, places data, and creating a 'GeoJSON'
based map on 'GitHub' 'gists'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pleiades versions 0.2.0 dated 2017-06-15 and 0.3.0 dated 2020-10-07
pleiades-0.2.0/pleiades/inst/doc/pleiades_vignette.Rmd |only pleiades-0.2.0/pleiades/inst/doc/pleiades_vignette.html |only pleiades-0.2.0/pleiades/inst/vign |only pleiades-0.2.0/pleiades/man/pleiades.Rd |only pleiades-0.2.0/pleiades/vignettes/pleiades_vignette.Rmd |only pleiades-0.3.0/pleiades/DESCRIPTION | 19 pleiades-0.3.0/pleiades/LICENSE | 2 pleiades-0.3.0/pleiades/MD5 | 53 - pleiades-0.3.0/pleiades/NEWS.md | 10 pleiades-0.3.0/pleiades/R/pl_cache.R | 8 pleiades-0.3.0/pleiades/R/pl_gist.R | 17 pleiades-0.3.0/pleiades/R/pl_places.R | 2 pleiades-0.3.0/pleiades/R/pl_search.R | 8 pleiades-0.3.0/pleiades/R/pl_status.R | 2 pleiades-0.3.0/pleiades/R/pleiades-package.r | 6 pleiades-0.3.0/pleiades/README.md | 432 --------------- pleiades-0.3.0/pleiades/build/vignette.rds |binary pleiades-0.3.0/pleiades/inst/doc/pleiades.Rmd |only pleiades-0.3.0/pleiades/inst/doc/pleiades.html |only pleiades-0.3.0/pleiades/man/pl_cache.Rd | 2 pleiades-0.3.0/pleiades/man/pl_gist.Rd | 17 pleiades-0.3.0/pleiades/man/pl_places.Rd | 2 pleiades-0.3.0/pleiades/man/pl_search.Rd | 4 pleiades-0.3.0/pleiades/man/pl_status.Rd | 2 pleiades-0.3.0/pleiades/man/pleiades-package.Rd |only pleiades-0.3.0/pleiades/tests/fixtures |only pleiades-0.3.0/pleiades/tests/testthat/helper-pleiades.R |only pleiades-0.3.0/pleiades/tests/testthat/test-pl_places.R | 4 pleiades-0.3.0/pleiades/tests/testthat/test-pl_search.R | 10 pleiades-0.3.0/pleiades/tests/testthat/test-pl_status.R | 4 pleiades-0.3.0/pleiades/vignettes/pleiades.Rmd |only pleiades-0.3.0/pleiades/vignettes/pleiades.Rmd.og |only 32 files changed, 103 insertions(+), 501 deletions(-)
Title: Parse Messy Geographic Coordinates
Description: Parse geographic coordinates from various formats
to decimal degree numeric values. Parse coordinates into
their parts (degree, minutes, seconds); calculate hemisphere
from coordinates; pull out individually degrees,
minutes, or seconds; add and subtract degrees, minutes,
and seconds. C++ code herein originally inspired from code
written by Jeffrey D. Bogan, but then completely re-written.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Alban Sagouis [ctb],
Jeffrey Bogan [ctb] (C++ code originally from Jeffrey Bogan, but
completely re-written),
Julien Brun [rev] (Julien Brun reviewed the package, see
https://github.com/ropensci/onboarding/issues/341),
Maria Munafó [rev] (Maria Munafó reviewed the package, see
https://github.com/ropensci/onboarding/issues/341),
rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between parzer versions 0.1.4 dated 2020-03-29 and 0.2.0 dated 2020-10-07
DESCRIPTION | 15 +-- MD5 | 31 +++--- NAMESPACE | 1 NEWS.md | 12 ++ R/RcppExports.R | 8 + R/parse_llstr.R |only R/parse_lon.R | 5 - R/parzer-package.R | 2 R/zzz.R | 16 ++- README.md | 177 +------------------------------------- build/vignette.rds |binary inst/doc/parzer.html | 11 ++ man/parse_llstr.Rd |only man/parzer-package.Rd | 2 src/RcppExports.cpp | 24 +++++ src/pz_split_llstr.cpp |only tests/testthat/test-parse_llstr.R |only tests/testthat/test-split_llstr.R |only tests/testthat/test-utils.R | 9 + 19 files changed, 112 insertions(+), 201 deletions(-)
Title: Dynamic Network Communities Detection and Generation
Description: Used for evolving network analysis regarding
community detection. Implements several algorithms that calculate communities
for graphs whose nodes and edges change over time.
Edges, which can have new nodes, can be added or deleted. Changes in the
communities are calculated without recalculating communities for the entire
graph.
REFERENCE: M. Cordeiro et al. (2016) <DOI:10.1007/s13278-016-0325-1>
G. Rossetti et al. (2017) <DOI:10.1007/s10994-016-5582-8>
G. Rossetti (2017) <DOI:10.1093/comnet/cnx016>
R. Sarmento (2019) <arXiv:1904.12593>.
Author: Rui P. Sarmento [aut, cre] (<https://orcid.org/0000-0003-1891-5295>),
Luís Lemos [aut],
Mário Cordeiro [ctb],
Giulio Rossetti [ctb]
Maintainer: Rui P. Sarmento <email@ruisarmento.com>
Diff between DynComm versions 2020.1.5 dated 2020-09-28 and 2020.1.6 dated 2020-10-07
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- build/partial.rdb |binary src/base/Cpp/algorithms/algorithmLouvain.h | 4 +- src/base/Cpp/framework/debug/debuggingInternals.h | 4 +- src/base/Cpp/framework/graph/graphUndirectedGroupable.h | 12 ++++---- src/base/Cpp/framework/time/timeFunctions.h | 24 +++++++++++----- 7 files changed, 36 insertions(+), 26 deletions(-)
Title: Lightweight and Feature Complete Unit Testing Framework
Description: Provides a lightweight (zero-dependency) and easy to use
unit testing framework. Main features: install tests with
the package. Test results are treated as data that can be stored and
manipulated. Test files are R scripts interspersed with test commands, that
can be programmed over. Fully automated build-install-test sequence for
packages. Skip tests when not run locally (e.g. on CRAN). Flexible and
configurable output printing. Compare computed output with output stored
with the package. Run tests in parallel. Extensible by other packages.
Report side effects.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>)
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between tinytest versions 1.2.2 dated 2020-06-18 and 1.2.3 dated 2020-10-07
DESCRIPTION | 8 +++--- MD5 | 28 +++++++++++++----------- NEWS | 9 +++++++ R/expectations.R | 4 ++- R/tinytest.R | 21 ++++++++++++++++++ build/vignette.rds |binary inst/doc/tinytest_examples.Rnw | 2 - inst/doc/tinytest_examples.pdf |binary inst/doc/using_tinytest.R | 38 +++++++++++++++++++-------------- inst/doc/using_tinytest.Rnw | 38 ++++++++++++++++++++++++++++++--- inst/doc/using_tinytest.pdf |binary inst/tinytest/runs/test_double_colon.R |only inst/tinytest/test_file.R | 7 ++++++ inst/tinytest/test_gh_issue_58.R |only vignettes/tinytest_examples.Rnw | 2 - vignettes/using_tinytest.Rnw | 38 ++++++++++++++++++++++++++++++--- 16 files changed, 153 insertions(+), 42 deletions(-)
Title: US Maps Including Alaska and Hawaii
Description: Obtain United States map data frames of varying region types (e.g. county,
state). The map data frames include Alaska and Hawaii conveniently placed to the
bottom left, as they appear in most maps of the US. Convenience functions for plotting
choropleths and working with FIPS codes are also provided.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.pl>
Diff between usmap versions 0.5.0 dated 2019-09-12 and 0.5.1 dated 2020-10-07
usmap-0.5.0/usmap/man/getFipsInfo.Rd |only usmap-0.5.1/usmap/DESCRIPTION | 16 - usmap-0.5.1/usmap/MD5 | 102 +++--- usmap-0.5.1/usmap/NEWS.md | 18 + usmap-0.5.1/usmap/R/datasets.R | 2 usmap-0.5.1/usmap/R/fips.R | 26 + usmap-0.5.1/usmap/R/plot-map.R | 15 usmap-0.5.1/usmap/R/transform.R | 4 usmap-0.5.1/usmap/R/usmap.R | 16 - usmap-0.5.1/usmap/README.md | 82 +---- usmap-0.5.1/usmap/build/vignette.rds |binary usmap-0.5.1/usmap/inst/doc/advanced-mapping.R | 4 usmap-0.5.1/usmap/inst/doc/advanced-mapping.Rmd | 4 usmap-0.5.1/usmap/inst/doc/advanced-mapping.html | 221 ++++++++++---- usmap-0.5.1/usmap/inst/doc/introduction.R | 14 usmap-0.5.1/usmap/inst/doc/introduction.Rmd | 6 usmap-0.5.1/usmap/inst/doc/introduction.html | 193 +++++++++--- usmap-0.5.1/usmap/inst/doc/mapping.R | 30 - usmap-0.5.1/usmap/inst/doc/mapping.Rmd | 6 usmap-0.5.1/usmap/inst/doc/mapping.html | 339 +++++++++++++--------- usmap-0.5.1/usmap/man/citypop.Rd | 4 usmap-0.5.1/usmap/man/countypop.Rd | 4 usmap-0.5.1/usmap/man/countypov.Rd | 4 usmap-0.5.1/usmap/man/dot-east_north_central.Rd | 4 usmap-0.5.1/usmap/man/dot-east_south_central.Rd | 4 usmap-0.5.1/usmap/man/dot-mid_atlantic.Rd | 4 usmap-0.5.1/usmap/man/dot-midwest_region.Rd | 4 usmap-0.5.1/usmap/man/dot-mountain.Rd | 4 usmap-0.5.1/usmap/man/dot-new_england.Rd | 4 usmap-0.5.1/usmap/man/dot-north_central_region.Rd | 4 usmap-0.5.1/usmap/man/dot-northeast_region.Rd | 4 usmap-0.5.1/usmap/man/dot-pacific.Rd | 4 usmap-0.5.1/usmap/man/dot-south_atlantic.Rd | 4 usmap-0.5.1/usmap/man/dot-south_region.Rd | 4 usmap-0.5.1/usmap/man/dot-west_north_central.Rd | 4 usmap-0.5.1/usmap/man/dot-west_region.Rd | 4 usmap-0.5.1/usmap/man/dot-west_south_central.Rd | 4 usmap-0.5.1/usmap/man/earthquakes.Rd | 6 usmap-0.5.1/usmap/man/fips.Rd | 6 usmap-0.5.1/usmap/man/fips_info.Rd | 3 usmap-0.5.1/usmap/man/get_fips_info.Rd |only usmap-0.5.1/usmap/man/map_with_data.Rd | 3 usmap-0.5.1/usmap/man/plot_usmap.Rd | 15 usmap-0.5.1/usmap/man/statepop.Rd | 4 usmap-0.5.1/usmap/man/statepov.Rd | 4 usmap-0.5.1/usmap/man/us_map.Rd | 7 usmap-0.5.1/usmap/man/usmap.Rd | 11 usmap-0.5.1/usmap/tests/testthat/test-fips-info.R | 4 usmap-0.5.1/usmap/tests/testthat/test-fips.R | 11 usmap-0.5.1/usmap/tests/testthat/test-plot.R | 63 ++-- usmap-0.5.1/usmap/vignettes/advanced-mapping.Rmd | 4 usmap-0.5.1/usmap/vignettes/introduction.Rmd | 6 usmap-0.5.1/usmap/vignettes/mapping.Rmd | 6 53 files changed, 828 insertions(+), 491 deletions(-)
Title: Summarize Data for Scientific Publication
Description: Create and format tables and APA statistics for
scientific publication. This includes making a 'Table 1'
to summarize demographics across groups, correlation tables
with significance indicated by stars, and extracting formatted
statistical summarizes from simple tests for in-text notation.
The package also includes functions for Winsorizing data based
on a Z-statistic cutoff.
Author: David Pagliaccio [aut, cre] (<https://orcid.org/0000-0002-1214-1965>)
Maintainer: David Pagliaccio <david.pagliaccio@gmail.com>
Diff between scipub versions 1.2.0 dated 2020-09-22 and 1.2.1 dated 2020-10-07
DESCRIPTION | 6 +- MD5 | 16 +++---- NEWS.md | 9 +++- R/gg_groupplot.R | 2 README.md | 5 +- inst/doc/scipub_vignette.R | 7 +++ inst/doc/scipub_vignette.Rmd | 40 ++++++++++++++++++ inst/doc/scipub_vignette.html | 89 ++++++++++++++++++++++++++++++++++++++++-- vignettes/scipub_vignette.Rmd | 40 ++++++++++++++++++ 9 files changed, 196 insertions(+), 18 deletions(-)
Title: r Client for OpenRefine API
Description: 'OpenRefine' (formerly 'Google Refine') is a popular, open source data cleaning software. This package enables users to programmatically trigger data transfer between R and 'OpenRefine'. Available functionality includes project import, export and deletion.
Author: VP Nagraj [aut, cre]
Maintainer: VP Nagraj <nagraj@nagraj.net>
Diff between rrefine versions 1.0 dated 2016-04-08 and 1.1.0 dated 2020-10-07
DESCRIPTION | 20 + MD5 | 44 ++-- NAMESPACE | 1 NEWS.md |only R/refine_delete.R | 56 +++-- R/refine_export.R | 82 +++++-- R/refine_upload.R | 81 ++++++- R/utils.R | 149 ++++++++++---- README.md |only build/vignette.rds |binary inst/doc/rrefine-vignette.R | 14 - inst/doc/rrefine-vignette.Rmd | 4 inst/doc/rrefine-vignette.html | 430 ++++++++++++++++++++++++++++++++++++----- man/lateformeeting.Rd | 7 man/lfm_clean.Rd | 7 man/refine_check.Rd | 12 - man/refine_delete.Rd | 27 +- man/refine_export.Rd | 39 ++- man/refine_id.Rd | 15 - man/refine_metadata.Rd | 16 + man/refine_path.Rd | 13 - man/refine_query.Rd |only man/refine_token.Rd |only man/refine_upload.Rd | 27 +- vignettes/rrefine-vignette.Rmd | 4 25 files changed, 804 insertions(+), 244 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides
a high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<arXiv:1902.08318> paper for more details about 'simdjson'. This package is
at present still a fairly thin and not fully complete wrapper that does not
aim to replace the existing and excellent 'JSON' packages for R.
Author: Dirk Eddelbuettel, Brendan Knapp
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.1 dated 2020-08-11 and 0.1.2 dated 2020-10-07
ChangeLog | 32 DESCRIPTION | 8 MD5 | 26 R/fparse.R | 26 README.md | 14 build/partial.rdb |binary inst/NEWS.Rd | 6 inst/include/RcppSimdJson/deserialize.hpp | 4 inst/include/RcppSimdJson/utils.hpp | 2 inst/include/simdjson.cpp |14138 ++++++++++++++++-------------- inst/include/simdjson.h | 2000 ++-- inst/tinytest/test_fparse_fload.R | 7 inst/tinytest/test_query.R | 53 man/fparse.Rd | 26 14 files changed, 8966 insertions(+), 7376 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Finn Lindgren [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.4-2 dated 2020-05-20 and 1.4-4 dated 2020-10-07
DESCRIPTION | 8 +- MD5 | 108 ++++++++++++++++---------------- R/AAA.R | 28 ++++++++ R/CRS-methods.R | 54 +++++++++++++--- R/Spatial-methods.R | 21 +++++- R/SpatialMultiPointsDataFrame-methods.R | 4 + R/SpatialPointsDataFrame-methods.R | 4 + R/projected.R | 75 ++++++++++++++++++---- build/vignette.rds |binary data/meuse.grid_ll.rda |binary inst/NEWS.Rd | 10 ++ inst/doc/csdacm.R | 36 +++++++--- inst/doc/csdacm.Rnw | 20 +++++ inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 2 man/00sp.Rd | 4 - man/CRS-class.Rd | 44 ++++++++++--- man/SpatialGridDataFrame-class.Rd | 2 man/SpatialPolygons-class.Rd | 2 man/SpatialPolygons.Rd | 2 man/aggregate.Rd | 2 man/gridlines.Rd | 4 - man/is.projected.Rd | 4 + man/over.Rd | 6 - man/spTransform.Rd | 2 man/spplot.Rd | 4 - src/gcdist.c | 6 - src/sp.h | 2 tests/agg.R | 1 tests/agg.Rout.save | 7 +- tests/base.R | 1 tests/base.Rout.save | 7 +- tests/fail1.R | 1 tests/fail1.Rout.save | 11 +-- tests/grid.R | 1 tests/grid.Rout.save | 11 +-- tests/over2.R | 1 tests/over2.Rout.save | 7 +- tests/pass1.R | 1 tests/pass1.Rout.save | 8 -- tests/point.in.polygon.R | 1 tests/point.in.polygon.Rout.save | 5 - tests/sel.R | 1 tests/sel.Rout.save | 7 +- tests/sp1.R | 1 tests/sp1.Rout.save | 7 +- tests/spDists.R | 1 tests/spDists.Rout.save | 5 - tests/spplot.R | 1 tests/spplot.Rout.save | 5 - tests/zerodist.R | 1 tests/zerodist.Rout.save | 7 +- vignettes/csdacm.Rnw | 20 +++++ 55 files changed, 402 insertions(+), 171 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Quantitative proteomics (Schubert et al 2017 <doi:10.1038/nprot.2017.040>) measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons.
The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values.
Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events.
Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options separating the data into sub-groups during normalization and testing.
Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrProteo versions 1.1.3 dated 2020-07-18 and 1.1.4 dated 2020-10-07
DESCRIPTION | 6 MD5 | 46 +-- R/combineMultFilterNAimput.R | 4 R/matrixNAneighbourImpute.R | 29 +- R/plotROC.R | 56 ++- R/readMaxQuantFile.R | 138 +++++++-- R/readPDExport.R | 225 ++++++++++++--- R/readProlineFile.R | 43 +-- R/readUCSCtable.R | 71 ++--- R/readUniProtExport.R | 10 R/summarizeForROC.R | 87 +++--- R/test2grp.R | 18 - R/testRobustToNAimputation.R | 55 +-- inst/doc/wrProteoVignette1.R | 33 +- inst/doc/wrProteoVignette1.Rmd | 50 ++- inst/doc/wrProteoVignette1.html | 507 ++++++++++++++++++------------------ inst/extdata/exampleProtDiscov1.txt | 2 man/plotROC.Rd | 5 man/readMaxQuantFile.Rd | 11 man/readPDExport.Rd | 26 + man/readProlineFile.Rd | 2 man/readUCSCtable.Rd | 14 man/test2grp.Rd | 2 vignettes/wrProteoVignette1.Rmd | 50 ++- 24 files changed, 900 insertions(+), 590 deletions(-)
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>),
Zachary Foster [ctb] (<https://orcid.org/0000-0002-5075-0948>),
Sam Levin [rev],
Margaret Siple [rev]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.1.9 dated 2020-05-31 and 0.2.0 dated 2020-10-07
taxlist-0.1.9/taxlist/R/NULLing.R |only taxlist-0.1.9/taxlist/R/StartMessage.R |only taxlist-0.2.0/taxlist/DESCRIPTION | 27 +- taxlist-0.2.0/taxlist/MD5 | 147 ++++++------ taxlist-0.2.0/taxlist/NAMESPACE | 3 taxlist-0.2.0/taxlist/NEWS.md | 20 - taxlist-0.2.0/taxlist/R/Extract.R | 42 +-- taxlist-0.2.0/taxlist/R/accepted_name.R | 47 ++- taxlist-0.2.0/taxlist/R/backup_object.R | 4 taxlist-0.2.0/taxlist/R/clean.R | 6 taxlist-0.2.0/taxlist/R/clean_strings.R | 4 taxlist-0.2.0/taxlist/R/count_taxa.R | 23 + taxlist-0.2.0/taxlist/R/df2taxlist.R | 35 ++ taxlist-0.2.0/taxlist/R/dissect_name.R | 2 taxlist-0.2.0/taxlist/R/get_children.R | 9 taxlist-0.2.0/taxlist/R/imports.R | 2 taxlist-0.2.0/taxlist/R/internal.R | 11 taxlist-0.2.0/taxlist/R/levels.R | 25 -- taxlist-0.2.0/taxlist/R/match_names.R | 75 +++--- taxlist-0.2.0/taxlist/R/merge_taxa.R | 17 - taxlist-0.2.0/taxlist/R/print_name.R | 14 - taxlist-0.2.0/taxlist/R/replace_x.R | 90 ++++--- taxlist-0.2.0/taxlist/R/subset.R | 5 taxlist-0.2.0/taxlist/R/summary.R | 46 +++ taxlist-0.2.0/taxlist/R/tax2traits.R | 20 - taxlist-0.2.0/taxlist/R/taxlist-class.R | 29 +- taxlist-0.2.0/taxlist/R/taxlist2taxmap.R | 37 +-- taxlist-0.2.0/taxlist/R/taxon_names.R | 20 - taxlist-0.2.0/taxlist/R/taxon_relations.R | 36 +- taxlist-0.2.0/taxlist/R/taxon_traits.R | 17 + taxlist-0.2.0/taxlist/R/taxon_views.R | 4 taxlist-0.2.0/taxlist/R/tnrs.R | 19 - taxlist-0.2.0/taxlist/R/tv2taxlist.R | 4 taxlist-0.2.0/taxlist/build/vignette.rds |binary taxlist-0.2.0/taxlist/data/Easplist.rda |binary taxlist-0.2.0/taxlist/inst/Cross.rda |only taxlist-0.2.0/taxlist/inst/doc/taxlist-intro.R | 36 +- taxlist-0.2.0/taxlist/inst/doc/taxlist-intro.Rmd | 44 +-- taxlist-0.2.0/taxlist/inst/doc/taxlist-intro.html | 88 ++++--- taxlist-0.2.0/taxlist/inst/wetlands_syntax.rda |only taxlist-0.2.0/taxlist/man/Extract.Rd | 24 - taxlist-0.2.0/taxlist/man/accepted_name.Rd | 4 taxlist-0.2.0/taxlist/man/backup_object.Rd | 4 taxlist-0.2.0/taxlist/man/clean.Rd | 2 taxlist-0.2.0/taxlist/man/count_taxa.Rd | 6 taxlist-0.2.0/taxlist/man/df2taxlist.Rd | 9 taxlist-0.2.0/taxlist/man/dissect_name.Rd | 2 taxlist-0.2.0/taxlist/man/figures |only taxlist-0.2.0/taxlist/man/get_children.Rd | 5 taxlist-0.2.0/taxlist/man/levels.Rd | 8 taxlist-0.2.0/taxlist/man/match_names.Rd | 33 +- taxlist-0.2.0/taxlist/man/merge_taxa.Rd | 3 taxlist-0.2.0/taxlist/man/print_name.Rd | 14 - taxlist-0.2.0/taxlist/man/replace_x.Rd | 73 +++-- taxlist-0.2.0/taxlist/man/subset.Rd | 3 taxlist-0.2.0/taxlist/man/summary.Rd | 16 + taxlist-0.2.0/taxlist/man/tax2traits.Rd | 4 taxlist-0.2.0/taxlist/man/taxlist-class.Rd | 11 taxlist-0.2.0/taxlist/man/taxlist2taxmap.Rd | 4 taxlist-0.2.0/taxlist/man/taxon_names.Rd | 14 - taxlist-0.2.0/taxlist/man/taxon_relations.Rd | 18 - taxlist-0.2.0/taxlist/man/taxon_traits.Rd | 9 taxlist-0.2.0/taxlist/man/taxon_views.Rd | 2 taxlist-0.2.0/taxlist/man/tv2taxlist.Rd | 4 taxlist-0.2.0/taxlist/tests/testthat/temp.rda |only taxlist-0.2.0/taxlist/tests/testthat/temp_2020-07-05.rda |only taxlist-0.2.0/taxlist/tests/testthat/temp_2020-07-08.rda |only taxlist-0.2.0/taxlist/tests/testthat/temp_2020-09-16.rda |only taxlist-0.2.0/taxlist/tests/testthat/temp_2020-10-02.rda |only taxlist-0.2.0/taxlist/tests/testthat/temp_2020-10-04.rda |only taxlist-0.2.0/taxlist/tests/testthat/temp_2020-10-07.rda |only taxlist-0.2.0/taxlist/tests/testthat/test-Extract.R | 16 - taxlist-0.2.0/taxlist/tests/testthat/test-clean.R | 2 taxlist-0.2.0/taxlist/tests/testthat/test-df2taxlist.R | 8 taxlist-0.2.0/taxlist/tests/testthat/test-load_last.R | 12 taxlist-0.2.0/taxlist/tests/testthat/test-match_names.R | 4 taxlist-0.2.0/taxlist/tests/testthat/test-taxon_relations.R | 8 taxlist-0.2.0/taxlist/tests/testthat/test-taxon_traits.R | 4 taxlist-0.2.0/taxlist/tests/testthat/test-tv2taxlist.R | 7 taxlist-0.2.0/taxlist/vignettes/taxlist-intro.Rmd | 44 +-- 80 files changed, 831 insertions(+), 554 deletions(-)
Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners). doi:10.18637/jss.v095.i14.
Author: Gianluca Baio [aut, cre]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between survHE versions 1.1 dated 2020-08-06 and 1.1.1 dated 2020-10-07
survHE-1.1.1/survHE/DESCRIPTION | 21 survHE-1.1.1/survHE/MD5 | 67 +- survHE-1.1.1/survHE/NAMESPACE | 8 survHE-1.1.1/survHE/R/data.R |only survHE-1.1.1/survHE/R/digitise.R | 12 survHE-1.1.1/survHE/R/fit_models.R |only survHE-1.1.1/survHE/R/global.R |only survHE-1.1.1/survHE/R/make.ipd.R | 12 survHE-1.1.1/survHE/R/make.surv.R | 566 ++--------------------- survHE-1.1.1/survHE/R/model.fit.plot.R | 307 +++++++----- survHE-1.1.1/survHE/R/plot.survHE.R | 264 ++-------- survHE-1.1.1/survHE/R/poly.weibull.R | 373 +++++++++------ survHE-1.1.1/survHE/R/print.survHE.R | 436 +---------------- survHE-1.1.1/survHE/R/psa.plot.R | 143 ++--- survHE-1.1.1/survHE/R/summary.survHE.R | 48 + survHE-1.1.1/survHE/R/survHE-package.R | 18 survHE-1.1.1/survHE/R/test.linear.assumptions.R | 1 survHE-1.1.1/survHE/R/utils_fit_models.R |only survHE-1.1.1/survHE/R/utils_make_surv.R |only survHE-1.1.1/survHE/R/utils_plot_survHE.R |only survHE-1.1.1/survHE/R/utils_print_survHE.R |only survHE-1.1.1/survHE/R/write.surv.R | 96 +-- survHE-1.1.1/survHE/data |only survHE-1.1.1/survHE/inst/CITATION |only survHE-1.1.1/survHE/inst/extdata |only survHE-1.1.1/survHE/man/data.Rd |only survHE-1.1.1/survHE/man/digitise.Rd | 14 survHE-1.1.1/survHE/man/fit.models.Rd | 21 survHE-1.1.1/survHE/man/make.ipd.Rd | 12 survHE-1.1.1/survHE/man/make.surv.Rd | 10 survHE-1.1.1/survHE/man/model.fit.plot.Rd | 21 survHE-1.1.1/survHE/man/plot.survHE.Rd | 60 +- survHE-1.1.1/survHE/man/poly.weibull.Rd | 8 survHE-1.1.1/survHE/man/print.survHE.Rd | 7 survHE-1.1.1/survHE/man/psa.plot.Rd | 15 survHE-1.1.1/survHE/man/summary.survHE.Rd | 9 survHE-1.1.1/survHE/man/survHE-package.Rd | 29 - survHE-1.1.1/survHE/man/write.surv.Rd | 30 - survHE-1.1/survHE/R/survHE.R |only survHE-1.1/survHE/man/test.linear.assumptions.Rd |only 40 files changed, 931 insertions(+), 1677 deletions(-)
Title: Smart Adaptive Recommendations
Description: 'Smart Adaptive Recommendations' (SAR) is the name of a fast, scalable, adaptive algorithm for personalized recommendations based on user transactions and item descriptions. It produces easily explainable/interpretable recommendations and handles "cold item" and "semi-cold user" scenarios. This package provides two implementations of 'SAR': a standalone implementation, and an interface to a web service in Microsoft's 'Azure' cloud: <https://github.com/Microsoft/Product-Recommendations/blob/master/doc/sar.md>. The former allows fast and easy experimentation, and the latter provides robust scalability and extra features for production use.
Author: Hong Ooi [aut, cre],
Microsoft Product Recommendations team [ctb] (source for MS sample
datasets),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between SAR versions 1.0.1 dated 2019-05-02 and 1.0.3 dated 2020-10-07
DESCRIPTION | 17 +++++++++-------- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 8 ++++++++ R/az_rec_model.R | 2 +- R/az_service.R | 2 +- R/cold_items_model.R | 8 ++++---- R/ms_data.R | 24 ++++++++++++++---------- R/onload.R | 12 ++++++------ R/predict_sar.R | 4 ++-- R/sar.R | 8 ++++---- README.md | 2 +- man/az_rec_service.Rd | 6 ++---- man/ms_catalog.Rd | 16 +++++++++------- man/ms_usage.Rd | 16 +++++++++------- man/rec_endpoint.Rd | 6 ++---- man/rec_model.Rd | 6 ++---- man/sar.Rd | 35 +++++++++++++++++++++++++++-------- man/user_predict.Rd | 10 ++++++++-- 18 files changed, 126 insertions(+), 90 deletions(-)
More information about modeltime.ensemble at CRAN
Permanent link
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bingsong@my.unthsc.edu>
Diff between mixIndependR versions 0.2.1 dated 2020-03-14 and 0.3.0 dated 2020-10-07
mixIndependR-0.2.1/mixIndependR/R/Prop_Pvalue.R |only mixIndependR-0.2.1/mixIndependR/man/Prop_Pvalue.Rd |only mixIndependR-0.3.0/mixIndependR/DESCRIPTION | 15 ++++---- mixIndependR-0.3.0/mixIndependR/MD5 | 35 ++++++++++++++------ mixIndependR-0.3.0/mixIndependR/NAMESPACE | 5 +- mixIndependR-0.3.0/mixIndependR/NEWS.md | 18 ++++++++++ mixIndependR-0.3.0/mixIndependR/R/AlleleFreq.R | 17 --------- mixIndependR-0.3.0/mixIndependR/R/DistAlleleShare.R | 2 - mixIndependR-0.3.0/mixIndependR/R/DistHetero.R | 1 mixIndependR-0.3.0/mixIndependR/R/counta.R | 15 -------- mixIndependR-0.3.0/mixIndependR/R/mixIndependK.R |only mixIndependR-0.3.0/mixIndependR/R/mixIndependX.R |only mixIndependR-0.3.0/mixIndependR/build |only mixIndependR-0.3.0/mixIndependR/inst |only mixIndependR-0.3.0/mixIndependR/man/mixIndependK.Rd |only mixIndependR-0.3.0/mixIndependR/man/mixIndependX.Rd |only mixIndependR-0.3.0/mixIndependR/tests/testthat.R | 9 ++--- mixIndependR-0.3.0/mixIndependR/vignettes |only 18 files changed, 61 insertions(+), 56 deletions(-)
Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end
is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
the GNU R language and environment for statistical computing and graphics.
While R can be used in batch mode, the r binary adds full support for
both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path
expression as the first line in scripts) as well as command-line use in
standard Unix pipelines. In other words, r provides the R language without
the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between littler versions 0.3.11 dated 2020-06-26 and 0.3.12 dated 2020-10-07
ChangeLog | 80 + DESCRIPTION | 10 MD5 | 44 README.md | 15 build/vignette.rds |binary configure | 18 inst/NEWS.Rd | 35 inst/doc/littler-examples.R |only inst/doc/littler-examples.Rmd | 18 inst/doc/littler-examples.html | 2372 ++++++++++------------------------------- inst/doc/littler-faq.R |only inst/doc/littler-faq.Rmd | 15 inst/doc/littler-faq.html | 1850 ++++--------------------------- inst/examples/c4c.r | 7 inst/examples/check.r | 8 inst/examples/com.r |only inst/examples/cos.r | 8 inst/examples/cow.r | 7 inst/examples/cranIncoming.r |only inst/examples/installBSPM.r |only inst/examples/installDeps.r |only inst/examples/installRSPM.r |only inst/examples/tt.r | 9 inst/examples/urlUpdate.r |only tests/simpleTests.R | 10 vignettes/littler-examples.Rmd | 18 vignettes/littler-faq.Rmd | 15 27 files changed, 1125 insertions(+), 3414 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Giuseppe Casalicchio [ctb] (<https://orcid.org/0000-0001-5324-5966>),
Stefan Coors [ctb] (<https://orcid.org/0000-0002-7465-2146>),
Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>),
Martin Binder [aut],
Marc Becker [ctb] (<https://orcid.org/0000-0002-8115-0400>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.6.0 dated 2020-09-13 and 0.7.0 dated 2020-10-07
mlr3-0.6.0/mlr3/R/helper_R6.R |only mlr3-0.6.0/mlr3/R/helper_future.R |only mlr3-0.6.0/mlr3/inst/references.bib |only mlr3-0.6.0/mlr3/man/as.data.table.Rd |only mlr3-0.7.0/mlr3/DESCRIPTION | 56 + mlr3-0.7.0/mlr3/MD5 | 243 ++++---- mlr3-0.7.0/mlr3/NAMESPACE | 4 mlr3-0.7.0/mlr3/NEWS.md | 15 mlr3-0.7.0/mlr3/R/BenchmarkResult.R | 303 ++++------ mlr3-0.7.0/mlr3/R/Learner.R | 15 mlr3-0.7.0/mlr3/R/LearnerClassif.R | 1 mlr3-0.7.0/mlr3/R/LearnerClassifFeatureless.R | 2 mlr3-0.7.0/mlr3/R/LearnerClassifRpart.R | 2 mlr3-0.7.0/mlr3/R/LearnerRegr.R | 1 mlr3-0.7.0/mlr3/R/LearnerRegrFeatureless.R | 2 mlr3-0.7.0/mlr3/R/LearnerRegrRpart.R | 2 mlr3-0.7.0/mlr3/R/Measure.R | 12 mlr3-0.7.0/mlr3/R/MeasureSimple.R | 4 mlr3-0.7.0/mlr3/R/PredictionData.R | 3 mlr3-0.7.0/mlr3/R/ResampleResult.R | 177 +++-- mlr3-0.7.0/mlr3/R/Resampling.R | 1 mlr3-0.7.0/mlr3/R/ResamplingBootstrap.R | 2 mlr3-0.7.0/mlr3/R/ResamplingCV.R | 8 mlr3-0.7.0/mlr3/R/ResamplingHoldout.R | 2 mlr3-0.7.0/mlr3/R/ResamplingLOO.R | 2 mlr3-0.7.0/mlr3/R/ResamplingRepeatedCV.R | 10 mlr3-0.7.0/mlr3/R/ResamplingSubsampling.R | 2 mlr3-0.7.0/mlr3/R/ResultData.R |only mlr3-0.7.0/mlr3/R/Task.R | 8 mlr3-0.7.0/mlr3/R/TaskClassif.R | 1 mlr3-0.7.0/mlr3/R/TaskClassif_german_credit.R | 2 mlr3-0.7.0/mlr3/R/TaskClassif_iris.R | 2 mlr3-0.7.0/mlr3/R/TaskClassif_spam.R | 2 mlr3-0.7.0/mlr3/R/TaskClassif_wine.R | 2 mlr3-0.7.0/mlr3/R/TaskRegr.R | 1 mlr3-0.7.0/mlr3/R/TaskSupervised.R | 2 mlr3-0.7.0/mlr3/R/TaskUnsupervised.R | 2 mlr3-0.7.0/mlr3/R/Task_rbind.R | 2 mlr3-0.7.0/mlr3/R/as_data_backend.R | 12 mlr3-0.7.0/mlr3/R/benchmark.R | 40 - mlr3-0.7.0/mlr3/R/bibentries.R |only mlr3-0.7.0/mlr3/R/fix_factor_levels.R | 2 mlr3-0.7.0/mlr3/R/helper.R | 24 mlr3-0.7.0/mlr3/R/mlr_learners.R | 2 mlr3-0.7.0/mlr3/R/mlr_measures.R | 2 mlr3-0.7.0/mlr3/R/mlr_sugar.R | 2 mlr3-0.7.0/mlr3/R/mlr_tasks.R | 3 mlr3-0.7.0/mlr3/R/predict.R | 2 mlr3-0.7.0/mlr3/R/reexports.R | 9 mlr3-0.7.0/mlr3/R/resample.R | 47 - mlr3-0.7.0/mlr3/R/worker.R | 2 mlr3-0.7.0/mlr3/R/zzz.R | 8 mlr3-0.7.0/mlr3/README.md | 16 mlr3-0.7.0/mlr3/build/partial.rdb |binary mlr3-0.7.0/mlr3/inst/testthat/helper_autotest.R | 11 mlr3-0.7.0/mlr3/inst/testthat/helper_expectations.R | 121 ++- mlr3-0.7.0/mlr3/man/BenchmarkResult.Rd | 47 - mlr3-0.7.0/mlr3/man/Learner.Rd | 8 mlr3-0.7.0/mlr3/man/LearnerClassif.Rd | 1 mlr3-0.7.0/mlr3/man/LearnerRegr.Rd | 1 mlr3-0.7.0/mlr3/man/PredictionData.Rd | 3 mlr3-0.7.0/mlr3/man/ResampleResult.Rd | 74 -- mlr3-0.7.0/mlr3/man/ResultData.Rd |only mlr3-0.7.0/mlr3/man/Task.Rd | 6 mlr3-0.7.0/mlr3/man/TaskClassif.Rd | 1 mlr3-0.7.0/mlr3/man/TaskRegr.Rd | 1 mlr3-0.7.0/mlr3/man/TaskSupervised.Rd | 2 mlr3-0.7.0/mlr3/man/TaskUnsupervised.Rd | 2 mlr3-0.7.0/mlr3/man/as_data_backend.Rd | 12 mlr3-0.7.0/mlr3/man/as_result_data.Rd |only mlr3-0.7.0/mlr3/man/mlr3-package.Rd | 11 mlr3-0.7.0/mlr3/man/mlr_learners.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_learners_classif.featureless.Rd | 4 mlr3-0.7.0/mlr3/man/mlr_learners_classif.rpart.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_learners_regr.featureless.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_learners_regr.rpart.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_measures.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.acc.Rd | 1 mlr3-0.7.0/mlr3/man/mlr_measures_classif.auc.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.bacc.Rd | 1 mlr3-0.7.0/mlr3/man/mlr_measures_classif.bbrier.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.ce.Rd | 1 mlr3-0.7.0/mlr3/man/mlr_measures_classif.costs.Rd | 1 mlr3-0.7.0/mlr3/man/mlr_measures_classif.dor.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fbeta.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fdr.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fn.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fnr.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fomr.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fp.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.fpr.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.logloss.Rd | 1 mlr3-0.7.0/mlr3/man/mlr_measures_classif.mbrier.Rd | 1 mlr3-0.7.0/mlr3/man/mlr_measures_classif.mcc.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.npv.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.ppv.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.prauc.Rd |only mlr3-0.7.0/mlr3/man/mlr_measures_classif.precision.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.recall.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.sensitivity.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.specificity.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.tn.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.tnr.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.tp.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_measures_classif.tpr.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_resamplings_bootstrap.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_resamplings_cv.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_resamplings_holdout.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_resamplings_loo.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_resamplings_repeated_cv.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_resamplings_subsampling.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_sugar.Rd | 2 mlr3-0.7.0/mlr3/man/mlr_tasks.Rd | 3 mlr3-0.7.0/mlr3/man/mlr_tasks_german_credit.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_tasks_iris.Rd | 5 mlr3-0.7.0/mlr3/man/mlr_tasks_spam.Rd | 4 mlr3-0.7.0/mlr3/man/mlr_tasks_wine.Rd | 4 mlr3-0.7.0/mlr3/man/reexports.Rd |only mlr3-0.7.0/mlr3/tests/testthat/test_PredictionClassif.R | 4 mlr3-0.7.0/mlr3/tests/testthat/test_PredictionRegr.R | 4 mlr3-0.7.0/mlr3/tests/testthat/test_Resampling.R | 14 mlr3-0.7.0/mlr3/tests/testthat/test_Task.R | 4 mlr3-0.7.0/mlr3/tests/testthat/test_benchmark.R | 148 ++-- mlr3-0.7.0/mlr3/tests/testthat/test_encapsulate.R | 4 mlr3-0.7.0/mlr3/tests/testthat/test_mlr_learners_regr_featureless.R | 2 mlr3-0.7.0/mlr3/tests/testthat/test_mlr_resampling_holdout.R | 17 mlr3-0.7.0/mlr3/tests/testthat/test_resample.R | 31 - 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Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Description: Analysis of plant pathogen pathotype survey data. Functions
provided calculate distribution of susceptibilities, distribution of
complexities with statistics, pathotype frequency distribution, as well as
diversity indices for pathotypes. This package is meant to be a direct
replacement for Herrmann, Löwer, Schachtel's (1999)
<doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS',
previously used for pathotype analysis.
Author: Austin G. McCoy [aut, ccp] (<https://orcid.org/0000-0003-2483-4184>),
Zachary Noel [aut, ccp] (<https://orcid.org/0000-0001-6375-8300>),
Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Martin Chilvers [aut] (<https://orcid.org/0000-0001-8832-1666>),
Zhian N. Kamvar [ctb, rev] (<https://orcid.org/0000-0003-1458-7108>),
Michigan Soybean Promotion Committee [fnd],
Project GREEEN [fnd],
North Central Soybean Research Program [fnd],
GRDC Project DAQ00186 [fnd]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between hagis versions 3.0.1 dated 2019-11-18 and 3.1.0 dated 2020-10-07
hagis-3.0.1/hagis/R/defunct.R |only hagis-3.0.1/hagis/man/hagis.Rd |only hagis-3.0.1/hagis/tests/testthat/test-defunct.R |only hagis-3.1.0/hagis/DESCRIPTION | 64 ++- hagis-3.1.0/hagis/MD5 | 64 ++- hagis-3.1.0/hagis/NAMESPACE | 3 hagis-3.1.0/hagis/NEWS.md | 43 +- hagis-3.1.0/hagis/R/calculate_complexities.R | 54 +-- hagis-3.1.0/hagis/R/calculate_diversities.R | 47 +- hagis-3.1.0/hagis/R/create_binary_matrix.R |only hagis-3.1.0/hagis/R/data.R | 28 + hagis-3.1.0/hagis/R/hagis-package.R | 15 hagis-3.1.0/hagis/R/internal_functions.R | 75 ++-- hagis-3.1.0/hagis/R/summarize_gene.R | 31 - hagis-3.1.0/hagis/R/zzz.R |only hagis-3.1.0/hagis/README.md | 74 +--- hagis-3.1.0/hagis/build/vignette.rds |binary hagis-3.1.0/hagis/data/sample_meta.rda |only hagis-3.1.0/hagis/inst/doc/betadiversity.R |only hagis-3.1.0/hagis/inst/doc/betadiversity.Rmd |only hagis-3.1.0/hagis/inst/doc/betadiversity.html |only hagis-3.1.0/hagis/inst/doc/hagis.R | 5 hagis-3.1.0/hagis/inst/doc/hagis.Rmd | 125 ++++--- hagis-3.1.0/hagis/inst/doc/hagis.html | 162 +++++----- hagis-3.1.0/hagis/man/P_sojae_survey.Rd | 8 hagis-3.1.0/hagis/man/calculate_complexities.Rd | 4 hagis-3.1.0/hagis/man/calculate_diversities.Rd | 8 hagis-3.1.0/hagis/man/create_binary_matrix.Rd |only hagis-3.1.0/hagis/man/hagis-package.Rd |only hagis-3.1.0/hagis/man/sample_meta.Rd |only hagis-3.1.0/hagis/man/summarize_gene.Rd | 8 hagis-3.1.0/hagis/tests/testthat/test-autoplot_hagis_complexities.R | 12 hagis-3.1.0/hagis/tests/testthat/test-autoplot_rps_summary.R | 14 hagis-3.1.0/hagis/tests/testthat/test-calculate_complexities.R | 5 hagis-3.1.0/hagis/tests/testthat/test-calculate_diversities.R | 14 hagis-3.1.0/hagis/tests/testthat/test-create_binary_matrix.R |only hagis-3.1.0/hagis/tests/testthat/test-diversities_table.R | 4 hagis-3.1.0/hagis/tests/testthat/test-individual_pathotypes.R | 15 hagis-3.1.0/hagis/vignettes/betadiversity.Rmd |only hagis-3.1.0/hagis/vignettes/hagis.Rmd | 125 ++++--- 40 files changed, 519 insertions(+), 488 deletions(-)
Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 2.0.1 dated 2019-08-26 and 3.0.0 dated 2020-10-07
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|only cmsaf-2.0.1/cmsaf/R/seas.anomaly.R |only cmsaf-2.0.1/cmsaf/R/seasmean.R |only cmsaf-2.0.1/cmsaf/R/seassum.R |only cmsaf-2.0.1/cmsaf/R/seasx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/sellonlatbox.R |only cmsaf-2.0.1/cmsaf/R/selmon.R |only cmsaf-2.0.1/cmsaf/R/selperiod.R |only cmsaf-2.0.1/cmsaf/R/selpoint.R |only cmsaf-2.0.1/cmsaf/R/selpoint.multi.R |only cmsaf-2.0.1/cmsaf/R/seltime.R |only cmsaf-2.0.1/cmsaf/R/selyear.R |only cmsaf-2.0.1/cmsaf/R/set_seasons.R |only cmsaf-2.0.1/cmsaf/R/simplelm.R |only cmsaf-2.0.1/cmsaf/R/simplelm2.R |only cmsaf-2.0.1/cmsaf/R/timmax.R |only cmsaf-2.0.1/cmsaf/R/timmean.R |only cmsaf-2.0.1/cmsaf/R/timmin.R |only cmsaf-2.0.1/cmsaf/R/timpctl.R |only cmsaf-2.0.1/cmsaf/R/timsd.R |only cmsaf-2.0.1/cmsaf/R/timsum.R |only cmsaf-2.0.1/cmsaf/R/timx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/trend.R |only cmsaf-2.0.1/cmsaf/R/wfldmean.R |only cmsaf-2.0.1/cmsaf/R/write_output_file.R |only cmsaf-2.0.1/cmsaf/R/write_output_file_trend.R |only cmsaf-2.0.1/cmsaf/R/xdpm_wrapper.R |only cmsaf-2.0.1/cmsaf/R/ydaymean.R |only cmsaf-2.0.1/cmsaf/R/year.anomaly.R |only cmsaf-2.0.1/cmsaf/R/yearmean.R |only cmsaf-2.0.1/cmsaf/R/yearsum.R |only cmsaf-2.0.1/cmsaf/R/ymonmax.R |only cmsaf-2.0.1/cmsaf/R/ymonmean.R |only cmsaf-2.0.1/cmsaf/R/ymonmin.R |only cmsaf-2.0.1/cmsaf/R/ymonsd.R |only cmsaf-2.0.1/cmsaf/R/ymonsum.R |only cmsaf-2.0.1/cmsaf/R/ymonx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/yseasmax.R |only cmsaf-2.0.1/cmsaf/R/yseasmean.R |only cmsaf-2.0.1/cmsaf/R/yseasmin.R |only cmsaf-2.0.1/cmsaf/R/yseassd.R |only cmsaf-2.0.1/cmsaf/R/yseasx_wrapper.R |only cmsaf-2.0.1/cmsaf/man/add_grid_info.Rd |only cmsaf-2.0.1/cmsaf/man/box_mergetime.Rd |only cmsaf-2.0.1/cmsaf/man/change_att.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.add.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.addc.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.cat.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.div.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.divc.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.mul.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.mulc.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.sub.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.subc.Rd |only cmsaf-2.0.1/cmsaf/man/dayrange.Rd |only cmsaf-2.0.1/cmsaf/man/divdpm.Rd |only cmsaf-2.0.1/cmsaf/man/extract.level.Rd |only cmsaf-2.0.1/cmsaf/man/extract.period.Rd |only cmsaf-2.0.1/cmsaf/man/fldmax.Rd |only cmsaf-2.0.1/cmsaf/man/fldmean.Rd |only cmsaf-2.0.1/cmsaf/man/fldmin.Rd |only cmsaf-2.0.1/cmsaf/man/get_time.Rd |only cmsaf-2.0.1/cmsaf/man/levbox_mergetime.Rd |only cmsaf-2.0.1/cmsaf/man/mon.anomaly.Rd |only cmsaf-2.0.1/cmsaf/man/monmax.Rd |only cmsaf-2.0.1/cmsaf/man/monmean.Rd |only cmsaf-2.0.1/cmsaf/man/monmin.Rd |only cmsaf-2.0.1/cmsaf/man/monsd.Rd |only cmsaf-2.0.1/cmsaf/man/monsum.Rd |only cmsaf-2.0.1/cmsaf/man/muldpm.Rd |only cmsaf-2.0.1/cmsaf/man/multimonmean.Rd |only cmsaf-2.0.1/cmsaf/man/multimonsum.Rd |only cmsaf-2.0.1/cmsaf/man/ncinfo.Rd |only cmsaf-2.0.1/cmsaf/man/read_ncvar.Rd |only cmsaf-2.0.1/cmsaf/man/remap.Rd |only cmsaf-2.0.1/cmsaf/man/seas.anomaly.Rd |only cmsaf-2.0.1/cmsaf/man/seasmean.Rd |only cmsaf-2.0.1/cmsaf/man/seassum.Rd |only cmsaf-2.0.1/cmsaf/man/sellonlatbox.Rd |only cmsaf-2.0.1/cmsaf/man/selmon.Rd |only cmsaf-2.0.1/cmsaf/man/selperiod.Rd |only cmsaf-2.0.1/cmsaf/man/selpoint.Rd |only cmsaf-2.0.1/cmsaf/man/selpoint.multi.Rd |only cmsaf-2.0.1/cmsaf/man/seltime.Rd |only cmsaf-2.0.1/cmsaf/man/selyear.Rd |only cmsaf-2.0.1/cmsaf/man/timmax.Rd |only cmsaf-2.0.1/cmsaf/man/timmean.Rd |only cmsaf-2.0.1/cmsaf/man/timmin.Rd |only cmsaf-2.0.1/cmsaf/man/timpctl.Rd |only cmsaf-2.0.1/cmsaf/man/timsd.Rd |only cmsaf-2.0.1/cmsaf/man/timsum.Rd |only cmsaf-2.0.1/cmsaf/man/trend.Rd |only cmsaf-2.0.1/cmsaf/man/wfldmean.Rd |only cmsaf-2.0.1/cmsaf/man/ydaymean.Rd |only cmsaf-2.0.1/cmsaf/man/year.anomaly.Rd |only cmsaf-2.0.1/cmsaf/man/yearmean.Rd |only cmsaf-2.0.1/cmsaf/man/yearsum.Rd |only cmsaf-2.0.1/cmsaf/man/ymonmax.Rd |only cmsaf-2.0.1/cmsaf/man/ymonmean.Rd |only cmsaf-2.0.1/cmsaf/man/ymonmin.Rd |only cmsaf-2.0.1/cmsaf/man/ymonsd.Rd |only cmsaf-2.0.1/cmsaf/man/ymonsum.Rd |only cmsaf-2.0.1/cmsaf/man/yseasmax.Rd |only cmsaf-2.0.1/cmsaf/man/yseasmean.Rd |only cmsaf-2.0.1/cmsaf/man/yseasmin.Rd |only cmsaf-2.0.1/cmsaf/man/yseassd.Rd |only cmsaf-2.0.1/cmsaf/tests/testdata |only cmsaf-2.0.1/cmsaf/tests/testthat |only cmsaf-2.0.1/cmsaf/tests/testthat.R |only cmsaf-3.0.0/cmsaf/DESCRIPTION | 44 cmsaf-3.0.0/cmsaf/MD5 | 333 cmsaf-3.0.0/cmsaf/NAMESPACE | 79 cmsaf-3.0.0/cmsaf/NEWS.md | 315 cmsaf-3.0.0/cmsaf/R/cmsaf.R | 64 cmsaf-3.0.0/cmsaf/R/get_grid.R | 4 cmsaf-3.0.0/cmsaf/R/release_questions.R |only cmsaf-3.0.0/cmsaf/R/run_toolbox.R | 46 cmsaf-3.0.0/cmsaf/inst/WORDLIST | 146 cmsaf-3.0.0/cmsaf/inst/toolbox/ColorspacePrivates.R |only cmsaf-3.0.0/cmsaf/inst/toolbox/global.R | 92 cmsaf-3.0.0/cmsaf/inst/toolbox/server.R | 8938 +++++++++----------- cmsaf-3.0.0/cmsaf/inst/toolbox/ui.R | 1027 +- cmsaf-3.0.0/cmsaf/inst/toolbox/www/style.css | 24 cmsaf-3.0.0/cmsaf/man/cmsaf.Rd | 82 cmsaf-3.0.0/cmsaf/man/run_toolbox.Rd | 5 cmsaf-3.0.0/cmsaf/tests/spelling.R | 2 cmsaf-3.0.0/cmsaf/tests/spelling.Rout.save | 50 199 files changed, 4950 insertions(+), 6301 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows',
'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gábor Csárdi [aut, cre],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between ps versions 1.3.4 dated 2020-08-11 and 1.4.0 dated 2020-10-07
DESCRIPTION | 10 - LICENSE.note |only MD5 | 141 +++++++------- NAMESPACE | 9 NEWS.md | 23 ++ R/disk.R |only R/errno.R | 2 R/low-level.R | 181 +++++++++++++----- R/memory.R |only R/os.R | 15 + R/system.R | 46 ++++ R/testthat-reporter.R | 6 R/utils.R | 18 + README.md | 2 man/errno.Rd | 2 man/ps_children.Rd | 4 man/ps_cmdline.Rd | 4 man/ps_connections.Rd | 4 man/ps_cpu_count.Rd | 2 man/ps_cpu_times.Rd | 4 man/ps_create_time.Rd | 4 man/ps_cwd.Rd | 4 man/ps_disk_partitions.Rd |only man/ps_disk_usage.Rd |only man/ps_environ.Rd | 6 man/ps_exe.Rd | 4 man/ps_get_nice.Rd |only man/ps_handle.Rd | 2 man/ps_interrupt.Rd | 2 man/ps_is_running.Rd | 4 man/ps_kill.Rd | 4 man/ps_memory_info.Rd | 4 man/ps_name.Rd | 4 man/ps_num_fds.Rd | 4 man/ps_num_threads.Rd | 4 man/ps_open_files.Rd | 4 man/ps_pid.Rd | 4 man/ps_ppid.Rd | 6 man/ps_resume.Rd | 4 man/ps_send_signal.Rd | 4 man/ps_status.Rd | 4 man/ps_suspend.Rd | 4 man/ps_system_memory.Rd |only man/ps_system_swap.Rd |only man/ps_terminal.Rd | 4 man/ps_terminate.Rd | 4 man/ps_tty_size.Rd |only man/ps_uids.Rd | 6 man/ps_username.Rd | 4 src/api-linux.c | 54 +++++ src/api-macos.c | 224 +++++++++++++++++++++-- src/api-posix.c | 98 ++++++++++ src/api-windows.c | 316 +++++++++++++++++++++++++++++++++ src/arch/macos/process_info.c | 8 src/arch/macos/process_info.h | 5 src/arch/windows/ntextapi.h | 6 src/arch/windows/process_handles.c | 7 src/arch/windows/process_handles.h | 5 src/arch/windows/process_info.c | 8 src/arch/windows/process_info.h | 5 src/common.c | 7 src/common.h | 5 src/dummy.c | 9 src/init.c | 7 src/linux.c | 7 src/macos.c | 7 src/posix.c | 7 src/posix.h | 5 src/ps-internal.h | 1 src/ps.h | 7 src/windows.c | 7 tests/testthat/test-cleanup-reporter.R | 18 + tests/testthat/test-finished.R | 1 tests/testthat/test-kill-tree.R | 51 ++++- tests/testthat/test-posix-zombie.R | 2 tests/testthat/test-posix.R | 2 76 files changed, 1138 insertions(+), 308 deletions(-)
Title: High-Dimensional Multiscale Online Changepoint Detection
Description: Implements the algorithm in Chen, Wang and Samworth (2020) <arxiv:2003.03668> for online detection of sudden mean changes in a sequence of high-dimensional observations. It also implements methods by Mei (2010) <doi:10.1093/biomet/asq010>, Xie and Siegmund (2013) <doi:10.1214/13-AOS1094> and Chan (2017) <doi:10.1214/17-AOS1546>.
Author: Yudong Chen, Tengyao Wang, Richard J. Samworth
Maintainer: Yudong Chen <yudong.chen@statslab.cam.ac.uk>
Diff between ocd versions 1.0 dated 2020-03-18 and 1.1 dated 2020-10-07
DESCRIPTION | 10 +-- MD5 | 23 +++++--- NAMESPACE | 2 R/ParkfieldSensors-data.R |only R/algorithms.R | 2 R/ocd.R | 125 +++++++++++++++++++++++++++++++++------------ README.md |only data |only man/ChangepointDetector.Rd | 21 ++++--- man/ParkfieldSensors.Rd |only man/accessor.Rd | 3 + man/getData.Rd | 7 +- man/setBaselineSD.Rd |only man/setStatus.Rd | 5 + man/update_param.Rd |only 15 files changed, 139 insertions(+), 59 deletions(-)
Title: Create Rich Command Line Applications
Description: Create rich command line applications, with colors, headings,
lists, alerts, progress bars, etc. It uses CSS for custom themes.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cliapp versions 0.1.0 dated 2018-12-16 and 0.1.1 dated 2020-10-07
DESCRIPTION | 8 +++---- MD5 | 44 +++++++++++++++++++++---------------------- NEWS.md | 7 ++++++ R/client.R | 2 - R/containers.R | 2 - R/package.R | 2 - R/simple-theme.R | 2 - R/utils.R | 8 +++++++ README.md | 11 +++++++--- man/cli_alert.Rd | 39 ++++++++++++++++++++++++++++---------- man/cli_div.Rd | 9 ++++++-- man/cli_dl.Rd | 10 +++++++-- man/cli_it.Rd | 9 ++++++-- man/cli_ol.Rd | 10 +++++++-- man/cli_par.Rd | 3 -- man/cli_progress_bar.Rd | 2 + man/cli_ul.Rd | 10 +++++++-- man/cli_verbatim.Rd | 2 - man/inline-markup.Rd | 6 ++--- man/simple_theme.Rd | 2 + man/start_app.Rd | 8 +++++-- man/themes.Rd | 4 +-- tests/testthat/test-themes.R | 4 --- 23 files changed, 137 insertions(+), 67 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' and 'mlr3proba'
with interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Quay Au [aut] (<https://orcid.org/0000-0002-5252-8902>),
Stefan Coors [aut] (<https://orcid.org/0000-0002-7465-2146>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3learners versions 0.4.0 dated 2020-09-25 and 0.4.1 dated 2020-10-07
mlr3learners-0.4.0/mlr3learners/inst/references.bib |only mlr3learners-0.4.1/mlr3learners/DESCRIPTION | 13 mlr3learners-0.4.1/mlr3learners/MD5 | 144 +++++----- mlr3learners-0.4.1/mlr3learners/NAMESPACE | 1 mlr3learners-0.4.1/mlr3learners/NEWS.md | 5 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifCVGlmnet.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifGlmnet.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifKKNN.R | 6 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifLDA.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifQDA.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifRanger.R | 4 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifSVM.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerClassifXgboost.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrCVGlmnet.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrGlmnet.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrKKNN.R | 6 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrKM.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrRanger.R | 4 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrSVM.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerRegrXgboost.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerSurvCVGlmnet.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerSurvGlmnet.R | 2 mlr3learners-0.4.1/mlr3learners/R/LearnerSurvRanger.R | 4 mlr3learners-0.4.1/mlr3learners/R/LearnerSurvXgboost.R | 2 mlr3learners-0.4.1/mlr3learners/R/bibentries.R |only mlr3learners-0.4.1/mlr3learners/R/helpers.R | 6 mlr3learners-0.4.1/mlr3learners/R/zzz.R | 11 mlr3learners-0.4.1/mlr3learners/README.md | 49 --- mlr3learners-0.4.1/mlr3learners/build/partial.rdb |binary mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.cv_glmnet.R | 6 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.glmnet.R | 8 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.kknn.R | 2 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.lda.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.logreg.R | 6 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.multinom.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.naive_bayes.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.qda.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.ranger.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.svm.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_classif.xgboost.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.cv_glmnet.R | 8 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.glmnet.R | 6 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.kknn.R | 2 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.km.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.lm.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.ranger.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.svm.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_regr.xgboost.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_surv.cv_glmnet.R | 6 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_surv.glmnet.R | 6 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_surv.ranger.R | 4 mlr3learners-0.4.1/mlr3learners/inst/paramtest/test_paramtest_surv.xgboost.R | 4 mlr3learners-0.4.1/mlr3learners/man/mlr3learners-package.Rd | 11 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.cv_glmnet.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.glmnet.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.kknn.Rd | 17 - mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.lda.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.qda.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.ranger.Rd | 11 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.svm.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_classif.xgboost.Rd | 6 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.cv_glmnet.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.glmnet.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.kknn.Rd | 17 - mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.km.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.ranger.Rd | 11 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.svm.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_regr.xgboost.Rd | 6 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_surv.cv_glmnet.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_surv.glmnet.Rd | 5 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_surv.ranger.Rd | 11 mlr3learners-0.4.1/mlr3learners/man/mlr_learners_surv.xgboost.Rd | 6 mlr3learners-0.4.1/mlr3learners/tests/testthat/test_classif_cv_glmnet.R | 1 mlr3learners-0.4.1/mlr3learners/tests/testthat/test_classif_glmnet.R | 1 74 files changed, 292 insertions(+), 248 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-14 0.4.9
2020-06-25 0.4.7
2020-04-16 0.4.6
2020-03-18 0.4.5
2020-02-24 0.4.4
2019-11-22 0.4.0
2018-10-06 0.3.6
2018-03-01 0.3.0
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' as described by Schauberger and Tutz (2019) <doi:10.18637/jss.v088.i09> and Schauberger and Tutz (2017) <doi:10.1177/1471082X17693086>. BTLLasso is a method to include different types of variables in paired comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between BTLLasso versions 0.1-10 dated 2019-03-25 and 0.1-11 dated 2020-10-07
DESCRIPTION | 11 - MD5 | 70 +++--- R/BTLLasso-package.R | 16 - R/BTLLasso.R | 2 R/boot.BTLLasso.R | 2 R/cv.BTLLasso.R | 2 R/paths.R | 2 R/plot.BTLLasso.R | 2 R/plot.boot.BTLLasso.R | 2 R/predict.BTLLasso.R | 2 R/print.BTLLasso.R | 2 R/print.boot.BTLLasso.R | 2 R/print.cv.BTLLasso.R | 2 R/response.BTLLasso.R | 2 man/BTLLasso-package.Rd | 304 ++++++++++++++-------------- man/BTLLasso.Rd | 431 ++++++++++++++++++++------------------- man/Buli1415.Rd | 178 ++++++++-------- man/Buli1516.Rd | 176 ++++++++-------- man/Buli1617.Rd | 176 ++++++++-------- man/Buli1718.Rd | 176 ++++++++-------- man/BuliResponse.Rd | 92 ++++---- man/GLES.Rd | 188 ++++++++--------- man/GLESsmall.Rd | 190 ++++++++--------- man/SimData.Rd | 178 ++++++++-------- man/boot.BTLLasso.Rd | 393 ++++++++++++++++++------------------ man/ctrl.BTLLasso.Rd | 487 +++++++++++++++++++++++---------------------- man/cv.BTLLasso.Rd | 474 ++++++++++++++++++++++--------------------- man/paths.Rd | 323 ++++++++++++++--------------- man/plot.BTLLasso.Rd | 386 ++++++++++++++++++----------------- man/plot.boot.BTLLasso.Rd | 382 ++++++++++++++++++----------------- man/predict.BTLLasso.Rd | 331 +++++++++++++++--------------- man/print.BTLLasso.Rd | 300 +++++++++++++-------------- man/print.boot.BTLLasso.Rd | 311 ++++++++++++++-------------- man/print.cv.BTLLasso.Rd | 306 ++++++++++++++-------------- man/response.BTLLasso.Rd | 171 ++++++++------- src/cppfunctions.cpp | 2 36 files changed, 3076 insertions(+), 2998 deletions(-)
Title: Atomic Force Microscope Image Analysis
Description: Provides Atomic Force Microscope images analysis such as Gaussian mixes identification, Power
Spectral Density, roughness against lengthscale, experimental variogram and variogram models,
fractal dimension and scale, 2D network analysis. The AFM images can be exported to STL format for 3D
printing.
Author: Mathieu Beauvais [aut, cre],
Irma Liascukiene [aut],
Jessem Landoulsi [aut]
Maintainer: Mathieu Beauvais <beauvais.escp@gmail.com>
Diff between AFM versions 1.2.6 dated 2019-06-08 and 2.0 dated 2020-10-07
AFM-1.2.6/AFM/man/AFMImageVariogramSlopesAnalysis-class.Rd |only AFM-2.0/AFM/DESCRIPTION | 12 AFM-2.0/AFM/MD5 | 129 ++--- AFM-2.0/AFM/NAMESPACE | 4 AFM-2.0/AFM/NEWS | 30 + AFM-2.0/AFM/R/AFMFractalDimensionAnalyser.R | 6 AFM-2.0/AFM/R/AFMGaussianMixAnalyser.R | 249 +++++++++- AFM-2.0/AFM/R/AFMImage.R | 16 AFM-2.0/AFM/R/AFMImageAnalyser.R | 9 AFM-2.0/AFM/R/AFMPSDAnalyser.R | 12 AFM-2.0/AFM/R/AFMReportMaker.R | 2 AFM-2.0/AFM/R/AFMVariogramAnalyser.R | 159 +++--- AFM-2.0/AFM/R/pkgname.R | 2 AFM-2.0/AFM/inst/CITATION | 17 AFM-2.0/AFM/inst/shiny/AFM-desktop/server.R | 207 ++++++-- AFM-2.0/AFM/inst/shiny/AFM-desktop/ui.R | 8 AFM-2.0/AFM/man/AFM.Rd | 3 AFM-2.0/AFM/man/AFMFractalDimensionAnalyser-getFractalDimensions.Rd | 3 AFM-2.0/AFM/man/AFMImage-class.Rd | 41 + AFM-2.0/AFM/man/AFMImage-extractAFMImage.Rd | 6 AFM-2.0/AFM/man/AFMImage-multiplyHeightsAFMImage.Rd | 2 AFM-2.0/AFM/man/AFMImage-simplifyAFMImage.Rd | 6 AFM-2.0/AFM/man/AFMImageAnalyser-class-initialize.Rd | 20 AFM-2.0/AFM/man/AFMImageFractalDimensionMethod-class.Rd | 4 AFM-2.0/AFM/man/AFMImageFractalDimensionsAnalysis-class.Rd | 7 AFM-2.0/AFM/man/AFMImageGaussianMixAnalysis-class.Rd | 35 + AFM-2.0/AFM/man/AFMImageNetworksAnalysis-class.Rd | 32 - AFM-2.0/AFM/man/AFMImagePSDAnalysis-class.Rd | 1 AFM-2.0/AFM/man/AFMImagePSDSlopesAnalysis-class.Rd | 1 AFM-2.0/AFM/man/AFMImageVariogramAnalyser-getAutomaticWidthForVariogramCalculation.Rd | 2 AFM-2.0/AFM/man/AFMImageVariogramAnalysis-class.Rd | 12 AFM-2.0/AFM/man/AFMImageVariogramAnalysis-evaluateVariogramModels-method.Rd | 6 AFM-2.0/AFM/man/AFMImageVariogramAnalysis-getDTModelEvaluation-method.Rd | 3 AFM-2.0/AFM/man/AFMImageVariogramAnalysis-getDTModelSillRange-method.Rd | 3 AFM-2.0/AFM/man/AFMImageVariogramModel-class.Rd | 15 AFM-2.0/AFM/man/AFMVariogramAnalyser-saveSpplotFromAFMImage.Rd | 9 AFM-2.0/AFM/man/PSD1DAgainstFrequency-methods.Rd | 1 AFM-2.0/AFM/man/PSD2DAgainstFrequency-methods.Rd | 4 AFM-2.0/AFM/man/RoughnessByLengthScale-methods.Rd | 3 AFM-2.0/AFM/man/analyse.Rd | 3 AFM-2.0/AFM/man/calculate3DModel-methods.Rd | 5 AFM-2.0/AFM/man/calculateNetworks-methods.Rd | 5 AFM-2.0/AFM/man/checkIsotropy.Rd | 2 AFM-2.0/AFM/man/displayColoredNetworkWithVerticesSize.Rd | 3 AFM-2.0/AFM/man/generateReportFromNanoscopeImageDirectory.Rd | 2 AFM-2.0/AFM/man/getAutoIntersectionForOmnidirectionalVariogram.Rd | 2 AFM-2.0/AFM/man/getAutoIntersectionForRoughnessAgainstLengthscale.Rd | 6 AFM-2.0/AFM/man/getIntersectionForRoughnessAgainstLengthscale.Rd | 8 AFM-2.0/AFM/man/getLogLogOmnidirectionalSlopeGraph.Rd | 3 AFM-2.0/AFM/man/getNetworkParameters-methods.Rd | 5 AFM-2.0/AFM/man/getNyquistSpatialFrequency-methods.Rd | 3 AFM-2.0/AFM/man/getPaddedAFMImage.Rd | 2 AFM-2.0/AFM/man/getRoughnessParameters-methods.Rd | 3 AFM-2.0/AFM/man/identifyEdgesFromCircles.Rd | 3 AFM-2.0/AFM/man/identifyMaxCircleRadius.Rd | 11 AFM-2.0/AFM/man/isAngleBetweenEdgesAlwaysSuperiorToMinAngle.Rd | 8 AFM-2.0/AFM/man/omniVariogramSlopeAnalysis-class.Rd |only AFM-2.0/AFM/man/performGaussianMixCalculation.Rd | 8 AFM-2.0/AFM/man/printVariogramModelEvaluations.Rd | 7 AFM-2.0/AFM/man/putAnalysisOnDisk-methods.Rd | 1 AFM-2.0/AFM/man/saveOnDiskIntersectionForRoughnessAgainstLengthscale.Rd | 6 AFM-2.0/AFM/man/shiftFFT2D.Rd | 2 AFM-2.0/AFM/man/shiftedPSDuv.Rd | 2 AFM-2.0/AFM/man/totalRMSRoughness.Rd | 2 AFM-2.0/AFM/man/transformAFMImageForNetworkAnalysis-methods.Rd | 5 AFM-2.0/AFM/tests/testthat/testAFMImageGaussianMixesExport.R |only AFM-2.0/AFM/tests/testthat/testAFMReportMaker.R | 1 67 files changed, 893 insertions(+), 296 deletions(-)
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb],
Li Wang [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.16.0 dated 2019-12-01 and 1.16.1 dated 2020-10-07
ChangeLog | 2 DESCRIPTION | 8 +-- MD5 | 114 +++++++++++++++++++++---------------------- R/access.R | 1 R/assignment.R | 1 R/coercion.R | 1 R/constructors.R | 1 R/fileio.R | 1 R/layout.R | 1 R/misc.R | 1 R/operators.R | 1 R/plot.R | 5 + R/printsum.R | 1 R/zzz.R | 3 - README.md | 2 build/vignette.rds |binary inst/CITATION | 6 +- inst/doc/networkVignette.pdf |binary man/add.edges.Rd | 2 man/add.vertices.Rd | 2 man/as.matrix.network.Rd | 2 man/as.network.matrix.Rd | 2 man/as.sociomatrix.Rd | 2 man/attribute.methods.Rd | 2 man/deletion.methods.Rd | 2 man/edgeset.constructors.Rd | 2 man/get.edges.Rd | 2 man/get.neighborhood.Rd | 2 man/is.adjacent.Rd | 2 man/loading.attributes.Rd | 2 man/network-operators.Rd | 2 man/network.Rd | 2 man/network.arrow.Rd | 2 man/network.density.Rd | 2 man/network.dyadcount.Rd | 2 man/network.edgecount.Rd | 2 man/network.extraction.Rd | 2 man/network.indicators.Rd | 2 man/network.initialize.Rd | 2 man/network.layout.Rd | 2 man/network.naedgecount.Rd | 2 man/network.size.Rd | 2 man/network.vertex.Rd | 2 man/permute.vertexIDs.Rd | 2 man/plot.network.Rd | 2 man/prod.network.Rd | 2 man/read.paj.Rd | 2 man/sum.network.Rd | 2 man/which.matrix.type.Rd | 2 src/Rinit.c | 1 src/access.c | 1 src/access.h | 1 src/constructors.c | 1 src/constructors.h | 1 src/layout.c | 1 src/layout.h | 1 src/utils.c | 1 src/utils.h | 1 58 files changed, 121 insertions(+), 99 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-30 0.9.0
2020-06-11 0.8.9
2020-03-17 0.8.8
2020-02-18 0.8.7
2020-01-17 0.8.5
2019-09-17 0.8.0
2019-07-25 0.7.12
2019-06-12 0.7.8
2019-03-26 0.7.0
2019-01-12 0.6.0
2018-10-03 0.5.2
2018-08-19 0.4.2
2018-06-11 0.3.35
2018-03-01 0.3.9
2018-01-24 0.2.3
2017-10-01 0.2.2-25
2017-08-03 0.2.2-3
2017-06-21 0.2.1-8
2017-05-14 0.2.1-4
Title: Statistical Methods for Regional Counts
Description: Implements statistical methods for analyzing the counts of areal data,
with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 1.2 dated 2020-05-26 and 1.3 dated 2020-10-07
smerc-1.2/smerc/R/casewin.R |only smerc-1.2/smerc/R/dc.test2.R |only smerc-1.2/smerc/R/dmst.test2.R |only smerc-1.2/smerc/R/edmst.test2.R |only smerc-1.2/smerc/R/elliptic.test2.R |only smerc-1.2/smerc/R/fast.test2.R |only smerc-1.2/smerc/R/flex.test2.R |only smerc-1.2/smerc/R/mlf.test2.R |only smerc-1.2/smerc/R/mlink.test2.R |only smerc-1.2/smerc/R/rflex.test2.R |only smerc-1.2/smerc/R/uls.test2.R |only smerc-1.2/smerc/man/arg_check_rflex_zones.Rd |only smerc-1.2/smerc/man/casewin.Rd |only smerc-1.3/smerc/DESCRIPTION | 17 smerc-1.3/smerc/MD5 | 222 ++-- smerc-1.3/smerc/NAMESPACE | 175 ++- smerc-1.3/smerc/NEWS | 2 smerc-1.3/smerc/R/RcppExports.R |only smerc-1.3/smerc/R/bn.zones.R |only smerc-1.3/smerc/R/color.clusters.R | 2 smerc-1.3/smerc/R/combine.zones.R | 46 - smerc-1.3/smerc/R/csg2.R | 4 smerc-1.3/smerc/R/dc.test.R |only smerc-1.3/smerc/R/dc.zones.R | 2 smerc-1.3/smerc/R/dmst.test.R |only smerc-1.3/smerc/R/dmst.zones.R | 2 smerc-1.3/smerc/R/edmst.sim.R | 90 +- smerc-1.3/smerc/R/edmst.test.R |only smerc-1.3/smerc/R/edmst.zones.R | 2 smerc-1.3/smerc/R/elliptic.test.R |only smerc-1.3/smerc/R/fast.test.R |only smerc-1.3/smerc/R/fast.zones.R | 122 +- smerc-1.3/smerc/R/flex.test.R |only smerc-1.3/smerc/R/flex_test.R |only smerc-1.3/smerc/R/flex_zones.R |only smerc-1.3/smerc/R/knn.R | 90 +- smerc-1.3/smerc/R/lget.R | 8 smerc-1.3/smerc/R/mlf.test.R |only smerc-1.3/smerc/R/mlf.zones.R | 154 +-- smerc-1.3/smerc/R/mlink.sim.R | 90 +- smerc-1.3/smerc/R/mlink.test.R |only smerc-1.3/smerc/R/mlink.zones.R | 114 +- smerc-1.3/smerc/R/mst.all.R | 4 smerc-1.3/smerc/R/nn2zones.R | 48 - smerc-1.3/smerc/R/nndist.R | 70 - smerc-1.3/smerc/R/nndup.R | 48 - smerc-1.3/smerc/R/nydf.R | 2 smerc-1.3/smerc/R/preamble.R | 4 smerc-1.3/smerc/R/rflex.midp.R | 116 +- smerc-1.3/smerc/R/rflex.test.R |only smerc-1.3/smerc/R/rflex.zones.R | 3 smerc-1.3/smerc/R/rflex_zones.R |only smerc-1.3/smerc/R/scan_stat.R |only smerc-1.3/smerc/R/sig_noc.R | 5 smerc-1.3/smerc/R/smerc-package.R |only smerc-1.3/smerc/R/tango.test.R | 2 smerc-1.3/smerc/R/uls.test.R |only smerc-1.3/smerc/build |only smerc-1.3/smerc/data/nypoly.rda |binary smerc-1.3/smerc/inst/doc |only smerc-1.3/smerc/inst/testdata-raw/create_bn_test_ref_rda.R |only smerc-1.3/smerc/inst/testdata-raw/create_flex_zones_ref_rda.R |only smerc-1.3/smerc/inst/testdata/bn_test_ref.rda |only smerc-1.3/smerc/inst/testdata/flex5_zones_ref.rda |only smerc-1.3/smerc/man/bn.zones.Rd |only smerc-1.3/smerc/man/cepp.weights.Rd | 78 - smerc-1.3/smerc/man/color.clusters.Rd | 80 - smerc-1.3/smerc/man/combine.zones.Rd | 52 - smerc-1.3/smerc/man/dc.test.Rd | 4 smerc-1.3/smerc/man/dc.zones.Rd | 2 smerc-1.3/smerc/man/dist.ellipse.Rd | 66 - smerc-1.3/smerc/man/dmst.test.Rd | 4 smerc-1.3/smerc/man/dmst.zones.Rd | 2 smerc-1.3/smerc/man/edmst.test.Rd | 4 smerc-1.3/smerc/man/edmst.zones.Rd | 2 smerc-1.3/smerc/man/elliptic.test.Rd | 2 smerc-1.3/smerc/man/fast.test.Rd | 2 smerc-1.3/smerc/man/fast.zones.Rd | 118 +- smerc-1.3/smerc/man/flex.test.Rd | 2 smerc-1.3/smerc/man/flex_test.Rd |only smerc-1.3/smerc/man/flex_zones.Rd |only smerc-1.3/smerc/man/lget.Rd | 4 smerc-1.3/smerc/man/logical2zones.Rd |only smerc-1.3/smerc/man/mlf.test.Rd | 2 smerc-1.3/smerc/man/mlink.test.Rd | 4 smerc-1.3/smerc/man/mlink.zones.Rd | 2 smerc-1.3/smerc/man/mst.all.Rd | 4 smerc-1.3/smerc/man/nn2zones.Rd | 52 - smerc-1.3/smerc/man/nndup.Rd | 54 - smerc-1.3/smerc/man/nydf.Rd | 2 smerc-1.3/smerc/man/rflex.test.Rd | 2 smerc-1.3/smerc/man/rflex_zones.Rd |only smerc-1.3/smerc/man/scan.nn.Rd | 102 +- smerc-1.3/smerc/man/scan_stat.Rd |only smerc-1.3/smerc/man/smerc.Rd |only smerc-1.3/smerc/man/tango.test.Rd | 2 smerc-1.3/smerc/man/uls.test.Rd | 2 smerc-1.3/smerc/man/uls.zones.Rd | 108 +- smerc-1.3/smerc/src |only smerc-1.3/smerc/tests/satscan_ny_out.txt | 368 ++++---- smerc-1.3/smerc/tests/scan_test_ny_poisson_elliptical_ubpop_10percent_penalty_medium.txt | 448 +++++----- smerc-1.3/smerc/tests/scan_test_ny_poisson_elliptical_ubpop_10percent_penalty_none.txt | 386 ++++---- smerc-1.3/smerc/tests/scan_test_ny_poisson_elliptical_ubpop_10percent_penalty_strong.txt | 448 +++++----- smerc-1.3/smerc/tests/test-all.R | 6 smerc-1.3/smerc/tests/testthat/test-bn.test.R | 134 +- smerc-1.3/smerc/tests/testthat/test-cepp.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-dc.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-dmst.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-edmst.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-elliptic.test-ref.R | 74 - smerc-1.3/smerc/tests/testthat/test-elliptical.test-a0.R | 113 +- smerc-1.3/smerc/tests/testthat/test-elliptical.test-a1.R | 113 +- smerc-1.3/smerc/tests/testthat/test-elliptical.test-ahalf.R | 105 +- smerc-1.3/smerc/tests/testthat/test-fast.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-flex-rflex-zones.R | 88 + smerc-1.3/smerc/tests/testthat/test-flex-zones-ref.R |only smerc-1.3/smerc/tests/testthat/test-flex.test-binomial.R | 92 +- smerc-1.3/smerc/tests/testthat/test-flex.test-poisson.R | 130 +- smerc-1.3/smerc/tests/testthat/test-flex.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-flex.test-sanity.R | 152 +-- smerc-1.3/smerc/tests/testthat/test-mlf.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-mlink.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-rflex.test-binomial.R | 3 smerc-1.3/smerc/tests/testthat/test-rflex.test-poisson.R | 2 smerc-1.3/smerc/tests/testthat/test-rflex.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-scan.test-sanity.R | 140 +-- smerc-1.3/smerc/tests/testthat/test-scan.test.R | 104 +- smerc-1.3/smerc/tests/testthat/test-scan_sim.R | 2 smerc-1.3/smerc/tests/testthat/test-scan_stat.R | 89 + smerc-1.3/smerc/tests/testthat/test-tango.test.R | 74 - smerc-1.3/smerc/tests/testthat/test-uls.test-ref.R | 64 - smerc-1.3/smerc/tests/testthat/test-uls_zones.R | 126 +- smerc-1.3/smerc/vignettes |only 133 files changed, 3101 insertions(+), 2938 deletions(-)
Title: Model Wrappers for Projection Methods
Description: Bindings for additional regression models for use
with the 'parsnip' package, including ordinary and spare partial least
squares models for regression and classification (Rohart et al (2017)
<doi:10.1371/journal.pcbi.1005752>).
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>),
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between plsmod versions 0.0.1 dated 2020-04-14 and 0.1.0 dated 2020-10-07
plsmod-0.0.1/plsmod/tests/testthat/class_examples.RData |only plsmod-0.0.1/plsmod/tests/testthat/reg_examples.RData |only plsmod-0.1.0/plsmod/DESCRIPTION | 8 - plsmod-0.1.0/plsmod/MD5 | 35 +++----- plsmod-0.1.0/plsmod/NEWS.md |only plsmod-0.1.0/plsmod/R/0_imports.R | 69 ++++++++++++++++ plsmod-0.1.0/plsmod/R/pls.R | 33 +++---- plsmod-0.1.0/plsmod/R/pls_data.R | 15 +-- plsmod-0.1.0/plsmod/R/predict.R | 2 plsmod-0.1.0/plsmod/R/wrapper.R | 33 +++---- plsmod-0.1.0/plsmod/README.md | 45 ++++++++-- plsmod-0.1.0/plsmod/inst/WORDLIST | 2 plsmod-0.1.0/plsmod/man/multi_predict.Rd | 2 plsmod-0.1.0/plsmod/man/pls.Rd | 24 ++--- plsmod-0.1.0/plsmod/man/pls_fit.Rd | 11 +- plsmod-0.1.0/plsmod/man/reexports.Rd | 2 plsmod-0.1.0/plsmod/tests/testthat/test-class-pls.R | 65 +++++++++------ plsmod-0.1.0/plsmod/tests/testthat/test-class-spls.R | 65 +++++++++------ plsmod-0.1.0/plsmod/tests/testthat/test-reg-pls.R | 51 +++++++---- plsmod-0.1.0/plsmod/tests/testthat/test-reg-spls.R | 49 +++++++---- 20 files changed, 326 insertions(+), 185 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-13 0.9.2-0
2020-01-10 0.9.1-9
2019-11-12 0.9.1-8
2019-10-27 0.9.1-7
2019-08-29 0.9.1-4
2019-08-06 0.9.1-3
2019-08-01 0.9.1-2
2019-07-26 0.9.1-1
2019-07-12 0.9.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-22 1.1.1-9
Title: High-Dimensional Mixed Graphical Models Estimation
Description: Provides weighted lasso framework for high-dimensional mixed data graph estimation.
In the graph estimation stage, the graph structure is estimated by maximizing the conditional
likelihood of one variable given the rest. We focus on the conditional loglikelihood of each variable
and fit separate regressions to estimate the parameters, much in the spirit of the neighborhood
selection approach proposed by Meinshausen-Buhlmann for the Gaussian Graphical Model and by Ravikumar
for the Ising Model. Currently, the discrete variables can only take two values. In the future, method
for general discrete data and for visualizing the estimated graph will be added.
For more details, see the linked paper.
Author: Mingyu Qi, Tianxi Li
Maintainer: Mingyu Qi <mq3sq@virginia.edu>
Diff between hmgm versions 1.0.2 dated 2019-12-16 and 1.0.3 dated 2020-10-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/hmgm-package.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: A Multiple Testing Procedure for High-Dimensional Mediation
Hypotheses
Description: A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression, the proposed method addresses an unmet methodological challenge.
Author: James Dai [aut, cre],
Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Diff between HDMT versions 1.0.1 dated 2019-12-05 and 1.0.2 dated 2020-10-07
HDMT-1.0.1/HDMT/R/fdrest.R |only HDMT-1.0.1/HDMT/R/fwerest.R |only HDMT-1.0.1/HDMT/R/nullestimation.R |only HDMT-1.0.1/HDMT/man/fdrest.Rd |only HDMT-1.0.1/HDMT/man/fwerest.Rd |only HDMT-1.0.1/HDMT/man/nullestimation.Rd |only HDMT-1.0.2/HDMT/DESCRIPTION | 12 - HDMT-1.0.2/HDMT/MD5 | 40 +++--- HDMT-1.0.2/HDMT/NAMESPACE | 3 HDMT-1.0.2/HDMT/R/adjust_quantile.R | 203 +++++++++++++++++---------------- HDMT-1.0.2/HDMT/R/fdr_est.R |only HDMT-1.0.2/HDMT/R/fwer_est.R |only HDMT-1.0.2/HDMT/R/null_estimation.R |only HDMT-1.0.2/HDMT/build/vignette.rds |binary HDMT-1.0.2/HDMT/inst/doc/HDMT.R | 38 ++---- HDMT-1.0.2/HDMT/inst/doc/HDMT.Rnw | 79 +++++------- HDMT-1.0.2/HDMT/inst/doc/HDMT.bib | 40 +++--- HDMT-1.0.2/HDMT/inst/doc/HDMT.pdf |binary HDMT-1.0.2/HDMT/man/adjust_quantile.Rd | 39 +++--- HDMT-1.0.2/HDMT/man/correct_qqplot.Rd | 24 +-- HDMT-1.0.2/HDMT/man/exercise_input.Rd | 73 ++++++----- HDMT-1.0.2/HDMT/man/fdr_est.Rd |only HDMT-1.0.2/HDMT/man/fwer_est.Rd |only HDMT-1.0.2/HDMT/man/null_estimation.Rd |only HDMT-1.0.2/HDMT/man/snp_input.Rd | 70 +++++------ HDMT-1.0.2/HDMT/vignettes/HDMT.Rnw | 79 +++++------- HDMT-1.0.2/HDMT/vignettes/HDMT.bib | 40 +++--- 27 files changed, 365 insertions(+), 375 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-20 2.0.3
2020-09-02 2.0.2
2020-05-10 1.4.0
2019-06-21 1.3.9
2019-03-08 1.3.8
2018-12-03 1.3.7
2018-07-14 1.3.6
2018-06-24 1.3.5
2018-06-10 1.3.4
2017-08-17 1.3.3.1
2017-08-12 1.3.3
2017-04-15 1.3.2