Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using
the Kannisto, Lee-Carter and related methods as described in
Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova, Nan Li and Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between MortCast versions 2.3-0 dated 2020-05-29 and 2.4-0 dated 2021-06-23
MortCast-2.3-0/MortCast/data/datalist |only MortCast-2.3-0/MortCast/src/Makevars |only MortCast-2.4-0/MortCast/ChangeLog | 8 + MortCast-2.4-0/MortCast/DESCRIPTION | 10 - MortCast-2.4-0/MortCast/MD5 | 62 ++++----- MortCast-2.4-0/MortCast/R/LC.R | 22 +-- MortCast-2.4-0/MortCast/R/MortCast-data.R | 4 MortCast-2.4-0/MortCast/R/MortCast.R | 3 MortCast-2.4-0/MortCast/R/kannisto.R | 32 +++-- MortCast-2.4-0/MortCast/R/life_table.R | 18 ++ MortCast-2.4-0/MortCast/R/other_methods.R | 58 +++++++-- MortCast-2.4-0/MortCast/build/partial.rdb |binary MortCast-2.4-0/MortCast/data/LQcoef.rda |binary MortCast-2.4-0/MortCast/data/MLT1Ylookup.rda |binary MortCast-2.4-0/MortCast/data/MLTlookup.rda |binary MortCast-2.4-0/MortCast/data/PMDadjcoef.rda |binary MortCast-2.4-0/MortCast/data/PMDrho.rda |binary MortCast-2.4-0/MortCast/man/LQcoef.Rd | 8 - MortCast-2.4-0/MortCast/man/MLTlookup.Rd | 6 MortCast-2.4-0/MortCast/man/MortCast-package.Rd | 5 MortCast-2.4-0/MortCast/man/PMDadjcoef.Rd | 6 MortCast-2.4-0/MortCast/man/PMDrho.Rd | 8 - MortCast-2.4-0/MortCast/man/cokannisto.Rd | 6 MortCast-2.4-0/MortCast/man/kannisto.Rd | 16 ++ MortCast-2.4-0/MortCast/man/kannisto.estimate.Rd | 2 MortCast-2.4-0/MortCast/man/kannisto.predict.Rd | 3 MortCast-2.4-0/MortCast/man/life.table.Rd | 13 +- MortCast-2.4-0/MortCast/man/lqgroup.Rd | 9 - MortCast-2.4-0/MortCast/man/mortcast.Rd | 18 +- MortCast-2.4-0/MortCast/man/mortcast.blend.Rd | 36 +++++ MortCast-2.4-0/MortCast/man/pmdgroup.Rd | 21 +-- MortCast-2.4-0/MortCast/src/init.c | 20 +-- MortCast-2.4-0/MortCast/src/life_tables.c | 143 ++++++++++++++++------- 33 files changed, 363 insertions(+), 174 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 ML framework with spatio-temporal resampling
methods to account for the presence of spatiotemporal autocorrelation
(STAC) in predictor variables. STAC may cause highly biased
performance estimates in cross-validation if ignored.
Author: Patrick Schratz [aut, cre] (<https://orcid.org/0000-0003-0748-6624>),
Marc Becker [aut] (<https://orcid.org/0000-0002-8115-0400>),
Jannes Muenchow [ctb] (<https://orcid.org/0000-0001-7834-4717>),
Michel Lang [ctb] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 0.4.0 dated 2021-06-03 and 0.4.1 dated 2021-06-23
mlr3spatiotempcv-0.4.0/mlr3spatiotempcv/tests/figs |only mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/DESCRIPTION | 12 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/MD5 | 186 +++++----- mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/NEWS.md | 7 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingRepeatedSpCVBlock.R | 3 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingRepeatedSpCVTiles.R | 9 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSpCVBlock.R | 12 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSpCVBuffer.R | 9 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSpCVCoords.R | 9 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSpCVDisc.R | 9 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSpCVEnv.R | 9 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSpCVTiles.R | 9 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/R/ResamplingSptCVCluto.R | 13 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/README.md | 14 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/build/partial.rdb |binary mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/inst/WORDLIST |only mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/inst/doc/mlr3spatiotempcv.html | 120 +++--- mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/inst/doc/spatiotemp-viz.R | 4 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/inst/doc/spatiotemp-viz.Rmd | 4 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/inst/doc/spatiotemp-viz.html | 60 +-- mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/_snaps |only mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/helper.R | 20 - mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/test-1-autoplot.R | 25 + mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/test-ResamplingRepeatedSpCVBlock.R | 2 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/test-ResamplingSpCVBlock.R | 15 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/test-ResamplingSptCVCluto.R | 1 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/tests/testthat/test-as_task.R | 1 mlr3spatiotempcv-0.4.1/mlr3spatiotempcv/vignettes/spatiotemp-viz.Rmd | 4 28 files changed, 316 insertions(+), 241 deletions(-)
More information about mlr3spatiotempcv at CRAN
Permanent link
Title: Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data
Description: A set of tools for parsing, manipulating, and graphing data
classified by a hierarchy (e.g. a taxonomy).
Author: Zachary Foster [aut, cre],
Niklaus Grunwald [ths],
Rob Gilmore [ctb]
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between metacoder versions 0.3.4 dated 2020-04-29 and 0.3.5 dated 2021-06-23
metacoder-0.3.4/metacoder/man/figures/README-unnamed-chunk-12-1.png |only metacoder-0.3.4/metacoder/man/figures/README-unnamed-chunk-15-1.png |only metacoder-0.3.4/metacoder/man/figures/README-unnamed-chunk-17-1.png |only metacoder-0.3.4/metacoder/man/figures/README-unnamed-chunk-19-1.png |only metacoder-0.3.4/metacoder/man/figures/readme_figure.png |only metacoder-0.3.5/metacoder/DESCRIPTION | 21 metacoder-0.3.5/metacoder/MD5 | 316 +++++++--- metacoder-0.3.5/metacoder/NAMESPACE | 182 +++++ metacoder-0.3.5/metacoder/NEWS.md | 12 metacoder-0.3.5/metacoder/R/as_phyloseq.R | 2 metacoder-0.3.5/metacoder/R/calculations--internal.R | 2 metacoder-0.3.5/metacoder/R/calculations.R | 28 metacoder-0.3.5/metacoder/R/heat_tree--internal.R | 2 metacoder-0.3.5/metacoder/R/heat_tree--legend.R | 17 metacoder-0.3.5/metacoder/R/heat_tree--mapping.R | 44 + metacoder-0.3.5/metacoder/R/heat_tree--vertex_size.R | 6 metacoder-0.3.5/metacoder/R/heat_tree.R | 30 metacoder-0.3.5/metacoder/R/heat_tree_matrix.R | 8 metacoder-0.3.5/metacoder/R/imports.R | 2 metacoder-0.3.5/metacoder/R/internal.R | 5 metacoder-0.3.5/metacoder/R/metacoder-package.R | 2 metacoder-0.3.5/metacoder/R/old_taxa--dataset_documentation.R |only metacoder-0.3.5/metacoder/R/old_taxa--globals.R |only metacoder-0.3.5/metacoder/R/old_taxa--hierarchies.R |only metacoder-0.3.5/metacoder/R/old_taxa--hierarchy.R |only metacoder-0.3.5/metacoder/R/old_taxa--imports.R |only metacoder-0.3.5/metacoder/R/old_taxa--internal.R |only metacoder-0.3.5/metacoder/R/old_taxa--lazyhelpers.R |only metacoder-0.3.5/metacoder/R/old_taxa--package.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxa.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--class.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--docs.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--internal.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--option_parsers.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--parsers.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--printers.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxmap--s3.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxon.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxon_database.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxon_id.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxon_name.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxon_rank.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxonomy--class.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxonomy--docs.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxonomy--internal.R |only metacoder-0.3.5/metacoder/R/old_taxa--taxonomy--s3.R |only metacoder-0.3.5/metacoder/R/old_taxa--temp.R |only metacoder-0.3.5/metacoder/R/old_taxa--zzz.R |only metacoder-0.3.5/metacoder/R/option_parsers.R | 2 metacoder-0.3.5/metacoder/R/parsers.R | 64 -- metacoder-0.3.5/metacoder/R/primersearch.R | 12 metacoder-0.3.5/metacoder/R/remove_ambiguous.R | 14 metacoder-0.3.5/metacoder/R/sequence_download.R | 99 ++- metacoder-0.3.5/metacoder/R/startup.R | 2 metacoder-0.3.5/metacoder/R/tools.R | 2 metacoder-0.3.5/metacoder/README.md | 168 +++-- metacoder-0.3.5/metacoder/build/vignette.rds |binary metacoder-0.3.5/metacoder/data/ex_taxmap.rda |only metacoder-0.3.5/metacoder/data/ranks_ref.rda |only metacoder-0.3.5/metacoder/inst/CITATION | 2 metacoder-0.3.5/metacoder/inst/doc/introduction.Rmd | 2 metacoder-0.3.5/metacoder/inst/doc/introduction.html | 195 ------ metacoder-0.3.5/metacoder/man/all_functions.Rd |only metacoder-0.3.5/metacoder/man/all_names.Rd |only metacoder-0.3.5/metacoder/man/arrange_obs.Rd |only metacoder-0.3.5/metacoder/man/arrange_taxa.Rd |only metacoder-0.3.5/metacoder/man/as_id.Rd |only metacoder-0.3.5/metacoder/man/branches.Rd |only metacoder-0.3.5/metacoder/man/calc_group_mean.Rd | 4 metacoder-0.3.5/metacoder/man/calc_group_median.Rd | 4 metacoder-0.3.5/metacoder/man/calc_group_rsd.Rd | 4 metacoder-0.3.5/metacoder/man/calc_group_stat.Rd | 4 metacoder-0.3.5/metacoder/man/calc_n_samples.Rd | 4 metacoder-0.3.5/metacoder/man/calc_obs_props.Rd | 4 metacoder-0.3.5/metacoder/man/calc_prop_samples.Rd | 4 metacoder-0.3.5/metacoder/man/calc_taxon_abund.Rd | 4 metacoder-0.3.5/metacoder/man/can_be_used_in_taxmap.Rd |only metacoder-0.3.5/metacoder/man/check_class_col.Rd |only metacoder-0.3.5/metacoder/man/check_for_pkg.Rd | 8 metacoder-0.3.5/metacoder/man/check_taxmap_data.Rd |only metacoder-0.3.5/metacoder/man/classifications.Rd |only metacoder-0.3.5/metacoder/man/compare_groups.Rd | 2 metacoder-0.3.5/metacoder/man/contains.Rd | 4 metacoder-0.3.5/metacoder/man/convert_base.Rd | 13 metacoder-0.3.5/metacoder/man/correct_taxon_names.Rd |only metacoder-0.3.5/metacoder/man/count_capture_groups.Rd |only metacoder-0.3.5/metacoder/man/counts_to_presence.Rd | 4 metacoder-0.3.5/metacoder/man/data_used.Rd |only metacoder-0.3.5/metacoder/man/database_list.Rd |only metacoder-0.3.5/metacoder/man/desc_font.Rd |only 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metacoder-0.3.5/metacoder/man/get_dataset.Rd |only metacoder-0.3.5/metacoder/man/get_dots_or_list.Rd |only metacoder-0.3.5/metacoder/man/get_sort_var.Rd |only metacoder-0.3.5/metacoder/man/grapes-greater-than-grapes.Rd | 4 metacoder-0.3.5/metacoder/man/heat_tree.Rd | 24 metacoder-0.3.5/metacoder/man/heat_tree_matrix.Rd | 2 metacoder-0.3.5/metacoder/man/hierarchies.Rd |only metacoder-0.3.5/metacoder/man/hierarchy.Rd |only metacoder-0.3.5/metacoder/man/highlight_taxon_ids.Rd |only metacoder-0.3.5/metacoder/man/id_classifications.Rd |only metacoder-0.3.5/metacoder/man/init_taxmap_data.Rd |only metacoder-0.3.5/metacoder/man/internodes.Rd |only metacoder-0.3.5/metacoder/man/is_ambiguous.Rd | 2 metacoder-0.3.5/metacoder/man/is_branch.Rd |only metacoder-0.3.5/metacoder/man/is_internode.Rd |only metacoder-0.3.5/metacoder/man/is_leaf.Rd |only metacoder-0.3.5/metacoder/man/is_root.Rd |only metacoder-0.3.5/metacoder/man/is_stem.Rd |only metacoder-0.3.5/metacoder/man/leaves.Rd |only 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metacoder-0.3.5/metacoder/man/simplify.Rd |only metacoder-0.3.5/metacoder/man/starts_with.Rd | 4 metacoder-0.3.5/metacoder/man/stems.Rd |only metacoder-0.3.5/metacoder/man/subtaxa.Rd |only metacoder-0.3.5/metacoder/man/subtaxa_apply.Rd |only metacoder-0.3.5/metacoder/man/supertaxa.Rd |only metacoder-0.3.5/metacoder/man/supertaxa_apply.Rd |only metacoder-0.3.5/metacoder/man/taxa-package.Rd |only metacoder-0.3.5/metacoder/man/taxa.Rd |only metacoder-0.3.5/metacoder/man/taxmap.Rd |only metacoder-0.3.5/metacoder/man/taxon.Rd |only metacoder-0.3.5/metacoder/man/taxon_database.Rd |only metacoder-0.3.5/metacoder/man/taxon_id.Rd |only metacoder-0.3.5/metacoder/man/taxon_ids.Rd |only metacoder-0.3.5/metacoder/man/taxon_indexes.Rd |only metacoder-0.3.5/metacoder/man/taxon_name.Rd |only metacoder-0.3.5/metacoder/man/taxon_names.Rd |only metacoder-0.3.5/metacoder/man/taxon_rank.Rd |only metacoder-0.3.5/metacoder/man/taxon_ranks.Rd |only metacoder-0.3.5/metacoder/man/taxonomy.Rd |only metacoder-0.3.5/metacoder/man/taxonomy_table.Rd |only metacoder-0.3.5/metacoder/man/tid_font.Rd |only metacoder-0.3.5/metacoder/man/to_percent.Rd |only metacoder-0.3.5/metacoder/man/transmute_obs.Rd |only metacoder-0.3.5/metacoder/man/unique_mapping.Rd | 6 metacoder-0.3.5/metacoder/man/validate_regex_key_pair.Rd |only metacoder-0.3.5/metacoder/man/validate_regex_match.Rd |only metacoder-0.3.5/metacoder/man/validate_taxmap_funcs.Rd |only metacoder-0.3.5/metacoder/man/zero_low_counts.Rd | 4 metacoder-0.3.5/metacoder/tests/testthat/test--taxa.R |only metacoder-0.3.5/metacoder/tests/testthat/test--taxmap.R |only metacoder-0.3.5/metacoder/tests/testthat/test--taxmap_parsers.R |only metacoder-0.3.5/metacoder/tests/testthat/test--taxonomy.R |only metacoder-0.3.5/metacoder/tests/testthat/test-taxon.R |only metacoder-0.3.5/metacoder/tests/testthat/test-taxon_id.R |only metacoder-0.3.5/metacoder/tests/testthat/test-taxon_name.R |only metacoder-0.3.5/metacoder/tests/testthat/test-taxon_rank.R |only metacoder-0.3.5/metacoder/vignettes/introduction.Rmd | 2 240 files changed, 1084 insertions(+), 626 deletions(-)
Title: QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Description: Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
For background, see the 2018 dissertation of P.M. Bourke <doi:10.18174/444415>.
Author: Peter Bourke [aut, cre],
Christine Hackett [ctb],
Chris Maliepaard [ctb],
Geert van Geest [ctb],
Roeland Voorrips [ctb],
Johan Willemsen [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polyqtlR versions 0.0.5 dated 2021-03-10 and 0.0.6 dated 2021-06-23
DESCRIPTION | 18 - MD5 | 29 +-- NAMESPACE | 1 R/accessory_functions.R | 35 +++ R/polyqtlR_functions.R | 370 +++++++++++++++++++++++++++------------- inst/doc/polyqtlR_vignette.R | 48 ++++- inst/doc/polyqtlR_vignette.html | 86 ++++++--- inst/doc/polyqtlR_vignette.rmd | 90 +++++++-- man/PVE.Rd | 17 - man/QTLscan.Rd | 6 man/check_cofactors.Rd |only man/count_recombinations.Rd | 2 man/fast_permute.Rd | 3 man/findQTLpeaks.Rd |only man/impute_dosages.Rd | 5 vignettes/QTLmodel.RDS |only vignettes/polyqtlR_vignette.rmd | 90 +++++++-- 17 files changed, 562 insertions(+), 238 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.
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 1.3.0 dated 2021-03-29 and 1.3.1 dated 2021-06-23
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS | 4 ++++ R/init.R | 2 +- build/vignette.rds |binary inst/doc/gert.html | 17 +++++++++-------- src/Makevars.ucrt |only src/Makevars.win | 2 +- src/clone.c | 20 ++++++++++++++++++++ 9 files changed, 46 insertions(+), 20 deletions(-)
Title: Sparse and Dense Multidimensional Array Storage Engine for Data
Science
Description: The data science storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.9.3 dated 2021-06-03 and 0.9.4 dated 2021-06-23
DESCRIPTION | 6 MD5 | 63 ++++++---- NAMESPACE | 13 ++ NEWS.md | 21 +++ R/Query.R | 15 ++ R/QueryCondition.R |only R/RcppExports.R | 16 ++ R/TileDBArray.R | 152 ++++++++++++++++++++++--- README.md | 4 configure | 35 +++-- configure.ac | 17 +- inst/doc/documentation.html | 18 +- inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 2 inst/include/tiledb.h | 8 + inst/tinytest/test_querycondition.R |only inst/tinytest/test_tiledbarray.R | 20 +++ man/query_condition-set-tiledb_array-method.Rd |only man/query_condition-tiledb_array-method.Rd |only man/return.array-set-tiledb_array-method.Rd |only man/return.array-tiledb_array-method.Rd |only man/return.matrix-set-tiledb_array-method.Rd | 2 man/return.matrix-tiledb_array-method.Rd | 2 man/tiledb_array-class.Rd | 4 man/tiledb_array.Rd | 10 + man/tiledb_query_add_range_with_type.Rd | 4 man/tiledb_query_condition-class.Rd |only man/tiledb_query_condition.Rd |only man/tiledb_query_condition_combine.Rd |only man/tiledb_query_condition_init.Rd |only man/tiledb_query_set_condition.Rd |only src/RcppExports.cpp | 54 ++++++++ src/finalizers.h | 11 + src/libtiledb.cpp | 128 +++++++++++++++++++++ tools/fetchTileDB.sh | 3 tools/fetchTileDBLib.R | 12 + tools/tiledbVersion.txt | 4 vignettes/introduction.Rmd | 2 38 files changed, 537 insertions(+), 91 deletions(-)
Title: Transforming and Harmonizing CCHS Variables
Description: Supporting the use of the Canadian Community Health Survey
(CCHS) by transforming variables from each cycle into harmonized,
consistent versions that span survey cycles (currently, 2001 to
2014). CCHS data used in this library is accessed and adapted in
accordance to the Statistics Canada Open Licence Agreement. This
package uses rec_with_table(), which was developed from 'sjmisc'
rec(). Lüdecke D (2018). "sjmisc: Data and Variable Transformation
Functions". Journal of Open Source Software, 3(26), 754.
<doi:10.21105/joss.00754>.
Author: Doug Manuel [aut, cph] (<https://orcid.org/0000-0003-0912-0845>),
Warsame Yusuf [aut, cre],
Rostyslav Vyuha [aut],
Carol Bennett [aut],
Yulric Sequeira [ctb],
The Ottawa Hospital [cph]
Maintainer: Warsame Yusuf <waryusuf@ohri.ca>
Diff between cchsflow versions 1.8.0 dated 2021-01-24 and 1.8.2 dated 2021-06-23
DESCRIPTION | 8 MD5 | 24 - NEWS.md | 16 R/age-categorical.R | 40 +- R/smoking.R | 13 README.md | 4 data/variable_details.RData |binary data/variables.RData |binary inst/extdata/variable_details.csv | 464 +++++++++++++------------- inst/extdata/variables.csv | 399 +++++++++++----------- man/pack_years_fun.Rd | 2 man/time_quit_smoking_fun.Rd | 11 tests/testdata/rec_with_table_test_data.RData |binary 13 files changed, 504 insertions(+), 477 deletions(-)
Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices
The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines. There
are over 1000 functions in total with an extensive test suite. The 'RcppGSL'
package provides an easy-to-use interface between 'GSL' data structures and
R using concepts from 'Rcpp' which is itself a package that eases the
interfaces between R and C++. This package also serves as a prime example of
how to build a package that uses 'Rcpp' to connect to another third-party
library. The 'autoconf' script, 'inline' plugin and example package can all
be used as a stanza to write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppGSL versions 0.3.8 dated 2020-06-21 and 0.3.9 dated 2021-06-23
ChangeLog | 26 ++++++++++++++++++++++++++ DESCRIPTION | 11 +++++++---- MD5 | 25 +++++++++++++------------ README.md | 3 ++- build/partial.rdb |binary build/vignette.rds |binary configure | 18 +++++++++--------- inst/NEWS.Rd | 10 ++++++++++ inst/doc/RcppGSL-intro.pdf |binary man/fastLm.Rd | 2 +- src/Makevars.ucrt |only src/Makevars.win | 4 ++-- tools/winlibs.R | 12 ++++++------ vignettes/RcppGSL-introduction.pdf |binary 14 files changed, 76 insertions(+), 35 deletions(-)
Title: Exact P-Values and Matching Confidence Intervals for Simple
Discrete Parametric Cases
Description: Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases (see Fay (2010) <doi:10.32614/rj-2010-008>).
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between exactci versions 1.3-3 dated 2017-10-02 and 1.4-2 dated 2021-06-23
ChangeLog | 12 + DESCRIPTION | 14 - MD5 | 20 + NAMESPACE | 1 R/exactpoissonCI.R | 464 ++++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/TwoSidedPoissonCIs.R |only inst/doc/TwoSidedPoissonCIs.Rmd |only inst/doc/TwoSidedPoissonCIs.html |only inst/doc/exactci.pdf |binary man/exactci-package.Rd | 4 tests |only vignettes/TwoSidedPoissonCIs.Rmd |only 13 files changed, 274 insertions(+), 241 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
RStudio [cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph]
(<https://orcid.org/0000-0002-8319-7624>),
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>),
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>),
Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Duncan Luguern [aut],
David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>,
dmkaplan2000),
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Shixiang Wang [aut, ctb] (<https://orcid.org/0000-0001-9855-7357>),
Jay Hesselberth [aut, ctb] (<https://orcid.org/0000-0002-6299-179X>),
Alfredo Hernández [ctb] (<https://orcid.org/0000-0002-2660-4545>),
Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>),
Stefano Coretta [ctb] (<https://orcid.org/0000-0001-9627-5532>,
stefanocoretta),
Alvaro Uzaheta [ctb] (auzaheta)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.19 dated 2021-03-04 and 0.20 dated 2021-06-23
DESCRIPTION | 6 MD5 | 84 ++++---- NEWS.md | 22 ++ R/copernicus_article.R | 24 +- R/joss_article.R | 2 R/rjournal_article.R | 2 inst/rmarkdown/templates/acm/resources/template.tex | 4 inst/rmarkdown/templates/acs/resources/template.tex | 4 inst/rmarkdown/templates/aea/resources/template.tex | 4 inst/rmarkdown/templates/agu/resources/template.tex | 4 inst/rmarkdown/templates/amq/resources/template.tex | 4 inst/rmarkdown/templates/ams/resources/template.tex | 4 inst/rmarkdown/templates/arxiv/resources/template.tex | 4 inst/rmarkdown/templates/asa/resources/template.tex | 4 inst/rmarkdown/templates/bioinformatics/resources/template.tex | 4 inst/rmarkdown/templates/biometrics/resources/template.tex | 4 inst/rmarkdown/templates/copernicus/resources/template.tex | 14 - inst/rmarkdown/templates/copernicus/skeleton/skeleton.Rmd | 38 +++ inst/rmarkdown/templates/elsevier/resources/template.tex | 13 - inst/rmarkdown/templates/frontiers/resources/template.tex | 4 inst/rmarkdown/templates/ieee/resources/template.tex | 4 inst/rmarkdown/templates/ims/resources/template.tex | 4 inst/rmarkdown/templates/jasa/resources/template.tex | 4 inst/rmarkdown/templates/joss/resources/template.tex | 4 inst/rmarkdown/templates/jss/resources/template.tex | 4 inst/rmarkdown/templates/lipics/skeleton/skeleton.Rmd | 8 inst/rmarkdown/templates/mdpi/resources/template.tex | 4 inst/rmarkdown/templates/mnras/resources/template.tex | 4 inst/rmarkdown/templates/oup/resources/template.tex | 96 +++++++++- inst/rmarkdown/templates/oup/skeleton/skeleton.Rmd | 41 +++- inst/rmarkdown/templates/peerj/resources/template.tex | 4 inst/rmarkdown/templates/pihph/resources/template.tex | 4 inst/rmarkdown/templates/plos/resources/template.tex | 4 inst/rmarkdown/templates/pnas/resources/template.tex | 4 inst/rmarkdown/templates/rjournal/resources/RJwrapper.tex | 4 inst/rmarkdown/templates/rjournal/resources/template.tex | 6 inst/rmarkdown/templates/rsos/resources/template.tex | 4 inst/rmarkdown/templates/rss/resources/template.tex | 4 inst/rmarkdown/templates/sage/resources/template.tex | 4 inst/rmarkdown/templates/sim/resources/template.tex | 4 inst/rmarkdown/templates/springer/resources/template.tex | 4 inst/rmarkdown/templates/tf/resources/template.tex | 4 man/copernicus_article.Rd | 18 + 43 files changed, 333 insertions(+), 157 deletions(-)
Title: Quantify the Balance of Phylogenetic Trees
Description: Measures the degree of balance for a given phylogenetic tree by
calculating the Total Cophenetic Index.
Reference: A. Mir, F. Rossello, L. A. Rotger (2013).
A new balance index for phylogenetic trees.
Math. Biosci. 241, 125-136 <doi:10.1016/j.mbs.2012.10.005>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TotalCopheneticIndex versions 2.0.0 dated 2021-01-28 and 2.0.1 dated 2021-06-23
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 2 +- inst/WORDLIST | 3 ++- tests/testthat/test-tci.R | 46 +++++++++++++++++++++++----------------------- 6 files changed, 44 insertions(+), 38 deletions(-)
More information about TotalCopheneticIndex at CRAN
Permanent link
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>
Diff between bbsBayes versions 2.3.6.2020 dated 2021-01-13 and 2.3.7.2020 dated 2021-06-23
bbsBayes-2.3.6.2020/bbsBayes/man/prepare_jags_data.Rd |only bbsBayes-2.3.7.2020/bbsBayes/DESCRIPTION | 8 - bbsBayes-2.3.7.2020/bbsBayes/LICENSE | 4 bbsBayes-2.3.7.2020/bbsBayes/MD5 | 31 ++-- bbsBayes-2.3.7.2020/bbsBayes/NAMESPACE | 2 bbsBayes-2.3.7.2020/bbsBayes/R/generate-map.R | 24 ++- bbsBayes-2.3.7.2020/bbsBayes/R/geofacet-plot.R | 18 ++ bbsBayes-2.3.7.2020/bbsBayes/R/load-map.R |only bbsBayes-2.3.7.2020/bbsBayes/R/plot-indices.R | 10 - bbsBayes-2.3.7.2020/bbsBayes/R/prepare-data.R |only bbsBayes-2.3.7.2020/bbsBayes/R/prepare-jags-data.R | 16 ++ bbsBayes-2.3.7.2020/bbsBayes/R/run-model.R | 2 bbsBayes-2.3.7.2020/bbsBayes/README.md | 14 +- bbsBayes-2.3.7.2020/bbsBayes/man/bbsBayes-deprecated.Rd | 108 +++++++++++++++- bbsBayes-2.3.7.2020/bbsBayes/man/generate_map.Rd | 5 bbsBayes-2.3.7.2020/bbsBayes/man/geofacet_plot.Rd | 5 bbsBayes-2.3.7.2020/bbsBayes/man/load_map.Rd |only bbsBayes-2.3.7.2020/bbsBayes/man/plot_indices.Rd | 3 bbsBayes-2.3.7.2020/bbsBayes/man/prepare_data.Rd |only 19 files changed, 207 insertions(+), 43 deletions(-)
Title: Using the Docker Container to Create R Workers on Local or Cloud
Platform
Description: This is the core package that provides both the user API and developer API to deploy
the parallel cluster on the cloud using the container service. The user can call
clusterPreset() to define the cloud service provider and container and makeDockerCluster()
to create the cluster. The developer should see "developer's cookbook" on how to define
the cloud provider and container.
Author: Jiefei Wang [aut, cre]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Diff between DockerParallel versions 1.0.3 dated 2021-06-07 and 1.0.4 dated 2021-06-23
DESCRIPTION | 6 MD5 | 27 - NEWS | 7 R/all-generics-CloudProvider.R | 41 + R/all-generics-ContainerProvider.R | 10 R/all-generics-base.R | 8 R/method-DockerCluster-utils.R | 17 R/method-DockerCluster.R | 917 +++++++++++++++++++------------------ README.md | 604 ++++++++++++------------ build/vignette.rds |binary inst/doc/developer-cookbook.html | 98 +-- inst/doc/vignette.Rmd |only inst/doc/vignette.html |only man/reconnectDockerCluster.Rd | 21 vignettes/package-structure.jpg |binary vignettes/vignette.Rmd |only 16 files changed, 906 insertions(+), 850 deletions(-)
More information about DockerParallel at CRAN
Permanent link
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>),
Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>),
Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>),
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.0.0 dated 2021-05-16 and 1.0.1 dated 2021-06-23
DESCRIPTION | 6 - MD5 | 15 +-- NEWS.md | 5 + README.md | 2 build/vignette.rds |binary inst/doc/api.html | 15 ++- inst/extdata/ccle_drug_response_extend.rda |only inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 68 ++++++++-------- inst/shinyapp/ui/help.R | 3 9 files changed, 63 insertions(+), 51 deletions(-)
Title: Field Observation Quick Analysis Toolkit
Description: Tools for quickly processing and analyzing
field observation data and air quality data. This
tools contain functions that facilitate analysis
in atmospheric chemistry (especially in ozone
pollution). Some functions of time series are also
applicable to other fields. For detail please view
homepage<https://github.com/tianshu129/foqat>.
Scientific Reference:
1. The Hydroxyl Radical (OH) Reactivity: Roger Atkinson and Janet Arey (2003) <doi:10.1021/cr0206420>.
2. Ozone Formation Potential (OFP): <https://ww2.arb.ca.gov/sites/default/files/classic/regact/2009/mir2009/mir10.pdf>.
3. TUV model: <https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model>.
Author: Tianshu Chen
Maintainer: Tianshu Chen <tianshu129@163.com>
Diff between foqat versions 1.6.4 dated 2021-03-28 and 1.6.5 dated 2021-06-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/loh.R | 2 -- R/ofp.R | 2 -- R/vocct.R | 2 -- man/loh.Rd | 3 --- man/ofp.Rd | 3 --- man/vocct.Rd | 3 --- 8 files changed, 11 insertions(+), 26 deletions(-)
Title: Interface to the 'qpmad' Quadratic Programming Solver
Description: Efficiently solve quadratic problems with linear inequality, equality and box constraints. The method used is outlined in D. Goldfarb, and A. Idnani (1983) <doi:10.1007/BF02591962>.
Author: Eric Anderson [aut, cre],
Alexander Sherikov [cph, ctb]
Maintainer: Eric Anderson <anderic1@gmx.com>
Diff between qpmadr versions 0.1.0 dated 2020-08-06 and 1.1.0-0 dated 2021-06-23
qpmadr-0.1.0/qpmadr/inst/include/qpmad/cholesky.h |only qpmadr-1.1.0-0/qpmadr/DESCRIPTION | 10 qpmadr-1.1.0-0/qpmadr/MD5 | 45 qpmadr-1.1.0-0/qpmadr/NAMESPACE | 1 qpmadr-1.1.0-0/qpmadr/NEWS.md | 7 qpmadr-1.1.0-0/qpmadr/R/RcppExports.R | 4 qpmadr-1.1.0-0/qpmadr/R/qpmad_package.R | 2 qpmadr-1.1.0-0/qpmadr/R/solve.R | 62 qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/active_set.h | 112 - qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/chosen_constraint.h | 36 qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/common.h | 21 qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/constraint_status.h | 22 qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/factorization_data.h | 355 +-- qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/givens.h | 240 +- qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/input_parser.h | 164 - qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/inverse.h | 28 qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/solver.h | 1008 +++++----- qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/solver_parameters.h | 50 qpmadr-1.1.0-0/qpmadr/inst/include/qpmad/testing.h | 117 - qpmadr-1.1.0-0/qpmadr/inst/tinytest/test_base.R | 14 qpmadr-1.1.0-0/qpmadr/man/qpmadParameters.Rd | 86 qpmadr-1.1.0-0/qpmadr/man/solveqp.Rd | 3 qpmadr-1.1.0-0/qpmadr/src/RcppExports.cpp | 13 qpmadr-1.1.0-0/qpmadr/src/qpmad_interface.cpp | 111 - 24 files changed, 1365 insertions(+), 1146 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 2.1-0 dated 2021-04-03 and 2.2-0 dated 2021-06-23
DESCRIPTION | 14 +-- MD5 | 30 +++---- NEWS | 194 +++++++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/Nickname.txt | 2 inst/doc/bugfixes.Rnw | 26 +++++- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 143 +++++++++++++++++++++++++++++---- inst/doc/updates.pdf |binary vignettes/bugfixes.Rnw | 26 +++++- vignettes/updates.Rnw | 143 +++++++++++++++++++++++++++++---- 16 files changed, 511 insertions(+), 68 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets on solid state drives. This bypasses limitation of physical memory size as well as limited bandwidth of database interfaces. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface. The data is memory mapped into R and then accessed using usual R list and array subscription operators. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as standalone C library. libMVL has simple C API making it easy to interchange of datasets with outside programs.
Author: Vladimir Dergachev [aut, cre] (<https://orcid.org/0000-0003-4708-6625>)
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 0.0.1.0 dated 2021-06-22 and 0.0.1.2 dated 2021-06-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/RMVL.R | 7 +++++-- src/libMVL.c | 5 +++++ 4 files changed, 16 insertions(+), 8 deletions(-)
More information about parallelMCMCcombine at CRAN
Permanent link
Title: Functions to Facilitate the Simulation of Large Scale Assessment
Data
Description: Provides functions to simulate data from large-scale educational
assessments, including background questionnaire data and cognitive item
responses that adhere to a multiple-matrix sampled design. The theoretical
foundation can be found on
Matta, T.H., Rutkowski, L., Rutkowski, D. et al. (2018)
<doi:10.1186/s40536-018-0068-8>.
Author: Tyler Matta [aut],
Leslie Rutkowski [aut],
David Rutkowski [aut],
Yuan-Ling Linda Liaw [aut],
Kondwani Kajera Mughogho [ctb],
Waldir Leoncio [aut, cre],
Sinan Yavuz [ctb],
Paul Bailey [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between lsasim versions 2.0.2 dated 2020-09-10 and 2.1.0 dated 2021-06-23
lsasim-2.0.2/lsasim/R/run_condition_checks.R |only lsasim-2.0.2/lsasim/man/run_condition_checks.Rd |only lsasim-2.0.2/lsasim/tests/testthat/test.betagenCmean.R |only lsasim-2.0.2/lsasim/tests/testthat/test.betagenCsd.R |only lsasim-2.1.0/lsasim/DESCRIPTION | 29 +- lsasim-2.1.0/lsasim/MD5 | 129 ++++++++-- lsasim-2.1.0/lsasim/NAMESPACE | 24 + lsasim-2.1.0/lsasim/R/anova.R |only lsasim-2.1.0/lsasim/R/attribute_cluster_labels.R |only lsasim-2.1.0/lsasim/R/beta_gen.R | 8 lsasim-2.1.0/lsasim/R/brr.R |only lsasim-2.1.0/lsasim/R/calc_n_tilde.R |only lsasim-2.1.0/lsasim/R/calc_replicate_weights.R |only lsasim-2.1.0/lsasim/R/calc_se_rho.R |only lsasim-2.1.0/lsasim/R/calc_var_between.R |only lsasim-2.1.0/lsasim/R/calc_var_tot.R |only lsasim-2.1.0/lsasim/R/calc_var_within.R |only lsasim-2.1.0/lsasim/R/check_n_N_class.R |only lsasim-2.1.0/lsasim/R/check_valid_structure.R |only lsasim-2.1.0/lsasim/R/cluster_gen.R |only lsasim-2.1.0/lsasim/R/cluster_gen_separate.R |only lsasim-2.1.0/lsasim/R/cluster_gen_together.R |only lsasim-2.1.0/lsasim/R/cluster_message.R |only lsasim-2.1.0/lsasim/R/convert_vector_to_list.R |only lsasim-2.1.0/lsasim/R/customize_summary.R |only lsasim-2.1.0/lsasim/R/draw_cluster_structure.R |only lsasim-2.1.0/lsasim/R/gen_X_W_cluster.R |only lsasim-2.1.0/lsasim/R/gen_variable_n.R | 13 - lsasim-2.1.0/lsasim/R/intraclass_cor.R |only lsasim-2.1.0/lsasim/R/irt_gen.R | 9 lsasim-2.1.0/lsasim/R/jackknife.R |only lsasim-2.1.0/lsasim/R/label_respondents.R |only lsasim-2.1.0/lsasim/R/lsasim.R | 7 lsasim-2.1.0/lsasim/R/misc.R |only lsasim-2.1.0/lsasim/R/pluralize.R |only lsasim-2.1.0/lsasim/R/print_anova_table.R |only lsasim-2.1.0/lsasim/R/questionnaire_gen.R | 35 +- lsasim-2.1.0/lsasim/R/ranges.R |only lsasim-2.1.0/lsasim/R/recalc_final_weights.R |only lsasim-2.1.0/lsasim/R/replicate_var.R |only lsasim-2.1.0/lsasim/R/response_gen.R | 66 ++--- lsasim-2.1.0/lsasim/R/rzeropois.R |only lsasim-2.1.0/lsasim/R/sample_from.R |only lsasim-2.1.0/lsasim/R/sample_within_range.R |only lsasim-2.1.0/lsasim/R/select.R |only lsasim-2.1.0/lsasim/R/summary.R |only lsasim-2.1.0/lsasim/R/summary_2.R |only lsasim-2.1.0/lsasim/R/trim_sample.R |only lsasim-2.1.0/lsasim/R/validate.R |only lsasim-2.1.0/lsasim/R/weight_responses.R |only lsasim-2.1.0/lsasim/R/whitelist_message.R |only lsasim-2.1.0/lsasim/build |only lsasim-2.1.0/lsasim/inst |only lsasim-2.1.0/lsasim/man/anova.lsasimcluster.Rd |only lsasim-2.1.0/lsasim/man/attribute_cluster_labels.Rd |only lsasim-2.1.0/lsasim/man/beta_gen.Rd | 10 lsasim-2.1.0/lsasim/man/brr.Rd |only lsasim-2.1.0/lsasim/man/calc_n_tilde.Rd |only lsasim-2.1.0/lsasim/man/calc_replicate_weights.Rd |only lsasim-2.1.0/lsasim/man/calc_se_rho.Rd |only lsasim-2.1.0/lsasim/man/calc_var_between.Rd |only lsasim-2.1.0/lsasim/man/calc_var_tot.Rd |only lsasim-2.1.0/lsasim/man/calc_var_within.Rd |only lsasim-2.1.0/lsasim/man/check_n_N_class.Rd |only lsasim-2.1.0/lsasim/man/check_valid_structure.Rd |only lsasim-2.1.0/lsasim/man/cluster_gen.Rd |only lsasim-2.1.0/lsasim/man/cluster_gen_separate.Rd |only lsasim-2.1.0/lsasim/man/cluster_gen_together.Rd |only lsasim-2.1.0/lsasim/man/cluster_message.Rd |only lsasim-2.1.0/lsasim/man/convert_vector_to_list.Rd |only lsasim-2.1.0/lsasim/man/customize_summary.Rd |only lsasim-2.1.0/lsasim/man/dot-onAttach.Rd |only lsasim-2.1.0/lsasim/man/draw_cluster_structure.Rd |only lsasim-2.1.0/lsasim/man/gen_X_W_cluster.Rd |only lsasim-2.1.0/lsasim/man/intraclass_cor.Rd |only lsasim-2.1.0/lsasim/man/jackknife.Rd |only lsasim-2.1.0/lsasim/man/label_respondents.Rd |only lsasim-2.1.0/lsasim/man/lsasim.Rd | 8 lsasim-2.1.0/lsasim/man/pluralize.Rd |only lsasim-2.1.0/lsasim/man/print_anova.Rd |only lsasim-2.1.0/lsasim/man/questionnaire_gen.Rd | 29 +- lsasim-2.1.0/lsasim/man/ranges.Rd |only lsasim-2.1.0/lsasim/man/recalc_final_weights.Rd |only lsasim-2.1.0/lsasim/man/replicate_var.Rd |only lsasim-2.1.0/lsasim/man/response_gen.Rd | 28 +- lsasim-2.1.0/lsasim/man/rzeropois.Rd |only lsasim-2.1.0/lsasim/man/sample_from.Rd |only lsasim-2.1.0/lsasim/man/sample_within_range.Rd |only lsasim-2.1.0/lsasim/man/select.Rd |only lsasim-2.1.0/lsasim/man/summary.lsasimcluster.Rd |only lsasim-2.1.0/lsasim/man/summary_2.Rd |only lsasim-2.1.0/lsasim/man/trim_sample.Rd |only lsasim-2.1.0/lsasim/man/validate_questionnaire_gen.Rd |only lsasim-2.1.0/lsasim/man/weight_responses.Rd |only lsasim-2.1.0/lsasim/man/whitelist_message.Rd |only lsasim-2.1.0/lsasim/tests/testthat/test.HugoReport.R |only lsasim-2.1.0/lsasim/tests/testthat/test.LindaReports.R | 8 lsasim-2.1.0/lsasim/tests/testthat/test.betagenCmeanCsd.R |only lsasim-2.1.0/lsasim/tests/testthat/test.clusterSamples.R |only lsasim-2.1.0/lsasim/tests/testthat/test.irt_gen.R |only lsasim-2.1.0/lsasim/tests/testthat/test.listOflists.R |only lsasim-2.1.0/lsasim/tests/testthat/test.randomClusterSampling.R |only lsasim-2.1.0/lsasim/vignettes |only 103 files changed, 279 insertions(+), 124 deletions(-)
Title: 'DataSHIELD' Implementation on Local Datasets
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This 'DataSHIELD Interface' implementation is for analyzing datasets living
in the current R session. The purpose of this is primarily for lightweight
'DataSHIELD' analysis package development.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>)
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between DSLite versions 1.2.0 dated 2021-03-16 and 1.3.0 dated 2021-06-23
DESCRIPTION | 16 +++++++------ MD5 | 29 +++++++++++++---------- NAMESPACE | 3 ++ R/DSLiteConnection.R | 24 +++++++++++++++---- R/DSLiteServer.R | 25 +++++++++++++++++--- README.md | 10 ++++---- build/vignette.rds |binary inst/doc/developing-with-dslite.Rmd | 2 - inst/doc/developing-with-dslite.html | 11 +++++++- inst/examples/datashield.R | 16 +++++++------ man/DSLiteServer.Rd | 32 +++++++++++++++++++++++--- man/dsAssignTable-DSLiteConnection-method.Rd | 4 +-- man/dsConnect-DSLiteDriver-method.Rd | 4 ++- man/dsIsCompleted-DSLiteResult-method.Rd |only man/dsKeepAlive-DSLiteConnection-method.Rd |only man/dsListProfiles-DSLiteConnection-method.Rd |only vignettes/developing-with-dslite.Rmd | 2 - 17 files changed, 128 insertions(+), 50 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
calculation of ancestor-descendant relationships;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.4.4 dated 2021-04-20 and 1.4.5 dated 2021-06-23
TreeTools-1.4.4/TreeTools/tests/figs |only TreeTools-1.4.5/TreeTools/DESCRIPTION | 11 TreeTools-1.4.5/TreeTools/MD5 | 96 ++-- TreeTools-1.4.5/TreeTools/NAMESPACE | 11 TreeTools-1.4.5/TreeTools/NEWS.md | 16 TreeTools-1.4.5/TreeTools/R/Combinatorics.R | 4 TreeTools-1.4.5/TreeTools/R/Information.R | 2 TreeTools-1.4.5/TreeTools/R/SplitFunctions.R | 8 TreeTools-1.4.5/TreeTools/R/Splits.R | 14 TreeTools-1.4.5/TreeTools/R/Support.R | 11 TreeTools-1.4.5/TreeTools/R/TotalCopheneticIndex.R | 6 TreeTools-1.4.5/TreeTools/R/data.R | 4 TreeTools-1.4.5/TreeTools/R/parse_files.R | 204 ++++++++-- TreeTools-1.4.5/TreeTools/R/phylo.R | 11 TreeTools-1.4.5/TreeTools/R/tree_display.R | 2 TreeTools-1.4.5/TreeTools/R/tree_generation.R | 2 TreeTools-1.4.5/TreeTools/R/tree_numbering.R | 24 + TreeTools-1.4.5/TreeTools/R/tree_properties.R | 4 TreeTools-1.4.5/TreeTools/R/tree_rearrangement.R | 45 ++ TreeTools-1.4.5/TreeTools/R/tree_shape.R | 11 TreeTools-1.4.5/TreeTools/build/partial.rdb |binary TreeTools-1.4.5/TreeTools/build/vignette.rds |binary TreeTools-1.4.5/TreeTools/inst/REFERENCES.bib | 4 TreeTools-1.4.5/TreeTools/inst/doc/filesystem-navigation.html | 201 --------- TreeTools-1.4.5/TreeTools/inst/doc/load-data.html | 201 --------- TreeTools-1.4.5/TreeTools/inst/doc/load-trees.html | 201 --------- TreeTools-1.4.5/TreeTools/man/AddTip.Rd | 2 TreeTools-1.4.5/TreeTools/man/ApeTime.Rd | 4 TreeTools-1.4.5/TreeTools/man/CollapseNode.Rd | 2 TreeTools-1.4.5/TreeTools/man/ConsensusWithout.Rd | 2 TreeTools-1.4.5/TreeTools/man/EndSentence.Rd |only TreeTools-1.4.5/TreeTools/man/Lobo.data.Rd | 5 TreeTools-1.4.5/TreeTools/man/MorphoBankDecode.Rd |only TreeTools-1.4.5/TreeTools/man/PhyToString.Rd | 3 TreeTools-1.4.5/TreeTools/man/ReadCharacters.Rd | 11 TreeTools-1.4.5/TreeTools/man/ReadTntTree.Rd | 8 TreeTools-1.4.5/TreeTools/man/RenumberTips.Rd | 3 TreeTools-1.4.5/TreeTools/man/Reorder.Rd | 15 TreeTools-1.4.5/TreeTools/man/RightmostCharacter.Rd | 8 TreeTools-1.4.5/TreeTools/man/SplitInformation.Rd | 2 TreeTools-1.4.5/TreeTools/man/TipLabels.Rd | 4 TreeTools-1.4.5/TreeTools/man/TreeShape.Rd | 4 TreeTools-1.4.5/TreeTools/man/Unquote.Rd |only TreeTools-1.4.5/TreeTools/tests/testthat/_snaps |only TreeTools-1.4.5/TreeTools/tests/testthat/test-Support.R | 19 TreeTools-1.4.5/TreeTools/tests/testthat/test-TotalCopheneticIndex.R | 4 TreeTools-1.4.5/TreeTools/tests/testthat/test-mst.R | 6 TreeTools-1.4.5/TreeTools/tests/testthat/test-parsers.R | 25 + TreeTools-1.4.5/TreeTools/tests/testthat/test-phylo.R | 7 TreeTools-1.4.5/TreeTools/tests/testthat/test-tree_rearrange.R | 3 50 files changed, 504 insertions(+), 726 deletions(-)
Title: Scrape the Web with Extra Power
Description: Tools for scraping information from webpages and other XML contents, using XPath or CSS selectors.
Author: Julien Boelaert <jubo.stats@gmail.com>
Maintainer: Julien Boelaert <jubo.stats@gmail.com>
Diff between scraEP versions 1.1 dated 2018-07-03 and 1.2 dated 2021-06-23
scraEP-1.1/scraEP/R/scraEP.R |only scraEP-1.1/scraEP/man/scraEP.Rd |only scraEP-1.2/scraEP/DESCRIPTION | 16 +- scraEP-1.2/scraEP/MD5 | 17 +- scraEP-1.2/scraEP/NAMESPACE | 8 - scraEP-1.2/scraEP/R/text-functions.R |only scraEP-1.2/scraEP/R/xscrape.R | 185 +++++++++++++++++++++++++------- scraEP-1.2/scraEP/data/wiki.rda |binary scraEP-1.2/scraEP/man/scraEP-package.Rd | 14 +- scraEP-1.2/scraEP/man/strcomp.Rd |only scraEP-1.2/scraEP/man/unaccent.Rd |only scraEP-1.2/scraEP/man/xscrape.Rd | 38 ++++-- 12 files changed, 204 insertions(+), 74 deletions(-)
Title: The Self-Controlled Case Series Method
Description: Various self-controlled case series models used to investigate
associations between time-varying exposures such as vaccines or
other drugs or non drug exposures and an adverse event can be
fitted. Detailed information on the self-controlled case series
method and its extensions with more examples can be found in
Farrington, P., Whitaker, H., and Ghebremichael Weldeselassie, Y.
(2018, ISBN: 978-1-4987-8159-6. Self-controlled Case Series studies:
A modelling Guide with R. Boca Raton: Chapman & Hall/CRC Press)
and <https://sccs-studies.info>.
Author: Yonas Ghebremichael Weldeselassie, Heather Whitaker, Paddy Farrington
Maintainer: "Yonas Ghebremichael-Weldeselassie" <y.weldeselassie@warwick.ac.uk>
Diff between SCCS versions 1.2 dated 2020-10-01 and 1.3 dated 2021-06-23
DESCRIPTION | 8 MD5 | 16 R/simulatesccsdata.R | 852 +++++++++++++++++++++++++-------------------------- man/SCCS-package.Rd | 94 ++--- man/eventdepenexp.Rd | 312 +++++++++--------- man/eventdepenobs.Rd | 302 +++++++++--------- man/formatdata.Rd | 282 ++++++++-------- man/nonparasccs.Rd | 234 +++++++------- man/quantsccs.Rd | 151 ++++----- 9 files changed, 1127 insertions(+), 1124 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Data
Description: Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data. See Krivitsky and Morris (2017) <doi:10.1214/16-AOAS1010>.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Steven M. Goodreau [ctb],
Martina Morris [ctb],
Kirk Li [ctb],
Emily N. Beylerian [ctb],
Michał Bojanowski [ctb] (<https://orcid.org/0000-0001-7503-852X>),
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <p.krivitsky@unsw.edu.au>
Diff between ergm.ego versions 0.9.0 dated 2021-06-21 and 1.0.0 dated 2021-06-23
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- R/summary.statistics.egor.R | 61 +++++++++++++++++++++----------------------- build/ergm.ego.pdf |binary build/partial.rdb |binary inst/CITATION | 4 +- inst/NEWS.Rd | 2 - 7 files changed, 43 insertions(+), 44 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between curl versions 4.3.1 dated 2021-04-30 and 4.3.2 dated 2021-06-23
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NEWS | 4 ++++ build/vignette.rds |binary inst/doc/intro.html | 47 +++++++++++++++++++++++++---------------------- inst/doc/windows.html | 3 +++ src/Makevars.ucrt |only src/Makevars.win | 4 ++-- 8 files changed, 44 insertions(+), 33 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-31 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-09 0.2.2
2020-07-21 0.2.0
2020-06-13 0.1.4
2019-06-10 0.1.3
2018-04-13 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-18 1.7.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-29 0.1
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Deo Salil [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] (<https://orcid.org/0000-0002-7111-0077>),
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>),
John Little [ctb],
Joselyn Chávez [ctb] (<https://orcid.org/0000-0002-4974-4591>),
Joseph Casillas [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Matthew Mark Strasiotto [ctb] (mstr3336),
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Klemm [ctb] (<https://orcid.org/0000-0002-5985-1737>),
Paul Lemmens [ctb],
Sean Lopp [ctb],
Silvia Canelon [ctb] (<https://orcid.org/0000-0003-1709-1394>),
Susan VanderPlas [ctb] (<https://orcid.org/0000-0002-3803-0972>),
Tuo Wang [ctb],
Waldir Leoncio [ctb],
Yongfu Liao [ctb],
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>),
Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.21 dated 2021-05-19 and 0.22 dated 2021-06-23
DESCRIPTION | 14 +++++++--- MD5 | 9 ++++-- build/vignette.rds |binary inst/rmarkdown/templates/xaringan/resources/glasgow_template.css |only inst/rmarkdown/templates/xaringan/resources/useR.css | 1 inst/rmarkdown/templates/xaringan/resources/uwm-fonts.css |only inst/rmarkdown/templates/xaringan/resources/uwm.css |only 7 files changed, 16 insertions(+), 8 deletions(-)
Title: Data Utility Functions
Description: Data utility functions for use in probability and statistics. Includes functions for computing higher-moments for samples and their decompositions.
Also includes utilities to examine functional mappings between factor variables and other variables in a data set.
Author: Ben O'Neill [aut, cre]
Maintainer: Ben O'Neill <ben.oneill@hotmail.com>
Diff between utilities versions 0.1.0 dated 2021-01-14 and 0.3.0 dated 2021-06-23
DESCRIPTION | 11 +++++------ MD5 | 16 ++++++++++++---- NAMESPACE | 1 + R/datasets.str.R |only R/log.R | 22 ++++++++++++++++++---- R/nlm.prob.R |only R/rm.attr.R |only R/softmax.R |only man/datasets.str.Rd |only man/log.Rd | 16 +++++++++++++--- man/nlm.prob.Rd |only man/rm.attr.Rd |only man/softmax.Rd |only 13 files changed, 49 insertions(+), 17 deletions(-)
Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under
various designs and sampling schemes. The main function, superbPlot(), can either return a plot
or a dataframe with the statistic and its precision interval so that other plotting package
can be used. See Cousineau (2017) <doi:10.5709/acp-0214-z> for a review or Cousineau (2005)
<doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012)
<doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>,
Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding
<doi:10.20982/tqmp.15.1.p001>.
Author: Denis Cousineau [aut, cre],
Bradley Harding [ctb],
Marc-Andre Goulet [ctb],
Jesika Walker [art]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between superb versions 0.9.5.0 dated 2021-04-21 and 0.9.7.5 dated 2021-06-23
DESCRIPTION | 18 +- MD5 | 181 ++++++++++++---------- NAMESPACE | 13 + NEWS.md | 33 ++++ R/CousineauLaurencelleLambda.R | 2 R/TMB1964r.R | 2 R/WelchDegreeOfFreedom.R | 6 R/dataFigure1.R | 2 R/dataFigure2.R | 2 R/dataFigure3.R | 2 R/dataFigure4.R | 2 R/functionsLogical.R | 32 +++ R/functionsPlotting_advanced.R | 43 ++--- R/functionsPlotting_base.R | 61 ++++--- R/functionsStatistical.R | 4 R/geom_superberrorbar.R |only R/makeTransparent.R |only R/showSignificance.R |only R/superb-package.R | 3 R/superbData.R | 21 +- R/superbPlot.R | 87 +++++++--- R/superbShiny.R |only R/testWinerCompoundSymmetry.R | 1 README.md | 65 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/REFERENCES.bib | 125 ++++++++++----- inst/doc/TheMakingOf.R | 215 ++++++++------------------ inst/doc/TheMakingOf.Rmd | 268 ++++++++++++--------------------- inst/doc/TheMakingOf.html | 212 ++++++++++++++------------ inst/doc/Vignette1.R | 11 - inst/doc/Vignette1.Rmd | 44 ++--- inst/doc/Vignette1.html | 40 ++-- inst/doc/Vignette2.R | 34 +--- inst/doc/Vignette2.Rmd | 87 +++++----- inst/doc/Vignette2.html | 60 +++---- inst/doc/Vignette3.R | 42 ++--- inst/doc/Vignette3.Rmd | 94 ++++++----- inst/doc/Vignette3.html | 38 ++-- inst/doc/Vignette4.R | 81 ++++----- inst/doc/Vignette4.Rmd | 148 ++++++++---------- inst/doc/Vignette4.html | 130 ++++++---------- inst/doc/Vignette5.R | 25 +-- inst/doc/Vignette5.Rmd | 58 +++---- inst/doc/Vignette5.html | 65 +++----- inst/doc/Vignette6.R | 10 - inst/doc/Vignette6.Rmd | 55 +++--- inst/doc/Vignette6.html | 65 ++++---- inst/doc/Vignette7.R | 26 +-- inst/doc/Vignette7.Rmd | 79 +++++---- inst/doc/Vignette7.html | 63 ++++--- inst/doc/Vignette8.R | 16 - inst/doc/Vignette8.Rmd | 53 +++--- inst/doc/Vignette8.html | 49 +++--- inst/doc/Vignette9.R |only inst/doc/Vignette9.Rmd |only inst/doc/Vignette9.html |only inst/doc/VignetteA.R |only inst/doc/VignetteA.Rmd |only inst/doc/VignetteA.html |only inst/doc/VignetteB.R |only inst/doc/VignetteB.Rmd |only inst/doc/VignetteB.html |only inst/superbShiny |only man/CousineauLaurencelleLambda.Rd | 2 man/TMB1964r.Rd | 2 man/WelchDegreeOfFreedom.Rd | 6 man/dataFigure1.Rd | 2 man/dataFigure2.Rd | 2 man/dataFigure3.Rd | 2 man/dataFigure4.Rd | 2 man/geom_superberrorbar.Rd |only man/makeTransparent.Rd |only man/precisionMeasureWithCustomDF.Rd | 4 man/showSignificance.Rd |only man/superb-package.Rd | 10 + man/superbData.Rd | 5 man/superbPlot.Rd | 7 man/superbPlot.bar.Rd | 2 man/superbPlot.halfwidthline.Rd | 2 man/superbPlot.line.Rd | 2 man/superbPlot.point.Rd | 2 man/superbPlot.pointindividualline.Rd | 2 man/superbPlot.pointjitter.Rd | 2 man/superbPlot.pointjitterviolin.Rd | 2 man/superbPlot.raincloud.Rd | 9 - man/superbShiny.Rd |only tests/testthat/test_showSignificance.R |only tests/testthat/test_superbPlot.R | 4 vignettes/TheMakingOf.Rmd | 268 ++++++++++++--------------------- vignettes/Vignette1.Rmd | 44 ++--- vignettes/Vignette2.Rmd | 87 +++++----- vignettes/Vignette3.Rmd | 94 ++++++----- vignettes/Vignette4.Rmd | 148 ++++++++---------- vignettes/Vignette5.Rmd | 58 +++---- vignettes/Vignette6.Rmd | 55 +++--- vignettes/Vignette7.Rmd | 79 +++++---- vignettes/Vignette8.Rmd | 53 +++--- vignettes/Vignette9.Rmd |only vignettes/VignetteA.Rmd |only vignettes/VignetteB.Rmd |only 102 files changed, 1886 insertions(+), 1848 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>),
Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>),
Xianying Tan [aut] (<https://orcid.org/0000-0002-6072-3521>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
RStudio, PBC [cph],
Adam Hyde [ctb] (paged.js in resources/js/),
Min-Zhong Lu [ctb] (resume.css in resources/css/),
Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.14 dated 2021-04-14 and 0.15 dated 2021-06-23
DESCRIPTION | 6 +-- MD5 | 22 +++++------ NEWS.md | 32 +++++++++++++--- R/chrome.R | 78 +++++++++++++++++++++++++---------------- R/paged.R | 1 README.md | 2 - inst/resources/css/default.css | 4 ++ inst/resources/css/jss.css | 22 +++++++++-- inst/resources/css/thesis.css | 4 ++ inst/resources/js/hooks.js | 1 man/chrome_print.Rd | 17 ++++---- man/find_chrome.Rd | 10 ++--- 12 files changed, 131 insertions(+), 68 deletions(-)
Title: Data and Functions for the Book Modern Statistical Graphics
Description: A companion to the Chinese book ``Modern Statistical Graphics''.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Peng Zhao [aut],
Lijia Yu [ctb],
Xiangyun Huang [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between MSG versions 0.6 dated 2020-11-30 and 0.7 dated 2021-06-23
DESCRIPTION | 12 - MD5 | 45 ++-- NEWS.md | 4 R/msg.R | 8 README.md | 2 demo/gradArrows1.R | 10 inst/examples/OLS-LMS2.R | 2 inst/examples/basketball.R | 4 inst/examples/coplot.R | 2 inst/examples/fourfoldplot.R | 6 inst/examples/gov-cn-pct.R | 2 inst/examples/gov-cn-pct2.R | 4 inst/examples/interaction-bubble-tikz.R | 2 inst/examples/interaction-bubble.R | 2 inst/examples/lines-demo.R | 5 inst/examples/murcia-ternary.R | 2 inst/examples/nightingale-ggplot2.R | 11 inst/examples/par1.R | 2 inst/examples/par2.R | 2 inst/examples/plot-region.R | 15 - inst/examples/plot-type-tikz.R |only inst/examples/survival2.R | 2 inst/examples/text.R | 6 inst/extdata/graphnr.csv | 360 +++++++++++++++----------------- 24 files changed, 262 insertions(+), 248 deletions(-)
Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jeffrey Horner [ctb],
Beilei Bian [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between mime versions 0.10 dated 2021-02-13 and 0.11 dated 2021-06-23
mime-0.10/mime/NEWS |only mime-0.11/mime/DESCRIPTION | 7 +++---- mime-0.11/mime/MD5 | 4 ++-- mime-0.11/mime/inst |only 4 files changed, 5 insertions(+), 6 deletions(-)
Title: Molecular Detection Mapping and Analysis Platform
Description: Runs a Shiny web application that merges raw 'qPCR' fluorescence data with related
metadata to visualize species presence/absence detection patterns and assess data quality.
The application calculates threshold values from raw fluorescence data using a method based
on the second derivative method, Luu-The et al (2005) <doi:10.2144/05382RR05>, and utilizes
the ‘chipPCR’ package by Rödiger, Burdukiewicz, & Schierack (2015) <doi:10.1093/bioinformatics/btv205>
to calculate Cq values. The application has the ability to connect to a custom developed MySQL
database to populate the applications interface. The application allows users to interact with
visualizations such as a dynamic map, amplification curves and standard curves, that allow for
zooming and/or filtering. It also enables the generation of customized exportable reports based
on filtered mapping data.
Author: Alka Benawra <alkabenawra@rogers.com>
Maintainer: Alka Benawra <alkabenawra@rogers.com>
Diff between MDMAPR versions 0.2.2 dated 2021-04-06 and 0.2.3 dated 2021-06-23
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)