Title: Create United States Uniform Cartogram Heatmaps
Description: The 'cartogram' heatmaps generated by the included methods
are an alternative to choropleth maps for the United States
and are based on work by the Washington Post graphics department in their report
on "The states most threatened by trade"
(<http://www.washingtonpost.com/wp-srv/special/business/states-most-threatened-by-trade/>).
"State bins" preserve as much of the geographic placement of the states as
possible but have the look and feel of a traditional heatmap. Functions are
provided that allow for use of a binned, discrete scale, a continuous scale
or manually specified colors depending on what is needed for the underlying data.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>),
Harold Gil [ctb] (fix for show.guide),
Brian Adams [ctb] (theme testing & feedback),
Thomas Wood [ctb] (Significant suggestions & testing that made new
features possible),
Mathew Kiang [ctb] (Minor fix for NA handling)
Maintainer: Bob Rudis <bob@rud.is>
Diff between statebins versions 1.2.2 dated 2015-12-21 and 1.4.0 dated 2020-07-08
statebins-1.2.2/statebins/man/statebins_continuous.Rd |only statebins-1.2.2/statebins/man/statebins_manual.Rd |only statebins-1.2.2/statebins/tests/test-all.R |only statebins-1.2.2/statebins/tests/testthat |only statebins-1.4.0/statebins/DESCRIPTION | 62 +- statebins-1.4.0/statebins/MD5 | 42 + statebins-1.4.0/statebins/NAMESPACE | 28 - statebins-1.4.0/statebins/R/aaa.R |only statebins-1.4.0/statebins/R/geom-rrect.r |only statebins-1.4.0/statebins/R/geom-rtile.R |only statebins-1.4.0/statebins/R/geom-statebins.r |only statebins-1.4.0/statebins/R/gutil.R |only statebins-1.4.0/statebins/R/statebins-package.R | 25 - statebins-1.4.0/statebins/R/statebins.R | 413 ++---------------- statebins-1.4.0/statebins/R/theme-statebin.R |only statebins-1.4.0/statebins/R/util.R |only statebins-1.4.0/statebins/data |only statebins-1.4.0/statebins/inst |only statebins-1.4.0/statebins/man/figures |only statebins-1.4.0/statebins/man/geom_statebins.Rd |only statebins-1.4.0/statebins/man/state_tbl.Rd |only statebins-1.4.0/statebins/man/statebins-package.Rd | 15 statebins-1.4.0/statebins/man/statebins.Rd | 87 +-- statebins-1.4.0/statebins/man/theme_statebins.Rd |only statebins-1.4.0/statebins/tests/tinytest.R |only 25 files changed, 215 insertions(+), 457 deletions(-)
Title: Model Elemental Fluxes in Fishes
Description: Model fluxes of carbon, nitrogen, and phosphorus with the use of a coupled
bioenergetics and stoichiometric model that incorporates flexible elemental limitation.
Additional functions to help the user to find parameters are included. Finally, functions to
extract and visualize results are available as well. For an introduction, see vignette.
For more information on the theoretical background of this model,
see Schiettekatte et al. (2020) <doi:10.1111/1365-2435.13618>.
Author: Nina M. D. Schiettekatte [aut, cre],
Diego Barneche [aut]
Maintainer: Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>
Diff between fishflux versions 0.0.1 dated 2020-07-03 and 0.0.1.1 dated 2020-07-08
DESCRIPTION | 6 - MD5 | 8 - README.md | 39 +++++-- inst/doc/intro_to_fishflux.html | 196 ++++++++++++++++++++-------------------- inst/stan/getB0.stan | 2 5 files changed, 132 insertions(+), 119 deletions(-)
Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language
('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a
list-based representation of 'EML' in R, so that 'EML' data can easily
be manipulated using standard 'R' tools. This makes this package an
effective backend for other 'R'-based tools working with 'EML.' By
abstracting away the complexity of 'XML' Schema, developers can
build around native 'R' list objects and not have to worry about satisfying
many of the additional constraints of set by the schema (such as element
ordering, which is handled automatically). Additionally, the 'JSON-LD'
representation enables the use of developer-friendly 'JSON' parsing and
serialization that may facilitate the use of 'EML' in contexts outside of 'R,'
as well as the informatics-friendly serializations such as 'RDF' and
'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Matthew B. Jones [aut, cph] (<https://orcid.org/0000-0003-0077-4738>),
Bryce Mecum [aut, cph] (<https://orcid.org/0000-0002-0381-3766>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between emld versions 0.4.0 dated 2020-02-05 and 0.5.0 dated 2020-07-08
DESCRIPTION | 6 MD5 | 22 NEWS.md | 8 R/eml_version.R | 25 R/validate_units.R | 6 build/vignette.rds |binary inst/doc/tutorial.html | 181 + inst/tests/eml-2.1.1/invalid |only inst/tests/eml-2.2.0/eml-2.2.0-milligramPerLiter.xml |only inst/tests/eml-2.2.0/eml-unitDictionary.xml | 1741 +++++++++++++++---- man/eml_version.Rd | 4 tests/testthat/test-validator.R | 9 tests/testthat/test-version.R | 12 13 files changed, 1574 insertions(+), 440 deletions(-)
Title: Hidden Markov Models of Character Evolution
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Author: Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Jeffrey Oliver [aut],
James Boyko [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>
Diff between corHMM versions 2.1 dated 2020-07-07 and 2.2 dated 2020-07-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/doc/corHMMv2.1-vignette.pdf |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Extra 'Recipes' for Text Processing
Description: Converting text to numerical features requires
specifically created procedures, which are implemented as steps
according to the 'recipes' package. These steps allows for
tokenization, filtering, counting (tf and tfidf) and feature hashing.
Author: Emil Hvitfeldt [aut, cre] (<https://orcid.org/0000-0002-0679-1945>)
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between textrecipes versions 0.2.3 dated 2020-05-22 and 0.3.0 dated 2020-07-08
DESCRIPTION | 18 MD5 | 84 - NAMESPACE | 6 NEWS.md | 6 R/0_imports.R | 2 R/RcppExports.R | 5 R/ngram.R | 22 R/stopwords.R | 9 R/text_normalization.R |only R/tokenlist.R | 4 R/utils-pipe.R | 2 README.md | 60 - inst/doc/Working-with-n-grams.html | 480 +++++----- inst/doc/cookbook---using-more-complex-recipes-involving-text.R | 6 inst/doc/cookbook---using-more-complex-recipes-involving-text.Rmd | 6 inst/doc/cookbook---using-more-complex-recipes-involving-text.html | 436 ++++----- inst/doc/tokenlist.html | 26 man/figures/logo.png |only man/pipe.Rd | 2 man/rcpp_ngram.Rd | 4 man/step_lda.Rd | 6 man/step_lemma.Rd | 6 man/step_ngram.Rd | 19 man/step_pos_filter.Rd | 6 man/step_sequence_onehot.Rd | 6 man/step_stem.Rd | 6 man/step_stopwords.Rd | 9 man/step_text_normalization.Rd |only man/step_textfeature.Rd | 6 man/step_texthash.Rd | 6 man/step_tf.Rd | 6 man/step_tfidf.Rd | 6 man/step_tokenfilter.Rd | 6 man/step_tokenize.Rd | 6 man/step_tokenmerge.Rd | 6 man/step_untokenize.Rd | 6 man/step_word_embeddings.Rd | 6 man/textrecipes-package.Rd | 2 src/RcppExports.cpp | 9 src/ngram.cpp | 52 - tests/testthat/test-ngram.R | 104 +- tests/testthat/test-stopwords.R | 4 tests/testthat/test-text_normalization.R |only tests/testthat/test-tokenlist.R | 85 + vignettes/cookbook---using-more-complex-recipes-involving-text.Rmd | 6 45 files changed, 927 insertions(+), 625 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 3.3 dated 2020-03-19 and 3.4 dated 2020-07-08
IsoplotR-3.3/IsoplotR/R/tests.R |only IsoplotR-3.4/IsoplotR/DESCRIPTION | 10 IsoplotR-3.4/IsoplotR/MD5 | 106 ++--- IsoplotR-3.4/IsoplotR/NAMESPACE | 1 IsoplotR-3.4/IsoplotR/R/ArAr.R | 4 IsoplotR-3.4/IsoplotR/R/KCa.R | 4 IsoplotR-3.4/IsoplotR/R/PD.R | 6 IsoplotR-3.4/IsoplotR/R/PbPb.R | 4 IsoplotR-3.4/IsoplotR/R/ThPb.R | 4 IsoplotR-3.4/IsoplotR/R/ThU.R | 18 IsoplotR-3.4/IsoplotR/R/UPb.R | 636 +++++++++++++++--------------- IsoplotR-3.4/IsoplotR/R/age.R | 66 +-- IsoplotR-3.4/IsoplotR/R/agespectrum.R | 12 IsoplotR-3.4/IsoplotR/R/cad.R | 124 ++--- IsoplotR-3.4/IsoplotR/R/central.R | 21 IsoplotR-3.4/IsoplotR/R/commonPb.R | 111 ++--- IsoplotR-3.4/IsoplotR/R/concordia.R | 73 ++- IsoplotR-3.4/IsoplotR/R/discfilter.R |only IsoplotR-3.4/IsoplotR/R/discordia.R | 4 IsoplotR-3.4/IsoplotR/R/errorellipse.R | 80 ++- IsoplotR-3.4/IsoplotR/R/evolution.R | 113 +++-- IsoplotR-3.4/IsoplotR/R/helioplot.R | 67 +-- IsoplotR-3.4/IsoplotR/R/io.R | 22 - IsoplotR-3.4/IsoplotR/R/isochron.R | 345 ++++++++-------- IsoplotR-3.4/IsoplotR/R/kde.R | 162 +++---- IsoplotR-3.4/IsoplotR/R/ludwig.R | 31 - IsoplotR-3.4/IsoplotR/R/peakfit.R | 160 ++++--- IsoplotR-3.4/IsoplotR/R/radialplot.R | 44 -- IsoplotR-3.4/IsoplotR/R/regression.R | 12 IsoplotR-3.4/IsoplotR/R/toolbox.R | 77 ++- IsoplotR-3.4/IsoplotR/R/weightedmean.R | 212 +++++----- IsoplotR-3.4/IsoplotR/R/york.R | 18 IsoplotR-3.4/IsoplotR/README.md | 4 IsoplotR-3.4/IsoplotR/inst/PbPb3.csv | 36 - IsoplotR-3.4/IsoplotR/inst/UPb7.csv | 42 - IsoplotR-3.4/IsoplotR/inst/UPb8.csv |only IsoplotR-3.4/IsoplotR/man/Pb0corr.Rd | 7 IsoplotR-3.4/IsoplotR/man/age.Rd | 112 +++-- IsoplotR-3.4/IsoplotR/man/agespectrum.Rd | 52 +- IsoplotR-3.4/IsoplotR/man/cad.Rd | 231 +++++++--- IsoplotR-3.4/IsoplotR/man/central.Rd | 3 IsoplotR-3.4/IsoplotR/man/concordia.Rd | 50 +- IsoplotR-3.4/IsoplotR/man/data2york.Rd | 14 IsoplotR-3.4/IsoplotR/man/discfilter.Rd |only IsoplotR-3.4/IsoplotR/man/diseq.Rd | 9 IsoplotR-3.4/IsoplotR/man/evolution.Rd | 41 + IsoplotR-3.4/IsoplotR/man/helioplot.Rd | 44 +- IsoplotR-3.4/IsoplotR/man/isochron.Rd | 403 ++++++++++++++----- IsoplotR-3.4/IsoplotR/man/kde.Rd | 414 ++++++++++++++----- IsoplotR-3.4/IsoplotR/man/ludwig.Rd | 10 IsoplotR-3.4/IsoplotR/man/mds.Rd | 33 + IsoplotR-3.4/IsoplotR/man/peakfit.Rd | 167 +++++-- IsoplotR-3.4/IsoplotR/man/radialplot.Rd | 418 ++++++++++++++----- IsoplotR-3.4/IsoplotR/man/read.data.Rd | 50 +- IsoplotR-3.4/IsoplotR/man/scatterplot.Rd | 65 ++- IsoplotR-3.4/IsoplotR/man/weightedmean.Rd | 423 ++++++++++++++----- 56 files changed, 3268 insertions(+), 1907 deletions(-)
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, restricted
quantile regression, and directional quantile classification. A vignette
is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and
included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code,
<https://orcid.org/0000-0002-7104-5826>)
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>
Diff between Qtools versions 1.5.1 dated 2019-12-13 and 1.5.2 dated 2020-07-08
DESCRIPTION | 26 ++++---- MD5 | 28 ++++---- NAMESPACE | 12 ++- NEWS | 23 ++++--- R/Qtools.R | 158 +++++++++++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/Qtools.R | 2 inst/doc/Qtools.html | 8 -- man/Qtools-internal.Rd | 1 man/Qtools-package.Rd | 6 - man/cmidecdf.Rd | 12 ++- man/midq2q.Rd |only man/midrq.Rd | 2 man/midrqControl.Rd | 7 +- man/plot.midq2q.Rd |only man/predict.qlss.Rd | 16 ++-- 16 files changed, 202 insertions(+), 99 deletions(-)
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty).
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <chadrien@ncc.go.jp>
Diff between mexhaz versions 1.7 dated 2019-12-10 and 1.8 dated 2020-07-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 12 +++++++++++- R/mexhaz.R | 7 ++----- R/predict.mexhaz.R | 16 +++++++++------- man/mexhaz.Rd | 3 +-- src/FrailtyAdaptL.c | 6 +++--- src/init.c | 36 ++++++++++++++++++------------------ 8 files changed, 55 insertions(+), 47 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.2.9 dated 2020-06-25 and 0.3.0 dated 2020-07-08
DESCRIPTION | 24 ++-- MD5 | 60 ++++++----- NEWS.md | 19 +++ R/zzz.R | 8 + README.md | 4 configure | 197 +++++++++++++++++++++++++++++---------- src/cqp.cpp | 19 +-- src/cwb/Makefile | 2 src/cwb/cl/attributes.c | 6 - src/cwb/cl/cdaccess.c | 2 src/cwb/cl/class-mapping.c | 14 +- src/cwb/cl/class-mapping.h | 4 src/cwb/cl/makecomps.c | 2 src/cwb/cl/storage.c | 3 src/cwb/config/platform/linux-64 | 2 src/cwb/cqp/Makefile | 16 +-- src/cwb/cqp/_options.h | 164 ++++++++++++++++---------------- src/cwb/cqp/corpmanag.c | 2 src/cwb/cqp/corpmanag.h | 4 src/cwb/cqp/cqp.h | 24 ++-- src/cwb/cqp/eval.c | 8 - src/cwb/cqp/eval.h | 15 +- src/cwb/cqp/lex.yy.c | 92 ------------------ src/cwb/cqp/options.h | 162 ++++++++++++++++---------------- src/cwb/cqp/parse_actions.c | 18 +-- src/cwb/cqp/parser.tab.c | 2 src/cwb/cqp/parser.y | 5 src/cwb/cqp/regex2dfa.c | 2 src/cwb/definitions.mk | 6 - src/env.h |only src/globalvars.h |only src/utils.h | 2 32 files changed, 467 insertions(+), 421 deletions(-)
Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains functions and
classes to be used in conjunction with other 'tidymodels' packages for
finding reasonable values of hyper-parameters in models, pre-processing
methods, and post-processing steps.
Author: Max Kuhn [aut, cre],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between tune versions 0.1.0 dated 2020-04-02 and 0.1.1 dated 2020-07-08
tune-0.1.0/tune/R/compat_dplyr.R |only tune-0.1.0/tune/R/tune_Bayes.R |only tune-0.1.0/tune/inst/examples |only tune-0.1.0/tune/tests/testthat/bayes_example.RData |only tune-0.1.0/tune/tests/testthat/svm_results.RData |only tune-0.1.1/tune/DESCRIPTION | 14 tune-0.1.1/tune/MD5 | 179 ++---- tune-0.1.1/tune/NAMESPACE | 81 ++ tune-0.1.1/tune/NEWS.md | 33 + tune-0.1.1/tune/R/0_imports.R | 20 tune-0.1.1/tune/R/checks.R | 138 +++- tune-0.1.1/tune/R/collect.R | 30 - tune-0.1.1/tune/R/compat-dplyr-old.R |only tune-0.1.1/tune/R/compat-dplyr.R |only tune-0.1.1/tune/R/compat-vctrs-helpers.R |only tune-0.1.1/tune/R/compat-vctrs.R |only tune-0.1.1/tune/R/conf_mat_resampled.R |only tune-0.1.1/tune/R/control.R | 56 + tune-0.1.1/tune/R/coord_obs_pred.R |only tune-0.1.1/tune/R/data.R | 2 tune-0.1.1/tune/R/extract.R | 19 tune-0.1.1/tune/R/filter_parameters.R |only tune-0.1.1/tune/R/grid_code_paths.R | 92 ++- tune-0.1.1/tune/R/grid_performance.R | 4 tune-0.1.1/tune/R/iteration_results.R |only tune-0.1.1/tune/R/last_fit.R | 10 tune-0.1.1/tune/R/merge.R | 3 tune-0.1.1/tune/R/min_grid.R | 5 tune-0.1.1/tune/R/outcome-names.R | 12 tune-0.1.1/tune/R/plots.R | 386 ++++++++++++- tune-0.1.1/tune/R/resample.R | 16 tune-0.1.1/tune/R/resample_results.R |only tune-0.1.1/tune/R/select_best.R | 29 tune-0.1.1/tune/R/symbol.R | 8 tune-0.1.1/tune/R/tunable.R | 116 +++ tune-0.1.1/tune/R/tune_args.R | 3 tune-0.1.1/tune/R/tune_bayes.R |only tune-0.1.1/tune/R/tune_grid.R | 94 ++- tune-0.1.1/tune/R/tune_results.R |only tune-0.1.1/tune/R/utils.R | 124 ++++ tune-0.1.1/tune/R/zzz.R | 31 - tune-0.1.1/tune/README.md | 77 +- tune-0.1.1/tune/data/example_ames_knn.RData |binary tune-0.1.1/tune/inst/WORDLIST | 2 tune-0.1.1/tune/man/autoplot.tune_results.Rd | 50 + tune-0.1.1/tune/man/conf_mat_resampled.Rd |only tune-0.1.1/tune/man/control_bayes.Rd | 6 tune-0.1.1/tune/man/control_grid.Rd | 9 tune-0.1.1/tune/man/coord_obs_pred.Rd |only tune-0.1.1/tune/man/empty_ellipses.Rd |only tune-0.1.1/tune/man/example_ames_knn.Rd | 2 tune-0.1.1/tune/man/filter_parameters.Rd |only tune-0.1.1/tune/man/fit_resamples.Rd | 2 tune-0.1.1/tune/man/merge.recipe.Rd | 3 tune-0.1.1/tune/man/outcome_names.Rd | 3 tune-0.1.1/tune/man/show_best.Rd | 12 tune-0.1.1/tune/man/tunable.Rd | 10 tune-0.1.1/tune/man/tune_accessor.Rd |only tune-0.1.1/tune/man/tune_args.Rd | 3 tune-0.1.1/tune/man/tune_bayes.Rd | 4 tune-0.1.1/tune/man/tune_grid.Rd | 4 tune-0.1.1/tune/tests/testthat/Rplots.pdf |only tune-0.1.1/tune/tests/testthat/helper-s3.R |only tune-0.1.1/tune/tests/testthat/knn_gp.rds |only tune-0.1.1/tune/tests/testthat/knn_grid.rds |binary tune-0.1.1/tune/tests/testthat/knn_results.rds |binary tune-0.1.1/tune/tests/testthat/knn_set.rds |binary tune-0.1.1/tune/tests/testthat/lm_bayes.rds |only tune-0.1.1/tune/tests/testthat/lm_resamples.rds |only tune-0.1.1/tune/tests/testthat/rcv_results.rds |binary tune-0.1.1/tune/tests/testthat/svm_reg_results.rds |only tune-0.1.1/tune/tests/testthat/svm_results.rds |only tune-0.1.1/tune/tests/testthat/test-GP.R | 69 -- tune-0.1.1/tune/tests/testthat/test-autoplot.R | 177 +++++ tune-0.1.1/tune/tests/testthat/test-bayes.R | 39 + tune-0.1.1/tune/tests/testthat/test-checks.R | 50 - tune-0.1.1/tune/tests/testthat/test-collect.R | 44 - tune-0.1.1/tune/tests/testthat/test-compat-dplyr-old.R |only tune-0.1.1/tune/tests/testthat/test-compat-dplyr.R |only tune-0.1.1/tune/tests/testthat/test-compat-vctrs-helpers.R |only tune-0.1.1/tune/tests/testthat/test-compat-vctrs.R |only tune-0.1.1/tune/tests/testthat/test-conf-mat-resampled.R |only tune-0.1.1/tune/tests/testthat/test-engine-parameters.R |only tune-0.1.1/tune/tests/testthat/test-estimate.R | 15 tune-0.1.1/tune/tests/testthat/test-extract.R | 49 + tune-0.1.1/tune/tests/testthat/test-filter-parameters.R |only tune-0.1.1/tune/tests/testthat/test-finalization.R |only tune-0.1.1/tune/tests/testthat/test-grid.R | 82 ++ tune-0.1.1/tune/tests/testthat/test-misc.R | 38 + tune-0.1.1/tune/tests/testthat/test-outcome-names.R |only tune-0.1.1/tune/tests/testthat/test-predictions.R | 56 - tune-0.1.1/tune/tests/testthat/test-resample.R | 49 + tune-0.1.1/tune/tests/testthat/test-select_best.R | 38 - tune-0.1.1/tune/tests/testthat/test-tunable.R | 7 tune-0.1.1/tune/tests/testthat/test_objects.RData |binary 95 files changed, 1876 insertions(+), 529 deletions(-)
Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.
Author: Max Kuhn [aut, cre],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between dials versions 0.0.7 dated 2020-06-10 and 0.0.8 dated 2020-07-08
dials-0.0.7/dials/tests/testthat/test_qual_params.R |only dials-0.0.8/dials/DESCRIPTION | 8 ++-- dials-0.0.8/dials/MD5 | 34 ++++++++++++-------- dials-0.0.8/dials/NAMESPACE | 21 ++++++++++++ dials-0.0.8/dials/NEWS.md | 4 ++ dials-0.0.8/dials/R/aaa_unknown.R | 8 +++- dials-0.0.8/dials/R/finalize.R | 22 ++++++++++++ dials-0.0.8/dials/R/param_engine_c50.R |only dials-0.0.8/dials/R/param_engine_cubist.R |only dials-0.0.8/dials/R/param_engine_earth.R |only dials-0.0.8/dials/R/param_engine_randomForest.R |only dials-0.0.8/dials/R/param_engine_ranger.R |only dials-0.0.8/dials/R/parameters.R | 2 - dials-0.0.8/dials/inst/doc/Basics.html | 16 +++++++++ dials-0.0.8/dials/man/c5_parameters.Rd |only dials-0.0.8/dials/man/cubist_parameters.Rd |only dials-0.0.8/dials/man/earth_parameters.Rd |only dials-0.0.8/dials/man/finalize.Rd | 6 +++ dials-0.0.8/dials/man/new-param.Rd | 2 - dials-0.0.8/dials/man/randomForest_parameters.Rd |only dials-0.0.8/dials/man/ranger_parameters.Rd |only dials-0.0.8/dials/man/update.parameters.Rd | 2 - dials-0.0.8/dials/tests/testthat/test_finalize.R | 8 ++-- dials-0.0.8/dials/tests/testthat/test_params.R |only 24 files changed, 108 insertions(+), 25 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>
Diff between bbsBayes versions 2.3.2.2020 dated 2020-06-27 and 2.3.3.2020 dated 2020-07-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/fetch-bbs-data.R | 18 ++++++++++++------ man/fetch_bbs_data.Rd | 3 ++- 4 files changed, 21 insertions(+), 14 deletions(-)
Title: Fast Rolling Functions for Seismology using 'Rcpp'
Description: Fast versions of seismic analysis functions that 'roll' over a
vector of values. See the 'RcppRoll' package for alternative
versions of basic statistical functions such as rolling mean,
median, etc.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Mary Templeton [aut],
Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between seismicRoll versions 1.1.3 dated 2018-12-04 and 1.1.4 dated 2020-07-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/findOutliers.Rd | 10 ++++++++-- man/seismicRoll.Rd | 6 +++++- src/source_files.cpp | 19 +++++++++++++++++++ 5 files changed, 40 insertions(+), 11 deletions(-)
Title: Confidentiality of Spatial Point Data
Description: Provides an automatic aggregation tool to manage point data privacy,
intended to be helpful for the production of official spatial data and for researchers.
The package pursues the data accuracy at the smallest possible areas preventing
individual information disclosure. The methodology, based on hierarchical geographic
data structures performs aggregation and local suppression of point data to ensure privacy
as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>.
The data structures are created following the guidelines for grid datasets from the
European Forum for Geography and Statistics.
Author: Raymond Lagonigro [aut, cre] (<https://orcid.org/0000-0002-8091-4296>),
Ramon Oller [aut] (<https://orcid.org/0000-0002-4333-0021>),
Joan Carles Martori [aut] (<https://orcid.org/0000-0002-8400-5487>)
Maintainer: Raymond Lagonigro <raymond.lagonigro@uvic.cat>
Diff between AQuadtree versions 1.0.0 dated 2020-03-13 and 1.0.1 dated 2020-07-08
AQuadtree-1.0.0/AQuadtree/inst/doc/AQuadtreeUse.pdf |only AQuadtree-1.0.0/AQuadtree/vignettes/AQuadtreeUse.html |only AQuadtree-1.0.1/AQuadtree/DESCRIPTION | 7 +-- AQuadtree-1.0.1/AQuadtree/MD5 | 36 ++++++++-------- AQuadtree-1.0.1/AQuadtree/NEWS |only AQuadtree-1.0.1/AQuadtree/R/AQuadtree-class.R | 17 +++++++ AQuadtree-1.0.1/AQuadtree/R/createAQuadtree.R | 19 ++++---- AQuadtree-1.0.1/AQuadtree/R/createGrid.R | 10 ++-- AQuadtree-1.0.1/AQuadtree/R/joinAQuadtrees.R | 6 ++ AQuadtree-1.0.1/AQuadtree/R/pointsToAQuadtree.R | 15 +++++- AQuadtree-1.0.1/AQuadtree/R/spatialPointsCellCodes.R | 13 +++++ AQuadtree-1.0.1/AQuadtree/build/vignette.rds |binary AQuadtree-1.0.1/AQuadtree/inst/doc/AQuadtreeUse.Rmd | 6 +- AQuadtree-1.0.1/AQuadtree/inst/doc/AQuadtreeUse.html |only AQuadtree-1.0.1/AQuadtree/man/AQuadtree-class.Rd | 16 ++++++- AQuadtree-1.0.1/AQuadtree/man/createAQuadtree.Rd | 6 +- AQuadtree-1.0.1/AQuadtree/man/createGrid.Rd | 8 +-- AQuadtree-1.0.1/AQuadtree/man/joinAQuadtrees.Rd | 6 ++ AQuadtree-1.0.1/AQuadtree/man/pointsToAQuadtree.Rd | 10 ++++ AQuadtree-1.0.1/AQuadtree/man/spatialPointsCellCodes.Rd | 8 +++ AQuadtree-1.0.1/AQuadtree/vignettes/AQuadtreeUse.Rmd | 6 +- 21 files changed, 136 insertions(+), 53 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test,
estimate, and analyze Stan models by accessing the header-only Stan library
provided by the 'StanHeaders' package. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference
via Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to quickly
and accurately evaluate gradients without burdening the user with the need to
derive the partial derivatives.
Author: Jiqiang Guo [aut],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Sebastian Weber [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Modrak Martin [ctb],
Trustees of Columbia University [cph],
Oleg Sklyar [cph] (R/cxxfunplus.R),
The R Core Team [cph] (R/pairs.R, R/dynGet.R),
Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R),
John Maddock [cph] (gamma.hpp),
Paul Bristow [cph] (gamma.hpp),
Nikhar Agrawal [cph] (gamma.hpp),
Christopher Kormanyos [cph] (gamma.hpp)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.19.3 dated 2020-02-11 and 2.21.1 dated 2020-07-08
DESCRIPTION | 30 MD5 | 763 ++++++++++++++-- NAMESPACE | 15 R/Rcpp_module_def.R | 48 - R/SBC.R | 61 + R/check_hmc_diagnostics.R | 6 R/cxxfunplus.R | 19 R/doctor_cppcode.R | 149 +-- R/exposeStanClass.R | 9 R/expose_stan_functions.R | 1 R/gqs_light.R | 2 R/loo.R | 125 ++ R/misc.R | 19 R/monitor.R | 33 R/plugin.R | 82 + R/rstan.R | 227 ++-- R/stan_plot.R | 3 R/stanc.R | 63 + R/stanfit-class.R | 1 R/stanmodel-class.R | 374 ++++--- R/zzz.R | 34 build/vignette.rds |binary inst/NEWS | 8 inst/doc/SBC.R | 3 inst/doc/SBC.Rmd | 6 inst/doc/SBC.html | 24 inst/doc/external.R | 2 inst/doc/external.Rmd | 9 inst/doc/external.html | 38 inst/doc/rstan.R | 4 inst/doc/rstan.Rmd | 4 inst/doc/rstan.html | 158 +-- inst/doc/stanfit-objects.R | 2 inst/doc/stanfit-objects.Rmd | 2 inst/doc/stanfit-objects.html | 255 ++--- inst/include/exporter.h | 4 inst/include/rstan/rcpp_module_def_for_rstan.hpp | 53 - inst/include/rstan/rstaninc.hpp | 1 inst/include/rstan_next |only man/plotting-functions.Rd | 2 man/rstan.Rd | 2 man/sbc.Rd | 7 man/stan.Rd | 2 man/stan_plot_diagnostics.Rd | 3 man/stanfit-method-loo-moment-match.Rd |only man/stanfit-method-loo.Rd | 89 + man/stanmodel-method-optimizing.Rd | 22 man/stanmodel-method-sampling.Rd | 2 src/Makevars | 24 src/Makevars.win | 17 src/Module.cpp |only src/init.cpp | 14 src/stan/analyze |only src/stan/callbacks |only src/stan/command |only src/stan/io |only src/stan/lang/ast |only src/stan/lang/ast.hpp |only src/stan/lang/compile_functions.hpp |only src/stan/lang/compiler.hpp |only src/stan/lang/function_signatures.h |only src/stan/lang/generator |only src/stan/lang/generator.hpp |only src/stan/lang/grammars/bare_type_grammar.hpp | 54 - src/stan/lang/grammars/bare_type_grammar_def.hpp | 93 - src/stan/lang/grammars/bare_type_grammar_inst.cpp | 9 src/stan/lang/grammars/block_var_decls_grammar_def.hpp | 284 +++-- src/stan/lang/grammars/block_var_decls_grammar_inst.cpp | 6 src/stan/lang/grammars/common_adaptors_def.hpp | 4 src/stan/lang/grammars/expression07_grammar.hpp | 51 - src/stan/lang/grammars/expression07_grammar_def.hpp | 58 - src/stan/lang/grammars/expression07_grammar_inst.cpp | 6 src/stan/lang/grammars/expression_grammar.hpp | 70 - src/stan/lang/grammars/expression_grammar_def.hpp | 157 +-- src/stan/lang/grammars/expression_grammar_inst.cpp | 6 src/stan/lang/grammars/functions_grammar.hpp | 72 - src/stan/lang/grammars/functions_grammar_def.hpp | 167 +-- src/stan/lang/grammars/functions_grammar_inst.cpp | 6 src/stan/lang/grammars/indexes_grammar.hpp | 91 - src/stan/lang/grammars/indexes_grammar_def.hpp | 158 +-- src/stan/lang/grammars/indexes_grammar_inst.cpp | 7 src/stan/lang/grammars/iterator_typedefs.hpp | 10 src/stan/lang/grammars/local_var_decls_grammar.hpp | 115 +- src/stan/lang/grammars/local_var_decls_grammar_def.hpp | 248 ++--- src/stan/lang/grammars/local_var_decls_grammar_inst.cpp | 6 src/stan/lang/grammars/program_grammar.hpp | 110 +- src/stan/lang/grammars/program_grammar_def.hpp | 252 ++--- src/stan/lang/grammars/program_grammar_inst.cpp | 6 src/stan/lang/grammars/semantic_actions.hpp | 40 src/stan/lang/grammars/semantic_actions_def.cpp | 439 ++++----- src/stan/lang/grammars/statement_2_grammar.hpp | 52 - src/stan/lang/grammars/statement_2_grammar_def.hpp | 92 - src/stan/lang/grammars/statement_2_grammar_inst.cpp | 6 src/stan/lang/grammars/statement_grammar.hpp | 190 +-- src/stan/lang/grammars/statement_grammar_def.hpp | 612 +++++------- src/stan/lang/grammars/statement_grammar_inst.cpp | 6 src/stan/lang/grammars/term_grammar.hpp | 169 +-- src/stan/lang/grammars/term_grammar_def.hpp | 654 +++++-------- src/stan/lang/grammars/term_grammar_inst.cpp | 6 src/stan/lang/grammars/whitespace_grammar.hpp | 21 src/stan/lang/grammars/whitespace_grammar_def.hpp | 31 src/stan/lang/grammars/whitespace_grammar_inst.cpp | 6 src/stan/lang/parser.hpp |only src/stan/lang/rethrow_located.hpp |only src/stan/mcmc |only src/stan/model |only src/stan/optimization |only src/stan/services |only src/stan/variational |only src/stan/version.hpp |only src/stan_fit.cpp |only src/stan_fit_base.cpp |only src/stan_fit_rccp.cpp |only vignettes/SBC.Rmd | 6 vignettes/external.Rmd | 9 vignettes/rstan.Rmd | 4 vignettes/stanfit-objects.Rmd | 2 117 files changed, 3896 insertions(+), 3316 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Project Nayuki [ctb] (Original author of underlying C++ code for
get_circumscribingcircle and lsm_p_circle),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between landscapemetrics versions 1.4.4 dated 2020-05-15 and 1.4.5 dated 2020-07-08
DESCRIPTION | 8 MD5 | 73 ++++---- NAMESPACE | 9 - NEWS.md | 11 + R/RcppExports.R | 4 R/calculate_lsm.R | 24 ++ R/get_boundaries.R | 200 +++++++++++++----------- R/get_centroids.R |only R/get_circumscribingcircle.R | 42 ++--- R/get_nearestneighbour.R | 237 +++++++++++------------------ R/lsm_c_gyrate_cv.R | 44 +++-- R/lsm_c_gyrate_mn.R | 44 +++-- R/lsm_c_gyrate_sd.R | 44 +++-- R/lsm_l_gyrate_cv.R | 41 +++-- R/lsm_l_gyrate_mn.R | 44 +++-- R/lsm_l_gyrate_sd.R | 41 +++-- R/lsm_p_core.R | 78 +++------ R/lsm_p_enn.R | 97 ++++------- R/lsm_p_gyrate.R | 84 +++++++--- R/lsm_p_ncore.R | 25 --- R/show_cores.R | 2 inst/doc/getstarted.html | 49 ++++- man/calculate_lsm.Rd | 19 +- man/get_boundaries.Rd | 60 ++++--- man/get_centroids.Rd |only man/get_nearestneighbour.Rd | 35 ++-- man/lsm_c_gyrate_cv.Rd | 19 +- man/lsm_c_gyrate_mn.Rd | 22 +- man/lsm_c_gyrate_sd.Rd | 19 +- man/lsm_l_gyrate_cv.Rd | 19 +- man/lsm_l_gyrate_mn.Rd | 22 +- man/lsm_l_gyrate_sd.Rd | 19 +- man/lsm_p_gyrate.Rd | 22 +- src/RcppExports.cpp | 16 + src/rcpp_get_nearest_neighbor.cpp | 24 ++ tests/testthat/test-get-boundaries.R | 92 +++++++---- tests/testthat/test-get-centroids.R |only tests/testthat/test-get-nearestneighbour.R | 51 +++--- tests/testthat/test-lsm-p-gyrate.R | 10 - 39 files changed, 941 insertions(+), 709 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: R Interface to Google Charts
Description: R interface to Google's chart tools, allowing users
to create interactive charts based on data frames. Charts
are displayed locally via the R HTTP help server. A modern
browser with an Internet connection is required and for some
charts a Flash player. The data remains local and is not
uploaded to Google.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb],
Ashley Baldry [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between googleVis versions 0.6.5 dated 2020-06-08 and 0.6.6 dated 2020-07-08
googleVis-0.6.5/googleVis/R/gvisIntensityMap.R |only googleVis-0.6.5/googleVis/demo/AnimatedGeoChart.R |only googleVis-0.6.5/googleVis/demo/WorldBank.R |only googleVis-0.6.5/googleVis/inst/brew |only googleVis-0.6.5/googleVis/inst/doc/Using_Roles_via_googleVis.R |only googleVis-0.6.5/googleVis/inst/doc/Using_Roles_via_googleVis.Rmd |only googleVis-0.6.5/googleVis/inst/doc/Using_Roles_via_googleVis.html |only googleVis-0.6.5/googleVis/inst/doc/Using_Trendlines_with_googleVis.R |only googleVis-0.6.5/googleVis/inst/doc/Using_Trendlines_with_googleVis.Rmd |only googleVis-0.6.5/googleVis/inst/doc/Using_Trendlines_with_googleVis.html |only googleVis-0.6.5/googleVis/inst/doc/Using_googleVis_with_knitr.R |only googleVis-0.6.5/googleVis/inst/doc/Using_googleVis_with_knitr.Rmd |only googleVis-0.6.5/googleVis/inst/doc/Using_googleVis_with_knitr.html |only googleVis-0.6.5/googleVis/inst/doc/googleVis.R |only googleVis-0.6.5/googleVis/inst/doc/googleVis.Rnw |only googleVis-0.6.5/googleVis/inst/doc/googleVis.pdf |only googleVis-0.6.5/googleVis/inst/gadgets |only googleVis-0.6.5/googleVis/inst/rsp |only googleVis-0.6.5/googleVis/man/gvisIntensityMap.Rd |only googleVis-0.6.5/googleVis/vignettes/Using_Roles_via_googleVis.Rmd |only googleVis-0.6.5/googleVis/vignettes/Using_Trendlines_with_googleVis.Rmd |only googleVis-0.6.5/googleVis/vignettes/Using_googleVis_with_knitr.Rmd |only googleVis-0.6.5/googleVis/vignettes/figures |only googleVis-0.6.5/googleVis/vignettes/googleVis.Rnw |only googleVis-0.6.5/googleVis/vignettes/mystyle.css |only googleVis-0.6.6/googleVis/DESCRIPTION | 16 googleVis-0.6.6/googleVis/MD5 | 83 googleVis-0.6.6/googleVis/NAMESPACE | 1 googleVis-0.6.6/googleVis/NEWS | 14 googleVis-0.6.6/googleVis/R/gvis.R | 9 googleVis-0.6.6/googleVis/R/gvisGeoChart.R | 58 googleVis-0.6.6/googleVis/R/gvisMap.R | 3 googleVis-0.6.6/googleVis/README.md | 18 googleVis-0.6.6/googleVis/build/googleVis.pdf |binary googleVis-0.6.6/googleVis/build/vignette.rds |binary googleVis-0.6.6/googleVis/demo/00Index | 2 googleVis-0.6.6/googleVis/demo/googleVis.R | 42 googleVis-0.6.6/googleVis/inst/doc/googleVis_examples.R | 25 googleVis-0.6.6/googleVis/inst/doc/googleVis_examples.Rmd | 36 googleVis-0.6.6/googleVis/inst/doc/googleVis_examples.html | 1413 ++-------- googleVis-0.6.6/googleVis/inst/doc/googleVis_intro.R |only googleVis-0.6.6/googleVis/inst/doc/googleVis_intro.Rmd |only googleVis-0.6.6/googleVis/inst/doc/googleVis_intro.html |only googleVis-0.6.6/googleVis/man/gvisGeoChart.Rd | 58 googleVis-0.6.6/googleVis/man/gvisMap.Rd | 3 googleVis-0.6.6/googleVis/vignettes/googleVis.bib | 4 googleVis-0.6.6/googleVis/vignettes/googleVis_examples.Rmd | 36 googleVis-0.6.6/googleVis/vignettes/googleVis_intro.Rmd |only 48 files changed, 461 insertions(+), 1360 deletions(-)
Title: Fetch and Analyze Data from 'WaterML' and 'WaterOneFlow' Web
Services
Description: Lets you connect to any of the 'Consortium of Universities for the Advancement of Hydrological Science, Inc.'
('CUAHSI') Water Data Center 'WaterOneFlow' web services
and read any 'WaterML' time series data file. To see list of available
web services, see <http://hiscentral.cuahsi.org>. All versions of 'WaterML'
(1.0, 1.1 and 2.0) and both types of the web service protocol ('SOAP' and 'REST') are supported.
The package has six data download functions: GetServices(): show all public web
services from the HIS Central Catalog. HISCentral_GetSites() and HISCentral_GetSeriesCatalog():
search for sites or time series from the HIS Central catalog based on geographic bounding box,
server, or keyword. GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server. GetSiteInfo(): Show what variables,
methods and quality control levels are available at the specific site. GetValues(): Given a site
code, variable code, start time and end time, fetch a data.frame of all the observation time
series data values. The GetValues() function can also parse 'WaterML' data from a custom URL or
from a local file. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a 'HydroServer Lite' Observations
Data Model ('ODM') database via the 'JSON' data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.9.0 dated 2020-02-12 and 1.9.5 dated 2020-07-08
DESCRIPTION | 13 LICENSE | 4 MD5 | 46 - NAMESPACE | 30 - R/GetServices.R | 156 ++--- R/GetSiteInfo.R | 1164 +++++++++++++++++++------------------- R/GetSites.R | 630 ++++++++++----------- R/GetValues.R | 1195 ++++++++++++++++++++-------------------- R/GetVariables.R | 454 +++++++-------- R/HISCentral_GetSeriesCatalog.R | 306 +++++----- R/HISCentral_GetSites.R | 276 ++++----- R/MakeSOAPEnvelope.R | 146 ++-- R/PackageDocumentation.R | 36 - R/WaterMLVersion.R | 88 +- R/WaterOneFlowNamespace.R | 62 +- R/WaterOneFlowVersion.R | 66 +- README.md | 28 build/vignette.rds |binary inst/CITATION | 40 - inst/doc/WaterML-Tutorial.R | 144 ++-- inst/doc/WaterML-Tutorial.Rmd | 314 +++++----- inst/doc/WaterML-Tutorial.html | 738 ++++++++++++------------ man/GetServices.Rd | 2 vignettes/WaterML-Tutorial.Rmd | 314 +++++----- 24 files changed, 3131 insertions(+), 3121 deletions(-)
More information about doebioresearch at CRAN
Permanent link
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Michael Sumner [ctb] (<https://orcid.org/0000-0002-2471-7511>),
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.4-2 dated 2020-07-01 and 0.4-3 dated 2020-07-08
DESCRIPTION | 10 - MD5 | 27 +- NAMESPACE | 1 NEWS.md | 8 R/ncdf.R | 284 ++++++++++++++++--------------- R/plot.R | 41 ++++ R/raster.R | 20 +- inst/doc/stars1.html | 17 - inst/doc/stars2.html | 4 inst/nc/sub.nc |only inst/nc/test_adaptor.cams_regional_fc.nc |only man/read_ncdf.Rd | 2 man/st_as_stars.Rd | 6 man/st_rgb.Rd |only tests/testthat/test_ncdf.R | 114 +++++++----- tests/testthat/test_rectilinear.R | 84 ++++----- 16 files changed, 362 insertions(+), 256 deletions(-)
Title: Statistical Modelling for Plant Size Distributions
Description: Developed for the following tasks. 1 ) Computing the probability density function,
cumulative distribution function, random generation, and estimating the parameters
of the eleven mixture models. 2 ) Point estimation of the parameters of two -
parameter Weibull distribution using twelve methods and three - parameter Weibull
distribution using nine methods. 3 ) The Bayesian inference for the three -
parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter
Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to
grouped data using three methods including approximated maximum likelihood,
expectation maximization, and maximum likelihood. 5 ) Estimating the parameters
of the gamma, log-normal, and Weibull mixture models fitted to the grouped data
through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve
fitted to the height - diameter observation, 7 ) Estimating parameters, computing
probability density function, cumulative distribution function, and generating
realizations from gamma shape mixture model introduced by Venturini et al. (2008)
<doi:10.1214/07-AOAS156> , 8 ) The Bayesian inference, computing probability density function,
cumulative distribution function, and generating realizations from four - parameter
Johnson SB distribution, and 9 ) Robust multiple linear regression analysis when error
term follows skewed t distribution.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>
Diff between ForestFit versions 0.6.0 dated 2020-06-27 and 0.6.1 dated 2020-07-08
DESCRIPTION | 29 ++++---- MD5 | 10 +-- R/ForestFit.R | 183 ++++++++++++++++++++++++++++---------------------------- man/rgsm.Rd | 2 man/rjsb.Rd | 2 man/skewtreg.Rd | 6 - 6 files changed, 118 insertions(+), 114 deletions(-)
Title: Estimation of Characteristics of Seasonal and Sporadic
Infectious Disease Outbreaks Using Generalized Additive
Modeling with Penalized Basis Splines
Description: Stochastic inference of infectious disease outcomes using generalized additive (mixed) models.
Author: Ben Artin [aut, cre, cph]
Maintainer: Ben Artin <ben@artins.org>
Diff between pspline.inference versions 0.23 dated 2020-07-01 and 0.24 dated 2020-07-08
pspline.inference-0.23/pspline.inference/vignettes/seasonal.csv |only pspline.inference-0.24/pspline.inference/DESCRIPTION | 17 pspline.inference-0.24/pspline.inference/MD5 | 18 pspline.inference-0.24/pspline.inference/README.md | 27 pspline.inference-0.24/pspline.inference/build/vignette.rds |binary pspline.inference-0.24/pspline.inference/inst/doc/seasonal.R | 22 pspline.inference-0.24/pspline.inference/inst/doc/seasonal.Rmd | 69 - pspline.inference-0.24/pspline.inference/inst/doc/seasonal.html | 497 ++++------ pspline.inference-0.24/pspline.inference/inst/extdata |only pspline.inference-0.24/pspline.inference/tests/testthat/test-estimate.R | 1 pspline.inference-0.24/pspline.inference/vignettes/seasonal.Rmd | 69 - 11 files changed, 286 insertions(+), 434 deletions(-)
More information about pspline.inference at CRAN
Permanent link
Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most
probable masses of a chemical compound given the frequencies of the composing
isotopes and their masses. It finds the smallest set of isotopologues with
a given probability. The probability is assumed to be that of the product of
multinomial distributions, each corresponding to one particular element and
parametrized by the frequencies of finding these elements in nature. These
numbers are supplied by IUPAC - the International Union of Pure and Applied
Chemistry.
Author: Mateusz Krzysztof Lacki and Michal Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>
Diff between IsoSpecR versions 2.1.0 dated 2020-05-27 and 2.1.1 dated 2020-07-08
DESCRIPTION | 8 - MD5 | 35 +++--- inst/CITATION | 15 ++ src/allocator.cpp | 15 +- src/allocator.h | 4 src/conf.h | 15 ++ src/cwrapper.cpp | 19 +++ src/cwrapper.h | 4 src/dirtyAllocator.cpp | 6 - src/dirtyAllocator.h | 4 src/fixedEnvelopes.cpp | 23 ++++ src/fixedEnvelopes.h | 4 src/isoSpec++.cpp | 26 ++-- src/isoSpec++.h | 8 - src/marginalTrek++.cpp | 272 +++++++++++++++++++++++++------------------------ src/marginalTrek++.h | 49 +++----- src/misc.h | 59 ++++++++++ src/platform.h | 2 src/pod_vector.h |only 19 files changed, 354 insertions(+), 214 deletions(-)
More information about UnifiedDoseFinding at CRAN
Permanent link
Title: Alt String Implementation
Description: Provides an extendable and performant 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] (Bundled PCRE2 code),
Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code),
University of Cambridge [cph] (Bundled PCRE2 code),
Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with
PCRE2),
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash
code)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.12.1 dated 2020-06-05 and 0.13.2 dated 2020-07-08
stringfish-0.12.1/stringfish/vignettes/bench_v1.png |only stringfish-0.13.2/stringfish/ChangeLog | 9 stringfish-0.13.2/stringfish/DESCRIPTION | 18 stringfish-0.13.2/stringfish/MD5 | 60 stringfish-0.13.2/stringfish/NAMESPACE | 11 stringfish-0.13.2/stringfish/R/RcppExports.R | 36 stringfish-0.13.2/stringfish/R/help_files.R | 154 + stringfish-0.13.2/stringfish/R/sf_functions.r | 38 stringfish-0.13.2/stringfish/R/zzz.R | 3 stringfish-0.13.2/stringfish/README.md | 73 stringfish-0.13.2/stringfish/configure | 81 - stringfish-0.13.2/stringfish/configure.ac | 65 stringfish-0.13.2/stringfish/inst/doc/vignette.R | 13 stringfish-0.13.2/stringfish/inst/doc/vignette.html | 175 +- stringfish-0.13.2/stringfish/inst/doc/vignette.rmd | 52 stringfish-0.13.2/stringfish/inst/include/sf_external.h | 18 stringfish-0.13.2/stringfish/inst/include/sf_internal.h | 129 + stringfish-0.13.2/stringfish/man/sf_ends.Rd |only stringfish-0.13.2/stringfish/man/sf_grepl.Rd | 6 stringfish-0.13.2/stringfish/man/sf_gsub.Rd | 6 stringfish-0.13.2/stringfish/man/sf_match.Rd |only stringfish-0.13.2/stringfish/man/sf_readLines.Rd | 2 stringfish-0.13.2/stringfish/man/sf_split.Rd |only stringfish-0.13.2/stringfish/man/sf_starts.Rd |only stringfish-0.13.2/stringfish/man/sf_tolower.Rd |only stringfish-0.13.2/stringfish/man/sf_toupper.Rd |only stringfish-0.13.2/stringfish/man/sf_trim.Rd |only stringfish-0.13.2/stringfish/man/sf_writeLines.Rd |only stringfish-0.13.2/stringfish/man/string_identical.Rd |only stringfish-0.13.2/stringfish/src/PCRE2/sljit/sljitConfigInternal.h | 2 stringfish-0.13.2/stringfish/src/RcppExports.cpp | 114 + stringfish-0.13.2/stringfish/src/sf_altrep.h | 4 stringfish-0.13.2/stringfish/src/sf_functions.cpp | 792 +++++++--- stringfish-0.13.2/stringfish/src/xxhash |only stringfish-0.13.2/stringfish/vignettes/bench_v2.png |only stringfish-0.13.2/stringfish/vignettes/vignette.rmd | 52 36 files changed, 1366 insertions(+), 547 deletions(-)
Title: A Grammar of Animated Graphics
Description: The grammar of graphics as implemented in the 'ggplot2' package has
been successful in providing a powerful API for creating static
visualisation. In order to extend the API for animated graphics this package
provides a completely new set of grammar, fully compatible with 'ggplot2'
for specifying transitions and animations in a flexible and extensible way.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
David Robinson [aut],
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between gganimate versions 1.0.5 dated 2020-02-09 and 1.0.6 dated 2020-07-08
DESCRIPTION | 8 - MD5 | 16 +- NEWS.md | 2 R/renderers.R | 3 build/vignette.rds |binary inst/doc/gganimate.html | 204 ++++++++++++++++++-------------- man/anim_save.Rd | 4 man/gif_file.Rd | 6 tests/testthat/test-transition-states.R | 2 9 files changed, 141 insertions(+), 104 deletions(-)
Title: World Register of Marine Species (WoRMS) Client
Description: Client for World Register of Marine Species
(<http://www.marinespecies.org/>). Includes functions for each
of the API methods, including searching for names by name, date and
common names, searching using external identifiers, fetching
synonyms, as well as fetching taxonomic children and
taxonomic classification.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between worrms versions 0.4.0 dated 2019-06-28 and 0.4.2 dated 2020-07-08
worrms-0.4.0/worrms/tests/fixtures/vcr_cassettes |only worrms-0.4.2/worrms/DESCRIPTION | 15 worrms-0.4.2/worrms/LICENSE | 2 worrms-0.4.2/worrms/MD5 | 153 - worrms-0.4.2/worrms/NEWS.md | 8 worrms-0.4.2/worrms/R/worrms-package.R | 4 worrms-0.4.2/worrms/README.md | 177 -- worrms-0.4.2/worrms/build/vignette.rds |binary worrms-0.4.2/worrms/inst/doc/worrms.Rmd | 220 +- worrms-0.4.2/worrms/inst/doc/worrms.html | 851 ++++++---- worrms-0.4.2/worrms/man/wm_children.Rd | 3 worrms-0.4.2/worrms/man/wm_records_date.Rd | 9 worrms-0.4.2/worrms/man/wm_records_name.Rd | 3 worrms-0.4.2/worrms/man/worrms-package.Rd | 6 worrms-0.4.2/worrms/tests/fixtures/wm_children.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_-error.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_error.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_marine_only_false.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_marine_only_true.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_name.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_children_offset.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_classification.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_classification_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_classification_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_common_id.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_common_id_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_common_id_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_distribution.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_distribution_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_distribution_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_external.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_external_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_external_fishbase.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_external_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_id2name.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_id2name_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_id2name_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_name2id.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_name2id_.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_name2id_many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_ranks_id.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_ranks_id_error.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_ranks_name.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_ranks_name_error.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_by_external__many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_by_external__tsn.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_by_external_fishbase.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_by_external_ncbi.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_by_external_tsn.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_error.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_record_plural_plural.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records__many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_common.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_common_fuzzy_false.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_common_fuzzy_true.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_common_offset.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_name.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_name_fuzzy.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_names.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_names_fuzzy.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_rank.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_rank_error.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_records_taxamatch.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_sources.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_sources__many.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_synonyms.yml |only worrms-0.4.2/worrms/tests/fixtures/wm_synonyms__many.yml |only worrms-0.4.2/worrms/tests/testthat/helper-worrms.R | 3 worrms-0.4.2/worrms/tests/testthat/test-wm_children.R | 6 worrms-0.4.2/worrms/tests/testthat/test-wm_record.R | 1 worrms-0.4.2/worrms/tests/testthat/test-wm_records_date.R | 3 worrms-0.4.2/worrms/tests/testthat/test-wm_records_name.R | 15 worrms-0.4.2/worrms/tests/testthat/test-wm_records_names.R | 12 worrms-0.4.2/worrms/tests/testthat/test-wm_records_taxamatch.R | 2 worrms-0.4.2/worrms/vignettes/worrms.Rmd | 220 +- worrms-0.4.2/worrms/vignettes/worrms.Rmd.og |only 79 files changed, 970 insertions(+), 743 deletions(-)
Title: S3 Generics for Bayesian Analyses
Description: Provides S3 generic methods and some default implementations
for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples.
The purpose of 'universals' is to reduce package dependencies and conflicts.
The 'nlist' package implements many of the methods for its 'nlist' class.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between universals versions 0.0.2 dated 2020-06-11 and 0.0.3 dated 2020-07-08
universals-0.0.2/universals/R/testing.R |only universals-0.0.2/universals/tests/testthat/test-bind-chains.R |only universals-0.0.2/universals/tests/testthat/test-converged-pars.R |only universals-0.0.2/universals/tests/testthat/test-converged-terms.R |only universals-0.0.2/universals/tests/testthat/test-converged.R |only universals-0.0.2/universals/tests/testthat/test-esr-pars.R |only universals-0.0.2/universals/tests/testthat/test-esr-terms.R |only universals-0.0.2/universals/tests/testthat/test-esr.R |only universals-0.0.2/universals/tests/testthat/test-nterms.R |only universals-0.0.2/universals/tests/testthat/test-pars.R |only universals-0.0.2/universals/tests/testthat/test-rhat-pars.R |only universals-0.0.2/universals/tests/testthat/test-rhat-terms.R |only universals-0.0.2/universals/tests/testthat/test-rhat.R |only universals-0.0.3/universals/DESCRIPTION | 21 - universals-0.0.3/universals/MD5 | 141 ++++------ universals-0.0.3/universals/NEWS.md | 5 universals-0.0.3/universals/R/bind-chains.R | 5 universals-0.0.3/universals/R/collapse-chains.R | 5 universals-0.0.3/universals/R/converged-pars.R | 6 universals-0.0.3/universals/R/converged-terms.R | 6 universals-0.0.3/universals/R/converged.R | 5 universals-0.0.3/universals/R/dims.R | 15 - universals-0.0.3/universals/R/esr-pars.R | 6 universals-0.0.3/universals/R/esr-terms.R | 5 universals-0.0.3/universals/R/esr.R | 5 universals-0.0.3/universals/R/estimates.R | 11 universals-0.0.3/universals/R/nchains.R | 13 universals-0.0.3/universals/R/ndims.R | 18 - universals-0.0.3/universals/R/niters.R | 10 universals-0.0.3/universals/R/npars.R | 4 universals-0.0.3/universals/R/npdims.R | 9 universals-0.0.3/universals/R/nsams.R | 13 universals-0.0.3/universals/R/nsims.R | 9 universals-0.0.3/universals/R/nterms.R | 15 - universals-0.0.3/universals/R/pars.R | 9 universals-0.0.3/universals/R/pdims.R | 10 universals-0.0.3/universals/R/rhat-pars.R | 6 universals-0.0.3/universals/R/rhat-terms.R | 6 universals-0.0.3/universals/R/rhat.R | 5 universals-0.0.3/universals/R/set-pars.R | 12 universals-0.0.3/universals/R/split-chains.R | 11 universals-0.0.3/universals/README.md | 6 universals-0.0.3/universals/man/bind_chains.Rd | 6 universals-0.0.3/universals/man/collapse_chains.Rd | 6 universals-0.0.3/universals/man/converged.Rd | 6 universals-0.0.3/universals/man/converged_pars.Rd | 7 universals-0.0.3/universals/man/converged_terms.Rd | 7 universals-0.0.3/universals/man/dims.Rd | 6 universals-0.0.3/universals/man/esr.Rd | 6 universals-0.0.3/universals/man/esr_pars.Rd | 7 universals-0.0.3/universals/man/esr_terms.Rd | 6 universals-0.0.3/universals/man/estimates.Rd | 11 universals-0.0.3/universals/man/nchains.Rd | 12 universals-0.0.3/universals/man/ndims.Rd | 7 universals-0.0.3/universals/man/niters.Rd | 10 universals-0.0.3/universals/man/npars.Rd | 5 universals-0.0.3/universals/man/npdims.Rd | 9 universals-0.0.3/universals/man/nsams.Rd | 13 universals-0.0.3/universals/man/nsims.Rd | 9 universals-0.0.3/universals/man/nterms.Rd | 15 - universals-0.0.3/universals/man/pars.Rd | 9 universals-0.0.3/universals/man/pdims.Rd | 10 universals-0.0.3/universals/man/rhat.Rd | 6 universals-0.0.3/universals/man/rhat_pars.Rd | 7 universals-0.0.3/universals/man/rhat_terms.Rd | 7 universals-0.0.3/universals/man/set_pars.Rd | 12 universals-0.0.3/universals/man/split_chains.Rd | 11 universals-0.0.3/universals/man/universals-package.Rd | 5 universals-0.0.3/universals/tests/testthat/test-collapse-chains.R | 16 - universals-0.0.3/universals/tests/testthat/test-estimates.R | 54 +++ universals-0.0.3/universals/tests/testthat/test-nchains.R | 17 - universals-0.0.3/universals/tests/testthat/test-niters.R | 14 universals-0.0.3/universals/tests/testthat/test-npdims.R | 20 + universals-0.0.3/universals/tests/testthat/test-nsams.R | 23 + universals-0.0.3/universals/tests/testthat/test-nsims.R | 12 universals-0.0.3/universals/tests/testthat/test-pdims.R | 19 + universals-0.0.3/universals/tests/testthat/test-set-pars.R | 48 +++ universals-0.0.3/universals/tests/testthat/test-split-chains.R | 28 + 78 files changed, 482 insertions(+), 376 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <http://cyclestreets.net/>;
calculation of route segment attributes such as bearing and aggregate flow;
and 'travel watershed' analysis.
See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Richard Ellison [aut],
Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>),
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Nikolai Berkoff [ctb] (Co-author of line2route),
Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10),
Mark Padgham [ctb],
Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.6.1 dated 2020-06-23 and 0.6.2 dated 2020-07-08
DESCRIPTION | 10 +++--- MD5 | 25 ++++++++------- NAMESPACE | 2 + NEWS.md | 7 ++++ R/route.R | 19 ++++++++--- R/route_google.R |only inst/doc/stplanr-od.html | 4 +- inst/doc/stplanr-routing.R | 47 ++++++++++++++++++++--------- inst/doc/stplanr-routing.Rmd | 67 +++++++++++++++++++++++++++++++++--------- inst/doc/stplanr-routing.html | 55 +++++++++++++++++++++------------- inst/doc/stplanr.html | 4 +- inst/test-route-local-large.R |only man/route.Rd | 4 +- man/route_google.Rd |only vignettes/stplanr-routing.Rmd | 67 +++++++++++++++++++++++++++++++++--------- 15 files changed, 223 insertions(+), 88 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Brooke Anderson [ctb],
Maëlle Salmon [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Alex Simmons [ctb],
Karthik Ram [ctb],
Hart Edmund [ctb],
rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 1.0.0 dated 2020-06-13 and 1.1.0 dated 2020-07-08
rnoaa-1.0.0/rnoaa/tests/fixtures/buoy_buoyid_case.yml |only rnoaa-1.0.0/rnoaa/tests/fixtures/homr.yml |only rnoaa-1.1.0/rnoaa/DESCRIPTION | 6 - rnoaa-1.1.0/rnoaa/MD5 | 76 +++++++--------- rnoaa-1.1.0/rnoaa/NEWS.md | 8 + rnoaa-1.1.0/rnoaa/R/argo.R | 7 - rnoaa-1.1.0/rnoaa/R/buoy.R | 5 - rnoaa-1.1.0/rnoaa/R/ncdc.r | 10 -- rnoaa-1.1.0/rnoaa/R/ncdc_datasets.r | 20 +--- rnoaa-1.1.0/rnoaa/R/ncdc_datatypes.r | 9 - rnoaa-1.1.0/rnoaa/README.md | 53 +++++------ rnoaa-1.1.0/rnoaa/build/vignette.rds |binary rnoaa-1.1.0/rnoaa/inst/doc/buoy_vignette.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/homr_vignette.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/ncdc_attributes.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/ncdc_vignette.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/ncdc_workflow.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/rnoaa.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/rnoaa_ropenaq.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/seaice_vignette.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/storms_vignette.html | 20 +++- rnoaa-1.1.0/rnoaa/inst/doc/swdi_vignette.html | 20 +++- rnoaa-1.1.0/rnoaa/man/argo.Rd | 3 rnoaa-1.1.0/rnoaa/man/buoy.Rd | 2 rnoaa-1.1.0/rnoaa/man/ncdc.Rd | 35 ------- rnoaa-1.1.0/rnoaa/man/ncdc_datasets.Rd | 15 --- rnoaa-1.1.0/rnoaa/man/ncdc_datatypes.Rd | 11 -- rnoaa-1.1.0/rnoaa/tests/testthat/test-arc2.R | 9 - rnoaa-1.1.0/rnoaa/tests/testthat/test-buoy.R | 21 +--- rnoaa-1.1.0/rnoaa/tests/testthat/test-check_response.r | 6 - rnoaa-1.1.0/rnoaa/tests/testthat/test-coops.R | 4 rnoaa-1.1.0/rnoaa/tests/testthat/test-cpc_prcp.R | 2 rnoaa-1.1.0/rnoaa/tests/testthat/test-ghcnd.R | 6 - rnoaa-1.1.0/rnoaa/tests/testthat/test-ghcnd_splitvars.R | 2 rnoaa-1.1.0/rnoaa/tests/testthat/test-homr.R | 53 +++++------ rnoaa-1.1.0/rnoaa/tests/testthat/test-meteo.R | 4 rnoaa-1.1.0/rnoaa/tests/testthat/test-seaice.R | 6 - rnoaa-1.1.0/rnoaa/tests/testthat/test-storm_events.R | 16 +-- rnoaa-1.1.0/rnoaa/tests/testthat/test-storms.R | 2 rnoaa-1.1.0/rnoaa/tests/testthat/test-vis_miss.R | 3 40 files changed, 325 insertions(+), 269 deletions(-)
Title: Recurrent Event Data Analysis
Description: Contains implementations of recurrent event data analysis routines
including (1) survival and recurrent event data simulation from
stochastic process point of view by the thinning method
proposed by Lewis and Shedler (1979) <doi:10.1002/nav.3800260304>
and the inversion method introduced in Cinlar (1975, ISBN:978-0486497976),
(2) the mean cumulative function (MCF) estimation by the
Nelson-Aalen estimator of the cumulative hazard rate function,
(3) two-sample recurrent event responses comparison with the pseudo-score
tests proposed by Lawless and Nadeau (1995) <doi:10.2307/1269617>,
(4) gamma frailty model with spline rate function following
Fu, et al. (2016) <doi:10.1080/10543406.2014.992524>.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>),
Haoda Fu [aut],
Jun Yan [ctb] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between reda versions 0.5.1 dated 2020-06-27 and 0.5.2 dated 2020-07-08
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/rateReg.R | 12 ++++++------ README.md | 13 +++---------- inst/CITATION | 2 +- inst/doc/reda-Recur.html | 6 +++--- inst/doc/reda-intro.html | 6 +++--- inst/doc/reda-simulate.html | 6 +++--- 10 files changed, 42 insertions(+), 40 deletions(-)
Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney and Riad Jarjour
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between proftools versions 0.99-2 dated 2016-01-13 and 0.99-3 dated 2020-07-08
proftools-0.99-2/proftools/README |only proftools-0.99-3/proftools/DESCRIPTION | 6 proftools-0.99-3/proftools/MD5 | 39 proftools-0.99-3/proftools/NAMESPACE | 5 proftools-0.99-3/proftools/R/callgrind.R |only proftools-0.99-3/proftools/R/flamegraph.R |only proftools-0.99-3/proftools/R/prof.R | 871 +++++------------ proftools-0.99-3/proftools/R/proftools.R | 6 proftools-0.99-3/proftools/README.md |only proftools-0.99-3/proftools/build/vignette.rds |binary proftools-0.99-3/proftools/inst/doc/proftools.R | 35 proftools-0.99-3/proftools/inst/doc/proftools.Rnw | 38 proftools-0.99-3/proftools/inst/doc/proftools.pdf |binary proftools-0.99-3/proftools/man/hotPaths.Rd | 3 proftools-0.99-3/proftools/man/plotProfileCallGraph.Rd | 7 proftools-0.99-3/proftools/man/profileCallGraph2Dot.Rd | 5 proftools-0.99-3/proftools/man/profileExpr.Rd | 8 proftools-0.99-3/proftools/man/readProfileData.Rd | 6 proftools-0.99-3/proftools/man/styles.Rd | 2 proftools-0.99-3/proftools/man/summaries.Rd | 10 proftools-0.99-3/proftools/vignettes/proftools.Rnw | 38 proftools-0.99-3/proftools/vignettes/proftools.bib | 56 - proftools-0.99-3/proftools/vignettes/shinyGUI.png |only 23 files changed, 435 insertions(+), 700 deletions(-)
Title: Management of Survey Data and Presentation of Analysis Results
Description: An infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) 'SPSS' and
'Stata' files is provided. Further, the package allows to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to 'LaTeX' and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.99.25.5 dated 2020-06-30 and 0.99.25.6 dated 2020-07-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/codebook-methods.R | 23 ++++++++++++++--------- R/dedup-labels.R | 5 +++-- inst/ChangeLog | 11 +++++++++++ inst/doc/anes48.html | 2 +- 6 files changed, 38 insertions(+), 21 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>),
Grant McDermott [ctb],
Karl Dunkle Werner [ctb],
Matthieu Stigler [ctb],
Daniel Lüdecke [ctb]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.8-5 dated 2019-12-17 and 2.8-5.1 dated 2020-07-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/startup.R | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6.6 dated 2020-05-16 and 4.6.7 dated 2020-07-08
DESCRIPTION | 12 +++++----- MD5 | 52 ++++++++++++++++++++++---------------------- NAMESPACE | 3 ++ NEWS | 5 ++++ R/by-lmBy.R | 2 - R/by-splitBy.R | 2 - R/by-subsetBy.R | 2 - R/by-summaryBy.R | 2 - R/by-transformBy.R | 2 - R/esticon.R | 4 ++- R/firstlastObs.R | 2 - R/interaction_plot.R |only R/linest_LSmeans.R | 2 - R/linest_compute.R | 2 - R/tidy.R | 4 +-- inst/doc/doby.pdf |binary inst/doc/linest-lsmeans.pdf |binary man/by-lmby.Rd | 2 - man/by-subset.Rd | 2 - man/by-summary.Rd | 2 - man/by-transform.Rd | 2 - man/esticon.Rd | 2 - man/firstlastobs.Rd | 2 - man/interaction-plot.Rd |only man/linest.Rd | 2 - man/ls-means.Rd | 2 - man/tidy-esticon.Rd | 2 - man/tidy-linest.Rd | 2 - 28 files changed, 64 insertions(+), 52 deletions(-)
Title: Extract Genotypes from a PLINK .bed File
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <cran@agrueneberg.info>
Diff between BEDMatrix versions 2.0.2 dated 2020-03-11 and 2.0.3 dated 2020-07-08
BEDMatrix-2.0.2/BEDMatrix/tests/testthat |only BEDMatrix-2.0.2/BEDMatrix/tests/testthat.R |only BEDMatrix-2.0.3/BEDMatrix/DESCRIPTION | 14 +-- BEDMatrix-2.0.3/BEDMatrix/MD5 | 30 ++++---- BEDMatrix-2.0.3/BEDMatrix/NEWS.md | 6 + BEDMatrix-2.0.3/BEDMatrix/R/BEDMatrix.R | 74 ++++++++++++--------- BEDMatrix-2.0.3/BEDMatrix/README.md | 4 - BEDMatrix-2.0.3/BEDMatrix/inst/include/BEDMatrix.h | 20 ++--- BEDMatrix-2.0.3/BEDMatrix/inst/tinytest |only BEDMatrix-2.0.3/BEDMatrix/man/BEDMatrix-class.Rd | 9 +- BEDMatrix-2.0.3/BEDMatrix/man/BEDMatrix-package.Rd | 5 - BEDMatrix-2.0.3/BEDMatrix/man/BEDMatrix.Rd | 12 +-- BEDMatrix-2.0.3/BEDMatrix/src/mapping.c | 12 --- BEDMatrix-2.0.3/BEDMatrix/tests/tinytest.R |only 14 files changed, 101 insertions(+), 85 deletions(-)
Title: Scale Mixture of Skew-Normal Linear Mixed Models
Description: It fits scale mixture of skew-normal linear mixed models using an expectation–maximization (EM) type algorithm, including some possibilities for modeling the within-subject dependence. Details can be found in Schumacher, Lachos and Matos (2020) <arXiv:2002.01040>.
Author: Fernanda L. Schumacher [aut, cre],
Larissa A. Matos [aut],
Victor H. Lachos [aut]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Diff between skewlmm versions 0.2.1 dated 2020-07-06 and 0.2.2 dated 2020-07-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 - R/auxfunctions-sim.R | 31 +++++++++++++++++++++---------- R/auxfunctions.R | 30 ++++++++++++++++++++---------- man/smsn.lmm.Rd | 4 ++-- 6 files changed, 52 insertions(+), 32 deletions(-)
Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
load the simulation data results of the DrugLogics software pipeline which predicts synergistic drug
combinations in cancer cell lines (developed by the DrugLogics research group
in NTNU). It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions/Matthews correlation coefficient score) or synergy prediction based on a given set
of gold standard synergies and find the average activity difference per network
node between all model group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be found.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between emba versions 0.1.5 dated 2020-07-01 and 0.1.6 dated 2020-07-08
DESCRIPTION | 8 - MD5 | 8 - NEWS.md | 4 inst/doc/emba.html | 172 ++++++++++++++++++++++------------------- tests/testthat/test-analysis.R | 38 ++++----- 5 files changed, 125 insertions(+), 105 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-14 0.1.1
2017-08-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-04 0.1.4
2019-03-17 0.1.3
2018-11-20 0.1.2
2018-10-28 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-14 1.1.0
2018-04-19 1.0.2
2017-11-20 1.0.1
2017-10-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-17 1.0.3
2015-08-05 1.0.2
2015-01-05 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-17 0.1.0
2016-11-08 0.0.8
2016-10-11 0.0.7
2016-10-06 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-02 1.0.3
2017-12-05 1.0.1
2017-11-22 1.0
2017-10-09 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-15 0.0.1.1
2020-05-25 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-06 1.1
2019-01-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-20 1.2.17