Title: Tools to Match Financial Portfolios with Climate Data
Description: These tools implement in R a fundamental part of
the software 'PACTA' (Paris Agreement Capital Transition Assessment),
which is a free tool that calculates the alignment between financial
portfolios and climate scenarios (<https://2degrees-investing.org/>).
Financial institutions use 'PACTA' to study how their capital
allocation impacts the climate. This package matches data from
financial portfolios to asset level data from market-intelligence
databases (e.g. power plant capacities, emission factors, etc.). This
is the first step to assess if a financial portfolio aligns with
climate goals.
Author: Mauro Lepore [aut, cre, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Jackson Hoffart [aut] (<https://orcid.org/0000-0002-8600-5042>),
Klaus Hagedorn [aut],
Florence Palandri [aut],
Evgeny Petrovsky [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between r2dii.match versions 0.0.3 dated 2020-06-30 and 0.0.4 dated 2020-08-13
r2dii.match-0.0.3/r2dii.match/R/restructure_loanbook_for_matching.R |only r2dii.match-0.0.3/r2dii.match/R/score_alias_similarity.R |only r2dii.match-0.0.3/r2dii.match/R/score_string_similarity.R |only r2dii.match-0.0.3/r2dii.match/tests/testthat/test-restructure_loanbook_for_matching.R |only r2dii.match-0.0.3/r2dii.match/tests/testthat/test-score_alias_similarity.R |only r2dii.match-0.0.3/r2dii.match/tests/testthat/test-score_string_similarity.R |only r2dii.match-0.0.4/r2dii.match/DESCRIPTION | 13 r2dii.match-0.0.4/r2dii.match/MD5 | 53 +- r2dii.match-0.0.4/r2dii.match/NAMESPACE | 7 r2dii.match-0.0.4/r2dii.match/NEWS.md | 14 r2dii.match-0.0.4/r2dii.match/R/add_sector_and_borderline.R | 3 r2dii.match-0.0.4/r2dii.match/R/crucial_columns.R |only r2dii.match-0.0.4/r2dii.match/R/imports.R | 20 r2dii.match-0.0.4/r2dii.match/R/match_name.R | 188 ++++--- r2dii.match-0.0.4/r2dii.match/R/prioritize.R | 5 r2dii.match-0.0.4/r2dii.match/R/restructure_ald.R |only r2dii.match-0.0.4/r2dii.match/R/select_chr.R | 2 r2dii.match-0.0.4/r2dii.match/R/to_alias.R | 7 r2dii.match-0.0.4/r2dii.match/R/uniquify_id_column.R | 18 r2dii.match-0.0.4/r2dii.match/README.md | 121 +--- r2dii.match-0.0.4/r2dii.match/inst/WORDLIST | 5 r2dii.match-0.0.4/r2dii.match/man/crucial_lbk.Rd |only r2dii.match-0.0.4/r2dii.match/man/match_name.Rd | 19 r2dii.match-0.0.4/r2dii.match/man/prioritize.Rd | 15 r2dii.match-0.0.4/r2dii.match/man/prioritize_level.Rd | 5 r2dii.match-0.0.4/r2dii.match/man/r2dii.match-package.Rd | 2 r2dii.match-0.0.4/r2dii.match/tests/testthat/helper-expect_names_match_name.R |only r2dii.match-0.0.4/r2dii.match/tests/testthat/helper-fake_lbk.R | 29 - r2dii.match-0.0.4/r2dii.match/tests/testthat/output/match_name-overwrite_warning.txt | 20 r2dii.match-0.0.4/r2dii.match/tests/testthat/output/match_name-sec_classif_unknown.txt | 2 r2dii.match-0.0.4/r2dii.match/tests/testthat/output/match_name-up266.txt |only r2dii.match-0.0.4/r2dii.match/tests/testthat/ref-match-name |only r2dii.match-0.0.4/r2dii.match/tests/testthat/test-match_name.R | 262 ++++++---- r2dii.match-0.0.4/r2dii.match/tests/testthat/test-restructure_ald.R |only 34 files changed, 477 insertions(+), 333 deletions(-)
Title: Tools for Working with 'Taxonomic' Databases
Description: Tools for working with 'taxonomic' databases, including
utilities for downloading databases, loading them into various
'SQL' databases, cleaning up files, and providing a 'SQL' connection
that can be used to do 'SQL' queries directly or used in 'dplyr'.
Author: Scott Chamberlain [aut, cre],
Zebulun Arendsee [aut]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between taxizedb versions 0.1.4 dated 2017-06-20 and 0.2.0 dated 2020-08-13
taxizedb-0.1.4/taxizedb/man/db_load.Rd |only taxizedb-0.1.4/taxizedb/tests/testthat/test-db_load.R |only taxizedb-0.2.0/taxizedb/DESCRIPTION | 32 taxizedb-0.2.0/taxizedb/LICENSE | 2 taxizedb-0.2.0/taxizedb/MD5 | 75 + taxizedb-0.2.0/taxizedb/NAMESPACE | 20 taxizedb-0.2.0/taxizedb/NEWS.md | 25 taxizedb-0.2.0/taxizedb/R/ap_children.R |only taxizedb-0.2.0/taxizedb/R/ap_classification.R |only taxizedb-0.2.0/taxizedb/R/ap_core.R |only taxizedb-0.2.0/taxizedb/R/ap_downstream.R |only taxizedb-0.2.0/taxizedb/R/ap_name2taxid.R |only taxizedb-0.2.0/taxizedb/R/ap_taxid2name.R |only taxizedb-0.2.0/taxizedb/R/ap_taxid2rank.R |only taxizedb-0.2.0/taxizedb/R/caching.R | 19 taxizedb-0.2.0/taxizedb/R/db_download.R | 444 +++++++++-- taxizedb-0.2.0/taxizedb/R/db_load.R | 198 ---- taxizedb-0.2.0/taxizedb/R/db_path.R |only taxizedb-0.2.0/taxizedb/R/rank_utils.R |only taxizedb-0.2.0/taxizedb/R/sql.R | 6 taxizedb-0.2.0/taxizedb/R/src.R | 63 + taxizedb-0.2.0/taxizedb/R/taxizedb-package.R | 136 ++- taxizedb-0.2.0/taxizedb/R/zzz.R | 40 taxizedb-0.2.0/taxizedb/README.md | 222 +---- taxizedb-0.2.0/taxizedb/build |only taxizedb-0.2.0/taxizedb/inst/doc |only taxizedb-0.2.0/taxizedb/inst/ignore/itis.R |only taxizedb-0.2.0/taxizedb/man/children.Rd |only taxizedb-0.2.0/taxizedb/man/classification.Rd |only taxizedb-0.2.0/taxizedb/man/db_download.Rd | 54 - taxizedb-0.2.0/taxizedb/man/db_load-defunct.Rd |only taxizedb-0.2.0/taxizedb/man/db_path.Rd |only taxizedb-0.2.0/taxizedb/man/downstream.Rd |only taxizedb-0.2.0/taxizedb/man/name2taxid.Rd |only taxizedb-0.2.0/taxizedb/man/sql_collect.Rd | 6 taxizedb-0.2.0/taxizedb/man/src_taxizedb.Rd | 31 taxizedb-0.2.0/taxizedb/man/taxid2name.Rd |only taxizedb-0.2.0/taxizedb/man/taxid2rank.Rd |only taxizedb-0.2.0/taxizedb/man/taxizedb-package.Rd | 129 ++- taxizedb-0.2.0/taxizedb/tests/testthat/helper-taxizedb.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-caching.R | 18 taxizedb-0.2.0/taxizedb/tests/testthat/test-children.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-classification.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-db_download.R | 2 taxizedb-0.2.0/taxizedb/tests/testthat/test-downstream.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-name2taxid.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-rank_utils.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-realthing.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-safety.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-sql_collect.R | 14 taxizedb-0.2.0/taxizedb/tests/testthat/test-src.R | 32 taxizedb-0.2.0/taxizedb/tests/testthat/test-taxid2name.R |only taxizedb-0.2.0/taxizedb/tests/testthat/test-taxid2rank.R |only taxizedb-0.2.0/taxizedb/vignettes |only 54 files changed, 961 insertions(+), 607 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes several measures for structural balance as introduced by Cartwright and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various centrality indices, and projections of signed two-mode networks introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between signnet versions 0.5.3 dated 2020-06-30 and 0.6.0 dated 2020-08-13
DESCRIPTION | 6 +- MD5 | 27 +++++----- NEWS.md | 5 + R/RcppExports.R | 4 - R/blockmodel.R | 24 +++++++-- R/data_avatar.R |only data/avatar.rda |only inst/doc/blockmodeling.html | 32 ++++++++---- inst/doc/centrality.html | 26 +++++++-- inst/doc/complex_matrices.html | 26 +++++++-- inst/doc/signed_2mode.html | 34 ++++++++---- inst/doc/signed_networks.html | 30 +++++++---- inst/doc/structural_balance.html | 40 +++++++++------ man/avatar.Rd |only src/RcppExports.cpp | 14 ++--- src/optimBlocks.cpp | 103 +++------------------------------------ 16 files changed, 193 insertions(+), 178 deletions(-)
Title: Coloring Wildlife Distributions in Space-Time
Description: Color and visualize wildlife distributions in
space-time using raster data. In addition to enabling display of
sequential change in distributions through the use of small multiples,
'colorist' provides functions for extracting several features of
interest from a sequence of distributions and for visualizing those
features using HCL (hue-chroma-luminance) color palettes. Resulting
maps allow for "fair" visual comparison of intensity values (e.g.,
occurrence, abundance, or density) across space and time and can be
used to address questions about where, when, and how consistently a
species, group, or individual is likely to be found.
Author: Justin Schuetz [aut] (<https://orcid.org/0000-0002-6163-538X>),
Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>),
Tom Auer [aut] (<https://orcid.org/0000-0001-8619-7147>)
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between colorist versions 0.1.0 dated 2020-03-26 and 0.1.1 dated 2020-08-13
colorist-0.1.0/colorist/data/datalist |only colorist-0.1.1/colorist/DESCRIPTION | 10 - colorist-0.1.1/colorist/MD5 | 38 ++-- colorist-0.1.1/colorist/NEWS.md | 7 colorist-0.1.1/colorist/R/data.R | 12 - colorist-0.1.1/colorist/R/map.R | 111 +++++++++----- colorist-0.1.1/colorist/R/metrics.R | 2 colorist-0.1.1/colorist/R/palette.R | 81 +++++++--- colorist-0.1.1/colorist/README.md | 27 +-- colorist-0.1.1/colorist/build |only colorist-0.1.1/colorist/inst |only colorist-0.1.1/colorist/man/elephant_ud.Rd | 2 colorist-0.1.1/colorist/man/fiespa_occ.Rd | 4 colorist-0.1.1/colorist/man/figures/README-elephant-1.png |binary colorist-0.1.1/colorist/man/fisher_ud.Rd | 4 colorist-0.1.1/colorist/man/map_multiples.Rd | 33 ++-- colorist-0.1.1/colorist/man/map_single.Rd | 45 +++-- colorist-0.1.1/colorist/man/palette_set.Rd | 7 colorist-0.1.1/colorist/vignettes |only 19 files changed, 242 insertions(+), 141 deletions(-)
Title: 'Comet' API for R
Description: A convenient 'R' wrapper to the 'Comet' API, which is a cloud
platform allowing you to track, compare, explain and optimize machine
learning experiments and models. Experiments can be viewed on the 'Comet'
online dashboard at <https://www.comet.ml>.
Author: Dean Attali [aut],
Doug Blank [cre]
Maintainer: Doug Blank <doug@comet.ml>
Diff between cometr versions 0.1.1 dated 2020-05-08 and 0.2.0 dated 2020-08-13
cometr-0.1.1/cometr/inst/train-examples/FeaturePlot.png |only cometr-0.1.1/cometr/inst/train-examples/Plot.png |only cometr-0.1.1/cometr/inst/train-examples/Rplots.pdf |only cometr-0.2.0/cometr/DESCRIPTION | 8 cometr-0.2.0/cometr/MD5 | 21 +- cometr-0.2.0/cometr/NAMESPACE | 1 cometr-0.2.0/cometr/NEWS.md |only cometr-0.2.0/cometr/R/experiment.R | 161 +++++++++++++--- cometr-0.2.0/cometr/R/utils.R | 26 ++ cometr-0.2.0/cometr/inst/train-examples/caret-example.R | 49 ++++ cometr-0.2.0/cometr/inst/train-examples/keras-example.R |only cometr-0.2.0/cometr/inst/train-examples/nnet-example.R |only cometr-0.2.0/cometr/man/Experiment.Rd | 29 ++ cometr-0.2.0/cometr/man/get_experiment.Rd |only cometr-0.2.0/cometr/tests/testthat/helper.R | 33 ++- 15 files changed, 264 insertions(+), 64 deletions(-)
Title: Create Tables for Reporting Clinical Trials
Description: Create Tables for Reporting Clinical Trials.
Calculates descriptive statistics and hypothesis tests,
arranges the results in a table ready for reporting with LaTeX, HTML or Word.
Author: Armin Ströbel [aut, cre] (<https://orcid.org/0000-0002-6873-5332>),
Alan Haynes [aut] (<https://orcid.org/0000-0003-1374-081X>)
Maintainer: Armin Ströbel <arminstroebel@web.de>
Diff between atable versions 0.1.7 dated 2020-07-14 and 0.1.8 dated 2020-08-13
DESCRIPTION | 6 ++-- MD5 | 20 ++++++++------- R/atable.R | 56 ++++++++++++++++++++++++++++++++++++++++--- R/atable_options.R | 16 +++++++++--- R/check_alias_mapping.R |only R/helper.R | 10 ------- inst/doc/atable_usage.pdf |binary man/atable.Rd | 24 ++++++++++++++++-- man/atable_options.Rd | 10 ++++++- man/check_alias_mapping.Rd |only tests/testthat/test_alias.R | 38 +++++++++++++++++++++++++++++ tests/testthat/test_atable.R | 19 ++++++++++++++ 12 files changed, 168 insertions(+), 31 deletions(-)
Title: In-place Operators for R
Description: It provides in-place operators for R
that are equivalent to '+=', '-=', '*=', '/=' in C++.
Those can be applied on integer|double vectors|matrices.
You have also access to sweep operations (in-place).
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between inplace versions 0.1.0 dated 2018-06-10 and 0.1.1 dated 2020-08-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- README.md | 8 ++++++-- man/inplace-package.Rd | 15 ++++++++++++--- tests/testthat/test-sweep.R | 2 +- 5 files changed, 28 insertions(+), 15 deletions(-)
Title: Vector Logistic Smooth Transition Models / Realized Covariances
Construction
Description: Allows the user to estimate a vector logistic smooth transition autoregressive model via maximum log-likelihood or nonlinear least squares. It further permits to test for linearity in the multivariate framework against a vector logistic smooth transition autoregressive model with a single transition variable. The estimation method is discussed in Terasvirta and Yang (2014, <doi:10.1108/S0731-9053(2013)0000031008>). Also, realized covariances can be constructed from stock market prices or returns, as explained in Andersen et al. (2001, <doi:10.1016/S0304-405X(01)00055-1>).
Author: Andrea Bucci [aut, cre, cph],
Giulio Palomba [aut],
Eduardo Rossi [aut],
Andrea Faragalli [ctb]
Maintainer: Andrea Bucci <andrea.bucci@unich.it>
Diff between starvars versions 0.1.7 dated 2020-05-04 and 0.1.8 dated 2020-08-13
starvars-0.1.7/starvars/man/predict.VLSTAR.Rd |only starvars-0.1.8/starvars/DESCRIPTION | 6 starvars-0.1.8/starvars/MD5 | 40 ++- starvars-0.1.8/starvars/NAMESPACE | 51 ++++ starvars-0.1.8/starvars/R/VLSTAR.R | 266 ++++++++--------------- starvars-0.1.8/starvars/R/VLSTARjoint.R | 113 +++++++--- starvars-0.1.8/starvars/R/coef.VLSTAR.R |only starvars-0.1.8/starvars/R/logLik.VLSTAR.R |only starvars-0.1.8/starvars/R/lrvarbart.R | 6 starvars-0.1.8/starvars/R/multiCUMSUM.R | 292 ++++++++++++++++++-------- starvars-0.1.8/starvars/R/plot.VLSTAR.R |only starvars-0.1.8/starvars/R/plot.vlstarpred.R |only starvars-0.1.8/starvars/R/predict.VLSTAR.R | 181 ++++++++++++++-- starvars-0.1.8/starvars/R/print.vlstarpred.R |only starvars-0.1.8/starvars/R/rcov.R | 148 +++++++------ starvars-0.1.8/starvars/R/summary.VLSTAR.R |only starvars-0.1.8/starvars/data/techprices.RData |only starvars-0.1.8/starvars/man/VLSTAR.Rd | 59 ++--- starvars-0.1.8/starvars/man/VLSTARjoint.Rd | 17 - starvars-0.1.8/starvars/man/coefficients.Rd |only starvars-0.1.8/starvars/man/logLik.Rd |only starvars-0.1.8/starvars/man/lrvarbart.Rd | 2 starvars-0.1.8/starvars/man/multiCUMSUM.Rd | 19 + starvars-0.1.8/starvars/man/plot.Rd |only starvars-0.1.8/starvars/man/predict.Rd |only starvars-0.1.8/starvars/man/rcov.Rd | 17 - starvars-0.1.8/starvars/man/summary.VLSTAR.Rd |only starvars-0.1.8/starvars/man/techprices.Rd |only 28 files changed, 767 insertions(+), 450 deletions(-)
Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to mixture
of dichotomous and polytomous data, calibrate online item parameters
(i.e., pretest and operational items), estimate examinees abilities,
and examine the IRT model-data fit on item-level in different ways
as well as provide useful functions related to unidimensional IRT models.
For the item parameter estimation, marginal maximum likelihood estimation
with expectation-maximization (MMLE-EM) algorithm
(Bock & Aitkin (1981) <doi:10.1007/BF02294168>) is used.
For the online calibration, Stocking's Method A
(Ban, Hanson, Wang, Yi, & Harris (2011) <doi:10.1111/j.1745-3984.2001.tb01123.x>)
and the fixed item parameter calibration (FIPC) method
(Kim (2006) <doi:10.1111/j.1745-3984.2006.00021.x>) are provided.
For the ability estimation, several popular scoring methods
(e.g., MLE, EAP, and MAP) are implemented. In terms of assessing the IRT
model-data fit, one of distinguished features of this package is that it
gives not only well-known item fit statistics (e.g., chi-square (X2),
likelihood ratio chi-square (G2), infit and oufit statistics, and
S-X2 statistic (Ames & Penfield (2015) <doi:10.1111/emip.12067>))
but also graphical displays to look at residuals between the observed
data and model-based predictions
(Hambleton, Swaminathan, & Rogers (1991, ISBN:9780803936478)).
In addition, there are many useful functions such as computing asymptotic
variance-covariance matrices of item parameter estimates (Li & Lissitz (2004)
<doi:10.1111/j.1745-3984.2004.tb01109.x>), importing item and/or ability
parameters from popular IRT software, running 'flexMIRT' (Cai, 2017)
through R, generating simulated data, computing the conditional
distribution of observed scores using the Lord-Wingersky recursion
formula (Lord & Wingersky (1984) <doi:10.1177/014662168400800409>),
computing the loglikelihood of individual items, computing the loglikelihood
of abilities, computing item and test information functions, computing item
and test characteristic curve functions, and plotting item and test
characteristic curves and item and test information functions.
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtplay versions 1.6.0 dated 2020-07-15 and 1.6.1 dated 2020-08-13
DESCRIPTION | 6 MD5 | 61 ++++---- NAMESPACE | 1 NEWS.md | 30 ++++ R/EMstep.R | 10 - R/est_irt.R | 357 +++++++++++++++++++++++++------------------------ R/est_item.R | 2 R/est_score.R | 281 ++++++++++++++++++++------------------ R/gen_weight.R | 2 R/getirt.R | 8 - R/hessian.R | 8 - R/inv_tcc.R | 59 +++----- R/irtmodel.R | 1 R/irtplay-package.R | 4 R/lwrc.R | 237 +++++++++++++++++--------------- R/plot_info.R | 13 + R/plot_irtfit.R | 15 -- R/post_den.R |only R/posterior.R | 17 +- R/print.R | 6 R/se_expinfo.R |only R/se_tcc.R | 10 - R/summary.R | 4 R/util.R | 5 README.md | 84 +++++------ data/LSAT6.rda |binary man/est_irt.Rd | 12 + man/est_item.Rd | 2 man/est_score.Rd | 15 +- man/gen.weight.Rd | 2 man/getirt.Rd | 6 man/irtplay-package.Rd | 4 man/post_den.Rd |only 33 files changed, 686 insertions(+), 576 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.4.0 dated 2020-07-17 and 0.5.0 dated 2020-08-13
DESCRIPTION | 6 +++--- MD5 | 26 ++++++++++++++++---------- NAMESPACE | 5 +++++ NEWS.md | 6 ++++++ R/compose.R |only R/enframe.R | 2 ++ R/leanify.R |only R/rd_info.R | 20 ++++++++++++++++++++ R/zzz.R | 2 +- README.md | 2 +- man/compose.Rd |only man/leanify_r6.Rd |only man/rd_info.Rd | 6 ++++++ tests/testthat/test_compose.R |only tests/testthat/test_cross_join.R | 2 +- tests/testthat/test_leanify.R |only tests/testthat/test_unnest.R | 2 +- 17 files changed, 62 insertions(+), 17 deletions(-)
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between robmixglm versions 1.1-0 dated 2020-06-18 and 1.1-1 dated 2020-08-13
DESCRIPTION | 8 - MD5 | 33 ++-- NAMESPACE | 3 R/RcppExports.R | 4 R/binomial.fit.robmixglm.R | 199 +++++++++++++--------------- R/fitnegbin.R |only R/gamma.fit.robmixglm.R | 147 ++++++++++----------- R/gaussian.fit.robmixglm.R | 96 ++++++------- R/nbinom.fit.robmixglm.R | 282 ++++++++++++++++++++++------------------- R/outlierTest.robmixglm.R | 130 +++++------------- R/poisson.fit.robmixglm.R | 85 +++++------- R/print.outlierTest.R | 14 +- R/robmixglm.R | 12 + R/truncpoisson.fit.robmixglm.R | 79 +++++------ inst/NEWS | 10 + man/outlierTest.robmixglm.Rd | 2 src/RcppExports.cpp | 16 -- src/fit.robmixglm.cpp | 28 ---- 18 files changed, 519 insertions(+), 629 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as 'Ghostscript' is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.8-1 dated 2020-05-25 and 0.9 dated 2020-08-13
DESCRIPTION | 10 +-- MD5 | 42 +++++++------- R/showtext.R | 112 ++++++++++++++++++++++----------------- R/zzz.R | 52 ++++++++++-------- README.md | 39 ++----------- build/vignette.rds |binary inst/NEWS.Rd | 33 +++++++++++ inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 36 +++--------- inst/doc/introduction.html | 85 +++++++++++++++++------------ man/showtext_auto.Rd | 12 +++- man/showtext_opts.Rd | 2 src/devfuns.c | 19 +++++- src/outline.c | 16 ++--- src/outline.h | 1 src/register_routines.c | 11 --- src/showtext-win.def | 4 - src/showtext.c | 128 +++++++++++++++++++++++++++------------------ src/util.c | 89 +++++++++++++++++-------------- src/util.h | 33 +++++++---- vignettes/introduction.Rmd | 36 +++--------- vignettes/load_fonts.png |only vignettes/source_han.png |only 23 files changed, 411 insertions(+), 351 deletions(-)
Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between RcmdrMisc versions 2.7-0 dated 2020-01-14 and 2.7-1 dated 2020-08-13
DESCRIPTION | 22 ++-- MD5 | 46 +++++---- NAMESPACE | 11 +- NEWS | 224 ++++++++++++++++++++++---------------------- R/Barplot.R | 150 +++++++++++++++-------------- R/Dotplot.R | 21 ++-- R/discretePlot.R | 6 + R/plots.R | 24 +++- R/readSAS.R | 48 ++++----- R/readSPSS.R | 110 ++++++++++----------- R/readStata.R | 48 ++++----- R/readXL.R | 46 ++++----- R/repeatedMeasuresPlot.R |only R/reshapeL2W.R |only R/reshapeW2L.R |only man/Barplot.Rd | 162 +++++++++++++++---------------- man/Dotplot.Rd | 2 man/Hist.Rd | 2 man/discretePlot.Rd | 2 man/indexplot.Rd | 2 man/readSAS.Rd | 71 ++++++------- man/readSPSS.Rd | 91 ++++++++--------- man/readStata.Rd | 74 +++++++------- man/readXL.Rd | 92 +++++++++--------- man/repeatedMeasuresPlot.Rd |only man/reshapeL2W.Rd |only man/reshapeW2L.Rd |only 27 files changed, 653 insertions(+), 601 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman [aut, cre],
Christopher Chang [ctb],
Xavi Puig [ctb],
Jan Wigginton [ctb]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.6.3 dated 2019-06-29 and 1.6.6 dated 2020-08-13
HardyWeinberg-1.6.3/HardyWeinberg/R/Chisquarex.R |only HardyWeinberg-1.6.6/HardyWeinberg/DESCRIPTION | 10 HardyWeinberg-1.6.6/HardyWeinberg/MD5 | 71 HardyWeinberg-1.6.6/HardyWeinberg/NAMESPACE | 4 HardyWeinberg-1.6.6/HardyWeinberg/R/Chisquare.R | 28 HardyWeinberg-1.6.6/HardyWeinberg/R/Chisquare.x.R | 38 HardyWeinberg-1.6.6/HardyWeinberg/R/HWExact.R | 4 HardyWeinberg-1.6.6/HardyWeinberg/R/HWLindley.R |only HardyWeinberg-1.6.6/HardyWeinberg/R/HWPerm.R | 22 HardyWeinberg-1.6.6/HardyWeinberg/R/HWTriExact.R | 4 HardyWeinberg-1.6.6/HardyWeinberg/R/HWf.R | 37 HardyWeinberg-1.6.6/HardyWeinberg/R/MakeCounts.R | 10 HardyWeinberg-1.6.6/HardyWeinberg/R/RcppExports.R | 6 HardyWeinberg-1.6.6/HardyWeinberg/R/auxlindley.R |only HardyWeinberg-1.6.6/HardyWeinberg/R/nearlyEqual.R |only HardyWeinberg-1.6.6/HardyWeinberg/R/subsamples.prob.R | 15 HardyWeinberg-1.6.6/HardyWeinberg/build/vignette.rds |binary HardyWeinberg-1.6.6/HardyWeinberg/inst/CITATION | 4 HardyWeinberg-1.6.6/HardyWeinberg/inst/doc/HardyWeinberg.R | 1 HardyWeinberg-1.6.6/HardyWeinberg/inst/doc/HardyWeinberg.Rnw | 2 HardyWeinberg-1.6.6/HardyWeinberg/inst/doc/HardyWeinberg.pdf |binary HardyWeinberg-1.6.6/HardyWeinberg/man/HWExact.Rd | 4 HardyWeinberg-1.6.6/HardyWeinberg/man/HWLindley.Rd |only HardyWeinberg-1.6.6/HardyWeinberg/man/HWMissing.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/HWPerm.Rd | 3 HardyWeinberg-1.6.6/HardyWeinberg/man/HWPower.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/HWTernaryPlot.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/HWf.Rd | 23 HardyWeinberg-1.6.6/HardyWeinberg/man/HardyWeinberg-package.Rd | 6 HardyWeinberg-1.6.6/HardyWeinberg/man/JPTmultiallelicsChr7.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/JPTmultiallelicsChrX.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/JPTsnps.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/JPTtriallelicsChr7.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/JPTtriallelicsChrX.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/man/MakeCounts.Rd | 3 HardyWeinberg-1.6.6/HardyWeinberg/man/Markers.Rd | 2 HardyWeinberg-1.6.6/HardyWeinberg/src/RcppExports.cpp | 31 HardyWeinberg-1.6.6/HardyWeinberg/vignettes/HardyWeinberg.Rnw | 2 HardyWeinberg-1.6.6/HardyWeinberg/vignettes/HardyWeinberg.bib | 886 +++++----- 39 files changed, 663 insertions(+), 569 deletions(-)
Title: Estimating the Sample Mean and Standard Deviation from Commonly
Reported Quantiles in Meta-Analysis
Description: Implements the methods of McGrath et al. (2020)
<doi:10.1177/0962280219889080> for estimating the sample mean and standard
deviation from commonly reported quantiles in meta-analysis. These methods
can be applied to studies that report the sample median, sample size, and
one or both of (i) the sample minimum and maximum values and (ii) the first
and third quartiles.
Author: Sean McGrath [aut, cre] (<https://orcid.org/0000-0002-7281-3516>),
XiaoFei Zhao [aut],
Russell Steele [aut],
Andrea Benedetti [aut] (<https://orcid.org/0000-0002-8314-9497>)
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>
Diff between estmeansd versions 0.2.0 dated 2019-03-26 and 0.2.1 dated 2020-08-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 20 ++++++++++---------- NEWS.md | 9 +++++++++ R/bc.mean.sd.R | 3 ++- R/qe.fit.R | 8 ++++---- R/qe.mean.sd.R | 2 +- README.md | 14 ++++++++------ man/bc.mean.sd.Rd | 14 +++++++++++--- man/plot.qe.fit.Rd | 19 +++++++++++++++---- man/qe.fit.Rd | 20 ++++++++++++++------ man/qe.mean.sd.Rd | 13 ++++++++++--- 11 files changed, 94 insertions(+), 47 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich (R package)
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.2.5 dated 2020-07-21 and 1.2.5.1 dated 2020-08-13
bartMachine-1.2.5.1/bartMachine/CHANGELOG | 5 +++ bartMachine-1.2.5.1/bartMachine/DESCRIPTION | 10 +++--- bartMachine-1.2.5.1/bartMachine/MD5 | 19 ++++++------- bartMachine-1.2.5.1/bartMachine/NAMESPACE | 1 bartMachine-1.2.5.1/bartMachine/R/bart_package_builders.R | 2 - bartMachine-1.2.5.1/bartMachine/R/bart_package_inits.R | 3 -- bartMachine-1.2.5.1/bartMachine/R/bart_package_summaries.R | 2 - bartMachine-1.2.5.1/bartMachine/R/zzz.R | 2 - bartMachine-1.2.5.1/bartMachine/inst/doc/bartMachine.pdf |binary bartMachine-1.2.5.1/bartMachine/inst/java/bart_java.jar |binary bartMachine-1.2.5/bartMachine/java/README |only 11 files changed, 22 insertions(+), 22 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph]
(<https://orcid.org/0000-0003-3092-2199>),
Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>),
Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>),
Joseph Brown [aut, cph],
Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>),
Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>),
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>),
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>),
RJ Ewing [aut, cph],
Olivier Gascuel [aut, cph],
Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>),
Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>),
Anthony Ives [aut, cph],
Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>),
Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>),
Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>),
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>),
Jim Lemon [aut, cph],
Guillaume Louvel [aut, cph],
Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>),
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>),
Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>),
Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.4 dated 2020-06-03 and 5.4-1 dated 2020-08-13
DESCRIPTION | 8 - MD5 | 70 +++++++-------- NAMESPACE | 4 R/as.bitsplits.R | 61 +++---------- R/dist.topo.R | 11 -- R/is.monophyletic.R | 5 - R/mst.R | 4 R/multi2di.R | 18 ++-- R/read.nexus.data.R | 53 ++++++++++++ R/rtree.R | 130 ++++++++++++++--------------- R/summary.phylo.R | 18 ++-- build/vignette.rds |binary inst/doc/MoranI.pdf |binary man/CADM.global.Rd | 2 man/MPR.Rd | 2 man/SDM.Rd | 2 man/ace.Rd | 2 man/additive.Rd | 2 man/boot.phylo.Rd | 2 man/ewLasso.Rd | 2 man/is.compatible.Rd | 2 man/mcmc.popsize.Rd | 9 -- man/multi2di.Rd | 7 + man/mvr.Rd | 2 man/njs.Rd | 6 - man/read.GenBank.Rd | 2 man/read.nexus.data.Rd | 9 +- man/rtree.Rd | 9 +- man/rtt.Rd | 2 man/trans.Rd | 2 man/treePop.Rd | 2 man/triangMtd.Rd | 2 src/ape.c | 12 +- src/bipartition.c | 137 ------------------------------- src/bitsplits.c | 215 ++++++++++++++++++++++++++++++------------------- src/dist_dna.c | 5 - 36 files changed, 385 insertions(+), 434 deletions(-)
Title: Power Analyses for Common Designs (Power to the People)
Description: Statistical power analysis for designs including t-tests, correlations,
multiple regression, ANOVA, mediation, and logistic regression. Functions accompany
Aberson (2019) <doi:10.4324/9781315171500>.
Author: Chris Aberson
Maintainer: Chris Aberson <cla18@humboldt.edu>
Diff between pwr2ppl versions 0.1.1 dated 2019-06-12 and 0.1.2 dated 2020-08-13
DESCRIPTION | 8 MD5 | 108 ++++----- NAMESPACE | 2 R/anc.R | 591 +++++++++++++++++++++++++++++++++++++++++++-------- R/anova2x2.R | 2 R/d_prec.R | 4 R/depb.R | 2 R/depcorr0.R | 2 R/lmm1w1b.R | 4 R/med.R | 8 R/medjs.R |only R/medserial.R |only R/propind.R | 1 R/tfromd.R | 14 - R/win1F.R | 2 R/win1bg1.R | 2 man/ChiGOF.Rd | 13 - man/LRcat.Rd | 3 man/LRcont.Rd | 3 man/MANOVA1f.Rd | 41 ++- man/MRC.Rd | 23 + man/MRC_all.Rd | 24 +- man/MRC_short2.Rd | 39 ++- man/MRC_shortcuts.Rd | 21 + man/R2ch.Rd | 21 + man/anc.Rd | 56 +++- man/anova1f_3.Rd | 14 + man/anova1f_3c.Rd | 18 + man/anova1f_4.Rd | 18 + man/anova1f_4c.Rd | 23 + man/anova2x2.Rd | 22 + man/anova2x2_se.Rd | 19 + man/d_prec.Rd | 4 man/depb.Rd | 5 man/depcorr0.Rd | 17 + man/indR2.Rd | 21 + man/indb.Rd | 20 + man/indcorr.Rd | 3 man/indt.Rd | 11 man/lmm1F.Rd | 21 + man/lmm1Ftrends.Rd | 21 + man/lmm1w1b.Rd | 43 +++ man/lmm2F.Rd | 59 ++++- man/lmm2Fse.Rd | 59 ++++- man/med.Rd | 29 ++ man/medjs.Rd |only man/medserial.Rd |only man/pairt.Rd | 3 man/propind.Rd | 7 man/regint.Rd | 16 + man/regintR2.Rd | 3 man/tfromd.Rd | 6 man/win1F.Rd | 23 + man/win1Ftrends.Rd | 21 + man/win1bg1.Rd | 43 +++ man/win2F.Rd | 59 ++++- man/win2Fse.Rd | 59 ++++- 57 files changed, 1334 insertions(+), 327 deletions(-)