Title: Integrating Ecosystem Remote Sensing Products to Derive EBV
Indicators
Description: Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biological organization that document biodiversity change. Freely available ecosystem remote sensing products (ERSP) are downloaded and integrated with data for national or regional domains to derive indicators for EBV in the class ecosystem structure (Pereira et al., 2013) <doi:10.1126/science.1229931>, including horizontal ecosystem extents, fragmentation, and information-theory indices. To process ERSP, users must provide a polygon or geographic administrative data map. Downloadable ERSP include Global Surface Water (Peckel et al., 2016) <doi:10.1038/nature20584>, Forest Change (Hansen et al., 2013) <doi:10.1126/science.1244693>, and Continuous Tree Cover data (Sexton et al., 2013) <doi:10.1080/17538947.2013.786146>.
Author: Wilson Lara Henao [aut, cre],
Victor Gutierrez-Velez [aut],
Ivan Gonzalez [ctb],
Maria C. Londono [ctb]
Maintainer: Wilson Lara Henao <wilarhen@gmail.com>
Diff between ecochange versions 2.9.1 dated 2022-11-01 and 2.9.3 dated 2023-02-07
DESCRIPTION | 12 +- MD5 | 36 +++---- NAMESPACE | 10 +- NEWS | 22 ++++ R/getGADM.R | 93 +++++++++++------- R/getrsp.R | 24 ++-- R/internal.R | 168 ++++++++++++++++++++++------------ R/plot.echanges.R | 7 + R/rsp2ebv.R | 17 +-- build/vignette.rds |binary inst/CITATION | 23 ++-- inst/doc/EcochangeTutorial.Rmd | 29 ++++- inst/doc/EcochangeTutorial.html | 196 +++++++++++++++++++++++----------------- man/getGADM.Rd | 33 +++--- man/getWRS.Rd | 8 - man/getrsp.Rd | 22 ++-- man/rsp2ebv.Rd | 30 +++--- man/tabuleRaster.Rd | 6 - vignettes/EcochangeTutorial.Rmd | 29 ++++- 19 files changed, 469 insertions(+), 296 deletions(-)
Title: Data for Comparing Species Distribution Modeling Methods
Description: Easy access to species distribution data for 6 regions in the world, for a total of 226 anonymised species. These data are described and made available by Elith et al (2020) <doi:10.17161/bi.v15i2.13384> to compare species distribution modelling methods.
Author: Robert J. Hijmans [aut] ,
Roozbeh Valavi [cre, aut],
Jane Elith [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between disdat versions 1.0-0 dated 2020-09-17 and 1.0-1 dated 2023-02-07
disdat-1.0-0/disdat/man/figures/interactfig.png |only disdat-1.0-1/disdat/DESCRIPTION | 10 disdat-1.0-1/disdat/MD5 | 31 disdat-1.0-1/disdat/R/disMapbook.R | 15 disdat-1.0-1/disdat/R/disOther.R | 2 disdat-1.0-1/disdat/build/vignette.rds |binary disdat-1.0-1/disdat/inst/CITATION | 9 disdat-1.0-1/disdat/inst/doc/data_vis.R | 37 disdat-1.0-1/disdat/inst/doc/data_vis.Rmd | 9 disdat-1.0-1/disdat/inst/doc/data_vis.html | 5556 +++++++++++++++++++++++- disdat-1.0-1/disdat/inst/doc/modeling.R | 6 disdat-1.0-1/disdat/inst/doc/modeling.Rmd | 6 disdat-1.0-1/disdat/inst/doc/modeling.html | 570 +- disdat-1.0-1/disdat/man/disData.Rd | 2 disdat-1.0-1/disdat/man/disdat-package.Rd | 3 disdat-1.0-1/disdat/vignettes/data_vis.Rmd | 9 disdat-1.0-1/disdat/vignettes/modeling.Rmd | 6 17 files changed, 5766 insertions(+), 505 deletions(-)
Title: Metrics of Difference for Comparing Pairs of Maps or Pairs of
Variables
Description: Metrics of difference for comparing pairs of variables or pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr. <rpontius@clarku.edu>, Ali Santacruz <amsantac@unal.edu.co>
Maintainer: Ali Santacruz <amsantac@unal.edu.co>
Diff between diffeR versions 0.0-6 dated 2019-01-22 and 0.0-7 dated 2023-02-07
DESCRIPTION | 18 +-- MD5 | 62 ++++++------ NAMESPACE | 12 +- R/MAD.R | 209 ++++++++++++++++++++---------------------- R/MADscatterplot.R | 13 ++ R/categoryComponentsPlot.R | 22 ++-- R/categorySourcesPlot.R | 22 ++-- R/composite.R | 48 ++++----- R/crosstabm.R | 36 ++++--- R/diffMetrics.R | 32 ++++++ R/diffTablej.R | 15 +++ R/differenceMR.R | 32 ++++-- R/memberships.R | 2 R/overallComponentsPlot.R | 42 ++++++-- R/overallSourcesPlot.R | 12 +- R/sample2pop.R | 13 ++ demo/composite.R | 32 ++---- demo/diffMetrics.R | 6 - man/MAD.Rd | 24 ++-- man/MADscatterplot.Rd | 18 +-- man/categoryComponentsPlot.Rd | 13 +- man/categorySourcesPlot.Rd | 19 +-- man/composite.Rd | 12 +- man/crosstabm.Rd | 12 +- man/diffMetrics.Rd | 4 man/diffTablej.Rd | 11 -- man/diffeR-package.Rd | 9 - man/differenceMR.Rd | 20 +--- man/memberships.Rd | 10 +- man/overallComponentsPlot.Rd | 19 ++- man/overallSourcesPlot.Rd | 19 +-- man/sample2pop.Rd | 9 + 32 files changed, 462 insertions(+), 365 deletions(-)
Title: Analyses of Evolutionary Time-Series
Description: Facilitates univariate and multivariate analysis of evolutionary sequences of phenotypic change. The package extends the modeling framework available in the 'paleoTS' package. Please see <https://klvoje.github.io/evoTS/index.html> for information about the package and the implemented models.
Author: Kjetil Lysne Voje [aut, cre]
Maintainer: Kjetil Lysne Voje <k.l.voje@nhm.uio.no>
Diff between evoTS versions 1.0.0 dated 2023-01-17 and 1.0.1 dated 2023-02-07
evoTS-1.0.0/evoTS/R/opt.multi.R |only evoTS-1.0.0/evoTS/man/opt.multi.R.Rd |only evoTS-1.0.1/evoTS/DESCRIPTION | 6 evoTS-1.0.1/evoTS/MD5 | 36 - evoTS-1.0.1/evoTS/NAMESPACE | 1 evoTS-1.0.1/evoTS/NEWS.md | 10 evoTS-1.0.1/evoTS/R/as.evoTS.BM.multi.fit.R | 6 evoTS-1.0.1/evoTS/R/as.evoTS.multi.URW.fit.R |only evoTS-1.0.1/evoTS/R/as.evoTS.multi.URW.shift.fit.R |only evoTS-1.0.1/evoTS/R/fit.multivariate.OU.R | 18 evoTS-1.0.1/evoTS/R/fit.multivariate.OU.user.defined.R | 22 - evoTS-1.0.1/evoTS/R/fit.multivariate.URW.shift.R | 370 +++++++++++++++-- evoTS-1.0.1/evoTS/R/opt.accel.single.R | 21 evoTS-1.0.1/evoTS/R/opt.accel.single.R.zero.corr.R | 25 - evoTS-1.0.1/evoTS/R/opt.decel.single.R | 23 - evoTS-1.0.1/evoTS/R/opt.decel.single.R.zero.corr.R | 27 - evoTS-1.0.1/evoTS/R/opt.single.R | 26 - evoTS-1.0.1/evoTS/R/opt.single.R.zero.corr.R | 13 evoTS-1.0.1/evoTS/README.md | 16 evoTS-1.0.1/evoTS/man/as.evoTS.multi.BW.fit.Rd | 3 evoTS-1.0.1/evoTS/man/as.evoTS.multi.URW.fit.Rd |only evoTS-1.0.1/evoTS/man/as.evoTS.multi.URW.shift.fit.Rd |only 22 files changed, 515 insertions(+), 108 deletions(-)
Title: Read and Write QOI Images
Description: The new QOI file format offers a very simple but efficient image compression algorithm. This package provides an easy and simple way to read, write and display bitmap images stored in the QOI (Quite Ok Image) format. It can read and write both files and in-memory raw vectors.
Author: Johannes Friedrich [aut, trl, cre],
Dominic Szablewski [cph]
Maintainer: Johannes Friedrich <Johannes.Friedrich@posteo.de>
Diff between qoi versions 0.0.3 dated 2022-04-25 and 0.0.4 dated 2023-02-07
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/init.c | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Tools for Poisson Data
Description: Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.
Author: Andrew Wheeler [aut, cre]
Maintainer: Andrew Wheeler <apwheele@gmail.com>
Diff between ptools versions 1.0.2 dated 2023-01-06 and 2.0.0 dated 2023-02-07
DESCRIPTION | 8 - MD5 | 30 +++--- NAMESPACE | 1 NEWS |only R/sp_features.R | 92 +++++++++++++++----- README.md | 30 ++++-- data/nyc_bor.rda |binary data/nyc_cafe.rda |binary data/nyc_liq.rda |binary data/nyc_shoot.rda |binary inst/doc/spat-feateng.R | 3 inst/doc/spat-feateng.Rmd | 3 inst/doc/spat-feateng.html | 198 ++++++++++++++++++++++----------------------- man/buff_sp.Rd |only man/prep_hexgrid.Rd | 4 man/vor_sp.Rd | 2 vignettes/spat-feateng.Rmd | 3 17 files changed, 212 insertions(+), 162 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 1.2.4 dated 2022-11-16 and 1.2.5 dated 2023-02-07
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 4 R/parsnip-exp_smoothing.R | 2 inst/doc/getting-started-with-modeltime.html | 223 +++++++++++++-------------- man/adam_reg.Rd | 6 man/exp_smoothing.Rd | 12 - tests/testthat/test-algo-exp_smoothing-ets.R | 17 +- 8 files changed, 147 insertions(+), 139 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations,
such as erosion and dilation, on data of arbitrary dimensionality. Can also
be used for finding connected components, resampling, filtering, smoothing
and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.6.2 dated 2022-08-10 and 1.6.3 dated 2023-02-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 ++++++ README.md | 2 +- build/partial.rdb |binary inst/tinytest/test-30-distance.R | 2 +- src/Array.h | 8 +++++++- src/lemon/maps.h | 15 +++++++++++++-- 8 files changed, 39 insertions(+), 16 deletions(-)
Title: Design of Optimum-Path Forest Classifiers
Description: The 'LibOPF' is a framework to develop pattern recognition techniques based on optimum-path forests (OPF), João P. Papa and Alexandre X. Falcão (2008) <doi:10.1007/978-3-540-89639-5_89>, with methods for supervised learning and data clustering.
Author: Rafael Junqueira Martarelli [aut, cre],
Joao Paulo Papa [aut],
Alexandre Xavier Falcao [cph]
Maintainer: Rafael Junqueira Martarelli <rfel.jm@gmail.com>
Diff between LibOPF versions 2.6.1 dated 2021-04-07 and 2.6.2 dated 2023-02-07
DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++----------------- src/code/OPF.c | 12 ++++++------ src/code/opf_accuracy.c | 6 +++--- src/code/opf_accuracy4label.c | 6 +++--- src/code/opf_classify.c | 8 ++++---- src/code/opf_cluster.c | 6 +++--- src/code/opf_distance.c | 4 ++-- src/code/opf_fold.c | 4 ++-- src/code/opf_info.c | 4 ++-- src/code/opf_learn.c | 6 +++--- src/code/opf_merge.c | 4 ++-- src/code/opf_pruning.c | 8 ++++---- src/code/opf_semi.c | 8 ++++---- src/code/opf_split.c | 8 ++++---- src/code/opf_train.c | 8 ++++---- src/code/opfknn_classify.c | 8 ++++---- src/code/opfknn_train.c | 8 ++++---- 18 files changed, 77 insertions(+), 77 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.0.1 dated 2022-12-11 and 1.0.2 dated 2023-02-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/grid.R | 5 ++++- inst/doc/Using_rerddap.html | 4 ++-- 5 files changed, 19 insertions(+), 11 deletions(-)
Title: Perform Power Analysis for the Random Intercept Cross-Lagged
Panel Model
Description: Perform user-friendly power analyses for the bivariate random
intercept cross-lagged panel model (RI-CLPM). The strategy as proposed
by Mulder (2022) <doi:10.1080/10705511.2022.2122467> is implemented.
Extended power analysis options include the use of bounded estimation,
inclusion of measurement error in the data generating model and
estimation model (i.e., the stable trait autoregressive trait state,
STARTS, model), imposing various constraints over time on the
parameters of the estimation model, among others.
Author: Jeroen Mulder [aut, cre] ,
Netherlands Organization for Scientific Research [fnd]
Maintainer: Jeroen Mulder <j.d.mulder@uu.nl>
Diff between powRICLPM versions 0.1.0 dated 2022-10-07 and 0.1.1 dated 2023-02-07
powRICLPM-0.1.0/powRICLPM/inst/doc/start.R |only powRICLPM-0.1.0/powRICLPM/inst/doc/start.Rmd |only powRICLPM-0.1.0/powRICLPM/inst/doc/start.html |only powRICLPM-0.1.0/powRICLPM/inst/extdata/power_preliminary.Rds |only powRICLPM-0.1.0/powRICLPM/tests/testthat/test-compute_Psi.R |only powRICLPM-0.1.0/powRICLPM/tests/testthat/test-summary.R |only powRICLPM-0.1.0/powRICLPM/vignettes/start.Rmd |only powRICLPM-0.1.1/powRICLPM/DESCRIPTION | 34 - powRICLPM-0.1.1/powRICLPM/MD5 | 98 ++--- powRICLPM-0.1.1/powRICLPM/NAMESPACE | 1 powRICLPM-0.1.1/powRICLPM/NEWS.md | 13 powRICLPM-0.1.1/powRICLPM/R/bootstrap-uncertainty.R | 8 powRICLPM-0.1.1/powRICLPM/R/check-give.R |only powRICLPM-0.1.1/powRICLPM/R/check-plot.R |only powRICLPM-0.1.1/powRICLPM/R/check-summary.R |only powRICLPM-0.1.1/powRICLPM/R/check.R | 166 --------- powRICLPM-0.1.1/powRICLPM/R/give.R | 32 + powRICLPM-0.1.1/powRICLPM/R/lavaan.R | 182 +++++----- powRICLPM-0.1.1/powRICLPM/R/plot.R | 160 ++++++-- powRICLPM-0.1.1/powRICLPM/R/powRICLPM.R | 22 - powRICLPM-0.1.1/powRICLPM/R/run.R | 46 +- powRICLPM-0.1.1/powRICLPM/R/summary.R | 21 - powRICLPM-0.1.1/powRICLPM/R/user-help.R |only powRICLPM-0.1.1/powRICLPM/README.md | 59 ++- powRICLPM-0.1.1/powRICLPM/build/partial.rdb |binary powRICLPM-0.1.1/powRICLPM/build/vignette.rds |binary powRICLPM-0.1.1/powRICLPM/inst/CITATION | 6 powRICLPM-0.1.1/powRICLPM/inst/doc/FAQ.Rmd | 2 powRICLPM-0.1.1/powRICLPM/inst/doc/FAQ.html | 1 powRICLPM-0.1.1/powRICLPM/inst/doc/Mulder2022.R | 70 ++- powRICLPM-0.1.1/powRICLPM/inst/doc/Mulder2022.Rmd | 78 ++-- powRICLPM-0.1.1/powRICLPM/inst/doc/Mulder2022.html | 150 ++++---- powRICLPM-0.1.1/powRICLPM/inst/doc/extensions.Rmd | 16 powRICLPM-0.1.1/powRICLPM/inst/doc/extensions.html | 43 +- powRICLPM-0.1.1/powRICLPM/inst/doc/mplus.R | 3 powRICLPM-0.1.1/powRICLPM/inst/doc/mplus.Rmd | 11 powRICLPM-0.1.1/powRICLPM/inst/doc/mplus.html | 23 - powRICLPM-0.1.1/powRICLPM/inst/doc/powRICLPM.R |only powRICLPM-0.1.1/powRICLPM/inst/doc/powRICLPM.Rmd |only powRICLPM-0.1.1/powRICLPM/inst/doc/powRICLPM.html |only powRICLPM-0.1.1/powRICLPM/inst/extdata/out_preliminary.RData |only powRICLPM-0.1.1/powRICLPM/man/check_Phi.Rd |only powRICLPM-0.1.1/powRICLPM/man/give.Rd | 84 ++-- powRICLPM-0.1.1/powRICLPM/man/plot.powRICLPM.Rd | 101 +++-- powRICLPM-0.1.1/powRICLPM/man/powRICLPM.Rd | 6 powRICLPM-0.1.1/powRICLPM/man/summary.powRICLPM.Rd | 10 powRICLPM-0.1.1/powRICLPM/tests/testthat/_snaps/summary.md | 22 - powRICLPM-0.1.1/powRICLPM/tests/testthat/test-checks-give.R |only powRICLPM-0.1.1/powRICLPM/tests/testthat/test-checks-plot.R |only powRICLPM-0.1.1/powRICLPM/tests/testthat/test-checks-summary.R |only powRICLPM-0.1.1/powRICLPM/tests/testthat/test-checks.R | 26 - powRICLPM-0.1.1/powRICLPM/tests/testthat/test-compute-population-values.R |only powRICLPM-0.1.1/powRICLPM/tests/testthat/test-constraints.R |only powRICLPM-0.1.1/powRICLPM/tests/testthat/test-give.R | 33 - powRICLPM-0.1.1/powRICLPM/tests/testthat/test-powRICLPM.R | 89 ---- powRICLPM-0.1.1/powRICLPM/tests/testthat/test-run.R | 4 powRICLPM-0.1.1/powRICLPM/vignettes/FAQ.Rmd | 2 powRICLPM-0.1.1/powRICLPM/vignettes/Mulder2022.Rmd | 78 ++-- powRICLPM-0.1.1/powRICLPM/vignettes/extensions.Rmd | 16 powRICLPM-0.1.1/powRICLPM/vignettes/mplus.Rmd | 11 powRICLPM-0.1.1/powRICLPM/vignettes/powRICLPM.Rmd |only 61 files changed, 859 insertions(+), 868 deletions(-)
Title: Interface to 'LMDB'
Description: Key-value store, implemented as a wrapper around 'LMDB';
the "lightning memory-mapped database" <https://www.symas.com/lmdb>.
'LMDB' is a transactional key value store that uses a memory map
for efficient access. This package wraps the entire 'LMDB'
interface (except duplicated keys), and provides objects for
transactions and cursors.
Author: Rich FitzJohn [aut, cre],
Howard Chu [aut, cph],
Symas Corporation [cph],
Martin Hedenfalk [aut, cph],
The OpenLDAP Foundation [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between thor versions 1.1.2 dated 2020-05-15 and 1.1.4 dated 2023-02-07
DESCRIPTION | 11 MD5 | 30 - README.md | 11 build/vignette.rds |binary cleanup.win |only inst/WORDLIST |only inst/doc/thor.Rmd | 4 inst/doc/thor.html | 1274 +++++++++++++++++++++-------------------------------- man/mdb_dbi.Rd | 2 man/mdb_env.Rd | 2 src/lmdb/README.md | 6 src/lmdb/mdb.c | 22 src/lmdb/mdb.patch | 72 ++ src/thor.c | 8 src/thor.h | 8 src/util.c | 2 vignettes/thor.Rmd | 4 17 files changed, 622 insertions(+), 834 deletions(-)
Title: Policy Learning
Description: Framework for evaluating user-specified finite stage policies and learning realistic policies via doubly robust loss functions. Policy learning methods include doubly robust restricted Q-learning, sequential policy tree learning and outcome weighted learning. See Nordland and Holst (2022) <arXiv:2212.02335> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.0 dated 2022-12-06 and 1.2 dated 2023-02-07
polle-1.0/polle/R/rqvl.R |only polle-1.0/polle/inst/sim/multi_actions.R |only polle-1.0/polle/inst/sim/multi_stage.R |only polle-1.0/polle/inst/sim/single_stage.R |only polle-1.0/polle/inst/sim/two_stage.R |only polle-1.0/polle/man/control_rqvl.Rd |only polle-1.0/polle/man/subset.policy_data.Rd |only polle-1.2/polle/DESCRIPTION | 23 polle-1.2/polle/MD5 | 146 +-- polle-1.2/polle/NAMESPACE | 44 polle-1.2/polle/NEWS.md | 9 polle-1.2/polle/R/Q_function.R | 117 +- polle-1.2/polle/R/drql.R |only polle-1.2/polle/R/earl.R | 11 polle-1.2/polle/R/fit_functions.R | 11 polle-1.2/polle/R/g_function.R | 160 ++- polle-1.2/polle/R/g_models.R | 321 +++++- polle-1.2/polle/R/helper_functions.R | 4 polle-1.2/polle/R/history_functions.R | 11 polle-1.2/polle/R/nuisance_functions.R | 57 - polle-1.2/polle/R/owl.R | 96 +- polle-1.2/polle/R/policy_data.R | 84 + polle-1.2/polle/R/policy_data_functions.R | 444 +++++++-- polle-1.2/polle/R/policy_def.R | 82 + polle-1.2/polle/R/policy_eval.R | 237 +--- polle-1.2/polle/R/policy_eval_functions.R |only polle-1.2/polle/R/policy_learn.R | 229 ---- polle-1.2/polle/R/policy_object_functions.R |only polle-1.2/polle/R/polle-package.R | 13 polle-1.2/polle/R/ptl.R | 208 ++-- polle-1.2/polle/R/q_models.R | 221 ++-- polle-1.2/polle/R/rql.R | 41 polle-1.2/polle/R/rwl.R | 11 polle-1.2/polle/R/simulation.R |only polle-1.2/polle/R/value_functions.R | 65 + polle-1.2/polle/inst/CITATION | 2 polle-1.2/polle/inst/sim/future.R | 1 polle-1.2/polle/man/conditional.Rd |only polle-1.2/polle/man/control_drql.Rd |only polle-1.2/polle/man/copy_policy_data.Rd | 1 polle-1.2/polle/man/fit_g_functions.Rd |only polle-1.2/polle/man/g_model.Rd | 62 - polle-1.2/polle/man/get_K.Rd | 1 polle-1.2/polle/man/get_action_set.Rd | 9 polle-1.2/polle/man/get_actions.Rd | 9 polle-1.2/polle/man/get_g_functions.Rd | 21 polle-1.2/polle/man/get_history.Rd | 3 polle-1.2/polle/man/get_history_names.Rd | 1 polle-1.2/polle/man/get_id.Rd | 9 polle-1.2/polle/man/get_id_stage.Rd | 9 polle-1.2/polle/man/get_n.Rd | 9 polle-1.2/polle/man/get_policy.Rd | 7 polle-1.2/polle/man/get_policy_actions.Rd | 22 polle-1.2/polle/man/get_policy_functions.Rd | 17 polle-1.2/polle/man/get_policy_object.Rd | 7 polle-1.2/polle/man/get_q_functions.Rd | 21 polle-1.2/polle/man/get_stage_action_sets.Rd |only polle-1.2/polle/man/get_utility.Rd | 9 polle-1.2/polle/man/nuisance_functions.Rd | 1 polle-1.2/polle/man/partial.Rd | 1 polle-1.2/polle/man/plot.policy_data.Rd |only polle-1.2/polle/man/plot.policy_eval.Rd |only polle-1.2/polle/man/policy.Rd | 5 polle-1.2/polle/man/policy_data.Rd | 22 polle-1.2/polle/man/policy_def.Rd | 4 polle-1.2/polle/man/policy_eval.Rd | 27 polle-1.2/polle/man/policy_learn.Rd | 37 polle-1.2/polle/man/predict.nuisance_functions.Rd | 25 polle-1.2/polle/man/q_model.Rd | 56 - polle-1.2/polle/man/reexports.Rd |only polle-1.2/polle/man/sim_multi_stage.Rd |only polle-1.2/polle/man/sim_single_stage.Rd |only polle-1.2/polle/man/sim_single_stage_multi_actions.Rd |only polle-1.2/polle/man/sim_two_stage.Rd |only polle-1.2/polle/man/sim_two_stage_multi_actions.Rd |only polle-1.2/polle/man/subset_id.Rd |only polle-1.2/polle/tests/testthat/test-g_empir.R |only polle-1.2/polle/tests/testthat/test-g_models.R |only polle-1.2/polle/tests/testthat/test-misc.R | 4 polle-1.2/polle/tests/testthat/test-policy_data.R | 204 +++- polle-1.2/polle/tests/testthat/test-policy_data_functions.R |only polle-1.2/polle/tests/testthat/test-policy_def.R | 39 polle-1.2/polle/tests/testthat/test-policy_eval.R | 292 +++++- polle-1.2/polle/tests/testthat/test-policy_learn.R | 570 +++--------- polle-1.2/polle/tests/testthat/test-policy_learn_drql.R |only polle-1.2/polle/tests/testthat/test-policy_learn_earl.R |only polle-1.2/polle/tests/testthat/test-policy_learn_owl.R |only polle-1.2/polle/tests/testthat/test-policy_learn_ptl.R |only polle-1.2/polle/tests/testthat/test-policy_learn_ql.R |only polle-1.2/polle/tests/testthat/test-policy_learn_rwl.R |only polle-1.2/polle/tests/testthat/test-q_models.R |only 91 files changed, 2405 insertions(+), 1747 deletions(-)
Title: Fit Models Derived from Point Processes to Species Distributions
using 'inlabru'
Description: Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models.
Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking.
We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them.
There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions.
An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Bob O'hara [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between PointedSDMs versions 1.2.0 dated 2023-01-16 and 1.2.1 dated 2023-02-07
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/dataOrganize.R | 6 ++++-- R/dataSDM.R | 31 ++++++++++++++++++++++--------- R/fitISDM.R | 4 ++-- R/makeLhoods.R | 4 ++-- README.md | 3 ++- inst/doc/Marked_Point_Process.html | 17 ++++++++++++----- inst/doc/Setophaga.Rmd | 2 +- inst/doc/Setophaga.html | 27 +++++++++++++++++---------- inst/doc/Solitary_tinamou.html | 13 ++++++++++--- inst/doc/Spatiotemporal_example.html | 17 ++++++++++++----- man/dataSDM.Rd | 4 ++-- vignettes/Setophaga.Rmd | 2 +- 14 files changed, 105 insertions(+), 61 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <Sylvain.Jasson@inrae.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.6-10 dated 2023-01-17 and 0.7-1 dated 2023-02-07
DESCRIPTION | 8 MD5 | 52 - src/Makevars.win | 3 src/apply.cc | 158 ++-- src/biginteger.cc | 34 - src/biginteger.h | 14 src/bigintegerR.cc | 1619 ++++++++++++++++++++++++++------------------------ src/bigintegerR.h | 8 src/bigmod.cc | 99 +-- src/bigmod.h | 220 +++--- src/bigrational.cc | 177 ++++- src/bigrational.h | 81 -- src/bigrationalR.cc | 776 ++++++++++++++--------- src/bigrationalR.h | 3 src/bigvec.cc | 259 ++----- src/bigvec.h | 50 + src/bigvec_q.cc | 4 src/bigvec_q.h | 5 src/extract_matrix.cc | 69 +- src/extract_matrix.h | 87 +- src/factor.cc | 21 src/factorize.cc | 5 src/matrix.cc | 769 ++++++++++++----------- src/matrixq.cc | 662 ++++++++++---------- src/solve.cc | 164 ++--- src/solve.h | 10 src/templateMatrix.h | 3 27 files changed, 2943 insertions(+), 2417 deletions(-)
Title: Process and Analyse Data from m-Path Sense
Description: Overcomes one of the major challenges in mobile (passive)
sensing, namely being able to pre-process the raw data that comes from
a mobile sensing app, specifically "m-Path Sense" <https://m-path.io>.
The main task of 'mpathsenser' is therefore to read "m-Path Sense"
JSON files into a database and provide several convenience functions
to aid in data processing.
Author: Koen Niemeijer [aut, cre] ,
Kristof Meers [ctb] ,
KU Leuven [cph, fnd]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>
Diff between mpathsenser versions 1.1.2 dated 2022-12-12 and 1.1.3 dated 2023-02-07
DESCRIPTION | 8 MD5 | 59 +- NEWS.md | 39 + R/database.R | 33 - R/import.R | 61 -- R/import_functions.R | 42 + R/linking.R | 95 ++- R/sensor_functions.R | 183 ------- R/utils.R | 76 -- README.md | 8 inst/doc/mpathsenser.html | 24 inst/extdata/dbdef.sql | 43 + inst/extdata/mpathsenser_db.pdf |binary inst/extdata/mpathsenser_db.png |binary inst/testdata/old_tests.json |only inst/testdata/test.db |binary inst/testdata/test.json | 162 +++--- man/add_gaps.Rd | 2 man/copy_db.Rd | 16 man/fix_jsons.Rd | 14 man/import.Rd | 21 man/link_db.Rd | 2 man/test_jsons.Rd | 22 man/unzip_data.Rd | 18 tests/testthat/test-data.R | 86 ++- tests/testthat/test-database.R | 532 +++++++++----------- tests/testthat/test-import.R | 860 +++++++++++++++++---------------- tests/testthat/test-import_functions.R | 107 +++- tests/testthat/test-linking.R | 80 ++- tests/testthat/test-sensor_functions.R | 3 tests/testthat/test-utils.R | 25 31 files changed, 1299 insertions(+), 1322 deletions(-)
Title: Easy Graphs for Data Visualisation and Linear Models for ANOVA
Description: Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practising code and teaching basics before users move on to more complex designs. See vignettes for details on usage <https://grafify-vignettes.netlify.app/>. Citation: <doi:10.5281/zenodo.5136508>.
Author: Avinash R Shenoy [cre, aut]
Maintainer: Avinash R Shenoy <a.shenoy@imperial.ac.uk>
Diff between grafify versions 3.0.0 dated 2022-10-23 and 3.0.1 dated 2023-02-07
grafify-3.0.0/grafify/R/plot_bar_sd.R |only grafify-3.0.0/grafify/man/plot_bar_sd.Rd |only grafify-3.0.0/grafify/tests/testthat/test-plot_bar_sd.R |only grafify-3.0.1/grafify/DESCRIPTION | 12 grafify-3.0.1/grafify/MD5 | 87 +++--- grafify-3.0.1/grafify/NAMESPACE | 1 grafify-3.0.1/grafify/NEWS.md | 23 + grafify-3.0.1/grafify/R/plot_3d_scatterbar.R | 124 ++++----- grafify-3.0.1/grafify/R/plot_3d_scatterbox.R | 105 +++---- grafify-3.0.1/grafify/R/plot_3d_scatterviolin.R | 213 ++++++---------- grafify-3.0.1/grafify/R/plot_4d_scatterbar.R | 34 +- grafify-3.0.1/grafify/R/plot_befafter_box.R | 189 ++++---------- grafify-3.0.1/grafify/R/plot_befafter_colours.R | 84 ++---- grafify-3.0.1/grafify/R/plot_befafter_shapes.R | 88 +++--- grafify-3.0.1/grafify/R/plot_dotbar_sd.R | 124 ++++----- grafify-3.0.1/grafify/R/plot_dotbox.R | 10 grafify-3.0.1/grafify/R/plot_dotviolin.R | 10 grafify-3.0.1/grafify/R/plot_grafify_palette.R | 18 - grafify-3.0.1/grafify/R/plot_histogram.R | 60 ++-- grafify-3.0.1/grafify/R/plot_lm_predict.R | 4 grafify-3.0.1/grafify/R/plot_point_sd.R | 115 +++++--- grafify-3.0.1/grafify/R/plot_qqline.R | 43 +-- grafify-3.0.1/grafify/R/plot_scatterbar_sd.R | 119 ++++---- grafify-3.0.1/grafify/R/plot_scatterbox.R | 87 +++--- grafify-3.0.1/grafify/R/plot_scatterviolin.R | 10 grafify-3.0.1/grafify/R/scale_colour_grafify.R | 2 grafify-3.0.1/grafify/R/theme_grafify.R | 5 grafify-3.0.1/grafify/build/partial.rdb |binary grafify-3.0.1/grafify/man/plot_3d_scatterbar.Rd | 5 grafify-3.0.1/grafify/man/plot_3d_scatterbox.Rd | 2 grafify-3.0.1/grafify/man/plot_3d_scatterviolin.Rd | 2 grafify-3.0.1/grafify/man/plot_4d_scatterbar.Rd | 3 grafify-3.0.1/grafify/man/plot_befafter_box.Rd | 5 grafify-3.0.1/grafify/man/plot_befafter_colours.Rd | 6 grafify-3.0.1/grafify/man/plot_befafter_shapes.Rd | 5 grafify-3.0.1/grafify/man/plot_dotbar_sd.Rd | 9 grafify-3.0.1/grafify/man/plot_dotbox.Rd | 6 grafify-3.0.1/grafify/man/plot_dotviolin.Rd | 6 grafify-3.0.1/grafify/man/plot_grafify_palette.Rd | 3 grafify-3.0.1/grafify/man/plot_histogram.Rd | 13 grafify-3.0.1/grafify/man/plot_point_sd.Rd | 30 +- grafify-3.0.1/grafify/man/plot_qqline.Rd | 9 grafify-3.0.1/grafify/man/plot_scatterbar_sd.Rd | 11 grafify-3.0.1/grafify/man/plot_scatterbox.Rd | 6 grafify-3.0.1/grafify/man/plot_scatterviolin.Rd | 6 grafify-3.0.1/grafify/man/theme_grafify.Rd | 5 46 files changed, 840 insertions(+), 859 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and
metadata from a PDF file. Also supports high quality rendering of PDF documents into
PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between pdftools versions 3.3.2 dated 2022-10-16 and 3.3.3 dated 2023-02-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ src/Makevars.win | 1 - src/bindings.cpp | 14 ++++++++++---- 5 files changed, 21 insertions(+), 12 deletions(-)
Title: Fast and Easy Quality Control of EWAS Results Files
Description: Tools for (automated and manual) quality control of
the results of Epigenome-Wide Association Studies.
Author: Peter J. van der Most,
Leanne K. Kupers,
Ilja Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>
Diff between QCEWAS versions 1.2-2 dated 2019-02-01 and 1.2-3 dated 2023-02-07
QCEWAS-1.2-2/QCEWAS/R/script_v12-2_package.R |only QCEWAS-1.2-2/QCEWAS/inst/doc/QCEWAS_Quick_Start_Guide_v110.docx |only QCEWAS-1.2-2/QCEWAS/inst/doc/QCEWAS_changelog_v122.txt |only QCEWAS-1.2-3/QCEWAS/DESCRIPTION | 12 +++--- QCEWAS-1.2-3/QCEWAS/MD5 | 18 +++++----- QCEWAS-1.2-3/QCEWAS/NAMESPACE | 1 QCEWAS-1.2-3/QCEWAS/R/script_v12-3_package.R |only QCEWAS-1.2-3/QCEWAS/inst/doc/QCEWAS_Quick_Start_Guide_v123.docx |only QCEWAS-1.2-3/QCEWAS/inst/doc/QCEWAS_changelog_v123.txt |only QCEWAS-1.2-3/QCEWAS/man/EWAS_QC.Rd | 4 +- QCEWAS-1.2-3/QCEWAS/man/EWAS_series.Rd | 3 + QCEWAS-1.2-3/QCEWAS/man/QCEWAS-package.Rd | 4 +- QCEWAS-1.2-3/QCEWAS/man/translate_header.Rd | 4 +- 13 files changed, 24 insertions(+), 22 deletions(-)
Title: Forest Estimations and Dendrometric Computations
Description: Computation of dendrometric and structural
parameters from forest inventory data. The objective is to provide an
user-friendly R package for researchers, ecologists, foresters,
statisticians, loggers and others persons who deal with forest inventory
data. Useful conversion of angle value from degree to radian, conversion from
angle to slope (in percentage) and their reciprocals as well as principal
angle determination are also included. Position and dispersion parameters
usually found in forest studies are implemented. The package contains
Fibonacci series, its extensions and the Golden Number computation.
Useful references are Arcadius Y. J. Akossou, Soufianou Arzouma,
Eloi Y. Attakpa, Noël H. Fonton and Kouami Kokou (2013) <doi:10.3390/d5010099>
and W. Bonou, R. Glele Kakaï, A.E. Assogbadjo, H.N. Fonton, B. Sinsin (2009)
<doi:10.1016/j.foreco.2009.05.032> .
Author: Narcisse Yehouenou [aut, cre],
Information and Communication Technology for you ONG [fnd]
Maintainer: Narcisse Yehouenou <narcisstar211@gmail.com>
Diff between dendrometry versions 0.0.1 dated 2022-08-22 and 0.0.2 dated 2023-02-07
DESCRIPTION | 10 MD5 | 66 +++--- NAMESPACE | 7 NEWS.md | 7 R/dendrometry.R | 495 ++++++++++++++++++++++++++++++++++++--------- build/partial.rdb |only demo/dendro.R | 1 demo/volume.R | 6 inst/doc/dendrometry.html | 27 -- man/Logging.Rd | 4 man/Tree.Rd | 5 man/angle2slope.Rd | 4 man/basal.Rd |only man/basal_i.Rd | 21 + man/circum.Rd |only man/dbh.Rd | 8 man/decrease.Rd | 4 man/decreaseMetric.Rd | 13 - man/deg.Rd | 6 man/dendrometry-package.Rd | 2 man/densityTree.Rd | 8 man/diameterMean.Rd | 12 - man/distanceH.Rd | 14 - man/factorize.Rd | 13 - man/fiboRate.Rd | 8 man/fibonacci.Rd | 12 - man/height.Rd | 4 man/makedata.Rd |only man/principal.Rd | 6 man/rad.Rd | 8 man/reducecoef.Rd | 7 man/sampleSize.Rd |only man/shape.Rd | 4 man/skewness.Rd | 3 man/slope2angle.Rd | 4 man/stacking.Rd |only man/volume.Rd | 2 37 files changed, 568 insertions(+), 223 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10. [...truncated...]
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 5.7 dated 2023-01-11 and 5.8 dated 2023-02-07
Directional-5.7/Directional/R/esag.datacontour.R |only Directional-5.7/Directional/R/kent.datacontour.R |only Directional-5.7/Directional/man/dkent.Rd |only Directional-5.7/Directional/man/esag.datacontour.Rd |only Directional-5.7/Directional/man/kent.contour.Rd |only Directional-5.7/Directional/man/kent.datacontour.Rd |only Directional-5.8/Directional/DESCRIPTION | 10 Directional-5.8/Directional/MD5 | 184 +++++++++------- Directional-5.8/Directional/NAMESPACE | 2 Directional-5.8/Directional/R/cipc.mle.R |only Directional-5.8/Directional/R/dcipc.R |only Directional-5.8/Directional/R/dgcpc.R |only Directional-5.8/Directional/R/dmixvmf.R |only Directional-5.8/Directional/R/dpurka.R | 2 Directional-5.8/Directional/R/dsespc.R |only Directional-5.8/Directional/R/dspcauchy.R |only Directional-5.8/Directional/R/dvmf.R | 2 Directional-5.8/Directional/R/dwood.R |only Directional-5.8/Directional/R/esag.reg.R |only Directional-5.8/Directional/R/gcpc.mle.R |only Directional-5.8/Directional/R/makefolds.R | 2 Directional-5.8/Directional/R/mixvmf.contour.R | 23 -- Directional-5.8/Directional/R/mixvmf.mle.R | 4 Directional-5.8/Directional/R/pc.test.R |only Directional-5.8/Directional/R/purka.contour.R |only Directional-5.8/Directional/R/purka.da.R | 2 Directional-5.8/Directional/R/purkada.pred.R | 2 Directional-5.8/Directional/R/rcipc.R |only Directional-5.8/Directional/R/rgcpc.R |only Directional-5.8/Directional/R/rmixvmf.R | 4 Directional-5.8/Directional/R/rsespc.R |only Directional-5.8/Directional/R/sespc.mle.R |only Directional-5.8/Directional/R/sipc.mle.R |only Directional-5.8/Directional/R/spcauchy.mle.R | 2 Directional-5.8/Directional/R/spchauchy.contour.R |only Directional-5.8/Directional/R/spher.esag.contour.R |only Directional-5.8/Directional/R/spher.kent.contour.R |only Directional-5.8/Directional/R/spher.mixvmf.contour.R |only Directional-5.8/Directional/R/spher.purka.contour.R |only Directional-5.8/Directional/R/spher.sespc.contour.R |only Directional-5.8/Directional/R/spher.spcauchy.contour.R |only Directional-5.8/Directional/R/spher.vmf.contour.R |only Directional-5.8/Directional/R/sphereplot.R | 35 ++- Directional-5.8/Directional/R/vmf.contour.R | 20 - Directional-5.8/Directional/R/vmf.kerncontour.R | 26 -- Directional-5.8/Directional/R/wood.mle.R | 5 Directional-5.8/Directional/man/Arotation.Rd | 2 Directional-5.8/Directional/man/Directional-package.Rd | 4 Directional-5.8/Directional/man/colspml.mle.Rd | 2 Directional-5.8/Directional/man/colwatsons.Rd | 2 Directional-5.8/Directional/man/cosnn.Rd | 3 Directional-5.8/Directional/man/desag.Rd |only Directional-5.8/Directional/man/dirda.cv.Rd | 4 Directional-5.8/Directional/man/dmixvmf.Rd |only Directional-5.8/Directional/man/dsespc.Rd |only Directional-5.8/Directional/man/dvm.Rd | 26 ++ Directional-5.8/Directional/man/dvmf.Rd | 34 +- Directional-5.8/Directional/man/dwood.Rd |only Directional-5.8/Directional/man/esag.contour.Rd | 28 +- Directional-5.8/Directional/man/esag.mle.Rd | 8 Directional-5.8/Directional/man/esag.reg.Rd |only Directional-5.8/Directional/man/esagda.pred.Rd | 2 Directional-5.8/Directional/man/f.rbing.Rd | 15 - Directional-5.8/Directional/man/fishkent.Rd | 3 Directional-5.8/Directional/man/hcf.aov.Rd | 2 Directional-5.8/Directional/man/hcf.boot.Rd | 4 Directional-5.8/Directional/man/hcf.circaov.Rd | 2 Directional-5.8/Directional/man/hcf.perm.Rd | 4 Directional-5.8/Directional/man/hcfcirc.boot.Rd | 4 Directional-5.8/Directional/man/hcfcirc.perm.Rd | 4 Directional-5.8/Directional/man/iag.reg.Rd | 9 Directional-5.8/Directional/man/iagesag.Rd | 4 Directional-5.8/Directional/man/kent.logcon.Rd | 3 Directional-5.8/Directional/man/kent.mle.Rd | 5 Directional-5.8/Directional/man/kuiper.Rd | 2 Directional-5.8/Directional/man/lambert.inv.Rd | 3 Directional-5.8/Directional/man/mediandir.Rd | 4 Directional-5.8/Directional/man/multivm.mle.Rd | 6 Directional-5.8/Directional/man/pc.test.Rd |only Directional-5.8/Directional/man/pcircpurka.Rd | 4 Directional-5.8/Directional/man/purka.mle.Rd | 4 Directional-5.8/Directional/man/purkada.pred.Rd | 6 Directional-5.8/Directional/man/racg.Rd | 2 Directional-5.8/Directional/man/rayleigh.Rd | 5 Directional-5.8/Directional/man/rbingham.Rd | 11 Directional-5.8/Directional/man/resag.Rd | 4 Directional-5.8/Directional/man/rfb.Rd | 11 Directional-5.8/Directional/man/rmatrixfisher.Rd | 11 Directional-5.8/Directional/man/rmixvmf.Rd | 12 - Directional-5.8/Directional/man/rot.matrix.Rd | 2 Directional-5.8/Directional/man/rotation.Rd | 3 Directional-5.8/Directional/man/rsespc.Rd |only Directional-5.8/Directional/man/rsop.Rd | 3 Directional-5.8/Directional/man/rvmf.Rd | 8 Directional-5.8/Directional/man/rvonmises.Rd | 51 +++- Directional-5.8/Directional/man/sespc.mle.Rd |only Directional-5.8/Directional/man/spher.esag.contour.Rd |only Directional-5.8/Directional/man/spher.mixvmf.contour.Rd |only Directional-5.8/Directional/man/spher.sespc.contour.Rd |only Directional-5.8/Directional/man/spher.vmf.contour.Rd |only Directional-5.8/Directional/man/spherconc.test.Rd | 2 Directional-5.8/Directional/man/sphereplot.Rd | 7 Directional-5.8/Directional/man/spml.fbed.Rd | 4 Directional-5.8/Directional/man/spml.mle.Rd | 22 + Directional-5.8/Directional/man/spml.regs.Rd | 2 Directional-5.8/Directional/man/vmf.contour.Rd | 48 +++- Directional-5.8/Directional/man/vmf.da.Rd | 6 Directional-5.8/Directional/man/vmf.kde.Rd | 3 Directional-5.8/Directional/man/vmf.kerncontour.Rd | 2 Directional-5.8/Directional/man/vmf.mle.Rd | 56 +++- Directional-5.8/Directional/man/vmfda.pred.Rd | 5 Directional-5.8/Directional/man/vmfkde.tune.Rd | 4 Directional-5.8/Directional/man/vmkde.tune.Rd | 4 Directional-5.8/Directional/man/wood.mle.Rd | 5 114 files changed, 494 insertions(+), 327 deletions(-)
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Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: State space modelling is an efficient and flexible framework for
statistical inference of a broad class of time series and other data. KFAS
includes computationally efficient functions for Kalman filtering, smoothing,
forecasting, and simulation of multivariate exponential family state space models,
with observations from Gaussian, Poisson, binomial, negative binomial, and gamma
distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske [aut, cre]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between KFAS versions 1.4.6 dated 2021-06-07 and 1.5.0 dated 2023-02-07
ChangeLog | 711 +++++------ DESCRIPTION | 9 MD5 | 236 +-- NAMESPACE | 2 R/KFAS-defunct.R | 106 - R/KFAS-package.R | 56 R/KFS.R | 1296 ++++++++++----------- R/SSMarima.R | 2 R/SSMcustom.R | 188 +-- R/SSMcycle.R | 190 +-- R/SSModel.R | 852 +++++++------- R/SSMregression.R | 392 +++--- R/SSMseasonal.R | 312 ++--- R/SSMtrend.R | 202 +-- R/approxSSM.R | 302 ++--- R/artransform.R | 46 R/checkModel.R | 292 ++-- R/coef.KFS.R | 218 +-- R/confint.R |only R/extract.SSModel.R | 564 ++++----- R/fitSSM.R | 520 ++++---- R/fitted.KFS.R | 106 - R/hatvalues.KFS.R | 98 - R/importanceSSM.R | 308 ++--- R/initTheta.R | 52 R/internalResids.R | 378 +++--- R/interval.R | 180 +- R/ldl.R | 74 - R/logLik.SSModel.R | 474 +++---- R/mvInnovations.R | 90 - R/plot.SSModel.R | 214 +-- R/predict.SSModel.R | 746 ++++++------ R/print.objects.R | 186 +-- R/rename_states.R | 48 R/residuals.KFS.R | 216 +-- R/rstandard.KFS.R | 79 + R/signals.R | 218 +-- R/simHelper.R | 90 - R/simulateSSM.R | 350 ++--- R/transformSSM.R | 330 ++--- R/zzz.R | 10 build/vignette.rds |binary inst/CITATION | 40 inst/doc/KFAS.R | 526 ++++---- inst/doc/KFAS.Rnw | 2224 ++++++++++++++++++------------------- inst/doc/KFAS.pdf |binary man/Extract.SSModel.Rd | 168 +- man/GlobalTemp.Rd | 92 - man/KFAS-defunct.Rd | 76 - man/KFAS.Rd | 1200 +++++++++---------- man/KFS.Rd | 568 ++++----- man/SSModel.Rd | 700 ++++++----- man/alcohol.Rd | 36 man/approxSSM.Rd | 224 +-- man/artransform.Rd | 68 - man/boat.Rd | 152 +- man/checkModel.Rd | 94 - man/coef.SSModel.Rd | 174 +- man/confint.KFS.Rd |only man/fitSSM.Rd | 394 +++--- man/fitted.SSModel.Rd | 122 +- man/hatvalues.KFS.Rd | 76 - man/importanceSSM.Rd | 216 +-- man/ldl.Rd | 64 - man/logLik.SSModel.Rd | 296 ++-- man/mvInnovations.Rd | 78 - man/plot.SSModel.Rd | 86 - man/predict.SSModel.Rd | 242 ++-- man/print.KFS.Rd | 42 man/print.SSModel.Rd | 32 man/rename_states.Rd | 62 - man/residuals.KFS.Rd | 80 - man/rstandard.KFS.Rd | 236 ++- man/sexratio.Rd | 108 - man/signal.Rd | 110 - man/simulateSSM.Rd | 242 ++-- man/transformSSM.Rd | 94 - src/approx.f90 | 331 ++--- src/approxloop.f90 | 210 +-- src/artransform.f90 | 40 src/covmeanw.f90 | 152 +- src/filter1step.f90 | 632 +++++----- src/filter1stepnovar.f90 | 158 +- src/filtersimfast.f90 | 110 - src/gloglik.f90 | 168 +- src/gsmoothall.f90 | 1076 ++++++++--------- src/isample.f90 | 346 ++--- src/isamplefilter.f90 | 432 +++---- src/kfilter.f90 | 180 +- src/kfilter2.f90 | 186 +-- src/kfstheta.f90 | 248 ++-- src/ldl.f90 | 70 - src/ldlssm.f90 | 164 +- src/marginalxx.f90 | 84 - src/mvfilter.f90 | 70 - src/ngfilter.f90 | 268 ++-- src/ngloglik.f90 | 314 ++--- src/ngsmooth.f90 | 248 ++-- src/predict.f90 | 96 - src/ptheta.f90 | 250 ++-- src/pytheta.f90 | 94 - src/simfilter.f90 | 292 ++-- src/simgaussian.f90 | 550 ++++----- src/simgaussianuncond.f90 | 418 +++--- src/smoothonestep.f90 | 262 ++-- src/smoothsim.f90 | 204 +-- src/smoothsimfast.f90 | 176 +- tests/test-all.R | 4 tests/testthat/testArima.R | 176 +- tests/testthat/testBasics.R | 100 - tests/testthat/testGLM.R | 648 +++++----- tests/testthat/testImportanceSSM.R | 64 - tests/testthat/testLMM.R | 72 - tests/testthat/testMisc.R | 62 - tests/testthat/testNumerical.R | 222 +-- tests/testthat/testPredict.R | 66 - tests/testthat/testSimulateSSM.R | 92 - tests/testthat/testStruct.R | 44 vignettes/KFAS.Rnw | 2224 ++++++++++++++++++------------------- vignettes/KFAS.bib | 828 ++++++------- 120 files changed, 16139 insertions(+), 15957 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@gmail.com>
Diff between REndo versions 2.4.7 dated 2022-10-21 and 2.4.8 dated 2023-02-07
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS.md | 7 +++++ data/dataCopDisCont.rda |binary tests/testthat/test-correctness_multilevel.R | 32 +++++++++++++-------------- 5 files changed, 31 insertions(+), 24 deletions(-)
Title: Model Selection with Bayesian Methods and Information Criteria
Description: Model selection and averaging for regression and mixtures, inclusing Bayesian model selection and information criteria (BIC, EBIC, AIC, GIC).
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck, Oriol Abril, Miquel Torrens
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 3.3.0 dated 2023-01-25 and 3.3.1 dated 2023-02-07
ChangeLog | 6 ++- DESCRIPTION | 11 +++-- MD5 | 25 ++++++------- NAMESPACE | 5 ++ R/AllClasses.R | 3 + R/infocriteria.R | 99 ++++++++++++++++++++++++++++++++++++++++++++++------ inst/doc/mombf.R | 5 ++ inst/doc/mombf.Rnw | 5 ++ inst/doc/mombf.pdf |binary man/bestBIC.Rd | 22 +++++++---- man/icfit-class.Rd |only src/Makevars | 2 - src/Makevars.win | 2 - vignettes/mombf.Rnw | 5 ++ 14 files changed, 149 insertions(+), 41 deletions(-)
Title: Make and Apply Customized Rounding Specifications for Tables
Description: Translate double and integer valued data into
character values formatted for tabulation in manuscripts
or other types of academic reports.
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>
Diff between table.glue versions 0.0.2 dated 2020-10-31 and 0.0.3 dated 2023-02-07
DESCRIPTION | 12 LICENSE | 4 MD5 | 95 +- NAMESPACE | 2 NEWS.md |only R/as_inline.R | 254 +++--- R/bracket_helpers.R | 454 ++++++----- R/check_args.R | 540 ++++++------- R/misc.R | 52 - R/nhanes.R | 112 +- R/round_spec.R | 984 ++++++++++++------------ R/table.glue-package.R | 16 R/table_ester.R | 608 +++++++-------- R/table_glue.R | 216 ++--- R/table_pvalue.R | 595 +++++++-------- R/table_value.R | 425 +++++----- README.md | 23 build/vignette.rds |binary inst/doc/default_rounder.Rmd | 150 +-- inst/doc/default_rounder.html | 290 +++---- inst/doc/table_guide.Rmd | 396 +++++----- inst/doc/table_guide.html | 1340 +++++++++++++++++----------------- man/as_inline.Rd | 80 +- man/bracket_drop.Rd | 151 ++- man/format_big.Rd | 76 - man/format_decimal.Rd | 74 - man/format_missing.Rd | 54 - man/format_small.Rd | 88 +- man/nhanes.Rd | 132 +-- man/round_half_up.Rd | 114 +- man/round_spec.Rd | 86 +- man/round_using_magnitude.Rd | 186 ++-- man/table.glue-package.Rd | 48 - man/table_ester.Rd | 238 +++--- man/table_glue.Rd | 132 +-- man/table_pvalue.Rd | 258 +++--- man/table_value.Rd | 78 - tests/testthat.R | 8 tests/testthat/test-as_inline.R | 268 +++--- tests/testthat/test-bracket_helpers.R | 199 ++--- tests/testthat/test-check_args.R | 104 +- tests/testthat/test-misc.R | 10 tests/testthat/test-round_spec.R | 90 +- tests/testthat/test-table_ester.R | 166 ++-- tests/testthat/test-table_glue.R | 28 tests/testthat/test-table_pvalue.R | 22 tests/testthat/test-table_value.R | 176 ++-- vignettes/default_rounder.Rmd | 150 +-- vignettes/table_guide.Rmd | 396 +++++----- 49 files changed, 5055 insertions(+), 4925 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.4.1 dated 2022-12-18 and 0.5.0 dated 2023-02-07
DESCRIPTION | 14 MD5 | 67 NAMESPACE | 10 NEWS.md | 273 ++- R/calibrate_to_sample.R | 2 R/generalized_bootstrap.R | 403 ++++- R/quadratic_forms.R | 436 +++++ R/quadratic_forms_of_survey_design_objects.R |only README.md | 17 build/vignette.rds |binary inst/CITATION |only inst/doc/bootstrap-replicates.R | 53 inst/doc/bootstrap-replicates.Rmd | 180 +- inst/doc/bootstrap-replicates.html | 771 ++++------ inst/doc/nonresponse-adjustments.R | 3 inst/doc/nonresponse-adjustments.Rmd | 27 inst/doc/nonresponse-adjustments.html | 711 +++------ inst/doc/sample-based-calibration.Rmd | 17 inst/doc/sample-based-calibration.html | 272 --- inst/doc/two-phase-sampling.R |only inst/doc/two-phase-sampling.Rmd |only inst/doc/two-phase-sampling.html |only man/as_gen_boot_design.Rd | 81 + man/get_design_quad_form.Rd |only man/get_nearest_psd_matrix.Rd |only man/ht_matrix_to_joint_probs.Rd |only man/is_psd_matrix.Rd |only man/make_gen_boot_factors.Rd | 6 man/make_quad_form_matrix.Rd | 5 man/make_twophase_quad_form.Rd |only man/rescale_reps.Rd |only man/svrep-package.Rd | 2 tests/testthat/test-generalized-bootstrap.R | 91 + tests/testthat/test-quadratic-forms.R | 21 tests/testthat/test-quadratic_forms_of_survey_design_objects.R |only vignettes/bootstrap-replicates.Rmd | 180 +- vignettes/nonresponse-adjustments.Rmd | 27 vignettes/references.bib | 48 vignettes/sample-based-calibration.Rmd | 17 vignettes/two-phase-sampling.Rmd |only vignettes/vignette-references.bib | 15 41 files changed, 2178 insertions(+), 1571 deletions(-)
Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple
GUI controls for R functions. These are built on the 'tcltk' package.
Uses could include changing a parameter on a graph by animating it
with a slider or a "doublebutton", up to more sophisticated control
panels.
Some functions for specific graphical tasks, referred to as 'cartoons',
are provided.
Author: Bowman, Bowman, Gibson and Crawford
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between rpanel versions 1.1-5.1 dated 2022-07-04 and 1.1-5.2 dated 2023-02-07
DESCRIPTION | 6 ++-- MD5 | 10 +++---- R/rp-geosim.r | 70 ++++++++++++++++++++++++++--------------------------- R/rp-likelihood.r | 66 ++++++++++++++++++++++++------------------------- R/rp-plot3d.r | 34 ++++++++++++------------- R/rp-regression2.r | 14 +++++----- 6 files changed, 100 insertions(+), 100 deletions(-)
Title: Penalized Elastic Net S/MM-Estimator of Regression
Description: Robust penalized (adaptive) elastic net S and M estimators for
linear regression. The methods are proposed in
Cohen Freue, G. V., Kepplinger, D., Salibián-Barrera, M., and Smucler, E.
(2019) <https://projecteuclid.org/euclid.aoas/1574910036>.
The package implements the extensions and algorithms described in
Kepplinger, D. (2020) <doi:10.14288/1.0392915>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pense versions 2.1.0 dated 2021-07-07 and 2.2.0 dated 2023-02-07
pense-2.1.0/pense/build/partial.rdb |only pense-2.1.0/pense/tests/testthat/testthat-problems.rds |only pense-2.1.0/pense/vignettes/computing_adapense_cache |only pense-2.1.0/pense/vignettes/computing_adapense_files |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_48807d83cc5fb6cf2463ef80d5d7ddd7.RData |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_48807d83cc5fb6cf2463ef80d5d7ddd7.rdb |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_48807d83cc5fb6cf2463ef80d5d7ddd7.rdx |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_22951aa6abea8973c9e5ba08064a8e38.RData |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_22951aa6abea8973c9e5ba08064a8e38.rdb |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_22951aa6abea8973c9e5ba08064a8e38.rdx |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_fa3f2d0727238f3562e13501679913fe.RData |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_fa3f2d0727238f3562e13501679913fe.rdb |only pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_fa3f2d0727238f3562e13501679913fe.rdx |only pense-2.2.0/pense/DESCRIPTION | 10 pense-2.2.0/pense/MD5 | 198 pense-2.2.0/pense/NAMESPACE | 4 pense-2.2.0/pense/NEWS.md | 8 pense-2.2.0/pense/R/autoconfig.win.R.in | 2 pense-2.2.0/pense/R/coef-methods.R | 2 pense-2.2.0/pense/R/constants.R |only pense-2.2.0/pense/R/control_options.R | 190 pense-2.2.0/pense/R/deprecated-functions.R | 22 pense-2.2.0/pense/R/elnet.R | 76 pense-2.2.0/pense/R/enpy.R | 6 pense-2.2.0/pense/R/pense_regression.R | 810 +-- pense-2.2.0/pense/R/pense_regression_args.R |only pense-2.2.0/pense/R/pensem_regression.R | 81 pense-2.2.0/pense/R/print-methods.R | 4 pense-2.2.0/pense/R/regmest_regression.R | 178 pense-2.2.0/pense/R/residuals-methods.R | 8 pense-2.2.0/pense/R/utilities-internal.R | 225 - 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Title: Functions for Optimal Matching
Description: Distance based bipartite matching using minimum cost flow, oriented
to matching of treatment and control groups in observational studies ('Hansen'
and 'Klopfer' 2006 <doi:10.1198/106186006X137047>). Routines are provided to
generate distances from generalised linear models (propensity score
matching), formulas giving variables on which to limit matched distances,
stratified or exact matching directives, or calipers, alone or in
combination.
Author: Ben Hansen [aut],
Mark Fredrickson [aut],
Josh Errickson [cre, aut],
Josh Buckner [aut],
Adam Rauh [ctb]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between optmatch versions 0.10.5 dated 2022-08-15 and 0.10.6 dated 2023-02-07
optmatch-0.10.5/optmatch/R/Optmatch.R |only optmatch-0.10.5/optmatch/R/subDivStrat.R |only optmatch-0.10.5/optmatch/tests/testthat/test.Optmatch.R |only optmatch-0.10.5/optmatch/tests/testthat/test.SubDivStrat.R |only optmatch-0.10.6/optmatch/DESCRIPTION | 39 optmatch-0.10.6/optmatch/MD5 | 92 - optmatch-0.10.6/optmatch/NAMESPACE | 15 optmatch-0.10.6/optmatch/NEWS.md | 6 optmatch-0.10.6/optmatch/R/InfinitySparseMatrix.R | 2 optmatch-0.10.6/optmatch/R/MCFSolutions.R |only optmatch-0.10.6/optmatch/R/Optmatch-package.R | 2 optmatch-0.10.6/optmatch/R/complementarySlackness.R |only optmatch-0.10.6/optmatch/R/edgelist.R |only optmatch-0.10.6/optmatch/R/fmatch.R | 384 ++++- optmatch-0.10.6/optmatch/R/fullmatch.R | 94 + optmatch-0.10.6/optmatch/R/makedist.R | 3 optmatch-0.10.6/optmatch/R/match_on.R | 2 optmatch-0.10.6/optmatch/R/max.controls.cap.R | 17 optmatch-0.10.6/optmatch/R/optmatchS3.R |only optmatch-0.10.6/optmatch/R/solve_reg_fm_prob.R |only optmatch-0.10.6/optmatch/R/zzzDistanceSpecification.R | 11 optmatch-0.10.6/optmatch/build/vignette.rds |binary optmatch-0.10.6/optmatch/inst/CITATION | 28 optmatch-0.10.6/optmatch/inst/doc/fullmatch-vignette.R | 21 optmatch-0.10.6/optmatch/inst/doc/fullmatch-vignette.Rmd | 21 optmatch-0.10.6/optmatch/inst/doc/fullmatch-vignette.html | 647 +++++++--- optmatch-0.10.6/optmatch/inst/doc/matching-from-foreign-software.html | 434 +++++- optmatch-0.10.6/optmatch/inst/doc/matching-within-subgroups.html | 381 ++++- optmatch-0.10.6/optmatch/man/InfinitySparseMatrix-class.Rd | 2 optmatch-0.10.6/optmatch/man/c.optmatch.Rd | 2 optmatch-0.10.6/optmatch/man/compare_optmatch.Rd | 2 optmatch-0.10.6/optmatch/man/edgelist.Rd |only optmatch-0.10.6/optmatch/man/evaluate_primal.Rd |only optmatch-0.10.6/optmatch/man/makeOptmatch.Rd | 2 optmatch-0.10.6/optmatch/man/match_on_szn_scale.Rd | 3 optmatch-0.10.6/optmatch/man/mcf_c_fns.Rd |only optmatch-0.10.6/optmatch/man/optmatch.Rd | 2 optmatch-0.10.6/optmatch/man/optmatch_restrictions.Rd | 2 optmatch-0.10.6/optmatch/man/optmatch_same_distance.Rd | 2 optmatch-0.10.6/optmatch/man/revise_ArcInfo_nodelabels.Rd |only optmatch-0.10.6/optmatch/man/update.optmatch.Rd | 2 optmatch-0.10.6/optmatch/src/map.cc | 2 optmatch-0.10.6/optmatch/tests/testthat/test.CBPS.R | 4 optmatch-0.10.6/optmatch/tests/testthat/test.DistanceSpecification.R | 10 optmatch-0.10.6/optmatch/tests/testthat/test.MCFSolutions.R |only optmatch-0.10.6/optmatch/tests/testthat/test.complementarySlackness.R |only optmatch-0.10.6/optmatch/tests/testthat/test.edgelist.R |only optmatch-0.10.6/optmatch/tests/testthat/test.feasible.R | 2 optmatch-0.10.6/optmatch/tests/testthat/test.fmatch.R | 293 ++-- optmatch-0.10.6/optmatch/tests/testthat/test.fullmatch.R | 96 - optmatch-0.10.6/optmatch/tests/testthat/test.optmatchS3.R |only optmatch-0.10.6/optmatch/tests/testthat/test.pairmatch.R | 51 optmatch-0.10.6/optmatch/tests/testthat/test.solve_reg_fm_prob.R |only optmatch-0.10.6/optmatch/tests/testthat/test.summary.optmatch.old.R | 4 optmatch-0.10.6/optmatch/tests/testthat/utilities.R |only optmatch-0.10.6/optmatch/vignettes/fullmatch-vignette.Rmd | 21 optmatch-0.10.6/optmatch/vignettes/hansenKlopfer2006JCGSfig2.png |only 57 files changed, 1966 insertions(+), 735 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <https://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.9.9 dated 2022-10-01 and 1.0.0 dated 2023-02-07
DESCRIPTION | 6 MD5 | 102 +-- R/partab.R | 9 inst/doc/parameter-table.html | 183 ++--- inst/partab |only inst/project/model/1001/1001.lst | 540 ++++++++-------- inst/project/model/1001/1001.xml | 1280 +++++++++++++++++++++------------------ inst/project/model/1001/mod.msf |binary inst/project/model/1001/mod.tab | 1012 +++++++++++++++--------------- inst/project/model/1001/mod2.tab | 1100 ++++++++++++++++----------------- inst/project/model/2001/2001.ctl | 2 inst/project/model/2001/2001.lst | 533 +++++++++++----- inst/project/model/2001/2001.xml | 652 ++++++++++++++----- inst/project/model/2001/mod.msf |binary inst/project/model/2001/mod.tab | 1020 +++++++++++++++---------------- inst/project/model/2001/mod2.tab | 1100 ++++++++++++++++----------------- inst/project/model/2002/2002.lst | 376 ++++++----- inst/project/model/2002/2002.xml | 862 +++++++++++++++----------- inst/project/model/2002/mod.msf |binary inst/project/model/2002/mod.tab | 1016 +++++++++++++++--------------- inst/project/model/2002/mod2.tab | 1100 ++++++++++++++++----------------- inst/project/model/2003/2003.lst | 352 ++++++---- inst/project/model/2003/2003.xml | 1045 +++++++++++++++++-------------- inst/project/model/2003/mod.msf |binary inst/project/model/2003/mod.tab | 556 ++++++++-------- inst/project/model/2003/mod2.tab | 32 inst/project/model/2004/2004.lst | 376 ++++++----- inst/project/model/2004/2004.xml | 1144 +++++++++++++++++++--------------- inst/project/model/2004/mod.msf |binary inst/project/model/2004/mod.tab | 560 ++++++++--------- inst/project/model/2004/mod2.tab | 30 inst/project/model/2005/2005.lst | 384 ++++++----- inst/project/model/2005/2005.xml | 1146 +++++++++++++++++++--------------- inst/project/model/2005/mod.msf |binary inst/project/model/2005/mod.tab | 552 ++++++++-------- inst/project/model/2005/mod2.tab | 32 inst/project/model/2006/2006.lst | 446 +++++++------ inst/project/model/2006/2006.xml | 1255 +++++++++++++++++++++----------------- inst/project/model/2006/mod.msf |binary inst/project/model/2006/mod.tab | 716 ++++++++++----------- inst/project/model/2006/mod2.tab | 766 +++++++++++------------ inst/project/model/2007/2007.lst | 523 ++++++++------- inst/project/model/2007/2007.xml | 1274 +++++++++++++++++++++----------------- inst/project/model/2007/mod.msf |binary inst/project/model/2007/mod.tab | 982 ++++++++++++++--------------- inst/project/model/2007/mod2.tab | 1100 ++++++++++++++++----------------- 46 files changed, 12987 insertions(+), 11177 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph]
,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 0.8.0 dated 2022-10-03 and 1.0.0 dated 2023-02-07
DESCRIPTION | 8 MD5 | 44 NEWS.md | 5 R/encoding.R | 23 R/inputChecks.R | 7 R/modelInputs.R | 5 R/predict.R | 17 README.md | 66 - inst/CITATION | 22 inst/doc/basic_usage.html | 163 +-- inst/doc/benchmark.html | 111 +- inst/doc/convergence.html | 111 +- inst/doc/data_formatting.R | 3 inst/doc/data_formatting.Rmd | 3 inst/doc/data_formatting.html | 204 ++-- inst/doc/interactions.html | 127 +- inst/doc/mnl_models.html | 139 +- inst/doc/mnl_models_weighted.html | 141 +- inst/doc/mxl_models.html | 129 +- inst/doc/predict.html | 129 +- inst/doc/summarizing_results.html | 1903 +++++++++++++++++--------------------- inst/doc/utility_models.html | 32 vignettes/data_formatting.Rmd | 3 23 files changed, 1656 insertions(+), 1739 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-09 1.3.0
2022-04-25 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-16 3.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-16 1.1.1
2018-04-13 1.1.0
2017-07-14 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-17 0.7.6
2021-01-18 0.7.5
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.1.0.0 dated 2022-12-15 and 2.1.0.1 dated 2023-02-07
DESCRIPTION | 6 MD5 | 104 - NEWS.md | 10 R/average_endpoints.R | 2 R/bnec.R | 4 R/helpers.R | 7 R/inits_functions.R | 6 R/sample_priors.R | 9 README.md | 15 build/vignette.rds |binary inst/doc/example1.Rmd | 864 ++++++------- inst/doc/example1.html | 1800 ++++++++++++++-------------- inst/doc/example2.Rmd | 572 ++++----- inst/doc/example2.html | 1506 ++++++++++++------------ inst/doc/example2b.Rmd | 976 +++++++-------- inst/doc/example2b.html | 1999 +++++++++++++++----------------- inst/doc/example3.Rmd | 392 +++--- inst/doc/example3.html | 1229 +++++++++---------- inst/doc/example4.Rmd | 394 +++--- inst/doc/example4.html | 1183 +++++++++--------- man/average_endpoints.Rd | 2 man/bayesnecfit-class.Rd | 148 +- man/beta_binomial2.Rd | 24 man/beta_binomial2_lpmf.Rd | 46 man/beta_binomial2_rng.Rd | 42 man/bnec.Rd | 452 +++---- man/bnecfit-class.Rd | 46 man/check_formula.Rd | 166 +- man/check_priors.Rd | 66 - man/expand_manec.Rd | 114 - man/expand_nec.Rd | 110 - man/herbicide.Rd | 84 - man/is_manecsummary.Rd | 34 man/is_necsummary.Rd | 28 man/log_lik_beta_binomial2.Rd | 38 man/make_brmsformula.Rd | 100 - man/manec_example.Rd | 42 man/manecsummary-class.Rd | 120 - man/nec_data.Rd | 36 man/necsummary-class.Rd | 88 - man/posterior_epred_beta_binomial2.Rd | 34 man/posterior_predict_beta_binomial2.Rd | 42 man/prebayesnecfit-class.Rd | 82 - man/pull_out.Rd | 102 - man/pull_prior.Rd | 50 man/show_params.Rd | 58 vignettes/example1.Rmd | 864 ++++++------- vignettes/example1.Rmd.orig | 2 vignettes/example2.Rmd | 572 ++++----- vignettes/example2.Rmd.orig | 4 vignettes/example2b.Rmd | 976 +++++++-------- vignettes/example3.Rmd | 392 +++--- vignettes/example4.Rmd | 394 +++--- 53 files changed, 8218 insertions(+), 8218 deletions(-)
Title: Tools for Handling Extraction of Features from Time Series
Description: Consolidates and calculates different sets of time-series features from multiple
'R' and 'Python' packages including 'Rcatch22' Henderson, T. (2021) <doi:10.5281/zenodo.5546815>,
'feasts' O'Hara-Wild, M., Hyndman, R., and Wang, E. (2021) <https://CRAN.R-project.org/package=feasts>,
'tsfeatures' Hyndman, R., Kang, Y., Montero-Manso, P., Talagala, T., Wang, E., Yang, Y., and O'Hara-Wild, M. (2020)
<https://CRAN.R-project.org/package=tsfeatures>, 'tsfresh' Christ, M., Braun, N., Neuffer, J.,
and Kempa-Liehr A.W. (2018) <doi:10.1016/j.neucom.2018.03.067>, 'TSFEL' Barandas, M., et al. (2020)
<doi:10.1016/j.softx.2020.100456>, and 'Kats' Facebook Infrastructure Data Science (2021)
<https://facebookresearch.github.io/Kats/>. Provides a standardised workflow from feature calculation to
feature processing, machine learning classification procedures, and the production of statistical graphics.
Author: Trent Henderson [cre, aut],
Annie Bryant [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between theft versions 0.4.1.1 dated 2022-11-17 and 0.4.2.3 dated 2023-02-07
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Title: Browse Over Longitudinal Data Graphically and Analytically in R
Description: Provides a framework of tools to summarise, visualise, and explore
longitudinal data. It builds upon the tidy time series data frames used in the
'tsibble' package, and is designed to integrate within the 'tidyverse', and
'tidyverts' (for time series) ecosystems. The methods implemented include
calculating features for understanding longitudinal data, including
calculating summary statistics such as quantiles, medians, and numeric ranges,
sampling individual series, identifying individual series representative of a
group, and extending the facet system in 'ggplot2' to facilitate exploration of samples of data. These methods are
fully described in the paper "brolgar: An R package to Browse Over
Longitudinal Data Graphically and Analytically in R", Nicholas Tierney,
Dianne Cook, Tania Prvan (2020) <arXiv:2012.01619>.
Author: Nicholas Tierney [aut, cre] ,
Di Cook [aut] ,
Tania Prvan [aut],
Stuart Lee [ctb],
Earo Wang [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between brolgar versions 0.1.2 dated 2021-08-25 and 1.0.0 dated 2023-02-07
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