Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.7.6 dated 2022-12-02 and 2.7.7 dated 2023-03-10
DESCRIPTION | 15 +-- MD5 | 127 +++++++++++++++------------- NAMESPACE | 3 NEWS.md | 72 +++++++++++++++- R/AAAA.R | 4 R/KSSL_VG_model.R | 18 +++- R/SDA-spatial.R | 12 +- R/SDA_query.R | 42 --------- R/SSURGO_spatial_query.R | 45 +++++----- R/WCS-utils.R | 9 ++ R/createSSURGO.R | 112 ++++++++++++++++++++++++- R/dbQueryNASIS.R | 21 ++-- R/estimateColorMixture.R | 6 - R/fetchNASIS.R | 68 +++++---------- R/fetchNASISWebReport.R | 18 ---- R/fetchNASIS_pedons.R | 9 -- R/fetchSCAN.R | 14 ++- R/fetchSoilGrids.R | 59 +++++++++---- R/fetchVegdata.R | 13 ++ R/get_NASIS_table_name_by_purpose.R | 6 - R/get_OSD.R | 2 R/get_RMF_from_NASIS_db.R | 27 ++++-- R/get_SDA_coecoclass.R | 2 R/get_SDA_cosurfmorph.R | 15 ++- R/get_SDA_interpretation.R | 4 R/get_SDA_pmgroupname.R | 27 ++++-- R/get_SSURGO_utils.R | 2 R/get_component_from_SDA.R | 115 +++++++++++++++++++++++++ R/get_cosoilmoist_from_SDA.R | 12 ++ R/get_ecosite_history_from_NASIS_db.R |only R/get_extended_data_from_NASIS_db.R | 21 ---- R/get_site_data_from_NASIS_db.R | 45 ++++++++-- R/mukey-WCS.R | 25 ++--- R/seriesExtent.R | 42 ++------- R/siblings.R | 2 R/simplifyArtifactData.R | 4 R/simplifyFragmentData.R | 2 R/soilDB-package.R | 12 +- R/uncode.R | 80 ++++++++++++++++-- R/utils.R | 55 ++++++------ build/partial.rdb |binary build/vignette.rds |only inst/CITATION | 10 +- inst/WORDLIST | 133 +++++++++++++++++++++++++++--- inst/doc |only man/SoilWeb_spatial_query.Rd | 5 - man/downloadSSURGO.Rd | 2 man/estimateColorMixture.Rd | 54 ++++++------ man/fetchNASIS.Rd | 57 +++++------- man/fetchSDA.Rd | 2 man/format_SQL_in_statement.Rd | 42 --------- man/get_NASIS_metadata.Rd | 13 ++ man/get_NASIS_table_metadata.Rd |only man/get_OSD.Rd | 2 man/get_RMF_from_NASIS_db.Rd |only man/get_SDA_coecoclass.Rd | 2 man/get_SDA_cosurfmorph.Rd | 3 man/get_SDA_pmgroupname.Rd | 3 man/get_ecosite_history_from_NASIS_db.Rd |only man/mukey.wcs.Rd | 21 ++-- man/soilDB-package.Rd | 12 +- tests/testthat/test-OSDquery.R | 3 tests/testthat/test-dbQueryNASIS.R | 64 +++++++------- tests/testthat/test-fetchSoilGrids.R | 5 - tests/testthat/test-get_SDA_pmgroupname.R | 12 ++ tests/testthat/test-siblings.R | 17 ++- vignettes |only 67 files changed, 1066 insertions(+), 563 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut] ,
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd],
Indrajeet Patil [ctb] ,
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Be [...truncated...]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between broom versions 1.0.3 dated 2023-01-25 and 1.0.4 dated 2023-03-10
DESCRIPTION | 32 +-- LICENSE | 4 MD5 | 312 ++++++++++++++++---------------- NEWS.md | 6 R/aaa-documentation-helper.R | 4 R/aer-tidiers.R | 15 - R/auc-tidiers.R | 6 R/bbmle-tidiers.R | 5 R/betareg-tidiers.R | 8 R/biglm-tidiers.R | 7 R/bingroup-tidiers.R | 18 - R/boot-tidiers.R | 41 ++-- R/broom-package.R | 3 R/btergm-tidiers.R | 29 +- R/car-tidiers.R | 20 +- R/caret-tidiers.R | 5 R/cluster-tidiers.R | 10 - R/cmprsk-tidiers.R | 19 + R/data-frame-tidiers.R | 1 R/drc-tidiers.R | 4 R/emmeans-tidiers.R | 27 +- R/epiR-tidiers.R | 28 +- R/ergm-tidiers.R | 11 - R/fixest-tidiers.R | 36 ++- R/gam-tidiers.R | 8 R/geepack-tidiers.R | 16 - R/glmnet-cv-glmnet-tidiers.R | 8 R/glmnet-glmnet-tidiers.R | 11 - R/gmm-tidiers.R | 6 R/hmisc-tidiers.R | 8 R/joinerml-tidiers.R | 17 - R/kendall-tidiers.R | 4 R/ks-tidiers.R | 4 R/lavaan-tidiers.R | 16 - R/leaps-tidiers.R | 4 R/lfe-tidiers.R | 74 +++---- R/list-optim-tidiers.R | 4 R/list-svd-tidiers.R | 6 R/lm-beta-tidiers.R | 8 R/lmodel2-tidiers.R | 4 R/lmtest-tidiers.R | 58 +++-- R/maps-tidiers.R | 8 R/margins-tidiers.R | 131 ++++++------- R/mass-fitdistr-tidiers.R | 3 R/mass-negbin-tidiers.R | 30 +-- R/mass-polr-tidiers.R | 28 +- R/mass-ridgelm-tidiers.R | 6 R/mass-rlm-tidiers.R | 7 R/mclust-tidiers.R | 17 - R/mediation-tidiers.R | 22 +- R/metafor-tidiers.R | 37 +-- R/mfx-tidiers.R | 151 ++++++++------- R/mgcv-tidiers.R | 10 - R/mlogit-tidiers.R | 74 +++---- R/muhaz-tidiers.R | 4 R/multcomp-tidiers.R | 12 - R/nnet-tidiers.R | 10 - R/nobs.R | 8 R/orcutt-tidiers.R | 2 R/ordinal-clm-tidiers.R | 4 R/ordinal-clmm-tidiers.R | 5 R/plm-tidiers.R | 6 R/polca-tidiers.R | 26 +- R/psych-tidiers.R | 10 - R/quantreg-nlrq-tidiers.R | 24 +- R/quantreg-rq-tidiers.R | 28 +- R/quantreg-rqs-tidiers.R | 6 R/robust-glmrob-tidiers.R | 15 - R/robust-lmrob-tidiers.R | 23 +- R/robustbase-glmrob-tidiers.R | 2 R/robustbase-lmrob-tidiers.R | 48 ++-- R/sp-tidiers.R | 66 ++++++ R/spdep-tidiers.R | 119 +++++------- R/speedglm-speedglm-tidiers.R | 4 R/speedglm-speedlm-tidiers.R | 5 R/stats-anova-tidiers.R | 82 ++++---- R/stats-arima-tidiers.R | 4 R/stats-decompose-tidiers.R | 4 R/stats-factanal-tidiers.R | 8 R/stats-glm-tidiers.R | 36 ++- R/stats-htest-tidiers.R | 24 +- R/stats-kmeans-tidiers.R | 13 - R/stats-lm-tidiers.R | 75 ++++--- R/stats-loess-tidiers.R | 2 R/stats-mlm-tidiers.R | 7 R/stats-nls-tidiers.R | 12 - R/stats-prcomp-tidiers.R | 28 +- R/stats-smooth.spline-tidiers.R | 10 - R/stats-summary-lm-tidiers.R | 55 +++-- R/stats-time-series-tidiers.R | 2 R/survey-tidiers.R | 21 +- R/survival-aareg-tidiers.R | 6 R/survival-cch-tidiers.R | 12 - R/survival-coxph-tidiers.R | 5 R/survival-pyears-tidiers.R | 6 R/survival-survdiff-tidiers.R | 2 R/survival-survexp-tidiers.R | 4 R/survival-survfit-tidiers.R | 13 - R/survival-survreg-tidiers.R | 14 - R/systemfit-tidiers.R | 6 R/tseries-tidiers.R | 6 R/utilities.R | 140 +++++++------- R/vars-tidiers.R | 21 +- R/zoo-tidiers.R | 16 - README.md | 8 inst/WORDLIST | 1 inst/doc/adding-tidiers.html | 4 inst/doc/available-methods.R | 18 + inst/doc/available-methods.Rmd | 18 + inst/doc/available-methods.html | 4 inst/doc/bootstrapping.html | 4 inst/doc/broom.R | 5 inst/doc/broom.Rmd | 5 inst/doc/broom.html | 35 +-- inst/doc/broom_and_dplyr.R | 36 +-- inst/doc/broom_and_dplyr.Rmd | 36 +-- inst/doc/broom_and_dplyr.html | 40 ++-- man/broom.Rd | 14 - man/null_tidiers.Rd | 2 man/sp_tidiers.Rd | 6 man/tidy.aov.Rd | 5 tests/testthat/test-boot.R | 4 tests/testthat/test-car.R | 17 - tests/testthat/test-cmprsk.R | 12 - tests/testthat/test-emmeans.R | 13 - tests/testthat/test-ergm.R | 3 tests/testthat/test-fixest.R | 21 +- tests/testthat/test-glmnetUtils.R | 4 tests/testthat/test-lfe.R | 66 ++++-- tests/testthat/test-list-xyz.R | 2 tests/testthat/test-lmtest.R | 8 tests/testthat/test-margins.R | 13 - tests/testthat/test-mass-negbin.R | 8 tests/testthat/test-metafor.R | 12 - tests/testthat/test-mfx.R | 2 tests/testthat/test-mgcv.R | 8 tests/testthat/test-nnet.R | 4 tests/testthat/test-robustbase.R | 4 tests/testthat/test-sp.R | 5 tests/testthat/test-spdep.R | 33 +-- tests/testthat/test-speedglm-speedglm.R | 1 tests/testthat/test-stats-anova.R | 28 +- tests/testthat/test-stats-glm.R | 11 + tests/testthat/test-stats-htest.R | 7 tests/testthat/test-stats-kmeans.R | 1 tests/testthat/test-stats-lm.R | 2 tests/testthat/test-stats-mlm.R | 1 tests/testthat/test-stats-summary-lm.R | 20 +- tests/testthat/test-survey.R | 18 + tests/testthat/test-survival-coxph.R | 6 tests/testthat/test-survival-survdiff.R | 4 tests/testthat/test-utilities.R | 72 +++---- tests/testthat/test-vars.R | 2 tests/testthat/test-zoo.R | 4 vignettes/available-methods.Rmd | 18 + vignettes/broom.Rmd | 5 vignettes/broom_and_dplyr.Rmd | 36 +-- 157 files changed, 1662 insertions(+), 1546 deletions(-)
Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service
(WFS) for vector data, Web Coverage Service (WCS), Catalogue Service (CSW) for ISO/OGC metadata, Web Processing Service (WPS) for data processes,
and associated standards such as the common web-service specification (OWS) and OGC Filter Encoding. Partial support is provided for the Web Map
Service (WMS). The purpose is to add support for additional OGC service standards such as Web Coverage Processing Service (WCPS), the Sensor
Observation Service (SOS), or even new standard services emerging such OGC API or SensorThings.
Author: Emmanuel Blondel [aut, cre] ,
Alexandre Bennici [ctb] ,
Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ows4R versions 0.3-3 dated 2023-01-12 and 0.3-4 dated 2023-03-10
DESCRIPTION | 10 ++--- MD5 | 30 ++++++++-------- NEWS.md | 14 ++++++- R/OWSHttpRequest.R | 4 ++ R/WFSFeatureType.R | 62 ++++++++++++++++++++++++++++++++--- R/WFSFeatureTypeElement.R | 22 +++++++++--- README.md | 37 ++++++++++++-------- inst/doc/csw.Rmd | 2 - inst/doc/csw.html | 2 - inst/doc/wcs.Rmd | 2 - inst/doc/wcs.html | 2 - man/WFSFeatureType.Rd | 49 +++++++++++++++++++++++++++ man/WFSFeatureTypeElement.Rd | 18 ++++++++++ tests/testthat/test_WCSClient_v2_0.R | 6 +-- vignettes/csw.Rmd | 2 - vignettes/wcs.Rmd | 2 - 16 files changed, 209 insertions(+), 55 deletions(-)
Title: Primary and Secondary Analyses for Micro-Randomized Trials
Description: Estimates marginal causal excursion effects and moderated causal excursion effects for micro-randomized trial (MRT). Applicable to MRT with binary treatment options and continuous or binary outcomes. The method for MRT with continuous outcomes is the weighted centered least squares (WCLS) by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274>. The method for MRT with binary outcomes is the estimator for marginal excursion effect (EMEE) by Qian et al. (2021) <doi:10.1093/biomet/asaa070>.
Author: Tianchen Qian [aut, cre] ,
Shaolin Xiang [aut],
Zhaoxi Cheng [aut],
Audrey Boruvka [ctb]
Maintainer: Tianchen Qian <t.qian@uci.edu>
Diff between MRTAnalysis versions 0.1.0 dated 2023-03-06 and 0.1.1 dated 2023-03-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 +++++- inst/doc/mrt-analysis.Rmd | 9 +++++---- inst/doc/mrt-analysis.html | 31 ++++++++++++++++++++----------- vignettes/mrt-analysis.Rmd | 9 +++++---- 6 files changed, 44 insertions(+), 29 deletions(-)
Title: Biodiversity Data from the Living Atlas Community
Description: The living atlas community provides tools to enable users to find,
access, combine and visualise data on biodiversity. 'galah' enables the R
community to directly access data and resources hosted by the living atlases.
Author: Martin Westgate [aut, cre],
Matilda Stevenson [aut],
Dax Kellie [aut],
Peggy Newman [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 1.5.1 dated 2023-01-13 and 1.5.2 dated 2023-03-10
DESCRIPTION | 6 MD5 | 112 +++++----- NAMESPACE | 3 NEWS.md | 13 + R/collect_occurrences.R | 39 ++- R/galah-package.R | 2 R/galah_down_to.R | 2 R/galah_filter.R | 16 + R/galah_geolocate.R | 2 R/galah_group_by.R | 3 R/galah_select.R | 10 R/search_all.R | 6 R/search_taxa.R | 7 R/select.R | 4 R/show_all.R | 4 R/show_values.R | 20 + R/url_GET.R | 10 R/url_download.R | 12 - R/utilities_internal.R | 18 + R/utilities_occurrences.R | 1 README.md | 111 +++++----- inst/doc/choosing_an_atlas.Rmd | 280 +++++++++++++------------- inst/doc/choosing_an_atlas.html | 278 ++++++++++++------------- inst/doc/download_data.Rmd | 86 +++---- inst/doc/download_data.html | 122 +++++------ inst/doc/look_up_information.Rmd | 147 ++++++------- inst/doc/look_up_information.html | 149 ++++++------- inst/doc/narrow_your_results.Rmd | 95 ++++---- inst/doc/narrow_your_results.html | 97 ++++----- inst/doc/piping.Rmd | 56 ++--- inst/doc/piping.html | 58 ++--- inst/doc/quick_start_guide.Rmd | 39 +-- inst/doc/quick_start_guide.html | 41 +-- man/figures/atlases_plot.png |only man/galah.Rd | 2 man/galah_geolocate.Rd | 2 man/search_all.Rd | 2 man/show_all.Rd | 2 tests/fixtures/IA_Sweden_show_all_fields.yml |only tests/fixtures/IA_Sweden_show_values.yml | 8 tests/testthat/test-galah_filter.R | 12 + tests/testthat/test-international-Austria.R | 2 tests/testthat/test-international-Brazil.R | 2 tests/testthat/test-international-Estonia.R | 2 tests/testthat/test-international-France.R | 2 tests/testthat/test-international-GBIF.R | 7 tests/testthat/test-international-Guatemala.R | 2 tests/testthat/test-international-Portugal.R | 2 tests/testthat/test-international-Spain.R | 2 tests/testthat/test-international-Sweden.R | 12 - tests/testthat/test-international-UK.R | 2 tests/testthat/test-show_values.R | 14 + vignettes/choosing_an_atlas.Rmd | 280 +++++++++++++------------- vignettes/download_data.Rmd | 86 +++---- vignettes/look_up_information.Rmd | 147 ++++++------- vignettes/narrow_your_results.Rmd | 95 ++++---- vignettes/piping.Rmd | 56 ++--- vignettes/quick_start_guide.Rmd | 39 +-- 58 files changed, 1378 insertions(+), 1251 deletions(-)
Title: A System of Soil Classification for Making and Interpreting Soil
Surveys
Description: Taxonomic dictionaries, formative element lists, and functions related to the maintenance, development and application of U.S. Soil Taxonomy.
Data and functionality are based on official U.S. Department of Agriculture sources including the latest edition of the Keys to Soil Taxonomy. Descriptions and metadata are obtained from the National Soil Information System or Soil Survey Geographic databases. Other sources are referenced in the data documentation.
Provides tools for understanding and interacting with concepts in the U.S. Soil Taxonomic System. Most of the current utilities are for working with taxonomic concepts at the "higher" taxonomic levels: Order, Suborder, Great Group, and Subgroup.
Author: Andrew Brown [aut, cre],
Dylan Beaudette [aut]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between SoilTaxonomy versions 0.2.2 dated 2022-10-17 and 0.2.3 dated 2023-03-10
DESCRIPTION | 10 +- MD5 | 62 +++++++----- NAMESPACE | 5 + NEWS.md | 12 ++ R/AAAAA.R | 3 R/SoilTaxonomy-package.R | 8 - R/data-documentation.R | 96 +++++++++++--------- R/extractSMR.R | 30 ++++-- R/formative-elements.R | 34 +++++-- R/getChildTaxa.R | 6 - R/getTaxonAtLevel.R | 67 ++++++++----- R/hierarchy.R | 45 +++++++++ R/higherTaxaCodes.R | 163 +++++++++++++++++++--------------- R/taxonTree.R |only README.md | 148 ++++++++++++++++++++++++++---- build/vignette.rds |binary data/ST_higher_taxa_codes_13th.rda |only data/ST_unique_list.rda |binary inst/CITATION | 10 +- inst/WORDLIST | 5 + inst/doc/diagnostics.html | 13 ++ inst/doc/family-level_taxonomy.html | 13 ++ inst/doc/taxon-letter-codes.html | 13 ++ man/ST.Rd | 7 + man/ST_family_classes.Rd | 2 man/ST_features.Rd | 2 man/ST_higher_taxa_codes_12th.Rd | 4 man/ST_higher_taxa_codes_13th.Rd |only man/SoilTaxonomy-package.Rd | 59 ++++++------ man/getTaxonAtLevel.Rd | 10 +- man/level_hierarchy.Rd |only man/taxonTree.Rd |only tests/testthat/test-extractSMR.R | 13 ++ tests/testthat/test-getTaxonAtLevel.R | 22 +++- tests/testthat/test-taxonTree.R |only 35 files changed, 584 insertions(+), 278 deletions(-)
Title: Generalized Linear Mixed Models with Robust Random Fields for
Spatiotemporal Modeling
Description: Implements Bayesian spatial and spatiotemporal
models that optionally allow for extreme spatial deviations through
time. 'glmmfields' uses a predictive process approach with random
fields implemented through a multivariate-t distribution instead of
the usual multivariate normal. Sampling is conducted with 'Stan'.
References: Anderson and Ward (2019) <doi:10.1002/ecy.2403>.
Author: Sean C. Anderson [aut, cre],
Eric J. Ward [aut],
Trustees of Columbia University [cph]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between glmmfields versions 0.1.4 dated 2020-07-09 and 0.1.7 dated 2023-03-10
glmmfields-0.1.4/glmmfields/R/zzz.R |only glmmfields-0.1.4/glmmfields/inst/include/meta_header.hpp |only glmmfields-0.1.4/glmmfields/src/Modules.cpp |only glmmfields-0.1.4/glmmfields/src/init.cpp |only glmmfields-0.1.4/glmmfields/src/stan_files |only glmmfields-0.1.4/glmmfields/tools |only glmmfields-0.1.7/glmmfields/DESCRIPTION | 15 glmmfields-0.1.7/glmmfields/MD5 | 62 - glmmfields-0.1.7/glmmfields/NAMESPACE | 2 glmmfields-0.1.7/glmmfields/NEWS.md | 16 glmmfields-0.1.7/glmmfields/R/fitting.R | 21 glmmfields-0.1.7/glmmfields/R/predict.R | 12 glmmfields-0.1.7/glmmfields/R/stan_pars.R | 3 glmmfields-0.1.7/glmmfields/R/stanmodels.R | 56 - glmmfields-0.1.7/glmmfields/build/vignette.rds |binary glmmfields-0.1.7/glmmfields/configure |only glmmfields-0.1.7/glmmfields/configure.win |only glmmfields-0.1.7/glmmfields/inst/CITATION | 24 glmmfields-0.1.7/glmmfields/inst/doc/spatial-glms.R | 17 glmmfields-0.1.7/glmmfields/inst/doc/spatial-glms.Rmd | 18 glmmfields-0.1.7/glmmfields/inst/doc/spatial-glms.html | 399 +++++----- glmmfields-0.1.7/glmmfields/inst/include/stan_meta_header.hpp |only glmmfields-0.1.7/glmmfields/inst/stan |only glmmfields-0.1.7/glmmfields/man/glmmfields.Rd | 8 glmmfields-0.1.7/glmmfields/man/predict.Rd | 5 glmmfields-0.1.7/glmmfields/src/Makevars | 23 glmmfields-0.1.7/glmmfields/src/Makevars.win | 24 glmmfields-0.1.7/glmmfields/src/RcppExports.cpp |only glmmfields-0.1.7/glmmfields/src/stanExports_glmmfields.cc |only glmmfields-0.1.7/glmmfields/src/stanExports_glmmfields.h |only glmmfields-0.1.7/glmmfields/tests/testthat/test-fit-ar-processes.R | 64 + glmmfields-0.1.7/glmmfields/tests/testthat/test-fit-basic.R | 63 + glmmfields-0.1.7/glmmfields/tests/testthat/test-fit-observation-models.R | 8 glmmfields-0.1.7/glmmfields/tests/testthat/test-fit-with-predictors.R | 2 glmmfields-0.1.7/glmmfields/tests/testthat/test-predict.R | 11 glmmfields-0.1.7/glmmfields/tests/testthat/test-stations.R | 74 + glmmfields-0.1.7/glmmfields/vignettes/spatial-glms.Rmd | 18 37 files changed, 560 insertions(+), 385 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available
from several federated data sources (mainly sources maintained by the
US Federal government). Currently, the package enables extraction from
seven datasets: The National Elevation Dataset digital elevation
models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset
(USGS); The Soil Survey Geographic (SSURGO) database from the National
Cooperative Soil Survey (NCSS), which is led by the Natural Resources
Conservation Service (NRCS) under the USDA; the Global Historical
Climatology Network (GHCN), coordinated by National Climatic Data
Center at NOAA; the Daymet gridded estimates of daily weather
parameters for North America, version 3, available from the Oak Ridge
National Laboratory's Distributed Active Archive Center (DAAC); the
International Tree Ring Data Bank; and the National Land Cover
Database (NLCD).
Author: R. Kyle Bocinsky [aut, cre, cph],
Dylan Beaudette [ctb],
Scott Chamberlain [ctb, rev],
Jeffrey Hollister [ctb],
Julia Gustavsen [rev]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 3.0.2 dated 2023-02-25 and 3.0.3 dated 2023-03-10
DESCRIPTION | 8 +-- MD5 | 38 +++++++++--------- NEWS.md | 9 ++++ R/DAYMET_FUNCTIONS.R | 12 ++--- R/NASS_FUNCTIONS.R | 2 R/NED_FUNCTIONS.R | 57 ++++++++++++++-------------- R/NHD_FUNCTIONS.R | 25 +++++++----- R/NLCD_FUNCTIONS.R | 2 README.md | 2 man/figures/README-GHCN-precipitation-1.png |binary man/figures/README-GHCN-temperature-1.png |binary man/figures/README-NED-1.png |binary man/figures/README-SSURGO-1.png |binary man/figures/README-SSURGO-area-1.png |binary man/get_nass_cdl.Rd | 2 man/get_ned.Rd | 12 +---- man/get_ned_tile.Rd | 5 -- man/get_nhd.Rd | 2 man/get_nlcd.Rd | 2 man/get_wbd.Rd | 2 20 files changed, 95 insertions(+), 85 deletions(-)
Title: Species Distribution Modeling and Ecological Niche Modeling
Description: Implements species distribution modeling and ecological niche
modeling, including: bias correction, spatial cross-validation, model
evaluation, raster interpolation, biotic "velocity" (speed and
direction of movement of a "mass" represented by a raster), interpolating
across a time series of rasters, and use of spatially imprecise records.
The heart of the package is a set of "training" functions which
automatically optimize model complexity based number of available
occurrences. These algorithms include MaxEnt, MaxNet, boosted regression
trees/gradient boosting machines, generalized additive models,
generalized linear models, natural splines, and random forests. To enhance
interoperability with other modeling packages, no new classes are created.
The package works with 'PROJ6' geodetic objects and coordinate reference
systems.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between enmSdmX versions 1.0.2 dated 2023-03-04 and 1.0.3 dated 2023-03-10
DESCRIPTION | 10 MD5 | 88 ++--- NEWS.md | 37 +- R/bioticVelocity.r | 4 R/enmSdmX.r | 2 R/geoFold.r | 8 R/geoThin.r | 4 R/globalx.r | 4 R/predictEnmSdm.r | 2 R/predictMaxNet.r | 2 R/trainBRT.r | 2 R/trainMaxEnt.r | 3 R/trainNS.r | 2 R/weightByDist.r | 4 man/bioticVelocity.Rd | 4 man/crss.Rd | 70 ++-- man/enmSdmX.Rd | 248 +++++++-------- man/evalAUC.Rd | 112 +++---- man/evalContBoyce.Rd | 250 +++++++-------- man/evalMultiAUC.Rd | 106 +++--- man/evalTSS.Rd | 150 ++++----- man/evalThreshold.Rd | 148 ++++----- man/evalThresholdStats.Rd | 160 +++++----- man/evalTjursR2.Rd | 118 +++---- man/examples/customCRS_examples.r | 2 man/examples/trainXYZ_examples.r | 4 man/geoFold.Rd | 8 man/geoThin.Rd | 4 man/globalx.Rd | 4 man/lemurs.Rd | 48 +-- man/mad0.Rd | 54 +-- man/mad1.Rd | 54 +-- man/predictEnmSdm.Rd | 524 ++++++++++++++++----------------- man/predictMaxEnt.Rd | 558 +++++++++++++++++------------------ man/predictMaxNet.Rd | 524 ++++++++++++++++----------------- man/summaryByCrossValid.Rd | 426 +++++++++++++------------- man/trainBRT.Rd | 6 man/trainByCrossValid.Rd | 504 +++++++++++++++---------------- man/trainGAM.Rd | 4 man/trainGLM.Rd | 4 man/trainMaxEnt.Rd | 600 +++++++++++++++++++------------------- man/trainMaxNet.Rd | 572 ++++++++++++++++++------------------ man/trainNS.Rd | 6 man/trainRF.Rd | 4 man/weightByDist.Rd | 4 45 files changed, 2731 insertions(+), 2721 deletions(-)
Title: Dose Titration Algorithm Tuning
Description: Dose Titration Algorithm Tuning (DTAT) is a methodologic framework
allowing dose individualization to be conceived as a continuous
learning process that begins in early-phase clinical trials and
continues throughout drug development, on into clinical practice.
This package includes code that researchers may use to reproduce
or extend key results of the DTAT research programme, plus tools
for trialists to design and simulate a '3+3/PC' dose-finding study.
Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and
Norris (2017c) <doi:10.1101/240846>.
Author: David C. Norris [aut, cre]
Maintainer: David C. Norris <david@precisionmethods.guru>
Diff between DTAT versions 0.3-4 dated 2020-06-14 and 0.3-5 dated 2023-03-10
DTAT-0.3-4/DTAT/inst/doc/widget_D3-viz.html |only DTAT-0.3-4/DTAT/inst/shiny-apps/Sim33PC/rsconnect |only DTAT-0.3-4/DTAT/inst/shiny-apps/TheCost/rsconnect |only DTAT-0.3-5/DTAT/DESCRIPTION | 14 - DTAT-0.3-5/DTAT/LICENSE | 2 DTAT-0.3-5/DTAT/MD5 | 34 +-- DTAT-0.3-5/DTAT/R/AllClass.R | 4 DTAT-0.3-5/DTAT/R/DTAT-package.R | 71 +++--- DTAT-0.3-5/DTAT/build/partial.rdb |binary DTAT-0.3-5/DTAT/build/vignette.rds |binary DTAT-0.3-5/DTAT/inst/doc/DTAT-package.bib | 4 DTAT-0.3-5/DTAT/inst/doc/Designing-33PC.html | 227 ++++++++++++---------- DTAT-0.3-5/DTAT/inst/shiny-apps/Sim33PC/app.R | 12 - DTAT-0.3-5/DTAT/man/DTAT-package.Rd | 10 DTAT-0.3-5/DTAT/man/Onoue.Friberg.Rd | 4 DTAT-0.3-5/DTAT/man/de.bioRxiv.240846.Rd | 2 DTAT-0.3-5/DTAT/man/dtat1000.Rd | 7 DTAT-0.3-5/DTAT/man/titration.Rd | 2 DTAT-0.3-5/DTAT/vignettes/DTAT-package.bib | 4 19 files changed, 219 insertions(+), 178 deletions(-)
Title: Penalized Transformation Models
Description: Partially penalized versions of specific transformation models
implemented in package 'mlt'. Available models include a fully parametric version
of the Cox model, other parametric survival models (Weibull, etc.), models for
binary and ordered categorical variables, normal and transformed-normal (Box-Cox type)
linear models, and continuous outcome logistic regression. Hyperparameter tuning
is facilitated through model-based optimization functionalities from package 'mlrMBO'.
The accompanying vignette describes the methodology used in 'tramnet' in detail.
Transformation models and model-based optimization are described in
Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
Bischl et al. (2016) <arxiv:1703.03373>, respectively.
Author: Lucas Kook [cre, aut],
Balint Tamasi [ctb],
Sandra Siegfried [ctb],
Samuel Pawel [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramnet versions 0.0-7 dated 2022-08-22 and 0.0-8 dated 2023-03-10
tramnet-0.0-7/tramnet/cleanup |only tramnet-0.0-8/tramnet/DESCRIPTION | 12 - tramnet-0.0-8/tramnet/MD5 | 31 ++-- tramnet-0.0-8/tramnet/R/methods.R | 9 - tramnet-0.0-8/tramnet/inst/doc/tramnet.R | 114 ++++++++-------- tramnet-0.0-8/tramnet/inst/doc/tramnet.Rnw | 93 ++++++------- tramnet-0.0-8/tramnet/inst/doc/tramnet.pdf |binary tramnet-0.0-8/tramnet/man/cvl_tramnet.Rd | 19 +- tramnet-0.0-8/tramnet/man/estfun.tramnet.Rd | 4 tramnet-0.0-8/tramnet/man/plot_path.Rd | 26 +-- tramnet-0.0-8/tramnet/man/prof_alpha.Rd | 17 +- tramnet-0.0-8/tramnet/man/prof_lambda.Rd | 20 +- tramnet-0.0-8/tramnet/man/tramnet.Rd | 30 ++-- tramnet-0.0-8/tramnet/tests/Colr-pen.R | 60 ++++---- tramnet-0.0-8/tramnet/tests/Colr-pen.Rout.save | 161 ++++++++++++++--------- tramnet-0.0-8/tramnet/vignettes/kook-hothorn.bib | 22 +++ tramnet-0.0-8/tramnet/vignettes/tramnet.Rnw | 93 ++++++------- 17 files changed, 389 insertions(+), 322 deletions(-)
Title: Structurally Guided Sampling
Description: Structurally guided sampling (SGS) approaches for airborne laser scanning (ALS; LIDAR). Primary functions provide means
to generate data-driven stratifications & methods for allocating samples. Intermediate functions for calculating and extracting important information
about input covariates and samples are also included. Processing outcomes are intended to help forest and environmental management
practitioners better optimize field sample placement as well as assess and augment existing sample networks in the context of data
distributions and conditions. ALS data is the primary intended use case, however any rasterized remote sensing data can be used,
enabling data-driven stratifications and sampling approaches.
Author: Tristan RH Goodbody [aut, cre, cph]
,
Nicholas C Coops [aut] ,
Martin Queinnec [aut]
Maintainer: Tristan RH Goodbody <goodbody.t@gmail.com>
Diff between sgsR versions 1.4.0 dated 2023-02-09 and 1.4.2 dated 2023-03-10
DESCRIPTION | 6 MD5 | 153 ++- NAMESPACE | 4 NEWS.md | 22 R/calculate_allocation_existing.R |only R/calculate_coobs.R | 5 R/calculate_distance.R | 5 R/calculate_pcomp.R | 5 R/calculate_representation.R | 19 R/extract_metrics.R | 36 R/extract_strata.R | 42 R/sample_ahels.R | 27 R/sample_balanced.R | 18 R/sample_clhs.R | 18 R/sample_existing.R | 469 +--------- R/sample_existing_balanced.R |only R/sample_existing_clhs.R |only R/sample_existing_srs.R |only R/sample_existing_strat.R |only R/sample_nc.R | 19 R/sample_srs.R | 18 R/sample_strat.R | 14 R/sample_sys_strat.R | 18 R/sample_systematic.R | 18 R/strat_breaks.R | 6 R/strat_kmeans.R | 6 R/strat_map.R | 8 R/strat_poly.R | 17 R/strat_quantiles.R | 6 R/utils-allocation-existing.R |only R/utils-existing.R |only R/utils-write.R |only README.md | 4 inst/doc/calculating.html | 12 inst/doc/sampling.R | 43 inst/doc/sampling.Rmd | 105 +- inst/doc/sampling.html | 885 +++++++++++--------- inst/doc/sgsR.html | 4 inst/doc/stratification.html | 4 man/allocating.Rd | 107 +- man/calculate_allocation.Rd | 1 man/calculate_allocation_existing.Rd |only man/calculate_coobs.Rd | 1 man/calculate_distance.Rd | 1 man/calculate_pcomp.Rd | 1 man/calculate_pop.Rd | 1 man/calculate_representation.Rd | 8 man/calculate_sampsize.Rd | 1 man/check_existing.Rd |only man/coords_existing.Rd |only man/prepare_existing.Rd |only man/sample_ahels.Rd | 3 man/sample_existing.Rd | 47 - man/sample_existing_balanced.Rd |only man/sample_existing_clhs.Rd |only man/sample_existing_srs.Rd |only man/sample_existing_strat.Rd |only man/sample_sys_strat.Rd | 206 ++-- man/take_samples.Rd |only man/vectorize.Rd | 84 - man/write.Rd |only tests/testthat/setup-testthat.R | 7 tests/testthat/test-calculate_allocation_existing.R |only tests/testthat/test-calculate_distance.R | 2 tests/testthat/test-calculate_pcomp.R | 2 tests/testthat/test-calculate_represenation.R | 4 tests/testthat/test-extract_metrics.R | 13 tests/testthat/test-extract_strata.R | 19 tests/testthat/test-sample_ahels.R | 4 tests/testthat/test-sample_balanced.R | 8 tests/testthat/test-sample_clhs.R | 3 tests/testthat/test-sample_existing.R | 84 - tests/testthat/test-sample_existing_balanced.R |only tests/testthat/test-sample_existing_clhs.R |only tests/testthat/test-sample_existing_srs.R |only tests/testthat/test-sample_existing_strat.R |only tests/testthat/test-sample_nc.R | 3 tests/testthat/test-sample_srs.R | 3 tests/testthat/test-sample_strat.R | 2 tests/testthat/test-sample_sys_strat.R | 7 tests/testthat/test-sample_systematic.R | 3 tests/testthat/test-strat_breaks.R | 2 tests/testthat/test-strat_kmeans.R | 2 tests/testthat/test-strat_map.R | 3 tests/testthat/test-strat_poly.R | 3 tests/testthat/test-strat_quantiles.R | 2 tests/testthat/test-utils-existing.R |only tests/testthat/test-utils-plot.R | 1 tests/testthat/test-utils-write.R |only vignettes/sampling.Rmd | 105 +- 90 files changed, 1307 insertions(+), 1452 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut],
Marly Gotti [aut],
Eli Miller [cre, aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Meth [...truncated...]
Maintainer: Eli Miller <eli.miller@atorusresearch.com>
Diff between riskmetric versions 0.2.0 dated 2023-02-22 and 0.2.1 dated 2023-03-10
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 5 ++ R/pkg_metric_error.R | 2 - R/pkg_ref_class_format.R | 2 - R/vctrs_list_of_pkg_metric.R | 2 - inst/doc/extending-riskmetric.html | 65 +++++++++++++++++-------------------- inst/doc/riskmetric.html | 57 +++++++++++++++----------------- 8 files changed, 76 insertions(+), 77 deletions(-)
Title: Unofficial API for Fedstat (Rosstat EMISS System) for Automatic
and Efficient Data Queries
Description: An API for automatic data queries to the fedstat <https://www.fedstat.ru>, using a small set of functions with a common interface.
Author: Denis Krylov [aut, cre],
Dmitry Kibalnikov [aut]
Maintainer: Denis Krylov <deniskrylovvit@gmail.com>
Diff between fedstatAPIr versions 0.2.0 dated 2022-01-14 and 1.0.0 dated 2023-03-10
fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_check_data_update.R |only fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_check_data_update_.R |only fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_get_data_ids_special_cases_handle.R |only fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_java_script_data_ids_parse_to_json.R |only fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_java_script_default_data_ids_object_ids_parse_to_json.R |only fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_parse_all_indicators_names.R |only fedstatAPIr-0.2.0/fedstatAPIr/R/fedstat_prepare_reference_data_for_check_data_update.R |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_check_data_update.Rd |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_check_data_update_.Rd |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_get_data_ids_special_cases_handle.Rd |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_java_script_data_ids_parse_to_json.Rd |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_java_script_default_data_ids_object_ids_parse_to_json.Rd |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_parse_all_indicators_names.Rd |only fedstatAPIr-0.2.0/fedstatAPIr/man/fedstat_prepare_reference_data_for_check_data_update.Rd |only fedstatAPIr-1.0.0/fedstatAPIr/DESCRIPTION | 26 - fedstatAPIr-1.0.0/fedstatAPIr/LICENSE | 2 fedstatAPIr-1.0.0/fedstatAPIr/MD5 | 57 +- fedstatAPIr-1.0.0/fedstatAPIr/NAMESPACE | 35 - fedstatAPIr-1.0.0/fedstatAPIr/NEWS.md | 23 fedstatAPIr-1.0.0/fedstatAPIr/R/fedstatAPIr-package.R |only fedstatAPIr-1.0.0/fedstatAPIr/R/fedstatAPIr.R | 5 fedstatAPIr-1.0.0/fedstatAPIr/R/fedstat_data_ids_filter.R | 249 ++++------ fedstatAPIr-1.0.0/fedstatAPIr/R/fedstat_data_load_with_filters.R | 52 +- fedstatAPIr-1.0.0/fedstatAPIr/R/fedstat_get_data_ids.R | 116 +--- fedstatAPIr-1.0.0/fedstatAPIr/R/fedstat_indicator_info.R |only fedstatAPIr-1.0.0/fedstatAPIr/R/fedstat_parse_sdmx_to_table.R | 157 ++---- fedstatAPIr-1.0.0/fedstatAPIr/R/fedstat_post_data_ids_filtered.R | 106 +--- fedstatAPIr-1.0.0/fedstatAPIr/R/parse_js1.R |only fedstatAPIr-1.0.0/fedstatAPIr/R/parse_js2.R |only fedstatAPIr-1.0.0/fedstatAPIr/R/utils.R | 18 fedstatAPIr-1.0.0/fedstatAPIr/README.md | 125 ++--- fedstatAPIr-1.0.0/fedstatAPIr/man/fedstatAPIr-package.Rd | 67 +- fedstatAPIr-1.0.0/fedstatAPIr/man/fedstat_data_ids_filter.Rd | 18 fedstatAPIr-1.0.0/fedstatAPIr/man/fedstat_data_load_with_filters.Rd | 36 - fedstatAPIr-1.0.0/fedstatAPIr/man/fedstat_get_data_ids.Rd | 166 +++--- fedstatAPIr-1.0.0/fedstatAPIr/man/fedstat_indicator_info.Rd |only fedstatAPIr-1.0.0/fedstatAPIr/man/fedstat_parse_sdmx_to_table.Rd | 32 - fedstatAPIr-1.0.0/fedstatAPIr/man/fedstat_post_data_ids_filtered.Rd | 20 fedstatAPIr-1.0.0/fedstatAPIr/man/parse_js1.Rd |only fedstatAPIr-1.0.0/fedstatAPIr/man/parse_js2.Rd |only 40 files changed, 615 insertions(+), 695 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.40.6-2 dated 2022-12-01 and 1.42.9 dated 2023-03-10
DESCRIPTION | 8 MD5 | 33 NEWS.md | 6 R/ggplot_as_list.R | 129 README.md | 3 build/vignette.rds |binary inst/doc/additional_examples.html | 4 inst/doc/getting_started.html | 4 inst/htmlwidgets/canvasXpress.js | 34 inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 2393 ++++++++++-------- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 8 inst/ui-examples/cX-function.R.gz |binary tests/testthat/setup.R | 3 tests/testthat/test-other-decorations.R | 22 tests/testthat/test-ui-correlation.R | 4 tests/testthat/test-ui-nonlinearfit.R | 20 tests/testthat/test-ui-upset.R |only 18 files changed, 1530 insertions(+), 1143 deletions(-)
Title: Edit an 'Antares' Simulation
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal
clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings.
'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Author: Veronique Bachelier [aut, cre],
Frederic Breant [aut],
Victor Perrier [aut],
Baptiste Seguinot [ctb],
Benoit Thieurmel [ctb],
Titouan Robert [ctb],
Jalal-Edine Zawam [ctb],
Etienne Sanchez [ctb],
Janus De Bondt [ctb],
Assil Mansouri [ctb],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between antaresEditObject versions 0.4.0 dated 2022-12-06 and 0.5.0 dated 2023-03-10
DESCRIPTION | 13 + MD5 | 53 ++++-- NAMESPACE | 12 + NEWS.md | 31 ++++ R/API.R | 4 R/cleanUpOutput.R |only R/computeTimeStampFromHourly.R | 2 R/computeTimeStepFromHourly.R |only R/createCluster.R | 7 R/editArea.R | 2 R/editCluster.R | 32 +++- R/playlist.R | 9 + R/updateAdequacySettings.R | 75 +++++++++ R/writeAntaresOutput.R | 27 ++- R/writeOutput.R | 82 +++++++++- R/zzz.R | 5 inst/doc/api-variant-management.R | 22 +- inst/doc/api-variant-management.Rmd | 2 inst/doc/api-variant-management.html | 153 ++++++++++---------- inst/doc/scenario-builder.html | 74 ++++++--- man/cleanUpOutput.Rd |only man/computeOtherFromHourlyMulti.Rd |only man/computeOtherFromHourlyYear.Rd |only man/computeTimeStampFromHourly.Rd | 3 man/convertConfigToAdq.Rd |only man/dot-dailyToWeekly.Rd |only man/dot-hourlyToOther.Rd |only man/updateAdequacySettings.Rd | 18 ++ tests/testthat/test-computeTimeStepFromHourly.R |only tests/testthat/test-compute_timeStamp_from_hourly.R | 36 ++-- tests/testthat/test-updateAdequacyPatch.R | 35 ++-- vignettes/api-variant-management.Rmd | 2 32 files changed, 487 insertions(+), 212 deletions(-)
More information about antaresEditObject at CRAN
Permanent link
Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data.
The namesake function mrbin() converts 1D
or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time. The function fia() ranks features according
to their impact on classifier models, especially artificial neural network models.
Author: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <matthias.s.klein@gmx.net>
Diff between mrbin versions 1.7.2 dated 2023-01-23 and 1.7.3 dated 2023-03-10
DESCRIPTION | 10 - MD5 | 32 +-- NEWS.md | 13 + R/mrbin.R | 459 +++++++++++++++++++++++++++------------------- build/vignette.rds |binary inst/CITATION | 4 inst/doc/mrbin.R | 1 inst/doc/mrbin.Rnw | 2 inst/doc/mrbin.pdf |binary inst/extdata/1/10/acqu |only inst/extdata/1/12/acqu |only inst/extdata/2/10/acqu |only inst/extdata/2/12/acqu |only inst/extdata/3/10/acqu |only inst/extdata/3/12/acqu |only man/fia.Rd | 7 man/plotResults.Rd | 4 man/setDilutionFactors.Rd | 5 man/setNoiseLevels.Rd | 9 vignettes/mrbin.Rnw | 2 20 files changed, 337 insertions(+), 211 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford [aut, cre] ,
Ian Durbach [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrdesign versions 2.8.0 dated 2023-01-18 and 2.8.2 dated 2023-03-10
DESCRIPTION | 10 ++++----- MD5 | 36 ++++++++++++++++++----------------- NAMESPACE | 7 +++++- NEWS | 17 ++++++++++++++++ R/En2.R | 2 - R/Lambda.R | 2 - R/Qpm.R | 2 - R/estimateSummary.R |only R/getdetectpar.R | 2 - R/methods.R | 34 ++++++++++++++++++--------------- R/optimalSpacing.R | 2 - R/run.scenarios.R | 39 +++++++++++++++++++++++++++++++++----- R/saturation.R | 2 - R/scenarioSummary.R | 6 ++--- R/utility.R | 4 +-- inst/CITATION | 5 ++-- man/estimateSummary.Rd |only man/run.scenarios.Rd | 46 ++++++++++++++++++++++++++++++++++++++++++--- man/secrdesign-package.Rd | 4 +-- man/summary.simulations.Rd | 9 ++++++-- 20 files changed, 166 insertions(+), 63 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Damir Pulatov [cre, aut],
Michel Lang [aut]
Maintainer: Damir Pulatov <damirpolat@protonmail.com>
Diff between mlr3cluster versions 0.1.6 dated 2022-12-22 and 0.1.7 dated 2023-03-10
mlr3cluster-0.1.6/mlr3cluster/man/mlr_measures_clust.db.Rd |only mlr3cluster-0.1.6/mlr3cluster/tests/testthat/test_unload.R |only mlr3cluster-0.1.7/mlr3cluster/DESCRIPTION | 8 mlr3cluster-0.1.7/mlr3cluster/MD5 | 26 +-- mlr3cluster-0.1.7/mlr3cluster/NAMESPACE | 4 mlr3cluster-0.1.7/mlr3cluster/NEWS.md | 5 mlr3cluster-0.1.7/mlr3cluster/R/MeasureClustInternal.R | 83 ++++++---- mlr3cluster-0.1.7/mlr3cluster/R/measures.R | 4 mlr3cluster-0.1.7/mlr3cluster/R/zzz.R | 14 - mlr3cluster-0.1.7/mlr3cluster/README.md | 9 - mlr3cluster-0.1.7/mlr3cluster/man/mlr_measures_clust.ch.Rd | 34 ---- mlr3cluster-0.1.7/mlr3cluster/man/mlr_measures_clust.dunn.Rd | 5 mlr3cluster-0.1.7/mlr3cluster/man/mlr_measures_clust.silhouette.Rd | 5 mlr3cluster-0.1.7/mlr3cluster/man/mlr_measures_clust.wss.Rd | 5 mlr3cluster-0.1.7/mlr3cluster/tests/testthat/helper_mlr3.R | 2 15 files changed, 97 insertions(+), 107 deletions(-)
Title: Create Interactive Web Maps with the JavaScript 'Leaflet'
Library
Description: Create and customize interactive maps using the 'Leaflet'
JavaScript library and the 'htmlwidgets' package. These maps can be used
directly from the R console, from 'RStudio', in Shiny applications and R Markdown
documents.
Author: Joe Cheng [aut, cre],
Bhaskar Karambelkar [aut],
Yihui Xie [aut],
Hadley Wickham [ctb],
Kenton Russell [ctb],
Kent Johnson [ctb],
Barret Schloerke [ctb],
jQuery Foundation and contributors [ctb, cph] ,
Vladimir Agafonkin [ctb, cph] ,
CloudMade [cph] [...truncated...]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between leaflet versions 2.1.1 dated 2022-03-25 and 2.1.2 dated 2023-03-10
DESCRIPTION | 8 +++---- MD5 | 50 ++++++++++++++++++++++++------------------------ NEWS | 11 ++++++++-- R/layers.R | 18 ++++++++--------- R/leaflet.R | 2 - R/mapPane.R | 2 - R/methods.R | 4 +-- R/normalize-sp.R | 23 +++++++++++----------- R/plugin-graticule.R | 2 - R/plugin-measure.R | 4 +-- R/plugin-minimap.R | 4 +-- R/plugin-providers.R | 2 - R/scalebar.R | 2 - man/addGraticule.Rd | 2 - man/addLayersControl.Rd | 2 - man/addMapPane.Rd | 2 - man/addMeasure.Rd | 4 +-- man/addMiniMap.Rd | 8 +++---- man/addProviderTiles.Rd | 2 - man/addScaleBar.Rd | 2 - man/easyButton.Rd | 8 +++---- man/leaflet.Rd | 8 +++---- man/makeIcon.Rd | 24 ++++------------------- man/map-layers.Rd | 32 +++++++++++++++--------------- man/map-methods.Rd | 18 ++++++++--------- man/map-options.Rd | 30 ++++++++++++++-------------- 26 files changed, 134 insertions(+), 140 deletions(-)
Title: Plots for Visualizing the Data Produced by the 'irace' Package
Description: Graphical visualization tools for analyzing the data produced by 'irace'. The 'iraceplot' package enables users to analyze the performance and the parameter space data sampled by the configuration during the search process. It provides a set of functions that generate different plots to visualize the configurations sampled during the execution of 'irace' and their performance. The functions just require the log file generated by 'irace' and, in some cases, they can be used with user-provided data.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Pablo Onate Marin [aut],
Leslie Perez Caceres [aut]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between iraceplot versions 1.0 dated 2022-12-19 and 1.1 dated 2023-03-10
DESCRIPTION | 14 +- MD5 | 44 ++++---- NAMESPACE | 9 + NEWS.md | 7 + R/ablation_plot.R |only R/boxplot_performance.R | 25 ++-- R/common.R | 1 R/configurations_display.R | 2 R/iraceplot-package.R | 4 R/plot_model.R | 2 R/reexport.R | 9 + R/sampling_frequency_iteration.R | 4 R/sampling_heatmap.R | 4 R/summarise_by_configuration.R |only README.md | 56 +++++----- build/vignette.rds |binary inst/doc/iraceplot_package.R | 9 - inst/doc/iraceplot_package.Rmd | 49 --------- inst/doc/iraceplot_package.html | 141 ++++++++++++++------------- inst/exdata/log-ablation-autoMOPSODTLZ.Rdata |only inst/template/report_html.Rmd | 20 +-- man/ablation_plot.Rd |only man/boxplot_performance.Rd | 4 man/read_ablogfile.Rd |only man/summarise_by_configuration.Rd |only vignettes/iraceplot_package.Rmd | 49 --------- 26 files changed, 196 insertions(+), 257 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including 'BLACS', 'PBLAS', and 'ScaLAPACK' in double precision via
'pbdMPI' based on 'ScaLAPACK' version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.3-3 dated 2022-10-26 and 0.3-4 dated 2023-03-10
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/CITATION | 24 ++++++++++++------------ src/BLACS/BI_BlacsErr.c | 3 ++- src/BLACS/BI_BlacsWarn.c | 3 ++- src/PBLAS/PTOOLS/PB_Cwarn.c | 3 ++- 7 files changed, 33 insertions(+), 25 deletions(-)
Title: Generalized Multipartite Networks
Description: We define generalized multipartite networks as the joint observation of several networks implying some common pre-specified groups of individuals. The aim is to fit an adapted version of the popular stochastic block model to multipartite networks, as described in Bar-hen, Barbillon and Donnet (2020) <arXiv:1807.10138>.
Author: Sophie Donnet [aut, cre] ,
Pierre Barbillon [aut]
Maintainer: Sophie Donnet <sophie.donnet@inrae.fr>
Diff between GREMLINS versions 0.2.0 dated 2020-11-25 and 0.2.1 dated 2023-03-10
GREMLINS-0.2.0/GREMLINS/R/plotMBM.R |only GREMLINS-0.2.0/GREMLINS/man/plotMBM.Rd |only GREMLINS-0.2.1/GREMLINS/DESCRIPTION | 18 GREMLINS-0.2.1/GREMLINS/MD5 | 44 GREMLINS-0.2.1/GREMLINS/NAMESPACE | 1 GREMLINS-0.2.1/GREMLINS/NEWS.md |only GREMLINS-0.2.1/GREMLINS/R/BMPOO.R | 4 GREMLINS-0.2.1/GREMLINS/R/GREMLINS_package.R | 1 GREMLINS-0.2.1/GREMLINS/R/multipartiteBM.R | 1 GREMLINS-0.2.1/GREMLINS/R/multipartiteBMFixedModel.R | 6 GREMLINS-0.2.1/GREMLINS/README.md | 33 GREMLINS-0.2.1/GREMLINS/build/vignette.rds |binary GREMLINS-0.2.1/GREMLINS/inst/doc/EcologicalNetwork.R | 5 GREMLINS-0.2.1/GREMLINS/inst/doc/EcologicalNetwork.Rmd | 8 GREMLINS-0.2.1/GREMLINS/inst/doc/EcologicalNetwork.html | 735 +++++--- GREMLINS-0.2.1/GREMLINS/inst/doc/Introduction.html | 647 +++++-- GREMLINS-0.2.1/GREMLINS/inst/doc/SimulatedNetwork.R | 2 GREMLINS-0.2.1/GREMLINS/inst/doc/SimulatedNetwork.Rmd | 4 GREMLINS-0.2.1/GREMLINS/inst/doc/SimulatedNetwork.html | 833 ++++++---- GREMLINS-0.2.1/GREMLINS/inst/plotMBM.R |only GREMLINS-0.2.1/GREMLINS/man/GREMLINS.Rd | 1 GREMLINS-0.2.1/GREMLINS/vignettes/EcologicalNetwork.Rmd | 8 GREMLINS-0.2.1/GREMLINS/vignettes/SimulatedNetwork.Rmd | 4 GREMLINS-0.2.1/GREMLINS/vignettes/biblio.bib | 2 GREMLINS-0.2.1/GREMLINS/vignettes/man/figures/README-plot-1.png |binary 25 files changed, 1470 insertions(+), 887 deletions(-)
Title: Build 'Docker Images' in 'Amazon SageMaker Studio' using 'Amazon
Web Service CodeBuild'
Description: Allows users to easily build custom 'docker images' <https://docs.docker.com/> from
'Amazon Web Service Sagemaker' <https://aws.amazon.com/sagemaker/> using
'Amazon Web Service CodeBuild' <https://aws.amazon.com/codebuild/>.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between smdocker versions 0.1.1 dated 2023-03-01 and 0.1.2 dated 2023-03-10
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 6 + R/builder.R | 4 - R/code_build.R | 1 R/main.R | 5 - R/sm_role.R | 15 +++- README.md | 9 ++ man/sm_build.Rd | 2 tests/testthat/test-sm-role.R | 139 +++++++++++++++++++++++++++++++++++++++++- 10 files changed, 184 insertions(+), 23 deletions(-)
Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] ,
Chao Cheng [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>
Diff between SASmarkdown versions 0.8.1 dated 2023-02-03 and 0.8.2 dated 2023-03-10
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- R/find_sas.r | 6 +++--- R/misc.r | 2 +- man/find_sas.Rd | 27 ++++++++++++++++----------- man/sas_collectcode.Rd | 32 +++++++++++++++++++------------- man/sas_enginesetup.rd | 11 ++++++++--- man/sas_output.Rd | 14 +++++++++----- man/saslog_hookset.rd | 12 ++++++++---- 9 files changed, 77 insertions(+), 52 deletions(-)
Title: Interface to the National Lakes Assessment
Description: Client for programmatic access to the 2007 and 2012 National
Lakes Assessment database <https://www.epa.gov/national-aquatic-resource-surveys/nla>
containing data for hundreds of lakes in the lower 48 states of the contiguous US.
Author: Jemma Stachelek [aut, cre]
Maintainer: Jemma Stachelek <jemma.stachelek@gmail.com>
Diff between nlaR versions 0.4.0 dated 2019-01-22 and 0.4.1 dated 2023-03-10
DESCRIPTION | 18 ++++++------- MD5 | 32 +++++++++++++----------- NEWS.md | 11 ++++---- R/compile.R | 41 +++++++++++-------------------- R/get.R | 23 +++++++++++++---- R/load.R | 27 +++++++++++++------- R/nlaR-package.R | 2 - R/utils.R | 6 +++- README.md | 48 ++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/comparison_2007-2012.html | 4 +-- inst/doc/summary_2012.html | 4 +-- man/nlaR-package.Rd | 1 man/nla_compile.Rd | 7 ++++- man/nla_get.Rd | 9 ++++++ man/nla_load.Rd | 6 ++-- tests |only 17 files changed, 138 insertions(+), 101 deletions(-)
Title: Adaptive Smoothing of Digital Images
Description: Implements tools for manipulation of digital
images and the Propagation Separation approach
by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1>
for smoothing digital images, see Polzehl and Tabelow (2007)
<DOI:10.18637/jss.v019.i01>.
Author: Karsten Tabelow <tabelow@wias-berlin.de>,
Joerg Polzehl <polzehl@wias-berlin.de>
Maintainer: Karsten Tabelow <tabelow@wias-berlin.de>
Diff between adimpro versions 0.9.3 dated 2021-01-11 and 0.9.5 dated 2023-03-10
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/aniso.r | 4 ++-- R/io2.R | 20 ++++++++++++++------ R/misc.r | 10 +++++++--- inst/CITATION | 32 +++++++++++++++----------------- 6 files changed, 49 insertions(+), 39 deletions(-)
Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre],
Daniel Herszenhut [aut] ,
Mark Padgham [aut],
Tom Buckley [aut],
Danton Noriega-Goodwin [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between tidytransit versions 1.4.1 dated 2023-02-01 and 1.5.0 dated 2023-03-10
DESCRIPTION | 10 MD5 | 61 ++-- NAMESPACE | 5 R/dates.R |only R/frequencies.R | 2 R/globals.R | 3 R/io.R | 17 - R/raptor.R | 16 - R/spatial.R | 11 R/spec.R | 496 ++++++++++++++++++--------------- R/tidygtfs.R | 86 ++++- R/time.R | 218 ++------------ R/travel_times.R | 4 R/utils.R | 13 R/validate_gtfs.R | 114 ++++--- inst/doc/frequency.html | 32 +- inst/doc/introduction.html | 56 +-- inst/doc/servicepatterns.html | 68 ++-- inst/doc/timetable.html | 115 +++---- inst/extdata/routing-NA-times.zip |only inst/extdata/routing.zip_gtfstools.rds |only man/as_tidygtfs.Rd |only man/duplicated_primary_keys.Rd |only man/get_stop_frequency.Rd | 2 man/gtfs_to_tidygtfs.Rd |only man/hhmmss_to_hms.Rd |only man/hhmmss_to_sec_split.Rd |only man/hhmmss_to_seconds.Rd |only man/raptor.Rd | 13 man/read_gtfs.Rd | 8 man/set_dates_services.Rd | 2 man/travel_times.Rd | 2 man/validate_gtfs.Rd | 18 - tests/testthat/test-as_tidygtfs.R |only tests/testthat/test-raptor.R | 65 ++-- tests/testthat/test-read-gtfs.R | 45 ++ tests/testthat/test-validate.R |only 37 files changed, 790 insertions(+), 692 deletions(-)
Title: Testing for Symmetry of Data and Model Residuals
Description: Implementations of a large number of tests for symmetry and their
bootstrap variants, which can be used for testing the symmetry of random
samples around a known or unknown mean. Functions are also there for testing
the symmetry of model residuals around zero. Currently, the supported models
are linear models and generalized autoregressive conditional
heteroskedasticity (GARCH) models (fitted with the 'fGarch' package). All
tests are implemented using the 'Rcpp' package which ensures great
performance of the code.
Author: Blagoje Ivanovic [aut, cre]
Bojana Milosevic [aut]
Marko Obradovic [aut]
Maintainer: Blagoje Ivanovic <blagoje.ivanovic@matf.bg.ac.rs>
Diff between symmetry versions 0.2.2 dated 2022-08-08 and 0.2.3 dated 2023-03-10
DESCRIPTION | 13 ++++++------- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/partial.rdb |binary src/bootstrap.cpp | 2 +- 5 files changed, 15 insertions(+), 12 deletions(-)
Title: ROC Curve Inference with and without Covariates
Description: Estimates the pooled (unadjusted) Receiver Operating Characteristic (ROC) curve, the covariate-adjusted ROC (AROC) curve, and the covariate-specific/conditional ROC (cROC) curve by different methods, both Bayesian and frequentist. Also, it provides functions to obtain ROC-based optimal cutpoints utilizing several criteria. Based on Erkanli, A. et al. (2006) <doi:10.1002/sim.2496>; Faraggi, D. (2003) <doi:10.1111/1467-9884.00350>; Gu, J. et al. (2008) <doi:10.1002/sim.3366>; Inacio de Carvalho, V. et al. (2013) <doi:10.1214/13-BA825>; Inacio de Carvalho, V., and Rodriguez-Alvarez, M.X. (2018) <arXiv:1806.00473>; Janes, H., and Pepe, M.S. (2009) <doi:10.1093/biomet/asp002>; Pepe, M.S. (1998) <http://www.jstor.org/stable/2534001?seq=1>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1016/j.csda.2010.07.018>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1007/s11222-010-9184-1>. Please see Rodriguez-Alvarez, M.X. and Inacio, V. (20208) [...truncated...]
Author: Maria Xose Rodriguez-Alvarez [aut, cre]
,
Vanda Inacio [aut]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@uvigo.es>
Diff between ROCnReg versions 1.0-7 dated 2021-12-20 and 1.0-8 dated 2023-03-10
DESCRIPTION | 8 ++++---- MD5 | 28 +++++++++++++++++++--------- NEWS | 4 ++++ R/compute.threshold.TPF.bnp.R |only R/compute.threshold.TPF.cROC.bnp.R |only R/compute.threshold.TPF.cROC.kernel.R |only R/compute.threshold.TPF.cROC.sp.R |only R/compute.threshold.TPF.kernel.R |only R/compute.threshold.TPF.pooledROC.BB.R |only R/compute.threshold.TPF.pooledROC.dpm.R |only R/compute.threshold.TPF.pooledROC.emp.R |only R/compute.threshold.TPF.pooledROC.kernel.R |only R/compute.threshold.TPF.sp.R |only R/compute.threshold.cROC.R | 10 ++++++++-- R/compute.threshold.pooledROC.R | 9 +++++++-- build/partial.rdb |binary inst/CITATION | 5 ++--- man/ROCnReg-package.Rd | 4 ++-- man/compute.threshold.cROC.Rd | 19 +++++++++++-------- man/compute.threshold.pooledROC.Rd | 15 +++++++++------ 20 files changed, 66 insertions(+), 36 deletions(-)
Title: An Simplified Implementation of the 'network' Package
Functionality
Description: An implementation of some of the core 'network' package functionality based on a
simplified data structure that is faster in many research applications. This package is designed
for back-end use in the 'statnet' family of packages, including 'EpiModel'. Support is provided for
binary and weighted, directed and undirected, bipartite and unipartite networks; no current
support for multigraphs, hypergraphs, or loops.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Adrien Le Guillou [aut],
Chad Klumb [aut],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between networkLite versions 1.0.1 dated 2023-01-25 and 1.0.5 dated 2023-03-10
DESCRIPTION | 8 ++--- MD5 | 13 ++++----- NEWS.md |only R/constructors.R | 54 ++++++++++++++++---------------------- R/networkLite-package.R | 4 +- man/constructors.Rd | 52 ++++++++++++++++-------------------- man/networkLite-package.Rd | 4 +- tests/testthat/test-networkLite.R | 11 +++++++ 8 files changed, 72 insertions(+), 74 deletions(-)
Title: Management of Survey Data and Presentation of Analysis Results
Description: An infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) 'SPSS' and
'Stata' files is provided. Further, the package allows to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to 'LaTeX' and HTML.
Author: Martin Elff
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.99.31.3 dated 2022-10-04 and 0.99.31.6 dated 2023-03-10
memisc-0.99.31.3/memisc/man/syntactic-sugar.Rd |only memisc-0.99.31.6/memisc/DESCRIPTION | 12 +-- memisc-0.99.31.6/memisc/MD5 | 30 ++++--- memisc-0.99.31.6/memisc/NAMESPACE | 8 ++ memisc-0.99.31.6/memisc/R/assign-if.R |only memisc-0.99.31.6/memisc/R/coarsen.R | 2 memisc-0.99.31.6/memisc/R/contrasts.R | 62 ++++++++++++---- memisc-0.99.31.6/memisc/R/dataset-methods.R | 15 +++ memisc-0.99.31.6/memisc/R/within-operators.R |only memisc-0.99.31.6/memisc/build/vignette.rds |binary memisc-0.99.31.6/memisc/inst/ChangeLog | 15 +++ memisc-0.99.31.6/memisc/inst/NEWS.Rd | 6 + memisc-0.99.31.6/memisc/inst/doc/anes48.html | 23 +++++ memisc-0.99.31.6/memisc/inst/doc/items.html | 2 memisc-0.99.31.6/memisc/man/assign-if.Rd |only memisc-0.99.31.6/memisc/man/attr-operators.Rd |only memisc-0.99.31.6/memisc/man/within-operators.Rd |only memisc-0.99.31.6/memisc/src/pspp-portableStream-for-R.c | 15 +++ memisc-0.99.31.6/memisc/src/pspp-system-for-R.c | 6 - 19 files changed, 151 insertions(+), 45 deletions(-)
Title: Analysis of fMRI Experiments
Description: Contains R-functions to perform an fMRI analysis as described in
Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>,
Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>,
Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>,
Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Brandon Whitcher [ctb],
Dames Sibylle [ctb]
Maintainer: Karsten Tabelow <tabelow@wias-berlin.de>
Diff between fmri versions 1.9.6 dated 2021-01-12 and 1.9.11 dated 2023-03-10
DESCRIPTION | 16 +-- MD5 | 64 +++++++------- NAMESPACE | 3 R/cluster.R | 216 ++++++++++++++++++++++++++++++++++++------------ R/detrend.R | 4 R/fmri.R | 7 - R/io.R | 10 +- R/lmslicetime.R | 13 +- R/misc.r | 2 R/plot.r | 27 ++++-- R/searchlight.r | 4 R/utilities.r | 14 +-- R/view23D.r | 2 inst/CITATION | 98 ++++++++++----------- man/ICAfingerprint.Rd | 4 man/cutroi.Rd | 2 man/fmri.cluster.Rd | 27 ++++-- man/fmri.detrend.Rd | 2 man/fmri.lm.Rd | 12 +- man/fmri.metaPar.Rd | 2 man/fmri.pvalue.Rd | 6 - man/fmri.searchlight.Rd | 2 man/fmri.sgroupICA.Rd | 4 man/fmri.smooth.Rd | 8 - man/fmri.stimulus.Rd | 2 man/plot.fmriICA.Rd | 10 +- man/plot.fmridata.Rd | 4 man/read.NIFTI.Rd | 6 - man/slicetiming.Rd | 6 - man/write.AFNI.Rd | 8 - man/write.ANALYZE.Rd | 2 man/write.NIFTI.Rd | 6 - src/clusterthresh.f | 11 +- 33 files changed, 369 insertions(+), 235 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Sta [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut],
Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.2.2 dated 2023-02-03 and 1.3.0 dated 2023-03-10
DESCRIPTION | 10 +-- MD5 | 51 ++++++++------- NAMESPACE | 4 - NEWS.md | 7 ++ R/heat_plot.R |only R/plot.SMCMallows.R | 3 R/smc_post_processing_functions.R | 36 ++++++++-- build/partial.rdb |binary inst/doc/SMC-Mallows.R | 2 inst/doc/SMC-Mallows.Rmd | 2 inst/doc/SMC-Mallows.html | 4 - inst/examples/heat_plot_example.R |only inst/examples/smc_post_processing_functions_example.R |only man/compute_posterior_intervals_alpha.Rd | 59 +++++++++++++++++- man/compute_posterior_intervals_rho.Rd | 59 +++++++++++++++++- man/compute_rho_consensus.Rd | 59 +++++++++++++++++- man/heat_plot.Rd |only man/smc_processing.Rd | 10 ++- src/misc.cpp | 15 ++++ src/misc.h | 1 src/smc_mallows_new_item_rank.cpp | 16 ++-- src/smc_mallows_new_users.cpp | 9 +- src/smc_mallows_new_users_funs.cpp | 7 -- src/test-leapandshift.cpp | 2 src/test-misc.cpp |only tests/testthat/test-heat_plot.R |only tests/testthat/test-smc_mallows_new_item_rank.R | 4 - tests/testthat/test-smc_post_processing.R |only tests/testthat/test-smc_updated_new_item_rank.R | 2 vignettes/SMC-Mallows.Rmd | 2 30 files changed, 288 insertions(+), 76 deletions(-)
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre] ,
Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.6.0.2 dated 2020-02-18 and 1.6.0.3 dated 2023-03-10
DESCRIPTION | 40 ++- LICENSE | 2 MD5 | 181 +++++++++------ NAMESPACE | 27 +- NEWS | 12 + NEWS.md | 22 + R/RcppExports.R | 88 +++++++ R/addLoggingWrapper.R | 49 +++- R/getID.R | 4 R/getLoggedValues.R | 7 R/makeBBOBFunction.R | 3 R/makeObjectiveFunction.R | 2 R/mof.SYMPARTrotated.R |only R/mof.SYMPARTsimple.R |only R/mof.dtlz2.R | 2 R/mof.dtlz5.R | 5 R/mof.dtlz6.R | 5 R/mof.dtlz7.R | 5 R/mof.mmf1.R |only R/mof.mmf10.R |only R/mof.mmf11.R |only R/mof.mmf12.R |only R/mof.mmf13.R |only R/mof.mmf14.R |only R/mof.mmf14a.R |only R/mof.mmf15.R |only R/mof.mmf15a.R |only R/mof.mmf1e.R |only R/mof.mmf1z.R |only R/mof.mmf2.R |only R/mof.mmf3.R |only R/mof.mmf4.R |only R/mof.mmf5.R |only R/mof.mmf6.R |only R/mof.mmf7.R |only R/mof.mmf8.R |only R/mof.mmf9.R |only R/mof.omni.R |only R/plot.autoplot.R | 44 ++- R/plot.helpers.R | 6 R/plot3D.R | 6 R/sof.aluffi-pentini.R | 2 R/sof.bent.cigar.R | 2 R/sof.complex.R | 2 R/sof.deflected.corrugated.spring.R | 2 R/sof.engvall.R | 2 R/sof.jennrichsampson.R | 2 R/sof.judge.R | 2 R/sof.kearfott.R | 2 R/sof.michalewicz.R | 4 R/sof.mpm2.R | 62 +---- R/sof.powell.sum.R | 2 R/visualizeParetoOptimalFront.R | 7 R/zzz.R | 5 inst/CITATION | 5 inst/mpm2.py | 35 +-- man/addLoggingWrapper.Rd | 11 man/autoplot.smoof_function.Rd | 21 + man/computeExpectedRunningTime.Rd | 10 man/getID.Rd | 6 man/makeAluffiPentiniFunction.Rd | 2 man/makeBBOBFunction.Rd | 2 man/makeBentCigarFunction.Rd | 2 man/makeComplexFunction.Rd | 2 man/makeDTLZ2Function.Rd | 3 man/makeDTLZ5Function.Rd | 6 man/makeDTLZ6Function.Rd | 6 man/makeDTLZ7Function.Rd | 6 man/makeDeflectedCorrugatedSpringFunction.Rd | 2 man/makeEngvallFunction.Rd | 2 man/makeJennrichSampsonFunction.Rd | 2 man/makeJudgeFunction.Rd | 2 man/makeKearfottFunction.Rd | 2 man/makeMMF10Function.Rd |only man/makeMMF11Function.Rd |only man/makeMMF12Function.Rd |only man/makeMMF13Function.Rd |only man/makeMMF14Function.Rd |only man/makeMMF14aFunction.Rd |only man/makeMMF15Function.Rd |only man/makeMMF15aFunction.Rd |only man/makeMMF1Function.Rd |only man/makeMMF1eFunction.Rd |only man/makeMMF1zFunction.Rd |only man/makeMMF2Function.Rd |only man/makeMMF3Function.Rd |only man/makeMMF4Function.Rd |only man/makeMMF5Function.Rd |only man/makeMMF6Function.Rd |only man/makeMMF7Function.Rd |only man/makeMMF8Function.Rd |only man/makeMMF9Function.Rd |only man/makeMPM2Function.Rd | 10 man/makeMultiObjectiveFunction.Rd | 20 + man/makeOmniTestFunction.Rd |only man/makeSYMPARTrotatedFunction.Rd |only man/makeSYMPARTsimpleFunction.Rd |only man/makeSingleObjectiveFunction.Rd | 24 +- man/mnof.Rd | 22 + man/plot1DNumeric.Rd | 9 man/plot2DNumeric.Rd | 12 - man/snof.Rd | 26 +- src/Makevars | 4 src/RcppExports.cpp | 315 +++++++++++++++++++++++++-- src/bbobStructures.h | 10 src/benchmarks.c | 4 src/benchmarks.h | 4 src/benchmarkshelper.c | 36 +-- src/benchmarkshelper.h | 10 src/mof.cec2019.cpp |only tests/testthat/Rplots.pdf |binary tests/testthat/test_filterFunctionByTags.R | 5 tests/testthat/test_logging.R | 5 tests/testthat/test_plotting.R | 15 + 114 files changed, 965 insertions(+), 299 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] ,
Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 3.2.0 dated 2021-11-26 and 3.2.1 dated 2023-03-10
DESCRIPTION | 8 +-- MD5 | 36 ++++++++--------- NAMESPACE | 2 NEWS.md | 15 ++++--- R/simulation.R | 22 +++++----- R/util.R | 5 -- build/partial.rdb |binary build/vignette.rds |binary data/exrates.RData |binary inst/CITATION | 78 +++++++++++++++++--------------------- inst/doc/article.pdf |binary inst/doc/article2.pdf |binary inst/include/stochvol.h | 68 ++++++++++++++++++++++++++++++++- inst/include/type_definitions.hpp | 10 ++++ man/logret.Rd | 4 - src/Makevars | 1 src/Makevars.win | 1 src/exports.cc | 5 ++ src/utils_latent_states.h | 7 --- 19 files changed, 164 insertions(+), 98 deletions(-)
Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random
Parameters
Description: An implementation of simulated maximum likelihood method for the estimation of Binary (Probit and Logit), Ordered (Probit and Logit) and Poisson models with random parameters for cross-sectional and longitudinal data as presented in Sarrias (2016) <doi:10.18637/jss.v074.i10>.
Author: Mauricio Sarrias [aut, cre] ,
Yves Croissant [ctb],
Achim Zeileis [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between Rchoice versions 0.3-5 dated 2022-04-20 and 0.3-6 dated 2023-03-10
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/hetprob.R | 52 +++++++++++++++++++++++++++------------------------- R/ivpml.R | 52 ++++++++++++++++++++++++++++++++++++++++++---------- inst/NEWS.Rd | 9 +++++++++ man/hetprob.Rd | 4 +--- 6 files changed, 89 insertions(+), 48 deletions(-)
Title: Useful Functions for Data Processing
Description: In ancient Chinese mythology, Bai Ze is a divine creature that knows the needs of everything.
'baizer' provides data processing functions frequently used by the author.
Hope this package also knows what you want!
Author: William Song [aut, cre]
Maintainer: William Song <william_swl@163.com>
Diff between baizer versions 0.2.0 dated 2023-03-03 and 0.3.0 dated 2023-03-10
DESCRIPTION | 6 MD5 | 54 ++++-- NAMESPACE | 20 ++ NEWS.md | 14 + R/IO.R | 43 +++++ R/baizer-package.R | 9 + R/dataframe.R | 138 +++++++++-------- R/numbers.R | 2 R/stat.R | 63 ++++++- R/tbflt.R |only R/utils-basic.R | 147 ++++++++++++++---- README.md | 295 +++++++++++++++++++++++++++++-------- man/cmdargs.Rd |only man/diff_index.Rd | 15 + man/fancy_count.Rd | 26 ++- man/fetch_char.Rd |only man/filterC.Rd |only man/fps_vector.Rd | 4 man/geom_mean.Rd |only man/ordered_slice.Rd | 2 man/pkglib.Rd |only man/same_index.Rd |only man/signif_round_string.Rd | 4 man/split_column.Rd | 8 - man/stat_fc.Rd | 6 man/tbflt.Rd |only tests/testthat/_snaps/dataframe.md | 103 ++++++++++-- tests/testthat/_snaps/stat.md | 100 ++++++++++-- tests/testthat/_snaps/tbflt.md |only tests/testthat/test-dataframe.R | 70 ++++++-- tests/testthat/test-stat.R | 20 ++ tests/testthat/test-tbflt.R |only tests/testthat/test-utils-basic.R | 70 ++++++++ 33 files changed, 952 insertions(+), 267 deletions(-)
Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect
in moderated regression and forming its confidence interval
by nonparametric bootstrapping as proposed in
Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Also includes simple-to-use
functions for computing conditional effects (unstandardized
or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] ,
David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between stdmod versions 0.2.1 dated 2022-10-09 and 0.2.6 dated 2023-03-10
DESCRIPTION | 10 MD5 | 68 +- NAMESPACE | 3 NEWS.md | 26 - R/coef_condeff.R |only R/condeff.R | 3 R/condeff_boot.R | 102 ++-- R/confint_condeff.R |only R/plotmod.R | 50 + R/print_cond_eff.R | 36 + R/print_stdmod.R | 4 R/print_summary_stdmod.R | 67 ++ R/std_selected_boot.R | 97 ++- R/summary_stdmod.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 39 - inst/doc/cond_effect.html | 422 +++++++++------- inst/doc/moderation.html | 593 ++++++++++++----------- inst/doc/plotmod.html | 472 ++++++++++-------- inst/doc/std_selected.html | 652 ++++++++++++++----------- inst/doc/stdmod.html | 732 +++++++++++++++-------------- inst/doc/stdmod_lavaan.html | 425 ++++++++-------- man/coef.cond_effect.Rd |only man/cond_effect.Rd | 13 man/confint.cond_effect.Rd |only man/print.cond_effect.Rd | 9 man/print.std_selected.Rd | 4 man/std_selected.Rd | 15 tests/testthat/test_condeff.R | 33 + tests/testthat/test_condeff_boot.R | 23 tests/testthat/test_condeff_boot_methods.R |only tests/testthat/test_condeff_methods.R |only tests/testthat/test_plotmod.R | 14 tests/testthat/test_plotmod_tumble.R | 16 tests/testthat/test_stdmod_selected.R | 41 + tests/testthat/test_stdmod_selected_fac.R | 35 + 38 files changed, 2324 insertions(+), 1684 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Traditional and spatial capture-mark-recapture analysis with
multiple non-invasive marks. The models implemented in 'multimark' combine
encounter history data arising from two different non-invasive "marks",
such as images of left-sided and right-sided pelage patterns of bilaterally
asymmetrical species, to estimate abundance and related demographic
parameters while accounting for imperfect detection. Bayesian models are
specified using simple formulae and fitted using Markov chain Monte Carlo.
Addressing deficiencies in currently available software, 'multimark' also
provides a user-friendly interface for performing Bayesian multimodel
inference using non-spatial or spatial capture-recapture data consisting of a single
conventional mark or multiple non-invasive marks. See McClintock (2015) <doi:10.1002/ece3.1676> and Maronde et al. (2020) <doi:10.1002/ece3.6990>.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] ,
Barry Brown [ctb] ,
James Lovato [ctb] ,
John Burkardt [ctb] ,
Cleve Moler [ctb] ,
Arjun Gopalaswamy [ctb]
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 2.1.5 dated 2022-10-18 and 2.1.6 dated 2023-03-10
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NEWS | 7 +++++ R/CJS.R | 2 - R/Closed.R | 4 +- inst/CITATION | 79 +++++++++++++++++++++++++++++++++++++++++----------------- 6 files changed, 77 insertions(+), 35 deletions(-)
Title: A Shiny Interface for Simple Data Management
Description: Launches a shiny application generating code to
view tables in several ways,
import/export tables,
modify tables,
make some basic graphics.
'IGoR' is a graphic user interface designed to help beginners
using simple functions around table management and exploration.
Inspired by 'Rcmdr', 'IGoR' is a code generator that, with simple inputs under a Shiny application,
provides R code mainly built around the 'tidyverse' or some packages in the direct line of the Mosaic project:
the 'rio' and 'ggformula' packages.
The generated code doesn't depend on IGoR and can be manually modified by the user or copied elsewhere.
Author: Jean-Luc Lipatz [aut, cre], Bernard Gestin [ctb]
Maintainer: Jean-Luc Lipatz <jllipatz@protonmail.com>
Diff between IGoRRR versions 0.3.2 dated 2022-03-17 and 0.3.4 dated 2023-03-10
DESCRIPTION | 12 +++++----- MD5 | 10 ++++---- NAMESPACE | 1 R/page_import.R | 61 ++++++++++++++++++++++++++++++++++++++++++++--------- inst/misc/news.txt | 4 +++ inst/text/FR.json | 7 +++++- 6 files changed, 73 insertions(+), 22 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the included version of Eigen [ctb, cph],
Timot [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.0.0 dated 2023-03-09 and 1.0.1 dated 2023-03-10
DESCRIPTION | 6 +- MD5 | 18 +++--- R/gpboost.R | 6 +- configure.ac | 2 man/gpb.cv.Rd | 6 +- man/gpb.grid.search.tune.parameters.Rd | 6 +- man/gpb.train.Rd | 6 +- man/gpb_shared_params.Rd | 6 +- man/gpboost.Rd | 6 +- src/include/GPBoost/likelihoods.h | 98 +++++++++++++++++++++++++-------- 10 files changed, 106 insertions(+), 54 deletions(-)
Title: Build Dirichlet Process Objects for Bayesian Modelling
Description: Perform nonparametric Bayesian analysis using Dirichlet
processes without the need to program the inference algorithms.
Utilise included pre-built models or specify custom
models and allow the 'dirichletprocess' package to handle the
Markov chain Monte Carlo sampling.
Our Dirichlet process objects can act as building blocks for a variety
of statistical models including and not limited to: density estimation,
clustering and prior distributions in hierarchical models.
See Teh, Y. W. (2011)
<https://www.stats.ox.ac.uk/~teh/research/npbayes/Teh2010a.pdf>,
among many other sources.
Author: Gordon J. Ross [aut],
Dean Markwick [aut, cre],
Kees Mulder [ctb] ,
Giovanni Sighinolfi [ctb],
Filippo Fiocchi [ctb]
Maintainer: Dean Markwick <dean.markwick@talk21.com>
Diff between dirichletprocess versions 0.4.0 dated 2020-06-13 and 0.4.1 dated 2023-03-10
DESCRIPTION | 15 MD5 | 89 +++-- NAMESPACE | 10 NEWS.md | 6 R/cluster_label_predict.R | 4 R/diagnostic_plots.R | 2 R/dirichlet_process_create.R | 1 R/dirichlet_process_gaussian_fixed_variance.R |only R/duplicate_cluster_remove.R | 107 +++--- R/fit.R | 2 R/likelihood.R | 14 R/likelihood_function.R | 5 R/mixing_distribution.R | 4 R/mvnormal_normal_wishart.R | 13 R/mvnormal_semi_conjugate.R | 5 R/normal_fixed_variance.R |only R/normal_inverse_gamma.R | 4 R/plot_dirichletprocess.R | 5 R/posterior_clusters.R | 7 R/print.R | 34 +- R/prior.R |only R/prior_clusters.R |only R/stick_breaking.R | 4 R/update_alpha_beta.R | 2 README.md | 51 +-- build/vignette.rds |binary inst/doc/dirichletprocess.R | 1 inst/doc/dirichletprocess.Rnw | 2 inst/doc/dirichletprocess.pdf |binary man/DirichletProcessCreate.Rd | 1 man/DirichletProcessGaussianFixedVariance.Rd |only man/GaussianFixedVarianceMixtureCreate.Rd |only man/Likelihood.Rd | 5 man/PosteriorDraw.Rd | 7 man/PosteriorParameters.Rd | 6 man/Predictive.Rd | 5 man/PriorClusters.Rd |only man/PriorDraw.Rd | 6 man/PriorFunction.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test_beta_uniform_gamma.R | 2 tests/testthat/test_duplicate_cluster_remove.R | 396 ++++++++++++------------- tests/testthat/test_gaussian_fixed_variance.R |only tests/testthat/test_global_parameter_update.R | 214 ++++++------- tests/testthat/test_mvnormal_normal_wishart.R | 4 tests/testthat/test_mvnormal_semi_conjugate.R | 8 tests/testthat/test_print.R | 33 ++ tests/testthat/test_prior.R |only tests/testthat/test_prior_clusters.R |only tests/testthat/test_update_g0.R | 238 +++++++-------- vignettes/dirichletprocess.Rnw | 2 51 files changed, 719 insertions(+), 595 deletions(-)
More information about dirichletprocess at CRAN
Permanent link
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 75 classes of statistical models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Marcio Augusto Diniz [ctb] ,
Noah Greifer [ctb] ,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.10.0 dated 2023-02-22 and 0.11.0 dated 2023-03-10
marginaleffects-0.10.0/marginaleffects/R/sanitize_transform_pre.R |only marginaleffects-0.10.0/marginaleffects/inst/tinytest/_tinyviztest |only marginaleffects-0.10.0/marginaleffects/inst/tinytest/_tinyviztest_review |only marginaleffects-0.11.0/marginaleffects/DESCRIPTION | 93 +- marginaleffects-0.11.0/marginaleffects/MD5 | 371 ++++------ marginaleffects-0.11.0/marginaleffects/NAMESPACE | 5 marginaleffects-0.11.0/marginaleffects/NEWS.md | 37 marginaleffects-0.11.0/marginaleffects/R/RcppExports.R |only marginaleffects-0.11.0/marginaleffects/R/backtransform.R | 16 marginaleffects-0.11.0/marginaleffects/R/broom.R | 6 marginaleffects-0.11.0/marginaleffects/R/ci.R | 11 marginaleffects-0.11.0/marginaleffects/R/comparisons.R | 129 +-- marginaleffects-0.11.0/marginaleffects/R/datagrid.R | 164 +--- marginaleffects-0.11.0/marginaleffects/R/get_averages.R | 6 marginaleffects-0.11.0/marginaleffects/R/get_contrast_data.R | 5 marginaleffects-0.11.0/marginaleffects/R/get_contrast_data_character.R | 9 marginaleffects-0.11.0/marginaleffects/R/get_contrast_data_factor.R | 9 marginaleffects-0.11.0/marginaleffects/R/get_contrasts.R | 26 marginaleffects-0.11.0/marginaleffects/R/get_model_matrix.R |only marginaleffects-0.11.0/marginaleffects/R/get_model_matrix_attribute.R |only marginaleffects-0.11.0/marginaleffects/R/get_modeldata.R | 11 marginaleffects-0.11.0/marginaleffects/R/get_predict.R | 17 marginaleffects-0.11.0/marginaleffects/R/get_se_delta.R | 2 marginaleffects-0.11.0/marginaleffects/R/hypotheses.R | 3 marginaleffects-0.11.0/marginaleffects/R/imputation.R | 2 marginaleffects-0.11.0/marginaleffects/R/marginal_means.R | 25 marginaleffects-0.11.0/marginaleffects/R/methods_afex.R | 10 marginaleffects-0.11.0/marginaleffects/R/methods_brms.R | 9 marginaleffects-0.11.0/marginaleffects/R/methods_ordinal.R | 13 marginaleffects-0.11.0/marginaleffects/R/methods_quantreg.R | 41 - marginaleffects-0.11.0/marginaleffects/R/methods_stats.R | 51 + marginaleffects-0.11.0/marginaleffects/R/package.R | 6 marginaleffects-0.11.0/marginaleffects/R/plot_comparisons.R | 12 marginaleffects-0.11.0/marginaleffects/R/plot_predictions.R | 6 marginaleffects-0.11.0/marginaleffects/R/plot_slopes.R | 2 marginaleffects-0.11.0/marginaleffects/R/predictions.R | 144 ++- marginaleffects-0.11.0/marginaleffects/R/print.R | 18 marginaleffects-0.11.0/marginaleffects/R/sanitize_comparison.R |only marginaleffects-0.11.0/marginaleffects/R/sanitize_condition.R | 9 marginaleffects-0.11.0/marginaleffects/R/sanitize_newdata.R | 38 + marginaleffects-0.11.0/marginaleffects/R/sanitize_variables.R | 62 - marginaleffects-0.11.0/marginaleffects/R/sanity_by.R | 4 marginaleffects-0.11.0/marginaleffects/R/sanity_dots.R | 10 marginaleffects-0.11.0/marginaleffects/R/sanity_model.R | 4 marginaleffects-0.11.0/marginaleffects/R/slopes.R | 16 marginaleffects-0.11.0/marginaleffects/R/type_dictionary.R | 3 marginaleffects-0.11.0/marginaleffects/R/utils.R | 25 marginaleffects-0.11.0/marginaleffects/README.md | 5 marginaleffects-0.11.0/marginaleffects/inst/WORDLIST | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/_tinysnapshot |only marginaleffects-0.11.0/marginaleffects/inst/tinytest/helpers.R | 5 marginaleffects-0.11.0/marginaleffects/inst/tinytest/stata/databases/Phobia.rds |only marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-backward.R |only marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-bugfix.R | 25 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-by.R | 38 - marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-comparisons-interaction.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-contrast.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-datagrid.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-df.R | 11 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-dots.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-equivalence.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-factor.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-hypotheses.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-hypothesis.R | 14 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-inferences.R | 3 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-interaction.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-marginal_means.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-marginaleffects.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-nested.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-newdata.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-p_adjust.R |only marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-AER.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-MASS.R | 12 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-MCMCglmm.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-MatchIt.R |only marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-Rchoice.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-afex.R | 22 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-aod.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-betareg.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-bife.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-biglm.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-blme.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-brglm2.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-brms-average.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-brms.R | 66 + marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-crch.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-estimatr.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-fixest.R | 18 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-gam.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-gamlss.R | 13 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-geepack.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-glmmTMB.R | 31 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-glmx.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-ivreg.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-lme4.R | 26 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-lmerTest.R | 10 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-mclogit.R | 13 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-mgcv.R | 12 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-mhurdle.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-mice.R | 32 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-mlogit.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-nlme.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-nnet.R | 3 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-ordinal.R | 20 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-plm.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-pscl.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-quantreg.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-rms.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-robust.R | 2 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-robustbase.R | 4 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-robustlmm.R | 6 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-rstanarm.R | 8 marginaleffects-0.11.0/marginaleffects/inst/tinytest/test-pkg-sampleSelection.R | 2 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More information about marginaleffects at CRAN
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Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
design functions for randomizing and assessing designs available as a
vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
The package 'dae' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between dae versions 3.2-14 dated 2023-01-13 and 3.2.15 dated 2023-03-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/Interaction.ABC.Plot.r | 5 ++++- R/designGGPlot.v1.r | 19 ++++++++++--------- R/designPlot.v2.r | 7 ++++--- build/partial.rdb |binary inst/NEWS.Rd | 4 ++++ inst/doc/DesignNotes.pdf |binary inst/doc/dae-manual.pdf |binary man/designRandomize.Rd | 9 +++++++-- 10 files changed, 42 insertions(+), 28 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models
applied to point-referenced and areal (lattice) data. Parameters
are estimated using various methods. Additional modeling features include anisotropy,
non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are
used to summarize, visualize, and compare models. Predictions at unobserved locations are
readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut],
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.2.0 dated 2022-11-11 and 0.3.0 dated 2023-03-10
spmodel-0.2.0/spmodel/man/AIC.spmod.Rd |only spmodel-0.2.0/spmodel/man/anova.spmod.Rd |only spmodel-0.2.0/spmodel/man/augment.spmod.Rd |only spmodel-0.2.0/spmodel/man/coef.spmod.Rd |only spmodel-0.2.0/spmodel/man/confint.spmod.Rd |only spmodel-0.2.0/spmodel/man/cooks.distance.spmod.Rd |only spmodel-0.2.0/spmodel/man/deviance.spmod.Rd |only spmodel-0.2.0/spmodel/man/fitted.spmod.Rd |only spmodel-0.2.0/spmodel/man/formula.spmod.Rd |only spmodel-0.2.0/spmodel/man/glance.spmod.Rd |only spmodel-0.2.0/spmodel/man/hatvalues.spmod.Rd |only spmodel-0.2.0/spmodel/man/influence.spmod.Rd |only spmodel-0.2.0/spmodel/man/labels.spmod.Rd |only spmodel-0.2.0/spmodel/man/logLik.spmod.Rd |only spmodel-0.2.0/spmodel/man/model.frame.spmod.Rd |only spmodel-0.2.0/spmodel/man/model.matrix.spmod.Rd |only spmodel-0.2.0/spmodel/man/plot.spmod.Rd |only spmodel-0.2.0/spmodel/man/predict.spmod.Rd |only spmodel-0.2.0/spmodel/man/predict.spmodRF.Rd |only spmodel-0.2.0/spmodel/man/print.spmod.Rd |only spmodel-0.2.0/spmodel/man/residuals.spmod.Rd |only spmodel-0.2.0/spmodel/man/summary.spmod.Rd |only spmodel-0.2.0/spmodel/man/tidy.spmod.Rd |only spmodel-0.2.0/spmodel/man/vcov.spmod.Rd |only spmodel-0.3.0/spmodel/DESCRIPTION | 10 spmodel-0.3.0/spmodel/MD5 | 217 - spmodel-0.3.0/spmodel/NAMESPACE | 120 spmodel-0.3.0/spmodel/NEWS.md | 35 spmodel-0.3.0/spmodel/R/AIC.R | 436 +-- spmodel-0.3.0/spmodel/R/PseudoR2.R | 94 spmodel-0.3.0/spmodel/R/anova.R | 441 +-- spmodel-0.3.0/spmodel/R/augment.R | 507 ++-- spmodel-0.3.0/spmodel/R/coef.R | 94 spmodel-0.3.0/spmodel/R/confint.R | 90 spmodel-0.3.0/spmodel/R/cooks.distance.R | 66 spmodel-0.3.0/spmodel/R/cov_betahat_adjust.R | 321 +- spmodel-0.3.0/spmodel/R/cov_initial_search.R | 2214 +++++++++--------- spmodel-0.3.0/spmodel/R/covmatrix.R | 190 - spmodel-0.3.0/spmodel/R/deviance.R | 70 spmodel-0.3.0/spmodel/R/esv.R | 320 +- spmodel-0.3.0/spmodel/R/fitted.R | 111 spmodel-0.3.0/spmodel/R/formula.R | 48 spmodel-0.3.0/spmodel/R/get_data_object.R | 867 +++---- spmodel-0.3.0/spmodel/R/get_eigenprods.R |only spmodel-0.3.0/spmodel/R/get_fitted.R | 326 +- spmodel-0.3.0/spmodel/R/get_initial_range.R | 158 - spmodel-0.3.0/spmodel/R/get_model_stats.R | 486 ++- spmodel-0.3.0/spmodel/R/get_randcov_list.R | 8 spmodel-0.3.0/spmodel/R/get_residuals.R | 60 spmodel-0.3.0/spmodel/R/glance.R | 106 spmodel-0.3.0/spmodel/R/glances.R | 132 - spmodel-0.3.0/spmodel/R/gloglik_products.R | 286 +- spmodel-0.3.0/spmodel/R/hatvalues.R | 68 spmodel-0.3.0/spmodel/R/influence.R | 76 spmodel-0.3.0/spmodel/R/labels.R | 50 spmodel-0.3.0/spmodel/R/logLik.R | 64 spmodel-0.3.0/spmodel/R/loocv.R | 453 +-- spmodel-0.3.0/spmodel/R/model.frame.R | 68 spmodel-0.3.0/spmodel/R/model.matrix.R | 56 spmodel-0.3.0/spmodel/R/partition_matrix.R | 52 spmodel-0.3.0/spmodel/R/partition_vector.R | 19 spmodel-0.3.0/spmodel/R/plot.R | 510 ++-- spmodel-0.3.0/spmodel/R/predict.R | 1786 +++++++------- spmodel-0.3.0/spmodel/R/print.R | 441 ++- spmodel-0.3.0/spmodel/R/randcov_vector.R | 21 spmodel-0.3.0/spmodel/R/residuals.R | 131 - spmodel-0.3.0/spmodel/R/spautor.R | 17 spmodel-0.3.0/spmodel/R/spautorRF.R | 28 spmodel-0.3.0/spmodel/R/spcov_initial.R | 2 spmodel-0.3.0/spmodel/R/spcov_matrix.R | 416 +-- spmodel-0.3.0/spmodel/R/spcov_matrixInv_de.R | 216 - spmodel-0.3.0/spmodel/R/spcov_optim2orig.R | 310 +- spmodel-0.3.0/spmodel/R/spcov_orig2optim.R | 722 ++--- spmodel-0.3.0/spmodel/R/splm.R | 785 +++--- spmodel-0.3.0/spmodel/R/splmRF.R | 32 spmodel-0.3.0/spmodel/R/spmodel-package.R | 3 spmodel-0.3.0/spmodel/R/sprnorm.R | 712 ++--- spmodel-0.3.0/spmodel/R/summary.R | 111 spmodel-0.3.0/spmodel/R/tidy.R | 238 + spmodel-0.3.0/spmodel/R/transform_anis.R | 47 spmodel-0.3.0/spmodel/R/varcomp.R |only spmodel-0.3.0/spmodel/R/vcov.R | 55 spmodel-0.3.0/spmodel/README.md | 22 spmodel-0.3.0/spmodel/inst/CITATION | 32 spmodel-0.3.0/spmodel/inst/doc/basics.Rmd | 7 spmodel-0.3.0/spmodel/inst/doc/basics.pdf |binary spmodel-0.3.0/spmodel/inst/doc/guide.R | 1 spmodel-0.3.0/spmodel/inst/doc/guide.Rmd | 1751 +++++++------- spmodel-0.3.0/spmodel/inst/doc/guide.pdf |binary spmodel-0.3.0/spmodel/inst/doc/technical.Rmd | 24 spmodel-0.3.0/spmodel/inst/doc/technical.pdf |binary spmodel-0.3.0/spmodel/inst/references.bib | 12 spmodel-0.3.0/spmodel/man/AIC.spmodel.Rd |only spmodel-0.3.0/spmodel/man/anova.spmodel.Rd |only spmodel-0.3.0/spmodel/man/augment.spmodel.Rd |only spmodel-0.3.0/spmodel/man/coef.spmodel.Rd |only spmodel-0.3.0/spmodel/man/confint.spmodel.Rd |only spmodel-0.3.0/spmodel/man/cooks.distance.spmodel.Rd |only spmodel-0.3.0/spmodel/man/covmatrix.Rd | 78 spmodel-0.3.0/spmodel/man/deviance.spmodel.Rd |only spmodel-0.3.0/spmodel/man/fitted.spmodel.Rd |only spmodel-0.3.0/spmodel/man/formula.spmodel.Rd |only spmodel-0.3.0/spmodel/man/glance.spmodel.Rd |only spmodel-0.3.0/spmodel/man/glances.Rd | 4 spmodel-0.3.0/spmodel/man/hatvalues.spmodel.Rd |only spmodel-0.3.0/spmodel/man/influence.spmodel.Rd |only spmodel-0.3.0/spmodel/man/labels.spmodel.Rd |only spmodel-0.3.0/spmodel/man/logLik.spmodel.Rd |only spmodel-0.3.0/spmodel/man/loocv.Rd | 8 spmodel-0.3.0/spmodel/man/model.frame.spmodel.Rd |only spmodel-0.3.0/spmodel/man/model.matrix.spmodel.Rd |only spmodel-0.3.0/spmodel/man/plot.spmodel.Rd |only spmodel-0.3.0/spmodel/man/predict.spmodel.Rd |only spmodel-0.3.0/spmodel/man/print.spmodel.Rd |only spmodel-0.3.0/spmodel/man/pseudoR2.Rd | 7 spmodel-0.3.0/spmodel/man/residuals.spmodel.Rd |only spmodel-0.3.0/spmodel/man/spautor.Rd | 10 spmodel-0.3.0/spmodel/man/spautorRF.Rd | 16 spmodel-0.3.0/spmodel/man/splm.Rd | 10 spmodel-0.3.0/spmodel/man/splmRF.Rd | 20 spmodel-0.3.0/spmodel/man/spmodel-package.Rd | 2 spmodel-0.3.0/spmodel/man/summary.spmodel.Rd |only spmodel-0.3.0/spmodel/man/tidy.spmodel.Rd |only spmodel-0.3.0/spmodel/man/varcomp.Rd |only spmodel-0.3.0/spmodel/man/vcov.spmodel.Rd |only spmodel-0.3.0/spmodel/tests/testthat/test-esv.R | 93 spmodel-0.3.0/spmodel/tests/testthat/test-generics.R | 6 spmodel-0.3.0/spmodel/tests/testthat/test-plot.R | 118 spmodel-0.3.0/spmodel/tests/testthat/test-residuals.R | 42 spmodel-0.3.0/spmodel/tests/testthat/test-spautor.R | 5 spmodel-0.3.0/spmodel/tests/testthat/test-splm.R | 5 spmodel-0.3.0/spmodel/tests/testthat/test-varcomp.R |only spmodel-0.3.0/spmodel/vignettes/basics.Rmd | 7 spmodel-0.3.0/spmodel/vignettes/guide.Rmd | 1751 +++++++------- spmodel-0.3.0/spmodel/vignettes/technical.Rmd | 24 135 files changed, 10051 insertions(+), 9306 deletions(-)
Title: Estimating Personalized Diagnostics Rules
Description: Recommend the optimal biomarker for disease screening or diagnosis based on patients' individual characteristics.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between persDx versions 0.3.0 dated 2023-03-04 and 0.4.0 dated 2023-03-10
persDx-0.3.0/persDx/R/02_np_lpd_surv_cov.r |only persDx-0.3.0/persDx/R/02_np_lpd_surv_cov2.r |only persDx-0.4.0/persDx/DESCRIPTION | 8 persDx-0.4.0/persDx/MD5 | 12 persDx-0.4.0/persDx/R/02_np_lpd_survival_cov1.r |only persDx-0.4.0/persDx/R/02_np_lpd_survival_cov2.r |only persDx-0.4.0/persDx/R/np_lpd.r | 353 +++++++++++------------ persDx-0.4.0/persDx/R/np_lpd_survival.r | 360 ++++++++++++------------ persDx-0.4.0/persDx/man/persDx-package.Rd | 4 9 files changed, 369 insertions(+), 368 deletions(-)
Title: Significance Tests for Palaeoenvironmental Reconstructions
Description: Several tests of quantitative palaeoenvironmental reconstructions
from microfossil assemblages, including the null model tests of the
statistically significant of reconstructions developed by Telford and Birks
(2011) <doi:10.1016/j.quascirev.2011.03.002>, and tests of the effect of
spatial autocorrelation on transfer function model performance using methods
from Telford and Birks (2009) <doi:10.1016/j.quascirev.2008.12.020> and
Trachsel and Telford (2016) <doi:10.5194/cp-12-1215-2016>. Age-depth models with
generalized mixed-effect regression from Heegaard et al (2005)
<doi:10.1191/0959683605hl836rr> are also included.
Author: Richard Telford [aut, cre, cph],
Mathias Trachsel [ctb]
Maintainer: Richard Telford <Richard.Telford@uib.no>
Diff between palaeoSig versions 2.0-7 dated 2023-01-26 and 2.1-3 dated 2023-03-10
DESCRIPTION | 17 +- MD5 | 44 +++-- NAMESPACE | 10 - NEWS.md | 41 +++++ R/1_randomTF.R | 17 +- R/coverage.plot.r | 16 +- R/jointsig.r | 2 R/plot.obscor.R | 9 - R/plot.palaeoSig.R | 13 - R/rne.R | 186 ++++++++++++++---------- R/simulate_species.r | 2 build/vignette.rds |binary inst/CITATION | 28 ++- inst/doc/h-block-crossvalidation.R | 86 +++++------ inst/doc/h-block-crossvalidation.Rmd | 89 ++++++----- inst/doc/h-block-crossvalidation.html | 257 +++++++++++++++++----------------- inst/doc/randomTF-spatial.R |only inst/doc/randomTF-spatial.Rmd |only inst/doc/randomTF-spatial.html |only man/obs.cor.Rd | 4 man/randomTF.Rd | 13 + man/rne.Rd | 34 +++- tests |only vignettes/h-block-crossvalidation.Rmd | 89 ++++++----- vignettes/randomTF-spatial.Rmd |only 25 files changed, 545 insertions(+), 412 deletions(-)
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between nser versions 1.4.4 dated 2022-12-14 and 1.4.5 dated 2023-03-10
DESCRIPTION | 12 +-- MD5 | 46 ++++++------ NAMESPACE | 1 R/fdii.R | 1 R/nseipo.R | 1 build/vignette.rds |binary inst/doc/bhav.html | 15 +--- inst/doc/bhavfos.html | 125 +++++++++++++++------------------ inst/doc/bhavpr.html | 125 +++++++++++++++------------------ inst/doc/bhavs.html | 125 +++++++++++++++------------------ inst/doc/bhavtoday.html | 125 +++++++++++++++------------------ inst/doc/dailydata.html | 125 +++++++++++++++------------------ inst/doc/daytomonth.html | 15 +--- inst/doc/daytoweek.html | 15 +--- inst/doc/fdii.html | 167 ++++++++++++++++++++------------------------- inst/doc/fobhav.html | 125 +++++++++++++++------------------ inst/doc/fobhavtoday.html | 125 +++++++++++++++------------------ inst/doc/nseindex.html | 15 +--- inst/doc/nseipo.html | 157 +++++++++++++++++++----------------------- inst/doc/nselive.html | 125 +++++++++++++++------------------ inst/doc/nseopen.html | 125 +++++++++++++++------------------ inst/doc/nsetree.html | 125 +++++++++++++++------------------ inst/doc/optbanknifty.html | 125 +++++++++++++++------------------ inst/doc/optnifty.html | 125 +++++++++++++++------------------ 24 files changed, 903 insertions(+), 1042 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.6.1 dated 2022-12-07 and 0.6.2 dated 2023-03-10
DESCRIPTION | 8 MD5 | 108 +- NEWS.md | 4 R/A_nhdplusTools.R | 934 ++++++++++---------- R/calc_network.R | 188 ++-- R/geoserver_tools.R | 772 ++++++++-------- R/get_codes.R | 700 +++++++-------- R/get_geometry.R | 280 +++--- R/get_hydro.R | 398 ++++---- R/get_network.R | 1242 +++++++++++++------------- R/get_vaa.R | 404 ++++---- R/hl_graph_utils.R | 235 ++--- R/index_nhdplus.R | 1232 +++++++++++++------------- R/plot_nhdplus.R | 1386 +++++++++++++++--------------- R/prep_nhdplus.R | 520 +++++------ R/rebuild_topology.R | 232 ++--- README.md | 15 inst/CITATION | 9 inst/doc/US_data.html | 194 +--- inst/doc/advanced_network.html | 8 inst/doc/indexing.html | 28 inst/doc/nhdplushr.html | 72 - inst/doc/plot_nhdplus.html | 18 man/download_vaa.Rd | 78 - man/fix_flowdir.Rd | 116 +- man/get_DM.Rd | 90 - man/get_flowline_index.Rd | 178 +-- man/get_hydro_location.Rd | 60 - man/get_levelpaths.Rd | 114 +- man/get_node.Rd | 76 - man/get_partial_length.Rd | 108 +- man/get_path_lengths.Rd | 100 +- man/get_path_members.Rd | 80 - man/get_pathlength.Rd | 54 - man/get_pfaf.Rd | 164 +-- man/get_tocomid.Rd | 108 +- man/get_vaa.Rd | 114 +- man/get_vaa_names.Rd | 76 - man/make_node_topology.Rd | 92 - man/plot_nhdplus.Rd | 324 +++---- man/rename_geometry.Rd | 46 man/rescale_measures.Rd | 70 - man/st_compatibalize.Rd | 62 - tests/testthat.R | 6 tests/testthat/test_00_plot_nhdplus.R | 426 ++++----- tests/testthat/test_03_get_functions.R | 568 ++++++------ tests/testthat/test_calc_network.R | 15 tests/testthat/test_get_codes.R | 246 ++--- tests/testthat/test_get_network.R | 522 +++++------ tests/testthat/test_get_path.R | 296 +++--- tests/testthat/test_get_path_lengths.R | 172 +-- tests/testthat/test_get_vaa.R | 66 - tests/testthat/test_index.R | 422 ++++----- tests/testthat/test_rebuild_topology.R | 268 ++--- tests/testthat/test_run_plus_attributes.R | 160 +-- 55 files changed, 7137 insertions(+), 7127 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.0.8 dated 2023-03-04 and 1.0.9 dated 2023-03-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/compile.R | 4 ++-- R/mrgsims.R | 16 +++++++++------- man/mrgsims_dplyr.Rd | 8 +++----- 5 files changed, 21 insertions(+), 21 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for descriptive statistics (e.g., frequency table, cross tabulation, multilevel descriptive statistics, multilevel R-squared measures, within-group and between-group correlation matrix, various effect size measures), data management (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and group scores, reading and writing SPSS and Excel files), missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), item analysis (e.g., coefficient alpha and omega, confirmatory factor analysis), and statistical analysis (e.g., confidence intervals, collinearity diagnostics, analysis of variance, t-test, z-test, sample size determination).
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.4.7 dated 2023-01-06 and 0.4.8 dated 2023-03-10
DESCRIPTION | 12 - MD5 | 54 +++--- NAMESPACE | 7 NEWS.md | 16 + R/aov.b.R | 8 R/aov.w.R | 2 R/center.R | 202 +++++++++++++++------- R/ci.mean.R | 2 R/ci.mean.w.R | 12 - R/ci.median.R | 161 ++++++++---------- R/cluster.scores.R | 225 ++++++++++++++++--------- R/freq.R | 4 R/item.reverse.R | 222 +++++++++++++++---------- R/multilevel.r2.R | 10 - R/multilevel.r2.manual.R |only R/print.misty.object.R | 52 +++++ R/rec.R | 389 ++++++++++++++++++++++++-------------------- R/restart.R |only R/run.mplus.R | 20 +- R/script.close.R |only R/script.new.R |only R/script.open.R |only R/script.save.R |only R/setsource.R |only man/center.Rd | 58 +++++- man/cluster.scores.Rd | 74 +++++--- man/item.reverse.Rd | 62 ++++--- man/multilevel.r2.manual.Rd |only man/rec.Rd | 88 +++++++-- man/restart.Rd |only man/script.close.Rd |only man/script.new.Rd |only man/script.open.Rd |only man/script.save.Rd |only man/setsource.Rd |only 35 files changed, 1060 insertions(+), 620 deletions(-)
Title: Data from Gapminder
Description: An excerpt of the data available at Gapminder.org. For each
of 142 countries, the package provides values for life expectancy, GDP
per capita, and population, every five years, from 1952 to 2007.
Author: Jennifer Bryan [aut, cre]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between gapminder versions 0.3.0 dated 2017-10-31 and 1.0.0 dated 2023-03-10
gapminder-0.3.0/gapminder/man/figures/README-demo-country-colors-base-1.png |only gapminder-0.3.0/gapminder/man/figures/README-demo-country-colors-ggplot2-1.png |only gapminder-0.3.0/gapminder/tests/testthat/continent_colors.rds |only gapminder-0.3.0/gapminder/tests/testthat/country_colors.rds |only gapminder-0.3.0/gapminder/tests/testthat/gapminder.rds |only gapminder-0.3.0/gapminder/tests/testthat/gapminder_unfiltered.rds |only gapminder-1.0.0/gapminder/DESCRIPTION | 38 - gapminder-1.0.0/gapminder/MD5 | 42 - gapminder-1.0.0/gapminder/NEWS.md | 6 gapminder-1.0.0/gapminder/R/country_codes.R | 21 gapminder-1.0.0/gapminder/R/country_colors.R | 101 +-- gapminder-1.0.0/gapminder/R/gapminder.R | 62 +- gapminder-1.0.0/gapminder/R/gapminder_unfiltered.R | 8 gapminder-1.0.0/gapminder/README.md | 296 +--------- gapminder-1.0.0/gapminder/build |only gapminder-1.0.0/gapminder/data/country_codes.rdata |binary gapminder-1.0.0/gapminder/inst/doc |only gapminder-1.0.0/gapminder/inst/extdata/country-codes.tsv | 2 gapminder-1.0.0/gapminder/man/country_codes.Rd | 21 gapminder-1.0.0/gapminder/man/country_colors.Rd | 97 +-- gapminder-1.0.0/gapminder/man/figures/README-test-drive-1.png |binary gapminder-1.0.0/gapminder/man/gapminder.Rd | 62 +- gapminder-1.0.0/gapminder/man/gapminder_unfiltered.Rd | 6 gapminder-1.0.0/gapminder/tests/testthat/_snaps |only gapminder-1.0.0/gapminder/tests/testthat/test-gapminder.R | 16 gapminder-1.0.0/gapminder/vignettes |only 26 files changed, 302 insertions(+), 476 deletions(-)
Title: Fuzzy Linear Regression
Description: Estimators for fuzzy linear regression. The functions estimate parameters of
fuzzy linear regression models with crisp or fuzzy independent variables (triangular
fuzzy numbers are supported). Implements multiple methods for parameter estimation and
algebraic operations with triangular fuzzy numbers. Includes functions for
summarising, printing and plotting the model fit. Calculates predictions from the
model and total error of fit. Individual methods are described in
Diamond (1988) <doi:10.1016/0020-0255(88)90047-3>,
Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004>,
Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98>,
Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008>,
Skrabanek, Marek & Pozdilkova (2021) <doi:10.3390/math9060685>,
Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>,
Zeng, Feng & Li (2017) <doi:10.1016/j.asoc.2016.09.029>.
Author: Pavel Skrabanek [aut, cph],
Natalia Martinkova [aut, cre, cph]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between fuzzyreg versions 0.6.1 dated 2023-03-09 and 0.6.2 dated 2023-03-10
DESCRIPTION | 8 MD5 | 14 NEWS.md | 4 build/vignette.rds |binary inst/doc/GettingStarted.R | 43 +- inst/doc/GettingStarted.Rmd | 103 +++-- inst/doc/GettingStarted.html | 794 +++++++++++++++++++++++-------------------- vignettes/GettingStarted.Rmd | 103 +++-- 8 files changed, 598 insertions(+), 471 deletions(-)
Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local database.
Author: Giorgio Comai [aut, cre, cph] ,
EDJNet [fnd]
Maintainer: Giorgio Comai <giorgio.comai@cci.tn.it>
Diff between tidywikidatar versions 0.5.6 dated 2023-01-31 and 0.5.7 dated 2023-03-10
DESCRIPTION | 6 - LICENSE | 2 MD5 | 40 ++++++----- NEWS.md | 6 + R/data.R | 5 + R/tw_get.R | 84 +++++++++++++++++++------ R/tw_get_image.R | 1 R/tw_get_p_wide.R | 11 +-- R/tw_get_qualifiers.R | 72 ++++++++++++++++++--- R/tw_get_wikipedia_category_members.R | 11 ++- R/tw_get_wikipedia_page_links.R | 11 +-- data/tw_test_items.rda |only man/tw_get.Rd | 19 +++++ man/tw_get_qualifiers.Rd | 19 +++++ man/tw_get_qualifiers_single.Rd | 19 +++++ man/tw_get_single.Rd | 22 +++++- man/tw_test_items.Rd |only tests/testthat/test-get.R | 6 + tests/testthat/test-get_image.R | 41 ++++++++++-- tests/testthat/test-get_others.R | 36 +++++++++- tests/testthat/test-get_property_same_length.R | 2 tests/testthat/test-get_qualifiers.R | 6 + 22 files changed, 327 insertions(+), 92 deletions(-)
Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) <doi:10.1214/08-STS254> . This test is useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers [aut, cre],
Mark Fredrickson [aut],
Ben Hansen [aut],
Josh Errickson [ctb]
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.3-2 dated 2023-02-03 and 0.3-3 dated 2023-03-10
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 +++- R/xtable.xbal.R | 2 ++ man/xtable.xbal.Rd | 3 +++ tests/testthat/test.plot.balancetest.R | 18 ++++++++++++++++++ tests/testthat/test.plot.xbal.R | 5 ++++- 7 files changed, 39 insertions(+), 11 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 2.2.0 dated 2022-11-16 and 2.2.1 dated 2023-03-10
DESCRIPTION | 10 +++--- MD5 | 14 ++++---- R/makePosColumns.R | 15 --------- R/stackDataFilesParallel.R | 49 ++++++++++++++++++++++++++++-- R/stackEddy.R | 72 +++++++++++++++++++++++++++++++++++++++++---- R/zipsByProduct.R | 7 +++- R/zipsByURI.R | 10 +++++- README.md | 5 +++ 8 files changed, 144 insertions(+), 38 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.3.6 dated 2023-02-06 and 1.4.0 dated 2023-03-10
DESCRIPTION | 14 +- MD5 | 43 ++++--- NEWS.md | 29 +++++ R/FilePsInput.R | 2 R/FileRepeatedInput.R | 1 R/FileSurveyInput.R | 1 R/coxph.R | 1 R/csvFileInput.R | 140 ++++++++++++++++--------- R/gee.R | 2 R/ggpairs.R | 71 +----------- R/jsBasicGadget.R | 269 +++++++++++++++++++++++++++++++++++++------------ R/jsPropensityGadget.R | 1 R/kaplan.R | 1 R/regress.R | 2 R/roc.R | 89 +++++++--------- R/tb1.R | 2 R/tb1simple.R | 14 +- R/timeroc.R | 2 inst/doc/jsmodule.html | 4 inst/www |only man/tb1simple.Rd | 4 man/tb1simple2.Rd | 4 man/tb1simpleUI.Rd | 4 23 files changed, 425 insertions(+), 275 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-04 0.3.0
2020-06-28 0.2.2
2019-01-21 0.2.0
2018-10-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-07 0.4.0
2018-09-20 0.3.0
2017-06-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-12 0.5.2
2020-07-30 0.5.0
2018-03-21 0.4.0
2017-04-11 0.3.4
2016-11-05 0.3.0
2016-01-28 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-17 1.0.5
2016-04-03 1.0.4
2015-12-14 1.0.3
2015-03-29 1.0.2
2015-01-25 1.0.1
2014-11-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-13 0.9.2
2020-01-29 0.9.0
2017-04-12 0.8.0
2016-12-22 0.3.0
2015-07-10 0.2.0
2014-01-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-23 1.0.0
2020-04-08 0.9.0
2019-05-03 0.8.6
2018-08-14 0.8.4
2018-07-19 0.8.2
2017-11-03 0.8.0
2016-11-23 0.6.4
2016-07-21 0.6.0
2016-02-15 0.5.6
2015-09-16 0.5.4
2015-08-05 0.5.2
2015-07-01 0.5.0
2015-04-27 0.4.7
2015-01-23 0.4.6
2014-07-22 0.4.1
2014-05-13 0.4.0
2013-11-12 0.3.6
2013-09-18 0.3.0
2013-08-12 0.2.0
2013-03-27 0.1.0
2012-02-19 0.0-5
2011-12-14 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-28 0.1.2
2021-01-28 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-02 0.3.0
2019-09-04 0.2.0
2017-09-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-05 1.0.1
2022-06-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-13 0.2.2
2020-09-10 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-30 0.2.0
2016-08-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-14 1.0.0
2020-10-08 0.2.1
2020-08-03 0.2.0