Title: Estimation of Characteristics of Seasonal and Sporadic
Infectious Disease Outbreaks Using Generalized Additive
Modeling with Penalized Basis Splines
Description: Inference of infectious disease outcomes using generalized additive
(mixed) models with penalized basis splines (P-Splines). See
<https://medrxiv.org/cgi/content/short/2020.07.14.20138180v1>.
Author: Ben Artin [aut, cre, cph]
Maintainer: Ben Artin <ben@artins.org>
Diff between pspline.inference versions 0.24 dated 2020-07-08 and 1.0.2 dated 2020-07-17
DESCRIPTION | 10 ++++++---- MD5 | 4 ++-- inst/doc/seasonal.html | 18 +++++++++--------- 3 files changed, 17 insertions(+), 15 deletions(-)
More information about pspline.inference at CRAN
Permanent link
Title: Tools for Creating Automated Courses
Description: Leverages the 'ari' package and other tools to create automated
courses from slides and a script. Also, uploads these to
'YouTube' and other services using 'tuber' package.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between ariExtra versions 0.2.9 dated 2020-07-07 and 0.2.10 dated 2020-07-17
DESCRIPTION | 8 +-- MD5 | 22 ++++---- NEWS.md | 4 + R/gs_ari.R | 2 R/make_ari_document.R | 2 R/pptx_notes.R | 25 +++++++++ R/rmd_to_ari.R | 91 ++++++++++++++++++++++------------- inst/doc/making_videos.html | 24 ++++----- inst/extdata/plumber_functions.R | 86 +++++++++++++++++++++++++++++++++ man/rmd_to_ari.Rd | 21 +++++++- tests/testthat/test-gs.R | 2 tests/testthat/test-rmd_to_ari.R | 100 +++++++++++++++++++++++++++++++++------ 12 files changed, 304 insertions(+), 83 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.900.1.0 dated 2020-06-09 and 0.9.900.2.0 dated 2020-07-17
ChangeLog | 11 +++++++ DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- build/vignette.rds |binary configure | 18 ++++++------ configure.ac | 4 +- inst/NEWS.Rd | 12 ++++++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/SpMat_meat.hpp | 7 ---- inst/include/armadillo_bits/arma_version.hpp | 2 - inst/include/armadillo_bits/op_sort_meat.hpp | 38 +++++++++++++++++---------- 12 files changed, 74 insertions(+), 48 deletions(-)
Title: Wildlife Sightability Modeling
Description: Uses logistic regression to model the probability of detection as a function of covariates.
This model is then used with observational survey data to estimate population size, while
accounting for uncertain detection. See Steinhorst and Samuel (1989).
Author: Fieberg John [aut],
Schwarz Carl James [aut, cre]
Maintainer: Schwarz Carl James <cschwarz.stat.sfu.ca@gmail.com>
Diff between SightabilityModel versions 1.3 dated 2014-10-04 and 1.4.0 dated 2020-07-17
DESCRIPTION | 22 MD5 | 85 - NAMESPACE | 26 R/MoosePopR.r |only R/SS.est.R | 295 ++-- R/SS.est.Ratio.R |only R/Sight.Est.R | 380 ++++- R/Sight.Est.Ratio.R |only R/SightabilityPopR.R |only R/Wong.est.R | 366 +++-- R/Wong.est.Ratio.R |only R/covtheta.R | 112 + R/data.R |only R/print.sightest.R | 100 - R/print.sightest_ratio.R |only R/summary.sightest.R | 69 - R/summary.sightest_ratio.R |only R/vardiff.R | 148 +- R/varlog.lam.R | 146 +- README.md |only build/vignette.rds |binary inst/CITATION | 38 inst/NEWS.Rd |only inst/doc/MoosePopR-SightabilityPopR-Demo.R |only inst/doc/MoosePopR-SightabilityPopR-Demo.Rmd |only inst/doc/MoosePopR-SightabilityPopR-Demo.html |only inst/doc/RatioEstimator.pdf |only inst/doc/RatioEstimator.pdf.asis |only inst/doc/SightabilityModel.R | 370 ++--- inst/doc/SightabilityModel.Rnw | 1664 +++++++++++++------------- inst/doc/SightabilityModel.pdf |binary inst/extdata |only man/MoosePopR.Rd |only man/SS.est.Ratio.Rd |only man/SS.est.Rd | 149 +- man/Sight.Est.Ratio.Rd |only man/Sight.Est.Rd | 339 ++--- man/SightabilityModel-package.Rd | 70 - man/SightabilityPopR.Rd |only man/Wong.est.Ratio.Rd |only man/Wong.est.Rd | 159 +- man/covtheta.Rd | 90 - man/exp.m.Rd | 60 man/g.fit.Rd | 48 man/gdat.Rd | 68 - man/obs.m.Rd | 77 - man/print.sightest.Rd | 52 man/sampinfo.m.Rd | 64 - man/summary.sightest.Rd | 57 man/vardiff.Rd | 109 - man/varlog.lam.Rd | 111 - vignettes/MoosePopR-SightabilityPopR-Demo.Rmd |only vignettes/RatioEstimator.pdf.asis |only vignettes/SightabilityModel.Rnw | 1664 +++++++++++++------------- vignettes/vignette.bib | 786 ++++++------ 55 files changed, 4134 insertions(+), 3590 deletions(-)
More information about SightabilityModel at CRAN
Permanent link
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
for Earthquake Description
Description: Estimation of the components of an ETAS (Epidemic Type Aftershock Sequence) model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive). New version 2.0.0: covariates have been introduced to explain the effects of external factors on the induced seismicity; the parametrization has been changed; Chiodi, Adelfio (2017)<doi:10.18637/jss.v076.i03>.
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi <marcello.chiodi@unipa.it>
Diff between etasFLP versions 2.0.0 dated 2020-05-05 and 2.1.0 dated 2020-07-17
etasFLP-2.0.0/etasFLP/data/californiacatalog.RData |only etasFLP-2.0.0/etasFLP/data/catalog.withcov.RData |only etasFLP-2.0.0/etasFLP/data/italycatalog.RData |only etasFLP-2.1.0/etasFLP/ChangeLog | 4 ++++ etasFLP-2.1.0/etasFLP/DESCRIPTION | 8 ++++---- etasFLP-2.1.0/etasFLP/MD5 | 18 +++++++++--------- etasFLP-2.1.0/etasFLP/NAMESPACE | 2 +- etasFLP-2.1.0/etasFLP/R/plot.etasclass.R | 7 ++++--- etasFLP-2.1.0/etasFLP/data/californiacatalog.rda |only etasFLP-2.1.0/etasFLP/data/catalog.withcov.rda |only etasFLP-2.1.0/etasFLP/data/italycatalog.rda |only etasFLP-2.1.0/etasFLP/man/etasFLP-package.Rd | 21 ++++++++++++--------- etasFLP-2.1.0/etasFLP/man/etasclass.Rd | 7 +++++-- 13 files changed, 39 insertions(+), 28 deletions(-)
Title: Spreadsheet Interface for Relational Databases
Description: Use 'SQLite3' as a database system via a complete SQL free R interface, treating the data as if it was a single spreadsheet.
Author: Benjamin Becker [aut, cre]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatDB versions 0.4.0 dated 2020-04-07 and 0.4.1 dated 2020-07-17
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only R/02_DB_creation.R | 11 ++++++----- README.md | 1 + tests/testthat/test_02_createDB.R | 9 +++++++++ 6 files changed, 24 insertions(+), 12 deletions(-)
Title: Climate AEMET Tools
Description: Tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API <https://opendata.aemet.es/> and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).
Author: Manuel Pizarro [aut, cre]
Maintainer: Manuel Pizarro <m.pizarro@csic.es>
Diff between climaemet versions 0.1.0 dated 2020-07-07 and 0.2.0 dated 2020-07-17
climaemet-0.1.0/climaemet/R/climaemet_news.R |only climaemet-0.1.0/climaemet/man/climaemet_news.Rd |only climaemet-0.1.0/climaemet/man/ggstripes_station.Rd |only climaemet-0.2.0/climaemet/DESCRIPTION | 24 climaemet-0.2.0/climaemet/MD5 | 60 - climaemet-0.2.0/climaemet/NAMESPACE | 29 climaemet-0.2.0/climaemet/NEWS.md | 16 climaemet-0.2.0/climaemet/R/aemet_tools.R | 472 ++++++++++---- climaemet-0.2.0/climaemet/R/climaemet_main.R | 311 ++++++++- climaemet-0.2.0/climaemet/R/plot_tools.R | 296 +++++++- climaemet-0.2.0/climaemet/README.md | 108 ++- climaemet-0.2.0/climaemet/man/aemet_daily_clim.Rd | 17 climaemet-0.2.0/climaemet/man/aemet_daily_period.Rd | 14 climaemet-0.2.0/climaemet/man/aemet_daily_period_all.Rd | 12 climaemet-0.2.0/climaemet/man/aemet_extremes_clim.Rd | 11 climaemet-0.2.0/climaemet/man/aemet_last_obs.Rd | 9 climaemet-0.2.0/climaemet/man/aemet_monthly_clim.Rd | 11 climaemet-0.2.0/climaemet/man/aemet_monthly_period.Rd | 14 climaemet-0.2.0/climaemet/man/aemet_monthly_period_all.Rd | 12 climaemet-0.2.0/climaemet/man/aemet_normal_clim.Rd | 7 climaemet-0.2.0/climaemet/man/aemet_normal_clim_all.Rd | 6 climaemet-0.2.0/climaemet/man/aemet_stations.Rd | 7 climaemet-0.2.0/climaemet/man/climaemet-package.Rd | 1 climaemet-0.2.0/climaemet/man/climatestripes_station.Rd |only climaemet-0.2.0/climaemet/man/climatogram_normal.Rd |only climaemet-0.2.0/climaemet/man/climatogram_period.Rd |only climaemet-0.2.0/climaemet/man/dms2decdegrees.Rd | 9 climaemet-0.2.0/climaemet/man/figures/climatogram.jpeg |only climaemet-0.2.0/climaemet/man/figures/stripes.jpeg |only climaemet-0.2.0/climaemet/man/figures/windrose.jpeg |only climaemet-0.2.0/climaemet/man/first_day_of_year.Rd | 10 climaemet-0.2.0/climaemet/man/get_data_aemet.Rd | 8 climaemet-0.2.0/climaemet/man/ggstripes.Rd | 21 climaemet-0.2.0/climaemet/man/ggwindrose.Rd |only climaemet-0.2.0/climaemet/man/last_day_of_year.Rd | 10 climaemet-0.2.0/climaemet/man/windrose_days.Rd |only climaemet-0.2.0/climaemet/man/windrose_period.Rd |only 37 files changed, 1208 insertions(+), 287 deletions(-)
Title: Single-Equation Penalized Error-Correction Selector (SPECS)
Description: Implementation of SPECS, your favourite Single-Equation Penalized Error-Correction Selector developed in
Smeekes and Wijler (2020) <arXiv:1809.08889>. SPECS provides a fully automated estimation procedure for large and potentially
(co)integrated datasets. The dataset in levels is converted to a conditional error-correction model, either by the user or
by means of the functions included in this package, and various specialised forms of penalized regression can be applied to
the model. Automated options for initializing and selecting a sequence of penalties, as well as the construction of penalty
weights via an initial estimator, are available. Moreover, the user may choose from a number of pre-specified deterministic
configurations to further simplify the model building process.
Author: Etienne Wijler [aut, cre],
Stephan Smeekes [aut] (<https://orcid.org/0000-0002-0157-639X>)
Maintainer: Etienne Wijler <e.wijler@maastrichtuniversity.nl>
Diff between specs versions 0.1.0 dated 2020-07-06 and 0.1.1 dated 2020-07-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/Unempl_GT.RData |binary src/specs.cpp | 5 +++-- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between set6 versions 0.1.5 dated 2020-07-01 and 0.1.6 dated 2020-07-17
DESCRIPTION | 6 MD5 | 138 +++++------ NEWS.md | 5 R/Properties.R | 105 +++++---- R/Set.R | 201 +++++++++-------- R/SetWrapper.R | 41 +-- R/SetWrapper_ComplementSet.R | 114 +++++---- R/SetWrapper_ExponentSet.R | 60 ++--- R/SetWrapper_PowersetSet.R | 62 +++-- R/SetWrapper_ProductSet.R | 88 ++++--- R/SetWrapper_UnionSet.R | 114 +++++---- R/Set_ConditionalSet.R | 109 +++++---- R/Set_FuzzySet.R | 170 ++++++++------ R/Set_FuzzySet_FuzzyTuple.R | 80 +++--- R/Set_Interval.R | 188 +++++++++------- R/Set_Interval_SpecialSet.R | 251 ++++++++++++--------- R/Set_LogicalSet.R | 10 R/Set_Tuple.R | 79 +++--- R/Set_UniversalSet.R | 36 +-- R/asFuzzySet.R | 92 ++++--- R/asInterval.R | 48 ++-- R/asSet.R | 51 ++-- R/assertions.R | 288 ++++++++++++++----------- R/atomic_coercions.R | 9 R/helpers.R | 185 +++++++++------- R/listSpecialSets.R | 27 +- R/operation_cleaner.R | 45 ++- R/operation_powerset.R | 58 ++--- R/operation_setcomplement.R | 260 ++++++++++++---------- R/operation_setintersect.R | 140 ++++++------ R/operation_setpower.R | 24 +- R/operation_setproduct.R | 75 +++--- R/operation_setsymdiff.R | 16 - R/operation_setunion.R | 236 +++++++++++--------- R/operators.R | 14 - R/set6-package.R | 2 R/set6.news.R | 5 R/setSymbol.R | 65 ++--- R/useUnicode.R | 8 R/zzz.R | 13 - build/vignette.rds |binary inst/doc/set6.html | 22 + tests/testthat.R | 1 tests/testthat/test-set6news.R | 2 tests/testthat/test_misc_helpers.R | 81 +++---- tests/testthat/test_misc_listspecialset.R | 2 tests/testthat/test_misc_unicode.R | 2 tests/testthat/test_operation_powerset.R | 47 ++-- tests/testthat/test_operations_setcomplement.R | 107 +++++---- tests/testthat/test_operations_setintersect.R | 110 +++++---- tests/testthat/test_operations_setpower.R | 29 +- tests/testthat/test_operations_setproduct.R | 70 +++--- tests/testthat/test_operations_setsymdiff.R | 25 +- tests/testthat/test_operations_setunion.R | 80 +++--- tests/testthat/test_properties.R | 4 tests/testthat/test_set.R | 224 +++++++++---------- tests/testthat/test_set_conditionalset.R | 30 +- tests/testthat/test_set_fuzzyset.R | 134 +++++------ tests/testthat/test_set_fuzzyset_fuzzytuple.R | 128 +++++------ tests/testthat/test_set_interval.R | 200 ++++++++--------- tests/testthat/test_set_interval_specialset.R | 14 - tests/testthat/test_set_logicalset.R | 4 tests/testthat/test_set_tuple.R | 104 ++++----- tests/testthat/test_set_universalset.R | 30 +- tests/testthat/test_setwrapper.R | 14 - tests/testthat/test_setwrapper_complementset.R | 16 - tests/testthat/test_setwrapper_exponentset.R | 12 - tests/testthat/test_setwrapper_powersetset.R | 38 +-- tests/testthat/test_setwrapper_productset.R | 40 ++- tests/testthat/test_setwrapper_unionset.R | 48 ++-- 70 files changed, 2813 insertions(+), 2323 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. This package includes functions to improve spatial-temporal modelling tasks using 'caret'. It prepares data for Leave-Location-Out and Leave-Time-Out cross-validation which are target-oriented validation strategies for spatial-temporal models. To decrease overfitting and improve model performances, the package implements a forward feature selection that selects suitable predictor variables in view to their contribution to the target-oriented performance.
Author: Hanna Meyer [cre, aut],
Chris Reudenbach [ctb],
Marvin Ludwig [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 0.4.1 dated 2020-05-19 and 0.4.2 dated 2020-07-17
DESCRIPTION | 12 MD5 | 43 - NEWS.md | 9 R/CAST-package.R | 3 R/CreateSpacetimeFolds.R | 17 R/aoa.R | 118 ++- R/ffs.R | 26 build/vignette.rds |binary inst/doc/AOA-tutorial.R | 60 - inst/doc/AOA-tutorial.Rmd | 14 inst/doc/AOA-tutorial.html | 57 - inst/doc/CAST-intro.R | 70 +- inst/doc/CAST-intro.Rmd | 64 +- inst/doc/CAST-intro.html | 1385 +++++++++++++++++++++++++------------------- man/CAST.Rd | 1 man/CreateSpacetimeFolds.Rd | 19 man/aoa.Rd | 48 - man/bss.Rd | 14 man/ffs.Rd | 18 man/plot_ffs.Rd | 14 vignettes/AOA-tutorial.Rmd | 14 vignettes/AOA-tutorial.md |only vignettes/CAST-intro.Rmd | 64 +- 23 files changed, 1233 insertions(+), 837 deletions(-)
Title: Modelling Pathways and Movement Potential Within a Landscape
(Version 1.7.4)
Description: Provides functionality to calculate cost surfaces based on slope (e.g. Herzog, 2010; Llobera and Sluckin, 2007 <doi:10.1016/j.jtbi.2007.07.020>; París Roche, 2002; Tobler, 1993), traversing slope (Bell and Lock, 2000), and landscape features (Llobera, 2000) to be used when modelling pathways and movement potential within a landscape (e.g. Llobera, 2015; Verhagen, 2013; White and Barber, 2012 <doi:10.1016/j.jas.2012.04.017>).
Author: Joseph Lewis [aut, cre]
Maintainer: Joseph Lewis <josephlewis1992@gmail.com>
Diff between leastcostpath versions 1.3.6 dated 2020-05-15 and 1.7.4 dated 2020-07-17
DESCRIPTION | 13 +- MD5 | 83 +++++++++------- NAMESPACE | 8 + NEWS.md | 45 ++++++++ R/PDI_validation.R |only R/add_dem_error.R |only R/calculate_slope.R |only R/cost.R |only R/cost_matrix.R | 4 R/create_CCP_lcps.R | 4 R/create_FETE_lcps.R | 4 R/create_banded_lcps.R | 4 R/create_barrier_cs.R | 26 +++-- R/create_feature_cs.R | 22 +++- R/create_lcp.R | 8 - R/create_lcp_density.R | 12 +- R/create_slope_cs.R | 216 +++++------------------------------------- R/create_stochastic_lcp.R |only R/create_traversal_cs.R | 16 ++- R/create_wide_lcp.R |only R/crop_cs.R |only R/neighbours.R |only R/validate_lcp.R | 2 R/wide_path_matrix.R |only README.md | 96 +++++++++++++++--- inst/doc/leastcostpath-1.R | 2 inst/doc/leastcostpath-1.Rmd | 6 - inst/doc/leastcostpath-1.html | 26 ++--- inst/doc/leastcostpath-2.Rmd | 4 inst/doc/leastcostpath-2.html | 92 +++++++++-------- man/PDI_validation.Rd |only man/add_dem_error.Rd |only man/cost_matrix.Rd | 7 - man/create_CCP_lcps.Rd | 3 man/create_FETE_lcps.Rd | 3 man/create_banded_lcps.Rd | 3 man/create_barrier_cs.Rd | 70 +++++++------ man/create_feature_cs.Rd | 9 + man/create_lcp.Rd | 3 man/create_lcp_density.Rd | 4 man/create_slope_cs.Rd | 106 ++++++++++---------- man/create_stochastic_lcp.Rd |only man/create_traversal_cs.Rd | 2 man/create_wide_lcp.Rd |only man/crop_cs.Rd |only man/neighbours_32.Rd |only man/neighbours_48.Rd |only man/validate_lcp.Rd | 3 man/wide_path_matrix.Rd |only vignettes/leastcostpath-1.Rmd | 6 - vignettes/leastcostpath-2.Rmd | 4 51 files changed, 487 insertions(+), 429 deletions(-)
Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the
'dialr' package.
Author: Danny Smith [aut, cre],
Google Inc. [ctb, cph] (libphonenumber),
Vonage Holdings Corp. [ctb, cph] (libphonenumber),
Ian Galpin [ctb, cph] (libphonenumber),
Ben Gertzfield [ctb, cph] (libphonenumber)
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialrjars versions 8.12.0 dated 2020-03-23 and 8.12.6 dated 2020-07-17
dialrjars-8.12.0/dialrjars/inst/java/carrier-1.126.jar |only dialrjars-8.12.0/dialrjars/inst/java/geocoder-2.136.jar |only dialrjars-8.12.0/dialrjars/inst/java/libphonenumber-8.12.0.jar |only dialrjars-8.12.0/dialrjars/inst/java/prefixmapper-2.136.jar |only dialrjars-8.12.6/dialrjars/DESCRIPTION | 8 +- dialrjars-8.12.6/dialrjars/MD5 | 12 ++-- dialrjars-8.12.6/dialrjars/NEWS.md | 30 ++++++++++ dialrjars-8.12.6/dialrjars/inst/java/carrier-1.132.jar |only dialrjars-8.12.6/dialrjars/inst/java/geocoder-2.142.jar |only dialrjars-8.12.6/dialrjars/inst/java/libphonenumber-8.12.6.jar |only dialrjars-8.12.6/dialrjars/inst/java/prefixmapper-2.142.jar |only 11 files changed, 40 insertions(+), 10 deletions(-)
Title: Discriminant Analysis Incorporating Individual Uncertainties
Description: The qda() function from package 'MASS' is extended to calculate a weighted linear (LDA) and quadratic discriminant analysis (QDA) by changing the group variances and group means based on cell-wise uncertainties.
The uncertainties can be derived e.g. through relative errors for each individual measurement (cell), not only row-wise or column-wise uncertainties.
The method can be applied compositional data (e.g. portions of substances, concentrations) and non-compositional data.
Author: Solveig Pospiech [aut, cre],
K. Gerald van den Boogaart [ctb]
Maintainer: Solveig Pospiech <s.pospiech@hzdr.de>
Diff between vdar versions 0.1.2-1 dated 2020-03-19 and 0.1.3 dated 2020-07-17
DESCRIPTION | 8 - MD5 | 28 ++-- NAMESPACE | 5 R/subfunctions.R | 52 ++++++-- R/weighted_DA.R | 295 ++++++++++++++++++++++++++++++++++++++-------- man/dataobs.Rd | 6 man/dataobs_coda.Rd | 6 man/datatrue.Rd | 6 man/datatrue_coda.Rd | 6 man/force_posdef.Rd | 2 man/generalized_mean.Rd | 6 man/uncertainties.Rd | 6 man/uncertainties_coda.Rd | 6 man/vlda.Rd | 20 +-- man/vqda.Rd | 18 +- 15 files changed, 359 insertions(+), 111 deletions(-)
Title: Searching for Footprints of Selection using 'Extended Haplotype
Homozygosity' Based Tests
Description: Population genetic data such as 'Single Nucleotide
Polymorphisms' (SNPs) is often used to identify genomic regions
that have been under recent natural or artificial selection
and might provide clues about the molecular mechanisms of adaptation.
One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH),
introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to
several statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
detecting positive or 'Darwinian' selection within a single population as well as
'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and
'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted
at differential selection between two populations.
Various plotting functions are also included to facilitate
visualization and interpretation of these statistics.
Due to changes in the API, albeit mostly minor,
versions 3.X are not compatible with versions 2.0.X.
Note: optionally, vcf files can be imported using package vcfR. That package
is currently removed from CRAN, but can still be installed from
<https://github.com/knausb/vcfR> following instructions there.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Alexander Klassmann <rehh@oneoverx.eu>
Diff between rehh versions 3.1.1 dated 2020-06-19 and 3.1.2 dated 2020-07-17
DESCRIPTION | 12 + MD5 | 34 ++--- NEWS.md | 4 R/data2haplohh.R | 218 +++++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/examples.R | 15 +- inst/doc/examples.Rmd | 19 +-- inst/doc/examples.html | 48 ++++--- inst/doc/rehh.R | 27 ++-- inst/doc/rehh.Rmd | 37 +++-- inst/doc/rehh.html | 72 ++++------- man/data2haplohh.Rd | 14 +- man/rehh-package.Rd | 3 tests/testthat/test_data2haplohh.R | 13 +- tests/testthat/test_error_messages.R | 136 ++++++++++++++++++++- tests/testthat/test_scan_hh.R | 3 vignettes/examples.Rmd | 19 +-- vignettes/rehh.Rmd | 37 +++-- 18 files changed, 481 insertions(+), 230 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.4 dated 2018-11-13 and 0.3.5 dated 2020-07-17
ChangeLog | 4 DESCRIPTION | 8 MD5 | 63 - NEWS.md | 4 R/configr.R | 15 R/configtype.R | 72 + R/merge.R | 2 R/parse.R | 2 build/vignette.rds |binary inst/doc/configr.R | 26 inst/doc/configr.html | 1418 +++++++++++++++++++------------------ inst/doc/filetypes.R | 2 inst/doc/filetypes.html | 466 ++++++------ inst/extdata/config.global.toml | 6 inst/extdata/config.simple.toml |only man/config.list.merge.Rd | 3 man/configr.Rd | 11 man/convert.config.Rd | 7 man/eval.config.Rd | 9 man/eval.config.merge.Rd | 7 man/eval.config.sections.Rd | 6 man/fetch.config.Rd | 9 man/get.config.type.Rd | 15 man/is.ini.file.Rd | 11 man/is.json.file.Rd | 9 man/is.toml.file.Rd | 9 man/is.yaml.file.Rd | 11 man/parse.extra.Rd | 13 man/read.config.Rd | 16 man/str2config.Rd | 4 man/write.config.Rd | 9 tests/testthat/test_a_configtype.R | 3 tests/testthat/test_k_parse.R | 2 33 files changed, 1222 insertions(+), 1020 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and function to adjust a variety of stochastic blockmodels (SBM).
Support at the moment Simple and Bipartite SBM (undirected and directed) for Bernoulli, Poisson and
Gaussian emission laws of the edges as described in Léger, 2016 <arxiv:1602.07587>.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
Sophie Donnet [aut],
großBM team [ctb],
Pierre Barbillon [ctb] (<https://orcid.org/0000-0002-7766-7693>)
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.2.0 dated 2020-07-07 and 0.2.1 dated 2020-07-17
DESCRIPTION | 8 MD5 | 38 +-- NEWS.md | 7 R/R6Class-BipartiteSBM_fit.R | 6 R/R6Class-SBM.R | 6 R/R6Class-SBM_fit.R | 2 R/R6Class-SimpleSBM_fit.R | 2 R/utils.R | 6 README.md | 8 inst/doc/SBM_fungus_tree_network.R | 18 + inst/doc/SBM_fungus_tree_network.Rmd | 25 ++ inst/doc/SBM_fungus_tree_network.html | 271 +++++++++++++--------- man/coef.SBM.Rd | 4 src/roundProduct.cpp | 3 tests/testthat/test-BipartiteSBM_fit.R | 47 +++ tests/testthat/test-BipartiteSBM_fit_covariates.R |only tests/testthat/test-BipartiteSBM_sampler.R | 2 tests/testthat/test-SimpleSBM_fit.R | 262 ++++++++++++++++++++- tests/testthat/test-SimpleSBM_fit_covariates.R |only tests/testthat/test-SimpleSBM_sampler.R | 2 vignettes/SBM_fungus_tree_network.Rmd | 25 ++ 21 files changed, 595 insertions(+), 147 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.3.0 dated 2020-06-03 and 0.4.0 dated 2020-07-17
DESCRIPTION | 8 ++--- MD5 | 46 +++++++++++++++++----------------- NAMESPACE | 3 ++ NEWS.md | 5 +++ R/check_packages_installed.R | 1 R/rd_info.R |only R/str_collapse.R | 16 ++++++++--- README.md | 3 -- man/Dictionary.Rd | 4 +- man/check_packages_installed.Rd | 1 man/compat-map.Rd | 2 - man/cross_join.Rd | 6 ++-- man/get_seed.Rd | 2 - man/map_values.Rd | 2 - man/rd_info.Rd |only man/require_namespaces.Rd | 2 - man/rowwise_table.Rd | 2 - man/sequence_helpers.Rd | 4 +- man/shuffle.Rd | 2 - man/str_collapse.Rd | 8 +++-- man/which_min.Rd | 2 - tests/testthat/test_as_short_string.R | 2 - tests/testthat/test_map.R | 2 - tests/testthat/test_map_values.R | 4 +- tests/testthat/test_topo_sort.R | 25 ++++++++---------- 25 files changed, 84 insertions(+), 68 deletions(-)
Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Author: S. Thomas Kelly [ctb],
S. Thomas Kelly [aut, cre],
Michael A. Black [aut, ths],
Robrecht Cannoodt [ctb],
Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>
Diff between graphsim versions 1.0.0 dated 2020-07-02 and 1.0.1 dated 2020-07-17
graphsim-1.0.0/graphsim/inst/doc/plots_directed.R |only graphsim-1.0.0/graphsim/inst/doc/plots_directed.Rmd |only graphsim-1.0.0/graphsim/inst/doc/simulate_expression.R |only graphsim-1.0.0/graphsim/inst/doc/simulate_expression.Rmd |only graphsim-1.0.0/graphsim/man/make_adjmatrix_graph.Rd |only graphsim-1.0.0/graphsim/man/make_state_matrix.Rd |only graphsim-1.0.0/graphsim/vignettes/demo.gif |only graphsim-1.0.0/graphsim/vignettes/demo2.gif |only graphsim-1.0.0/graphsim/vignettes/simulate_expression.md |only graphsim-1.0.0/graphsim/vignettes/simulate_expression_files |only graphsim-1.0.1/graphsim/DESCRIPTION | 22 - graphsim-1.0.1/graphsim/MD5 | 68 +--- graphsim-1.0.1/graphsim/NEWS.md | 8 graphsim-1.0.1/graphsim/R/adjmat.R | 21 + graphsim-1.0.1/graphsim/R/commonlink.R | 21 + graphsim-1.0.1/graphsim/R/distance.R | 26 + graphsim-1.0.1/graphsim/R/generate.R | 29 + graphsim-1.0.1/graphsim/R/graphsim-package.R |only graphsim-1.0.1/graphsim/R/laplacian.R | 19 + graphsim-1.0.1/graphsim/R/plot_directed.R | 19 + graphsim-1.0.1/graphsim/R/sigma.R | 23 + graphsim-1.0.1/graphsim/R/state.R | 24 + graphsim-1.0.1/graphsim/README.md | 74 +++- graphsim-1.0.1/graphsim/build/vignette.rds |binary graphsim-1.0.1/graphsim/inst/CITATION | 55 +-- graphsim-1.0.1/graphsim/inst/doc/plots_directed.html | 164 ++++----- graphsim-1.0.1/graphsim/inst/doc/plots_directed.html.asis |only graphsim-1.0.1/graphsim/inst/doc/simulate_expression.html | 165 +++++----- graphsim-1.0.1/graphsim/inst/doc/simulate_expression.html.asis |only graphsim-1.0.1/graphsim/man/generate_expression.Rd | 43 ++ graphsim-1.0.1/graphsim/man/graphsim-package.Rd |only graphsim-1.0.1/graphsim/man/make_adjmatrix.Rd |only graphsim-1.0.1/graphsim/man/make_commonlink.Rd | 34 ++ graphsim-1.0.1/graphsim/man/make_distance.Rd | 39 ++ graphsim-1.0.1/graphsim/man/make_laplacian.Rd | 32 + graphsim-1.0.1/graphsim/man/make_sigma.Rd | 37 ++ graphsim-1.0.1/graphsim/man/make_state.Rd |only graphsim-1.0.1/graphsim/man/plot_directed.Rd | 28 + graphsim-1.0.1/graphsim/vignettes/plots_directed.Rmd | 4 graphsim-1.0.1/graphsim/vignettes/plots_directed.html.asis |only graphsim-1.0.1/graphsim/vignettes/simulate_expression.Rmd | 72 ++-- graphsim-1.0.1/graphsim/vignettes/simulate_expression.html.asis |only 42 files changed, 716 insertions(+), 311 deletions(-)
Title: Dynamic Model Averaging and Dynamic Model Selection for
Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University
of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between fDMA versions 2.2.5 dated 2020-04-03 and 2.2.6 dated 2020-07-17
DESCRIPTION | 10 +-- MD5 | 26 +++++----- NAMESPACE | 2 NEWS | 10 +++ R/altf.R | 116 +++++++++++++++++---------------------------- R/altf2.R | 15 +++-- R/tvp.R | 2 build/vignette.rds |binary inst/CITATION | 14 +++-- inst/doc/fDMA_vignette.pdf |binary man/altf.Rd | 25 +++------ man/altf2.Rd | 28 ++++------ man/altf3.Rd | 19 ++----- man/altf4.Rd | 17 +----- 14 files changed, 122 insertions(+), 162 deletions(-)
Title: Change Point Detection in Genomic Sequences
Description: Estimation of number and location of change points in
mean-shift (piecewise constant) models. Particularly useful (but not confined) to
model genomic sequences of continuous measurements.
Author: Vito M.R. Muggeo
Maintainer: Vito M.R. Muggeo <vito.muggeo@unipa.it>
Diff between cumSeg versions 1.2 dated 2019-01-18 and 1.3 dated 2020-07-17
DESCRIPTION | 10 +-- MD5 | 17 +++-- NAMESPACE | 6 - NEWS |only R/jumpoints.R | 24 +++++-- R/plot.aCGHsegmented.R | 147 ++++++++++++++++++++++++++++++--------------- R/print.aCGHsegmented.R |only man/cumSeg-package.Rd | 10 +-- man/jumpoints.Rd | 12 ++- man/plot.aCGHsegmented.Rd | 11 +++ man/print.aCGHsegmented.Rd |only 11 files changed, 159 insertions(+), 78 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via Three. JAGS types of models may be fitted: 1) With explanatory variables only, boral fits independent column Generalized Linear Models (GLMs) to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui [aut, cre],
Wade Blanchard [aut]
Maintainer: Francis K.C. Hui <fhui28@gmail.com>
Diff between boral versions 1.8.1 dated 2020-06-05 and 1.9 dated 2020-07-17
DESCRIPTION | 19 MD5 | 102 ++-- NAMESPACE | 53 +- R/auxilaryfunctions.R | 558 ++++++++++------------ R/boral.jags.R | 1008 ++++++++++++++++++++--------------------- R/calclogLfunctions.R | 168 +++--- R/checkfunctions.R | 125 ++--- R/getcorrelations.R | 114 ++-- R/getmeasures.R | 376 +++++++-------- R/hpdintervals.R | 42 - R/lvsplots.R | 183 +++---- R/makejagsboralmodel.R | 123 +---- R/makejagsboralnullmodel.R | 106 +--- R/plotboral.R | 49 - R/predictfn.R | 109 +--- R/simdatafunctions.R | 424 ++++++++--------- R/summaryboral.R | 159 +++--- R/tidyboral.R | 81 +-- R/unseenfunctions.R | 267 ++++------ R/varpart.R |only R/ztnbinom.R |only R/ztpoisson.R |only build/boral.pdf |only build/partial.rdb |binary inst/NEWS.Rd | 22 man/about.distributions.Rd | 8 man/about.lvs.Rd | 5 man/about.ssvs.Rd | 5 man/about.traits.Rd | 5 man/boral.Rd | 15 man/calc.condlogLik.Rd | 5 man/calc.logLik.lv0.Rd | 5 man/calc.marglogLik.Rd | 7 man/calc.varpart.Rd | 5 man/coefsplot.Rd | 5 man/create.life.Rd | 7 man/ds.residuals.Rd | 5 man/figures |only man/fitted.boral.Rd | 9 man/get.dic.Rd | 5 man/get.enviro.cor.Rd | 5 man/get.hpdintervals.Rd | 5 man/get.mcmcsamples.Rd | 5 man/get.measures.Rd | 9 man/get.more.measures.Rd | 9 man/get.residual.cor.Rd | 5 man/lvsplot.Rd | 5 man/make.jagsboralmodel.Rd | 7 man/make.jagsboralnullmodel.Rd | 7 man/plot.boral.Rd | 5 man/predict.boral.Rd | 10 man/summary.boral.Rd | 5 man/tidyboral.Rd | 5 53 files changed, 2050 insertions(+), 2211 deletions(-)
Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression
(Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang Zhou [ctb],
Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xiaoleiliu@mail.hzau.edu.cn>
Diff between rMVP versions 1.0.0 dated 2020-05-07 and 1.0.3 dated 2020-07-17
CHANGELOG |only DESCRIPTION | 13 ++-- MD5 | 43 ++++++++------- NAMESPACE | 57 ++++++++++++++----- R/MVP.Data.r | 13 +--- R/MVP.FaSTLMM.LL.r | 16 +---- R/MVP.FarmCPU.r | 30 +++++++++- R/MVP.K.VanRaden.r | 52 +++++++++--------- R/MVP.MLM.r | 14 ++-- R/MVP.PCA.r | 22 +++---- R/MVP.Report.r | 19 ++++-- R/MVP.Utility.r | 1 R/MVP.r | 23 +++++--- R/RcppExports.R | 16 +++-- R/exports.R |only man/MVP.Report.QQplot.Rd | 2 man/reexports.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 60 +++++++++++++-------- src/assoc.cpp | 39 +++++++++---- src/data_converter.cpp | 89 ++++++++++++++++--------------- src/impute.cpp | 25 ++++---- src/kinship.cpp | 134 ++++++++++++++++++++++++++++++++++++++--------- 24 files changed, 424 insertions(+), 248 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.1.0 dated 2020-03-11 and 1.1.1 dated 2020-07-17
SDMtune-1.1.0/SDMtune/R/SDMtune.R |only SDMtune-1.1.0/SDMtune/inst/doc/SDMtune.R |only SDMtune-1.1.0/SDMtune/inst/doc/SDMtune.Rmd |only SDMtune-1.1.0/SDMtune/inst/doc/SDMtune.html |only SDMtune-1.1.0/SDMtune/man/SDMtune-pkg.Rd |only SDMtune-1.1.0/SDMtune/man/figures/logo.svg |only SDMtune-1.1.0/SDMtune/tests/spelling.R |only SDMtune-1.1.0/SDMtune/vignettes/SDMtune.Rmd |only SDMtune-1.1.1/SDMtune/DESCRIPTION | 34 - SDMtune-1.1.1/SDMtune/MD5 | 338 +++++----- SDMtune-1.1.1/SDMtune/NAMESPACE | 71 -- SDMtune-1.1.1/SDMtune/NEWS.md | 19 SDMtune-1.1.1/SDMtune/R/ANN-class.R | 7 SDMtune-1.1.1/SDMtune/R/BRT-class.R | 7 SDMtune-1.1.1/SDMtune/R/Maxent-class.R | 4 SDMtune-1.1.1/SDMtune/R/Maxnet-class.R | 3 SDMtune-1.1.1/SDMtune/R/RF-class.R | 7 SDMtune-1.1.1/SDMtune/R/SDMmodel-class.R | 17 SDMtune-1.1.1/SDMtune/R/SDMmodel2MaxEnt.R | 14 SDMtune-1.1.1/SDMtune/R/SDMmodelCV-class.R | 18 SDMtune-1.1.1/SDMtune/R/SDMtune-class.R | 11 SDMtune-1.1.1/SDMtune/R/SDMtune-package.R |only SDMtune-1.1.1/SDMtune/R/SWD-class.R | 11 SDMtune-1.1.1/SDMtune/R/addSamplesToBg.R | 12 SDMtune-1.1.1/SDMtune/R/aicc.R | 29 SDMtune-1.1.1/SDMtune/R/auc.R | 29 SDMtune-1.1.1/SDMtune/R/chart-utils.R | 30 SDMtune-1.1.1/SDMtune/R/checkMaxentInstallation.R |only SDMtune-1.1.1/SDMtune/R/confMatrix.R | 25 SDMtune-1.1.1/SDMtune/R/corVar.R | 17 SDMtune-1.1.1/SDMtune/R/doJk.R | 44 - SDMtune-1.1.1/SDMtune/R/getTunableArgs.R |only SDMtune-1.1.1/SDMtune/R/gridSearch.R | 46 - SDMtune-1.1.1/SDMtune/R/maxentTh.R | 6 SDMtune-1.1.1/SDMtune/R/maxentVarImp.R | 18 SDMtune-1.1.1/SDMtune/R/mergeSWD.R | 29 SDMtune-1.1.1/SDMtune/R/modelReport.R | 37 - SDMtune-1.1.1/SDMtune/R/optimizeModel.R | 69 +- SDMtune-1.1.1/SDMtune/R/plotCor.R | 54 - SDMtune-1.1.1/SDMtune/R/plotJk.R | 27 SDMtune-1.1.1/SDMtune/R/plotPA.R | 57 - SDMtune-1.1.1/SDMtune/R/plotPred.R | 44 - SDMtune-1.1.1/SDMtune/R/plotROC.R | 32 SDMtune-1.1.1/SDMtune/R/plotResponse.R | 86 +- SDMtune-1.1.1/SDMtune/R/plotVarImp.R | 23 SDMtune-1.1.1/SDMtune/R/predict-ANN.R | 6 SDMtune-1.1.1/SDMtune/R/predict-BRT.R | 6 SDMtune-1.1.1/SDMtune/R/predict-Maxent.R | 15 SDMtune-1.1.1/SDMtune/R/predict-RF.R | 6 SDMtune-1.1.1/SDMtune/R/predict-SDMmodel.R | 106 +-- SDMtune-1.1.1/SDMtune/R/predict-SDMmodelCV.R | 114 +-- SDMtune-1.1.1/SDMtune/R/prepareSWD.R | 17 SDMtune-1.1.1/SDMtune/R/randomFolds.R | 25 SDMtune-1.1.1/SDMtune/R/randomSearch.R | 38 - 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Title: Spatial Objects of the Czech Republic
Description: Administrative regions and other spatial objects of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between RCzechia versions 1.5.0 dated 2020-05-04 and 1.5.1 dated 2020-07-17
DESCRIPTION | 10 MD5 | 12 NEWS.md | 5 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/vignette.html | 496 ++++++++++++++++---------------- tests/testthat/test-1-data-structures.R | 4 7 files changed, 276 insertions(+), 251 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ctb],
Duncan Golicher [ctb],
Josh Gray [ctb],
Jonathan A. Greenberg [ctb],
Paul Hiemstra [ctb],
Kassel Hingee [ctb],
Institute for Mathematics Applied Geosciences [cph],
Charles Karney [ctb],
Matteo Mattiuzzi [ctb],
Steven Mosher [ctb],
Jakub Nowosad [ctb],
Edzer Pebesma [ctb],
Oscar Perpinan Lamigueiro [ctb],
Etienne B. Racine [ctb],
Barry Rowlingson [ctb],
Ashton Shortridge [ctb],
Bill Venables [ctb],
Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.3-7 dated 2020-06-27 and 3.3-13 dated 2020-07-17
raster-3.3-13/raster/DESCRIPTION | 10 ++-- raster-3.3-13/raster/MD5 | 44 ++++++++++---------- raster-3.3-13/raster/R/bind.R | 65 ++++++++++++++++-------------- raster-3.3-13/raster/R/buffer.R | 6 ++ raster-3.3-13/raster/R/coverPolygons.R | 27 ++++-------- raster-3.3-13/raster/R/cropSpatial.R | 24 ++++++----- raster-3.3-13/raster/R/erase.R | 23 ++++++---- raster-3.3-13/raster/R/intersect_sp.R | 65 +++++++++++++++++------------- raster-3.3-13/raster/R/netCDFtoRasterCD.R | 8 ++- raster-3.3-13/raster/R/print.R | 2 raster-3.3-13/raster/R/trim.R | 23 +++++----- raster-3.3-13/raster/R/union_sp.R | 15 ++++-- raster-3.3-13/raster/R/xyValuesBuffer.R | 4 + raster-3.3-13/raster/inst/tests |only raster-3.3-13/raster/man/density.Rd | 2 raster-3.3-13/raster/man/plot.Rd | 2 raster-3.3-13/raster/man/strech.Rd | 10 ++-- raster-3.3-13/raster/man/zoom.Rd | 2 raster-3.3-13/raster/src/terrain.cpp | 7 +-- raster-3.3-7/raster/tests |only 20 files changed, 184 insertions(+), 155 deletions(-)
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of predicates (is_* functions) to check the state of your
variables, and assertions (assert_* functions) to throw errors if they
aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: ORPHANED
Diff between assertive versions 0.3-5 dated 2016-12-30 and 0.3-5.1 dated 2020-07-17
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-24 0.0-2
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that wraps 'install.packages',
'remotes::install_github', 'versions::install.versions', and 'base::require'
that allows for reproducible workflows. As with other functions in a
reproducible workflow, this package emphasizes functions that return the
same result whether it is the first or subsequent times running the function.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.0.4 dated 2020-06-05 and 0.0.5 dated 2020-07-17
Require-0.0.4/Require/man/tempFilesAndFolders.Rd |only Require-0.0.4/Require/tests/testit/tmp.txt |only Require-0.0.5/Require/DESCRIPTION | 12 Require-0.0.5/Require/MD5 | 51 +- Require-0.0.5/Require/NAMESPACE | 2 Require-0.0.5/Require/NEWS.md | 15 Require-0.0.5/Require/R/CRAN.R | 6 Require-0.0.5/Require/R/Require-helpers.R | 201 +++++---- Require-0.0.5/Require/R/Require.R | 15 Require-0.0.5/Require/R/extract.R | 23 - Require-0.0.5/Require/R/helpers.R | 25 - Require-0.0.5/Require/R/pkgDep.R | 207 ++++++++- Require-0.0.5/Require/R/pkgSnapshot.R | 2 Require-0.0.5/Require/R/setLibPaths.R | 2 Require-0.0.5/Require/README.md | 7 Require-0.0.5/Require/man/Require-internals.Rd | 1 Require-0.0.5/Require/man/Require.Rd | 2 Require-0.0.5/Require/man/checkPath.Rd | 3 Require-0.0.5/Require/man/extractPkgName.Rd | 71 +-- Require-0.0.5/Require/man/pkgDep.Rd | 60 ++ Require-0.0.5/Require/man/setLibPaths.Rd | 2 Require-0.0.5/Require/man/tempdir2.Rd |only Require-0.0.5/Require/man/tempfile2.Rd |only Require-0.0.5/Require/man/trimVersionNumber.Rd |only Require-0.0.5/Require/tests/testit/packageVersions.txt | 376 ++++------------- Require-0.0.5/Require/tests/testit/test-helpers.R | 3 Require-0.0.5/Require/tests/testit/test-packages.R | 53 +- Require-0.0.5/Require/tests/testit/test-packagesLong.R | 14 Require-0.0.5/Require/tests/testit/test-pkgDep.R | 20 29 files changed, 644 insertions(+), 529 deletions(-)
Title: Toolkit for Data Analytics in Human Resources
Description: Transform and analyze workforce data in meaningful ways for human resources (HR) analytics. Get started with workforce planning using a simple Shiny app.
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>
Diff between hR versions 0.2.1 dated 2019-11-10 and 0.2.2 dated 2020-07-17
DESCRIPTION | 10 +- MD5 | 32 +++--- NAMESPACE | 3 R/hierarchyLong.R | 27 +---- R/hierarchyStats.R |only R/hierarchyValid.R |only R/hierarchyWide.R | 29 +---- README.md | 2 build/vignette.rds |binary inst/doc/hR.R | 38 ++++++- inst/doc/hR.Rmd | 41 +++++++- inst/doc/hR.html | 219 ++++++++++++++++++++++++++++---------------- inst/workforcePlanApp/app.R | 6 - man/hierarchyLong.Rd | 4 man/hierarchyStats.Rd |only man/hierarchyValid.Rd |only man/hierarchyWide.Rd | 4 man/workforceHistory.Rd | 6 - vignettes/hR.Rmd | 41 +++++++- 19 files changed, 290 insertions(+), 172 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>
Diff between dipsaus versions 0.0.8 dated 2020-06-23 and 0.0.9 dated 2020-07-17
dipsaus-0.0.8/dipsaus/man/dev_create.Rd |only dipsaus-0.0.9/dipsaus/DESCRIPTION | 13 dipsaus-0.0.9/dipsaus/MD5 | 66 +- dipsaus-0.0.9/dipsaus/NAMESPACE | 17 dipsaus-0.0.9/dipsaus/NEWS.md | 26 dipsaus-0.0.9/dipsaus/R/graphics.R | 77 ++ dipsaus-0.0.9/dipsaus/R/language.R | 39 + dipsaus-0.0.9/dipsaus/R/map-s3.R | 4 dipsaus-0.0.9/dipsaus/R/persist.R | 4 dipsaus-0.0.9/dipsaus/R/shiny-inputbindings.R | 51 + dipsaus-0.0.9/dipsaus/R/strings.R | 144 ++++- dipsaus-0.0.9/dipsaus/R/utils-package.R | 61 ++ dipsaus-0.0.9/dipsaus/R/utils-rstudio.R |only dipsaus-0.0.9/dipsaus/R/utils.R | 46 + dipsaus-0.0.9/dipsaus/build/vignette.rds |binary dipsaus-0.0.9/dipsaus/inst/doc/async_evaluator.html | 236 ++++---- dipsaus-0.0.9/dipsaus/inst/doc/r_expr_addons.Rmd | 2 dipsaus-0.0.9/dipsaus/inst/doc/r_expr_addons.html | 298 +++++------ dipsaus-0.0.9/dipsaus/inst/doc/shiny_customized_widgets.html | 102 ++- dipsaus-0.0.9/dipsaus/inst/doc/utility_functions.html | 170 +++--- dipsaus-0.0.9/dipsaus/man/PersistContainer.Rd | 2 dipsaus-0.0.9/dipsaus/man/add_to_session.Rd |only dipsaus-0.0.9/dipsaus/man/ask_yesno.Rd | 21 dipsaus-0.0.9/dipsaus/man/capture_expr.Rd |only dipsaus-0.0.9/dipsaus/man/clear_env.Rd |only dipsaus-0.0.9/dipsaus/man/do_nothing.Rd |only dipsaus-0.0.9/dipsaus/man/graphic-devices.Rd |only dipsaus-0.0.9/dipsaus/man/map.Rd | 3 dipsaus-0.0.9/dipsaus/man/prepare_install.Rd | 15 dipsaus-0.0.9/dipsaus/man/print_directory_tree.Rd |only dipsaus-0.0.9/dipsaus/man/restart_session.Rd |only dipsaus-0.0.9/dipsaus/man/rs_active_project.Rd |only dipsaus-0.0.9/dipsaus/man/rs_avail.Rd |only dipsaus-0.0.9/dipsaus/man/rs_exec.Rd |only dipsaus-0.0.9/dipsaus/man/rs_focus_console.Rd |only dipsaus-0.0.9/dipsaus/man/rs_save_all.Rd |only dipsaus-0.0.9/dipsaus/man/rs_select_path.Rd |only dipsaus-0.0.9/dipsaus/man/rs_viewer.Rd |only dipsaus-0.0.9/dipsaus/man/shiny_is_running.Rd |only dipsaus-0.0.9/dipsaus/man/test_farg.Rd |only dipsaus-0.0.9/dipsaus/tests/testthat/test.maps.R | 8 dipsaus-0.0.9/dipsaus/tests/testthat/test.queues.R | 2 dipsaus-0.0.9/dipsaus/vignettes/r_expr_addons.Rmd | 2 43 files changed, 956 insertions(+), 453 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-15 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-18 0.0.8
2015-02-10 0.0.3
Title: Assertions for Checking the State of R
Description: A set of predicates and assertions for checking the state and
capabilities of R, the operating system it is running on, and the IDE
being used. This is mainly for use by other package developers who
want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: ORPHANED
Diff between assertive.reflection versions 0.0-4 dated 2016-12-30 and 0.0-4.1 dated 2020-07-17
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- tests/testthat/test-r-has-capabilities.R | 8 +++++++- 3 files changed, 14 insertions(+), 9 deletions(-)
More information about assertive.reflection at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-03 1.0.2