Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <https://cyclestreets.net/> and
calculation of route segment attributes such as bearing.
The package implements the 'travel flow aggregration' method
described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779>.
Further information on the package's aim and scope can be found
in the vignettes and in a paper in the R Journal
(Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Richard Ellison [aut],
Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>),
Barry Rowlingson [ctb],
Nick Bearman [ctb],
Nikolai Berkoff [ctb],
Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10),
Mark Padgham [ctb],
Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.8.0 dated 2020-10-28 and 0.8.1 dated 2021-01-07
stplanr-0.8.0/stplanr/vignettes/rsconnect |only stplanr-0.8.1/stplanr/DESCRIPTION | 24 stplanr-0.8.1/stplanr/MD5 | 159 stplanr-0.8.1/stplanr/NAMESPACE | 13 stplanr-0.8.1/stplanr/NEWS.md | 13 stplanr-0.8.1/stplanr/R/SpatialLinesNetwork.R | 136 stplanr-0.8.1/stplanr/R/catchmentArea.R | 14 stplanr-0.8.1/stplanr/R/geo_projected.R | 14 stplanr-0.8.1/stplanr/R/gps.R | 2 stplanr-0.8.1/stplanr/R/line_breakup.R | 3 stplanr-0.8.1/stplanr/R/linefuns.R | 8 stplanr-0.8.1/stplanr/R/loadABS.R | 6 stplanr-0.8.1/stplanr/R/od-funs.R | 73 stplanr-0.8.1/stplanr/R/oneway.R | 17 stplanr-0.8.1/stplanr/R/overline.R | 470 - stplanr-0.8.1/stplanr/R/rnet-clean.R | 233 stplanr-0.8.1/stplanr/R/rnet_boundary_points.R |only stplanr-0.8.1/stplanr/R/rnet_group.R |only stplanr-0.8.1/stplanr/R/route.R | 292 stplanr-0.8.1/stplanr/R/route_bikecitizens.R |only stplanr-0.8.1/stplanr/R/route_cyclestreets.R | 8 stplanr-0.8.1/stplanr/R/route_funs.R | 14 stplanr-0.8.1/stplanr/R/route_google.R | 6 stplanr-0.8.1/stplanr/R/route_local.R | 26 stplanr-0.8.1/stplanr/R/route_osrm.R |only stplanr-0.8.1/stplanr/R/slope.R | 45 stplanr-0.8.1/stplanr/R/stplanr-package.R | 1 stplanr-0.8.1/stplanr/R/toptail.R | 6 stplanr-0.8.1/stplanr/README.md | 2 stplanr-0.8.1/stplanr/build/partial.rdb |only stplanr-0.8.1/stplanr/inst/doc/stplanr-od.Rmd | 4 stplanr-0.8.1/stplanr/inst/doc/stplanr-od.html | 4171 ---------- stplanr-0.8.1/stplanr/inst/doc/stplanr-paper.html | 252 stplanr-0.8.1/stplanr/inst/doc/stplanr-parallel.html | 236 stplanr-0.8.1/stplanr/inst/doc/stplanr-route-nets.html | 236 stplanr-0.8.1/stplanr/inst/doc/stplanr-routing.html | 236 stplanr-0.8.1/stplanr/inst/doc/stplanr.html | 256 stplanr-0.8.1/stplanr/man/SpatialLinesNetwork.Rd | 2 stplanr-0.8.1/stplanr/man/angle_diff.Rd | 4 stplanr-0.8.1/stplanr/man/calc_catchment.Rd | 4 stplanr-0.8.1/stplanr/man/calc_catchment_sum.Rd | 2 stplanr-0.8.1/stplanr/man/calc_moving_catchment.Rd | 2 stplanr-0.8.1/stplanr/man/calc_network_catchment.Rd | 2 stplanr-0.8.1/stplanr/man/find_network_nodes.Rd | 2 stplanr-0.8.1/stplanr/man/geo_buffer.Rd | 10 stplanr-0.8.1/stplanr/man/geo_length.Rd | 2 stplanr-0.8.1/stplanr/man/geo_projected.Rd | 2 stplanr-0.8.1/stplanr/man/geo_toptail.Rd | 2 stplanr-0.8.1/stplanr/man/gsection.Rd | 4 stplanr-0.8.1/stplanr/man/islines.Rd | 2 stplanr-0.8.1/stplanr/man/line2route.Rd | 1 stplanr-0.8.1/stplanr/man/line2routeRetry.Rd | 1 stplanr-0.8.1/stplanr/man/lineLabels.Rd | 2 stplanr-0.8.1/stplanr/man/line_bearing.Rd | 2 stplanr-0.8.1/stplanr/man/line_breakup.Rd | 2 stplanr-0.8.1/stplanr/man/od_aggregate_from.Rd | 2 stplanr-0.8.1/stplanr/man/od_aggregate_to.Rd | 2 stplanr-0.8.1/stplanr/man/od_coords2line.Rd | 12 stplanr-0.8.1/stplanr/man/od_id.Rd | 3 stplanr-0.8.1/stplanr/man/od_oneway.Rd | 4 stplanr-0.8.1/stplanr/man/overline.Rd | 60 stplanr-0.8.1/stplanr/man/overline_intersection.Rd | 17 stplanr-0.8.1/stplanr/man/overline_spatial.Rd |only stplanr-0.8.1/stplanr/man/plot-SpatialLinesNetwork-ANY-method.Rd | 2 stplanr-0.8.1/stplanr/man/plot-sfNetwork-ANY-method.Rd | 2 stplanr-0.8.1/stplanr/man/read_table_builder.Rd | 4 stplanr-0.8.1/stplanr/man/rnet_boundary_points.Rd |only stplanr-0.8.1/stplanr/man/rnet_breakup_vertices.Rd | 81 stplanr-0.8.1/stplanr/man/rnet_group.Rd |only stplanr-0.8.1/stplanr/man/route.Rd | 32 stplanr-0.8.1/stplanr/man/route_bikecitizens.Rd |only stplanr-0.8.1/stplanr/man/route_dodgr.Rd | 1 stplanr-0.8.1/stplanr/man/route_google.Rd | 6 stplanr-0.8.1/stplanr/man/route_local.Rd | 10 stplanr-0.8.1/stplanr/man/route_osrm.Rd |only stplanr-0.8.1/stplanr/man/route_rolling_average.Rd | 2 stplanr-0.8.1/stplanr/man/route_rolling_gradient.Rd | 4 stplanr-0.8.1/stplanr/man/route_sequential_dist.Rd | 6 stplanr-0.8.1/stplanr/man/route_slope_matrix.Rd | 15 stplanr-0.8.1/stplanr/man/route_slope_vector.Rd | 4 stplanr-0.8.1/stplanr/man/route_transportapi_public.Rd | 1 stplanr-0.8.1/stplanr/man/sln2points.Rd | 4 stplanr-0.8.1/stplanr/man/sum_network_links.Rd | 8 stplanr-0.8.1/stplanr/man/sum_network_routes.Rd | 32 stplanr-0.8.1/stplanr/vignettes/references.bib | 2 stplanr-0.8.1/stplanr/vignettes/stplanr-od.Rmd | 4 86 files changed, 1250 insertions(+), 6094 deletions(-)
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between robmixglm versions 1.2-0 dated 2020-08-26 and 1.2-1 dated 2021-01-07
robmixglm-1.2-0/robmixglm/vignettes/Untitled.Rmd |only robmixglm-1.2-1/robmixglm/DESCRIPTION | 8 +- robmixglm-1.2-1/robmixglm/MD5 | 29 ++++---- robmixglm-1.2-1/robmixglm/R/binomial.fit.robmixglm.R | 2 robmixglm-1.2-1/robmixglm/R/fitnegbin.R | 6 - robmixglm-1.2-1/robmixglm/R/gamma.fit.robmixglm.R | 2 robmixglm-1.2-1/robmixglm/R/gaussian.fit.robmixglm.R | 52 ++++++++------- robmixglm-1.2-1/robmixglm/R/nbinom.fit.robmixglm.R | 19 ----- robmixglm-1.2-1/robmixglm/R/outlierTest.robmixglm.R | 5 - robmixglm-1.2-1/robmixglm/R/poisson.fit.robmixglm.R | 7 -- robmixglm-1.2-1/robmixglm/R/robmixglm.R | 9 ++ robmixglm-1.2-1/robmixglm/R/truncpoisson.fit.robmixglm.R | 4 - robmixglm-1.2-1/robmixglm/inst/NEWS | 10 ++ robmixglm-1.2-1/robmixglm/inst/doc/robmixglm-package.pdf |binary robmixglm-1.2-1/robmixglm/man/outlierTest.robmixglm.Rd | 2 robmixglm-1.2-1/robmixglm/man/robmixglm.Rd | 23 ++++-- 16 files changed, 91 insertions(+), 87 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Brooke Anderson [ctb],
Maëlle Salmon [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Alex Simmons [ctb],
Karthik Ram [ctb],
Hart Edmund [ctb],
rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 1.2.0 dated 2020-10-06 and 1.3.0 dated 2021-01-07
rnoaa-1.2.0/rnoaa/README.md |only rnoaa-1.2.0/rnoaa/build |only rnoaa-1.2.0/rnoaa/inst/doc |only rnoaa-1.2.0/rnoaa/vignettes |only rnoaa-1.3.0/rnoaa/DESCRIPTION | 9 - rnoaa-1.3.0/rnoaa/MD5 | 148 ++++++++++------------ rnoaa-1.3.0/rnoaa/NEWS.md | 18 ++ rnoaa-1.3.0/rnoaa/R/bsw.R | 7 - rnoaa-1.3.0/rnoaa/R/buoy.R | 8 - rnoaa-1.3.0/rnoaa/R/coops.R | 4 rnoaa-1.3.0/rnoaa/R/cpc.R | 7 - rnoaa-1.3.0/rnoaa/R/ersst.R | 31 ++-- rnoaa-1.3.0/rnoaa/R/ghcnd.R | 52 ++++--- rnoaa-1.3.0/rnoaa/R/ghcnd_search.R | 2 rnoaa-1.3.0/rnoaa/R/ghcnd_stations.R | 2 rnoaa-1.3.0/rnoaa/R/globals.R | 5 rnoaa-1.3.0/rnoaa/R/helpers_ghcnd.R | 8 - rnoaa-1.3.0/rnoaa/R/homr.R | 2 rnoaa-1.3.0/rnoaa/R/isd.R | 2 rnoaa-1.3.0/rnoaa/R/lcd.R | 4 rnoaa-1.3.0/rnoaa/R/meteo_distance.R | 13 + rnoaa-1.3.0/rnoaa/R/meteo_utils.r | 6 rnoaa-1.3.0/rnoaa/R/ncdc_datacats.r | 1 rnoaa-1.3.0/rnoaa/R/ncdc_datasets.r | 1 rnoaa-1.3.0/rnoaa/R/ncdc_datatypes.r | 1 rnoaa-1.3.0/rnoaa/R/ncdc_locs.r | 1 rnoaa-1.3.0/rnoaa/R/ncdc_locs_cats.r | 1 rnoaa-1.3.0/rnoaa/R/ncdc_stations.r | 1 rnoaa-1.3.0/rnoaa/R/rnoaa-package.r | 9 - rnoaa-1.3.0/rnoaa/R/seaice.r | 2 rnoaa-1.3.0/rnoaa/R/storm_events.R | 2 rnoaa-1.3.0/rnoaa/R/swdi.r | 4 rnoaa-1.3.0/rnoaa/R/tornadoes.R | 1 rnoaa-1.3.0/rnoaa/R/units-ghcnd.R | 4 rnoaa-1.3.0/rnoaa/R/vis_miss.R | 2 rnoaa-1.3.0/rnoaa/man/argo.Rd | 5 rnoaa-1.3.0/rnoaa/man/bsw.Rd | 7 - rnoaa-1.3.0/rnoaa/man/buoy.Rd | 10 - rnoaa-1.3.0/rnoaa/man/coops.Rd | 4 rnoaa-1.3.0/rnoaa/man/cpc_prcp.Rd | 7 - rnoaa-1.3.0/rnoaa/man/ersst.Rd | 24 ++- rnoaa-1.3.0/rnoaa/man/ghcnd.Rd | 14 +- rnoaa-1.3.0/rnoaa/man/ghcnd_search.Rd | 6 rnoaa-1.3.0/rnoaa/man/ghcnd_stations.Rd | 1 rnoaa-1.3.0/rnoaa/man/homr.Rd | 3 rnoaa-1.3.0/rnoaa/man/isd.Rd | 1 rnoaa-1.3.0/rnoaa/man/lcd.Rd | 3 rnoaa-1.3.0/rnoaa/man/meteo_nearby_stations.Rd | 2 rnoaa-1.3.0/rnoaa/man/meteo_pull_monitors.Rd | 6 rnoaa-1.3.0/rnoaa/man/meteo_tidy_ghcnd.Rd | 10 - rnoaa-1.3.0/rnoaa/man/ncdc.Rd | 2 rnoaa-1.3.0/rnoaa/man/ncdc_datacats.Rd | 5 rnoaa-1.3.0/rnoaa/man/ncdc_datasets.Rd | 5 rnoaa-1.3.0/rnoaa/man/ncdc_datatypes.Rd | 5 rnoaa-1.3.0/rnoaa/man/ncdc_locs.Rd | 5 rnoaa-1.3.0/rnoaa/man/ncdc_locs_cats.Rd | 5 rnoaa-1.3.0/rnoaa/man/ncdc_stations.Rd | 5 rnoaa-1.3.0/rnoaa/man/rnoaa-package.Rd | 9 - rnoaa-1.3.0/rnoaa/man/sea_ice.Rd | 2 rnoaa-1.3.0/rnoaa/man/storm_events.Rd | 3 rnoaa-1.3.0/rnoaa/man/swdi.Rd | 4 rnoaa-1.3.0/rnoaa/man/tornadoes.Rd | 3 rnoaa-1.3.0/rnoaa/man/vis_miss.Rd | 1 rnoaa-1.3.0/rnoaa/tests/files/201609.nc |binary rnoaa-1.3.0/rnoaa/tests/files/20166.nc |binary rnoaa-1.3.0/rnoaa/tests/files/20167.nc |binary rnoaa-1.3.0/rnoaa/tests/files/20168.nc |binary rnoaa-1.3.0/rnoaa/tests/fixtures/ersst1.yml | 16 +- rnoaa-1.3.0/rnoaa/tests/fixtures/ersst2.yml | 16 +- rnoaa-1.3.0/rnoaa/tests/fixtures/ersst3.yml | 16 +- rnoaa-1.3.0/rnoaa/tests/fixtures/ersst4.yml | 16 +- rnoaa-1.3.0/rnoaa/tests/testthat/test-ghcnd.R | 55 +++++++- rnoaa-1.3.0/rnoaa/tests/testthat/test-homr.R | 6 rnoaa-1.3.0/rnoaa/tests/testthat/test-tornadoes.R | 1 74 files changed, 331 insertions(+), 310 deletions(-)
Title: API Wrapper Around 'Postcodes.io'
Description: Free UK geocoding using data from Office for National Statistics.
It is using several functions to get information about post codes, outward
codes, reverse geocoding, nearest post codes/outward codes, validation, or
randomly generate a post code. API wrapper around <https://postcodes.io>.
Author: Eryk Walczak [aut, cre] (<https://orcid.org/0000-0001-8724-462X>),
Claudia Vitolo [rev] (<https://orcid.org/0000-0002-4252-1176>),
Robin Lovelace [rev] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Eryk Walczak <eryk.j.walczak@gmail.com>
Diff between PostcodesioR versions 0.1.1 dated 2019-08-24 and 0.3.0 dated 2021-01-07
DESCRIPTION | 12 MD5 | 56 +- NAMESPACE | 1 NEWS.md | 12 R/bulk_postcode_lookup.R | 13 R/nearest_outcode.R | 2 R/nearest_postcode.R | 2 R/place_lookup.R | 2 R/place_query.R | 2 R/postcode_lookup.R | 30 + R/random_place.R | 2 R/scottish_postcode_lookup.R |only R/terminated_postcode.R | 4 README.md | 54 +- build/vignette.rds |binary inst/doc/Introduction.R | 61 +- inst/doc/Introduction.Rmd | 22 + inst/doc/Introduction.html | 544 ++++++++++++++----------- man/figures |only man/outcode_reverse_geocoding.Rd | 3 man/place_lookup.Rd | 2 man/place_query.Rd | 2 man/postcode_lookup.Rd | 9 man/random_place.Rd | 2 man/reverse_geocoding.Rd | 9 man/scottish_postcode_lookup.Rd |only man/terminated_postcode.Rd | 4 tests/testthat/test-bulk_postcode_lookup.R | 5 tests/testthat/test-postcode_lookup.R | 14 tests/testthat/test-scottish_postcode_lookup.R |only vignettes/Introduction.Rmd | 22 + 31 files changed, 568 insertions(+), 323 deletions(-)
Title: Agglomerative Partitioning Framework for Dimension Reduction
Description: A fast and flexible framework for agglomerative
partitioning. 'partition' uses an approach called
Direct-Measure-Reduce to create new variables that maintain the
user-specified minimum level of information. Each reduced variable is
also interpretable: the original variables map to one and only one
variable in the reduced data set. 'partition' is flexible, as well:
how variables are selected to reduce, how information loss is
measured, and the way data is reduced can all be customized.
'partition' is based on the Partition framework discussed in Millstein
et al. (2020) <doi: 10.1093/bioinformatics/btz661>.
Author: Joshua Millstein [aut],
Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between partition versions 0.1.2 dated 2020-05-24 and 0.1.3 dated 2021-01-07
DESCRIPTION | 13 +++-- MD5 | 35 ++++++++-------- NEWS.md | 4 + R/data.R | 3 - R/simulate_block.R | 5 +- README.md | 17 ++++++- build/partial.rdb |only build/vignette.rds |binary inst/doc/extending-partition.html | 30 ++++++++++++- inst/doc/introduction-to-partition.html | 32 +++++++++++++- man/baxter_data.Rd | 3 - tests/testthat/helper-df.R | 2 tests/testthat/test-mappings-and-scores-work.R | 11 ++--- tests/testthat/test-misc-partitioner-arguments.R | 15 +++--- tests/testthat/test-partition-objects-are-well-shaped.R | 15 +++--- tests/testthat/test-partitioners-helpers-work.R | 12 +++++ tests/testthat/test-partitioners-reduce-correctly.R | 1 tests/testthat/test-permutations-return-correctly.R | 7 +-- tests/testthat/test-plots-are-plotting.R | 19 ++++---- 19 files changed, 149 insertions(+), 75 deletions(-)
Title: Estimation of Intrinsic and Extrinsic Noise from Single-Cell
Data
Description: Functions to calculate estimates of intrinsic and extrinsic noise from the two-reporter single-cell experiment, as in Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186. Functions implement multiple estimators developed for unbiasedness or min Mean Squared Error (MSE) in Fu, A. Q. and Pachter, L. (2016). Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Statistical Applications in Genetics and Molecular Biology, 15(6), 447-471.
Author: Audrey Qiuyan Fu and Lior Pachter
Maintainer: Audrey Q. Fu <audreyqyfu@gmail.com>
Diff between noise versions 1.0 dated 2016-07-28 and 1.0.1 dated 2021-01-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/partial.rdb |binary man/computeExtrinsicNoise.Rd | 5 +---- man/computeExtrinsicNoiseKnownCor.Rd | 4 ---- man/computeIntrinsicNoise.Rd | 5 +---- 6 files changed, 12 insertions(+), 22 deletions(-)
Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written
for the purpose of more efficiently understanding and sharing the results of
(primarily) regression analyses. There are also a number of miscellaneous
functions for statistical and programming purposes. Just about everything
supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <jacob.long@sc.edu>
Diff between jtools versions 2.1.1 dated 2020-11-16 and 2.1.2 dated 2021-01-07
DESCRIPTION | 6 MD5 | 25 NEWS.md | 4 R/export_summ.R | 2 R/summ.R | 20 build/partial.rdb |only build/vignette.rds |binary inst/doc/effect_plot.html | 339 +---------- inst/doc/summ.html | 1359 ---------------------------------------------- inst/doc/svycor.html | 303 ---------- man/summ.glm.Rd | 4 man/summ.lm.Rd | 4 man/summ.merMod.Rd | 552 +++++++++--------- tests/testthat/Rplots.pdf |binary 14 files changed, 402 insertions(+), 2216 deletions(-)
Title: Goodness-of-Fit Tests in High-Dimensional GLMs
Description: Methodology for testing nonlinearity in the conditional mean function
in low- or high-dimensional generalized linear models, and the significance of
(potentially large) groups of predictors. Details on the algorithms can be
found in the paper by Jankova, Shah, Buehlmann and Samworth (2019)
<arXiv:1908.03606>.
Author: Jana Jankova [aut, cre], Rajen Shah [aut], Peter Buehlmann [aut], Richard Samworth [aut]
Maintainer: Jana Jankova <jana.jankova@gmail.com>
Diff between GRPtests versions 0.1.0 dated 2019-10-11 and 0.1.1 dated 2021-01-07
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 1 + R/GRPgrouptest.R | 1 - R/GRPtest.R | 5 ++--- R/helpers.R | 26 ++++++++++++++++++-------- man/GRPtest.Rd | 2 +- 7 files changed, 33 insertions(+), 24 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman <broman@wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, Brian Yandell, and R Core Team
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.46-2 dated 2020-03-11 and 1.47-9 dated 2021-01-07
qtl-1.46-2/qtl/inst/LICENSE.txt |only qtl-1.47-9/qtl/DESCRIPTION | 14 - qtl-1.47-9/qtl/MD5 | 103 +++++------ qtl-1.47-9/qtl/NAMESPACE | 2 qtl-1.47-9/qtl/NEWS.md | 34 +++ qtl-1.47-9/qtl/R/find_large_intervals.R |only qtl-1.47-9/qtl/R/phyloqtl_scan.R | 16 + qtl-1.47-9/qtl/R/pull_stuff.R | 26 ++ qtl-1.47-9/qtl/R/read.cross.R | 15 - qtl-1.47-9/qtl/R/util.R | 15 - qtl-1.47-9/qtl/README.md | 2 qtl-1.47-9/qtl/build/vignette.rds |binary qtl-1.47-9/qtl/data/badorder.RData |binary qtl-1.47-9/qtl/data/bristle3.RData |binary qtl-1.47-9/qtl/data/bristleX.RData |binary qtl-1.47-9/qtl/data/fake.4way.RData |binary qtl-1.47-9/qtl/data/fake.bc.RData |binary qtl-1.47-9/qtl/data/fake.f2.RData |binary qtl-1.47-9/qtl/data/hyper.RData |binary qtl-1.47-9/qtl/data/listeria.RData |binary qtl-1.47-9/qtl/data/locations.RData |binary qtl-1.47-9/qtl/data/map10.RData |binary qtl-1.47-9/qtl/data/mapthis.RData |binary qtl-1.47-9/qtl/data/multitrait.RData |binary qtl-1.47-9/qtl/inst/INSTALL_ME.txt | 16 - qtl-1.47-9/qtl/inst/doc/Sources/MQM/MQM-tour.aux | 6 qtl-1.47-9/qtl/inst/doc/Sources/MQM/MQM-tour.dvi |binary qtl-1.47-9/qtl/inst/doc/Sources/MQM/MQM-tour.log | 206 +++++++++++++++------- qtl-1.47-9/qtl/inst/doc/Sources/MQM/SweaveIt.Rout | 2 qtl-1.47-9/qtl/inst/doc/bcsft.R | 1 qtl-1.47-9/qtl/inst/doc/bcsft.Rnw | 2 qtl-1.47-9/qtl/inst/doc/bcsft.pdf |binary qtl-1.47-9/qtl/inst/doc/rqtltour.pdf |binary qtl-1.47-9/qtl/inst/doc/rqtltour2.pdf |binary qtl-1.47-9/qtl/man/a.starting.point.Rd | 4 qtl-1.47-9/qtl/man/addloctocross.Rd | 4 qtl-1.47-9/qtl/man/argmax.geno.Rd | 2 qtl-1.47-9/qtl/man/calc.genoprob.Rd | 2 qtl-1.47-9/qtl/man/effectscan.Rd | 2 qtl-1.47-9/qtl/man/findDupMarkers.Rd | 2 qtl-1.47-9/qtl/man/find_large_intervals.Rd |only qtl-1.47-9/qtl/man/hyper.Rd | 2 qtl-1.47-9/qtl/man/mqmplotmultitrait.Rd | 2 qtl-1.47-9/qtl/man/plot.map.Rd | 2 qtl-1.47-9/qtl/man/plot.pxg.Rd | 2 qtl-1.47-9/qtl/man/plot.rf.Rd | 2 qtl-1.47-9/qtl/man/plot.scanone.Rd | 4 qtl-1.47-9/qtl/man/plot.scantwo.Rd | 2 qtl-1.47-9/qtl/man/plotLodProfile.Rd | 2 qtl-1.47-9/qtl/man/plotModel.Rd | 2 qtl-1.47-9/qtl/man/read.cross.Rd | 9 qtl-1.47-9/qtl/man/sim.geno.Rd | 2 qtl-1.47-9/qtl/man/write.cross.Rd | 2 qtl-1.47-9/qtl/vignettes/bcsft.Rnw | 2 54 files changed, 325 insertions(+), 186 deletions(-)
Title: Doubly Robust Difference-in-Differences Estimators
Description: Implements the locally efficient doubly robust difference-in-differences (DiD)
estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
<doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
regression estimators (also implemented in the package) to form estimators with
more attractive statistical properties. Two different estimation methods can be used
to estimate the nuisance functions.
Author: Pedro H. C. Sant'Anna [aut, cre],
Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedro.h.santanna@vanderbilt.edu>
Diff between DRDID versions 1.0.0 dated 2020-05-18 and 1.0.1 dated 2021-01-07
DESCRIPTION | 18 - MD5 | 97 +++---- NEWS.md | 26 +- R/drdid.R | 7 R/drdid_imp_panel.R | 13 - R/drdid_imp_rc.R | 7 R/drdid_imp_rc1.R | 7 R/drdid_package.R | 4 R/drdid_panel.R | 13 - R/drdid_rc.R | 16 + R/drdid_rc1.R | 16 + R/ipw_did_panel.R | 13 - R/ipw_did_rc.R | 13 - R/ipwdid.R | 7 R/nsw.R | 4 R/nsw_long.R | 4 R/ordid.R | 6 R/pre_process_drdid.R | 452 +++++++++++++++++------------------ R/pscore.cal.R | 114 +++++--- R/reg_did_panel.R | 9 R/reg_did_rc.R | 12 R/sim_rc.R | 4 R/std_ipw_did_panel.R | 7 R/std_ipw_did_rc.R | 6 R/wols.br.panel.R | 46 +-- R/wols_rc.R | 75 +++-- README.md | 122 ++++----- build |only inst/CITATION | 7 inst/WORDLIST | 1 man/DRDID-package.Rd | 4 man/drdid.Rd | 7 man/drdid_imp_panel.Rd | 7 man/drdid_imp_rc.Rd | 7 man/drdid_imp_rc1.Rd | 7 man/drdid_panel.Rd | 4 man/drdid_rc.Rd | 4 man/drdid_rc1.Rd | 4 man/ipw_did_panel.Rd | 7 man/ipw_did_rc.Rd | 7 man/ipwdid.Rd | 7 man/nsw.Rd | 4 man/nsw_long.Rd | 4 man/ordid.Rd | 6 man/reg_did_panel.Rd | 6 man/reg_did_rc.Rd | 6 man/sim_rc.Rd | 4 man/std_ipw_did_panel.Rd | 6 man/std_ipw_did_rc.Rd | 6 tests/testthat/test_errors.R | 548 +++++++++++++++++++++---------------------- 50 files changed, 926 insertions(+), 855 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova & Martinkova, 2017, <doi:10.1111/jedm.12158>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.3.5 dated 2020-08-24 and 1.3.7 dated 2021-01-07
DESCRIPTION | 16 +- MD5 | 97 +++++++------ NAMESPACE | 4 NEWS.md | 48 +++++- R/GMAT.R | 8 - R/GMAT2.R | 10 - R/GMAT2key.R | 10 - R/GMAT2test.R | 10 - R/GMATkey.R | 8 - R/GMATtest.R | 8 - R/MLR.R | 6 R/MSATB.R | 6 R/MSATBkey.R | 6 R/MSATBtest.R | 6 R/NLR.R | 144 +++++++++++--------- R/ORD.R | 6 R/ddfMLR.R | 8 + R/difNLR-package.R | 48 +++--- R/difNLR.R | 334 ++++++++++++++++++++++++++++-------------------- R/difORD.R | 3 R/estimNLR.R | 109 ++++++++++++++- R/genNLR.R | 6 R/startNLR.R | 6 README.md | 27 +++ build |only inst/CITATION | 16 +- man/GMAT.Rd | 8 - man/GMAT2.Rd | 10 - man/GMAT2key.Rd | 10 - man/GMAT2test.Rd | 10 - man/GMATkey.Rd | 8 - man/GMATtest.Rd | 8 - man/MLR.Rd | 6 man/MSATB.Rd | 6 man/MSATBkey.Rd | 6 man/MSATBtest.Rd | 6 man/NLR.Rd | 24 ++- man/ORD.Rd | 6 man/coef.difNLR.Rd | 14 +- man/ddfMLR.Rd | 6 man/difNLR-package.Rd | 43 +++--- man/difNLR.Rd | 236 ++++++++++++++++++++------------- man/difORD.Rd | 3 man/estimNLR.Rd | 1 man/genNLR.Rd | 6 man/logLik.difNLR.Rd | 14 +- man/plot.difNLR.Rd | 14 +- man/predict.difNLR.Rd | 14 +- man/residuals.difNLR.Rd | 14 +- man/startNLR.Rd | 6 50 files changed, 886 insertions(+), 543 deletions(-)
Title: Southwest Fisheries Science Center Shipboard DAS Data Processing
Description: Process and summarize shipboard
'DAS' <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data
produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz'
<https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>.
This package standardizes and streamlines basic DAS data processing,
and includes a PDF with the DAS data format requirements.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>)
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between swfscDAS versions 0.4.0 dated 2020-06-30 and 0.5.0 dated 2021-01-07
swfscDAS-0.4.0/swfscDAS/inst/das_sample_strata.csv |only swfscDAS-0.5.0/swfscDAS/DESCRIPTION | 24 swfscDAS-0.5.0/swfscDAS/MD5 | 74 swfscDAS-0.5.0/swfscDAS/NAMESPACE | 230 +- swfscDAS-0.5.0/swfscDAS/NEWS.md | 23 swfscDAS-0.5.0/swfscDAS/R/das_check.R | 160 + swfscDAS-0.5.0/swfscDAS/R/das_chop_condition.R | 22 swfscDAS-0.5.0/swfscDAS/R/das_chop_equallength.R | 37 swfscDAS-0.5.0/swfscDAS/R/das_chop_section.R | 9 swfscDAS-0.5.0/swfscDAS/R/das_effort.R | 113 + swfscDAS-0.5.0/swfscDAS/R/das_effort_strata.R |only swfscDAS-0.5.0/swfscDAS/R/das_format_pdf.R | 8 swfscDAS-0.5.0/swfscDAS/R/das_intersects_strata.R | 95 - swfscDAS-0.5.0/swfscDAS/R/das_process.R | 5 swfscDAS-0.5.0/swfscDAS/R/das_read.R | 30 swfscDAS-0.5.0/swfscDAS/R/das_segdata.R | 69 swfscDAS-0.5.0/swfscDAS/R/das_sight.R | 140 - swfscDAS-0.5.0/swfscDAS/R/swfscDAS-internal.R | 53 swfscDAS-0.5.0/swfscDAS/R/swfscDAS-package.R | 14 swfscDAS-0.5.0/swfscDAS/README.md | 24 swfscDAS-0.5.0/swfscDAS/build/vignette.rds |binary swfscDAS-0.5.0/swfscDAS/inst/das_sample_stratum.csv | 10 swfscDAS-0.5.0/swfscDAS/inst/doc/DAS_data_join.html | 114 - swfscDAS-0.5.0/swfscDAS/inst/doc/swfscDAS.R | 18 swfscDAS-0.5.0/swfscDAS/inst/doc/swfscDAS.Rmd | 27 swfscDAS-0.5.0/swfscDAS/inst/doc/swfscDAS.html | 1001 ++++++------ swfscDAS-0.5.0/swfscDAS/man/das_check.Rd | 93 - swfscDAS-0.5.0/swfscDAS/man/das_chop_condition.Rd | 15 swfscDAS-0.5.0/swfscDAS/man/das_chop_equallength.Rd | 6 swfscDAS-0.5.0/swfscDAS/man/das_chop_section.Rd | 6 swfscDAS-0.5.0/swfscDAS/man/das_effort.Rd | 347 ++-- swfscDAS-0.5.0/swfscDAS/man/das_effort_strata.Rd |only swfscDAS-0.5.0/swfscDAS/man/das_format_pdf.Rd | 8 swfscDAS-0.5.0/swfscDAS/man/das_intersects_strata.Rd | 197 +- swfscDAS-0.5.0/swfscDAS/man/das_process.Rd | 5 swfscDAS-0.5.0/swfscDAS/man/das_read.Rd | 30 swfscDAS-0.5.0/swfscDAS/man/das_segdata.Rd | 13 swfscDAS-0.5.0/swfscDAS/man/das_sight.Rd | 129 - swfscDAS-0.5.0/swfscDAS/tests/testthat/test-effort_strata.R |only swfscDAS-0.5.0/swfscDAS/vignettes/swfscDAS.Rmd | 27 40 files changed, 1837 insertions(+), 1339 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 1.17-0 dated 2020-02-07 and 1.20-2 dated 2021-01-07
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NAMESPACE | 5 ++--- NEWS | 24 ++++++++++++++++++++++++ R/resolve.defaults.R | 11 ++++++----- R/utiltext.R | 26 +------------------------- inst/doc/packagesizes.txt | 6 +++++- man/do.call.matched.Rd | 7 ++++++- man/do.call.without.Rd | 6 +++++- man/orderstats.Rd |only man/spatstat.utils-internal.Rd | 6 ------ src/init.c | 1 + tests/tekst.R | 1 - 13 files changed, 67 insertions(+), 59 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system (DES) to
implement a complete data-to-decisions, reproducible workflow.
The core DES components facilitate modularity, and easily enable the user
to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the DES project.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>),
Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>),
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES.core versions 1.0.3 dated 2020-09-12 and 1.0.5 dated 2021-01-07
SpaDES.core-1.0.3/SpaDES.core/man/paddedFloatToChar.Rd |only SpaDES.core-1.0.3/SpaDES.core/tests/testthat/test-updateList.R |only SpaDES.core-1.0.5/SpaDES.core/DESCRIPTION | 32 SpaDES.core-1.0.5/SpaDES.core/MD5 | 185 +- SpaDES.core-1.0.5/SpaDES.core/NAMESPACE | 22 SpaDES.core-1.0.5/SpaDES.core/NEWS.md | 18 SpaDES.core-1.0.5/SpaDES.core/R/cache.R | 22 SpaDES.core-1.0.5/SpaDES.core/R/checkpoint.R | 1 SpaDES.core-1.0.5/SpaDES.core/R/copy.R | 2 SpaDES.core-1.0.5/SpaDES.core/R/downloadData.R | 49 SpaDES.core-1.0.5/SpaDES.core/R/helpers.R | 12 SpaDES.core-1.0.5/SpaDES.core/R/memory.R | 12 SpaDES.core-1.0.5/SpaDES.core/R/misc-methods.R | 211 -- SpaDES.core-1.0.5/SpaDES.core/R/module-define.R | 19 SpaDES.core-1.0.5/SpaDES.core/R/module-dependencies-methods.R | 26 SpaDES.core-1.0.5/SpaDES.core/R/module-repository.R | 65 SpaDES.core-1.0.5/SpaDES.core/R/module-template.R | 66 SpaDES.core-1.0.5/SpaDES.core/R/moduleMetadata.R | 16 SpaDES.core-1.0.5/SpaDES.core/R/options.R | 7 SpaDES.core-1.0.5/SpaDES.core/R/plotting-diagrams.R | 30 SpaDES.core-1.0.5/SpaDES.core/R/progress.R | 4 SpaDES.core-1.0.5/SpaDES.core/R/project-template.R | 9 SpaDES.core-1.0.5/SpaDES.core/R/reexports.R |only SpaDES.core-1.0.5/SpaDES.core/R/restart.R | 6 SpaDES.core-1.0.5/SpaDES.core/R/simList-accessors.R | 63 SpaDES.core-1.0.5/SpaDES.core/R/simList-class.R | 12 SpaDES.core-1.0.5/SpaDES.core/R/simulation-parseModule.R | 19 SpaDES.core-1.0.5/SpaDES.core/R/simulation-simInit.R | 25 SpaDES.core-1.0.5/SpaDES.core/R/simulation-spades.R | 229 ++ SpaDES.core-1.0.5/SpaDES.core/R/spades-core-deprecated.R | 92 + SpaDES.core-1.0.5/SpaDES.core/R/spades-core-package.R | 4 SpaDES.core-1.0.5/SpaDES.core/R/times.R | 71 SpaDES.core-1.0.5/SpaDES.core/R/zzz.R | 6 SpaDES.core-1.0.5/SpaDES.core/README.md | 7 SpaDES.core-1.0.5/SpaDES.core/build/vignette.rds |binary SpaDES.core-1.0.5/SpaDES.core/inst/WORDLIST | 97 - SpaDES.core-1.0.5/SpaDES.core/inst/doc/i-introduction.Rmd | 2 SpaDES.core-1.0.5/SpaDES.core/inst/doc/i-introduction.html | 522 ++--- SpaDES.core-1.0.5/SpaDES.core/inst/doc/ii-modules.R | 4 SpaDES.core-1.0.5/SpaDES.core/inst/doc/ii-modules.Rmd | 8 SpaDES.core-1.0.5/SpaDES.core/inst/doc/ii-modules.html | 907 +++++----- SpaDES.core-1.0.5/SpaDES.core/inst/doc/iii-cache.html | 641 ++----- SpaDES.core-1.0.5/SpaDES.core/inst/doc/iv-advanced.R | 3 SpaDES.core-1.0.5/SpaDES.core/inst/doc/iv-advanced.Rmd | 3 SpaDES.core-1.0.5/SpaDES.core/inst/doc/iv-advanced.html | 261 -- SpaDES.core-1.0.5/SpaDES.core/inst/doc/v-automated-testing.R |only SpaDES.core-1.0.5/SpaDES.core/inst/doc/v-automated-testing.Rmd |only SpaDES.core-1.0.5/SpaDES.core/inst/doc/v-automated-testing.html |only SpaDES.core-1.0.5/SpaDES.core/inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R | 4 SpaDES.core-1.0.5/SpaDES.core/inst/sampleModules/caribouMovement/caribouMovement.R | 7 SpaDES.core-1.0.5/SpaDES.core/inst/sampleModules/fireSpread/fireSpread.R | 4 SpaDES.core-1.0.5/SpaDES.core/inst/sampleModules/randomLandscapes/randomLandscapes.R | 10 SpaDES.core-1.0.5/SpaDES.core/inst/templates/LICENSE.template | 2 SpaDES.core-1.0.5/SpaDES.core/inst/templates/module.R.template | 10 SpaDES.core-1.0.5/SpaDES.core/inst/templates/module.Rmd.template | 2 SpaDES.core-1.0.5/SpaDES.core/inst/templates/modulePartialMeta.R.template | 4 SpaDES.core-1.0.5/SpaDES.core/inst/templates/render-module-rmd.yaml.template | 52 SpaDES.core-1.0.5/SpaDES.core/man/Plot.Rd | 2 SpaDES.core-1.0.5/SpaDES.core/man/SpaDES.core-package.Rd | 4 SpaDES.core-1.0.5/SpaDES.core/man/bindrows.Rd |only SpaDES.core-1.0.5/SpaDES.core/man/createsOutput.Rd | 2 SpaDES.core-1.0.5/SpaDES.core/man/doEvent.Rd | 9 SpaDES.core-1.0.5/SpaDES.core/man/expectsInput.Rd | 2 SpaDES.core-1.0.5/SpaDES.core/man/loadPackages.Rd | 4 SpaDES.core-1.0.5/SpaDES.core/man/moduleDiagram.Rd | 25 SpaDES.core-1.0.5/SpaDES.core/man/moduleMetadata.Rd | 14 SpaDES.core-1.0.5/SpaDES.core/man/newModule.Rd | 2 SpaDES.core-1.0.5/SpaDES.core/man/newProject.Rd | 1 SpaDES.core-1.0.5/SpaDES.core/man/objectDiagram.Rd | 8 SpaDES.core-1.0.5/SpaDES.core/man/pkgEnv.Rd | 2 SpaDES.core-1.0.5/SpaDES.core/man/reexports.Rd |only SpaDES.core-1.0.5/SpaDES.core/man/robustDigest.Rd | 7 SpaDES.core-1.0.5/SpaDES.core/man/simInitAnd.Rd | 4 SpaDES.core-1.0.5/SpaDES.core/man/simList-accessors-metadata.Rd | 17 SpaDES.core-1.0.5/SpaDES.core/man/spades.Rd | 42 SpaDES.core-1.0.5/SpaDES.core/man/spadesOptions.Rd | 6 SpaDES.core-1.0.5/SpaDES.core/man/spadesTime.Rd | 20 SpaDES.core-1.0.5/SpaDES.core/man/timeConversion.Rd | 18 SpaDES.core-1.0.5/SpaDES.core/man/updateList.Rd | 21 SpaDES.core-1.0.5/SpaDES.core/man/use_gha.Rd |only SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-cache.R | 14 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-checkpoint.R | 13 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-conditionalEvents.R | 4 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-downloadData.R | 4 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-futureEvents.R |only SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-load.R | 8 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-mod.R | 11 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-module-deps-methods.R | 12 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-module-template.R | 2 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-multipleModulePaths.R | 4 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-objectSynonyms.R | 50 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-save.R | 3 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-simList.R | 30 SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-simulation.R | 95 - SpaDES.core-1.0.5/SpaDES.core/tests/testthat/test-timeunits.R | 6 SpaDES.core-1.0.5/SpaDES.core/vignettes/i-introduction.Rmd | 2 SpaDES.core-1.0.5/SpaDES.core/vignettes/ii-modules.Rmd | 8 SpaDES.core-1.0.5/SpaDES.core/vignettes/iv-advanced.Rmd | 3 SpaDES.core-1.0.5/SpaDES.core/vignettes/v-automated-testing.Rmd |only 99 files changed, 2178 insertions(+), 2186 deletions(-)
Title: Spatial Capture-Recapture (SCR) Methods Using 'nimble'
Description: Provides utility functions, distributions, and methods for improving Markov chain Monte Carlo (MCMC) sampling efficiency for ecological Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) models. The methods provided implement the techniques presented in "Estimation of Large-Scale Spatial Capture-Recapture Models" (Turek, et al (2020) <doi:10.1101/2020.05.07.081182>).
Author: Richard Bischof [aut],
Daniel Turek [aut, cre],
Cyril Milleret [aut],
Torbjørn Ergon [aut],
Pierre Dupont [aut],
Perry de Valpine [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleSCR versions 0.1.0 dated 2020-08-20 and 0.1.1 dated 2021-01-07
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++++--------- NAMESPACE | 4 ++++ R/dHabitatMask.R | 2 +- R/dbinomLocal_normal.R |only R/dbinom_sparseLocalSCR.R | 36 +++++++++++++++++++++--------------- R/getLocalObjects.R |only R/getLocalTraps.R | 14 ++++++++++++-- R/scaleCoordsToHabitatGrid.R |only R/zzz.R | 16 ++++++++++++++++ man/dHabitatMask.Rd | 2 +- man/dbinomLocal_normal.Rd |only man/dbinom_sparseLocalSCR.Rd | 4 ++-- man/getLocalObjects.Rd |only man/getLocalTraps.Rd | 4 ++-- man/scaleCoordsToHabitatGrid.Rd |only 16 files changed, 78 insertions(+), 36 deletions(-)
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Description: Methods for analyzing and using quartets displayed on a collection of gene trees,
primarily to make inferences about the species tree or network under the multi-species
coalescent model. These include quartet hypothesis tests for the model, as developed by
Mitchell et al. (2019) <doi:10.1214/19-EJS1576>, simplex plots of quartet concordance factors
as presented by Allman et al. (2020) <doi:10.1101/2020.02.13.948083>, species tree inference methods
based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and
Yourdkhani and Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, and the NANUQ algorithm for inference of level-1
species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>. Software announcement by
Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.
Author: Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
John Rhodes [aut, cre] (<https://orcid.org/0000-0001-9921-1091>)
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Diff between MSCquartets versions 1.0.5 dated 2019-12-16 and 1.1.0 dated 2021-01-07
MSCquartets-1.0.5/MSCquartets/man/MSCquartets.Rd |only MSCquartets-1.1.0/MSCquartets/DESCRIPTION | 36 + MSCquartets-1.1.0/MSCquartets/MD5 | 54 +- MSCquartets-1.1.0/MSCquartets/NAMESPACE | 5 MSCquartets-1.1.0/MSCquartets/R/ExpectedCFs.R |only MSCquartets-1.1.0/MSCquartets/R/MSCquartets.R | 17 MSCquartets-1.1.0/MSCquartets/R/NANUQ.R | 48 +- MSCquartets-1.1.0/MSCquartets/R/ParallelTable.R |only MSCquartets-1.1.0/MSCquartets/R/QuartetTally.R | 8 MSCquartets-1.1.0/MSCquartets/R/SimplexPlot.R | 15 MSCquartets-1.1.0/MSCquartets/R/TreeQuartetDist.R | 26 - MSCquartets-1.1.0/MSCquartets/R/TreeQuartetHypTest.R | 258 +++++++------- MSCquartets-1.1.0/MSCquartets/R/WQDCrecursive.R | 4 MSCquartets-1.1.0/MSCquartets/R/pHist.R | 4 MSCquartets-1.1.0/MSCquartets/build/partial.rdb |binary MSCquartets-1.1.0/MSCquartets/inst/REFERENCES.bib | 238 +++++++----- MSCquartets-1.1.0/MSCquartets/man/MSCquartets-package.Rd |only MSCquartets-1.1.0/MSCquartets/man/NANUQ.Rd | 30 + MSCquartets-1.1.0/MSCquartets/man/NANUQdist.Rd | 16 MSCquartets-1.1.0/MSCquartets/man/QDC.Rd | 12 MSCquartets-1.1.0/MSCquartets/man/WQDC.Rd | 25 - MSCquartets-1.1.0/MSCquartets/man/dataGeneTreeSample.Rd | 4 MSCquartets-1.1.0/MSCquartets/man/dataHeliconiusMartin.Rd | 8 MSCquartets-1.1.0/MSCquartets/man/dataYeastRokas.Rd | 6 MSCquartets-1.1.0/MSCquartets/man/estimateEdgeLengths.Rd | 3 MSCquartets-1.1.0/MSCquartets/man/expectedCFs.Rd |only MSCquartets-1.1.0/MSCquartets/man/quartetNetworkDist.Rd | 6 MSCquartets-1.1.0/MSCquartets/man/quartetTable.Rd | 2 MSCquartets-1.1.0/MSCquartets/man/quartetTableParallel.Rd |only MSCquartets-1.1.0/MSCquartets/man/quartetTreeTest.Rd | 10 MSCquartets-1.1.0/MSCquartets/man/quartetTreeTestInd.Rd | 11 31 files changed, 509 insertions(+), 337 deletions(-)
Title: Index Numbers in Social Sciences
Description: We provide an R tool for teaching in Social Sciences. It allows the computation of index numbers. It is a measure of the evolution of a fixed magnitude for only a product of for several products. It is very useful in Social Sciences. Among others, we obtain simple index numbers (in chain or in serie), index numbers for not only a product or weighted index numbers as the Laspeyres index (Laspeyres, 1864), the Paasche index (Paasche, 1874) or the Fisher index (Lapedes, 1978).
Author: Alejandro Saavedra-Nieves, Paula Saavedra-Nieves
Maintainer: Alejandro Saavedra-Nieves <alejandro.saavedra.nieves@gmail.com>
Diff between IndexNumber versions 1.2 dated 2020-06-04 and 1.3 dated 2021-01-07
DESCRIPTION | 8 ++--- MD5 | 30 +++++++++++----------- R/aggregated.index.number.R | 55 ++++++++++++++++++++++++++++++++++++++--- R/edgeworth.index.number.R | 26 ++++++++++++++----- R/fisher.index.number.R | 26 ++++++++++++++----- R/index.number.chain.R | 10 +++++++ R/index.number.serie.R | 10 ++++++- R/laspeyres.index.number.R | 31 ++++++++++++++++------- R/paasche.index.number.R | 31 ++++++++++++++++------- build/partial.rdb |binary man/IndexNumber-package.Rd | 4 ++ man/aggregated.index.number.Rd | 10 +++++-- man/edgeworth.index.number.Rd | 6 ++-- man/fisher.index.number.Rd | 2 + man/laspeyres.index.number.Rd | 4 +- man/paasche.index.number.Rd | 4 +- 16 files changed, 195 insertions(+), 62 deletions(-)
Title: Create 'Formattable' Data Structures
Description: Provides functions to create formattable vectors and data frames.
'Formattable' vectors are printed with text formatting, and formattable
data frames are printed with multiple types of formatting in HTML
to improve the readability of data presented in tabular form rendered in
web pages.
Author: Kun Ren [aut, cre],
Kenton Russell [aut]
Maintainer: Kun Ren <ken@renkun.me>
Diff between formattable versions 0.2.0.1 dated 2016-08-05 and 0.2.1 dated 2021-01-07
DESCRIPTION | 13 MD5 | 126 - NEWS | 2 R/formattable.R | 14 R/formatter.R | 13 R/style.R | 8 R/utils.R | 6 README.md | 58 build/vignette.rds |binary inst/doc/formattable-data-frame.R | 41 inst/doc/formattable-data-frame.Rmd | 8 inst/doc/formattable-data-frame.html | 2461 +++++++++++++---------------------- inst/doc/introduction.R | 37 inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 524 +++++-- man/accounting.Rd | 9 man/area.Rd | 1 man/as.datatable.Rd | 1 man/as.datatable.formattable.Rd | 1 man/as.htmlwidget.Rd | 1 man/as.htmlwidget.formattable.Rd | 1 man/color_bar.Rd | 1 man/color_text.Rd | 1 man/color_tile.Rd | 1 man/comma.Rd | 6 man/csscolor.Rd | 1 man/currency.Rd | 28 man/digits.Rd | 1 man/format_table.Rd | 13 man/formattable-package.Rd | 1 man/formattable.Date.Rd | 4 man/formattable.POSIXct.Rd | 10 man/formattable.POSIXlt.Rd | 10 man/formattable.Rd | 1 man/formattable.data.frame.Rd | 10 man/formattable.default.Rd | 4 man/formattable.factor.Rd | 4 man/formattable.logical.Rd | 4 man/formattable.numeric.Rd | 4 man/formattableOutput.Rd | 1 man/formatter.Rd | 1 man/gradient.Rd | 4 man/icontext.Rd | 14 man/is.formattable.Rd | 1 man/normalize.Rd | 1 man/normalize_bar.Rd | 1 man/percent.Rd | 3 man/prefix.Rd | 1 man/proportion.Rd | 1 man/proportion_bar.Rd | 1 man/qrank.Rd | 1 man/renderFormattable.Rd | 1 man/scientific.Rd | 1 man/style.Rd | 5 man/suffix.Rd | 1 man/vmap.Rd | 1 tests/testthat/test-formats.R | 74 - tests/testthat/test-formattable.R | 49 tests/testthat/test-formatter.R | 85 - tests/testthat/test-style.R | 34 tests/testthat/test-transform.R | 10 tests/testthat/test-utils.R | 2 vignettes/formattable-data-frame.Rmd | 8 vignettes/introduction.Rmd | 4 64 files changed, 1679 insertions(+), 2059 deletions(-)
Title: Fast Inference for Large Spatial Datasets using BRISC
Description: Fits bootstrap with univariate spatial regression models using Bootstrap for Rapid Inference on Spatial Covariances (BRISC) for large datasets using nearest neighbor Gaussian processes detailed in Saha and Datta (2018) <doi:10.1002/sta4.184>.
Author: Arkajyoti Saha [aut, cre],
Abhirup Datta [aut],
Jorge Nocedal [ctb],
Naoaki Okazaki [ctb]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Diff between BRISC versions 0.2.0 dated 2019-08-19 and 1.0.0 dated 2021-01-07
DESCRIPTION | 8 - MD5 | 35 ++-- NAMESPACE | 3 R/BRISC_correlation.R |only R/BRISC_decorrelation.R |only R/BRISC_simulation.R |only R/Brisc_Variogram.CI.R | 6 R/bootstrap_brisc.R | 2 R/estimation.R | 74 ++++++++- R/prediction.R | 37 +--- R/zzz.R |only man/BRISC_bootstrap.Rd | 23 +- man/BRISC_correlation.Rd |only man/BRISC_decorrelation.Rd |only man/BRISC_estimation.Rd | 102 ++++++++----- man/BRISC_prediction.Rd | 29 ++- man/BRISC_simulation.Rd |only man/BRISC_variogram.ci.Rd | 19 +- src/BRISC.cpp | 353 +++++++++++++++++++++++++++++++++++++++++++-- src/BRISC_Predict.cpp | 2 src/util.cpp | 142 +++++++++++++++++- src/util.h | 2 22 files changed, 693 insertions(+), 144 deletions(-)
Title: Estimating Hierarchical Linear Models for Single-Case Designs
Description: Provides a set of tools for estimating hierarchical linear
models and effect sizes based on data from single-case designs.
Functions are provided for calculating standardized mean difference effect sizes that
are directly comparable to standardized mean differences estimated from between-subjects randomized experiments,
as described in Hedges, Pustejovsky, and Shadish (2012) <DOI:10.1002/jrsm.1052>;
Hedges, Pustejovsky, and Shadish (2013) <DOI:10.1002/jrsm.1086>; and
Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>.
Includes an interactive web interface.
Author: James Pustejovsky [aut, cre],
Man Chen [aut],
Bethany Hamilton [aut]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between scdhlm versions 0.5.1 dated 2020-11-30 and 0.5.2 dated 2021-01-07
DESCRIPTION | 8 MD5 | 95 +++++----- NEWS.md | 6 R/HPS-ES-functions.R | 4 R/REML-ES-functions.R | 2 R/scdhlm-package.r | 41 ++-- R/scdhlm.R | 33 +-- R/simulation-functions.R | 10 - build/partial.rdb |only inst/doc/Estimating-effect-sizes.Rmd | 4 inst/doc/Estimating-effect-sizes.html | 52 ++--- inst/shiny-examples/scdhlm/code-chunks/clean-example-nofilter-TR.R | 10 - inst/shiny-examples/scdhlm/code-chunks/clean-example-nofilter.R | 11 - inst/shiny-examples/scdhlm/code-chunks/clean-inputdata-nofilter-TR.R | 10 - inst/shiny-examples/scdhlm/code-chunks/clean-inputdata-nofilter.R | 11 - inst/shiny-examples/scdhlm/code-chunks/load-dat.R | 12 - inst/shiny-examples/scdhlm/code-chunks/load-excel.R | 6 inst/shiny-examples/scdhlm/code-chunks/load-from-function.R | 3 inst/shiny-examples/scdhlm/markdown/Accessing_scdhlm.Rmd | 1 inst/shiny-examples/scdhlm/markdown/Accessing_scdhlm.md | 1 inst/shiny-examples/scdhlm/markdown/scdhlm.md | 4 inst/shiny-examples/scdhlm/rsconnect/shinyapps.io/jepusto/scdhlm.dcf | 4 inst/shiny-examples/scdhlm/server.R | 31 ++- man/AlberMorgan.Rd | 2 man/Anglesea.Rd | 4 man/BartonArwood.Rd | 2 man/Bryant2018.Rd | 2 man/Lambert.Rd | 2 man/Laski.Rd | 2 man/MB1results.Rd | 2 man/MB2results.Rd | 2 man/MB4results.Rd | 2 man/Rodriguez.Rd | 2 man/Romaniuk.Rd | 3 man/Ruiz.Rd | 2 man/Saddler.Rd | 4 man/Salazar.Rd | 2 man/Schutte.Rd | 4 man/Thiemann2001.Rd | 2 man/Thiemann2004.Rd | 2 man/compare_RML_HPS.Rd | 2 man/effect_size_ABk.Rd | 2 man/effect_size_MB.Rd | 2 man/g_REML.Rd | 2 man/simulate.g_REML.Rd | 4 man/simulate_MB2.Rd | 2 man/simulate_MB4.Rd | 2 tests/testthat/test_graphing_functions.R | 8 vignettes/Estimating-effect-sizes.Rmd | 4 49 files changed, 237 insertions(+), 191 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.16 dated 2019-07-23 and 1.0.17 dated 2021-01-07
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/gene_atomization.R | 38 +++++++++++++++++++------------------- R/readabs.R | 2 +- R/readabsnew.R | 4 ++-- data/HGNCdata.rda |binary 6 files changed, 33 insertions(+), 33 deletions(-)
More information about peopleanalyticsdata at CRAN
Permanent link
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
For additional documentation refer to the following article:
Ranghetti et al. (2020) <doi:10.1016/j.cageo.2020.104473>.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.3.9 dated 2020-10-14 and 1.4.0 dated 2021-01-07
DESCRIPTION | 9 MD5 | 303 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 38 +++ R/abs2rel.R | 5 R/add_rgb_image.R | 5 R/add_tile_suffix.R |only R/build_example_param_file.R | 5 R/calcindex.R | 7 R/check_gdal.R | 5 R/check_gui_deps.R | 5 R/check_param_list.R | 5 R/check_sen2r_deps.R | 5 R/compute_s2_paths.R | 36 ++- R/comsub.R | 5 R/create_indices_db.R | 10 R/create_s2_dop.R | 5 R/expand_path.R | 10 R/expect_equal_crs.R | 5 R/fix_envi_format.R | 5 R/gdalUtil.R | 17 - R/gdal_abs2rel.R | 5 R/gdal_warp.R | 252 ++++++++++++------------ R/gdalwarp_grid.R | 13 - R/gipp.R | 12 - R/give_write_permission.R | 7 R/helpers_extent.R | 5 R/ignorelist.R | 5 R/init_python.R | 5 R/install_aria2.R | 5 R/install_sen2cor.R | 9 R/list_indices.R | 5 R/load_binpaths.R | 7 R/mountpoint.R | 5 R/nn.R | 5 R/path_check.R | 2 R/print_message.R | 5 R/projpar.R | 5 R/raster_metadata.R | 5 R/s2_calcindices.R | 10 R/s2_dop.R | 5 R/s2_download.R | 61 ++++-- R/s2_gui.R | 11 - R/s2_list.R | 21 +- R/s2_mask.R | 14 - R/s2_merge.R | 5 R/s2_order.R | 7 R/s2_rgb.R | 11 - R/s2_thumbnails.R | 15 - R/s2_tiles.R | 5 R/s2_translate.R | 76 ++++++- R/safe_getMetadata.R | 5 R/safe_is_online.R | 12 - R/safe_shortname.R | 27 +- R/safelist-class.R | 5 R/scihub_login.R | 14 - R/sen2cor.R | 11 - R/sen2r.R | 270 +++++++++++++++++--------- R/sen2r_getElements.R | 7 R/sen2r_process_report.R | 7 R/smooth_mask.R | 5 R/st_as_text_2.R | 34 +-- R/st_crs2.R | 5 R/str_pad2.R | 5 R/tiles_intersects.R | 5 R/trace_functions.R | 5 build/partial.rdb |only inst/CITATION | 2 inst/doc/installation.Rmd | 6 inst/doc/installation.html | 6 inst/doc/sen2r_cmd.R | 6 inst/doc/sen2r_cmd.Rmd | 73 +++---- inst/doc/sen2r_cmd.html | 76 +++---- inst/extdata/settings/indices.json | 4 man/abs2rel.Rd | 5 man/add_rgb_image.Rd | 5 man/add_tile_suffix.Rd |only man/build_example_param_file.Rd | 5 man/calcindex.Rd | 5 man/check_gdal.Rd | 5 man/check_gui_deps.Rd | 5 man/check_param_list.Rd | 5 man/check_sen2r_deps.Rd | 5 man/compute_s2_paths.Rd | 5 man/comsub.Rd | 5 man/create_indices_db.Rd | 5 man/create_s2_dop.Rd | 5 man/expand_path.Rd | 5 man/expect_equal_crs.Rd | 5 man/fix_envi_format.Rd | 5 man/gdalUtil.Rd | 17 - man/gdal_abs2rel_rel2abs.Rd | 5 man/gdal_warp.Rd | 33 +-- man/gdalwarp_grid.Rd | 13 - man/gipp.Rd | 5 man/gipp_init.Rd | 5 man/give_write_permission.Rd | 7 man/ignorelist.Rd | 5 man/init_python.Rd | 5 man/install_aria2.Rd | 5 man/install_sen2cor.Rd | 9 man/list_indices.Rd | 5 man/load_binpaths.Rd | 5 man/load_extent.Rd | 5 man/mountpoint.Rd | 5 man/nn.Rd | 5 man/normalize_path.Rd | 5 man/path_check.Rd | 2 man/print_message.Rd | 5 man/projpar.Rd | 5 man/raster2rgb.Rd | 5 man/raster_metadata.Rd | 5 man/s2_calcindices.Rd | 10 man/s2_dop.Rd | 5 man/s2_download.Rd | 7 man/s2_gui.Rd | 5 man/s2_list.Rd | 7 man/s2_mask.Rd | 14 - man/s2_merge.Rd | 5 man/s2_order.Rd | 7 man/s2_rgb.Rd | 11 - man/s2_thumbnails.Rd | 5 man/s2_tiles.Rd | 5 man/s2_translate.Rd | 5 man/safe_getMetadata.Rd | 5 man/safe_is_online.Rd | 7 man/safe_shortname.Rd | 10 man/safelist-class.Rd | 5 man/scihub_login.Rd | 7 man/sen2cor.Rd | 11 - man/sen2r.Rd | 31 +-- man/sen2r_getElements.Rd | 5 man/sen2r_process_report.Rd | 7 man/smooth_mask.Rd | 5 man/st_crs2.Rd | 5 man/stack2rgb.Rd | 5 man/str_pad2.Rd | 5 man/tiles_intersects.Rd | 5 man/trace_function.Rd | 5 tests/testthat/setup-scihub_creds.R | 6 tests/testthat/test-gdal_warp.R | 75 +++---- tests/testthat/test-s2_download.R | 23 ++ tests/testthat/test-s2_list.R | 21 ++ tests/testthat/test-s2_order.R | 44 +++- tests/testthat/test-scihub_login.R | 1 tests/testthat/test-sen2cor.R | 37 +-- tests/testthat/test-sen2r-01_merge.R | 1 tests/testthat/test-sen2r-02_warp.R | 5 tests/testthat/test-sen2r-03_mask.R | 1 tests/testthat/test-sen2r-04_indices.R | 1 tests/testthat/test-sen2r-05_rgb.R | 1 tests/testthat/test-sen2r-06_ignorelist.R | 1 vignettes/installation.Rmd | 6 vignettes/sen2r_cmd.Rmd | 73 +++---- 154 files changed, 1318 insertions(+), 1092 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.12.3 dated 2020-11-25 and 0.12.4 dated 2021-01-07
DESCRIPTION | 6 MD5 | 226 ++++++++------- NAMESPACE | 1 NEWS.md | 50 +++ R/R.R | 68 +++- R/actions.R | 1 R/available-packages.R | 92 +++++- R/bootstrap.R | 94 ++++-- R/check.R | 4 R/ci.R |only R/clean.R | 2 R/config-defaults.R | 18 + R/config.R | 12 R/cran.R |only R/dependencies.R | 25 + R/description.R | 2 R/download.R | 136 +++++++-- R/extsoft.R | 2 R/file-backed.R | 14 R/files.R | 6 R/hydrate.R | 23 - R/imbue.R | 3 R/imports.R | 3 R/init.R | 8 R/install.R | 187 +++++++------ R/libpaths.R | 6 R/load.R | 7 R/lockfile-api.R | 6 R/lockfile.R | 6 R/package.R |only R/packages.R | 284 -------------------- R/patch.R | 23 + R/paths.R | 25 - R/preflight.R | 2 R/project.R | 21 + R/python-conda.R | 4 R/python-virtualenv.R | 4 R/rebuild.R | 12 R/remotes.R | 23 - R/repos.R | 10 R/restart.R | 2 R/restore.R | 41 +- R/retrieve.R | 155 ++++++++-- R/rspm.R | 2 R/scaffold.R | 6 R/scope.R | 13 R/skip.R | 5 R/snapshot.R | 76 +++-- R/status.R | 37 +- R/temp.R | 12 R/tests.R | 98 ++++-- R/testthat-reporter.R | 7 R/unload.R | 2 R/update.R | 13 R/upgrade.R | 1 R/use-python.R | 2 R/utils-format.R | 8 R/utils.R | 6 R/verbose.R | 2 README.md | 2 build/vignette.rds |binary inst/config.yml | 14 inst/doc/ci.html | 3 inst/doc/collaborating.html | 3 inst/doc/docker.html | 8 inst/doc/faq.html | 4 inst/doc/local-sources.Rmd | 6 inst/doc/local-sources.html | 9 inst/doc/lockfile.html | 5 inst/doc/mran.html | 4 inst/doc/packages.Rmd | 15 + inst/doc/packages.html | 8 inst/doc/python.html | 3 inst/doc/renv.html | 10 inst/doc/rsconnect.R |only inst/doc/rsconnect.Rmd |only inst/doc/rsconnect.html |only inst/resources/activate.R | 94 ++++-- man/config.Rd | 4 man/dependencies.Rd | 12 man/install.Rd | 2 man/paths.Rd | 25 - tests/testthat/helper-aaa.R | 31 ++ tests/testthat/local/skeleton/skeleton_1.0.0.tar.gz |only tests/testthat/local/skeleton/skeleton_1.0.0.tgz |only tests/testthat/resources/empty-label.Rmd |only tests/testthat/resources/evil.Rmd | 1 tests/testthat/resources/knitr-reused-chunks.Rmd |only tests/testthat/test-actions.R | 18 + tests/testthat/test-activate.R | 2 tests/testthat/test-available-packages.R | 33 ++ tests/testthat/test-bioconductor.R | 10 tests/testthat/test-bootstrap.R | 21 + tests/testthat/test-cache.R | 2 tests/testthat/test-dependencies.R | 12 tests/testthat/test-description.R | 1 tests/testthat/test-download.R | 11 tests/testthat/test-file-backed.R | 4 tests/testthat/test-files.R | 28 - tests/testthat/test-hydrate.R | 2 tests/testthat/test-init.R | 17 - tests/testthat/test-install.R | 69 ++++ tests/testthat/test-json.R | 2 tests/testthat/test-load.R | 2 tests/testthat/test-lockfile.R | 6 tests/testthat/test-paths.R | 2 tests/testthat/test-profiles.R | 4 tests/testthat/test-properties.R | 2 tests/testthat/test-python.R | 8 tests/testthat/test-r.R | 2 tests/testthat/test-remotes.R | 2 tests/testthat/test-restore.R | 47 ++- tests/testthat/test-retrieve.R | 15 + tests/testthat/test-scope.R | 15 + tests/testthat/test-snapshot.R | 23 + tests/testthat/test-update.R | 3 vignettes/ide-publish.png |only vignettes/local-sources.Rmd | 6 vignettes/packages.Rmd | 15 + vignettes/rsconnect.Rmd |only 120 files changed, 1619 insertions(+), 932 deletions(-)
Title: Phylogenetic Monte Carlo
Description: Monte Carlo based model choice for applied phylogenetics of
continuous traits. Method described in Carl Boettiger, Graham Coop,
Peter Ralph (2012) Is your phylogeny informative? Measuring
the power of comparative methods, Evolution 66 (7)
2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between pmc versions 1.0.3 dated 2018-05-17 and 1.0.4 dated 2021-01-07
pmc-1.0.3/pmc/inst/doc/pmc_tutorial.R |only pmc-1.0.4/pmc/DESCRIPTION | 12 pmc-1.0.4/pmc/MD5 | 25 - pmc-1.0.4/pmc/NEWS | 5 pmc-1.0.4/pmc/README.md | 12 pmc-1.0.4/pmc/build/vignette.rds |binary pmc-1.0.4/pmc/inst/CITATION | 2 pmc-1.0.4/pmc/inst/doc/pmc_tutorial.Rmd | 54 ++- pmc-1.0.4/pmc/inst/doc/pmc_tutorial.html | 248 ++++++++++------- pmc-1.0.4/pmc/man/figures/README-unnamed-chunk-3-1.png |binary pmc-1.0.4/pmc/man/pmc.Rd | 17 - pmc-1.0.4/pmc/vignettes/fig |only pmc-1.0.4/pmc/vignettes/pmc_tutorial.Rmd | 54 ++- 13 files changed, 274 insertions(+), 155 deletions(-)
Title: Interactive Studio for Explanatory Model Analysis
Description: Automate the explanatory analysis of machine learning predictive models.
Generate advanced interactive model explanations in the form of a serverless HTML
site with only one line of code. This tool is model agnostic, therefore compatible
with most of the black box predictive models and frameworks. The main function
computes various (instance and dataset level) model explanations and produces
a customisable dashboard, which consists of multiple panels for plots with their
short descriptions. Easily save the dashboard and share it with others. Tools
for Explanatory Model Analysis unite with tools for Exploratory Data Analysis
to give a broad overview of the model behavior.
Author: Hubert Baniecki [aut, cre] (<https://orcid.org/0000-0001-6661-5364>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>),
Piotr Piatyszek [ctb]
Maintainer: Hubert Baniecki <hbaniecki@gmail.com>
Diff between modelStudio versions 2.1.0 dated 2020-11-22 and 2.1.1 dated 2021-01-07
DESCRIPTION | 6 - MD5 | 36 +++---- NEWS.md | 3 R/modelStudio.R | 102 +++++++++---------- inst/doc/ms-perks-features.Rmd | 20 +-- inst/doc/ms-perks-features.html | 18 +-- inst/doc/ms-r-python-examples.Rmd | 2 inst/doc/ms-r-python-examples.html | 6 - man/modelStudio.Rd | 101 +++++++++---------- tests/testthat.R | 4 tests/testthat/test_2_0.R | 138 +++++++++++++-------------- tests/testthat/test_2_1.R | 3 tests/testthat/test_modelStudio.R | 18 ++- tests/testthat/test_ms_update_observations.R | 55 +++++----- tests/testthat/test_ms_update_options.R | 48 ++++----- tests/testthat/test_objects.R | 37 +++---- tests/testthat/test_warnings_and_errors.R | 43 ++++---- vignettes/ms-perks-features.Rmd | 20 +-- vignettes/ms-r-python-examples.Rmd | 2 19 files changed, 343 insertions(+), 319 deletions(-)
Title: MCMC Generalised Linear Mixed Models
Description: Fits Multi-response Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Diff between MCMCglmm versions 2.29 dated 2019-04-24 and 2.30 dated 2021-01-07
.Rinstignore | 6 DESCRIPTION | 10 MD5 | 52 NAMESPACE | 5 R/MCMCglmm.R | 2707 +++++++++++++++++++++++----------------------- R/buildZ.R | 6 R/inverseA.R | 6 R/pkk.R |only R/predict.MCMCglmm.R | 31 R/simulate.MCMCglmm.R | 13 build/vignette.rds |binary inst/CITATION | 4 inst/doc/CourseNotes.pdf |binary inst/doc/Overview.pdf |binary man/BTdata.Rd | 2 man/BTped.Rd | 2 man/MCMCglmm.Rd | 6 man/PlodiaPO.Rd | 2 man/PlodiaR.Rd | 2 man/PlodiaRB.Rd | 2 man/SShorns.Rd | 2 man/pkk.Rd |only man/rIW.Rd | 2 src/MCMCglmm.cc | 119 +- src/MCMCglmm.h | 5 src/pkk.c |only src/pkkR.cc |only vignettes/CourseNotes.bib | 440 +++++++ vignettes/Figures/TEST.R | 19 vignettes/Overview.bib | 584 +++++++++ 30 files changed, 2644 insertions(+), 1383 deletions(-)
Title: Selecting Attributes
Description: Functions for selecting attributes from a given dataset. Attribute
subset selection is the process of identifying and removing as much of the
irrelevant and redundant information as possible.
Author: Piotr Romanski, Lars Kotthoff
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Diff between FSelector versions 0.31 dated 2018-05-16 and 0.32 dated 2021-01-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cutoff.R | 4 ++-- R/discretize.R | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Extracts Tabular Data from Excel Reports
Description: Removes metadata and summary formatting from Excel reports, so that
data from those reports can more easily be loaded into R. Currently works with
.xlsx and .xls format files.
Author: Christopher Burch [aut, cre] (<https://orcid.org/0000-0001-6934-3325>)
Maintainer: Christopher Burch <cmburch@cmburch.me>
Diff between excelstrippr versions 0.1.1 dated 2021-01-05 and 0.1.2 dated 2021-01-07
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- NEWS.md | 9 ++++-- R/extract_data.R | 22 ++++++++------ R/strip_metadata.R | 22 +++++++++++--- README.md | 36 ++++++++++++++---------- man/extract_data.Rd | 74 +++++++++++++++++++++++++------------------------- man/strip_metadata.Rd | 53 +++++++++++++++++++---------------- 8 files changed, 133 insertions(+), 103 deletions(-)
Title: Environmental Interpolation using Spatial Kernel Density
Estimation
Description: Estimates an ecological niche using occurrence data, covariates, and kernel
density-based estimation methods. For a single species with presence and absence data,
the 'envi' package uses the spatial relative risk function that is estimated using the
'sparr' package. Details about the 'sparr' package methods can be found in the tutorial:
Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can
be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about
relative risk functions using kernel density estimation can be found in J. F. Bithell
(1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] (<https://orcid.org/0000-0001-9477-8582>),
Lance A. Waller [ctb, ths] (<https://orcid.org/0000-0001-5002-8886>),
Emory University [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between envi versions 0.1.3 dated 2020-12-21 and 0.1.6 dated 2021-01-07
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++------- NEWS.md | 11 ++++++++ R/package.R | 2 - build/partial.rdb |only man/envi-package.Rd | 2 - tests/testthat/test-lrren.R | 46 +++++++++++++++++++++++-------------- tests/testthat/test-perlrren.R | 18 +++++++------- tests/testthat/test-plot_cv.R | 14 ++++++++++- tests/testthat/test-plot_obs.R | 12 +++++++++ tests/testthat/test-plot_predict.R | 12 +++++++++ 11 files changed, 102 insertions(+), 42 deletions(-)
Title: Filter and Plot RNA Biotypes
Description: Analyze and plot the abundance of different RNA biotypes present in a count matrix, this evaluation can be useful if you want to test different strategies of normalization or analyze a particular biotype in a differential gene expression analysis.
Author: Luiz Antonio de Jesus Rocha [aut, cre, cph]
Maintainer: Luiz Antonio de Jesus Rocha <luiz.rocha@unifesp.br>
Diff between BioInsight versions 0.1.0 dated 2020-08-17 and 0.2.0 dated 2021-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/describeRNA.R | 22 +++++++++++----------- R/revealRNA.R | 7 ++----- 4 files changed, 19 insertions(+), 22 deletions(-)
Title: Downloading Time Series from ALFRED Database for Various
Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases.
Its functions return tidy data frames for different releases of the specified time series.
Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between alfred versions 0.1.9 dated 2021-01-04 and 0.1.10 dated 2021-01-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 1 + R/get_alfred_series.R | 9 +++++++-- inst/doc/alfred.html | 4 ++-- tests/testthat/test_download.R | 1 + 7 files changed, 21 insertions(+), 13 deletions(-)
Title: Wizardry Code Meta Testing
Description: Meta testing is the ability to test a function without having to
provide its parameter values.
Those values will be generated, based on semantic naming of parameters, as
introduced by package 'wyz.code.offensiveProgramming'.
Value generation logic can be completed with your own data types
and generation schemes. This to meet your most specific requirements and to
answer to a wide variety of usages, from general use case to very specific
ones.
While using meta testing, it becomes easier to generate stress test
campaigns, non-regression test campaigns and robustness test campaigns, as
generated tests can be saved and reused from session to session.
Main benefits of using 'wyz.code.metaTesting' is ability to discover valid
and invalid function parameter combinations, ability to infer valid
parameter values, and to provide smart summaries that allows you to focus
on dysfunctional cases.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>
Diff between wyz.code.metaTesting versions 1.1.12 dated 2020-04-22 and 1.1.20 dated 2021-01-07
wyz.code.metaTesting-1.1.12/wyz.code.metaTesting/inst/doc/releases.R |only wyz.code.metaTesting-1.1.12/wyz.code.metaTesting/inst/doc/releases.Rmd |only wyz.code.metaTesting-1.1.12/wyz.code.metaTesting/inst/doc/releases.html |only wyz.code.metaTesting-1.1.12/wyz.code.metaTesting/vignettes/releases.Rmd |only wyz.code.metaTesting-1.1.12/wyz.code.metaTesting/vignettes/vignette-common.R |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/DESCRIPTION | 8 wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/MD5 | 21 - wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/build/partial.rdb |binary wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/build/vignette.rds |binary wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/inst/doc/release-notes.R |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/inst/doc/release-notes.Rmd |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/inst/doc/release-notes.html |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/inst/extdata |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/tests/testthat/test_computeArgumentsCombination.R | 209 +++++++--- wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/vignettes/common-style.R |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/vignettes/release-notes.Rmd |only wyz.code.metaTesting-1.1.20/wyz.code.metaTesting/vignettes/style.css | 8 17 files changed, 184 insertions(+), 62 deletions(-)
More information about wyz.code.metaTesting at CRAN
Permanent link
Title: Convert Between 'WKT' and 'GeoJSON'
Description: Convert 'WKT' to 'GeoJSON' and 'GeoJSON' to 'WKT'. Functions
included for converting between 'GeoJSON' to 'WKT', creating both
'GeoJSON' features, and non-features, creating 'WKT' from R objects
(e.g., lists, data.frames, vectors), and linting 'WKT'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Os Keyes [aut] (author of code in src/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between wellknown versions 0.7.0 dated 2020-10-20 and 0.7.2 dated 2021-01-07
wellknown-0.7.0/wellknown/README.md |only wellknown-0.7.2/wellknown/DESCRIPTION | 15 +++++++++------ wellknown-0.7.2/wellknown/MD5 | 8 ++++---- wellknown-0.7.2/wellknown/NEWS.md | 8 ++++++++ wellknown-0.7.2/wellknown/src/Makevars |only wellknown-0.7.2/wellknown/src/centroid.cpp | 7 +++++-- 6 files changed, 26 insertions(+), 12 deletions(-)
Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function that is estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] (<https://orcid.org/0000-0001-9477-8582>),
Elena Hsieh [ctb] (<https://orcid.org/0000-0003-3969-6597>),
Debashis Ghosh [ctb] (<https://orcid.org/0000-0001-6618-1316>),
Lance A. Waller [ctb] (<https://orcid.org/0000-0001-5002-8886>),
NCI [cph]
Maintainer: Ian D. Buller <ian.buller@nih.gov>
Diff between gateR versions 0.1.4 dated 2020-11-30 and 0.1.6 dated 2021-01-07
DESCRIPTION | 8 ++--- MD5 | 45 +++++++++++++++---------------- NAMESPACE | 2 + NEWS.md | 14 +++++++++ R/gating.R | 62 ++++++++++++++++++++++++++++--------------- R/lotrrs.R | 54 ++++++++++++++++++++++++++----------- R/package.R | 6 ++-- R/pval_correct.R | 2 - R/pval_plot.R | 3 -- R/randCyto.R | 2 - R/rrs.R | 41 ++++++++++++++++++++-------- R/utils.R | 2 - README.md | 2 - build/partial.rdb |only inst/doc/vignette.html | 12 ++++---- man/gateR-package.Rd | 4 +- man/gating.Rd | 18 ++++++++---- man/lotrrs.Rd | 18 ++++++++---- man/randCyto.Rd | 2 - man/rrs.Rd | 18 ++++++++---- tests/testthat/test-gating.R | 11 ++++++- tests/testthat/test-lotrrs.R | 4 +- tests/testthat/test-rrs.R | 4 +- vignettes/vignette.Rmd | 6 ++-- 24 files changed, 221 insertions(+), 119 deletions(-)
Title: An Alternative to the Kruskal-Wallis Based on the Kendall Tau
Distance
Description: The Concordance Test is a non-parametric method for testing whether two o more samples originate from the same distribution. It extends the Kendall Tau correlation coefficient when there are only two groups. For details, see Monge (2019) <arXiv:1912.12880v1>.
Author: Javier Alcaraz [aut],
Laura Anton-Sanchez [aut, cre],
Juan Francisco Monge [aut]
Maintainer: Laura Anton-Sanchez <l.anton@umh.es>
Diff between ConcordanceTest versions 0.1.0 dated 2020-09-28 and 1.0.0 dated 2021-01-07
ConcordanceTest-0.1.0/ConcordanceTest/man/CT_Critical_Values_Sim.Rd |only ConcordanceTest-0.1.0/ConcordanceTest/man/CT_Distribution_Sim.Rd |only ConcordanceTest-0.1.0/ConcordanceTest/man/CT_Hyphotesis_Test.Rd |only ConcordanceTest-1.0.0/ConcordanceTest/DESCRIPTION | 10 ConcordanceTest-1.0.0/ConcordanceTest/MD5 | 23 ConcordanceTest-1.0.0/ConcordanceTest/NAMESPACE | 4 ConcordanceTest-1.0.0/ConcordanceTest/NEWS.md |only ConcordanceTest-1.0.0/ConcordanceTest/R/functions.R | 798 +++------- ConcordanceTest-1.0.0/ConcordanceTest/man/CT_Coefficient.Rd | 8 ConcordanceTest-1.0.0/ConcordanceTest/man/CT_Critical_Values.Rd | 22 ConcordanceTest-1.0.0/ConcordanceTest/man/CT_Density_Plot.Rd | 17 ConcordanceTest-1.0.0/ConcordanceTest/man/CT_Distribution.Rd | 23 ConcordanceTest-1.0.0/ConcordanceTest/man/CT_Hypothesis_Test.Rd |only ConcordanceTest-1.0.0/ConcordanceTest/man/CT_Probability_Plot.Rd | 18 ConcordanceTest-1.0.0/ConcordanceTest/man/Permutations_With_Repetition.Rd | 11 15 files changed, 324 insertions(+), 610 deletions(-)
More information about ConcordanceTest at CRAN
Permanent link
Title: Variance Components Testing for Linear and Nonlinear Mixed
Effects Models
Description: An implementation of the Likelihood ratio Test (LRT) for testing that,
in a (non)linear mixed effects model, the variances of a subset of the random
effects are equal to zero. There is no restriction on the subset of variances
that can be tested: for example, it is possible to test that all the variances
are equal to zero. Note that the implemented test is asymptotic.
This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'.
Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Author: Charlotte Baey [aut, cre] (<https://orcid.org/0000-0002-1413-1058>),
Estelle Kuhn [aut]
Maintainer: Charlotte Baey <charlotte.baey@univ-lille.fr>
Diff between varTestnlme versions 0.2.0 dated 2020-07-07 and 1.0.0 dated 2021-01-07
varTestnlme-0.2.0/varTestnlme/R/approxWeights.R |only varTestnlme-0.2.0/varTestnlme/R/bootstrapFIM.R |only varTestnlme-0.2.0/varTestnlme/R/chiBarObject.R |only varTestnlme-0.2.0/varTestnlme/R/extractFIMnlme.R |only varTestnlme-0.2.0/varTestnlme/R/funcCO.R |only varTestnlme-0.2.0/varTestnlme/R/funcStruct.R |only varTestnlme-0.2.0/varTestnlme/R/getVarCovlme4.R |only varTestnlme-0.2.0/varTestnlme/R/getVarCovnlme.R |only varTestnlme-0.2.0/varTestnlme/R/loadMessage.R |only varTestnlme-0.2.0/varTestnlme/R/plot.varTestObject.R |only varTestnlme-0.2.0/varTestnlme/R/print.varTestObject.R |only varTestnlme-0.2.0/varTestnlme/R/summary.varTestObject.R |only varTestnlme-0.2.0/varTestnlme/R/varTest.R |only varTestnlme-0.2.0/varTestnlme/R/varTestObject.R |only varTestnlme-0.2.0/varTestnlme/R/weightsChiBarSquare.R |only varTestnlme-0.2.0/varTestnlme/man/chiBarSquareObject-class.Rd |only varTestnlme-0.2.0/varTestnlme/man/dfchisqbar-methods.Rd |only varTestnlme-0.2.0/varTestnlme/man/extractFIMnlme.Rd |only varTestnlme-0.2.0/varTestnlme/man/funcStruct.Rd |only varTestnlme-0.2.0/varTestnlme/man/getVarCovlme4.Rd |only varTestnlme-0.2.0/varTestnlme/man/getVarCovnlme.Rd |only varTestnlme-0.2.0/varTestnlme/man/pchisqbar-methods.Rd |only varTestnlme-0.2.0/varTestnlme/man/plot.varTestObject.Rd |only varTestnlme-0.2.0/varTestnlme/man/print.varTestObject.Rd |only varTestnlme-0.2.0/varTestnlme/man/summary.varTestObject.Rd |only varTestnlme-0.2.0/varTestnlme/man/varTest.Rd |only varTestnlme-0.2.0/varTestnlme/man/varTestObject-class.Rd |only varTestnlme-0.2.0/varTestnlme/man/varTestnlme-internal.Rd |only varTestnlme-1.0.0/varTestnlme/DESCRIPTION | 14 varTestnlme-1.0.0/varTestnlme/MD5 | 76 -- varTestnlme-1.0.0/varTestnlme/NAMESPACE | 25 varTestnlme-1.0.0/varTestnlme/NEWS.md | 5 varTestnlme-1.0.0/varTestnlme/R/chibarsquare.R |only varTestnlme-1.0.0/varTestnlme/R/constraintsFn.R |only varTestnlme-1.0.0/varTestnlme/R/generics.R |only varTestnlme-1.0.0/varTestnlme/R/lme4_utilities.R |only varTestnlme-1.0.0/varTestnlme/R/lme_utilities.R |only varTestnlme-1.0.0/varTestnlme/R/pkgName.R |only varTestnlme-1.0.0/varTestnlme/R/saemix_utilities.R |only varTestnlme-1.0.0/varTestnlme/R/varCompTest.lme.R |only varTestnlme-1.0.0/varTestnlme/R/varCompTest.merMod.R |only varTestnlme-1.0.0/varTestnlme/R/varCompTest.saemix.R |only varTestnlme-1.0.0/varTestnlme/README.md | 30 varTestnlme-1.0.0/varTestnlme/inst/doc/varTestnlme.R | 73 - varTestnlme-1.0.0/varTestnlme/inst/doc/varTestnlme.Rmd | 92 +- varTestnlme-1.0.0/varTestnlme/inst/doc/varTestnlme.html | 373 +++++++--- varTestnlme-1.0.0/varTestnlme/man/approxWeights.Rd | 5 varTestnlme-1.0.0/varTestnlme/man/bootinvFIM.Rd | 11 varTestnlme-1.0.0/varTestnlme/man/bootinvFIM.lme.Rd |only varTestnlme-1.0.0/varTestnlme/man/bootinvFIM.merMod.Rd |only varTestnlme-1.0.0/varTestnlme/man/bootinvFIM.saemix.Rd |only varTestnlme-1.0.0/varTestnlme/man/dfChiBarSquare.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractStruct.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractStruct.lme.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractStruct.merMod.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractStruct.saemix.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractVarCov.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractVarCov.lme.Rd |only varTestnlme-1.0.0/varTestnlme/man/extractVarCov.merMod.Rd |only varTestnlme-1.0.0/varTestnlme/man/objFunction.Rd |only varTestnlme-1.0.0/varTestnlme/man/pckName.Rd |only varTestnlme-1.0.0/varTestnlme/man/varCompTest.Rd |only varTestnlme-1.0.0/varTestnlme/man/weightsChiBarSquare.Rd | 38 - varTestnlme-1.0.0/varTestnlme/vignettes/varTestnlme.Rmd | 92 +- varTestnlme-1.0.0/varTestnlme/vignettes/web_only/fim.Rmd | 12 65 files changed, 515 insertions(+), 331 deletions(-)
Title: Genotype by Environment (GxE) Analysis
Description: Analysis of multi environment data of plant breeding experiments
following the analyses described in Malosetti, Ribaut,
and van Eeuwijk (2013), <doi:10.3389/fphys.2013.00044>.
One of a series of statistical genetic packages for streamlining the analysis of
typical plant breeding experiments developed by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://www.vsni.co.uk/software/asreml-r>).
Author: Bart-Jan van Rossum [aut, cre],
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie J Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Willem Kruijer [ctb] (<https://orcid.org/0000-0001-7179-1733>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGxE versions 1.0.3 dated 2020-11-09 and 1.0.4 dated 2021-01-07
DESCRIPTION | 10 MD5 | 55 ++--- NEWS.md | 6 R/chkFuncs.R | 7 R/createVarComp.R | 4 R/data.R | 4 R/gxeAmmi.R | 13 - R/gxeFw.R | 25 ++ R/gxeMegaEnv.R | 11 - README.md | 22 -- build/partial.rdb |only data/dropsPheno.rda |binary inst/doc/statgenGxE.R | 8 inst/doc/statgenGxE.Rmd | 10 inst/doc/statgenGxE.html | 384 ++++++++----------------------------- man/CRDR.Rd | 2 man/dropsPheno.Rd | 4 man/gxeMegaEnv.Rd | 2 man/herit.Rd | 2 man/statgenGxE-package.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-gxeAmmi.R | 12 - tests/testthat/test-gxeFW.R | 11 + tests/testthat/test-gxeMegaEnv.R | 14 - tests/testthat/test-gxeStability.R | 2 tests/testthat/test-gxeVarComp.R | 21 +- tests/testthat/test-plots.R | 5 tests/testthat/test-summaries.R | 2 vignettes/statgenGxE.Rmd | 10 29 files changed, 244 insertions(+), 404 deletions(-)
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks (walk,
bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks
<https://github.com/conveyal/r5>. The package allows users to
generate detailed routing analysis or calculate travel time matrices
using seamless parallel computing on top of the R5 Java machine.
Author: Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>),
Rafael H. M. Pereira [aut, cre]
(<https://orcid.org/0000-0003-2125-7465>),
Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>),
Carlos Kaue Vieira Braga [aut]
(<https://orcid.org/0000-0002-6104-7297>),
Matthew Wigginton Conway [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 0.3-0 dated 2021-01-05 and 0.3-1 dated 2021-01-07
DESCRIPTION | 8 MD5 | 25 - NEWS.md | 31 +- R/detailed_itineraries.R | 621 ++++++++++++++++++++++---------------------- R/download_r5.R | 193 ++++++------- R/setup_r5.R | 244 ++++++++--------- R/travel_time_matrix.R | 452 ++++++++++++++++---------------- R/utils.R | 105 +++++-- R/zzz.R | 2 inst/doc/intro_to_r5r.html | 23 - man/detailed_itineraries.Rd | 6 man/download_metadata.Rd |only man/select_mode.Rd | 4 man/travel_time_matrix.Rd | 5 14 files changed, 895 insertions(+), 824 deletions(-)
Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits the Poisson-Tweedie generalized linear mixed
model described in Signorelli et al. (2020,
<doi:10.1177/1471082X20936017>). Likelihood approximation based on
adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre, cph]
(<https://orcid.org/0000-0002-8102-3356>),
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between ptmixed versions 1.0.1 dated 2020-10-26 and 1.0.2 dated 2021-01-07
DESCRIPTION | 14 ++-- MD5 | 42 +++++++------- NAMESPACE | 34 +++++------ R/makespaghetti.R | 6 ++ inst/CITATION | 6 +- inst/NEWS.md | 12 +++- inst/doc/Overview_functionalities_ptmixed.Rmd | 24 ++++---- inst/doc/Overview_functionalities_ptmixed.html | 75 ++++++++++++++----------- man/df1.Rd | 6 +- man/loglik.pt.1re.Rd | 22 +------ man/make.spaghetti.Rd | 36 +++--------- man/nbglm.Rd | 14 +--- man/nbmixed.Rd | 33 +++-------- man/pmf.Rd | 19 +----- man/ptglm.Rd | 16 +---- man/ptmixed.Rd | 39 ++++--------- man/ranef.Rd | 10 +-- man/simulate_ptglmm.Rd | 18 +----- man/summary.ptglm.Rd | 6 +- man/summary.ptglmm.Rd | 8 +- man/wald.test.Rd | 8 +- vignettes/Overview_functionalities_ptmixed.Rmd | 24 ++++---- 22 files changed, 213 insertions(+), 259 deletions(-)
Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating precision-recall curves under various conditions.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between prcbench versions 0.8.2 dated 2020-03-26 and 0.9.1 dated 2021-01-07
DESCRIPTION | 12 MD5 | 67 ++-- NEWS.md | 8 R/data_interface.R | 2 R/data_zzz.R | 300 +++++++++++------- R/g_autoplot.R | 6 R/g_print.R | 2 R/main_benchmark.R | 6 R/main_evalcurves.R | 8 R/prcbench.R | 2 R/tool_interface.R | 6 R/tool_java.R | 9 R/tool_rlib.R | 2 R/tool_zzz.R | 280 +++++++---------- README.md | 202 +++++++----- build/vignette.rds |binary inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 542 ++++++++++++++++++++++++---------- java/auc2/src/auc2/AUCWrapper.java | 2 man/TestDataB.Rd | 47 ++ man/TestDataC.Rd | 95 +++-- man/ToolAUCCalculator.Rd | 74 ++-- man/ToolIFBase.Rd | 82 +++-- man/ToolPRROC.Rd | 69 ++-- man/ToolPerfMeas.Rd | 29 - man/ToolROCR.Rd | 31 - man/Toolprecrec.Rd | 45 +- man/figures |only man/prcbench.Rd | 2 tests/testthat.R | 3 tests/testthat/test_main_evalcurves.R | 6 tests/testthat/test_plot_autoplot.R | 5 tests/testthat/test_print.R | 2 tests/testthat/test_tool_userd.R | 4 vignettes/introduction.Rmd | 8 35 files changed, 1164 insertions(+), 802 deletions(-)
Title: Ensemble Sampler for Affine-Invariant MCMC
Description: Provides ensemble samplers for
affine-invariant Monte Carlo Markov Chain, which allow a faster
convergence for badly scaled estimation problems. Two samplers are
proposed: the 'differential.evolution' sampler from ter Braak and
Vrugt (2008) <doi:10.1007/s11222-008-9104-9> and the 'stretch' sampler
from Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65>.
Author: Hugo Gruson [cre, aut, cph] (<https://orcid.org/0000-0002-4094-1476>),
Sanda Dejanic [aut, cph],
Andreas Scheidegger [aut, cph]
(<https://orcid.org/0000-0003-2575-2172>)
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between mcmcensemble versions 2.0 dated 2020-10-17 and 2.1 dated 2021-01-07
mcmcensemble-2.0/mcmcensemble/R/MCMCEnsembleSampler-package.R |only mcmcensemble-2.0/mcmcensemble/man/figures/README-unnamed-chunk-4-1.svg |only mcmcensemble-2.0/mcmcensemble/man/figures/README-unnamed-chunk-4-2.svg |only mcmcensemble-2.1/mcmcensemble/DESCRIPTION | 13 - mcmcensemble-2.1/mcmcensemble/MD5 | 36 ++- mcmcensemble-2.1/mcmcensemble/NAMESPACE | 2 mcmcensemble-2.1/mcmcensemble/NEWS.md | 19 + mcmcensemble-2.1/mcmcensemble/R/MCMCEnsemble.R | 14 - mcmcensemble-2.1/mcmcensemble/R/d.e.mcmc.R | 98 +++++----- mcmcensemble-2.1/mcmcensemble/R/mcmcensemble-package.R |only mcmcensemble-2.1/mcmcensemble/R/s.m.mcmc.R | 85 ++++---- mcmcensemble-2.1/mcmcensemble/README.md | 65 +++++- mcmcensemble-2.1/mcmcensemble/build/partial.rdb |binary mcmcensemble-2.1/mcmcensemble/build/vignette.rds |only mcmcensemble-2.1/mcmcensemble/inst |only mcmcensemble-2.1/mcmcensemble/man/MCMCEnsemble.Rd | 6 mcmcensemble-2.1/mcmcensemble/man/d.e.mcmc.Rd | 3 mcmcensemble-2.1/mcmcensemble/man/figures/README-example-de-1.svg |only mcmcensemble-2.1/mcmcensemble/man/figures/README-example-stretch-1.svg |only mcmcensemble-2.1/mcmcensemble/man/mcmcensemble-package.Rd | 2 mcmcensemble-2.1/mcmcensemble/tests/testthat/test-MCMCEnsemble.R | 19 + mcmcensemble-2.1/mcmcensemble/tests/testthat/test-convergence.R |only mcmcensemble-2.1/mcmcensemble/vignettes |only 23 files changed, 228 insertions(+), 134 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb]
(<https://orcid.org/0000-0002-0705-1287>),
Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.4.4 dated 2020-06-27 and 0.4.5 dated 2021-01-07
heatwaveR-0.4.4/heatwaveR/R/geom2plotly.R |only heatwaveR-0.4.4/heatwaveR/man/plotly_helpers.Rd |only heatwaveR-0.4.4/heatwaveR/tests/testthat/test-geom2plotly.R |only heatwaveR-0.4.5/heatwaveR/DESCRIPTION | 18 heatwaveR-0.4.5/heatwaveR/MD5 | 79 - heatwaveR-0.4.5/heatwaveR/NAMESPACE | 3 heatwaveR-0.4.5/heatwaveR/NEWS.md | 540 +++++----- heatwaveR-0.4.5/heatwaveR/R/block_average.R | 6 heatwaveR-0.4.5/heatwaveR/R/category.R | 31 heatwaveR-0.4.5/heatwaveR/R/clim_spread.R | 2 heatwaveR-0.4.5/heatwaveR/R/detect_event.R | 47 heatwaveR-0.4.5/heatwaveR/R/exceedance.R | 183 +-- heatwaveR-0.4.5/heatwaveR/R/geoms.R | 9 heatwaveR-0.4.5/heatwaveR/R/graph_functions.R | 9 heatwaveR-0.4.5/heatwaveR/R/make_whole.R | 40 heatwaveR-0.4.5/heatwaveR/R/proto_event.R | 1 heatwaveR-0.4.5/heatwaveR/R/ts2clm.R | 11 heatwaveR-0.4.5/heatwaveR/README.md | 18 heatwaveR-0.4.5/heatwaveR/build/vignette.rds |binary heatwaveR-0.4.5/heatwaveR/inst/doc/OISST_preparation.Rmd | 2 heatwaveR-0.4.5/heatwaveR/inst/doc/OISST_preparation.html | 16 heatwaveR-0.4.5/heatwaveR/inst/doc/complex_clims.html | 200 +-- heatwaveR-0.4.5/heatwaveR/inst/doc/detection_and_visualisation.html | 75 - heatwaveR-0.4.5/heatwaveR/inst/doc/event_categories.html | 24 heatwaveR-0.4.5/heatwaveR/inst/doc/exceedance.html | 18 heatwaveR-0.4.5/heatwaveR/inst/doc/gridded_event_detection.R | 18 heatwaveR-0.4.5/heatwaveR/inst/doc/gridded_event_detection.Rmd | 20 heatwaveR-0.4.5/heatwaveR/inst/doc/gridded_event_detection.html | 36 heatwaveR-0.4.5/heatwaveR/man/category.Rd | 6 heatwaveR-0.4.5/heatwaveR/man/detect_event.Rd | 6 heatwaveR-0.4.5/heatwaveR/man/exceedance.Rd | 16 heatwaveR-0.4.5/heatwaveR/man/make_whole.Rd | 2 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-category.R | 16 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-clim_calc.R | 2 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-clim_spread.R | 4 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-detect_event.R | 18 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-exceedance.R | 32 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-make_whole.R | 12 heatwaveR-0.4.5/heatwaveR/tests/testthat/test-smooth_percentile.R | 2 heatwaveR-0.4.5/heatwaveR/vignettes/OISST_preparation.Rmd | 2 heatwaveR-0.4.5/heatwaveR/vignettes/bibliography.bib | 1 heatwaveR-0.4.5/heatwaveR/vignettes/gridded_event_detection.Rmd | 20 42 files changed, 793 insertions(+), 752 deletions(-)
Title: Freedom from Disease
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997, <doi:10.1016/s0167-5877(97)00081-0>). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002, <doi:10.1016/S0167-5877(01)00245-8>). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka <ian.kopacka@ages.at>
Diff between FFD versions 1.0-6 dated 2015-02-24 and 1.0-8 dated 2021-01-07
DESCRIPTION | 19 ++++++++------- MD5 | 10 ++++---- NAMESPACE | 7 ++++- R/FFD_GUI-internal.R | 60 ++++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/FFD-intro.pdf |binary 6 files changed, 53 insertions(+), 43 deletions(-)
Title: Analysis of Eye Data
Description: There is no ophthalmic researcher who has not had headaches from
the handling of visual acuity entries. Different notations, untidy entries.
This shall now be a matter of the past. Eye makes it as easy as pie to work
with VA data - easy cleaning, easy conversion between
Snellen, logMAR, ETDRS letters, and qualitative visual acuity
shall never pester you again. The eye
package automates the pesky task to count number of patients and eyes,
and can help to clean data with easy re-coding for right and left eyes.
It also contains functions to help reshaping eye side specific variables
between wide and long format. Visual acuity conversion is based on
Schulze-Bonsel et al. (2006) <doi:10.1167/iovs.05-0981>,
Gregori et al. (2010) <doi:10.1097/iae.0b013e3181d87e04>,
Beck et al. (2003) <doi:10.1016/s0002-9394(02)01825-1> and
Bach (2007) <http:michaelbach.de/sci/acuity.html>.
Author: Tjebo Heeren [aut, cre] (<https://orcid.org/0000-0001-5297-2301>),
Antoine Fabri [ctb]
Maintainer: Tjebo Heeren <tjebo@gmx.de>
Diff between eye versions 0.1.0 dated 2020-06-25 and 1.0.0 dated 2021-01-07
eye-0.1.0/eye/data/amd.rda |only eye-0.1.0/eye/man/age.Rd |only eye-0.1.0/eye/man/amd.Rd |only eye-0.1.0/eye/man/va_dissect.Rd |only eye-1.0.0/eye/DESCRIPTION | 38 - eye-1.0.0/eye/MD5 | 99 +- eye-1.0.0/eye/NAMESPACE | 18 eye-1.0.0/eye/NEWS.md | 39 + eye-1.0.0/eye/R/VAclassConversion.R |only eye-1.0.0/eye/R/blink.R | 7 eye-1.0.0/eye/R/check_plausible.R |only eye-1.0.0/eye/R/data.R | 51 - eye-1.0.0/eye/R/eye.R | 4 eye-1.0.0/eye/R/eyes.R | 137 ++-- eye-1.0.0/eye/R/getElem.R | 30 eye-1.0.0/eye/R/recodeye.R | 178 +++-- eye-1.0.0/eye/R/reveal.R | 2 eye-1.0.0/eye/R/sysdata.rda |binary eye-1.0.0/eye/R/tools.R | 61 + eye-1.0.0/eye/R/va.R | 311 ++++----- eye-1.0.0/eye/R/va_cleaner.R | 82 +- eye-1.0.0/eye/R/va_methods.R | 302 ++++---- eye-1.0.0/eye/R/which_va.R | 65 - eye-1.0.0/eye/README.md | 420 +++++------- eye-1.0.0/eye/build/partial.rdb |only eye-1.0.0/eye/build/vignette.rds |binary eye-1.0.0/eye/data/va_chart.rda |binary eye-1.0.0/eye/inst/CITATION |only eye-1.0.0/eye/inst/doc/eye.R | 81 +- eye-1.0.0/eye/inst/doc/eye.Rmd | 204 ++---- eye-1.0.0/eye/inst/doc/eye.html | 911 ++++++++++++++------------- eye-1.0.0/eye/man/VAclasses.Rd |only eye-1.0.0/eye/man/VAwrapper.Rd |only eye-1.0.0/eye/man/blink.Rd | 3 eye-1.0.0/eye/man/clean_va.Rd | 32 eye-1.0.0/eye/man/convertQuali.Rd |only eye-1.0.0/eye/man/eye.Rd | 5 eye-1.0.0/eye/man/eyes.Rd | 59 - eye-1.0.0/eye/man/getElem.Rd | 21 eye-1.0.0/eye/man/getage.Rd |only eye-1.0.0/eye/man/introduceNA.Rd |only eye-1.0.0/eye/man/parse_snellen.Rd |only eye-1.0.0/eye/man/plausibility_methods.Rd |only eye-1.0.0/eye/man/recodeye.Rd | 53 + eye-1.0.0/eye/man/snellen_steps.Rd | 38 - eye-1.0.0/eye/man/tidyNA.Rd |only eye-1.0.0/eye/man/va.Rd | 118 +-- eye-1.0.0/eye/man/va_chart.Rd | 14 eye-1.0.0/eye/man/va_methods.Rd | 83 +- eye-1.0.0/eye/man/va_mixed.Rd |only eye-1.0.0/eye/man/warnings.Rd |only eye-1.0.0/eye/man/which_va.Rd | 17 eye-1.0.0/eye/tests/testthat/test-blink.R | 5 eye-1.0.0/eye/tests/testthat/test-eyes.R | 56 - eye-1.0.0/eye/tests/testthat/test-internal.R | 1 eye-1.0.0/eye/tests/testthat/test-myop.R | 1 eye-1.0.0/eye/tests/testthat/test-recodeye.R |only eye-1.0.0/eye/tests/testthat/test-reveal.R | 3 eye-1.0.0/eye/tests/testthat/test-va.R | 140 ++-- eye-1.0.0/eye/vignettes/eye.Rmd | 204 ++---- 60 files changed, 1991 insertions(+), 1902 deletions(-)
Title: Estimate Time Varying Reproduction Numbers from Epidemic Curves
Description: Tools to quantify transmissibility throughout
an epidemic from the analysis of time series of incidence as described in
Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004)
<doi:10.1093/aje/kwh255>.
Author: Anne Cori [aut, cre] (<https://orcid.org/0000-0002-8443-9162>),
Simon Cauchemez [ctb],
Neil M. Ferguson [ctb] (<https://orcid.org/0000-0002-1154-8093>),
Christophe Fraser [ctb] (<https://orcid.org/0000-0003-2399-9657>),
Elisabeth Dahlqwist [ctb] (<https://orcid.org/0000-0001-5797-6803>),
P. Alex Demarsh [ctb],
Thibaut Jombart [ctb] (<https://orcid.org/0000-0003-2226-8692>),
Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>),
Justin Lessler [ctb] (<https://orcid.org/0000-0002-9741-8109>),
Shikun Li [ctb],
Jonathan A. Polonsky [ctb] (<https://orcid.org/0000-0002-8634-4255>),
Jake Stockwin [ctb],
Robin Thompson [ctb] (<https://orcid.org/0000-0001-8545-5212>),
Rolina van Gaalen [ctb]
Maintainer: Anne Cori <a.cori@imperial.ac.uk>
Diff between EpiEstim versions 2.2-3 dated 2020-05-29 and 2.2-4 dated 2021-01-07
DESCRIPTION | 8 MD5 | 20 README.md | 2 build/vignette.rds |binary data/Flu1918.rda |binary data/Measles1861.rda |binary data/MockRotavirus.rda |binary data/SARS2003.rda |binary data/Smallpox1972.rda |binary inst/doc/demo.html | 1329 +++++++++++++++++++++------------------------ tests/testthat/test-plot.R | 12 11 files changed, 672 insertions(+), 699 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.1.9 dated 2020-11-18 and 0.1.10 dated 2021-01-07
dm-0.1.10/dm/DESCRIPTION | 23 +- dm-0.1.10/dm/MD5 | 114 +++++------- dm-0.1.10/dm/NEWS.md | 9 + dm-0.1.10/dm/R/db-helpers.R | 41 ++++ dm-0.1.10/dm/R/dm-from-src.R | 17 + dm-0.1.10/dm/R/financial-db-con.R | 1 dm-0.1.10/dm/R/financial.R | 1 dm-0.1.10/dm/R/global.R | 2 dm-0.1.10/dm/R/key-helpers.R | 4 dm-0.1.10/dm/R/pkgdown.R | 2 dm-0.1.10/dm/R/primary-keys.R | 22 ++ dm-0.1.10/dm/README.md | 68 +++---- dm-0.1.10/dm/inst/doc/dm.html | 44 ---- dm-0.1.10/dm/inst/doc/howto-dm-copy.html | 60 +----- dm-0.1.10/dm/inst/doc/howto-dm-db.html | 46 ----- dm-0.1.10/dm/inst/doc/howto-dm-df.html | 48 ----- dm-0.1.10/dm/inst/doc/howto-dm-rows.html | 58 +----- dm-0.1.10/dm/inst/doc/howto-dm-theory.html | 56 +----- dm-0.1.10/dm/inst/doc/tech-dm-cdm.html | 44 ---- dm-0.1.10/dm/inst/doc/tech-dm-class.html | 126 ++++---------- dm-0.1.10/dm/inst/doc/tech-dm-draw.html | 44 ---- dm-0.1.10/dm/inst/doc/tech-dm-filter.html | 62 +----- dm-0.1.10/dm/inst/doc/tech-dm-join.html | 44 ---- dm-0.1.10/dm/inst/doc/tech-dm-low-level.html | 44 ---- dm-0.1.10/dm/inst/doc/tech-dm-naming.html | 40 ---- dm-0.1.10/dm/inst/doc/tech-dm-zoom.html | 46 ----- dm-0.1.10/dm/tests/testthat/_snaps/bind.md |only dm-0.1.10/dm/tests/testthat/_snaps/check-cardinalities.md |only dm-0.1.10/dm/tests/testthat/_snaps/dm.md |only dm-0.1.10/dm/tests/testthat/_snaps/draw-dm |only dm-0.1.10/dm/tests/testthat/_snaps/error-helpers.md |only dm-0.1.10/dm/tests/testthat/_snaps/format.md |only dm-0.1.10/dm/tests/testthat/_snaps/key-helpers.md |only dm-0.1.10/dm/tests/testthat/_snaps/paste.md | 5 dm-0.1.10/dm/tests/testthat/_snaps/primary-keys.md |only dm-0.1.10/dm/tests/testthat/_snaps/rows-db.md |only dm-0.1.10/dm/tests/testthat/_snaps/tidyselect.md |only dm-0.1.10/dm/tests/testthat/helper-print.R | 2 dm-0.1.10/dm/tests/testthat/helper-src.R | 8 dm-0.1.10/dm/tests/testthat/test-bind.R | 28 +-- dm-0.1.10/dm/tests/testthat/test-check-cardinalities.R | 73 ++++---- dm-0.1.10/dm/tests/testthat/test-dm-from-src.R | 56 +++++- dm-0.1.10/dm/tests/testthat/test-dm.R | 21 +- dm-0.1.10/dm/tests/testthat/test-draw-dm.R | 30 +-- dm-0.1.10/dm/tests/testthat/test-error-helpers.R | 118 ++++++------- dm-0.1.10/dm/tests/testthat/test-format.R | 24 +- dm-0.1.10/dm/tests/testthat/test-key-helpers.R | 14 - dm-0.1.10/dm/tests/testthat/test-learn.R | 37 ++++ dm-0.1.10/dm/tests/testthat/test-paste.R | 4 dm-0.1.10/dm/tests/testthat/test-primary-keys.R | 33 ++- dm-0.1.10/dm/tests/testthat/test-rows-db.R | 56 +++--- dm-0.1.10/dm/tests/testthat/test-tidyselect.R | 12 - dm-0.1.9/dm/man/financial_db_con.Rd |only dm-0.1.9/dm/tests/testthat/_snaps/draw-dm.md |only dm-0.1.9/dm/tests/testthat/out |only 55 files changed, 623 insertions(+), 964 deletions(-)
Title: Wrapper for the UN OCHA ReliefWeb Disaster Events API
Description: Access and manage the application programming interface (API) of the United Nations Office for the Coordination of Humanitarian Affairs' (OCHA) ReliefWeb disaster events at <https://reliefweb.int/disasters/>. The package requires a minimal number of dependencies. It offers functionality to retrieve a user-defined sample of disaster events from ReliefWeb, providing an easy alternative to scraping the ReliefWeb website. It enables a seamless integration of regular data updates into the research work flow.
Author: Christoph Dworschak [aut, cre]
(<https://orcid.org/0000-0003-0196-9545>)
Maintainer: Christoph Dworschak <c.dworschak@essex.ac.uk>
Diff between disastr.api versions 1.0.2 dated 2021-01-06 and 1.0.3 dated 2021-01-07
DESCRIPTION | 12 +++---- MD5 | 12 +++---- NEWS.md | 6 +++ R/disastr.api.R | 2 - R/disastr.api.internal.R | 4 +- README.md | 79 +++++++++++++++++++++++------------------------ man/disastr.api.Rd | 2 - 7 files changed, 61 insertions(+), 56 deletions(-)
Title: Set of Tools to Compute Various Climate Indices
Description: Set of tools to compute metrics and indices for climate analysis.
The package provides functions to compute extreme indices, evaluate the
agreement between models and combine theses models into an ensemble. Multi-model
time series of climate indices can be computed either after averaging the 2-D
fields from different models provided they share a common grid or by combining
time series computed on the model native grid. Indices can be assigned weights
and/or combined to construct new indices.
Author: BSC-CNS [aut, cph],
Nuria Perez-Zanon [aut, cre] (<https://orcid.org/0000-0001-8568-3071>),
Nicolau Manubens [ctb],
Alasdair Hunter [aut],
Louis-Philippe Caron [ctb]
Maintainer: Nuria Perez-Zanon <nuria.perez@bsc.es>
Diff between ClimProjDiags versions 0.1.0 dated 2020-01-21 and 0.1.1 dated 2021-01-07
DESCRIPTION | 14 +- MD5 | 10 - NAMESPACE | 1 R/Climdex.R | 282 ------------------------------------------------------- R/Extremes.R | 3 R/WaveDuration.R | 122 ----------------------- 6 files changed, 22 insertions(+), 410 deletions(-)
Title: Bayesian Mixture Models with JAGS
Description: Fits finite mixture models of univariate Gaussian distributions using JAGS within a Bayesian framework.
Author: Bettina Gruen [aut, cre] (<https://orcid.org/0000-0001-7265-4773>),
Martyn Plummer [ctb] (<https://orcid.org/0000-0001-5130-6497>)
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between bayesmix versions 0.7-4 dated 2015-07-01 and 0.7-5 dated 2021-01-07
DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 4 ++-- inst/NEWS.Rd | 5 +++++ 3 files changed, 21 insertions(+), 16 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Description: Algorithms to create prognostic biomarkers using biological genesets or networks.
Author: Syed Haider [aut, cre],
Paul C. Boutros [aut],
Michal Grzadkowski [ctb]
Maintainer: Syed Haider <Syed.Haider@icr.ac.uk>
Diff between SIMMS versions 1.3.0 dated 2020-06-05 and 1.3.1 dated 2021-01-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/create.KM.plot.R | 2 +- R/create.sensitivity.plot.R | 2 +- inst/doc/Using-SIMMS.html | 6 +++--- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: FAB Confidence Intervals
Description: Frequentist assisted by Bayes (FAB) confidence interval
construction. See 'Adaptive multigroup confidence intervals with constant
coverage' by Yu and Hoff <DOI:10.1093/biomet/asy009> and
'Exact adaptive confidence intervals for linear regression coefficients'
by Hoff and Yu <DOI:10.1214/18-EJS1517>.
Author: Peter Hoff and Chaoyu Yu
Maintainer: Peter Hoff <peter.hoff@duke.edu>
Diff between fabCI versions 0.1 dated 2017-01-06 and 0.2 dated 2021-01-07
fabCI-0.1/fabCI/man/wfabz.Rd |only fabCI-0.2/fabCI/DESCRIPTION | 14 ++++++++----- fabCI-0.2/fabCI/MD5 | 34 +++++++++++++++++++------------- fabCI-0.2/fabCI/NAMESPACE | 11 +++++----- fabCI-0.2/fabCI/NEWS.md |only fabCI-0.2/fabCI/R/data.R | 4 +-- fabCI-0.2/fabCI/R/fabregCI.R |only fabCI-0.2/fabCI/R/fabtCI.R | 10 ++++++--- fabCI-0.2/fabCI/R/fabzCI.R | 40 ++++---------------------------------- fabCI-0.2/fabCI/R/multifabCI.R | 2 - fabCI-0.2/fabCI/R/multifabCIhom.R | 13 ++++++------ fabCI-0.2/fabCI/man/ebayes_est.Rd |only fabCI-0.2/fabCI/man/fabregCI.Rd |only fabCI-0.2/fabCI/man/fabtCI.Rd | 2 - fabCI-0.2/fabCI/man/fabtwzCI.Rd | 2 - fabCI-0.2/fabCI/man/fabtzCI.Rd |only fabCI-0.2/fabCI/man/fabzCI.Rd | 2 - fabCI-0.2/fabCI/man/hhetmodel.Rd | 2 - fabCI-0.2/fabCI/man/hhommodel.Rd | 2 - fabCI-0.2/fabCI/man/radon.Rd | 1 fabCI-0.2/fabCI/man/sfabz.Rd |only fabCI-0.2/fabCI/man/umauregCI.Rd |only 22 files changed, 62 insertions(+), 77 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <Sylvain.Jasson@inrae.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.6-1 dated 2020-10-01 and 0.6-2 dated 2021-01-07
ChangeLog | 10 - DESCRIPTION | 8 MD5 | 8 configure | 523 +++++++++++++++++++++++++++++++++++++++++++++++++++++++---- configure.ac | 20 +- 5 files changed, 522 insertions(+), 47 deletions(-)
Title: Plot Publication-Grade Gene and Genome Maps
Description: Draws gene or genome maps and comparisons between these, in a
publication-grade manner. Starting from simple, common files, it will
draw postscript or PDF files that can be sent as such to journals.
Author: Lionel Guy <lionel.guy@imbim.uu.se>
Maintainer: Lionel Guy <lionel.guy@imbim.uu.se>
Diff between genoPlotR versions 0.8.10 dated 2020-12-10 and 0.8.11 dated 2021-01-07
DESCRIPTION | 13 +++++-------- MD5 | 24 ++++++++++++------------ NEWS | 6 ++++++ R/genoPlotR.R | 2 +- R/read_comparison.R | 2 +- R/read_mauve_backbone.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary data/barto.RData |binary data/chrY_subseg.RData |binary data/mauve_bbone.RData |binary data/three_genes.RData |binary inst/doc/genoPlotR.pdf |binary 13 files changed, 26 insertions(+), 23 deletions(-)
Title: Sequential Forward Floating Selection using Jeffries-Matusita
Distance
Description: Feature selection using Sequential Forward Floating feature Selection and Jeffries-Matusita distance. It returns a suboptimal set of features to use for image classification. Reference: Dalponte, M., Oerka, H.O., Gobakken, T., Gianelle, D. & Naesset, E. (2013). Tree Species Classification in Boreal Forests With Hyperspectral Data. IEEE Transactions on Geoscience and Remote Sensing, 51, 2632-2645, <DOI:10.1109/TGRS.2012.2216272>.
Author: Michele Dalponte and Hans Ole Oerka
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>
Diff between varSel versions 0.1 dated 2016-11-04 and 0.2 dated 2021-01-07
varSel-0.1/varSel/data/datalist |only varSel-0.2/varSel/DESCRIPTION | 10 +- varSel-0.2/varSel/MD5 | 13 +- varSel-0.2/varSel/R/varSelSFFS.R | 167 ++++++++++++++++++++---------------- varSel-0.2/varSel/man/BHATdist.Rd | 7 - varSel-0.2/varSel/man/JMdist.Rd | 7 - varSel-0.2/varSel/man/dat.Rd | 5 - varSel-0.2/varSel/man/varSelSFFS.Rd | 13 +- 8 files changed, 121 insertions(+), 101 deletions(-)
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Iago Giné-Vázquez [ctb],
Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.8.5 dated 2020-05-28 and 2.8.6 dated 2021-01-07
sjmisc-2.8.5/sjmisc/R/to_factor.R |only sjmisc-2.8.5/sjmisc/R/to_label.R |only sjmisc-2.8.5/sjmisc/man/to_character.Rd |only sjmisc-2.8.5/sjmisc/man/to_factor.Rd |only sjmisc-2.8.5/sjmisc/man/to_label.Rd |only sjmisc-2.8.6/sjmisc/DESCRIPTION | 17 +- sjmisc-2.8.6/sjmisc/MD5 | 128 +++++++++----------- sjmisc-2.8.6/sjmisc/NAMESPACE | 7 - sjmisc-2.8.6/sjmisc/NEWS.md | 15 ++ sjmisc-2.8.6/sjmisc/R/S3-methods.R | 4 sjmisc-2.8.6/sjmisc/R/count_na.R | 2 sjmisc-2.8.6/sjmisc/R/de_mean.R | 2 sjmisc-2.8.6/sjmisc/R/descr.R | 2 sjmisc-2.8.6/sjmisc/R/dicho.R | 2 sjmisc-2.8.6/sjmisc/R/frq.R | 4 sjmisc-2.8.6/sjmisc/R/group_var.R | 2 sjmisc-2.8.6/sjmisc/R/is_crossed.R | 2 sjmisc-2.8.6/sjmisc/R/move_column.R | 18 ++ sjmisc-2.8.6/sjmisc/R/re-exports.R |only sjmisc-2.8.6/sjmisc/R/rec.R | 6 sjmisc-2.8.6/sjmisc/R/recode_to.R | 2 sjmisc-2.8.6/sjmisc/R/ref_lvl.R | 4 sjmisc-2.8.6/sjmisc/R/remove_vars.R | 4 sjmisc-2.8.6/sjmisc/R/replace_na.R | 2 sjmisc-2.8.6/sjmisc/R/round_num.R | 2 sjmisc-2.8.6/sjmisc/R/row_count.R | 2 sjmisc-2.8.6/sjmisc/R/row_sums.R | 2 sjmisc-2.8.6/sjmisc/R/set_na.R | 2 sjmisc-2.8.6/sjmisc/R/split_var.R | 4 sjmisc-2.8.6/sjmisc/R/std.R | 2 sjmisc-2.8.6/sjmisc/R/tidy_values.R | 2 sjmisc-2.8.6/sjmisc/R/to_dummy.R | 9 + sjmisc-2.8.6/sjmisc/R/to_value.R | 6 sjmisc-2.8.6/sjmisc/R/var_type.R | 4 sjmisc-2.8.6/sjmisc/R/zap_inf.R | 2 sjmisc-2.8.6/sjmisc/README.md | 4 sjmisc-2.8.6/sjmisc/build/partial.rdb |binary sjmisc-2.8.6/sjmisc/build/vignette.rds |binary sjmisc-2.8.6/sjmisc/inst/doc/design_philosophy.html | 14 +- sjmisc-2.8.6/sjmisc/inst/doc/exploringdatasets.Rmd | 2 sjmisc-2.8.6/sjmisc/inst/doc/exploringdatasets.html | 16 ++ sjmisc-2.8.6/sjmisc/inst/doc/recodingvariables.Rmd | 2 sjmisc-2.8.6/sjmisc/inst/doc/recodingvariables.html | 16 ++ sjmisc-2.8.6/sjmisc/man/count_na.Rd | 2 sjmisc-2.8.6/sjmisc/man/descr.Rd | 2 sjmisc-2.8.6/sjmisc/man/dicho.Rd | 23 --- sjmisc-2.8.6/sjmisc/man/frq.Rd | 4 sjmisc-2.8.6/sjmisc/man/group_var.Rd | 23 --- sjmisc-2.8.6/sjmisc/man/has_na.Rd | 2 sjmisc-2.8.6/sjmisc/man/is_crossed.Rd | 2 sjmisc-2.8.6/sjmisc/man/move_columns.Rd | 18 ++ sjmisc-2.8.6/sjmisc/man/rec.Rd | 2 sjmisc-2.8.6/sjmisc/man/recode_to.Rd | 23 --- sjmisc-2.8.6/sjmisc/man/reexports.Rd | 10 + sjmisc-2.8.6/sjmisc/man/ref_lvl.Rd | 4 sjmisc-2.8.6/sjmisc/man/remove_var.Rd | 2 sjmisc-2.8.6/sjmisc/man/replace_na.Rd | 2 sjmisc-2.8.6/sjmisc/man/row_count.Rd | 2 sjmisc-2.8.6/sjmisc/man/row_sums.Rd | 2 sjmisc-2.8.6/sjmisc/man/split_var.Rd | 25 --- sjmisc-2.8.6/sjmisc/man/std.Rd | 23 --- sjmisc-2.8.6/sjmisc/man/tidy_values.Rd | 2 sjmisc-2.8.6/sjmisc/man/to_dummy.Rd | 2 sjmisc-2.8.6/sjmisc/man/to_value.Rd | 5 sjmisc-2.8.6/sjmisc/man/var_type.Rd | 4 sjmisc-2.8.6/sjmisc/man/zap_inf.Rd | 2 sjmisc-2.8.6/sjmisc/vignettes/exploringdatasets.Rmd | 2 sjmisc-2.8.6/sjmisc/vignettes/recodingvariables.Rmd | 2 68 files changed, 256 insertions(+), 248 deletions(-)
Title: Bayesian Reliability Estimation
Description: Functionality for the most common single test reliability estimates:
Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower bound and coefficient omega.
The Bayesian estimates are provided with credible intervals.
The frequentist estimates are provided with bootstrapped confidence intervals
The method for the Bayesian estimates, except for omega, is sampling from the posterior inverse 'Wishart'
for the covariance matrix based measures
(see 'Murphy', 2007, <https://www.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>.
In the case of omega it is 'Gibbs' Sampling from the joint conditional distributions of a single factor model
('Lee', 2007, <doi:10.1002/9780470024737>).
The glb method uses adjusted code from the 'Rcsdp' package by 'Hector Corrada Bravo',
<https://CRAN.R-project.org/package=Rcsdp>. This process applies a slightly adjusted solving algorithm
from the 'CSDP' library by 'Brian Borchers' <https://github.com/coin-or/Csdp/wiki>,
<doi:10.1080/10556789908805765>, but is wrapped in 'RcppArmadillo'.
Guttman's Lambda-4 is from 'Benton' (2015) <doi:10.1007/978-3-319-07503-7_19>.
The principal factor analysis for a version of frequentist omega is from 'Schlegel' (2017)
<https://www.r-bloggers.com/2017/03/iterated-principal-factor-method-of-factor-analysis-with-r/>.
The analytic confidence interval of alpha is from 'Bonett' and 'Wright' (2015) <doi:10.1002/job.1960>.
Author: Julius M. Pfadt [aut, cre],
Don van den Bergh [aut],
Joris Goosen [aut]
Maintainer: Julius M. Pfadt <julius.pfadt@gmail.com>
Diff between Bayesrel versions 0.7.0.2 dated 2020-11-18 and 0.7.0.3 dated 2021-01-07
Bayesrel-0.7.0.2/Bayesrel/R/omega_gibbs_sampler.R |only Bayesrel-0.7.0.3/Bayesrel/DESCRIPTION | 8 ++--- Bayesrel-0.7.0.3/Bayesrel/MD5 | 12 +++---- Bayesrel-0.7.0.3/Bayesrel/R/boot_apply_functions.R | 33 ++++++++++++--------- Bayesrel-0.7.0.3/Bayesrel/R/omegaUni_Gibbs.R |only Bayesrel-0.7.0.3/Bayesrel/R/omega_fit.R | 22 ++++++++------ Bayesrel-0.7.0.3/Bayesrel/R/princ_fac.R | 2 - Bayesrel-0.7.0.3/Bayesrel/build/partial.rdb |binary 8 files changed, 44 insertions(+), 33 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Werner Stahel [ctb] (Functions: compresid2way(), f.robftest(), last(),
p.scales(), p.dnorm()),
Andreas Ruckstuhl [ctb] (Functions: p.arrows(), p.profileTraces(),
p.res.2x()),
Christian Keller [ctb] (Functions: histBxp(), p.tachoPlot()),
Kjetil Halvorsen [ctb] (Functions: KSd(), ecdf.ksCI()),
Alain Hauser [ctb] (Functions: cairoSwd(), is.whole(),
toLatex.numeric()*),
Christoph Buser [ctb] (to function Duplicated()),
Lorenz Gygax [ctb] (to function p.res.2fact()),
Bill Venables [ctb] (Functions: empty.dimnames(), primes()),
Tony Plate [ctb] (to inv.seq()),
Isabelle Fl<fc>ckiger [ctb],
Marcel Wolbers [ctb],
Markus Keller [ctb],
Sandrine Dudoit [ctb],
Jane Fridlyand [ctb],
Greg Snow [ctb] (to loessDemo()),
Henrik Aa. Nielsen [ctb] (to loessDemo()),
Vincent Carey [ctb],
Ben Bolker [ctb],
Philippe Grosjean [ctb],
Fr<e9>d<e9>ric Ibanez [ctb],
Caterina Savi [ctb],
Charles Geyer [ctb],
Jens Oehlschl<e4>gel [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-7 dated 2020-05-07 and 1.1-8 dated 2021-01-07
DESCRIPTION | 16 +++++++++------- MD5 | 26 ++++++++++++++------------ NAMESPACE | 5 +++++ R/hatMat.R | 2 +- R/misc-goodies.R | 2 +- R/pkgDesc.R |only R/sessionInfo-ext.R | 22 +++++++++++++--------- R/unix/package-props.R | 1 - inst/NEWS.Rd | 21 +++++++++++++++++++++ man/AsciiToInt.Rd | 18 +++++++++--------- man/pkgDesc.Rd |only man/read.org.table.Rd | 4 ++-- man/sessionInfoX.Rd | 20 ++++++++++++++++++-- tests/posdef.R | 2 +- tests/posdef.Rout.save | 2 +- 15 files changed, 95 insertions(+), 46 deletions(-)
Title: Install the 'Natverse' Packages from Scratch
Description: Provides streamlined installation for packages from the 'natverse',
a suite of R packages for computational neuroanatomy built on top of the
'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete
'natverse' suite requires a 'GitHub' user account and personal access token
'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.
Author: Sridhar Jagannathan [aut, cre]
(<https://orcid.org/0000-0002-2078-1145>),
Gregory Jefferis [aut] (<https://orcid.org/0000-0002-0587-9355>)
Maintainer: Sridhar Jagannathan <j.sridharrajan@gmail.com>
Diff between natmanager versions 0.4.6 dated 2020-07-06 and 0.4.7 dated 2021-01-07
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/utils.R | 16 ++++++++++++++++ R/zzz.R | 6 +++--- README.md | 11 ++++++----- inst/WORDLIST | 7 ++++--- tests/testthat/test-install.R | 14 ++++++++++++++ 8 files changed, 61 insertions(+), 24 deletions(-)
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bingsong@my.unthsc.edu>
Diff between mixIndependR versions 0.4.3 dated 2020-11-30 and 0.4.4 dated 2021-01-07
DESCRIPTION | 7 MD5 | 113 +-- NAMESPACE | 60 - NEWS.md | 147 ++-- R/AlleleFreq.R | 50 - R/AlleleShare.R | 114 +-- R/Dist_SimuChisq.R | 54 - R/FreqAlleleShare.R | 36 - R/FreqHetero.R | 36 - R/GenotypeFreq.R | 76 +- R/HWE_Chisq.R | 58 - R/Heterozygous.R | 50 - R/RealProAlleleShare.R | 30 R/Simulate_DistK.R | 46 - R/Simulate_DistX.R | 50 - R/mixIndependK.R | 62 - R/mixIndependX.R | 62 - R/mixexample-data.R | 34 - R/read_vcf_gt.R | 48 - R/splitGenotype.R | 78 +- README.md | 58 - build/vignette.rds |binary inst/CITATION |only inst/doc/BasicGenetics.R | 76 +- inst/doc/BasicGenetics.Rmd | 156 ++-- inst/doc/BasicGenetics.html | 816 +++++++++++++------------- inst/doc/DistributionBuildingNComparison.R | 90 +- inst/doc/DistributionBuildingNComparison.Rmd | 126 ++-- inst/doc/DistributionBuildingNComparison.html | 780 ++++++++++++------------ inst/doc/HypothesisTest.R | 98 +-- inst/doc/HypothesisTest.Rmd | 130 ++-- inst/doc/HypothesisTest.html | 776 ++++++++++++------------ man/AlleleFreq.Rd | 58 - man/AlleleShare.Rd | 60 - man/ComposPare_K.Rd | 58 - man/ComposPare_X.Rd | 58 - man/DistAlleleShare.Rd | 56 - man/DistHetero.Rd | 54 - man/Dist_SimuChisq.Rd | 62 - man/ExpProAlleleShare.Rd | 60 - man/FreqAlleleShare.Rd | 48 - man/FreqHetero.Rd | 48 - man/GenotypeFreq.Rd | 66 +- man/HWE.Chisq.Rd | 76 +- man/Heterozygous.Rd | 56 - man/RealProAlleleShare.Rd | 48 - man/RxpHetero.Rd | 78 +- man/Simulate_DistK.Rd | 56 - man/Simulate_DistX.Rd | 60 - man/counta.Rd | 54 - man/mixIndependK.Rd | 62 - man/mixIndependX.Rd | 62 - man/mixexample.Rd | 54 - man/read_vcf_gt.Rd | 50 - man/splitGenotype.Rd | 66 +- vignettes/BasicGenetics.Rmd | 156 ++-- vignettes/DistributionBuildingNComparison.Rmd | 126 ++-- vignettes/HypothesisTest.Rmd | 130 ++-- 58 files changed, 3069 insertions(+), 3010 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-16 dated 2020-06-16 and 1.1-0 dated 2021-01-07
randomLCA-1.0-16/randomLCA/R/bestlca.R |only randomLCA-1.1-0/randomLCA/DESCRIPTION | 11 randomLCA-1.1-0/randomLCA/MD5 | 72 +- randomLCA-1.1-0/randomLCA/NAMESPACE | 10 randomLCA-1.1-0/randomLCA/R/bestfixedlca.R |only randomLCA-1.1-0/randomLCA/R/besttrandomlca.R |only randomLCA-1.1-0/randomLCA/R/fitAdaptRandom.R | 556 ++++++++++----------- randomLCA-1.1-0/randomLCA/R/fitAdaptRandom2.R | 40 - randomLCA-1.1-0/randomLCA/R/outcomeProbs.R | 7 randomLCA-1.1-0/randomLCA/R/randomLCA.R | 90 --- randomLCA-1.1-0/randomLCA/R/refit.randomLCA.R | 77 +- randomLCA-1.1-0/randomLCA/build/partial.rdb |only randomLCA-1.1-0/randomLCA/inst/NEWS | 6 randomLCA-1.1-0/randomLCA/man/AIC.Rd | 2 randomLCA-1.1-0/randomLCA/man/AIC3.Rd | 2 randomLCA-1.1-0/randomLCA/man/BIC.Rd | 2 randomLCA-1.1-0/randomLCA/man/calcCond2Prob.Rd | 2 randomLCA-1.1-0/randomLCA/man/calcCondProb.Rd | 2 randomLCA-1.1-0/randomLCA/man/calcMargProb.Rd | 2 randomLCA-1.1-0/randomLCA/man/classProbs.Rd | 2 randomLCA-1.1-0/randomLCA/man/dentistry.Rd | 6 randomLCA-1.1-0/randomLCA/man/fitted.Rd | 2 randomLCA-1.1-0/randomLCA/man/genderrole.Rd | 18 randomLCA-1.1-0/randomLCA/man/hivtests.Rd | 6 randomLCA-1.1-0/randomLCA/man/logLik.Rd | 2 randomLCA-1.1-0/randomLCA/man/maxPostClass.Rd | 4 randomLCA-1.1-0/randomLCA/man/myocardial.Rd | 2 randomLCA-1.1-0/randomLCA/man/outcomeProbs.Rd | 2 randomLCA-1.1-0/randomLCA/man/pap.Rd | 22 randomLCA-1.1-0/randomLCA/man/plot.Rd | 4 randomLCA-1.1-0/randomLCA/man/postClassProbs.Rd | 2 randomLCA-1.1-0/randomLCA/man/print.randomLCA.Rd | 2 randomLCA-1.1-0/randomLCA/man/randomLCA.Rd | 15 randomLCA-1.1-0/randomLCA/man/ranef.Rd | 2 randomLCA-1.1-0/randomLCA/man/refit.Rd | 4 randomLCA-1.1-0/randomLCA/man/simulate.Rd | 4 randomLCA-1.1-0/randomLCA/man/summary.randomLCA.Rd | 2 randomLCA-1.1-0/randomLCA/man/symptoms.Rd | 8 randomLCA-1.1-0/randomLCA/man/uterinecarcinoma.Rd | 4 39 files changed, 471 insertions(+), 523 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function knn() from package 'nabor' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Dominic Russel [ctb],
Luigi Ranghetti [ctb],
Charles F.F Karney [ctb, cph] (Author of included C code from
'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.4.0 dated 2020-10-18 and 0.4.1 dated 2021-01-07
nngeo-0.4.0/nngeo/R/st_split_junctions.R |only nngeo-0.4.0/nngeo/man/st_split_junctions.Rd |only nngeo-0.4.1/nngeo/DESCRIPTION | 8 +++++--- nngeo-0.4.1/nngeo/MD5 | 20 +++++++++----------- nngeo-0.4.1/nngeo/NAMESPACE | 1 - nngeo-0.4.1/nngeo/NEWS.md | 9 ++++++++- nngeo-0.4.1/nngeo/R/st_ellipse.R | 8 ++++---- nngeo-0.4.1/nngeo/R/st_remove_holes.R | 28 +++++++++++++++++++++++++--- nngeo-0.4.1/nngeo/inst/doc/intro.pdf |binary nngeo-0.4.1/nngeo/man/nngeo-package.Rd | 1 + nngeo-0.4.1/nngeo/man/st_ellipse.Rd | 8 ++++---- nngeo-0.4.1/nngeo/man/st_remove_holes.Rd | 13 ++++++++++++- 12 files changed, 68 insertions(+), 28 deletions(-)
Title: Managing, Querying and Analyzing Tokenized Text
Description: Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations).
Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences),
similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages,
and the possibility to reconstruct original text from tokens to facilitate interpretation.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between corpustools versions 0.4.2 dated 2020-01-23 and 0.4.4 dated 2021-01-07
corpustools-0.4.2/corpustools/R/collocations.r |only corpustools-0.4.2/corpustools/R/lookup_method.r |only corpustools-0.4.2/corpustools/man/add_collocation_label.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-compare_corpus.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-compare_documents.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-compare_subset.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-dtm.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-feature_associations.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-feature_stats.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-kwic.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-search_contexts.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-search_features.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-semnet.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-semnet_window.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-set_special.Rd |only corpustools-0.4.2/corpustools/man/tCorpus-cash-top_features.Rd |only corpustools-0.4.4/corpustools/DESCRIPTION | 19 corpustools-0.4.4/corpustools/MD5 | 256 - corpustools-0.4.4/corpustools/NAMESPACE | 17 corpustools-0.4.4/corpustools/R/1_tcorpus.r | 134 corpustools-0.4.4/corpustools/R/RcppExports.R | 16 corpustools-0.4.4/corpustools/R/compare_corpora.r | 7 corpustools-0.4.4/corpustools/R/compare_documents.r | 7 corpustools-0.4.4/corpustools/R/create_tcorpus.r | 170 - corpustools-0.4.4/corpustools/R/data.r | 15 corpustools-0.4.4/corpustools/R/deprecated.r | 685 ---- corpustools-0.4.4/corpustools/R/dictionaries.r |only corpustools-0.4.4/corpustools/R/document_term_matrix.r | 16 corpustools-0.4.4/corpustools/R/documentation_methods.r | 117 corpustools-0.4.4/corpustools/R/ego_network.r | 2 corpustools-0.4.4/corpustools/R/feature_associations.r | 17 corpustools-0.4.4/corpustools/R/get_quoted_text.r |only corpustools-0.4.4/corpustools/R/import_tcorpus.r |only corpustools-0.4.4/corpustools/R/kwic.r | 7 corpustools-0.4.4/corpustools/R/lda.r | 17 corpustools-0.4.4/corpustools/R/merge_tcorpus.r | 4 corpustools-0.4.4/corpustools/R/multitokens.r |only corpustools-0.4.4/corpustools/R/overlap_highlight.r |only corpustools-0.4.4/corpustools/R/plot_words.r | 22 corpustools-0.4.4/corpustools/R/positions.r | 41 corpustools-0.4.4/corpustools/R/preprocessing.r | 2 corpustools-0.4.4/corpustools/R/print_text.r | 76 corpustools-0.4.4/corpustools/R/query.r |only corpustools-0.4.4/corpustools/R/rsyntax.r |only corpustools-0.4.4/corpustools/R/rsyntax_convenience.r |only corpustools-0.4.4/corpustools/R/search.r | 222 - corpustools-0.4.4/corpustools/R/search_contexts.r | 47 corpustools-0.4.4/corpustools/R/search_dictionary.r | 164 - corpustools-0.4.4/corpustools/R/search_features.r | 71 corpustools-0.4.4/corpustools/R/search_results.r | 4 corpustools-0.4.4/corpustools/R/semnet.r | 8 corpustools-0.4.4/corpustools/R/semnet_plotting.r | 4 corpustools-0.4.4/corpustools/R/smoothing.r | 4 corpustools-0.4.4/corpustools/R/subset_tcorpus.r | 9 corpustools-0.4.4/corpustools/R/tokenize.r | 20 corpustools-0.4.4/corpustools/R/udpipe.r | 121 corpustools-0.4.4/corpustools/R/udpipe_coref.r |only corpustools-0.4.4/corpustools/R/udpipe_tcorpus.r |only corpustools-0.4.4/corpustools/R/udpipe_tqueries.r |only corpustools-0.4.4/corpustools/R/udpipe_transformations.r |only corpustools-0.4.4/corpustools/R/util.r | 19 corpustools-0.4.4/corpustools/build/vignette.rds |binary corpustools-0.4.4/corpustools/data/sotu_texts.rda |binary corpustools-0.4.4/corpustools/data/tc_sotu_udpipe.rda |only corpustools-0.4.4/corpustools/inst/doc/corpustools.R | 147 - corpustools-0.4.4/corpustools/inst/doc/corpustools.Rmd | 26 corpustools-0.4.4/corpustools/inst/doc/corpustools.html | 1394 ++++++---- corpustools-0.4.4/corpustools/man/add_multitoken_label.Rd |only corpustools-0.4.4/corpustools/man/agg_label.Rd |only corpustools-0.4.4/corpustools/man/aggregate_rsyntax.Rd |only corpustools-0.4.4/corpustools/man/as.tcorpus.default.Rd | 2 corpustools-0.4.4/corpustools/man/backbone_filter.Rd | 12 corpustools-0.4.4/corpustools/man/browse_hits.Rd | 16 corpustools-0.4.4/corpustools/man/browse_texts.Rd | 55 corpustools-0.4.4/corpustools/man/compare_corpus.Rd | 16 corpustools-0.4.4/corpustools/man/compare_documents.Rd | 20 corpustools-0.4.4/corpustools/man/compare_subset.Rd | 21 corpustools-0.4.4/corpustools/man/corenlp_tokens.Rd | 4 corpustools-0.4.4/corpustools/man/count_tcorpus.Rd | 10 corpustools-0.4.4/corpustools/man/create_tcorpus.Rd | 62 corpustools-0.4.4/corpustools/man/docfreq_filter.Rd | 10 corpustools-0.4.4/corpustools/man/dtm_compare.Rd | 14 corpustools-0.4.4/corpustools/man/dtm_wordcloud.Rd | 14 corpustools-0.4.4/corpustools/man/ego_semnet.Rd | 16 corpustools-0.4.4/corpustools/man/emoticon_dict.Rd | 4 corpustools-0.4.4/corpustools/man/feature_associations.Rd | 20 corpustools-0.4.4/corpustools/man/fold_rsyntax.Rd |only corpustools-0.4.4/corpustools/man/get_dtm.Rd | 36 corpustools-0.4.4/corpustools/man/get_global_i.Rd | 7 corpustools-0.4.4/corpustools/man/get_kwic.Rd | 21 corpustools-0.4.4/corpustools/man/merge_tcorpora.Rd | 12 corpustools-0.4.4/corpustools/man/plot.contextHits.Rd | 2 corpustools-0.4.4/corpustools/man/plot.featureAssociations.Rd | 7 corpustools-0.4.4/corpustools/man/plot.featureHits.Rd | 2 corpustools-0.4.4/corpustools/man/plot.vocabularyComparison.Rd | 15 corpustools-0.4.4/corpustools/man/plot_semnet.Rd | 27 corpustools-0.4.4/corpustools/man/plot_words.Rd | 21 corpustools-0.4.4/corpustools/man/preprocess_tokens.Rd | 26 corpustools-0.4.4/corpustools/man/search_contexts.Rd | 15 corpustools-0.4.4/corpustools/man/search_dictionary.Rd | 23 corpustools-0.4.4/corpustools/man/search_features.Rd | 41 corpustools-0.4.4/corpustools/man/semnet.Rd | 13 corpustools-0.4.4/corpustools/man/semnet_window.Rd | 16 corpustools-0.4.4/corpustools/man/set_network_attributes.Rd | 13 corpustools-0.4.4/corpustools/man/sgt.Rd | 2 corpustools-0.4.4/corpustools/man/sotu_texts.Rd | 4 corpustools-0.4.4/corpustools/man/stopwords_list.Rd | 4 corpustools-0.4.4/corpustools/man/subset.tCorpus.Rd | 6 corpustools-0.4.4/corpustools/man/subset_query.Rd | 15 corpustools-0.4.4/corpustools/man/tCorpus-cash-annotate_rsyntax.Rd |only corpustools-0.4.4/corpustools/man/tCorpus-cash-code_dictionary.Rd | 12 corpustools-0.4.4/corpustools/man/tCorpus-cash-code_features.Rd | 7 corpustools-0.4.4/corpustools/man/tCorpus-cash-feats_to_columns.Rd | 4 corpustools-0.4.4/corpustools/man/tCorpus-cash-fold_rsyntax.Rd |only corpustools-0.4.4/corpustools/man/tCorpus-cash-get.Rd | 3 corpustools-0.4.4/corpustools/man/tCorpus-cash-lda_fit.Rd | 17 corpustools-0.4.4/corpustools/man/tCorpus-cash-merge.Rd |only corpustools-0.4.4/corpustools/man/tCorpus-cash-replace_dictionary.Rd | 2 corpustools-0.4.4/corpustools/man/tCorpus-cash-search_recode.Rd | 8 corpustools-0.4.4/corpustools/man/tCorpus-cash-set.Rd | 2 corpustools-0.4.4/corpustools/man/tCorpus-cash-set_name.Rd | 2 corpustools-0.4.4/corpustools/man/tCorpus-cash-subset.Rd | 44 corpustools-0.4.4/corpustools/man/tCorpus-cash-subset_query.Rd | 6 corpustools-0.4.4/corpustools/man/tCorpus-cash-udpipe_clauses.Rd |only corpustools-0.4.4/corpustools/man/tCorpus-cash-udpipe_coref.Rd |only corpustools-0.4.4/corpustools/man/tCorpus-cash-udpipe_quotes.Rd |only corpustools-0.4.4/corpustools/man/tCorpus_data.Rd | 2 corpustools-0.4.4/corpustools/man/tc_plot_tree.Rd |only corpustools-0.4.4/corpustools/man/tc_sotu_udpipe.Rd |only corpustools-0.4.4/corpustools/man/tokenWindowOccurence.Rd | 13 corpustools-0.4.4/corpustools/man/tokens_to_tcorpus.Rd | 41 corpustools-0.4.4/corpustools/man/top_features.Rd | 13 corpustools-0.4.4/corpustools/man/transform_rsyntax.Rd |only corpustools-0.4.4/corpustools/man/udpipe_clause_tqueries.Rd |only corpustools-0.4.4/corpustools/man/udpipe_quote_tqueries.Rd |only corpustools-0.4.4/corpustools/man/udpipe_simplify.Rd |only corpustools-0.4.4/corpustools/man/udpipe_spanquote_tqueries.Rd |only corpustools-0.4.4/corpustools/man/udpipe_tcorpus.Rd |only corpustools-0.4.4/corpustools/src/QueryIter.cpp | 11 corpustools-0.4.4/corpustools/src/RcppExports.cpp | 58 corpustools-0.4.4/corpustools/src/collapse_terms.cpp | 2 corpustools-0.4.4/corpustools/src/coref.cpp |only corpustools-0.4.4/corpustools/src/dictionary_lookup.cpp | 72 corpustools-0.4.4/corpustools/src/hit_ids_and.cpp | 4 corpustools-0.4.4/corpustools/src/ngrams.cpp | 1 corpustools-0.4.4/corpustools/src/parse_query.cpp | 117 corpustools-0.4.4/corpustools/tests/testthat/test_advanced_search.r | 32 corpustools-0.4.4/corpustools/tests/testthat/test_compare_documents.r | 4 corpustools-0.4.4/corpustools/tests/testthat/test_dictionary_lookup.r | 25 corpustools-0.4.4/corpustools/tests/testthat/test_search_contexts.r | 15 corpustools-0.4.4/corpustools/tests/testthat/test_search_features.r | 20 corpustools-0.4.4/corpustools/tests/testthat/test_tcorpus.r | 34 corpustools-0.4.4/corpustools/vignettes/corpustools.Rmd | 26 153 files changed, 2675 insertions(+), 2453 deletions(-)
Title: Execution of Multiple Clustering Algorithm
Description: The design of this package allows us to run different clustering packages and compare the results between them, to determine which algorithm behaves best from the data provided.
Author: Luis Alfonso Perez Martos [aut, cre]
Maintainer: Luis Alfonso Perez Martos <lapm0001@gmail.com>
Diff between Clustering versions 1.7.1 dated 2020-12-04 and 1.7.2 dated 2021-01-07
Clustering-1.7.1/Clustering/vignettes/img/variable_false.png |only Clustering-1.7.1/Clustering/vignettes/img/variable_true.png |only Clustering-1.7.2/Clustering/DESCRIPTION | 8 Clustering-1.7.2/Clustering/MD5 | 16 Clustering-1.7.2/Clustering/inst/doc/Clustering.R | 2 Clustering-1.7.2/Clustering/inst/doc/Clustering.Rmd | 155 +- Clustering-1.7.2/Clustering/inst/doc/Clustering.pdf |binary Clustering-1.7.2/Clustering/vignettes/Clustering.Rmd | 155 +- Clustering-1.7.2/Clustering/vignettes/bibliography.bib | 738 ++++++----- Clustering-1.7.2/Clustering/vignettes/img/tab_graph.png |binary 10 files changed, 614 insertions(+), 460 deletions(-)
Title: Comparing Single Cases to Small Samples
Description: When comparing single cases to control populations and no parameters are known researchers and clinicians must estimate these with a control sample. This is often done when testing a case's abnormality on some variable or testing abnormality of the discrepancy between two variables. Appropriate frequentist and Bayesian methods for doing this are here implemented, including tests allowing for the inclusion of covariates. These have been developed first and foremost by John Crawford and Paul Garthwaite, e.g. in Crawford and Howell (1998) <doi:10.1076/clin.12.4.482.7241>, Crawford and Garthwaite (2005) <doi:10.1037/0894-4105.19.3.318>, Crawford and Garthwaite (2007) <doi:10.1080/02643290701290146> and Crawford, Garthwaite and Ryan (2011) <doi:10.1016/j.cortex.2011.02.017>. The package is also equipped with power calculators for each method.
Author: Jonathan Rittmo [aut, cre] (<https://orcid.org/0000-0001-5075-0166>),
Robert McIntosh [aut] (<https://orcid.org/0000-0002-7615-6699>)
Maintainer: Jonathan Rittmo <j.rittmo@gmail.com>
Diff between singcar versions 0.1.1 dated 2020-10-29 and 0.1.2 dated 2021-01-07
DESCRIPTION | 6 MD5 | 51 +- NEWS.md | 8 R/BSDT.R | 42 - R/BSDT_cov.R | 40 - R/BTD.R | 25 - R/BTD_cov.R | 33 - R/RSDT.R | 44 - R/TD.R | 27 - R/UDT.R | 44 - R/deficit_power.R | 9 R/dissoc_power.R | 12 build/partial.rdb |only build/vignette.rds |binary inst/doc/singcar_vignette.R | 2 inst/doc/singcar_vignette.Rmd | 2 inst/doc/singcar_vignette.html | 763 +++++++++++----------------------- man/BSDT.Rd | 6 man/BSDT_cov.Rd | 2 man/BTD.Rd | 4 man/BTD_cov.Rd | 6 man/RSDT.Rd | 4 man/TD.Rd | 8 man/UDT.Rd | 4 tests/testthat/test-BTD_cov.R | 4 tests/testthat/test-power_functions.R | 148 ++++++ vignettes/singcar_vignette.Rmd | 2 27 files changed, 600 insertions(+), 696 deletions(-)
Title: 'Rcpp' Interface to 'PostgreSQL'
Description: Fully 'DBI'-compliant 'Rcpp'-backed interface to
'PostgreSQL' <https://www.postgresql.org/>, an open-source relational
database.
Author: Hadley Wickham [aut],
Jeroen Ooms [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph],
R Consortium [fnd],
Tomoaki Nishiyama [ctb] (Code for encoding vectors into strings derived
from RPostgreSQL)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RPostgres versions 1.2.1 dated 2020-09-28 and 1.3.0 dated 2021-01-07
RPostgres-1.2.1/RPostgres/src/configure.bash |only RPostgres-1.3.0/RPostgres/DESCRIPTION | 13 - RPostgres-1.3.0/RPostgres/MD5 | 53 ++-- RPostgres-1.3.0/RPostgres/NAMESPACE | 1 RPostgres-1.3.0/RPostgres/NEWS.md | 18 + RPostgres-1.3.0/RPostgres/R/PqConnection.R | 117 +++++++++ RPostgres-1.3.0/RPostgres/R/PqResult.R | 26 ++ RPostgres-1.3.0/RPostgres/R/RcppExports.R | 4 RPostgres-1.3.0/RPostgres/R/quote.R | 14 - RPostgres-1.3.0/RPostgres/README.md | 4 RPostgres-1.3.0/RPostgres/build |only RPostgres-1.3.0/RPostgres/configure | 122 +++++++++- RPostgres-1.3.0/RPostgres/inst |only RPostgres-1.3.0/RPostgres/man/Postgres.Rd | 10 RPostgres-1.3.0/RPostgres/man/Redshift.Rd | 2 RPostgres-1.3.0/RPostgres/man/postgresWaitForNotify.Rd |only RPostgres-1.3.0/RPostgres/man/quote.Rd | 3 RPostgres-1.3.0/RPostgres/src/DbConnection.cpp | 43 +++ RPostgres-1.3.0/RPostgres/src/DbConnection.h | 1 RPostgres-1.3.0/RPostgres/src/PqColumnDataSource.cpp | 88 +++++-- RPostgres-1.3.0/RPostgres/src/PqColumnDataSource.h | 2 RPostgres-1.3.0/RPostgres/src/PqResultImpl.cpp | 8 RPostgres-1.3.0/RPostgres/src/RcppExports.cpp | 13 + RPostgres-1.3.0/RPostgres/src/connection.cpp | 5 RPostgres-1.3.0/RPostgres/tests/testthat/helper-DBItest.R | 7 RPostgres-1.3.0/RPostgres/tests/testthat/test-DBItest.R | 2 RPostgres-1.3.0/RPostgres/tests/testthat/test-dbWriteTable.R | 30 ++ RPostgres-1.3.0/RPostgres/tests/testthat/test-timezone.R |only RPostgres-1.3.0/RPostgres/tests/testthat/test-waitForNotify.R |only RPostgres-1.3.0/RPostgres/vignettes |only 30 files changed, 504 insertions(+), 82 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs; one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut], Sam Weerahandi [ctb], Malwane Ananda [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between onewaytests versions 2.4 dated 2019-08-19 and 2.5 dated 2021-01-07
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/ag.test.R | 3 ++- R/aov.test.R | 3 ++- R/bf.test.R | 3 ++- R/box.test.R | 3 ++- R/describe.R | 3 ++- R/gp.test.R | 3 ++- R/gplot.R | 3 ++- R/homog.test.R | 3 ++- R/james.test.R | 3 ++- R/johansen.test.R | 3 ++- R/kw.test.R | 3 ++- R/mw.test.R | 3 ++- R/nor.test.R | 3 ++- R/paircomp.R | 2 ++ R/paircomp.jt.R | 2 ++ R/ss.test.R | 3 ++- R/st.test.R | 3 ++- R/welch.test.R | 3 ++- R/wt.test.R | 3 ++- man/gp.test.Rd | 6 ++++-- 22 files changed, 67 insertions(+), 44 deletions(-)
Title: Pedigree, Genetic Merit and Phenotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with (non)random mating followed by (non)random selection with different patterns in males and females.
Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between pedSimulate versions 0.0.4 dated 2020-04-26 and 0.1.1 dated 2021-01-07
DESCRIPTION | 12 - MD5 | 20 +- NAMESPACE | 1 NEWS.md | 7 R/assortative.R |only R/fs_mate_finder.R | 18 +- R/pedSimulate.R | 26 +-- R/pp_mate_finder.R | 18 +- R/simulatePed.R | 383 ++++++++++++++++++++++++---------------------- man/assortative.Rd |only man/pedSimulte-package.Rd | 26 +-- man/simulatePed.Rd | 62 ++++--- 12 files changed, 313 insertions(+), 260 deletions(-)
Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points
Detection
Description: A retake on the Genie algorithm - a robust
hierarchical clustering method
(Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>).
Now faster and more memory efficient; determining the whole hierarchy
for datasets of 10M points in low dimensional Euclidean spaces or
100K points in high-dimensional ones takes only 1-2 minutes.
Allows clustering with respect to mutual reachability distances
so that it can act as a noise point detector or a robustified version of
'HDBSCAN*' (that is able to detect a predefined number of
clusters and hence it does not dependent on the somewhat
fragile 'eps' parameter).
The package also features an implementation of economic inequity indices
(the Gini, Bonferroni index) and external cluster validity measures
(partition similarity scores; e.g., the adjusted Rand, Fowlkes-Mallows,
adjusted mutual information, pair sets index).
See also the 'Python' version of 'genieclust' available on 'PyPI', which
supports sparse data, more metrics, and even larger datasets.
Author: Marek Gagolewski [aut, cre, cph]
(<https://orcid.org/0000-0003-0637-6028>),
Maciej Bartoszuk [ctb],
Anna Cena [ctb],
Peter M. Larsen [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between genieclust versions 0.9.4 dated 2020-07-31 and 0.9.7 dated 2021-01-07
DESCRIPTION | 12 +++---- MD5 | 53 +++++++++++++++---------------- NEWS | 23 ++++++++++++- R/RcppExports.R | 4 ++ R/gclust.R | 31 ++++++++++-------- R/genieclust-package.R | 29 ++++++++++------- R/mst.R | 73 ++++++++++++++++++++----------------------- man/emst_mlpack.Rd | 12 +------ man/gclust.Rd | 2 - man/mst.Rd | 6 +-- src/RcppExports.cpp | 14 ++++++++ src/c_argfuns.h | 4 +- src/c_common.h | 4 +- src/c_compare_partitions.h | 4 +- src/c_disjoint_sets.h | 4 +- src/c_distance.h | 4 +- src/c_genie.h | 4 +- src/c_gini_disjoint_sets.h | 4 +- src/c_inequity.h | 4 +- src/c_int_dict.h | 4 +- src/c_matrix.h | 4 +- src/c_mst.h | 30 ++++++++--------- src/c_postprocess.h | 4 +- src/c_preprocess.h | 4 +- src/r_compare_partitions.cpp | 4 +- src/r_emst.cpp |only src/r_gclust.cpp | 35 +------------------- src/r_inequity.cpp | 4 +- 28 files changed, 195 insertions(+), 185 deletions(-)
Title: Regression Spline Functions and Classes
Description: Constructs basis matrix of B-splines, M-splines
I-splines, convex splines (C-splines), periodic M-splines,
natural cubic splines, generalized Bernstein polynomials,
and their integrals (except C-splines) and derivatives
of given order by close-form recursive formulas.
It also contains a C++ head-only library integrated with Rcpp.
See De Boor (1978) <doi:10.1002/zamm.19800600129>,
Ramsay (1988) <doi:10.1214/ss/1177012761>, and
Meyer (2008) <doi:10.1214/08-AOAS167>
for more information about the spline basis.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>),
Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between splines2 versions 0.3.1 dated 2020-07-14 and 0.4.1 dated 2021-01-07
DESCRIPTION | 23 - MD5 | 139 +++--- NAMESPACE | 4 NEWS.md | 68 ++- R/RcppExports.R | 45 -- R/bSpline.R | 40 + R/bernsteinPoly.R | 4 R/cSpline.R | 68 +-- R/dbs.R | 19 R/deriv.R | 130 +++--- R/iSpline.R | 14 R/ibs.R | 10 R/mSpline.R | 79 ++- R/misc.R | 24 - R/naturalSpline.R |only R/predict.R | 87 ++-- R/print.R | 8 R/splines2-package.R | 4 README.md | 155 +++++-- build/vignette.rds |binary inst/CITATION | 4 inst/bib/splines2.bib | 15 inst/doc/splines2-intro.R | 47 +- inst/doc/splines2-intro.Rmd | 129 ++++-- inst/doc/splines2-intro.html | 479 ++++++++--------------- inst/doc/splines2-wi-rcpp.Rmd | 76 ++- inst/doc/splines2-wi-rcpp.html | 399 +++++-------------- inst/examples/ex-bSpline.R | 5 inst/examples/ex-bernsteinPoly.R | 5 inst/examples/ex-cSpline.R | 5 inst/examples/ex-iSpline.R | 5 inst/examples/ex-ibs.R | 7 inst/examples/ex-mSpline.R | 29 + inst/examples/ex-naturalSpline.R |only inst/include/splines2Armadillo.h | 4 inst/include/splines2Armadillo/BSpline.h | 94 +--- inst/include/splines2Armadillo/BernsteinPoly.h | 60 +- inst/include/splines2Armadillo/CSpline.h | 2 inst/include/splines2Armadillo/ISpline.h | 2 inst/include/splines2Armadillo/MSpline.h | 79 +-- inst/include/splines2Armadillo/NaturalSpline.h |only inst/include/splines2Armadillo/PeriodicMSpline.h |only inst/include/splines2Armadillo/SplineBase.h | 150 +++++-- inst/include/splines2Armadillo/common.h | 2 inst/include/splines2Armadillo/utils.h | 19 inst/tinytest/test-bernsteinPoly.R | 37 + inst/tinytest/test-cSpline.R | 3 inst/tinytest/test-deriv.R | 4 inst/tinytest/test-iSpline.R | 3 inst/tinytest/test-mSpline.R | 274 +++++++++++++ inst/tinytest/test-naturalSpline.R |only inst/tinytest/test-predict.R | 3 inst/tinytest/test-print.R | 4 man/bSpline.Rd | 39 + man/bernsteinPoly.Rd | 5 man/cSpline.Rd | 30 - man/dbs.Rd | 29 - man/deriv.Rd | 27 - man/iSpline.Rd | 21 - man/ibs.Rd | 31 - man/mSpline.Rd | 100 +++- man/naturalSpline.Rd |only man/predict.Rd | 22 - man/splines2.Rd | 2 src/BSpline_export.cpp | 20 src/BernsteinPoly_export.cpp | 6 src/CSpline_export.cpp | 61 -- src/ISpline_export.cpp | 108 ----- src/MSpline_export.cpp | 77 ++- src/NaturalSpline_export.cpp |only src/RcppExports.cpp | 110 +---- tests/tinytest.R | 2 vignettes/splines2-intro.Rmd | 129 ++++-- vignettes/splines2-wi-rcpp.Rmd | 76 ++- 74 files changed, 2099 insertions(+), 1662 deletions(-)
Title: Shiny Control Panel
Description: Add shiny inputs with one or more inline buttons that grow and shrink with inputs.
Also add tool tips to input buttons and styling and messages for input validation.
Author: Alex Pickering
Maintainer: Alex Pickering <alexvpickering@gmail.com>
Diff between shinypanel versions 0.1.2 dated 2020-10-16 and 0.1.4 dated 2021-01-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 +++++++- R/selectizeInputWithButtons.R | 2 +- R/textInputWithButtons.R | 8 ++++---- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at
the University of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster,
Brendan McArdle, Ben Stevenson, Chris Wild
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.1-29 dated 2020-09-18 and 3.1-30 dated 2021-01-07
s20x-3.1-29/s20x/data/airpass.df.txt.gz |only s20x-3.1-29/s20x/data/apples.df.txt.gz |only s20x-3.1-29/s20x/data/arousal.df.txt.gz |only s20x-3.1-29/s20x/data/beer.df.txt.gz |only s20x-3.1-29/s20x/data/body.df.txt.gz |only s20x-3.1-29/s20x/data/books.df.txt.gz |only s20x-3.1-29/s20x/data/bursary.df.txt.gz |only s20x-3.1-29/s20x/data/butterfat.df.txt.gz |only s20x-3.1-29/s20x/data/camplake.df.txt.gz |only s20x-3.1-29/s20x/data/chalk.df.txt.gz |only s20x-3.1-29/s20x/data/computer.df.txt.gz |only s20x-3.1-29/s20x/data/course.df.txt.gz |only s20x-3.1-29/s20x/data/course2way.df.txt.gz |only s20x-3.1-29/s20x/data/diamonds.df.txt.gz |only s20x-3.1-29/s20x/data/fire.df.txt.gz |only s20x-3.1-29/s20x/data/fruitfly.df.txt.gz |only s20x-3.1-29/s20x/data/house.df.txt.gz |only s20x-3.1-29/s20x/data/incomes.df.txt.gz |only s20x-3.1-29/s20x/data/lakemary.df.txt.gz |only s20x-3.1-29/s20x/data/larain.df.txt.gz |only s20x-3.1-29/s20x/data/mazda.df.txt.gz |only s20x-3.1-29/s20x/data/mening.df.txt.gz |only s20x-3.1-29/s20x/data/mergers.df.txt.gz |only s20x-3.1-29/s20x/data/mozart.df.txt.gz |only s20x-3.1-29/s20x/data/nail.df.txt.gz |only s20x-3.1-29/s20x/data/oysters.df.txt.gz |only s20x-3.1-29/s20x/data/peru.df.txt.gz |only s20x-3.1-29/s20x/data/rain.df.txt.gz |only s20x-3.1-29/s20x/data/seeds.df.txt.gz |only s20x-3.1-29/s20x/data/sheep.df.txt.gz |only s20x-3.1-29/s20x/data/skulls.df.txt.gz |only s20x-3.1-29/s20x/data/soyabean.df.txt.gz |only s20x-3.1-29/s20x/data/teach.df.txt.gz |only s20x-3.1-29/s20x/data/technitron.df.txt.gz |only s20x-3.1-29/s20x/data/thyroid.df.txt.gz |only s20x-3.1-29/s20x/data/toothpaste.df.txt.gz |only s20x-3.1-29/s20x/data/zoo.df.txt.gz |only s20x-3.1-30/s20x/DESCRIPTION | 10 ++- s20x-3.1-30/s20x/MD5 | 84 ++++++++++++++--------------- s20x-3.1-30/s20x/R/boxqq.r | 4 - s20x-3.1-30/s20x/R/estimateContrasts1.R | 12 +++- s20x-3.1-30/s20x/R/src-package.R | 22 +++++++ s20x-3.1-30/s20x/data/airpass.df.rda |only s20x-3.1-30/s20x/data/apples.df.rda |only s20x-3.1-30/s20x/data/arousal.df.rda |only s20x-3.1-30/s20x/data/beer.df.rda |only s20x-3.1-30/s20x/data/body.df.rda |only s20x-3.1-30/s20x/data/books.df.rda |only s20x-3.1-30/s20x/data/bursary.df.rda |only s20x-3.1-30/s20x/data/butterfat.df.rda |only s20x-3.1-30/s20x/data/camplake.df.rda |only s20x-3.1-30/s20x/data/chalk.df.rda |only s20x-3.1-30/s20x/data/computer.df.rda |only s20x-3.1-30/s20x/data/course.df.rda |only s20x-3.1-30/s20x/data/course2way.df.rda |only s20x-3.1-30/s20x/data/diamonds.df.rda |only s20x-3.1-30/s20x/data/fire.df.rda |only s20x-3.1-30/s20x/data/fruitfly.df.rda |only s20x-3.1-30/s20x/data/house.df.rda |only s20x-3.1-30/s20x/data/incomes.df.rda |only s20x-3.1-30/s20x/data/lakemary.df.rda |only s20x-3.1-30/s20x/data/larain.df.rda |only s20x-3.1-30/s20x/data/mazda.df.rda |only s20x-3.1-30/s20x/data/mening.df.rda |only s20x-3.1-30/s20x/data/mergers.df.rda |only s20x-3.1-30/s20x/data/mozart.df.rda |only s20x-3.1-30/s20x/data/nail.df.rda |only s20x-3.1-30/s20x/data/oysters.df.rda |only s20x-3.1-30/s20x/data/peru.df.rda |only s20x-3.1-30/s20x/data/rain.df.rda |only s20x-3.1-30/s20x/data/seeds.df.rda |only s20x-3.1-30/s20x/data/sheep.df.rda |only s20x-3.1-30/s20x/data/skulls.df.rda |only s20x-3.1-30/s20x/data/snapper.df.rda |only s20x-3.1-30/s20x/data/soyabean.df.rda |only s20x-3.1-30/s20x/data/teach.df.rda |only s20x-3.1-30/s20x/data/technitron.df.rda |only s20x-3.1-30/s20x/data/thyroid.df.rda |only s20x-3.1-30/s20x/data/toothpaste.df.rda |only s20x-3.1-30/s20x/data/zoo.df.rda |only s20x-3.1-30/s20x/man/snapper.df.Rd |only 81 files changed, 82 insertions(+), 50 deletions(-)
Title: Database Interface and 'MariaDB' Driver
Description: Implements a 'DBI'-compliant interface to 'MariaDB'
(<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>)
databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RMariaDB versions 1.0.11 dated 2020-12-16 and 1.1.0 dated 2021-01-07
RMariaDB-1.0.11/RMariaDB/tests/testthat/testthat-problems.rds |only RMariaDB-1.1.0/RMariaDB/DESCRIPTION | 14 +- RMariaDB-1.1.0/RMariaDB/MD5 | 45 +++---- RMariaDB-1.1.0/RMariaDB/NEWS.md | 15 ++ RMariaDB-1.1.0/RMariaDB/R/MariaDBConnection.R | 4 RMariaDB-1.1.0/RMariaDB/R/MariaDBResult.R | 3 RMariaDB-1.1.0/RMariaDB/R/coerce.R | 36 ++++- RMariaDB-1.1.0/RMariaDB/R/connect.R | 61 +++++++++- RMariaDB-1.1.0/RMariaDB/R/default.R | 12 - RMariaDB-1.1.0/RMariaDB/R/query.R | 19 ++- RMariaDB-1.1.0/RMariaDB/R/quote.R | 17 ++ RMariaDB-1.1.0/RMariaDB/R/table.R | 11 + RMariaDB-1.1.0/RMariaDB/configure | 7 - RMariaDB-1.1.0/RMariaDB/man/dbConnect-MariaDBDriver-method.Rd | 23 +++ RMariaDB-1.1.0/RMariaDB/man/mariadb-quoting.Rd | 3 RMariaDB-1.1.0/RMariaDB/src/MariaBinding.cpp | 7 - RMariaDB-1.1.0/RMariaDB/src/MariaResultPrep.cpp | 3 RMariaDB-1.1.0/RMariaDB/src/MariaRow.cpp | 6 RMariaDB-1.1.0/RMariaDB/src/MariaTypes.cpp | 6 RMariaDB-1.1.0/RMariaDB/src/MariaTypes.h | 4 RMariaDB-1.1.0/RMariaDB/tests/testthat/helper-DBItest.R | 4 RMariaDB-1.1.0/RMariaDB/tests/testthat/test-DBItest.R | 2 RMariaDB-1.1.0/RMariaDB/tests/testthat/test-queries.R | 2 RMariaDB-1.1.0/RMariaDB/tests/testthat/test-timezone.R |only RMariaDB-1.1.0/RMariaDB/tools/tz.sql |only 25 files changed, 240 insertions(+), 64 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between 'GRASS' 7 geographical
information system and R, based on starting R from within the 'GRASS' 'GIS'
environment, or running free-standing R in a temporary 'GRASS' location;
the package provides facilities for using all 'GRASS' commands from the
R command line. This package may not be used for 'GRASS' 6, for which
'spgrass6' should be used.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Rainer Krug [ctb] (<https://orcid.org/0000-0002-7490-0066>),
Markus Neteler [ctb] (<https://orcid.org/0000-0003-1916-1966>),
Sebastian Jeworutzki [ctb] (<https://orcid.org/0000-0002-2671-5253>),
Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>)
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.2-3 dated 2020-12-07 and 0.2-4 dated 2021-01-07
rgrass7-0.2-3/rgrass7/ChangeLog |only rgrass7-0.2-3/rgrass7/inst/ChangeLog |only rgrass7-0.2-4/rgrass7/DESCRIPTION | 26 ++++--- rgrass7-0.2-4/rgrass7/MD5 | 14 ++-- rgrass7-0.2-4/rgrass7/NAMESPACE | 2 rgrass7-0.2-4/rgrass7/NEWS.md |only rgrass7-0.2-4/rgrass7/R/initGRASS.R | 30 +++++++- rgrass7-0.2-4/rgrass7/R/xml1.R | 93 ++++++++++++++++++++++++++- rgrass7-0.2-4/rgrass7/inst/pre_git_ChangeLog |only rgrass7-0.2-4/rgrass7/man/execGRASS.Rd | 25 ++++++- 10 files changed, 163 insertions(+), 27 deletions(-)
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 1.6.2 dated 2021-01-04 and 1.6.3 dated 2021-01-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/RCzechia.R | 2 +- R/sysdata.rda |binary inst/doc/vignette.html | 16 ++++++++-------- man/RCzechia-package.Rd | 2 +- 7 files changed, 24 insertions(+), 20 deletions(-)
Title: Xsimd C++ Header-Only Library Files
Description: This header-only library provides modern, portable C++ wrappers for SIMD
intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512).
By placing this library in this package, we offer an efficient distribution system for
Xsimd <https://github.com/xtensor-stack/xsimd> for R packages using CRAN.
Author: Marc A. Suchard [aut, cre],
Andrew J. Holbrook [aut],
Observational Health Data Sciences and Informatics [cph],
Johan Mabille [cph, ctb] (author and copyright holder of Xsimd library
under a BSD-3 license),
Sylvain Corlay [cph, ctb] (author and copyright holder of Xsimd library
under a BSD-3 license),
Alexander J. Lee [cph, ctb] (author and copyright holder of
FeatureDetector library under a CC0 1.0 license)
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between RcppXsimd versions 7.1.4 dated 2019-07-18 and 7.1.5 dated 2021-01-07
DESCRIPTION | 12 ++++---- MD5 | 25 ++++++++++-------- NAMESPACE | 2 + NEWS.md | 9 +++++- R/RcppXsimd.R | 50 +++++++++++++++++++++++++++++++++--- README.md | 2 - man/RcppXsimd.Rd | 1 man/getNEONFlags.Rd |only man/supportsNEON.Rd |only src/FeatureDetector/cpu.cpp |only src/FeatureDetector/cpu_aarch64.cpp |only src/FeatureDetector/cpu_aarch64.h |only src/Makevars | 2 - src/Makevars.win | 2 - src/RcppXsimd.cpp | 16 ++++++++++- tests/testthat/test-SIMD.R | 6 ++-- 16 files changed, 98 insertions(+), 29 deletions(-)
Title: Implementation of the 'PROCESS' Macro
Description: Perform moderation, mediation, moderated mediation and moderated moderation.
Inspired from famous 'PROCESS' macro for 'SPSS' and 'SAS' created by Andrew Hayes.
Author: Keon-Woong Moon [aut, cre],
Sokyoung Hong [ctb]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between processR versions 0.2.3 dated 2020-01-27 and 0.2.6 dated 2021-01-07
DESCRIPTION | 18 ++--- MD5 | 62 +++++++++---------- NAMESPACE | 5 + NEWS.md | 22 ++++++ R/condPlot2.R | 2 R/drawModel.R | 71 ++++++++++++++-------- R/modSummary.R | 4 - R/modelsSummary.R | 51 +++++++++++----- R/statisticalDiagram.R | 2 README.md | 12 --- build/vignette.rds |binary inst/doc/processR.Rmd | 2 inst/doc/processR.html | 146 +++++++++++++++++++++++++++++++++++++--------- man/caskets.Rd | 6 + man/condPlot2.Rd | 2 man/disaster.Rd | 6 + man/drawModel.Rd | 5 + man/education.Rd | 6 + man/estress.Rd | 6 + man/glbwarm.Rd | 6 + man/modSummary.Rd | 4 - man/modelsSummaryTable.Rd | 8 +- man/moreModels.Rd | 6 + man/nodes.Rd | 6 + man/numberSubscript.Rd | 4 - man/parrows.Rd | 6 + man/pmacro.Rd | 6 + man/pmi.Rd | 6 + man/protest.Rd | 6 + man/teachers.Rd | 6 + man/teams.Rd | 6 + vignettes/processR.Rmd | 2 32 files changed, 342 insertions(+), 158 deletions(-)
Title: Several Methods for Procedural Name Generation
Description: A small, dependency-free way to generate random names. Methods
provided include the adjective-surname approach of Docker containers
('<https://github.com/moby/moby/blob/master/pkg/namesgenerator/names-generator.go'),
and combinations of common English or Spanish words.
Author: Michael Mahoney [aut, cre] (<https://orcid.org/0000-0003-2402-304X>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between proceduralnames versions 0.1.0 dated 2021-01-05 and 0.1.1 dated 2021-01-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/docker_names.R | 8 ++++++-- R/english_names.R | 4 +++- R/spanish_names.R | 4 +++- data/common_words.rda |binary 7 files changed, 27 insertions(+), 13 deletions(-)
More information about proceduralnames at CRAN
Permanent link
Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator
Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics)
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.11.2 dated 2020-05-28 and 0.12.0 dated 2021-01-07
DESCRIPTION | 19 MD5 | 149 +- NEWS.md | 5 R/etc_utils_autoplot.R | 24 R/etc_utils_dataframe.R | 4 R/etc_utils_plot.R | 40 R/etc_utils_validate_args.R | 14 R/etc_utils_validate_obj.R | 2 R/g_auc.R | 2 R/g_auc_ci.R | 4 R/g_fortify.R | 65 - R/g_part.R | 4 R/g_pauc.R | 2 R/mm1_create_mmdat.R | 2 R/mm2_join_data.R | 8 R/mm3_reformat_data.R | 2 R/mm4_format_nfold.R | 4 R/pl2_pipeline_main_aucroc.R | 13 R/pl2_pipeline_main_basic.R | 20 R/pl2_pipeline_main_rocprc.R | 18 R/pl3_calc_auc_with_u.R | 2 R/pl4_calc_measures.R | 4 R/precrec.R | 2 README.md | 189 ++- build/vignette.rds |binary inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 984 +++++++++++------- man/auc_ci.Rd | 2 man/figures |only man/part.Rd | 2 src/precrec_misc.cpp | 16 src/precrec_mmx.cpp | 45 src/precrec_plx.cpp | 27 tests/testthat.R | 3 tests/testthat/test_g_auc.R | 8 tests/testthat/test_g_auc_ci.R | 14 tests/testthat/test_g_autoplot1_pl.R | 2 tests/testthat/test_g_autoplot2_curves.R | 66 - tests/testthat/test_g_autoplot3_points.R | 66 - tests/testthat/test_g_datamatrix1_curves.R | 10 tests/testthat/test_g_datamatrix2_points.R | 18 tests/testthat/test_g_datamatrix3_aucroc.R | 2 tests/testthat/test_g_fortify1_pl.R | 2 tests/testthat/test_g_fortify2_curves.R | 2 tests/testthat/test_g_fortify3_points.R | 2 tests/testthat/test_g_part.R | 10 tests/testthat/test_g_pauc.R | 8 tests/testthat/test_g_plot2_curves.R | 44 tests/testthat/test_g_plot3_points.R | 52 tests/testthat/test_g_print.R | 10 tests/testthat/test_main_evalmod.R | 38 tests/testthat/test_mm1_1_mmdata.R | 4 tests/testthat/test_mm1_2_mmdata_mnames.R | 2 tests/testthat/test_mm1_3_mmdata_nfold.R | 78 - tests/testthat/test_mm2_1_join_datasets.R | 26 tests/testthat/test_mm2_2_join_scores.R | 16 tests/testthat/test_mm2_3_join_labels.R | 7 tests/testthat/test_mm3_1_reformat_data_scores.R | 7 tests/testthat/test_mm3_2_reformat_data_labels.R | 2 tests/testthat/test_mm3_3_reformat_data_main.R | 8 tests/testthat/test_mm3_4_reformat_data_singleclass.R |only tests/testthat/test_mm4_1_format_nfold.R | 2 tests/testthat/test_pl1_1_pl_main.R | 14 tests/testthat/test_pl2_1_pl_main_rocprc.R | 12 tests/testthat/test_pl2_2_pl_main_basic.R | 10 tests/testthat/test_pl2_3_pl_main_aucroc.R | 10 tests/testthat/test_pl3_1_create_confmats.R | 2 tests/testthat/test_pl3_2_calc_auc_with_u.R | 8 tests/testthat/test_pl4_1_calc_measures.R | 2 tests/testthat/test_pl5_1_create_roc.R | 2 tests/testthat/test_pl5_2_create_prc.R | 2 tests/testthat/test_pl5_3_create_curves.R | 2 tests/testthat/test_pl6_1_calc_avg_points.R | 10 tests/testthat/test_pl6_2_calc_avg_curves.R | 10 tests/testthat/test_uc1_usecases.R | 12 tests/testthat/test_uc2_usecases.R |only vignettes/introduction.Rmd | 4 77 files changed, 1312 insertions(+), 975 deletions(-)
Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models,
and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint,
Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or
'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.6.4 dated 2020-12-15 and 0.6.5 dated 2021-01-07
modelsummary-0.6.4/modelsummary/R/easystats.R |only modelsummary-0.6.4/modelsummary/R/extract_statistic_override.R |only modelsummary-0.6.4/modelsummary/man/DinM.Rd |only modelsummary-0.6.4/modelsummary/man/assert_dependency.Rd |only modelsummary-0.6.4/modelsummary/man/check_dependency.Rd |only modelsummary-0.6.4/modelsummary/man/clean_stars.Rd |only modelsummary-0.6.4/modelsummary/man/coef_map_felm_iv.Rd |only modelsummary-0.6.4/modelsummary/man/datasummary_extract.Rd |only modelsummary-0.6.4/modelsummary/man/datasummary_skim_categorical.Rd |only modelsummary-0.6.4/modelsummary/man/datasummary_skim_dataset.Rd |only modelsummary-0.6.4/modelsummary/man/datasummary_skim_numeric.Rd |only modelsummary-0.6.4/modelsummary/man/extract_estimates.Rd |only modelsummary-0.6.4/modelsummary/man/extract_gof.Rd |only modelsummary-0.6.4/modelsummary/man/extract_models.Rd |only modelsummary-0.6.4/modelsummary/man/extract_statistic_override.Rd |only modelsummary-0.6.4/modelsummary/man/factory.Rd |only modelsummary-0.6.4/modelsummary/man/factory_dataframe.Rd |only modelsummary-0.6.4/modelsummary/man/factory_flextable.Rd |only modelsummary-0.6.4/modelsummary/man/factory_gt.Rd |only modelsummary-0.6.4/modelsummary/man/factory_huxtable.Rd |only modelsummary-0.6.4/modelsummary/man/factory_kableExtra.Rd |only modelsummary-0.6.4/modelsummary/man/fmt_labels_md.Rd |only modelsummary-0.6.4/modelsummary/man/glance.modelsummary_list.Rd |only modelsummary-0.6.4/modelsummary/man/glance_custom.default.Rd |only modelsummary-0.6.4/modelsummary/man/glance_custom.fixest.Rd |only modelsummary-0.6.4/modelsummary/man/glance_easystats.Rd |only modelsummary-0.6.4/modelsummary/man/gof_map_build.Rd |only modelsummary-0.6.4/modelsummary/man/make_stars.Rd |only modelsummary-0.6.4/modelsummary/man/make_stars_note.Rd |only modelsummary-0.6.4/modelsummary/man/pad.Rd |only modelsummary-0.6.4/modelsummary/man/parse_output_arg.Rd |only modelsummary-0.6.4/modelsummary/man/replace_dict.Rd |only modelsummary-0.6.4/modelsummary/man/rounding.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_add_rows.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_align.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_coef.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_conf_level.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_ds_nesting_factor.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_ds_right_handed_formula.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_estimate.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_factory.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_fmt.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_gof.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_model_names.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_notes.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_output.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_stars.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_statistic.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_statistic_override.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_tidy.Rd |only modelsummary-0.6.4/modelsummary/man/sanity_title.Rd |only modelsummary-0.6.4/modelsummary/man/tidy.modelsummary_list.Rd |only modelsummary-0.6.4/modelsummary/man/tidy_custom.default.Rd |only modelsummary-0.6.4/modelsummary/man/tidy_easystats.Rd |only modelsummary-0.6.4/modelsummary/man/tidy_felm_iv.Rd |only modelsummary-0.6.4/modelsummary/tests/figs/modelplot |only modelsummary-0.6.4/modelsummary/tests/testthat/test-glance_custom.R |only modelsummary-0.6.4/modelsummary/tests/testthat/test-supported.R |only modelsummary-0.6.5/modelsummary/DESCRIPTION | 8 modelsummary-0.6.5/modelsummary/MD5 | 294 ++++------ modelsummary-0.6.5/modelsummary/NAMESPACE | 4 modelsummary-0.6.5/modelsummary/NEWS.md | 14 modelsummary-0.6.5/modelsummary/R/bind.R | 9 modelsummary-0.6.5/modelsummary/R/convenience.R | 8 modelsummary-0.6.5/modelsummary/R/datasummary.R | 2 modelsummary-0.6.5/modelsummary/R/datasummary_balance.R | 55 + modelsummary-0.6.5/modelsummary/R/datasummary_df.R | 2 modelsummary-0.6.5/modelsummary/R/datasummary_extract.R | 7 modelsummary-0.6.5/modelsummary/R/datasummary_functions.R | 127 +++- modelsummary-0.6.5/modelsummary/R/datasummary_skim.R | 26 modelsummary-0.6.5/modelsummary/R/extract_estimates.R | 109 ++- modelsummary-0.6.5/modelsummary/R/extract_gof.R | 127 ++-- modelsummary-0.6.5/modelsummary/R/extract_vcov.R |only modelsummary-0.6.5/modelsummary/R/factory.R | 1 modelsummary-0.6.5/modelsummary/R/factory_dataframe.R | 2 modelsummary-0.6.5/modelsummary/R/factory_flextable.R | 2 modelsummary-0.6.5/modelsummary/R/factory_gt.R | 2 modelsummary-0.6.5/modelsummary/R/factory_huxtable.R | 2 modelsummary-0.6.5/modelsummary/R/factory_kableExtra.R | 23 modelsummary-0.6.5/modelsummary/R/glance_custom.R | 10 modelsummary-0.6.5/modelsummary/R/gof_map.R | 2 modelsummary-0.6.5/modelsummary/R/modelplot.R | 42 - modelsummary-0.6.5/modelsummary/R/modelsummary.R | 294 ++++++---- modelsummary-0.6.5/modelsummary/R/modelsummary_list.R | 4 modelsummary-0.6.5/modelsummary/R/modelsummary_wide.R | 153 +++-- modelsummary-0.6.5/modelsummary/R/parse_output_arg.R | 142 ++-- modelsummary-0.6.5/modelsummary/R/reexport.R | 27 modelsummary-0.6.5/modelsummary/R/sanity_checks.R | 154 +++-- modelsummary-0.6.5/modelsummary/R/stars.R | 15 modelsummary-0.6.5/modelsummary/R/supported_models.R |only modelsummary-0.6.5/modelsummary/R/tidy_custom.R | 8 modelsummary-0.6.5/modelsummary/R/utils_pad.R | 2 modelsummary-0.6.5/modelsummary/R/utils_replace.R | 2 modelsummary-0.6.5/modelsummary/R/utils_rounding.R | 11 modelsummary-0.6.5/modelsummary/README.md | 208 ++----- modelsummary-0.6.5/modelsummary/build/modelsummary.pdf |binary modelsummary-0.6.5/modelsummary/man/All.Rd | 1 modelsummary-0.6.5/modelsummary/man/AllObs.Rd | 1 modelsummary-0.6.5/modelsummary/man/Arguments.Rd | 1 modelsummary-0.6.5/modelsummary/man/DropEmpty.Rd | 1 modelsummary-0.6.5/modelsummary/man/Factor.Rd | 1 modelsummary-0.6.5/modelsummary/man/Format.Rd | 1 modelsummary-0.6.5/modelsummary/man/Heading.Rd | 1 modelsummary-0.6.5/modelsummary/man/Histogram.Rd | 6 modelsummary-0.6.5/modelsummary/man/Max.Rd | 18 modelsummary-0.6.5/modelsummary/man/Mean.Rd | 18 modelsummary-0.6.5/modelsummary/man/Median.Rd | 18 modelsummary-0.6.5/modelsummary/man/Min.Rd | 18 modelsummary-0.6.5/modelsummary/man/Multicolumn.Rd | 1 modelsummary-0.6.5/modelsummary/man/N.Rd | 9 modelsummary-0.6.5/modelsummary/man/NPercent.Rd | 6 modelsummary-0.6.5/modelsummary/man/NUnique.Rd | 11 modelsummary-0.6.5/modelsummary/man/Ncol.Rd | 6 modelsummary-0.6.5/modelsummary/man/P0.Rd | 18 modelsummary-0.6.5/modelsummary/man/P100.Rd | 18 modelsummary-0.6.5/modelsummary/man/P25.Rd | 18 modelsummary-0.6.5/modelsummary/man/P50.Rd | 18 modelsummary-0.6.5/modelsummary/man/P75.Rd | 18 modelsummary-0.6.5/modelsummary/man/Paste.Rd | 1 modelsummary-0.6.5/modelsummary/man/Percent.Rd | 1 modelsummary-0.6.5/modelsummary/man/PercentMissing.Rd | 4 modelsummary-0.6.5/modelsummary/man/PlusMinus.Rd | 1 modelsummary-0.6.5/modelsummary/man/RowFactor.Rd | 1 modelsummary-0.6.5/modelsummary/man/RowNum.Rd | 1 modelsummary-0.6.5/modelsummary/man/SD.Rd | 18 modelsummary-0.6.5/modelsummary/man/Var.Rd | 18 modelsummary-0.6.5/modelsummary/man/datasummary.Rd | 16 modelsummary-0.6.5/modelsummary/man/datasummary_balance.Rd | 15 modelsummary-0.6.5/modelsummary/man/datasummary_correlation.Rd | 12 modelsummary-0.6.5/modelsummary/man/datasummary_df.Rd | 14 modelsummary-0.6.5/modelsummary/man/datasummary_skim.Rd | 12 modelsummary-0.6.5/modelsummary/man/get_estimates.Rd |only modelsummary-0.6.5/modelsummary/man/get_gof.Rd |only modelsummary-0.6.5/modelsummary/man/glance_custom.Rd | 4 modelsummary-0.6.5/modelsummary/man/modelplot.Rd | 17 modelsummary-0.6.5/modelsummary/man/modelsummary.Rd | 197 ++++-- modelsummary-0.6.5/modelsummary/man/modelsummary_wide.Rd | 83 +- modelsummary-0.6.5/modelsummary/man/msummary.Rd | 194 ++++-- modelsummary-0.6.5/modelsummary/man/supported_models.Rd |only modelsummary-0.6.5/modelsummary/man/tidy_custom.Rd | 8 modelsummary-0.6.5/modelsummary/tests/figs/coef-map-color-shape-background.svg |only modelsummary-0.6.5/modelsummary/tests/figs/coef-omit.svg |only modelsummary-0.6.5/modelsummary/tests/figs/multiple-plots-facet.svg |only modelsummary-0.6.5/modelsummary/tests/figs/multiple-plots-vanilla.svg |only modelsummary-0.6.5/modelsummary/tests/figs/vanilla.svg |only modelsummary-0.6.5/modelsummary/tests/testthat/known_output/datasummary_balance_penguins.html | 18 modelsummary-0.6.5/modelsummary/tests/testthat/known_output/msummary_latex_simple.tex |only modelsummary-0.6.5/modelsummary/tests/testthat/known_output/output-file.jpg |only modelsummary-0.6.5/modelsummary/tests/testthat/known_output/output-file.md |only modelsummary-0.6.5/modelsummary/tests/testthat/known_output/output-file.rtf |only modelsummary-0.6.5/modelsummary/tests/testthat/known_output/output-file.tex |only modelsummary-0.6.5/modelsummary/tests/testthat/known_output/output-file.txt |only modelsummary-0.6.5/modelsummary/tests/testthat/test-add_columns.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-add_rows.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-bad-input.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-coef_map.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-coef_omit.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-coef_rename.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-custom.R |only modelsummary-0.6.5/modelsummary/tests/testthat/test-datasummary.R | 6 modelsummary-0.6.5/modelsummary/tests/testthat/test-datasummary_balance.R | 72 +- modelsummary-0.6.5/modelsummary/tests/testthat/test-datasummary_correlation.R | 1 modelsummary-0.6.5/modelsummary/tests/testthat/test-datasummary_df.R | 6 modelsummary-0.6.5/modelsummary/tests/testthat/test-datasummary_skim.R | 62 +- modelsummary-0.6.5/modelsummary/tests/testthat/test-ellipses.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-estimate.R |only modelsummary-0.6.5/modelsummary/tests/testthat/test-exponentiate.R |only modelsummary-0.6.5/modelsummary/tests/testthat/test-extract_estimates.R | 2 modelsummary-0.6.5/modelsummary/tests/testthat/test-flextable.R | 6 modelsummary-0.6.5/modelsummary/tests/testthat/test-fmt.R | 4 modelsummary-0.6.5/modelsummary/tests/testthat/test-glue.R | 4 modelsummary-0.6.5/modelsummary/tests/testthat/test-gof.R | 30 - modelsummary-0.6.5/modelsummary/tests/testthat/test-gt.R | 4 modelsummary-0.6.5/modelsummary/tests/testthat/test-huxtable.R | 11 modelsummary-0.6.5/modelsummary/tests/testthat/test-interaction.R | 5 modelsummary-0.6.5/modelsummary/tests/testthat/test-kableExtra.R | 4 modelsummary-0.6.5/modelsummary/tests/testthat/test-latex.R |only modelsummary-0.6.5/modelsummary/tests/testthat/test-modelplot.R | 16 modelsummary-0.6.5/modelsummary/tests/testthat/test-modelsummary_list.R | 36 - modelsummary-0.6.5/modelsummary/tests/testthat/test-modelsummary_wide.R | 86 ++ modelsummary-0.6.5/modelsummary/tests/testthat/test-rounding.R |only modelsummary-0.6.5/modelsummary/tests/testthat/test-stars.R | 42 + modelsummary-0.6.5/modelsummary/tests/testthat/test-statistic.R | 4 modelsummary-0.6.5/modelsummary/tests/testthat/test-statistic_override.R | 50 + modelsummary-0.6.5/modelsummary/tests/testthat/test-unsupported.R | 8 modelsummary-0.6.5/modelsummary/tests/testthat/test-vcov.R |only 186 files changed, 2021 insertions(+), 1193 deletions(-)
Title: Functions for the Logitnormal Distribution
Description: Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between logitnorm versions 0.8.37 dated 2018-07-30 and 0.8.38 dated 2021-01-07
DESCRIPTION | 10 - MD5 | 52 +++--- R/logitnorm.R | 155 ++++++++++--------- build/vignette.rds |binary inst/doc/logitnorm.R | 12 - inst/doc/logitnorm.Rmd | 268 ++++++++++++++++----------------- inst/doc/logitnorm.html | 12 - inst/unitTests/runitLogitnorm.R | 4 inst/unitTests/runitmodeLogitnorm.R | 88 +++++----- inst/unitTests/runitmomentsLogitnorm.R | 64 ++++--- man/dlogitnorm.Rd | 68 ++++---- man/invlogit.Rd | 44 ++--- man/logit.Rd | 44 ++--- man/logitnorm-package.Rd | 110 ++++++------- man/modeLogitnorm.Rd | 38 ++-- man/momentsLogitnorm.Rd | 54 +++--- man/plogitnorm.Rd | 44 ++--- man/qlogitnorm.Rd | 44 ++--- man/rlogitnorm.Rd | 40 ++-- man/twCoefLogitnorm.Rd | 85 +++++----- man/twCoefLogitnormCi.Rd | 62 +++---- man/twCoefLogitnormE.Rd | 87 +++++----- man/twCoefLogitnormMLE.Rd | 72 ++++---- man/twCoefLogitnormMLEFlat.Rd | 40 ++-- man/twCoefLogitnormN.Rd | 78 ++++----- man/twSigmaLogitnorm.Rd | 60 +++---- vignettes/logitnorm.Rmd | 268 ++++++++++++++++----------------- 27 files changed, 966 insertions(+), 937 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Diff between llama versions 0.9.3 dated 2020-05-22 and 0.9.4 dated 2021-01-07
DESCRIPTION | 8 ++++---- LICENSE | 4 ++-- MD5 | 14 +++++++------- NEWS | 3 +++ R/classify.R | 8 ++++---- R/classifyPairs.R | 8 ++++---- R/regression.R | 4 ++-- man/llama-package.Rd | 21 ++++++++++----------- 8 files changed, 36 insertions(+), 34 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] (jQuery library),
Vladimir Agafonkin [ctb, cph] (Leaflet library),
CloudMade [cph] (Leaflet library),
Leaflet contributors [ctb] (Leaflet library),
Brandon Copeland [ctb, cph] (leaflet-measure plugin),
Joerg Dietrich [ctb, cph] (Leaflet.Terminator plugin),
Benjamin Becquet [ctb, cph] (Leaflet.MagnifyingGlass plugin),
Norkart AS [ctb, cph] (Leaflet.MiniMap plugin),
L. Voogdt [ctb, cph] (Leaflet.awesome-markers plugin),
Daniel Montague [ctb, cph] (Leaflet.EasyButton plugin),
Kartena AB [ctb, cph] (Proj4Leaflet plugin),
Robert Kajic [ctb, cph] (leaflet-locationfilter plugin),
Mapbox [ctb, cph] (leaflet-omnivore plugin),
Michael Bostock [ctb, cph] (topojson),
RStudio [cph]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between leaflet versions 2.0.3 dated 2019-11-16 and 2.0.4.1 dated 2021-01-07
leaflet-2.0.3/leaflet/inst/htmlwidgets/plugins/Proj4Leaflet/proj4-compressed.js |only leaflet-2.0.4.1/leaflet/DESCRIPTION | 14 leaflet-2.0.4.1/leaflet/MD5 | 118 leaflet-2.0.4.1/leaflet/NEWS | 15 leaflet-2.0.4.1/leaflet/R/colors.R | 26 leaflet-2.0.4.1/leaflet/R/data.R | 4 leaflet-2.0.4.1/leaflet/R/layers.R | 20 leaflet-2.0.4.1/leaflet/R/leaflet.R | 2 leaflet-2.0.4.1/leaflet/R/mapPane.R | 2 leaflet-2.0.4.1/leaflet/R/methods.R | 4 leaflet-2.0.4.1/leaflet/R/plugin-graticule.R | 2 leaflet-2.0.4.1/leaflet/R/plugin-measure.R | 4 leaflet-2.0.4.1/leaflet/R/plugin-minimap.R | 4 leaflet-2.0.4.1/leaflet/R/plugin-providers.R | 2 leaflet-2.0.4.1/leaflet/R/scalebar.R | 2 leaflet-2.0.4.1/leaflet/README.md | 15 leaflet-2.0.4.1/leaflet/data/atlStorms2005.rda |binary leaflet-2.0.4.1/leaflet/data/breweries91.rda |binary leaflet-2.0.4.1/leaflet/data/gadmCHE.rda |binary leaflet-2.0.4.1/leaflet/inst/htmlwidgets/leaflet.js | 1000 +- leaflet-2.0.4.1/leaflet/inst/htmlwidgets/leaflet.yaml | 10 leaflet-2.0.4.1/leaflet/inst/htmlwidgets/lib/leaflet/leaflet.js | 4 leaflet-2.0.4.1/leaflet/inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js | 2 leaflet-2.0.4.1/leaflet/inst/htmlwidgets/plugins/Proj4Leaflet/proj4.min.js |only leaflet-2.0.4.1/leaflet/inst/legacy/www/leaflet-src.js | 3696 +++++----- leaflet-2.0.4.1/leaflet/inst/legacy/www/leaflet.js | 4 leaflet-2.0.4.1/leaflet/man/addAwesomeMarkers.Rd | 20 leaflet-2.0.4.1/leaflet/man/addGraticule.Rd | 14 leaflet-2.0.4.1/leaflet/man/addLayersControl.Rd | 14 leaflet-2.0.4.1/leaflet/man/addLegend.Rd | 32 leaflet-2.0.4.1/leaflet/man/addMapPane.Rd | 2 leaflet-2.0.4.1/leaflet/man/addMeasure.Rd | 27 leaflet-2.0.4.1/leaflet/man/addMiniMap.Rd | 32 leaflet-2.0.4.1/leaflet/man/addProviderTiles.Rd | 25 leaflet-2.0.4.1/leaflet/man/addRasterImage.Rd | 17 leaflet-2.0.4.1/leaflet/man/addScaleBar.Rd | 19 leaflet-2.0.4.1/leaflet/man/addSimpleGraticule.Rd | 13 leaflet-2.0.4.1/leaflet/man/addTerminator.Rd | 11 leaflet-2.0.4.1/leaflet/man/atlStorms2005.Rd | 4 leaflet-2.0.4.1/leaflet/man/awesomeIcons.Rd | 16 leaflet-2.0.4.1/leaflet/man/breweries91.Rd | 4 leaflet-2.0.4.1/leaflet/man/colorNumeric.Rd | 80 leaflet-2.0.4.1/leaflet/man/deprecated.Rd | 9 leaflet-2.0.4.1/leaflet/man/derivePoints.Rd | 10 leaflet-2.0.4.1/leaflet/man/derivePolygons.Rd | 11 leaflet-2.0.4.1/leaflet/man/dispatch.Rd | 9 leaflet-2.0.4.1/leaflet/man/easyButton.Rd | 14 leaflet-2.0.4.1/leaflet/man/gadmCHE.Rd | 8 leaflet-2.0.4.1/leaflet/man/icons.Rd | 28 leaflet-2.0.4.1/leaflet/man/leaflet.Rd | 48 leaflet-2.0.4.1/leaflet/man/leafletDependencies.Rd | 4 leaflet-2.0.4.1/leaflet/man/leafletProxy.Rd | 8 leaflet-2.0.4.1/leaflet/man/leafletSizingPolicy.Rd | 9 leaflet-2.0.4.1/leaflet/man/makeAwesomeIcon.Rd | 16 leaflet-2.0.4.1/leaflet/man/makeIcon.Rd | 22 leaflet-2.0.4.1/leaflet/man/map-layers.Rd | 330 leaflet-2.0.4.1/leaflet/man/map-methods.Rd | 4 leaflet-2.0.4.1/leaflet/man/map-options.Rd | 135 leaflet-2.0.4.1/leaflet/man/providers.Rd | 4 leaflet-2.0.4.1/leaflet/man/validateCoords.Rd | 3 leaflet-2.0.4.1/leaflet/tests/testthat/test-normalize-2.R | 2 61 files changed, 3292 insertions(+), 2662 deletions(-)
Title: Easy Access to 'ggplot2' Commands
Description: Provides a series of aliases to commonly used but difficult
to remember 'ggplot2' sequences.
Author: Jonathan Carroll [aut, cre] (<https://orcid.org/0000-0002-1404-5264>),
Alicia Schep [aut] (<https://orcid.org/0000-0002-3915-0618>),
Jonathan Sidi [aut] (<https://orcid.org/0000-0002-4222-1819>),
Bob Rudis [ctb] (<https://orcid.org/0000-0001-5670-2640>),
Mohamed El Fodil Ihaddaden [ctb],
Thomas Neitmann [ctb]
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>
Diff between ggeasy versions 0.1.2 dated 2020-03-19 and 0.1.3 dated 2021-01-07
ggeasy-0.1.2/ggeasy/tests/README.md |only ggeasy-0.1.3/ggeasy/DESCRIPTION | 14 ggeasy-0.1.3/ggeasy/MD5 | 62 +- ggeasy-0.1.3/ggeasy/NAMESPACE | 1 ggeasy-0.1.3/ggeasy/NEWS.md | 6 ggeasy-0.1.3/ggeasy/R/text.R | 6 ggeasy-0.1.3/ggeasy/README.md | 47 - ggeasy-0.1.3/ggeasy/build/vignette.rds |binary ggeasy-0.1.3/ggeasy/inst/doc/shortcuts.html | 366 +++---------- ggeasy-0.1.3/ggeasy/inst/doc/tests_and_coverage.Rmd | 159 ++--- ggeasy-0.1.3/ggeasy/inst/doc/tests_and_coverage.html | 495 ++++++------------ ggeasy-0.1.3/ggeasy/man/easy_change_text.Rd | 3 ggeasy-0.1.3/ggeasy/man/figures/example-1.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-10.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-11.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-2.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-3.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-4.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-5.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-6.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-7.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-8.png |binary ggeasy-0.1.3/ggeasy/man/figures/example-9.png |binary ggeasy-0.1.3/ggeasy/man/figures/logo.gif |only ggeasy-0.1.3/ggeasy/man/figures/logo.png |binary ggeasy-0.1.3/ggeasy/man/figures/teach-1.png |binary ggeasy-0.1.3/ggeasy/man/figures/teach-2.png |binary ggeasy-0.1.3/ggeasy/tests/testthat/test-labs.R | 59 +- ggeasy-0.1.3/ggeasy/tests/testthat/test-legend.R | 86 +-- ggeasy-0.1.3/ggeasy/tests/testthat/test-remove-axis.R | 42 - ggeasy-0.1.3/ggeasy/tests/testthat/test-rotate.R | 30 - ggeasy-0.1.3/ggeasy/tests/testthat/test-text.R | 12 ggeasy-0.1.3/ggeasy/vignettes/tests_and_coverage.Rmd | 159 ++--- 33 files changed, 645 insertions(+), 902 deletions(-)
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in
handy if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.9.0 dated 2020-12-02 and 1.10.0 dated 2021-01-07
fakemake-1.10.0/fakemake/DESCRIPTION | 6 fakemake-1.10.0/fakemake/MD5 | 39 +- fakemake-1.10.0/fakemake/NEWS.md | 11 fakemake-1.10.0/fakemake/R/make.R |only fakemake-1.10.0/fakemake/R/makefiles.R |only fakemake-1.10.0/fakemake/R/makelists.R | 54 ++++ fakemake-1.10.0/fakemake/build/vignette.rds |binary fakemake-1.10.0/fakemake/inst/NEWS.rd |only fakemake-1.10.0/fakemake/inst/doc/An_Introduction_to_fakemake.html | 34 +- fakemake-1.10.0/fakemake/inst/doc/Building_Packages.Rmd | 6 fakemake-1.10.0/fakemake/inst/doc/Building_Packages.html | 133 ++++++---- fakemake-1.10.0/fakemake/inst/runit_tests/runit-make.R |only fakemake-1.10.0/fakemake/inst/runit_tests/runit-xmake.R | 14 - fakemake-1.10.0/fakemake/inst/templates/Makefile_testing |only fakemake-1.10.0/fakemake/inst/templates/all.Rout |only fakemake-1.10.0/fakemake/inst/templates/error2.Rout |only fakemake-1.10.0/fakemake/inst/templates/message1.Rout |only fakemake-1.10.0/fakemake/inst/templates/message2.Rout |only fakemake-1.10.0/fakemake/inst/templates/warning2.Rout |only fakemake-1.10.0/fakemake/man/make.Rd | 47 ++- fakemake-1.10.0/fakemake/man/provide_make_list.Rd | 4 fakemake-1.10.0/fakemake/man/read_makefile.Rd | 2 fakemake-1.10.0/fakemake/man/visualize.Rd | 2 fakemake-1.10.0/fakemake/man/write_makefile.Rd | 2 fakemake-1.10.0/fakemake/vignettes/Building_Packages.Rmd | 6 fakemake-1.9.0/fakemake/R/main.R |only 26 files changed, 254 insertions(+), 106 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.28.0 dated 2020-11-19 and 0.30.0 dated 2021-01-07
DESCRIPTION | 12 +++---- MD5 | 49 ++++++++++++++++---------------- NAMESPACE | 2 + NEWS.md | 4 ++ R/S3_glance.R | 22 +++----------- R/S3_nobs.R | 6 +++ R/estimatr_difference_in_means.R | 2 - R/estimatr_horvitz_thompson.R | 2 - R/estimatr_iv_robust.R | 2 - R/estimatr_lm_lin.R | 4 +- R/estimatr_lm_robust.R | 8 ++--- build |only man/difference_in_means.Rd | 2 - man/estimatr_glancers.Rd | 48 +++++++++++++++---------------- man/horvitz_thompson.Rd | 2 - man/iv_robust.Rd | 2 - man/lm_lin.Rd | 4 +- man/lm_robust.Rd | 8 ++--- tests/testthat/test-iv-robust-fes.R | 2 + tests/testthat/test-iv-robust.R | 2 + tests/testthat/test-lm-robust-fes.R | 6 +++ tests/testthat/test-lm-robust.R | 3 + tests/testthat/test-lm-robust_emmeans.R | 10 +++++- tests/testthat/test-lm-robust_margins.R | 8 +++-- tests/testthat/test-modelsummary.R | 18 ++++++----- tests/testthat/test-starprep.R | 2 + 26 files changed, 129 insertions(+), 101 deletions(-)
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building
simulation program 'EnergyPlus'(<https://energyplus.net>), which
enables programmatic navigation, modification of 'EnergyPlus' models
and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuan.jia@bears-berkeley.sg>
Diff between eplusr versions 0.13.0 dated 2020-08-28 and 0.14.0 dated 2021-01-07
DESCRIPTION | 15 MD5 | 106 - NEWS.md | 2187 ++++++++++++++++++++------------------- R/constants.R | 10 R/epw.R | 38 R/geom.R | 34 R/group.R | 152 +- R/idd.R | 2 R/idf.R | 107 + R/idfobj-sch.R | 9 R/idfobj.R | 10 R/impl-epw.R | 220 +++ R/impl-geom.R | 11 R/impl-idf.R | 107 + R/impl-idfobj-sch.R | 2 R/impl-idfobj.R | 2 R/impl-sql.R | 394 ------- R/install.R | 36 R/job.R | 52 R/param.R | 37 R/parse.R | 14 R/run.R | 31 R/sql.R | 2 R/sysdata.rda |binary R/transition.R | 797 +++++++++++++- R/validate.R | 2 R/viewer.R | 2 README.md | 61 - inst/CITATION | 2 man/EplusGroupJob.Rd | 41 man/EplusJob.Rd | 15 man/Epw.Rd | 17 man/Idd.Rd | 2 man/Idf.Rd | 13 man/IdfGeometry.Rd | 2 man/IdfObject.Rd | 10 man/IdfViewer.Rd | 2 man/ParametricJob.Rd | 15 man/expand_idf_dots_object.Rd | 2 man/figures/logo.svg | 954 ++++++++--------- man/run_model.Rd | 3 tests/testthat/test-epw.R | 18 tests/testthat/test-geom.R | 2 tests/testthat/test-group.R | 18 tests/testthat/test-idf.R | 2 tests/testthat/test-idfobj-sch.R | 4 tests/testthat/test-impl-epw.R | 21 tests/testthat/test-impl-idf.R | 5 tests/testthat/test-install.R | 6 tests/testthat/test-param.R | 4 tests/testthat/test-run.R | 7 tests/testthat/test-sql.R | 283 ----- tests/testthat/test-transition.R | 530 +++++++-- tests/testthat/test-utils.R | 2 54 files changed, 3705 insertions(+), 2715 deletions(-)
Title: Diffs for R Objects
Description: Generate a colorized diff of two R objects for an intuitive
visualization of their differences.
Author: Brodie Gaslam [aut, cre],
Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff
Algorithm)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between diffobj versions 0.3.2 dated 2020-10-05 and 0.3.3 dated 2021-01-07
diffobj-0.3.2/diffobj/inst/doc/metacomp.R |only diffobj-0.3.2/diffobj/inst/doc/metacomp.Rmd |only diffobj-0.3.2/diffobj/inst/doc/metacomp.html |only diffobj-0.3.2/diffobj/tests/run.R |only diffobj-0.3.2/diffobj/tests/scaling.R |only diffobj-0.3.2/diffobj/tests/testthat |only diffobj-0.3.2/diffobj/vignettes/metacomp.Rmd |only diffobj-0.3.3/diffobj/DESCRIPTION | 8 diffobj-0.3.3/diffobj/MD5 | 532 ++++++++--------- diffobj-0.3.3/diffobj/NEWS.md | 8 diffobj-0.3.3/diffobj/R/capt.R | 2 diffobj-0.3.3/diffobj/R/check.R | 2 diffobj-0.3.3/diffobj/R/core.R | 2 diffobj-0.3.3/diffobj/R/diff.R | 2 diffobj-0.3.3/diffobj/R/finalizer.R | 2 diffobj-0.3.3/diffobj/R/get.R | 2 diffobj-0.3.3/diffobj/R/guides.R | 2 diffobj-0.3.3/diffobj/R/html.R | 2 diffobj-0.3.3/diffobj/R/hunks.R | 9 diffobj-0.3.3/diffobj/R/layout.R | 2 diffobj-0.3.3/diffobj/R/misc.R | 2 diffobj-0.3.3/diffobj/R/myerssimple.R | 2 diffobj-0.3.3/diffobj/R/pager.R | 2 diffobj-0.3.3/diffobj/R/rdiff.R | 2 diffobj-0.3.3/diffobj/R/rds.R | 2 diffobj-0.3.3/diffobj/R/s4.R | 9 diffobj-0.3.3/diffobj/R/set.R | 2 diffobj-0.3.3/diffobj/R/styles.R | 2 diffobj-0.3.3/diffobj/R/subset.R | 2 diffobj-0.3.3/diffobj/R/summmary.R | 2 diffobj-0.3.3/diffobj/R/system.R | 2 diffobj-0.3.3/diffobj/R/text.R | 2 diffobj-0.3.3/diffobj/R/tochar.R | 2 diffobj-0.3.3/diffobj/R/trim.R | 2 diffobj-0.3.3/diffobj/R/word.R | 2 diffobj-0.3.3/diffobj/README.md | 19 diffobj-0.3.3/diffobj/build/vignette.rds |binary diffobj-0.3.3/diffobj/inst/COPYRIGHTS | 2 diffobj-0.3.3/diffobj/inst/doc/diffobj.Rmd | 2 diffobj-0.3.3/diffobj/inst/doc/diffobj.html | 12 diffobj-0.3.3/diffobj/inst/doc/embed.html | 10 diffobj-0.3.3/diffobj/inst/script/diffobj.js | 2 diffobj-0.3.3/diffobj/src/diff.c | 2 diffobj-0.3.3/diffobj/src/diff.h | 2 diffobj-0.3.3/diffobj/tests/_helper |only diffobj-0.3.3/diffobj/tests/startup.Rs |only diffobj-0.3.3/diffobj/tests/test-atomic.R |only diffobj-0.3.3/diffobj/tests/test-atomic.Rout.save |only diffobj-0.3.3/diffobj/tests/test-banner.R |only diffobj-0.3.3/diffobj/tests/test-banner.Rout.save |only diffobj-0.3.3/diffobj/tests/test-capture.R |only diffobj-0.3.3/diffobj/tests/test-capture.Rout.save |only diffobj-0.3.3/diffobj/tests/test-check.R |only diffobj-0.3.3/diffobj/tests/test-check.Rout.save |only diffobj-0.3.3/diffobj/tests/test-context.R |only diffobj-0.3.3/diffobj/tests/test-context.Rout.save |only diffobj-0.3.3/diffobj/tests/test-core.R |only diffobj-0.3.3/diffobj/tests/test-core.Rout.save |only diffobj-0.3.3/diffobj/tests/test-diffChr.R |only diffobj-0.3.3/diffobj/tests/test-diffChr.Rout.save |only diffobj-0.3.3/diffobj/tests/test-diffDeparse.R |only diffobj-0.3.3/diffobj/tests/test-diffDeparse.Rout.save |only diffobj-0.3.3/diffobj/tests/test-diffObj.R |only diffobj-0.3.3/diffobj/tests/test-diffObj.Rout.save |only diffobj-0.3.3/diffobj/tests/test-diffPrint.R |only diffobj-0.3.3/diffobj/tests/test-diffPrint.Rout.save |only diffobj-0.3.3/diffobj/tests/test-diffStr.R |only diffobj-0.3.3/diffobj/tests/test-diffStr.Rout.save |only diffobj-0.3.3/diffobj/tests/test-file.R |only diffobj-0.3.3/diffobj/tests/test-file.Rout.save |only diffobj-0.3.3/diffobj/tests/test-guide.R |only diffobj-0.3.3/diffobj/tests/test-guide.Rout.save |only diffobj-0.3.3/diffobj/tests/test-html.R |only diffobj-0.3.3/diffobj/tests/test-html.Rout.save |only diffobj-0.3.3/diffobj/tests/test-limit.R |only diffobj-0.3.3/diffobj/tests/test-limit.Rout.save |only diffobj-0.3.3/diffobj/tests/test-methods.R |only diffobj-0.3.3/diffobj/tests/test-methods.Rout.save |only diffobj-0.3.3/diffobj/tests/test-misc.R |only diffobj-0.3.3/diffobj/tests/test-misc.Rout.save |only diffobj-0.3.3/diffobj/tests/test-pager.R |only diffobj-0.3.3/diffobj/tests/test-pager.Rout.save |only diffobj-0.3.3/diffobj/tests/test-rdiff.R |only diffobj-0.3.3/diffobj/tests/test-rdiff.Rout.save |only diffobj-0.3.3/diffobj/tests/test-s4.R |only diffobj-0.3.3/diffobj/tests/test-s4.Rout.save |only diffobj-0.3.3/diffobj/tests/test-scaling.R |only diffobj-0.3.3/diffobj/tests/test-ses.R |only diffobj-0.3.3/diffobj/tests/test-ses.Rout.save |only diffobj-0.3.3/diffobj/tests/test-style.R |only diffobj-0.3.3/diffobj/tests/test-style.Rout.save |only diffobj-0.3.3/diffobj/tests/test-subset.R |only diffobj-0.3.3/diffobj/tests/test-subset.Rout.save |only diffobj-0.3.3/diffobj/tests/test-summary.R |only diffobj-0.3.3/diffobj/tests/test-summary.Rout.save |only diffobj-0.3.3/diffobj/tests/test-text.R |only diffobj-0.3.3/diffobj/tests/test-text.Rout.save |only diffobj-0.3.3/diffobj/tests/test-trim.R |only diffobj-0.3.3/diffobj/tests/test-trim.Rout.save |only diffobj-0.3.3/diffobj/tests/test-warnings.R |only diffobj-0.3.3/diffobj/tests/test-warnings.Rout.save |only diffobj-0.3.3/diffobj/tests/zz-test-check.R |only diffobj-0.3.3/diffobj/vignettes/diffobj.Rmd | 2 103 files changed, 361 insertions(+), 304 deletions(-)
Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2020) <arXiv:2101.00086>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between calculus versions 0.2.1 dated 2020-03-23 and 0.3.0 dated 2021-01-07
calculus-0.2.1/calculus/R/det.R |only calculus-0.2.1/calculus/R/inverse.R |only calculus-0.2.1/calculus/R/kronecker.R |only calculus-0.2.1/calculus/R/levicivita.R |only calculus-0.2.1/calculus/R/trace.R |only calculus-0.2.1/calculus/R/utilities.R |only calculus-0.2.1/calculus/man/det.Rd |only calculus-0.2.1/calculus/man/diag.Rd |only calculus-0.2.1/calculus/man/grapes-matrix-grapes.Rd |only calculus-0.2.1/calculus/man/inverse.Rd |only calculus-0.2.1/calculus/man/kronecker.Rd |only calculus-0.2.1/calculus/man/levicivita.Rd |only calculus-0.2.1/calculus/man/trace.Rd |only calculus-0.3.0/calculus/DESCRIPTION | 23 calculus-0.3.0/calculus/MD5 | 158 +- calculus-0.3.0/calculus/NAMESPACE | 23 calculus-0.3.0/calculus/NEWS.md | 10 calculus-0.3.0/calculus/R/contraction.R |only calculus-0.3.0/calculus/R/delta.R |only calculus-0.3.0/calculus/R/derivative.R | 393 ++--- calculus-0.3.0/calculus/R/einstein.R | 115 - calculus-0.3.0/calculus/R/epsilon.R |only calculus-0.3.0/calculus/R/evaluate.R | 139 - calculus-0.3.0/calculus/R/hermite.R | 81 - calculus-0.3.0/calculus/R/integral.R | 247 +-- calculus-0.3.0/calculus/R/mxdet.R |only calculus-0.3.0/calculus/R/mxinv.R |only calculus-0.3.0/calculus/R/mxtr.R |only calculus-0.3.0/calculus/R/ode.R |only calculus-0.3.0/calculus/R/operators.R | 1322 ++++++++++------- calculus-0.3.0/calculus/R/package.R | 9 calculus-0.3.0/calculus/R/partitions.R | 29 calculus-0.3.0/calculus/R/taylor.R | 86 - calculus-0.3.0/calculus/R/utils.R |only calculus-0.3.0/calculus/README.md | 897 ----------- calculus-0.3.0/calculus/build |only calculus-0.3.0/calculus/inst |only calculus-0.3.0/calculus/man/c2e.Rd | 29 calculus-0.3.0/calculus/man/calculus-package.Rd |only calculus-0.3.0/calculus/man/contraction.Rd |only calculus-0.3.0/calculus/man/cross.Rd | 30 calculus-0.3.0/calculus/man/curl.Rd | 120 + calculus-0.3.0/calculus/man/delta.Rd |only calculus-0.3.0/calculus/man/derivative.Rd | 144 + calculus-0.3.0/calculus/man/diagonal.Rd |only calculus-0.3.0/calculus/man/divergence.Rd | 102 - calculus-0.3.0/calculus/man/e2c.Rd | 29 calculus-0.3.0/calculus/man/einstein.Rd | 52 calculus-0.3.0/calculus/man/epsilon.Rd |only calculus-0.3.0/calculus/man/evaluate.Rd | 88 - calculus-0.3.0/calculus/man/figures |only calculus-0.3.0/calculus/man/gradient.Rd | 102 - calculus-0.3.0/calculus/man/grapes-diff-grapes.Rd | 30 calculus-0.3.0/calculus/man/grapes-div-grapes.Rd | 30 calculus-0.3.0/calculus/man/grapes-dot-grapes.Rd | 31 calculus-0.3.0/calculus/man/grapes-inner-grapes.Rd | 34 calculus-0.3.0/calculus/man/grapes-kronecker-grapes.Rd | 28 calculus-0.3.0/calculus/man/grapes-outer-grapes.Rd | 32 calculus-0.3.0/calculus/man/grapes-prod-grapes.Rd | 30 calculus-0.3.0/calculus/man/grapes-sum-grapes.Rd | 30 calculus-0.3.0/calculus/man/hermite.Rd | 54 calculus-0.3.0/calculus/man/hessian.Rd | 91 - calculus-0.3.0/calculus/man/index.Rd | 45 calculus-0.3.0/calculus/man/integral.Rd | 137 - calculus-0.3.0/calculus/man/jacobian.Rd |only calculus-0.3.0/calculus/man/laplacian.Rd | 106 - calculus-0.3.0/calculus/man/mx.Rd |only calculus-0.3.0/calculus/man/mxdet.Rd |only calculus-0.3.0/calculus/man/mxinv.Rd |only calculus-0.3.0/calculus/man/mxtr.Rd |only calculus-0.3.0/calculus/man/ode.Rd |only calculus-0.3.0/calculus/man/partitions.Rd | 25 calculus-0.3.0/calculus/man/taylor.Rd | 64 calculus-0.3.0/calculus/man/wrap.Rd | 26 calculus-0.3.0/calculus/src/calculus.cpp | 499 +++--- calculus-0.3.0/calculus/tests |only calculus-0.3.0/calculus/vignettes |only 77 files changed, 2858 insertions(+), 2662 deletions(-)
Title: A Bootstrap-Based Heterogeneity Test for Meta-Analysis
Description: Implements a bootstrap-based heterogeneity test for standardized mean differences (d), Fisher-transformed Pearson's correlations (r), and natural-logarithm-transformed odds ratio (or) in meta-analysis studies. Depending on the presence of moderators, this Monte Carlo based test can be implemented in the random- or mixed-effects model. This package uses rma() function from the R package 'metafor' to obtain parameter estimates and likelihoods, so installation of R package 'metafor' is required. This approach refers to the studies of Anscombe (1956) <doi:10.2307/2332926>, Haldane (1940) <doi:10.2307/2332614>, Hedges (1981) <doi:10.3102/10769986006002107>, Hedges & Olkin (1985, ISBN:978-0123363800), Silagy, Lancaster, Stead, Mant, & Fowler (2004) <doi:10.1002/14651858.CD000146.pub2>, Viechtbauer (2010) <doi:10.18637/jss.v036.i03>, and Zuckerman (1994, ISBN:978-0521432009).
Author: Ge Jiang [aut, cre],
Han Du [aut],
Zijun Ke [ctb]
Maintainer: Ge Jiang <gejiang2@illinois.edu>
Diff between boot.heterogeneity versions 0.1.1 dated 2020-09-21 and 1.1.2 dated 2021-01-07
DESCRIPTION | 10 MD5 | 32 - NAMESPACE | 3 R/Internal.R | 113 +++- R/boot.d.R | 93 ++- R/boot.fcor.R | 121 +++-- R/boot.lnOR.R | 67 +- README.md | 5 build/vignette.rds |binary inst/doc/boot.heterogeneity.R | 48 +- inst/doc/boot.heterogeneity.Rmd | 136 +++-- inst/doc/boot.heterogeneity.html | 929 ++++++++++++++++++++++----------------- man/boot.d.Rd | 32 - man/boot.fcor.Rd | 32 - man/boot.lnOR.Rd | 34 - tests/testthat/test_bt.R | 6 vignettes/boot.heterogeneity.Rmd | 136 +++-- 17 files changed, 1101 insertions(+), 696 deletions(-)
More information about boot.heterogeneity at CRAN
Permanent link
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for: 1. single response multiple regression, see Papageorgiou, G. (2018) <doi: 10.32614/RJ-2018-069>, 2. multivariate response multiple regression, with nonparametric models for the means, the variances and the correlation matrix, with variable selection, see Papageorgiou, G. and Marshall, B. C. (2020) <doi: 10.1080/10618600.2020.1739534>, 3. joint mean-covariance models for multivariate responses, see Papageorgiou, G. (2020), and 4.Dirichlet process mixtures, see Papageorgiou, G. (2019) <doi: 10.1111/anzs.12273>.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.1.4 dated 2020-05-08 and 2.1.5 dated 2021-01-07
BNSP-2.1.4/BNSP/src/LongMultWish.c |only BNSP-2.1.5/BNSP/DESCRIPTION | 15 +- BNSP-2.1.5/BNSP/MD5 | 39 +++--- BNSP-2.1.5/BNSP/NAMESPACE | 5 BNSP-2.1.5/BNSP/R/bnpLongMulti.R | 201 +++++++++++++++++++++++++++++++----- BNSP-2.1.5/BNSP/R/bnpMulti.R | 14 +- BNSP-2.1.5/BNSP/R/mvrm.R | 5 BNSP-2.1.5/BNSP/R/plot.R | 37 ++++-- BNSP-2.1.5/BNSP/data/ami.rda |only BNSP-2.1.5/BNSP/data/simD2.rda |only BNSP-2.1.5/BNSP/inst/CITATION | 12 +- BNSP-2.1.5/BNSP/man/BNSP-package.Rd | 12 +- BNSP-2.1.5/BNSP/man/ami.rd |only BNSP-2.1.5/BNSP/man/lmrm.Rd |only BNSP-2.1.5/BNSP/man/mvrm.Rd | 7 - BNSP-2.1.5/BNSP/man/simD.rd | 2 BNSP-2.1.5/BNSP/man/simD2.rd |only BNSP-2.1.5/BNSP/src/LongMult.c | 82 +++++++------- BNSP-2.1.5/BNSP/src/LongMultG.c | 45 ++++---- BNSP-2.1.5/BNSP/src/LongMultGV.c | 35 +++--- BNSP-2.1.5/BNSP/src/OneResLtnt.c | 5 BNSP-2.1.5/BNSP/src/sampling.h | 66 +++++++++++ BNSP-2.1.5/BNSP/src/spec.BCM.h | 8 - BNSP-2.1.5/BNSP/src/test.c |only 24 files changed, 420 insertions(+), 170 deletions(-)
Title: Create Area-Proportional Venn Diagrams from Biological Lists
Description: Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen et al. (2008) <doi:10.1186/1471-2164-9-488>.
Author: Tim Hulsen [aut, cre] (<https://orcid.org/0000-0002-0208-8443>)
Maintainer: Tim Hulsen <thulsen@gmail.com>
Diff between BioVenn versions 1.1.0 dated 2020-11-20 and 1.1.1 dated 2021-01-07
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/draw.venn.R | 22 ++-------------------- 3 files changed, 7 insertions(+), 25 deletions(-)
Title: Sparse Matrix Format with Data on Disk
Description: Provides a sparse matrix format with data stored on disk, to be
used in both R and C++. This is intended for more efficient use of sparse
data in C++ and also when parallelizing, since data on disk does not need
copying. Only a limited number of features will be implemented. For now,
conversion can be performed from a 'dgCMatrix' or a 'dsCMatrix' from R
package 'Matrix'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigsparser versions 0.4.0 dated 2020-08-24 and 0.4.1 dated 2021-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/include/bigsparser/EigenMatrixReplacement.h | 3 ++- inst/include/bigsparser/SFBM.h | 10 +++++++++- 4 files changed, 17 insertions(+), 8 deletions(-)
Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine.
Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate
models (counterfactual patient-level quantities, for example the individual treatment effect),
(3) subgroup identification models (find subsets of patients with similar treatment effects),
and (4) parameter estimation and inference (for the overall population and discovered subgroups).
These tools can directly feed into stratified medicine algorithms including PRISM
(patient response identifiers for stratified medicine; Jemielita and Mehrotra 2019
<arXiv:1912.03337>. PRISM is a flexible and general framework which accepts
user-created models/functions. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>
Diff between StratifiedMedicine versions 1.0.2 dated 2020-08-03 and 1.0.3 dated 2021-01-07
DESCRIPTION | 8 MD5 | 66 - NEWS.md | 4 R/PRISM.R | 14 R/filter_train.R | 2 R/learners.R | 15 R/ple_train.R | 17 R/plot.R | 21 R/plot_dependence.R | 29 R/plot_forest.R | 2 R/plot_ggparty.R | 56 - R/plot_ple.R | 27 R/submod_train.R | 2 README.md | 15 build/partial.rdb |only build/vignette.rds |binary inst/doc/SM_PRISM.R | 349 +++---- inst/doc/SM_PRISM.Rmd | 13 inst/doc/SM_PRISM.html | 1783 +++++++++++++++++------------------- inst/doc/SM_User_Models.R | 344 +++--- inst/doc/SM_User_Models.html | 1084 ++++++++++----------- man/PRISM.Rd | 9 man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/figures/README-example-6.png |binary man/figures/README-example-7.png |binary man/filter_train.Rd | 2 man/ple_train.Rd | 9 man/plot.PRISM.Rd | 17 man/submod_train.Rd | 2 tests/testthat/test-ple_waterfall.R |only vignettes/SM_PRISM.Rmd | 13 35 files changed, 2001 insertions(+), 1902 deletions(-)
More information about StratifiedMedicine at CRAN
Permanent link
Title: Query Random User Data from the Random User Generator API
Description: Generate random user data from the Random User Generator API.
For more information, see <https://randomuser.me/>.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between radous versions 0.1.0 dated 2020-11-05 and 0.1.1 dated 2021-01-07
DESCRIPTION | 8 MD5 | 8 R/get_data.R | 41 +++ README.md | 408 +++++++++++++++++++++--------------- tests/testthat/test-test_get_data.R | 7 5 files changed, 288 insertions(+), 184 deletions(-)
Title: Efficient Network Enrichment Analysis Test
Description: Includes functions and examples to compute NEAT, the Network Enrichment Analysis Test described in Signorelli et al. (2016, <DOI:10.1186/s12859-016-1203-6>).
Author: Mirko Signorelli [aut, cre, cph]
(<https://orcid.org/0000-0002-8102-3356>),
Veronica Vinciotti [ctb],
Ernst Wit [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between neat versions 1.2.2 dated 2020-10-22 and 1.2.3 dated 2021-01-07
DESCRIPTION | 18 +++--- MD5 | 14 ++-- build/vignette.rds |binary inst/CITATION | 4 - inst/NEWS.md | 7 ++ inst/doc/neat.Rmd | 6 +- inst/doc/neat.html | 156 ++++++++++++++++++++++++++++++++++------------------- vignettes/neat.Rmd | 6 +- 8 files changed, 134 insertions(+), 77 deletions(-)