Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.26.0 dated 2019-06-29 and 0.26.1 dated 2019-06-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 7 +++++++ src/libgit2/src/xdiff/xdiffi.c | 2 +- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
('ODE', 'DAE', 'DDE')
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations ('ODE'), of
partial differential equations ('PDE'), of differential
algebraic equations ('DAE'), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK'
collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk'
and a C-implementation of solvers of the 'Runge-Kutta' family with
fixed or variable time steps. The package contains routines
designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D
partial differential equations ('PDE') that have been converted
to 'ODEs' by numerical differencing.
Author: Karline Soetaert [aut],
Thomas Petzoldt [aut, cre],
R. Woodrow Setzer [aut],
odepack authors [cph]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.21 dated 2018-05-09 and 1.23 dated 2019-06-29
DESCRIPTION | 8 MD5 | 38 - NEWS | 9 R/daspk.R | 1112 +++++++++++++++++++++++----------------------- R/lsoda.R | 492 ++++++++++---------- R/lsodar.R | 4 R/lsode.R | 652 +++++++++++++------------- R/radau.R | 644 +++++++++++++------------- R/vode.R | 4 R/zvode.R | 4 build/vignette.rds |binary data/ccl4data.rda |binary inst/CITATION | 2 inst/doc/compiledCode.pdf |binary inst/doc/deSolve.pdf |binary man/deSolve.Rd | 310 ++++++------ man/plot.deSolve.Rd | 11 src/errmsg.f | 41 - src/lags.c | 2 src/rprintf.c | 20 20 files changed, 1661 insertions(+), 1692 deletions(-)
Title: Efficient Computations of Standard Clustering Comparison
Measures
Description: Implements an efficient O(n) algorithm based on bucket-sorting for
fast computation of standard clustering comparison measures. Available measures
include adjusted Rand index (ARI), normalized information distance (NID),
normalized mutual information (NMI), adjusted mutual information (AMI),
normalized variation information (NVI) and entropy, as described in Vinh et al (2009)
<doi:10.1145/1553374.1553511>.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
Guillem Rigaill [aut],
Valentin Dervieux [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inra.fr>
Diff between aricode versions 0.1.1 dated 2018-05-02 and 0.1.2 dated 2019-06-29
aricode-0.1.1/aricode/inst/tests |only aricode-0.1.2/aricode/DESCRIPTION | 13 ++++++----- aricode-0.1.2/aricode/MD5 | 28 +++++++++++++----------- aricode-0.1.2/aricode/NAMESPACE | 1 aricode-0.1.2/aricode/NEWS | 3 ++ aricode-0.1.2/aricode/R/RcppExports.R | 4 +++ aricode-0.1.2/aricode/R/aricode-package.R | 3 +- aricode-0.1.2/aricode/R/aricode.R | 33 +++++++++++++++++++++++++++-- aricode-0.1.2/aricode/inst/check_speed.R |only aricode-0.1.2/aricode/man/AMI.Rd |only aricode-0.1.2/aricode/man/aricode.Rd | 3 +- aricode-0.1.2/aricode/man/entropy.Rd | 2 - aricode-0.1.2/aricode/src/RcppExports.cpp | 13 +++++++++++ aricode-0.1.2/aricode/src/aricode.cpp | 34 ++++++++++++++++++++++++++++++ aricode-0.1.2/aricode/tests |only 15 files changed, 113 insertions(+), 24 deletions(-)
Title: Phylogenies with Annotations
Description: Functions to read and write APE-compatible phylogenetic
trees in NEXUS and Newick formats, while preserving annotations.
Author: Daniel Beer [aut], Anusha Beer [aut]
Maintainer: Daniel Beer <dlbeer@gmail.com>
Diff between phylotate versions 1.2 dated 2018-01-29 and 1.3 dated 2019-06-29
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS | 6 + R/format.R | 9 +- R/mbattrs.R | 30 ++++---- R/newick.R | 160 +++++++++++++++++++++++++------------------- R/nexus.R | 178 ++++++++++++++++++++++++------------------------- R/tokenize.R | 70 +++++++++---------- man/mb_attrs.Rd | 2 man/print_annotated.Rd | 8 +- man/write_annotated.Rd | 8 +- tests/round_trip.R | 66 ++++++++++++------ 12 files changed, 316 insertions(+), 251 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.2 dated 2019-03-09 and 5.5.3 dated 2019-06-29
dtwclust-5.5.2/dtwclust/inst/doc/parallelization-considerations.R |only dtwclust-5.5.2/dtwclust/inst/doc/timing-experiments.R |only dtwclust-5.5.3/dtwclust/DESCRIPTION | 12 dtwclust-5.5.3/dtwclust/MD5 | 89 dtwclust-5.5.3/dtwclust/NAMESPACE | 1 dtwclust-5.5.3/dtwclust/R/CENTROIDS-shape-extraction.R | 2 dtwclust-5.5.3/dtwclust/R/CLUSTERING-compare-clusterings.R | 1964 ++++---- dtwclust-5.5.3/dtwclust/R/CLUSTERING-repeat-clustering.R | 257 - dtwclust-5.5.3/dtwclust/R/CLUSTERING-tsclust-controls.R | 3 dtwclust-5.5.3/dtwclust/R/GENERICS-cvi.R | 4 dtwclust-5.5.3/dtwclust/R/S4-TSClusters-methods.R | 2278 +++++----- dtwclust-5.5.3/dtwclust/R/pkg.R | 346 - dtwclust-5.5.3/dtwclust/build/vignette.rds |binary dtwclust-5.5.3/dtwclust/data/dtwclustTimings.rda |binary dtwclust-5.5.3/dtwclust/inst/NEWS.Rd | 31 dtwclust-5.5.3/dtwclust/inst/doc/dtwclust.Rnw | 10 dtwclust-5.5.3/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-5.5.3/dtwclust/inst/doc/parallelization-considerations.Rmd | 4 dtwclust-5.5.3/dtwclust/inst/doc/parallelization-considerations.html | 7 dtwclust-5.5.3/dtwclust/inst/doc/timing-experiments.Rmd | 12 dtwclust-5.5.3/dtwclust/inst/doc/timing-experiments.html | 47 dtwclust-5.5.3/dtwclust/man/cvi.Rd | 4 dtwclust-5.5.3/dtwclust/man/dtwclust-package.Rd | 1 dtwclust-5.5.3/dtwclust/man/shape_extraction.Rd | 2 dtwclust-5.5.3/dtwclust/man/tsclust-controls.Rd | 3 dtwclust-5.5.3/dtwclust/src/Makevars | 1 dtwclust-5.5.3/dtwclust/src/Makevars.win | 5 dtwclust-5.5.3/dtwclust/src/centroids/dba.cpp | 67 dtwclust-5.5.3/dtwclust/src/centroids/sdtw-cent.cpp | 46 dtwclust-5.5.3/dtwclust/src/distmat/distmat.cpp | 6 dtwclust-5.5.3/dtwclust/src/distmat/distmat.h | 14 dtwclust-5.5.3/dtwclust/src/distmat/dtw-lb.cpp | 32 dtwclust-5.5.3/dtwclust/src/distmat/fillers.cpp | 85 dtwclust-5.5.3/dtwclust/src/tadpole/tadpole.cpp | 68 dtwclust-5.5.3/dtwclust/src/utils/ParallelWorker.cpp |only dtwclust-5.5.3/dtwclust/src/utils/ParallelWorker.h |only dtwclust-5.5.3/dtwclust/src/utils/utils.cpp | 31 dtwclust-5.5.3/dtwclust/tests/testthat.R | 2 dtwclust-5.5.3/dtwclust/tests/testthat/helper-all.R | 2 dtwclust-5.5.3/dtwclust/tests/testthat/setup-rngkind.R |only dtwclust-5.5.3/dtwclust/tests/testthat/system/invalid-inputs.R | 338 - dtwclust-5.5.3/dtwclust/tests/testthat/test-01-unit.R | 16 dtwclust-5.5.3/dtwclust/tests/testthat/test-02-integration.R | 10 dtwclust-5.5.3/dtwclust/tests/testthat/test-04-system.R | 26 dtwclust-5.5.3/dtwclust/vignettes/REFERENCES.bib | 20 dtwclust-5.5.3/dtwclust/vignettes/dtwclust.Rnw | 10 dtwclust-5.5.3/dtwclust/vignettes/parallelization-considerations.Rmd | 4 dtwclust-5.5.3/dtwclust/vignettes/timing-experiments.Rmd | 12 48 files changed, 2987 insertions(+), 2885 deletions(-)
Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected
Areas (WDPA). Data is obtained from Protected Planet
<http://protectedplanet.net>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between wdpar versions 0.0.3 dated 2019-04-09 and 1.0.0 dated 2019-06-29
DESCRIPTION | 15 ++++++++------- MD5 | 28 ++++++++++++++-------------- NEWS.md | 9 +++++++++ R/wdpa_clean.R | 2 +- R/wdpa_fetch.R | 2 +- R/wdpa_url.R | 2 +- README.md | 7 +++++-- inst/CITATION | 2 +- inst/doc/wdpar.Rmd | 4 ++-- inst/doc/wdpar.html | 11 ++++++----- tests/testthat/test_internal.R | 4 ++-- tests/testthat/test_wdpa_clean.R | 12 ++++++------ tests/testthat/test_wdpa_fetch.R | 4 ++-- tests/testthat/test_wdpa_read.R | 4 ++-- vignettes/wdpar.Rmd | 4 ++-- 15 files changed, 62 insertions(+), 48 deletions(-)
Title: Read, Validate, Analyze, and Map Files in the General Transit
Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Flavio Poletti [aut],
Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Mark Padgham [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb],
Kearey Smith [ctb],
Dave Vautin [ctb],
Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>
Diff between tidytransit versions 0.5.0 dated 2019-05-20 and 0.5.1 dated 2019-06-29
DESCRIPTION | 6 MD5 | 39 ++-- NAMESPACE | 2 R/import.R | 93 +---------- R/raptor.R | 11 - R/summary.R |only R/utils.R | 3 build/vignette.rds |binary inst/doc/frequency.Rmd | 14 + inst/doc/frequency.html | 190 ++++++++++------------- inst/doc/introduction.R | 3 inst/doc/introduction.Rmd | 12 + inst/doc/introduction.html | 110 ++++++------- inst/doc/servicepatterns.html | 302 +++++++++++++++++--------------------- inst/doc/timetable.html | 226 ++++++++++++---------------- inst/extdata/sample-feed-bom.zip |only man/summary.gtfs.Rd |only tests/testthat/test-import-gtfs.R | 9 + tests/testthat/test-raptor.R | 21 ++ tests/testthat/test-utils.R | 24 +-- vignettes/frequency.Rmd | 14 + vignettes/introduction.Rmd | 12 + 22 files changed, 508 insertions(+), 583 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns
of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.4.1 dated 2019-05-28 and 1.4.2 dated 2019-06-29
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 7 +++++++ R/dim.R | 9 +++++++-- R/type-sum.R | 3 ++- build/pillar.pdf |binary tests/testthat/test-dim.R |only 7 files changed, 25 insertions(+), 11 deletions(-)
Title: High Precise Measurement of R Expressions Execution Time
Description: Provides infrastructure to accurately measure and compare
the execution time of R expressions.
Author: Artem Klevtsov [aut, cre],
Anton Antonov [ctb],
Philipp Upravitelev [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between benchr versions 0.2.2 dated 2018-07-15 and 0.2.3 dated 2019-06-29
benchr-0.2.2/benchr/tests/testthat |only benchr-0.2.2/benchr/tests/testthat.R |only benchr-0.2.3/benchr/DESCRIPTION | 10 +- benchr-0.2.3/benchr/MD5 | 58 +++++++------- benchr-0.2.3/benchr/R/benchmark.R | 63 ++++++++------- benchr-0.2.3/benchr/R/benchr-package.R | 9 +- benchr-0.2.3/benchr/R/boxplot.R | 92 ++++++++++++---------- benchr-0.2.3/benchr/R/mean.R | 49 ++++++----- benchr-0.2.3/benchr/R/order.R | 16 +-- benchr-0.2.3/benchr/R/plot.R | 73 +++++++++-------- benchr-0.2.3/benchr/R/print.R | 72 +++++++++-------- benchr-0.2.3/benchr/R/summary.R | 25 +++--- benchr-0.2.3/benchr/R/units.R | 111 ++++++++++++++------------- benchr-0.2.3/benchr/R/utils.R | 63 +++++++-------- benchr-0.2.3/benchr/R/zzz.R | 2 benchr-0.2.3/benchr/inst |only benchr-0.2.3/benchr/man/benchmark.Rd | 1 benchr-0.2.3/benchr/man/benchr.Rd | 8 - benchr-0.2.3/benchr/man/boxplot.benchmark.Rd | 7 - benchr-0.2.3/benchr/man/mean.benchmark.Rd | 7 - benchr-0.2.3/benchr/man/plot.benchmark.Rd | 10 +- benchr-0.2.3/benchr/man/print.benchmark.Rd | 14 +-- benchr-0.2.3/benchr/man/summary.benchmark.Rd | 7 - benchr-0.2.3/benchr/tests/tinytest.R |only 24 files changed, 374 insertions(+), 323 deletions(-)
Title: Client for the News API
Description: Interface to gather news from the 'News API', based on a multilevel query <https://newsapi.org/>. A personal API key is required.
Author: Preu Frie [aut, pro],
Buhl Yannik [aut, cre],
Schulze Lars [aut],
Dix Jan [aut, pro]
Maintainer: Buhl Yannik <ybuhl@posteo.de>
Diff between newsanchor versions 0.1.0 dated 2019-03-05 and 0.1.1 dated 2019-06-29
newsanchor-0.1.0/newsanchor/inst/doc/scrape-nyt.R |only newsanchor-0.1.0/newsanchor/inst/doc/scrape-nyt.Rmd |only newsanchor-0.1.0/newsanchor/inst/doc/scrape-nyt.html |only newsanchor-0.1.0/newsanchor/vignettes/scrape-nyt.Rmd |only newsanchor-0.1.1/newsanchor/DESCRIPTION | 10 newsanchor-0.1.1/newsanchor/MD5 | 24 newsanchor-0.1.1/newsanchor/NAMESPACE | 1 newsanchor-0.1.1/newsanchor/NEWS.md | 7 newsanchor-0.1.1/newsanchor/R/set_api_key.R | 14 newsanchor-0.1.1/newsanchor/build/vignette.rds |binary newsanchor-0.1.1/newsanchor/inst/doc/usage-newsanchor.html | 399 +++++++--- newsanchor-0.1.1/newsanchor/man/set_api_key.Rd | 8 newsanchor-0.1.1/newsanchor/tests/testthat.R | 2 newsanchor-0.1.1/newsanchor/tests/testthat/test_get_everything.R | 2 newsanchor-0.1.1/newsanchor/tests/testthat/test_set_api_key.R | 16 15 files changed, 344 insertions(+), 139 deletions(-)
Title: Fast Gaussian Process Computation Using Vecchia's Approximation
Description: Functions for fitting and doing predictions with
Gaussian process models using Vecchia's (1988) approximation.
Package also includes functions for reordering input locations,
finding ordered nearest neighbors (with help from 'FNN' package),
grouping operations, and conditional simulations.
Covariance functions for spatial and spatial-temporal data
on Euclidean domains and spheres are provided. The original
approximation is due to Vecchia (1988)
<http://www.jstor.org/stable/2345768>, and the reordering and
grouping methods are from Guinness (2018)
<doi:10.1080/00401706.2018.1437476>.
Model fitting employs a Fisher scoring algorithm described
in Guinness (2019) <arXiv:1905.08374>.
Author: Joseph Guinness [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Joseph Guinness <joeguinness@gmail.com>
Diff between GpGp versions 0.1.1 dated 2019-01-30 and 0.2.0 dated 2019-06-29
GpGp-0.1.1/GpGp/R/profile_likelihoods.R |only GpGp-0.1.1/GpGp/build |only GpGp-0.1.1/GpGp/inst/doc |only GpGp-0.1.1/GpGp/man/Linv_mult_grouped.Rd |only GpGp-0.1.1/GpGp/man/matern_space_time.Rd |only GpGp-0.1.1/GpGp/man/matern_sphere_time.Rd |only GpGp-0.1.1/GpGp/man/proflik_mean.Rd |only GpGp-0.1.1/GpGp/man/proflik_mean_grouped.Rd |only GpGp-0.1.1/GpGp/man/proflik_mean_variance.Rd |only GpGp-0.1.1/GpGp/man/proflik_mean_variance_grouped.Rd |only GpGp-0.1.1/GpGp/man/proflik_variance.Rd |only GpGp-0.1.1/GpGp/man/proflik_variance_grouped.Rd |only GpGp-0.1.1/GpGp/man/vecchia_Linv_grouped.Rd |only GpGp-0.1.1/GpGp/man/vecchia_loglik.Rd |only GpGp-0.1.1/GpGp/man/vecchia_loglik_grouped.Rd |only GpGp-0.1.1/GpGp/src/covfuns.cpp |only GpGp-0.1.1/GpGp/src/covfuns.h |only GpGp-0.1.1/GpGp/src/vecchia_fun_grouped.h |only GpGp-0.1.1/GpGp/src/vecchia_functions.cpp |only GpGp-0.1.1/GpGp/src/vecchia_functions_grouped.cpp |only GpGp-0.1.1/GpGp/src/vecchiafun.h |only GpGp-0.1.1/GpGp/vignettes |only GpGp-0.2.0/GpGp/DESCRIPTION | 25 GpGp-0.2.0/GpGp/MD5 | 138 - GpGp-0.2.0/GpGp/NAMESPACE | 21 GpGp-0.2.0/GpGp/NEWS.md | 45 GpGp-0.2.0/GpGp/R/GpGp.R | 55 GpGp-0.2.0/GpGp/R/RcppExports.R | 994 ++++++++-- GpGp-0.2.0/GpGp/R/argo2016.R |only GpGp-0.2.0/GpGp/R/fisher_scoring.R |only GpGp-0.2.0/GpGp/R/fit_model.R | 722 +++++-- GpGp-0.2.0/GpGp/R/nearest_neighbor_functions.R | 36 GpGp-0.2.0/GpGp/R/penalties.R |only GpGp-0.2.0/GpGp/R/predictions.R | 72 GpGp-0.2.0/GpGp/R/simulation_functions.R | 26 GpGp-0.2.0/GpGp/data/argo2016.RData |only GpGp-0.2.0/GpGp/data/datalist |only GpGp-0.2.0/GpGp/man/GpGp.Rd | 53 GpGp-0.2.0/GpGp/man/L_mult.Rd | 6 GpGp-0.2.0/GpGp/man/L_t_mult.Rd |only GpGp-0.2.0/GpGp/man/Linv_mult.Rd | 4 GpGp-0.2.0/GpGp/man/Linv_t_mult.Rd |only GpGp-0.2.0/GpGp/man/argo2016.Rd |only GpGp-0.2.0/GpGp/man/cond_sim.Rd | 35 GpGp-0.2.0/GpGp/man/condition_number.Rd |only GpGp-0.2.0/GpGp/man/expit.Rd |only GpGp-0.2.0/GpGp/man/exponential_anisotropic2D.Rd |only GpGp-0.2.0/GpGp/man/exponential_anisotropic3D.Rd |only GpGp-0.2.0/GpGp/man/exponential_isotropic.Rd |only GpGp-0.2.0/GpGp/man/exponential_nonstat_var.Rd |only GpGp-0.2.0/GpGp/man/exponential_scaledim.Rd |only GpGp-0.2.0/GpGp/man/exponential_spacetime.Rd |only GpGp-0.2.0/GpGp/man/exponential_sphere.Rd |only GpGp-0.2.0/GpGp/man/exponential_sphere_warp.Rd |only GpGp-0.2.0/GpGp/man/exponential_spheretime.Rd |only GpGp-0.2.0/GpGp/man/exponential_spheretime_warp.Rd |only GpGp-0.2.0/GpGp/man/fast_Gp_sim.Rd | 17 GpGp-0.2.0/GpGp/man/fast_Gp_sim_Linv.Rd | 4 GpGp-0.2.0/GpGp/man/find_ordered_nn.Rd | 20 GpGp-0.2.0/GpGp/man/find_ordered_nn_brute.Rd | 8 GpGp-0.2.0/GpGp/man/fisher_scoring.Rd |only GpGp-0.2.0/GpGp/man/fit_model.Rd | 87 GpGp-0.2.0/GpGp/man/get_linkfun.Rd |only GpGp-0.2.0/GpGp/man/get_penalty.Rd |only GpGp-0.2.0/GpGp/man/get_start_parms.Rd |only GpGp-0.2.0/GpGp/man/matern_anisotropic2D.Rd |only GpGp-0.2.0/GpGp/man/matern_anisotropic3D.Rd |only GpGp-0.2.0/GpGp/man/matern_isotropic.Rd | 15 GpGp-0.2.0/GpGp/man/matern_nonstat_var.Rd |only GpGp-0.2.0/GpGp/man/matern_scaledim.Rd |only GpGp-0.2.0/GpGp/man/matern_spacetime.Rd |only GpGp-0.2.0/GpGp/man/matern_sphere.Rd | 17 GpGp-0.2.0/GpGp/man/matern_sphere_warp.Rd |only GpGp-0.2.0/GpGp/man/matern_spheretime.Rd |only GpGp-0.2.0/GpGp/man/matern_spheretime_warp.Rd |only GpGp-0.2.0/GpGp/man/pen_hi.Rd |only GpGp-0.2.0/GpGp/man/pen_lo.Rd |only GpGp-0.2.0/GpGp/man/pen_loglo.Rd |only GpGp-0.2.0/GpGp/man/predictions.Rd | 31 GpGp-0.2.0/GpGp/man/sph_grad_xyz.Rd |only GpGp-0.2.0/GpGp/man/summary.GpGp_fit.Rd |only GpGp-0.2.0/GpGp/man/test_likelihood_object.Rd |only GpGp-0.2.0/GpGp/man/vecchia_Linv.Rd | 34 GpGp-0.2.0/GpGp/man/vecchia_grouped_meanzero_loglik.Rd |only GpGp-0.2.0/GpGp/man/vecchia_grouped_profbeta_loglik.Rd |only GpGp-0.2.0/GpGp/man/vecchia_grouped_profbeta_loglik_grad_info.Rd |only GpGp-0.2.0/GpGp/man/vecchia_meanzero_loglik.Rd |only GpGp-0.2.0/GpGp/man/vecchia_profbeta_loglik.Rd |only GpGp-0.2.0/GpGp/man/vecchia_profbeta_loglik_grad_info.Rd |only GpGp-0.2.0/GpGp/src/Makevars |only GpGp-0.2.0/GpGp/src/Makevars.win |only GpGp-0.2.0/GpGp/src/RcppExports.cpp | 647 ++++++ GpGp-0.2.0/GpGp/src/basis.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_01.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_02.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_03.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_04.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_05.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_06.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_07.h |only GpGp-0.2.0/GpGp/src/covmatrix_funs_08.h |only GpGp-0.2.0/GpGp/src/matrix_mult.cpp |only GpGp-0.2.0/GpGp/src/onepass.h |only GpGp-0.2.0/GpGp/src/vecchia_loglik_grad_info.cpp |only GpGp-0.2.0/GpGp/tests/testthat/test_covfuns.R |only GpGp-0.2.0/GpGp/tests/testthat/test_fisher.R |only GpGp-0.2.0/GpGp/tests/testthat/test_loglik.R | 97 GpGp-0.2.0/GpGp/tests/testthat/test_proflik.R | 85 109 files changed, 2619 insertions(+), 675 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.11-1 dated 2019-02-01 and 2.11-2 dated 2019-06-29
DESCRIPTION | 12 +- MD5 | 43 ++++----- NAMESPACE | 4 R/BiodiversityRGUI.R | 2 R/accumcomp.R | 14 ++- R/accumplot.R | 16 ++- R/ensemble.calibrate.models.R | 54 +++++++++--- R/ensemble.calibrate.weights.R | 183 +++++++++++++++++++++++++++-------------- R/ensemble.environmentalThin.R | 102 +++++++++++++++++++--- R/ensemble.plot.R | 2 R/ensemble.raster.R | 4 R/ensemble.spatialThin.R | 30 ++++-- R/ensemble.weights.R | 3 inst/ChangeLog | 54 ++++++++++++ inst/etc/BiodiversityGUI.R | 140 ++++++++++++++++++++++++++++--- inst/etc/Rcmdr-menus.txt | 1 inst/etc/Thumbs.db |only man/accumresult.Rd | 29 ++++-- man/ensemble.Rd | 8 - man/ensemble.batch.Rd | 4 man/ensemble.raster.Rd | 4 man/ensemble.spatialThin.Rd | 16 ++- man/ifri.Rd | 2 23 files changed, 546 insertions(+), 181 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.25.2 dated 2019-03-19 and 0.26.0 dated 2019-06-29
DESCRIPTION | 6 - MD5 | 64 +++++----- NAMESPACE | 5 NEWS | 31 +++++ R/commit.R | 115 ++++++++++++++----- R/index.R | 50 ++++---- R/repository.R | 59 ++++++++++ R/tag.R | 31 +++-- R/time.R | 2 inst/AUTHORS | 2 man/commits.Rd | 45 +++++++ man/lookup_commit.Rd |only man/tag.Rd | 26 +++- src/git2r.c | 5 src/git2r_S3.c | 2 src/git2r_S3.h | 3 src/git2r_odb.c | 2 src/git2r_reference.c | 9 + src/git2r_revwalk.c | 216 ++++++++++++++++++++++++++++++++++++- src/git2r_revwalk.h | 5 src/git2r_tag.c | 91 ++++++++++----- src/git2r_tag.h | 4 src/libgit2/include/git2/version.h | 4 src/libgit2/src/attr_file.c | 12 -- src/libgit2/src/config_file.c | 3 src/libgit2/src/fileops.c | 9 + src/libgit2/src/ignore.c | 4 src/libgit2/src/odb.c | 9 + src/libgit2/src/patch_parse.c | 35 ++--- src/libgit2/src/xdiff/xdiffi.c | 2 tests/commits_path.R |only tests/pull.R | 13 +- tests/time.R | 6 - tests/when.R | 8 - 34 files changed, 678 insertions(+), 200 deletions(-)
Title: Generation of ENVIREM Variables
Description: Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables.
Author: Pascal O. Title, Jordan B. Bemmels
Maintainer: Pascal Title <ptitle@iu.edu>
Diff between envirem versions 1.5 dated 2019-06-14 and 2.0 dated 2019-06-29
DESCRIPTION | 18 +++--- MD5 | 69 +++++++++++++---------- NAMESPACE | 8 ++ R/ETsolradRasters.R |only R/aridityIndexThornthwaite.R | 25 +++++++- R/assignNames.R |only R/climaticMoistureIndex.R | 11 +++ R/createEnv.R |only R/dataTypeCheck.R | 2 R/embergerQ.R | 19 +++++- R/envirem-package.R | 26 +++----- R/generateRasters.R | 54 +++++++++++++----- R/layerCreation.R | 116 +++++++++++++++++++++------------------ R/monthCountByTemp.R | 10 ++- R/monthlyPET.R | 14 ++-- R/otherTempExtremes.R | 8 +- R/pacificCentric.R | 4 - R/petExtremes.R | 13 +++- R/split_raster.R | 5 + R/thermicityIndex.R | 2 R/varnames.R |only R/verifyFileStructure.R | 118 ++++++++++++++++++++++++---------------- R/verifyRasterNames.R |only R/zzz.R | 3 + man/ETsolradRasters.Rd |only man/aridityIndexThornthwaite.Rd | 14 ++++ man/assignNames.Rd |only man/climaticMoistureIndex.Rd | 7 +- man/dataTypeCheck.Rd | 2 man/embergerQ.Rd | 5 + man/envirem.Rd | 22 ++----- man/generateRasters.Rd | 22 ++++++- man/layerCreation.Rd | 16 ++++- man/otherTempExtremes.Rd | 2 man/pacificCentric.Rd | 4 - man/petExtremes.Rd | 9 ++- man/split_raster.Rd | 5 + man/varnames.Rd |only man/verifyFileStructure.Rd | 34 ++++++++--- man/verifyRasterNames.Rd |only 40 files changed, 430 insertions(+), 237 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-12 0.1.1
2019-06-04 0.1.0
Title: Clustering via Stochastic Approximation and Gaussian Mixture
Models
Description: Computes clustering by fitting Gaussian mixture models (GMM) via stochastic approximation following the methods of Nguyen and Jones (2018) <doi:10.1201/9780429446177>. It also provides some test data generation and plotting functionality to assist with this process.
Author: Andrew T. Jones, Hien D. Nguyen
Maintainer: Andrew T. Jones <andrewthomasjones@gmail.com>
Diff between SAGMM versions 0.2.3 dated 2019-05-09 and 0.2.4 dated 2019-06-29
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NAMESPACE | 1 - NEWS.md | 4 ++++ R/main.R | 2 +- 5 files changed, 14 insertions(+), 12 deletions(-)
Title: Species Trait Data from Around the Web
Description: Species trait data from many different sources, including
sequence data from 'NCBI', plant trait data from 'BETYdb', plant data
from the USDA plants database, data from 'EOL' 'Traitbank',
Coral traits data (<https://coraltraits.org>), 'Birdlife' International,
and more.
Author: Scott Chamberlain [aut, cre],
Zachary Foster [aut],
Ignasi Bartomeus [aut],
David LeBauer [aut],
Chris Black [aut],
David Harris [aut],
Rupert Collins [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between traits versions 0.4.0 dated 2019-06-07 and 0.4.2 dated 2019-06-29
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 12 ++++++++++++ R/betydb.R | 11 ++--------- R/ncbi_searcher.R | 6 +++--- R/taxa_search.R | 9 +++++---- man/taxa_search.Rd | 4 ++-- 7 files changed, 33 insertions(+), 27 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman [aut, cre],
Christopher Chang [ctb],
Xavi Puig [ctb],
Jan Wigginton [ctb]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.6.2 dated 2019-04-14 and 1.6.3 dated 2019-06-29
DESCRIPTION | 8 ++++---- MD5 | 28 +++++++++++++++++----------- R/loglik.1.R |only R/loglik.2.R |only R/loglik.3.R |only R/loglik.4.R |only R/loglik.5.R |only R/loglik.6.R |only build/vignette.rds |binary inst/doc/HardyWeinberg.R | 2 +- inst/doc/HardyWeinberg.Rnw | 4 ++-- inst/doc/HardyWeinberg.pdf |binary man/HardyWeinberg-package.Rd | 4 ++-- src/RcppExports.cpp | 1 - src/SNPHWEX.cpp | 12 +++++++----- src/support.cpp | 1 + vignettes/HardyWeinberg.Rnw | 4 ++-- vignettes/HardyWeinberg.bib | 7 ++++++- 18 files changed, 42 insertions(+), 29 deletions(-)
Title: Tunes AdaBoost, Support Vector Machines, and Gradient Boosting
Machines
Description: Contains two functions that are intended to make
tuning supervised learning methods easy. The eztune function uses a
genetic algorithm or Hooke-Jeeves optimizer to find the best
set of tuning parameters. The user can choose the optimizer, the
learning method, and if optimization will be based on accuracy
obtained through validation error, cross validation, or resubstitution.
The function eztune.cv will compute a cross validated error rate. The purpose
of eztune_cv is to provide a cross validated accuracy or MSE when
resubstitution or validation data are used for optimization because
error measures from both approaches can be misleading.
Author: Jill Lundell [aut, cre]
Maintainer: Jill Lundell <jflundell@gmail.com>
Diff between EZtune versions 1.0.0 dated 2018-10-14 and 2.0.0 dated 2019-06-29
EZtune-1.0.0/EZtune/R/ada_binary.R |only EZtune-1.0.0/EZtune/R/eztune.cv.R |only EZtune-1.0.0/EZtune/R/gbm_binary.R |only EZtune-1.0.0/EZtune/R/svm_binary.R |only EZtune-1.0.0/EZtune/README.md |only EZtune-1.0.0/EZtune/man/EZtune-package.Rd |only EZtune-1.0.0/EZtune/man/eztune.cv.Rd |only EZtune-2.0.0/EZtune/DESCRIPTION | 24 ++-- EZtune-2.0.0/EZtune/MD5 | 46 +++++---- EZtune-2.0.0/EZtune/NAMESPACE | 4 EZtune-2.0.0/EZtune/R/ada_bin.R |only EZtune-2.0.0/EZtune/R/ada_bin_ga.R |only EZtune-2.0.0/EZtune/R/cv_tests.R |only EZtune-2.0.0/EZtune/R/eztune.R | 152 ++++++++++++++++-------------- EZtune-2.0.0/EZtune/R/eztune_cv.R |only EZtune-2.0.0/EZtune/R/gbm_bin.R |only EZtune-2.0.0/EZtune/R/gbm_bin_ga.R |only EZtune-2.0.0/EZtune/R/gbm_reg.R |only EZtune-2.0.0/EZtune/R/gbm_reg_ga.R |only EZtune-2.0.0/EZtune/R/lichen.R | 4 EZtune-2.0.0/EZtune/R/misc.R |only EZtune-2.0.0/EZtune/R/mullein.R | 6 - EZtune-2.0.0/EZtune/R/mulleinTest.R | 2 EZtune-2.0.0/EZtune/R/svm_bin.R |only EZtune-2.0.0/EZtune/R/svm_bin_ga.R |only EZtune-2.0.0/EZtune/R/svm_reg.R |only EZtune-2.0.0/EZtune/R/svm_reg_ga.R |only EZtune-2.0.0/EZtune/build |only EZtune-2.0.0/EZtune/inst/doc |only EZtune-2.0.0/EZtune/man/eztune.Rd | 97 +++++++++++-------- EZtune-2.0.0/EZtune/man/eztune_cv.Rd |only EZtune-2.0.0/EZtune/man/lichen.Rd | 4 EZtune-2.0.0/EZtune/man/mullein.Rd | 6 - EZtune-2.0.0/EZtune/man/mulleinTest.Rd | 2 EZtune-2.0.0/EZtune/vignettes |only 35 files changed, 197 insertions(+), 150 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.8.1 dated 2019-05-14 and 0.8.2 dated 2019-06-29
DESCRIPTION | 27 +- MD5 | 162 ++++++++--------- NAMESPACE | 5 NEWS.md | 48 ++++- R/RcppExports.R | 4 R/bench-compare.r | 2 R/case_when.R | 10 + R/colwise-distinct.R | 15 - R/colwise-mutate.R | 4 R/colwise.R | 12 - R/compat-lazyeval.R | 2 R/count-tally.R | 2 R/dataframe.R | 11 - R/funs-predicates.R | 2 R/funs.R | 24 +- R/group-by.r | 5 R/group-indices.R | 2 R/group_map.R | 17 + R/group_nest.R | 2 R/group_split.R | 8 R/grouped-df.r | 8 R/manip.r | 13 - R/rank.R | 3 R/recode.R | 1 R/reexport-tibble.r | 3 R/rowwise.r | 2 R/tbl-cube.r | 8 R/tbl-df.r | 14 - R/tbl.r | 30 +-- R/top-n.R | 55 +++-- R/utils-expr.R | 2 R/utils.r | 4 README.md | 4 build/dplyr.pdf |binary inst/doc/programming.html | 10 - inst/include/dplyr/data/DataMask.h | 11 - inst/include/dplyr/hybrid/Column.h | 4 inst/include/dplyr/hybrid/Expression.h | 6 inst/include/dplyr/hybrid/scalar_result/first_last.h | 73 +++++-- inst/include/dplyr/hybrid/scalar_result/mean_sd_var.h | 4 inst/include/dplyr/hybrid/scalar_result/min_max.h | 4 inst/include/dplyr/hybrid/scalar_result/n_distinct.h | 2 inst/include/dplyr/hybrid/scalar_result/sum.h | 4 inst/include/dplyr/hybrid/vector_result/in.h | 2 inst/include/dplyr/hybrid/vector_result/lead_lag.h | 4 inst/include/dplyr/hybrid/vector_result/ntile.h | 2 inst/include/dplyr/hybrid/vector_result/rank.h | 14 + inst/include/dplyr/hybrid/vector_result/row_number.h | 2 inst/include/dplyr/symbols.h | 4 inst/include/dplyr/visitors/order/OrderVisitorImpl.h | 28 ++ inst/include/dplyr/visitors/vector/VectorVisitorImpl.h | 5 inst/include/tools/SlicingIndex.h | 11 - inst/include/tools/comparisons.h | 23 ++ man/bench_compare.Rd | 2 man/case_when.Rd | 10 + man/distinct_all.Rd | 10 - man/reexports.Rd | 3 man/tally.Rd | 2 man/tbl_vars.Rd | 4 man/top_n.Rd | 37 ++- src/RcppExports.cpp | 9 src/arrange.cpp | 2 src/group_indices.cpp | 14 - src/init.cpp | 7 src/mutate.cpp | 6 tests/testthat/test-arrange.r | 16 + tests/testthat/test-colwise-filter.R | 3 tests/testthat/test-colwise-mutate.R | 51 +++++ tests/testthat/test-colwise-select.R | 2 tests/testthat/test-colwise.R | 1 tests/testthat/test-funs.R | 8 tests/testthat/test-group-by.r | 19 + tests/testthat/test-group_data.R | 5 tests/testthat/test-group_map.R | 20 ++ tests/testthat/test-group_split.R | 12 - tests/testthat/test-hybrid-traverse.R | 1 tests/testthat/test-mutate.r | 24 ++ tests/testthat/test-overscope.R | 15 - tests/testthat/test-summarise.r | 8 tests/testthat/test-tbl-cube.R | 4 tests/testthat/test-tbl.R | 9 tests/testthat/test-top-n.R | 13 + 82 files changed, 727 insertions(+), 314 deletions(-)
Title: Detrend Images
Description: Detrend fluorescence microscopy image series for fluorescence
fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This
package contains functionality published in a 2016 paper
<doi:10.1093/bioinformatics/btx434> but it has been extended since then with
the Robin Hood algorithm and thus contains unpublished work.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths, cph]
(<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between detrendr versions 0.6.2 dated 2019-06-15 and 0.6.3 dated 2019-06-29
DESCRIPTION | 20 ++++++++++---------- MD5 | 24 +++++++++++++++--------- NEWS.md | 11 +++++++++-- R/dir_detrend.R | 14 ++++++++++++++ README.md |only build/vignette.rds |binary inst/WORDLIST | 3 +++ inst/doc/batch-mode.html | 4 ++-- inst/doc/linescan-data.R |only inst/doc/linescan-data.Rmd |only inst/doc/linescan-data.html |only inst/doc/single-images.html | 10 +++++----- inst/extdata/linescan.tif |only tests/testthat/test-dir-detrend.R | 4 +++- tests/testthat/test-smooth.R | 10 +++++++--- vignettes/linescan-data.Rmd |only 16 files changed, 68 insertions(+), 32 deletions(-)