Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 0.2 dated 2018-09-30 and 0.3 dated 2018-12-07
landscapemetrics-0.2/landscapemetrics/man/rcpp_get_adjacency.Rd |only landscapemetrics-0.2/landscapemetrics/man/rcpp_get_pairs.Rd |only landscapemetrics-0.2/landscapemetrics/src/get_adjacency.cpp |only landscapemetrics-0.2/landscapemetrics/src/get_adjacency.h |only landscapemetrics-0.2/landscapemetrics/src/get_composition_vector.cpp |only landscapemetrics-0.2/landscapemetrics/src/get_coocurrence_vector.cpp |only landscapemetrics-0.2/landscapemetrics/src/rcpp_circle.cpp |only landscapemetrics-0.3/landscapemetrics/DESCRIPTION | 75 - landscapemetrics-0.3/landscapemetrics/MD5 | 394 +++--- landscapemetrics-0.3/landscapemetrics/NAMESPACE | 25 landscapemetrics-0.3/landscapemetrics/NEWS.md | 31 landscapemetrics-0.3/landscapemetrics/R/RcppExports.R | 62 - landscapemetrics-0.3/landscapemetrics/R/calculate_lsm.R | 464 +++---- landscapemetrics-0.3/landscapemetrics/R/check_landscape.R |only landscapemetrics-0.3/landscapemetrics/R/construct_buffer.R | 4 landscapemetrics-0.3/landscapemetrics/R/extract_lsm.R | 85 + landscapemetrics-0.3/landscapemetrics/R/get_adjacencies.R | 19 landscapemetrics-0.3/landscapemetrics/R/get_boundaries.R |only landscapemetrics-0.3/landscapemetrics/R/get_circumscribingcircle.R | 65 - landscapemetrics-0.3/landscapemetrics/R/get_nearestneighbour.R | 14 landscapemetrics-0.3/landscapemetrics/R/get_patches.R | 253 +++- landscapemetrics-0.3/landscapemetrics/R/get_unique_values.R |only landscapemetrics-0.3/landscapemetrics/R/landscapemetrics-package.R | 8 landscapemetrics-0.3/landscapemetrics/R/list_lsm.R |only landscapemetrics-0.3/landscapemetrics/R/lsm_c_ai.R | 52 landscapemetrics-0.3/landscapemetrics/R/lsm_c_area_cv.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_area_mn.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_area_sd.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_ca.R | 248 ++-- landscapemetrics-0.3/landscapemetrics/R/lsm_c_cai_sd.R | 2 landscapemetrics-0.3/landscapemetrics/R/lsm_c_circle_cv.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_circle_mn.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_c_circle_sd.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_c_clumpy.R | 60 landscapemetrics-0.3/landscapemetrics/R/lsm_c_cohesion.R | 37 landscapemetrics-0.3/landscapemetrics/R/lsm_c_core_cv.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_c_core_mn.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_c_core_sd.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_c_cpland.R | 35 landscapemetrics-0.3/landscapemetrics/R/lsm_c_dcad.R | 29 landscapemetrics-0.3/landscapemetrics/R/lsm_c_dcore_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_dcore_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_dcore_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_division.R | 18 landscapemetrics-0.3/landscapemetrics/R/lsm_c_ed.R | 27 landscapemetrics-0.3/landscapemetrics/R/lsm_c_enn_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_enn_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_enn_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_frac_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_frac_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_frac_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_gyrate_cv.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_c_gyrate_mn.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_c_gyrate_sd.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_c_iji.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_c_lpi.R | 16 landscapemetrics-0.3/landscapemetrics/R/lsm_c_lsi.R | 33 landscapemetrics-0.3/landscapemetrics/R/lsm_c_mesh.R | 18 landscapemetrics-0.3/landscapemetrics/R/lsm_c_ndca.R | 18 landscapemetrics-0.3/landscapemetrics/R/lsm_c_nlsi.R | 30 landscapemetrics-0.3/landscapemetrics/R/lsm_c_np.R | 17 landscapemetrics-0.3/landscapemetrics/R/lsm_c_pafrac.R | 20 landscapemetrics-0.3/landscapemetrics/R/lsm_c_para_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_para_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_para_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_pd.R | 20 landscapemetrics-0.3/landscapemetrics/R/lsm_c_pladj.R | 13 landscapemetrics-0.3/landscapemetrics/R/lsm_c_pland.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_c_shape_cv.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_shape_mn.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_shape_sd.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_c_split.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_c_tca.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_c_te.R | 80 - landscapemetrics-0.3/landscapemetrics/R/lsm_l_ai.R | 24 landscapemetrics-0.3/landscapemetrics/R/lsm_l_area_cv.R | 11 landscapemetrics-0.3/landscapemetrics/R/lsm_l_area_mn.R | 11 landscapemetrics-0.3/landscapemetrics/R/lsm_l_area_sd.R | 11 landscapemetrics-0.3/landscapemetrics/R/lsm_l_cai_cv.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_l_cai_mn.R | 11 landscapemetrics-0.3/landscapemetrics/R/lsm_l_cai_sd.R | 11 landscapemetrics-0.3/landscapemetrics/R/lsm_l_circle_cv.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_l_circle_mn.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_l_circle_sd.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_l_cohesion.R | 35 landscapemetrics-0.3/landscapemetrics/R/lsm_l_condent.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_l_contag.R | 9 landscapemetrics-0.3/landscapemetrics/R/lsm_l_core_cv.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_l_core_mn.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_l_core_sd.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_l_dcad.R | 18 landscapemetrics-0.3/landscapemetrics/R/lsm_l_dcore_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_dcore_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_dcore_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_division.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_l_ed.R | 33 landscapemetrics-0.3/landscapemetrics/R/lsm_l_enn_cv.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_l_enn_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_enn_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_ent.R | 9 landscapemetrics-0.3/landscapemetrics/R/lsm_l_frac_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_frac_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_frac_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_gyrate_cv.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_l_gyrate_mn.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_l_gyrate_sd.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_l_iji.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_l_joinent.R | 8 landscapemetrics-0.3/landscapemetrics/R/lsm_l_lpi.R | 13 landscapemetrics-0.3/landscapemetrics/R/lsm_l_lsi.R | 23 landscapemetrics-0.3/landscapemetrics/R/lsm_l_mesh.R | 13 landscapemetrics-0.3/landscapemetrics/R/lsm_l_msidi.R | 12 landscapemetrics-0.3/landscapemetrics/R/lsm_l_msiei.R | 16 landscapemetrics-0.3/landscapemetrics/R/lsm_l_mutinf.R | 11 landscapemetrics-0.3/landscapemetrics/R/lsm_l_ndca.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_np.R | 3 landscapemetrics-0.3/landscapemetrics/R/lsm_l_pafrac.R | 30 landscapemetrics-0.3/landscapemetrics/R/lsm_l_para_cv.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_para_mn.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_para_sd.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_pd.R | 28 landscapemetrics-0.3/landscapemetrics/R/lsm_l_pladj.R | 9 landscapemetrics-0.3/landscapemetrics/R/lsm_l_pr.R | 2 landscapemetrics-0.3/landscapemetrics/R/lsm_l_prd.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_l_rpr.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_l_shape_cv.R | 10 landscapemetrics-0.3/landscapemetrics/R/lsm_l_shape_mn.R | 10 landscapemetrics-0.3/landscapemetrics/R/lsm_l_shape_sd.R | 10 landscapemetrics-0.3/landscapemetrics/R/lsm_l_shdi.R | 15 landscapemetrics-0.3/landscapemetrics/R/lsm_l_shei.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_l_sidi.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_siei.R | 7 landscapemetrics-0.3/landscapemetrics/R/lsm_l_split.R | 14 landscapemetrics-0.3/landscapemetrics/R/lsm_l_ta.R | 6 landscapemetrics-0.3/landscapemetrics/R/lsm_l_tca.R | 5 landscapemetrics-0.3/landscapemetrics/R/lsm_l_te.R | 32 landscapemetrics-0.3/landscapemetrics/R/lsm_p_area.R | 33 landscapemetrics-0.3/landscapemetrics/R/lsm_p_cai.R | 23 landscapemetrics-0.3/landscapemetrics/R/lsm_p_circle.R | 162 ++ landscapemetrics-0.3/landscapemetrics/R/lsm_p_contig.R | 49 landscapemetrics-0.3/landscapemetrics/R/lsm_p_core.R | 74 - landscapemetrics-0.3/landscapemetrics/R/lsm_p_enn.R | 153 ++ landscapemetrics-0.3/landscapemetrics/R/lsm_p_frac.R | 22 landscapemetrics-0.3/landscapemetrics/R/lsm_p_gyrate.R | 118 + landscapemetrics-0.3/landscapemetrics/R/lsm_p_ncore.R | 233 +++ landscapemetrics-0.3/landscapemetrics/R/lsm_p_para.R | 19 landscapemetrics-0.3/landscapemetrics/R/lsm_p_perim.R | 75 - landscapemetrics-0.3/landscapemetrics/R/lsm_p_shape.R | 19 landscapemetrics-0.3/landscapemetrics/R/matrix_to_raster.R |only landscapemetrics-0.3/landscapemetrics/R/options_landscapemetrics.R |only landscapemetrics-0.3/landscapemetrics/R/pad_raster.R | 54 landscapemetrics-0.3/landscapemetrics/R/raster_to_points.R |only landscapemetrics-0.3/landscapemetrics/R/sample_lsm.R | 21 landscapemetrics-0.3/landscapemetrics/R/show_cores.R | 220 +-- landscapemetrics-0.3/landscapemetrics/R/show_correlation.R | 10 landscapemetrics-0.3/landscapemetrics/R/show_lsm.R |only landscapemetrics-0.3/landscapemetrics/R/show_patches.R | 181 +- landscapemetrics-0.3/landscapemetrics/data/lsm_abbreviations_names.rda |binary landscapemetrics-0.3/landscapemetrics/inst/doc/getstarted.R | 70 - landscapemetrics-0.3/landscapemetrics/inst/doc/getstarted.Rmd | 108 + landscapemetrics-0.3/landscapemetrics/inst/doc/getstarted.html | 613 +++++++--- landscapemetrics-0.3/landscapemetrics/man/calculate_lsm.Rd | 38 landscapemetrics-0.3/landscapemetrics/man/check_landscape.Rd |only landscapemetrics-0.3/landscapemetrics/man/extract_lsm.Rd | 56 landscapemetrics-0.3/landscapemetrics/man/get_adjacencies.Rd | 15 landscapemetrics-0.3/landscapemetrics/man/get_boundaries.Rd |only landscapemetrics-0.3/landscapemetrics/man/get_circumscribingcircle.Rd | 39 landscapemetrics-0.3/landscapemetrics/man/get_nearestneighbour.Rd | 12 landscapemetrics-0.3/landscapemetrics/man/get_patches.Rd | 48 landscapemetrics-0.3/landscapemetrics/man/get_unique_values.Rd |only landscapemetrics-0.3/landscapemetrics/man/landscapemetrics.Rd | 15 landscapemetrics-0.3/landscapemetrics/man/list_lsm.Rd |only landscapemetrics-0.3/landscapemetrics/man/lsm_c_cai_sd.Rd | 2 landscapemetrics-0.3/landscapemetrics/man/lsm_c_ed.Rd | 4 landscapemetrics-0.3/landscapemetrics/man/lsm_c_pafrac.Rd | 2 landscapemetrics-0.3/landscapemetrics/man/lsm_l_ed.Rd | 4 landscapemetrics-0.3/landscapemetrics/man/matrix_to_raster.Rd |only landscapemetrics-0.3/landscapemetrics/man/options_landscapemetrics.Rd |only landscapemetrics-0.3/landscapemetrics/man/raster_to_points.Rd |only landscapemetrics-0.3/landscapemetrics/man/sample_lsm.Rd | 2 landscapemetrics-0.3/landscapemetrics/man/show_cores.Rd | 23 landscapemetrics-0.3/landscapemetrics/man/show_lsm.Rd |only landscapemetrics-0.3/landscapemetrics/man/show_patches.Rd | 18 landscapemetrics-0.3/landscapemetrics/src/RcppExports.cpp | 135 +- landscapemetrics-0.3/landscapemetrics/src/get_class_index_map.cpp |only landscapemetrics-0.3/landscapemetrics/src/get_class_index_map.h |only landscapemetrics-0.3/landscapemetrics/src/rcpp_create_neighborhood.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_create_neighborhood.h |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_boundaries.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_boundaries.h |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_circle.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_composition_vector.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_coocurrence_matrix.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_coocurrence_matrix.h |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_coocurrence_matrix_diag.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_coocurrence_matrix_diag.h |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_coocurrence_vector.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_coocurrence_vector.h |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_unique_values.cpp |only landscapemetrics-0.3/landscapemetrics/src/rcpp_get_unique_values.h |only landscapemetrics-0.3/landscapemetrics/tests/testthat/helper-brick.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/helper-landscapes.R | 8 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-calculate-lsm.R | 56 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-check-landscape.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-extract-lsm.R | 19 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-get-adjacencies.R | 60 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-get-boundaries.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-get-circumscribungcircle.R | 38 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-get-nearestneighbour.R | 2 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-get-unique-values.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-list-lsm.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-lsm-p-circle.R | 4 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-lsm-p-perim.R | 21 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-matrix-to-raster.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-raster-to-points.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-rcpp-get-coocurrence-matrix.R | 10 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-rcpp-get-entropy.R | 3 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-show-cores.R | 33 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-show-lsm.R |only landscapemetrics-0.3/landscapemetrics/tests/testthat/test-show-patches.R | 28 landscapemetrics-0.3/landscapemetrics/tests/testthat/test-unique-values.R |only landscapemetrics-0.3/landscapemetrics/vignettes/getstarted.Rmd | 108 + 222 files changed, 4057 insertions(+), 2173 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph],
Robert Rigby [aut],
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb],
Fernanda De Bastiani [ctb],
Raydonal Ospina [ctb],
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [ctb],
Marco Enea [ctb],
Alexios Ghalanos [ctb],
Christos Argyropoulos [ctb],
Almond Stocker [ctb],
Jens Lichter [ctb],
Stanislaus Stadlmann [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 5.1-0 dated 2018-10-06 and 5.1-1 dated 2018-12-07
DESCRIPTION | 8 MD5 | 102 +++---- NAMESPACE | 8 R/BB.R | 41 +- R/BI.R | 130 ++++----- R/BNB.R | 29 -- R/DELAPORT.R | 29 -- R/DoubleBinomial.R | 37 +- R/GAF.R |only R/GB2.R | 4 R/GIG.R | 22 + R/GeneralisedPoisson.R | 4 R/IG.R | 3 R/LG.R | 25 - R/NBF.R | 4 R/NBI.R | 200 +++++++------- R/NBII.R | 253 ++++++++--------- R/NET.R | 18 + R/PIG.R | 4 R/SHASHo.R | 21 + R/SI.R | 15 - R/SICHEL-10-09-12.R | 10 R/ST2.R | 606 +++++++++++++++++++++--------------------- R/ST3.R | 610 +++++++++++++++++++++--------------------- R/ST3C.R | 18 + R/ST4.R | 699 +++++++++++++++++++++++++------------------------ R/ST5.R | 536 +++++++++++++++++++------------------ R/WARING_BOB.r | 44 +-- R/YULE.R | 22 - R/ZABI.R | 2 R/ZABNB.R | 408 ++++++++++++++-------------- R/ZAIG.R | 66 +--- R/ZALG.R | 10 R/ZANBI.R | 316 +++++++++++----------- R/ZAP.R | 10 R/ZAPIG.R | 292 ++++++++++---------- R/ZASICHEL.R | 268 +++++++++--------- R/ZAZIPF.R | 10 R/ZIBI.R | 2 R/ZIBNB.R | 398 ++++++++++++++------------- R/ZINBI.R | 288 ++++++++++---------- R/ZIP.R | 5 R/ZIP2.R | 4 R/ZIPF.R | 4 R/ZIPIG.R | 128 ++++---- R/ZISICHEL.R | 303 ++++++++++----------- R/logNO.R | 4 R/plottingDist.R |only build/partial.rdb |binary man/BE.Rd | 2 man/GAF.Rd |only man/NOF.Rd | 38 +- man/ZAIG.Rd | 5 man/count_1_31.Rd |only 54 files changed, 3162 insertions(+), 2903 deletions(-)
Title: Market Area Models for Retail and Service Locations
Description: Market area models are used to analyze and predict store choices and market areas concerning retail and service locations. This package is a more user-friendly wrapper of the functions in the package 'MCI' (Wieland 2017) providing market area analysis using the Huff Model or the Multiplicative Competitive Interaction (MCI) Model. In 'MCI2', also a function for creating transport costs matrices is provided.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between MCI2 versions 1.0.0 dated 2018-11-29 and 1.1.0 dated 2018-12-07
DESCRIPTION | 8 +-- MD5 | 21 ++++++--- NAMESPACE | 2 R/checkod.R |only R/huff.R | 1 R/huff.newdest.R | 2 R/huff.optim.R |only R/mcimat.create.R | 2 R/tcmat.create.R | 98 ++++++++++++++++++++++++++++++++++------------ R/to.tcmat.R |only data/HaslachDistricts.rda |binary man/huff.optim.Rd |only man/tcmat.create.Rd | 34 ++++++++++++--- man/to.tcmat.Rd |only 14 files changed, 123 insertions(+), 45 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.5-2 dated 2018-07-25 and 1.5-3 dated 2018-12-07
ChangeLog | 12 +++++++++ DESCRIPTION | 8 +++--- MD5 | 32 +++++++++++++------------ NAMESPACE | 4 +-- R/gp.R | 2 - R/laGP.R | 66 +++++++++++++++++++++++++++++------------------------ R/laGP_sep.R | 38 +++++++++++++++++------------- R/parallel.R | 2 - R/randLine.R |only README | 6 ++-- build/vignette.rds |binary inst/CITATION | 39 +++++++++++++++---------------- inst/doc/laGP.pdf |binary man/aGP.Rd | 26 +++++++++++--------- man/alcGP.Rd | 5 ++++ man/blhs.Rd | 4 +-- man/laGP.Rd | 28 ++++++++++++---------- man/randLine.Rd |only 18 files changed, 154 insertions(+), 118 deletions(-)
Title: Analysis of Multiplex Cytometric Bead Assays
Description: Reproducible and automated analysis of multiplex bead assays such
as CBA (Morgan et al. 2004; <doi: 10.1016/j.clim.2003.11.017>), LEGENDplex
(Yu et al. 2015; <doi: 10.1084/jem.20142318>), and MACSPlex (Miltenyi
Biotec 2014; Application note: Data acquisition and analysis without the
MACSQuant analyzer;
<https://www.miltenyibiotec.com/upload/assets/IM0021608.PDF>). The
package provides functions for streamlined reading of fcs files, and
identification of bead clusters and analyte expression. The package eases
the calculation of standard curves and the subsequent calculation of the
analyte concentration.
Author: Ulrik Stervbo [aut, cre] (<https://orcid.org/0000-0002-2831-8868>)
Maintainer: Ulrik Stervbo <ulrik.stervbo@gmail.com>
Diff between beadplexr versions 0.1.0 dated 2018-03-09 and 0.2.0 dated 2018-12-07
beadplexr-0.1.0/beadplexr/inst/resources/legendplex_human_th_cytokine_panel_13-plex.yml |only beadplexr-0.1.0/beadplexr/tests/testthat/testdata |only beadplexr-0.2.0/beadplexr/DESCRIPTION | 42 beadplexr-0.2.0/beadplexr/LICENSE | 2 beadplexr-0.2.0/beadplexr/MD5 | 115 beadplexr-0.2.0/beadplexr/NAMESPACE | 1 beadplexr-0.2.0/beadplexr/NEWS.md | 15 beadplexr-0.2.0/beadplexr/R/analyte_mfi.R | 2 beadplexr-0.2.0/beadplexr/R/calc_conc.R | 6 beadplexr-0.2.0/beadplexr/R/cluster_events.R | 50 beadplexr-0.2.0/beadplexr/R/data.R | 11 beadplexr-0.2.0/beadplexr/R/identify_analyte.R | 6 beadplexr-0.2.0/beadplexr/R/panel_information.R | 43 beadplexr-0.2.0/beadplexr/R/read_fcs.R | 12 beadplexr-0.2.0/beadplexr/R/utils.R | 29 beadplexr-0.2.0/beadplexr/R/visualisations.R | 19 beadplexr-0.2.0/beadplexr/README.md | 42 beadplexr-0.2.0/beadplexr/build/vignette.rds |binary beadplexr-0.2.0/beadplexr/inst/CITATION |only beadplexr-0.2.0/beadplexr/inst/WORDLIST |only beadplexr-0.2.0/beadplexr/inst/doc/cba_macsplex_example.Rmd | 4 beadplexr-0.2.0/beadplexr/inst/doc/cba_macsplex_example.html | 181 - beadplexr-0.2.0/beadplexr/inst/doc/legendplex-analysis.R | 4 beadplexr-0.2.0/beadplexr/inst/doc/legendplex-analysis.Rmd | 40 beadplexr-0.2.0/beadplexr/inst/doc/legendplex-analysis.html | 399 +- beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_adipokine_panel_13-plex.yml |only beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_anti-virus_response_panel_13-plex.yml |only beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_cd8-nk_panel_13-plex.yml |only beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_cytokine_panel_2_13-plex.yml | 49 beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_growth_factor_panel_13-plex.yml | 49 beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_inflammation_panel_13-plex.yml |only beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_metabolic_panel_1_4-plex.yml |only beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_proinflammatory_chemokine_panel_13-plex.yml | 49 beadplexr-0.2.0/beadplexr/inst/resources/legendplex_human_t_helper_cytokine_panels_13-plex.yml |only beadplexr-0.2.0/beadplexr/inst/testdata |only beadplexr-0.2.0/beadplexr/man/apply_compensation.Rd | 2 beadplexr-0.2.0/beadplexr/man/assign_analyte_id.Rd | 3 beadplexr-0.2.0/beadplexr/man/calc_analyte_mfi.Rd | 2 beadplexr-0.2.0/beadplexr/man/calc_centre.Rd | 4 beadplexr-0.2.0/beadplexr/man/calc_dist_to_centre.Rd | 2 beadplexr-0.2.0/beadplexr/man/calc_std_conc.Rd | 3 beadplexr-0.2.0/beadplexr/man/cluster_events.Rd | 44 beadplexr-0.2.0/beadplexr/man/despeckle.Rd | 4 beadplexr-0.2.0/beadplexr/man/do_find_turning_points.Rd | 4 beadplexr-0.2.0/beadplexr/man/facs_plot.Rd | 2 beadplexr-0.2.0/beadplexr/man/figures/beadplexr2.gpl |only beadplexr-0.2.0/beadplexr/man/figures/logo.png |binary beadplexr-0.2.0/beadplexr/man/figures/logo.svg | 1554 ++++------ beadplexr-0.2.0/beadplexr/man/ident_bead_pop.Rd | 4 beadplexr-0.2.0/beadplexr/man/identify_analyte.Rd | 9 beadplexr-0.2.0/beadplexr/man/identify_assay_analyte.Rd | 8 beadplexr-0.2.0/beadplexr/man/load_panel.Rd | 14 beadplexr-0.2.0/beadplexr/man/lplex.Rd | 11 beadplexr-0.2.0/beadplexr/man/panel_name_file.Rd | 2 beadplexr-0.2.0/beadplexr/man/plot_concentrations.Rd | 4 beadplexr-0.2.0/beadplexr/man/read_fcs.Rd | 8 beadplexr-0.2.0/beadplexr/man/trim_population.Rd | 5 beadplexr-0.2.0/beadplexr/tests/testthat/test_calc_conc.R | 43 beadplexr-0.2.0/beadplexr/tests/testthat/test_cluster_events.R | 26 beadplexr-0.2.0/beadplexr/tests/testthat/test_identify_assay_analyte.R | 50 beadplexr-0.2.0/beadplexr/tests/testthat/test_panel_information.R | 10 beadplexr-0.2.0/beadplexr/tests/testthat/test_panel_information_file_structure.R | 2 beadplexr-0.2.0/beadplexr/vignettes/cba_macsplex_example.Rmd | 4 beadplexr-0.2.0/beadplexr/vignettes/legendplex-analysis.Rmd | 40 64 files changed, 1600 insertions(+), 1434 deletions(-)
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from eBird
(<http://ebird.org>), an online tool for recording bird observations.
Public access to the full eBird database is via the eBird Basic Dataset
(EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable
text file. This package is an interface to AWK for extracting data from the
EBD based on taxonomic, spatial, or temporal filters, to produce a
manageable file size that can be imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>),
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.3.0 dated 2018-10-04 and 0.3.1 dated 2018-12-07
DESCRIPTION | 12 MD5 | 32 - NEWS.md | 5 R/auk-filter.r | 5 R/auk-protocol.r | 16 R/auk-rollup.r | 7 R/auk-sampling.r | 6 R/auk-unique.r | 42 + R/auk-version.r | 2 R/filter-repeat-visits.r | 2 R/format-unmarked-occu.r | 16 inst/doc/auk.html | 1028 ++++++++++++++---------------------- inst/doc/development.html | 334 ++--------- man/auk_protocol.Rd | 13 man/auk_unique.Rd | 18 tests/testthat/test_auk-keep-drop.r | 8 tests/testthat/test_auk-unique.r | 19 17 files changed, 616 insertions(+), 949 deletions(-)
Title: World Development Indicators (World Bank)
Description: Search, extract and format data from the World Bank's
World Development Indicators.
Author: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between WDI versions 2.5 dated 2018-04-10 and 2.5.1 dated 2018-12-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 28 +++++++++++++++++----------- R/WDI_data.R | 1 + data/WDI_data.RData |binary man/WDI_data.Rd | 1 + 6 files changed, 28 insertions(+), 20 deletions(-)
Title: Lomb-Scargle Periodogram
Description: Computes the Lomb-Scargle Periodogram for unevenly sampled time series. Includes a randomization procedure to obtain reliable p-values.
Author: Thomas Ruf, partially based on C original by Press et al. (Numerical Recipes)
Maintainer: Thomas Ruf <Thomas.Ruf@vetmeduni.ac.at>
Diff between lomb versions 1.0 dated 2013-10-20 and 1.1 dated 2018-12-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 6 ++++++ R/lspfunctions.R | 1 + 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Interactive shiny application for analysis of educational tests and
their items.
Author: Patricia Martinkova [aut, cre],
Adela Drabinova [aut],
Ondrej Leder [aut],
Jakub Houdek [aut],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.2.8 dated 2018-09-28 and 1.2.9 dated 2018-12-07
DESCRIPTION | 23 MD5 | 85 NAMESPACE | 3 NEWS | 153 R/DDplot.R | 222 R/DistractorAnalysis.R | 17 R/ItemAnalysis.R |only R/dataMedical.R | 2 R/dataMedicalgraded.R | 2 R/dataMedicaltest.R | 2 R/gDisrim.R | 114 R/ggWrightMap.R | 22 R/plotDIFLogistic.R | 6 R/plotDIFirt.R | 7 R/plotDistractorAnalysis.R | 28 README.md | 9 inst/CITATION | 4 inst/shiny-examples/ShinyItemAnalysis/counter.Rdata |binary inst/shiny-examples/ShinyItemAnalysis/reporthtml.Rmd | 98 inst/shiny-examples/ShinyItemAnalysis/reportpdf.Rmd | 140 inst/shiny-examples/ShinyItemAnalysis/server.R | 932 +-- inst/shiny-examples/ShinyItemAnalysis/server/DIF.R | 263 - inst/shiny-examples/ShinyItemAnalysis/server/Data.R | 260 - inst/shiny-examples/ShinyItemAnalysis/server/IRT.R | 2335 ++++++++-- inst/shiny-examples/ShinyItemAnalysis/server/Regression.R | 102 inst/shiny-examples/ShinyItemAnalysis/server/Reliability.R | 19 inst/shiny-examples/ShinyItemAnalysis/server/Setting.R |only inst/shiny-examples/ShinyItemAnalysis/server/Summary.R | 45 inst/shiny-examples/ShinyItemAnalysis/server/TraditionalAnalysis.R | 87 inst/shiny-examples/ShinyItemAnalysis/server/Validity.R | 200 inst/shiny-examples/ShinyItemAnalysis/ui.R | 325 - inst/shiny-examples/ShinyItemAnalysis/ui/About.R | 18 inst/shiny-examples/ShinyItemAnalysis/ui/Data.R | 91 inst/shiny-examples/ShinyItemAnalysis/ui/IRT.R | 1170 ++--- man/DDplot.Rd | 73 man/DistractorAnalysis.Rd | 13 man/ItemAnalysis.Rd |only man/dataMedical.Rd | 2 man/dataMedicalgraded.Rd | 2 man/dataMedicaltest.Rd | 2 man/gDiscrim.Rd | 56 man/ggWrightMap.Rd | 22 man/plotDIFLogistic.Rd | 4 man/plotDIFirt.Rd | 3 man/plotDistractorAnalysis.Rd | 28 45 files changed, 4918 insertions(+), 2071 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of 'RJSONIO', but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with a web API. The implementation is
based on the mapping described in the vignette (Ooms, 2014). In addition to
converting JSON data from/to R objects, 'jsonlite' contains functions to
stream, validate, and prettify JSON data. The unit tests included with the
package verify that all edge cases are encoded and decoded consistently for
use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between jsonlite versions 1.5 dated 2017-06-01 and 1.6 dated 2018-12-07
jsonlite-1.5/jsonlite/R/rbind.pages.R |only jsonlite-1.5/jsonlite/inst/doc/json-opencpu.R |only jsonlite-1.5/jsonlite/inst/doc/json-opencpu.Rnw |only jsonlite-1.5/jsonlite/vignettes/json-opencpu.Rnw |only jsonlite-1.6/jsonlite/DESCRIPTION | 8 jsonlite-1.6/jsonlite/MD5 | 69 +- jsonlite-1.6/jsonlite/NAMESPACE | 3 jsonlite-1.6/jsonlite/NEWS | 11 jsonlite-1.6/jsonlite/R/asJSON.difftime.R |only jsonlite-1.6/jsonlite/R/fromJSON.R | 12 jsonlite-1.6/jsonlite/R/rbind_pages.R |only jsonlite-1.6/jsonlite/R/read_json.R | 20 jsonlite-1.6/jsonlite/R/unbox.R | 2 jsonlite-1.6/jsonlite/build/vignette.rds |binary jsonlite-1.6/jsonlite/inst/doc/json-aaquickstart.html | 234 ++++++++- jsonlite-1.6/jsonlite/inst/doc/json-apis.Rmd | 182 ++----- jsonlite-1.6/jsonlite/inst/doc/json-apis.html | 387 ++++++++++----- jsonlite-1.6/jsonlite/inst/doc/json-mapping.pdf |binary jsonlite-1.6/jsonlite/inst/doc/json-opencpu.pdf |binary jsonlite-1.6/jsonlite/inst/doc/json-opencpu.pdf.asis |only jsonlite-1.6/jsonlite/inst/doc/json-paging.Rmd | 162 +----- jsonlite-1.6/jsonlite/inst/doc/json-paging.html | 372 +++++++++----- jsonlite-1.6/jsonlite/man/fromJSON.Rd | 24 jsonlite-1.6/jsonlite/man/prettify.Rd | 1 jsonlite-1.6/jsonlite/man/rbind_pages.Rd | 17 jsonlite-1.6/jsonlite/man/read_json.Rd | 12 jsonlite-1.6/jsonlite/src/Makevars | 14 jsonlite-1.6/jsonlite/src/prettify.c | 5 jsonlite-1.6/jsonlite/src/push_parser.c | 41 - jsonlite-1.6/jsonlite/src/register.c | 58 ++ jsonlite-1.6/jsonlite/src/row_collapse.c | 8 jsonlite-1.6/jsonlite/src/validate.c | 12 jsonlite-1.6/jsonlite/src/yajl/api/yajl_common.h | 2 jsonlite-1.6/jsonlite/tests/testthat/test-libjson-utf8.R | 13 jsonlite-1.6/jsonlite/vignettes/json-apis.Rmd | 182 ++----- jsonlite-1.6/jsonlite/vignettes/json-apis.Rmd.orig | 30 - jsonlite-1.6/jsonlite/vignettes/json-opencpu.Rnw.orig |only jsonlite-1.6/jsonlite/vignettes/json-opencpu.pdf.asis |only jsonlite-1.6/jsonlite/vignettes/json-paging.Rmd | 162 +----- jsonlite-1.6/jsonlite/vignettes/json-paging.Rmd.orig | 30 - 40 files changed, 1173 insertions(+), 900 deletions(-)
Title: An Algorithm for Morphometric Characters Selection and
Statistical Validation in Morphological Taxonomy
Description: An algorithm which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between VARSEDIG versions 1.8 dated 2018-08-29 and 1.9 dated 2018-12-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- data/characiformes.RData |binary data/scorpaeniformes.RData |binary man/VARSEDIG.Rd | 3 ++- man/VIDTAXA.Rd | 38 ++++++++++++++++++++++++-------------- 6 files changed, 34 insertions(+), 23 deletions(-)
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith
(2019) <doi:10.1093/sysbio/syy083>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>),
Klaus Schliep [cph] (<https://orcid.org/0000-0003-2941-0161>),
Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 0.2.0 dated 2018-09-11 and 0.2.1 dated 2018-12-07
DESCRIPTION | 37 +++++---- MD5 | 134 +++++++++++++++++++---------------- NAMESPACE | 14 +++ NEWS.md | 29 +++++++ R/IWScore.R | 12 +-- R/Partitions.R |only R/Ratchet.R | 4 + R/RcppExports.R |only R/ReleaseQuestions.R |only R/Support.R | 70 ++++++++++++------ R/data.R | 3 R/helper_functions.R | 5 - R/mpl_morphy_objects.R | 5 - R/mpl_morphyex.R | 2 R/parse_files.R | 79 +++++++++++--------- R/phylo.R | 3 R/pp_ProfileScore.R | 22 +++-- R/pp_info_extra_step.r | 4 - R/tree_numbering.R | 12 +-- R/tree_rearrangement.R | 70 ++++++++++++++++++ README.md | 6 - build/partial.rdb |binary inst/CITATION | 22 +++-- inst/REFERENCES.bib | 9 +- inst/doc/getting-started.html | 4 - inst/doc/inapplicable.Rmd | 2 inst/doc/inapplicable.html | 12 +-- inst/doc/load-data.html | 8 +- inst/doc/profile-scores.html | 4 - inst/doc/profile.Rmd | 5 - inst/doc/profile.html | 6 - man/CollapseNode.Rd |only man/DescendantEdges.Rd | 4 - man/DropSingleSplits.Rd |only man/ICSteps.Rd | 4 - man/IWScore.Rd | 10 +- man/NonDuplicateRoot.Rd | 3 man/ProfileScore.Rd | 18 ++-- man/Ratchet.Rd | 4 - man/ReadTntTree.Rd | 19 +++- man/RearrangeEdges.Rd | 3 man/Renumber.Rd | 3 man/RenumberTree.Rd | 4 - man/SPR.Rd | 3 man/SingleCharMorphy.Rd | 5 - man/SplitFrequency.Rd | 20 +---- man/SplitsRepeated.Rd |only man/Subtree.Rd | 5 - man/Tree2Splits.Rd |only man/TreeSearch.Rd | 3 man/UniqueSplits.Rd |only man/congreveLamsdellMatrices.Rd | 3 man/inapplicable.citations.Rd | 7 + man/inapplicable.datasets.Rd | 7 + man/inapplicable.phyData.Rd | 7 + src/RMorphy.c | 34 +++----- src/RMorphy.h | 1 src/RcppExports.cpp |only src/TreeSearch-init.c | 7 + src/ape_reorder.h | 2 src/build_postorder.h | 47 ++++++------ src/morphy.h | 15 +-- src/mpl.c | 35 ++++----- src/mpl.h | 18 ++-- src/mplerror.h | 2 src/phangorn_bip.cpp |only src/renumber_tree.h | 26 +++--- tests/testthat/test-Partitions.R |only tests/testthat/test-Support.R |only tests/testthat/test-mpl-search.R | 40 ---------- tests/testthat/test-parsers.R | 3 tests/testthat/test-tree-rearrange.R | 23 ++++++ vignettes/inapplicable.Rmd | 2 vignettes/profile.Rmd | 5 - 74 files changed, 576 insertions(+), 399 deletions(-)
Title: The Serial Interface Package
Description: Enables reading and writing binary and ASCII data to
RS232/RS422/RS485 or any other virtual serial interfaces of the
computer.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>
Diff between serial versions 2.0 dated 2018-12-05 and 2.1.2 dated 2018-12-07
DESCRIPTION | 6 ++-- MD5 | 19 +++++++------ NAMESPACE | 1 R/init.R | 2 - R/pkgname.R | 1 R/serial.R | 58 ++++++++++++++++++++++++++++++++++++------ man/nBytesInQueue.Rd |only man/read.serialConnection.Rd | 11 ++++++- man/serial.Rd | 1 man/serialConnection.Rd | 2 - man/write.serialConnection.Rd | 3 ++ 11 files changed, 81 insertions(+), 23 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<http://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 1.6-2 dated 2018-08-03 and 2.0-0 dated 2018-12-07
icesTAF-1.6-2/icesTAF/R/read.dls.R |only icesTAF-1.6-2/icesTAF/R/tafpng.R |only icesTAF-1.6-2/icesTAF/R/write.dls.R |only icesTAF-1.6-2/icesTAF/man/read.dls.Rd |only icesTAF-1.6-2/icesTAF/man/tafpng.Rd |only icesTAF-1.6-2/icesTAF/man/write.dls.Rd |only icesTAF-2.0-0/icesTAF/DESCRIPTION | 12 ++-- icesTAF-2.0-0/icesTAF/MD5 | 79 ++++++++++++++------------- icesTAF-2.0-0/icesTAF/NAMESPACE | 9 ++- icesTAF-2.0-0/icesTAF/NEWS | 23 +++++++ icesTAF-2.0-0/icesTAF/R/clean.R | 23 ++++++- icesTAF-2.0-0/icesTAF/R/deps.R | 2 icesTAF-2.0-0/icesTAF/R/dos2unix.R | 7 +- icesTAF-2.0-0/icesTAF/R/download.R | 7 +- icesTAF-2.0-0/icesTAF/R/icesTAF-package.R | 9 ++- icesTAF-2.0-0/icesTAF/R/make.R | 2 icesTAF-2.0-0/icesTAF/R/makeAll.R | 8 +- icesTAF-2.0-0/icesTAF/R/makeTAF.R | 5 - icesTAF-2.0-0/icesTAF/R/mkdir.R | 10 +-- icesTAF-2.0-0/icesTAF/R/os.unix.R |only icesTAF-2.0-0/icesTAF/R/os.windows.R |only icesTAF-2.0-0/icesTAF/R/rmdir.R |only icesTAF-2.0-0/icesTAF/R/sourceAll.R | 8 +- icesTAF-2.0-0/icesTAF/R/sourceTAF.R | 15 ++--- icesTAF-2.0-0/icesTAF/R/taf.library.R |only icesTAF-2.0-0/icesTAF/R/taf.png.R |only icesTAF-2.0-0/icesTAF/R/taf.skeleton.R | 8 +- icesTAF-2.0-0/icesTAF/R/taf.unzip.R |only icesTAF-2.0-0/icesTAF/R/write.taf.R | 10 +++ icesTAF-2.0-0/icesTAF/data/catage.long.rda |binary icesTAF-2.0-0/icesTAF/data/catage.taf.rda |binary icesTAF-2.0-0/icesTAF/data/catage.xtab.rda |binary icesTAF-2.0-0/icesTAF/data/summary.taf.rda |binary icesTAF-2.0-0/icesTAF/data/taf.colors.rda |binary icesTAF-2.0-0/icesTAF/man/clean.Rd | 17 ++++- icesTAF-2.0-0/icesTAF/man/dos2unix.Rd | 7 +- icesTAF-2.0-0/icesTAF/man/download.Rd | 7 +- icesTAF-2.0-0/icesTAF/man/icesTAF-package.Rd | 9 ++- icesTAF-2.0-0/icesTAF/man/make.Rd | 2 icesTAF-2.0-0/icesTAF/man/makeAll.Rd | 6 -- icesTAF-2.0-0/icesTAF/man/mkdir.Rd | 10 +-- icesTAF-2.0-0/icesTAF/man/os.unix.Rd |only icesTAF-2.0-0/icesTAF/man/rmdir.Rd |only icesTAF-2.0-0/icesTAF/man/sourceAll.Rd | 6 -- icesTAF-2.0-0/icesTAF/man/sourceTAF.Rd | 11 +-- icesTAF-2.0-0/icesTAF/man/taf.library.Rd |only icesTAF-2.0-0/icesTAF/man/taf.png.Rd |only icesTAF-2.0-0/icesTAF/man/taf.unzip.Rd |only icesTAF-2.0-0/icesTAF/man/write.taf.Rd | 8 ++ 49 files changed, 191 insertions(+), 129 deletions(-)
Title: Functions Related to ICES Advice
Description: A collection of functions that facilitate computational steps
related to advice for fisheries management, according to ICES guidelines.
These include methods for calculating reference points and model diagnostics.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Anne Cooper [aut]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesAdvice versions 1.4-2 dated 2018-06-26 and 2.0-0 dated 2018-12-07
DESCRIPTION | 15 +++++++++------ MD5 | 40 ++++++++++++++++++++++------------------ NAMESPACE | 2 ++ NEWS | 9 +++++++++ R/Bpa.R | 3 +++ R/DLS3.2.R | 3 +++ R/Fpa.R | 5 ++++- R/icesAdvice-package.R | 14 +++++++++++--- R/icesRound.R | 2 +- R/read.dls.R |only R/sigmaCI.R | 7 +++++-- R/sigmaPA.R | 7 +++++-- R/write.dls.R |only data/shake.rda |binary man/Bpa.Rd | 3 +++ man/DLS3.2.Rd | 3 +++ man/Fpa.Rd | 5 ++++- man/icesAdvice-package.Rd | 13 ++++++++++--- man/icesRound.Rd | 2 +- man/read.dls.Rd |only man/sigmaCI.Rd | 7 +++++-- man/sigmaPA.Rd | 7 +++++-- man/write.dls.Rd |only 23 files changed, 105 insertions(+), 42 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: This is a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download (and re-arrange, in the
case of NDVI3g.v0) the half-monthly data sets from
<https://ecocast.arc.nasa.gov/data/pub/gimms/>; import downloaded files from
ENVI binary (NDVI3g.v0) or NetCDF format (NDVI3g.v1) directly into R based
on the widespread 'raster' package; conduct quality control; and generate
monthly composites (e.g., maximum values) from the half-monthly input data.
As a special gimmick, a method is included to conveniently apply the
Mann-Kendall trend test upon 'Raster*' images, optionally featuring
trend-free pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between gimms versions 1.1.0 dated 2018-01-12 and 1.1.1 dated 2018-12-07
DESCRIPTION | 11 ++++++----- MD5 | 43 ++++++++++++++++++++++--------------------- NEWS | 9 +++++++++ NEWS.md | 9 +++++++++ R/gimmsControls.R | 4 +--- R/monthlyComposite.R | 4 +--- R/monthlyIndices.R | 9 +++++---- R/oldNaming.R | 2 -- R/qualityControl.R | 4 +--- R/rasterizeGimms.R | 14 ++++---------- R/significantTau.R | 14 ++++---------- README.md | 6 ++++++ build |only data/bale3g.v1.rda |binary data/kili3g.v0.rda |binary man/downloadGimms.Rd | 4 ++-- man/monthlyComposite.Rd | 4 ++-- man/monthlyIndices.Rd | 9 +++++---- man/oldNaming.Rd | 2 -- man/qualityControl.Rd | 4 ++-- man/rasterizeGimms.Rd | 4 ++-- man/rearrangeFiles.Rd | 4 ++-- man/significantTau.Rd | 18 ++++++------------ 23 files changed, 89 insertions(+), 89 deletions(-)
Title: 32-Bit Floats
Description: R comes with a suite of utilities for linear algebra with "numeric"
(double precision) vectors/matrices. However, sometimes single precision (or
less!) is more than enough for a particular task. This package extends R's
linear algebra facilities to include 32-bit float (single precision) data.
Float vectors/matrices have half the precision of their "numeric"-type
counterparts but are generally faster to numerically operate on, for a
performance vs accuracy trade-off. The internal representation is an S4
class, which allows us to keep the syntax identical to that of base R's.
Interaction between floats and base types for binary operators is generally
possible; in these cases, type promotion always defaults to the higher
precision. The package ships with copies of the single precision 'BLAS' and
'LAPACK', which are automatically built in the event they are not available
on the system.
Author: Drew Schmidt [aut, cre, cph],
Wei-Chen Chen [aut],
Dmitriy Selivanov [ctb] (improvements in external package linking),
ORNL [cph]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between float versions 0.2-0 dated 2018-08-06 and 0.2-1 dated 2018-12-07
float-0.2-0/float/R/machine.r |only float-0.2-0/float/man/machine_float.Rd |only float-0.2-1/float/ChangeLog | 6 float-0.2-1/float/DESCRIPTION | 13 float-0.2-1/float/MD5 | 176 +++++------ float-0.2-1/float/NAMESPACE | 1 float-0.2-1/float/R/02-flags.r | 66 +++- float-0.2-1/float/R/backsolve.r | 1 float-0.2-1/float/R/binary.r | 2 float-0.2-1/float/R/chol.r | 1 float-0.2-1/float/R/chol2inv.r | 1 float-0.2-1/float/R/colSums.r | 1 float-0.2-1/float/R/cond.r | 1 float-0.2-1/float/R/converters.r | 1 float-0.2-1/float/R/crossprod.r | 1 float-0.2-1/float/R/eigen.r | 1 float-0.2-1/float/R/extremes.r | 1 float-0.2-1/float/R/float-package.r | 15 float-0.2-1/float/R/isSymmetric.r | 1 float-0.2-1/float/R/math.r | 7 float-0.2-1/float/R/matmult.r | 1 float-0.2-1/float/R/na.r | 1 float-0.2-1/float/R/norm.r | 1 float-0.2-1/float/R/print.r | 42 ++ float-0.2-1/float/R/qr.r | 1 float-0.2-1/float/R/rand.r | 1 float-0.2-1/float/R/scale.r | 21 + float-0.2-1/float/R/solve.r | 1 float-0.2-1/float/R/special.r |only float-0.2-1/float/R/sum.r | 1 float-0.2-1/float/R/svd.r | 1 float-0.2-1/float/R/sweep.r | 1 float-0.2-1/float/R/xpose.r | 1 float-0.2-1/float/R/zzz.r | 33 +- float-0.2-1/float/README.md | 2 float-0.2-1/float/cleanup | 1 float-0.2-1/float/configure | 525 --------------------------------- float-0.2-1/float/configure.ac | 10 float-0.2-1/float/data |only float-0.2-1/float/inst/doc/float.Rnw | 21 + float-0.2-1/float/inst/doc/float.pdf |binary float-0.2-1/float/man/Machine_float.Rd |only float-0.2-1/float/man/NA_float_.Rd |only float-0.2-1/float/man/NaNf.Rd |only float-0.2-1/float/man/arithmetic.Rd | 45 +- float-0.2-1/float/man/backsolve.Rd | 13 float-0.2-1/float/man/bind.Rd | 3 float-0.2-1/float/man/bracket.Rd | 3 float-0.2-1/float/man/c.Rd | 1 float-0.2-1/float/man/chol.Rd | 1 float-0.2-1/float/man/chol2inv.Rd | 1 float-0.2-1/float/man/colsums.Rd | 7 float-0.2-1/float/man/comparison.Rd | 1 float-0.2-1/float/man/converters.Rd | 15 float-0.2-1/float/man/crossprod.Rd | 1 float-0.2-1/float/man/diag.Rd | 1 float-0.2-1/float/man/dims.Rd | 11 float-0.2-1/float/man/eigen.Rd | 1 float-0.2-1/float/man/extremes.Rd | 5 float-0.2-1/float/man/float-package.Rd | 1 float-0.2-1/float/man/float.Rd | 1 float-0.2-1/float/man/float32.Rd | 1 float-0.2-1/float/man/hyperbolic.Rd | 9 float-0.2-1/float/man/is.float.Rd | 1 float-0.2-1/float/man/isSymmetric.Rd | 1 float-0.2-1/float/man/log.Rd | 3 float-0.2-1/float/man/mathis.Rd | 3 float-0.2-1/float/man/matmult.Rd | 3 float-0.2-1/float/man/miscmath.Rd | 3 float-0.2-1/float/man/na.Rd | 5 float-0.2-1/float/man/names.Rd | 9 float-0.2-1/float/man/norm.Rd | 1 float-0.2-1/float/man/print-float32.Rd | 9 float-0.2-1/float/man/qr.Rd | 3 float-0.2-1/float/man/rand.Rd | 7 float-0.2-1/float/man/rcond.Rd | 5 float-0.2-1/float/man/rep.Rd | 1 float-0.2-1/float/man/round.Rd | 5 float-0.2-1/float/man/scale.Rd | 1 float-0.2-1/float/man/solve.Rd | 1 float-0.2-1/float/man/specialmath.Rd | 3 float-0.2-1/float/man/sum.Rd | 1 float-0.2-1/float/man/svd.Rd | 3 float-0.2-1/float/man/sweep.Rd | 5 float-0.2-1/float/man/trig.Rd | 11 float-0.2-1/float/man/xpose.Rd | 3 float-0.2-1/float/src/Makevars.in | 12 float-0.2-1/float/src/Makevars.win | 9 float-0.2-1/float/src/NA.c | 4 float-0.2-1/float/src/install.libs.R |only float-0.2-1/float/src/scale.c | 16 - float-0.2-1/float/vignettes/float.Rnw | 21 + 92 files changed, 411 insertions(+), 820 deletions(-)
Title: Fixed Effects Nonlinear Maximum Likelihood Models
Description: Efficient estimation of maximum likelihood models with multiple fixed-effects. Standard-errors can easily and flexibly be clustered and estimations exported.
Author: Laurent Berge [aut, cre]
Maintainer: Laurent Berge <laurent.berge@uni.lu>
Diff between FENmlm versions 2.3 dated 2018-11-15 and 2.3.1 dated 2018-12-07
DESCRIPTION | 8 - MD5 | 22 +-- R/MiscFuns.R | 113 +++++++++++++++-- R/RcppExports.R | 72 +++++------ R/femlm.R | 73 ++++++----- inst/NEWS.Rd | 24 +++ inst/doc/FENmlm.html | 37 +++-- man/femlm.Rd | 4 man/res2table.Rd | 2 man/res2tex.Rd | 6 src/RcppExports.cpp | 280 ++++++++++++++++++++++---------------------- src/Rcpp_get_derivative.cpp | 4 12 files changed, 387 insertions(+), 258 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-04 0.0.2
2018-05-11 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-18 1.05
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/svn-trunk/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.1-4 dated 2018-01-28 and 0.1-5 dated 2018-12-07
lwgeom-0.1-4/lwgeom/R/geodetic.R |only lwgeom-0.1-4/lwgeom/man/lw_geodetic.Rd |only lwgeom-0.1-5/lwgeom/DESCRIPTION | 16 ++-- lwgeom-0.1-5/lwgeom/MD5 | 75 +++++++++++-------- lwgeom-0.1-5/lwgeom/NAMESPACE | 18 ++++ lwgeom-0.1-5/lwgeom/NEWS.md | 16 ++++ lwgeom-0.1-5/lwgeom/R/RcppExports.R | 24 ++++++ lwgeom-0.1-5/lwgeom/R/bearing.R | 2 lwgeom-0.1-5/lwgeom/R/bounding_circle.R | 2 lwgeom-0.1-5/lwgeom/R/clockwise.R |only lwgeom-0.1-5/lwgeom/R/geod.R |only lwgeom-0.1-5/lwgeom/R/geohash.R | 6 - lwgeom-0.1-5/lwgeom/R/init.R | 17 ---- lwgeom-0.1-5/lwgeom/R/perimeter.R |only lwgeom-0.1-5/lwgeom/R/snap_to_grid.R | 11 +- lwgeom-0.1-5/lwgeom/R/split.R | 41 ++++++++++ lwgeom-0.1-5/lwgeom/R/startpoint.R |only lwgeom-0.1-5/lwgeom/R/transform.R | 27 ++++--- lwgeom-0.1-5/lwgeom/R/wkt.R |only lwgeom-0.1-5/lwgeom/configure | 7 + lwgeom-0.1-5/lwgeom/configure.ac | 7 + lwgeom-0.1-5/lwgeom/man/geod.Rd |only lwgeom-0.1-5/lwgeom/man/perimeter.Rd |only lwgeom-0.1-5/lwgeom/man/st_astext.Rd |only lwgeom-0.1-5/lwgeom/man/st_force_polygon_cw.Rd |only lwgeom-0.1-5/lwgeom/man/st_geohash.Rd | 4 - lwgeom-0.1-5/lwgeom/man/st_is_polygon_cw.Rd |only lwgeom-0.1-5/lwgeom/man/st_linesubstring.Rd |only lwgeom-0.1-5/lwgeom/man/st_snap_to_grid.Rd | 11 +- lwgeom-0.1-5/lwgeom/man/st_split.Rd | 4 - lwgeom-0.1-5/lwgeom/man/st_startpoint.Rd |only lwgeom-0.1-5/lwgeom/man/st_transform_proj.Rd | 13 +-- lwgeom-0.1-5/lwgeom/src/Makevars.in | 3 lwgeom-0.1-5/lwgeom/src/Makevars.win | 3 lwgeom-0.1-5/lwgeom/src/RcppExports.cpp | 77 ++++++++++++++++++++ lwgeom-0.1-5/lwgeom/src/geodetic.cpp | 7 + lwgeom-0.1-5/lwgeom/src/liblwgeom/lwutil.c | 8 +- lwgeom-0.1-5/lwgeom/src/lwgeom.cpp | 70 +++++++++++++++++- lwgeom-0.1-5/lwgeom/src/sub.cpp |only lwgeom-0.1-5/lwgeom/tests/azimuth.Rout.save | 10 +- lwgeom-0.1-5/lwgeom/tests/dist.Rout.save | 10 +- lwgeom-0.1-5/lwgeom/tests/geod.Rout.save | 14 +-- lwgeom-0.1-5/lwgeom/tests/perimeter.R |only lwgeom-0.1-5/lwgeom/tests/perimeter.Rout.save |only lwgeom-0.1-5/lwgeom/tests/testthat.Rout.save | 12 +-- lwgeom-0.1-5/lwgeom/tests/testthat/test-as_text.R |only lwgeom-0.1-5/lwgeom/tests/testthat/test-clockwise.R |only lwgeom-0.1-5/lwgeom/tests/testthat/test_lwgeom.R | 21 +++++ 48 files changed, 412 insertions(+), 124 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for multiple random effects allowing the specification of variance-covariance structures for random effects and allowing the fit of heterogeneous and special variance models (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson, Direct-Inversion Average Information and Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) to include multiple relationship matrices or other covariance structures. Spatial models can be fitted using the two-dimensional spline functionality in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 3.7 dated 2018-12-04 and 3.7.1 dated 2018-12-07
DESCRIPTION | 6 MD5 | 34 +- NAMESPACE | 2 R/FUN_plotting.R | 19 + R/FUN_special.R | 23 + R/mmer.R | 107 ++++++--- inst/doc/sommer.Rmd | 6 inst/doc/sommer.pdf |binary inst/doc/sommer.start.Rmd | 4 inst/doc/sommer.start.pdf |binary man/mmer.Rd | 2 man/mmer2.Rd | 2 man/sommer-package.Rd | 6 src/MNR.cpp | 7 vignettes/sommer.Rmd | 6 vignettes/sommer.html | 279 +++++++++++------------ vignettes/sommer.start.Rmd | 4 vignettes/sommer.start.html | 520 +++++++++++++++++++++----------------------- 18 files changed, 544 insertions(+), 483 deletions(-)
Title: Ecological Inference and Higher-Dimension Data Management
Description: Provides methods for analyzing R by C ecological contingency
tables using the extreme case analysis, ecological regression,
and Multinomial-Dirichlet ecological inference models. Also
provides tools for manipulating higher-dimension data objects.
Author: Olivia Lau <olivia.lau@post.harvard.edu>, Ryan T. Moore
<rtm@american.edu>, Michael Kellermann <mrkellermann@gmail.com>
Maintainer: Michael Kellermann <mrkellermann@gmail.com>
Diff between eiPack versions 0.1-7 dated 2012-01-13 and 0.1-8 dated 2018-12-07
eiPack-0.1-7/eiPack/R/density.plot.R |only eiPack-0.1-7/eiPack/R/density.plot.default.R |only eiPack-0.1-7/eiPack/R/density.plot.lambdaMD.R |only eiPack-0.1-7/eiPack/R/density.plot.lambdaReg.R |only eiPack-0.1-7/eiPack/R/density.plot.lambdaRegBayes.R |only eiPack-0.1-8/eiPack/DESCRIPTION | 24 eiPack-0.1-8/eiPack/INDEX | 54 - eiPack-0.1-8/eiPack/LICENSE | 52 - eiPack-0.1-8/eiPack/MD5 | 55 - eiPack-0.1-8/eiPack/NAMESPACE | 68 +- eiPack-0.1-8/eiPack/R/densityplot.R |only eiPack-0.1-8/eiPack/R/densityplot.default.R |only eiPack-0.1-8/eiPack/R/densityplot.lambdaMD.R |only eiPack-0.1-8/eiPack/R/densityplot.lambdaReg.R |only eiPack-0.1-8/eiPack/R/densityplot.lambdaRegBayes.R |only eiPack-0.1-8/eiPack/R/ei.MD.bayes.R | 312 +++++----- eiPack-0.1-8/eiPack/R/tuneMD.R | 172 ++--- eiPack-0.1-8/eiPack/demo/lambda.MD.R | 2 eiPack-0.1-8/eiPack/demo/lambda.reg.R | 2 eiPack-0.1-8/eiPack/demo/lambda.reg.bayes.R | 2 eiPack-0.1-8/eiPack/man/bounds.Rd | 102 +-- eiPack-0.1-8/eiPack/man/density.plot.Rd | 105 +-- eiPack-0.1-8/eiPack/man/ei.MD.bayes.Rd | 582 ++++++++++---------- eiPack-0.1-8/eiPack/man/ei.reg.Rd | 146 ++--- eiPack-0.1-8/eiPack/man/ei.reg.bayes.Rd | 126 ++-- eiPack-0.1-8/eiPack/man/lambda.MD.Rd | 92 +-- eiPack-0.1-8/eiPack/man/lambda.reg.Rd | 124 ++-- eiPack-0.1-8/eiPack/man/lambda.reg.bayes.Rd | 60 +- eiPack-0.1-8/eiPack/man/mergeMD.Rd | 94 +-- eiPack-0.1-8/eiPack/man/plot.bounds.Rd | 77 +- eiPack-0.1-8/eiPack/man/senc.Rd | 78 +- eiPack-0.1-8/eiPack/src/eiutil.c | 6 eiPack-0.1-8/eiPack/src/init.c |only eiPack-0.1-8/eiPack/src/rbyceicov4.c | 2 34 files changed, 1178 insertions(+), 1159 deletions(-)
Title: Shadow Text Grob and Layer
Description: Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'.
These functions create/draw text grob with background shadow.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between shadowtext versions 0.0.3 dated 2018-09-29 and 0.0.4 dated 2018-12-07
DESCRIPTION | 8 - MD5 | 24 +-- NAMESPACE | 38 ++--- R/geom-shadowtext.R | 232 +++++++++++++++---------------- R/shadowtext-grob.R | 166 +++++++++++----------- build/vignette.rds |binary inst/doc/shadowtext.R | 78 +++++----- inst/doc/shadowtext.Rmd | 150 ++++++++++---------- inst/doc/shadowtext.html | 348 +++++++++++++++++++++++------------------------ man/geom_shadowtext.Rd | 100 ++++++------- man/reexports.Rd | 32 ++-- man/shadowtextGrob.Rd | 118 +++++++-------- vignettes/shadowtext.Rmd | 150 ++++++++++---------- 13 files changed, 722 insertions(+), 722 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrdesign versions 2.5.4 dated 2017-12-04 and 2.5.5 dated 2018-12-07
secrdesign-2.5.4/secrdesign/R/Twenty20.R |only secrdesign-2.5.4/secrdesign/man/figures |only secrdesign-2.5.5/secrdesign/DESCRIPTION | 13 secrdesign-2.5.5/secrdesign/MD5 | 59 ++- secrdesign-2.5.5/secrdesign/NAMESPACE | 15 secrdesign-2.5.5/secrdesign/NEWS | 16 secrdesign-2.5.5/secrdesign/R/methods.R | 3 secrdesign-2.5.5/secrdesign/R/optimalSpacing.R | 215 ++++++----- secrdesign-2.5.5/secrdesign/R/power.R |only secrdesign-2.5.5/secrdesign/R/run.scenarios.R | 134 ++++-- secrdesign-2.5.5/secrdesign/R/scenarioSummary.R | 24 + secrdesign-2.5.5/secrdesign/R/select.stats.R | 4 secrdesign-2.5.5/secrdesign/build |only secrdesign-2.5.5/secrdesign/inst/doc/secrdesign-manual.pdf |binary secrdesign-2.5.5/secrdesign/inst/doc/secrdesign-vignette.R |only secrdesign-2.5.5/secrdesign/inst/doc/secrdesign-vignette.Rmd |only secrdesign-2.5.5/secrdesign/inst/doc/secrdesign-vignette.pdf |only secrdesign-2.5.5/secrdesign/man/optimalSpacing.Rd | 15 secrdesign-2.5.5/secrdesign/man/predict.simulations.Rd | 4 secrdesign-2.5.5/secrdesign/man/run.scenarios.Rd | 17 secrdesign-2.5.5/secrdesign/man/scenarioSummary.Rd | 5 secrdesign-2.5.5/secrdesign/man/secrdesign-package.Rd | 4 secrdesign-2.5.5/secrdesign/vignettes |only 23 files changed, 339 insertions(+), 189 deletions(-)
Title: Additive Main Effects and Multiplicative Interaction Model
Stability Parameters
Description: Computes various stability parameters from Additive Main Effects
and Multiplicative Interaction (AMMI) analysis results such as Modified
AMMI Stability Value (MASV), Sums of the Absolute Value of the Interaction
Principal Component Scores (SIPC), Sum Across Environments of
Genotype-Environment Interaction Modelled by AMMI (AMGE), Sum Across
Environments of Absolute Value of Genotype-Environment Interaction Modelled
by AMMI (AV_(AMGE)), AMMI Stability Index (ASI), Modified ASI (MASI), AMMI
Based Stability Parameter (ASTAB), Annicchiarico's D Parameter (DA), Zhang's
D Parameter (DZ), Averages of the Squared Eigenvector Values (EV), Stability
Measure Based on Fitted AMMI Model (FA), Absolute Value of the Relative
Contribution of IPCs to the Interaction (Za). Further calculates the
Simultaneous Selection Index for Yield and Stability from the computed
stability parameters. See the vignette for complete list of citations for
the methods implemented.
Author: B. C. Ajay [aut, cre] (<https://orcid.org/0000-0001-7222-8483>),
J. Aravind [aut] (<https://orcid.org/0000-0002-4791-442X>),
R. Abdul Fiyaz [aut],
ICAR [cph] (https://www.icar.org.in)
Maintainer: B. C. Ajay <ajaygpb@yahoo.co.in>
Diff between ammistability versions 0.1.0 dated 2018-08-13 and 0.1.1 dated 2018-12-07
DESCRIPTION | 12 +++-- MD5 | 48 +++++++++++----------- NEWS.md | 9 ++++ R/AMGE.AMMI.R | 5 +- R/ASI.AMMI.R | 5 +- R/ASTAB.AMMI.R | 5 +- R/AVAMGE.AMMI.R | 5 +- R/DA.AMMI.R | 5 +- R/DZ.AMMI.R | 5 +- R/EV.AMMI.R | 5 +- R/FA.AMMI.R | 5 +- R/MASI.AMMI.R | 8 +++ R/MASV.AMMI.R | 5 +- R/SIPC.AMMI.R | 5 +- R/SSI.R | 2 R/ZA.AMMI.R | 5 +- README.md | 54 ++++++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 - inst/doc/Introduction.Rmd | 95 ++++++++++++++++++++++++++++++++++++--------- inst/doc/Introduction.pdf |binary man/SSI.Rd | 2 vignettes/Introduction.Rmd | 95 ++++++++++++++++++++++++++++++++++++--------- vignettes/stability.rda |binary 25 files changed, 280 insertions(+), 104 deletions(-)
Title: Parametric Models for Survival Data
Description: Executes simple parametric models for right-censored
survival data. Functionality emulates capabilities in 'Minitab', including
fitting right-censored data, assessing fit, plotting survival functions,
and summary statistics and probabilities.
Author: Ashley Jacobson [aut, cre],
Victor Wilson [aut],
Shannon Pileggi [aut]
Maintainer: Ashley Jacobson <ashleypjacobson@gmail.com>
Diff between parmsurvfit versions 0.0.1 dated 2018-10-08 and 0.1.0 dated 2018-12-07
parmsurvfit-0.0.1/parmsurvfit/R/plot_qqsurv.R |only parmsurvfit-0.0.1/parmsurvfit/man/plot_qqsurv.Rd |only parmsurvfit-0.1.0/parmsurvfit/DESCRIPTION | 28 - parmsurvfit-0.1.0/parmsurvfit/MD5 | 33 + parmsurvfit-0.1.0/parmsurvfit/NAMESPACE | 2 parmsurvfit-0.1.0/parmsurvfit/R/parmsurvfit.R | 2 parmsurvfit-0.1.0/parmsurvfit/R/plot_ppsurv.R |only parmsurvfit-0.1.0/parmsurvfit/R/surv_prob.R | 40 +- parmsurvfit-0.1.0/parmsurvfit/README.md | 87 ++++ parmsurvfit-0.1.0/parmsurvfit/build/vignette.rds |binary parmsurvfit-0.1.0/parmsurvfit/inst/doc/parmsurvfit_vig.R | 87 +++- parmsurvfit-0.1.0/parmsurvfit/inst/doc/parmsurvfit_vig.Rmd | 176 ++++----- parmsurvfit-0.1.0/parmsurvfit/inst/doc/parmsurvfit_vig.html | 227 ++++++------ parmsurvfit-0.1.0/parmsurvfit/man/figures |only parmsurvfit-0.1.0/parmsurvfit/man/parmsurvfit.Rd | 2 parmsurvfit-0.1.0/parmsurvfit/man/plot_ppsurv.Rd |only parmsurvfit-0.1.0/parmsurvfit/man/surv_prob.Rd | 14 parmsurvfit-0.1.0/parmsurvfit/vignettes/parmsurvfit_vig.Rmd | 176 ++++----- 18 files changed, 527 insertions(+), 347 deletions(-)
Title: Converts 'R' Objects to Javascript Object Notation (JSON)
Description: Converts 'R' objects into Javascript Object Notation (JSON) using
the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between jsonify versions 0.1.1 dated 2018-10-14 and 0.1.2 dated 2018-12-07
DESCRIPTION | 14 ++--- MD5 | 36 ++++++------ NAMESPACE | 1 NEWS.md |only R/RcppExports.R | 36 ++++++------ R/jsondf-package.R | 1 R/to_json.R | 57 ++++++++++---------- README.md | 34 +++++++++++- inst/include/jsonify/to_json/dataframe.hpp | 8 +- inst/include/jsonify/to_json/matrix.hpp | 12 ++-- inst/include/jsonify/to_json/vectors.hpp | 20 +++---- inst/include/jsonify/to_json/writers.hpp | 61 +++++++++++++-------- inst/include/jsonify/utils.hpp | 22 +++++++ man/to_json.Rd | 34 +++++++----- src/RcppExports.cpp | 81 ++++++++++++++++------------- src/to_json.cpp | 36 ++++++------ tests/testthat/test-to_json_dataframe.R | 24 +++++++- tests/testthat/test-to_json_lists.R | 13 ++++ tests/testthat/test-to_json_vectors.R | 16 +++++ tests/testthat/test-unbox.R |only 20 files changed, 318 insertions(+), 188 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers
can be painful. Dealing with authentication, server state,
and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three
contexts that mock the network connection in different ways, as well as
testing functions to assert that HTTP requests were---or were
not---made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables one to write vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 3.2.0 dated 2018-11-09 and 3.2.2 dated 2018-12-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/expect-header.R | 1 + R/trace.R | 15 ++++++++++++++- 5 files changed, 27 insertions(+), 9 deletions(-)