Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-16 0.1-10
2013-12-11 0.1-8
2013-06-17 0.1-7
2011-03-11 0.1-03
2010-03-07 0.1-02
2008-06-13 0.1-00
Title: Index of Local Sensitivity to Nonignorability
Description: The current version provides functions to compute, print and summarize the Index of Sensitivity to Nonignorability (ISNI) in the generalized linear model for independent data, and in the marginal multivariate Gaussian model and the linear mixed model for longitudinal/clustered data. It allows for arbitrary patterns of missingness in the regression outcomes caused by dropout and/or intermittent missingness. One can compute the sensitivity index without estimating any nonignorable models or positing specific magnitude of nonignorability. Thus ISNI provides a simple quantitative assessment of how robust the standard estimates assuming missing at random is with respect to the assumption of ignorability. For a tutorial, download at <http://huixie.people.uic.edu/Research/ISNI_R_tutorial.pdf>. For more details, see Troxel Ma and Heitjan (2004) and Xie and Heitjan (2004) <doi:10.1191/1740774504cn005oa> and Ma Troxel and Heitjan (2005) <doi:10.1002/sim.2107> and Xie (2008) <doi:10.1002/sim.3117> and Xie (2012) <doi:10.1016/j.csda.2010.11.021> and Xie and Qian (2012) <doi:10.1002/jae.1157>.
Author: Hui Xie <huixie@uic.edu>, Weihua Gao, Baodong Xing, Daniel Heitjan, Donald Hedeker, Chengbo Yuan
Maintainer: Hui Xie <huixie@uic.edu>
Diff between isni versions 0.3 dated 2018-06-16 and 0.4 dated 2019-02-04
DESCRIPTION | 6 ++--- MD5 | 9 ++++--- NEWS.md |only R/isnilmm.R | 25 +++++++++++++++------- R/isnimgm.R | 50 ++++++++++++++++++++++++++++++++++++++------ inst/doc/isni_vignette.html | 24 ++++++++++----------- 6 files changed, 82 insertions(+), 32 deletions(-)
Title: Functions to Import Data from 'z-Tree' into R
Description: Read '.xls' and '.sbj' files which are written by the
Microsoft Windows program 'z-Tree'. The latter is a software for
developing and carrying out economic experiments
(see <http://www.ztree.uzh.ch/> for more information).
Author: Oliver Kirchkamp
Maintainer: Oliver Kirchkamp <oliver@kirchkamp.de>
Diff between zTree versions 1.0.5 dated 2019-01-02 and 1.0.6 dated 2019-02-04
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NAMESPACE | 1 - NEWS.md | 2 ++ R/zTreeSbj.R | 2 +- R/zTreeTables.R | 4 ++-- build/partial.rdb |binary 7 files changed, 17 insertions(+), 15 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://www.laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] (Enable the support of .lax file and
extra byte attributes),
Martin Isenburg [cph] (Is the author of the LASlib and LASzip
libraries),
David Auty [ctb] (Reviewed the documentation),
Pierrick Marie [ctb] (Helped to compile LASlib code in R),
Tiago de Conto [ctb] (Implemented the -thin_with_voxel filter method)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between rlas versions 1.2.9 dated 2018-10-25 and 1.3.0 dated 2019-02-04
rlas-1.2.9/rlas/R/checkers.r |only rlas-1.2.9/rlas/man/header_add_extrabytes.Rd |only rlas-1.2.9/rlas/man/header_create.Rd |only rlas-1.3.0/rlas/DESCRIPTION | 16 rlas-1.3.0/rlas/MD5 | 59 - rlas-1.3.0/rlas/NAMESPACE | 58 + rlas-1.3.0/rlas/NEWS.md | 8 rlas-1.3.0/rlas/R/RcppExports.R | 8 rlas-1.3.0/rlas/R/check_content.r |only rlas-1.3.0/rlas/R/deprecated.r |only rlas-1.3.0/rlas/R/header_tools.r | 234 ++++- rlas-1.3.0/rlas/R/las_specifications.r |only rlas-1.3.0/rlas/R/readLAS.r | 12 rlas-1.3.0/rlas/R/writeLAS.r | 24 rlas-1.3.0/rlas/README.md | 40 rlas-1.3.0/rlas/inst/include/lasdefinitions.hpp | 8 rlas-1.3.0/rlas/inst/include/rlasextrabytesattributes.h |only rlas-1.3.0/rlas/inst/include/rlasstreamer.h | 57 - rlas-1.3.0/rlas/man/check.Rd | 32 rlas-1.3.0/rlas/man/crs_tools.Rd |only rlas-1.3.0/rlas/man/deprecated.Rd |only rlas-1.3.0/rlas/man/extra_bytes_attribute_tools.Rd |only rlas-1.3.0/rlas/man/las_specification_tools.Rd |only rlas-1.3.0/rlas/man/public_header_block_tools.Rd |only rlas-1.3.0/rlas/man/read.las.Rd | 12 rlas-1.3.0/rlas/src/LASlib/lasfilter.cpp | 63 + rlas-1.3.0/rlas/src/Makevars | 1 rlas-1.3.0/rlas/src/Makevars.win | 1 rlas-1.3.0/rlas/src/RcppExports.cpp | 38 rlas-1.3.0/rlas/src/fast.cpp | 2 rlas-1.3.0/rlas/src/readLAS.cpp | 6 rlas-1.3.0/rlas/src/readheader.cpp | 83 + rlas-1.3.0/rlas/src/rlasextrabytesattributes.cpp |only rlas-1.3.0/rlas/src/rlasstreamer.cpp | 445 ++++------ rlas-1.3.0/rlas/src/writeLAS.cpp | 669 +++++----------- rlas-1.3.0/rlas/tests/testthat/test-header_tools.R | 23 rlas-1.3.0/rlas/tests/testthat/test-writelas.R | 59 + 37 files changed, 1033 insertions(+), 925 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for
the sample selection bias from observed outcomes in matching
markets. This includes one-sided matching of agents into
groups as well as two-sided matching of students to schools.
The package also contains algorithms to find stable matchings
in the three most common matching problems: the stable roommates
problem, the college admissions problem, and the house
allocation problem.
Author: Thilo Klein [aut, cre],
Robert Aue [ctb],
Sven Giegerich [ctb],
Alexander Sauer [ctb]
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 1.0-0 dated 2018-12-04 and 1.0-1 dated 2019-02-04
DESCRIPTION | 11 +- MD5 | 48 ++++----- NAMESPACE | 1 NEWS.md | 12 +- R/hri.R | 212 +++++++++++++++++++++-------------------- R/hri2.R | 7 - R/iaa.R | 60 +++++------ R/rsd.R | 121 +++++++++++------------ R/stabit.R | 1 R/stabit2.R | 3 R/ttc.R | 60 +++++------ R/ttc2.R | 57 +++++------ R/ttcc.R | 45 ++++---- R/xlogit.data.R |only build/vignette.rds |binary inst/doc/matching.pdf |binary inst/include/params.h | 96 +++++++++--------- man/hri.Rd | 4 man/iaa.Rd | 6 - man/matchingMarkets-package.Rd | 2 man/rsd.Rd | 2 man/stabit.Rd | 1 man/ttc.Rd | 10 - man/ttc2.Rd | 10 - man/ttcc.Rd | 10 - man/xlogit.data.Rd |only 26 files changed, 402 insertions(+), 377 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Identification of the Factors Affecting Species Richness
Description: It identifies the factors significantly related to species richness, and their relative contribution, using multiple regressions and support vector machine models. It uses an output file of 'ModestR' (<http://www.ipez.es/ModestR>) with data of richness of the species and environmental variables in a cell size defined by the user. The residuals of the support vector machine model are shown on a map. Negative residuals may be potential areas with undiscovered and/or unregistered species, or areas with decreased species richness due to the negative effect of anthropogenic factors.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between FactorsR versions 1.3 dated 2018-12-06 and 1.4 dated 2019-02-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- data/adworld.RData |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Download Data from Mexico's Air Quality Information System
Description: Easy-to-use functions for downloading air quality data from the
Mexican National Air Quality Information System (SINAICA). Allows you to
query pollution and meteorological parameters from more than a hundred
monitoring stations located throughout Mexico. See <https://sinaica.inecc.gob.mx>
for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Diff between rsinaica versions 0.6.0 dated 2018-10-24 and 0.6.1 dated 2019-02-04
DESCRIPTION | 6 - MD5 | 8 +- NEWS.md | 4 + R/sinaica_station_data.R | 139 ++++++++++++++++++----------------- R/sinaica_station_params_and_dates.R | 88 +++++++++++++--------- 5 files changed, 140 insertions(+), 105 deletions(-)
Title: Analysis of MHC Data in Non-Model Species
Description: Ten tools for analysis of major histocompatibility complex (MHC) data in non-
model species. The functions are tailored for amplicon data sets that have been
filtered using the 'dada2' method (for more information visit
<https://benjjneb.github.io/dada2>), but even other data sets can be analysed,
if the data tables are formatted according to the description in each function.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The HpltFind() function infers putative haplotypes from families in the data
set.
The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of
the haplotype inference.
The PapaDiv() function compares parent pairs in the data set and calculate their
joint MHC diversity, taking into account sequence variants that occur in both
parents.
The MeanPdist() function calculates the mean p-distance from pairwise
comparisons sequences in each sample in a data set. The function includes the
option to specify which codons to compare.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates a fasta file for each sample in the data
set.
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.1.0 dated 2017-10-23 and 1.1.1 dated 2019-02-04
DESCRIPTION | 8 +- LICENSE | 2 MD5 | 14 ++-- NEWS.md | 7 ++ R/GetHpltTable_func_20170924.R | 4 + R/GetReplTable_func_20170924.R | 4 + R/HpltFind_func_20170924.R | 123 +++++++++++++++++++++-------------------- R/PapaDiv_func_20170924.R | 2 8 files changed, 91 insertions(+), 73 deletions(-)
More information about safetyGraphics at CRAN
Permanent link
Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at <http://www.phidot.org/software/mark/downloads/>
but is not open source.
Author: Jeff Laake <jefflaake@gmail.com> with code contributions from Eldar
Rakhimberdiev, Ben Augustine, Daniel Turek and Brett McClintock and example data and analysis
from Bret Collier, Jay Rotella, David Pavlacky, Andrew Paul, Luke Eberhart-
Phillips, and Jake Ivan.
Maintainer: Jeff Laake <jefflaake@gmail.com>
Diff between RMark versions 2.2.5 dated 2018-07-13 and 2.2.6 dated 2019-02-04
DESCRIPTION | 15 +- MD5 | 47 ++++--- NEWS | 28 ++++ R/RMark-package.R | 114 +++++++++++++++++- R/collect.model.names.R | 8 - R/collect.models.R | 2 R/compute.design.data.R | 271 +++++++++++++++++++++---------------------- R/covariate.predictions.r | 26 ++-- R/export.MARK.r | 17 ++ R/export.chdata.R | 1 R/make.design.data.R | 191 +++++++++++++++--------------- R/make.mark.model.R | 126 +++++++++++-------- R/process.data.R | 62 ++++++--- data/Density.r |only data/Density.txt |only data/NSpeciesOcc.rda |only inst/DerivedPar.txt | 4 inst/MarkModels.pdf |binary inst/models.txt | 7 - inst/parameters.txt | 25 +++ man/Burnham.Rd | 2 man/Density.Rd |only man/NSpeciesOcc.Rd |only man/collect.models.Rd | 2 man/compute.design.data.Rd | 4 man/covariate.predictions.Rd | 26 ++-- man/process.data.Rd | 2 27 files changed, 605 insertions(+), 375 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis
of chemical toxicokinetics ("TK") as in Pearce et al. (2017)
<doi:10.18637/jss.v079.i04>. Chemical-specific in vitro
data have been obtained from relatively high throughput
experiments. Both physiologically-based ("PBTK") and empirical
(e.g., one compartment) "TK" models can be parameterized for
several hundred chemicals and multiple species. These models are
solved efficiently, often using compiled (C-based) code. A Monte
Carlo sampler is included for simulating biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and measurement limitations. Calibrated methods are included for
predicting tissue:plasma partition coefficients and volume of
distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for
in vitro-in vivo extrapolation ("IVIVE") of high throughput
screening data (e.g., Tox21, ToxCast) to real-world exposures via
reverse dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre],
Robert Pearce [aut],
Caroline Ring [aut],
Greg Honda [aut],
Jimena Davis [ctb],
Nisha Sipes [ctb],
Barbara Wetmore [ctb],
Woodrow Setzer [ctb]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.8 dated 2018-01-23 and 1.9 dated 2019-02-04
httk-1.8/httk/R/3compPBPKmodel_inits.R |only httk-1.8/httk/R/pbtk1comp_inits.R |only httk-1.8/httk/R/vLiverPBPK_inits.R |only httk-1.8/httk/man/Wetmore_Css.Rd |only httk-1.8/httk/man/Wetmore_Oral_Equiv.Rd |only httk-1.8/httk/man/get_wetmore_cheminfo.Rd |only httk-1.8/httk/man/sipes.data.Rd |only httk-1.9/httk/DESCRIPTION | 61 httk-1.9/httk/MD5 | 361 - httk-1.9/httk/NAMESPACE | 4 httk-1.9/httk/NEWS |binary httk-1.9/httk/R/Calc_Hepatic_Clearance.r | 39 httk-1.9/httk/R/Calc_elimination_rate.R | 105 httk-1.9/httk/R/Calc_ratioblood2plasma.R | 27 httk-1.9/httk/R/Calc_volume_of_distribution.R | 63 httk-1.9/httk/R/Parameterize_PBTK.r | 25 httk-1.9/httk/R/Parameterize_SteadyState.R | 52 httk-1.9/httk/R/Predict_partitioning_Schmitt.R | 12 httk-1.9/httk/R/add_chemtable.R | 204 httk-1.9/httk/R/age_draw_smooth.R | 8 httk-1.9/httk/R/armitage.R |only httk-1.9/httk/R/available_rblood2plasma.R | 47 httk-1.9/httk/R/calc_analytic_css.R | 414 + httk-1.9/httk/R/calc_chem_stats.R | 1 httk-1.9/httk/R/calc_css.R | 96 httk-1.9/httk/R/calc_mc_css.R | 198 httk-1.9/httk/R/calc_mc_oral_equiv.R | 50 httk-1.9/httk/R/ckd_epi_eq.R | 8 httk-1.9/httk/R/convert_httk.R | 213 httk-1.9/httk/R/data.R | 122 httk-1.9/httk/R/draw_fup_clint.R | 193 httk-1.9/httk/R/estimate_gfr.R | 8 httk-1.9/httk/R/estimate_gfr_ped.R | 8 httk-1.9/httk/R/estimate_hematocrit.R | 8 httk-1.9/httk/R/gen_age_height_weight.R | 8 httk-1.9/httk/R/gen_height_weight.R | 8 httk-1.9/httk/R/get_Wetmore_Css.R | 8 httk-1.9/httk/R/get_Wetmore_Oral_Equiv.R | 6 httk-1.9/httk/R/get_Wetmore_cheminfo.R | 2 httk-1.9/httk/R/get_chem_id.R | 2 httk-1.9/httk/R/get_cheminfo.R | 2 httk-1.9/httk/R/get_gfr_category.R | 8 httk-1.9/httk/R/get_httk_params.R | 59 httk-1.9/httk/R/get_rblood2plasma.R | 5 httk-1.9/httk/R/get_weight_class.R | 8 httk-1.9/httk/R/hematocrit_infants.R | 8 httk-1.9/httk/R/honda.ivive.R |only httk-1.9/httk/R/httkpop.R | 10 httk-1.9/httk/R/httkpop_bio.R | 8 httk-1.9/httk/R/httkpop_direct_resample.R | 8 httk-1.9/httk/R/httkpop_direct_resample_inner.R | 8 httk-1.9/httk/R/httkpop_generate.R | 10 httk-1.9/httk/R/httkpop_virtual_indiv.R | 8 httk-1.9/httk/R/ionization_functions.R | 204 httk-1.9/httk/R/load_sipes2017.R | 35 httk-1.9/httk/R/modelinfo_1comp.R |only httk-1.9/httk/R/modelinfo_3comp.R |only httk-1.9/httk/R/modelinfo_3compss.R |only httk-1.9/httk/R/modelinfo_PBTK.R |only httk-1.9/httk/R/modelinfo_Schmitt.R |only httk-1.9/httk/R/monte_carlo.R | 5 httk-1.9/httk/R/parameterize_1comp.R | 131 httk-1.9/httk/R/parameterize_schmitt.R | 16 httk-1.9/httk/R/r_left_censored_norm.R | 6 httk-1.9/httk/R/solve_1comp.R | 28 httk-1.9/httk/R/solve_3comp.R | 12 httk-1.9/httk/R/solve_pbtk.R | 12 httk-1.9/httk/R/sysdata.rda |only httk-1.9/httk/R/tissue_mass_functions.R | 782 +-- httk-1.9/httk/R/tissue_masses_flows.R | 7 httk-1.9/httk/R/tissue_scale.R | 8 httk-1.9/httk/R/utils.R | 16 httk-1.9/httk/R/zzz.R |only httk-1.9/httk/build/partial.rdb |binary httk-1.9/httk/build/vignette.rds |binary httk-1.9/httk/data/Tables.RData |binary httk-1.9/httk/data/armitage_input.RData |only httk-1.9/httk/data/datalist | 4 httk-1.9/httk/data/httkpop.RData |binary httk-1.9/httk/data/vignettes.RData |binary httk-1.9/httk/data/well_param.RData |only httk-1.9/httk/inst/doc/Honda_2018_updated_armitage.R |only httk-1.9/httk/inst/doc/Honda_2018_updated_armitage.Rmd |only httk-1.9/httk/inst/doc/Honda_2018_updated_armitage.html |only httk-1.9/httk/inst/doc/Pearce_2017_partitioning_plots.R | 1 httk-1.9/httk/inst/doc/Pearce_2017_partitioning_plots.Rmd | 1 httk-1.9/httk/inst/doc/Pearce_2017_partitioning_plots.html | 987 ++-- httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_age_dist.html | 416 + httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.R | 15 httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.Rmd | 103 httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.html | 2070 +++++---- httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.html | 990 ++-- httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.html | 586 +- httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.html | 546 +- httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.html | 1112 ++-- httk-1.9/httk/inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.html | 546 +- httk-1.9/httk/inst/doc/Ring_2017_vignette01_subpopulations.R | 2 httk-1.9/httk/inst/doc/Ring_2017_vignette01_subpopulations.Rmd | 2 httk-1.9/httk/inst/doc/Ring_2017_vignette01_subpopulations.html | 504 +- httk-1.9/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.html | 924 ++-- httk-1.9/httk/inst/doc/Ring_2017_vignette03_paper_fig2.html | 454 +- httk-1.9/httk/inst/doc/Ring_2017_vignette04_paper_fig3.html | 578 +- httk-1.9/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.Rmd | 12 httk-1.9/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.html | 838 ++- httk-1.9/httk/inst/doc/Ring_2017_vignette06_aerplotting.html | 1059 ++-- httk-1.9/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.html | 784 ++- httk-1.9/httk/inst/doc/Wambaugh_2018_Figures.R | 4 httk-1.9/httk/inst/doc/Wambaugh_2018_Figures.Rmd | 4 httk-1.9/httk/inst/doc/Wambaugh_2018_Figures.html | 2240 +++++----- httk-1.9/httk/man/Calc_elimination_rate.Rd | 9 httk-1.9/httk/man/Calc_ratioblood2plasma.Rd | 5 httk-1.9/httk/man/Parameterize_PBTK.Rd | 2 httk-1.9/httk/man/Sipes2017.Rd |only httk-1.9/httk/man/age_dist_smooth.Rd | 13 httk-1.9/httk/man/age_draw_smooth.Rd | 11 httk-1.9/httk/man/armitage_estimate_sarea.Rd |only httk-1.9/httk/man/armitage_eval.Rd |only httk-1.9/httk/man/armitage_input.Rd |only httk-1.9/httk/man/blood_mass_correct.Rd | 1 httk-1.9/httk/man/blood_weight.Rd | 10 httk-1.9/httk/man/bmiage.Rd | 12 httk-1.9/httk/man/body_surface_area.Rd | 1 httk-1.9/httk/man/bone_mass_age.Rd | 1 httk-1.9/httk/man/brain_mass.Rd | 1 httk-1.9/httk/man/calc_analytic_css.Rd | 159 httk-1.9/httk/man/calc_css.Rd | 4 httk-1.9/httk/man/calc_ionization.Rd | 11 httk-1.9/httk/man/calc_mc_css.Rd | 90 httk-1.9/httk/man/calc_mc_oral_equiv.Rd | 47 httk-1.9/httk/man/ckd_epi_eq.Rd | 10 httk-1.9/httk/man/convert_httk.Rd | 40 httk-1.9/httk/man/draw_fup_clint.Rd | 38 httk-1.9/httk/man/estimate_gfr.Rd | 10 httk-1.9/httk/man/estimate_gfr_ped.Rd | 10 httk-1.9/httk/man/estimate_hematocrit.Rd | 10 httk-1.9/httk/man/figures |only httk-1.9/httk/man/gen_age_height_weight.Rd | 10 httk-1.9/httk/man/gen_height_weight.Rd | 10 httk-1.9/httk/man/get_cheminfo.Rd | 2 httk-1.9/httk/man/get_gfr_category.Rd | 10 httk-1.9/httk/man/get_httk_params.Rd | 64 httk-1.9/httk/man/get_lit_cheminfo.Rd |only httk-1.9/httk/man/get_lit_css.Rd |only httk-1.9/httk/man/get_lit_oral_equiv.Rd |only httk-1.9/httk/man/get_weight_class.Rd | 10 httk-1.9/httk/man/hematocrit_infants.Rd | 10 httk-1.9/httk/man/httk-package.Rd | 34 httk-1.9/httk/man/httkpop.Rd |only httk-1.9/httk/man/httkpop_bio.Rd | 10 httk-1.9/httk/man/httkpop_direct_resample.Rd | 10 httk-1.9/httk/man/httkpop_direct_resample_inner.Rd | 14 httk-1.9/httk/man/httkpop_generate.Rd | 13 httk-1.9/httk/man/httkpop_virtual_indiv.Rd | 21 httk-1.9/httk/man/is_in_inclusive.Rd | 10 httk-1.9/httk/man/kidney_mass_children.Rd | 1 httk-1.9/httk/man/liver_mass_children.Rd | 2 httk-1.9/httk/man/load_sipes2017.Rd | 12 httk-1.9/httk/man/lung_mass_children.Rd | 1 httk-1.9/httk/man/mcnally_dt.Rd | 12 httk-1.9/httk/man/nhanes_mec_svy.Rd | 12 httk-1.9/httk/man/pancreas_mass_children.Rd | 1 httk-1.9/httk/man/parameterize_1comp.Rd | 6 httk-1.9/httk/man/r_left_censored_norm.Rd | 1 httk-1.9/httk/man/rfun.Rd | 10 httk-1.9/httk/man/sipes2017.table.Rd |only httk-1.9/httk/man/skeletal_muscle_mass.Rd | 1 httk-1.9/httk/man/skeletal_muscle_mass_children.Rd | 1 httk-1.9/httk/man/skin_mass_bosgra.Rd | 1 httk-1.9/httk/man/solve_1comp_pk.Rd | 10 httk-1.9/httk/man/solve_3comp_pbpk.Rd | 11 httk-1.9/httk/man/solve_pbtk.Rd | 11 httk-1.9/httk/man/spleen_mass_children.Rd | 1 httk-1.9/httk/man/spline_heightweight.Rd | 12 httk-1.9/httk/man/spline_hematocrit.Rd | 12 httk-1.9/httk/man/spline_serumcreat.Rd | 12 httk-1.9/httk/man/tissue_masses_flows.Rd | 10 httk-1.9/httk/man/tissue_scale.Rd | 10 httk-1.9/httk/man/well_param.Rd |only httk-1.9/httk/man/wfl.Rd | 12 httk-1.9/httk/tests/1comp_test.R |only httk-1.9/httk/tests/1comp_test.Rout.save |only httk-1.9/httk/tests/3comp_test.R |only httk-1.9/httk/tests/3comp_test.Rout.save |only httk-1.9/httk/tests/3compss_test.R |only httk-1.9/httk/tests/3compss_test.Rout.save |only httk-1.9/httk/tests/adddata_test.R |only httk-1.9/httk/tests/adddata_test.Rout.save |only httk-1.9/httk/tests/cheminfo_test.R | 11 httk-1.9/httk/tests/cheminfo_test.Rout.save | 30 httk-1.9/httk/tests/ivive_test.R |only httk-1.9/httk/tests/ivive_test.Rout.save |only httk-1.9/httk/tests/other_tests.R | 6 httk-1.9/httk/tests/other_tests.Rout.save | 127 httk-1.9/httk/tests/pbtk_test.R |only httk-1.9/httk/tests/pbtk_test.Rout.save |only httk-1.9/httk/vignettes/Honda_2018_updated_armitage.Rmd |only httk-1.9/httk/vignettes/Pearce_2017_partitioning_plots.Rmd | 1 httk-1.9/httk/vignettes/Ring_2017_supplemental_vignette_globalsensitivityanalysis.Rmd | 103 httk-1.9/httk/vignettes/Ring_2017_vignette01_subpopulations.Rmd | 2 httk-1.9/httk/vignettes/Ring_2017_vignette05b_plothowgatejohnson.Rmd | 12 httk-1.9/httk/vignettes/Wambaugh_2018_Figures.Rmd | 4 201 files changed, 12603 insertions(+), 7125 deletions(-)
Title: Probability Functions and Generalized Regression Models for
Stable Distributions
Description: Density, distribution, quantile and hazard functions of a
stable variate; generalized regression models for the parameters
of a stable distribution. See the README for how to make equivalent calls
to those of 'stabledist'. See github for Journal article.
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the
CRAN version),
Philippe Lambert [aut]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between stable versions 1.1.3 dated 2018-05-26 and 1.1.4 dated 2019-02-04
stable-1.1.3/stable/man/Stable.Rd |only stable-1.1.4/stable/DESCRIPTION | 8 stable-1.1.4/stable/MD5 | 20 stable-1.1.4/stable/NAMESPACE | 2 stable-1.1.4/stable/NEWS.md | 6 stable-1.1.4/stable/R/stable.r | 241 +++++++--- stable-1.1.4/stable/man/Links.Rd | 5 stable-1.1.4/stable/man/Parameter_Conversion.Rd | 3 stable-1.1.4/stable/man/Parameter_Conversion_Nolan_pm1_pm0.Rd | 1 stable-1.1.4/stable/man/stable.Rd |only stable-1.1.4/stable/man/stable.mode.Rd | 9 stable-1.1.4/stable/man/stablereg.Rd | 29 - 12 files changed, 216 insertions(+), 108 deletions(-)
Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre],
Ben Armstrong [aut],
Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between dlnm versions 2.3.6 dated 2018-09-12 and 2.3.8 dated 2019-02-04
DESCRIPTION | 8 +- MD5 | 110 ++++++++++++++++++------------------ NEWS.md | 18 +++++ R/Predict.matrix.cb.smooth.R | 2 R/cbPen.R | 2 R/checkcrossbasis.R | 2 R/checkgroup.R | 2 R/checkonebasis.R | 2 R/coef.crosspred.R | 2 R/coef.crossreduce.R | 2 R/cr.R | 2 R/crossbasis.R | 2 R/crosspred.R | 4 - R/crossreduce.R | 4 - R/equalknots.R | 2 R/exphist.R | 54 +++++++---------- R/fci.R | 2 R/findrank.R | 2 R/getcoef.R | 2 R/getlink.R | 2 R/getvcov.R | 2 R/integer.R | 2 R/lin.R | 2 R/lines.crosspred.R | 8 +- R/lines.crossreduce.R | 4 - R/logknots.R | 2 R/mkXpred.R | 2 R/mkaddSlag.R | 2 R/mkat.R | 2 R/mkcen.R | 2 R/mklag.R | 2 R/onAttach.R | 2 R/onebasis.R | 2 R/plot.crosspred.R | 4 - R/plot.crossreduce.R | 4 - R/points.crosspred.R | 8 +- R/points.crossreduce.R | 4 - R/poly.R | 2 R/ps.R | 2 R/seqlag.R | 2 R/smooth.construct.cb.smooth.spec.R | 2 R/strata.R | 2 R/summary.crossbasis.R | 2 R/summary.crosspred.R | 2 R/summary.crossreduce.R | 2 R/summary.onebasis.R | 2 R/thr.R | 2 R/vcov.crosspred.R | 2 R/vcov.crossreduce.R | 2 build/vignette.rds |binary inst/NEWS | 18 +++++ inst/doc/dlnmExtended.pdf |binary inst/doc/dlnmOverview.pdf |binary inst/doc/dlnmPenalized.pdf |binary inst/doc/dlnmTS.pdf |binary man/exphist.Rd | 6 - 56 files changed, 179 insertions(+), 149 deletions(-)
Title: A Data Specification Format and Interface
Description: Creates a data specification that describes the columns of a
table (data.frame). Provides methods to read, write, and update the
specification. Checks whether a table matches its specification. See
specification.data.frame(),read.spec(), write.spec(), as.csv.spec(),
respecify.character(), and %matches%.data.frame().
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between spec versions 0.1.3 dated 2017-04-13 and 0.1.6 dated 2019-02-04
DESCRIPTION | 6 ++-- MD5 | 11 +++++--- NAMESPACE | 3 ++ R/spec.R | 61 ++++++++++++++++++++++++++++++++++++++++++++++ man/guidetext.Rd | 3 ++ man/specify.Rd |only man/specify.character.Rd |only man/specify.data.frame.Rd |only 8 files changed, 77 insertions(+), 7 deletions(-)
Title: Data-Driven Plot Design
Description: Designs plots in terms of core structure. See 'example(metaplot)'.
Primary arguments are (unquoted) column names; order and type (numeric or not)
dictate the resulting plot. Specify any y variables, x variable, any groups variable,
and any conditioning variables to metaplot() to generate density plots, boxplots,
mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot()
to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide'
are honored, producing fully annotated plots with minimal effort. Attribute 'guide'
is typically units, but may be encoded() to provide interpretations of categorical
values (see '?encode'). Utility unpack() transforms scalar column attributes to row
values and pack() does the reverse, supporting tool-neutral storage of metadata along
with primary data. The package supports customizable aesthetics such as such as reference
lines, unity lines, smooths, log transformation, and linear fits. The user may choose
between trellis and ggplot output. Compact syntax and integrated metadata promote workflow
scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between metaplot versions 0.8.0 dated 2018-09-30 and 0.8.2 dated 2019-02-04
DESCRIPTION | 6 ++-- MD5 | 10 +++--- NAMESPACE | 1 R/categorical.R | 56 ++++++++++++++++++------------------- R/scatter.R | 68 ++++++++++++++++++++++++++++++---------------- man/scatter_data_frame.Rd | 6 ++-- 6 files changed, 85 insertions(+), 62 deletions(-)
Title: Multivariate Normal and Elliptically-Contoured Repeated
Measurements Models
Description: Functions for fitting various normal theory (growth
curve) and elliptically-contoured repeated measurements models
with ARMA and random effects dependence.
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the
CRAN version)
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between growth versions 1.1.0 dated 2016-12-08 and 1.1.1 dated 2019-02-04
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NAMESPACE | 2 +- NEWS.md | 8 ++++++++ R/carma.r | 4 ++-- R/elliptic.r | 2 +- man/carma.Rd | 23 ++++++++++++----------- man/corgram.Rd | 1 - man/elliptic.Rd | 27 ++++++++++++++------------- man/pergram.Rd | 10 +++++----- man/potthoff.Rd | 7 +++---- man/rmaov.Rd | 7 +++---- src/growth_init.c |only 13 files changed, 66 insertions(+), 58 deletions(-)
Title: Estimating the Sample Mean and Standard Deviation from Commonly
Reported Quantiles in Meta-Analysis
Description: Implements the methods of McGrath et al. (in preparation) for
estimating the sample mean and standard deviation from commonly reported
quantiles in meta-analysis. These methods can be applied to studies that
report the sample median, sample size, and one or both of (i) the sample
minimum and maximum values and (ii) the first and third quartiles.
Author: Sean McGrath [aut, cre] (<https://orcid.org/0000-0002-7281-3516>),
XiaoFei Zhao [aut],
Russell Steele [aut],
Andrea Benedetti [aut] (<https://orcid.org/0000-0002-8314-9497>)
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>
Diff between estmeansd versions 0.1.0 dated 2019-01-11 and 0.1.1 dated 2019-02-04
DESCRIPTION | 22 ++++++++++++---------- MD5 | 9 +++++---- R/bc.mean.sd.R | 3 +-- R/get.scenario.R |only R/qe.fit.R | 13 ++++++------- man/qe.fit.Rd | 6 +++--- 6 files changed, 27 insertions(+), 26 deletions(-)
Title: Bender Client
Description: R client for Bender Hyperparameters optimizer : <https://bender.dreem.com>
The R client allows you to communicate with the Bender API and therefore submit some new trials within your R script itself.
Author: Dylan Heirstraeten
Maintainer: Valentin Thorey <valentin@dreem.com>
Diff between bender versions 0.1.0 dated 2019-01-20 and 0.1.1 dated 2019-02-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/bender.R | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-31 0.2.2
Title: A Systematic Data Wrangling Idiom
Description: Supports systematic scrutiny, modification, and integration of
data. The function status() counts rows that have missing values in
grouping columns (returned by na() ), have non-unique combinations of
grouping columns (returned by dup() ), and that are not locally sorted
(returned by unsorted() ). Functions enumerate() and itemize() give
sorted unique combinations of columns, with or without occurrence counts,
respectively. Function ignore() drops columns in x that are present in y,
and informative() drops columns in x that are entirely NA; constant() returns
values that are constant, given a key. Data that have defined unique
combinations of grouping values behave more predictably during merge operations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between wrangle versions 0.4 dated 2017-04-13 and 0.5.1 dated 2019-02-04
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++++-- NAMESPACE | 7 +++++++ R/constant.R |only man/constant.Rd |only man/constant.data.frame.Rd |only man/constant.grouped_df.Rd |only 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.8.3 dated 2018-09-30 and 0.8.6 dated 2019-02-04
DESCRIPTION | 6 MD5 | 12 - R/likebut.R | 9 R/partab.R | 4 R/superset.R | 8 inst/doc/parameter-table.html | 392 +++++++++++++++++++++++++++++++++--------- man/meta.character.Rd | 4 7 files changed, 338 insertions(+), 97 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre] (<https://orcid.org/0000-0002-9999-1558>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Scott Jackson [aut],
Mikko Korpela [ctb]
Maintainer: ORPHANED
Diff between ggmap versions 2.6.2 dated 2019-01-23 and 3.0.0 dated 2019-02-04
ggmap-2.6.2/ggmap/R/help.R |only ggmap-2.6.2/ggmap/R/mutate_geocode.R |only ggmap-2.6.2/ggmap/R/zzz.R |only ggmap-2.6.2/ggmap/man/distQueryCheck.Rd |only ggmap-2.6.2/ggmap/man/mutate_geocode.Rd |only ggmap-2.6.2/ggmap/man/routeQueryCheck.Rd |only ggmap-3.0.0/ggmap/DESCRIPTION | 36 - ggmap-3.0.0/ggmap/MD5 | 158 ++++--- ggmap-3.0.0/ggmap/NAMESPACE | 90 +++- ggmap-3.0.0/ggmap/NEWS | 74 +++ ggmap-3.0.0/ggmap/R/LonLat2XY.R | 2 ggmap-3.0.0/ggmap/R/OSM_scale_lookup.R | 3 ggmap-3.0.0/ggmap/R/attach.R |only ggmap-3.0.0/ggmap/R/bb2bbox.R | 2 ggmap-3.0.0/ggmap/R/calc_zoom.r | 2 ggmap-3.0.0/ggmap/R/coord_map.R |only ggmap-3.0.0/ggmap/R/file_drawer.R | 2 ggmap-3.0.0/ggmap/R/geocode.R | 583 ++++++++++++++-------------- ggmap-3.0.0/ggmap/R/geom_leg.R | 2 ggmap-3.0.0/ggmap/R/get_cloudmademap.R | 198 ++++----- ggmap-3.0.0/ggmap/R/get_googlemap.R | 589 ++++++++++++----------------- ggmap-3.0.0/ggmap/R/get_map.R | 114 ++--- ggmap-3.0.0/ggmap/R/get_navermap.R | 248 +----------- ggmap-3.0.0/ggmap/R/get_openstreetmap.R | 137 +++--- ggmap-3.0.0/ggmap/R/get_stamenmap.R | 492 ++++++++++++------------ ggmap-3.0.0/ggmap/R/gglocator.R | 128 ++++-- ggmap-3.0.0/ggmap/R/ggmap-defunct.R |only ggmap-3.0.0/ggmap/R/ggmap-package.R |only ggmap-3.0.0/ggmap/R/ggmap.R | 100 ++-- ggmap-3.0.0/ggmap/R/ggmap_options.R |only ggmap-3.0.0/ggmap/R/ggplot2.R | 8 ggmap-3.0.0/ggmap/R/helpers.R | 22 - ggmap-3.0.0/ggmap/R/mapdist.R | 358 +++++++++++------ ggmap-3.0.0/ggmap/R/print.R | 12 ggmap-3.0.0/ggmap/R/qmap.R | 80 --- ggmap-3.0.0/ggmap/R/qmplot.R | 11 ggmap-3.0.0/ggmap/R/register_google.R |only ggmap-3.0.0/ggmap/R/revgeocode.R | 246 +++++++----- ggmap-3.0.0/ggmap/R/route.R | 510 ++++++++++++++++--------- ggmap-3.0.0/ggmap/R/theme_inset.R | 21 - ggmap-3.0.0/ggmap/R/theme_nothing.R | 46 +- ggmap-3.0.0/ggmap/R/trek.R |only ggmap-3.0.0/ggmap/README.md | 233 +++++++++-- ggmap-3.0.0/ggmap/data/crime.rda |binary ggmap-3.0.0/ggmap/man/LonLat2XY.Rd | 7 ggmap-3.0.0/ggmap/man/OSM_scale_lookup.Rd | 4 ggmap-3.0.0/ggmap/man/XY2LonLat.Rd | 7 ggmap-3.0.0/ggmap/man/bb2bbox.Rd | 3 ggmap-3.0.0/ggmap/man/calc_zoom.Rd | 3 ggmap-3.0.0/ggmap/man/crime.Rd | 7 ggmap-3.0.0/ggmap/man/file_drawer.Rd | 1 ggmap-3.0.0/ggmap/man/geocode.Rd | 136 +++--- ggmap-3.0.0/ggmap/man/geom_leg.Rd | 47 +- ggmap-3.0.0/ggmap/man/get_cloudmademap.Rd | 53 +- ggmap-3.0.0/ggmap/man/get_googlemap.Rd | 184 +++++---- ggmap-3.0.0/ggmap/man/get_map.Rd | 92 ++-- ggmap-3.0.0/ggmap/man/get_navermap.Rd | 75 +-- ggmap-3.0.0/ggmap/man/get_openstreetmap.Rd | 40 - ggmap-3.0.0/ggmap/man/get_stamenmap.Rd | 256 +++++------- ggmap-3.0.0/ggmap/man/ggimage.Rd | 1 ggmap-3.0.0/ggmap/man/gglocator.Rd | 50 +- ggmap-3.0.0/ggmap/man/ggmap-defunct.Rd |only ggmap-3.0.0/ggmap/man/ggmap.Rd | 86 +--- ggmap-3.0.0/ggmap/man/ggmap_options.Rd |only ggmap-3.0.0/ggmap/man/ggmapplot.Rd | 7 ggmap-3.0.0/ggmap/man/hadley.Rd | 1 ggmap-3.0.0/ggmap/man/inset.Rd | 1 ggmap-3.0.0/ggmap/man/inset_raster.Rd | 3 ggmap-3.0.0/ggmap/man/legs2route.Rd | 10 ggmap-3.0.0/ggmap/man/make_bbox.Rd | 1 ggmap-3.0.0/ggmap/man/mapdist.Rd | 74 ++- ggmap-3.0.0/ggmap/man/print.ggmap.Rd | 11 ggmap-3.0.0/ggmap/man/qmap.Rd | 42 -- ggmap-3.0.0/ggmap/man/qmplot.Rd | 20 ggmap-3.0.0/ggmap/man/reexports.Rd |only ggmap-3.0.0/ggmap/man/register_google.Rd |only ggmap-3.0.0/ggmap/man/revgeocode.Rd | 56 +- ggmap-3.0.0/ggmap/man/route.Rd | 82 ++-- ggmap-3.0.0/ggmap/man/theme_inset.Rd | 1 ggmap-3.0.0/ggmap/man/theme_nothing.Rd | 8 ggmap-3.0.0/ggmap/man/trek.Rd |only ggmap-3.0.0/ggmap/man/wind.Rd | 7 ggmap-3.0.0/ggmap/man/zips.Rd | 9 ggmap-3.0.0/ggmap/tests |only ggmap-3.0.0/ggmap/tools |only 85 files changed, 3135 insertions(+), 2757 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 0.3.1 dated 2018-12-07 and 0.3.2 dated 2019-02-04
DESCRIPTION | 46 - MD5 | 44 - NAMESPACE | 2 NEWS.md | 5 R/auk-clean.r | 237 +++---- R/auk-filter.r | 1193 +++++++++++++++++++-------------------- R/auk-protocol.r | 12 R/auk-select.r | 182 ++--- R/auk-set-awk-path.r | 120 +-- R/auk-set-ebd-path.r | 104 +-- R/auk-split.r | 7 R/auk-version.r | 2 R/pipe.r | 4 R/utils.r | 266 ++++---- build/vignette.rds |binary inst/doc/auk.html | 1056 +++++++++++++++++++++------------- inst/doc/development.html | 356 +++++++++-- man/auk_protocol.Rd | 11 man/reexports.Rd | 2 tests/testthat/test_auk-ebd.r | 166 ++--- tests/testthat/test_auk-filter.r | 397 ++++++------ tests/testthat/test_auk-split.r | 110 +-- tests/testthat/test_unmarked.r | 105 +-- 23 files changed, 2452 insertions(+), 1975 deletions(-)
Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with
corresponding random forest for conditional transformation models
as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>)
and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between trtf versions 0.3-4 dated 2019-01-16 and 0.3-5 dated 2019-02-04
trtf-0.3-4/trtf/tests/GBSG2-Ex.Rout.save |only trtf-0.3-4/trtf/tests/regtest-traforest.Rout.save |only trtf-0.3-4/trtf/tests/regtest-trafotree.Rout.save |only trtf-0.3-5/trtf/DESCRIPTION | 8 ++++---- trtf-0.3-5/trtf/MD5 | 22 +++++++++++++++++----- trtf-0.3-5/trtf/inst/NEWS.Rd | 6 ++++++ trtf-0.3-5/trtf/inst/survival_forests |only 7 files changed, 27 insertions(+), 9 deletions(-)
Title: Shiny Application of Medical and Pharmaceutical Statistics
Description: The web-based statistical fundamentals, tests, and models, aiming to facilitate researchers to analyze medical, pharmaceutical and genomic data.
Author: Yi Zhou [cre, aut] (<https://orcid.org/0000-0001-9254-324>)
Maintainer: Yi Zhou <zhou-y@phs.osaka-u.ac.jp>
Diff between mephas versions 0.1.0 dated 2019-02-01 and 1.0.0 dated 2019-02-04
mephas-0.1.0/mephas/R/MFSdistributiont.R |only mephas-0.1.0/mephas/R/advertisement.R |only mephas-0.1.0/mephas/R/coloncancer.R |only mephas-0.1.0/mephas/R/insurance.R |only mephas-0.1.0/mephas/R/lung.R |only mephas-0.1.0/mephas/R/server.anova.R |only mephas-0.1.0/mephas/R/server.dist.R |only mephas-0.1.0/mephas/R/server.nptest.R |only mephas-0.1.0/mephas/R/server.pcapls.R |only mephas-0.1.0/mephas/R/server.proptest.R |only mephas-0.1.0/mephas/R/server.rctab.R |only mephas-0.1.0/mephas/R/server.reg.R |only mephas-0.1.0/mephas/R/server.t.R |only mephas-0.1.0/mephas/R/stop.R |only mephas-0.1.0/mephas/R/ttest.p1.ui.R |only mephas-0.1.0/mephas/R/ttest.p2.ui.R |only mephas-0.1.0/mephas/R/ttest.p3.ui.R |only mephas-0.1.0/mephas/R/ui.anova.R |only mephas-0.1.0/mephas/R/ui.dist.R |only mephas-0.1.0/mephas/R/ui.nptest.R |only mephas-0.1.0/mephas/R/ui.pcapls.R |only mephas-0.1.0/mephas/R/ui.proptest.R |only mephas-0.1.0/mephas/R/ui.rctab.R |only mephas-0.1.0/mephas/R/ui.reg.R |only mephas-0.1.0/mephas/R/ui.t.R |only mephas-0.1.0/mephas/data |only mephas-0.1.0/mephas/man/MFSstop.Rd |only mephas-0.1.0/mephas/man/advertisement.Rd |only mephas-0.1.0/mephas/man/coloncancer.Rd |only mephas-0.1.0/mephas/man/insurance.Rd |only mephas-0.1.0/mephas/man/lung.Rd |only mephas-0.1.0/mephas/man/server.anova.Rd |only mephas-0.1.0/mephas/man/server.dist.Rd |only mephas-0.1.0/mephas/man/server.nptest.Rd |only mephas-0.1.0/mephas/man/server.pcapls.Rd |only mephas-0.1.0/mephas/man/server.proptest.Rd |only mephas-0.1.0/mephas/man/server.rctab.Rd |only mephas-0.1.0/mephas/man/server.reg.Rd |only mephas-0.1.0/mephas/man/server.t.Rd |only mephas-0.1.0/mephas/man/ttest.p1.ui.Rd |only mephas-0.1.0/mephas/man/ttest.p2.ui.Rd |only mephas-0.1.0/mephas/man/ttest.p3.ui.Rd |only mephas-0.1.0/mephas/man/ui.anova.Rd |only mephas-0.1.0/mephas/man/ui.dist.Rd |only mephas-0.1.0/mephas/man/ui.nptest.Rd |only mephas-0.1.0/mephas/man/ui.pcapls.Rd |only mephas-0.1.0/mephas/man/ui.proptest.Rd |only mephas-0.1.0/mephas/man/ui.rctab.Rd |only mephas-0.1.0/mephas/man/ui.reg.Rd |only mephas-0.1.0/mephas/man/ui.t.Rd |only mephas-1.0.0/mephas/DESCRIPTION | 33 - mephas-1.0.0/mephas/MD5 | 87 -- mephas-1.0.0/mephas/NAMESPACE | 35 - mephas-1.0.0/mephas/NEWS.md |only mephas-1.0.0/mephas/R/MFSanova.R | 556 ++++++++++++++++++ mephas-1.0.0/mephas/R/MFSdistribution.R |only mephas-1.0.0/mephas/R/MFSnptest.R | 426 ++++++++++++++ mephas-1.0.0/mephas/R/MFSpcapls.R | 720 +++++++++++++++++++++++- mephas-1.0.0/mephas/R/MFSproptest.R | 396 +++++++++++++ mephas-1.0.0/mephas/R/MFSrctabtest.R | 296 +++++++++ mephas-1.0.0/mephas/R/MFSreg.R | 867 ++++++++++++++++++++++++++++- mephas-1.0.0/mephas/R/MFSttest.R | 843 ++++++++++++++++++++++++++++ mephas-1.0.0/mephas/R/pls.data.ui.R |only mephas-1.0.0/mephas/R/pls.ui.R |only mephas-1.0.0/mephas/R/reg.data.ui.R | 4 mephas-1.0.0/mephas/R/sysdata.rda |binary mephas-1.0.0/mephas/README.md |only mephas-1.0.0/mephas/inst |only mephas-1.0.0/mephas/man/MFSdistribution.Rd | 2 mephas-1.0.0/mephas/man/MFSpcapls.Rd | 2 mephas-1.0.0/mephas/man/pls.data.ui.Rd |only mephas-1.0.0/mephas/man/pls.ui.Rd |only 72 files changed, 4126 insertions(+), 141 deletions(-)
Title: Infinite Mixtures of Infinite Factor Analysers and Related
Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2018) <arXiv:1701.07010v4>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
Author: Keefe Murphy [aut, cre],
Cinzia Viroli [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between IMIFA versions 2.0.0 dated 2018-05-01 and 2.1.0 dated 2019-02-04
IMIFA-2.0.0/IMIFA/man/IMIFA.Rd |only IMIFA-2.0.0/IMIFA/man/sim_IMIFA_data.Rd |only IMIFA-2.1.0/IMIFA/DESCRIPTION | 20 IMIFA-2.1.0/IMIFA/MD5 | 100 IMIFA-2.1.0/IMIFA/NAMESPACE | 14 IMIFA-2.1.0/IMIFA/R/Diagnostics.R | 706 ++-- IMIFA-2.1.0/IMIFA/R/FullConditionals.R | 1637 ++++++---- IMIFA-2.1.0/IMIFA/R/Gibbs_FA.R | 54 IMIFA-2.1.0/IMIFA/R/Gibbs_IFA.R | 79 IMIFA-2.1.0/IMIFA/R/Gibbs_IMFA.R | 214 - IMIFA-2.1.0/IMIFA/R/Gibbs_IMIFA.R | 315 - IMIFA-2.1.0/IMIFA/R/Gibbs_MFA.R | 111 IMIFA-2.1.0/IMIFA/R/Gibbs_MIFA.R | 208 - IMIFA-2.1.0/IMIFA/R/Gibbs_OMFA.R | 139 IMIFA-2.1.0/IMIFA/R/Gibbs_OMIFA.R | 217 - IMIFA-2.1.0/IMIFA/R/IMIFA.R | 19 IMIFA-2.1.0/IMIFA/R/MainFunction.R | 546 +-- IMIFA-2.1.0/IMIFA/R/PlottingFunctions.R | 902 +++-- IMIFA-2.1.0/IMIFA/R/SimulateData.R | 235 + IMIFA-2.1.0/IMIFA/README.md | 8 IMIFA-2.1.0/IMIFA/build/vignette.rds |binary IMIFA-2.1.0/IMIFA/inst/CITATION | 26 IMIFA-2.1.0/IMIFA/inst/NEWS.md | 104 IMIFA-2.1.0/IMIFA/inst/doc/IMIFA.R | 16 IMIFA-2.1.0/IMIFA/inst/doc/IMIFA.Rmd | 35 IMIFA-2.1.0/IMIFA/inst/doc/IMIFA.html | 118 IMIFA-2.1.0/IMIFA/man/G_moments.Rd | 14 IMIFA-2.1.0/IMIFA/man/G_priorDensity.Rd | 6 IMIFA-2.1.0/IMIFA/man/IMIFA-package.Rd |only IMIFA-2.1.0/IMIFA/man/Ledermann.Rd | 7 IMIFA-2.1.0/IMIFA/man/MGP_check.Rd | 12 IMIFA-2.1.0/IMIFA/man/Procrustes.Rd | 3 IMIFA-2.1.0/IMIFA/man/Zsimilarity.Rd | 8 IMIFA-2.1.0/IMIFA/man/bnpControl.Rd | 76 IMIFA-2.1.0/IMIFA/man/get_IMIFA_results.Rd | 60 IMIFA-2.1.0/IMIFA/man/gumbel_max.Rd | 4 IMIFA-2.1.0/IMIFA/man/heat_legend.Rd | 14 IMIFA-2.1.0/IMIFA/man/mat2cols.Rd | 11 IMIFA-2.1.0/IMIFA/man/mcmc_IMIFA.Rd | 40 IMIFA-2.1.0/IMIFA/man/mgpControl.Rd | 44 IMIFA-2.1.0/IMIFA/man/mixfaControl.Rd | 52 IMIFA-2.1.0/IMIFA/man/pareto_scale.Rd |only IMIFA-2.1.0/IMIFA/man/plot.Results_IMIFA.Rd | 34 IMIFA-2.1.0/IMIFA/man/plot_cols.Rd | 10 IMIFA-2.1.0/IMIFA/man/psi_hyper.Rd | 58 IMIFA-2.1.0/IMIFA/man/rDirichlet.Rd | 6 IMIFA-2.1.0/IMIFA/man/scores_MAP.Rd |only IMIFA-2.1.0/IMIFA/man/shift_GA.Rd | 5 IMIFA-2.1.0/IMIFA/man/show_IMIFA_digit.Rd | 7 IMIFA-2.1.0/IMIFA/man/show_digit.Rd | 2 IMIFA-2.1.0/IMIFA/man/sim_IMIFA.Rd |only IMIFA-2.1.0/IMIFA/man/storeControl.Rd | 21 IMIFA-2.1.0/IMIFA/vignettes/IMIFA.Rmd | 35 IMIFA-2.1.0/IMIFA/vignettes/res_olive_IMIFA__Edited-Vignette-only-Version.rda |binary 54 files changed, 3708 insertions(+), 2644 deletions(-)
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.0 dated 2018-07-18 and 1.0.1 dated 2019-02-04
DESCRIPTION | 25 - MD5 | 47 +- NAMESPACE | 12 R/assertions.R |only R/install_packages.R | 2 R/mapdf.R | 9 R/package.R | 19 R/safe_tempdir.R |only R/tibble.R | 16 README.md | 20 - build/vignette.rds |binary inst/NEWS | 70 ++- inst/doc/functionality.R | 38 + inst/doc/functionality.Rmd | 56 ++ inst/doc/functionality.html | 641 ++++++++++++++++++++++++++------- man/all_in.Rd |only man/dynutils.Rd | 19 man/extract_row_to_list.Rd | 3 man/has_names.Rd |only man/is_bounded.Rd |only man/is_single_numeric.Rd |only man/mapdf.Rd | 5 man/safe_tempdir.Rd |only tests/testthat/test-assertions.R |only tests/testthat/test-install_packages.R | 10 tests/testthat/test-mapdf.R | 20 - tests/testthat/test-safe_tempdir.R |only tests/testthat/test-tibble.R | 39 +- vignettes/functionality.Rmd | 56 ++ 29 files changed, 898 insertions(+), 209 deletions(-)
Title: Bayesian Framework for Computational Modeling
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>),
the present package aims to provide a framework for conducting Bayesian
analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the
Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>).
The initial version includes several modules for conducting Bayesian
equivalents of chi-squared tests, analysis of variance (ANOVA),
multiple (hierarchical) regression, softmax regression, and for fitting data
(e.g., structural equation modeling).
Author: Øystein Olav Skaar [aut, cre]
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>
Diff between bfw versions 0.3.0 dated 2018-11-04 and 0.4.0 dated 2019-02-04
bfw-0.3.0/bfw/inst/doc/fit_latent_data.md |only bfw-0.3.0/bfw/inst/doc/fit_observed_data.md |only bfw-0.3.0/bfw/inst/doc/metric.md |only bfw-0.3.0/bfw/inst/doc/plot_mean.md |only bfw-0.3.0/bfw/inst/doc/regression.md |only bfw-0.4.0/bfw/DESCRIPTION | 10 bfw-0.4.0/bfw/MD5 | 48 - bfw-0.4.0/bfw/NAMESPACE | 6 bfw-0.4.0/bfw/NEWS.md | 29 bfw-0.4.0/bfw/R/basic_functions.R | 8 bfw-0.4.0/bfw/R/mcmc.R | 18 bfw-0.4.0/bfw/R/mcmc_misc.R | 57 + bfw-0.4.0/bfw/R/plot_parse.R | 8 bfw-0.4.0/bfw/R/settings.R | 9 bfw-0.4.0/bfw/R/stats_metric.R | 522 +++++++------- bfw-0.4.0/bfw/R/stats_nominal.R | 5 bfw-0.4.0/bfw/README.md | 19 bfw-0.4.0/bfw/inst/doc/fit_latent_data.html | 582 +++++----------- bfw-0.4.0/bfw/inst/doc/fit_observed_data.html | 940 ++++++++++---------------- bfw-0.4.0/bfw/inst/doc/metric.html | 492 +++---------- bfw-0.4.0/bfw/inst/doc/plot_mean.html | 468 +++--------- bfw-0.4.0/bfw/inst/doc/regression.html | 482 +++---------- bfw-0.4.0/bfw/man/ComputeHDI.Rd | 4 bfw-0.4.0/bfw/man/ETA.Rd | 8 bfw-0.4.0/bfw/man/InverseHDI.Rd |only bfw-0.4.0/bfw/man/ParsePlot.Rd | 4 bfw-0.4.0/bfw/man/RunMCMC.Rd | 20 bfw-0.4.0/bfw/man/bfw.Rd | 13 28 files changed, 1402 insertions(+), 2350 deletions(-)
Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre],
Björn Bähre [aut] (aha and power diagrams),
Carsten Gottschlich [aut] (simplex and shortlist),
Valentin Hartmann [aut] (semidiscrete1),
Florian Heinemann [aut] (transport_track),
Bernhard Schmitzer [aut] (shielding),
Jörn Schrieber [aut] (subsampling),
Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.10-0 dated 2019-01-02 and 0.11-0 dated 2019-02-04
DESCRIPTION | 12 +++++---- MD5 | 16 +++++++----- NAMESPACE | 5 +++ NEWS | 28 ++++++++++++++++++++++ R/fundament.R | 61 +++++++++++++++++++++++++++++++++--------------- R/subsampling.R |only inst/CITATION | 3 +- man/subwasserstein.Rd |only man/wasserstein.Rd | 7 +++-- src/semidiscrete_p1.cpp | 3 -- 10 files changed, 98 insertions(+), 37 deletions(-)
Title: Area-Proportional Euler and Venn Diagrams with Ellipses
Description: Generate area-proportional Euler diagrams
using numerical optimization. An Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Diagrams may be fit with ellipses and circles via
a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>),
A. Jonathan R. Godfrey [ctb],
Peter Gustafsson [ctb],
David H. Eberly [ctb] (geometric algorithms),
Emanuel Huber [ctb] (root solver code)
Maintainer: Johan Larsson <mail@larssonjohan.com>
Diff between eulerr versions 5.0.0 dated 2018-11-05 and 5.1.0 dated 2019-02-04
DESCRIPTION | 14 - MD5 | 59 +++-- NAMESPACE | 8 NEWS.md | 37 +++ R/euler.R | 363 ++--------------------------------- R/eulerr_options.R | 2 R/fit_diagram.R |only R/parse_input.R |only R/plot.euler.R | 210 ++++++++++---------- R/print.euler.R | 62 +++++ R/sysdata.rda |only R/utils.R | 21 ++ R/venn.R |only build/vignette.rds |binary inst/doc/introduction.html | 28 ++ inst/doc/under-the-hood.Rmd | 2 inst/doc/under-the-hood.html | 6 inst/doc/venn-diagrams.R |only inst/doc/venn-diagrams.Rmd |only inst/doc/venn-diagrams.html |only inst/doc/visualization.html | 28 ++ man/euler.Rd | 4 man/eulerr-package.Rd | 1 man/figures/README-plot_method-1.png |binary man/is_integer.Rd |only man/is_real.Rd |only man/plot.euler.Rd | 14 + man/print.euler.Rd | 9 man/print.venn.Rd |only man/venn.Rd |only tests/testthat/test-assertions.R | 8 tests/testthat/test-inputs.R | 38 +++ tests/testthat/test-plotting.R | 81 ++++--- tests/testthat/test-printing.R |only tests/testthat/test-utils.R | 2 vignettes/under-the-hood.Rmd | 2 vignettes/venn-diagrams.Rmd |only 37 files changed, 464 insertions(+), 535 deletions(-)
Title: Searching for Footprints of Selection using "Extended Haplotype
Homozygosity" Based Tests
Description: Population genetic data in form of "Single Nucleotide
Polymorphisms" (SNPs) is often used to identify genomic regions
that have been under recent natural or artificial selection
and might provide clues about the molecular mechanisms of adaptation.
The concept of an "Extended Haplotype Homozygosity" (EHH), introduced by
(Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several
derived statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: "iHS" (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
detecting selection within a single population as well as
"Rsb" (Tang 2007) <doi:10.1371/journal.pbio.0050171> and
"XP-EHH" (Sabeti 2007) <doi:10.1038/nature06250> to detect
(differential) selection between two populations.
Various plotting functions are also included to facilitate
visualization and interpretation of these statistics.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@inra.fr>
Diff between rehh versions 2.0.2 dated 2016-11-18 and 2.0.3 dated 2019-02-04
rehh-2.0.2/rehh/inst/doc/rehh.pdf |only rehh-2.0.2/rehh/vignettes/rehh.html |only rehh-2.0.3/rehh/ChangeLog | 15 rehh-2.0.3/rehh/DESCRIPTION | 31 - rehh-2.0.3/rehh/MD5 | 78 +-- rehh-2.0.3/rehh/NAMESPACE | 7 rehh-2.0.3/rehh/R/bifurcation.diagram.R | 28 - rehh-2.0.3/rehh/R/calc_ehh.R | 28 - rehh-2.0.3/rehh/R/calc_ehhs.R | 34 + rehh-2.0.3/rehh/R/distribplot.R | 10 rehh-2.0.3/rehh/R/ies2xpehh.R | 6 rehh-2.0.3/rehh/R/ihh2ihs.R | 127 +++-- rehh-2.0.3/rehh/R/ihsplot.R | 20 rehh-2.0.3/rehh/R/rsbplot.R | 20 rehh-2.0.3/rehh/R/scan_hh.R | 3 rehh-2.0.3/rehh/R/xpehhplot.R | 20 rehh-2.0.3/rehh/build/vignette.rds |binary rehh-2.0.3/rehh/inst/CITATION | 9 rehh-2.0.3/rehh/inst/doc/rehh.R | 214 ++------- rehh-2.0.3/rehh/inst/doc/rehh.Rmd | 649 +++++++++++++---------------- rehh-2.0.3/rehh/inst/doc/rehh.html |only rehh-2.0.3/rehh/man/bifurcation.diagram.Rd | 33 - rehh-2.0.3/rehh/man/calc_ehh.Rd | 31 - rehh-2.0.3/rehh/man/calc_ehhs.Rd | 24 - rehh-2.0.3/rehh/man/data2haplohh.Rd | 28 - rehh-2.0.3/rehh/man/distribplot.Rd | 11 rehh-2.0.3/rehh/man/ies2rsb.Rd | 11 rehh-2.0.3/rehh/man/ies2xpehh.Rd | 15 rehh-2.0.3/rehh/man/ihh2ihs.Rd | 14 rehh-2.0.3/rehh/man/ihsplot.Rd | 10 rehh-2.0.3/rehh/man/make.example.files.Rd | 13 rehh-2.0.3/rehh/man/rehh-package.Rd | 41 + rehh-2.0.3/rehh/man/rsbplot.Rd | 8 rehh-2.0.3/rehh/man/scan_hh.Rd | 27 - rehh-2.0.3/rehh/man/xpehhplot.Rd | 14 rehh-2.0.3/rehh/src/CALL_EHH.c | 5 rehh-2.0.3/rehh/src/CALL_EHHS.c | 5 rehh-2.0.3/rehh/src/CALL_SCAN_HH.c | 9 rehh-2.0.3/rehh/src/hh_utils.c | 61 +- rehh-2.0.3/rehh/src/hh_utils.h | 2 rehh-2.0.3/rehh/src/rehh_init.c |only rehh-2.0.3/rehh/vignettes/rehh.Rmd | 649 +++++++++++++---------------- 42 files changed, 1136 insertions(+), 1174 deletions(-)
Title: Econometric Analysis of Explosive Time Series
Description: Testing for and dating periods of explosive dynamics
(exuberance) in time series using recursive unit root tests as proposed
by Phillips, P. C., Shi, S. and Yu, J. (2015a) <doi:10.1111/iere.12132>.
Simulation of a variety of periodically-collapsing bubble processes. The
estimation code utilizes the matrix inversion lemma of the recursive least
squares algorithm which results in significant speed improvements.
Author: Kostas Vasilopoulos [cre, aut],
Eftymios Pavlidis [aut],
Simon Spavound [aut],
EnrÃqeu MatrÃnez-GarcÃa [aut]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Diff between exuber versions 0.1.0 dated 2018-06-17 and 0.2.0 dated 2019-02-04
exuber-0.1.0/exuber/R/internal.R |only exuber-0.1.0/exuber/R/misc.R |only exuber-0.1.0/exuber/R/report.R |only exuber-0.1.0/exuber/R/rls.r |only exuber-0.1.0/exuber/man/index.Rd |only exuber-0.1.0/exuber/man/plot.radf.Rd |only exuber-0.1.0/exuber/man/report.Rd |only exuber-0.1.0/exuber/src/srls_gsadf_cpp.cpp |only exuber-0.1.0/exuber/tests/testthat/test-report.R |only exuber-0.2.0/exuber/DESCRIPTION | 36 +- exuber-0.2.0/exuber/MD5 | 92 ++++--- exuber-0.2.0/exuber/NAMESPACE | 64 ++++- exuber-0.2.0/exuber/NEWS.md |only exuber-0.2.0/exuber/R/RcppExports.R | 7 exuber-0.2.0/exuber/R/autoplot.R |only exuber-0.2.0/exuber/R/col_names.R |only exuber-0.2.0/exuber/R/data-crit.R |only exuber-0.2.0/exuber/R/deprecate.R |only exuber-0.2.0/exuber/R/exuber-package.r | 13 - exuber-0.2.0/exuber/R/index.R |only exuber-0.2.0/exuber/R/mc_cv.R | 212 ++++++++-------- exuber-0.2.0/exuber/R/radf.R | 175 +++++++------- exuber-0.2.0/exuber/R/reexports.R |only exuber-0.2.0/exuber/R/sb_cv.R |only exuber-0.2.0/exuber/R/simul.R | 114 ++++----- exuber-0.2.0/exuber/R/summary.R |only exuber-0.2.0/exuber/R/utils.R |only exuber-0.2.0/exuber/R/wb_cv.R | 250 +++++++------------- exuber-0.2.0/exuber/R/zzz.R |only exuber-0.2.0/exuber/README.md | 128 +++++++--- exuber-0.2.0/exuber/data |only exuber-0.2.0/exuber/inst/CITATION | 29 +- exuber-0.2.0/exuber/inst/figures |only exuber-0.2.0/exuber/man/autoplot.datestamp.Rd |only exuber-0.2.0/exuber/man/autoplot.radf.Rd |only exuber-0.2.0/exuber/man/col_names.Rd | 6 exuber-0.2.0/exuber/man/crit.Rd |only exuber-0.2.0/exuber/man/datestamp.Rd |only exuber-0.2.0/exuber/man/diagnostics.Rd |only exuber-0.2.0/exuber/man/exuber-deprecated.Rd |only exuber-0.2.0/exuber/man/exuber.Rd | 12 exuber-0.2.0/exuber/man/index.radf.Rd |only exuber-0.2.0/exuber/man/mc_cv.Rd | 24 + exuber-0.2.0/exuber/man/pipe.Rd |only exuber-0.2.0/exuber/man/print.ggarrange.Rd |only exuber-0.2.0/exuber/man/radf.Rd | 22 - exuber-0.2.0/exuber/man/reexports.Rd |only exuber-0.2.0/exuber/man/sb_cv.Rd |only exuber-0.2.0/exuber/man/sim_blan.Rd | 6 exuber-0.2.0/exuber/man/sim_dgp1.Rd | 6 exuber-0.2.0/exuber/man/sim_dgp2.Rd | 8 exuber-0.2.0/exuber/man/sim_evans.Rd | 19 - exuber-0.2.0/exuber/man/summary.Rd |only exuber-0.2.0/exuber/man/wb_cv.Rd | 34 +- exuber-0.2.0/exuber/src/Makevars |only exuber-0.2.0/exuber/src/Makevars.win |only exuber-0.2.0/exuber/src/RcppExports.cpp | 17 - exuber-0.2.0/exuber/src/rls_gsadf.cpp |only exuber-0.2.0/exuber/tests/testthat/helper.R | 53 +++- exuber-0.2.0/exuber/tests/testthat/test-autoplot.R |only exuber-0.2.0/exuber/tests/testthat/test-col_names.R |only exuber-0.2.0/exuber/tests/testthat/test-cv.R | 126 ++++++++-- exuber-0.2.0/exuber/tests/testthat/test-fortify.R |only exuber-0.2.0/exuber/tests/testthat/test-index.R |only exuber-0.2.0/exuber/tests/testthat/test-panel.R |only exuber-0.2.0/exuber/tests/testthat/test-radf.R | 91 +------ exuber-0.2.0/exuber/tests/testthat/test-sim.R | 9 exuber-0.2.0/exuber/tests/testthat/test-summary.R |only 68 files changed, 852 insertions(+), 701 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt,
Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara,
Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs,
Helene Wagner
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan versions 2.5-3 dated 2018-10-25 and 2.5-4 dated 2019-02-04
DESCRIPTION | 8 - MD5 | 38 +++--- R/RsquareAdj.R | 38 +++--- R/decorana.R | 2 R/goodness.cca.R | 5 R/ordiParseFormula.R | 11 + R/ordiplot.R | 3 R/panel.ordi.R | 4 R/plot.cca.R | 6 - R/summary.cca.R | 2 build/partial.rdb |binary inst/NEWS.Rd | 52 ++++++++ inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary inst/doc/partitioning.pdf |binary man/RsquareAdj.Rd | 8 - man/decostand.Rd | 2 man/simper.Rd | 30 ++--- tests/cca-object-tests.Rout.save | 226 +++++++++++++++++++-------------------- 20 files changed, 257 insertions(+), 178 deletions(-)
Title: Example Data for R Package 'vortexR'
Description: Contains selected data from two publications,
Campbell 'et' 'al'. (2016) <DOI:10.1080/14486563.2015.1028486>
and 'Pacioni' 'et' 'al'. (2017) <DOI:10.1071/PC17002>.
The data is provided both as raw outputs from the population viability
analysis software 'Vortex' and packaged as R objects.
The R package 'vortexR' uses the raw data provided here to illustrate its
functionality of parsing raw 'Vortex' output into R objects.
Author: Carlo Pacioni [aut, cre],
Florian W. Mayer [aut]
Maintainer: Carlo Pacioni <C.Pacioni@Murdoch.edu.au>
Diff between vortexRdata versions 1.0.3 dated 2017-03-25 and 1.0.5 dated 2019-02-04
DESCRIPTION | 19 ++++++++++--------- MD5 | 37 +++++++++++++++++++------------------ NEWS.md |only R/vortexRdata_pkg_data.R | 36 ++++++++++++++++++------------------ README.md | 8 +++++++- data/pac.clas.pairw.rda |binary inst/CITATION | 2 +- man/campbell.Rd | 2 +- man/pac.clas.Nadults.Rd | 2 +- man/pac.clas.Ne.Rd | 2 +- man/pac.clas.Rd | 4 ++-- man/pac.clas.lookup.Rd | 2 +- man/pac.clas.pairw.Rd | 2 +- man/pac.lhs.Rd | 4 ++-- man/pac.run.lhs.Rd | 4 ++-- man/pac.yr.Rd | 2 +- man/pacioni.Rd | 2 +- man/sta.evy5.Rd | 2 +- man/sta.evy5.b11.Rd | 4 ++-- man/sta.main.Rd | 2 +- 20 files changed, 72 insertions(+), 64 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: Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Flavio Poletti [aut],
Angela Li [aut],
Mark Padgham [aut],
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 0.3.5 dated 2018-10-28 and 0.3.6 dated 2019-02-04
DESCRIPTION | 17 +++---- MD5 | 44 +++++++++--------- NAMESPACE | 3 - R/frequencies.R | 12 +++- R/globals.R | 4 + R/import.R | 20 +++----- R/service.R | 2 R/spec.R | 12 ++-- R/time.R | 80 ++++++++++++++++++--------------- R/validate.R | 4 - inst/doc/GTFS-table-relationships.R | 1 inst/doc/GTFS-table-relationships.Rmd | 1 inst/doc/GTFS-table-relationships.html | 59 +++++++++++------------- inst/doc/introduction.html | 37 +++++++-------- inst/extdata/sample-feed-fixed.zip |only man/get_date_service_table.Rd | 4 - man/import_gtfs.Rd | 2 man/read_gtfs.Rd | 2 man/set_hms_times.Rd | 4 - tests/testthat/test-import-gtfs.R | 17 +++---- tests/testthat/test-main.R | 5 -- tests/testthat/test-time.R |only tests/testthat/test_headways.R | 2 vignettes/GTFS-table-relationships.Rmd | 1 24 files changed, 171 insertions(+), 162 deletions(-)
Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming with
palettes spread over many packages with many different API's. This packages
aims to collect all color palettes across the R ecosystem under the same
package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between paletteer versions 0.1.0 dated 2018-07-10 and 0.2.0 dated 2019-02-04
paletteer-0.1.0/paletteer/build |only paletteer-0.1.0/paletteer/inst/doc |only paletteer-0.1.0/paletteer/vignettes |only paletteer-0.2.0/paletteer/DESCRIPTION | 13 paletteer-0.2.0/paletteer/LICENSE.note | 18 + paletteer-0.2.0/paletteer/MD5 | 45 +- paletteer-0.2.0/paletteer/NEWS.md | 7 paletteer-0.2.0/paletteer/R/data.R | 35 +- paletteer-0.2.0/paletteer/R/paletteer_c_wrappers.R | 69 ++- paletteer-0.2.0/paletteer/README.md | 175 ++++++---- paletteer-0.2.0/paletteer/data/palettes_c_names.rda |binary paletteer-0.2.0/paletteer/data/palettes_d.rda |binary paletteer-0.2.0/paletteer/data/palettes_d_names.rda |binary paletteer-0.2.0/paletteer/data/palettes_dynamic_names.rda |binary paletteer-0.2.0/paletteer/man/figures/README-unnamed-chunk-2-1.png |binary paletteer-0.2.0/paletteer/man/figures/README-unnamed-chunk-3-1.png |binary paletteer-0.2.0/paletteer/man/figures/README-unnamed-chunk-4-1.png |binary paletteer-0.2.0/paletteer/man/ggplot2-scales-discrete.Rd | 12 paletteer-0.2.0/paletteer/man/paleteer-c-wrapper.Rd | 6 paletteer-0.2.0/paletteer/man/paletteer-package.Rd | 10 paletteer-0.2.0/paletteer/man/palettes_c_names.Rd | 12 paletteer-0.2.0/paletteer/man/palettes_d.Rd | 5 paletteer-0.2.0/paletteer/man/palettes_d_names.Rd | 10 paletteer-0.2.0/paletteer/man/palettes_dynamic_names.Rd | 8 24 files changed, 271 insertions(+), 154 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>),
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>),
Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>),
Rune Haubo Bojesen Christensen [ctb]
(<https://orcid.org/0000-0002-4494-3399>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Bin Dai [ctb],
Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>),
Gabor Grothendieck [ctb],
Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>),
John Fox [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-19 dated 2018-11-10 and 1.1-20 dated 2019-02-04
lme4-1.1-19/lme4/R/bootMer.r |only lme4-1.1-20/lme4/DESCRIPTION | 6 - lme4-1.1-20/lme4/MD5 | 65 +++++++-------- lme4-1.1-20/lme4/R/allFit.R | 13 +-- lme4-1.1-20/lme4/R/bootMer.R |only lme4-1.1-20/lme4/R/checkConv.R | 1 lme4-1.1-20/lme4/R/lmer.R | 2 lme4-1.1-20/lme4/R/lmerControl.R | 4 lme4-1.1-20/lme4/R/methods.R | 4 lme4-1.1-20/lme4/R/profile.R | 32 ++++--- lme4-1.1-20/lme4/R/utilities.R | 1 lme4-1.1-20/lme4/R/vcconv.R | 2 lme4-1.1-20/lme4/inst/NEWS.Rd | 34 ++++++-- lme4-1.1-20/lme4/man/confint.merMod.Rd | 2 lme4-1.1-20/lme4/man/lmerControl.Rd | 3 lme4-1.1-20/lme4/man/ranef.Rd | 9 -- lme4-1.1-20/lme4/tests/AAAtest-all.R | 10 +- lme4-1.1-20/lme4/tests/Rplots.pdf |binary lme4-1.1-20/lme4/tests/lme4_nlme.R | 40 ++++++--- lme4-1.1-20/lme4/tests/lmer-0.R | 44 ++++++---- lme4-1.1-20/lme4/tests/lmer-1.R | 22 ++--- lme4-1.1-20/lme4/tests/lmer-1.Rout.save | 43 ++++------ lme4-1.1-20/lme4/tests/minval.R | 10 +- lme4-1.1-20/lme4/tests/modFormula.R | 25 ++++-- lme4-1.1-20/lme4/tests/priorWeightsModComp.R | 104 ++++++++++++++++++++----- lme4-1.1-20/lme4/tests/profile-tst.R | 33 +++++-- lme4-1.1-20/lme4/tests/refit.R | 14 --- lme4-1.1-20/lme4/tests/testthat/test-allFit.R |only lme4-1.1-20/lme4/tests/testthat/test-lmer.R | 8 - lme4-1.1-20/lme4/tests/testthat/test-methods.R | 36 ++++---- lme4-1.1-20/lme4/tests/testthat/test-predict.R | 73 ++++++++--------- lme4-1.1-20/lme4/tests/testthat/test-ranef.R | 43 +++++----- lme4-1.1-20/lme4/tests/testthat/test-resids.R | 12 +- lme4-1.1-20/lme4/tests/testthat/test-summary.R | 32 +++++-- lme4-1.1-20/lme4/vignettes/lmer.Rnw | 7 + 35 files changed, 446 insertions(+), 288 deletions(-)
Title: Data Manipulation Verbs for the Spatial Classes
Description: Methods for 'dplyr' verbs for 'sp' 'Spatial' classes. The basic
verbs that modify data attributes, remove or re-arrange rows are supported
and provide complete 'Spatial' analogues of the input data. The group by
and summarize work flow returns a non-topological spatial union. There is
limited support for joins, with left and inner to copy attributes from
another table.
Author: Michael D. Sumner [aut, cre],
Joscha Legewie [ctb],
Jussi Jousimo [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between spdplyr versions 0.1.3 dated 2017-06-02 and 0.2.0 dated 2019-02-04
DESCRIPTION | 8 MD5 | 18 +- NAMESPACE | 6 NEWS.md | 4 R/sdplyr-Spatial.r | 33 +++- README.md | 29 ++- build/vignette.rds |binary inst/doc/spdplyr.html | 408 +++++++++++++++++++++++++++++++++++++++----------- man/dplyr-S3.Rd | 1 man/dplyr-Spatial.Rd | 20 -- 10 files changed, 387 insertions(+), 140 deletions(-)
Title: R2s for Regression Models
Description: Three methods to calculate R2 for models with correlated errors,
including Phylogenetic GLS, Phylogenetic Logistic Regression, Linear Mixed
Models (LMMs), and Generalized Linear Mixed Models (GLMMs). See details in
Ives 2018 <doi:10.1093/sysbio/syy060>.
Author: Anthony Ives [aut, cre],
Daijiang Li [ctb]
Maintainer: Anthony Ives <arives@wisc.edu>
Diff between rr2 versions 1.0.0 dated 2018-11-04 and 1.0.1 dated 2019-02-04
DESCRIPTION | 10 +- MD5 | 27 +++--- NAMESPACE | 1 NEWS.md |only R/r2.R | 13 ++- R/r2_lik.R | 37 ++++++++- R/r2_pred.R | 186 +++++++++++++++++++++++++++++----------------- R/r2_resid.R | 79 ++++++++++++++++--- R/utils.R | 2 README.md | 34 +++++++- man/R2.Rd | 13 ++- man/R2.lik.Rd | 11 ++ man/R2.pred.Rd | 18 ++-- man/R2.resid.Rd | 12 ++ tests/testthat/test_r2s.R | 5 + 15 files changed, 326 insertions(+), 122 deletions(-)
Title: Fast Symbolic Multivariate Polynomials
Description: Fast manipulation of symbolic multivariate polynomials
using the 'Map' class of the Standard Template Library. The package
uses print and coercion methods from the 'mpoly' package (Kahle 2013,
"Multivariate polynomials in R". The R Journal, 5(1):162), but offers
speed improvements. It is comparable in speed to the 'spray' package
for sparse arrays, but retains the symbolic benefits of 'mpoly'.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between mvp versions 1.0-2 dated 2019-01-14 and 1.0-5 dated 2019-02-04
mvp-1.0-2/mvp/inst/doc/mvp.html |only mvp-1.0-5/mvp/DESCRIPTION | 17 - mvp-1.0-5/mvp/MD5 | 35 +- mvp-1.0-5/mvp/NAMESPACE | 1 mvp-1.0-5/mvp/R/RcppExports.R | 12 mvp-1.0-5/mvp/R/skimpy.R | 58 +++- mvp-1.0-5/mvp/build/partial.rdb |only mvp-1.0-5/mvp/build/vignette.rds |binary mvp-1.0-5/mvp/inst/doc/mvp.R | 70 +++-- mvp-1.0-5/mvp/inst/doc/mvp.Rmd | 532 ++++++++++++++++++++------------------ mvp-1.0-5/mvp/inst/doc/mvp.pdf |only mvp-1.0-5/mvp/man/deriv.Rd | 2 mvp-1.0-5/mvp/man/horner.Rd |only mvp-1.0-5/mvp/man/mvp-package.Rd |only mvp-1.0-5/mvp/man/ooom.Rd |only mvp-1.0-5/mvp/man/subs.Rd | 3 mvp-1.0-5/mvp/man/taylor.Rd |only mvp-1.0-5/mvp/src/RcppExports.cpp | 47 +++ mvp-1.0-5/mvp/src/skimpy.cpp | 97 ++++++ mvp-1.0-5/mvp/tests/aac.R | 2 mvp-1.0-5/mvp/tests/foursquare.R | 8 mvp-1.0-5/mvp/vignettes/mvp.Rmd | 532 ++++++++++++++++++++------------------ 22 files changed, 861 insertions(+), 555 deletions(-)
Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or
.dat) that has an accompanying setup file (.sps or .sas). These file
combinations are sometimes referred to as .txt+.sps, .txt+.sas,
.dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas
pair in which the setup file contains instructions to open that text
file. It will NOT open other text files, .sav, .sas, or .por data
files. Fixed-width ASCII files with setup files are common in older
(pre-2000) government data.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 1.4.0 dated 2018-06-18 and 2.0.0 dated 2019-02-04
asciiSetupReader-1.4.0/asciiSetupReader/R/parse_spss_setup.R |only asciiSetupReader-1.4.0/asciiSetupReader/inst/doc/Introduction_to_asciiReader.R |only asciiSetupReader-1.4.0/asciiSetupReader/inst/doc/Introduction_to_asciiReader.Rmd |only asciiSetupReader-1.4.0/asciiSetupReader/inst/doc/Introduction_to_asciiReader.html |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/1980_leoka.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/1981_SHR.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/1985_UCR_offenses_known.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/1986_UCR_offenses_known.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/1987_SHR.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/1988_SHR.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/2000_UCR_offenses_known.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/ca_vital_sps.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/crosswalk_sps.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/parole_survey.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/parole_survey_sps.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/prisoners.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/sacramento.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/sex_offender_notification.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/sex_offender_notification_sps.zip |only asciiSetupReader-1.4.0/asciiSetupReader/inst/testdata/ucr_property_stolen_1998.zip |only asciiSetupReader-1.4.0/asciiSetupReader/tests/testthat/test-parse-value-labels.R |only asciiSetupReader-1.4.0/asciiSetupReader/tests/testthat/test-spss-parser.R |only asciiSetupReader-1.4.0/asciiSetupReader/vignettes/Introduction_to_asciiReader.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/DESCRIPTION | 40 asciiSetupReader-2.0.0/asciiSetupReader/LICENSE |only asciiSetupReader-2.0.0/asciiSetupReader/MD5 | 116 +- asciiSetupReader-2.0.0/asciiSetupReader/NAMESPACE | 3 asciiSetupReader-2.0.0/asciiSetupReader/NEWS.md | 30 asciiSetupReader-2.0.0/asciiSetupReader/R/helper.R | 130 +- asciiSetupReader-2.0.0/asciiSetupReader/R/make_sps_setup.R |only asciiSetupReader-2.0.0/asciiSetupReader/R/parse_setup.R |only asciiSetupReader-2.0.0/asciiSetupReader/R/read_ascii_setup.R |only asciiSetupReader-2.0.0/asciiSetupReader/R/sas.R | 145 -- asciiSetupReader-2.0.0/asciiSetupReader/R/spss.R | 88 - asciiSetupReader-2.0.0/asciiSetupReader/R/utils.R | 116 +- asciiSetupReader-2.0.0/asciiSetupReader/README.md | 167 --- asciiSetupReader-2.0.0/asciiSetupReader/build/vignette.rds |binary asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/Introduction_to_asciiSetupReader.R |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/Introduction_to_asciiSetupReader.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/Introduction_to_asciiSetupReader.html |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/making-an-sps-file.R |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/making-an-sps-file.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/making-an-sps-file.html |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/parsing-an-sps-or-sas-file.R |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/parsing-an-sps-or-sas-file.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/inst/doc/parsing-an-sps-or-sas-file.html |only asciiSetupReader-2.0.0/asciiSetupReader/inst/extdata/sacramento.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1980_leoka_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1980_leoka_sps.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1981_SHR_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1985_UCR_offenses_known_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1986_UCR_offenses_known_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1987_SHR_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/1988_SHR_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/2000_UCR_offenses_known_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/2006_UCR_offenses_known_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/2017_sadc_sas_input_program.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/2017_sadc_spss_input_program.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/ca_vital.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/ca_vital.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/corrections_prison_admissions_1991_2016.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/corrections_prison_admissions_1991_2016.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/crosswalk.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/crosswalk.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/jail_survey_1987.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/jail_survey_1987.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/jail_survey_1987.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/jail_survey_2010.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/jail_survey_2010.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/ncvs_1979_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/ncvs_1979_sps.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/parole_survey.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/parole_survey.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/prisoners_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/sacramento_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/sex_offender_notification.sas |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/sex_offender_notification.sps |only asciiSetupReader-2.0.0/asciiSetupReader/inst/testdata/ucr_property_stolen_1998_sas.zip |only asciiSetupReader-2.0.0/asciiSetupReader/man/make_sps_setup.Rd |only asciiSetupReader-2.0.0/asciiSetupReader/man/parse_setup.Rd |only asciiSetupReader-2.0.0/asciiSetupReader/man/read_ascii_setup.Rd |only asciiSetupReader-2.0.0/asciiSetupReader/man/sas_ascii_reader.Rd | 19 asciiSetupReader-2.0.0/asciiSetupReader/man/spss_ascii_reader.Rd | 15 asciiSetupReader-2.0.0/asciiSetupReader/tests/spelling.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/setup.R | 533 ++++++---- asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-all-value-labels-assigned.R | 422 +++++-- asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-column-names.R | 146 +- asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-missing-values.R | 117 -- asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-parse-value-labels-sas.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-parse-value-labels-sps.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-parser-missing-sas.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-parser-missing-sps.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-parser-sas.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-parser-spss.R |only asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-silent.R | 268 ++--- asciiSetupReader-2.0.0/asciiSetupReader/tests/testthat/test-value-labels.R | 26 asciiSetupReader-2.0.0/asciiSetupReader/vignettes/Introduction_to_asciiSetupReader.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/vignettes/making-an-sps-file.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/vignettes/parsing-an-sps-or-sas-file.Rmd |only asciiSetupReader-2.0.0/asciiSetupReader/vignettes/setup_file_example.sps |only 100 files changed, 1336 insertions(+), 1045 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for all URL-handling needs, including encoding and decoding,
parsing, parameter extraction and modification. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Os Keyes [aut, cre], Jay Jacobs [aut, cre], Drew Schmidt [aut],
Mark Greenaway [ctb], Bob Rudis [ctb], Alex Pinto [ctb], Maryam Khezrzadeh [ctb], Peter Meilstrup [ctb],
Adam M. Costello [cph], Jeff Bezanson [cph], Peter Meilstrup [ctb], Xueyuan Jiang [ctb]
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between urltools versions 1.7.1 dated 2018-08-03 and 1.7.2 dated 2019-02-04
DESCRIPTION | 14 +++++------ MD5 | 16 ++++++------- NEWS | 6 ++++- R/suffix.R | 4 ++- R/zzz.R | 4 +-- data/suffix_dataset.rda |binary man/suffix_extract.Rd | 2 + man/urltools.Rd | 1 tests/testthat/test_suffixes.R | 48 ++++++++++++++++++++--------------------- 9 files changed, 51 insertions(+), 44 deletions(-)
Title: Read, Validate, and Analyze 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. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Flavio Poletti [aut],
Angela Li [aut],
Mark Padgham [aut],
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 trread versions 0.2.5 dated 2018-07-28 and 0.2.7 dated 2019-02-04
trread-0.2.5/trread/README |only trread-0.2.5/trread/inst/doc/read-gtfs-files.R |only trread-0.2.5/trread/inst/doc/read-gtfs-files.Rmd |only trread-0.2.5/trread/inst/doc/read-gtfs-files.html |only trread-0.2.5/trread/man/list_files.Rd |only trread-0.2.5/trread/man/validate_gtfs_structure.Rd |only trread-0.2.5/trread/vignettes/read-gtfs-files.Rmd |only trread-0.2.7/trread/DESCRIPTION | 48 + trread-0.2.7/trread/MD5 | 77 ++ trread-0.2.7/trread/NAMESPACE | 25 trread-0.2.7/trread/R/data.R |only trread-0.2.7/trread/R/frequencies.R |only trread-0.2.7/trread/R/globals.R | 16 trread-0.2.7/trread/R/import.R | 304 ++++++---- trread-0.2.7/trread/R/joins.R |only trread-0.2.7/trread/R/plot.R |only trread-0.2.7/trread/R/service.R |only trread-0.2.7/trread/R/spec.R | 243 +++++--- trread-0.2.7/trread/R/time.R |only trread-0.2.7/trread/R/transitfeeds.R |only trread-0.2.7/trread/R/validate.R | 362 ++++--------- trread-0.2.7/trread/build/vignette.rds |binary trread-0.2.7/trread/data |only trread-0.2.7/trread/inst/doc/GTFS-table-relationships.R |only trread-0.2.7/trread/inst/doc/GTFS-table-relationships.Rmd |only trread-0.2.7/trread/inst/doc/GTFS-table-relationships.html |only trread-0.2.7/trread/inst/doc/introduction.R |only trread-0.2.7/trread/inst/doc/introduction.Rmd |only trread-0.2.7/trread/inst/doc/introduction.html |only trread-0.2.7/trread/inst/extdata/sample-feed-fixed.zip |only trread-0.2.7/trread/man/clear_api_key.Rd |only trread-0.2.7/trread/man/count_service_trips.Rd |only trread-0.2.7/trread/man/download_from_url.Rd | 3 trread-0.2.7/trread/man/feedlist_df.Rd |only trread-0.2.7/trread/man/filter_feedlist.Rd |only trread-0.2.7/trread/man/filter_stop_times_by_hour.Rd |only trread-0.2.7/trread/man/filter_stops.Rd |only trread-0.2.7/trread/man/get_api_key.Rd |only trread-0.2.7/trread/man/get_date_service_table.Rd |only trread-0.2.7/trread/man/get_feed.Rd |only trread-0.2.7/trread/man/get_feedlist.Rd |only trread-0.2.7/trread/man/get_route_frequency.Rd |only trread-0.2.7/trread/man/get_stop_frequency.Rd |only trread-0.2.7/trread/man/gt_as_dt.Rd |only trread-0.2.7/trread/man/gtfs_obj.Rd |only trread-0.2.7/trread/man/has_api_key.Rd |only trread-0.2.7/trread/man/import_gtfs.Rd | 8 trread-0.2.7/trread/man/most_frequent_service.Rd |only trread-0.2.7/trread/man/read_gtfs.Rd |only trread-0.2.7/trread/man/route_type_names_df.Rd |only trread-0.2.7/trread/man/service_by_dow.Rd |only trread-0.2.7/trread/man/set_api_key.Rd |only trread-0.2.7/trread/man/set_hms_times.Rd |only trread-0.2.7/trread/man/shape_for_route.Rd |only trread-0.2.7/trread/man/shape_route_service.Rd |only trread-0.2.7/trread/man/shapes_for_routes.Rd |only trread-0.2.7/trread/man/unzip_file.Rd | 4 trread-0.2.7/trread/tests/testthat/test-import-gtfs.R | 80 -- trread-0.2.7/trread/tests/testthat/test-main.R |only trread-0.2.7/trread/tests/testthat/test-time.R |only trread-0.2.7/trread/tests/testthat/test_headways.R |only trread-0.2.7/trread/vignettes/GTFS-table-relationships.Rmd |only trread-0.2.7/trread/vignettes/figures |only trread-0.2.7/trread/vignettes/introduction.Rmd |only 64 files changed, 588 insertions(+), 582 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 2.5.6 dated 2019-01-26 and 2.5.7 dated 2019-02-04
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/methods.R | 9 ++++++++- man/Lambda.Rd | 2 +- man/secrdesign-package.Rd | 10 +++++----- 6 files changed, 32 insertions(+), 17 deletions(-)
Title: Utility Functions for Parametric Multi-State Models
Description: Provides functions for working with multi-state modelling,
such as efficient simulation routines for estimating transition probabilities and length of stay.
It is designed as an extension to multi-state modelling capabilities provided with the 'flexsurv'
package (see Jackson (2016) <doi:10.18637/jss.v070.i08>).
Author: Stuart Lacy
Maintainer: Stuart Lacy <stuart.lacy@gmail.com>
Diff between multistateutils versions 1.2.0 dated 2018-07-21 and 1.2.2 dated 2019-02-04
multistateutils-1.2.0/multistateutils/man/des-package.Rd |only multistateutils-1.2.2/multistateutils/DESCRIPTION | 20 multistateutils-1.2.2/multistateutils/MD5 | 50 multistateutils-1.2.2/multistateutils/NEWS.md | 10 multistateutils-1.2.2/multistateutils/R/cohort.R | 34 multistateutils-1.2.2/multistateutils/R/length_of_stay.R | 84 multistateutils-1.2.2/multistateutils/R/msprep2.R | 116 multistateutils-1.2.2/multistateutils/R/transition_probabilities.R | 58 multistateutils-1.2.2/multistateutils/R/utils.R | 64 multistateutils-1.2.2/multistateutils/README.md | 285 - multistateutils-1.2.2/multistateutils/build/vignette.rds |binary multistateutils-1.2.2/multistateutils/inst/doc/Examples.R | 20 multistateutils-1.2.2/multistateutils/inst/doc/Examples.Rmd | 21 multistateutils-1.2.2/multistateutils/inst/doc/Examples.html | 2732 ++-------- multistateutils-1.2.2/multistateutils/man/cohort_simulation.Rd | 23 multistateutils-1.2.2/multistateutils/man/length_of_stay.Rd | 21 multistateutils-1.2.2/multistateutils/man/msprep2.Rd | 21 multistateutils-1.2.2/multistateutils/man/plot_predicted_pathway.Rd | 4 multistateutils-1.2.2/multistateutils/man/predict_transitions.Rd | 19 multistateutils-1.2.2/multistateutils/src/simulation.cpp | 10 multistateutils-1.2.2/multistateutils/src/state.cpp | 2 multistateutils-1.2.2/multistateutils/src/transitions.cpp | 2 multistateutils-1.2.2/multistateutils/tests/testthat/test_cohort.R | 39 multistateutils-1.2.2/multistateutils/tests/testthat/test_lengthofstay.R | 55 multistateutils-1.2.2/multistateutils/tests/testthat/test_transitionprobs.R | 118 multistateutils-1.2.2/multistateutils/vignettes/Examples.Rmd | 21 multistateutils-1.2.2/multistateutils/vignettes/treatmentpathways.png |only 27 files changed, 1212 insertions(+), 2617 deletions(-)
More information about multistateutils at CRAN
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Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs, pairwise comparisons, graphical approaches, assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 1.9 dated 2018-10-18 and 2.0 dated 2019-02-04
DESCRIPTION | 9 +++++---- MD5 | 46 +++++++++++++++++++++++----------------------- R/ag.test.R | 7 +++++-- R/aov.test.R | 7 +++++-- R/bf.test.R | 7 +++++-- R/describe.R | 7 +++++-- R/gplot.R | 7 +++++-- R/homog.test.R | 7 +++++-- R/james.test.R | 7 +++++-- R/kw.test.R | 7 +++++-- R/nor.test.R | 7 +++++-- R/paircomp.R | 5 +++-- R/paircomp.jt.R | 4 ++-- R/welch.test.R | 7 +++++-- man/ag.test.Rd | 13 ++++++++++++- man/aov.test.Rd | 6 +++++- man/bf.test.Rd | 6 +++++- man/describe.Rd | 2 +- man/gplot.Rd | 2 +- man/homog.test.Rd | 2 +- man/james.test.Rd | 5 ++++- man/kw.test.Rd | 5 ++++- man/nor.test.Rd | 2 +- man/welch.test.Rd | 6 +++++- 24 files changed, 122 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-17 0.1.7
2017-05-30 0.1.6
2017-05-04 0.1.4
2016-09-14 0.1.3
2016-06-01 0.1.0.0