Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing,
to use separately or with the book "Visual Statistics. Use R!":
Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>.
Most useful functions:
Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering;
Recode() which does multiple recoding in a fast, simple and flexible way;
Misclass() which outputs confusion matrix even if classes are not concerted;
Overlap() which calculates overlaps of convex hulls from any projection;
Biarrows() which converts any scatterplot into biplot;
and Pleiad() which is fast and flexible correlogram.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Core Team [ctb]
Maintainer: Alexey Shipunov <dactylorhiza@gmail.com>
Diff between shipunov versions 1.7 dated 2020-03-18 and 1.8 dated 2020-06-02
DESCRIPTION | 22 ++++++++++----- MD5 | 56 ++++++++++++++++++++-------------------- NEWS | 14 ++++++++++ R/aaa.r | 36 +++++--------------------- R/alldups.r | 2 - R/bclust.r | 34 ++++++++++++++++++------ R/dotcharts.r | 72 ++++++++++++++++++++++++++-------------------------- R/fill.r | 1 R/hulls.r | 8 ++--- R/misclass.r | 38 +++++++++++++++------------ R/pleiad.r | 8 ++--- R/ploth.r |only TODO | 21 +++++++++++++-- man/Alldups.Rd | 8 ++--- man/Biarrows.Rd | 15 ++-------- man/Ditto.Rd | 8 +++++ man/Gradd.Rd | 9 +++--- man/Gridmoon.Rd | 3 +- man/Hcoords.Rd | 35 +++++++++++++++++++++++-- man/Hulls.Rd | 31 +++++++++++++--------- man/MDSv.Rd | 4 +- man/Misclass.Rd | 24 ++++++++++------- man/Pleiad.Rd | 45 ++++++++++++++++++++++---------- man/Ploth.Rd | 22 +++++++++++---- man/Rpart2newick.Rd | 4 +- man/Rresults.Rd | 2 - man/Str.Rd | 23 +++++++--------- man/Tcoords.Rd |only man/Xpager.Rd | 2 - man/keys.Rd | 31 +++++++++++++++++----- 30 files changed, 353 insertions(+), 225 deletions(-)
Title: Statistical Analysis of Point Processes
Description: Functions for statistical analysis of point processes.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>
Diff between SAPP versions 1.0.7 dated 2016-10-05 and 1.0.8 dated 2020-06-02
SAPP-1.0.7/SAPP/inst/doc/SAPP-guide_e.pdf |only SAPP-1.0.7/SAPP/inst/doc/SAPP-guide_j.pdf |only SAPP-1.0.8/SAPP/DESCRIPTION | 11 SAPP-1.0.8/SAPP/MD5 | 85 - SAPP-1.0.8/SAPP/NAMESPACE | 8 SAPP-1.0.8/SAPP/R/SAPP.R | 1532 +++++++++++++++--------------- SAPP-1.0.8/SAPP/build |only SAPP-1.0.8/SAPP/data/Brastings.rda |binary SAPP-1.0.8/SAPP/data/PProcess.rda |binary SAPP-1.0.8/SAPP/data/PoissonData.rda |binary SAPP-1.0.8/SAPP/data/SelfExcit.rda |binary SAPP-1.0.8/SAPP/data/main2003JUL26.rda |binary SAPP-1.0.8/SAPP/data/res2003JUL26.rda |binary SAPP-1.0.8/SAPP/inst/doc/SAPP.Rnw |only SAPP-1.0.8/SAPP/inst/doc/SAPP.pdf |only SAPP-1.0.8/SAPP/inst/doc/changes.txt | 45 SAPP-1.0.8/SAPP/man/Brastings.Rd | 11 SAPP-1.0.8/SAPP/man/SAPP-package.Rd | 20 SAPP-1.0.8/SAPP/man/eptren.Rd | 75 - SAPP-1.0.8/SAPP/man/etarpp.Rd | 55 - SAPP-1.0.8/SAPP/man/etasap.Rd | 21 SAPP-1.0.8/SAPP/man/etasim.Rd | 11 SAPP-1.0.8/SAPP/man/linlin.Rd | 14 SAPP-1.0.8/SAPP/man/linsim.Rd | 6 SAPP-1.0.8/SAPP/man/momori.Rd | 15 SAPP-1.0.8/SAPP/man/pgraph.Rd | 24 SAPP-1.0.8/SAPP/man/ptspec.Rd | 10 SAPP-1.0.8/SAPP/man/respoi.Rd | 20 SAPP-1.0.8/SAPP/man/simbvh.Rd | 23 SAPP-1.0.8/SAPP/src/aftpoi.f | 227 ++-- SAPP-1.0.8/SAPP/src/eptren.c | 2 SAPP-1.0.8/SAPP/src/eptrenf.f | 24 SAPP-1.0.8/SAPP/src/etarpp.c | 2 SAPP-1.0.8/SAPP/src/etas.f | 69 - SAPP-1.0.8/SAPP/src/etasap.c | 2 SAPP-1.0.8/SAPP/src/etasim.c | 2 SAPP-1.0.8/SAPP/src/init.c |only SAPP-1.0.8/SAPP/src/linlin.c | 2 SAPP-1.0.8/SAPP/src/linlinf.f | 12 SAPP-1.0.8/SAPP/src/linsim.c | 2 SAPP-1.0.8/SAPP/src/momori.c | 2 SAPP-1.0.8/SAPP/src/pgraph.c | 2 SAPP-1.0.8/SAPP/src/pgraphf.f | 1 SAPP-1.0.8/SAPP/src/ptspec.c | 2 SAPP-1.0.8/SAPP/src/respoi.c | 2 SAPP-1.0.8/SAPP/src/simbvh.c | 2 SAPP-1.0.8/SAPP/vignettes |only 47 files changed, 1301 insertions(+), 1040 deletions(-)
Title: River Network Distance Computation and Applications
Description: Reads river network shape files and computes network distances.
Also included are a variety of computation and graphical tools designed
for fisheries telemetry research, such as minimum home range, kernel density
estimation, and clustering analysis using empirical k-functions with
a bootstrap envelope. Tools are also provided for editing the river
networks, meaning there is no reliance on external software.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matt.tyers@alaska.gov>
Diff between riverdist versions 0.15.1 dated 2020-05-22 and 0.15.2 dated 2020-06-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 3 --- NEWS.md | 2 +- R/dataset_help.R | 3 --- inst/doc/riverdist_vignette.html | 6 +++--- man/riverdist-package.Rd | 4 ++-- 7 files changed, 16 insertions(+), 22 deletions(-)
Title: Simulating Forest Growth using the 3-PG Model
Description: Provides a flexible and easy-to-use interface for the Physiological Processes Predicting Growth (3-PG) model written in Fortran. The r3PG serves as a flexible and easy-to-use interface for the 3-PGpjs (monospecific, evenaged and evergreen forests) described in Landsberg & Waring (1997) <doi:10.1016/S0378-1127(97)00026-1> and the 3-PGmix (deciduous, uneven-aged or mixed-species forests) described in Forrester & Tang (2016) <doi:10.1016/j.ecolmodel.2015.07.010>.
Author: Volodymyr Trotsiuk [aut, cre] (<https://orcid.org/0000-0002-8363-656X>),
Florian Hartig [aut] (<https://orcid.org/0000-0002-6255-9059>),
David Forrester [aut]
Maintainer: Volodymyr Trotsiuk <vtrotsiuk@gmail.com>
Diff between r3PG versions 0.1.1 dated 2020-05-19 and 0.1.2 dated 2020-06-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 8 ++++++++ R/run_3PG.R | 3 ++- build/partial.rdb |binary src/md_3PG.f95 | 16 +++++++++++----- tests/testthat/test-vba.R | 2 +- 7 files changed, 31 insertions(+), 16 deletions(-)
Title: Markov Random Field Models for Image Analysis
Description: Model fitting, sampling and visualization
for the (Hidden) Markov Random Field model with pairwise interactions and
general interaction structure from
Freguglia, Garcia & Bicas (2020) <doi:10.1002/env.2613>,
which has many popular models used in 2-dimensional lattices
as particular cases, like the Ising Model and Potts Model.
Author: Victor Freguglia [aut, cre] (<https://orcid.org/0000-0002-6189-4453>)
Maintainer: Victor Freguglia <victorfreguglia@gmail.com>
Diff between mrf2d versions 0.2.0 dated 2020-02-21 and 0.3 dated 2020-06-02
mrf2d-0.2.0/mrf2d/inst/doc/mrf2d.R |only mrf2d-0.2.0/mrf2d/inst/doc/mrf2d.Rmd |only mrf2d-0.2.0/mrf2d/inst/doc/mrf2d.html |only mrf2d-0.2.0/mrf2d/vignettes/mrf2d.Rmd |only mrf2d-0.3/mrf2d/DESCRIPTION | 13 mrf2d-0.3/mrf2d/MD5 | 137 +-- mrf2d-0.3/mrf2d/NAMESPACE | 62 - mrf2d-0.3/mrf2d/NEWS.md | 10 mrf2d-0.3/mrf2d/R/RcppExports.R | 126 +- mrf2d-0.3/mrf2d/R/array_vector_conversions.R | 304 +++--- mrf2d-0.3/mrf2d/R/basis_functions.R | 211 ++-- mrf2d-0.3/mrf2d/R/cpmrf2d.R |only mrf2d-0.3/mrf2d/R/example_data.R | 85 + mrf2d-0.3/mrf2d/R/family.R | 111 +- mrf2d-0.3/mrf2d/R/fit_ghm.R | 435 +++++----- mrf2d-0.3/mrf2d/R/fit_icm.R | 36 mrf2d-0.3/mrf2d/R/fit_sa.R | 288 +++--- mrf2d-0.3/mrf2d/R/mrf2d.R |only mrf2d-0.3/mrf2d/R/mrfi_class.R | 323 ++++--- mrf2d-0.3/mrf2d/R/mrfi_methods.R | 352 ++++---- mrf2d-0.3/mrf2d/R/plot.R | 152 +-- mrf2d-0.3/mrf2d/R/pseudo_likelihood.R | 279 +++--- mrf2d-0.3/mrf2d/R/rmrf.R | 329 +++---- mrf2d-0.3/mrf2d/R/suf_stat.R | 226 +++-- mrf2d-0.3/mrf2d/R/zzz.R | 12 mrf2d-0.3/mrf2d/README.md | 299 +++--- mrf2d-0.3/mrf2d/build/partial.rdb |binary mrf2d-0.3/mrf2d/build/vignette.rds |binary mrf2d-0.3/mrf2d/data/bold5000.rda |only mrf2d-0.3/mrf2d/data/field1.rda |only mrf2d-0.3/mrf2d/data/hfield1.rda |only mrf2d-0.3/mrf2d/inst/REFERENCES.bib | 147 +-- mrf2d-0.3/mrf2d/inst/doc/mrf2d-family.R |only mrf2d-0.3/mrf2d/inst/doc/mrf2d-family.Rmd |only mrf2d-0.3/mrf2d/inst/doc/mrf2d-family.html |only mrf2d-0.3/mrf2d/man/Z_potts.Rd | 50 - mrf2d-0.3/mrf2d/man/basis_functions.Rd | 86 + mrf2d-0.3/mrf2d/man/bold5000.Rd |only mrf2d-0.3/mrf2d/man/cpmrf2d.Rd |only mrf2d-0.3/mrf2d/man/data_examples.Rd |only mrf2d-0.3/mrf2d/man/dplot.Rd | 108 +- mrf2d-0.3/mrf2d/man/figures/README-Y_example_plot-1.png |binary mrf2d-0.3/mrf2d/man/figures/README-Z_example_plot-1.png |binary mrf2d-0.3/mrf2d/man/figures/README-example_interacions-1.png |binary mrf2d-0.3/mrf2d/man/figures/README-example_interacions-2.png |binary mrf2d-0.3/mrf2d/man/figures/README-example_interacions-3.png |binary mrf2d-0.3/mrf2d/man/figures/README-plot_interaction-1.png |binary mrf2d-0.3/mrf2d/man/figures/README-results_plot-1.png |binary mrf2d-0.3/mrf2d/man/figures/README-results_plot-2.png |binary mrf2d-0.3/mrf2d/man/figures/README-results_plot-3.png |binary mrf2d-0.3/mrf2d/man/fit_ghm.Rd | 231 ++--- mrf2d-0.3/mrf2d/man/fit_pl.Rd | 128 +- mrf2d-0.3/mrf2d/man/fit_sa.Rd | 238 ++--- mrf2d-0.3/mrf2d/man/mrf2d-family.Rd | 134 +-- mrf2d-0.3/mrf2d/man/mrf2d-package.Rd |only mrf2d-0.3/mrf2d/man/mrfi-class.Rd | 140 +-- mrf2d-0.3/mrf2d/man/mrfi-operations.Rd | 80 - mrf2d-0.3/mrf2d/man/mrfi-subsetting.Rd | 59 - mrf2d-0.3/mrf2d/man/mrfi.Rd | 100 +- mrf2d-0.3/mrf2d/man/pl_mrf2d.Rd | 91 +- mrf2d-0.3/mrf2d/man/plot.mrfi.Rd | 91 +- mrf2d-0.3/mrf2d/man/rmrf2d.Rd | 240 ++--- mrf2d-0.3/mrf2d/man/smr_array.Rd | 97 +- mrf2d-0.3/mrf2d/man/smr_stat.Rd | 96 +- mrf2d-0.3/mrf2d/tests/testthat.R | 8 mrf2d-0.3/mrf2d/tests/testthat/test-array_vector_conversions.R | 50 - mrf2d-0.3/mrf2d/tests/testthat/test-basis_functions.R | 44 - mrf2d-0.3/mrf2d/tests/testthat/test-cohist.R |only mrf2d-0.3/mrf2d/tests/testthat/test-cp_mrf2d.R |only mrf2d-0.3/mrf2d/tests/testthat/test-fit_ghm.R | 87 +- mrf2d-0.3/mrf2d/tests/testthat/test-fit_icm.R | 8 mrf2d-0.3/mrf2d/tests/testthat/test-fit_sa.R | 30 mrf2d-0.3/mrf2d/tests/testthat/test-mrfi_class.R | 85 + mrf2d-0.3/mrf2d/tests/testthat/test-plot.R | 8 mrf2d-0.3/mrf2d/tests/testthat/test-pseudo_likelihood.R | 88 +- mrf2d-0.3/mrf2d/tests/testthat/test-rmrf2d.R | 106 +- mrf2d-0.3/mrf2d/tests/testthat/test-smr_functions.R | 42 mrf2d-0.3/mrf2d/tests/testthat/test-suf_stat.R | 16 mrf2d-0.3/mrf2d/vignettes/mrf2d-family.Rmd |only 79 files changed, 3383 insertions(+), 3095 deletions(-)
Title: Keyword Assisted Topic Model
Description: Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2020) <arXiv:2004.05964>.
Author: Shusei Eshima [aut, cre] (<https://orcid.org/0000-0003-3613-4046>),
Tomoya Sasaki [aut],
William Lowe [ctb],
Kosuke Imai [aut]
Maintainer: Shusei Eshima <shuseieshima@g.harvard.edu>
Diff between keyATM versions 0.2.0 dated 2020-05-23 and 0.2.2 dated 2020-06-02
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 11 ++++++++++- R/keyATMvb.R | 1 + R/model.R | 2 +- src/LDA_base.cpp | 1 + src/keyATM_meta.cpp | 2 +- tests/testthat/test-Initialization.R | 6 +++++- tests/testthat/test-keyATM.R | 1 + tests/testthat/test-keyATMHeterogeneity.R | 6 +++--- tests/testthat/test-plot.R | 2 +- tests/testthat/test-weightedLDA.R | 7 ++++--- 12 files changed, 45 insertions(+), 28 deletions(-)
Title: Health-Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health-economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
R Core Team [ctb] (hesim uses some slightly modified C functions from
base R)
Maintainer: Devin Incerti <devin.incerti@gmail.com>
Diff between hesim versions 0.3.0 dated 2020-05-25 and 0.3.1 dated 2020-06-02
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- inst/doc/expected-values.html | 4 ++-- inst/doc/getting-started.html | 20 ++++++++++---------- inst/doc/icea.html | 4 ++-- inst/doc/intro.html | 4 ++-- inst/doc/markov-inhomogeneous.html | 4 ++-- inst/doc/mlogit.html | 4 ++-- inst/doc/mstate.html | 4 ++-- inst/doc/psm.html | 4 ++-- src/indiv-ctstm.cpp | 6 +++--- 11 files changed, 40 insertions(+), 40 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Stephanie Lobaugh [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.3.0 dated 2020-04-17 and 1.3.1 dated 2020-06-02
gtsummary-1.3.0/gtsummary/R/tidyselect_to_list.R |only gtsummary-1.3.0/gtsummary/inst/rmarkdown_example/gtsummary_rmarkdown_html.docx |only gtsummary-1.3.0/gtsummary/inst/rmarkdown_example/gtsummary_rmarkdown_html.html |only gtsummary-1.3.0/gtsummary/inst/rmarkdown_example/gtsummary_rmarkdown_html.log |only gtsummary-1.3.0/gtsummary/inst/rmarkdown_example/gtsummary_rmarkdown_html.rtf |only gtsummary-1.3.0/gtsummary/man/figures/bold_p_stack_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/modify_anova_ex1.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_col_ex1.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_col_ex2.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_lm_bold_p_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_lm_sort_p_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_reg_nevent_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_stat_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_sum_bold_p_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_sum_q_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_sum_q_ex1.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_sum_sort_p_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_uv_q_ex2.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_uvglm_bold_p_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_uvglm_sort_p_ex.png |only gtsummary-1.3.0/gtsummary/man/figures/tbl_uvr_q_ex.png |only gtsummary-1.3.0/gtsummary/man/img |only gtsummary-1.3.1/gtsummary/DESCRIPTION | 18 gtsummary-1.3.1/gtsummary/MD5 | 428 gtsummary-1.3.1/gtsummary/NAMESPACE | 16 gtsummary-1.3.1/gtsummary/NEWS.md | 69 gtsummary-1.3.1/gtsummary/R/add_global_p.R | 38 gtsummary-1.3.1/gtsummary/R/add_nevent.R | 15 gtsummary-1.3.1/gtsummary/R/add_overall.R | 5 gtsummary-1.3.1/gtsummary/R/add_p.R | 72 gtsummary-1.3.1/gtsummary/R/add_q.R | 35 gtsummary-1.3.1/gtsummary/R/add_stat.R |only gtsummary-1.3.1/gtsummary/R/add_stat_label.R | 127 gtsummary-1.3.1/gtsummary/R/as_flextable.R | 73 gtsummary-1.3.1/gtsummary/R/as_gt.R | 16 gtsummary-1.3.1/gtsummary/R/as_huxtable.R |only gtsummary-1.3.1/gtsummary/R/as_kable.R | 3 gtsummary-1.3.1/gtsummary/R/as_kable_extra.R | 26 gtsummary-1.3.1/gtsummary/R/as_tibble.R | 61 gtsummary-1.3.1/gtsummary/R/bold_p.R | 10 gtsummary-1.3.1/gtsummary/R/combine_terms.R | 33 gtsummary-1.3.1/gtsummary/R/gtsummary-package.R | 3 gtsummary-1.3.1/gtsummary/R/inline_text.R | 54 gtsummary-1.3.1/gtsummary/R/modify_footnote.R |only gtsummary-1.3.1/gtsummary/R/modify_header.R | 93 gtsummary-1.3.1/gtsummary/R/modify_spanning_header.R |only gtsummary-1.3.1/gtsummary/R/print.R | 67 gtsummary-1.3.1/gtsummary/R/reexport.R | 9 gtsummary-1.3.1/gtsummary/R/select_helpers.R | 25 gtsummary-1.3.1/gtsummary/R/set_gtsummary_theme.R |only gtsummary-1.3.1/gtsummary/R/sort_p.R | 10 gtsummary-1.3.1/gtsummary/R/sysdata.rda |only gtsummary-1.3.1/gtsummary/R/tbl_cross.R | 56 gtsummary-1.3.1/gtsummary/R/tbl_merge.R | 14 gtsummary-1.3.1/gtsummary/R/tbl_regression.R | 28 gtsummary-1.3.1/gtsummary/R/tbl_stack.R | 34 gtsummary-1.3.1/gtsummary/R/tbl_summary.R | 93 gtsummary-1.3.1/gtsummary/R/tbl_survfit.R | 7 gtsummary-1.3.1/gtsummary/R/tbl_survival.R | 2 gtsummary-1.3.1/gtsummary/R/tbl_uvregression.R | 11 gtsummary-1.3.1/gtsummary/R/theme_gtsummary.R |only gtsummary-1.3.1/gtsummary/R/utils-add_p.R | 144 gtsummary-1.3.1/gtsummary/R/utils-gtsummary_core.R | 294 gtsummary-1.3.1/gtsummary/R/utils-misc.R |only gtsummary-1.3.1/gtsummary/R/utils-tbl_regression.R | 31 gtsummary-1.3.1/gtsummary/R/utils-tbl_summary.R | 239 gtsummary-1.3.1/gtsummary/R/vetted_models.R | 8 gtsummary-1.3.1/gtsummary/README.md | 26 gtsummary-1.3.1/gtsummary/build/gtsummary.pdf |17604 ++++++---- gtsummary-1.3.1/gtsummary/build/vignette.rds |binary gtsummary-1.3.1/gtsummary/inst/WORDLIST | 3 gtsummary-1.3.1/gtsummary/inst/doc/gallery.R | 70 gtsummary-1.3.1/gtsummary/inst/doc/gallery.Rmd | 81 gtsummary-1.3.1/gtsummary/inst/doc/gallery.html | 1450 gtsummary-1.3.1/gtsummary/inst/doc/global_options.Rmd | 7 gtsummary-1.3.1/gtsummary/inst/doc/global_options.html | 121 gtsummary-1.3.1/gtsummary/inst/doc/gtsummary_definition.Rmd | 4 gtsummary-1.3.1/gtsummary/inst/doc/gtsummary_definition.html | 639 gtsummary-1.3.1/gtsummary/inst/doc/inline_text.R | 2 gtsummary-1.3.1/gtsummary/inst/doc/inline_text.Rmd | 2 gtsummary-1.3.1/gtsummary/inst/doc/inline_text.html | 190 gtsummary-1.3.1/gtsummary/inst/doc/rmarkdown.R | 8 gtsummary-1.3.1/gtsummary/inst/doc/rmarkdown.Rmd | 10 gtsummary-1.3.1/gtsummary/inst/doc/rmarkdown.html | 312 gtsummary-1.3.1/gtsummary/inst/doc/tbl_regression.R | 25 gtsummary-1.3.1/gtsummary/inst/doc/tbl_regression.Rmd | 40 gtsummary-1.3.1/gtsummary/inst/doc/tbl_regression.html | 487 gtsummary-1.3.1/gtsummary/inst/doc/tbl_summary.R | 26 gtsummary-1.3.1/gtsummary/inst/doc/tbl_summary.Rmd | 41 gtsummary-1.3.1/gtsummary/inst/doc/tbl_summary.html | 666 gtsummary-1.3.1/gtsummary/inst/doc/themes.R |only gtsummary-1.3.1/gtsummary/inst/doc/themes.Rmd |only gtsummary-1.3.1/gtsummary/inst/doc/themes.html |only gtsummary-1.3.1/gtsummary/man/add_global_p.Rd | 64 gtsummary-1.3.1/gtsummary/man/add_global_p.tbl_regression.Rd | 152 gtsummary-1.3.1/gtsummary/man/add_global_p.tbl_uvregression.Rd | 109 gtsummary-1.3.1/gtsummary/man/add_n.Rd | 2 gtsummary-1.3.1/gtsummary/man/add_nevent.Rd | 56 gtsummary-1.3.1/gtsummary/man/add_nevent.tbl_regression.Rd | 112 gtsummary-1.3.1/gtsummary/man/add_nevent.tbl_uvregression.Rd | 124 gtsummary-1.3.1/gtsummary/man/add_overall.Rd | 2 gtsummary-1.3.1/gtsummary/man/add_p.tbl_cross.Rd | 1 gtsummary-1.3.1/gtsummary/man/add_p.tbl_summary.Rd | 4 gtsummary-1.3.1/gtsummary/man/add_q.Rd | 25 gtsummary-1.3.1/gtsummary/man/add_stat.Rd |only gtsummary-1.3.1/gtsummary/man/add_stat_label.Rd | 48 gtsummary-1.3.1/gtsummary/man/as_flextable.Rd | 4 gtsummary-1.3.1/gtsummary/man/as_gt.Rd | 137 gtsummary-1.3.1/gtsummary/man/as_huxtable.gtsummary.Rd |only gtsummary-1.3.1/gtsummary/man/as_kable.Rd | 119 gtsummary-1.3.1/gtsummary/man/as_kable_extra.Rd | 1 gtsummary-1.3.1/gtsummary/man/as_tibble.gtsummary.Rd | 127 gtsummary-1.3.1/gtsummary/man/bold_italicize_labels_levels.Rd | 6 gtsummary-1.3.1/gtsummary/man/bold_p.Rd | 94 gtsummary-1.3.1/gtsummary/man/combine_terms.Rd | 220 gtsummary-1.3.1/gtsummary/man/deprecated.Rd | 78 gtsummary-1.3.1/gtsummary/man/figures/README-tbl_summary_print_extra-1.png |binary gtsummary-1.3.1/gtsummary/man/figures/add_nevent_ex.png |only gtsummary-1.3.1/gtsummary/man/figures/add_p_cross_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/add_p_cross_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/add_p_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/add_p_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/add_q_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/add_q_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/add_stat_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/add_stat_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/add_stat_label_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/add_stat_label_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/as_gt_ex.png |binary gtsummary-1.3.1/gtsummary/man/figures/bold_p_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/bold_p_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/combine_terms_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/combine_terms_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/combine_terms_ex3.png |binary gtsummary-1.3.1/gtsummary/man/figures/gt_output_formats.PNG |binary gtsummary-1.3.1/gtsummary/man/figures/inline_text_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/modify_footnote_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/modify_footnote_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/modify_footnote_ex3.png |only gtsummary-1.3.1/gtsummary/man/figures/modify_header_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/modify_header_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/select_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/set_gtsummary_theme_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/sort_p_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/sort_p_ex2.png |only gtsummary-1.3.1/gtsummary/man/figures/spanning_header_ex1.png |only gtsummary-1.3.1/gtsummary/man/figures/tbl_bold_ital_ex.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_cross_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_cross_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_lm_global_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_merge_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_merge_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_n_ex.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_nostrata_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_overall_ex.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_regression_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_regression_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_regression_ex3.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_stack_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_stack_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_strata_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_summary_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_summary_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_summary_ex3.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_survfit_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_survfit_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_uv_ex1.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_uv_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_uv_global_ex2.png |binary gtsummary-1.3.1/gtsummary/man/figures/tbl_uv_nevent_ex.png |binary gtsummary-1.3.1/gtsummary/man/gtsummary-package.Rd | 100 gtsummary-1.3.1/gtsummary/man/gtsummary_logo.Rd | 36 gtsummary-1.3.1/gtsummary/man/inline_text.Rd | 52 gtsummary-1.3.1/gtsummary/man/inline_text.tbl_cross.Rd | 14 gtsummary-1.3.1/gtsummary/man/inline_text.tbl_regression.Rd | 176 gtsummary-1.3.1/gtsummary/man/inline_text.tbl_summary.Rd | 4 gtsummary-1.3.1/gtsummary/man/inline_text.tbl_survfit.Rd | 4 gtsummary-1.3.1/gtsummary/man/inline_text.tbl_survival.Rd | 171 gtsummary-1.3.1/gtsummary/man/inline_text.tbl_uvregression.Rd | 184 gtsummary-1.3.1/gtsummary/man/modify_footnote.Rd |only gtsummary-1.3.1/gtsummary/man/modify_header.Rd | 86 gtsummary-1.3.1/gtsummary/man/modify_spanning_header.Rd |only gtsummary-1.3.1/gtsummary/man/print_gtsummary.Rd | 55 gtsummary-1.3.1/gtsummary/man/reexports.Rd | 78 gtsummary-1.3.1/gtsummary/man/select_helpers.Rd | 2 gtsummary-1.3.1/gtsummary/man/set_gtsummary_theme.Rd |only gtsummary-1.3.1/gtsummary/man/sort_p.Rd | 86 gtsummary-1.3.1/gtsummary/man/style_percent.Rd | 74 gtsummary-1.3.1/gtsummary/man/style_pvalue.Rd | 86 gtsummary-1.3.1/gtsummary/man/style_ratio.Rd | 86 gtsummary-1.3.1/gtsummary/man/style_sigfig.Rd | 86 gtsummary-1.3.1/gtsummary/man/tbl_cross.Rd | 10 gtsummary-1.3.1/gtsummary/man/tbl_merge.Rd | 14 gtsummary-1.3.1/gtsummary/man/tbl_regression.Rd | 313 gtsummary-1.3.1/gtsummary/man/tbl_stack.Rd | 19 gtsummary-1.3.1/gtsummary/man/tbl_summary.Rd | 37 gtsummary-1.3.1/gtsummary/man/tbl_survfit.Rd | 176 gtsummary-1.3.1/gtsummary/man/tbl_survival.survfit.Rd | 259 gtsummary-1.3.1/gtsummary/man/tbl_uvregression.Rd | 382 gtsummary-1.3.1/gtsummary/man/theme_gtsummary.Rd |only gtsummary-1.3.1/gtsummary/man/trial.Rd | 56 gtsummary-1.3.1/gtsummary/man/vetted_models.Rd | 124 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_global_p.R | 21 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_n.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_nevent.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_overall.R | 5 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_p.R | 77 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_q.R | 21 gtsummary-1.3.1/gtsummary/tests/testthat/test-add_stat.R |only gtsummary-1.3.1/gtsummary/tests/testthat/test-add_stat_label.R | 16 gtsummary-1.3.1/gtsummary/tests/testthat/test-as_gt.R | 58 gtsummary-1.3.1/gtsummary/tests/testthat/test-as_huxtable.R |only gtsummary-1.3.1/gtsummary/tests/testthat/test-as_tibble.R | 44 gtsummary-1.3.1/gtsummary/tests/testthat/test-combine_terms.R | 18 gtsummary-1.3.1/gtsummary/tests/testthat/test-inline_text.R | 39 gtsummary-1.3.1/gtsummary/tests/testthat/test-modify_footnote.R |only gtsummary-1.3.1/gtsummary/tests/testthat/test-modify_spanning_header.R |only gtsummary-1.3.1/gtsummary/tests/testthat/test-select_helpers.R | 2 gtsummary-1.3.1/gtsummary/tests/testthat/test-set_gtsummary_theme.R |only gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_cross.R | 48 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_merge.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_regression.R | 29 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_stack.R | 3 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_summary.R | 20 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_summary_input_checks.R | 14 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_survfit.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_survival.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-tbl_uvregression.R | 9 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-clogit.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-coxph.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-geeglm.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-glm.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-glmer.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-lm.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-lmer.R | 1 gtsummary-1.3.1/gtsummary/tests/testthat/test-vetted_models-survreg.R | 1 gtsummary-1.3.1/gtsummary/vignettes/gallery.Rmd | 81 gtsummary-1.3.1/gtsummary/vignettes/global_options.Rmd | 7 gtsummary-1.3.1/gtsummary/vignettes/gtsummary_definition.Rmd | 4 gtsummary-1.3.1/gtsummary/vignettes/inline_text.Rmd | 2 gtsummary-1.3.1/gtsummary/vignettes/rmarkdown.Rmd | 10 gtsummary-1.3.1/gtsummary/vignettes/tbl_regression.Rmd | 40 gtsummary-1.3.1/gtsummary/vignettes/tbl_summary.Rmd | 41 gtsummary-1.3.1/gtsummary/vignettes/themes.Rmd |only 244 files changed, 17415 insertions(+), 11543 deletions(-)
Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574> and
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565>.
Also contains functions to simulate the diversity-dependent
process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 4.3 dated 2020-04-01 and 4.4 dated 2020-06-02
DESCRIPTION | 10 ++++----- MD5 | 23 +++++++++++---------- R/dd_utils.R | 24 ++++++++++++++++------ man/bd_ML.Rd | 28 ++++++++++++++++++-------- man/dd_KI_ML.Rd | 43 ++++++++++++++++++++++++++-------------- man/dd_LR.Rd | 27 +++++++++++++++++++------ man/dd_ML.Rd | 28 ++++++++++++++++++-------- man/dd_MS_ML.Rd | 41 +++++++++++++++++++++++++------------- man/dd_MS_loglik.Rd | 3 -- man/dd_SR_ML.Rd | 39 ++++++++++++++++++++++++------------ man/dd_multiple_KI_loglik.Rd | 11 ++++++++-- man/optimizer.Rd | 15 ++++++++++++- tests/testthat/test-optimizer.R |only 13 files changed, 200 insertions(+), 92 deletions(-)
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita,
Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 1.0.6 dated 2019-08-04 and 1.0.7 dated 2020-06-02
DESCRIPTION | 8 MD5 | 77 +-- NAMESPACE | 156 +++--- R/accept.calculate.r | 40 - R/combine.chains.r | 38 - R/ifm.missing.MCMC.R | 734 ++++++++++++++--------------- R/ifm.naive.MCMC.R | 578 +++++++++++------------ R/ifm.robust.MCMC.R | 760 +++++++++++++++---------------- R/prop.state.z.r | 86 +-- R/prop.year.missing.r | 58 +- R/range_raster.R | 1 README.md |only build/vignette.rds |binary data/cabrera.rda |binary data/landscape_change.rda |binary data/mc_df.rda |binary data/occ.landscape.rda |binary data/occ.landscape2.rda |binary data/param1.rda |binary data/param2.rda |binary data/rg_exp.rda |binary data/rland.rda |binary data/simulatedifm.rda |binary inst/CITATION | 36 - inst/doc/landscape_simulation-knitr.R | 1 inst/doc/landscape_simulation-knitr.Rnw | 280 +++++------ inst/doc/landscape_simulation-knitr.pdf |binary inst/doc/parameter_estimation-knitr.R | 1 inst/doc/parameter_estimation-knitr.Rnw | 390 +++++++-------- inst/doc/parameter_estimation-knitr.pdf |binary inst/doc/range_expansion-knitr.R | 1 inst/doc/range_expansion-knitr.Rnw | 220 ++++---- inst/doc/range_expansion-knitr.pdf |binary inst/examples/landmask.asc | 262 +++++----- inst/examples/landmask.asc.aux.xml | 40 - inst/examples/presences.asc | 86 +-- inst/examples/presences.asc.aux.xml | 40 - vignettes/landscape_simulation-knitr.Rnw | 280 +++++------ vignettes/parameter_estimation-knitr.Rnw | 390 +++++++-------- vignettes/range_expansion-knitr.Rnw | 220 ++++---- 40 files changed, 2391 insertions(+), 2392 deletions(-)
Title: Utilities for 'big.matrix' Objects from Package 'bigmemory'
Description: Extend the 'bigmemory' package with various analytics.
Functions 'bigkmeans' and 'binit' may also be used with native R objects.
For 'tapply'-like functions, the bigtabulate package may also be helpful.
For linear algebra support, see 'bigalgebra'. For mutex (locking) support
for advanced shared-memory usage, see 'synchronicity'.
Author: John W. Emerson [cre, aut],
Michael J. Kane [aut],
Saksham Chandra [ctb]
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between biganalytics versions 1.1.14 dated 2016-02-18 and 1.1.20 dated 2020-06-02
biganalytics-1.1.14/biganalytics/src/Makevars |only biganalytics-1.1.20/biganalytics/DESCRIPTION | 27 ++- biganalytics-1.1.20/biganalytics/MD5 | 27 +-- biganalytics-1.1.20/biganalytics/R/apply.R | 3 biganalytics-1.1.20/biganalytics/cleanup |only biganalytics-1.1.20/biganalytics/configure | 6 biganalytics-1.1.20/biganalytics/man/apply-methods.Rd | 5 biganalytics-1.1.20/biganalytics/man/biganalytics-package.Rd | 9 - biganalytics-1.1.20/biganalytics/man/bigkmeans.Rd | 1 biganalytics-1.1.20/biganalytics/man/biglm.big.matrix.Rd | 23 ++ biganalytics-1.1.20/biganalytics/man/binit.Rd | 1 biganalytics-1.1.20/biganalytics/man/summary.stat.Rd | 40 ++--- biganalytics-1.1.20/biganalytics/src/biganalytics_init.c |only biganalytics-1.1.20/biganalytics/src/hash.cpp | 1 biganalytics-1.1.20/biganalytics/src/summary_stat.cpp | 88 +++++------ biganalytics-1.1.20/biganalytics/tests |only 16 files changed, 130 insertions(+), 101 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/divisions-committees/lidar-division/laser-las-file-format-exchange-activities>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://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 1.3.5 dated 2020-02-04 and 1.3.6 dated 2020-06-02
DESCRIPTION | 10 MD5 | 29 +- NEWS.md | 13 + R/RcppExports.R | 4 R/check_content.r | 4 R/header_tools.r | 67 +++-- R/las_specifications.r | 385 ++++++++++---------------------- R/readLAS.r | 28 +- README.md | 2 man/las_specification_tools.Rd | 1 man/read.las.Rd | 14 - src/RcppExports.cpp | 10 src/readheader.cpp | 15 + tests/testthat/test-header_tools.R |only tests/testthat/test-las-specification.R | 34 ++ tests/testthat/test-readlas.R | 12 16 files changed, 312 insertions(+), 316 deletions(-)
Title: Gene-Based Association Analysis for Complex Traits
Description: Gene based association test between a group of SNPs and traits
including familial (both continuous and binary) traits, multivariate
continuous (both independent and familial) traits and longitudinal
continuous traits. Part of methods were previously published in Maity et al
(2012) <doi:10.1002/gepi.21663>, Chen et al (2013)
<doi:10.1002/gepi.21703>, Yan et al (2015) <doi:10.1159/000375409>, Yan et
al (2015) <doi:10.1534/genetics.115.178590> and Yan et al (2015)
<doi:10.1159/000445057>.
Author: Qi Yan
Maintainer: Qi Yan <qiy17@pitt.edu>
Diff between KMgene versions 1.2 dated 2017-11-22 and 1.3 dated 2020-06-02
KMgene-1.2/KMgene/R/c.KMgene.R |only KMgene-1.2/KMgene/R/coxlr.fit.R |only KMgene-1.2/KMgene/R/ginv_s.R |only KMgene-1.2/KMgene/R/pchisqsum2.R |only KMgene-1.2/KMgene/R/saddle.R |only KMgene-1.2/KMgene/src |only KMgene-1.3/KMgene/DESCRIPTION | 36 +++---- KMgene-1.3/KMgene/MD5 | 120 +++++++++++--------------- KMgene-1.3/KMgene/NAMESPACE | 21 ---- KMgene-1.3/KMgene/R/CoxKM.R | 132 +---------------------------- KMgene-1.3/KMgene/R/FKM.R | 6 - KMgene-1.3/KMgene/R/FKMO.R | 6 - KMgene-1.3/KMgene/R/FbKM.R | 8 - KMgene-1.3/KMgene/R/FbKMO.R | 6 - KMgene-1.3/KMgene/R/LKM.R | 6 - KMgene-1.3/KMgene/R/LKMO.R | 6 - KMgene-1.3/KMgene/R/LKM_Int.R | 2 KMgene-1.3/KMgene/R/MFKM.R | 9 - KMgene-1.3/KMgene/R/MFKMO.R | 7 + KMgene-1.3/KMgene/R/MFKMO_Null_Model.R | 18 +-- KMgene-1.3/KMgene/R/MFKM_Null_Model.R | 18 +-- KMgene-1.3/KMgene/R/MKM.R | 6 - KMgene-1.3/KMgene/R/MKMO.R | 6 - KMgene-1.3/KMgene/R/prepCoxKM.R | 127 --------------------------- KMgene-1.3/KMgene/data/LKM_numID_int.RData |binary KMgene-1.3/KMgene/man/CoxKM.Rd | 22 +++- KMgene-1.3/KMgene/man/CoxKM_data.Rd | 7 - KMgene-1.3/KMgene/man/FKM.Rd | 9 - KMgene-1.3/KMgene/man/FKMO.Rd | 25 +++-- KMgene-1.3/KMgene/man/FKMO_Null_Model.Rd | 3 KMgene-1.3/KMgene/man/FKM_Null_Model.Rd | 3 KMgene-1.3/KMgene/man/FKM_charID.Rd | 3 KMgene-1.3/KMgene/man/FKM_numID.Rd | 3 KMgene-1.3/KMgene/man/FbKM.Rd | 18 +-- KMgene-1.3/KMgene/man/FbKMO.Rd | 21 ++-- KMgene-1.3/KMgene/man/FbKMO_Null_Model.Rd | 6 - KMgene-1.3/KMgene/man/FbKM_Null_Model.Rd | 6 - KMgene-1.3/KMgene/man/FbKM_charID.Rd | 3 KMgene-1.3/KMgene/man/FbKM_numID.Rd | 3 KMgene-1.3/KMgene/man/LKM.Rd | 9 - KMgene-1.3/KMgene/man/LKMO.Rd | 21 ++-- KMgene-1.3/KMgene/man/LKMO_Null_Model.Rd | 3 KMgene-1.3/KMgene/man/LKM_Int.Rd | 17 ++- KMgene-1.3/KMgene/man/LKM_Null_Model.Rd | 3 KMgene-1.3/KMgene/man/LKM_charID.Rd | 3 KMgene-1.3/KMgene/man/LKM_numID.Rd | 3 KMgene-1.3/KMgene/man/LKM_numID_int.Rd | 3 KMgene-1.3/KMgene/man/MFKM.Rd | 22 ++-- KMgene-1.3/KMgene/man/MFKMO.Rd | 23 +++-- KMgene-1.3/KMgene/man/MFKMO_Null_Model.Rd | 20 +++- KMgene-1.3/KMgene/man/MFKM_Null_Model.Rd | 20 +++- KMgene-1.3/KMgene/man/MFKM_charID.Rd | 3 KMgene-1.3/KMgene/man/MFKM_numID.Rd | 3 KMgene-1.3/KMgene/man/MKM.Rd | 20 ++-- KMgene-1.3/KMgene/man/MKMO.Rd | 23 +++-- KMgene-1.3/KMgene/man/MKMO_Null_Model.Rd | 3 KMgene-1.3/KMgene/man/MKM_Null_Model.Rd | 3 KMgene-1.3/KMgene/man/MKM_charID.Rd | 5 - KMgene-1.3/KMgene/man/MKM_numID.Rd | 5 - KMgene-1.3/KMgene/man/prepCoxKM.Rd | 14 ++- 60 files changed, 327 insertions(+), 571 deletions(-)
Title: Causal Inference for Multiple Treatments with a Binary Outcome
Description: Different methods to conduct causal inference for multiple treatments with a binary outcome, including regression adjustment, vector matching, Bayesian additive regression trees, targeted maximum likelihood and inverse probability of treatment weighting using different generalized propensity score models such as multinomial logistic regression, generalized boosted models and super learner. For more details, see the paper by Liangyuan Hu (2020) <doi:10.1177/0962280220921909>.
Author: Liangyuan Hu [aut],
Chenyang Gu [aut],
Michael Lopez [aut],
Jiayi Ji [aut, cre]
Maintainer: Jiayi Ji <Jiayi.Ji@mountsinai.org>
Diff between CIMTx versions 0.1.0 dated 2020-04-15 and 0.2.0 dated 2020-06-02
CIMTx-0.1.0/CIMTx/R/ate_fun.R |only CIMTx-0.1.0/CIMTx/R/att_fun.R |only CIMTx-0.1.0/CIMTx/man/ate_fun.Rd |only CIMTx-0.1.0/CIMTx/man/att_fun.Rd |only CIMTx-0.2.0/CIMTx/DESCRIPTION | 10 CIMTx-0.2.0/CIMTx/MD5 | 56 ++-- CIMTx-0.2.0/CIMTx/NAMESPACE | 2 CIMTx-0.2.0/CIMTx/R/bart_multiTrt.R | 11 CIMTx-0.2.0/CIMTx/R/bart_multiTrt_ate.R | 333 ++++++++++----------------- CIMTx-0.2.0/CIMTx/R/bart_multiTrt_att.R | 238 +++++++++++++------ CIMTx-0.2.0/CIMTx/R/causal_multi_treat.R | 36 ++ CIMTx-0.2.0/CIMTx/R/iptw_multiTrt.R | 18 - CIMTx-0.2.0/CIMTx/R/iptw_multiTrt_ate.R | 275 ++++++++++------------ CIMTx-0.2.0/CIMTx/R/iptw_multiTrt_att.R | 304 ++++++++++++------------ CIMTx-0.2.0/CIMTx/R/readj_multiTrt.R | 12 CIMTx-0.2.0/CIMTx/R/readj_multiTrt_att.R | 158 +++++++++--- CIMTx-0.2.0/CIMTx/R/regadj_multiTrt_ate.R | 165 ++++++++----- CIMTx-0.2.0/CIMTx/R/tmle.R | 181 ++++++++++---- CIMTx-0.2.0/CIMTx/R/vm_multiTrt_att.R | 203 +++++++++------- CIMTx-0.2.0/CIMTx/man/bart_multiTrt.Rd | 9 CIMTx-0.2.0/CIMTx/man/bart_multiTrt_ate.Rd | 4 CIMTx-0.2.0/CIMTx/man/bart_multiTrt_att.Rd | 12 CIMTx-0.2.0/CIMTx/man/causal_multi_treat.Rd | 16 - CIMTx-0.2.0/CIMTx/man/iptw_multiTrt.Rd | 24 - CIMTx-0.2.0/CIMTx/man/iptw_multiTrt_ate.Rd | 13 - CIMTx-0.2.0/CIMTx/man/iptw_multiTrt_att.Rd | 16 - CIMTx-0.2.0/CIMTx/man/regadj_multiTrt.Rd | 9 CIMTx-0.2.0/CIMTx/man/regadj_multiTrt_ate.Rd | 5 CIMTx-0.2.0/CIMTx/man/regadj_multiTrt_att.Rd | 8 CIMTx-0.2.0/CIMTx/man/tmle.Rd | 9 CIMTx-0.2.0/CIMTx/man/vm_multiTrt_att.Rd | 9 31 files changed, 1211 insertions(+), 925 deletions(-)
Title: Spatially Varying and Spatio-Temporal Dynamic Linear Models
Description: Fits, spatially predicts, and temporally forecasts space-time data using Gaussian Process (GP): (1) spatially varying coefficient process models and (2) spatio-temporal dynamic linear models. Bakar et al., (2016) <doi:10.1080/00949655.2015.1038267>. Bakar et al., (2015) <doi:10.1111/rssc.12103>.
Author: K. Shuvo Bakar, Philip Kokic, Huidong Jin
Maintainer: Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between spTDyn versions 2.0 dated 2017-10-24 and 2.0.1 dated 2020-06-02
DESCRIPTION | 8 - MD5 | 12 +- NAMESPACE | 12 -- R/useful_commands.R | 230 ---------------------------------------------------- inst/CITATION | 18 ++-- inst/ChangeLog | 9 +- src/mathematics.c | 6 - 7 files changed, 32 insertions(+), 263 deletions(-)
Title: Rolling Entry Matching
Description: Functions to perform propensity score matching on rolling entry interventions for which a suitable "entry" date is not observed for nonparticipants. For more details, please reference Witman et al. (2018) <https://onlinelibrary.wiley.com/doi/abs/10.1111/1475-6773.13086>.
Author: Rob Chew [aut, cre], Kasey Jones [aut, cre], Mahin Manley [aut], Allison Witman [res], Chris Beadles [res], Yiyan Liu [res], Ann Larson [res]
Maintainer: Rob Chew <rchew@rti.org>
Diff between rollmatch versions 2.0.1 dated 2019-02-19 and 2.0.2 dated 2020-06-02
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- R/utility_functions.R | 4 ++-- 3 files changed, 10 insertions(+), 9 deletions(-)
Title: Point-in-Polyhedron Test (2D and 3D)
Description: Function pip3d() tests whether a point in 3D space is
within, exactly on, or outside an enclosed surface defined by a triangular mesh.
Function pip2d() tests whether a point in 2D space is within, exactly on, or outside a polygon.
For a reference, see: Liu et al., A new point containment test algorithm based on preprocessing
and determining triangles, Computer-Aided Design 42(12):1143-1150.
Author: Jose M. Maisog, Yuan Wang, George Luta, Jianfei Liu
Maintainer: Jose M. Maisog <bravas02@gmail.com>
Diff between ptinpoly versions 2.4 dated 2014-08-27 and 2.8 dated 2020-06-02
DESCRIPTION | 20 +++++++++++--------- MD5 | 18 +++++++++--------- data/comb.rda |binary data/faces.rda |binary data/fractal.rda |binary data/queries.rda |binary data/spiral.rda |binary data/verts.rda |binary src/kodtree.h | 3 ++- src/pinpolyhedronA.cc | 19 ++++++++++++------- 10 files changed, 34 insertions(+), 26 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Davide Vega, Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from these libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 3.3 dated 2020-05-08 and 3.3.1 dated 2020-06-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/src/community/modularity.hpp | 2 ++ src/src/community/normalized_mutual_information.hpp | 2 ++ 4 files changed, 10 insertions(+), 6 deletions(-)
Title: The Multivariate Normal and t Distributions, and Their Truncated
Versions
Description: Functions are provided for computing the density and the
distribution function of d-dimensional normal and "t" random variables,
possibly truncated (on one side or two sides, with componentwise choice),
and for generating random vectors sampled from these distributions,
except sampling from the truncated "t". Moments of arbitrary order of
a truncated normal are computed, and converted to cumulants up to order 4.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d=3, d>2, if d denotes the dimensionality.
Author: Adelchi Azzalini [aut, cre],
Alan Genz [aut] (most Fortran code),
Alan Miller [ctb] (Fortran routine PHI),
Michael J. Wichura [ctb] (Fortran routine PHINV),
G. W. Hill [ctb] (Fortran routine STDINV),
Yihong Ge [ctb] (Fortran routines BNVU and MVBVU).
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 1.5-7 dated 2020-04-30 and 2.0.0 dated 2020-06-02
mnormt-1.5-7/mnormt/COPYING |only mnormt-1.5-7/mnormt/ChangeLog |only mnormt-1.5-7/mnormt/man/dmnorm.Rd |only mnormt-1.5-7/mnormt/man/dmt.Rd |only mnormt-2.0.0/mnormt/DESCRIPTION | 31 ++++++++++++------ mnormt-2.0.0/mnormt/MD5 | 26 +++++++++------ mnormt-2.0.0/mnormt/NAMESPACE | 1 mnormt-2.0.0/mnormt/NEWS | 36 +++++++++++++-------- mnormt-2.0.0/mnormt/R/mnormt.R | 41 +++++++++++++++++++++--- mnormt-2.0.0/mnormt/R/sample_mardia.R | 2 - mnormt-2.0.0/mnormt/R/truncNT.R |only mnormt-2.0.0/mnormt/man/mnorm.Rd |only mnormt-2.0.0/mnormt/man/mnormt-package.Rd | 50 ++++++++++++++++++------------ mnormt-2.0.0/mnormt/man/mom.mtruncnorm.Rd |only mnormt-2.0.0/mnormt/man/mom2cum.Rd |only mnormt-2.0.0/mnormt/man/mt.Rd |only mnormt-2.0.0/mnormt/man/mtruncnorm.Rd |only mnormt-2.0.0/mnormt/man/mtrunct.Rd |only mnormt-2.0.0/mnormt/man/recintab.Rd |only mnormt-2.0.0/mnormt/src/mnormt_init.c |only mnormt-2.0.0/mnormt/src/tvpack.f |only 21 files changed, 126 insertions(+), 61 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press).
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between GE versions 0.1.1 dated 2020-05-24 and 0.1.3 dated 2020-06-02
DESCRIPTION | 9 - MD5 | 74 +++++++----- NAMESPACE | 7 + R/CARA.R | 6 - R/CRRA.R | 18 ++- R/SCES_A.R | 3 R/gemCanonicalDynamicMacroeconomic_3_2.R |only R/gemInputOutputTable_easy_5_4.R | 2 R/gemMoney_3_2.R | 42 ++----- R/gemQuasilinearPureExchange_2_2.R |only R/gemRobinson_3_2.R | 36 +++++- R/gemTax_5_4.R | 14 +- R/intertemporal_utility.R | 6 - R/makePolicyIncomeTax.R |only R/makePolicyStickyPrice.R |only R/makePolicySupply.R |only R/makePolicyTechnologyChange.R |only R/node_insert.R | 30 +++-- R/node_print.R | 4 R/node_set.R | 5 R/policyMarketClearingPrice.R |only R/ratio_adjust.R | 18 +-- R/sdm2.R | 162 ++++++++++++++++++---------- R/sdm_dstl.R | 2 man/CARA.Rd | 6 - man/CRRA.Rd | 16 ++ man/SCES_A.Rd | 3 man/gemCanonicalDynamicMacroeconomic_3_2.Rd |only man/gemInputOutputTable_easy_5_4.Rd | 2 man/gemMoney_3_2.Rd | 25 ++-- man/gemQuasilinearPureExchange_2_2.Rd |only man/gemRobinson_3_2.Rd | 36 +++++- man/gemTax_5_4.Rd | 14 +- man/intertemporal_utility.Rd | 6 - man/makePolicyIncomeTax.Rd |only man/makePolicyStickyPrice.Rd |only man/makePolicySupply.Rd |only man/makePolicyTechnologyChange.Rd |only man/node_insert.Rd | 23 ++- man/node_print.Rd | 4 man/node_set.Rd | 7 + man/policyMarketClearingPrice.Rd |only man/ratio_adjust.Rd | 7 - man/sdm2.Rd | 56 +++++++-- man/sdm_dstl.Rd | 2 45 files changed, 437 insertions(+), 208 deletions(-)
Title: Gradient Boosting
Description: Functional gradient descent algorithm for a variety of convex and non-convex loss functions, for both classical and robust regression and classification problems. See Wang (2011) <doi:10.2202/1557-4679.1304>, Wang (2012) <doi:10.3414/ME11-02-0020>, Wang (2018) <doi:10.1080/10618600.2018.1424635>, Wang (2018) <doi:10.1214/18-EJS1404>.
Author: Zhu Wang [aut, cre] (<https://orcid.org/0000-0002-0773-0052>),
Torsten Hothorn [ctb]
Maintainer: Zhu Wang <wangz1@uthscsa.edu>
Diff between bst versions 0.3-20 dated 2020-04-30 and 0.3-21 dated 2020-06-02
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 3 --- build/vignette.rds |binary inst/doc/cancer.pdf |binary inst/doc/khan.pdf |binary inst/doc/mcl.pdf |binary inst/doc/pros.pdf |binary 8 files changed, 11 insertions(+), 14 deletions(-)
Title: Generates Networks from BTS Data
Description: A flexible tool that allows generating bespoke
air transport statistics for urban studies based on publicly available
data from the Bureau of Transport Statistics (BTS) in the United States
<https://www.transtats.bts.gov/databases.asp?Mode_ID=1&Mode_Desc=Aviation&Subject_ID2=0>.
Author: Filipe Teixeira [aut, cre]
Maintainer: Filipe Teixeira <Filipe.MarquesTeixeira@Ugent.be>
Diff between skynet versions 1.3.0 dated 2018-12-12 and 1.3.8 dated 2020-06-02
DESCRIPTION | 19 +++--- MD5 | 65 ++++++++++++--------- NAMESPACE | 9 ++ NEWS.md | 12 +++ R/data_carriers.R | 9 ++ R/download_db1b.R | 14 +++- R/download_ontime.R |only R/download_t100.R | 2 R/download_t100_int.R |only R/import_db1b.R | 4 - R/import_ontime.R |only R/import_t100.R | 33 +++++++--- R/make_net_trip.R |only R/netPath.R | 32 ++++++---- R/skynet.R | 4 - build/vignette.rds |binary data/aircraft_type.rda |only inst/doc/skynet.R | 8 +- inst/doc/skynet.html | 102 +++++++++++++++++++++------------ inst/extdata/Ontime_2011_1.csv |only man/MetroFull.Rd | 4 - man/MetroLookup.Rd | 4 - man/OD_Sample.Rd | 4 - man/aircraft_type.Rd |only man/airportCode.Rd | 4 - man/airportCodeFull.Rd | 4 - man/airportMaster.Rd | 4 - man/carriers.Rd | 4 - man/download_ontime.Rd |only man/download_t100_int.Rd |only man/import_ontime.Rd |only man/make_net_dir.Rd | 11 ++- man/make_net_trip.Rd |only man/make_net_und.Rd | 12 +++ tests/testthat/test_download_db1b.R |only tests/testthat/test_download_ontime.R |only tests/testthat/test_download_t100.R |only tests/testthat/test_import_ontime.R |only tests/testthat/test_import_t100.R | 4 - tests/testthat/test_netPath.R | 2 tests/testthat/test_smallerfunctions.R | 10 +-- 41 files changed, 259 insertions(+), 121 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.9.4 dated 2020-05-04 and 0.9.5 dated 2020-06-02
DESCRIPTION | 8 MD5 | 10 NEWS.md | 4 R/forestcox.R | 2 build/vignette.rds |binary inst/doc/jstable.html | 940 ++++++++++++++++++++++++++++++-------------------- 6 files changed, 588 insertions(+), 376 deletions(-)
Title: Helpful Functions from Oliver Wyman Actuarial Consulting
Description: Makes difficult operations easy. Includes these types of functions:
shorthand, type conversion, data wrangling, and workflow.
Also includes some helpful data objects: NA strings, U.S. state list, color blind charting colors.
Built and shared by Oliver Wyman Actuarial Consulting. Accepting proposed contributions through GitHub.
Author: Oliver Wyman Actuarial Consulting [aut, cph],
Bryce Chamberlain [aut, cre],
Scott Sobel [ctb],
Rajesh Sahasrabuddhe [ctb]
Maintainer: Bryce Chamberlain <bryce.chamberlain@oliverwyman.com>
Diff between easyr versions 0.3-1 dated 2020-03-20 and 0.4-0 dated 2020-06-02
easyr-0.3-1/easyr/man/rjoinf.Rd |only easyr-0.4-0/easyr/DESCRIPTION | 14 - easyr-0.4-0/easyr/MD5 | 184 +++++++-------- easyr-0.4-0/easyr/NAMESPACE | 1 easyr-0.4-0/easyr/NEWS | 2 easyr-0.4-0/easyr/R/atype.R | 7 easyr-0.4-0/easyr/R/begin.R | 6 easyr-0.4-0/easyr/R/bindf-joinf.R | 123 +++------- easyr-0.4-0/easyr/R/char2fac.R | 10 easyr-0.4-0/easyr/R/coalf.R | 23 + easyr-0.4-0/easyr/R/dict.R | 27 -- easyr-0.4-0/easyr/R/drows.R | 2 easyr-0.4-0/easyr/R/fldict.R | 20 + easyr-0.4-0/easyr/R/fmat.R | 20 + easyr-0.4-0/easyr/R/isval.R | 2 easyr-0.4-0/easyr/R/jrepl.R | 18 - easyr-0.4-0/easyr/R/nanull.R | 2 easyr-0.4-0/easyr/R/read.any.R | 34 +- easyr-0.4-0/easyr/R/sch.R | 82 ++++++ easyr-0.4-0/easyr/R/sumnum.R | 2 easyr-0.4-0/easyr/R/tcol.R | 5 easyr-0.4-0/easyr/R/todate.R | 5 easyr-0.4-0/easyr/R/totype.R | 2 easyr-0.4-0/easyr/R/usepkg.R | 4 easyr-0.4-0/easyr/R/utils.R | 55 ++++ easyr-0.4-0/easyr/R/validateequal.R | 44 +-- easyr-0.4-0/easyr/R/xldate.R | 2 easyr-0.4-0/easyr/README.md | 10 easyr-0.4-0/easyr/man/atype.Rd | 124 ++++------ easyr-0.4-0/easyr/man/begin.Rd | 51 ++-- easyr-0.4-0/easyr/man/binbyvol.Rd | 66 ++--- easyr-0.4-0/easyr/man/bindf.Rd | 90 +++---- easyr-0.4-0/easyr/man/cache.init.Rd | 89 +++---- easyr-0.4-0/easyr/man/cache.ok.Rd | 66 ++--- easyr-0.4-0/easyr/man/cblind.Rd | 4 easyr-0.4-0/easyr/man/cc.Rd | 52 ++-- easyr-0.4-0/easyr/man/char2fac.Rd | 50 ++-- easyr-0.4-0/easyr/man/charnum.Rd | 65 ++--- easyr-0.4-0/easyr/man/checkeq.Rd | 59 ++-- easyr-0.4-0/easyr/man/clear.cache.Rd | 44 +-- easyr-0.4-0/easyr/man/coalf.Rd | 46 +-- easyr-0.4-0/easyr/man/crun.Rd | 40 +-- easyr-0.4-0/easyr/man/ddiff.Rd | 56 ++-- easyr-0.4-0/easyr/man/dict.Rd | 66 ++--- easyr-0.4-0/easyr/man/drows.Rd | 52 ++-- easyr-0.4-0/easyr/man/ecopy.Rd | 49 ++-- easyr-0.4-0/easyr/man/eq.Rd | 54 ++-- easyr-0.4-0/easyr/man/fac2char.Rd | 4 easyr-0.4-0/easyr/man/fjoinf.Rd | 109 ++++----- easyr-0.4-0/easyr/man/fldict.Rd | 89 +++---- easyr-0.4-0/easyr/man/fmat.Rd | 86 +++---- easyr-0.4-0/easyr/man/getbetterint.Rd | 44 +-- easyr-0.4-0/easyr/man/getinfo.Rd | 108 ++++----- easyr-0.4-0/easyr/man/hashfiles.Rd | 53 ++-- easyr-0.4-0/easyr/man/headers_row.Rd | 54 ++-- easyr-0.4-0/easyr/man/ijoinf.Rd | 106 ++++---- easyr-0.4-0/easyr/man/isval.Rd | 74 +++--- easyr-0.4-0/easyr/man/jrepl.Rd | 117 ++++----- easyr-0.4-0/easyr/man/likedate.Rd | 72 ++---- easyr-0.4-0/easyr/man/ljoinf.Rd | 109 ++++----- easyr-0.4-0/easyr/man/match.factors.Rd | 94 +++---- easyr-0.4-0/easyr/man/mdiff.Rd | 52 ++-- easyr-0.4-0/easyr/man/namesx.Rd | 56 ++-- easyr-0.4-0/easyr/man/nanull.Rd | 72 +++--- easyr-0.4-0/easyr/man/nastrings.Rd | 4 easyr-0.4-0/easyr/man/pad0.Rd | 50 ++-- easyr-0.4-0/easyr/man/qdiff.Rd | 52 ++-- easyr-0.4-0/easyr/man/rany_fixColNames.Rd | 44 +-- easyr-0.4-0/easyr/man/read.any.Rd | 225 ++++++++----------- easyr-0.4-0/easyr/man/read.txt.Rd | 64 ++--- easyr-0.4-0/easyr/man/runfolder.Rd | 75 ++---- easyr-0.4-0/easyr/man/rx.Rd | 54 ++-- easyr-0.4-0/easyr/man/save.cache.Rd | 72 +++--- easyr-0.4-0/easyr/man/sch.Rd | 66 +++-- easyr-0.4-0/easyr/man/spl.Rd | 62 ++--- easyr-0.4-0/easyr/man/states.Rd | 4 easyr-0.4-0/easyr/man/strx.Rd | 44 +-- easyr-0.4-0/easyr/man/sumnum.Rd | 70 ++--- easyr-0.4-0/easyr/man/tcmsg.Rd | 60 ++--- easyr-0.4-0/easyr/man/tcol.Rd | 66 ++--- easyr-0.4-0/easyr/man/tcwarn.Rd | 60 ++--- easyr-0.4-0/easyr/man/tobool.Rd | 77 +++--- easyr-0.4-0/easyr/man/todate.Rd | 105 ++++---- easyr-0.4-0/easyr/man/tonum.Rd | 102 +++----- easyr-0.4-0/easyr/man/usepkg.Rd | 47 ++- easyr-0.4-0/easyr/man/validate.equal.Rd | 115 ++++----- easyr-0.4-0/easyr/man/w.Rd | 60 ++--- easyr-0.4-0/easyr/man/xldate.Rd | 93 +++---- easyr-0.4-0/easyr/man/ydiff.Rd | 52 ++-- easyr-0.4-0/easyr/tests/testthat/test-files/test.pdf |only easyr-0.4-0/easyr/tests/testthat/test_bindf-joinf.R | 29 +- easyr-0.4-0/easyr/tests/testthat/test_hashfiles.R | 2 easyr-0.4-0/easyr/tests/testthat/test_read.any.R | 13 + easyr-0.4-0/easyr/tests/testthat/test_sch.R | 31 ++ 94 files changed, 2469 insertions(+), 2457 deletions(-)
Title: Simulation of Longitudinal Data
Description: Simulation and visualization of complex
models for longitudinal data. The models are encoded using the model coding
language 'Mlxtran' and automatically converted into C++ codes.
That allows one to implement very easily complex ODE-based models and complex
statistical models, including mixed effects models, for continuous, count,
categorical, and time-to-event data.
Author: Marc Lavielle [aut, cre],
Esther Ilinca [ctb],
Raphael Kuate [ctb]
Maintainer: Marc Lavielle <Marc.Lavielle@inria.fr>
Diff between mlxR versions 4.1.0 dated 2019-10-11 and 4.1.3 dated 2020-06-02
DESCRIPTION | 8 ++--- MD5 | 42 +++++++++++++++--------------- NAMESPACE | 1 R/mlxComputeRCleaner.R | 68 ++++++++++++++++++++++++------------------------- R/monolix2simulx.R | 3 +- R/prctilemlx.R | 7 +---- R/processing_monolix.R | 9 +++--- R/readdatamlx.R | 26 ++++++++++-------- R/simpopmlx.R | 2 - R/simulx.R | 14 +++++++++- man/catplotmlx.Rd | 12 +++++++- man/exposure.Rd | 15 ++++++++-- man/kmplotmlx.Rd | 15 ++++++++-- man/mlxplore.Rd | 9 +++++- man/monolix2simulx.Rd | 10 +++++-- man/prctilemlx.Rd | 15 ++++++++-- man/readDatamlx.Rd | 17 ++++++++++-- man/shinymlx.Rd | 17 +++++++++--- man/simpopmlx.Rd | 10 +++++-- man/simulx.Rd | 25 +++++++++++++----- man/statmlx.Rd | 3 -- man/writeDatamlx.Rd | 16 ++++++++--- 22 files changed, 225 insertions(+), 119 deletions(-)
Title: Busca CEPs Brasileiros
Description: Retorna detalhes de dados de CEPs brasileiros, bairros, logradouros
e tal. (Returns info of Brazilian postal codes, city names, addresses
and so on.)
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between cepR versions 0.1.0 dated 2017-07-04 and 0.1.1 dated 2020-06-02
cepR-0.1.0/cepR/R/busca_cidade.R |only cepR-0.1.0/cepR/R/sp.R |only cepR-0.1.0/cepR/R/xxx.R |only cepR-0.1.0/cepR/data |only cepR-0.1.0/cepR/man/busca_cidade.Rd |only cepR-0.1.0/cepR/man/sp.Rd |only cepR-0.1.1/cepR/DESCRIPTION | 16 +++-- cepR-0.1.1/cepR/MD5 | 28 ++++------ cepR-0.1.1/cepR/NAMESPACE | 5 - cepR-0.1.1/cepR/NEWS.md |only cepR-0.1.1/cepR/R/busca_cep.R | 37 ++----------- cepR-0.1.1/cepR/R/busca_cidades.R |only cepR-0.1.1/cepR/R/busca_estado.R | 35 ++++-------- cepR-0.1.1/cepR/R/busca_latlon.R | 39 ++------------ cepR-0.1.1/cepR/R/parse_api.R |only cepR-0.1.1/cepR/R/utils.R |only cepR-0.1.1/cepR/README.md | 95 +++++++++++++++++++---------------- cepR-0.1.1/cepR/man/busca_cidades.Rd |only cepR-0.1.1/cepR/man/busca_estado.Rd | 16 ++++- cepR-0.1.1/cepR/man/pipe.Rd | 2 20 files changed, 119 insertions(+), 154 deletions(-)
Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and robustness analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.20.0 dated 2020-05-18 and 1.21.0 dated 2020-06-02
DESCRIPTION | 8 MD5 | 28 NAMESPACE | 33 - NEWS | 7 R/base.R | 5 R/sensiHSIC.R | 1367 +++++++++++++++++++++---------------------- R/sobolshap_knn.R |only man/decoupling.Rd | 15 man/sensiHSIC.Rd | 320 +++++----- man/sensitivity-package.Rd | 13 man/shapleyLinearGaussian.Rd | 5 man/shapleyPermEx.Rd | 2 man/shapleyPermRand.Rd | 4 man/shapleySubsetMc.Rd | 4 man/sobolrank.Rd | 2 man/sobolshap_knn.Rd |only 16 files changed, 950 insertions(+), 863 deletions(-)
Title: A Code Generator for ODE-Based Models
Description: Provides an R6 class and several utility methods to
facilitate the implementation of models based on ordinary
differential equations. The heart of the package is a code generator
that creates compiled 'Fortran' (or 'R') code which can be passed to
a numerical solver. There is direct support for solvers contained
in packages 'deSolve' and 'rootSolve'.
Author: David Kneis <david.kneis@tu-dresden.de>
Maintainer: David Kneis <david.kneis@tu-dresden.de>
Diff between rodeo versions 0.7.5 dated 2019-11-29 and 0.7.6 dated 2020-06-02
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- README.md | 2 +- build/vignette.rds |binary inst/doc/rodeoVignette.R | 2 +- inst/doc/rodeoVignette.Rmd | 32 -------------------------------- inst/doc/rodeoVignette.pdf |binary man/exportDF.Rd | 15 ++++++++++++--- man/rodeo-class.Rd | 6 ------ man/stoiCreate.Rd | 9 +++++++-- vignettes/rodeoVignette.Rmd | 32 -------------------------------- 11 files changed, 36 insertions(+), 92 deletions(-)
Title: Spatio-Temporal Bayesian Modelling
Description: Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems. Bakar and Sahu (2015) <doi:10.18637/jss.v063.i15>.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between spTimer versions 3.3 dated 2018-11-10 and 3.3.1 dated 2020-06-02
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 6 ------ R/useful_commands.R | 4 ++-- inst/ChangeLog | 8 ++++++++ src/gibbs_ar.c | 13 ++++++++++--- src/gibbs_gp.c | 7 +++++-- src/gibbs_gpp.c | 7 +++++-- src/mathematics.c | 4 ++++ 9 files changed, 46 insertions(+), 27 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Giuseppe Casalicchio [ctb] (<https://orcid.org/0000-0001-5324-5966>),
Stefan Coors [ctb] (<https://orcid.org/0000-0002-7465-2146>),
Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>),
Martin Binder [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.2.0 dated 2020-04-17 and 0.3.0 dated 2020-06-02
DESCRIPTION | 16 +++---- MD5 | 54 ++++++++++++------------- NEWS.md | 9 ++++ R/DataBackendCbind.R | 6 +- R/Measure.R | 13 ++++-- R/Resampling.R | 4 - R/ResamplingBootstrap.R | 2 R/ResamplingCV.R | 2 R/ResamplingCustom.R | 2 R/ResamplingHoldout.R | 2 R/ResamplingInsample.R | 2 R/ResamplingRepeatedCV.R | 2 R/ResamplingSubsampling.R | 2 R/Task.R | 84 +++++++++++++++++++++++----------------- R/TaskClassif.R | 7 ++- R/Task_rbind.R | 4 - R/benchmark.R | 31 ++++---------- R/helper.R | 14 ------ R/resample.R | 21 +++------- README.md | 12 ++--- build/partial.rdb |binary inst/testthat/helper_autotest.R | 33 ++++++++------- man/Measure.Rd | 13 ++++-- man/Task.Rd | 18 +++++++- man/TaskClassif.Rd | 10 ++++ tests/testthat/test_Task.R | 18 ++++++++ tests/testthat/test_benchmark.R | 2 tests/testthat/test_parallel.R | 22 ++++++---- 28 files changed, 228 insertions(+), 177 deletions(-)
Title: Interactive 'ggplot2' Layer and Theme Aesthetic Editor
Description: Interactively edit 'ggplot2' layer and theme aesthetics definitions.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between ggedit versions 0.3.0 dated 2018-07-03 and 0.3.1 dated 2020-06-02
DESCRIPTION | 18 +++++++++--------- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/class_layer.R | 10 +++++----- R/ggedit.R | 2 +- README.md | 14 ++++++++------ man/fetch_layer_aes.Rd | 8 ++++++-- man/ggEdit_Module.Rd | 12 ++++++++++-- man/ggedit.Rd | 2 +- man/ggeditOpts.Rd | 6 +++++- man/grapes-greater-than-grapes.Rd | 2 +- man/pList.Rd | 4 +++- 12 files changed, 61 insertions(+), 41 deletions(-)
Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions
from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>.
'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates
the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are
also provided to generate the gambin distribution and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre],
Michael Krabbe Borregaard [aut],
Karl Ugland [aut],
Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>
Diff between gambin versions 2.4.3 dated 2020-02-03 and 2.4.4 dated 2020-06-02
DESCRIPTION | 6 MD5 | 33 +- NAMESPACE | 1 NEWS.md | 5 R/deconstruct_gambin.R | 20 + R/gambin-package.R | 71 ++++-- R/print_summary_gambin.R | 2 R/summary_gambin.R | 8 inst/doc/overview.R | 8 inst/doc/overview.Rmd | 34 ++- inst/doc/overview.html | 402 +++++++++++++++++++++++++++--------- man/deconstruct_modes.Rd | 19 + man/gambin-package.Rd | 65 +++-- man/summary.gambin.Rd | 2 tests/testthat/test_deconstruct.R |only tests/testthat/test_fitAbundances.R | 5 vignettes/overview.Rmd | 34 ++- vignettes/refs.bib | 4 18 files changed, 516 insertions(+), 203 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures
and centrality indices <doi:10.3758/s13428-017-0862-1>. Allows for flexible
specification of any undirected network estimation procedure in R, and offers
default sets for various estimation routines.
Author: Sacha Epskamp [aut, cre],
Eiko I. Fried [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 1.4.2 dated 2020-05-15 and 1.4.3 dated 2020-06-02
DESCRIPTION | 6 - MD5 | 4 - R/comparePlot.R | 190 ++++++++++++++++++++++++++++---------------------------- 3 files changed, 100 insertions(+), 100 deletions(-)
Title: Cartography for Statistical Analysis
Description: Creating maps for statistical analysis such as proportional circles, chroropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity.
The great features are :
- Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technology).
- Create interactive maps through zoom and pop-up ('leaflet' technology).
- Create frozen maps with the possibility to add labels.
Author: Sébastien CALVET - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [cre, aut],
Sophie AUDRIC - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [aut],
SED - DR Hauts-de-France - INSEE [ctb],
PSAR-SL - DR Auvergne-Rhone-Alpes - INSEE [ctb],
PSAR-EEP - DR Occitanie - INSEE [ctb],
SED - DR Pays-de-la-Loire - INSEE [ctb]
Maintainer: Sébastien CALVET <sebastien.calvet@insee.fr>
Diff between oceanis versions 1.0.7 dated 2020-04-02 and 1.7.3 dated 2020-06-02
DESCRIPTION | 18 ++-- MD5 | 84 +++++++++--------- NAMESPACE | 180 ++++++++++++++++++++-------------------- NEWS | 31 ++++++ R/leaflet_classes.R | 4 R/leaflet_classes_ronds.R | 4 R/leaflet_joignantes.R | 6 - R/leaflet_oursins.R | 4 R/leaflet_ronds.R | 4 R/leaflet_ronds_classes.R | 4 R/leaflet_saphirs.R | 4 R/leaflet_typo.R | 4 R/plot_classes.R | 39 +++++--- R/plot_classes_ronds.R | 74 ++++++++++------ R/plot_joignantes.R | 28 ++++-- R/plot_ronds.R | 28 ++++-- R/plot_ronds_classes.R | 70 +++++++++------ R/plot_saphirs.R | 29 ++++-- R/plot_typo.R | 57 +++++++----- R/plot_typo_symboles.R | 79 ++++++++++------- R/sf_pays973.R | 5 + R/sf_paysm.R | 5 + R/sf_reg01.R | 3 R/sf_reg02.R | 3 R/sf_reg03.R | 5 + R/sf_reg04.R | 5 + R/sf_reg06.R | 5 + R/shiny_classes.R | 4 R/shiny_classes_ronds.R | 4 R/shiny_joignantes.R | 4 R/shiny_oursins.R | 4 R/shiny_ronds.R | 4 R/shiny_ronds_classes.R | 4 R/shiny_saphirs.R | 4 R/shiny_typo.R | 4 build/vignette.rds |binary inst/doc/integration_shiny.html | 4 inst/doc/oceanis.html | 19 +--- inst/extdata/pays973.dbf |binary inst/extdata/pays973.prj | 2 inst/extdata/pays973.shp |binary inst/extdata/pays973.shx |binary man/donnees.Rd | 6 - 43 files changed, 499 insertions(+), 346 deletions(-)
Title: Collection of Scripts for Interface Between 'Cornerstone' and
'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'.
The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>)
is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster.
The engineers incorporate intensified hands-on statistics into their projects.
They benefit from an intuitive and uniquely designed graphical Workmap concept: you design
experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon,
immediately, interactively, and without any programming.
While 'Cornerstone's' interface to the statistical programming language 'R' has been available
since version 6.0, the latest interface with 'R' is even much more efficient.
'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the
standard 'Cornerstone' GUI.
Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R'
routines, immediately and without the need to deal with programming code.
Additionally, your 'R' programming team develops corresponding 'R' packages detached from
'Cornerstone' in their favorite 'R' environment.
Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel
(<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@camline.academy>
Diff between CornerstoneR versions 2.0.0 dated 2020-05-17 and 2.0.1 dated 2020-06-02
CornerstoneR-2.0.0/CornerstoneR/tests/testthat/test_functionList.R |only CornerstoneR-2.0.1/CornerstoneR/DESCRIPTION | 6 CornerstoneR-2.0.1/CornerstoneR/MD5 | 44 +- CornerstoneR-2.0.1/CornerstoneR/NAMESPACE | 1 CornerstoneR-2.0.1/CornerstoneR/NEWS.md | 6 CornerstoneR-2.0.1/CornerstoneR/R/matchNearestNeighbor.R | 1 CornerstoneR-2.0.1/CornerstoneR/R/reshapeWide.R | 7 CornerstoneR-2.0.1/CornerstoneR/R/showVersions.R |only CornerstoneR-2.0.1/CornerstoneR/build/vignette.rds |binary CornerstoneR-2.0.1/CornerstoneR/inst/csdata/functionList.txt | 2 CornerstoneR-2.0.1/CornerstoneR/inst/doc/fitFunction.html | 134 ++------ CornerstoneR-2.0.1/CornerstoneR/inst/doc/matchNearestNeighbor.html | 58 +-- CornerstoneR-2.0.1/CornerstoneR/inst/doc/mosaicPlot.html | 40 -- CornerstoneR-2.0.1/CornerstoneR/inst/doc/randomForest.html | 106 ++---- CornerstoneR-2.0.1/CornerstoneR/inst/doc/redirectDataset.html | 52 +-- CornerstoneR-2.0.1/CornerstoneR/inst/doc/reshape.R | 7 CornerstoneR-2.0.1/CornerstoneR/inst/doc/reshape.Rmd | 19 - CornerstoneR-2.0.1/CornerstoneR/inst/doc/reshape.html | 163 ++++------ CornerstoneR-2.0.1/CornerstoneR/inst/doc/showVersions.R |only CornerstoneR-2.0.1/CornerstoneR/inst/doc/showVersions.Rmd |only CornerstoneR-2.0.1/CornerstoneR/inst/doc/showVersions.html |only CornerstoneR-2.0.1/CornerstoneR/inst/variablesdialog/reshapeWide.xml | 2 CornerstoneR-2.0.1/CornerstoneR/man/showVersions.Rd |only CornerstoneR-2.0.1/CornerstoneR/tests/testthat/test_misc.R |only CornerstoneR-2.0.1/CornerstoneR/tests/testthat/test_reshape.R | 20 + CornerstoneR-2.0.1/CornerstoneR/vignettes/reshape.Rmd | 19 - CornerstoneR-2.0.1/CornerstoneR/vignettes/showVersions.Rmd |only 27 files changed, 292 insertions(+), 395 deletions(-)
Title: Creating Contact and Social Networks
Description: Process spatially- and temporally-discrete data into contact and
social networks, and facilitate network analysis by randomizing
individuals' movement paths and/or related categorical variables. To use
this package, users need only have a dataset containing spatial data
(i.e., latitude/longitude, or planar x & y coordinates), individual IDs
relating spatial data to specific individuals, and date/time information
relating spatial locations to temporal locations. The functionality of this
package ranges from data "cleaning" via multiple filtration functions, to
spatial and temporal data interpolation, and network creation and analysis.
Functions within this package are not limited to describing interpersonal
contacts. Package functions can also identify and quantify "contacts"
between individuals and fixed areas (e.g., home ranges, water bodies,
buildings, etc.). As such, this package is an incredibly useful resource
for facilitating epidemiological, ecological, ethological and sociological
research.
Author: Trevor Farthing [aut, cre],
Daniel Dawson [aut],
Cristina Lanzas [ctb]
Maintainer: Trevor Farthing <tsfarthi@ncsu.edu>
Diff between contact versions 1.2.2 dated 2020-04-13 and 1.2.3 dated 2020-06-02
contact-1.2.2/contact/inst/doc/Using_the_contact_package_v1_2_2.R |only contact-1.2.2/contact/inst/doc/Using_the_contact_package_v1_2_2.Rmd |only contact-1.2.2/contact/inst/doc/Using_the_contact_package_v1_2_2.html |only contact-1.2.2/contact/vignettes/Using_the_contact_package_v1_2_2.Rmd |only contact-1.2.3/contact/DESCRIPTION | 6 contact-1.2.3/contact/MD5 | 32 ++--- contact-1.2.3/contact/NAMESPACE | 2 contact-1.2.3/contact/R/contactCompare_binom.R |only contact-1.2.3/contact/R/contactCompare_chisq.R | 64 +++++++--- contact-1.2.3/contact/R/ntwrkEdges.R | 51 +++++-- contact-1.2.3/contact/R/socialEdges.R |only contact-1.2.3/contact/R/tempAggregate.R | 6 contact-1.2.3/contact/R/timeBlock.append.R | 2 contact-1.2.3/contact/build/vignette.rds |binary contact-1.2.3/contact/inst/doc/Using_the_contact_package_v1_2_3.R |only contact-1.2.3/contact/inst/doc/Using_the_contact_package_v1_2_3.Rmd |only contact-1.2.3/contact/inst/doc/Using_the_contact_package_v1_2_3.html |only contact-1.2.3/contact/man/contactCompare_binom.Rd |only contact-1.2.3/contact/man/contactCompare_chisq.Rd | 41 ++++-- contact-1.2.3/contact/man/ntwrkEdges.Rd | 2 contact-1.2.3/contact/man/socialEdges.Rd |only contact-1.2.3/contact/man/timeBlock.append.Rd | 2 contact-1.2.3/contact/vignettes/Using_the_contact_package_v1_2_3.Rmd |only 23 files changed, 137 insertions(+), 71 deletions(-)
More information about shinySearchbar at CRAN
Permanent link
Title: Cell-Type-Specific Association Testing in Bulk Omics Experiments
Description: In bulk epigenome/transcriptome experiments, molecular expression
is measured in a tissue, which is a mixture of multiple types of cells.
This package tests association of a disease/phenotype with a molecular marker
for each cell type.
The proportion of cell types in each sample needs to be given as input.
The package is applicable to epigenome-wide association study (EWAS) and
differential gene expression analysis.
Takeuchi and Kato (submitted)
"omicwas: cell-type-specific epigenome-wide and transcriptome association study".
Author: Fumihiko Takeuchi [aut, cre] (<https://orcid.org/0000-0003-3185-5661>)
Maintainer: Fumihiko Takeuchi <fumihiko@takeuchi.name>
Diff between omicwas versions 0.3.1 dated 2020-02-19 and 0.7.0 dated 2020-06-02
omicwas-0.3.1/omicwas/data/datalist |only omicwas-0.7.0/omicwas/DESCRIPTION | 18 omicwas-0.7.0/omicwas/MD5 | 42 omicwas-0.7.0/omicwas/NAMESPACE | 11 omicwas-0.7.0/omicwas/R/GSE42861small.R | 2 omicwas-0.7.0/omicwas/R/GTExsmall.R |only omicwas-0.7.0/omicwas/R/ctcisQTL.R | 149 -- omicwas-0.7.0/omicwas/R/lmridgeLW76.R |only omicwas-0.7.0/omicwas/R/omicwas.R | 882 +++++++++++++++-- omicwas-0.7.0/omicwas/README.md | 14 omicwas-0.7.0/omicwas/build |only omicwas-0.7.0/omicwas/data/GSE79262small.RData |binary omicwas-0.7.0/omicwas/data/GTExsmall.RData |only omicwas-0.7.0/omicwas/inst |only omicwas-0.7.0/omicwas/man/GSE42861small.Rd | 6 omicwas-0.7.0/omicwas/man/GSE79262small.Rd | 4 omicwas-0.7.0/omicwas/man/GTExsmall.Rd |only omicwas-0.7.0/omicwas/man/ctassoc.Rd | 102 + omicwas-0.7.0/omicwas/man/ctcisQTL.Rd | 46 omicwas-0.7.0/omicwas/tests/GSE42861smallresult.RData |binary omicwas-0.7.0/omicwas/tests/GSE42861smallresult2.RData |only omicwas-0.7.0/omicwas/tests/GTExsmallresult.RData |only omicwas-0.7.0/omicwas/tests/ctcisQTL.out.txt | 202 +-- omicwas-0.7.0/omicwas/tests/testthat/testctcisQTL.R | 4 omicwas-0.7.0/omicwas/tests/testthat/testomicwas.R | 31 omicwas-0.7.0/omicwas/vignettes |only 26 files changed, 1108 insertions(+), 405 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 5.2 dated 2020-02-10 and 5.3 dated 2020-06-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 10 +++++++--- NEWS | 3 +++ data/Acidity.rda |binary data/Enzyme.rda |binary data/Galaxy.rda |binary 7 files changed, 20 insertions(+), 13 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Originally described in Kamvar, Tabima, and Grünwald (2014)
<doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and
Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [aut] (<https://orcid.org/0000-0002-3603-2691>),
Sydney E. Everhart [ctb, dtc] (<https://orcid.org/0000-0002-5773-1280>),
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb]
(<https://orcid.org/0000-0002-7324-7448>),
Erik Sotka [ctb],
Brian J. Knaus [ctb] (<https://orcid.org/0000-0003-1665-4343>),
Patrick G. Meirmans [ctb] (<https://orcid.org/0000-0002-6395-8107>),
Frédéric D. Chevalier [ctb] (<https://orcid.org/0000-0003-2611-8106>),
Niklaus J. Grünwald [ths] (<https://orcid.org/0000-0003-1656-7602>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.8.5 dated 2020-02-25 and 2.8.6 dated 2020-06-02
DESCRIPTION | 11 - MD5 | 69 +++--- NEWS.md | 25 ++ R/Index_calculations.r | 76 ++++--- R/bitwise.r | 89 ++++---- R/check_data.R | 2 R/distances.r | 2 R/file_handling.r | 54 +++-- R/ia_jackknife.R | 93 ++++----- R/internal.r | 45 +--- R/pipe.R | 2 R/print_methods.r | 2 R/sample_schemes.r | 12 - R/zzz.r | 2 build/vignette.rds |binary data/Aeut.rda |binary data/Pinf.rda |binary data/Pram.rda |binary data/monpop.rda |binary data/old_Pinf.rda |binary data/old_partial_clone.rda |binary data/partial_clone.rda |binary inst/doc/algo.pdf |binary inst/doc/mlg.html | 392 +++++++++++++++++++------------------ inst/doc/poppr_manual.html | 444 ++++++++++++++++++++++--------------------- man/Aeut.Rd | 6 man/Pinf.Rd | 6 man/Pram.Rd | 6 man/genetic_distance.Rd | 4 man/monpop.Rd | 6 man/partial_clone.Rd | 6 man/win.ia.Rd | 2 tests/testthat/genalex |only tests/testthat/test-import.R | 15 + tests/testthat/test-plots.R | 2 tests/testthat/test-winia.R | 5 36 files changed, 750 insertions(+), 628 deletions(-)
Title: Bayesian Model Averaging for Random and Fixed Effects
Meta-Analysis
Description: Computes the posterior model probabilities for standard meta-analysis models
(null model vs. alternative model assuming either fixed- or random-effects, respectively).
These posterior probabilities are used to estimate the overall mean effect size
as the weighted average of the mean effect size estimates of the random- and
fixed-effect model as proposed by Gronau, Van Erp, Heck, Cesario, Jonas, &
Wagenmakers (2017, <doi:10.1080/23743603.2017.1326760>). The user can define
a wide range of non-informative or informative priors for the mean effect size
and the heterogeneity coefficient. Moreover, using pre-compiled Stan models,
meta-analysis with continuous and discrete moderators with Jeffreys-Zellner-Siow (JZS)
priors can be fitted and tested. This allows to compute Bayes factors and
perform Bayesian model averaging across random- and fixed-effects meta-analysis
with and without moderators. For a primer on Bayesian model-averaged meta-analysis,
see Gronau, Heck, Berkhout, Haaf, & Wagenmakers (2020, <doi:10.31234/osf.io/97qup>).
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>),
Quentin F. Gronau [ctb],
Eric-Jan Wagenmakers [ctb]
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>
Diff between metaBMA versions 0.6.2 dated 2019-09-16 and 0.6.3 dated 2020-06-02
DESCRIPTION | 23 +++++++----- MD5 | 55 +++++++++++++++--------------- NEWS | 6 +++ R/bma.R | 54 +++++++++++++++++++---------- R/metaBMA.R | 4 +- R/meta_bma.R | 10 +++++ R/meta_stan.R | 3 + build/vignette.rds |binary inst/CITATION |only inst/doc/metaBMA.R | 10 ++--- inst/doc/metaBMA.html | 45 ++++++++++-------------- man/bma.Rd | 10 ++++- man/facial_feedback.Rd | 6 ++- man/metaBMA-package.Rd | 5 ++ man/meta_bma.Rd | 27 ++++++++++++-- man/meta_default.Rd | 3 - man/meta_fixed.Rd | 20 ++++++++-- man/meta_ordered.Rd | 22 +++++++++--- man/meta_random.Rd | 24 +++++++++---- man/plot_forest.Rd | 12 +++++- man/plot_posterior.Rd | 10 ++++- man/power_pose.Rd | 10 ++++- man/prior.Rd | 10 ++++- man/towels.Rd | 6 ++- tests/testthat/test_H0_logml.R | 6 ++- tests/testthat/test_bma.R | 14 ++++--- tests/testthat/test_gronau2017powerpose.R | 14 +++---- tests/testthat/test_integrate.R | 8 +++- tests/testthat/test_stan.R | 8 ++-- 29 files changed, 282 insertions(+), 143 deletions(-)
Title: Convert Between 'R' Objects and Javascript Object Notation
(JSON)
Description: Conversions between 'R' objects and Javascript Object Notation (JSON) using
the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
Author: David Cooley [aut, cre],
Chris Muir [ctb],
Brendan Knapp [ctb] (<https://orcid.org/0000-0003-3284-4972>)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between jsonify versions 1.2.0 dated 2020-05-30 and 1.2.1 dated 2020-06-02
DESCRIPTION | 8 - MD5 | 10 +- NEWS.md | 4 inst/doc/jsonify.html | 4 inst/include/jsonify/from_json/from_json.hpp | 59 +++++++++++- inst/include/jsonify/from_json/simplify/simplify.hpp | 90 ++++++++++--------- 6 files changed, 119 insertions(+), 56 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.6.3 dated 2019-01-30 and 1.6.4 dated 2020-06-02
DESCRIPTION | 12 MD5 | 74 ++-- NEWS.md | 6 R/06-simplegeom-obj.R | 7 R/bufferPoint.R | 2 R/start-geojob.R | 9 build/vignette.rds |binary inst/doc/custom_data_sources.R | 94 +++--- inst/doc/custom_data_sources.html | 372 +++++++++++++++++++------ inst/doc/geoknife.html | 563 ++++++++++++++++++++++++++------------ inst/doc/plot_geotiff.R | 48 +-- inst/doc/plot_geotiff.html | 371 ++++++++++++++++++++----- man/XML-method.Rd | 1 man/abstract-datagroup.Rd | 1 man/algorithm-webprocess.Rd | 1 man/attribute.Rd | 1 man/bufferPoint.Rd | 2 man/check-geojob.Rd | 1 man/datagroup-methods.Rd | 1 man/download.Rd | 1 man/email-method.Rd | 1 man/geojob-methods.Rd | 3 man/geom.Rd | 1 man/inputs-webprocess.Rd | 3 man/parseTimeseries.Rd | 2 man/query.Rd | 1 man/simplegeom-methods.Rd | 1 man/start-methods.Rd | 2 man/times-webdata.Rd | 1 man/times_query-method.Rd | 1 man/url.Rd | 1 man/values.Rd | 1 man/variables_query-method.Rd | 1 man/version.Rd | 1 man/wait.Rd | 1 man/webdata-methods.Rd | 7 man/webgeom-methods.Rd | 5 man/webprocess-methods.Rd | 9 38 files changed, 1130 insertions(+), 479 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees
Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon, Matthew Pennell, Chad Brock, Joseph Brown, Wendell Challenger,
Jon Eastman, Rich FitzJohn, Rich Glor, Gene Hunt, Liam Revell, Graham Slater,
Josef Uyeda, and Jason Weir
Maintainer: Luke Harmon <lukeh@uidaho.edu>
Diff between geiger versions 2.0.6.4 dated 2020-01-25 and 2.0.7 dated 2020-06-02
ChangeLog | 68 DESCRIPTION | 18 MD5 | 156 - NAMESPACE | 336 ++-- R/TESTING.R | 1202 +++++++------- R/congruify.R | 910 +++++------ R/deprecated.R | 318 +-- R/disparity.R | 533 +++--- R/diversification.R | 496 +++--- R/diversitree.R | 4 R/edges.R | 452 ++--- R/examples.R | 222 +- R/glomogram.R | 312 +-- R/internal.R | 254 +-- R/likelihood.R | 865 +++++----- R/mecca.R | 3028 ++++++++++++++++++------------------- R/medusa.R | 2647 ++++++++++++++++---------------- R/plotting.R | 1446 ++++++++--------- R/postpred.R | 560 +++--- R/proposals.R | 1741 ++++++++++----------- R/rjmcmc.R | 552 +++--- R/simulation.R | 556 +++--- R/traits-fossil.R | 1533 +++++++++---------- R/traits.R | 2125 +++++++++++++------------- R/utilities-misc.R | 16 R/utilities-phylo.R | 3781 +++++++++++++++++++++++------------------------ R/utilities-print.R | 645 ++++---- R/utilities-stat.R | 316 +-- README.md | 86 - inst/CITATION | 145 - man/aicm.Rd | 86 - man/aicw.Rd | 66 man/aov.phylo.Rd | 114 - man/bd.ms.Rd | 152 - man/calibrate.mecca.Rd | 178 +- man/calibrate.rjmcmc.Rd | 88 - man/congruify.phylo.Rd | 112 - man/dcount.Rd | 86 - man/drop.extinct.Rd | 96 - man/dtt.Rd | 154 - man/fitContinuous.Rd | 394 ++-- man/fitContinuousMCMC.Rd | 212 +- man/fitDiscrete.Rd | 251 +-- man/gbresolve.Rd | 124 - man/geiger-data.Rd | 234 +- man/geiger-defunct.Rd | 156 - man/geiger-examples.Rd | 22 man/geiger-internal.Rd | 183 +- man/geiger-package.Rd | 48 man/load.rjmcmc.Rd | 116 - man/make.gbm.Rd | 148 - man/mecca.Rd | 296 +-- man/medusa.Rd | 172 +- man/name.check.Rd | 94 - man/nh.test.Rd | 152 - man/nodelabel.phylo.Rd | 250 +-- man/plot.medusa.Rd | 106 - man/pp.mcmc.Rd | 283 +-- man/r8s.phylo.Rd | 150 - man/ratematrix.Rd | 82 - man/rc.Rd | 116 - man/rescale.Rd | 182 +- man/rjmcmc.bm.Rd | 228 +- man/sim.bd.Rd | 90 - man/sim.bdtree.Rd | 116 - man/sim.char.Rd | 126 - man/startingpt.mecca.Rd | 132 - man/subset.phylo.Rd | 66 man/tips.Rd | 64 man/to.auteur.Rd | 70 man/treedata.Rd | 76 src/APE_reorder_phylo.c | 1 src/branches.cpp | 110 - src/init.c | 1 src/mkn.c | 30 src/mkn.h | 2 src/pic.c | 4 src/util.c | 33 src/utilities.cpp | 203 +- 79 files changed, 15858 insertions(+), 15720 deletions(-)
Title: Simple Visualisation with 'ggplot2' and 'leaflet' Wrappers
Description: Provides 'ggplot2' and 'leaflet' wrapper functions designed to simplify the creation of high quality graph and map visualisations. These functions only require inputs of data, variables and titles to provide beautiful interactive or image visualisations. However they allow for more flexibility if required. The intent is that high quality well-designed graphs and maps can be made more consistently with less effort, code and expertise than would otherwise be required.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 1.1.3 dated 2020-05-14 and 1.1.4 dated 2020-06-02
simplevis-1.1.3/simplevis/data/nz_region.rda |only simplevis-1.1.3/simplevis/man/nz_region.Rd |only simplevis-1.1.4/simplevis/DESCRIPTION | 6 +++--- simplevis-1.1.4/simplevis/MD5 | 16 +++++++--------- simplevis-1.1.4/simplevis/NEWS.md | 4 ++++ simplevis-1.1.4/simplevis/R/data.R | 13 ------------- simplevis-1.1.4/simplevis/R/other.R | 10 ---------- simplevis-1.1.4/simplevis/inst/doc/simplevis.html | 4 ++-- simplevis-1.1.4/simplevis/man/pal_point_set1.Rd | 8 +------- simplevis-1.1.4/simplevis/man/pal_snz.Rd | 8 +------- 10 files changed, 18 insertions(+), 51 deletions(-)
Title: Tools for Post-Hoc Analysis
Description: Implements a range of facilities for post-hoc analysis and
summarizing linear models, generalized linear models and
generalized linear mixed models, including grouping and clustering
via pairwise comparisons using graph representations and efficient
algorithms for finding maximal cliques of a graph.
Includes also non-parametric toos for post-hoc analysis.
It has S3 methods for printing summarizing, and producing plots,
line and barplots suitable for post-hoc analyses.
Author: Rodrigo Labouriau [aut, cre] (<https://orcid.org/0000-0001-8713-6864>)
Maintainer: Rodrigo Labouriau <rodrigo.labouriau@math.au.dk>
Diff between postHoc versions 0.1.1 dated 2020-03-24 and 0.1.3 dated 2020-06-02
DESCRIPTION | 12 - MD5 | 26 ++- NAMESPACE | 10 + R/AuxiliarFunctions.R | 21 ++ R/GroupClustering.R | 298 +++++++++++++++++++++++++++++++++++++---- R/Methods4PostHoc.R | 2 R/OldCompatibility.R |only build |only inst |only man/ExtractCI.Rd | 5 man/FormGroupsClusters.Rd | 3 man/GroupClusterEffects.Rd |only man/KruskalWallisAllPvalues.Rd |only man/MedianBootCI.Rd |only man/posthoc.Rd | 16 +- man/posthocKW.Rd |only vignettes |only 17 files changed, 342 insertions(+), 51 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order (Baker, 1975) <ISBN:9780120748556>.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 1.0.0 dated 2019-12-08 and 1.0.1 dated 2020-06-02
DESCRIPTION | 12 ++--- MD5 | 14 +++--- R/Pade.R | 14 +++--- README.md | 102 +++++++++++++++++++++++++++++++++------------ build |only inst/CITATION |only inst/NEWS.Rd | 43 +++++++++++++----- man/Pade-package.Rd | 23 +++++++--- tests/testthat/test-Pade.R | 8 +++ 9 files changed, 156 insertions(+), 60 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 1.2.19 dated 2020-05-14 and 1.2.23 dated 2020-06-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/analysis.R | 30 +++++++++++++++++++----------- R/array.R | 3 ++- R/group.R | 3 ++- R/table.R | 58 ++++++++++++++++++++++++++++++---------------------------- 6 files changed, 62 insertions(+), 50 deletions(-)
Title: In Silico Quantitative Genetics
Description: Accomplish high performance simulations in quantitative genetics.
The molecular genetic components are represented by R6/C++ classes and methods.
The core computational algorithm is implemented using bitsets according to
<doi:10.1534/g3.119.400373>. A mix between low and high level interfaces
provides great flexibility and allows user defined extensions and a wide range of
applications.
Author: Fernando H. Toledo [aut, cre] (<https://orcid.org/0000-0003-0158-643X>)
International Maize and Wheat Improvement Center [cph]
Maintainer: Fernando H. Toledo <f.toledo@cgiar.org>
Diff between isqg versions 1.2 dated 2019-02-13 and 1.3 dated 2020-06-02
isqg-1.2/isqg/inst/include/isqg/Sifter.hpp |only isqg-1.2/isqg/src/Sifter.cpp |only isqg-1.3/isqg/DESCRIPTION | 24 +- isqg-1.3/isqg/MD5 | 49 +++--- isqg-1.3/isqg/NAMESPACE | 4 isqg-1.3/isqg/R/Functions.R | 45 +---- isqg-1.3/isqg/R/Hooks.R | 1 isqg-1.3/isqg/R/ISQG.R | 7 isqg-1.3/isqg/R/Mating.R | 9 - isqg-1.3/isqg/R/R6Classes.R | 96 ++++++++--- isqg-1.3/isqg/R/Trait.R | 2 isqg-1.3/isqg/build |only isqg-1.3/isqg/inst/CITATION |only isqg-1.3/isqg/inst/REFERENCES.bib |only isqg-1.3/isqg/inst/extdata |only isqg-1.3/isqg/inst/include/isqg.h | 2 isqg-1.3/isqg/inst/include/isqg/FwdDefs.hpp | 11 - isqg-1.3/isqg/inst/include/isqg/isqg.hpp | 21 +- isqg-1.3/isqg/man/Data.Rd | 4 isqg-1.3/isqg/man/Genotype.Rd | 2 isqg-1.3/isqg/man/ISQG.Rd | 6 isqg-1.3/isqg/man/Specie.Rd | 125 +++++++++++++++ isqg-1.3/isqg/man/Specimen.Rd | 227 +++++++++++++++++++++++++++- isqg-1.3/isqg/man/Trait.Rd | 92 ++++++++++- isqg-1.3/isqg/man/dot-decode.Rd |only isqg-1.3/isqg/man/dot-fuse.Rd |only isqg-1.3/isqg/man/set_specie.Rd | 44 +---- isqg-1.3/isqg/src/Makevars | 2 isqg-1.3/isqg/src/Makevars.win | 2 29 files changed, 605 insertions(+), 170 deletions(-)
Title: Check, Install and Load CRAN & USGS GRAN Packages
Description: The function `install_load` checks the local R library(ies) to see
if the required package(s) is/are installed or not. If the package(s)
is/are not installed, then the package(s) will be installed along with
the required dependency(ies). This function pulls source or
binary packages from the Rstudio-sponsored CRAN mirror and/or
the USGS GRAN Repository. Lastly, the chosen package(s)
is/are loaded. The function `load_package` simply loads the provided
packages. If this package does not fit your needs, then you may want to
consider these other R packages: 'needs', 'easypackages', 'pacman', 'pak',
'anyLib', and/or 'librarian'.
Author: maloneypatr [aut, cre], Irucka Embry [aut, ctb]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Diff between install.load versions 1.2.1 dated 2016-07-12 and 1.2.3 dated 2020-06-02
install.load-1.2.1/install.load/LICENSE.note |only install.load-1.2.3/install.load/DESCRIPTION | 24 +++++++++--------- install.load-1.2.3/install.load/LICENSE |only install.load-1.2.3/install.load/MD5 | 21 +++++++++------- install.load-1.2.3/install.load/NAMESPACE | 3 ++ install.load-1.2.3/install.load/NEWS.md | 10 ++++++- install.load-1.2.3/install.load/R/install.load.R |only install.load-1.2.3/install.load/R/install_load.R | 26 +++++++++++++------- install.load-1.2.3/install.load/R/load_package.R | 10 +++++-- install.load-1.2.3/install.load/README.md | 8 +++--- install.load-1.2.3/install.load/inst |only install.load-1.2.3/install.load/man/install.load.Rd |only install.load-1.2.3/install.load/man/install_load.Rd | 20 ++++++++------- install.load-1.2.3/install.load/man/load_package.Rd | 12 +++------ 14 files changed, 82 insertions(+), 52 deletions(-)
Title: Index Construction for Time Series Data
Description: Derivation of indexes for benchmarking purposes. A methodology with flexible number of constituents is implemented. Also functions for market capitalization and volume weighted indexes with fixed number of constituents are available. The main function of the package, indexComp(), provides the derived index, suitable for analysis purposes. The functions indexUpdate(), indexMemberSelection() and indexMembersUpdate() are components of indexComp() and enable one to construct and continuously update an index, e.g. for display on a website. The methodology behind the functions provided gets introduced in Trimborn and Haerdle (2018) <doi:10.1016/j.jempfin.2018.08.004>.
Author: Simon Trimborn <trimborn.econometrics@gmail.com>
Maintainer: Simon Trimborn <trimborn.econometrics@gmail.com>
Diff between IndexConstruction versions 0.1-2 dated 2019-10-24 and 0.1-3 dated 2020-06-02
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 4 +--- data/CryptoData.RData |binary data/datalist | 2 +- 5 files changed, 12 insertions(+), 14 deletions(-)
More information about IndexConstruction at CRAN
Permanent link
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management
procedures for data-limited fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
M. Bryan [ctb],
HF. Geremont [ctb],
C. Grandin [ctb],
W. Harford [ctb],
Q. Huynh [ctb],
C. Walters [ctb]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 5.4.3 dated 2020-04-16 and 5.4.4 dated 2020-06-02
DLMtool-5.4.3/DLMtool/data/Generic_Fleet.RData |only DLMtool-5.4.3/DLMtool/data/Generic_Obs.RData |only DLMtool-5.4.3/DLMtool/data/datalist |only DLMtool-5.4.4/DLMtool/DESCRIPTION | 12 DLMtool-5.4.4/DLMtool/MD5 | 259 ++--- DLMtool-5.4.4/DLMtool/NAMESPACE | 2 DLMtool-5.4.4/DLMtool/NEWS.md | 15 DLMtool-5.4.4/DLMtool/R/Data_make_update.R | 42 DLMtool-5.4.4/DLMtool/R/DefineClasses.r | 58 - DLMtool-5.4.4/DLMtool/R/MPs_SupportingFunctions.R | 1 DLMtool-5.4.4/DLMtool/R/MSE_functions.R | 93 + DLMtool-5.4.4/DLMtool/R/Misc_Exported.R | 14 DLMtool-5.4.4/DLMtool/R/Misc_Internal.R | 51 - DLMtool-5.4.4/DLMtool/R/PMobjects.R | 6 DLMtool-5.4.4/DLMtool/R/SampleOM.R | 120 +- DLMtool-5.4.4/DLMtool/R/Turing.R | 4 DLMtool-5.4.4/DLMtool/R/popdyn.R | 14 DLMtool-5.4.4/DLMtool/R/runMSE.r | 73 + DLMtool-5.4.4/DLMtool/R/sysdata.rda |binary DLMtool-5.4.4/DLMtool/data/Albacore.RData |binary DLMtool-5.4.4/DLMtool/data/Atlantic_mackerel.RData |binary DLMtool-5.4.4/DLMtool/data/Blue_shark.RData |binary DLMtool-5.4.4/DLMtool/data/Bluefin_tuna.RData |binary DLMtool-5.4.4/DLMtool/data/Bluefin_tuna_WAtl.RData |binary DLMtool-5.4.4/DLMtool/data/Butterfish.RData |binary DLMtool-5.4.4/DLMtool/data/China_rockfish.RData |binary DLMtool-5.4.4/DLMtool/data/Cobia.RData |binary DLMtool-5.4.4/DLMtool/data/DataDescription.RData |binary DLMtool-5.4.4/DLMtool/data/DecE_Dom.RData |binary DLMtool-5.4.4/DLMtool/data/DecE_HDom.RData |binary DLMtool-5.4.4/DLMtool/data/DecE_NDom.RData |binary DLMtool-5.4.4/DLMtool/data/Example_datafile.RData |binary DLMtool-5.4.4/DLMtool/data/FlatE_Dom.RData |binary DLMtool-5.4.4/DLMtool/data/FlatE_HDom.RData |binary DLMtool-5.4.4/DLMtool/data/FlatE_NDom.RData |binary DLMtool-5.4.4/DLMtool/data/FleetDescription.RData |binary DLMtool-5.4.4/DLMtool/data/Generic_DecE.RData |binary DLMtool-5.4.4/DLMtool/data/Generic_FlatE.RData |binary DLMtool-5.4.4/DLMtool/data/Generic_IncE.RData |binary DLMtool-5.4.4/DLMtool/data/Generic_fleet.RData |only DLMtool-5.4.4/DLMtool/data/Generic_obs.RData |only DLMtool-5.4.4/DLMtool/data/Gulf_blue_tilefish.RData |binary DLMtool-5.4.4/DLMtool/data/Herring.RData |binary DLMtool-5.4.4/DLMtool/data/ImpDescription.RData |binary DLMtool-5.4.4/DLMtool/data/Imprecise_Biased.RData |binary DLMtool-5.4.4/DLMtool/data/Imprecise_Unbiased.RData |binary DLMtool-5.4.4/DLMtool/data/IncE_HDom.RData |binary DLMtool-5.4.4/DLMtool/data/IncE_NDom.RData |binary DLMtool-5.4.4/DLMtool/data/LHdatabase.RData |binary DLMtool-5.4.4/DLMtool/data/Low_Effort_Non_Target.RData |binary DLMtool-5.4.4/DLMtool/data/MSEDescription.RData |binary DLMtool-5.4.4/DLMtool/data/Mackerel.RData |binary DLMtool-5.4.4/DLMtool/data/OMDescription.RData |binary DLMtool-5.4.4/DLMtool/data/ObsDescription.RData |binary DLMtool-5.4.4/DLMtool/data/Overages.RData |binary DLMtool-5.4.4/DLMtool/data/Perfect_Imp.RData |binary DLMtool-5.4.4/DLMtool/data/Perfect_Info.RData |binary DLMtool-5.4.4/DLMtool/data/Porgy.RData |binary DLMtool-5.4.4/DLMtool/data/Precise_Biased.RData |binary DLMtool-5.4.4/DLMtool/data/Precise_Unbiased.RData |binary DLMtool-5.4.4/DLMtool/data/Red_snapper.RData |binary DLMtool-5.4.4/DLMtool/data/ReqData.RData |binary DLMtool-5.4.4/DLMtool/data/Rockfish.RData |binary DLMtool-5.4.4/DLMtool/data/SimulatedData.RData |binary DLMtool-5.4.4/DLMtool/data/Simulation_1.RData |binary DLMtool-5.4.4/DLMtool/data/Snapper.RData |binary DLMtool-5.4.4/DLMtool/data/Sole.RData |binary DLMtool-5.4.4/DLMtool/data/StockDescription.RData |binary DLMtool-5.4.4/DLMtool/data/Target_All_Fish.RData |binary DLMtool-5.4.4/DLMtool/data/Targeting_Small_Fish.RData |binary DLMtool-5.4.4/DLMtool/data/Toothfish.RData |binary DLMtool-5.4.4/DLMtool/data/ourReefFish.RData |binary DLMtool-5.4.4/DLMtool/data/testOM.RData |binary DLMtool-5.4.4/DLMtool/data/tiny.RData |binary DLMtool-5.4.4/DLMtool/man/AvC.Rd | 122 +- DLMtool-5.4.4/DLMtool/man/AvC_MLL.Rd | 124 +- DLMtool-5.4.4/DLMtool/man/BK.Rd | 228 ++-- DLMtool-5.4.4/DLMtool/man/CC1.Rd | 214 ++-- DLMtool-5.4.4/DLMtool/man/CompSRA.Rd | 150 +- DLMtool-5.4.4/DLMtool/man/DBSRA.Rd | 224 ++-- DLMtool-5.4.4/DLMtool/man/DCAC.Rd | 354 +++---- DLMtool-5.4.4/DLMtool/man/DD.Rd | 174 +-- DLMtool-5.4.4/DLMtool/man/DDe.Rd | 166 +-- DLMtool-5.4.4/DLMtool/man/DTe40.Rd | 132 +- DLMtool-5.4.4/DLMtool/man/Data-class.Rd | 446 ++++---- DLMtool-5.4.4/DLMtool/man/DataDescription.Rd | 2 DLMtool-5.4.4/DLMtool/man/DynF.Rd | 168 +-- DLMtool-5.4.4/DLMtool/man/EtargetLopt.Rd | 120 +- DLMtool-5.4.4/DLMtool/man/FMSYref.Rd | 132 +- DLMtool-5.4.4/DLMtool/man/Fadapt.Rd | 210 ++-- DLMtool-5.4.4/DLMtool/man/Fdem.Rd | 174 +-- DLMtool-5.4.4/DLMtool/man/Fratio.Rd | 244 ++-- DLMtool-5.4.4/DLMtool/man/GB_CC.Rd | 140 +- DLMtool-5.4.4/DLMtool/man/GB_slope.Rd | 164 +-- DLMtool-5.4.4/DLMtool/man/GB_target.Rd | 176 +-- DLMtool-5.4.4/DLMtool/man/Gcontrol.Rd | 172 +-- DLMtool-5.4.4/DLMtool/man/ICI.Rd | 200 +-- DLMtool-5.4.4/DLMtool/man/IT5.Rd | 154 +-- DLMtool-5.4.4/DLMtool/man/ITM.Rd | 106 +- DLMtool-5.4.4/DLMtool/man/ITe5.Rd | 142 +- DLMtool-5.4.4/DLMtool/man/Imp-class.Rd | 82 - DLMtool-5.4.4/DLMtool/man/Iratio.Rd | 152 +-- DLMtool-5.4.4/DLMtool/man/Islope1.Rd | 202 ++-- DLMtool-5.4.4/DLMtool/man/Itarget1.Rd | 226 ++-- DLMtool-5.4.4/DLMtool/man/Itarget1_MPA.Rd | 176 +-- DLMtool-5.4.4/DLMtool/man/ItargetE1.Rd | 210 ++-- DLMtool-5.4.4/DLMtool/man/LBSPR.Rd | 200 +-- DLMtool-5.4.4/DLMtool/man/Lratio_BHI.Rd | 198 +-- DLMtool-5.4.4/DLMtool/man/LstepCC1.Rd | 306 +++--- DLMtool-5.4.4/DLMtool/man/LstepCE1.Rd | 210 ++-- DLMtool-5.4.4/DLMtool/man/Ltarget1.Rd | 266 ++--- DLMtool-5.4.4/DLMtool/man/LtargetE1.Rd | 180 +-- DLMtool-5.4.4/DLMtool/man/MCD.Rd | 138 +- DLMtool-5.4.4/DLMtool/man/MRreal.Rd | 122 +- DLMtool-5.4.4/DLMtool/man/MSEDescription.Rd | 32 DLMtool-5.4.4/DLMtool/man/OM-class.Rd | 504 +++++----- DLMtool-5.4.4/DLMtool/man/Rcontrol.Rd | 216 ++-- DLMtool-5.4.4/DLMtool/man/Rec-class.Rd | 98 - DLMtool-5.4.4/DLMtool/man/SBT1.Rd | 238 ++-- DLMtool-5.4.4/DLMtool/man/SPMSY.Rd | 150 +- DLMtool-5.4.4/DLMtool/man/SPSRA.Rd | 168 +-- DLMtool-5.4.4/DLMtool/man/SPmod.Rd | 162 +-- DLMtool-5.4.4/DLMtool/man/SPslope.Rd | 186 +-- DLMtool-5.4.4/DLMtool/man/YPR.Rd | 184 +-- DLMtool-5.4.4/DLMtool/man/checkMSE.Rd | 124 +- DLMtool-5.4.4/DLMtool/man/curE.Rd | 122 +- DLMtool-5.4.4/DLMtool/man/matlenlim.Rd | 230 ++-- DLMtool-5.4.4/DLMtool/man/runCOSEWIC.Rd | 280 ++--- DLMtool-5.4.4/DLMtool/man/summary-Data.Rd | 62 - DLMtool-5.4.4/DLMtool/man/testOM.Rd | 32 DLMtool-5.4.4/DLMtool/src/genLenComp.cpp | 3 DLMtool-5.4.4/DLMtool/tests/manual/test-code/test-OM_functions.R | 12 DLMtool-5.4.4/DLMtool/tests/manual/test-code/test-cpars.R | 6 133 files changed, 5556 insertions(+), 5323 deletions(-)
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ddpcr versions 1.14 dated 2020-03-23 and 1.15 dated 2020-06-02
DESCRIPTION | 6 MD5 | 18 NEWS.md | 6 R/aaa.R | 12 R/outliers.R | 2 inst/doc/algorithm.html | 420 +++++++------ inst/doc/extend.html | 825 +++++++++++++------------ inst/doc/overview.html | 1272 ++++++++++++++++++---------------------- inst/doc/technical_details.html | 409 +++++++----- tests/testthat/test-utils.R | 4 10 files changed, 1521 insertions(+), 1453 deletions(-)
Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more
accessible to students and professionals from Epidemiology and
Public Health related disciplines. Includes a function to report
coefficients and confidence intervals from models using robust
standard errors (when available), functions that expand 'ggplot2'
plots and functions relevant for introductory papers in Epidemiology
or Public Health. Please note that use of the
provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre],
Frank Harell [ctb],
John Fox [ctb],
R-Core [ctb]
Maintainer: Josie Athens <josie.athens@otago.ac.nz>
Diff between pubh versions 1.1.12 dated 2020-04-26 and 1.1.14 dated 2020-06-02
DESCRIPTION | 16 - MD5 | 40 +-- NAMESPACE | 4 R/descriptive_functions.R | 7 R/display_functions.R | 6 R/epi_functions.R | 6 R/plot_functions.R | 13 - build/vignette.rds |binary data/Oncho.rda |binary inst/doc/introduction.R | 9 inst/doc/introduction.Rmd | 19 - inst/doc/introduction.html | 119 ++++------ inst/doc/regression.R | 49 ++-- inst/doc/regression.Rmd | 55 ++-- inst/doc/regression.html | 513 ++++++++++++++++++++++----------------------- man/cross_tab.Rd | 8 man/glm_coef.Rd | 4 man/multiple.Rd | 7 man/odds_trend.Rd | 6 vignettes/introduction.Rmd | 19 - vignettes/regression.Rmd | 55 ++-- 21 files changed, 486 insertions(+), 469 deletions(-)
Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC)
classification system using R and C++.
Author: Peter DeWitt [aut],
Tell Bennett [aut],
James Feinstein [aut],
Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@ucdenver.edu>
Diff between pccc versions 1.0.4 dated 2020-05-15 and 1.0.5 dated 2020-06-02
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 8 R/ccc.R | 2 R/get_codes.R | 2 data/comparability.rda |binary data/pccc_icd10_dataset.rda |binary data/pccc_icd9_dataset.rda |binary inst/doc/pccc-example.html | 4 inst/doc/pccc-icd-codes.html | 759 +++++++++++++++++++++++++++++++++++++++++-- inst/doc/pccc-overview.html | 4 man/ccc.Rd | 15 12 files changed, 774 insertions(+), 50 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-09 0.8.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-11 0.1.3
2017-10-11 0.1.2
2017-09-25 0.1.0
2017-09-25 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-29 2.0.2
2019-05-29 2.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-03 0.4.0
2020-02-03 0.3.2
2020-01-29 0.3.1
2020-01-14 0.3.0
2019-11-04 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-19 2.1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-21 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-22 0.3.0
2018-03-13 0.2.0
2018-02-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-12 0.1.0
Title: Latin Hypercube Designs (LHDs) Algorithms
Description: Contains different algorithms for efficient Latin Hypercube Designs (LHDs) with flexible sizes. Our package is comprehensive since it is capable of generating nearly orthogonal LHDs, maximin distance LHDs, and maximum projection LHDs. Documentation for each algorithm includes useful information and explanation along with corresponding references. This package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, design of computer experiments.
Author: Hongzhi Wang, Qian Xiao, Abhyuday Mandal
Maintainer: Hongzhi Wang <hw34508@uga.edu>
Diff between LHD versions 0.1.3 dated 2020-04-14 and 1.1.0 dated 2020-06-02
DESCRIPTION | 8 MD5 | 64 +- NAMESPACE | 3 NEWS.md | 21 R/AvgAbsCor.R |only R/GA.R | 393 ++++++++++++-- R/LaPSO.R | 416 +++++++++++++-- R/MaxAbsCor.R |only R/MaxProCriterion.R |only R/OA2LHD.R | 25 R/OASA.R | 256 +++++++-- R/SA.R | 181 +++++- R/SA2008.R | 360 +++++++++++-- R/SLHD.R | 877 +++++++++++++++++++++++++++++---- R/dij.R | 2 R/phi_p.R | 12 R/rLHD.R | 3 inst/doc/Vignette_for_LHD.R | 88 ++- inst/doc/Vignette_for_LHD.Rmd | 134 +++-- inst/doc/Vignette_for_LHD.html | 490 +++++++++--------- man/AvgAbsCor.Rd |only man/GA.Rd | 35 - man/LaPSO.Rd | 49 + man/MaxAbsCor.Rd |only man/MaxProCriterion.Rd |only man/OA2LHD.Rd | 24 man/OASA.Rd | 60 +- man/SA.Rd | 44 + man/SA2008.Rd | 46 + man/SLHD.Rd | 58 +- man/dij.Rd | 2 man/phi_p.Rd | 12 man/rLHD.Rd | 3 tests/testthat/testmyfunctions_part1.R | 24 tests/testthat/testmyfunctions_part2.R | 24 vignettes/Vignette_for_LHD.Rmd | 134 +++-- 36 files changed, 2905 insertions(+), 943 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data
analysis, drake rebuilds intermediate data objects when their
dependencies change, and it skips work when the results are already up
to date. Not every execution starts from scratch, there is native
support for parallel and distributed computing, and completed projects
have tangible evidence that they are reproducible. Extensive
documentation, from beginner-friendly tutorials to practical examples
and more, is available at the reference website
<https://docs.ropensci.org/drake/> and the online manual
<https://books.ropensci.org/drake/>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>),
Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>),
Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Ellis Hughes [ctb],
Matthew Mark Strasiotto [ctb],
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 7.12.1 dated 2020-05-14 and 7.12.2 dated 2020-06-02
DESCRIPTION | 6 ++-- MD5 | 22 +++++++------- NEWS.md | 7 ++++ R/dynamic.R | 1 R/store_outputs.R | 15 ++++++++++ R/transform_plan.R | 42 ++++++++++++++++------------ build/drake.pdf |binary tests/scenarios/run.sh | 1 tests/testthat/test-6-visuals.R | 2 + tests/testthat/test-7-deprecate.R | 1 tests/testthat/test-7-dsl.R | 19 ++++++++++++ tests/testthat/test-9-dynamic.R | 57 ++++++++++++++++++++++++++++++++++++-- 12 files changed, 139 insertions(+), 34 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-29 0.0-55.1
2014-07-20 0.0-55
2013-01-31 0.0-54
2012-10-09 0.0-53
2012-06-20 0.0-52
2012-06-09 0.0-51
2012-04-03 0.0-49
2011-12-04 0.0-48
2011-10-27 0.0-47
2011-10-24 0.0-46
2011-09-02 0.0-45
2011-07-23 0.0-44
2011-04-30 0.0-43
2011-02-18 0.0-42
2011-01-11 0.0-41
2010-07-29 0.0-39
2010-07-09 0.0-38
2010-07-02 0.0-37
2010-06-25 0.0-36
2010-05-22 0.0-35
2010-05-19 0.0-34
2010-05-06 0.0-33
2010-03-25 0.0-32
2010-02-28 0.0-31
2009-09-09 0.0-30
2009-02-10 0.0-26
2009-02-03 0.0-25
2009-01-28 0.0-24
2009-01-27 0.0-23
2008-12-18 0.0-22
2008-11-17 0.0-21
2008-10-13 0.0-20
2008-09-02 0.0-19
2008-08-31 0.0-18
2008-08-27 0.0-17
2008-08-22 0.0-16
2008-08-11 0.0-15
2008-08-08 0.0-14
2008-07-20 0.0-11
2008-07-20 0.0-13
2008-05-06 0.0-9
2008-04-24 0.0-8
2008-01-23 0.0-7
2007-11-07 0.0-6
2007-09-21 0.0-5
2007-08-09 0.0-4
2007-08-02 0.0-3
2007-07-16 0.0-2
2007-07-12 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-26 1.6-3
2020-01-12 1.6-1
2019-01-23 1.5-5
2019-01-09 1.5-4
2018-09-18 1.5-3
2018-07-09 1.5-2
2017-11-28 1.5
2017-06-19 1.4-2
2016-07-19 1.3-4
2016-01-28 1.3-1
2015-09-16 1.2-5
2015-02-10 1.1-5
2014-09-06 1.1-1
2014-05-15 1.0-5
2013-11-14 1.0
2013-03-19 0.4-11
2012-11-10 0.4
2012-07-08 0.3-42
2011-11-18 0.3-40
2011-09-08 0.3-39
2011-06-30 0.3-36
2011-05-19 0.3-35
2011-05-16 0.3-34
2011-05-04 0.3-32
2011-03-31 0.3-30
2010-12-09 0.3-28
2010-11-30 0.3-27
2010-09-19 0.3-24
2010-07-24 0.3-12
2010-07-07 0.3-10
2010-06-29 0.3-7
2010-06-29 0.3-8
2010-06-26 0.3-6
2010-06-23 0.3-5
2010-06-22 0.3-4
2010-06-15 0.3-3
2010-06-13 0.3-2
2010-06-10 0.3-1
2010-05-29 0.3
2010-03-19 0.2-1
2010-03-17 0.2
2010-01-04 0.1