Title: Flexible Genotyping for Polyploids
Description: Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allele bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. Also provided are functions to
simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
functions to calculate oracle genotyping error rates, oracle_mis(), and
correlation with the true genotypes, oracle_cor(). These latter two
functions are useful for read depth calculations. Run
browseVignettes(package = "updog") in R for example usage. See
Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between updog versions 2.0.2 dated 2020-07-21 and 2.1.1 dated 2021-10-25
DESCRIPTION | 19 - MD5 | 104 ++++---- NAMESPACE | 5 NEWS.md | 18 + R/RcppExports.R | 6 R/ashdog.R | 23 + R/data.R | 10 R/multidog.R | 343 ++++++++++++++++++++++---- R/oracle.R | 10 R/plot_geno.R | 6 R/pp.R | 2 R/rflexdog.R | 8 R/updog.R | 15 - README.md | 29 +- build/partial.rdb |only build/vignette.rds |binary inst/doc/multidog.R | 22 + inst/doc/multidog.Rmd | 264 +++++++++++--------- inst/doc/multidog.html | 455 +++++++++++------------------------ inst/doc/oracle_calculations.html | 320 +++++------------------- inst/doc/simulate_ngs.html | 464 +++++++++++------------------------- inst/doc/smells_like_updog.html | 342 ++++++-------------------- man/export_vcf.Rd |only man/flexdog.Rd | 6 man/flexdog_full.Rd | 13 - man/multidog.Rd | 78 ++++-- man/oracle_cor.Rd | 2 man/oracle_cor_from_joint.Rd | 2 man/oracle_joint.Rd | 2 man/oracle_mis.Rd | 2 man/oracle_mis_from_joint.Rd | 2 man/oracle_mis_vec.Rd | 2 man/oracle_mis_vec_from_joint.Rd | 2 man/oracle_plot.Rd | 2 man/plot.flexdog.Rd | 4 man/plot.multidog.Rd | 4 man/plot_geno.Rd | 4 man/rflexdog.Rd | 4 man/rgeno.Rd | 4 man/snpdat.Rd | 6 man/uitdewilligen.Rd | 4 man/updog-package.Rd | 10 src/RcppExports.cpp | 5 src/oracle.cpp | 6 tests/testthat/test_dbetabinom.R | 273 ++++++++++----------- tests/testthat/test_f1_genotyping.R | 80 +++--- tests/testthat/test_flexdog.R | 404 ++++++++++++++++--------------- tests/testthat/test_gradients.R | 18 + tests/testthat/test_objectives.R | 310 ++++++++++++------------ tests/testthat/test_oracle.R | 10 tests/testthat/test_rflexdog.R | 4 tests/testthat/test_utils.R | 11 tests/testthat/test_wikmat.R | 2 vignettes/multidog.Rmd | 264 +++++++++++--------- 54 files changed, 1888 insertions(+), 2117 deletions(-)
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction
from noisy and high-dimensional data. It facilitates identification of patterns representing underlying
groups on all samples in a data set. Based on Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA.
(2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014)
Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Author: Stefano Cacciatore [aut, trl, cre]
(<https://orcid.org/0000-0001-7052-7156>),
Leonardo Tenori [aut] (<https://orcid.org/0000-0001-6438-059X>)
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 1.7 dated 2021-09-27 and 1.8 dated 2021-10-25
KODAMA-1.7/KODAMA/inst/doc/KODAMA.html |only KODAMA-1.8/KODAMA/DESCRIPTION | 8 - KODAMA-1.8/KODAMA/MD5 | 26 +++--- KODAMA-1.8/KODAMA/NAMESPACE | 62 +++++++------- KODAMA-1.8/KODAMA/R/KOD.R | 26 +++++- KODAMA-1.8/KODAMA/build/vignette.rds |binary KODAMA-1.8/KODAMA/inst/doc/KODAMA.R | 28 +++--- KODAMA-1.8/KODAMA/inst/doc/KODAMA.Rmd | 32 ++++--- KODAMA-1.8/KODAMA/inst/doc/KODAMA.pdf |only KODAMA-1.8/KODAMA/man/MetRef.Rd | 2 KODAMA-1.8/KODAMA/man/USA.Rd | 2 KODAMA-1.8/KODAMA/man/categorical.test.Rd | 105 +++++++++++++----------- KODAMA-1.8/KODAMA/man/continuous.test.Rd | 127 ++++++++++++++++-------------- KODAMA-1.8/KODAMA/man/lymphoma.Rd | 2 KODAMA-1.8/KODAMA/vignettes/KODAMA.Rmd | 32 ++++--- 15 files changed, 255 insertions(+), 197 deletions(-)
Title: Efficient Doubly Robust Population Size Estimation
Description: Estimation of the total population size from capture-recapture data efficiently and with low bias implementing the methods from Das M, Kennedy EH, and Jewell NP (2021) <arXiv:2104.14091>. The estimator is doubly robust against errors in the estimation of the intermediate nuisance parameters. Users can choose from the flexible estimation models provided in the package, or use any other preferred model.
Author: Manjari Das [aut, cre] (<https://orcid.org/0000-0002-6781-6368>),
Edward H. Kennedy [aut] (<https://orcid.org/0000-0002-1510-8175>)
Maintainer: Manjari Das <manjari8d@gmail.com>
Diff between drpop versions 0.0.1 dated 2021-10-11 and 0.0.2 dated 2021-10-25
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only R/popsize.R | 5 ++--- R/tmle.R | 18 +++++++++--------- tests/testthat/testdrpop.R | 8 ++++---- 6 files changed, 23 insertions(+), 23 deletions(-)
Title: Bayesian Screening and Variable Selection
Description: Performs Bayesian variable screening and selection for ultra-high dimensional linear regression models.
Author: Dongjin Li [aut, cre], Somak Dutta [aut], Vivekananda Roy [ctb]
Maintainer: Dongjin Li <liyangxiaobei@gmail.com>
Diff between bravo versions 2.0.1 dated 2021-09-22 and 2.1.1 dated 2021-10-25
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/sven.R | 10 +++++----- man/bits.Rd | 8 ++++---- man/sven.Rd | 3 +++ src/RcppExports.cpp | 5 +++++ 6 files changed, 27 insertions(+), 19 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.9 dated 2021-02-23 and 0.10 dated 2021-10-25
DESCRIPTION | 8 +- MD5 | 58 +++++++++--------- NAMESPACE | 10 +++ NEWS | 7 ++ R/03_modelformation_generateParameterTable.R | 2 R/03_modelformation_labtoind.R | 12 +-- R/03_modelformation_tsData.R | 57 ++++++++++------- R/15_lvm_identify.R | 14 ++-- R/18_dlvm1_identify.R | 4 - R/19_tsdlvm1_identify.R | 8 +- R/21_Ising_identify.R | 4 - R/22_ml_lvm_identify.R | 8 +- R/a_models_dlvm1.R | 7 +- R/a_models_ml_tsdlvm1.R | 87 ++++++++++++++++++++------- R/a_models_ml_tslvgvar.R | 20 ++++++ R/b_modelexpansions_addMIs.R | 6 - R/e_modelmodifications_groupequal.R | 4 - R/e_modelmodifications_groupfree.R | 2 R/e_modelmodifications_intersectionmodel.R | 2 R/e_modelmodifications_partialprune.R | 5 - R/e_modelmodifications_unionmodel.R | 2 R/f_convenience_CIplot.R |only R/f_convenience_MIs.R | 14 +--- R/f_convenience_modelCompare.R | 2 R/f_convenience_parameters.R | 8 +- build/partial.rdb |binary data/Jonas.RData |binary man/CIplot.Rd |only man/ml_tsdlvm1.Rd | 17 ++++- man/var1_family.Rd | 3 man/varcov_family.Rd | 22 ++++++ 31 files changed, 262 insertions(+), 131 deletions(-)
Title: Common S3 Generics not Provided by Base R Methods Related to
Model Fitting
Description: In order to reduce potential package dependencies
and conflicts, generics provides a number of commonly used S3
generics.
Author: Hadley Wickham [aut, cre],
Max Kuhn [aut],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between generics versions 0.1.0 dated 2020-10-31 and 0.1.1 dated 2021-10-25
generics-0.1.0/generics/tests/testthat/helper-expect_known_cat.R |only generics-0.1.0/generics/tests/testthat/helper-skip_if_below_r_version.R |only generics-0.1.0/generics/tests/testthat/test-generics-extension.R |only generics-0.1.0/generics/tests/testthat/test-multiple-packages.R |only generics-0.1.0/generics/tests/testthat/test-s4.R |only generics-0.1.0/generics/tests/testthat/test-same-rd.R |only generics-0.1.0/generics/tests/testthat/test-single-package.R |only generics-0.1.0/generics/tests/testthat/test-special-cases.R |only generics-0.1.0/generics/tests/testthat/testGenericsExtension/test-1.txt |only generics-0.1.0/generics/tests/testthat/testMultiMethod/test-1.txt |only generics-0.1.0/generics/tests/testthat/testMultiPackage/test-1.txt |only generics-0.1.0/generics/tests/testthat/testS4Docs/test-1.txt |only generics-0.1.0/generics/tests/testthat/testS4Docs/test-2.txt |only generics-0.1.0/generics/tests/testthat/testSameRd/test-1.txt |only generics-0.1.0/generics/tests/testthat/testSingleMethod/test-1.txt |only generics-0.1.1/generics/DESCRIPTION | 14 ++-- generics-0.1.1/generics/MD5 | 34 +++------- generics-0.1.1/generics/NAMESPACE | 2 generics-0.1.1/generics/NEWS.md | 4 + generics-0.1.1/generics/R/docs.R | 4 - generics-0.1.1/generics/R/explore.R |only generics-0.1.1/generics/R/tune_args.R |only generics-0.1.1/generics/R/utils.R |only generics-0.1.1/generics/README.md | 16 ++-- generics-0.1.1/generics/build/generics.pdf |binary generics-0.1.1/generics/man/explore.Rd |only generics-0.1.1/generics/man/tune_args.Rd |only generics-0.1.1/generics/tests/testthat/_snaps |only generics-0.1.1/generics/tests/testthat/test-docs.R |only 29 files changed, 35 insertions(+), 39 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
Austin Dickey [ctb],
Matthias Grenié [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb],
Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.12 dated 2021-07-07 and 0.4.13 dated 2021-10-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/fortify_surv.R | 2 +- R/plotlib.R | 1 - build/vignette.rds |binary inst/doc/plot_pca.html | 9 +++------ tests/testthat/test-surv.R | 11 +++++++++++ 8 files changed, 31 insertions(+), 19 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.6-9.1 dated 2021-02-23 and 0.6-9.2 dated 2021-10-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 15 ++++++++++++++- configure.ac | 18 ++++++++---------- 4 files changed, 29 insertions(+), 18 deletions(-)
Title: Transforming and Harmonizing CCHS Variables
Description: Supporting the use of the Canadian Community Health Survey
(CCHS) by transforming variables from each cycle into harmonized,
consistent versions that span survey cycles (currently, 2001 to
2018). CCHS data used in this library is accessed and adapted in
accordance to the Statistics Canada Open Licence Agreement. This
package uses rec_with_table(), which was developed from 'sjmisc'
rec(). Lüdecke D (2018). "sjmisc: Data and Variable Transformation
Functions". Journal of Open Source Software, 3(26), 754.
<doi:10.21105/joss.00754>.
Author: Doug Manuel [aut, cph] (<https://orcid.org/0000-0003-0912-0845>),
Warsame Yusuf [aut, cre],
Rostyslav Vyuha [aut],
Kitty Chen [aut],
Carol Bennett [aut],
Yulric Sequeira [ctb],
The Ottawa Hospital [cph]
Maintainer: Warsame Yusuf <waryusuf@ohri.ca>
Diff between cchsflow versions 1.8.2 dated 2021-06-23 and 2.0.0 dated 2021-10-25
cchsflow-1.8.2/cchsflow/tests/testthat/test-binge-drinker.R |only cchsflow-1.8.2/cchsflow/tests/testthat/test-percent-time-canada.R |only cchsflow-2.0.0/cchsflow/DESCRIPTION | 17 cchsflow-2.0.0/cchsflow/MD5 | 92 cchsflow-2.0.0/cchsflow/NAMESPACE | 12 cchsflow-2.0.0/cchsflow/NEWS.md | 56 cchsflow-2.0.0/cchsflow/R/alcohol.R | 484 + cchsflow-2.0.0/cchsflow/R/bmi.R | 180 cchsflow-2.0.0/cchsflow/R/data.R | 91 cchsflow-2.0.0/cchsflow/R/diet.R | 88 cchsflow-2.0.0/cchsflow/R/immigration.R |only cchsflow-2.0.0/cchsflow/R/percent-time-canada.R | 75 cchsflow-2.0.0/cchsflow/R/physical-activity.R |only cchsflow-2.0.0/cchsflow/R/recode-with-table.R | 32 cchsflow-2.0.0/cchsflow/R/smoking.R | 204 cchsflow-2.0.0/cchsflow/README.md | 10 cchsflow-2.0.0/cchsflow/data/cchs2015_2016_p.RData |only cchsflow-2.0.0/cchsflow/data/cchs2017_2018_p.RData |only cchsflow-2.0.0/cchsflow/data/variable_details.RData |binary cchsflow-2.0.0/cchsflow/data/variables.RData |binary cchsflow-2.0.0/cchsflow/inst/extdata/sample_variable_details.csv | 2 cchsflow-2.0.0/cchsflow/inst/extdata/variable_details.csv | 3700 +++++----- cchsflow-2.0.0/cchsflow/inst/extdata/variables.csv | 288 cchsflow-2.0.0/cchsflow/man/SMKG040_fun.Rd |only cchsflow-2.0.0/cchsflow/man/adjusted_bmi_fun.Rd |only cchsflow-2.0.0/cchsflow/man/bmi_fun_cat.Rd |only cchsflow-2.0.0/cchsflow/man/cchs2001_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2003_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2005_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2007_2008_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2009_2010_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2010_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2011_2012_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2012_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2013_2014_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2014_p.Rd | 2 cchsflow-2.0.0/cchsflow/man/cchs2015_2016_p.Rd |only cchsflow-2.0.0/cchsflow/man/cchs2017_2018_p.Rd |only cchsflow-2.0.0/cchsflow/man/diet_score_fun.Rd | 10 cchsflow-2.0.0/cchsflow/man/diet_score_fun_cat.Rd |only cchsflow-2.0.0/cchsflow/man/energy_exp_fun.Rd |only cchsflow-2.0.0/cchsflow/man/immigration_fun.Rd |only cchsflow-2.0.0/cchsflow/man/low_drink_long_fun.Rd |only cchsflow-2.0.0/cchsflow/man/low_drink_score_fun.Rd |only cchsflow-2.0.0/cchsflow/man/low_drink_score_fun1.Rd |only cchsflow-2.0.0/cchsflow/man/low_drink_short_fun.Rd |only cchsflow-2.0.0/cchsflow/man/pack_years_fun.Rd | 10 cchsflow-2.0.0/cchsflow/man/pack_years_fun_cat.Rd |only cchsflow-2.0.0/cchsflow/man/pct_time_fun.Rd | 2 cchsflow-2.0.0/cchsflow/man/pct_time_fun_cat.Rd |only cchsflow-2.0.0/cchsflow/man/smoke_simple_fun.Rd | 6 cchsflow-2.0.0/cchsflow/tests/testdata/rec_with_table_test_data.RData |binary cchsflow-2.0.0/cchsflow/tests/testthat/test-alcohol.R |only cchsflow-2.0.0/cchsflow/tests/testthat/test-bmi.R | 21 cchsflow-2.0.0/cchsflow/tests/testthat/test-data.R | 44 cchsflow-2.0.0/cchsflow/tests/testthat/test-diet.R |only cchsflow-2.0.0/cchsflow/tests/testthat/test-immigration.R |only cchsflow-2.0.0/cchsflow/tests/testthat/test-physical-activity.R |only cchsflow-2.0.0/cchsflow/tests/testthat/test-smoking.R | 24 59 files changed, 3554 insertions(+), 1914 deletions(-)
Title: Number Names
Description: Converts numeric vectors to character vectors of English
number names. Provides conversion to cardinals, ordinals, numerators,
and denominators. Supports negative and non-integer numbers.
Author: Alexander Rossell Hayes [aut, cre]
(<https://orcid.org/0000-0001-9412-0457>),
Eli Pousson [ctb]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between nombre versions 0.3.0 dated 2020-09-12 and 0.4.0 dated 2021-10-25
nombre-0.3.0/nombre/R/set_config.R |only nombre-0.3.0/nombre/R/zzz.R |only nombre-0.3.0/nombre/man/reexports.Rd |only nombre-0.3.0/nombre/man/set_config.Rd |only nombre-0.3.0/nombre/tests/testthat/test-set_config.R |only nombre-0.4.0/nombre/DESCRIPTION | 38 +- nombre-0.4.0/nombre/MD5 | 43 +- nombre-0.4.0/nombre/NAMESPACE | 5 nombre-0.4.0/nombre/NEWS.md | 11 nombre-0.4.0/nombre/R/adverbial.R | 3 nombre-0.4.0/nombre/R/cardinal.R | 36 -- nombre-0.4.0/nombre/R/collective.R | 12 nombre-0.4.0/nombre/R/convert_fraction.R | 29 + nombre-0.4.0/nombre/R/denominator.R | 6 nombre-0.4.0/nombre/R/ordinal.R | 4 nombre-0.4.0/nombre/R/ratio.R |only nombre-0.4.0/nombre/R/test_helpers.R |only nombre-0.4.0/nombre/README.md | 339 +++++++++---------- nombre-0.4.0/nombre/man/adverbial.Rd | 12 nombre-0.4.0/nombre/man/cardinal.Rd | 62 +-- nombre-0.4.0/nombre/man/collective.Rd | 29 - nombre-0.4.0/nombre/man/denominator.Rd | 16 nombre-0.4.0/nombre/man/nombre-package.Rd | 10 nombre-0.4.0/nombre/man/numerator.Rd | 3 nombre-0.4.0/nombre/man/ordinal.Rd | 11 nombre-0.4.0/nombre/man/ratio.Rd |only nombre-0.4.0/nombre/tests/testthat/test-ratio.R |only 27 files changed, 329 insertions(+), 340 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. MXL models assume uncorrelated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) "Discrete Choice Methods with Simulation, 2nd Edition" <doi:10.1017/CBO9780511805271>.
Author: John Helveston [aut, cre, cph]
(<https://orcid.org/0000-0002-2657-9191>),
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 0.3.0 dated 2021-08-13 and 0.4.0 dated 2021-10-25
logitr-0.3.0/logitr/inst/doc/predict_choices.R |only logitr-0.3.0/logitr/inst/doc/predict_choices.Rmd |only logitr-0.3.0/logitr/inst/doc/predict_choices.html |only logitr-0.3.0/logitr/inst/doc/predict_probs.R |only logitr-0.3.0/logitr/inst/doc/predict_probs.Rmd |only logitr-0.3.0/logitr/inst/doc/predict_probs.html |only logitr-0.3.0/logitr/inst/example/data_formatting.R |only logitr-0.3.0/logitr/inst/example/interactions.R |only logitr-0.3.0/logitr/inst/example/mnl_models.R |only logitr-0.3.0/logitr/inst/example/mnl_models_weighted.R |only logitr-0.3.0/logitr/inst/example/mxl_models.R |only logitr-0.3.0/logitr/inst/example/predict_choices.R |only logitr-0.3.0/logitr/inst/example/predict_probs.R |only logitr-0.3.0/logitr/inst/extdata/choices_mnl_pref.Rds |only logitr-0.3.0/logitr/inst/extdata/choices_mnl_wtp.Rds |only logitr-0.3.0/logitr/inst/extdata/choices_mxl_pref.Rds |only logitr-0.3.0/logitr/inst/extdata/choices_mxl_wtp.Rds |only logitr-0.3.0/logitr/inst/extdata/int_model_price_brand.Rds |only logitr-0.3.0/logitr/inst/extdata/int_model_price_feat.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_pref.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_pref_dannon.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_pref_dummies.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_pref_weight.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_wtp.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_wtp_unweighted.Rds |only logitr-0.3.0/logitr/inst/extdata/mnl_wtp_weighted.Rds |only logitr-0.3.0/logitr/inst/extdata/model_price_feat_mxl.Rds |only logitr-0.3.0/logitr/inst/extdata/probs_mnl_pref.Rds |only logitr-0.3.0/logitr/inst/extdata/probs_mnl_wtp.Rds |only logitr-0.3.0/logitr/inst/extdata/probs_mxl_pref.Rds |only logitr-0.3.0/logitr/inst/extdata/probs_mxl_wtp.Rds |only logitr-0.3.0/logitr/man/figures/logitr-hex.ai |only logitr-0.3.0/logitr/man/figures/logitr-hex.png |only logitr-0.3.0/logitr/vignettes/predict_choices.Rmd |only logitr-0.3.0/logitr/vignettes/predict_probs.Rmd |only logitr-0.4.0/logitr/DESCRIPTION | 8 logitr-0.4.0/logitr/MD5 | 162 +--- logitr-0.4.0/logitr/NAMESPACE | 6 logitr-0.4.0/logitr/NEWS.md | 23 logitr-0.4.0/logitr/R/additionalInfo.R | 18 logitr-0.4.0/logitr/R/data.R | 4 logitr-0.4.0/logitr/R/encoding.R | 2 logitr-0.4.0/logitr/R/inputChecks.R | 77 + logitr-0.4.0/logitr/R/logitr.R | 123 ++- logitr-0.4.0/logitr/R/methods.R | 125 ++- logitr-0.4.0/logitr/R/modelInputs.R | 179 ++-- logitr-0.4.0/logitr/R/optimLoop.R | 12 logitr-0.4.0/logitr/R/predict.R | 510 +++++++------ logitr-0.4.0/logitr/R/tools.R | 5 logitr-0.4.0/logitr/R/wtp.R | 63 + logitr-0.4.0/logitr/README.md | 16 logitr-0.4.0/logitr/build/partial.rdb |binary logitr-0.4.0/logitr/build/vignette.rds |binary logitr-0.4.0/logitr/data/yogurt.rda |binary logitr-0.4.0/logitr/inst/CITATION | 4 logitr-0.4.0/logitr/inst/doc/basic_usage.R | 98 +- logitr-0.4.0/logitr/inst/doc/basic_usage.Rmd | 116 +- logitr-0.4.0/logitr/inst/doc/basic_usage.html | 222 ++--- logitr-0.4.0/logitr/inst/doc/data_formatting.R | 41 - logitr-0.4.0/logitr/inst/doc/data_formatting.Rmd | 43 - logitr-0.4.0/logitr/inst/doc/data_formatting.html | 146 +-- logitr-0.4.0/logitr/inst/doc/interactions.R | 92 +- logitr-0.4.0/logitr/inst/doc/interactions.Rmd | 103 +- logitr-0.4.0/logitr/inst/doc/interactions.html | 280 ++++--- logitr-0.4.0/logitr/inst/doc/mnl_models.R | 55 - logitr-0.4.0/logitr/inst/doc/mnl_models.Rmd | 56 - logitr-0.4.0/logitr/inst/doc/mnl_models.html | 288 +++---- logitr-0.4.0/logitr/inst/doc/mnl_models_weighted.R | 74 - logitr-0.4.0/logitr/inst/doc/mnl_models_weighted.Rmd | 49 - logitr-0.4.0/logitr/inst/doc/mnl_models_weighted.html | 417 +++++----- logitr-0.4.0/logitr/inst/doc/mxl_models.R | 8 logitr-0.4.0/logitr/inst/doc/mxl_models.Rmd | 14 logitr-0.4.0/logitr/inst/doc/mxl_models.html | 384 ++++----- logitr-0.4.0/logitr/inst/doc/predict.R |only logitr-0.4.0/logitr/inst/doc/predict.Rmd |only logitr-0.4.0/logitr/inst/doc/predict.html |only logitr-0.4.0/logitr/inst/example/examples.R |only logitr-0.4.0/logitr/inst/extdata/mxl_pref.Rds |binary logitr-0.4.0/logitr/inst/extdata/mxl_wtp.Rds |binary logitr-0.4.0/logitr/man/figures/logo.ai |only logitr-0.4.0/logitr/man/figures/logo.png |only logitr-0.4.0/logitr/man/fitted.logitr.Rd |only logitr-0.4.0/logitr/man/logitr.Rd | 74 + logitr-0.4.0/logitr/man/miscmethods.logitr.Rd | 8 logitr-0.4.0/logitr/man/predict.logitr.Rd |only logitr-0.4.0/logitr/man/predictChoices.Rd | 30 logitr-0.4.0/logitr/man/predictProbs.Rd | 24 logitr-0.4.0/logitr/man/recodeData.Rd | 2 logitr-0.4.0/logitr/man/residuals.logitr.Rd |only logitr-0.4.0/logitr/man/rmdchunks/dataFormat.Rmd | 4 logitr-0.4.0/logitr/man/se.Rd |only logitr-0.4.0/logitr/man/se.logitr.Rd |only logitr-0.4.0/logitr/man/vcov.logitr.Rd |only logitr-0.4.0/logitr/man/wtp.Rd | 16 logitr-0.4.0/logitr/man/wtp.logitr.Rd |only logitr-0.4.0/logitr/man/wtpCompare.Rd | 10 logitr-0.4.0/logitr/man/yogurt.Rd | 4 logitr-0.4.0/logitr/tests/testthat/test_predict.R |only logitr-0.4.0/logitr/tests/testthat/test_startPars.R | 30 logitr-0.4.0/logitr/vignettes/basic_usage.Rmd | 116 +- logitr-0.4.0/logitr/vignettes/data_formatting.Rmd | 43 - logitr-0.4.0/logitr/vignettes/interactions.Rmd | 103 +- logitr-0.4.0/logitr/vignettes/mnl_models.Rmd | 56 - logitr-0.4.0/logitr/vignettes/mnl_models_weighted.Rmd | 49 - logitr-0.4.0/logitr/vignettes/mxl_models.Rmd | 14 logitr-0.4.0/logitr/vignettes/predict.Rmd |only logitr-0.4.0/logitr/vignettes/probs.png |binary 107 files changed, 2271 insertions(+), 2135 deletions(-)
Title: Subgroup Treatment Effect Estimation in Clinical Trials
Description: Naive and adjusted treatment effect estimation for subgroups. Model
averaging (Bornkamp et.al, 2016 <doi:10.1002/pst.1796>) and bagging
(Rosenkranz, 2016 <doi:10.1002/bimj.201500147>) are proposed to address the
problem of selection bias in treatment effect estimates for subgroups.
The package can be used for all commonly encountered type of outcomes in
clinical trials (continuous, binary, survival, count). Additional functions
are provided to build the subgroup variables to be used and to plot the
results using forest plots. For details, see Ballarini et.al. (2021) <doi:10.18637/jss.v099.i14>.
Author: Nicolas Ballarini [aut, cre],
Bjoern Bornkamp [aut],
Marius Thomas [aut, cre],
Baldur Magnusson [ctb]
Maintainer: Nicolas Ballarini <nicoballarini@gmail.com>
Diff between subtee versions 0.3-7.1 dated 2021-02-25 and 1.0.0 dated 2021-10-25
DESCRIPTION | 10 MD5 | 23 - build/vignette.rds |binary inst/CITATION |only inst/doc/plotting_functions.html | 388 ++++++---------------------- inst/doc/subbuild_function.html | 496 ++++++++++--------------------------- inst/doc/subtee_package.html | 522 +++++++++++---------------------------- man/bagged.Rd | 4 man/get_prca_data.Rd | 4 man/modav.Rd | 4 man/plot.subtee.Rd | 5 man/subbuild.Rd | 222 ++++++++-------- man/unadj.Rd | 4 13 files changed, 517 insertions(+), 1165 deletions(-)
Title: 'Prevision.io' R SDK
Description: For working with the 'Prevision.io' AI model management platform's API <https://prevision.io/>.
Author: Florian Laroumagne [aut, cre],
Prevision.io Inc [cph]
Maintainer: Florian Laroumagne <florian.laroumagne@prevision.io>
Diff between previsionio versions 11.3.0 dated 2021-10-13 and 11.3.1 dated 2021-10-25
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 18 +++++++++++++++++- R/deployment.R | 4 ++-- R/folder.R | 2 +- R/pipeline.R | 4 ++-- R/project.R | 16 ++++++++-------- R/zzz.R | 2 +- man/create_deployment_model.Rd | 4 ++-- man/create_pipeline.Rd | 4 ++-- man/create_project_user.Rd | 4 ++-- man/update_project_user_role.Rd | 2 +- tests/testthat/test-experiment.R | 2 +- tests/testthat/test-project.R | 2 +- 14 files changed, 56 insertions(+), 40 deletions(-)
Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: Includes tools to calculate statistical power, minimum detectable effect size (MDES), MDES difference (MDESD), and minimum required sample size for various multilevel randomized experiments (MRE) with continuous outcomes.
Accomodates 14 types of MRE designs to detect main treatment effect, seven types of MRE designs to detect moderated treatment effect (2-1-1, 2-1-2, 2-2-1, 2-2-2, 3-3-1, 3-3-2, and 3-3-3 designs; <total.lev> - <trt.lev> - <mod.lev>),
five types of MRE designs to detect mediated treatment effects (2-1-1, 2-2-1, 3-1-1, 3-2-1, and 3-3-1 designs; <trt.lev> - <med.lev> - <out.lev>), four types of partially nested (PN) design to detect main treatment effect,
and three types of PN designs to detect mediated treatment effects (2/1, 3/1, 3/2; <trt.arm.lev> / <ctrl.arm.lev>).
See 'PowerUp!' Excel series at <https://www.causalevaluation.org/>.
Author: Metin Bulus [aut, cre],
Nianbo Dong [aut],
Benjamin Kelcey [aut],
Jessaca Spybrook [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between PowerUpR versions 1.0.4 dated 2019-06-01 and 1.1.0 dated 2021-10-25
PowerUpR-1.0.4/PowerUpR/R/bcra3f2.R |only PowerUpR-1.0.4/PowerUpR/R/bcra4f3.R |only PowerUpR-1.0.4/PowerUpR/R/bira2c1.R |only PowerUpR-1.0.4/PowerUpR/R/bira2f1.R |only PowerUpR-1.0.4/PowerUpR/R/bira2r1.R |only PowerUpR-1.0.4/PowerUpR/R/bira3r1.R |only PowerUpR-1.0.4/PowerUpR/R/bira4r1.R |only PowerUpR-1.0.4/PowerUpR/R/cra2r2.R |only PowerUpR-1.0.4/PowerUpR/R/cra3r3.R |only PowerUpR-1.0.4/PowerUpR/R/cra4r4.R |only PowerUpR-1.0.4/PowerUpR/R/depdef.R |only PowerUpR-1.0.4/PowerUpR/R/ira1r1.R |only PowerUpR-1.0.4/PowerUpR/man/PowerUpR-deprecated.Rd |only PowerUpR-1.0.4/PowerUpR/man/bcra3f2.Rd |only PowerUpR-1.0.4/PowerUpR/man/bcra4f3.Rd |only PowerUpR-1.0.4/PowerUpR/man/bira2c1.Rd |only PowerUpR-1.0.4/PowerUpR/man/bira2f1.Rd |only PowerUpR-1.0.4/PowerUpR/man/bira2r1.Rd |only PowerUpR-1.0.4/PowerUpR/man/bira3r1.Rd |only PowerUpR-1.0.4/PowerUpR/man/bira4r1.Rd |only PowerUpR-1.0.4/PowerUpR/man/cra2r2.Rd |only PowerUpR-1.0.4/PowerUpR/man/cra3r3.Rd |only PowerUpR-1.0.4/PowerUpR/man/cra4r4.Rd |only PowerUpR-1.0.4/PowerUpR/man/ira1r1.Rd |only PowerUpR-1.1.0/PowerUpR/DESCRIPTION | 14 PowerUpR-1.1.0/PowerUpR/MD5 | 97 +- PowerUpR-1.1.0/PowerUpR/NAMESPACE | 59 + PowerUpR-1.1.0/PowerUpR/NEWS.md | 9 PowerUpR-1.1.0/PowerUpR/R/bcra3r2.R | 153 ++++ PowerUpR-1.1.0/PowerUpR/R/bcra4r2.R | 17 PowerUpR-1.1.0/PowerUpR/R/bcra4r3.R | 12 PowerUpR-1.1.0/PowerUpR/R/bira2.R |only PowerUpR-1.1.0/PowerUpR/R/bira3.R |only PowerUpR-1.1.0/PowerUpR/R/bira4.R |only PowerUpR-1.1.0/PowerUpR/R/conv.R | 47 - PowerUpR-1.1.0/PowerUpR/R/cra2.R |only PowerUpR-1.1.0/PowerUpR/R/cra3.R |only PowerUpR-1.1.0/PowerUpR/R/cra4.R |only PowerUpR-1.1.0/PowerUpR/R/error.R | 133 ++- PowerUpR-1.1.0/PowerUpR/R/ira.R |only PowerUpR-1.1.0/PowerUpR/R/med_pn.R |only PowerUpR-1.1.0/PowerUpR/R/plot.R | 85 +- PowerUpR-1.1.0/PowerUpR/R/replication.R |only PowerUpR-1.1.0/PowerUpR/R/t1t2.R | 6 PowerUpR-1.1.0/PowerUpR/R/utils.R | 156 +--- PowerUpR-1.1.0/PowerUpR/README.md | 33 PowerUpR-1.1.0/PowerUpR/build/partial.rdb |only PowerUpR-1.1.0/PowerUpR/build/vignette.rds |binary PowerUpR-1.1.0/PowerUpR/inst/CITATION | 8 PowerUpR-1.1.0/PowerUpR/inst/doc/three_level_cluster_randomized_trial.R | 12 PowerUpR-1.1.0/PowerUpR/inst/doc/three_level_cluster_randomized_trial.Rmd | 18 PowerUpR-1.1.0/PowerUpR/inst/doc/three_level_cluster_randomized_trial.html | 349 ++++++++-- PowerUpR-1.1.0/PowerUpR/inst/doc/vectorization_over_arbitary_parameters.R |only PowerUpR-1.1.0/PowerUpR/inst/doc/vectorization_over_arbitary_parameters.html |only PowerUpR-1.1.0/PowerUpR/inst/doc/vectorization_over_arbitary_parameters.rmd |only PowerUpR-1.1.0/PowerUpR/man/PowerUpR-package.Rd | 2 PowerUpR-1.1.0/PowerUpR/man/bcra3r2.Rd | 57 + PowerUpR-1.1.0/PowerUpR/man/bcra4r2.Rd | 17 PowerUpR-1.1.0/PowerUpR/man/bcra4r3.Rd | 13 PowerUpR-1.1.0/PowerUpR/man/bira2.Rd |only PowerUpR-1.1.0/PowerUpR/man/bira3.Rd |only PowerUpR-1.1.0/PowerUpR/man/bira4.Rd |only PowerUpR-1.1.0/PowerUpR/man/conv.Rd | 2 PowerUpR-1.1.0/PowerUpR/man/cra2.Rd |only PowerUpR-1.1.0/PowerUpR/man/cra3.Rd |only PowerUpR-1.1.0/PowerUpR/man/cra4.Rd |only PowerUpR-1.1.0/PowerUpR/man/ira.Rd |only PowerUpR-1.1.0/PowerUpR/man/med_pn.Rd |only PowerUpR-1.1.0/PowerUpR/man/plot.Rd | 10 PowerUpR-1.1.0/PowerUpR/man/replication.Rd |only PowerUpR-1.1.0/PowerUpR/man/t1t2.Rd | 2 PowerUpR-1.1.0/PowerUpR/vignettes/three_level_cluster_randomized_trial.Rmd | 18 PowerUpR-1.1.0/PowerUpR/vignettes/vectorization_over_arbitary_parameters.rmd |only 73 files changed, 913 insertions(+), 416 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 1.4.3 dated 2020-06-02 and 1.5 dated 2021-10-25
DESCRIPTION | 15 MD5 | 94 NAMESPACE | 228 +- NEWS | 331 +-- R/Smetric.R | 244 +- R/bootInclude.R | 132 - R/bootTable.R | 791 +++---- R/bootThreshold.R | 200 - R/bootnet.R | 1678 +++++++-------- R/bootnetResultsMethods.R | 160 - R/centralityCompare.R | 384 +-- R/checkInput.R | 709 +++--- R/comparePlot.R | 196 - R/defaultFunctions.R | 4273 ++++++++++++++++++++------------------- R/estimateNetwork.R | 453 ++-- R/multiverse.R | 162 - R/netSimulator.R | 668 +++--- R/netSimulator_methods.R | 209 - R/parSim.R | 276 +- R/plotMethod.R | 1818 ++++++++-------- R/printMethod.R | 289 +- R/replicationSimulator.R | 322 +- R/replicationSimulator_methods.R | 100 R/simGraph.R | 182 - R/summaryMethod.R | 359 +-- R/transformations.R | 52 R/zzz.R | 94 inst/CITATION | 26 man/IsingGenerator.Rd | 46 man/binarize.Rd | 70 man/bootInclude.Rd | 132 - man/bootThreshold.Rd | 140 - man/bootnet-package.Rd | 56 man/bootnet.Rd | 368 +-- man/corStability.Rd | 110 - man/differenceTest.Rd | 152 - man/estimateNetwork.Rd | 630 ++--- man/genGGM.Rd | 94 man/ggmGenerator.Rd | 66 man/multiverse.Rd | 50 man/netSimulator.Rd | 359 +-- man/null.Rd | 50 man/plot.bootnet.Rd | 220 +- man/plot.netSimulator.Rd | 152 - man/plotBootnetResult.Rd | 70 man/print.bootnet.Rd | 56 man/summary.bootnet.Rd | 72 man/transformation.Rd | 50 48 files changed, 8847 insertions(+), 8541 deletions(-)
Title: Spatial Capture-Recapture (SCR) Methods Using 'nimble'
Description: Provides utility functions, distributions, and methods for improving Markov chain Monte Carlo (MCMC) sampling efficiency for ecological Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) models. The methods provided implement the techniques presented in "Estimation of Large-Scale Spatial Capture-Recapture Models" (Turek, et al (2021); Eco-sphere 12(2):e03385. <doi:10.1002/ecs2.3385>).
Author: Richard Bischof [aut],
Daniel Turek [aut, cre],
Cyril Milleret [aut],
Torbjørn Ergon [aut],
Pierre Dupont [aut],
Soumen Dey [aut],
Wei Zhang [aut],
Perry de Valpine [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleSCR versions 0.1.2 dated 2021-07-01 and 0.1.3 dated 2021-10-25
DESCRIPTION | 26 + MD5 | 93 +++-- NAMESPACE | 41 ++ R/calcWindowSizes.R |only R/dbernppAC.R |only R/dbernppACmovement_exp.R |only R/dbernppACmovement_normal.R |only R/dbernppDetection_normal.R |only R/dbernppLocalACmovement_exp.R |only R/dbernppLocalACmovement_normal.R |only R/dbernppLocalDetection_normal.R |only R/dbinomLocal_normal.R | 2 R/dnormalizer.R |only R/dpoisLocal_normal.R | 4 R/dpoisppAC.R |only R/dpoisppDetection_normal.R |only R/dpoisppLocalDetection_normal.R |only R/getLocalObjects.R | 8 R/getMidPointNodes.R |only R/getSparseY.R | 4 R/getWindowCoords.R |only R/getWindowIndex.R |only R/integrateIntensityLocal_exp.R |only R/integrateIntensityLocal_normal.R |only R/integrateIntensity_exp.R |only R/integrateIntensity_normal.R |only R/makeConstantNimbleFunction.R |only R/marginalVoidProbIntegrand.R |only R/marginalVoidProbNumIntegration.R |only R/scaleCoordsToHabitatGrid.R | 2 R/stratRejectionSampler_exp.R |only R/stratRejectionSampler_normal.R |only R/zzz.R | 186 +++++++++- build/vignette.rds |binary inst/NEWS |only inst/doc/Point_Process.R |only inst/doc/Point_Process.Rmd |only inst/doc/Point_Process.html |only inst/doc/Simulate_and_fit_SCR_models_with_dbinomLocal_normal.Rmd | 4 inst/doc/Simulate_and_fit_SCR_models_with_dbinomLocal_normal.html | 10 inst/doc/wolverine_example.html | 4 inst/extdata/pointProcess_samples.RData |only inst/extdata/pointProcess_samples1.RData |only man/calcWindowSizes.Rd |only man/dbernppAC.Rd |only man/dbernppACmovement_exp.Rd |only man/dbernppACmovement_normal.Rd |only man/dbernppDetection_normal.Rd |only man/dbernppLocalACmovement_exp.Rd |only man/dbernppLocalACmovement_normal.Rd |only man/dbernppLocalDetection_normal.Rd |only man/dbinomLocal_normal.Rd | 2 man/dnormalizer.Rd |only man/dpoisLocal_normal.Rd | 4 man/dpoisppAC.Rd |only man/dpoisppDetection_normal.Rd |only man/dpoisppLocalDetection_normal.Rd |only man/getLocalObjects.Rd | 6 man/getMidPointNodes.Rd |only man/getSparseY.Rd | 2 man/getWindowCoords.Rd |only man/getWindowIndex.Rd |only man/integrateIntensityLocal_exp.Rd |only man/integrateIntensityLocal_normal.Rd |only man/integrateIntensity_exp.Rd |only man/integrateIntensity_normal.Rd |only man/makeConstantNimbleFunction.Rd |only man/marginalVoidProbIntegrand.Rd |only man/marginalVoidProbNumIntegration.Rd |only man/stratRejectionSampler_exp.Rd |only man/stratRejectionSampler_normal.Rd |only tests/testthat/test-dbinomLocal_normal.R | 9 vignettes/Point_Process.Rmd |only vignettes/Simulate_and_fit_SCR_models_with_dbinomLocal_normal.Rmd | 4 vignettes/references.bib | 10 75 files changed, 363 insertions(+), 58 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>
Diff between twang versions 2.4 dated 2021-07-26 and 2.5 dated 2021-10-25
DESCRIPTION | 10 +- MD5 | 16 +-- build/vignette.rds |binary inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.R | 170 ++++++++--------------------------------- inst/doc/twang.pdf |binary inst/doc/twang.rnw | 212 ++++++++++++++++++++++++++-------------------------- vignettes/twang.rnw | 212 ++++++++++++++++++++++++++-------------------------- 9 files changed, 258 insertions(+), 362 deletions(-)
Title: Multivariate Normal Functions for Sparse Covariance and
Precision Matrices
Description: Computes multivariate normal (MVN) densities, and
samples from MVN distributions, when the covariance or
precision matrix is sparse.
Author: Michael Braun [aut, cre, cph] (<https://orcid.org/0000-0003-4774-2119>)
Maintainer: Michael Braun <braunm@smu.edu>
Diff between sparseMVN versions 0.2.1.1 dated 2018-03-26 and 0.2.2 dated 2021-10-25
sparseMVN-0.2.1.1/sparseMVN/inst/doc/sparseMVN.R |only sparseMVN-0.2.1.1/sparseMVN/inst/doc/sparseMVN.Rnw |only sparseMVN-0.2.1.1/sparseMVN/inst/doc/sparseMVN.bib |only sparseMVN-0.2.1.1/sparseMVN/inst/doc/sparseMVN.pdf |only sparseMVN-0.2.1.1/sparseMVN/vignettes/sparseMVN.Rnw |only sparseMVN-0.2.2/sparseMVN/DESCRIPTION | 27 ++-- sparseMVN-0.2.2/sparseMVN/MD5 | 29 ++--- sparseMVN-0.2.2/sparseMVN/NEWS | 19 +-- sparseMVN-0.2.2/sparseMVN/R/dmvn-sparse.R |only sparseMVN-0.2.2/sparseMVN/R/rmvn-sparse.R | 79 +------------- sparseMVN-0.2.2/sparseMVN/R/sparseMVN.R | 3 sparseMVN-0.2.2/sparseMVN/build/vignette.rds |binary sparseMVN-0.2.2/sparseMVN/inst/doc/sparseMVN2.R |only sparseMVN-0.2.2/sparseMVN/inst/doc/sparseMVN2.Rmd |only sparseMVN-0.2.2/sparseMVN/inst/doc/sparseMVN2.html |only sparseMVN-0.2.2/sparseMVN/man/dmvn.sparse.Rd |only sparseMVN-0.2.2/sparseMVN/man/rmvn.sparse.Rd | 16 -- sparseMVN-0.2.2/sparseMVN/man/sparseMVN-package.Rd | 14 ++ sparseMVN-0.2.2/sparseMVN/tests/testthat/test_sparseMVN.R | 36 +++--- sparseMVN-0.2.2/sparseMVN/vignettes/.install_extras | 1 sparseMVN-0.2.2/sparseMVN/vignettes/banded.png |only sparseMVN-0.2.2/sparseMVN/vignettes/block_arrow.png |only sparseMVN-0.2.2/sparseMVN/vignettes/sparseMVN2.Rmd |only 23 files changed, 92 insertions(+), 132 deletions(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Description: Provides functions for multivariate and propensity score matching
and for finding optimal balance based on a genetic search algorithm.
A variety of univariate and multivariate metrics to
determine if balance has been obtained are also provided. For
details, see the paper by Jasjeet Sekhon
(2007, <doi:10.18637/jss.v042.i07>).
Author: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>
Maintainer: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>
Diff between Matching versions 4.9-10 dated 2021-10-09 and 4.9-11 dated 2021-10-25
Matching-4.9-10/Matching/cleanup |only Matching-4.9-10/Matching/configure |only Matching-4.9-10/Matching/configure.ac |only Matching-4.9-10/Matching/src/Makevars.in |only Matching-4.9-11/Matching/DESCRIPTION | 8 ++++---- Matching-4.9-11/Matching/MD5 | 9 +++------ Matching-4.9-11/Matching/build/partial.rdb |binary Matching-4.9-11/Matching/src/Makevars |only 8 files changed, 7 insertions(+), 10 deletions(-)
Title: Dual Empirical Likelihood Inference under Density Ratio Models
in the Presence of Multiple Samples
Description: Dual empirical likelihood (DEL) inference under semiparametric density ratio models (DRM) in the presence of multiple samples, including population cumulative distribution function estimation, quantile estimation and comparison, density estimation, composite hypothesis testing for DRM parameters which encompasses testing for changes in population distribution functions as a special case, etc.
Author: Song Cai
Maintainer: Song Cai <scai@math.carleton.ca>
Diff between drmdel versions 1.3.1 dated 2015-01-21 and 1.3.2 dated 2021-10-25
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ src/utilities.c | 3 ++- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Differential Analysis with Random Reference Genes
Description: Differential Analysis of short RNA transcripts that can be modeled by either Poisson or Negative binomial distribution. The statistical methodology implemented in this package is based on the random selection of references genes (Desaulle et al. (2021) <arXiv:2103.09872>).
Author: Dorota Desaulle [aut, cre] (<https://orcid.org/0000-0002-3419-9447>),
Yves Rozenholc [aut] (<https://orcid.org/0000-0002-3907-5101>)
Maintainer: Dorota Desaulle <dorota.desaulle@u-paris.fr>
Diff between DArand versions 0.0.1.0 dated 2021-09-27 and 0.0.1.1 dated 2021-10-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/DArand.R | 4 +++- man/DArand.Rd | 5 ++++- tests/testthat/test-DArand.R | 8 ++++---- 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and direct
extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR',
'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma'
and 'xz'.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Ondrej Holy [cph] (archive_write_add_filter implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between archive versions 1.1.1 dated 2021-10-13 and 1.1.2 dated 2021-10-25
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/zzz.R | 1 + README.md | 6 +++--- build/archive.pdf |binary src/archive_extract.cpp | 2 +- src/archive_write_files.cpp | 3 +-- 8 files changed, 20 insertions(+), 16 deletions(-)
Title: Multi-Level Vector Autoregression
Description: Estimates the multi-level vector autoregression model on time-series data.
Three network structures are obtained: temporal networks, contemporaneous
networks and between-subjects networks.
Author: Sacha Epskamp [aut, cre],
Marie K. Deserno [aut],
Laura F. Bringmann [aut],
Myrthe Veenman [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between mlVAR versions 0.4.4 dated 2019-10-21 and 0.5 dated 2021-10-25
DESCRIPTION | 18 ++- MD5 | 18 +-- NAMESPACE | 6 + NEWS | 11 + R/S3Methods.R | 20 ++- R/lmer_murmur.R | 19 +-- R/mlVAR.R | 52 +++++++- R/mlVARsamplesize.R | 301 +++++++++++++++++++++++++++++++++++++++------------- R/modelMatrix.R | 5 man/mlVARsample.Rd | 57 ++++++++- 10 files changed, 384 insertions(+), 123 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.0.6 dated 2021-10-09 and 0.0.7 dated 2021-10-25
DESCRIPTION | 13 ++++-- MD5 | 28 ++++++++------ NAMESPACE | 1 NEWS.md | 5 ++ R/grid-draw-utilities.R | 20 ++++++++++ R/method-grid-draw.R | 90 +++++++++++++++++++++++++++++------------------- R/scales.R | 44 ++++++++++++++++------- R/utilities.R | 11 +++++ R/zzz.R |only inst/CITATION |only inst/doc/ggbreak.R | 7 +++ inst/doc/ggbreak.Rmd | 14 +++++++ inst/doc/ggbreak.html | 26 ++++++++----- man/scale_break.Rd | 12 +++++- man/scale_cut.Rd | 12 +++++- vignettes/ggbreak.Rmd | 14 +++++++ 16 files changed, 216 insertions(+), 81 deletions(-)
Title: Interface to 'fastai'
Description: The 'fastai' <https://docs.fast.ai/index.html> library
simplifies training fast and accurate neural networks
using modern best practices. It is based on research
in to deep learning best practices undertaken
at 'fast.ai', including 'out of the box' support
for vision, text, tabular, audio, time series, and
collaborative filtering models.
Author: Turgut Abdullayev [ctb, cre, cph, aut]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>
Diff between fastai versions 2.0.9 dated 2021-07-28 and 2.1.0 dated 2021-10-25
fastai-2.0.9/fastai/tests/testthat/test-GAN.R |only fastai-2.0.9/fastai/tests/testthat/test-experimental.R |only fastai-2.0.9/fastai/tests/testthat/test-generics-tensor.R |only fastai-2.0.9/fastai/tests/testthat/test-image.R |only fastai-2.0.9/fastai/tests/testthat/test-medical.R |only fastai-2.0.9/fastai/tests/testthat/test-medical_image_render.R |only fastai-2.0.9/fastai/tests/testthat/test-model_load.R |only fastai-2.0.9/fastai/tests/testthat/test-modify.R |only fastai-2.0.9/fastai/tests/testthat/test-nn_module.R |only fastai-2.0.9/fastai/tests/testthat/test-predict_medical.R |only fastai-2.0.9/fastai/tests/testthat/test-pretrained_in_cnn_learner.R |only fastai-2.0.9/fastai/tests/testthat/test-regression.R |only fastai-2.0.9/fastai/tests/testthat/test-tabular.R |only fastai-2.0.9/fastai/tests/testthat/test-text-load.R |only fastai-2.0.9/fastai/tests/testthat/test-text.R |only fastai-2.0.9/fastai/tests/testthat/test-time-series.R |only fastai-2.1.0/fastai/DESCRIPTION | 8 +-- fastai-2.1.0/fastai/MD5 | 24 +--------- fastai-2.1.0/fastai/R/install_fastai.R | 12 ++--- fastai-2.1.0/fastai/README.md | 11 ++-- fastai-2.1.0/fastai/build/vignette.rds |binary 21 files changed, 20 insertions(+), 35 deletions(-)
Title: Generative Art with 'ggplot2'
Description: Provides algorithms for creating artworks in the 'ggplot2' language that incorporate some form of randomness.
Author: Koen Derks [aut, cre]
Maintainer: Koen Derks <koen-derks@hotmail.com>
Diff between aRtsy versions 0.1.3 dated 2021-09-26 and 0.1.4 dated 2021-10-25
DESCRIPTION | 15 +-- MD5 | 33 ++++--- NAMESPACE | 1 NEWS.md | 12 ++ R/RcppExports.R | 8 + R/canvas_ant.R | 3 R/canvas_flow.R | 41 +++++---- R/canvas_maze.R |only R/canvas_nebula.R | 4 R/colorPalette.R | 65 +++++++++++++- README.md | 157 ++++++++++++++++++++---------------- inst/CITATION | 4 man/canvas_flow.Rd | 18 ++-- man/canvas_maze.Rd |only man/colorPalette.Rd | 6 - src/RcppExports.cpp | 23 ++++- src/canvas_flow.cpp | 9 -- src/canvas_maze.cpp |only tests/testthat/test-all-paintings.R | 50 ++++++----- 19 files changed, 287 insertions(+), 162 deletions(-)
Title: Port of the S+ "Robust Library"
Description: Methods for robust statistics, a state of the art in the early
2000s, notably for robust regression and robust multivariate analysis.
Author: Jiahui Wang,
Ruben Zamar <ruben@stat.ubc.ca>,
Alfio Marazzi <Alfio.Marazzi@inst.hospvd.ch>,
Victor Yohai <vyohai@dm.uba.ar>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Ricardo Maronna <maron@mate.unlp.edu.ar>,
Eric Zivot <ezivot@u.washington.edu>,
David Rocke <dmrocke@ucdavis.edu>,
Doug Martin,
Martin Maechler <maechler@stat.math.ethz.ch>,
Kjell Konis <kjell.konis@me.com>.
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between robust versions 0.5-0.0 dated 2020-03-07 and 0.6-0 dated 2021-10-25
DESCRIPTION | 9 MD5 | 12 NAMESPACE | 20 R/library.q | 4 man/OverlaidDenPlot.fdfm.Rd | 8 src/compatibility.c | 1 tests/Examples/robust-Ex.Rout.save | 2291 ++++++++++++++++++------------------- 7 files changed, 1182 insertions(+), 1163 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are
otherwise performed manually. This includes setting up unit testing,
test coverage, continuous integration, Git, 'GitHub', licenses,
'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
Malcolm Barrett [aut] (<https://orcid.org/0000-0003-0299-5825>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between usethis versions 2.1.0 dated 2021-10-16 and 2.1.2 dated 2021-10-25
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS.md | 10 ++++++++++ R/git-default-branch.R | 25 ++++++++++++++++++++++--- R/release.R | 3 ++- man/git-default-branch.Rd | 2 +- 6 files changed, 48 insertions(+), 18 deletions(-)
Title: Advanced 'tryCatch()' and 'try()' Functions
Description: Advanced tryCatch() and try() functions for better error handling
(logging, stack trace with source code references and support for post-mortem analysis via dump files).
Author: Juergen Altfeld [aut, cre, cph],
Charles Epaillard [ctb],
Brandon Bertelsen [ctb],
Valerian Wrobel [ctb]
Maintainer: Juergen Altfeld <jaltfeld@altfeld-im.de>
Diff between tryCatchLog versions 1.2.4 dated 2021-05-21 and 1.3.1 dated 2021-10-25
tryCatchLog-1.2.4/tryCatchLog/tests/testthat/build_log_output_test_data_2.txt |only tryCatchLog-1.2.4/tryCatchLog/tests/testthat/out2.txt |only tryCatchLog-1.3.1/tryCatchLog/DESCRIPTION | 12 - tryCatchLog-1.3.1/tryCatchLog/MD5 | 34 ++-- tryCatchLog-1.3.1/tryCatchLog/NEWS.md | 27 +++ tryCatchLog-1.3.1/tryCatchLog/R/limited_Labels_Compact.R | 27 ++- tryCatchLog-1.3.1/tryCatchLog/R/tryCatchLog.R | 37 ++++ tryCatchLog-1.3.1/tryCatchLog/R/tryLog.R | 4 tryCatchLog-1.3.1/tryCatchLog/inst/doc/90_appendix.Rmd_child | 2 tryCatchLog-1.3.1/tryCatchLog/inst/doc/tryCatchLog-intro.html | 6 tryCatchLog-1.3.1/tryCatchLog/man/limitedLabelsCompact.Rd | 10 - tryCatchLog-1.3.1/tryCatchLog/man/tryCatchLog.Rd | 12 + tryCatchLog-1.3.1/tryCatchLog/man/tryLog.Rd | 5 tryCatchLog-1.3.1/tryCatchLog/tests/testthat/expected_full_stack_trace.txt | 66 ------- tryCatchLog-1.3.1/tryCatchLog/tests/testthat/expected_log_output.txt |only tryCatchLog-1.3.1/tryCatchLog/tests/testthat/test_build_log_output.R | 4 tryCatchLog-1.3.1/tryCatchLog/tests/testthat/test_logging_of_conditions.R |only tryCatchLog-1.3.1/tryCatchLog/tests/testthat/test_silent_warnings.R | 3 tryCatchLog-1.3.1/tryCatchLog/tests/testthat/test_user_defined_conditions.R | 83 ++++------ tryCatchLog-1.3.1/tryCatchLog/vignettes/90_appendix.Rmd_child | 2 20 files changed, 180 insertions(+), 154 deletions(-)
More information about simplermarkdown at CRAN
Permanent link
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Richard M. Heiberger [ctb] (formatHex(), *Bin, *Dec),
John C. Nash [ctb] (hjkMpfr(), origin of unirootR()),
Hans W. Borchers [ctb] (optimizeR(*, "GoldenRatio"); origin of
hjkMpfr())
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.8-5 dated 2021-10-06 and 0.8-6 dated 2021-10-25
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 13 +++++++++++++ inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.pdf |binary man/Bessel_mpfr.Rd | 22 ++++++++++++---------- src/convert.c | 25 +++++++++++++++---------- 10 files changed, 54 insertions(+), 34 deletions(-)
Title: Multimodal and Multilevel Network Analysis
Description: A set of tools that extend common social network analysis packages
for analysing multimodal and multilevel networks.
It includes functions for one- and two-mode (and sometimes three-mode)
centrality, centralization, clustering, and constraint,
as well as for one- and two-mode network regression and block-modelling.
All functions operate with matrices, edge lists,
and 'igraph', 'network'/'sna', and 'tidygraph' objects.
The package is released as a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Author: James Hollway [cph, cre, aut, ctb] (IHEID,
<https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 0.8.1 dated 2021-10-22 and 0.8.2 dated 2021-10-25
DESCRIPTION | 16 +- MD5 | 28 +-- NAMESPACE | 4 NEWS.md | 23 +++ R/blockmodel.R | 5 R/blockmodel_visualisation.R | 2 R/coercion.R | 3 R/reexports_ggplot2.R | 4 R/to.R | 27 +++ inst/doc/blockmodel.R | 13 - inst/doc/blockmodel.Rmd | 76 +++++++-- inst/doc/blockmodel.html | 328 ++++++++++++++++++++++--------------------- man/reexports.Rd | 3 man/to.Rd | 4 vignettes/blockmodel.Rmd | 76 +++++++-- 15 files changed, 374 insertions(+), 238 deletions(-)
Title: Kaya Identity Data for Nations and Regions
Description: Provides data for Kaya identity variables (population, gross
domestic product, primary energy consumption, and energy-related
CO2 emissions) for the world and for individual nations, and
utility functions for looking up data, plotting trends of
Kaya variables, and plotting the fuel mix for a given country
or region. The Kaya identity (Yoichi Kaya and Keiichi Yokobori,
"Environment, Energy, and Economy: Strategies for Sustainability"
(United Nations University Press, 1998) and
<https://en.wikipedia.org/wiki/Kaya_identity>) expresses a nation's
or region's greenhouse gas emissions in terms of its population,
per-capita Gross Domestic Product, the energy intensity of its
economy, and the carbon-intensity of its energy supply.
Author: Jonathan Gilligan [cre, aut] (<https://orcid.org/0000-0003-1375-6686>)
Maintainer: Jonathan Gilligan <jonathan.gilligan@vanderbilt.edu>
Diff between kayadata versions 0.5.1 dated 2021-03-27 and 1.0.0 dated 2021-10-25
kayadata-0.5.1/kayadata/tests/figs |only kayadata-1.0.0/kayadata/DESCRIPTION | 10 - kayadata-1.0.0/kayadata/MD5 | 45 ++--- kayadata-1.0.0/kayadata/NAMESPACE | 2 kayadata-1.0.0/kayadata/NEWS.md | 13 + kayadata-1.0.0/kayadata/R/kaya.R | 2 kayadata-1.0.0/kayadata/R/kayadata.R | 5 kayadata-1.0.0/kayadata/R/plot_kaya.R | 4 kayadata-1.0.0/kayadata/build/partial.rdb |binary kayadata-1.0.0/kayadata/build/vignette.rds |binary kayadata-1.0.0/kayadata/data/fuel_mix.rda |binary kayadata-1.0.0/kayadata/data/kaya_data.rda |binary kayadata-1.0.0/kayadata/inst/WORDLIST | 34 ++-- kayadata-1.0.0/kayadata/inst/doc/kayadata.html | 42 ++--- kayadata-1.0.0/kayadata/inst/doc/policy_analysis.html | 78 ++++------ kayadata-1.0.0/kayadata/man/figures/README-plot-fuel-mix-1.png |binary kayadata-1.0.0/kayadata/man/figures/README-plot-kaya-1.png |binary kayadata-1.0.0/kayadata/man/figures/README-plot-kaya-world-1.png |binary kayadata-1.0.0/kayadata/man/kayadata-package.Rd | 2 kayadata-1.0.0/kayadata/tests/testthat/_snaps |only 20 files changed, 120 insertions(+), 117 deletions(-)
Title: Explanatory Item Response Modeling for Dichotomous and
Polytomous Items
Description: Analysis of dichotomous and polytomous response data using the explanatory item response modeling framework, as described in Bulut, Gorgun, & Yildirim-Erbasli (2021) <doi:10.3390/psych3030023>, Stanke & Bulut (2019) <doi:10.21449/ijate.515085>, and De Boeck & Wilson (2004) <doi:10.1007/978-1-4757-3990-9>. Generalized linear mixed modeling is used for estimating the effects of item-related and person-related variables on dichotomous and polytomous item responses.
Author: Okan Bulut [aut, cre] (<https://orcid.org/0000-0001-5853-1267>)
Maintainer: Okan Bulut <bulut@ualberta.ca>
Diff between eirm versions 0.4 dated 2021-07-04 and 0.5 dated 2021-10-25
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 6 ++++++ R/eirm.R | 51 ++++++++++++++++++++++++++++++++++++++++++--------- R/polyreformat.R | 2 +- inst/CITATION | 38 +++++++++++++++++++++++++------------- man/eirm.Rd | 19 ++++++++++++++++++- 8 files changed, 105 insertions(+), 36 deletions(-)
More information about DominoPredictionLogging at CRAN
Permanent link
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.6.9 dated 2021-08-16 and 1.7.0 dated 2021-10-25
castor-1.6.9/castor/R/get_trait_depth.R |only castor-1.6.9/castor/man/get_trait_depth.Rd |only castor-1.7.0/castor/DESCRIPTION | 10 castor-1.7.0/castor/MD5 | 96 +- castor-1.7.0/castor/NAMESPACE | 7 castor-1.7.0/castor/R/RcppExports.R | 8 castor-1.7.0/castor/R/asr_max_parsimony.R | 2 castor-1.7.0/castor/R/auxiliary_routines.R | 12 castor-1.7.0/castor/R/collapse_monofurcations.R | 2 castor-1.7.0/castor/R/collapse_tree_at_resolution.R | 2 castor-1.7.0/castor/R/consentrait_depth.R |only castor-1.7.0/castor/R/discrete_trait_depth.R |only castor-1.7.0/castor/R/fit_hbd_pdr_on_grid.R | 6 castor-1.7.0/castor/R/generate_gene_tree_msc.R | 2 castor-1.7.0/castor/R/generate_gene_tree_msc_hgt_dl.R | 4 castor-1.7.0/castor/R/generate_random_tree.R | 2 castor-1.7.0/castor/R/generate_tree_hbd_reverse.R | 2 castor-1.7.0/castor/R/generate_tree_hbds.R | 2 castor-1.7.0/castor/R/generate_tree_with_evolving_rates.R | 2 castor-1.7.0/castor/R/get_subtree_at_node.R | 2 castor-1.7.0/castor/R/get_subtree_with_tips.R | 2 castor-1.7.0/castor/R/get_subtrees_at_nodes.R | 2 castor-1.7.0/castor/R/is_bifurcating.R |only castor-1.7.0/castor/R/join_rooted_trees.R | 2 castor-1.7.0/castor/R/merge_nodes_to_multifurcations.R | 2 castor-1.7.0/castor/R/merge_short_edges.R | 2 castor-1.7.0/castor/R/multifurcations_to_bifurcations.R | 2 castor-1.7.0/castor/R/read_tree.R | 2 castor-1.7.0/castor/R/reorder_tree_edges.R | 5 castor-1.7.0/castor/R/root_at_midpoint.R | 3 castor-1.7.0/castor/R/root_at_node.R | 2 castor-1.7.0/castor/R/root_in_edge.R | 1 castor-1.7.0/castor/R/root_via_outgroup.R | 1 castor-1.7.0/castor/R/simulate_dsse.R | 2 castor-1.7.0/castor/R/simulate_tdsse.R | 2 castor-1.7.0/castor/R/spline_coefficients.R |only castor-1.7.0/castor/R/split_tree_at_height.R | 2 castor-1.7.0/castor/R/tree_from_branching_ages.R | 2 castor-1.7.0/castor/R/tree_from_sampling_branching_ages.R | 2 castor-1.7.0/castor/R/trim_tree_at_height.R | 2 castor-1.7.0/castor/man/asr_max_parsimony.Rd | 6 castor-1.7.0/castor/man/asr_mk_model.Rd | 2 castor-1.7.0/castor/man/consentrait_depth.Rd |only castor-1.7.0/castor/man/discrete_trait_depth.Rd |only castor-1.7.0/castor/man/evaluate_spline.Rd | 7 castor-1.7.0/castor/man/fit_hbd_pdr_on_best_grid_size.Rd | 2 castor-1.7.0/castor/man/fit_hbd_pdr_on_grid.Rd | 2 castor-1.7.0/castor/man/geographic_acf.Rd | 2 castor-1.7.0/castor/man/get_trait_acf.Rd | 2 castor-1.7.0/castor/man/is_bifurcating.Rd |only castor-1.7.0/castor/man/root_at_midpoint.Rd | 2 castor-1.7.0/castor/man/spline_coefficients.Rd |only castor-1.7.0/castor/src/RcppExports.cpp | 44 + castor-1.7.0/castor/src/phylogenetics_cpp_routines.cpp | 580 ++++++++++++-- 54 files changed, 674 insertions(+), 174 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-11 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-09 0.2.0
2021-01-21 0.1.1
2021-01-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-21 0.2.5
2017-07-13 0.2.0
2017-04-07 0.1.1
2017-04-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-09 3.3.0
2021-04-13 3.2.1
2021-03-22 3.2.0
2020-12-08 3.1.1
2020-11-18 3.1.0
Title: Framework for Specifying and Simulating Individual Based Models
Description: A framework which provides users a set of useful primitive elements for
specifying individual based simulation models, with special attention models for
infectious disease epidemiology. Users build models by specifying variables for
each characteristic of individuals in the simulated population by using data
structures exposed by the package. The package provides efficient methods for
finding subsets of individuals based on these variables, or cohorts. Cohorts can
then be targeted for variable updates or scheduled for events. Variable updates
queued during a time step are executed at the end of a discrete time step, and
the code places no restrictions on how individuals are allowed to interact.
These data structures are designed to provide an intuitive way for users to turn
their conceptual model of a system into executable code, which is fast and
memory efficient.
Author: Giovanni Charles [aut, cre] (<https://orcid.org/0000-0002-7024-1200>),
Sean L. Wu [aut] (<https://orcid.org/0000-0002-5781-9493>),
Peter Winskill [aut] (<https://orcid.org/0000-0003-3001-4959>),
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Giovanni Charles <giovanni.charles@gmail.com>
Diff between individual versions 0.1.6 dated 2021-10-14 and 0.1.7 dated 2021-10-25
DESCRIPTION | 8 MD5 | 72 +- NEWS.md | 4 R/bitset.R | 48 - R/catch-routine-registration.R | 2 R/categorical_variable.R | 14 R/double_variable.R | 8 R/event.R | 12 R/integer_variable.R | 10 R/prefab.R | 88 +-- R/render.R | 22 R/targeted_event.R | 12 README.md | 61 +- inst/doc/API.html | 728 +++++++++++++++------------ inst/doc/Contributing.html | 402 ++++++++------ inst/doc/Performance.html | 676 ++++++++++++++----------- inst/doc/Tutorial.html | 646 +++++++++++++---------- inst/include/Event.h | 3 man/Bitset.Rd | 48 - man/CategoricalVariable.Rd | 10 man/DoubleVariable.Rd | 8 man/Event.Rd | 12 man/IntegerVariable.Rd | 10 man/Render.Rd | 22 man/TargetedEvent.Rd | 12 man/bernoulli_process.Rd | 10 man/categorical_count_renderer_process.Rd | 10 man/fixed_probability_multinomial_process.Rd | 12 man/infection_age_process.Rd | 22 man/multi_probability_bernoulli_process.Rd | 10 man/multi_probability_multinomial_process.Rd | 10 man/reschedule_listener.Rd | 8 man/update_category_listener.Rd | 6 src/RcppExports.cpp | 9 src/categorical_variable.cpp | 3 tests/testthat/test-categoricalvariable.R | 21 tests/testthat/test-cpp.R | 5 37 files changed, 1732 insertions(+), 1332 deletions(-)
Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation to analyze data
shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Sido Haakma [aut, cre] (<https://orcid.org/0000-0003-1278-9144>),
Tommy de Boer [aut] (<https://orcid.org/0000-0002-4492-7225>),
Fleur Kelpin [aut] (<https://orcid.org/0000-0003-1527-5130>),
MOLGENIS org [cph, fnd]
Maintainer: Sido Haakma <s.haakma@rug.nl>
Diff between DSMolgenisArmadillo versions 1.3.7 dated 2021-10-14 and 1.4.0 dated 2021-10-25
DESCRIPTION | 10 +-- MD5 | 18 +++--- NEWS.md | 6 +- R/ArmadilloConnection.R | 13 ++++ R/ArmadilloDriver.R | 13 +++- man/DSMolgenisArmadillo-package.Rd | 6 -- man/dsConnect-ArmadilloDriver-method.Rd | 3 + tests/testthat/helper.R | 2 tests/testthat/test-ArmadilloConnection.R | 31 ++++++++++ tests/testthat/test-ArmadilloDriver.R | 88 +++++++++++++++++++++++++----- 10 files changed, 154 insertions(+), 36 deletions(-)
More information about DSMolgenisArmadillo at CRAN
Permanent link
Title: Simulated Goodness-of-Fit Tests for Discrete Distributions
Description: Implements Monte Carlo simulations for
goodness-of-fit (GOF) tests for discrete distributions. This
includes tests based on the Chi-squared statistic, the
log-likelihood-ratio (G^2) statistic, the Freeman-Tukey
(Hellinger-distance) statistic, the Kolmogorov-Smirnov
statistic, the Cramer-von Mises statistic as described in
Choulakian, Lockhart and Stephens (1994) <doi:10.2307/3315828>,
and the root-mean-square statistic, see Perkins,
Tygert, and Ward (2011) <doi:10.1016/j.amc.2011.03.124>.
Author: Josh McCormick [aut, cre]
Maintainer: Josh McCormick <josh.mccormick@aya.yale.edu>
Diff between discretefit versions 0.0.0 dated 2021-10-08 and 0.1.0 dated 2021-10-25
discretefit-0.0.0/discretefit/src/chisq_gof.cpp |only discretefit-0.0.0/discretefit/src/ks_gof.cpp |only discretefit-0.0.0/discretefit/src/rms_gof.cpp |only discretefit-0.0.0/discretefit/src/utils.h |only discretefit-0.1.0/discretefit/DESCRIPTION | 22 discretefit-0.1.0/discretefit/MD5 | 54 +- discretefit-0.1.0/discretefit/NAMESPACE | 2 discretefit-0.1.0/discretefit/NEWS.md |only discretefit-0.1.0/discretefit/R/RcppExports.R | 16 discretefit-0.1.0/discretefit/R/chisq_gof.R | 94 ++- discretefit-0.1.0/discretefit/R/cvm_gof.R |only discretefit-0.1.0/discretefit/R/ft_gof.R |only discretefit-0.1.0/discretefit/R/g_gof.R | 30 + discretefit-0.1.0/discretefit/R/ks_gof.R | 29 + discretefit-0.1.0/discretefit/R/rms_gof.R | 30 + discretefit-0.1.0/discretefit/R/utils.R | 4 discretefit-0.1.0/discretefit/README.md | 246 +++++----- discretefit-0.1.0/discretefit/inst/doc/package_introduction.R | 44 - discretefit-0.1.0/discretefit/inst/doc/package_introduction.Rmd | 113 ++-- discretefit-0.1.0/discretefit/inst/doc/package_introduction.html | 177 ++++--- discretefit-0.1.0/discretefit/man/chisq_gof.Rd | 15 discretefit-0.1.0/discretefit/man/cvm_gof.Rd |only discretefit-0.1.0/discretefit/man/ft_gof.Rd |only discretefit-0.1.0/discretefit/man/g_gof.Rd | 21 discretefit-0.1.0/discretefit/man/ks_gof.Rd | 15 discretefit-0.1.0/discretefit/man/rms_gof.Rd | 15 discretefit-0.1.0/discretefit/src/RcppExports.cpp | 51 -- discretefit-0.1.0/discretefit/src/discretefit.h | 30 + discretefit-0.1.0/discretefit/src/simulate_p.cpp | 115 ++-- discretefit-0.1.0/discretefit/src/statistics.cpp | 42 + discretefit-0.1.0/discretefit/tests/testthat/test-results.R | 99 +++- discretefit-0.1.0/discretefit/tests/testthat/test-stats.R |only discretefit-0.1.0/discretefit/vignettes/package_introduction.Rmd | 113 ++-- 33 files changed, 830 insertions(+), 547 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC)
as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations,
and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring.
GPC compare two groups of observations (intervention vs. control group)
regarding several prioritized endpoints to estimate the probability that a random observation drawn from
one group performs better than a random observation drawn from the other group (Mann-Whitney parameter).
The net benefit and win ratio statistics,
i.e. the difference and ratio between the probabilities relative to the intervention and control groups,
can then also be estimated. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>),
non-parametric bootstrap, or permutations.
The software enables the use of thresholds of minimal importance difference,
stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [ctb],
Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 2.3.0 dated 2021-04-23 and 2.3.5 dated 2021-10-25
DESCRIPTION | 26 MD5 | 259 ++- NAMESPACE | 143 +- NEWS | 388 +++-- R/0-onLoad.R | 16 R/1-setGeneric.R | 124 - R/BuyseMultComp.R |only R/BuyseTTEM.R | 1290 +++++++++---------- R/BuyseTest-Peron.R | 628 ++++----- R/BuyseTest-check.R | 968 +++++++------- R/BuyseTest-inference.R | 772 ++++------- R/BuyseTest-initialization.R | 1419 ++++++++++----------- R/BuyseTest-package.R | 101 - R/BuyseTest-print.R | 324 ++-- R/BuyseTest.R | 1355 ++++++++++---------- R/BuyseTest.options.R | 208 +-- R/PairScore.R | 106 - R/RcppExports.R | 415 +++--- R/S4-BuysePower-show.R | 88 - R/S4-BuysePower-summary.R | 402 +++--- R/S4-BuysePower.R | 134 +- R/S4-BuyseTest-coef.R | 357 +++-- R/S4-BuyseTest-confint.R | 1604 ++++++++++++------------ R/S4-BuyseTest-get.R | 1387 ++++++++++---------- R/S4-BuyseTest-sensitivity.R | 951 +++++++------- R/S4-BuyseTest-show.R | 98 - R/S4-BuyseTest-summary.R | 1064 ++++++++-------- R/S4-BuyseTest.R | 564 ++++---- R/S4-BuyseTest.options.R | 436 +++--- R/auc.R | 644 +++++---- R/brier.R |only R/constStrata.R | 176 +- R/discreteRoot.R | 532 ++++---- R/iid.prodlim.R | 372 ++--- R/normexp.R | 416 +++--- R/performance.R |only R/powerBuyseTest.R | 1049 ++++++++------- R/predict.logit.R |only R/simBuyseTest.R | 1076 ++++++++-------- R/simCompetingRisks.R | 282 ++-- R/valid.R | 950 +++++++------- build/vignette.rds |binary inst/CITATION | 96 - inst/doc-Wilcoxon |only inst/doc/overview.pdf |binary inst/doc/overview.pdf.asis | 10 inst/doc/wilcoxonTest.pdf |only inst/doc/wilcoxonTest.pdf.asis |only inst/optim-iid/FCT_calcOnePair.h | 1724 +++++++++++++------------- man/BuyseMultComp.Rd |only man/BuyseTTEM.Rd | 148 +- man/BuyseTest-package.Rd | 82 - man/BuyseTest.Rd | 581 ++++---- man/BuyseTest.options-class.Rd | 36 man/BuyseTest.options-methods.Rd | 44 man/BuyseTest.options.Rd | 67 - man/GPC_cpp.Rd | 340 ++--- man/S4BuysePower-class.Rd | 36 man/S4BuysePower-show.Rd | 50 man/S4BuysePower-summary.Rd | 118 - man/S4BuyseTest-class.Rd | 36 man/S4BuyseTest-coef.Rd | 106 - man/S4BuyseTest-confint.Rd | 228 +-- man/S4BuyseTest-getCount.Rd | 56 man/S4BuyseTest-getIid.Rd | 115 - man/S4BuyseTest-getPairScore.Rd | 286 ++-- man/S4BuyseTest-getPseudovalue.Rd | 138 +- man/S4BuyseTest-getSurvival.Rd | 116 - man/S4BuyseTest-sensitivity.Rd | 176 +- man/S4BuyseTest-show.Rd | 50 man/S4BuyseTest-summary.Rd | 287 ++-- man/auc.Rd | 152 +- man/autoplot.sensitivity.Rd | 100 - man/boot2pvalue.Rd | 170 +- man/calcIntegralSurv2_cpp.Rd | 94 - man/coef.BuyseTestAuc.Rd | 38 man/coef.BuyseTestBrier.Rd |only man/confint.BuyseTestAuc.Rd | 38 man/confint.BuyseTestBrier.Rd |only man/constStrata.Rd | 120 - man/discreteRoot.Rd | 62 man/dot-calcIntegralCif_cpp.Rd | 98 - man/dot-calcIntegralSurv_cpp.Rd | 84 - man/dot-colCenter_cpp.Rd | 38 man/dot-colMultiply_cpp.Rd | 38 man/dot-colScale_cpp.Rd | 38 man/dot-information.logit.Rd |only man/dot-rowCenter_cpp.Rd | 38 man/dot-rowCumProd_cpp.Rd | 34 man/dot-rowCumSum_cpp.Rd | 34 man/dot-rowMultiply_cpp.Rd | 38 man/dot-rowScale_cpp.Rd | 38 man/dot-score.logit.Rd |only man/dot-vcov.logit.Rd |only man/iid.BuyseTestAuc.Rd |only man/iid.BuyseTestBrier.Rd |only man/iid.prodlim.Rd | 82 - man/internal-initialization.Rd | 242 +-- man/internal-print.Rd | 82 - man/performance.Rd |only man/pnormexp.Rd | 58 man/pnormweibull.Rd | 64 man/powerBuyseTest.Rd | 204 +-- man/predict.BuyseTTEM.Rd | 52 man/predict.logit.Rd |only man/qnormexp.Rd | 46 man/qnormweibull.Rd | 76 - man/simCompetingRisks.Rd | 208 +-- man/simulation.Rd | 292 ++-- man/testArgs.Rd | 87 - man/validFCTs.Rd | 310 ++-- src/FCT_buyseTest.cpp | 702 +++++----- src/FCT_calcAllPairs.h | 58 src/FCT_calcOnePair.h | 33 src/FCT_calcStatistic.h | 357 +++-- src/RcppExports.cpp | 18 tests/testthat.R | 83 - tests/testthat/test-BuysePower.R | 396 +++-- tests/testthat/test-BuyseTTEM.R | 504 +++---- tests/testthat/test-BuyseTest-CR.R | 466 +++---- tests/testthat/test-BuyseTest-PairScore.R | 238 +-- tests/testthat/test-BuyseTest-Pairs.R | 1196 +++++++++--------- tests/testthat/test-BuyseTest-checkValues.R | 1085 ++++++++-------- tests/testthat/test-BuyseTest-correctionTTE.R | 446 +++--- tests/testthat/test-BuyseTest-engine.R | 218 +-- tests/testthat/test-BuyseTest-iid.R | 1519 ++++++++++++---------- tests/testthat/test-BuyseTest-neutralAsUnif.R | 204 +-- tests/testthat/test-BuyseTest-operator.R | 198 +- tests/testthat/test-BuyseTest-previousBug.R | 1015 +++++++-------- tests/testthat/test-BuyseTest-resampling.R | 1198 +++++++++--------- tests/testthat/test-auc.R | 218 ++- tests/testthat/test-initSurvival.R | 438 +++--- tests/testthat/test-initThreshold.R | 168 +- tests/testthat/test-otherPackages.R | 296 ++-- vignettes/overview.pdf.asis | 10 vignettes/vignette_CR.Rmd | 146 +- vignettes/wilcoxonTest.pdf.asis |only 137 files changed, 20597 insertions(+), 19718 deletions(-)
Title: Bayesian Time-Stratified Population Analysis
Description: Provides advanced Bayesian methods to estimate
abundance and run-timing from temporally-stratified
Petersen mark-recapture experiments. Methods include
hierarchical modelling of the capture probabilities
and spline smoothing of the daily run size. Theory
described in Bonner and Schwarz (2011)
<doi:10.1111/j.1541-0420.2011.01599.x>.
Author: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com> and
Simon J Bonner <sbonner6@uwo.ca>
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between BTSPAS versions 2021.11.1 dated 2021-10-11 and 2021.11.2 dated 2021-10-25
DESCRIPTION | 8 MD5 | 50 +-- NEWS.md | 5 R/RunTime.R | 2 R/TimeStratPetersenDiagErrorWHChinook2_fit.R | 17 - R/TimeStratPetersenDiagErrorWHChinook_fit.R | 78 ++--- R/TimeStratPetersenDiagErrorWHSteel_fit.R | 53 +-- R/TimeStratPetersenDiagError_fit.R | 67 +--- R/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.R | 77 ++-- R/TimeStratPetersenNonDiagErrorNP_fit.R | 75 +--- R/TimeStratPetersenNonDiagError_fit.R | 71 +--- R/plot_logit.R | 22 - R/zzz.R | 2 build/partial.rdb |binary inst/doc/a-Diagonal-model.html | 309 +++++++++----------- inst/doc/b-Diagonal-model-with-multiple-ages.html | 38 +- inst/doc/c-Non-diagonal-model.html | 34 +- inst/doc/d-Non-diagonal-with-fall-back-model.html | 24 - inst/doc/e-Bias-from-incomplete-sampling.html | 32 +- inst/doc/f-Interpolating-run-earlier-and-later.html | 12 man/TimeStratPetersenDiagErrorWHChinook_fit.Rd | 9 man/TimeStratPetersenDiagErrorWHSteel_fit.Rd | 6 man/TimeStratPetersenDiagError_fit.Rd | 10 man/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.Rd | 6 man/TimeStratPetersenNonDiagErrorNP_fit.Rd | 6 man/TimeStratPetersenNonDiagError_fit.Rd | 6 26 files changed, 500 insertions(+), 519 deletions(-)
Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between maotai versions 0.2.1 dated 2021-09-21 and 0.2.2 dated 2021-10-25
maotai-0.2.1/maotai/R/aux_hiddenDAS.R |only maotai-0.2.1/maotai/R/aux_hiddenR.R |only maotai-0.2.2/maotai/DESCRIPTION | 6 - maotai-0.2.2/maotai/MD5 | 20 ++--- maotai-0.2.2/maotai/NEWS.md | 6 + maotai-0.2.2/maotai/R/RcppExports.R | 12 +++ maotai-0.2.2/maotai/R/aux_hidden_compute.R |only maotai-0.2.2/maotai/R/aux_hidden_dist.R |only maotai-0.2.2/maotai/R/aux_hidden_operation.R |only maotai-0.2.2/maotai/build/partial.rdb |binary maotai-0.2.2/maotai/src/RcppExports.cpp | 47 +++++++++++ maotai-0.2.2/maotai/src/cpp_casket.cpp | 2 maotai-0.2.2/maotai/src/cpp_smacof.cpp |only maotai-0.2.2/maotai/src/src_computations.cpp | 107 ++++++++++++++++++++++++++- 14 files changed, 184 insertions(+), 16 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. (2014) <doi:10.4172/2155-6180.1000189> "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 10.5-0 dated 2020-12-11 and 10.5-1 dated 2021-10-25
DESCRIPTION | 12 MD5 | 30 R/mma.r | 17 build/vignette.rds |binary inst/doc/MMAvignette.R | 44 inst/doc/MMAvignette.html | 1026 +++++----- vignettes/MMAvignette_files/figure-html/unnamed-chunk-10-2.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-10-3.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-13-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-17-2.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-18-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-19-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-22-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-23-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-23-4.png |binary 16 files changed, 582 insertions(+), 547 deletions(-)
Title: Computing Variances and Covariances, Visualization and Missing
Data Solution for Multivariate Meta-Analysis
Description: Collection of functions to compute covariances for different effect sizes, data visualization, and single and multiple imputations for missing data. Effect sizes include correlation (r), mean difference (MD), standardized mean difference (SMD), log odds ratio (logOR), log risk ratio (logRR), and risk difference (RD).
Author: Min Lu <m.lu6@umiami.edu>
Maintainer: Min Lu <m.lu6@umiami.edu>
Diff between metavcov versions 2.1.1 dated 2021-10-07 and 2.1.2 dated 2021-10-25
DESCRIPTION | 12 +- MD5 | 52 +++++----- NAMESPACE | 11 +- R/lgOR.vcov.R | 24 +++- R/lgRR.vcov.R | 22 +++- R/md.vcov.R | 18 ++- R/metafixed.R | 3 R/metami.R | 47 ++++++--- R/mix.vcov.R | 238 ++++++++++++++++++++++++++++++++++++------------ R/plotCI.R | 25 +++-- R/r.vcov.R | 33 ++++-- R/rd.vcov.R | 22 +++- R/smd.vcov.R | 31 ++++-- inst/NEWS | 57 +++++++---- man/lgor_lgrr.Rd | 7 - man/lgor_rd.Rd | 7 - man/lgrr_rd.Rd | 7 - man/md_lgor.Rd | 5 - man/md_lgrr.Rd | 5 - man/md_rd.Rd | 5 - man/md_smd.Rd | 5 - man/metavcov-package.Rd | 2 man/r.vcov.Rd | 2 man/smd.vcov.Rd | 13 +- man/smd_lgor.Rd | 7 - man/smd_lgrr.Rd | 7 - man/smd_rd.Rd | 7 - 27 files changed, 436 insertions(+), 238 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.0.5 dated 2021-10-05 and 4.0.6 dated 2021-10-25
DESCRIPTION | 10 - MD5 | 82 +++++---- NAMESPACE | 3 NEWS | 38 ++++ R/BarChart.R | 38 ++-- R/Plot.R | 43 ++++- R/Regression.R | 10 - R/SummaryStats.R | 14 - R/interact.R |only R/pivot.R | 75 ++++---- R/reg.zKfold.R | 4 R/zzz.R | 11 + inst/doc/BarChart.R | 2 inst/doc/BarChart.Rmd | 11 + inst/doc/BarChart.html | 23 +- inst/doc/Customize.html | 4 inst/doc/Extract.html | 22 +- inst/doc/Histogram.Rmd | 10 + inst/doc/Histogram.html | 9 - inst/doc/Means.R | 2 inst/doc/Means.Rmd | 4 inst/doc/Means.html | 34 ++-- inst/doc/Plot.Rmd | 19 ++ inst/doc/Plot.html | 69 ++++---- inst/doc/Regression.html | 50 ++--- inst/doc/pivot.R | 7 inst/doc/pivot.Rmd | 23 +- inst/doc/pivot.html | 397 +++++++++++++++++++++++------------------------ inst/doc/utilities.html | 18 +- inst/shiny_examples |only man/BarChart.Rd | 2 man/Plot.Rd | 2 man/interact.Rd |only man/pivot.Rd | 2 vignettes/BarChart.Rmd | 11 + vignettes/Histogram.Rmd | 10 + vignettes/Means.Rmd | 4 vignettes/Plot.Rmd | 19 ++ vignettes/pivot.Rmd | 23 +- 39 files changed, 633 insertions(+), 472 deletions(-)
Title: The Hyperdirichlet Distribution, Mark 2
Description: A suite of routines for the hyperdirichlet distribution; supersedes the 'hyperdirichlet' package.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between hyper2 versions 2.0-0 dated 2021-03-04 and 2.0-1 dated 2021-10-25
hyper2-2.0-0/hyper2/data/formula1.R |only hyper2-2.0-0/hyper2/inst/NBA.Rmd |only hyper2-2.0-0/hyper2/inst/NBA.txt |only hyper2-2.0-0/hyper2/inst/T20.Rmd |only hyper2-2.0-0/hyper2/inst/T20.txt |only hyper2-2.0-0/hyper2/inst/T20_analysis.R |only hyper2-2.0-0/hyper2/inst/chess.bib |only hyper2-2.0-0/hyper2/inst/chess.txt |only hyper2-2.0-0/hyper2/inst/collusion_chess_draws.Rnw |only hyper2-2.0-0/hyper2/inst/collusion_curacao1962.R |only hyper2-2.0-0/hyper2/inst/collusion_detection.R |only hyper2-2.0-0/hyper2/inst/cook.Rmd |only hyper2-2.0-0/hyper2/inst/cook_repeated.Rmd |only hyper2-2.0-0/hyper2/inst/cooking_weekly.txt |only hyper2-2.0-0/hyper2/inst/counterstrike.R |only hyper2-2.0-0/hyper2/inst/counterstrike.Rmd |only hyper2-2.0-0/hyper2/inst/counterstrike_random.R |only hyper2-2.0-0/hyper2/inst/curacao1962.txt |only hyper2-2.0-0/hyper2/inst/curacao1962_candidates.txt |only hyper2-2.0-0/hyper2/inst/curacao1962_individual_games.R |only hyper2-2.0-0/hyper2/inst/curacao1962_threeplayers.R |only hyper2-2.0-0/hyper2/inst/curacao1962_threeplayers_rest_monster.Rmd |only hyper2-2.0-0/hyper2/inst/curling.Rmd |only hyper2-2.0-0/hyper2/inst/curling.txt |only hyper2-2.0-0/hyper2/inst/eurovision.Rmd |only hyper2-2.0-0/hyper2/inst/eurovision.txt |only hyper2-2.0-0/hyper2/inst/f1points.Rmd |only hyper2-2.0-0/hyper2/inst/f1points_Omaker.R |only hyper2-2.0-0/hyper2/inst/formula1.Rmd |only hyper2-2.0-0/hyper2/inst/formula1_1995.txt |only hyper2-2.0-0/hyper2/inst/formula1_1996.txt |only hyper2-2.0-0/hyper2/inst/formula1_1997.txt |only hyper2-2.0-0/hyper2/inst/formula1_1998.txt |only hyper2-2.0-0/hyper2/inst/formula1_1999.txt |only hyper2-2.0-0/hyper2/inst/formula1_2000.txt |only hyper2-2.0-0/hyper2/inst/formula1_2001.txt |only hyper2-2.0-0/hyper2/inst/formula1_2002.txt |only hyper2-2.0-0/hyper2/inst/formula1_2003.txt |only hyper2-2.0-0/hyper2/inst/formula1_2004.txt |only hyper2-2.0-0/hyper2/inst/formula1_2005.txt |only hyper2-2.0-0/hyper2/inst/formula1_2006.txt |only hyper2-2.0-0/hyper2/inst/formula1_2007.txt |only hyper2-2.0-0/hyper2/inst/formula1_2008.txt |only hyper2-2.0-0/hyper2/inst/formula1_2009.txt |only hyper2-2.0-0/hyper2/inst/formula1_2010.txt |only hyper2-2.0-0/hyper2/inst/formula1_2011.txt |only hyper2-2.0-0/hyper2/inst/formula1_2012.txt |only hyper2-2.0-0/hyper2/inst/formula1_2013.txt |only hyper2-2.0-0/hyper2/inst/formula1_2014.txt |only hyper2-2.0-0/hyper2/inst/formula1_2015.txt |only hyper2-2.0-0/hyper2/inst/formula1_2016.txt |only hyper2-2.0-0/hyper2/inst/formula1_2017.txt |only hyper2-2.0-0/hyper2/inst/formula1_2018.txt |only hyper2-2.0-0/hyper2/inst/formula1_2019.txt |only hyper2-2.0-0/hyper2/inst/formula1_allyears.R |only hyper2-2.0-0/hyper2/inst/formula1_allyears.Rmd |only hyper2-2.0-0/hyper2/inst/formula1_conditions.txt |only hyper2-2.0-0/hyper2/inst/formula1_points.Rmd |only hyper2-2.0-0/hyper2/inst/formula1_top9.Rmd |only hyper2-2.0-0/hyper2/inst/gbbo_series10.R |only hyper2-2.0-0/hyper2/inst/gbbo_series9.R |only hyper2-2.0-0/hyper2/inst/gradient.Rmd |only hyper2-2.0-0/hyper2/inst/handover.Rmd |only hyper2-2.0-0/hyper2/inst/handover.txt |only hyper2-2.0-0/hyper2/inst/home_advantage.Rmd |only hyper2-2.0-0/hyper2/inst/icons.Rmd |only hyper2-2.0-0/hyper2/inst/icons.txt |only hyper2-2.0-0/hyper2/inst/interzonal.Rmd |only hyper2-2.0-0/hyper2/inst/jester-data-3.csv |only hyper2-2.0-0/hyper2/inst/jester.Rmd |only hyper2-2.0-0/hyper2/inst/karate.Rmd |only hyper2-2.0-0/hyper2/inst/karate.txt |only hyper2-2.0-0/hyper2/inst/kka.Rmd |only hyper2-2.0-0/hyper2/inst/laura_confidence_interval.R |only hyper2-2.0-0/hyper2/inst/loser.Rmd |only hyper2-2.0-0/hyper2/inst/masterchef.Rmd |only hyper2-2.0-0/hyper2/inst/masterchef_series6_allrounds.R |only hyper2-2.0-0/hyper2/inst/moto.Rmd |only hyper2-2.0-0/hyper2/inst/motoGP_2019.txt |only hyper2-2.0-0/hyper2/inst/notthewinner.Rmd |only hyper2-2.0-0/hyper2/inst/order.Rmd |only hyper2-2.0-0/hyper2/inst/ordertable_to_ranktable.Rmd |only hyper2-2.0-0/hyper2/inst/ordertrans.Rmd |only hyper2-2.0-0/hyper2/inst/pentathlon.Rmd |only hyper2-2.0-0/hyper2/inst/pentathlon.txt |only hyper2-2.0-0/hyper2/inst/powerboat.Rmd |only hyper2-2.0-0/hyper2/inst/powerboat.txt |only hyper2-2.0-0/hyper2/inst/red_bus_blue_bus.Rmd |only hyper2-2.0-0/hyper2/inst/retain.Rmd |only hyper2-2.0-0/hyper2/inst/rock_paper_scissors_monster.Rmd |only hyper2-2.0-0/hyper2/inst/rowing.Rmd |only hyper2-2.0-0/hyper2/inst/rowing.txt |only hyper2-2.0-0/hyper2/inst/rowing_minimal.txt |only hyper2-2.0-0/hyper2/inst/skating.Rmd |only hyper2-2.0-0/hyper2/inst/skating.txt |only hyper2-2.0-0/hyper2/inst/soling.Rmd |only hyper2-2.0-0/hyper2/inst/soling.txt |only hyper2-2.0-0/hyper2/inst/soling_qf.txt |only hyper2-2.0-0/hyper2/inst/soling_rr1.txt |only hyper2-2.0-0/hyper2/inst/soling_rr2.txt |only hyper2-2.0-0/hyper2/inst/stockholm1962.txt |only hyper2-2.0-0/hyper2/inst/stockholm1962_matches.txt |only hyper2-2.0-0/hyper2/inst/table_tennis_serve.Rmd |only hyper2-2.0-0/hyper2/inst/tennis.Rmd |only hyper2-2.0-0/hyper2/inst/universities.Rmd |only hyper2-2.0-0/hyper2/inst/universities.txt |only hyper2-2.0-0/hyper2/inst/volleyball.Rmd |only hyper2-2.0-0/hyper2/inst/volleyball.txt |only hyper2-2.0-0/hyper2/inst/volvo.Rmd |only hyper2-2.0-0/hyper2/inst/volvo.txt |only hyper2-2.0-0/hyper2/inst/wikipedia.txt |only hyper2-2.0-0/hyper2/inst/wikipedia_refdesk.txt |only hyper2-2.0-0/hyper2/inst/zurich1953_candidates.txt |only hyper2-2.0-1/hyper2/DESCRIPTION | 12 hyper2-2.0-1/hyper2/MD5 | 287 +++------- hyper2-2.0-1/hyper2/NAMESPACE | 7 hyper2-2.0-1/hyper2/R/hyper2.R | 144 +++-- hyper2-2.0-1/hyper2/R/keep.R | 10 hyper2-2.0-1/hyper2/R/psubs.R |only hyper2-2.0-1/hyper2/R/tests.R | 43 + hyper2-2.0-1/hyper2/build/hyper2.pdf |binary hyper2-2.0-1/hyper2/build/partial.rdb |binary hyper2-2.0-1/hyper2/build/vignette.rds |binary hyper2-2.0-1/hyper2/data/NBA.rda |binary hyper2-2.0-1/hyper2/data/T20.rda |binary hyper2-2.0-1/hyper2/data/chess.rda |binary hyper2-2.0-1/hyper2/data/counterstrike.rda |binary hyper2-2.0-1/hyper2/data/curling.rda |binary hyper2-2.0-1/hyper2/data/eurodance.rda |only hyper2-2.0-1/hyper2/data/eurovision.rda |binary hyper2-2.0-1/hyper2/data/formula1.rda |only hyper2-2.0-1/hyper2/data/handover.rda |binary hyper2-2.0-1/hyper2/data/icons.rda |binary hyper2-2.0-1/hyper2/data/interzonal.rda |binary hyper2-2.0-1/hyper2/data/jester.rda |binary hyper2-2.0-1/hyper2/data/karate.rda |binary hyper2-2.0-1/hyper2/data/kka.rda |binary hyper2-2.0-1/hyper2/data/masterchef.rda |binary hyper2-2.0-1/hyper2/data/moto.rda |binary hyper2-2.0-1/hyper2/data/pentathlon.rda |binary hyper2-2.0-1/hyper2/data/powerboat.rda |binary hyper2-2.0-1/hyper2/data/rowing.rda |binary hyper2-2.0-1/hyper2/data/skating.rda |binary hyper2-2.0-1/hyper2/data/soling.rda |binary hyper2-2.0-1/hyper2/data/surfing.rda |only hyper2-2.0-1/hyper2/data/table_tennis.rda |binary hyper2-2.0-1/hyper2/data/tennis.rda |binary hyper2-2.0-1/hyper2/data/universities.rda |binary hyper2-2.0-1/hyper2/data/volleyball.rda |binary hyper2-2.0-1/hyper2/data/volvo.rda |binary hyper2-2.0-1/hyper2/inst/CITATION | 4 hyper2-2.0-1/hyper2/inst/doc/hyper2.R | 6 hyper2-2.0-1/hyper2/inst/doc/hyper2.Rnw | 46 - hyper2-2.0-1/hyper2/inst/doc/hyper2.pdf |binary hyper2-2.0-1/hyper2/inst/doc/icons.html | 29 - hyper2-2.0-1/hyper2/inst/doc/integration.R | 53 - hyper2-2.0-1/hyper2/inst/doc/integration.Rnw | 52 + hyper2-2.0-1/hyper2/inst/doc/integration.pdf |binary hyper2-2.0-1/hyper2/man/B.Rd | 13 hyper2-2.0-1/hyper2/man/T20.Rd | 4 hyper2-2.0-1/hyper2/man/as.ordertable.Rd | 4 hyper2-2.0-1/hyper2/man/chess.Rd | 2 hyper2-2.0-1/hyper2/man/consistency.Rd |only hyper2-2.0-1/hyper2/man/counterstrike.Rd | 5 hyper2-2.0-1/hyper2/man/dirichlet.Rd | 30 - hyper2-2.0-1/hyper2/man/eurodance.Rd |only hyper2-2.0-1/hyper2/man/eurovision.Rd | 1 hyper2-2.0-1/hyper2/man/figures |only hyper2-2.0-1/hyper2/man/ggrl.Rd | 28 hyper2-2.0-1/hyper2/man/gradient.Rd | 18 hyper2-2.0-1/hyper2/man/head.hyper2.Rd | 9 hyper2-2.0-1/hyper2/man/hyper2-package.Rd | 2 hyper2-2.0-1/hyper2/man/hyper2.Rd | 25 hyper2-2.0-1/hyper2/man/icons.Rd | 2 hyper2-2.0-1/hyper2/man/interzonal.Rd | 2 hyper2-2.0-1/hyper2/man/jester.Rd | 3 hyper2-2.0-1/hyper2/man/keep.Rd | 1 hyper2-2.0-1/hyper2/man/loglik.Rd | 60 +- hyper2-2.0-1/hyper2/man/masterchef.Rd | 6 hyper2-2.0-1/hyper2/man/matrix2supp.Rd | 1 hyper2-2.0-1/hyper2/man/maxp.Rd | 12 hyper2-2.0-1/hyper2/man/mult_grid.Rd | 2 hyper2-2.0-1/hyper2/man/ordertable.Rd | 4 hyper2-2.0-1/hyper2/man/ordertable2supp.Rd | 4 hyper2-2.0-1/hyper2/man/ordertrans.Rd | 15 hyper2-2.0-1/hyper2/man/powerboat.Rd | 6 hyper2-2.0-1/hyper2/man/profile.Rd | 8 hyper2-2.0-1/hyper2/man/psubs.Rd |only hyper2-2.0-1/hyper2/man/pwa.Rd | 24 hyper2-2.0-1/hyper2/man/ranktable.Rd | 3 hyper2-2.0-1/hyper2/man/rhyper2.Rd | 4 hyper2-2.0-1/hyper2/man/rp.Rd | 3 hyper2-2.0-1/hyper2/man/rrank.Rd | 15 hyper2-2.0-1/hyper2/man/skating.Rd | 2 hyper2-2.0-1/hyper2/man/suplist.Rd | 5 hyper2-2.0-1/hyper2/man/surfing.Rd |only hyper2-2.0-1/hyper2/man/tennis.Rd | 13 hyper2-2.0-1/hyper2/man/tests.Rd | 36 - hyper2-2.0-1/hyper2/man/tidy.Rd | 1 hyper2-2.0-1/hyper2/man/universities.Rd | 6 hyper2-2.0-1/hyper2/man/volleyball.Rd | 2 hyper2-2.0-1/hyper2/man/zapweak.Rd | 8 hyper2-2.0-1/hyper2/man/zipf.Rd |only hyper2-2.0-1/hyper2/vignettes/hyper2.Rnw | 46 - hyper2-2.0-1/hyper2/vignettes/hyper2.bib | 8 hyper2-2.0-1/hyper2/vignettes/integration.Rnw | 52 + 206 files changed, 642 insertions(+), 546 deletions(-)
Title: Convert Decimals to Fractions
Description: Provides functions for converting decimals to a
matrix of numerators and denominators or a character vector of
fractions. Supports mixed or improper fractions, finding common
denominators for vectors of fractions, limiting denominators to powers
of ten, and limiting denominators to a maximum value. Also includes
helper functions for finding the least common multiple and greatest
common divisor for a vector of integers. Implemented using C++ for
maximum speed.
Author: Alexander Rossell Hayes [aut, cre, cph]
(<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between fracture versions 0.1.3 dated 2021-05-25 and 0.2.0 dated 2021-10-25
DESCRIPTION | 11 MD5 | 31 +- NAMESPACE | 38 +-- NEWS.md | 13 + R/RcppExports.R | 30 +- R/check_dots_empty0.R |only R/frac_mat.R | 56 +++- R/fracture.R | 13 - README.md | 378 ++++++++++++++++---------------- man/frac_mat.Rd | 8 man/fracture-package.Rd | 9 man/fracture.Rd | 8 src/RcppExports.cpp | 5 tests/testthat/_snaps |only tests/testthat/test-check_dots_empty0.R |only tests/testthat/test-frac_mat.R | 4 tests/testthat/test-frac_style.R | 35 -- tests/testthat/test-fracture.R | 36 ++- 18 files changed, 375 insertions(+), 300 deletions(-)