Title: Divisia Monetary Aggregates Index
Description: Functions to calculate Divisia monetary aggregates index as given in Barnett, W. A. (1980) (<DOI:10.1016/0304-4076(80)90070-6>).
Author: Muhammad Yaseen [aut, cre],
Ahmad Nadeem [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between dmai versions 0.4.0 dated 2019-05-18 and 0.5.0 dated 2024-03-23
DESCRIPTION | 16 +++++++--------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/dmaiIntro-package.R | 1 - README.md | 8 ++++---- man/dmai.Rd | 3 +-- man/dmaiIntro.Rd | 2 -- 7 files changed, 22 insertions(+), 24 deletions(-)
Title: Useful Libraries for Building a Java Based GUI under R
Description: Useful libraries for building a Java based GUI under R are provided.
Author: Kornelius Rohmeyer , see COPYRIGHTS file for the authors of the java libraries
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between CommonJavaJars versions 1.0-6 dated 2018-07-09 and 1.1-0 dated 2024-03-23
CommonJavaJars-1.0-6/CommonJavaJars/R/showGuide.R |only CommonJavaJars-1.0-6/CommonJavaJars/inst/java/log4j-1.2.17.jar |only CommonJavaJars-1.0-6/CommonJavaJars/man/showGuide.Rd |only CommonJavaJars-1.1-0/CommonJavaJars/DESCRIPTION | 9 ++- CommonJavaJars-1.1-0/CommonJavaJars/MD5 | 19 ++++--- CommonJavaJars-1.1-0/CommonJavaJars/NAMESPACE | 1 CommonJavaJars-1.1-0/CommonJavaJars/build/vignette.rds |binary CommonJavaJars-1.1-0/CommonJavaJars/inst/COPYRIGHTS | 10 ++-- CommonJavaJars-1.1-0/CommonJavaJars/inst/NOTICE.txt |only CommonJavaJars-1.1-0/CommonJavaJars/inst/doc/CommonJavaJars.pdf |binary CommonJavaJars-1.1-0/CommonJavaJars/inst/java/log4j-1.2-api-2.23.1.jar |only CommonJavaJars-1.1-0/CommonJavaJars/inst/java/log4j-api-2.23.1.jar |only CommonJavaJars-1.1-0/CommonJavaJars/inst/java/log4j-core-2.23.1.jar |only CommonJavaJars-1.1-0/CommonJavaJars/man/CommonJavaJars-package.Rd | 25 ++++------ 14 files changed, 32 insertions(+), 32 deletions(-)
More information about CommonJavaJars at CRAN
Permanent link
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Description: Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
and the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>. Software
announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.
Author: Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
John Rhodes [aut, cre]
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Diff between MSCquartets versions 1.3.2 dated 2023-10-27 and 2.0 dated 2024-03-23
MSCquartets-1.3.2/MSCquartets/R/MSCquartets.R |only MSCquartets-2.0/MSCquartets/DESCRIPTION | 33 ++++--- MSCquartets-2.0/MSCquartets/LICENSE | 2 MSCquartets-2.0/MSCquartets/MD5 | 62 ++++++++------ MSCquartets-2.0/MSCquartets/NAMESPACE | 33 +++++++ MSCquartets-2.0/MSCquartets/R/MSCquartets-package.R |only MSCquartets-2.0/MSCquartets/R/NANUQ.R | 5 - MSCquartets-2.0/MSCquartets/R/ParallelTableCpp.R | 3 MSCquartets-2.0/MSCquartets/R/QuartetTally.R | 8 + MSCquartets-2.0/MSCquartets/R/RcppExports.R | 60 ++++++++++++- MSCquartets-2.0/MSCquartets/R/TreeOfBlobs.R |only MSCquartets-2.0/MSCquartets/R/TreeQuartetHypTest.R | 4 MSCquartets-2.0/MSCquartets/build/partial.rdb |binary MSCquartets-2.0/MSCquartets/inst/REFERENCES.bib | 8 - MSCquartets-2.0/MSCquartets/man/BQinference.Rd |only MSCquartets-2.0/MSCquartets/man/MSCquartets-package.Rd | 18 +++- MSCquartets-2.0/MSCquartets/man/T1density.Rd | 2 MSCquartets-2.0/MSCquartets/man/T3density.Rd | 2 MSCquartets-2.0/MSCquartets/man/TINNIK.Rd |only MSCquartets-2.0/MSCquartets/man/TINNIKdist.Rd |only MSCquartets-2.0/MSCquartets/man/collapseEdges.Rd |only MSCquartets-2.0/MSCquartets/man/compatibleSplits.Rd |only MSCquartets-2.0/MSCquartets/man/cutDensity.Rd |only MSCquartets-2.0/MSCquartets/man/dataGeneTreeSample.Rd | 2 MSCquartets-2.0/MSCquartets/man/dataHeliconiusMartin.Rd | 2 MSCquartets-2.0/MSCquartets/man/dataYeastRokas.Rd | 2 MSCquartets-2.0/MSCquartets/man/initBquartets.Rd |only MSCquartets-2.0/MSCquartets/man/nodeGroups.Rd |only MSCquartets-2.0/MSCquartets/man/pTableYeastRokas.Rd | 5 - MSCquartets-2.0/MSCquartets/man/quartetBTinferencePlot.Rd |only MSCquartets-2.0/MSCquartets/man/quartetCutMLE.Rd |only MSCquartets-2.0/MSCquartets/man/quartetCutTest.Rd |only MSCquartets-2.0/MSCquartets/man/quartetCutTestInd.Rd |only MSCquartets-2.0/MSCquartets/man/quartetTable.Rd | 10 ++ MSCquartets-2.0/MSCquartets/man/quartetTallyCpp.Rd | 12 ++ MSCquartets-2.0/MSCquartets/man/sortQuartetTableRows.Rd | 2 MSCquartets-2.0/MSCquartets/man/treeFromSplits.Rd |only MSCquartets-2.0/MSCquartets/man/treeOfBlobs.Rd |only MSCquartets-2.0/MSCquartets/src/QuartetTallyCpp.cpp | 23 ++++- MSCquartets-2.0/MSCquartets/src/RcppExports.cpp | 48 +++++++++- MSCquartets-2.0/MSCquartets/src/TINNIKcpp.cpp |only 41 files changed, 267 insertions(+), 79 deletions(-)
Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end
is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
the GNU R language and environment for statistical computing and graphics.
While R can be used in batch mode, the r binary adds full support for
both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path
expression as the first line in scripts) as well as command-line use in
standard Unix pipelines. In other words, r provides the R language without
the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between littler versions 0.3.19 dated 2023-12-17 and 0.3.20 dated 2024-03-23
ChangeLog | 99 +++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++-- MD5 | 31 +++++++------ R/init.R | 19 ++------ build/vignette.rds |binary configure | 18 +++---- configure.ac | 2 inst/NEWS.Rd | 26 +++++++++++ inst/examples/ciw.r |only inst/examples/doi2bib.r |only inst/examples/installDeps2.r |only inst/examples/installRub.r | 4 - inst/examples/rcc.r | 4 - inst/examples/tt.r | 11 +++- inst/examples/tttf.r | 16 +++++- inst/examples/tttl.r | 12 +++-- src/Makevars.in | 2 src/littler.c | 8 ++- 18 files changed, 204 insertions(+), 58 deletions(-)
Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation,
dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via
bootstrap and recursive sandwich estimation. Estimation and
inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv).
Extension to continuous treatment variables. Wallace et al. (2017)
<DOI:10.18637/jss.v080.i02>; Simoneau et al. (2020)
<DOI:10.1080/00949655.2020.1793341>.
Author: Michael Wallace, Erica E M Moodie, David A Stephens, Gabrielle Simoneau, Shannon T. Holloway and Juliana Schulz
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DTRreg versions 2.1 dated 2024-03-14 and 2.2 dated 2024-03-23
DESCRIPTION | 10 MD5 | 14 - NEWS | 4 R/DTRreg.R | 4 R/DWsurv.R | 4 R/dtrProcedure.R | 4 R/utils.R | 2 man/DWSurv.Rd | 660 +++++++++++++++++++++++++++---------------------------- 8 files changed, 355 insertions(+), 347 deletions(-)
Title: Tools to Download and Work with USDA Cropscape Data
Description: Downloads USDA National Agricultural Statistics Service (NASS)
cropscape data for a specified state. Utilities for fips, abbreviation,
and name conversion are also provided. Full functionality requires an
internet connection, but data sets can be cached for later off-line use.
Author: Jonathan Lisic [cre],
Lu Chen [aut],
Jemma Stachelek [ctb]
Maintainer: Jonathan Lisic <jlisic@gmail.com>
Diff between cdlTools versions 0.15 dated 2020-06-27 and 1.13 dated 2024-03-23
DESCRIPTION | 22 +++++++------ MD5 | 56 +++++++++++++++++---------------- NAMESPACE | 9 +++++ R/createComparableCDL.R | 76 +++++++++++++++++++++++++++++++-------------- R/data.R | 4 +- R/fips.R | 54 ++++++++++++++++++++++++++----- R/getCDL.R | 66 ++++++++++++++++++++++++++------------- R/getCDL_bbox.R |only R/metadata.R |only data/stateNames.rda |binary data/varNamesCDL.rda |binary inst/CITATION | 41 +++++++++++++++--------- man/census2010FIPS.Rd | 8 ++-- man/corn.Rd | 4 +- man/cotton.Rd | 4 +- man/createComparableCDL.Rd | 24 +++++++++++--- man/cultivated.Rd | 4 +- man/durumWheat.Rd | 4 +- man/fips.Rd | 7 ++-- man/getCDL.Rd | 25 ++++++++++---- man/getCDL_bbox.Rd |only man/metadata.Rd |only man/nothing.Rd | 4 +- man/pasture.Rd | 4 +- man/projCDL.Rd | 4 +- man/soybeans.Rd | 4 +- man/springWheat.Rd | 4 +- man/stateNames.Rd | 6 ++- man/varNamesCDL.Rd | 4 +- man/water.Rd | 4 +- man/winterWheat.Rd | 4 +- 31 files changed, 309 insertions(+), 137 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] ,
Posit Software, PBC [cph, fnd],
Alessandro Gasparini [ctb] ,
Benjie Gillam [ctb],
Claus Thorn Ekstroem [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Deo Salil [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] ,
Inaki Ucar [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.29 dated 2024-02-09 and 0.30 dated 2024-03-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/vignette.rds |binary inst/rmarkdown/templates/xaringan/resources/js/ws-handler.js | 3 +-- inst/rmarkdown/templates/xaringan/resources/rutgers.css | 8 ++++---- 5 files changed, 13 insertions(+), 14 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre] ,
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb],
Romain Lesur [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.29 dated 2024-02-09 and 0.30 dated 2024-03-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/dynamic.R | 3 ++- inst/resources/ws-reload.js | 3 +-- inst/resources/ws-update.js | 3 +-- 5 files changed, 11 insertions(+), 12 deletions(-)
Title: Download Data from Brazil's Population Census
Description: Download data from Brazil's population census. The package is built
on top of the 'Arrow' platform <https://arrow.apache.org/docs/r/>,
which allows users to work with larger-than-memory census data using
'dplyr' familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.
Author: Rafael H. M. Pereira [aut, cre]
,
Rogerio J. Barbosa [aut] ,
Diego Rabatone Oliveira [ctb],
Neal Richardson [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between censobr versions 0.3.1 dated 2024-02-23 and 0.3.2 dated 2024-03-23
DESCRIPTION | 13 +-- MD5 | 20 ++-- NEWS.md | 10 ++ R/read_tracts.R | 17 ++-- R/utils.R | 15 --- inst/doc/censobr.html | 8 - inst/doc/census_tracts_data.html | 158 ++++++++------------------------------ inst/doc/documentation.html | 4 man/arrow_open_dataset.Rd | 4 man/read_tracts.Rd | 3 tests/testthat/test_read_tracts.R | 12 ++ 11 files changed, 96 insertions(+), 168 deletions(-)
Title: Regularized Linear Modeling with Tidy Data
Description: An extension to the 'R' tidy data environment for automated machine learning. The package allows fitting and cross validation of linear regression and classification algorithms on grouped data.
Author: Johann Pfitzinger [aut, cre]
Maintainer: Johann Pfitzinger <johann.pfitzinger@gmail.com>
Diff between tidyfit versions 0.7.0 dated 2024-02-26 and 0.7.1 dated 2024-03-23
DESCRIPTION | 8 +-- MD5 | 72 +++++++++++++-------------- NEWS.md | 4 + R/explain.R | 2 R/explain.tidyfit.models.R | 2 R/explain_methods.R | 22 ++++---- R/fit.quantile.R | 8 +-- R/fit.quantile_rf.R | 6 +- R/fit.rf.R | 2 R/fit.svm.R | 4 - R/model_definition.R | 29 ++++++++-- inst/doc/Predicting_Boston_House_Prices.html | 6 +- man/explain.Rd | 2 man/explain.tidyfit.models.Rd | 2 tests/testthat/test-adalasso.R | 1 tests/testthat/test-bayes.R | 1 tests/testthat/test-blasso.R | 1 tests/testthat/test-bma.R | 1 tests/testthat/test-boost.R | 1 tests/testthat/test-bridge.R | 1 tests/testthat/test-cor.R | 1 tests/testthat/test-enet.R | 1 tests/testthat/test-gets.R | 1 tests/testthat/test-glm.R | 1 tests/testthat/test-glmm.R | 2 tests/testthat/test-hfr.R | 1 tests/testthat/test-lasso.R | 1 tests/testthat/test-lm.R | 1 tests/testthat/test-pcr.R | 1 tests/testthat/test-plsr.R | 1 tests/testthat/test-quantile.R | 1 tests/testthat/test-quantile_rf.R | 1 tests/testthat/test-rf.R | 1 tests/testthat/test-ridge.R | 1 tests/testthat/test-robust.R | 1 tests/testthat/test-spikeslab.R | 1 tests/testthat/test-svm.R | 1 37 files changed, 117 insertions(+), 76 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Recursive Partitioning ('RPART') or step wise regression models are fit. Nested cross validation (or analogous for the random forest) is used to estimate and compare performances between these models.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied with the 'path=TRUE' options when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by default.
When fitting not a relaxed lasso model but an elastic-net model, then the R-packages 'nestedcv' <https://cran.r-project.org/package=nestedcv>, 'glmnetSE' <http [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.4-3 dated 2024-03-03 and 0.4-4 dated 2024-03-23
glmnetr-0.4-3/glmnetr/R/RandomForest_240220.R |only glmnetr-0.4-3/glmnetr/R/aicreg_230218.R |only glmnetr-0.4-3/glmnetr/R/ann_tab_cv_240202.R |only glmnetr-0.4-3/glmnetr/R/cv.glmnetr_240224.R |only glmnetr-0.4-3/glmnetr/R/cv.stepreg_240202.R |only glmnetr-0.4-3/glmnetr/R/nested.glmnetr_240301.R |only glmnetr-0.4-3/glmnetr/R/plot.cv.glmnetr_240224.R |only glmnetr-0.4-3/glmnetr/R/plot.perf.glmnetr_240226.R |only glmnetr-0.4-3/glmnetr/R/predict_ann_tab_230714.R |only glmnetr-0.4-3/glmnetr/R/stepreg_230218.R |only glmnetr-0.4-3/glmnetr/R/summary.cv.glmnetr_230508.R |only glmnetr-0.4-3/glmnetr/R/summary.nested.glmnetr_240301.R |only glmnetr-0.4-3/glmnetr/R/tools_240301.R |only glmnetr-0.4-3/glmnetr/R/xgbm_tuned_240224.R |only glmnetr-0.4-3/glmnetr/inst/doc/An_Overview_of_glmnetr_240301.pdf |only glmnetr-0.4-3/glmnetr/inst/doc/An_Overview_of_glmnetr_240301.pdf.asis |only glmnetr-0.4-3/glmnetr/inst/doc/Using_ann_tab_cv_240301.pdf |only glmnetr-0.4-3/glmnetr/inst/doc/Using_ann_tab_cv_240301.pdf.asis |only glmnetr-0.4-3/glmnetr/inst/doc/Using_stepreg_240301.pdf |only glmnetr-0.4-3/glmnetr/inst/doc/Using_stepreg_240301.pdf.asis |only glmnetr-0.4-3/glmnetr/vignettes/An_Overview_of_glmnetr_240301.Rmd |only glmnetr-0.4-3/glmnetr/vignettes/An_Overview_of_glmnetr_240301.pdf.asis |only glmnetr-0.4-3/glmnetr/vignettes/Using_ann_tab_cv_240301.Rmd |only glmnetr-0.4-3/glmnetr/vignettes/Using_ann_tab_cv_240301.pdf.asis |only glmnetr-0.4-3/glmnetr/vignettes/Using_stepreg_240301.Rmd |only glmnetr-0.4-3/glmnetr/vignettes/Using_stepreg_240301.pdf.asis |only glmnetr-0.4-4/glmnetr/DESCRIPTION | 12 glmnetr-0.4-4/glmnetr/MD5 | 167 +++++----- glmnetr-0.4-4/glmnetr/NAMESPACE | 10 glmnetr-0.4-4/glmnetr/R/RandomForest_240322.R |only glmnetr-0.4-4/glmnetr/R/aicreg_240322.R |only glmnetr-0.4-4/glmnetr/R/ann_tab_cv_240322.R |only glmnetr-0.4-4/glmnetr/R/cv.glmnetr_240322.R |only glmnetr-0.4-4/glmnetr/R/cv.stepreg_240322.R |only glmnetr-0.4-4/glmnetr/R/nested.glmnetr_240322.R |only glmnetr-0.4-4/glmnetr/R/plot.cv.glmnetr_240322.R |only glmnetr-0.4-4/glmnetr/R/plot.perf.glmnetr_240322.R |only glmnetr-0.4-4/glmnetr/R/predict_240322.R |only glmnetr-0.4-4/glmnetr/R/predict_ann_tab_240322.R |only glmnetr-0.4-4/glmnetr/R/rederive_240322.R |only glmnetr-0.4-4/glmnetr/R/stepreg_240322.R |only glmnetr-0.4-4/glmnetr/R/summary.cv.glmnetr_240322.R |only glmnetr-0.4-4/glmnetr/R/summary.nested.glmnetr_240322.R |only glmnetr-0.4-4/glmnetr/R/tools_240322.R |only glmnetr-0.4-4/glmnetr/R/xgbm_tuned_240322.R |only glmnetr-0.4-4/glmnetr/build/vignette.rds |binary glmnetr-0.4-4/glmnetr/inst/doc/An_Overview_of_glmnetr_240322.pdf |only glmnetr-0.4-4/glmnetr/inst/doc/An_Overview_of_glmnetr_240322.pdf.asis |only glmnetr-0.4-4/glmnetr/inst/doc/Using_ann_tab_cv_240322.pdf |only glmnetr-0.4-4/glmnetr/inst/doc/Using_ann_tab_cv_240322.pdf.asis |only glmnetr-0.4-4/glmnetr/inst/doc/Using_stepreg_240322.pdf |only glmnetr-0.4-4/glmnetr/inst/doc/Using_stepreg_240322.pdf.asis |only glmnetr-0.4-4/glmnetr/man/aicreg.Rd | 5 glmnetr-0.4-4/glmnetr/man/ann_tab_cv.Rd | 4 glmnetr-0.4-4/glmnetr/man/ann_tab_cv_best.Rd | 16 glmnetr-0.4-4/glmnetr/man/best.preds.Rd | 7 glmnetr-0.4-4/glmnetr/man/bsint.Rd | 2 glmnetr-0.4-4/glmnetr/man/calceloss.Rd | 2 glmnetr-0.4-4/glmnetr/man/cox.sat.dev.Rd | 5 glmnetr-0.4-4/glmnetr/man/cv.glmnetr.Rd | 4 glmnetr-0.4-4/glmnetr/man/cv.stepreg.Rd | 5 glmnetr-0.4-4/glmnetr/man/devrat_.Rd | 5 glmnetr-0.4-4/glmnetr/man/diff_time.Rd | 5 glmnetr-0.4-4/glmnetr/man/diff_time1.Rd | 2 glmnetr-0.4-4/glmnetr/man/dtstndrz.Rd | 4 glmnetr-0.4-4/glmnetr/man/factor.foldid.Rd | 5 glmnetr-0.4-4/glmnetr/man/get.foldid.Rd | 4 glmnetr-0.4-4/glmnetr/man/getlamgam.Rd | 2 glmnetr-0.4-4/glmnetr/man/glmnetr.Rd | 4 glmnetr-0.4-4/glmnetr/man/glmnetr.compcv.Rd | 13 glmnetr-0.4-4/glmnetr/man/glmnetr.compcv0.Rd | 2 glmnetr-0.4-4/glmnetr/man/glmnetr.simdata.Rd | 4 glmnetr-0.4-4/glmnetr/man/glmnetr_devratio.Rd | 2 glmnetr-0.4-4/glmnetr/man/glmnetr_seed.Rd | 5 glmnetr-0.4-4/glmnetr/man/glmnetrll_1fold.Rd | 2 glmnetr-0.4-4/glmnetr/man/nested.glmnetr.Rd | 70 ++-- glmnetr-0.4-4/glmnetr/man/plot.cv.glmnetr.Rd | 2 glmnetr-0.4-4/glmnetr/man/plot.glmnetr.Rd | 2 glmnetr-0.4-4/glmnetr/man/plot.nested.glmnetr.Rd | 39 +- glmnetr-0.4-4/glmnetr/man/plot_perf_glmnetr.Rd | 35 +- glmnetr-0.4-4/glmnetr/man/predict.cv.glmnetr.Rd | 4 glmnetr-0.4-4/glmnetr/man/predict.cv.stepreg.Rd | 5 glmnetr-0.4-4/glmnetr/man/predict.glmnetr.Rd | 2 glmnetr-0.4-4/glmnetr/man/predict.nested.glmnetr.Rd | 4 glmnetr-0.4-4/glmnetr/man/predict_ann_tab.Rd | 5 glmnetr-0.4-4/glmnetr/man/predict_nested_rf.Rd |only glmnetr-0.4-4/glmnetr/man/predict_nested_xgb.Rd |only glmnetr-0.4-4/glmnetr/man/prednn_tl.Rd | 2 glmnetr-0.4-4/glmnetr/man/preds_1.Rd | 2 glmnetr-0.4-4/glmnetr/man/print.nested.glmnetr.Rd | 4 glmnetr-0.4-4/glmnetr/man/print.rf_tune.Rd | 5 glmnetr-0.4-4/glmnetr/man/rederive_rf.Rd |only glmnetr-0.4-4/glmnetr/man/rederive_xgb.Rd |only glmnetr-0.4-4/glmnetr/man/rf_tune.Rd | 9 glmnetr-0.4-4/glmnetr/man/rf_xbhat.Rd |only glmnetr-0.4-4/glmnetr/man/roundperf.Rd | 5 glmnetr-0.4-4/glmnetr/man/rpart_xbhat.Rd |only glmnetr-0.4-4/glmnetr/man/stepreg.Rd | 5 glmnetr-0.4-4/glmnetr/man/summary.cv.glmnetr.Rd | 4 glmnetr-0.4-4/glmnetr/man/summary.cv.stepreg.Rd | 5 glmnetr-0.4-4/glmnetr/man/summary.nested.glmnetr.Rd | 11 glmnetr-0.4-4/glmnetr/man/summary.rf_tune.Rd | 5 glmnetr-0.4-4/glmnetr/man/summary.stepreg.Rd | 5 glmnetr-0.4-4/glmnetr/man/wtlast.Rd | 2 glmnetr-0.4-4/glmnetr/man/wtmiddle.Rd | 2 glmnetr-0.4-4/glmnetr/man/wtzero.Rd | 2 glmnetr-0.4-4/glmnetr/man/xgb.simple.Rd | 7 glmnetr-0.4-4/glmnetr/man/xgb.tuned.Rd | 19 - glmnetr-0.4-4/glmnetr/man/xgb_xbhat.Rd |only glmnetr-0.4-4/glmnetr/vignettes/An_Overview_of_glmnetr_240322.Rmd |only glmnetr-0.4-4/glmnetr/vignettes/An_Overview_of_glmnetr_240322.pdf.asis |only glmnetr-0.4-4/glmnetr/vignettes/Using_ann_tab_cv_240322.Rmd |only glmnetr-0.4-4/glmnetr/vignettes/Using_ann_tab_cv_240322.pdf.asis |only glmnetr-0.4-4/glmnetr/vignettes/Using_stepreg_240322.Rmd |only glmnetr-0.4-4/glmnetr/vignettes/Using_stepreg_240322.pdf.asis |only 115 files changed, 339 insertions(+), 221 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to
Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>,
Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>,
Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>,
Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>,
Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and
Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.
Author: France Mentre [aut],
Romain Leroux [aut, cre],
Jeremy Seurat [aut],
Lucie Fayette [aut],
Emmanuelle Comets [ctb],
Sylvie Retout [ctb]
Maintainer: Romain Leroux <romain.leroux@inserm.fr>
Diff between PFIM versions 6.0.2 dated 2023-11-24 and 6.0.3 dated 2024-03-23
PFIM-6.0.2/PFIM/man/plot.Rd |only PFIM-6.0.2/PFIM/vignettes/Example02_EvaluationPopFIM_files |only PFIM-6.0.3/PFIM/DESCRIPTION | 10 PFIM-6.0.3/PFIM/MD5 | 553 ++++------ PFIM-6.0.3/PFIM/NAMESPACE | 5 PFIM-6.0.3/PFIM/R/Design.R | 44 PFIM-6.0.3/PFIM/R/Evaluation.R | 207 +++ PFIM-6.0.3/PFIM/R/FedorovWynnAlgorithm.R | 138 ++ PFIM-6.0.3/PFIM/R/Fim.R | 93 - PFIM-6.0.3/PFIM/R/GenericMethods.R | 106 + PFIM-6.0.3/PFIM/R/LibraryOfPKModels.R | 96 - PFIM-6.0.3/PFIM/R/Model.R | 4 PFIM-6.0.3/PFIM/R/MultiplicativeAlgorithm.R | 56 - PFIM-6.0.3/PFIM/R/Optimization.R | 201 +++ PFIM-6.0.3/PFIM/R/OptimizationAlgorithm.R | 69 + PFIM-6.0.3/PFIM/R/PFIM-package.R | 11 PFIM-6.0.3/PFIM/R/PFIMProject.R | 1 PFIM-6.0.3/PFIM/R/PlotEvaluation.R | 114 +- PFIM-6.0.3/PFIM/build/partial.rdb |binary PFIM-6.0.3/PFIM/build/vignette.rds |binary PFIM-6.0.3/PFIM/inst/doc/Example01.R | 279 +++-- PFIM-6.0.3/PFIM/inst/doc/Example01.Rmd | 309 +++-- PFIM-6.0.3/PFIM/inst/doc/Example01.html | 474 +++++--- PFIM-6.0.3/PFIM/inst/doc/Example02.R | 160 +- PFIM-6.0.3/PFIM/inst/doc/Example02.Rmd | 161 +- PFIM-6.0.3/PFIM/inst/doc/Example02.html | 240 ++-- PFIM-6.0.3/PFIM/man/Administration-class.Rd | 56 - PFIM-6.0.3/PFIM/man/AdministrationConstraints-class.Rd | 52 PFIM-6.0.3/PFIM/man/BayesianFim-class.Rd | 22 PFIM-6.0.3/PFIM/man/Combined1-class.Rd | 54 PFIM-6.0.3/PFIM/man/Constant-class.Rd | 52 PFIM-6.0.3/PFIM/man/Design-class.Rd | 56 - PFIM-6.0.3/PFIM/man/Distribution-class.Rd | 46 PFIM-6.0.3/PFIM/man/EvaluateArm.Rd | 52 PFIM-6.0.3/PFIM/man/EvaluateDesign.Rd | 48 PFIM-6.0.3/PFIM/man/EvaluateErrorModelDerivatives.Rd | 44 PFIM-6.0.3/PFIM/man/EvaluateFisherMatrix.Rd | 70 - PFIM-6.0.3/PFIM/man/EvaluateModel.Rd | 94 - PFIM-6.0.3/PFIM/man/EvaluateVarianceFIM.Rd | 62 - PFIM-6.0.3/PFIM/man/EvaluateVarianceModel.Rd | 48 PFIM-6.0.3/PFIM/man/Evaluation-class.Rd | 60 - PFIM-6.0.3/PFIM/man/FedorovWynnAlgorithm-class.Rd | 62 - PFIM-6.0.3/PFIM/man/FedorovWynnAlgorithm_Rcpp.Rd | 98 - PFIM-6.0.3/PFIM/man/Fim-class.Rd | 54 PFIM-6.0.3/PFIM/man/IndividualFim-class.Rd | 22 PFIM-6.0.3/PFIM/man/LibraryOfModels-class.Rd | 48 PFIM-6.0.3/PFIM/man/LibraryOfPDModels.Rd | 22 PFIM-6.0.3/PFIM/man/LibraryOfPKModels.Rd | 22 PFIM-6.0.3/PFIM/man/LibraryOfPKPDModels-class.Rd | 22 PFIM-6.0.3/PFIM/man/LogNormal-class.Rd | 22 PFIM-6.0.3/PFIM/man/Model-class.Rd | 64 - PFIM-6.0.3/PFIM/man/ModelAnalytic-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelAnalyticBolus-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelAnalyticBolusSteadyState-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelAnalyticInfusion-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelAnalyticInfusionSteadyState-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelAnalyticSteadyState-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelBolus-class.Rd | 20 PFIM-6.0.3/PFIM/man/ModelError-class.Rd | 20 PFIM-6.0.3/PFIM/man/ModelInfusion-class.Rd | 20 PFIM-6.0.3/PFIM/man/ModelODE-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelODEBolus-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelODEDoseInEquations-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelODEDoseNotInEquations-class.Rd | 20 PFIM-6.0.3/PFIM/man/ModelODEInfusion-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelODEInfusionDoseInEquations-class.Rd | 22 PFIM-6.0.3/PFIM/man/ModelParameter-class.Rd | 52 PFIM-6.0.3/PFIM/man/MultiplicativeAlgorithm-class.Rd | 58 - PFIM-6.0.3/PFIM/man/MultiplicativeAlgorithm_Rcpp.Rd | 74 - PFIM-6.0.3/PFIM/man/Normal-class.Rd | 22 PFIM-6.0.3/PFIM/man/Optimization-class.Rd | 72 - PFIM-6.0.3/PFIM/man/OptimizationAlgorithm-class.Rd | 48 PFIM-6.0.3/PFIM/man/PFIM-package.Rd | 15 PFIM-6.0.3/PFIM/man/PFIMProject-class.Rd | 48 PFIM-6.0.3/PFIM/man/PGBOAlgorithm-class.Rd | 70 - PFIM-6.0.3/PFIM/man/PSOAlgorithm-class.Rd | 60 - PFIM-6.0.3/PFIM/man/PlotEvaluation-class.Rd | 22 PFIM-6.0.3/PFIM/man/PopulationFim-class.Rd | 22 PFIM-6.0.3/PFIM/man/Proportional-class.Rd | 52 PFIM-6.0.3/PFIM/man/Report.Rd | 58 - PFIM-6.0.3/PFIM/man/SamplingTimeConstraints-class.Rd | 58 - PFIM-6.0.3/PFIM/man/SamplingTimes-class.Rd | 48 PFIM-6.0.3/PFIM/man/SimplexAlgorithm-class.Rd | 56 - PFIM-6.0.3/PFIM/man/addModel.Rd | 44 PFIM-6.0.3/PFIM/man/addModels.Rd | 44 PFIM-6.0.3/PFIM/man/checkSamplingTimeConstraintsForContinuousOptimization.Rd | 76 - PFIM-6.0.3/PFIM/man/checkValiditySamplingConstraint.Rd | 40 PFIM-6.0.3/PFIM/man/convertPKModelAnalyticToPKModelODE.Rd | 54 PFIM-6.0.3/PFIM/man/defineModel.Rd | 44 PFIM-6.0.3/PFIM/man/defineModelFromLibraryOfModels.Rd | 44 PFIM-6.0.3/PFIM/man/defineModelType.Rd | 44 PFIM-6.0.3/PFIM/man/defineModelUserDefined.Rd | 44 PFIM-6.0.3/PFIM/man/definePKModel.Rd | 80 - PFIM-6.0.3/PFIM/man/definePKPDModel.Rd | 114 +- PFIM-6.0.3/PFIM/man/fisher.simplex.Rd | 42 PFIM-6.0.3/PFIM/man/fun.amoeba.Rd | 64 - PFIM-6.0.3/PFIM/man/generateFimsFromConstraints.Rd | 44 PFIM-6.0.3/PFIM/man/generateReportEvaluation.Rd | 118 +- PFIM-6.0.3/PFIM/man/generateReportOptimization.Rd | 156 +- PFIM-6.0.3/PFIM/man/generateSamplingsFromSamplingConstraints.Rd | 40 PFIM-6.0.3/PFIM/man/generateTables.Rd | 50 PFIM-6.0.3/PFIM/man/getAdjustedGradient.Rd | 50 PFIM-6.0.3/PFIM/man/getAdministration.Rd | 44 PFIM-6.0.3/PFIM/man/getAdministrationConstraint.Rd | 44 PFIM-6.0.3/PFIM/man/getAdministrations.Rd | 42 PFIM-6.0.3/PFIM/man/getAdministrationsConstraints.Rd | 40 PFIM-6.0.3/PFIM/man/getArms.Rd | 48 PFIM-6.0.3/PFIM/man/getColumnAndParametersNamesFIM.Rd | 58 - PFIM-6.0.3/PFIM/man/getColumnAndParametersNamesFIMInLatex.Rd | 58 - PFIM-6.0.3/PFIM/man/getConditionNumberFixedEffects.Rd | 40 PFIM-6.0.3/PFIM/man/getConditionNumberVarianceEffects.Rd | 46 PFIM-6.0.3/PFIM/man/getContent.Rd | 40 PFIM-6.0.3/PFIM/man/getCorrelationMatrix.Rd | 9 PFIM-6.0.3/PFIM/man/getDataFrameResults.Rd | 13 PFIM-6.0.3/PFIM/man/getDcriterion.Rd | 9 PFIM-6.0.3/PFIM/man/getDelta.Rd | 40 PFIM-6.0.3/PFIM/man/getDerivatives.Rd | 40 PFIM-6.0.3/PFIM/man/getDescription.Rd | 40 PFIM-6.0.3/PFIM/man/getDesigns.Rd | 40 PFIM-6.0.3/PFIM/man/getDeterminant.Rd | 9 PFIM-6.0.3/PFIM/man/getDistribution.Rd | 40 PFIM-6.0.3/PFIM/man/getDose.Rd | 46 PFIM-6.0.3/PFIM/man/getEigenValues.Rd | 40 PFIM-6.0.3/PFIM/man/getElementaryProtocols.Rd | 46 PFIM-6.0.3/PFIM/man/getEquation.Rd | 40 PFIM-6.0.3/PFIM/man/getEquations.Rd | 40 PFIM-6.0.3/PFIM/man/getEquationsAfterInfusion.Rd | 40 PFIM-6.0.3/PFIM/man/getEquationsDuringInfusion.Rd | 40 PFIM-6.0.3/PFIM/man/getEvaluationFIMResults.Rd | 40 PFIM-6.0.3/PFIM/man/getEvaluationInitialDesignResults.Rd | 40 PFIM-6.0.3/PFIM/man/getFim.Rd | 4 PFIM-6.0.3/PFIM/man/getFisherMatrix.Rd | 9 PFIM-6.0.3/PFIM/man/getFixedEffects.Rd | 40 PFIM-6.0.3/PFIM/man/getFixedMu.Rd | 40 PFIM-6.0.3/PFIM/man/getFixedOmega.Rd | 40 PFIM-6.0.3/PFIM/man/getFixedParameters.Rd | 40 PFIM-6.0.3/PFIM/man/getFixedTimes.Rd | 40 PFIM-6.0.3/PFIM/man/getInitialConditions.Rd | 46 PFIM-6.0.3/PFIM/man/getIterationAndCriteria.Rd | 40 PFIM-6.0.3/PFIM/man/getLambda.Rd | 40 PFIM-6.0.3/PFIM/man/getLibraryPDModels.Rd | 40 PFIM-6.0.3/PFIM/man/getLibraryPKModels.Rd | 40 PFIM-6.0.3/PFIM/man/getMinSampling.Rd | 40 PFIM-6.0.3/PFIM/man/getModel.Rd | 40 PFIM-6.0.3/PFIM/man/getModelEquations.Rd | 40 PFIM-6.0.3/PFIM/man/getModelError.Rd | 46 PFIM-6.0.3/PFIM/man/getModelErrorParametersValues.Rd | 40 PFIM-6.0.3/PFIM/man/getModelFromLibrary.Rd | 40 PFIM-6.0.3/PFIM/man/getModelParameters.Rd | 40 PFIM-6.0.3/PFIM/man/getModelParametersValues.Rd | 40 PFIM-6.0.3/PFIM/man/getMu.Rd | 48 PFIM-6.0.3/PFIM/man/getName.Rd | 72 - PFIM-6.0.3/PFIM/man/getNames.Rd | 40 PFIM-6.0.3/PFIM/man/getNumberOfArms.Rd | 40 PFIM-6.0.3/PFIM/man/getNumberOfIterations.Rd | 40 PFIM-6.0.3/PFIM/man/getNumberOfParameters.Rd | 40 PFIM-6.0.3/PFIM/man/getNumberOfTimesByWindows.Rd | 40 PFIM-6.0.3/PFIM/man/getNumberOfsamplingsOptimisable.Rd | 40 PFIM-6.0.3/PFIM/man/getOdeSolverParameters.Rd | 46 PFIM-6.0.3/PFIM/man/getOmega.Rd | 48 PFIM-6.0.3/PFIM/man/getOptimalDesign.Rd | 40 PFIM-6.0.3/PFIM/man/getOptimalFrequencies.Rd |only PFIM-6.0.3/PFIM/man/getOptimalWeights.Rd | 40 PFIM-6.0.3/PFIM/man/getOptimizationResults.Rd | 40 PFIM-6.0.3/PFIM/man/getOptimizer.Rd | 40 PFIM-6.0.3/PFIM/man/getOptimizerParameters.Rd | 40 PFIM-6.0.3/PFIM/man/getOutcome.Rd | 68 - PFIM-6.0.3/PFIM/man/getOutcomes.Rd | 46 PFIM-6.0.3/PFIM/man/getOutcomesEvaluation.Rd | 40 PFIM-6.0.3/PFIM/man/getOutcomesForEvaluation.Rd | 40 PFIM-6.0.3/PFIM/man/getOutcomesGradient.Rd | 40 PFIM-6.0.3/PFIM/man/getPDModel.Rd | 44 PFIM-6.0.3/PFIM/man/getPKModel.Rd | 44 PFIM-6.0.3/PFIM/man/getPKPDModel.Rd | 44 PFIM-6.0.3/PFIM/man/getParameters.Rd | 54 PFIM-6.0.3/PFIM/man/getPlotOptions.Rd | 38 PFIM-6.0.3/PFIM/man/getProportionsOfSubjects.Rd | 40 PFIM-6.0.3/PFIM/man/getRSE.Rd | 10 PFIM-6.0.3/PFIM/man/getSE.Rd | 9 PFIM-6.0.3/PFIM/man/getSamplingTime.Rd | 44 PFIM-6.0.3/PFIM/man/getSamplingTimeConstraint.Rd | 44 PFIM-6.0.3/PFIM/man/getSamplingTimes.Rd | 40 PFIM-6.0.3/PFIM/man/getSamplingTimesConstraints.Rd | 40 PFIM-6.0.3/PFIM/man/getSamplings.Rd | 48 PFIM-6.0.3/PFIM/man/getSamplingsWindows.Rd | 40 PFIM-6.0.3/PFIM/man/getShrinkage.Rd | 10 PFIM-6.0.3/PFIM/man/getSigmaInter.Rd | 40 PFIM-6.0.3/PFIM/man/getSigmaSlope.Rd | 40 PFIM-6.0.3/PFIM/man/getSize.Rd | 46 PFIM-6.0.3/PFIM/man/getTau.Rd | 40 PFIM-6.0.3/PFIM/man/getTimeDose.Rd | 40 PFIM-6.0.3/PFIM/man/getTinf.Rd | 40 PFIM-6.0.3/PFIM/man/getVarianceEffects.Rd | 40 PFIM-6.0.3/PFIM/man/getcError.Rd | 40 PFIM-6.0.3/PFIM/man/isDoseInEquations.Rd | 40 PFIM-6.0.3/PFIM/man/isModelAnalytic.Rd | 40 PFIM-6.0.3/PFIM/man/isModelBolus.Rd | 44 PFIM-6.0.3/PFIM/man/isModelInfusion.Rd | 40 PFIM-6.0.3/PFIM/man/isModelODE.Rd | 40 PFIM-6.0.3/PFIM/man/isModelSteadyState.Rd | 40 PFIM-6.0.3/PFIM/man/optimize.Rd | 76 - PFIM-6.0.3/PFIM/man/parametersForComputingGradient.Rd | 40 PFIM-6.0.3/PFIM/man/plotEvaluation.Rd |only PFIM-6.0.3/PFIM/man/plotFrequencies.Rd |only PFIM-6.0.3/PFIM/man/plotOutcomesEvaluation.Rd | 52 PFIM-6.0.3/PFIM/man/plotOutcomesGradient.Rd | 52 PFIM-6.0.3/PFIM/man/plotRSE.Rd | 44 PFIM-6.0.3/PFIM/man/plotSE.Rd | 44 PFIM-6.0.3/PFIM/man/plotSensitivityIndice.Rd |only PFIM-6.0.3/PFIM/man/plotShrinkage.Rd | 44 PFIM-6.0.3/PFIM/man/plotWeights.Rd | 52 PFIM-6.0.3/PFIM/man/reportTablesAdministration.Rd | 40 PFIM-6.0.3/PFIM/man/reportTablesDesign.Rd | 40 PFIM-6.0.3/PFIM/man/reportTablesFIM.Rd | 58 - PFIM-6.0.3/PFIM/man/reportTablesModelError.Rd | 40 PFIM-6.0.3/PFIM/man/reportTablesModelParameters.Rd | 40 PFIM-6.0.3/PFIM/man/reportTablesPlot.Rd | 44 PFIM-6.0.3/PFIM/man/reportTablesSamplingConstraints.Rd | 40 PFIM-6.0.3/PFIM/man/resizeFisherMatrix.Rd | 44 PFIM-6.0.3/PFIM/man/run.Rd | 46 PFIM-6.0.3/PFIM/man/setAdministrations.Rd | 48 PFIM-6.0.3/PFIM/man/setArm.Rd | 44 PFIM-6.0.3/PFIM/man/setArms.Rd | 52 PFIM-6.0.3/PFIM/man/setContent.Rd | 44 PFIM-6.0.3/PFIM/man/setDerivatives.Rd | 44 PFIM-6.0.3/PFIM/man/setDescription.Rd | 44 PFIM-6.0.3/PFIM/man/setDesigns.Rd | 44 PFIM-6.0.3/PFIM/man/setDistribution.Rd | 44 PFIM-6.0.3/PFIM/man/setDose.Rd | 44 PFIM-6.0.3/PFIM/man/setEquation.Rd | 44 PFIM-6.0.3/PFIM/man/setEquations.Rd | 44 PFIM-6.0.3/PFIM/man/setEquationsAfterInfusion.Rd | 44 PFIM-6.0.3/PFIM/man/setEquationsDuringInfusion.Rd | 44 PFIM-6.0.3/PFIM/man/setEvaluationFIMResults.Rd | 44 PFIM-6.0.3/PFIM/man/setEvaluationInitialDesignResults.Rd | 44 PFIM-6.0.3/PFIM/man/setFim.Rd | 44 PFIM-6.0.3/PFIM/man/setFimTypeToString.Rd | 40 PFIM-6.0.3/PFIM/man/setFisherMatrix.Rd | 44 PFIM-6.0.3/PFIM/man/setFixedEffects.Rd | 40 PFIM-6.0.3/PFIM/man/setFixedMu.Rd | 44 PFIM-6.0.3/PFIM/man/setFixedOmega.Rd | 44 PFIM-6.0.3/PFIM/man/setInitialConditions.Rd | 50 PFIM-6.0.3/PFIM/man/setIterationAndCriteria.Rd | 44 PFIM-6.0.3/PFIM/man/setModel.Rd | 44 PFIM-6.0.3/PFIM/man/setModelError.Rd | 44 PFIM-6.0.3/PFIM/man/setModelFromLibrary.Rd | 44 PFIM-6.0.3/PFIM/man/setMu.Rd | 52 PFIM-6.0.3/PFIM/man/setName.Rd | 58 - PFIM-6.0.3/PFIM/man/setNumberOfArms.Rd | 44 PFIM-6.0.3/PFIM/man/setOdeSolverParameters.Rd | 44 PFIM-6.0.3/PFIM/man/setOmega.Rd | 52 PFIM-6.0.3/PFIM/man/setOptimalDesign.Rd | 44 PFIM-6.0.3/PFIM/man/setOptimalWeights.Rd | 44 PFIM-6.0.3/PFIM/man/setOptimizationResults.Rd | 44 PFIM-6.0.3/PFIM/man/setOutcome.Rd | 52 PFIM-6.0.3/PFIM/man/setOutcomes.Rd | 44 PFIM-6.0.3/PFIM/man/setOutcomesEvaluation.Rd | 44 PFIM-6.0.3/PFIM/man/setOutcomesForEvaluation.Rd | 44 PFIM-6.0.3/PFIM/man/setOutcomesGradient.Rd | 44 PFIM-6.0.3/PFIM/man/setParameters.Rd | 84 - PFIM-6.0.3/PFIM/man/setSamplingConstraintForOptimization.Rd | 40 PFIM-6.0.3/PFIM/man/setSamplingTime.Rd | 44 PFIM-6.0.3/PFIM/man/setSamplingTimes.Rd | 44 PFIM-6.0.3/PFIM/man/setSamplingTimesConstraints.Rd | 44 PFIM-6.0.3/PFIM/man/setSamplings.Rd | 44 PFIM-6.0.3/PFIM/man/setShrinkage.Rd | 58 - PFIM-6.0.3/PFIM/man/setSigmaInter.Rd | 44 PFIM-6.0.3/PFIM/man/setSigmaSlope.Rd | 44 PFIM-6.0.3/PFIM/man/setSize.Rd | 62 - PFIM-6.0.3/PFIM/man/setTau.Rd | 44 PFIM-6.0.3/PFIM/man/setTimeDose.Rd | 44 PFIM-6.0.3/PFIM/man/setTinf.Rd | 44 PFIM-6.0.3/PFIM/man/setVarianceEffects.Rd | 40 PFIM-6.0.3/PFIM/man/setcError.Rd | 44 PFIM-6.0.3/PFIM/man/show.Rd | 102 - PFIM-6.0.3/PFIM/tests/testthat/test_PKModels-PFIM.R | 261 ---- PFIM-6.0.3/PFIM/tests/testthat/test_PKPDModels-PFIM.R | 58 - PFIM-6.0.3/PFIM/vignettes/Example01.Rmd | 309 +++-- PFIM-6.0.3/PFIM/vignettes/Example02.Rmd | 161 +- 279 files changed, 7957 insertions(+), 6974 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include propensity score weighting using generalized linear models, gradient
boosting machines, the covariate balancing propensity score algorithm, inverse probability tilting, Bayesian additive regression trees, and
SuperLearner, and directly estimating balancing weights using entropy balancing, energy balancing, and optimization-based weights. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.14.2 dated 2023-05-23 and 1.0.0 dated 2024-03-23
WeightIt-0.14.2/WeightIt/R/utilities.R |only WeightIt-0.14.2/WeightIt/R/weightit2method.R |only WeightIt-1.0.0/WeightIt/DESCRIPTION | 17 WeightIt-1.0.0/WeightIt/MD5 | 127 - WeightIt-1.0.0/WeightIt/NAMESPACE | 68 WeightIt-1.0.0/WeightIt/NEWS.md | 34 WeightIt-1.0.0/WeightIt/R/ESS.R |only WeightIt-1.0.0/WeightIt/R/SHARED.R | 112 - WeightIt-1.0.0/WeightIt/R/WeightIt-package.R |only WeightIt-1.0.0/WeightIt/R/as.weightit.R | 145 + WeightIt-1.0.0/WeightIt/R/calibrate.R |only WeightIt-1.0.0/WeightIt/R/chk-utilities.R | 15 WeightIt-1.0.0/WeightIt/R/dist_functions.R | 40 WeightIt-1.0.0/WeightIt/R/functions_for_processing.R | 546 +++-- WeightIt-1.0.0/WeightIt/R/get_w_from_ps.R |only WeightIt-1.0.0/WeightIt/R/glm_weightit.R |only WeightIt-1.0.0/WeightIt/R/make_full_rank.R |only WeightIt-1.0.0/WeightIt/R/mlogit_weightit.R |only WeightIt-1.0.0/WeightIt/R/msmdata.R |only WeightIt-1.0.0/WeightIt/R/sbps.R | 141 + WeightIt-1.0.0/WeightIt/R/summary.weightit.R |only WeightIt-1.0.0/WeightIt/R/trim.R | 271 ++ WeightIt-1.0.0/WeightIt/R/weightit.R | 393 +-- WeightIt-1.0.0/WeightIt/R/weightit.fit.R | 560 ++--- WeightIt-1.0.0/WeightIt/R/weightit2bart.R |only WeightIt-1.0.0/WeightIt/R/weightit2cbps.R |only WeightIt-1.0.0/WeightIt/R/weightit2ebal.R |only WeightIt-1.0.0/WeightIt/R/weightit2energy.R |only WeightIt-1.0.0/WeightIt/R/weightit2gbm.R |only WeightIt-1.0.0/WeightIt/R/weightit2glm.R |only WeightIt-1.0.0/WeightIt/R/weightit2ipt.R |only WeightIt-1.0.0/WeightIt/R/weightit2npcbps.R |only WeightIt-1.0.0/WeightIt/R/weightit2optweight.R |only WeightIt-1.0.0/WeightIt/R/weightit2ps.R |only WeightIt-1.0.0/WeightIt/R/weightit2super.R |only WeightIt-1.0.0/WeightIt/R/weightit2user.R |only WeightIt-1.0.0/WeightIt/R/weightitMSM.R | 348 +-- WeightIt-1.0.0/WeightIt/R/zzz.R |only WeightIt-1.0.0/WeightIt/README.md | 173 - WeightIt-1.0.0/WeightIt/build/WeightIt.pdf |binary WeightIt-1.0.0/WeightIt/build/stage23.rdb |only WeightIt-1.0.0/WeightIt/build/vignette.rds |binary WeightIt-1.0.0/WeightIt/inst/doc/WeightIt.R | 42 WeightIt-1.0.0/WeightIt/inst/doc/WeightIt.Rmd | 40 WeightIt-1.0.0/WeightIt/inst/doc/WeightIt.html | 363 +-- WeightIt-1.0.0/WeightIt/inst/doc/estimating-effects.R | 225 -- WeightIt-1.0.0/WeightIt/inst/doc/estimating-effects.Rmd | 298 +- WeightIt-1.0.0/WeightIt/inst/doc/estimating-effects.html | 1486 ++++++++------ WeightIt-1.0.0/WeightIt/inst/doc/installing-packages.Rmd | 26 WeightIt-1.0.0/WeightIt/inst/doc/installing-packages.html | 138 - WeightIt-1.0.0/WeightIt/man/ESS.Rd | 40 WeightIt-1.0.0/WeightIt/man/WeightIt-package.Rd |only WeightIt-1.0.0/WeightIt/man/as.weightit.Rd | 133 - WeightIt-1.0.0/WeightIt/man/calibrate.Rd |only WeightIt-1.0.0/WeightIt/man/get_w_from_ps.Rd | 284 +- WeightIt-1.0.0/WeightIt/man/glm_weightit.Rd |only WeightIt-1.0.0/WeightIt/man/make_full_rank.Rd | 60 WeightIt-1.0.0/WeightIt/man/method_bart.Rd | 101 WeightIt-1.0.0/WeightIt/man/method_cbps.Rd | 143 - WeightIt-1.0.0/WeightIt/man/method_ebal.Rd | 106 WeightIt-1.0.0/WeightIt/man/method_energy.Rd | 145 - WeightIt-1.0.0/WeightIt/man/method_gbm.Rd | 207 + WeightIt-1.0.0/WeightIt/man/method_glm.Rd | 208 + WeightIt-1.0.0/WeightIt/man/method_ipt.Rd |only WeightIt-1.0.0/WeightIt/man/method_npcbps.Rd | 103 WeightIt-1.0.0/WeightIt/man/method_optweight.Rd | 130 - WeightIt-1.0.0/WeightIt/man/method_super.Rd | 161 - WeightIt-1.0.0/WeightIt/man/method_user.Rd | 62 WeightIt-1.0.0/WeightIt/man/msmdata.Rd | 49 WeightIt-1.0.0/WeightIt/man/sbps.Rd | 188 - WeightIt-1.0.0/WeightIt/man/summary.weightit.Rd | 90 WeightIt-1.0.0/WeightIt/man/trim.Rd | 127 - WeightIt-1.0.0/WeightIt/man/weightit.Rd | 297 +- WeightIt-1.0.0/WeightIt/man/weightit.fit.Rd | 242 +- WeightIt-1.0.0/WeightIt/man/weightitMSM.Rd | 269 +- WeightIt-1.0.0/WeightIt/vignettes/WeightIt.Rmd | 40 WeightIt-1.0.0/WeightIt/vignettes/estimating-effects.Rmd | 298 +- WeightIt-1.0.0/WeightIt/vignettes/installing-packages.Rmd | 26 WeightIt-1.0.0/WeightIt/vignettes/references.bib | 95 79 files changed, 5371 insertions(+), 3841 deletions(-)
Title: Tukey g-&-h Distribution
Description: Functions for density,
cumulative density, quantile and
simulation of Tukey g-and-h (1977)
distributions. The quantile-based
transformation (Hoaglin 1985
<doi:10.1002/9781118150702.ch11>) and
its reverse transformation, as well as
the letter-value based estimates
(Hoaglin 1985), are also provided.
Author: Tingting Zhan [aut, cre, cph],
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between TukeyGH77 versions 0.1.0 dated 2024-03-19 and 0.1.1 dated 2024-03-23
TukeyGH77-0.1.0/TukeyGH77/R/qGH2z.R |only TukeyGH77-0.1.0/TukeyGH77/R/z2qGH.R |only TukeyGH77-0.1.0/TukeyGH77/man/qGH2z.Rd |only TukeyGH77-0.1.0/TukeyGH77/man/z2qGH.Rd |only TukeyGH77-0.1.1/TukeyGH77/DESCRIPTION | 38 ++++++++------ TukeyGH77-0.1.1/TukeyGH77/MD5 | 32 ++++++------ TukeyGH77-0.1.1/TukeyGH77/NAMESPACE | 11 +++- TukeyGH77-0.1.1/TukeyGH77/NEWS.md | 3 - TukeyGH77-0.1.1/TukeyGH77/R/0info.R | 9 ++- TukeyGH77-0.1.1/TukeyGH77/R/GH2z.R |only TukeyGH77-0.1.1/TukeyGH77/R/TukeyGH.R | 39 ++++++-------- TukeyGH77-0.1.1/TukeyGH77/R/helper.R | 56 ++------------------- TukeyGH77-0.1.1/TukeyGH77/R/letterValue.R |only TukeyGH77-0.1.1/TukeyGH77/R/vuniroot2.R | 11 ++-- TukeyGH77-0.1.1/TukeyGH77/R/z2GH.R |only TukeyGH77-0.1.1/TukeyGH77/man/GH2z.Rd |only TukeyGH77-0.1.1/TukeyGH77/man/TukeyGH.Rd | 26 +++------ TukeyGH77-0.1.1/TukeyGH77/man/TukeyGH77-package.Rd | 9 +++ TukeyGH77-0.1.1/TukeyGH77/man/TukeyGH_helper.Rd | 39 +++++++------- TukeyGH77-0.1.1/TukeyGH77/man/letterValue.Rd |only TukeyGH77-0.1.1/TukeyGH77/man/vuniroot2.Rd | 9 +-- TukeyGH77-0.1.1/TukeyGH77/man/z2GH.Rd |only 22 files changed, 128 insertions(+), 154 deletions(-)