Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
Author: Guangchuang Yu [aut, cre, cph]
,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.1.6 dated 2024-08-28 and 0.1.7 dated 2024-10-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 4 ++++ NEWS.md | 5 +++++ R/operator.R | 14 ++++++++++---- R/treedata-function.R |only inst/doc/ggfun.html | 6 +++--- man/td_filter.Rd |only man/td_mutate.Rd |only man/td_unnest.Rd |only 10 files changed, 34 insertions(+), 15 deletions(-)
Title: Motivational Quotes and Shakespearean Bard–bits for Personal
Projects
Description: Generate motivational quotes and Shakespearean word combinations (bard–bits) that a user can consider for their personal projects. Each of the package functions takes two arguments, cat which default to any, and a a numeric or character seed to ensure reproducible results.
Author: JP Monteagudo [aut, cre, cph]
Maintainer: JP Monteagudo <jpmonteagudo2014@gmail.com>
Diff between despair versions 0.1.0 dated 2024-08-22 and 0.1.1 dated 2024-10-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 +++++-- R/demotivate.R | 3 ++- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Patrick J. Breheny [aut, cre] ,
Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.0.0 dated 2024-10-11 and 4.1.0 dated 2024-10-23
DESCRIPTION | 8 +-- MD5 | 84 ++++++++++++++++++++--------------------- NEWS.md | 10 ++++ R/coef-cv-plmm.R | 2 R/coef-plmm.R | 2 R/create_design.R | 17 +++----- R/create_design_filebacked.R | 1 R/create_design_in_memory.R | 12 ++--- R/cv-plmm.R | 29 +++++++++++++- R/loss-plmm.R | 2 R/plmm.R | 32 +++++++++++++-- R/plmm_checks.R | 1 R/plot-cv-plmm.R | 2 R/plot-plmm.R | 2 R/predict-plmm.R | 2 R/print-summary-cv-plmm.R | 2 R/print-summary-plmm.R | 2 R/summary-cv-plmm.R | 2 R/summary-plmm.R | 2 R/untransform.R | 2 README.md | 28 +++++++++++-- data/admix.rda |binary inst/doc/getting-started.R | 9 ++++ inst/doc/getting-started.Rmd | 19 +++++++-- inst/doc/getting-started.html | 32 +++++++++++---- inst/tinytest/test_cv.R | 2 inst/tinytest/test_plmm.R | 4 - man/coef.cv_plmm.Rd | 2 man/coef.plmm.Rd | 2 man/create_design.Rd | 18 ++------ man/create_design_in_memory.Rd | 4 - man/cv_plmm.Rd | 12 ++++- man/plmm.Rd | 12 ++++- man/plmm_loss.Rd | 2 man/plot.cv_plmm.Rd | 2 man/plot.plmm.Rd | 2 man/predict.plmm.Rd | 2 man/print.summary.cv_plmm.Rd | 2 man/print.summary.plmm.Rd | 2 man/summary.cv_plmm.Rd | 2 man/summary.plmm.Rd | 2 src/plmm_init.c | 1 vignettes/getting-started.Rmd | 19 +++++++-- 43 files changed, 268 insertions(+), 128 deletions(-)
Title: Maximum Likelihood Estimation of Various Univariate and
Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre],
Sofia Piperaki [aut],
Muhammad Imran [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MLE versions 1.1 dated 2024-09-10 and 1.2 dated 2024-10-23
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/positive.mle.R | 41 +++++++++++++++++++++++++++++++++++++++++ man/MLE-package.Rd | 4 ++-- man/positive.mle.Rd | 6 +++++- 6 files changed, 60 insertions(+), 13 deletions(-)
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.9.4 dated 2024-09-03 and 2.9.6 dated 2024-10-23
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ inst/NEWS | 7 +++++++ inst/doc/distrMod.pdf |binary man/0distrMod-package.Rd | 6 +++--- man/fiCov.Rd | 2 +- tests/Examples/distrMod-Ex.Rout.save | 2 +- 7 files changed, 26 insertions(+), 19 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 [aut, cre],
Simon J Bonner [aut]
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between BTSPAS versions 2024.5.9 dated 2024-05-10 and 2024.11.1 dated 2024-10-23
DESCRIPTION | 24 ++++++++++++++------- MD5 | 26 +++++++++++------------ NEWS.md | 6 +++++ R/TimeStratPetersenDiagErrorWHChinook2_fit.R | 2 - R/TimeStratPetersenDiagErrorWHChinook_fit.R | 2 - R/TimeStratPetersenDiagErrorWHSteel_fit.R | 2 - R/TimeStratPetersenDiagError_fit.R | 7 ++++-- R/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.R | 2 - R/TimeStratPetersenNonDiagErrorNP_fit.R | 2 - R/TimeStratPetersenNonDiagError_fit.R | 3 +- R/run_jags.R | 14 +++++++++++- R/zzz.R | 11 +-------- build/partial.rdb |binary build/vignette.rds |binary 14 files changed, 62 insertions(+), 39 deletions(-)
Title: Extract 'REDCap' Databases into Tidy 'Tibble's
Description: Convert 'REDCap' exports into tidy tables for easy handling of 'REDCap' repeat instruments and event arms.
Author: Richard Hanna [aut, cre] ,
Stephan Kadauke [aut] ,
Ezra Porter [aut]
Maintainer: Richard Hanna <richardshanna91@gmail.com>
Diff between REDCapTidieR versions 1.1.1 dated 2024-04-16 and 1.2.0 dated 2024-10-23
DESCRIPTION | 12 +- MD5 | 55 ++++++----- NAMESPACE | 21 ++++ NEWS.md | 15 ++- R/REDCapTidieR-package.R | 19 ++- R/checks.R | 125 +++++++++++++++++++++++++ R/clean_redcap_long.R | 76 +++++++++++++-- R/combine_checkboxes.R |only R/read_redcap.R | 93 ++++++++++++++++-- R/utils.R | 82 ++++++++++++---- README.md | 3 build/vignette.rds |binary inst/WORDLIST | 8 + inst/doc/REDCapTidieR.Rmd | 2 inst/doc/REDCapTidieR.html | 116 ++++++++--------------- man/add_event_mapping.Rd | 5 - man/check_equal_col_summaries.Rd |only man/check_fields_are_checkboxes.Rd |only man/check_fields_exist.Rd |only man/check_metadata_fields_exist.Rd |only man/combine_and_repair_tbls.Rd |only man/combine_checkboxes.Rd |only man/convert_checkbox_vals.Rd |only man/extract_metadata_tibble.Rd |only man/get_metadata_spec.Rd |only man/get_repeat_event_types.Rd |only man/read_redcap.Rd | 4 man/replace_true.Rd |only tests/testthat/_snaps/write.md | 154 +++++++++++++++++++++++++++---- tests/testthat/test-checks.R | 69 +++++++++++++ tests/testthat/test-clean_redcap_long.R | 29 +++-- tests/testthat/test-combine_checkboxes.R |only tests/testthat/test-read_redcap.R | 40 ++++++++ tests/testthat/test-utils.R | 46 ++++++++- vignettes/REDCapTidieR.Rmd | 2 35 files changed, 785 insertions(+), 191 deletions(-)
Title: Modelling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted
eigenvector maps.
Author: Guillaume Guenard [aut, cre] ,
Pierre Legendre [ctb]
Maintainer: Guillaume Guenard <guillaume.guenard@umontreal.ca>
Diff between MPSEM versions 0.4-4 dated 2024-09-04 and 0.5-1 dated 2024-10-23
DESCRIPTION | 10 - MD5 | 42 ++--- NAMESPACE | 4 R/MPSEM-package.R | 6 R/PEM-class.R | 4 R/PEM-functions.R | 143 ++++++++---------- R/dstGraph.R |only R/dst_idx.R |only R/global.R |only R/graph-class.R | 4 R/graph-functions.R | 4 R/lm-utils.R | 4 R/trait-simulator.R | 8 - build/partial.rdb |binary inst/doc/REM_with_MPSEM.R | 2 inst/doc/REM_with_MPSEM.Rmd | 2 inst/doc/REM_with_MPSEM.html | 341 +++++++++++++++++++++---------------------- man/MPSEM-package.Rd | 2 man/PEM-functions.Rd | 41 ++--- man/dstGraph.Rd |only src/MPSEM.c | 161 ++++++++++++++++---- src/MPSEM.h | 36 ++-- src/init.c | 8 - vignettes/REM_with_MPSEM.Rmd | 2 24 files changed, 466 insertions(+), 358 deletions(-)
Title: Fit, Simulate, and Diagnose Hierarchical Exponential-Family
Models for Big Networks
Description: A toolbox for analyzing and simulating large networks based on hierarchical exponential-family random graph models (HERGMs).'bigergm' implements the estimation for large networks efficiently building on the 'lighthergm' and 'hergm' packages. Moreover, the package contains tools for simulating networks with local dependence to assess the goodness-of-fit.
Author: Cornelius Fritz [aut, cre],
Michael Schweinberger [aut],
Shota Komatsu [aut],
Juan Nelson Martinez Dahbura [aut],
Takanori Nishida [aut],
Angelo Mele [aut]
Maintainer: Cornelius Fritz <corneliusfritz2010@gmail.com>
Diff between bigergm versions 1.2.2 dated 2024-10-03 and 1.2.3 dated 2024-10-23
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- vignettes/bigergm.html | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: Synthetic Population Generator
Description: Generates high-entropy integer synthetic populations from marginal and (optionally) seed data using quasirandom sampling,
in arbitrary dimensionality (Smith, Lovelace and Birkin (2017) <doi:10.18564/jasss.3550>).
The package also provides an implementation of the Iterative Proportional Fitting (IPF) algorithm (Zaloznik (2011) <doi:10.13140/2.1.2480.9923>).
Author: Andrew Smith [aut, cre],
Steven Johnson [ctb] ,
Massachusetts Institute of Technology [cph] ,
John Burkhardt [ctb, cph] ,
G Bhattacharjee [ctb]
Maintainer: Andrew Smith <andrew@friarswood.net>
Diff between humanleague versions 2.3.1 dated 2024-02-24 and 2.3.2 dated 2024-10-23
DESCRIPTION | 6 ++-- MD5 | 17 ++++++------- src/Integerise.cpp | 1 src/Microsynthesis.h | 21 ++++++---------- src/NDArrayUtils.h | 19 ++++++++++++++ src/TestNDArray.cpp | 56 ------------------------------------------- src/TestSobol.cpp | 65 +++++++++++++++++++++++--------------------------- src/TestStatFuncs.cpp | 1 src/UnitTester.cpp | 2 - tests/test_errors.py |only 10 files changed, 71 insertions(+), 117 deletions(-)
Title: Data Mining Classification and Regression Methods
Description: Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions. Versions: 1.4.7 improved Importance function and examples, minor error fixes; 1.4.6 / 1.4.5 / 1.4.4 new automated machine learning (AutoML) and ensembles, via improved fit(), mining() and mparheuristic() functions, and new categorical preprocessing, via improved delevels() function; 1.4.3 new metrics (e.g., macro precision, explained variance), new "lssvm" model and improved mparheuristic() function; 1.4.2 new "NMAE" metric, "xgboost" and "cv.glmnet" models (16 classification and 18 regression models); 1.4.1 new tutorial and more robust version; 1.4 - new classification and regression models, with a total of 14 classification and 15 regression methods, including: Decision Trees, Neural Networks, Support Vector Machines, Random Forests, Bagging and Boosting; 1.3 and 1.3.1 - new classification and regression metrics; [...truncated...]
Author: Paulo Cortez [aut, cre]
Maintainer: Paulo Cortez <pcortez@dsi.uminho.pt>
Diff between rminer versions 1.4.6 dated 2020-08-28 and 1.4.7 dated 2024-10-23
DESCRIPTION | 11 - MD5 | 39 +++--- R/metrics.R | 2 R/model.R | 294 ++++++++++++++++++++++++++++++++------------------- R/plots.R | 21 ++- R/preprocess.R | 6 - build |only data/sa_tree.rda |binary man/CasesSeries.Rd | 2 man/Importance.Rd | 52 ++++++++- man/crossvaldata.Rd | 2 man/delevels.Rd | 2 man/fit.Rd | 70 ++++++------ man/lforecast.Rd | 2 man/mgraph.Rd | 3 man/mining.Rd | 6 - man/mmetric.Rd | 4 man/mparheuristic.Rd | 9 - man/sa_fri1.Rd | 2 man/sin1reg.Rd | 2 man/vecplot.Rd | 4 21 files changed, 333 insertions(+), 200 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Laura Marshall [cre],
Jeff Laake [aut],
David Miller [aut],
Felix Petersma [aut],
Len Thomas [ctb],
David Borchers [ctb],
Jon Bishop [ctb],
Jonah McArthur [ctb],
Eric Rexstad [rev]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.3.0 dated 2023-12-18 and 3.0.0 dated 2024-10-23
DESCRIPTION | 32 +++- MD5 | 74 +++++++---- NAMESPACE | 1 NEWS | 15 ++ R/adj.cos.R |only R/adj.herm.R |only R/adj.poly.R |only R/adj.series.grad.cos.R |only R/adj.series.grad.herm.R |only R/adj.series.grad.poly.R |only R/check.mono.R | 37 +++-- R/ddf.R | 15 +- R/ddf.ds.R | 22 ++- R/detfct.fit.R | 3 R/detfct.fit.mono.R | 43 +++--- R/detfct.fit.opt.R | 291 +++++++++++++++++++++++++++++++++++--------- R/distpdf.grad.R |only R/flnl.constr.grad.R |only R/flnl.grad.R |only R/gstdint.R | 4 R/integratepdf.grad.R |only R/keyfct.grad.hn.R |only R/keyfct.grad.hz.R |only R/mcds_tools.R | 36 +++-- R/mrds-package.R | 33 ++++ R/nlminb_wrapper.R | 2 R/rescale_pars.R | 2 R/zzz.R | 8 - README.md | 2 build/partial.rdb |binary man/adj.cos.Rd |only man/adj.herm.Rd |only man/adj.poly.Rd |only man/adj.series.grad.cos.Rd |only man/adj.series.grad.herm.Rd |only man/adj.series.grad.poly.Rd |only man/check.mono.Rd | 6 man/ddf.Rd | 15 +- man/detfct.fit.opt.Rd | 7 - man/distpdf.grad.Rd |only man/flnl.constr.grad.neg.Rd |only man/flnl.grad.Rd |only man/integratepdf.grad.Rd |only man/keyfct.grad.hn.Rd |only man/keyfct.grad.hz.Rd |only man/mcds_dot_exe.Rd | 35 +++-- man/mrds-package.Rd | 6 man/mrds_opt.Rd | 201 +++++++++++++++++------------- man/nlminb_wrapper.Rd | 2 man/rescale_pars.Rd | 2 50 files changed, 623 insertions(+), 271 deletions(-)
Title: K-Means for Joint Longitudinal Data
Description: An implementation of k-means specifically design
to cluster joint trajectories (longitudinal data on
several variable-trajectories).
Like 'kml', it provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical
interface for choosing the 'best' number of clusters. In addition, the 3D graph
representing the mean joint-trajectories of each cluster can be exported through
LaTeX in a 3D dynamic rotating PDF graph.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Patrice Kiener [ctb],
Jean-Baptiste Pingault [ctb]
Maintainer: Christophe Genolini <christophe.genolini@free.fr>
Diff between kml3d versions 2.4.6.1 dated 2023-12-13 and 2.5.0 dated 2024-10-23
DESCRIPTION | 30 ++++++++++++++---------------- MD5 | 26 +++++++++++++------------- NEWS | 11 +++++++++++ man/ClusterLongData3d-class.Rd | 24 ++++++++++++------------ man/clusterLongData3d.Rd | 2 +- man/generateArtificialLongData3d.Rd | 6 +++--- man/kml3d-package.Rd | 8 ++++---- man/kml3d.Rd | 20 ++++++++++---------- man/parKml3d.Rd | 12 ++++++------ man/plot.Rd | 18 +++++++++++------- man/plot3d.Rd | 16 ++++++++-------- man/plot3dPdf.Rd | 17 ++++++++++------- man/plotMean3d.Rd | 12 ++++++------ man/plotTraj3d.Rd | 12 ++++++------ 14 files changed, 115 insertions(+), 99 deletions(-)
Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design
to cluster longitudinal data. It provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Patrice Kiener [ctb]
Maintainer: Christophe Genolini <christophe.genolini@free.fr>
Diff between kml versions 2.4.6.1 dated 2023-12-13 and 2.5.0 dated 2024-10-23
DESCRIPTION | 25 +- MD5 | 24 +- NEWS | 28 +++ man/ClusterLongData-class.Rd | 380 ++++++++++++++++++++++--------------------- man/ParKml-class.Rd | 232 +++++++++++++------------- man/choice.Rd | 260 +++++++++++++++-------------- man/getBestPostProba.Rd | 106 +++++------ man/kml-package.Rd | 302 +++++++++++++++++----------------- man/kml.Rd | 286 ++++++++++++++++---------------- man/parKml.Rd | 240 +++++++++++++-------------- man/plot.Rd | 279 +++++++++++++++---------------- man/plotMeans.Rd | 173 +++++++++---------- man/plotTraj.Rd | 189 ++++++++++----------- 13 files changed, 1294 insertions(+), 1230 deletions(-)
Title: General Unified Threshold Model of Survival for Bees using
Bayesian Inference
Description: Tools to calibrate, validate, and make predictions with the
General Unified Threshold model of Survival adapted for Bee species. The
model is presented in the publication from Baas, J., Goussen, B., Miles, M.,
Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and
Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G.,
van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the
GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011)
<doi:10.1021/es103092a>.
The authors are grateful to Bayer A.G. for its financial support.
Author: Benoit Goussen [aut, cre] ,
Liubov Zakharova [ctb],
Romoli Carlo [ctb],
Bayer AG [cph],
ibacon GmbH [cph]
Maintainer: Benoit Goussen <benoit.goussen@ibacon.com>
Diff between BeeGUTS versions 1.1.3 dated 2023-09-18 and 1.3.0 dated 2024-10-23
DESCRIPTION | 21 MD5 | 86 NAMESPACE | 12 NEWS.md | 11 R/BeeGUTS-Internal.R | 4 R/BeeGUTS-package.R | 38 R/LCx.R | 75 R/ShortTimeEffects.R |only R/TimeReinforcedToxicity.R |only R/plotBeeGUTS.R | 160 + R/ppc.R | 28 R/predictBeeGUTS.R | 19 R/predictBeeGUTS2.R |only R/readData.R | 6 R/stanmodels.R | 3 R/validateBeeGUTS.R | 148 + README.md | 123 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/Tutorial.R | 2 inst/doc/Tutorial.Rmd | 11 inst/doc/Tutorial.html | 58 inst/stan/GUTS_hb_only.stan |only man/BeeGUTS-package.Rd | 34 man/ShortTimeEffects.Rd |only man/ShortTimeEffects.beeSurvFit.Rd |only man/TRT.Rd |only man/TRT.beeSurvFit.Rd |only man/correlation_plot.Rd |only man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/ppc.beeSurvValidation.Rd |only man/predict.beeSurvFit.Rd | 4 man/predict2.Rd |only man/priorposterior_plot.Rd |only man/validate.Rd | 10 man/validate.beeSurvFit.Rd | 10 src/RcppExports.cpp | 2 src/stanExports_GUTS_IT.h | 2762 +++++++++++++-------------- src/stanExports_GUTS_SD.h | 2664 ++++++++++++-------------- src/stanExports_GUTS_hb_only.cc |only src/stanExports_GUTS_hb_only.h |only vignettes/Tutorial.Rmd | 11 vignettes/man/figures/Tutorial-example-1.png |binary vignettes/man/figures/Tutorial-example-2.png |binary vignettes/man/figures/Tutorial-example-3.png |binary vignettes/man/figures/Tutorial-example-4.png |binary vignettes/man/figures/Tutorial-example-5.png |binary 51 files changed, 3390 insertions(+), 2912 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/data-documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <bskinner@neh.gov>
Diff between rscorecard versions 0.29.0 dated 2024-08-30 and 0.30.0 dated 2024-10-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/sysdata.rda |binary 4 files changed, 10 insertions(+), 6 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.3.0 dated 2024-08-19 and 3.4.0 dated 2024-10-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 ++++- R/makeDF.R | 4 ++-- man/Rlabkey-package.Rd | 4 ++-- 5 files changed, 16 insertions(+), 13 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]
Maintainer: Romain Leroux <romain.leroux@inserm.fr>
Diff between PFIM versions 6.0.3 dated 2024-03-23 and 6.1 dated 2024-10-23
PFIM-6.0.3/PFIM/man/ModelODEBolus-class.Rd |only PFIM-6.1/PFIM/DESCRIPTION | 24 PFIM-6.1/PFIM/MD5 | 653 ++++--- PFIM-6.1/PFIM/NAMESPACE | 62 PFIM-6.1/PFIM/R/Administration.R | 10 PFIM-6.1/PFIM/R/AdministrationConstraints.R | 7 PFIM-6.1/PFIM/R/Arm.R | 99 + PFIM-6.1/PFIM/R/Combined1.R | 11 PFIM-6.1/PFIM/R/Constant.R | 11 PFIM-6.1/PFIM/R/Design.R | 254 +- PFIM-6.1/PFIM/R/Distribution.R | 6 PFIM-6.1/PFIM/R/Evaluation.R | 236 +- PFIM-6.1/PFIM/R/FedorovWynnAlgorithm.R | 174 -- PFIM-6.1/PFIM/R/Fim.R | 33 PFIM-6.1/PFIM/R/GenericMethods.R | 4 PFIM-6.1/PFIM/R/LibraryOfModels.R | 7 PFIM-6.1/PFIM/R/LibraryOfPKModels.R | 241 +- PFIM-6.1/PFIM/R/LibraryOfPKPDModels.R | 5 PFIM-6.1/PFIM/R/LogNormal.R | 6 PFIM-6.1/PFIM/R/Model.R | 141 + PFIM-6.1/PFIM/R/ModelAnalytic.R | 507 ++--- PFIM-6.1/PFIM/R/ModelAnalyticBolus.R | 11 PFIM-6.1/PFIM/R/ModelAnalyticBolusSteadyState.R | 10 PFIM-6.1/PFIM/R/ModelAnalyticInfusion.R | 800 ++++----- PFIM-6.1/PFIM/R/ModelAnalyticInfusionSteadyState.R | 812 ++++----- PFIM-6.1/PFIM/R/ModelAnalyticSteadyState.R | 515 ++---- PFIM-6.1/PFIM/R/ModelBolus.R | 14 PFIM-6.1/PFIM/R/ModelError.R | 11 PFIM-6.1/PFIM/R/ModelInfusion.R | 14 PFIM-6.1/PFIM/R/ModelODE.R | 17 PFIM-6.1/PFIM/R/ModelODEBolus.R | 542 ++---- PFIM-6.1/PFIM/R/ModelODEDoseInEquations.R | 515 ++---- PFIM-6.1/PFIM/R/ModelODEDoseNotInEquations.R | 416 ++-- PFIM-6.1/PFIM/R/ModelODEInfusion.R | 18 PFIM-6.1/PFIM/R/ModelODEInfusionDoseInEquations.R | 432 ++--- PFIM-6.1/PFIM/R/ModelParameter.R | 9 PFIM-6.1/PFIM/R/MultiplicativeAlgorithm.R | 191 +- PFIM-6.1/PFIM/R/Normal.R | 6 PFIM-6.1/PFIM/R/Optimization.R | 168 - PFIM-6.1/PFIM/R/OptimizationAlgorithm.R | 42 PFIM-6.1/PFIM/R/PFIM-package.R | 16 PFIM-6.1/PFIM/R/PFIMProject.R | 9 PFIM-6.1/PFIM/R/PGBOAlgorithm.R | 37 PFIM-6.1/PFIM/R/PSOAlgorithm.R | 38 PFIM-6.1/PFIM/R/PlotEvaluation.R | 170 - PFIM-6.1/PFIM/R/PopulationFim.R | 857 +++++----- PFIM-6.1/PFIM/R/Proportional.R | 11 PFIM-6.1/PFIM/R/SamplingTimeConstraints.R | 12 PFIM-6.1/PFIM/R/SamplingTimes.R | 9 PFIM-6.1/PFIM/R/SimplexAlgorithm.R | 12 PFIM-6.1/PFIM/build/partial.rdb |binary PFIM-6.1/PFIM/build/vignette.rds |binary PFIM-6.1/PFIM/inst/doc/Example01.R | 58 PFIM-6.1/PFIM/inst/doc/Example01.Rmd | 8 PFIM-6.1/PFIM/inst/doc/Example01.html | 213 +- PFIM-6.1/PFIM/inst/doc/Example02.R | 48 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/templateEvaluationBayesianFim.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/templateEvaluationIndividualFim.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/templateEvaluationPopulationFim.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_FedorovAlgorithm.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_PGBOAlgorithm.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_PSOAlgorithm.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_SimplexAlgorithm.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_evaluation.Rmd | 2 PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_multiplicativeAlgorithm.Rmd | 2 PFIM-6.1/PFIM/man/Administration-class.Rd | 56 PFIM-6.1/PFIM/man/AdministrationConstraints-class.Rd | 52 PFIM-6.1/PFIM/man/BayesianFim-class.Rd | 22 PFIM-6.1/PFIM/man/Combined1-class.Rd | 54 PFIM-6.1/PFIM/man/Constant-class.Rd | 52 PFIM-6.1/PFIM/man/Design-class.Rd | 56 PFIM-6.1/PFIM/man/Distribution-class.Rd | 46 PFIM-6.1/PFIM/man/EvaluateArm.Rd | 54 PFIM-6.1/PFIM/man/EvaluateDesign.Rd | 48 PFIM-6.1/PFIM/man/EvaluateErrorModelDerivatives.Rd | 44 PFIM-6.1/PFIM/man/EvaluateFisherMatrix.Rd | 70 PFIM-6.1/PFIM/man/EvaluateModel.Rd | 96 - PFIM-6.1/PFIM/man/EvaluateModelGradient.Rd |only PFIM-6.1/PFIM/man/EvaluateVarianceFIM.Rd | 62 PFIM-6.1/PFIM/man/EvaluateVarianceModel.Rd | 50 PFIM-6.1/PFIM/man/Evaluation-class.Rd | 60 PFIM-6.1/PFIM/man/FedorovWynnAlgorithm-class.Rd | 62 PFIM-6.1/PFIM/man/FedorovWynnAlgorithm_Rcpp.Rd | 98 - PFIM-6.1/PFIM/man/Fim-class.Rd | 54 PFIM-6.1/PFIM/man/IndividualFim-class.Rd | 22 PFIM-6.1/PFIM/man/LibraryOfModels-class.Rd | 48 PFIM-6.1/PFIM/man/LibraryOfPDModels.Rd | 22 PFIM-6.1/PFIM/man/LibraryOfPKModels.Rd | 22 PFIM-6.1/PFIM/man/LibraryOfPKPDModels-class.Rd | 22 PFIM-6.1/PFIM/man/LogNormal-class.Rd | 22 PFIM-6.1/PFIM/man/Model-class.Rd | 64 PFIM-6.1/PFIM/man/ModelAnalytic-class.Rd | 22 PFIM-6.1/PFIM/man/ModelAnalyticBolus-class.Rd | 22 PFIM-6.1/PFIM/man/ModelAnalyticBolusSteadyState-class.Rd | 22 PFIM-6.1/PFIM/man/ModelAnalyticInfusion-class.Rd | 22 PFIM-6.1/PFIM/man/ModelAnalyticInfusionSteadyState-class.Rd | 22 PFIM-6.1/PFIM/man/ModelAnalyticSteadyState-class.Rd | 22 PFIM-6.1/PFIM/man/ModelBolus-class.Rd | 20 PFIM-6.1/PFIM/man/ModelError-class.Rd | 20 PFIM-6.1/PFIM/man/ModelInfusion-class.Rd | 20 PFIM-6.1/PFIM/man/ModelODE-class.Rd | 22 PFIM-6.1/PFIM/man/ModelODEDoseInEquations-class.Rd | 22 PFIM-6.1/PFIM/man/ModelODEDoseNotInEquations-class.Rd | 20 PFIM-6.1/PFIM/man/ModelODEInfusion-class.Rd | 22 PFIM-6.1/PFIM/man/ModelODEInfusionDoseInEquations-class.Rd | 22 PFIM-6.1/PFIM/man/ModelParameter-class.Rd | 52 PFIM-6.1/PFIM/man/MultiplicativeAlgorithm-class.Rd | 59 PFIM-6.1/PFIM/man/MultiplicativeAlgorithm_Rcpp.Rd | 74 PFIM-6.1/PFIM/man/Normal-class.Rd | 22 PFIM-6.1/PFIM/man/Optimization-class.Rd | 72 PFIM-6.1/PFIM/man/OptimizationAlgorithm-class.Rd | 48 PFIM-6.1/PFIM/man/PFIM-package.Rd | 22 PFIM-6.1/PFIM/man/PFIMProject-class.Rd | 48 PFIM-6.1/PFIM/man/PGBOAlgorithm-class.Rd | 70 PFIM-6.1/PFIM/man/PSOAlgorithm-class.Rd | 60 PFIM-6.1/PFIM/man/PlotEvaluation-class.Rd | 22 PFIM-6.1/PFIM/man/PopulationFim-class.Rd | 22 PFIM-6.1/PFIM/man/Proportional-class.Rd | 52 PFIM-6.1/PFIM/man/Report.Rd | 58 PFIM-6.1/PFIM/man/SamplingTimeConstraints-class.Rd | 58 PFIM-6.1/PFIM/man/SamplingTimes-class.Rd | 48 PFIM-6.1/PFIM/man/SimplexAlgorithm-class.Rd | 56 PFIM-6.1/PFIM/man/addModel.Rd | 44 PFIM-6.1/PFIM/man/addModels.Rd | 44 PFIM-6.1/PFIM/man/checkSamplingTimeConstraintsForContinuousOptimization.Rd | 76 PFIM-6.1/PFIM/man/checkValiditySamplingConstraint.Rd | 40 PFIM-6.1/PFIM/man/computeVMat.Rd |only PFIM-6.1/PFIM/man/convertPKModelAnalyticToPKModelODE.Rd | 54 PFIM-6.1/PFIM/man/dataForArmEvaluation.Rd |only PFIM-6.1/PFIM/man/defineModel.Rd | 44 PFIM-6.1/PFIM/man/defineModelEquationsFromStringToFunction.Rd |only PFIM-6.1/PFIM/man/defineModelFromLibraryOfModels.Rd | 44 PFIM-6.1/PFIM/man/defineModelType.Rd | 44 PFIM-6.1/PFIM/man/defineModelUserDefined.Rd | 44 PFIM-6.1/PFIM/man/definePKModel.Rd | 80 PFIM-6.1/PFIM/man/definePKPDModel.Rd | 114 - PFIM-6.1/PFIM/man/fisher.simplex.Rd | 42 PFIM-6.1/PFIM/man/fun.amoeba.Rd | 64 PFIM-6.1/PFIM/man/generateFimsFromConstraints.Rd | 44 PFIM-6.1/PFIM/man/generateReportEvaluation.Rd | 118 - PFIM-6.1/PFIM/man/generateReportOptimization.Rd | 156 - PFIM-6.1/PFIM/man/generateSamplingsFromSamplingConstraints.Rd | 40 PFIM-6.1/PFIM/man/generateTables.Rd | 50 PFIM-6.1/PFIM/man/getAdjustedGradient.Rd | 50 PFIM-6.1/PFIM/man/getAdministration.Rd | 44 PFIM-6.1/PFIM/man/getAdministrationConstraint.Rd | 44 PFIM-6.1/PFIM/man/getAdministrations.Rd | 42 PFIM-6.1/PFIM/man/getAdministrationsConstraints.Rd | 40 PFIM-6.1/PFIM/man/getArms.Rd | 48 PFIM-6.1/PFIM/man/getColumnAndParametersNamesFIM.Rd | 58 PFIM-6.1/PFIM/man/getColumnAndParametersNamesFIMInLatex.Rd | 58 PFIM-6.1/PFIM/man/getConditionNumberFixedEffects.Rd | 40 PFIM-6.1/PFIM/man/getConditionNumberVarianceEffects.Rd | 46 PFIM-6.1/PFIM/man/getContent.Rd | 40 PFIM-6.1/PFIM/man/getDataForArmEvaluation.Rd |only PFIM-6.1/PFIM/man/getDataFrameResults.Rd | 10 PFIM-6.1/PFIM/man/getDelta.Rd | 40 PFIM-6.1/PFIM/man/getDerivatives.Rd | 40 PFIM-6.1/PFIM/man/getDescription.Rd | 40 PFIM-6.1/PFIM/man/getDesigns.Rd | 40 PFIM-6.1/PFIM/man/getDistribution.Rd | 40 PFIM-6.1/PFIM/man/getDose.Rd | 46 PFIM-6.1/PFIM/man/getEigenValues.Rd | 40 PFIM-6.1/PFIM/man/getElementaryProtocols.Rd | 46 PFIM-6.1/PFIM/man/getEquation.Rd | 40 PFIM-6.1/PFIM/man/getEquations.Rd | 40 PFIM-6.1/PFIM/man/getEquationsAfterInfusion.Rd | 40 PFIM-6.1/PFIM/man/getEquationsDuringInfusion.Rd | 40 PFIM-6.1/PFIM/man/getEvaluationFIMResults.Rd | 40 PFIM-6.1/PFIM/man/getEvaluationInitialDesignResults.Rd | 40 PFIM-6.1/PFIM/man/getFixedEffects.Rd | 40 PFIM-6.1/PFIM/man/getFixedMu.Rd | 40 PFIM-6.1/PFIM/man/getFixedOmega.Rd | 40 PFIM-6.1/PFIM/man/getFixedParameters.Rd | 40 PFIM-6.1/PFIM/man/getFixedTimes.Rd | 40 PFIM-6.1/PFIM/man/getInitialConditions.Rd | 46 PFIM-6.1/PFIM/man/getIterationAndCriteria.Rd | 40 PFIM-6.1/PFIM/man/getLambda.Rd | 40 PFIM-6.1/PFIM/man/getLibraryPDModels.Rd | 40 PFIM-6.1/PFIM/man/getLibraryPKModels.Rd | 40 PFIM-6.1/PFIM/man/getMinSampling.Rd | 40 PFIM-6.1/PFIM/man/getModel.Rd | 40 PFIM-6.1/PFIM/man/getModelEquations.Rd | 40 PFIM-6.1/PFIM/man/getModelError.Rd | 46 PFIM-6.1/PFIM/man/getModelErrorParametersValues.Rd | 40 PFIM-6.1/PFIM/man/getModelFromLibrary.Rd | 40 PFIM-6.1/PFIM/man/getModelParameters.Rd | 40 PFIM-6.1/PFIM/man/getModelParametersValues.Rd | 40 PFIM-6.1/PFIM/man/getMu.Rd | 48 PFIM-6.1/PFIM/man/getName.Rd | 72 PFIM-6.1/PFIM/man/getNames.Rd | 40 PFIM-6.1/PFIM/man/getNumberOfArms.Rd | 40 PFIM-6.1/PFIM/man/getNumberOfIterations.Rd | 40 PFIM-6.1/PFIM/man/getNumberOfParameters.Rd | 40 PFIM-6.1/PFIM/man/getNumberOfTimesByWindows.Rd | 40 PFIM-6.1/PFIM/man/getNumberOfsamplingsOptimisable.Rd | 40 PFIM-6.1/PFIM/man/getOdeSolverParameters.Rd | 46 PFIM-6.1/PFIM/man/getOmega.Rd | 48 PFIM-6.1/PFIM/man/getOptimalDesign.Rd | 40 PFIM-6.1/PFIM/man/getOptimalWeights.Rd | 40 PFIM-6.1/PFIM/man/getOptimizationResults.Rd | 40 PFIM-6.1/PFIM/man/getOptimizer.Rd | 40 PFIM-6.1/PFIM/man/getOptimizerParameters.Rd | 40 PFIM-6.1/PFIM/man/getOutcome.Rd | 68 PFIM-6.1/PFIM/man/getOutcomes.Rd | 46 PFIM-6.1/PFIM/man/getOutcomesEvaluation.Rd | 40 PFIM-6.1/PFIM/man/getOutcomesForEvaluation.Rd | 40 PFIM-6.1/PFIM/man/getOutcomesGradient.Rd | 40 PFIM-6.1/PFIM/man/getPDModel.Rd | 44 PFIM-6.1/PFIM/man/getPKModel.Rd | 44 PFIM-6.1/PFIM/man/getPKPDModel.Rd | 44 PFIM-6.1/PFIM/man/getParameters.Rd | 54 PFIM-6.1/PFIM/man/getPlotOptions.Rd | 38 PFIM-6.1/PFIM/man/getProportionsOfSubjects.Rd | 40 PFIM-6.1/PFIM/man/getSamplingTime.Rd | 44 PFIM-6.1/PFIM/man/getSamplingTimeConstraint.Rd | 44 PFIM-6.1/PFIM/man/getSamplingTimes.Rd | 40 PFIM-6.1/PFIM/man/getSamplingTimesConstraints.Rd | 40 PFIM-6.1/PFIM/man/getSamplings.Rd | 48 PFIM-6.1/PFIM/man/getSamplingsWindows.Rd | 40 PFIM-6.1/PFIM/man/getSigmaInter.Rd | 40 PFIM-6.1/PFIM/man/getSigmaSlope.Rd | 40 PFIM-6.1/PFIM/man/getSize.Rd | 46 PFIM-6.1/PFIM/man/getTau.Rd | 40 PFIM-6.1/PFIM/man/getTimeDose.Rd | 40 PFIM-6.1/PFIM/man/getTinf.Rd | 40 PFIM-6.1/PFIM/man/getVariables.Rd |only PFIM-6.1/PFIM/man/getVarianceEffects.Rd | 40 PFIM-6.1/PFIM/man/getWeightThreshold.Rd |only PFIM-6.1/PFIM/man/getcError.Rd | 40 PFIM-6.1/PFIM/man/initialize-Administration-method.Rd |only PFIM-6.1/PFIM/man/initialize-AdministrationConstraints-method.Rd |only PFIM-6.1/PFIM/man/initialize-Arm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Combined1-method.Rd |only PFIM-6.1/PFIM/man/initialize-Constant-method.Rd |only PFIM-6.1/PFIM/man/initialize-Design-method.Rd |only PFIM-6.1/PFIM/man/initialize-Distribution-method.Rd |only PFIM-6.1/PFIM/man/initialize-Evaluation-method.Rd |only PFIM-6.1/PFIM/man/initialize-FedorovWynnAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Fim-method.Rd |only PFIM-6.1/PFIM/man/initialize-LibraryOfModels-method.Rd |only PFIM-6.1/PFIM/man/initialize-LibraryOfPKPDModels-method.Rd |only PFIM-6.1/PFIM/man/initialize-LogNormal-method.Rd |only PFIM-6.1/PFIM/man/initialize-Model-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalytic-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticBolus-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticBolusSteadyState-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticInfusion-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticInfusionSteadyState-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticSteadyState-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelBolus-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelError-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelInfusion-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelParameter-method.Rd |only PFIM-6.1/PFIM/man/initialize-MultiplicativeAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Normal-method.Rd |only PFIM-6.1/PFIM/man/initialize-Optimization-method.Rd |only PFIM-6.1/PFIM/man/initialize-OptimizationAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-PFIMProject-method.Rd |only PFIM-6.1/PFIM/man/initialize-PGBOAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-PSOAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Proportional-method.Rd |only PFIM-6.1/PFIM/man/initialize-SamplingTimeConstraints-method.Rd |only PFIM-6.1/PFIM/man/initialize-SamplingTimes-method.Rd |only PFIM-6.1/PFIM/man/initialize-SimplexAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/isDoseInEquations.Rd | 40 PFIM-6.1/PFIM/man/isModelAnalytic.Rd | 40 PFIM-6.1/PFIM/man/isModelBolus.Rd | 44 PFIM-6.1/PFIM/man/isModelInfusion.Rd | 40 PFIM-6.1/PFIM/man/isModelODE.Rd | 40 PFIM-6.1/PFIM/man/isModelSteadyState.Rd | 40 PFIM-6.1/PFIM/man/optimize.Rd | 76 PFIM-6.1/PFIM/man/parametersForComputingGradient.Rd | 42 PFIM-6.1/PFIM/man/plotEvaluation.Rd | 44 PFIM-6.1/PFIM/man/plotFrequencies.Rd | 8 PFIM-6.1/PFIM/man/plotOutcomesEvaluation.Rd | 62 PFIM-6.1/PFIM/man/plotOutcomesGradient.Rd | 52 PFIM-6.1/PFIM/man/plotRSE.Rd | 44 PFIM-6.1/PFIM/man/plotSE.Rd | 44 PFIM-6.1/PFIM/man/plotSensitivityIndice.Rd | 44 PFIM-6.1/PFIM/man/plotShrinkage.Rd | 44 PFIM-6.1/PFIM/man/plotWeights.Rd | 50 PFIM-6.1/PFIM/man/reportTablesAdministration.Rd | 40 PFIM-6.1/PFIM/man/reportTablesDesign.Rd | 40 PFIM-6.1/PFIM/man/reportTablesFIM.Rd | 58 PFIM-6.1/PFIM/man/reportTablesModelError.Rd | 40 PFIM-6.1/PFIM/man/reportTablesModelParameters.Rd | 40 PFIM-6.1/PFIM/man/reportTablesPlot.Rd | 44 PFIM-6.1/PFIM/man/reportTablesSamplingConstraints.Rd | 40 PFIM-6.1/PFIM/man/resizeFisherMatrix.Rd | 44 PFIM-6.1/PFIM/man/run.Rd | 46 PFIM-6.1/PFIM/man/setAdministrations.Rd | 48 PFIM-6.1/PFIM/man/setArm.Rd | 44 PFIM-6.1/PFIM/man/setArms.Rd | 52 PFIM-6.1/PFIM/man/setContent.Rd | 44 PFIM-6.1/PFIM/man/setDataForArmEvaluation.Rd |only PFIM-6.1/PFIM/man/setDataForModelEvaluation.Rd |only PFIM-6.1/PFIM/man/setDerivatives.Rd | 44 PFIM-6.1/PFIM/man/setDescription.Rd | 44 PFIM-6.1/PFIM/man/setDesigns.Rd | 44 PFIM-6.1/PFIM/man/setDistribution.Rd | 44 PFIM-6.1/PFIM/man/setDose.Rd | 44 PFIM-6.1/PFIM/man/setEquation.Rd | 44 PFIM-6.1/PFIM/man/setEquations.Rd | 44 PFIM-6.1/PFIM/man/setEquationsAfterInfusion.Rd | 44 PFIM-6.1/PFIM/man/setEquationsDuringInfusion.Rd | 44 PFIM-6.1/PFIM/man/setEvaluationFIMResults.Rd | 44 PFIM-6.1/PFIM/man/setEvaluationInitialDesignResults.Rd | 44 PFIM-6.1/PFIM/man/setFim.Rd | 44 PFIM-6.1/PFIM/man/setFimTypeToString.Rd | 40 PFIM-6.1/PFIM/man/setFisherMatrix.Rd | 44 PFIM-6.1/PFIM/man/setFixedEffects.Rd | 40 PFIM-6.1/PFIM/man/setFixedMu.Rd | 44 PFIM-6.1/PFIM/man/setFixedOmega.Rd | 44 PFIM-6.1/PFIM/man/setInitialConditions.Rd | 50 PFIM-6.1/PFIM/man/setIterationAndCriteria.Rd | 44 PFIM-6.1/PFIM/man/setModel.Rd | 44 PFIM-6.1/PFIM/man/setModelError.Rd | 44 PFIM-6.1/PFIM/man/setModelFromLibrary.Rd | 44 PFIM-6.1/PFIM/man/setMu.Rd | 52 PFIM-6.1/PFIM/man/setName.Rd | 58 PFIM-6.1/PFIM/man/setNumberOfArms.Rd | 44 PFIM-6.1/PFIM/man/setOdeSolverParameters.Rd | 44 PFIM-6.1/PFIM/man/setOmega.Rd | 52 PFIM-6.1/PFIM/man/setOptimalDesign.Rd | 44 PFIM-6.1/PFIM/man/setOptimalWeights.Rd | 44 PFIM-6.1/PFIM/man/setOptimizationResults.Rd | 44 PFIM-6.1/PFIM/man/setOutcome.Rd | 52 PFIM-6.1/PFIM/man/setOutcomes.Rd | 44 PFIM-6.1/PFIM/man/setOutcomesEvaluation.Rd | 44 PFIM-6.1/PFIM/man/setOutcomesForEvaluation.Rd | 44 PFIM-6.1/PFIM/man/setOutcomesGradient.Rd | 44 PFIM-6.1/PFIM/man/setParameters.Rd | 84 PFIM-6.1/PFIM/man/setSamplingConstraintForOptimization.Rd | 40 PFIM-6.1/PFIM/man/setSamplingTime.Rd | 44 PFIM-6.1/PFIM/man/setSamplingTimes.Rd | 44 PFIM-6.1/PFIM/man/setSamplingTimesConstraints.Rd | 44 PFIM-6.1/PFIM/man/setSamplings.Rd | 44 PFIM-6.1/PFIM/man/setShrinkage.Rd | 58 PFIM-6.1/PFIM/man/setSigmaInter.Rd | 44 PFIM-6.1/PFIM/man/setSigmaSlope.Rd | 44 PFIM-6.1/PFIM/man/setSize.Rd | 62 PFIM-6.1/PFIM/man/setTau.Rd | 44 PFIM-6.1/PFIM/man/setTimeDose.Rd | 44 PFIM-6.1/PFIM/man/setTinf.Rd | 44 PFIM-6.1/PFIM/man/setVarianceEffects.Rd | 40 PFIM-6.1/PFIM/man/setcError.Rd | 44 PFIM-6.1/PFIM/man/show.Rd | 102 - PFIM-6.1/PFIM/tests/testthat/test_PKModels-PFIM.R | 25 PFIM-6.1/PFIM/vignettes/Example01.Rmd | 8 350 files changed, 9619 insertions(+), 9801 deletions(-)
Title: Generate Random Walks Compatible with the 'tidyverse'
Description: Generates random walks of various types by providing a set of functions
that are compatible with the 'tidyverse'. The functions provided in the package
make it simple to create random walks with a variety of properties, such as
how many simulations to run, how many steps to take, and the distribution of
random walk itself.
Author: Steven Sanderson [aut, cre, cph]
,
Antti Rask [aut, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between RandomWalker versions 0.1.0 dated 2024-09-15 and 0.2.0 dated 2024-10-23
DESCRIPTION | 10 MD5 | 62 +-- NAMESPACE | 7 NEWS.md | 26 + R/00_global_variables.R | 10 R/auto-rw30.R | 13 R/gen-brown-motion-geometric.R | 10 R/gen-brown-motion.R | 10 R/gen-discrete-walk.R | 9 R/gen-random-normal-walk-drift.R | 12 R/gen-random-normal-walk.R | 8 R/helpers.R | 379 +++++++++++++++++++ R/plt-visualize-walks.R | 385 +++++++++++++------- R/vec-running-quantile.R |only README.md | 68 ++- inst/doc/getting-started.Rmd | 194 +++++----- inst/doc/getting-started.html | 32 - man/brownian_motion.Rd | 10 man/convert_snake_to_title_case.Rd | 85 ++-- man/discrete_walk.Rd | 9 man/figures/README-random_walk_visual_example-1.png |binary man/generate_caption.Rd | 97 ++--- man/geometric_brownian_motion.Rd | 10 man/get_attributes.Rd |only man/rand_walk_helper.Rd | 111 +++-- man/random_normal_drift_walk.Rd | 12 man/random_normal_walk.Rd | 8 man/running_quantile.Rd |only man/rw30.Rd | 13 man/std_cum_max_augment.Rd |only man/std_cum_mean_augment.Rd |only man/std_cum_min_augment.Rd |only man/std_cum_prod_augment.Rd |only man/std_cum_sum_augment.Rd |only man/visualize_walks.Rd | 36 + vignettes/getting-started.Rmd | 194 +++++----- 36 files changed, 1197 insertions(+), 623 deletions(-)
Title: Adverse Events Analysis Using 'metalite'
Description: Analyzes adverse events in clinical trials using the 'metalite'
data structure. The package simplifies the workflow to create
production-ready tables, listings, and figures discussed in the
adverse events analysis chapters of
"R for Clinical Study Reports and Submission"
by Zhang et al. (2022) <https://r4csr.org/>.
Author: Yilong Zhang [aut],
Yujie Zhao [aut, cre],
Benjamin Wang [aut],
Nan Xiao [aut],
Sarad Nepal [aut],
Madhusudhan Ginnaram [aut],
Venkatesh Burla [ctb],
Ruchitbhai Patel [aut],
Brian Lang [aut],
Xuan Deng [aut],
Hiroaki Fukuda [aut],
Bing Liu [aut],
Jee [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between metalite.ae versions 0.1.2 dated 2024-04-16 and 0.1.3 dated 2024-10-23
DESCRIPTION | 10 MD5 | 93 - NEWS.md | 79 R/avg.R | 201 +- R/data.R | 11 R/empty_table.R |only R/extend_ae_specific.R | 60 R/fmt.R | 2 R/format_ae_specific.R | 154 + R/format_ae_specific_subgroup.R | 1 R/tlf_ae_exp_adj.R | 120 - R/tlf_ae_listing.R | 126 - R/tlf_ae_specific.R | 314 +-- R/tlf_ae_specific_subgroup.R | 250 +- R/tlf_ae_summary.R | 136 - data/metalite_ae_adexsum.rda |only inst/doc/ae-listing.html | 2 inst/doc/ae-specific-subgroup.html | 16 inst/doc/ae-specific.R | 24 inst/doc/ae-specific.Rmd | 49 inst/doc/ae-specific.html | 254 +- inst/doc/ae-summary.R | 3 inst/doc/ae-summary.Rmd | 8 inst/doc/ae-summary.html | 17 inst/doc/metalite-ae.html | 2 man/extend_ae_specific_events.Rd | 2 man/extend_ae_specific_inference.Rd | 6 man/format_ae_specific.Rd | 41 man/format_ae_summary.Rd | 31 man/metalite.ae-package.Rd | 2 man/metalite_ae_adexsum.Rd |only tests/testthat/test-independent-testing-avg_duration.R | 5 tests/testthat/test-independent-testing-avg_event.R | 28 tests/testthat/test-independent-testing-empty_table.R |only tests/testthat/test-independent-testing-extend_ae_specific.R | 2 tests/testthat/test-independent-testing-format_ae_specific.R | 26 tests/testthat/test-independent-testing-tlf_ae_specific.R | 33 tests/testthat/test-independent-testing-tlf_ae_specific_subgroup.R | 2 vignettes/ae-specific.Rmd | 49 vignettes/ae-summary.Rmd | 8 vignettes/fig/ae0specific.png |binary vignettes/pdf/ae0specific0sub0gender1.pdf |binary vignettes/pdf/ae0specific1.pdf |binary vignettes/pdf/ae0specific2.pdf |binary vignettes/pdf/empty_ae0specific.pdf |only vignettes/pdf/mock_ae0specific1.pdf |binary vignettes/rtf/ae0specific0sub0gender1.rtf | 864 ++++----- vignettes/rtf/ae0specific1.rtf | 342 +-- vignettes/rtf/ae0specific2.rtf | 894 +++++----- vignettes/rtf/mock_ae0specific1.rtf | 2 50 files changed, 2456 insertions(+), 1813 deletions(-)
Title: Acknowledge all Contributors to a Project
Description: Acknowledge all contributors to a project via a single
function call. The function appends to a 'README' or other specified
file(s) a table with names of all individuals who contributed via code
or repository issues. The package also includes several additional
functions to extract and quantify contributions to any repository.
Author: Mark Padgham [aut, cre],
Chris Hartgerink [aut],
Maelle Salmon [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between allcontributors versions 0.2.0 dated 2024-05-16 and 0.2.2 dated 2024-10-23
allcontributors-0.2.0/allcontributors/tests/testthat/getcontribs/api |only allcontributors-0.2.0/allcontributors/tests/testthat/getcontribs/api.github.com |only allcontributors-0.2.2/allcontributors/DESCRIPTION | 22 - allcontributors-0.2.2/allcontributors/MD5 | 43 +- allcontributors-0.2.2/allcontributors/NEWS.md | 15 allcontributors-0.2.2/allcontributors/R/add-contributors.R | 14 allcontributors-0.2.2/allcontributors/R/github-contribs-issue.R | 2 allcontributors-0.2.2/allcontributors/R/github.R | 104 +---- allcontributors-0.2.2/allcontributors/R/urlcheck.R | 10 allcontributors-0.2.2/allcontributors/R/utils.R | 2 allcontributors-0.2.2/allcontributors/README.md |only allcontributors-0.2.2/allcontributors/build/vignette.rds |binary allcontributors-0.2.2/allcontributors/inst/doc/allcontributors.Rmd | 170 ++++----- allcontributors-0.2.2/allcontributors/inst/doc/allcontributors.html | 174 +++++----- allcontributors-0.2.2/allcontributors/inst/httptest2/redact.R | 10 allcontributors-0.2.2/allcontributors/man/allcontributors-package.Rd | 14 allcontributors-0.2.2/allcontributors/man/get_contributors.Rd | 2 allcontributors-0.2.2/allcontributors/man/get_gh_code_contributors.Rd | 2 allcontributors-0.2.2/allcontributors/man/get_gh_contrib_issue.Rd | 2 allcontributors-0.2.2/allcontributors/man/get_gh_issue_people.Rd | 2 allcontributors-0.2.2/allcontributors/man/get_gh_issue_titles.Rd | 2 allcontributors-0.2.2/allcontributors/tests/testthat/getcontribs/gh-api |only allcontributors-0.2.2/allcontributors/vignettes/allcontributors.Rmd | 170 ++++----- 23 files changed, 376 insertions(+), 384 deletions(-)
More information about allcontributors at CRAN
Permanent link
Title: Access the 'Strava' API
Description: Functions to access data from the 'Strava v3 API' <https://developers.strava.com/>.
Author: Marcus W. Beck [cre],
Pedro Villarroel [aut],
Daniel Padfield [aut],
Lorenzo Gaborini [aut],
Niklas von Maltzahn [aut]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between rStrava versions 1.3.1 dated 2024-03-26 and 1.3.2 dated 2024-10-23
DESCRIPTION | 12 +-- MD5 | 123 ++++++++++++++++++------------------- NAMESPACE | 1 NEWS.md |only R/athl_fun.R | 9 +- R/athlind_fun.R | 7 +- R/compile_activities.R | 8 +- R/compile_activity_streams.R | 7 +- R/compile_segment.R | 6 - R/get_KOMs.R | 7 +- R/get_activity.R | 10 ++- R/get_activity_list.R | 5 + R/get_activity_streams.R | 4 - R/get_athlete.R | 5 + R/get_club.R | 2 R/get_efforts_list.R | 9 +- R/get_elev_prof.R | 5 + R/get_gear.R | 5 + R/get_heat_map.R | 5 + R/get_laps.R | 7 +- R/get_leaderboard.R | 7 +- R/get_pages.R | 8 +- R/get_segment.R | 11 ++- R/get_starred.R | 5 + R/get_streams.R | 10 ++- R/plot_spdsplits.R | 5 + R/url_activities.R | 6 + R/url_athlete.R | 10 ++- R/url_clubs.R | 8 +- R/url_gear.R | 4 + R/url_segment.R | 7 +- R/url_streams.R | 7 +- man/athl_fun.Rd | 6 - man/athlind_fun.Rd | 2 man/compile_activities.Rd | 2 man/compile_activity_streams.Rd | 4 - man/compile_segment.Rd | 6 - man/figures/unnamed-chunk-12-1.png |binary man/figures/unnamed-chunk-13-1.png |binary man/figures/unnamed-chunk-13-2.png |binary man/figures/unnamed-chunk-17-1.png |binary man/get_KOMs.Rd | 4 - man/get_activity.Rd | 4 - man/get_activity_list.Rd | 2 man/get_activity_streams.Rd | 4 - man/get_athlete.Rd | 2 man/get_club.Rd | 2 man/get_efforts_list.Rd | 6 - man/get_elev_prof.Rd | 2 man/get_gear.Rd | 2 man/get_heat_map.Rd | 2 man/get_laps.Rd | 66 +++++++++---------- man/get_leaderboard.Rd | 4 - man/get_segment.Rd | 8 +- man/get_starred.Rd | 2 man/get_streams.Rd | 4 - man/plot_spdsplits.Rd | 2 man/seltime_fun.Rd | 52 +++++++-------- man/url_activities.Rd | 2 man/url_athlete.Rd | 2 man/url_clubs.Rd | 4 - man/url_segment.Rd | 4 - man/url_streams.Rd | 4 - 63 files changed, 308 insertions(+), 221 deletions(-)
Title: Cluster Analysis with Missing Values by Multiple Imputation
Description: Allows clustering of incomplete observations by addressing missing values using multiple imputation. For achieving this goal, the methodology consists in three steps, following Audigier and Niang 2022 <doi:10.1007/s11634-022-00519-1>. I) Missing data imputation using dedicated models. Four multiple imputation methods are proposed, two are based on joint modelling and two are fully sequential methods, as discussed in Audigier et al. (2021) <doi:10.48550/arXiv.2106.04424>. II) cluster analysis of imputed data sets. Six clustering methods are available (distances-based or model-based), but custom methods can also be easily used. III) Partition pooling. The set of partitions is aggregated using Non-negative Matrix Factorization based method. An associated instability measure is computed by bootstrap (see Fang, Y. and Wang, J., 2012 <doi:10.1016/j.csda.2011.09.003>). Among applications, this instability measure can be used to choose a number of clusters with missing value [...truncated...]
Author: Vincent Audigier [aut, cre] ,
Hang Joon Kim [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between clusterMI versions 1.2.1 dated 2024-07-07 and 1.2.2 dated 2024-10-23
DESCRIPTION | 10 - MD5 | 32 ++- R/choosem.R | 21 +- R/choosenbclust.R | 14 - R/clusterMI.R | 69 +++----- R/fastnmf.R | 135 +++++++++------- R/imputedata.R | 22 ++ R/initfastnmf.intern.R |only R/mclustboot.intern.R | 41 +++- R/overimpute.R | 2 inst/doc/clusterMI.R | 3 inst/doc/clusterMI.Rmd | 4 inst/doc/clusterMI.html | 398 ++++++++++++++++++++++++------------------------ man/clusterMI.Rd | 24 -- man/fastnmf.Rd | 32 +-- man/initfastnmf.Rd |only man/overimpute.Rd | 2 vignettes/clusterMI.Rmd | 4 18 files changed, 421 insertions(+), 392 deletions(-)
Title: Open Population Capture-Recapture
Description: Non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between openCR versions 2.2.6 dated 2023-11-27 and 2.2.7 dated 2024-10-23
openCR-2.2.6/openCR/R/getD.R |only openCR-2.2.7/openCR/DESCRIPTION | 8 +-- openCR-2.2.7/openCR/MD5 | 53 ++++++++++------------ openCR-2.2.7/openCR/NEWS | 8 +++ openCR-2.2.7/openCR/R/openCR.fit.R | 7 +- openCR-2.2.7/openCR/R/utility.R | 4 - openCR-2.2.7/openCR/build/partial.rdb |binary openCR-2.2.7/openCR/build/vignette.rds |binary openCR-2.2.7/openCR/inst/doc/openCR-vignette.Rmd | 6 +- openCR-2.2.7/openCR/inst/doc/openCR-vignette.pdf |binary openCR-2.2.7/openCR/man/AIC.openCR.Rd | 2 openCR-2.2.7/openCR/man/LLsurface.Rd | 4 - openCR-2.2.7/openCR/man/cumMove.Rd | 5 +- openCR-2.2.7/openCR/man/kernel.Rd | 4 - openCR-2.2.7/openCR/man/microtus.Rd | 2 openCR-2.2.7/openCR/man/openCR-defunct.Rd | 2 openCR-2.2.7/openCR/man/openCR-internal.Rd | 2 openCR-2.2.7/openCR/man/openCR-package.Rd | 6 +- openCR-2.2.7/openCR/man/openCR.fit.Rd | 10 ++-- openCR-2.2.7/openCR/man/par.openCR.fit.Rd | 4 - openCR-2.2.7/openCR/man/read.inp.Rd | 2 openCR-2.2.7/openCR/man/simulate.Rd | 8 +-- openCR-2.2.7/openCR/man/strata.Rd | 2 openCR-2.2.7/openCR/man/stratify.Rd | 8 +-- openCR-2.2.7/openCR/man/ucare.Rd | 2 openCR-2.2.7/openCR/man/utility.Rd | 2 openCR-2.2.7/openCR/src/prwiparallel.cpp | 30 ++++++------ openCR-2.2.7/openCR/vignettes/openCR-vignette.Rmd | 6 +- 28 files changed, 99 insertions(+), 88 deletions(-)
Title: Cite 'R' Packages on the Fly in 'R Markdown' and 'Quarto'
Description: References and cites 'R' and 'R' packages on the fly in 'R
Markdown' and 'Quarto'. 'pakret' provides a minimalistic API that
generates preformatted citations of 'R' and 'R' packages, and adds
their reference to a '.bib' file directly from within your document.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between pakret versions 0.2.1 dated 2024-10-10 and 0.2.2 dated 2024-10-23
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/checkers.R | 15 ++++++++++++++- R/pakret.R | 4 ++++ R/pkrt-set.R | 11 ++++++----- R/utils-local.R | 22 ++++++++++++++-------- README.md | 17 ++++++++--------- tests/testthat/_snaps/onload.md | 4 ++-- tests/testthat/test-onload.R | 4 ++-- tests/testthat/test-pkrt-set.R | 34 ++++++++++++++++++++++++++++++++-- tests/testthat/test-pkrt.R | 5 +++-- 12 files changed, 105 insertions(+), 45 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.5 dated 2024-07-08 and 0.5.6 dated 2024-10-23
DESCRIPTION | 8 - MD5 | 52 +++---- NEWS.md | 8 + R/jskm.R | 187 +++++++++++++++++++++++----- R/svyjskm.R | 198 +++++++++++++++++++++++++----- README.md | 12 - inst/doc/jskm.html | 36 ++--- man/figures/README-unnamed-chunk-1-1.png |binary man/figures/README-unnamed-chunk-1-2.png |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary man/figures/README-unnamed-chunk-7-3.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-8-2.png |binary man/figures/README-unnamed-chunk-8-3.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/jskm.Rd | 5 man/svyjskm.Rd | 7 - tests/testthat/test-km.R | 12 + 27 files changed, 401 insertions(+), 124 deletions(-)
Title: Random Forest with Multivariate Longitudinal Predictors
Description: Based on random forest principle, 'DynForest' is able to include
multiple longitudinal predictors to provide individual predictions.
Longitudinal predictors are modeled through the random forest. The
methodology is fully described for a survival outcome in:
Devaux, Helmer, Genuer & Proust-Lima (2023)
<doi: 10.1177/09622802231206477>.
Author: Anthony Devaux [aut, cre] ,
Robin Genuer [aut] ,
Cecile Proust-Lima [aut] ,
Louis Capitaine [aut]
Maintainer: Anthony Devaux <anthony.devauxbarault@gmail.com>
Diff between DynForest versions 1.1.3 dated 2024-03-22 and 1.2.0 dated 2024-10-23
DynForest-1.1.3/DynForest/R/DynForest.R |only DynForest-1.1.3/DynForest/R/compute_OOBerror.R |only DynForest-1.1.3/DynForest/R/compute_VIMP.R |only DynForest-1.1.3/DynForest/R/compute_gVIMP.R |only DynForest-1.1.3/DynForest/R/getTree.R |only DynForest-1.1.3/DynForest/R/getTreeNodes.R |only DynForest-1.1.3/DynForest/R/var_depth.R |only DynForest-1.1.3/DynForest/inst/doc/Introduction.R |only DynForest-1.1.3/DynForest/inst/doc/Introduction.Rmd |only DynForest-1.1.3/DynForest/inst/doc/Introduction.html |only DynForest-1.1.3/DynForest/inst/doc/factor.R |only DynForest-1.1.3/DynForest/inst/doc/factor.Rmd |only DynForest-1.1.3/DynForest/inst/doc/factor.html |only DynForest-1.1.3/DynForest/inst/doc/numeric.R |only DynForest-1.1.3/DynForest/inst/doc/numeric.Rmd |only DynForest-1.1.3/DynForest/inst/doc/numeric.html |only DynForest-1.1.3/DynForest/inst/doc/surv.R |only DynForest-1.1.3/DynForest/inst/doc/surv.Rmd |only DynForest-1.1.3/DynForest/inst/doc/surv.html |only DynForest-1.1.3/DynForest/man/DynForest.Rd |only DynForest-1.1.3/DynForest/man/DynTree.Rd |only DynForest-1.1.3/DynForest/man/DynTree_surv.Rd |only DynForest-1.1.3/DynForest/man/Fact.partitions.Rd |only DynForest-1.1.3/DynForest/man/OOB.rfshape.Rd |only DynForest-1.1.3/DynForest/man/OOB.tree.Rd |only DynForest-1.1.3/DynForest/man/checking.Rd |only DynForest-1.1.3/DynForest/man/combine_times.Rd |only DynForest-1.1.3/DynForest/man/compute_OOBerror.Rd |only DynForest-1.1.3/DynForest/man/compute_VIMP.Rd |only DynForest-1.1.3/DynForest/man/compute_gVIMP.Rd |only DynForest-1.1.3/DynForest/man/getParamMM.Rd |only DynForest-1.1.3/DynForest/man/getTree.Rd |only DynForest-1.1.3/DynForest/man/getTreeNodes.Rd |only DynForest-1.1.3/DynForest/man/impurity.Rd |only DynForest-1.1.3/DynForest/man/impurity_split.Rd |only DynForest-1.1.3/DynForest/man/plot.DynForest.Rd |only DynForest-1.1.3/DynForest/man/pred.MMT.Rd |only DynForest-1.1.3/DynForest/man/predRE.Rd |only DynForest-1.1.3/DynForest/man/predict.DynForest.Rd |only DynForest-1.1.3/DynForest/man/print.DynForest.Rd |only DynForest-1.1.3/DynForest/man/rf_shape_para.Rd |only DynForest-1.1.3/DynForest/man/summary.DynForest.Rd |only DynForest-1.1.3/DynForest/man/var_depth.Rd |only DynForest-1.1.3/DynForest/man/var_split_factor.Rd |only DynForest-1.1.3/DynForest/man/var_split_long.Rd |only DynForest-1.1.3/DynForest/man/var_split_num.Rd |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestRPaper_CIF.png |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestR_VIMP_gVIMP.png |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestR_factor_mindepth.png |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestR_mindepth.png |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestR_mindepth_scalar.png |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestR_mtrytuned.png |only DynForest-1.1.3/DynForest/vignettes/Figures/DynForestR_predCIF.png |only 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DynForest-1.2.0/DynForest/R/dynforest.R |only DynForest-1.2.0/DynForest/R/getParamMM.R | 1 DynForest-1.2.0/DynForest/R/get_tree.R |only DynForest-1.2.0/DynForest/R/get_treenodes.R |only DynForest-1.2.0/DynForest/R/impurity.R | 1 DynForest-1.2.0/DynForest/R/impurity_split.R | 1 DynForest-1.2.0/DynForest/R/plot.R | 94 +++-- DynForest-1.2.0/DynForest/R/predRE.R | 1 DynForest-1.2.0/DynForest/R/pred_MMT.R | 1 DynForest-1.2.0/DynForest/R/predict.R | 31 + DynForest-1.2.0/DynForest/R/print.R | 105 +++--- DynForest-1.2.0/DynForest/R/rf_shape_para.R | 1 DynForest-1.2.0/DynForest/R/summary.R | 34 +- DynForest-1.2.0/DynForest/R/var_split_factor.R | 1 DynForest-1.2.0/DynForest/R/var_split_long.R | 1 DynForest-1.2.0/DynForest/R/var_split_num.R | 1 DynForest-1.2.0/DynForest/README.md | 12 DynForest-1.2.0/DynForest/build/vignette.rds |binary DynForest-1.2.0/DynForest/inst/doc/classification.R |only DynForest-1.2.0/DynForest/inst/doc/classification.Rmd |only 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Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.2.0 dated 2024-09-09 and 1.3.0 dated 2024-10-23
REDCapR-1.2.0/REDCapR/inst/test-data/checkboxes-1 |only REDCapR-1.2.0/REDCapR/inst/test-data/decimal-comma |only REDCapR-1.2.0/REDCapR/inst/test-data/decimal-comma-and-dot |only REDCapR-1.2.0/REDCapR/inst/test-data/decimal-dot |only REDCapR-1.2.0/REDCapR/inst/test-data/delete-multiple-arm |only REDCapR-1.2.0/REDCapR/inst/test-data/delete-single-arm |only REDCapR-1.2.0/REDCapR/inst/test-data/longitudinal-single-arm |only REDCapR-1.2.0/REDCapR/inst/test-data/problematic-dictionary |only REDCapR-1.2.0/REDCapR/inst/test-data/problematic-values |only REDCapR-1.2.0/REDCapR/inst/test-data/project-clinical-trial |only REDCapR-1.2.0/REDCapR/inst/test-data/project-dag |only REDCapR-1.2.0/REDCapR/inst/test-data/project-longitudinal |only REDCapR-1.2.0/REDCapR/inst/test-data/project-russian |only REDCapR-1.2.0/REDCapR/inst/test-data/project-simple |only REDCapR-1.2.0/REDCapR/inst/test-data/project-survey |only REDCapR-1.2.0/REDCapR/inst/test-data/repeating-instruments |only REDCapR-1.2.0/REDCapR/inst/test-data/specific-redcapr/log-read/2020-08-10.R |only REDCapR-1.2.0/REDCapR/inst/test-data/specific-redcapr/log-read/2021-07-11-record3-user.R |only REDCapR-1.2.0/REDCapR/inst/test-data/super-wide |only REDCapR-1.2.0/REDCapR/inst/test-data/super-wide-3 |only REDCapR-1.2.0/REDCapR/inst/test-data/super-wide-metadata |only REDCapR-1.2.0/REDCapR/inst/test-data/validation-types-v1 |only REDCapR-1.2.0/REDCapR/inst/test-data/vignette-repeating |only REDCapR-1.3.0/REDCapR/DESCRIPTION | 9 REDCapR-1.3.0/REDCapR/LICENSE | 4 REDCapR-1.3.0/REDCapR/MD5 | 767 - REDCapR-1.3.0/REDCapR/NAMESPACE | 108 REDCapR-1.3.0/REDCapR/NEWS.md | 12 REDCapR-1.3.0/REDCapR/R/REDCapR-package.R | 132 REDCapR-1.3.0/REDCapR/R/constant.R | 462 REDCapR-1.3.0/REDCapR/R/create-batch-glossary.R | 208 REDCapR-1.3.0/REDCapR/R/helpers-testing.R | 146 REDCapR-1.3.0/REDCapR/R/kernel-api.R | 238 REDCapR-1.3.0/REDCapR/R/metadata-utilities.R | 270 REDCapR-1.3.0/REDCapR/R/project-dag-write.R | 363 REDCapR-1.3.0/REDCapR/R/project-delete-multiple-arm.R | 219 REDCapR-1.3.0/REDCapR/R/project-delete-single-arm.R | 223 REDCapR-1.3.0/REDCapR/R/project-simple.R | 332 REDCapR-1.3.0/REDCapR/R/redcap-arm-export.R | 372 REDCapR-1.3.0/REDCapR/R/redcap-column-sanitize.R | 128 REDCapR-1.3.0/REDCapR/R/redcap-dag-read.R | 334 REDCapR-1.3.0/REDCapR/R/redcap-delete.R | 432 REDCapR-1.3.0/REDCapR/R/redcap-event-instruments.R | 366 REDCapR-1.3.0/REDCapR/R/redcap-event-read.R | 368 REDCapR-1.3.0/REDCapR/R/redcap-file-download-oneshot.R | 520 REDCapR-1.3.0/REDCapR/R/redcap-file-upload-oneshot.R | 400 REDCapR-1.3.0/REDCapR/R/redcap-instrument-download.R | 464 REDCapR-1.3.0/REDCapR/R/redcap-instruments.R | 332 REDCapR-1.3.0/REDCapR/R/redcap-log-read.R | 446 REDCapR-1.3.0/REDCapR/R/redcap-metadata-coltypes.R | 1025 - REDCapR-1.3.0/REDCapR/R/redcap-metadata-read.R | 438 REDCapR-1.3.0/REDCapR/R/redcap-metadata-write.R | 316 REDCapR-1.3.0/REDCapR/R/redcap-next-free-record-name.R | 284 REDCapR-1.3.0/REDCapR/R/redcap-project-info-read.R | 604 - REDCapR-1.3.0/REDCapR/R/redcap-project.R | 266 REDCapR-1.3.0/REDCapR/R/redcap-read-eav-oneshot.R | 708 - REDCapR-1.3.0/REDCapR/R/redcap-read-oneshot-eav.R | 818 - REDCapR-1.3.0/REDCapR/R/redcap-read-oneshot.R | 808 - REDCapR-1.3.0/REDCapR/R/redcap-read.R | 1232 +- REDCapR-1.3.0/REDCapR/R/redcap-report.R | 498 REDCapR-1.3.0/REDCapR/R/redcap-survey-link-export-oneshot.R | 342 REDCapR-1.3.0/REDCapR/R/redcap-users-export.R | 450 REDCapR-1.3.0/REDCapR/R/redcap-variables.R | 346 REDCapR-1.3.0/REDCapR/R/redcap-version.R | 218 REDCapR-1.3.0/REDCapR/R/redcap-write-oneshot.R | 406 REDCapR-1.3.0/REDCapR/R/redcap-write.R | 424 REDCapR-1.3.0/REDCapR/R/retrieve-credential.R | 796 - REDCapR-1.3.0/REDCapR/R/sanitize-token.R | 198 REDCapR-1.3.0/REDCapR/R/skippers.R | 14 REDCapR-1.3.0/REDCapR/R/utilities.R | 236 REDCapR-1.3.0/REDCapR/R/validate.R | 830 - REDCapR-1.3.0/REDCapR/README.md | 190 REDCapR-1.3.0/REDCapR/build/vignette.rds |binary REDCapR-1.3.0/REDCapR/inst/WORDLIST | 316 REDCapR-1.3.0/REDCapR/inst/doc/BasicREDCapROperations.R | 182 REDCapR-1.3.0/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 344 REDCapR-1.3.0/REDCapR/inst/doc/BasicREDCapROperations.html | 1457 +- REDCapR-1.3.0/REDCapR/inst/doc/SecurityDatabase.Rmd | 696 - REDCapR-1.3.0/REDCapR/inst/doc/SecurityDatabase.html | 1440 +- REDCapR-1.3.0/REDCapR/inst/doc/TroubleshootingApiCalls.R | 38 REDCapR-1.3.0/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 1064 - REDCapR-1.3.0/REDCapR/inst/doc/TroubleshootingApiCalls.html | 2119 +-- REDCapR-1.3.0/REDCapR/inst/doc/advanced-redcapr-operations.R | 278 REDCapR-1.3.0/REDCapR/inst/doc/advanced-redcapr-operations.Rmd | 542 REDCapR-1.3.0/REDCapR/inst/doc/advanced-redcapr-operations.html | 1479 +- REDCapR-1.3.0/REDCapR/inst/doc/longitudinal-and-repeating.R | 252 REDCapR-1.3.0/REDCapR/inst/doc/longitudinal-and-repeating.Rmd | 850 - REDCapR-1.3.0/REDCapR/inst/doc/longitudinal-and-repeating.html | 5545 ++++------ REDCapR-1.3.0/REDCapR/inst/doc/workflow-read.R | 210 REDCapR-1.3.0/REDCapR/inst/doc/workflow-read.Rmd | 864 - REDCapR-1.3.0/REDCapR/inst/doc/workflow-read.html | 4411 +++---- REDCapR-1.3.0/REDCapR/inst/doc/workflow-write.R | 34 REDCapR-1.3.0/REDCapR/inst/doc/workflow-write.Rmd | 836 - REDCapR-1.3.0/REDCapR/inst/doc/workflow-write.html | 1555 +- REDCapR-1.3.0/REDCapR/inst/misc/bad.credentials | 16 REDCapR-1.3.0/REDCapR/inst/misc/conflicting-rows.credentials | 16 REDCapR-1.3.0/REDCapR/inst/misc/dev-2.credentials |only REDCapR-1.3.0/REDCapR/inst/misc/example.credentials | 74 REDCapR-1.3.0/REDCapR/inst/misc/out-of-order.credentials | 16 REDCapR-1.3.0/REDCapR/inst/misc/plugin-redirection.yml |only REDCapR-1.3.0/REDCapR/inst/misc/project-redirection.yml |only REDCapR-1.3.0/REDCapR/inst/misc/skeleton.credentials | 38 REDCapR-1.3.0/REDCapR/inst/misc/validation-transformation.yml | 280 REDCapR-1.3.0/REDCapR/inst/misc/vignette.css | 72 REDCapR-1.3.0/REDCapR/inst/misc/zero-rows.credentials | 12 REDCapR-1.3.0/REDCapR/inst/test-data/project-color-boxes/Readme.md | 106 REDCapR-1.3.0/REDCapR/inst/test-data/project-color-boxes/data.csv | 8 REDCapR-1.3.0/REDCapR/inst/test-data/project-color-boxes/dictionary.csv | 6 REDCapR-1.3.0/REDCapR/inst/test-data/projects |only REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/delete/multiple-arm-four-records.R | 70 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/delete/single-arm-four-records.R | 14 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/1-arm.R | 16 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-both-arms.R | 48 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-only-arm-1.R | 34 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-only-arm-2.R | 28 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/no-arms.R | 2 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/instruments/default.R | 12 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/log-read/2024-10-11.R |only REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/longitudinal.R | 254 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/problematic-dictionary.R | 18 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/repeating-instruments.R | 34 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/simple.R | 54 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/validation-types.R | 108 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-all-three.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-demographics.R | 64 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-health.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-race_and_ethnicity.R | 42 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal.R | 120 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/super-wide-3-subset.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/all-test-projects.R | 319 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/chicago.R | 86 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/simple.R | 84 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-plumbing/longitudinal.R | 72 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-plumbing/repeated.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-plumbing/simple.R | 14 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-repeating-sparse/default.R | 28 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-false.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-true.R | 51 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/col_types.R | 48 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/default.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/error-bad-token.R | 104 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/export_checkbox_label.R | 62 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/filter-character.R | 18 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/filter-numeric.R | 26 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label-and-dag-one-single-batch.R | 64 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label-and-dag-three-tiny-batches.R | 64 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label-header.R | 54 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label.R | 62 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/na.R | 104 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/raw-and-dag.R | 48 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/raw.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-fields-without-record-id.R | 12 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-fields-zero-length.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-fields.R | 8 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-forms-only-1st.R | 24 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-forms-without-record-id.R | 18 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-forms.R | 32 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-records-zero-length.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-records.R | 34 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-clinical-trial/default.R | 1998 +-- REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-dag/assigned-to-dag-a.R | 22 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-dag/no-assignment.R | 22 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/blank-for-gray-false.R | 99 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/blank-for-gray-true.R | 99 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/default.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/filter-character.R | 27 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/filter-numeric.R | 43 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-fields-zero-length.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-fields.R | 25 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-forms.R | 71 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-records-zero-length.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-records.R | 61 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-false.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-true.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/default.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/filter-character.R | 16 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/filter-numeric.R | 26 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/label-and-dag.R | 56 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/label-header.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/raw-and-dag.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/raw.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/specify-forms.R | 34 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-false.R | 50 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-true.R | 78 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/col_types.R | 102 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/default.R | 100 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/export_checkbox_label.R | 114 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/filter-character.R | 70 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/filter-numeric.R | 80 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/force-character-type.R | 102 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/label-and-dag.R | 118 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/label-header.R | 106 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/label.R | 114 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/na.R | 104 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/raw-and-dag.R | 104 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/raw.R | 100 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-fields-without-record-id.R | 22 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-fields-zero-length.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-fields.R | 8 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms-only-1st.R | 48 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms-only-2nd.R | 34 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms-without-record-id.R | 32 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms.R | 74 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-records-zero-length.R | 46 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-records.R | 34 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/report/col_types.R | 24 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/report/default.R | 25 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/report/export_checkbox_label.R | 30 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/report/force-character-type.R | 26 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/report/label-header.R | 106 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/report/raw.R | 24 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/test-project/read-insert-and-update.R | 40 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/users-export/with-dags--user.R | 33 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/users-export/with-dags--user_form.R | 9 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/users-export/without-dags--user.R | 35 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/users-export/without-dags--user_form.R | 13 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/variables/default.R | 36 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-batch/default.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-batch/update-one-field.R | 92 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-batch/update-two-fields.R | 92 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-dag/after.R | 16 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-dag/before.R | 14 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/default.R | 96 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/one-field.R | 92 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/overwrite-true.R | 90 REDCapR-1.3.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/two-fields.R | 92 REDCapR-1.3.0/REDCapR/man/REDCapR-package.Rd | 212 REDCapR-1.3.0/REDCapR/man/collapse_vector.Rd | 60 REDCapR-1.3.0/REDCapR/man/constant.Rd | 232 REDCapR-1.3.0/REDCapR/man/create_batch_glossary.Rd | 122 REDCapR-1.3.0/REDCapR/man/figures/logo.svg | 278 REDCapR-1.3.0/REDCapR/man/kernel_api.Rd | 150 REDCapR-1.3.0/REDCapR/man/metadata_utilities.Rd | 188 REDCapR-1.3.0/REDCapR/man/redcap_arm_export.Rd | 178 REDCapR-1.3.0/REDCapR/man/redcap_column_sanitize.Rd | 112 REDCapR-1.3.0/REDCapR/man/redcap_dag_read.Rd | 168 REDCapR-1.3.0/REDCapR/man/redcap_delete.Rd | 226 REDCapR-1.3.0/REDCapR/man/redcap_event_instruments.Rd | 204 REDCapR-1.3.0/REDCapR/man/redcap_event_read.Rd | 182 REDCapR-1.3.0/REDCapR/man/redcap_file_download_oneshot.Rd | 290 REDCapR-1.3.0/REDCapR/man/redcap_file_upload_oneshot.Rd | 264 REDCapR-1.3.0/REDCapR/man/redcap_instrument_download.Rd | 274 REDCapR-1.3.0/REDCapR/man/redcap_instruments.Rd | 172 REDCapR-1.3.0/REDCapR/man/redcap_log_read.Rd | 260 REDCapR-1.3.0/REDCapR/man/redcap_metadata_coltypes.Rd | 346 REDCapR-1.3.0/REDCapR/man/redcap_metadata_read.Rd | 194 REDCapR-1.3.0/REDCapR/man/redcap_metadata_write.Rd | 200 REDCapR-1.3.0/REDCapR/man/redcap_next_free_record_name.Rd | 168 REDCapR-1.3.0/REDCapR/man/redcap_project.Rd | 168 REDCapR-1.3.0/REDCapR/man/redcap_project_info_read.Rd | 318 REDCapR-1.3.0/REDCapR/man/redcap_read.Rd | 640 - REDCapR-1.3.0/REDCapR/man/redcap_read_eav_oneshot.Rd | 350 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REDCapR-1.3.0/REDCapR/tests/test-all.R | 19 REDCapR-1.3.0/REDCapR/tests/testthat/test-arm-export.R | 260 REDCapR-1.3.0/REDCapR/tests/testthat/test-column-sanitize.R | 70 REDCapR-1.3.0/REDCapR/tests/testthat/test-constant.R | 196 REDCapR-1.3.0/REDCapR/tests/testthat/test-create-batch-glossary.R | 198 REDCapR-1.3.0/REDCapR/tests/testthat/test-create-credential-local.R | 74 REDCapR-1.3.0/REDCapR/tests/testthat/test-dag-read.R | 156 REDCapR-1.3.0/REDCapR/tests/testthat/test-delete.R | 406 REDCapR-1.3.0/REDCapR/tests/testthat/test-event-instruments.R | 369 REDCapR-1.3.0/REDCapR/tests/testthat/test-event-read.R | 331 REDCapR-1.3.0/REDCapR/tests/testthat/test-file-oneshot.R | 1166 +- REDCapR-1.3.0/REDCapR/tests/testthat/test-instruments-metadata.R | 156 REDCapR-1.3.0/REDCapR/tests/testthat/test-instruments.R | 180 REDCapR-1.3.0/REDCapR/tests/testthat/test-log-read.R | 148 REDCapR-1.3.0/REDCapR/tests/testthat/test-metadata-coltypes.R | 460 REDCapR-1.3.0/REDCapR/tests/testthat/test-metadata-read.R | 634 - REDCapR-1.3.0/REDCapR/tests/testthat/test-metadata-utilities.R | 380 REDCapR-1.3.0/REDCapR/tests/testthat/test-metadata-write.R | 110 REDCapR-1.3.0/REDCapR/tests/testthat/test-next-free-record-name.R | 185 REDCapR-1.3.0/REDCapR/tests/testthat/test-project-info-read.R | 225 REDCapR-1.3.0/REDCapR/tests/testthat/test-project.R | 158 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 382 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-batch-plumbing.R | 178 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-batch-repeating-sparse.R | 246 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-batch-simple.R | 1800 +-- REDCapR-1.3.0/REDCapR/tests/testthat/test-read-batch-survey.R | 214 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-clinical-trial.R | 86 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-dag.R | 90 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-decimal-comma.R | 232 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-decimal-dot.R | 176 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-eav-oneshot.R | 699 - REDCapR-1.3.0/REDCapR/tests/testthat/test-read-errors.R | 184 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-oneshot-eav.R | 683 - REDCapR-1.3.0/REDCapR/tests/testthat/test-read-oneshot.R | 1542 +- REDCapR-1.3.0/REDCapR/tests/testthat/test-read-russian.R | 88 REDCapR-1.3.0/REDCapR/tests/testthat/test-read-superwide.R | 292 REDCapR-1.3.0/REDCapR/tests/testthat/test-report.R | 342 REDCapR-1.3.0/REDCapR/tests/testthat/test-retrieve-credential-local.R | 358 REDCapR-1.3.0/REDCapR/tests/testthat/test-retrieve-credential-mssql.R | 332 REDCapR-1.3.0/REDCapR/tests/testthat/test-sanitize.R | 146 REDCapR-1.3.0/REDCapR/tests/testthat/test-skippers.R | 22 REDCapR-1.3.0/REDCapR/tests/testthat/test-survey-link-export-oneshot.R | 133 REDCapR-1.3.0/REDCapR/tests/testthat/test-users-export.R | 248 REDCapR-1.3.0/REDCapR/tests/testthat/test-utilities-collapse_vector.R | 40 REDCapR-1.3.0/REDCapR/tests/testthat/test-utilities-replace_nas_with_explicit.R | 160 REDCapR-1.3.0/REDCapR/tests/testthat/test-validate-field-names.R | 106 REDCapR-1.3.0/REDCapR/tests/testthat/test-validate-no-logical.R | 165 REDCapR-1.3.0/REDCapR/tests/testthat/test-validate-record-id-name.R | 78 REDCapR-1.3.0/REDCapR/tests/testthat/test-validate-repeat.R | 66 REDCapR-1.3.0/REDCapR/tests/testthat/test-validate-uniqueness.R | 220 REDCapR-1.3.0/REDCapR/tests/testthat/test-validate.R | 182 REDCapR-1.3.0/REDCapR/tests/testthat/test-variables.R | 186 REDCapR-1.3.0/REDCapR/tests/testthat/test-version.R | 90 REDCapR-1.3.0/REDCapR/tests/testthat/test-write-batch.R | 416 REDCapR-1.3.0/REDCapR/tests/testthat/test-write-dag.R | 426 REDCapR-1.3.0/REDCapR/tests/testthat/test-write-error.R | 309 REDCapR-1.3.0/REDCapR/tests/testthat/test-write-oneshot.R | 564 - REDCapR-1.3.0/REDCapR/vignettes/BasicREDCapROperations.Rmd | 344 REDCapR-1.3.0/REDCapR/vignettes/SecurityDatabase.Rmd | 696 - REDCapR-1.3.0/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 1064 - REDCapR-1.3.0/REDCapR/vignettes/advanced-redcapr-operations.Rmd | 542 REDCapR-1.3.0/REDCapR/vignettes/longitudinal-and-repeating.Rmd | 850 - REDCapR-1.3.0/REDCapR/vignettes/workflow-read.Rmd | 864 - REDCapR-1.3.0/REDCapR/vignettes/workflow-write.Rmd | 836 - 334 files changed, 42643 insertions(+), 42584 deletions(-)
Title: Quantitative Evaluation of the Native Fertility of Tropical
Soils
Description: An implementation of the QUEFTS (Quantitative Evaluation of the Native Fertility of Tropical Soils) model. The model (1) estimates native nutrient (N, P, K) supply of soils from a few soil chemical properties; and (2) computes crop yield given that supply, crop parameters, fertilizer application, and crop attainable yield. See Janssen et al. (1990) <doi:10.1016/0016-7061(90)90021-Z> for the technical details and Sattari et al. (2014) <doi:10.1016/j.fcr.2013.12.005> for a recent evaluation and improvements.
Author: Robert J. Hijmans [cre, aut],
Pieter Pypers [ctb, aut],
Joost Wolff [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between Rquefts versions 1.2-3 dated 2023-10-24 and 1.2-4 dated 2024-10-23
DESCRIPTION | 8 MD5 | 52 ++--- NAMESPACE | 14 - R/RcppExports.R | 14 - R/a_generic_functions.R | 126 +++++++------- R/fcc.R | 244 +++++++++++++-------------- R/ferti_funs.R | 104 +++++------ R/nutSupply.R | 264 ++++++++++++++--------------- R/rquefts.R | 270 +++++++++++++++--------------- R/spatial.R | 134 +++++++-------- R/zzz.R | 2 build/partial.rdb |binary inst/extdata/fertilizers.csv | 60 +++--- inst/extdata/old_quefts_crop_pars.csv | 58 +++--- inst/extdata/quefts_crop_pars.csv | 58 +++--- man/Rquefts-package.Rd | 46 ++--- man/batch.Rd | 92 +++++----- man/fertApp.Rd | 88 ++++----- man/fertilizer.Rd | 76 ++++---- man/nutSupply.Rd | 98 +++++------ man/predict.Rd | 124 +++++++------- man/quefts.Rd | 300 ++++++++++++++++------------------ man/quefts_biom.Rd | 76 ++++---- man/quefts_crop.Rd | 80 ++++----- man/quefts_fert.Rd | 68 +++---- man/quefts_soil.Rd | 74 ++++---- man/revSupply.Rd | 104 +++++------ 27 files changed, 1316 insertions(+), 1318 deletions(-)
Title: Count Regression Models Based on the Bell Distribution
Description: Bell regression models for count data with overdispersion. The implemented models account for ordinary and zero-inflated regression models under both frequentist and Bayesian approaches. Theoretical details regarding the models implemented in the package can be found in Castellares et al. (2018) <doi:10.1016/j.apm.2017.12.014> and Lemonte et al. (2020) <doi:10.1080/02664763.2019.1636940>.
Author: Fabio Demarqui [aut, cre, cph]
,
Marcos Prates [ctb] ,
Fredy Caceres [ctb],
Andrew Johnson [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Diff between bellreg versions 0.0.2.1 dated 2024-06-17 and 0.0.2.2 dated 2024-10-23
bellreg-0.0.2.1/bellreg/man/Bell.Rd |only bellreg-0.0.2.2/bellreg/DESCRIPTION | 8 bellreg-0.0.2.2/bellreg/MD5 | 34 +- bellreg-0.0.2.2/bellreg/NAMESPACE | 4 bellreg-0.0.2.2/bellreg/NEWS.md | 5 bellreg-0.0.2.2/bellreg/R/bell.R |only bellreg-0.0.2.2/bellreg/R/belldist.R | 15 bellreg-0.0.2.2/bellreg/R/bellreg-package.R | 2 bellreg-0.0.2.2/bellreg/R/bellreg.R | 2 bellreg-0.0.2.2/bellreg/README.md | 10 bellreg-0.0.2.2/bellreg/build/partial.rdb |binary bellreg-0.0.2.2/bellreg/build/vignette.rds |binary bellreg-0.0.2.2/bellreg/inst/doc/bellreg.html | 99 +++--- bellreg-0.0.2.2/bellreg/inst/doc/zibellreg.html | 127 ++++---- bellreg-0.0.2.2/bellreg/inst/stan/bellreg.stan | 5 bellreg-0.0.2.2/bellreg/inst/stan/zibellreg.stan | 2 bellreg-0.0.2.2/bellreg/man/Belldist.Rd |only bellreg-0.0.2.2/bellreg/man/bell.Rd |only bellreg-0.0.2.2/bellreg/src/stanExports_bellreg.h | 301 ++++++++++---------- bellreg-0.0.2.2/bellreg/src/stanExports_zibellreg.h | 4 20 files changed, 325 insertions(+), 293 deletions(-)
Title: Multivariate Normal Hypothesis Testing
Description: Hypothesis testing of the parameters of multivariate normal distributions, including the testing of a single mean vector, two mean vectors, multiple mean vectors, a single covariance matrix, multiple covariance matrices, a mean and a covariance matrix simultaneously, and the testing of independence of multivariate normal random vectors. Huixuan, Gao (2005, ISBN:9787301078587), "Applied Multivariate Statistical Analysis".
Author: Xifeng Zhang [aut, cre]
Maintainer: Xifeng Zhang <cnxifeng9819@163.com>
Diff between MNormTest versions 1.1.0 dated 2024-10-22 and 1.1.1 dated 2024-10-23
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 8 +++++--- tests/testthat/test-covTest.multi.R | 2 +- tests/testthat/test-covTest.single.R | 6 +++--- tests/testthat/test-indTest.multi.R | 4 ++-- tests/testthat/test-meanTest.multi.R | 2 +- tests/testthat/test-meanTest.single.R | 4 ++-- tests/testthat/test-meanTest.two.R | 6 +++--- tests/testthat/test-meancov.Test.R | 2 +- 10 files changed, 30 insertions(+), 28 deletions(-)
Title: The Lawson-Hanson Algorithm for Non-Negative Least Squares
(NNLS)
Description: An R interface to the Lawson-Hanson implementation of an
algorithm for non-negative least squares (NNLS). Also allows
the combination of non-negative and non-positive constraints.
Author: Katharine M. Mullen [aut],
Ivo H. M. van Stokkum [aut],
Katharine Mullen [cre]
Maintainer: Katharine Mullen <mullenkate@gmail.com>
Diff between nnls versions 1.5 dated 2023-09-11 and 1.6 dated 2024-10-23
DESCRIPTION | 22 +++++++++++++++++----- MD5 | 8 ++++---- NEWS | 4 ++++ src/lawson_hanson_nnls.f | 11 +++++++++-- src/nnnpls.f | 13 +++++++++++-- 5 files changed, 45 insertions(+), 13 deletions(-)
Title: Design and Analysis of Mixture Experiments
Description: Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson [aut, cre],
Cameron Willden [aut],
Greg Piepel [ctb]
Maintainer: John Lawson <lawson@byu.edu>
Diff between mixexp versions 1.2.7 dated 2022-05-27 and 1.2.7.1 dated 2024-10-23
DESCRIPTION | 13 +++++-------- MD5 | 5 +++-- src/cnvrt.f | 3 ++- src/init.c |only 4 files changed, 10 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-08 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-21 0.4.4.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-26 1.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-08 2.2-7
2023-06-02 2.2-6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-14 0.1.3
Title: Classification Models with Copula Functions
Description: Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.
Author: Rogelio Salinas Gutierrez [aut, cre, cph]
,
Angelica Hernandez Quintero [aut, cph]
,
Pedro Abraham Montoya Calzada [aut, cph]
,
Carlos Alberto Lopez Hernandez [aut, cph]
,
Juan Manuel Marquez Romero [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rsalinas@correo.uaa.mx>
Diff between MLCOPULA versions 1.0.0 dated 2024-06-06 and 1.0.1 dated 2024-10-23
DESCRIPTION | 6 +++--- MD5 | 40 +++++++++++++++++++++++----------------- NAMESPACE | 1 + R/aux_mi_report.R |only R/classification_report.R |only R/copulaClassifier.R | 3 ++- R/copulaPredict.R | 5 +++-- R/join_all.R | 14 ++++++++------ R/join_amh.R | 14 ++++++++------ R/join_clayton.R | 12 +++++++----- R/join_frank.R | 12 +++++++----- R/join_gaussian.R | 13 +++++++------ R/join_grid.R | 13 ++++++++----- R/join_gumbel.R | 13 ++++++++----- R/join_joe.R | 14 ++++++++------ R/mi_cop.R | 2 +- R/mi_gaussian.R |only R/mi_report.R |only R/train_independent.R |only R/train_normal.R | 2 +- build/partial.rdb |binary man/classification_report.Rd |only man/copulaClassifier.Rd | 42 +++++++++++++++++++++--------------------- man/copulaPredict.Rd | 16 ++++++++++------ 24 files changed, 126 insertions(+), 96 deletions(-)
Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that
uses techniques from topology to analyze high-dimensional data. Here we
implement Mapper, an algorithm from this area developed by Singh, Mémoli and
Carlsson (2007) which generalizes the concept of a
Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>
Diff between mappeR versions 1.1.0 dated 2024-10-16 and 1.2.0 dated 2024-10-23
mappeR-1.1.0/mappeR/R/arboretum.R |only mappeR-1.1.0/mappeR/R/viewmaster-hub.R |only mappeR-1.1.0/mappeR/R/watering_hole.R |only mappeR-1.1.0/mappeR/man/get_single_linkage_clusters.Rd |only mappeR-1.1.0/mappeR/man/run_slink.Rd |only mappeR-1.2.0/mappeR/DESCRIPTION | 11 mappeR-1.2.0/mappeR/MD5 | 68 +-- mappeR-1.2.0/mappeR/NEWS.md | 5 mappeR-1.2.0/mappeR/R/art_studio.R | 16 mappeR-1.2.0/mappeR/R/baskin_robbins.R |only mappeR-1.2.0/mappeR/R/cartography_chamber.R | 266 +++--------- mappeR-1.2.0/mappeR/R/cluster_factory.R |only mappeR-1.2.0/mappeR/R/quilting_hut.R | 25 - mappeR-1.2.0/mappeR/R/stats_hub.R |only mappeR-1.2.0/mappeR/R/viewmaster-library.R |only mappeR-1.2.0/mappeR/README.md | 9 mappeR-1.2.0/mappeR/man/compute_tightness.Rd | 7 mappeR-1.2.0/mappeR/man/convert_to_clusters.Rd | 2 mappeR-1.2.0/mappeR/man/create_1D_mapper_object.Rd | 8 mappeR-1.2.0/mappeR/man/create_ball_mapper_object.Rd | 2 mappeR-1.2.0/mappeR/man/create_bins.Rd | 6 mappeR-1.2.0/mappeR/man/create_clusterball_mapper_object.Rd | 4 mappeR-1.2.0/mappeR/man/create_mapper_object.Rd | 10 mappeR-1.2.0/mappeR/man/create_single_bin.Rd | 6 mappeR-1.2.0/mappeR/man/cut_dendrogram.Rd | 7 mappeR-1.2.0/mappeR/man/eccentricity_filter.Rd | 2 mappeR-1.2.0/mappeR/man/get_bin_vector.Rd | 2 mappeR-1.2.0/mappeR/man/get_cluster_sizes.Rd | 4 mappeR-1.2.0/mappeR/man/get_cluster_tightness_vector.Rd | 8 mappeR-1.2.0/mappeR/man/get_clustered_data.Rd | 2 mappeR-1.2.0/mappeR/man/get_clusters.Rd | 4 mappeR-1.2.0/mappeR/man/get_edge_weights.Rd | 7 mappeR-1.2.0/mappeR/man/get_hierarchical_clusters.Rd |only mappeR-1.2.0/mappeR/man/get_tallest_branch.Rd | 2 mappeR-1.2.0/mappeR/man/mappeR-package.Rd | 2 mappeR-1.2.0/mappeR/man/process_dendrograms.Rd | 7 mappeR-1.2.0/mappeR/man/run_cluster_machine.Rd | 4 mappeR-1.2.0/mappeR/man/run_link.Rd |only mappeR-1.2.0/mappeR/man/subset_dists.Rd | 2 mappeR-1.2.0/mappeR/tests/testthat/Rplots.pdf |only mappeR-1.2.0/mappeR/tests/testthat/test-inputs.R | 10 41 files changed, 225 insertions(+), 283 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre],
Niklas von Hertzen [aut]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.6.6 dated 2024-05-14 and 1.6.7 dated 2024-10-23
DESCRIPTION | 30 +++++++++++++++--------------- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ README.md | 9 ++++----- inst/app/global.R | 2 ++ inst/app/tools/app/about.md | 2 +- inst/app/tools/app/tutorials.md | 2 +- inst/app/tools/data/manage.R | 2 -- inst/app/tools/help/report_rmd.Rmd | 2 ++ inst/app/tools/help/report_rmd.md | 2 ++ inst/app/www/style.css | 4 ++-- 11 files changed, 43 insertions(+), 36 deletions(-)
Title: Simulating Nonhomogeneous Poisson Point Processes
Description: Simulates events from one dimensional nonhomogeneous Poisson point processes (NHPPPs) as per Trikalinos and Sereda (2024, <doi:10.48550/arXiv.2402.00358>). Functions are based on three algorithms that provably sample from a target NHPPP: the time-transformation of a homogeneous Poisson process (of intensity one) via the inverse of the integrated intensity function (Cinlar E, "Theory of stochastic processes" (1975, ISBN:0486497996)); the generation of a Poisson number of order statistics from a fixed density function; and the thinning of a majorizing NHPPP via an acceptance-rejection scheme (Lewis PAW, Shedler, GS (1979) <doi:10.1002/nav.3800260304>).
Author: Thomas Trikalinos [aut, cre, cph]
,
Yuliia Sereda [aut]
Maintainer: Thomas Trikalinos <thomas_trikalinos@brown.edu>
Diff between nhppp versions 0.1.4 dated 2024-05-28 and 1.0.0 dated 2024-10-23
nhppp-0.1.4/nhppp/R/vdraw_intensity_step_regular.R |only nhppp-0.1.4/nhppp/R/vdraw_intensity_step_regular_R.R |only nhppp-0.1.4/nhppp/R/vdraw_sc_step_regular_R.R |only nhppp-0.1.4/nhppp/R/vztdraw_intensity_step_regular_R.R |only nhppp-0.1.4/nhppp/R/vztdraw_sc_step_regular.R |only nhppp-0.1.4/nhppp/R/vztdraw_sc_step_regular_R.R |only nhppp-0.1.4/nhppp/man/vdraw_intensity_step_regular.Rd |only nhppp-0.1.4/nhppp/man/vdraw_intensity_step_regular_R.Rd |only nhppp-0.1.4/nhppp/man/vdraw_sc_step_regular_R.Rd |only nhppp-0.1.4/nhppp/man/vztdraw_intensity_step_regular_R.Rd |only nhppp-0.1.4/nhppp/man/vztdraw_sc_step_regular.Rd |only nhppp-0.1.4/nhppp/man/vztdraw_sc_step_regular_R.Rd |only nhppp-0.1.4/nhppp/tests/testthat/test-ppp_n.R |only nhppp-0.1.4/nhppp/tests/testthat/test-ppp_orderstat.R |only nhppp-0.1.4/nhppp/tests/testthat/test-ppp_sequential.R |only nhppp-0.1.4/nhppp/tests/testthat/test-vdraw_intensity_step_regular_R.R |only nhppp-0.1.4/nhppp/tests/testthat/test-vztdraw_intensity_step_regular_R.R |only nhppp-0.1.4/nhppp/tests/testthat/test-vztdraw_sc_step_regular_R.R |only nhppp-1.0.0/nhppp/DESCRIPTION | 17 nhppp-1.0.0/nhppp/MD5 | 293 +++++----- nhppp-1.0.0/nhppp/NAMESPACE | 19 nhppp-1.0.0/nhppp/NEWS.md | 6 nhppp-1.0.0/nhppp/R/data.R |only nhppp-1.0.0/nhppp/R/draw.R | 63 +- nhppp-1.0.0/nhppp/R/draw_cumulative_intensity.R |only nhppp-1.0.0/nhppp/R/draw_cumulative_intensity_inversion.R | 35 - nhppp-1.0.0/nhppp/R/draw_cumulative_intensity_orderstats.R | 33 - nhppp-1.0.0/nhppp/R/draw_intensity.R | 105 +-- nhppp-1.0.0/nhppp/R/draw_intensity_line.R |only nhppp-1.0.0/nhppp/R/draw_intensity_step.R | 28 nhppp-1.0.0/nhppp/R/draw_sc_linear.R | 38 - nhppp-1.0.0/nhppp/R/draw_sc_loglinear.R | 30 - nhppp-1.0.0/nhppp/R/draw_sc_step.R | 35 - nhppp-1.0.0/nhppp/R/draw_sc_step_regular.R | 22 nhppp-1.0.0/nhppp/R/matrix_cumsum_columns.R | 3 nhppp-1.0.0/nhppp/R/matrix_cumsum_columns_inplace.R | 3 nhppp-1.0.0/nhppp/R/matrix_diff_columns.R | 3 nhppp-1.0.0/nhppp/R/matrix_diff_columns_inplace.R | 3 nhppp-1.0.0/nhppp/R/ppp.R |only nhppp-1.0.0/nhppp/R/ppp2.R |only nhppp-1.0.0/nhppp/R/ppp_exactly_n.R |only nhppp-1.0.0/nhppp/R/ppp_n.R | 6 nhppp-1.0.0/nhppp/R/ppp_next_n.R | 12 nhppp-1.0.0/nhppp/R/ppp_orderstat.R | 5 nhppp-1.0.0/nhppp/R/ppp_sequential.R | 6 nhppp-1.0.0/nhppp/R/utils-calculus.R | 1 nhppp-1.0.0/nhppp/R/utils-helper.R | 29 nhppp-1.0.0/nhppp/R/utils-invert_bijection.R | 2 nhppp-1.0.0/nhppp/R/utils-linear.R | 95 +-- nhppp-1.0.0/nhppp/R/utils-rngstream.R | 14 nhppp-1.0.0/nhppp/R/utils-vectorized.R | 7 nhppp-1.0.0/nhppp/R/vdraw.R | 103 ++- nhppp-1.0.0/nhppp/R/vdraw_cumulative_intensity.R |only nhppp-1.0.0/nhppp/R/vdraw_intensity.R |only nhppp-1.0.0/nhppp/R/vdraw_intensity_step_regular_cpp.R | 92 +-- nhppp-1.0.0/nhppp/R/vdraw_intensity_step_regular_forcezt.R |only nhppp-1.0.0/nhppp/R/vdraw_sc_step_regular.R | 91 +-- nhppp-1.0.0/nhppp/R/vdraw_sc_step_regular_cpp.R | 88 +-- nhppp-1.0.0/nhppp/R/vztdraw_intensity.R |only nhppp-1.0.0/nhppp/R/vztdraw_intensity_step_regular.R | 144 +++- nhppp-1.0.0/nhppp/R/vztdraw_sc_step_regular_cpp.R | 92 +-- nhppp-1.0.0/nhppp/R/ztdraw_cumulative_intensity.R | 28 nhppp-1.0.0/nhppp/R/ztdraw_intensity.R | 100 +-- nhppp-1.0.0/nhppp/R/ztdraw_intensity_line.R |only nhppp-1.0.0/nhppp/R/ztdraw_intensity_step.R | 28 nhppp-1.0.0/nhppp/R/ztdraw_sc_linear.R | 39 - nhppp-1.0.0/nhppp/R/ztdraw_sc_loglinear.R | 37 - nhppp-1.0.0/nhppp/R/ztppp.R | 12 nhppp-1.0.0/nhppp/README.md | 47 - nhppp-1.0.0/nhppp/build/partial.rdb |binary nhppp-1.0.0/nhppp/build/vignette.rds |only nhppp-1.0.0/nhppp/data |only nhppp-1.0.0/nhppp/inst/doc |only nhppp-1.0.0/nhppp/man/Lambda_exp_form.Rd | 11 nhppp-1.0.0/nhppp/man/Lambda_inv_exp_form.Rd | 11 nhppp-1.0.0/nhppp/man/Lambda_inv_linear_form.Rd | 11 nhppp-1.0.0/nhppp/man/Lambda_linear_form.Rd | 11 nhppp-1.0.0/nhppp/man/annual_mortality_rates_2015.Rd |only nhppp-1.0.0/nhppp/man/check_ppp_sample_validity.Rd | 12 nhppp-1.0.0/nhppp/man/check_ppp_vector_validity.Rd | 1 nhppp-1.0.0/nhppp/man/compare_ppp_vectors.Rd | 1 nhppp-1.0.0/nhppp/man/draw.Rd | 32 - nhppp-1.0.0/nhppp/man/draw_cumulative_intensity.Rd |only nhppp-1.0.0/nhppp/man/draw_cumulative_intensity_inversion.Rd | 17 nhppp-1.0.0/nhppp/man/draw_cumulative_intensity_orderstats.Rd | 17 nhppp-1.0.0/nhppp/man/draw_intensity.Rd | 40 - nhppp-1.0.0/nhppp/man/draw_intensity_line.Rd |only nhppp-1.0.0/nhppp/man/draw_intensity_step.Rd | 21 nhppp-1.0.0/nhppp/man/draw_sc_linear.Rd | 18 nhppp-1.0.0/nhppp/man/draw_sc_loglinear.Rd | 18 nhppp-1.0.0/nhppp/man/draw_sc_step.Rd | 14 nhppp-1.0.0/nhppp/man/draw_sc_step_regular.Rd | 10 nhppp-1.0.0/nhppp/man/expect_no_error.Rd | 1 nhppp-1.0.0/nhppp/man/inverse_with_uniroot.Rd | 1 nhppp-1.0.0/nhppp/man/inverse_with_uniroot_sorted.Rd | 1 nhppp-1.0.0/nhppp/man/make_cumulative_Lambda_matrix.Rd | 1 nhppp-1.0.0/nhppp/man/make_lambda_matrix.Rd | 1 nhppp-1.0.0/nhppp/man/make_range_t_matrix.Rd | 1 nhppp-1.0.0/nhppp/man/mat_cumsum_columns.Rd | 1 nhppp-1.0.0/nhppp/man/mat_cumsum_columns_with_scalar_ceiling.Rd | 1 nhppp-1.0.0/nhppp/man/mat_cumsum_columns_with_vector_ceiling.Rd | 1 nhppp-1.0.0/nhppp/man/mat_diff_columns.Rd | 1 nhppp-1.0.0/nhppp/man/matrix_cumsum_columns.Rd |only nhppp-1.0.0/nhppp/man/matrix_cumsum_columns_inplace.Rd |only nhppp-1.0.0/nhppp/man/matrix_diff_columns.Rd |only nhppp-1.0.0/nhppp/man/matrix_diff_columns_inplace.Rd |only nhppp-1.0.0/nhppp/man/nhppp-package.Rd | 1 nhppp-1.0.0/nhppp/man/ppp.Rd |only nhppp-1.0.0/nhppp/man/ppp2.Rd |only nhppp-1.0.0/nhppp/man/ppp_exactly_n.Rd |only nhppp-1.0.0/nhppp/man/ppp_n.Rd | 4 nhppp-1.0.0/nhppp/man/ppp_next_n.Rd | 4 nhppp-1.0.0/nhppp/man/ppp_orderstat.Rd | 4 nhppp-1.0.0/nhppp/man/ppp_sequential.Rd | 4 nhppp-1.0.0/nhppp/man/read_code.Rd | 1 nhppp-1.0.0/nhppp/man/rng_stream_rexp.Rd | 1 nhppp-1.0.0/nhppp/man/rng_stream_rpois.Rd | 1 nhppp-1.0.0/nhppp/man/rng_stream_runif.Rd | 1 nhppp-1.0.0/nhppp/man/rng_stream_rztpois.Rd | 1 nhppp-1.0.0/nhppp/man/rztpois.Rd | 7 nhppp-1.0.0/nhppp/man/simpson_num_integr.Rd | 1 nhppp-1.0.0/nhppp/man/vdraw.Rd | 59 +- nhppp-1.0.0/nhppp/man/vdraw_cumulative_intensity.Rd |only nhppp-1.0.0/nhppp/man/vdraw_intensity.Rd |only nhppp-1.0.0/nhppp/man/vdraw_intensity_step_regular_cpp.Rd | 49 - nhppp-1.0.0/nhppp/man/vdraw_intensity_step_regular_forcezt.Rd |only nhppp-1.0.0/nhppp/man/vdraw_sc_step_regular.Rd | 46 + nhppp-1.0.0/nhppp/man/vdraw_sc_step_regular_cpp.Rd | 37 - nhppp-1.0.0/nhppp/man/vztdraw_intensity.Rd |only nhppp-1.0.0/nhppp/man/vztdraw_intensity_step_regular.Rd | 49 - nhppp-1.0.0/nhppp/man/vztdraw_sc_step_regular_cpp.Rd | 34 - nhppp-1.0.0/nhppp/man/ztdraw_cumulative_intensity.Rd | 18 nhppp-1.0.0/nhppp/man/ztdraw_intensity.Rd | 40 - nhppp-1.0.0/nhppp/man/ztdraw_intensity_line.Rd |only nhppp-1.0.0/nhppp/man/ztdraw_intensity_step.Rd | 21 nhppp-1.0.0/nhppp/man/ztdraw_sc_linear.Rd | 18 nhppp-1.0.0/nhppp/man/ztdraw_sc_loglinear.Rd | 22 nhppp-1.0.0/nhppp/man/ztppp.Rd | 10 nhppp-1.0.0/nhppp/tests/testthat/test-draw.R | 11 nhppp-1.0.0/nhppp/tests/testthat/test-draw_cumulative_intensity.R |only nhppp-1.0.0/nhppp/tests/testthat/test-draw_cumulative_intensity_inversion.R | 40 - nhppp-1.0.0/nhppp/tests/testthat/test-draw_cumulative_intensity_orderstats.R | 13 nhppp-1.0.0/nhppp/tests/testthat/test-draw_intensity.R | 44 - nhppp-1.0.0/nhppp/tests/testthat/test-draw_intensity_line.R |only nhppp-1.0.0/nhppp/tests/testthat/test-draw_intensity_step.R | 11 nhppp-1.0.0/nhppp/tests/testthat/test-draw_sc_linear.R | 24 nhppp-1.0.0/nhppp/tests/testthat/test-draw_sc_loglinear.R | 6 nhppp-1.0.0/nhppp/tests/testthat/test-draw_sc_step.R | 22 nhppp-1.0.0/nhppp/tests/testthat/test-draw_sc_step_regular.R | 21 nhppp-1.0.0/nhppp/tests/testthat/test-ppp.R |only nhppp-1.0.0/nhppp/tests/testthat/test-ppp2.R |only nhppp-1.0.0/nhppp/tests/testthat/test-ppp_agreement.R | 164 ++--- nhppp-1.0.0/nhppp/tests/testthat/test-ppp_exactly_n.R |only nhppp-1.0.0/nhppp/tests/testthat/test-ppp_next_n.R | 13 nhppp-1.0.0/nhppp/tests/testthat/test-utils-linear.R | 20 nhppp-1.0.0/nhppp/tests/testthat/test-utils-rng_stream.R | 6 nhppp-1.0.0/nhppp/tests/testthat/test-vdraw_cumulative_intensity.R |only nhppp-1.0.0/nhppp/tests/testthat/test-vdraw_intensity_step_regular_cpp.R | 59 +- nhppp-1.0.0/nhppp/tests/testthat/test-vdraw_intensity_step_regular_forcezt.R |only nhppp-1.0.0/nhppp/tests/testthat/test-vdraw_sc_step_regular.R | 90 ++- nhppp-1.0.0/nhppp/tests/testthat/test-vdraw_sc_step_regular_cpp.R | 76 +- nhppp-1.0.0/nhppp/tests/testthat/test-vztdraw_intensity_step_regular.R |only nhppp-1.0.0/nhppp/tests/testthat/test-vztdraw_sc_step_regular_cpp.R | 46 + nhppp-1.0.0/nhppp/tests/testthat/test-ztdraw_cumulative_intensity.R | 17 nhppp-1.0.0/nhppp/tests/testthat/test-ztdraw_intensity.R | 93 --- nhppp-1.0.0/nhppp/tests/testthat/test-ztdraw_intensity_line.R |only nhppp-1.0.0/nhppp/tests/testthat/test-ztdraw_intensity_step.R | 11 nhppp-1.0.0/nhppp/tests/testthat/test-ztdraw_sc_linear.R | 8 nhppp-1.0.0/nhppp/tests/testthat/test-ztdraw_sc_loglinear.R | 8 nhppp-1.0.0/nhppp/tests/testthat/test-ztnhppp_agreement.R | 80 +- nhppp-1.0.0/nhppp/tests/testthat/test-ztppp.R | 9 nhppp-1.0.0/nhppp/vignettes |only 172 files changed, 1761 insertions(+), 1633 deletions(-)