Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.0-3 dated 2023-01-28 and 3.0-5 dated 2023-04-22
DESCRIPTION | 17 +--- MD5 | 46 +++++------ NEWS | 17 ++++ build/vignette.rds |binary demo/data.R | 6 - inst/CITATION | 98 +++++++++-------------- inst/doc/bugfixes.R | 18 ++-- inst/doc/bugfixes.Rnw | 9 +- inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 149 ++++++++++++++++++------------------ inst/doc/datasets.Rnw | 14 +++ inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 4 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 21 ++--- inst/doc/updates.Rnw | 190 +++++++++++++++++++++++++++++++++++++++------- inst/doc/updates.pdf |binary man/macros/defns.Rd | 4 man/spatstat-package.Rd | 4 vignettes/bugfixes.Rnw | 9 +- vignettes/datasets.Rnw | 14 +++ vignettes/updates.Rnw | 190 +++++++++++++++++++++++++++++++++++++++------- 24 files changed, 566 insertions(+), 244 deletions(-)
Title: Power Analysis and Sample Size Calculation
Description: Power analysis and sample size calculation for Welch and Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) t-tests including Monte-Carlo simulations of empirical power and type-I-error. Power and sample size calculation for Wilcoxon rank sum and signed rank tests via Monte-Carlo simulations. Power and sample size required for the evaluation of a diagnostic test(-system) (Flahault et al. (2005), <doi:10.1016/j.jclinepi.2004.12.009>; Dobbin and Simon (2007), <doi:10.1093/biostatistics/kxj036>) as well as for a single proportion (Fleiss et al. (2003), ISBN:978-0-471-52629-2; Piegorsch (2004), <doi:10.1016/j.csda.2003.10.002>; Thulin (2014), <doi:10.1214/14-ejs909>), comparing two negative binomial rates (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>), and ANCOVA (Shieh (2020), <doi:10.1007/s11336-019-09692-3>).
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKpower versions 0.6 dated 2023-04-10 and 0.7 dated 2023-04-22
DESCRIPTION | 10 - MD5 | 35 +-- NAMESPACE | 3 NEWS | 7 R/powerANCOVA.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/MKpower.R | 33 +++ inst/doc/MKpower.Rmd | 61 +++++- inst/doc/MKpower.html | 412 +++++++++++++++++++++++++++++++------------ man/0MKpower-package.Rd | 9 man/histSimPower.Rd | 6 man/power.ancova.Rd |only man/power.diagnostic.test.Rd | 2 man/power.hsu.t.test.Rd | 2 man/power.nb.test.Rd | 2 man/power.welch.t.test.Rd | 2 man/qqunifSimPower.Rd | 2 vignettes/MKpower.Rmd | 61 +++++- vignettes/MKpower.bib | 16 + 20 files changed, 507 insertions(+), 156 deletions(-)
Title: Lemna Ecotox Effect Model
Description: The reference implementation of model equations and default
parameters for the toxicokinetic-toxicodynamic (TKTD) model of the Lemna
(duckweed) aquatic plant. Lemna is a standard test macrophyte used in ecotox
effect studies. The model was described and published by the SETAC Europe
Interest Group Effect Modeling. It is a refined description of the Lemna
TKTD model published by Schmitt et al. (2013)
<doi:10.1016/j.ecolmodel.2013.01.017>.
Author: Nils Kehrein [aut, cre],
SETAC Europe IG Effect Modeling [ccp]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between lemna versions 1.0.0 dated 2022-05-10 and 1.0.1 dated 2023-04-22
DESCRIPTION | 8 MD5 | 32 - NEWS.md | 6 R/lemna_ode.R | 262 +++++------ README.md | 190 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lemna-introduction.html | 181 ++++--- inst/doc/lemna-verification.html | 203 ++++---- man/effect.Rd | 6 man/lemna.Rd | 6 man/param_defaults.Rd | 240 +++++----- src/lemna.c | 10 tests/testthat/test-param.R | 6 tests/testthat/test-verify-variable.R | 11 vignettes/mmc2.r | 346 +++++++------- vignettes/mmc3.r | 798 +++++++++++++++++----------------- 17 files changed, 1166 insertions(+), 1139 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 2.1.4 dated 2023-04-02 and 2.1.5 dated 2023-04-22
DESCRIPTION | 6 +-- MD5 | 26 ++++++++-------- NAMESPACE | 6 +++ NEWS.md | 17 ++++++++++ R/nlmixr2_md5.R | 2 - R/nmObjGet.R | 67 ++++++++++++++++++++++++++++++++++++------- R/rxsolve.R | 11 +++++++ R/sharedControl.R | 4 ++ R/splitModelRxUiGet.R | 30 +++++++++++++++++-- man/getValidNlmixrControl.Rd | 3 + man/nlmixr2Est.Rd | 3 + man/nmObjGetData.Rd | 12 +++++++ tests/testthat/test-cwres.R | 1 tests/testthat/test-nonmu.R | 3 + 14 files changed, 161 insertions(+), 30 deletions(-)
Title: Penalized Poisson Pseudo Maximum Likelihood Regression
Description: A set of tools that enables efficient estimation of penalized
Poisson Pseudo Maximum Likelihood regressions, using lasso or ridge penalties, for models
that feature one or more sets of high-dimensional fixed effects. The methodology is based on
Breinlich, Corradi, Rocha, Ruta, Santos Silva, and Zylkin (2021) <http://hdl.handle.net/10986/35451>
and takes advantage of the method of alternating projections of Gaure (2013)
<doi:10.1016/j.csda.2013.03.024> for dealing with HDFE, as well as
the coordinate descent algorithm of Friedman, Hastie and Tibshirani (2010)
<doi:10.18637/jss.v033.i01> for fitting lasso regressions. The package is also able to carry out
cross-validation and to implement the plugin lasso of Belloni, Chernozhukov, Hansen and Kozbur (2016)
<doi:10.1080/07350015.2015.1102733>.
Author: Diego Ferreras Garrucho [aut],
Tom Zylkin [aut],
Joao Cruz [cre]
Maintainer: Joao Cruz <jm01780@surrey.ac.uk>
Diff between penppml versions 0.2.1 dated 2022-12-16 and 0.2.2 dated 2023-04-22
DESCRIPTION | 6 - MD5 | 38 ++++----- NEWS.md | 5 + R/bootstrap.R | 32 ++++---- R/iceberg.R | 8 +- R/mlfitppml_int.R | 9 +- R/penhdfeppml_cluster_int.R | 35 +++++++- R/penhdfeppml_int.R | 7 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-penppml.R | 4 - inst/doc/intro-to-penppml.Rmd | 8 +- inst/doc/intro-to-penppml.html | 160 +++++++++++++++++++++++------------------ man/bootstrap.Rd | 17 +--- man/iceberg.Rd | 2 man/mlfitppml_int.Rd | 5 + man/penhdfeppml_cluster_int.Rd | 11 ++ man/penhdfeppml_int.Rd | 5 + man/plugin_lasso_int.Rd | 4 - vignettes/intro-to-penppml.Rmd | 8 +- 20 files changed, 216 insertions(+), 148 deletions(-)
Title: Test Overlapping of Polygons Against Random Rotation
Description: Tests the observed overlapping polygon area in a collection of polygons against a null model of random rotation, as explained in De la Cruz et al. (2017) <doi:10.13140/RG.2.2.12825.72801>.
Author: Marcelino de la Cruz Rot
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between overlapptest versions 1.2-4 dated 2021-03-15 and 1.3 dated 2023-04-22
DESCRIPTION | 10 ++-- MD5 | 20 ++++---- R/check.ventana.R | 49 +++++++++++--------- build/vignette.rds |binary data/Astragalus.rda |binary data/Sesleria.rda |binary inst/doc/Readshapefiles.R | 92 +++++++++++++++++++++------------------ inst/doc/Readshapefiles.Rnw | 101 ++++++++++++++++++++++--------------------- inst/doc/Readshapefiles.pdf |binary man/test.intersection.Rd | 20 +++++--- vignettes/Readshapefiles.Rnw | 101 ++++++++++++++++++++++--------------------- 11 files changed, 214 insertions(+), 179 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.10.0 dated 2023-03-20 and 2.11.0 dated 2023-04-22
DESCRIPTION | 8 +- MD5 | 30 ++++----- NEWS.md | 4 + R/abfit.R | 103 ++++++++++++++++++++------------- R/mrs_data_display.R | 5 + R/mrs_data_proc.R | 11 ++- R/mrs_read_pfile.R | 16 ++++- R/mrs_read_rda.R | 4 + inst/doc/spant-intro.html | 106 +++++++++++++++++----------------- inst/doc/spant-preprocessing.html | 4 - man/abfit_opts.Rd | 10 ++- man/set_lw.Rd | 5 + tests/testthat/abfit_res_coarse.rds |binary tests/testthat/abfit_res_default.rds |binary tests/testthat/abfit_res_fine.rds |binary tests/testthat/abfit_res_no_optim.rds |binary 16 files changed, 187 insertions(+), 119 deletions(-)
Title: Pedigree Inference from SNPs
Description: Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 2.5.3 dated 2023-03-21 and 2.5.6 dated 2023-04-22
sequoia-2.5.3/sequoia/inst/doc/vignette-main.pdf |only sequoia-2.5.3/sequoia/vignettes/vignette-main.html |only sequoia-2.5.6/sequoia/DESCRIPTION | 8 ++++---- sequoia-2.5.6/sequoia/MD5 | 21 ++++++++++----------- sequoia-2.5.6/sequoia/NEWS.md | 10 ++++++++++ sequoia-2.5.6/sequoia/R/CalcBYprobs.R | 6 +++--- sequoia-2.5.6/sequoia/R/ComparePeds.R | 4 ++-- sequoia-2.5.6/sequoia/build/vignette.rds |binary sequoia-2.5.6/sequoia/inst/doc/vignette-age.pdf |binary sequoia-2.5.6/sequoia/inst/doc/vignette-main.Rmd | 20 ++++++++++---------- sequoia-2.5.6/sequoia/inst/doc/vignette-main.html |only sequoia-2.5.6/sequoia/src/Sequoia.f90 | 14 ++++++-------- sequoia-2.5.6/sequoia/vignettes/vignette-main.Rmd | 20 ++++++++++---------- 13 files changed, 55 insertions(+), 48 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Melissa Hallow [aut],
Wenping Wang [aut],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Cleve Moler [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Gilber [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.0.12 dated 2023-03-28 and 2.0.13 dated 2023-04-22
rxode2-2.0.12/rxode2/tests/testthat/test-rxSumProd-1.qs |only rxode2-2.0.13/rxode2/DESCRIPTION | 6 rxode2-2.0.13/rxode2/MD5 | 35 +- rxode2-2.0.13/rxode2/NAMESPACE | 1 rxode2-2.0.13/rxode2/NEWS.md | 8 rxode2-2.0.13/rxode2/R/mu.R | 6 rxode2-2.0.13/rxode2/R/piping-ini.R | 60 +--- rxode2-2.0.13/rxode2/R/rxUiBlessed.R | 2 rxode2-2.0.13/rxode2/R/rxode2_md5.R | 2 rxode2-2.0.13/rxode2/R/rxsolve.R | 5 rxode2-2.0.13/rxode2/R/ui-rename.R | 4 rxode2-2.0.13/rxode2/README.md | 157 ++++--------- rxode2-2.0.13/rxode2/build/vignette.rds |binary rxode2-2.0.13/rxode2/inst/doc/rxode2-syntax.html | 14 - rxode2-2.0.13/rxode2/man/rxSolve.Rd | 3 rxode2-2.0.13/rxode2/tests/testthat/test-iCov.R |only rxode2-2.0.13/rxode2/tests/testthat/test-piping-ini.R | 69 +++++ rxode2-2.0.13/rxode2/tests/testthat/test-rxSumProd.R | 5 rxode2-2.0.13/rxode2/tests/testthat/test-ui-rename.R | 33 ++ rxode2-2.0.13/rxode2/tests/testthat/test-ui-single-theta.R |only 20 files changed, 228 insertions(+), 182 deletions(-)
Title: Power Simulation for Sequential Analyses and Multiple Hypotheses
Description: Calculates, via simulation, power and appropriate stopping
alpha boundaries (and/or futility bounds) for sequential analyses (i.e.,
group sequential design) as well as for multiple hypotheses (multiple tests
included in an analysis), given any specified global error rate. This enables
the sequential use of practically any significance test, as long as the
underlying data can be simulated in advance to a reasonable approximation.
Lukács (2022) <doi:10.21105/joss.04643>.
Author: Gaspar Lukacs [aut, cre]
Maintainer: Gaspar Lukacs <lkcsgaspar@gmail.com>
Diff between POSSA versions 0.6.3 dated 2023-03-14 and 0.6.4 dated 2023-04-22
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++++++++++- build |only inst |only vignettes |only 5 files changed, 24 insertions(+), 6 deletions(-)
Title: Methods and Tools for Bayesian Dynamic Conditional Correlation
GARCH(1,1) Model
Description: Bayesian estimation of dynamic conditional correlation GARCH model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade-Filho, M.G., (2014). <doi:10.1080/02664763.2013.839635>.
Author: Jose Augusto Fiorucci [aut, cre, cph]
,
Ricardo Sanders Ehlers [aut, cph]
,
Francisco Louzada [aut, cph]
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>
Diff between bayesDccGarch versions 3.0.3 dated 2021-10-05 and 3.0.4 dated 2023-04-22
ChangeLog | 2 DESCRIPTION | 6 MD5 | 16 +- R/mainFunctions.R | 10 - README.md | 4 man/bayesDccGarch-package.Rd | 4 man/predict.bayesDccGarch.Rd | 2 src/bayesDccGarch.c | 12 - src/matrixOperations.h | 272 +++++++++++++++++++++---------------------- 9 files changed, 164 insertions(+), 164 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-28 0.1.3
2023-01-17 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-03 0.4.11
2017-07-08 0.4.3
2016-02-11 0.4.1
2016-02-08 0.4
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez [aut, cre],
Jose Emmanuel Chacon [cph],
Carlos Aguero [cph],
Jorge Arce [cph]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 3.0.13 dated 2022-07-16 and 3.1.0 dated 2023-04-22
RSDA-3.0.13/RSDA/R/sym_interval_tsne.R |only RSDA-3.0.13/RSDA/man/plot.sym_tsne.Rd |only RSDA-3.0.13/RSDA/man/sym.tsne.Rd |only RSDA-3.1.0/RSDA/DESCRIPTION | 14 RSDA-3.1.0/RSDA/MD5 | 36 - RSDA-3.1.0/RSDA/NAMESPACE | 7 RSDA-3.1.0/RSDA/R/RSDA.R | 14 RSDA-3.1.0/RSDA/R/read_sym_table.R | 3 RSDA-3.1.0/RSDA/R/sym_interval_umap.R | 29 RSDA-3.1.0/RSDA/R/symbolic_df.R | 96 ++ RSDA-3.1.0/RSDA/R/symbolic_objects.R | 3 RSDA-3.1.0/RSDA/build/vignette.rds |binary RSDA-3.1.0/RSDA/inst/doc/introduction.R | 42 - RSDA-3.1.0/RSDA/inst/doc/introduction.Rmd | 55 - RSDA-3.1.0/RSDA/inst/doc/introduction.html | 999 +++++++++++------------------ RSDA-3.1.0/RSDA/man/RSDA.Rd | 4 RSDA-3.1.0/RSDA/man/plot.sym_umap.Rd | 2 RSDA-3.1.0/RSDA/man/sym.umap.Rd | 31 RSDA-3.1.0/RSDA/man/tbl_subset_col.Rd |only RSDA-3.1.0/RSDA/man/var.length.Rd | 2 RSDA-3.1.0/RSDA/vignettes/introduction.Rmd | 55 - 21 files changed, 579 insertions(+), 813 deletions(-)