Title: Maximum-Likelihood Perfect Phylogeny Inference at Scale
Description: Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).
Author: Teng Gao [cre, aut],
Evan Biederstedt [aut],
Peter Kharchenko [aut],
Yufeng Wu [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Diff between scistreer versions 1.0.0 dated 2022-11-21 and 1.0.1 dated 2022-11-24
DESCRIPTION | 9 +++++---- MD5 | 29 ++++++++++++++++++----------- NAMESPACE | 3 +++ R/data.R | 16 ++++++++++++++-- R/scistreer.R | 26 ++++++++++++++++++++------ R/zzz.R |only README.md | 4 +++- data/gtree_small.rda |only data/mut_nodes_small.rda |only data/tree_upgma.rda |only man/get_mut_graph.Rd | 2 +- man/gtree_small.Rd |only man/mut_nodes_small.Rd |only man/mut_to_tree.Rd | 4 +++- man/perform_nni.Rd | 4 +++- man/score_tree.Rd | 8 +++++--- man/tree_upgma.Rd |only src/Makevars | 2 +- src/Makevars.win | 2 +- 19 files changed, 77 insertions(+), 32 deletions(-)
Title: MULTIplex NEtworks with Shared Structure
Description: Model fitting and simulation for Gaussian and logistic inner
product MultiNeSS models for multiplex networks. The package implements
a convex fitting algorithm with fully adaptive parameter tuning,
including options for edge cross-validation. For more details see
MacDonald et al. (2020).
Author: Peter W. MacDonald [aut, cre]
Maintainer: Peter W. MacDonald <pwmacdon@umich.edu>
Diff between multiness versions 1.0.1 dated 2022-11-21 and 1.0.2 dated 2022-11-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/multiness_fit.R | 6 +++--- README.md | 4 ++-- man/multiness_fit.Rd | 6 +++--- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: NanoString Quality Control Dashboard
Description: NanoString nCounter data are gene expression assays
where there is no need for the use of enzymes or amplification
protocols and work with fluorescent barcodes (Geiss et al. (2018)
<doi:10.1038/nbt1385>). Each barcode is assigned a
messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its
target can be counted. As a result each count of a specific barcode
represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString
quality Control dasHbOard) is able to analyse the exported NanoString
nCounter data and facilitates the user in performing a quality
control. 'NACHO' does this by visualising quality control metrics,
expression of control genes, principal components and sample specific
size factors in an interactive web application.
Author: Mickael Canouil [aut, cre] ,
Roderick Slieker [aut] ,
Gerard Bouland [aut]
Maintainer: Mickael Canouil <mickael@canouil.dev>
Diff between NACHO versions 2.0.0 dated 2022-05-31 and 2.0.1 dated 2022-11-24
DESCRIPTION | 10 MD5 | 16 - NEWS.md | 9 README.md | 22 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/NACHO-analysis.html | 227 +++++++------------ inst/doc/NACHO.R | 80 +++--- inst/doc/NACHO.html | 498 ++++++++++++++----------------------------- 9 files changed, 334 insertions(+), 528 deletions(-)
Title: Assembling Long Gene Copies from Short Read Data
Description: Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.
Author: Lei Yang
Maintainer: Lei Yang <leiyangslu@gmail.com>
Diff between copyseparator versions 1.1.0 dated 2022-07-06 and 1.2.0 dated 2022-11-24
DESCRIPTION | 10 +- MD5 | 18 ++-- NAMESPACE | 4 + NEWS.md | 6 + R/copy_assemble.R | 7 + R/copy_separate.R | 2 R/copy_validate.R | 4 - R/sep_assem.R | 131 +++++++++++++++++------------------ inst/doc/Usage_of_copyseparator.html | 124 +++++++++++++++++---------------- man/sep_assem.Rd | 8 +- 10 files changed, 166 insertions(+), 148 deletions(-)
Title: INsulin Secretion ANalysEr
Description: A user-friendly interface, using Shiny, to analyse glucose-stimulated insulin secretion (GSIS)
assays in pancreatic beta cells or islets.
The package allows the user to import several sets of experiments from different spreadsheets
and to perform subsequent steps: summarise in a tidy format, visualise data quality
and compare experimental conditions without omitting to account for technical confounders
such as the date of the experiment or the technician.
Together, insane is a comprehensive method that optimises pre-processing and analyses of
GSIS experiments in a friendly-user interface.
The Shiny App was initially designed for EndoC-betaH1 cell line following method described
in Ndiaye et al., 2017 (<doi:10.1016/j.molmet.2017.03.011>).
Author: Mickael Canouil [aut, cre]
Maintainer: Mickael Canouil <mickael@canouil.dev>
Diff between insane versions 0.1.0 dated 2020-11-04 and 1.0.0 dated 2022-11-24
insane-0.1.0/insane/vignettes/copy_protocol.R |only insane-1.0.0/insane/DESCRIPTION | 18 - insane-1.0.0/insane/MD5 | 19 - insane-1.0.0/insane/NEWS.md | 11 insane-1.0.0/insane/README.md | 67 ++-- insane-1.0.0/insane/build/vignette.rds |binary insane-1.0.0/insane/inst/doc/insane.html | 297 +++++++++----------- insane-1.0.0/insane/inst/doc/protocol.html | 171 ++++++----- insane-1.0.0/insane/man/figures/README-template.gif |binary insane-1.0.0/insane/man/go_insane.Rd | 5 insane-1.0.0/insane/man/insane-package.Rd | 15 - 11 files changed, 314 insertions(+), 289 deletions(-)
Title: Irucka Embry's Miscellaneous USGS Functions
Description: A collection of Irucka Embry's miscellaneous USGS functions
(processing .exp and .psf files, statistical error functions,
"+" dyadic operator for use with NA, creating ADAPS and QW
spreadsheet files, calculating saturated enthalpy). Irucka created these
functions while a Cherokee Nation Technology Solutions (CNTS) United States
Geological Survey (USGS) Contractor and/or USGS employee.
Author: Irucka Embry [aut, cre], Anne Hoos [ctb], and Timothy H. Diehl [ctb]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Diff between ie2misc versions 0.8.8 dated 2022-01-21 and 0.9.0 dated 2022-11-24
DESCRIPTION | 16 ++++++------ MD5 | 57 +++++++++++++++++++++---------------------- NAMESPACE | 50 +++++++++++++++++++++++++++---------- NEWS.md | 17 +++++++++++- R/adaps.R | 20 +++++++-------- R/dr.R | 22 +++++++++------- R/expFileOutput.R | 20 +++++++-------- R/ie2misc.R | 15 +++++++++-- R/madstat.R | 15 +++++++---- R/mae.R | 20 +++++++++------ R/mape.R | 20 +++++++++------ R/na_operator.R | 11 +++++--- R/psfFileChange.R | 18 ++++++------- R/qw.R | 21 +++++++-------- R/rmse.R | 19 ++++++++------ R/sat_enthalpy.R | 24 +++++++++--------- R/vnse.R | 22 +++++++++------- man/adaps.Rd | 2 - man/dr.Rd | 14 ++++++---- man/expFileOutput.Rd | 2 - man/grapes-plus-na-grapes.Rd | 7 +++-- man/ie2misc.Rd |only man/madstat.Rd | 13 ++++++--- man/mae.Rd | 12 ++++++--- man/mape.Rd | 12 ++++++--- man/psfFileChange.Rd | 2 - man/qw.Rd | 2 - man/rmse.Rd | 11 +++++--- man/sat_enthalpy.Rd | 4 +-- man/vnse.Rd | 14 ++++++---- 30 files changed, 291 insertions(+), 191 deletions(-)
Title: Irregularly Observed Autoregressive Models
Description: Data sets, functions and scripts with examples to implement autoregressive models for irregularly observed time series. The models available in this package are the irregular autoregressive model (Eyheramendy et al.(2018) <doi:10.1093/mnras/sty2487>), the complex irregular autoregressive model (Elorrieta et al.(2019) <doi:10.1051/0004-6361/201935560>) and the bivariate irregular autoregressive model (Elorrieta et al.(2021) <doi:10.1093/mnras/stab1216>).
Author: Elorrieta Felipe [aut, cre],
Ojeda Cesar [aut],
Eyheramendy Susana [aut],
Palma Wilfredo [aut]
Maintainer: Elorrieta Felipe <felipe.elorrieta@usach.cl>
Diff between iAR versions 1.1.0 dated 2022-07-11 and 1.2.0 dated 2022-11-24
iAR-1.1.0/iAR/R/BIARsmoothing.R |only iAR-1.1.0/iAR/R/IARTest2.R |only iAR-1.1.0/iAR/R/IARsmoothing.R |only iAR-1.1.0/iAR/man/BIARLL.Rd |only iAR-1.1.0/iAR/man/BIARsmoothing.Rd |only iAR-1.1.0/iAR/man/IARTest2.Rd |only iAR-1.1.0/iAR/man/IARsmoothing.Rd |only iAR-1.1.0/iAR/src/BIARLL.cpp |only iAR-1.2.0/iAR/DESCRIPTION | 8 - iAR-1.2.0/iAR/MD5 | 106 +++++++++++--------- iAR-1.2.0/iAR/NAMESPACE | 16 ++- iAR-1.2.0/iAR/R/BIARinterpolation.R |only iAR-1.2.0/iAR/R/BIARkalman.R | 2 iAR-1.2.0/iAR/R/CIARinterpolation.R |only iAR-1.2.0/iAR/R/CIARkalman.R | 142 ++++++++++++++-------------- iAR-1.2.0/iAR/R/Forecast_iARModels.R |only iAR-1.2.0/iAR/R/IARPermutation.R |only iAR-1.2.0/iAR/R/IARfit.R | 14 +- iAR-1.2.0/iAR/R/IARforecast.R |only iAR-1.2.0/iAR/R/IARgamma.R | 114 +++++++++++----------- iAR-1.2.0/iAR/R/IARgforecast.R |only iAR-1.2.0/iAR/R/IARginterpolation.R |only iAR-1.2.0/iAR/R/IARinterpolation.R |only iAR-1.2.0/iAR/R/IARkalman.R | 8 - iAR-1.2.0/iAR/R/IARloglik.R | 162 ++++++++++++++++---------------- iAR-1.2.0/iAR/R/IARt.R | 108 ++++++++++----------- iAR-1.2.0/iAR/R/IARtest.R | 76 ++++++++------- iAR-1.2.0/iAR/R/IARtinterpolation.R |only iAR-1.2.0/iAR/R/RcppExports.R | 160 ++++++++++++++++--------------- iAR-1.2.0/iAR/R/foldlc.R | 6 - iAR-1.2.0/iAR/R/iAR.R | 4 iAR-1.2.0/iAR/build/partial.rdb |binary iAR-1.2.0/iAR/man/BIARfit.Rd | 4 iAR-1.2.0/iAR/man/BIARforecast.Rd |only iAR-1.2.0/iAR/man/BIARinterpolation.Rd |only iAR-1.2.0/iAR/man/BIARphikalman.Rd | 8 - iAR-1.2.0/iAR/man/CIARfit.Rd | 4 iAR-1.2.0/iAR/man/CIARforecast.Rd | 13 +- iAR-1.2.0/iAR/man/CIARinterpolation.Rd |only iAR-1.2.0/iAR/man/CIARkalman.Rd | 8 - iAR-1.2.0/iAR/man/CIARphikalman.Rd | 10 + iAR-1.2.0/iAR/man/Forecast_iARModels.Rd |only iAR-1.2.0/iAR/man/IARPermutation.Rd |only iAR-1.2.0/iAR/man/IARTest.Rd | 53 +++++----- iAR-1.2.0/iAR/man/IARfit.Rd | 6 - iAR-1.2.0/iAR/man/IARforecast.Rd |only iAR-1.2.0/iAR/man/IARgforecast.Rd |only iAR-1.2.0/iAR/man/IARginterpolation.Rd |only iAR-1.2.0/iAR/man/IARinterpolation.Rd |only iAR-1.2.0/iAR/man/IARkalman.Rd | 6 - iAR-1.2.0/iAR/man/IARloglik.Rd | 6 - iAR-1.2.0/iAR/man/IARphigamma.Rd | 6 - iAR-1.2.0/iAR/man/IARphikalman.Rd | 10 + iAR-1.2.0/iAR/man/IARphiloglik.Rd | 6 - iAR-1.2.0/iAR/man/IARphit.Rd | 10 + iAR-1.2.0/iAR/man/IARtinterpolation.Rd |only iAR-1.2.0/iAR/man/foldlc.Rd | 2 iAR-1.2.0/iAR/src/BIARfit.cpp | 6 - iAR-1.2.0/iAR/src/BIARforecast.cpp |only iAR-1.2.0/iAR/src/BIARphikalman.cpp | 79 ++++++++++++++- iAR-1.2.0/iAR/src/CIARfit.cpp | 6 - iAR-1.2.0/iAR/src/CIARforecast.cpp | 17 +-- iAR-1.2.0/iAR/src/CIARphikalman.cpp | 45 ++++++-- iAR-1.2.0/iAR/src/IARphigamma.cpp | 8 + iAR-1.2.0/iAR/src/IARphikalman.cpp | 51 +++++++--- iAR-1.2.0/iAR/src/IARphiloglik.cpp | 10 - iAR-1.2.0/iAR/src/IARphit.cpp | 12 +- iAR-1.2.0/iAR/src/RcppExports.cpp | 109 +++++++++++---------- 68 files changed, 794 insertions(+), 627 deletions(-)
Title: Bridge to System Package Manager
Description: Enables binary package installations on Linux distributions.
Provides functions to manage packages via the distribution's package
manager. Also provides transparent integration with R's install.packages()
and a fallback mechanism. When installed as a system package, interacts
with the system's package manager without requiring administrative
privileges via an integrated D-Bus service; otherwise, uses sudo.
Currently, the following backends are supported: DNF, APT, ALPM.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between bspm versions 0.3.10 dated 2022-08-05 and 0.4.0 dated 2022-11-24
DESCRIPTION | 8 +-- MD5 | 36 +++++++-------- NAMESPACE | 1 NEWS.md | 8 +++ R/bridge.R | 28 ++++++----- R/integration.R | 71 ++++++++++++++++++++++++++++-- R/manager.R | 45 ++++++++++--------- README.md | 1 inst/service/backend/__init__.py | 2 inst/service/backend/_utils.py | 22 ++++++++- inst/service/backend/alpm.py | 92 ++++++++++++++++++++++++--------------- inst/service/backend/apt.py | 39 +++++++++++++--- inst/service/backend/dnf.py | 46 +++++++++++++++---- inst/service/bspm.py | 72 +++++++++++++++++++----------- inst/tinytest/test_integration.R | 2 inst/tinytest/test_manager.R | 6 -- inst/tinytest/test_manager_ci.R | 5 ++ man/integration.Rd | 10 +++- man/manager.Rd | 19 ++++---- 19 files changed, 358 insertions(+), 155 deletions(-)
Title: Haplotype Trend Regression with eXtra Flexibility (HTRX)
Description: Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Barrie W, Yang Y, Attfield K E, et al (2022) <doi:10.1101/2022.09.23.509097>.
Author: Yaoling Yang [aut, cre] ,
Daniel Lawson [aut]
Maintainer: Yaoling Yang <yaoling.yang@bristol.ac.uk>
Diff between HTRX versions 1.0.7 dated 2022-10-11 and 1.1.0 dated 2022-11-24
HTRX-1.0.7/HTRX/R/tenfold_split.R |only HTRX-1.0.7/HTRX/man/tenfold_split.Rd |only HTRX-1.1.0/HTRX/DESCRIPTION | 8 HTRX-1.1.0/HTRX/MD5 | 42 +- HTRX-1.1.0/HTRX/NAMESPACE | 2 HTRX-1.1.0/HTRX/R/computeR2.R | 18 - HTRX-1.1.0/HTRX/R/data_split.R |only HTRX-1.1.0/HTRX/R/do_cumulative_htrx.R | 341 ++++++++++++++-------- HTRX-1.1.0/HTRX/R/do_cv.R | 451 ++++++++++++++++++------------ HTRX-1.1.0/HTRX/R/do_cv_direct.R |only HTRX-1.1.0/HTRX/R/htrx_max.R | 96 ++++-- HTRX-1.1.0/HTRX/R/htrx_nfeatures.R |only HTRX-1.1.0/HTRX/R/make_htrx.R | 20 - HTRX-1.1.0/HTRX/R/pkgname.R | 20 - HTRX-1.1.0/HTRX/R/themodel.R | 12 HTRX-1.1.0/HTRX/README.md | 38 +- HTRX-1.1.0/HTRX/man/HTRX-package.Rd | 19 - HTRX-1.1.0/HTRX/man/computeR2.Rd | 16 - HTRX-1.1.0/HTRX/man/data_split.Rd |only HTRX-1.1.0/HTRX/man/do_cumulative_htrx.Rd | 162 ++++++---- HTRX-1.1.0/HTRX/man/do_cv.Rd | 137 +++++---- HTRX-1.1.0/HTRX/man/do_cv_direct.Rd |only HTRX-1.1.0/HTRX/man/htrx_max.Rd | 33 +- HTRX-1.1.0/HTRX/man/htrx_nfeatures.Rd |only HTRX-1.1.0/HTRX/man/make_htrx.Rd | 16 - HTRX-1.1.0/HTRX/man/themodel.Rd | 12 26 files changed, 890 insertions(+), 553 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.3.1 dated 2022-11-07 and 4.3.2 dated 2022-11-24
DESCRIPTION | 12 +-- MD5 | 29 ++++---- R/InitErgmTerm.R | 2 R/ergm-terms-index.R | 94 +++++++++++++++++------------ R/ergm_proposal.R | 37 ++++++++--- build/ergm.pdf |binary build/vignette.rds |binary inst/CITATION | 4 - inst/NEWS.Rd | 16 ++++ inst/doc/ergm-term-crossRef.html | 22 +++--- inst/doc/ergm.pdf |binary inst/doc/nodal_attributes.html | 4 - man/ergm_proposal_table.Rd | 19 +++++ tests/testthat/test-ergm-proposal-unload.R |only tests/testthat/test-ergm-term-doc.R | 13 ++++ tests/testthat/test-term-edgecov.R | 22 +++++- 16 files changed, 188 insertions(+), 86 deletions(-)
Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin'
from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Samra Goumri [aut],
Zauad Shahreer Abeer [aut],
Eduard Szoecs [ctb]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between datamods versions 1.3.4 dated 2022-09-01 and 1.4.0 dated 2022-11-24
DESCRIPTION | 18 ++++--- MD5 | 87 +++++++++++++++++++--------------- NAMESPACE | 34 +++++++++++++ NEWS.md | 7 ++ R/data.R |only R/edit-data-utils.R |only R/edit-data.R |only R/filter-data.R | 31 +++++++++--- R/import-copypaste.R | 3 - R/import-file.R | 7 +- R/import-globalenv.R | 5 + R/import-googlesheets.R | 3 - R/import-modal.R | 18 +++++-- R/import-url.R | 5 + R/sample-data.R |only R/select-group.R |only R/update-variables.R | 16 ++++-- R/utils.R | 26 +++++++++- R/zzz.R | 2 README.md | 15 ++--- build/vignette.rds |binary data |only inst/doc/datamods.R | 7 ++ inst/doc/datamods.Rmd | 53 +++++++++++--------- inst/doc/datamods.html | 80 +++++++++++++++++-------------- inst/doc/i18n.html | 39 +++++++++++++-- inst/i18n/al.csv | 23 ++++++++ inst/i18n/cn.csv | 23 ++++++++ inst/i18n/de.csv | 23 ++++++++ inst/i18n/es.csv | 25 +++++++++ inst/i18n/fr.csv | 24 +++++++++ inst/i18n/kr.csv | 23 ++++++++ inst/i18n/mk.csv | 23 ++++++++ inst/i18n/pt.csv | 23 ++++++++ inst/i18n/tr.csv | 23 ++++++++ man/demo_edit.Rd |only man/edit-data.Rd |only man/figures/datamods-sample.png |only man/filter-data.Rd | 4 - man/import-copypaste.Rd | 4 - man/import-file.Rd | 8 +-- man/import-globalenv.Rd | 4 - man/import-googlesheets.Rd | 4 - man/import-modal.Rd | 19 ++++++- man/import-url.Rd | 16 +++--- man/module-sample.Rd |only man/select-group.Rd |only tests/testthat/test-edit-data.R |only tests/testthat/test-filter-data.R | 16 +++--- vignettes/datamods.Rmd | 53 +++++++++++--------- vignettes/figures/datamods-sample.png |only 51 files changed, 607 insertions(+), 187 deletions(-)
Title: Composite-Based Structural Equation Modeling
Description: Estimate, assess, test, and study linear, nonlinear, hierarchical
and multigroup structural equation models using composite-based approaches
and procedures, including estimation techniques such as partial least squares
path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc),
generalized structured component analysis (GSCA), generalized structured
component analysis with uniqueness terms (GSCAm), generalized canonical
correlation analysis (GCCA), principal component analysis (PCA),
factor score regression (FSR) using sum score, regression or
bartlett scores (including bias correction using Croon’s approach),
as well as several tests and typical postestimation procedures
(e.g., verify admissibility of the estimates, assess the model fit,
test the model fit etc.).
Author: Manuel E. Rademaker [aut] ,
Florian Schuberth [aut, cre] ,
Tamara Schamberger [ctb] ,
Michael Klesel [ctb] ,
Theo K. Dijkstra [ctb],
Joerg Henseler [ctb]
Maintainer: Florian Schuberth <f.schuberth@utwente.nl>
Diff between cSEM versions 0.4.0 dated 2021-04-19 and 0.5.0 dated 2022-11-24
cSEM-0.4.0/cSEM/tests/comparisons/results_cf_model.xls |only cSEM-0.4.0/cSEM/tests/comparisons/results_composite_model.xls |only cSEM-0.5.0/cSEM/DESCRIPTION | 37 cSEM-0.5.0/cSEM/MD5 | 277 cSEM-0.5.0/cSEM/NAMESPACE | 2 cSEM-0.5.0/cSEM/R/00_csem.R | 28 cSEM-0.5.0/cSEM/R/00_foreman.R | 6 cSEM-0.5.0/cSEM/R/csem_model.R | 4 cSEM-0.5.0/cSEM/R/csem_resample.R | 66 cSEM-0.5.0/cSEM/R/estimators_paths.R | 2 cSEM-0.5.0/cSEM/R/estimators_weights.R | 85 cSEM-0.5.0/cSEM/R/exportToExcel.R | 11 cSEM-0.5.0/cSEM/R/helper_assess.R | 428 cSEM-0.5.0/cSEM/R/helper_csem.R | 2 cSEM-0.5.0/cSEM/R/helper_foreman.R | 85 cSEM-0.5.0/cSEM/R/helper_infer.R | 2 cSEM-0.5.0/cSEM/R/helper_predict.R |only cSEM-0.5.0/cSEM/R/helper_test_MGD.R | 10 cSEM-0.5.0/cSEM/R/plot.cSEMNonlinearEffects.R | 4 cSEM-0.5.0/cSEM/R/postestimate_assess.R | 98 cSEM-0.5.0/cSEM/R/postestimate_doIPMA.R | 10 cSEM-0.5.0/cSEM/R/postestimate_infer.R | 2 cSEM-0.5.0/cSEM/R/postestimate_predict.R | 598 cSEM-0.5.0/cSEM/R/postestimate_summarize.R | 7 cSEM-0.5.0/cSEM/R/postestimate_test_CVPAT.R |only cSEM-0.5.0/cSEM/R/postestimate_test_MGD.R | 10 cSEM-0.5.0/cSEM/R/postestimate_test_OMF.R | 53 cSEM-0.5.0/cSEM/R/postestimate_test_hausman.R | 4 cSEM-0.5.0/cSEM/R/postestimate_verify.R | 6 cSEM-0.5.0/cSEM/R/print.cSEMAssess.R | 42 cSEM-0.5.0/cSEM/R/print.cSEMPredict.R | 251 cSEM-0.5.0/cSEM/R/print.cSEMTestCVPAT.R |only cSEM-0.5.0/cSEM/R/print.cSEMTestHausman.R | 2 cSEM-0.5.0/cSEM/R/print.cSEMTestMGD.R | 2 cSEM-0.5.0/cSEM/R/print.cSEMTestMICOM.R | 6 cSEM-0.5.0/cSEM/R/print.cSEMTestOMF.R | 10 cSEM-0.5.0/cSEM/R/zz_arguments.R | 74 cSEM-0.5.0/cSEM/R/zz_datasets.R | 123 cSEM-0.5.0/cSEM/R/zz_helper_print.R | 31 cSEM-0.5.0/cSEM/R/zz_templates.R | 4 cSEM-0.5.0/cSEM/README.md | 413 cSEM-0.5.0/cSEM/build/cSEM.pdf |16519 +++++----- cSEM-0.5.0/cSEM/build/partial.rdb |binary cSEM-0.5.0/cSEM/build/vignette.rds |binary cSEM-0.5.0/cSEM/data/Benitezetal2020.RData |only cSEM-0.5.0/cSEM/inst/REFERENCES.bib | 91 cSEM-0.5.0/cSEM/inst/REFERENCES.bib.sav.tmp |only cSEM-0.5.0/cSEM/inst/doc/Notation.html | 236 cSEM-0.5.0/cSEM/inst/doc/Terminology.html | 247 cSEM-0.5.0/cSEM/inst/doc/Using-assess.Rmd | 4 cSEM-0.5.0/cSEM/inst/doc/Using-assess.html | 1025 cSEM-0.5.0/cSEM/inst/doc/cSEM.Rmd | 13 cSEM-0.5.0/cSEM/inst/doc/cSEM.html | 871 cSEM-0.5.0/cSEM/inst/examples/example_assess.R | 5 cSEM-0.5.0/cSEM/inst/examples/example_infer.R | 2 cSEM-0.5.0/cSEM/inst/examples/example_predict.R | 62 cSEM-0.5.0/cSEM/inst/examples/example_resamplecSEMResults.R | 4 cSEM-0.5.0/cSEM/inst/examples/example_testOMF.R | 2 cSEM-0.5.0/cSEM/inst/examples/example_verify.R | 2 cSEM-0.5.0/cSEM/man/Anime.Rd | 4 cSEM-0.5.0/cSEM/man/Benitezetal2020.Rd |only cSEM-0.5.0/cSEM/man/BergamiBagozzi2000.Rd | 35 cSEM-0.5.0/cSEM/man/ITFlex.Rd | 4 cSEM-0.5.0/cSEM/man/LancelotMiltgenetal2016.Rd | 2 cSEM-0.5.0/cSEM/man/Russett.Rd | 4 cSEM-0.5.0/cSEM/man/SQ.Rd | 4 cSEM-0.5.0/cSEM/man/Switching.Rd | 4 cSEM-0.5.0/cSEM/man/Yooetal2000.Rd | 4 cSEM-0.5.0/cSEM/man/adjustAlpha.Rd | 70 cSEM-0.5.0/cSEM/man/args_assess_dotdotdot.Rd | 2 cSEM-0.5.0/cSEM/man/args_default.Rd | 52 cSEM-0.5.0/cSEM/man/assess.Rd | 37 cSEM-0.5.0/cSEM/man/cSEM-package.Rd | 8 cSEM-0.5.0/cSEM/man/calculate2ndStage.Rd | 58 cSEM-0.5.0/cSEM/man/calculateAVE.Rd | 2 cSEM-0.5.0/cSEM/man/calculateCompositeVCV.Rd | 46 cSEM-0.5.0/cSEM/man/calculateConstructVCV.Rd | 52 cSEM-0.5.0/cSEM/man/calculateCorrectionFactors.Rd | 112 cSEM-0.5.0/cSEM/man/calculateDistance.Rd | 78 cSEM-0.5.0/cSEM/man/calculateFLCriterion.Rd | 2 cSEM-0.5.0/cSEM/man/calculateFR.Rd | 48 cSEM-0.5.0/cSEM/man/calculateHTMT.Rd | 52 cSEM-0.5.0/cSEM/man/calculateIndicatorCor.Rd | 126 cSEM-0.5.0/cSEM/man/calculateInnerWeightsPLS.Rd | 124 cSEM-0.5.0/cSEM/man/calculateMAE.Rd |only cSEM-0.5.0/cSEM/man/calculateModelSelectionCriteria.Rd | 2 cSEM-0.5.0/cSEM/man/calculateOuterWeightsPLS.Rd | 78 cSEM-0.5.0/cSEM/man/calculateParameterDifference.Rd | 66 cSEM-0.5.0/cSEM/man/calculateReliabilities.Rd | 104 cSEM-0.5.0/cSEM/man/calculateWeightsGSCA.Rd | 126 cSEM-0.5.0/cSEM/man/calculateWeightsGSCAm.Rd | 144 cSEM-0.5.0/cSEM/man/calculateWeightsKettenring.Rd | 86 cSEM-0.5.0/cSEM/man/calculateWeightsPCA.Rd | 64 cSEM-0.5.0/cSEM/man/calculateWeightsPLS.Rd | 174 cSEM-0.5.0/cSEM/man/calculateWeightsUnit.Rd | 74 cSEM-0.5.0/cSEM/man/checkConvergence.Rd | 86 cSEM-0.5.0/cSEM/man/classifyConstructs.Rd | 68 cSEM-0.5.0/cSEM/man/convertModel.Rd | 60 cSEM-0.5.0/cSEM/man/csem.Rd | 31 cSEM-0.5.0/cSEM/man/csem_arguments.Rd | 64 cSEM-0.5.0/cSEM/man/csem_model.Rd | 138 cSEM-0.5.0/cSEM/man/csem_results.Rd | 2 cSEM-0.5.0/cSEM/man/csem_test.Rd | 42 cSEM-0.5.0/cSEM/man/distance_measures.Rd | 8 cSEM-0.5.0/cSEM/man/doIPMA.Rd | 10 cSEM-0.5.0/cSEM/man/estimatePath.Rd | 2 cSEM-0.5.0/cSEM/man/fit_measures.Rd | 34 cSEM-0.5.0/cSEM/man/foreman.Rd | 308 cSEM-0.5.0/cSEM/man/getParameterNames.Rd | 70 cSEM-0.5.0/cSEM/man/handleArgs.Rd | 38 cSEM-0.5.0/cSEM/man/infer.Rd | 2 cSEM-0.5.0/cSEM/man/inference_helper.Rd | 4 cSEM-0.5.0/cSEM/man/nonlinear_estimation_utilities.Rd | 76 cSEM-0.5.0/cSEM/man/parseModel.Rd | 296 cSEM-0.5.0/cSEM/man/plot.cSEMNonlinearEffects.Rd | 4 cSEM-0.5.0/cSEM/man/plot.cSEMPredict.Rd | 40 cSEM-0.5.0/cSEM/man/predict.Rd | 174 cSEM-0.5.0/cSEM/man/print.cSEMPlotPredict.Rd | 40 cSEM-0.5.0/cSEM/man/print.cSEMPredict.Rd | 8 cSEM-0.5.0/cSEM/man/print.cSEMTestCVPAT.Rd |only cSEM-0.5.0/cSEM/man/processData.Rd | 76 cSEM-0.5.0/cSEM/man/reliability.Rd | 8 cSEM-0.5.0/cSEM/man/resampleData.Rd | 482 cSEM-0.5.0/cSEM/man/resamplecSEMResults.Rd | 32 cSEM-0.5.0/cSEM/man/satisfaction.Rd | 4 cSEM-0.5.0/cSEM/man/satisfaction_gender.Rd | 4 cSEM-0.5.0/cSEM/man/scaleWeights.Rd | 46 cSEM-0.5.0/cSEM/man/setDominantIndicator.Rd | 66 cSEM-0.5.0/cSEM/man/setStartingValues.Rd | 52 cSEM-0.5.0/cSEM/man/testCVPAT.Rd |only cSEM-0.5.0/cSEM/man/testHausman.Rd | 4 cSEM-0.5.0/cSEM/man/testMGD.Rd | 6 cSEM-0.5.0/cSEM/man/testOMF.Rd | 6 cSEM-0.5.0/cSEM/man/threecommonfactors.Rd | 8 cSEM-0.5.0/cSEM/man/verify.Rd | 7 cSEM-0.5.0/cSEM/tests/comparisons/Compare_to_ADANCO_and_matrixpls_cf_model.R | 53 cSEM-0.5.0/cSEM/tests/comparisons/Compare_to_ADANCO_and_matrixpls_composite_model.R | 31 cSEM-0.5.0/cSEM/tests/comparisons/results_cf_model_adanco_2_2_1_centroid.xls |only cSEM-0.5.0/cSEM/tests/comparisons/results_composite_model_adanco_2_2_1_centroid.xls |only cSEM-0.5.0/cSEM/tests/other_tests/test_progressr_on_ubuntu.R | 4 cSEM-0.5.0/cSEM/tests/testthat/test-assess.R | 5 cSEM-0.5.0/cSEM/tests/testthat/test-csem.r | 3 cSEM-0.5.0/cSEM/tests/testthat/test-main.R | 29 cSEM-0.5.0/cSEM/tests/testthat/test-predict.R | 14 cSEM-0.5.0/cSEM/vignettes/Using-assess.Rmd | 4 cSEM-0.5.0/cSEM/vignettes/cSEM.Rmd | 13 146 files changed, 14831 insertions(+), 11457 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
Fragpipe(da Veiga et al 2020, <doi:10.1038/s41592-020-0912-y>), MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), MassChroq (Valot et al 2011] <doi:10.1002/pmic.201100120>), ProteomeDiscoverer,
OpenMS (<doi:10.1038/nmeth.3959>) and Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>). Meta-data provided in sdrf format can be integrated to the analysis.
Quantitative proteomics measurements frequently contain multiple NA values, due to [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.6.0 dated 2022-03-01 and 1.7.0.1 dated 2022-11-24
wrProteo-1.6.0/wrProteo/inst/extdata/conta1.fasta |only wrProteo-1.7.0.1/wrProteo/DESCRIPTION | 27 wrProteo-1.7.0.1/wrProteo/MD5 | 98 wrProteo-1.7.0.1/wrProteo/NAMESPACE | 4 wrProteo-1.7.0.1/wrProteo/R/AucRoc.R | 14 wrProteo-1.7.0.1/wrProteo/R/combineMultFilterNAimput.R | 4 wrProteo-1.7.0.1/wrProteo/R/corColumnOrder.R | 176 wrProteo-1.7.0.1/wrProteo/R/matrixNAinspect.R | 53 wrProteo-1.7.0.1/wrProteo/R/matrixNAneighbourImpute.R | 28 wrProteo-1.7.0.1/wrProteo/R/readFasta2.R | 26 wrProteo-1.7.0.1/wrProteo/R/readFragpipeFile.R |only wrProteo-1.7.0.1/wrProteo/R/readMassChroQFile.R | 145 wrProteo-1.7.0.1/wrProteo/R/readMaxQuantFile.R | 686 + wrProteo-1.7.0.1/wrProteo/R/readMaxQuantPeptides.R |only wrProteo-1.7.0.1/wrProteo/R/readProlineFile.R | 342 wrProteo-1.7.0.1/wrProteo/R/readProtDiscovFile.R | 775 - wrProteo-1.7.0.1/wrProteo/R/readProtDiscovPeptides.R |only wrProteo-1.7.0.1/wrProteo/R/readSampleMetaData.R |only wrProteo-1.7.0.1/wrProteo/R/readSdrf.R | 57 wrProteo-1.7.0.1/wrProteo/R/removeSampleInList.R | 3 wrProteo-1.7.0.1/wrProteo/R/replMissingProtNames.R | 4 wrProteo-1.7.0.1/wrProteo/R/summarizeForROC.R | 115 wrProteo-1.7.0.1/wrProteo/R/testRobustToNAimputation.R | 83 wrProteo-1.7.0.1/wrProteo/build/vignette.rds |binary wrProteo-1.7.0.1/wrProteo/inst/doc/wrProteoVignette1.R | 82 wrProteo-1.7.0.1/wrProteo/inst/doc/wrProteoVignette1.Rmd | 379 wrProteo-1.7.0.1/wrProteo/inst/doc/wrProteoVignette1.html | 2145 +++- wrProteo-1.7.0.1/wrProteo/inst/doc/wrProteoVignetteUPS1.R | 143 wrProteo-1.7.0.1/wrProteo/inst/doc/wrProteoVignetteUPS1.Rmd | 242 wrProteo-1.7.0.1/wrProteo/inst/doc/wrProteoVignetteUPS1.html | 4341 ++++++---- wrProteo-1.7.0.1/wrProteo/inst/extdata/conta1.fasta.gz |only wrProteo-1.7.0.1/wrProteo/inst/extdata/parameters.txt.gz |only wrProteo-1.7.0.1/wrProteo/inst/extdata/peptides_tinyMQ.txt.gz |only wrProteo-1.7.0.1/wrProteo/inst/extdata/pxd001819_PD_InputFiles.txt.gz |only wrProteo-1.7.0.1/wrProteo/inst/extdata/pxd001819f_PL.xlsx |only wrProteo-1.7.0.1/wrProteo/inst/extdata/summary.txt.gz |only wrProteo-1.7.0.1/wrProteo/inst/extdata/tinyFragpipe1.tsv.gz |only wrProteo-1.7.0.1/wrProteo/man/AucROC.Rd | 10 wrProteo-1.7.0.1/wrProteo/man/VolcanoPlotW2.Rd | 3 wrProteo-1.7.0.1/wrProteo/man/combineMultFilterNAimput.Rd | 4 wrProteo-1.7.0.1/wrProteo/man/corColumnOrder.Rd | 25 wrProteo-1.7.0.1/wrProteo/man/matrixNAinspect.Rd | 14 wrProteo-1.7.0.1/wrProteo/man/readFasta2.Rd | 2 wrProteo-1.7.0.1/wrProteo/man/readFragpipeFile.Rd |only wrProteo-1.7.0.1/wrProteo/man/readMassChroQFile.Rd | 23 wrProteo-1.7.0.1/wrProteo/man/readMaxQuantFile.Rd | 74 wrProteo-1.7.0.1/wrProteo/man/readMaxQuantPeptides.Rd |only wrProteo-1.7.0.1/wrProteo/man/readProlineFile.Rd | 29 wrProteo-1.7.0.1/wrProteo/man/readProtDiscovFile.Rd | 42 wrProteo-1.7.0.1/wrProteo/man/readProtDiscovPeptides.Rd |only wrProteo-1.7.0.1/wrProteo/man/readSampleMetaData.Rd |only wrProteo-1.7.0.1/wrProteo/man/readSdrf.Rd | 25 wrProteo-1.7.0.1/wrProteo/man/removeSampleInList.Rd | 7 wrProteo-1.7.0.1/wrProteo/man/replMissingProtNames.Rd | 2 wrProteo-1.7.0.1/wrProteo/man/summarizeForROC.Rd | 49 wrProteo-1.7.0.1/wrProteo/man/testRobustToNAimputation.Rd | 13 wrProteo-1.7.0.1/wrProteo/vignettes/wrProteoVignette1.Rmd | 379 wrProteo-1.7.0.1/wrProteo/vignettes/wrProteoVignetteUPS1.Rmd | 242 58 files changed, 7067 insertions(+), 3848 deletions(-)
Title: Renewal Method for Extreme Values Extrapolation
Description: Peaks Over Threshold (POT) or 'methode du renouvellement'. The
distribution for the excesses can be chosen, and heterogeneous data
(including historical data or block data) can be used in a
Maximum-Likelihood framework.
Author: Yves Deville <deville.yves@alpestat.com>, IRSN <renext@irsn.fr>
Maintainer: Lucie Pheulpin <lucie.pheulpin@irsn.fr>
Diff between Renext versions 3.1-0 dated 2016-07-04 and 3.1-3 dated 2022-11-24
ChangeLog | 35 +++++ DESCRIPTION | 15 +- MD5 | 32 ++--- R/Ren2gev.R | 35 ++++- R/Renouv4.R | 23 ++- R/SandT.R | 4 R/gof.date.R | 1 R/iniMAXOTS.R | 275 ++++++++++++++++++++++++++++++----------------- R/randomRendata.R | 17 ++ build/partial.rdb |binary inst/doc/RenextGuide.pdf |binary man/Brest.Rd | 4 man/LRExp.test.Rd | 2 man/Lomax.Rd | 2 man/Renext-package.Rd | 24 ++-- man/Renouv.Rd | 6 - man/fGEV.MAX.Rd | 16 +- 17 files changed, 319 insertions(+), 172 deletions(-)
Title: Optimal Analysis of Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.0.0 dated 2022-06-26 and 3.1.0 dated 2022-11-24
TestGardener-3.0.0/TestGardener/R/ConditionalSimulation.R |only TestGardener-3.0.0/TestGardener/man/ConditionalSimulation.Rd |only TestGardener-3.1.0/TestGardener/DESCRIPTION | 35 + TestGardener-3.1.0/TestGardener/MD5 | 66 +-- TestGardener-3.1.0/TestGardener/NAMESPACE | 5 TestGardener-3.1.0/TestGardener/R/Analyze.R | 42 + TestGardener-3.1.0/TestGardener/R/Entropy.plot.R | 57 +- TestGardener-3.1.0/TestGardener/R/Hcurve.R |only TestGardener-3.1.0/TestGardener/R/Power.plot.R | 54 +- TestGardener-3.1.0/TestGardener/R/Wpca.plot.R | 36 - TestGardener-3.1.0/TestGardener/R/dataSimulation.R |only TestGardener-3.1.0/TestGardener/R/entropies.R |only TestGardener-3.1.0/TestGardener/R/make.dataList.R | 7 TestGardener-3.1.0/TestGardener/R/scoreDensity.R | 4 TestGardener-3.1.0/TestGardener/R/theta2arclen.R | 15 TestGardener-3.1.0/TestGardener/R/thetasearch.R |only TestGardener-3.1.0/TestGardener/inst/NEWS.Rd | 15 TestGardener-3.1.0/TestGardener/inst/doc/Quantshort.R | 57 +- TestGardener-3.1.0/TestGardener/inst/doc/Quantshort.Rmd | 111 +++-- TestGardener-3.1.0/TestGardener/inst/doc/Quantshort.html | 239 ++++++----- TestGardener-3.1.0/TestGardener/inst/doc/SDS.html | 36 - TestGardener-3.1.0/TestGardener/man/Analyze.Rd | 2 TestGardener-3.1.0/TestGardener/man/ArcLength.plot.Rd | 4 TestGardener-3.1.0/TestGardener/man/Entropy.plot.Rd | 2 TestGardener-3.1.0/TestGardener/man/Hcurve.Rd |only TestGardener-3.1.0/TestGardener/man/ICC.plot.Rd | 2 TestGardener-3.1.0/TestGardener/man/Power.plot.Rd | 2 TestGardener-3.1.0/TestGardener/man/Sensitivity.plot.Rd | 2 TestGardener-3.1.0/TestGardener/man/TG_density.fd.Rd | 4 TestGardener-3.1.0/TestGardener/man/Wpca.plot.Rd | 8 TestGardener-3.1.0/TestGardener/man/dataSimulation.Rd |only TestGardener-3.1.0/TestGardener/man/density_plot.Rd | 2 TestGardener-3.1.0/TestGardener/man/entropies.Rd |only TestGardener-3.1.0/TestGardener/man/scoreDensity.Rd | 2 TestGardener-3.1.0/TestGardener/man/scorePerformance.Rd | 8 TestGardener-3.1.0/TestGardener/man/theta.distn.Rd | 2 TestGardener-3.1.0/TestGardener/man/theta2arclen.Rd | 7 TestGardener-3.1.0/TestGardener/man/thetasearch.Rd |only TestGardener-3.1.0/TestGardener/vignettes/Quantshort.Rmd | 111 +++-- 39 files changed, 588 insertions(+), 349 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-13 dated 2022-04-02 and 1.1-14 dated 2022-11-24
DESCRIPTION | 15 ++++++++------- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 2 +- R/Ftest-rlm.R | 4 ++-- R/TA.plot.R | 10 ++++++++-- R/diagDA.R | 6 +++--- R/misc-goodies.R | 21 +++++++++++++++++---- R/pkgDesc.R | 2 +- R/prettylab.R | 2 +- R/sessionInfo-ext.R | 8 ++++---- R/u.goodies.R | 2 +- R/zzz.R | 19 +++++++++++++++---- inst/NEWS.Rd | 25 ++++++++++++++++++++++++- man/TA.plot.Rd | 2 +- man/diagDA.Rd | 2 +- man/eaxis.Rd | 2 +- man/ellipsePoints.Rd | 4 ++-- man/hatMat.Rd | 2 +- man/helppdf.Rd | 6 +++--- man/polyn.eval.Rd | 31 ++++++++++++++++++++++++++++--- man/read.org.table.Rd | 7 ++++++- 21 files changed, 148 insertions(+), 64 deletions(-)
Title: Safe Anytime-Valid Inference
Description: Functions to design and apply tests that are anytime valid. The
functions can be used to design hypothesis tests in the prospective/randomised
control trial setting or in the observational/retrospective setting. The
resulting tests remain valid under both optional stopping and optional
continuation. The current version includes safe t-tests and safe tests of
two proportions. For details on the theory of safe tests, see
Grunwald, de Heide and Koolen (2019) "Safe Testing" <arXiv:1906.07801>,
for details on safe logrank tests see ter Schure, Perez-Ortiz, Ly and Grunwald
(2020) "The Safe Logrank Test: Error Control under Continuous Monitoring with
Unlimited Horizon" <arXiv:2011.06931v3> and Turner, Ly and Grunwald (2021)
"Safe Tests and Always-Valid Confidence Intervals for contingency tables and
beyond" <arXiv:2106.02693> for details on safe contingency table tests.
Author: Rosanne Turner [aut],
Alexander Ly [cre, aut],
Muriel Felipe Perez-Ortiz [ctb],
Judith ter Schure [ctb],
Peter Grunwald [ctb]
Maintainer: Alexander Ly <a.ly@jasp-stats.org>
Diff between safestats versions 0.8.6 dated 2022-02-01 and 0.8.7 dated 2022-11-24
DESCRIPTION | 12 MD5 | 124 - NEWS.md | 8 R/helpers.R | 62 R/logRankTest.R | 121 + R/safe2x2Test.R | 4 R/safeS3Methods.R | 40 R/tTest.R | 239 ++ R/zTest.R | 196 +- build/vignette.rds |binary inst/doc/contingency-tables-vignette.R | 38 inst/doc/contingency-tables-vignette.Rmd | 38 inst/doc/contingency-tables-vignette.html | 686 ++++++-- inst/doc/safestats-vignette.Rmd | 18 inst/doc/safestats-vignette.html | 817 ++++++++-- man/checkAndReturnsEsMinParameterSide.Rd | 8 man/computeBetaBatchSafeZ.Rd | 4 man/computeBetaSafeT.Rd | 4 man/computeBetaSafeZ.Rd | 4 man/computeBootObj.Rd | 4 man/computeConfidenceIntervalZ.Rd | 4 man/computeEsMinSafeT.Rd | 4 man/computeLogrankBetaFrom.Rd | 4 man/computeLogrankNEvents.Rd | 4 man/computeMinEsBatchSafeZ.Rd | 4 man/computeNPlanBatchSafeT.Rd | 4 man/computeNPlanBatchSafeZ.Rd | 4 man/computeNPlanSafeT.Rd | 4 man/computeNPlanSafeZ.Rd | 4 man/designFreqT.Rd | 6 man/designFreqZ.Rd | 4 man/designPilotSafeT.Rd | 6 man/designPilotSafeZ.Rd | 6 man/designSafeLogrank.Rd | 6 man/designSafeT.Rd | 6 man/designSafeTwoProportions.Rd | 2 man/designSafeZ.Rd | 6 man/getNameAlternative.Rd | 4 man/plotSafeTDesignSampleSizeProfile.Rd | 4 man/rLogrank.Rd | 8 man/replicateTTests.Rd | 6 man/safeLogrankTest.Rd | 10 man/safeTTestStat.Rd | 2 man/safeTTestStatAlpha.Rd | 2 man/safeTTestStatTDensity.Rd | 2 man/safeZTest.Rd | 2 man/safeZTestStat.Rd | 4 man/sampleLogrankStoppingTimes.Rd | 4 man/sampleStoppingTimesSafeT.Rd | 4 man/sampleStoppingTimesSafeZ.Rd | 4 man/selectivelyContinueTTestCombineData.Rd | 4 man/simulate.safeDesign.Rd | 2 tests/testthat/test-nonExportedFunctions.R | 4 vignettes/contingency-tables-vignette.Rmd | 38 vignettes/safe2x2VignetteData/safe2x2ConfidenceOdds.Rdata |binary vignettes/safe2x2VignetteData/safe2x2Coverage.Rdata |binary vignettes/safe2x2VignetteData/safe2x2DesignObject.Rdata |binary vignettes/safe2x2VignetteData/safe2x2DiffRestrictedDesign.Rdata |binary vignettes/safe2x2VignetteData/safe2x2SimFisher.Rdata |binary vignettes/safe2x2VignetteData/safe2x2SimObject.Rdata |binary vignettes/safe2x2VignetteData/safe2x2UnbalancedDesignObject.Rdata |binary vignettes/safe2x2VignetteData/safe2x2UnbalancedSimObject.Rdata |binary vignettes/safestats-vignette.Rmd | 18 63 files changed, 1958 insertions(+), 669 deletions(-)
Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings.
The 'rsurveycto' R package uses the 'SurveyCTO' REST API
<https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html>
to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's
and to download file attachments. The package also has limited support to
write datasets to a server.
Author: Jake Hughey [aut, cre],
Robert On [aut]
Maintainer: Jake Hughey <jake@agency.fund>
Diff between rsurveycto versions 0.1.2 dated 2022-10-24 and 0.1.4 dated 2022-11-24
DESCRIPTION | 14 +-- MD5 | 41 +++++----- NAMESPACE | 2 R/scto_auth.R | 21 +++-- R/scto_get_attachments.R | 17 ++-- R/scto_get_form_definitions.R |only R/scto_meta.R | 20 +++-- R/scto_read.R | 96 ++++++++++++------------ R/scto_read_utils.R | 46 ++++++----- R/scto_write.R | 12 ++- R/utils.R | 21 +++-- man/scto_auth.Rd | 4 - man/scto_get_attachments.Rd | 5 - man/scto_get_form_definitions.Rd |only man/scto_meta.Rd | 6 + man/scto_read.Rd | 37 ++++----- man/scto_write.Rd | 2 tests/testthat/setup.R | 6 + tests/testthat/test-scto-get-attachments.R | 3 tests/testthat/test-scto-get-form-definitions.R |only tests/testthat/test-scto-meta.R | 3 tests/testthat/test-scto-read.R | 14 ++- tests/testthat/test-scto-write.R | 3 23 files changed, 212 insertions(+), 161 deletions(-)
Title: General Transit Feed Specification (GTFS) Editing and Analysing
Tools
Description: Utility functions to read, manipulate, analyse and write
transit feeds in the General Transit Feed Specification (GTFS) data
format.
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Pedro R. Andrade [aut] ,
Joao Bazzo [aut] ,
Mark Padgham [ctb],
Marcus Saraiva [ctb] ,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between gtfstools versions 1.1.0 dated 2022-05-24 and 1.2.0 dated 2022-11-24
gtfstools-1.1.0/gtfstools/inst/CITATION |only gtfstools-1.2.0/gtfstools/DESCRIPTION | 14 gtfstools-1.2.0/gtfstools/MD5 | 47 gtfstools-1.2.0/gtfstools/NAMESPACE | 1 gtfstools-1.2.0/gtfstools/NEWS.md | 20 gtfstools-1.2.0/gtfstools/R/download_validator.R |only gtfstools-1.2.0/gtfstools/R/gtfstools.R | 3 gtfstools-1.2.0/gtfstools/R/set_trip_speed.R | 43 gtfstools-1.2.0/gtfstools/R/validate_gtfs.R | 444 ++--- gtfstools-1.2.0/gtfstools/R/write_gtfs.R | 16 gtfstools-1.2.0/gtfstools/README.md | 38 gtfstools-1.2.0/gtfstools/build/vignette.rds |binary gtfstools-1.2.0/gtfstools/inst/doc/filtering.R | 13 gtfstools-1.2.0/gtfstools/inst/doc/filtering.Rmd | 13 gtfstools-1.2.0/gtfstools/inst/doc/gtfstools.Rmd | 4 gtfstools-1.2.0/gtfstools/inst/doc/gtfstools.html | 4 gtfstools-1.2.0/gtfstools/inst/doc/validating.R |only gtfstools-1.2.0/gtfstools/inst/doc/validating.Rmd |only gtfstools-1.2.0/gtfstools/inst/doc/validating.html |only gtfstools-1.2.0/gtfstools/man/download_validator.Rd |only gtfstools-1.2.0/gtfstools/man/figures/html_validation_report.png |only gtfstools-1.2.0/gtfstools/man/gtfstools.Rd | 3 gtfstools-1.2.0/gtfstools/man/validate_gtfs.Rd | 117 - gtfstools-1.2.0/gtfstools/tests/testthat/test-download_validator.R |only gtfstools-1.2.0/gtfstools/tests/testthat/test-set_trip_speed.R | 36 gtfstools-1.2.0/gtfstools/tests/testthat/test-validate_gtfs.R | 748 +++------- gtfstools-1.2.0/gtfstools/vignettes/filtering.Rmd | 13 gtfstools-1.2.0/gtfstools/vignettes/gtfstools.Rmd | 4 gtfstools-1.2.0/gtfstools/vignettes/validating.Rmd |only 29 files changed, 692 insertions(+), 889 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.18 dated 2022-09-29 and 2.3.19 dated 2022-11-24
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------- NEWS.md | 5 +++ build/vignette.rds |binary inst/doc/manual.R | 4 +-- inst/doc/manual.Rmd | 4 +-- inst/doc/manual.html | 66 ++++++++++++++++++++++++++++++++------------------- src/knn.cpp | 9 +++--- src/tgstat.cpp | 11 ++++---- vignettes/manual.Rmd | 4 +-- 10 files changed, 78 insertions(+), 53 deletions(-)
Title: Generalized Extended Triangular Designs ('GETdesigns')
Description: Since their introduction by Bose and Nair (1939) <https://www.jstor.org/stable/40383923>, partially balanced incomplete block (PBIB) designs remain an important class of incomplete block designs. The concept of association scheme was used by Bose and Shimamoto (1952) <doi:10.1080/01621459.1952.10501161> for the classification of these designs. The constraint of resources always motivates the experimenter to advance towards PBIB designs, more specifically to higher associate class PBIB designs from balanced incomplete block designs. It is interesting to note that many times higher associate PBIB designs perform better than their counterpart lower associate PBIB designs for the same set of parameters v, b, r, k and lambda_i (i=1,2...m). This package contains functions named GETD() for generating m-associate (m>=2) class PBIB designs along with parameters (v, b, r, k and lambda_i, i = 1, 2,…,m) based on Generalized Triangular (GT) Association Scheme. It also calculates the [...truncated...]
Author: Mohd Harun [aut, ctb],
Cini Varghese [aut, ctb],
Ashutosh Dalal [aut, cre]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between GETdesigns versions 1.0.0 dated 2022-11-22 and 1.1.0 dated 2022-11-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/GETD.R | 21 +++++++-------------- 3 files changed, 12 insertions(+), 19 deletions(-)
Title: Geospatial Data Integration
Description: Geospatial data integration framework that merges raster, spatial polygon, and (dynamic) spatial points data into a spatial (panel) data frame at any geographical resolution.
Author: Karsten Donnay and Andrew M. Linke
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Diff between geomerge versions 0.3.2 dated 2020-04-06 and 0.3.3 dated 2022-11-24
DESCRIPTION | 13 +++--- MD5 | 24 ++++++------ NAMESPACE | 5 +- NEWS | 4 ++ R/generateGrid.R | 12 +++--- R/geomerge.R | 28 +++++++------- R/geomerge.merge.R | 6 +-- R/plot.geomerge.R | 6 +-- R/print.geomerge.R | 6 +-- R/summary.geomerge.R | 6 +-- README.md | 6 +-- man/generateGrid.Rd | 14 +++++-- man/geomerge.Rd | 97 +++++++++++++++++++++++++++++++++++++++++++++------ 13 files changed, 157 insertions(+), 70 deletions(-)
More information about butterflyOptions at CRAN
Permanent link
Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques.
Intrinsic dimension estimation methods for exploratory analysis are also provided.
For more details on the package, see the paper by You and Shung (2022) <doi:10.1016/j.simpa.2022.100414>.
Author: Kisung You [aut, cre] ,
Changhee Suh [ctb],
Dennis Shung [ctb]
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between Rdimtools versions 1.1.0 dated 2022-09-22 and 1.1.1 dated 2022-11-24
DESCRIPTION | 12 +++---- MD5 | 34 ++++++++++----------- NAMESPACE | 2 - NEWS.md | 5 +++ R/Rdimtools-package.R | 2 - R/auxchecks.R | 3 + R/nonlinear_MVE.R | 48 +++++++++++++++++-------------- R/nonlinear_MVU.R | 45 ++++++++++++++++++++--------- R/nonlinear_NNP.R | 4 +- README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/nonlinear_MVE.Rd | 32 ++++++++++---------- man/nonlinear_MVU.Rd | 16 +++++----- man/nonlinear_NNP.Rd | 4 +- vignettes/quick-start.html | 8 ++--- 18 files changed, 125 insertions(+), 92 deletions(-)
Title: Iterated Ordinary Least Squares Regression
Description: Addresses the 'log of zero' by developing a new family of
estimators called iterated Ordinary Least Squares.
This family nests standard approaches such as log-linear and
Poisson regressions, offers several computational advantages,
and corresponds to the correct way to perform the popular
log(Y + 1) transformation. For more details about how to use it,
see the notebook at: <https://www.davidbenatia.com/>.
Author: Nassim Zbalah [cre],
David Benatia [aut]
Maintainer: Nassim Zbalah <nas66.nz@gmail.com>
Diff between IOLS versions 0.1.0 dated 2022-11-08 and 0.1.1 dated 2022-11-24
IOLS-0.1.0/IOLS/R/plot_iOLS.R |only IOLS-0.1.0/IOLS/R/plot_iOLS_path.R |only IOLS-0.1.0/IOLS/man/plot.Rd |only IOLS-0.1.1/IOLS/DESCRIPTION | 6 ++-- IOLS-0.1.1/IOLS/MD5 | 31 +++++++++++++------------ IOLS-0.1.1/IOLS/NAMESPACE | 3 +- IOLS-0.1.1/IOLS/R/iOLS.R | 21 ++++++++++++----- IOLS-0.1.1/IOLS/R/iOLS_path.R | 17 ++++++++++---- IOLS-0.1.1/IOLS/R/iOLS_path_plot.R |only IOLS-0.1.1/IOLS/R/iOLS_plot.R |only IOLS-0.1.1/IOLS/R/lambda_test.R | 18 +++++++++++++- IOLS-0.1.1/IOLS/R/print_Lambda_test.R | 26 +++++++++++++++++---- IOLS-0.1.1/IOLS/R/print_iOLS.R | 29 ++++++++++++++++-------- IOLS-0.1.1/IOLS/R/print_iOLS_path.R | 31 +++++++++++++++++++------ IOLS-0.1.1/IOLS/man/iOLS.Rd | 6 +--- IOLS-0.1.1/IOLS/man/iOLS_path.Rd | 16 +++++++++++-- IOLS-0.1.1/IOLS/man/iOLS_path_plot.Rd |only IOLS-0.1.1/IOLS/man/iOLS_plot.Rd |only IOLS-0.1.1/IOLS/man/lambda_test.Rd | 2 - IOLS-0.1.1/IOLS/man/print.Rd | 41 ++++++++++++++++++++-------------- 20 files changed, 171 insertions(+), 76 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut] ,
Vincent Arel-Bundock [aut, ctb]
,
Alex Hayes [rev] ,
Grant McDermott [ [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.18.7 dated 2022-11-18 and 0.18.8 dated 2022-11-24
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 6 R/check_if_installed.R | 8 R/format_message.R | 2 inst/doc/display.html | 298 +++++++++++++++----------------- man/check_if_installed.Rd | 8 man/format_message.Rd | 2 tests/testthat/test-standardize_names.R | 7 9 files changed, 175 insertions(+), 178 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.7.0 dated 2022-09-13 and 0.7.1 dated 2022-11-24
DESCRIPTION | 11 MD5 | 80 ++-- NAMESPACE | 4 NEWS.md | 29 + R/api_get.R | 5 R/filters.R | 16 R/finbif_collections.R | 15 R/finbif_metadata.R | 39 +- R/finbif_occurrence.R | 134 +++++-- R/finbif_occurrence_load.R | 83 +++- R/finbif_records.R | 23 + R/finbif_request_token.R | 5 R/finbif_taxa.R | 2 R/methods.R | 48 ++ R/sysdata.rda |binary R/utils.R | 27 + R/variables.R | 26 + README.md | 6 build/vignette.rds |binary data/finland_map.rda |binary inst/NEWS.Rd | 29 + inst/doc/finbif.html | 111 +++--- inst/doc/v02_occurrence_data.html | 111 +++--- inst/doc/v03_selecting_variables.html | 111 +++--- inst/doc/v04_metadata.Rmd | 27 - inst/doc/v04_metadata.html | 138 ++++---- inst/doc/v05_filtering.html | 111 +++--- inst/doc/v06_plotting.html | 111 +++--- man/filters.Rd | 16 man/finbif_collections.Rd | 7 man/finbif_last_mod.Rd |only man/finbif_taxa.Rd | 2 man/variables.Rd | 26 + tests/testthat/HBF.49382.zip |only tests/testthat/_snaps/local-finbif_occurrence_load.md | 304 +++++++++++++++++- tests/testthat/helper-finbif.R | 2 tests/testthat/laji-data-new-col.tsv |only tests/testthat/test-finbif_last_mod.R |only tests/testthat/test-finbif_occurrence.R | 34 +- tests/testthat/test-local-finbif_occurrence_load.R | 25 + tests/testthat/test-metadata.R | 4 tests/testthat/test-utils.R | 9 vignettes/v04_metadata.Rmd | 27 - 43 files changed, 1188 insertions(+), 570 deletions(-)
Title: Working with netCDF for Essential Biodiversity Variables
Description: The concept of Essential Biodiversity Variables (EBV) comes with a
data structure based on the Network Common Data Form (netCDF).
The 'ebvcube' 'R' package provides functionality to easily create, access and
visualise this data. The EBV netCDFs can be downloaded from the EBV Data
Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
Author: Luise Quoss [aut, cre] ,
Nestor Fernandez [aut] ,
Christian Langer [aut] ,
Jose Valdez [aut] ,
Henrique Miguel Pereira [aut]
Maintainer: Luise Quoss <luise.quoss@idiv.de>
Diff between ebvcube versions 0.1.1 dated 2022-11-09 and 0.1.2 dated 2022-11-24
ebvcube-0.1.1/ebvcube/tests/testthat/test-ebv_attribute.R |only ebvcube-0.1.1/ebvcube/tests/testthat/test-ebv_create.R |only ebvcube-0.1.2/ebvcube/DESCRIPTION | 6 ebvcube-0.1.2/ebvcube/MD5 | 70 ebvcube-0.1.2/ebvcube/NEWS.md | 16 ebvcube-0.1.2/ebvcube/R/ebv_add_data.R | 6 ebvcube-0.1.2/ebvcube/R/ebv_analyse.R | 5 ebvcube-0.1.2/ebvcube/R/ebv_attribute.R | 167 ebvcube-0.1.2/ebvcube/R/ebv_create.R | 2077 +++++----- ebvcube-0.1.2/ebvcube/R/ebv_download.R | 2 ebvcube-0.1.2/ebvcube/R/ebv_map.R | 5 ebvcube-0.1.2/ebvcube/R/ebv_properties.R | 2 ebvcube-0.1.2/ebvcube/R/ebv_read.R | 6 ebvcube-0.1.2/ebvcube/R/ebv_read_bb.R | 6 ebvcube-0.1.2/ebvcube/R/ebv_read_shp.R | 6 ebvcube-0.1.2/ebvcube/R/ebv_resample.R | 8 ebvcube-0.1.2/ebvcube/R/ebv_trend.R | 5 ebvcube-0.1.2/ebvcube/R/ebv_utils.R | 52 ebvcube-0.1.2/ebvcube/R/ebv_write.R | 2 ebvcube-0.1.2/ebvcube/inst/docs/ebvcube_0.1.2.pdf |only ebvcube-0.1.2/ebvcube/inst/extdata/martins_comcom_id1_20220208_v1.nc |binary ebvcube-0.1.2/ebvcube/inst/extdata/testdata/pereira_csar_bes_sim_20220830_4d.nc |binary ebvcube-0.1.2/ebvcube/inst/extdata/testdata/test_att.nc |binary ebvcube-0.1.2/ebvcube/inst/extdata/testdata/test_create.nc |binary ebvcube-0.1.2/ebvcube/man/ebv_add_data.Rd | 4 ebvcube-0.1.2/ebvcube/man/ebv_analyse.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_attribute.Rd | 4 ebvcube-0.1.2/ebvcube/man/ebv_create.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_download.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_map.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_properties.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_read.Rd | 4 ebvcube-0.1.2/ebvcube/man/ebv_read_bb.Rd | 4 ebvcube-0.1.2/ebvcube/man/ebv_read_shp.Rd | 4 ebvcube-0.1.2/ebvcube/man/ebv_resample.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_trend.Rd | 2 ebvcube-0.1.2/ebvcube/man/ebv_write.Rd | 2 ebvcube-0.1.2/ebvcube/tests/testthat/test-ebv_manipulate.R |only 38 files changed, 1271 insertions(+), 1206 deletions(-)
More information about StatTeacherAssistant at CRAN
Permanent link
Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative
signal is expected to be localized, a series of filters determine which peak
signals are characterized by an implausible spatial distribution. The filters
reduce the dataset dimensionality and increase its information vs noise ratio,
improving the quality of the unsupervised analysis results, reducing data
dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese@outlook.com>
Diff between SPUTNIK versions 1.4 dated 2021-10-18 and 1.4.1 dated 2022-11-24
DESCRIPTION | 16 MD5 | 160 +-- NAMESPACE | 152 +-- NEWS | 166 +-- R/add_rem_border.R | 110 +- R/binary_refimg.R | 232 ++-- R/construct_funcs.R | 292 ++--- R/continuous_refimg.R | 154 +-- R/data_funcs.R | 190 +-- R/examples/filter_count.R | 70 - R/examples/filter_csr.R | 64 - R/examples/filter_global.R | 66 - R/examples/filter_split.R | 50 R/examples/graph_funcs.R | 62 - R/examples/msImage_binOtsu.R | 16 R/examples/msImage_closeImage.R | 22 R/examples/msImage_invertImage.R | 16 R/examples/msImage_plot.R | 16 R/examples/msImage_removeSmallObjects.R | 18 R/examples/msImage_smoothImage.R | 16 R/examples/msiDataset_binKmeans.R | 30 R/examples/msiDataset_getters.R | 36 R/examples/msiDataset_transform.R | 46 R/examples/sparseness.R | 36 R/filter_count.R | 318 +++--- R/filter_csr.R | 436 ++++---- R/filter_global.R | 274 ++--- R/filter_split.R | 460 ++++----- R/generic_funcs.R | 62 - R/graph_funcs.R | 390 +++---- R/is_funcs.R | 258 ++--- R/ms.image_class.R | 94 - R/ms.image_methods.R | 574 +++++------ R/msi.dataset_class.R | 156 +-- R/msi.dataset_funcs.R | 864 ++++++++--------- R/msi.dataset_methods.R | 1462 ++++++++++++++--------------- R/mz_funcs.R | 430 ++++---- R/sparseness_funcs.R | 254 ++--- README.md |only inst/CITATION | 32 man/CSRPeaksFilter.Rd | 218 ++-- man/NMI.Rd | 62 - man/PCAImage-msi.dataset-method.Rd | 50 man/SSIM.Rd | 70 - man/applyPeaksFilter-msi.dataset-method.Rd | 116 +- man/binKmeans-msi.dataset-method.Rd | 90 - man/binKmeans2-msi.dataset-method.Rd | 122 +- man/binOtsu-ms.image-method.Rd | 56 - man/binSupervised-msi.dataset-method.Rd | 102 +- man/bladderMALDIRompp2010.Rd | 56 - man/closeImage-ms.image-method.Rd | 66 - man/countPixelsFilter.Rd | 228 ++-- man/createPeaksFilter.Rd | 76 - man/getIntensityMat-msi.dataset-method.Rd | 78 - man/getMZ-msi.dataset-method.Rd | 76 - man/getShapeMSI-msi.dataset-method.Rd | 76 - man/gini.index.Rd | 110 +- man/globalPeaksFilter.Rd | 212 ++-- man/invertImage-ms.image-method.Rd | 56 - man/ms.image-class.Rd | 46 man/msImage.Rd | 70 - man/msi.dataset-class.Rd | 78 - man/msiDataset.Rd | 96 - man/normIntensity-msi.dataset-method.Rd | 190 +-- man/numDetectedMSI-msi.dataset-method.Rd | 44 man/ovarianDESIDoria2016.Rd | 56 - man/plot.Rd | 64 - man/refImageBinaryKmeans.Rd | 66 - man/refImageBinaryKmeansMulti.Rd | 112 +- man/refImageBinaryOtsu.Rd | 36 man/refImageBinarySVM.Rd | 68 - man/refImageContinuous.Rd | 55 - man/removeSmallObjects-ms.image-method.Rd | 70 - man/scatter.ratio.Rd | 94 - man/smoothImage-ms.image-method.Rd | 62 - man/spatial.chaos.Rd | 112 +- man/splitPeaksFilter.Rd | 240 ++-- man/totalIonCountMSI-msi.dataset-method.Rd | 44 man/varTransform-msi.dataset-method.Rd | 110 +- tests |only 80 files changed, 5873 insertions(+), 5860 deletions(-)
Title: Rearranging Data
Description: Arrange data by a set of methods. Use rearrangers to reorder
data points and mutators to change their values. From basic utilities,
to centering the greatest value, to swirling in 3-dimensional space,
'rearrr' enables creativity when plotting and experimenting with data.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between rearrr versions 0.3.1 dated 2022-08-28 and 0.3.2 dated 2022-11-24
DESCRIPTION | 11 +- MD5 | 138 ++++++++++++++-------------- NEWS.md | 10 ++ R/angle.R | 14 +- R/apply_transformation_matrix.R | 26 +++-- R/circularize.R | 48 +++++---- R/cluster_groups.R | 46 +++++---- R/create_dimming_fn.R | 12 +- R/dim_values.R | 18 ++- R/expand_distances.R | 70 +++++++------- R/expand_distances_each.R | 96 ++++++++++--------- R/flip_values.R | 26 +++-- R/generate_clusters.R | 25 ++--- R/generate_wave.R | 22 ++-- R/helpers.R | 8 + R/hexagonalize.R | 48 +++++---- R/rotate_2d.R | 28 +++-- R/rotate_3d.R | 46 +++++---- R/shear_2d.R | 38 ++++--- R/shear_3d.R | 36 ++++--- R/square.R | 48 +++++---- R/swirl_2d.R | 26 +++-- R/swirl_3d.R | 80 ++++++++-------- R/table_of_content_markdown.R | 3 R/transfer_centroids.R | 12 +- R/triangularize.R | 48 +++++---- README.md | 3 build/rearrr.pdf |binary man/angle.Rd | 14 +- man/apply_transformation_matrix.Rd | 26 +++-- man/circularize.Rd | 48 +++++---- man/cluster_groups.Rd | 46 +++++---- man/create_dimming_fn.Rd | 12 +- man/dim_values.Rd | 18 ++- man/expand_distances.Rd | 70 +++++++------- man/expand_distances_each.Rd | 96 ++++++++++--------- man/flip_values.Rd | 26 +++-- man/generate_clusters.Rd | 25 ++--- man/hexagonalize.Rd | 48 +++++---- man/rotate_2d.Rd | 28 +++-- man/rotate_3d.Rd | 46 +++++---- man/shear_2d.Rd | 38 ++++--- man/shear_3d.Rd | 36 ++++--- man/square.Rd | 48 +++++---- man/swirl_2d.Rd | 26 +++-- man/swirl_3d.Rd | 80 ++++++++-------- man/triangularize.Rd | 48 +++++---- tests/testthat.R | 4 tests/testthat/test_angle.R | 8 - tests/testthat/test_closest_to.R | 16 +-- tests/testthat/test_cluster_groups.R | 8 - tests/testthat/test_create_dimming_fn.R | 3 tests/testthat/test_create_origin_fn.R | 3 tests/testthat/test_dim_values.R | 16 +-- tests/testthat/test_distance.R | 8 - tests/testthat/test_expand_distances.R | 20 ++-- tests/testthat/test_expand_distances_each.R | 16 +-- tests/testthat/test_flip_values.R | 16 +-- tests/testthat/test_n_fn.R | 11 +- tests/testthat/test_pair_extremes.R | 4 tests/testthat/test_positition_funcs.R | 8 - tests/testthat/test_rev_windows.R | 4 tests/testthat/test_roll_values.R | 12 +- tests/testthat/test_rotate_2d.R | 32 +++--- tests/testthat/test_rotate_3d.R | 16 +-- tests/testthat/test_scalers.R | 4 tests/testthat/test_shear_2d.R | 32 +++--- tests/testthat/test_shear_3d.R | 32 +++--- tests/testthat/test_swirl_2d.R | 36 +++---- tests/testthat/test_swirl_3d.R | 16 +-- 70 files changed, 1157 insertions(+), 933 deletions(-)
Title: Creating Groups from Data
Description: Methods for dividing data into groups.
Create balanced partitions and cross-validation folds.
Perform time series windowing and general grouping and splitting of data.
Balance existing groups with up- and downsampling or collapse them to fewer groups.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between groupdata2 versions 2.0.1 dated 2022-08-28 and 2.0.2 dated 2022-11-24
DESCRIPTION | 12 - MD5 | 66 +++---- NEWS.md | 10 + R/collapse_groups.R | 4 R/collapse_groups_auto_tuning.R | 8 R/collapse_groups_by.R | 4 R/helpers.R | 16 + R/run_by_group.R | 2 R/summarize_balances.R | 4 R/summarize_group_cols.R | 6 R/summarizers.R | 6 build/groupdata2.pdf |binary inst/doc/automatic_groups_with_groupdata2.html | 4 inst/doc/cross-validation_with_groupdata2.R | 15 + inst/doc/cross-validation_with_groupdata2.Rmd | 17 +- inst/doc/cross-validation_with_groupdata2.html | 166 ++++++++++---------- inst/doc/description_of_groupdata2.R | 16 - inst/doc/description_of_groupdata2.Rmd | 16 - inst/doc/description_of_groupdata2.html | 6 inst/doc/introduction_to_groupdata2.html | 4 inst/doc/time_series_with_groupdata2.R | 8 inst/doc/time_series_with_groupdata2.Rmd | 8 inst/doc/time_series_with_groupdata2.html | 6 man/collapse_groups.Rd | 4 man/collapse_groups_by.Rd | 4 tests/testthat.R | 4 tests/testthat/test_collapse_groups.R | 4 tests/testthat/test_fold.R | 2 tests/testthat/test_numerically_balanced_grouping.R | 3 tests/testthat/test_summarize_balances.R | 2 tests/testthat/test_summarizers.R | 2 vignettes/cross-validation_with_groupdata2.Rmd | 17 +- vignettes/description_of_groupdata2.Rmd | 16 - vignettes/time_series_with_groupdata2.Rmd | 8 34 files changed, 258 insertions(+), 212 deletions(-)
Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input
data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre] ,
Brent Thorne [ctb] ,
Diego Hernangomez [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between ggspatial versions 1.1.6 dated 2022-07-08 and 1.1.7 dated 2022-11-24
ggspatial-1.1.6/ggspatial/tests/testthat/_snaps |only ggspatial-1.1.6/ggspatial/tests/testthat/rosm.cache |only ggspatial-1.1.7/ggspatial/DESCRIPTION | 8 ggspatial-1.1.7/ggspatial/MD5 | 105 +--------- ggspatial-1.1.7/ggspatial/NAMESPACE | 2 ggspatial-1.1.7/ggspatial/NEWS.md | 5 ggspatial-1.1.7/ggspatial/R/geom-polypath.R | 38 +-- ggspatial-1.1.7/ggspatial/R/ggspatial-package.R | 2 ggspatial-1.1.7/ggspatial/R/layer-spatial-raster.R | 10 ggspatial-1.1.7/ggspatial/R/layer-spatial-stars.R | 8 ggspatial-1.1.7/ggspatial/R/layer-spatial-terra.R | 8 ggspatial-1.1.7/ggspatial/R/layer-spatial.R | 2 ggspatial-1.1.7/ggspatial/man/figures/README-fig-layer-spatial-sf-1.png |binary ggspatial-1.1.7/ggspatial/man/geom_polypath.Rd | 7 ggspatial-1.1.7/ggspatial/man/layer_spatial.Rd | 2 ggspatial-1.1.7/ggspatial/tests/testthat/test-annotation-map-tile.R | 24 -- ggspatial-1.1.7/ggspatial/tests/testthat/test-layer-spatial-raster.R | 2 ggspatial-1.1.7/ggspatial/tests/testthat/test-layer-spatial-stars.R | 2 ggspatial-1.1.7/ggspatial/tests/testthat/test-layer-spatial-terra.R | 2 19 files changed, 65 insertions(+), 162 deletions(-)
Title: Visualisation of High-Throughput Behavioural (i.e. Ethomics)
Data
Description: Extension of 'ggplot2' providing layers, scales and preprocessing functions
useful to represent behavioural variables that are recorded over multiple animals and days.
This package is part of the 'rethomics' framework <https://rethomics.github.io/>.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between ggetho versions 0.3.6 dated 2020-04-29 and 0.3.7 dated 2022-11-24
DESCRIPTION | 15 ++-- MD5 | 22 +++--- R/ggetho.R | 7 +- R/stat-ld-annotations.R | 4 - R/stat-pop-etho.R | 7 +- man/geom_peak.Rd | 50 +++++++++------ man/ggetho.Rd | 21 ++++-- man/ggspectro.Rd | 12 ++- man/stat_ld_annotations.Rd | 55 ++++++++++------ man/stat_pop_etho.Rd | 60 +++++++++++------- man/stat_tile_etho.Rd | 67 +++++++++++++------- man/time_scales.Rd | 148 +++++++++++++++++++++++++++++++++------------ 12 files changed, 312 insertions(+), 156 deletions(-)
Title: Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Description: Deliver the full functionality of 'ECharts' with minimal overhead. 'echarty' users build R lists for 'ECharts' API. Lean set of powerful commands.
Author: Larry Helgason [cre, aut, cph],
John Coene [aut, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>
Diff between echarty versions 1.4.7 dated 2022-08-28 and 1.5.0 dated 2022-11-24
echarty-1.4.7/echarty/R/echarty-package.R |only echarty-1.4.7/echarty/man/echarty-package.Rd |only echarty-1.5.0/echarty/DESCRIPTION | 8 echarty-1.5.0/echarty/MD5 | 46 echarty-1.5.0/echarty/NEWS.md | 19 echarty-1.5.0/echarty/R/echarty.R | 1951 ++++++++++-------- echarty-1.5.0/echarty/R/examples.R | 8 echarty-1.5.0/echarty/inst/htmlwidgets/echarty.js | 576 ++--- echarty-1.5.0/echarty/inst/js/echarts.min.js | 4 echarty-1.5.0/echarty/inst/js/lottie-parser.js |only echarty-1.5.0/echarty/inst/js/world.js |only echarty-1.5.0/echarty/inst/themes/dark-mushroom.js | 7 echarty-1.5.0/echarty/man/Introduction.Rd |only echarty-1.5.0/echarty/man/ec.clmn.Rd | 24 echarty-1.5.0/echarty/man/ec.examples.Rd | 8 echarty-1.5.0/echarty/man/ec.init.Rd | 25 echarty-1.5.0/echarty/man/ec.theme.Rd | 4 echarty-1.5.0/echarty/man/ec.upd.Rd | 6 echarty-1.5.0/echarty/man/ec.util.Rd | 93 echarty-1.5.0/echarty/man/ecr.band.Rd | 20 echarty-1.5.0/echarty/man/ecr.ebars.Rd | 48 echarty-1.5.0/echarty/man/ecs.exec.Rd | 2 echarty-1.5.0/echarty/tests/testthat/test-ec.clmn.R | 93 echarty-1.5.0/echarty/tests/testthat/test-ec.util.R |only echarty-1.5.0/echarty/tests/testthat/test-other.R | 83 echarty-1.5.0/echarty/tests/testthat/test-presets.R | 68 echarty-1.5.0/echarty/tests/testthat/test-renderers.R | 88 27 files changed, 1810 insertions(+), 1371 deletions(-)
Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this,
R developers can use variables, inheritance, and functions to generate
dynamic style sheets. The package uses the 'Sass CSS' extension language,
which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut],
Timothy Mastny [aut],
Richard Iannone [aut] ,
Barret Schloerke [aut] ,
Carson Sievert [aut, cre] ,
Christophe Dervieux [ctb] ,
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] ,
Greter Marcel [ctb, cph] ,
Mifsud Michael [ct [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.4.3 dated 2022-11-19 and 0.4.4 dated 2022-11-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 +++++++- inst/doc/sass.html | 4 ++-- src/Makevars | 2 +- src/Makevars.win | 2 +- 6 files changed, 19 insertions(+), 13 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions in a recent version is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.2.18 dated 2022-10-04 and 2.2.19 dated 2022-11-24
DESCRIPTION | 88 +++----- MD5 | 58 ++--- NEWS.md | 15 + src/vendor/boost/lexical_cast/detail/converter_lexical_streams.hpp | 6 src/vendor/boost/mpl/vector/aux_/preprocessed/plain |only src/vendor/boost/preprocessor/control/detail/edg |only src/vendor/boost/preprocessor/list/detail/edg |only src/vendor/boost/preprocessor/repetition/detail/edg |only tests/testthat.R | 8 tests/testthat/test-affinity.R | 27 +- tests/testthat/test-astyle.R | 2 tests/testthat/test-basic-types.R | 8 tests/testthat/test-blob.R | 2 tests/testthat/test-column-info.R | 2 tests/testthat/test-data-type.R | 2 tests/testthat/test-dbClearResult.R | 2 tests/testthat/test-dbConnect.R | 2 tests/testthat/test-dbSendQuery.R | 41 +-- tests/testthat/test-dbWriteTable.R | 2 tests/testthat/test-dbWriteTableAutoincrement.R | 2 tests/testthat/test-encoding.R | 110 ++++------ tests/testthat/test-error.R | 2 tests/testthat/test-exception.R | 2 tests/testthat/test-extendedTypes.R | 20 - tests/testthat/test-json.R | 6 tests/testthat/test-readonly.R | 2 tests/testthat/test-regularExpressions.R | 2 tests/testthat/test-sd.R | 2 tests/testthat/test-sqliteCopyDatabase.R | 2 tests/testthat/test-sqliteQuickColumn.R | 2 tests/testthat/test-transactions.R | 2 31 files changed, 199 insertions(+), 220 deletions(-)
Title: Relational Event Models
Description: Tools to fit relational event models.
Author: Carter T. Butts <buttsc@uci.edu>
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between relevent versions 1.1 dated 2021-09-22 and 1.2 dated 2022-11-24
ChangeLog | 10 ++++++ DESCRIPTION | 8 ++--- MD5 | 15 +++++---- R/data.proc.R |only R/rem.R | 2 - R/rem.dyad.R | 64 ++++++++++++++++++++++++++++++---------- TODO |only man/as.sociomatrix.eventlist.Rd |only man/rem.dyad.Rd | 24 +++++++++++++-- src/utils.c | 4 +- 10 files changed, 97 insertions(+), 30 deletions(-)
Title: Diversity Indices for Numerical Matrices
Description: Methods to calculate indices of diversity on numerical matrices based on information theory. The rationale behind the package is described in Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039> and Rocchini, Marcantonio,..., Ricotta (2021) <doi:10.1101/2021.01.23.427872>.
Author: Matteo Marcantonio [aut, cre],
Martina Iannacito [aut, ctb],
Elisa Marchetto [ctb],
Elisa Thouverai [aut, ctb],
Michele Torresani [aut, ctb],
Daniele Da Re [aut],
Clara Tattoni [aut],
Giovanni Bacaro [aut],
Saverio Vicario [aut, ctb],
Carlo Ricotta [ [...truncated...]
Maintainer: Matteo Marcantonio <marcantoniomatteo@gmail.com>
Diff between rasterdiv versions 0.2-5.2 dated 2022-03-29 and 0.3.1 dated 2022-11-24
rasterdiv-0.2-5.2/rasterdiv/inst/doc/rasterdiv_advanced_multimensionRao.R |only rasterdiv-0.2-5.2/rasterdiv/inst/doc/rasterdiv_advanced_multimensionRao.Rmd |only rasterdiv-0.2-5.2/rasterdiv/inst/doc/rasterdiv_advanced_multimensionRao.html |only rasterdiv-0.2-5.2/rasterdiv/vignettes/rasterdiv_advanced_multimensionRao.Rmd |only rasterdiv-0.3.1/rasterdiv/DESCRIPTION | 14 rasterdiv-0.3.1/rasterdiv/MD5 | 46 - rasterdiv-0.3.1/rasterdiv/NAMESPACE | 2 rasterdiv-0.3.1/rasterdiv/NEWS.md | 12 rasterdiv-0.3.1/rasterdiv/R/mpaRaoAreaS.R |only rasterdiv-0.3.1/rasterdiv/R/paRao.R | 356 +++++----- rasterdiv-0.3.1/rasterdiv/R/paRaoAreaS.R | 1 rasterdiv-0.3.1/rasterdiv/TODO | 2 rasterdiv-0.3.1/rasterdiv/build/vignette.rds |binary rasterdiv-0.3.1/rasterdiv/inst/CITATION |only rasterdiv-0.3.1/rasterdiv/inst/WORDLIST | 6 rasterdiv-0.3.1/rasterdiv/inst/_pkgdown.yml |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_advanced_multidimension_Rao.R |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_advanced_multidimension_Rao.Rmd |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_advanced_multidimension_Rao.html |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_area_based_Rao.R |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_area_based_Rao.Rmd |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_area_based_Rao.html |only rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_basics.R | 40 - rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_basics.Rmd | 55 - rasterdiv-0.3.1/rasterdiv/inst/doc/rasterdiv_basics.html | 143 +--- rasterdiv-0.3.1/rasterdiv/man/mpaRaoAreaS.Rd |only rasterdiv-0.3.1/rasterdiv/man/mpaRaoS.Rd | 2 rasterdiv-0.3.1/rasterdiv/man/paRaoP.Rd | 1 rasterdiv-0.3.1/rasterdiv/man/paRaoS.Rd | 1 rasterdiv-0.3.1/rasterdiv/vignettes/rasterdiv_advanced_multidimension_Rao.Rmd |only rasterdiv-0.3.1/rasterdiv/vignettes/rasterdiv_area_based_Rao.Rmd |only rasterdiv-0.3.1/rasterdiv/vignettes/rasterdiv_basics.Rmd | 55 - 32 files changed, 355 insertions(+), 381 deletions(-)
Title: Gaussian Process Fitting
Description: Fits a Gaussian process model to data. Gaussian processes
are commonly used in computer experiments to fit an interpolating model.
The model is stored as an 'R6' object and can be easily updated with new
data. There are options to run in parallel, and 'Rcpp'
has been used to speed up calculations.
For more info about Gaussian process software, see Erickson et al. (2018)
<doi:10.1016/j.ejor.2017.10.002>.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between GauPro versions 0.2.5 dated 2022-11-14 and 0.2.6 dated 2022-11-24
DESCRIPTION | 18 - MD5 | 65 ++-- NAMESPACE | 3 NEWS.md | 13 R/GauPro_Gauss_LOO.R | 10 R/GauPro_S3.R | 73 ++++ R/convert_X_with_formula_back.R |only R/kernel_Cubic.R | 3 R/kernel_Factor.R | 2 R/kernel_OrderedFactor.R | 2 R/kernel_base.R | 66 +++- R/kernel_ignoreinds.R | 3 R/kernel_model.R | 371 ++++++++++++++++++++++--- R/kernel_model_LOO.R | 126 ++++---- R/kernel_product.R | 1 R/kernel_sum.R | 1 README.md | 2 inst/doc/CrossValidationErrorCorrection.html | 20 - inst/doc/GauPro.html | 4 inst/doc/IntroductionToGPs.html | 4 inst/doc/derivatives.html | 4 inst/doc/surface_derivatives.html | 4 man/Cubic.Rd | 3 man/FactorKernel.Rd | 2 man/GauPro_Gauss_LOO.Rd | 12 man/GauPro_kernel.Rd | 10 man/GauPro_kernel_model.Rd | 76 ++++- man/GauPro_kernel_model_LOO.Rd | 7 man/OrderedFactorKernel.Rd | 2 man/print.summary.GauPro.Rd |only man/summary.GauPro.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/test_Gauss_GauPro_LOO.R | 14 tests/testthat/test_kernel_model_LOO.R |only tests/testthat/test_kernel_model_and_kernels.R | 269 +++++++++++++++--- tests/testthat/test_kernels_right_type.R | 39 ++ 36 files changed, 1007 insertions(+), 222 deletions(-)
Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as
proposed by Ruegamer et al. (2021) <arXiv:2104.02705>.
Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre],
Florian Pfisterer [ctb],
Philipp Baumann [ctb],
Chris Kolb [ctb],
Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between deepregression versions 0.3 dated 2022-11-16 and 0.3.1 dated 2022-11-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/orthogonalization.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
More information about deepregression at CRAN
Permanent link
Title: Bayes Factors, Model Choice and Variable Selection in Linear
Models
Description: Conceived to calculate Bayes factors in Linear models and then to provide a formal Bayesian answer to testing and variable selection problems. From a theoretical side, the emphasis in this package is placed on the prior distributions and it allows a wide range of them: Jeffreys (1961); Zellner and Siow(1980)<DOI:10.1007/bf02888369>; Zellner and Siow(1984); Zellner (1986)<DOI:10.2307/2233941>; Fernandez et al. (2001)<DOI:10.1016/s0304-4076(00)00076-2>; Liang et al. (2008)<DOI:10.1198/016214507000001337> and Bayarri et al. (2012)<DOI:10.1214/12-aos1013>. The interaction with the package is through a friendly interface that syntactically mimics the well-known lm() command of R. The resulting objects can be easily explored providing the user very valuable information (like marginal, joint and conditional inclusion probabilities of potential variables; the highest posterior probability model, HPM; the median probability model, MPM) about the structure of the t [...truncated...]
Author: Gonzalo Garcia-Donato [aut],
Anabel Forte [aut, cre],
Carlos Vergara-Hernandez [ctb]
Maintainer: Anabel Forte <anabel.forte@uv.es>
Diff between BayesVarSel versions 2.0.1 dated 2020-02-18 and 2.2.3 dated 2022-11-24
BayesVarSel-2.0.1/BayesVarSel/README.md |only BayesVarSel-2.0.1/BayesVarSel/build |only BayesVarSel-2.0.1/BayesVarSel/inst/doc |only BayesVarSel-2.0.1/BayesVarSel/vignettes |only BayesVarSel-2.2.3/BayesVarSel/DESCRIPTION | 13 BayesVarSel-2.2.3/BayesVarSel/MD5 | 65 BayesVarSel-2.2.3/BayesVarSel/NEWS.md | 13 BayesVarSel-2.2.3/BayesVarSel/R/Btest.R | 102 BayesVarSel-2.2.3/BayesVarSel/R/Bvs.R | 317 - BayesVarSel-2.2.3/BayesVarSel/R/GibbsBvs.R | 333 + BayesVarSel-2.2.3/BayesVarSel/R/GibbsBvsF.R | 24 BayesVarSel-2.2.3/BayesVarSel/R/package.R | 149 BayesVarSel-2.2.3/BayesVarSel/R/plotBvs.R | 6 BayesVarSel-2.2.3/BayesVarSel/data/OBICE.rdata |only BayesVarSel-2.2.3/BayesVarSel/man/Btest.Rd | 50 BayesVarSel-2.2.3/BayesVarSel/man/Bvs.Rd | 54 BayesVarSel-2.2.3/BayesVarSel/man/GibbsBvs.Rd | 15 BayesVarSel-2.2.3/BayesVarSel/man/GibbsBvsF.Rd | 17 BayesVarSel-2.2.3/BayesVarSel/man/Hald.Rd | 6 BayesVarSel-2.2.3/BayesVarSel/man/OBICE.Rd |only BayesVarSel-2.2.3/BayesVarSel/man/Ozone35.Rd | 6 BayesVarSel-2.2.3/BayesVarSel/man/SDM.Rd | 6 BayesVarSel-2.2.3/BayesVarSel/src/BayesVarSel_init.c | 56 BayesVarSel-2.2.3/BayesVarSel/src/Gibbsauxiliaryfuncs.c | 2 BayesVarSel-2.2.3/BayesVarSel/src/allBF.c | 194 BayesVarSel-2.2.3/BayesVarSel/src/allBF.h | 4 BayesVarSel-2.2.3/BayesVarSel/src/main.c | 3970 ++++++++++++++++ BayesVarSel-2.2.3/BayesVarSel/src/mainGibbs.c | 3046 ++++++++++++ BayesVarSel-2.2.3/BayesVarSel/src/mainSingle.c | 42 BayesVarSel-2.2.3/BayesVarSel/src/priorprob.c | 15 30 files changed, 8200 insertions(+), 305 deletions(-)
Title: Spatial Objects of the Czech Republic
Description: Administrative regions and other spatial objects of the Czech Republic.
Author: Jindra Lacko [aut, cre]
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between RCzechia versions 1.9.4 dated 2022-10-06 and 1.10.0 dated 2022-11-24
RCzechia-1.10.0/RCzechia/DESCRIPTION | 14 RCzechia-1.10.0/RCzechia/MD5 | 63 ++-- RCzechia-1.10.0/RCzechia/NEWS.md | 8 RCzechia-1.10.0/RCzechia/R/downloader.R | 13 RCzechia-1.10.0/RCzechia/R/ok_to_proceed.R | 5 RCzechia-1.10.0/RCzechia/R/vyskopis.R | 51 ++- RCzechia-1.10.0/RCzechia/README.md | 14 RCzechia-1.10.0/RCzechia/build/vignette.rds |binary RCzechia-1.10.0/RCzechia/inst/doc/vignette.Rmd | 32 +- RCzechia-1.10.0/RCzechia/inst/doc/vignette.html | 153 ++++------ RCzechia-1.10.0/RCzechia/man/vyskopis.Rd | 39 +- RCzechia-1.10.0/RCzechia/tests/testthat/test-1-casti.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-chr-uzemi.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-kraje.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-lesy.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-obce.R | 8 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-okresy.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-orp.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-relief.R | 43 +- RCzechia-1.10.0/RCzechia/tests/testthat/test-1-republika.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-transport.R | 8 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-vodstvo.R | 10 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-volby.R | 8 RCzechia-1.10.0/RCzechia/tests/testthat/test-1-zip-codes.R | 4 RCzechia-1.10.0/RCzechia/tests/testthat/test-2-code-internal.R |only RCzechia-1.10.0/RCzechia/tests/testthat/test-2-code-public.R |only RCzechia-1.10.0/RCzechia/vignettes/brno-center-1.png |binary RCzechia-1.10.0/RCzechia/vignettes/census-1.png |binary RCzechia-1.10.0/RCzechia/vignettes/ctverce-1.png |binary RCzechia-1.10.0/RCzechia/vignettes/geocode-1.png |binary RCzechia-1.10.0/RCzechia/vignettes/relief-1.png |binary RCzechia-1.10.0/RCzechia/vignettes/senat-1.png |binary RCzechia-1.10.0/RCzechia/vignettes/vignette.Rmd | 32 +- RCzechia-1.9.4/RCzechia/tests/testthat/test-2-code.R |only 34 files changed, 260 insertions(+), 273 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 0.8.3 dated 2022-10-20 and 0.8.4 dated 2022-11-24
graphlayouts-0.8.3/graphlayouts/man/graphlayouts.Rd |only graphlayouts-0.8.4/graphlayouts/DESCRIPTION | 6 graphlayouts-0.8.4/graphlayouts/MD5 | 23 + graphlayouts-0.8.4/graphlayouts/NEWS.md | 5 graphlayouts-0.8.4/graphlayouts/R/graphlayouts.R | 9 graphlayouts-0.8.4/graphlayouts/R/layout_dynamic.R | 2 graphlayouts-0.8.4/graphlayouts/R/layout_manipulate.R | 9 graphlayouts-0.8.4/graphlayouts/README.md | 34 +- graphlayouts-0.8.4/graphlayouts/man/graphlayouts-package.Rd |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-graph_manipulate.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-layout_dynamic.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-layout_large_graphs.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-layout_manipulate.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-layout_multilevel.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-layout_spectral.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-layouts.R |only graphlayouts-0.8.4/graphlayouts/tests/testthat/test-stress_majorization.R | 128 +++++++++- 17 files changed, 177 insertions(+), 39 deletions(-)