Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph] ,
Matthew Collins [aut] ,
Scott Chamberlain [ctb],
Kevin Love [ctb],
Hem Nalini Morzaria-Luna [ctb],
Michelle L. Gaynor [ctb, aut],
Jesse Bennett [cre]
Maintainer: Jesse Bennett <j3553@ufl.edu>
Diff between ridigbio versions 0.4.0 dated 2024-09-03 and 0.4.1 dated 2024-09-30
DESCRIPTION | 8 MD5 | 48 NEWS.md | 5 inst/doc/BadCoordinateID.html | 4 inst/doc/BasicUsage.Rmd | 127 inst/doc/BasicUsage.html | 26 inst/doc/Fields.R | 157 inst/doc/Fields.Rmd | 210 inst/doc/Fields.html |22924 +++++++++++++++++++++++++++++++++++++++++- inst/doc/FindTissue.Rmd | 30 inst/doc/FindTissue.html | 49 inst/doc/IDDataFlags.Rmd | 10 inst/doc/MediaAPIDemo.R | 71 inst/doc/MediaAPIDemo.Rmd | 62 inst/doc/MediaAPIDemo.html | 99 inst/doc/ModifiedDataID.Rmd | 18 inst/doc/RecordAPIDemo.Rmd | 30 inst/doc/RecordAPIDemo.html | 139 vignettes/BasicUsage.Rmd | 127 vignettes/Fields.Rmd | 210 vignettes/FindTissue.Rmd | 30 vignettes/IDDataFlags.Rmd | 10 vignettes/MediaAPIDemo.Rmd | 62 vignettes/ModifiedDataID.Rmd | 18 vignettes/RecordAPIDemo.Rmd | 30 25 files changed, 23652 insertions(+), 852 deletions(-)
Title: Bayesian Modelling of Extremal Dependence in Time Series
Description: Characterisation of the extremal dependence structure of time series, avoiding pre-processing and filtering as done typically with peaks-over-threshold methods. It uses the conditional approach of Heffernan and Tawn (2004) <DOI:10.1111/j.1467-9868.2004.02050.x> which is very flexible in terms of extremal and asymptotic dependence structures, and Bayesian methods improve efficiency and allow for deriving measures of uncertainty. For example, the extremal index, related to the size of clusters in time, can be estimated and samples from its posterior distribution obtained.
Author: Thomas Lugrin [aut, cre, cph]
Maintainer: Thomas Lugrin <thomas.lugrin@alumni.epfl.ch>
Diff between tsxtreme versions 0.3.3 dated 2021-04-23 and 0.3.4 dated 2024-09-30
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NEWS.md | 18 ++++++++++-------- build/partial.rdb |binary src/etfit.cpp | 26 +++++++++++++------------- src/etfit.h | 2 +- src/etfit_externC.cpp | 4 ++-- src/init.c | 2 +- 8 files changed, 41 insertions(+), 38 deletions(-)
Title: Cholesky Decomposition of the Wishart Distribution
Description: Sampling from the Cholesky factorization of a Wishart random
variable, sampling from the inverse Wishart distribution, sampling from
the Cholesky factorization of an inverse Wishart random variable, sampling
from the pseudo Wishart distribution, sampling from the generalized
inverse Wishart distribution, computing densities for the Wishart
and inverse Wishart distributions, and computing the multivariate gamma
and digamma functions. Provides a header file so the C functions can be
called directly from other programs.
Author: Geoffrey Thompson [aut, cre] ,
R Core Team [ctb]
Maintainer: Geoffrey Thompson <gzthompson@gmail.com>
Diff between CholWishart versions 1.1.2.1 dated 2024-09-23 and 1.1.4 dated 2024-09-30
CholWishart-1.1.2.1/CholWishart/man/CholWishart.Rd |only CholWishart-1.1.4/CholWishart/DESCRIPTION | 13 CholWishart-1.1.4/CholWishart/MD5 | 22 CholWishart-1.1.4/CholWishart/NEWS.md | 5 CholWishart-1.1.4/CholWishart/R/CholWishart-package.r | 5 CholWishart-1.1.4/CholWishart/README.md | 38 CholWishart-1.1.4/CholWishart/build/partial.rdb |binary CholWishart-1.1.4/CholWishart/build/vignette.rds |binary CholWishart-1.1.4/CholWishart/inst/doc/wishart.html | 591 +++++++++++---- CholWishart-1.1.4/CholWishart/man/CholWishart-package.Rd |only CholWishart-1.1.4/CholWishart/man/dWishart.Rd | 4 CholWishart-1.1.4/CholWishart/man/lmvgamma.Rd | 4 CholWishart-1.1.4/CholWishart/src/rCholWishart.c | 8 13 files changed, 486 insertions(+), 204 deletions(-)
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 0.2.0 dated 2024-07-01 and 1.2.1 dated 2024-09-30
vectorsurvR-0.2.0/vectorsurvR/R/ProcessAbunAnom.R |only vectorsurvR-1.2.1/vectorsurvR/DESCRIPTION | 8 vectorsurvR-1.2.1/vectorsurvR/MD5 | 60 vectorsurvR-1.2.1/vectorsurvR/NAMESPACE | 3 vectorsurvR-1.2.1/vectorsurvR/R/data.R | 18 vectorsurvR-1.2.1/vectorsurvR/R/getAbundance.R | 6 vectorsurvR-1.2.1/vectorsurvR/R/getArthroCollections.R | 89 vectorsurvR-1.2.1/vectorsurvR/R/getInfectionRate.R | 6 vectorsurvR-1.2.1/vectorsurvR/R/getPools.R | 46 vectorsurvR-1.2.1/vectorsurvR/R/getRegions.R |only vectorsurvR-1.2.1/vectorsurvR/R/getSites.R |only vectorsurvR-1.2.1/vectorsurvR/R/getToken.R | 6 vectorsurvR-1.2.1/vectorsurvR/R/getVectorIndex.R | 8 vectorsurvR-1.2.1/vectorsurvR/R/globals.R | 12 vectorsurvR-1.2.1/vectorsurvR/R/plotInfectionRate.R | 2 vectorsurvR-1.2.1/vectorsurvR/R/processAbunAnom.R |only vectorsurvR-1.2.1/vectorsurvR/data/sample_collections.rda |binary vectorsurvR-1.2.1/vectorsurvR/data/sample_pools.rda |binary vectorsurvR-1.2.1/vectorsurvR/inst/doc/vectorsurvR.R | 294 vectorsurvR-1.2.1/vectorsurvR/inst/doc/vectorsurvR.Rmd | 612 + vectorsurvR-1.2.1/vectorsurvR/inst/doc/vectorsurvR.html | 5262 +++++++++++++- vectorsurvR-1.2.1/vectorsurvR/man/getAbundance.Rd | 4 vectorsurvR-1.2.1/vectorsurvR/man/getArthroCollections.Rd | 8 vectorsurvR-1.2.1/vectorsurvR/man/getInfectionRate.Rd | 4 vectorsurvR-1.2.1/vectorsurvR/man/getPools.Rd | 6 vectorsurvR-1.2.1/vectorsurvR/man/getRegions.Rd |only vectorsurvR-1.2.1/vectorsurvR/man/getSites.Rd |only vectorsurvR-1.2.1/vectorsurvR/man/getToken.Rd | 2 vectorsurvR-1.2.1/vectorsurvR/man/getVectorIndex.Rd | 6 vectorsurvR-1.2.1/vectorsurvR/man/plotInfectionRate.Rd | 2 vectorsurvR-1.2.1/vectorsurvR/man/processAbunAnom.Rd | 6 vectorsurvR-1.2.1/vectorsurvR/man/sample_collections.Rd | 7 vectorsurvR-1.2.1/vectorsurvR/man/sample_pools.Rd | 10 vectorsurvR-1.2.1/vectorsurvR/vignettes/vectorsurvR.Rmd | 612 + 34 files changed, 6981 insertions(+), 118 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.
Author: Thomas Jaki [aut, cre] ,
Dominique-Laurent Couturier [aut]
,
Dominic Magirr [aut],
Nikita Mozgunov [aut] ,
Philip Pallmann [aut]
Maintainer: Thomas Jaki <thomas.jaki@pm.me>
Diff between MAMS versions 2.0.2 dated 2024-04-12 and 3.0.0 dated 2024-09-30
MAMS-2.0.2/MAMS/R/generics.R |only MAMS-2.0.2/MAMS/R/mams.R |only MAMS-2.0.2/MAMS/R/mams.sim.R |only MAMS-2.0.2/MAMS/R/new.bounds.R |only MAMS-2.0.2/MAMS/R/ordinal.mams.R |only MAMS-2.0.2/MAMS/R/stepdown.mams.R |only MAMS-2.0.2/MAMS/R/stepdown.update.R |only MAMS-2.0.2/MAMS/R/tite.mams.R |only MAMS-2.0.2/MAMS/man/MAMS-package.Rd |only MAMS-2.0.2/MAMS/man/MAMS.News.Rd |only MAMS-2.0.2/MAMS/man/figures |only MAMS-2.0.2/MAMS/man/generic.Rd |only MAMS-2.0.2/MAMS/man/mams.Rd |only MAMS-3.0.0/MAMS/DESCRIPTION | 11 MAMS-3.0.0/MAMS/MD5 | 51 ++-- MAMS-3.0.0/MAMS/NAMESPACE | 72 ++++-- MAMS-3.0.0/MAMS/R/MAMS-package.R |only MAMS-3.0.0/MAMS/R/dtl.R |only MAMS-3.0.0/MAMS/R/generic.R |only MAMS-3.0.0/MAMS/R/internal.R | 24 -- MAMS-3.0.0/MAMS/R/sep.R |only MAMS-3.0.0/MAMS/R/simultaneous.R |only MAMS-3.0.0/MAMS/build/partial.rdb |binary MAMS-3.0.0/MAMS/inst/NEWS | 14 + MAMS-3.0.0/MAMS/man/MAMS.Rd |only MAMS-3.0.0/MAMS/man/MAMSNews.Rd |only MAMS-3.0.0/MAMS/man/dot-onAttach.Rd |only MAMS-3.0.0/MAMS/man/mams.sim.Rd | 300 +++++++++++++++------------ MAMS-3.0.0/MAMS/man/new.bounds.Rd | 254 +++++++++++++--------- MAMS-3.0.0/MAMS/man/ordinal.mams.Rd | 273 ++++++++++++++++-------- MAMS-3.0.0/MAMS/man/plot.MAMS.Rd |only MAMS-3.0.0/MAMS/man/plot.MAMS.stepdown.Rd |only MAMS-3.0.0/MAMS/man/print.MAMS.Rd |only MAMS-3.0.0/MAMS/man/print.MAMS.stepdown.Rd |only MAMS-3.0.0/MAMS/man/stepdown.mams.Rd | 169 ++++++++------- MAMS-3.0.0/MAMS/man/stepdown.update.Rd | 209 ++++++++++-------- MAMS-3.0.0/MAMS/man/summary.MAMS.Rd |only MAMS-3.0.0/MAMS/man/summary.MAMS.stepdown.Rd |only MAMS-3.0.0/MAMS/man/tite.mams.Rd | 197 ++++++++++------- MAMS-3.0.0/MAMS/src/prodsum123.c | 19 - 40 files changed, 934 insertions(+), 659 deletions(-)
Title: Regional Frequency Analysis using L-Moments
Description: Functions for regional frequency analysis
using the methods of J. R. M. Hosking and J. R. Wallis (1997),
"Regional frequency analysis: an approach based on L-moments".
Author: J. R. M. Hosking [aut, cre]
Maintainer: J. R. M. Hosking <jrmhosking@gmail.com>
Diff between lmomRFA versions 3.6 dated 2023-08-29 and 3.8 dated 2024-09-30
DESCRIPTION | 20 +-- MD5 | 28 ++-- NEWS | 15 ++ R/lmomRFA.r | 4 build/vignette.rds |binary data/Appalach.rda |binary data/Cascades.rda |binary data/Maxwind.rda |binary inst/doc/RegSim.pdf |binary inst/lmomRFA-manual.pdf |binary man/lmomRFA-package.Rd | 2 man/regtst.Rd | 2 man/summary.regtst.Rd | 2 src/lmomRFA-lmom.f | 293 ++++++++++++++++++++++++++---------------------- src/lmomRFA.f | 16 +- 15 files changed, 212 insertions(+), 170 deletions(-)
Title: L-Moments
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples; parameter
estimation; L-moment ratio diagram; plot vs. quantiles of an
extreme-value distribution.
Author: J. R. M. Hosking [aut, cre]
Maintainer: J. R. M. Hosking <jrmhosking@gmail.com>
Diff between lmom versions 3.0 dated 2023-08-29 and 3.2 dated 2024-09-30
DESCRIPTION | 14 + MD5 | 30 +-- NEWS | 28 +++ R/lmom.r | 51 +++-- inst/lmom-manual.pdf |binary man/lmom-package.Rd | 2 man/lmrd.Rd | 12 - man/lmrp.Rd | 10 - man/pel-functions.Rd | 5 src/dqagie.f | 4 src/dqagse.f | 2 src/dqelg.f | 2 src/dqk15i.f | 10 - src/dqk21.f | 6 src/lmoments.f | 445 +++++++++++++++++++++++++++------------------------ src/samlm.f | 2 16 files changed, 351 insertions(+), 272 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals, inspired by
Python's Literal String Interpolation
<https://www.python.org/dev/peps/pep-0498/> and Docstrings
<https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted
String Literals
<https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.
Author: Jim Hester [aut] ,
Jennifer Bryan [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between glue versions 1.7.0 dated 2024-01-09 and 1.8.0 dated 2024-09-30
glue-1.7.0/glue/R/compat-s3-register.R |only glue-1.7.0/glue/man/glue-deprecated.Rd |only glue-1.8.0/glue/DESCRIPTION | 10 glue-1.8.0/glue/MD5 | 52 ++--- glue-1.8.0/glue/NAMESPACE | 8 glue-1.8.0/glue/NEWS.md | 26 ++ glue-1.8.0/glue/R/glue-package.R |only glue-1.8.0/glue/R/glue.R | 37 +-- glue-1.8.0/glue/R/sql.R | 14 - glue-1.8.0/glue/R/utils.R | 4 glue-1.8.0/glue/R/vctrs.R | 9 glue-1.8.0/glue/R/zzz.R | 10 glue-1.8.0/glue/README.md | 297 ++++++++--------------------- glue-1.8.0/glue/build/vignette.rds |binary glue-1.8.0/glue/inst/doc/engines.Rmd | 4 glue-1.8.0/glue/inst/doc/engines.html | 8 glue-1.8.0/glue/inst/doc/glue.R |only glue-1.8.0/glue/inst/doc/glue.Rmd |only glue-1.8.0/glue/inst/doc/glue.html |only glue-1.8.0/glue/inst/doc/transformers.html | 4 glue-1.8.0/glue/inst/doc/wrappers.R |only glue-1.8.0/glue/inst/doc/wrappers.Rmd |only glue-1.8.0/glue/inst/doc/wrappers.html |only glue-1.8.0/glue/man/glue-package.Rd |only glue-1.8.0/glue/man/glue.Rd | 5 glue-1.8.0/glue/man/glue_col.Rd | 3 glue-1.8.0/glue/man/glue_safe.Rd | 3 glue-1.8.0/glue/man/glue_sql.Rd | 8 glue-1.8.0/glue/tests/testthat/test-glue.R | 4 glue-1.8.0/glue/tests/testthat/test-sql.R | 8 glue-1.8.0/glue/vignettes/engines.Rmd | 4 glue-1.8.0/glue/vignettes/glue.Rmd |only glue-1.8.0/glue/vignettes/wrappers.Rmd |only 33 files changed, 203 insertions(+), 315 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get star [...truncated...]
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
Rider Johnson [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 16.2 dated 2024-06-27 and 16.3 dated 2024-09-30
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/bubblePlot.R | 7 +++++-- R/describe.R | 14 ++++++++++---- man/quilt.plot.Rd | 15 ++++++++------- man/sim.Krig.Rd | 2 +- man/xline.Rd | 2 +- 7 files changed, 36 insertions(+), 26 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included. (Pokotylo, Mozharovskyi and Dyckerhoff, 2019 <doi:10.18637/jss.v091.i05>).
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut],
Stanislav Nagy [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.3.15 dated 2024-01-12 and 1.3.16 dated 2024-09-30
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- man/ddalpha-package.Rd | 4 ++-- man/ddalpha.train.Rd | 8 ++++---- man/depth.L2.Rd | 4 ++-- man/depth.Mahalanobis.Rd | 4 ++-- man/depth.betaSkeleton.Rd | 4 ++-- man/depth.potential.Rd | 2 +- man/depth.simplicialVolume.Rd | 4 ++-- man/depth.space.Mahalanobis.Rd | 4 ++-- man/depth.space.potential.Rd | 2 +- man/depth.space.simplicialVolume.Rd | 4 ++-- man/depth.space.spatial.Rd | 4 ++-- man/depth.spatial.Rd | 4 ++-- src/depth.fd.f | 13 ------------- 15 files changed, 42 insertions(+), 55 deletions(-)
Title: Power Calculation for Stepped Wedge Cluster Randomized Trials
Description: To meet the needs of statistical power calculation for stepped wedge cluster randomized trials, we developed this software. Different parameters can be specified by users for different scenarios, including: cross-sectional and cohort designs, binary and continuous outcomes, marginal (GEE) and conditional models (mixed effects model), three link functions (identity, log, logit links), with and without time effects (the default specification assumes no-time-effect) under exchangeable, nested exchangeable and block exchangeable correlation structures. Unequal numbers of clusters per sequence are also allowed. The methods included in this package: Zhou et al. (2020) <doi:10.1093/biostatistics/kxy031>, Li et al. (2018) <doi:10.1111/biom.12918>. Supplementary documents can be found at: <https://ysph.yale.edu/cmips/research/software/study-design-power-calculation/swdpwr/>. The Shiny app for swdpwr can be accessed at: <https://jiachenchen322.shinyapps.io/swdpwr_shinyapp/&g [...truncated...]
Author: Jiachen Chen [cre, aut],
Xin Zhou [aut],
Fan Li [aut],
Donna Spiegelman. [aut]
Maintainer: Jiachen Chen <jiachen.chen322@gmail.com>
Diff between swdpwr versions 1.9 dated 2023-09-28 and 1.10 dated 2024-09-30
DESCRIPTION | 30 +++++++++++++++++++++++------- MD5 | 8 ++++---- R/swdpower.R | 11 +++++++++-- man/swdpower.Rd | 11 +++++++++-- man/swdpwr-package.Rd | 2 +- 5 files changed, 46 insertions(+), 16 deletions(-)
Title: Dynamic OpenAPI/Swagger Client
Description: Access services specified in OpenAPI (formerly Swagger) format.
It is not a code generator. Client is generated dynamically as a list of R
functions.
Author: Darko Bergant [aut],
Marcel Ramos [cre, ctb] ,
Alexandru Mahmoud [ctb],
Sean Davis [ctb],
Martin Morgan [ctb]
Maintainer: Marcel Ramos <marcel.ramos@sph.cuny.edu>
Diff between rapiclient versions 0.1.6 dated 2024-08-21 and 0.1.8 dated 2024-09-30
DESCRIPTION | 8 +-- MD5 | 18 ++++---- NEWS.md | 20 +++++++++ R/operations.R | 64 +++++++++++++++++++---------- inst/extdata/sample_specs/petstore.json | 2 man/get_api.Rd | 8 ++- man/rapiclient-package.Rd | 2 tests/testthat/test_external_api.R | 18 ++------ tests/testthat/test_operations.R | 70 +++++++++++++++++++++++++++++--- tests/testthat/test_utilities.R | 4 + 10 files changed, 158 insertions(+), 56 deletions(-)
Title: Complementary Package to 'nicheROVER' and 'SIBER'
Description: Provides functions complementary to packages 'nicheROVER' and 'SIBER'
allowing the user to extract Bayesian estimates from data objects created
by the packages 'nicheROVER' and 'SIBER'. Please see the following
publications for detailed methods on 'nicheROVER' and 'SIBER'
Hansen et al. (2015) <doi:10.1890/14-0235.1>,
Jackson et al. (2011) <doi:10.1111/j.1365-2656.2011.01806.x>, and
Layman et al. (2007) <doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2>,
respectfully.
Author: Benjamin L. Hlina [aut, cre]
Maintainer: Benjamin L. Hlina <benjamin.hlina@gmail.com>
Diff between nichetools versions 0.3.1 dated 2024-09-06 and 0.3.2 dated 2024-09-30
DESCRIPTION | 6 MD5 | 56 +-- R/data.R | 2 R/extract_layman.R | 9 R/extract_mu.R | 99 +++++-- R/extract_overlap.R | 3 R/extract_sigma.R | 142 +++++++--- R/extract_similarities.R | 4 R/zzz.R | 3 data/post_sam_siber.rda |binary inst/doc/using-nichetools-with-the-package-SIBER.R | 14 inst/doc/using-nichetools-with-the-package-SIBER.Rmd | 16 - inst/doc/using-nichetools-with-the-package-SIBER.html | 27 - inst/doc/using-nichetools-with-the-package-nicheROVER.R | 56 +-- inst/doc/using-nichetools-with-the-package-nicheROVER.Rmd | 68 ++-- inst/doc/using-nichetools-with-the-package-nicheROVER.html | 109 +++---- man/extract_layman.Rd | 9 man/extract_mu.Rd | 49 ++- man/extract_sigma.Rd | 12 man/extract_similarities.Rd | 4 man/post_sam_siber.Rd | 2 tests/testthat/test-extract_laymans.R | 23 + tests/testthat/test-extract_mu.R | 148 +++++++++- tests/testthat/test-extract_niche_size.R | 103 +++++-- tests/testthat/test-extract_overlap.R | 7 tests/testthat/test-extract_sigma.R | 183 +++++++++++-- tests/testthat/test-extract_similarities.R | 46 +-- vignettes/using-nichetools-with-the-package-SIBER.Rmd | 16 - vignettes/using-nichetools-with-the-package-nicheROVER.Rmd | 68 ++-- 29 files changed, 871 insertions(+), 413 deletions(-)
Title: A 'shiny' Application for the (Audio-)Visualization of Adverse
Event Profiles
Description: Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Author: Nicole Rethemeier [aut],
Christoph Tasto [aut],
Steffen Jeske [aut],
Bodo Kirsch [cre]
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Diff between adepro versions 4.1.0 dated 2024-04-25 and 4.1.2 dated 2024-09-30
adepro-4.1.0/adepro/inst/app |only adepro-4.1.2/adepro/DESCRIPTION | 26 ++++++++++++++++++++----- adepro-4.1.2/adepro/MD5 | 32 +++++++++++++------------------ adepro-4.1.2/adepro/R/adae.R | 2 - adepro-4.1.2/adepro/R/adsl.R | 2 - adepro-4.1.2/adepro/R/launch_adepro.R | 10 ++++----- adepro-4.1.2/adepro/R/my.symbols.R | 1 adepro-4.1.2/adepro/R/server.R |only adepro-4.1.2/adepro/R/ui.R |only adepro-4.1.2/adepro/README.md | 12 +++++------ adepro-4.1.2/adepro/inst/doc/adepro.html | 4 +-- adepro-4.1.2/adepro/man/adae_data.Rd | 2 - adepro-4.1.2/adepro/man/adsl.Rd | 2 - adepro-4.1.2/adepro/man/my.symbols.Rd | 1 adepro-4.1.2/adepro/man/server.Rd |only adepro-4.1.2/adepro/man/ui.Rd |only 16 files changed, 54 insertions(+), 40 deletions(-)
Title: Classification with Matrix Variate Normal and t Distributions
Description: Provides sampling and density functions for matrix
variate normal, t, and inverted t distributions; ML estimation for matrix
variate normal and t distributions using the EM algorithm,
including some restrictions on the parameters; and classification by linear and
quadratic discriminant analysis for matrix variate normal and t
distributions described in Thompson et al. (2019) <doi:10.1080/10618600.2019.1696208>.
Performs clustering with matrix variate normal and t mixture models.
Author: Geoffrey Thompson [aut, cre] ,
B. D. Ripley [ctb, cph] ,
W. N. Venables [ctb, cph]
Maintainer: Geoffrey Thompson <gzthompson@gmail.com>
Diff between MixMatrix versions 0.2.6 dated 2021-11-16 and 0.2.8 dated 2024-09-30
MixMatrix-0.2.6/MixMatrix/man/MixMatrix.Rd |only MixMatrix-0.2.8/MixMatrix/DESCRIPTION | 24 MixMatrix-0.2.8/MixMatrix/MD5 | 52 MixMatrix-0.2.8/MixMatrix/NAMESPACE | 1 MixMatrix-0.2.8/MixMatrix/NEWS.md | 6 MixMatrix-0.2.8/MixMatrix/R/MixMatrix.R | 7 MixMatrix-0.2.8/MixMatrix/R/matrixnorm.R | 2 MixMatrix-0.2.8/MixMatrix/R/mixnorm.R | 2 MixMatrix-0.2.8/MixMatrix/R/mlmatrixt.R | 2 MixMatrix-0.2.8/MixMatrix/README.md | 54 MixMatrix-0.2.8/MixMatrix/build/partial.rdb |binary MixMatrix-0.2.8/MixMatrix/build/vignette.rds |binary MixMatrix-0.2.8/MixMatrix/inst/doc/discriminant-analysis.R | 2 MixMatrix-0.2.8/MixMatrix/inst/doc/discriminant-analysis.html | 794 ++++---- MixMatrix-0.2.8/MixMatrix/inst/doc/matrix-t-estimation.R | 2 MixMatrix-0.2.8/MixMatrix/inst/doc/matrix-t-estimation.html | 898 +++++---- MixMatrix-0.2.8/MixMatrix/inst/doc/matrixnormal.R | 2 MixMatrix-0.2.8/MixMatrix/inst/doc/matrixnormal.html | 912 +++++----- MixMatrix-0.2.8/MixMatrix/inst/doc/mixturemodel.R | 2 MixMatrix-0.2.8/MixMatrix/inst/doc/mixturemodel.html | 620 +++--- MixMatrix-0.2.8/MixMatrix/man/MLmatrixnorm.Rd | 6 MixMatrix-0.2.8/MixMatrix/man/MLmatrixt.Rd | 10 MixMatrix-0.2.8/MixMatrix/man/MixMatrix-package.Rd |only MixMatrix-0.2.8/MixMatrix/man/matrixlda.Rd | 4 MixMatrix-0.2.8/MixMatrix/man/matrixmixture.Rd | 4 MixMatrix-0.2.8/MixMatrix/man/matrixqda.Rd | 10 MixMatrix-0.2.8/MixMatrix/src/Makevars | 1 MixMatrix-0.2.8/MixMatrix/src/Makevars.win | 1 28 files changed, 1928 insertions(+), 1490 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute effect sizes and statistical tests if needed.
Author: Dan Chaltiel [aut, cre] ,
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.7.0 dated 2023-11-12 and 0.8.0 dated 2024-09-30
crosstable-0.7.0/crosstable/inst/doc/crosstable-install.Rmd |only crosstable-0.7.0/crosstable/inst/doc/crosstable-install.html |only crosstable-0.7.0/crosstable/vignettes/crosstable-install.Rmd |only crosstable-0.8.0/crosstable/DESCRIPTION | 8 crosstable-0.8.0/crosstable/MD5 | 113 +-- crosstable-0.8.0/crosstable/NAMESPACE | 8 crosstable-0.8.0/crosstable/NEWS.md | 27 crosstable-0.8.0/crosstable/R/compact.R | 2 crosstable-0.8.0/crosstable/R/cross_by.R | 9 crosstable-0.8.0/crosstable/R/cross_categorical.R | 57 + crosstable-0.8.0/crosstable/R/cross_numeric.R | 1 crosstable-0.8.0/crosstable/R/cross_survival.R | 5 crosstable-0.8.0/crosstable/R/crosstable.R | 53 - crosstable-0.8.0/crosstable/R/flextable.R | 79 +- crosstable-0.8.0/crosstable/R/labels.R | 8 crosstable-0.8.0/crosstable/R/officer.R | 85 +- crosstable-0.8.0/crosstable/R/options.R | 85 ++ crosstable-0.8.0/crosstable/R/pivot.R | 61 +- crosstable-0.8.0/crosstable/R/utils.R | 93 ++- crosstable-0.8.0/crosstable/build/vignette.rds |binary crosstable-0.8.0/crosstable/inst/doc/crosstable-report.R | 5 crosstable-0.8.0/crosstable/inst/doc/crosstable-report.Rmd | 103 --- crosstable-0.8.0/crosstable/inst/doc/crosstable-report.html | 166 ++--- crosstable-0.8.0/crosstable/inst/doc/crosstable-selection.R | 4 crosstable-0.8.0/crosstable/inst/doc/crosstable-selection.html | 34 - crosstable-0.8.0/crosstable/inst/doc/crosstable.R | 2 crosstable-0.8.0/crosstable/inst/doc/crosstable.html | 28 crosstable-0.8.0/crosstable/inst/doc/percent_pattern.R | 4 crosstable-0.8.0/crosstable/inst/doc/percent_pattern.html | 14 crosstable-0.8.0/crosstable/man/as_flextable.Rd | 194 +++--- crosstable-0.8.0/crosstable/man/body_add_gg2.Rd | 110 +-- crosstable-0.8.0/crosstable/man/body_add_legend.Rd | 4 crosstable-0.8.0/crosstable/man/body_add_normal.Rd | 198 +++--- crosstable-0.8.0/crosstable/man/body_add_table_list.Rd | 2 crosstable-0.8.0/crosstable/man/body_add_table_section.Rd | 2 crosstable-0.8.0/crosstable/man/body_add_title.Rd | 3 crosstable-0.8.0/crosstable/man/body_replace_text_at_bkms.Rd | 4 crosstable-0.8.0/crosstable/man/crosstable-package.Rd | 1 crosstable-0.8.0/crosstable/man/crosstable.Rd | 295 +++++----- crosstable-0.8.0/crosstable/man/crosstable_options.Rd | 42 + crosstable-0.8.0/crosstable/man/ct_compact.Rd | 2 crosstable-0.8.0/crosstable/man/generate_autofit_macro.Rd | 59 +- crosstable-0.8.0/crosstable/man/get_label.Rd | 98 +-- crosstable-0.8.0/crosstable/man/get_percent_pattern.Rd | 5 crosstable-0.8.0/crosstable/man/transpose_crosstable.Rd | 5 crosstable-0.8.0/crosstable/tests/testthat/_snaps/by_factor.md | 23 crosstable-0.8.0/crosstable/tests/testthat/_snaps/effects_snap.md | 48 - crosstable-0.8.0/crosstable/tests/testthat/_snaps/flextable.md | 181 +++--- crosstable-0.8.0/crosstable/tests/testthat/_snaps/methods.md | 6 crosstable-0.8.0/crosstable/tests/testthat/_snaps/options.md | 71 +- crosstable-0.8.0/crosstable/tests/testthat/_snaps/quick_surv.md |only crosstable-0.8.0/crosstable/tests/testthat/helper-init_dataset.R | 7 crosstable-0.8.0/crosstable/tests/testthat/test-by_factor.R | 46 + crosstable-0.8.0/crosstable/tests/testthat/test-crosstable.R | 31 - crosstable-0.8.0/crosstable/tests/testthat/test-flextable.R | 19 crosstable-0.8.0/crosstable/tests/testthat/test-methods.R | 3 crosstable-0.8.0/crosstable/tests/testthat/test-options.R | 35 + crosstable-0.8.0/crosstable/tests/testthat/test-quick_surv.R |only crosstable-0.8.0/crosstable/tests/testthat/test-tests.R | 2 crosstable-0.8.0/crosstable/vignettes/crosstable-report.Rmd | 103 --- 60 files changed, 1427 insertions(+), 1226 deletions(-)
Title: Heart Rate Variability Analysis of ECG Data
Description: Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis. See Garcia et al. (2017) <DOI:10.1007/978-3-319-65355-6>.
Author: Leandro Rodriguez-Linares [aut, cre],
Xose Vila [aut],
Maria Jose Lado [aut],
Arturo Mendez [aut],
Abraham Otero [aut],
Constantino Antonio Garcia [aut],
Matti Lassila [ctb]
Maintainer: Leandro Rodriguez-Linares <leandro@uvigo.es>
Diff between RHRV versions 4.2.7 dated 2022-10-31 and 5.0.0 dated 2024-09-30
DESCRIPTION | 15 MD5 | 84 ++-- NAMESPACE | 42 +- R/RHRVEasy.R |only R/Utils.R | 121 ++++++- R/easyFreqAnalysis.R |only R/easyNonlinearAnalysis.R |only R/easyScalingRegionEstimation.R |only R/easyStatsFunctions.R |only R/easyTimeAnalysis.R |only R/zzz.R |only build/vignette.rds |binary inst/doc/RHRV-quickstart.html | 636 ++++++++++++++++++++++++------------- inst/doc/RHRVEasy.R |only inst/doc/RHRVEasy.Rmd |only inst/doc/RHRVEasy.html |only man/AnalyzePowerBandsByEpisodes.Rd | 12 man/BuildTakens.Rd | 1 man/CalculateCorrDim.Rd | 34 + man/CalculateDFA.Rd | 23 - man/CalculateEmbeddingDim.Rd | 15 man/CalculateEnergyInPSDBands.Rd | 17 man/CalculateInfDim.Rd | 37 +- man/CalculateMaxLyapunov.Rd | 32 + man/CalculatePSD.Rd | 10 man/CalculateSampleEntropy.Rd | 23 - man/CalculateTimeLag.Rd | 11 man/EstimatePSDSlope.Rd | 17 man/ExtractTimeSegment.Rd | 1 man/LoadBeatVector.Rd | 4 man/NonlinearityTests.Rd | 7 man/OverplotEpisodes.Rd | 18 - man/PlotHR.Rd | 24 - man/PlotNIHR.Rd | 24 - man/PlotPSD.Rd | 33 + man/PlotPowerBand.Rd | 24 - man/PlotSinglePowerBand.Rd | 28 + man/PlotSpectrogram.Rd | 38 +- man/PoincarePlot.Rd | 23 - man/RHRV-package.Rd | 8 man/RHRVEasy.Rd |only man/RHRVEasyStats.Rd |only man/RQA.Rd | 16 man/RecurrencePlot.Rd | 11 man/SaveHRVIndices.Rd |only man/SurrogateTest.Rd | 19 - man/Window.Rd | 1 man/getNormSpectralUnits.Rd | 8 man/nonLinearNoiseReduction.Rd | 9 vignettes/RHRVEasy.Rmd |only 50 files changed, 1000 insertions(+), 426 deletions(-)
Title: Cohort Generation for the OMOP Common Data Model
Description: Generate cohorts and subsets using an Observational
Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database.
Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or
SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Author: Anthony Sena [aut, cre],
Jamie Gilbert [aut],
Gowtham Rao [aut],
Martijn Schuemie [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <sena@ohdsi.org>
Diff between CohortGenerator versions 0.11.1 dated 2024-09-15 and 0.11.2 dated 2024-09-30
DESCRIPTION | 8 +++--- MD5 | 32 ++++++++++++------------ NEWS.md | 7 ++++- R/NegativeControlCohorts.R | 1 README.md | 1 inst/doc/CreatingCohortSubsetDefinitions.Rmd | 2 - inst/doc/CreatingCohortSubsetDefinitions.html | 4 +-- inst/doc/GeneratingCohorts.Rmd | 2 - inst/doc/GeneratingCohorts.pdf |binary inst/doc/SamplingCohorts.Rmd | 2 - inst/doc/SamplingCohorts.pdf |binary inst/sql/sql_server/CreateResultsDataModel.sql | 18 ++++++------- inst/sql/sql_server/NegativeControlOutcomes.sql | 1 man/CohortGenerator-package.Rd | 4 +-- vignettes/CreatingCohortSubsetDefinitions.Rmd | 2 - vignettes/GeneratingCohorts.Rmd | 2 - vignettes/SamplingCohorts.Rmd | 2 - 17 files changed, 48 insertions(+), 40 deletions(-)
More information about CohortGenerator at CRAN
Permanent link
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb],
Qing Yu [ctb],
Wouter van der Bijl [ctb],
Joan Maspons [ctb],
Rutger Vos [ctb],
Paul Bastide [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.6.2 dated 2020-06-22 and 2.6.5 dated 2024-09-30
DESCRIPTION | 18 +-- MD5 | 48 ++++---- NAMESPACE | 5 R/OU1d.R | 2 R/mace.R |only R/phyloglm.R | 109 ++++++++++++++---- R/phyloglmstep.R | 8 - R/phylolm.R | 208 ++++++++++++++++++++++-------------- R/phylostep.R | 26 ++++ R/rTrait.R | 186 ++++++++++++++++---------------- R/tools.R | 6 - README.md | 7 - inst/CITATION | 25 ++-- man/mace.Rd |only man/phyloglm-methods.Rd | 2 man/phyloglm.Rd | 6 - man/phyloglmstep.Rd | 2 man/phylolm-methods.Rd | 10 + man/phylolm-package.Rd | 6 - man/phylolm.Rd | 17 +- man/phylostep.Rd | 3 man/rTrait.Rd | 102 ++++++++--------- man/three.point.compute.Rd | 127 +++++++++++---------- src/Makevars | 2 tests/testthat/testErrors.R |only tests/testthat/testMethods.R |only tests/testthat/testREML.R |only tests/testthat/testStartingBounds.R |only 28 files changed, 542 insertions(+), 383 deletions(-)
Title: Functions and Datasets for the Data Science Course at IBAW
Description: A collection of useful functions and datasets for the Data Science
Course at IBAW.
Author: Stefan Lanz [aut, cre]
Maintainer: Stefan Lanz <slanz1137@gmail.com>
Diff between ibawds versions 0.6.0 dated 2024-03-08 and 1.0.0 dated 2024-09-30
DESCRIPTION | 24 ++- MD5 | 42 +++--- NAMESPACE | 1 R/cran_packages.R | 14 -- R/data.R | 6 R/find_similar_colour.R | 32 ++-- R/grading_tables.R | 4 R/install.R | 252 ++++++++++++++++++++++++++++++++++-- R/rescale.R | 9 - R/voronoi.R | 38 +++-- README.md | 27 +++ build/partial.rdb |binary data/cran_history.rda |binary inst/WORDLIST | 2 man/check_ibawds_setup.Rd |only man/cran_history.Rd | 2 man/downgrade_packages.Rd | 26 +++ man/ibawds-package.Rd | 6 man/noisy_data.Rd | 4 tests/spelling.R |only tests/testthat/test-cran_packages.R | 2 tests/testthat/test-data.R | 12 + tests/testthat/test-install.R | 71 +++++++++- 23 files changed, 468 insertions(+), 106 deletions(-)
Title: Advanced Factor Manipulation Utilities
Description: Provides a collection of utility functions for manipulating and analyzing factor vectors in R. It offers tools for filtering, splitting, combining, and reordering factor levels based on various criteria. The package is designed to simplify common tasks in categorical data analysis, making it easier to work with factors in a flexible and efficient manner.
Author: Kai Guo [aut, cre]
Maintainer: Kai Guo <guokai8@gmail.com>
Diff between fctutils versions 0.0.6 dated 2024-09-24 and 0.0.7 dated 2024-09-30
fctutils-0.0.6/fctutils/man/fct_apply.Rd |only fctutils-0.0.6/fctutils/man/fct_char_freq.Rd |only fctutils-0.0.6/fctutils/man/fct_collapse_lev.Rd |only fctutils-0.0.6/fctutils/man/fct_combine.Rd |only fctutils-0.0.6/fctutils/man/fct_concat.Rd |only fctutils-0.0.6/fctutils/man/fct_count.Rd |only fctutils-0.0.6/fctutils/man/fct_decode.Rd |only fctutils-0.0.6/fctutils/man/fct_dummy.Rd |only fctutils-0.0.6/fctutils/man/fct_duplicates.Rd |only fctutils-0.0.6/fctutils/man/fct_encode.Rd |only fctutils-0.0.6/fctutils/man/fct_extract.Rd |only fctutils-0.0.6/fctutils/man/fct_factorize.Rd |only fctutils-0.0.6/fctutils/man/fct_filter_freq.Rd |only fctutils-0.0.6/fctutils/man/fct_filter_func.Rd |only fctutils-0.0.6/fctutils/man/fct_filter_pos.Rd |only fctutils-0.0.6/fctutils/man/fct_freq.Rd |only fctutils-0.0.6/fctutils/man/fct_group_by_prefix.Rd |only fctutils-0.0.6/fctutils/man/fct_impute.Rd |only fctutils-0.0.6/fctutils/man/fct_insert.Rd |only fctutils-0.0.6/fctutils/man/fct_intersect.Rd |only fctutils-0.0.6/fctutils/man/fct_len.Rd |only fctutils-0.0.6/fctutils/man/fct_level_lengths.Rd |only fctutils-0.0.6/fctutils/man/fct_level_order.Rd |only fctutils-0.0.6/fctutils/man/fct_level_stats.Rd |only fctutils-0.0.6/fctutils/man/fct_map_func.Rd |only fctutils-0.0.6/fctutils/man/fct_mapping.Rd |only fctutils-0.0.6/fctutils/man/fct_merge.Rd |only fctutils-0.0.6/fctutils/man/fct_merge_similar.Rd |only fctutils-0.0.6/fctutils/man/fct_na.Rd |only fctutils-0.0.6/fctutils/man/fct_pad_levels.Rd |only fctutils-0.0.6/fctutils/man/fct_pattern_replace.Rd |only fctutils-0.0.6/fctutils/man/fct_pos.Rd |only fctutils-0.0.6/fctutils/man/fct_regex_freq.Rd |only fctutils-0.0.6/fctutils/man/fct_remove_levels.Rd |only fctutils-0.0.6/fctutils/man/fct_rename_levels.Rd |only fctutils-0.0.6/fctutils/man/fct_reorder_within.Rd |only fctutils-0.0.6/fctutils/man/fct_replace.Rd |only fctutils-0.0.6/fctutils/man/fct_replace_na.Rd |only fctutils-0.0.6/fctutils/man/fct_replace_pattern.Rd |only fctutils-0.0.6/fctutils/man/fct_reverse.Rd |only fctutils-0.0.6/fctutils/man/fct_rollup.Rd |only fctutils-0.0.6/fctutils/man/fct_sample_levels.Rd |only fctutils-0.0.6/fctutils/man/fct_sort.Rd |only fctutils-0.0.6/fctutils/man/fct_sort_custom.Rd |only fctutils-0.0.6/fctutils/man/fct_split.Rd |only fctutils-0.0.6/fctutils/man/fct_split_levels.Rd |only fctutils-0.0.6/fctutils/man/fct_sub.Rd |only fctutils-0.0.6/fctutils/man/fct_substr_freq.Rd |only fctutils-0.0.6/fctutils/man/fct_table.Rd |only fctutils-0.0.6/fctutils/man/fct_union.Rd |only fctutils-0.0.6/fctutils/man/fct_unique_comb.Rd |only fctutils-0.0.7/fctutils/DESCRIPTION | 6 fctutils-0.0.7/fctutils/MD5 | 130 +++++++-------- fctutils-0.0.7/fctutils/NAMESPACE | 103 ++++++------ fctutils-0.0.7/fctutils/R/fct_comp.R |only fctutils-0.0.7/fctutils/R/fct_misc.R | 146 +++++++---------- fctutils-0.0.7/fctutils/R/single_fct.R | 74 ++++---- fctutils-0.0.7/fctutils/R/single_filter.R | 20 +- fctutils-0.0.7/fctutils/R/single_insert.R | 14 - fctutils-0.0.7/fctutils/R/single_replace.R | 31 ++- fctutils-0.0.7/fctutils/R/single_split.R | 10 - fctutils-0.0.7/fctutils/R/two_fct.R | 36 ++-- fctutils-0.0.7/fctutils/inst/doc/fctutils.R | 94 +++++------ fctutils-0.0.7/fctutils/inst/doc/fctutils.Rmd | 170 ++++++++++---------- fctutils-0.0.7/fctutils/inst/doc/fctutils.html | 176 ++++++++++----------- fctutils-0.0.7/fctutils/man/ft_apply.Rd |only fctutils-0.0.7/fctutils/man/ft_char_freq.Rd |only fctutils-0.0.7/fctutils/man/ft_collapse_lev.Rd |only fctutils-0.0.7/fctutils/man/ft_combine.Rd |only fctutils-0.0.7/fctutils/man/ft_concat.Rd |only fctutils-0.0.7/fctutils/man/ft_count.Rd |only fctutils-0.0.7/fctutils/man/ft_decode.Rd |only fctutils-0.0.7/fctutils/man/ft_dummy.Rd |only fctutils-0.0.7/fctutils/man/ft_duplicates.Rd |only fctutils-0.0.7/fctutils/man/ft_encode.Rd |only fctutils-0.0.7/fctutils/man/ft_extract.Rd |only fctutils-0.0.7/fctutils/man/ft_factorize.Rd |only fctutils-0.0.7/fctutils/man/ft_filter_freq.Rd |only fctutils-0.0.7/fctutils/man/ft_filter_func.Rd |only fctutils-0.0.7/fctutils/man/ft_filter_pos.Rd |only fctutils-0.0.7/fctutils/man/ft_freq.Rd |only fctutils-0.0.7/fctutils/man/ft_group_by_prefix.Rd |only fctutils-0.0.7/fctutils/man/ft_impute.Rd |only fctutils-0.0.7/fctutils/man/ft_insert.Rd |only fctutils-0.0.7/fctutils/man/ft_intersect.Rd |only fctutils-0.0.7/fctutils/man/ft_len.Rd |only fctutils-0.0.7/fctutils/man/ft_level_lengths.Rd |only fctutils-0.0.7/fctutils/man/ft_level_order.Rd |only fctutils-0.0.7/fctutils/man/ft_level_stats.Rd |only fctutils-0.0.7/fctutils/man/ft_map_func.Rd |only fctutils-0.0.7/fctutils/man/ft_mapping.Rd |only fctutils-0.0.7/fctutils/man/ft_merge.Rd |only fctutils-0.0.7/fctutils/man/ft_merge_similar.Rd |only fctutils-0.0.7/fctutils/man/ft_na.Rd |only fctutils-0.0.7/fctutils/man/ft_pad_levels.Rd |only fctutils-0.0.7/fctutils/man/ft_pairs.Rd |only fctutils-0.0.7/fctutils/man/ft_pattern_replace.Rd |only fctutils-0.0.7/fctutils/man/ft_pos.Rd |only fctutils-0.0.7/fctutils/man/ft_regex_freq.Rd |only fctutils-0.0.7/fctutils/man/ft_remove_levels.Rd |only fctutils-0.0.7/fctutils/man/ft_rename_levels.Rd |only fctutils-0.0.7/fctutils/man/ft_reorder_within.Rd |only fctutils-0.0.7/fctutils/man/ft_replace.Rd |only fctutils-0.0.7/fctutils/man/ft_replace_na.Rd |only fctutils-0.0.7/fctutils/man/ft_replace_pattern.Rd |only fctutils-0.0.7/fctutils/man/ft_reverse.Rd |only fctutils-0.0.7/fctutils/man/ft_rollup.Rd |only fctutils-0.0.7/fctutils/man/ft_sample_levels.Rd |only fctutils-0.0.7/fctutils/man/ft_sort.Rd |only fctutils-0.0.7/fctutils/man/ft_sort_custom.Rd |only fctutils-0.0.7/fctutils/man/ft_split.Rd |only fctutils-0.0.7/fctutils/man/ft_split_levels.Rd |only fctutils-0.0.7/fctutils/man/ft_sub.Rd |only fctutils-0.0.7/fctutils/man/ft_substr_freq.Rd |only fctutils-0.0.7/fctutils/man/ft_table.Rd |only fctutils-0.0.7/fctutils/man/ft_union.Rd |only fctutils-0.0.7/fctutils/man/ft_unique_comb.Rd |only fctutils-0.0.7/fctutils/vignettes/fctutils.Rmd | 170 ++++++++++---------- 118 files changed, 591 insertions(+), 589 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-09 0.4.0
2019-03-11 0.3.7
2019-03-07 0.3.6
2018-07-08 0.3.4
2018-02-19 0.3.2
Title: Supporting Functions Maintained by Zhen Lu
Description: Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.
Author: Zhen Lu [aut, cre]
Maintainer: Zhen Lu <luzh29@mail2.sysu.edu.cn>
Diff between lulab.utils versions 0.0.2 dated 2024-09-10 and 0.0.3 dated 2024-09-30
DESCRIPTION | 6 - MD5 | 10 +- NAMESPACE | 1 NEWS.md | 17 ++-- R/utilities.R | 147 +++++++++++++++++++++++++++----------- man/test_mirror.Rd |only tests/testthat/test-test_mirror.R |only 7 files changed, 126 insertions(+), 55 deletions(-)
Title: Machine Learning Model Explainer
Description: It enables detailed interpretation of complex classification and regression models through Shapley analysis including data-driven characterization of subgroups of individuals. Furthermore, it facilitates multi-measure model evaluation, model fairness, and decision curve analysis. Additionally, it offers enhanced visualizations with interactive elements.
Author: Ramtin Zargari Marandi [aut, cre]
Maintainer: Ramtin Zargari Marandi <ramtin.zargari.marandi@regionh.dk>
Diff between explainer versions 1.0.1 dated 2024-04-18 and 1.0.2 dated 2024-09-30
DESCRIPTION | 11 MD5 | 49 ++- NAMESPACE | 7 R/SHAPclust.R | 530 +++++++++++++++++++-------------------- R/ShapFeaturePlot.R | 164 ++++++------ R/eCM_plot.R | 248 +++++++++--------- R/eDecisionCurve.R | 304 +++++++++++----------- R/eFairness.R | 309 +++++++++++----------- R/eROC_plot.R | 297 +++++++++++---------- R/eSHAP_plot.R | 492 ++++++++++++++++++------------------ R/eSHAP_plot_multiclass.R |only R/eSHAP_plot_reg.R | 415 +++++++++++++++--------------- R/eperformance.R | 582 ++++++++++++++++++++++--------------------- R/shapPartialPlot.R | 164 ++++++------ README.md | 4 build |only inst/doc |only man/SHAPclust.Rd | 4 man/ShapFeaturePlot.Rd | 2 man/ShapPartialPlot.Rd | 2 man/eCM_plot.Rd | 2 man/eDecisionCurve.Rd | 2 man/eFairness.Rd | 2 man/eROC_plot.Rd | 2 man/eSHAP_plot.Rd | 8 man/eSHAP_plot_multiclass.Rd |only vignettes |only 27 files changed, 1846 insertions(+), 1754 deletions(-)
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, [...truncated...]
Author: Marie-Laure Delignette-Muller [aut]
,
Elise Billoir [aut] ,
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.5-2 dated 2024-01-31 and 2.6-0 dated 2024-09-30
DRomics-2.5-2/DRomics/tests/examplewithNAvalues.R |only DRomics-2.5-2/DRomics/tests/examplewithRNAseq.R |only DRomics-2.5-2/DRomics/tests/examplewithanchoringdata.R |only DRomics-2.5-2/DRomics/tests/examplewithinsitudata.R |only DRomics-2.5-2/DRomics/tests/examplewithmetabolomic.R |only DRomics-2.5-2/DRomics/tests/examplewithmicroarray.R |only DRomics-2.5-2/DRomics/tests/examplewithnoreplicate.R |only DRomics-2.5-2/DRomics/tests/testAIC.R |only DRomics-2.5-2/DRomics/tests/test_selectgroups.R |only DRomics-2.5-2/DRomics/tests/testbmdcalc.R |only DRomics-2.5-2/DRomics/tests/testbmdplotwithgradient.R |only DRomics-2.5-2/DRomics/tests/testplotfit.R |only DRomics-2.5-2/DRomics/tests/testresidualtests.R |only DRomics-2.5-2/DRomics/tests/testscaling.R |only DRomics-2.5-2/DRomics/tests/testsensitivityplot.R |only DRomics-2.5-2/DRomics/tests/testthat/test_bmdcalc.R |only DRomics-2.5-2/DRomics/tests/testthat/test_drcfit.R |only DRomics-2.5-2/DRomics/tests/testthat/test_itemselect.R |only DRomics-2.6-0/DRomics/DESCRIPTION | 10 DRomics-2.6-0/DRomics/MD5 | 132 DRomics-2.6-0/DRomics/NEWS.md | 16 DRomics-2.6-0/DRomics/R/PCAdataplot.R | 86 DRomics-2.6-0/DRomics/R/RNAseqdata.R | 155 DRomics-2.6-0/DRomics/R/bmdboot.R | 569 +- DRomics-2.6-0/DRomics/R/bmdcalc.R | 375 - DRomics-2.6-0/DRomics/R/bmdfilter.R | 66 DRomics-2.6-0/DRomics/R/bmdplot.R | 206 DRomics-2.6-0/DRomics/R/bmdplotwithgradient.R | 262 - DRomics-2.6-0/DRomics/R/continuousanchoringdata.R | 116 DRomics-2.6-0/DRomics/R/curvesplot.R | 333 - DRomics-2.6-0/DRomics/R/drcfit.R | 2073 ++++----- DRomics-2.6-0/DRomics/R/ecdfplotwithCI.R | 78 DRomics-2.6-0/DRomics/R/ecdfquantileplot.R | 18 DRomics-2.6-0/DRomics/R/formatdata4DRomics.R | 15 DRomics-2.6-0/DRomics/R/itemselect.R | 175 DRomics-2.6-0/DRomics/R/metabolomicdata.R | 97 DRomics-2.6-0/DRomics/R/microarraydata.R | 98 DRomics-2.6-0/DRomics/R/omicdata.R | 10 DRomics-2.6-0/DRomics/R/onAttach.R | 22 DRomics-2.6-0/DRomics/R/selectgroups.R | 81 DRomics-2.6-0/DRomics/R/sensitivityplot.R | 149 DRomics-2.6-0/DRomics/R/targetplot.R | 77 DRomics-2.6-0/DRomics/R/trendplot.R | 78 DRomics-2.6-0/DRomics/R/util-basicandfitfunc.R | 261 - DRomics-2.6-0/DRomics/R/util-plotfunc.R | 127 DRomics-2.6-0/DRomics/build/partial.rdb |binary DRomics-2.6-0/DRomics/build/vignette.rds |binary DRomics-2.6-0/DRomics/inst/DRomics-shiny/install.R | 2 DRomics-2.6-0/DRomics/inst/DRomics-shiny/rinstall.txt | 2 DRomics-2.6-0/DRomics/inst/DRomics-shiny/ui.R | 6 DRomics-2.6-0/DRomics/inst/DRomicsInterpreter-shiny/install.R | 2 DRomics-2.6-0/DRomics/inst/DRomicsInterpreter-shiny/rinstall.txt | 2 DRomics-2.6-0/DRomics/inst/DRomicsInterpreter-shiny/server.R | 27 DRomics-2.6-0/DRomics/inst/DRomicsInterpreter-shiny/ui.R | 9 DRomics-2.6-0/DRomics/inst/doc/DRomics_vignette.R | 150 DRomics-2.6-0/DRomics/inst/doc/DRomics_vignette.Rmd | 175 DRomics-2.6-0/DRomics/inst/doc/DRomics_vignette.html | 2152 +++------- DRomics-2.6-0/DRomics/man/PCAdataplot.Rd | 2 DRomics-2.6-0/DRomics/man/RNAseqdata.Rd | 20 DRomics-2.6-0/DRomics/man/continuousanchoringdata.Rd | 10 DRomics-2.6-0/DRomics/man/curvesplot.Rd | 68 DRomics-2.6-0/DRomics/man/drcfit.Rd | 9 DRomics-2.6-0/DRomics/man/itemselect.Rd | 14 DRomics-2.6-0/DRomics/man/metabolomicdata.Rd | 10 DRomics-2.6-0/DRomics/man/microarraydata.Rd | 16 DRomics-2.6-0/DRomics/man/targetplot.Rd | 2 DRomics-2.6-0/DRomics/tests/testthat/testAIC.R |only DRomics-2.6-0/DRomics/tests/testthat/test_windows_bmdcalc.R |only DRomics-2.6-0/DRomics/tests/testthat/test_windows_drcfit.R |only DRomics-2.6-0/DRomics/tests/testthat/test_windows_itemselect.R |only DRomics-2.6-0/DRomics/tests/testthat/testbmdcalc.R |only DRomics-2.6-0/DRomics/tests/testthat/testbmdplotwithgradient.R |only DRomics-2.6-0/DRomics/tests/testthat/testplotfit.R |only DRomics-2.6-0/DRomics/tests/testthat/testresidualtests.R |only DRomics-2.6-0/DRomics/tests/testthat/testscaling.R |only DRomics-2.6-0/DRomics/tests/testthat/testselectgroups.R |only DRomics-2.6-0/DRomics/tests/testthat/testsensitivityplot.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithNAvalues.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithRNAseq.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithanchoringdata.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithinsitudata.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithmetabolomic.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithmicroarray.R |only DRomics-2.6-0/DRomics/tests/testthat/testwithnoreplicate.R |only DRomics-2.6-0/DRomics/vignettes/DRomics_vignette.Rmd | 175 85 files changed, 3726 insertions(+), 4812 deletions(-)
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing,
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
The package is described in detail in Polzehl J, Papafitsoros K, Tabelow K (2020).
Patch-Wise Adaptive Weights Smoothing in R. Journal of Statistical Software, 95(6), 1-27.
<doi:10.18637/jss.v095.i06>,
Usage of the package in MR imaging is illustrated in Polzehl and Tabelow (2023),
Magnetic Resonance Brain Imaging, 2nd Ed. Appendix A, Springer, Use R! Series.
<doi:10.1007/978-3-031-38949-8>.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.5-5 dated 2024-02-07 and 2.5-6 dated 2024-09-30
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/partial.rdb |binary inst/doc/aws-Example.pdf |binary src/awslp.f | 8 ++++---- src/caws.f | 4 ++-- src/estimateComplexSigma.f | 2 +- src/pcaws.f | 7 ++++--- src/smooth3d.f | 4 ++-- src/smse3.f | 6 +++--- src/varest.f | 8 ++++---- 11 files changed, 34 insertions(+), 33 deletions(-)
Title: Image Registration Using the 'NiftyReg' Library
Description: Provides an 'R' interface to the 'NiftyReg' image registration tools
<https://github.com/KCL-BMEIS/niftyreg>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden [cre, aut] ,
Marc Modat [aut],
Benoit Presles [aut],
Thanasis Anthopoulos [aut],
Pankaj Daga [aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.8.3 dated 2024-06-20 and 2.8.4 dated 2024-09-30
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 15 ++++++++++++++- NEWS | 18 ++++++++++++++++++ R/affine.R | 44 ++++++++++++++++++++++++++++++++++---------- R/zzz.R | 2 +- src/AffineMatrix.cpp | 18 +++++------------- src/AffineMatrix.h | 2 +- src/reg-lib/_reg_aladin.cpp | 6 +++--- 9 files changed, 90 insertions(+), 43 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://wikis.ec.europa.eu/pages/viewpage.action?pageId=44165555>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.23.1 dated 2024-03-26 and 0.23.2 dated 2024-09-30
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 8 +++++++- R/load_cfg.R | 2 +- README.md | 2 +- inst/tinytest/test_restatapi.R | 6 +++--- 6 files changed, 22 insertions(+), 16 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization", Riviere Marie-Karelle et
al. (2016) <doi:10.1177/0962280216631763>.
Author: Marie-Karelle Riviere [aut],
Jacques-Henri Jourdan [aut, cre]
Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@cnrs.fr>
Diff between dfmta versions 1.7-3 dated 2022-05-03 and 1.7-6 dated 2024-09-30
DESCRIPTION | 20 ++++++++++++++------ MD5 | 18 +++++++++--------- build/partial.rdb |binary configure | 52 ++++++++++++++++++++++------------------------------ configure.ac | 10 +--------- man/mtaBin_next.Rd | 2 +- man/mtaBin_sim.Rd | 2 +- src/Makevars.in | 1 - src/Makevars.win | 1 - src/dfmta.cpp | 8 ++++---- 10 files changed, 52 insertions(+), 62 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies where toxicity rates are supposed to increase with both agents.
Author: Marie-Karelle Riviere [aut],
Jacques-Henri Jourdan [aut, cre]
Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@cnrs.fr>
Diff between dfcomb versions 3.1-1 dated 2023-01-07 and 3.1-4 dated 2024-09-30
DESCRIPTION | 20 ++++++++++++++------ MD5 | 6 +++--- build/partial.rdb |binary src/logistic.cpp | 10 +++++----- 4 files changed, 22 insertions(+), 14 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available. The package has a companion paper: Boeck, M., Feldkircher, M. and F. Huber (2022) "BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R", Journal of Statistical Software, Vol. 104(9), pp. 1-28 <doi:10.18 [...truncated...]
Author: Maximilian Boeck [aut, cre] ,
Martin Feldkircher [aut] ,
Florian Huber [aut] ,
Darjus Hosszejni [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@fau.de>
Diff between BGVAR versions 2.5.7 dated 2024-07-07 and 2.5.8 dated 2024-09-30
DESCRIPTION | 10 +- MD5 | 44 ++++++------ NEWS | 4 + R/BGVAR.R | 24 ++++--- R/fevd.R | 8 +- R/hd.R | 4 - R/irf.R | 4 - R/plot.R | 5 - R/predict.R | 8 ++ R/utils.R | 146 +++++++++++++++++++++---------------------- README.md | 2 inst/doc/examples.html | 166 ++++++++++++++++++++++++------------------------- man/bgvar.Rd | 8 +- man/fevd.Rd | 4 - man/gfevd.Rd | 4 - man/hd.Rd | 4 - man/irf.Rd | 4 - man/lps.Rd | 2 man/plot.Rd | 5 - man/predict.Rd | 2 man/rmse.Rd | 2 src/BVAR_linear.cpp | 88 ++++++++++++------------- src/helper.cpp | 6 - 23 files changed, 288 insertions(+), 266 deletions(-)
Title: Find Clinical Trial Sites Under-Reporting Adverse Events
Description: Monitoring of Adverse Event (AE) reporting in clinical trials is
important for patient safety. Sites that are under-reporting AEs can be detected
using Bootstrap-based simulations that simulate overall AE reporting. Based on the
simulation an AE under-reporting probability is assigned to each site in a
given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).
Author: Bjoern Koneswarakantha [aut, cre, cph]
,
F. Hoffmann-La Roche Ltd [cph]
Maintainer: Bjoern Koneswarakantha <bjoern.koneswarakantha@roche.com>
Diff between simaerep versions 0.5.0 dated 2024-04-03 and 0.6.0 dated 2024-09-30
simaerep-0.5.0/simaerep/man/eval_sites_deprecated.Rd |only simaerep-0.6.0/simaerep/DESCRIPTION | 15 simaerep-0.6.0/simaerep/MD5 | 63 - simaerep-0.6.0/simaerep/NAMESPACE | 18 simaerep-0.6.0/simaerep/NEWS.md | 7 simaerep-0.6.0/simaerep/R/0_imports.R | 6 simaerep-0.6.0/simaerep/R/S3_orivisit.R | 19 simaerep-0.6.0/simaerep/R/S3_simaerep.R | 325 +++++++- simaerep-0.6.0/simaerep/R/inframe.R |only simaerep-0.6.0/simaerep/R/simaerep.R | 399 +++++----- simaerep-0.6.0/simaerep/R/simaerep_plot.R | 132 ++- simaerep-0.6.0/simaerep/R/simulate_test_data.R | 145 +++ simaerep-0.6.0/simaerep/README.md | 103 ++ simaerep-0.6.0/simaerep/inst/WORDLIST | 21 simaerep-0.6.0/simaerep/man/eval_sites.Rd | 3 simaerep-0.6.0/simaerep/man/figures/README-unnamed-chunk-2-1.png |binary simaerep-0.6.0/simaerep/man/figures/README-unnamed-chunk-3-1.png |only simaerep-0.6.0/simaerep/man/figures/README-unnamed-chunk-4-1.png |only simaerep-0.6.0/simaerep/man/max_rank.Rd |only simaerep-0.6.0/simaerep/man/p_adjust_bh_inframe.Rd |only simaerep-0.6.0/simaerep/man/prune_to_visit_med75_inframe.Rd |only simaerep-0.6.0/simaerep/man/sim_inframe.Rd |only simaerep-0.6.0/simaerep/man/sim_ur.Rd |only simaerep-0.6.0/simaerep/man/sim_ur_scenarios.Rd | 5 simaerep-0.6.0/simaerep/man/simaerep.Rd | 95 +- simaerep-0.6.0/simaerep/man/simaerep_inframe.Rd |only simaerep-0.6.0/simaerep/tests/testthat/_snaps/S3_simaerep.md | 2 simaerep-0.6.0/simaerep/tests/testthat/_snaps/eval_sites.md | 18 simaerep-0.6.0/simaerep/tests/testthat/_snaps/validation/study-025.svg | 13 simaerep-0.6.0/simaerep/tests/testthat/_snaps/validation/study-050.svg | 15 simaerep-0.6.0/simaerep/tests/testthat/_snaps/validation/study-075.svg | 15 simaerep-0.6.0/simaerep/tests/testthat/_snaps/validation/study-100.svg | 15 simaerep-0.6.0/simaerep/tests/testthat/test_S3_simaerep.R | 84 ++ simaerep-0.6.0/simaerep/tests/testthat/test_check_df_visit.R | 2 simaerep-0.6.0/simaerep/tests/testthat/test_data.R | 111 ++ simaerep-0.6.0/simaerep/tests/testthat/test_eval_sites.R | 20 simaerep-0.6.0/simaerep/tests/testthat/test_inframe.R |only simaerep-0.6.0/simaerep/tests/testthat/test_site_aggr.R | 2 38 files changed, 1198 insertions(+), 455 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for analyses of multiple social networks are delivered with this
package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' makes
possible, among other things, to create and manipulate multiplex, multimode, and
multilevel network data with different formats. Effective ways are available to treat
multiple networks with routines that combine algebraic systems like the partially ordered
semigroup with decomposition procedures or semiring structures with the relational
bundles occurring in different types of multivariate networks. 'multiplex' provides also
an algebraic approach for affiliation networks through Galois derivations between families
of the pairs of subsets in the two domains of the network with visualization options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 3.4 dated 2024-07-30 and 3.7 dated 2024-09-30
DESCRIPTION | 8 +- MD5 | 122 +++++++++++++++++++++--------------------- R/comps.R | 15 ++++- R/diagram.levels.R | 2 R/read.gml.R | 4 - R/rel.sys.R | 7 ++ build/vignette.rds |binary inst/CHANGELOG | 11 +++ inst/doc/TwoModeNetworks.R | 43 +++++++------- inst/doc/TwoModeNetworks.Rnw | 92 +++++++++++++++++-------------- inst/doc/TwoModeNetworks.pdf |binary man/as.semigroup.Rd | 25 ++++---- man/as.signed.Rd | 10 +-- man/as.strings.Rd | 19 +++--- man/bundle.census.Rd | 30 +++++----- man/bundles.Rd | 53 ++++++++---------- man/cngr.Rd | 20 +++--- man/comps.Rd | 31 +++++----- man/cph.Rd | 26 +++----- man/decomp.Rd | 12 ++-- man/diagram.Rd | 19 +++--- man/diagram.levels.Rd | 33 ++++++----- man/dichot.Rd | 10 ++- man/edgeT.Rd | 11 +-- man/edgel.Rd | 12 ++-- man/expos.Rd | 17 ++--- man/fact.Rd | 10 +-- man/fltr.Rd | 30 +++++----- man/galois.Rd | 10 ++- man/green.rel.Rd | 14 ++-- man/hasse.Rd | 8 +- man/hierar.Rd | 27 +++------ man/incubs.Rd | 19 +++--- man/mlvl.Rd | 12 +--- man/mnplx.Rd | 11 +-- man/multiplex-package.Rd | 27 ++++----- man/neighb.Rd | 15 ++--- man/pacnet.Rd | 6 +- man/partial.order.Rd | 27 ++++----- man/perm.Rd | 10 +-- man/pfvn.Rd | 5 - man/pi.rels.Rd | 12 +--- man/prev.Rd | 5 - man/rbox.Rd | 21 +++---- man/read.dl.Rd | 11 +-- man/read.gml.Rd | 18 +++--- man/reduc.Rd | 7 -- man/rel.sys.Rd | 59 +++++++++++--------- man/rm.isol.Rd | 10 +-- man/semigroup.Rd | 16 ++--- man/semiring.Rd | 22 +++---- man/signed.Rd | 18 ++---- man/strings.Rd | 18 ++---- man/summaryBundles.Rd | 23 +++---- man/transf.Rd | 22 +++---- man/wordT.Rd | 32 +++++------ man/write.dat.Rd | 15 ++--- man/write.dl.Rd | 10 +-- man/write.edgel.Rd | 4 - man/write.gml.Rd | 2 man/zbind.Rd | 10 +-- vignettes/TwoModeNetworks.Rnw | 92 +++++++++++++++++-------------- 62 files changed, 660 insertions(+), 630 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.2.8 dated 2024-07-03 and 1.2.9 dated 2024-09-30
cmsafvis-1.2.8/cmsafvis/tests/spelling.Rout.save |only cmsafvis-1.2.9/cmsafvis/DESCRIPTION | 8 +++--- cmsafvis-1.2.9/cmsafvis/MD5 | 17 ++++++------- cmsafvis-1.2.9/cmsafvis/NEWS.md | 6 ++++ cmsafvis-1.2.9/cmsafvis/R/fieldmean_plot.R | 2 - cmsafvis-1.2.9/cmsafvis/R/plot_abs_map.R | 25 +++++++++++++++++-- cmsafvis-1.2.9/cmsafvis/R/plot_abs_map_mean.R | 27 +++++++++++++++++---- cmsafvis-1.2.9/cmsafvis/R/plot_fieldmean.R | 21 ++++++++++++++-- cmsafvis-1.2.9/cmsafvis/R/plot_fieldmean_and_map.R | 23 +++++++++++++++-- cmsafvis-1.2.9/cmsafvis/inst/WORDLIST | 1 10 files changed, 104 insertions(+), 26 deletions(-)
Title: Calculate and Visualize 'SNOTEL' Snow Data and Seasonality
Description: Programmatic interface to the 'SNOTEL' snow data
(<https://www.nrcs.usda.gov/programs-initiatives/sswsf-snow-survey-and-water-supply-forecasting-program>). Provides easy downloads of snow
data into your R work space or a local directory. Additional post-processing
routines to extract snow season indexes are provided.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between snotelr versions 1.4 dated 2024-05-23 and 1.5 dated 2024-09-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/snotel_download.r | 2 +- R/snotel_metric.r | 5 +++-- build/vignette.rds |binary inst/doc/snotelr-vignette.html | 4 ++-- tests/testthat/test_snotel_functions.r | 18 +++++++++--------- 7 files changed, 24 insertions(+), 23 deletions(-)
Title: Minimal and Uncluttered Package Documentation
Description: Generates simple and beautiful one-page HTML reference manuals
with package documentation. Math rendering and syntax highlighting are done
server-side in R such that no JavaScript libraries are needed in the
browser, which makes the documentation portable and fast to load.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between postdoc versions 1.2.2 dated 2023-10-18 and 1.4.0 dated 2024-09-30
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS | 7 +++++++ R/manual.R | 8 +++++++- inst/help-template/manual.html | 8 ++++---- 5 files changed, 29 insertions(+), 16 deletions(-)
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using
functions that handle messy data, dropouts, and other problematic cases.
Create IDs, calculate the time, transfer
variables between app data frames, and delete sensitive information.
Review your experimental data prior to running
the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code.
Information on 'oTree' is found in Chen, D. L., Schonger, M., &
Wickens, C. (2016) <doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.1.0 dated 2024-07-04 and 1.2.0 dated 2024-09-30
gmoTree-1.1.0/gmoTree/inst/extdata/exp_data_2.1.0 |only gmoTree-1.1.0/gmoTree/inst/extdata/exp_data_2.2.4 |only gmoTree-1.1.0/gmoTree/inst/extdata/exp_data_5.4.0subapp |only gmoTree-1.1.0/gmoTree/inst/extdata/exp_wrong_data |only gmoTree-1.1.0/gmoTree/inst/extdata/old_one |only gmoTree-1.2.0/gmoTree/DESCRIPTION | 49 gmoTree-1.2.0/gmoTree/MD5 | 386 + gmoTree-1.2.0/gmoTree/NAMESPACE | 6 gmoTree-1.2.0/gmoTree/NEWS.md | 12 gmoTree-1.2.0/gmoTree/R/apptime.R | 326 - gmoTree-1.2.0/gmoTree/R/assignv.R | 4 gmoTree-1.2.0/gmoTree/R/assignv_to_aaw.R | 11 gmoTree-1.2.0/gmoTree/R/codebook.R |only gmoTree-1.2.0/gmoTree/R/constant_col.R | 4 gmoTree-1.2.0/gmoTree/R/delete_cases.R | 51 gmoTree-1.2.0/gmoTree/R/delete_dropouts.R | 41 gmoTree-1.2.0/gmoTree/R/delete_duplicate.R | 7 gmoTree-1.2.0/gmoTree/R/delete_plabels.R | 10 gmoTree-1.2.0/gmoTree/R/delete_sessions.R | 67 gmoTree-1.2.0/gmoTree/R/extime.R | 185 gmoTree-1.2.0/gmoTree/R/import_otree.R | 39 gmoTree-1.2.0/gmoTree/R/make_ids.R | 49 gmoTree-1.2.0/gmoTree/R/messy_chat.R | 41 gmoTree-1.2.0/gmoTree/R/messy_time.R | 31 gmoTree-1.2.0/gmoTree/R/oTree.R | 2 gmoTree-1.2.0/gmoTree/R/pagesec.R | 40 gmoTree-1.2.0/gmoTree/R/show_constant.R | 3 gmoTree-1.2.0/gmoTree/R/show_dropouts.R | 14 gmoTree-1.2.0/gmoTree/README.md | 33 gmoTree-1.2.0/gmoTree/build/vignette.rds |binary gmoTree-1.2.0/gmoTree/inst/CITATION | 6 gmoTree-1.2.0/gmoTree/inst/WORDLIST | 3 gmoTree-1.2.0/gmoTree/inst/doc/codebook.R |only gmoTree-1.2.0/gmoTree/inst/doc/codebook.Rmd |only gmoTree-1.2.0/gmoTree/inst/doc/codebook.html |only gmoTree-1.2.0/gmoTree/inst/doc/intro_to_gmoTree.R | 7 gmoTree-1.2.0/gmoTree/inst/doc/intro_to_gmoTree.Rmd | 36 gmoTree-1.2.0/gmoTree/inst/doc/intro_to_gmoTree.html | 1022 ++-- gmoTree-1.2.0/gmoTree/inst/extdata/ocode_new |only gmoTree-1.2.0/gmoTree/inst/extdata/ocode_z |only gmoTree-1.2.0/gmoTree/inst/rmd |only gmoTree-1.2.0/gmoTree/man/apptime.Rd | 14 gmoTree-1.2.0/gmoTree/man/assignv.Rd | 4 gmoTree-1.2.0/gmoTree/man/assignv_to_aaw.Rd | 11 gmoTree-1.2.0/gmoTree/man/codebook.Rd |only gmoTree-1.2.0/gmoTree/man/delete_cases.Rd | 49 gmoTree-1.2.0/gmoTree/man/delete_dropouts.Rd | 20 gmoTree-1.2.0/gmoTree/man/delete_duplicate.Rd | 6 gmoTree-1.2.0/gmoTree/man/delete_plabels.Rd | 8 gmoTree-1.2.0/gmoTree/man/delete_sessions.Rd | 65 gmoTree-1.2.0/gmoTree/man/extime.Rd | 16 gmoTree-1.2.0/gmoTree/man/import_otree.Rd | 30 gmoTree-1.2.0/gmoTree/man/make_ids.Rd | 12 gmoTree-1.2.0/gmoTree/man/messy_chat.Rd | 16 gmoTree-1.2.0/gmoTree/man/messy_time.Rd | 14 gmoTree-1.2.0/gmoTree/man/oTree.Rd | 2 gmoTree-1.2.0/gmoTree/man/pagesec.Rd | 4 gmoTree-1.2.0/gmoTree/man/show_constant.Rd | 2 gmoTree-1.2.0/gmoTree/man/show_dropouts.Rd | 14 gmoTree-1.2.0/gmoTree/tests/testthat/testdata |only gmoTree-1.2.0/gmoTree/tests/testthat/tests.R | 3331 +++++++--------- gmoTree-1.2.0/gmoTree/tests/testthat/tests_codebook.R |only gmoTree-1.2.0/gmoTree/vignettes/app.png |only gmoTree-1.2.0/gmoTree/vignettes/codebook.Rmd |only gmoTree-1.2.0/gmoTree/vignettes/intro.png |only gmoTree-1.2.0/gmoTree/vignettes/intro_to_gmoTree.Rmd | 36 gmoTree-1.2.0/gmoTree/vignettes/structure.png |only gmoTree-1.2.0/gmoTree/vignettes/title.png |only 68 files changed, 3220 insertions(+), 2919 deletions(-)
Title: Co-Ranking Matrix
Description: Calculates the co-ranking matrix to assess the
quality of a dimensionality reduction.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <guido.kraemer@uni-leipzig.de>
Diff between coRanking versions 0.2.4 dated 2023-03-20 and 0.2.5 dated 2024-09-30
DESCRIPTION | 10 ++--- MD5 | 16 ++++----- README.md | 3 + build/vignette.rds |binary inst/doc/coranking.R | 8 ++-- inst/doc/coranking.html | 29 ++++++++-------- man/coRanking-package.Rd | 2 - src/coranking.cpp | 2 - src/coranking_main.cpp | 82 +++++++++++++++++++++++------------------------ 9 files changed, 77 insertions(+), 75 deletions(-)
Title: Individual-Based Forest Growth Simulator 'TROLL'
Description: 'TROLL' is coded in C++ and it typically simulates hundreds of
thousands of individuals over hundreds of years. The 'rcontroll' R package
is a wrapper of 'TROLL'. 'rcontroll' includes functions that generate inputs
for simulations and run simulations. Finally, it is possible to analyse
the 'TROLL' outputs through tables, figures, and maps taking advantage of
other R visualisation packages. 'rcontroll' also offers the possibility to
generate a virtual LiDAR point cloud that corresponds to a snapshot of
the simulated forest.
Author: Sylvain Schmitt [aut, cre] ,
Guillaume Salzet [aut] ,
Fabian Fischer [aut] ,
Isabelle Marechaux [aut] ,
Jerome Chave [aut]
Maintainer: Sylvain Schmitt <sylvain.m.schmitt@gmail.com>
Diff between rcontroll versions 0.1.1 dated 2023-09-07 and 0.1.2 dated 2024-09-30
rcontroll-0.1.1/rcontroll/tools |only rcontroll-0.1.2/rcontroll/DESCRIPTION | 6 - rcontroll-0.1.2/rcontroll/MD5 | 48 +++++++-------- rcontroll-0.1.2/rcontroll/NEWS.md | 8 ++ rcontroll-0.1.2/rcontroll/R/autoplot.troll.R | 3 rcontroll-0.1.2/rcontroll/R/generate_climate.R | 10 +-- rcontroll-0.1.2/rcontroll/R/rcontroll.R | 2 rcontroll-0.1.2/rcontroll/R/troll.R | 6 - rcontroll-0.1.2/rcontroll/R/update_parameters.trollsim.R | 15 ++-- rcontroll-0.1.2/rcontroll/R/zzz.R | 2 rcontroll-0.1.2/rcontroll/build/vignette.rds |binary rcontroll-0.1.2/rcontroll/inst/doc/climate.R | 40 +++++------- rcontroll-0.1.2/rcontroll/inst/doc/climate.Rmd | 17 ++--- rcontroll-0.1.2/rcontroll/inst/doc/climate.html | 25 +++---- rcontroll-0.1.2/rcontroll/inst/doc/lidar.R | 6 - rcontroll-0.1.2/rcontroll/inst/doc/lidar.html | 48 ++++++--------- rcontroll-0.1.2/rcontroll/inst/doc/troll.R | 2 rcontroll-0.1.2/rcontroll/inst/doc/troll.html | 4 - rcontroll-0.1.2/rcontroll/inst/doc/workflow.R | 6 - rcontroll-0.1.2/rcontroll/inst/doc/workflow.html | 10 --- rcontroll-0.1.2/rcontroll/inst/figures/nouragues.png |only rcontroll-0.1.2/rcontroll/man/rcontroll.Rd | 1 rcontroll-0.1.2/rcontroll/man/trollCpp.Rd | 16 ++--- rcontroll-0.1.2/rcontroll/src/Makevars.ucrt | 17 ++--- rcontroll-0.1.2/rcontroll/src/troll_rcpp.cpp | 46 ++++++++++---- rcontroll-0.1.2/rcontroll/vignettes/climate.Rmd | 17 ++--- 26 files changed, 181 insertions(+), 174 deletions(-)
Title: Power Analysis for PLS Classification
Description: It estimates power and sample size for Partial Least Squares-based methods described in Andreella, et al., (2024), <doi:10.48550/arXiv.2403.10289>.
Author: Angela Andreella [aut, cre]
Maintainer: Angela Andreella <angela.andreella@unive.it>
Diff between powerPLS versions 0.1.0 dated 2024-03-21 and 0.2.0 dated 2024-09-30
powerPLS-0.1.0/powerPLS/R/umor_acqueo.R |only powerPLS-0.1.0/powerPLS/data/umor_acqueo.rda |only powerPLS-0.1.0/powerPLS/man/sim_Tscore.Rd |only powerPLS-0.1.0/powerPLS/man/umor_acqueo.Rd |only powerPLS-0.2.0/powerPLS/DESCRIPTION | 11 - powerPLS-0.2.0/powerPLS/MD5 | 64 +++---- powerPLS-0.2.0/powerPLS/NAMESPACE | 5 powerPLS-0.2.0/powerPLS/NEWS.md |only powerPLS-0.2.0/powerPLS/R/IDA.R | 10 - powerPLS-0.2.0/powerPLS/R/PLSc.R | 42 ++-- powerPLS-0.2.0/powerPLS/R/R2Test.R | 77 +++++--- powerPLS-0.2.0/powerPLS/R/aqueous_humour.R |only powerPLS-0.2.0/powerPLS/R/computePower.R | 210 ++++++++++------------- powerPLS-0.2.0/powerPLS/R/computeSampleSize.R | 41 ++-- powerPLS-0.2.0/powerPLS/R/computeWT.R | 20 +- powerPLS-0.2.0/powerPLS/R/global.R |only powerPLS-0.2.0/powerPLS/R/mccTest.R | 109 ++++++++--- powerPLS-0.2.0/powerPLS/R/ptPLSc.R | 19 +- powerPLS-0.2.0/powerPLS/R/scoreTest.R | 103 ++++++++--- powerPLS-0.2.0/powerPLS/R/sim_Tscore.R | 31 --- powerPLS-0.2.0/powerPLS/R/sim_XY.R | 90 +++++++-- powerPLS-0.2.0/powerPLS/R/simulatePilotData.R | 28 +-- powerPLS-0.2.0/powerPLS/R/wheezing.R |only powerPLS-0.2.0/powerPLS/README.md | 6 powerPLS-0.2.0/powerPLS/data/aqueous_humour.rda |only powerPLS-0.2.0/powerPLS/data/wheezing.rda |only powerPLS-0.2.0/powerPLS/man/IDA.Rd | 12 - powerPLS-0.2.0/powerPLS/man/PLSc.Rd | 42 ++-- powerPLS-0.2.0/powerPLS/man/R2Test.Rd | 31 ++- powerPLS-0.2.0/powerPLS/man/aqueous_humour.Rd |only powerPLS-0.2.0/powerPLS/man/computePower.Rd | 48 +++-- powerPLS-0.2.0/powerPLS/man/computeSampleSize.Rd | 41 ++-- powerPLS-0.2.0/powerPLS/man/computeWT.Rd | 20 +- powerPLS-0.2.0/powerPLS/man/mccTest.Rd | 33 ++- powerPLS-0.2.0/powerPLS/man/ptPLSc.Rd | 21 +- powerPLS-0.2.0/powerPLS/man/scoreTest.Rd | 31 ++- powerPLS-0.2.0/powerPLS/man/sim_XY.Rd | 36 ++- powerPLS-0.2.0/powerPLS/man/simulatePilotData.Rd | 31 ++- powerPLS-0.2.0/powerPLS/man/wheezing.Rd |only 39 files changed, 712 insertions(+), 500 deletions(-)
Title: Multivariate Morphometric Analysis
Description: Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package is described in Šlenker et al. 2022.
Author: Marek Slenker [aut, cre] ,
Petr Koutecky [ctb] ,
Karol Marhold [ctb]
Maintainer: Marek Slenker <marek.slenker@savba.sk>
Diff between MorphoTools2 versions 1.0.1.1 dated 2023-02-19 and 1.0.2.0 dated 2024-09-30
DESCRIPTION | 21 +- MD5 | 42 ++-- NAMESPACE | 3 R/pcoa.calc.R | 3 R/plot.addLabels.characters.R | 166 +++++++++++++--- R/plot.biplot.R |only R/plot.characters.R | 30 ++ R/plot.points.R | 7 build/vignette.rds |binary inst/doc/MorphoTools2_tutorial.R | 54 ++++- inst/doc/MorphoTools2_tutorial.Rmd | 84 ++++++-- inst/doc/MorphoTools2_tutorial.pdf |binary man/nmds.calc.Rd | 2 man/plot3Dpoints.Rd | 2 man/plotAddEllipses.Rd | 2 man/plotAddLabels.characters.Rd | 5 man/plotAddLegend.Rd | 4 man/plotBiplot.Rd |only man/plotPoints.Rd | 2 tests/testthat/test.pcoa.calc.R | 3 tests/testthat/test.plot.addLabels.characters_hist.R | 2 tests/testthat/test.plot.addLabels.characters_scatter.R | 2 vignettes/MorphoTools2_tutorial.Rmd | 84 ++++++-- 23 files changed, 413 insertions(+), 105 deletions(-)
Title: Generate Generative Data for a Data Source
Description: Generative Adversarial Networks are applied to generate generative data for a data source. A generative model consisting of a generator and a discriminator network is trained. During iterative training the distribution of generated data is converging to that of the data source. Direct applications of generative data are the created functions for data evaluation and missing data completion. A software service for accelerated training of generative models on graphics processing units is available. Reference: Goodfellow et al. (2014) <doi:10.48550/arXiv.1406.2661>.
Author: Werner Mueller [aut, cre]
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganGenerativeData versions 2.0.2 dated 2024-06-23 and 2.1.2 dated 2024-09-30
ganGenerativeData-2.0.2/ganGenerativeData/man/gdCalculateDensityValueQuantile.Rd |only ganGenerativeData-2.1.2/ganGenerativeData/DESCRIPTION | 16 + ganGenerativeData-2.1.2/ganGenerativeData/MD5 | 29 +- ganGenerativeData-2.1.2/ganGenerativeData/NAMESPACE | 3 ganGenerativeData-2.1.2/ganGenerativeData/R/RcppExports.R | 25 ++ ganGenerativeData-2.1.2/ganGenerativeData/R/gdPlotProjection.R | 1 ganGenerativeData-2.1.2/ganGenerativeData/R/gdService.R | 2 ganGenerativeData-2.1.2/ganGenerativeData/man/ganGenerativeData-package.Rd | 98 +++++++++- ganGenerativeData-2.1.2/ganGenerativeData/man/gdCalculateDensityValue.Rd | 2 ganGenerativeData-2.1.2/ganGenerativeData/man/gdDensityValueInverseQuantile.Rd |only ganGenerativeData-2.1.2/ganGenerativeData/man/gdDensityValueQuantile.Rd |only ganGenerativeData-2.1.2/ganGenerativeData/man/gdServiceTrain.Rd | 2 ganGenerativeData-2.1.2/ganGenerativeData/src/RcppExports.cpp | 22 +- ganGenerativeData-2.1.2/ganGenerativeData/src/dataSource.h | 10 - ganGenerativeData-2.1.2/ganGenerativeData/src/density.h | 74 +++++-- ganGenerativeData-2.1.2/ganGenerativeData/src/gdInt.cpp | 53 ++++- ganGenerativeData-2.1.2/ganGenerativeData/src/generativeData.h | 7 17 files changed, 280 insertions(+), 64 deletions(-)
More information about ganGenerativeData at CRAN
Permanent link
Title: Simultaneous Selection by Trait and WAASB Index
Description: This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot generated by the 'metan'. The aim of the current package is to effectively distinguish the top-ranked genotypes in MET (Multi-Environmental Trials). For a detailed explanation of the process of obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the manual included in this package as well as the study by Olivoto & Lúcio (2020) <doi:10.1111/2041-210X.13384>. In this context, "WAASB" refers to the "Weighted Average of Absolute Scores" provided by Olivoto et al. (2019) <doi:10.2134/agronj2019.03.0220>, which quantifies the stability of genotypes across different environments using linear mixed-effect models. To run the package, you need to extract the "WAASB" and "WAASBY" coefficients using the 'metan' and apply them. This tool utilizes PCA (Principal Component Analysis) and differentiates the entries which may be genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a c [...truncated...]
Author: Ali Arminian [aut, cre, cph]
Maintainer: Ali Arminian <abeyran@gmail.com>
Diff between rYWAASB versions 0.1 dated 2024-08-28 and 0.2 dated 2024-09-30
rYWAASB-0.1/rYWAASB/build/partial.rdb |only rYWAASB-0.1/rYWAASB/inst/extdata/ryassb.xlsx |only rYWAASB-0.1/rYWAASB/man/rYWAASB.Rd |only rYWAASB-0.2/rYWAASB/DESCRIPTION | 26 - rYWAASB-0.2/rYWAASB/MD5 | 60 ++- rYWAASB-0.2/rYWAASB/NAMESPACE | 27 + rYWAASB-0.2/rYWAASB/NEWS.md |only rYWAASB-0.2/rYWAASB/R/PCA_biplot.R |only rYWAASB-0.2/rYWAASB/R/bar_plot1.R | 93 +++-- rYWAASB-0.2/rYWAASB/R/bar_plot2.R | 71 ++-- rYWAASB-0.2/rYWAASB/R/nbclust.R |only rYWAASB-0.2/rYWAASB/R/rYWAASB.R | 90 +++-- rYWAASB-0.2/rYWAASB/R/ranki.R | 130 ++++++- rYWAASB-0.2/rYWAASB/README.md | 6 rYWAASB-0.2/rYWAASB/build/stage23.rdb |only rYWAASB-0.2/rYWAASB/build/vignette.rds |binary rYWAASB-0.2/rYWAASB/data/maize.rda |binary rYWAASB-0.2/rYWAASB/inst/doc/rYWAASB_manual.R | 104 +++++- rYWAASB-0.2/rYWAASB/inst/doc/rYWAASB_manual.Rmd | 157 +++++++-- rYWAASB-0.2/rYWAASB/inst/doc/rYWAASB_manual.html | 385 +++++++++++++++-------- rYWAASB-0.2/rYWAASB/inst/extdata/Iris.xls |only rYWAASB-0.2/rYWAASB/inst/extdata/chickpea.xls |only rYWAASB-0.2/rYWAASB/inst/extdata/maize.xls |binary rYWAASB-0.2/rYWAASB/man/PCA_biplot.Rd |only rYWAASB-0.2/rYWAASB/man/bar_plot1.Rd | 39 -- rYWAASB-0.2/rYWAASB/man/bar_plot2.Rd | 40 -- rYWAASB-0.2/rYWAASB/man/data_ge.Rd | 16 rYWAASB-0.2/rYWAASB/man/figures |only rYWAASB-0.2/rYWAASB/man/maize.Rd | 31 + rYWAASB-0.2/rYWAASB/man/nbclust.Rd |only rYWAASB-0.2/rYWAASB/man/rYWAASB-package.Rd |only rYWAASB-0.2/rYWAASB/man/ranki.Rd | 99 ++++- rYWAASB-0.2/rYWAASB/vignettes/rYWAASB_manual.Rmd | 157 +++++++-- 33 files changed, 1064 insertions(+), 467 deletions(-)
Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'.
This package provides a Database Interface 'DBI' compliant
driver for 'R' to access 'PostgreSQL' database systems.
In order to build and install this package from source, 'PostgreSQL'
itself must be present your system to provide 'PostgreSQL' functionality
via its libraries and header files. These files are provided as
'postgresql-devel' package under some Linux distributions.
On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway [aut],
Dirk Eddelbuettel [aut],
Tomoaki Nishiyama [aut, cre],
Sameer Kumar Prayaga [aut] ,
Neil Tiffin [aut]
Maintainer: Tomoaki Nishiyama <tomoaki@sci.u-toyama.ac.jp>
Diff between RPostgreSQL versions 0.7-6 dated 2024-01-11 and 0.7-7 dated 2024-09-30
RPostgreSQL-0.7-6/RPostgreSQL/tests/connectWithNull.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/connectWithNull.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/createTableMixedCaseTest.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/createTableMixedCaseTest.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dataTypeTests.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dataTypeTests.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dateTZ.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dateTZ.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/datetimeTests.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/datetimeTests.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/datetimestampwrite.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/datetimestampwrite.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbColumnInfo.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbColumnInfo.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbExistsIssue.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbExistsIssue.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbExistsq.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbExistsq.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbExistsqc.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbExistsqc.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbGetQueryParams.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbGetQueryParams.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbListFields.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbListFields.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbTransactionTests.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbTransactionTests.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbWriteTableSchema.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbWriteTableSchema.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbWriteTableTest.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbWriteTableTest.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbWriteTabletypes.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbWriteTabletypes.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbtemptable.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/dbtemptable.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/escape.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/escape.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/loadDriverAndConnect.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/loadDriverAndConnect.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/openSendQuery.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/openSendQuery.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/selectWithAlias.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/selectWithAlias.Rout.save |only RPostgreSQL-0.7-6/RPostgreSQL/tests/utf.R |only RPostgreSQL-0.7-6/RPostgreSQL/tests/utf.Rout.save |only RPostgreSQL-0.7-7/RPostgreSQL/ChangeLog | 12 ++ RPostgreSQL-0.7-7/RPostgreSQL/DESCRIPTION | 35 +++++- RPostgreSQL-0.7-7/RPostgreSQL/MD5 | 55 +--------- RPostgreSQL-0.7-7/RPostgreSQL/inst/NEWS | 3 RPostgreSQL-0.7-7/RPostgreSQL/src/RS-pgsql-copy.c | 4 RPostgreSQL-0.7-7/RPostgreSQL/src/RS-pgsql-pqexecparams.c | 4 RPostgreSQL-0.7-7/RPostgreSQL/tests/test-RPostgreSQL.R |only 51 files changed, 53 insertions(+), 60 deletions(-)
Title: Quality Control for Label-Free Proteomics Expression Data
Description: Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluati [...truncated...]
Author: Kabilan S [aut, cre],
Dr Shashi Bhushan Lal [aut, ths],
Dr Sudhir Srivastava [aut, ths],
Dr Krishna Kumar Chaturvedi [ths],
Dr Yasin Jeshima K [ths],
Dr Ramasubramanian V [ths],
Dr Girish Kumar Jha [ctb]
Maintainer: Kabilan S <kabilan151414@gmail.com>
Diff between lfproQC versions 0.3.0 dated 2024-09-13 and 1.3.0 dated 2024-09-30
lfproQC-0.3.0/lfproQC/vignettes/images/flow1.jpg |only lfproQC-1.3.0/lfproQC/DESCRIPTION | 6 lfproQC-1.3.0/lfproQC/MD5 | 24 lfproQC-1.3.0/lfproQC/NEWS | 38 lfproQC-1.3.0/lfproQC/R/MAplot_DE_fn.R | 2 lfproQC-1.3.0/lfproQC/R/best_combination.R | 416 +++- lfproQC-1.3.0/lfproQC/R/volcanoplot_DE_fn.R | 2 lfproQC-1.3.0/lfproQC/README.md | 8 lfproQC-1.3.0/lfproQC/inst/doc/user_guide.R | 22 lfproQC-1.3.0/lfproQC/inst/doc/user_guide.Rmd | 22 lfproQC-1.3.0/lfproQC/inst/doc/user_guide.html | 1971 ----------------------- lfproQC-1.3.0/lfproQC/man/best_combination.Rd | 23 lfproQC-1.3.0/lfproQC/vignettes/images/flow1.png |only lfproQC-1.3.0/lfproQC/vignettes/user_guide.Rmd | 22 14 files changed, 406 insertions(+), 2150 deletions(-)
Title: Bayesian Regression Models with Global-Local Shrinkage Priors
Description: Fits linear or generalized linear regression models using Bayesian global-local shrinkage prior hierarchies as described in Polson and Scott (2010) <doi:10.1093/acprof:oso/9780199694587.003.0017>. Provides an efficient implementation of ridge, lasso, horseshoe and horseshoe+ regression with logistic, Gaussian, Laplace, Student-t, Poisson or geometric distributed targets using the algorithms summarized in Makalic and Schmidt (2016) <doi:10.48550/arXiv.1611.06649>.
Author: Daniel F. Schmidt [aut, cph, cre]
,
Enes Makalic [aut, cph]
Maintainer: Daniel F. Schmidt <daniel.schmidt@monash.edu>
Diff between bayesreg versions 1.2 dated 2021-03-29 and 1.3 dated 2024-09-30
DESCRIPTION | 19 MD5 | 16 NAMESPACE | 3 R/bayesreg-package.R | 59 +- R/bayesreg.R | 1343 ++++++++++++++++++++++++++++++------------------ man/bayesreg-package.Rd | 56 +- man/bayesreg.Rd | 54 + man/predict.bayesreg.Rd | 13 man/summary.bayesreg.Rd | 14 9 files changed, 1042 insertions(+), 535 deletions(-)
Title: Routines for Performing Empirical Calibration of Observational
Study Estimates
Description: Routines for performing empirical calibration of observational
study estimates. By using a set of negative control hypotheses we can
estimate the empirical null distribution of a particular observational
study setup. This empirical null distribution can be used to compute a
calibrated p-value, which reflects the probability of observing an
estimated effect size when the null hypothesis is true taking both random
and systematic error into account. A similar approach can be used to
calibrate confidence intervals, using both negative and positive controls.
For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and
Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Author: Martijn Schuemie [aut, cre] ,
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EmpiricalCalibration versions 3.1.2 dated 2023-12-21 and 3.1.3 dated 2024-09-30
DESCRIPTION | 10 - MD5 | 24 +- NEWS.md | 10 - R/ConfidenceIntervalCalibration.R | 104 +++++------ R/EmpiricalCalibrationUsingMcmc.R | 118 +++++++------ README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/EmpiricalCiCalibrationVignette.pdf |binary inst/doc/EmpiricalMaxSprtCalibrationVignette.pdf |binary inst/doc/EmpiricalPCalibrationVignette.pdf |binary tests/testthat/test-EmpiricalCalibrationUsingAsymptotics.R | 16 + tests/testthat/test-empiricalCalibrationUsingMcmc.R | 18 + 13 files changed, 180 insertions(+), 124 deletions(-)
More information about EmpiricalCalibration at CRAN
Permanent link
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related
to spatial data science, while serving as a basis for other packages maintained
by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.2.1 dated 2024-09-23 and 0.3.0 dated 2024-09-30
sdsfun-0.2.1/sdsfun/inst/extdata/henan.geojson |only sdsfun-0.2.1/sdsfun/inst/extdata/snnu.geojson |only sdsfun-0.3.0/sdsfun/DESCRIPTION | 13 sdsfun-0.3.0/sdsfun/MD5 | 43 +- sdsfun-0.3.0/sdsfun/NAMESPACE | 6 sdsfun-0.3.0/sdsfun/NEWS.md | 17 sdsfun-0.3.0/sdsfun/R/RcppExports.R |only sdsfun-0.3.0/sdsfun/R/dummy_var.R |only sdsfun-0.3.0/sdsfun/R/fuzzyoverlay.R |only sdsfun-0.3.0/sdsfun/R/sdsfun-package.R |only sdsfun-0.3.0/sdsfun/R/sf_helpers.R | 315 ++++++++-------- sdsfun-0.3.0/sdsfun/R/spdep_helpers.R | 313 +++++++++------ sdsfun-0.3.0/sdsfun/R/spwt.R | 49 +- sdsfun-0.3.0/sdsfun/R/zzz.R |only sdsfun-0.3.0/sdsfun/README.md | 2 sdsfun-0.3.0/sdsfun/inst/extdata/gzma.gpkg |only sdsfun-0.3.0/sdsfun/man/dummy_tbl.Rd |only sdsfun-0.3.0/sdsfun/man/dummy_vector.Rd |only sdsfun-0.3.0/sdsfun/man/fuzzyoverlay.Rd |only sdsfun-0.3.0/sdsfun/man/sf_geometry_name.Rd | 4 sdsfun-0.3.0/sdsfun/man/sf_geometry_type.Rd | 4 sdsfun-0.3.0/sdsfun/man/sf_utm_proj_wgs84.Rd | 4 sdsfun-0.3.0/sdsfun/man/spdep_contiguity_swm.Rd | 8 sdsfun-0.3.0/sdsfun/man/spdep_nb.Rd |only sdsfun-0.3.0/sdsfun/man/spdep_skater.Rd |only sdsfun-0.3.0/sdsfun/src |only sdsfun-0.3.0/sdsfun/tests/testthat/test-dummy_var.R |only sdsfun-0.3.0/sdsfun/tests/testthat/test-sf_helpers.R | 18 sdsfun-0.3.0/sdsfun/tests/testthat/test-spdep_helpers.R | 134 +++--- 29 files changed, 530 insertions(+), 400 deletions(-)
Title: Prediction Limits for Poisson Distribution
Description: Prediction limits for the Poisson distribution
are produced from both frequentist and Bayesian viewpoints. Limiting results
are provided in a Bayesian setting with uniform, Jeffreys and gamma as prior
distributions. More details on the methodology are discussed in Bejleri and
Nandram (2018) <doi:10.1080/03610926.2017.1373814> and Bejleri, Sartore and
Nandram (2021) <doi:10.1007/s42952-021-00157-x>.
Author: Valbona Bejleri [aut] ,
Luca Sartore [aut, cre] ,
Balgobin Nandram [aut]
Maintainer: Luca Sartore <drwolf85@gmail.com>
Diff between plpoisson versions 0.3.0 dated 2022-05-10 and 0.3.1 dated 2024-09-30
DESCRIPTION | 8 +-- MD5 | 14 ++--- NEWS | 125 +++++++++++++++++++++++++++-------------------- README.md | 3 - build/partial.rdb |binary inst/INSTALL.md | 4 - man/plpoisson-package.Rd | 4 - src/plpbootstrap.c | 8 +-- 8 files changed, 92 insertions(+), 74 deletions(-)