Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] ,
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.5-32 dated 2022-05-10 and 1.6-2 dated 2022-11-08
rgdal-1.5-32/rgdal/man/project.Rd |only rgdal-1.5-32/rgdal/man/readGDAL.Rd |only rgdal-1.5-32/rgdal/man/readOGR.Rd |only rgdal-1.5-32/rgdal/man/wrappers.Rd |only rgdal-1.5-32/rgdal/man/writeOGR.Rd |only rgdal-1.6-2/rgdal/DESCRIPTION | 8 rgdal-1.6-2/rgdal/MD5 | 66 rgdal-1.6-2/rgdal/NAMESPACE | 258 - rgdal-1.6-2/rgdal/NEWS.md | 16 rgdal-1.6-2/rgdal/R/AAA.R | 6 rgdal-1.6-2/rgdal/R/Class-CRSx.R | 1 rgdal-1.6-2/rgdal/R/gdal.R | 2 rgdal-1.6-2/rgdal/R/ogr.R | 6 rgdal-1.6-2/rgdal/R/ogr_sp.R | 3 rgdal-1.6-2/rgdal/R/ogr_write.R | 1 rgdal-1.6-2/rgdal/R/project.R | 1 rgdal-1.6-2/rgdal/R/sp_gdal.R | 6 rgdal-1.6-2/rgdal/R/wrappers.R | 1 rgdal-1.6-2/rgdal/build/vignette.rds |binary rgdal-1.6-2/rgdal/configure | 2452 ++++------ rgdal-1.6-2/rgdal/configure.ac | 16 rgdal-1.6-2/rgdal/inst/SVN_VERSION | 2 rgdal-1.6-2/rgdal/inst/doc/CRS_projections_transformations.html | 158 rgdal-1.6-2/rgdal/inst/doc/OGR_shape_encoding.pdf |binary rgdal-1.6-2/rgdal/inst/doc/PROJ6_GDAL3.html | 122 rgdal-1.6-2/rgdal/man/CRS-class.Rd | 16 rgdal-1.6-2/rgdal/man/GDALDriver-class.Rd | 6 rgdal-1.6-2/rgdal/man/rgdal-deprecated.Rd |only rgdal-1.6-2/rgdal/man/showWKT.Rd | 11 rgdal-1.6-2/rgdal/src/Makevars.ucrt | 8 rgdal-1.6-2/rgdal/src/Makevars.win | 5 rgdal-1.6-2/rgdal/src/gdal-bindings.cpp | 4 rgdal-1.6-2/rgdal/src/ogr_proj.cpp | 2 rgdal-1.6-2/rgdal/src/proj6.cpp | 2 rgdal-1.6-2/rgdal/src/proj_network7.cpp | 6 rgdal-1.6-2/rgdal/src/projectit.cpp | 2 rgdal-1.6-2/rgdal/src/rgdal.h | 14 37 files changed, 1580 insertions(+), 1621 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-25 1.2.1
2022-05-18 1.1.4
2022-03-21 1.1.3
2022-03-08 1.1.1
2022-03-02 1.1.0
Title: Hierarchical Exponential-Family Random Graph Models
Description: Hierarchical exponential-family random graph models with local dependence. See Schweinberger and Luna (2018) <doi:10.18637/jss.v085.i01>.
Author: Michael Schweinberger [cre, aut],
Mark S. Handcock [aut],
Sergii Babkin [aut],
Jonathan R. Stewart [aut],
Duy Q. Vu [aut],
Pamela Luna [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@psu.edu>
Diff between hergm versions 4.1-9 dated 2022-06-10 and 4.1-10 dated 2022-11-08
DESCRIPTION | 26 +++++++++++++------------- MD5 | 6 +++--- R/helper.functions.R | 2 +- man/hergm.terms.Rd | 22 +++++++++++----------- 4 files changed, 28 insertions(+), 28 deletions(-)
Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: A geomorphology-based hydrological modelling for transferring
streamflow measurements from gauged to ungauged catchments. Inverse
modelling enables to estimate net rainfall from streamflow measurements
following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>.
Resulting net rainfall is then estimated on the ungauged catchments
by spatial interpolation in order to finally simulate streamflow
following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] ,
Christophe Cudennec [ths] ,
Tom Loree [ctb],
Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>
Diff between transfR versions 1.0.0 dated 2022-10-05 and 1.0.1 dated 2022-11-08
DESCRIPTION | 12 MD5 | 25 - build/partial.rdb |binary inst/CITATION |only inst/REFERENCES.bib | 12 inst/doc/V01_get_started.Rmd | 2 inst/doc/V01_get_started.html | 143 +++---- inst/doc/V02_inputs_preparation_stars.html | 139 +++---- inst/doc/V03_inputs_preparation_whitebox.R | 37 + inst/doc/V03_inputs_preparation_whitebox.Rmd | 46 +- inst/doc/V03_inputs_preparation_whitebox.html | 484 +++++++++++++------------- man/transfR.Rd | 10 vignettes/V01_get_started.Rmd | 2 vignettes/V03_inputs_preparation_whitebox.Rmd | 46 +- 14 files changed, 506 insertions(+), 452 deletions(-)
Title: Machine Learning and Inference for Topological Data Analysis
Description: Topological data analysis is a powerful tool for finding non-linear global structure
in whole datasets. 'TDApplied' aims to bridge topological data analysis with data, statistical
and machine learning practitioners so that more analyses may benefit from the
power of topological data analysis. The main tool of topological data analysis is
persistent homology, which computes a shape descriptor of a dataset, called
a persistence diagram. There are five goals of this package: (1) convert persistence diagrams
computed using the two main R packages for topological data analysis into a data frame,
(2) implement fast versions of both distance and kernel calculations
for pairs of persistence diagrams, (3) provide methods for machine learning
and inference for persistence diagrams which scale well, (4) deliver a fast implementation
of persistent homology via a python interface, and (5) contribute tools for the interpretation of
persistence diagrams.
Author: Shael Brown [aut, cre],
Dr. Reza Farivar [aut, fnd]
Maintainer: Shael Brown <shaelebrown@gmail.com>
Diff between TDApplied versions 0.1.3 dated 2022-10-02 and 2.0.0 dated 2022-11-08
DESCRIPTION | 17 MD5 | 79 +- NAMESPACE | 7 NEWS.md | 8 R/TDApplied.R | 12 R/bootstrap.R |only R/convert.R | 13 R/distance_calculations.R | 79 ++ R/inference.R | 6 R/kernel_calculations.R | 8 R/machine_learning.R | 14 R/plot.R |only R/python_functions.R |only R/utilities.R | 7 README.md | 51 + build/partial.rdb |binary exec |only inst/doc/ML_and_Inference.R | 496 +++++++++------ inst/doc/ML_and_Inference.Rmd | 655 +++++++++++++-------- inst/doc/ML_and_Inference.html | 996 +++++++++++++++----------------- man/PyH.Rd |only man/TDApplied.Rd | 9 man/bootstrap_persistence_thresholds.Rd |only man/check_PyH_setup.Rd |only man/check_ripser.Rd |only man/diagram_distance.Rd | 9 man/diagram_kernel.Rd | 6 man/diagram_kkmeans.Rd | 2 man/diagram_kpca.Rd | 4 man/diagram_ksvm.Rd | 2 man/diagram_mds.Rd | 2 man/distance_matrix.Rd | 2 man/gram_matrix.Rd | 2 man/import_ripser.Rd |only man/independence_test.Rd | 4 man/permutation_test.Rd | 2 man/plot_diagram.Rd |only man/predict_diagram_kkmeans.Rd | 2 man/predict_diagram_kpca.Rd | 2 man/predict_diagram_ksvm.Rd | 2 tests/testthat/test-bootstrap.R |only tests/testthat/test-distance.R | 74 ++ tests/testthat/test-inference.R | 6 tests/testthat/test-plot.R |only tests/testthat/test-python.R |only vignettes/ML_and_Inference.Rmd | 655 +++++++++++++-------- vignettes/REFERENCES.bib | 33 + 47 files changed, 1964 insertions(+), 1302 deletions(-)
Title: Wrangle, Analyze, and Visualize Animal Movement Data
Description: Tools to import, clean, and visualize movement data,
particularly from motion capture systems such as Optitrack's
'Motive', the Straw Lab's 'Flydra', or from other sources. We provide
functions to remove artifacts, standardize tunnel position and tunnel
axes, select a region of interest, isolate specific trajectories, fill
gaps in trajectory data, and calculate 3D and per-axis velocity. For
experiments of visual guidance, we also provide functions that use
subject position to estimate perception of visual stimuli.
Author: Vikram B. Baliga [aut, cre] ,
Melissa S. Armstrong [aut] ,
Eric R. Press [aut] ,
Anne-Sophie Bonnet-Lebrun [rev],
Marco Sciaini [rev]
Maintainer: Vikram B. Baliga <vbaliga87@gmail.com>
Diff between pathviewr versions 1.1.3 dated 2022-08-22 and 1.1.5 dated 2022-11-08
DESCRIPTION | 8 MD5 | 52 NEWS.md | 8 R/analytical_functions.R | 2380 +++++++++++++------------- R/plotting_functions.R | 69 R/utility_functions.R | 15 README.md | 6 inst/doc/data-import-cleaning.html | 4 inst/doc/managing-frame-gaps.Rmd | 414 ++-- inst/doc/managing-frame-gaps.html | 4 inst/doc/visual-perception-functions.Rmd | 772 ++++---- inst/doc/visual-perception-functions.html | 4 man/plot_by_subject.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-angular_functions.R | 98 - tests/testthat/test-calc_min_dist_box.R | 162 - tests/testthat/test-calc_min_dist_v.R | 162 - tests/testthat/test-exclude_by_velocity.R | 84 tests/testthat/test-get_header.R | 34 tests/testthat/test-get_sf.R | 280 +-- tests/testthat/test-get_vis_angle.R | 284 +-- tests/testthat/test-plot_by_subject.R | 396 ++-- tests/testthat/test-plot_viewr_trajectories.R | 438 ++-- tests/testthat/test-relabel_viewr_axes.R | 40 tests/testthat/test-visualize_frame_gap.R | 154 - vignettes/managing-frame-gaps.Rmd | 414 ++-- vignettes/visual-perception-functions.Rmd | 772 ++++---- 27 files changed, 3536 insertions(+), 3523 deletions(-)
Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service
(WFS) for vector data, Web Coverage Service (WCS), Catalogue Service (CSW) for ISO/OGC metadata, Web Processing Service (WPS) for data processes,
and associated standards such as the common web-service specification (OWS) and OGC Filter Encoding. Partial support is provided for the Web Map
Service (WMS). The purpose is to add support for additional OGC service standards such as Web Coverage Processing Service (WCPS), the Sensor
Observation Service (SOS), or even new standard services emerging such OGC API or SensorThings.
Author: Emmanuel Blondel [aut, cre] ,
Alexandre Bennici [ctb] ,
Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ows4R versions 0.3-1 dated 2022-08-19 and 0.3-2 dated 2022-11-08
DESCRIPTION | 21 +++++------ MD5 | 66 +++++++++++++++++------------------ NAMESPACE | 2 - NEWS.md | 17 +++++++-- R/OGCAbstractObject.R | 3 + R/OWSGetCapabilities.R | 2 - R/WCSClient.R | 23 ++++++------ R/WCSCoverageSummary.R | 40 +++++++++++---------- R/WCSDescribeCoverage.R | 2 + R/WCSGSElevationDomain.R | 3 + R/WCSGSTimeDomain.R | 3 - R/WCSGetCoverage.R | 14 ++++--- R/WFSFeatureType.R | 2 - R/WFSGetFeature.R | 2 - R/WMSGetFeatureInfo.R | 2 - R/WPSDescribeProcess.R | 2 - R/WPSExecute.R | 2 - README.md | 9 +++- inst/doc/wcs.Rmd | 6 ++- inst/doc/wcs.html | 6 ++- man/OWSGetCapabilities.Rd | 2 - man/WCSClient.Rd | 22 +++++++---- man/WCSCoverageSummary.Rd | 14 +++---- man/WCSDescribeCoverage.Rd | 3 + man/WCSGSElevationDomain.Rd | 3 + man/WCSGSTimeDomain.Rd | 2 - man/WCSGetCoverage.Rd | 3 + man/WFSFeatureType.Rd | 2 - man/WFSGetFeature.Rd | 2 - man/WMSGetFeatureInfo.Rd | 2 - man/WPSDescribeProcess.Rd | 2 - man/WPSExecute.Rd | 2 - tests/testthat/test_WCSClient_v2_0.R | 10 ++--- vignettes/wcs.Rmd | 6 ++- 34 files changed, 175 insertions(+), 127 deletions(-)
Title: Access Scottish Health and Social Care Open Data
Description: Allows potential users of Scottish Health and Social Care Open Data
(<https://www.opendata.nhs.scot/>) to easily explore and extract the
available data.
Author: James Hardy [aut, cre]
Maintainer: James Hardy <jrh-dev@protonmail.com>
Diff between odns versions 1.0.1 dated 2022-08-07 and 1.0.2 dated 2022-11-08
DESCRIPTION | 8 ++-- MD5 | 55 +++++++++++++++------------ NAMESPACE | 1 NEWS.md | 15 +++++++ R/all_packages.R | 24 ++++++++---- R/all_resources.R | 23 +++++++---- R/cap_url.R | 2 - R/detect_error.R | 4 +- R/get_data.R | 16 +++++--- R/get_resource.R | 3 + R/nrow_resource.R | 8 +++- R/package_metadata.R | 8 +++- R/resource_data_items.R |only R/resource_metadata.R | 49 ++++++++++++------------ README.md | 35 +++++++++++++++-- build/vignette.rds |binary inst/doc/using_odns.Rmd | 53 +++++++++++++++++++++++--- inst/doc/using_odns.html | 58 ++++++++++++++++++++++++----- man/get_resource.Rd | 3 + man/resource_data_items.Rd |only man/resource_metadata.Rd | 13 +++--- tests/testthat/test-all_packages.R | 6 +-- tests/testthat/test-all_resources.R | 5 +- tests/testthat/test-get_data.R | 12 +++--- tests/testthat/test-nrow_resource.R | 2 - tests/testthat/test-package_metadata.R | 4 +- tests/testthat/test-resource_data_items.R |only tests/testthat/test-resource_metadata.R | 14 +++---- tests/testthat/test_data/res_meta.rda |only tests/testthat/test_data/res_meta_fail.rda |only vignettes/using_odns.Rmd | 53 +++++++++++++++++++++++--- 31 files changed, 339 insertions(+), 135 deletions(-)
Title: Spatio-Network Generalised Linear Mixed Models for Areal Unit
and Network Data
Description: Implements a class of univariate and multivariate spatio-network generalised linear mixed models for areal unit and network data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson. Spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution following the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>). Network structures are modelled by a set of random effects that reflect a multiple membership structure (Browne et al. (2001) <doi:10.1177/1471082X0100100202>).
Author: George Gerogiannis, Mark Tranmer, Duncan Lee
Maintainer: George Gerogiannis <g.gerogiannis.1@research.gla.ac.uk>
Diff between netcmc versions 1.0.1 dated 2022-06-28 and 1.0.2 dated 2022-11-08
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 5 ++--- R/multivariateBinomialNetworkLeroux.R | 2 +- R/multivariateBinomialNetworkRand.R | 2 +- R/multivariateGaussianNetworkLerouxMH.R | 2 +- R/multivariateGaussianNetworkRand.R | 2 +- R/multivariatePoissonNetworkLeroux.R | 2 +- R/multivariatePoissonNetworkRand.R | 2 +- R/print.netcmc.R |only R/univariateBinomialNetworkLeroux.R | 2 +- R/univariateGaussianNetworkLerouxMH.R | 2 +- R/univariatePoissonNetworkLeroux.R | 2 +- man/print.netcmc.Rd |only 14 files changed, 28 insertions(+), 27 deletions(-)
Title: 'NetCDF' Geometry and Time Series
Description: Tools to create time series and geometry 'NetCDF' files.
Author: David Blodgett [aut, cre],
Luke Winslow [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between ncdfgeom versions 1.1.3 dated 2022-07-14 and 1.1.4 dated 2022-11-08
ncdfgeom-1.1.3/ncdfgeom/vignettes/geometry_cache |only ncdfgeom-1.1.4/ncdfgeom/DESCRIPTION | 10 ncdfgeom-1.1.4/ncdfgeom/MD5 | 16 - ncdfgeom-1.1.4/ncdfgeom/build/vignette.rds |binary ncdfgeom-1.1.4/ncdfgeom/inst/doc/geometry.html | 126 +++++---- ncdfgeom-1.1.4/ncdfgeom/inst/doc/ncdfgeom.html | 132 +++++----- ncdfgeom-1.1.4/ncdfgeom/inst/doc/timeseries.html | 124 ++++----- ncdfgeom-1.1.4/ncdfgeom/tests/testthat/test_create_cell_geometry.R | 2 8 files changed, 213 insertions(+), 197 deletions(-)
Title: Comprehensive GO Terms Comparison Between Species
Description: Supports the assessment of functional enrichment analyses obtained for several lists of genes and provides a workflow to analyze them between two species via weighted graphs. Methods are described in Sosa et al. (2022) (Submitted to Genomics).
Author: Chrystian Camilo Sosa [aut, cre, cph]
,
Diana Carolina Clavijo-Buritica [aut],
Mauricio Alberto Quimbaya [aut],
Maria Victoria Diaz [ctb],
Camila Riccio Rengifo [ctb],
Nicolas Lopez-Rozo [ctb],
Arlen James Mosquera [ctb],
Andres Álvarez [ctb]
Maintainer: Chrystian Camilo Sosa <ccsosaa@javerianacali.edu.co>
Diff between GOCompare versions 1.0.1 dated 2022-04-29 and 1.0.2 dated 2022-11-08
DESCRIPTION | 17 - MD5 | 27 +- NAMESPACE | 1 R/GOCompare-package.R | 8 R/compareGOspecies.R | 440 ++++++++++++++++++++++++++++++--------------- R/evaluateCAT_species.R | 3 R/evaluateGO_species.R | 3 R/graph_GOspecies.R | 132 ++++++++++--- R/graph_two_GOspecies.R | 189 ++++++++++++++----- R/mostFrequentGOs.R | 3 build |only man/GOCompare-package.Rd | 8 man/compareGOspecies.Rd | 16 + man/graphGOspecies.Rd | 82 ++++++-- man/graph_two_GOspecies.Rd | 116 ++++++++--- 15 files changed, 748 insertions(+), 297 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut, cre],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between geoknife versions 1.6.8 dated 2022-09-21 and 1.6.9 dated 2022-11-08
DESCRIPTION | 6 - MD5 | 22 +++---- NEWS.md | 9 ++ R/inputs-webprocess.R | 1 inst/CITATION | 2 inst/doc/custom_data_sources.Rmd | 2 inst/doc/custom_data_sources.html | 117 +++++++++++++++++++------------------- inst/doc/geoknife.html | 117 ++++++++++++++++++-------------------- inst/doc/plot_geotiff.html | 115 ++++++++++++++++++------------------- inst/unnamed-chunk-6-1.png |binary man/inputs-webprocess.Rd | 2 vignettes/custom_data_sources.Rmd | 2 12 files changed, 202 insertions(+), 193 deletions(-)
Title: Bayesian Adaptive Randomization
Description: Bayesian adaptive randomization is also called outcome adaptive randomization, which is increasingly used in clinical trials.
Author: Chia-Wei Hsu [aut, cre],
Haitao Pan [aut]
Maintainer: Chia-Wei Hsu <Chia-Wei.Hsu@stjude.org>
Diff between BAR versions 0.1.0 dated 2022-11-07 and 0.1.1 dated 2022-11-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/get_oc_BAR.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Tools for Plant Ecophysiology & Modeling
Description: Contains modeling and analytical tools for plant ecophysiology.
MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer,
Berry (1980) <doi:10.1007/BF00386231> model as described in Buckley and
Diaz-Espejo (2015) <doi:10.1111/pce.12459>. It uses units to ensure that
parameters are properly specified and transformed before calculations.
Temperature response functions get automatically "baked" into all
parameters based on leaf temperature following Bernacchi et al. (2002)
<doi:10.1104/pp.008250>. The package includes boundary layer, cuticular,
stomatal, and mesophyll conductances to CO2, which each can vary on the
upper and lower portions of the leaf. Use straightforward functions to
simulate photosynthesis over environmental gradients such as Photosynthetic
Photon Flux Density (PPFD) and leaf temperature, or over trait gradients
such as CO2 conductance or photochemistry.
ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) <doi:10.1007/BF00386231>)
and [...truncated...]
Author: Joseph Stinziano [aut] ,
Cassaundra Roback [aut],
Demi Sargent [aut],
Bridget Murphy [aut],
Patrick Hudson [aut, dtc],
Chris Muir [aut, cre]
Maintainer: Chris Muir <cdmuir@hawaii.edu>
Diff between photosynthesis versions 2.0.3 dated 2022-08-12 and 2.1.0 dated 2022-11-08
photosynthesis-2.0.3/photosynthesis/R/check_dependencies.R |only photosynthesis-2.0.3/photosynthesis/inst/doc/photosynthesis-curve-fitting-sensitivity-analyses.R |only photosynthesis-2.0.3/photosynthesis/inst/doc/photosynthesis-curve-fitting-sensitivity-analyses.Rmd |only photosynthesis-2.0.3/photosynthesis/inst/doc/photosynthesis-curve-fitting-sensitivity-analyses.html |only photosynthesis-2.0.3/photosynthesis/man/check_dependencies.Rd |only photosynthesis-2.0.3/photosynthesis/man/figures/README-parallel-example-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-10-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-11-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-11-2.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-11-3.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-12-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-12-2.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-12-3.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-12-4.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-13-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-6-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-6-2.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-7-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-7-2.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-2.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-3.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-4.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-5.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-6.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-8-7.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-9-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-9-2.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-9-3.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-unnamed-chunk-9-4.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-use-tealeaves-example-1.png |only photosynthesis-2.0.3/photosynthesis/man/figures/README-use-tealeaves-example-2.png |only photosynthesis-2.0.3/photosynthesis/man/gw2gc.Rd |only photosynthesis-2.0.3/photosynthesis/vignettes/photosynthesis-curve-fitting-sensitivity-analyses.Rmd |only photosynthesis-2.1.0/photosynthesis/DESCRIPTION | 20 photosynthesis-2.1.0/photosynthesis/MD5 | 163 - 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Title: Load and Process Passive Acoustic Data
Description: Tools for loading and processing passive acoustic data. Read in data
that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite
processing functions, and export data for reports or external modeling tools. Parameter
calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>,
Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)
<doi:10.1121/1.3479549>.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Emily Griffiths [ctb],
Michael Oswald [ctb],
Simone Baumann-Pickering [ctb],
Julie Oswald [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMpal versions 0.16.0 dated 2022-03-06 and 0.17.0 dated 2022-11-08
DESCRIPTION | 12 MD5 | 61 +-- NAMESPACE | 4 NEWS.md | 718 ++++++++++++++++------------------------ R/AllClass.R | 12 R/addBinaries.R | 21 - R/addDatabase.R | 25 - R/addGps.R | 10 R/addHydrophoneDepth.R | 237 ++++++------- R/addNote.R |only R/addRecordings.R | 76 +++- R/bindStudies.R | 15 R/calculateAverageSpectra.R | 132 ------- R/calculateICI.R | 3 R/filter.R | 66 +++ R/getBinaryData.R | 14 R/getClipData.R |only R/getDetectorData.R | 13 R/plotGram.R | 101 +++-- R/processPgDetections.R | 113 ++++-- R/removeNote.R |only R/setSpecies.R | 14 R/utils.R | 248 ++++++++++--- R/wavUtils.R |only R/writeEventClips.R | 505 ++++++++++++---------------- README.md | 5 inst/extdata/Example.sqlite3 |binary man/addHydrophoneDepth.Rd | 2 man/addNote.Rd |only man/getClipData.Rd |only man/plotGram.Rd | 13 man/processPgDetections.Rd | 3 man/removeNote.Rd |only man/writeEventClips.Rd | 8 tests/testthat/test-workStudy.R | 62 ++- 35 files changed, 1273 insertions(+), 1220 deletions(-)
Title: Multivariate Conditional Volatility Modelling and Forecasting
Description: Methods and tools for estimating, simulating and forecasting of so-called BEKK-models (named after Baba, Engle, Kraft and Kroner) based on the fast Berndt–Hall–Hall–Hausman (BHHH) algorithm described in Hafner and Herwartz (2008) <doi:10.1007/s00184-007-0130-y>.
Author: Markus J. Fuelle [aut],
Christian M. Hafner [aut],
Helmut Herwartz [aut],
Alexander Lange [aut, cre]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>
Diff between BEKKs versions 1.3.1 dated 2022-10-03 and 1.4.0 dated 2022-11-08
BEKKs-1.3.1/BEKKs/man/bekk_forecast.Rd |only BEKKs-1.3.1/BEKKs/man/bekk_sim.Rd |only BEKKs-1.4.0/BEKKs/DESCRIPTION | 6 BEKKs-1.4.0/BEKKs/LICENSE | 4 BEKKs-1.4.0/BEKKs/MD5 | 124 BEKKs-1.4.0/BEKKs/NAMESPACE | 144 BEKKs-1.4.0/BEKKs/R/BEKKs.R | 85 BEKKs-1.4.0/BEKKs/R/Portmanteau_test.R | 153 BEKKs-1.4.0/BEKKs/R/RcppExports.R | 494 +- BEKKs-1.4.0/BEKKs/R/VaR.R | 557 +- BEKKs-1.4.0/BEKKs/R/backtest.R | 422 +- BEKKs-1.4.0/BEKKs/R/bekk_fit.R | 1766 ++++---- BEKKs-1.4.0/BEKKs/R/bekk_fit_methods.R | 339 - BEKKs-1.4.0/BEKKs/R/bekk_forecast.R | 2066 +++++----- BEKKs-1.4.0/BEKKs/R/bekk_functions.R | 240 - BEKKs-1.4.0/BEKKs/R/bekk_mc_eval.R | 90 BEKKs-1.4.0/BEKKs/R/bekk_sim.R | 246 - BEKKs-1.4.0/BEKKs/R/bekk_spec.R | 134 BEKKs-1.4.0/BEKKs/R/bekk_starting_values.R | 812 +-- BEKKs-1.4.0/BEKKs/R/extract_csd.R | 32 BEKKs-1.4.0/BEKKs/R/matrix_stuff.R | 198 BEKKs-1.4.0/BEKKs/R/plot.backtest.R | 172 BEKKs-1.4.0/BEKKs/R/plot.bekk.R | 150 BEKKs-1.4.0/BEKKs/R/plot.var.R | 276 - BEKKs-1.4.0/BEKKs/R/plot.virf.R | 130 BEKKs-1.4.0/BEKKs/R/summary.backtest.R | 264 - BEKKs-1.4.0/BEKKs/R/summary.bekk.R | 420 +- BEKKs-1.4.0/BEKKs/R/summary.var.R | 68 BEKKs-1.4.0/BEKKs/R/virf.R | 706 +-- BEKKs-1.4.0/BEKKs/R/zzz.R | 8 BEKKs-1.4.0/BEKKs/build/BEKKs.pdf |binary BEKKs-1.4.0/BEKKs/man/BEKKs.Rd | 99 BEKKs-1.4.0/BEKKs/man/GoldStocksBonds.Rd | 54 BEKKs-1.4.0/BEKKs/man/StocksBonds.Rd | 50 BEKKs-1.4.0/BEKKs/man/VaR.Rd | 94 BEKKs-1.4.0/BEKKs/man/backtest.Rd | 112 BEKKs-1.4.0/BEKKs/man/bekk_fit.Rd | 146 BEKKs-1.4.0/BEKKs/man/bekk_fit_methods.Rd | 88 BEKKs-1.4.0/BEKKs/man/bekk_spec.Rd | 64 BEKKs-1.4.0/BEKKs/man/portmanteau.test.Rd | 50 BEKKs-1.4.0/BEKKs/man/predict.Rd |only BEKKs-1.4.0/BEKKs/man/simulate.Rd |only BEKKs-1.4.0/BEKKs/man/virf.Rd | 106 BEKKs-1.4.0/BEKKs/tests/testthat.R | 8 BEKKs-1.4.0/BEKKs/tests/testthat/test-Grid_Search.R | 16 BEKKs-1.4.0/BEKKs/tests/testthat/test-asymmetric_grid_search.R | 40 BEKKs-1.4.0/BEKKs/tests/testthat/test-bekk_fit.R | 198 BEKKs-1.4.0/BEKKs/tests/testthat/test-bekk_forecast.R | 294 - BEKKs-1.4.0/BEKKs/tests/testthat/test-bekk_sim.R | 118 BEKKs-1.4.0/BEKKs/tests/testthat/test-bhh_bekk.R | 18 BEKKs-1.4.0/BEKKs/tests/testthat/test-commutation_mat.R | 52 BEKKs-1.4.0/BEKKs/tests/testthat/test-duplication_mat.R | 52 BEKKs-1.4.0/BEKKs/tests/testthat/test-elimination_mat.R | 80 BEKKs-1.4.0/BEKKs/tests/testthat/test-inv_gen.R | 24 BEKKs-1.4.0/BEKKs/tests/testthat/test-loglike_bekk.R | 46 BEKKs-1.4.0/BEKKs/tests/testthat/test-loglike_bekk_asymm.R | 74 BEKKs-1.4.0/BEKKs/tests/testthat/test-score_bekk.R | 38 BEKKs-1.4.0/BEKKs/tests/testthat/test-score_dbekk.R | 34 BEKKs-1.4.0/BEKKs/tests/testthat/test-score_sbekk.R | 34 BEKKs-1.4.0/BEKKs/tests/testthat/test-valid_asymm_bekk.R | 78 BEKKs-1.4.0/BEKKs/tests/testthat/test-valid_bekk.R | 126 BEKKs-1.4.0/BEKKs/tests/testthat/test-virf.R | 32 BEKKs-1.4.0/BEKKs/tests/testthat/test_score_bekk_asymm.R | 48 BEKKs-1.4.0/BEKKs/tests/testthat/test_score_dbekk_asymm.R | 44 BEKKs-1.4.0/BEKKs/tests/testthat/test_score_sbekk_asymm.R | 38 65 files changed, 6251 insertions(+), 6210 deletions(-)
Title: Artificial Intelligence Systems and Observer Performance
Description: Analyzing the performance of artificial intelligence
(AI) systems/algorithms characterized by a 'search-and-report'
strategy. Historically observer performance has dealt with
measuring radiologists' performances in search tasks, e.g., searching
for lesions in medical images and reporting them, but the implicit
location information has been ignored. The implemented methods apply
to analyzing the absolute and relative performances of AI systems,
comparing AI performance to a group of human readers or optimizing the
reporting threshold of an AI system. In addition to performing historical
receiver operating receiver operating characteristic (ROC) analysis
(localization information ignored), the software also performs
free-response receiver operating characteristic (FROC)
analysis, where lesion localization information is used. A book
using the software has been published: Chakraborty DP: Observer
Performance Methods for Diagnostic Imaging - Foundations, Modeling,
and Applications with R-B [...truncated...]
Author: Dev Chakraborty [cre, aut, cph],
Peter Phillips [ctb],
Xuetong Zhai [aut]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>
Diff between RJafroc versions 2.1.1 dated 2022-08-12 and 2.1.2 dated 2022-11-08
RJafroc-2.1.1/RJafroc/R/DfReadLrocDataFile.R |only RJafroc-2.1.1/RJafroc/R/SimulateRoiDataset.R |only RJafroc-2.1.1/RJafroc/R/UtilIntrinsic2PhysicalRSM.R |only RJafroc-2.1.1/RJafroc/R/UtilPhysical2IntrinsicRSM.R |only RJafroc-2.1.1/RJafroc/R/test2Functions.R |only RJafroc-2.1.1/RJafroc/inst/extdata/CrossedModalities.xlsx |only RJafroc-2.1.1/RJafroc/inst/extdata/findings.txt |only RJafroc-2.1.1/RJafroc/inst/extdata/jaf_truth.txt |only RJafroc-2.1.1/RJafroc/man/DfReadLrocDataFile.Rd |only RJafroc-2.1.1/RJafroc/man/RSM_erf.Rd |only RJafroc-2.1.1/RJafroc/man/RSM_xFROC.Rd |only RJafroc-2.1.1/RJafroc/man/RSM_yFROC.Rd |only RJafroc-2.1.1/RJafroc/man/UtilIntrinsic2PhysicalRSM.Rd |only RJafroc-2.1.1/RJafroc/man/UtilPhysical2IntrinsicRSM.Rd |only RJafroc-2.1.1/RJafroc/man/funs.Rd |only RJafroc-2.1.2/RJafroc/DESCRIPTION | 20 RJafroc-2.1.2/RJafroc/MD5 | 155 +- RJafroc-2.1.2/RJafroc/NAMESPACE | 14 RJafroc-2.1.2/RJafroc/NEWS.md | 277 +++- RJafroc-2.1.2/RJafroc/R/ChisqrGoodnessOfFit.R | 10 RJafroc-2.1.2/RJafroc/R/DfFroc2Roc.R | 8 RJafroc-2.1.2/RJafroc/R/DfReadCrossedModalities.R | 14 RJafroc-2.1.2/RJafroc/R/EnvironmentVariables.R | 8 RJafroc-2.1.2/RJafroc/R/FitCorCbm.R | 45 RJafroc-2.1.2/RJafroc/R/FitRsmRoc.R | 134 +- RJafroc-2.1.2/RJafroc/R/IgnoreSimulateRoiDataset.R |only RJafroc-2.1.2/RJafroc/R/PlotBinormalFit.R | 2 RJafroc-2.1.2/RJafroc/R/PlotCBMFit.R | 2 RJafroc-2.1.2/RJafroc/R/PlotRsmOperatingCharacteristics.R | 69 - RJafroc-2.1.2/RJafroc/R/PlotSupport.R | 6 RJafroc-2.1.2/RJafroc/R/RcppExports.R | 28 RJafroc-2.1.2/RJafroc/R/SimulateFrocDataset.R | 12 RJafroc-2.1.2/RJafroc/R/SimulateLrocDataset.R | 15 RJafroc-2.1.2/RJafroc/R/SsFrocNhRsmModel.R | 46 RJafroc-2.1.2/RJafroc/R/StSignificanceTestingCadVsRad.R | 2 RJafroc-2.1.2/RJafroc/R/StSignificanceTestingCrossedModalities.R | 6 RJafroc-2.1.2/RJafroc/R/UtilAnalyticalAucsRSM.R | 73 - RJafroc-2.1.2/RJafroc/R/UtilAnalyticalAucsRSM_R.R |only RJafroc-2.1.2/RJafroc/R/UtilIntrinsic2RSM.R |only RJafroc-2.1.2/RJafroc/R/UtilLesionWeightsMatrix.R | 31 RJafroc-2.1.2/RJafroc/R/UtilRSM2Intrinsic.R |only RJafroc-2.1.2/RJafroc/R/rsmFormulae.R | 273 ++-- RJafroc-2.1.2/RJafroc/inst/cranSubmission/cran-comments-last-submission.md |only RJafroc-2.1.2/RJafroc/inst/cranSubmission/cranSubmission.R | 31 RJafroc-2.1.2/RJafroc/man/ChisqrGoodnessOfFit.Rd | 2 RJafroc-2.1.2/RJafroc/man/DfFroc2Roc.Rd | 8 RJafroc-2.1.2/RJafroc/man/DfReadCrossedModalities.Rd | 15 RJafroc-2.1.2/RJafroc/man/FitRsmRoc.Rd | 8 RJafroc-2.1.2/RJafroc/man/PlotRsmOperatingCharacteristics.Rd | 29 RJafroc-2.1.2/RJafroc/man/RJafroc-package.Rd | 583 ++++------ RJafroc-2.1.2/RJafroc/man/RSM_LLF.Rd |only RJafroc-2.1.2/RJafroc/man/RSM_NLF.Rd |only RJafroc-2.1.2/RJafroc/man/RSM_pdfD.Rd | 6 RJafroc-2.1.2/RJafroc/man/RSM_pdfN.Rd | 4 RJafroc-2.1.2/RJafroc/man/RSM_wLLF.Rd |only RJafroc-2.1.2/RJafroc/man/RSM_xROC.Rd | 4 RJafroc-2.1.2/RJafroc/man/RSM_yROC.Rd | 6 RJafroc-2.1.2/RJafroc/man/SimulateFrocDataset.Rd | 6 RJafroc-2.1.2/RJafroc/man/SimulateLrocDataset.Rd | 8 RJafroc-2.1.2/RJafroc/man/SsFrocNhRsmModel.Rd | 8 RJafroc-2.1.2/RJafroc/man/StSignificanceTestingCrossedModalities.Rd | 6 RJafroc-2.1.2/RJafroc/man/UtilAnalyticalAucsRSM.Rd | 30 RJafroc-2.1.2/RJafroc/man/UtilIntrinsic2RSM.Rd |only RJafroc-2.1.2/RJafroc/man/UtilRSM2Intrinsic.Rd |only RJafroc-2.1.2/RJafroc/src/CommonFuncs.h | 12 RJafroc-2.1.2/RJafroc/src/RcppExports.cpp | 64 - RJafroc-2.1.2/RJafroc/src/RsmFuncs.cpp | 37 RJafroc-2.1.2/RJafroc/src/SmAucInt.cpp | 18 RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Fitting/RsmRoc.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Fitting/RsmRocDegenerate.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Plots/lrocData-LROC-lists.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Plots/lrocData-LROC-vectors.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Plots/lrocData-LROC.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Plots/lrocData-ROC-lists.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Plots/lrocData-ROC.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/SimulateDatasets/SimulateFrocDataset.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/SimulateDatasets/SimulateRocDataset.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/SsPower/FROC-dataset04.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/goodValues361/Utils/Intrinsic2PhysicalRSM.rds |binary RJafroc-2.1.2/RJafroc/tests/testthat/test-Df2RJafrocDataset.R | 4 RJafroc-2.1.2/RJafroc/tests/testthat/test-DfReadCrossedModalities.R | 36 RJafroc-2.1.2/RJafroc/tests/testthat/test-DfXroc2Xroc.R | 30 RJafroc-2.1.2/RJafroc/tests/testthat/test-LrocFomCheck.R | 152 +- RJafroc-2.1.2/RJafroc/tests/testthat/test-PlotEmpiricalOperatingCharacteristics.R | 61 - RJafroc-2.1.2/RJafroc/tests/testthat/test-RSM-formulae.R | 69 - RJafroc-2.1.2/RJafroc/tests/testthat/test-SsSampleSizeFroc.R | 2 RJafroc-2.1.2/RJafroc/tests/testthat/test-UtilIntrinsic2Physical.R | 6 RJafroc-2.1.2/RJafroc/tests/testthat/test-lesDistr-weights.R | 33 RJafroc-2.1.2/RJafroc/tests/testthat/test-model-aucs.R | 40 RJafroc-2.1.2/RJafroc/tests/testthat/test-predicted-plots.R | 87 + RJafroc-2.1.2/RJafroc/tests/testthat/test-simulate-datasets.R | 4 91 files changed, 1361 insertions(+), 1298 deletions(-)
Title: Create and Maintain a Relational Database of Data from
PubMed/MEDLINE
Description: Provides a simple interface for extracting various elements from
the publicly available PubMed XML files, incorporating PubMed's regular
updates, and combining the data with the NIH Open Citation Collection. See
Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between pmparser versions 1.0.10 dated 2022-04-28 and 1.0.11 dated 2022-11-08
DESCRIPTION | 8 MD5 | 28 - NEWS.md | 3 build/vignette.rds |binary inst/doc/data_dictionary.html | 14 tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db |binary tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db |binary tests/testthat/parsing_tables/get_parsing_tables_no_suffix.rds |binary tests/testthat/parsing_tables/get_parsing_tables_with_suffix.rds |binary tests/testthat/pubmed_sample/file_info_predown_all.csv | 280 ++++++++++ tests/testthat/pubmed_sample/open_citation_collection.zip |binary tests/testthat/pubmed_sample/pmdb_sample_create.db |binary tests/testthat/pubmed_sample/pmdb_sample_update.db |binary tests/testthat/pubmed_sample/pubmed22n1114.rds |binary tests/testthat/pubmed_sample/pubmed22n1115.rds |binary 15 files changed, 308 insertions(+), 25 deletions(-)
Title: Fitting and Tuning Regularized Cause-Specific Cox Models with
Elastic-Net Penalty
Description: Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.
Author: Shahin Roshani [aut, cre, cph]
Maintainer: Shahin Roshani <s.roshani@nki.nl>
Diff between CSCNet versions 0.1.1 dated 2022-10-06 and 0.1.2 dated 2022-11-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 13 +++++++------ R/penCSC.R | 18 ++++++++++++------ R/predict.penCSC.R | 12 ++++++++++-- R/tune_penCSC.R | 6 +++++- inst/doc/CSCNet.html | 18 +++++++++--------- 7 files changed, 52 insertions(+), 33 deletions(-)
Title: Variance Function Program
Description: Variance function estimation for models proposed by W. Sadler in his variance function program
('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is
to fit multiple variance functions to a data set and consequently assess which function reflects
the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship
is of great importance when individual test-results are used for defining follow-up treatment of patients.
Author: Andre Schuetzenmeister [cre, aut],
Florian Dufey [aut],
Andrea Geistanger [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VFP versions 1.4 dated 2021-12-20 and 1.4.1 dated 2022-11-08
VFP-1.4.1/VFP/DESCRIPTION | 10 +- VFP-1.4.1/VFP/MD5 | 27 +++---- VFP-1.4.1/VFP/NAMESPACE | 1 VFP-1.4.1/VFP/R/fit.R | 4 - VFP-1.4.1/VFP/R/methods.R | 4 - VFP-1.4.1/VFP/R/plot.R | 6 - VFP-1.4.1/VFP/R/utils.R | 2 VFP-1.4.1/VFP/build/vignette.rds |binary VFP-1.4.1/VFP/inst/ChangeLog.txt | 7 + VFP-1.4.1/VFP/inst/doc/VFP_package_vignette.html | 53 +++++++++----- VFP-1.4.1/VFP/man/VFP-Package.Rd | 4 - VFP-1.4.1/VFP/vignettes/figures/deriveCx_examples_2-1.png |binary VFP-1.4.1/VFP/vignettes/figures/deriveCx_examples_3-1.png |binary VFP-1.4.1/VFP/vignettes/figures/deriveCx_examples_4-1.png |binary VFP-1.4/VFP/inst/doc/How_to_work_with_package_VFP.pdf |only 15 files changed, 72 insertions(+), 46 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1> and for a tutorial on some of the main functions available here, see Gilleland (2022) <doi: 10.5065/4px3-5a05>.
Author: Eric Gilleland [aut, cre],
Kim Elmore [ctb],
Caren Marzban [ctb],
Matt Pocernich [ctb],
Gregor Skok [ctb]
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 1.0 dated 2022-07-19 and 1.0-1 dated 2022-11-08
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 +- inst/CITATION | 8 ++++---- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Regression Models with Break-Points / Change-Points (with
Possibly Random Effects) Estimation
Description: Given a regression model, segmented `updates' it by adding one or more segmented
(i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in
in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 1.6-0 dated 2022-05-31 and 1.6-1 dated 2022-11-08
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ NEWS | 11 +++++++++++ R/plot.segmented.R | 4 ++-- R/plot.segmented.lme.r | 26 ++++++++++++++++++++------ R/points.segmented.r | 3 ++- R/segmented.lme.r | 4 ++-- R/segmented.numeric.R | 13 +++++++++---- R/selgmented.r | 14 +++++++++++--- R/summary.segmented.lme.r | 2 +- inst/CITATION | 16 +++++++++++++++- man/aapc.Rd | 2 +- man/plot.segmented.lme.Rd | 4 ++-- man/points.segmented.Rd | 7 ++++--- man/segmented-package.Rd | 4 ++-- man/segmented.Rd | 2 +- man/segmented.lme.Rd | 27 +++++++++++++++------------ man/summary.segmented.lme.Rd | 10 +++++----- man/vcov.segmented.lme.Rd | 4 ++-- 19 files changed, 127 insertions(+), 70 deletions(-)
Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between jagshelper versions 0.1.9 dated 2022-11-01 and 0.1.11 dated 2022-11-08
DESCRIPTION | 8 - MD5 | 29 ++-- NAMESPACE | 1 NEWS.md | 6 R/jagshelper1.R | 245 ++++++++++++++++++++++++++++++++++++-- README.md | 3 inst/doc/jagshelper-vignette.R | 3 inst/doc/jagshelper-vignette.Rmd | 7 - inst/doc/jagshelper-vignette.html | 15 +- man/check_Rhat.Rd | 2 man/jagshelper-package.Rd | 4 man/plotRhats.Rd | 2 man/plotdens.Rd |only man/traceworstRhat.Rd | 2 tests/testthat/test_jagshelper.R | 11 + vignettes/jagshelper-vignette.Rmd | 7 - 16 files changed, 304 insertions(+), 41 deletions(-)
Title: Geographically Optimal Similarity
Description: Understanding spatial association is essential for spatial
statistical inference, including factor exploration and spatial prediction.
Geographically optimal similarity (GOS) model is an effective method
for spatial prediction, as described in Yongze Song (2022)
<doi:10.1007/s11004-022-10036-8>. GOS was developed based on
the geographical similarity principle, as described in Axing Zhu (2018)
<doi:10.1080/19475683.2018.1534890>. GOS has advantages in
more accurate spatial prediction using fewer samples and
critically reduced prediction uncertainty.
Author: Yongze Song [aut, cre]
Maintainer: Yongze Song <yongze.song@outlook.com>
Diff between geosimilarity versions 1.1 dated 2022-05-17 and 2.2 dated 2022-11-08
DESCRIPTION | 31 ++++--- INDEX | 3 MD5 | 26 ++++- NAMESPACE | 14 +++ R/bestkappa.R |only R/data.R | 32 ++++--- R/gos.R | 243 +++++++++++++++++++++++++++---------------------------- R/zzz.R |only build |only data/grid.rda |only inst |only man/bestkappa.Rd |only man/gos.Rd | 5 - man/grid.Rd |only vignettes |only 15 files changed, 200 insertions(+), 154 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.9.0 dated 2022-07-08 and 2.9.2 dated 2022-11-08
DESCRIPTION | 10 ++--- MD5 | 10 ++--- R/BAT.R | 93 ++++++++++++++++++++++++++++++++++++--------------- man/alpha.Rd | 4 +- man/hyper.quality.Rd | 2 - man/rao.Rd | 2 - 6 files changed, 80 insertions(+), 41 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.
Author: Pavel N. Krivitsky [aut, cre] ,
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between tergm versions 4.1.0 dated 2022-06-22 and 4.1.1 dated 2022-11-08
tergm-4.1.0/tergm/R/AAA.R |only tergm-4.1.0/tergm/man/Change-ergmTerm.Rd |only tergm-4.1.0/tergm/man/Cross-ergmTerm.Rd |only tergm-4.1.0/tergm/man/Diss-ergmTerm.Rd |only tergm-4.1.0/tergm/man/EdgeAges-ergmTerm.Rd |only tergm-4.1.0/tergm/man/Form-ergmTerm.Rd |only tergm-4.1.0/tergm/man/Persist-ergmTerm.Rd |only tergm-4.1.0/tergm/man/degrange.mean.age-ergmTerm.Rd |only tergm-4.1.0/tergm/man/degree.mean.age-ergmTerm.Rd |only tergm-4.1.0/tergm/man/discord-ergmHint.Rd |only tergm-4.1.0/tergm/man/discordBDStratTNT-ergmProposal.Rd |only tergm-4.1.0/tergm/man/discordTNT-ergmProposal.Rd |only tergm-4.1.0/tergm/man/edge.ages-ergmTerm.Rd |only tergm-4.1.0/tergm/man/edgecov.ages-ergmTerm.Rd |only tergm-4.1.0/tergm/man/edgecov.mean.age-ergmTerm.Rd |only tergm-4.1.0/tergm/man/edges.ageinterval-ergmTerm.Rd |only tergm-4.1.0/tergm/man/mean.age-ergmTerm.Rd |only tergm-4.1.0/tergm/man/nodefactor.mean.age-ergmTerm.Rd |only tergm-4.1.0/tergm/man/nodemix.mean.age-ergmTerm.Rd |only tergm-4.1.0/tergm/man/staticDiscordTNT-ergmProposal.Rd |only tergm-4.1.1/tergm/DESCRIPTION | 13 tergm-4.1.1/tergm/LICENSE | 1 tergm-4.1.1/tergm/MD5 | 72 +- tergm-4.1.1/tergm/R/InitErgmTerm.duration.R | 51 - tergm-4.1.1/tergm/R/simulate.tergm.R | 4 tergm-4.1.1/tergm/R/summary.statistics.networkDynamic.R | 16 tergm-4.1.1/tergm/build/tergm.pdf |binary tergm-4.1.1/tergm/build/vignette.rds |binary tergm-4.1.1/tergm/inst/CITATION | 6 tergm-4.1.1/tergm/inst/NEWS.Rd | 28 tergm-4.1.1/tergm/inst/doc/tergm4_conversion.html | 204 +++++- tergm-4.1.1/tergm/man/Change-ergmTerm-4236ef3c.Rd |only tergm-4.1.1/tergm/man/Cross-ergmTerm-03ab5578.Rd |only tergm-4.1.1/tergm/man/Diss-ergmTerm-f48278bd.Rd |only tergm-4.1.1/tergm/man/EdgeAges-ergmTerm-dcd27226.Rd |only tergm-4.1.1/tergm/man/Form-ergmTerm-fa13d505.Rd |only tergm-4.1.1/tergm/man/Persist-ergmTerm-34b51891.Rd |only tergm-4.1.1/tergm/man/combine_networks.Rd | 12 tergm-4.1.1/tergm/man/degrangemeanage-ergmTerm-26c66071.Rd |only tergm-4.1.1/tergm/man/degreemeanage-ergmTerm-405409f9.Rd |only tergm-4.1.1/tergm/man/discord-ergmHint-3608365e.Rd |only tergm-4.1.1/tergm/man/discordBDStratTNT-ergmProposal-9267ec8b.Rd |only tergm-4.1.1/tergm/man/discordTNT-ergmProposal-bc75dff0.Rd |only tergm-4.1.1/tergm/man/edgeages-ergmTerm-07c50367.Rd |only tergm-4.1.1/tergm/man/edgecovages-ergmTerm-8222522a.Rd |only tergm-4.1.1/tergm/man/edgecovmeanage-ergmTerm-46204f5f.Rd |only tergm-4.1.1/tergm/man/edgesageinterval-ergmTerm-3ea18dd0.Rd |only tergm-4.1.1/tergm/man/is.durational.Rd | 6 tergm-4.1.1/tergm/man/meanage-ergmTerm-8d81c4e1.Rd |only tergm-4.1.1/tergm/man/nodefactormeanage-ergmTerm-11ed6b41.Rd |only tergm-4.1.1/tergm/man/nodemixmeanage-ergmTerm-f93ece12.Rd |only tergm-4.1.1/tergm/man/staticDiscordTNT-ergmProposal-b73a241d.Rd |only tergm-4.1.1/tergm/src/discordTNT.c | 47 + tergm-4.1.1/tergm/tests/testthat/test-discord-proposals.R | 301 ++++++++++ tergm-4.1.1/tergm/tests/testthat/test-durational-terms.R | 4 tergm-4.1.1/tergm/tests/testthat/test-lasttoggle.R | 2 tergm-4.1.1/tergm/tests/testthat/test-summary-networkDynamic.R |only 57 files changed, 596 insertions(+), 171 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: A set of tools for processing and modeling high-throughput and
high-content chemical screening data. The package was developed for the
the chemical screening data generated by the US EPA ToxCast program, but
can be used for diverse chemical screening efforts.
Author: Richard S Judson [ctb, ths],
Dayne L Filer [aut],
Jason Brown [cre],
Sarah E Davidson-Fritz [ctb] ,
Madison Feshuk [ctb] ,
Lori Kolaczkowski [ctb],
Todd Zurlinden [ctb],
Parth Kothiya [ctb],
Woodrow R Setzer [ctb],
Matthew T Martin [ctb, ths],
Katie [...truncated...]
Maintainer: Jason Brown <brown.jason@epa.gov>
Diff between tcpl versions 3.0.0 dated 2022-08-31 and 3.0.1 dated 2022-11-08
DESCRIPTION | 10 MD5 | 142 ++++----- NEWS | 5 R/mc4.R | 14 R/mc4_mthds.R | 6 R/tcplFit2.R | 9 R/tcplLoadConcUnit.R | 8 build/vignette.rds |binary inst/doc/Assay_Registration.html | 112 +++---- inst/doc/Data_processing-Archive_tcpl_v2.html | 210 ++++++------- inst/doc/Data_processing.R | 161 +++++----- inst/doc/Data_processing.Rmd | 180 ++++++----- inst/doc/Data_processing.html | 405 +++++++++++++------------- inst/doc/Data_retrieval.R | 8 inst/doc/Data_retrieval.Rmd | 10 inst/doc/Data_retrieval.html | 171 +++++----- inst/doc/Introduction_Appendices.R | 2 inst/doc/Introduction_Appendices.Rmd | 8 inst/doc/Introduction_Appendices.html | 141 ++++----- man/MC2_Methods.Rd | 108 +++--- man/MC3_Methods.Rd | 294 +++++++++--------- man/MC4_Methods.Rd | 98 +++--- man/MC5_Methods.Rd | 90 ++--- man/MC6_Methods.Rd | 132 ++++---- man/Models.Rd | 292 +++++++++--------- man/SC1_Methods.Rd | 184 +++++------ man/assay_funcs.Rd | 142 ++++----- man/blineShift.Rd | 56 +-- man/dot-buildAssayQ.Rd | 54 +-- man/dot-convertNames.Rd | 38 +- man/dot-plateHeat.Rd | 68 ++-- man/dot-prepField.Rd | 44 +- man/flareFunc.Rd | 56 +-- man/hill_utils.Rd | 142 ++++----- man/interlaceFunc.Rd | 62 +-- man/is.odd.Rd | 50 +-- man/lu.Rd | 82 ++--- man/lw.Rd | 82 ++--- man/mthd_funcs.Rd | 176 +++++------ man/query_funcs.Rd | 134 ++++---- man/registerMthd.Rd | 58 +-- man/rgstr_funcs.Rd | 184 +++++------ man/sink.reset.Rd | 48 +-- man/tcplAICProb.Rd | 78 ++--- man/tcplAddModel.Rd | 124 +++---- man/tcplAppend.Rd | 48 +-- man/tcplCascade.Rd | 64 ++-- man/tcplCode2CASN.Rd | 60 +-- man/tcplCytoPt.Rd | 246 +++++++-------- man/tcplDelete.Rd | 54 +-- man/tcplFit.Rd | 118 +++---- man/tcplFit2.Rd | 5 man/tcplListFlds.Rd | 56 +-- man/tcplLoadChem.Rd | 118 +++---- man/tcplLoadClib.Rd | 126 ++++---- man/tcplLoadConcUnit.Rd | 44 +- man/tcplLoadUnit.Rd | 44 +- man/tcplLvlCount.Rd | 106 +++--- man/tcplMakeAeidMultiPlts.Rd | 80 ++--- man/tcplMakeAeidPlts.Rd | 128 ++++---- man/tcplMakeChidMultiPlts.Rd | 80 ++--- man/tcplMultiplot.Rd | 72 ++-- man/tcplPlotFitc.Rd | 58 +-- man/tcplPlotM4ID.Rd | 98 +++--- man/tcplPlotPlate.Rd | 114 +++---- man/tcplPrepOtpt.Rd | 114 +++---- man/tcplSubsetChid.Rd | 134 ++++---- man/tcplVarMat.Rd | 252 ++++++++-------- man/tcplWriteLvl0.Rd | 82 ++--- vignettes/Data_processing.Rmd | 180 ++++++----- vignettes/Data_retrieval.Rmd | 10 vignettes/Introduction_Appendices.Rmd | 8 72 files changed, 3543 insertions(+), 3434 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Uses by default the 's2'
package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] ,
Roger Bivand [ctb] ,
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] ,
Kirill Mueller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-8 dated 2022-07-14 and 1.0-9 dated 2022-11-08
DESCRIPTION | 12 MD5 | 109 - NAMESPACE | 3 NEWS.md | 16 R/RcppExports.R | 8 R/aggregate.R | 2 R/bbox.R | 2 R/break_antimeridian.R |only R/gdal_utils.R | 6 R/geom-measures.R | 21 R/geom-transformers.R | 4 R/init.R | 6 R/make_grid.R | 11 R/s2.R | 14 R/sample.R | 30 R/sf.R | 2 R/sfc.R | 2 R/spatstat.R | 6 R/stars.R | 34 R/tidyverse.R | 8 R/transform.R | 14 configure | 2864 +++++++++++++++++++++---------------------- configure.ac | 16 inst/doc/sf1.Rmd | 2 inst/doc/sf1.html | 126 - inst/doc/sf2.html | 6 inst/doc/sf4.html | 2 inst/doc/sf7.html | 18 inst/docker/arrow |only inst/docker/devel/Dockerfile | 32 inst/docker/gdal/Dockerfile | 10 man/gdal.Rd | 52 man/gdal_utils.Rd | 2 man/geos_unary.Rd | 4 man/s2.Rd | 2 man/st_break_antimeridian.Rd |only man/st_coordinates.Rd | 2 man/st_geometry.Rd | 2 man/st_sample.Rd | 7 man/st_transform.Rd | 13 man/tidyverse.Rd | 9 man/vctrs.Rd | 4 src/Makevars.ucrt | 7 src/Makevars.win | 4 src/RcppExports.cpp | 38 src/gdal_read.cpp | 22 src/gdal_utils.cpp | 39 src/gdal_write.cpp | 3 src/geos.cpp | 4 src/mdim.cpp | 431 +++++- tests/gdal_geom.Rout.save | 15 tests/geos.Rout.save | 10 tests/sfc.Rout.save | 17 tests/spatstat.Rout.save | 8 tests/testthat/test_read.R | 2 tests/testthat/test_write.R | 1 vignettes/sf1.Rmd | 2 57 files changed, 2273 insertions(+), 1813 deletions(-)
Title: Record Linkage Functions for Linking and Deduplicating Data Sets
Description: Provides functions for linking and deduplicating data sets.
Methods based on a stochastic approach are implemented as well as
classification algorithms from the machine learning domain. For details,
see our paper "The RecordLinkage Package: Detecting Errors in Data"
Sariyar M / Borg A (2010) <doi:10.32614/RJ-2010-017>.
Author: Murat Sariyar [aut, cre],
Andreas Borg [aut]
Maintainer: Murat Sariyar <murat.sariyar@bfh.ch>
Diff between RecordLinkage versions 0.4-12.2 dated 2022-01-09 and 0.4-12.4 dated 2022-11-08
DESCRIPTION | 6 ++-- MD5 | 50 ++++++++++++++++++------------------- NEWS | 17 ++++++------ R/phonetics.r | 4 +-- R/strcmp.r | 8 +++--- R/summary.r | 4 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BigData.pdf |binary inst/doc/EVT.pdf |binary inst/doc/Supervised.pdf |binary inst/doc/WeightBased.pdf |binary inst/doc/WeightBased.rnw | 2 - man/RLBigData-constructors.rd | 27 ++++++-------------- man/RLdata.rd | 8 ++---- man/compare.rd | 56 ++++++++++++------------------------------ man/deleteNULLs.Rd | 56 ++++++++++++++++++++---------------------- man/epiWeights.Rd | 39 ++++++++--------------------- man/internals.Rd | 2 - man/phonetics.Rd | 3 -- man/stochastic.rd | 15 +++-------- man/strcmp.rd | 25 ++++++------------ man/trainSupv.Rd | 4 --- src/mygllm.c | 18 ++++++------- src/sqlite_extensions.c | 7 +++-- vignettes/WeightBased.rnw | 2 - 26 files changed, 141 insertions(+), 212 deletions(-)
Title: Toolbox for Pseudo and Quasi Random Number Generation and Random
Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators,
multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister
algorithm (<doi:10.1007/978-3-540-74496-2_36>) and WELL (<doi:10.1145/1132973.1132974>)
generators); (2) quasi random generators - the Torus algorithm, the
Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some
generator tests - the gap test, the serial test, the poker test, see, e.g.,
Gentle (2003) <doi:10.1007/b97336>.
Take a look at the Distribution task view of types and tests of random number generators.
The package can be provided without the 'rngWELL' dependency on demand.
Package in Memoriam of Diethelm and Barbara Wuertz.
Author: R code by Yohan Chalabi [ctb], Christophe Dutang [aut, cre], Petr Savicky [aut],
Diethelm Wuertz [aut]; C code of Knuth-TAOCP RNG by Donald Knuth [aut];
C code of Torus, Halton and Sobol sequences by Christophe Dutang [aut, cre];
C code of SFMT algor [...truncated...]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between randtoolbox versions 2.0.2 dated 2022-08-16 and 2.0.3 dated 2022-11-08
DESCRIPTION | 20 +++-- MD5 | 66 ++++++++--------- R/pseudoRNG.R | 3 R/quasiRNG.R | 18 ++-- R/runifInterface.R | 153 +++++++++++++++++++--------------------- build/partial.rdb |only build/vignette.rds |binary inst/NEWS | 15 +++ inst/doc/fullpres.pdf |binary inst/doc/shortintro.pdf |binary man/colltest.Rd | 4 - man/colltestsparse.Rd | 5 - man/freqtest.Rd | 4 - man/gaptest.Rd | 4 - man/ordertest.Rd | 4 - man/overall-doc.Rd | 13 +-- man/pokertest.Rd | 4 - man/pseudoRNG.Rd | 37 ++++----- man/quasiRNG.Rd | 35 ++++----- man/runifInterface.Rd | 2 man/serialtest.Rd | 6 - man/sobol-test-func.Rd | 4 - src/LowDiscrepancy-halton.c | 8 +- src/LowDiscrepancy-halton.h | 9 ++ src/congruRand.c | 36 +++++---- src/congruRand.h | 13 ++- src/init.c | 24 ++++-- src/knuthTAOCP2002.c | 15 +++ src/randtoolbox.c | 12 ++- src/randtoolbox.h | 10 ++ src/runifInterface.c | 12 ++- src/runifInterface.h | 17 +++- src/version.c | 2 tests/test-knuthTAOCP.R |only tests/test-runifInterface-LCG.R | 58 ++++++++------- 35 files changed, 351 insertions(+), 262 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.11 dated 2022-09-25 and 2.12 dated 2022-11-08
DESCRIPTION | 10 - MD5 | 117 +++++++++--------- NAMESPACE | 2 R/TheilSen.R | 2 R/calendarPlot.R | 55 ++++++-- R/corPlot.R | 11 + R/getMeta.R | 323 ++++++++++++++++++++++++++++++++------------------ R/import.2.R | 103 +++++++-------- R/importADMS.R | 103 +++++++-------- R/importAQE.R | 44 +++--- R/importAURN.R | 219 ++++++++++++++++----------------- R/importAURNCsv.R | 21 +-- R/importEUR.R | 198 +++++++++++++++--------------- R/importKCL.R | 71 +++++----- R/importLocal.R |only R/importNI.R | 48 +++---- R/importSAQN.R | 49 +++---- R/importTraj.R | 47 +++---- R/importUKAQ.R | 311 +++++++++++++++++++++++------------------------- R/importWAQN.R | 48 +++---- R/linearRelation.R | 27 +++- R/percentileRose.R | 13 +- R/polarAnnulus.R | 13 +- R/polarCluster.R | 32 +++- R/polarDiff.R | 9 + R/polarFreq.R | 144 +++++++++++----------- R/polarPlot.R | 24 ++- R/scatterPlot.R | 18 +- R/smoothTrend.R | 21 +-- R/summaryPlot.R | 214 +++++++++++++++------------------ R/timePlot.R | 9 - R/timeProp.R | 7 - R/timeVariation.R | 7 - R/trajCluster.R | 226 +++++++++++++++++----------------- R/trajLevel.R | 10 + R/trendLevel.R | 7 - R/windRose.R | 262 +++++++++++++++++++--------------------- man/TheilSen.Rd | 2 man/calendarPlot.Rd | 5 man/corPlot.Rd | 5 man/importAURN.Rd | 31 +++- man/importEurope.Rd | 6 man/importMeta.Rd | 16 +- man/linearRelation.Rd | 5 man/percentileRose.Rd | 5 man/polarAnnulus.Rd | 5 man/polarCluster.Rd | 5 man/polarDiff.Rd | 14 ++ man/polarFreq.Rd | 5 man/polarPlot.Rd | 5 man/scatterPlot.Rd | 5 man/smoothTrend.Rd | 5 man/summaryPlot.Rd | 210 +++++++++++++++----------------- man/timePlot.Rd | 5 man/timeProp.Rd | 5 man/timeVariation.Rd | 5 man/trajCluster.Rd | 8 - man/trajLevel.Rd | 5 man/trendLevel.Rd | 5 man/windRose.Rd | 52 +++++--- 60 files changed, 1757 insertions(+), 1482 deletions(-)
Title: Compute and Illustrate the Multiple Facets of Functional
Diversity
Description: Computing functional traits-based distances between pairs of
species for species gathered in assemblages allowing to build several
functional spaces. The package allows to compute functional diversity
indices assessing the distribution of species (and of their dominance) in a
given functional space for each assemblage and the overlap between
assemblages in a given functional space, see: Chao et al. (2018)
<doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>,
Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al.
(2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009)
<doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included.
Visit the 'mFD' website for more information, documentation and examples.
Author: Camille Magneville [aut, cre, cph]
,
Nicolas Loiseau [aut] ,
Camille Albouy [aut] ,
Nicolas Casajus [aut] ,
Thomas Claverie [aut] ,
Arthur Escalas [aut] ,
Fabien Leprieur [aut] ,
Eva Maire [aut] ,
David Mouillot [aut] ,
Sebastien Villeger [aut]
Maintainer: Camille Magneville <camille.magneville@gmail.com>
Diff between mFD versions 1.0.1 dated 2021-12-16 and 1.0.2 dated 2022-11-08
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 19 R/check_inputs.R | 4 R/plot_beta_indices.R | 6 R/quality_fspaces.R | 8 README.md | 11 build/vignette.rds |binary inst/CITATION | 12 inst/doc/Compute_and_interpret_quality_of_functional_spaces.R | 2 inst/doc/Compute_and_interpret_quality_of_functional_spaces.Rmd | 2 inst/doc/Compute_and_interpret_quality_of_functional_spaces.html | 6 inst/doc/Compute_functional_hill_indices.html | 4 inst/doc/Continuous_traits_framework.html | 4 inst/doc/Customised_plots.R |only inst/doc/Customised_plots.Rmd |only inst/doc/Customised_plots.html |only inst/doc/How_to_deal_with_Functional_Entities.R | 2 inst/doc/How_to_deal_with_Functional_Entities.Rmd | 4 inst/doc/How_to_deal_with_Functional_Entities.html | 145 ++-- inst/doc/mFD_general_workflow.R | 92 +- inst/doc/mFD_general_workflow.Rmd | 26 inst/doc/mFD_general_workflow.html | 309 ++++++++-- inst/sticker |only man/figures/hexasticker_mFD.png |binary vignettes/Compute_and_interpret_quality_of_functional_spaces.Rmd | 2 vignettes/Customised_plots.Rmd |only vignettes/How_to_deal_with_Functional_Entities.Rmd | 4 vignettes/mFD_general_workflow.Rmd | 26 29 files changed, 509 insertions(+), 237 deletions(-)
Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a
combination of narrative, figures, videos, exercises, and quizzes to
create self-paced tutorials for learning about R and R packages.
Author: Garrick Aden-Buie [aut, cre] ,
Barret Schloerke [aut] ,
JJ Allaire [aut, ccp],
Alexander Rossell Hayes [ctb] ,
Nischal Shrestha [ctb] ,
Angela Li [ctb] ,
RStudio [cph, fnd],
Ajax.org B.V. [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Payne [ctb, cph] ,
J [...truncated...]
Maintainer: Garrick Aden-Buie <garrick@rstudio.com>
Diff between learnr versions 0.11.1 dated 2022-10-19 and 0.11.2 dated 2022-11-08
learnr-0.11.1/learnr/tests/testthat/tutorials/basic.html |only learnr-0.11.1/learnr/tests/testthat/tutorials/hint-copy/hint-copy.html |only learnr-0.11.1/learnr/tests/testthat/tutorials/hint-div/hint-div.html |only learnr-0.11.1/learnr/tests/testthat/tutorials/hint-div/hint-next.html |only learnr-0.11.1/learnr/tests/testthat/tutorials/hint-next/hint-next.html |only learnr-0.11.1/learnr/tests/testthat/tutorials/knitr-hooks_empty-exercise/duplicate-label.html |only learnr-0.11.2/learnr/DESCRIPTION | 12 +-- learnr-0.11.2/learnr/MD5 | 32 ++++------ learnr-0.11.2/learnr/NAMESPACE | 2 learnr-0.11.2/learnr/NEWS.md | 8 ++ learnr-0.11.2/learnr/R/exercise.R | 2 learnr-0.11.2/learnr/R/learnr-package.R | 2 learnr-0.11.2/learnr/R/quiz.R | 8 -- learnr-0.11.2/learnr/build/vignette.rds |binary learnr-0.11.2/learnr/inst/doc/shinyapps-publishing.Rmd | 2 learnr-0.11.2/learnr/inst/doc/shinyapps-publishing.html | 7 -- learnr-0.11.2/learnr/man/rmd-fragments/learnr-install.Rmd | 2 learnr-0.11.2/learnr/man/rmd-fragments/learnr-overview.Rmd | 2 learnr-0.11.2/learnr/tests/testthat/test-exercise.R | 22 ++++++ learnr-0.11.2/learnr/vignettes/shinyapps-publishing.Rmd | 2 20 files changed, 56 insertions(+), 47 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.2.1 dated 2022-05-24 and 1.2.2 dated 2022-11-08
dexter-1.2.1/dexter/NEWS |only dexter-1.2.2/dexter/DESCRIPTION | 10 dexter-1.2.2/dexter/MD5 | 58 +-- dexter-1.2.2/dexter/NEWS.md |only dexter-1.2.2/dexter/R/dexter.R | 192 +--------- dexter-1.2.2/dexter/R/enorm.R | 28 + dexter-1.2.2/dexter/R/individual_differences.R | 41 +- dexter-1.2.2/dexter/R/misc.R | 9 dexter-1.2.2/dexter/R/oplike.R | 18 dexter-1.2.2/dexter/R/plausible_scores.R | 9 dexter-1.2.2/dexter/R/plots.R | 27 - dexter-1.2.2/dexter/R/profile_analysis.R | 2 dexter-1.2.2/dexter/R/reparam.R | 1 dexter-1.2.2/dexter/R/resp_data.R | 11 dexter-1.2.2/dexter/R/standards.R | 22 - dexter-1.2.2/dexter/R/suf_stats.R | 9 dexter-1.2.2/dexter/R/tia.R | 56 ++ dexter-1.2.2/dexter/build/vignette.rds |binary dexter-1.2.2/dexter/inst/doc/DIF_vignette.html | 23 - dexter-1.2.2/dexter/inst/doc/Equating.html | 33 + dexter-1.2.2/dexter/inst/doc/Plausible_Values.html | 27 - dexter-1.2.2/dexter/inst/doc/Test_Individual_differences.html | 31 - dexter-1.2.2/dexter/inst/doc/dexter.html | 77 ++-- dexter-1.2.2/dexter/inst/doc/profile-plots.html | 20 - dexter-1.2.2/dexter/man/distractor_plot.Rd | 3 dexter-1.2.2/dexter/man/tia_tables.Rd | 7 dexter-1.2.2/dexter/src/data.cpp | 21 - dexter-1.2.2/dexter/tests/testthat/test_data_selection.R | 24 - dexter-1.2.2/dexter/tests/testthat/test_database.R | 20 + dexter-1.2.2/dexter/tests/testthat/test_enorm.R | 1 dexter-1.2.2/dexter/tests/testthat/test_profiles.R | 2 31 files changed, 404 insertions(+), 378 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-03 0.7.3
2019-05-15 0.7
2018-01-28 0.6.4
Title: Fake Web Apps for HTTP Testing
Description: Create a web app that makes it easier to test web clients
without using the internet. It includes a web app framework with path
matching, parameters and templates. Can parse various 'HTTP' request
bodies. Can send 'JSON' data or files from the disk. Includes a web app
that implements the <https://httpbin.org> web service.
Author: Gabor Csardi [aut, cre],
RStudio, Pbc. [cph],
Civetweb contributors [ctb] ,
Redoc contributors [ctb] ,
L. Peter Deutsch [ctb] ,
Martin Purschke [ctb] ,
Aladdin Enterprises [cph] ,
Maelle Salmon [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between webfakes versions 1.1.5 dated 2022-10-25 and 1.1.6 dated 2022-11-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/app-process.R | 5 +++++ R/response.R | 9 ++++++++- 5 files changed, 28 insertions(+), 8 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial
transport data and non-motorized modes. Create geographic "desire
lines" from origin-destination (OD) data (building on the 'od'
package); calculate routes on the transport network locally and via
interfaces to routing services such as <https://cyclestreets.net/>;
calculate route segment attributes such as bearing. The package
implements the 'travel flow aggregration' method described in Morgan
and Lovelace (2020) <doi:10.1177/2399808320942779>. Further
information on the package's aim and scope can be found in the
vignettes and in a paper in the R Journal (Lovelace and Ellison 2018)
<doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] ,
Richard Ellison [aut],
Malcolm Morgan [aut] ,
Barry Rowlingson [ctb],
Nick Bearman [ctb],
Nikolai Berkoff [ctb],
Scott Chamberlain [rev] ,
Mark Padgham [ctb],
Andrea Gilardi [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 1.0.1 dated 2022-08-19 and 1.0.2 dated 2022-11-08
DESCRIPTION | 8 - MD5 | 106 +++++++++++++------------- NEWS.md | 4 R/data.R | 22 +++-- R/geo_projected.R | 4 R/oneway.R | 2 R/overline.R | 8 + README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/stplanr-od.html | 142 ++++++++++++++++++----------------- inst/doc/stplanr-paper.html | 158 ++++++++++++++++++++------------------- inst/doc/stplanr-parallel.html | 124 ++++++++++++++++-------------- inst/doc/stplanr-route-nets.html | 124 ++++++++++++++++-------------- inst/doc/stplanr-routing.html | 127 ++++++++++++++++--------------- inst/doc/stplanr.Rmd | 2 inst/doc/stplanr.html | 150 +++++++++++++++++++------------------ man/bbox_scale.Rd | 4 man/cents_sf.Rd | 17 ++++ man/destinations_sf.Rd | 13 ++- man/flow.Rd | 28 ++++++ man/flow_dests.Rd | 14 ++- man/flowlines_sf.Rd | 13 ++- man/geo_bb.Rd | 4 man/geo_bb_matrix.Rd | 4 man/geo_buffer.Rd | 11 ++ man/geo_length.Rd | 11 ++ man/geo_projected.Rd | 11 ++ man/geo_select_aeq.Rd | 11 ++ man/od2line.Rd | 1 man/od2odf.Rd | 1 man/od_aggregate_from.Rd | 1 man/od_aggregate_to.Rd | 1 man/od_coords.Rd | 1 man/od_coords2line.Rd | 1 man/od_data_lines.Rd | 17 ++++ man/od_data_routes.Rd | 17 ++++ man/od_data_sample.Rd | 17 ++++ man/od_id.Rd | 3 man/od_id_order.Rd | 16 +++ man/od_oneway.Rd | 1 man/od_to_odmatrix.Rd | 1 man/odmatrix_to_od.Rd | 1 man/osm_net_example.Rd | 17 ++++ man/overline.Rd | 4 man/points2flow.Rd | 1 man/points2odf.Rd | 1 man/quadrant.Rd | 6 + man/read_table_builder.Rd | 16 +++ man/route_network_sf.Rd | 13 ++- man/routes_fast_sf.Rd | 13 ++- man/routes_slow_sf.Rd | 13 ++- man/zones_sf.Rd | 17 ++++ vignettes/stplanr.Rmd | 2 54 files changed, 813 insertions(+), 492 deletions(-)
Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with 'mlr3',
e.g. grid search, random search, generalized simulated annealing and
iterated racing. Various termination criteria can be set and
combined. The class 'AutoTuner' provides a convenient way to perform
nested resampling in combination with 'mlr3'.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.15.0 dated 2022-10-21 and 0.16.0 dated 2022-11-08
DESCRIPTION | 27 +-- MD5 | 57 +++--- NAMESPACE | 5 NEWS.md | 6 R/AutoTuner.R | 8 R/CallbackTuning.R |only R/ContextEval.R |only R/ObjectiveTuning.R | 45 +++-- R/TunerIrace.R | 10 - R/TuningInstanceMulticrit.R | 7 R/TuningInstanceSingleCrit.R | 9 - R/auto_tuner.R | 5 R/mlr_callbacks.R |only R/reexport.R | 9 + R/tune.R | 6 R/zzz.R | 5 README.md | 311 ++++++++++++++++-------------------- build/partial.rdb |binary inst/WORDLIST | 9 + man/AutoTuner.Rd | 10 - man/CallbackTuning.Rd |only man/ContextEval.Rd |only man/ObjectiveTuning.Rd | 8 man/TuningInstanceMultiCrit.Rd | 8 man/TuningInstanceSingleCrit.Rd | 8 man/auto_tuner.Rd | 6 man/callback_tuning.Rd |only man/mlr3tuning.backup.Rd |only man/mlr3tuning.early_stopping.Rd |only man/mlr_tuners_irace.Rd | 3 man/reexports.Rd | 5 man/ti.Rd | 2 man/tune.Rd | 6 tests/testthat/test_mlr_callbacks.R |only 34 files changed, 325 insertions(+), 250 deletions(-)
Title: History Matching and Emulation Package
Description: A set of objects and functions for Bayes Linear emulation and history matching.
Core functionality includes automated training of emulators to data, diagnostic functions
to ensure suitability, and a variety of proposal methods for generating 'waves' of points.
For details on the mathematical background, there are many papers available on the topic
(see references attached to function help files); for details of the functions in this package,
consult the manual or help files.
Author: Andrew Iskauskas [aut, cre]
Maintainer: Andrew Iskauskas <andrew.iskauskas@durham.ac.uk>
Diff between hmer versions 1.0.1 dated 2022-05-17 and 1.2.0 dated 2022-11-08
DESCRIPTION | 15 - MD5 | 212 +++++++++--------- NAMESPACE | 3 NEWS.md | 22 + R/Emulator.R | 214 +++++++++++------- R/VarianceEmulator.R | 210 +++++++++++------- R/correlations.R | 11 R/derivative_functions.R | 6 R/diagnosticplots.R | 10 R/diagnostics.R | 72 +++++- R/fullwave.R | 14 - R/genpoints.R | 274 +++++++++++++++++------- R/implausibility.R | 21 + R/modelbuilding.R | 12 - R/multiwaveplot.R | 10 R/plotting.R | 4 R/utils.R | 77 +++++- build/vignette.rds |binary data/SIREmulators.rda |binary data/SIRMultiWaveEmulators.rda |binary inst/doc/demonstrating-the-hmer-package.Rmd | 28 -- inst/doc/demonstrating-the-hmer-package.html | 69 ++---- inst/doc/emulationhandbook.Rmd | 38 +-- inst/doc/emulationhandbook.html | 188 ++++++++-------- inst/doc/low-dimensional-examples.Rmd | 71 +++--- inst/doc/low-dimensional-examples.html | 180 ++++++++------- inst/doc/stochasticandbimodalemulation.Rmd | 6 inst/doc/stochasticandbimodalemulation.html | 55 ++-- man/analyze_diagnostic.Rd | 11 man/bimodal_emulator_from_data.Rd | 3 man/directional_proposal.Rd | 6 man/full_wave.Rd | 6 man/generate_new_runs.Rd | 18 + man/nth_implausible.Rd | 7 man/simulator_plot.Rd | 3 man/variance_emulator_from_data.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test-em_building.R | 8 tests/testthat/test-emulator.R | 7 tests/testthat/test-exp_sq.R | 28 +- tests/testthat/test-gamma_exp.R | 20 - tests/testthat/test-get_dist.R | 3 tests/testthat/test-implausibility.R | 8 tests/testthat/test-matern.R | 34 +- tests/testthat/test-orn_uhl.R | 22 - tests/testthat/test-point_gen.R | 2 tests/testthat/test-rat_quad.R | 32 +- tests/testthat/test-validation_diag.R | 13 - tests/testthat/test-variance_ems.R | 4 vignettes/demo-em-plot-2.png |binary vignettes/demo-em-plot-3.png |binary vignettes/demo-em-plot-4.png |binary vignettes/demo-em-plot-augment-1.png |binary vignettes/demo-em-plot-imp-1.png |binary vignettes/demo-em-plot-imp-2.png |binary vignettes/demo-gen-new-runs-1.png |binary vignettes/demo-lattice-plot-1.png |binary vignettes/demo-multi-wave-plots-1.png |binary vignettes/demo-plot-waves-1.png |binary vignettes/demo-validate-1.png |binary vignettes/demonstrating-the-hmer-package.Rmd | 28 -- vignettes/emulationhandbook.Rmd | 38 +-- vignettes/handbook-bad-design-diagnostic-1.png |binary vignettes/handbook-bad_design_generation-1.png |binary vignettes/handbook-behaviour-plot-1.png |binary vignettes/handbook-behaviour-plot-2.png |binary vignettes/handbook-output-active-1-1.png |binary vignettes/handbook-output-active-1-2.png |binary vignettes/handbook-transformed-imp-1.png |binary vignettes/low-dimensional-examples.Rmd | 71 +++--- vignettes/lowdim-changed-2d-validation-1.png |binary vignettes/lowdim-gen-1d-points-2-1.png |binary vignettes/lowdim-gen-2d-points-2-1.png |binary vignettes/lowdim-gen-2d-points-first-1.png |binary vignettes/lowdim-plot-1d-results-first-1.png |binary vignettes/lowdim-plot-2d-ems-1.png |binary vignettes/lowdim-plot-2d-ems-2.png |binary vignettes/lowdim-plot-2d-ems-corr-1.png |binary vignettes/lowdim-plot-2d-ems-imp-1.png |binary vignettes/lowdim-plot-2d-ems-imp-2.png |binary vignettes/lowdim-plot-2d-ems-with-augment-1.png |binary vignettes/lowdim-plot-2d-imp-2-1.png |binary vignettes/lowdim-plot-2d-waves-1.png |binary vignettes/lowdim-plot-2d-waves-2.png |binary vignettes/lowdim-plot-2d-waves-3.png |binary vignettes/lowdim-validate-2d-ems-1.png |binary vignettes/lowdim-validate-2d-ems-2-1.png |binary vignettes/lowdim-wave-2-1d-1.png |binary vignettes/stoch-bimodal-demo-1.png |binary vignettes/stoch-bimodal-imp-1.png |binary vignettes/stoch-bimodal-indiv-imp-1.png |binary vignettes/stoch-bimodal-indiv-imp-2.png |binary vignettes/stoch-plot-bimodal-1.png |binary vignettes/stoch-plot-bimodal-2.png |binary vignettes/stoch-plot-stoch-ems-1.png |binary vignettes/stoch-plot-stoch-ems-2.png |binary vignettes/stoch-plot-stoch-imp-1.png |binary vignettes/stoch-plot-stoch-var-1.png |binary vignettes/stoch-propose-bimodal-1.png |binary vignettes/stoch-propose-var-em-1.png |binary vignettes/stoch-validate-bimodal-1.png |binary vignettes/stoch-validate-bimodal-2.png |binary vignettes/stoch-validate-stoch-em-1.png |binary vignettes/stoch-validate-stoch-em-2.png |binary vignettes/stoch-validate-stoch-em-3.png |binary vignettes/stoch-validate-var-em-1.png |binary vignettes/stochasticandbimodalemulation.Rmd | 6 107 files changed, 1312 insertions(+), 891 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, following Marcon, Traissac, Puech, and Lang (2015) <doi:10.18637/jss.v067.c03>.
Includes classical functions (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M).
Relies on 'spatstat' for some core calculation.
Author: Eric Marcon [aut, cre] ,
Gabriel Lang [aut] ,
Stephane Traissac [aut] ,
Florence Puech [aut]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between dbmss versions 2.7-10 dated 2022-07-10 and 2.7-11 dated 2022-11-08
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS.md | 11 +++++++++++ R/KinhomEnvelope.R | 2 +- R/Kmmhat.R | 2 +- R/Ktest.r | 2 ++ R/autoplot.R | 4 ++-- build/vignette.rds |binary inst/doc/dbmss.html | 13 ++++++++++--- man/Ktest.Rd | 4 ++++ man/autoplot.Rd | 2 +- 12 files changed, 48 insertions(+), 24 deletions(-)
Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readMzXmlData versions 2.8.1 dated 2015-09-16 and 2.8.2 dated 2022-11-08
readMzXmlData-2.8.1/readMzXmlData/man/grepNumeric.Rd |only readMzXmlData-2.8.2/readMzXmlData/DESCRIPTION | 13 +- readMzXmlData-2.8.2/readMzXmlData/MD5 | 51 +++++----- readMzXmlData-2.8.2/readMzXmlData/NAMESPACE | 2 readMzXmlData-2.8.2/readMzXmlData/NEWS | 5 readMzXmlData-2.8.2/readMzXmlData/R/attribute-functions.R | 2 readMzXmlData-2.8.2/readMzXmlData/R/base64-functions.R | 2 readMzXmlData-2.8.2/readMzXmlData/R/grep-functions.R | 6 - readMzXmlData-2.8.2/readMzXmlData/R/package.R | 4 readMzXmlData-2.8.2/readMzXmlData/R/parseMzXml.R | 4 readMzXmlData-2.8.2/readMzXmlData/R/readMzXmlDir-functions.R | 2 readMzXmlData-2.8.2/readMzXmlData/R/readMzXmlFile-functions.R | 6 - readMzXmlData-2.8.2/readMzXmlData/R/revfregexpr-functions.R | 2 readMzXmlData-2.8.2/readMzXmlData/man/attributeTimeToDouble.Rd | 11 -- readMzXmlData-2.8.2/readMzXmlData/man/attributeToDouble.Rd | 11 -- readMzXmlData-2.8.2/readMzXmlData/man/attributeToString.Rd | 11 -- readMzXmlData-2.8.2/readMzXmlData/man/base64-decode.Rd | 17 +-- readMzXmlData-2.8.2/readMzXmlData/man/grepDouble.Rd |only readMzXmlData-2.8.2/readMzXmlData/man/grepNumber.Rd |only readMzXmlData-2.8.2/readMzXmlData/man/grepSubString.Rd | 9 - readMzXmlData-2.8.2/readMzXmlData/man/mzXmlHandlers.Rd | 11 -- readMzXmlData-2.8.2/readMzXmlData/man/parseMzXml.Rd | 3 readMzXmlData-2.8.2/readMzXmlData/man/readMzXmlData-defunct.Rd | 5 readMzXmlData-2.8.2/readMzXmlData/man/readMzXmlData-package.Rd | 21 +--- readMzXmlData-2.8.2/readMzXmlData/man/readMzXmlDir.Rd | 22 ++-- readMzXmlData-2.8.2/readMzXmlData/man/readMzXmlFile-internal.Rd | 9 - readMzXmlData-2.8.2/readMzXmlData/man/readMzXmlFile.Rd | 15 +- readMzXmlData-2.8.2/readMzXmlData/man/revfregexpr.Rd | 3 28 files changed, 127 insertions(+), 120 deletions(-)
Title: Genomic Prediction of Hybrid Performance
Description: Performs genomic prediction of hybrid performance using eight GS methods including GBLUP, BayesB, RKHS, PLS, LASSO, Elastic net, Random forest and XGBoost. It also provides fast cross-validation and mating design scheme for training population (Xu S et al (2016) <doi:10.1111/tpj.13242>; Xu S (2017) <doi:10.1534/g3.116.038059>).
Author: Yang Xu, Guangning Yu, Yanru Cui, Shizhong Xu, Chenwu Xu
Maintainer: Yang Xu <xuyang_89@126.com>
Diff between predhy versions 1.2.0 dated 2021-08-16 and 1.2.1 dated 2022-11-08
predhy-1.2.0/predhy/R/cv.r |only predhy-1.2.1/predhy/DESCRIPTION | 10 - predhy-1.2.1/predhy/MD5 | 18 +- predhy-1.2.1/predhy/NAMESPACE | 3 predhy-1.2.1/predhy/R/convertgen.R | 210 ++++++++++++------------- predhy-1.2.1/predhy/R/cv.R |only predhy-1.2.1/predhy/R/hybrid.predict_NCII.R |only predhy-1.2.1/predhy/R/import_packages.R | 3 predhy-1.2.1/predhy/R/predhy.predict.R | 16 - predhy-1.2.1/predhy/man/convertgen.Rd | 7 predhy-1.2.1/predhy/man/cv.Rd | 13 - predhy-1.2.1/predhy/man/predhy.predict_NCII.Rd |only 12 files changed, 150 insertions(+), 130 deletions(-)
Title: Outlier Detection Using Partitioning Clustering Algorithms
Description: An object is called "outlier" if it remarkably deviates from the other objects in a data set. Outlier detection is the process to find outliers by using the methods that are based on distance measures, clustering and spatial methods (Ben-Gal, 2005 <ISBN 0-387-24435-2>). It is one of the intensively studied research topics for identification of novelties, frauds, anomalies, deviations or exceptions in addition to its use for outlier removing in data processing. This package provides the implementations of some novel approaches to detect the outliers based on typicality degrees that are obtained with the soft partitioning clustering algorithms such as Fuzzy C-means and its variants.
Author: Zeynel Cebeci [aut, cre] ,
Cagatay Cebeci [ctb] ,
Yalcin Tahtali [ctb]
Maintainer: Zeynel Cebeci <zcebeci@cukurova.edu.tr>
Diff between odetector versions 1.0.0 dated 2022-10-04 and 1.0.1 dated 2022-11-08
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- inst/NEWS.Rd | 5 +++++ inst/doc/odetector.Rmd | 2 +- inst/doc/odetector.html | 18 +++++++++--------- vignettes/odetector.Rmd | 2 +- 6 files changed, 26 insertions(+), 21 deletions(-)
Title: Latent Unknown Clustering Integrating Multi-View Data
Description: An implementation of the LUCID model (Peng (2019) <doi:10.1093/bioinformatics/btz667>).
LUCID conducts integrated clustering using exposures, omics data (and outcome
as an option). An EM algorithm is implemented to estimate MLE of the LUCID model.
LUCIDus features integrated variable selection, incorporation of missing omics
data, bootstrap inference, prediction and visualization of the model.
Author: Yinqi Zhao [aut, cre] ,
David Conti [ths] ,
Jesse Goodrich [ctb] ,
Cheng Peng [ctb]
Maintainer: Yinqi Zhao <yinqiz@usc.edu>
Diff between LUCIDus versions 2.2 dated 2022-08-07 and 2.2.1 dated 2022-11-08
LUCIDus-2.2.1/LUCIDus/DESCRIPTION | 39 +++++++++++++++------ LUCIDus-2.2.1/LUCIDus/MD5 | 21 ++++++----- LUCIDus-2.2.1/LUCIDus/NEWS.md | 6 ++- LUCIDus-2.2.1/LUCIDus/R/est_lucid.R | 5 ++ LUCIDus-2.2.1/LUCIDus/build/vignette.rds |binary LUCIDus-2.2.1/LUCIDus/inst/CITATION | 41 +++++++++++++++-------- LUCIDus-2.2.1/LUCIDus/inst/doc/LUCIDus.R |only LUCIDus-2.2.1/LUCIDus/inst/doc/LUCIDus.Rmd |only LUCIDus-2.2.1/LUCIDus/inst/doc/LUCIDus.html |only LUCIDus-2.2.1/LUCIDus/vignettes/DAG.png |binary LUCIDus-2.2.1/LUCIDus/vignettes/LUCIDus.Rmd |only LUCIDus-2.2.1/LUCIDus/vignettes/workflow.png |only LUCIDus-2.2/LUCIDus/inst/doc/LUCID_vignette.R |only LUCIDus-2.2/LUCIDus/inst/doc/LUCID_vignette.Rmd |only LUCIDus-2.2/LUCIDus/inst/doc/LUCID_vignette.html |only LUCIDus-2.2/LUCIDus/vignettes/LUCID_vignette.Rmd |only 16 files changed, 76 insertions(+), 36 deletions(-)
Title: Local Control Strategy for Robust Analysis of Cross-Sectional
Data
Description: Especially when cross-sectional data are observational, effects of treatment
selection bias and confounding are revealed by using the Nonparametric and Unsupervised
"preprocessing" methods central to Local Control (LC) Strategy. The LC objective is
to estimate the "effect-size distribution" that best quantifies a potentially causal
relationship between a numeric y-Outcome variable and a t-Treatment or e-Exposure
variable. Treatment variables are binary {either 1 = "new" or 0 = "control"}, while
Exposure variables vary continuously over a finite range. LC Strategy starts by
CLUSTERING experimental units (individual patients, US Counties, etc.) on their
X-confounder characteristics. Clusters represent exclusive and exhaustive BLOCKS of
relatively well-matched units. The implicit statistical model for LC is thus simple
one-way ANOVA. Within-Block measures of effect-size are Local Rank Correlations (LRCs)
when Exposure is numeric with (many) more than two levels. Otherwise, Treatment choic [...truncated...]
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between LocalControlStrategy versions 1.3.3 dated 2019-08-29 and 1.4 dated 2022-11-08
DESCRIPTION | 41 ++++++++++++++++++------------------ MD5 | 24 ++++++++++++--------- R/LCsetup.R | 19 +++++++++++----- build/partial.rdb |binary data/datalist |only data/pci15k.rda |binary data/pmdata.rda |only data/radon.rda |binary demo/00Index | 1 demo/pmdata.R |only man/LocalControlStrategy-package.Rd | 14 ++++++------ man/lrcagg.Rd | 12 +++++----- man/ltdagg.Rd | 6 ++--- man/pmdata.Rd |only man/reveal.data.Rd | 2 - 15 files changed, 66 insertions(+), 53 deletions(-)
More information about LocalControlStrategy at CRAN
Permanent link
Title: Hydro-Meteorology Time-Series
Description: Functions for the management and treatment of hydrology and
meteorology time-series stored in a 'Sqlite' data base.
Author: Pierre Chevallier [aut, cre]
Maintainer: Pierre Chevallier <pierre.chevallier@ird.fr>
Diff between htsr versions 1.1.4 dated 2022-04-17 and 1.1.5 dated 2022-11-08
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- R/f_convert.R | 3 ++- R/h_addna.R |only build/vignette.rds |binary inst/doc/htsr-package.Rmd | 4 +++- inst/doc/htsr-package.html | 19 +++++++++++-------- man/f_convert.Rd | 2 +- man/h_addna.Rd |only vignettes/htsr-package.Rmd | 4 +++- 10 files changed, 34 insertions(+), 24 deletions(-)
Title: High-Dimensional Shrinkage Optimal Portfolios
Description: Constructs shrinkage estimators of high-dimensional mean-variance portfolios and performs
high-dimensional tests on optimality of a given portfolio. The techniques developed in
Bodnar et al. (2018) <doi:10.1016/j.ejor.2017.09.028>, Bodnar et al. (2019)
<doi:10.1109/TSP.2019.2929964>, Bodnar et al. (2020) <doi:10.1109/TSP.2020.3037369>
are central to the package. They provide simple and feasible estimators and tests for optimal
portfolio weights, which are applicable for 'large p and large n' situations where p is the
portfolio dimension (number of stocks) and n is the sample size. The package also includes tools
for constructing portfolios based on shrinkage estimators of the mean vector and covariance matrix
as well as a new Bayesian estimator for the Markowitz efficient frontier recently developed by
Bauder et al. (2021) <doi:10.1080/14697688.2020.1748214>.
Author: Taras Bodnar [aut] ,
Solomiia Dmytriv [aut] ,
Yarema Okhrin [aut] ,
Dmitry Otryakhin [aut, cre] ,
Nestor Parolya [aut]
Maintainer: Dmitry Otryakhin <d.otryakhin.acad@protonmail.ch>
Diff between HDShOP versions 0.1.2 dated 2021-10-23 and 0.1.3 dated 2022-11-08
HDShOP-0.1.2/HDShOP/NEWS.md |only HDShOP-0.1.3/HDShOP/DESCRIPTION | 8 HDShOP-0.1.3/HDShOP/MD5 | 36 +- HDShOP-0.1.3/HDShOP/NAMESPACE | 6 HDShOP-0.1.3/HDShOP/R/BDOPS_2020.R | 2 HDShOP-0.1.3/HDShOP/R/HDShOP-package.R | 4 HDShOP-0.1.3/HDShOP/R/S3_custom_portfol.R | 32 +- HDShOP-0.1.3/HDShOP/R/S3_tradit_portfol.R | 42 ++ HDShOP-0.1.3/HDShOP/R/S3_weights_portfol.R | 160 +++++++++- HDShOP-0.1.3/HDShOP/R/case_c_gr_1.R |only HDShOP-0.1.3/HDShOP/R/dispatchers.R | 76 +++- HDShOP-0.1.3/HDShOP/build/partial.rdb |binary HDShOP-0.1.3/HDShOP/inst/REFERENCES.bib | 9 HDShOP-0.1.3/HDShOP/man/MVShrinkPortfolio.Rd | 55 ++- HDShOP-0.1.3/HDShOP/man/MeanVar_portfolio.Rd | 2 HDShOP-0.1.3/HDShOP/man/new_GMV_portfolio_weights_BDPS19.Rd | 23 + HDShOP-0.1.3/HDShOP/man/new_MV_portfolio_traditional.Rd | 7 HDShOP-0.1.3/HDShOP/man/new_MV_portfolio_weights_BDOPS21.Rd | 27 + HDShOP-0.1.3/HDShOP/tests/testthat/test_T_stat.R | 2 HDShOP-0.1.3/HDShOP/tests/testthat/test_shrink_covar_methods.R | 35 ++ 20 files changed, 448 insertions(+), 78 deletions(-)
Title: Freedom from Disease
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997, <doi:10.1016/s0167-5877(97)00081-0>). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002, <doi:10.1016/S0167-5877(01)00245-8>). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka <ian.kopacka@ages.at>
Diff between FFD versions 1.0-8 dated 2021-01-07 and 1.0-9 dated 2022-11-08
FFD-1.0-8/FFD/src |only FFD-1.0-9/FFD/DESCRIPTION | 15 - FFD-1.0-9/FFD/MD5 | 16 - FFD-1.0-9/FFD/NAMESPACE | 2 FFD-1.0-9/FFD/R/FFD_GUI-internal.R | 12 - FFD-1.0-9/FFD/R/computeAposterioriError.R | 338 +++++++++++++++--------------- FFD-1.0-9/FFD/build/vignette.rds |binary FFD-1.0-9/FFD/inst/doc/FFD-intro.R | 324 ++++++++++++++-------------- FFD-1.0-9/FFD/inst/doc/FFD-intro.pdf |binary 9 files changed, 361 insertions(+), 346 deletions(-)
Title: Modelling and Analysis of Dynamic Computer Experiments
Description: Emulating and solving inverse problems for dynamic computer experiments.
It contains two major functionalities: (1) localized GP model for large-scale
dynamic computer experiments using the algorithm proposed by
Zhang et al. (2018) <arXiv:1611.09488>; (2) solving inverse problems
in dynamic computer experiments. The current version only supports 64-bit
version of R.
Author: Ru Zhang [aut, cre],
Chunfang Devon Lin [aut],
Pritam Ranjan [aut],
Robert B Gramacy [ctb],
Nicolas Devillard [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Peihuang Lu-Chen [ctb],
Berend Hasselman [ctb],
Ja [...truncated...]
Maintainer: Ru Zhang <heavenmarshal@gmail.com>
Diff between DynamicGP versions 1.1-8 dated 2022-04-12 and 1.1-9 dated 2022-11-08
DESCRIPTION | 8 - MD5 | 14 +- src/gp_sep.cpp | 6 - src/gpseplm.cpp | 8 - src/include/gp_sep.hpp | 2 src/include/gpseplm.hpp | 4 src/linalg.c | 252 ++++++++++++++++++++++++------------------------ src/nwout.c | 2 8 files changed, 150 insertions(+), 146 deletions(-)
Title: Continuous Time Meta-Analysis ('CoTiMA')
Description: The 'CoTiMA' package performs meta-analyses of correlation matrices of repeatedly measured variables taken from
studies that used different time intervals. Different time intervals between measurement occasions impose problems for
meta-analyses because the effects (e.g. cross-lagged effects) cannot be simply aggregated, for example, by means of common
fixed or random effects analysis. However, continuous time math, which is applied in 'CoTiMA', can be used to extrapolate or
intrapolate the results from all studies to any desired time lag. By this, effects obtained in studies that used different
time intervals can be meta-analyzed. 'CoTiMA' fits models to empirical data using the structural equation model (SEM) package
'ctsem', the effects specified in a SEM are related to parameters that are not directly included in the model (i.e.,
continuous time parameters; together, they represent the continuous time structural equation model, CTSEM). Statistical
model comparisons and significance [...truncated...]
Author: Christian Dormann [aut, cph],
Markus Homberg [aut, com, cre],
Christina Guthier [ctb],
Manuel Voelkle [ctb]
Maintainer: Markus Homberg <cotima@uni-mainz.de>
Diff between CoTiMA versions 0.5.4 dated 2022-01-20 and 0.6.2 dated 2022-11-08
DESCRIPTION | 12 MD5 | 300 ++++++------- NAMESPACE | 10 R/ctmaAllInvFit.R | 58 +- R/ctmaBiG.R | 3 R/ctmaEmpCov.R | 2 R/ctmaFit.R | 254 +++++++++-- R/ctmaInit.R | 759 ++++++++++++++++++++++------------ R/ctmaLabels.R | 69 ++- R/ctmaOptimizeFit.R |only R/ctmaOptimizeInit.R | 60 ++ R/ctmaPlot.R | 217 ++++++++- R/ctmaPower.R | 19 R/ctmaPrep.R | 9 R/ctmaSV.R | 2 R/ctmaScaleInits.R |only R/ctmaShapeRawData.R |only R/ctmaStanctArgs.R | 6 build/vignette.rds |binary data/A128.rda |binary data/A313.rda |binary data/CoTiMABiG_D_BO.rda |binary data/CoTiMAFullFit_3.rda |binary data/CoTiMAFullFit_6.rda |binary data/CoTiMAFullFit_6_new.rda |binary data/CoTiMAFullInv23Fit_6.rda |binary data/CoTiMAFullInvEq23Fit_6.rda |binary data/CoTiMAInitFit_3.rda |binary data/CoTiMAInitFit_6.rda |binary data/CoTiMAInitFit_6_NUTS.rda |binary data/CoTiMAInitFit_6_new.rda |binary data/CoTiMAInitFit_D_BO.rda |binary data/CoTiMAMod1onFullFit_6.rda |binary data/CoTiMAMod1onFullFit_6_cats12.rda |binary data/CoTiMAMod2on23Fit_6.rda |binary data/CoTiMAPart134Inv3Fit_6.rda |binary data/CoTiMAPower_D_BO.rda |binary data/CoTiMAoptimFit313.rda |binary data/CoTiMAstudyList_3.rda |binary data/CoTiMAstudyList_6.rda |binary data/CoTiMAstudyList_6_new.rda |binary data/addedByResearcher2.rda |binary data/addedByResearcher3.rda |binary data/addedByResearcher313.rda |binary data/ageM128.rda |binary data/ageM18.rda |binary data/ageM2.rda |binary data/ageM201.rda |binary data/ageM3.rda |binary data/ageM313.rda |binary data/ageM32.rda |binary data/ageSD128.rda |binary data/ageSD18.rda |binary data/ageSD2.rda |binary data/ageSD201.rda |binary data/ageSD3.rda |binary data/ageSD313.rda |binary data/ageSD32.rda |binary data/alphas128.rda |binary data/alphas313.rda |binary data/burnout128.rda |binary data/burnout18.rda |binary data/burnout2.rda |binary data/burnout201.rda |binary data/burnout3.rda |binary data/burnout313.rda |binary data/burnout32.rda |binary data/combineVariables128.rda |binary data/combineVariablesNames128.rda |binary data/country128.rda |binary data/country18.rda |binary data/country2.rda |binary data/country201.rda |binary data/country3.rda |binary data/country313.rda |binary data/country32.rda |binary data/delta_t128.rda |binary data/delta_t18.rda |binary data/delta_t2.rda |binary data/delta_t201.rda |binary data/delta_t3.rda |binary data/delta_t313.rda |binary data/delta_t32.rda |binary data/demands128.rda |binary data/demands18.rda |binary data/demands2.rda |binary data/demands201.rda |binary data/demands3.rda |binary data/demands313.rda |binary data/demands32.rda |binary data/dl_link.rda |binary data/empcov128.rda |binary data/empcov18.rda |binary data/empcov2.rda |binary data/empcov201.rda |binary data/empcov3.rda |binary data/empcov313.rda |binary data/empcov32.rda |binary data/malePercent128.rda |binary data/malePercent18.rda |binary data/malePercent2.rda |binary data/malePercent201.rda |binary data/malePercent3.rda |binary data/malePercent313.rda |binary data/malePercent32.rda |binary data/moderator128.rda |binary data/moderator18.rda |binary data/moderator2.rda |binary data/moderator201.rda |binary data/moderator3.rda |binary data/moderator313.rda |binary data/moderator32.rda |binary data/moderatorLabels.rda |binary data/moderatorValues.rda |binary data/occupation128.rda |binary data/occupation18.rda |binary data/occupation2.rda |binary data/occupation201.rda |binary data/occupation3.rda |binary data/occupation313.rda |binary data/occupation32.rda |binary data/pairwiseN128.rda |binary data/pubList_8.rda |binary data/rawdata128.rda |binary data/recodeVariables128.rda |binary data/results128.rda |binary data/sampleSize128.rda |binary data/sampleSize18.rda |binary data/sampleSize2.rda |binary data/sampleSize201.rda |binary data/sampleSize3.rda |binary data/sampleSize313.rda |binary data/sampleSize32.rda |binary data/source128.rda |binary data/source2.rda |binary data/source201.rda |binary data/source3.rda |binary data/source313.rda |binary data/targetVariables128.rda |binary data/targetVariables2.rda |binary data/targetVariables3.rda |binary data/targetVariables313.rda |binary data/variableNames128.rda |binary inst/doc/CoTiMA_User_Guide.pdf |binary man/CoTiMAStanctArgs.Rd | 2 man/ctmaAllInvFit.Rd | 17 man/ctmaFit.Rd | 23 - man/ctmaInit.Rd | 27 - man/ctmaLabels.Rd | 15 man/ctmaOptimizeFit.Rd |only man/ctmaOptimizeInit.Rd | 26 + man/ctmaPower.Rd | 5 man/ctmaScaleInits.Rd |only man/ctmaShapeRawData.Rd |only 154 files changed, 1321 insertions(+), 574 deletions(-)
Title: Tools to Conduct Meteorological Normalisation on Air Quality
Data
Description: An integrated set of tools to allow data users to conduct
meteorological normalisation on air quality data. This meteorological
normalisation technique uses predictive random forest models to remove
variation of pollutant concentrations so trends and interventions can be
explored in a robust way. For examples, see Grange et al. (2018)
<doi:10.5194/acp-18-6223-2018> and Grange and Carslaw (2019)
<doi:10.1016/j.scitotenv.2018.10.344>.
Author: Stuart K. Grange [cre, aut]
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>
Diff between rmweather versions 0.1.51 dated 2020-06-15 and 0.2.4 dated 2022-11-08
rmweather-0.1.51/rmweather/NEWS.md |only rmweather-0.1.51/rmweather/README.md |only rmweather-0.2.4/rmweather/DESCRIPTION | 14 +- rmweather-0.2.4/rmweather/MD5 | 53 +++++---- rmweather-0.2.4/rmweather/NAMESPACE | 8 + rmweather-0.2.4/rmweather/R/base_re_exports.R | 2 rmweather-0.2.4/rmweather/R/data_london.R | 4 rmweather-0.2.4/rmweather/R/dplyr_re_exports.R | 4 rmweather-0.2.4/rmweather/R/rmw_calculate_model_errors.R |only rmweather-0.2.4/rmweather/R/rmw_do_all.R | 4 rmweather-0.2.4/rmweather/R/rmw_model_nested_sets.R |only rmweather-0.2.4/rmweather/R/rmw_nest_for_modelling.R |only rmweather-0.2.4/rmweather/R/rmw_normalise.R | 57 +++++----- rmweather-0.2.4/rmweather/R/rmw_partial_dependencies.R | 39 ++++-- rmweather-0.2.4/rmweather/R/rmw_predict.R | 10 + rmweather-0.2.4/rmweather/R/rmw_predict_nested_partial_dependencies.R |only rmweather-0.2.4/rmweather/R/rmw_predict_nested_sets.R |only rmweather-0.2.4/rmweather/R/rmw_predict_nested_sets_by_year.R |only rmweather-0.2.4/rmweather/R/rmw_prepare_data.R | 9 - rmweather-0.2.4/rmweather/R/rmw_train_model.R | 9 - rmweather-0.2.4/rmweather/R/rmweather_helpers.R | 10 + rmweather-0.2.4/rmweather/R/zzz.R | 8 + rmweather-0.2.4/rmweather/inst/CITATION | 2 rmweather-0.2.4/rmweather/man/base-functions.Rd |only rmweather-0.2.4/rmweather/man/data_london.Rd | 4 rmweather-0.2.4/rmweather/man/dplyr-functions.Rd |only rmweather-0.2.4/rmweather/man/rmw_calculate_model_errors.Rd |only rmweather-0.2.4/rmweather/man/rmw_model_nested_sets.Rd |only rmweather-0.2.4/rmweather/man/rmw_nest_for_modelling.Rd |only rmweather-0.2.4/rmweather/man/rmw_partial_dependencies.Rd | 16 ++ rmweather-0.2.4/rmweather/man/rmw_predict_nested_partial_dependencies.Rd |only rmweather-0.2.4/rmweather/man/rmw_predict_nested_sets.Rd |only rmweather-0.2.4/rmweather/man/rmw_predict_nested_sets_by_year.Rd |only rmweather-0.2.4/rmweather/man/system_cpu_core_count.Rd | 5 rmweather-0.2.4/rmweather/man/zzz.Rd |only rmweather-0.2.4/rmweather/tests/testthat/test_02_rmw_functions.R | 9 + 36 files changed, 173 insertions(+), 94 deletions(-)
Title: Import, Clean and Update Data from the New Zealand Freshwater
Fish Database
Description: Access the New Zealand Freshwater Fish Database from R and a few functions to clean the data once in R.
Author: Finnbar Lee [aut, cre],
Nick Young [aut]
Maintainer: Finnbar Lee <lee.finnbar@gmail.com>
Diff between nzffdr versions 2.0.0 dated 2022-01-16 and 2.1.0 dated 2022-11-08
nzffdr-2.0.0/nzffdr/R/nzffdr_old.R |only nzffdr-2.0.0/nzffdr/man/nzffd_add.Rd |only nzffdr-2.0.0/nzffdr/man/nzffd_fill.Rd |only nzffdr-2.1.0/nzffdr/DESCRIPTION | 11 - nzffdr-2.1.0/nzffdr/MD5 | 36 +-- nzffdr-2.1.0/nzffdr/NAMESPACE | 4 nzffdr-2.1.0/nzffdr/NEWS.md | 20 + nzffdr-2.1.0/nzffdr/R/nzffdr_add_dates.R | 19 + nzffdr-2.1.0/nzffdr/R/nzffdr_clean.R | 6 nzffdr-2.1.0/nzffdr/R/nzffdr_get_table.R | 4 nzffdr-2.1.0/nzffdr/R/nzffdr_import.R | 37 +-- nzffdr-2.1.0/nzffdr/R/nzffdr_ind_lengths.R | 2 nzffdr-2.1.0/nzffdr/R/nzffdr_widen_habitat.R | 9 nzffdr-2.1.0/nzffdr/README.md | 185 +++-------------- nzffdr-2.1.0/nzffdr/man/figures/unnamed-chunk-10-1.png |only nzffdr-2.1.0/nzffdr/man/nzffdr_add_dates.Rd | 2 nzffdr-2.1.0/nzffdr/man/nzffdr_clean.Rd | 6 nzffdr-2.1.0/nzffdr/man/nzffdr_get_table.Rd | 4 nzffdr-2.1.0/nzffdr/man/nzffdr_import.Rd | 19 + nzffdr-2.1.0/nzffdr/man/nzffdr_ind_lengths.Rd | 2 nzffdr-2.1.0/nzffdr/man/nzffdr_widen_habitat.Rd | 3 21 files changed, 144 insertions(+), 225 deletions(-)
Title: Multiple Geometric Shape Point Layer for 'ggplot2'
Description: To create the multiple polygonal point layer for easily discernible shapes,
we developed the package, it is like the 'geom_point' of 'ggplot2'.
It can be used to draw the scatter plot.
Author: Shuangbin Xu [aut, cre]
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Diff between ggstar versions 1.0.3 dated 2021-12-03 and 1.0.4 dated 2022-11-08
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/scale-starshape.R | 28 ++++++++++++++++------------ R/utilities.R | 2 ++ build/vignette.rds |binary inst/doc/ggstar.html | 35 +++++++++++++++++------------------ man/geom_star.Rd | 20 ++++++++++++-------- man/scale_manual.Rd | 1 + man/scale_starshape.Rd | 1 + man/scale_starshape_identity.Rd | 5 +++-- man/starshape_pal.Rd |only 13 files changed, 74 insertions(+), 56 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.20.2 dated 2022-07-04 and 1.22 dated 2022-11-08
gam-1.20.2/gam/man/random.Rd |only gam-1.20.2/gam/man/s.Rd |only gam-1.22/gam/ChangeLog | 6 gam-1.22/gam/DESCRIPTION | 13 gam-1.22/gam/MD5 | 149 +++++----- gam-1.22/gam/NAMESPACE | 97 +++++- gam-1.22/gam/R/anova.gam.R | 50 +++ gam-1.22/gam/R/anova.gamlist.R | 3 gam-1.22/gam/R/as.anova.R | 1 gam-1.22/gam/R/as.data.frame.lo.smooth.R | 3 gam-1.22/gam/R/assign.list.R | 1 gam-1.22/gam/R/gam-package.R |only gam-1.22/gam/R/gam.R | 188 +++++++++++++ gam-1.22/gam/R/gam.control.R | 26 + gam-1.22/gam/R/gam.exact.R | 40 ++ gam-1.22/gam/R/gam.fit.R | 2 gam-1.22/gam/R/gam.lo.R | 2 gam-1.22/gam/R/gam.match.R | 1 gam-1.22/gam/R/gam.nlchisq.R | 1 gam-1.22/gam/R/gam.random.R | 69 ++++ gam-1.22/gam/R/gam.s.R | 68 ++++ gam-1.22/gam/R/gam.scope.R | 43 ++ gam-1.22/gam/R/gam.smoothers.R | 33 ++ gam-1.22/gam/R/gam.sp.R | 1 gam-1.22/gam/R/gamlist.R | 1 gam-1.22/gam/R/general.wam.R | 1 gam-1.22/gam/R/gplot.R | 1 gam-1.22/gam/R/gplot.default.R | 2 gam-1.22/gam/R/gplot.factor.R | 3 gam-1.22/gam/R/gplot.list.R | 3 gam-1.22/gam/R/gplot.matrix.R | 3 gam-1.22/gam/R/gplot.numeric.R | 3 gam-1.22/gam/R/labels.gam.R | 3 gam-1.22/gam/R/lo.R | 95 ++++++ gam-1.22/gam/R/lo.wam.R | 1 gam-1.22/gam/R/na.gam.replace.R | 35 ++ gam-1.22/gam/R/newdata.predict.gam.R | 1 gam-1.22/gam/R/plot.gam.R | 88 ++++++ gam-1.22/gam/R/plot.preplot.gam.R | 3 gam-1.22/gam/R/polylo.R | 1 gam-1.22/gam/R/predict.gam.R | 89 ++++++ gam-1.22/gam/R/preplot.gam.R | 4 gam-1.22/gam/R/print.gam.R | 3 gam-1.22/gam/R/print.gamex.R | 3 gam-1.22/gam/R/print.stepanova.R | 2 gam-1.22/gam/R/print.summary.gam.R | 3 gam-1.22/gam/R/random.R | 2 gam-1.22/gam/R/s.R | 2 gam-1.22/gam/R/s.wam.R | 1 gam-1.22/gam/R/step.gam.R | 103 +++++++ gam-1.22/gam/R/subset.smooth.R | 2 gam-1.22/gam/R/summary.gam.R | 4 gam-1.22/gam/R/ylim.scale.R | 1 gam-1.22/gam/README.md |only gam-1.22/gam/man/anova.gam.Rd | 97 +++--- gam-1.22/gam/man/gam-internal.Rd | 13 gam-1.22/gam/man/gam-package.Rd |only gam-1.22/gam/man/gam.Rd | 447 +++++++++++++++---------------- gam-1.22/gam/man/gam.control.Rd | 65 ++-- gam-1.22/gam/man/gam.data.Rd | 36 +- gam-1.22/gam/man/gam.exact.Rd | 109 ++++--- gam-1.22/gam/man/gam.random.Rd |only gam-1.22/gam/man/gam.s.Rd |only gam-1.22/gam/man/gam.scope.Rd | 96 +++--- gam-1.22/gam/man/gam.smoothers.Rd | 54 +-- gam-1.22/gam/man/kyphosis.Rd | 36 +- gam-1.22/gam/man/lo.Rd | 203 +++++++------- gam-1.22/gam/man/na.gam.replace.Rd | 59 ++-- gam-1.22/gam/man/plot.gam.Rd | 172 +++++++---- gam-1.22/gam/man/predict.gam.Rd | 166 ++++++----- gam-1.22/gam/man/step.gam.Rd | 193 +++++++------ gam-1.22/gam/src/backfit.f | 2 gam-1.22/gam/src/bsplvd.f | 8 gam-1.22/gam/src/bvalue.f | 2 gam-1.22/gam/src/linear.f | 30 ++ gam-1.22/gam/src/lo.f | 15 - gam-1.22/gam/src/loessc.c | 43 +- gam-1.22/gam/src/loessf.f | 54 ++- gam-1.22/gam/src/splsm.f | 12 79 files changed, 2218 insertions(+), 954 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.6.0 dated 2022-06-07 and 0.6.1 dated 2022-11-08
dlookr-0.6.0/dlookr/NEWS |only dlookr-0.6.1/dlookr/DESCRIPTION | 8 dlookr-0.6.1/dlookr/MD5 | 47 dlookr-0.6.1/dlookr/NAMESPACE | 1 dlookr-0.6.1/dlookr/NEWS.md |only dlookr-0.6.1/dlookr/R/dlookr.R | 2 dlookr-0.6.1/dlookr/R/html_eda.R | 800 ++++++++---- dlookr-0.6.1/dlookr/R/report.R | 36 dlookr-0.6.1/dlookr/R/report_tbl_dbi.R | 38 dlookr-0.6.1/dlookr/R/target_by.R | 32 dlookr-0.6.1/dlookr/inst/CITATION |only dlookr-0.6.1/dlookr/inst/doc/EDA.html | 269 ++-- dlookr-0.6.1/dlookr/inst/doc/diagonosis.html | 5 dlookr-0.6.1/dlookr/inst/doc/introduce.html | 5 dlookr-0.6.1/dlookr/inst/doc/transformation.html | 28 dlookr-0.6.1/dlookr/inst/report/02_RunEDA.Rnw | 3 dlookr-0.6.1/dlookr/inst/report/02_RunEDA_KR.Rnw | 3 dlookr-0.6.1/dlookr/inst/report/EDA_Report.Rmd | 3 dlookr-0.6.1/dlookr/inst/report/EDA_Report_KR.Rmd | 3 dlookr-0.6.1/dlookr/inst/report/eda_paged_temp.Rmd | 18 dlookr-0.6.1/dlookr/inst/report/eda_temp.Rmd | 10 dlookr-0.6.1/dlookr/man/diagnose_paged_report.data.frame.Rd | 2 dlookr-0.6.1/dlookr/man/diagnose_paged_report.tbl_dbi.Rd | 2 dlookr-0.6.1/dlookr/man/eda_paged_report.data.frame.Rd | 2 dlookr-0.6.1/dlookr/man/eda_paged_report.tbl_dbi.Rd | 2 dlookr-0.6.1/dlookr/man/transformation_paged_report.Rd | 2 26 files changed, 899 insertions(+), 422 deletions(-)