Title: Benchmarking and Visualization Toolkit for Penalized Cox Models
Description: Creates nomogram visualizations for penalized Cox regression
models, with the support of reproducible survival model building,
validation, calibration, and comparison for high-dimensional data.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut],
Miao-Zhu Li [aut],
Frank Harrell [ctb] ,
Sergej Potapov [ctb] ,
Werner Adler [ctb] ,
Matthias Schmid [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 6.0.2 dated 2023-04-24 and 6.0.3 dated 2024-03-02
DESCRIPTION | 16 +++---- MD5 | 72 ++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 9 ++++ R/1_1_model.R | 77 ++++++++++++++++++++++++++++-------- R/1_2_model_tune.R | 13 ++---- R/1_3_model_method.R | 13 +++--- R/2_2_convert_model.R | 10 +++- R/2_3_survial_curves.R | 18 ++++---- R/3_1_validate.R | 33 ++++++--------- R/3_2_validate_utils.R | 39 +++++------------- R/3_3_validate_method.R | 24 +++-------- R/3_4_validate_external.R | 6 +- R/3_5_validate_external_utils.R | 33 ++++----------- R/3_6_validate_external_method.R | 18 +++----- R/4_1_calibrate.R | 31 +++++--------- R/4_2_calibrate_utils.R | 26 ++++++------ R/4_3_calibrate_method.R | 45 ++++----------------- R/4_4_calibrate_external.R | 8 +-- R/4_5_calibrate_external_utils.R | 6 +- R/4_6_calibrate_external_method.R | 13 +++--- R/4_7_kmplot.R | 17 ++++--- R/5_1_compare_by_validate.R | 26 +++--------- R/5_2_compare_by_validate_method.R | 19 ++++---- R/5_3_compare_by_calibrate.R | 26 +++--------- R/5_4_compare_by_calibrate_method.R | 17 ++++--- R/rms_nomogram_method.R | 1 build/vignette.rds |binary inst/doc/hdnom.R | 22 +++++----- inst/doc/hdnom.html | 22 +++------- man/fit_aenet.Rd | 2 man/fit_enet.Rd | 2 man/fit_flasso.Rd | 2 man/fit_mcp.Rd | 2 man/fit_mnet.Rd | 2 man/fit_scad.Rd | 2 man/fit_snet.Rd | 2 37 files changed, 313 insertions(+), 362 deletions(-)
Title: Network Analysis of Immune Repertoire
Description: Pipelines for studying the adaptive immune repertoire of T cells
and B cells via network analysis based on receptor sequence similarity.
Relate clinical outcomes to immune repertoires based on their network
properties, or to particular clusters and clones within a repertoire.
Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.
Author: Brian Neal [aut, cre],
Hai Yang [aut],
Daniil Matveev [aut],
Phi Long Le [aut],
Li Zhang [cph, aut]
Maintainer: Brian Neal <Brian.Neal@ucsf.edu>
Diff between NAIR versions 1.0.3 dated 2024-01-09 and 1.0.4 dated 2024-03-02
DESCRIPTION | 8 MD5 | 40 +- NEWS.md | 17 R/RcppExports.R | 8 R/argchecks_mid.R | 2 R/arghecks_upper.R | 34 + R/network_analysis.R | 40 +- R/utils.R | 3 inst/doc/buildRepSeqNetwork.html | 2 inst/doc/cluster_analysis.html | 6 inst/doc/supplementary.html | 3 man/generateAdjacencyMatrix.Rd | 5 src/RcppExports.cpp | 46 ++ src/dropDegreeZero.cpp |only src/dropDegreeZero.h |only src/hamAdjacencyMatSparse.cpp | 50 +- src/hamDistBounded.cpp | 11 src/hamDistBounded.h | 4 src/levAdjacencyMatSparse.cpp | 52 +- src/levDistBounded.cpp | 10 src/patternAdjacencyMatSparse.cpp |only src/sortAdjacencyMatSparse.cpp |only tests/testthat/test_functions.R | 673 ++++++++++++++++++++------------------ 23 files changed, 592 insertions(+), 422 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford [aut, cre] ,
Ian Durbach [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrdesign versions 2.8.2 dated 2023-03-10 and 2.9.0 dated 2024-03-02
DESCRIPTION | 8 +- MD5 | 34 ++++---- NAMESPACE | 2 NEWS | 20 +++++ R/estimateSummary.R | 23 +++-- R/methods.R | 19 +++- R/onAttach.R | 3 R/rbind.estimatetables.R | 50 ++++++------ R/run.scenarios.R | 180 ++++++++++++++++++++++++++++++--------------- R/select.stats.R | 32 ++++---- R/transformOutput.R |only R/utility.R | 23 +++++ man/estimateSummary.Rd | 5 + man/run.scenarios.Rd | 16 +++- man/secrdesign-internal.Rd | 26 ++++++ man/secrdesign-package.Rd | 4 - man/select.stats.Rd | 2 man/transformOutput.Rd |only src/secrdesignarma.cpp | 15 +++ 19 files changed, 315 insertions(+), 147 deletions(-)
Title: Companion Datasets and Functions for Research Design in the
Social Sciences
Description: Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design in the Social Sciences: Declaration, Diagnosis, and Redesign" <https://book.declaredesign.org>. 'rdss' includes datasets, helper functions, and plotting components to enable use and replication of the book.
Author: Graeme Blair [aut, cre] ,
Alexander Coppock [aut] ,
Macartan Humphreys [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between rdss versions 1.0.6 dated 2024-02-20 and 1.0.8 dated 2024-03-02
rdss-1.0.6/rdss/tests/testthat/test-zzz-process-tracing.R |only rdss-1.0.8/rdss/DESCRIPTION | 8 ++++---- rdss-1.0.8/rdss/MD5 | 14 +++++++------- rdss-1.0.8/rdss/NEWS.md | 4 ++++ rdss-1.0.8/rdss/R/data.R | 2 +- rdss-1.0.8/rdss/R/get_replication_file.R | 10 ++++++++-- rdss-1.0.8/rdss/man/clingingsmith_etal.Rd | 4 ++-- rdss-1.0.8/rdss/man/get_rdss_file.Rd | 7 +++++-- rdss-1.0.8/rdss/tests/testthat/test-process-tracing.R |only 9 files changed, 31 insertions(+), 18 deletions(-)
Title: R Access to Mass-Spec Data
Description: R-based access to mass-spectrometry (MS) data. While many packages
exist to process MS data, many of these make it difficult to
access the underlying mass-to-charge ratio (m/z), intensity, and
retention time of the files
themselves. This package is designed to format MS data in a tidy fashion and
allows the user perform the plotting and analysis.
Author: William Kumler [aut, cre, cph],
Ricardo Cunha [ctb],
Ethan Bass [ctb]
Maintainer: William Kumler <wkumler@uw.edu>
Diff between RaMS versions 1.3.4 dated 2023-12-13 and 1.4.0 dated 2024-03-02
RaMS-1.3.4/RaMS/inst/extdata/DDApos_2.mzML.gz |only RaMS-1.3.4/RaMS/inst/extdata/DDApos_2.mzXML.gz |only RaMS-1.4.0/RaMS/DESCRIPTION | 8 RaMS-1.4.0/RaMS/MD5 | 105 ++- RaMS-1.4.0/RaMS/NAMESPACE | 2 RaMS-1.4.0/RaMS/NEWS.md | 15 RaMS-1.4.0/RaMS/R/extraHelperFunctions.R | 206 +++++++ RaMS-1.4.0/RaMS/R/grabMSdataCode.R | 73 +- RaMS-1.4.0/RaMS/R/grabMzmlFunctions.R | 244 +++++++-- RaMS-1.4.0/RaMS/R/grabMzxmlFunctions.R | 212 ++++++-- RaMS-1.4.0/RaMS/R/minifyMSFunctions.R | 59 ++ RaMS-1.4.0/RaMS/README.md | 19 RaMS-1.4.0/RaMS/inst/CITATION |only RaMS-1.4.0/RaMS/inst/doc/Intro-to-RaMS.html | 263 +++------- RaMS-1.4.0/RaMS/inst/doc/Intro-to-tmzML.html | 4 RaMS-1.4.0/RaMS/inst/doc/Minifying-files-with-RaMS.R | 14 RaMS-1.4.0/RaMS/inst/doc/Minifying-files-with-RaMS.Rmd | 22 RaMS-1.4.0/RaMS/inst/doc/Minifying-files-with-RaMS.html | 74 -- RaMS-1.4.0/RaMS/inst/doc/RaMS-and-friends.R | 2 RaMS-1.4.0/RaMS/inst/doc/RaMS-and-friends.Rmd | 2 RaMS-1.4.0/RaMS/inst/doc/RaMS-and-friends.html | 36 - RaMS-1.4.0/RaMS/inst/doc/speed_size_comparison.html | 4 RaMS-1.4.0/RaMS/inst/extdata/Blank_129I_1L_pos_20240207-MS3.mzML.gz |only RaMS-1.4.0/RaMS/inst/extdata/Blank_129I_1L_pos_20240207-MS3.mzXML.gz |only RaMS-1.4.0/RaMS/inst/extdata/LB12HL_AB.mzML.gz |binary RaMS-1.4.0/RaMS/inst/extdata/LB12HL_AB.mzXML.gz |binary RaMS-1.4.0/RaMS/inst/extdata/LB12HL_CD.mzML.gz |binary RaMS-1.4.0/RaMS/inst/extdata/LB12HL_EF.mzML.gz |binary RaMS-1.4.0/RaMS/inst/extdata/S30657.mzML.gz |only RaMS-1.4.0/RaMS/inst/extdata/S30657.mzXML.gz |only RaMS-1.4.0/RaMS/man/editMSfileRTs.Rd |only RaMS-1.4.0/RaMS/man/grabAccessionData.Rd | 4 RaMS-1.4.0/RaMS/man/grabMSdata.Rd | 46 - RaMS-1.4.0/RaMS/man/grabMzmlBPC.Rd | 6 RaMS-1.4.0/RaMS/man/grabMzmlData.Rd | 59 +- RaMS-1.4.0/RaMS/man/grabMzmlMS1.Rd | 6 RaMS-1.4.0/RaMS/man/grabMzmlMS2.Rd | 8 RaMS-1.4.0/RaMS/man/grabMzmlMS3.Rd |only RaMS-1.4.0/RaMS/man/grabMzxmlBPC.Rd | 6 RaMS-1.4.0/RaMS/man/grabMzxmlData.Rd | 25 RaMS-1.4.0/RaMS/man/grabMzxmlMS1.Rd | 6 RaMS-1.4.0/RaMS/man/grabMzxmlMS2.Rd | 8 RaMS-1.4.0/RaMS/man/grabMzxmlMS3.Rd |only RaMS-1.4.0/RaMS/man/minifyMSdata.Rd | 6 RaMS-1.4.0/RaMS/man/mz_group.Rd | 150 ++--- RaMS-1.4.0/RaMS/man/pmppm.Rd | 56 +- RaMS-1.4.0/RaMS/man/qplotMS1data.Rd | 130 ++-- RaMS-1.4.0/RaMS/man/trapz.Rd | 78 +- RaMS-1.4.0/RaMS/tests/testthat/setup-load.R | 24 RaMS-1.4.0/RaMS/tests/testthat/test_EICthings.R | 10 RaMS-1.4.0/RaMS/tests/testthat/test_basics.R | 73 ++ RaMS-1.4.0/RaMS/tests/testthat/test_editRTs.R |only RaMS-1.4.0/RaMS/tests/testthat/test_errors_n_messes.R | 2 RaMS-1.4.0/RaMS/tests/testthat/test_extras.R | 6 RaMS-1.4.0/RaMS/tests/testthat/test_minify.R | 20 RaMS-1.4.0/RaMS/tests/testthat/test_mzML_mzXML_equality.R | 52 - RaMS-1.4.0/RaMS/tests/testthat/test_tmzML_things.R | 2 RaMS-1.4.0/RaMS/vignettes/Minifying-files-with-RaMS.Rmd | 22 RaMS-1.4.0/RaMS/vignettes/RaMS-and-friends.Rmd | 2 59 files changed, 1355 insertions(+), 816 deletions(-)
Title: Synthesise and Correlate Rating-Scale Data
Description: Synthesise rating-scale data with predefined
first & second moments (mean & standard deviation) and, optionally,
correlate multiple vectors with predefined correlation matrix.
Also generate synthetic rating-scale data with predefined Cronbach's Alpha.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>
Diff between LikertMakeR versions 0.1.5 dated 2022-12-22 and 0.2.0 dated 2024-03-02
LikertMakeR-0.1.5/LikertMakeR/tests/testthat/test_lcor.R |only LikertMakeR-0.1.5/LikertMakeR/tests/testthat/test_lexact.R |only LikertMakeR-0.1.5/LikertMakeR/tests/testthat/test_lfast.R |only LikertMakeR-0.2.0/LikertMakeR/DESCRIPTION | 32 LikertMakeR-0.2.0/LikertMakeR/MD5 | 58 LikertMakeR-0.2.0/LikertMakeR/NAMESPACE | 25 LikertMakeR-0.2.0/LikertMakeR/NEWS.md | 61 LikertMakeR-0.2.0/LikertMakeR/R/RcppExports.R |only LikertMakeR-0.2.0/LikertMakeR/R/alpha.R |only LikertMakeR-0.2.0/LikertMakeR/R/eigenvalues.R |only LikertMakeR-0.2.0/LikertMakeR/R/lcor.R | 103 - LikertMakeR-0.2.0/LikertMakeR/R/lexact.R | 103 - LikertMakeR-0.2.0/LikertMakeR/R/lfast.R | 52 LikertMakeR-0.2.0/LikertMakeR/R/makeCorrAlpha.R |only LikertMakeR-0.2.0/LikertMakeR/R/makeItems.R |only LikertMakeR-0.2.0/LikertMakeR/README.md | 594 ++++-- LikertMakeR-0.2.0/LikertMakeR/build/vignette.rds |binary LikertMakeR-0.2.0/LikertMakeR/inst/CITATION | 5 LikertMakeR-0.2.0/LikertMakeR/inst/doc/LikertMakeR_vignette.R | 352 +++ LikertMakeR-0.2.0/LikertMakeR/inst/doc/LikertMakeR_vignette.Rmd | 883 +++++++--- LikertMakeR-0.2.0/LikertMakeR/inst/doc/LikertMakeR_vignette.html | 882 +++++++-- LikertMakeR-0.2.0/LikertMakeR/man/alpha.Rd |only LikertMakeR-0.2.0/LikertMakeR/man/eigenvalues.Rd |only LikertMakeR-0.2.0/LikertMakeR/man/lcor.Rd | 32 LikertMakeR-0.2.0/LikertMakeR/man/lexact.Rd | 42 LikertMakeR-0.2.0/LikertMakeR/man/lfast.Rd | 7 LikertMakeR-0.2.0/LikertMakeR/man/makeCorrAlpha.Rd |only LikertMakeR-0.2.0/LikertMakeR/man/makeItems.Rd |only LikertMakeR-0.2.0/LikertMakeR/src |only LikertMakeR-0.2.0/LikertMakeR/tests/testthat.R | 4 LikertMakeR-0.2.0/LikertMakeR/tests/testthat/test-alpha.R |only LikertMakeR-0.2.0/LikertMakeR/tests/testthat/test-eigenvalues.R |only LikertMakeR-0.2.0/LikertMakeR/tests/testthat/test-lcor.R |only LikertMakeR-0.2.0/LikertMakeR/tests/testthat/test-lfast.R |only LikertMakeR-0.2.0/LikertMakeR/tests/testthat/test-makeCorrAlpha.R |only LikertMakeR-0.2.0/LikertMakeR/tests/testthat/test-makeItems.R |only LikertMakeR-0.2.0/LikertMakeR/vignettes/LikertMakeR_1.png |only LikertMakeR-0.2.0/LikertMakeR/vignettes/LikertMakeR_2.png |only LikertMakeR-0.2.0/LikertMakeR/vignettes/LikertMakeR_vignette.Rmd | 883 +++++++--- 39 files changed, 2950 insertions(+), 1168 deletions(-)
Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using
a headless browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre],
Gabor Csardi [aut],
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd],
Ascent Digital Services [cph, ccp]
Maintainer: Winston Chang <winston@posit.co>
Diff between shinytest versions 1.5.3 dated 2023-03-24 and 1.5.4 dated 2024-03-02
DESCRIPTION | 22 +++++++++++----------- MD5 | 6 +++--- NEWS.md | 4 ++++ README.md | 2 ++ 4 files changed, 20 insertions(+), 14 deletions(-)
Title: Data on Base and Recommended Packages for Current and Previous
Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 4.3.2.0 dated 2023-11-29 and 4.3.3.0 dated 2024-03-02
DESCRIPTION | 8 +- MD5 | 17 +++-- NEWS.md | 10 +++ README.md | 88 +++++++++++++++---------------- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary tests |only 9 files changed, 69 insertions(+), 54 deletions(-)
Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing
and managing large amounts of data. This package provides a nearly
feature complete, object oriented wrapper for the 'HDF5' API
<https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes.
Additionally, functionality is added so that 'HDF5' objects behave very
similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre],
Mario Annau [aut],
Novartis Institute for BioMedical Research [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between hdf5r versions 1.3.9 dated 2024-01-14 and 1.3.10 dated 2024-03-02
DESCRIPTION | 6 - MD5 | 94 +++++++++++----------- R/Common_functions.R | 122 ++++++++++++++--------------- R/R6Classes.R | 2 R/R6Classes_H5A.R | 14 +-- R/R6Classes_H5D.R | 28 +++--- R/R6Classes_H5File.R | 10 +- R/R6Classes_H5P.R | 142 +++++++++++++++++----------------- R/R6Classes_H5R.R | 4 R/R6Classes_H5S.R | 48 +++++------ R/R6Classes_H5T.R | 78 +++++++++---------- R/adapt_during_onLoad.R | 6 - R/high_level_UI.R | 4 inst/doc/hdf5r.R | 4 inst/doc/hdf5r.Rmd | 156 +++++++++++++++++++------------------- inst/doc/hdf5r.html | 8 - man/H5A-class.Rd | 18 ++-- man/H5D-class.Rd | 66 ++++++++-------- man/H5File-class.Rd | 122 ++++++++++++++--------------- man/H5Group-class.Rd | 112 +++++++++++++-------------- man/H5P-class.Rd | 8 - man/H5P_ATTRIBUTE_CREATE-class.Rd | 4 man/H5P_CLASS-class.Rd | 2 man/H5P_DATASET_ACCESS-class.Rd | 4 man/H5P_DATASET_CREATE-class.Rd | 50 ++++++------ man/H5P_DATASET_XFER-class.Rd | 14 +-- man/H5P_FILE_ACCESS-class.Rd | 4 man/H5P_FILE_CREATE-class.Rd | 20 ++-- man/H5P_LINK_ACCESS-class.Rd | 12 +- man/H5P_LINK_CREATE-class.Rd | 8 - man/H5P_OBJECT_COPY-class.Rd | 4 man/H5P_OBJECT_CREATE-class.Rd | 12 +- man/H5R_DATASET_REGION-class.Rd | 2 man/H5R_OBJECT-class.Rd | 2 man/H5RefClass-class.Rd | 12 +- man/H5S-class.Rd | 50 ++++++------ man/H5S_H5D_subset_assign.Rd | 4 man/H5T-class.Rd | 72 ++++++++--------- man/H5T_ARRAY-class.Rd | 6 - man/H5T_COMPOUND-class.Rd | 2 man/H5T_FLOAT-class.Rd | 16 +-- man/H5T_INTEGER-class.Rd | 4 man/H5T_STRING-class.Rd | 10 +- man/H5T_VLEN-class.Rd | 2 man/text_to_dtype.Rd | 2 src/Makevars.ucrt | 22 ++++- src/convert.c | 2 vignettes/hdf5r.Rmd | 156 +++++++++++++++++++------------------- 48 files changed, 784 insertions(+), 766 deletions(-)
Title: Interactive Tables, Calendars and Charts for the Web
Description: Create interactive tables, calendars and charts with 'TOAST UI' <https://ui.toast.com/> libraries to
integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
NHN FE Development Lab [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between toastui versions 0.3.1 dated 2024-02-09 and 0.3.2 dated 2024-03-02
DESCRIPTION | 6 +-- MD5 | 28 +++++++-------- NEWS.md | 12 ++++++ R/datagrid.R | 5 ++ R/grid-editor.R | 8 +++- R/grid-proxy.R | 20 +++++++++-- R/onLoad.R | 2 - R/toastui-package.R | 9 ++--- data/rolling_stones_50.rda |binary data/rolling_stones_500.rda |binary inst/htmlwidgets/datagrid.js | 2 - inst/htmlwidgets/datagrid.js.LICENSE.txt | 2 - man/datagrid.Rd | 3 + man/grid_editor_date.Rd | 55 ++++++++++++++++++++++++++----- man/grid_proxy_delete_row.Rd | 12 +++--- 15 files changed, 120 insertions(+), 44 deletions(-)
Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time. For more information, please check the following paper:
Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.1-8 dated 2021-11-12 and 1.2-32 dated 2024-03-02
sdm-1.1-8/sdm/README.md |only sdm-1.1-8/sdm/inst/external/predictors.grd |only sdm-1.1-8/sdm/inst/external/predictors.gri |only sdm-1.2-32/sdm/DESCRIPTION | 14 sdm-1.2-32/sdm/MD5 | 126 + sdm-1.2-32/sdm/NAMESPACE | 20 sdm-1.2-32/sdm/R/AAAClasses.R | 435 +++++- sdm-1.2-32/sdm/R/adapt.R |only sdm-1.2-32/sdm/R/background.R |only sdm-1.2-32/sdm/R/coordinates.R | 78 + sdm-1.2-32/sdm/R/ensemble.R | 1809 +++++++++++++--------------- sdm-1.2-32/sdm/R/evaluates.R | 104 + sdm-1.2-32/sdm/R/features.R |only sdm-1.2-32/sdm/R/getData.R | 22 sdm-1.2-32/sdm/R/gui.R | 10 sdm-1.2-32/sdm/R/impute.R |only sdm-1.2-32/sdm/R/installAll.R | 6 sdm-1.2-32/sdm/R/maxNet.R |only sdm-1.2-32/sdm/R/modelFrame.R | 314 ---- sdm-1.2-32/sdm/R/niche.R | 316 ++++ sdm-1.2-32/sdm/R/nicheSimilarity.R |only sdm-1.2-32/sdm/R/pca.R |only sdm-1.2-32/sdm/R/plot.R | 48 sdm-1.2-32/sdm/R/predict.R | 803 +++++++----- sdm-1.2-32/sdm/R/responseCurve.R | 104 + sdm-1.2-32/sdm/R/sdm.R | 805 ++---------- sdm-1.2-32/sdm/R/sdmData.R | 1490 ++++++++++++++++------- sdm-1.2-32/sdm/R/sdmFormula.R | 771 ++++++++--- sdm-1.2-32/sdm/R/sdmMethods.R | 189 -- sdm-1.2-32/sdm/R/sdmSetting.R |only sdm-1.2-32/sdm/R/show.R | 128 + sdm-1.2-32/sdm/R/subset.R | 8 sdm-1.2-32/sdm/R/utilities.R |only sdm-1.2-32/sdm/R/varImp.R | 170 ++ sdm-1.2-32/sdm/build/vignette.rds |binary sdm-1.2-32/sdm/inst/external/predictors.tif |only sdm-1.2-32/sdm/inst/external/sp1.cpg |only sdm-1.2-32/sdm/inst/external/sp1.dbf |only sdm-1.2-32/sdm/inst/external/sp1.prj |only sdm-1.2-32/sdm/inst/external/sp1.shp |only sdm-1.2-32/sdm/inst/external/sp1.shx |only sdm-1.2-32/sdm/inst/external/sp2.cpg |only sdm-1.2-32/sdm/inst/external/sp2.dbf |only sdm-1.2-32/sdm/inst/external/sp2.prj |only sdm-1.2-32/sdm/inst/external/sp2.shp |only sdm-1.2-32/sdm/inst/external/sp2.shx |only sdm-1.2-32/sdm/inst/methods/sdm/gam.R | 8 sdm-1.2-32/sdm/inst/methods/sdm/maxNet.R |only sdm-1.2-32/sdm/man/adapt.Rd |only sdm-1.2-32/sdm/man/add.Rd | 10 sdm-1.2-32/sdm/man/arithm.Rd | 12 sdm-1.2-32/sdm/man/as.data.frame.Rd | 18 sdm-1.2-32/sdm/man/background.Rd |only sdm-1.2-32/sdm/man/boxplot.Rd | 2 sdm-1.2-32/sdm/man/coordinates.Rd | 22 sdm-1.2-32/sdm/man/density.Rd | 2 sdm-1.2-32/sdm/man/ensemble.Rd | 74 - sdm-1.2-32/sdm/man/evaluates.Rd | 10 sdm-1.2-32/sdm/man/extractIndex.Rd | 2 sdm-1.2-32/sdm/man/featuresFrame-class.Rd | 2 sdm-1.2-32/sdm/man/getModelInfo.Rd | 2 sdm-1.2-32/sdm/man/gui.Rd | 2 sdm-1.2-32/sdm/man/installAll.Rd | 2 sdm-1.2-32/sdm/man/names.Rd | 2 sdm-1.2-32/sdm/man/niche.Rd | 12 sdm-1.2-32/sdm/man/nicheSimilarity.Rd |only sdm-1.2-32/sdm/man/pca.Rd |only sdm-1.2-32/sdm/man/predict.Rd | 68 - sdm-1.2-32/sdm/man/read.sdm.Rd | 2 sdm-1.2-32/sdm/man/response.Rd | 5 sdm-1.2-32/sdm/man/roc.Rd | 2 sdm-1.2-32/sdm/man/sdm.Rd | 24 sdm-1.2-32/sdm/man/sdmData.Rd | 62 sdm-1.2-32/sdm/man/sdmModel-class.Rd | 5 sdm-1.2-32/sdm/man/sdmSetting.Rd | 27 sdm-1.2-32/sdm/man/sdmdata-class.Rd | 2 sdm-1.2-32/sdm/man/subset.Rd | 2 sdm-1.2-32/sdm/man/varImportance.Rd | 45 78 files changed, 4818 insertions(+), 3378 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.1 dated 2024-02-19 and 1.0.2 dated 2024-03-02
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 2 ++ R/CommonFun.R | 26 +++++++++++++++++++------- R/FD_Fun.R | 10 +++++++--- R/PD_Fun.R | 9 +++++++-- R/TD_Fun.R | 10 ++++++++-- inst/doc/Introduction.pdf |binary 8 files changed, 53 insertions(+), 24 deletions(-)
Title: Mixed Effects Cox Models
Description: Fit Cox proportional hazards models containing both
fixed and random effects. The random effects can have a general form, of which
familial interactions (a "kinship" matrix) is a particular special case.
Note that the simplest case of a mixed effects Cox model, i.e. a single random
per-group intercept, is also called a "frailty" model. The approach is based
on Ripatti and Palmgren, Biometrics 2002.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau.terry@mayo.edu>
Diff between coxme versions 2.2-18.1 dated 2022-10-03 and 2.2-19 dated 2024-03-02
coxme-2.2-18.1/coxme/vignettes/figures |only coxme-2.2-19/coxme/DESCRIPTION | 6 +-- coxme-2.2-19/coxme/MD5 | 52 ++++++++++++++++-------------- coxme-2.2-19/coxme/NAMESPACE | 3 + coxme-2.2-19/coxme/R/anova.coxme.R | 8 +--- coxme-2.2-19/coxme/R/anova.coxmelist.R | 4 -- coxme-2.2-19/coxme/R/coxme.R | 3 - coxme-2.2-19/coxme/R/print.coxme.R | 2 - coxme-2.2-19/coxme/R/summary.coxme.R |only coxme-2.2-19/coxme/build/vignette.rds |binary coxme-2.2-19/coxme/inst/NEWS.Rd | 5 ++ coxme-2.2-19/coxme/inst/NEWS.Rd.orig |only coxme-2.2-19/coxme/inst/doc/coxme.pdf |binary coxme-2.2-19/coxme/inst/doc/laplace.pdf |binary coxme-2.2-19/coxme/inst/doc/lmekin.R | 4 +- coxme-2.2-19/coxme/inst/doc/lmekin.Rnw | 4 +- coxme-2.2-19/coxme/inst/doc/lmekin.pdf |binary coxme-2.2-19/coxme/inst/doc/variance.R | 2 - coxme-2.2-19/coxme/inst/doc/variance.Rnw | 2 - coxme-2.2-19/coxme/inst/doc/variance.pdf |binary coxme-2.2-19/coxme/man/print.coxme.Rd | 11 ------ coxme-2.2-19/coxme/man/summary.coxme.Rd |only coxme-2.2-19/coxme/noweb/all.nw |only coxme-2.2-19/coxme/noweb/all.pdf |only coxme-2.2-19/coxme/noweb/all.tex |only coxme-2.2-19/coxme/noweb/basic.Rnw | 3 - coxme-2.2-19/coxme/noweb/code.nw | 7 +--- coxme-2.2-19/coxme/noweb/fit.Rnw | 4 +- coxme-2.2-19/coxme/noweb/test2.r |only coxme-2.2-19/coxme/vignettes/lmekin.Rnw | 4 +- coxme-2.2-19/coxme/vignettes/variance.Rnw | 2 - 31 files changed, 58 insertions(+), 68 deletions(-)
Title: Routines for Block Diagonal Symmetric Matrices
Description: This is a special case of sparse matrices, used by coxme.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>
Diff between bdsmatrix versions 1.3-6 dated 2022-06-03 and 1.3-7 dated 2024-03-02
bdsmatrix-1.3-6/bdsmatrix/inst/NEWS.Rd.orig |only bdsmatrix-1.3-7/bdsmatrix/DESCRIPTION | 8 ++++---- bdsmatrix-1.3-7/bdsmatrix/MD5 | 7 +++---- bdsmatrix-1.3-7/bdsmatrix/R/gchol.bdsmatrix.R | 16 +++++++--------- bdsmatrix-1.3-7/bdsmatrix/inst/NEWS.Rd | 4 ++++ 5 files changed, 18 insertions(+), 17 deletions(-)
Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette.
'tinycodet' primarily focuses on 4 aspects.
1) Safer decimal (in)equality testing, safer atomic conversions, and other functions for safer coding.
2) A new package import system,
that attempts to combine the benefits of using a package without attaching it,
with the benefits of attaching a package.
3) Extending the string manipulation capabilities of the 'stringi' R package.
4) Reducing repetitive code.
Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between tinycodet versions 0.4.1 dated 2024-02-17 and 0.4.5 dated 2024-03-02
tinycodet-0.4.1/tinycodet/src/alloc_stri_locate_ith.cpp |only tinycodet-0.4.5/tinycodet/DESCRIPTION | 9 + tinycodet-0.4.5/tinycodet/MD5 | 34 ++++-- tinycodet-0.4.5/tinycodet/NAMESPACE | 4 tinycodet-0.4.5/tinycodet/NEWS.md | 5 + tinycodet-0.4.5/tinycodet/R/RcppExports.R | 20 +++- tinycodet-0.4.5/tinycodet/R/form.R |only tinycodet-0.4.5/tinycodet/R/pro.R |only tinycodet-0.4.5/tinycodet/R/safer_match.R |only tinycodet-0.4.5/tinycodet/R/str_search.R | 4 tinycodet-0.4.5/tinycodet/R/stri_locate_ith.R | 9 + tinycodet-0.4.5/tinycodet/R/tinycodet_safer.R | 8 + tinycodet-0.4.5/tinycodet/inst/tinytest/count/count_number_of_tests.R | 2 tinycodet-0.4.5/tinycodet/inst/tinytest/regular/test-decimal-eq.R | 3 tinycodet-0.4.5/tinycodet/inst/tinytest/regular/test-form.R |only tinycodet-0.4.5/tinycodet/inst/tinytest/regular/test-pro.R |only tinycodet-0.4.5/tinycodet/man/aaa1_tinycodet_safer.Rd | 8 + tinycodet-0.4.5/tinycodet/man/form.Rd |only tinycodet-0.4.5/tinycodet/man/pro.Rd |only tinycodet-0.4.5/tinycodet/man/safer_partialmatch.Rd |only tinycodet-0.4.5/tinycodet/man/str_search.Rd | 4 tinycodet-0.4.5/tinycodet/src/RcppExports.cpp | 50 +++++++--- tinycodet-0.4.5/tinycodet/src/rcpp_stri_locate_ith.cpp |only 23 files changed, 115 insertions(+), 45 deletions(-)
Title: Solvers for Maximum Weight Connected Subgraph Problem and Its
Variants
Description: Algorithms for solving various Maximum
Weight Connected Subgraph Problems, including variants with
budget constraints, cardinality constraints, weighted edges and signals.
The package represents an R interface to high-efficient solvers based on
relax-and-cut approach (Álvarez-Miranda E., Sinnl M. (2017) <doi:10.1016/j.cor.2017.05.015>)
mixed-integer programming (Loboda A., Artyomov M., and Sergushichev A. (2016) <doi:10.1007/978-3-319-43681-4_17>)
and simulated annealing.
Author: Alexander Loboda [aut, cre],
Nikolay Poperechnyi [aut],
Eduardo Alvarez-Miranda [aut],
Markus Sinnl [aut],
Alexey Sergushichev [aut],
Paul Hosler Jr. [cph] ,
www.hamcrest.org [cph] ,
Barak Naveh and Contributors [cph] ,
The Apache Software Foundation [...truncated...]
Maintainer: Alexander Loboda <aleks.loboda@gmail.com>
Diff between mwcsr versions 0.1.7 dated 2023-05-16 and 0.1.8 dated 2024-03-02
DESCRIPTION | 6 MD5 | 16 - inst/doc/tutorial.R | 2 inst/doc/tutorial.html | 321 ++++++++++++++++++++-------------------- src/sgmwcs/components.cpp | 18 +- src/sgmwcs/cut.cpp | 5 src/sgmwcs/include/components.h | 3 src/sgmwcs/relax_and_cut.cpp | 27 ++- src/sgmwcs/variable.cpp | 2 9 files changed, 214 insertions(+), 186 deletions(-)
Title: Compound Annual Growth Rate
Description: A time series usually does not have a uniform growth rate. Compound Annual Growth Rate measures the average annual growth over a given period. More details can be found in Bardhan et al. (2022) <DOI:10.18805/ag.D-5418>.
Author: Debopam Rakshit [aut, cre],
Dwaipayan Bardhan [aut]
Maintainer: Debopam Rakshit <rakshitdebopam@yahoo.com>
Diff between CAGR versions 0.1.0 dated 2023-11-09 and 1.1.0 dated 2024-03-02
DESCRIPTION | 15 +++---- MD5 | 9 ++-- NAMESPACE | 3 + R/CAGR.R | 111 +++++++++++++++++++++++++++++++++++++++++++++++++++++- man/data.first.Rd |only man/data.last.Rd |only man/n.years.Rd |only 7 files changed, 126 insertions(+), 12 deletions(-)
Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In the process, causal effects, adjacency matrices, and other essential parameters of the complex biological networks, [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.1 dated 2024-02-28 and 0.0.2 dated 2024-03-02
DESCRIPTION | 6 +- MD5 | 18 ++++-- R/NetworkMotif.R | 47 ++++++++++++----- R/RGM.R | 30 +---------- README.md | 80 ++++++++++++++++++++++-------- man/NetworkMotif.Rd | 23 ++++++-- man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-11-2.png |only man/figures/README-unnamed-chunk-11-3.png |only man/figures/README-unnamed-chunk-12-1.png |only man/figures/README-unnamed-chunk-8-1.png |binary src/Generate.cpp | 15 ++--- 12 files changed, 136 insertions(+), 83 deletions(-)
Title: Gaussian Processes for Estimating Causal Exposure Response
Curves
Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint <arXiv:2105.03454>.
Author: Naeem Khoshnevis [aut, cre] ,
Boyu Ren [aut] ,
Tanujit Dey [ctb] ,
Danielle Braun [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Diff between GPCERF versions 0.2.2 dated 2024-02-16 and 0.2.3 dated 2024-03-02
DESCRIPTION | 6 - MD5 | 76 ++++++++------- NEWS.md | 13 ++ R/compute_deriv_weights_gp.R | 2 R/compute_m_sigma.R | 40 +++++--- R/estimate_cerf_gp.R | 85 +++++++++++++---- R/estimate_cerf_nngp.R | 88 ++++++++++++++--- R/estimate_noise_gp.R | 9 - R/find_optimal_nn.R | 4 README.md | 37 +++++-- build/vignette.rds |binary inst/CITATION | 2 inst/doc/A-Note-on-Choosing-Hyperparameters.R |only inst/doc/A-Note-on-Choosing-Hyperparameters.Rmd |only inst/doc/A-Note-on-Choosing-Hyperparameters.html |only inst/doc/Developers-Guide.R |only inst/doc/Developers-Guide.Rmd |only inst/doc/Developers-Guide.html |only inst/doc/GPCERF.R | 6 + inst/doc/GPCERF.Rmd | 13 ++ inst/doc/GPCERF.html | 108 +++++++++++----------- inst/doc/Nearest-neighbor-Gaussian-Processes.R | 8 + inst/doc/Nearest-neighbor-Gaussian-Processes.Rmd | 8 + inst/doc/Nearest-neighbor-Gaussian-Processes.html | 32 +++--- inst/doc/Standard-Gaussian-Processes.R | 6 + inst/doc/Standard-Gaussian-Processes.Rmd | 6 + inst/doc/Standard-Gaussian-Processes.html | 22 ++-- man/compute_deriv_weights_gp.Rd | 2 man/compute_m_sigma.Rd | 16 +-- man/estimate_cerf_gp.Rd | 34 +++++- man/estimate_cerf_nngp.Rd | 34 +++++- man/estimate_noise_gp.Rd | 7 - man/figures/png/readme_gp.png |binary man/figures/png/readme_nngp.png |binary tests/testthat/test-compute_m_sigma.R | 13 ++ tests/testthat/test-estimate_cerf_gp.R | 30 ++++++ tests/testthat/test-estimate_cerf_nngp.R | 30 ++++-- tests/testthat/test-estimate_noise_gp.R | 2 vignettes/A-Note-on-Choosing-Hyperparameters.Rmd |only vignettes/Developers-Guide.Rmd |only vignettes/GPCERF.Rmd | 13 ++ vignettes/Nearest-neighbor-Gaussian-Processes.Rmd | 8 + vignettes/Standard-Gaussian-Processes.Rmd | 6 + 43 files changed, 542 insertions(+), 224 deletions(-)
Title: Core Tools for Packages in the 'fable' Framework
Description: Provides tools, helpers and data structures for
developing models and time series functions for 'fable' and extension
packages. These tools support a consistent and tidy interface for time
series modelling and analysis.
Author: Mitchell O'Hara-Wild [aut, cre]
,
Rob Hyndman [aut],
Earo Wang [aut] ,
Di Cook [ctb],
George Athanasopoulos [ctb],
David Holt [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fabletools versions 0.4.0 dated 2024-02-09 and 0.4.1 dated 2024-03-02
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS.md | 10 ++++++++++ R/accuracy.R | 2 +- R/features.R | 3 ++- R/generate.R | 2 +- R/model.R | 3 ++- R/plot.R | 10 +++++++--- R/utils.R | 3 ++- build/fabletools.pdf |binary man/features.Rd | 4 +++- man/generate.mdl_df.Rd | 2 +- man/interval_accuracy_measures.Rd | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-accuracy.R | 2 +- 15 files changed, 48 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-23 0.93
2024-02-15 0.92
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-31 3.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-18 2024.2-1
2021-03-02 2021.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-26 2020.2-1
2015-12-16 2015.12-1
2014-11-25 2014.11-1
2013-03-07 2013.3-2
2012-09-20 2012.6-1
2012-05-02 2012.4-1
2011-11-28 2011.11-2
2011-11-03 2011.11-1
2011-03-23 2011.3-1
2011-01-20 2009.12-1
2009-10-18 2009.10-2
2009-10-13 2009.10-1
2009-07-26 2009.7-1
2008-10-19 2008.10-1
2007-12-02 2007.11-1
2007-07-13 2007.7-1
2007-05-13 2007.5-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-25 0.1.13
2022-03-11 0.1.12
2022-02-16 0.1.11
2021-09-11 0.1.9
2021-04-17 0.1.8
2021-03-09 0.1.7
2021-02-09 0.1.6
2021-01-17 0.1.5
2020-11-18 0.1.4
2020-11-11 0.1.3
2020-11-03 0.1.2
2020-10-20 0.1.1
2020-10-15 0.1.0
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as 'Ghostscript' is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.9-6 dated 2023-05-03 and 0.9-7 dated 2024-03-02
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/introduction.html | 4 ++-- src/Makevars.ucrt | 13 +++++++++++-- 6 files changed, 31 insertions(+), 14 deletions(-)
Title: Convert R Graphics to Flash Animations
Description: Using the 'Ming' library
<https://github.com/libming/libming> to create Flash animations.
Users can either use the 'SWF' device swf() to generate 'SWF' file
directly through plotting functions like plot() and lines(),
or convert images of other formats ('SVG', 'PNG', 'JPEG') into 'SWF'.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between R2SWF versions 0.9-8 dated 2022-11-17 and 0.9-9 dated 2024-03-02
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- inst/NEWS.Rd | 9 +++++++++ src/Makevars.ucrt | 19 ++++++++++++++++--- 4 files changed, 34 insertions(+), 11 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre] ,
Joshua Cook [ctb],
Clara Jegousse [ctb],
Miaozhu Li [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 3.0.0 dated 2023-03-08 and 3.0.1 dated 2024-03-02
DESCRIPTION | 8 ++--- MD5 | 25 ++++++++-------- NEWS.md | 10 ++++++ R/discrete-igv.R | 2 - build/vignette.rds |binary inst/doc/ggsci-faq.R |only inst/doc/ggsci-faq.Rmd | 75 ++++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/ggsci-faq.html | 53 +++++++++++++++++++++++++++++++++ inst/doc/ggsci.R | 8 ++--- inst/doc/ggsci.Rmd | 2 - inst/doc/ggsci.html | 66 +++++++++++++++++++----------------------- man/pal_igv.Rd | 2 - vignettes/ggsci-faq.Rmd | 75 ++++++++++++++++++++++++++++++++++++++++++++++++ vignettes/ggsci.Rmd | 2 - 14 files changed, 268 insertions(+), 60 deletions(-)
Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>. Different research methods during Q-matrix validating are available.
Author: Haijiang Qin [aut, cre, cph],
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 0.1.4 dated 2024-02-04 and 0.1.5 dated 2024-03-02
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ R/CDM.R | 34 +++++++++++++++++----------------- R/Mmatrix.R | 2 +- R/PVAF.R | 2 +- R/R2.R | 4 ++-- R/fit.R | 6 +++--- R/sim.Q.R | 2 +- R/sim.data.R | 4 ++-- R/validation.R | 26 +++++++++++++------------- man/CDM.Rd | 34 +++++++++++++++++----------------- man/fit.Rd | 6 +++--- man/get.Mmatrix.Rd | 2 +- man/get.PVAF.Rd | 2 +- man/get.R2.Rd | 4 ++-- man/sim.Q.Rd | 2 +- man/sim.data.Rd | 4 ++-- man/validation.Rd | 26 +++++++++++++------------- tests/demo.R | 2 +- 19 files changed, 104 insertions(+), 104 deletions(-)