Title: Spatial and Spatiotemporal Relative Risk
Description: Provides functions to estimate kernel-smoothed spatial and spatio-temporal densities and relative risk functions, and perform subsequent inference. Methodological details can be found in the accompanying tutorial: Davies et al. (2018) <DOI:10.1002/sim.7577>.
Author: Tilman M. Davies [aut, cre],
Jonathan C. Marshall [aut]
Maintainer: Tilman M. Davies <tilman.davies@otago.ac.nz>
Diff between sparr versions 2.3-15 dated 2024-07-07 and 2.3-16 dated 2025-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/tol.classify.R | 19 ++++++++++++++++++- man/sparr-package.Rd | 4 ++-- 4 files changed, 27 insertions(+), 10 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.10 dated 2025-02-05 and 0.5.11 dated 2025-03-19
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 2 NEWS.md | 6 + R/jskm.R | 154 +++++++++++++++++++++++++++++++++++++++++++++++++- R/svyjskm.R | 161 +++++++++++++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/jskm.html | 10 +-- man/jskm.Rd | 12 +++ man/svyjskm.Rd | 13 +++- 10 files changed, 349 insertions(+), 35 deletions(-)
Title: Bayesian Analysis of List Experiments with Prior Information
Description: Estimates Bayesian models of list experiments with informative priors. It includes functionalities to estimate different types of list experiment models with varying prior information. See Lu and Traunmüller (2021) <doi:10.2139/ssrn.3871089> for examples and details of estimation.
Author: Xiao Lu [aut, cre],
Richard Traunmueller [aut]
Maintainer: Xiao Lu <xiao.lu.research@gmail.com>
Diff between bayeslist versions 0.0.1.4 dated 2024-11-28 and 0.0.1.5 dated 2025-03-19
DESCRIPTION | 6 +-- MD5 | 42 ++++++++++++------------- inst/stan/model_misreport_aux.stan | 14 ++++---- inst/stan/model_misreport_cmp.stan | 10 ++--- inst/stan/model_misreport_doublelist.stan | 18 +++++----- inst/stan/model_misreport_infonorm.stan | 14 ++++---- inst/stan/model_misreport_noaux.stan | 6 +-- inst/stan/model_outcome_aux.stan | 12 +++---- inst/stan/model_outcome_cmp.stan | 8 ++-- inst/stan/model_outcome_doublelist.stan | 12 +++---- inst/stan/model_outcome_infonorm.stan | 8 ++-- inst/stan/model_outcome_noaux.stan | 4 +- inst/stan/model_predict_aux.stan | 14 ++++---- inst/stan/model_predict_aux_linear.stan | 14 ++++---- inst/stan/model_predict_cmp.stan | 10 ++--- inst/stan/model_predict_cmp_linear.stan | 10 ++--- inst/stan/model_predict_doublelist.stan | 18 +++++----- inst/stan/model_predict_doublelist_linear.stan | 18 +++++----- inst/stan/model_predict_infonorm.stan | 10 ++--- inst/stan/model_predict_infonorm_linear.stan | 10 ++--- inst/stan/model_predict_noaux.stan | 6 +-- inst/stan/model_predict_noaux_linear.stan | 6 +-- 22 files changed, 135 insertions(+), 135 deletions(-)
Title: Create Images of Volumetric Brain Data in NIfTI Format Using
'ggplot2' Syntax
Description: A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data.
Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and
themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects,
inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.
Author: Michael Hallquist [aut, cre]
Maintainer: Michael Hallquist <michael.hallquist@gmail.com>
Diff between ggbrain versions 0.8.1 dated 2023-03-21 and 0.9.0 dated 2025-03-19
ggbrain-0.8.1/ggbrain/inst/extdata/Schaefer_200_7networks_2009c_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/abspe_ptfce_fwep_0.05.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/decision_onset_zstat_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/echange_overall_zstat_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/mni_template_2009c_3mm.nii.gz |only ggbrain-0.8.1/ggbrain/inst/extdata/pe_ptfce_fwep_0.05.nii.gz |only ggbrain-0.8.1/ggbrain/man/annotate_panel.Rd |only ggbrain-0.9.0/ggbrain/DESCRIPTION | 10 ggbrain-0.9.0/ggbrain/MD5 | 98 ggbrain-0.9.0/ggbrain/NAMESPACE | 13 ggbrain-0.9.0/ggbrain/NEWS.md | 17 ggbrain-0.9.0/ggbrain/R/contrast_parser.R | 48 ggbrain-0.9.0/ggbrain/R/ggb.R | 98 ggbrain-0.9.0/ggbrain/R/ggbrain_images.R | 19 ggbrain-0.9.0/ggbrain/R/ggbrain_label.R | 6 ggbrain-0.9.0/ggbrain/R/ggbrain_layer.R | 82 ggbrain-0.9.0/ggbrain/R/ggbrain_layer_brain.R | 19 ggbrain-0.9.0/ggbrain/R/ggbrain_layer_outline.R | 20 ggbrain-0.9.0/ggbrain/R/ggbrain_panel.R | 19 ggbrain-0.9.0/ggbrain/R/ggbrain_plot.R | 56 ggbrain-0.9.0/ggbrain/R/ggbrain_slices.R | 89 ggbrain-0.9.0/ggbrain/R/sugar.R | 134 - ggbrain-0.9.0/ggbrain/build/vignette.rds |binary ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_aesthetics.R | 44 ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_aesthetics.Rmd | 4 ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_aesthetics.html | 694 ++--- ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_introduction.R | 92 ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_introduction.Rmd | 169 - ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_introduction.html | 1099 +++----- ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_labels.R | 190 + ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_labels.Rmd | 300 ++ ggbrain-0.9.0/ggbrain/inst/doc/ggbrain_labels.html | 1247 +++++++--- ggbrain-0.9.0/ggbrain/inst/extdata/Schaefer2018_200Parcels_7Networks_order_2009c_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/Schaefer_200_7networks_2009c_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/Schaefer_200_7networks_labels.csv | 402 +-- ggbrain-0.9.0/ggbrain/inst/extdata/Yeo2011_7Networks_ColorLUT.txt |only ggbrain-0.9.0/ggbrain/inst/extdata/abspe_ptfce_fwep_0.05_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/echange_ptfce_fwep_0.05_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/feedback_onset_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/mni_template_2009c_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/inst/extdata/pe_ptfce_fwep_0.05_2mm.nii.gz |only ggbrain-0.9.0/ggbrain/man/annotate_slice.Rd |only ggbrain-0.9.0/ggbrain/man/define.Rd | 12 ggbrain-0.9.0/ggbrain/man/geom_brain.Rd | 10 ggbrain-0.9.0/ggbrain/man/geom_outline.Rd | 6 ggbrain-0.9.0/ggbrain/man/ggb.Rd | 2 ggbrain-0.9.0/ggbrain/man/ggbrain_plot.Rd | 4 ggbrain-0.9.0/ggbrain/man/ggbrain_slices.Rd | 13 ggbrain-0.9.0/ggbrain/man/images.Rd | 2 ggbrain-0.9.0/ggbrain/man/montage.Rd | 2 ggbrain-0.9.0/ggbrain/man/plot.ggb.Rd | 12 ggbrain-0.9.0/ggbrain/man/plot.ggbrain_patchwork.Rd |only ggbrain-0.9.0/ggbrain/man/plus-.ggbrain_images.Rd | 4 ggbrain-0.9.0/ggbrain/man/render.Rd | 35 ggbrain-0.9.0/ggbrain/man/render.ggb.Rd |only ggbrain-0.9.0/ggbrain/man/slices.Rd | 2 ggbrain-0.9.0/ggbrain/vignettes/ggbrain_aesthetics.Rmd | 4 ggbrain-0.9.0/ggbrain/vignettes/ggbrain_introduction.Rmd | 169 - ggbrain-0.9.0/ggbrain/vignettes/ggbrain_labels.Rmd | 300 ++ 59 files changed, 3499 insertions(+), 2047 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features.
All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] ,
Edzer Pebesma [ctb] ,
Roger Bivand [ctb],
Jeroen Ooms [ctb] ,
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kaminski [cph] [...truncated...]
Maintainer: Marius Appel <marius.appel@hs-bochum.de>
Diff between gdalcubes versions 0.7.0 dated 2024-03-06 and 0.7.1 dated 2025-03-19
gdalcubes-0.7.0/gdalcubes/src/gdalcubes/src/fscache_cube.h |only gdalcubes-0.7.0/gdalcubes/src/gdalcubes/src/stream_apply_chunk.cpp |only gdalcubes-0.7.0/gdalcubes/src/gdalcubes/src/stream_apply_chunk.h |only gdalcubes-0.7.1/gdalcubes/DESCRIPTION | 12 gdalcubes-0.7.1/gdalcubes/LICENSE | 2 gdalcubes-0.7.1/gdalcubes/MD5 | 253 ++++------ gdalcubes-0.7.1/gdalcubes/NEWS.md | 5 gdalcubes-0.7.1/gdalcubes/R/config.R | 2 gdalcubes-0.7.1/gdalcubes/R/cube.R | 4 gdalcubes-0.7.1/gdalcubes/R/gdalcubes.R | 3 gdalcubes-0.7.1/gdalcubes/R/view.R | 2 gdalcubes-0.7.1/gdalcubes/build/vignette.rds |binary gdalcubes-0.7.1/gdalcubes/configure | 26 - gdalcubes-0.7.1/gdalcubes/configure.ac | 2 gdalcubes-0.7.1/gdalcubes/inst/CITATION | 44 - gdalcubes-0.7.1/gdalcubes/inst/COPYRIGHTS | 92 +-- gdalcubes-0.7.1/gdalcubes/inst/doc/gc01_MODIS.Rmd | 4 gdalcubes-0.7.1/gdalcubes/inst/doc/gc01_MODIS.html | 23 gdalcubes-0.7.1/gdalcubes/inst/formats/CHIRPS_v2_0_daily_p05_tif.json | 34 - gdalcubes-0.7.1/gdalcubes/inst/formats/CHIRPS_v2_0_monthly_p05_tif.json | 34 - gdalcubes-0.7.1/gdalcubes/inst/formats/ESA_CCI_SM_ACTIVE.json | 96 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/ESA_CCI_SM_PASSIVE.json | 96 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/GPM_IMERG_3B_DAY_GIS_V06A.json | 80 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/L8_L1TP.json | 120 ++-- gdalcubes-0.7.1/gdalcubes/inst/formats/L8_SR.json | 158 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD09GA.json | 96 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD10A2.json | 44 - gdalcubes-0.7.1/gdalcubes/inst/formats/MxD11A1.json | 72 +- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD11A2.json | 88 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD13A2.json | 84 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD13A3.json | 84 +-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD13Q1.json | 104 ++-- gdalcubes-0.7.1/gdalcubes/inst/formats/MxD14A2.json | 42 - gdalcubes-0.7.1/gdalcubes/inst/formats/PlanetScope_3B_AnalyticMS_SR.json | 72 +- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L1C.json | 158 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L1C_AWS.json | 160 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L2A.json | 164 +++--- gdalcubes-0.7.1/gdalcubes/inst/formats/Sentinel2_L2A_THEIA.json | 118 ++-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_aggregate_space.R | 120 ++-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_aggregate_time.R | 122 ++-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_apply_pixel.R | 78 +-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_as_json.R | 32 - gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_crop.R | 52 +- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_cube_view.R | 134 ++--- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_rename_bands.R | 24 gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_selection.R | 98 +-- gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_slice_space.R | 24 gdalcubes-0.7.1/gdalcubes/inst/tinytest/test_slice_time.R | 24 gdalcubes-0.7.1/gdalcubes/man/add_collection_format.Rd | 50 - gdalcubes-0.7.1/gdalcubes/man/add_images.Rd | 74 +- gdalcubes-0.7.1/gdalcubes/man/aggregate_space.Rd | 112 ++-- gdalcubes-0.7.1/gdalcubes/man/aggregate_time.Rd | 100 +-- gdalcubes-0.7.1/gdalcubes/man/animate.Rd | 134 ++--- gdalcubes-0.7.1/gdalcubes/man/apply_pixel.Rd | 100 +-- gdalcubes-0.7.1/gdalcubes/man/apply_pixel.array.Rd | 66 +- gdalcubes-0.7.1/gdalcubes/man/apply_pixel.cube.Rd | 188 +++---- gdalcubes-0.7.1/gdalcubes/man/apply_time.Rd | 130 ++--- gdalcubes-0.7.1/gdalcubes/man/apply_time.array.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/apply_time.cube.Rd | 172 +++--- gdalcubes-0.7.1/gdalcubes/man/as_array.Rd | 80 +-- gdalcubes-0.7.1/gdalcubes/man/as_json.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/bands.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/chunk_apply.Rd | 114 ++-- gdalcubes-0.7.1/gdalcubes/man/collection_formats.Rd | 54 +- gdalcubes-0.7.1/gdalcubes/man/create_image_collection.Rd | 164 +++--- gdalcubes-0.7.1/gdalcubes/man/crop.Rd | 130 ++--- gdalcubes-0.7.1/gdalcubes/man/cube_view.Rd | 158 +++--- gdalcubes-0.7.1/gdalcubes/man/dim.cube.Rd | 70 +- gdalcubes-0.7.1/gdalcubes/man/dimension_bounds.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/dimension_values.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/dimensions.Rd | 70 +- gdalcubes-0.7.1/gdalcubes/man/dot-copy_cube.Rd | 42 - gdalcubes-0.7.1/gdalcubes/man/extent.Rd | 66 +- gdalcubes-0.7.1/gdalcubes/man/extract_geom.Rd | 218 ++++---- gdalcubes-0.7.1/gdalcubes/man/fill_time.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/filter_geom.Rd | 126 ++-- gdalcubes-0.7.1/gdalcubes/man/filter_pixel.Rd | 98 +-- gdalcubes-0.7.1/gdalcubes/man/gdalcubes.Rd | 58 +- gdalcubes-0.7.1/gdalcubes/man/gdalcubes_gdal_has_geos.Rd | 28 - gdalcubes-0.7.1/gdalcubes/man/gdalcubes_gdalformats.Rd | 28 - gdalcubes-0.7.1/gdalcubes/man/gdalcubes_gdalversion.Rd | 28 - gdalcubes-0.7.1/gdalcubes/man/gdalcubes_options.Rd | 144 ++--- gdalcubes-0.7.1/gdalcubes/man/gdalcubes_selection.Rd | 180 +++---- gdalcubes-0.7.1/gdalcubes/man/gdalcubes_set_gdal_config.Rd | 46 - gdalcubes-0.7.1/gdalcubes/man/image_collection.Rd | 62 +- gdalcubes-0.7.1/gdalcubes/man/image_mask.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/join_bands.Rd | 98 +-- gdalcubes-0.7.1/gdalcubes/man/json_cube.Rd | 102 ++-- gdalcubes-0.7.1/gdalcubes/man/memsize.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/names.cube.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/nbands.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/ncdf_cube.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/nt.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/nx.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/ny.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/pack_minmax.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/plot.cube.Rd | 218 ++++---- gdalcubes-0.7.1/gdalcubes/man/print.cube.Rd | 62 +- gdalcubes-0.7.1/gdalcubes/man/print.cube_view.Rd | 44 - gdalcubes-0.7.1/gdalcubes/man/print.image_collection.Rd | 60 +- gdalcubes-0.7.1/gdalcubes/man/proj4.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/raster_cube.Rd | 126 ++-- gdalcubes-0.7.1/gdalcubes/man/read_chunk_as_array.Rd | 102 ++-- gdalcubes-0.7.1/gdalcubes/man/reduce_space.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/reduce_space.array.Rd | 72 +- gdalcubes-0.7.1/gdalcubes/man/reduce_space.cube.Rd | 146 ++--- gdalcubes-0.7.1/gdalcubes/man/reduce_time.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/reduce_time.array.Rd | 68 +- gdalcubes-0.7.1/gdalcubes/man/reduce_time.cube.Rd | 182 +++---- gdalcubes-0.7.1/gdalcubes/man/rename_bands.Rd | 98 +-- gdalcubes-0.7.1/gdalcubes/man/select_bands.Rd | 94 +-- gdalcubes-0.7.1/gdalcubes/man/select_time.Rd | 90 +-- gdalcubes-0.7.1/gdalcubes/man/size.Rd | 70 +- gdalcubes-0.7.1/gdalcubes/man/slice_space.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/slice_time.Rd | 92 +-- gdalcubes-0.7.1/gdalcubes/man/srs.Rd | 64 +- gdalcubes-0.7.1/gdalcubes/man/st_as_stars.cube.Rd | 76 +-- gdalcubes-0.7.1/gdalcubes/man/stac_image_collection.Rd | 112 ++-- gdalcubes-0.7.1/gdalcubes/man/stack_cube.Rd | 160 +++--- gdalcubes-0.7.1/gdalcubes/man/write_chunk_from_array.Rd | 96 +-- gdalcubes-0.7.1/gdalcubes/man/write_ncdf.Rd | 152 +++--- gdalcubes-0.7.1/gdalcubes/man/write_tif.Rd | 158 +++--- gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/build_info.h | 12 gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/external/date.h | 8 gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/external/tinyexpr/tinyexpr.c | 23 gdalcubes-0.7.1/gdalcubes/src/gdalcubes/src/external/tinyexpr/tinyexpr.h | 2 gdalcubes-0.7.1/gdalcubes/tests/tinytest.R | 14 gdalcubes-0.7.1/gdalcubes/tools/winlibs.R | 24 gdalcubes-0.7.1/gdalcubes/vignettes/gc01_MODIS.Rmd | 4 129 files changed, 5134 insertions(+), 5097 deletions(-)
Title: '2bit' 'C' Library
Description: A trimmed down copy of the "kent-core source tree"
turned into a 'C' library for manipulation of '.2bit' files.
See <https://genome.ucsc.edu/FAQ/FAQformat.html#format7>
for a quick overview of the '2bit' format. The "kent-core source tree"
can be found here: <https://github.com/ucscGenomeBrowser/kent-core/>.
Only the '.c' and '.h' files from the source tree that are related
to manipulation of '.2bit' files were kept. Note that the package
is primarily useful to developers of other R packages who wish
to use the '2bit' 'C' library in their own 'C'/'C++' code.
Author: Herve Pages [aut, cre],
UC Regents [cph]
Maintainer: Herve Pages <hpages.on.github@gmail.com>
Diff between Rtwobitlib versions 0.3.8 dated 2025-03-18 and 0.3.9 dated 2025-03-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary src/kent/Makefile.Rtwobitlib | 3 ++- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Description: Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and
NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in
Allman et al.(2024) (forth [...truncated...]
Author: Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
Kristina Wicke [aut],
John Rhodes [aut, cre]
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Diff between MSCquartets versions 3.1 dated 2025-03-07 and 3.2 dated 2025-03-19
DESCRIPTION | 6 ++-- MD5 | 10 ++++---- R/ToBtoLevel1.R | 2 - R/evonetMisc.R | 63 +++++++++++++++++++++++++-------------------------- build/partial.rdb |binary man/resolveLevel1.Rd | 2 - 6 files changed, 42 insertions(+), 41 deletions(-)
Title: Bayesian Analysis of Dynamic Generalized Linear Models
Description: Provide routines for filtering and smoothing, forecasting, sampling and Bayesian analysis of Dynamic Generalized Linear Models using the methodology described in Alves et al. (2024)<doi:10.48550/arXiv.2201.05387> and dos Santos Jr. et al. (2024)<doi:10.48550/arXiv.2403.13069>.
Author: Silvaneo dos Santos Jr. [aut, cre],
Mariane Branco Alves [aut],
Helio dos Santos Migon [aut]
Maintainer: Silvaneo dos Santos Jr. <silvaneojunior@utexas.edu>
Diff between kDGLM versions 1.2.0 dated 2024-05-25 and 1.2.7 dated 2025-03-19
kDGLM-1.2.0/kDGLM/man/TF_block.Rd |only kDGLM-1.2.7/kDGLM/DESCRIPTION | 16 kDGLM-1.2.7/kDGLM/MD5 | 117 - kDGLM-1.2.7/kDGLM/NAMESPACE | 14 kDGLM-1.2.7/kDGLM/R/func_helper.R | 130 - kDGLM-1.2.7/kDGLM/R/kernel_gamma.R | 24 kDGLM-1.2.7/kDGLM/R/kernel_poisson.R | 3 kDGLM-1.2.7/kDGLM/R/kernels.R | 71 kDGLM-1.2.7/kDGLM/R/main.R | 284 +++ kDGLM-1.2.7/kDGLM/R/plot_helper.R | 10 kDGLM-1.2.7/kDGLM/R/priors.R | 36 kDGLM-1.2.7/kDGLM/R/structure_helper.R | 317 +++ kDGLM-1.2.7/kDGLM/build/partial.rdb |binary kDGLM-1.2.7/kDGLM/build/vignette.rds |binary kDGLM-1.2.7/kDGLM/inst/apalike.csl | 1172 ++++++------- kDGLM-1.2.7/kDGLM/inst/doc/example1.R | 142 - kDGLM-1.2.7/kDGLM/inst/doc/example1.Rmd | 19 kDGLM-1.2.7/kDGLM/inst/doc/example1.html | 2225 ++++++++++++++++++++++++-- kDGLM-1.2.7/kDGLM/inst/doc/fitting.R | 104 - kDGLM-1.2.7/kDGLM/inst/doc/fitting.html | 26 kDGLM-1.2.7/kDGLM/inst/doc/intro.R | 56 kDGLM-1.2.7/kDGLM/inst/doc/intro.Rmd | 75 kDGLM-1.2.7/kDGLM/inst/doc/intro.html | 2144 ++++++++++++++++++++++++- kDGLM-1.2.7/kDGLM/inst/doc/outcomes.R | 37 kDGLM-1.2.7/kDGLM/inst/doc/outcomes.Rmd | 3 kDGLM-1.2.7/kDGLM/inst/doc/outcomes.html | 29 kDGLM-1.2.7/kDGLM/inst/doc/structures.R | 308 +-- kDGLM-1.2.7/kDGLM/inst/doc/structures.Rmd | 22 kDGLM-1.2.7/kDGLM/inst/doc/structures.html | 58 kDGLM-1.2.7/kDGLM/man/CAR_prior.Rd | 11 kDGLM-1.2.7/kDGLM/man/Gamma.Rd | 3 kDGLM-1.2.7/kDGLM/man/analytic_filter.Rd | 4 kDGLM-1.2.7/kDGLM/man/block_mult.Rd | 1 kDGLM-1.2.7/kDGLM/man/block_rename.Rd | 1 kDGLM-1.2.7/kDGLM/man/block_superpos.Rd | 1 kDGLM-1.2.7/kDGLM/man/coef.fitted_dlm.Rd | 1 kDGLM-1.2.7/kDGLM/man/eval_dlm_norm_const.Rd | 91 - kDGLM-1.2.7/kDGLM/man/ffs_block.Rd |only kDGLM-1.2.7/kDGLM/man/fit_model.Rd | 322 +-- kDGLM-1.2.7/kDGLM/man/fit_model_single.Rd | 46 kDGLM-1.2.7/kDGLM/man/forecast.fitted_dlm.Rd | 1 kDGLM-1.2.7/kDGLM/man/formula.to.structure.Rd |only kDGLM-1.2.7/kDGLM/man/generic_smoother.Rd | 4 kDGLM-1.2.7/kDGLM/man/harmonic_block.Rd | 7 kDGLM-1.2.7/kDGLM/man/intervention.Rd | 1 kDGLM-1.2.7/kDGLM/man/joint_prior.Rd | 96 - kDGLM-1.2.7/kDGLM/man/kdglm.Rd |only kDGLM-1.2.7/kDGLM/man/noise_block.Rd | 6 kDGLM-1.2.7/kDGLM/man/noticeSARI.Rd | 60 kDGLM-1.2.7/kDGLM/man/polynomial_block.Rd | 7 kDGLM-1.2.7/kDGLM/man/reexports.Rd | 40 kDGLM-1.2.7/kDGLM/man/regression_block.Rd | 15 kDGLM-1.2.7/kDGLM/man/simulate.fitted_dlm.Rd | 103 - kDGLM-1.2.7/kDGLM/man/smoothing.Rd | 55 kDGLM-1.2.7/kDGLM/man/specify.dlm_block.Rd | 79 kDGLM-1.2.7/kDGLM/man/summary.dlm_block.Rd | 1 kDGLM-1.2.7/kDGLM/man/tf_block.Rd |only kDGLM-1.2.7/kDGLM/man/update.fitted_dlm.Rd | 1 kDGLM-1.2.7/kDGLM/vignettes/example1.Rmd | 19 kDGLM-1.2.7/kDGLM/vignettes/intro.Rmd | 75 kDGLM-1.2.7/kDGLM/vignettes/outcomes.Rmd | 3 kDGLM-1.2.7/kDGLM/vignettes/structures.Rmd | 22 62 files changed, 6705 insertions(+), 1813 deletions(-)
Title: Statistical Combination of Diagnostic Tests
Description: A system for combining two diagnostic tests using various approaches
that include statistical and machine-learning-based methodologies.
These approaches are divided into four groups: linear combination
methods, non-linear combination methods, mathematical operators,
and machine learning algorithms. See
the <https://biotools.erciyes.edu.tr/dtComb/> website
for more information, documentation, and examples.
Author: Serra Ilayda Yerlitas [aut, ctb],
Serra Bersan Gengec [aut, ctb],
Necla Kochan [aut, ctb],
Gozde Erturk Zararsiz [aut, ctb],
Selcuk Korkmaz [aut, ctb],
Gokmen Zararsiz [aut, ctb, cre]
Maintainer: Gokmen Zararsiz <gokmen.zararsiz@gmail.com>
Diff between dtComb versions 1.0.4 dated 2024-10-11 and 1.0.5 dated 2025-03-19
dtComb-1.0.4/dtComb/data/exampleData1.rda |only dtComb-1.0.4/dtComb/man/exampleData1.Rd |only dtComb-1.0.5/dtComb/DESCRIPTION | 8 dtComb-1.0.5/dtComb/LICENSE | 2 dtComb-1.0.5/dtComb/MD5 | 70 ++-- dtComb-1.0.5/dtComb/R/data.R | 14 dtComb-1.0.5/dtComb/R/linComb.R | 36 +- dtComb-1.0.5/dtComb/R/mathComb.R | 10 dtComb-1.0.5/dtComb/R/mlComb.R | 6 dtComb-1.0.5/dtComb/R/nonlinComb.R | 4 dtComb-1.0.5/dtComb/R/plotComb.R | 278 ++++++++-------- dtComb-1.0.5/dtComb/R/predict.dtComb.R | 6 dtComb-1.0.5/dtComb/R/standardization.R | 304 +++++++++--------- dtComb-1.0.5/dtComb/data/laparoscopy.rda |only dtComb-1.0.5/dtComb/inst/doc/vignettedtComb.R | 14 dtComb-1.0.5/dtComb/inst/doc/vignettedtComb.Rnw | 16 dtComb-1.0.5/dtComb/inst/doc/vignettedtComb.pdf |binary dtComb-1.0.5/dtComb/man/helper_PCL.Rd | 6 dtComb-1.0.5/dtComb/man/helper_PT.Rd | 6 dtComb-1.0.5/dtComb/man/helper_TS.Rd | 6 dtComb-1.0.5/dtComb/man/helper_minimax.Rd | 6 dtComb-1.0.5/dtComb/man/helper_minmax.Rd | 6 dtComb-1.0.5/dtComb/man/laparoscopy.Rd |only dtComb-1.0.5/dtComb/man/linComb.Rd | 6 dtComb-1.0.5/dtComb/man/mathComb.Rd | 6 dtComb-1.0.5/dtComb/man/mlComb.Rd | 6 dtComb-1.0.5/dtComb/man/nonlinComb.Rd | 4 dtComb-1.0.5/dtComb/man/plotComb.Rd | 6 dtComb-1.0.5/dtComb/man/predict.dtComb.Rd | 6 dtComb-1.0.5/dtComb/man/std.train.Rd | 4 dtComb-1.0.5/dtComb/man/transform_math.Rd | 4 dtComb-1.0.5/dtComb/tests/testthat/test-linComb.R | 6 dtComb-1.0.5/dtComb/tests/testthat/test-mathComb.R | 4 dtComb-1.0.5/dtComb/tests/testthat/test-mlComb.R | 4 dtComb-1.0.5/dtComb/tests/testthat/test-nonlinComb.R | 4 dtComb-1.0.5/dtComb/tests/testthat/test-predComb.R | 6 dtComb-1.0.5/dtComb/tests/testthat/test-standardize.R | 6 dtComb-1.0.5/dtComb/vignettes/vignettedtComb.Rnw | 16 38 files changed, 443 insertions(+), 443 deletions(-)
Title: Estimations using Conley Standard Errors
Description: Functions calculating Conley (1999) <doi:10.1016/S0304-4076(98)00084-0> standard errors. The package started by merging and extending multiple packages and
other published scripts on this econometric technique. It strongly emphasizes computational optimization. Details are available in the function documentation and in
the vignette.
Author: Christian Dueben [aut, cre],
Richard Bluhm [cph],
Luis Calderon [cph],
Darin Christensen [cph],
Timothy Conley [cph],
Thiemo Fetzer [cph],
Leander Heldring [cph]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>
Diff between conleyreg versions 0.1.7 dated 2022-03-03 and 0.1.8 dated 2025-03-19
DESCRIPTION | 16 MD5 | 54 +- NEWS.md | 4 R/conleyreg.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/conleyreg_introduction.R | 8 inst/doc/conleyreg_introduction.html | 670 +++++++++++++++++++++++++++++++---- src/Makevars | 12 src/Makevars.win | 12 src/XeeXhC.cpp | 1 src/XeeXhC.h | 1 src/XeeXhC_R.cpp | 1 src/dist_mat.cpp | 1 src/distance_functions.cpp | 1 src/distance_functions.h | 1 src/distance_matrices.cpp | 1 src/distance_matrices.h | 1 src/isbalanced.cpp | 3 src/lp.cpp | 1 src/lp_filling.cpp | 1 src/lp_filling.h | 1 src/lp_filling_R.cpp | 1 src/lp_vcov.cpp | 1 src/ols.cpp | 1 src/openmp_installed.cpp | 1 src/time_dist.cpp | 1 28 files changed, 646 insertions(+), 155 deletions(-)
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Tymoteusz Kwiecinski [aut, cre]
,
Jakub Grzywaczewski [aut],
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>
Diff between SerolyzeR versions 1.0.0 dated 2025-03-07 and 1.1.0 dated 2025-03-19
DESCRIPTION | 11 MD5 | 71 +-- NAMESPACE | 2 R/classes-model.R | 227 +++++++++--- R/classes-plate.R | 37 +- R/classes-plate_builder.R | 42 ++ R/config.R | 2 R/generate_report.R | 404 ++++++++++------------ R/parser-xponent.R | 10 R/parser.R | 125 ++++-- R/plots-standard_curve.R | 6 R/process-dir.R | 151 +++++--- R/process-file.R | 71 ++- R/process-plate.R | 189 ++++------ README.md | 4 build/vignette.rds |binary inst/doc/example_script.R | 23 - inst/doc/example_script.Rmd | 76 +++- inst/doc/example_script.html | 199 ++++++---- inst/img/report_warnings.png |only inst/templates/levey_jennings_report_template.Rmd | 68 ++- inst/templates/plate_report_template.Rmd | 95 +++-- man/Model.Rd | 8 man/Plate.Rd | 38 +- man/PlateBuilder.Rd | 12 man/handle_high_dose_hook.Rd | 4 man/process_dir.Rd | 164 ++++++-- man/process_file.Rd | 95 +++-- man/process_plate.Rd | 154 ++++---- man/read_luminex_data.Rd | 109 ++++- man/translate_sample_names_to_sample_types.Rd | 3 tests/testthat/test-generate_report.R | 1 tests/testthat/test-model.R | 71 +++ tests/testthat/test-parser.R | 9 tests/testthat/test-process-dir.R | 53 ++ tests/testthat/test-process-plate.R | 17 vignettes/example_script.Rmd | 76 +++- 37 files changed, 1733 insertions(+), 894 deletions(-)
Title: Web Scraping and Bibliometric Analysis of MDPI Journals
Description: Provides comprehensive tools to scrape and analyze data from the MDPI journals. It allows users to extract metrics such as submission-to-acceptance times, article types, and whether articles are part of special issues. The package can also visualize this information through plots. Additionally, 'MDPIexploreR' offers tools to explore patterns of self-citations within articles and provides insights into guest-edited special issues.
Author: Pablo Gomez Barreiro [aut, cre]
Maintainer: Pablo Gomez Barreiro <pablogomezbr@hotmail.es>
Diff between MDPIexploreR versions 0.2.0 dated 2024-10-15 and 0.3.0 dated 2025-03-19
MDPIexploreR-0.2.0/MDPIexploreR/inst/doc/introduction_MDPIexploreR.R |only MDPIexploreR-0.2.0/MDPIexploreR/inst/doc/introduction_MDPIexploreR.Rmd |only MDPIexploreR-0.2.0/MDPIexploreR/inst/doc/introduction_MDPIexploreR.html |only MDPIexploreR-0.2.0/MDPIexploreR/vignettes/introduction_MDPIexploreR.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/DESCRIPTION | 11 MDPIexploreR-0.3.0/MDPIexploreR/MD5 | 64 ++- MDPIexploreR-0.3.0/MDPIexploreR/NAMESPACE | 4 MDPIexploreR-0.3.0/MDPIexploreR/NEWS.md | 29 + MDPIexploreR-0.3.0/MDPIexploreR/R/MDPI_journals.R | 7 MDPIexploreR-0.3.0/MDPIexploreR/R/article_find.R | 2 MDPIexploreR-0.3.0/MDPIexploreR/R/article_info.R | 13 MDPIexploreR-0.3.0/MDPIexploreR/R/global.R | 7 MDPIexploreR-0.3.0/MDPIexploreR/R/guest_editor_info.R | 183 ---------- MDPIexploreR-0.3.0/MDPIexploreR/R/plot_articles.R | 88 ++++ MDPIexploreR-0.3.0/MDPIexploreR/R/selfcite_check.R | 2 MDPIexploreR-0.3.0/MDPIexploreR/R/special_issue_find.R | 2 MDPIexploreR-0.3.0/MDPIexploreR/R/special_issue_info.R |only MDPIexploreR-0.3.0/MDPIexploreR/R/topic_find.R |only MDPIexploreR-0.3.0/MDPIexploreR/R/topic_info.R |only MDPIexploreR-0.3.0/MDPIexploreR/README.md | 22 + MDPIexploreR-0.3.0/MDPIexploreR/build/vignette.rds |binary MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/article_functions.R |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/article_functions.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/article_functions.html |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/plot_articles.R |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/plot_articles.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/inst/doc/plot_articles.html |only MDPIexploreR-0.3.0/MDPIexploreR/man/MDPI_journals.Rd | 46 +- MDPIexploreR-0.3.0/MDPIexploreR/man/agriculture.Rd | 58 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/article_find.Rd | 44 +- MDPIexploreR-0.3.0/MDPIexploreR/man/article_info.Rd | 80 ++-- MDPIexploreR-0.3.0/MDPIexploreR/man/clean_names.Rd | 40 +- MDPIexploreR-0.3.0/MDPIexploreR/man/guest_editor_info.Rd | 85 ++-- MDPIexploreR-0.3.0/MDPIexploreR/man/horticulturae.Rd | 58 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/plot_articles.Rd | 50 +- MDPIexploreR-0.3.0/MDPIexploreR/man/selfcite_check.Rd | 58 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/special_issue_find.Rd | 56 +-- MDPIexploreR-0.3.0/MDPIexploreR/man/special_issue_info.Rd |only MDPIexploreR-0.3.0/MDPIexploreR/man/topic_find.Rd |only MDPIexploreR-0.3.0/MDPIexploreR/man/topic_info.Rd |only MDPIexploreR-0.3.0/MDPIexploreR/vignettes/article_functions.Rmd |only MDPIexploreR-0.3.0/MDPIexploreR/vignettes/plot_articles.Rmd |only 42 files changed, 498 insertions(+), 511 deletions(-)
Title: Robust Bayesian Elastic Net
Description: As heavy-tailed error distribution and outliers in the response variable widely exist, models which are robust to data contamination are highly demanded. Here, we develop a novel robust Bayesian variable selection method with elastic net penalty. In particular, the spike-and-slab priors have been incorporated to impose sparsity. An efficient Gibbs sampler has been developed to facilitate computation.The core modules of the package have been developed in 'C++' and R.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu@ksu.edu>
Diff between Bayenet versions 0.2 dated 2024-04-05 and 0.3 dated 2025-03-19
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/Bayenet-package.R | 8 ++++---- R/Bayenet.R | 2 +- R/Qenet.R | 2 +- R/Qenetss.R | 2 +- R/robust.R | 4 ++-- man/Bayenet-package.Rd | 8 ++++---- man/Bayenet.Rd | 2 +- 9 files changed, 28 insertions(+), 28 deletions(-)
Title: Vegetation Imaging Spectroscopy Analyzer
Description: Provides easy-to-use tools for data analysis and visualization for hyperspectral remote sensing (also known as imaging spectroscopy), with
a particular focus on vegetation hyperspectral data analysis. It consists of a set of functions, ranging from the organization of hyperspectral data
in the proper data structure for spectral feature selection, calculation of vegetation index, multivariate analysis, as well as to the visualization
of spectra and results of analysis in the 'ggplot2' style.
Author: Kang Yu [aut, cre]
Maintainer: Kang Yu <kang.yu@outlook.com>
Diff between visa versions 0.1.0 dated 2021-04-20 and 1.0.0 dated 2025-03-19
visa-0.1.0/visa/R/data-specdb.R |only visa-0.1.0/visa/R/ggspectra.R |only visa-0.1.0/visa/data/NSpec.DB.rda |only visa-0.1.0/visa/man/NSpec.DB.Rd |only visa-0.1.0/visa/man/SpectraDataFrame-class.Rd |only visa-0.1.0/visa/man/SpectraDataFrame.Rd |only visa-0.1.0/visa/man/SpectraDatabase-class.Rd |only visa-0.1.0/visa/man/SpectraMaxtrix-class.Rd |only visa-0.1.0/visa/man/ggplot.Rd |only visa-0.1.0/visa/man/wavelength-methods.Rd |only visa-1.0.0/visa/DESCRIPTION | 24 visa-1.0.0/visa/MD5 | 96 +- visa-1.0.0/visa/NAMESPACE | 67 + visa-1.0.0/visa/NEWS.md | 10 visa-1.0.0/visa/R/Spectra-class.R | 81 +- visa-1.0.0/visa/R/cm.nsr.R | 112 +-- visa-1.0.0/visa/R/cm.rbd3.R |only visa-1.0.0/visa/R/cm.sr.R | 108 +-- visa-1.0.0/visa/R/data-specdf.R | 6 visa-1.0.0/visa/R/data-speclib.R |only visa-1.0.0/visa/R/find.bestBands.R |only visa-1.0.0/visa/R/ggplot-method.R | 5 visa-1.0.0/visa/R/ggplot.cm.R |only visa-1.0.0/visa/R/ggplot.lmfit.R | 80 +- visa-1.0.0/visa/R/ggplot.spectra.R |only visa-1.0.0/visa/R/nsr.R |only visa-1.0.0/visa/R/plt.2dcm.R |only visa-1.0.0/visa/R/plt.3dcm_best.R |only visa-1.0.0/visa/R/spectra.R | 6 visa-1.0.0/visa/R/sr.R | 47 - visa-1.0.0/visa/R/visa.R | 14 visa-1.0.0/visa/R/wavelength.R | 67 + visa-1.0.0/visa/README.md | 29 visa-1.0.0/visa/build/vignette.rds |binary visa-1.0.0/visa/data/NSpec.Lib.rda |only visa-1.0.0/visa/inst/CITATION | 6 visa-1.0.0/visa/inst/doc/visa.R | 64 + visa-1.0.0/visa/inst/doc/visa.Rmd | 105 ++- visa-1.0.0/visa/inst/doc/visa.html | 707 ++++++++++++++++----- visa-1.0.0/visa/man/NSpec.DF.Rd | 6 visa-1.0.0/visa/man/NSpec.Lib.Rd |only visa-1.0.0/visa/man/Spectra-class.Rd | 124 +-- visa-1.0.0/visa/man/SpectraDataframe-class.Rd |only visa-1.0.0/visa/man/SpectraDataframe.Rd |only visa-1.0.0/visa/man/SpectraLibrary-class.Rd |only visa-1.0.0/visa/man/SpectraMatrix-class.Rd |only visa-1.0.0/visa/man/cm.nsr.Rd | 39 - visa-1.0.0/visa/man/cm.rbd3.Rd |only visa-1.0.0/visa/man/cm.sr.Rd | 36 - visa-1.0.0/visa/man/find.bestBands.Rd |only visa-1.0.0/visa/man/ggplot-method.Rd | 37 - visa-1.0.0/visa/man/ggplot.cm.Rd |only visa-1.0.0/visa/man/ggplot.spectra.Rd |only visa-1.0.0/visa/man/ndvi2.Rd | 2 visa-1.0.0/visa/man/nsr.Rd |only visa-1.0.0/visa/man/plt.2dcm.Rd |only visa-1.0.0/visa/man/plt.3dcm_best.Rd |only visa-1.0.0/visa/man/spectra-methods.Rd | 86 +- visa-1.0.0/visa/man/sr.Rd | 23 visa-1.0.0/visa/man/visa.Rd | 21 visa-1.0.0/visa/man/wavelength.Rd |only visa-1.0.0/visa/tests/testthat.R | 6 visa-1.0.0/visa/tests/testthat/test-ggplot.lmfit.R | 15 visa-1.0.0/visa/vignettes/visa.Rmd | 105 ++- visa-1.0.0/visa/vignettes/visa.txt | 174 ++++- 65 files changed, 1504 insertions(+), 804 deletions(-)
Title: Mixed Integer Evolution Strategies
Description: Evolutionary black box optimization algorithms building on the
'bbotk' package. 'miesmuschel' offers both ready-to-use optimization
algorithms, as well as their fundamental building blocks that can be used to
manually construct specialized optimization loops. The Mixed Integer Evolution
Strategies as described by Li et al. (2013) <doi:10.1162/EVCO_a_00059> can be
implemented, as well as the multi-objective optimization algorithms NSGA-II
by Deb, Pratap, Agarwal, and Meyarivan (2002) <doi:10.1109/4235.996017>.
Author: Martin Binder [aut, cre],
Lennart Schneider [ctb] ,
Susanne Dandl [ctb] ,
Andreas Hofheinz [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between miesmuschel versions 0.0.4-2 dated 2024-07-09 and 0.0.4-3 dated 2025-03-19
DESCRIPTION | 6 +++--- MD5 | 29 +++++++++++++++-------------- NEWS.md | 10 +++++++--- R/FiltorMaybe.R | 4 ++-- R/FiltorNull.R | 4 ++-- R/FiltorProxy.R | 4 ++-- R/FiltorSurrogateProgressive.R | 4 ++-- R/FiltorSurrogateTournament.R | 4 ++-- R/OperatorCombination.R | 2 +- inst/tinytest/helper_mutators.R | 11 +++++++++++ inst/tinytest/test_mutator_sequential.R |only man/dict_filtors_maybe.Rd | 4 ++-- man/dict_filtors_null.Rd | 4 ++-- man/dict_filtors_proxy.Rd | 4 ++-- man/dict_filtors_surprog.Rd | 4 ++-- man/dict_filtors_surtour.Rd | 4 ++-- 16 files changed, 57 insertions(+), 41 deletions(-)
Title: Client for 'GoFigr.io'
Description: Integrates with your 'RMarkdown' documents to automatically publish
figures to the <https://GoFigr.io> service. Supports both 'knitr' and interactive
execution within 'RStudio'.
Author: Maciej Pacula [cre, aut],
Flagstaff Solutions, LLC [cph]
Maintainer: Maciej Pacula <maciej@gofigr.io>
Diff between gofigR versions 0.2.2 dated 2025-02-07 and 0.3.1 dated 2025-03-19
gofigR-0.2.2/gofigR/man/capture.Rd |only gofigR-0.2.2/gofigR/man/plot_interactive.Rd |only gofigR-0.2.2/gofigR/man/plot_knitr.Rd |only gofigR-0.2.2/gofigR/man/plot_rstudio.Rd |only gofigR-0.2.2/gofigR/man/plot_script.Rd |only gofigR-0.3.1/gofigR/DESCRIPTION | 9 gofigR-0.3.1/gofigR/MD5 | 34 - gofigR-0.3.1/gofigR/NAMESPACE | 9 gofigR-0.3.1/gofigR/R/api.R | 3 gofigR-0.3.1/gofigR/R/context.R |only gofigR-0.3.1/gofigR/R/gfconfig.R | 11 gofigR-0.3.1/gofigR/R/integrations.R | 684 ++++++++--------------- gofigR-0.3.1/gofigR/R/watermark.R | 45 + gofigR-0.3.1/gofigR/README.md | 99 +-- gofigR-0.3.1/gofigR/man/CONFIG_PATH.Rd |only gofigR-0.3.1/gofigR/man/check_configured.Rd |only gofigR-0.3.1/gofigR/man/enable.Rd | 8 gofigR-0.3.1/gofigR/man/get_execution_context.Rd |only gofigR-0.3.1/gofigR/man/get_title.Rd |only gofigR-0.3.1/gofigR/man/ggwatermark.Rd |only gofigR-0.3.1/gofigR/man/intercept.Rd | 13 gofigR-0.3.1/gofigR/man/is_intercept_on.Rd |only gofigR-0.3.1/gofigR/man/publish.Rd |only gofigR-0.3.1/gofigR/man/publish_base.Rd |only gofigR-0.3.1/gofigR/man/watermark_generator.Rd | 6 25 files changed, 397 insertions(+), 524 deletions(-)
Title: Download and Processing of Automatic Weather Stations (AWS) Data
of INMET-Brazil
Description: A compilation of functions to download and processing AWS data of INMET-Brazil, with the purpose of reference evapotranspiration (ETo) estimation. The package aims to make meteorological and agricultural data analysis more parsimonious.
Author: Roberto Filgueiras [aut, cre] ,
Luan P. Venancio [aut] ,
Catariny C. Aleman [aut] ,
Fernando F. da Cunha [aut]
Maintainer: Roberto Filgueiras <betofilgueiras@gmail.com>
Diff between BrazilMet versions 0.2.0 dated 2022-10-27 and 0.3.0 dated 2025-03-19
BrazilMet-0.2.0/BrazilMet/man/figures/desktop.ini |only BrazilMet-0.3.0/BrazilMet/DESCRIPTION | 12 BrazilMet-0.3.0/BrazilMet/MD5 | 38 BrazilMet-0.3.0/BrazilMet/NAMESPACE | 82 - BrazilMet-0.3.0/BrazilMet/NEWS.md | 11 BrazilMet-0.3.0/BrazilMet/R/atmospheric_parameters.R | 27 BrazilMet-0.3.0/BrazilMet/R/conversion_factor_for_radiations.R | 57 - BrazilMet-0.3.0/BrazilMet/R/daily_download_AWS_INMET.R | 462 +++++----- BrazilMet-0.3.0/BrazilMet/R/daily_eto_FAO56.R | 174 +-- BrazilMet-0.3.0/BrazilMet/R/eto_hs.R | 14 BrazilMet-0.3.0/BrazilMet/R/etp_thorntwaite.R |only BrazilMet-0.3.0/BrazilMet/R/hourly_download_AWS_INMET.R |only BrazilMet-0.3.0/BrazilMet/R/radiation_parameters.R | 355 +++---- BrazilMet-0.3.0/BrazilMet/R/see_stations_info.R | 4 BrazilMet-0.3.0/BrazilMet/R/variables_air_humidity_2.R | 107 +- BrazilMet-0.3.0/BrazilMet/R/wind_speed_variables.R | 4 BrazilMet-0.3.0/BrazilMet/README.md |only BrazilMet-0.3.0/BrazilMet/man/daily_eto_FAO56.Rd | 6 BrazilMet-0.3.0/BrazilMet/man/download_AWS_INMET_daily.Rd | 10 BrazilMet-0.3.0/BrazilMet/man/eto_hs.Rd | 62 - BrazilMet-0.3.0/BrazilMet/man/etp_thorntwaite.Rd |only BrazilMet-0.3.0/BrazilMet/man/hourly_weather_station_download.Rd |only BrazilMet-0.3.0/BrazilMet/man/radiation_conversion.Rd | 6 23 files changed, 763 insertions(+), 668 deletions(-)
Title: Management and Processing of Autonomous Recording Unit (ARU)
Data
Description: Parse Autonomous Recording Unit (ARU) data and for sub-sampling recordings.
Extract Metadata from your recordings, select a subset of recordings for
interpretation, and prepare files for processing on the
'WildTrax' <https://wildtrax.ca/> platform. Read and process metadata
from recordings collected using the SongMeter and BAR-LT types of ARUs.
Author: David Hope [aut, cre] ,
Steffi LaZerte [aut] ,
Government of Canada [cph, fnd]
Maintainer: David Hope <david.hope@ec.gc.ca>
Diff between ARUtools versions 0.7.1 dated 2024-10-08 and 0.7.2 dated 2025-03-19
DESCRIPTION | 12 MD5 | 48 +- NEWS.md | 9 R/calc_sun.R | 4 R/checks.R | 3 R/create_dirs.R | 6 README.md | 2 build/vignette.rds |binary inst/doc/ARUtools.R | 6 inst/doc/ARUtools.html | 136 ++++---- inst/doc/Misc.R | 54 +-- inst/doc/SubSample.R | 86 ++--- inst/doc/SubSample.html | 502 +++++++++++++++---------------- inst/doc/customizing.R | 2 inst/doc/customizing.html | 518 ++++++++++++++++---------------- inst/doc/multisampling.html | 436 +++++++++++++------------- inst/doc/spatial.html | 306 +++++++++--------- inst/doc/timezones.html | 92 ++--- man/create_lookaround.Rd | 102 +++--- man/get_pattern.Rd | 44 +- man/guess_ARU_type.Rd | 50 +-- man/meta_clean_logs.Rd | 72 ++-- man/set_pattern.Rd | 58 +-- tests/testthat/_snaps/08_selections.md | 8 tests/testthat/test-02_clean_metadata.R | 8 25 files changed, 1286 insertions(+), 1278 deletions(-)
Title: Convert Digital Images into 'SpatRaster' Objects
Description: Generate 'SpatRaster' objects, as defined by the 'terra'
package, from digital images, using a specified spatial object as a
geographical reference.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rasterpic versions 0.2.6 dated 2024-12-17 and 0.3.0 dated 2025-03-19
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 107 +++---- R/rasterpic_img.R | 576 +++++++++++++++++++-------------------- README.md | 55 +++ build/vignette.rds |binary inst/doc/rasterpic.html | 10 inst/schemaorg.json | 4 tests/testthat/test-fileformat.R | 3 tests/testthat/test-nlayers.R | 1 10 files changed, 420 insertions(+), 360 deletions(-)
Title: Functions for Stochastic Search Variable Selection (SSVS)
Description: Functions for performing stochastic search variable selection (SSVS)
for binary and continuous outcomes and visualizing the results.
SSVS is a Bayesian variable selection method used to estimate the probability
that individual predictors should be included in a regression model.
Using MCMC estimation, the method samples thousands of regression models
in order to characterize the model uncertainty regarding both the predictor
set and the regression parameters. For details see Bainter, McCauley, Wager,
and Losin (2020) Improving practices for selecting a subset of important
predictors in psychology: An application to predicting pain, Advances in
Methods and Practices in Psychological Science 3(1), 66-80
<DOI:10.1177/2515245919885617>.
Author: Sierra Bainter [cre, aut] ,
Thomas McCauley [aut],
Mahmoud Fahmy [aut],
Dean Attali [aut]
Maintainer: Sierra Bainter <sbainter@miami.edu>
Diff between SSVS versions 2.0.0 dated 2022-05-29 and 2.1.0 dated 2025-03-19
DESCRIPTION | 23 +++---- MD5 | 40 ++++++++---- NAMESPACE | 6 + NEWS.md | 4 + R/SSVS.R | 6 + R/SSVS_MI.R |only R/imputed_mtcars.R |only R/plot.R | 19 +++-- R/plot_MI.R |only R/summary.R | 1 R/summary_MI.R |only R/utils-pipe.R |only R/utils.R | 6 + README.md | 112 +++++++++++++++++++++++++++-------- data/imputed_mtcars.RData |only inst/shiny/www/logo.png |binary man/figures/README-binary-plot-1.png |binary man/figures/README-plot-1.png |binary man/figures/logo.png |binary man/imputed_mtcars.Rd |only man/pipe.Rd |only man/plot.ssvs.Rd | 2 man/plot.ssvs_mi.Rd |only man/print.ssvs_mi_summary.Rd |only man/ssvs.Rd | 2 man/ssvs_mi.Rd |only man/summary.ssvs_mi.Rd |only 27 files changed, 158 insertions(+), 63 deletions(-)
Title: General Purpose Client for 'ERDDAP™' Servers
Description: General purpose R client for 'ERDDAP™' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP™' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Salvador Jesus Fernandez Bejarano [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.2.0 dated 2024-12-11 and 1.2.1 dated 2025-03-19
DESCRIPTION | 8 ++-- MD5 | 36 +++++++++--------- NEWS.md | 6 +++ R/convert_time.R | 11 +++++ R/convert_units.R | 11 +++++ R/fipscounty.R | 11 +++++ R/grid.R | 22 ++++++++++- R/keywords.R | 12 +++++- R/servers.R | 11 +++++ R/table.R | 22 ++++++++++- R/version.R | 11 +++++ R/zzz.r | 12 +++++- build/vignette.rds |binary inst/doc/Using_rerddap.R | 43 ++++----------------- inst/doc/Using_rerddap.Rmd | 50 ++++++------------------- inst/doc/Using_rerddap.html | 87 +++++++++++++++----------------------------- inst/doc/rerddap.html | 5 +- vignettes/Using_rerddap.Rmd | 50 ++++++------------------- vignettes/ifrPSA.png |binary 19 files changed, 206 insertions(+), 202 deletions(-)
Title: The Fill-Mask Association Test
Description: The Fill-Mask Association Test ('FMAT')
<doi:10.1037/pspa0000396>
is an integrative and probability-based method using
Masked Language Models to measure conceptual associations
(e.g., attitudes, biases, stereotypes, social norms, cultural values)
as propositions in natural language.
Supported language models include 'BERT'
<doi:10.48550/arXiv.1810.04805> and its variants available at 'Hugging Face'
<https://huggingface.co/models?pipeline_tag=fill-mask>.
Methodological references and installation guidance are provided at
<https://psychbruce.github.io/FMAT/>.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between FMAT versions 2024.7 dated 2024-07-29 and 2025.3 dated 2025-03-19
DESCRIPTION | 14 +- MD5 | 20 ++- NAMESPACE | 5 NEWS.md | 8 + R/FMAT.R | 251 +++++++++++++++++++++++++++++++++++++++--------- README.md | 33 +++--- man/BERT_download.Rd | 5 man/BERT_info.Rd | 14 +- man/BERT_info_date.Rd |only man/FMAT_load.Rd | 2 man/FMAT_run.Rd | 2 man/set_cache_folder.Rd |only 12 files changed, 276 insertions(+), 78 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.9.0 dated 2024-11-23 and 0.10.0 dated 2025-03-19
DESCRIPTION | 15 +- MD5 | 120 +++++++++++----------- NEWS.md | 5 R/LearnerClassifCVGlmnet.R | 15 ++ R/LearnerClassifGlmnet.R | 14 +- R/LearnerClassifKKNN.R | 2 R/LearnerClassifLogReg.R | 58 +++++++--- R/LearnerClassifNnet.R | 2 R/LearnerClassifRanger.R | 12 +- R/LearnerClassifXgboost.R | 61 +++++++---- R/LearnerRegrCVGlmnet.R | 12 +- R/LearnerRegrGlmnet.R | 12 +- R/LearnerRegrKKNN.R | 2 R/LearnerRegrKM.R | 4 R/LearnerRegrLM.R | 45 +++++++- R/LearnerRegrNnet.R | 2 R/LearnerRegrRanger.R | 12 +- R/LearnerRegrXgboost.R | 38 ++++-- R/helpers_glmnet.R | 32 +++++ R/helpers_ranger.R | 23 ++++ build/partial.rdb |binary inst/paramtest/test_paramtest_classif.cv_glmnet.R | 6 - inst/paramtest/test_paramtest_classif.glmnet.R | 7 - inst/paramtest/test_paramtest_classif.logreg.R | 6 - inst/paramtest/test_paramtest_classif.xgboost.R | 2 inst/paramtest/test_paramtest_regr.cv_glmnet.R | 6 - inst/paramtest/test_paramtest_regr.glmnet.R | 7 - inst/paramtest/test_paramtest_regr.lm.R | 6 - inst/paramtest/test_paramtest_regr.xgboost.R | 2 man/mlr3learners-package.Rd | 1 man/mlr_learners_classif.cv_glmnet.Rd | 10 + man/mlr_learners_classif.glmnet.Rd | 11 +- man/mlr_learners_classif.kknn.Rd | 2 man/mlr_learners_classif.lda.Rd | 2 man/mlr_learners_classif.log_reg.Rd | 13 ++ man/mlr_learners_classif.multinom.Rd | 2 man/mlr_learners_classif.naive_bayes.Rd | 2 man/mlr_learners_classif.nnet.Rd | 2 man/mlr_learners_classif.qda.Rd | 2 man/mlr_learners_classif.ranger.Rd | 15 ++ man/mlr_learners_classif.svm.Rd | 2 man/mlr_learners_classif.xgboost.Rd | 12 +- man/mlr_learners_regr.cv_glmnet.Rd | 10 + man/mlr_learners_regr.glmnet.Rd | 11 +- man/mlr_learners_regr.kknn.Rd | 2 man/mlr_learners_regr.km.Rd | 4 man/mlr_learners_regr.lm.Rd | 13 ++ man/mlr_learners_regr.nnet.Rd | 2 man/mlr_learners_regr.ranger.Rd | 15 ++ man/mlr_learners_regr.svm.Rd | 2 man/mlr_learners_regr.xgboost.Rd | 12 +- tests/testthat/test_classif_glmnet.R | 41 +++++++ tests/testthat/test_classif_kknn.R | 2 tests/testthat/test_classif_log_reg.R | 55 ++++++++++ tests/testthat/test_classif_ranger.R | 11 +- tests/testthat/test_classif_xgboost.R | 69 ++++++++---- tests/testthat/test_regr_glmnet.R | 38 ++++++ tests/testthat/test_regr_kknn.R | 2 tests/testthat/test_regr_lm.R | 48 ++++++++ tests/testthat/test_regr_ranger.R | 10 + tests/testthat/test_regr_xgboost.R | 43 +++++-- 61 files changed, 787 insertions(+), 207 deletions(-)
Title: Mathijs Deen's Miscellaneous Auxiliaries
Description: Provides a variety of functions useful for data analysis,
selection, manipulation, and graphics.
Author: Mathijs Deen [aut, cre]
Maintainer: Mathijs Deen <dev@mathijsdeen.com>
Diff between MDMA versions 1.1.0 dated 2024-04-25 and 2.0.0 dated 2025-03-19
MDMA-1.1.0/MDMA/R/posteriorModelOdds.R |only MDMA-1.1.0/MDMA/man/posteriorModelOdds.Rd |only MDMA-2.0.0/MDMA/DESCRIPTION | 14 MDMA-2.0.0/MDMA/MD5 | 127 ++- MDMA-2.0.0/MDMA/NAMESPACE | 169 +++-- MDMA-2.0.0/MDMA/NEWS |only MDMA-2.0.0/MDMA/R/CEA.R |only MDMA-2.0.0/MDMA/R/CEAC.R |only MDMA-2.0.0/MDMA/R/QIDS-data.R | 30 MDMA-2.0.0/MDMA/R/R2.vglm.R |only MDMA-2.0.0/MDMA/R/auc.R | 42 - MDMA-2.0.0/MDMA/R/check.R | 264 ++++---- MDMA-2.0.0/MDMA/R/coefsLogReg.R | 62 - MDMA-2.0.0/MDMA/R/corList.R | 44 - MDMA-2.0.0/MDMA/R/currency2unicode.R |only MDMA-2.0.0/MDMA/R/dPPC2.R | 150 ++-- MDMA-2.0.0/MDMA/R/f2Local.R |only MDMA-2.0.0/MDMA/R/frequencies.R | 46 - MDMA-2.0.0/MDMA/R/gnomes-data.R |only MDMA-2.0.0/MDMA/R/inRange.R | 108 +-- MDMA-2.0.0/MDMA/R/keep.R | 62 - MDMA-2.0.0/MDMA/R/m.R | 56 - MDMA-2.0.0/MDMA/R/ni.R | 32 MDMA-2.0.0/MDMA/R/pMM.R |only MDMA-2.0.0/MDMA/R/plotDistribution.R | 138 ++-- MDMA-2.0.0/MDMA/R/probeInteraction.R | 366 +++++------ MDMA-2.0.0/MDMA/R/rci.R | 42 - MDMA-2.0.0/MDMA/R/roc.R | 368 +++++------ MDMA-2.0.0/MDMA/R/tTest.R | 460 +++++++------- MDMA-2.0.0/MDMA/R/wtp.R |only MDMA-2.0.0/MDMA/R/zzz.R |only MDMA-2.0.0/MDMA/data/QIDS.rda |binary MDMA-2.0.0/MDMA/data/gnomes.rda |only MDMA-2.0.0/MDMA/man/CEA.Rd |only MDMA-2.0.0/MDMA/man/CEAC.Rd |only MDMA-2.0.0/MDMA/man/QIDS.Rd | 50 - MDMA-2.0.0/MDMA/man/R2.vglm.Rd |only MDMA-2.0.0/MDMA/man/auc.Rd | 56 - MDMA-2.0.0/MDMA/man/check.Rd | 150 ++-- MDMA-2.0.0/MDMA/man/coefsLogReg.Rd | 62 - MDMA-2.0.0/MDMA/man/corList.Rd | 56 - MDMA-2.0.0/MDMA/man/currency2unicode.Rd |only MDMA-2.0.0/MDMA/man/dPPC2.Rd | 104 +-- MDMA-2.0.0/MDMA/man/f2Local.Rd |only MDMA-2.0.0/MDMA/man/figures/lifecycle-archived.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-defunct.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-deprecated.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-experimental.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-maturing.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-questioning.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-soft-deprecated.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-stable.svg | 44 - MDMA-2.0.0/MDMA/man/figures/lifecycle-superseded.svg | 44 - MDMA-2.0.0/MDMA/man/frequencies.Rd | 50 - MDMA-2.0.0/MDMA/man/gnomes.Rd |only MDMA-2.0.0/MDMA/man/grapes-inRange-grapes.Rd | 74 +- MDMA-2.0.0/MDMA/man/grapes-ni-grapes.Rd | 60 - MDMA-2.0.0/MDMA/man/grapes-withinRange-grapes.Rd | 76 +- MDMA-2.0.0/MDMA/man/keep.Rd | 74 +- MDMA-2.0.0/MDMA/man/m.Rd | 68 +- MDMA-2.0.0/MDMA/man/pMM.Rd |only MDMA-2.0.0/MDMA/man/plot.CEA.Rd |only MDMA-2.0.0/MDMA/man/plot.CEAC.Rd |only MDMA-2.0.0/MDMA/man/plot.probeInteraction.Rd | 108 +-- MDMA-2.0.0/MDMA/man/plot.roc.Rd | 150 ++-- MDMA-2.0.0/MDMA/man/plotDistribution.Rd | 140 ++-- MDMA-2.0.0/MDMA/man/print.check.lm.Rd | 64 - MDMA-2.0.0/MDMA/man/print.probeInteraction.Rd | 62 - MDMA-2.0.0/MDMA/man/print.tTest.Rd | 60 - MDMA-2.0.0/MDMA/man/print.wtp.Rd |only MDMA-2.0.0/MDMA/man/probeInteraction.Rd | 114 +-- MDMA-2.0.0/MDMA/man/rci.Rd | 72 +- MDMA-2.0.0/MDMA/man/roc.Rd | 82 +- MDMA-2.0.0/MDMA/man/summary.tTest.Rd | 68 +- MDMA-2.0.0/MDMA/man/tTest.Rd | 152 ++-- MDMA-2.0.0/MDMA/man/wtp.Rd |only MDMA-2.0.0/MDMA/tests |only 77 files changed, 2496 insertions(+), 2432 deletions(-)
Title: Generating Features for a Cohort
Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Author: Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Jenna Reps [aut],
Anthony Sena [aut],
Ger Inberg [aut, cre],
Observational Health Data Science and Informatics [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between FeatureExtraction versions 3.7.2 dated 2024-10-18 and 3.8.0 dated 2025-03-19
FeatureExtraction-3.7.2/FeatureExtraction/inst/java/SqlRender-1.15.0.jar |only FeatureExtraction-3.7.2/FeatureExtraction/inst/java/featureExtraction-3.7.1-SNAPSHOT.jar |only FeatureExtraction-3.8.0/FeatureExtraction/DESCRIPTION | 10 FeatureExtraction-3.8.0/FeatureExtraction/MD5 | 95 +- FeatureExtraction-3.8.0/FeatureExtraction/NEWS.md | 8 FeatureExtraction-3.8.0/FeatureExtraction/R/Aggregation.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/CompareCohorts.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/CovariateData.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DefaultCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DefaultTemporalCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DefaultTemporalSequenceCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/DetailedCovariateSettings.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/FeatureExtraction.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/GetCovariates.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/GetCovariatesFromCohortAttributes.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/GetCovariatesFromOtherCohorts.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/GetDefaultCovariates.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/HelperFunctions.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/R/Normalization.R | 5 FeatureExtraction-3.8.0/FeatureExtraction/R/Table1.R | 4 FeatureExtraction-3.8.0/FeatureExtraction/R/UnitTestHelperFunctions.R | 2 FeatureExtraction-3.8.0/FeatureExtraction/build/vignette.rds |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/csv/PrespecTemporalAnnualAnalysis.csv |only FeatureExtraction-3.8.0/FeatureExtraction/inst/csv/jarChecksum.txt | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.R | 160 ++-- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.R | 112 +-- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.R | 216 +++--- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.R | 224 +++--- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.R | 236 +++---- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.R | 232 +++---- FeatureExtraction-3.8.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.pdf |binary FeatureExtraction-3.8.0/FeatureExtraction/inst/java/SqlRender-1.19.1.jar |only FeatureExtraction-3.8.0/FeatureExtraction/inst/java/featureExtraction-3.8.0-SNAPSHOT.jar |only FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/DomainConcept.sql | 20 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/GetAttrCovariates.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/GetHdpsCovariates.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/IncludeDescendants.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/inst/sql/sql_server/RemoveCovariateTempTables.sql | 2 FeatureExtraction-3.8.0/FeatureExtraction/java/org/ohdsi/featureExtraction/FeatureExtraction.java | 326 +++++----- FeatureExtraction-3.8.0/FeatureExtraction/java/org/ohdsi/featureExtraction/ReadCSVFile.java | 2 FeatureExtraction-3.8.0/FeatureExtraction/java/org/ohdsi/featureExtraction/ReadCSVFileWithHeader.java | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbCohortAttrCovariatesData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbCohortBasedCovariatesData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbCovariateData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/man/getDbDefaultCovariateData.Rd | 2 FeatureExtraction-3.8.0/FeatureExtraction/tests/testthat/test-DetailedCovariateSettings.R | 2 51 files changed, 892 insertions(+), 816 deletions(-)
More information about FeatureExtraction at CRAN
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Title: Apply Transformations to Data
Description: Provides a set of functions for data transformations.
Transformations are performed on character and numeric data. As the scope of the package is
within Student Analytics, there are functions focused around the academic year.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvconverter versions 0.5.10 dated 2024-06-11 and 0.7.0 dated 2025-03-19
vvconverter-0.5.10/vvconverter/tests/testthat/test-month_name.R |only vvconverter-0.5.10/vvconverter/tests/testthat/test-test-yes-no.R |only vvconverter-0.5.10/vvconverter/tests/testthat/test-transform-logical-yes-no.R |only vvconverter-0.7.0/vvconverter/DESCRIPTION | 6 +-- vvconverter-0.7.0/vvconverter/MD5 | 12 ++---- vvconverter-0.7.0/vvconverter/R/month_name.R | 10 ++++- vvconverter-0.7.0/vvconverter/R/test_yes_no.R | 7 +++ vvconverter-0.7.0/vvconverter/R/transform_logical_yes_no.R | 20 +++++++++- vvconverter-0.7.0/vvconverter/tests/testthat/test_clean_multiple_underscores.R |only 9 files changed, 41 insertions(+), 14 deletions(-)
Title: 'Rcpp' Implementation of Dirichlet Process Regression
Description: 'Rcpp' reimplementation of the the Bayesian non-parametric Dirichlet Process Regression model for penalized regression first published in Zeng and Zhou (2017) <doi:10.1038/s41467-017-00470-2>. A full Bayesian version is implemented with Gibbs sampling, as well as a faster but less accurate variational Bayes approximation.
Author: Mohammad Abu Gazala [cre, aut],
Daniel Nachun [ctb],
Ping Zeng [ctb]
Maintainer: Mohammad Abu Gazala <abugazalamohammad@gmail.com>
Diff between RcppDPR versions 0.1.9 dated 2025-03-15 and 0.1.10 dated 2025-03-19
RcppDPR-0.1.10/RcppDPR/DESCRIPTION | 6 ++--- RcppDPR-0.1.10/RcppDPR/MD5 | 11 +++------- RcppDPR-0.1.10/RcppDPR/NEWS.md | 2 + RcppDPR-0.1.10/RcppDPR/src/ldr.cpp | 13 +++--------- RcppDPR-0.1.10/RcppDPR/src/root_solver.cpp | 2 - RcppDPR-0.1.9/RcppDPR/inst/extdata/data/in/mouse_hs1940.bed |only RcppDPR-0.1.9/RcppDPR/inst/extdata/data/in/mouse_hs1940.bim |only RcppDPR-0.1.9/RcppDPR/inst/extdata/data/in/mouse_hs1940.fam |only 8 files changed, 14 insertions(+), 20 deletions(-)
Title: Probability Computations on Pedigrees
Description: An implementation of the Elston-Stewart algorithm for
calculating pedigree likelihoods given genetic marker data (Elston and
Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is
extended to allow inbred founders. 'pedprobr' is part of the
'pedsuite', a collection of packages for pedigree analysis in R. In
particular, 'pedprobr' depends on 'pedtools' for pedigree
manipulations and 'pedmut' for mutation modelling. For more
information, see 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedprobr versions 0.9.4 dated 2024-05-08 and 0.9.5 dated 2025-03-19
DESCRIPTION | 16 ++-- MD5 | 42 +++++------ NEWS.md | 19 ++++- R/genoCombinations.R | 4 - R/likelihood.R | 11 +-- R/likelihood2.R | 3 R/merlin.R | 2 R/oneMarkerDistribution.R | 131 +++++++++++++++++++++++++++--------- R/startdata.R | 26 ++++--- R/twoMarkerDistribution.R | 62 +++++++++-------- R/utils.R | 18 +--- README.md | 55 ++++++++++----- build/partial.rdb |binary man/genoCombinations.Rd | 4 - man/likelihood.Rd | 10 -- man/merlin.Rd | 2 man/oneMarkerDistribution.Rd | 69 +++++++++++------- man/pedprobr-package.Rd | 2 man/twoMarkerDistribution.Rd | 44 +++++------- tests/testthat/test-likelihood.R | 14 ++- tests/testthat/test-oneMarkerDist.R | 77 ++++++++++++--------- tests/testthat/test-twoMarkerDist.R | 92 ++++++++++++------------- 22 files changed, 424 insertions(+), 279 deletions(-)
Title: Processing Force-Plate Data
Description: Process raw force-plate data (txt-files) by segmenting them into trials and, if needed, calculating (user-defined) descriptive
statistics of variables for user-defined time bins (relative to trigger onsets) for each trial. When segmenting the data a baseline
correction, a filter, and a data imputation can be applied if needed. Experimental data can also be processed and combined with the
segmented force-plate data. This procedure is suggested by Johannsen et al. (2023) <doi:10.6084/m9.figshare.22190155> and some of the
options (e.g., choice of low-pass filter) are also suggested by Winter (2009) <doi:10.1002/9780470549148>.
Author: Raphael Hartmann [aut, cre] ,
Anton Koger [aut, ctb] ,
Leif Johannsen [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between forceplate versions 1.1-3 dated 2024-03-12 and 1.1-4 dated 2025-03-19
DESCRIPTION | 14 ++-- MD5 | 6 +- R/segment_fp_data.R | 138 ++++++++++++++++++++++++++++++++++--------------- man/segment_fp_data.Rd | 74 +++++++++++++++----------- 4 files changed, 150 insertions(+), 82 deletions(-)
Title: Execute Pharmacometric Models Using 'shiny'
Description: Execute Nonlinear Mixed Effects (NLME) models for pharmacometrics using a 'shiny'
interface. Specify engine parameters and select from different run options, including
simple estimation, stepwise covariate search, bootstrapping, simulation, visual predictive
check, and more. Models are executed using the 'Certara.RsNLME' package.
Author: James Craig [aut, cre],
Mike Talley [aut],
Vitalii Nazarov [aut],
Certara USA, Inc [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.RsNLME.ModelExecutor versions 3.0.1 dated 2025-01-07 and 3.0.2 dated 2025-03-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 5 ++++- R/modelExecutorUI.R | 6 ++---- 4 files changed, 12 insertions(+), 11 deletions(-)
More information about Certara.RsNLME.ModelExecutor at CRAN
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Title: Calculate Indices of Dynamic Interaction for Wildlife Tracking
Data
Description: Dynamic interaction refers to spatial-temporal associations in the movements of two (or more) animals. This package provides tools for calculating a suite of indices used for quantifying dynamic interaction with wildlife telemetry data. For more information on each of the methods employed see the references within. The package (as of version >= 0.3) also has new tools for automating contact analysis in large tracking datasets. The package (as of version 1.0) uses the 'move2' class of objects for working with tracking dataset.
Author: Jed Long [aut, cre, cph]
Maintainer: Jed Long <jed.long@uwo.ca>
Diff between wildlifeDI versions 1.0.0 dated 2024-03-22 and 1.0.1 dated 2025-03-19
DESCRIPTION | 14 +- MD5 | 22 +-- NEWS | 4 R/Prox.R | 2 R/checkTO.R | 2 R/conProcess.R | 6 - R/wildlifeDI-package.r | 5 README.md | 118 +++++++-------------- build/vignette.rds |binary inst/doc/wildlifeDI-vignette-contact_analysis.html | 80 +++++++------- inst/doc/wildlifeDI-vignette.html | 18 +-- man/wildlifeDI-package.Rd | 9 + 12 files changed, 131 insertions(+), 149 deletions(-)
More information about CohortPathways at CRAN
Permanent link
More information about CohortSurvival at CRAN
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Title: Programmatic Access to the European Central Bank's Data Portal
Description: Provides an interface to the European Central Bank's Data
Portal API, allowing for programmatic retrieval of a vast quantity
of statistical data.
Author: Eric Persson [aut, cre],
Franz X. Mohr [ctb]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ecb versions 0.4.2 dated 2023-04-20 and 0.4.3 dated 2025-03-19
ecb-0.4.2/ecb/inst/doc/ecb_sdw.R |only ecb-0.4.2/ecb/inst/doc/ecb_sdw.Rmd |only ecb-0.4.2/ecb/inst/doc/ecb_sdw.html |only ecb-0.4.2/ecb/vignettes/ecb_sdw.Rmd |only ecb-0.4.2/ecb/vignettes/phillips_plot-1.png |only ecb-0.4.3/ecb/DESCRIPTION | 30 - ecb-0.4.3/ecb/MD5 | 39 -- ecb-0.4.3/ecb/NAMESPACE | 14 ecb-0.4.3/ecb/R/get_historical_sdw.R | 96 ++--- ecb-0.4.3/ecb/R/main.R | 533 +++++++++++++--------------- ecb-0.4.3/ecb/build/vignette.rds |binary ecb-0.4.3/ecb/inst/doc/ecb_edp.R |only ecb-0.4.3/ecb/inst/doc/ecb_edp.Rmd |only ecb-0.4.3/ecb/inst/doc/ecb_edp.html |only ecb-0.4.3/ecb/man/convert_dates.Rd | 44 +- ecb-0.4.3/ecb/man/get_data.Rd | 134 +++---- ecb-0.4.3/ecb/man/get_dataflows.Rd | 42 +- ecb-0.4.3/ecb/man/get_description.Rd | 40 +- ecb-0.4.3/ecb/man/get_dimensions.Rd | 46 +- ecb-0.4.3/ecb/tests/testthat.R | 8 ecb-0.4.3/ecb/tests/testthat/tests.R | 116 +++--- ecb-0.4.3/ecb/vignettes/ecb_edp.Rmd |only ecb-0.4.3/ecb/vignettes/hicp_plot-1.png |binary ecb-0.4.3/ecb/vignettes/screenshot.png |binary ecb-0.4.3/ecb/vignettes/screenshot2.png |binary 25 files changed, 567 insertions(+), 575 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-10 1.2.1
2024-03-05 1.2.0
2024-01-08 1.1.0
2023-08-24 1.0.4
2023-07-01 1.0.3
2023-06-21 1.0.2
2023-02-12 1.0.1
2023-01-06 1.0.0
2022-08-25 0.11.7
2022-02-01 0.11.6
2022-01-20 0.11.5
2021-03-16 0.11.4
2020-06-22 0.10.6
2020-06-16 0.10.5
2020-01-27 0.9.5
2020-01-14 0.9.4
2019-12-05 0.9.3
2019-05-17 0.9.2
Title: Fitting (Exponential/Diffusion) RT-MPT Models
Description: Fit (exponential or diffusion) response-time extended multinomial processing tree (RT-MPT) models
by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003> and Klauer, Hartmann, and Meyer-Grant (submitted).
The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models,
but also latencies. This enables it to estimate process completion times and encoding plus motor execution times
next to the process probabilities of traditional MPTs. 'rtmpt' is a hierarchical Bayesian framework and posterior
samples are sampled using a Metropolis-within-Gibbs sampler (for exponential RT-MPTs) or Hamiltonian-within-Gibbs
sampler (for diffusion RT-MPTs).
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Constantin G. Meyer-Grant [aut, ctb],
Henrik Singmann [ctb, aut],
Jean Marie Linhart [ctb],
Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 2.0-2 dated 2025-01-23 and 2.0-3 dated 2025-03-19
DESCRIPTION | 6 +- MD5 | 28 ++++++------ R/call_rtmpt.R | 95 +++++++++++++++++++++++++++--------------- R/get_indices.R | 1 R/get_infofile.R | 2 R/make_mcmc.R | 4 - R/print_rtmpt.R | 2 R/simulate_rtmpt.R | 2 R/simulate_rtmpt_SBC.R | 2 inst/doc/rtmpt_guideline.html | 4 - man/fit_drtmpt.Rd | 2 man/fit_ertmpt.Rd | 2 src/diagnosis.cpp | 60 +++++++++++++++----------- src/main.cpp | 6 ++ src/r_wrapper.cpp | 43 ++++++++++--------- 15 files changed, 157 insertions(+), 102 deletions(-)
Title: Calculate Surface/Image Texture Indexes
Description: Methods for the computation of surface/image texture indices using a geostatistical based approach (Trevisani et al. (2023) <doi:10.1016/j.geomorph.2023.108838>). It provides various functions for the computation of surface texture indices (e.g., omnidirectional roughness and roughness anisotropy), including the ones based on the robust MAD estimator. The kernels included in the software permit also to calculate the surface/image texture indices directly from the input surface (i.e., without de-trending) using increments of order 2. It also provides the new radial roughness index (RRI), representing the improvement of the popular topographic roughness index (TRI). The framework can be easily extended with ad-hoc surface/image texture indices.
Author: Sebastiano Trevisani [aut, cre]
,
Ilich Alexander [ctb] ,
Zakharko Taras [ctb]
Maintainer: Sebastiano Trevisani <strevisani@iuav.it>
Diff between SurfRough versions 0.0.1.0 dated 2024-08-30 and 0.0.1.1 dated 2025-03-19
DESCRIPTION | 15 + MD5 | 29 ++- NAMESPACE | 14 + R/GeostTextureLibrarySharedRoxy.R | 336 +++++++++++++++++++++++++++++++++++--- R/RcppExports.R |only R/package.R |only README.md | 8 man/Madscan.Rd | 91 +++++----- man/Meanscan.Rd | 73 ++++---- man/RRI.Rd | 99 ++++++----- man/RRIK3.Rd |only man/RRIMax.Rd |only man/RRIMin.Rd |only man/Trik2.Rd | 91 +++++----- man/Trik2.SpatRaster.Rd |only man/Trik2.numeric.Rd |only man/circularDispersionGV.Rd | 53 +++-- man/circularDispersionNV.Rd | 55 +++--- src |only 19 files changed, 602 insertions(+), 262 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, and custom transformations.
An export function helps to generate
html, word, and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.63.0 dated 2025-03-01 and 0.64.0 dated 2025-03-19
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------ NAMESPACE | 6 +++ NEWS.md | 34 ++++++++++++++---- R/anova.R | 92 +++++++++++++++++++++++++++++++++++++++++++------ R/fetch.R |only R/mplm.R | 6 +-- R/plm.R | 7 +++ R/plm_contrasts.R | 4 +- R/print-export-plm.R | 16 +++++--- R/private-regression.R | 33 ++++++++--------- R/private_options.R | 2 - R/scan.R | 2 + man/anova.sc_plm.Rd | 52 +++++++++++++++++++++++---- man/fetch.Rd |only 15 files changed, 219 insertions(+), 69 deletions(-)
Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elemental indexes are first calculated for a collection
of elemental aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.8.1 dated 2024-09-12 and 0.8.2 dated 2025-03-19
DESCRIPTION | 15 MD5 | 207 ++- NAMESPACE | 14 NEWS.md | 47 R/aggregate.piar_index.R | 301 +++-- R/aggregation_structure-class.R | 10 R/aggregation_structure.R | 20 R/as_aggregation_structure.R | 3 R/as_index.R | 65 - R/chain.R | 19 R/coerce-aggregation_structure.R | 60 - R/coerce-index.R | 47 R/contrib.R | 94 + R/cut.piar_aggregation_structure.R |only R/elemental_index.R | 132 -- R/expand_classification.R | 33 R/extract.piar_index.R | 187 +-- R/head.piar_index.R | 2 R/helpers.R |only R/impute_prices.R | 58 R/index-class.R | 41 R/is.na.piar_index.R | 2 R/levels.piar_aggregation_structure.R | 10 R/levels.piar_index.R | 10 R/mean.piar_index.R | 155 +- R/merge.piar_index.R | 6 R/price_relative.R | 18 R/split.piar_index.R | 27 R/split_classification.R |only R/stack.piar_index.R | 10 R/time.piar_index.R | 8 R/update.aggregation_structure.R | 17 R/weights.piar_aggregation_structure.R | 22 R/window.piar_index.R | 46 README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/adjust-weights.R |only inst/doc/adjust-weights.Rmd |only inst/doc/adjust-weights.html |only inst/doc/contributions.R |only inst/doc/contributions.Rmd |only inst/doc/contributions.html |only inst/doc/imputation.R |only inst/doc/imputation.Rmd |only inst/doc/imputation.html |only inst/doc/index-number-formulas.R |only inst/doc/index-number-formulas.Rmd |only inst/doc/index-number-formulas.html |only inst/doc/matrix-aggregation.R |only inst/doc/matrix-aggregation.Rmd |only inst/doc/matrix-aggregation.html |only inst/doc/multiple-baskets.R |only inst/doc/multiple-baskets.Rmd |only inst/doc/multiple-baskets.html |only inst/doc/multiple-data-sources.R |only inst/doc/multiple-data-sources.Rmd |only inst/doc/multiple-data-sources.html |only inst/doc/multiple-dimensions.R |only inst/doc/multiple-dimensions.Rmd |only inst/doc/multiple-dimensions.html |only inst/doc/piar.R | 314 ----- inst/doc/piar.Rmd | 575 +-------- inst/doc/piar.html | 992 +++-------------- inst/doc/spatial-price-index.R |only inst/doc/spatial-price-index.Rmd |only inst/doc/spatial-price-index.html |only inst/doc/subperiods.R |only inst/doc/subperiods.Rmd |only inst/doc/subperiods.html |only inst/doc/superlative-aggregation.R |only inst/doc/superlative-aggregation.Rmd |only inst/doc/superlative-aggregation.html |only man/aggregate.piar_index.Rd | 27 man/aggregation_structure.Rd | 5 man/as.data.frame.piar_index.Rd | 20 man/as.matrix.piar_aggregation_structure.Rd | 33 man/as.ts.piar_index.Rd |only man/as_aggregation_structure.Rd | 3 man/as_index.Rd | 14 man/chain.Rd | 1 man/contrib.Rd | 23 man/cut.piar_aggregation_structure.Rd |only man/elemental_index.Rd | 15 man/expand_classification.Rd | 7 man/head.piar_index.Rd | 1 man/impute_prices.Rd | 12 man/is.na.piar_index.Rd | 1 man/levels.piar_aggregation_structure.Rd | 1 man/levels.piar_index.Rd | 5 man/mean.piar_index.Rd | 5 man/merge.piar_index.Rd | 1 man/split.piar_index.Rd | 5 man/split_classification.Rd |only man/stack.piar_index.Rd | 1 man/sub-.piar_index.Rd | 1 man/time.piar_index.Rd | 6 man/update.piar_aggregation_structure.Rd | 5 man/weights.piar_aggregation_structure.Rd | 9 man/window.piar_index.Rd | 1 tests/Examples/piar-Ex.Rout.save | 160 ++ tests/test-making-price-indexes.R | 2 tests/test-making-price-indexes.Rout.save | 2 tests/testthat/test-aggregate.R | 49 tests/testthat/test-aggregation-structure-attributes.R | 40 tests/testthat/test-aggregation_structure.R | 28 tests/testthat/test-as.ts.R |only tests/testthat/test-as_index.R | 32 tests/testthat/test-coerce-aggregation-structure.R | 11 tests/testthat/test-coerce-index.R | 23 tests/testthat/test-contrib.R | 51 tests/testthat/test-cut.R |only tests/testthat/test-expand_classification.R | 3 tests/testthat/test-extract-index.R | 23 tests/testthat/test-split.R | 6 tests/testthat/test-split_classification.R |only tests/testthat/test-stack.R | 2 tests/testthat/test-update.R | 36 vignettes/adjust-weights.Rmd |only vignettes/contributions.Rmd |only vignettes/imputation.Rmd |only vignettes/index-number-formulas.Rmd |only vignettes/matrix-aggregation.Rmd |only vignettes/multiple-baskets.Rmd |only vignettes/multiple-data-sources.Rmd |only vignettes/multiple-dimensions.Rmd |only vignettes/piar.Rmd | 575 +-------- vignettes/spatial-price-index.Rmd |only vignettes/subperiods.Rmd |only vignettes/superlative-aggregation.Rmd |only 131 files changed, 2002 insertions(+), 2819 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 10.0.0 dated 2025-03-12 and 10.0.1 dated 2025-03-19
DESCRIPTION | 11 +++--- LICENSE | 2 - MD5 | 22 ++++++------ NAMESPACE | 2 + NEWS.md | 4 ++ R/msigdbr-check-data.R | 55 +++++++++++++++++++------------- R/msigdbr-package.R | 3 + R/msigdbr.R | 68 ++++++++++++++++++++++----------------- README.md | 8 ---- build/partial.rdb |binary man/msigdbr_check_data.Rd | 5 ++ tests/testthat/test-msigdbr.R | 72 +++++++++++------------------------------- 12 files changed, 122 insertions(+), 130 deletions(-)
Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a
C API that can be used to write high-performance C and C++
geometry operations using R as an interface. Headers are provided
to make linking to and using these functions from C++ code as
easy and as safe as possible. This package contains an internal
copy of the 'GEOS' library to guarantee the best possible
consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] ,
GEOS authors [aut],
Martin Davis [ctb, cph],
Benjamin Campbell [ctb, cph],
Tomasz Sowa [ctb, cph],
Christian Kaiser [ctb, cph],
David Skea [ctb, cph],
Daniel Baston [ctb, cph],
Sandro Santilli [ctb, cph],
Mateusz Loskot [...truncated...]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between libgeos versions 3.11.1-2 dated 2023-11-29 and 3.11.1-3 dated 2025-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 10 +++++++--- src/geos_include/nlohmann_json.hpp | 4 ++-- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.9.2 dated 2025-03-12 and 0.10.1 dated 2025-03-19
DESCRIPTION | 16 ++++++++-------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 5 +++++ NEWS.md | 15 ++++++++++++--- R/countTokens.R |only R/gemini.R | 8 +++++--- R/gemini_audio.R | 19 +++++++++++-------- R/gemini_chat.R | 16 +++++++++++----- R/gemini_image.R | 16 +++++++++++----- R/gen_docs.R | 2 -- R/setEnv.R |only R/vertex.R | 2 +- man/countTokens.Rd |only man/gemini.Rd | 2 +- man/gemini_audio.Rd | 2 +- man/gemini_chat.Rd | 2 +- man/gemini_image.Rd | 2 +- man/setEnv.Rd |only 18 files changed, 85 insertions(+), 52 deletions(-)