Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.28-1 dated 2024-09-14 and 0.4.29 dated 2024-11-22
DESCRIPTION | 8 +-- MD5 | 28 +++++----- NEWS.md | 5 + R/read-fmi-cum.R | 2 R/read-tuv-file.r | 99 +++++++++++++++++++++++++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 24 ++++----- inst/doc/user-guide.Rmd | 4 - inst/doc/user-guide.html | 114 ++++++++++++++++++++++---------------------- man/qtuv_s.e.irrad.Rd | 12 +++- man/read_fmi2mspct.Rd | 2 tests/testthat/test-macam.R | 6 +- tests/testthat/test-oo.R | 72 +++++++++++++-------------- vignettes/user-guide.Rmd | 4 - 15 files changed, 227 insertions(+), 153 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.3.2 dated 2024-02-08 and 1.4.0 dated 2024-11-22
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Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 0.9.1 dated 2024-02-21 and 1.0.0 dated 2024-11-22
slendr-0.9.1/slendr/R/engines.R |only slendr-0.9.1/slendr/inst/doc/vignette-07-backends.R |only slendr-0.9.1/slendr/inst/doc/vignette-07-backends.Rmd |only slendr-0.9.1/slendr/inst/doc/vignette-07-backends.html |only slendr-0.9.1/slendr/inst/doc/vignette-09-paper.R |only slendr-0.9.1/slendr/inst/doc/vignette-09-paper.Rmd |only slendr-0.9.1/slendr/inst/doc/vignette-09-paper.html |only slendr-0.9.1/slendr/vignettes/vignette-07-backends.Rmd |only slendr-0.9.1/slendr/vignettes/vignette-09-paper.Rmd |only slendr-1.0.0/slendr/DESCRIPTION | 8 slendr-1.0.0/slendr/MD5 | 263 +++--- slendr-1.0.0/slendr/NAMESPACE | 4 slendr-1.0.0/slendr/NEWS.md | 38 slendr-1.0.0/slendr/R/compilation.R | 158 ++- slendr-1.0.0/slendr/R/extensions.R |only slendr-1.0.0/slendr/R/extract_parameters.R |only slendr-1.0.0/slendr/R/interface.R | 67 - slendr-1.0.0/slendr/R/msprime.R |only slendr-1.0.0/slendr/R/print.R | 12 slendr-1.0.0/slendr/R/slim.R |only slendr-1.0.0/slendr/R/tree-sequences.R | 184 +++- slendr-1.0.0/slendr/R/tspop.R | 6 slendr-1.0.0/slendr/R/utils.R | 20 slendr-1.0.0/slendr/R/visualization.R | 33 slendr-1.0.0/slendr/R/zzz.R | 8 slendr-1.0.0/slendr/README.md | 35 slendr-1.0.0/slendr/build/partial.rdb |only slendr-1.0.0/slendr/build/vignette.rds |binary slendr-1.0.0/slendr/inst/doc/vignette-00-installation.Rmd | 6 slendr-1.0.0/slendr/inst/doc/vignette-00-installation.html | 28 slendr-1.0.0/slendr/inst/doc/vignette-01-tutorial.R | 4 slendr-1.0.0/slendr/inst/doc/vignette-01-tutorial.Rmd | 16 slendr-1.0.0/slendr/inst/doc/vignette-01-tutorial.html | 43 - 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Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Functions for
analysis of resulting respirometry data are also provided. This package
provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk [aut, cre]
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 2.0.0 dated 2024-07-18 and 2.0.1 dated 2024-11-22
DESCRIPTION | 20 +++++++++++++------- MD5 | 6 +++--- NEWS | 3 +++ R/import_firesting.R | 27 ++++++++++++++++++++++----- 4 files changed, 41 insertions(+), 15 deletions(-)
Title: Search Spaces for 'mlr3'
Description: Collection of search spaces for hyperparameter optimization in the
'mlr3' ecosystem. It features ready-to-use search spaces for many popular
machine learning algorithms. The search spaces are from scientific articles
and work for a wide range of data sets.
Author: Marc Becker [cre, aut] ,
Michel Lang [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuningspaces versions 0.5.1 dated 2024-06-21 and 0.5.2 dated 2024-11-22
DESCRIPTION | 12 +++---- MD5 | 20 ++++++------ NEWS.md | 4 ++ R/TuningSpace.R | 26 ++++++++++------ R/bibentries.R | 11 +++--- R/tuning_spaces_rbv1.R | 4 +- R/tuning_spaces_rbv2.R | 4 +- R/zzz.R | 2 + README.md | 62 ++++++++++++++++++++++----------------- man/TuningSpace.Rd | 24 +++++++++------ man/mlr_tuning_spaces_default.Rd | 5 +-- 11 files changed, 101 insertions(+), 73 deletions(-)
More information about mlr3tuningspaces at CRAN
Permanent link
Title: Digitization of Phytosociological Relevés
Description: Simple and fast tool for transforming phytosociological
vegetation data into digital form for the following analysis.
Danihelka, Chrtek, and Kaplan (2012, ISSN:00327786).
Hennekens, and Schaminée (2001) <doi:10.2307/3237010>.
Tichý (2002) <doi:10.1111/j.1654-1103.2002.tb02069.x>.
Wickham, François, Henry, Müller (2022) <https://CRAN.R-project.org/package=dplyr>.
Author: Premysl Kral [aut, cre] ,
Jan Douda [aut]
Maintainer: Premysl Kral <kralp@fzp.czu.cz>
Diff between Rveg versions 0.1.5 dated 2024-06-26 and 0.1.6 dated 2024-11-22
Rveg-0.1.5/Rveg/inst/doc/Rveg.R |only Rveg-0.1.5/Rveg/man/tvToRveg.Rd |only Rveg-0.1.6/Rveg/DESCRIPTION | 6 Rveg-0.1.6/Rveg/MD5 | 45 Rveg-0.1.6/Rveg/NAMESPACE | 3 Rveg-0.1.6/Rveg/R/CreateChecklist.R | 8 Rveg-0.1.6/Rveg/R/RvegCheck.R | 7 Rveg-0.1.6/Rveg/R/RvegCombine.R | 1 Rveg-0.1.6/Rveg/R/RvegLoad.R |only Rveg-0.1.6/Rveg/R/RvegToJuice.R | 123 +- Rveg-0.1.6/Rveg/R/addReleve.R | 347 +++++- Rveg-0.1.6/Rveg/R/createTABLE.R | 233 +++- Rveg-0.1.6/Rveg/build/vignette.rds |binary Rveg-0.1.6/Rveg/inst/doc/Rveg.Rmd | 1359 +++++++++++++++++++----- Rveg-0.1.6/Rveg/inst/doc/Rveg.pdf |binary Rveg-0.1.6/Rveg/inst/extdata/example_dbHEAD.csv | 39 Rveg-0.1.6/Rveg/inst/extdata/example_dbREL.csv | 65 - Rveg-0.1.6/Rveg/inst/extdata/tvexport.csv | 146 +- Rveg-0.1.6/Rveg/man/CreateChecklist.Rd | 4 Rveg-0.1.6/Rveg/man/RvegCheck.Rd | 3 Rveg-0.1.6/Rveg/man/RvegCombine.Rd | 1 Rveg-0.1.6/Rveg/man/RvegLoad.Rd |only Rveg-0.1.6/Rveg/man/RvegToJuice.Rd | 1 Rveg-0.1.6/Rveg/man/TvToRveg.Rd |only Rveg-0.1.6/Rveg/man/addReleve.Rd | 9 Rveg-0.1.6/Rveg/vignettes/Rveg.Rmd | 1359 +++++++++++++++++++----- 26 files changed, 2983 insertions(+), 776 deletions(-)
Title: Interactive 3D Visualization of Molecular Structures
Description: Provides an 'htmlwidgets' <https://www.htmlwidgets.org/> interface to 'NGL.js' <http://nglviewer.org/ngl/api/>.
'NGLvieweR' can be used to visualize and interact with protein databank ('PDB') and structural files in R and Shiny applications.
It includes a set of API functions to manipulate the viewer after creation in Shiny.
Author: Niels van der Velden [aut, cre],
Alexander Rose [cph]
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>
Diff between NGLVieweR versions 1.3.1 dated 2021-06-01 and 1.4.0 dated 2024-11-22
DESCRIPTION | 10 MD5 | 90 - NAMESPACE | 76 NEWS.md | 30 R/NGLVieweR-shiny.R | 204 +- R/NGLVieweR.R | 1249 +++++++++----- R/NGLVieweR_example.R | 92 - R/api.R | 1727 ++++++++++--------- README.md | 111 - build/vignette.rds |binary inst/doc/NGLVieweR.R | 761 +++++--- inst/doc/NGLVieweR.Rmd | 1023 +++++++---- inst/doc/NGLVieweR.html | 2959 ++++++++++++++++++++++++++++------ inst/examples/API/app.R | 40 inst/examples/addSelection/app.R | 90 - inst/examples/multiStructureSelection |only inst/examples/updateColor/app.R | 3 inst/examples/updateZoomMove/app.R | 19 inst/htmlwidgets/NGLVieweR.js | 816 +++++---- inst/htmlwidgets/NGLVieweR.yaml | 24 man/NGLVieweR.Rd | 17 man/NGLVieweR_example.Rd | 7 man/addRepresentation.Rd | 30 man/addSelection.Rd | 20 man/addStructure.Rd |only man/figures/click_interaction.PNG |only man/removeSelection.Rd | 3 man/selectionParameters.Rd |only man/setFocus.Rd | 3 man/setPosition.Rd |only man/setQuality.Rd | 6 man/setRock.Rd | 6 man/setRotation.Rd |only man/setScale.Rd |only man/setSpin.Rd | 6 man/setSuperpose.Rd |only man/snapShot.Rd | 9 man/stageParameters.Rd | 9 man/updateColor.Rd | 10 man/updateFocus.Rd | 5 man/updateFullscreen.Rd | 3 man/updateRepresentation.Rd | 13 man/updateRock.Rd | 19 man/updateSelection.Rd | 10 man/updateSpin.Rd | 11 man/updateStage.Rd | 11 man/updateVisibility.Rd | 10 man/updateZoomMove.Rd | 30 man/zoomMove.Rd | 43 vignettes/NGLVieweR.Rmd | 1023 +++++++---- 50 files changed, 6938 insertions(+), 3690 deletions(-)
Title: Bayesian Estimation of the Additive Main Effects and
Multiplicative Interaction Model
Description: Performs Bayesian estimation of the additive main effects and multiplicative interaction (AMMI) model. The method is explained in Crossa, J., Perez-Elizalde, S., Jarquin, D., Cotes, J.M., Viele, K., Liu, G. and Cornelius, P.L. (2011) (<doi:10.2135/cropsci2010.06.0343>).
Author: Muhammad Yaseen [aut, cre],
Jose Crossa [aut, ctb],
Sergio Perez-Elizalde [aut, ctb],
Diego Jarquin [aut, ctb],
Jose Miguel Cotes [aut, ctb],
Kert Viele [aut, ctb],
Genzhou Liu [aut, ctb],
Paul L. Cornelius [aut, ctb],
Julian Garcia Abadillo Velasco [...truncated...]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between bayesammi versions 0.2.0 dated 2024-10-15 and 0.3.0 dated 2024-11-22
DESCRIPTION | 30 +++++++++++--------- MD5 | 14 +++++---- NAMESPACE | 13 +++++++++ NEWS.md | 11 +++++++ R/bayes_ammi.R | 78 ++++++++++++++++++++++++++++++++++++++---------------- R/biplots.R |only README.md | 26 +++++++----------- man/bayes_ammi.Rd | 2 - man/biplots.Rd |only 9 files changed, 114 insertions(+), 60 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg],
Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.0.3 dated 2023-07-10 and 1.0.5 dated 2024-11-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/data.R | 2 +- build/vignette.rds |binary man/mock.vccc.Rd | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.7.2 dated 2024-09-23 and 3.7.3 dated 2024-11-22
DESCRIPTION | 6 +++--- MD5 | 32 +++++++++++++++++++++----------- NAMESPACE | 7 +++++++ NEWS.md | 10 ++++++++++ R/Class_definitions.R | 14 ++++++++------ R/Data_Functions.R | 2 -- R/Empirical_MP.R |only R/MSE_functions.R | 4 +++- R/SAM2OM.R |only R/Splot.R |only R/popdyn.R | 5 ++--- R/runMSE.R | 3 ++- man/Emp.Rd |only man/Splot.Rd |only man/doHCR.Rd |only man/doIfreq.Rd |only man/doRec.Rd |only man/quantile_plot.Rd |only man/runMP.Rd | 3 --- man/select_MP.Rd | 38 +++++++++++++++++++------------------- man/smoothy.Rd |only src/LinInter.cpp | 3 ++- 22 files changed, 77 insertions(+), 50 deletions(-)
Title: Fast Approximation of Time-Varying Infectious Disease
Transmission Rates
Description: A fast method for approximating time-varying infectious disease
transmission rates from disease incidence time series and other
data, based on a discrete time approximation of an SEIR model, as
analyzed in Jagan et al. (2020) <doi:10.1371/journal.pcbi.1008124>.
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between fastbeta versions 0.3.0 dated 2024-05-17 and 0.3.1 dated 2024-11-22
fastbeta-0.3.0/fastbeta/R/fastbeta.affine.R |only fastbeta-0.3.0/fastbeta/R/fastbeta.bootstrap.R |only fastbeta-0.3.1/fastbeta/DESCRIPTION | 14 - fastbeta-0.3.1/fastbeta/MD5 | 54 ++-- fastbeta-0.3.1/fastbeta/NAMESPACE | 3 fastbeta-0.3.1/fastbeta/R/fastbeta.R | 228 ++++++++++++++++++++- fastbeta-0.3.1/fastbeta/R/ptpi.R | 9 fastbeta-0.3.1/fastbeta/R/seir.R | 211 +++++++++++++------ fastbeta-0.3.1/fastbeta/data/seir.ts01.R | 6 fastbeta-0.3.1/fastbeta/data/seir.ts02.R | 6 fastbeta-0.3.1/fastbeta/inst/NEWS.Rd | 55 ++++- fastbeta-0.3.1/fastbeta/man/deconvolve.Rd | 4 fastbeta-0.3.1/fastbeta/man/fastbeta-defunct.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta-deprecated.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta-notyet.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta-package.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta.Rd | 24 +- fastbeta-0.3.1/fastbeta/man/fastbeta.bootstrap.Rd | 12 - fastbeta-0.3.1/fastbeta/man/fastbeta.matrix.Rd |only fastbeta-0.3.1/fastbeta/man/ptpi.Rd | 16 - fastbeta-0.3.1/fastbeta/man/seir.Rd | 42 ++- fastbeta-0.3.1/fastbeta/man/seir.auxiliary.Rd |only fastbeta-0.3.1/fastbeta/man/seir.library.Rd | 2 fastbeta-0.3.1/fastbeta/man/smallpox.Rd | 2 fastbeta-0.3.1/fastbeta/src/Makevars |only fastbeta-0.3.1/fastbeta/src/fastbeta-win.def |only fastbeta-0.3.1/fastbeta/src/fastbeta.c | 19 - fastbeta-0.3.1/fastbeta/src/init.c | 25 +- fastbeta-0.3.1/fastbeta/src/ptpi.c | 52 ++-- fastbeta-0.3.1/fastbeta/src/seir.c | 47 ++-- fastbeta-0.3.1/fastbeta/tests/fastbeta.R | 2 fastbeta-0.3.1/fastbeta/tests/ptpi.R | 2 fastbeta-0.3.1/fastbeta/tests/seir.R | 8 33 files changed, 609 insertions(+), 234 deletions(-)
Title: Easy Access to High-Resolution Daily Climate Data for Europe
Description: Get high-resolution (1 km) daily climate data (precipitation,
minimum and maximum temperatures) for points and polygons within
Europe.
Author: Veronica Cruz-Alonso [aut, cre, cph]
,
Francisco Rodriguez-Sanchez [aut, cph]
,
Christoph Pucher [aut] ,
Paloma Ruiz-Benito [aut] ,
Julen Astigarraga [aut] ,
Mathias Neumann [aut] ,
Sophia Ratcliffe [aut]
Maintainer: Veronica Cruz-Alonso <veronica.cral@gmail.com>
Diff between easyclimate versions 0.2.1 dated 2023-07-11 and 0.2.2 dated 2024-11-22
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 4 R/build_url.R | 104 ++--- R/get_daily_climate.R | 2 R/get_daily_climate_single.R | 660 +++++++++++++++++------------------ README.md | 32 + man/easyclimate-package.Rd | 4 man/get_daily_climate.Rd | 2 tests/testthat/test-build_url.R | 50 +- tests/testthat/test-period_to_days.R | 87 ++-- 11 files changed, 495 insertions(+), 478 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.0.1 dated 2024-09-24 and 4.0.2 dated 2024-11-22
OlinkAnalyze-4.0.1/OlinkAnalyze/tests/data |only OlinkAnalyze-4.0.2/OlinkAnalyze/DESCRIPTION | 8 OlinkAnalyze-4.0.2/OlinkAnalyze/MD5 | 94 +++--- OlinkAnalyze-4.0.2/OlinkAnalyze/NEWS.md | 8 OlinkAnalyze-4.0.2/OlinkAnalyze/R/olink_normalization_utils.R | 52 ++- OlinkAnalyze-4.0.2/OlinkAnalyze/R/read_npx_parquet.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/R/sysdata.rda |binary OlinkAnalyze-4.0.2/OlinkAnalyze/build/vignette.rds |binary OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/LOD.html | 8 OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/OutlierExclusion.html | 30 +- OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/Vignett.html | 28 +- OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.Rmd | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.html | 26 - OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_introduction.html | 22 - OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/plate_randomizer.html | 16 - OlinkAnalyze-4.0.2/OlinkAnalyze/man/olink_norm_input_assay_overlap.Rd | 11 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md | 24 - OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/_snaps/npxProcessing.md | 130 ++++----- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/data |only OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/helper-get_example_olink_data.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_anova.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_boxplot.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_bridgeselector.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_heatmap.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_one_non_parametric.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_ordinalRegression.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_plate_randomizer.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_ttest.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Volcano_plot.R | 5 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-dist_plot.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-linear_mixed_model.R | 6 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-npxProcessing.R | 6 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_Pathway_Enrichment.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 86 +++++- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization_n.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization_product.R | 99 ++++--- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 136 ++++++---- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_qc_plot.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-pca_plot.R | 6 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-umap_plot.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test_Olink_wilcox.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/vignettes/bridging_E3072toEHT.Rmd | 4 43 files changed, 521 insertions(+), 342 deletions(-)
Title: Implementation of LT-FH++
Description: Implementation of LT-FH++, an extension of
the liability threshold family history (LT-FH) model.
LT-FH++ uses a Gibbs sampler for sampling from the truncated
multivariate normal distribution and allows for
flexible family structures. LT-FH++ was first described in
Pedersen, Emil M., et al. (2022)
<doi:10.1016/j.ajhg.2022.01.009>
as an extension to LT-FH with more flexible family structures,
and again as the age-dependent liability threshold (ADuLT) model
Pedersen, Emil M., et al. (2023)
<doi:10.1038/s41467-023-41210-z>
as an alternative to traditional time-to-event genome-wide
association studies, where family history was not considered.
Author: Emil Michael Pedersen [aut, cre],
Florian Prive [aut, ths],
Bjarni Johann Vilhjalmsson [ths],
Esben Agerbo [ths],
Jette Steinbach [aut],
Lucas Rasmussen [ctb]
Maintainer: Emil Michael Pedersen <emp@ph.au.dk>
Diff between LTFHPlus versions 2.1.1 dated 2024-02-12 and 2.1.2 dated 2024-11-22
DESCRIPTION | 14 +++++++------- MD5 | 14 ++++++++------ NEWS.md | 14 +++++++++----- R/Simulate_under_LTM.R | 12 ++++++------ R/tmp.R |only R/tmp2.R |only man/LTFHPlus-package.Rd | 2 +- man/simulate_under_LTM.Rd | 2 +- man/simulate_under_LTM_multi.Rd | 6 +++--- 9 files changed, 35 insertions(+), 29 deletions(-)
Title: "Eating the Liver of Data Science"
Description: Offers a suite of helper functions to simplify various data science techniques for non-experts. This package aims to enable individuals with only a minimal level of coding knowledge to become acquainted with these techniques in an accessible manner. Inspired by an ancient Persian idiom, we liken this process to "eating the liver of data science," suggesting a deep and intimate engagement with the field of data science. This package includes functions for tasks such as data partitioning for out-of-sample testing, calculating Mean Squared Error (MSE) to assess prediction accuracy, and data transformations (z-score and min-max). In addition to these helper functions, the 'liver' package also features several intriguing datasets valuable for multivariate analysis.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.17 dated 2024-10-28 and 1.18 dated 2024-11-22
liver-1.17/liver/R/transform.R |only liver-1.17/liver/man/transform.Rd |only liver-1.18/liver/DESCRIPTION | 6 liver-1.18/liver/MD5 | 34 ++-- liver-1.18/liver/NAMESPACE | 2 liver-1.18/liver/NEWS.md | 8 + liver-1.18/liver/R/kNN.R | 12 - liver-1.18/liver/R/kNN.plot.R | 216 +++++++++++++-------------- liver-1.18/liver/R/partition.R | 28 +-- liver-1.18/liver/R/scaler.R |only liver-1.18/liver/inst/doc/liver-example.R | 60 +++---- liver-1.18/liver/inst/doc/liver-example.Rmd | 68 ++++---- liver-1.18/liver/inst/doc/liver-example.html | 54 +++--- liver-1.18/liver/man/kNN.Rd | 8 - liver-1.18/liver/man/kNN.plot.Rd | 20 +- liver-1.18/liver/man/minmax.Rd | 6 liver-1.18/liver/man/partition.Rd | 7 liver-1.18/liver/man/scaler.Rd |only liver-1.18/liver/man/zscore.Rd | 6 liver-1.18/liver/vignettes/liver-example.Rmd | 68 ++++---- 20 files changed, 305 insertions(+), 298 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables <doi:10.18637/jss.v111.i02>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <madslindskou@gmail.com>
Diff between sparta versions 0.8.4 dated 2022-04-12 and 1.0.1 dated 2024-11-22
DESCRIPTION | 13 - MD5 | 29 +-- NAMESPACE | 1 NEWS.md | 5 R/api_converters.R | 2 R/api_sparta.R | 2 R/helpers_sparta.R | 1 build/vignette.rds |binary inst/CITATION |only inst/doc/using_sparta.R | 2 inst/doc/using_sparta.html | 341 ++++++++++++++++++++++++++------------------- man/as_sparta.Rd | 3 man/merge.Rd | 3 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 16 files changed, 245 insertions(+), 166 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.15.0 dated 2024-10-29 and 0.15.1 dated 2024-11-22
DESCRIPTION | 9 +++++---- MD5 | 18 +++++++++--------- NEWS.md | 11 ++++++++++- R/handler_notifier.R | 1 - R/handler_ntfy.R | 6 ++---- R/handler_rpushbullet.R | 8 ++++---- build/vignette.rds |binary man/handler_notifier.Rd | 1 - man/handler_ntfy.Rd | 8 +++----- man/handler_rpushbullet.Rd | 11 ++++++++--- 10 files changed, 41 insertions(+), 32 deletions(-)
Title: Download and Import Open Street Map Data Extracts
Description: Match, download, convert and import Open Street Map data extracts
obtained from several providers.
Author: Andrea Gilardi [aut, cre] ,
Robin Lovelace [aut] ,
Barry Rowlingson [ctb] ,
Salva Fernandez [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/395>),
Nicholas Potter [rev] for
rOpenSci, see
<https://github.com/ropensci/soft [...truncated...]
Maintainer: Andrea Gilardi <andrea.gilardi@polimi.it>
Diff between osmextract versions 0.5.1 dated 2024-04-30 and 0.5.2 dated 2024-11-22
DESCRIPTION | 12 - MD5 | 68 +++--- NEWS.md | 314 +++++++++++++++--------------- R/data.R | 2 R/download.R | 2 R/get-key-values.R | 2 R/get-network.R | 78 ++----- R/get.R | 64 ++---- R/vectortranslate.R | 23 +- inst/WORDLIST | 1 inst/doc/osmextract.R | 310 +++++++++++++++-------------- inst/doc/osmextract.Rmd | 36 +-- inst/doc/osmextract.html | 151 +++++++------- inst/doc/providers.R | 8 inst/doc/providers.html | 7 inst/doc/providers_comparisons.R | 8 inst/doc/providers_comparisons.html | 24 +- inst/osmconf.ini | 9 man/figures/README-iow1-1.png |binary man/figures/README-points-lines-iow-1.png |binary man/figures/README-points-lines-iow-2.png |binary man/oe_download.Rd | 13 - man/oe_find.Rd | 14 - man/oe_get.Rd | 64 ++---- man/oe_get_boundary.Rd | 8 man/oe_get_keys.Rd | 6 man/oe_get_network.Rd | 23 +- man/oe_match.Rd | 34 +-- man/oe_read.Rd | 27 +- man/oe_vectortranslate.Rd | 18 - man/openstreetmap_fr_zones.Rd | 2 tests/testthat/_snaps/get-keys.md | 60 ++--- tests/testthat/test-get-keys.R | 2 tests/testthat/test-get-network.R | 35 +++ vignettes/osmextract.Rmd | 36 +-- 35 files changed, 750 insertions(+), 711 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.4.0 dated 2024-11-21 and 0.4.1 dated 2024-11-22
DESCRIPTION | 6 MD5 | 20 +-- NEWS.md | 8 + R/MaestroPipeline.R | 16 ++ R/MaestroPipelineList.R | 32 ++++- inst/doc/maestro-4-advanced-scheduling.html | 14 +- inst/doc/maestro-5-directed-acyclic-graphs.html | 24 +-- man/MaestroPipeline.Rd | 42 ++++++ man/MaestroPipelineList.Rd | 4 tests/testthat/_snaps/dags.md | 28 ++++ tests/testthat/test-dags.R | 148 ++++++++++++++++++++++++ 11 files changed, 302 insertions(+), 40 deletions(-)
Title: Ternary Plots
Description: Ternary plots made simple. This package allows to create
ternary plots using 'graphics'. It provides functions to display the
data in the ternary space, to add or tune graphical elements and to
display statistical summaries. It also includes common ternary
diagrams which are useful for the archaeologist (e.g. soil texture
charts, ceramic phase diagram).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between isopleuros versions 1.2.0 dated 2024-01-08 and 1.3.0 dated 2024-11-22
DESCRIPTION | 29 +- MD5 | 108 +++++---- NAMESPACE | 1 NEWS.md | 8 R/AllGenerics.R | 70 ++++-- R/coordinates.R | 2 R/isopleuros-internal.R | 18 + R/isopleuros-package.R | 2 R/ternary_arrows.R | 2 R/ternary_axes.R | 2 R/ternary_box.R | 2 R/ternary_contour.R | 15 - R/ternary_crosshairs.R | 7 R/ternary_density.R | 19 - R/ternary_ellipse.R | 8 R/ternary_grid.R | 6 R/ternary_hull.R | 15 - R/ternary_image.R |only R/ternary_labels.R | 255 +++++++++++++++------- R/ternary_lines.R | 7 R/ternary_mean.R | 8 R/ternary_pca.R | 7 R/ternary_plot.R | 34 -- R/ternary_polygon.R | 6 R/ternary_segments.R | 2 R/ternary_text.R | 16 - R/ternary_title.R | 2 R/ternary_window.R |only R/triangle_phase.R | 4 R/triangle_soil.R | 4 README.md | 38 +-- build/partial.rdb |binary inst/examples/ex-image.R |only inst/examples/ex-plot.R | 9 inst/tinytest/_tinysnapshot/image_density.svg |only inst/tinytest/_tinysnapshot/image_interpolate.svg |only inst/tinytest/_tinysnapshot/image_rgb.svg |only inst/tinytest/_tinysnapshot/zoom_x.svg | 78 +++--- inst/tinytest/_tinysnapshot/zoom_y.svg | 78 +++--- inst/tinytest/_tinysnapshot/zoom_z.svg | 63 ++--- inst/tinytest/test_plot.R | 8 inst/tinytest/test_scale.R | 12 + inst/tinytest/test_statistics.R | 56 ++-- inst/tinytest/test_tiles.R |only man/coordinates_cartesian.Rd | 8 man/coordinates_ternary.Rd | 5 man/isopleuros-package.Rd | 3 man/ternary_arrows.Rd | 1 man/ternary_crosshairs.Rd | 1 man/ternary_density.Rd | 5 man/ternary_hull.Rd | 10 man/ternary_image.Rd |only man/ternary_labels.Rd | 24 +- man/ternary_lines.Rd | 1 man/ternary_plot.Rd | 15 - man/ternary_points.Rd | 7 man/ternary_polygon.Rd | 1 man/ternary_segments.Rd | 1 man/ternary_text.Rd | 19 + 59 files changed, 673 insertions(+), 429 deletions(-)
Title: Hyperbolic DEA Estimation
Description: Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Author: Alexander Oettl [cre, aut] ,
Daniel Gulde [aut]
Maintainer: Alexander Oettl <alexoettl34@gmail.com>
Diff between hyperbolicDEA versions 1.0.1 dated 2024-11-19 and 1.0.2 dated 2024-11-22
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/check_arguments.R | 4 +--- 3 files changed, 6 insertions(+), 8 deletions(-)
Title: Three-Way / Multigroup Data Analysis Through Densities
Description: The data consist of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides tools to create or manage such data and functional methods (principal component analysis, multidimensional scaling, cluster analysis, discriminant analysis...) for such probability densities.
Author: Rachid Boumaza [aut],
Pierre Santagostini [aut, cre],
Smail Yousfi [aut],
Gilles Hunault [ctb],
Julie Bourbeillon [ctb],
Besnik Pumo [ctb],
Sabine Demotes-Mainard [aut]
Maintainer: Pierre Santagostini <pierre.santagostini@agrocampus-ouest.fr>
Diff between dad versions 4.1.2 dated 2023-08-30 and 4.1.5 dated 2024-11-22
DESCRIPTION | 40 ++++++++++-- MD5 | 52 +++++++-------- build/vignette.rds |binary inst/doc/dad-intro.Rmd | 2 inst/doc/dad-intro.html | 8 +- inst/doc/mds-discrete-distributions.Rmd | 2 inst/doc/mds-discrete-distributions.html | 14 ++-- man/associations.Rd | 2 man/associations.folder.Rd | 2 man/castles.dated.Rd | 2 man/castles.nondated.Rd | 2 man/departments.Rd | 10 +-- man/dspg.Rd | 26 +++---- man/dspgd2015.Rd | 26 +++---- man/dstatis.inter.Rd | 5 - man/kurtosis.folder.Rd | 6 - man/mdsdd.Rd | 2 man/mtgplant1.Rd | 2 man/mtgplant2.Rd | 2 man/plotframes.Rd | 94 ++++++++++++++-------------- man/roseflowers.Rd | 2 man/roseleaves.Rd | 2 man/roses.Rd | 36 +++++----- man/skewness.folder.Rd | 102 +++++++++++++++---------------- man/varietyleaves.Rd | 2 vignettes/dad-intro.Rmd | 2 vignettes/mds-discrete-distributions.Rmd | 2 27 files changed, 238 insertions(+), 209 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre],
Muhammed Ali Yilmaz [aut],
Ozgur Asar [ctb],
Ozlem Ilk [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 2.9 dated 2023-09-13 and 3.0 dated 2024-11-22
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- R/confInt.R | 2 +- man/boxcoxmeta.Rd | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Implementation of the SVM-Maj Algorithm
Description: Implements the SVM-Maj algorithm to train data with support vector machine
<doi:10.1007/s11634-008-0020-9>.
This algorithm uses two efficient updates, one for linear kernel and one
for the nonlinear kernel.
Author: Hoksan Yip [aut, cre],
Patrick J.F. Groenen [aut],
Georgi Nalbantov [aut]
Maintainer: Hoksan Yip <hoksan@gmail.com>
Diff between SVMMaj versions 0.2.9.2 dated 2024-08-19 and 0.2.9.3 dated 2024-11-22
DESCRIPTION | 10 MD5 | 72 ++-- R/classification.R | 44 +- R/data.R | 102 +++--- R/hinge.R | 217 ++++++------- R/ispline.R | 167 +++++----- R/normalize.R | 169 +++++----- R/plotsvmmaj.R | 175 +++++------ R/predict.R | 140 ++++---- R/printsvmmaj.R | 213 +++++++------ R/roccurve.R | 79 ++--- R/svmmaj.R | 515 +++++++++++++++++--------------- R/svmmajcrossval.R | 551 ++++++++++++++++++----------------- R/update.R | 142 ++++----- build/vignette.rds |binary inst/doc/paper.R | 131 ++++---- inst/doc/paper.Rnw | 133 ++++---- inst/doc/paper.pdf |binary man/auc.Rd | 2 man/classification.Rd | 12 man/diabetes.Rd | 14 man/getHinge.Rd | 24 - man/isb.Rd | 24 - man/normalize.Rd | 6 man/plot.hinge.Rd | 4 man/plot.svmmajcrossval.Rd | 6 man/predict.svmmaj.Rd | 4 man/print.svmmaj.Rd | 34 +- man/print.svmmajcrossval.Rd | 2 man/svmmaj.Rd | 48 +-- man/svmmajcrossval.Rd | 8 man/transformdata.Rd | 6 man/voting.Rd | 30 - tests/test_all.R | 2 tests/testthat/test_svmmaj.R | 178 +++++------ tests/testthat/test_svmmajcrossval.R | 53 ++- vignettes/paper.Rnw | 133 ++++---- 37 files changed, 1791 insertions(+), 1659 deletions(-)
Title: Utilities Dealing with Solar Time Such as Sun Position and Time
of Sunrise
Description: Provide utilities to work with solar time,
i.e. where noon is exactly when sun culminates.
Provides functions for computing sun position and times of sunrise and sunset.
Author: Thomas Wutzler [aut, cre]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between solartime versions 0.0.2 dated 2021-04-22 and 0.0.4 dated 2024-11-22
DESCRIPTION | 16 MD5 | 51 +-- NAMESPACE | 1 NEWS.md | 10 R/utilSolarTime.R | 47 ++ build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/overview.Rmd | 16 inst/doc/overview.html | 471 ++++++++++++++++++++++------- man/computeDayLength.Rd | 38 +- man/computeDayLengthDoy.Rd | 52 +-- man/computeIsDayByHour.Rd | 48 +- man/computeIsDayByLocation.Rd | 82 ++--- man/computeSolarToLocalTimeDifference.Rd | 74 ++-- man/computeSunPosition.Rd | 38 +- man/computeSunPositionDoyHour.Rd | 88 ++--- man/computeSunriseHour.Rd | 50 +-- man/computeSunriseHourDoy.Rd | 84 ++--- man/computeSunsetHour.Rd | 50 +-- man/computeSunsetHourDoy.Rd | 80 ++-- man/getFractionalHours.Rd | 34 +- man/getHoursAheadOfUTC.Rd | 36 +- man/getSolarTimeHour.Rd | 36 +- man/setLocalTimeZone.Rd |only tests/spelling.R |only tests/testthat/test_compute_sun_position.R |only tools/README-eccentricityPlot-1.png |binary vignettes/overview.Rmd | 16 28 files changed, 870 insertions(+), 552 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models for conditional quantile functions:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press,
<doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression,
CRC Press, <doi:10.1201/9781315120256>.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] ,
Pin Tian Ng [ctb] ,
Blaise Melly [ctb] ,
Achim Zeileis [ctb] ,
Philip Grosjean [ctb] ,
Cleve Moler [ctb] ,
Yousef Saad [ctb] ,
Victor Chernozhukov [ctb] ,
Ivan Fernandez-Val [ctb] ,
Martin Maechler [c [...truncated...]
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.99 dated 2024-10-22 and 5.99.1 dated 2024-11-22
DESCRIPTION | 10 ++- MD5 | 22 ++++---- R/sfn.R | 123 +++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/ChangeLog | 8 +++ inst/doc/rq.pdf |binary man/akj.Rd | 2 man/sfn.control.Rd | 51 +++++++++----------- src/chlfct.f | 5 + src/quantreg_init.c | 2 src/srqfn.f | 74 +++++++++++++++-------------- src/srqfnc.f | 132 +++++++++++++++++++++++++++------------------------- 12 files changed, 227 insertions(+), 202 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 0.3.1 dated 2024-09-21 and 0.4.0 dated 2024-11-22
omopgenerics-0.3.1/omopgenerics/R/methodParticipants.R |only omopgenerics-0.3.1/omopgenerics/man/participants.Rd |only omopgenerics-0.3.1/omopgenerics/tests/testthat/test-methodParticipants.R |only omopgenerics-0.4.0/omopgenerics/DESCRIPTION | 15 omopgenerics-0.4.0/omopgenerics/MD5 | 233 omopgenerics-0.4.0/omopgenerics/NAMESPACE | 23 omopgenerics-0.4.0/omopgenerics/R/addSettings.R |only omopgenerics-0.4.0/omopgenerics/R/assert.R | 136 omopgenerics-0.4.0/omopgenerics/R/casting.R | 21 omopgenerics-0.4.0/omopgenerics/R/cdmFromTables.R | 5 omopgenerics-0.4.0/omopgenerics/R/classAchillesTable.R | 5 omopgenerics-0.4.0/omopgenerics/R/classCdmReference.R | 155 omopgenerics-0.4.0/omopgenerics/R/classCdmSource.R | 10 omopgenerics-0.4.0/omopgenerics/R/classCdmTable.R | 23 omopgenerics-0.4.0/omopgenerics/R/classCodelist.R | 32 omopgenerics-0.4.0/omopgenerics/R/classCodelistWithDetails.R | 35 omopgenerics-0.4.0/omopgenerics/R/classCohortTable.R | 109 omopgenerics-0.4.0/omopgenerics/R/classConceptSetExpression.R | 59 omopgenerics-0.4.0/omopgenerics/R/classOmopTable.R | 23 omopgenerics-0.4.0/omopgenerics/R/classSummarisedResult.R | 532 - omopgenerics-0.4.0/omopgenerics/R/columns.R |only omopgenerics-0.4.0/omopgenerics/R/combineStrata.R | 4 omopgenerics-0.4.0/omopgenerics/R/compute.R | 57 omopgenerics-0.4.0/omopgenerics/R/exportCodelist.R | 79 omopgenerics-0.4.0/omopgenerics/R/exportConceptSetExpression.R | 85 omopgenerics-0.4.0/omopgenerics/R/exportSummarisedResult.R | 19 omopgenerics-0.4.0/omopgenerics/R/filter.R |only omopgenerics-0.4.0/omopgenerics/R/importCodelist.R | 40 omopgenerics-0.4.0/omopgenerics/R/importConceptSetExpression.R | 84 omopgenerics-0.4.0/omopgenerics/R/importSummarisedResult.R | 77 omopgenerics-0.4.0/omopgenerics/R/methodBind.R | 17 omopgenerics-0.4.0/omopgenerics/R/methodDropTable.R | 2 omopgenerics-0.4.0/omopgenerics/R/methodInsertTable.R | 2 omopgenerics-0.4.0/omopgenerics/R/methodSettings.R | 1 omopgenerics-0.4.0/omopgenerics/R/methodSuppress.R | 88 omopgenerics-0.4.0/omopgenerics/R/methodTidy.R |only omopgenerics-0.4.0/omopgenerics/R/overwriteClasses.R | 2 omopgenerics-0.4.0/omopgenerics/R/pivot.R |only omopgenerics-0.4.0/omopgenerics/R/recordCohortAttrition.R | 2 omopgenerics-0.4.0/omopgenerics/R/split.R |only omopgenerics-0.4.0/omopgenerics/R/summary.R | 18 omopgenerics-0.4.0/omopgenerics/R/sysdata.rda |binary omopgenerics-0.4.0/omopgenerics/R/unite.R |only omopgenerics-0.4.0/omopgenerics/R/utilities.R | 26 omopgenerics-0.4.0/omopgenerics/R/validate.R | 270 omopgenerics-0.4.0/omopgenerics/README.md | 37 omopgenerics-0.4.0/omopgenerics/inst/doc/codelists.R | 19 omopgenerics-0.4.0/omopgenerics/inst/doc/codelists.Rmd | 19 omopgenerics-0.4.0/omopgenerics/inst/doc/codelists.html | 47 omopgenerics-0.4.0/omopgenerics/inst/doc/cohorts.R | 48 omopgenerics-0.4.0/omopgenerics/inst/doc/cohorts.Rmd | 48 omopgenerics-0.4.0/omopgenerics/inst/doc/cohorts.html | 233 omopgenerics-0.4.0/omopgenerics/inst/doc/reexport.Rmd | 10 omopgenerics-0.4.0/omopgenerics/inst/doc/reexport.html | 7 omopgenerics-0.4.0/omopgenerics/inst/doc/summarised_result.R | 283 omopgenerics-0.4.0/omopgenerics/inst/doc/summarised_result.Rmd | 497 + omopgenerics-0.4.0/omopgenerics/inst/doc/summarised_result.html | 4130 +++++++++- omopgenerics-0.4.0/omopgenerics/man/addSettings.Rd |only omopgenerics-0.4.0/omopgenerics/man/additionalColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/cdmName.Rd | 1 omopgenerics-0.4.0/omopgenerics/man/compute.cdm_table.Rd | 11 omopgenerics-0.4.0/omopgenerics/man/emptyAchillesTable.Rd | 2 omopgenerics-0.4.0/omopgenerics/man/exportCodelist.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/exportConceptSetExpression.Rd | 5 omopgenerics-0.4.0/omopgenerics/man/filterAdditional.Rd |only omopgenerics-0.4.0/omopgenerics/man/filterGroup.Rd |only omopgenerics-0.4.0/omopgenerics/man/filterSettings.Rd |only omopgenerics-0.4.0/omopgenerics/man/filterStrata.Rd |only omopgenerics-0.4.0/omopgenerics/man/groupColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/importCodelist.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/importConceptSetExpression.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/newSummarisedResult.Rd | 44 omopgenerics-0.4.0/omopgenerics/man/omopColumns.Rd | 9 omopgenerics-0.4.0/omopgenerics/man/omopgenerics-package.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/pivotEstimates.Rd |only omopgenerics-0.4.0/omopgenerics/man/print.codelist_with_details.Rd | 6 omopgenerics-0.4.0/omopgenerics/man/print.conceptSetExpression.Rd | 26 omopgenerics-0.4.0/omopgenerics/man/reexports.Rd | 5 omopgenerics-0.4.0/omopgenerics/man/settingsColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitAdditional.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitAll.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitGroup.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitStrata.Rd |only omopgenerics-0.4.0/omopgenerics/man/strataColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/summary.summarised_result.Rd | 2 omopgenerics-0.4.0/omopgenerics/man/suppress.summarised_result.Rd | 26 omopgenerics-0.4.0/omopgenerics/man/tidy.summarised_result.Rd |only omopgenerics-0.4.0/omopgenerics/man/tidyColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/uniteAdditional.Rd |only omopgenerics-0.4.0/omopgenerics/man/uniteGroup.Rd |only omopgenerics-0.4.0/omopgenerics/man/uniteStrata.Rd |only omopgenerics-0.4.0/omopgenerics/man/validateCohortArgument.Rd | 4 omopgenerics-0.4.0/omopgenerics/man/validateCohortIdArgument.Rd | 10 omopgenerics-0.4.0/omopgenerics/man/validateNewColumn.Rd |only omopgenerics-0.4.0/omopgenerics/man/validateResultArgument.Rd | 22 omopgenerics-0.4.0/omopgenerics/tests/testthat/_snaps/utilities.md | 2 omopgenerics-0.4.0/omopgenerics/tests/testthat/setup.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-addSettings.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-assert.R | 33 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCdmReference.R | 1 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCodelist.R | 49 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCodelistWithDetails.R | 38 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCohortTable.R | 104 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classConceptSetExpression.R | 233 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classSummarisedResult.R | 70 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-cohortCodelist.R | 113 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-columns.R | 41 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-combineStrata.R | 23 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-emptyObjects.R | 23 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-exportCodelist.R | 54 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-exportConceptSetExpression.R | 75 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-exportSummarisedResult.R | 21 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-filter.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-importCodelist.R | 36 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-importConceptSetExpression.R | 132 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-importSummarisedResult.R | 147 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodBind.R | 82 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodComputeTable.R | 13 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodDropSourceTable.R | 2 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodInsertTable.R | 1 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodReadSourceTable.R | 2 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodSummary.R | 7 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodSuppress.R | 52 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodTidy.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-overwriteClasses.R | 9 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-pivot.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-prefix.R | 6 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-recordCohortAttrition.R | 1 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-split.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-unite.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-utilities.R | 63 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-validate.R | 200 omopgenerics-0.4.0/omopgenerics/vignettes/codelists.Rmd | 19 omopgenerics-0.4.0/omopgenerics/vignettes/cohorts.Rmd | 48 omopgenerics-0.4.0/omopgenerics/vignettes/reexport.Rmd | 10 omopgenerics-0.4.0/omopgenerics/vignettes/summarised_result.Rmd | 497 + 136 files changed, 7965 insertions(+), 2094 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.2.4 dated 2024-11-13 and 2.2.5 dated 2024-11-22
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/MVar.pt-package.Rd | 6 +++--- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Multivariate Analysis
Description: Multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.2.4 dated 2024-11-13 and 2.2.5 dated 2024-11-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/MVar-package.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Easily Handling Data from the ‘m-Path’ Platform
Description: Provides tools for importing and cleaning Experience Sampling
Method (ESM) data collected via the 'm-Path' platform. The goal is
to provide with a few utility functions to be able to read and perform
some common operations in ESM data collected through the 'm-Path'
platform (<https://m-path.io/landing/>). Functions include raw data
handling, format standardization, and basic data checks, as well as to
calculate the response rate in data from ESM studies.
Author: Merijn Mestdagh [aut, cre] ,
Lara Navarrete [aut],
Koen Niemeijer [aut] ,
m-Path Software [cph]
Maintainer: Merijn Mestdagh <merijn.mestdagh@m-path.io>
Diff between mpathr versions 1.0.1 dated 2024-10-21 and 1.0.2 dated 2024-11-22
mpathr-1.0.1/mpathr/man/figures/README-pressure-1.png |only mpathr-1.0.1/mpathr/man/figures/logo2.png |only mpathr-1.0.1/mpathr/man/figures/logo2.svg |only mpathr-1.0.2/mpathr/DESCRIPTION | 6 +-- mpathr-1.0.2/mpathr/MD5 | 17 ++++----- mpathr-1.0.2/mpathr/NEWS.md | 18 ++++++++++ mpathr-1.0.2/mpathr/R/cast_vec.R | 15 ++++++++ mpathr-1.0.2/mpathr/R/read_mpath.R | 19 ++++++++--- mpathr-1.0.2/mpathr/README.md | 12 +++++- mpathr-1.0.2/mpathr/build/vignette.rds |binary mpathr-1.0.2/mpathr/tests/testthat/test-cast_vec.R | 31 ++++++++++++++++++ 11 files changed, 98 insertions(+), 20 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 10.0.0 dated 2024-07-26 and 11.0.0 dated 2024-11-22
ggblanket-10.0.0/ggblanket/R/unexported.R |only ggblanket-10.0.0/ggblanket/man/weave_col_palette_c.Rd |only ggblanket-10.0.0/ggblanket/man/weave_col_palette_d.Rd |only ggblanket-10.0.0/ggblanket/man/weave_col_palette_o.Rd |only ggblanket-11.0.0/ggblanket/DESCRIPTION | 10 ggblanket-11.0.0/ggblanket/MD5 | 303 +- ggblanket-11.0.0/ggblanket/NAMESPACE | 5 ggblanket-11.0.0/ggblanket/NEWS.md | 10 ggblanket-11.0.0/ggblanket/R/aes.R | 8 ggblanket-11.0.0/ggblanket/R/flex_mode.R | 56 ggblanket-11.0.0/ggblanket/R/gg_blanket.R | 15 ggblanket-11.0.0/ggblanket/R/gg_qq.R | 28 ggblanket-11.0.0/ggblanket/R/gg_ribbon.R | 25 ggblanket-11.0.0/ggblanket/R/gg_smooth.R | 1 ggblanket-11.0.0/ggblanket/R/label_every_nth.R |only ggblanket-11.0.0/ggblanket/R/set_blanket.R | 158 - ggblanket-11.0.0/ggblanket/R/weave.R | 268 +- ggblanket-11.0.0/ggblanket/inst/WORDLIST | 2 ggblanket-11.0.0/ggblanket/inst/doc/ggblanket.R | 23 ggblanket-11.0.0/ggblanket/inst/doc/ggblanket.Rmd | 32 ggblanket-11.0.0/ggblanket/inst/doc/ggblanket.html | 163 - ggblanket-11.0.0/ggblanket/man/aes_colour_contrast.Rd | 130 - ggblanket-11.0.0/ggblanket/man/aes_colour_darken.Rd | 122 - ggblanket-11.0.0/ggblanket/man/figures/README-unnamed-chunk-2-1.png |binary ggblanket-11.0.0/ggblanket/man/gg_area.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_bar.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_bin_2d.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_blanket.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_boxplot.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_col.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_contour.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_contour_filled.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_crossbar.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_density.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_density_2d.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_density_2d_filled.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_errorbar.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_freqpoly.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_function.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_hex.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_histogram.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_jitter.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_label.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_line.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_linerange.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_path.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_point.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_pointrange.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_polygon.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_qq.Rd | 6 ggblanket-11.0.0/ggblanket/man/gg_quantile.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_raster.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_rect.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_ribbon.Rd | 3 ggblanket-11.0.0/ggblanket/man/gg_rug.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_segment.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_sf.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_smooth.Rd | 3 ggblanket-11.0.0/ggblanket/man/gg_step.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_text.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_tile.Rd | 2 ggblanket-11.0.0/ggblanket/man/gg_violin.Rd | 2 ggblanket-11.0.0/ggblanket/man/label_every_nth.Rd |only ggblanket-11.0.0/ggblanket/man/set_blanket.Rd | 276 -- ggblanket-11.0.0/ggblanket/man/weave_col_palettes.Rd |only ggblanket-11.0.0/ggblanket/man/weave_geom_defaults.Rd | 142 - ggblanket-11.0.0/ggblanket/man/weave_theme.Rd | 4 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-area.svg | 6 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-bar.svg | 68 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-bin-2d.svg | 664 ++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-blanket.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-boxplot.svg | 58 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-col.svg | 66 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-contour-filled.svg | 118 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-crossbar.svg | 66 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-density-2d-filled.svg | 118 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-density.svg | 38 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-errorbar.svg | 70 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-freqpoly.svg | 20 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-hex.svg | 730 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-histogram.svg | 820 +++---- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-label.svg | 82 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-linerange.svg | 54 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-point.svg | 778 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-pointrange.svg | 66 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-polygon.svg | 128 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-raster.svg | 92 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-rect.svg | 104 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-ribbon.svg | 6 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-smooth.svg | 106 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-text.svg | 76 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-tile.svg | 44 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-violin.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/1.svg | 48 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/10.svg | 116 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/11.svg | 104 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/12.svg | 180 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/13.svg | 140 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/2.svg | 32 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/3.svg | 370 +-- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/5.svg | 148 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/6.svg | 4 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/7.svg | 66 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/8.svg | 68 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/article-go-further/9.svg | 480 ++-- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/1.svg | 118 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/10.svg | 118 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/11.svg | 54 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/12.svg | 154 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/2.svg | 16 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/3.svg | 754 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/4.svg | 118 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/5.svg | 16 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/6.svg | 754 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/7.svg | 16 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/8.svg | 754 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/col_palette/9.svg | 754 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/ggproto-etc/all-3.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/ggproto-etc/default.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/ggproto-etc/geomviolin.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/ggproto-etc/positiondodge.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/ggproto-etc/statydensity.svg | 64 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/labelled/labelled.svg | 92 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/modes/dark-mode-r.svg | 1124 +++++----- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/modes/light-mode-b.svg | 20 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/modes/light-mode-r.svg | 1124 +++++----- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/modes/light-mode-t.svg | 20 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/numeric-col/light-mode-b.svg | 942 ++++---- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/numeric-col/light-mode-r.svg | 936 ++++---- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/numeric-col/light-mode-t.svg | 850 +++---- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/set_blanket/2.svg | 780 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/set_blanket/3.svg | 778 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/set_blanket/4.svg | 800 +++---- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/set_blanket/5.svg | 808 +++---- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/set_blanket/6.svg | 168 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/symmetric/1.svg | 60 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/symmetric/2.svg | 60 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/10.svg | 20 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/11.svg | 200 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/13.svg | 272 +- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/14.svg | 48 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/15.svg | 110 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/16.svg | 4 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/17.svg | 148 - ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/18.svg | 94 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/19.svg | 94 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/2.svg | 778 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/20.svg | 778 +++--- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/21.svg | 272 +- ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/3.svg | 60 ggblanket-11.0.0/ggblanket/tests/testthat/_snaps/vignette-ggblanket/4.svg | 180 - 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Title: Calibration, Validation, and Simulation of TKTD Models
Description: Eases the use of ecotoxicological effect models. Can simulate
common toxicokinetic-toxicodynamic (TK/TD) models such as
General Unified Threshold models of Survival (GUTS) and Lemna. It can
derive effects and effect profiles (EPx) from scenarios. It supports the
use of 'tidyr' workflows employing the pipe symbol. Time-consuming
tasks can be parallelized.
Author: Nils Kehrein [aut, cre],
Dirk Nickisch [aut],
Peter Vermeiren [aut],
Torben Wittwer [ctb],
Johannes Witt [ctb],
Andre Gergs [ctb]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between cvasi versions 1.2.0 dated 2024-09-23 and 1.3.1 dated 2024-11-22
cvasi-1.2.0/cvasi/R/class-Algae.R |only cvasi-1.2.0/cvasi/R/class-Deb.R |only cvasi-1.2.0/cvasi/R/class-GutsRed.R |only cvasi-1.2.0/cvasi/R/class-Lemna.R |only cvasi-1.2.0/cvasi/R/class-Myriophyllum.R |only cvasi-1.2.0/cvasi/R/class-parameter_set.R |only cvasi-1.2.0/cvasi/R/import.R |only cvasi-1.2.0/cvasi/R/morse.R |only cvasi-1.2.0/cvasi/man/import_exposure_text.Rd |only cvasi-1.2.0/cvasi/man/morse.Rd |only cvasi-1.2.0/cvasi/src/algae_TKTD.c |only cvasi-1.2.0/cvasi/tests/testthat/test-simulate_Lemna.R |only cvasi-1.3.1/cvasi/DESCRIPTION | 32 cvasi-1.3.1/cvasi/MD5 | 229 cvasi-1.3.1/cvasi/NAMESPACE | 15 cvasi-1.3.1/cvasi/NEWS.md | 28 cvasi-1.3.1/cvasi/R/calibrate.R | 9 cvasi-1.3.1/cvasi/R/class-EffectScenario.R | 3 cvasi-1.3.1/cvasi/R/class-ParameterSet.R |only cvasi-1.3.1/cvasi/R/class-ScenarioSequence.R | 6 cvasi-1.3.1/cvasi/R/class-Transferable.R | 2 cvasi-1.3.1/cvasi/R/data.R | 4 cvasi-1.3.1/cvasi/R/dose_response.R | 93 cvasi-1.3.1/cvasi/R/effect.R | 15 cvasi-1.3.1/cvasi/R/fx.R | 82 cvasi-1.3.1/cvasi/R/get.R | 8 cvasi-1.3.1/cvasi/R/globals.R | 13 cvasi-1.3.1/cvasi/R/has.R | 6 cvasi-1.3.1/cvasi/R/import_morse.R |only cvasi-1.3.1/cvasi/R/import_toxswa.R | 398 - cvasi-1.3.1/cvasi/R/is.R | 2 cvasi-1.3.1/cvasi/R/man-deb.R |only cvasi-1.3.1/cvasi/R/man-lemna.R |only cvasi-1.3.1/cvasi/R/man-macrophytes.R |only cvasi-1.3.1/cvasi/R/model-algae.R |only cvasi-1.3.1/cvasi/R/model-deb_abj.R |only cvasi-1.3.1/cvasi/R/model-debtox.R | 37 cvasi-1.3.1/cvasi/R/model-guts_red.R |only cvasi-1.3.1/cvasi/R/model-lemna_schmitt.R |only cvasi-1.3.1/cvasi/R/model-lemna_setac.R |only cvasi-1.3.1/cvasi/R/model-myriophyllum.R |only cvasi-1.3.1/cvasi/R/plot.R |only cvasi-1.3.1/cvasi/R/plotting.r | 39 cvasi-1.3.1/cvasi/R/set.R | 12 cvasi-1.3.1/cvasi/R/set_exposure.R | 22 cvasi-1.3.1/cvasi/R/set_param.R | 10 cvasi-1.3.1/cvasi/R/simulate.R | 95 cvasi-1.3.1/cvasi/R/solver.R | 505 - cvasi-1.3.1/cvasi/R/survival.R | 6 cvasi-1.3.1/cvasi/README.md |only cvasi-1.3.1/cvasi/data/Rsubcapitata.rda |binary cvasi-1.3.1/cvasi/data/americamysis.rda |binary cvasi-1.3.1/cvasi/data/focusd1.rda |binary cvasi-1.3.1/cvasi/data/minnow_it.rda |binary cvasi-1.3.1/cvasi/data/minnow_sd.rda |binary cvasi-1.3.1/cvasi/inst/doc/cvasi-1-manual.R | 14 cvasi-1.3.1/cvasi/inst/doc/cvasi-1-manual.Rmd | 11 cvasi-1.3.1/cvasi/inst/doc/cvasi-1-manual.html | 17 cvasi-1.3.1/cvasi/inst/doc/cvasi-2-howto.R | 18 cvasi-1.3.1/cvasi/inst/doc/cvasi-2-howto.Rmd | 20 cvasi-1.3.1/cvasi/inst/doc/cvasi-2-howto.html | 24 cvasi-1.3.1/cvasi/man/Algae-models.Rd | 12 cvasi-1.3.1/cvasi/man/Algae_Simple.Rd | 30 cvasi-1.3.1/cvasi/man/Algae_TKTD.Rd | 30 cvasi-1.3.1/cvasi/man/Algae_Weber.Rd | 30 cvasi-1.3.1/cvasi/man/DEB-models.Rd | 12 cvasi-1.3.1/cvasi/man/DEB_abj.Rd | 21 cvasi-1.3.1/cvasi/man/DEBtox.Rd | 30 cvasi-1.3.1/cvasi/man/GUTS-RED-models.Rd | 10 cvasi-1.3.1/cvasi/man/GUTS_RED_IT.Rd | 2 cvasi-1.3.1/cvasi/man/GUTS_RED_SD.Rd | 2 cvasi-1.3.1/cvasi/man/Lemna-models.Rd | 10 cvasi-1.3.1/cvasi/man/Lemna_SETAC.Rd | 62 cvasi-1.3.1/cvasi/man/Lemna_Schmitt.Rd | 58 cvasi-1.3.1/cvasi/man/Macrophyte-models.Rd | 10 cvasi-1.3.1/cvasi/man/Myrio.Rd | 43 cvasi-1.3.1/cvasi/man/Myrio_log.Rd | 43 cvasi-1.3.1/cvasi/man/Myriophyllum-models.Rd | 10 cvasi-1.3.1/cvasi/man/Rsubcapitata.Rd | 2 cvasi-1.3.1/cvasi/man/Scenarios.Rd | 10 cvasi-1.3.1/cvasi/man/Transferable.Rd | 10 cvasi-1.3.1/cvasi/man/dose_response.Rd | 10 cvasi-1.3.1/cvasi/man/figures |only cvasi-1.3.1/cvasi/man/focusd1.Rd | 2 cvasi-1.3.1/cvasi/man/fx.Rd | 19 cvasi-1.3.1/cvasi/man/get_model.Rd | 2 cvasi-1.3.1/cvasi/man/get_tag.Rd | 2 cvasi-1.3.1/cvasi/man/import_morse.Rd |only cvasi-1.3.1/cvasi/man/import_swash.Rd | 6 cvasi-1.3.1/cvasi/man/import_toxswa.Rd | 63 cvasi-1.3.1/cvasi/man/minnow_it.Rd | 2 cvasi-1.3.1/cvasi/man/minnow_sd.Rd | 2 cvasi-1.3.1/cvasi/man/parameter_set.Rd | 5 cvasi-1.3.1/cvasi/man/plot.Rd |only cvasi-1.3.1/cvasi/man/plot_epx.Rd | 2 cvasi-1.3.1/cvasi/man/plot_ppc.Rd | 3 cvasi-1.3.1/cvasi/man/plot_ppc_combi.Rd | 6 cvasi-1.3.1/cvasi/man/plot_scenario.Rd | 10 cvasi-1.3.1/cvasi/man/plot_sd.Rd | 3 cvasi-1.3.1/cvasi/man/set_mode_of_action.Rd | 7 cvasi-1.3.1/cvasi/man/set_param.Rd | 96 cvasi-1.3.1/cvasi/man/set_times.Rd | 2 cvasi-1.3.1/cvasi/man/simulate_batch.Rd | 35 cvasi-1.3.1/cvasi/man/solver.Rd | 81 cvasi-1.3.1/cvasi/man/survival.Rd | 6 cvasi-1.3.1/cvasi/src/algae_simple.c | 11 cvasi-1.3.1/cvasi/src/algae_tktd.c |only cvasi-1.3.1/cvasi/src/algae_weber.c | 13 cvasi-1.3.1/cvasi/src/deb_abj.c | 18 cvasi-1.3.1/cvasi/src/lemna_schmitt.c | 50 cvasi-1.3.1/cvasi/src/lemna_setac.c |only cvasi-1.3.1/cvasi/src/myriophyllum.c | 31 cvasi-1.3.1/cvasi/tests/data/TOXSWA/testonil.out | 3531 ---------- cvasi-1.3.1/cvasi/tests/data/morse |only cvasi-1.3.1/cvasi/tests/testthat/_snaps/verify_guts.md | 12 cvasi-1.3.1/cvasi/tests/testthat/lemna_helpers.R |only cvasi-1.3.1/cvasi/tests/testthat/morse_guts-red.R | 8 cvasi-1.3.1/cvasi/tests/testthat/test-calibrate.R | 2 cvasi-1.3.1/cvasi/tests/testthat/test-epx.R | 11 cvasi-1.3.1/cvasi/tests/testthat/test-get.R | 4 cvasi-1.3.1/cvasi/tests/testthat/test-import_morse.R |only cvasi-1.3.1/cvasi/tests/testthat/test-import_toxswa.R | 167 cvasi-1.3.1/cvasi/tests/testthat/test-plot.R |only cvasi-1.3.1/cvasi/tests/testthat/test-set.R | 84 cvasi-1.3.1/cvasi/tests/testthat/test-set_exposure.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_batch.R | 28 cvasi-1.3.1/cvasi/tests/testthat/test-simulate_lemna_schmitt.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_lemna_setac.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_sequence.R | 2 cvasi-1.3.1/cvasi/vignettes/cvasi-1-manual.Rmd | 11 cvasi-1.3.1/cvasi/vignettes/cvasi-2-howto.Rmd | 20 131 files changed, 1302 insertions(+), 5277 deletions(-)
Title: Carbon-Related Assessment of Silvicultural Concepts
Description: A simulation model and accompanying functions that support
assessing silvicultural concepts on the forest estate level with a focus on
the CO2 uptake by wood growth and CO2 emissions by forest operations. For
achieving this, a virtual forest estate area is split into the areas covered
by typical phases of the silvicultural concept of interest. Given initial
area shares of these phases, the dynamics of these areas is simulated. The
typical carbon stocks and flows which are known for all phases are
attributed post-hoc to the areas and upscaled to the estate level. CO2
emissions by forest operations are estimated based on the amounts and
dimensions of the harvested timber. Probabilities of damage events are taken
into account.
Author: Peter Biber [aut, cre, cph] ,
Stefano Grigolato [ctb] ,
Julia Schmucker [ctb] ,
Enno Uhl [ctb] ,
Hans Pretzsch [ctb]
Maintainer: Peter Biber <p.biber@tum.de>
Diff between care4cmodel versions 1.0.2 dated 2024-06-04 and 1.0.3 dated 2024-11-22
DESCRIPTION | 10 MD5 | 20 - NEWS.md | 18 R/co2_evaluation.R | 6 R/plot_c4c_co2_result.R | 14 R/setup_simulation.R | 4 README.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started-with-care4cmodel.html | 498 ++++++++++++------------- man/setup_statevars.Rd | 4 11 files changed, 292 insertions(+), 285 deletions(-)
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 24.10.3 dated 2024-10-03 and 24.11.2 dated 2024-11-22
REDCapCAST-24.10.3/REDCapCAST/R/create_instrument_meta.R |only REDCapCAST-24.10.3/REDCapCAST/inst/doc/Introduction.R |only REDCapCAST-24.10.3/REDCapCAST/inst/doc/Introduction.Rmd |only REDCapCAST-24.10.3/REDCapCAST/inst/doc/Introduction.html |only REDCapCAST-24.10.3/REDCapCAST/man/server_factory.Rd |only REDCapCAST-24.10.3/REDCapCAST/man/ui_factory.Rd |only REDCapCAST-24.10.3/REDCapCAST/vignettes/Introduction.Rmd |only REDCapCAST-24.11.2/REDCapCAST/DESCRIPTION | 32 REDCapCAST-24.11.2/REDCapCAST/MD5 | 79 REDCapCAST-24.11.2/REDCapCAST/NAMESPACE | 27 REDCapCAST-24.11.2/REDCapCAST/NEWS.md | 34 REDCapCAST-24.11.2/REDCapCAST/R/as_factor.R |only REDCapCAST-24.11.2/REDCapCAST/R/ds2dd_detailed.R | 439 +++-- REDCapCAST-24.11.2/REDCapCAST/R/export_redcap_instrument.R |only REDCapCAST-24.11.2/REDCapCAST/R/redcapcast_data.R | 3 REDCapCAST-24.11.2/REDCapCAST/R/shiny_cast.R | 268 ++- REDCapCAST-24.11.2/REDCapCAST/README.md | 51 REDCapCAST-24.11.2/REDCapCAST/build/vignette.rds |binary REDCapCAST-24.11.2/REDCapCAST/data/redcapcast_data.csv |only REDCapCAST-24.11.2/REDCapCAST/data/redcapcast_data.rda |binary REDCapCAST-24.11.2/REDCapCAST/data/redcapcast_meta.rda |binary REDCapCAST-24.11.2/REDCapCAST/inst/WORDLIST | 26 REDCapCAST-24.11.2/REDCapCAST/inst/doc/Database-creation.R | 54 REDCapCAST-24.11.2/REDCapCAST/inst/doc/Database-creation.Rmd | 2 REDCapCAST-24.11.2/REDCapCAST/inst/doc/Database-creation.html | 859 ---------- REDCapCAST-24.11.2/REDCapCAST/inst/doc/REDCapCAST.R |only REDCapCAST-24.11.2/REDCapCAST/inst/doc/REDCapCAST.Rmd |only REDCapCAST-24.11.2/REDCapCAST/inst/doc/REDCapCAST.html |only REDCapCAST-24.11.2/REDCapCAST/inst/shiny-examples |only REDCapCAST-24.11.2/REDCapCAST/man/REDCapCAST-package.Rd | 4 REDCapCAST-24.11.2/REDCapCAST/man/all_na.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/as_factor.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/cast_data_overview.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/cast_meta_overview.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/compact_vec.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/create_instrument_meta.Rd | 25 REDCapCAST-24.11.2/REDCapCAST/man/ds2dd_detailed.Rd | 35 REDCapCAST-24.11.2/REDCapCAST/man/export_redcap_instrument.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/fct2num.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/file_extension.Rd | 6 REDCapCAST-24.11.2/REDCapCAST/man/get_attr.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/guess_time_only.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/haven_all_levels.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/named_levels.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/nav_bar_page.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/numchar2fct.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/parse_data.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/possibly_roman.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/redcapcast_data.Rd | 3 REDCapCAST-24.11.2/REDCapCAST/man/set_attr.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/shiny_cast.Rd | 7 REDCapCAST-24.11.2/REDCapCAST/man/var2fct.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/vec2choice.Rd |only REDCapCAST-24.11.2/REDCapCAST/tests/testthat/test-ds2dd.R |only REDCapCAST-24.11.2/REDCapCAST/vignettes/Database-creation.Rmd | 2 REDCapCAST-24.11.2/REDCapCAST/vignettes/REDCapCAST.Rmd |only 56 files changed, 864 insertions(+), 1092 deletions(-)
Title: Neutrosophic Statistics
Description: Analyzes data involving imprecise and vague information. Provides summary statistics and describes the characteristics of neutrosophic data, as defined by Florentin Smarandache (2013).<ISBN:9781599732749>.
Author: Zahid Khan [aut],
Zsolt T. Kosztyan [aut, cre]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between neutrostat versions 0.0.1 dated 2024-10-11 and 0.0.2 dated 2024-11-22
DESCRIPTION | 7 ++++--- MD5 | 18 ++++++++++++++++-- NAMESPACE | 40 ++++++++++++++++++++++++++++++++++++++++ R/nexp.R |only R/ngam.R |only R/nlap.R |only R/nnorm.R |only R/nray.R |only R/nwbl.R |only inst |only man/nexp.Rd |only man/ngam.Rd |only man/nlap.Rd |only man/nnorm.Rd |only man/nray.Rd |only man/nwbl.Rd |only 16 files changed, 60 insertions(+), 5 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.0.9 dated 2024-09-25 and 1.0.10 dated 2024-11-22
DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/DESCRIPTION | 9 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/MD5 | 205 ++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/NAMESPACE | 1 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/NEWS.md | 5 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDaysSupply.R | 117 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugDose.R | 104 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugExposureDuration.R | 33 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugQuantity.R | 28 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugRoutes.R | 47 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugSig.R | 40 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugSourceConcepts.R | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugType.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugsMissing.R | 72 + DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkVerbatimEndDate.R | 38 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/executeChecks.R | 181 ++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/getDrugRecords.R | 18 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/getDrugStrength.R | 21 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/ingredientDescendantsInDb.R | 103 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/mockDrugExposure.R | 423 +++++----- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/obscureCounts.R | 13 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/runBenchmark.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/shiny.R | 1 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/summariseChecks.R | 128 +-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/utils.R | 59 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/README.md | 166 ++- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/build/vignette.rds |binary DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DaysSupply.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DaysSupply.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DaysSupply.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.html | 122 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDose.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDose.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDose.html | 122 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDuration.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDuration.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDuration.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSig.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSig.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSig.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.html | 122 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugTypes.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugTypes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugTypes.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.Rmd | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.html | 180 ++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Missingness.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Missingness.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Missingness.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Quantity.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Quantity.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Quantity.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Routes.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Routes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Routes.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data/eunomia.zip |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/dataPlotPanel.R | 235 +++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/global.R | 17 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/metaDataPanel.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/mock.zip |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/plots.R | 93 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/server.R | 165 ++- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/tests/testthat/test-shinytest2.R | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/ui.R | 21 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/utils.R | 57 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/executeChecks.Rd | 3 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/executeChecksSingleIngredient.Rd | 2 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/runBenchmarkExecuteSingleIngredient.Rd |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/writeResultToDisk.Rd | 3 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-CheckDrugSig.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-CheckVerbatimEndDate.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-GetDrugRecords.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-MockDrugExposure.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-ObscureCounts.R | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-SummariseChecks.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-SyntheaSqlServer.R | 17 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDaysSupply.R | 58 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugDose.R | 84 + DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugExposureDuration.R | 49 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugMissings.R | 56 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugQuantity.R | 27 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugRoutes.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugSourceConcepts.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugTypes.R | 52 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-executeChecks.R | 266 ++++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-runBenchmark.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-utils.R | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DaysSupply.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DiagnosticsSummary.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugDose.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugDuration.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugSig.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugSourceConcepts.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugTypes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/IntroductionToDrugExposureDiagnostics.Rmd | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/Missingness.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/Quantity.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/Routes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/VerbatimEndDate.Rmd | 8 DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data/mock.zip |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-checkDrugSig.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-checkVerbatimEndDate.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-getDrugRecords.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-mockDrugExposure.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-summariseChecks.R |only 112 files changed, 3242 insertions(+), 2025 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Document a Universe of Packages
Description: Creates a data frame containing the metadata associated with
the documentation of a collection of R packages. It allows for linking
topic names to their corresponding documentation online. If you
maintain a universe meta-package, it helps create a comprehensive
reference for its website.
Author: Mauro Lepore [aut, cre, cph]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between dverse versions 0.0.1 dated 2024-11-05 and 0.1.0 dated 2024-11-22
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS.md | 26 ++++++- R/document_universe.R | 103 ++++++++++------------------ R/s3_strip_class.R | 3 R/search_documentation.R | 13 +-- README.md | 104 +++++++++++++++++++++-------- inst/WORDLIST | 11 +-- man/document_universe.Rd | 6 + tests/testthat/test-document_universe.R | 38 ++++++++-- tests/testthat/test-search_documentation.R | 12 --- 11 files changed, 201 insertions(+), 143 deletions(-)
Title: Bootstrapping in Different One-Way and Two-Way ANOVA
Description: To address the violation of the assumption of normally distributed variables, researchers frequently employ bootstrapping. Building upon established packages for R (Sigmann et al. (2024) <doi:10.32614/CRAN.package.afex>, Lenth (2024) <doi:10.32614/CRAN.package.emmeans>), we provide bootstrapping functions to approximate a normal distribution of the parameter estimates for between-subject, within-subject, and mixed one-way and two-way ANOVA.
Author: Lisa-Marie Segbert [aut],
Christian Bloetner [aut, cre]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between AOboot versions 0.1.0 dated 2024-09-03 and 0.1.1 dated 2024-11-22
DESCRIPTION | 8 MD5 | 8 R/AObootMixed.R | 1338 ++++++++++++++++++++++++++-------------------------- man/AObootMixed.Rd | 4 man/AObootWithin.Rd | 4 5 files changed, 685 insertions(+), 677 deletions(-)
Title: Matching Adjusted Indirect Comparison
Description: Facilitates performing matching adjusted indirect comparison
(MAIC) analysis where the endpoint of interest is either time-to-event
(e.g. overall survival) or binary (e.g. objective tumor response). The method
is described by Signorovitch et al (2012) <doi:10.1016/j.jval.2012.05.004>.
Author: Gregory Chen [aut],
Michael Seo [aut],
Isaac Gravestock [aut, cre],
Miranta Antoniou [ctb],
Chrysostomos Kalyvas [ctb],
MSD, Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between maicplus versions 0.1.0 dated 2024-11-10 and 0.1.1 dated 2024-11-22
maicplus-0.1.0/maicplus/tests/testthat/Rplots.pdf |only maicplus-0.1.1/maicplus/DESCRIPTION | 10 +- maicplus-0.1.1/maicplus/MD5 | 37 ++++------ maicplus-0.1.1/maicplus/NEWS.md | 4 + maicplus-0.1.1/maicplus/R/maic_anchored.R | 24 +++--- maicplus-0.1.1/maicplus/R/maic_unanchored.R | 4 - maicplus-0.1.1/maicplus/inst/doc/anchored_binary.R | 2 maicplus-0.1.1/maicplus/inst/doc/anchored_binary.Rmd | 2 maicplus-0.1.1/maicplus/inst/doc/anchored_binary.html | 12 +-- maicplus-0.1.1/maicplus/inst/doc/anchored_survival.html | 4 - maicplus-0.1.1/maicplus/inst/doc/calculating_weights.html | 6 - maicplus-0.1.1/maicplus/inst/doc/introduction.html | 4 - maicplus-0.1.1/maicplus/inst/doc/kaplan_meier_plots.html | 16 ++-- maicplus-0.1.1/maicplus/inst/doc/unanchored_binary.R | 10 +- maicplus-0.1.1/maicplus/inst/doc/unanchored_binary.Rmd | 10 +- maicplus-0.1.1/maicplus/inst/doc/unanchored_binary.html | 4 - maicplus-0.1.1/maicplus/inst/doc/unanchored_survival.html | 4 - maicplus-0.1.1/maicplus/tests/testthat/_snaps/maic_anchored.md | 16 ++-- maicplus-0.1.1/maicplus/vignettes/anchored_binary.Rmd | 2 maicplus-0.1.1/maicplus/vignettes/unanchored_binary.Rmd | 10 +- 20 files changed, 95 insertions(+), 86 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.16 dated 2024-08-19 and 1.0.17 dated 2024-11-22
DESCRIPTION | 8 ++-- MD5 | 52 ++++++++++++++--------------- NEWS.md | 5 ++ R/data.R | 4 ++ build/vignette.rds |binary data/municipality_key.rda |binary data/municipality_key_2013.rda |binary data/municipality_key_2014.rda |binary data/municipality_key_2015.rda |binary data/municipality_key_2016.rda |binary data/municipality_key_2017.rda |binary data/municipality_key_2018.rda |binary data/municipality_key_2019.rda |binary data/municipality_key_2020.rda |binary data/municipality_key_2021.rda |binary data/municipality_key_2022.rda |binary data/municipality_key_2023.rda |binary data/municipality_key_2024.rda |binary inst/doc/geofi_datasets.R | 10 ++--- inst/doc/geofi_datasets.html | 30 ++++++++-------- inst/doc/geofi_joining_attribute_data.R | 10 ++--- inst/doc/geofi_joining_attribute_data.html | 4 +- inst/doc/geofi_making_maps.R | 10 ++--- inst/doc/geofi_making_maps.html | 32 ++++++++--------- inst/doc/geofi_spatial_analysis.R | 10 ++--- inst/doc/geofi_spatial_analysis.html | 18 +++++----- man/municipality_key_2024.Rd | 4 ++ 27 files changed, 105 insertions(+), 92 deletions(-)
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 3.4.2 dated 2024-09-20 and 3.4.3 dated 2024-11-22
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/bsroc.R | 1 + R/plot.metadiag.R | 4 +++- R/plotcompare.R | 3 ++- R/plotcredibility.R | 3 ++- 7 files changed, 32 insertions(+), 13 deletions(-)
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis (<https://www.reconverse.org>).
Author: Tim Taylor [aut, cre] ,
Thibaut Jombart [ctb]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 2.5.0 dated 2024-10-06 and 2.6.0 dated 2024-11-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 29 +++++++++++++++++++++++++++++ R/incidence.R | 24 +++++++++++++++--------- R/plot.R | 6 +++++- R/utils.R | 2 ++ build/vignette.rds |binary inst/doc/incidence2.html | 34 +++++++++++++++++----------------- 8 files changed, 79 insertions(+), 38 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
Diff between vDiveR versions 2.0.0 dated 2024-09-12 and 2.0.1 dated 2024-11-22
vDiveR-2.0.0/vDiveR/R/plot_conservationLevel.R |only vDiveR-2.0.0/vDiveR/R/plot_worldmap.R |only vDiveR-2.0.0/vDiveR/man/plot_conservationLevel.Rd |only vDiveR-2.0.0/vDiveR/man/plot_worldmap.Rd |only vDiveR-2.0.1/vDiveR/DESCRIPTION | 14 vDiveR-2.0.1/vDiveR/MD5 | 50 vDiveR-2.0.1/vDiveR/NAMESPACE | 11 vDiveR-2.0.1/vDiveR/NEWS.md | 5 vDiveR-2.0.1/vDiveR/R/json2csv.R | 3 vDiveR-2.0.1/vDiveR/R/metadata_extraction.R | 2 vDiveR-2.0.1/vDiveR/R/plot_conservation_level.R |only vDiveR-2.0.1/vDiveR/R/plot_correlation.R | 2 vDiveR-2.0.1/vDiveR/R/plot_dynamics_protein.R | 68 vDiveR-2.0.1/vDiveR/R/plot_dynamics_proteome.R | 116 vDiveR-2.0.1/vDiveR/R/plot_entropy.R | 31 vDiveR-2.0.1/vDiveR/R/plot_time.R | 2 vDiveR-2.0.1/vDiveR/R/plot_world_map.R |only vDiveR-2.0.1/vDiveR/R/sample_data.R | 2 vDiveR-2.0.1/vDiveR/data/metadata.rda |binary vDiveR-2.0.1/vDiveR/data/protein_2hosts.rda |binary vDiveR-2.0.1/vDiveR/inst/extdata/city_mapper.csv |87098 ++++++++++----------- vDiveR-2.0.1/vDiveR/man/metadata.Rd | 2 vDiveR-2.0.1/vDiveR/man/metadata_extraction.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_conservation_level.Rd |only vDiveR-2.0.1/vDiveR/man/plot_dynamics_protein.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_dynamics_proteome.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_entropy.Rd | 4 vDiveR-2.0.1/vDiveR/man/plot_time.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_world_map.Rd |only vDiveR-2.0.1/vDiveR/tests/testthat/test-json2csv.R | 4 30 files changed, 42621 insertions(+), 44801 deletions(-)
Title: Robust Score Testing in GLMs, by Sign-Flip Contributions
Description: Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.
Author: Livio Finos [cre, aut] ,
Jelle J. Goeman [ctb],
Jesse Hemerik [ctb],
Riccardo De Santis [ctb]
Maintainer: Livio Finos <livio.finos@unipd.it>
Diff between flipscores versions 1.2.0 dated 2022-08-15 and 1.3.1 dated 2024-11-22
DESCRIPTION | 22 +++- MD5 | 31 ++++-- NAMESPACE | 37 ++++---- R/anova_flipscores.R | 7 - R/compute_flips.R |only R/compute_scores.R | 201 +++++++++++++++++++++++++++++---------------- R/flipscores-package.R |only R/flipscores.R | 107 +++++++++++++++++------ R/flipscores_package.R | 6 - R/make_flips.R |only R/utility_functions.R | 23 +++-- R/utiliy_score_functions.R | 119 +++++++++++++------------- build |only man/anova.flipscores.Rd | 84 +++++++++--------- man/compute_scores.Rd | 4 man/flipscores-method.Rd | 50 +++++------ man/flipscores-package.Rd | 20 +++- man/flipscores.Rd | 40 +++++--- man/make_flips.Rd |only 19 files changed, 459 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-15 1.6.6
2022-04-10 1.6.5
2022-03-29 1.6.4
2021-10-07 1.6.3
2021-03-22 1.6.2
2020-10-01 1.6.0
2019-10-22 1.5.2
2019-08-06 1.5.1
2019-06-05 1.5.0
2018-09-19 1.4.9
2018-05-07 1.4.8
2017-07-08 1.4.6
2017-06-09 1.4.5
2017-03-12 1.4.3
2017-02-11 1.4.1
2016-12-19 1.3.9
2016-11-30 1.3.8
2016-04-20 1.0.7-1
2016-01-06 1.0.7
2015-07-21 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-22 2.4.6
2022-04-28 2.4.5
2021-03-20 2.4.4
2020-12-10 2.4.3
2020-10-01 2.4.2
2020-07-27 2.4.1
2020-07-09 2.4.0
2019-11-15 2.3.0
2019-01-31 2.2.0
2018-12-05 2.1.3
2018-10-17 2.1.2
2018-08-17 2.1.1
2018-03-14 2.1.0
2017-05-23 2.0.8
2017-02-11 2.0.4
2016-12-01 2.0.2
2015-09-16 1.0.1
2015-08-02 1.0.0
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.11.4 dated 2023-12-10 and 0.11.5 dated 2024-11-22
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- inst/doc/networkDynamic.R | 2 +- inst/doc/networkDynamic.Rnw | 2 +- inst/doc/networkDynamic.pdf |binary man/Newcomb.Rd | 4 ++-- man/add.active.Rd | 12 ++++++------ man/age.at.Rd | 2 +- man/as.networkDynamic.Rd | 4 ++-- man/is.active.Rd | 4 ++-- man/network.extensions.Rd | 2 +- man/persistent_ids.Rd | 2 +- man/print.networkDynamic.Rd | 2 +- man/tea_functions.Rd | 2 +- vignettes/networkDynamic.Rnw | 2 +- 16 files changed, 41 insertions(+), 39 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-29 0.1.0
2020-01-15 0.0.2
2018-08-16 0.0.1