Title: Parse, Read, and Edit 'TOML'
Description: A toolkit for working with 'TOML' files in R while preserving
formatting, comments, and structure. 'tomledit' enables serialization of R
objects such as lists, data.frames, numeric, logical, and date vectors.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between tomledit versions 0.1.0 dated 2025-02-13 and 0.1.1 dated 2025-04-09
DESCRIPTION | 12 +++++--- MD5 | 37 ++++++++++++++------------ NEWS.md |only R/modify.R | 2 - R/toml.R | 4 +- README.md |only configure | 15 ---------- configure.win | 15 ---------- man/tomledit-package.Rd | 4 ++ src/Makevars.in | 14 +++++----- src/Makevars.win.in | 25 ++++++----------- src/rust/Cargo.lock | 67 +++++++++++++++++++++++++++--------------------- src/rust/Cargo.toml | 3 +- src/rust/src/array.rs | 13 +++++++++ src/rust/src/item.rs | 9 +++++- src/rust/src/lib.rs | 7 ++--- src/rust/src/table.rs | 37 ++++++++++++-------------- src/rust/src/values.rs | 5 ++- src/rust/vendor.tar.xz |binary tools/config.R |only tools/msrv.R | 4 +- 21 files changed, 138 insertions(+), 135 deletions(-)
Title: The FPCdpca Criterion on Distributed Principal Component
Analysis
Description: We consider optimal subset selection in the setting that one needs to use only one data subset to represent the whole data set with minimum information loss, and devise a novel intersection-based criterion on selecting optimal subset, called as the FPC criterion, to handle with the optimal sub-estimator in distributed principal component analysis; That is, the FPCdpca. The philosophy of the package is described in Guo G. (2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Jiarui Li [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between FPCdpca versions 0.1.0 dated 2024-05-27 and 0.2.0 dated 2025-04-09
DESCRIPTION | 23 +++++++---- MD5 | 38 +++++++++++-------- NAMESPACE | 26 ++++++------- R/Depca.R | 90 +++++++++++++++++++++++---------------------- R/Dpca.R | 40 ++++++++++++++------ R/Drp.R | 6 ++- R/Drpca.R | 6 ++- R/Drsvd.R | 98 ++++++++++++++++++++++++++++---------------------- R/Dsvd.R | 6 ++- R/FPC.R | 4 +- data |only man/Depca.Rd | 78 +++++++++++++++++++++------------------ man/Dpca.Rd | 65 +++++++++++++++++++++------------ man/Drp.Rd | 55 +++++++++++++++------------- man/Drpca.Rd | 53 ++++++++++++++------------- man/Drsvd.Rd | 78 ++++++++++++++++++++------------------- man/Dsvd.Rd | 59 ++++++++++++++---------------- man/FPC.Rd | 49 +++++++++++++------------ man/review.Rd |only man/riboflavin.Rd |only man/riboflavinv100.Rd |only 21 files changed, 434 insertions(+), 340 deletions(-)
Title: Regularized Joint Assignment Forest with Treatment Arm
Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] ,
Xinyi Zhang [aut, cre, cph] ,
Jann Spiess [aut, cph] ,
Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>
Diff between rjaf versions 0.1.2 dated 2025-02-16 and 0.1.3 dated 2025-04-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++-- R/rjaf.R | 41 ++++++++++++++++++++++++----------------- man/rjaf.Rd | 16 +++++++++------- src/RcppExports.cpp | 10 ++++------ src/rjaf.cpp | 14 ++------------ tests/testthat/test-rjaf.R | 4 ++-- 8 files changed, 53 insertions(+), 56 deletions(-)
Title: Lookup Geolocation and Proxy Information using 'IP2Location.io'
API
Description: Query for enriched data such as country, region, city, latitude & longitude, ZIP code, time zone, Autonomous System, Internet Service Provider, domain, net speed, International direct dialing (IDD) code, area code, weather station data, mobile data, elevation, usage type, address type, advertisement category, fraud score, and proxy data with an IP address. You can also query a list of hosted domain names for the IP address too.
This package uses the 'IP2Location.io' API to query this data. To get started with a free API key, sign up here <https://www.ip2location.io/sign-up?ref=1>.
Author: IP2Location.io [aut, cre]
Maintainer: IP2Location.io <support@ip2location.io>
Diff between ip2locationio versions 1.0.0 dated 2024-10-31 and 1.1.0 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NAMESPACE | 1 + R/IP2Locationio.R | 29 +++++++++++++++++++++++++++++ man/lookupHostedDomain.Rd |only 5 files changed, 38 insertions(+), 7 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.80 dated 2025-01-30 and 2.0.81 dated 2025-04-09
DESCRIPTION | 8 - MD5 | 14 +-- NEWS | 9 +- inst/doc/epiR_descriptive.html | 16 +-- inst/doc/epiR_measures_of_association.html | 12 +- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 14 +-- man/epi.edr.Rd | 127 +++++++++++++++-------------- 8 files changed, 110 insertions(+), 94 deletions(-)
Title: Visualizing of Distributions of Covariance Matrices
Description: Visualizing of distributions of covariance matrices.
The package implements the methodology described in Tokuda, T., Goodrich, B., Van Mechelen, I., Gelman, A., & Tuerlinckx, F. (2012) <https://sites.stat.columbia.edu/gelman/research/unpublished/Visualization.pdf>.
Author: Tomoki Tokuda [aut],
Ben Goodrich [ctb],
Iven Van Mechelen [ctb],
Andrew Gelman [ctb],
Francis Tuerlinckx [ctb],
Kristof Meers [cre]
Maintainer: Kristof Meers <kristof.meers+cran@kuleuven.be>
Diff between VisCov versions 1.5.0 dated 2024-12-04 and 1.6.0 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md |only R/VisCov.R | 16 +++++++++++++++- man/VisCov.Rd | 2 +- 5 files changed, 24 insertions(+), 9 deletions(-)
Title: Phylogenetic Analysis with Discrete Character Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Author: Martin R. Smith [aut, cre, cph]
,
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 1.5.1 dated 2024-05-23 and 1.6.0 dated 2025-04-09
TreeSearch-1.5.1/TreeSearch/R/mpl_visualise.R |only TreeSearch-1.6.0/TreeSearch/DESCRIPTION | 10 TreeSearch-1.6.0/TreeSearch/MD5 | 174 TreeSearch-1.6.0/TreeSearch/NAMESPACE | 437 TreeSearch-1.6.0/TreeSearch/NEWS.md | 634 TreeSearch-1.6.0/TreeSearch/R/AdditionTree.R | 264 TreeSearch-1.6.0/TreeSearch/R/Bootstrap.R | 10 TreeSearch-1.6.0/TreeSearch/R/Concordance.R | 104 TreeSearch-1.6.0/TreeSearch/R/Consistency.R | 172 TreeSearch-1.6.0/TreeSearch/R/CustomSearch.R | 45 TreeSearch-1.6.0/TreeSearch/R/IWScore.R | 29 TreeSearch-1.6.0/TreeSearch/R/Jackknife.R | 9 TreeSearch-1.6.0/TreeSearch/R/MaximizeParsimony.R | 1937 +- TreeSearch-1.6.0/TreeSearch/R/NNI.R | 22 TreeSearch-1.6.0/TreeSearch/R/PlotCharacter.R | 953 - TreeSearch-1.6.0/TreeSearch/R/PolEscapa.R | 250 TreeSearch-1.6.0/TreeSearch/R/RandomTreeScore.R | 2 TreeSearch-1.6.0/TreeSearch/R/Ratchet.R | 19 TreeSearch-1.6.0/TreeSearch/R/SPR.R | 53 TreeSearch-1.6.0/TreeSearch/R/Sectorial.R | 7 TreeSearch-1.6.0/TreeSearch/R/SuccessiveApproximations.R | 5 TreeSearch-1.6.0/TreeSearch/R/TBR.R | 20 TreeSearch-1.6.0/TreeSearch/R/TaxonInfluence.R | 388 TreeSearch-1.6.0/TreeSearch/R/data.R | 417 TreeSearch-1.6.0/TreeSearch/R/data_manipulation.R | 448 TreeSearch-1.6.0/TreeSearch/R/length_range.R | 592 TreeSearch-1.6.0/TreeSearch/R/mpl_morphy_objects.R | 13 TreeSearch-1.6.0/TreeSearch/R/tree_length.R | 28 TreeSearch-1.6.0/TreeSearch/R/tree_rearrangement.R | 12 TreeSearch-1.6.0/TreeSearch/build/partial.rdb |binary TreeSearch-1.6.0/TreeSearch/build/vignette.rds |binary TreeSearch-1.6.0/TreeSearch/inst/Parsimony/app.R | 7305 +++++----- TreeSearch-1.6.0/TreeSearch/inst/Parsimony/log.lg |only TreeSearch-1.6.0/TreeSearch/inst/Parsimony/www/app.css | 256 TreeSearch-1.6.0/TreeSearch/inst/REFERENCES.bib | 1204 - TreeSearch-1.6.0/TreeSearch/inst/WORDLIST | 498 TreeSearch-1.6.0/TreeSearch/inst/apa-old-doi-prefix.csl | 2306 ++- TreeSearch-1.6.0/TreeSearch/inst/doc/custom.html | 30 TreeSearch-1.6.0/TreeSearch/inst/doc/getting-started.Rmd | 136 TreeSearch-1.6.0/TreeSearch/inst/doc/getting-started.html | 11 TreeSearch-1.6.0/TreeSearch/inst/doc/profile-scores.html | 24 TreeSearch-1.6.0/TreeSearch/inst/doc/profile.R | 4 TreeSearch-1.6.0/TreeSearch/inst/doc/profile.Rmd | 294 TreeSearch-1.6.0/TreeSearch/inst/doc/profile.html | 68 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-search.R | 4 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-search.Rmd | 722 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-search.html | 230 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-space.R | 10 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-space.html | 32 TreeSearch-1.6.0/TreeSearch/man/AdditionTree.Rd | 125 TreeSearch-1.6.0/TreeSearch/man/AllSPR.Rd | 76 TreeSearch-1.6.0/TreeSearch/man/CharacterLength.Rd | 125 TreeSearch-1.6.0/TreeSearch/man/ConcordantInformation.Rd | 115 TreeSearch-1.6.0/TreeSearch/man/Consistency.Rd | 151 TreeSearch-1.6.0/TreeSearch/man/DoubleNNI.Rd | 65 TreeSearch-1.6.0/TreeSearch/man/JackLabels.Rd | 140 TreeSearch-1.6.0/TreeSearch/man/Jackknife.Rd | 192 TreeSearch-1.6.0/TreeSearch/man/LengthAdded.Rd | 161 TreeSearch-1.6.0/TreeSearch/man/MaximizeParsimony.Rd | 624 TreeSearch-1.6.0/TreeSearch/man/MorphyTreeLength.Rd | 172 TreeSearch-1.6.0/TreeSearch/man/NNI.Rd | 239 TreeSearch-1.6.0/TreeSearch/man/PlotCharacter.Rd | 238 TreeSearch-1.6.0/TreeSearch/man/Ratchet.Rd | 444 TreeSearch-1.6.0/TreeSearch/man/RearrangeEdges.Rd | 161 TreeSearch-1.6.0/TreeSearch/man/SPR.Rd | 232 TreeSearch-1.6.0/TreeSearch/man/SiteConcordance.Rd | 189 TreeSearch-1.6.0/TreeSearch/man/StopUnlessBifurcating.Rd | 47 TreeSearch-1.6.0/TreeSearch/man/SuccessiveApproximations.Rd | 143 TreeSearch-1.6.0/TreeSearch/man/TBR.Rd | 224 TreeSearch-1.6.0/TreeSearch/man/TBRWarning.Rd | 84 TreeSearch-1.6.0/TreeSearch/man/TaxonInfluence.Rd | 293 TreeSearch-1.6.0/TreeSearch/man/TreeLength.Rd | 186 TreeSearch-1.6.0/TreeSearch/man/TreeSearch.Rd | 301 TreeSearch-1.6.0/TreeSearch/man/cSPR.Rd | 64 TreeSearch-1.6.0/TreeSearch/man/dot-NonDuplicateRoot.Rd | 94 TreeSearch-1.6.0/TreeSearch/man/inapplicable.datasets.Rd | 325 TreeSearch-1.6.0/TreeSearch/tests/testthat/_snaps/PlotCharacter/plotchar-consensus.svg |only TreeSearch-1.6.0/TreeSearch/tests/testthat/_snaps/PlotCharacter/plotchar-invar-ambig.svg |only TreeSearch-1.6.0/TreeSearch/tests/testthat/_snaps/PlotCharacter/plotchar-invariant.svg |only TreeSearch-1.6.0/TreeSearch/tests/testthat/test-AdditionTree.R | 192 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-Concordance.R | 291 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-Consistency.R | 116 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-CustomSearch.R | 272 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-Jackknife.R | 92 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-PlotCharacter.R | 307 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-SPR.R |only TreeSearch-1.6.0/TreeSearch/tests/testthat/test-pp-random-tree.R | 279 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-zzz-tree-rearrange.R | 540 TreeSearch-1.6.0/TreeSearch/vignettes/getting-started.Rmd | 136 TreeSearch-1.6.0/TreeSearch/vignettes/profile.Rmd | 294 TreeSearch-1.6.0/TreeSearch/vignettes/tree-search.Rmd | 722 91 files changed, 15137 insertions(+), 13502 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.2.0 dated 2025-03-07 and 2.3.0 dated 2025-04-09
DESCRIPTION | 8 MD5 | 34 +-- NAMESPACE | 3 NEWS | 11 + R/EGM.R | 486 ++++++++++----------------------------------- R/EGM.compare.R | 74 +++++- R/EGM.optimizations.R |only R/UVA.R | 495 +++++++++++++++++++++++----------------------- R/bootEGA.R | 4 R/community.detection.R | 3 R/helpers.R | 31 ++ R/itemDiagnostics.R |only R/itemStability.R | 236 +++++++++++----------- R/oldsimEGM.R |only R/simEGM.R | 514 ++++++++++-------------------------------------- man/EGM.Rd | 26 -- man/EGM.compare.Rd | 28 ++ man/UVA.Rd | 18 - man/itemDiagnostics.Rd |only man/simEGM.Rd | 26 -- 20 files changed, 755 insertions(+), 1242 deletions(-)
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are:
flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>),
fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>),
rubber band based cartogram (Dougenik et al. (1985)
<doi:10.1111/j.0033-0124.1985.00075.x>).
Author: Pierre-Andre Cornillon [aut, cre],
Florent Demoraes [aut],
Flow-Based-Cartograms [cph]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between cartogramR versions 1.2-0 dated 2024-09-03 and 1.5-0 dated 2025-04-09
cartogramR-1.2-0/cartogramR/src/Makevars |only cartogramR-1.5-0/cartogramR/DESCRIPTION | 35 cartogramR-1.5-0/cartogramR/MD5 | 38 cartogramR-1.5-0/cartogramR/R/cartogramR.R | 130 +- cartogramR-1.5-0/cartogramR/R/cartogramR_options.R | 64 - cartogramR-1.5-0/cartogramR/cleanup |only cartogramR-1.5-0/cartogramR/configure |only cartogramR-1.5-0/cartogramR/inst/cc |only cartogramR-1.5-0/cartogramR/man/cartogramR_options.Rd | 27 cartogramR-1.5-0/cartogramR/src/Makevars.in |only cartogramR-1.5-0/cartogramR/src/Makevars.win | 24 cartogramR-1.5-0/cartogramR/src/cartogram.c | 88 - cartogramR-1.5-0/cartogramR/src/cartogram.h | 2 cartogramR-1.5-0/cartogramR/src/cartogramR.c | 316 ++++- cartogramR-1.5-0/cartogramR/src/checkring.c | 4 cartogramR-1.5-0/cartogramR/src/dcn.c | 972 ++++++++++++------ cartogramR-1.5-0/cartogramR/src/dcn.h | 5 cartogramR-1.5-0/cartogramR/src/diff_integrate.c | 42 cartogramR-1.5-0/cartogramR/src/ffb_integrate.c | 108 +- cartogramR-1.5-0/cartogramR/src/fill_with_density.c | 25 cartogramR-1.5-0/cartogramR/src/init.c | 2 cartogramR-1.5-0/cartogramR/src/iocartogramR.c | 4 cartogramR-1.5-0/cartogramR/src/myomp.h |only 23 files changed, 1313 insertions(+), 573 deletions(-)
Title: Watch the File System for Changes
Description: R binding for 'libfswatch', a file system monitoring library. Watch
files, or directories recursively, for changes in the background. Log
activity, or run an R function every time a change event occurs.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between watcher versions 0.1.2 dated 2025-02-25 and 0.1.3 dated 2025-04-09
DESCRIPTION | 7 ++++--- MD5 | 23 ++++++++++++----------- NEWS.md | 6 ++++++ R/watch.R | 4 ++-- configure | 27 +++++++++++++-------------- configure.ucrt |only configure.win | 43 ++++++++++++++++++++++++++++++------------- man/watcher.Rd | 4 ++-- src/Makevars.ucrt | 2 +- src/Makevars.win | 4 ++-- src/fswatch-5c443d2.tar.gz |binary src/watcher.c | 7 +++++++ tests/testthat/test-watch.R | 16 +++++++++++++++- 13 files changed, 94 insertions(+), 49 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.6 dated 2025-03-02 and 1.0.7 dated 2025-04-09
DESCRIPTION | 6 +- MD5 | 20 +++---- R/OR.R | 1 R/constants.R | 21 +++++++ R/list_shuffle.R | 5 - README.md | 6 +- inst/doc/add_today_date_to_filenames_quickcode.html | 54 ++++++++++---------- inst/doc/nullish_coalescing_operator_r.html | 4 - inst/doc/quickcode_r_introduction.html | 4 - inst/doc/track_function_usage_r.html | 4 - man/const.Rd | 22 ++++++++ 11 files changed, 95 insertions(+), 52 deletions(-)
Title: Multivariate Time Series Data Imputation
Description: This is an EM algorithm based method for imputation of missing values in multivariate normal time series. The imputation algorithm accounts for both spatial and temporal correlation structures. Temporal patterns can be modeled using an ARIMA(p,d,q), optionally with seasonal components, a non-parametric cubic spline or generalized additive models with exogenous covariates. This algorithm is specially tailored for climate data with missing measurements from several monitors along a given region.
Author: Washington Junger [aut, cre],
Antonio Ponce de Leon [ctb]
Maintainer: Washington Junger <wjunger@ims.uerj.br>
Diff between mtsdi versions 0.3.5 dated 2018-01-23 and 0.3.7 dated 2025-04-09
DESCRIPTION | 17 ++++++++++------- MD5 | 14 +++++++------- man/internal.Rd | 1 + man/mkjnw.Rd | 4 ++-- man/mnimput.Rd | 16 ++++++++-------- man/plot.mtsdi.Rd | 4 ++-- man/print.mtsdi.Rd | 2 +- man/print.summary.mtsdi.Rd | 2 +- 8 files changed, 32 insertions(+), 28 deletions(-)
Title: Analysis of Archaeological Mortality Data
Description: A collection of functions for the analysis of archaeological mortality
data (on the topic see e.g. Chamberlain 2006
<https://books.google.de/books?id=nG5FoO_becAC&lpg=PA27&ots=LG0b_xrx6O&dq=life%20table%20archaeology&pg=PA27#v=onepage&q&f=false>).
It takes demographic data in different formats and displays the result in a standard life table
as well as plots the relevant indices (percentage of deaths, survivorship, probability of death,
life expectancy, percentage of population). It also checks for possible biases in the age
structure and applies corrections to life tables.
Author: Nils Mueller-Scheessel [aut, cre, cph]
,
Martin Hinz [aut],
Clemens Schmid [aut],
Christoph Rinne [aut],
Daniel Knitter [aut],
Wolfgang Hamer [aut],
Dirk Seidensticker [aut],
Franziska Faupel [aut],
Carolin Tietze [aut],
Nicole Grunert [aut]
Maintainer: Nils Mueller-Scheessel <nils.mueller-scheessel@ufg.uni-kiel.de>
Diff between mortAAR versions 1.1.7 dated 2025-01-12 and 1.1.8 dated 2025-04-09
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Title: Homomorphic Computations in R
Description: Homomorphic computations in R for privacy-preserving applications. Currently only
the Paillier Scheme is implemented.
Author: Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between homomorpheR versions 0.2-2 dated 2019-01-23 and 0.3 dated 2025-04-09
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Title: Quantitative Pest Risk Assessment at the Entry Step
Description: Supports risk assessors in performing the entry step of the
quantitative Pest Risk Assessment. It allows the estimation of the
amount of a plant pest entering a risk assessment area (in terms of
founder populations) through the calculation of the imported
commodities that could be potential pathways of pest entry, and the
development of a pathway model. Two 'Shiny' apps based on the
functionalities of the package are included, that simplify the process
of assessing the risk of entry of plant pests. The approach is based
on the work of the European Food Safety Authority (EFSA PLH Panel et
al., 2018) <doi:10.2903/j.efsa.2018.5350>.
Author: Martina Cendoya [aut, cre] ,
Maria Chiara Rosace [aut]
Maintainer: Martina Cendoya <cendoya_marmar@gva.es>
Diff between qPRAentry versions 0.1.0 dated 2024-12-17 and 0.1.1 dated 2025-04-09
DESCRIPTION | 16 +-- MD5 | 20 ++-- NEWS.md | 5 + R/mod_ntrade_redistribution.R | 7 + R/utils.R | 26 +++-- README.md | 33 ++++-- inst/doc/qPRAentry_workflow.R | 45 ++++++--- inst/doc/qPRAentry_workflow.Rmd | 36 ++++++- inst/doc/qPRAentry_workflow.html | 191 +++++++++++++++++++-------------------- man/qPRAentry-package.Rd | 8 + vignettes/qPRAentry_workflow.Rmd | 36 ++++++- 11 files changed, 272 insertions(+), 151 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] ,
Laura DeCicco [ctb],
Emily Riederer [rev],
Margaret Siple [rev],
Cagri Alican [rev]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.6.1 dated 2024-10-10 and 0.6.2 dated 2025-04-09
DESCRIPTION | 8 +- MD5 | 24 +++---- NEWS.md | 130 +++++++++++++++++++++++++----------------- R/fixreg.R | 20 +++--- R/regions.R | 20 +++++- build/vignette.rds |binary inst/doc/interactive.R | 6 + inst/doc/interactive.html | 31 +++++----- inst/doc/nigeria-maps.R | 4 + inst/doc/nigeria-maps.html | 29 ++++----- man/fix_region.Rd | 16 ++--- man/naijR.Rd | 8 ++ tests/testthat/test-regions.R | 11 ++- 13 files changed, 188 insertions(+), 119 deletions(-)
Title: Interpretable Machine Learning and Statistical Inference with
Accumulated Local Effects (ALE)
Description: Accumulated Local Effects (ALE) were initially developed as a model-agnostic approach for global explanations of the results of black-box machine learning algorithms. ALE has a key advantage over other approaches like partial dependency plots (PDP) and SHapley Additive exPlanations (SHAP): its values represent a clean functional decomposition of the model. As such, ALE values are not affected by the presence or absence of interactions among variables in a mode. Moreover, its computation is relatively rapid. This package reimplements the algorithms for calculating ALE data and develops highly interpretable visualizations for plotting these ALE values. It also extends the original ALE concept to add bootstrap-based confidence intervals and ALE-based statistics that can be used for statistical inference. For more details, see Okoli, Chitu. 2023. “Statistical Inference Using Machine Learning and Classical Techniques Based on Accumulated Local Effects (ALE).” arXiv. <doi:10.48550/arXiv.2 [...truncated...]
Author: Chitu Okoli [aut, cre]
Maintainer: Chitu Okoli <Chitu.Okoli@skema.edu>
Diff between ale versions 0.3.1 dated 2025-03-10 and 0.5.0 dated 2025-04-09
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Title: R Wrapper to Access a Wide Range of Germany's Federal
Statistical System Databases Based on the GENESIS Web Service
RESTful API of the German Federal Statistical Office
(Statistisches Bundesamt/Destatis)
Description: A RESTful API wrapper for accessing the GENESIS database of
the German Federal Statistical Office (Destatis) as well as its Census
Database and the database of Germany's regional statistics. Supports data
search functions, credential management, result caching, and handling
remote background jobs for large datasets.
Author: Yannik Buhl [aut, cre],
Zoran Kovacevic [aut] ,
Dorian Le Jeune [aut],
Long Nguyen [aut] ,
Johannes Ritter [aut]
Maintainer: Yannik Buhl <ybuhl@posteo.de>
Diff between restatis versions 0.2.0 dated 2024-07-25 and 0.3.0 dated 2025-04-09
restatis-0.2.0/restatis/R/gen_meta_data.R |only restatis-0.2.0/restatis/R/utils.R |only restatis-0.2.0/restatis/man/gen_metadata_stats.Rd |only restatis-0.2.0/restatis/man/gen_metadata_tab.Rd |only restatis-0.2.0/restatis/man/gen_metadata_val.Rd |only restatis-0.2.0/restatis/man/gen_metadata_var.Rd |only restatis-0.2.0/restatis/man/rev_database_function.Rd |only restatis-0.2.0/restatis/tests/testthat/catalogue1/api/catalogue/tables-30cbd2.json |only restatis-0.2.0/restatis/tests/testthat/catalogue2/api/catalogue/statistics-f5c1c1.json |only restatis-0.2.0/restatis/tests/testthat/catalogue3/api/catalogue/cubes-57cf25.json |only restatis-0.2.0/restatis/tests/testthat/catalogue4/api/catalogue/cubes-e28931.json |only restatis-0.2.0/restatis/tests/testthat/catalogue4/api/catalogue/statistics-c47d1c.json |only restatis-0.2.0/restatis/tests/testthat/catalogue4/api/catalogue/tables-e234ed.json |only restatis-0.2.0/restatis/tests/testthat/catalogue5/api/catalogue/tables-5b59e0.json |only 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Title: Exploratory Chemometrics for 2D Spectroscopy
Description: A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.
Author: Bryan A. Hanson [aut, cre]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec2D versions 0.5.0 dated 2021-10-11 and 0.5.1 dated 2025-04-09
DESCRIPTION | 10 +++--- MD5 | 64 +++++++++++++++++++++-------------------- NAMESPACE | 24 --------------- NEWS.md | 6 +++ R/AlignArraysMBO.R | 1 R/ChemoSpec2D-package.R | 8 +---- R/cleanArgs2D.R | 3 - R/createScale.R | 1 R/drawScale.R | 1 R/evalArrayOverlapMBO.R | 1 R/findExtreme.R | 1 R/findZeros.R | 1 R/getAlignOrder.R | 1 R/getPN.R | 1 R/hats_alignSpectra2D.R | 2 - R/makeArray.R | 24 --------------- R/makeArray2.R |only R/mapColors.R | 1 R/noiseSurface.R | 1 R/onAttach.R | 2 - R/plotEngine.R | 1 R/rescale.R | 1 R/shiftArray.R | 1 R/showHist.R | 1 R/symAroundZero.R | 1 R/unstack.R | 1 build/vignette.rds |binary data/MUD1.RData |binary data/MUD2.RData |binary inst/doc/ChemoSpec2D.pdf |binary inst/tinytest/test_makeArray.R | 5 +-- man/ChemoSpec2D-package.Rd | 8 +++++ man/hats_alignSpectra2D.Rd | 2 - vignettes/pinp.cls |only 34 files changed, 60 insertions(+), 114 deletions(-)
Title: Machine Learning Immunogenicity and Vaccine Response Analysis
Description: Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Author: Ivan Tomic [aut, cre, cph] ,
Adriana Tomic [aut, ctb, cph, fnd]
,
Stephanie Hao [aut]
Maintainer: Ivan Tomic <info@ivantomic.com>
Diff between immunaut versions 1.0.0 dated 2024-10-25 and 1.0.2 dated 2025-04-09
DESCRIPTION | 15 MD5 | 54 +- NAMESPACE | 20 NEWS.md |only R/functions.R | 761 +++++++++++++++++++++++++++--------- R/immunaut.R | 238 ++++++++--- R/immunautLAIV-data.R |only R/utils.R | 191 +++++---- R/zzz.R | 3 README.md | 134 +++--- data/immunautDemo.rda |binary data/immunautLAIV.rda |only man/auto_simon_ml.Rd | 36 + man/calculate_tsne.Rd | 16 man/castAllStringsToNA.Rd | 7 man/cluster_tsne_density.Rd | 12 man/cluster_tsne_hierarchical.Rd | 15 man/cluster_tsne_knn_louvain.Rd | 39 - man/cluster_tsne_mclust.Rd | 14 man/find_optimal_resolution.Rd | 42 - man/generate_demo_data.Rd | 2 man/immunaut.Rd | 98 ++-- man/immunautLAIV.Rd |only man/isNumeric.Rd | 1 man/is_var_empty.Rd | 1 man/pick_best_cluster_modularity.Rd |only man/pick_best_cluster_overall.Rd |only man/pick_best_cluster_silhouette.Rd |only man/pick_best_cluster_simon.Rd |only man/preProcessData.Rd | 21 man/preProcessResample.Rd | 7 man/remove_outliers.Rd | 9 32 files changed, 1147 insertions(+), 589 deletions(-)
Title: Fast and Scalable Single Cell Differential Expression Analysis
using Mixed-Effects Models
Description: A fast and scalable linear mixed-effects model (LMM) estimation algorithm
for analysis of single-cell differential expression. The algorithm uses
summary-level statistics and requires less computer memory to fit the LMM.
Author: Changjiang Xu [aut, cre],
Gary Bader [aut]
Maintainer: Changjiang Xu <changjiang.xu@utoronto.ca>
Diff between FLASHMM versions 1.2.0 dated 2025-03-31 and 1.2.1 dated 2025-04-09
DESCRIPTION | 6 MD5 | 14 +- NEWS.md | 2 README.md | 74 ++++++++--- inst/doc/FLASHMM-vignette.R | 19 +- inst/doc/FLASHMM-vignette.Rmd | 25 ++- inst/doc/FLASHMM-vignette.html | 267 ++++++++++++++++++++--------------------- vignettes/FLASHMM-vignette.Rmd | 25 ++- 8 files changed, 241 insertions(+), 191 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible
outcome to evaluate the effectiveness of a new therapy (the true endpoint) is
difficult to measure. In such a situation, it can be an effective strategy to
replace the true endpoint by a (bio)marker that is easier to measure and that
allows for a prediction of the treatment effect on the true endpoint (a
surrogate endpoint). The package 'Surrogate' allows for an evaluation of the
appropriateness of a candidate surrogate endpoint based on the meta-analytic,
information-theoretic, and causal-inference frameworks. Part of this software
has been developed using funding provided from the European Union's Seventh
Framework Programme for research, technological development and demonstration
(Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt
University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland
Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut],
Florian Stijven [aut],
Fenny Ong [aut],
Dries De Witte [aut],
Gokce Deliorman [aut],
Paul Meyvisch [aut],
Alvaro Poveda [aut],
Ariel Alonso [aut],
Hannah Ensor [aut],
Christoper Weir [aut],
Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>
Diff between Surrogate versions 3.3.3 dated 2025-02-11 and 3.4.0 dated 2025-04-09
DESCRIPTION | 10 ++++++---- MD5 | 14 ++++++++++---- NAMESPACE | 3 +++ NEWS.md | 12 ++++++++++++ R/ICA_alpha_ContCont.R |only R/ICA_t.R |only man/ICA_alpha_ContCont.Rd |only man/ICA_t.Rd |only man/Surrogate-package.Rd | 1 + tests/testthat/test_ICA_alpha_ContCont.R |only tests/testthat/test_ICA_t.R |only 11 files changed, 32 insertions(+), 8 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@unimib.it>
Diff between osmextract versions 0.5.2 dated 2024-11-22 and 0.5.3 dated 2025-04-09
DESCRIPTION | 10 MD5 | 52 +- NEWS.md | 332 ++++++------ R/get-network.R | 3 R/get.R | 8 R/match.R | 35 + R/utils.R | 21 build/vignette.rds |binary data/bbbike_zones.rda |binary data/geofabrik_zones.rda |binary data/openstreetmap_fr_zones.rda |binary inst/WORDLIST | 1 inst/doc/osmextract.R | 11 inst/doc/osmextract.Rmd | 28 + inst/doc/osmextract.html | 774 +++++++++++++++--------------- inst/doc/providers.html | 2 inst/doc/providers_comparisons.html | 14 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/geofabrik_zones.Rd | 2 man/oe_get.Rd | 8 man/oe_get_network.Rd | 3 man/oe_match.Rd | 17 man/osmextract-package.Rd | 2 tests/testthat/test-match.R | 19 vignettes/osmextract.Rmd | 28 + 27 files changed, 790 insertions(+), 580 deletions(-)
Title: Analyze Data from Electronic Adherence Monitoring Devices
Description: Medication adherence, defined as medication-taking behavior that aligns with the agreed-upon
treatment protocol, is critical for realizing the benefits of prescription medications.
Medication adherence can be assessed using electronic adherence monitoring devices (EAMDs),
pill bottles or boxes that contain a computer chip that records the date and time of each
opening (or “actuation”). Before researchers can use EAMD data, they must apply a series of
decision rules to transform actuation data into adherence data.
The purpose of this R package ('oncmap') is to transform EAMD actuations in the form of a raw .csv file,
information about the patient, regimen, and non-monitored periods into two daily adherence values --
Dose Taken and Correct Dose Taken.
Author: Michal Kouril [aut, cre] ,
Meghan McGrady [aut] ,
Mara Constance [aut] ,
Kevin Hommel [aut]
Maintainer: Michal Kouril <Michal.Kouril@cchmc.org>
Diff between oncmap versions 0.1.5 dated 2025-01-27 and 0.1.7 dated 2025-04-09
DESCRIPTION | 8 ++-- LICENSE | 2 - MD5 | 25 +++++++------- NEWS.md |only R/adherence_preprocess.R | 45 ++++++++++++------------- R/globals.R | 9 ++--- R/process_eamd.R | 36 +++++++++++--------- R/read_input.R | 46 +++++++++++++++++--------- R/report_adherence.R | 36 ++++++++++---------- build/vignette.rds |binary tests/testthat/test-adherence_preprocessing.R | 6 +-- tests/testthat/test-detect.R | 4 +- tests/testthat/test-process_eamd-script.R | 40 +++++++++++++--------- tests/testthat/test-process_eamd.R | 14 +++---- 14 files changed, 150 insertions(+), 121 deletions(-)
Title: Distributed Gaussian Process Calculations
Description: Distributes Gaussian process calculations across nodes
in a distributed memory setting, using Rmpi. The bigGP class
provides high-level methods for maximum likelihood with normal data,
prediction, calculation of uncertainty (i.e., posterior covariance
calculations), and simulation of realizations. In addition, bigGP
provides an API for basic matrix calculations with distributed
covariance matrices, including Cholesky decomposition, back/forwardsolve,
crossproduct, and matrix multiplication.
Author: Christopher Paciorek [aut, cre],
Benjamin Lipshitz [aut],
Prabhat [ctb],
Cari Kaufman [ctb],
Tina Zhuo [ctb],
Rollin Thomas [ctb]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between bigGP versions 0.1.8 dated 2023-04-25 and 0.1.9 dated 2025-04-09
DESCRIPTION | 10 MD5 | 14 NEWS | 6 build/partial.rdb |binary configure | 2957 ++++++++++++++++++++++++++++-------------------------- configure.ac | 18 data/SN2011fe.rda |binary man/bigGP.exit.Rd | 4 8 files changed, 1582 insertions(+), 1427 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-6 dated 2024-04-17 and 0.3-7 dated 2025-04-09
DESCRIPTION | 10 ++++---- MD5 | 10 ++++---- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++ inst/doc/tbm_supplement.R | 54 ++++++++++++++++++++++---------------------- inst/doc/tbm_supplement.pdf |binary 6 files changed, 44 insertions(+), 37 deletions(-)
Title: Spectrally Deconfounded Models
Description: Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.48550/arXiv.2502.03969>).
Author: Markus Ulmer [aut, cre, cph] ,
Cyrill Scheidegger [aut]
Maintainer: Markus Ulmer <markus.ulmer@stat.math.ethz.ch>
Diff between SDModels versions 1.0.4 dated 2025-02-19 and 1.0.7 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 13 +++++++++++++ R/SDTree.R | 5 +++-- R/paths.R | 6 +++++- R/predict.R | 28 +++++++++++++++++++++++++--- README.md | 8 +++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Runtime.R | 26 +++++++++++++------------- inst/doc/Runtime.html | 7 ++++--- man/predict.SDForest.Rd | 5 ++++- tests/testthat/test-anchor.R | 6 ++++++ tests/testthat/test-parallel.R | 16 ++++++++++++---- tests/testthat/test-tree.R | 41 +++++++++++++++++++++++++++++++++++++++++ 15 files changed, 149 insertions(+), 48 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph]
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.2.2-4 dated 2024-03-10 and 2.2.2-5 dated 2025-04-09
DESCRIPTION | 10 +-- MD5 | 18 +++--- R/template_huiwalter.R | 3 - build/vignette.rds |binary configure | 8 +- configure.ac | 6 +- inst/doc/UserGuide.pdf |binary inst/doc/quickjags.R | 24 ++++---- inst/doc/quickjags.html | 130 +++++++++++++++++++++++------------------------- man/runjags-package.Rd | 2 10 files changed, 98 insertions(+), 103 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon realms (C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package complements the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.0.0 dated 2025-01-07 and 1.1.1 dated 2025-04-09
rice-1.0.0/rice/R/calc.R |only rice-1.0.0/rice/man/overlap.Rd |only rice-1.1.1/rice/DESCRIPTION | 15 - rice-1.1.1/rice/MD5 | 115 ++++---- rice-1.1.1/rice/NAMESPACE | 8 rice-1.1.1/rice/NEWS.md | 15 + rice-1.1.1/rice/R/calibrate.R | 106 +++++-- rice-1.1.1/rice/R/marine.R | 195 +++++++------- rice-1.1.1/rice/R/plots.R | 177 +++++++----- rice-1.1.1/rice/R/realms.R | 325 ++++++++++++++++++----- rice-1.1.1/rice/R/rice-package.R | 4 rice-1.1.1/rice/R/rice.R | 61 ++++ rice-1.1.1/rice/R/sets.R | 114 +++++++- rice-1.1.1/rice/R/sources.R |only rice-1.1.1/rice/build/partial.rdb |binary rice-1.1.1/rice/build/vignette.rds |binary rice-1.1.1/rice/data/shells.rda |binary rice-1.1.1/rice/inst/doc/rice.R | 32 +- rice-1.1.1/rice/inst/doc/rice.Rmd | 60 +++- rice-1.1.1/rice/inst/doc/rice.html | 473 ++++++++++++++++++---------------- rice-1.1.1/rice/man/BCADtoD14C.Rd | 5 rice-1.1.1/rice/man/BCADtoF14C.Rd | 5 rice-1.1.1/rice/man/BCADtocalBP.Rd | 2 rice-1.1.1/rice/man/BCADtopMC.Rd | 5 rice-1.1.1/rice/man/C14toD14C.Rd | 4 rice-1.1.1/rice/man/C14toF14C.Rd | 6 rice-1.1.1/rice/man/C14tocalBP.Rd | 2 rice-1.1.1/rice/man/C14topMC.Rd | 4 rice-1.1.1/rice/man/D14CtoC14.Rd | 4 rice-1.1.1/rice/man/F14CtoC14.Rd | 4 rice-1.1.1/rice/man/as.bin.Rd | 2 rice-1.1.1/rice/man/as.one.Rd | 2 rice-1.1.1/rice/man/calBPtoBCAD.Rd | 2 rice-1.1.1/rice/man/calBPtoD14C.Rd | 5 rice-1.1.1/rice/man/calBPtoF14C.Rd | 5 rice-1.1.1/rice/man/calBPtopMC.Rd | 5 rice-1.1.1/rice/man/caldist.Rd | 3 rice-1.1.1/rice/man/calib.t.Rd | 3 rice-1.1.1/rice/man/calibrate.Rd | 8 rice-1.1.1/rice/man/clean.Rd | 9 rice-1.1.1/rice/man/contaminate.Rd | 9 rice-1.1.1/rice/man/draw.ccurve.Rd | 3 rice-1.1.1/rice/man/find.shells.Rd | 20 + rice-1.1.1/rice/man/fractions.Rd | 2 rice-1.1.1/rice/man/fromto.Rd |only rice-1.1.1/rice/man/howmanyC14.Rd |only rice-1.1.1/rice/man/hpd.Rd | 8 rice-1.1.1/rice/man/l.calib.Rd | 3 rice-1.1.1/rice/man/map.shells.Rd | 18 + rice-1.1.1/rice/man/muck.Rd | 9 rice-1.1.1/rice/man/older.Rd | 3 rice-1.1.1/rice/man/overlapping.Rd |only rice-1.1.1/rice/man/p.range.Rd | 3 rice-1.1.1/rice/man/push.gamma.Rd | 8 rice-1.1.1/rice/man/push.normal.Rd | 5 rice-1.1.1/rice/man/r.calib.Rd | 3 rice-1.1.1/rice/man/shells.mean.Rd | 2 rice-1.1.1/rice/man/span.Rd |only rice-1.1.1/rice/man/spread.Rd | 4 rice-1.1.1/rice/man/weighted_means.Rd | 2 rice-1.1.1/rice/man/younger.Rd | 3 rice-1.1.1/rice/vignettes/rice.Rmd | 60 +++- 62 files changed, 1300 insertions(+), 650 deletions(-)
Title: Spatial Phylogenetic Analysis
Description: Conduct various analyses on spatial phylogenetic diversity patterns.
Use your data on an evolutionary tree and geographic distributions of the
terminal taxa to compute diversity and endemism metrics, test significance
with null model randomization, analyze community turnover and biotic
regionalization, and perform spatial conservation prioritizations. All
functions support quantitative community data in addition to binary data.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
Diff between phylospatial versions 1.0.0 dated 2025-01-24 and 1.1.0 dated 2025-04-09
DESCRIPTION | 24 +++--- MD5 | 54 +++++++------ NAMESPACE | 1 NEWS.md |only R/phylospatial.R | 7 + R/ps_canape.R | 4 - R/ps_diversity.R | 143 ++++++++++++++++++++++++++++++------- R/ps_ordinate.R | 2 R/ps_rand.R | 26 ++++-- README.md | 18 ++-- inst/doc/alpha-diversity.R | 11 +- inst/doc/alpha-diversity.Rmd | 36 +++++---- inst/doc/alpha-diversity.html | 86 +++++++++++++--------- inst/doc/beta-diversity.R | 2 inst/doc/phylospatial-data.R | 2 inst/doc/phylospatial-data.Rmd | 4 - inst/doc/phylospatial-data.html | 8 +- inst/doc/prioritization.R | 2 man/clade_dist.Rd |only man/phylospatial-package.Rd | 4 - man/ps_canape.Rd | 4 - man/ps_diversity.Rd | 63 ++++++++++------ man/ps_ordinate.Rd | 3 man/ps_rand.Rd | 18 ++-- tests/testthat/test-phylospatial.R | 1 tests/testthat/test-ps_diversity.R | 66 +++++++++++------ tests/testthat/test-ps_rand.R | 1 vignettes/alpha-diversity.Rmd | 36 +++++---- vignettes/phylospatial-data.Rmd | 4 - 29 files changed, 410 insertions(+), 220 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre] ,
Stephane Dray [ctb] ,
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Peter Li [ctb],
Luiz Droubi [ctb],
James Riley [ctb],
Antoine de Falguerolles [ctb],
Monique Graf [ctb],
Neville Verlander [ctb],
Brian [...truncated...]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.9-1 dated 2023-08-09 and 0.9-3 dated 2025-04-09
DESCRIPTION | 30 ++++++++++++-------- MD5 | 52 +++++++++++++++++------------------ NEWS.md | 18 +++++++++++- build/partial.rdb |binary build/vignette.rds |binary data/Armada.RData |binary inst/WORDLIST | 14 +++++++++ inst/doc/Snow_deaths-duplicates.R | 14 ++++----- inst/doc/Snow_deaths-duplicates.Rmd | 2 - inst/doc/Snow_deaths-duplicates.html | 20 ++++++------- man/Arbuthnot.Rd | 2 - man/Armada.Rd | 38 ++++++++++++++++--------- man/Cavendish.Rd | 2 - man/Cholera.Rd | 2 - man/CholeraDeaths1849.Rd | 2 - man/Galton.Rd | 3 +- man/GaltonFamilies.Rd | 2 - man/Guerry.Rd | 2 - man/HistData-package.Rd | 2 - man/Michelson.Rd | 2 - man/Minard.Rd | 22 ++++---------- man/PearsonLee.Rd | 5 ++- man/PolioTrials.Rd | 2 - man/Pollen.Rd | 2 - man/Pyx.Rd | 21 ++++++++++++++ man/Snow.Rd | 13 ++++++-- vignettes/Snow_deaths-duplicates.Rmd | 2 - 27 files changed, 172 insertions(+), 102 deletions(-)
Title: Fit a Penalized Constrained Continuation Ratio Model for
Predicting an Ordinal Response
Description: Penalized methods are useful for fitting over-parameterized models. This package includes functions for restructuring an ordinal
response dataset for fitting continuation ratio models for datasets where the number of covariates exceeds the sample size or when
there is collinearity among the covariates. The 'glmnet' fitting algorithm is used to fit the continuation ratio model after data restructuring.
Author: Kellie J. Archer [aut, cre]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between glmnetcr versions 1.0.6 dated 2020-07-03 and 1.0.7 dated 2025-04-09
DESCRIPTION | 14 ++++++++------ MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary data/diabetes.rda |binary inst/CITATION | 36 +++++++++++++++--------------------- inst/NEWS.Rd | 5 +++++ inst/doc/glmnetcr.pdf |binary man/diabetes.Rd | 2 +- man/glmnetcr-package.Rd | 2 +- man/glmnetcr.Rd | 2 +- 11 files changed, 41 insertions(+), 40 deletions(-)
Title: An Adaptive Lifting Scheme Algorithm
Description: Adaptive wavelet lifting transforms for signal denoising using optimal local neighbourhood regression, from Nunes et al. (2006) <doi:10.1007/s11222-006-6560-y>.
Author: Matt Nunes [aut, cre],
Marina Knight [aut],
Guy Nason [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between adlift versions 1.4-5 dated 2023-03-22 and 1.4-6 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/Amatdual.Rd | 2 +- man/fwtnp.Rd | 2 +- src/adlift.c | 32 ++++++++++++++++++++++++++++---- 5 files changed, 38 insertions(+), 14 deletions(-)
Title: Climate Classification According to Several Indices
Description: Classification of climate according to Koeppen - Geiger, of aridity
indices, of continentality indices, of water balance after Thornthwaite, of
viticultural bioclimatic indices. Drawing climographs: Thornthwaite, Peguy,
Bagnouls-Gaussen.
Author: Emanuele Eccel [aut],
Fabio Zottele [aut, cre],
Emanuele Cordano [aut],
Giambattista Toller [aut],
Fondazione Edmund Mach [cph]
Maintainer: Fabio Zottele <fabio.zottele@fmach.it>
Diff between ClimClass versions 2.1.0 dated 2016-08-04 and 2.1.1 dated 2025-04-09
DESCRIPTION | 19 +- MD5 | 66 ++++----- NEWS.md | 24 ++- R/ClimClass.R | 7 - R/as.datcli.R | 186 +++++++++++++-------------- R/peguy.R | 286 ++++++++++++++++++++---------------------- R/thornthwaite.R | 2 man/ClimClass.Rd | 23 ++- man/ExAtRa.Rd | 7 - man/P.Rd | 5 man/RDI.Rd | 20 +- man/Tm.Rd | 5 man/Tn.Rd | 5 man/Trent_climate.Rd | 1 man/Tx.Rd | 5 man/W_balance.Rd | 5 man/arid.Rd | 16 +- man/arid_ind_tables.Rd | 5 man/as.datcli.Rd | 27 ++- man/bagn_gau.Rd | 23 ++- man/clima_81_10.Rd | 5 man/climate.Rd | 1 man/coeff_rad.Rd | 5 man/contin.Rd | 16 +- man/continental_ind_tables.Rd | 5 man/coord_elev.Rd | 5 man/koeppen_geiger.Rd | 15 +- man/lista_cli.Rd | 5 man/oiv_ind.Rd | 25 ++- man/peguy.Rd | 27 ++- man/plot.thornthwaite.Rd | 24 ++- man/quantiles.Rd | 5 man/thornt_lst.Rd | 5 man/thornthwaite.Rd | 236 +++++++++++++++++----------------- 34 files changed, 606 insertions(+), 510 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments (GUI)
Description: A 'Shiny' application to access the functionalities and datasets of the 'archeofrag' package for spatial analysis in archaeology from refitting data. Quick and seamless exploration of archaeological refitting datasets, focusing on physical refits only. Features include: built-in documentation and convenient workflow, plot generation and exports, exploration of spatial units merging solutions, simulation of archaeological site formation processes, support for parallel computing, R code generation to re-execute simulations and ensure reproducibility, code generation for the 'openMOLE' model exploration software. A demonstration of the app is available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag.gui versions 1.0.0 dated 2025-03-10 and 1.1.0 dated 2025-04-09
DESCRIPTION | 10 - MD5 | 10 - NAMESPACE | 6 NEWS.md | 5 R/app_server.R | 495 +++++++++++++++++++++++++++++++++++++++++++++++++-------- R/app_ui.R | 171 ++++++++++++++----- 6 files changed, 580 insertions(+), 117 deletions(-)
More information about archeofrag.gui at CRAN
Permanent link
Title: Analysis of Differential Behaviour of SPARRA Score Across
Demographic Groups
Description: The SPARRA risk score (Scottish Patients At Risk of admission and Re-Admission) estimates yearly risk of emergency hospital admission using electronic health records on a monthly basis for most of the Scottish population. This package implements a suite of functions used to analyse the behaviour and performance of the score, focusing particularly on differential performance over demographically-defined groups. It includes useful utility functions to plot receiver-operator-characteristic, precision-recall and calibration curves, draw stock human figures, estimate counterfactual quantities without the need to re-compute risk scores, to simulate a semi-realistic dataset. Our manuscript can be found at: <doi:10.1371/journal.pdig.0000675>.
Author: Ioanna Thoma [aut] ,
Catalina Vallejos [ctb] ,
Louis Aslett [ctb] ,
Jill Ireland [ctb] ,
Simon Rogers [ctb] ,
James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>
Diff between SPARRAfairness versions 0.0.0.2 dated 2024-11-07 and 0.1.0.0 dated 2025-04-09
SPARRAfairness-0.0.0.2/SPARRAfairness/inst/doc/SPARRAfairness_example.html |only SPARRAfairness-0.1.0.0/SPARRAfairness/DESCRIPTION | 10 SPARRAfairness-0.1.0.0/SPARRAfairness/MD5 | 18 SPARRAfairness-0.1.0.0/SPARRAfairness/NEWS.md | 4 SPARRAfairness-0.1.0.0/SPARRAfairness/build/vignette.rds |binary SPARRAfairness-0.1.0.0/SPARRAfairness/data/all_data.RData |binary SPARRAfairness-0.1.0.0/SPARRAfairness/data/decomposition_matrix.RData |binary SPARRAfairness-0.1.0.0/SPARRAfairness/inst/doc/SPARRAfairness_example.Rmd | 6 SPARRAfairness-0.1.0.0/SPARRAfairness/inst/doc/SPARRAfairness_example.pdf |only SPARRAfairness-0.1.0.0/SPARRAfairness/vignettes/SPARRAfairness.bib | 898 ---------- SPARRAfairness-0.1.0.0/SPARRAfairness/vignettes/SPARRAfairness_example.Rmd | 6 11 files changed, 53 insertions(+), 889 deletions(-)
More information about SPARRAfairness at CRAN
Permanent link
Title: Get Spanish Origin-Destination Data
Description: Gain seamless access to origin-destination (OD) data from the
Spanish Ministry of Transport, hosted at
<https://www.transportes.gob.es/ministerio/proyectos-singulares/estudios-de-movilidad-con-big-data/opendata-movilidad>.
This package simplifies the management of these large datasets by
providing tools to download zone boundaries, handle associated
origin-destination data, and process it efficiently with the 'duckdb'
database interface. Local caching minimizes repeated downloads,
streamlining workflows for researchers and analysts. Extensive
documentation is available at
<https://ropenspain.github.io/spanishoddata/index.html>, offering
guides on creating static and dynamic mobility flow visualizations and
transforming large datasets into analysis-ready formats.
Author: Egor Kotov [aut, cre] ,
Robin Lovelace [aut] ,
Eugeni Vidal-Tortosa [ctb]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between spanishoddata versions 0.1.0 dated 2024-12-18 and 0.1.1 dated 2025-04-09
DESCRIPTION | 12 MD5 | 139 ++++---- NAMESPACE | 2 NEWS.md | 22 + R/available-data.R | 4 R/cite.R |only R/codebook.R | 3 R/connect.R | 13 R/convert.R | 5 R/data-dir.R | 8 R/dev-tools.R | 2 R/disconnect.R | 3 R/download_data.R | 4 R/duckdb-helpers.R | 4 R/get-zones.R | 3 R/get.R | 24 + R/internal-utils.R | 59 +++ R/onload.R |only R/quick-get.R | 139 ++++---- R/spanishoddata-package.R |only README.md | 168 ++++++---- build/vignette.rds |binary inst/CITATION | 69 ++-- inst/doc/convert.html | 83 +--- inst/doc/convert.qmd | 46 +- inst/doc/quick-get.R | 9 inst/doc/quick-get.html | 46 +- inst/doc/quick-get.qmd | 27 - inst/doc/v1-2020-2021-mitma-data-codebook.R | 5 inst/doc/v1-2020-2021-mitma-data-codebook.html | 158 ++++----- inst/doc/v1-2020-2021-mitma-data-codebook.qmd | 41 +- inst/doc/v2-2022-onwards-mitma-data-codebook.html | 146 ++++---- inst/doc/v2-2022-onwards-mitma-data-codebook.qmd | 31 + inst/extdata/sql-queries/v1-od-distritos-clean-csv-view-en.sql | 7 inst/extdata/sql-queries/v1-od-distritos-clean-csv-view-es.sql | 4 inst/extdata/sql-queries/v1-od-municipios-clean-csv-view-en.sql | 2 inst/extdata/sql-queries/v2-od-distritos-clean-csv-view-en.sql | 5 inst/extdata/sql-queries/v2-od-gau-clean-csv-view-en.sql | 2 inst/extdata/sql-queries/v2-od-municipios-clean-csv-view-en.sql | 2 inst/schemaorg.json | 26 + inst/vignette-include/install-package.qmd | 17 - inst/vignette-include/overall-approach.qmd | 2 man/figures/README-desire-lines-1.png |binary man/figures/README-distritos-1.png |binary man/figures/flows_plot_all_districts.png |binary man/figures/flows_plot_barcelona.png |binary man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/figures/zones_barcelona_fua_plot.png |binary man/figures/zones_barcelona_plot.png |only man/spanishoddata-package.Rd |only man/spod_available_data.Rd | 2 man/spod_cite.Rd |only man/spod_codebook.Rd | 2 man/spod_connect.Rd | 4 man/spod_convert.Rd | 2 man/spod_disconnect.Rd | 2 man/spod_download.Rd | 2 man/spod_duckdb_limit_resources.Rd | 2 man/spod_duckdb_od.Rd | 2 man/spod_get.Rd | 4 man/spod_get_data_dir.Rd | 2 man/spod_get_valid_dates.Rd | 4 man/spod_get_zones.Rd | 2 man/spod_graphql_valid_dates.Rd |only man/spod_quick_get_od.Rd | 4 man/spod_set_data_dir.Rd | 2 tests/testthat/test-quick-get.R | 43 -- vignettes/convert.qmd | 46 +- vignettes/media/flows_plot_barcelona.svg |only vignettes/private |only vignettes/quick-get.qmd | 27 - vignettes/references.bib | 30 - vignettes/v1-2020-2021-mitma-data-codebook.qmd | 41 +- vignettes/v2-2022-onwards-mitma-data-codebook.qmd | 31 + 77 files changed, 922 insertions(+), 674 deletions(-)
Title: Radiation and Photovoltaic Systems
Description: Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Author: Oscar Perpinan Lamigueiro [cre, aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@upm.es>
Diff between solaR versions 0.46 dated 2021-10-19 and 0.47 dated 2025-04-09
DESCRIPTION | 10 ++-- MD5 | 88 +++++++++++++++++++++---------------------- R/corrFdKt.R | 4 - R/fCompD.R | 8 +-- R/fCompI.R | 6 +- R/fProd.R | 6 +- R/fTemp.R | 4 - R/prodGCPV.R | 2 R/prodPVPS.R | 2 README.md | 13 +----- build/partial.rdb |binary inst/CITATION | 4 - man/G0-class.Rd | 4 - man/Gef-class.Rd | 4 - man/HQCurve.Rd | 4 - man/NmgSFB.Rd | 4 - man/ProdGCPV-class.Rd | 4 - man/ProdPVPS-class.Rd | 4 - man/Shade-class.Rd | 6 +- man/Sol-class.Rd | 4 - man/calcG0.Rd | 4 - man/calcGef.Rd | 4 - man/calcShd.Rd | 4 - man/calcSol.Rd | 4 - man/compareLosses-methods.Rd | 4 - man/fBTd.Rd | 4 - man/fCompD.Rd | 4 - man/fCompI.Rd | 4 - man/fInclin.Rd | 4 - man/fProd.Rd | 4 - man/fPump.Rd | 4 - man/fSolD.Rd | 4 - man/fSolI.Rd | 4 - man/fSombra.Rd | 6 +- man/fTemp.Rd | 4 - man/fTheta.Rd | 4 - man/indexD-methods.Rd | 9 ++++ man/indexI-methods.Rd | 6 ++ man/local2UTC.Rd | 4 - man/optimShd.Rd | 6 +- man/prodGCPV.Rd | 4 - man/prodPVPS.Rd | 4 - man/pumpCoef.Rd | 6 +- man/window-methods.Rd | 2 man/writeSolar.Rd | 8 +-- 45 files changed, 153 insertions(+), 143 deletions(-)
Title: Spatial ARCH and GARCH Models (spGARCH)
Description: A collection of functions to deal with spatial and spatiotemporal autoregressive conditional heteroscedasticity (spatial ARCH and GARCH models) by Otto, Schmid, Garthoff (2018, Spatial Statistics) <doi:10.1016/j.spasta.2018.07.005>: simulation of spatial ARCH-type processes (spARCH, log/exponential-spARCH, complex-spARCH); quasi-maximum-likelihood estimation of the parameters of spARCH models and spatial autoregressive models with spARCH disturbances, diagnostic checks, visualizations.
Author: Philipp Otto [cre, aut]
Maintainer: Philipp Otto <philipp.otto89@gmail.com>
Diff between spGARCH versions 0.2.2 dated 2020-09-02 and 0.2.3 dated 2025-04-09
DESCRIPTION | 16 +- MD5 | 33 ++--- R/RcppExports.R | 94 +++++++-------- R/zzz.R | 56 ++++---- build |only inst/CITATION | 65 +++++----- man/extractAIC.spARCH.Rd | 66 +++++----- man/fitted.spARCH.Rd | 58 ++++----- man/logLik.spARCH.Rd | 62 ++++----- man/plot.spARCH.Rd | 76 ++++++------ man/qml.SARspARCH.Rd | 274 +++++++++++++++++++++---------------------- man/qml.spARCH.Rd | 260 ++++++++++++++++++++--------------------- man/residuals.spARCH.Rd | 58 ++++----- man/spARCHsim.Rd | 238 +++++++++++++++++++------------------- man/spGARCH.Rd | 33 ++--- man/spGARCHsim.Rd | 294 +++++++++++++++++++++++------------------------ man/summary.spARCH.Rd | 134 ++++++++++----------- src/RcppExports.cpp | 5 18 files changed, 921 insertions(+), 901 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>,
a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD),
its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD).
Due to the possible portability issues CRAN version no longer supports OpenMP, but you can install OpenMP-supported version
from GitHub: <https://github.com/helske/Rlibeemd/>.
Author: Jouni Helske [aut, cre] ,
Perttu Luukko [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between Rlibeemd versions 1.4.3 dated 2023-09-05 and 1.4.4 dated 2025-04-09
ChangeLog | 7 +++++ DESCRIPTION | 10 +++---- MD5 | 58 +++++++++++++++++++++++---------------------- R/Rlibeemd-package.R | 2 - R/emd_num_imfs.R | 2 - R/zzz.R | 7 ++--- README.md |only configure | 2 - man/Rlibeemd.Rd | 16 ++++++++++++ src/Makevars.in | 1 src/Makevars.win | 1 src/RcppExports.cpp | 4 +-- src/array.h | 26 +++----------------- src/array_complex.h |only src/bemd.c | 36 ++++++++++++++++++--------- src/bemd.h | 21 +++++++++------- src/bemdR.cpp | 14 +++++++--- src/ceemdan.c | 6 ++-- src/ceemdanR.cpp | 2 - src/eemd.h | 21 +++++++--------- src/eemdR.cpp | 2 - src/eemd_routine.c | 4 +-- src/emd.c | 8 +++--- src/emd.h | 8 +++--- src/emd_num_imfsR.cpp | 4 +-- src/extras.h | 4 --- src/extrema.c | 8 +++--- src/extrema.h | 2 - src/spline.c | 4 +-- src/workspace.h | 22 ++++++++--------- tests/testthat/test-bemd.R | 2 - 31 files changed, 162 insertions(+), 142 deletions(-)
Title: Estimation of Optimal Size for a Holdout Set for Updating a
Predictive Score
Description: Predictive scores must be updated with care, because actions taken on the basis of existing risk scores causes bias in risk estimates from the updated score. A holdout set is a straightforward way to manage this problem: a proportion of the population is 'held-out' from computation of the previous risk score. This package provides tools to estimate a size for this holdout set and associated errors. Comprehensive vignettes are included. Please see: Haidar-Wehbe S, Emerson SR, Aslett LJM, Liley J (2022) <doi:10.48550/arXiv.2202.06374> (to appear in Annals of Applied Statistics) for details of methods.
Author: Sami Haidar-Wehbe [aut],
Sam Emerson [aut] ,
Louis Aslett [aut] ,
James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>
Diff between OptHoldoutSize versions 0.1.0.0 dated 2022-02-18 and 0.1.0.1 dated 2025-04-09
OptHoldoutSize-0.1.0.0/OptHoldoutSize/inst/doc/ASPRE_example.html |only OptHoldoutSize-0.1.0.0/OptHoldoutSize/inst/doc/comparison_of_algorithms.html |only OptHoldoutSize-0.1.0.0/OptHoldoutSize/inst/doc/simulated_example.html |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/DESCRIPTION | 10 OptHoldoutSize-0.1.0.1/OptHoldoutSize/MD5 | 57 ++-- OptHoldoutSize-0.1.0.1/OptHoldoutSize/NEWS.md | 6 OptHoldoutSize-0.1.0.1/OptHoldoutSize/R/OptHoldoutSize_estimation.R | 2 OptHoldoutSize-0.1.0.1/OptHoldoutSize/build/vignette.rds |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/aspre_emulation.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/aspre_parametric.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_a_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_cost_a_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_cost_e_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_e_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/data_example_simulation.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/data_nextpoint_em.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/data_nextpoint_par.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ohs_array.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ohs_resample.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/params_aspre.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/ASPRE_example.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/ASPRE_example.pdf |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/comparison_of_algorithms.R | 12 - OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/comparison_of_algorithms.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/comparison_of_algorithms.pdf |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/simulated_example.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/simulated_example.pdf |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/man/optimal_holdout_size.Rd | 2 OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/ASPRE_example.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/ASPRE_example.html |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/comparison_of_algorithms.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/optimal_holdout_sizing.bib | 117 ---------- OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/simulated_example.Rmd | 4 33 files changed, 66 insertions(+), 164 deletions(-)
More information about OptHoldoutSize at CRAN
Permanent link
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 and 'CrewT ImoVifa' ('Topcon Tempo') with partial implementations on the Centervue Compass, Kowa AP 7000 and Android phones. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph] ,
David Lawson [ctb, cph],
Ivan Marin-Franch [ctb, cph],
Matthias Muller [ctb],
Jonathan Denniss [ctb, cph],
Astrid Zeman [ctb],
Giovanni Montesano [ctb]
Maintainer: Andrew Turpin <andrew.turpin@lei.org.au>
Diff between OPI versions 3.0.2 dated 2024-07-09 and 3.0.4 dated 2025-04-09
DESCRIPTION | 10 +-- MD5 | 102 +++++++++++++++++++------------------ NEWS.md | 8 ++ R/Compass.r | 8 ++ R/Display.r | 10 +++ R/ImoVifa.r | 18 +++++- R/MAIA.r |only R/Octopus600.r | 2 R/Octopus900.r | 5 + R/PhoneHMD.r | 10 +++ R/PicoVR.r | 10 +++ R/SimGaussian.r | 1 R/SimHenson.r | 6 +- R/SimHensonRT.r | 16 ++--- R/SimNo.r | 5 + R/SimYes.r | 5 + R/full_threshold.r | 4 + R/opi.r | 23 ++++++-- R/zest.r | 4 - README.md | 4 - man/ZEST.Rd | 4 - man/dot-opi_env.Rd | 2 man/full_threshold.Rd | 4 + man/opiClose.Rd | 1 man/opiClose_for_Display.Rd | 2 man/opiClose_for_ImoVifa.Rd | 2 man/opiClose_for_MAIA.Rd |only man/opiClose_for_PhoneHMD.Rd | 2 man/opiClose_for_PicoVR.Rd | 2 man/opiInitialise.Rd | 1 man/opiInitialise_for_Display.Rd | 2 man/opiInitialise_for_ImoVifa.Rd | 2 man/opiInitialise_for_MAIA.Rd |only man/opiInitialise_for_PhoneHMD.Rd | 2 man/opiInitialise_for_PicoVR.Rd | 2 man/opiPresent.Rd | 1 man/opiPresent_for_Display.Rd | 2 man/opiPresent_for_ImoVifa.Rd | 10 ++- man/opiPresent_for_MAIA.Rd |only man/opiPresent_for_PhoneHMD.Rd | 2 man/opiPresent_for_PicoVR.Rd | 2 man/opiPresent_for_SimHensonRT.Rd | 7 -- man/opiQueryDevice.Rd | 1 man/opiQueryDevice_for_Display.Rd | 2 man/opiQueryDevice_for_ImoVifa.Rd | 2 man/opiQueryDevice_for_MAIA.Rd |only man/opiQueryDevice_for_PhoneHMD.Rd | 2 man/opiQueryDevice_for_PicoVR.Rd | 2 man/opiSetup.Rd | 1 man/opiSetup_for_Display.Rd | 2 man/opiSetup_for_ImoVifa.Rd | 2 man/opiSetup_for_MAIA.Rd |only man/opiSetup_for_PhoneHMD.Rd | 2 man/opiSetup_for_PicoVR.Rd | 2 tests/testthat/test-opiPresent.r | 6 +- 55 files changed, 232 insertions(+), 95 deletions(-)
Title: Generating Funky Heatmaps for Data Frames
Description: Allows generating heatmap-like visualisations for data
frames. Funky heatmaps can be fine-tuned by providing annotations of the
columns and rows, which allows assigning multiple palettes or geometries
or grouping rows and columns together in categories.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut] ,
Louise Deconinck [ctb] ,
Artuur Couckuyt [ctb] ,
Nick Markov [ctb] ,
Luke Zappia [ctb]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between funkyheatmap versions 0.5.1 dated 2025-01-15 and 0.5.2 dated 2025-04-09
funkyheatmap-0.5.1/funkyheatmap/inst/doc/mtcars.R |only funkyheatmap-0.5.1/funkyheatmap/inst/doc/mtcars.Rmd |only funkyheatmap-0.5.1/funkyheatmap/inst/doc/mtcars.html |only funkyheatmap-0.5.1/funkyheatmap/vignettes/mtcars.Rmd |only funkyheatmap-0.5.2/funkyheatmap/DESCRIPTION | 6 +- funkyheatmap-0.5.2/funkyheatmap/MD5 | 28 ++++++---- funkyheatmap-0.5.2/funkyheatmap/NEWS.md | 6 ++ funkyheatmap-0.5.2/funkyheatmap/README.md | 13 +++- funkyheatmap-0.5.2/funkyheatmap/build/partial.rdb |binary funkyheatmap-0.5.2/funkyheatmap/build/vignette.rds |binary funkyheatmap-0.5.2/funkyheatmap/inst/doc/funkyheatmap.R |only funkyheatmap-0.5.2/funkyheatmap/inst/doc/funkyheatmap.Rmd |only funkyheatmap-0.5.2/funkyheatmap/inst/doc/funkyheatmap.html |only funkyheatmap-0.5.2/funkyheatmap/inst/doc/scIB.html | 10 +++ funkyheatmap-0.5.2/funkyheatmap/vignettes/funkyheatmap.Rmd |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/automatic.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/automatic.svg |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/manual.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/manual.svg |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/straight.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/straight.svg |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/vengine.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/vengine.svg |only 23 files changed, 45 insertions(+), 18 deletions(-)
Title: Find Clinical Trial Sites Under-Reporting Adverse Events
Description: Monitoring of Adverse Event (AE) reporting in clinical trials is
important for patient safety. Sites that are under-reporting AEs can be detected
using Bootstrap-based simulations that simulate overall AE reporting. Based on the
simulation an AE under-reporting probability is assigned to each site in a
given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).
Author: Bjoern Koneswarakantha [aut, cre, cph]
,
F. Hoffmann-La Roche Ltd [cph]
Maintainer: Bjoern Koneswarakantha <bjoern.koneswarakantha@roche.com>
Diff between simaerep versions 0.6.0 dated 2024-09-30 and 0.7.0 dated 2025-04-09
simaerep-0.6.0/simaerep/R/lint.R |only simaerep-0.7.0/simaerep/DESCRIPTION | 8 simaerep-0.7.0/simaerep/MD5 | 79 +-- simaerep-0.7.0/simaerep/NAMESPACE | 2 simaerep-0.7.0/simaerep/NEWS.md | 9 simaerep-0.7.0/simaerep/R/S3_orivisit.R | 43 + simaerep-0.7.0/simaerep/R/S3_simaerep.R | 184 ++++--- simaerep-0.7.0/simaerep/R/inframe.R | 170 ++++-- simaerep-0.7.0/simaerep/R/simaerep.R | 247 ++++++---- simaerep-0.7.0/simaerep/R/simaerep_plot.R | 224 ++++----- simaerep-0.7.0/simaerep/R/simulate_test_data.R | 154 ++++-- simaerep-0.7.0/simaerep/README.md | 14 simaerep-0.7.0/simaerep/inst/WORDLIST | 3 simaerep-0.7.0/simaerep/man/aggr_duplicated_visits.Rd | 4 simaerep-0.7.0/simaerep/man/check_df_visit.Rd | 4 simaerep-0.7.0/simaerep/man/eval_sites.Rd | 14 simaerep-0.7.0/simaerep/man/exp_implicit_missing_visits.Rd | 4 simaerep-0.7.0/simaerep/man/figures/README-unnamed-chunk-3-1.png |binary simaerep-0.7.0/simaerep/man/figures/README-unnamed-chunk-4-1.png |binary simaerep-0.7.0/simaerep/man/get_site_mean_ae_dev.Rd | 4 simaerep-0.7.0/simaerep/man/orivisit.Rd | 4 simaerep-0.7.0/simaerep/man/p_adjust_bh_inframe.Rd | 2 simaerep-0.7.0/simaerep/man/plot.simaerep.Rd | 5 simaerep-0.7.0/simaerep/man/plot_study.Rd | 8 simaerep-0.7.0/simaerep/man/plot_visit_med75.Rd | 8 simaerep-0.7.0/simaerep/man/sim_inframe.Rd | 4 simaerep-0.7.0/simaerep/man/sim_test_data_events.Rd |only simaerep-0.7.0/simaerep/man/sim_test_data_study.Rd | 11 simaerep-0.7.0/simaerep/man/simaerep.Rd | 11 simaerep-0.7.0/simaerep/man/simaerep_inframe.Rd | 5 simaerep-0.7.0/simaerep/man/site_aggr.Rd | 10 simaerep-0.7.0/simaerep/tests/testthat/_snaps/eval_sites.md | 12 simaerep-0.7.0/simaerep/tests/testthat/test_S3_orivisit.R | 33 + simaerep-0.7.0/simaerep/tests/testthat/test_S3_simaerep.R | 16 simaerep-0.7.0/simaerep/tests/testthat/test_check_df_visit.R | 2 simaerep-0.7.0/simaerep/tests/testthat/test_data.R | 67 ++ simaerep-0.7.0/simaerep/tests/testthat/test_event_names.R |only simaerep-0.7.0/simaerep/tests/testthat/test_get_portf_perf.R | 2 simaerep-0.7.0/simaerep/tests/testthat/test_inframe.R | 6 simaerep-0.7.0/simaerep/tests/testthat/test_plot.R | 84 +++ simaerep-0.7.0/simaerep/tests/testthat/test_sim_sites.R | 64 ++ simaerep-0.7.0/simaerep/tests/testthat/test_sim_studies.R | 14 42 files changed, 1078 insertions(+), 457 deletions(-)
Title: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Description: Individual based simulations of hybridizing populations,
where the accumulation of junctions is tracked. Furthermore,
mathematical equations are provided to verify simulation outcomes.
Both simulations and mathematical equations are based on Janzen
(2018, <doi:10.1101/058107>) and Janzen (2022,
<doi:10.1111/1755-0998.13519>).
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between junctions versions 2.1.1 dated 2025-03-12 and 2.1.3 dated 2025-04-09
DESCRIPTION | 8 - MD5 | 32 ++--- NEWS.md | 137 ++++++++++++------------ README.md | 4 build/vignette.rds |binary inst/doc/Overview_of_the_junctions_package.html | 12 +- inst/doc/junctions_vignette.R | 24 ++-- inst/doc/junctions_vignette.html | 4 inst/doc/phased_and_unphased_data.html | 68 +++++------ man/junctions-package.Rd | 6 + tests/testthat/test-backcrossing.R | 1 tests/testthat/test-estim_time_haploid.R | 2 tests/testthat/test-marker_dist.R | 4 tests/testthat/test-one-chrom.R | 1 tests/testthat/test-phased-error.R | 1 tests/testthat/test-phased.R | 2 tests/testthat/test-unphased.R | 12 -- 17 files changed, 159 insertions(+), 159 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre]
,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 3.5.1 dated 2024-04-23 and 3.5.2 dated 2025-04-09
ggplot2-3.5.1/ggplot2/man/is.Coord.Rd |only ggplot2-3.5.1/ggplot2/man/is.facet.Rd |only ggplot2-3.5.1/ggplot2/man/is.ggplot.Rd |only ggplot2-3.5.1/ggplot2/man/is.theme.Rd |only ggplot2-3.5.2/ggplot2/DESCRIPTION | 8 ggplot2-3.5.2/ggplot2/MD5 | 140 ggplot2-3.5.2/ggplot2/NAMESPACE | 18 ggplot2-3.5.2/ggplot2/NEWS.md | 1487 +++++----- ggplot2-3.5.2/ggplot2/R/aes.R | 4 ggplot2-3.5.2/ggplot2/R/coord-.R | 16 ggplot2-3.5.2/ggplot2/R/coord-cartesian-.R | 2 ggplot2-3.5.2/ggplot2/R/facet-.R | 20 ggplot2-3.5.2/ggplot2/R/fortify.R | 2 ggplot2-3.5.2/ggplot2/R/geom-.R | 3 ggplot2-3.5.2/ggplot2/R/geom-defaults.R | 48 ggplot2-3.5.2/ggplot2/R/ggproto.R | 21 ggplot2-3.5.2/ggplot2/R/guide-.R | 10 ggplot2-3.5.2/ggplot2/R/guide-axis.R | 2 ggplot2-3.5.2/ggplot2/R/guide-colorbar.R | 3 ggplot2-3.5.2/ggplot2/R/guide-legend.R | 3 ggplot2-3.5.2/ggplot2/R/guides-.R | 14 ggplot2-3.5.2/ggplot2/R/labels.R | 33 ggplot2-3.5.2/ggplot2/R/layer.R | 7 ggplot2-3.5.2/ggplot2/R/margins.R | 6 ggplot2-3.5.2/ggplot2/R/plot-build.R | 12 ggplot2-3.5.2/ggplot2/R/plot-construction.R | 6 ggplot2-3.5.2/ggplot2/R/plot.R | 15 ggplot2-3.5.2/ggplot2/R/position-.R | 4 ggplot2-3.5.2/ggplot2/R/scale-.R | 4 ggplot2-3.5.2/ggplot2/R/scale-colour.R | 2 ggplot2-3.5.2/ggplot2/R/stat-.R | 4 ggplot2-3.5.2/ggplot2/R/stat-ellipse.R | 2 ggplot2-3.5.2/ggplot2/R/theme-current.R | 4 ggplot2-3.5.2/ggplot2/R/theme-elements.R | 18 ggplot2-3.5.2/ggplot2/R/theme.R | 21 ggplot2-3.5.2/ggplot2/README.md | 12 ggplot2-3.5.2/ggplot2/build/vignette.rds |binary ggplot2-3.5.2/ggplot2/inst/doc/extending-ggplot2.Rmd | 2 ggplot2-3.5.2/ggplot2/inst/doc/extending-ggplot2.html | 160 - ggplot2-3.5.2/ggplot2/inst/doc/ggplot2-in-packages.R | 10 ggplot2-3.5.2/ggplot2/inst/doc/ggplot2-in-packages.html | 4 ggplot2-3.5.2/ggplot2/inst/doc/ggplot2-specs.html | 90 ggplot2-3.5.2/ggplot2/inst/doc/ggplot2.html | 54 ggplot2-3.5.2/ggplot2/man/element.Rd | 6 ggplot2-3.5.2/ggplot2/man/figures/README-example-1.png |binary ggplot2-3.5.2/ggplot2/man/get_geom_defaults.Rd |only ggplot2-3.5.2/ggplot2/man/ggplot2-ggproto.Rd | 4 ggplot2-3.5.2/ggplot2/man/ggplot_gtable.Rd | 4 ggplot2-3.5.2/ggplot2/man/ggproto.Rd | 9 ggplot2-3.5.2/ggplot2/man/guide_colourbar.Rd | 2 ggplot2-3.5.2/ggplot2/man/is_tests.Rd |only ggplot2-3.5.2/ggplot2/man/labs.Rd | 7 ggplot2-3.5.2/ggplot2/man/stat_ellipse.Rd | 2 ggplot2-3.5.2/ggplot2/tests/testthat/Rplots.pdf |binary ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-cartesian.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-flip.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-map.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-transform.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord_sf.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-basic.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-check-overlap.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-positive-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-text-dodged-into-rows-cols.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-vertical-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-zero-breaks.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-zero-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/test-function-args.R | 2 ggplot2-3.5.2/ggplot2/tests/testthat/test-ggsave.R | 6 ggplot2-3.5.2/ggplot2/tests/testthat/test-labels.R | 65 ggplot2-3.5.2/ggplot2/tests/testthat/test-theme.R | 12 ggplot2-3.5.2/ggplot2/tests/testthat/test-utilities-checks.R | 29 ggplot2-3.5.2/ggplot2/vignettes/extending-ggplot2.Rmd | 2 74 files changed, 1394 insertions(+), 1406 deletions(-)
Title: Pre-Processing of 'GENEActiv' Data
Description: Analytics to read in and segment raw 'GENEActiv' accelerometer data into epochs and events.
For more details on the 'GENEActiv' device, see <https://activinsights.com/resources/geneactiv-support-1-2/>.
Author: Joss Langford [aut],
Ian Long [aut],
Jia Ying Chua [aut, cre],
Activinsights Ltd [cph]
Maintainer: Jia Ying Chua <jiayingc@activinsights.com>
Diff between GENEAcore versions 1.0.0 dated 2025-04-01 and 1.0.1 dated 2025-04-09
DESCRIPTION | 8 MD5 | 26 R/MPI_calibrate.R | 560 +++++++------- R/MPI_create.R | 1368 +++++++++++++++++------------------ R/MPI_detect.R | 788 ++++++++++---------- R/aggregate_periods.R | 508 ++++++------ R/geneacore.R | 492 ++++++------ R/sample_binfile.R | 316 ++++---- inst/doc/GENEAcore.Rmd | 990 ++++++++++++------------- tests/testthat/test-MPI_calibrate.R | 3 tests/testthat/test-MPI_create.R | 29 tests/testthat/test-sample_binfile.R | 9 tests/testthat/test-step_counter.R | 93 +- vignettes/GENEAcore.Rmd | 990 ++++++++++++------------- 14 files changed, 3092 insertions(+), 3088 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.10 dated 2025-01-08 and 0.5.11 dated 2025-04-09
DESCRIPTION | 23 ++- MD5 | 52 ++++---- NEWS.md | 6 R/format_value.R | 242 +++++++++++++++++++++++++++------------ R/generics.R | 14 +- R/matrix_form.R | 1 R/mpf_exporters.R | 40 ++++-- R/pagination.R | 36 +++-- R/tostring.R | 18 +- build/vignette.rds |binary inst/WORDLIST | 5 inst/doc/formatters.html | 13 +- man/export_as_pdf.Rd | 7 - man/export_as_rtf.Rd | 4 man/export_as_txt.Rd | 7 - man/format_value.Rd | 12 + man/formatters-package.Rd | 6 man/make_row_df.Rd | 10 + man/matrix_form.Rd | 10 + man/mpf_to_rtf.Rd | 5 man/paginate_indices.Rd | 10 + man/propose_column_widths.Rd | 11 + man/round_fmt.Rd | 15 +- man/tostring.Rd | 7 - man/vert_pag_indices.Rd | 7 - tests/testthat/test-formatters.R | 125 ++++++++++++++++++++ tests/testthat/test-pagination.R | 2 27 files changed, 520 insertions(+), 168 deletions(-)
Title: Easy Management of File Names
Description: Create descriptive file names with ease. New file names are
automatically (but optionally) time stamped and placed in date stamped
directories. Streamline your analysis pipeline with input and output file
names that have informative tags and proper file extensions.
Author: David J. H. Shih [aut, cre]
Maintainer: David J. H. Shih <djh.shih@gmail.com>
Diff between filenamer versions 0.2.4 dated 2024-04-04 and 0.3 dated 2025-04-09
DESCRIPTION | 16 +++++++++----- MD5 | 10 ++++----- R/filename.R | 45 +++++++++++++++++++++++++++++++++++------ R/make_path.R | 4 ++- man/as.character.filename.Rd | 6 ++++- tests/testthat/test_filename.R | 7 ++++++ 6 files changed, 69 insertions(+), 19 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Description: Utility package containing:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear estimates.
3) Restrict functions to a smaller domain.
4) Miscellaneous other utilities.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6.25 dated 2025-01-30 and 4.6.26 dated 2025-04-09
DESCRIPTION | 6 MD5 | 54 +++--- NAMESPACE | 12 + NEWS.md | 8 R/DATA_doby.R | 117 +++++++++++-- R/NAMESPACE_doby.R | 5 R/a_handle_dots_and_symbols.R |only R/by_lmBy.R | 68 +++++--- R/by_splitBy.R | 160 ++++++++++++++---- R/by_transformBy.R | 2 R/doby_utilities.R | 1 R/linear_modelling.R |only R/linest_matrix.R | 15 + R/plot_functions.r | 70 ++++++-- data/child_growth.RData |only data/crickets.RData |binary data/shoes.RData |binary data/wine.RData |only inst/doc/doby.html | 355 +++++++++++++++++++++--------------------- inst/doc/linest_lsmeans.pdf |binary inst/doc/section_fun.html | 222 +++++++++++--------------- man/add_int.Rd |only man/add_pred.Rd |only man/add_resid.Rd |only man/by-lmby.Rd | 8 man/by-split.Rd | 45 +++-- man/child_growth.Rd |only man/crickets.Rd | 21 +- man/data-wine.Rd |only man/income.Rd | 26 --- man/plot_lm.Rd | 8 man/reciprocal.Rd |only man/response.Rd |only man/shoes.Rd |only 34 files changed, 725 insertions(+), 478 deletions(-)
Title: A Repository of Bayesian Networks from the Academic Literature
Description: A collection of Bayesian networks (discrete, Gaussian, and conditional linear Gaussian) collated from recent academic literature. The 'bnRep_summary' object provides an overview of the Bayesian networks in the repository and the package documentation includes details about the variables in each network. A Shiny app to explore the repository can be launched with 'bnRep_app()' and is available online at <https://manueleleonelli.shinyapps.io/bnRep>. Reference: 'M. Leonelli' (2025) <doi:10.1016/j.neucom.2025.129502>.
Author: Manuele Leonelli [aut, cre, cph]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnRep versions 0.0.2 dated 2024-10-01 and 0.0.3 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 10 ++++++---- inst/CITATION | 9 ++++----- inst/doc/overview.html | 2 +- 5 files changed, 19 insertions(+), 18 deletions(-)
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre]
,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 0.1.2 dated 2023-11-27 and 0.3.0 dated 2025-04-09
aedseo-0.1.2/aedseo/R/aedseo.R |only aedseo-0.1.2/aedseo/R/tsd.R |only aedseo-0.1.2/aedseo/R/utils-pipe.R |only aedseo-0.1.2/aedseo/build/partial.rdb |only aedseo-0.1.2/aedseo/inst/doc/aedseo_introduction.R |only aedseo-0.1.2/aedseo/inst/doc/aedseo_introduction.Rmd |only aedseo-0.1.2/aedseo/inst/doc/aedseo_introduction.html |only aedseo-0.1.2/aedseo/man/pipe.Rd |only aedseo-0.1.2/aedseo/man/predict.aedseo.Rd |only aedseo-0.1.2/aedseo/man/summary.aedseo.Rd |only aedseo-0.1.2/aedseo/tests/testthat/test-aedseo.R |only aedseo-0.1.2/aedseo/tests/testthat/test-tsd.R |only aedseo-0.1.2/aedseo/vignettes/aedseo_introduction.Rmd |only aedseo-0.3.0/aedseo/DESCRIPTION | 46 aedseo-0.3.0/aedseo/MD5 | 125 +- aedseo-0.3.0/aedseo/NAMESPACE | 28 aedseo-0.3.0/aedseo/NEWS.md | 64 + aedseo-0.3.0/aedseo/R/0_documentation.R |only aedseo-0.3.0/aedseo/R/1_utils.R |only aedseo-0.3.0/aedseo/R/aedseo-package.R | 18 aedseo-0.3.0/aedseo/R/autoplot.R | 587 ++++++++-- aedseo-0.3.0/aedseo/R/combined_seasonal_output.R |only aedseo-0.3.0/aedseo/R/consecutive_growth_warnings.R |only aedseo-0.3.0/aedseo/R/epi_calendar.R | 46 aedseo-0.3.0/aedseo/R/fit_growth_rate.R | 20 aedseo-0.3.0/aedseo/R/fit_percentiles.R |only aedseo-0.3.0/aedseo/R/generate_seasonal_data.R |only aedseo-0.3.0/aedseo/R/historical_summary.R |only aedseo-0.3.0/aedseo/R/plot.R | 89 - aedseo-0.3.0/aedseo/R/predict.R | 88 - aedseo-0.3.0/aedseo/R/seasonal_burden_levels.R |only aedseo-0.3.0/aedseo/R/seasonal_onset.R |only aedseo-0.3.0/aedseo/R/summary.R | 286 +++- aedseo-0.3.0/aedseo/R/to_time_series.R |only aedseo-0.3.0/aedseo/README.md | 61 - aedseo-0.3.0/aedseo/build/vignette.rds |binary aedseo-0.3.0/aedseo/inst/doc/aedseo.R |only aedseo-0.3.0/aedseo/inst/doc/aedseo.Rmd |only aedseo-0.3.0/aedseo/inst/doc/aedseo.html |only aedseo-0.3.0/aedseo/inst/doc/burden_levels.R |only aedseo-0.3.0/aedseo/inst/doc/burden_levels.Rmd |only aedseo-0.3.0/aedseo/inst/doc/burden_levels.html |only aedseo-0.3.0/aedseo/inst/doc/generate_seasonal_wave.R |only aedseo-0.3.0/aedseo/inst/doc/generate_seasonal_wave.Rmd |only aedseo-0.3.0/aedseo/inst/doc/generate_seasonal_wave.html |only aedseo-0.3.0/aedseo/inst/doc/seasonal_onset.R |only aedseo-0.3.0/aedseo/inst/doc/seasonal_onset.Rmd |only aedseo-0.3.0/aedseo/inst/doc/seasonal_onset.html |only aedseo-0.3.0/aedseo/man/aedseo-package.Rd | 7 aedseo-0.3.0/aedseo/man/aedseo.Rd | 81 - aedseo-0.3.0/aedseo/man/autoplot.Rd | 206 ++- aedseo-0.3.0/aedseo/man/combined_seasonal_output.Rd |only aedseo-0.3.0/aedseo/man/consecutive_growth_warnings.Rd |only aedseo-0.3.0/aedseo/man/epi_calendar.Rd | 27 aedseo-0.3.0/aedseo/man/figures/lifecycle-archived.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-defunct.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-deprecated.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-experimental.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-maturing.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-questioning.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-soft-deprecated.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-stable.svg | 58 aedseo-0.3.0/aedseo/man/figures/lifecycle-superseded.svg | 42 aedseo-0.3.0/aedseo/man/fit_growth_rate.Rd | 21 aedseo-0.3.0/aedseo/man/fit_percentiles.Rd |only aedseo-0.3.0/aedseo/man/generate_seasonal_data.Rd |only aedseo-0.3.0/aedseo/man/historical_summary.Rd |only aedseo-0.3.0/aedseo/man/plot.Rd | 79 - aedseo-0.3.0/aedseo/man/predict.tsd_onset.Rd |only aedseo-0.3.0/aedseo/man/seasonal_burden_levels.Rd |only aedseo-0.3.0/aedseo/man/seasonal_onset.Rd |only aedseo-0.3.0/aedseo/man/summary.tsd_burden_levels.Rd |only aedseo-0.3.0/aedseo/man/summary.tsd_onset.Rd |only aedseo-0.3.0/aedseo/man/to_time_series.Rd |only aedseo-0.3.0/aedseo/man/tsd.Rd | 59 - aedseo-0.3.0/aedseo/tests/testthat.R | 24 aedseo-0.3.0/aedseo/tests/testthat/helper-setup.R |only aedseo-0.3.0/aedseo/tests/testthat/test-combined_seasonal_output.R |only aedseo-0.3.0/aedseo/tests/testthat/test-consecutive_growth_warnings.R |only aedseo-0.3.0/aedseo/tests/testthat/test-epi_calendar.R | 50 aedseo-0.3.0/aedseo/tests/testthat/test-fit_growth_rate.R | 8 aedseo-0.3.0/aedseo/tests/testthat/test-fit_percentiles.R |only aedseo-0.3.0/aedseo/tests/testthat/test-generate_seasonal_data.R |only aedseo-0.3.0/aedseo/tests/testthat/test-historical_summary.R |only aedseo-0.3.0/aedseo/tests/testthat/test-predict.R | 195 ++- aedseo-0.3.0/aedseo/tests/testthat/test-seasonal_burden_levels.R |only aedseo-0.3.0/aedseo/tests/testthat/test-seasonal_onset.R |only aedseo-0.3.0/aedseo/tests/testthat/test-summary.R | 101 + aedseo-0.3.0/aedseo/tests/testthat/test-to_time_series.R |only aedseo-0.3.0/aedseo/vignettes/aedseo.Rmd |only aedseo-0.3.0/aedseo/vignettes/burden_levels.Rmd |only aedseo-0.3.0/aedseo/vignettes/generate_seasonal_wave.Rmd |only aedseo-0.3.0/aedseo/vignettes/seasonal_onset.Rmd |only 93 files changed, 1749 insertions(+), 961 deletions(-)
Title: Computing Graph Structures on WikiPathways
Description: Converts pathways from 'WikiPathways' GPML format or
'KEGG' KGML format into 'igraph' objects. Includes tools to find all
cycles in the resulting graphs and determine which ones involve
negative feedback (inhibition).
Author: Kevin R. Coombes [aut, cre],
Polina Bombina [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between WayFindR versions 0.1.2 dated 2024-04-10 and 0.3.1 dated 2025-04-09
WayFindR-0.1.2/WayFindR/inst/doc/WayFindR_graphs.R |only WayFindR-0.1.2/WayFindR/inst/doc/WayFindR_graphs.Rmd |only WayFindR-0.1.2/WayFindR/inst/doc/WayFindR_graphs.html |only WayFindR-0.1.2/WayFindR/vignettes/WayFindR_graphs.Rmd |only WayFindR-0.3.1/WayFindR/DESCRIPTION | 25 +- WayFindR-0.3.1/WayFindR/MD5 | 49 +++-- WayFindR-0.3.1/WayFindR/NAMESPACE | 25 ++ WayFindR-0.3.1/WayFindR/R/05-toIgraph.R | 2 WayFindR-0.3.1/WayFindR/R/09-ellipse.R |only WayFindR-0.3.1/WayFindR/R/10-keggUtil.R |only WayFindR-0.3.1/WayFindR/R/11-graphNEL.R |only WayFindR-0.3.1/WayFindR/R/12-kgml.R |only WayFindR-0.3.1/WayFindR/R/sysdata.rda |binary WayFindR-0.3.1/WayFindR/R/zzz.R |only WayFindR-0.3.1/WayFindR/build/vignette.rds |binary WayFindR-0.3.1/WayFindR/data/edgeColors.rda |binary WayFindR-0.3.1/WayFindR/data/edgeTypes.rda |binary WayFindR-0.3.1/WayFindR/data/nodeColors.rda |binary WayFindR-0.3.1/WayFindR/data/nodeShapes.rda |binary WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_getStarted.html | 121 +++++++------- WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_metrics.R |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_metrics.Rmd |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_metrics.html |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_plots.R |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_plots.Rmd |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_plots.html |only WayFindR-0.3.1/WayFindR/inst/pathways/kegg_hsa00510.xml |only WayFindR-0.3.1/WayFindR/inst/profile |only WayFindR-0.3.1/WayFindR/man/02-util.Rd | 4 WayFindR-0.3.1/WayFindR/man/03-main.Rd | 80 +++++---- WayFindR-0.3.1/WayFindR/man/10-kgml-util.Rd |only WayFindR-0.3.1/WayFindR/man/11-coerce.Rd |only WayFindR-0.3.1/WayFindR/tests/06-testShapes.R |only WayFindR-0.3.1/WayFindR/tests/10-testKeggUtil.R |only WayFindR-0.3.1/WayFindR/tests/11-testkgml.R |only WayFindR-0.3.1/WayFindR/vignettes/WayFindR_metrics.Rmd |only WayFindR-0.3.1/WayFindR/vignettes/WayFindR_plots.Rmd |only 37 files changed, 182 insertions(+), 124 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Author: Richard S Judson [ctb, ths] ,
Dayne L Filer [aut],
Jason Brown [ctb] ,
Sarah E Davidson-Fritz [ctb] ,
Madison Feshuk [cre] ,
Carter Thunes [ctb],
Ashley Ko [ctb],
Kelly Carstens [ctb] ,
Todd Zurlinden [ctb] ,
Lori Kolaczkowski [ctb],
Kurt Dunham [ctb [...truncated...]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between tcpl versions 3.2.0 dated 2024-10-09 and 3.2.1 dated 2025-04-09
DESCRIPTION | 18 MD5 | 10 NEWS.md | 4 build/vignette.rds |binary inst/doc/Introduction_Appendices.html | 2813 +++++++++++++++++----------------- tests/testthat/_snaps/tcplDefine.md | 350 ++-- 6 files changed, 1610 insertions(+), 1585 deletions(-)
Title: Quantile-Frequency Analysis (QFA) of Time Series
Description: Quantile-frequency analysis (QFA) of time series based on trigonometric quantile regression.
Spline quantile regression (SQR) for regression coefficient estimation.
References:
[1] Li, T.-H. (2012) "Quantile periodograms," Journal of the American Statistical
Association, 107, 765–776, <doi:10.1080/01621459.2012.682815>.
[2] Li, T.-H. (2014) Time Series with Mixed Spectra, CRC Press, <doi:10.1201/b15154>
[3] Li, T.-H. (2022) "Quantile Fourier transform, quantile series, and nonparametric
estimation of quantile spectra," <doi:10.48550/arXiv.2211.05844>.
[4] Li, T.-H. (2024) "Quantile crossing spectrum and spline autoregression
estimation," <doi:10.48550/arXiv.2412.02513>.
[5] Li, T.-H. (2024) "Spline autoregression method for estimation of quantile spectrum,"
<doi:10.48550/arXiv.2412.17163>.
[6] Li, T.-H., and Megiddo, N. (2025) "Spline quantile regression,"
<doi:10.48550/arXiv.2501.03883>.
Author: Ta-Hsin Li [cre, aut]
Maintainer: Ta-Hsin Li <thl024@outlook.com>
Diff between qfa versions 4.0 dated 2025-01-08 and 4.1 dated 2025-04-09
qfa-4.0/qfa/R/qfa4.0.R |only qfa-4.1/qfa/DESCRIPTION | 16 ++++---- qfa-4.1/qfa/MD5 | 66 ++++++++++++++++++------------------ qfa-4.1/qfa/R/qfa4.1.R |only qfa-4.1/qfa/man/per.Rd | 2 - qfa-4.1/qfa/man/qacf.Rd | 2 - qfa-4.1/qfa/man/qcser.Rd | 2 - qfa-4.1/qfa/man/qdft.Rd | 2 - qfa-4.1/qfa/man/qdft2qacf.Rd | 2 - qfa-4.1/qfa/man/qdft2qper.Rd | 2 - qfa-4.1/qfa/man/qdft2qser.Rd | 2 - qfa-4.1/qfa/man/qfa.plot.Rd | 2 - qfa-4.1/qfa/man/qkl.divergence.Rd | 2 - qfa-4.1/qfa/man/qper.Rd | 2 - qfa-4.1/qfa/man/qper2.Rd | 2 - qfa-4.1/qfa/man/qser.Rd | 2 - qfa-4.1/qfa/man/qser2ar.Rd | 2 - qfa-4.1/qfa/man/qser2qacf.Rd | 2 - qfa-4.1/qfa/man/qser2sar.Rd | 2 - qfa-4.1/qfa/man/qspec.ar.Rd | 2 - qfa-4.1/qfa/man/qspec.lw.Rd | 2 - qfa-4.1/qfa/man/qspec.sar.Rd | 2 - qfa-4.1/qfa/man/qspec2qcoh.Rd | 2 - qfa-4.1/qfa/man/sar.eq.bootstrap.Rd | 2 - qfa-4.1/qfa/man/sar.eq.test.Rd | 2 - qfa-4.1/qfa/man/sar.gc.bootstrap.Rd | 2 - qfa-4.1/qfa/man/sar.gc.coef.Rd | 2 - qfa-4.1/qfa/man/sar.gc.test.Rd | 2 - qfa-4.1/qfa/man/sqdft.Rd | 8 ++-- qfa-4.1/qfa/man/sqdft.fit.Rd | 6 +-- qfa-4.1/qfa/man/sqr.Rd | 6 +-- qfa-4.1/qfa/man/sqr.fit.Rd | 4 +- qfa-4.1/qfa/man/sqr.fit.optim.Rd | 2 - qfa-4.1/qfa/man/tqr.fit.Rd | 2 - qfa-4.1/qfa/man/tsqr.fit.Rd | 2 - 35 files changed, 81 insertions(+), 79 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland [aut, cre]
,
Tahir Mehmood [ctb],
Solve Saeboe [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.12 dated 2024-05-22 and 0.9.13 dated 2025-04-09
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/REP.R | 2 ++ R/T2.R | 7 ++++++- R/filters.R | 2 +- R/stpls.R | 7 +++++-- man/VIP.Rd | 2 +- man/rep_pls.Rd | 2 ++ man/stpls.Rd | 7 +++++-- 10 files changed, 40 insertions(+), 21 deletions(-)
Title: Photosynthetic Gas Exchange Analysis
Description: Read, process, fit, and analyze photosynthetic gas exchange
measurements. Documentation is provided by several vignettes; also see
Lochocki, Salesse-Smith, & McGrath (2025) <doi:10.1111/pce.15501>.
Author: Edward B. Lochocki [cre, aut] ,
Coralie E. Salesse-Smith [aut]
,
Justin M. McGrath [aut] ,
PhotoGEA authors [cph]
Maintainer: Edward B. Lochocki <eloch@illinois.edu>
Diff between PhotoGEA versions 1.3.1 dated 2025-04-08 and 1.3.2 dated 2025-04-09
DESCRIPTION | 8 ++-- MD5 | 23 +++++++------ NAMESPACE | 3 + NEWS.md | 8 +++- R/check_response_curve_data.R | 19 ++++++----- R/exdf.R | 50 ++++++++++++++++++++---------- README.md | 4 ++ inst/doc/PhotoGEA.html | 2 - man/read_cr3000.Rd | 2 - man/read_licor_6800_Excel.Rd | 4 +- man/read_licor_6800_plaintext.Rd | 2 - tests/testthat/test-factorize_id_column.R | 15 +++++++-- tests/testthat/test-rbind.exdf.R |only 13 files changed, 91 insertions(+), 49 deletions(-)
Title: A Nondecimated Lifting Transform for Signal Denoising
Description: Uses a modified lifting algorithm on which it builds the
nondecimated lifting transform. It has applications in wavelet
shrinkage.
Author: Marina Knight [aut],
Matt Nunes [aut, cre]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between nlt versions 2.2-1 dated 2018-07-10 and 2.2-2 dated 2025-04-09
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- man/fwtnpperm.Rd | 4 ++-- man/transmatdualperm.Rd | 6 +++--- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Named Capture to Data Tables
Description: User-friendly functions for extracting a data
table (row for each match, column for each group)
from non-tabular text data using regular expressions,
and for melting columns that match a regular expression.
Patterns are defined using a readable syntax
that makes it easy to build complex patterns
in terms of simpler, re-usable sub-patterns.
Named R arguments are translated to column names
in the output; capture groups without names are used
internally in order to provide a standard interface
to three regular expression 'C' libraries
('PCRE', 'RE2', 'ICU').
Output can also include numeric columns via
user-specified type conversion functions.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between nc versions 2025.1.21 dated 2025-01-21 and 2025.3.24 dated 2025-04-09
DESCRIPTION | 6 MD5 | 28 NAMESPACE | 1 NEWS | 4 R/alevels.R |only build/vignette.rds |binary inst/doc/v0-overview.html | 372 +++--- inst/doc/v1-capture-first.html | 1278 +++++++++++---------- inst/doc/v2-capture-all.html | 878 +++++++------- inst/doc/v3-capture-melt.html | 956 ++++++++------- inst/doc/v4-comparisons.html | 1942 ++++++++++++++++---------------- inst/doc/v5-helpers.html | 382 +++--- inst/doc/v6-engines.html | 317 +++-- inst/doc/v7-capture-glob.html | 957 ++++++++------- man/alevels.Rd |only tests/testthat/test-CRAN-alternatives.R | 26 16 files changed, 3791 insertions(+), 3356 deletions(-)
Title: Resampling Algorithms for 'mlr3' Framework
Description: A supervised learning algorithm inputs a train set,
and outputs a prediction function, which can be used on a test set.
If each data point belongs to a subset
(such as geographic region, year, etc), then
how do we know if subsets are similar enough so that
we can get accurate predictions on one subset,
after training on Other subsets?
And how do we know if training on All subsets would improve
prediction accuracy, relative to training on the Same subset?
SOAK, Same/Other/All K-fold cross-validation, <doi:10.48550/arXiv.2410.08643>
can be used to answer these question, by fixing a test subset,
training models on Same/Other/All subsets, and then
comparing test error rates (Same versus Other and Same versus All).
Also provides code for estimating how many train samples
are required to get accurate predictions on a test set.
Author: Toby Hocking [aut, cre] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Jakob Richter [ctb] ,
Patrick Schratz [ctb] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [ctb],
Florian Pfisterer [ctb] ,
Raphael Sonabend [ctb] , [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between mlr3resampling versions 2024.9.6 dated 2024-09-11 and 2025.3.30 dated 2025-04-09
DESCRIPTION | 40 MD5 | 52 NAMESPACE | 11 NEWS | 178 R/ResamplingBase.R | 166 R/ResamplingSameOtherCV.R | 244 R/ResamplingSameOtherSizesCV.R | 357 R/ResamplingVariableSizeTrainCV.R | 190 R/pvalue.R |only R/score.R | 50 R/zzz.R | 37 build/vignette.rds |binary inst/doc/Newer_resamplers.R | 1069 - inst/doc/Newer_resamplers.Rmd | 1671 +- inst/doc/Newer_resamplers.html | 3717 ++-- inst/doc/Older_resamplers.R | 1944 +- inst/doc/Older_resamplers.Rmd | 2888 +-- inst/doc/Older_resamplers.html |26117 ++++++++++++++++++----------------- man/AZtrees.Rd | 120 man/ResamplingSameOtherCV.Rd | 355 man/ResamplingSameOtherSizesCV.Rd | 422 man/ResamplingVariableSizeTrainCV.Rd | 310 man/pvalue.Rd |only man/score.Rd | 139 tests/testthat.R | 4 tests/testthat/test-CRAN.R | 888 - vignettes/Newer_resamplers.Rmd | 1671 +- vignettes/Older_resamplers.Rmd | 2888 +-- 28 files changed, 23573 insertions(+), 21955 deletions(-)
More information about mlr3resampling at CRAN
Permanent link
Title: Wrapper for 'minimap2'
Description: Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li <me@liheng.org>.
*SPECIAL NOTES
1. Examples can only be run from 'GitHub' installation.
2. 'conda' or 'mamba' must be used to install 'minimapR' on your system.
3. For Windows users, 'minimap2' and 'samtools' can be installed via MSYS2, instructions are provided when 'minimap2_installation()' is run.
Li, Heng (2018) <doi:10.1093/bioinformatics/bty191> "Minimap2: pairwise alignment for nucleotide sequences".
Author: Jake Reed [aut, cre] ,
Pradyun Pulipaka [ctb]
Maintainer: Jake Reed <hreed.ga@gmail.com>
Diff between minimapR versions 0.0.1.1 dated 2025-03-30 and 0.0.1.3 dated 2025-04-09
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/minimapR-helper.R | 16 ++++++++++++++-- inst/doc/minimapR.html | 22 +++++++++++----------- 4 files changed, 33 insertions(+), 20 deletions(-)
Title: Continuous Confidence Interval Plots using t-Distribution
Description: Provides an extension to 'ggplot2'
(Wickham, 2016, <doi:10.1007/978-3-319-24277-4>) for creating two types of
continuous confidence interval plots (Violin CI and Gradient CI plots),
typically for the sample mean. These plots contain multiple user-defined
confidence areas with varying colours, defined by the underlying
t-distribution used to compute standard confidence intervals for the mean of
the normal distribution when the variance is unknown. Two types of plots are
available, a gradient plot with rectangular areas, and a violin plot where
the shape (horizontal width) is defined by the probability density function
of the t-distribution. These visualizations are studied in
(Helske, Helske, Cooper, Ynnerman, and Besancon, 2021)
<doi:10.1109/TVCG.2021.3073466>.
Author: Jouni Helske [aut, cre]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between ggstudent versions 0.1.1-1 dated 2020-05-11 and 0.1.2 dated 2025-04-09
DESCRIPTION | 30 ++++++++++++++---------- MD5 | 12 ++++----- R/statStudent.R | 17 ++++++++----- README.md | 15 ++++++++---- man/GeomStudent.Rd | 4 ++- man/StatStudent.Rd | 4 ++- man/geom_student.Rd | 64 ++++++++++++++++++++-------------------------------- 7 files changed, 75 insertions(+), 71 deletions(-)
Title: Rename and Encode Data Frames Using External Crosswalk Files
Description: A pair of functions for renaming and encoding data frames
using external crosswalk files. It is especially useful when
constructing master data sets from multiple smaller data
sets that do not name or encode variables consistently
across files. Based on similar commands in 'Stata'.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between crosswalkr versions 0.2.6 dated 2020-01-08 and 0.3.0 dated 2025-04-09
DESCRIPTION | 26 +- MD5 | 33 +-- NEWS.md | 4 R/crosswalkr.R | 5 R/data.R | 22 ++ build/vignette.rds |binary data/sttercrosswalk.rda |only inst/doc/collapse.R | 2 inst/doc/collapse.Rmd | 2 inst/doc/collapse.html | 230 +++++++++++++----------- inst/doc/crosswalkr.R | 6 inst/doc/crosswalkr.html | 375 +++++++++++++++++++++++----------------- inst/extdata/sttercrosswalk.rda |only man/crosswalkr.Rd | 14 + man/encodefrom.Rd | 4 man/renamefrom.Rd | 4 man/stcrosswalk.Rd | 6 man/sttercrosswalk.Rd |only vignettes/collapse.Rmd | 2 19 files changed, 431 insertions(+), 304 deletions(-)
Title: Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent
for Irregularly Sampled Time Series
Description: Implementation of Hurst exponent estimators based on complex-valued lifting wavelet energy from Knight, M. I and Nunes, M. A. (2018) <doi:10.1007/s11222-018-9820-8>.
Author: Matt Nunes [aut, cre],
Marina Knight [aut]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between CliftLRD versions 0.1-1 dated 2018-07-18 and 0.1-2 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/CliftLRD-package.Rd | 2 +- man/liftHurstC.Rd | 8 ++++---- man/liftHurstCC.Rd | 8 ++++---- man/meanC.Rd | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2025.1.21 dated 2025-01-21 and 2025.4.1 dated 2025-04-09
DESCRIPTION | 6 MD5 | 22 +- NEWS | 4 R/predict.R | 13 + build/vignette.rds |binary inst/doc/Custom_Plots.html | 200 +++++++++++--------------- inst/doc/Custom_References.html | 278 ++++++++++++++++-------------------- inst/doc/Custom_Units.html | 213 ++++++++++++--------------- inst/doc/cum_median.html | 210 +++++++++++---------------- inst/doc/regex.html | 238 +++++++++++++------------------ inst/doc/sparse.html | 306 +++++++++++++++++++--------------------- tests/testthat/test-CRAN.R | 5 12 files changed, 677 insertions(+), 818 deletions(-)
Title: Conduct Simulation Studies with a Minimal Amount of Source Code
Description: Tool for statistical simulations that have two components.
One component generates the data and the other one
analyzes the data. The main aims of the package are the reduction
of the administrative source code (mainly loops and management code for the
results) and a simple applicability of the package that allows the user to
quickly learn how to work with it. Parallel computing is
also supported. Finally, convenient functions are provided to summarize the
simulation results.
Author: Marsel Scheer [aut, cre]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between simTool versions 1.1.7 dated 2020-09-22 and 1.1.8 dated 2025-04-09
DESCRIPTION | 13 MD5 | 24 - NEWS.md |only R/expand_tibble.R | 2 R/extract_fun_and_parameter.R | 11 R/print.eval_tibbles.R | 1 README.md |only build/vignette.rds |binary inst/doc/simTool.R | 350 +++++++-------- inst/doc/simTool.Rmd | 8 inst/doc/simTool.html | 923 +++++++++++++++++++++++++----------------- man/expand_tibble.Rd | 2 man/print.eval_tibbles.Rd | 1 vignettes/simTool.Rmd | 8 14 files changed, 781 insertions(+), 562 deletions(-)
Title: Model-Free Covariate Selection
Description: Model-free selection of covariates under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011). Marginal co-ordinate hypothesis testing is used in situations where all covariates are continuous while kernel-based smoothing appropriate for mixed data is used otherwise.
Author: Jenny Haeggstroem [aut, cre],
Emma Persson [aut],
Sandy Weisberg [aut]
Maintainer: Jenny Haeggstroem <jenny.haggstrom@umu.se>
Diff between CovSel versions 1.2.1 dated 2015-11-09 and 1.2.2 dated 2025-04-09
DESCRIPTION | 21 +++++++++++++++------ MD5 | 12 ++++++++---- NAMESPACE | 9 +++++++-- R/dr.R |only R/psave.R |only R/psir.R |only R/zzz.R |only man/cov.sel.Rd | 2 +- man/lalonde.Rd | 2 +- 9 files changed, 32 insertions(+), 14 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/data-documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between rscorecard versions 0.30.0 dated 2024-10-23 and 0.31.0 dated 2025-04-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 10 +++++++--- R/sysdata.rda |binary man/rscorecard.Rd | 2 +- tests/testthat/test-get.R | 6 +++--- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Model Infectious Disease Parameters from Serosurveys
Description: An easy-to-use and efficient tool to estimate infectious diseases parameters using serological data. Implemented models include SIR models (basic_sir_model(), static_sir_model(), mseir_model(), sir_subpops_model()), parametric models (polynomial_model(), fp_model()), nonparametric models (lp_model()), semiparametric models (penalized_splines_model()), hierarchical models (hierarchical_bayesian_model()).
The package is based on the book "Modeling Infectious Disease Parameters Based on Serological and Social Contact Data: A Modern Statistical Perspective" (Hens, Niel & Shkedy, Ziv & Aerts, Marc & Faes, Christel & Damme, Pierre & Beutels, Philippe., 2013) <doi:10.1007/978-1-4614-4072-7>.
Author: Anh Phan Truong Quynh [aut, cre],
Nguyen Pham Nguyen The [aut],
Long Bui Thanh [aut],
Tuyen Huynh [aut],
Thinh Ong [aut] ,
Marc Choisy [aut]
Maintainer: Anh Phan Truong Quynh <anhptq@oucru.org>
Diff between serosv versions 1.0.1 dated 2024-10-18 and 1.1.0 dated 2025-04-09
DESCRIPTION | 21 +- MD5 | 142 ++++++++++-------- NAMESPACE | 14 + NEWS.md | 5 R/compare_models.R |only R/correct_prevalence.R |only R/fractional_polynomial_models.R | 40 ++--- R/hierarchical_bayesian_model.R | 27 +-- R/mixture_model.R | 2 R/nonparametric.R | 28 +-- R/plots.R | 15 + R/polynomial_models.R | 66 ++------ R/semiparametric_models.R | 29 +-- R/stanmodels.R | 3 R/utils.R | 49 ++++++ R/weibull_model.R | 30 +-- README.md | 57 ++++++- build/vignette.rds |binary inst/doc/data_transformation.Rmd | 2 inst/doc/data_transformation.html | 2 inst/doc/hierarchical_model.R | 4 inst/doc/hierarchical_model.Rmd | 4 inst/doc/hierarchical_model.html | 136 +++++++++-------- inst/doc/imperfect_test.R |only inst/doc/imperfect_test.Rmd |only inst/doc/imperfect_test.html |only inst/doc/linelisting_vs_aggregated.R |only inst/doc/linelisting_vs_aggregated.Rmd |only inst/doc/linelisting_vs_aggregated.html |only inst/doc/model_selection.R |only inst/doc/model_selection.Rmd |only inst/doc/model_selection.html |only inst/doc/nonparametric_model.R | 8 - inst/doc/nonparametric_model.Rmd | 8 - inst/doc/nonparametric_model.html | 10 - inst/doc/parametric_model.R | 40 +---- inst/doc/parametric_model.Rmd | 44 +---- inst/doc/parametric_model.html | 165 +++------------------ inst/doc/semiparametric_model.R | 11 - inst/doc/semiparametric_model.Rmd | 15 + inst/doc/semiparametric_model.html | 75 ++++----- inst/doc/visualizing_model.R | 10 - inst/doc/visualizing_model.Rmd | 10 - inst/doc/visualizing_model.html | 42 ++--- inst/stan/fra_2.stan | 4 inst/stan/fra_3.stan | 4 inst/stan/log_logistic.stan | 4 inst/stan/prevalence_correction.stan |only man/compare_models.Rd |only man/correct_prevalence.Rd |only man/farrington_model.Rd | 19 -- man/figures/README-unnamed-chunk-48-1.png |only man/figures/README-unnamed-chunk-49-1.png |only man/figures/README-unnamed-chunk-49-2.png |only man/find_best_fp_powers.Rd | 10 - man/fp_model.Rd | 12 - man/hierarchical_bayesian_model.Rd | 15 - man/lp_model.Rd | 21 -- man/penalized_spline_model.Rd | 16 -- man/polynomial_model.Rd | 28 --- man/transform_data.Rd | 4 man/weibull_model.Rd | 17 -- src/RcppExports.cpp | 2 src/stanExports_fra_2.h | 8 - src/stanExports_fra_3.h | 8 - src/stanExports_log_logistic.h | 8 - src/stanExports_prevalence_correction.cc |only src/stanExports_prevalence_correction.h |only tests/testthat/test-fractional-polynomial-models.R | 6 tests/testthat/test-hierarchical_bayesian_model.R | 6 tests/testthat/test-nonparametric.R | 6 tests/testthat/test-penalized_spline_model.R | 23 +- tests/testthat/test-polynomial-models.R | 27 +-- tests/testthat/test-weibull-model.R | 8 - vignettes/data_transformation.Rmd | 2 vignettes/hierarchical_model.Rmd | 4 vignettes/imperfect_test.Rmd |only vignettes/linelisting_vs_aggregated.Rmd |only vignettes/model_selection.Rmd |only vignettes/nonparametric_model.Rmd | 8 - vignettes/parametric_model.Rmd | 44 +---- vignettes/semiparametric_model.Rmd | 15 + vignettes/visualizing_model.Rmd | 10 - 83 files changed, 640 insertions(+), 813 deletions(-)