Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The [...truncated...]
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.26.25 dated 2023-05-17 and 2.26.26 dated 2023-05-30
DESCRIPTION | 6 - MD5 | 18 ++-- inst/doc/stanmath.R | 4 - inst/doc/stanmath.Rmd | 14 +-- inst/doc/stanmath.html | 18 ++-- inst/include/stan/math/fwd/core/operator_multiplication.hpp | 47 ++++++++++++ inst/include/stan/math/rev/core/operator_multiplication.hpp | 43 ++++++++++ inst/include/sundials/sundials_memory.h | 4 - src/sundials/sundials_memory.c | 4 - vignettes/stanmath.Rmd | 14 +-- 10 files changed, 131 insertions(+), 41 deletions(-)
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis (<https://www.reconverse.org>).
Author: Tim Taylor [aut, cre] ,
Thibaut Jombart [ctb]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 2.0.0 dated 2023-03-17 and 2.1.0 dated 2023-05-30
DESCRIPTION | 6 +- MD5 | 20 +++--- NEWS.md | 26 ++++++++ R/complete_dates.R | 51 ++++++++++++++--- R/incidence.R | 24 +++++++- R/utils.R | 22 +++++++ inst/doc/incidence2.Rmd | 1 inst/doc/incidence2.html | 139 +++++++++++++++++++++++------------------------ man/complete_dates.Rd | 24 +++++--- man/incidence.Rd | 14 +++- vignettes/incidence2.Rmd | 1 11 files changed, 224 insertions(+), 104 deletions(-)
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Author: Kenneth Hoehn [aut, cre],
Cole Jensen [ctb],
Susanna Marquez [ctb],
Jason Vander Heiden [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.hoehn@yale.edu>
Diff between dowser versions 1.1.0 dated 2022-10-04 and 1.2.0 dated 2023-05-30
dowser-1.1.0/dowser/vignettes/isotype_model.txt |only dowser-1.1.0/dowser/vignettes/temp |only dowser-1.2.0/dowser/DESCRIPTION | 29 dowser-1.2.0/dowser/MD5 | 233 dowser-1.2.0/dowser/NAMESPACE | 5 dowser-1.2.0/dowser/R/Classes.R | 2 dowser-1.2.0/dowser/R/Clones.R | 1799 +++-- dowser-1.2.0/dowser/R/Germlines.R | 820 +- dowser-1.2.0/dowser/R/Plotting.R | 8 dowser-1.2.0/dowser/R/Statistics.R | 59 dowser-1.2.0/dowser/R/TreeFunctions.R | 4431 ++++++++------ dowser-1.2.0/dowser/R/zzz.R |only dowser-1.2.0/dowser/build/vignette.rds |binary dowser-1.2.0/dowser/inst/CITATION | 2 dowser-1.2.0/dowser/inst/doc/Building-Trees-Vignette.Rmd | 1 dowser-1.2.0/dowser/inst/doc/Building-Trees-Vignette.pdf |binary dowser-1.2.0/dowser/inst/doc/Discrete-Trait-Vignette.Rmd | 5 dowser-1.2.0/dowser/inst/doc/Discrete-Trait-Vignette.pdf |binary dowser-1.2.0/dowser/inst/doc/Germlines-Vignette.Rmd | 3 dowser-1.2.0/dowser/inst/doc/Germlines-Vignette.pdf |binary dowser-1.2.0/dowser/inst/doc/Measurable-Evolution.Rmd | 1 dowser-1.2.0/dowser/inst/doc/Measurable-Evolution.pdf |binary dowser-1.2.0/dowser/inst/doc/Plotting-Trees-Vignette.Rmd | 1 dowser-1.2.0/dowser/inst/doc/Plotting-Trees-Vignette.pdf |binary dowser-1.2.0/dowser/inst/doc/Quickstart-Vignette.Rmd | 1 dowser-1.2.0/dowser/inst/doc/Quickstart-Vignette.pdf |binary dowser-1.2.0/dowser/inst/doc/Sequences-Vignette.Rmd | 1 dowser-1.2.0/dowser/inst/doc/Sequences-Vignette.pdf |binary dowser-1.2.0/dowser/man/airrClone-class.Rd | 2 dowser-1.2.0/dowser/man/buildIgphyml.Rd | 6 dowser-1.2.0/dowser/man/buildPML.Rd | 11 dowser-1.2.0/dowser/man/buildRAxML.Rd |only dowser-1.2.0/dowser/man/calcRF.Rd |only dowser-1.2.0/dowser/man/findSwitches.Rd | 5 dowser-1.2.0/dowser/man/formatClones.Rd | 96 dowser-1.2.0/dowser/man/getBootstraps.Rd |only dowser-1.2.0/dowser/man/getSeq.Rd | 2 dowser-1.2.0/dowser/man/getSubTaxa.Rd |only dowser-1.2.0/dowser/man/getTrees.Rd | 28 dowser-1.2.0/dowser/man/rerootTree.Rd | 4 dowser-1.2.0/dowser/vignettes/Building-Trees-Vignette.Rmd | 1 dowser-1.2.0/dowser/vignettes/Discrete-Trait-Vignette.Rmd | 5 dowser-1.2.0/dowser/vignettes/Germlines-Vignette.Rmd | 3 dowser-1.2.0/dowser/vignettes/Measurable-Evolution.Rmd | 1 dowser-1.2.0/dowser/vignettes/Plotting-Trees-Vignette.Rmd | 1 dowser-1.2.0/dowser/vignettes/Quickstart-Vignette.Rmd | 1 dowser-1.2.0/dowser/vignettes/Sequences-Vignette.Rmd | 1 47 files changed, 4393 insertions(+), 3175 deletions(-)
Title: Generate Code Lists for the OMOP Common Data Model
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 1.2.0 dated 2023-05-04 and 1.3.0 dated 2023-05-30
DESCRIPTION | 6 - MD5 | 15 ++- NAMESPACE | 1 NEWS.md | 3 R/getICD10StandardCodes.R |only R/mockVocabRef.R | 39 +++++++- inst/doc/a01_Introduction_to_CodelistGenerator.html | 76 ++++++++--------- inst/doc/a02_Candidate_codes_OA.html | 88 +++++++++----------- man/getICD10StandardCodes.Rd |only tests/testthat/test-getICD10StandardCodes.R |only 10 files changed, 129 insertions(+), 99 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Accessing the Flipside Crypto ShroomDK API
Description: Programmatic access to Flipside Crypto data via the Compass RPC API: <https://api-docs.flipsidecrypto.xyz/>. As simple as auto_paginate_query() but with core functions as needed for troubleshooting. Note, 0.1.1 support deprecated 2023-05-31.
Author: Carlos Mercado
Maintainer: Carlos Mercado <carlos.mercado@flipsidecrypto.com>
Diff between shroomDK versions 0.2.0 dated 2023-05-11 and 0.2.1 dated 2023-05-30
DESCRIPTION | 6 - MD5 | 20 ++--- R/auto_paginate_query.R | 67 +++++++++++++++-- R/clean_query.R | 5 - R/create_query_token.R | 17 ++-- R/get_query_from_token.R | 43 +++++------ README.md | 169 ++++++++++++++++++++++++++++++-------------- man/auto_paginate_query.Rd | 19 +++- man/clean_query.Rd | 5 - man/create_query_token.Rd | 13 ++- man/get_query_from_token.Rd | 3 11 files changed, 249 insertions(+), 118 deletions(-)
Title: Sensitivity Analysis with Time-to-Event Outcomes
Description: Performs a dual-parameter sensitivity analysis of treatment effect to unmeasured confounding in observational studies with either survival or competing risks outcomes. Huang, R., Xu, R. and Dulai, P.S.(2020) <doi:10.1002/sim.8672>.
Author: Rong Huang, Ronghui Xu
Maintainer: Rong Huang <roh019@ucsd.edu>
Diff between survSens versions 0.1.0 dated 2020-04-29 and 1.1.0 dated 2023-05-30
DESCRIPTION | 16 +++++----- MD5 | 30 +++++++++---------- NAMESPACE | 6 ++- R/comprSensitivity.R | 70 +++++++++++++++++++++++++++++++++++++++------ R/compr_EM_variance.R | 8 ++--- R/compr_stoEM_ipw.R | 38 +++++++++++++++++++++++- R/compr_stoEM_regression.R | 69 ++++++++++++++++++++++++++++++++++++++++---- R/plotsens.R | 40 +++++++++++++++++++------ R/survSensitivity.R | 45 +++++++++++++++++++++++++--- R/surv_EM_variance.R | 2 - R/surv_stoEM_ipw.R | 27 ++++++++++++++--- R/surv_stoEM_regression.R | 43 +++++++++++++++++++++++++-- README.md | 62 +++++++++++++++++++++++++++++++++++---- data/tau.res.rda |binary man/plotsens.Rd | 10 ++---- man/tau.res.Rd | 6 ++- 16 files changed, 390 insertions(+), 82 deletions(-)
Title: Access Elevation Data from Various APIs
Description: Several web services are available that provide access to elevation
data. This package provides access to several of those services and
returns elevation data either as a SpatialPointsDataFrame from
point elevation services or as a raster object from raster
elevation services. Currently, the package supports access to the
Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>,
the Open Topography Global Datasets API <https://opentopography.org/developers/>,
and the USGS Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.
Author: Jeffrey Hollister [aut, cre] ,
Tarak Shah [ctb],
Alec L. Robitaille [ctb] ,
Marcus W. Beck [rev] ,
Mike Johnson [ctb]
Maintainer: Jeffrey Hollister <hollister.jeff@epa.gov>
Diff between elevatr versions 0.4.2 dated 2022-01-07 and 0.4.4 dated 2023-05-30
DESCRIPTION | 12 MD5 | 25 R/get_elev_point.R | 68 - R/get_elev_raster.R | 50 R/internal.R | 36 README.md | 49 build/vignette.rds |binary inst/CITATION | 4 inst/bug.R |only inst/doc/introduction_to_elevatr.R | 8 inst/doc/introduction_to_elevatr.Rmd | 8 inst/doc/introduction_to_elevatr.html | 1888 +++++++++++++++++++++++++++------- man/get_elev_raster.Rd | 2 vignettes/introduction_to_elevatr.Rmd | 8 14 files changed, 1708 insertions(+), 450 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-17 0.3.1
2016-11-05 0.3.0
2016-08-28 0.2.0
2016-07-20 0.1.0
Title: Nested Dichotomy Logistic Regression Models
Description: Provides functions for specifying and fitting nested
dichotomy logistic regression models for a multi-category response and
methods for summarising and plotting those models. Nested dichotomies are
statistically independent, and hence provide an additive decomposition
of tests for the overall 'polytomous' response. When the dichotomies
make sense substantively, this method can be a simpler alternative to
the standard 'multinomial' logistic model which compares response
categories to a reference level. See: J. Fox (2016), "Applied
Regression Analysis and Generalized Linear Models", 3rd Ed., ISBN
1452205663.
Author: John Fox [aut] ,
Michael Friendly [aut, cre] ,
Achim Zeileis [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between nestedLogit versions 0.2.1 dated 2023-05-15 and 0.3.0 dated 2023-05-30
nestedLogit-0.2.1/nestedLogit/R/plot.nested.R |only nestedLogit-0.2.1/nestedLogit/inst/doc/plotting.R |only nestedLogit-0.2.1/nestedLogit/inst/doc/plotting.Rmd |only nestedLogit-0.2.1/nestedLogit/inst/doc/plotting.html |only nestedLogit-0.2.1/nestedLogit/vignettes/plotting.Rmd |only nestedLogit-0.3.0/nestedLogit/DESCRIPTION | 15 nestedLogit-0.3.0/nestedLogit/MD5 | 71 - nestedLogit-0.3.0/nestedLogit/NAMESPACE | 13 nestedLogit-0.3.0/nestedLogit/NEWS.md | 17 nestedLogit-0.3.0/nestedLogit/R/as.data.frame.predict.R |only nestedLogit-0.3.0/nestedLogit/R/broomMethods.R | 2 nestedLogit-0.3.0/nestedLogit/R/models.R | 6 nestedLogit-0.3.0/nestedLogit/R/nested.R | 29 nestedLogit-0.3.0/nestedLogit/R/nestedMethods.R | 185 +++ nestedLogit-0.3.0/nestedLogit/R/plot.nested-ci.R |only nestedLogit-0.3.0/nestedLogit/build/vignette.rds |binary nestedLogit-0.3.0/nestedLogit/inst/WORDLIST | 18 nestedLogit-0.3.0/nestedLogit/inst/doc/nestedLogit.R | 26 nestedLogit-0.3.0/nestedLogit/inst/doc/nestedLogit.Rmd | 88 + nestedLogit-0.3.0/nestedLogit/inst/doc/nestedLogit.html | 491 +++++----- nestedLogit-0.3.0/nestedLogit/inst/doc/plotting-ggplot.R |only nestedLogit-0.3.0/nestedLogit/inst/doc/plotting-ggplot.Rmd |only nestedLogit-0.3.0/nestedLogit/inst/doc/plotting-ggplot.html |only nestedLogit-0.3.0/nestedLogit/inst/doc/standard-errors.Rmd |only nestedLogit-0.3.0/nestedLogit/inst/doc/standard-errors.html |only nestedLogit-0.3.0/nestedLogit/man/as.data.frame.predictNestedLogit.Rd |only nestedLogit-0.3.0/nestedLogit/man/broomMethods.Rd | 2 nestedLogit-0.3.0/nestedLogit/man/models.Rd | 3 nestedLogit-0.3.0/nestedLogit/man/nestedLogit.Rd | 9 nestedLogit-0.3.0/nestedLogit/man/nestedMethods.Rd | 41 nestedLogit-0.3.0/nestedLogit/man/partials/methods.Rmd | 4 nestedLogit-0.3.0/nestedLogit/man/plot.nestedLogit.Rd | 16 nestedLogit-0.3.0/nestedLogit/tests/testthat/test-fitted-probs.R | 7 nestedLogit-0.3.0/nestedLogit/tests/testthat/test-probs-SEs.R |only nestedLogit-0.3.0/nestedLogit/vignettes/apalike.csl |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-alt-plot-1.png |binary nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-ggplot-alt1-1.png |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-ggplot-dichot1-1.png |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-ggplot-dichot2-1.png |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-ggplot-logit-1.png |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-ggplot-p1-1.png |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-ggplot-p2-1.png |only nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-matplot-1.png |binary nestedLogit-0.3.0/nestedLogit/vignettes/fig/wlf-plot-1.png |binary nestedLogit-0.3.0/nestedLogit/vignettes/nestedLogit.Rmd | 88 + nestedLogit-0.3.0/nestedLogit/vignettes/plotting-ggplot.Rmd |only nestedLogit-0.3.0/nestedLogit/vignettes/references.bib | 37 nestedLogit-0.3.0/nestedLogit/vignettes/standard-errors.Rmd |only 48 files changed, 783 insertions(+), 385 deletions(-)
Title: Interface to the 'Microsoft 365' Suite of Cloud Services
Description: An interface to the 'Microsoft 365' (formerly known as 'Office 365') suite of cloud services, building on the framework supplied by the 'AzureGraph' package. Enables access from R to data stored in 'Teams', 'SharePoint Online' and 'OneDrive', including the ability to list drive folder contents, upload and download files, send messages, and retrieve data lists. Also provides a full-featured 'Outlook' email client, with the ability to send emails and manage emails and mail folders.
Author: Hong Ooi [aut, cre],
Roman Zenka [ctb],
Robert Ashton [ctb],
Philip Zheng [ctb],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between Microsoft365R versions 2.3.4 dated 2022-03-16 and 2.4.0 dated 2023-05-30
DESCRIPTION | 16 MD5 | 126 ++--- NEWS.md | 17 R/Microsoft365R.R | 24 + R/add_methods.R | 2 R/build_email_request.R | 4 R/client.R | 2 R/make_email_attachments.R | 9 R/ms_channel.R | 6 R/ms_chat.R | 6 R/ms_chat_message.R | 6 R/ms_drive.R | 216 ++++++--- R/ms_drive_item.R | 456 ++++++++++++++++--- R/ms_list.R | 6 R/ms_list_item.R | 4 R/ms_outlook.R | 6 R/ms_outlook_attachment.R | 4 R/ms_outlook_email.R | 6 R/ms_outlook_folder.R | 8 R/ms_outlook_object.R | 10 R/ms_plan.R | 6 R/ms_plan_bucket.R | 6 R/ms_plan_task.R | 6 R/ms_site.R | 6 R/ms_team.R | 6 R/ms_team_member.R | 4 R/normalize_src.R |only README.md | 8 build/vignette.rds |binary inst/app_registration.md | 2 inst/doc/auth.html | 325 +++++++++---- inst/doc/od_sp.Rmd | 17 inst/doc/od_sp.html | 387 ++++++++++------ inst/doc/outlook.html | 591 ++++++++++++++----------- inst/doc/scripted.Rmd | 10 inst/doc/scripted.html | 437 +++++++++++------- inst/doc/shiny.Rmd | 4 inst/doc/shiny.html | 334 ++++++++------ inst/doc/teams.html | 475 ++++++++++++-------- man/add_methods.Rd | 8 man/client.Rd | 2 man/microsoft365r_options.Rd |only man/ms_channel.Rd | 6 man/ms_chat.Rd | 6 man/ms_chat_message.Rd | 6 man/ms_drive.Rd | 98 +++- man/ms_drive_item.Rd | 74 ++- man/ms_list.Rd | 6 man/ms_list_item.Rd | 4 man/ms_outlook.Rd | 18 man/ms_outlook_attachment.Rd | 4 man/ms_outlook_email.Rd | 6 man/ms_outlook_folder.Rd | 20 man/ms_plan.Rd | 6 man/ms_plan_bucket.Rd | 6 man/ms_plan_task.Rd | 6 man/ms_site.Rd | 6 man/ms_team.Rd | 6 man/ms_team_member.Rd | 4 tests/testthat/test01_onedrive.R | 98 ++++ tests/testthat/test01a_onedrive_conntransfer.R |only tests/testthat/test01b_onedrive_copymove.R |only tests/testthat/test02_business_onedrive.R | 2 vignettes/od_sp.Rmd | 17 vignettes/scripted.Rmd | 10 vignettes/shiny.Rmd | 4 66 files changed, 2670 insertions(+), 1311 deletions(-)
Title: Robust Bayesian Survival Analysis
Description: A framework for estimating ensembles of parametric survival models
with different parametric families. The RoBSA framework uses Bayesian
model-averaging to combine the competing parametric survival models into
a model ensemble, weights the posterior parameter distributions based on
posterior model probabilities and uses Bayes factors to test for the
presence or absence of the individual predictors or preference for a
parametric family (Bartoš, Aust & Haaf, 2022, <doi:10.1186/s12874-022-01676-9>).
The user can define a wide range of informative priors for all parameters
of interest. The package provides convenient functions for summary, visualizations,
fit diagnostics, and prior distribution calibration.
Author: Frantisek Bartos [aut, cre] ,
Julia M. Haaf [ths] ,
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBSA versions 1.0.1 dated 2023-03-13 and 1.0.2 dated 2023-05-30
DESCRIPTION | 10 - MD5 | 85 ++++----- NAMESPACE | 1 NEWS.md | 7 R/check-input-and-settings.R | 6 R/check-priors-and-models.R | 14 + R/diagnostics.R | 2 R/fit-and-marglik.R | 2 R/priors.R | 31 +++ R/summary.R | 74 +++++-- R/utilities.R | 5 build/partial.rdb |binary inst/REFERENCES.bib | 9 man/RoBSA-package.Rd | 70 +++---- man/RoBSA.Rd | 330 +++++++++++++++++------------------ man/RoBSA_control.Rd | 142 +++++++-------- man/calibrate_meta_analytic.Rd | 82 ++++---- man/calibrate_quartiles.Rd | 108 +++++------ man/check_RoBSA.Rd | 40 ++-- man/check_setup.Rd | 274 ++++++++++++++--------------- man/contr.meandif.Rd |only man/contr.orthonormal.Rd | 60 +++--- man/default_prior.Rd | 78 ++++---- man/diagnostics.Rd | 186 +++++++++---------- man/exp-aft.Rd | 130 ++++++------- man/extract_flexsurv.Rd | 42 ++-- man/gamma-aft.Rd | 134 +++++++------- man/is.RoBSA.Rd | 34 +-- man/llogis-aft.Rd | 134 +++++++------- man/lnorm-aft.Rd | 134 +++++++------- man/plot.RoBSA.Rd | 194 ++++++++++---------- man/plot_models.Rd | 182 +++++++++---------- man/plot_prediction.Rd | 268 ++++++++++++++-------------- man/predict.RoBSA.Rd | 126 ++++++------- man/print.RoBSA.Rd | 44 ++-- man/print.summary.RoBSA.Rd | 44 ++-- man/prior.Rd | 170 +++++++++--------- man/prior_factor.Rd | 188 ++++++++++--------- man/prior_informed.Rd | 138 +++++++------- man/prior_informed_medicine_names.Rd | 38 ++-- man/prior_none.Rd | 80 ++++---- man/summary.RoBSA.Rd | 246 +++++++++++++------------- man/update.RoBSA.Rd | 296 +++++++++++++++---------------- man/weibull-aft.Rd | 134 +++++++------- 44 files changed, 2232 insertions(+), 2140 deletions(-)
Title: Bootstrap a Clustering Solution to Establish the Stability of
the Clusters
Description: Providing a cluster allocation for n samples, either with an $n \times p$ data matrix or an $n \times n$ distance
matrix, a bootstrap procedure is performed. The proportion of bootstrap replicates where a pair of samples
cluster in the same cluster indicates who tightly the samples in a particular cluster clusters together.
Author: Sugnet Lubbe [aut, cre, cph]
Maintainer: Sugnet Lubbe <slubbe@sun.ac.za>
Diff between ClusBoot versions 1.0 dated 2019-12-13 and 1.0.1 dated 2023-05-30
ClusBoot-1.0.1/ClusBoot/DESCRIPTION | 36 ++++---- ClusBoot-1.0.1/ClusBoot/LICENSE |only ClusBoot-1.0.1/ClusBoot/MD5 | 26 ++--- ClusBoot-1.0.1/ClusBoot/NAMESPACE | 11 +- ClusBoot-1.0.1/ClusBoot/R/data.R |only ClusBoot-1.0.1/ClusBoot/R/funcs.R |only ClusBoot-1.0.1/ClusBoot/data/case.study.psychiatrist.rda |only ClusBoot-1.0.1/ClusBoot/man/boot.silhouette.Rd | 67 +++++---------- ClusBoot-1.0.1/ClusBoot/man/case.study.psychiatrist.Rd |only ClusBoot-1.0.1/ClusBoot/man/clusboot.Rd | 67 +++++---------- ClusBoot-1.0.1/ClusBoot/man/complete.linkage.Rd | 55 ++++-------- ClusBoot-1.0.1/ClusBoot/man/figures |only ClusBoot-1.0.1/ClusBoot/man/plot.clusboot.Rd | 67 +++++---------- ClusBoot-1.0/ClusBoot/R/boot.silhouette.R |only ClusBoot-1.0/ClusBoot/R/clusboot.R |only ClusBoot-1.0/ClusBoot/R/complete.linkage.R |only ClusBoot-1.0/ClusBoot/R/plot.clusboot.R |only ClusBoot-1.0/ClusBoot/build |only ClusBoot-1.0/ClusBoot/data/case_study_psychiatrist.rda |only ClusBoot-1.0/ClusBoot/man/ClusBoot-package.Rd |only ClusBoot-1.0/ClusBoot/man/case_study_psychiatrist.Rd |only 21 files changed, 133 insertions(+), 196 deletions(-)
Title: Call Rust Code from R using the 'extendr' Crate
Description: Provides functions to compile and load Rust code from R, similar
to how 'Rcpp' or 'cpp11' allow easy interfacing with C++ code. Also provides
helper functions to create R packages that use Rust code. Under the hood,
the Rust crate 'extendr' is used to do all the heavy lifting.
Author: Claus O. Wilke [aut] ,
Andy Thomason [aut],
Mossa M. Reimert [aut],
Ilia Kosenkov [aut, cre] ,
Hiroaki Yutani [aut] ,
Malcolm Barrett [aut] ,
Josiah Parry [ctb]
Maintainer: Ilia Kosenkov <ilia.kosenkov@outlook.com>
Diff between rextendr versions 0.2.0 dated 2021-06-15 and 0.3.0 dated 2023-05-30
rextendr-0.2.0/rextendr/R/clean_code.R |only rextendr-0.2.0/rextendr/R/install_libR_bindings.R |only rextendr-0.2.0/rextendr/R/ui.R |only rextendr-0.2.0/rextendr/tests/testthat/teardown.R |only rextendr-0.2.0/rextendr/tests/testthat/test-helper-functions.R |only rextendr-0.3.0/rextendr/DESCRIPTION | 36 rextendr-0.3.0/rextendr/LICENSE | 4 rextendr-0.3.0/rextendr/MD5 | 153 - rextendr-0.3.0/rextendr/NAMESPACE | 76 rextendr-0.3.0/rextendr/NEWS.md | 42 rextendr-0.3.0/rextendr/R/clean.R |only rextendr-0.3.0/rextendr/R/eval.R | 191 + rextendr-0.3.0/rextendr/R/features.R |only rextendr-0.3.0/rextendr/R/find_exports.R | 115 rextendr-0.3.0/rextendr/R/function_options.R |only rextendr-0.3.0/rextendr/R/generate_toml.R |only rextendr-0.3.0/rextendr/R/helpers.r |only rextendr-0.3.0/rextendr/R/knitr_engine.R | 133 - rextendr-0.3.0/rextendr/R/license_note.R |only rextendr-0.3.0/rextendr/R/make_module_macro.R | 54 rextendr-0.3.0/rextendr/R/register_extendr.R | 385 +-- rextendr-0.3.0/rextendr/R/rextendr.R | 28 rextendr-0.3.0/rextendr/R/rextendr_document.R | 40 rextendr-0.3.0/rextendr/R/rust_sitrep.R |only rextendr-0.3.0/rextendr/R/sanitize_code.R |only rextendr-0.3.0/rextendr/R/setup.R |only rextendr-0.3.0/rextendr/R/source.R | 914 ++++--- rextendr-0.3.0/rextendr/R/toml_serialization.R | 577 ++-- rextendr-0.3.0/rextendr/R/track_rust_source.R | 325 -- rextendr-0.3.0/rextendr/R/try_save_all.R | 30 rextendr-0.3.0/rextendr/R/use_extendr.R | 423 ++- rextendr-0.3.0/rextendr/R/utils.R |only rextendr-0.3.0/rextendr/R/write_file.R | 46 rextendr-0.3.0/rextendr/R/zzz.R | 78 rextendr-0.3.0/rextendr/README.md | 165 - 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Title: Non-Parametric Concordance Coefficient
Description: A non-parametric test for multi-observer concordance and
differences between concordances in (un)balanced data.
Author: Rowan Kuiper [cre, aut] ,
Remco Hoogenboezem [aut],
Sjoerd Huisman [ctb] ,
Pieter Sonneveld [ths],
Mark van Duin [ths]
Maintainer: Rowan Kuiper <r.kuiper.emc@gmail.com>
Diff between nopaco versions 1.0.6 dated 2019-07-06 and 1.0.7 dated 2023-05-30
nopaco-1.0.6/nopaco/NEWS |only nopaco-1.0.6/nopaco/src/Makevars.win |only nopaco-1.0.7/nopaco/DESCRIPTION | 12 nopaco-1.0.7/nopaco/MD5 | 37 +- nopaco-1.0.7/nopaco/NEWS.md |only nopaco-1.0.7/nopaco/R/concordance.test.R | 351 +++++++++++---------------- nopaco-1.0.7/nopaco/R/onLoad.R | 6 nopaco-1.0.7/nopaco/R/zzz.R | 303 ++++++++++++++--------- nopaco-1.0.7/nopaco/build/vignette.rds |binary nopaco-1.0.7/nopaco/inst/CITATION | 2 nopaco-1.0.7/nopaco/inst/doc/nopaco.R | 1 nopaco-1.0.7/nopaco/inst/doc/nopaco.pdf |binary nopaco-1.0.7/nopaco/man/coef-methods.Rd | 6 nopaco-1.0.7/nopaco/man/concordance.test.Rd | 17 - nopaco-1.0.7/nopaco/man/convertionMethods.Rd | 6 nopaco-1.0.7/nopaco/man/getPsi-methods.Rd | 6 nopaco-1.0.7/nopaco/man/scores.Rd | 6 nopaco-1.0.7/nopaco/src/Makevars | 1 nopaco-1.0.7/nopaco/src/bootstrapCI.cpp | 4 nopaco-1.0.7/nopaco/src/getPsi.cpp | 116 ++++---- nopaco-1.0.7/nopaco/src/getPsi.h | 1 21 files changed, 463 insertions(+), 412 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.0.7 dated 2023-03-14 and 1.0.8 dated 2023-05-30
DESCRIPTION | 10 +++--- MD5 | 48 +++++++++++++++---------------- NAMESPACE | 1 R/GeoCompositeLik.r | 27 +---------------- R/GeoCompositeLik2.R | 70 +++++++++++++++++++++++++--------------------- R/GeoFit.r | 2 - R/GeoFit2.R | 2 - R/GeoIndCompositeLik2.R | 25 +--------------- R/GeoLik.r | 36 +++++++++++------------ R/GeoQQ.R | 44 ++++++++++++++-------------- R/GeoSim.r | 11 +++---- R/GeoSimCopula.R | 12 ++++++- R/Geovarestbootstrap.R | 10 +++++- R/Utility.r | 19 +++++++++--- man/CompIndLik2.Rd | 2 - man/CompLik.Rd | 2 - man/CompLik2.Rd | 2 - man/GeoFit.Rd | 2 - man/GeoFit2.Rd | 2 - man/GeoQQ.Rd | 4 +- man/GeoSim.Rd | 3 + man/GeoSimCopula.Rd | 3 + man/GeoVarestbootstrap.Rd | 6 ++- man/Lik.Rd | 2 - src/Distributions.c | 45 ++++++++++++++++++++++++++++- 25 files changed, 215 insertions(+), 175 deletions(-)
Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.5.3 dated 2023-05-03 and 3.5.4 dated 2023-05-30
FIESTA-3.5.3/FIESTA/data/ref_cond.rda |only FIESTA-3.5.3/FIESTA/data/ref_conversion.rda |only FIESTA-3.5.3/FIESTA/data/ref_plt.rda |only FIESTA-3.5.3/FIESTA/data/ref_popType.rda |only FIESTA-3.5.3/FIESTA/data/ref_shp.rda |only FIESTA-3.5.3/FIESTA/data/ref_species.rda |only FIESTA-3.5.3/FIESTA/data/ref_titles.rda |only FIESTA-3.5.3/FIESTA/data/ref_tree.rda |only FIESTA-3.5.3/FIESTA/man/DEFAULT_NODATA.Rd |only FIESTA-3.5.3/FIESTA/man/ref_ALP.Rd |only FIESTA-3.5.4/FIESTA/DESCRIPTION | 16 FIESTA-3.5.4/FIESTA/MD5 | 176 +- FIESTA-3.5.4/FIESTA/NAMESPACE | 20 FIESTA-3.5.4/FIESTA/R/DBgetEvalid.R | 142 +- FIESTA-3.5.4/FIESTA/R/DBgetPlots.R | 191 +-- FIESTA-3.5.4/FIESTA/R/DBgetStrata.R | 8 FIESTA-3.5.4/FIESTA/R/DBgetXY.R | 29 FIESTA-3.5.4/FIESTA/R/FIESTA-package.R | 192 --- FIESTA-3.5.4/FIESTA/R/aaa.R | 2 FIESTA-3.5.4/FIESTA/R/check.auxiliary.R | 9 FIESTA-3.5.4/FIESTA/R/check.popdataPLT.R | 24 FIESTA-3.5.4/FIESTA/R/check.popdataVOL.R | 12 FIESTA-3.5.4/FIESTA/R/check.rowcol.R | 47 FIESTA-3.5.4/FIESTA/R/check.rowcolPB.R | 3 FIESTA-3.5.4/FIESTA/R/check.tree.R | 124 -- FIESTA-3.5.4/FIESTA/R/datLUTnm.R | 8 FIESTA-3.5.4/FIESTA/R/datLUTspp.R |only FIESTA-3.5.4/FIESTA/R/datSumTree.R | 736 ++++++------ FIESTA-3.5.4/FIESTA/R/datSumTreeDom.R | 979 ++++++++-------- FIESTA-3.5.4/FIESTA/R/modGBpop.R | 33 FIESTA-3.5.4/FIESTA/R/modGBratio.R | 13 FIESTA-3.5.4/FIESTA/R/modGBtree.R | 12 FIESTA-3.5.4/FIESTA/R/modMApop.R | 24 FIESTA-3.5.4/FIESTA/R/modMAtree.R | 8 FIESTA-3.5.4/FIESTA/R/modSApop.R | 24 FIESTA-3.5.4/FIESTA/R/modSAtree.R | 4 FIESTA-3.5.4/FIESTA/R/modWFpop.R | 16 FIESTA-3.5.4/FIESTA/R/modWFtree.R | 8 FIESTA-3.5.4/FIESTA/R/re_exports.R | 39 FIESTA-3.5.4/FIESTA/R/spClipPoint.R | 7 FIESTA-3.5.4/FIESTA/R/spClipRast.R | 35 FIESTA-3.5.4/FIESTA/R/spExtractPoly.R | 8 FIESTA-3.5.4/FIESTA/R/spExtractRast.R | 9 FIESTA-3.5.4/FIESTA/R/spGetAuxiliary.R | 15 FIESTA-3.5.4/FIESTA/R/spGetEstUnit.R | 10 FIESTA-3.5.4/FIESTA/R/spGetPlots.R | 5 FIESTA-3.5.4/FIESTA/R/spGetStates.R | 2 FIESTA-3.5.4/FIESTA/R/spGetStrata.R | 9 FIESTA-3.5.4/FIESTA/R/spGetXY.R | 14 FIESTA-3.5.4/FIESTA/R/spMakeSpatialPoints.R | 24 FIESTA-3.5.4/FIESTA/R/spPoly2Rast.R | 10 FIESTA-3.5.4/FIESTA/R/spReprojectRaster.R | 4 FIESTA-3.5.4/FIESTA/R/spReprojectVector.R | 3 FIESTA-3.5.4/FIESTA/R/spZonalRast.R | 2 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_GB.R | 2 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_GB.Rmd | 2 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_GB.html | 1099 +++++++++--------- FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_MA.R | 3 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_MA.Rmd | 3 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_MA.html | 569 ++++----- FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_PB.R | 3 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_PB.Rmd | 3 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_PB.html | 5 FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_SA.html | 90 - FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_dat.html | 304 ++-- FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_sp.R | 80 - FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_sp.Rmd | 89 - FIESTA-3.5.4/FIESTA/inst/doc/FIESTA_tutorial_sp.html | 632 +++++----- FIESTA-3.5.4/FIESTA/man/DBgetPlots.Rd | 6 FIESTA-3.5.4/FIESTA/man/datLUTspp.Rd |only FIESTA-3.5.4/FIESTA/man/datSumTree.Rd | 16 FIESTA-3.5.4/FIESTA/man/datSumTreeDom.Rd | 18 FIESTA-3.5.4/FIESTA/man/modGBpop.Rd | 3 FIESTA-3.5.4/FIESTA/man/modGBratio.Rd | 2 FIESTA-3.5.4/FIESTA/man/modGBtree.Rd | 2 FIESTA-3.5.4/FIESTA/man/modMApop.Rd | 3 FIESTA-3.5.4/FIESTA/man/modSApop.Rd | 3 FIESTA-3.5.4/FIESTA/man/ref_codes.Rd | 2 FIESTA-3.5.4/FIESTA/man/ref_cond.Rd | 20 FIESTA-3.5.4/FIESTA/man/ref_conversion.Rd | 9 FIESTA-3.5.4/FIESTA/man/ref_estvar.Rd | 2 FIESTA-3.5.4/FIESTA/man/ref_plt.Rd | 20 FIESTA-3.5.4/FIESTA/man/ref_popType.Rd | 9 FIESTA-3.5.4/FIESTA/man/ref_shp.Rd | 21 FIESTA-3.5.4/FIESTA/man/ref_species.Rd | 23 FIESTA-3.5.4/FIESTA/man/ref_titles.Rd | 9 FIESTA-3.5.4/FIESTA/man/ref_tree.Rd | 20 FIESTA-3.5.4/FIESTA/man/spGetEstUnit.Rd | 3 FIESTA-3.5.4/FIESTA/man/spGetStates.Rd | 2 FIESTA-3.5.4/FIESTA/man/spMakeSpatialPoints.Rd | 27 FIESTA-3.5.4/FIESTA/man/spReprojectVector.Rd | 3 FIESTA-3.5.4/FIESTA/vignettes/FIESTA_tutorial_GB.Rmd | 2 FIESTA-3.5.4/FIESTA/vignettes/FIESTA_tutorial_MA.Rmd | 3 FIESTA-3.5.4/FIESTA/vignettes/FIESTA_tutorial_PB.Rmd | 3 FIESTA-3.5.4/FIESTA/vignettes/FIESTA_tutorial_sp.Rmd | 89 - 95 files changed, 3100 insertions(+), 3160 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Data
Description: Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data. See Krivitsky and Morris (2017) <doi:10.1214/16-AOAS1010>.
Author: Pavel N. Krivitsky [aut, cre] ,
Steven M. Goodreau [ctb],
Martina Morris [ctb],
Kirk Li [ctb],
Emily N. Beylerian [ctb],
Michal Bojanowski [ctb] ,
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm.ego versions 1.0.1 dated 2022-05-26 and 1.1.0 dated 2023-05-30
DESCRIPTION | 18 +++--- LICENSE | 3 - MD5 | 91 ++++++++++++++++----------------- NAMESPACE | 2 R/EgoStat.R | 2 R/EgoStat.duration.R | 2 R/EgoStat.node.attr.R | 2 R/InitErgmTerm.R | 2 R/control.ergm.ego.R | 2 R/control.simulate.ergm.ego.R | 2 R/degreedist.R | 2 R/egor.R | 38 ++++++++----- R/ergm.ego.R | 15 ++--- R/fmhfit.R | 2 R/gof.ergm.ego.R | 46 ++++++---------- R/predict.ergmego.R | 2 R/reweight.egor.R | 2 R/simulate.ergm.ego.R | 40 ++++++++------ R/summary.ergm.ego.R | 2 R/summary.statistics.egor.R | 2 R/zzz.R | 2 build/ergm.ego.pdf |binary build/stage23.rdb |only data/fmhfit.rda |binary inst/CITATION | 36 ++++++------- inst/NEWS.Rd | 37 +++++++++++++ man/EgoStat-internal.Rd | 30 +++++----- man/ergm.ego.Rd | 3 + man/nodal_attributes-API.Rd | 4 - man/simulate.ergm.ego.Rd | 25 +++++---- man/summary_formula.egor.Rd | 4 - man/template_network.Rd | 21 ++++++- src/changestats.c | 2 src/include_stubs.c | 2 src/init.c | 2 tests/testthat.R | 2 tests/testthat/test-EgoStat.R | 2 tests/testthat/test-boot_jack.R | 2 tests/testthat/test-coef_recovery.R | 2 tests/testthat/test-degreedist.R | 2 tests/testthat/test-drop.R | 2 tests/testthat/test-gof.ergm.ego.R | 2 tests/testthat/test-mixingmatrix.R | 2 tests/testthat/test-netsize.adj.R | 2 tests/testthat/test-predict.ergm.ego.R | 2 tests/testthat/test-statmismatch.R | 2 tests/testthat/test-table_ppop.R | 81 ++++++++--------------------- 47 files changed, 291 insertions(+), 257 deletions(-)
Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of 40
different coding schemes, convert between coding schemes, and assign
region descriptors.
Author: Vincent Arel-Bundock [aut, cre]
,
CJ Yetman [ctb] ,
Nils Enevoldsen [ctb] ,
Samuel Meichtry [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.4.0 dated 2022-05-04 and 1.5.0 dated 2023-05-30
DESCRIPTION | 10 +-- MD5 | 38 ++++++++------ NAMESPACE | 1 NEWS.md | 11 +++- R/codelist.R | 5 + R/countrycode.R | 27 +++++++--- R/countryname.R | 10 +++ R/get_dictionary.R |only data/codelist.rda |binary data/codelist_panel.rda |binary inst/CITATION | 31 +++++++---- man/codelist.Rd | 5 + man/countrycode-package.Rd | 4 - man/get_dictionary.Rd |only tests/testthat/data-known-name-variations.R | 4 + tests/testthat/test-basic.R | 11 ++++ tests/testthat/test-codelist.R | 4 - tests/testthat/test-corner-cases.R | 73 ++++++++++++++++++++++++++++ tests/testthat/test-countryname.R | 4 - tests/testthat/test-custom-dictionary.R |only tests/testthat/test-dictionary_attributes.R |only tests/testthat/test-regex-internal.R | 5 + 22 files changed, 191 insertions(+), 52 deletions(-)
Title: Additional Operators for Image Models
Description: Implements additional operators for computer vision models, including
operators necessary for image segmentation and object detection deep learning
models.
Author: Daniel Falbel [aut, cre],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchvisionlib versions 0.3.0 dated 2022-10-31 and 0.4.0 dated 2023-05-30
DESCRIPTION | 9 +++----- MD5 | 30 +++++++++++++++------------ NAMESPACE | 1 NEWS.md | 5 ++++ R/RcppExports.R | 8 +++++++ R/ops.R | 3 +- R/package.R | 2 - R/reader.R |only inst/def/torchvisionlib.def | 2 + inst/include/torchvisionlib/exports.h | 12 ++++++++++ inst/include/torchvisionlib/torchvisionlib.h | 2 + man/ops_ps_roi_align.Rd | 7 +++--- man/vision_read_jpeg.Rd |only src/RcppExports.cpp | 24 +++++++++++++++++++++ src/exports.cpp | 8 +++++++ src/exports.h | 2 + tests/testthat/imgs |only tests/testthat/test-reader.R |only 18 files changed, 92 insertions(+), 23 deletions(-)
More information about torchvisionlib at CRAN
Permanent link
Title: Robust Bayesian T-Test
Description: An implementation of Bayesian model-averaged t-test that allows
users to draw inference about the presence vs absence of the effect,
heterogeneity of variances, and outliers. The 'RoBTT' packages estimates model
ensembles of models created as a combination of the competing hypotheses and uses
Bayesian model-averaging to combine the models using posterior model probabilities.
Users can obtain the model-averaged posterior distributions and inclusion Bayes
factors which account for the uncertainty in the data generating process
(Maier et al., 2022, <doi:10.31234/osf.io/d5zwc>).
Users can define a wide range of informative priors for all parameters
of interest. The package provides convenient functions for summary, visualizations,
and fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBTT versions 1.0.2 dated 2023-03-30 and 1.1.0 dated 2023-05-30
RoBTT-1.0.2/RoBTT/src/Makevars |only RoBTT-1.1.0/RoBTT/DESCRIPTION | 11 RoBTT-1.1.0/RoBTT/MD5 | 54 RoBTT-1.1.0/RoBTT/NAMESPACE | 6 RoBTT-1.1.0/RoBTT/NEWS.md | 9 RoBTT-1.1.0/RoBTT/R/RoBTT-package.R | 3 RoBTT-1.1.0/RoBTT/R/check-input-and-settings.R | 120 RoBTT-1.1.0/RoBTT/R/diagnostics.R |only RoBTT-1.1.0/RoBTT/R/plot.R | 81 RoBTT-1.1.0/RoBTT/R/utilities.R | 2 RoBTT-1.1.0/RoBTT/build/partial.rdb |binary RoBTT-1.1.0/RoBTT/build/vignette.rds |binary RoBTT-1.1.0/RoBTT/inst/doc/Introduction_to_RoBTT.html | 4 RoBTT-1.1.0/RoBTT/inst/stan/beta.stan | 4 RoBTT-1.1.0/RoBTT/inst/stan/gamma.stan | 4 RoBTT-1.1.0/RoBTT/inst/stan/include/common_functions.stan | 22 RoBTT-1.1.0/RoBTT/inst/stan/lognormal.stan | 4 RoBTT-1.1.0/RoBTT/inst/stan/normal.stan | 4 RoBTT-1.1.0/RoBTT/inst/stan/t.stan | 6 RoBTT-1.1.0/RoBTT/man/check_setup.Rd |only RoBTT-1.1.0/RoBTT/man/diagnostics.Rd |only RoBTT-1.1.0/RoBTT/man/plot.RoBTT.Rd | 4 RoBTT-1.1.0/RoBTT/man/rho2logsdr.Rd |only RoBTT-1.1.0/RoBTT/src/Makevars.win | 4 RoBTT-1.1.0/RoBTT/src/stanExports_beta.h | 3028 +++++------- RoBTT-1.1.0/RoBTT/src/stanExports_gamma.h | 3020 +++++------- RoBTT-1.1.0/RoBTT/src/stanExports_lognormal.h | 3030 +++++------- RoBTT-1.1.0/RoBTT/src/stanExports_normal.h | 2846 ++++-------- RoBTT-1.1.0/RoBTT/src/stanExports_t.h | 3312 +++++--------- RoBTT-1.1.0/RoBTT/tests/testthat/test-0-CRAN.R | 34 RoBTT-1.1.0/RoBTT/tests/testthat/test-4-diagnostics.R |only 31 files changed, 6556 insertions(+), 9056 deletions(-)
Title: Reading Ontologies into R
Description: Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017 <doi:10.1093/bioinformatics/btw763>.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyIndex versions 2.10 dated 2022-08-24 and 2.11 dated 2023-05-30
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/data.R | 2 +- inst/CITATION | 26 ++++++++++++-------------- inst/doc/intro-to-ontologyX.html | 4 ++-- inst/doc/reading-ontologies.html | 4 ++-- 6 files changed, 26 insertions(+), 28 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.
Author: Pavel N. Krivitsky [aut, cre] ,
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between tergm versions 4.1.1 dated 2022-11-08 and 4.2.0 dated 2023-05-30
tergm-4.1.1/tergm/R/combine.networks.R |only tergm-4.1.1/tergm/R/ergmlhs.R |only tergm-4.1.1/tergm/R/print.combined_networks.R |only tergm-4.1.1/tergm/man/combine_networks.Rd |only tergm-4.1.1/tergm/man/split.network.Rd |only tergm-4.1.1/tergm/man/uncombine_network.Rd |only tergm-4.1.1/tergm/src/changestat_netseries.h |only tergm-4.1.1/tergm/src/changestats_netseries.c |only tergm-4.2.0/tergm/DESCRIPTION | 32 - tergm-4.2.0/tergm/LICENSE | 2 tergm-4.2.0/tergm/MD5 | 203 ++++----- tergm-4.2.0/tergm/NAMESPACE | 10 tergm-4.2.0/tergm/R/InitErgmConstraint.hints.R | 2 tergm-4.2.0/tergm/R/InitErgmProposal.DynMLE.R | 2 tergm-4.2.0/tergm/R/InitErgmProposal.DynMoME.R | 2 tergm-4.2.0/tergm/R/InitErgmTerm.EGMME.R | 64 ++ tergm-4.2.0/tergm/R/InitErgmTerm.duration.R | 2 tergm-4.2.0/tergm/R/InitErgmTerm.netseries.R | 217 +++------- tergm-4.2.0/tergm/R/control.simulate.stergm.R | 2 tergm-4.2.0/tergm/R/control.simulate.tergm.R | 2 tergm-4.2.0/tergm/R/control.stergm.R | 2 tergm-4.2.0/tergm/R/control.tergm.R | 4 tergm-4.2.0/tergm/R/impute.network.list.R | 2 tergm-4.2.0/tergm/R/is.durational.R | 2 tergm-4.2.0/tergm/R/is.lasttoggle.R | 2 tergm-4.2.0/tergm/R/simulate.stergm.R | 2 tergm-4.2.0/tergm/R/simulate.tergm.R | 29 - tergm-4.2.0/tergm/R/stergm.R | 12 tergm-4.2.0/tergm/R/stergm.utils.R | 2 tergm-4.2.0/tergm/R/summary.statistics.networkDynamic.R | 2 tergm-4.2.0/tergm/R/tergm-deprecated.R | 2 tergm-4.2.0/tergm/R/tergm-package.R | 2 tergm-4.2.0/tergm/R/tergm.CMLE.R | 10 tergm-4.2.0/tergm/R/tergm.EGMME.GD.R | 2 tergm-4.2.0/tergm/R/tergm.EGMME.R | 6 tergm-4.2.0/tergm/R/tergm.EGMME.SA.R | 2 tergm-4.2.0/tergm/R/tergm.EGMME.initialfit.R | 2 tergm-4.2.0/tergm/R/tergm.R | 25 - tergm-4.2.0/tergm/R/tergm.getMCMCsample.R | 2 tergm-4.2.0/tergm/R/tergm.godfather.R | 2 tergm-4.2.0/tergm/R/zzz.R | 4 tergm-4.2.0/tergm/build/stage23.rdb |only tergm-4.2.0/tergm/build/tergm.pdf |binary tergm-4.2.0/tergm/build/vignette.rds |binary tergm-4.2.0/tergm/inst/CITATION | 24 - tergm-4.2.0/tergm/inst/NEWS.Rd | 27 + tergm-4.2.0/tergm/man/Change-ergmTerm-4236ef3c.Rd | 16 tergm-4.2.0/tergm/man/Cross-ergmTerm-03ab5578.Rd | 12 tergm-4.2.0/tergm/man/Diss-ergmTerm-f48278bd.Rd | 16 tergm-4.2.0/tergm/man/Form-ergmTerm-fa13d505.Rd | 16 tergm-4.2.0/tergm/man/Persist-ergmTerm-34b51891.Rd | 16 tergm-4.2.0/tergm/man/control.tergm.Rd | 3 tergm-4.2.0/tergm/man/simulate.stergm.Rd | 2 tergm-4.2.0/tergm/man/simulate.tergm.Rd | 2 tergm-4.2.0/tergm/man/stergm.Rd | 9 tergm-4.2.0/tergm/man/tergm.Rd | 21 tergm-4.2.0/tergm/src/DynSA.c | 2 tergm-4.2.0/tergm/src/DynSA.h | 2 tergm-4.2.0/tergm/src/MCMCDyn.c | 2 tergm-4.2.0/tergm/src/MCMCDyn.h | 2 tergm-4.2.0/tergm/src/MHproposals_DynMLE.c | 2 tergm-4.2.0/tergm/src/changestats_auxnet.c | 2 tergm-4.2.0/tergm/src/changestats_duration.c | 2 tergm-4.2.0/tergm/src/changestats_duration.h | 2 tergm-4.2.0/tergm/src/changestats_lasttoggle.c | 2 tergm-4.2.0/tergm/src/changestats_lasttoggle.h | 2 tergm-4.2.0/tergm/src/changestats_operator.c | 2 tergm-4.2.0/tergm/src/discordTNT.c | 2 tergm-4.2.0/tergm/src/godfather.c | 2 tergm-4.2.0/tergm/src/godfather.h | 2 tergm-4.2.0/tergm/src/include_stubs.c | 2 tergm-4.2.0/tergm/src/init.c | 2 tergm-4.2.0/tergm/src/tergm_changestats_auxnet.h | 2 tergm-4.2.0/tergm/src/tergm_model.h | 2 tergm-4.2.0/tergm/tests/degree.mean.age.R | 2 tergm-4.2.0/tergm/tests/dynamic_EGMME.R | 2 tergm-4.2.0/tergm/tests/dynamic_MLE_blockdiag.R | 2 tergm-4.2.0/tergm/tests/dynamic_MLE_blockdiag.bipartite.R | 48 +- tergm-4.2.0/tergm/tests/sim_gf_sum.R | 2 tergm-4.2.0/tergm/tests/simulate_networkDynamic.R | 2 tergm-4.2.0/tergm/tests/tergm_offset_tests.R | 2 tergm-4.2.0/tergm/tests/tergm_parallel.R | 2 tergm-4.2.0/tergm/tests/testthat.R | 2 tergm-4.2.0/tergm/tests/testthat/helper-CMLE.R | 4 tergm-4.2.0/tergm/tests/testthat/test-CMLE-2-bip.R | 2 tergm-4.2.0/tergm/tests/testthat/test-CMLE-2-dir.R | 2 tergm-4.2.0/tergm/tests/testthat/test-CMLE-2-und.R | 2 tergm-4.2.0/tergm/tests/testthat/test-CMLE-bip.R | 2 tergm-4.2.0/tergm/tests/testthat/test-CMLE-dir.R | 2 tergm-4.2.0/tergm/tests/testthat/test-CMLE-und.R | 2 tergm-4.2.0/tergm/tests/testthat/test-EGMME-errors.R | 2 tergm-4.2.0/tergm/tests/testthat/test-EGMME-initialfit.R | 2 tergm-4.2.0/tergm/tests/testthat/test-EGMME-simple.R | 2 tergm-4.2.0/tergm/tests/testthat/test-basis.R |only tergm-4.2.0/tergm/tests/testthat/test-discord-proposals.R | 2 tergm-4.2.0/tergm/tests/testthat/test-durational-terms.R | 2 tergm-4.2.0/tergm/tests/testthat/test-edgelist_with_lasttoggle.R | 2 tergm-4.2.0/tergm/tests/testthat/test-extract-formulae.R | 6 tergm-4.2.0/tergm/tests/testthat/test-lasttoggle.R | 2 tergm-4.2.0/tergm/tests/testthat/test-networkLite.R |only tergm-4.2.0/tergm/tests/testthat/test-nwelt.R | 2 tergm-4.2.0/tergm/tests/testthat/test-simulate.R | 30 - tergm-4.2.0/tergm/tests/testthat/test-summary-networkDynamic.R | 2 tergm-4.2.0/tergm/tests/testthat/test-term-.SubsetStatistics.R | 6 tergm-4.2.0/tergm/tests/testthat/test-term-Change.R | 6 tergm-4.2.0/tergm/tests/testthat/test-term-Cross.R | 6 tergm-4.2.0/tergm/tests/testthat/test-term-EdgeAges.R | 2 tergm-4.2.0/tergm/tests/testthat/test-terms-Form-Persist-Diss.R | 4 108 files changed, 540 insertions(+), 476 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.13 dated 2022-09-14 and 0.2.14 dated 2023-05-30
BayesTools-0.2.13/BayesTools/tests |only BayesTools-0.2.14/BayesTools/DESCRIPTION | 14 BayesTools-0.2.14/BayesTools/MD5 | 453 +--------- BayesTools-0.2.14/BayesTools/NAMESPACE | 27 BayesTools-0.2.14/BayesTools/NEWS.md | 27 BayesTools-0.2.14/BayesTools/R/BayesTools-package.R | 2 BayesTools-0.2.14/BayesTools/R/JAGS-diagnostics.R | 112 +- BayesTools-0.2.14/BayesTools/R/JAGS-fit.R | 123 +- BayesTools-0.2.14/BayesTools/R/JAGS-formula.R | 304 +++++- BayesTools-0.2.14/BayesTools/R/JAGS-marglik.R | 74 - BayesTools-0.2.14/BayesTools/R/distributions-mpoint.R |only BayesTools-0.2.14/BayesTools/R/distributions-point.R | 10 BayesTools-0.2.14/BayesTools/R/marginal-distributions.R |only BayesTools-0.2.14/BayesTools/R/model-averaging-plots.R | 289 +++++- BayesTools-0.2.14/BayesTools/R/model-averaging.R | 116 ++ BayesTools-0.2.14/BayesTools/R/priors-density.R | 39 BayesTools-0.2.14/BayesTools/R/priors-plot.R | 181 ++- BayesTools-0.2.14/BayesTools/R/priors-print.R | 12 BayesTools-0.2.14/BayesTools/R/priors-tools.R | 50 + BayesTools-0.2.14/BayesTools/R/priors.R | 434 ++++++--- BayesTools-0.2.14/BayesTools/R/summary-tables.R | 381 +++++++- BayesTools-0.2.14/BayesTools/R/tools.R | 43 BayesTools-0.2.14/BayesTools/build/partial.rdb |binary BayesTools-0.2.14/BayesTools/build/vignette.rds |binary BayesTools-0.2.14/BayesTools/inst/doc/ComparisonR.html | 133 +- BayesTools-0.2.14/BayesTools/inst/doc/SpikeAndSlab.html | 133 +- BayesTools-0.2.14/BayesTools/man/BayesTools_ensemble_tables.Rd | 49 - BayesTools-0.2.14/BayesTools/man/BayesTools_model_tables.Rd | 38 BayesTools-0.2.14/BayesTools/man/JAGS_diagnostics.Rd | 14 BayesTools-0.2.14/BayesTools/man/JAGS_evaluate_formula.Rd | 66 - BayesTools-0.2.14/BayesTools/man/JAGS_fit.Rd | 4 BayesTools-0.2.14/BayesTools/man/Savage_Dickey_BF.Rd |only BayesTools-0.2.14/BayesTools/man/add_column.Rd | 70 - BayesTools-0.2.14/BayesTools/man/contr.independent.Rd |only BayesTools-0.2.14/BayesTools/man/contr.meandif.Rd |only BayesTools-0.2.14/BayesTools/man/is.prior.Rd | 10 BayesTools-0.2.14/BayesTools/man/marginal_inference.Rd |only BayesTools-0.2.14/BayesTools/man/marginal_posterior.Rd |only BayesTools-0.2.14/BayesTools/man/mix_posteriors.Rd | 4 BayesTools-0.2.14/BayesTools/man/mpoint.Rd |only BayesTools-0.2.14/BayesTools/man/parameter_names.Rd | 76 - BayesTools-0.2.14/BayesTools/man/plot_marginal.Rd |only BayesTools-0.2.14/BayesTools/man/plot_models.Rd | 2 BayesTools-0.2.14/BayesTools/man/prior_factor.Rd | 12 BayesTools-0.2.14/BayesTools/man/remove_column.Rd |only BayesTools-0.2.14/BayesTools/man/transform_factor_samples.Rd |only BayesTools-0.2.14/BayesTools/man/transform_meandif_samples.Rd |only BayesTools-0.2.14/BayesTools/man/transform_orthonormal_samples.Rd | 48 - 48 files changed, 2104 insertions(+), 1246 deletions(-)
Title: Taxometric Analysis
Description: We provide functions to perform taxometric analyses. This package contains 46 functions, but only 5 should be called directly by users. CheckData() should be run prior to any taxometric analysis to ensure that the data are appropriate for taxometric analysis. RunTaxometrics() performs taxometric analyses for a sample of data. RunCCFIProfile() performs a series of taxometric analyses to generate a CCFI profile. CreateData() generates a sample of categorical or dimensional data. ClassifyCases() assigns cases to groups using the base-rate classification method.
Author: John Ruscio <ruscio@tcnj.edu> and Shirley Wang <shirleywang@g.harvard.edu>
Maintainer: John Ruscio <ruscio@tcnj.edu>
Diff between RTaxometrics versions 3.2 dated 2021-03-20 and 3.2.1 dated 2023-05-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 4 +++- R/print.profile.R | 4 +--- R/print.taxometrics.R | 4 +--- man/RunLMode.Rd | 6 +++--- man/RunMAXEIG.Rd | 6 +++--- 7 files changed, 21 insertions(+), 23 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>.
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Jan Linnenbrink [aut],
Philipp Otto [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 0.8.0 dated 2023-05-21 and 0.8.1 dated 2023-05-30
DESCRIPTION | 6 MD5 | 29 +-- NEWS.md | 5 inst/doc/cast01-CAST-intro.html | 8 inst/doc/cast02-AOA-tutorial.R | 17 - inst/doc/cast02-AOA-tutorial.Rmd | 19 +- inst/doc/cast02-AOA-tutorial.html | 356 +++++++++++++++++++------------------- inst/doc/cast03-AOA-parallel.R | 7 inst/doc/cast03-AOA-parallel.Rmd | 7 inst/doc/cast03-AOA-parallel.html | 35 +-- inst/doc/cast04-plotgeodist.html | 4 inst/extdata/bioclim.grd | 27 +- inst/extdata/bioclim.grd.aux.xml |only inst/extdata/bioclim.gri |binary vignettes/cast02-AOA-tutorial.Rmd | 19 +- vignettes/cast03-AOA-parallel.Rmd | 7 16 files changed, 279 insertions(+), 267 deletions(-)
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Katriona Goldmann [aut]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.6.2 dated 2023-05-15 and 0.6.4 dated 2023-05-30
DESCRIPTION | 6 +-- MD5 | 33 +++++++++---------- NAMESPACE | 1 NEWS.md | 13 +++++++ R/nestcv.train.R | 17 +++++++++ R/nestedcv.R | 26 +++++++++++++-- R/shap.R | 49 ++++++++++++++++++---------- R/varImp.R | 58 ++++++++++++++++++++------------- inst/CITATION |only inst/doc/nestedcv.html | 74 ++++++++++++++++++++----------------------- inst/doc/nestedcv_shap.html | 6 +-- man/barplot_var_stability.Rd | 8 ++-- man/cva.glmnet.Rd | 5 ++ man/nestcv.glmnet.Rd | 6 +++ man/nestcv.train.Rd | 6 +++ man/plot_shap_bar.Rd | 12 ++++++ man/plot_shap_beeswarm.Rd | 5 ++ man/plot_var_stability.Rd | 8 ++-- 18 files changed, 220 insertions(+), 113 deletions(-)
Title: Tools for Exploring Multivariate Data via ICS/ICA
Description: Implementation of Tyler, Critchley, Duembgen and Oja's (JRSS B, 2009,
<doi:10.1111/j.1467-9868.2009.00706.x>) and Oja, Sirkia and Eriksson's
(AJS, 2006, <https://www.ajs.or.at/index.php/ajs/article/view/vol35,%20no2%263%20-%207>) method of two different
scatter matrices to obtain an invariant coordinate system or independent
components, depending on the underlying assumptions.
Author: Klaus Nordhausen, Hannu Oja, David E. Tyler
Maintainer: Klaus Nordhausen <klaus.k.nordhausen@jyu.fi>
Diff between ICS versions 1.3-1 dated 2018-03-02 and 1.3-2 dated 2023-05-30
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/CHANGES | 7 +++++++ inst/CITATION | 24 +++++++----------------- inst/doc/ICS.R | 1 - inst/doc/ICS.pdf |binary man/ICS-package.Rd | 6 +++--- man/ics2.Rd | 2 +- 9 files changed, 34 insertions(+), 38 deletions(-)
Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [ctb, ctr],
Tim Schreier [ctb, ctr],
Luis Winckelman [ctb, ctr],
Quirin Stier [ctb, ctr],
Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between GeneralizedUmatrix versions 1.2.5 dated 2022-11-28 and 1.2.6 dated 2023-05-30
DESCRIPTION | 11 MD5 | 40 NAMESPACE | 3 R/GeneralizedUmatrix.R | 9 R/TopviewTopographicMap.R | 26 R/XYcoords2LinesColumns.R | 42 R/plotTopographicMap.R | 54 R/sESOM4BMUs.R | 2 R/tileGUM.R | 73 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/GeneralizedUmatrix.html | 2488 ++++++++++++++++++++++++-------------- man/GeneralizedUmatrix-package.Rd | 2 man/GeneralizedUmatrix.Rd | 4 man/TopviewTopographicMap.Rd | 14 man/XYcoords2LinesColumns.Rd | 4 man/plotTopographicMap.Rd | 12 man/sESOM4BMUs.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 21 files changed, 1757 insertions(+), 1035 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: Collection of Tools for LGD Rating Model Development
Description: The goal of this package is to cover the most common steps in Loss Given Default (LGD) rating model development.
The main procedures available are those that refer to bivariate and multivariate analysis. In particular two statistical methods for
multivariate analysis are currently implemented – OLS regression and fractional logistic regression.
Both methods are also available within different blockwise model designs and both have customized stepwise algorithms.
Descriptions of these customized designs are available in Siddiqi (2016) <doi:10.1002/9781119282396.ch10> and
Anderson, R.A. (2021) <doi:10.1093/oso/9780192844194.001.0001>.
Although they are explained for PD model, the same designs are applicable for LGD model with different underlying regression methods
(OLS and fractional logistic regression). To cover other important steps for LGD model development, it is recommended to use
'LGDtoolkit' package along with 'PDtoolkit', and 'monobin' (or 'monobinShiny') packages.
A [...truncated...]
Author: Andrija Djurovic [aut, cre]
Maintainer: Andrija Djurovic <djandrija@gmail.com>
Diff between LGDtoolkit versions 0.1.0 dated 2023-03-08 and 0.2.0 dated 2023-05-30
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++++------ NAMESPACE | 4 ++++ NEWS.md | 6 ++++++ R/03_STEP_FWD.R | 4 ++-- R/04_STEP_RPC.R | 2 +- R/12_HETEROGENEITY.R |only R/13_HOMOGENEITY.R |only README.md | 2 +- man/heterogeneity.Rd |only man/homogeneity.Rd |only 11 files changed, 29 insertions(+), 14 deletions(-)
Title: Extra Recipes for Encoding Predictors
Description: Predictors can be converted to one or more numeric
representations using a variety of methods. Effect encodings using
simple generalized linear models <arXiv:1611.09477> or nonlinear
models <arXiv:1604.06737> can be used. There are also functions for
dimension reduction and other approaches.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between embed versions 1.1.0 dated 2023-04-14 and 1.1.1 dated 2023-05-30
DESCRIPTION | 10 - MD5 | 110 +++++++++--------- NAMESPACE | 2 NEWS.md | 8 + R/collapse_stringdist.R | 2 R/discretize_cart.R | 23 ++- R/discretize_xgb.R | 21 ++- R/embed-package.R | 2 R/embed.R | 26 +++- R/feature_hash.R | 4 R/lencode_bayes.R | 24 ++-- R/lencode_glm.R | 16 ++ R/lencode_mixed.R | 22 ++- R/pca_sparse.R | 22 ++- R/pca_sparse_bayes.R | 21 ++- R/pca_truncated.R | 21 ++- R/umap.R | 10 + R/woe.R | 20 ++- man/step_collapse_stringdist.Rd | 2 man/step_discretize_cart.Rd | 2 man/step_lencode_bayes.Rd | 2 man/step_lencode_glm.Rd | 2 man/step_lencode_mixed.Rd | 2 man/step_pca_sparse.Rd | 2 man/step_pca_sparse_bayes.Rd | 2 man/step_umap.Rd | 2 man/step_woe.Rd | 2 tests/testthat/_snaps/collapse_cart.md | 32 ++--- tests/testthat/_snaps/collapse_stringdist.md | 32 ++--- tests/testthat/_snaps/discretize_cart.md | 93 ++++++++++----- tests/testthat/_snaps/discretize_xgb.md | 67 ++++++++--- tests/testthat/_snaps/embed.md | 44 ++++++- tests/testthat/_snaps/feature_hash.md | 44 ++++++- tests/testthat/_snaps/lencode_bayes.md | 87 ++++++++++---- tests/testthat/_snaps/lencode_glm.md | 67 ++++++++--- tests/testthat/_snaps/lencode_mixed.md | 67 ++++++++--- tests/testthat/_snaps/pca_sparse.md | 78 ++++++++++++- tests/testthat/_snaps/pca_sparse_bayes.md | 44 ++++++- tests/testthat/_snaps/pca_truncated.md | 44 ++++++- tests/testthat/_snaps/umap.md | 44 ++++++- tests/testthat/_snaps/woe.md | 65 ++++++++--- tests/testthat/test-collapse_cart.R | 62 +++++----- tests/testthat/test-collapse_stringdist.R | 76 +++++++----- tests/testthat/test-discretize_cart.R | 115 +++++++++++-------- tests/testthat/test-discretize_xgb.R | 102 ++++++++++------- tests/testthat/test-embed.R | 127 +++++++++++++-------- tests/testthat/test-feature_hash.R | 99 +++++++++++----- tests/testthat/test-helpers.R | 1 tests/testthat/test-lencode_bayes.R | 120 +++++++++++++------- tests/testthat/test-lencode_glm.R | 102 +++++++++++------ tests/testthat/test-lencode_mixed.R | 107 +++++++++++------- tests/testthat/test-pca_sparse.R | 128 +++++++++++++++++---- tests/testthat/test-pca_sparse_bayes.R | 159 ++++++++++++++++++--------- tests/testthat/test-pca_truncated.R | 106 +++++++++++++++--- tests/testthat/test-umap.R | 99 ++++++++++------ tests/testthat/test-woe.R | 134 +++++++++++++++------- 56 files changed, 1926 insertions(+), 801 deletions(-)
Title: CRAN Task Views
Description: Infrastructure for task views to CRAN-style repositories: Querying task views and installing the associated
packages (client-side tools), generating HTML pages and storing task view information in the repository
(server-side tools).
Author: Achim Zeileis [aut, cre] ,
Kurt Hornik [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ctv versions 0.9-4 dated 2022-11-05 and 0.9-5 dated 2023-05-30
DESCRIPTION | 16 +++------- MD5 | 18 +++++------ NEWS.md | 14 ++++++++ R/ctv-md.R | 19 ++++++------ R/ctv-server.R | 25 +++++++++------- build/vignette.rds |binary inst/CITATION | 37 ++++++++++++++++------- inst/doc/ctv-howto.Rmd | 30 +++++++++---------- inst/doc/ctv-howto.html | 75 ++++++++++++++++++++++++------------------------ vignettes/ctv-howto.Rmd | 30 +++++++++---------- 10 files changed, 147 insertions(+), 117 deletions(-)
Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Author: Bryan A. Hanson [aut, cre] ,
Tejasvi Gupta [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpecUtils versions 1.0.2 dated 2022-12-05 and 1.0.3 dated 2023-05-30
ChemoSpecUtils-1.0.2/ChemoSpecUtils/inst/tinytest/test_chkArgs.R |only ChemoSpecUtils-1.0.2/ChemoSpecUtils/inst/tinytest/test_chkGraphicsOpt.R |only ChemoSpecUtils-1.0.2/ChemoSpecUtils/inst/tinytest/test_chkSpectra.Spectra2D.R |only ChemoSpecUtils-1.0.2/ChemoSpecUtils/inst/tinytest/test_rowDist.R |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/DESCRIPTION | 14 ChemoSpecUtils-1.0.3/ChemoSpecUtils/MD5 | 200 +++++----- ChemoSpecUtils-1.0.3/ChemoSpecUtils/NEWS.md | 5 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/ChemoSpecUtils-package.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/GraphicsOptions.R | 32 - ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/addEllipseInfo.R | 11 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/addLegend.R | 15 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/addMethod.R | 11 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/check4Gaps.R | 6 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/checkForPackageWithVersion.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/chkArgs.R | 95 ++++ ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/chkGraphicsOpt.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/chkReqGraphicsPkgs.R | 11 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/chkSpectra.R | 5 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/chkSpectra.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/chkSpectra.Spectra2D.R | 19 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/colLeaf.R | 16 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/colorSymbol.R | 23 - ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/computeEllipses.R | 11 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/conColScheme.R | 9 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/distPlot.R | 15 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/documentation_functions.R |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/drawEllipses.R | 13 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/drawPoints.R | 15 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/extraData.R | 9 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/findNA.R | 31 + ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/getExtremeCoords.R | 11 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/getLimits.R | 13 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/getVarExplained.R | 10 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/ggAddLegend.R | 8 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/ggAnnotate.R | 6 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/ggRepel.R | 6 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/groupNcolor.R | 17 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/hcaScores.R | 6 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/hcaScores.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/hcaScores.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/labelExtremes.R | 9 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/onAttach.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/plotHCA.R | 10 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/plotScores.R | 13 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/plotScores.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/plotScores.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/plotScree.R | 7 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/plotScree.default.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/prepLegendCoords.R | 6 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/remGrpSam.R | 13 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeFreq.R | 12 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeFreq.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeFreq.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeGroup.R | 7 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeGroup.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeGroup.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeSample.R | 7 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeSample.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/removeSample.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/rowDist.R | 142 +++---- ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sampleDist.R | 66 +-- ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sampleDist.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sampleDist.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/scorePlot.R | 6 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/shrinkLeaf.R | 13 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sumGroups.R | 5 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sumGroups.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sumGroups.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sumSpectra.R | 5 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sumSpectra.Spectra.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/sumSpectra.Spectra2D.R | 2 ChemoSpecUtils-1.0.3/ChemoSpecUtils/R/updateGroups.R | 8 ChemoSpecUtils-1.0.3/ChemoSpecUtils/inst/tinytest/test-chkArgs.R |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/inst/tinytest/test-chkSpectra.Spectra2D.R | 16 ChemoSpecUtils-1.0.3/ChemoSpecUtils/inst/tinytest/test-findNA.R |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/GraphicsOptions.Rd | 72 +-- ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/check4Gaps.Rd | 5 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/checkForPackageWithVersion.Rd | 4 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/chkSpectra.Rd | 11 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/colorSymbol.Rd | 39 + ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/conColScheme.Rd | 9 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-addEllipseInfo.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-addLegend.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-addMethod.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-chkArgs.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-chkReqGraphicsPkgs.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-colLeaf.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-computeEllipses.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-distPlot.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-drawEllipses.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-drawPoints.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-extraData.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-findNA.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-getExtremeCoords.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-getLimits.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-getVarExplained.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-ggAddLegend.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-ggAnnotate.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-ggRepel.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-groupNcolor.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-labelExtremes.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-plotHCA.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-prepLegendCoords.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-remGrpSam.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-scorePlot.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/dot-shrinkLeaf.Rd |only ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/hcaScores.Rd | 18 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/plotScores.Rd | 40 -- ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/plotScree.Rd | 17 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/removeFreq.Rd | 12 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/removeGroup.Rd | 7 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/removeSample.Rd | 7 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/rowDist.Rd | 146 +++---- ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/sampleDist.Rd | 68 +-- ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/sumGroups.Rd | 15 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/sumSpectra.Rd | 5 ChemoSpecUtils-1.0.3/ChemoSpecUtils/man/updateGroups.Rd | 8 117 files changed, 827 insertions(+), 688 deletions(-)
More information about ChemoSpecUtils at CRAN
Permanent link
Title: Functions to Create Publication-Quality Plots
Description: Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.
Author: Paul Boutros [aut, cre],
Christine P'ng [ctb],
Jeff Green [ctb],
Stephenie Prokopec [ctb],
Ontario Institute for Cancer Research [cph],
The R Core Team [cph],
The R Foundation [cph],
Robert Gentleman [ctb],
Ross Ihaka [ctb],
Caden Bugh [ctb],
Dan Kni [...truncated...]
Maintainer: Paul Boutros <PBoutros@mednet.ucla.edu>
Diff between BoutrosLab.plotting.general versions 7.0.5 dated 2023-01-06 and 7.0.8 dated 2023-05-30
BoutrosLab.plotting.general-7.0.5/BoutrosLab.plotting.general/R/print.to.file.R |only BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/DESCRIPTION | 8 - BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/MD5 | 55 ++++---- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/NEWS | 39 ++++++ BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.barplot.R | 48 +++---- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.boxplot.R | 59 +-------- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.densityplot.R | 14 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.dotmap.R | 14 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.heatmap.R | 65 ---------- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.hexbinplot.R | 14 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.histogram.R | 55 ++++---- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.manhattanplot.R | 15 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.multipanelplot.R | 52 +++----- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.polygonplot.R | 15 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.qqplot.comparison.R | 19 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.qqplot.fit.R | 20 --- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.scatterplot.R | 15 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.segplot.R | 14 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.stripplot.R | 14 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/create.violinplot.R | 18 -- BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/export.to.file.R |only BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/R/legend.grob.R | 17 ++ BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/README.md |only BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/build/vignette.rds |binary BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/inst/doc/PlottingGuide.pdf |binary BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/man/create.barplot.Rd | 2 BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/man/create.boxplot.Rd | 23 +++ BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/man/create.histogram.Rd | 14 ++ BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/man/create.scatterplot.Rd | 2 BoutrosLab.plotting.general-7.0.8/BoutrosLab.plotting.general/man/create.segplot.Rd | 2 30 files changed, 215 insertions(+), 398 deletions(-)
More information about BoutrosLab.plotting.general at CRAN
Permanent link
Title: Delaunay and Voronoï Tessellations
Description: Delaunay and Voronoï tessellations, with emphasis on the
two-dimensional and the three-dimensional cases (the package provides
functions to plot the tessellations for these cases). Delaunay
tessellations are computed in C with the help of the 'Qhull' library
<http://www.qhull.org/>.
Author: Stephane Laurent [aut, cre],
C. B. Barber [cph] ,
The Geometry Center [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between tessellation versions 2.1.2 dated 2023-03-08 and 2.1.3 dated 2023-05-30
DESCRIPTION | 8 MD5 | 14 NEWS.md | 5 R/voronoi.R | 927 ++++++++++++++++++++++++++++------------------------------ man/Edge2.Rd | 30 - man/Edge3.Rd | 30 - man/IEdge2.Rd | 18 - man/IEdge3.Rd | 18 - 8 files changed, 527 insertions(+), 523 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] ,
Avi Srivastava [aut] ,
Paul Hoffman [ctb] ,
Rahul Satija [ctb]
Maintainer: Tim Stuart <stuartt@gis.a-star.edu.sg>
Diff between Signac versions 1.9.0 dated 2022-12-08 and 1.10.0 dated 2023-05-30
Signac-1.10.0/Signac/DESCRIPTION | 18 +- Signac-1.10.0/Signac/MD5 | 38 ++-- Signac-1.10.0/Signac/NAMESPACE | 6 Signac-1.10.0/Signac/NEWS.md | 19 ++ Signac-1.10.0/Signac/R/generics.R | 6 Signac-1.10.0/Signac/R/heatmaps.R | 90 ++++------ Signac-1.10.0/Signac/R/motifs.R | 8 Signac-1.10.0/Signac/R/objects.R | 9 + Signac-1.10.0/Signac/R/preprocessing.R | 39 ++++ Signac-1.10.0/Signac/R/utilities.R | 55 ++++-- Signac-1.10.0/Signac/R/visualization.R | 164 ++++++++++++++++++- Signac-1.10.0/Signac/build/partial.rdb |binary Signac-1.10.0/Signac/data/blacklist_hg38_unified.rda |binary Signac-1.10.0/Signac/inst/CITATION | 12 - Signac-1.10.0/Signac/man/AddMotifs.Rd | 8 Signac-1.10.0/Signac/man/DensityScatter.Rd |only Signac-1.10.0/Signac/man/FindTopFeatures.Rd | 4 Signac-1.10.0/Signac/man/LinkPlot.Rd | 5 Signac-1.10.0/Signac/man/Signac-package.Rd | 2 Signac-1.10.0/Signac/src/Makevars.win | 1 Signac-1.9.0/Signac/src/Makevars |only 21 files changed, 360 insertions(+), 124 deletions(-)
Title: Colour Palettes Based on the Scientific Colour-Maps
Description: Colour choice in information visualisation is important in order to
avoid being mislead by inherent bias in the used colour palette. The 'scico'
package provides access to the perceptually uniform and colour-blindness
friendly palettes developed by Fabio Crameri and released under the
"Scientific Colour-Maps" moniker. The package contains 24 different palettes
and includes both diverging and sequential types.
Author: Thomas Lin Pedersen [aut, cre]
,
Fabio Crameri [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between scico versions 1.3.1 dated 2022-08-19 and 1.4.0 dated 2023-05-30
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/palette.R | 42 +++++++++++++++++++++++++++++++++--------- R/sysdata.rda |binary README.md | 6 +++--- build/partial.rdb |binary man/scico.Rd | 14 ++++++++++++-- man/scico_data.Rd | 6 ++++-- man/scico_palette_show.Rd | 11 ++++++++++- 10 files changed, 80 insertions(+), 31 deletions(-)
Title: Analysis and Visualisation of Benchmark Experiments
Description: Implements methods for post-hoc analysis and
visualisation of benchmark experiments, for 'mlr3' and beyond.
Author: Sonabend Raphael [aut] ,
Florian Pfisterer [aut] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Sebastian Fischer [cre, ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3benchmark versions 0.1.5 dated 2023-03-14 and 0.1.6 dated 2023-05-30
DESCRIPTION | 6 - MD5 | 29 ++++----- NAMESPACE | 3 NEWS.md | 4 + R/BenchmarkAggr.R | 85 +++++++++++++++++++++++---- R/autoplot.BenchmarkAggr.R | 2 README.md | 3 man/BenchmarkAggr.Rd | 6 - man/as.BenchmarkAggr.Rd | 8 +- man/as_benchmark_aggr.Rd |only man/autoplot.BenchmarkAggr.Rd | 2 man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-8-2.png |binary tests/testthat/test_BenchmarkAggr.R | 21 +++++- tests/testthat/test_autoplot_BenchmarkAggr.R | 2 16 files changed, 127 insertions(+), 44 deletions(-)
Title: Swarm Intelligence for Self-Organized Clustering
Description: Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called Databionic swarm (DBS) is introduced which was published in Thrun, M.C., Ultsch A.: "Swarm Intelligence for Self-Organized Clustering" (2020), Artificial Intelligence, <DOI:10.1016/j.artint.2020.103237>. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matri [...truncated...]
Author: Michael Thrun [aut, cre, cph] ,
Quirin Stier [aut, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DatabionicSwarm versions 1.1.6 dated 2022-11-29 and 1.2.0 dated 2023-05-30
DESCRIPTION | 20 MD5 | 53 NAMESPACE | 6 R/DBSclustering.R | 131 + R/Delaunay4Points.R | 45 R/DelaunayClassificationError.R | 9 R/GeneratePswarmVisualization.R | 4 R/Pswarm.R | 7 R/RcppExports.R | 4 R/ShortestGraphPathsC.R | 3 R/getCartesianCoordinates.R | 53 R/sESOM4BMUs.R | 226 +-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/NEWS | 10 inst/doc/DatabionicSwarm.html | 2496 +++++++++++++++++++++++-------------- man/DBSclustering.Rd | 11 man/Delaunay4Points.Rd | 5 man/DelaunayClassificationError.Rd | 5 man/GeneratePswarmVisualization.Rd | 5 man/Pswarm.Rd | 7 man/sESOM4BMUs.Rd | 5 src/DatabionicSwarm_init.c | 3 src/Makevars | 23 src/Makevars.win | 28 src/RcppExports.cpp | 19 src/trainstepC2.cpp |only 28 files changed, 1996 insertions(+), 1186 deletions(-)
More information about DatabionicSwarm at CRAN
Permanent link
Title: Bayesian Inference and Model Selection for Stochastic Epidemics
Description: Bayesian analysis for stochastic extensions of non-linear
dynamic systems using advanced computational algorithms. Described in Bouranis, L.,
Demiris, N., Kalogeropoulos, K., and Ntzoufras, I. (2022) <arXiv:2211.15229>.
Author: Lampros Bouranis [aut, cre, cph]
,
European Union [fnd]
Maintainer: Lampros Bouranis <bernadette.aueb@gmail.com>
Diff between Bernadette versions 1.1.2 dated 2023-05-25 and 1.1.3 dated 2023-05-30
DESCRIPTION | 6 ++-- MD5 | 46 ++++++++++++++++++------------------- R/misc.R | 3 -- R/posterior_contactmatrix.R | 25 +++++++++++++++++--- R/posterior_infections.R | 48 ++++++++++++++++++++++++++++++++++----- R/posterior_mortality.R | 48 ++++++++++++++++++++++++++++++++++----- R/posterior_rt.R | 48 ++++++++++++++++++++++++++++++++++----- R/posterior_transmrate.R | 48 ++++++++++++++++++++++++++++++++++----- R/stan_igbm.R | 23 ++++++++++++++++-- R/stan_igbm.fit.R | 2 - R/summary.stangbm.R | 25 +++++++++++++++++--- inst/doc/Bernadette.html | 2 - inst/stan/igbm.stan | 2 - man/plot_posterior_cm.Rd | 23 ++++++++++++++++-- man/plot_posterior_infections.Rd | 23 ++++++++++++++++-- man/plot_posterior_mortality.Rd | 23 ++++++++++++++++-- man/plot_posterior_rt.Rd | 23 ++++++++++++++++-- man/plot_posterior_transmrate.Rd | 23 ++++++++++++++++-- man/posterior_infections.Rd | 23 ++++++++++++++++-- man/posterior_mortality.Rd | 23 ++++++++++++++++-- man/posterior_rt.Rd | 23 ++++++++++++++++-- man/posterior_transmrate.Rd | 23 ++++++++++++++++-- man/stan_igbm.Rd | 23 ++++++++++++++++-- man/summary.stanigbm.Rd | 23 ++++++++++++++++-- 24 files changed, 481 insertions(+), 98 deletions(-)
Title: Assertions to Check Properties of Code
Description: A set of predicates and assertions for checking the properties of
code. This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually want to
use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.code versions 0.0-3 dated 2018-10-21 and 0.0-4 dated 2023-05-30
assertive.code-0.0-3/assertive.code/NEWS |only assertive.code-0.0-4/assertive.code/DESCRIPTION | 15 assertive.code-0.0-4/assertive.code/MD5 | 24 assertive.code-0.0-4/assertive.code/NEWS.md |only assertive.code-0.0-4/assertive.code/R/is-code.R | 868 +++++----- assertive.code-0.0-4/assertive.code/README.md | 113 - assertive.code-0.0-4/assertive.code/man/has_arg.Rd | 7 assertive.code-0.0-4/assertive.code/man/is_binding_locked.Rd | 10 assertive.code-0.0-4/assertive.code/man/is_existing.Rd | 24 assertive.code-0.0-4/assertive.code/man/is_if_condition.Rd | 3 assertive.code-0.0-4/assertive.code/man/is_loaded.Rd | 14 assertive.code-0.0-4/assertive.code/man/is_valid_r_code.Rd | 3 assertive.code-0.0-4/assertive.code/man/is_valid_variable_name.Rd | 25 assertive.code-0.0-4/assertive.code/tests/testthat/test-is-code.R | 301 +-- 14 files changed, 723 insertions(+), 684 deletions(-)
More information about assertive.code at CRAN
Permanent link
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] ,
Zoltan Herczeg [ctb, cph] ,
University of Cambridge [cph] ,
Tilera Corporation [cph] ,
Yann Collet [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.15.7 dated 2022-04-13 and 0.15.8 dated 2023-05-30
ChangeLog | 5 ++++ DESCRIPTION | 10 ++++---- MD5 | 30 +++++++++++++------------- R/zz_help_files.R | 10 ++++---- README.md | 8 ++---- build/vignette.rds |binary inst/doc/vignette.R | 18 +++++++++++++++ inst/doc/vignette.html | 3 -- inst/doc/vignette.rmd | 26 +++++++++++++++++----- man/string_identical.Rd | 7 ++++++ src/Makevars.in | 1 src/Makevars.win | 1 src/PCRE2/pcre2.h | 2 - src/sf_functions.cpp | 22 ++++++++++++------- tests/tests.r | 55 +++++++++++++++++++++++++++++++++++++++--------- vignettes/vignette.rmd | 26 +++++++++++++++++----- 16 files changed, 159 insertions(+), 65 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevedata versions 0.9.0 dated 2023-01-19 and 1.0.0 dated 2023-05-30
DESCRIPTION | 8 +++--- MD5 | 56 +++++++++++++++++++++++++++------------------ NEWS.md | 18 ++++++++++++++ R/rd-Datasaurus.R | 1 R/rd-ESS10NO.R | 2 - R/rd-LOTI.R | 4 +-- R/rd-ODGI.R | 4 +-- R/rd-OODTPT.R |only R/rd-PRDEG.R |only R/rd-coffee_imports.R | 28 ++++++++++++++++------ R/rd-eurostate_codes.R |only R/rd-thatcher_approval.R | 3 -- R/rd-wbd_example.R |only README.md | 13 ++++------ build/partial.rdb |binary data/LOTI.rda |binary data/ODGI.rda |binary data/OODTPT.rda |only data/PRDEG.rda |only data/coffee_imports.rda |binary data/eurostat_codes.rda |only data/thatcher_approval.rda |binary data/turnips.rda |binary data/ukg_eeri.rda |binary data/wbd_example.rda |only man/Datasaurus.Rd | 1 man/ESS10NO.Rd | 2 - man/LOTI.Rd | 4 +-- man/ODGI.Rd | 4 +-- man/OODTPT.Rd |only man/PRDEG.Rd |only man/coffee_imports.Rd | 28 ++++++++++++++++------ man/eurostat_codes.Rd |only man/thatcher_approval.Rd | 3 -- man/wbd_example.Rd |only 35 files changed, 116 insertions(+), 63 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.6.0 dated 2023-01-23 and 0.6.1 dated 2023-05-30
inti-0.6.0/inti/R/include_figure.R |only inti-0.6.0/inti/man/include_figure.Rd |only inti-0.6.1/inti/DESCRIPTION | 8 inti-0.6.1/inti/MD5 | 51 ++-- inti-0.6.1/inti/NAMESPACE | 2 inti-0.6.1/inti/NEWS.md | 23 ++ inti-0.6.1/inti/R/gdoc2qmd.R | 108 +++++++++- inti-0.6.1/inti/R/include_pdf.R |only inti-0.6.1/inti/R/table2qmd.R | 18 - inti-0.6.1/inti/R/tarpuy_plex.R | 57 ++--- inti-0.6.1/inti/R/tarpuy_traits.R | 35 +-- inti-0.6.1/inti/build/partial.rdb |binary inti-0.6.1/inti/build/vignette.rds |binary inti-0.6.1/inti/inst/doc/apps.html | 2 inti-0.6.1/inti/inst/doc/rticles.html | 2 inti-0.6.1/inti/inst/doc/yupana.R | 38 +-- inti-0.6.1/inti/inst/doc/yupana.Rmd | 32 +- inti-0.6.1/inti/inst/doc/yupana.html | 2 inti-0.6.1/inti/inst/style.docx |only inti-0.6.1/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 6 inti-0.6.1/inti/inst/tarpuy/server.R | 38 ++- inti-0.6.1/inti/inst/tarpuy/ui.R | 48 +++- inti-0.6.1/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 6 inti-0.6.1/inti/man/gdoc2qmd.Rd | 4 inti-0.6.1/inti/man/include_pdf.Rd |only inti-0.6.1/inti/man/table2qmd.Rd | 4 inti-0.6.1/inti/man/tarpuy_plex.Rd | 7 inti-0.6.1/inti/man/tarpuy_traits.Rd | 6 inti-0.6.1/inti/vignettes/yupana.Rmd | 32 +- 29 files changed, 341 insertions(+), 188 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] ,
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.3.1 dated 2022-05-20 and 1.3.3 dated 2023-05-30
DESCRIPTION | 29 MD5 | 66 NAMESPACE | 205 - R/ClusterAccuracy.R | 188 - R/ClusterApply.R | 43 R/ClusterCount.R | 58 R/ClusterCreateClassification.R | 54 R/ClusterEqualWeighting.R | 3 R/ClusterMCC.R | 78 R/ClusterUpsamplingMinority.R | 18 R/ClusterabilityMDplot.R | 46 R/CrossEntropyClustering.R |only R/DBscan.R | 37 R/DatabionicSwarmClustering.R | 318 +- R/GapStatistic.R |only R/HierarchicalClusterData.R | 4 R/HierarchicalClusterDists.R | 4 R/MeanShiftClustering.R |only R/kmeansClustering.R | 168 + build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/FCPS.R | 208 - inst/doc/FCPS.html | 5019 ++++++++++++++++++------------------- man/ClusterApply.Rd | 17 man/ClusterCount.Rd | 19 man/ClusterCreateClassification.Rd | 14 man/ClusterDistances.Rd | 2 man/ClusterInterDistances.Rd | 2 man/ClusterMCC.Rd | 125 man/ClusterabilityMDplot.Rd | 219 - man/CrossEntropyClustering.Rd |only man/DBscan.Rd | 7 man/DatabionicSwarmClustering.Rd | 291 +- man/GapStatistic.Rd |only man/MeanShiftClustering.Rd |only man/kmeansClustering.Rd | 35 37 files changed, 3802 insertions(+), 3479 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Multiple or Multilayer Networks
Description: A set of extensions for the 'ergm' package to fit multilayer/multiplex/multirelational networks and samples of multiple networks. 'ergm.multi' is a part of the Statnet suite of packages for network analysis. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Krivitsky, Coletti, and Hens (2022) <doi:10.48550/arXiv.2202.03685>.
Author: Pavel N. Krivitsky [aut, cre] ,
Mark S. Handcock [ctb],
David R. Hunter [ctb],
Chad Klumb [ctb],
Pietro Coletti [ctb],
Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm.multi versions 0.1.2 dated 2023-01-05 and 0.2.0 dated 2023-05-30
DESCRIPTION | 20 LICENSE | 2 MD5 | 124 +++--- NAMESPACE | 2 R/InitErgmConstraint.R | 2 R/InitErgmProposal.blockdiag.R | 2 R/InitErgmTerm.R | 2 R/InitErgmTerm.dgw_sp.R | 2 R/InitErgmTerm.multilayer.R | 18 R/InitErgmTerm.multinet.R | 6 R/InitErgmTerm.spcache.multilayer.R | 2 R/InitWtErgmTerm.multinet.R | 2 R/block_blacklist.R | 4 R/combine.networks.R | 30 - R/data.R | 2 R/ergm.multi-package.R | 2 R/ergmlhs.R | 2 R/gofN.R | 202 ++++++++-- R/marg_cond_sim.R | 10 R/print.combined_networks.R | 2 R/zzz.R | 4 build/ergm.multi.pdf |binary build/partial.rdb |binary build/stage23.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/NEWS.Rd | 23 + inst/doc/Goeyvaerts_reproduction.R | 7 inst/doc/Goeyvaerts_reproduction.Rmd | 7 inst/doc/Goeyvaerts_reproduction.html | 125 +++++- inst/include/ergm.multi_MHblockdiag.h | 2 inst/include/ergm.multi_changestat_multilayer.h | 2 inst/include/ergm.multi_changestat_multilayer_common.do_not_include_directly.h | 2 inst/include/ergm.multi_stubs.c | 2 man/gofN.Rd | 79 +-- man/plot.gofN.Rd |only src/MHproposals_block.c | 2 src/MHproposals_block.h | 2 src/changestats_dgw_sp_ML.c | 2 src/changestats_dgw_sp_ML.h | 2 src/changestats_multilayer.c | 2 src/changestats_multinet.c | 2 src/changestats_spcache_ML.c | 2 src/ergm.multi_changestat_multinet.h | 2 src/ergm.multi_changestat_multinet_common.do_not_include_directly.h | 2 src/ergm.multi_wtchangestat_multinet.h | 2 src/include_stubs.c | 2 src/init.c | 2 src/mean_var.c | 2 src/wtchangestats_multinet.c | 2 tests/testthat.R | 2 tests/testthat/test-multilayer-CMB.R | 2 tests/testthat/test-multilayer-MLE.R | 2 tests/testthat/test-multilayer-MPLE.R | 2 tests/testthat/test-multilayer-direction.R | 2 tests/testthat/test-multilayer-heterogeneous-directedness.R | 2 tests/testthat/test-multilayer-mutuality.R | 2 tests/testthat/test-multilayer-summary.R | 2 tests/testthat/test-multilayer-triadic.R | 2 tests/testthat/test-multilayer.R | 2 tests/testthat/test-multinet.R | 2 tests/testthat/test-subnetcache.R | 2 tests/testthat/test-term-dgwesp-ml.R | 2 vignettes/Goeyvaerts_reproduction.Rmd | 7 64 files changed, 523 insertions(+), 237 deletions(-)
Title: Interact with 'Condor' from R via SSH
Description: Interact with 'Condor' from R via SSH connection. Files are first
uploaded from user machine to submitter machine, and the job is then submitted
from the submitter machine to 'Condor'. Functions are provided to submit,
list, and download 'Condor' jobs from R. 'Condor' is an open source
high-throughput computing software framework for distributed parallelization
of computationally intensive tasks.
Author: Arni Magnusson [aut, cre],
Jemery Day [ctb],
Thomas Teears [ctb]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between condor versions 1.0.0 dated 2023-04-03 and 1.0.1 dated 2023-05-30
DESCRIPTION | 12 ++++++---- MD5 | 32 ++++++++++++++-------------- NEWS.md | 13 +++++++++++ R/condor-package.R | 3 ++ R/condor_dir.R | 42 +++++++++++++++++++++++++++---------- R/condor_download.R | 17 +++++++++++---- R/condor_log.R | 51 +++++++++++++++++++++++++++++++++++----------- R/condor_q.R | 5 ++++ R/condor_submit.R | 5 ++++ R/summary.condor_log.R | 7 ++++++ man/condor-package.Rd | 3 ++ man/condor_dir.Rd | 13 +++++++++-- man/condor_download.Rd | 15 +++++++++---- man/condor_log.Rd | 16 ++++++++++++-- man/condor_q.Rd | 5 ++++ man/condor_submit.Rd | 5 ++++ man/summary.condor_log.Rd | 7 ++++++ 17 files changed, 194 insertions(+), 57 deletions(-)
Title: Spatial Dynamic Panel Data Modeling
Description: Spatial model calculation for static and dynamic panel data models, weights matrix creation and Bayesian model comparison.
Bayesian model comparison methods were described by 'LeSage' (2014) <doi:10.1016/j.spasta.2014.02.002>.
The 'Lee'-'Yu' transformation approach is described in 'Yu', 'De Jong' and 'Lee' (2008) <doi:10.1016/j.jeconom.2008.08.002>, 'Lee' and 'Yu' (2010) <doi:10.1016/j.jeconom.2009.08.001> and 'Lee' and 'Yu' (2010) <doi:10.1017/S0266466609100099>.
Author: Rozeta Simonovska [aut, cre]
Maintainer: Rozeta Simonovska <simonovska.r@gmail.com>
Diff between SDPDmod versions 0.0.2 dated 2023-04-13 and 0.0.3 dated 2023-05-30
DESCRIPTION | 8 +++--- MD5 | 10 +++---- NEWS.md | 4 +++ R/SDPDm.R | 2 - build/vignette.rds |binary inst/doc/spatial_model.html | 58 ++++++++++++++++++++++---------------------- 6 files changed, 43 insertions(+), 39 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory models can be estimated with quadrature (EM)
or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modeling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models, including mixture and zero-inflated response models,
are supported.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.38.1 dated 2023-02-27 and 1.39 dated 2023-05-30
DESCRIPTION | 6 MD5 | 50 +- NEWS.md | 13 R/DIF.R | 101 ++++- R/DRF.R | 186 ++++++--- R/SIBTEST.R | 820 +++++++++++++++++++++++++++++------------ R/expected.test.R | 6 R/fscores.R | 5 R/fscores.internal.R | 50 +- R/itemfit.R | 2 R/itemplot.R | 6 R/mirtCluster.R | 5 R/utils.R | 19 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mirt-vignettes.html | 204 ++++++---- man/DIF.Rd | 45 ++ man/DRF.Rd | 24 - man/SIBTEST.Rd | 126 +++++- man/expected.test.Rd | 4 man/fscores.Rd | 5 man/itemplot.Rd | 6 man/mirtCluster.Rd | 3 tests/tests/test-11-discrete.R | 3 tests/tests/test-16-DCIRT.R | 14 tests/tests/test-17-DIF_DRF.R | 15 26 files changed, 1228 insertions(+), 490 deletions(-)
Title: L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments,
and Many Distributions
Description: Extensive functions for L-moments (LMs) and probability-weighted moments
(PWMs), parameter estimation for distributions, LM computation for distributions, and
L-moment ratio diagrams. Maximum likelihood and maximum product of spacings estimation
are also available. LMs for right-tail and left-tail censoring by known or unknown threshold
and by indicator variable are available. Asymmetric (asy) trimmed LMs (TL-moments, TLMs) are
supported. LMs of residual (resid) and reversed (rev) residual life are implemented along
with 13 quantile function operators for reliability and survival analyses. Exact analytical
bootstrap estimates of order statistics, LMs, and variances-covariances of LMs are provided.
The Harri-Coble Tau34-squared Normality Test is available. Distribution support with
"L" (LMs), "TL" (TLMs) and added (+) support for right-tail censoring (RC) encompasses:
Asy Exponential (Exp) Power [L], Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L],
Gamma [L], Generalized (Gen) Exp [...truncated...]
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between lmomco versions 2.4.7 dated 2022-08-26 and 2.4.9 dated 2023-05-30
DESCRIPTION | 8 MD5 | 722 +++++++++++++++++++++--------------------- NAMESPACE | 2 NEWS |only R/cvm.test.lmomco.R | 2 R/disfitqua.R | 2 R/headrick.sheng.lalpha.R | 89 ++++- R/pp.R | 27 + R/tau34sq.normtest.R | 2 R/zzz.R | 2 build/partial.rdb |binary inst/CITATION | 4 man/Apwm2BpwmRC.Rd | 6 man/BEhypergeo.Rd | 2 man/Bpwm2ApwmRC.Rd | 6 man/LaguerreHalf.Rd | 2 man/Lcomoment.Lk12.Rd | 4 man/Lcomoment.Wk.Rd | 4 man/Lcomoment.coefficients.Rd | 4 man/Lcomoment.correlation.Rd | 4 man/Lcomoment.matrix.Rd | 4 man/T2prob.Rd | 2 man/TLmom.Rd | 4 man/TLmoms.Rd | 4 man/add.lmomco.axis.Rd | 2 man/add.log.axis.Rd | 2 man/are.lmom.valid.Rd | 2 man/are.par.valid.Rd | 4 man/are.paraep4.valid.Rd | 4 man/are.parcau.valid.Rd | 4 man/are.paremu.valid.Rd | 4 man/are.parexp.valid.Rd | 4 man/are.pargam.valid.Rd | 4 man/are.pargep.valid.Rd | 4 man/are.pargev.valid.Rd | 2 man/are.pargld.valid.Rd | 4 man/are.parglo.valid.Rd | 4 man/are.pargno.valid.Rd | 5 man/are.pargov.valid.Rd | 4 man/are.pargpa.valid.Rd | 4 man/are.pargum.valid.Rd | 4 man/are.parkap.valid.Rd | 4 man/are.parkmu.valid.Rd | 4 man/are.parkur.valid.Rd | 4 man/are.parlap.valid.Rd | 4 man/are.parlmrq.valid.Rd | 4 man/are.parln3.valid.Rd | 4 man/are.parnor.valid.Rd | 4 man/are.parpdq3.valid.Rd | 2 man/are.parpdq4.valid.Rd | 2 man/are.parpe3.valid.Rd | 4 man/are.parray.valid.Rd | 4 man/are.parrevgum.valid.Rd | 4 man/are.parrice.valid.Rd | 4 man/are.parsla.valid.Rd | 4 man/are.parst3.valid.Rd | 4 man/are.partexp.valid.Rd | 4 man/are.partri.valid.Rd | 4 man/are.parwak.valid.Rd | 4 man/are.parwei.valid.Rd | 4 man/bfrlmomco.Rd | 2 man/cdf2lmom.Rd | 4 man/cdf2lmoms.Rd | 4 man/cdfaep4.Rd | 2 man/cdfcau.Rd | 2 man/cdfemu.Rd | 2 man/cdfexp.Rd | 2 man/cdfgam.Rd | 2 man/cdfgep.Rd | 2 man/cdfgld.Rd | 2 man/cdfglo.Rd | 4 man/cdfgno.Rd | 5 man/cdfgov.Rd | 2 man/cdfgum.Rd | 2 man/cdfkap.Rd | 2 man/cdfkmu.Rd | 2 man/cdfkur.Rd | 2 man/cdflap.Rd | 2 man/cdflmrq.Rd | 2 man/cdfln3.Rd | 2 man/cdfnor.Rd | 2 man/cdfpe3.Rd | 2 man/cdfray.Rd | 2 man/cdfrevgum.Rd | 2 man/cdfrice.Rd | 2 man/cdfsla.Rd | 2 man/cdfst3.Rd | 2 man/cdftexp.Rd | 2 man/cdftri.Rd | 2 man/cdfwak.Rd | 2 man/cdfwei.Rd | 2 man/check.fs.Rd | 7 man/check.pdf.Rd | 4 man/cmlmomco.Rd | 2 man/cvm.test.lmomco.Rd | 6 man/dat2bernqua.Rd | 87 ++--- man/dat2bernquaf.Rd | 18 - man/disfitqua.Rd | 6 man/dist.list.Rd | 2 man/dlmomco.Rd | 2 man/expect.max.ostat.Rd | 2 man/f2f.Rd | 4 man/f2flo.Rd | 4 man/f2fpds.Rd | 4 man/fliplmoms.Rd | 2 man/flo2f.Rd | 4 man/fpds2f.Rd | 4 man/freq.curve.all.Rd | 7 man/gen.freq.curves.Rd | 2 man/genci.simple.Rd | 2 man/grv2prob.Rd | 2 man/harmonic.mean.Rd | 4 man/headrick.sheng.lalpha.Rd | 180 +++++++++- man/hlmomco.Rd | 2 man/is.aep4.Rd | 4 man/is.cau.Rd | 4 man/is.emu.Rd | 4 man/is.exp.Rd | 4 man/is.gam.Rd | 4 man/is.gep.Rd | 4 man/is.gev.Rd | 4 man/is.gld.Rd | 4 man/is.glo.Rd | 4 man/is.gno.Rd | 4 man/is.gov.Rd | 4 man/is.gpa.Rd | 4 man/is.gum.Rd | 4 man/is.kap.Rd | 4 man/is.kmu.Rd | 4 man/is.kur.Rd | 4 man/is.lap.Rd | 4 man/is.lmrq.Rd | 4 man/is.ln3.Rd | 4 man/is.nor.Rd | 4 man/is.pdq3.Rd | 2 man/is.pdq4.Rd | 2 man/is.pe3.Rd | 4 man/is.ray.Rd | 4 man/is.revgum.Rd | 4 man/is.rice.Rd | 4 man/is.sla.Rd | 4 man/is.st3.Rd | 4 man/is.texp.Rd | 4 man/is.tri.Rd | 4 man/is.wak.Rd | 4 man/is.wei.Rd | 4 man/lcomoms2.Rd | 4 man/lkhlmomco.Rd | 2 man/lmom.ub.Rd | 4 man/lmom2par.Rd | 2 man/lmom2pwm.Rd | 2 man/lmom2vec.Rd | 6 man/lmomRCmark.Rd | 4 man/lmomTLgld.Rd | 2 man/lmomTLgpa.Rd | 2 man/lmomaep4.Rd | 2 man/lmomcau.Rd | 2 man/lmomco-package.Rd | 3 man/lmomcohash.Rd |only man/lmomemu.Rd | 2 man/lmomexp.Rd | 2 man/lmomgam.Rd | 2 man/lmomgep.Rd | 2 man/lmomgev.Rd | 2 man/lmomgld.Rd | 2 man/lmomglo.Rd | 2 man/lmomgno.Rd | 5 man/lmomgov.Rd | 2 man/lmomgpa.Rd | 2 man/lmomgpaRC.Rd | 2 man/lmomgum.Rd | 2 man/lmomkap.Rd | 2 man/lmomkmu.Rd | 2 man/lmomkur.Rd | 2 man/lmomlap.Rd | 2 man/lmomlmrq.Rd | 4 man/lmomln3.Rd | 2 man/lmompe3.Rd | 2 man/lmomray.Rd | 2 man/lmomrevgum.Rd | 2 man/lmomrice.Rd | 2 man/lmoms.Rd | 4 man/lmoms.bernstein.Rd | 6 man/lmoms.bootbarvar.Rd | 6 man/lmoms.cov.Rd | 7 man/lmomsRCmark.Rd | 4 man/lmomsla.Rd | 2 man/lmomst3.Rd | 2 man/lmomtexp.Rd | 2 man/lmomtri.Rd | 2 man/lmomwak.Rd | 2 man/lmomwei.Rd | 2 man/lmorph.Rd | 4 man/lmrdia.Rd | 4 man/lmrdiscord.Rd | 4 man/lrv2prob.Rd | 2 man/lrzlmomco.Rd | 2 man/mle2par.Rd | 17 man/mps2par.Rd | 2 man/nonexceeds.Rd | 6 man/par2cdf.Rd | 2 man/par2cdf2.Rd | 2 man/par2lmom.Rd | 2 man/par2qua.Rd | 2 man/par2qua2.Rd | 4 man/par2qua2lo.Rd | 4 man/par2vec.Rd | 2 man/parTLgld.Rd | 2 man/parTLgpa.Rd | 2 man/paraep4.Rd | 2 man/parcau.Rd | 2 man/paremu.Rd | 2 man/parexp.Rd | 2 man/pargam.Rd | 2 man/pargep.Rd | 2 man/pargev.Rd | 2 man/pargld.Rd | 2 man/parglo.Rd | 5 man/pargno.Rd | 5 man/pargov.Rd | 2 man/pargpa.Rd | 2 man/pargpaRC.Rd | 2 man/pargum.Rd | 2 man/parkap.Rd | 2 man/parkmu.Rd | 2 man/parkur.Rd | 2 man/parlap.Rd | 2 man/parlmrq.Rd | 2 man/parln3.Rd | 2 man/parnor.Rd | 2 man/parpe3.Rd | 5 man/parray.Rd | 2 man/parrevgum.Rd | 2 man/parrice.Rd | 2 man/pars2x.Rd | 2 man/parsla.Rd | 2 man/parst3.Rd | 2 man/partexp.Rd | 2 man/partri.Rd | 2 man/parwak.Rd | 2 man/parwei.Rd | 2 man/pdfaep4.Rd | 2 man/pdfcau.Rd | 2 man/pdfemu.Rd | 2 man/pdfexp.Rd | 2 man/pdfgam.Rd | 2 man/pdfgep.Rd | 2 man/pdfgld.Rd | 2 man/pdfglo.Rd | 2 man/pdfgno.Rd | 5 man/pdfgov.Rd | 2 man/pdfgum.Rd | 2 man/pdfkap.Rd | 2 man/pdfkmu.Rd | 2 man/pdfkur.Rd | 2 man/pdflap.Rd | 2 man/pdflmrq.Rd | 2 man/pdfln3.Rd | 2 man/pdfnor.Rd | 2 man/pdfpe3.Rd | 2 man/pdfray.Rd | 2 man/pdfrevgum.Rd | 2 man/pdfrice.Rd | 2 man/pdfsla.Rd | 2 man/pdfst3.Rd | 2 man/pdftexp.Rd | 2 man/pdftri.Rd | 2 man/pdfwak.Rd | 2 man/pdfwei.Rd | 2 man/pfactor.bernstein.Rd | 4 man/plmomco.Rd | 2 man/plotlmrdia.Rd | 2 man/plotradarlmr.Rd | 2 man/pmoms.Rd | 8 man/pp.Rd | 29 - man/pp.f.Rd | 6 man/pp.median.Rd | 16 man/prettydist.Rd | 2 man/prob2T.Rd | 2 man/prob2grv.Rd | 2 man/prob2lrv.Rd | 2 man/pwm.Rd | 6 man/pwm.beta2alpha.Rd | 6 man/pwm.gev.Rd | 6 man/pwm.pp.Rd | 6 man/pwm.ub.Rd | 6 man/pwm2lmom.Rd | 2 man/pwm2vec.Rd | 6 man/pwmLC.Rd | 6 man/pwmRC.Rd | 6 man/qlmomco.Rd | 2 man/qua.ostat.Rd | 2 man/qua2ci.cov.Rd | 2 man/qua2ci.simple.Rd | 2 man/quaaep4.Rd | 2 man/quaaep4kapmix.Rd | 2 man/quacau.Rd | 2 man/quaemu.Rd | 2 man/quaexp.Rd | 2 man/quagam.Rd | 2 man/quagep.Rd | 2 man/quagld.Rd | 2 man/quaglo.Rd | 2 man/quagno.Rd | 5 man/quagov.Rd | 2 man/quagum.Rd | 2 man/quakap.Rd | 2 man/quakmu.Rd | 2 man/quakur.Rd | 2 man/qualap.Rd | 2 man/qualmrq.Rd | 2 man/qualn3.Rd | 2 man/quanor.Rd | 2 man/quape3.Rd | 2 man/quaray.Rd | 2 man/quarevgum.Rd | 2 man/quarice.Rd | 2 man/quasla.Rd | 2 man/quast3.Rd | 2 man/quatexp.Rd | 2 man/quatri.Rd | 2 man/quawak.Rd | 2 man/quawei.Rd | 2 man/ralmomco.Rd | 2 man/reslife.lmoms.Rd | 2 man/riglmomco.Rd | 2 man/rlmomco.Rd | 2 man/rmlmomco.Rd | 2 man/rmvarlmomco.Rd | 2 man/rralmomco.Rd | 2 man/rreslife.lmoms.Rd | 2 man/rrmlmomco.Rd | 2 man/rrmvarlmomco.Rd | 2 man/sentiv.curve.Rd | 2 man/slmomco.Rd | 2 man/stttlmomco.Rd | 2 man/supdist.Rd | 6 man/tau34sq.normtest.Rd | 5 man/theoLmoms.Rd | 4 man/theoLmoms.max.ostat.Rd | 2 man/theoTLmoms.Rd | 2 man/theopwms.Rd | 4 man/tlmr2par.Rd | 2 man/tlmrcau.Rd | 4 man/tlmrexp.Rd | 4 man/tlmrgev.Rd | 4 man/tlmrglo.Rd | 4 man/tlmrgno.Rd | 7 man/tlmrgpa.Rd | 4 man/tlmrgum.Rd | 4 man/tlmrln3.Rd | 4 man/tlmrnor.Rd | 4 man/tlmrpe3.Rd | 4 man/tlmrray.Rd | 4 man/tttlmomco.Rd | 2 man/vec2TLmom.Rd | 2 man/vec2lmom.Rd | 2 man/vec2par.Rd | 2 man/vec2pwm.Rd | 2 man/x2pars.Rd | 2 man/x2xlo.Rd | 4 man/z.par2cdf.Rd | 2 man/z.par2qua.Rd | 2 363 files changed, 1212 insertions(+), 1011 deletions(-)