Title: A friendly MCMC framework
Description: Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC)
framework for implementing Metropolis-Hastings algorithm in a modular way
allowing users to specify automatic convergence checker, personalized
transition kernels, and out-of-the-box multiple MCMC chains using
parallel computing. Most of the methods implemented in this package can
be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods
included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5>
Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5>
Robust Adaptive Metropolis, and Thawornwattana et
al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Author: George Vega Yon [aut, cre] ,
Paul Marjoram [ctb, ths] ,
National Cancer Institute [fnd] ,
Fabian Scheipl [rev]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between fmcmc versions 0.5-1 dated 2022-01-13 and 0.5-2 dated 2023-08-29
DESCRIPTION | 10 MD5 | 26 - NEWS.md | 5 R/imports.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/NEWS | 25 - inst/doc/advanced-features.html | 518 +++++++++++++++++++--------------- inst/doc/user-defined-kernels.html | 354 +++++++++++++---------- inst/doc/workflow-with-fmcmc.html | 561 +++++++++++++++++++++---------------- man/fmcmc.Rd | 8 man/kernel_new.Rd | 6 man/mcmc-loop.Rd | 6 14 files changed, 877 insertions(+), 650 deletions(-)
Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: Francois Rousset [aut, cre, cph]
,
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 4.3.20 dated 2023-07-06 and 4.4.0 dated 2023-08-29
DESCRIPTION | 10 - MD5 | 143 ++++++++++++------------ NAMESPACE | 5 R/HLFactorList.R | 78 +++++++++---- R/HLfit_Internals.R | 39 ++---- R/HLfit_b_internals.R | 11 + R/HLframes.R | 36 ++++-- R/LR.R | 56 ++++++--- R/calc_LRT.R | 4 R/combinepar.R | 18 +-- R/confint.R | 5 R/constructors_IMRFs.R | 20 ++- R/corMatern.R | 10 - R/corrHLfit-internals.R | 53 +++----- R/correlationFns.R | 6 - R/cov_new_fix.R | 90 +++++++++++---- R/determine_spprec.R | 8 + R/extractors.R | 69 +++++++++-- R/fit_as_ZX.R | 18 ++- R/fitme.R | 3 R/fitme_body.R | 2 R/fitmecorrHLfit_body_internals.R | 9 + R/generateName.R | 70 ++++------- R/geo_info.R | 37 ++++-- R/hatvalues.R | 20 +++ R/mapMM.R | 5 R/multiFRK.R | 51 ++++++-- R/newPLS.R | 14 +- R/postfit_internals.R | 98 +++++++--------- R/predict.R | 105 +++++++++++++---- R/predict_mv.R | 70 ++++++++--- R/preprocess.R | 127 ++++++++++++++------- R/preprocess_MV.R | 88 +++++++------- R/preprocess_internals.R | 44 ++++++- R/profile.R | 4 R/sXaug_EigenDense_QRP_Chol_scaled.R | 7 - R/sXaug_sparsePrecisions.R | 2 R/safe_opt.R | 6 - R/simulate.HL.R | 133 +++++++++++++++++----- R/spaMM.data.R | 8 + R/spaMM_boot.R | 49 +++++--- R/update.HL.R | 41 +++--- R/utils.R | 2 inst/NEWS.Rd | 26 ++++ man/AIC.Rd | 2 man/DoF.Rd |only man/HLfit.Rd | 38 +++--- man/IMRF.Rd | 21 ++- man/MaternIMRF.Rd | 3 man/anova.HLfit.Rd | 9 - man/div_info.Rd | 2 man/fitmv.Rd | 29 ++-- man/get_cPredVar.Rd | 6 - man/get_matrix.Rd | 3 man/mv.Rd | 3 man/poisson.Rd | 2 man/predict.Rd | 6 - man/setNbThreads.Rd | 2 man/simulate.Rd | 15 +- man/spaMM-internal.Rd | 2 man/spaMM.Rd | 2 man/spaMM_boot.Rd | 6 - man/update.Rd | 20 ++- man/vcov.Rd | 17 ++ tests/plot1.pdf |only tests/plot2.pdf |only tests/testthat/extralong/test-composite-extra.R | 9 + tests/testthat/extralong/test-mv-extra.R | 72 +++++++----- tests/testthat/test-LLM.R | 16 ++ tests/testthat/test-adjacency-corrMatrix.R | 16 +- tests/testthat/test-fixedLRT.R | 6 - tests/testthat/test-mv.R | 3 tests/testthat/test-simulate.R | 5 tests/testthat/test-spaMM.R | 2 74 files changed, 1311 insertions(+), 706 deletions(-)
Title: Axis Labeling
Description: Functions which provide a range of axis labeling algorithms.
Author: Justin Talbot,
Maintainer: Nuno Sempere <nuno.semperelh@gmail.com>
Diff between labeling versions 0.4.2 dated 2020-10-20 and 0.4.3 dated 2023-08-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/labeling-package.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in parallel,
so metadata resolution and package downloads are fast. Metadata and package
files are cached on the local disk as well. 'pak' has a dependency solver,
so it finds version conflicts before performing the installation. This
version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.5.1 dated 2023-04-27 and 0.6.0 dated 2023-08-29
pak-0.5.1/pak/tests/testthat/test-system-requirements.R |only pak-0.6.0/pak/DESCRIPTION | 22 +-- pak-0.6.0/pak/MD5 | 95 +++++++++------- pak-0.6.0/pak/NAMESPACE | 12 ++ pak-0.6.0/pak/NEWS.md | 49 ++++++++ pak-0.6.0/pak/R/confirmation.R | 20 +++ pak-0.6.0/pak/R/dev-mode.R | 2 pak-0.6.0/pak/R/docs.R | 27 +++- pak-0.6.0/pak/R/library.R | 2 pak-0.6.0/pak/R/package.R | 8 - pak-0.6.0/pak/R/pak-cleanup.R | 2 pak-0.6.0/pak/R/pak-update.R | 7 + pak-0.6.0/pak/R/repo.R | 51 ++++---- pak-0.6.0/pak/R/search.R | 1 pak-0.6.0/pak/R/subprocess.R | 1 pak-0.6.0/pak/R/sysreqs.R |only pak-0.6.0/pak/R/sysreqsdocs.R |only pak-0.6.0/pak/R/system-requirements.R | 39 ++++++ pak-0.6.0/pak/R/utils.R | 4 pak-0.6.0/pak/man/chunks/sysreqs.Rmd |only pak-0.6.0/pak/man/chunks/sysreqs.md |only pak-0.6.0/pak/man/chunks/tldr.Rmd | 2 pak-0.6.0/pak/man/figures/lifecycle-archived.svg |only pak-0.6.0/pak/man/figures/lifecycle-defunct.svg |only pak-0.6.0/pak/man/figures/lifecycle-deprecated.svg |only pak-0.6.0/pak/man/figures/lifecycle-experimental.svg |only pak-0.6.0/pak/man/figures/lifecycle-maturing.svg |only pak-0.6.0/pak/man/figures/lifecycle-questioning.svg |only pak-0.6.0/pak/man/figures/lifecycle-soft-deprecated.svg |only pak-0.6.0/pak/man/figures/lifecycle-stable.svg |only pak-0.6.0/pak/man/figures/lifecycle-superseded.svg |only pak-0.6.0/pak/man/figures/tldr-cran.svg | 2 pak-0.6.0/pak/man/get-started.Rd | 2 pak-0.6.0/pak/man/lib_status.Rd | 5 pak-0.6.0/pak/man/local_system_requirements.Rd | 28 ++++ pak-0.6.0/pak/man/package-dependency-types.Rd | 2 pak-0.6.0/pak/man/pak-config.Rd | 4 pak-0.6.0/pak/man/pak.Rd | 3 pak-0.6.0/pak/man/pak_cleanup.Rd | 2 pak-0.6.0/pak/man/pak_package_sources.Rd | 2 pak-0.6.0/pak/man/pkg_deps.Rd | 5 pak-0.6.0/pak/man/pkg_deps_tree.Rd | 3 pak-0.6.0/pak/man/pkg_download.Rd | 5 pak-0.6.0/pak/man/pkg_install.Rd | 3 pak-0.6.0/pak/man/pkg_name_check.Rd | 4 pak-0.6.0/pak/man/pkg_remove.Rd | 3 pak-0.6.0/pak/man/pkg_status.Rd | 5 pak-0.6.0/pak/man/pkg_sysreqs.Rd |only pak-0.6.0/pak/man/repo_add.Rd | 88 ++++++-------- pak-0.6.0/pak/man/repo_status.Rd | 2 pak-0.6.0/pak/man/sysreqs.Rd |only pak-0.6.0/pak/man/sysreqs_check_installed.Rd |only pak-0.6.0/pak/man/sysreqs_db_list.Rd |only pak-0.6.0/pak/man/sysreqs_db_match.Rd |only pak-0.6.0/pak/man/sysreqs_db_update.Rd |only pak-0.6.0/pak/man/sysreqs_is_supported.Rd |only pak-0.6.0/pak/man/sysreqs_list_system_packages.Rd |only pak-0.6.0/pak/man/sysreqs_platforms.Rd |only pak-0.6.0/pak/tests/testthat/test-repo.R | 38 ++++-- pak-0.6.0/pak/tools/dynamic-help.R | 8 - 60 files changed, 377 insertions(+), 181 deletions(-)
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Spencer Pease [ctb],
Thomas Bergamaschi [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.4.15 dated 2023-07-05 and 0.4.16 dated 2023-08-29
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/MazamaCoreUtils.R | 1 + inst/doc/error-handling.html | 12 ++++++------ inst/doc/logging.html | 32 ++++++++++++++++---------------- man/MazamaCoreUtils.Rd | 1 + 7 files changed, 38 insertions(+), 32 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Get Silhouettes of Organisms from PhyloPic
Description: Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>)
to fetch silhouette images of organisms. Includes functions for adding
silhouettes to both base R plots and ggplot2 plots.
Author: William Gearty [aut, cre] ,
Lewis A. Jones [aut] ,
Scott Chamberlain [aut] ,
David Miller [ctb]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between rphylopic versions 1.1.1 dated 2023-07-08 and 1.2.0 dated 2023-08-29
DESCRIPTION | 14 MD5 | 105 ++- NAMESPACE | 10 NEWS.md | 145 ++--- R/add_phylopic.r | 35 - R/add_phylopic_base.r | 62 +- R/browse_phylopic.R |only R/geom_phylopic.R | 286 ++++++++-- R/get_attribution.R | 128 +++- R/get_phylopic.R | 16 R/get_uuid.R | 42 + R/phylopic_utils.R | 92 ++- R/pick_phylopic.R | 18 R/zzz.r | 24 README.md | 22 build/vignette.rds |binary inst/doc/a-getting-started.R | 14 inst/doc/a-getting-started.Rmd | 17 inst/doc/a-getting-started.html | 36 - inst/doc/b-advanced-ggplot.R | 53 + inst/doc/b-advanced-ggplot.Rmd | 65 +- inst/doc/b-advanced-ggplot.html | 279 +++++---- inst/doc/c-advanced-base.R | 35 - inst/doc/c-advanced-base.Rmd | 40 - inst/doc/c-advanced-base.html | 220 ++++--- man/add_phylopic.Rd | 25 man/add_phylopic_base.Rd | 25 man/browse_phylopic.Rd |only man/geom_phylopic.Rd | 39 + man/get_attribution.Rd | 26 man/get_phylopic.Rd | 18 man/get_uuid.Rd | 11 man/phylopic_key_glyph.Rd |only man/pick_phylopic.Rd | 7 man/plot_phylopic.Rd |only man/recolor_phylopic.Rd | 15 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/add_phylopic/phylopic-in-background.svg | 30 - tests/testthat/_snaps/add_phylopic/phylopics-on-top-of-plot.svg | 96 +-- tests/testthat/_snaps/add_phylopic_base/phylopic-in-background.svg | 4 tests/testthat/_snaps/add_phylopic_base/phylopics-on-top-of-plot.svg | 96 +-- tests/testthat/_snaps/geom_phylopic/geom-phylopic.svg | 40 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-img.svg |only tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-larger-glyphs.svg |only tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-uuid.svg |only tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph.svg |only tests/testthat/_snaps/phylopic_utils |only tests/testthat/test-add_phylopic.R | 7 tests/testthat/test-add_phylopic_base.R | 11 tests/testthat/test-browse_phylopic.R |only tests/testthat/test-geom_phylopic.R | 117 +++- tests/testthat/test-get_attribution.R | 12 tests/testthat/test-get_phylopic.R | 4 tests/testthat/test-get_uuid.R | 15 tests/testthat/test-phylopic_utils.R | 29 - vignettes/a-getting-started.Rmd | 17 vignettes/b-advanced-ggplot.Rmd | 65 +- vignettes/c-advanced-base.Rmd | 40 - 58 files changed, 1755 insertions(+), 752 deletions(-)
Title: Multilevel Mediation Analysis
Description: Do multilevel mediation analysis with generalized additive multilevel models. The analysis method is described in Yu and Li (2020), "Third-Variable Effect Analysis with Multilevel Additive Models", PLoS ONE 15(10): e0241072.
Author: Qingzhao Yu, Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mlma versions 6.2-1 dated 2022-05-16 and 6.3-1 dated 2023-08-29
DESCRIPTION | 10 MD5 | 16 NAMESPACE | 1 R/mlma.r | 32 - build/vignette.rds |binary inst/doc/MLMAvignette.html | 833 +++++++++++++++++++++++++++++++-------------- man/boot.mlma.Rd | 2 man/data.org.Rd | 13 man/mlma-package.Rd | 7 9 files changed, 614 insertions(+), 300 deletions(-)
Title: Fitting Univariate Censored Linear Regression Model with
Autoregressive Errors
Description: It fits a univariate left, right, or interval censored linear regression model
with autoregressive errors, considering the normal or the Student-t distribution for the
innovations. It provides estimates and standard errors of the parameters, predicts
future observations, and supports missing values on the dependent variable.
References used for this package:
Schumacher, F. L., Lachos, V. H., & Dey, D. K. (2017). Censored regression models with
autoregressive errors: A likelihood-based perspective. Canadian Journal of Statistics,
45(4), 375-392 <doi:10.1002/cjs.11338>.
Schumacher, F. L., Lachos, V. H., Vilca-Labra, F. E., & Castro, L. M. (2018). Influence
diagnostics for censored regression models with autoregressive errors. Australian & New
Zealand Journal of Statistics, 60(2), 209-229 <doi:10.1111/anzs.12229>.
Valeriano, K. A., Schumacher, F. L., Galarza, C. E., & Matos, L. A. (2021). Censored
autoregressive regression models with Student-t innovations. arX [...truncated...]
Author: Fernanda L. Schumacher [aut, cre]
,
Katherine A. L. Valeriano [ctb]
,
Victor H. Lachos [ctb] ,
Christian G. Morales [ctb] ,
Larissa A. Matos [ctb]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Diff between ARCensReg versions 2.1 dated 2016-09-10 and 3.0.1 dated 2023-08-29
ARCensReg-2.1/ARCensReg/R/princfunctionGerar.R |only ARCensReg-3.0.1/ARCensReg/DESCRIPTION | 73 +++ ARCensReg-3.0.1/ARCensReg/MD5 | 51 +- ARCensReg-3.0.1/ARCensReg/NAMESPACE | 42 +- ARCensReg-3.0.1/ARCensReg/NEWS.md |only ARCensReg-3.0.1/ARCensReg/R/ARtCensReg_final.R |only ARCensReg-3.0.1/ARCensReg/R/ARtCensReg_utils.R |only ARCensReg-3.0.1/ARCensReg/R/RcppExports.R |only ARCensReg-3.0.1/ARCensReg/R/auxfunctions.R | 264 +++++-------- ARCensReg-3.0.1/ARCensReg/R/finalfunction.R | 342 +++++++++++------ ARCensReg-3.0.1/ARCensReg/R/finalfunctionDiag.R | 81 ++-- ARCensReg-3.0.1/ARCensReg/R/finalfunctionGerar.R | 102 ++++- ARCensReg-3.0.1/ARCensReg/R/princfunction.R | 423 +++++++--------------- ARCensReg-3.0.1/ARCensReg/R/princfunctionDiag.R | 45 +- ARCensReg-3.0.1/ARCensReg/README.md |only ARCensReg-3.0.1/ARCensReg/build |only ARCensReg-3.0.1/ARCensReg/inst |only ARCensReg-3.0.1/ARCensReg/man/ARtCensReg.Rd |only ARCensReg-3.0.1/ARCensReg/man/InfDiag.Rd | 142 +++---- ARCensReg-3.0.1/ARCensReg/man/arcensreg.Rd | 234 ++++++------ ARCensReg-3.0.1/ARCensReg/man/cloudceiling.Rd | 57 +- ARCensReg-3.0.1/ARCensReg/man/figures |only ARCensReg-3.0.1/ARCensReg/man/phosphorus.Rd | 86 ++-- ARCensReg-3.0.1/ARCensReg/man/plot.InfDiag.Rd |only ARCensReg-3.0.1/ARCensReg/man/plot.Rd |only ARCensReg-3.0.1/ARCensReg/man/plot.residARpCRM.Rd |only ARCensReg-3.0.1/ARCensReg/man/predict.Rd |only ARCensReg-3.0.1/ARCensReg/man/print.Rd |only ARCensReg-3.0.1/ARCensReg/man/rARCens.Rd | 101 +++-- ARCensReg-3.0.1/ARCensReg/man/residuals.Rd |only ARCensReg-3.0.1/ARCensReg/man/summary.Rd |only ARCensReg-3.0.1/ARCensReg/src |only 32 files changed, 1099 insertions(+), 944 deletions(-)
Title: Life History Metrics from Matrix Population Models
Description: Functions for calculating life history metrics using matrix
population models ('MPMs'). Described in Jones et al. (2021)
<doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] ,
Danny Buss [ctb],
Pol Capdevila [aut] ,
Hal Caswell [aut] ,
Judy P. Che-Castaldo [aut] ,
Richard A. Hinrichsen [aut] ,
John Jackson [aut] ,
Tamora James [aut] ,
Owen Jones [aut, cre] ,
Sam Levin [aut] ,
William K. Petry [aut] ,
[...truncated...]
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rage versions 1.4.0 dated 2023-04-10 and 1.5.0 dated 2023-08-29
Rage-1.4.0/Rage/tests/testthat/test-checkValidMat.R |only Rage-1.5.0/Rage/DESCRIPTION | 18 Rage-1.5.0/Rage/MD5 | 216 +++--- Rage-1.5.0/Rage/NAMESPACE | 5 Rage-1.5.0/Rage/NEWS.md | 9 Rage-1.5.0/Rage/R/Rage-package.R |only Rage-1.5.0/Rage/R/data.R | 14 Rage-1.5.0/Rage/R/entropy_k.R | 4 Rage-1.5.0/Rage/R/gen_time.R | 70 +- Rage-1.5.0/Rage/R/globals.R | 4 Rage-1.5.0/Rage/R/is_leslie_matrix.R |only Rage-1.5.0/Rage/R/leslie_collapse.R |only Rage-1.5.0/Rage/R/life_expect.R | 252 ++++--- Rage-1.5.0/Rage/R/lifetable_convert.R | 4 Rage-1.5.0/Rage/R/longevity.R | 19 Rage-1.5.0/Rage/R/mature_.R | 5 Rage-1.5.0/Rage/R/mpm_collapse.R | 11 Rage-1.5.0/Rage/R/mpm_standardize.R | 10 Rage-1.5.0/Rage/R/mpm_to_.R | 32 Rage-1.5.0/Rage/R/mpm_to_table.R | 39 - Rage-1.5.0/Rage/R/name_stages.R | 11 Rage-1.5.0/Rage/R/net_repro_rate.R | 25 Rage-1.5.0/Rage/R/perturb_matrix.R | 7 Rage-1.5.0/Rage/R/perturb_stochastic.R | 14 Rage-1.5.0/Rage/R/perturb_trans.R | 50 - Rage-1.5.0/Rage/R/perturb_vr.R | 16 Rage-1.5.0/Rage/R/plot_life_cycle.R | 10 Rage-1.5.0/Rage/R/pop_vectors.R | 15 Rage-1.5.0/Rage/R/qsd_converge.R | 19 Rage-1.5.0/Rage/R/repro_stages.R | 33 Rage-1.5.0/Rage/R/shape_rep.R | 28 Rage-1.5.0/Rage/R/shape_surv.R | 26 Rage-1.5.0/Rage/R/standard_stages.R | 5 Rage-1.5.0/Rage/R/utils.R | 76 +- Rage-1.5.0/Rage/R/vital_rates.R | 31 Rage-1.5.0/Rage/R/vr_mat.R | 5 Rage-1.5.0/Rage/R/vr_vec.R | 12 Rage-1.5.0/Rage/README.md | 23 Rage-1.5.0/Rage/build/partial.rdb |only Rage-1.5.0/Rage/build/vignette.rds |binary Rage-1.5.0/Rage/data/leslie_mpm1.rda |only Rage-1.5.0/Rage/inst/WORDLIST | 20 Rage-1.5.0/Rage/inst/doc/a01_GettingStarted.R | 32 Rage-1.5.0/Rage/inst/doc/a01_GettingStarted.Rmd | 32 Rage-1.5.0/Rage/inst/doc/a01_GettingStarted.html | 483 +++++++------- Rage-1.5.0/Rage/inst/doc/a02_VitalRates.html | 224 +++--- Rage-1.5.0/Rage/inst/doc/a03_LifeHistoryTraits.R | 45 - Rage-1.5.0/Rage/inst/doc/a03_LifeHistoryTraits.Rmd | 56 - Rage-1.5.0/Rage/inst/doc/a03_LifeHistoryTraits.html | 189 +++-- Rage-1.5.0/Rage/inst/doc/a04_AgeFromStage.R | 13 Rage-1.5.0/Rage/inst/doc/a04_AgeFromStage.Rmd | 13 Rage-1.5.0/Rage/inst/doc/a04_AgeFromStage.html | 255 +++---- Rage-1.5.0/Rage/inst/doc/a05_SuggestedQualityControl.html | 4 Rage-1.5.0/Rage/man/Rage-package.Rd |only Rage-1.5.0/Rage/man/age_from_stage.Rd | 32 Rage-1.5.0/Rage/man/entropy_k.Rd | 4 Rage-1.5.0/Rage/man/gen_time.Rd | 64 + Rage-1.5.0/Rage/man/is_leslie_matrix.Rd |only Rage-1.5.0/Rage/man/leslie_collapse.Rd |only Rage-1.5.0/Rage/man/leslie_mpm1.Rd |only Rage-1.5.0/Rage/man/life_expect.Rd | 90 +- Rage-1.5.0/Rage/man/lifetable_convert.Rd | 4 Rage-1.5.0/Rage/man/longevity.Rd | 15 Rage-1.5.0/Rage/man/mpm_collapse.Rd | 7 Rage-1.5.0/Rage/man/mpm_rearrange.Rd | 2 Rage-1.5.0/Rage/man/mpm_split.Rd | 2 Rage-1.5.0/Rage/man/mpm_standardize.Rd | 12 Rage-1.5.0/Rage/man/mpm_to_table.Rd | 29 Rage-1.5.0/Rage/man/name_stages.Rd | 9 Rage-1.5.0/Rage/man/net_repro_rate.Rd | 23 Rage-1.5.0/Rage/man/perturb_trans.Rd | 46 - Rage-1.5.0/Rage/man/perturb_vr.Rd | 4 Rage-1.5.0/Rage/man/pop_vectors.Rd | 12 Rage-1.5.0/Rage/man/repro_stages.Rd | 10 Rage-1.5.0/Rage/man/shape_rep.Rd | 18 Rage-1.5.0/Rage/man/shape_surv.Rd | 4 Rage-1.5.0/Rage/man/standard_stages.Rd | 2 Rage-1.5.0/Rage/man/vital_rates.Rd | 5 Rage-1.5.0/Rage/man/vr_mat.Rd | 3 Rage-1.5.0/Rage/man/vr_vec.Rd | 12 Rage-1.5.0/Rage/tests/testthat/test-checkValidStartLife.R | 3 Rage-1.5.0/Rage/tests/testthat/test-entropy_d.R | 4 Rage-1.5.0/Rage/tests/testthat/test-entropy_k.R | 6 Rage-1.5.0/Rage/tests/testthat/test-gen_time.R | 29 Rage-1.5.0/Rage/tests/testthat/test-is_leslie_matrix.R |only Rage-1.5.0/Rage/tests/testthat/test-leslie_collapse.R |only Rage-1.5.0/Rage/tests/testthat/test-life_expect.R | 12 Rage-1.5.0/Rage/tests/testthat/test-longevity.R | 8 Rage-1.5.0/Rage/tests/testthat/test-mature_.R | 6 Rage-1.5.0/Rage/tests/testthat/test-mature_distrib.R | 6 Rage-1.5.0/Rage/tests/testthat/test-meanMat.R | 4 Rage-1.5.0/Rage/tests/testthat/test-mpm_collapse.R | 18 Rage-1.5.0/Rage/tests/testthat/test-mpm_rearrange.R | 16 Rage-1.5.0/Rage/tests/testthat/test-mpm_split.R | 2 Rage-1.5.0/Rage/tests/testthat/test-mpm_standardize.R | 2 Rage-1.5.0/Rage/tests/testthat/test-mpm_to_.R | 17 Rage-1.5.0/Rage/tests/testthat/test-mpm_to_table.R | 35 - Rage-1.5.0/Rage/tests/testthat/test-name_stages.R | 10 Rage-1.5.0/Rage/tests/testthat/test-net_repro_rate.R | 16 Rage-1.5.0/Rage/tests/testthat/test-perturb_matrix.R | 5 Rage-1.5.0/Rage/tests/testthat/test-perturb_stochastic.R | 2 Rage-1.5.0/Rage/tests/testthat/test-perturb_trans.R | 4 Rage-1.5.0/Rage/tests/testthat/test-perturb_vr.R | 12 Rage-1.5.0/Rage/tests/testthat/test-plot_life_cycle.R | 6 Rage-1.5.0/Rage/tests/testthat/test-qsd_converge.R | 11 Rage-1.5.0/Rage/tests/testthat/test-repro_stages.R | 6 Rage-1.5.0/Rage/tests/testthat/test-shape_rep.R | 6 Rage-1.5.0/Rage/tests/testthat/test-shape_surv.R | 8 Rage-1.5.0/Rage/tests/testthat/test-standard_stages.R | 6 Rage-1.5.0/Rage/tests/testthat/test-vital_rates.R | 12 Rage-1.5.0/Rage/tests/testthat/test-vr_mat.R | 6 Rage-1.5.0/Rage/tests/testthat/test-vr_vec.R | 12 Rage-1.5.0/Rage/vignettes/a01_GettingStarted.Rmd | 32 Rage-1.5.0/Rage/vignettes/a03_LifeHistoryTraits.Rmd | 56 - Rage-1.5.0/Rage/vignettes/a04_AgeFromStage.Rmd | 13 115 files changed, 1817 insertions(+), 1467 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04> and in Skaltsa et al (2010, 2012) <doi:10.1002/bimj.200900294>, <doi:10.1002/sim.4369>.
Author: Sara Perez-Jaume [aut, cre],
Natalia Pallares [aut],
Konstantina Skaltsa [aut]
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.9.1 dated 2023-04-11 and 2.9.2 dated 2023-08-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/ThresholdROC-package.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Renewal Method for Extreme Values Extrapolation
Description: Peaks Over Threshold (POT) or 'methode du renouvellement'. The
distribution for the excesses can be chosen, and heterogeneous data
(including historical data or block data) can be used in a
Maximum-Likelihood framework.
Author: Yves Deville <deville.yves@alpestat.com>, Lise Bardet <lise.bardet@irsn.fr>
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between Renext versions 3.1-3 dated 2022-11-24 and 3.1-4 dated 2023-08-29
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- build/partial.rdb |binary inst/doc/RenextGuide.pdf |binary man/Renext-package.Rd | 2 +- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Outright Tool for the Analysis of Spatial Inequalities and
Segregation
Description: A set of indexes and tests for the analysis of social segregation.
Author: Mihai Tivadar <mihai.tivadar@inrae.fr>
Maintainer: Mihai Tivadar <mihai.tivadar@inrae.fr>
Diff between OasisR versions 3.0.2 dated 2020-05-27 and 3.1.0 dated 2023-08-29
DESCRIPTION | 23 ++++---- MD5 | 27 +++++----- R/DataDoc.R | 2 R/GeoFunctions.R | 140 ++++++++++++++++++++++++++++-------------------------- R/SegFunctions.R | 21 +++----- inst/CITATION | 2 man/GreHSize.Rd | 2 man/ISDuncan.Rd | 92 +++++++++++++++++------------------ man/area.Rd | 6 +- man/boundaries.Rd | 8 +-- man/contig.Rd | 8 +-- man/distance.Rd | 8 +-- man/distcenter.Rd | 8 +-- man/perimeter.Rd | 6 +- tests |only 15 files changed, 180 insertions(+), 173 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.6.2 dated 2023-03-10 and 0.7.0 dated 2023-08-29
DESCRIPTION | 10 MD5 | 94 ++- NAMESPACE | 14 NEWS.md | 496 ++++++++++---------- R/downloading_tools.R | 556 +++++++++++------------ R/get_hydro.R | 2 R/get_network.R | 2 R/get_nhdplushr.R | 651 +++++++++++++-------------- R/get_vaa.R | 137 +++++ R/hl_graph_utils.R | 4 R/index_nhdplus.R | 5 R/rescale_catchments.R |only README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 26 - inst/doc/US_data.Rmd | 710 ++++++++++++++--------------- inst/doc/US_data.html | 735 +++++++++++++++---------------- inst/doc/advanced_network.Rmd | 570 ++++++++++++------------ inst/doc/advanced_network.html | 299 ++++++------ inst/doc/indexing.Rmd | 530 +++++++++++----------- inst/doc/indexing.html | 532 +++++++++++----------- inst/doc/nhdplusTools.Rmd | 158 +++--- inst/doc/nhdplusTools.html | 6 inst/doc/nhdplushr.Rmd | 416 ++++++++--------- inst/doc/nhdplushr.html | 368 +++++++-------- inst/doc/plot_nhdplus.Rmd | 532 +++++++++++----------- inst/doc/plot_nhdplus.html | 404 ++++++++--------- man/download_nhdplushr.Rd | 66 +- man/download_vaa.Rd | 2 man/get_catchment_characteristics.Rd |only man/get_characteristics_metadata.Rd |only man/get_vaa.Rd | 2 man/get_vaa_names.Rd | 2 man/make_standalone.Rd | 122 ++--- man/rescale_catchment_characteristics.Rd |only tests/testthat.R | 6 tests/testthat/data/rescale_data.rds |only tests/testthat/helper.R | 78 +-- tests/testthat/test_01_get_nldi.R | 618 +++++++++++++------------- tests/testthat/test_02_subset_extras.R | 452 +++++++++---------- tests/testthat/test_get_nhdplushr.R | 356 +++++++-------- tests/testthat/test_get_vaa.R | 110 +++- tests/testthat/test_navigate.R | 20 tests/testthat/test_rescale_catchments.R |only vignettes/US_data.Rmd | 710 ++++++++++++++--------------- vignettes/advanced_network.Rmd | 570 ++++++++++++------------ vignettes/indexing.Rmd | 530 +++++++++++----------- vignettes/nhdplusTools.Rmd | 158 +++--- vignettes/nhdplushr.Rmd | 416 ++++++++--------- vignettes/plot_nhdplus.Rmd | 532 +++++++++++----------- 51 files changed, 6114 insertions(+), 5895 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu and Li (2022) (ISBN: 9780367365479) "Statistical Methods for Mediation, Confounding and Moderation Analysis Using R and SAS", published by Chapman and Hall/CRC; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 10.6-1 dated 2022-05-16 and 10.7-1 dated 2023-08-29
DESCRIPTION | 8 MD5 | 34 R/mma.r | 220 + build/vignette.rds |binary inst/doc/MMAvignette.html | 1346 ++++++---- man/boot.med.Rd | 4 man/boot.mod.Rd | 4 man/mma-package.Rd | 7 man/mma.Rd | 4 man/summary.mma.Rd | 5 vignettes/MMAvignette_files/figure-html/unnamed-chunk-10-3.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-13-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-19-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-22-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-23-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-23-2.png |binary vignettes/vignettebib.bib | 5 18 files changed, 1032 insertions(+), 605 deletions(-)
Title: Convert Large Numbers to Bigq Format
Description: This function converts mfpr, numeric, or character strings representing numbers to bigq format without loss of precision.
Author: Carl Witthoft [aut, cre]
Maintainer: Carl Witthoft <cellocgw@gmail.com>
Diff between go2bigq versions 1.0 dated 2022-03-29 and 2.0.1 dated 2023-08-29
DESCRIPTION | 13 +++++++------ MD5 | 9 +++++---- R/go2bigq.R | 14 ++++++++++---- build |only man/go2bigq-package.Rd | 18 +++++++++--------- man/go2bigq.Rd | 6 +++--- 6 files changed, 34 insertions(+), 26 deletions(-)
Title: Bindings to the 'Geospatial Data Abstraction Library' Raster API
Description: Interface to the raster API of the 'Geospatial Data Abstraction
Library' ('GDAL') supporting manual creation of uninitialized datasets,
creation from existing raster as template, low level I/O, configuration of
virtual raster (VRT), coordinate transformation, and access to 'gdalwarp'
for reprojection. Includes selected 'GDAL' algorithms and functions for
working with spatial reference systems. Calling signatures resemble the
native C, C++ and Python APIs provided by the 'GDAL' project
(<https://gdal.org>). Bindings are implemented via 'Rcpp' exposed class
along with several stand-alone functions. Additional functionality
includes: class 'RunningStats' for efficient summary statistics on large
data streams; class 'CmbTable' for counting unique combinations of integers
with a hash table; raster overlay to identify and count unique pixel
combinations across multiple input layers; raster calculation by evaluating
any R expression on a stack of layers with pixel coordinates available [...truncated...]
Author: Chris Toney [aut, cre],
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <chris.toney@usda.gov>
Diff between gdalraster versions 1.3.0 dated 2023-06-29 and 1.4.0 dated 2023-08-29
DESCRIPTION | 37 ++--- MD5 | 70 +++++---- NEWS.md | 18 ++ R/RcppExports.R | 60 +++++--- R/display.R | 216 ++++++++++++++++++------------ R/gdalraster.R | 83 +++++++++-- R/gdalraster_proc.R | 110 ++++++++++++--- R/running_stats.R | 2 README.md | 7 build/vignette.rds |binary cleanup | 1 configure | 18 +- configure.ac | 2 inst/doc/raster-api-tutorial.R | 1 inst/doc/raster-api-tutorial.Rmd | 1 inst/doc/raster-api-tutorial.html | 24 +-- man/DEFAULT_DEM_PROC.Rd |only man/GDALRaster-class.Rd | 83 +++++++++-- man/RunningStats-class.Rd | 2 man/dem_proc.Rd |only man/gdalraster-package.Rd | 11 - man/inv_project.Rd | 7 man/plot_raster.Rd | 108 ++++++++------- man/transform_xy.Rd | 9 - src/RcppExports.cpp | 60 +++++--- src/cmb_table.cpp | 4 src/gdal_exp.cpp | 270 +++++++++++++++++++++++--------------- src/gdalraster.cpp | 260 +++++++++++++++++++++++++++--------- src/gdalraster.h | 49 ++++-- src/running_stats.cpp | 2 src/transform.cpp | 63 ++++++-- tests |only vignettes/raster-api-tutorial.Rmd | 1 33 files changed, 1065 insertions(+), 514 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. (2021) <doi:10.18637/jss.v100.i06>.
Author: Edgar Merkle [aut, cre] ,
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb]
,
Terrence D. Jorgensen [ctb] ,
Huub Hoofs [ctb] ,
Rens van de Schoot [ctb] ,
Andrew Johnson [ctb] ,
Matthew Emery [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.4-8 dated 2023-06-12 and 0.5-1 dated 2023-08-29
DESCRIPTION | 8 MD5 | 45 - NEWS.md | 10 R/blav_fit_measures.R | 15 R/blav_model_loglik.R | 68 ++ R/blav_object_inspect.R | 47 + R/blav_object_methods.R | 131 ---- R/blav_predict.R | 26 R/blav_utils.R | 26 R/blavaan.R | 221 +++++-- R/ctr_bayes_fit.R | 3 R/ctr_ppmc.R | 2 R/lav_export_stanmarg.R | 633 ++++++++++++++------- R/lvgqs.R | 142 ++++ R/stanmarg_data.R | 519 +++++++++-------- inst/stan/stanmarg.stan | 1366 +++++++++++++++++++++++++++++++++++++--------- inst/testdata/sysdata.rda |binary man/blavCompare.Rd | 2 man/blavInspect.Rd | 14 man/blavPredict.Rd | 4 man/dpriors.Rd | 2 man/plot.blavaan.Rd | 2 src |only 23 files changed, 2362 insertions(+), 924 deletions(-)
Title: AIRR Data Representation Reference Library
Description: Schema definitions and read, write and validation tools for data
formatted in accordance with the AIRR Data Representation schemas defined
by the AIRR Community <http://docs.airr-community.org>.
Author: Jason Vander Heiden [aut, cre],
Susanna Marquez [aut],
Scott Christley [aut],
Katharina Imkeller [aut],
Ulrik Stervbo [aut],
AIRR Community [cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between airr versions 1.4.1 dated 2022-08-28 and 1.5.0 dated 2023-08-29
airr-1.4.1/airr/tests |only airr-1.5.0/airr/DESCRIPTION | 10 airr-1.5.0/airr/MD5 | 23 airr-1.5.0/airr/NEWS.md | 6 airr-1.5.0/airr/inst/doc/Usage-Vignette.html | 289 ++--- airr-1.5.0/airr/inst/extdata/airr-schema.yaml | 1086 ++++++++++++--------- airr-1.5.0/airr/inst/extdata/germline-example.json | 784 +++++++-------- 7 files changed, 1185 insertions(+), 1013 deletions(-)
Title: Influential Cases in Structural Equation Modeling
Description: Sensitivity analysis in structural equation modeling using
influence measures and diagnostic plots. Support leave-one-out casewise
sensitivity analysis presented by Pek and MacCallum (2011)
<doi:10.1080/00273171.2011.561068> and approximate casewise influence
using scores and casewise likelihood.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semfindr versions 0.1.5 dated 2023-06-19 and 0.1.5.4 dated 2023-08-29
DESCRIPTION | 8 +- MD5 | 40 ++++++------ NEWS.md | 20 ++++++ R/mahalanobis_exo.R | 12 --- R/mahalanobis_rerun.R | 41 +++---------- R/pars_id.R | 50 +++++++++++++++- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/casewise_scores.html | 6 - inst/doc/semfindr.html | 28 ++++---- inst/doc/user_id.html | 6 - man/mahalanobis_predictors.Rd | 8 -- man/mahalanobis_rerun.Rd | 9 -- man/pars_id.Rd | 28 ++++++++ tests/testthat/test-est_change_loo_multi_select_by_op.R | 39 ++++++++++++ tests/testthat/test-mahalanobis_exo_multi_missing.R | 14 +++- tests/testthat/test-mahalanobis_exo_single_missing.R | 9 ++ tests/testthat/test-mahalanobis_multi_missing.R | 18 +++++ tests/testthat/test-mahalanobis_single_missing.R | 8 ++ vignettes/articles/multiple_group.Rmd | 20 +++--- 21 files changed, 248 insertions(+), 118 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is
natively supported (including from SSL/HTTPS), compressed files can be read
directly without explicit decompression, and fast import packages are used where
appropriate. An additional convenience function, 'convert()', provides a simple
method for converting between file types.
Author: Jason Becker [ctb],
Chung-hong Chan [aut, cre] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick Kennedy [ctb],
Ryan Pr [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 0.5.29 dated 2021-11-22 and 0.5.30 dated 2023-08-29
rio-0.5.29/rio/inst/examples |only rio-0.5.29/rio/tests/test-all.R |only rio-0.5.29/rio/tests/testthat/files |only rio-0.5.30/rio/DESCRIPTION | 25 rio-0.5.30/rio/MD5 | 188 rio-0.5.30/rio/NAMESPACE | 288 - rio-0.5.30/rio/NEWS.md | 890 +-- rio-0.5.30/rio/R/arg_reconcile.R | 248 rio-0.5.30/rio/R/characterize.R | 190 rio-0.5.30/rio/R/compression.R | 196 rio-0.5.30/rio/R/convert.R | 86 rio-0.5.30/rio/R/convert_google_url.R | 22 rio-0.5.30/rio/R/export.R | 338 - rio-0.5.30/rio/R/export_list.R | 158 rio-0.5.30/rio/R/export_methods.R | 650 +- rio-0.5.30/rio/R/extensions.R | 146 rio-0.5.30/rio/R/gather_attrs.R | 136 rio-0.5.30/rio/R/import.R | 324 - rio-0.5.30/rio/R/import_list.R | 326 - rio-0.5.30/rio/R/import_methods.R | 954 +-- rio-0.5.30/rio/R/is_file_text.R | 78 rio-0.5.30/rio/R/onLoad.R | 26 rio-0.5.30/rio/R/remote_to_local.R | 138 rio-0.5.30/rio/R/rio.R | 59 rio-0.5.30/rio/R/set_class.R | 42 rio-0.5.30/rio/R/standardize_attributes.R | 116 rio-0.5.30/rio/R/suggestions.R | 96 rio-0.5.30/rio/R/utils.R | 230 rio-0.5.30/rio/README.md | 683 +- rio-0.5.30/rio/build/vignette.rds |binary rio-0.5.30/rio/inst/CITATION | 21 rio-0.5.30/rio/inst/doc/rio.R | 180 rio-0.5.30/rio/inst/doc/rio.html | 2733 +++++++--- rio-0.5.30/rio/man/arg_reconcile.Rd | 154 rio-0.5.30/rio/man/get_ext.Rd | 34 rio-0.5.30/rio/man/import.Rd | 2 rio-0.5.30/rio/man/import_list.Rd | 2 rio-0.5.30/rio/man/rio.Rd | 27 rio-0.5.30/rio/po/R-rio.pot | 296 - rio-0.5.30/rio/tests/testdata |only rio-0.5.30/rio/tests/testthat.R |only rio-0.5.30/rio/tests/testthat/test_arg_reconcile.R | 354 - rio-0.5.30/rio/tests/testthat/test_characterize.R | 62 rio-0.5.30/rio/tests/testthat/test_compress.R | 60 rio-0.5.30/rio/tests/testthat/test_convert.R | 62 rio-0.5.30/rio/tests/testthat/test_errors.R | 74 rio-0.5.30/rio/tests/testthat/test_export_list.R | 88 rio-0.5.30/rio/tests/testthat/test_extensions.R | 48 rio-0.5.30/rio/tests/testthat/test_format_R.R | 30 rio-0.5.30/rio/tests/testthat/test_format_arff.R | 24 rio-0.5.30/rio/tests/testthat/test_format_csv.R | 128 rio-0.5.30/rio/tests/testthat/test_format_csv_gz.R | 24 rio-0.5.30/rio/tests/testthat/test_format_csvy.R | 30 rio-0.5.30/rio/tests/testthat/test_format_dbf.R | 32 rio-0.5.30/rio/tests/testthat/test_format_dif.R | 12 rio-0.5.30/rio/tests/testthat/test_format_dta.R | 79 rio-0.5.30/rio/tests/testthat/test_format_eviews.R | 12 rio-0.5.30/rio/tests/testthat/test_format_external_packages.R | 46 rio-0.5.30/rio/tests/testthat/test_format_feather.R | 26 rio-0.5.30/rio/tests/testthat/test_format_fortran.R | 16 rio-0.5.30/rio/tests/testthat/test_format_fst.R | 26 rio-0.5.30/rio/tests/testthat/test_format_fwf.R | 72 rio-0.5.30/rio/tests/testthat/test_format_html.R | 68 rio-0.5.30/rio/tests/testthat/test_format_json.R | 44 rio-0.5.30/rio/tests/testthat/test_format_matlab.R | 32 rio-0.5.30/rio/tests/testthat/test_format_mtp.R | 8 rio-0.5.30/rio/tests/testthat/test_format_ods.R | 51 rio-0.5.30/rio/tests/testthat/test_format_parquet.R | 20 rio-0.5.30/rio/tests/testthat/test_format_psv.R | 24 rio-0.5.30/rio/tests/testthat/test_format_pzfx.R | 41 rio-0.5.30/rio/tests/testthat/test_format_rdata.R | 84 rio-0.5.30/rio/tests/testthat/test_format_rds.R | 44 rio-0.5.30/rio/tests/testthat/test_format_rec.R | 8 rio-0.5.30/rio/tests/testthat/test_format_sas.R | 36 rio-0.5.30/rio/tests/testthat/test_format_sav.R | 142 rio-0.5.30/rio/tests/testthat/test_format_syd.R | 12 rio-0.5.30/rio/tests/testthat/test_format_tsv.R | 24 rio-0.5.30/rio/tests/testthat/test_format_xls.R | 62 rio-0.5.30/rio/tests/testthat/test_format_xml.R | 48 rio-0.5.30/rio/tests/testthat/test_format_yml.R | 32 rio-0.5.30/rio/tests/testthat/test_gather_attrs.R | 102 rio-0.5.30/rio/tests/testthat/test_identical.R | 114 rio-0.5.30/rio/tests/testthat/test_import_list.R | 188 rio-0.5.30/rio/tests/testthat/test_install_formats.R | 41 rio-0.5.30/rio/tests/testthat/test_is_file_text.R | 147 rio-0.5.30/rio/tests/testthat/test_matrix.R | 30 rio-0.5.30/rio/tests/testthat/test_remote.R | 88 rio-0.5.30/rio/tests/testthat/test_set_class.R | 58 rio-0.5.30/rio/vignettes/rio.Rmd | 538 - 89 files changed, 7370 insertions(+), 6103 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.6.1.0 dated 2023-08-10 and 0.12.6.3.0 dated 2023-08-29
ChangeLog | 19 + DESCRIPTION | 8 MD5 | 40 +- configure | 18 - configure.ac | 2 inst/NEWS.Rd | 27 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 2 inst/include/armadillo_bits/SpSubview_bones.hpp | 22 - inst/include/armadillo_bits/SpValProxy_bones.hpp | 25 - inst/include/armadillo_bits/SpValProxy_meat.hpp | 56 +-- inst/include/armadillo_bits/arma_config.hpp | 7 inst/include/armadillo_bits/arma_rng.hpp | 348 +++++++++++++++----- inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_setup.hpp | 7 inst/include/armadillo_bits/config.hpp | 17 inst/include/armadillo_bits/diskio_bones.hpp | 2 inst/include/armadillo_bits/diskio_meat.hpp | 122 +++++-- inst/include/armadillo_bits/field_bones.hpp | 2 inst/include/armadillo_bits/subview_field_bones.hpp | 26 - 21 files changed, 515 insertions(+), 237 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Edgar Merkle [ctb],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Ad [...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-14 dated 2023-06-13 and 0.7-15 dated 2023-08-29
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/determine.subgroups.R | 10 +++++++++- R/final.org.R | 20 +++++++++++++------- R/get.params.R | 8 ++++++-- R/gimme.R | 19 +++++++++++++++---- R/search.paths.ms.R | 6 +----- build/vignette.rds |binary data/HRFsim.rda |binary data/ms.fit.rda |binary data/simData.rda |binary data/simDataLV.rda |binary data/ts.rda |binary inst/doc/gimme_vignette.html | 4 ++-- inst/doc/hrfgimme-vignette.html | 4 ++-- man/final.org.Rd | 3 --- man/search.paths.ms.Rd | 6 ------ 17 files changed, 68 insertions(+), 52 deletions(-)
Title: Generalized Autoregressive Score Models
Description: Estimation, forecasting, and simulation of generalized
autoregressive score (GAS) models of Creal, Koopman, and Lucas (2013)
<doi:10.1002/jae.1279> and Harvey (2013) <doi:10.1017/cbo9781139540933>.
Model specification allows for various data types and distributions,
different parametrizations, exogenous variables, joint and separate modeling
of exogenous variables and dynamics, higher score and autoregressive orders,
custom and unconditional initial values of time-varying parameters, fixed
and bounded values of coefficients, and missing values. Model estimation is
performed by the maximum likelihood method and the Hessian matrix.
Author: Vladimir Holy [aut, cre]
Maintainer: Vladimir Holy <vladimir.holy@vse.cz>
Diff between gasmodel versions 0.5.0 dated 2023-08-26 and 0.5.1 dated 2023-08-29
DESCRIPTION | 6 MD5 | 50 ++--- NEWS.md | 3 R/helper_check.R | 15 + R/main_bootstrap.R | 363 +++++++++++++++++++++++++------------- R/main_estimate.R | 3 R/main_filter.R | 3 R/main_forecast.R | 12 - R/main_simulate.R | 2 R/wrappers_parallel.R | 3 build/partial.rdb |binary inst/doc/case_durations.Rmd | 4 inst/doc/case_durations.html | 4 inst/doc/case_rankings.Rmd | 2 inst/doc/case_rankings.html | 2 inst/doc/distributions.html | 4 man/gas.Rd | 3 man/gas_bootstrap.Rd | 17 + man/gas_filter.Rd | 3 man/gas_forecast.Rd | 12 - man/gas_simulate.Rd | 2 man/wrappers_parallel.Rd | 2 vignettes/case_durations.Rmd | 4 vignettes/case_durations.Rmd.orig | 4 vignettes/case_rankings.Rmd | 2 vignettes/case_rankings.Rmd.orig | 2 26 files changed, 341 insertions(+), 186 deletions(-)
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [aut],
Xianying Tan [aut],
JJ Allaire [ctb],
Maximilian Girlich [ctb],
Greg Freedman Ellis [ctb],
Johannes Rauh [ctb],
SpryMedia Limited [ctb, cph] ,
Brian Reavis [ctb, cph] ,
Leon Gersen [ctb, cph] ,
Bartek Szopka [ct [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.28 dated 2023-05-18 and 0.29 dated 2023-08-29
DT-0.28/DT/inst/examples/DT-click/rsconnect |only DT-0.28/DT/inst/examples/DT-edit/rsconnect |only DT-0.28/DT/inst/examples/DT-filter/rsconnect |only DT-0.28/DT/inst/examples/DT-info/rsconnect |only DT-0.28/DT/inst/examples/DT-proxy/rsconnect |only DT-0.28/DT/inst/examples/DT-radio/rsconnect |only DT-0.28/DT/inst/examples/DT-rows/rsconnect |only DT-0.28/DT/inst/examples/DT-scroller/rsconnect |only DT-0.28/DT/inst/examples/DT-scroller/www |only DT-0.28/DT/inst/examples/DT-selection/rsconnect |only DT-0.29/DT/DESCRIPTION | 10 +++++----- DT-0.29/DT/MD5 | 22 ++++++---------------- DT-0.29/DT/R/datatables.R | 7 ++++++- DT-0.29/DT/R/shiny.R | 2 ++ DT-0.29/DT/build/vignette.rds |binary DT-0.29/DT/inst/doc/DT.html | 10 +++++----- DT-0.29/DT/inst/htmlwidgets/datatables.js | 2 +- 17 files changed, 25 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-08 0.1-5
2016-12-05 0.1-4
2013-12-10 0.1-3
Title: A 'FRACTRAN' Interpreter and Some Helper Functions
Description: 'FRACTRAN' is an obscure yet tantalizing programming language invented by John Conway of 'Game of Life' fame. The code consists of a sequence of fractions. The rules are simple. First, select an integer to initialize the process. Second, multiply the integer by the first fraction. If an integer results, start again with the new integer. If not, try the next fraction. Finally, if no such multiplication yields an integer, terminate the program. For more information, see <https://en.wikipedia.org/wiki/FRACTRAN> .
Author: Carl Witthoft [aut, cre]
Maintainer: Carl Witthoft <cellocgw@gmail.com>
Diff between Rfractran versions 1.0 dated 2020-06-25 and 1.0.1 dated 2023-08-29
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- build/partial.rdb |binary man/fracDo.Rd | 2 +- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Multiple Mediation Analysis for Big Data Sets
Description: Used for general multiple mediation analysis with big data sets.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mmabig versions 3.1-0 dated 2022-05-14 and 3.2-0 dated 2023-08-29
DESCRIPTION | 8 MD5 | 10 build/vignette.rds |binary inst/doc/MMABIGvignette.html | 1108 +++++++++++++++++++++++-------------------- man/mmabig-package.Rd | 7 vignettes/vignette.bib | 8 6 files changed, 620 insertions(+), 521 deletions(-)
Title: Configurable Function for Solving Families of Nonlinear
Equations
Description: This is designed for use with an arbitrary set of equations with
an arbitrary set of unknowns.
The user selects "fixed" values for enough unknowns to leave as many variables as
there are equations, which in most cases means the system is properly
defined and a unique solution exists. The function, the fixed values
and initial values for the remaining unknowns are fed to a nonlinear backsolver.
The original version of "TK!Solver" , now a product of Universal Technical Systems (<https://www.uts.com>) was the inspiration for this function.
Author: Carl Witthoft
Maintainer: Carl Witthoft <cellocgw@gmail.com>
Diff between ktsolve versions 1.3 dated 2020-04-25 and 1.3.1 dated 2023-08-29
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Matched Samples that are Balanced and Representative by Design
Description: Includes functions for the construction of matched samples that are balanced and representative by design. Among others, these functions can be used for matching in observational studies with treated and control units, with cases and controls, in related settings with instrumental variables, and in discontinuity designs. Also, they can be used for the design of randomized experiments, for example, for matching before randomization. By default, 'designmatch' uses the 'highs' optimization solver, but its performance is greatly enhanced by the 'Gurobi' optimization solver and its associated R interface. For their installation, please follow the instructions at <https://www.gurobi.com/documentation/quickstart.html> and <https://www.gurobi.com/documentation/7.0/refman/r_api_overview.html>. We have also included directions in the gurobi_installation file in the inst folder.
Author: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>, Cinar Kilcioglu <ckilcioglu16@gsb.columbia.edu>, Juan P. Vielma <jvielma@mit.edu>, Eric R. Cohn <ericcohn@g.harvard.edu>
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>
Diff between designmatch versions 0.5.3 dated 2023-07-10 and 0.5.4 dated 2023-08-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/designmatch-package.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Counting Codes in a Text and Preparing Data for Analysis
Description: Data analysis frequently requires coding, in particular when data are collected by interviews, by observations or even by questionnaires. Therefore, code counting and data preparation are necessary phases to carry out the analysis. Thus, the analysts will wish to count the codes inserted in a text (tokenization and counting of a list of pre-established codes) and to carry out the preparation of the data (feature scaling min-max normalization, Zscore, Box and Cox transformation, Yeo and Johnson transformation, median absolute deviation). For Box and Cox (1964) <https://www.jstor.org/stable/2984418> transformation, optimal Lambda is calculated by correlation coefficient test inspired of Lye (1993) <doi:10.1139/l93-101>. The same method is used for the calculation of the optimal lambda for Yeo and Johnson (2000) <doi:10.1093/biomet/87.4.954> transformation. Median absolute deviation is calculated on the basis of Leys et al (1993) <doi:10.1016/j.jesp.2013.03.013>. P [...truncated...]
Author: Philippe Cohard [aut, cre]
Maintainer: Philippe Cohard <p.cohard@laposte.net>
Diff between codecountR versions 0.0.2.0 dated 2023-08-16 and 0.0.2.1 dated 2023-08-29
codecountR-0.0.2.0/codecountR/R/piBloom.R |only codecountR-0.0.2.0/codecountR/man/piBloom.Rd |only codecountR-0.0.2.1/codecountR/DESCRIPTION | 6 +++--- codecountR-0.0.2.1/codecountR/MD5 | 12 ++++++------ codecountR-0.0.2.1/codecountR/NAMESPACE | 2 +- codecountR-0.0.2.1/codecountR/R/BoxAndCox.R | 2 +- codecountR-0.0.2.1/codecountR/R/YeoAndJohnson.R | 2 +- codecountR-0.0.2.1/codecountR/R/piBlom.R |only codecountR-0.0.2.1/codecountR/man/piBlom.Rd |only 9 files changed, 12 insertions(+), 12 deletions(-)
Title: Hydro-Meteorology Time-Series
Description: Functions for the management and treatment of hydrology and
meteorology time-series stored in a 'Sqlite' data base.
Author: Pierre Chevallier [aut, cre]
Maintainer: Pierre Chevallier <pierre.chevallier@mailo.com>
Diff between htsr versions 2.0.1 dated 2023-06-29 and 2.1.0 dated 2023-08-29
htsr-2.0.1/htsr/R/ds_dismeas.R |only htsr-2.0.1/htsr/R/htsr.R |only htsr-2.0.1/htsr/R/p_bar_app.R |only htsr-2.0.1/htsr/R/p_line_app.R |only htsr-2.0.1/htsr/inst/extdata/app_dismeas |only htsr-2.0.1/htsr/inst/extdata/app_exphts/app.R |only htsr-2.0.1/htsr/inst/extdata/app_invent/app.R |only htsr-2.0.1/htsr/inst/extdata/app_plothts/app.R |only htsr-2.0.1/htsr/inst/extdata/app_sensor/app.R |only htsr-2.0.1/htsr/inst/extdata/app_station/app.R |only htsr-2.0.1/htsr/inst/extdata/app_tstep/app.R |only htsr-2.0.1/htsr/inst/extdata/fichier_discalib.RData |only htsr-2.0.1/htsr/inst/extdata/fichier_fhts.RData |only htsr-2.0.1/htsr/inst/extdata/fichier_fsq.RData |only htsr-2.0.1/htsr/inst/extdata/settings.RData |only htsr-2.0.1/htsr/man/ds_dismeas.Rd |only htsr-2.0.1/htsr/man/htsr.Rd |only htsr-2.0.1/htsr/man/p_bar_app.Rd |only htsr-2.0.1/htsr/man/p_line_app.Rd |only htsr-2.1.0/htsr/DESCRIPTION | 14 - htsr-2.1.0/htsr/MD5 | 102 +++++------ htsr-2.1.0/htsr/NAMESPACE | 6 htsr-2.1.0/htsr/R/d_convert_weewx.R | 5 htsr-2.1.0/htsr/R/d_exp_hts.R | 69 +++---- htsr-2.1.0/htsr/R/d_inventory.R | 2 htsr-2.1.0/htsr/R/d_sensor.R | 4 htsr-2.1.0/htsr/R/ds_exp_hts.R | 17 - htsr-2.1.0/htsr/R/ds_inventory.R | 9 - htsr-2.1.0/htsr/R/ds_sensor.R | 5 htsr-2.1.0/htsr/R/ds_station.R | 8 htsr-2.1.0/htsr/R/h_common.R | 3 htsr-2.1.0/htsr/R/hs_tstep.R | 13 - htsr-2.1.0/htsr/R/htsr-package.R | 11 - htsr-2.1.0/htsr/R/p_bar.R | 135 +++++---------- htsr-2.1.0/htsr/R/p_line.R | 144 +++++----------- htsr-2.1.0/htsr/R/ps_plothts.R | 33 --- htsr-2.1.0/htsr/R/z_set.R | 117 ++++++++----- htsr-2.1.0/htsr/build/vignette.rds |binary htsr-2.1.0/htsr/inst/doc/htsr-package.Rmd | 35 +-- htsr-2.1.0/htsr/inst/doc/htsr-package.html | 44 ++-- htsr-2.1.0/htsr/inst/extdata/app_exphts/server.R |only htsr-2.1.0/htsr/inst/extdata/app_exphts/settings.RData |only htsr-2.1.0/htsr/inst/extdata/app_exphts/ui.R |only htsr-2.1.0/htsr/inst/extdata/app_invent/server.R |only htsr-2.1.0/htsr/inst/extdata/app_invent/ui.R |only htsr-2.1.0/htsr/inst/extdata/app_plothts/conf.RData |only htsr-2.1.0/htsr/inst/extdata/app_plothts/fil.RData |only htsr-2.1.0/htsr/inst/extdata/app_plothts/server.R |only htsr-2.1.0/htsr/inst/extdata/app_plothts/settings.RData |only htsr-2.1.0/htsr/inst/extdata/app_plothts/ui.R |only htsr-2.1.0/htsr/inst/extdata/app_sensor/server.R |only htsr-2.1.0/htsr/inst/extdata/app_sensor/ui.R |only htsr-2.1.0/htsr/inst/extdata/app_station/server.R |only htsr-2.1.0/htsr/inst/extdata/app_station/ui.R |only htsr-2.1.0/htsr/inst/extdata/app_tstep/server.R |only htsr-2.1.0/htsr/inst/extdata/app_tstep/ui.R |only htsr-2.1.0/htsr/man/d_convert_weewx.Rd | 5 htsr-2.1.0/htsr/man/d_exp_hts.Rd | 20 +- htsr-2.1.0/htsr/man/d_inventory.Rd | 2 htsr-2.1.0/htsr/man/ds_exp_hts.Rd | 12 - htsr-2.1.0/htsr/man/ds_inventory.Rd | 7 htsr-2.1.0/htsr/man/ds_sensor.Rd | 2 htsr-2.1.0/htsr/man/ds_station.Rd | 2 htsr-2.1.0/htsr/man/hs_tstep.Rd | 10 - htsr-2.1.0/htsr/man/htsr-package.Rd |only htsr-2.1.0/htsr/man/p_bar.Rd | 73 -------- htsr-2.1.0/htsr/man/p_line.Rd | 92 ---------- htsr-2.1.0/htsr/man/ps_plothts.Rd | 20 -- htsr-2.1.0/htsr/man/z_set.Rd | 79 +++++++- htsr-2.1.0/htsr/vignettes/htsr-package.Rmd | 35 +-- 70 files changed, 475 insertions(+), 660 deletions(-)
Title: Allan Variance
Description: Implements the allan variance and allan variance linear regression estimator for latent time series models. More details about the method can be found, for example, in Guerrier, S., Molinari, R., & Stebler, Y. (2016) <doi:10.1109/LSP.2016.2541867>.
Author: Stephane Guerrier [aut, cre],
James Balamuta [aut],
Gaetan Bakalli [aut],
Roberto Molinari [aut],
Justin Lee [aut],
Ahmed Radi [aut],
Haotian Xu [aut],
Yuming Zhang [aut],
Nathanael Claussen [aut],
Lionel Voirol [ctb]
Maintainer: Stephane Guerrier <stef.guerrier@gmail.com>
Diff between avar versions 0.1.2 dated 2022-07-11 and 0.1.3 dated 2023-08-29
DESCRIPTION | 10 MD5 | 8 R/av-package.r | 1 build/vignette.rds |binary inst/doc/avar-example.html | 462 +++++++++++++++++++++++++++++++++------------ 5 files changed, 355 insertions(+), 126 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al.(2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
Weibull to censored and/or weighted data. Multiple distributions can
be averaged using Akaike Information Criteria. Confidence intervals
on hazard concentrations and proportions are produced by parametric
bootstrapping.
Author: Joe Thorley [aut, cre, ctr] ,
Carl Schwarz [aut, ctr],
Rebecca Fisher [ctb],
David Fox [ctb],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb], [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 1.0.4 dated 2023-05-17 and 1.0.5 dated 2023-08-29
DESCRIPTION | 6 - MD5 | 30 ++--- NEWS.md | 7 + R/bcanz.R | 14 ++ R/censored.R | 14 ++ R/seeds.R | 14 ++ build/vignette.rds |binary inst/WORDLIST | 12 -- inst/doc/distributions.html | 38 +++--- inst/doc/exposure-plots.html | 66 +++++------ inst/doc/faqs.html | 52 ++++---- inst/doc/small-sample-bias-ref.html | 4 inst/doc/ssdtools.html | 214 ++++++++++++++++++------------------ tests/testthat/test-hc.R | 84 ++++++++++---- tests/testthat/test-hp.R | 67 ++++++++--- tests/testthat/test-predict.R | 14 ++ 16 files changed, 380 insertions(+), 256 deletions(-)
Title: Fast Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis. Implements the method described in (Luu, 2016)
<DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020)
<DOI:10.1093/molbev/msaa053>.
Author: Keurcien Luu [aut],
Michael Blum [aut],
Florian Prive [aut, cre],
Eric Bazin [ctb],
Nicolas Duforet-Frebourg [ctb]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between pcadapt versions 4.3.3 dated 2020-05-05 and 4.3.5 dated 2023-08-29
DESCRIPTION | 22 ++-- MD5 | 64 ++++++------- NAMESPACE | 2 NEWS.md | 135 +++++++++++++++++++---------- R/RcppExports.R | 2 R/bed2matrix.R | 2 R/iram.R | 3 R/pcadapt.R | 2 R/plotUtils.R | 1 README.md | 10 +- inst/CITATION | 23 ++-- man/bed2matrix.Rd | 54 +++++------ man/get.pc.Rd | 34 +++---- man/get.pop.names.Rd | 38 ++++---- man/get.score.color.Rd | 44 ++++----- man/get_statistics.Rd | 50 +++++----- man/hist_plot.Rd | 38 ++++---- man/manhattan_plot.Rd | 58 ++++++------ man/pcadapt.Rd | 226 ++++++++++++++++++++++++------------------------- man/ped2pcadapt.Rd | 34 +++---- man/plot.pcadapt.Rd | 142 +++++++++++++++--------------- man/print_convert.Rd | 46 ++++----- man/qq_plot.Rd | 32 +++--- man/read.pcadapt.Rd | 100 ++++++++++----------- man/run.pcadapt.Rd | 20 ++-- man/score_plot.Rd | 62 ++++++------- man/scree_plot.Rd | 38 ++++---- man/vcf2pcadapt.Rd | 44 ++++----- man/vcf_convert.Rd | 42 ++++----- man/writeBed.Rd | 36 +++---- src/Makevars | 2 src/RcppExports.cpp | 5 + src/vcfUtils.cpp | 2 33 files changed, 736 insertions(+), 677 deletions(-)
Title: Determining and Evaluating High-Risk Zones
Description: Functions for determining and evaluating high-risk zones and
simulating and thinning point process data, as described in 'Determining
high risk zones using point process methodology - Realization by building
an R package' Seibold (2012) <http://highriskzone.r-forge.r-project.org/Bachelorarbeit.pdf>
and 'Determining high-risk zones for unexploded World War II bombs by using point
process methodology', Mahling et al. (2013) <doi:10.1111/j.1467-9876.2012.01055.x>.
Author: Heidi Seibold <Heidi.Seibold@uzh.ch>, Monia Mahling
<monia.mahling@stat.uni-muenchen.de>, Sebastian Linne
<Sebastian.Linne@campus.lmu.de>, Felix Guenther
<felix.guenther@stat.uni-muenchen.de>
Maintainer: Rickmer Schulte <R.Schulte@campus.lmu.de>
Diff between highriskzone versions 1.4.8 dated 2022-11-22 and 1.4.9 dated 2023-08-29
DESCRIPTION | 14 +++++------ MD5 | 8 +++--- NAMESPACE | 3 +- R/est_intens_spde.R | 9 ++++--- R/highriskzone-package.R | 58 +++++++++++++++++++++++------------------------ 5 files changed, 48 insertions(+), 44 deletions(-)
Title: Generating Funky Heatmaps for Data Frames
Description: Allows generating heatmap-like visualisations for benchmark data
frames. Funky heatmaps can be fine-tuned by providing annotations of the
columns and rows, which allows assigning multiple palettes or geometries
or grouping rows and columns together in categories.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between funkyheatmap versions 0.3.0 dated 2023-03-01 and 0.4.0 dated 2023-08-29
funkyheatmap-0.3.0/funkyheatmap/inst/doc/dynbenchmark.R |only funkyheatmap-0.3.0/funkyheatmap/inst/doc/dynbenchmark.Rmd |only funkyheatmap-0.3.0/funkyheatmap/inst/doc/dynbenchmark.html |only funkyheatmap-0.3.0/funkyheatmap/inst/doc/executable.Rmd |only funkyheatmap-0.3.0/funkyheatmap/inst/doc/executable.html |only funkyheatmap-0.3.0/funkyheatmap/inst/doc/nextflow.Rmd |only funkyheatmap-0.3.0/funkyheatmap/inst/doc/nextflow.html |only funkyheatmap-0.3.0/funkyheatmap/vignettes/dynbenchmark.Rmd |only funkyheatmap-0.3.0/funkyheatmap/vignettes/executable.Rmd |only funkyheatmap-0.3.0/funkyheatmap/vignettes/nextflow.Rmd |only funkyheatmap-0.4.0/funkyheatmap/DESCRIPTION | 19 funkyheatmap-0.4.0/funkyheatmap/MD5 | 111 +- funkyheatmap-0.4.0/funkyheatmap/NAMESPACE | 6 funkyheatmap-0.4.0/funkyheatmap/NEWS.md | 47 funkyheatmap-0.4.0/funkyheatmap/R/add_column_if_missing.R | 4 funkyheatmap-0.4.0/funkyheatmap/R/calculate_column_positions.R | 11 funkyheatmap-0.4.0/funkyheatmap/R/calculate_geom_positions.R | 491 +--------- funkyheatmap-0.4.0/funkyheatmap/R/calculate_row_positions.R | 6 funkyheatmap-0.4.0/funkyheatmap/R/compose_ggplot.R | 104 +- funkyheatmap-0.4.0/funkyheatmap/R/compute_bounds.R |only funkyheatmap-0.4.0/funkyheatmap/R/create_legends.R |only funkyheatmap-0.4.0/funkyheatmap/R/dynbenchmark_data.R | 4 funkyheatmap-0.4.0/funkyheatmap/R/funky_heatmap.R | 145 ++ funkyheatmap-0.4.0/funkyheatmap/R/funkyheatmap-package.R | 9 funkyheatmap-0.4.0/funkyheatmap/R/geom_rounded_rect.R | 34 funkyheatmap-0.4.0/funkyheatmap/R/make_geom_data_processor.R | 51 - funkyheatmap-0.4.0/funkyheatmap/R/position_arguments.R |only funkyheatmap-0.4.0/funkyheatmap/R/scale_minmax.R | 2 funkyheatmap-0.4.0/funkyheatmap/R/scib_data.R |only funkyheatmap-0.4.0/funkyheatmap/R/score_to_funky_rectangle.R | 12 funkyheatmap-0.4.0/funkyheatmap/R/verify_column_groups.R | 6 funkyheatmap-0.4.0/funkyheatmap/R/verify_column_info.R | 26 funkyheatmap-0.4.0/funkyheatmap/R/verify_data.R | 18 funkyheatmap-0.4.0/funkyheatmap/R/verify_legends.R |only funkyheatmap-0.4.0/funkyheatmap/R/verify_palettes.R | 46 funkyheatmap-0.4.0/funkyheatmap/R/verify_row_groups.R | 6 funkyheatmap-0.4.0/funkyheatmap/R/verify_row_info.R | 6 funkyheatmap-0.4.0/funkyheatmap/README.md | 22 funkyheatmap-0.4.0/funkyheatmap/build/partial.rdb |binary funkyheatmap-0.4.0/funkyheatmap/build/vignette.rds |binary funkyheatmap-0.4.0/funkyheatmap/data/scib_summary.rda |only funkyheatmap-0.4.0/funkyheatmap/inst/REFERENCES.bib | 14 funkyheatmap-0.4.0/funkyheatmap/inst/doc/mtcars.R | 10 funkyheatmap-0.4.0/funkyheatmap/inst/doc/mtcars.Rmd | 10 funkyheatmap-0.4.0/funkyheatmap/inst/doc/mtcars.html | 32 funkyheatmap-0.4.0/funkyheatmap/inst/doc/scIB.R |only funkyheatmap-0.4.0/funkyheatmap/inst/doc/scIB.Rmd |only funkyheatmap-0.4.0/funkyheatmap/inst/doc/scIB.html |only funkyheatmap-0.4.0/funkyheatmap/man/funky_heatmap.Rd | 51 - funkyheatmap-0.4.0/funkyheatmap/man/funkyheatmap-package.Rd | 6 funkyheatmap-0.4.0/funkyheatmap/man/geom_rounded_rect.Rd | 2 funkyheatmap-0.4.0/funkyheatmap/man/position_arguments.Rd |only funkyheatmap-0.4.0/funkyheatmap/man/scib_summary.Rd |only funkyheatmap-0.4.0/funkyheatmap/man/verify_column_groups.Rd | 8 funkyheatmap-0.4.0/funkyheatmap/man/verify_column_info.Rd | 8 funkyheatmap-0.4.0/funkyheatmap/man/verify_legends.Rd |only funkyheatmap-0.4.0/funkyheatmap/man/verify_palettes.Rd | 8 funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-calculate_column_positions.R |only funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-calculate_row_positions.R |only funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-funky_heatmap.R | 10 funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-image_geom.R |only funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-verify_column_info.R | 8 funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-verify_data.R | 2 funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test-verify_palettes.R | 2 funkyheatmap-0.4.0/funkyheatmap/tests/testthat/test_images |only funkyheatmap-0.4.0/funkyheatmap/vignettes/images |only funkyheatmap-0.4.0/funkyheatmap/vignettes/mtcars.Rmd | 10 funkyheatmap-0.4.0/funkyheatmap/vignettes/scIB.Rmd |only 68 files changed, 618 insertions(+), 749 deletions(-)
Title: Accuracy and Precision of Measurements
Description: N>=3 methods are used to measure each of n items.
The data are used to estimate simultaneously systematic error (bias)
and random error (imprecision). Observed measurements for each method
or device are assumed to be linear functions of the unknown true values
and the errors are assumed normally distributed. Pairwise calibration
curves and plots can be easily generated. Unlike the 'ncb.od' function,
the 'omx' function builds a one-factor measurement error model using 'OpenMx'
and allows missing values, uses full information maximum likelihood to
estimate parameters, and provides both likelihood-based and bootstrapped
confidence intervals for all parameters, in addition to Wald-type intervals.
Author: Richard A. Bilonick <rabilonick@gmail.com>
Maintainer: Richard A. Bilonick <rabilonick@gmail.com>
Diff between merror versions 2.0.2 dated 2015-11-03 and 3.0 dated 2023-08-29
DESCRIPTION | 21 ++++++++++++--------- MD5 | 17 ++++++++++++----- NAMESPACE | 1 + R/alpha.beta.sigma.R |only R/globals.R |only R/omx.R |only data/pm2.5.rda |binary data/redshift.rda |only man/alpha.beta.sigma.Rd |only man/cplot.Rd | 22 +++++++++++++++++++--- man/ncb.od.Rd | 25 ++++++++++++++----------- man/omx.Rd |only man/redshift.Rd |only 13 files changed, 58 insertions(+), 28 deletions(-)
Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive
Q-Learning, Q-Learning, weighted learning, and value-search methods based on
Augmented Inverse Probability Weighted Estimators and Inverse Probability
Weighted Estimators. Dynamic Treatment Regimes: Statistical Methods for
Precision Medicine, Tsiatis, A. A., Davidian, M. D., Holloway, S. T., and Laber, E. B.,
Chapman & Hall/CRC Press, 2020, ISBN:978-1-4987-6977-8.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DynTxRegime versions 4.12 dated 2023-04-25 and 4.14 dated 2023-08-29
DESCRIPTION | 8 MD5 | 136 ++--- NEWS | 140 +++-- R/A_List.R | 2 R/A_ModelObj_DecisionPointList.R | 1 R/A_ModelObj_SubsetList.R | 1 R/B_TxObj.R | 2 R/B_TxSubset.R | 2 R/C_TypedFit.R | 2 R/C_TypedFitObj.R | 396 ++++++++-------- R/D_OutcomeNoFit.R | 2 R/D_OutcomeObj.R | 2 R/D_newModel.R | 224 ++++----- R/E_class_IQLearnFS_C.R | 362 +++++++------- R/E_class_IQLearnFS_ME.R | 260 +++++----- R/E_class_IQLearnFS_VHet.R | 6 R/E_class_IQLearnSS.R | 366 +++++++------- R/E_class_QLearn.R | 2 R/F_PropensityFit.R | 2 R/F_PropensityObj.R | 2 R/H_class_OptimalSeq.R | 4 R/I_ClassificationFit.R | 3 R/I_ClassificationObj.R | 4 R/J_class_OptimalClass.R | 2 R/L_LogitSurrogate.R | 6 R/M_OptimBasic.R | 2 R/M_OptimObj.R | 2 R/N_CVInfo.R | 2 R/N_CVInfoObj.R | 4 R/O_Learning.R | 788 ++++++++++++++++---------------- R/P_class_.owl.R | 3 R/P_class_OWL.R | 3 R/P_owl.R | 392 +++++++-------- R/Q_class_RWL.R | 3 R/R_class_BOWL.R | 552 +++++++++++----------- R/S_class_EARL.R | 3 R/internalTest.R | 367 +++++++------- man/ModelObj_DecisionPointList-class.Rd | 2 man/ModelObj_SubsetList-class.Rd | 2 man/cycleList.Rd | 4 man/newBOWL.Rd | 4 man/newCVInfo.Rd | 4 man/newCVInfoObj.Rd | 8 man/newClassificationFit.Rd | 6 man/newClassificationObj.Rd | 4 man/newEARL.Rd | 5 man/newIQLearnFS_C.Rd | 4 man/newIQLearnFS_ME.Rd | 4 man/newIQLearnFS_VHet.Rd | 4 man/newIQLearnSS.Rd | 4 man/newLearning.Rd | 4 man/newModel.Rd | 4 man/newOWL.Rd | 5 man/newOptim.Rd | 4 man/newOptimObj.Rd | 4 man/newOptimalClass.Rd | 4 man/newOptimalSeq.Rd | 4 man/newOutcomeFit.Rd | 4 man/newOutcomeObj.Rd | 4 man/newPropensityFit.Rd | 4 man/newPropensityObj.Rd | 4 man/newQLearn.Rd | 4 man/newRWL-methods.Rd | 2 man/newRWL.Rd | 4 man/newTxObj.Rd | 4 man/newTxSubset.Rd | 4 man/newTypedFit.Rd | 4 man/newTypedFitObj.Rd | 4 man/seqFunc.Rd | 4 69 files changed, 2094 insertions(+), 2094 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 0.0.8 dated 2023-03-16 and 1.0.0 dated 2023-08-29
DESCRIPTION | 9 +- MD5 | 62 ++++++++------- NAMESPACE | 1 NEWS.md |only R/assign_to_R_env.R | 2 R/clean_path_name.R | 2 R/clear.R | 4 - R/close_all_connections.R | 2 R/dt_row_to_string.R |only R/equals2.R | 3 R/firstup.R | 4 - R/get_current_timestamp.R | 3 R/is.empty.R | 2 R/notin.R | 2 R/string_replacements.R | 2 R/time_diff_print.R | 4 + R/trim.space.R | 2 R/vgsub.R | 2 README.md | 130 +++++++++++++++++++++++++-------- man/assign_to_R_env.Rd | 2 man/clean_path_name.Rd | 2 man/clear.Rd | 2 man/close_all_connections.Rd | 2 man/dt_row_to_string.Rd |only man/equals2.Rd | 3 man/firstup.Rd | 4 - man/get_current_timestamp.Rd | 3 man/grapes-notin-grapes.Rd | 2 man/is.empty.Rd | 2 man/string_replacements.Rd | 2 man/time_diff_print.Rd | 4 + man/trim.space.Rd | 2 man/vgsub.Rd | 2 tests/testthat/test-dt_row_to_string.R |only 34 files changed, 178 insertions(+), 90 deletions(-)
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting
intent.
Author: Kirill Mueller [aut] ,
Lorenz Walthert [cre, aut],
Indrajeet Patil [ctb]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.10.1 dated 2023-06-05 and 1.10.2 dated 2023-08-29
DESCRIPTION | 8 MD5 | 116 ++--- NEWS.md | 20 R/nest.R | 2 R/parse.R | 1 R/rules-line-breaks.R | 22 - R/set-assert-args.R | 2 R/testing.R | 2 R/ui-caching.R | 4 inst/doc/caching.html | 14 inst/doc/customizing_styler.R | 10 inst/doc/customizing_styler.Rmd | 10 inst/doc/customizing_styler.html | 290 +++++++------- inst/doc/detect-alignment.html | 180 ++++---- inst/doc/distribute_custom_style_guides.html | 36 - inst/doc/remove_rules.html | 162 +++---- inst/doc/strict.html | 2 inst/doc/styler.html | 110 ++--- man/is_insufficiently_parsed_string.Rd | 2 man/set_line_break_after_opening_if_call_is_multi_line.Rd | 11 man/set_line_break_if_call_is_multi_line.Rd | 16 tests/testthat/test-cache-low-level-api.R | 16 tests/testthat/test-create_token.R | 2 tests/testthat/test-create_tree.R | 2 tests/testthat/test-curly-curly.R | 2 tests/testthat/test-exception_handling.R | 2 tests/testthat/test-helpers.R | 2 tests/testthat/test-identify-roxygen-examples.R | 2 tests/testthat/test-indention_curly.R | 2 tests/testthat/test-indention_fun_calls.R | 2 tests/testthat/test-indention_multiple.R | 2 tests/testthat/test-indention_operators.R | 2 tests/testthat/test-indention_round_brackets.R | 2 tests/testthat/test-insertion_comment_interaction.R | 2 tests/testthat/test-line_breaks_and_other.R | 2 tests/testthat/test-line_breaks_fun_call.R | 1 tests/testthat/test-math_token_spacing.R | 2 tests/testthat/test-parsing.R | 2 tests/testthat/test-relocate_eq_assign.R | 1 tests/testthat/test-rmd.R | 2 tests/testthat/test-rnw.R | 2 tests/testthat/test-roundtrip.R | 3 tests/testthat/test-roxygen-examples-parse.R | 2 tests/testthat/test-scope-AsIs.R | 2 tests/testthat/test-scope-character.R | 2 tests/testthat/test-serialize_tests.R | 2 tests/testthat/test-spacing.R | 2 tests/testthat/test-square_brackets.R | 2 tests/testthat/test-start_line.R | 2 tests/testthat/test-strict.R | 2 tests/testthat/test-tidyeval.R | 2 tests/testthat/test-token_adding_removing.R | 2 tests/testthat/test-unary.R | 2 tests/testthat/test-unindention.R | 2 tests/testthat/test-unindention_regex.R | 1 tests/testthat/test-utils.R | 2 tests/testthat/test-varia.R | 2 tests/testthat/tests-cache-require-serial.R | 2 vignettes/customizing_styler.Rmd | 10 59 files changed, 535 insertions(+), 581 deletions(-)
Title: Identification of Somatic Mutation-Driven Immune Cells
Description: A computing tool is developed to automated identify somatic mutation-driven immune cells. The operation modes including: i) inferring the relative abundance matrix of tumor-infiltrating immune cells and integrating it with a particular gene mutation status, ii) detecting differential immune cells with respect to the gene mutation status and converting the abundance matrix of significant differential immune cell into two binary matrices (one for up-regulated and one for down-regulated), iii) identifying somatic mutation-driven immune cells by comparing the gene mutation status with each immune cell in the binary matrices across all samples, and iv) visualization of immune cell abundance of samples in different mutation status..
Author: Baotong Zheng, Junwei Han
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SMDIC versions 0.1.3 dated 2020-11-13 and 0.1.4 dated 2023-08-29
SMDIC-0.1.3/SMDIC/R/data.R |only SMDIC-0.1.3/SMDIC/README.md |only SMDIC-0.1.3/SMDIC/data/datalist |only SMDIC-0.1.4/SMDIC/DESCRIPTION | 12 SMDIC-0.1.4/SMDIC/MD5 | 49 - SMDIC-0.1.4/SMDIC/NAMESPACE | 82 +- SMDIC-0.1.4/SMDIC/R/GetExampleData.R | 88 +- SMDIC-0.1.4/SMDIC/R/SMDIC-package.R | 18 SMDIC-0.1.4/SMDIC/R/exp2cell.R | 960 +++++++++++++-------------- SMDIC-0.1.4/SMDIC/R/getEnvironmentData.R | 18 SMDIC-0.1.4/SMDIC/R/maf2matrix.R | 132 +-- SMDIC-0.1.4/SMDIC/R/mutcorcell.R | 580 ++++++++-------- SMDIC-0.1.4/SMDIC/R/visualization.R | 731 ++++++++++----------- SMDIC-0.1.4/SMDIC/build/vignette.rds |binary SMDIC-0.1.4/SMDIC/inst/doc/SMDIC.R | 22 SMDIC-0.1.4/SMDIC/inst/doc/SMDIC.Rmd | 2 SMDIC-0.1.4/SMDIC/inst/doc/SMDIC.html | 687 ++++++++++++------- SMDIC-0.1.4/SMDIC/inst/extdata/example.maf | 998 ++++++++++++++--------------- SMDIC-0.1.4/SMDIC/man/SMDIC-package.Rd | 18 SMDIC-0.1.4/SMDIC/man/envData.Rd | 44 - SMDIC-0.1.4/SMDIC/man/exp2cell.Rd | 2 SMDIC-0.1.4/SMDIC/man/figures/manual.pdf |binary SMDIC-0.1.4/SMDIC/man/heatmapcell.Rd | 118 +-- SMDIC-0.1.4/SMDIC/man/plotCoocMutex.Rd | 84 +- SMDIC-0.1.4/SMDIC/man/plotwaterfall.Rd | 111 +-- SMDIC-0.1.4/SMDIC/man/survcell.Rd | 130 +-- SMDIC-0.1.4/SMDIC/vignettes/SMDIC.Rmd | 2 27 files changed, 2518 insertions(+), 2370 deletions(-)
Title: Tools for Calculating Hypocycloids, Epicycloids, Hypotrochoids,
and Epitrochoids
Description: Tools for calculating coordinate representations of
hypocycloids, epicyloids, hypotrochoids, and epitrochoids
(altogether called 'cycloids' here) with different scaling
and positioning options. The cycloids can be visualised with
any appropriate graphics function in R.
Author: Peter Biber
Maintainer: Peter Biber <castor.fiber@gmx.de>
Diff between cycloids versions 1.0.1 dated 2023-04-30 and 1.0.2 dated 2023-08-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ man/cycloids-package.Rd | 7 ------- 4 files changed, 11 insertions(+), 14 deletions(-)
Title: International Cricket Data
Description: Data on international and other major cricket matches from
ESPNCricinfo <https://www.espncricinfo.com> and Cricsheet <https://cricsheet.org>.
This package provides some functions to download the data into tibbles ready
for analysis.
Author: Rob Hyndman [aut, cre],
Charles Gray [aut],
Sayani Gupta [aut],
Timothy Hyndman [aut],
Hassan Rafique [aut],
Jacquie Tran [aut],
Puwasala Gamakumara [ctb],
Alex Whan [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between cricketdata versions 0.2.2 dated 2023-02-18 and 0.2.3 dated 2023-08-29
cricketdata-0.2.2/cricketdata/man/cricketdata.Rd |only cricketdata-0.2.3/cricketdata/DESCRIPTION | 25 ++--- cricketdata-0.2.3/cricketdata/MD5 | 46 +++++----- cricketdata-0.2.3/cricketdata/NAMESPACE | 2 cricketdata-0.2.3/cricketdata/NEWS.md | 4 cricketdata-0.2.3/cricketdata/R/cricketdata.R | 24 +---- cricketdata-0.2.3/cricketdata/R/data.R | 8 - cricketdata-0.2.3/cricketdata/R/fetch_cricket_data.R | 8 + cricketdata-0.2.3/cricketdata/R/fetch_player_meta.R | 33 +++---- cricketdata-0.2.3/cricketdata/R/update_player_meta.R | 10 +- cricketdata-0.2.3/cricketdata/build/vignette.rds |binary cricketdata-0.2.3/cricketdata/data/cricsheet_codes.rda |binary cricketdata-0.2.3/cricketdata/data/player_meta.rda |binary cricketdata-0.2.3/cricketdata/inst/doc/cricinfo.html | 8 - cricketdata-0.2.3/cricketdata/inst/doc/cricketdata_R_pkg.html | 6 - cricketdata-0.2.3/cricketdata/inst/doc/cricsheet.R | 4 cricketdata-0.2.3/cricketdata/inst/doc/cricsheet.Rmd | 26 ++--- cricketdata-0.2.3/cricketdata/inst/doc/cricsheet.html | 40 +++----- cricketdata-0.2.3/cricketdata/man/cricketdata-package.Rd |only cricketdata-0.2.3/cricketdata/man/cricsheet_codes.Rd | 4 cricketdata-0.2.3/cricketdata/man/fetch_player_meta.Rd | 2 cricketdata-0.2.3/cricketdata/man/player_meta.Rd | 4 cricketdata-0.2.3/cricketdata/man/reexports.Rd | 2 cricketdata-0.2.3/cricketdata/man/update_player_meta.Rd | 2 cricketdata-0.2.3/cricketdata/vignettes/cricsheet.Rmd | 26 ++--- 25 files changed, 138 insertions(+), 146 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.15.2 dated 2022-12-16 and 1.15.3 dated 2023-08-29
DESCRIPTION | 9 + MD5 | 6 - README | 231 ----------------------------------------------- man/timetools-package.Rd | 13 -- 4 files changed, 8 insertions(+), 251 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph]
,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Julien Ruffault [ctb],
Francois Pimont [ctb] ,
Herve Cochard [ctb] ,
Aitor Amezte [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 3.1.3 dated 2023-08-23 and 3.1.4 dated 2023-08-29
medfate-3.1.3/medfate/tests/testthat/Rplots.pdf |only medfate-3.1.4/medfate/DESCRIPTION | 8 +-- medfate-3.1.4/medfate/MD5 | 11 ++-- medfate-3.1.4/medfate/src/fuelstructure.cpp | 43 +++++++++++-------- medfate-3.1.4/medfate/src/growth.cpp | 8 +-- medfate-3.1.4/medfate/src/spwb.cpp | 9 ++- medfate-3.1.4/medfate/src/transpiration_advanced.cpp | 4 + 7 files changed, 47 insertions(+), 36 deletions(-)
Title: Individual and Group Farm Sustainability Assessments using the
IDEA4 Method
Description: Collection of tools to automate the processing of data collected though the IDEA4 method (see Zahm et al. (2018) <doi:10.1051/cagri/2019004> ). Starting from the original data collecting files this packages provides functions to compute IDEA indicators, draw modern and aesthetic plots, and produce a wide range of reporting materials.
Author: David Carayon [aut, cre, cph]
Maintainer: David Carayon <david.carayon@inrae.fr>
Diff between IDEATools versions 3.5.0 dated 2023-08-08 and 3.5.1 dated 2023-08-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/write_idea.R | 4 ++-- man/figures/logo.png |binary 5 files changed, 12 insertions(+), 9 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 1.1.0 dated 2023-08-16 and 1.1.1 dated 2023-08-29
DESCRIPTION | 8 +- MD5 | 36 ++++----- R/GeoCV.R | 16 ++-- R/GeoCompositeLik2.R | 2 R/GeoCorrFct.r | 10 ++ R/GeoCovmatrix.r | 7 + R/GeoFit.r | 5 - R/GeoFit2.R | 10 ++ R/GeoIndCompositeLik2.R | 8 +- R/GeoKrig.r | 183 +++++++++++++++++++++++----------------------- R/GeoKrigloc.R | 6 - R/GeoResiduals.r | 2 R/Utility.r | 19 ++-- man/GeoCorrFct.Rd | 12 +-- man/GeoCovmatrix.Rd | 33 +++++--- man/GeoFit.Rd | 10 +- man/GeoTests.Rd | 2 src/CorrelationFunction.c | 59 +++++++++----- src/Utility.c | 1 19 files changed, 243 insertions(+), 186 deletions(-)
Title: Extreme Value Statistics and Quantile Estimation
Description: Fit, plot and compare several (extreme value) distribution functions.
Compute (truncated) distribution quantile estimates and plot return periods on a linear scale.
On the fitting method, see Asquith (2011): Distributional Analysis with L-moment Statistics [...] ISBN 1463508417.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between extremeStat versions 1.5.5 dated 2023-04-08 and 1.5.8 dated 2023-08-29
DESCRIPTION | 8 MD5 | 14 build/vignette.rds |binary inst/doc/extremeStat.R | 290 +++---- inst/doc/extremeStat.Rmd | 6 inst/doc/extremeStat.html | 1491 ++++++++++++++++++++--------------------- tests/testthat/test-quantile.R | 18 vignettes/extremeStat.Rmd | 6 8 files changed, 920 insertions(+), 913 deletions(-)
Title: Download and Import the HUGO Gene Nomenclature Committee
('HGNC') Data Set into R
Description: A set of routines to quickly download and import the 'HGNC'
data set on mapping of gene symbols to gene entries in other popular
databases or resources.
Author: Ramiro Magno [aut, cre] ,
Ana-Teresa Maia [aut] ,
CINTESIS [cph, fnd],
Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Diff between hgnc versions 0.1.3 dated 2023-06-29 and 0.1.4 dated 2023-08-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/list_archives.R | 4 ++-- README.md | 54 +++++++++++++++++++++++++++--------------------------- 5 files changed, 40 insertions(+), 36 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.7.7 dated 2023-03-10 and 2.7.8 dated 2023-08-29
DESCRIPTION | 8 MD5 | 119 - NAMESPACE | 3 NEWS.md | 20 R/AAAA.R | 16 R/ISSR800.R | 2 R/ROSETTA.R | 2 R/SDA_query.R | 27 R/WCS-utils.R | 30 R/fetchEDIT_tools.R | 2 R/fetchKSSL.R | 6 R/fetchNASIS_components.R | 10 R/fetchOSD.R | 4 R/fetchSCAN.R | 71 - R/fetchSoilGrids.R | 110 + R/fetchVegdata.R | 4 R/get_SDA_coecoclass.R | 38 R/get_SDA_hydric.R | 6 R/get_SDA_interpretation.R | 8 R/get_SDA_muaggatt.R | 5 R/get_SDA_pmgroupname.R | 2 R/get_SDA_property.R | 46 R/get_SSURGO_utils.R | 73 - R/get_component_data_from_NASIS_db.R | 36 R/get_component_from_GDB.R | 221 ++- R/get_component_from_SDA.R | 19 R/get_ecosite_history_from_NASIS_db.R | 2 R/get_vegplot_data_from_NASIS_db.R | 102 + R/mukey-WCS.R | 31 R/seriesExtent.R | 4 R/siblings.R | 4 R/simplifyFragmentData.R | 3 R/soilColorWCS.R | 2 R/soilDB-package.R | 3 R/uncode.R | 2 R/utils.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/fetchNASIS.R | 192 +- inst/doc/fetchNASIS.html | 2027 +------------------------------ inst/doc/wcs-ssurgo.R |only inst/doc/wcs-ssurgo.Rmd |only inst/doc/wcs-ssurgo.html |only man/NASISChoiceList.Rd | 2 man/ROSETTA.Rd | 2 man/fetchGDB.Rd | 3 man/fetchOSD.Rd | 2 man/fetchSCAN.Rd | 6 man/fetchSoilGrids.Rd | 47 man/fetchVegdata.Rd | 9 man/get_EDIT_ecoclass_by_geoUnit.Rd | 2 man/get_SDA_coecoclass.Rd | 3 man/loafercreek.Rd | 4 man/mukey.wcs.Rd | 4 man/seriesExtent.Rd | 2 tests/testthat/test-SDA_query.R | 3 tests/testthat/test-fetchSCAN.R | 9 tests/testthat/test-fetchSoilGrids.R | 4 tests/testthat/test-get_SDA_coecoclass.R | 9 tests/testthat/test-get_SDA_property.R | 10 tests/testthat/test-get_SSURGO_utils.R |only tests/testthat/test-simplifyColorData.R | 3 vignettes/wcs-ssurgo.Rmd |only 63 files changed, 964 insertions(+), 2432 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Zeke Marshall [ctb] ,
Thomas Etherington [ctb] ,
Janosch Heinermann [ctb]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 2.0.3 dated 2023-03-13 and 2.0.4 dated 2023-08-29
DESCRIPTION | 8 MD5 | 16 NEWS.md | 280 ++++++------- R/reconstruct_pattern_cluster.R | 836 +++++++++++++++++++--------------------- R/reconstruct_pattern_hetero.R | 772 ++++++++++++++++++------------------ R/reconstruct_pattern_homo.R | 820 +++++++++++++++++++-------------------- R/reconstruct_pattern_marks.R | 688 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/get_started.html | 88 ++-- 9 files changed, 1744 insertions(+), 1764 deletions(-)
Title: Rasch Sampler
Description: MCMC based sampling of binary matrices with fixed margins as used in exact Rasch model tests.
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Norman D. Verhelst [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between RaschSampler versions 0.8-8 dated 2015-07-23 and 0.8-9 dated 2023-08-29
DESCRIPTION | 8 +-- MD5 | 15 +++--- NAMESPACE | 2 R/rsampler.R | 97 ++++++++++++++++++++++---------------------- R/rsextrmat.R | 35 +++++++++------ R/rsextrobj.R | 68 ++++++++++++++++-------------- R/rstats.R | 54 +++++++++++++----------- man/RaschSampler-package.Rd | 9 ---- src/init.c |only 9 files changed, 148 insertions(+), 140 deletions(-)
Title: Experience Life Tables
Description: Build experience life tables.
Author: Julien Tomas, Frederic Planchet, Wassim Youssef
Maintainer: Wassim Youssef <Wassim.G.Youssef@gmail.com>
Diff between ELT versions 1.6 dated 2016-04-11 and 1.7 dated 2023-08-29
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-06 1.1.1
2021-03-11 1.1
2020-05-27 1.0
Title: Fit a Collection of Curves to Single Cohort Decomposition Data
Description: There is a long tradition of studying the flux of carbon from the biosphere to the atmosphere by following a particular cohort of litter (wood, leaves, roots, or other organic material) through time. The resulting data are mass remaining and time. A variety of functional forms may be used to fit the resulting data. Some work better empirically. Some are better connected to a process-based understanding. Some have a small number of free parameters; others have more. This package matches decomposition data to a family of these curves using likelihood--based fitting. This package is based on published research by Cornwell & Weedon (2013) <doi:10.1111/2041-210X.12138>.
Author: Will Cornwell [aut, cre] ,
James Weedon [aut],
Guofang Liu [ctb]
Maintainer: Will Cornwell <wcornwell@gmail.com>
Diff between litterfitter versions 0.1.2 dated 2022-09-15 and 0.1.3 dated 2023-08-29
DESCRIPTION | 16 +-- LICENSE | 2 MD5 | 35 ++++--- NAMESPACE | 8 + NEWS.md |only R/internal.R | 29 ++++++ R/litterFitter-package.R | 3 R/output-fxns.R | 92 ++++++++++---------- README.md | 5 - build/vignette.rds |binary inst/CITATION | 22 ++-- inst/doc/litterfitter.html | 137 +++++++++++++++---------------- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/litterfitter.Rd | 24 +++++ man/plot.litfit.Rd | 35 ++++--- man/predict_from_fit.Rd |only man/simulate_and_check.Rd |only man/steady_state.Rd | 36 ++++---- tests/testthat/test-fit_litter.R | 14 +-- 20 files changed, 267 insertions(+), 191 deletions(-)
Title: Regional Frequency Analysis using L-Moments
Description: Functions for regional frequency analysis using the methods
of J. R. M. Hosking and J. R. Wallis (1997), "Regional frequency analysis:
an approach based on L-moments".
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking <jrmhosking@gmail.com>
Diff between lmomRFA versions 3.5 dated 2023-02-19 and 3.6 dated 2023-08-29
lmomRFA-3.5/lmomRFA/src/samlm.f |only lmomRFA-3.6/lmomRFA/DESCRIPTION | 8 lmomRFA-3.6/lmomRFA/MD5 | 22 lmomRFA-3.6/lmomRFA/NEWS | 33 lmomRFA-3.6/lmomRFA/build/vignette.rds |binary lmomRFA-3.6/lmomRFA/data/Appalach.rda |binary lmomRFA-3.6/lmomRFA/data/Cascades.rda |binary lmomRFA-3.6/lmomRFA/data/Maxwind.rda |binary lmomRFA-3.6/lmomRFA/inst/doc/RegSim.pdf |binary lmomRFA-3.6/lmomRFA/inst/lmomRFA-manual.pdf |binary lmomRFA-3.6/lmomRFA/man/regdata.Rd | 2 lmomRFA-3.6/lmomRFA/src/lmomRFA-lmom.f |only lmomRFA-3.6/lmomRFA/src/lmomRFA.f | 2191 +++++----------------------- 13 files changed, 441 insertions(+), 1815 deletions(-)
Title: L-Moments
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples; parameter
estimation; L-moment ratio diagram; plot vs. quantiles of an
extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking <jrmhosking@gmail.com>
Diff between lmom versions 2.9 dated 2022-05-29 and 3.0 dated 2023-08-29
DESCRIPTION | 8 MD5 | 32 +- NEWS | 25 +- R/lmom.r | 4 inst/CITATION | 7 inst/lmom-manual.pdf |binary man/cdfgev.Rd | 4 man/cdfgpa.Rd | 2 man/lmrd.Rd | 4 man/pel-functions.Rd | 12 + src/dqagie.f | 28 +- src/dqagse.f | 30 +- src/dqelg.f | 24 +- src/dqk15i.f | 16 - src/dqk21.f | 16 - src/lmoments.f | 581 +++++++++++++++++++++++++++++++-------------------- src/samlm.f | 20 + 17 files changed, 490 insertions(+), 323 deletions(-)