Title: A Modification of Fleiss' Kappa in Case of Nominal and Ordinal
Variables
Description: The kappa statistic implemented by Fleiss is a very popular index for assessing the reliability of agreement among multiple observers. It is used both in the psychological and in the psychiatric field. Other fields of application are typically medicine, biology and engineering. Unfortunately,the kappa statistic may behave inconsistently in case of strong agreement between raters, since this index assumes lower values than it would have been expected. We propose a modification kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo simulations are used both to testing statistical hypotheses and to calculating percentile bootstrap confidence intervals based on proposed statistic in case of nominal and ordinal data.
Author: Daniele Giardiello [cre],
Piero Quatto [aut],
Enrico Ripamonti [aut],
Stefano Vigliani [ctb]
Maintainer: Daniele Giardiello <daniele.giardiello1@gmail.com>
Diff between raters versions 2.0.3 dated 2023-08-19 and 2.0.4 dated 2024-05-29
DESCRIPTION | 9 - MD5 | 14 - R/concordance.R | 412 ++++++++++++++++++++++++++++------------------------- R/wlin.conc.R | 262 ++++++++++++++++----------------- R/wquad.conc.R | 265 +++++++++++++++++----------------- man/concordance.Rd | 22 +- man/wlin.conc.Rd | 18 +- man/wquad.conc.Rd | 18 +- 8 files changed, 531 insertions(+), 489 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
Huijuan Xu [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Teun Post [ctb],
Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 2.1.1 dated 2024-02-01 and 2.1.2 dated 2024-05-29
DESCRIPTION | 13 - MD5 | 29 ++- NAMESPACE | 9 + NEWS.md | 4 R/hardReexports.R | 422 +++++++++++++++++++++++++++++++++++++++++-------- R/utils.R | 9 + README.md | 13 - man/bobyqaControl.Rd |only man/bootstrapFit.Rd | 19 +- man/foceiControl.Rd | 15 + man/lbfgsb3cControl.Rd |only man/n1qn1Control.Rd |only man/newuoaControl.Rd |only man/nlmControl.Rd |only man/nlmeControl.Rd | 5 man/nlminbControl.Rd |only man/nlsControl.Rd |only man/optimControl.Rd |only man/saemControl.Rd | 10 + man/uobyqaControl.Rd |only 20 files changed, 457 insertions(+), 91 deletions(-)
Title: Empirical Likelihood Ratio Test/Confidence Interval for AUC or
pAUC
Description: Test hypotheses and construct confidence intervals for AUC (area under Receiver
Operating Characteristic curve) and pAUC (partial area under ROC curve), from the
given two samples of test data with disease/healthy subjects. The method used is
based on TWO SAMPLE empirical likelihood and PROFILE empirical likelihood, as described in
<https://www.ms.uky.edu/~mai/research/eAUC1.pdf>.
Author: Mai Zhou [aut, cre, cph],
Xue Ding [aut],
Yumin Zhao [aut]
Maintainer: Mai Zhou <maizhou@gmail.com>
Diff between emplikAUC versions 0.3 dated 2023-01-13 and 0.4 dated 2024-05-29
DESCRIPTION | 14 +++++++------ MD5 | 18 ++++++++++------ NAMESPACE | 2 - R/el2test4auc.R | 8 +++---- R/myEstPaucT.R | 3 +- R/smooth0.R |only R/smoothLvec.R |only inst/doc/emplikAUCvig.pdf |binary man/emplikAUC-internal.Rd | 49 +++++++++++++++++++++------------------------- man/smooth0.Rd |only man/smooth3vec.Rd | 2 - man/smoothLvec.Rd |only 12 files changed, 50 insertions(+), 46 deletions(-)
Title: Accelerated Oblique Random Forests
Description: Fit, interpret, and compute predictions with oblique random
forests. Includes support for partial dependence, variable importance,
passing customized functions for variable importance and identification
of linear combinations of features. Methods for the oblique random
survival forest are described in Jaeger et al., (2023)
<DOI:10.1080/10618600.2023.2231048>.
Author: Byron Jaeger [aut, cre] ,
Nicholas Pajewski [ctb],
Sawyer Welden [ctb],
Christopher Jackson [rev],
Marvin Wright [rev],
Lukas Burk [rev]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>
Diff between aorsf versions 0.1.4 dated 2024-05-03 and 0.1.5 dated 2024-05-29
DESCRIPTION | 6 MD5 | 19 +- NEWS.md | 262 ++++++++++++++++++++-------------------- R/orsf_R6.R | 43 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/aorsf.html | 30 ++-- inst/doc/fast.html | 4 inst/doc/oobag.html | 6 inst/doc/pd.html | 254 +++++++++++++++++++------------------- tests/testthat/test-na_action.R |only 11 files changed, 328 insertions(+), 296 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-25 1.0.4
2023-05-04 1.0.3
2023-03-07 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-09 1.0.1
2023-09-25 1.0.0
2016-07-22 0.6.1
2016-07-14 0.6.0
2016-06-13 0.5.2
2016-05-30 0.5.1
2016-02-04 0.5.0
Title: Spatial Analysis of Vectra Immunoflourescent Data
Description: Visualization and analysis of Vectra Immunoflourescent
data. Options for calculating both the univariate and bivariate Ripley's K
are included. Calculations are performed using a permutation-based
approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.
Author: Jordan Creed [aut],
Ram Thapa [aut],
Christopher Wilson [aut],
Alex Soupir [aut],
Oscar Ospina [aut],
Julia Wrobel [aut],
Brooke Fridley [cph],
Fridley Lab [cre]
Maintainer: Fridley Lab <fridley.lab@moffitt.org>
Diff between spatialTIME versions 1.3.4-3 dated 2024-03-11 and 1.3.4-4 dated 2024-05-29
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- R/bi_nn_g2.R | 12 ++++++------ R/create_mif.R | 14 +++++++------- R/ripleys_k.R | 2 +- R/utils-helpers.R | 2 +- README.md | 11 +++++++++-- inst/doc/intro.html | 18 +++++++++--------- 8 files changed, 46 insertions(+), 38 deletions(-)
Title: Blind Source Separation for Multivariate Spatio-Temporal Data
Description: Simultaneous/joint diagonalization of local autocovariance matrices to estimate spatio-temporally uncorrelated random fields.
Author: Christoph Muehlmann [aut] ,
Nikolaus Piccolotto [aut] ,
Claudia Cappello [aut] ,
Sandra De Iaco [aut] ,
Klaus Nordhausen [aut, cre]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between SpaceTimeBSS versions 0.3-0 dated 2023-07-20 and 0.4-0 dated 2024-05-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ data/meteo_veneto.RData |binary inst/ChangeLog.txt | 7 ++++++- man/SpaceTimeBSS-package.Rd | 17 ++++++++++------- src/lacov.cpp | 6 +++--- src/stkmat.cpp | 6 +++--- 7 files changed, 32 insertions(+), 24 deletions(-)
Title: Create 'shiny' Applications for Cox Proportional Hazards Models
Description: Takes one or more fitted Cox proportional hazards models and writes
a 'shiny' application to a directory specified by the user. The 'shiny'
application displays predicted survival curves based on user input, and
contains none of the original data used to create the Cox model or models.
The goal is towards visualization and presentation of predicted survival
curves.
Author: Harrison Clement [aut, cre],
Subodh Selukar [aut],
Stanley Pounds [aut],
St Jude Children's Research Hospital [fnd]
Maintainer: Harrison Clement <harrisonclement16@gmail.com>
Diff between shinyCox versions 1.0.1 dated 2023-08-23 and 1.1.0 dated 2024-05-29
shinyCox-1.0.1/shinyCox/LICENSE |only shinyCox-1.1.0/shinyCox/DESCRIPTION | 10 shinyCox-1.1.0/shinyCox/MD5 | 35 shinyCox-1.1.0/shinyCox/NAMESPACE | 49 - shinyCox-1.1.0/shinyCox/NEWS.md | 11 shinyCox-1.1.0/shinyCox/R/confints.R |only shinyCox-1.1.0/shinyCox/R/cox_predictions.R | 851 ++++++++++------------ shinyCox-1.1.0/shinyCox/R/misc_functions.R | 240 +++--- shinyCox-1.1.0/shinyCox/R/shine_coxph.R | 11 shinyCox-1.1.0/shinyCox/R/shiny_blocks.R | 176 ++-- shinyCox-1.1.0/shinyCox/R/shinybuilder.R | 24 shinyCox-1.1.0/shinyCox/README.md | 152 +-- shinyCox-1.1.0/shinyCox/man/cox_KM_plots.Rd | 147 +-- shinyCox-1.1.0/shinyCox/man/cox_times_table.Rd | 162 ++-- shinyCox-1.1.0/shinyCox/man/get_confint.Rd |only shinyCox-1.1.0/shinyCox/man/make_coxph.Rd | 70 - shinyCox-1.1.0/shinyCox/man/predict_one_coxfit.Rd | 86 +- shinyCox-1.1.0/shinyCox/man/predict_se.Rd |only shinyCox-1.1.0/shinyCox/man/prep_coxfit.Rd | 68 - shinyCox-1.1.0/shinyCox/man/shine_coxph.Rd | 182 ++-- shinyCox-1.1.0/shinyCox/man/surv_pred_info.Rd |only 21 files changed, 1157 insertions(+), 1117 deletions(-)
Title: Take Screenshots (Screen Capture) from R Command
Description: Take screenshots from R command and locate an image position.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
Diff between screenshot versions 0.9.0 dated 2023-08-14 and 0.9.1 dated 2024-05-29
screenshot-0.9.0/screenshot/R/locat_image.R |only screenshot-0.9.0/screenshot/R/utils-pipe.R |only screenshot-0.9.0/screenshot/man/pipe.Rd |only screenshot-0.9.1/screenshot/DESCRIPTION | 15 screenshot-0.9.1/screenshot/LICENSE | 4 screenshot-0.9.1/screenshot/MD5 | 70 - screenshot-0.9.1/screenshot/NAMESPACE | 42 screenshot-0.9.1/screenshot/NEWS.md | 8 screenshot-0.9.1/screenshot/R/clipboard.R |only screenshot-0.9.1/screenshot/R/data.R |only screenshot-0.9.1/screenshot/R/display.R |only screenshot-0.9.1/screenshot/R/locate_image.R |only screenshot-0.9.1/screenshot/R/screenshot.R | 6 screenshot-0.9.1/screenshot/R/utils-rlang.R | 3 screenshot-0.9.1/screenshot/README.md | 39 screenshot-0.9.1/screenshot/data |only screenshot-0.9.1/screenshot/inst/WORDLIST | 2 screenshot-0.9.1/screenshot/man/bitmap2png.Rd |only screenshot-0.9.1/screenshot/man/clipboard2bitmap.Rd |only screenshot-0.9.1/screenshot/man/clipboard_sample.Rd |only screenshot-0.9.1/screenshot/man/compare_table.Rd | 52 screenshot-0.9.1/screenshot/man/count_val_freq.Rd | 50 screenshot-0.9.1/screenshot/man/create_header.Rd |only screenshot-0.9.1/screenshot/man/display_corner.Rd |only screenshot-0.9.1/screenshot/man/display_size.Rd |only screenshot-0.9.1/screenshot/man/figures |only screenshot-0.9.1/screenshot/man/get_clipboard_image.Rd |only screenshot-0.9.1/screenshot/man/get_os.Rd | 36 screenshot-0.9.1/screenshot/man/hay2needle.Rd | 62 - screenshot-0.9.1/screenshot/man/hex2little_endian.Rd |only screenshot-0.9.1/screenshot/man/image2gray_matrix.Rd | 44 screenshot-0.9.1/screenshot/man/index2xy.Rd | 52 screenshot-0.9.1/screenshot/man/install_screenshot.Rd | 72 - screenshot-0.9.1/screenshot/man/is_all_same.Rd | 40 screenshot-0.9.1/screenshot/man/locate_image.Rd | 121 + screenshot-0.9.1/screenshot/man/locate_ndl_in_hay.Rd | 80 - screenshot-0.9.1/screenshot/man/save_bmp.Rd |only screenshot-0.9.1/screenshot/man/save_clipboard_image.Rd |only screenshot-0.9.1/screenshot/man/screenshot.Rd | 72 - screenshot-0.9.1/screenshot/man/screenshot_exists.Rd | 46 screenshot-0.9.1/screenshot/man/xy_pos.Rd | 56 screenshot-0.9.1/screenshot/tests/testthat.R | 24 screenshot-0.9.1/screenshot/tests/testthat/test-find_needle.R | 6 screenshot-0.9.1/screenshot/tools/clipboard.R |only screenshot-0.9.1/screenshot/tools/cran-comments-1st.md |only screenshot-0.9.1/screenshot/tools/screenshot.bat | 606 +++++----- screenshot-0.9.1/screenshot/tools/screenshot_0.bat |only 47 files changed, 832 insertions(+), 776 deletions(-)
Title: Estimation of Fuzzy Poverty Measures
Description: Estimates fuzzy measures of poverty and deprivation. It also estimates the sampling variance of these measures using bootstrap or jackknife repeated replications.
Author: Federico Crescenzi [aut, cre] ,
Lorenzo Mori [aut] ,
Gianni Betti [ctb]
Maintainer: Federico Crescenzi <federico.crescenzi@unitus.it>
Diff between FuzzyPovertyR versions 2.0.1 dated 2024-02-14 and 2.1.0 dated 2024-05-29
FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/FuzzyPoverty_class.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_FL.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_ZBM.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_belhadj2011.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_belhadj2015.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_chakravarty.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_cz.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_equate.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_mu.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_objective.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_tfr.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_verma.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fm_verma2.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fs_fuzzyScaleItem.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fs_modified_sum.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fs_mu.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fs_objective.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/fs_wb.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/R/weighted_quantile.R |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/FN.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/FuzzyPoverty.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/FuzzySupplementary.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/Fuzzy_conv.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/MemberhsipGradesMatrix.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/belhadj2015.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/bootP.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_Chakravarty.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_FL.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_TFR.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_ZBM.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_belhadj2011.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_belhadj2015.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_cerioli.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_equate.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_mu.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_mu2.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_mu_TFR.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_objective.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_verma.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fm_verma2.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fs_mu.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fs_objective.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/fuzzyScaleItem.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/modifiedSum.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/ub1.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/ub2.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/wb.jh.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/weighted_quantile.Rd |only FuzzyPovertyR-2.0.1/FuzzyPovertyR/man/z_fun.Rd |only FuzzyPovertyR-2.1.0/FuzzyPovertyR/DESCRIPTION | 12 FuzzyPovertyR-2.1.0/FuzzyPovertyR/MD5 | 129 FuzzyPovertyR-2.1.0/FuzzyPovertyR/NAMESPACE | 2 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/HCR.R | 71 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/Not_exp_fun.R |only FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/eq_predicate.R | 137 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fm_construct.R | 264 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fm_var.R | 416 - FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_construct.R | 182 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_construct_all.R | 94 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_equate.R | 106 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_order.R | 110 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_plot.R | 202 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_summary.R | 82 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_transform.R | 80 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_var.R | 333 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/fs_weight.R | 112 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/plot_method.R | 288 FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/summary_method.R | 101 FuzzyPovertyR-2.1.0/FuzzyPovertyR/build/vignette.rds |binary FuzzyPovertyR-2.1.0/FuzzyPovertyR/inst/WORDLIST |only FuzzyPovertyR-2.1.0/FuzzyPovertyR/inst/doc/FuzzyPovertyR.R | 335 FuzzyPovertyR-2.1.0/FuzzyPovertyR/inst/doc/FuzzyPovertyR.Rmd | 961 +- FuzzyPovertyR-2.1.0/FuzzyPovertyR/inst/doc/FuzzyPovertyR.html | 3621 +++++----- FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/HCR.Rd | 9 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/eq_predicate.Rd | 34 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/eusilc.Rd | 60 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fm_construct.Rd | 156 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fm_var.Rd | 96 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_construct.Rd | 43 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_construct_all.Rd | 35 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_equate.Rd | 35 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_order.Rd | 14 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_transform.Rd | 14 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_var.Rd | 69 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/fs_weight.Rd | 25 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/plot.FuzzyMonetary.Rd | 13 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/plot.FuzzySupplementary.Rd | 12 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/summary.FuzzyMonetary.Rd | 14 FuzzyPovertyR-2.1.0/FuzzyPovertyR/man/summary.FuzzySupplementary.Rd | 13 FuzzyPovertyR-2.1.0/FuzzyPovertyR/vignettes/FuzzyPovertyR.Rmd | 961 +- FuzzyPovertyR-2.1.0/FuzzyPovertyR/vignettes/bib.bib | 670 - 91 files changed, 5695 insertions(+), 4216 deletions(-)
Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools
for making reproducible and reusable content in R.
The two workhorse functions are Cache() and prepInputs(). Cache()
allows for nested caching, is robust to environments and objects with
environments (like functions), and has deals with some classes of
file-backed R objects e.g., from terra and raster packages.
Both functions have been developed to
be foundational components of data retrieval
and processing in continuous workflow situations. In both functions,
efforts are made to make the first and subsequent calls of functions have
the same result, but faster at subsequent times by way of checksums
and digesting. Several features are still under development, including
cloud storage of cached objects, allowing for sharing between users. Several
advanced options are available, see ?reproducibleOptions().
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [aut] ,
Tati Micheletti [ctb] ,
Ceres Barros [ctb] ,
Ian Eddy [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 2.0.12 dated 2024-04-15 and 2.1.0 dated 2024-05-29
DESCRIPTION | 30 MD5 | 135 +- NAMESPACE | 15 NEWS.md | 35 R/DBI.R | 307 ++-- R/cache-helpers.R | 10 R/cache.R | 343 +++-- R/checksums.R | 49 R/cloud.R | 2 R/convertPaths.R | 3 R/download.R | 178 +- R/exportedMethods.R | 835 +++++++----- R/gis.R | 6 R/helpers.R | 182 -- R/listNamed.R |only R/messages.R | 333 +++++ R/options.R | 26 R/paths.R | 64 R/postProcess.R | 89 + R/postProcessTo.R | 720 +++++++---- R/preProcess.R | 339 +++-- R/prepInputs.R | 641 +++++---- R/robustDigest.R | 20 R/showCacheEtc.R | 151 +- R/zzz.R | 24 README.md | 2 inst/WORDLIST | 18 inst/doc/Intro-to-Cache.Rmd | 2 inst/doc/Intro-to-Cache.html | 1872 ++++++++++++++--------------- inst/examples/example_assessDataType.R | 2 inst/examples/example_postProcessTo.R |only man/Cache.Rd | 15 man/CacheGeo.Rd | 8 man/CacheHelpers.Rd | 94 - man/Checksums.Rd | 6 man/assessDataType.Rd | 2 man/digest.Rd | 3 man/dot-isMemoised.Rd |only man/dotWrap.Rd | 6 man/exportedMethods.Rd | 30 man/fastMask.Rd | 4 man/gdalwarpFns.Rd |only man/keepOrigGeom.Rd |only man/listNamed.Rd |only man/loadFile.Rd |only man/messageColoured.Rd | 59 man/pkgEnv.Rd | 20 man/postProcessTo.Rd | 46 man/preProcess.Rd | 4 man/prepInputs.Rd | 28 man/remapFilenames.Rd |only man/reproducibleOptions.Rd | 22 man/retry.Rd | 2 man/saveToCache.Rd | 6 man/viewCache.Rd | 24 tests/testthat/helper-allEqual.R | 31 tests/testthat/setup.R | 22 tests/testthat/test-cache.R | 243 ++- tests/testthat/test-cacheGeo.R | 2 tests/testthat/test-cacheHelpers.R | 79 - tests/testthat/test-cloud.R | 9 tests/testthat/test-copy.R | 4 tests/testthat/test-devMode.R | 4 tests/testthat/test-gis.R | 2 tests/testthat/test-misc.R | 24 tests/testthat/test-paths.R |only tests/testthat/test-postProcess.R | 18 tests/testthat/test-postProcessTerra.R | 1 tests/testthat/test-preProcessDoesntWork.R | 35 tests/testthat/test-preProcessWorks.R | 8 tests/testthat/test-prepInputs.R | 710 +++++----- tests/testthat/test-robustDigest.R | 25 vignettes/Intro-to-Cache.Rmd | 2 73 files changed, 4836 insertions(+), 3195 deletions(-)
Title: Pivotal Methods for Bayesian Relabelling and k-Means Clustering
Description: Collection of pivotal algorithms
for: relabelling the MCMC chains in order to undo the label
switching problem in Bayesian mixture models;
fitting sparse finite mixtures;
initializing the centers of the classical k-means algorithm
in order to obtain a better clustering solution.
For further details see
Egidi, Pappadà, Pauli and Torelli (2018b)<ISBN:9788891910233>.
Author: Leonardo Egidi[aut, cre],
Roberta Pappada[aut],
Francesco Pauli[aut],
Nicola Torelli[aut]
Maintainer: Leonardo Egidi <legidi@units.it>
Diff between pivmet versions 0.5.0 dated 2023-02-22 and 0.6.0 dated 2024-05-29
pivmet-0.5.0/pivmet/R/bayes_mcmc.R |only pivmet-0.5.0/pivmet/R/musk.R |only pivmet-0.5.0/pivmet/R/pivotal.R |only pivmet-0.5.0/pivmet/R/plot.R |only pivmet-0.5.0/pivmet/R/relab.R |only pivmet-0.5.0/pivmet/R/sim.R |only pivmet-0.5.0/pivmet/tests/testthat/test-bayesMCMC.R |only pivmet-0.5.0/pivmet/tests/testthat/test-bayesMCMCbiv.R |only pivmet-0.5.0/pivmet/tests/testthat/test-mus.R |only pivmet-0.6.0/pivmet/DESCRIPTION | 12 pivmet-0.6.0/pivmet/MD5 | 45 pivmet-0.6.0/pivmet/NEWS.md | 6 pivmet-0.6.0/pivmet/R/piv_KMeans.R |only pivmet-0.6.0/pivmet/R/piv_MCMC.R |only pivmet-0.6.0/pivmet/R/piv_plot.R |only pivmet-0.6.0/pivmet/R/piv_rel.R |only pivmet-0.6.0/pivmet/R/piv_sel.R |only pivmet-0.6.0/pivmet/R/piv_sim.R |only pivmet-0.6.0/pivmet/README.md | 140 - pivmet-0.6.0/pivmet/build/vignette.rds |binary pivmet-0.6.0/pivmet/inst/doc/K-means_clustering_using_the_MUS_algorithm.html | 530 +++- pivmet-0.6.0/pivmet/inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.html | 1067 ++++++---- pivmet-0.6.0/pivmet/man/piv_KMeans.Rd | 2 pivmet-0.6.0/pivmet/man/piv_MCMC.Rd | 2 pivmet-0.6.0/pivmet/man/piv_plot.Rd | 2 pivmet-0.6.0/pivmet/man/piv_rel.Rd | 2 pivmet-0.6.0/pivmet/man/piv_sel.Rd | 2 pivmet-0.6.0/pivmet/man/piv_sim.Rd | 2 pivmet-0.6.0/pivmet/tests/testthat/test_piv_KMeans.R |only pivmet-0.6.0/pivmet/tests/testthat/test_piv_MCMC.R |only pivmet-0.6.0/pivmet/tests/testthat/test_piv_rel.R |only pivmet-0.6.0/pivmet/tests/testthat/test_piv_sel.R |only pivmet-0.6.0/pivmet/tests/testthat/testthat.R | 5 33 files changed, 1225 insertions(+), 592 deletions(-)
Title: Conducts Mokken Scale Analysis
Description: Contains functions for performing Mokken
scale analysis on test and questionnaire data.
It includes an automated item selection algorithm, and various checks of model assumptions.
Author: L. Andries van der Ark [aut, cre],
Letty Koopman [aut],
J. Hendrik Straat [ctb],
Don van den Bergh [ctb]
Maintainer: L. Andries van der Ark <L.A.vanderArk@uva.nl>
Diff between mokken versions 3.1.0 dated 2023-06-26 and 3.1.1 dated 2024-05-29
DESCRIPTION | 8 MD5 | 20 R/check.iio.R | 1212 ++++++++++++++++++++++++++--------------- R/internalFunctions.R | 5 R/plot.iio.class.R | 6 R/summary.iio.class.R | 9 R/summary.monotonicity.class.R | 2 build/partial.rdb |binary data/trog.rda |only man/check.iio.Rd | 30 - man/mokken-package.Rd | 30 - man/trog.Rd |only 12 files changed, 872 insertions(+), 450 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre],
Joao Carmezim [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.3.0 dated 2024-05-10 and 0.4.0 dated 2024-05-29
flowchart-0.3.0/flowchart/R/clinic_patient.R |only flowchart-0.3.0/flowchart/R/clinic_visit.R |only flowchart-0.3.0/flowchart/data/clinic_patient.rda |only flowchart-0.3.0/flowchart/data/clinic_visit.rda |only flowchart-0.3.0/flowchart/man/clinic_patient.Rd |only flowchart-0.3.0/flowchart/man/clinic_visit.Rd |only flowchart-0.4.0/flowchart/DESCRIPTION | 6 flowchart-0.4.0/flowchart/MD5 | 58 +- flowchart-0.4.0/flowchart/NEWS.md | 14 flowchart-0.4.0/flowchart/R/as_fc.R | 4 flowchart-0.4.0/flowchart/R/fc_draw.R | 10 flowchart-0.4.0/flowchart/R/fc_export.R | 28 - flowchart-0.4.0/flowchart/R/fc_filter.R | 6 flowchart-0.4.0/flowchart/R/fc_merge.R | 19 flowchart-0.4.0/flowchart/R/fc_modify.R | 50 - flowchart-0.4.0/flowchart/R/fc_split.R | 6 flowchart-0.4.0/flowchart/R/fc_stack.R | 25 flowchart-0.4.0/flowchart/README.md | 6 flowchart-0.4.0/flowchart/build/vignette.rds |binary flowchart-0.4.0/flowchart/data/safo.rda |binary flowchart-0.4.0/flowchart/inst/doc/flowchart.R | 199 +++---- flowchart-0.4.0/flowchart/inst/doc/flowchart.Rmd | 304 ++++++----- flowchart-0.4.0/flowchart/inst/doc/flowchart.html | 577 +++++++++++----------- flowchart-0.4.0/flowchart/man/as_fc.Rd | 4 flowchart-0.4.0/flowchart/man/fc_draw.Rd | 10 flowchart-0.4.0/flowchart/man/fc_export.Rd | 22 flowchart-0.4.0/flowchart/man/fc_filter.Rd | 6 flowchart-0.4.0/flowchart/man/fc_merge.Rd | 19 flowchart-0.4.0/flowchart/man/fc_modify.Rd | 50 - flowchart-0.4.0/flowchart/man/fc_split.Rd | 6 flowchart-0.4.0/flowchart/man/fc_stack.Rd | 23 flowchart-0.4.0/flowchart/man/figures |only flowchart-0.4.0/flowchart/vignettes/flowchart.Rmd | 304 ++++++----- 33 files changed, 894 insertions(+), 862 deletions(-)
Title: Auxiliary Data Package for Our Main Package 'dartR'
Description: Data package for 'dartR'. Provides data sets to run examples in 'dartR'.
This was necessary due to the size limit imposed by 'CRAN'. The data in 'dartR.data'
is needed to run the examples provided in the 'dartR' functions.
All available data sets are either based on actual data (but reduced in size)
and/or simulated data sets to allow the fast execution of examples and demonstration
of the functions.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.data versions 1.0.2 dated 2022-11-16 and 1.0.8 dated 2024-05-29
dartR.data-1.0.2/dartR.data/README.md |only dartR.data-1.0.2/dartR.data/data/bandicoot.rda |only dartR.data-1.0.2/dartR.data/data/platypus.rda |only dartR.data-1.0.8/dartR.data/DESCRIPTION | 18 +++-- dartR.data-1.0.8/dartR.data/MD5 | 36 +++++++--- dartR.data-1.0.8/dartR.data/NAMESPACE | 3 dartR.data-1.0.8/dartR.data/R/datasets.r | 74 ++++++++++++++++++++++ dartR.data-1.0.8/dartR.data/R/zzz.R |only dartR.data-1.0.8/dartR.data/build |only dartR.data-1.0.8/dartR.data/data/EYR.rda |only dartR.data-1.0.8/dartR.data/data/LBP.rda |only dartR.data-1.0.8/dartR.data/data/YTH.rda |only dartR.data-1.0.8/dartR.data/data/bandicoot.gl.rda |only dartR.data-1.0.8/dartR.data/data/platypus.gl.rda |only dartR.data-1.0.8/dartR.data/data/possums.gl.rda |binary dartR.data-1.0.8/dartR.data/data/testset.gl.rda |binary dartR.data-1.0.8/dartR.data/data/testset.gs.rda |binary dartR.data-1.0.8/dartR.data/inst/CITATION | 20 ++++- dartR.data-1.0.8/dartR.data/man/EYR.Rd |only dartR.data-1.0.8/dartR.data/man/LBP.Rd |only dartR.data-1.0.8/dartR.data/man/YTH.Rd |only dartR.data-1.0.8/dartR.data/man/figures |only dartR.data-1.0.8/dartR.data/man/platy.Rd | 13 +++ dartR.data-1.0.8/dartR.data/man/zzz.Rd |only 24 files changed, 144 insertions(+), 20 deletions(-)
Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph]
,
Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>
Diff between snvecR versions 3.9.3 dated 2024-04-24 and 3.9.4 dated 2024-05-29
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/analyze_grid_td-ed.html | 410 ++++++++++++++++++------------------- tests/testthat/test-get_solution.R | 2 8 files changed, 222 insertions(+), 216 deletions(-)
Title: Optimal Regression Design under the Second-Order Least Squares
Estimator
Description: With given inputs that include number of points, discrete design space, a measure of skewness, models and parameter value, this package calculates the objective value, optimal designs and plot the equivalence theory under A- and D-optimal criteria under the second-order Least squares estimator. This package is based on the paper "Properties of optimal regression designs under the second-order least squares estimator" by Chi-Kuang Yeh and Julie Zhou (2021) <doi:10.1007/s00362-018-01076-6>.
Author: Chi-Kuang Yeh [aut, cre] ,
Julie Zhou [aut, ctb],
Jason Hou-Liu [ctb]
Maintainer: Chi-Kuang Yeh <chi-kuang.yeh@uwaterloo.ca>
Diff between SLSEdesign versions 0.0.2 dated 2024-05-27 and 0.0.3 dated 2024-05-29
DESCRIPTION | 17 +++++---- MD5 | 22 ++++++------ NAMESPACE | 1 R/Aopt.R | 43 ++++++++--------------- R/Dopt.R | 29 +++++++-------- R/plot_weight.R | 2 - inst/doc/SLSEdesign.R | 6 +-- inst/doc/SLSEdesign.Rmd | 6 +-- inst/doc/SLSEdesign.html | 86 ++++++++++++++++++++--------------------------- man/Aopt.Rd | 13 +++---- man/Dopt.Rd | 10 ++--- vignettes/SLSEdesign.Rmd | 6 +-- 12 files changed, 104 insertions(+), 137 deletions(-)
Title: A Soil Survey Toolkit
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: Dylan Beaudette [cre, aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut],
USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between sharpshootR versions 2.3 dated 2024-04-08 and 2.3.1 dated 2024-05-29
DESCRIPTION | 14 ++++++-------- MD5 | 12 ++++++------ NAMESPACE | 5 ----- NEWS.md | 4 ++++ R/component.adj.matrix.R | 16 +++++++++++----- R/dailyWB.R | 4 +++- tests/testthat/Rplots.pdf |binary 7 files changed, 30 insertions(+), 25 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Cole C. Monnahan [ctb, cph] ,
Mollie Brooks [ct [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.5.0 dated 2024-04-03 and 0.6.0 dated 2024-05-29
DESCRIPTION | 8 - MD5 | 60 ++++++------- NEWS.md | 47 ++++++++++ R/cross-val.R | 3 R/dharma.R | 145 +++++++++++++++++++------------- R/families.R | 36 +++++-- R/fit.R | 97 ++++++++++----------- R/index.R | 31 ++---- R/methods.R | 12 -- R/predict.R | 44 ++------- R/print.R | 4 R/priors.R | 1 R/residuals.R | 31 ++++++ R/tmb-sim.R | 18 ++- R/utils.R | 100 +++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/COPYRIGHTS | 4 inst/WORDLIST |only inst/doc/model-description.html | 4 man/dharma_residuals.Rd | 52 ++++------- man/families.Rd | 7 - man/sdmTMB.Rd | 3 man/simulate.sdmTMB.Rd | 3 src/sdmTMB.cpp | 37 ++++---- tests/testthat/Rplots.pdf |binary tests/testthat/test-3-families.R | 1 tests/testthat/test-5-residuals.R | 39 ++++++++ tests/testthat/test-dharma.R | 8 - tests/testthat/test-extra-time.R | 145 +++++++++++++++++++++++++++++++- tests/testthat/test-random-intercepts.R | 27 +++++ tests/testthat/test-tinyVAST.R |only 32 files changed, 636 insertions(+), 331 deletions(-)
Title: A Statistical Framework for the Analysis of Japanese Kanji
Characters
Description: Various tools and data sets that support the study of kanji, including their morphology, decomposition and concepts of distance and similarity between them.
Author: Dominic Schuhmacher [aut, cre]
,
Lennart Finke [aut]
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between kanjistat versions 0.9.1 dated 2023-05-23 and 0.14.0 dated 2024-05-29
DESCRIPTION | 34 - MD5 | 79 +- NAMESPACE | 13 NEWS.md | 107 +++ R/RcppExports.R |only R/bezier.R |only R/distance_transforms.R |only R/kanji1.R | 124 +++ R/kanji2.R | 338 ++++++---- R/kanji_neighborhoods.R |only R/kanjimat.R | 24 R/kanjistat-package.R | 109 +++ R/kanjivec.R | 23 R/read_kanjidic2.R |only R/stroke_edit_distance.R |only R/utilities.R | 89 ++ R/zzz.R | 4 README.md | 32 build/partial.rdb |binary build/vignette.rds |binary data/dstrokedit.rda |only data/dyehli.rda |only data/pooledsimilarity.rda |only inst/doc/kanjistat.html | 135 +++ man/compare_neighborhoods.Rd |only man/convert_kanji.Rd |only man/distdata.Rd |only man/figures/hair_kvecdend_sm.svg |only man/figures/hair_kveckanji_sm.svg |only man/figures/treesplan_sm.png |only man/figures/treestrans_sm.png |only man/fivetrees.Rd | 4 man/kanjidata.Rd | 4 man/kanjidist.Rd | 40 - man/kanjidistmat.Rd | 8 man/kanjimat.Rd | 6 man/kanjivec.Rd | 15 man/pooled_similarity.Rd |only man/read_kanjidic2.Rd |only man/sedist.Rd |only src |only tests/testthat/_data_and_more_snaps/kanjidic2-2023-365_ichihagi.xml |only tests/testthat/_data_and_more_snaps/kanjidic2_listref_ichihagi.rda |only tests/testthat/_data_and_more_snaps/kanjivec_flatten_ref_yuumail.rds |binary tests/testthat/_data_and_more_snaps/kanjivec_ref_fuji.rds |binary tests/testthat/helper.R | 1 tests/testthat/test-bezier.R |only tests/testthat/test-kanji1.R | 223 ++++++ tests/testthat/test-kanjimat.R | 5 tests/testthat/test-kanjivec.R | 17 tests/testthat/test-read_kanjidic2.R |only tests/testthat/test-stroke_edit_distance.R |only 52 files changed, 1199 insertions(+), 235 deletions(-)
Title: Genotype-by-Environment Interaction in Polygenic Score Models
Description: A novel PRS model is introduced to enhance the prediction accuracy by utilising GxE effects. This package performs Genome Wide Association Studies (GWAS) and Genome Wide Environment Interaction Studies (GWEIS) using a discovery dataset. The package has the ability to obtain polygenic risk scores (PRSs) for a target sample. Finally it predicts the risk values of each individual in the target sample. Users have the choice of using existing models (Li et al., 2015) <doi:10.1093/annonc/mdu565>, (Pandis et al., 2013) <doi:10.1093/ejo/cjt054>, (Peyrot et al., 2018) <doi:10.1016/j.biopsych.2017.09.009> and (Song et al., 2022) <doi:10.1038/s41467-022-32407-9>, as well as newly proposed models for genomic risk prediction (refer to the URL for more details).
Author: Dovini Jayasinghe [aut, cre, cph],
Hong Lee [aut, cph],
Moksedul Momin [aut, cph]
Maintainer: Dovini Jayasinghe <dovini.jayasinghe@mymail.unisa.edu.au>
Diff between GxEprs versions 1.1 dated 2023-10-03 and 1.2 dated 2024-05-29
DESCRIPTION | 8 - MD5 | 20 +-- R/GWAS_binary.R | 136 +++++++++++++------------- R/GWEIS_binary.R | 183 +++++++++++++++++------------------ R/PRS_binary.R | 102 +++++++++---------- R/summary_permuted_binary.R | 12 +- R/summary_permuted_quantitative.R | 18 ++- man/GWAS_binary.Rd | 6 - man/GWEIS_binary.Rd | 15 +- man/PRS_binary.Rd | 6 - man/summary_permuted_quantitative.Rd | 2 11 files changed, 261 insertions(+), 247 deletions(-)
Title: Download Data from the CSO 'PxStat' API
Description: Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide
format. The Central Statistics Office (CSO) is the national statistical institute of Ireland
and 'PxStat' is the CSOs online database of Official Statistics. This database contains current
and historical data series compiled from CSO statistical releases and is accessed at
<http://data.cso.ie>.
The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides
access to 'PxStat' data in JSON-stat format at <http://data.cso.ie>.
This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.
Author: Eoin Horgan [aut] ,
Conor Crowley [aut, cre],
Vytas Vaiciulis [aut],
Mervyn O'Luing [aut],
James O'Rourke [aut]
Maintainer: Conor Crowley <conor.crowley@cso.ie>
Diff between csodata versions 1.4.2 dated 2023-08-11 and 1.5.0 dated 2024-05-29
DESCRIPTION | 9 - MD5 | 36 ++-- NEWS.md | 14 + R/cso_get_data.R | 22 +- R/cso_get_geo.R | 10 - R/cso_get_meta.R | 26 +- R/cso_get_toc.R | 19 +- R/csodata.R | 3 build/vignette.rds |binary inst/doc/quick_start_guide.R | 4 inst/doc/quick_start_guide.html | 354 +++++++++++++++++++--------------------- man/cso_get_content.Rd | 4 man/cso_get_data.Rd | 8 man/cso_get_interval.Rd | 6 man/cso_get_meta.Rd | 6 man/cso_get_toc.Rd | 6 man/cso_get_var_values.Rd | 4 man/cso_get_vars.Rd | 6 man/csodata.Rd | 20 ++ 19 files changed, 297 insertions(+), 260 deletions(-)
Title: Probabilistic Reconciliation via Conditioning
Description: Provides methods for probabilistic reconciliation of hierarchical forecasts of time series.
The available methods include analytical Gaussian reconciliation (Corani et al., 2021)
<doi:10.1007/978-3-030-67664-3_13>,
MCMC reconciliation of count time series (Corani et al., 2024)
<doi:10.1016/j.ijforecast.2023.04.003>,
Bottom-Up Importance Sampling (Zambon et al., 2024)
<doi:10.1007/s11222-023-10343-y>,
methods for the reconciliation of mixed hierarchies (Mix-Cond and TD-cond)
(Zambon et al., 2024. The 40th Conference on Uncertainty in Artificial Intelligence, accepted).
Author: Dario Azzimonti [aut, cre] ,
Nicolo Rubattu [aut] ,
Lorenzo Zambon [aut] ,
Giorgio Corani [aut]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between bayesRecon versions 0.2.0 dated 2023-12-19 and 0.3.0 dated 2024-05-29
bayesRecon-0.2.0/bayesRecon/R/M3_example.R |only bayesRecon-0.2.0/bayesRecon/R/carparts_example.R |only bayesRecon-0.2.0/bayesRecon/R/extr_mkt_events.R |only bayesRecon-0.2.0/bayesRecon/R/extr_mkt_events_basefc.R |only bayesRecon-0.2.0/bayesRecon/R/infantMortality.R |only bayesRecon-0.2.0/bayesRecon/R/reconc.R |only bayesRecon-0.2.0/bayesRecon/R/reconc_MH.R |only bayesRecon-0.2.0/bayesRecon/tests/testthat/test-examples.R |only bayesRecon-0.2.0/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_373057e17e36714cc0eaca92f649f5e7.RData |only bayesRecon-0.2.0/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_373057e17e36714cc0eaca92f649f5e7.rdb |only bayesRecon-0.2.0/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_373057e17e36714cc0eaca92f649f5e7.rdx |only bayesRecon-0.2.0/bayesRecon/vignettes/bayesRecon_vignette_cache |only bayesRecon-0.3.0/bayesRecon/DESCRIPTION | 20 bayesRecon-0.3.0/bayesRecon/MD5 | 113 +- bayesRecon-0.3.0/bayesRecon/NAMESPACE | 7 bayesRecon-0.3.0/bayesRecon/NEWS.md | 16 bayesRecon-0.3.0/bayesRecon/R/PMF.R |only bayesRecon-0.3.0/bayesRecon/R/bayesRecon-package.R | 57 - bayesRecon-0.3.0/bayesRecon/R/data.R |only bayesRecon-0.3.0/bayesRecon/R/hierarchy.R | 127 ++ bayesRecon-0.3.0/bayesRecon/R/reconc_BUIS.R |only bayesRecon-0.3.0/bayesRecon/R/reconc_MCMC.R |only bayesRecon-0.3.0/bayesRecon/R/reconc_MixCond.R |only bayesRecon-0.3.0/bayesRecon/R/reconc_TDcond.R |only bayesRecon-0.3.0/bayesRecon/R/reconc_gaussian.R |only bayesRecon-0.3.0/bayesRecon/R/shrink_cov.R | 5 bayesRecon-0.3.0/bayesRecon/R/utils.R | 550 +++++++--- bayesRecon-0.3.0/bayesRecon/README.md | 56 - bayesRecon-0.3.0/bayesRecon/build/vignette.rds |binary bayesRecon-0.3.0/bayesRecon/data/M5_CA1_basefc.rda |only bayesRecon-0.3.0/bayesRecon/inst/doc/bayesRecon.R | 4 bayesRecon-0.3.0/bayesRecon/inst/doc/bayesRecon.Rmd | 4 bayesRecon-0.3.0/bayesRecon/inst/doc/bayesRecon.html | 53 bayesRecon-0.3.0/bayesRecon/inst/doc/mixed_reconciliation.R |only bayesRecon-0.3.0/bayesRecon/inst/doc/mixed_reconciliation.Rmd |only bayesRecon-0.3.0/bayesRecon/inst/doc/mixed_reconciliation.html |only bayesRecon-0.3.0/bayesRecon/inst/doc/reconciliation_properties.R | 14 bayesRecon-0.3.0/bayesRecon/inst/doc/reconciliation_properties.Rmd | 18 bayesRecon-0.3.0/bayesRecon/inst/doc/reconciliation_properties.html | 36 bayesRecon-0.3.0/bayesRecon/man/M3_example.Rd | 2 bayesRecon-0.3.0/bayesRecon/man/M5_CA1_basefc.Rd |only bayesRecon-0.3.0/bayesRecon/man/PMF.get_mean.Rd |only bayesRecon-0.3.0/bayesRecon/man/PMF.get_quantile.Rd |only bayesRecon-0.3.0/bayesRecon/man/PMF.get_var.Rd |only bayesRecon-0.3.0/bayesRecon/man/PMF.sample.Rd |only bayesRecon-0.3.0/bayesRecon/man/PMF.summary.Rd |only bayesRecon-0.3.0/bayesRecon/man/bayesRecon-package.Rd | 55 - bayesRecon-0.3.0/bayesRecon/man/carparts_example.Rd | 15 bayesRecon-0.3.0/bayesRecon/man/extr_mkt_events.Rd | 16 bayesRecon-0.3.0/bayesRecon/man/extr_mkt_events_basefc.Rd | 19 bayesRecon-0.3.0/bayesRecon/man/infantMortality.Rd | 6 bayesRecon-0.3.0/bayesRecon/man/reconc_BUIS.Rd | 27 bayesRecon-0.3.0/bayesRecon/man/reconc_MCMC.Rd | 20 bayesRecon-0.3.0/bayesRecon/man/reconc_MixCond.Rd |only bayesRecon-0.3.0/bayesRecon/man/reconc_TDcond.Rd |only bayesRecon-0.3.0/bayesRecon/man/reconc_gaussian.Rd | 18 bayesRecon-0.3.0/bayesRecon/man/schaferStrimmer_cov.Rd | 5 bayesRecon-0.3.0/bayesRecon/tests/testthat/dataForTests/Weekly-Gaussian_S.csv | 196 +-- bayesRecon-0.3.0/bayesRecon/tests/testthat/dataForTests/Weekly-Gaussian_basef.csv | 196 +-- bayesRecon-0.3.0/bayesRecon/tests/testthat/dataForTests/generate_weeklyTestData.R |only bayesRecon-0.3.0/bayesRecon/tests/testthat/test-PMF.R |only bayesRecon-0.3.0/bayesRecon/tests/testthat/test-hierarchy.R | 42 bayesRecon-0.3.0/bayesRecon/tests/testthat/test-reconc_BUIS_gaussian.R |only bayesRecon-0.3.0/bayesRecon/tests/testthat/test-reconc_MCMC.R | 2 bayesRecon-0.3.0/bayesRecon/tests/testthat/test-reconc_MixCond.R |only bayesRecon-0.3.0/bayesRecon/tests/testthat/test-reconc_TDcond.R |only bayesRecon-0.3.0/bayesRecon/tests/testthat/test-sample_funs.R |only bayesRecon-0.3.0/bayesRecon/tests/testthat/test-schaferStrimmer.R | 3 bayesRecon-0.3.0/bayesRecon/tests/testthat/test-weightswarn.R | 18 bayesRecon-0.3.0/bayesRecon/vignettes/bayesRecon.Rmd | 4 bayesRecon-0.3.0/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_2e65ff6a059f3ffe08f8f520ad9729bb.RData |only bayesRecon-0.3.0/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_2e65ff6a059f3ffe08f8f520ad9729bb.rdb |only bayesRecon-0.3.0/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_2e65ff6a059f3ffe08f8f520ad9729bb.rdx |only bayesRecon-0.3.0/bayesRecon/vignettes/img/M5store_hier.png |only bayesRecon-0.3.0/bayesRecon/vignettes/mixed_reconciliation.Rmd |only bayesRecon-0.3.0/bayesRecon/vignettes/reconciliation_properties.Rmd | 18 bayesRecon-0.3.0/bayesRecon/vignettes/references.bib | 63 - 77 files changed, 1236 insertions(+), 569 deletions(-)
Title: 'nonmem2rx' Converts 'NONMEM' Models to 'rxode2'
Description: 'NONMEM' has been a tool for running nonlinear mixed
effects models since the 80s and is still used today (Bauer 2019
<doi:10.1002/psp4.12404>). This tool allows you to convert
'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016)
<doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax
(Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2'
syntax requires the residual specification to be included and it
is not always translated. If available, the 'rxode2' model will
read in the 'NONMEM' data and compare the simulation for the
population model ('PRED') individual model ('IPRED') and residual
model ('IWRES') to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rx [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Philip Delff [ctb],
Gabriel Staples [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nonmem2rx versions 0.1.3 dated 2023-12-12 and 0.1.4 dated 2024-05-29
nonmem2rx-0.1.3/nonmem2rx/inst/doc/rxode2-validate.R |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/rxode2-validate.Rmd |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/rxode2-validate.html |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-extra-items.R |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-extra-items.Rmd |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-extra-items.html |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-new-dosing-with-covs.R |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-new-dosing-with-covs.Rmd |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-new-dosing-with-covs.html |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-new-dosing.R |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-new-dosing.Rmd |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-new-dosing.html |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-uncertainty.R |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-uncertainty.Rmd |only nonmem2rx-0.1.3/nonmem2rx/inst/doc/simulate-uncertainty.html |only nonmem2rx-0.1.3/nonmem2rx/vignettes/rxode2-validate.Rmd |only nonmem2rx-0.1.3/nonmem2rx/vignettes/simulate-extra-items.Rmd |only nonmem2rx-0.1.3/nonmem2rx/vignettes/simulate-new-dosing-with-covs.Rmd |only nonmem2rx-0.1.3/nonmem2rx/vignettes/simulate-new-dosing.Rmd |only nonmem2rx-0.1.3/nonmem2rx/vignettes/simulate-uncertainty.Rmd |only nonmem2rx-0.1.4/nonmem2rx/DESCRIPTION | 8 nonmem2rx-0.1.4/nonmem2rx/MD5 | 73 nonmem2rx-0.1.4/nonmem2rx/NEWS.md | 29 nonmem2rx-0.1.4/nonmem2rx/R/RcppExports.R | 4 nonmem2rx-0.1.4/nonmem2rx/R/fromNonmemToRxId.R |only nonmem2rx-0.1.4/nonmem2rx/R/linCmt.R | 21 nonmem2rx-0.1.4/nonmem2rx/R/lst.R | 12 nonmem2rx-0.1.4/nonmem2rx/R/nminfo.R | 8 nonmem2rx-0.1.4/nonmem2rx/R/nmtab.R | 18 nonmem2rx-0.1.4/nonmem2rx/R/nonmem2rx.R | 8 nonmem2rx-0.1.4/nonmem2rx/R/readCov.R | 24 nonmem2rx-0.1.4/nonmem2rx/R/readInNonmemInput.R | 24 nonmem2rx-0.1.4/nonmem2rx/R/records.R | 23 nonmem2rx-0.1.4/nonmem2rx/R/validate.R | 57 nonmem2rx-0.1.4/nonmem2rx/R/xml.R | 79 nonmem2rx-0.1.4/nonmem2rx/build/vignette.rds |binary nonmem2rx-0.1.4/nonmem2rx/inst/abbrev.g | 8 nonmem2rx-0.1.4/nonmem2rx/inst/data.g | 2 nonmem2rx-0.1.4/nonmem2rx/inst/doc/import-nonmem.html | 928 nonmem2rx-0.1.4/nonmem2rx/src/RcppExports.cpp | 9 nonmem2rx-0.1.4/nonmem2rx/src/abbrev.g.d_parser.h |10652 +++++----- nonmem2rx-0.1.4/nonmem2rx/src/data.g.d_parser.h | 539 nonmem2rx-0.1.4/nonmem2rx/src/init.c | 5 nonmem2rx-0.1.4/nonmem2rx/src/nonmemId.cpp | 28 nonmem2rx-0.1.4/nonmem2rx/tests/testthat/_snaps/vdiff/first-plot.svg | 2 nonmem2rx-0.1.4/nonmem2rx/tests/testthat/test-abbrev.R | 36 nonmem2rx-0.1.4/nonmem2rx/tests/testthat/test-data.R | 3 nonmem2rx-0.1.4/nonmem2rx/tests/testthat/test-nonmem-id.R | 15 48 files changed, 6445 insertions(+), 6170 deletions(-)
Title: Fast Backward Elimination Based on Information Criterion
Description: Performs backward elimination with similar syntax to
the stepAIC() function from the 'MASS' package. A bounding algorithm is
used to avoid fitting unnecessary models, making it much faster.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jacob-seedorff@uiowa.edu>
Diff between fastbackward versions 1.0.0 dated 2024-05-22 and 1.0.1 dated 2024-05-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 5 +++++ R/fastbackward.R | 7 ++++++- 4 files changed, 19 insertions(+), 9 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb],
Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 2.3.2 dated 2024-03-28 and 2.3.3 dated 2024-05-29
DESCRIPTION | 6 MD5 | 62 ++++---- NEWS.md | 11 + R/datasets.R | 67 ++++++++- README.md | 292 ++++++++++++++++++++++------------------- data/advantage_details.rda |binary data/advantage_movement.rda |binary data/boot_mapping.rda |binary data/castaway_details.rda |binary data/castaways.rda |binary data/challenge_description.rda |binary data/challenge_results.rda |binary data/challenge_summary.rda |only data/confessionals.rda |binary data/episode_summary.rda |only data/episodes.rda |binary data/jury_votes.rda |binary data/season_summary.rda |binary data/tribe_colours.rda |binary data/tribe_mapping.rda |binary data/viewers.rda |binary data/vote_history.rda |binary man/auction_details.Rd | 3 man/boot_mapping.Rd | 2 man/castaways.Rd | 2 man/challenge_description.Rd | 2 man/challenge_results.Rd | 4 man/challenge_summary.Rd |only man/episode_summary.Rd |only man/episodes.Rd | 1 man/season_summary.Rd | 4 man/survivor_auction.Rd | 3 man/tribe_mapping.Rd | 2 tests/testthat/tests.R | 60 ++++++++ 34 files changed, 342 insertions(+), 179 deletions(-)
Title: Creating Standalone and Composite Plots in 'ggplot2' for
Publications
Description: Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun (Sam) Min <seung.min@mail.mcgill.ca>
Diff between smplot2 versions 0.2.2 dated 2024-05-22 and 0.2.3 dated 2024-05-29
smplot2-0.2.2/smplot2/R/attach.R |only smplot2-0.2.2/smplot2/R/sm_add_arrow.R |only smplot2-0.2.2/smplot2/R/sm_add_line.R |only smplot2-0.2.2/smplot2/R/sm_add_polygon.R |only smplot2-0.2.2/smplot2/R/sm_add_rect.R |only smplot2-0.2.2/smplot2/man/sm_add_arrow.Rd |only smplot2-0.2.2/smplot2/man/sm_add_line.Rd |only smplot2-0.2.2/smplot2/man/sm_add_polygon.Rd |only smplot2-0.2.2/smplot2/man/sm_add_rect.Rd |only smplot2-0.2.3/smplot2/DESCRIPTION | 14 - smplot2-0.2.3/smplot2/MD5 | 70 +++----- smplot2-0.2.3/smplot2/NAMESPACE | 162 ++++++++++--------- smplot2-0.2.3/smplot2/NEWS.md | 23 ++ smplot2-0.2.3/smplot2/R/aaa.R |only smplot2-0.2.3/smplot2/R/sm_add_legend.R | 4 smplot2-0.2.3/smplot2/R/sm_bar2.R | 42 ++++ smplot2-0.2.3/smplot2/R/sm_boxplot2.R | 28 ++- smplot2-0.2.3/smplot2/R/sm_common_axis.R | 15 + smplot2-0.2.3/smplot2/R/sm_forest2.R | 38 +++- smplot2-0.2.3/smplot2/R/sm_hist.R | 33 +++ smplot2-0.2.3/smplot2/R/sm_plot_clean.R | 6 smplot2-0.2.3/smplot2/R/sm_pointplot.R | 26 ++- smplot2-0.2.3/smplot2/R/sm_put_together.R | 228 ++++++++++++++++++++++++--- smplot2-0.2.3/smplot2/R/sm_raincloud.R | 40 +++- smplot2-0.2.3/smplot2/R/sm_slope.R | 69 ++++++-- smplot2-0.2.3/smplot2/R/sm_slope_mean.R |only smplot2-0.2.3/smplot2/R/sm_statCorr.R | 54 +++++- smplot2-0.2.3/smplot2/R/sm_stdErr.R | 2 smplot2-0.2.3/smplot2/R/sm_violin.R | 33 +++ smplot2-0.2.3/smplot2/R/zzz.R |only smplot2-0.2.3/smplot2/README.md | 5 smplot2-0.2.3/smplot2/inst |only smplot2-0.2.3/smplot2/man/sm_bar.Rd | 11 - smplot2-0.2.3/smplot2/man/sm_boxplot.Rd | 9 - smplot2-0.2.3/smplot2/man/sm_forest.Rd | 9 - smplot2-0.2.3/smplot2/man/sm_hist.Rd | 7 smplot2-0.2.3/smplot2/man/sm_pointplot.Rd | 4 smplot2-0.2.3/smplot2/man/sm_put_together.Rd | 58 ++++-- smplot2-0.2.3/smplot2/man/sm_raincloud.Rd | 7 smplot2-0.2.3/smplot2/man/sm_slope.Rd | 26 +-- smplot2-0.2.3/smplot2/man/sm_slope_mean.Rd |only smplot2-0.2.3/smplot2/man/sm_statCorr.Rd | 18 +- smplot2-0.2.3/smplot2/man/sm_violin.Rd | 11 - 43 files changed, 792 insertions(+), 260 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 2.0.8 dated 2024-01-31 and 2.0.9 dated 2024-05-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/vpcPlot.R | 2 +- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial economics,
addressing a variety of topics covered in Scheuch, Voigt, and Weiss (2023) <doi:10.1201/b23237>.
The package is designed to provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information and resources
related to the book, visit <https://www.tidy-finance.org/r/index.html>.
Author: Christoph Scheuch [aut, cre] ,
Stefan Voigt [aut] ,
Patrick Weiss [aut]
Maintainer: Christoph Scheuch <christoph.scheuch@gmail.com>
Diff between tidyfinance versions 0.1.0 dated 2024-03-05 and 0.2.0 dated 2024-05-29
DESCRIPTION | 14 MD5 | 63 - NAMESPACE | 1 NEWS.md | 18 R/check_supported_type.R |only R/disconnect_connection.R |only R/download_data.R | 1317 --------------------------- R/download_data_factors.R |only R/download_data_macro_predictors.R |only R/download_data_wrds.R |only R/download_data_wrds_ccm_links.R |only R/download_data_wrds_clean_trace.R |only R/download_data_wrds_compustat.R |only R/download_data_wrds_crsp.R |only R/download_data_wrds_fisd.R |only R/get_wrds_connection.R | 24 R/global_variables.R |only R/list_supported_types.R |only R/set_wrds_credentials.R |only build/vignette.rds |only inst/doc |only man/check_supported_type.Rd | 2 man/disconnection_connection.Rd | 2 man/download_data_factors.Rd | 2 man/download_data_factors_ff.Rd | 3 man/download_data_factors_q.Rd | 2 man/download_data_macro_predictors.Rd | 2 man/download_data_wrds.Rd | 8 man/download_data_wrds_ccm_links.Rd | 2 man/download_data_wrds_clean_trace.Rd | 2 man/download_data_wrds_compustat.Rd | 2 man/download_data_wrds_crsp.Rd | 4 man/download_data_wrds_fisd.Rd | 2 man/list_supported_types.Rd | 2 man/list_supported_types_ff.Rd | 2 man/list_supported_types_macro_predictors.Rd | 2 man/list_supported_types_q.Rd | 2 man/list_supported_types_wrds.Rd | 2 man/set_wrds_credentials.Rd |only vignettes |only 40 files changed, 94 insertions(+), 1386 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The [...truncated...]
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.32.8 dated 2024-05-21 and 2.32.9 dated 2024-05-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/stanmath.html | 6 +++--- inst/include/stan/math/memory/stack_alloc.hpp | 4 +++- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Quantitative Trading Framework
Description: Collection of functions to retrieve financial data from various sources, including brokerage and exchange platforms, financial websites, and data providers. Includes functions to retrieve account information, portfolio information, and place/cancel orders from different brokers. Additionally, allows users to download historical data such as earnings, dividends, stock splits.
Author: Vyacheslav Arbuzov[cph, cre, aut], Sergey Edunov[aut]
Maintainer: Vyacheslav Arbuzov <arbuzov1989@gmail.com>
Diff between rusquant versions 1.0.5 dated 2024-01-29 and 1.1.1 dated 2024-05-29
DESCRIPTION | 10 ++-- MD5 | 82 +++++++++++++++++++----------------- NAMESPACE | 2 NEWS | 5 -- NEWS.md | 10 +++- R/auth.R |only R/cancelOrder.R | 12 ----- R/getAccounts.R | 66 +++++++++++------------------ R/getDividends.R | 27 ++++------- R/getEarnings.R | 27 +++-------- R/getEconomic.R | 26 +++-------- R/getIPO.R | 24 +++------- R/getOrderbook.R | 52 +++++++++++++++++----- R/getOrders.R | 13 ----- R/getPortfolio.R | 14 ------ R/getSplits.R | 14 ------ R/getSymbolList.r | 67 +++++++++++++++++++++++------ R/getSymbols.Algopack.R | 95 ++++++++++++++++++++++++------------------ R/getSymbols.Alor.R | 12 ----- R/getSymbols.Comon.R |only R/getSymbols.Finam.R | 14 ------ R/getSymbols.Gigapack.R | 23 ++-------- R/getSymbols.MarketWatch.R | 58 ++++++++++++++----------- R/getSymbols.Mfd.R | 14 ------ R/getSymbols.Moex.R | 22 +-------- R/getSymbols.Poloniex.R | 16 +------ R/getSymbols.Rusquant.R | 15 ------ R/getSymbols.Tinkoff.R | 15 ------ R/getTradelog.R | 64 ++++++++++++++++++++++------ R/getTrades.R | 14 ------ R/placeOrder.R | 13 ----- man/auth.Rd |only man/getDividends.Rd | 4 - man/getEarnings.Rd | 4 - man/getEconomic.Rd | 4 - man/getIPO.Rd | 2 man/getOrderbook.Rd | 6 ++ man/getSymbolList.Rd | 4 + man/getSymbols.Algopack.Rd | 32 ++++++++++---- man/getSymbols.Comon.Rd |only man/getSymbols.Gigapack.Rd | 2 man/getSymbols.MarketWatch.Rd | 9 +-- man/getSymbols.Poloniex.Rd | 1 man/getTradelog.Rd | 8 +++ 44 files changed, 427 insertions(+), 475 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 2.0.9 dated 2024-01-31 and 2.0.10 dated 2024-05-29
DESCRIPTION | 6 +- MD5 | 8 +- NEWS.md | 4 + R/computingutil.R | 143 +++++++++++++++++++++++++++------------------------- man/bootstrapFit.Rd | 19 ++++-- 5 files changed, 98 insertions(+), 82 deletions(-)
Title: Download Map Data from GISCO API - Eurostat
Description: Tools to download data from the GISCO (Geographic Information
System of the Commission) Eurostat database
<https://ec.europa.eu/eurostat/web/gisco>. Global and European map
data available. This package is in no way officially related to or
endorsed by Eurostat.
Author: Diego Hernangomez [aut, cre, cph]
,
EuroGeographics [cph] ,
Vincent Arel-Bundock [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 0.4.2 dated 2024-03-27 and 0.5.0 dated 2024-05-29
DESCRIPTION | 10 - MD5 | 77 ++++---- NAMESPACE | 12 + NEWS.md | 50 +++-- R/giscoR-package.R | 2 R/gisco_addressapi.R |only R/gisco_get_airports.R | 8 R/gisco_get_countries.R | 2 R/gisco_get_education.R |only R/gisco_get_grid.R | 4 R/gisco_get_healthcare.R | 16 - R/gisco_get_lau.R | 2 R/gisco_get_nuts.R | 4 R/gisco_get_postalcodes.R | 18 +- R/gisco_get_urban_audit.R | 2 README.md | 6 build/vignette.rds |binary data/gisco_coastallines.rda |binary data/gisco_countries.rda |binary data/gisco_countrycode.rda |binary data/gisco_db.rda |binary data/gisco_nuts.rda |binary inst/WORDLIST | 11 + inst/doc/giscoR.Rmd | 16 + inst/doc/giscoR.html | 244 ++++++++++++++-------------- inst/schemaorg.json | 4 man/chunks |only man/gisco_addressapi.Rd |only man/gisco_get.Rd | 2 man/gisco_get_airports.Rd | 5 man/gisco_get_education.Rd |only man/gisco_get_grid.Rd | 4 man/gisco_get_healthcare.Rd | 15 + man/gisco_get_lau.Rd | 6 man/gisco_get_nuts.Rd | 4 man/gisco_get_postalcodes.Rd | 7 man/gisco_get_urban_audit.Rd | 6 tests/testthat/test-gisco_addressapi.R |only tests/testthat/test-gisco_attributions.R | 52 ++--- tests/testthat/test-gisco_get_education.R |only tests/testthat/test-gisco_get_urban_audit.R | 5 vignettes/giscoR-1.png |binary vignettes/giscoR.Rmd | 16 + 43 files changed, 340 insertions(+), 270 deletions(-)
Title: Generalized Power Analysis for LATE
Description: An implementation of the generalized power analysis for the local average treatment effect (LATE), proposed by Bansak (2020) <doi:10.1214/19-STS732>. Power analysis is in the context of estimating the LATE (also known as the complier average causal effect, or CACE), with calculations based on a test of the null hypothesis that the LATE equals 0 with a two-sided alternative. The method uses standardized effect sizes to place a conservative bound on the power under minimal assumptions. Package allows users to recover power, sample size requirements, or minimum detectable effect sizes. Package also allows users to work with absolute effects rather than effect sizes, to specify an additional assumption to narrow the bounds, and to incorporate covariate adjustment.
Author: Kirk Bansak [aut],
Eddie Yang [aut, cre]
Maintainer: Eddie Yang <z5yang@ucsd.edu>
Diff between powerLATE versions 0.1.1 dated 2020-09-27 and 0.1.2 dated 2024-05-29
DESCRIPTION | 13 +++++------ MD5 | 48 +++++++++++++++++++++---------------------- R/equal_ordered.R | 2 - R/equal_ordered_cov.R | 6 ++--- R/equal_unordered.R | 2 - R/equal_unordered_cov.R | 6 ++--- R/onAttach.R | 2 - R/powerLATE.R | 3 -- R/powerLATE_cov.R | 3 -- R/print_powerLATE.R | 15 ++++++------- R/unequal_ordered.R | 2 - R/unequal_ordered_cov.R | 6 ++--- R/unequal_unordered.R | 2 - R/unequal_unordered_cov.R | 6 ++--- README.md | 40 +++++++++++++++++++++-------------- man/dot-onAttach.Rd | 2 - man/equal.ordered.Rd | 2 - man/equal.ordered.cov.Rd | 2 - man/equal.unordered.Rd | 2 - man/equal.unordered.cov.Rd | 2 - man/print.powerLATE.Rd | 10 ++------ man/unequal.ordered.Rd | 2 - man/unequal.ordered.cov.Rd | 2 - man/unequal.unordered.Rd | 2 - man/unequal.unordered.cov.Rd | 2 - 25 files changed, 92 insertions(+), 92 deletions(-)
Title: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Description: A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.
Author: Daniel Greene, Sylvia Richardson and Ernest Turro
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between BeviMed versions 5.8 dated 2021-01-31 and 5.10 dated 2024-05-29
DESCRIPTION | 11 MD5 | 100 ++-- NAMESPACE | 79 +-- R/RcppExports.R | 14 R/convenience.R | 37 - R/functions.R | 23 R/generics.R | 6 build/vignette.rds |binary inst/CITATION | 36 - inst/doc/Guide.R | 142 +++--- inst/doc/Guide.Rnw | 4 inst/doc/Guide.pdf |binary inst/doc/Intro.R | 38 - inst/doc/Intro.html | 671 +++++++++++++++++++---------- inst/doc/vcf.R | 20 inst/doc/vcf.html | 547 +++++++++++++++++------ man/CI_gamma1_evidence.Rd | 56 +- man/bevimed.Rd | 92 +-- man/bevimed_m.Rd | 215 ++++----- man/bevimed_polytomous.Rd | 92 +-- man/call_cpp.Rd | 221 ++++----- man/conditional_prob_pathogenic.Rd | 40 - man/expected_explained.Rd | 40 - man/explaining_variants.Rd | 40 - man/extract_conditional_prob_pathogenic.Rd | 40 - man/extract_expected_explained.Rd | 40 - man/extract_explaining_variants.Rd | 40 - man/extract_gamma1_evidence.Rd | 40 - man/extract_prob_association.Rd | 44 - man/extract_prob_pathogenic.Rd | 44 - man/gamma0_evidence.Rd | 44 - man/gamma1_evidence.Rd | 40 - man/log_BF.Rd | 48 +- man/print.BeviMed.Rd | 44 - man/print.BeviMed_m.Rd | 44 - man/print.BeviMed_summary.Rd | 42 - man/prob_association.Rd | 44 - man/prob_association_m.Rd | 52 +- man/prob_pathogenic.Rd | 44 - man/stack_BeviMeds.Rd | 34 - man/stop_chain.Rd | 116 ++--- man/subset_variants.Rd | 36 - man/sum_ML_over_PP.Rd | 38 - man/summary.BeviMed.Rd | 62 +- man/summary.BeviMed_m.Rd | 94 ++-- man/tune_proposal_sds.Rd | 86 +-- man/tune_temperatures.Rd | 42 - src/RcppExports.cpp | 15 src/sampling.cpp | 32 + src/sampling.h | 2 vignettes/Guide.Rnw | 4 51 files changed, 2153 insertions(+), 1582 deletions(-)
Title: Single Cell Oriented Reconstruction of PANDA Individual
Optimized Networks
Description: Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
Author: Daniel Osorio [aut, cre] ,
Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between SCORPION versions 1.0.1 dated 2022-09-22 and 1.0.2 dated 2024-05-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/makeSuperCells.R | 3 ++- R/scorpion.R | 10 +++++++--- man/scorpion.Rd | 7 +++++-- 5 files changed, 22 insertions(+), 14 deletions(-)
More information about CurricularAnalytics at CRAN
Permanent link
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] ,
Abhraneel Sarma [ctb],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Amar Al-Zubaidi [ctb],
Andre Simon [ctb] ,
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] ,
Ben Baumer [ctb], [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.46 dated 2024-04-06 and 1.47 dated 2024-05-29
knitr-1.46/knitr/inst/doc/datatables.R |only knitr-1.46/knitr/inst/doc/docco-classic.R |only knitr-1.46/knitr/inst/doc/docco-linear.R |only knitr-1.46/knitr/inst/doc/knit_expand.R |only knitr-1.46/knitr/inst/doc/knit_print.R |only knitr-1.46/knitr/inst/doc/knitr-html.R |only knitr-1.46/knitr/inst/doc/knitr-intro.R |only knitr-1.46/knitr/inst/doc/knitr-markdown.R |only knitr-1.47/knitr/DESCRIPTION | 10 knitr-1.47/knitr/MD5 | 262 ++++++++++----------- knitr-1.47/knitr/R/block.R | 4 knitr-1.47/knitr/R/cache.R | 8 knitr-1.47/knitr/R/citation.R | 18 - knitr-1.47/knitr/R/header.R | 2 knitr-1.47/knitr/R/highlight.R | 2 knitr-1.47/knitr/R/output.R | 2 knitr-1.47/knitr/R/parser.R | 14 - knitr-1.47/knitr/R/table.R | 5 knitr-1.47/knitr/R/themes.R | 6 knitr-1.47/knitr/R/utils.R | 5 knitr-1.47/knitr/build/vignette.rds |binary knitr-1.47/knitr/inst/doc/datatables.Rmd | 4 knitr-1.47/knitr/inst/doc/datatables.html | 6 knitr-1.47/knitr/inst/doc/docco-classic.Rmd | 2 knitr-1.47/knitr/inst/doc/docco-classic.html | 10 knitr-1.47/knitr/inst/doc/docco-linear.Rmd | 2 knitr-1.47/knitr/inst/doc/docco-linear.html | 6 knitr-1.47/knitr/inst/doc/knit_expand.Rmd | 2 knitr-1.47/knitr/inst/doc/knit_expand.html | 28 +- knitr-1.47/knitr/inst/doc/knit_print.Rmd | 2 knitr-1.47/knitr/inst/doc/knit_print.html | 31 +- knitr-1.47/knitr/inst/doc/knitr-html.Rhtml | 2 knitr-1.47/knitr/inst/doc/knitr-html.html | 6 knitr-1.47/knitr/inst/doc/knitr-intro.Rmd | 2 knitr-1.47/knitr/inst/doc/knitr-intro.html | 18 - 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-26 1.0.0
2016-09-22 0.9.99
2016-08-15 0.9.9
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Maximum likelihood estimation of smooth transition vector
autoregressive models with various types of transition weight functions,
conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2024) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2024) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.0.0 dated 2024-05-27 and 1.0.1 dated 2024-05-29
sstvars-1.0.0/sstvars/src/Makevars |only sstvars-1.0.0/sstvars/src/Makevars.os |only sstvars-1.0.1/sstvars/DESCRIPTION | 17 +++++++++------- sstvars-1.0.1/sstvars/MD5 | 12 ++++------- sstvars-1.0.1/sstvars/NEWS.md | 6 ++++- sstvars-1.0.1/sstvars/README.md | 7 ++++++ sstvars-1.0.1/sstvars/configure | 21 ++++++++++++++------ sstvars-1.0.1/sstvars/inst/doc/sstvars-vignette.pdf |binary 8 files changed, 42 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-24 0.0.5
2017-12-05 0.0.4
2017-03-05 0.0.3
2016-11-30 0.0.2
2016-11-11 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-25 0.13.0
2023-01-23 0.12.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-02 0.6.1
2023-02-27 0.6.0