Title: Supplementary Distributions
Description: Ten distributions supplementing those built into R.
Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi
squared, Spearman's rho, maximum F ratio, the Pearson product
moment correlation coefficient, Johnson distributions, normal
scores and generalized hypergeometric distributions.
Author: Bob Wheeler [aut],
Thorsten Pohlert [ctb, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between SuppDists versions 1.1-9.8 dated 2024-09-03 and 1.1-9.9 dated 2025-03-23
DESCRIPTION | 8 - MD5 | 10 - inst/NEWS.Rd | 9 + src/dists.cpp | 366 +++++++++++++++++++++++++++++----------------------------- src/dists.h | 48 +++---- src/wheeler.h | 6 6 files changed, 228 insertions(+), 219 deletions(-)
Title: Robust Effect Size Index (RESI) Estimation
Description: Summarize model output using a robust effect size index. The index is introduced in Vandekar, Tao, & Blume (2020, <doi:10.1007/s11336-020-09698-2>). Software paper available at <doi:10.18637/jss.v112.i03>.
Author: Megan Jones [aut, cre],
Kaidi Kang [aut],
Simon Vandekar [aut]
Maintainer: Megan Jones <megan.n.taylor@vanderbilt.edu>
Diff between RESI versions 1.2.4 dated 2024-01-16 and 1.3.0 dated 2025-03-23
DESCRIPTION | 14 ++++++------- MD5 | 46 ++++++++++++++++++++++++--------------------- NAMESPACE | 2 + NEWS.md | 6 +++++ R/S2chisq.R |only R/S2z.R |only R/chisq2S.R | 2 - R/f2S.R | 2 - R/internal_functions.R | 2 - R/resi.R | 12 ++++++----- R/resi_pe.R | 6 ++--- R/t2S.R | 2 - R/z2S.R | 2 - README.md | 1 build/vignette.rds |binary inst/CITATION | 23 +++++++++++++++------- inst/doc/RESI.R | 2 - inst/doc/RESI.html | 2 - man/S2chisq.Rd |only man/S2z.Rd |only man/chisq2S.Rd | 2 - man/f2S.Rd | 2 - man/resi.Rd | 12 ++++++----- man/t2S.Rd | 2 - man/z2S.Rd | 2 - tests/testthat/test-resi.R | 5 ++++ 26 files changed, 90 insertions(+), 59 deletions(-)
Title: Fitting Hidden Markov Models to Financial Data
Description: Fitting (hierarchical) hidden Markov models to financial data
via maximum likelihood estimation. See Oelschläger, L. and Adam, T.
"Detecting Bearish and Bullish Markets in Financial Time Series Using
Hierarchical Hidden Markov Models" (2021, Statistical Modelling)
<doi:10.1177/1471082X211034048> for a reference on the method. A user guide
is provided by the accompanying software paper "fHMM: Hidden Markov Models
for Financial Time Series in R", Oelschläger, L., Adam, T., and Michels, R.
(2024, Journal of Statistical Software) <doi:10.18637/jss.v109.i09>.
Author: Lennart Oelschlaeger [aut, cre]
,
Timo Adam [aut] ,
Rouven Michels [aut]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between fHMM versions 1.4.1 dated 2024-09-16 and 1.4.2 dated 2025-03-23
DESCRIPTION | 10 MD5 | 258 NAMESPACE | 236 NEWS.md | 278 R/RcppExports.R | 22 R/compare_models.R | 152 R/compute_T_star.R | 174 R/compute_ci.R | 122 R/compute_residuals.R | 238 R/data_and_models.R | 612 R/decode_states.R | 350 R/download_data.R | 305 R/fHMM_colors.R | 152 R/fHMM_controls.R | 1846 +- R/fHMM_data.R | 432 R/fHMM_events.R | 116 R/fHMM_likelihood.R | 478 R/fHMM_model.R | 898 - R/fHMM_parameters.R | 2192 +- R/fHMM_sdds.R | 320 R/fit_model.R | 500 R/get_initial_values.R | 652 R/helpers.R | 124 R/parameter_labels.R | 132 R/plot.R | 1536 +- R/read_data.R | 462 R/reorder_states.R | 264 R/simulate_hmm.R | 416 README.md | 627 build/partial.rdb |binary build/vignette.rds |binary inst/doc/fHMM.R | 14 inst/doc/fHMM.Rmd | 108 inst/doc/fHMM.html | 934 - inst/doc/v01_model_definition.R | 14 inst/doc/v01_model_definition.Rmd | 104 inst/doc/v01_model_definition.html | 866 - inst/doc/v02_controls.R | 86 inst/doc/v02_controls.Rmd | 176 inst/doc/v02_controls.html | 1002 - inst/doc/v03_data_management.R | 88 inst/doc/v03_data_management.Rmd | 184 inst/doc/v03_data_management.html | 922 - inst/doc/v04_model_estimation.R | 82 inst/doc/v04_model_estimation.Rmd | 252 inst/doc/v04_model_estimation.html | 1136 - inst/doc/v05_state_decoding_and_prediction.R | 52 inst/doc/v05_state_decoding_and_prediction.Rmd | 148 inst/doc/v05_state_decoding_and_prediction.html | 948 - inst/doc/v06_model_checking.R | 46 inst/doc/v06_model_checking.Rmd | 132 inst/doc/v06_model_checking.html | 920 - inst/doc/v07_model_selection.R | 32 inst/doc/v07_model_selection.Rmd | 108 inst/doc/v07_model_selection.html | 914 - inst/extdata/dax.csv |18024 ++++++++++++------------ man/compare_models.Rd | 60 man/compute_T_star.Rd | 58 man/compute_ci.Rd | 54 man/compute_residuals.Rd | 48 man/dax.Rd | 70 man/dax_model_2n.Rd | 82 man/dax_model_3t.Rd | 92 man/dax_vw_model.Rd | 94 man/decode_states.Rd | 138 man/download_data.Rd | 134 man/fHMM-package.Rd | 62 man/fHMM_colors.Rd | 80 man/fHMM_data.Rd | 140 man/fHMM_events.Rd | 82 man/fHMM_model.Rd | 178 man/fHMM_parameters.Rd | 324 man/fHMM_sdds.Rd | 126 man/fit_model.Rd | 338 man/get_initial_values.Rd | 98 man/ll_hmm.Rd | 256 man/nLL_hhmm.Rd | 44 man/nLL_hmm.Rd | 44 man/parameter_labels.Rd | 40 man/parameter_transformations.Rd | 458 man/plot.fHMM_data.Rd | 70 man/plot.fHMM_model.Rd | 118 man/plot_ll.Rd | 46 man/plot_pr.Rd | 40 man/plot_sdds.Rd | 52 man/plot_ts.Rd | 86 man/prepare_data.Rd | 60 man/read_data.Rd | 58 man/reorder_states.Rd | 96 man/set_controls.Rd | 652 man/sim_model_2gamma.Rd | 78 man/simulate_hmm.Rd | 270 man/simulate_observations.Rd | 82 man/spx.Rd | 72 man/unemp.Rd | 54 man/unemp_spx_model_3_2.Rd | 86 man/vw.Rd | 70 tests/testthat.R | 8 tests/testthat/test-compare_models.R | 40 tests/testthat/test-compute_T_star.R | 84 tests/testthat/test-compute_ci.R | 26 tests/testthat/test-compute_residuals.R | 46 tests/testthat/test-data_and_models.R | 88 tests/testthat/test-decode_states.R | 60 tests/testthat/test-download_data.R | 170 tests/testthat/test-fHMM_colors.R | 70 tests/testthat/test-fHMM_controls.R | 1260 - tests/testthat/test-fHMM_data.R | 120 tests/testthat/test-fHMM_events.R | 56 tests/testthat/test-fHMM_likelihood.R | 66 tests/testthat/test-fHMM_model.R | 96 tests/testthat/test-fHMM_parameters.R | 426 tests/testthat/test-fHMM_sdds.R | 214 tests/testthat/test-fit_model.R | 178 tests/testthat/test-get_initial_values.R | 118 tests/testthat/test-helpers.R | 88 tests/testthat/test-parameter_labels.R | 68 tests/testthat/test-plot.R | 232 tests/testthat/test-read_data.R | 42 tests/testthat/test-reorder_states.R | 12 tests/testthat/test-simulate_hmm.R | 100 vignettes/fHMM.Rmd | 108 vignettes/ref.bib | 662 vignettes/v01_model_definition.Rmd | 104 vignettes/v02_controls.Rmd | 176 vignettes/v03_data_management.Rmd | 184 vignettes/v04_model_estimation.Rmd | 252 vignettes/v05_state_decoding_and_prediction.Rmd | 148 vignettes/v06_model_checking.Rmd | 132 vignettes/v07_model_selection.Rmd | 108 130 files changed, 25920 insertions(+), 25908 deletions(-)
Title: Non-Parametric Dissolution Profile Analysis
Description: Similarity of dissolution profiles is assessed using the
similarity factor f2 according to the EMA guideline (European
Medicines Agency 2010) "On the investigation of bioequivalence".
Dissolution profiles are regarded as similar if the f2 value is
between 50 and 100. For the applicability of the similarity factor f2,
the variability between profiles needs to be within certain limits.
Often, this constraint is violated. One possibility in this situation
is to resample the measured profiles in order to obtain a bootstrap
estimate of f2 (Shah et al. (1998) <doi:10.1023/A:1011976615750>).
Other alternatives are the model-independent non-parametric
multivariate confidence region (MCR) procedure (Tsong et al. (1996)
<doi:10.1177/009286159603000427>) or the T2-test for equivalence
procedure (Hoffelder (2016)
<https://www.ecv.de/suse_item.php?suseId=Z|pi|8430>). Functions for
estimation of f1, f2, bootstrap f2, MCR / T2-test for equivalence
procedure are implemented.
Author: Pius Dahinden [aut, cre],
Tillotts Pharma AG [cph, fnd]
Maintainer: Pius Dahinden <pius.dahinden@tillotts.com>
Diff between disprofas versions 0.2.0 dated 2024-06-10 and 0.2.1 dated 2025-03-23
disprofas-0.2.0/disprofas/README.md |only disprofas-0.2.0/disprofas/man/examples/examples_get_hotellings.R |only disprofas-0.2.0/disprofas/man/get_hotellings.Rd |only disprofas-0.2.0/disprofas/tests/testthat/test-get_hotellings.R |only disprofas-0.2.1/disprofas/DESCRIPTION | 10 - disprofas-0.2.1/disprofas/MD5 | 32 ++--- disprofas-0.2.1/disprofas/NAMESPACE | 2 disprofas-0.2.1/disprofas/NEWS.md | 10 + disprofas-0.2.1/disprofas/R/generic.R | 8 - disprofas-0.2.1/disprofas/R/statistics.R | 25 ---- disprofas-0.2.1/disprofas/build/partial.rdb |binary disprofas-0.2.1/disprofas/man/figures/README-example-1-1.png |binary disprofas-0.2.1/disprofas/man/figures/README-example-4-1.png |binary disprofas-0.2.1/disprofas/man/figures/README-example-5a-step-4-1.png |binary disprofas-0.2.1/disprofas/man/figures/README-example-5b-step-4-1.png |binary disprofas-0.2.1/disprofas/tests/testthat/test-generic_bootstrap_f2.R | 5 disprofas-0.2.1/disprofas/tests/testthat/test-generic_mimcr.R | 54 ++++------ disprofas-0.2.1/disprofas/tests/testthat/test-generic_mztia.R | 17 ++- disprofas-0.2.1/disprofas/tests/testthat/test-get_T2_two.R | 2 19 files changed, 73 insertions(+), 92 deletions(-)
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Description: Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
Author: Zheng Ren [aut, cre, cph] ,
Andrew Chen [aut, cph] ,
Elizabeth Horwath [ctb]
Maintainer: Zheng Ren <zren1422@gmail.com>
Diff between ComBatFamQC versions 1.0.5 dated 2025-03-17 and 1.0.6 dated 2025-03-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/Help_Func.R | 2 +- R/comfam_shiny.R | 4 ++-- inst/figure/ComBatFamQC.png |binary tests/testthat/test-age_shiny.R | 1 + tests/testthat/test-comfam_shiny.R | 1 + 8 files changed, 20 insertions(+), 14 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as four vignettes. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 2.4.3 dated 2024-03-19 and 2.5.3 dated 2025-03-23
DESCRIPTION | 8 +- MD5 | 100 +++++++++++++++-------------- NAMESPACE | 2 R/df2latex.R | 56 ++++++++++------ R/hare.r |only R/rd2html.R | 12 ++- R/vJoin.R | 75 +++++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 10 -- inst/NEWS.Rd | 43 +++++++++++- inst/doc/factor.R |only inst/doc/factor.Rnw |only inst/doc/factor.pdf |only inst/doc/intro.R | 92 +++++++++++++++------------ inst/doc/intro.Rnw | 80 ++++++++++++++--------- inst/doc/intro.pdf |binary inst/doc/mediation.R | 14 ++-- inst/doc/mediation.pdf |binary inst/doc/mediation.rnw | 35 +++++----- inst/doc/omega.R | 44 +++++++++---- inst/doc/omega.Rnw | 74 ++++++++++++++++++---- inst/doc/omega.pdf |binary inst/doc/overview.R | 151 +++++++++++++++++++++++++-------------------- inst/doc/overview.Rnw | 92 +++++++++++++++++++++------ inst/doc/overview.pdf |binary man/GERAS.Rd | 2 man/Schutz.Rd | 2 man/ability.Rd | 13 ++- man/bfi.Rd | 10 ++ man/big5.100.adjectives.Rd | 18 ++++- man/blant.Rd | 10 ++ man/blot.Rd | 9 ++ man/burt.Rd | 9 +- man/cubits.Rd | 5 + man/df2latex.Rd | 4 - man/dfOrder.Rd | 2 man/epi.Rd | 12 ++- man/hare.Rd |only man/heights.Rd | 11 ++- man/iqitems.Rd | 8 +- man/msq.Rd | 21 ++++-- man/msqR.rd | 10 ++ man/psychTools.Rd | 2 man/read.clipboard.Rd | 30 ++++++-- man/spengler.Rd | 2 man/usaf.Rd | 2 man/vJoin.Rd | 5 + man/zola.Rd | 2 vignettes/factor.Rnw |only vignettes/intro.Rnw | 80 ++++++++++++++--------- vignettes/mediation.rnw | 35 +++++----- vignettes/omega.Rnw | 74 ++++++++++++++++++---- vignettes/overview.Rnw | 92 +++++++++++++++++++++------ 54 files changed, 915 insertions(+), 443 deletions(-)
Title: Wrapper for the National Bank of Poland API
Description: Use the <https://api.nbp.pl/> API through R. Retrieve
currency exchange rates and gold prices data published by the
National Bank of Poland in form of convenient R objects.
Author: Ryszard Szymanski [aut, cre]
Maintainer: Ryszard Szymanski <ryszard.szymanski@outlook.com>
Diff between rnbp versions 0.2.1 dated 2021-06-07 and 0.2.2 dated 2025-03-23
DESCRIPTION | 11 MD5 | 158 - NAMESPACE | 36 NEWS.md | 4 R/endpoint_common.R | 8 R/endpoint_goldprice.R | 374 ++-- R/endpoint_rates.R | 490 +++-- R/endpoint_tables.R | 399 ++-- R/nbp_api_response.R | 46 R/parser.R | 56 R/query_builder.R | 88 - R/request_helpers.R | 41 R/utils_assertions.R | 68 R/utils_testers.R | 64 README.md | 174 +- build/vignette.rds |binary inst/doc/rnbp.R | 108 - inst/doc/rnbp.Rmd | 192 +- inst/doc/rnbp.html | 832 +++++----- man/add_json_format.Rd | 40 man/add_path_part.Rd | 42 man/create_request.Rd | 46 man/dot-goldprice_base_url.Rd | 22 man/dot-rates_base_url.Rd | 22 man/dot-send_gold_endpoint_request.Rd | 34 man/dot-send_rates_endpoint_request.Rd | 34 man/dot-send_tables_endpoint_request.Rd | 34 man/dot-tables_base_url.Rd | 22 man/figures/README-exchangerate_table-1.png |binary man/figures/README-gold_price-1.png |binary man/figures/README-rates-1.png |binary man/get_current_exchangerate.Rd | 92 - man/get_current_exchangerate_table.Rd | 84 - man/get_current_goldprice.Rd | 78 man/get_exchangerate_from.Rd | 110 - man/get_exchangerate_from_interval.Rd | 110 - man/get_exchangerate_table_from.Rd | 103 - man/get_exchangerate_tables_from_interval.Rd | 102 - man/get_goldprice_from.Rd | 98 - man/get_goldprice_from_interval.Rd | 98 - man/get_last_n_exchangerate_tables.Rd | 88 - man/get_last_n_exchangerates.Rd | 96 - man/get_last_n_goldprices.Rd | 84 - man/get_todays_exchangerate.Rd | 100 - man/get_todays_exchangerate_table.Rd | 92 - man/get_todays_goldprice.Rd | 86 - man/is_count.Rd | 36 man/is_date.Rd | 36 man/is_integer.Rd | 36 man/is_nbp_api_response.Rd | 38 man/nbp_api_base_url.Rd | 22 tests/testthat.R | 8 tests/testthat/api.nbp.pl/api/cenyzlota-7315b4.json | 12 tests/testthat/api.nbp.pl/api/cenyzlota/2019-07-12-7315b4.json | 12 tests/testthat/api.nbp.pl/api/cenyzlota/2019-07-15/2019-07-16-7315b4.json | 20 tests/testthat/api.nbp.pl/api/cenyzlota/last/2-7315b4.json | 20 tests/testthat/api.nbp.pl/api/cenyzlota/today-7315b4.json | 12 tests/testthat/api.nbp.pl/api/exchangerates/rates/a/EUR-7315b4.json | 24 tests/testthat/api.nbp.pl/api/exchangerates/rates/a/EUR/2019-07-03-7315b4.json | 24 tests/testthat/api.nbp.pl/api/exchangerates/rates/a/EUR/2019-07-11/2019-07-13-7315b4.json | 34 tests/testthat/api.nbp.pl/api/exchangerates/rates/a/EUR/last/2-7315b4.json | 34 tests/testthat/api.nbp.pl/api/exchangerates/rates/a/EUR/today-7315b4.json | 24 tests/testthat/api.nbp.pl/api/exchangerates/tables/a-7315b4.json | 38 tests/testthat/api.nbp.pl/api/exchangerates/tables/a/2019-07-03-7315b4.json | 38 tests/testthat/api.nbp.pl/api/exchangerates/tables/a/2019-07-08/2019-07-09-7315b4.json | 72 tests/testthat/api.nbp.pl/api/exchangerates/tables/a/last/2-7315b4.json | 72 tests/testthat/api.nbp.pl/api/exchangerates/tables/a/last/68-7315b4.R | 2 tests/testthat/api.nbp.pl/api/exchangerates/tables/a/today-7315b4.json | 38 tests/testthat/api.nbp.pl/api/exchangerates/tables/b/today-7315b4.R | 2 tests/testthat/api.nbp.pl/api/exchangerates/tables/z-7315b4.R | 2 tests/testthat/helper.R | 2 tests/testthat/resources/test-parser-currency_table.json | 38 tests/testthat/test-endpoint_goldprice.R | 102 - tests/testthat/test-endpoint_rates.R | 232 +- tests/testthat/test-endpoint_tables.R | 278 +-- tests/testthat/test-parser.R | 2 tests/testthat/test-query_builder.R | 36 tests/testthat/test-utils_assertions.R | 82 tests/testthat/test-utils_testers.R | 46 vignettes/rnbp.Rmd | 192 +- 80 files changed, 3319 insertions(+), 3213 deletions(-)
Title: 'Shiny' Applications for the R Package 'Luminescence'
Description: A collection of 'shiny' applications for the R package
'Luminescence'. These mainly, but not exclusively, include applications for
plotting chronometric data from e.g. luminescence or radiocarbon dating. It
further provides access to bootstraps tooltip and popover functionality and
contains the 'jscolor.js' library with a custom 'shiny' output binding.
Author: Christoph Burow [aut, cre] ,
Urs Tilmann Wolpert [aut],
Sebastian Kreutzer [aut] ,
Marco Colombo [aut] ,
R Luminescence Package Team [ctb],
Jan Odvarko [cph] ,
AnalytixWare [cph] ,
RStudio [cph]
Maintainer: Christoph Burow <christoph.burow@gmx.net>
Diff between RLumShiny versions 0.2.3 dated 2022-01-31 and 0.2.4 dated 2025-03-23
DESCRIPTION | 37 ++--- MD5 | 68 ++++----- NAMESPACE | 1 NEWS.md | 221 +++++++++++++++++-------------- R/RLumShiny.R | 5 R/addin.R | 14 - R/app_RLum.R | 38 ++--- R/jscolor.R | 73 +++++----- R/module_aboutTab.R | 4 inst/shiny/KDE/server.R | 49 ++---- inst/shiny/KDE/ui.R | 75 +++++----- inst/shiny/RCarb/server.R | 2 inst/shiny/abanico/server.R | 32 +--- inst/shiny/abanico/ui.R | 185 ++++++++++++++----------- inst/shiny/cosmicdose/Global.R | 4 inst/shiny/cosmicdose/server.R | 149 ++++++++++---------- inst/shiny/cosmicdose/ui.R | 71 ++++++--- inst/shiny/doserecovery/server.R | 37 +---- inst/shiny/doserecovery/ui.R | 106 ++++++++------ inst/shiny/fading/server.R | 2 inst/shiny/fastratio/UI.R | 42 ++--- inst/shiny/histogram/server.R | 21 -- inst/shiny/histogram/ui.R | 93 ++++++++----- inst/shiny/radialplot/server.R | 62 ++++---- inst/shiny/radialplot/ui.R | 114 ++++++++------- inst/shiny/scalegamma/server.R | 12 - inst/shiny/scalegamma/ui.R | 5 inst/shiny/surfaceexposure/server.R | 148 ++++++++++---------- inst/shiny/teststimulationpower/server.R | 7 inst/shiny/teststimulationpower/ui.R | 4 inst/shiny/transformCW/Server.R | 10 - inst/shiny/transformCW/UI.R | 14 - man/RLumShiny-package.Rd | 28 +++ man/app_RLum.Rd | 39 ++--- man/jscolorInput.Rd | 30 ++-- 35 files changed, 943 insertions(+), 859 deletions(-)
Title: Extracting and Visualizing Paleobiodiversity
Description: Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.
Author: Darius Nau [aut, cre]
Maintainer: Darius Nau <dariusnau@gmx.at>
Diff between paleoDiv versions 0.4.0 dated 2024-10-17 and 0.4.6 dated 2025-03-23
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 15 +++ R/paleoDiv.R | 128 +++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/Paleobiodiversity_analysis.R | 2 inst/doc/Paleobiodiversity_analysis.Rmd | 2 man/multijitter.Rd | 3 man/ts.periods.Rd | 5 - man/ts.stages.Rd | 5 - man/violins.Rd | 9 ++ vignettes/Paleobiodiversity_analysis.Rmd | 2 12 files changed, 158 insertions(+), 41 deletions(-)
Title: Render Markdown with 'commonmark'
Description: Render Markdown to full and lightweight HTML/LaTeX documents with
the 'commonmark' package. This package has been superseded by 'litedown'.
Author: Yihui Xie [aut, cre] ,
JJ Allaire [aut],
Jeffrey Horner [aut],
Henrik Bengtsson [ctb],
Jim Hester [ctb],
Yixuan Qiu [ctb],
Kohske Takahashi [ctb],
Adam November [ctb],
Nacho Caballero [ctb],
Jeroen Ooms [ctb],
Thomas Leeper [ctb],
Joe Cheng [ctb],
An [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between markdown versions 1.13 dated 2024-06-04 and 2.0 dated 2025-03-23
markdown-1.13/markdown/tests/smartypants.R |only markdown-2.0/markdown/DESCRIPTION | 10 markdown-2.0/markdown/MD5 | 23 markdown-2.0/markdown/NAMESPACE | 2 markdown-2.0/markdown/NEWS.md | 4 markdown-2.0/markdown/R/package.R | 2 markdown-2.0/markdown/R/render.R | 399 +------- markdown-2.0/markdown/R/rmarkdown.R | 52 - markdown-2.0/markdown/R/utils.R | 851 ------------------- markdown-2.0/markdown/inst/examples/render-options.R | 2 markdown-2.0/markdown/man/mark.Rd | 67 - markdown-2.0/markdown/man/markdown_options.Rd | 87 - markdown-2.0/markdown/tests/tests.Rout.save | 21 13 files changed, 97 insertions(+), 1423 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between magick versions 2.8.5 dated 2024-09-20 and 2.8.6 dated 2025-03-23
DESCRIPTION | 7 ++-- MD5 | 14 ++++---- build/vignette.rds |binary inst/doc/intro.R | 12 +++---- inst/doc/intro.html | 89 +++++++++++++++++++++++++++++----------------------- src/Makevars.in | 6 +-- src/Makevars.win | 15 ++++---- tools/winlibs.R | 11 +++--- 8 files changed, 85 insertions(+), 69 deletions(-)
Title: Just Analysis Methods Base
Description: Just analysis methods ('jam') base functions
focused on bioinformatics.
Version- and gene-centric alphanumeric sort,
unique name and version assignment, colorized console and 'HTML' output,
color ramp and palette manipulation,
'Rmarkdown' cache import, styled 'Excel' worksheet import and export,
interpolated raster output from smooth scatter and image plots,
list to delimited vector, efficient list tools.
Author: James M. Ward [aut, cre, cph]
Maintainer: James M. Ward <jmw86069@gmail.com>
Diff between jamba versions 1.0.2 dated 2025-03-10 and 1.0.4 dated 2025-03-23
DESCRIPTION | 6 +- MD5 | 22 ++++----- NEWS.md | 41 +++++++++++++++++ R/jamba-kable-coloring.R | 2 R/jamba-utils.R | 89 ++++++++++++++++++++++++++++++------- inst/doc/jamba-vignette.R | 2 inst/doc/jamba-vignette.Rmd | 2 inst/doc/jamba-vignette.html | 12 ++-- man/check_pkg_installed.Rd | 67 ++++++++++++++++++++++----- man/kable_coloring.Rd | 2 tests/testthat/test-getColorRamp.R | 17 ++++--- vignettes/jamba-vignette.Rmd | 2 12 files changed, 204 insertions(+), 60 deletions(-)
Title: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size
bitmap arrays using 'librsvg2'. The resulting bitmap can be written to
e.g. png, jpeg or webp format. In addition, the package can convert
images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms [aut, cre] ,
Salim Brueggemann [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between rsvg versions 2.6.1 dated 2024-09-20 and 2.6.2 dated 2025-03-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- build/vignette.rds |binary cleanup | 1 - inst/doc/svg-css.html | 7 ++++--- src/Makevars.in | 5 +++++ src/Makevars.win | 20 ++++++++++---------- tools/winlibs.R | 13 ++++++------- 8 files changed, 35 insertions(+), 31 deletions(-)
Title: Open Source OCR Engine
Description: Bindings to 'Tesseract':
a powerful optical character recognition (OCR) engine that supports over 100 languages.
The engine is highly configurable in order to tune the detection algorithms and
obtain the best possible results.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between tesseract versions 5.2.2 dated 2024-10-04 and 5.2.3 dated 2025-03-23
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/doc/intro.R | 4 ++-- inst/doc/intro.html | 12 ++++++------ src/Makevars.in | 8 ++++---- src/Makevars.win | 24 ++++++++++++------------ src/tesseract.cpp | 4 ++-- tools/winlibs.R | 27 ++++++++++----------------- 9 files changed, 47 insertions(+), 54 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft
PowerPoint' documents from R. The package focuses on tabular and
graphical reporting from R; it also provides two functions that let
users get document content into data objects. A set of functions lets
add and remove images, tables and paragraphs of text in new or
existing documents. The package does not require any installation of
Microsoft products to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Stefan Moog [aut],
Mark Heckmann [aut] ,
ArData [cph],
Frank Hangler [ctb] ,
Liz Sander [ctb] ,
Anton Victorson [ctb] ,
Jon Calder [ctb] ,
John Harrold [ctb] ,
John Muschelli [ctb] ,
Bill Denney [ctb] ,
Nikolai Beck [ctb] ,
Gr [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.6.7 dated 2024-10-09 and 0.6.8 dated 2025-03-23
officer-0.6.7/officer/tests/testthat/test-ppt-notes.R |only officer-0.6.8/officer/DESCRIPTION | 25 officer-0.6.8/officer/MD5 | 95 +- officer-0.6.8/officer/NAMESPACE | 30 officer-0.6.8/officer/NEWS.md | 20 officer-0.6.8/officer/R/dev-utils.R | 2 officer-0.6.8/officer/R/docx_add.R | 93 +- officer-0.6.8/officer/R/docx_settings.R | 15 officer-0.6.8/officer/R/openxml_content_type.R | 1 officer-0.6.8/officer/R/ph_location.R | 401 ++++++++-- officer-0.6.8/officer/R/post-proc.R | 19 officer-0.6.8/officer/R/ppt_notes.R | 2 officer-0.6.8/officer/R/ppt_ph_manipulate.R | 2 officer-0.6.8/officer/R/ppt_ph_with_methods.R | 129 +++ officer-0.6.8/officer/R/pptx_slide_manip.R | 139 +++ officer-0.6.8/officer/R/utils.R | 77 + officer-0.6.8/officer/inst/examples/example_add_slide.R |only officer-0.6.8/officer/inst/examples/example_phs_with.R |only officer-0.6.8/officer/inst/examples/example_slide_visible.R |only officer-0.6.8/officer/man/add_slide.Rd | 40 officer-0.6.8/officer/man/body_add.Rd | 20 officer-0.6.8/officer/man/body_add_gg.Rd | 12 officer-0.6.8/officer/man/body_add_img.Rd | 17 officer-0.6.8/officer/man/body_add_plot.Rd | 21 officer-0.6.8/officer/man/body_replace_gg_at_bkm.Rd | 5 officer-0.6.8/officer/man/fortify_location.Rd | 6 officer-0.6.8/officer/man/move_slide.Rd | 4 officer-0.6.8/officer/man/on_slide.Rd | 4 officer-0.6.8/officer/man/ph_location.Rd | 17 officer-0.6.8/officer/man/ph_location_fullsize.Rd | 4 officer-0.6.8/officer/man/ph_location_id.Rd | 2 officer-0.6.8/officer/man/ph_location_label.Rd | 11 officer-0.6.8/officer/man/ph_location_left.Rd | 6 officer-0.6.8/officer/man/ph_location_right.Rd | 6 officer-0.6.8/officer/man/ph_location_template.Rd | 10 officer-0.6.8/officer/man/ph_location_type.Rd | 2 officer-0.6.8/officer/man/ph_with.Rd | 97 +- officer-0.6.8/officer/man/phs_with.Rd |only officer-0.6.8/officer/man/remove_slide.Rd | 4 officer-0.6.8/officer/man/resolve_location.Rd |only officer-0.6.8/officer/man/roxygen |only officer-0.6.8/officer/man/set_notes.Rd | 4 officer-0.6.8/officer/man/slide-visible.Rd |only officer-0.6.8/officer/man/stop_if_not_in_slide_range.Rd |only officer-0.6.8/officer/tests/testthat/docs_dir/test-slides-visible.pptx |only officer-0.6.8/officer/tests/testthat/setup.R |only officer-0.6.8/officer/tests/testthat/test-docx-add.R | 71 + officer-0.6.8/officer/tests/testthat/test-docx-misc.R | 11 officer-0.6.8/officer/tests/testthat/test-pptx-add.R | 236 ----- officer-0.6.8/officer/tests/testthat/test-pptx-info.R | 31 officer-0.6.8/officer/tests/testthat/test-pptx-misc.R | 81 +- officer-0.6.8/officer/tests/testthat/test-pptx-notes.R |only officer-0.6.8/officer/tests/testthat/test-pptx-ph-location.R |only officer-0.6.8/officer/tests/testthat/test-utils.R | 60 + officer-0.6.8/officer/tests/testthat/utils.R | 1 55 files changed, 1277 insertions(+), 556 deletions(-)
Title: Introductory Statistics with R
Description: Data sets and scripts for text examples and exercises in
P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Author: Peter Dalgaard [aut, cre]
Maintainer: Peter Dalgaard <pd.mes@cbs.dk>
Diff between ISwR versions 2.0-9 dated 2024-10-10 and 2.0-10 dated 2025-03-23
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- data/IgM.rda |binary data/alkfos.rda |binary data/bcmort.rda |binary data/caesarean.rda |binary data/coking.rda |binary data/ewrates.rda |binary data/fake.trypsin.rda |binary data/heart.rate.rda |binary data/intake.rda |binary data/lung.rda |binary data/nickel.expand.rda |binary data/nickel.rda |binary data/react.rda |binary data/red.cell.folate.rda |binary data/stroke.rda |binary data/tb.dilute.rda |binary data/zelazo.rda |binary tests/allscripts.Rout.save | 19 ++++++++++--------- 20 files changed, 33 insertions(+), 32 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia [aut],
Silvia Castiglione [aut, cre],
Carmela Serio [aut],
Giorgia Girardi [aut],
Alessandro Mondanaro [aut],
Marina Melchionna [aut],
Mirko Di Febbraro [aut],
Antonio Profico [aut],
Francesco Carotenuto [aut]
Maintainer: Silvia Castiglione <silvia.castiglione@unina.it>
Diff between RRphylo versions 2.8.1 dated 2024-08-22 and 3.0.0 dated 2025-03-23
RRphylo-2.8.1/RRphylo/NEWS.md |only RRphylo-2.8.1/RRphylo/inst/doc/overfitRR.Rmd |only RRphylo-2.8.1/RRphylo/inst/doc/overfitRR.html |only RRphylo-2.8.1/RRphylo/inst/doc/swapONE.Rmd |only RRphylo-2.8.1/RRphylo/inst/doc/swapONE.html |only RRphylo-2.8.1/RRphylo/vignettes/overfitRR.Rmd |only RRphylo-2.8.1/RRphylo/vignettes/plotting-data.Rda |only RRphylo-2.8.1/RRphylo/vignettes/swapONE.Rmd |only RRphylo-3.0.0/RRphylo/DESCRIPTION | 77 RRphylo-3.0.0/RRphylo/MD5 | 286 ++- RRphylo-3.0.0/RRphylo/NAMESPACE | 302 ++- RRphylo-3.0.0/RRphylo/R/DataFelids.R | 8 RRphylo-3.0.0/RRphylo/R/PGLS_fossil.R | 40 RRphylo-3.0.0/RRphylo/R/RRphylo.R | 344 +--- RRphylo-3.0.0/RRphylo/R/StableTraitsR.R | 4 RRphylo-3.0.0/RRphylo/R/angle.matrix.R | 39 RRphylo-3.0.0/RRphylo/R/auxilliary.functions.R | 91 + RRphylo-3.0.0/RRphylo/R/colorbar.R | 41 RRphylo-3.0.0/RRphylo/R/compRates.R |only RRphylo-3.0.0/RRphylo/R/conv.map.R | 59 RRphylo-3.0.0/RRphylo/R/cutPhylo.R | 33 RRphylo-3.0.0/RRphylo/R/distNodes.R | 128 - RRphylo-3.0.0/RRphylo/R/evo.dir.R | 65 RRphylo-3.0.0/RRphylo/R/geiger_functions.R | 49 RRphylo-3.0.0/RRphylo/R/getGenus.R | 25 RRphylo-3.0.0/RRphylo/R/getMommy.R | 11 RRphylo-3.0.0/RRphylo/R/getSis.R | 4 RRphylo-3.0.0/RRphylo/R/makeFossil.R | 2 RRphylo-3.0.0/RRphylo/R/makeL.R | 2 RRphylo-3.0.0/RRphylo/R/makeL1.R | 2 RRphylo-3.0.0/RRphylo/R/move.lineage.R | 131 - RRphylo-3.0.0/RRphylo/R/namesCompare.R | 150 + RRphylo-3.0.0/RRphylo/R/node.paths.R | 2 RRphylo-3.0.0/RRphylo/R/overfitPGLS.R |only RRphylo-3.0.0/RRphylo/R/overfitRR.R | 874 +---------- RRphylo-3.0.0/RRphylo/R/overfitSC.R |only RRphylo-3.0.0/RRphylo/R/overfitSS.R |only RRphylo-3.0.0/RRphylo/R/overfitST.R |only RRphylo-3.0.0/RRphylo/R/phyloclust.R | 33 RRphylo-3.0.0/RRphylo/R/plotConv.R | 53 RRphylo-3.0.0/RRphylo/R/plotRR.R | 51 RRphylo-3.0.0/RRphylo/R/plotRates.R | 15 RRphylo-3.0.0/RRphylo/R/plotShift.R | 241 +-- RRphylo-3.0.0/RRphylo/R/plotTrend.R | 80 - RRphylo-3.0.0/RRphylo/R/print.RRphyloList.R |only RRphylo-3.0.0/RRphylo/R/random.evolvability.test.R | 23 RRphylo-3.0.0/RRphylo/R/rate.map.R | 62 RRphylo-3.0.0/RRphylo/R/rateHistory.R |only RRphylo-3.0.0/RRphylo/R/resampleTree.R |only RRphylo-3.0.0/RRphylo/R/rescaleRR.R | 8 RRphylo-3.0.0/RRphylo/R/retrieve.angles.R | 105 - RRphylo-3.0.0/RRphylo/R/scaleTree.R | 73 RRphylo-3.0.0/RRphylo/R/search.conv.R | 1398 ++++++------------ RRphylo-3.0.0/RRphylo/R/search.shift.R | 453 ++--- RRphylo-3.0.0/RRphylo/R/search.trend.R | 115 - RRphylo-3.0.0/RRphylo/R/setBM.R | 7 RRphylo-3.0.0/RRphylo/R/sizedsubtree.R | 10 RRphylo-3.0.0/RRphylo/R/swapONE.R | 9 RRphylo-3.0.0/RRphylo/R/tree.merger.R | 366 +++- RRphylo-3.0.0/RRphylo/R/treeCompare.R | 214 +- RRphylo-3.0.0/RRphylo/README.md | 23 RRphylo-3.0.0/RRphylo/build/vignette.rds |binary RRphylo-3.0.0/RRphylo/data/DataFelids.rda |binary RRphylo-3.0.0/RRphylo/inst/CITATION | 18 RRphylo-3.0.0/RRphylo/inst/doc/Alternative-trees.Rmd |only RRphylo-3.0.0/RRphylo/inst/doc/Alternative-trees.html |only RRphylo-3.0.0/RRphylo/inst/doc/Plotting-tools.Rmd | 148 + RRphylo-3.0.0/RRphylo/inst/doc/Plotting-tools.html | 499 +++--- RRphylo-3.0.0/RRphylo/inst/doc/RRphylo.Rmd | 4 RRphylo-3.0.0/RRphylo/inst/doc/RRphylo.html | 24 RRphylo-3.0.0/RRphylo/inst/doc/Tree-Manipulation.Rmd | 528 ++---- RRphylo-3.0.0/RRphylo/inst/doc/Tree-Manipulation.html | 804 ++++++---- RRphylo-3.0.0/RRphylo/inst/doc/overfit.Rmd |only RRphylo-3.0.0/RRphylo/inst/doc/overfit.html |only RRphylo-3.0.0/RRphylo/inst/doc/search.conv.Rmd | 548 +------ RRphylo-3.0.0/RRphylo/inst/doc/search.conv.html | 53 RRphylo-3.0.0/RRphylo/inst/doc/search.shift.Rmd | 71 RRphylo-3.0.0/RRphylo/inst/doc/search.shift.html | 278 --- RRphylo-3.0.0/RRphylo/inst/doc/search.trend.Rmd | 16 RRphylo-3.0.0/RRphylo/inst/doc/search.trend.html | 26 RRphylo-3.0.0/RRphylo/inst/figures |only RRphylo-3.0.0/RRphylo/man/DataApes.Rd | 74 RRphylo-3.0.0/RRphylo/man/DataCetaceans.Rd | 66 RRphylo-3.0.0/RRphylo/man/DataFelids.Rd | 64 RRphylo-3.0.0/RRphylo/man/DataOrnithodirans.Rd | 64 RRphylo-3.0.0/RRphylo/man/DataSimians.Rd | 36 RRphylo-3.0.0/RRphylo/man/DataUng.Rd | 60 RRphylo-3.0.0/RRphylo/man/PGLS_fossil.Rd | 267 +-- RRphylo-3.0.0/RRphylo/man/RRphylo-defunct.Rd | 30 RRphylo-3.0.0/RRphylo/man/RRphylo-deprecated.Rd | 16 RRphylo-3.0.0/RRphylo/man/RRphylo-package.Rd | 48 RRphylo-3.0.0/RRphylo/man/RRphylo.Rd | 416 ++--- RRphylo-3.0.0/RRphylo/man/StableTraitsR.Rd | 204 +- RRphylo-3.0.0/RRphylo/man/angle.matrix.Rd | 282 +-- RRphylo-3.0.0/RRphylo/man/colorbar.Rd | 178 +- RRphylo-3.0.0/RRphylo/man/compRates.Rd |only RRphylo-3.0.0/RRphylo/man/conv.map.Rd | 252 +-- RRphylo-3.0.0/RRphylo/man/cutPhylo.Rd | 111 - RRphylo-3.0.0/RRphylo/man/distNodes.Rd | 94 - RRphylo-3.0.0/RRphylo/man/evo.dir.Rd | 368 ++-- RRphylo-3.0.0/RRphylo/man/fix.poly.Rd | 162 +- RRphylo-3.0.0/RRphylo/man/getGenus.Rd | 70 RRphylo-3.0.0/RRphylo/man/getMommy.Rd | 78 - RRphylo-3.0.0/RRphylo/man/getSis.Rd | 72 RRphylo-3.0.0/RRphylo/man/lollipoPlot.Rd | 108 - RRphylo-3.0.0/RRphylo/man/makeFossil.Rd | 74 RRphylo-3.0.0/RRphylo/man/makeL.Rd | 64 RRphylo-3.0.0/RRphylo/man/makeL1.Rd | 64 RRphylo-3.0.0/RRphylo/man/move.lineage.Rd | 182 +- RRphylo-3.0.0/RRphylo/man/namesCompare.Rd | 112 - RRphylo-3.0.0/RRphylo/man/node.paths.Rd | 70 RRphylo-3.0.0/RRphylo/man/overfitPGLS.Rd |only RRphylo-3.0.0/RRphylo/man/overfitRR.Rd | 480 ++---- RRphylo-3.0.0/RRphylo/man/overfitSC.Rd |only RRphylo-3.0.0/RRphylo/man/overfitSS.Rd |only RRphylo-3.0.0/RRphylo/man/overfitST.Rd |only RRphylo-3.0.0/RRphylo/man/phyloclust.Rd | 96 - RRphylo-3.0.0/RRphylo/man/plotConv.Rd | 30 RRphylo-3.0.0/RRphylo/man/plotRR.Rd | 155 + RRphylo-3.0.0/RRphylo/man/plotRates.Rd | 146 - RRphylo-3.0.0/RRphylo/man/plotShift.Rd | 72 RRphylo-3.0.0/RRphylo/man/plotTrend.Rd | 234 +-- RRphylo-3.0.0/RRphylo/man/random.evolvability.test.Rd | 161 +- RRphylo-3.0.0/RRphylo/man/rate.map.Rd | 198 +- RRphylo-3.0.0/RRphylo/man/rateHistory.Rd |only RRphylo-3.0.0/RRphylo/man/resampleTree.Rd |only RRphylo-3.0.0/RRphylo/man/rescaleRR.Rd | 166 +- RRphylo-3.0.0/RRphylo/man/retrieve.angles.Rd | 357 ++-- RRphylo-3.0.0/RRphylo/man/scaleTree.Rd | 191 +- RRphylo-3.0.0/RRphylo/man/search.conv.Rd | 317 ++-- RRphylo-3.0.0/RRphylo/man/search.shift.Rd | 347 ++-- RRphylo-3.0.0/RRphylo/man/search.trend.Rd | 448 ++--- RRphylo-3.0.0/RRphylo/man/setBM.Rd | 187 +- RRphylo-3.0.0/RRphylo/man/sig2BM.Rd | 76 RRphylo-3.0.0/RRphylo/man/sizedsubtree.Rd | 87 - RRphylo-3.0.0/RRphylo/man/swapONE.Rd | 124 - RRphylo-3.0.0/RRphylo/man/tips.Rd | 62 RRphylo-3.0.0/RRphylo/man/tree.merger.Rd | 400 +++-- RRphylo-3.0.0/RRphylo/man/treeCompare.Rd | 81 - RRphylo-3.0.0/RRphylo/man/treedataMatch.Rd | 91 - RRphylo-3.0.0/RRphylo/vignettes/Alternative-trees.Rmd |only RRphylo-3.0.0/RRphylo/vignettes/Plotting-tools.Rmd | 148 + RRphylo-3.0.0/RRphylo/vignettes/RRphylo.Rmd | 4 RRphylo-3.0.0/RRphylo/vignettes/Tree-Manipulation.Rmd | 528 ++---- RRphylo-3.0.0/RRphylo/vignettes/figs |only RRphylo-3.0.0/RRphylo/vignettes/functions4vignettes.R |only RRphylo-3.0.0/RRphylo/vignettes/overfit.Rmd |only RRphylo-3.0.0/RRphylo/vignettes/search.conv.Rmd | 548 +------ RRphylo-3.0.0/RRphylo/vignettes/search.shift.Rmd | 71 RRphylo-3.0.0/RRphylo/vignettes/search.trend.Rmd | 16 150 files changed, 8292 insertions(+), 10340 deletions(-)
Title: Creation, Reading and Validation of 'mzqc' Files
Description: Reads, writes and validates 'mzQC' files. The 'mzQC' format is a
standardized file format for the exchange, transmission, and archiving of
quality metrics derived from biological mass spectrometry data, as defined
by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative)
Quality Control working group.
See <https://hupo-psi.github.io/mzQC/> for details.
Author: Chris Bielow [aut, cre] ,
David Jimenez-Morales [rev, ctb]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between rmzqc versions 0.5.4 dated 2024-04-16 and 0.5.5 dated 2025-03-23
DESCRIPTION | 10 LICENSE | 4 MD5 | 151 NEWS.md | 6 R/conversion.R | 63 R/io.R | 88 R/mzQC.R | 1427 R/obo.R | 4 R/overview.R |only R/rmzqc-package.R | 12 R/rmzqc.R | 14 R/templates.R | 9 R/validator.R | 188 README.md | 9 build/vignette.rds |binary inst/cv/pato.obo |44716 +++++++++++++++--------------- inst/cv/psi-ms.obo |49134 +++++++++++++++++----------------- inst/cv/uo.obo | 8150 ++--- inst/doc/basic_guide.R | 5 inst/doc/basic_guide.Rmd | 7 inst/doc/basic_guide.html | 19 inst/doc/using_a_custom_cv.Rmd | 144 inst/doc/using_a_custom_cv.html | 18 inst/doc/validation_guide.R | 32 inst/doc/validation_guide.Rmd | 104 inst/doc/validation_guide.html | 4 man/CV_.Rd | 235 man/MzQCDateTime-class.Rd | 54 man/MzQCanalysisSoftware-class.Rd | 54 man/MzQCbaseQuality-class.Rd | 38 man/MzQCcontrolledVocabulary-class.Rd | 56 man/MzQCcvParameter-class.Rd | 60 man/MzQCinputFile-class.Rd | 48 man/MzQCmetadata-class.Rd | 46 man/MzQCmzQC-class.Rd | 62 man/MzQCqualityMetric-class.Rd | 52 man/MzQCrunQuality-class.Rd | 22 man/MzQCsetQuality-class.Rd | 24 man/NULL_to_NA.Rd | 42 man/NULL_to_charNA.Rd | 42 man/check_type.Rd | 68 man/filenameToCV.Rd | 74 man/fromDatatoMzQC.Rd | 44 man/fromDatatoMzQCobj.Rd | 44 man/getCVInfo.Rd | 26 man/getCVSingleton.Rd | 22 man/getCVTemplate.Rd | 42 man/getDefaultCV.Rd | 28 man/getLatest_PSICV_URL.Rd | 24 man/getLocal_CV_Version.Rd | 36 man/getQualityMetricTemplate.Rd | 47 man/getSyntaxValidator.Rd | 22 man/hasFileSuffix.Rd | 62 man/isUndefined.Rd | 64 man/isValidMzQC.Rd | 74 man/localFileToURI.Rd | 40 man/readMZQC.Rd | 34 man/removeFileSuffix.Rd | 52 man/removeIfExists.Rd | 34 man/rmzqc-package.Rd | 56 man/toAnalysisSoftware.Rd | 60 man/toQCMetric.Rd | 121 man/validateFromFile.Rd | 40 man/validateFromObj.Rd | 50 man/validateFromString.Rd | 50 man/writeMZQC.Rd | 40 tests/testthat.R | 8 tests/testthat/test-mzQC.R | 80 tests/testthat/test_conversion.R | 42 tests/testthat/test_io.R | 34 tests/testthat/test_misc.R | 130 tests/testthat/test_obo.R | 94 tests/testthat/test_templates.R | 38 tests/testthat/test_validate.R | 72 vignettes/basic_guide.Rmd | 7 vignettes/using_a_custom_cv.Rmd | 144 vignettes/validation_guide.Rmd | 104 77 files changed, 53620 insertions(+), 53540 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.7.0 dated 2025-01-24 and 0.8.0 dated 2025-03-23
tinytable-0.7.0/tinytable/inst/tinytest/_tinysnapshot/html-images-portable.html |only tinytable-0.8.0/tinytable/DESCRIPTION | 13 - tinytable-0.8.0/tinytable/MD5 | 103 ++++------ tinytable-0.8.0/tinytable/NAMESPACE | 1 tinytable-0.8.0/tinytable/NEWS.md | 17 + tinytable-0.8.0/tinytable/R/escape.R | 2 tinytable-0.8.0/tinytable/R/finalize_bootstrap.R | 5 tinytable-0.8.0/tinytable/R/format_tt.R | 19 + tinytable-0.8.0/tinytable/R/package.R | 8 tinytable-0.8.0/tinytable/R/print.R | 46 +++- tinytable-0.8.0/tinytable/R/sanity.R | 15 + tinytable-0.8.0/tinytable/R/style_bootstrap.R | 11 - tinytable-0.8.0/tinytable/R/style_grid.R | 2 tinytable-0.8.0/tinytable/R/style_tt.R | 4 tinytable-0.8.0/tinytable/R/tt_bootstrap.R | 21 +- tinytable-0.8.0/tinytable/README.md | 97 ++++----- tinytable-0.8.0/tinytable/build/partial.rdb |binary tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 28 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-html_tutorial_01.html | 46 ++-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue165_html_centering_style.html | 68 +++--- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_01_html.html | 36 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_02_html.html | 38 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-alignment.html | 52 ++--- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-bootstrap_css.html | 36 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-borders.html | 20 - tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-caption.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-conditional_styling.html | 28 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-font_size.html | 36 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-footnote.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-formatting.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-heatmap.html | 96 ++++----- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-images.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-individual_cells.html | 28 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-issue297.txt | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-issue58.html | 36 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-issue88.html | 28 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-issue92.html | 36 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-line_break.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-merge_cells.html | 30 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-missing_value.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-omit_headers.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-spanning_cells.html | 34 +-- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-striped.html | 24 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-striped_orange.html | 28 +- tinytable-0.8.0/tinytable/inst/tinytest/_tinysnapshot/html-vectorized_color_j.html | 48 ++-- tinytable-0.8.0/tinytable/inst/tinytest/helpers.R | 53 +++-- tinytable-0.8.0/tinytable/inst/tinytest/test-format_tt.R | 25 +- tinytable-0.8.0/tinytable/inst/tinytest/test-group_tt.R | 5 tinytable-0.8.0/tinytable/inst/tinytest/test-html.R | 33 +-- tinytable-0.8.0/tinytable/inst/tinytest/test-markdown.R | 4 tinytable-0.8.0/tinytable/inst/tinytest/test-pdf.R | 2 tinytable-0.8.0/tinytable/inst/tinytest/test-theme.R | 18 + tinytable-0.8.0/tinytable/inst/tinytest/test-tibble.R | 7 53 files changed, 807 insertions(+), 672 deletions(-)