Title: Hierarchical Bayesian Vector Autoregression
Description: Estimation of hierarchical Bayesian vector autoregressive models.
Implements hierarchical prior selection for conjugate priors in the fashion
of Giannone, Lenza & Primiceri (2015) <doi:10.1162/REST_a_00483>. Functions
to compute and identify impulse responses, calculate forecasts,
forecast error variance decompositions and scenarios are available.
Several methods to print, plot and summarise results facilitate analysis.
Author: Nikolas Kuschnig [aut, cre] (<https://orcid.org/0000-0002-6642-2543>),
Lukas Vashold [aut],
Michael McCracken [dtc],
Serena Ng [dtc]
Maintainer: Nikolas Kuschnig <nikolas.kuschnig@wu.ac.at>
Diff between BVAR versions 0.2.2 dated 2020-02-20 and 1.0.0 dated 2020-05-05
BVAR-0.2.2/BVAR/inst/REFERENCES.bib |only BVAR-0.2.2/BVAR/man/as.mcmc.bvar.Rd |only BVAR-0.2.2/BVAR/man/bv_plot_trace.Rd |only BVAR-0.2.2/BVAR/man/companion.bvar.Rd |only BVAR-0.2.2/BVAR/man/logLik.bvar.Rd |only BVAR-1.0.0/BVAR/DESCRIPTION | 29 +- BVAR-1.0.0/BVAR/LICENSE | 6 BVAR-1.0.0/BVAR/MD5 | 149 ++++++---- BVAR-1.0.0/BVAR/NAMESPACE | 19 + BVAR-1.0.0/BVAR/NEWS.md | 61 +++- BVAR-1.0.0/BVAR/R/10_bvar.R | 436 +++++++++++++++----------------- BVAR-1.0.0/BVAR/R/11_input.R | 67 +--- BVAR-1.0.0/BVAR/R/12_aux.R | 266 ++++++++++++++----- BVAR-1.0.0/BVAR/R/13_mvtnorm.R |only BVAR-1.0.0/BVAR/R/15_prep_data.R | 177 ++++++++---- BVAR-1.0.0/BVAR/R/20_ml.R | 111 ++++---- BVAR-1.0.0/BVAR/R/21_draw.R | 54 +-- BVAR-1.0.0/BVAR/R/22_get.R | 42 +-- BVAR-1.0.0/BVAR/R/30_metropolis_setup.R | 62 ++-- BVAR-1.0.0/BVAR/R/35_metropolis_print.R | 7 BVAR-1.0.0/BVAR/R/40_priors_setup.R | 48 +-- BVAR-1.0.0/BVAR/R/41_minnesota.R | 152 +++++++---- BVAR-1.0.0/BVAR/R/42_dummy.R | 71 ++--- BVAR-1.0.0/BVAR/R/43_sur_soc.R | 16 - BVAR-1.0.0/BVAR/R/45_priors_print.R | 34 +- BVAR-1.0.0/BVAR/R/50_fcast_setup.R | 83 ++++-- BVAR-1.0.0/BVAR/R/51_fcast_compute.R | 27 - BVAR-1.0.0/BVAR/R/52_fcast_cond.R |only BVAR-1.0.0/BVAR/R/54_predict.R | 141 +++++++--- BVAR-1.0.0/BVAR/R/55_fcast_print.R | 64 ++-- BVAR-1.0.0/BVAR/R/58_fcast_plot.R | 163 ++++++++--- BVAR-1.0.0/BVAR/R/60_irf_setup.R | 102 ++++--- BVAR-1.0.0/BVAR/R/61_irf_compute.R | 36 +- BVAR-1.0.0/BVAR/R/62_sign_restr.R | 20 - BVAR-1.0.0/BVAR/R/63_fevd.R | 21 - BVAR-1.0.0/BVAR/R/64_irf_method.R | 200 ++++++++------ BVAR-1.0.0/BVAR/R/65_irf_print.R | 94 +++--- BVAR-1.0.0/BVAR/R/68_irf_plot.R | 134 ++++++--- BVAR-1.0.0/BVAR/R/80_coda.R | 113 +++++--- BVAR-1.0.0/BVAR/R/81_parallel.R |only BVAR-1.0.0/BVAR/R/85_transform.R |only BVAR-1.0.0/BVAR/R/90_print.R | 24 - BVAR-1.0.0/BVAR/R/91_plot.R | 134 +++++---- BVAR-1.0.0/BVAR/R/92_coef.R | 92 +++--- BVAR-1.0.0/BVAR/R/93_density.R | 62 ++-- BVAR-1.0.0/BVAR/R/94_logLik.R | 23 - BVAR-1.0.0/BVAR/R/95_fitted.R | 97 +++---- BVAR-1.0.0/BVAR/R/96_summary.R | 45 +-- BVAR-1.0.0/BVAR/R/97_companion.R | 90 ++++-- BVAR-1.0.0/BVAR/R/BVAR-package.R | 22 + BVAR-1.0.0/BVAR/R/data.R | 49 ++- BVAR-1.0.0/BVAR/R/deprecated.R | 164 ------------ BVAR-1.0.0/BVAR/R/zzz.R |only BVAR-1.0.0/BVAR/build |only BVAR-1.0.0/BVAR/data/fred_md.rda |only BVAR-1.0.0/BVAR/data/fred_qd.rda |binary BVAR-1.0.0/BVAR/inst/CITATION | 36 +- BVAR-1.0.0/BVAR/inst/doc |only BVAR-1.0.0/BVAR/inst/fred_trans.csv |only BVAR-1.0.0/BVAR/inst/tinytest |only BVAR-1.0.0/BVAR/man/BVAR-package.Rd | 20 + BVAR-1.0.0/BVAR/man/bv_dummy.Rd | 46 ++- BVAR-1.0.0/BVAR/man/bv_fcast.Rd | 54 ++- BVAR-1.0.0/BVAR/man/bv_irf.Rd | 54 +-- BVAR-1.0.0/BVAR/man/bv_metropolis.Rd | 56 ++-- BVAR-1.0.0/BVAR/man/bv_minnesota.Rd | 93 +++--- BVAR-1.0.0/BVAR/man/bv_priors.Rd | 48 +-- BVAR-1.0.0/BVAR/man/bvar.Rd | 176 +++++++----- BVAR-1.0.0/BVAR/man/coda.Rd |only BVAR-1.0.0/BVAR/man/coef.bvar.Rd | 52 +-- BVAR-1.0.0/BVAR/man/companion.Rd |only BVAR-1.0.0/BVAR/man/density.bvar.Rd | 67 ++-- BVAR-1.0.0/BVAR/man/fitted.bvar.Rd | 55 ++-- BVAR-1.0.0/BVAR/man/fred_qd.Rd | 52 ++- BVAR-1.0.0/BVAR/man/fred_transform.Rd |only BVAR-1.0.0/BVAR/man/irf.bvar.Rd | 75 ++--- BVAR-1.0.0/BVAR/man/par_bvar.Rd |only BVAR-1.0.0/BVAR/man/plot.bvar.Rd | 73 ++--- BVAR-1.0.0/BVAR/man/plot.bvar_fcast.Rd | 86 +++--- BVAR-1.0.0/BVAR/man/plot.bvar_irf.Rd | 77 +++-- BVAR-1.0.0/BVAR/man/predict.bvar.Rd | 73 ++--- BVAR-1.0.0/BVAR/man/summary.bvar.Rd | 29 +- BVAR-1.0.0/BVAR/tests |only BVAR-1.0.0/BVAR/vignettes |only 84 files changed, 2798 insertions(+), 2231 deletions(-)
Title: Cox Mixed-Effects Models for Genome-Wide Association Studies
Description: Fast algorithms for fitting a Cox mixed-effects model for e.g., genome-wide association studies. See Liang He and Alexander Kulminski (2019) <doi:10.1101/729285>.
Author: Liang He
Maintainer: Liang He <liang.he@duke.edu>
Diff between coxmeg versions 1.0.10 dated 2020-03-20 and 1.0.11 dated 2020-05-05
DESCRIPTION | 12 +- MD5 | 18 +-- R/coxmeg.R | 17 ++- R/coxmeg_m.R | 16 ++- R/coxmeg_plink.R | 16 ++- R/fit_ppl.R | 18 ++- build/partial.rdb |binary inst/doc/COXMEG_example.Rmd | 2 inst/doc/COXMEG_example.html | 208 +++++++++++++++++++++---------------------- vignettes/COXMEG_example.Rmd | 2 10 files changed, 164 insertions(+), 145 deletions(-)
Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] (<https://orcid.org/0000-0003-4092-8228>),
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] (<https://orcid.org/0000-0003-0532-4824>),
Ken Andersen [aut, cph] (<https://orcid.org/0000-0002-8478-3430>),
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.0.0 dated 2020-04-04 and 2.0.1 dated 2020-05-05
DESCRIPTION | 6 +- MD5 | 67 +++++++++++++++++---------------- NAMESPACE | 2 NEWS.md | 28 ++++++++++++- R/MizerParams-class.R | 2 R/extension.R | 29 ++++++++++++++ R/newMultispeciesParams.R | 8 +-- R/project_methods.R | 8 +-- R/setFishing.R | 8 +++ R/setInitialValues.R | 16 ++++++- R/setInteraction.R | 14 +++--- R/setPredKernel.R | 2 R/setResource.R | 36 ++++++++--------- R/species_params.R | 16 ++++--- R/summary_methods.R | 8 ++- R/upgrade.R | 11 ++++- R/wrapper_functions.R | 2 data/NS_params.RData |binary man/emptyParams.Rd | 2 man/getEncounter.Rd | 2 man/mizerEncounter.Rd | 2 man/newMultispeciesParams.Rd | 18 ++++---- man/setInitialValues.Rd | 3 - man/setInteraction.Rd | 2 man/setParams.Rd | 12 ++--- man/setRateFunction.Rd | 15 +++++++ man/setResource.Rd | 14 +++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-MizerParams.R | 26 ------------ tests/testthat/test-extension.R | 14 ++++++ tests/testthat/test-setFishing.R |only tests/testthat/test-setInitialValues.R | 18 ++++++++ tests/testthat/test-setParams.R | 23 ----------- tests/testthat/test-setResource.R |only tests/testthat/test-species_params.R |only tests/testthat/test-summary_methods.R | 22 ++++++++++ 36 files changed, 273 insertions(+), 163 deletions(-)
Title: Detection of Statistically Significant Combinations of SNPs in
Association Mapping
Description: A significant pattern mining-based toolbox for region-based genome-wide association studies and higher-order epistasis analyses, implementing the methods described in Llinares-López et al. (2017) <doi:10.1093/bioinformatics/btx071>.
Author: Felipe Llinares-López [aut, cph],
Laetitia Papaxanthos [aut, cph],
Damian Roqueiro [aut, cph],
Matthew Baker [ctr],
Mikołaj Rybiński [ctr],
Uwe Schmitt [ctr],
Dean Bodenham [aut, cre, cph],
Karsten Borgwardt [aut, fnd, cph]
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>
Diff between CASMAP versions 0.6.0 dated 2018-07-18 and 0.6.1 dated 2020-05-05
DESCRIPTION | 6 MD5 | 14 - build/vignette.rds |binary inst/doc/intro.html | 167 ++++++++++--------- inst/include/FilterIntervals.h | 234 +++++++++++++-------------- inst/include/SignificantIntervalSearchFais.h | 4 inst/include/chi2.h | 66 +++---- inst/include/gamma.h | 26 +-- 8 files changed, 270 insertions(+), 247 deletions(-)
Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data.
Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU),
and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters
can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized
in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>,
Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>,
Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>,
Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, and
Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanovic [aut, cre]
Maintainer: Mladen Jovanovic <coach.mladen.jovanovic@gmail.com>
Diff between shorts versions 0.0.1 dated 2020-04-23 and 1.0.0 dated 2020-05-05
shorts-0.0.1/shorts/R/model_using_instant_velocity.R |only shorts-0.0.1/shorts/R/model_using_split_times.R |only shorts-0.0.1/shorts/man/figures/shorts-logo.png |only shorts-0.0.1/shorts/man/mixed_model_using_instant_velocity.Rd |only shorts-0.0.1/shorts/man/mixed_model_using_split_times.Rd |only shorts-0.0.1/shorts/man/model_using_instant_velocity.Rd |only shorts-0.0.1/shorts/man/model_using_split_times.Rd |only shorts-1.0.0/shorts/DESCRIPTION | 14 shorts-1.0.0/shorts/MD5 | 65 + shorts-1.0.0/shorts/NAMESPACE | 18 shorts-1.0.0/shorts/NEWS.md | 21 shorts-1.0.0/shorts/R/find_functions.R |only shorts-1.0.0/shorts/R/format_splits.R | 17 shorts-1.0.0/shorts/R/mixed_model_using_splits.R |only shorts-1.0.0/shorts/R/model_using_radar.R |only shorts-1.0.0/shorts/R/model_using_splits.R |only shorts-1.0.0/shorts/R/predict_functions.R | 78 +- shorts-1.0.0/shorts/README.md | 387 +++++++--- shorts-1.0.0/shorts/build |only shorts-1.0.0/shorts/data/radar_gun_data.rda |binary shorts-1.0.0/shorts/data/split_times.rda |binary shorts-1.0.0/shorts/inst/CITATION | 4 shorts-1.0.0/shorts/inst/doc |only shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-10-1.png |only shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-11-1.png |binary shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-12-1.png |only shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-14-1.png |only shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-4-1.png |binary shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-5-1.png |binary shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-7-1.png |binary shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-8-1.png |only shorts-1.0.0/shorts/man/figures/README-unnamed-chunk-9-1.png |binary shorts-1.0.0/shorts/man/figures/logo.png |only shorts-1.0.0/shorts/man/find_functions.Rd |only shorts-1.0.0/shorts/man/format_splits.Rd | 3 shorts-1.0.0/shorts/man/mixed_model_split_times.Rd |only shorts-1.0.0/shorts/man/mixed_model_using_radar.Rd |only shorts-1.0.0/shorts/man/model_split_times.Rd |only shorts-1.0.0/shorts/man/model_using_radar.Rd |only shorts-1.0.0/shorts/man/predict_kinematics.Rd | 64 + shorts-1.0.0/shorts/man/radar_gun_data.Rd | 6 shorts-1.0.0/shorts/man/split_times.Rd | 6 shorts-1.0.0/shorts/vignettes |only 43 files changed, 516 insertions(+), 167 deletions(-)
Title: Modern Logging for the R Ecosystem
Description: An effortless 'ndjson' (newline-delimited 'JSON') logger, with two primary
log-writing interfaces. It provides a set of wrappings for base R's
message(), warning(), and stop() functions that maintain identical
functionality, but also log the handler message to an 'ndjson' log file.
'loggit' also exports its internal 'loggit()' function for powerful and
configurable custom logging. No change in existing code is necessary to use
this package, and should only require additions to fully leverage the power
of the logging system. 'loggit' also provides a log reader for reading an
'ndjson' log file into a data frame, log rotation, and live echo of the
'ndjson' log messages to terminal 'stdout' for log capture by external
systems (like containers). 'loggit' is ideal for Shiny apps, data pipelines,
modeling work flows, and more. Please see the vignettes for detailed example
use cases.
Author: Ryan Price [cre, aut]
Maintainer: Ryan Price <ryapric@gmail.com>
Diff between loggit versions 1.2.0 dated 2020-03-16 and 2.0.0 dated 2020-05-05
loggit-1.2.0/loggit/man/agree_to_upcoming_loggit_updates.Rd |only loggit-1.2.0/loggit/man/getLogFile.Rd |only loggit-1.2.0/loggit/man/getTimestampFormat.Rd |only loggit-1.2.0/loggit/man/get_logs.Rd |only loggit-1.2.0/loggit/man/setLogFile.Rd |only loggit-1.2.0/loggit/man/setTimestampFormat.Rd |only loggit-2.0.0/loggit/DESCRIPTION | 34 +-- loggit-2.0.0/loggit/LICENSE | 2 loggit-2.0.0/loggit/MD5 | 53 +++- loggit-2.0.0/loggit/NAMESPACE | 14 - loggit-2.0.0/loggit/NEWS.md | 55 +++++ loggit-2.0.0/loggit/R/configurations.R | 91 +++----- loggit-2.0.0/loggit/R/handlers.R | 47 +--- loggit-2.0.0/loggit/R/json.R |only loggit-2.0.0/loggit/R/loggit.R | 128 +++--------- loggit-2.0.0/loggit/R/utils.R |only loggit-2.0.0/loggit/R/zzz.R | 16 - loggit-2.0.0/loggit/build |only loggit-2.0.0/loggit/inst |only loggit-2.0.0/loggit/man/get_logfile.Rd |only loggit-2.0.0/loggit/man/get_timestamp_format.Rd |only loggit-2.0.0/loggit/man/handlers.Rd | 39 --- loggit-2.0.0/loggit/man/loggit.Rd | 38 +-- loggit-2.0.0/loggit/man/read_logs.Rd |only loggit-2.0.0/loggit/man/read_ndjson.Rd |only loggit-2.0.0/loggit/man/rotate_logs.Rd |only loggit-2.0.0/loggit/man/set_logfile.Rd |only loggit-2.0.0/loggit/man/set_timestamp_format.Rd |only loggit-2.0.0/loggit/man/write_ndjson.Rd |only loggit-2.0.0/loggit/tests/testthat/helpers.R |only loggit-2.0.0/loggit/tests/testthat/test_handlers.R |only loggit-2.0.0/loggit/tests/testthat/test_json.R |only loggit-2.0.0/loggit/tests/testthat/test_loggit.R | 89 ++------ loggit-2.0.0/loggit/tests/testthat/test_utils.R |only loggit-2.0.0/loggit/vignettes |only 35 files changed, 267 insertions(+), 339 deletions(-)
Title: Grouped Statistical Analyses in a Tidy Way
Description: Collection of functions to run statistical tests
across all combinations of multiple grouping variables.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between groupedstats versions 0.2.2 dated 2020-04-05 and 1.0.0 dated 2020-05-05
DESCRIPTION | 10 MD5 | 24 - NAMESPACE | 8 NEWS.md | 7 R/grouped_aov.R | 23 - R/lm_effsize_ci.R | 118 ++---- README.md | 177 ++++----- man/figures/README-grouped_summary3-1.png |binary man/grouped_aov.Rd | 4 man/lm_effsize_ci.Rd | 23 - man/lm_effsize_standardizer.Rd | 15 tests/testthat/test-grouped_summary.R | 2 tests/testthat/test-lm_effsize_ci.R | 538 ------------------------------ 13 files changed, 179 insertions(+), 770 deletions(-)
Title: An Interface to Google Drive
Description: Manage Google Drive files from R.
Author: Lucy D'Agostino McGowan [aut],
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between googledrive versions 1.0.0 dated 2019-08-19 and 1.0.1 dated 2020-05-05
DESCRIPTION | 13 ++--- LICENSE | 4 - MD5 | 80 ++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 16 ++++++ R/dribble.R | 5 +- R/drive_auth.R | 1 R/drive_find.R | 5 ++ R/drive_get.R | 9 ++- R/drive_reveal_path.R | 2 R/drive_share.R | 24 +++++++++ R/drive_update.R | 2 R/drive_upload.R | 2 R/request_make.R | 6 +- R/sysdata.rda |binary R/utils.R | 5 ++ build/vignette.rds |binary inst/WORDLIST |only inst/doc/googledrive.html | 11 +--- man/as_dribble.Rd | 6 +- man/drive_auth.Rd | 15 ++++-- man/drive_auth_configure.Rd | 5 +- man/drive_cp.Rd | 3 - man/drive_create.Rd | 10 +++- man/drive_deauth.Rd | 5 +- man/drive_download.Rd | 9 ++- man/drive_find.Rd | 15 ++++-- man/drive_get.Rd | 18 +++++-- man/drive_has_token.Rd | 7 +- man/drive_mkdir.Rd | 10 +++- man/drive_mv.Rd | 3 - man/drive_put.Rd | 13 ++--- man/drive_reveal.Rd | 6 +- man/drive_share.Rd | 26 +++++++++- man/drive_token.Rd | 7 +- man/drive_upload.Rd | 11 +++- man/googledrive-package.Rd | 4 - man/request_generate.Rd | 14 ++++- man/request_make.Rd | 15 +++--- tests/spelling.R |only tests/testthat/test-drive_find.R | 8 +-- tests/testthat/test-generate_request.R | 5 +- 42 files changed, 263 insertions(+), 138 deletions(-)
Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.3.5 dated 2020-02-03 and 1.4.0 dated 2020-05-05
dispRity-1.3.5/dispRity/src/char.diff.c |only dispRity-1.3.5/dispRity/src/char.diff.hamming.c |only dispRity-1.4.0/dispRity/DESCRIPTION | 14 dispRity-1.4.0/dispRity/MD5 | 149 +++--- dispRity-1.4.0/dispRity/NAMESPACE | 5 dispRity-1.4.0/dispRity/NEWS.md | 19 dispRity-1.4.0/dispRity/R/adonis.dispRity.R | 13 dispRity-1.4.0/dispRity/R/adonis.dispRity_fun.R | 2 dispRity-1.4.0/dispRity/R/boot.matrix.R | 86 ++- dispRity-1.4.0/dispRity/R/boot.matrix_fun.R | 16 dispRity-1.4.0/dispRity/R/char.diff.R | 431 ++++++++++--------- dispRity-1.4.0/dispRity/R/char.diff_fun.R | 100 ++-- dispRity-1.4.0/dispRity/R/chrono.subsets.R | 94 ++-- dispRity-1.4.0/dispRity/R/chrono.subsets_fun.R | 249 ++++++---- dispRity-1.4.0/dispRity/R/custom.subsets.R | 32 - dispRity-1.4.0/dispRity/R/dispRity.R | 73 ++- dispRity-1.4.0/dispRity/R/dispRity.metric.R | 125 +++++ dispRity-1.4.0/dispRity/R/dispRity.utilities.R | 40 - dispRity-1.4.0/dispRity/R/dispRity_fun.R | 90 +++ dispRity-1.4.0/dispRity/R/get.bin.ages.R | 6 dispRity-1.4.0/dispRity/R/make.demo.data.R | 69 ++- dispRity-1.4.0/dispRity/R/make.metric.R | 29 - dispRity-1.4.0/dispRity/R/model.test_fun.R | 4 dispRity-1.4.0/dispRity/R/null.test_fun.R | 11 dispRity-1.4.0/dispRity/R/plot.char.diff.R |only dispRity-1.4.0/dispRity/R/plot.char.diff_fun.R |only dispRity-1.4.0/dispRity/R/plot.dispRity.R | 22 dispRity-1.4.0/dispRity/R/plot.dispRity_fun.R | 17 dispRity-1.4.0/dispRity/R/print.dispRity.R | 43 + dispRity-1.4.0/dispRity/R/sanitizing.R | 54 ++ dispRity-1.4.0/dispRity/R/slice.tree.R | 4 dispRity-1.4.0/dispRity/R/slice.tree_fun.R | 83 +-- dispRity-1.4.0/dispRity/R/summary.dispRity.R | 8 dispRity-1.4.0/dispRity/R/summary.dispRity_fun.R | 16 dispRity-1.4.0/dispRity/R/test.dispRity_fun.R | 8 dispRity-1.4.0/dispRity/R/tree.age.R | 2 dispRity-1.4.0/dispRity/R/tree.age_fun.R | 4 dispRity-1.4.0/dispRity/R/zzz.R | 2 dispRity-1.4.0/dispRity/data/BeckLee_ages.rda |binary dispRity-1.4.0/dispRity/data/BeckLee_disparity.rda |binary dispRity-1.4.0/dispRity/data/BeckLee_mat50.rda |binary dispRity-1.4.0/dispRity/data/BeckLee_mat99.rda |binary dispRity-1.4.0/dispRity/data/BeckLee_tree.rda |binary dispRity-1.4.0/dispRity/data/disparity.rda |binary dispRity-1.4.0/dispRity/inst/References.bib | 17 dispRity-1.4.0/dispRity/man/BeckLee.Rd | 4 dispRity-1.4.0/dispRity/man/BeckLee_disparity.Rd | 4 dispRity-1.4.0/dispRity/man/Claddis.ordination.Rd | 5 dispRity-1.4.0/dispRity/man/adonis.dispRity.Rd | 14 dispRity-1.4.0/dispRity/man/boot.matrix.Rd | 17 dispRity-1.4.0/dispRity/man/char.diff.Rd | 94 +++- dispRity-1.4.0/dispRity/man/check.morpho.Rd | 11 dispRity-1.4.0/dispRity/man/chrono.subsets.Rd | 6 dispRity-1.4.0/dispRity/man/custom.subsets.Rd | 2 dispRity-1.4.0/dispRity/man/dispRity.metric.Rd | 21 dispRity-1.4.0/dispRity/man/dispRity.through.time.Rd | 3 dispRity-1.4.0/dispRity/man/disparity.Rd | 4 dispRity-1.4.0/dispRity/man/dtt.dispRity.Rd | 11 dispRity-1.4.0/dispRity/man/extinction.subsets.Rd | 3 dispRity-1.4.0/dispRity/man/extract.dispRity.Rd | 9 dispRity-1.4.0/dispRity/man/make.metric.Rd | 4 dispRity-1.4.0/dispRity/man/matrix.dispRity.Rd | 10 dispRity-1.4.0/dispRity/man/model.test.Rd | 12 dispRity-1.4.0/dispRity/man/model.test.sim.Rd | 16 dispRity-1.4.0/dispRity/man/model.test.wrapper.Rd | 23 - dispRity-1.4.0/dispRity/man/null.test.Rd | 14 dispRity-1.4.0/dispRity/man/pair.plot.Rd | 13 dispRity-1.4.0/dispRity/man/plot.char.diff.Rd | 21 dispRity-1.4.0/dispRity/man/plot.dispRity.Rd | 29 + dispRity-1.4.0/dispRity/man/reduce.matrix.Rd | 3 dispRity-1.4.0/dispRity/man/rescale.dispRity.Rd | 3 dispRity-1.4.0/dispRity/man/sim.morpho.Rd | 13 dispRity-1.4.0/dispRity/man/slice.tree.Rd | 2 dispRity-1.4.0/dispRity/man/space.maker.Rd | 10 dispRity-1.4.0/dispRity/man/summary.dispRity.Rd | 12 dispRity-1.4.0/dispRity/man/test.dispRity.Rd | 14 dispRity-1.4.0/dispRity/src/bitwise.dist.c |only dispRity-1.4.0/dispRity/src/dispRity.h | 5 78 files changed, 1575 insertions(+), 774 deletions(-)
Title: Music Notation Syntax, Manipulation, Analysis and Transcription
in R
Description: Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing and analyzing musical information in R.
The music notation framework facilitates creating and analyzing music data in notation form.
Music data can be viewed, manipulated and analyzed while in different forms of representation based around different data structures: strings and data frames.
Each representation offers advantages over the other for different use cases.
Music syntax can be entered directly and represented in character strings to minimize the formatting overhead of data entry by using simple data structures, for example when wanting to quickly enter and transcribe short pieces of music to sheet music or tablature.
The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation.
The same music data can also be organized in tidy data frames, allowing for a more familiar and powerful approach to the analysis of large amounts of structured music data.
Functions are available for mapping seamlessly between these data structures and their representations of musical information.
The package also provides API wrapper functions for transcribing musical representations in R into guitar tablature ("tabs") and basic sheet music using the 'LilyPond' backend (<http://lilypond.org>).
'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax.
The package generates 'LilyPond' files from R code and can pass them to 'LilyPond' to be rendered into sheet music pdf files.
The package offers nominal MIDI file output support in conjunction with rendering sheet music.
The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>
Diff between tabr versions 0.4.2 dated 2020-03-17 and 0.4.3 dated 2020-05-05
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NAMESPACE | 2 ++ NEWS.md | 5 +++++ R/class_methods.R | 4 ++++ R/freq.R | 29 ++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/tabr-prog-chords.html | 32 ++++++++++++++++---------------- man/ratio_to_cents.Rd |only tests/testthat/test-freq.R | 16 ++++++++++++---- 10 files changed, 79 insertions(+), 32 deletions(-)
Title: Companion Software for the Coursera Statistics with R
Specialization
Description: Data and functions to support Bayesian and frequentist inference and decision making
for the Coursera Specialization "Statistics with R".
See <https://github.com/StatsWithR/statsr> for more information.
Author: Colin Rundel [aut],
Mine Cetinkaya-Rundel [aut],
Merlise Clyde [aut, cre],
David Banks [aut]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between statsr versions 0.1-0 dated 2018-05-08 and 0.2.0 dated 2020-05-05
statsr-0.1-0/statsr/R/BF_app.R |only statsr-0.1-0/statsr/R/bayes_single_mean_JZS.R |only statsr-0.1-0/statsr/R/bayes_single_mean_sim.R |only statsr-0.1-0/statsr/R/bayes_single_mean_theo.R |only statsr-0.1-0/statsr/R/tapwater.R |only statsr-0.1-0/statsr/R/zinc.R |only statsr-0.1-0/statsr/data/tapwater.rda |only statsr-0.1-0/statsr/data/zinc.rda |only statsr-0.1-0/statsr/man/BF_app.Rd |only statsr-0.1-0/statsr/man/figures |only statsr-0.1-0/statsr/man/tapwater.Rd |only statsr-0.1-0/statsr/man/zinc.Rd |only statsr-0.2.0/statsr/DESCRIPTION | 48 +--- statsr-0.2.0/statsr/LICENSE |only statsr-0.2.0/statsr/MD5 | 96 ++++---- statsr-0.2.0/statsr/NAMESPACE | 2 statsr-0.2.0/statsr/NEWS.md | 9 statsr-0.2.0/statsr/R/ames_sampling_dist.R | 14 - statsr-0.2.0/statsr/R/atheism.R | 2 statsr-0.2.0/statsr/R/bandit_posterior.R | 87 ++++---- statsr-0.2.0/statsr/R/bandit_sim.R | 35 --- statsr-0.2.0/statsr/R/bayes_inference.R | 248 ++--------------------- statsr-0.2.0/statsr/R/bayes_single_mean.R |only statsr-0.2.0/statsr/R/bayes_two_mean.R | 112 ++++++---- statsr-0.2.0/statsr/R/calc_streak.R | 2 statsr-0.2.0/statsr/R/credible_interval.R | 15 - statsr-0.2.0/statsr/R/globals.R |only statsr-0.2.0/statsr/R/inference.R | 27 -- statsr-0.2.0/statsr/R/plot_ss.R | 26 -- statsr-0.2.0/statsr/R/rep_sample_n.R | 5 statsr-0.2.0/statsr/R/rstudio.R | 3 statsr-0.2.0/statsr/R/statsr.R | 18 - statsr-0.2.0/statsr/README.md |only statsr-0.2.0/statsr/inst/lab.css | 121 ++++++----- statsr-0.2.0/statsr/man/allow_shiny.Rd | 5 statsr-0.2.0/statsr/man/ames.Rd | 6 statsr-0.2.0/statsr/man/ames_sampling_dist.Rd | 11 - statsr-0.2.0/statsr/man/arbuthnot.Rd | 6 statsr-0.2.0/statsr/man/atheism.Rd | 8 statsr-0.2.0/statsr/man/bandit_posterior.Rd | 14 - statsr-0.2.0/statsr/man/bandit_sim.Rd | 36 --- statsr-0.2.0/statsr/man/bayes_inference.Rd | 116 ++-------- statsr-0.2.0/statsr/man/brfss.Rd | 6 statsr-0.2.0/statsr/man/calc_streak.Rd | 4 statsr-0.2.0/statsr/man/credible_interval_app.Rd | 14 - statsr-0.2.0/statsr/man/evals.Rd | 6 statsr-0.2.0/statsr/man/inference.Rd | 59 ++--- statsr-0.2.0/statsr/man/kobe_basket.Rd | 6 statsr-0.2.0/statsr/man/mlb11.Rd | 6 statsr-0.2.0/statsr/man/nc.Rd | 6 statsr-0.2.0/statsr/man/nycflights.Rd | 6 statsr-0.2.0/statsr/man/plot_bandit_posterior.Rd | 11 - statsr-0.2.0/statsr/man/plot_ss.Rd | 11 - statsr-0.2.0/statsr/man/present.Rd | 6 statsr-0.2.0/statsr/man/rep_sample_n.Rd | 8 statsr-0.2.0/statsr/man/statsr.Rd | 19 - statsr-0.2.0/statsr/man/wage.Rd | 6 57 files changed, 405 insertions(+), 841 deletions(-)
Title: Spatial Management and Assessment of Demersal Resources for
Trawl Fisheries
Description: A tool for assessing bio-economic feedback in
different management scenarios (D'Andrea et al., 2020
<doi:10.1111/2041-210X.13394>). 'smartR' (Spatial Management and Assessment
of demersal Resources for Trawl fisheries) combines information from different
tasks gathered within the European Data Collection Framework for the fishery
sector. The 'smartR' package implements the SMART model (Russo et al., 2014
<doi:10.1371/journal.pone.0086222>), through the object-oriented
programming paradigm, and within this package it is possible to achieve the
complete set of analyses required by the SMART approach: from the editing and
formatting of the raw data; the construction and maintenance of coherent
datasets; the numerical and visual inspection of the generated metadata; to
the final simulation of management scenarios and the forecast of their
effects. The interaction between the user and the application could take
place through invocation of methods via the command line or could be entirely
committed to the graphical user interfaces (GUI).
Author: Lorenzo D'Andrea, Tommaso Russo, Antonio Parisi, Stefano Cataudella
Maintainer: Lorenzo D'Andrea <dandrea.lorenz@gmail.com>
Diff between smartR versions 0.62.0 dated 2018-11-30 and 0.62.3 dated 2020-05-05
smartR-0.62.0/smartR/inst/SMART_Logo.2.jpg |only smartR-0.62.3/smartR/DESCRIPTION | 23 smartR-0.62.3/smartR/MD5 | 39 smartR-0.62.3/smartR/NAMESPACE | 1 smartR-0.62.3/smartR/R/smart_class.R | 9739 +++++++++++++------------- smartR-0.62.3/smartR/R/smart_funct.R | 225 smartR-0.62.3/smartR/R/smart_gui.R | 2959 +++---- smartR-0.62.3/smartR/R/smart_plots.R | 137 smartR-0.62.3/smartR/build |only smartR-0.62.3/smartR/inst/doc |only smartR-0.62.3/smartR/inst/model/bertGrow.jags | 44 smartR-0.62.3/smartR/inst/model/gompGrow.jags | 44 smartR-0.62.3/smartR/inst/smartR_Workflow.png |only smartR-0.62.3/smartR/man/FishFleet.Rd | 452 - smartR-0.62.3/smartR/man/FisheryBySpecie.Rd | 192 smartR-0.62.3/smartR/man/SampleMap.Rd | 370 smartR-0.62.3/smartR/man/SmartProject.Rd | 436 - smartR-0.62.3/smartR/man/SurveyBySpecie.Rd | 196 smartR-0.62.3/smartR/man/smartR.Rd | 80 smartR-0.62.3/smartR/man/smartRgui.Rd | 48 smartR-0.62.3/smartR/vignettes |only 21 files changed, 7497 insertions(+), 7488 deletions(-)
Title: Iterative Solvers for (Sparse) Linear System of Equations
Description: Solving a system of linear equations is one of the most fundamental
computational problems for many fields of mathematical studies, such as
regression problems from statistics or numerical partial differential equations.
We provide basic stationary iterative solvers such as Jacobi, Gauss-Seidel,
Successive Over-Relaxation and SSOR methods. Nonstationary, also known as
Krylov subspace methods are also provided. Sparse matrix computation is also supported
in that solving large and sparse linear systems can be manageable using 'Matrix' package
along with 'RcppArmadillo'. For a more detailed description, see a book by Saad (2003)
<doi:10.1137/1.9780898718003>.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between Rlinsolve versions 0.3.0 dated 2018-07-14 and 0.3.1 dated 2020-05-05
DESCRIPTION | 17 ++++----- MD5 | 87 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 - NEWS.md |only R/aux_FISCH.R | 2 - R/auxiliary.R | 18 +++++++++ R/init.R | 27 +++++++++++++- R/lsolve_BICG.R | 3 + R/lsolve_BICGSTAB.R | 3 + R/lsolve_CG.R | 3 + R/lsolve_CGS.R | 3 + R/lsolve_CHEBY.R | 3 + R/lsolve_GMRES.R | 3 + R/lsolve_GS.R | 7 ++- R/lsolve_JACOBI.R | 3 + R/lsolve_QMR.R | 5 ++ R/lsolve_SOR.R | 3 + R/lsolve_SSOR.R | 3 + R/package-Rlinsolve.R | 7 ++- build/partial.rdb |binary man/Rlinsolve.Rd | 5 +- man/aux_FISCH.Rd | 2 - man/basic_GS.Rd | 12 +++++- man/basic_JACOBI.Rd | 13 ++++++- man/basic_SOR.Rd | 13 ++++++- man/basic_SSOR.Rd | 13 ++++++- man/krylov_BICG.Rd | 12 +++++- man/krylov_BICGSTAB.Rd | 12 +++++- man/krylov_CG.Rd | 13 ++++++- man/krylov_CGS.Rd | 13 ++++++- man/krylov_CHEBY.Rd | 13 ++++++- man/krylov_GMRES.Rd | 13 ++++++- man/krylov_QMR.Rd | 14 ++++++- src/Makevars | 2 - src/Makevars.win | 2 - src/krylov_bicg.cpp | 1 src/krylov_bicgstab.cpp | 1 src/krylov_cgs.cpp | 1 src/krylov_cheby.cpp | 1 src/krylov_gmres.cpp | 9 ++-- src/krylov_qmr.cpp | 1 src/method_gs.cpp | 1 src/method_jacobi.cpp | 1 src/method_sor.cpp | 1 src/method_ssor.cpp | 1 45 files changed, 266 insertions(+), 103 deletions(-)
Title: Compose Interoperable Analysis Pipelines & Put Them in
Production
Description: Enables data scientists to compose pipelines of analysis which consist of data manipulation, exploratory analysis & reporting, as well as modeling steps. Data scientists can use tools of their choice through an R interface, and compose interoperable pipelines between R, Spark, and Python.
Credits to Mu Sigma for supporting the development of the package.
Note - To enable pipelines involving Spark tasks, the package uses the 'SparkR' package.
The SparkR package needs to be installed to use Spark as an engine within a pipeline. SparkR is distributed natively with Apache Spark and is not distributed on CRAN. The SparkR version needs to directly map to the Spark version (hence the native distribution), and care needs to be taken to ensure that this is configured properly.
To install SparkR from Github, run the following command if you know the Spark version: 'devtools::install_github('apache/spark@v2.x.x', subdir='R/pkg')'.
The other option is to install SparkR by running the following terminal commands if Spark has already been installed: '$ export SPARK_HOME=/path/to/spark/directory && cd $SPARK_HOME/R/lib/SparkR/ && R -e "devtools::install('.')"'.
Author: Naren Srinivasan [aut],
Zubin Dowlaty [aut],
Sanjay [ctb],
Neeratyoy Mallik [ctb],
Anoop S [ctb],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between analysisPipelines versions 1.0.0 dated 2019-01-08 and 1.0.1 dated 2020-05-05
DESCRIPTION | 10 MD5 | 18 R/core-functions.R | 3 inst/doc/Analysis_pipelines_for_working_with_Python_functions.html | 379 +++- inst/doc/Analysis_pipelines_for_working_with_R_dataframes.html | 819 ++++++---- inst/doc/Analysis_pipelines_for_working_with_sparkR.html | 397 +++- inst/doc/Interoperable_Pipelines.html | 618 +++++-- inst/doc/Meta_Pipelines.html | 569 ++++-- inst/doc/Streaming_pipelines_for_working_Apache_Spark_Structured_Streaming.html | 535 ++++-- inst/doc/Using_pipelines_inside_shiny_widgets.html | 341 +++- 10 files changed, 2673 insertions(+), 1016 deletions(-)
More information about analysisPipelines at CRAN
Permanent link
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement. A new functionality is added in version 1.0.9 for estimating the time delay between doubly-lensed light curves observed in two bands.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, Aneta Siemiginowska, and Zhirui Hu
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.9 dated 2020-05-03 and 1.0.10 dated 2020-05-05
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/timedelay-package.Rd | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press).
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between GE versions 0.0.8 dated 2020-05-01 and 0.0.9 dated 2020-05-05
GE-0.0.8/GE/R/gemMoney_CES_3_2.R |only GE-0.0.8/GE/man/gemMoney_CES_3_2.Rd |only GE-0.0.9/GE/DESCRIPTION | 9 GE-0.0.9/GE/MD5 | 60 +-- GE-0.0.9/GE/NAMESPACE | 4 GE-0.0.9/GE/R/CES.R | 2 GE-0.0.9/GE/R/apply_expand.grid.R |only GE-0.0.9/GE/R/demand_coefficient.R | 27 - GE-0.0.9/GE/R/dst_plot.R | 3 GE-0.0.9/GE/R/gemInputOutputTable_2_8_4.R | 33 - GE-0.0.9/GE/R/gemInputOutputTable_5_4.R | 10 GE-0.0.9/GE/R/gemInputOutputTable_7_4.R | 16 GE-0.0.9/GE/R/gemInputOutputTable_8_8.R | 20 - GE-0.0.9/GE/R/gemInputOutputTable_CES_3_3.R | 10 GE-0.0.9/GE/R/gemInputOutputTable_Leontief_3_3.R | 10 GE-0.0.9/GE/R/gemInputOutputTable_easy_5_4.R | 12 GE-0.0.9/GE/R/gemMoney_3_2.R |only GE-0.0.9/GE/R/gemStandardInputOutputTable_7_4.R | 12 GE-0.0.9/GE/R/rate_to_beta.R | 11 GE-0.0.9/GE/R/sdm_dstl.R | 396 +++++++++++++++++--- GE-0.0.9/GE/man/CES.Rd | 1 GE-0.0.9/GE/man/apply_expand.grid.Rd |only GE-0.0.9/GE/man/demand_coefficient.Rd | 27 - GE-0.0.9/GE/man/gemInputOutputTable_2_8_4.Rd | 10 GE-0.0.9/GE/man/gemInputOutputTable_5_4.Rd | 10 GE-0.0.9/GE/man/gemInputOutputTable_7_4.Rd | 13 GE-0.0.9/GE/man/gemInputOutputTable_8_8.Rd | 11 GE-0.0.9/GE/man/gemInputOutputTable_CES_3_3.Rd | 9 GE-0.0.9/GE/man/gemInputOutputTable_Leontief_3_3.Rd | 9 GE-0.0.9/GE/man/gemInputOutputTable_easy_5_4.Rd | 11 GE-0.0.9/GE/man/gemMoney_3_2.Rd |only GE-0.0.9/GE/man/gemStandardInputOutputTable_7_4.Rd | 11 GE-0.0.9/GE/man/rate_to_beta.Rd | 11 GE-0.0.9/GE/man/sdm_dstl.Rd | 396 +++++++++++++++++--- 34 files changed, 926 insertions(+), 228 deletions(-)
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
for Earthquake Description
Description: Estimation of the components of an ETAS (Epidemic Type Aftershock Sequence) model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive). New version 2.0.0: covariates have been introduced to explain the effects of external factors on the induced seismicity; the parametrization has been changed; Chiodi, Adelfio (2017)<doi:10.18637/jss.v076.i03>.
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi <marcello.chiodi@unipa.it>
Diff between etasFLP versions 1.4.0 dated 2017-01-05 and 2.0.0 dated 2020-05-05
etasFLP-1.4.0/etasFLP/R/embedding.rect.cat.eps.R |only etasFLP-1.4.0/etasFLP/R/etas.mod2.R |only etasFLP-1.4.0/etasFLP/R/etasFLP-internal.R |only etasFLP-1.4.0/etasFLP/R/flp1.etas.nlm.R |only etasFLP-2.0.0/etasFLP/ChangeLog | 37 + etasFLP-2.0.0/etasFLP/DESCRIPTION | 23 etasFLP-2.0.0/etasFLP/MD5 | 76 +- etasFLP-2.0.0/etasFLP/NAMESPACE | 16 etasFLP-2.0.0/etasFLP/R/cat.select.R |only etasFLP-2.0.0/etasFLP/R/compare.etasclass.R | 9 etasFLP-2.0.0/etasFLP/R/embedding.rect.cat.epsNEW.R |only etasFLP-2.0.0/etasFLP/R/eqcat.R | 2 etasFLP-2.0.0/etasFLP/R/etas.mod2NEW.R |only etasFLP-2.0.0/etasFLP/R/etas.starting.R | 6 etasFLP-2.0.0/etasFLP/R/etasclass.R | 532 ++++++++++++-------- etasFLP-2.0.0/etasFLP/R/flp1.etas.nlmNEW.R |only etasFLP-2.0.0/etasFLP/R/flpkspace.R | 5 etasFLP-2.0.0/etasFLP/R/generaloptimizationNEW.R |only etasFLP-2.0.0/etasFLP/R/kde2d.integral.R | 24 etasFLP-2.0.0/etasFLP/R/kde2dnew.fortran.R | 40 - etasFLP-2.0.0/etasFLP/R/plot.eqcat.R | 16 etasFLP-2.0.0/etasFLP/R/plot.etasclass.R | 142 ++--- etasFLP-2.0.0/etasFLP/R/plot.profile.etasclass.R | 2 etasFLP-2.0.0/etasFLP/R/print.etasclass.R | 2 etasFLP-2.0.0/etasFLP/R/profile.etasclass.R | 62 -- etasFLP-2.0.0/etasFLP/R/summary.etasclass.R | 8 etasFLP-2.0.0/etasFLP/data/californiacatalog.RData |binary etasFLP-2.0.0/etasFLP/data/catalog.withcov.RData |only etasFLP-2.0.0/etasFLP/data/italycatalog.RData |binary etasFLP-2.0.0/etasFLP/inst/CITATION | 4 etasFLP-2.0.0/etasFLP/man/bwd.nrd.Rd | 12 etasFLP-2.0.0/etasFLP/man/catalog.withcov.Rd |only etasFLP-2.0.0/etasFLP/man/compare.etasclass.Rd | 4 etasFLP-2.0.0/etasFLP/man/eqcat.Rd | 21 etasFLP-2.0.0/etasFLP/man/etas.starting.Rd | 28 - etasFLP-2.0.0/etasFLP/man/etasFLP-internal.Rd | 23 etasFLP-2.0.0/etasFLP/man/etasFLP-package.Rd | 21 etasFLP-2.0.0/etasFLP/man/etasclass.Rd | 237 ++++++-- etasFLP-2.0.0/etasFLP/man/kde2dnew.fortran.Rd | 25 etasFLP-2.0.0/etasFLP/man/plot.etasclass.Rd | 24 etasFLP-2.0.0/etasFLP/man/profile.etasclass.Rd | 166 +++--- etasFLP-2.0.0/etasFLP/man/summary.etasclass.Rd | 126 +++- etasFLP-2.0.0/etasFLP/src/Makevars |only etasFLP-2.0.0/etasFLP/src/etasFLP.h |only etasFLP-2.0.0/etasFLP/src/fortran_etas_code.f90 | 462 +++-------------- etasFLP-2.0.0/etasFLP/src/init.c |only 46 files changed, 1054 insertions(+), 1101 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Export Data Frames to Excel 'xlsx' Format
Description: Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'.
Fast and no Java or Excel required.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
John McNamara [cph] (Author of libxlsxwriter (see AUTHORS and COPYRIGHT
files for details))
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between writexl versions 1.2 dated 2019-11-27 and 1.3 dated 2020-05-05
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 6 ++++++ R/write_xlsx.R | 15 +++++++++++++-- inst/WORDLIST | 4 ++++ man/write_xlsx.Rd | 6 +++++- src/include/xlsxwriter/common.h | 13 ++++++++----- src/libxlsxwriter/workbook.c | 16 ++++++++-------- src/write_xlsx.c | 14 +++++++++----- tests/testthat/test-performance.R | 1 + 10 files changed, 67 insertions(+), 34 deletions(-)
Title: Generalized Hyperbolic Distribution and Its Special Cases
Description: Detailed functionality for working
with the univariate and multivariate Generalized Hyperbolic
distribution and its special cases (Hyperbolic (hyp), Normal
Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t
and Gaussian distribution). Especially, it contains fitting
procedures, an AIC-based model selection routine, and functions
for the computation of density, quantile, probability, random
variates, expected shortfall and some portfolio optimization
and plotting routines as well as the likelihood ratio test. In
addition, it contains the Generalized Inverse Gaussian
distribution. See Chapter 3 of A. J. McNeil, R. Frey, and P. Embrechts.
Quantitative risk management: Concepts, techniques and tools.
Princeton University Press, Princeton (2005).
Author: Marc Weibel, David Luethi, Wolfgang Breymann
Maintainer: Marc Weibel <marc.weibel@quantsulting.ch>
Diff between ghyp versions 1.6.0 dated 2020-04-21 and 1.6.1 dated 2020-05-05
ChangeLog | 7 + DESCRIPTION | 12 +- MD5 | 23 ++-- NAMESPACE | 8 + R/ghyp-attribution.R |only R/ghypClasses.R | 54 +++++++++++ R/ghypGenericMethods.R | 111 ++++++++++++++++++++++- R/ghypPlots.R |only README.md | 2 build/vignette.rds |binary inst/doc/Generalized_Hyperbolic_Distribution.R | 1 inst/doc/Generalized_Hyperbolic_Distribution.pdf |binary man/ESghyp.attribution.Rd |only man/ghyp.attribution-class.Rd |only man/plot-ghyp.attribution.Rd |only 15 files changed, 196 insertions(+), 22 deletions(-)
Title: Fast Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis. Implements the method described in (Luu, 2016)
<DOI:10.1111/1755-0998.12592>.
Author: Keurcien Luu [aut],
Michael Blum [aut],
Florian Privé [aut, cre],
Eric Bazin [ctb],
Nicolas Duforet-Frebourg [ctb]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between pcadapt versions 4.3.1 dated 2020-02-28 and 4.3.3 dated 2020-05-05
DESCRIPTION | 17 ++++++++++------- MD5 | 21 ++++++++++++--------- NEWS.md |only R/bed2matrix.R | 4 ++-- R/pcadaptUtils.R | 2 +- R/plotUtils.R | 4 ++-- README.md | 40 ++++++++++++++++++---------------------- inst/CITATION |only inst/WORDLIST |only man/bed2matrix.Rd | 4 ++-- man/get.score.color.Rd | 2 +- man/plot.pcadapt.Rd | 2 +- man/scree_plot.Rd | 2 +- 13 files changed, 50 insertions(+), 48 deletions(-)
Title: Combination Matrix Axis for 'ggplot2' to Create 'UpSet' Plots
Description: Replace the standard x-axis in 'ggplots' with a combination matrix
to visualize complex set overlaps. 'UpSet' has introduced a new way to visualize
the overlap of sets as an alternative to Venn diagrams.
This package provides a simple way to produce such plots using 'ggplot2'.
In addition it can convert any categorical axis into a combination
matrix axis.
Author: Constantin Ahlmann-Eltze [aut, cre]
(<https://orcid.org/0000-0002-3762-068X>)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Diff between ggupset versions 0.2.1 dated 2020-03-29 and 0.3.0 dated 2020-05-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/axis_combmatrix.R | 34 ++++++++++++++-------------------- tests/testthat/test-axis_combmatrix.R | 5 +++++ 5 files changed, 32 insertions(+), 27 deletions(-)
Title: Bayesian t-Test
Description: Provides an Markov-Chain-Monte-Carlo algorithm for Bayesian t-tests on the effect size. The underlying Gibbs sampler is based on a two-component Gaussian mixture and approximates the posterior distributions of the effect size, the difference of means and difference of standard deviations. A posterior analysis of the effect size via the region of practical equivalence is provided, too. For more details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between bayest versions 1.1 dated 2019-12-13 and 1.2 dated 2020-05-05
DESCRIPTION | 13 MD5 | 6 R/bayest.R | 1434 ++++++++++++++++++++++++++++++++++-------------------- build/partial.rdb |binary 4 files changed, 921 insertions(+), 532 deletions(-)
Title: Quickly View Data Frames in 'Excel', Build Folder Paths and
Create Date Vectors
Description: Contains several useful navigation helper functions, including easily building
folder paths, quick viewing dataframes in 'Excel', creating date vectors and changing the
console prompt to reflect time.
Author: Nico Katzke [aut, cre]
Maintainer: Nico Katzke <nfkatzke@gmail.com>
Diff between rmsfuns versions 1.0.0.0 dated 2020-04-27 and 1.0.0.1 dated 2020-05-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Safe_Return.portfolio.R | 2 +- inst/doc/rmsfuns.html | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results and where your package stands in the
CRAN submission queue in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 1.1.5 dated 2020-04-07 and 1.2.1 dated 2020-05-05
DESCRIPTION | 12 ++--- MD5 | 28 ++++++------ NAMESPACE | 5 ++ NEWS.md | 7 +++ R/cran_details.R | 2 R/cran_flavors.R |only R/cran_results.R | 13 +++-- R/foghorn.R | 11 ++--- build/vignette.rds |binary inst/doc/foghorn.html | 58 ++++++++++++-------------- man/cran_details.Rd | 34 +++++++-------- man/cran_results.Rd | 34 +++++++-------- man/n_cran_flavors.Rd |only man/summary_cran_results.Rd | 8 +-- tests/testthat/test-foghorn.R | 72 +++++++++++++++++++++++++-------- tests/testthat/test-n_cran_platforms.R | 65 +++++++++++++++++++++-------- 16 files changed, 215 insertions(+), 134 deletions(-)
Title: Construction and Evaluation of Metamodels
Description: Estimation, validation and prediction of models of different types : linear models, additive models, MARS,PolyMARS and Kriging.
Author: D. Dupuy and C. Helbert
Maintainer: C. Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceEval versions 1.4 dated 2015-06-15 and 1.5 dated 2020-05-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 3 +-- 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Global Sensitivity Analysis in Physiologically Based Kinetic
Modeling
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic/toxicokinetic model with multivariate outputs. The package also provides some functions to check the convergence and sensitivity of model parameters.
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>),
Brad Reisfeld [aut],
Weihsueh A. Chiu [aut] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <nhsieh@cvm.tamu.edu>
Diff between pksensi versions 1.1.5 dated 2020-02-05 and 1.1.6 dated 2020-05-05
DESCRIPTION | 14 +++++----- MD5 | 30 +++++++++++------------ NEWS.md | 5 +++ R/check.R | 50 ++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/pbpk_apap.R | 30 +++++++++++------------ inst/doc/pbpk_apap.Rmd | 4 +-- inst/doc/pbpk_apap.html | 16 +++++------- inst/doc/pbtk1cpt.R | 62 ++++++++++++++++++++++++------------------------ inst/doc/pbtk1cpt.html | 12 +++------ man/check.Rd | 21 +++++++++++++--- man/compile_model.Rd | 8 ++++-- man/rfast99.Rd | 12 +++++++-- man/solve_fun.Rd | 22 +++++++++++++---- man/solve_mcsim.Rd | 38 ++++++++++++++++++++++++----- vignettes/pbpk_apap.Rmd | 4 +-- 16 files changed, 202 insertions(+), 126 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.4.3 dated 2019-12-20 and 1.4.4 dated 2020-05-05
DESCRIPTION | 23 ++++++++++++----------- MD5 | 16 +++++++++------- NAMESPACE | 6 ------ NEWS.md | 9 +++++++++ R/deprecated.R |only R/dim.R | 4 ++-- R/type-sum.R | 25 ++----------------------- build/pillar.pdf |binary man/deprecated.Rd |only man/type_sum.Rd | 5 +---- 10 files changed, 35 insertions(+), 53 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Relies on the easystats ecosystem (Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between correlation versions 0.2.0 dated 2020-04-09 and 0.2.1 dated 2020-05-05
DESCRIPTION | 6 +- MD5 | 22 +++++----- NEWS.md | 24 ++++++++++- R/cor_to_pcor.R | 13 ++++-- R/correlation.R | 79 ++++++++++++++++++++------------------ R/methods.easycorrelation.R | 3 + R/print.easycormatrix.R | 3 - man/cor_test.Rd | 19 ++++++--- man/correlation.Rd | 35 ++++++++++------ man/distance_mahalanobis.Rd | 68 ++++++++++++++++---------------- tests/testthat/test-cor_test.R | 7 ++- tests/testthat/test-cor_to_pcor.R | 10 ++-- 12 files changed, 174 insertions(+), 115 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Simulation tools for management strategy evaluation are provided for the 'DLMtool' operating model to inform data-rich fisheries.
'MSEtool' provides complementary assessment models of varying complexity with standardized reporting, diagnostic tools for evaluating
assessment models within closed-loop simulation, and helper functions for building more complex operating models and management procedures.
Author: Quang Huynh [aut],
Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
Chris Grandin [ctb] (iSCAM functions)
Maintainer: Tom Carruthers <t.carruthers@oceans.ubc.ca>
Diff between MSEtool versions 1.5.0 dated 2020-03-24 and 1.6.0 dated 2020-05-05
MSEtool-1.5.0/MSEtool/inst/include/DD_SS.hpp |only MSEtool-1.5.0/MSEtool/inst/include/cDD_SS.hpp |only MSEtool-1.5.0/MSEtool/man/Data-rich-MP.Rd |only MSEtool-1.6.0/MSEtool/DESCRIPTION | 8 MSEtool-1.6.0/MSEtool/MD5 | 139 ++-- MSEtool-1.6.0/MSEtool/NAMESPACE | 5 MSEtool-1.6.0/MSEtool/NEWS.md | 6 MSEtool-1.6.0/MSEtool/R/SRA_scope.R | 91 +- MSEtool-1.6.0/MSEtool/R/SRA_scope_data.R | 6 MSEtool-1.6.0/MSEtool/R/assess_DD.R | 254 ++----- MSEtool-1.6.0/MSEtool/R/assess_SCA.R | 13 MSEtool-1.6.0/MSEtool/R/assess_SCA2.R | 13 MSEtool-1.6.0/MSEtool/R/assess_SCA_Pope.R | 13 MSEtool-1.6.0/MSEtool/R/assess_SP.R | 14 MSEtool-1.6.0/MSEtool/R/assess_SSS.R |only MSEtool-1.6.0/MSEtool/R/assess_VPA.R | 22 MSEtool-1.6.0/MSEtool/R/assess_cDD.R | 201 +---- MSEtool-1.6.0/MSEtool/R/define_S4_class_SRA.R | 58 + MSEtool-1.6.0/MSEtool/R/define_S4_class_assess.R | 2 MSEtool-1.6.0/MSEtool/R/define_S4_class_profile.R | 20 MSEtool-1.6.0/MSEtool/R/report_DD_TMB.R | 64 - MSEtool-1.6.0/MSEtool/R/report_SCA.R | 59 - MSEtool-1.6.0/MSEtool/R/report_SCA_Pope.R | 55 - MSEtool-1.6.0/MSEtool/R/report_SP.R | 44 - MSEtool-1.6.0/MSEtool/R/report_SSS.R |only MSEtool-1.6.0/MSEtool/R/report_VPA.R | 42 - MSEtool-1.6.0/MSEtool/R/report_cDD.R | 44 - MSEtool-1.6.0/MSEtool/R/report_spict.R | 37 + MSEtool-1.6.0/MSEtool/R/z_MPs.R | 43 - MSEtool-1.6.0/MSEtool/build/vignette.rds |binary MSEtool-1.6.0/MSEtool/inst/doc/Delay_difference.Rmd | 4 MSEtool-1.6.0/MSEtool/inst/doc/Delay_difference.html | 8 MSEtool-1.6.0/MSEtool/inst/doc/MSEtool.R | 6 MSEtool-1.6.0/MSEtool/inst/doc/MSEtool.Rmd | 37 - MSEtool-1.6.0/MSEtool/inst/doc/MSEtool.html | 121 +-- MSEtool-1.6.0/MSEtool/inst/doc/SCA.Rmd | 4 MSEtool-1.6.0/MSEtool/inst/doc/SCA.html | 8 MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope.Rmd | 188 ----- MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope.html | 158 ---- MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope_eq.R |only MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope_eq.Rmd |only MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope_eq.html |only MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope_sel.R |only MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope_sel.Rmd |only MSEtool-1.6.0/MSEtool/inst/doc/SRA_scope_sel.html |only MSEtool-1.6.0/MSEtool/inst/doc/Surplus_production.Rmd | 4 MSEtool-1.6.0/MSEtool/inst/doc/Surplus_production.html | 8 MSEtool-1.6.0/MSEtool/inst/doc/VPA.Rmd | 4 MSEtool-1.6.0/MSEtool/inst/doc/VPA.html | 8 MSEtool-1.6.0/MSEtool/inst/doc/multiMSE.R | 18 MSEtool-1.6.0/MSEtool/inst/doc/multiMSE.Rmd | 21 MSEtool-1.6.0/MSEtool/inst/doc/multiMSE.html | 581 ++++++++--------- MSEtool-1.6.0/MSEtool/inst/include/DD.hpp | 81 +- MSEtool-1.6.0/MSEtool/inst/include/SCA.hpp | 3 MSEtool-1.6.0/MSEtool/inst/include/SCA2.hpp | 3 MSEtool-1.6.0/MSEtool/inst/include/SCA_Pope.hpp | 3 MSEtool-1.6.0/MSEtool/inst/include/SP.hpp | 3 MSEtool-1.6.0/MSEtool/inst/include/cDD.hpp | 37 - MSEtool-1.6.0/MSEtool/inst/include/functions.hpp | 2 MSEtool-1.6.0/MSEtool/man/Albacore_TwoFleet.Rd | 58 - MSEtool-1.6.0/MSEtool/man/Assessment-class.Rd | 296 ++++---- MSEtool-1.6.0/MSEtool/man/DD_TMB.Rd | 332 ++++----- MSEtool-1.6.0/MSEtool/man/Model-based-MP.Rd |only MSEtool-1.6.0/MSEtool/man/SRA-class.Rd | 119 ++- MSEtool-1.6.0/MSEtool/man/SRA_scope.Rd | 23 MSEtool-1.6.0/MSEtool/man/SSS.Rd |only MSEtool-1.6.0/MSEtool/man/VPA.Rd | 229 +++--- MSEtool-1.6.0/MSEtool/man/profile.Rd | 106 +-- MSEtool-1.6.0/MSEtool/src/MSEtool.cpp | 6 MSEtool-1.6.0/MSEtool/vignettes/Delay_difference.Rmd | 4 MSEtool-1.6.0/MSEtool/vignettes/MSEtool.Rmd | 37 - MSEtool-1.6.0/MSEtool/vignettes/SCA.Rmd | 4 MSEtool-1.6.0/MSEtool/vignettes/SRA_scope.Rmd | 188 ----- MSEtool-1.6.0/MSEtool/vignettes/SRA_scope_eq.Rmd |only MSEtool-1.6.0/MSEtool/vignettes/SRA_scope_sel.Rmd |only MSEtool-1.6.0/MSEtool/vignettes/Surplus_production.Rmd | 4 MSEtool-1.6.0/MSEtool/vignettes/VPA.Rmd | 4 MSEtool-1.6.0/MSEtool/vignettes/multiMSE.Rmd | 21 78 files changed, 1661 insertions(+), 2333 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-24 1.0-8
2016-03-03 1.0-7
2014-12-21 1.0-6
2014-02-24 1.0-5
2009-04-27 1.0-4
2009-03-31 1.0-3
2009-02-11 1.0-2
2008-12-15 1.0-1
2008-12-11 1.0