Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for
feature selection in high-dimensional regressions proposed in
Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>,
with support for multi-step adaptive MCP-net (MSAMNet) and
multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between msaenet versions 3.1 dated 2019-05-17 and 3.1.1 dated 2024-03-03
msaenet-3.1.1/msaenet/DESCRIPTION | 11 msaenet-3.1.1/msaenet/MD5 | 86 ++-- msaenet-3.1.1/msaenet/NEWS.md | 54 +- msaenet-3.1.1/msaenet/R/aenet.R | 25 - msaenet-3.1.1/msaenet/R/amnet.R | 25 - msaenet-3.1.1/msaenet/R/asnet.R | 25 - msaenet-3.1.1/msaenet/R/msaenet-eval.R | 12 msaenet-3.1.1/msaenet/R/msaenet-inspect.R | 60 +-- msaenet-3.1.1/msaenet/R/msaenet-package.R | 20 - msaenet-3.1.1/msaenet/R/msaenet-sim.R | 36 - msaenet-3.1.1/msaenet/R/msaenet-tune-glmnet.R | 25 - msaenet-3.1.1/msaenet/R/msaenet-tune-ncvreg.R | 53 +- msaenet-3.1.1/msaenet/R/msaenet-utils.R | 43 +- msaenet-3.1.1/msaenet/R/msaenet.R | 41 -- msaenet-3.1.1/msaenet/R/msamnet.R | 45 -- msaenet-3.1.1/msaenet/R/msasnet.R | 45 -- msaenet-3.1.1/msaenet/R/plot-msaenet.R | 112 ++--- msaenet-3.1.1/msaenet/R/predict-msaenet.R | 6 msaenet-3.1.1/msaenet/R/print-msaenet.R | 7 msaenet-3.1.1/msaenet/R/utils.R |only msaenet-3.1.1/msaenet/README.md | 97 ++-- msaenet-3.1.1/msaenet/build/partial.rdb |only msaenet-3.1.1/msaenet/build/vignette.rds |binary msaenet-3.1.1/msaenet/inst/CITATION | 24 - msaenet-3.1.1/msaenet/inst/doc/msaenet.R | 24 - msaenet-3.1.1/msaenet/inst/doc/msaenet.Rmd | 18 msaenet-3.1.1/msaenet/inst/doc/msaenet.html | 434 ++++++++++++---------- msaenet-3.1.1/msaenet/inst/logo |only msaenet-3.1.1/msaenet/man/aenet.Rd | 27 - msaenet-3.1.1/msaenet/man/amnet.Rd | 26 - msaenet-3.1.1/msaenet/man/asnet.Rd | 26 - msaenet-3.1.1/msaenet/man/figures |only msaenet-3.1.1/msaenet/man/msaenet-package.Rd | 32 - msaenet-3.1.1/msaenet/man/msaenet.Rd | 31 + msaenet-3.1.1/msaenet/man/msaenet.sim.binomial.Rd | 11 msaenet-3.1.1/msaenet/man/msaenet.sim.cox.Rd | 11 msaenet-3.1.1/msaenet/man/msaenet.sim.gaussian.Rd | 11 msaenet-3.1.1/msaenet/man/msaenet.sim.poisson.Rd | 11 msaenet-3.1.1/msaenet/man/msaenet.tune.glmnet.Rd | 17 msaenet-3.1.1/msaenet/man/msaenet.tune.ncvreg.Rd | 18 msaenet-3.1.1/msaenet/man/msamnet.Rd | 30 + msaenet-3.1.1/msaenet/man/msasnet.Rd | 30 + msaenet-3.1.1/msaenet/man/plot.msaenet.Rd | 44 +- msaenet-3.1.1/msaenet/vignettes/msaenet.Rmd | 18 msaenet-3.1/msaenet/LICENSE |only 45 files changed, 945 insertions(+), 726 deletions(-)
Title: Additional Themes, Theme Components and Utilities for 'ggplot2'
Description: A compilation of extra 'ggplot2' themes, scales and utilities, including a
spell check function for plot label fields and an overall emphasis on typography.
A copy of the 'Google' font 'Roboto Condensed' is also included.
Author: Bob Rudis [aut, cre] ,
Patrick Kennedy [ctb],
Philipp Reiner [ctb],
Dan Wilson [ctb] ,
Xavier Adam [ctb],
Google [cph] ,
IBM [cph] ,
Goldman Sachs [cph] ,
Impallari Type [cph] ,
Jacob Barnett [ctb],
Thomas J. Leeper [ctb] ,
Joris Meys [ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between hrbrthemes versions 0.8.0 dated 2020-03-06 and 0.8.7 dated 2024-03-03
hrbrthemes-0.8.0/hrbrthemes/R/ipsum-pdf.R |only hrbrthemes-0.8.0/hrbrthemes/R/ipsum.r |only hrbrthemes-0.8.0/hrbrthemes/R/tinyhand.R |only hrbrthemes-0.8.0/hrbrthemes/R/titillium-web.R |only hrbrthemes-0.8.0/hrbrthemes/build |only hrbrthemes-0.8.0/hrbrthemes/inst/doc |only hrbrthemes-0.8.0/hrbrthemes/inst/fonts/plex-sans |only hrbrthemes-0.8.0/hrbrthemes/inst/fonts/public-sans |only hrbrthemes-0.8.0/hrbrthemes/inst/fonts/roboto-slab |only hrbrthemes-0.8.0/hrbrthemes/inst/fonts/tinyhand |only hrbrthemes-0.8.0/hrbrthemes/inst/fonts/titillium-web |only hrbrthemes-0.8.0/hrbrthemes/inst/rmarkdown |only hrbrthemes-0.8.0/hrbrthemes/man/TinyHand.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/TitilliumWeb.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/import_tinyhand.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/import_titillium_web.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/ipsum.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/ipsum_pdf.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/theme_ipsum_tw.Rd |only hrbrthemes-0.8.0/hrbrthemes/man/theme_tinyhand.Rd |only hrbrthemes-0.8.0/hrbrthemes/vignettes |only hrbrthemes-0.8.7/hrbrthemes/DESCRIPTION | 32 +-- hrbrthemes-0.8.7/hrbrthemes/MD5 | 150 +++++---------- hrbrthemes-0.8.7/hrbrthemes/NAMESPACE | 27 +- hrbrthemes-0.8.7/hrbrthemes/R/color.r | 16 + hrbrthemes-0.8.7/hrbrthemes/R/econ-sans.R | 38 +-- hrbrthemes-0.8.7/hrbrthemes/R/ft.R | 22 +- hrbrthemes-0.8.7/hrbrthemes/R/goldmansans.R |only hrbrthemes-0.8.7/hrbrthemes/R/hrbrthemes-package.R | 2 hrbrthemes-0.8.7/hrbrthemes/R/inter.R |only hrbrthemes-0.8.7/hrbrthemes/R/modern.r | 22 +- hrbrthemes-0.8.7/hrbrthemes/R/plexsans.R | 43 +--- hrbrthemes-0.8.7/hrbrthemes/R/public-sans.R | 43 +--- hrbrthemes-0.8.7/hrbrthemes/R/roboto-condensed.r | 42 ++-- hrbrthemes-0.8.7/hrbrthemes/R/scales.r | 150 ++++++++++++--- hrbrthemes-0.8.7/hrbrthemes/R/theme-ipsum.r | 24 +- hrbrthemes-0.8.7/hrbrthemes/R/utils.r | 77 ------- hrbrthemes-0.8.7/hrbrthemes/R/zzz.r | 43 ++-- hrbrthemes-0.8.7/hrbrthemes/inst/COPYRIGHTS | 100 ++++++++++ hrbrthemes-0.8.7/hrbrthemes/inst/fonts/goldman-sans |only hrbrthemes-0.8.7/hrbrthemes/man/ArialNarrow.Rd | 4 hrbrthemes-0.8.7/hrbrthemes/man/EconSansCondensed.Rd | 8 hrbrthemes-0.8.7/hrbrthemes/man/GoldmanSans.Rd |only hrbrthemes-0.8.7/hrbrthemes/man/Inter.Rd |only hrbrthemes-0.8.7/hrbrthemes/man/PlexSans.Rd | 6 hrbrthemes-0.8.7/hrbrthemes/man/PublicSans.Rd | 10 - hrbrthemes-0.8.7/hrbrthemes/man/RobotoCondensed.Rd | 6 hrbrthemes-0.8.7/hrbrthemes/man/figures/README-an-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-ax1-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-ax2-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-ax3-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-ft-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-ps-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-rc-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-sc-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-sp-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/figures/README-tw-1.png |binary hrbrthemes-0.8.7/hrbrthemes/man/ft_cols.Rd | 6 hrbrthemes-0.8.7/hrbrthemes/man/gg_check.Rd | 2 hrbrthemes-0.8.7/hrbrthemes/man/hrbrthemes.Rd | 8 hrbrthemes-0.8.7/hrbrthemes/man/import_econ_sans.Rd | 6 hrbrthemes-0.8.7/hrbrthemes/man/import_goldman_sans.Rd |only hrbrthemes-0.8.7/hrbrthemes/man/import_inter.Rd |only hrbrthemes-0.8.7/hrbrthemes/man/import_plex_sans.Rd | 6 hrbrthemes-0.8.7/hrbrthemes/man/import_public_sans.Rd | 6 hrbrthemes-0.8.7/hrbrthemes/man/scale_ft.Rd | 29 ++ hrbrthemes-0.8.7/hrbrthemes/man/scale_ipsum.Rd | 29 ++ hrbrthemes-0.8.7/hrbrthemes/man/scale_x_percent.Rd | 13 + hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum.Rd | 2 hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum_es.Rd | 10 - hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum_gs.Rd |only hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum_inter.Rd |only hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum_ps.Rd | 10 - hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum_pub.Rd | 10 - hrbrthemes-0.8.7/hrbrthemes/man/theme_ipsum_rc.Rd | 8 hrbrthemes-0.8.7/hrbrthemes/tests/testthat/_snaps |only 76 files changed, 564 insertions(+), 446 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Recursive Partitioning ('RPART') or step wise regression models are fit. Nested cross validation (or analogous for the random forest) is used to estimate and compare performances between these models.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied with the 'path=TRUE' options when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by default.
When fitting not a relaxed lasso model but an elastic-net model, then the R-packages 'nestedcv' <https://cran.r-project.org/package=nestedcv>, 'glmnetSE' <http [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.4-2 dated 2024-02-08 and 0.4-3 dated 2024-03-03
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Title: Reconstruction Set Test
Description: Contains logic for sample-level variable set scoring using randomized reduced rank reconstruction error.
Frost, H. Robert (2023) "Reconstruction Set Test (RESET): a computationally efficient method for
single sample gene set testing based on randomized reduced rank reconstruction error" <doi:10.1101/2023.04.03.535366>.
Author: H. Robert Frost [aut, cre]
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between RESET versions 0.2.1 dated 2023-08-20 and 0.2.2 dated 2024-03-03
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 5 +++++ R/RESET.R | 11 ++++++++++- build/vignette.rds |binary inst/doc/RESET_PBMC3K_BioCarta_LogNormalization.pdf |binary inst/doc/RESET_pbmc_small.pdf |binary man/RESET-package.Rd | 2 +- 8 files changed, 26 insertions(+), 12 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.3.2 dated 2024-01-31 and 1.3.5 dated 2024-03-03
greeks-1.3.2/greeks/vignettes/Greeks_UI.png |only greeks-1.3.5/greeks/DESCRIPTION | 8 greeks-1.3.5/greeks/MD5 | 58 +-- greeks-1.3.5/greeks/R/BS_European_Greeks.R | 10 greeks-1.3.5/greeks/R/BS_Geometric_Asian_Greeks.R | 12 greeks-1.3.5/greeks/R/BS_Implied_Volatility.R | 15 greeks-1.3.5/greeks/R/BS_Malliavin_Asian_Greeks.R | 18 - greeks-1.3.5/greeks/R/Binomial_American_Greeks.R | 13 greeks-1.3.5/greeks/R/Greeks.R | 109 ++++++ greeks-1.3.5/greeks/R/Greeks_UI.R | 19 + greeks-1.3.5/greeks/R/Implied_Volatility.R | 17 greeks-1.3.5/greeks/R/Malliavin_Asian_Greeks.R | 20 + greeks-1.3.5/greeks/R/Malliavin_European_Greeks.R | 12 greeks-1.3.5/greeks/R/Malliavin_Geometric_Asian_Greeks.R | 23 + greeks-1.3.5/greeks/build/partial.rdb |only greeks-1.3.5/greeks/inst/doc/using_greeks.Rmd | 2 greeks-1.3.5/greeks/man/BS_European_Greeks.Rd | 140 ++++---- greeks-1.3.5/greeks/man/BS_Geometric_Asian_Greeks.Rd | 13 greeks-1.3.5/greeks/man/BS_Implied_Volatility.Rd | 16 greeks-1.3.5/greeks/man/BS_Malliavin_Asian_Greeks.Rd | 173 +++++----- greeks-1.3.5/greeks/man/Binomial_American_Greeks.Rd | 13 greeks-1.3.5/greeks/man/Greeks.Rd | 123 ++++++- greeks-1.3.5/greeks/man/Greeks_UI.Rd | 17 greeks-1.3.5/greeks/man/Implied_Volatility.Rd | 16 greeks-1.3.5/greeks/man/Malliavin_Asian_Greeks.Rd | 19 - greeks-1.3.5/greeks/man/Malliavin_European_Greeks.Rd | 12 greeks-1.3.5/greeks/man/Malliavin_Geometric_Asian_Greeks.Rd | 23 + greeks-1.3.5/greeks/man/figures |only greeks-1.3.5/greeks/src/Binomial_American_Greeks.cpp | 25 - greeks-1.3.5/greeks/tests/testthat/test-Binomial_American_Greeks.R | 43 -- greeks-1.3.5/greeks/vignettes/GreeksUI.png |only greeks-1.3.5/greeks/vignettes/using_greeks.Rmd | 2 32 files changed, 696 insertions(+), 275 deletions(-)
Title: Fish Migration Monitoring
Description: Graphical outputs and treatment for a database of fish pass
monitoring. It is a part of the 'STACOMI' open source project developed in
France by the French Office for Biodiversity institute to centralize
data obtained by fish pass monitoring. This version is available in French and
English. See <http://stacomir.r-forge.r-project.org/> for more information on
'STACOMI'.
Author: Cedric Briand [aut, cre],
Marion Legrand [aut],
Beaulaton Laurent [ctb],
Boulenger Clarisse [ctb],
Lafage Denis [ctb],
Grall Sebastien [ctb]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>
Diff between stacomiR versions 0.6.0.7 dated 2022-07-18 and 0.6.1 dated 2024-03-03
stacomiR-0.6.0.7/stacomiR/R/ref_period.R |only stacomiR-0.6.0.7/stacomiR/man/getvalue-ref_period-method.Rd |only stacomiR-0.6.0.7/stacomiR/man/ref_period-class.Rd |only stacomiR-0.6.0.7/stacomiR/tests/testthat/import_coe20092015.csv |only stacomiR-0.6.1/stacomiR/.Rinstignore | 3 stacomiR-0.6.1/stacomiR/DESCRIPTION | 34 stacomiR-0.6.1/stacomiR/MD5 | 197 stacomiR-0.6.1/stacomiR/NAMESPACE | 7 stacomiR-0.6.1/stacomiR/NEWS.md | 28 stacomiR-0.6.1/stacomiR/R/data.R | 6 stacomiR-0.6.1/stacomiR/R/fungraph.R | 29 stacomiR-0.6.1/stacomiR/R/ref_coe.R | 2 stacomiR-0.6.1/stacomiR/R/ref_dc.R | 11 stacomiR-0.6.1/stacomiR/R/report_annual.R | 24 stacomiR-0.6.1/stacomiR/R/report_dc.R | 2 stacomiR-0.6.1/stacomiR/R/report_df.R | 2 stacomiR-0.6.1/stacomiR/R/report_env.R | 11 stacomiR-0.6.1/stacomiR/R/report_ge_weight.R | 8 stacomiR-0.6.1/stacomiR/R/report_mig.R | 153 stacomiR-0.6.1/stacomiR/R/report_mig_env.R | 626 - stacomiR-0.6.1/stacomiR/R/report_mig_interannual.R | 3557 +++++----- stacomiR-0.6.1/stacomiR/R/report_mig_mult.R | 45 stacomiR-0.6.1/stacomiR/R/report_sample_char.R | 20 stacomiR-0.6.1/stacomiR/R/report_sea_age.R | 13 stacomiR-0.6.1/stacomiR/R/report_silver_eel.R | 36 stacomiR-0.6.1/stacomiR/R/report_species.R | 6 stacomiR-0.6.1/stacomiR/R/stacomi.R | 20 stacomiR-0.6.1/stacomiR/R/stacomiR-package.R | 6 stacomiR-0.6.1/stacomiR/build/vignette.rds |binary stacomiR-0.6.1/stacomiR/data/r_mig.rda |binary stacomiR-0.6.1/stacomiR/inst/doc/stacomir.R | 49 stacomiR-0.6.1/stacomiR/inst/doc/stacomir.Rmd | 19 stacomiR-0.6.1/stacomiR/inst/doc/stacomir.html | 641 + stacomiR-0.6.1/stacomiR/inst/examples/report_dc-example.R | 4 stacomiR-0.6.1/stacomiR/inst/examples/report_mig-example.R | 2 stacomiR-0.6.1/stacomiR/inst/examples/report_mig_interannual-example.R | 34 stacomiR-0.6.1/stacomiR/inst/examples/report_mig_mult-example.R | 6 stacomiR-0.6.1/stacomiR/inst/po/en@quot |only stacomiR-0.6.1/stacomiR/inst/po/fr/LC_MESSAGES/R-stacomiR.mo |binary stacomiR-0.6.1/stacomiR/man/calcule-report_mig-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/calcule-report_mig_mult-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/charge-ref_choice-method.Rd | 1 stacomiR-0.6.1/stacomiR/man/charge-report_mig_mult-method.Rd | 6 stacomiR-0.6.1/stacomiR/man/charge-report_sea_age-method.Rd | 4 stacomiR-0.6.1/stacomiR/man/charge-report_silver_eel-method.Rd | 6 stacomiR-0.6.1/stacomiR/man/choice_c-report_mig_mult-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/coef_durif.Rd | 2 stacomiR-0.6.1/stacomiR/man/connect-report_mig-method.Rd | 19 stacomiR-0.6.1/stacomiR/man/fn_connect_report_mig_interannual.Rd |only stacomiR-0.6.1/stacomiR/man/fun_report_mig_interannual.Rd | 9 stacomiR-0.6.1/stacomiR/man/fun_stage_durif.Rd | 2 stacomiR-0.6.1/stacomiR/man/model-report_ge_weight-method.Rd | 8 stacomiR-0.6.1/stacomiR/man/plot-report_dc-missing-method.Rd | 6 stacomiR-0.6.1/stacomiR/man/plot-report_df-missing-method.Rd | 6 stacomiR-0.6.1/stacomiR/man/plot-report_mig-ANY-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/plot-report_mig_interannual-missing-method.Rd | 37 stacomiR-0.6.1/stacomiR/man/plot-report_mig_mult-missing-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/plot-report_sea_age-missing-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/plot-report_silver_eel-missing-method.Rd | 2 stacomiR-0.6.1/stacomiR/man/plot-report_species-missing-method.Rd | 6 stacomiR-0.6.1/stacomiR/man/print-report_mig-method.Rd | 17 stacomiR-0.6.1/stacomiR/man/r_mig.Rd | 4 stacomiR-0.6.1/stacomiR/man/ref_choice-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_coe-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_dc-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_df-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_horodate-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_list-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_par-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_parqual-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_parquan-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_stage-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_taxa-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/ref_year-class.Rd | 1 stacomiR-0.6.1/stacomiR/man/report_dc-class.Rd | 4 stacomiR-0.6.1/stacomiR/man/report_mig-class.Rd | 2 stacomiR-0.6.1/stacomiR/man/report_mig_interannual-class.Rd | 38 stacomiR-0.6.1/stacomiR/man/report_mig_mult-class.Rd | 6 stacomiR-0.6.1/stacomiR/man/stacomi.Rd | 6 stacomiR-0.6.1/stacomiR/man/summary-report_mig_interannual-method.Rd | 4 stacomiR-0.6.1/stacomiR/man/supprime-report_mig_interannual-method.Rd | 4 stacomiR-0.6.1/stacomiR/man/write_database-report_mig-method.Rd | 7 stacomiR-0.6.1/stacomiR/po/R-fr.mo |only stacomiR-0.6.1/stacomiR/po/R-fr.po | 252 stacomiR-0.6.1/stacomiR/po/R-stacomiR.pot | 105 stacomiR-0.6.1/stacomiR/tests/testthat/helper.R | 67 stacomiR-0.6.1/stacomiR/tests/testthat/test-00-functions.R | 12 stacomiR-0.6.1/stacomiR/tests/testthat/test-00-stacomir.R | 42 stacomiR-0.6.1/stacomiR/tests/testthat/test-00-zrefclasses.R | 39 stacomiR-0.6.1/stacomiR/tests/testthat/test-01-report_mig_mult.R | 42 stacomiR-0.6.1/stacomiR/tests/testthat/test-02-report_mig.R | 98 stacomiR-0.6.1/stacomiR/tests/testthat/test-03-report_df.R | 10 stacomiR-0.6.1/stacomiR/tests/testthat/test-04-report_dc.R | 10 stacomiR-0.6.1/stacomiR/tests/testthat/test-05-report_sample_char.R | 12 stacomiR-0.6.1/stacomiR/tests/testthat/test-06-report_mig_interannual.R | 206 stacomiR-0.6.1/stacomiR/tests/testthat/test-07-report_sea_age.R | 22 stacomiR-0.6.1/stacomiR/tests/testthat/test-08-report_silver_eel.R | 31 stacomiR-0.6.1/stacomiR/tests/testthat/test-09-report_annual.R | 38 stacomiR-0.6.1/stacomiR/tests/testthat/test-10-report_env.R | 8 stacomiR-0.6.1/stacomiR/tests/testthat/test-11-report_mig_env.R | 12 stacomiR-0.6.1/stacomiR/tests/testthat/test-12-report_mig_char.R | 34 stacomiR-0.6.1/stacomiR/tests/testthat/test-13-report_species.R | 48 stacomiR-0.6.1/stacomiR/tests/testthat/test-14-report_ge_weight.R | 47 stacomiR-0.6.1/stacomiR/vignettes/stacomir.Rmd | 19 104 files changed, 3898 insertions(+), 3087 deletions(-)
Title: Running Operations for Vectors
Description: Lightweight library for rolling windows operations. Package enables
full control over the window length, window lag and a time indices. With a runner
one can apply any R function on a rolling windows. The package eases work with
equally and unequally spaced time series.
Author: Dawid Kaledkowski [aut, cre]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@gmail.com>
Diff between runner versions 0.4.3 dated 2023-03-21 and 0.4.4 dated 2024-03-03
DESCRIPTION | 8 MD5 | 80 - R/RcppExports.R | 141 +-- R/run.R | 235 ++--- R/run_by.R | 48 - R/utils.R | 34 README.md | 36 build/vignette.rds |binary inst/doc/apply_any_r_function.R | 19 inst/doc/apply_any_r_function.Rmd | 53 - inst/doc/apply_any_r_function.html | 84 - inst/doc/built-in_functions.R | 52 - inst/doc/built-in_functions.Rmd | 52 - inst/doc/built-in_functions.html | 73 - inst/doc/runner_examples.R | 51 - inst/doc/runner_examples.Rmd | 83 + inst/doc/runner_examples.html | 185 ++-- man/dot-check_unresolved_at.Rd | 2 man/dot-check_unresolved_difftime.Rd | 2 man/dot-is_datetime_valid.Rd | 2 man/dot-k_by.Rd | 4 man/fill_run.Rd | 6 man/lag_run.Rd | 2 man/length_run.Rd | 4 man/max_run.Rd | 18 man/mean_run.Rd | 12 man/min_run.Rd | 10 man/run_by.Rd | 50 - man/runner.Rd | 38 man/streak_run.Rd | 8 man/sum_run.Rd | 8 man/which_run.Rd | 8 man/window_run.Rd | 6 src/fill_run.cpp | 38 src/lag_run.cpp | 113 +- src/length_run.cpp | 45 - src/minmax_run.cpp | 34 src/runner.cpp | 1533 ++++++++++++++++++++++------------- vignettes/apply_any_r_function.Rmd | 53 - vignettes/built-in_functions.Rmd | 52 - vignettes/runner_examples.Rmd | 83 + 41 files changed, 1987 insertions(+), 1378 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and multivariate (<doi:10.1186/s12711-022-00730-w>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.5 dated 2023-11-21 and 2.2.6 dated 2024-03-03
DESCRIPTION | 8 +-- MD5 | 21 ++++----- R/RcppExports.R | 16 ++++++ R/cv.R | 25 +++++++++- man/bWGR.Rd | 4 - man/em.Rd | 8 +++ man/mvr.Rd | 6 ++ man/xtra.Rd | 7 +-- src/RcppExports.cpp | 67 ++++++++++++++++++++++++++-- src/mega20231111.cpp | 82 +++++++++++++++++++---------------- src/mega20240303.cpp |only src/wgr20210213.cpp | 118 +++++++++++++++++++++++++++++++++++++++++++++++++++ 12 files changed, 297 insertions(+), 65 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.10.2 dated 2024-02-24 and 0.10.3 dated 2024-03-03
DESCRIPTION | 6 - MD5 | 20 ++--- NEWS.md | 7 + R/get.R | 2 R/query.R | 159 +++++++++++++++++++++++++++++++++---------- R/zzz.R | 9 ++ inst/WORDLIST | 12 ++- inst/doc/nodbi-overview.html | 46 ++++++------ man/docdb_get.Rd | 2 man/docdb_query.Rd | 6 + tests/testthat/core-nodbi.R | 10 ++ 11 files changed, 199 insertions(+), 80 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 12.1. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood e [...truncated...]
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.3.3 dated 2024-01-21 and 0.3.4 dated 2024-03-03
DESCRIPTION | 6 - MD5 | 9 +- R/All.R | 209 ++++++++++++++------------------------------------------ R/RainAPI.R |only man/RainEA.Rd |only man/RainSEPA.Rd |only man/Zdists.Rd | 6 - 7 files changed, 66 insertions(+), 164 deletions(-)
Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder
reliability coefficient alpha and bootstrapped uncertainty estimates
(Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to
make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb]
Maintainer: Alexander Staudt <staudtlex@live.de>
Diff between icr versions 0.6.4 dated 2023-11-28 and 0.6.5 dated 2024-03-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot_icr.R | 2 ++ R/print_icr.R | 3 +++ 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Weighted and Directed Networks
Description: Assortativity coefficients, centrality measures,
and clustering coefficients for weighted and directed networks.
Rewiring unweighted networks with given assortativity coefficients.
Generating general preferential attachment networks.
Author: Yelie Yuan [aut, cre],
Tiandong Wang [aut],
Jun Yan [aut],
Panpan Zhang [aut]
Maintainer: Yelie Yuan <yelie.yuan@uconn.edu>
Diff between wdnet versions 1.2.2 dated 2023-09-06 and 1.2.3 dated 2024-03-03
DESCRIPTION | 25 ++++++------------- MD5 | 44 +++++++++++++++++----------------- NEWS.md | 5 +++ R/RcppExports.R | 2 - R/assortativity.R | 2 - R/centrality.R | 38 +++++++++++++++--------------- R/cls_rpacontrol.R | 2 - R/cls_wdnet.R | 2 - R/clustercoef.R | 4 +-- R/compile_pref.R | 2 - R/joint_dist.R | 2 - R/rewire.R | 18 +++++++------- R/rpa_control.R | 10 +++---- R/rpanet.R | 2 - R/rpanet_internal.R | 2 - R/utils.R | 2 - R/wdnet-package.R | 2 - README.md | 2 - inst/CITATION | 53 ++++++++++++++++++++++++++++++------------ man/centrality.Rd | 36 ++++++++++++++-------------- man/clustcoef.Rd | 2 - man/dprewire.Rd | 16 ++++++------ man/rpa_control_preference.Rd | 8 +++--- 23 files changed, 151 insertions(+), 130 deletions(-)
Title: Classes and Methods for 'IP' Addresses
Description: Provides S4 classes for Internet Protocol (IP) versions 4 and 6 addresses and efficient methods for 'IP' addresses comparison, arithmetic, bit manipulation and lookup. Both 'IPv4' and 'IPv6' arbitrary ranges are also supported as well as internationalized (IDN) domain lookup with and 'whois' query.
Author: Thomas Soubiran [aut, cre]
Maintainer: Thomas Soubiran <thomas.soubiran@univ-lille.fr>
Diff between IP versions 0.1.2 dated 2024-01-10 and 0.1.3 dated 2024-03-03
DESCRIPTION | 8 ++-- MD5 | 15 ++++--- R/Rip-ipv4.R | 101 +++++++++++++++++++++++++++++++++++++++++++++++++++- R/Rip-ipv6.R | 100 +++++++++++++++++++++++++++++++++++++-------------- man/varia.Rd | 13 +++++- src/Makevars.ucrt |only src/Makevars.win | 4 +- src/Rip-host-info.c | 12 ++++-- tools/winlibs.R | 23 +++++++---- 9 files changed, 220 insertions(+), 56 deletions(-)
Title: Download Data from Kobotoolbox to R
Description: Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
Author: Asitav Sen [aut, cre, cph]
Maintainer: Asitav Sen <hello@asitavsen.com>
Diff between KoboconnectR versions 1.2.1 dated 2022-10-18 and 1.2.2 dated 2024-03-03
DESCRIPTION | 11 MD5 | 52 +-- NEWS.md | 7 R/Koboconnect.R | 370 +++++++++++++--------------- R/other.R | 202 +++++++-------- build/vignette.rds |binary inst/doc/Usage.R | 30 +- inst/doc/Usage.Rmd | 30 +- inst/doc/Usage.html | 36 +- man/get_kobo_token.Rd | 4 man/kobo_df_download.Rd | 4 man/kobo_export_create.Rd | 4 man/kobo_exports.Rd | 4 man/kobo_media_downloader.Rd | 4 man/kobo_xls_dl.Rd | 4 man/kobotools_api.Rd | 6 man/kobotools_kpi_data.Rd | 6 tests/spelling.R | 9 tests/testthat/test-get_kobo_token.R | 14 - tests/testthat/test-kobo_df_download.R | 23 - tests/testthat/test-kobo_export_create.R | 70 +++-- tests/testthat/test-kobo_exports.R | 2 tests/testthat/test-kobo_media_downloader.R | 10 tests/testthat/test-kobo_xls_dl.R | 2 tests/testthat/test-kobotools_api.R | 17 - tests/testthat/test-kobotools_kpi_data.R | 26 - vignettes/Usage.Rmd | 30 +- 27 files changed, 504 insertions(+), 473 deletions(-)
Title: Structurally Guided Sampling
Description: Structurally guided sampling (SGS) approaches for airborne laser scanning (ALS; LIDAR). Primary functions provide means
to generate data-driven stratifications & methods for allocating samples. Intermediate functions for calculating and extracting important information
about input covariates and samples are also included. Processing outcomes are intended to help forest and environmental management
practitioners better optimize field sample placement as well as assess and augment existing sample networks in the context of data
distributions and conditions. ALS data is the primary intended use case, however any rasterized remote sensing data can be used,
enabling data-driven stratifications and sampling approaches.
Author: Tristan RH Goodbody [aut, cre, cph]
,
Nicholas C Coops [aut] ,
Martin Queinnec [aut]
Maintainer: Tristan RH Goodbody <goodbody.t@gmail.com>
Diff between sgsR versions 1.4.4 dated 2023-06-13 and 1.4.5 dated 2024-03-03
DESCRIPTION | 12 MD5 | 89 ++-- NEWS.md | 4 R/calculate_allocation_existing.R | 1 R/calculate_coobs.R | 2 R/calculate_lhsOpt.R | 2 R/calculate_pop.R | 2 R/calculate_sampsize.R | 6 R/sample_ahels.R | 2 R/sample_balanced.R | 10 R/sample_existing_balanced.R | 3 R/sample_existing_clhs.R | 1 R/sample_existing_srs.R | 1 R/sample_existing_strat.R | 2 R/utils-existing.R | 3 R/utils-vectorization.R | 4 R/utils-write.R | 3 inst/WORDLIST |only inst/doc/calculating.R | 8 inst/doc/calculating.html | 25 - inst/doc/sampling.R | 2 inst/doc/sampling.html | 656 +++++++++++++++++----------------- inst/doc/sgsR.R | 2 inst/doc/sgsR.html | 4 inst/doc/stratification.R | 2 inst/doc/stratification.html | 27 + man/calculate_allocation_existing.Rd | 128 +++--- man/calculate_coobs.Rd | 4 man/calculate_distance.Rd | 2 man/calculate_lhsOpt.Rd | 2 man/calculate_pcomp.Rd | 2 man/calculate_pop.Rd | 4 man/calculate_representation.Rd | 2 man/calculate_sampsize.Rd | 8 man/check_existing.Rd | 56 +- man/coords_existing.Rd | 36 - man/prepare_existing.Rd | 74 +-- man/sample_ahels.Rd | 2 man/sample_balanced.Rd | 7 man/sample_existing_balanced.Rd | 84 ++-- man/sample_existing_clhs.Rd | 90 ++-- man/sample_existing_srs.Rd | 48 +- man/sample_existing_strat.Rd | 70 +-- man/take_samples.Rd | 50 +- tests/spelling.R |only tests/testthat/Rplots.pdf |only tests/testthat/test-sample_balanced.R | 4 47 files changed, 791 insertions(+), 755 deletions(-)
Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One
Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in the console or in txt, html or pdf files. Download the package documentation (html index, README, NEWS, pdf manual, vignettes, source code, binaries) with a single instruction. Visualize the package dependencies and CRAN checks. Compare the package versions, unload and install the packages and their dependencies in a safe order. Explore CRAN archives. Use the above functions for task view maintenance. Access web search engines from the console thanks to 80+ bookmarks. All functions accept standard and non-standard evaluation.
Author: Patrice Kiener [aut, cre]
Maintainer: Patrice Kiener <rpackages@inmodelia.com>
Diff between RWsearch versions 5.0.5 dated 2022-02-22 and 5.1.4 dated 2024-03-03
DESCRIPTION | 12 MD5 | 45 NAMESPACE | 4 NEWS | 40 R/RWsearch-package.R |only R/a_intro.R | 159 -- R/h_R.R | 40 R/p_html.R | 2 R/p_inst.R | 11 R/s_crandb_tvdb.R | 14 R/s_sos.R | 29 build/vignette.rds |binary inst/doc/RWsearch-1-Introduction.html | 738 ++++++++--- inst/doc/RWsearch-2-Display-Download-Documentation.html | 708 +++++++---- inst/doc/RWsearch-3-Package-versions-and-dependencies.html | 539 ++++++-- inst/doc/RWsearch-4-Tools-for-taskviews.html | 836 ++++++++----- inst/doc/RWsearch-5-Web-search-engines.html | 259 +++- man/RWsearch-package.Rd | 6 man/crandb.Rd | 3 man/h_R.Rd | 6 man/p_html.Rd | 2 man/p_inst.Rd | 6 man/s_crandb_tvdb.Rd | 14 man/s_sos.Rd | 13 24 files changed, 2387 insertions(+), 1099 deletions(-)
Title: The CDK Libraries Packaged for R
Description: An R interface to the Chemistry Development Kit, a Java library
for chemoinformatics. Given the size of the library itself, this package is
not expected to change very frequently. To make use of the CDK within R, it is
suggested that you use the 'rcdk' package. Note that it is possible to directly
interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more
idiomatic way. The CDK library itself is released as LGPL and the sources can be
obtained from <https://github.com/cdk/cdk>.
Author: Rajarshi Guha [aut] ,
Zachary Charlop-Powers [cre] ,
CDK Project [ctb, cph]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdklibs versions 2.8 dated 2022-09-25 and 2.9 dated 2024-03-03
rcdklibs-2.8/rcdklibs/inst/cont/beam-core-1.3.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/beam-func-1.3.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-atomtype-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-charges-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-cip-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-control-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-core-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-ctab-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-data-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-datadebug-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-depict-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-dict-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-diff-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-extra-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-fingerprint-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-forcefield-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-formula-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-fragment-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-group-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-hash-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-inchi-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-interfaces-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-io-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-ioformats-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-ionpot-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-isomorphism-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-jniinchi-support-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-legacy-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-libiocml-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-libiomd-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-model-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-pcore-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-pdb-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-pdbcml-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsar-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsaratomic-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarbond-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarcml-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarionpot-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarmolecular-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarprotein-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-reaction-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-render-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-renderawt-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-renderbasic-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-renderextra-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-sdg-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-signature-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-silent-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-smarts-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-smiles-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-standard-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-structgen-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-tautomer-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-valencycheck-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cmlxom-4.3.jar |only rcdklibs-2.8/rcdklibs/inst/cont/euclid-2.3.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-api-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-core-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-darwin-aarch64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-darwin-x86-64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-linux-arm-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-linux-x86-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-linux-x86-64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-win32-x86-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-win32-x86-64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/joda-time-2.11.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/log4j-1.2-api-2.18.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/log4j-api-2.18.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/log4j-core-2.18.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/serializer-2.7.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xalan-2.7.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xercesImpl-2.12.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xml-apis-1.4.01.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xom-1.3.7.jar |only rcdklibs-2.9/rcdklibs/DESCRIPTION | 25 - rcdklibs-2.9/rcdklibs/MD5 | 159 ++++------ rcdklibs-2.9/rcdklibs/NAMESPACE | 4 rcdklibs-2.9/rcdklibs/NEWS.md | 6 rcdklibs-2.9/rcdklibs/R/rcdklibs.R | 3 rcdklibs-2.9/rcdklibs/README.md | 6 rcdklibs-2.9/rcdklibs/inst/cont/beam-core-1.3.5.jar |only rcdklibs-2.9/rcdklibs/inst/cont/beam-func-1.3.5.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-atomtype-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-charges-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-cip-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-control-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-core-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-ctab-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-data-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-datadebug-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-depict-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-dict-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-diff-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-extra-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-fingerprint-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-forcefield-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-formula-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-fragment-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-group-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-hash-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-inchi-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-interfaces-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-io-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-ioformats-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-ionpot-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-isomorphism-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-jniinchi-support-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-legacy-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-libiocml-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-libiomd-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-model-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-pcore-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-pdb-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qm-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsar-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsaratomic-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsarbond-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsarcml-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsarionpot-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsarmolecular-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-qsarprotein-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-reaction-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-render-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-renderawt-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-renderbasic-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-renderextra-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-sdg-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-signature-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-silent-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-smarts-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-smiles-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-standard-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-structgen-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-tautomer-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cdk-valencycheck-2.9.jar |only rcdklibs-2.9/rcdklibs/inst/cont/cmlxom-4.5.jar |only rcdklibs-2.9/rcdklibs/inst/cont/euclid-2.5.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-api-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-core-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-darwin-aarch64-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-darwin-x86-64-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-linux-aarch64-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-linux-arm-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-linux-x86-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-linux-x86-64-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-win32-x86-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/jna-inchi-win32-x86-64-1.2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/joda-time-2.12.5.jar |only rcdklibs-2.9/rcdklibs/inst/cont/log4j-1.2-api-2.20.0.jar |only rcdklibs-2.9/rcdklibs/inst/cont/log4j-api-2.20.0.jar |only rcdklibs-2.9/rcdklibs/inst/cont/log4j-core-2.20.0.jar |only rcdklibs-2.9/rcdklibs/inst/cont/xml-apis-1.0.b2.jar |only rcdklibs-2.9/rcdklibs/inst/cont/xom-1.3.9.jar |only rcdklibs-2.9/rcdklibs/man/figures |only 155 files changed, 107 insertions(+), 96 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions K1, K2, K3, K4 and K7 to characterize
distributions with left and right, symmetric or asymmetric fat tails in market
finance, neuroscience and other disciplines. Two algorithms to estimate with
a high accuracy distribution parameters, quantiles, value-at-risk and expected
shortfall. Include power hyperbolas and power hyperbolic functions.
Author: Patrice Kiener [aut, cre]
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.8-0 dated 2021-03-12 and 1.8-5 dated 2024-03-03
FatTailsR-1.8-0/FatTailsR/R/a_FatTailsR-package.R |only FatTailsR-1.8-0/FatTailsR/R/b_data.R |only FatTailsR-1.8-5/FatTailsR/DESCRIPTION | 15 +++-- FatTailsR-1.8-5/FatTailsR/MD5 | 65 +++++++++++----------- FatTailsR-1.8-5/FatTailsR/NEWS | 27 ++++++++- FatTailsR-1.8-5/FatTailsR/R/FatTailsR-package.R |only FatTailsR-1.8-5/FatTailsR/R/a_data.R |only FatTailsR-1.8-5/FatTailsR/R/b_fatreturns.R |only FatTailsR-1.8-5/FatTailsR/R/c_trigohp.R | 2 FatTailsR-1.8-5/FatTailsR/R/f_kiener1.R | 4 - FatTailsR-1.8-5/FatTailsR/R/g_kiener2.R | 4 - FatTailsR-1.8-5/FatTailsR/R/h_kiener3.R | 4 - FatTailsR-1.8-5/FatTailsR/R/i_kiener4.R | 4 - FatTailsR-1.8-5/FatTailsR/R/j_kiener7.R | 4 - FatTailsR-1.8-5/FatTailsR/R/m_laplaceroll.R | 12 ++-- FatTailsR-1.8-5/FatTailsR/inst/CITATION | 16 +++-- FatTailsR-1.8-5/FatTailsR/man/FatTailsR.Rd | 13 ++++ FatTailsR-1.8-5/FatTailsR/man/ckiener1234.Rd | 9 ++- FatTailsR-1.8-5/FatTailsR/man/dfData.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/elevate.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/exfit0.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/extractData.Rd | 56 +----------------- FatTailsR-1.8-5/FatTailsR/man/fatreturns.Rd | 5 + FatTailsR-1.8-5/FatTailsR/man/getDSdata.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/kiener1.Rd | 16 +++-- FatTailsR-1.8-5/FatTailsR/man/kiener2.Rd | 19 ++++-- FatTailsR-1.8-5/FatTailsR/man/kiener3.Rd | 22 ++++--- FatTailsR-1.8-5/FatTailsR/man/kiener4.Rd | 22 ++++--- FatTailsR-1.8-5/FatTailsR/man/kiener7.Rd | 4 - FatTailsR-1.8-5/FatTailsR/man/kmoments.Rd | 3 - FatTailsR-1.8-5/FatTailsR/man/laplacegaussnorm.Rd | 12 ++-- FatTailsR-1.8-5/FatTailsR/man/mData.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/pprobs0.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/tData.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/xData.Rd | 2 FatTailsR-1.8-5/FatTailsR/man/zData.Rd | 2 36 files changed, 189 insertions(+), 167 deletions(-)
Title: An Interface to Crypto Data Sources
Description: Allows you to connect to data sources across the
crypto ecosystem. This data can enable a range of activity such as
portfolio tracking, programmatic trading, or industry analysis.
Author: Trevor French [aut, cre]
Maintainer: Trevor French <FrenchTrevor@outlook.com>
Diff between cryptotrackr versions 1.1.0 dated 2023-12-07 and 1.2.0 dated 2024-03-03
cryptotrackr-1.1.0/cryptotrackr/R/helium.R |only cryptotrackr-1.1.0/cryptotrackr/man/helium_block_at_hash.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_block_at_height.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_block_descriptions.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_block_stats.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_blockchain_stats.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_height.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_token_supply.Rd |only cryptotrackr-1.1.0/cryptotrackr/man/helium_transactions_at_height.Rd |only cryptotrackr-1.2.0/cryptotrackr/DESCRIPTION | 8 cryptotrackr-1.2.0/cryptotrackr/MD5 | 93 ++++++---- cryptotrackr-1.2.0/cryptotrackr/R/binance_us.R | 19 -- cryptotrackr-1.2.0/cryptotrackr/R/blockchain_dot_com.R | 24 +- cryptotrackr-1.2.0/cryptotrackr/R/cex_io.R | 35 ++- cryptotrackr-1.2.0/cryptotrackr/R/coinbase.R | 74 ++++++- cryptotrackr-1.2.0/cryptotrackr/R/coingecko.R | 16 - cryptotrackr-1.2.0/cryptotrackr/R/coinlist.R | 11 - cryptotrackr-1.2.0/cryptotrackr/R/crypto_dot_com.R | 20 +- cryptotrackr-1.2.0/cryptotrackr/R/gemini.R | 12 - cryptotrackr-1.2.0/cryptotrackr/R/huobi.R | 4 cryptotrackr-1.2.0/cryptotrackr/R/kraken.R | 20 +- cryptotrackr-1.2.0/cryptotrackr/R/kucoin.R | 4 cryptotrackr-1.2.0/cryptotrackr/R/magic_eden.R | 20 +- cryptotrackr-1.2.0/cryptotrackr/R/nifty_gateway.R | 8 cryptotrackr-1.2.0/cryptotrackr/R/okcoin.R | 10 - cryptotrackr-1.2.0/cryptotrackr/R/paxos.R | 10 - cryptotrackr-1.2.0/cryptotrackr/R/solana.R |only cryptotrackr-1.2.0/cryptotrackr/README.md | 8 cryptotrackr-1.2.0/cryptotrackr/man/amberdata_spot_pairs.Rd | 86 ++++----- cryptotrackr-1.2.0/cryptotrackr/man/amberdata_spot_reference.Rd | 84 ++++----- cryptotrackr-1.2.0/cryptotrackr/man/cex_io_ohlcv.Rd | 3 cryptotrackr-1.2.0/cryptotrackr/man/cex_io_ticker.Rd | 3 cryptotrackr-1.2.0/cryptotrackr/man/coinbase_accounts.Rd | 11 - cryptotrackr-1.2.0/cryptotrackr/man/coinbase_api_call.Rd | 4 cryptotrackr-1.2.0/cryptotrackr/man/coinbase_candles.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/coingecko_vs_currencies.Rd | 2 cryptotrackr-1.2.0/cryptotrackr/man/coinlist_symbols.Rd | 3 cryptotrackr-1.2.0/cryptotrackr/man/figures/solana.png |only cryptotrackr-1.2.0/cryptotrackr/man/solana_api_call.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_assemble_key_pair.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_assemble_list.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_assemble_request_body.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_account_info.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_block.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_block_height.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_genesis_hash.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_health.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_identity.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_inflation_rate.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_recent_prioritization_fees.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_signature_for_address.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_slot.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_supply.Rd |only cryptotrackr-1.2.0/cryptotrackr/man/solana_get_version.Rd |only cryptotrackr-1.2.0/cryptotrackr/tests |only 55 files changed, 345 insertions(+), 247 deletions(-)
Title: Modeling Earthquake Data Using 'ETAS' Model
Description: Fits the space-time Epidemic Type Aftershock Sequence
('ETAS') model to earthquake catalogs using a stochastic 'declustering'
approach. The 'ETAS' model is a 'spatio-temporal' marked point process
model and a special case of the 'Hawkes' process. The package is based
on a Fortran program by 'Jiancang Zhuang'
(available at <http://bemlar.ism.ac.jp/zhuang/software.html>),
which is modified and translated into C++ and C such that it
can be called from R. Parallel computing with 'OpenMP' is possible
on supported platforms.
Author: Abdollah Jalilian [aut, cre] ,
Jiancang Zhuang [ctb]
Maintainer: Abdollah Jalilian <stat4aj@gmail.com>
Diff between ETAS versions 0.5.1 dated 2022-11-28 and 0.6.1 dated 2024-03-03
DESCRIPTION | 8 MD5 | 45 - R/RcppExports.R | 24 R/decluster.R | 5 R/etas.R | 23 R/etasfit.R | 4 R/lambda.R | 6 R/morisitaindex.R | 2 R/poisstest.R | 6 R/rates.R | 7 R/resid.etas.R | 3 README.md | 1 build/partial.rdb |binary build/vignette.rds |binary configure | 1415 ++++++++++++++++++++------------- configure.ac | 46 - inst/doc/usingETASWeapper.pdf |binary man/ETAS-internal.Rd | 23 man/etas.Rd | 16 man/resid.etas.Rd | 2 src/Makevars.in | 1 src/RcppExports.cpp | 60 - src/fitMP.cpp | 1794 +++++++++++++++++++++--------------------- src/funcs.h |only 24 files changed, 1960 insertions(+), 1531 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] ,
Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@icloud.com>
Diff between stochvol versions 3.2.3 dated 2023-11-26 and 3.2.4 dated 2024-03-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/plotting.R | 9 ++------- inst/doc/article.pdf |binary inst/doc/article2.pdf |binary 5 files changed, 9 insertions(+), 14 deletions(-)
Title: Ecological Inference by Linear Programming under Homogeneity
Description: Provides a bunch of algorithms based on linear programming for estimating, under
the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices)
using mainly aggregate data (from voting units).
References:
Pavía and Romero (2022) <doi:10.1177/00491241221092725>.
Pavía (2023) <doi:10.1007/s43545-023-00658-y>.
Pavía and Romero (2024) <doi:10.1093/jrsssa/qnae013>.
Pavía (2024) A local convergent ecological inference algorithm for RxC tables.
Pavía and Penadés (2024). A bottom-up approach for ecological inference.
Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>.
Acknowledgements:
The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.
Author: Jose M. Pavia [aut, cre] ,
Rafael Romero [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between lphom versions 0.3.5-4 dated 2024-02-20 and 0.3.5-5 dated 2024-03-03
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 8 ++++++++ R/adjust2integers.R | 14 +++++++------- R/auxiliar.R | 19 +++++++++++++++---- R/lclphom.R | 11 +++++++++-- R/lp_apriori.R | 11 +++++++++-- R/lphom.R | 11 +++++++++-- R/nslphom.R | 11 +++++++++-- R/plot.R | 3 ++- R/rslphom.R | 11 +++++++++-- R/tslphom.R | 11 +++++++++-- man/lclphom.Rd | 11 +++++++++-- man/lp_apriori.Rd | 11 +++++++++-- man/lphom.Rd | 11 +++++++++-- man/nslphom.Rd | 11 +++++++++-- man/rslphom.Rd | 11 +++++++++-- man/tslphom.Rd | 11 +++++++++-- 18 files changed, 161 insertions(+), 57 deletions(-)
Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo
standard errors of commonly used summary statistics. This package is modelled
on the 'simsum' user-written command in 'Stata' (White I.R., 2010
<https://www.stata-journal.com/article.html?article=st0200>), further extending
it with additional performance measures and functionality.
Author: Alessandro Gasparini [aut, cre]
,
Ian R. White [aut]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>
Diff between rsimsum versions 0.11.3 dated 2022-08-17 and 0.13.0 dated 2024-03-03
rsimsum-0.11.3/rsimsum/man/rsimsum.Rd |only rsimsum-0.13.0/rsimsum/DESCRIPTION | 11 rsimsum-0.13.0/rsimsum/MD5 | 140 - rsimsum-0.13.0/rsimsum/NEWS.md | 33 rsimsum-0.13.0/rsimsum/R/autoplot.multisimsum.R | 5 rsimsum-0.13.0/rsimsum/R/autoplot.simsum.R | 17 rsimsum-0.13.0/rsimsum/R/autoplot.summary.multisimsum.R | 4 rsimsum-0.13.0/rsimsum/R/autoplot.summary.simsum.R | 4 rsimsum-0.13.0/rsimsum/R/data.R | 2 rsimsum-0.13.0/rsimsum/R/performance.R | 63 rsimsum-0.13.0/rsimsum/R/plot-types.R | 56 rsimsum-0.13.0/rsimsum/R/print.multisimsum.R | 2 rsimsum-0.13.0/rsimsum/R/print.simsum.R | 2 rsimsum-0.13.0/rsimsum/R/print.summary.multisimsum.R | 8 rsimsum-0.13.0/rsimsum/R/print.summary.simsum.R | 8 rsimsum-0.13.0/rsimsum/R/rsimsum-package.R | 15 rsimsum-0.13.0/rsimsum/R/simsum.R | 47 rsimsum-0.13.0/rsimsum/R/summary.multisimsum.R | 9 rsimsum-0.13.0/rsimsum/R/summary.simsum.R | 3 rsimsum-0.13.0/rsimsum/R/tidy.R | 6 rsimsum-0.13.0/rsimsum/R/utils.R | 29 rsimsum-0.13.0/rsimsum/README.md | 28 rsimsum-0.13.0/rsimsum/build/partial.rdb |binary rsimsum-0.13.0/rsimsum/build/vignette.rds |binary rsimsum-0.13.0/rsimsum/data/tt.rda |binary rsimsum-0.13.0/rsimsum/inst/CITATION | 5 rsimsum-0.13.0/rsimsum/inst/doc/A-introduction.R | 6 rsimsum-0.13.0/rsimsum/inst/doc/A-introduction.Rmd | 48 rsimsum-0.13.0/rsimsum/inst/doc/A-introduction.html | 920 +++++----- rsimsum-0.13.0/rsimsum/inst/doc/B-relhaz.html | 646 +++---- rsimsum-0.13.0/rsimsum/inst/doc/C-plotting.R | 3 rsimsum-0.13.0/rsimsum/inst/doc/C-plotting.Rmd | 20 rsimsum-0.13.0/rsimsum/inst/doc/C-plotting.html | 413 ++-- rsimsum-0.13.0/rsimsum/inst/doc/D-nlp.html | 77 rsimsum-0.13.0/rsimsum/inst/doc/E-custom-inputs.R | 10 rsimsum-0.13.0/rsimsum/inst/doc/E-custom-inputs.Rmd | 14 rsimsum-0.13.0/rsimsum/inst/doc/E-custom-inputs.html | 529 ++--- rsimsum-0.13.0/rsimsum/inst/doc/F-rsimsumtidyverse.html | 161 + rsimsum-0.13.0/rsimsum/man/autoplot.multisimsum.Rd | 3 rsimsum-0.13.0/rsimsum/man/autoplot.simsum.Rd | 3 rsimsum-0.13.0/rsimsum/man/autoplot.summary.multisimsum.Rd | 3 rsimsum-0.13.0/rsimsum/man/autoplot.summary.simsum.Rd | 3 rsimsum-0.13.0/rsimsum/man/figures/README-ba-1.png |binary rsimsum-0.13.0/rsimsum/man/figures/README-density-1.png |binary rsimsum-0.13.0/rsimsum/man/figures/README-hex-1.png |binary rsimsum-0.13.0/rsimsum/man/figures/README-lolly-1.png |binary rsimsum-0.13.0/rsimsum/man/figures/README-nlp-1.png |binary rsimsum-0.13.0/rsimsum/man/figures/README-ridgeline-1.png |binary rsimsum-0.13.0/rsimsum/man/figures/README-zipper-1.png |binary rsimsum-0.13.0/rsimsum/man/multisimsum.Rd | 27 rsimsum-0.13.0/rsimsum/man/print.summary.multisimsum.Rd | 8 rsimsum-0.13.0/rsimsum/man/print.summary.simsum.Rd | 8 rsimsum-0.13.0/rsimsum/man/rsimsum-package.Rd |only rsimsum-0.13.0/rsimsum/man/simsum.Rd | 31 rsimsum-0.13.0/rsimsum/man/summary.multisimsum.Rd | 7 rsimsum-0.13.0/rsimsum/man/summary.simsum.Rd | 1 rsimsum-0.13.0/rsimsum/man/tidy.Rd | 4 rsimsum-0.13.0/rsimsum/man/tt.Rd | 2 rsimsum-0.13.0/rsimsum/tests/testthat/test-#15.R | 16 rsimsum-0.13.0/rsimsum/tests/testthat/test-#26.R | 6 rsimsum-0.13.0/rsimsum/tests/testthat/test-#41.R |only rsimsum-0.13.0/rsimsum/tests/testthat/test-#45.R |only rsimsum-0.13.0/rsimsum/tests/testthat/test-#47.R |only rsimsum-0.13.0/rsimsum/tests/testthat/test-#55.R |only rsimsum-0.13.0/rsimsum/tests/testthat/test-autoplot.R | 16 rsimsum-0.13.0/rsimsum/tests/testthat/test-ci.limits.R | 4 rsimsum-0.13.0/rsimsum/tests/testthat/test-multisimsum.R | 10 rsimsum-0.13.0/rsimsum/tests/testthat/test-performance-math.R | 4 rsimsum-0.13.0/rsimsum/tests/testthat/test-simsum.R | 10 rsimsum-0.13.0/rsimsum/tests/testthat/test-summary.multisimsum.R | 3 rsimsum-0.13.0/rsimsum/tests/testthat/test-summary.simsum.R | 1 rsimsum-0.13.0/rsimsum/vignettes/A-introduction.Rmd | 48 rsimsum-0.13.0/rsimsum/vignettes/C-plotting.Rmd | 20 rsimsum-0.13.0/rsimsum/vignettes/E-custom-inputs.Rmd | 14 74 files changed, 1983 insertions(+), 1613 deletions(-)
Title: Genome-Wide Association Study with SNP-Set Methods
Description: By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.
Author: Kosuke Hamazaki [aut, cre],
Hiroyoshi Iwata [aut, ctb]
Maintainer: Kosuke Hamazaki <hamazaki@ut-biomet.org>
Diff between RAINBOWR versions 0.1.33 dated 2023-09-12 and 0.1.35 dated 2024-03-03
DESCRIPTION | 8 MD5 | 60 ++--- NEWS.md | 16 + R/RGWAS.epistasis.R | 2 R/RGWAS.multisnp.R | 2 R/RGWAS.multisnp.interaction.R | 2 R/RGWAS.normal.R | 2 R/RGWAS.normal.interaction.R | 2 R/RGWAS.twostep.R | 2 R/RGWAS.twostep.epi.R | 2 R/Rice_geno_score.R | 2 R/SS_gwas.R | 2 R/functions_for_RGWAS.R | 46 ++++ R/other_useful_functions.R | 338 ++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/RAINBOWR.R | 24 +- inst/doc/RAINBOWR.html | 396 +++++++++++++++++++------------------- man/CalcThreshold.Rd | 11 - man/RAINBOWR.Rd | 2 man/RGWAS.epistasis.Rd | 2 man/RGWAS.multisnp.Rd | 2 man/RGWAS.multisnp.interaction.Rd | 2 man/RGWAS.normal.Rd | 2 man/RGWAS.normal.interaction.Rd | 2 man/RGWAS.twostep.Rd | 2 man/RGWAS.twostep.epi.Rd | 2 man/Rice_geno_score.Rd | 2 man/SS_gwas.Rd | 2 man/estNetwork.Rd | 39 +++ man/estPhylo.Rd | 35 +++ src/EMM_functions.cpp | 6 31 files changed, 609 insertions(+), 408 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.8.0.0 dated 2024-02-08 and 0.12.8.1.0 dated 2024-03-03
ChangeLog | 16 ++++ DESCRIPTION | 8 +- MD5 | 34 +++++----- README.md | 37 +++++++---- build/partial.rdb |binary build/vignette.rds |binary configure | 18 ++--- configure.ac | 2 inst/NEWS.Rd | 13 ++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_setup.hpp | 2 inst/include/armadillo_bits/op_norm_meat.hpp | 81 ++++++++++++++----------- inst/include/armadillo_bits/spop_norm_meat.hpp | 10 ++- inst/include/armadillo_bits/translate_blas.hpp | 12 +++ src/RcppArmadillo.cpp | 4 - src/fastLm.cpp | 4 - 18 files changed, 155 insertions(+), 88 deletions(-)
Title: A Compilation of Some Frequently Used R Functions
Description: The NOT functions and a simple compilation of various functions for easy usage. Shorthand code to save memory usage.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 0.6 dated 2023-12-03 and 0.7 dated 2024-03-03
quickcode-0.6/quickcode/R/cv.gm.R |only quickcode-0.6/quickcode/R/g.mean.R |only quickcode-0.6/quickcode/R/sd.gm.R |only quickcode-0.6/quickcode/R/tracker.R |only quickcode-0.6/quickcode/man/geo.cv.Rd |only quickcode-0.6/quickcode/man/geo.mean.Rd |only quickcode-0.6/quickcode/man/geo.sd.Rd |only quickcode-0.7/quickcode/DESCRIPTION | 6 quickcode-0.7/quickcode/MD5 | 55 +++--- quickcode-0.7/quickcode/NAMESPACE | 12 + quickcode-0.7/quickcode/NEWS.md | 14 + quickcode-0.7/quickcode/R/0.7_combo_func1.R |only quickcode-0.7/quickcode/R/0.7_equations2.R |only quickcode-0.7/quickcode/R/aaa.R | 17 + quickcode-0.7/quickcode/R/clean.R | 2 quickcode-0.7/quickcode/R/data_rep.R |only quickcode-0.7/quickcode/R/decommissionedPkg.R | 23 ++ quickcode-0.7/quickcode/R/equations1.R |only quickcode-0.7/quickcode/R/filename.R |only quickcode-0.7/quickcode/R/libraryAll.R | 8 quickcode-0.7/quickcode/R/mult.R |only quickcode-0.7/quickcode/R/not.empty.R | 18 ++ quickcode-0.7/quickcode/R/once.R | 9 - quickcode-0.7/quickcode/R/randomImage.R | 7 quickcode-0.7/quickcode/R/supervariable.R |only quickcode-0.7/quickcode/README.md | 86 ++++++++-- quickcode-0.7/quickcode/inst/doc/quickcode_r_introduction.html | 4 quickcode-0.7/quickcode/man/data_rep.Rd |only quickcode-0.7/quickcode/man/fAddDate.Rd |only quickcode-0.7/quickcode/man/genRandImg.Rd | 8 quickcode-0.7/quickcode/man/geostats.Rd |only quickcode-0.7/quickcode/man/machine_learning.Rd |only quickcode-0.7/quickcode/man/multiply.Rd |only quickcode-0.7/quickcode/man/newSuperVar.Rd |only quickcode-0.7/quickcode/man/not.exists.Rd |only quickcode-0.7/quickcode/man/rDecomPkg.Rd | 9 - quickcode-0.7/quickcode/man/read.csv.print.Rd |only quickcode-0.7/quickcode/man/read.table.print.Rd |only quickcode-0.7/quickcode/man/setOnce.Rd | 4 quickcode-0.7/quickcode/man/strsplit.bool.Rd |only quickcode-0.7/quickcode/man/strsplit.num.Rd |only 41 files changed, 224 insertions(+), 58 deletions(-)
Title: Polynomials in R
Description: Implements univariate polynomial operations in R, including
polynomial arithmetic, finding zeros, plotting, and some operations on
lists of polynomials.
Author: Bill Venables, with contribution by Kurt Hornik, Georgi Boshnakov and Brian Ripley.
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between PolynomF versions 2.0-5 dated 2022-05-01 and 2.0-8 dated 2024-03-03
DESCRIPTION | 12 MD5 | 16 R/Orthogonal_polynomials.R | 385 +++++------ R/RcppExports.R | 22 build/vignette.rds |binary inst/doc/polynomials.R | 348 +++++----- inst/doc/polynomials.Rmd | 875 ++++++++++++------------- inst/doc/polynomials.html | 1559 ++++++++++++++++++++++----------------------- vignettes/polynomials.Rmd | 875 ++++++++++++------------- 9 files changed, 2093 insertions(+), 1999 deletions(-)