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 3.1.1 dated 2024-03-03 and 3.1.2 dated 2024-05-10
msaenet-3.1.1/msaenet/inst/logo |only msaenet-3.1.2/msaenet/DESCRIPTION | 10 - msaenet-3.1.2/msaenet/MD5 | 44 +++--- msaenet-3.1.2/msaenet/NEWS.md | 115 ++++++++++++----- msaenet-3.1.2/msaenet/R/amnet.R | 2 msaenet-3.1.2/msaenet/R/asnet.R | 2 msaenet-3.1.2/msaenet/R/msamnet.R | 2 msaenet-3.1.2/msaenet/R/msasnet.R | 2 msaenet-3.1.2/msaenet/R/plot-msaenet.R | 26 ++- msaenet-3.1.2/msaenet/README.md | 6 msaenet-3.1.2/msaenet/build/partial.rdb |binary msaenet-3.1.2/msaenet/build/vignette.rds |binary msaenet-3.1.2/msaenet/inst/WORDLIST |only msaenet-3.1.2/msaenet/inst/doc/msaenet.R | 16 +- msaenet-3.1.2/msaenet/inst/doc/msaenet.Rmd | 106 +++++++++++---- msaenet-3.1.2/msaenet/inst/doc/msaenet.html | 43 +++--- msaenet-3.1.2/msaenet/man/amnet.Rd | 2 msaenet-3.1.2/msaenet/man/asnet.Rd | 2 msaenet-3.1.2/msaenet/man/figures/README-msaenet-1.png |binary msaenet-3.1.2/msaenet/man/figures/README-msamnet-1.png |binary msaenet-3.1.2/msaenet/man/figures/README-msasnet-1.png |binary msaenet-3.1.2/msaenet/man/msamnet.Rd | 2 msaenet-3.1.2/msaenet/man/msasnet.Rd | 2 msaenet-3.1.2/msaenet/vignettes/msaenet.Rmd | 106 +++++++++++---- 24 files changed, 323 insertions(+), 165 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.9.1 dated 2024-05-07 and 0.9.2 dated 2024-05-10
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 9 ++ R/lag.R | 2 R/sset.R | 15 +++ README.md | 230 ++++++++++++++++++++++++++++++------------------------------ man/lag.Rd | 2 man/sset.Rd | 15 +++ src/lag.cpp | 131 +++++++++++++++++++++------------- 9 files changed, 249 insertions(+), 177 deletions(-)
Title: Optimal Convex M-Estimation for Linear Regression via Antitonic
Score Matching
Description: Performs linear regression with respect to a data-driven convex loss function that is chosen to minimize the asymptotic covariance of the resulting M-estimator. The convex loss function is estimated in 5 steps: (1) form an initial OLS (ordinary least squares) or LAD (least absolute deviation) estimate of the regression coefficients; (2) use the resulting residuals to obtain a kernel estimator of the error density; (3) estimate the score function of the errors by differentiating the logarithm of the kernel density estimate; (4) compute the L2 projection of the estimated score function onto the set of decreasing functions; (5) take a negative antiderivative of the projected score function estimate. Newton's method (with Hessian modification) is then used to minimize the convex empirical risk function. Further details of the method are given in Feng et al. (2024) <doi:10.48550/arXiv.2403.16688>.
Author: Yu-Chun Kao [aut],
Min Xu [aut, cre],
Oliver Y. Feng [aut],
Richard J. Samworth [aut]
Maintainer: Min Xu <min.cut@gmail.com>
Diff between asm versions 0.1.0 dated 2024-04-25 and 0.2.0 dated 2024-05-10
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- R/asm.R | 24 +++++++++++++++++++----- man/predict.asm.Rd | 8 ++++++++ 4 files changed, 37 insertions(+), 13 deletions(-)
Title: Get Water Attributes Visually in R
Description: Provides methods to Get Water Attributes Visually in R ('gwavr'). This allows the user to point and click on areas within the United States and get back hydrological data, e.g. flowlines, catchments, basin boundaries, comids, etc.
Author: Joshua Erickson [aut, cre]
Maintainer: Joshua Erickson <joshualerickson@gmail.com>
Diff between gwavr versions 0.2.0 dated 2022-03-28 and 0.3.1 dated 2024-05-10
gwavr-0.2.0/gwavr/man/get_Basin.Rd |only gwavr-0.2.0/gwavr/man/get_NLDI.Rd |only gwavr-0.2.0/gwavr/man/get_NLDI_catchments.Rd |only gwavr-0.2.0/gwavr/man/get_whitebox_basin.Rd |only gwavr-0.2.0/gwavr/man/nldi_basin_function.Rd |only gwavr-0.3.1/gwavr/DESCRIPTION | 19 gwavr-0.3.1/gwavr/MD5 | 57 gwavr-0.3.1/gwavr/NAMESPACE | 11 gwavr-0.3.1/gwavr/NEWS.md | 20 gwavr-0.3.1/gwavr/R/basin.R | 284 +-- gwavr-0.3.1/gwavr/R/data.R |only gwavr-0.3.1/gwavr/R/globals.R | 4 gwavr-0.3.1/gwavr/R/modules.R | 1320 +++++++++++++- gwavr-0.3.1/gwavr/R/nhdplus.R | 268 +- gwavr-0.3.1/gwavr/R/nldi.R | 534 ++--- gwavr-0.3.1/gwavr/R/streamnetwork.R |only gwavr-0.3.1/gwavr/R/usgsdv.R |only gwavr-0.3.1/gwavr/R/usgsinst.R |only gwavr-0.3.1/gwavr/R/utils.R | 622 +++++- gwavr-0.3.1/gwavr/README.md | 142 - gwavr-0.3.1/gwavr/data |only gwavr-0.3.1/gwavr/inst/www/legend.png |only gwavr-0.3.1/gwavr/man/add_select_script.Rd |only gwavr-0.3.1/gwavr/man/basinMod.Rd | 14 gwavr-0.3.1/gwavr/man/basinModUI.Rd | 2 gwavr-0.3.1/gwavr/man/convert_sf_geocollection.Rd |only gwavr-0.3.1/gwavr/man/df_site_new.Rd |only gwavr-0.3.1/gwavr/man/get_basin_interactively.Rd | 120 - gwavr-0.3.1/gwavr/man/get_nhdplus_interactively.Rd | 94 gwavr-0.3.1/gwavr/man/get_nldi_interactively.Rd | 68 gwavr-0.3.1/gwavr/man/get_stream_network_interactively.Rd |only gwavr-0.3.1/gwavr/man/get_usgs_dv_interactively.Rd |only gwavr-0.3.1/gwavr/man/get_usgs_iv_interactively.Rd |only gwavr-0.3.1/gwavr/man/rename_geometry.Rd |only gwavr-0.3.1/gwavr/man/streamnetworkMod.Rd |only gwavr-0.3.1/gwavr/man/streamnetworkModUI.Rd |only gwavr-0.3.1/gwavr/man/usgsdvMod.Rd |only gwavr-0.3.1/gwavr/man/usgsdvModUI.Rd |only gwavr-0.3.1/gwavr/man/usgsinstMod.Rd |only gwavr-0.3.1/gwavr/man/usgsinstModUI.Rd |only gwavr-0.3.1/gwavr/tests/testthat |only gwavr-0.3.1/gwavr/tests/testthat.R |only 42 files changed, 2675 insertions(+), 904 deletions(-)
Title: Bayesian Spatial Analysis
Description: For Bayesian inference with spatial data, provides exploratory spatial analysis tools, multiple spatial model specifications, spatial model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health surveillance data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.
Author: Connor Donegan [aut, cre] ,
Mitzi Morris [ctb],
Amy Tims [ctb]
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Diff between geostan versions 0.6.0 dated 2024-04-16 and 0.6.1 dated 2024-05-10
DESCRIPTION | 10 - MD5 | 55 +++--- NAMESPACE | 5 NEWS.md | 17 ++ R/convenience-functions.R | 164 ++++++++++++++++---- R/geostan_fit-methods.R | 25 +-- R/moran.R | 4 R/raster-analysis.R | 2 README.md | 45 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/measuring-sa.Rmd | 10 - inst/doc/measuring-sa.html | 148 ++++++++++++------ inst/doc/raster-regression.html | 89 ++++++----- inst/doc/spatial-me-models.html | 246 ++++++++++++++++--------------- inst/doc/spatial-weights-matrix.R |only inst/doc/spatial-weights-matrix.Rmd |only inst/doc/spatial-weights-matrix.html |only man/edges.Rd | 19 ++ man/eigen_grid.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |binary man/geostan-package.Rd | 18 ++ man/mc.Rd | 2 man/me_diag.Rd | 2 man/moran_plot.Rd | 2 man/n_nbs.Rd |only man/predict.geostan_fit.Rd | 14 - man/shape2mat.Rd | 48 ++++-- man/sp_diag.Rd | 2 vignettes/measuring-sa.Rmd | 10 - vignettes/spatial-weights-matrix.Rmd |only 31 files changed, 590 insertions(+), 349 deletions(-)
Title: Bayesian Time-Stratified Population Analysis
Description: Provides advanced Bayesian methods to estimate
abundance and run-timing from temporally-stratified
Petersen mark-recapture experiments. Methods include
hierarchical modelling of the capture probabilities
and spline smoothing of the daily run size. Theory
described in Bonner and Schwarz (2011)
<doi:10.1111/j.1541-0420.2011.01599.x>.
Author: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com> and
Simon J Bonner <sbonner6@uwo.ca>
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between BTSPAS versions 2024.4.1 dated 2024-03-15 and 2024.5.9 dated 2024-05-10
DESCRIPTION | 8 ++-- MD5 | 30 +++++++++--------- NEWS.md | 7 +++- R/TimeStratPetersenDiagError.R | 2 - R/TimeStratPetersenDiagErrorWHChinook2_fit.R | 24 +++++++++----- R/TimeStratPetersenDiagErrorWHChinook_fit.R | 23 ++++++++----- R/TimeStratPetersenDiagErrorWHSteel_fit.R | 26 +++++++++------ R/TimeStratPetersenDiagError_fit.R | 38 ++++++++++++++--------- R/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.R | 25 +++++++++------ R/TimeStratPetersenNonDiagErrorNP_fit.R | 25 +++++++++------ R/TimeStratPetersenNonDiagError_fit.R | 24 +++++++++----- R/initial_values.R | 6 ++- R/zzz.R | 2 - build/partial.rdb |binary build/vignette.rds |binary man/TimeStratPetersenDiagError_fit.Rd | 5 ++- 16 files changed, 149 insertions(+), 96 deletions(-)
Title: Polynomial Spline Routines
Description: Routines for the polynomial spline fitting routines
hazard regression, hazard estimation with flexible tails, logspline,
lspec, polyclass, and polymars, by C. Kooperberg and co-authors.
Author: Charles Kooperberg [aut, cre],
Cleve Moler [ctb] ,
Jack Dongarra [ctb]
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between polspline versions 1.1.24 dated 2023-10-26 and 1.1.25 dated 2024-05-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/polspline.R | 56 ++++++++++++++++++++++++++++---------------------------- src/nlsd.c | 2 +- 4 files changed, 36 insertions(+), 36 deletions(-)
Title: Routines for Logspline Density Estimation
Description: Contains routines for logspline density estimation.
The function oldlogspline() uses the same algorithm as the logspline package
version 1.0.x; i.e. the Kooperberg and Stone (1992)
algorithm (with an improved interface). The recommended routine logspline()
uses an algorithm from Stone et al (1997) <DOI:10.1214/aos/1031594728>.
Author: Charles Kooperberg [aut, cre],
Cleve Moler [ctb] ,
Jack Dongarra [ctb]
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between logspline versions 2.1.21 dated 2023-10-26 and 2.1.22 dated 2024-05-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/logspline.R | 53 +++++++++++++++++++++++++++-------------------------- src/lsdall.c | 1 - src/nlsd.c | 2 +- 5 files changed, 36 insertions(+), 36 deletions(-)
Title: A Simple Author Handler for Scientific Writing
Description: Handles and formats author information in scientific writing
in 'R Markdown' and 'Quarto'. 'plume' provides easy-to-use and
flexible tools for injecting author metadata in 'YAML' headers as well
as generating author and contribution lists (among others) as strings
from tabular data.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between plume versions 0.2.3 dated 2024-01-29 and 0.2.4 dated 2024-05-10
plume-0.2.3/plume/R/credit_roles.R |only plume-0.2.3/plume/inst/CITATION |only plume-0.2.4/plume/DESCRIPTION | 6 plume-0.2.4/plume/MD5 | 59 plume-0.2.4/plume/NEWS.md | 56 plume-0.2.4/plume/R/checkers.R | 87 - plume-0.2.4/plume/R/context-binder.R | 2 plume-0.2.4/plume/R/credit-roles.R |only plume-0.2.4/plume/R/icon.R | 2 plume-0.2.4/plume/R/plume-handler.R | 25 plume-0.2.4/plume/R/plume-quarto.R | 18 plume-0.2.4/plume/R/plume.R | 50 plume-0.2.4/plume/R/utils.R | 2 plume-0.2.4/plume/R/yaml.R | 4 plume-0.2.4/plume/README.md | 12 plume-0.2.4/plume/build/vignette.rds |binary plume-0.2.4/plume/inst/doc/comprehensive-affiliation-schema.R | 8 plume-0.2.4/plume/inst/doc/comprehensive-affiliation-schema.html | 4 plume-0.2.4/plume/inst/doc/plume-workflow.R | 14 plume-0.2.4/plume/inst/doc/plume-workflow.Rmd | 16 plume-0.2.4/plume/inst/doc/plume-workflow.html | 22 plume-0.2.4/plume/inst/doc/plume.R | 78 plume-0.2.4/plume/inst/doc/plume.Rmd | 47 plume-0.2.4/plume/inst/doc/plume.html | 854 +++++----- plume-0.2.4/plume/inst/doc/working-in-other-languages.R | 2 plume-0.2.4/plume/inst/doc/working-in-other-languages.html | 4 plume-0.2.4/plume/tests/testthat/helper-plume.R | 8 plume-0.2.4/plume/tests/testthat/test-get-orcids.R | 2 plume-0.2.4/plume/tests/testthat/test-icon.R | 2 plume-0.2.4/plume/tests/testthat/test-set-status.R | 5 plume-0.2.4/plume/vignettes/plume-workflow.Rmd | 16 plume-0.2.4/plume/vignettes/plume.Rmd | 47 32 files changed, 730 insertions(+), 722 deletions(-)
Title: Model-Free Functional Chi-Squared and Exact Tests
Description: Statistical hypothesis testing methods for
inferring model-free functional dependency using asymptotic
chi-squared or exact distributions. Functional test
statistics are asymmetric and functionally optimal, unique
from other related statistics. Tests in this package reveal
evidence for causality based on the causality-by-
functionality principle. They include asymptotic functional
chi-squared tests (Zhang & Song 2013) <doi:10.48550/arXiv.1311.2707>,
an adapted functional chi-squared test (Kumar & Song 2022)
<doi:10.1093/bioinformatics/btac206>,
and an exact functional test (Zhong & Song 2019)
<doi:10.1109/TCBB.2018.2809743> (Nguyen et al. 2020)
<doi:10.24963/ijcai.2020/372>. The normalized functional
chi-squared test was used by Best Performer 'NMSUSongLab'
in HPN-DREAM (DREAM8) Breast Cancer Network Inference
Challenges (Hill et al. 2016) <doi:10.1038/nmeth.3773>. A
function index (Zhong & Song 2019)
<doi:10.1186/s12920-019-0565-9> ( [...truncated...]
Author: Yang Zhang [aut],
Hua Zhong [aut] ,
Hien Nguyen [aut] ,
Ruby Sharma [aut] ,
Sajal Kumar [aut] ,
Yiyi Li [aut] ,
Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.5.3 dated 2023-05-25 and 2.5.4 dated 2024-05-10
FunChisq-2.5.3/FunChisq/src/EFTNetwork.cpp |only FunChisq-2.5.3/FunChisq/src/EFTNetwork.h |only FunChisq-2.5.3/FunChisq/src/EFT_DQP.cpp |only FunChisq-2.5.3/FunChisq/src/EFT_DQP.h |only FunChisq-2.5.4/FunChisq/DESCRIPTION | 18 FunChisq-2.5.4/FunChisq/MD5 | 40 - FunChisq-2.5.4/FunChisq/NEWS.md | 36 + FunChisq-2.5.4/FunChisq/build/partial.rdb |binary FunChisq-2.5.4/FunChisq/build/vignette.rds |binary FunChisq-2.5.4/FunChisq/inst/doc/adapted.fun.chisq.test.R | 12 FunChisq-2.5.4/FunChisq/inst/doc/adapted.fun.chisq.test.html | 238 ++++----- FunChisq-2.5.4/FunChisq/inst/doc/exact.fun.test.html | 53 +- FunChisq-2.5.4/FunChisq/inst/doc/patterns.html | 276 +++++------ FunChisq-2.5.4/FunChisq/man/EFT.Rd | 2 FunChisq-2.5.4/FunChisq/src/fastEnu.cpp |only FunChisq-2.5.4/FunChisq/src/fastEnu.h |only FunChisq-2.5.4/FunChisq/src/fastEnuNode.cpp |only FunChisq-2.5.4/FunChisq/src/fastEnuNode.h |only FunChisq-2.5.4/FunChisq/src/main.cpp | 12 FunChisq-2.5.4/FunChisq/tests/testthat/test_AdpFunChisq.R | 39 - FunChisq-2.5.4/FunChisq/tests/testthat/test_EFT.R | 20 FunChisq-2.5.4/FunChisq/tests/testthat/test_FunChisq.R | 14 FunChisq-2.5.4/FunChisq/tests/testthat/test_NoiseModel.R | 2 FunChisq-2.5.4/FunChisq/tests/testthat/test_conditional_FC.R | 36 - FunChisq-2.5.4/FunChisq/tests/testthat/test_simulate.R | 23 25 files changed, 438 insertions(+), 383 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.0.3 dated 2024-03-18 and 5.1.0 dated 2024-05-10
Seurat-5.0.3/Seurat/tests/testdata/visium/raw_probe_bc_matrix.h5 |only Seurat-5.1.0/Seurat/DESCRIPTION | 14 Seurat-5.1.0/Seurat/MD5 | 161 ++-- Seurat-5.1.0/Seurat/NAMESPACE | 7 Seurat-5.1.0/Seurat/NEWS.md | 18 Seurat-5.1.0/Seurat/R/convenience.R | 12 Seurat-5.1.0/Seurat/R/differential_expression.R | 2 Seurat-5.1.0/Seurat/R/generics.R | 2 Seurat-5.1.0/Seurat/R/integration.R | 28 Seurat-5.1.0/Seurat/R/integration5.R | 4 Seurat-5.1.0/Seurat/R/objects.R | 106 ++- Seurat-5.1.0/Seurat/R/preprocessing.R | 329 +++++++--- Seurat-5.1.0/Seurat/R/preprocessing5.R | 5 Seurat-5.1.0/Seurat/R/reexports.R | 8 Seurat-5.1.0/Seurat/R/sketching.R | 13 Seurat-5.1.0/Seurat/R/tree.R | 42 - Seurat-5.1.0/Seurat/R/utilities.R | 140 ++-- Seurat-5.1.0/Seurat/R/visualization.R | 148 +++- Seurat-5.1.0/Seurat/build/Seurat.pdf |binary Seurat-5.1.0/Seurat/build/stage23.rdb |binary Seurat-5.1.0/Seurat/man/AddAzimuthResults.Rd | 1 Seurat-5.1.0/Seurat/man/AddAzimuthScores.Rd | 1 Seurat-5.1.0/Seurat/man/BridgeCellsRepresentation.Rd | 1 Seurat-5.1.0/Seurat/man/BuildClusterTree.Rd | 8 Seurat-5.1.0/Seurat/man/BuildNicheAssay.Rd | 3 Seurat-5.1.0/Seurat/man/CCAIntegration.Rd | 1 Seurat-5.1.0/Seurat/man/CellsByImage.Rd | 1 Seurat-5.1.0/Seurat/man/CountSketch.Rd | 1 Seurat-5.1.0/Seurat/man/CreateCategoryMatrix.Rd | 1 Seurat-5.1.0/Seurat/man/FastRPCAIntegration.Rd | 1 Seurat-5.1.0/Seurat/man/FetchResidualSCTModel.Rd | 1 Seurat-5.1.0/Seurat/man/FetchResiduals_reference.Rd | 1 Seurat-5.1.0/Seurat/man/FindBridgeAnchor.Rd | 1 Seurat-5.1.0/Seurat/man/FindBridgeIntegrationAnchors.Rd | 1 Seurat-5.1.0/Seurat/man/FindBridgeTransferAnchors.Rd | 1 Seurat-5.1.0/Seurat/man/FindMarkers.Rd | 2 Seurat-5.1.0/Seurat/man/GaussianSketch.Rd | 1 Seurat-5.1.0/Seurat/man/GetTissueCoordinates.Rd | 3 Seurat-5.1.0/Seurat/man/HVFInfo.SCTAssay.Rd | 1 Seurat-5.1.0/Seurat/man/ISpatialDimPlot.Rd | 11 Seurat-5.1.0/Seurat/man/ISpatialFeaturePlot.Rd | 4 Seurat-5.1.0/Seurat/man/ImageDimPlot.Rd | 2 Seurat-5.1.0/Seurat/man/ImageFeaturePlot.Rd | 2 Seurat-5.1.0/Seurat/man/JointPCAIntegration.Rd | 1 Seurat-5.1.0/Seurat/man/LeverageScore.Rd | 1 Seurat-5.1.0/Seurat/man/LinkedPlots.Rd | 5 Seurat-5.1.0/Seurat/man/Load10X_Spatial.Rd | 6 Seurat-5.1.0/Seurat/man/NNtoGraph.Rd | 1 Seurat-5.1.0/Seurat/man/PrepareBridgeReference.Rd | 1 Seurat-5.1.0/Seurat/man/ProjectData.Rd | 1 Seurat-5.1.0/Seurat/man/ProjectDimReduc.Rd | 1 Seurat-5.1.0/Seurat/man/ProjectIntegration.Rd | 1 Seurat-5.1.0/Seurat/man/PseudobulkExpression.Rd | 86 ++ Seurat-5.1.0/Seurat/man/RPCAIntegration.Rd | 1 Seurat-5.1.0/Seurat/man/Radius.Rd | 14 Seurat-5.1.0/Seurat/man/Read10X_Coordinates.Rd |only Seurat-5.1.0/Seurat/man/Read10X_Image.Rd | 24 Seurat-5.1.0/Seurat/man/Read10X_ScaleFactors.Rd |only Seurat-5.1.0/Seurat/man/Read10X_probe_metadata.Rd | 1 Seurat-5.1.0/Seurat/man/ScaleFactors.Rd | 3 Seurat-5.1.0/Seurat/man/SelectIntegrationFeatures5.Rd | 1 Seurat-5.1.0/Seurat/man/SelectSCTIntegrationFeatures.Rd | 1 Seurat-5.1.0/Seurat/man/Seurat-package.Rd | 1 Seurat-5.1.0/Seurat/man/SingleSpatialPlot.Rd | 10 Seurat-5.1.0/Seurat/man/SketchData.Rd | 1 Seurat-5.1.0/Seurat/man/SpatialPlot.Rd | 18 Seurat-5.1.0/Seurat/man/TransferSketchLabels.Rd | 1 Seurat-5.1.0/Seurat/man/UnSketchEmbeddings.Rd | 1 Seurat-5.1.0/Seurat/man/VisiumV2-class.Rd |only Seurat-5.1.0/Seurat/src/RcppExports.cpp | 2 Seurat-5.1.0/Seurat/tests/testdata/visium/spatial/scalefactors_json.json | 2 Seurat-5.1.0/Seurat/tests/testdata/visium/spatial/tissue_hires_image.png |only Seurat-5.1.0/Seurat/tests/testdata/visium/spatial/tissue_lowres_image.png |binary Seurat-5.1.0/Seurat/tests/testdata/visium_hd |only Seurat-5.1.0/Seurat/tests/testthat/test_differential_expression.R | 24 Seurat-5.1.0/Seurat/tests/testthat/test_integratedata.R | 6 Seurat-5.1.0/Seurat/tests/testthat/test_load_10X.R | 227 ++++++ Seurat-5.1.0/Seurat/tests/testthat/test_spatial.R |only Seurat-5.1.0/Seurat/tests/testthat/test_transferdata.R | 6 Seurat-5.1.0/Seurat/tests/testthat/test_tree.R |only Seurat-5.1.0/Seurat/tests/testthat/test_utilities.R | 109 +++ 81 files changed, 1257 insertions(+), 389 deletions(-)
Title: 'Amazon Web Services' Storage Services
Description: Interface to 'Amazon Web Services' storage services,
including 'Simple Storage Service' ('S3') and more
<https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.storage versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 164 +++++------ R/backup_interfaces.R | 4 R/backup_operations.R | 42 ++ R/backup_service.R | 2 R/backupstorage_service.R | 2 R/dlm_service.R | 4 R/ebs_operations.R | 26 - R/ebs_service.R | 4 R/efs_service.R | 2 R/finspacedata_service.R | 2 R/fsx_operations.R | 32 +- R/fsx_service.R | 2 R/glacier_service.R | 2 R/omics_interfaces.R | 26 - R/omics_operations.R | 71 ++-- R/omics_service.R | 12 R/recyclebin_service.R | 2 R/s3_interfaces.R | 8 R/s3_operations.R | 47 +-- R/s3_service.R | 2 R/s3control_operations.R | 15 - R/s3control_service.R | 4 R/s3outposts_service.R | 2 R/storagegateway_interfaces.R | 2 R/storagegateway_operations.R | 14 R/storagegateway_service.R | 8 man/backup_list_backup_job_summaries.Rd | 15 - man/backup_list_backup_jobs.Rd | 14 man/backup_list_recovery_points_by_resource.Rd | 13 man/dlm.Rd | 2 man/ebs.Rd | 2 man/ebs_get_snapshot_block.Rd | 2 man/ebs_put_snapshot_block.Rd | 4 man/ebs_start_snapshot.Rd | 20 - man/fsx_create_file_system.Rd | 9 man/fsx_create_storage_virtual_machine.Rd | 14 man/fsx_describe_shared_vpc_configuration.Rd | 2 man/fsx_describe_snapshots.Rd | 4 man/omics.Rd | 10 man/omics_accept_share.Rd | 6 man/omics_create_sequence_store.Rd | 5 man/omics_create_share.Rd | 13 man/omics_create_workflow.Rd | 2 man/omics_delete_share.Rd | 6 man/omics_get_share.Rd | 6 man/omics_get_workflow.Rd | 4 man/omics_list_multipart_read_set_uploads.Rd | 2 man/omics_list_shares.Rd | 9 man/omics_list_workflows.Rd | 4 man/omics_start_run.Rd | 15 - man/s3_abort_multipart_upload.Rd | 2 man/s3_complete_multipart_upload.Rd | 2 man/s3_copy_object.Rd | 2 man/s3_create_bucket.Rd | 2 man/s3_create_multipart_upload.Rd | 2 man/s3_delete_bucket.Rd | 2 man/s3_delete_bucket_policy.Rd | 2 man/s3_delete_object.Rd | 2 man/s3_delete_objects.Rd | 2 man/s3_get_bucket_policy.Rd | 2 man/s3_get_object.Rd | 2 man/s3_get_object_attributes.Rd | 2 man/s3_head_bucket.Rd | 2 man/s3_head_object.Rd | 2 man/s3_list_multipart_uploads.Rd | 2 man/s3_list_objects.Rd | 2 man/s3_list_objects_v2.Rd | 7 man/s3_list_parts.Rd | 2 man/s3_put_bucket_policy.Rd | 2 man/s3_put_object.Rd | 2 man/s3_upload_part.Rd | 2 man/s3_upload_part_copy.Rd | 2 man/s3control.Rd | 2 man/s3control_create_access_point.Rd | 7 man/s3control_get_multi_region_access_point.Rd | 2 man/s3control_get_multi_region_access_point_policy.Rd | 2 man/s3control_get_multi_region_access_point_policy_status.Rd | 2 man/s3control_list_jobs.Rd | 4 man/storagegateway.Rd | 6 man/storagegateway_describe_tapes.Rd | 6 man/storagegateway_notify_when_uploaded.Rd | 4 man/storagegateway_shutdown_gateway.Rd | 4 83 files changed, 454 insertions(+), 326 deletions(-)
Title: 'Amazon Web Services' Networking & Content Delivery Services
Description: Interface to 'Amazon Web Services' networking and content
delivery services, including 'Route 53' Domain Name System service,
'CloudFront' content delivery, load balancing, and more
<https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.networking versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 146 +++++----- R/apigateway_operations.R | 6 R/apigateway_service.R | 2 R/apigatewaymanagementapi_service.R | 2 R/apigatewayv2_service.R | 2 R/appfabric_service.R | 2 R/appmesh_service.R | 2 R/arczonalshift_service.R | 2 R/backupgateway_service.R | 2 R/cloudfront_operations.R | 59 ++-- R/cloudfront_service.R | 15 - R/directconnect_service.R | 2 R/elb_service.R | 2 R/elbv2_operations.R | 13 R/elbv2_service.R | 2 R/globalaccelerator_interfaces.R | 14 R/globalaccelerator_operations.R | 63 ++-- R/globalaccelerator_service.R | 6 R/networkfirewall_service.R | 2 R/networkmanager_service.R | 2 R/route53_interfaces.R | 4 R/route53_operations.R | 15 - R/route53_service.R | 2 R/route53domains_interfaces.R | 10 R/route53domains_operations.R | 117 ++++---- R/route53domains_service.R | 2 R/route53recoverycluster_service.R | 4 R/route53recoverycontrolconfig_service.R | 2 R/route53recoveryreadiness_service.R | 2 R/route53resolver_interfaces.R | 14 R/route53resolver_operations.R | 146 +++++++++- R/route53resolver_service.R | 2 R/servicediscovery_operations.R | 14 R/servicediscovery_service.R | 4 R/telconetworkbuilder_service.R | 2 R/vpclattice_service.R | 2 man/apigateway_create_model.Rd | 2 man/apigateway_update_model.Rd | 2 man/cloudfront.Rd | 12 man/cloudfront_create_invalidation.Rd | 2 man/cloudfront_create_key_value_store.Rd | 10 man/cloudfront_create_realtime_log_config.Rd | 7 man/cloudfront_delete_key_value_store.Rd | 8 man/cloudfront_describe_key_value_store.Rd | 6 man/cloudfront_list_distributions_by_web_acl_id.Rd | 8 man/cloudfront_list_key_value_stores.Rd | 10 man/cloudfront_update_key_value_store.Rd | 10 man/elbv2_create_load_balancer.Rd | 13 man/globalaccelerator.Rd | 4 man/globalaccelerator_advertise_byoip_cidr.Rd | 5 man/globalaccelerator_create_cross_account_attachment.Rd | 13 man/globalaccelerator_delete_cross_account_attachment.Rd | 2 man/globalaccelerator_deprovision_byoip_cidr.Rd | 5 man/globalaccelerator_list_cross_account_resource_accounts.Rd | 4 man/globalaccelerator_list_cross_account_resources.Rd | 6 man/globalaccelerator_provision_byoip_cidr.Rd | 7 man/globalaccelerator_update_cross_account_attachment.Rd | 16 - man/globalaccelerator_withdraw_byoip_cidr.Rd | 5 man/route53_get_geo_location.Rd | 2 man/route53_update_health_check.Rd | 5 man/route53domains_register_domain.Rd | 44 +-- man/route53domains_transfer_domain.Rd | 33 +- man/route53domains_update_domain_contact.Rd | 5 man/route53domains_update_domain_contact_privacy.Rd | 39 +- man/route53recoverycluster.Rd | 2 man/route53resolver_create_firewall_rule.Rd | 37 ++ man/route53resolver_create_resolver_endpoint.Rd | 9 man/route53resolver_delete_firewall_rule.Rd | 29 + man/route53resolver_update_firewall_rule.Rd | 37 ++ man/servicediscovery.Rd | 2 man/servicediscovery_discover_instances.Rd | 5 man/servicediscovery_list_services.Rd | 4 man/servicediscovery_register_instance.Rd | 4 74 files changed, 737 insertions(+), 373 deletions(-)
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Title: 'Amazon Web Services' Machine Learning Services
Description: Interface to 'Amazon Web Services' machine learning services,
including 'SageMaker' managed machine learning service, natural
language processing, speech recognition, translation, and more
<https://aws.amazon.com/machine-learning/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.machine.learning versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 248 +++---- R/augmentedairuntime_service.R | 2 R/bedrock_interfaces.R | 120 +++ R/bedrock_operations.R | 563 ++++++++++++++-- R/bedrock_service.R | 30 R/bedrockruntime_interfaces.R | 4 R/bedrockruntime_operations.R | 114 ++- R/bedrockruntime_service.R | 9 R/comprehend_operations.R | 11 R/comprehend_service.R | 2 R/comprehendmedical_service.R | 2 R/elasticinference_operations.R | 2 R/elasticinference_service.R | 2 R/forecastqueryservice_service.R | 2 R/forecastservice_service.R | 2 R/frauddetector_service.R | 2 R/lexmodelbuildingservice_service.R | 2 R/lexmodelsv2_interfaces.R | 82 ++ R/lexmodelsv2_operations.R | 210 +++++ R/lexmodelsv2_service.R | 8 R/lexruntimeservice_service.R | 2 R/lexruntimev2_service.R | 2 R/lookoutequipment_interfaces.R | 14 R/lookoutequipment_operations.R | 16 R/lookoutequipment_service.R | 2 R/lookoutmetrics_service.R | 2 R/machinelearning_service.R | 2 R/panorama_service.R | 2 R/personalize_interfaces.R | 14 R/personalize_operations.R | 84 +- R/personalize_service.R | 12 R/personalizeevents_service.R | 2 R/personalizeruntime_operations.R | 8 R/personalizeruntime_service.R | 2 R/polly_service.R | 2 R/rekognition_interfaces.R | 8 R/rekognition_service.R | 8 R/sagemaker_interfaces.R | 64 + R/sagemaker_operations.R | 183 +++-- R/sagemaker_service.R | 10 R/sagemakeredgemanager_service.R | 2 R/sagemakerfeaturestoreruntime_operations.R | 2 R/sagemakerfeaturestoreruntime_service.R | 2 R/sagemakergeospatialcapabilities_service.R | 2 R/sagemakermetrics_service.R | 2 R/sagemakerruntime_service.R | 2 R/textract_service.R | 2 R/transcribeservice_interfaces.R | 6 R/transcribeservice_service.R | 2 R/translate_service.R | 2 R/voiceid_service.R | 2 man/bedrock.Rd | 28 man/bedrock_create_evaluation_job.Rd |only man/bedrock_create_guardrail.Rd |only man/bedrock_create_guardrail_version.Rd |only man/bedrock_create_model_customization_job.Rd | 31 man/bedrock_create_provisioned_model_throughput.Rd | 53 + man/bedrock_delete_custom_model.Rd | 2 man/bedrock_delete_guardrail.Rd |only man/bedrock_delete_provisioned_model_throughput.Rd | 6 man/bedrock_get_custom_model.Rd | 4 man/bedrock_get_evaluation_job.Rd |only man/bedrock_get_guardrail.Rd |only man/bedrock_get_model_customization_job.Rd | 2 man/bedrock_get_provisioned_model_throughput.Rd | 6 man/bedrock_list_custom_models.Rd | 7 man/bedrock_list_evaluation_jobs.Rd |only man/bedrock_list_foundation_models.Rd | 16 man/bedrock_list_guardrails.Rd |only man/bedrock_list_provisioned_model_throughputs.Rd | 34 man/bedrock_list_tags_for_resource.Rd | 2 man/bedrock_stop_evaluation_job.Rd |only man/bedrock_stop_model_customization_job.Rd | 2 man/bedrock_tag_resource.Rd | 4 man/bedrock_untag_resource.Rd | 4 man/bedrock_update_guardrail.Rd |only man/bedrock_update_provisioned_model_throughput.Rd | 21 man/bedrockruntime.Rd | 7 man/bedrockruntime_invoke_model.Rd | 58 + man/bedrockruntime_invoke_model_with_response_stream.Rd | 53 + man/comprehend_contains_pii_entities.Rd | 3 man/comprehend_detect_pii_entities.Rd | 4 man/comprehend_start_pii_entities_detection_job.Rd | 4 man/lexmodelsv2.Rd | 6 man/lexmodelsv2_create_bot_replica.Rd |only man/lexmodelsv2_create_intent.Rd | 8 man/lexmodelsv2_delete_bot_replica.Rd |only man/lexmodelsv2_describe_bot_replica.Rd |only man/lexmodelsv2_list_bot_alias_replicas.Rd |only man/lexmodelsv2_list_bot_replicas.Rd |only man/lexmodelsv2_list_bot_version_replicas.Rd |only man/lexmodelsv2_update_intent.Rd | 8 man/lookoutequipment_create_model.Rd | 7 man/lookoutequipment_list_labels.Rd | 2 man/lookoutequipment_update_model.Rd | 7 man/personalize.Rd | 10 man/personalize_create_campaign.Rd | 16 man/personalize_create_solution.Rd | 29 man/personalize_list_solutions.Rd | 4 man/personalize_list_tags_for_resource.Rd | 2 man/personalize_tag_resource.Rd | 2 man/personalize_untag_resource.Rd | 6 man/personalize_update_campaign.Rd | 15 man/personalizeruntime_get_personalized_ranking.Rd | 2 man/personalizeruntime_get_recommendations.Rd | 4 man/rekognition.Rd | 3 man/sagemaker.Rd | 8 man/sagemaker_create_app_image_config.Rd | 9 man/sagemaker_create_auto_ml_job.Rd | 2 man/sagemaker_create_domain.Rd | 4 man/sagemaker_create_feature_group.Rd | 15 man/sagemaker_create_image.Rd | 2 man/sagemaker_create_image_version.Rd | 5 man/sagemaker_create_model_package.Rd | 11 man/sagemaker_create_presigned_domain_url.Rd | 2 man/sagemaker_create_space.Rd | 6 man/sagemaker_create_training_job.Rd | 6 man/sagemaker_create_user_profile.Rd | 2 man/sagemaker_delete_hyper_parameter_tuning_job.Rd |only man/sagemaker_delete_space.Rd | 2 man/sagemaker_describe_model_package_group.Rd | 2 man/sagemaker_describe_space.Rd | 2 man/sagemaker_list_spaces.Rd | 2 man/sagemaker_update_app_image_config.Rd | 5 man/sagemaker_update_cluster.Rd | 4 man/sagemaker_update_cluster_software.Rd |only man/sagemaker_update_domain.Rd | 2 man/sagemaker_update_endpoint.Rd | 8 man/sagemaker_update_feature_group.Rd | 5 man/sagemaker_update_model_package.Rd | 17 man/sagemaker_update_space.Rd | 2 man/sagemakerfeaturestoreruntime_delete_record.Rd | 2 tests/testthat/test_bedrock.R | 8 134 files changed, 1929 insertions(+), 576 deletions(-)
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Title: 'Amazon Web Services' End User Computing Services
Description: Interface to 'Amazon Web Services' end user computing
services, including collaborative document editing, mobile intranet,
and more <https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.end.user.computing versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 76 +++-- R/appstream_operations.R | 4 R/appstream_service.R | 2 R/ivschat_service.R | 12 R/nimblestudio_service.R | 2 R/workdocs_service.R | 2 R/worklink_service.R | 2 R/workmail_service.R | 2 R/workmailmessageflow_service.R | 2 R/workspaces_interfaces.R | 82 ++++++ R/workspaces_operations.R | 192 ++++++++++++++- R/workspaces_service.R | 10 R/workspacesweb_interfaces.R | 28 +- R/workspacesweb_operations.R | 78 +++--- R/workspacesweb_service.R | 2 man/ivschat.Rd | 10 man/workspaces.Rd | 8 man/workspaces_accept_account_link_invitation.Rd |only man/workspaces_create_account_link_invitation.Rd |only man/workspaces_delete_account_link_invitation.Rd |only man/workspaces_describe_workspaces.Rd | 5 man/workspaces_get_account_link.Rd |only man/workspaces_list_account_links.Rd |only man/workspaces_reject_account_link_invitation.Rd |only man/workspacesweb_create_browser_settings.Rd | 2 man/workspacesweb_create_identity_provider.Rd | 6 man/workspacesweb_create_ip_access_settings.Rd | 2 man/workspacesweb_create_network_settings.Rd | 2 man/workspacesweb_create_portal.Rd | 18 - man/workspacesweb_create_trust_store.Rd | 2 man/workspacesweb_create_user_access_logging_settings.Rd | 2 man/workspacesweb_create_user_settings.Rd | 2 man/workspacesweb_tag_resource.Rd | 2 man/workspacesweb_update_browser_settings.Rd | 2 man/workspacesweb_update_identity_provider.Rd | 6 man/workspacesweb_update_ip_access_settings.Rd | 2 man/workspacesweb_update_network_settings.Rd | 2 man/workspacesweb_update_portal.Rd | 16 - man/workspacesweb_update_trust_store.Rd | 2 man/workspacesweb_update_user_access_logging_settings.Rd | 2 man/workspacesweb_update_user_settings.Rd | 2 42 files changed, 453 insertions(+), 146 deletions(-)
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Title: R Interface to 'Mapbox' Web Services
Description: Includes support for 'Mapbox' Navigation APIs, including directions,
isochrones, and route optimization; the Search API for forward and reverse geocoding;
the Maps API for interacting with 'Mapbox' vector tilesets and visualizing
'Mapbox' maps in R; and 'Mapbox Tiling Service' and 'tippecanoe' for generating map tiles.
See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
Author: Kyle Walker [aut, cre],
Eli Pousson [ctb],
Anthony North [ctb, cph],
Miles McBain [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapboxapi versions 0.5.3 dated 2023-10-16 and 0.6 dated 2024-05-10
DESCRIPTION | 15 - MD5 | 25 + NAMESPACE | 6 R/mapboxapi-package.R | 6 R/search.R | 538 ++++++++++++++++++++++++++++++++++++--- R/zzz.R | 3 README.md | 69 ++--- inst |only man/geocoder_as_sf.Rd |only man/geocoder_as_xy.Rd |only man/get_geocoder_dependencies.Rd |only man/mapboxGeocoderInput.Rd |only man/mapboxapi.Rd | 10 man/mb_batch_geocode.Rd |only man/mb_geocode.Rd | 33 +- tools |only 16 files changed, 604 insertions(+), 101 deletions(-)
Title: Cluster-Preserving Multivariate Joint Grid Discretization
Description: Discretize multivariate continuous data using a grid
that captures the joint distribution via preserving clusters in
the original data (Wang et al. 2020) <doi:10.1145/3388440.3412415>.
Joint grid discretization is applicable as a data transformation step
to prepare data for model-free inference of association, function, or
causality.
Author: Jiandong Wang [aut],
Sajal Kumar [aut] ,
Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between GridOnClusters versions 0.1.0 dated 2022-01-28 and 0.1.0.1 dated 2024-05-10
GridOnClusters-0.1.0.1/GridOnClusters/DESCRIPTION | 13 GridOnClusters-0.1.0.1/GridOnClusters/MD5 | 14 GridOnClusters-0.1.0.1/GridOnClusters/NEWS.md | 9 GridOnClusters-0.1.0.1/GridOnClusters/build/partial.rdb |binary GridOnClusters-0.1.0.1/GridOnClusters/build/vignette.rds |binary GridOnClusters-0.1.0.1/GridOnClusters/inst/doc/Examples.html | 536 ++++++---- GridOnClusters-0.1.0.1/GridOnClusters/tests/testthat/test-GridOnClusters.R | 86 - GridOnClusters-0.1.0/GridOnClusters/src/Makevars |only GridOnClusters-0.1.0/GridOnClusters/src/Makevars.win |only 9 files changed, 439 insertions(+), 219 deletions(-)
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Title: FaaS (Function as a Service) Package
Description: Allows users to create and deploy the workflow with multiple functions
in Function-as-a-Service (FaaS) cloud computing platforms.
The 'FaaSr' package makes it simpler for R developers to use FaaS platforms by providing the following functionality:
1) Parsing and validating a JSON-based payload compliant to 'FaaSr' schema supporting multiple FaaS platforms
2) Invoking user functions written in R in a Docker container (derived from rocker), using a list generated from
the parser as argument
3) Downloading/uploading of files from/to S3 buckets using simple primitives
4) Logging to files in S3 buckets
5) Triggering downstream actions supporting multiple FaaS platforms
6) Generating FaaS-specific API calls to simplify the registering of a user's workflow with a FaaS platform
Supported FaaS platforms:
Apache OpenWhisk <https://openwhisk.apache.org/>
GitHub Actions <https://github.com/features/actions>
Amazon Web Services (AWS) Lambda <https://aws.amazon.com/lambda/>
Support [...truncated...]
Author: Figueiredo Renato [aut, cre, ths, cph]
,
Park Sungjae [aut],
Mu Nan [ctb],
Ku Yun-Jung [ctb],
Daneshmand Vahid [ctb],
Thomas R. Quinn [aut],
Carey Cayelan [ctb]
Maintainer: Figueiredo Renato <renatof@ufl.edu>
Diff between FaaSr versions 1.1.2 dated 2024-02-27 and 1.2.1 dated 2024-05-10
DESCRIPTION | 9 +- MD5 | 47 ++++++++------- NAMESPACE | 2 NEWS.md | 13 ++++ R/faasr_abort_on_multiple_invocations.R | 10 +-- R/faasr_arrow_s3_bucket.R | 12 ++- R/faasr_client_api_aws-lambda.R | 26 +++++--- R/faasr_client_api_github-actions.R | 2 R/faasr_client_api_openwhisk.R | 4 - R/faasr_delete_file.R | 1 R/faasr_get_file.R | 1 R/faasr_get_folder_list.R |only R/faasr_init_log_folder.R | 3 R/faasr_put_file.R | 1 R/faasr_start.R | 5 + R/faasr_test.R |only README.md | 15 +++- inst/WORDLIST | 17 ----- man/faasr_delete_file.Rd | 2 man/faasr_get_file.Rd | 2 man/faasr_get_folder_list.Rd |only man/faasr_put_file.Rd | 2 man/faasr_register_workflow_aws_lambda.Rd | 8 ++ man/faasr_register_workflow_aws_lambda_function_build.Rd | 3 man/faasr_register_workflow_openwhisk.Rd | 3 man/faasr_test.Rd |only man/figures |only 27 files changed, 112 insertions(+), 76 deletions(-)
Title: 'Amazon Web Services' Developer Tools Services
Description: Interface to 'Amazon Web Services' developer tools services,
including version control, continuous integration and deployment, and
more <https://aws.amazon.com/products/developer-tools/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.developer.tools versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 176 +- R/cloud9_operations.R | 15 R/cloud9_service.R | 2 R/cloudcontrolapi_service.R | 2 R/codeartifact_interfaces.R | 122 + R/codeartifact_operations.R | 676 ++++++++-- R/codeartifact_service.R | 93 + R/codebuild_interfaces.R | 90 + R/codebuild_operations.R | 382 +++++ R/codebuild_service.R | 9 R/codecatalyst_interfaces.R | 2 R/codecatalyst_operations.R | 3 R/codecatalyst_service.R | 2 R/codecommit_service.R | 2 R/codedeploy_service.R | 2 R/codeguruprofiler_service.R | 2 R/codegurureviewer_service.R | 2 R/codegurusecurity_operations.R | 2 R/codegurusecurity_service.R | 2 R/codepipeline_interfaces.R | 36 R/codepipeline_operations.R | 36 R/codepipeline_service.R | 3 R/codestar_service.R | 2 R/codestarconnections_interfaces.R | 12 R/codestarconnections_operations.R | 14 R/codestarconnections_service.R | 2 R/codestarnotifications_service.R | 2 R/devopsguru_operations.R | 6 R/devopsguru_service.R | 2 R/drs_interfaces.R | 70 - R/drs_operations.R | 2 R/drs_service.R | 2 R/fis_interfaces.R | 26 R/fis_operations.R | 22 R/fis_service.R | 8 R/wellarchitected_interfaces.R | 46 R/wellarchitected_operations.R | 90 + R/wellarchitected_service.R | 8 R/xray_operations.R | 2 R/xray_service.R | 2 man/cloud9_create_environment_ec2.Rd | 13 man/codeartifact.Rd | 75 - man/codeartifact_copy_package_versions.Rd | 19 man/codeartifact_create_package_group.Rd |only man/codeartifact_delete_package.Rd | 16 man/codeartifact_delete_package_group.Rd |only man/codeartifact_delete_package_versions.Rd | 19 man/codeartifact_describe_package.Rd | 16 man/codeartifact_describe_package_group.Rd |only man/codeartifact_describe_package_version.Rd | 18 man/codeartifact_dispose_package_versions.Rd | 17 man/codeartifact_get_associated_package_group.Rd |only man/codeartifact_get_package_version_asset.Rd | 18 man/codeartifact_get_package_version_readme.Rd | 20 man/codeartifact_list_allowed_repositories_for_group.Rd |only man/codeartifact_list_associated_packages.Rd |only man/codeartifact_list_package_groups.Rd |only man/codeartifact_list_package_version_assets.Rd | 18 man/codeartifact_list_package_version_dependencies.Rd | 18 man/codeartifact_list_package_versions.Rd | 15 man/codeartifact_list_packages.Rd | 9 man/codeartifact_list_sub_package_groups.Rd |only man/codeartifact_put_package_origin_configuration.Rd | 9 man/codeartifact_update_package_group.Rd |only man/codeartifact_update_package_group_origin_configuration.Rd |only man/codeartifact_update_package_versions_status.Rd | 10 man/codebuild.Rd | 7 man/codebuild_batch_get_fleets.Rd |only man/codebuild_create_fleet.Rd |only man/codebuild_delete_fleet.Rd |only man/codebuild_import_source_credentials.Rd | 2 man/codebuild_list_fleets.Rd |only man/codebuild_start_build.Rd | 23 man/codebuild_update_fleet.Rd |only man/codecatalyst_create_dev_environment.Rd | 3 man/codepipeline.Rd | 1 man/codepipeline_list_pipeline_executions.Rd | 3 man/codepipeline_rollback_stage.Rd |only man/codestarconnections_create_sync_configuration.Rd | 9 man/codestarconnections_update_sync_configuration.Rd | 9 man/fis.Rd | 6 man/fis_create_target_account_configuration.Rd | 4 man/fis_delete_target_account_configuration.Rd | 2 man/fis_get_experiment_target_account_configuration.Rd | 2 man/fis_get_target_account_configuration.Rd | 2 man/fis_list_experiments.Rd | 8 man/fis_start_experiment.Rd | 9 man/fis_update_target_account_configuration.Rd | 2 man/wellarchitected.Rd | 6 man/wellarchitected_create_workload.Rd | 5 man/wellarchitected_get_global_settings.Rd |only man/wellarchitected_list_lens_review_improvements.Rd | 4 man/wellarchitected_update_global_settings.Rd | 9 man/wellarchitected_update_integration.Rd |only man/wellarchitected_update_lens_review.Rd | 5 man/wellarchitected_update_workload.Rd | 5 tests/testthat/test_codebuild.R | 4 98 files changed, 1939 insertions(+), 488 deletions(-)
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Title: 'Amazon Web Services' Database Services
Description: Interface to 'Amazon Web Services' database services,
including 'Relational Database Service' ('RDS'), 'DynamoDB' 'NoSQL'
database, and more <https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.database versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 296 +++--- R/dax_service.R | 2 R/docdb_interfaces.R | 22 R/docdb_operations.R | 54 + R/docdb_service.R | 3 R/docdbelastic_interfaces.R | 60 - R/docdbelastic_operations.R | 347 +++++-- R/docdbelastic_service.R | 53 - R/dynamodb_interfaces.R | 60 + R/dynamodb_operations.R | 295 +++++ R/dynamodb_service.R | 6 R/dynamodbstreams_service.R | 2 R/elasticache_interfaces.R | 12 R/elasticache_operations.R | 17 R/elasticache_service.R | 2 R/keyspaces_interfaces.R | 20 R/keyspaces_operations.R | 111 ++ R/keyspaces_service.R | 7 R/lakeformation_interfaces.R | 6 R/lakeformation_operations.R | 30 R/lakeformation_service.R | 2 R/memorydb_service.R | 2 R/neptune_service.R | 2 R/neptunedata_service.R | 2 R/qldb_service.R | 2 R/qldbsession_service.R | 2 R/rds_interfaces.R | 136 ++ R/rds_operations.R | 542 +++++++++-- R/rds_service.R | 8 R/rdsdataservice_service.R | 2 R/redshift_interfaces.R | 26 R/redshift_operations.R | 117 +- R/redshift_service.R | 3 R/redshiftdataapiservice_service.R | 2 R/redshiftserverless_operations.R | 58 - R/redshiftserverless_service.R | 2 R/simpledb_service.R | 2 R/timestreamquery_interfaces.R | 26 R/timestreamquery_operations.R | 74 + R/timestreamquery_service.R | 4 R/timestreamwrite_operations.R | 2 R/timestreamwrite_service.R | 2 man/docdb.Rd | 3 man/docdb_switchover_global_cluster.Rd |only man/docdbelastic.Rd | 50 - man/docdbelastic_copy_cluster_snapshot.Rd |only man/docdbelastic_create_cluster.Rd | 52 - man/docdbelastic_create_cluster_snapshot.Rd | 12 man/docdbelastic_delete_cluster.Rd | 6 man/docdbelastic_delete_cluster_snapshot.Rd | 7 man/docdbelastic_get_cluster.Rd | 6 man/docdbelastic_get_cluster_snapshot.Rd | 6 man/docdbelastic_list_cluster_snapshots.Rd | 29 man/docdbelastic_list_clusters.Rd | 14 man/docdbelastic_list_tags_for_resource.Rd | 6 man/docdbelastic_restore_cluster_from_snapshot.Rd | 34 man/docdbelastic_start_cluster.Rd |only man/docdbelastic_stop_cluster.Rd |only man/docdbelastic_tag_resource.Rd | 8 man/docdbelastic_untag_resource.Rd | 8 man/docdbelastic_update_cluster.Rd | 38 man/dynamodb.Rd | 4 man/dynamodb_batch_get_item.Rd | 8 man/dynamodb_batch_write_item.Rd | 6 man/dynamodb_create_backup.Rd | 3 man/dynamodb_create_table.Rd | 18 man/dynamodb_delete_item.Rd | 3 man/dynamodb_delete_resource_policy.Rd |only man/dynamodb_delete_table.Rd | 3 man/dynamodb_describe_continuous_backups.Rd | 5 man/dynamodb_describe_contributor_insights.Rd | 3 man/dynamodb_describe_kinesis_streaming_destination.Rd | 3 man/dynamodb_describe_table.Rd | 3 man/dynamodb_describe_table_replica_auto_scaling.Rd | 3 man/dynamodb_describe_time_to_live.Rd | 3 man/dynamodb_disable_kinesis_streaming_destination.Rd | 11 man/dynamodb_enable_kinesis_streaming_destination.Rd | 11 man/dynamodb_export_table_to_point_in_time.Rd | 5 man/dynamodb_get_item.Rd | 3 man/dynamodb_get_resource_policy.Rd |only man/dynamodb_list_backups.Rd | 3 man/dynamodb_list_contributor_insights.Rd | 3 man/dynamodb_put_item.Rd | 3 man/dynamodb_put_resource_policy.Rd |only man/dynamodb_query.Rd | 5 man/dynamodb_restore_table_to_point_in_time.Rd | 2 man/dynamodb_scan.Rd | 7 man/dynamodb_update_continuous_backups.Rd | 3 man/dynamodb_update_contributor_insights.Rd | 3 man/dynamodb_update_item.Rd | 3 man/dynamodb_update_kinesis_streaming_destination.Rd |only man/dynamodb_update_table.Rd | 11 man/dynamodb_update_table_replica_auto_scaling.Rd | 3 man/dynamodb_update_time_to_live.Rd | 3 man/elasticache_create_cache_cluster.Rd | 2 man/elasticache_create_replication_group.Rd | 7 man/elasticache_modify_cache_cluster.Rd | 3 man/elasticache_modify_replication_group.Rd | 3 man/keyspaces.Rd | 5 man/keyspaces_create_table.Rd | 33 man/keyspaces_get_table_auto_scaling_settings.Rd |only man/keyspaces_restore_table.Rd | 20 man/keyspaces_update_table.Rd | 26 man/lakeformation_create_lake_format_identi_center_config.Rd | 13 man/lakeformation_update_lake_format_identi_center_config.Rd | 15 man/rds.Rd | 6 man/rds_create_blue_green_deployment.Rd | 9 man/rds_create_custom_db_engine_version.Rd | 10 man/rds_create_db_cluster.Rd | 23 man/rds_create_db_cluster_parameter_group.Rd | 2 man/rds_create_db_instance.Rd | 36 man/rds_create_db_instance_read_replica.Rd | 16 man/rds_create_db_shard_group.Rd |only man/rds_create_event_subscription.Rd | 8 man/rds_create_integration.Rd | 11 man/rds_delete_custom_db_engine_version.Rd | 10 man/rds_delete_db_shard_group.Rd |only man/rds_describe_db_clusters.Rd | 2 man/rds_describe_db_engine_versions.Rd | 3 man/rds_describe_db_shard_groups.Rd |only man/rds_describe_engine_default_parameters.Rd | 1 man/rds_describe_global_clusters.Rd | 9 man/rds_describe_orderable_db_instance_options.Rd | 7 man/rds_modify_activity_stream.Rd | 2 man/rds_modify_custom_db_engine_version.Rd | 10 man/rds_modify_db_cluster.Rd | 19 man/rds_modify_db_instance.Rd | 29 man/rds_modify_db_shard_group.Rd |only man/rds_modify_integration.Rd |only man/rds_reboot_db_shard_group.Rd |only man/rds_restore_db_instance_from_db_snapshot.Rd | 23 man/rds_restore_db_instance_from_s3.Rd | 18 man/rds_restore_db_instance_to_point_in_time.Rd | 18 man/redshift.Rd | 1 man/redshift_associate_data_share_consumer.Rd | 4 man/redshift_authorize_data_share.Rd | 4 man/redshift_authorize_snapshot_access.Rd | 14 man/redshift_create_cluster.Rd | 10 man/redshift_deauthorize_data_share.Rd | 4 man/redshift_describe_data_shares.Rd | 2 man/redshift_describe_data_shares_for_consumer.Rd | 4 man/redshift_describe_data_shares_for_producer.Rd | 4 man/redshift_disassociate_data_share_consumer.Rd | 4 man/redshift_list_recommendations.Rd |only man/redshift_modify_cluster.Rd | 16 man/redshift_restore_from_cluster_snapshot.Rd | 4 man/redshiftserverless_create_scheduled_action.Rd | 22 man/redshiftserverless_create_workgroup.Rd | 8 man/redshiftserverless_update_scheduled_action.Rd | 22 man/redshiftserverless_update_workgroup.Rd | 8 man/timestreamquery.Rd | 2 man/timestreamquery_describe_account_settings.Rd |only man/timestreamquery_prepare_query.Rd | 2 man/timestreamquery_update_account_settings.Rd |only tests/testthat/test_rds.R | 4 tests/testthat/test_redshift.R | 4 tests/testthat/test_timestreamquery.R | 4 158 files changed, 2591 insertions(+), 809 deletions(-)
Title: 'Amazon Web Services' Customer Engagement Services
Description: Interface to 'Amazon Web Services' customer engagement
services, including 'Simple Email Service', 'Connect' contact center
service, and more <https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.customer.engagement versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 125 +- R/connect_interfaces.R | 38 R/connect_operations.R | 438 +++++++++ R/connect_service.R | 2 R/connectcampaignservice_interfaces.R | 6 R/connectcampaignservice_service.R | 2 R/connectcases_interfaces.R | 64 + R/connectcases_operations.R | 144 +++ R/connectcases_service.R | 10 R/connectcontactlens_service.R | 2 R/connectparticipant_operations.R | 7 R/connectparticipant_service.R | 4 R/connectwisdomservice_service.R | 2 R/customerprofiles_service.R | 2 R/pinpoint_interfaces.R | 8 R/pinpoint_service.R | 2 R/pinpointemail_operations.R | 4 R/pinpointemail_service.R | 2 R/pinpointsmsvoice_service.R | 2 R/pinpointsmsvoicev2_interfaces.R | 162 +++ R/pinpointsmsvoicev2_operations.R | 453 +++++++++- R/pinpointsmsvoicev2_service.R | 28 R/ses_operations.R | 4 R/ses_service.R | 2 R/sesv2_interfaces.R | 6 R/sesv2_operations.R | 12 R/sesv2_service.R | 2 man/connect_associate_instance_storage_config.Rd | 16 man/connect_create_security_profile.Rd | 16 man/connect_create_user.Rd | 9 man/connect_get_current_metric_data.Rd | 14 man/connect_get_metric_data.Rd | 8 man/connect_get_metric_data_v2.Rd | 275 +++++- man/connect_get_traffic_distribution.Rd | 5 man/connect_monitor_contact.Rd | 2 man/connect_start_chat_contact.Rd | 6 man/connect_stop_contact.Rd | 2 man/connect_update_security_profile.Rd | 14 man/connectcases.Rd | 8 man/connectcases_create_case.Rd | 14 man/connectcases_delete_field.Rd |only man/connectcases_delete_layout.Rd |only man/connectcases_delete_template.Rd |only man/connectcases_get_case_audit_events.Rd |only man/connectcases_update_case.Rd | 8 man/connectparticipant.Rd | 2 man/connectparticipant_complete_attachment_upload.Rd | 2 man/connectparticipant_send_event.Rd | 5 man/pinpointsmsvoicev2.Rd | 24 man/pinpointsmsvoicev2_associate_protect_configuration.Rd |only man/pinpointsmsvoicev2_create_event_destination.Rd | 2 man/pinpointsmsvoicev2_create_protect_configuration.Rd |only man/pinpointsmsvoicev2_delete_accoun_defaul_protec_config.Rd |only man/pinpointsmsvoicev2_delete_media_message_spend_limit_override.Rd |only man/pinpointsmsvoicev2_delete_protect_configuration.Rd |only man/pinpointsmsvoicev2_describe_protect_configurations.Rd |only man/pinpointsmsvoicev2_disassociate_protect_configuration.Rd |only man/pinpointsmsvoicev2_get_prote_confi_count_rule_set.Rd |only man/pinpointsmsvoicev2_request_phone_number.Rd | 2 man/pinpointsmsvoicev2_send_destination_number_verification_code.Rd | 2 man/pinpointsmsvoicev2_send_media_message.Rd |only man/pinpointsmsvoicev2_send_text_message.Rd | 7 man/pinpointsmsvoicev2_send_voice_message.Rd | 5 man/pinpointsmsvoicev2_set_account_default_protect_configuration.Rd |only man/pinpointsmsvoicev2_set_media_message_spend_limit_override.Rd |only man/pinpointsmsvoicev2_updat_prote_confi_count_rule_set.Rd |only man/pinpointsmsvoicev2_update_protect_configuration.Rd |only man/sesv2_put_account_details.Rd | 4 man/sesv2_send_email.Rd | 2 man/sesv2_update_contact.Rd | 2 tests/testthat/test_pinpointsmsvoicev2.R | 8 72 files changed, 1785 insertions(+), 220 deletions(-)
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Title: 'Amazon Web Services' Application Integration Services
Description: Interface to 'Amazon Web Services' application integration
services, including 'Simple Queue Service' ('SQS') message queue,
'Simple Notification Service' ('SNS') publish/subscribe messaging, and
more <https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.application.integration versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 +- MD5 | 79 +++++++++++----------- R/eventbridge_interfaces.R | 4 - R/eventbridge_operations.R | 32 -------- R/eventbridge_service.R | 2 R/eventbridgepipes_service.R | 2 R/eventbridgescheduler_service.R | 2 R/locationservice_interfaces.R | 6 - R/locationservice_operations.R | 38 +++++++++- R/locationservice_service.R | 2 R/mq_service.R | 2 R/mwaa_interfaces.R | 2 R/mwaa_operations.R | 2 R/mwaa_service.R | 2 R/resourceexplorer_service.R | 2 R/schemas_service.R | 2 R/sfn_interfaces.R | 12 +++ R/sfn_operations.R | 34 +++++++++ R/sfn_service.R | 5 - R/sns_interfaces.R | 18 ++--- R/sns_operations.R | 47 +++++++++---- R/sns_service.R | 2 R/sqs_service.R | 2 R/swf_service.R | 2 man/eventbridge_put_rule.Rd | 26 ------- man/locationservice_create_route_calculator.Rd | 2 man/locationservice_get_map_glyphs.Rd | 2 man/locationservice_get_place.Rd | 34 +++++++++ man/mwaa_create_environment.Rd | 2 man/sfn.Rd | 3 man/sfn_validate_state_machine_definition.Rd |only man/sns_create_platform_application.Rd | 3 man/sns_create_platform_endpoint.Rd | 5 - man/sns_delete_endpoint.Rd | 2 man/sns_delete_platform_application.Rd | 2 man/sns_get_endpoint_attributes.Rd | 3 man/sns_get_platform_application_attributes.Rd | 2 man/sns_list_endpoints_by_platform_application.Rd | 5 - man/sns_list_platform_applications.Rd | 3 man/sns_set_endpoint_attributes.Rd | 3 man/sns_set_platform_application_attributes.Rd | 16 +++- 41 files changed, 258 insertions(+), 164 deletions(-)
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Title: 'Amazon Web Services' Analytics Services
Description: Interface to 'Amazon Web Services' 'analytics' services,
including 'Elastic MapReduce' 'Hadoop' and 'Spark' big data service,
'Elasticsearch' search engine, and more <https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.analytics versions 0.5.0 dated 2024-01-09 and 0.6.0 dated 2024-05-10
DESCRIPTION | 8 MD5 | 311 ++++---- R/athena_interfaces.R | 2 R/athena_operations.R | 11 R/athena_service.R | 2 R/cloudsearch_service.R | 2 R/cloudsearchdomain_service.R | 2 R/datapipeline_service.R | 2 R/datazone_interfaces.R | 134 +++ R/datazone_operations.R | 378 +++++++++- R/datazone_service.R | 18 R/elasticsearchservice_interfaces.R | 28 R/elasticsearchservice_operations.R | 32 R/elasticsearchservice_service.R | 3 R/emr_interfaces.R | 16 R/emr_operations.R | 38 + R/emr_service.R | 3 R/entityresolution_interfaces.R | 144 +++ R/entityresolution_operations.R | 360 +++++++++ R/entityresolution_service.R | 14 R/firehose_interfaces.R | 6 R/firehose_operations.R | 54 - R/firehose_service.R | 19 R/glue_interfaces.R | 18 R/glue_operations.R | 49 + R/glue_service.R | 4 R/gluedatabrew_service.R | 2 R/healthlake_interfaces.R | 8 R/healthlake_service.R | 2 R/ivs_interfaces.R | 76 +- R/ivs_operations.R | 216 +++++ R/ivs_service.R | 135 ++- R/ivsrealtime_interfaces.R | 6 R/ivsrealtime_service.R | 2 R/kafka_interfaces.R | 4 R/kafka_service.R | 2 R/kafkaconnect_interfaces.R | 64 + R/kafkaconnect_operations.R | 156 +++- R/kafkaconnect_service.R | 6 R/kendra_operations.R | 48 - R/kendra_service.R | 14 R/kendraranking_service.R | 2 R/kinesis_operations.R | 2 R/kinesis_service.R | 2 R/kinesisanalytics_service.R | 2 R/kinesisanalyticsv2_interfaces.R | 6 R/kinesisanalyticsv2_operations.R | 98 +- R/kinesisanalyticsv2_service.R | 35 R/mturk_operations.R | 2 R/mturk_service.R | 2 R/opensearchingestion_operations.R | 2 R/opensearchingestion_service.R | 2 R/opensearchservice_interfaces.R | 30 R/opensearchservice_operations.R | 42 + R/opensearchservice_service.R | 14 R/opensearchserviceserverless_operations.R | 4 R/opensearchserviceserverless_service.R | 2 R/quicksight_interfaces.R | 44 - R/quicksight_operations.R | 155 +++- R/quicksight_service.R | 5 man/athena_import_notebook.Rd | 11 man/datazone.Rd | 16 man/datazone_accept_predictions.Rd | 8 man/datazone_cancel_metadata_generation_run.Rd |only man/datazone_create_asset.Rd | 2 man/datazone_create_listing_change_set.Rd | 18 man/datazone_create_subscription_request.Rd | 2 man/datazone_delete_domain.Rd | 9 man/datazone_delete_listing.Rd | 8 man/datazone_delete_project.Rd | 5 man/datazone_delete_time_series_data_points.Rd |only man/datazone_get_listing.Rd | 10 man/datazone_get_metadata_generation_run.Rd |only man/datazone_get_time_series_data_point.Rd |only man/datazone_list_environments.Rd | 2 man/datazone_list_metadata_generation_runs.Rd |only man/datazone_list_projects.Rd | 2 man/datazone_list_time_series_data_points.Rd |only man/datazone_post_time_series_data_points.Rd |only man/datazone_reject_predictions.Rd | 9 man/datazone_search.Rd | 2 man/datazone_search_listings.Rd | 7 man/datazone_search_types.Rd | 4 man/datazone_start_metadata_generation_run.Rd |only man/elasticsearchservice.Rd | 1 man/elasticsearchservice_cancel_domain_config_change.Rd |only man/emr.Rd | 1 man/emr_set_unhealthy_node_replacement.Rd |only man/entityresolution.Rd | 12 man/entityresolution_add_policy_statement.Rd |only man/entityresolution_batch_delete_unique_id.Rd |only man/entityresolution_create_id_mapping_workflow.Rd | 4 man/entityresolution_create_id_namespace.Rd |only man/entityresolution_delete_id_namespace.Rd |only man/entityresolution_delete_policy_statement.Rd |only man/entityresolution_get_id_namespace.Rd |only man/entityresolution_get_match_id.Rd | 7 man/entityresolution_get_policy.Rd |only man/entityresolution_list_id_namespaces.Rd |only man/entityresolution_put_policy.Rd |only man/entityresolution_start_id_mapping_job.Rd | 4 man/entityresolution_update_id_mapping_workflow.Rd | 7 man/entityresolution_update_id_namespace.Rd |only man/firehose.Rd | 17 man/firehose_create_delivery_stream.Rd | 28 man/firehose_delete_delivery_stream.Rd | 14 man/firehose_describe_delivery_stream.Rd | 3 man/firehose_put_record.Rd | 5 man/firehose_update_destination.Rd | 5 man/glue.Rd | 2 man/glue_get_unfiltered_table_metadata.Rd | 47 + man/ivs.Rd | 118 +-- man/ivs_create_channel.Rd | 14 man/ivs_create_playback_restriction_policy.Rd |only man/ivs_delete_playback_restriction_policy.Rd |only man/ivs_get_playback_restriction_policy.Rd |only man/ivs_list_channels.Rd | 3 man/ivs_list_playback_restriction_policies.Rd |only man/ivs_untag_resource.Rd | 2 man/ivs_update_channel.Rd | 18 man/ivs_update_playback_restriction_policy.Rd |only man/kafkaconnect.Rd | 4 man/kafkaconnect_create_connector.Rd | 11 man/kafkaconnect_create_custom_plugin.Rd | 5 man/kafkaconnect_create_worker_configuration.Rd | 5 man/kafkaconnect_delete_worker_configuration.Rd |only man/kafkaconnect_list_custom_plugins.Rd | 8 man/kafkaconnect_list_tags_for_resource.Rd |only man/kafkaconnect_list_worker_configurations.Rd | 9 man/kafkaconnect_tag_resource.Rd |only man/kafkaconnect_untag_resource.Rd |only man/kendra.Rd | 12 man/kendra_create_index.Rd | 4 man/kendra_delete_index.Rd | 4 man/kendra_delete_thesaurus.Rd | 4 man/kendra_describe_index.Rd | 4 man/kendra_describe_thesaurus.Rd | 4 man/kendra_query.Rd | 5 man/kendra_retrieve.Rd | 5 man/kendra_update_data_source.Rd | 4 man/kendra_update_index.Rd | 14 man/kinesisanalyticsv2.Rd | 33 man/kinesisanalyticsv2_add_appli_cloud_watch_loggi_optio.Rd | 6 man/kinesisanalyticsv2_create_application.Rd | 10 man/kinesisanalyticsv2_delet_appli_cloud_watch_loggi_optio.Rd | 6 man/kinesisanalyticsv2_delete_application.Rd | 2 man/kinesisanalyticsv2_delete_application_vpc_configuration.Rd | 5 man/kinesisanalyticsv2_describe_application.Rd | 9 man/kinesisanalyticsv2_discover_input_schema.Rd | 2 man/kinesisanalyticsv2_list_applications.Rd | 5 man/kinesisanalyticsv2_start_application.Rd | 8 man/kinesisanalyticsv2_stop_application.Rd | 9 man/kinesisanalyticsv2_tag_resource.Rd | 5 man/kinesisanalyticsv2_untag_resource.Rd | 9 man/kinesisanalyticsv2_update_applic_mainte_config.Rd | 6 man/kinesisanalyticsv2_update_application.Rd | 16 man/opensearchservice.Rd | 9 man/opensearchservice_cancel_domain_config_change.Rd |only man/opensearchservice_create_domain.Rd | 5 man/opensearchservice_update_domain_config.Rd | 5 man/quicksight.Rd | 3 man/quicksight_create_account_subscription.Rd | 47 + man/quicksight_generate_embed_url_for_anonymous_user.Rd | 12 man/quicksight_generate_embed_url_for_registered_user.Rd | 7 man/quicksight_register_user.Rd | 11 man/quicksight_start_dashboard_snapshot_job.Rd | 5 man/quicksight_update_folder_permissions.Rd | 6 man/quicksight_update_ip_restriction.Rd | 11 man/quicksight_update_spice_capacity_configuration.Rd |only man/quicksight_update_user.Rd | 11 tests/testthat/test_entityresolution.R | 4 tests/testthat/test_ivs.R | 4 172 files changed, 2819 insertions(+), 831 deletions(-)
More information about paws.analytics at CRAN
Permanent link
Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to sets of time series. Users can build dynamic nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2022) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.0 dated 2024-05-06 and 1.1.1 dated 2024-05-10
mvgam-1.1.0/mvgam/inst/doc/SS_model.svg |only mvgam-1.1.0/mvgam/inst/doc/vignette.rds |only mvgam-1.1.1/mvgam/DESCRIPTION | 8 mvgam-1.1.1/mvgam/MD5 | 108 mvgam-1.1.1/mvgam/NEWS.md | 9 mvgam-1.1.1/mvgam/R/add_nmixture.R | 2 mvgam-1.1.1/mvgam/R/loo.mvgam.R | 274 mvgam-1.1.1/mvgam/R/mvgam.R | 4536 ++++++------ mvgam-1.1.1/mvgam/README.md | 70 mvgam-1.1.1/mvgam/inst/doc/data_in_mvgam.R | 115 mvgam-1.1.1/mvgam/inst/doc/data_in_mvgam.Rmd | 2 mvgam-1.1.1/mvgam/inst/doc/data_in_mvgam.html | 194 mvgam-1.1.1/mvgam/inst/doc/forecast_evaluation.R | 133 mvgam-1.1.1/mvgam/inst/doc/forecast_evaluation.Rmd | 32 mvgam-1.1.1/mvgam/inst/doc/forecast_evaluation.html | 845 +- mvgam-1.1.1/mvgam/inst/doc/mvgam_overview.R | 228 mvgam-1.1.1/mvgam/inst/doc/mvgam_overview.Rmd | 96 mvgam-1.1.1/mvgam/inst/doc/mvgam_overview.html | 1378 +-- mvgam-1.1.1/mvgam/inst/doc/nmixtures.R | 188 mvgam-1.1.1/mvgam/inst/doc/nmixtures.Rmd | 2 mvgam-1.1.1/mvgam/inst/doc/nmixtures.html | 286 mvgam-1.1.1/mvgam/inst/doc/shared_states.R | 154 mvgam-1.1.1/mvgam/inst/doc/shared_states.Rmd | 45 mvgam-1.1.1/mvgam/inst/doc/shared_states.html | 461 - mvgam-1.1.1/mvgam/inst/doc/time_varying_effects.R | 159 mvgam-1.1.1/mvgam/inst/doc/time_varying_effects.Rmd | 52 mvgam-1.1.1/mvgam/inst/doc/time_varying_effects.html | 709 - mvgam-1.1.1/mvgam/inst/doc/trend_formulas.R | 277 mvgam-1.1.1/mvgam/inst/doc/trend_formulas.Rmd | 121 mvgam-1.1.1/mvgam/inst/doc/trend_formulas.html | 778 -- mvgam-1.1.1/mvgam/man/figures/README-beta_sim-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-13-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-14-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-15-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-16-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-17-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-18-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-19-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-20-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-21-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-22-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-23-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-24-1.png |binary mvgam-1.1.1/mvgam/man/figures/README-unnamed-chunk-8-1.png |binary mvgam-1.1.1/mvgam/man/mvgam_marginaleffects.Rd | 2 mvgam-1.1.1/mvgam/src/trend_funs.cpp | 18 mvgam-1.1.1/mvgam/tests/testthat/setup.R | 1 mvgam-1.1.1/mvgam/tests/testthat/test-example_processing.R | 1 mvgam-1.1.1/mvgam/tests/testthat/test-sim_mvgam.R | 77 mvgam-1.1.1/mvgam/vignettes/data_in_mvgam.Rmd | 2 mvgam-1.1.1/mvgam/vignettes/forecast_evaluation.Rmd | 32 mvgam-1.1.1/mvgam/vignettes/mvgam_overview.Rmd | 96 mvgam-1.1.1/mvgam/vignettes/nmixtures.Rmd | 2 mvgam-1.1.1/mvgam/vignettes/shared_states.Rmd | 45 mvgam-1.1.1/mvgam/vignettes/time_varying_effects.Rmd | 52 mvgam-1.1.1/mvgam/vignettes/trend_formulas.Rmd | 121 56 files changed, 5488 insertions(+), 6223 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of larg [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.14.2 dated 2024-02-28 and 1.15.0.3 dated 2024-05-10
wrMisc-1.14.2/wrMisc/inst/doc/doc |only wrMisc-1.15.0.3/wrMisc/DESCRIPTION | 11 wrMisc-1.15.0.3/wrMisc/MD5 | 159 - wrMisc-1.15.0.3/wrMisc/NAMESPACE | 1 wrMisc-1.15.0.3/wrMisc/R/adjustUnitPrefix.R | 136 - wrMisc-1.15.0.3/wrMisc/R/buildTree.R | 28 wrMisc-1.15.0.3/wrMisc/R/checkFilePath.R | 233 +- wrMisc-1.15.0.3/wrMisc/R/checkUnitPrefix.R |only wrMisc-1.15.0.3/wrMisc/R/coinPermTest.R | 19 wrMisc-1.15.0.3/wrMisc/R/colMedSds.R | 43 wrMisc-1.15.0.3/wrMisc/R/colSds.R | 19 wrMisc-1.15.0.3/wrMisc/R/colorAccording2.R | 44 wrMisc-1.15.0.3/wrMisc/R/combineRedundLinesInList.R | 9 wrMisc-1.15.0.3/wrMisc/R/combineReplFromListToMatr.R | 29 wrMisc-1.15.0.3/wrMisc/R/concatMatch.R | 8 wrMisc-1.15.0.3/wrMisc/R/convToNum.R | 9 wrMisc-1.15.0.3/wrMisc/R/fusePairs.R | 8 wrMisc-1.15.0.3/wrMisc/R/htmlSpecCharConv.R | 38 wrMisc-1.15.0.3/wrMisc/R/linModelSelect.R | 10 wrMisc-1.15.0.3/wrMisc/R/makeMAList.R | 44 wrMisc-1.15.0.3/wrMisc/R/matchMatrixLinesToRef.R | 172 - wrMisc-1.15.0.3/wrMisc/R/moderTest2grp.R | 74 wrMisc-1.15.0.3/wrMisc/R/moderTestXgrp.R | 52 wrMisc-1.15.0.3/wrMisc/R/normalizeThis.R | 47 wrMisc-1.15.0.3/wrMisc/R/organizeAsListOfRepl.R | 6 wrMisc-1.15.0.3/wrMisc/R/pVal2lfdr.R | 43 wrMisc-1.15.0.3/wrMisc/R/packageDownloadStat.R | 30 wrMisc-1.15.0.3/wrMisc/R/protectSpecChar.R | 31 wrMisc-1.15.0.3/wrMisc/R/randIndFx.R | 23 wrMisc-1.15.0.3/wrMisc/R/readCsvBatch.R | 25 wrMisc-1.15.0.3/wrMisc/R/readTabulatedBatch.R | 137 - wrMisc-1.15.0.3/wrMisc/R/readVarColumns.R | 10 wrMisc-1.15.0.3/wrMisc/R/readXlsxBatch.R | 45 wrMisc-1.15.0.3/wrMisc/R/rowMedSds.R | 28 wrMisc-1.15.0.3/wrMisc/R/sampNoDeMArrayLM.R | 28 wrMisc-1.15.0.3/wrMisc/R/searchLinesAtGivenSlope.R | 48 wrMisc-1.15.0.3/wrMisc/R/stableMode.R | 36 wrMisc-1.15.0.3/wrMisc/R/stdErrMedBoot.R | 26 wrMisc-1.15.0.3/wrMisc/R/test2factLimma.R | 78 wrMisc-1.15.0.3/wrMisc/R/trimRedundText.R | 64 wrMisc-1.15.0.3/wrMisc/R/writeCsv.R | 22 wrMisc-1.15.0.3/wrMisc/build/vignette.rds |binary wrMisc-1.15.0.3/wrMisc/inst/doc/wrMiscVignette1.R | 28 wrMisc-1.15.0.3/wrMisc/inst/doc/wrMiscVignette1.Rmd | 59 wrMisc-1.15.0.3/wrMisc/inst/doc/wrMiscVignette1.html | 1787 ++++++---------- wrMisc-1.15.0.3/wrMisc/man/adjustUnitPrefix.Rd | 32 wrMisc-1.15.0.3/wrMisc/man/buildTree.Rd | 5 wrMisc-1.15.0.3/wrMisc/man/checkFilePath.Rd | 23 wrMisc-1.15.0.3/wrMisc/man/checkUnitPrefix.Rd |only wrMisc-1.15.0.3/wrMisc/man/coinPermTest.Rd | 7 wrMisc-1.15.0.3/wrMisc/man/colMedSds.Rd | 8 wrMisc-1.15.0.3/wrMisc/man/colSds.Rd | 8 wrMisc-1.15.0.3/wrMisc/man/colorAccording2.Rd | 13 wrMisc-1.15.0.3/wrMisc/man/combineReplFromListToMatr.Rd | 8 wrMisc-1.15.0.3/wrMisc/man/convToNum.Rd | 9 wrMisc-1.15.0.3/wrMisc/man/dot-chooseGrpCol.Rd | 17 wrMisc-1.15.0.3/wrMisc/man/dot-trimFromEnd.Rd | 6 wrMisc-1.15.0.3/wrMisc/man/dot-trimFromStart.Rd | 6 wrMisc-1.15.0.3/wrMisc/man/dot-trimLeft.Rd | 4 wrMisc-1.15.0.3/wrMisc/man/dot-trimRight.Rd | 4 wrMisc-1.15.0.3/wrMisc/man/htmlSpecCharConv.Rd | 2 wrMisc-1.15.0.3/wrMisc/man/makeMAList.Rd | 4 wrMisc-1.15.0.3/wrMisc/man/matchMatrixLinesToRef.Rd | 3 wrMisc-1.15.0.3/wrMisc/man/moderTest2grp.Rd | 19 wrMisc-1.15.0.3/wrMisc/man/normalizeThis.Rd | 2 wrMisc-1.15.0.3/wrMisc/man/pVal2lfdr.Rd | 6 wrMisc-1.15.0.3/wrMisc/man/packageDownloadStat.Rd | 10 wrMisc-1.15.0.3/wrMisc/man/protectSpecChar.Rd | 3 wrMisc-1.15.0.3/wrMisc/man/randIndFx.Rd | 13 wrMisc-1.15.0.3/wrMisc/man/readCsvBatch.Rd | 2 wrMisc-1.15.0.3/wrMisc/man/readTabulatedBatch.Rd | 2 wrMisc-1.15.0.3/wrMisc/man/readVarColumns.Rd | 4 wrMisc-1.15.0.3/wrMisc/man/readXlsxBatch.Rd | 5 wrMisc-1.15.0.3/wrMisc/man/rowMedSds.Rd | 16 wrMisc-1.15.0.3/wrMisc/man/sampNoDeMArrayLM.Rd | 8 wrMisc-1.15.0.3/wrMisc/man/searchLinesAtGivenSlope.Rd | 6 wrMisc-1.15.0.3/wrMisc/man/stableMode.Rd | 2 wrMisc-1.15.0.3/wrMisc/man/stdErrMedBoot.Rd | 14 wrMisc-1.15.0.3/wrMisc/man/test2factLimma.Rd | 19 wrMisc-1.15.0.3/wrMisc/man/trimRedundText.Rd | 3 wrMisc-1.15.0.3/wrMisc/vignettes/wrMiscVignette1.Rmd | 59 81 files changed, 2143 insertions(+), 1956 deletions(-)
Title: Gaussian Process Models for Scalar and Functional Inputs
Description: Construction and smart selection of Gaussian process models
for analysis of computer experiments
with emphasis on treatment of functional inputs that are regularly sampled. This package
offers: (i) flexible modeling of functional-input regression
problems through the fairly general Gaussian process model; (ii)
built-in dimension reduction for functional inputs; (iii)
heuristic optimization of the structural parameters of the model
(e.g., active inputs, kernel function, type of distance).
An in-depth tutorial in the use of funGp is provided in
Betancourt et al. (2024) <doi:10.18637/jss.v109.i05> and
Metamodeling background is provided in
Betancourt et al. (2020) <doi:10.1016/j.ress.2020.106870>.
The algorithm for structural parameter optimization is described
in <https://hal.science/hal-02532713>.
Author: Jose Betancourt [cre, aut],
Francois Bachoc [aut],
Thierry Klein [aut],
Jeremy Rohmer [aut],
Yves Deville [ctb],
Deborah Idier [ctb]
Maintainer: Jose Betancourt <fungp.rpack@gmail.com>
Diff between funGp versions 0.3.2 dated 2023-04-25 and 1.0.0 dated 2024-05-10
DESCRIPTION | 16 +++++----- MD5 | 53 ++++++++++++++++----------------- NEWS.md | 18 +++++++++++ R/0_funGp_Doc.R | 39 ++++++++---------------- R/1_Xfgpm_Class.R | 36 +++++++++++----------- R/1_fgpm_Class.R | 44 +++++++++++++-------------- R/2_fgpKern_Class.R | 8 ++--- R/2_fgpProj_Class.R | 2 - R/3_ant_admin.R | 21 +++++++++++-- R/7_blackBoxFunctions.R | 32 ++++++++++---------- R/7_plottingFunctions.R | 18 +++++------ R/7_plottingFunctionsStandard.R | 12 +++---- README.md | 13 +++++--- build/partial.rdb |binary inst |only man/Xfgpm-class.Rd | 13 +++----- man/black-boxes.Rd | 32 ++++++++++---------- man/decay.Rd | 9 ++--- man/decay2probs.Rd | 9 ++--- man/fgpm-class.Rd | 14 +++----- man/fgpm.Rd | 30 ++++++++++-------- man/fgpm_factory.Rd | 23 ++++++++------ man/funGp-package.Rd | 64 ++++++++++++++++++++++++---------------- man/get_active_in.Rd | 9 ++++- man/kernel-class.Rd | 8 ++--- man/plot-fgpm-method.Rd | 12 +++---- man/proj-Class.Rd | 2 - man/which_on.Rd | 12 ++++++- 28 files changed, 300 insertions(+), 249 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre],
Joao Carmezim [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.2.0 dated 2024-04-09 and 0.3.0 dated 2024-05-10
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 8 +++++++ R/fc_split.R | 50 +++++++++++++++++++++++++++++++++++------------- README.md | 2 - inst/doc/flowchart.html | 2 - 6 files changed, 55 insertions(+), 23 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 1.0.6 dated 2024-04-29 and 1.0.7 dated 2024-05-10
rtpcr-1.0.6/rtpcr/R/qpcrANCOVA.r |only rtpcr-1.0.6/rtpcr/R/qpcrANOVA.r |only rtpcr-1.0.6/rtpcr/man/qpcrANCOVA.Rd |only rtpcr-1.0.6/rtpcr/man/qpcrANOVA.Rd |only rtpcr-1.0.7/rtpcr/DESCRIPTION | 8 rtpcr-1.0.7/rtpcr/MD5 | 58 - rtpcr-1.0.7/rtpcr/NAMESPACE | 5 rtpcr-1.0.7/rtpcr/R/multiplot.r | 2 rtpcr-1.0.7/rtpcr/R/oneFACTORplot.r | 81 +- rtpcr-1.0.7/rtpcr/R/package_data.r | 6 rtpcr-1.0.7/rtpcr/R/qpcrANOVAFC.r |only rtpcr-1.0.7/rtpcr/R/qpcrANOVARE.r |only rtpcr-1.0.7/rtpcr/R/qpcrMeans.r |only rtpcr-1.0.7/rtpcr/R/qpcrREPEATED.r | 51 - rtpcr-1.0.7/rtpcr/R/qpcrTTEST.r | 6 rtpcr-1.0.7/rtpcr/R/qpcrTTESTplot.r | 7 rtpcr-1.0.7/rtpcr/R/threeFACTORplot.r | 79 + rtpcr-1.0.7/rtpcr/R/twoFACTORplot.r | 94 +- rtpcr-1.0.7/rtpcr/data/data_efficiency.rda |binary rtpcr-1.0.7/rtpcr/inst/doc/vignette.R | 81 +- rtpcr-1.0.7/rtpcr/inst/doc/vignette.Rmd | 131 ++- rtpcr-1.0.7/rtpcr/inst/doc/vignette.html | 843 +++++++++++++++------ rtpcr-1.0.7/rtpcr/inst/extdata/data_efficiency.csv | 44 - rtpcr-1.0.7/rtpcr/man/data_efficiency.Rd | 5 rtpcr-1.0.7/rtpcr/man/multiplot.Rd | 2 rtpcr-1.0.7/rtpcr/man/oneFACTORplot.Rd | 10 rtpcr-1.0.7/rtpcr/man/qpcrANOVAFC.Rd |only rtpcr-1.0.7/rtpcr/man/qpcrANOVARE.Rd |only rtpcr-1.0.7/rtpcr/man/qpcrMeans.Rd |only rtpcr-1.0.7/rtpcr/man/qpcrREPEATED.Rd | 15 rtpcr-1.0.7/rtpcr/man/qpcrTTEST.Rd | 4 rtpcr-1.0.7/rtpcr/man/qpcrTTESTplot.Rd | 4 rtpcr-1.0.7/rtpcr/man/threeFACTORplot.Rd | 10 rtpcr-1.0.7/rtpcr/man/twoFACTORplot.Rd | 33 rtpcr-1.0.7/rtpcr/vignettes/vignette.Rmd | 131 ++- 35 files changed, 1164 insertions(+), 546 deletions(-)
Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Description: Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Munday [ctb],
Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.4.0 dated 2023-09-26 and 1.5.0 dated 2024-05-10
EpiNow2-1.4.0/EpiNow2/R/adjust.R |only EpiNow2-1.4.0/EpiNow2/R/dist.R |only EpiNow2-1.4.0/EpiNow2/inst/templates |only EpiNow2-1.4.0/EpiNow2/man/dist_spec_plus.Rd |only EpiNow2-1.4.0/EpiNow2/man/figures/unnamed-chunk-13-1.png |only EpiNow2-1.4.0/EpiNow2/man/figures/unnamed-chunk-14-1.png |only EpiNow2-1.4.0/EpiNow2/man/figures/unnamed-chunk-15-1.png |only EpiNow2-1.4.0/EpiNow2/man/figures/unnamed-chunk-17-1.png |only EpiNow2-1.4.0/EpiNow2/man/figures/unnamed-chunk-18-1.png |only EpiNow2-1.4.0/EpiNow2/man/figures/unnamed-chunk-19-1.png |only EpiNow2-1.4.0/EpiNow2/man/fit_model_with_vb.Rd |only EpiNow2-1.4.0/EpiNow2/man/tune_inv_gamma.Rd |only EpiNow2-1.4.0/EpiNow2/man/update_list.Rd |only EpiNow2-1.4.0/EpiNow2/tests/testthat/test-models |only EpiNow2-1.4.0/EpiNow2/tests/testthat/test-simulate_infections.R |only EpiNow2-1.5.0/EpiNow2/DESCRIPTION | 45 EpiNow2-1.5.0/EpiNow2/MD5 | 506 EpiNow2-1.5.0/EpiNow2/NAMESPACE | 73 EpiNow2-1.5.0/EpiNow2/NEWS.md | 73 EpiNow2-1.5.0/EpiNow2/R/EpiNow2-package.R | 2 EpiNow2-1.5.0/EpiNow2/R/checks.R |only EpiNow2-1.5.0/EpiNow2/R/create.R | 542 EpiNow2-1.5.0/EpiNow2/R/data.R | 44 EpiNow2-1.5.0/EpiNow2/R/deprecated.R |only EpiNow2-1.5.0/EpiNow2/R/dist_spec.R |only EpiNow2-1.5.0/EpiNow2/R/epinow-internal.R | 32 EpiNow2-1.5.0/EpiNow2/R/epinow.R | 108 EpiNow2-1.5.0/EpiNow2/R/estimate_delay.R |only EpiNow2-1.5.0/EpiNow2/R/estimate_infections.R | 575 EpiNow2-1.5.0/EpiNow2/R/estimate_secondary.R | 329 EpiNow2-1.5.0/EpiNow2/R/estimate_truncation.R | 263 EpiNow2-1.5.0/EpiNow2/R/extract.R | 209 EpiNow2-1.5.0/EpiNow2/R/fit.R |only EpiNow2-1.5.0/EpiNow2/R/get.R | 196 EpiNow2-1.5.0/EpiNow2/R/opts.R | 692 EpiNow2-1.5.0/EpiNow2/R/plot.R | 112 EpiNow2-1.5.0/EpiNow2/R/regional_epinow.R | 140 EpiNow2-1.5.0/EpiNow2/R/report.R | 166 EpiNow2-1.5.0/EpiNow2/R/setup.R | 55 EpiNow2-1.5.0/EpiNow2/R/simulate_infections.R | 334 EpiNow2-1.5.0/EpiNow2/R/simulate_secondary.R |only EpiNow2-1.5.0/EpiNow2/R/stan.R |only EpiNow2-1.5.0/EpiNow2/R/summarise.R | 148 EpiNow2-1.5.0/EpiNow2/R/utilities.R | 84 EpiNow2-1.5.0/EpiNow2/README.md | 513 EpiNow2-1.5.0/EpiNow2/build/partial.rdb |binary EpiNow2-1.5.0/EpiNow2/build/vignette.rds |binary EpiNow2-1.5.0/EpiNow2/data/example_generation_time.rda |only EpiNow2-1.5.0/EpiNow2/data/example_incubation_period.rda |only EpiNow2-1.5.0/EpiNow2/data/example_reporting_delay.rda |only EpiNow2-1.5.0/EpiNow2/data/example_truncated.rda |only EpiNow2-1.5.0/EpiNow2/inst/CITATION | 21 EpiNow2-1.5.0/EpiNow2/inst/WORDLIST | 36 EpiNow2-1.5.0/EpiNow2/inst/doc/EpiNow2.Rmd |only EpiNow2-1.5.0/EpiNow2/inst/doc/EpiNow2.html |only EpiNow2-1.5.0/EpiNow2/inst/doc/case-studies.R | 2 EpiNow2-1.5.0/EpiNow2/inst/doc/epinow.Rmd |only EpiNow2-1.5.0/EpiNow2/inst/doc/epinow.html |only EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections.R | 2 EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections.Rmd | 4 EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections.html | 4 EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections_options.Rmd |only EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections_options.html |only EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections_workflow.Rmd |only EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_infections_workflow.html |only EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_secondary.R | 2 EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_truncation.R | 2 EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_truncation.Rmd | 8 EpiNow2-1.5.0/EpiNow2/inst/doc/estimate_truncation.html | 8 EpiNow2-1.5.0/EpiNow2/inst/doc/gaussian_process_implementation_details.R | 2 EpiNow2-1.5.0/EpiNow2/inst/extdata |only EpiNow2-1.5.0/EpiNow2/inst/stan/data/delays.stan | 17 EpiNow2-1.5.0/EpiNow2/inst/stan/data/observation_model.stan | 1 EpiNow2-1.5.0/EpiNow2/inst/stan/data/observations.stan | 4 EpiNow2-1.5.0/EpiNow2/inst/stan/data/simulation_delays.stan | 10 EpiNow2-1.5.0/EpiNow2/inst/stan/data/simulation_rt.stan | 4 EpiNow2-1.5.0/EpiNow2/inst/stan/estimate_infections.stan | 237 EpiNow2-1.5.0/EpiNow2/inst/stan/estimate_secondary.stan | 46 EpiNow2-1.5.0/EpiNow2/inst/stan/estimate_truncation.stan | 29 EpiNow2-1.5.0/EpiNow2/inst/stan/functions/delays.stan | 70 EpiNow2-1.5.0/EpiNow2/inst/stan/functions/generated_quantities.stan | 24 EpiNow2-1.5.0/EpiNow2/inst/stan/functions/infections.stan | 6 EpiNow2-1.5.0/EpiNow2/inst/stan/functions/observation_model.stan | 57 EpiNow2-1.5.0/EpiNow2/inst/stan/functions/pmfs.stan | 53 EpiNow2-1.5.0/EpiNow2/inst/stan/functions/secondary.stan | 26 EpiNow2-1.5.0/EpiNow2/inst/stan/simulate_infections.stan | 38 EpiNow2-1.5.0/EpiNow2/inst/stan/simulate_secondary.stan | 47 EpiNow2-1.5.0/EpiNow2/man/Distributions.Rd |only EpiNow2-1.5.0/EpiNow2/man/EpiNow2-package.Rd | 9 EpiNow2-1.5.0/EpiNow2/man/add_day_of_week.Rd | 3 EpiNow2-1.5.0/EpiNow2/man/adjust_infection_to_report.Rd | 83 EpiNow2-1.5.0/EpiNow2/man/allocate_delays.Rd | 3 EpiNow2-1.5.0/EpiNow2/man/allocate_empty.Rd | 3 EpiNow2-1.5.0/EpiNow2/man/apply_tolerance.Rd |only EpiNow2-1.5.0/EpiNow2/man/backcalc_opts.Rd | 11 EpiNow2-1.5.0/EpiNow2/man/bootstrapped_dist_fit.Rd | 7 EpiNow2-1.5.0/EpiNow2/man/c.dist_spec.Rd | 19 EpiNow2-1.5.0/EpiNow2/man/calc_summary_measures.Rd | 2 EpiNow2-1.5.0/EpiNow2/man/calc_summary_stats.Rd | 4 EpiNow2-1.5.0/EpiNow2/man/check_reports_valid.Rd |only EpiNow2-1.5.0/EpiNow2/man/check_stan_delay.Rd |only EpiNow2-1.5.0/EpiNow2/man/clean_regions.Rd | 6 EpiNow2-1.5.0/EpiNow2/man/collapse.Rd |only EpiNow2-1.5.0/EpiNow2/man/construct_output.Rd | 4 EpiNow2-1.5.0/EpiNow2/man/convert_to_logmean.Rd | 2 EpiNow2-1.5.0/EpiNow2/man/convert_to_logsd.Rd | 2 EpiNow2-1.5.0/EpiNow2/man/convert_to_natural.Rd |only EpiNow2-1.5.0/EpiNow2/man/convolve_and_scale.Rd |only EpiNow2-1.5.0/EpiNow2/man/copy_results_to_latest.Rd | 4 EpiNow2-1.5.0/EpiNow2/man/create_backcalc_data.Rd | 15 EpiNow2-1.5.0/EpiNow2/man/create_clean_reported_cases.Rd | 41 EpiNow2-1.5.0/EpiNow2/man/create_complete_cases.Rd |only EpiNow2-1.5.0/EpiNow2/man/create_delay_inits.Rd |only EpiNow2-1.5.0/EpiNow2/man/create_future_rt.Rd | 10 EpiNow2-1.5.0/EpiNow2/man/create_gp_data.Rd | 16 EpiNow2-1.5.0/EpiNow2/man/create_initial_conditions.Rd | 9 EpiNow2-1.5.0/EpiNow2/man/create_obs_model.Rd | 16 EpiNow2-1.5.0/EpiNow2/man/create_rt_data.Rd | 14 EpiNow2-1.5.0/EpiNow2/man/create_shifted_cases.Rd | 46 EpiNow2-1.5.0/EpiNow2/man/create_stan_args.Rd | 31 EpiNow2-1.5.0/EpiNow2/man/create_stan_data.Rd | 48 EpiNow2-1.5.0/EpiNow2/man/create_stan_delays.Rd | 12 EpiNow2-1.5.0/EpiNow2/man/delay_opts.Rd | 35 EpiNow2-1.5.0/EpiNow2/man/discretise.Rd |only EpiNow2-1.5.0/EpiNow2/man/dist_fit.Rd | 15 EpiNow2-1.5.0/EpiNow2/man/dist_skel.Rd | 33 EpiNow2-1.5.0/EpiNow2/man/dist_spec.Rd | 100 EpiNow2-1.5.0/EpiNow2/man/epinow.Rd | 117 EpiNow2-1.5.0/EpiNow2/man/epinow2_cmdstan_model.Rd |only EpiNow2-1.5.0/EpiNow2/man/epinow2_rstan_model.Rd |only EpiNow2-1.5.0/EpiNow2/man/epinow2_stan_model.Rd |only EpiNow2-1.5.0/EpiNow2/man/estimate_delay.Rd | 11 EpiNow2-1.5.0/EpiNow2/man/estimate_infections.Rd | 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EpiNow2-1.5.0/EpiNow2/man/plot_CrIs.Rd | 6 EpiNow2-1.5.0/EpiNow2/man/plot_estimates.Rd | 44 EpiNow2-1.5.0/EpiNow2/man/plot_summary.Rd | 6 EpiNow2-1.5.0/EpiNow2/man/plus-.dist_spec.Rd | 33 EpiNow2-1.5.0/EpiNow2/man/print.dist_spec.Rd | 21 EpiNow2-1.5.0/EpiNow2/man/process_region.Rd | 7 EpiNow2-1.5.0/EpiNow2/man/process_regions.Rd | 10 EpiNow2-1.5.0/EpiNow2/man/regional_epinow.Rd | 116 EpiNow2-1.5.0/EpiNow2/man/regional_runtimes.Rd | 32 EpiNow2-1.5.0/EpiNow2/man/regional_summary.Rd | 40 EpiNow2-1.5.0/EpiNow2/man/report_cases.Rd | 52 EpiNow2-1.5.0/EpiNow2/man/report_plots.Rd | 33 EpiNow2-1.5.0/EpiNow2/man/rstan_opts.Rd | 21 EpiNow2-1.5.0/EpiNow2/man/rstan_sampling_opts.Rd | 18 EpiNow2-1.5.0/EpiNow2/man/rstan_vb_opts.Rd | 22 EpiNow2-1.5.0/EpiNow2/man/rt_opts.Rd | 8 EpiNow2-1.5.0/EpiNow2/man/run_region.Rd | 57 EpiNow2-1.5.0/EpiNow2/man/sample_approx_dist.Rd | 11 EpiNow2-1.5.0/EpiNow2/man/save_estimate_infections.Rd | 4 EpiNow2-1.5.0/EpiNow2/man/save_input.Rd | 10 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EpiNow2-1.5.0/EpiNow2/man/trunc_opts.Rd | 32 EpiNow2-1.5.0/EpiNow2/man/update_horizon.Rd | 10 EpiNow2-1.5.0/EpiNow2/man/update_secondary_args.Rd | 17 EpiNow2-1.5.0/EpiNow2/src/stanExports_dist_fit.h | 1485 - EpiNow2-1.5.0/EpiNow2/src/stanExports_estimate_infections.h | 9333 +++++----- EpiNow2-1.5.0/EpiNow2/src/stanExports_estimate_secondary.h | 5570 +++-- EpiNow2-1.5.0/EpiNow2/src/stanExports_estimate_truncation.h | 4706 ++--- EpiNow2-1.5.0/EpiNow2/src/stanExports_simulate_infections.h | 6941 +++---- EpiNow2-1.5.0/EpiNow2/src/stanExports_simulate_secondary.h | 4794 ++--- EpiNow2-1.5.0/EpiNow2/tests/testthat/_snaps/calc_CrI.md | 8 EpiNow2-1.5.0/EpiNow2/tests/testthat/_snaps/calc_CrIs.md | 18 EpiNow2-1.5.0/EpiNow2/tests/testthat/_snaps/calc_summary_measures.md | 18 EpiNow2-1.5.0/EpiNow2/tests/testthat/_snaps/calc_summary_stats.md | 10 EpiNow2-1.5.0/EpiNow2/tests/testthat/_snaps/simulate-infections.md |only EpiNow2-1.5.0/EpiNow2/tests/testthat/_snaps/simulate-secondary.md |only EpiNow2-1.5.0/EpiNow2/tests/testthat/setup.R | 8 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-adjust_infection_to_report.R | 37 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-checks.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-create_clean_reported_cases.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-create_future-rt.R | 4 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-create_obs_model.R | 36 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-create_stan_args.R | 5 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-create_stan_data.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-delays.R | 111 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-dist.R | 50 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-dist_spec.R | 378 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-epinow.R | 214 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-estimate_infections.R | 56 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-estimate_secondary.R | 159 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-estimate_truncation.R | 124 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-forecast-infections.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-get_dist.R | 18 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-opts.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-plot_estimates.R | 8 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-regional_epinow.R | 45 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-regional_runtimes.R | 12 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-regional_summary.R | 18 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-report_cases.R | 39 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-report_plots.R | 8 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-seeding-time.R | 14 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-simulate-infections.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-simulate-secondary.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-stan-convole.R | 1 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-stan-generated_quantities.R |only EpiNow2-1.5.0/EpiNow2/tests/testthat/test-stan-infections.R | 20 EpiNow2-1.5.0/EpiNow2/tests/testthat/test-stan-secondary.R | 26 EpiNow2-1.5.0/EpiNow2/vignettes/EpiNow2-unnamed-chunk-11-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/EpiNow2-unnamed-chunk-15-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/EpiNow2.Rmd |only EpiNow2-1.5.0/EpiNow2/vignettes/EpiNow2.Rmd.orig |only EpiNow2-1.5.0/EpiNow2/vignettes/epinow-epinow-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/epinow-regional_epinow-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/epinow-regional_epinow_multiple-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/epinow.Rmd |only EpiNow2-1.5.0/EpiNow2/vignettes/epinow.Rmd.orig |only EpiNow2-1.5.0/EpiNow2/vignettes/estimate_infections.Rmd | 4 EpiNow2-1.5.0/EpiNow2/vignettes/estimate_infections_options-bp-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/estimate_infections_options-data-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/estimate_infections_options-default-1.png |only EpiNow2-1.5.0/EpiNow2/vignettes/estimate_infections_options-fixed-1.png |only 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EpiNow2-1.5.0/EpiNow2/vignettes/estimate_truncation.Rmd | 8 EpiNow2-1.5.0/EpiNow2/vignettes/precompile.R |only 303 files changed, 21996 insertions(+), 21078 deletions(-)
Title: Linguistic Phonetic Fieldwork Tools
Description: There are a lot of different typical tasks that have to be solved during phonetic research and experiments. This includes creating a presentation that will contain all stimuli, renaming and concatenating multiple sound files recorded during a session, automatic annotation in 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Boersma & Weenink 2020 <https://www.fon.hum.uva.nl/praat/>), creating an html table with annotations and spectrograms, and converting multiple formats ('Praat' TextGrid, 'ELAN', 'EXMARaLDA', 'Audacity', subtitles '.srt', and 'FLEx' flextext). All of these tasks can be solved by a mixture of different tools (any programming language has programs for automatic renaming, and Praat contains scripts for concatenating and renaming files, etc.). 'phonfieldwork' provides a functionality that will make it easier to solve those tasks independently of any additional tools. You can also compare the functionality with ot [...truncated...]
Author: George Moroz [aut, cre] ,
Jonathan Keane [rev] ,
Niko Partanen [rev] ,
Valeria Buntiakova [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between phonfieldwork versions 0.0.13 dated 2024-04-15 and 0.0.14 dated 2024-05-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/utils.r | 2 +- build/vignette.rds |binary inst/doc/data_manipulation_with_tidyverse.html | 2 +- inst/doc/ethical_research_with_phonfieldwork.html | 4 ++-- inst/doc/phonfieldwork.html | 5 +++-- 8 files changed, 25 insertions(+), 16 deletions(-)
Title: Likelihood Based Inference
Description: Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference.
Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between LBI versions 0.1.0 dated 2023-12-12 and 0.1.1 dated 2024-05-10
LBI-0.1.0/LBI/man/RRL.Rd |only LBI-0.1.1/LBI/DESCRIPTION | 6 +++--- LBI-0.1.1/LBI/MD5 | 16 ++++++++-------- LBI-0.1.1/LBI/R/LInorm.R | 2 +- LBI-0.1.1/LBI/R/LInormVar.R | 2 +- LBI-0.1.1/LBI/R/LRT.R | 20 +++++++++----------- LBI-0.1.1/LBI/R/OneTwo.R | 8 ++++---- LBI-0.1.1/LBI/inst/NEWS.Rd | 6 ++++++ LBI-0.1.1/LBI/man/LIbin.Rd | 4 +--- LBI-0.1.1/LBI/man/RRLI.Rd |only 10 files changed, 33 insertions(+), 31 deletions(-)
Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including
those where counts or mortality rates of the reference population are
used. Currently supported: excess hazard models (Dickman, Sloggett,
Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean
survival times, relative/net survival (in particular the Ederer II
(Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and
Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and
standardized incidence and mortality ratios, all of which can be
easily adjusted for by covariates such as age. Fast splitting and
aggregation of 'Lexis' objects (from package 'Epi') and other
computations achieved using 'data.table'.
Author: Joonas Miettinen [cre, aut] ,
Matti Rantanen [aut],
Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between popEpi versions 0.4.11 dated 2023-08-23 and 0.4.12 dated 2024-05-10
popEpi-0.4.11/popEpi/tests/testthat/Rplots.pdf |only popEpi-0.4.12/popEpi/DESCRIPTION | 8 popEpi-0.4.12/popEpi/LICENSE | 4 popEpi-0.4.12/popEpi/MD5 | 69 +++---- popEpi-0.4.12/popEpi/NAMESPACE | 9 popEpi-0.4.12/popEpi/NEWS.md | 50 +++-- popEpi-0.4.12/popEpi/R/fractional_years.R | 2 popEpi-0.4.12/popEpi/R/mean_survival.R | 20 -- popEpi-0.4.12/popEpi/R/utility_functions.R | 8 popEpi-0.4.12/popEpi/README.md | 109 ++++------- popEpi-0.4.12/popEpi/build/partial.rdb |binary popEpi-0.4.12/popEpi/build/vignette.rds |binary popEpi-0.4.12/popEpi/inst/doc/sir.R | 8 popEpi-0.4.12/popEpi/inst/doc/sir.html | 28 +- popEpi-0.4.12/popEpi/inst/doc/survtab_examples.html | 50 ++--- popEpi-0.4.12/popEpi/man/RPL.Rd | 2 popEpi-0.4.12/popEpi/man/Surv.Rd | 12 - popEpi-0.4.12/popEpi/man/lines.sirspline.Rd | 4 popEpi-0.4.12/popEpi/man/lines.survtab.Rd | 4 popEpi-0.4.12/popEpi/man/plot.sirspline.Rd | 4 popEpi-0.4.12/popEpi/man/plot.survtab.Rd | 4 popEpi-0.4.12/popEpi/man/popEpi-package.Rd | 116 ++++++------ popEpi-0.4.12/popEpi/man/print.survtab.Rd | 4 popEpi-0.4.12/popEpi/man/rate.Rd | 8 popEpi-0.4.12/popEpi/man/relpois.Rd | 6 popEpi-0.4.12/popEpi/man/relpois_ag.Rd | 6 popEpi-0.4.12/popEpi/man/rpcurve.Rd | 4 popEpi-0.4.12/popEpi/man/sir.Rd | 6 popEpi-0.4.12/popEpi/man/sir_exp.Rd | 4 popEpi-0.4.12/popEpi/man/sir_ratio.Rd | 4 popEpi-0.4.12/popEpi/man/sirspline.Rd | 10 - popEpi-0.4.12/popEpi/man/summary.survtab.Rd | 4 popEpi-0.4.12/popEpi/man/survmean.Rd | 87 ++++----- popEpi-0.4.12/popEpi/man/survtab.Rd | 4 popEpi-0.4.12/popEpi/man/survtab_ag.Rd | 4 popEpi-0.4.12/popEpi/tests/testthat/test_survtab_observed.R | 109 ++++++----- 36 files changed, 399 insertions(+), 372 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-14 1.2.1
2021-12-10 1.2
2021-04-08 1.1
2021-01-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-10 0.5.1
2018-05-07 0.5.0
2017-07-26 0.4.3
Title: R Interface for Apache Sedona
Description: R interface for 'Apache Sedona' based on 'sparklyr'
(<https://sedona.apache.org>).
Author: Apache Sedona [aut, cre],
Jia Yu [ctb, cph],
Yitao Li [aut, cph] ,
The Apache Software Foundation [cph],
RStudio [cph]
Maintainer: Apache Sedona <private@sedona.apache.org>
Diff between apache.sedona versions 1.5.2 dated 2024-05-07 and 1.5.3 dated 2024-05-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dependencies.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-25 1.0.7
2019-12-17 1.0.6
2018-10-29 1.0.5
2017-11-30 1.0.4
2017-11-22 1.0.3
Title: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')
Description: Wrapper functions that interface with 'FSL'
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with 'FSL'
completely in R, where you pass R objects of class 'nifti', implemented by
package 'oro.nifti', and the function executes an 'FSL' command and returns an R
object of class 'nifti' if desired.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 2.25.2 dated 2022-08-25 and 2.25.3 dated 2024-05-10
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 4 R/fsl_cluster.R | 16 +- R/rpi_orient.R | 6 build/vignette.rds |binary inst/doc/dti_data.R | 2 inst/doc/dti_data.html | 313 +++++++++++++++++++++++++++---------------------- inst/doc/fslr.html | 182 +++++++++++++++++----------- man/fsl_cluster.Rd | 16 +- man/rpi_orient.Rd | 6 11 files changed, 332 insertions(+), 241 deletions(-)
Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply
formats to data frames or vectors. The package aims to provide
functionality similar to that of SAS® formats. Formats are assigned to
the format attribute on data frame columns. Then when the fdata()
function is called, a new data frame is created with the column data
formatted as specified. The package also contains a value() function
to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fmtr versions 1.6.3 dated 2024-01-09 and 1.6.4 dated 2024-05-10
DESCRIPTION | 10 +- MD5 | 114 +++++++++++++------------- NAMESPACE | 2 NEWS.md | 10 ++ R/fapply.R | 4 R/fcat.R | 22 ++--- R/flist.R | 175 ++++++++++++++++++++++++++++++++++++----- R/fmt.R | 39 +++++++-- R/fmtr.R | 3 build/vignette.rds |binary inst/doc/fmtr-convenience.html | 4 inst/doc/fmtr-example1.html | 2 inst/doc/fmtr-example2.html | 2 inst/doc/fmtr-fapply.html | 6 - inst/doc/fmtr-fapply2.html | 6 - inst/doc/fmtr-faq.R | 23 +++++ inst/doc/fmtr-faq.Rmd | 39 +++++++++ inst/doc/fmtr-faq.html | 33 +++++++ inst/doc/fmtr-fcat.html | 6 - inst/doc/fmtr-fdata.html | 6 - inst/doc/fmtr-helpers.html | 4 inst/doc/fmtr.R | 10 +- inst/doc/fmtr.Rmd | 8 - inst/doc/fmtr.html | 10 +- man/as.data.frame.fcat.Rd | 2 man/as.data.frame.fmt.Rd | 2 man/as.data.frame.fmt_lst.Rd | 6 - man/as.fcat.data.frame.Rd | 2 man/as.fcat.fmt_lst.Rd | 2 man/as.fcat.list.Rd | 2 man/as.fcat.tbl_df.Rd | 2 man/as.flist.Rd | 64 ++++++++++---- man/as.flist.data.frame.Rd | 66 +++++++++++---- man/as.flist.fcat.Rd | 66 +++++++++++---- man/as.flist.list.Rd | 6 - man/as.flist.tbl_df.Rd | 66 +++++++++++---- man/as.fmt.data.frame.Rd | 12 +- man/condition.Rd | 2 man/fcat.Rd | 2 man/flist.Rd | 66 +++++++++++---- man/fmtr.Rd | 9 ++ man/is.fcat.Rd | 2 man/is.flist.Rd | 6 - man/is.format.Rd | 2 man/labels.fmt.Rd | 2 man/print.fcat.Rd | 2 man/print.fmt.Rd | 2 man/print.fmt_lst.Rd | 6 - man/read.fcat.Rd | 6 - man/read.flist.Rd |only man/value.Rd | 2 man/write.fcat.Rd | 8 - man/write.flist.Rd |only tests/testthat/test-fapply.R | 16 +++ tests/testthat/test-fcat.R | 19 ++++ tests/testthat/test-flist.R | 71 +++++++++++++--- tests/testthat/test-fmt.R | 92 +++++++++++++++++++++ vignettes/fmtr-faq.Rmd | 39 +++++++++ vignettes/fmtr.Rmd | 8 - 59 files changed, 908 insertions(+), 290 deletions(-)