Title: Dose Escalation Design in Phase I Oncology Trial Using Bayesian
Logistic Regression Modeling
Description: Design dose escalation using Bayesian logistic regression modeling in Phase I oncology trial.
Author: Furong Sun <furongs@vt.edu>, Zhonggai Li <zli@bostonbiomedical.com>
Maintainer: Furong Sun <furongs@vt.edu>
Diff between blrm versions 1.0-1 dated 2019-06-24 and 1.0-2 dated 2022-07-06
ChangeLog | 8 DESCRIPTION | 12 - MD5 | 16 - NAMESPACE | 4 R/blrm_combo_ms.R | 252 +++++++++-------------- R/blrm_combo_ss.R | 494 +++++++++++++++++++++------------------------- R/blrm_mono_ms.R | 577 ++++++++++++++++++++++++++---------------------------- R/blrm_mono_ss.R | 360 ++++++++++++++++----------------- man/blrm.Rd | 288 ++++++++++++++------------ 9 files changed, 965 insertions(+), 1046 deletions(-)
Title: Functions for Web Development
Description: Organizational framework for web development in R including functions to
serve static and dynamic content via HTTP methods, includes the html5 package to
create HTML pages, and offers other utility functions for common tasks related
to web development.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between webdeveloper versions 1.0.0 dated 2022-06-22 and 1.0.1 dated 2022-07-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/webdeveloper.R | 31 ++++++++++++++++++------------- man/serveHTTP.Rd | 12 ++++++++---- 4 files changed, 32 insertions(+), 23 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).
Other 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 large data-sets by combining very close values.
Many times large experimental datasets need some additional filtering, adequate functions are provided.
Batch reading (or writing) of sets of files and combining data to arrays is supported, too.
Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.9.1 dated 2022-04-13 and 1.9.2 dated 2022-07-06
wrMisc-1.9.1/wrMisc/inst/doc/doc |only wrMisc-1.9.2/wrMisc/DESCRIPTION | 8 wrMisc-1.9.2/wrMisc/MD5 | 33 wrMisc-1.9.2/wrMisc/NAMESPACE | 5 wrMisc-1.9.2/wrMisc/R/combineAsN.R |only wrMisc-1.9.2/wrMisc/R/confInt.R |only wrMisc-1.9.2/wrMisc/R/moderTestXgrp.R | 9 wrMisc-1.9.2/wrMisc/R/replicateStructure.R | 18 wrMisc-1.9.2/wrMisc/R/rowGrpSums.R |only wrMisc-1.9.2/wrMisc/R/sortByNRepeated.R |only wrMisc-1.9.2/wrMisc/R/stableMode.R | 17 wrMisc-1.9.2/wrMisc/inst/doc/wrMiscVignette1.R | 19 wrMisc-1.9.2/wrMisc/inst/doc/wrMiscVignette1.Rmd | 45 - wrMisc-1.9.2/wrMisc/inst/doc/wrMiscVignette1.html | 968 +++++++++++----------- wrMisc-1.9.2/wrMisc/man/combineAsN.Rd |only wrMisc-1.9.2/wrMisc/man/confInt.Rd |only wrMisc-1.9.2/wrMisc/man/moderTestXgrp.Rd | 3 wrMisc-1.9.2/wrMisc/man/rowGrpSums.Rd |only wrMisc-1.9.2/wrMisc/man/sortByNRepeated.Rd |only wrMisc-1.9.2/wrMisc/man/stableMode.Rd | 10 wrMisc-1.9.2/wrMisc/vignettes/wrMiscVignette1.Rmd | 45 - 21 files changed, 684 insertions(+), 496 deletions(-)
Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for
single-case designs, including several non-overlap measures and parametric
effect size measures, and for estimating the gradual effects model developed
by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>.
Standard errors and confidence intervals (based on the assumption that the outcome
measurements are mutually independent) are provided for the subset of effect sizes
indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre],
Man Chen [aut],
Daniel M. Swan [aut],
Paulina Grekov [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between SingleCaseES versions 0.6.0 dated 2022-06-03 and 0.6.1 dated 2022-07-06
SingleCaseES-0.6.0/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/markdown/using_batch.md |only SingleCaseES-0.6.0/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/markdown/using_single.md |only SingleCaseES-0.6.1/SingleCaseES/DESCRIPTION | 16 SingleCaseES-0.6.1/SingleCaseES/MD5 | 61 SingleCaseES-0.6.1/SingleCaseES/NEWS.md | 11 SingleCaseES-0.6.1/SingleCaseES/R/data-processing.R | 48 SingleCaseES-0.6.1/SingleCaseES/R/non-overlap-measures.R | 19 SingleCaseES-0.6.1/SingleCaseES/R/parametric-measures.R | 8 SingleCaseES-0.6.1/SingleCaseES/inst/doc/Effect-size-definitions.Rmd | 66 SingleCaseES-0.6.1/SingleCaseES/inst/doc/Effect-size-definitions.html | 685 +- SingleCaseES-0.6.1/SingleCaseES/inst/doc/Using-SingleCaseES.R | 116 SingleCaseES-0.6.1/SingleCaseES/inst/doc/Using-SingleCaseES.Rmd | 568 -- SingleCaseES-0.6.1/SingleCaseES/inst/doc/Using-SingleCaseES.html | 2576 ++++------ SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/code-chunks/bcalc-aggregate-inputdata.R | 9 SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/code-chunks/bcalc-noaggregate-inputdata.R | 9 SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/code-chunks/dat-clean.R |only SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/markdown/About.md | 9 SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/markdown/Accessing.md | 90 SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/markdown/using_multiple_series.md |only SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/markdown/using_single_series.md |only SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/server.R | 142 SingleCaseES-0.6.1/SingleCaseES/inst/shiny-examples/SCD-effect-sizes/ui.R | 18 SingleCaseES-0.6.1/SingleCaseES/man/calc_phase_pairs.Rd | 28 SingleCaseES-0.6.1/SingleCaseES/tests/spelling.R | 4 SingleCaseES-0.6.1/SingleCaseES/tests/testdata/ex_issue73.csv |only SingleCaseES-0.6.1/SingleCaseES/tests/testdata/ex_issue74.csv |only SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-Pustejovsky-2015.R | 2 SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-Pustejovsky-2018-LRR.R | 4 SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-SCD-effect-sizes.R | 330 + SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-calc-phase-pairs.R | 32 SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-directional-arguments.R | 2 SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-tarlow-2017.R | 10 SingleCaseES-0.6.1/SingleCaseES/tests/testthat/test-trunc-constant.R | 31 SingleCaseES-0.6.1/SingleCaseES/vignettes/Effect-size-definitions.Rmd | 66 SingleCaseES-0.6.1/SingleCaseES/vignettes/Using-SingleCaseES.Rmd | 568 -- 35 files changed, 2755 insertions(+), 2773 deletions(-)
Title: R-Squared Measures for Multilevel Models
Description: Generates both total- and level-specific R-squared measures from
Rights and Sterba’s (2019) <doi:10.1037/met0000184> framework of R-squared measures for multilevel
models with random intercepts and/or slopes, which is based on a complete
decomposition of variance. Additionally generates graphical
representations of these R-squared measures to allow visualizing and
interpreting all measures in the framework together as an integrated set.
This framework subsumes 10 previously-developed R-squared measures for
multilevel models as special cases of 5 measures from the framework, and it
also includes several newly-developed measures. Measures in the framework
can be used to compute R-squared differences when comparing multilevel
models (following procedures in Rights & Sterba (2020) <doi:10.1080/00273171.2019.1660605>).
Author: Mairead Shaw [aut, cre],
Jason Rights [aut],
Sonya Sterba [aut],
Jessica Flake [aut]
Maintainer: Mairead Shaw <mairead.shaw@mail.mcgill.ca>
Diff between r2mlm versions 0.3.1 dated 2021-11-03 and 0.3.2 dated 2022-07-06
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- NEWS.md | 11 +++++++++++ R/r2mlm.R | 23 ++++++++++++----------- R/r2mlm3_manual.R | 2 ++ R/r2mlm_comp.R | 8 ++++---- R/r2mlm_comp_manual.R | 2 ++ R/r2mlm_long_manual.R | 3 ++- R/r2mlm_manual.R | 4 ++++ man/r2mlm.Rd | 16 +++++++++------- 11 files changed, 62 insertions(+), 39 deletions(-)
Title: Information Matrices for 'lmeStruct' and 'glsStruct' Objects
Description: Provides analytic derivatives and information matrices for
fitted linear mixed effects (lme) models and generalized least squares (gls) models
estimated using lme() (from package 'nlme') and gls() (from package 'nlme'), respectively.
The package includes functions for estimating the sampling variance-covariance of variance
component parameters using the inverse Fisher information. The variance components include
the parameters of the random effects structure (for lme models), the variance structure,
and the correlation structure. The expected and average forms of the Fisher information matrix
are used in the calculations, and models estimated by full maximum likelihood or
restricted maximum likelihood are supported. The package also includes a function for estimating
standardized mean difference effect sizes (Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>)
based on fitted lme or gls models.
Author: James Pustejovsky [aut] ,
Man Chen [aut, cre]
Maintainer: Man Chen <manchen9005@gmail.com>
Diff between lmeInfo versions 0.2.0 dated 2022-06-15 and 0.2.1 dated 2022-07-06
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/information-matrices.R | 1 + build/partial.rdb |binary inst/doc/Information-matrices-for-fitted-LME-models.html | 4 ++-- tests/testthat/test-weird-variable-names.R |only 7 files changed, 16 insertions(+), 10 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny'
apps and R markdown documents. A tree allows to represent hierarchical
data (e.g. the contents of a directory). Similar to the 'shinyTree'
package but offers more features and options, such as the grid
extension, restricting the drag-and-drop behavior, and settings for
the search functionality. It is possible to attach some data to the
nodes of a tree and then to get these data in 'Shiny' when a node is
selected. Also provides a 'Shiny' gadget allowing to manipulate one or
more folders, and a 'Shiny' module allowing to navigate in the server
side file system.
Author: Stephane Laurent [aut, cre],
jQuery contributors [ctb, cph] ,
Ivan Bozhanov [ctb, cph] ,
Vedran Opacic [ctb, cph] ,
Avi Deitcher [ctb, cph] ,
Philip Hutchison [ctb, cph] ,
Terence Eden [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 2.0.0 dated 2022-06-08 and 2.1.0 dated 2022-07-06
jsTreeR-2.0.0/jsTreeR/inst/htmlwidgets/OtherIcons |only jsTreeR-2.0.0/jsTreeR/inst/htmlwidgets/SuperTinyIcons |only jsTreeR-2.1.0/jsTreeR/DESCRIPTION | 48 jsTreeR-2.1.0/jsTreeR/MD5 | 1837 ++++++++---- jsTreeR-2.1.0/jsTreeR/NAMESPACE | 2 jsTreeR-2.1.0/jsTreeR/NEWS.md | 7 jsTreeR-2.1.0/jsTreeR/R/jstree.R | 29 jsTreeR-2.1.0/jsTreeR/R/jstreeExamples.R | 3 jsTreeR-2.1.0/jsTreeR/R/zzz.R | 53 jsTreeR-2.1.0/jsTreeR/README.md | 2 jsTreeR-2.1.0/jsTreeR/inst/examples/SuperTinyIcons/global.R | 28 jsTreeR-2.1.0/jsTreeR/inst/examples/SuperTinyIcons/server.R | 2 jsTreeR-2.1.0/jsTreeR/inst/examples/SuperTinyIcons/ui.R | 16 jsTreeR-2.1.0/jsTreeR/inst/examples/SuperTinyIcons/www |only jsTreeR-2.1.0/jsTreeR/inst/examples/imageIcon |only jsTreeR-2.1.0/jsTreeR/inst/htmlwidgets/jstreer.yaml | 8 jsTreeR-2.1.0/jsTreeR/inst/www/OtherIcons |only jsTreeR-2.1.0/jsTreeR/inst/www/SuperTinyIcons |only jsTreeR-2.1.0/jsTreeR/man/jstree.Rd | 11 jsTreeR-2.1.0/jsTreeR/man/jstreeExample.Rd | 3 20 files changed, 1455 insertions(+), 594 deletions(-)
Title: Tools for Clinical Research
Description: Every research team have their own script for data management, statistics and
most importantly hemodynamic indices. The purpose is to standardize scripts
utilized in clinical research. The hemodynamic indices can be used in a long-format dataframe,
and add both periods of interest (trigger-periods), and delete artifacts with deleter-files.
Transfer function analysis (Claassen et al. (2016) <doi:10.1177/0271678X15626425>) and
Mx (Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>) can be calculated using this package.
Author: Markus Harboe Olsen [cre, aut],
Christian Riberholt [ctb],
Ronan Berg [ctb],
Kirsten Moeller [ctb],
Janus Christian Jakobsen [ctb],
Aksel Karl Georg Jensen [ctb]
Maintainer: Markus Harboe Olsen <oel@oelfam.com>
Diff between clintools versions 0.9.4 dated 2022-06-22 and 0.9.5 dated 2022-07-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/dilations.R | 40 +++++++++++++++++++++++----------------- man/dilations.Rd | 5 ++++- 5 files changed, 39 insertions(+), 25 deletions(-)
Title: Classification of RNA Sequences using Complex Network and
Information Theory
Description: It makes the creation of networks from sequences of RNA, with this is done the abstraction of characteristics of these networks with a methodology of maximum entropy for the purpose of making a classification between the classes of the sequences. There are two data present in the 'BASiNET' package, "mRNA", and "ncRNA" with 10 sequences. These sequences were taken from the data set used in the article (LI, Aimin; ZHANG, Junying; ZHOU, Zhongyin, 2014) <doi:10.1186/1471-2105-15-311>, these sequences are used to run examples.
Author: Murilo Montanini Breve [aut] ,
Matheus Henrique Pimenta-Zanon [aut]
,
Fabricio Martins Lopes [aut, cre]
Maintainer: Fabricio Martins Lopes <fabricio@utfpr.edu.br>
Diff between BASiNETEntropy versions 0.99.3 dated 2022-07-05 and 0.99.4 dated 2022-07-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/classify.R | 1 - README.md | 6 +++--- inst/doc/BASiNETEntropy.html | 4 ++-- 5 files changed, 13 insertions(+), 14 deletions(-)
More information about BASiNETEntropy at CRAN
Permanent link
Title: R Interface to 'Quarto' Markdown Publishing System
Description: Convert R Markdown documents and 'Jupyter' notebooks to a variety of
output formats using 'Quarto'.
Author: JJ Allaire [aut, cre]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between quarto versions 1.1 dated 2022-01-06 and 1.2 dated 2022-07-06
quarto-1.1/quarto/man/quarto.Rd |only quarto-1.1/quarto/man/quarto_serve.Rd |only quarto-1.2/quarto/DESCRIPTION | 16 quarto-1.2/quarto/MD5 | 30 quarto-1.2/quarto/NAMESPACE | 3 quarto-1.2/quarto/R/publish.R | 2 quarto-1.2/quarto/R/quarto-package.R | 1 quarto-1.2/quarto/R/quarto.R | 12 quarto-1.2/quarto/R/render.R | 6 quarto-1.2/quarto/R/run.R | 20 quarto-1.2/quarto/README.md | 42 + quarto-1.2/quarto/build |only quarto-1.2/quarto/inst |only quarto-1.2/quarto/man/figures |only quarto-1.2/quarto/man/quarto_render.Rd | 4 quarto-1.2/quarto/man/quarto_run.Rd |only quarto-1.2/quarto/man/quarto_version.Rd |only quarto-1.2/quarto/tests/testthat/test-quarto.R |only quarto-1.2/quarto/tests/testthat/test.html | 911 ++++++++++++++++++------- quarto-1.2/quarto/vignettes |only 20 files changed, 770 insertions(+), 277 deletions(-)
Title: Tidy Model Stacking
Description: Model stacking is an ensemble technique
that involves training a model to combine the outputs of many
diverse statistical models, and has been shown to improve
predictive performance in a variety of settings. 'stacks'
implements a grammar for 'tidymodels'-aligned model stacking.
Author: Simon Couch [aut, cre],
Max Kuhn [aut],
RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between stacks versions 0.2.3 dated 2022-05-12 and 1.0.0 dated 2022-07-06
DESCRIPTION | 10 +++--- MD5 | 24 ++++++++-------- NEWS.md | 40 +++++++++++++++++++++------ R/add_candidates.R | 3 +- R/expressions.R | 2 - README.md | 2 + inst/doc/basics.R | 4 +- inst/doc/basics.Rmd | 4 +- inst/doc/basics.html | 38 +++++++++++-------------- inst/doc/classification.html | 62 +++++++++++++++++++++--------------------- man/stacks_description.Rd | 2 - tests/testthat/test_predict.R | 28 ++++++++++++++++++ vignettes/basics.Rmd | 4 +- 13 files changed, 136 insertions(+), 87 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.1.0 dated 2022-04-15 and 3.1.1 dated 2022-07-06
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- R/generic.predict.rfsrc.R | 2 +- R/rfsrc.R | 4 ++-- configure | 18 +++++++++--------- configure.ac | 2 +- data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/housing.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/peakVO2.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary data/wine.rda |binary inst/NEWS | 11 +++++++++-- man/randomForestSRC_package.Rd | 6 ++---- man/tune.rfsrc.Rd | 2 +- 20 files changed, 49 insertions(+), 44 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Retrieve Data from MacLeish Field Station
Description: Download data from the Ada and Archibald MacLeish Field
Station in Whately, MA. The Ada
and Archibald MacLeish Field Station is a 260-acre patchwork of
forest and farmland located in West Whately, MA that provides opportunities
for faculty and students to pursue environmental research, outdoor
education, and low-impact recreation
(see <https://www.smith.edu/about-smith/sustainable-smith/macleish> for more information).
This package contains
weather data over several years, and spatial data on various man-made and
natural structures.
Author: Benjamin S. Baumer [aut, cre] ,
Rose Goueth [aut],
Wencong Li [aut],
Weijia Zhang [ctb],
Nicholas Horton [ctb],
Dominique Kelly [aut] ,
Albert Y. Kim [aut]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between macleish versions 0.3.8 dated 2021-09-11 and 0.3.9 dated 2022-07-06
DESCRIPTION | 18 - MD5 | 15 - NAMESPACE | 5 NEWS.md | 5 R/phenocam.R |only build/vignette.rds |binary data/macleish_layers.rda |binary inst/doc/macleish.html | 441 ++++++++++++++++++++++++----------------- man/phenocam_image_url.Rd |only tests/testthat/test-phenocam.R |only 10 files changed, 293 insertions(+), 191 deletions(-)
Title: Easy Dockerfile Creation from R
Description: Build a Dockerfile straight from your R session.
'dockerfiler' allows you to create step by step a Dockerfile, and
provide convenient tools to wrap R code inside this Dockerfile.
Author: Colin Fay [cre, aut] ,
Vincent Guyader [aut] ,
Josiah Parry [aut] ,
Sebastien Rochette [aut]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between dockerfiler versions 0.1.4 dated 2021-09-03 and 0.2.0 dated 2022-07-06
dockerfiler-0.1.4/dockerfiler/tests/testthat/DESC_ |only dockerfiler-0.1.4/dockerfiler/tests/testthat/test-dockerignore.R |only dockerfiler-0.2.0/dockerfiler/DESCRIPTION | 48 + dockerfiler-0.2.0/dockerfiler/MD5 | 43 + dockerfiler-0.2.0/dockerfiler/NAMESPACE | 4 dockerfiler-0.2.0/dockerfiler/NEWS.md | 4 dockerfiler-0.2.0/dockerfiler/R/dock_from_desc.R | 46 + dockerfiler-0.2.0/dockerfiler/R/dock_from_renv.R |only dockerfiler-0.2.0/dockerfiler/R/dockerfile.R | 95 +-- dockerfiler-0.2.0/dockerfiler/R/dockerfiler-package.R |only dockerfiler-0.2.0/dockerfiler/R/dockerignore.R | 31 + dockerfiler-0.2.0/dockerfiler/build/vignette.rds |binary dockerfiler-0.2.0/dockerfiler/inst/DESCRIPTION |only dockerfiler-0.2.0/dockerfiler/inst/doc/dockerfile-from-renv-lock.R |only dockerfiler-0.2.0/dockerfiler/inst/doc/dockerfile-from-renv-lock.Rmd |only dockerfiler-0.2.0/dockerfiler/inst/doc/dockerfile-from-renv-lock.html |only dockerfiler-0.2.0/dockerfiler/inst/doc/dockerfiler.html | 214 ++++++++ dockerfiler-0.2.0/dockerfiler/inst/renv_Dockefile |only dockerfiler-0.2.0/dockerfiler/man/Dockerfile.Rd | 246 +--------- dockerfiler-0.2.0/dockerfiler/man/dock_from_renv.Rd |only dockerfiler-0.2.0/dockerfiler/man/docker_ignore_add.Rd | 2 dockerfiler-0.2.0/dockerfiler/man/dockerfiler-package.Rd |only dockerfiler-0.2.0/dockerfiler/man/dockerfiles.Rd | 10 dockerfiler-0.2.0/dockerfiler/man/gen_base_image.Rd |only dockerfiler-0.2.0/dockerfiler/man/get_sysreqs.Rd | 4 dockerfiler-0.2.0/dockerfiler/tests/testthat/DESCRIPTION |only dockerfiler-0.2.0/dockerfiler/tests/testthat/renv.lock |only dockerfiler-0.2.0/dockerfiler/tests/testthat/test-dock_from_desc.R | 192 +++---- dockerfiler-0.2.0/dockerfiler/tests/testthat/test-dock_from_renv.R |only dockerfiler-0.2.0/dockerfiler/tests/testthat/test-dockerbuild.R |only dockerfiler-0.2.0/dockerfiler/vignettes/dockerfile-from-renv-lock.Rmd |only 31 files changed, 480 insertions(+), 459 deletions(-)
Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre]
,
Bjoern-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between baseline versions 1.3-1 dated 2020-09-12 and 1.3-4 dated 2022-07-06
DESCRIPTION | 27 MD5 | 140 +- NAMESPACE | 56 - NEWS | 82 - R/aaa.R | 72 + R/baseline.R | 244 +++-- R/baseline.TAP.R | 144 ++- R/baseline.als.R | 277 +++-- R/baseline.fillPeaks.R | 425 ++++----- R/baseline.irls.R | 288 +++--- R/baseline.lowpass.R | 85 + R/baseline.medianWindow.R | 135 +- R/baseline.modpolyfit.R | 99 +- R/baseline.package.R |only R/baseline.peakDetection.R | 858 +++++++++--------- R/baseline.rfbaseline.R | 88 + R/baseline.rollingBall.R | 244 ++--- R/baseline.shirley.R | 221 +++- R/baselineGUI.R | 676 +++++++------- R/baselineGUI2.R | 802 +++++++++-------- R/custom.baseline.R | 146 +-- R/datasets.R |only R/globals.R | 16 R/optimWizard.R | 979 ++++++++++---------- R/optimisation.R | 1837 ++++++++++++++++++++++++--------------- R/plotBaseline.R | 328 +++--- R/plotOptim.R | 866 +++++++++--------- README.md | 35 data/datalist | 6 inst/CITATION | 30 man/PLSRTest-class.Rd | 82 - man/XPSdata.Rd | 68 - man/algorithm.Rd | 58 - man/baseline-class.Rd | 110 +- man/baseline-package.Rd | 170 +-- man/baseline.Rd | 150 +-- man/baseline.TAP.Rd | 112 +- man/baseline.als.Rd | 84 - man/baseline.fillPeaks.Rd | 80 - man/baseline.irls.Rd | 70 - man/baseline.lowpass.Rd | 78 - man/baseline.medianWindow.Rd | 80 - man/baseline.modpolyfit.Rd | 82 - man/baseline.peakDetection.Rd | 110 +- man/baseline.rfbaseline.Rd | 104 +- man/baseline.rollingBall.Rd | 72 - man/baseline.shirley.Rd | 182 +-- man/baselineAlg-class.Rd | 140 +- man/baselineAlgResult-class.Rd | 120 +- man/baselineAlgTest-class.Rd | 94 - man/baselineAlgorithms.Rd | 94 - man/baselineAlgorithmsGUI.Rd | 56 - man/baselineEnv.Rd | 78 - man/baselineGUI.Rd | 68 - man/custom.baseline.Rd | 140 +- man/doOptim.Rd | 122 +- man/funcName.Rd | 56 - man/getBaseline.Rd | 96 +- man/ind.min.Rd | 56 - man/milk.Rd | 70 - man/name.Rd | 52 - man/optimWizard.Rd | 77 - man/overall.min.Rd | 62 - man/param.Rd | 68 - man/param.ind.min.Rd | 62 - man/plotBaseline.Rd | 124 +- man/plotOptim.Rd | 56 - man/predictionResult-class.Rd | 106 +- man/predictionTest-class.Rd | 40 man/qualMeas.Rd | 156 +-- man/ridgeRegressionTest-class.Rd | 74 - man/runTest.Rd | 130 +- 72 files changed, 7216 insertions(+), 5879 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Eamon B. O'Dea [c [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 4.2 dated 2022-04-11 and 4.3 dated 2022-07-06
DESCRIPTION | 10 ++--- MD5 | 92 +++++++++++++++++++++++++-------------------------- R/bake.R | 30 +++++++++++++--- R/bsmc2.R | 4 +- R/csnippet.R | 7 +++ R/distributions.R | 2 - R/flow.R | 21 ++++------- R/plot.R | 2 - R/pomp_fun.R | 2 - R/rprocess_spec.R | 2 - R/sannbox.R | 2 - R/time.R | 12 ++++++ R/workhorses.R | 91 ++++++++++++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary data/LondonYorke.rda |binary data/bsflu.rda |binary data/ebolaWA2014.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 31 ++++++++++++++++- inst/NEWS.Rd | 13 +++++++ man/bake.Rd | 21 +++++++++-- man/bsflu.Rd | 17 ++++----- man/bsmc2.Rd | 4 +- man/csnippet.Rd | 9 ++++ man/distributions.Rd | 2 - man/dmeasure.Rd | 10 ++++- man/dprior.Rd | 2 - man/dprocess.Rd | 9 ++++ man/ebola.Rd | 6 +-- man/emeasure.Rd | 8 +++- man/flow.Rd | 10 ++++- man/kf.Rd | 43 ++++++++++++----------- man/nlf.Rd | 22 ++++++------ man/plot.Rd | 2 - man/probe_match.Rd | 12 ++++-- man/rinit.Rd | 2 - man/rmeasure.Rd | 8 +++- man/rprior.Rd | 2 - man/rprocess.Rd | 9 ++++ man/rprocess_spec.Rd | 2 - man/rw2.Rd | 19 ++++++---- man/skeleton.Rd | 8 +++- man/spect_match.Rd | 7 ++- man/time.Rd | 5 ++ man/traj_match.Rd | 20 +++++++---- man/vmeasure.Rd | 8 +++- 47 files changed, 408 insertions(+), 180 deletions(-)
Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a
series of functions related to sample size and power calculations for common analysis in the healthcare
field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and
proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients,
regression coefficients (linear, logistic and Cox), linear mixed model,
Cronbach's alpha, interobserver agreement, intraclass correlation coefficients,
limit of agreement on Bland-Altman plots,
area under the curve, sensitivity and specificity incorporating the prevalence of disease.
You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.
Author: Rogerio Boff Borges [aut, cre]
,
Guilherme Serpa Azambuja [aut]
,
Aline Castello Branco Mancuso [aut]
,
Vanessa Bielefeldt Leotti [aut]
,
Vânia Naomi Hirakata [aut] ,
Suzi Alves Camey [aut] ,
Stela Maris de Jezus Castro [aut]
,
Hospital de Clinicas d [...truncated...]
Maintainer: Rogerio Boff Borges <roborges@hcpa.edu.br>
Diff between PSS.Health versions 0.4.0 dated 2022-03-29 and 0.5.1 dated 2022-07-06
DESCRIPTION | 20 MD5 | 35 NAMESPACE | 8 R/PSS_Health.R | 9 build/vignette.rds |binary inst/PSS.Health/R/mod_desvio_padrao_agrupado.R |only inst/PSS.Health/R/modulo_1_media.R |only inst/PSS.Health/R/modulo_2_medias_dependentes.R |only inst/PSS.Health/R/modulo_2_medias_independentes.R |only inst/PSS.Health/R/modulo_2_proporcoes_independentes.R |only inst/PSS.Health/R/modulo_anova_uma_via.R |only inst/PSS.Health/R/modulo_auc.R |only inst/PSS.Health/R/modulo_cox.R |only inst/PSS.Health/R/modulo_kappa.R |only inst/PSS.Health/R/modulo_mc_nemar.R |only inst/PSS.Health/R/modulo_medidas_repetidas.R | 552 inst/PSS.Health/R/modulo_nao_inferioridade.R |only inst/PSS.Health/R/modulo_qui_quadrado.R |only inst/PSS.Health/R/modulo_regressao_linear.R |only inst/PSS.Health/R/modulo_regressao_logistica.R |only inst/PSS.Health/R/translation.R |only inst/PSS.Health/global.R | 362 inst/PSS.Health/server.R |12453 ++++++------------ inst/PSS.Health/ui.R | 4683 ------ inst/PSS.Health/www/Logo_ufrgs.jpg |only inst/PSS.Health/www/Logomarca_hcpa.png |only man/PSS_Health.Rd | 6 27 files changed, 4915 insertions(+), 13213 deletions(-)
Title: Single-Cell Integrator and Batch Effect Remover
Description: Remove batch effects by projecting query batches into the reference batch space.
Author: Dailin Gan [aut, cre] ,
Jun Li [aut]
Maintainer: Dailin Gan <dgan@nd.edu>
Diff between SCIBER versions 0.1.2 dated 2022-06-22 and 0.1.3 dated 2022-07-06
DESCRIPTION | 10 ++++++---- MD5 | 7 ++++++- build |only inst |only vignettes |only 5 files changed, 12 insertions(+), 5 deletions(-)
Title: Obtain Suggested Coordinate Reference System Information for
Spatial Data
Description: Uses data from the 'EPSG' Registry to look up suitable coordinate reference
system transformations for spatial datasets in R. Returns a data frame with 'CRS' codes
that can be used for 'CRS' transformation and mapping projects. Please see
the 'EPSG' Dataset Terms of Use at <https://epsg.org/terms-of-use.html> for more information.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between crsuggest versions 0.3.1 dated 2021-05-14 and 0.4 dated 2022-07-06
DESCRIPTION | 10 +++--- MD5 | 15 ++++----- NAMESPACE | 2 + R/crsuggest-package.R | 2 - R/guess_crs.R | 56 +++++++++++++++++++++++++++++---- R/suggest_crs.R | 83 ++++++++++++++++++++++++++++++++++++++++++++------ man/guess_crs.Rd | 11 ++++-- man/suggest_crs.Rd | 3 - man/view_crs.Rd |only 9 files changed, 148 insertions(+), 34 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Mueller [aut, cre] ,
Antoine Fabri [ctb],
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
Indrajeet Patil [ctb] ,
Maelle Salmon [ctb] ,
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>
Diff between dm versions 0.2.8 dated 2022-04-08 and 0.3.0 dated 2022-07-06
dm-0.2.8/dm/R/dm-from-src.R |only dm-0.2.8/dm/R/rows-db.R |only dm-0.2.8/dm/man/dm_get_referencing_tables.Rd |only dm-0.2.8/dm/man/dm_is_referenced.Rd |only dm-0.2.8/dm/man/dm_join_to_tbl.Rd |only dm-0.2.8/dm/man/get_returned_rows.Rd |only dm-0.2.8/dm/man/rows-db.Rd |only dm-0.2.8/dm/tests/testthat/test-dm-from-src.R |only dm-0.2.8/dm/tests/testthat/test-rows-db.R |only dm-0.3.0/dm/DESCRIPTION | 39 dm-0.3.0/dm/LICENSE | 2 dm-0.3.0/dm/MD5 | 423 ++++---- dm-0.3.0/dm/NAMESPACE | 52 - dm-0.3.0/dm/NEWS.md | 67 + dm-0.3.0/dm/R/aaa-dbplyr.R | 32 dm-0.3.0/dm/R/add-tbl.R | 2 dm-0.3.0/dm/R/build_copy_queries.R | 13 dm-0.3.0/dm/R/code-generation.R |only dm-0.3.0/dm/R/data-model-helpers.R | 31 dm-0.3.0/dm/R/datamodelr-code.R | 75 - dm-0.3.0/dm/R/db-helpers.R | 31 dm-0.3.0/dm/R/db-interface.R | 8 dm-0.3.0/dm/R/disambiguate.R | 8 dm-0.3.0/dm/R/disentangle.R |only dm-0.3.0/dm/R/dm.R | 386 ++++--- dm-0.3.0/dm/R/dm_from_con.R |only dm-0.3.0/dm/R/dm_get_con.R |only dm-0.3.0/dm/R/dm_wrap.R | 5 dm-0.3.0/dm/R/dplyr.R | 20 dm-0.3.0/dm/R/draw-dm.R | 46 dm-0.3.0/dm/R/enum_ops.R |only dm-0.3.0/dm/R/enumerate_all_paths.R |only dm-0.3.0/dm/R/examine-constraints.R | 4 dm-0.3.0/dm/R/filter-dm.R | 54 + dm-0.3.0/dm/R/filter-helpers.R | 3 dm-0.3.0/dm/R/financial-db-con.R | 8 dm-0.3.0/dm/R/financial.R | 2 dm-0.3.0/dm/R/flatten.R | 73 - dm-0.3.0/dm/R/foreign-keys.R | 25 dm-0.3.0/dm/R/global.R | 45 dm-0.3.0/dm/R/graph.R | 33 dm-0.3.0/dm/R/import.R | 1 dm-0.3.0/dm/R/json_nest.R |only dm-0.3.0/dm/R/json_nest_join.R |only dm-0.3.0/dm/R/json_pack.R |only dm-0.3.0/dm/R/json_pack_join.R |only dm-0.3.0/dm/R/key-helpers.R | 7 dm-0.3.0/dm/R/learn.R | 386 ++----- dm-0.3.0/dm/R/meta.R |only dm-0.3.0/dm/R/mssql.R |only dm-0.3.0/dm/R/nycflights13.R | 9 dm-0.3.0/dm/R/pack_join.R | 30 dm-0.3.0/dm/R/paste.R | 3 dm-0.3.0/dm/R/pixarfilms.R | 12 dm-0.3.0/dm/R/postgres.R |only dm-0.3.0/dm/R/primary-keys.R | 17 dm-0.3.0/dm/R/ptype.R | 3 dm-0.3.0/dm/R/reexport.R | 3 dm-0.3.0/dm/R/rows-dm.R | 72 + dm-0.3.0/dm/R/rows-truncate.R | 32 dm-0.3.0/dm/R/select-tbl.R | 2 dm-0.3.0/dm/R/select.R | 6 dm-0.3.0/dm/R/test-dm.R | 4 dm-0.3.0/dm/R/tidyr.R | 3 dm-0.3.0/dm/R/utils.R | 9 dm-0.3.0/dm/R/validate.R | 49 dm-0.3.0/dm/R/zoom.R | 12 dm-0.3.0/dm/R/zzx-deprecated.R | 8 dm-0.3.0/dm/R/zzz.R | 8 dm-0.3.0/dm/README.md | 65 - dm-0.3.0/dm/build/vignette.rds |binary dm-0.3.0/dm/inst/doc/dm.R | 36 dm-0.3.0/dm/inst/doc/dm.Rmd | 95 - dm-0.3.0/dm/inst/doc/dm.html | 525 +++++++--- dm-0.3.0/dm/inst/doc/howto-dm-copy.Rmd | 44 dm-0.3.0/dm/inst/doc/howto-dm-copy.html | 615 +++++++++--- dm-0.3.0/dm/inst/doc/howto-dm-db.R | 31 dm-0.3.0/dm/inst/doc/howto-dm-db.Rmd | 73 - dm-0.3.0/dm/inst/doc/howto-dm-db.html | 647 +++++++++---- dm-0.3.0/dm/inst/doc/howto-dm-df.R | 9 dm-0.3.0/dm/inst/doc/howto-dm-df.Rmd | 52 - dm-0.3.0/dm/inst/doc/howto-dm-df.html | 557 ++++++++--- dm-0.3.0/dm/inst/doc/howto-dm-rows.R | 11 dm-0.3.0/dm/inst/doc/howto-dm-rows.Rmd | 74 - dm-0.3.0/dm/inst/doc/howto-dm-rows.html | 518 +++++++--- dm-0.3.0/dm/inst/doc/howto-dm-theory.R | 20 dm-0.3.0/dm/inst/doc/howto-dm-theory.Rmd | 89 + dm-0.3.0/dm/inst/doc/howto-dm-theory.html | 573 +++++++++-- dm-0.3.0/dm/inst/doc/tech-dm-cdm.Rmd | 3 dm-0.3.0/dm/inst/doc/tech-dm-cdm.html | 254 ++++- dm-0.3.0/dm/inst/doc/tech-dm-class.R | 24 dm-0.3.0/dm/inst/doc/tech-dm-class.Rmd | 50 - dm-0.3.0/dm/inst/doc/tech-dm-class.html | 394 ++++++- dm-0.3.0/dm/inst/doc/tech-dm-draw.R | 2 dm-0.3.0/dm/inst/doc/tech-dm-draw.Rmd | 14 dm-0.3.0/dm/inst/doc/tech-dm-draw.html | 328 +++++- dm-0.3.0/dm/inst/doc/tech-dm-filter.html | 374 ++++++- dm-0.3.0/dm/inst/doc/tech-dm-join.R | 23 dm-0.3.0/dm/inst/doc/tech-dm-join.Rmd | 52 - dm-0.3.0/dm/inst/doc/tech-dm-join.html | 389 ++++++- dm-0.3.0/dm/inst/doc/tech-dm-low-level.R | 3 dm-0.3.0/dm/inst/doc/tech-dm-low-level.Rmd | 17 dm-0.3.0/dm/inst/doc/tech-dm-low-level.html | 348 ++++++ dm-0.3.0/dm/inst/doc/tech-dm-naming.Rmd | 18 dm-0.3.0/dm/inst/doc/tech-dm-naming.html | 252 ++++- dm-0.3.0/dm/inst/doc/tech-dm-zoom.R | 2 dm-0.3.0/dm/inst/doc/tech-dm-zoom.Rmd | 18 dm-0.3.0/dm/inst/doc/tech-dm-zoom.html | 330 +++++- dm-0.3.0/dm/man/check_key.Rd | 7 dm-0.3.0/dm/man/copy_dm_to.Rd | 2 dm-0.3.0/dm/man/deprecated.Rd | 49 dm-0.3.0/dm/man/dm.Rd | 55 - dm-0.3.0/dm/man/dm_add_fk.Rd | 2 dm-0.3.0/dm/man/dm_add_pk.Rd | 2 dm-0.3.0/dm/man/dm_disambiguate_cols.Rd | 6 dm-0.3.0/dm/man/dm_draw.Rd | 27 dm-0.3.0/dm/man/dm_examine_constraints.Rd | 4 dm-0.3.0/dm/man/dm_flatten_to_tbl.Rd | 40 dm-0.3.0/dm/man/dm_from_con.Rd |only dm-0.3.0/dm/man/dm_from_src.Rd | 29 dm-0.3.0/dm/man/dm_get_all_fks.Rd | 2 dm-0.3.0/dm/man/dm_get_all_pks.Rd | 2 dm-0.3.0/dm/man/dm_get_con.Rd |only dm-0.3.0/dm/man/dm_get_filters.Rd | 31 dm-0.3.0/dm/man/dm_has_pk.Rd | 2 dm-0.3.0/dm/man/dm_nrow.Rd | 2 dm-0.3.0/dm/man/dm_nycflights13.Rd | 12 dm-0.3.0/dm/man/dm_paste.Rd | 2 dm-0.3.0/dm/man/dm_pixarfilms.Rd | 6 dm-0.3.0/dm/man/dm_ptype.Rd | 3 dm-0.3.0/dm/man/dm_rename.Rd | 2 dm-0.3.0/dm/man/dm_rm_fk.Rd | 2 dm-0.3.0/dm/man/dm_rm_pk.Rd | 2 dm-0.3.0/dm/man/dm_rm_tbl.Rd | 2 dm-0.3.0/dm/man/dm_select.Rd | 2 dm-0.3.0/dm/man/dm_select_tbl.Rd | 2 dm-0.3.0/dm/man/dm_set_colors.Rd | 7 dm-0.3.0/dm/man/dm_validate.Rd |only dm-0.3.0/dm/man/dm_wrap_tbl.Rd | 5 dm-0.3.0/dm/man/dm_zoom_to.Rd | 3 dm-0.3.0/dm/man/dplyr_join.Rd | 9 dm-0.3.0/dm/man/dplyr_table_manipulation.Rd | 8 dm-0.3.0/dm/man/glimpse.dm.Rd |only dm-0.3.0/dm/man/json_nest.Rd |only dm-0.3.0/dm/man/json_nest_join.Rd |only dm-0.3.0/dm/man/json_pack.Rd |only dm-0.3.0/dm/man/json_pack_join.Rd |only dm-0.3.0/dm/man/materialize.Rd | 2 dm-0.3.0/dm/man/pack_join.Rd | 25 dm-0.3.0/dm/man/pull_tbl.Rd | 4 dm-0.3.0/dm/man/reexports.Rd | 3 dm-0.3.0/dm/man/rows-dm.Rd | 19 dm-0.3.0/dm/man/tidyr_table_manipulation.Rd | 2 dm-0.3.0/dm/man/utils_table_manipulation.Rd | 2 dm-0.3.0/dm/tests/testthat/_snaps/bind.md | 16 dm-0.3.0/dm/tests/testthat/_snaps/check_suggested.md | 2 dm-0.3.0/dm/tests/testthat/_snaps/code-generation.md |only dm-0.3.0/dm/tests/testthat/_snaps/df/db-interface.md | 136 +- dm-0.3.0/dm/tests/testthat/_snaps/df/meta |only dm-0.3.0/dm/tests/testthat/_snaps/disentangle.md |only dm-0.3.0/dm/tests/testthat/_snaps/dm.md | 291 +++++ dm-0.3.0/dm/tests/testthat/_snaps/dm_nest_tbl.md | 8 dm-0.3.0/dm/tests/testthat/_snaps/dm_wrap.md | 32 dm-0.3.0/dm/tests/testthat/_snaps/dplyr.md | 4 dm-0.3.0/dm/tests/testthat/_snaps/draw-dm.md | 46 dm-0.3.0/dm/tests/testthat/_snaps/duckdb |only dm-0.3.0/dm/tests/testthat/_snaps/enum-ops.md |only dm-0.3.0/dm/tests/testthat/_snaps/enumerate_all_paths.md |only dm-0.3.0/dm/tests/testthat/_snaps/error-helpers.md | 4 dm-0.3.0/dm/tests/testthat/_snaps/filter-dm.md | 66 - dm-0.3.0/dm/tests/testthat/_snaps/json.md |only dm-0.3.0/dm/tests/testthat/_snaps/json_nest.md |only dm-0.3.0/dm/tests/testthat/_snaps/json_pack.md |only dm-0.3.0/dm/tests/testthat/_snaps/learn.md |only dm-0.3.0/dm/tests/testthat/_snaps/maria |only dm-0.3.0/dm/tests/testthat/_snaps/meta.md |only dm-0.3.0/dm/tests/testthat/_snaps/mssql/db-interface.md | 18 dm-0.3.0/dm/tests/testthat/_snaps/mssql/meta |only dm-0.3.0/dm/tests/testthat/_snaps/mssql/meta.md |only dm-0.3.0/dm/tests/testthat/_snaps/paste.md | 2 dm-0.3.0/dm/tests/testthat/_snaps/postgres/db-interface.md | 18 dm-0.3.0/dm/tests/testthat/_snaps/postgres/meta |only dm-0.3.0/dm/tests/testthat/_snaps/rows-db.md | 117 +- dm-0.3.0/dm/tests/testthat/_snaps/rows-dm.md | 108 +- dm-0.3.0/dm/tests/testthat/_snaps/sqlite/db-interface.md | 18 dm-0.3.0/dm/tests/testthat/_snaps/tidyselect.md | 6 dm-0.3.0/dm/tests/testthat/_snaps/upgrade.md | 8 dm-0.3.0/dm/tests/testthat/_snaps/zzx-deprecated.md | 22 dm-0.3.0/dm/tests/testthat/helper-config-db.R | 5 dm-0.3.0/dm/tests/testthat/helper-print.R | 6 dm-0.3.0/dm/tests/testthat/helper-skip.R | 9 dm-0.3.0/dm/tests/testthat/helper-src.R | 77 + dm-0.3.0/dm/tests/testthat/helper-sync.R |only dm-0.3.0/dm/tests/testthat/test-add-tbl.R | 5 dm-0.3.0/dm/tests/testthat/test-bind.R | 4 dm-0.3.0/dm/tests/testthat/test-check_suggested.R | 2 dm-0.3.0/dm/tests/testthat/test-code-generation.R |only dm-0.3.0/dm/tests/testthat/test-db-helpers.R | 17 dm-0.3.0/dm/tests/testthat/test-db-interface.R | 6 dm-0.3.0/dm/tests/testthat/test-disentangle.R |only dm-0.3.0/dm/tests/testthat/test-dm.R | 54 + dm-0.3.0/dm/tests/testthat/test-dplyr-src.R | 6 dm-0.3.0/dm/tests/testthat/test-dplyr.R | 29 dm-0.3.0/dm/tests/testthat/test-enum-ops.R |only dm-0.3.0/dm/tests/testthat/test-enumerate_all_paths.R |only dm-0.3.0/dm/tests/testthat/test-error-helpers.R | 2 dm-0.3.0/dm/tests/testthat/test-examine-constraints.R | 1 dm-0.3.0/dm/tests/testthat/test-flatten.R | 34 dm-0.3.0/dm/tests/testthat/test-foreign-keys.R | 2 dm-0.3.0/dm/tests/testthat/test-json.R |only dm-0.3.0/dm/tests/testthat/test-json_nest.R |only dm-0.3.0/dm/tests/testthat/test-json_pack.R |only dm-0.3.0/dm/tests/testthat/test-learn.R | 224 +++- dm-0.3.0/dm/tests/testthat/test-meta.R |only dm-0.3.0/dm/tests/testthat/test-nest.R | 2 dm-0.3.0/dm/tests/testthat/test-pack_join.R | 32 dm-0.3.0/dm/tests/testthat/test-pool-support.R | 4 dm-0.3.0/dm/tests/testthat/test-rows-dm.R | 22 dm-0.3.0/dm/tests/testthat/test-table-surgery.R | 2 dm-0.3.0/dm/tests/testthat/test-tidyselect.R | 9 dm-0.3.0/dm/tests/testthat/test-upgrade.R | 8 dm-0.3.0/dm/tests/testthat/test-validate.R | 73 + dm-0.3.0/dm/tests/testthat/test-zoom.R | 1 dm-0.3.0/dm/tests/testthat/test-zzx-deprecated.R | 2 dm-0.3.0/dm/tests/testthat/test_dm_from_con.R |only dm-0.3.0/dm/vignettes/dm.Rmd | 95 - dm-0.3.0/dm/vignettes/howto-dm-copy.Rmd | 44 dm-0.3.0/dm/vignettes/howto-dm-db.Rmd | 73 - dm-0.3.0/dm/vignettes/howto-dm-df.Rmd | 52 - dm-0.3.0/dm/vignettes/howto-dm-rows.Rmd | 74 - dm-0.3.0/dm/vignettes/howto-dm-theory.Rmd | 89 + dm-0.3.0/dm/vignettes/setup/setup.R | 11 dm-0.3.0/dm/vignettes/tech-dm-cdm.Rmd | 3 dm-0.3.0/dm/vignettes/tech-dm-class.Rmd | 50 - dm-0.3.0/dm/vignettes/tech-dm-draw.Rmd | 14 dm-0.3.0/dm/vignettes/tech-dm-join.Rmd | 52 - dm-0.3.0/dm/vignettes/tech-dm-low-level.Rmd | 17 dm-0.3.0/dm/vignettes/tech-dm-naming.Rmd | 18 dm-0.3.0/dm/vignettes/tech-dm-zoom.Rmd | 18 239 files changed, 8437 insertions(+), 3211 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-01 0.1.1
Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2021,
<doi:10.1021/acs.analchem.1c00123>). Supported features include reading
spectral data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay
smoothing of spectral intensities with smooth_intens(), correcting
background noise with subtr_bg() in accordance with Zhao et al. (2007)
<doi:10.1366/000370207782597003>, and identifying spectra using an onboard
reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>).
Analyzed spectra can be shared with the Open Specy community. A Shiny app is
available via run_app() or online at
<https://openanalysis.org/openspecy/>.
Author: Win Cowger [cre, aut] ,
Zacharias Steinmetz [aut] ,
Andrew Gray [ctb] ,
Hannah Hapich [ctb] ,
Jennifer Lynch [ctb, dtc] ,
Hannah De Frond [ctb, dtc] ,
Keenan Munno [ctb, dtc] ,
Chelsea Rochman [ctb, dtc] ,
Sebastian Primpke [ctb, dtc] ,
Orestis Herod [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>
Diff between OpenSpecy versions 0.9.3 dated 2021-10-13 and 0.9.5 dated 2022-07-06
OpenSpecy-0.9.3/OpenSpecy/inst/shiny/data/costs.csv |only OpenSpecy-0.9.3/OpenSpecy/inst/shiny/data/donations.csv |only OpenSpecy-0.9.5/OpenSpecy/DESCRIPTION | 18 OpenSpecy-0.9.5/OpenSpecy/MD5 | 30 OpenSpecy-0.9.5/OpenSpecy/NEWS.md | 19 OpenSpecy-0.9.5/OpenSpecy/README.md | 13 OpenSpecy-0.9.5/OpenSpecy/build/partial.rdb |binary OpenSpecy-0.9.5/OpenSpecy/build/vignette.rds |binary OpenSpecy-0.9.5/OpenSpecy/inst/doc/sop.Rmd | 4 OpenSpecy-0.9.5/OpenSpecy/inst/doc/sop.html | 659 ++++++++- OpenSpecy-0.9.5/OpenSpecy/inst/shiny/server.R | 135 - OpenSpecy-0.9.5/OpenSpecy/inst/shiny/ui.R | 995 +++++++------- OpenSpecy-0.9.5/OpenSpecy/inst/shiny/www/dancing.jpg |only OpenSpecy-0.9.5/OpenSpecy/inst/shiny/www/favicon.png |only OpenSpecy-0.9.5/OpenSpecy/man/OpenSpecy-package.Rd | 8 OpenSpecy-0.9.5/OpenSpecy/man/share_spec.Rd | 3 OpenSpecy-0.9.5/OpenSpecy/tests/testthat/test-read_spec.R | 3 OpenSpecy-0.9.5/OpenSpecy/vignettes/sop.Rmd | 4 18 files changed, 1252 insertions(+), 639 deletions(-)
Title: Multiple Approximate Kernel Learning (MAKL)
Description: R package associated with the Multiple Approximate Kernel Learning (MAKL) algorithm proposed in <doi:10.1093/bioinformatics/btac241>. The algorithm fits multiple approximate kernel learning (MAKL) models that are fast, scalable and interpretable.
Author: Ayyuece Beguem Bektaş [aut, cre]
,
Mehmet Goenen [aut]
Maintainer: Ayyuece Beguem Bektaş <ayyucebektas17@ku.edu.tr>
Diff between MAKL versions 1.0.0 dated 2022-01-17 and 1.0.1 dated 2022-07-06
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------ R/makl_test.R | 34 ++++++++++---------------- R/makl_train.R | 58 ++++++++++++++++++++------------------------- inst/doc/makl_example.Rmd | 8 +++--- inst/doc/makl_example.html | 11 ++++---- man/makl_test.Rd | 13 +++------- man/makl_train.Rd | 11 +++----- vignettes/makl_example.Rmd | 8 +++--- 9 files changed, 75 insertions(+), 92 deletions(-)
Title: High Performance Colour Space Manipulation
Description: The encoding of colour can be handled in many different ways,
using different colour spaces. As different colour spaces have
different uses, efficient conversion between these representations are
important. The 'farver' package provides a set of functions that gives
access to very fast colour space conversion and comparisons
implemented in C++, and offers speed improvements over the
'convertColor' function in the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Berendea Nicolae [aut] ,
Romain Francois [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between farver versions 2.1.0 dated 2021-02-28 and 2.1.1 dated 2022-07-06
DESCRIPTION | 55 +++++++++++++------------------ MD5 | 34 +++++++++---------- NAMESPACE | 2 - NEWS.md | 5 ++ R/aaa.R | 5 +- R/compare_colour.R | 4 +- R/convert_colour.R | 4 +- R/decode.R | 2 - R/encode.R | 13 +++++-- R/farver-package.R | 8 +++- R/modify.R | 16 +++++---- R/native.R | 4 +- README.md | 49 ++++++++++++++------------- man/farver-package.Rd | 10 +---- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary src/init.cpp | 18 +++++----- tests/testthat.R | 8 ++++ 18 files changed, 124 insertions(+), 113 deletions(-)
Title: Assembling Long Gene Copies from Short Read Data
Description: Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.
Author: Lei Yang
Maintainer: Lei Yang <leiyangslu@gmail.com>
Diff between copyseparator versions 1.0.0 dated 2022-05-24 and 1.1.0 dated 2022-07-06
DESCRIPTION | 6 - MD5 | 22 ++-- NAMESPACE | 4 NEWS.md | 14 ++ R/copy_assemble.R | 259 ++++++++++++++++++++++++++++++++++++------------- R/copy_detect.R | 52 +++++---- R/copy_separate.R | 97 ++++++++++-------- R/copy_validate.R | 2 R/sep_assem.R |only R/subset_downsize.R | 8 - man/copy_separate.Rd | 13 ++ man/sep_assem.Rd |only man/subset_downsize.Rd | 2 13 files changed, 327 insertions(+), 152 deletions(-)
Title: Bayesian Quantile Regression for Ordinal Models
Description: Package provides functions for estimating Bayesian quantile regression with ordinal outcomes,
computing the covariate effects, model comparison measures, and inefficiency factor. The generic
ordinal model with 3 or more outcomes (labeled OR1 model) is estimated by a combination of Gibbs
sampling and Metropolis-Hastings algorithm. Whereas an ordinal model with exactly 3 outcomes
(labeled OR2 model) is estimated using Gibbs sampling only. For each model framework, there is a
specific function for estimation. The summary output produces estimates for regression quantiles
and two measures of model comparison — log of marginal likelihood and Deviance Information Criterion
(DIC). The package also has specific functions for computing the covariate effects and other functions
that aids either the estimation or inference in quantile ordinal models.
Rahman, M. A. (2016).“Bayesian Quantile Regression for Ordinal Models.” Bayesian
Analysis, II(I): 1-24 <doi: 10.1214/15-BA939>.
Yu, K., and Moyeed, R. A. (2001). “Bayesian Quantile Regression.” Statistics and
Probability Letters, 54(4): 437–447 <doi: 10.1016/S0167-7152(01)00124-9>.
Koenker, R., and Bassett, G. (1978).“Regression Quantiles.” Econometrica,
46(1): 33-50 <doi: 10.2307/1913643>.
Chib, S. (1995). “Marginal likelihood from the Gibbs output.” Journal of
the American Statistical Association, 90(432):1313–1321, 1995. <doi: 10.1080/01621459.1995.10476635>.
Chib, S., and Jeliazkov, I. (2001). “Marginal likelihood from the
Metropolis-Hastings output.” Journal of the American Statistical Association, 96(453):270–281, 2001. <doi: 10.1198/016214501750332848>.
Author: Mohammad Arshad Rahman Developer [aut],
Prajual Maheshwari [cre]
Maintainer: Prajual Maheshwari <prajual1391@gmail.com>
Diff between bqror versions 1.3.0 dated 2021-11-21 and 1.4.0 dated 2022-07-06
bqror-1.3.0/bqror/man/covariateEffect_or1.Rd |only bqror-1.3.0/bqror/man/covariateEffect_or2.Rd |only bqror-1.3.0/bqror/man/deviance_or1.Rd |only bqror-1.3.0/bqror/man/deviance_or2.Rd |only bqror-1.3.0/bqror/man/drawbeta_or1.Rd |only bqror-1.3.0/bqror/man/drawbeta_or2.Rd |only bqror-1.3.0/bqror/man/drawdelta_or1.Rd |only bqror-1.3.0/bqror/man/drawlatent_or1.Rd |only bqror-1.3.0/bqror/man/drawlatent_or2.Rd |only bqror-1.3.0/bqror/man/drawnu_or2.Rd |only bqror-1.3.0/bqror/man/drawsigma_or2.Rd |only bqror-1.3.0/bqror/man/draww_or1.Rd |only bqror-1.3.0/bqror/man/infactor_or1.Rd |only bqror-1.3.0/bqror/man/infactor_or2.Rd |only bqror-1.3.0/bqror/man/logMargLikelihood_or1.Rd |only bqror-1.3.0/bqror/man/logMargLikelihood_or2.Rd |only bqror-1.3.0/bqror/man/qrnegLogLike_or2.Rd |only bqror-1.3.0/bqror/man/qrnegLogLikensum_or1.Rd |only bqror-1.3.0/bqror/man/quantreg_or1.Rd |only bqror-1.3.0/bqror/man/quantreg_or2.Rd |only bqror-1.3.0/bqror/man/traceplot_or1.Rd |only bqror-1.3.0/bqror/man/traceplot_or2.Rd |only bqror-1.4.0/bqror/DESCRIPTION | 31 bqror-1.4.0/bqror/MD5 | 86 +- bqror-1.4.0/bqror/NAMESPACE | 47 - bqror-1.4.0/bqror/R/ORI.R | 1013 +++++++++++++----------- bqror-1.4.0/bqror/R/ORII.R | 799 +++++++++--------- bqror-1.4.0/bqror/R/bqror.R | 55 - bqror-1.4.0/bqror/R/data.R | 168 +-- bqror-1.4.0/bqror/data/Policy_Opinion.RData |binary bqror-1.4.0/bqror/man/Educational_Attainment.Rd | 33 bqror-1.4.0/bqror/man/Policy_Opinion.Rd | 29 bqror-1.4.0/bqror/man/alcdf.Rd | 18 bqror-1.4.0/bqror/man/alcdfstd.Rd | 14 bqror-1.4.0/bqror/man/bqror.Rd | 54 - bqror-1.4.0/bqror/man/covEffectOR1.Rd |only bqror-1.4.0/bqror/man/covEffectOR2.Rd |only bqror-1.4.0/bqror/man/data25j3.Rd | 21 bqror-1.4.0/bqror/man/data25j4.Rd | 23 bqror-1.4.0/bqror/man/data50j3.Rd | 21 bqror-1.4.0/bqror/man/data50j4.Rd | 23 bqror-1.4.0/bqror/man/data75j3.Rd | 21 bqror-1.4.0/bqror/man/data75j4.Rd | 23 bqror-1.4.0/bqror/man/devianceOR1.Rd |only bqror-1.4.0/bqror/man/devianceOR2.Rd |only bqror-1.4.0/bqror/man/drawbetaOR1.Rd |only bqror-1.4.0/bqror/man/drawbetaOR2.Rd |only bqror-1.4.0/bqror/man/drawdeltaOR1.Rd |only bqror-1.4.0/bqror/man/drawlatentOR1.Rd |only bqror-1.4.0/bqror/man/drawlatentOR2.Rd |only bqror-1.4.0/bqror/man/drawnuOR2.Rd |only bqror-1.4.0/bqror/man/drawsigmaOR2.Rd |only bqror-1.4.0/bqror/man/drawwOR1.Rd |only bqror-1.4.0/bqror/man/infactorOR1.Rd |only bqror-1.4.0/bqror/man/infactorOR2.Rd |only bqror-1.4.0/bqror/man/logLik.bqrorOR1.Rd |only bqror-1.4.0/bqror/man/logMargLikeOR1.Rd |only bqror-1.4.0/bqror/man/logMargLikeOR2.Rd |only bqror-1.4.0/bqror/man/qrminfundtheorem.Rd | 26 bqror-1.4.0/bqror/man/qrnegLogLikeOR2.Rd |only bqror-1.4.0/bqror/man/qrnegLogLikensumOR1.Rd |only bqror-1.4.0/bqror/man/quantregOR1.Rd |only bqror-1.4.0/bqror/man/quantregOR2.Rd |only bqror-1.4.0/bqror/man/rndald.Rd | 14 bqror-1.4.0/bqror/tests |only 65 files changed, 1285 insertions(+), 1234 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>,
Judith H. Pa [...truncated...]
Maintainer: Thimo Kasper <thimo.kasper@plus.ac.at>
Diff between dynRB versions 0.16 dated 2021-05-11 and 0.17 dated 2022-07-06
DESCRIPTION | 10 MD5 | 12 - build/vignette.rds |binary inst/doc/TutorialdynRB.R | 14 - inst/doc/TutorialdynRB.Rmd | 15 - inst/doc/TutorialdynRB.html | 478 +++++++++++++++++++++++++++----------------- vignettes/TutorialdynRB.Rmd | 15 - 7 files changed, 338 insertions(+), 206 deletions(-)
Title: UK Epidemiological Data Management
Description: Contains utilities and functions for the cleaning, processing and
management of patient level public health data for surveillance
and analysis held by the UK Health Security Agency, UKHSA.
Author: Alex Bhattacharya [aut, cre]
Maintainer: Alex Bhattacharya <alex.bhatt@gmail.com>
Diff between epidm versions 1.0.2 dated 2022-02-15 and 1.0.3 dated 2022-07-06
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/respeciate_generic.R | 13 +++++++++++++ R/sql_connect.R | 2 +- README.md | 5 +++-- 6 files changed, 34 insertions(+), 12 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
three public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', <https://clinicaltrials.gov/>) and
the 'ISRCTN' (<http://www.isrctn.com/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite' or 'MongoDB'; via package 'nodbi').
Functions are included to identify de-duplicated records,
to easily find and extract variables (fields) of interest even
from complex nesting as used by the registers, and
to update previous queries.
The package can be used for meta-analysis and trend-analysis of
the design and conduct as well as for results of clinical trials.
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.9.1 dated 2022-04-24 and 1.10.0 dated 2022-07-06
DESCRIPTION | 8 MD5 | 28 - NAMESPACE | 3 NEWS.md | 267 ++++++------------- R/main.R | 91 +++--- R/utils.R | 71 +++-- README.md | 23 + inst/doc/ctrdata_install.pdf |binary inst/doc/ctrdata_retrieve.pdf |binary inst/doc/ctrdata_summarise.pdf |binary inst/tinytest/test_ctrdata_ctrfindactivesubstance.R | 6 inst/tinytest/test_ctrdata_other_functions.R | 4 man/ctrFindActiveSubstanceSynonyms.Rd | 2 man/ctrLoadQueryIntoDb.Rd | 10 man/figures/README-ctrdata_results_neuroblastoma.png |binary 15 files changed, 249 insertions(+), 264 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. The central algorithm is
Fisher scoring and iterative reweighted least squares.
At the heart of this package are the vector generalized linear
and additive model (VGLM/VGAM) classes. VGLMs can be loosely
thought of as multivariate GLMs. VGAMs are data-driven
VGLMs that use smoothing. The book "Vector Generalized
Linear and Additive Models: With an Implementation in R"
(Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
the statistical framework and the package. Currently only
fixed-effects models are implemented. Many (100+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE. The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Hauck-Donner effect detection is implemented.
Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas Yee [aut, cre] ,
Cleve Moler [ctb]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.1-6 dated 2022-02-14 and 1.1-7 dated 2022-07-06
VGAM-1.1-6/VGAM/man/fill.Rd |only VGAM-1.1-7/VGAM/DESCRIPTION | 11 VGAM-1.1-7/VGAM/MD5 | 666 ++++++------ VGAM-1.1-7/VGAM/NAMESPACE | 6 VGAM-1.1-7/VGAM/NEWS | 28 VGAM-1.1-7/VGAM/R/aamethods.q | 9 VGAM-1.1-7/VGAM/R/family.actuary.R | 1153 +++++++++++++--------- VGAM-1.1-7/VGAM/R/family.aunivariate.R | 827 +++++++++------- VGAM-1.1-7/VGAM/R/family.binomial.R | 73 - VGAM-1.1-7/VGAM/R/family.bivariate.R | 538 ++++++---- VGAM-1.1-7/VGAM/R/family.categorical.R | 272 ++--- VGAM-1.1-7/VGAM/R/family.censored.R | 15 VGAM-1.1-7/VGAM/R/family.circular.R | 30 VGAM-1.1-7/VGAM/R/family.exp.R | 120 +- VGAM-1.1-7/VGAM/R/family.extremes.R | 421 +++++--- VGAM-1.1-7/VGAM/R/family.functions.R | 3 VGAM-1.1-7/VGAM/R/family.gait0.R | 520 ++++++++-- VGAM-1.1-7/VGAM/R/family.gaitd.R | 421 ++++++-- VGAM-1.1-7/VGAM/R/family.genetic.R | 155 +-- VGAM-1.1-7/VGAM/R/family.glmgam.R | 220 ++-- VGAM-1.1-7/VGAM/R/family.nbd.R | 259 +++-- VGAM-1.1-7/VGAM/R/family.normal.R | 360 ++++--- VGAM-1.1-7/VGAM/R/family.oneinf.R | 4 VGAM-1.1-7/VGAM/R/family.qreg.R | 718 ++++++++------ VGAM-1.1-7/VGAM/R/family.rcim.R | 8 VGAM-1.1-7/VGAM/R/family.rrr.R | 45 VGAM-1.1-7/VGAM/R/family.survival.R | 90 + VGAM-1.1-7/VGAM/R/family.univariate.R | 1380 +++++++++++++++++--------- VGAM-1.1-7/VGAM/R/family.zeroinf.R | 1435 ++++++++++++++++------------ VGAM-1.1-7/VGAM/R/links.q | 67 - VGAM-1.1-7/VGAM/R/model.matrix.vglm.q | 56 - VGAM-1.1-7/VGAM/R/residuals.vlm.q | 93 + VGAM-1.1-7/VGAM/R/rrvglm.control.q | 2 VGAM-1.1-7/VGAM/build/partial.rdb |binary VGAM-1.1-7/VGAM/data/Huggins89.t1.rda |binary VGAM-1.1-7/VGAM/data/Huggins89table1.rda |binary VGAM-1.1-7/VGAM/data/alclevels.rda |binary VGAM-1.1-7/VGAM/data/alcoff.rda |binary VGAM-1.1-7/VGAM/data/auuc.rda |binary VGAM-1.1-7/VGAM/data/backPain.rda |binary VGAM-1.1-7/VGAM/data/backPain2.rda |binary VGAM-1.1-7/VGAM/data/beggs.rda |binary VGAM-1.1-7/VGAM/data/car.all.rda |binary VGAM-1.1-7/VGAM/data/cfibrosis.rda |binary VGAM-1.1-7/VGAM/data/corbet.rda |binary VGAM-1.1-7/VGAM/data/crashbc.rda |binary VGAM-1.1-7/VGAM/data/crashf.rda |binary VGAM-1.1-7/VGAM/data/crashi.rda |binary VGAM-1.1-7/VGAM/data/crashmc.rda |binary VGAM-1.1-7/VGAM/data/crashp.rda |binary VGAM-1.1-7/VGAM/data/crashtr.rda |binary VGAM-1.1-7/VGAM/data/deermice.rda |binary VGAM-1.1-7/VGAM/data/ducklings.rda |binary VGAM-1.1-7/VGAM/data/finney44.rda |binary VGAM-1.1-7/VGAM/data/flourbeetle.rda |binary VGAM-1.1-7/VGAM/data/hspider.rda |binary VGAM-1.1-7/VGAM/data/lakeO.rda |binary VGAM-1.1-7/VGAM/data/leukemia.rda |binary VGAM-1.1-7/VGAM/data/lpossums.rda |only VGAM-1.1-7/VGAM/data/marital.nz.rda |binary VGAM-1.1-7/VGAM/data/melbmaxtemp.rda |binary VGAM-1.1-7/VGAM/data/pneumo.rda |binary VGAM-1.1-7/VGAM/data/prinia.rda |binary VGAM-1.1-7/VGAM/data/ruge.rda |binary VGAM-1.1-7/VGAM/data/toxop.rda |binary VGAM-1.1-7/VGAM/data/venice.rda |binary VGAM-1.1-7/VGAM/data/venice90.rda |binary VGAM-1.1-7/VGAM/data/wine.rda |binary VGAM-1.1-7/VGAM/man/Select.Rd | 2 VGAM-1.1-7/VGAM/man/acat.Rd | 16 VGAM-1.1-7/VGAM/man/alaplaceUC.Rd | 22 VGAM-1.1-7/VGAM/man/anovavglm.Rd | 54 - VGAM-1.1-7/VGAM/man/backPain.Rd | 6 VGAM-1.1-7/VGAM/man/beggs.Rd | 8 VGAM-1.1-7/VGAM/man/bell.Rd | 4 VGAM-1.1-7/VGAM/man/benfUC.Rd | 13 VGAM-1.1-7/VGAM/man/benini.Rd | 25 VGAM-1.1-7/VGAM/man/beniniUC.Rd | 20 VGAM-1.1-7/VGAM/man/betaII.Rd | 30 VGAM-1.1-7/VGAM/man/betaR.Rd | 45 VGAM-1.1-7/VGAM/man/betabinomUC.Rd | 76 - VGAM-1.1-7/VGAM/man/betabinomial.Rd | 87 - VGAM-1.1-7/VGAM/man/betabinomialff.Rd | 114 +- VGAM-1.1-7/VGAM/man/betaff.Rd | 70 - VGAM-1.1-7/VGAM/man/betageomUC.Rd | 18 VGAM-1.1-7/VGAM/man/betageometric.Rd | 32 VGAM-1.1-7/VGAM/man/betanormUC.Rd | 22 VGAM-1.1-7/VGAM/man/betaprime.Rd | 17 VGAM-1.1-7/VGAM/man/biamhcop.Rd | 9 VGAM-1.1-7/VGAM/man/biamhcopUC.Rd | 4 VGAM-1.1-7/VGAM/man/biclaytoncop.Rd | 30 VGAM-1.1-7/VGAM/man/biclaytoncopUC.Rd | 12 VGAM-1.1-7/VGAM/man/bifgmcop.Rd | 27 VGAM-1.1-7/VGAM/man/bifgmcopUC.Rd | 4 VGAM-1.1-7/VGAM/man/bifgmexp.Rd | 28 VGAM-1.1-7/VGAM/man/bifrankcop.Rd | 32 VGAM-1.1-7/VGAM/man/bifrankcopUC.Rd | 4 VGAM-1.1-7/VGAM/man/bigamma.mckay.Rd | 50 VGAM-1.1-7/VGAM/man/bigumbelIexp.Rd | 26 VGAM-1.1-7/VGAM/man/bilogisUC.Rd | 26 VGAM-1.1-7/VGAM/man/bilogistic.Rd | 61 - VGAM-1.1-7/VGAM/man/binom2.or.Rd | 111 +- VGAM-1.1-7/VGAM/man/binom2.orUC.Rd | 84 - VGAM-1.1-7/VGAM/man/binom2.rho.Rd | 37 VGAM-1.1-7/VGAM/man/binom2.rhoUC.Rd | 49 VGAM-1.1-7/VGAM/man/binomialff.Rd | 3 VGAM-1.1-7/VGAM/man/binormal.Rd | 15 VGAM-1.1-7/VGAM/man/binormalUC.Rd | 18 VGAM-1.1-7/VGAM/man/binormalcop.Rd | 40 VGAM-1.1-7/VGAM/man/binormcopUC.Rd | 4 VGAM-1.1-7/VGAM/man/biplackettcop.Rd | 25 VGAM-1.1-7/VGAM/man/biplackettcopUC.Rd | 12 VGAM-1.1-7/VGAM/man/biplot-methods.Rd | 8 VGAM-1.1-7/VGAM/man/bisa.Rd | 36 VGAM-1.1-7/VGAM/man/bisaUC.Rd | 13 VGAM-1.1-7/VGAM/man/bistudentt.Rd | 33 VGAM-1.1-7/VGAM/man/bistudenttUC.Rd | 49 VGAM-1.1-7/VGAM/man/bmi.nz.Rd | 12 VGAM-1.1-7/VGAM/man/borel.tanner.Rd | 33 VGAM-1.1-7/VGAM/man/bortUC.Rd | 10 VGAM-1.1-7/VGAM/man/brat.Rd | 12 VGAM-1.1-7/VGAM/man/bratt.Rd | 16 VGAM-1.1-7/VGAM/man/cardUC.Rd | 16 VGAM-1.1-7/VGAM/man/cratio.Rd | 22 VGAM-1.1-7/VGAM/man/cumulative.Rd | 46 VGAM-1.1-7/VGAM/man/dagum.Rd | 70 - VGAM-1.1-7/VGAM/man/dagumUC.Rd | 38 VGAM-1.1-7/VGAM/man/deermice.Rd | 33 VGAM-1.1-7/VGAM/man/deplot.lmscreg.Rd | 39 VGAM-1.1-7/VGAM/man/depvar.Rd | 4 VGAM-1.1-7/VGAM/man/df.residual.Rd | 8 VGAM-1.1-7/VGAM/man/dgaitdplot.Rd | 63 - VGAM-1.1-7/VGAM/man/diffzeta.Rd | 27 VGAM-1.1-7/VGAM/man/diffzetaUC.Rd | 9 VGAM-1.1-7/VGAM/man/dirichlet.Rd | 51 VGAM-1.1-7/VGAM/man/dirmul.old.Rd | 75 - VGAM-1.1-7/VGAM/man/dirmultinomial.Rd | 96 + VGAM-1.1-7/VGAM/man/double.cens.normal.Rd | 25 VGAM-1.1-7/VGAM/man/double.expbinomial.Rd | 124 +- VGAM-1.1-7/VGAM/man/drop1.Rd | 73 - VGAM-1.1-7/VGAM/man/eexpUC.Rd | 14 VGAM-1.1-7/VGAM/man/enormUC.Rd | 7 VGAM-1.1-7/VGAM/man/erlang.Rd | 34 VGAM-1.1-7/VGAM/man/eunifUC.Rd | 16 VGAM-1.1-7/VGAM/man/explink.Rd | 29 VGAM-1.1-7/VGAM/man/felix.Rd | 6 VGAM-1.1-7/VGAM/man/felixUC.Rd | 3 VGAM-1.1-7/VGAM/man/fff.Rd | 44 VGAM-1.1-7/VGAM/man/fill1.Rd |only VGAM-1.1-7/VGAM/man/fisherzlink.Rd | 38 VGAM-1.1-7/VGAM/man/fisk.Rd | 28 VGAM-1.1-7/VGAM/man/fiskUC.Rd | 11 VGAM-1.1-7/VGAM/man/fittedvlm.Rd | 35 VGAM-1.1-7/VGAM/man/foldnormUC.Rd | 20 VGAM-1.1-7/VGAM/man/foldnormal.Rd | 52 - VGAM-1.1-7/VGAM/man/foldsqrtlink.Rd | 56 - VGAM-1.1-7/VGAM/man/frechet.Rd | 80 + VGAM-1.1-7/VGAM/man/frechetUC.Rd | 16 VGAM-1.1-7/VGAM/man/freund61.Rd | 64 - VGAM-1.1-7/VGAM/man/gaitdbinomUC.Rd | 16 VGAM-1.1-7/VGAM/man/gaitdlog.Rd | 20 VGAM-1.1-7/VGAM/man/gaitdlogUC.Rd | 8 VGAM-1.1-7/VGAM/man/gaitdnbinomUC.Rd | 30 VGAM-1.1-7/VGAM/man/gaitdnbinomial.Rd | 111 +- VGAM-1.1-7/VGAM/man/gaitdpoisUC.Rd | 82 - VGAM-1.1-7/VGAM/man/gaitdpoisson.Rd | 157 +-- VGAM-1.1-7/VGAM/man/gaitdzeta.Rd | 14 VGAM-1.1-7/VGAM/man/gaitzetaUC.Rd | 21 VGAM-1.1-7/VGAM/man/gengammaUC.Rd | 2 VGAM-1.1-7/VGAM/man/genpois1UC.Rd | 10 VGAM-1.1-7/VGAM/man/gevUC.Rd | 32 VGAM-1.1-7/VGAM/man/gompertzUC.Rd | 7 VGAM-1.1-7/VGAM/man/gpdUC.Rd | 26 VGAM-1.1-7/VGAM/man/gumbelIIUC.Rd | 10 VGAM-1.1-7/VGAM/man/gumbelUC.Rd | 6 VGAM-1.1-7/VGAM/man/hdeff.Rd | 16 VGAM-1.1-7/VGAM/man/hspider.Rd | 43 VGAM-1.1-7/VGAM/man/huber.Rd | 28 VGAM-1.1-7/VGAM/man/huberUC.Rd | 38 VGAM-1.1-7/VGAM/man/hypersecant.Rd | 41 VGAM-1.1-7/VGAM/man/hzetaUC.Rd | 12 VGAM-1.1-7/VGAM/man/iam.Rd | 72 - VGAM-1.1-7/VGAM/man/identitylink.Rd | 10 VGAM-1.1-7/VGAM/man/inv.binomial.Rd | 32 VGAM-1.1-7/VGAM/man/inv.gaussianff.Rd | 32 VGAM-1.1-7/VGAM/man/inv.lomax.Rd | 20 VGAM-1.1-7/VGAM/man/inv.lomaxUC.Rd | 15 VGAM-1.1-7/VGAM/man/inv.paralogistic.Rd | 38 VGAM-1.1-7/VGAM/man/inv.paralogisticUC.Rd | 27 VGAM-1.1-7/VGAM/man/is.buggy.Rd | 47 VGAM-1.1-7/VGAM/man/is.parallel.Rd | 4 VGAM-1.1-7/VGAM/man/is.zero.Rd | 15 VGAM-1.1-7/VGAM/man/kendall.tau.Rd | 20 VGAM-1.1-7/VGAM/man/kumar.Rd | 30 VGAM-1.1-7/VGAM/man/kumarUC.Rd | 26 VGAM-1.1-7/VGAM/man/laplace.Rd | 37 VGAM-1.1-7/VGAM/man/laplaceUC.Rd | 18 VGAM-1.1-7/VGAM/man/leipnik.Rd | 58 - VGAM-1.1-7/VGAM/man/lerch.Rd | 18 VGAM-1.1-7/VGAM/man/leukemia.Rd | 5 VGAM-1.1-7/VGAM/man/levy.Rd | 42 VGAM-1.1-7/VGAM/man/lgammaUC.Rd | 26 VGAM-1.1-7/VGAM/man/lgammaff.Rd | 35 VGAM-1.1-7/VGAM/man/lino.Rd | 42 VGAM-1.1-7/VGAM/man/linoUC.Rd | 3 VGAM-1.1-7/VGAM/man/lms.bcg.Rd | 37 VGAM-1.1-7/VGAM/man/lms.bcn.Rd | 102 + VGAM-1.1-7/VGAM/man/lms.yjn.Rd | 82 - VGAM-1.1-7/VGAM/man/logF.Rd | 23 VGAM-1.1-7/VGAM/man/logUC.Rd | 4 VGAM-1.1-7/VGAM/man/logistic.Rd | 18 VGAM-1.1-7/VGAM/man/logitlink.Rd | 91 - VGAM-1.1-7/VGAM/man/logitoffsetlink.Rd | 13 VGAM-1.1-7/VGAM/man/loglapUC.Rd | 26 VGAM-1.1-7/VGAM/man/loglaplace.Rd | 113 +- VGAM-1.1-7/VGAM/man/loglinb2.Rd | 39 VGAM-1.1-7/VGAM/man/loglinb3.Rd | 47 VGAM-1.1-7/VGAM/man/loglink.Rd | 32 VGAM-1.1-7/VGAM/man/logloglink.Rd | 22 VGAM-1.1-7/VGAM/man/lomaxUC.Rd | 9 VGAM-1.1-7/VGAM/man/lpossums.Rd |only VGAM-1.1-7/VGAM/man/lqnorm.Rd | 47 VGAM-1.1-7/VGAM/man/lvplot.Rd | 2 VGAM-1.1-7/VGAM/man/lvplot.qrrvglm.Rd | 191 +-- VGAM-1.1-7/VGAM/man/lvplot.rrvglm.Rd | 177 ++- VGAM-1.1-7/VGAM/man/makeham.Rd | 6 VGAM-1.1-7/VGAM/man/makehamUC.Rd | 20 VGAM-1.1-7/VGAM/man/maxwell.Rd | 8 VGAM-1.1-7/VGAM/man/maxwellUC.Rd | 9 VGAM-1.1-7/VGAM/man/mccullagh89.Rd | 6 VGAM-1.1-7/VGAM/man/melbmaxtemp.Rd | 8 VGAM-1.1-7/VGAM/man/meplot.Rd | 9 VGAM-1.1-7/VGAM/man/micmen.Rd | 58 - VGAM-1.1-7/VGAM/man/mix2exp.Rd | 6 VGAM-1.1-7/VGAM/man/mix2normal.Rd | 113 +- VGAM-1.1-7/VGAM/man/mix2poisson.Rd | 63 - VGAM-1.1-7/VGAM/man/model.framevlm.Rd | 19 VGAM-1.1-7/VGAM/man/model.matrixvlm.Rd | 11 VGAM-1.1-7/VGAM/man/moffset.Rd | 25 VGAM-1.1-7/VGAM/man/multinomial.Rd | 79 - VGAM-1.1-7/VGAM/man/negbinomial.Rd | 220 ++-- VGAM-1.1-7/VGAM/man/notdocumentedyet.Rd | 5 VGAM-1.1-7/VGAM/man/olym.Rd | 42 VGAM-1.1-7/VGAM/man/paralogisticUC.Rd | 4 VGAM-1.1-7/VGAM/man/paretoIVUC.Rd | 32 VGAM-1.1-7/VGAM/man/perks.Rd | 20 VGAM-1.1-7/VGAM/man/poissonff.Rd | 6 VGAM-1.1-7/VGAM/man/posbernUC.Rd | 40 VGAM-1.1-7/VGAM/man/posbernoulli.b.Rd | 75 - VGAM-1.1-7/VGAM/man/posbernoulli.t.Rd | 111 +- VGAM-1.1-7/VGAM/man/posbernoulli.tb.Rd | 128 +- VGAM-1.1-7/VGAM/man/posbinomial.Rd | 82 - VGAM-1.1-7/VGAM/man/posgeomUC.Rd | 4 VGAM-1.1-7/VGAM/man/posnegbinomial.Rd | 130 +- VGAM-1.1-7/VGAM/man/posnormUC.Rd | 8 VGAM-1.1-7/VGAM/man/posnormal.Rd | 67 - VGAM-1.1-7/VGAM/man/prinia.Rd | 15 VGAM-1.1-7/VGAM/man/propodds.Rd | 61 - VGAM-1.1-7/VGAM/man/qrrvglm.control.Rd | 496 ++++++--- VGAM-1.1-7/VGAM/man/qtplot.lmscreg.Rd | 20 VGAM-1.1-7/VGAM/man/qvar.Rd | 17 VGAM-1.1-7/VGAM/man/rayleighUC.Rd | 14 VGAM-1.1-7/VGAM/man/rcqo.Rd | 141 +- VGAM-1.1-7/VGAM/man/rec.exp1.Rd | 34 VGAM-1.1-7/VGAM/man/rec.normal.Rd | 55 - VGAM-1.1-7/VGAM/man/reciprocallink.Rd | 10 VGAM-1.1-7/VGAM/man/residualsvglm.Rd | 96 + VGAM-1.1-7/VGAM/man/rhobitlink.Rd | 35 VGAM-1.1-7/VGAM/man/riceUC.Rd | 29 VGAM-1.1-7/VGAM/man/riceff.Rd | 34 VGAM-1.1-7/VGAM/man/rigff.Rd | 16 VGAM-1.1-7/VGAM/man/rootogram4vglm.Rd | 6 VGAM-1.1-7/VGAM/man/round2.Rd | 30 VGAM-1.1-7/VGAM/man/rrar.Rd | 26 VGAM-1.1-7/VGAM/man/rrvglm-class.Rd | 17 VGAM-1.1-7/VGAM/man/rrvglm.Rd | 53 - VGAM-1.1-7/VGAM/man/rrvglm.control.Rd | 111 +- VGAM-1.1-7/VGAM/man/rrvglm.optim.control.Rd | 32 VGAM-1.1-7/VGAM/man/ruge.Rd | 19 VGAM-1.1-7/VGAM/man/sc.t2UC.Rd | 4 VGAM-1.1-7/VGAM/man/sinmadUC.Rd | 7 VGAM-1.1-7/VGAM/man/slashUC.Rd | 3 VGAM-1.1-7/VGAM/man/sratio.Rd | 14 VGAM-1.1-7/VGAM/man/studentt.Rd | 53 - VGAM-1.1-7/VGAM/man/tobit.Rd | 117 +- VGAM-1.1-7/VGAM/man/tobitUC.Rd | 18 VGAM-1.1-7/VGAM/man/topple.Rd | 13 VGAM-1.1-7/VGAM/man/toppleUC.Rd | 21 VGAM-1.1-7/VGAM/man/toxop.Rd | 8 VGAM-1.1-7/VGAM/man/triangle.Rd | 53 - VGAM-1.1-7/VGAM/man/triangleUC.Rd | 2 VGAM-1.1-7/VGAM/man/trplot.Rd | 24 VGAM-1.1-7/VGAM/man/trplot.qrrvglm.Rd | 62 - VGAM-1.1-7/VGAM/man/truncparetoUC.Rd | 6 VGAM-1.1-7/VGAM/man/truncweibull.Rd | 36 VGAM-1.1-7/VGAM/man/undocumented-methods.Rd | 7 VGAM-1.1-7/VGAM/man/uninormal.Rd | 38 VGAM-1.1-7/VGAM/man/vcovvlm.Rd | 9 VGAM-1.1-7/VGAM/man/venice.Rd | 43 VGAM-1.1-7/VGAM/man/vgam-class.Rd | 38 VGAM-1.1-7/VGAM/man/vgam.Rd | 128 +- VGAM-1.1-7/VGAM/man/vgam.control.Rd | 45 VGAM-1.1-7/VGAM/man/vglm.Rd | 184 ++- VGAM-1.1-7/VGAM/man/vglm.control.Rd | 13 VGAM-1.1-7/VGAM/man/vglmff-class.Rd | 17 VGAM-1.1-7/VGAM/man/vonmises.Rd | 31 VGAM-1.1-7/VGAM/man/vplot.profile.Rd | 9 VGAM-1.1-7/VGAM/man/vsmooth.spline.Rd | 51 VGAM-1.1-7/VGAM/man/waitakere.Rd | 6 VGAM-1.1-7/VGAM/man/waldff.Rd | 10 VGAM-1.1-7/VGAM/man/weibull.mean.Rd | 39 VGAM-1.1-7/VGAM/man/weibullR.Rd | 81 + VGAM-1.1-7/VGAM/man/weightsvglm.Rd | 15 VGAM-1.1-7/VGAM/man/wine.Rd | 40 VGAM-1.1-7/VGAM/man/yeo.johnson.Rd | 10 VGAM-1.1-7/VGAM/man/yulesimon.Rd | 21 VGAM-1.1-7/VGAM/man/yulesimonUC.Rd | 10 VGAM-1.1-7/VGAM/man/zabinomUC.Rd | 29 VGAM-1.1-7/VGAM/man/zageomUC.Rd | 23 VGAM-1.1-7/VGAM/man/zanegbinUC.Rd | 35 VGAM-1.1-7/VGAM/man/zapoisUC.Rd | 20 VGAM-1.1-7/VGAM/man/zetaUC.Rd | 13 VGAM-1.1-7/VGAM/man/zibinomUC.Rd | 18 VGAM-1.1-7/VGAM/man/zigeomUC.Rd | 25 VGAM-1.1-7/VGAM/man/zinegbinUC.Rd | 24 VGAM-1.1-7/VGAM/man/zipfUC.Rd | 15 VGAM-1.1-7/VGAM/man/zipfmbUC.Rd | 45 VGAM-1.1-7/VGAM/man/zipoisUC.Rd | 59 - VGAM-1.1-7/VGAM/man/zipoisson.Rd | 210 ++-- VGAM-1.1-7/VGAM/man/zoabetaUC.Rd | 18 VGAM-1.1-7/VGAM/src/lms.f | 9 VGAM-1.1-7/VGAM/src/rgam.f | 32 VGAM-1.1-7/VGAM/src/tyeepolygamma.f | 5 VGAM-1.1-7/VGAM/src/vgam.f | 250 ++-- VGAM-1.1-7/VGAM/src/vlinpack1.f | 5 VGAM-1.1-7/VGAM/src/vmux.f | 80 - 336 files changed, 12265 insertions(+), 8185 deletions(-)
Title: Simultaneously Impute the Missing and Censored Values
Description: Implementing a multiple imputation algorithm for multivariate data with missing and censored values under a coarsening at random assumption (Heitjan and Rubin, 1991<doi:10.1214/aos/1176348396>). The multiple imputation algorithm is based on the data augmentation algorithm proposed by Tanner and Wong (1987)<doi:10.1080/01621459.1987.10478458>. The Gibbs sampling algorithm is adopted to to update the model parameters and draw imputations of the coarse data.
Author: Hesen Li
Maintainer: Hesen Li <li.hesen.21@gmail.com>
Diff between mvnimpute versions 1.0.0 dated 2022-06-23 and 1.0.1 dated 2022-07-06
mvnimpute-1.0.0/mvnimpute/NEWS.md |only mvnimpute-1.0.0/mvnimpute/build |only mvnimpute-1.0.0/mvnimpute/inst |only mvnimpute-1.0.0/mvnimpute/vignettes |only mvnimpute-1.0.1/mvnimpute/DESCRIPTION | 9 +- mvnimpute-1.0.1/mvnimpute/MD5 | 38 ++++------ mvnimpute-1.0.1/mvnimpute/R/acf.R | 57 +--------------- mvnimpute-1.0.1/mvnimpute/R/avg.plot.R | 67 +++---------------- mvnimpute-1.0.1/mvnimpute/R/conv.plot.R | 17 ++++ mvnimpute-1.0.1/mvnimpute/R/data.generation.new.R | 7 - mvnimpute-1.0.1/mvnimpute/R/marg.plot.R | 64 +++--------------- mvnimpute-1.0.1/mvnimpute/R/multiple.imputation.R | 19 ++--- mvnimpute-1.0.1/mvnimpute/R/visual.plot.R | 2 mvnimpute-1.0.1/mvnimpute/README.md | 26 ++----- mvnimpute-1.0.1/mvnimpute/man/acf.calc.Rd | 59 +--------------- mvnimpute-1.0.1/mvnimpute/man/avg.plot.Rd | 63 ++--------------- mvnimpute-1.0.1/mvnimpute/man/conv.plot.Rd | 16 +++- mvnimpute-1.0.1/mvnimpute/man/data.generation.Rd | 2 mvnimpute-1.0.1/mvnimpute/man/marg.plot.Rd | 61 ++--------------- mvnimpute-1.0.1/mvnimpute/man/multiple.imputation.Rd | 19 ++--- mvnimpute-1.0.1/mvnimpute/man/visual.plot.Rd | 2 21 files changed, 128 insertions(+), 400 deletions(-)
Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.3.0.1 dated 2021-09-15 and 2.3.1 dated 2022-07-06
DESCRIPTION | 8 MD5 | 588 +- NAMESPACE | 512 - NEWS.md | 1515 ++--- R/MizerParams-class.R | 1670 +++--- R/MizerSim-class.R | 716 +- R/RcppExports.R | 14 R/animateSpectra.R | 208 R/calibrate.R | 360 - R/compareParams.R | 198 R/customFunction.R | 114 R/data.R | 252 R/deprecated.R | 1024 +-- R/extension.R | 590 +- R/get_initial_n.R | 92 R/helpers.R | 24 R/manipulate_species.R | 937 +-- R/match.R | 266 - R/mizer-package.R | 82 R/newMultispeciesParams.R | 650 +- R/newSingleSpeciesParams.R | 400 - R/plotBiomassObservedVsModel.R | 416 - R/plotYieldObservedVsModel.R | 388 - R/plots.R | 2650 +++++----- R/pred_kernel_funcs.R | 260 R/project.R | 844 +-- R/project_methods.R | 1340 ++--- R/rate_functions.R | 1789 +++--- R/reproduction.R | 418 - R/resource_dynamics.R | 162 R/saveParams.R | 174 R/selectivity_funcs.R | 250 R/setBevertonHolt.R | 645 +- R/setColours.R | 196 R/setExtMort.R | 288 - R/setFishing.R | 1304 ++-- R/setInitialValues.R | 316 - R/setInteraction.R | 232 R/setMaxIntakeRate.R | 234 R/setMetabolicRate.R | 250 R/setMetadata.R | 178 R/setPredKernel.R | 670 +- R/setReproduction.R | 784 +- R/setResource.R | 556 +- R/setSearchVolume.R | 250 R/species_params.R | 968 +-- R/steady.R | 734 +- R/summary_methods.R | 1610 +++--- R/test-helpers.R | 22 R/upgrade.R | 672 +- R/wrapper_functions.R | 1192 ++-- README.md | 352 - inst/CITATION | 42 inst/WORDLIST | 387 - inst/examples/supplementary_material.R | 1008 +-- inst/extdata/NS_f_history.csv | 90 inst/extdata/NS_interaction.csv | 26 inst/extdata/NS_species_params.csv | 26 inst/shiny/selectivity_effects/app.R | 1071 ++-- inst/shiny/selectivity_effects/hake_mullet.RDS |binary man/BevertonHoltRDD.Rd | 94 man/MizerParams-class.Rd | 360 - man/MizerParams.Rd | 126 man/MizerSim-class.Rd | 122 man/MizerSim.Rd | 56 man/N.Rd | 54 man/NOther.Rd | 36 man/NS_interaction.Rd | 58 man/NS_params.Rd | 70 man/NS_sim.Rd | 62 man/NS_species_params.Rd | 78 man/NS_species_params_gears.Rd | 80 man/RickerRDD.Rd | 70 man/SheperdRDD.Rd | 70 man/addSpecies.Rd | 168 man/animateSpectra.Rd | 142 man/box_pred_kernel.Rd | 67 man/calibrateBiomass.Rd | 92 man/calibrateYield.Rd | 82 man/compareParams.Rd | 52 man/constantEggRDI.Rd | 108 man/constantRDD.Rd | 66 man/constant_other.Rd | 42 man/customFunction.Rd | 112 man/default_pred_kernel_params.Rd | 40 man/different.Rd | 40 man/distanceMaxRelRDI.Rd | 66 man/distanceSSLogN.Rd | 70 man/double_sigmoid_length.Rd | 93 man/emptyParams.Rd | 126 man/figures/Beverton-Holt-plot-1.png |binary man/figures/unnamed-chunk-4-1.png |binary man/finalN.Rd | 68 man/finalNOther.Rd | 36 man/gear_params.Rd | 136 man/getBiomass.Rd | 107 man/getCommunitySlope.Rd | 150 man/getComponent.Rd | 48 man/getCriticalFeedingLevel.Rd | 38 man/getDiet.Rd | 154 man/getEGrowth.Rd | 160 man/getERepro.Rd | 166 man/getEReproAndGrowth.Rd | 202 man/getESpawning.Rd | 166 man/getEffort.Rd | 48 man/getEncounter.Rd | 224 man/getFMort.Rd | 213 man/getFMortGear.Rd | 172 man/getFeedingLevel.Rd | 202 man/getGrowthCurves.Rd | 100 man/getM2.Rd | 164 man/getM2Background.Rd | 154 man/getMeanMaxWeight.Rd | 124 man/getMeanWeight.Rd | 110 man/getMort.Rd | 182 man/getN.Rd | 107 man/getParams.Rd | 46 man/getPhiPrey.Rd | 84 man/getPredMort.Rd | 170 man/getPredRate.Rd | 166 man/getProportionOfLargeFish.Rd | 154 man/getRDD.Rd | 152 man/getRDI.Rd | 184 man/getRates.Rd | 156 man/getReproductionLevel.Rd | 60 man/getResourceMort.Rd | 154 man/getSSB.Rd | 71 man/getTimes.Rd | 42 man/getYield.Rd | 104 man/getYieldGear.Rd | 80 man/getZ.Rd | 180 man/get_f0_default.Rd | 68 man/get_gamma_default.Rd | 54 man/get_h_default.Rd | 62 man/get_initial_n.Rd | 64 man/get_ks_default.Rd | 56 man/get_phi.Rd | 50 man/get_required_reproduction.Rd | 36 man/get_size_range_array.Rd | 114 man/get_time_elements.Rd | 54 man/idxFinalT.Rd | 58 man/indicator_functions.Rd | 44 man/initialN-set.Rd | 62 man/initialNOther-set.Rd | 44 man/initialNResource-set.Rd | 58 man/initial_effort.Rd | 104 man/inter.Rd | 42 man/knife_edge.Rd | 45 man/log_breaks.Rd | 50 man/lognormal_pred_kernel.Rd | 83 man/matchBiomasses.Rd | 104 man/matchYields.Rd | 96 man/mizer-package.Rd | 122 man/mizerEGrowth.Rd | 140 man/mizerERepro.Rd | 146 man/mizerEReproAndGrowth.Rd | 198 man/mizerEncounter.Rd | 204 man/mizerFMort.Rd | 152 man/mizerFMortGear.Rd | 88 man/mizerFeedingLevel.Rd | 168 man/mizerMort.Rd | 154 man/mizerPredMort.Rd | 138 man/mizerPredRate.Rd | 146 man/mizerRDI.Rd | 172 man/mizerRates.Rd | 134 man/mizerResourceMort.Rd | 136 man/newCommunityParams.Rd | 250 man/newMultispeciesParams.Rd | 1238 ++-- man/newSingleSpeciesParams.Rd | 242 man/newTraitParams.Rd | 410 - man/noRDD.Rd | 58 man/plotBiomass.Rd | 234 man/plotBiomassObservedVsModel.Rd | 218 man/plotDataFrame.Rd | 110 man/plotDiet.Rd | 114 man/plotFMort.Rd | 164 man/plotFeedingLevel.Rd | 214 man/plotGrowthCurves.Rd | 190 man/plotM2.Rd | 154 man/plotMizerSim.Rd | 164 man/plotPredMort.Rd | 162 man/plotSpectra.Rd | 270 - man/plotYield.Rd | 192 man/plotYieldGear.Rd | 164 man/plotYieldObservedVsModel.Rd | 206 man/plotting_functions.Rd | 186 man/power_law_pred_kernel.Rd | 105 man/project.Rd | 242 man/projectToSteady.Rd | 126 man/project_simple.Rd | 174 man/reexports.Rd | 32 man/removeSpecies.Rd | 66 man/renameSpecies.Rd | 56 man/resource_constant.Rd | 63 man/resource_params.Rd | 138 man/resource_semichemostat.Rd | 143 man/saveParams.Rd | 54 man/scaleModel.Rd | 96 man/setBevertonHolt.Rd | 264 man/setColours.Rd | 124 man/setComponent.Rd | 110 man/setExtMort.Rd | 236 man/setFishing.Rd | 376 - man/setInitialValues.Rd | 112 man/setInteraction.Rd | 180 man/setMaxIntakeRate.Rd | 160 man/setMetabolicRate.Rd | 170 man/setMetadata.Rd | 126 man/setParams.Rd | 1104 ++-- man/setPredKernel.Rd | 284 - man/setRateFunction.Rd | 178 man/setReproduction.Rd | 402 - man/setResource.Rd | 270 - man/setRmax.Rd | 238 man/setSearchVolume.Rd | 176 man/set_community_model.Rd | 274 - man/set_multispecies_model.Rd | 130 man/set_species_param_default.Rd | 58 man/set_trait_model.Rd | 318 - man/sigmoid_length.Rd | 61 man/sigmoid_weight.Rd | 49 man/species_params.Rd | 321 - man/steady.Rd | 120 man/summary-MizerParams-method.Rd | 40 man/summary-MizerSim-method.Rd | 40 man/summary_functions.Rd | 54 man/truncated_lognormal_pred_kernel.Rd | 85 man/upgradeParams.Rd | 112 man/upgradeSim.Rd | 106 man/validGearParams.Rd | 118 man/validParams.Rd | 34 man/validSpeciesParams.Rd | 86 man/valid_species_arg.Rd | 62 man/w.Rd | 178 tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/plotBiomassObservedVsModel/plotbiomassobservedvsmodel.svg | 250 tests/testthat/_snaps/plotYieldObservedVsModel/plotyieldobservedvsmodel.svg | 222 tests/testthat/_snaps/plots/plot-biomass.svg | 146 tests/testthat/_snaps/plots/plot-diet.svg | 234 tests/testthat/_snaps/plots/plot-feeding-level-critical.svg | 150 tests/testthat/_snaps/plots/plot-feeding-level.svg | 130 tests/testthat/_snaps/plots/plot-growth-curves-panel.svg | 974 +-- tests/testthat/_snaps/plots/plot-growth-curves.svg | 138 tests/testthat/_snaps/plots/plot-single-growth-curve.svg | 140 tests/testthat/_snaps/plots/plot-spectra.svg | 150 tests/testthat/_snaps/plots/plot-yield-by-gear.svg | 132 tests/testthat/_snaps/plots/plot-yield.svg | 142 tests/testthat/_snaps/plots/plotfishing-mortality.svg | 130 tests/testthat/_snaps/plots/plotfmort-truncated.svg | 126 tests/testthat/_snaps/plots/plotpredation-mortality.svg | 130 tests/testthat/_snaps/plots/plotpredmort-truncated.svg | 122 tests/testthat/test-MizerParams-class.R | 182 tests/testthat/test-MizerSim-class.R | 116 tests/testthat/test-analytic_results.R | 444 - tests/testthat/test-animateSpectra.R | 20 tests/testthat/test-backwards_compatibility.R | 282 - tests/testthat/test-calibrate.R | 126 tests/testthat/test-compareParams.R | 80 tests/testthat/test-customFunction.R | 30 tests/testthat/test-extension.R | 370 - tests/testthat/test-get_initial_n.R | 38 tests/testthat/test-manipulate_species.R | 478 - tests/testthat/test-match.R | 132 tests/testthat/test-newMultispeciesParams.R | 102 tests/testthat/test-newSingleSpeciesParams.R | 20 tests/testthat/test-plotBiomassObservedVsModel.R | 112 tests/testthat/test-plotYieldObservedVsModel.R | 108 tests/testthat/test-plots.R | 270 - tests/testthat/test-pred_kernel_funcs.R | 42 tests/testthat/test-project.R | 492 - tests/testthat/test-project_methods.R | 1141 ++-- tests/testthat/test-reproduction.R | 76 tests/testthat/test-resource_dynamics.R | 122 tests/testthat/test-selectivity_funcs.R | 144 tests/testthat/test-setBevertonHolt.R | 266 - tests/testthat/test-setColours.R | 92 tests/testthat/test-setExtMort.R | 124 tests/testthat/test-setFishing.R | 548 +- tests/testthat/test-setInitialValues.R | 140 tests/testthat/test-setInteraction.R | 66 tests/testthat/test-setMaxIntakeRate.R | 112 tests/testthat/test-setMetabolicRate.R | 126 tests/testthat/test-setMetadata.R | 36 tests/testthat/test-setPredKernel.R | 186 tests/testthat/test-setReproduction.R | 286 - tests/testthat/test-setResource.R | 300 - tests/testthat/test-setSearchVolume.R | 108 tests/testthat/test-single_species.R | 92 tests/testthat/test-species_params.R | 250 tests/testthat/test-steady.R | 240 tests/testthat/test-summary_methods.R | 709 +- tests/testthat/test-upgrade.R | 112 tests/testthat/test-wrapper_functions.R | 246 vignettes/.install_extras | 2 296 files changed, 34910 insertions(+), 34575 deletions(-)
Title: Genetic Linkage Maps in Autopolyploids
Description: Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologues. For situations where pairwise analysis has
limited power, the algorithm relies on the multilocus likelihood
obtained through a hidden Markov model (HMM). For more detail,
please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378>
and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.
Author: Marcelo Mollinari [aut, cre] ,
Gabriel Gesteira [aut] ,
Guilhereme Pereira [ctb] ,
Augusto Garcia [ctb] ,
Zhao-Bang Zeng [ctb] ,
Katharine Preedy [ctb, cph] ,
Robert Gentleman [cph] ,
Ross Ihaka [cph] ,
R Foundation [cph] ,
R-core [cph]
Maintainer: Marcelo Mollinari <mmollin@ncsu.edu>
Diff between mappoly versions 0.3.0 dated 2022-01-11 and 0.3.1 dated 2022-07-06
DESCRIPTION | 15 - MD5 | 49 ++-- NAMESPACE | 1 NEWS.md | 4 R/group.R | 198 +++++++++--------- R/haplotype_map_utils.R | 19 - R/marker_info.R | 5 R/mds.R | 12 - R/merge_maps.R | 48 ++-- R/poly_cross_simulate.R | 2 R/rf_list_to_matrix.R | 3 R/utils.R | 26 +- README.md | 29 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/mappoly_startguide.Rmd | 2 inst/doc/mappoly_startguide.html | 158 +++++++++++--- man/generate_all_link_phases_elim_equivalent_haplo.Rd | 3 man/group_mappoly.Rd | 4 man/mds_mappoly.Rd | 5 man/poly_cross_simulate.Rd | 2 src/RcppExports.cpp | 5 src/quality_lod_hmm.cpp |only tests/testthat/test-cahe_twopts.R | 2 tests/testthat/test-utility_func.R | 3 vignettes/mappoly_startguide.Rmd | 2 26 files changed, 375 insertions(+), 222 deletions(-)
Title: Bayesian Multinomial Logistic Normal Regression
Description: Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation
and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for
scalability. 'fido' replaces the previous package 'stray'.
Author: Justin Silverman [aut],
Kim Roche [ctb],
Michelle Nixon [ctb, cre]
Maintainer: Michelle Nixon
<pistner@psu.edu>
Diff between fido versions 1.0.1 dated 2022-05-17 and 1.0.2 dated 2022-07-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 7 ++++++- R/fidofit_methods.R | 4 +--- inst/doc/non-linear-models.html | 4 ++-- man/sample_prior.pibblefit.Rd | 4 +--- tests/testthat/test-pibble.R | 6 +++--- 7 files changed, 23 insertions(+), 22 deletions(-)
Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and
'geospatial' data from the British Columbia Data Catalogue
(<https://catalogue.data.gov.bc.ca/>). Search catalogue data records
based on keywords, data licence, sector, data format, and B.C.
government organization. View metadata directly in R, download many
data formats, and query 'geospatial' data available via the B.C.
government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>
Diff between bcdata versions 0.3.1 dated 2022-05-24 and 0.3.2 dated 2022-07-06
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++-------- NAMESPACE | 10 ++---- NEWS.md | 5 +++ R/bcdata-package.R | 4 ++ R/bcdc-web-services.R | 14 ++++----- R/cql-translator.R | 33 +++++------------------ R/utils-classes.R | 6 ++-- man/bcdc_query_geodata.Rd | 14 ++++----- man/mutate.Rd | 2 - man/select.Rd | 4 +- tests/testthat/test-bcdc-get-citation.R | 2 + tests/testthat/test-query-geodata-base-methods.R | 4 ++ 13 files changed, 63 insertions(+), 67 deletions(-)
Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to
version, share, deploy, and monitor a trained model. Functions handle
both recording and checking the model's input data prototype, and
predicting from a remote API endpoint. The 'vetiver' package is
extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] ,
RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between vetiver versions 0.1.5 dated 2022-05-25 and 0.1.6 dated 2022-07-06
vetiver-0.1.5/vetiver/R/deploy-rsconnect.R |only vetiver-0.1.6/vetiver/DESCRIPTION | 22 +-- vetiver-0.1.6/vetiver/MD5 | 70 +++++----- vetiver-0.1.6/vetiver/NAMESPACE | 5 vetiver-0.1.6/vetiver/NEWS.md | 16 ++ vetiver-0.1.6/vetiver/R/attach-pkgs.R | 4 vetiver-0.1.6/vetiver/R/dashboard.R |only vetiver-0.1.6/vetiver/R/monitor.R | 21 +-- vetiver-0.1.6/vetiver/R/open-api-spec.R | 1 vetiver-0.1.6/vetiver/R/ptype.R | 5 vetiver-0.1.6/vetiver/R/rsconnect.R |only vetiver-0.1.6/vetiver/R/vetiver-package.R | 4 vetiver-0.1.6/vetiver/R/write-docker.R | 38 ++--- vetiver-0.1.6/vetiver/R/write-plumber.R | 11 + vetiver-0.1.6/vetiver/README.md | 6 vetiver-0.1.6/vetiver/inst/doc/model-card.html | 4 vetiver-0.1.6/vetiver/inst/doc/vetiver.html | 10 - vetiver-0.1.6/vetiver/inst/rmarkdown/templates/vetiver_dashboard |only vetiver-0.1.6/vetiver/man/attach_pkgs.Rd | 2 vetiver-0.1.6/vetiver/man/vetiver_compute_metrics.Rd | 27 ++- vetiver-0.1.6/vetiver/man/vetiver_create_rsconnect_bundle.Rd |only vetiver-0.1.6/vetiver/man/vetiver_dashboard.Rd |only vetiver-0.1.6/vetiver/man/vetiver_deploy_rsconnect.Rd | 27 +++ vetiver-0.1.6/vetiver/man/vetiver_write_docker.Rd | 17 +- vetiver-0.1.6/vetiver/man/vetiver_write_plumber.Rd | 11 + vetiver-0.1.6/vetiver/tests/testthat/_snaps/api.md | 3 vetiver-0.1.6/vetiver/tests/testthat/_snaps/choose-version.md | 3 vetiver-0.1.6/vetiver/tests/testthat/_snaps/create-ptype.md | 5 vetiver-0.1.6/vetiver/tests/testthat/_snaps/dashboard.md |only vetiver-0.1.6/vetiver/tests/testthat/_snaps/predict.md | 10 - vetiver-0.1.6/vetiver/tests/testthat/_snaps/ranger.md | 5 vetiver-0.1.6/vetiver/tests/testthat/_snaps/rsconnect.md |only vetiver-0.1.6/vetiver/tests/testthat/_snaps/write-docker.md | 22 +-- vetiver-0.1.6/vetiver/tests/testthat/_snaps/write-plumber.md | 19 ++ vetiver-0.1.6/vetiver/tests/testthat/skeleton.html |only vetiver-0.1.6/vetiver/tests/testthat/test-dashboard.R |only vetiver-0.1.6/vetiver/tests/testthat/test-monitor.R | 9 - vetiver-0.1.6/vetiver/tests/testthat/test-rsconnect.R |only vetiver-0.1.6/vetiver/tests/testthat/test-write-docker.R | 3 vetiver-0.1.6/vetiver/tests/testthat/test-write-plumber.R | 15 ++ vetiver-0.1.6/vetiver/vignettes/vetiver-templates.png |binary 41 files changed, 254 insertions(+), 141 deletions(-)
Title: Explore Temporal Signal of Molecular Phylogenies
Description: Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels.
Author: Guangchuang Yu [aut, cre, cph]
,
Xuanan Zhu [aut],
Jianfeng Lin [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between shinyTempSignal versions 0.0.2 dated 2022-04-14 and 0.0.3 dated 2022-07-06
DESCRIPTION | 12 ++-- MD5 | 10 +-- NAMESPACE | 4 - R/app_server.R | 159 +++++++++++++++++++++++++++++++++++++++----------------- R/app_ui.R | 3 + R/dateNumeric.R | 12 ++-- 6 files changed, 133 insertions(+), 67 deletions(-)
More information about shinyTempSignal at CRAN
Permanent link