Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 3.4.0 dated 2022-11-19 and 3.4.1 dated 2022-12-05
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 4 ++++ build/partial.rdb |binary 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.24 dated 2022-10-18 and 0.10.25 dated 2022-12-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/db-apply.c | 6 +++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 2.0.4 dated 2022-10-17 and 2.0.5 dated 2022-12-05
DESCRIPTION | 6 ++-- MD5 | 20 ++++++------- NEWS | 3 ++ build/vignette.rds |binary inst/doc/bignum.html | 46 +++++++++++++------------------ inst/doc/crypto_hashing.html | 22 +++++---------- inst/doc/keys.html | 62 +++++++++++++++++++------------------------ inst/doc/secure_rng.html | 32 +++++++++------------- src/bcrypt/blf.h | 13 ++------- src/bcrypt/blowfish.c | 14 +-------- src/hash.c | 5 ++- 11 files changed, 93 insertions(+), 130 deletions(-)
Title: NanoString Quality Control Dashboard
Description: NanoString nCounter data are gene expression assays
where there is no need for the use of enzymes or amplification
protocols and work with fluorescent barcodes (Geiss et al. (2018)
<doi:10.1038/nbt1385>). Each barcode is assigned a
messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its
target can be counted. As a result each count of a specific barcode
represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString
quality Control dasHbOard) is able to analyse the exported NanoString
nCounter data and facilitates the user in performing a quality
control. 'NACHO' does this by visualising quality control metrics,
expression of control genes, principal components and sample specific
size factors in an interactive web application.
Author: Mickael Canouil [aut, cre] ,
Roderick Slieker [aut] ,
Gerard Bouland [aut]
Maintainer: Mickael Canouil <pro@mickael.canouil.dev>
Diff between NACHO versions 2.0.1 dated 2022-11-24 and 2.0.2 dated 2022-12-05
DESCRIPTION | 18 ++++---- MD5 | 20 ++++----- NEWS.md | 10 ++++ R/autoplot.R | 28 ++++++++----- R/render.R | 2 inst/doc/NACHO-analysis.html | 8 +-- inst/doc/NACHO.html | 88 +++++++++++++++++++++++++------------------ man/NACHO-package.Rd | 2 man/autoplot.nacho.Rd | 2 man/print.nacho.Rd | 2 man/render.Rd | 2 11 files changed, 108 insertions(+), 74 deletions(-)
Title: INsulin Secretion ANalysEr
Description: A user-friendly interface, using Shiny, to analyse glucose-stimulated insulin secretion (GSIS)
assays in pancreatic beta cells or islets.
The package allows the user to import several sets of experiments from different spreadsheets
and to perform subsequent steps: summarise in a tidy format, visualise data quality
and compare experimental conditions without omitting to account for technical confounders
such as the date of the experiment or the technician.
Together, insane is a comprehensive method that optimises pre-processing and analyses of
GSIS experiments in a friendly-user interface.
The Shiny App was initially designed for EndoC-betaH1 cell line following method described
in Ndiaye et al., 2017 (<doi:10.1016/j.molmet.2017.03.011>).
Author: Mickael Canouil [aut, cre]
Maintainer: Mickael Canouil <pro@mickael.canouil.dev>
Diff between insane versions 1.0.0 dated 2022-11-24 and 1.0.1 dated 2022-12-05
DESCRIPTION | 19 +++++++++---------- MD5 | 17 +++++++++-------- NAMESPACE | 2 -- NEWS.md | 10 ++++++++++ R/go_insane.R | 1 - build/partial.rdb |only inst/app/app.R | 22 +++++++++++----------- inst/doc/insane.html | 4 ++-- man/go_insane.Rd | 2 +- man/insane-package.Rd | 6 +++--- 10 files changed, 45 insertions(+), 38 deletions(-)
Title: Minimal and Uncluttered Package Documentation
Description: Generates simple and beautiful one-page HTML reference manuals
with package documentation. Math rendering and syntax highlighting are done
server-side in R such that no JavaScript libraries are needed in the
browser, which makes the documentation portable and fast to load.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between postdoc versions 1.0.0 dated 2022-11-28 and 1.1.0 dated 2022-12-05
DESCRIPTION | 8 +++--- MD5 | 7 +++--- NEWS |only R/manual.R | 61 ++++++++++++++++++++++++++++++++++++++++++----------- man/html_manual.Rd | 4 +++ 5 files changed, 61 insertions(+), 19 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 1.9.1 dated 2022-10-05 and 1.9.2 dated 2022-12-05
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ build/vignette.rds |binary inst/doc/gert.html | 23 +++++++++++++++-------- src/branch.c | 2 +- src/clone.c | 4 ++-- 7 files changed, 30 insertions(+), 20 deletions(-)
Title: Count Regression for Correlated Observations with the
Beta-Binomial
Description: Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.
Author: Bryan D Martin [aut, cre],
Daniela Witten [aut],
Amy D Willis [aut]
Maintainer: Bryan D Martin <bmartin6@uw.edu>
Diff between corncob versions 0.3.0 dated 2022-09-23 and 0.3.1 dated 2022-12-05
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/doc/corncob-intro.pdf |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Robust One-Way ANOVA Tests under Heteroscedasticity and
Nonnormality
Description: Robust tests (RW, RPB and RGF) are provided for testing the equality of several long-tailed symmetric (LTS) means when the variances are unknown and arbitrary. RW, RPB and RGF tests are robust versions of Welch's F test proposed by Welch (1951) <doi:10.2307/2332579>, parametric bootstrap test proposed by Krishnamoorthy et. al (2007) <doi:10.1016/j.csda.2006.09.039>; and generalized F test proposed by Weerahandi (1995) <doi:10.2307/2532947>;, respectively. These tests are based on the modified maximum likelihood (MML) estimators proposed by Tiku(1967, 1968) <doi:10.2307/2333859>, <doi:10.1080/01621459.1968.11009228>.
Author: Gamze Guven [aut, cre],
Sukru Acitas [aut],
Birdal Senoglu [aut]
Maintainer: Gamze Guven <gamzeguven@ogu.edu.tr>
Diff between RobustANOVA versions 0.2.0 dated 2022-11-09 and 0.3.0 dated 2022-12-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- man/RGF.Rd | 2 +- man/RPB.Rd | 2 +- man/RW.Rd | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Markov-Switching GARCH Models
Description: Fit (by Maximum Likelihood or MCMC/Bayesian), simulate, and forecast various Markov-Switching GARCH models as described in Ardia et al. (2019) <doi:10.18637/jss.v091.i04>.
Author: David Ardia [aut] ,
Keven Bluteau [aut, cre] ,
Kris Boudt [ctb] ,
Leopoldo Catania [aut] ,
Alexios Ghalanos [ctb],
Brian Peterson [ctb],
Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@usherbrooke.ca>
Diff between MSGARCH versions 2.50 dated 2022-01-15 and 2.51 dated 2022-12-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 2 ++ build/partial.rdb |binary src/Mapping.cpp | 8 ++++---- 5 files changed, 14 insertions(+), 12 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.4.5 dated 2022-09-30 and 0.5.0 dated 2022-12-05
DESCRIPTION | 16 MD5 | 77 +- NAMESPACE | 4 NEWS.md | 15 R/dark-or-light.R | 8 R/geom-grob.R | 201 ++++-- R/geom-label-linked.r | 151 +++- R/geom-label-npc.r | 1 R/geom-margin-arrow.r | 4 R/geom-margin-grob.r | 11 R/geom-margin-point.r | 4 R/geom-plot.R | 174 +++-- R/geom-point-linked.r | 189 ++++-- R/geom-quadrant-lines.R | 4 R/geom-table.R | 151 +++- R/geom-text-linked.r | 274 ++++++-- R/geom-text-npc.r | 65 -- R/stat-group-counts.R |only R/stat-panel-counts.R |only R/stat-quadrant-counts.R | 50 - README.md | 194 +++--- build/vignette.rds |binary inst/doc/grammar-extensions.R | 237 +------ inst/doc/grammar-extensions.Rmd | 393 ++---------- inst/doc/grammar-extensions.html | 1206 ++++++++++++++++----------------------- inst/doc/nudge-examples.R |only inst/doc/nudge-examples.Rmd |only inst/doc/nudge-examples.html |only man/geom_grob.Rd | 158 +++-- man/geom_plot.Rd | 132 ++-- man/geom_point_s.Rd | 79 ++ man/geom_quadrant_lines.Rd | 5 man/geom_table.Rd | 101 ++- man/geom_text_npc.Rd | 88 +- man/geom_text_s.Rd | 234 +++++-- man/geom_x_margin_arrow.Rd | 4 man/geom_x_margin_grob.Rd | 43 + man/geom_x_margin_point.Rd | 4 man/ggpp-ggproto.Rd | 7 man/stat_panel_counts.Rd |only man/stat_quadrant_counts.Rd | 10 vignettes/grammar-extensions.Rmd | 393 ++---------- vignettes/nudge-examples.Rmd |only 43 files changed, 2347 insertions(+), 2340 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, binary data from GENEA devices (not for sale), and .cwa-format and .wav-format data from 'Axivity' <https://axivity.com>. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 0.2.4 dated 2022-10-09 and 0.2.6 dated 2022-12-05
DESCRIPTION | 10 +++++---- MD5 | 16 +++++++-------- R/readAxivity.R | 8 ++++--- R/readGENEActiv.R | 12 +++++++---- R/readWav.R | 44 +++++++++++++++++++++++++++++------------- inst/NEWS.Rd | 10 +++++++++ man/GGIRread-package.Rd | 4 +-- man/resample.Rd | 2 - tests/testthat/test_readWav.R | 2 - 9 files changed, 72 insertions(+), 36 deletions(-)
Title: {{mustache}} for R, Logicless Templating
Description: Implements 'Mustache' logicless templating.
Author: Edwin de Jonge
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between whisker versions 0.4 dated 2019-08-28 and 0.4.1 dated 2022-12-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/tag2delim.Rd | 2 -- 3 files changed, 6 insertions(+), 8 deletions(-)
Title: Draw Sectors
Description: Some useful functions that can use 'grid' and 'ggplot2' to plot sectors and interact with 'Seurat' to plot gene expression percentages. Also, there are some examples of how to draw sectors in 'ComplexHeatmap'.
Author: Pengdong Yan [aut, cre, cph]
Maintainer: Pengdong Yan <yanpd01@gmail.com>
Diff between ggsector versions 1.6.5 dated 2022-12-05 and 1.6.6 dated 2022-12-05
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/sector_df.R | 1 + inst/doc/ggsector.R | 6 +++--- inst/doc/ggsector.Rmd | 6 +++--- inst/doc/ggsector.html | 6 +++--- vignettes/ggsector.Rmd | 6 +++--- 7 files changed, 22 insertions(+), 21 deletions(-)
Title: Tools for Analyzing Finite Mixture Models
Description: Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, multivariate normal, multinomial, gamma), various Reliability Mixture Models (RMMs), mixtures-of-regressions settings (linear regression, logistic regression, Poisson regression, linear regression with changepoints, predictor-dependent mixing proportions, random effects regressions, hierarchical mixtures-of-experts), and tools for selecting the number of components (bootstrapping the likelihood ratio test statistic, mixturegrams, and model selection criteria). Bayesian estimation of mixtures-of-linear-regressions models is available as well as a novel data depth method for obtaining credible bands. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).
Author: Derek Young [aut, cre] ,
Tatiana Benaglia [aut],
Didier Chauveau [aut],
David Hunter [aut],
Kedai Cheng [aut],
Ryan Elmore [ctb],
Thomas Hettmansperger [ctb],
Hoben Thomas [ctb],
Fengjuan Xuan [ctb]
Maintainer: Derek Young <derek.young@uky.edu>
Diff between mixtools versions 1.2.0 dated 2020-02-07 and 2.0.0 dated 2022-12-05
DESCRIPTION | 17 - MD5 | 101 ++++--- NAMESPACE | 24 + NEWS | 25 + R/bootcomp.R | 70 ++--- R/bootse.R | 16 - R/gammamixEM.R | 8 R/lambda.R | 22 + R/plotly_FDR.R |only R/plotly_compCDF.R |only R/plotly_ellipse.R |only R/plotly_expRMM.R |only R/plotly_ise.npEM.R |only R/plotly_mixEM.R |only R/plotly_mixMCMC.R |only R/plotly_mixturegram.R |only R/plotly_npEM.R |only R/plotly_post.beta.R |only R/plotly_seq.npEM.R |only R/plotly_spEMN01.R |only R/plotly_spRMM.R |only R/plotly_weibullRMM.R |only R/regmixEMloc.R | 143 +++++----- R/segregmixEM.R | 602 +++++++++++++++++++++++----------------------- R/summary.mixEM.R | 4 R/zzz.R | 4 build/vignette.rds |binary inst/CITATION | 44 +-- inst/doc/mixtools.pdf |binary man/RTdata2.Rd | 2 man/boot.comp.Rd | 4 man/boot.se.Rd | 4 man/compCDF.Rd | 6 man/expRMM_EM.Rd | 2 man/figures |only man/hmeEM.Rd | 4 man/logisregmixEM.Rd | 4 man/mixtools-internal.Rd | 5 man/multmixEM.Rd | 4 man/mvnormalmixEM.Rd | 4 man/normalmixEM.Rd | 6 man/normalmixEM2comp.Rd | 6 man/normalmixMMlc.Rd | 2 man/plotexpRMM.Rd | 2 man/plotly_FDR.Rd |only man/plotly_compCDF.Rd |only man/plotly_ellipse.Rd |only man/plotly_expRMM.Rd |only man/plotly_ise.npEM.Rd |only man/plotly_mixEM.Rd |only man/plotly_mixMCMC.Rd |only man/plotly_mixturegram.Rd |only man/plotly_npEM.Rd |only man/plotly_post.beta.Rd |only man/plotly_seq.npEM.Rd |only man/plotly_spEMN01.Rd |only man/plotly_spRMM.Rd |only man/plotly_weibullRMM.Rd |only man/plotspRMM.Rd | 2 man/plotweibullRMM.Rd | 2 man/poisregmixEM.Rd | 4 man/post.beta.Rd | 4 man/regmixEM.Rd | 10 man/spRMM_SEM.Rd | 2 man/summary.spRMM.Rd | 2 man/weibullRMM_SEM.Rd | 2 66 files changed, 622 insertions(+), 541 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 0.99.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-14 0.99.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-10 1.0.1.1
2013-10-31 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-04 1.0.4
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Katriona Goldmann [aut]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.4.0 dated 2022-10-23 and 0.4.4 dated 2022-12-05
DESCRIPTION | 6 MD5 | 52 ++-- NAMESPACE | 11 NEWS.md | 16 + R/innercv_roc.R | 212 +++++++++++++++-- R/nestcv.train.R | 29 +- R/nestcv_SuperLearner.R | 2 R/nestedcv.R | 62 +---- R/outercv.R | 56 +++- R/predSummary.R |only R/randomsample.R | 68 +++++ R/smote.R | 4 build/vignette.rds |binary inst/doc/nestedcv.R | 96 ++++++- inst/doc/nestedcv.Rmd | 164 +++++++++++-- inst/doc/nestedcv.html | 587 +++++++++++++++++++++++++++++++----------------- man/innercv_preds.Rd |only man/innercv_roc.Rd | 17 - man/innercv_summary.Rd |only man/nestcv.glmnet.Rd | 4 man/nestcv.train.Rd | 4 man/outercv.Rd | 5 man/predSummary.Rd | 15 - man/randomsample.Rd | 69 +++++ man/train_preds.Rd |only man/train_roc.Rd |only man/train_summary.Rd |only vignettes/fig1.svg | 134 ---------- vignettes/fig2.svg | 157 ------------ vignettes/nestedcv.Rmd | 164 +++++++++++-- 30 files changed, 1244 insertions(+), 690 deletions(-)
Title: Shiny App for Grey Forecasting Model
Description: The 'Greymodels' Shiny app is an interactive interface for statistical modelling and forecasting using grey-based models. It covers several state-of-the-art univariate and multivariate grey models. A user friendly interface allows users to easily compare the performance of different models for prediction and among others, visualize graphical plots of predicted values within user chosen confidence intervals. Chang, C. (2019) <doi:10.24818/18423264/53.1.19.11>, Li, K., Zhang, T. (2019) <doi:10.1007/s12667-019-00344-0>, Ou, S. (2012) <doi:10.1016/j.compag.2012.03.007>, Li, S., Zhou, M., Meng, W., Zhou, W. (2019) <doi:10.1080/23307706.2019.1666310>, Xie, N., Liu, S. (2009) <doi:10.1016/j.apm.2008.01.011>, Shao, Y., Su, H. (2012) <doi:10.1016/j.aasri.2012.06.003>, Xie, N., Liu, S., Yang, Y., Yuan, C. (2013) <doi:10.1016/j.apm.2012.10.037>, Li, S., Miao, Y., Li, G., Ikram, M. (2020) <doi:10.1016/j.matcom.2019.12.020>, Che, X., Luo, Y., He, Z. ( [...truncated...]
Author: Jahajeeah Havisha [aut, cre],
Saib Aslam Aly [aut]
Maintainer: Jahajeeah Havisha <hjahajeeah@utm.ac.mu>
Diff between Greymodels versions 2.0 dated 2022-11-27 and 2.0.1 dated 2022-12-05
DESCRIPTION | 6 MD5 | 10 NAMESPACE | 2 R/CIplots_igndgm12.R | 3 R/app.R | 2 R/app_ui.R | 2797 +++++++++++++++++++++++++-------------------------- 6 files changed, 1413 insertions(+), 1407 deletions(-)
Title: Create 'Ascii' Screen Casts from R Scripts
Description: Record 'asciicast' screen casts from R scripts. Convert them
to animated SVG images, to be used in 'README' files, or blog posts.
Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast'
'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.
Author: Gabor Csardi [aut, cre],
Romain Francois [aut],
Mario Nebl [aut] ,
Marcin Kulik [aut]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between asciicast versions 2.2.1 dated 2022-11-21 and 2.3.0 dated 2022-12-05
DESCRIPTION | 6 +- MD5 | 36 +++++++------- NEWS.md | 12 ++++ R/asciicast.R | 7 +- R/debug.R |only R/embed.R | 48 ++++++++++++------ R/knitr.R | 66 ++++++++++++++++++++++++- R/parameters.R | 4 + R/svg.R | 51 ++++++++++++++++++- R/test.R | 2 README.md | 69 +++++++++++++++------------ man/asciicast-package.Rd | 4 + man/asciicast_start_process.Rd | 6 +- man/expect_snapshot_r_process.Rd | 2 man/figures/README-/unnamed-chunk-3-dark.svg |only man/figures/README-/unnamed-chunk-3.svg | 2 man/figures/README-/unnamed-chunk-5-dark.svg |only man/figures/README-/unnamed-chunk-5.svg | 2 man/figures/README-/unnamed-chunk-7-dark.svg |only man/figures/README-/unnamed-chunk-7.svg | 2 man/record.Rd | 6 +- 21 files changed, 244 insertions(+), 81 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-04 0.2.1
2017-09-18 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-22 2.0.6
2018-04-29 2.0.5
2018-04-16 2.0.4
2018-04-06 2.0.3
2018-03-10 2.0.2
2018-01-05 2.0.1
2017-10-23 1.0.8
2017-09-23 1.0.7
2017-06-07 1.0.6
2017-06-02 1.0.5
2017-03-04 1.0.4
2017-02-09 1.0.3
2017-01-27 1.0.2
2017-01-15 1.0.1
2017-01-14 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-13 1.0.2
2013-01-13 1.0.3
2013-01-11 1.0.1
2008-02-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-04 1.3.9
2021-08-06 1.3.8
2021-03-18 1.3.7
2021-01-13 1.3.6
2020-11-23 1.3.5
2020-11-12 1.3.4
2020-01-09 1.3.3
2019-09-10 1.3.2
2019-07-25 1.3.1
2019-06-28 1.3.0
2018-11-17 1.2.2
2018-08-08 1.2.1
2018-06-07 1.2.0
2018-03-06 1.1.2
2018-02-14 1.1.1
2018-01-16 1.1.0
2017-12-13 1.0.1
2017-11-09 1.0.0
Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions
based on R base graphics, interval management functions and svg importation
functions among others. Also include stereographic projection functions,
and other functions made to deal with large datasets while keeping options
to get into the details of the data.
When using for publication please cite
Sebastien Wouters, Anne-Christine Da Silva, Frederic Boulvain and
Xavier Devleeschouwer, 2021. The R Journal 13:2, 153-178.
The palaeomagnetism functions are based on:
Tauxe, L., 2010. Essentials of Paleomagnetism. University of California
Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>;
Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural
Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge
University Press, 289 pp.;
Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections
with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205,
<doi: 10.1016/j.ca [...truncated...]
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <wouterseb@gmail.com>
Diff between StratigrapheR versions 1.2.5 dated 2022-05-10 and 1.3.0 dated 2022-12-05
DESCRIPTION | 8 - MD5 | 85 +++++++++++------- NAMESPACE | 19 ++++ NEWS | 25 +++++ R/StratigrapheR.R | 10 +- R/as.lim.R | 16 +-- R/centresvg.R | 5 + R/changejoint.R |only R/changesvg.R | 16 +++ R/clipsvg.R | 14 ++ R/collection.R |only R/collections.R |only R/framesvg.R | 8 + R/is.clockwise.R |only R/is.joint.R |only R/litholog.R | 72 +++++++++++++-- R/memento.R | 239 +++++++++++++++++++++++++++++++++++---------------- R/minorAxisTicks.R | 10 +- R/multigons.R | 224 +++++++++++++++++++++++------------------------ R/nlegend.R | 6 - R/octapos.R |only R/octashift.R |only R/outliner.R |only R/placesvg.R | 6 + R/pointsvg.R | 68 +++++++++++++- R/profiler.R |only R/shift.R | 165 ++++++++++++++++++++++++++++------- R/symbology.R |only R/trace.lim.R |only R/weld.R | 2 R/weldjoint.R |only R/weldlog.R | 53 ++++------- R/weldprofile.R |only data/oufti99.rda |only man/StratigrapheR.Rd | 2 man/as.lim.Rd | 16 +-- man/changejoint.Rd |only man/collection.Rd |only man/collections.Rd |only man/framesvg.Rd | 2 man/is.clockwise.Rd |only man/is.joint.Rd |only man/litholog.Rd | 20 ++-- man/memento.Rd | 47 +++++++--- man/multigons.Rd | 6 - man/nlegend.Rd | 4 man/octapos.Rd |only man/octashift.Rd |only man/outliner.Rd |only man/pointsvg.Rd | 8 + man/profiler.Rd |only man/shift.Rd | 48 +++++++++- man/symbology.Rd |only man/trace.lim.Rd |only man/weldjoint.Rd |only man/weldlog.Rd | 2 man/weldprofile.Rd |only 57 files changed, 860 insertions(+), 346 deletions(-)
Title: Draw Sectors
Description: Some useful functions that can use 'grid' and 'ggplot2' to plot sectors and interact with 'Seurat' to plot gene expression percentages. Also, there are some examples of how to draw sectors in 'ComplexHeatmap'.
Author: Pengdong Yan [aut, cre, cph]
Maintainer: Pengdong Yan <yanpd01@gmail.com>
Diff between ggsector versions 1.6.1 dated 2022-11-28 and 1.6.5 dated 2022-12-05
ggsector-1.6.1/ggsector/R/0_reexport.R |only ggsector-1.6.1/ggsector/R/1_sector_df.R |only ggsector-1.6.1/ggsector/R/1_sector_ggplot.R |only ggsector-1.6.1/ggsector/R/1_sector_grid.R |only ggsector-1.6.1/ggsector/R/1_sector_seurat.R |only ggsector-1.6.1/ggsector/R/2_pie_df.R |only ggsector-1.6.5/ggsector/DESCRIPTION | 6 ggsector-1.6.5/ggsector/MD5 | 33 - ggsector-1.6.5/ggsector/R/ggplot.R |only ggsector-1.6.5/ggsector/R/grid.R |only ggsector-1.6.5/ggsector/R/reexport.R |only ggsector-1.6.5/ggsector/R/sector_df.R |only ggsector-1.6.5/ggsector/R/seurat.R |only ggsector-1.6.5/ggsector/inst/doc/ggsector.R | 214 ++++++++++- ggsector-1.6.5/ggsector/inst/doc/ggsector.Rmd | 271 +++++++++++++- ggsector-1.6.5/ggsector/inst/doc/ggsector.html | 453 ++++++++++++++++++------- ggsector-1.6.5/ggsector/man/draw_key_sector.Rd | 2 ggsector-1.6.5/ggsector/man/geom_sector.Rd | 175 ++++++--- ggsector-1.6.5/ggsector/man/reexports.Rd | 2 ggsector-1.6.5/ggsector/man/sectorGrob.Rd | 2 ggsector-1.6.5/ggsector/man/sector_df.Rd | 2 ggsector-1.6.5/ggsector/man/seurat.Rd | 40 +- ggsector-1.6.5/ggsector/vignettes/ggsector.Rmd | 271 +++++++++++++- 23 files changed, 1168 insertions(+), 303 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-12 0.1.26
2019-12-12 0.1.25
2019-12-12 0.1.24
2019-11-03 0.1.23
2019-10-13 0.1.22
2019-10-10 0.1.21
2019-10-07 0.1.20
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-05 1.1.4
2015-05-02 1.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-03 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-25 2.0-6
2015-04-07 2.0-5
2014-08-25 2.0-4
2014-05-23 2.0-3
2013-10-25 2.0-2
2013-08-20 2.0-1
2010-05-06 1.0-1
2009-12-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-23 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-20 1.1
2014-01-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-24 0.5.5
2020-09-12 0.5.2
2020-07-23 0.5.0
2020-01-15 0.4.9
2019-09-23 0.4.8
2019-08-06 0.4.7
2019-02-09 0.4.5
2018-11-08 0.4.4
2018-09-10 0.4.3
2018-07-14 0.4.2
2018-04-10 0.4.0
2017-10-28 0.3.5
2017-10-26 0.3.4
2017-10-05 0.3.3
2017-08-17 0.3.2
2017-08-14 0.3.1
2017-08-01 0.3.0
2017-07-08 0.2.7
2017-04-01 0.2.6
2017-03-31 0.2.5
2017-02-15 0.2.4
2017-02-07 0.2.3
2016-10-24 0.2.2
2016-10-15 0.2.1
2016-09-16 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-20 1.2.2
2022-06-22 1.2.1
2022-05-30 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-04 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-10 0.2.5.2
2021-11-29 0.2.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-21 0.0.2
2018-04-16 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-16 1.0.2
2021-12-01 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-28 1.4.0
2020-05-12 1.3.0
2020-04-02 1.2.0
2020-02-23 1.1.0
2020-01-18 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-01 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-23 1.1.4
2016-07-08 1.1.2
2016-07-05 1.1
2016-07-05 1.1.1
2016-03-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-05 2.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-08 0.1.3
2017-08-29 0.1
Title: High Mach Finds Routes for Supersonic Aircraft
Description: For supersonic aircraft, flying subsonic over land,
High Mach finds the best route between airports. Allows for coastal buffer and
potentially closed regions. Uses a minimal model of aircraft
performance: the focus is on time saved versus subsonic flight, rather
than on vertical flight profile. For modelling and forecasting, not for planning your
flight!
Author: David Marsh [aut, cre],
Enrico Spinielli [ctb],
EUROCONTROL [fnd, cph]
Maintainer: David Marsh <david6marsh@gmail.com>
Diff between himach versions 0.3.0 dated 2022-06-09 and 0.3.1 dated 2022-12-05
himach-0.3.0/himach/tests/spelling.R |only himach-0.3.1/himach/DESCRIPTION | 13 himach-0.3.1/himach/MD5 | 55 + himach-0.3.1/himach/NEWS.md | 7 himach-0.3.1/himach/R/grids.R | 26 himach-0.3.1/himach/R/maps.R | 49 - himach-0.3.1/himach/R/routes.R | 91 +-- himach-0.3.1/himach/R/utils.R | 18 himach-0.3.1/himach/README.md | 77 +- himach-0.3.1/himach/build/vignette.rds |binary himach-0.3.1/himach/inst/WORDLIST | 2 himach-0.3.1/himach/inst/doc/Supersonic_Routes.html | 250 ++++---- himach-0.3.1/himach/inst/doc/Supersonic_Routes_in_depth.html | 311 +++++------ himach-0.3.1/himach/man/find_route.Rd | 3 himach-0.3.1/himach/man/find_routes.Rd | 2 himach-0.3.1/himach/tests/spelling.Rout.save |only himach-0.3.1/himach/tests/testthat/_snaps |only himach-0.3.1/himach/tests/testthat/known/test_multiroute |binary himach-0.3.1/himach/tests/testthat/spelling.R |only himach-0.3.1/himach/tests/testthat/test-zzz.R | 12 himach-0.3.1/himach/tests/testthat/test_grid.R | 25 himach-0.3.1/himach/tests/testthat/test_map.R | 9 himach-0.3.1/himach/tests/testthat/test_routes.R | 49 - himach-0.3.1/himach/tests/testthat/test_utils.R | 34 - himach-0.3.1/himach/vignettes/buffer_example.png |binary himach-0.3.1/himach/vignettes/buffer_island_example.png |binary himach-0.3.1/himach/vignettes/polar_examples.png |binary himach-0.3.1/himach/vignettes/refuel_examples_pacific.png |binary himach-0.3.1/himach/vignettes/three_routes.png |binary 29 files changed, 531 insertions(+), 502 deletions(-)
Title: LiDAR Data Voxelisation
Description: Read, manipulate and write voxel spaces. Voxel spaces are
read from text-based output files of the 'AMAPVox' software. 'AMAPVox'
is a LiDAR point cloud voxelisation software that aims at estimating
leaf area through several theoretical/numerical approaches. See more
in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the
technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.
Author: Gregoire Vincent [aut],
Julien Heurtebize [aut],
Philippe Verley [aut, cre]
Maintainer: Philippe Verley <philippe.verley@ird.fr>
Diff between AMAPVox versions 0.12.0 dated 2022-08-24 and 0.12.1 dated 2022-12-05
DESCRIPTION | 6 +- MD5 | 22 ++++---- NEWS.md | 6 ++ R/PlantArea.R | 4 - R/Utils-voxel.R | 6 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/AMAPVox.html | 111 ++++++++++++++++++++++----------------------- inst/doc/Installation.html | 111 ++++++++++++++++++++++----------------------- inst/doc/Publications.html | 15 ++---- inst/doc/Voxelization.html | 111 ++++++++++++++++++++++----------------------- inst/doc/amapvox-gui.html | 111 ++++++++++++++++++++++----------------------- 12 files changed, 253 insertions(+), 250 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-24 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-11 2.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-21 0.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-11 0.9.3
2017-11-23 0.9.2
2017-02-24 0.9.1
2017-02-09 0.9.0
2015-02-20 0.8-3
2014-09-24 0.8-2
2014-01-06 0.8-0
2013-11-11 0.7-9
2013-08-28 0.7-8
2013-07-22 0.7-5
2013-04-04 0.7-4
2013-03-16 0.7-3
2013-01-04 0.7-2
2012-11-26 0.7-1
2012-04-02 0.7-0
2011-12-28 0.6-8
2011-11-04 0.6-7
2011-10-26 0.6-6
2011-09-08 0.6-5
2011-08-07 0.6-4
2011-07-31 0.6-3
2011-05-30 0.6-2
2011-03-24 0.6-1
2011-02-22 0.6-0
2011-02-06 0.5-9
2011-02-03 0.5-8
2010-03-14 0.5.0
2010-02-15 0.4.9
2009-04-04 0.4.5
2009-03-01 0.4.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-13 0.2.6
2018-07-13 0.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-07 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-19 1.1.1
2021-01-07 1.1.0
2019-12-16 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-20 0.1.1
2018-07-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-10 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-29 2.0.2
2016-12-21 2.0.1
2016-12-05 2.0.0
2016-10-29 1.0.0
2016-05-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-20 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-16 1.2.1
2016-11-07 1.2
2015-09-20 1.1
2014-08-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-19 1.2.5
2022-03-31 1.2.3
2022-03-25 1.2.2
2022-01-18 1.1.0
2021-11-20 1.0.11
2021-10-21 0.5.6
2021-10-05 0.5.5
2021-09-22 0.5.4
2019-03-04 0.5.3
2019-02-14 0.5.1
2019-02-10 0.5
2017-04-14 0.3.25
2017-04-13 0.3.23
2017-04-06 0.3.21
2017-03-21 0.3.20
2016-12-25 0.3.15
2016-12-23 0.3.8
2016-10-11 0.3.3.1
2016-09-12 0.3.3
2016-09-09 0.3.2
2016-06-29 0.2.1.1
2016-06-23 0.2.1
2016-04-23 0.1.0
2015-12-15 0.0.14
2015-11-05 0.0.12
2015-07-10 0.0.10
2015-06-03 0.0.7
2015-04-20 0.0.2
2015-04-09 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-24 1.2.3
2020-11-12 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-03 1.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-14 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-13 1.2.1
2019-12-13 1.1
2018-04-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-01 2.0
2017-10-02 1.3
2017-05-23 1.2
2017-05-22 1.1
2017-03-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-21 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-17 1.0.1
2021-08-16 1.0.0
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <siacus@iq.harvard.edu>
Diff between yuima versions 1.15.15 dated 2022-09-09 and 1.15.18 dated 2022-12-05
DESCRIPTION | 6 MD5 | 16 - NEWS | 14 R/IC.R | 799 ++++++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/IC.Rd | 11 man/rng.Rd | 532 +++++++++++++++++------------------ src/ae.cpp | 15 - src/euler.c | 6 9 files changed, 767 insertions(+), 632 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <sebastian.calonico@columbia.edu>, Matias D. Cattaneo <cattaneo@princeton.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@princeton.edu>
Maintainer: Sebastian Calonico <sebastian.calonico@columbia.edu>
Diff between rdrobust versions 2.1.0 dated 2022-10-28 and 2.1.1 dated 2022-12-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rdrobust.R | 2 +- man/rdrobust-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Quantity Calculus for R Vectors
Description: Integration of the 'units' and 'errors' packages for a complete
quantity calculus system for R vectors, matrices and arrays, with automatic
propagation, conversion, derivation and simplification of magnitudes and
uncertainties. Documentation about 'units' and 'errors' is provided in the
papers by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>) and
by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in
those packages as vignettes; see 'citation("quantities")' for details.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between quantities versions 0.1.6 dated 2021-02-21 and 0.2.0 dated 2022-12-05
DESCRIPTION | 14 MD5 | 93 ++-- NAMESPACE | 14 NEWS.md | 19 R/errors.R | 105 +++- R/init.R | 18 R/math.R | 4 R/misc.R | 27 - R/quantities.R | 2 R/units.R | 24 - R/utils.R | 7 README.md | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 70 ++- inst/doc/introduction.Rmd | 124 +++++ inst/doc/introduction.html | 846 +++++++++++++++---------------------- inst/doc/parsing.Rmd | 2 inst/doc/parsing.html | 313 ++----------- man/Extract.quantities.Rd | 10 man/as.data.frame.quantities.Rd | 3 man/c.quantities.Rd | 4 man/correl.Rd |only man/errors.Rd | 41 + man/groupGeneric.quantities.Rd | 6 man/units.Rd | 19 src/RcppExports.cpp | 5 tests/testthat/_snaps |only tests/testthat/helper-quantities.R | 7 tests/testthat/test-correl.R |only tests/testthat/test-math.R | 8 tests/testthat/test-misc.R | 38 + tests/testthat/test-ops.R | 2 tests/testthat/test-parse.R | 2 tests/testthat/test-plot.R |only tests/testthat/test-quantities.R | 46 +- tests/testthat/test-summary.R | 2 tests/testthat/test-tidyverse.R | 25 - tests/testthat/test-utils.R | 8 vignettes/introduction.Rmd | 124 +++++ vignettes/parsing.Rmd | 2 41 files changed, 1094 insertions(+), 952 deletions(-)
Title: Interface to 'Phylocom'
Description: Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>),
a library for analysis of 'phylogenetic' community structure and
character evolution. Includes low level methods for interacting with
the three executables, as well as higher level interfaces for methods
like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
Author: Jeroen Ooms [aut],
Scott Chamberlain [aut] ,
Cam Webb [cph] ),
David Ackerly [cph] ),
Steven Kembel [cph] ),
Luna Luisa Sanchez Reyes [aut, cre]
Maintainer: Luna Luisa Sanchez Reyes <sanchez.reyes.luna@gmail.com>
Diff between phylocomr versions 0.3.2 dated 2019-12-20 and 0.3.3 dated 2022-12-05
DESCRIPTION | 32 +- MD5 | 53 ++-- NEWS.md | 10 R/phylocomr-inputs.R | 12 R/phylocomr-package.R | 10 R/phylomatic.R | 5 README.md | 461 +++++++++++++++++--------------------- build/partial.rdb |only build/vignette.rds |binary inst/doc/phylocomr.Rmd | 2 inst/doc/phylocomr.html | 119 +++------ man/figures/unnamed-chunk-9-1.png |binary man/ph_phylomatic.Rd | 2 man/phylocomr-inputs.Rd | 2 man/phylocomr-package.Rd | 2 src/Makevars | 2 src/libphylocom/combase.c | 2 src/libphylocom/comstruct.c | 9 src/libphylocom/ecomain.c | 6 src/libphylocom/ecovolve.h | 25 -- src/libphylocom/io.c | 6 src/libphylocom/phylocom.h | 256 ++++++++++----------- src/libphylocom/phylomatic.c | 4 src/nothing.c | 2 tests/testthat/test-bladj.R | 10 tests/testthat/test-comtrait.R | 9 tests/testthat/test-phylomatic.R | 170 +++++++------- vignettes/phylocomr.Rmd | 2 28 files changed, 582 insertions(+), 631 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 0.3.1 dated 2022-10-31 and 0.4 dated 2022-12-05
openxlsx2-0.3.1/openxlsx2/man/merge_borders.Rd |only openxlsx2-0.3.1/openxlsx2/man/merge_cellXfs.Rd |only openxlsx2-0.3.1/openxlsx2/man/merge_fills.Rd |only openxlsx2-0.3.1/openxlsx2/man/merge_fonts.Rd |only openxlsx2-0.3.1/openxlsx2/man/merge_numFmts.Rd |only openxlsx2-0.3.1/openxlsx2/man/wb_chart_sheet.Rd |only openxlsx2-0.4/openxlsx2/DESCRIPTION | 12 openxlsx2-0.4/openxlsx2/MD5 | 128 - openxlsx2-0.4/openxlsx2/NAMESPACE | 11 openxlsx2-0.4/openxlsx2/NEWS.md | 58 openxlsx2-0.4/openxlsx2/R/all-equal.R | 214 -- openxlsx2-0.4/openxlsx2/R/asserts.R | 15 openxlsx2-0.4/openxlsx2/R/baseXML.R | 641 ++++++++ openxlsx2-0.4/openxlsx2/R/class-chart-sheet.R | 117 + openxlsx2-0.4/openxlsx2/R/class-workbook-wrappers.R | 175 ++ openxlsx2-0.4/openxlsx2/R/class-workbook.R | 774 +++++++--- openxlsx2-0.4/openxlsx2/R/class-worksheet.R | 155 +- openxlsx2-0.4/openxlsx2/R/dates.R | 99 - openxlsx2-0.4/openxlsx2/R/expect-wrapper.R | 3 openxlsx2-0.4/openxlsx2/R/helperFunctions.R | 3 openxlsx2-0.4/openxlsx2/R/openxlsx2.R | 1 openxlsx2-0.4/openxlsx2/R/pugixml.R | 21 openxlsx2-0.4/openxlsx2/R/readWorkbook.R | 19 openxlsx2-0.4/openxlsx2/R/utils.R | 17 openxlsx2-0.4/openxlsx2/R/wb_functions.R | 153 + openxlsx2-0.4/openxlsx2/R/wb_load.R | 207 ++ openxlsx2-0.4/openxlsx2/R/wb_styles.R | 198 -- openxlsx2-0.4/openxlsx2/R/write.R | 46 openxlsx2-0.4/openxlsx2/build/vignette.rds |binary openxlsx2-0.4/openxlsx2/inst/AUTHORS | 1 openxlsx2-0.4/openxlsx2/inst/WORDLIST | 42 openxlsx2-0.4/openxlsx2/inst/doc/openxlsx2_basic_manual.Rmd | 6 openxlsx2-0.4/openxlsx2/inst/doc/openxlsx2_basic_manual.html | 24 openxlsx2-0.4/openxlsx2/inst/include/pugixml/pugiconfig.hpp | 2 openxlsx2-0.4/openxlsx2/inst/include/pugixml/pugixml.cpp | 2 openxlsx2-0.4/openxlsx2/inst/include/pugixml/pugixml.hpp | 4 openxlsx2-0.4/openxlsx2/man/dataframe_to_dims.Rd |only openxlsx2-0.4/openxlsx2/man/named_region.Rd | 45 openxlsx2-0.4/openxlsx2/man/openxlsx2.Rd | 1 openxlsx2-0.4/openxlsx2/man/read_xlsx.Rd | 7 openxlsx2-0.4/openxlsx2/man/set_cell_style.Rd | 45 openxlsx2-0.4/openxlsx2/man/wbChartSheet.Rd | 83 + openxlsx2-0.4/openxlsx2/man/wbWorkbook.Rd | 193 ++ openxlsx2-0.4/openxlsx2/man/wbWorksheet.Rd | 128 + openxlsx2-0.4/openxlsx2/man/wb_add_chart_xml.Rd |only openxlsx2-0.4/openxlsx2/man/wb_add_drawing.Rd |only openxlsx2-0.4/openxlsx2/man/wb_add_mschart.Rd |only openxlsx2-0.4/openxlsx2/man/wb_data.Rd |only openxlsx2-0.4/openxlsx2/man/wb_grid_lines.Rd | 4 openxlsx2-0.4/openxlsx2/man/wb_load.Rd | 8 openxlsx2-0.4/openxlsx2/man/wb_read.Rd | 9 openxlsx2-0.4/openxlsx2/man/wb_save.Rd | 3 openxlsx2-0.4/openxlsx2/man/wb_set_bookview.Rd |only openxlsx2-0.4/openxlsx2/src/helper_functions.cpp | 4 openxlsx2-0.4/openxlsx2/src/pugi.cpp | 3 openxlsx2-0.4/openxlsx2/tests/testthat/test-asserts.R | 1 openxlsx2-0.4/openxlsx2/tests/testthat/test-class-chart-sheet.R | 1 openxlsx2-0.4/openxlsx2/tests/testthat/test-class-comment.R | 11 openxlsx2-0.4/openxlsx2/tests/testthat/test-class-workbook-wrappers.R | 65 openxlsx2-0.4/openxlsx2/tests/testthat/test-class-workbook.R | 162 ++ openxlsx2-0.4/openxlsx2/tests/testthat/test-class-worksheet.R | 51 openxlsx2-0.4/openxlsx2/tests/testthat/test-fill_merged_cells.R | 22 openxlsx2-0.4/openxlsx2/tests/testthat/test-helper_functions.R | 2 openxlsx2-0.4/openxlsx2/tests/testthat/test-loading_workbook.R | 25 openxlsx2-0.4/openxlsx2/tests/testthat/test-pugixml.R | 24 openxlsx2-0.4/openxlsx2/tests/testthat/test-read_sources.R | 113 + openxlsx2-0.4/openxlsx2/tests/testthat/test-save.R | 25 openxlsx2-0.4/openxlsx2/tests/testthat/test-wb_functions.R | 42 openxlsx2-0.4/openxlsx2/tests/testthat/test-wb_styles.R | 30 openxlsx2-0.4/openxlsx2/tests/testthat/test-write.R | 25 openxlsx2-0.4/openxlsx2/vignettes/openxlsx2_basic_manual.Rmd | 6 71 files changed, 3337 insertions(+), 949 deletions(-)
Title: Iterated Function Systems
Description: Iterated Function Systems Estimator as in Iacus and La Torre (2005) <doi:10.1155/JAMDS.2005.33>.
Author: S. M. Iacus
Maintainer: Stefano M. Iacus <siacus@iq.harvard.edu>
Diff between ifs versions 0.1.9 dated 2022-08-10 and 0.1.10 dated 2022-12-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/ifs.c | 4 +++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.0.4 dated 2022-11-30 and 1.0.5 dated 2022-12-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- src/CompositeLikelihoodCond2.c | 3 --- src/Distributions.c | 39 ++++++++++++++++++++------------------- src/GeoModels_init.c | 6 +++--- 5 files changed, 31 insertions(+), 33 deletions(-)
Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Author: Bryan A. Hanson [aut, cre] ,
Tejasvi Gupta [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpecUtils versions 1.0.0 dated 2021-10-10 and 1.0.2 dated 2022-12-05
DESCRIPTION | 16 +++++----- MD5 | 36 ++++++++++++------------ NAMESPACE | 4 -- NEWS.md | 5 +++ R/GraphicsOptions.R | 2 - R/addLegend.R | 4 +- R/drawEllipses.R | 46 ++++++++++++++++-------------- R/ggAddLegend.R | 73 ++++++++++++++++++++++++++++++++++--------------- R/prepLegendCoords.R | 56 +++++++++++++++++++++++-------------- R/rowDist.R | 2 - R/scorePlot.R | 50 +++++++++++++++++---------------- build/partial.rdb |binary data/Col12.RData |binary data/Col7.RData |binary data/Col8.RData |binary data/Sym12.RData |binary data/Sym8.RData |binary man/GraphicsOptions.Rd | 2 - man/rowDist.Rd | 2 - 19 files changed, 175 insertions(+), 123 deletions(-)
More information about ChemoSpecUtils at CRAN
Permanent link
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.3.3 dated 2019-05-08 and 1.3.5 dated 2022-12-05
DESCRIPTION | 14 MD5 | 62 +-- R/align.R | 2 R/aphid.R | 4 R/derivePHMM.R | 10 README.md | 7 build/vignette.rds |binary inst/doc/aphid-vignette.R | 30 - inst/doc/aphid-vignette.Rmd | 5 inst/doc/aphid-vignette.html | 845 ++++++++++++++++++++++++++++++++++--------- man/Viterbi.Rd | 33 + man/align.Rd | 105 ++++- man/aphid.Rd | 5 man/backward.Rd | 15 man/casino.Rd | 6 man/deriveHMM.Rd | 11 man/derivePHMM.Rd | 174 ++++++-- man/forward.Rd | 15 man/generate.Rd | 15 man/globins.Rd | 6 man/map.Rd | 15 man/plot.HMM.Rd | 3 man/plot.PHMM.Rd | 11 man/posterior.Rd | 3 man/substitution.Rd | 6 man/train.Rd | 48 +- man/weight.Rd | 6 man/writePHMM.Rd | 3 src/ViterbiC.cpp | 10 src/utils.cpp | 20 - vignettes/aphid-vignette.Rmd | 5 vignettes/aphid.bib | 12 32 files changed, 1126 insertions(+), 380 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-17 1.4
2019-02-09 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-12 3.12.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-17 1.0.4
2019-05-14 1.0.3
2013-04-24 1.0.2
2012-03-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-18 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-17 1.0-3
2016-05-17 1.0-0
2015-01-04 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-06 1.1.2
2015-11-18 1.1.1
2013-02-17 1.1
2013-02-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-09 3.5
2022-04-20 3.4
2020-02-11 3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-10 1.3.4
2014-03-10 1.3.1
2013-10-01 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-10 0.8-2
2018-04-11 0.8-1
2017-06-05 0.8
2017-05-23 0.7
2017-04-02 0.6
2017-04-02 0.6-1
2016-10-04 0.5
2016-05-18 0.4
2016-04-27 0.3
2016-03-14 0.2
2016-02-16 0.1