Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut, cre]
(<https://orcid.org/0000-0002-0315-8888>),
Tae Seung Kang [aut],
Sai Bhargav Yalamanchi [aut],
Mildenberger Thoralf [ctb] (<https://orcid.org/0000-0001-7242-1873>),
Deepak Yadav [aut],
Ignacio Cordón [aut] (<https://orcid.org/0000-0002-3152-0231>),
Vandit Jain [ctb],
Toni Giorgino [ctb] (<https://orcid.org/0000-0001-6449-0596>),
Richèl J.C. Bilderbeek [ctb] (<https://orcid.org/0000-0003-1107-7049>),
Daniel Ebbert [ctb] (<https://orcid.org/0000-0003-3666-7205>),
Shreyash Maheshwari [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.8.5 dated 2020-05-21 and 0.8.5-2 dated 2020-09-08
ChangeLog | 2 DESCRIPTION | 17 ++--- MD5 | 47 +++++++------ NEWS | 4 - R/statisticalTests.R | 64 +++++++++++-------- R/sysdata.rda |binary build/vignette.rds |binary data/blanden.rda |binary data/craigsendi.rda |binary data/holson.rda |binary data/kullback.rda |binary data/preproglucacon.rda |binary data/rain.rda |binary data/sales.rda |binary data/tm_abs.rda |binary inst/doc/an_introduction_to_markovchain_package.R | 2 inst/doc/an_introduction_to_markovchain_package.Rmd | 4 - inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/gsoc_2017_additions.pdf |binary inst/doc/higher_order_markov_chains.pdf |binary man/statisticalTests.Rd | 6 + tests/testthat/Rplots.pdf |binary tests/testthat/testStatisticalTests.R |only tests/testthat/testetm.R | 59 ++++++++++------- vignettes/an_introduction_to_markovchain_package.Rmd | 4 - 25 files changed, 123 insertions(+), 86 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>),
Lukas Lohse [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.3.2.0 dated 2020-06-18 and 0.3.3.0 dated 2020-09-08
DESCRIPTION | 17 +- MD5 | 54 +++--- NEWS | 8 + R/helper.R | 16 -- R/plots.R | 14 + R/simulateResiduals.R | 6 R/tests.R | 176 ++++++++++++++++------ inst/doc/DHARMa.R | 48 ++++++ inst/doc/DHARMa.Rmd | 68 +++++++- inst/doc/DHARMa.html | 271 ++++++++++++++++++++-------------- inst/examples/simulateResidualsHelp.R | 15 - inst/examples/testOutliersHelp.R | 2 inst/examples/testsHelp.R | 8 - man/getQuantile.Rd | 4 man/hist.DHARMa.Rd | 5 man/outliers.Rd | 4 man/recalculateResiduals.Rd | 15 - man/residuals.DHARMa.Rd | 15 - man/simulateResiduals.Rd | 22 +- man/testDispersion.Rd | 8 - man/testGeneric.Rd | 13 - man/testOutliers.Rd | 19 +- man/testResiduals.Rd | 8 - man/testUniformity.Rd | 8 - man/testZeroInflation.Rd | 8 - tests/testthat/Rplots.pdf |binary tests/testthat/testModelTypes.R | 24 +-- vignettes/DHARMa.Rmd | 68 +++++++- 28 files changed, 610 insertions(+), 314 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: We provide a toolbox to fit and simulate a univariate or multivariate damped random walk process that is also known as an Ornstein-Uhlenbeck process or a continuous-time autoregressive model of the first order, i.e., CAR(1) or CARMA(1, 0). This process is suitable for analyzing univariate or multivariate time series data with irregularly-spaced observation times and heteroscedastic measurement errors. When it comes to the multivariate case, the number of data points (measurements/observations) available at each observation time does not need to be the same, and the length of each time series can vary. The number of time series data sets that can be modeled simultaneously is limited to ten in this version of the package. We use Kalman-filtering to evaluate the resulting likelihood function, which leads to a scalable and efficient computation in finding maximum likelihood estimates of the model parameters or in drawing their posterior samples. Please pay attention to loading the data if this package is used for astronomical data analyses; see the details in the manual. Also see Hu and Tak (2020) <arXiv:2005.08049>.
Author: Zhirui Hu and Hyungsuk Tak
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.1 dated 2020-05-19 and 1.0.2 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/drw.R | 7 ++++++- man/Rdrw-package.Rd | 4 ++-- 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Exploring and Testing the Toolchain and System Libraries
Description: A collection of helper functions that interface with the appropriate
system utilities to learn about the build environment. Lets you explore 'make'
rules to test the local configuration, or query 'pkg-config' to find compiler
flags and libs needed for building packages with external dependencies. Also
contains tools to analyze which libraries that a installed R package linked to
by inspecting output from 'ldd' in combination with information from your
distribution package manager, e.g. 'rpm' or 'dpkg'. Finally the package provides
Windows-specific utilities to automatically find or install the suitable version
of the 'Rtools' build environment, and diagnose some common problems.
Author: Jeroen Ooms [aut, cre, cph] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between maketools versions 1.0.0 dated 2020-08-05 and 1.1.0 dated 2020-09-08
DESCRIPTION | 30 ++++++++++++------------------ MD5 | 12 ++++++------ R/info.R | 2 ++ R/make.R | 2 +- R/pkgconfig.R | 2 +- R/sysdeps.R | 6 ++++-- tests/testthat/test-sysdeps.R | 4 +++- 7 files changed, 29 insertions(+), 29 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<https://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the 'GBIF'
tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 3.2.0 dated 2020-07-23 and 3.3.0 dated 2020-09-08
DESCRIPTION | 8 +- MD5 | 93 ++++++++++++++--------------- NEWS.md | 13 ++++ R/dataset_metrics.r | 2 R/dataset_search.r | 2 R/gbif_issues.R | 12 ++- R/gbif_names.R | 4 - R/installations.r | 2 R/name_lookup.r | 2 R/name_suggest.r | 2 R/networks.r | 2 R/nodes.r | 2 R/occ_count.r | 4 - R/occ_data.R | 21 +++++- R/occ_download.R | 4 - R/occ_issues.r | 2 R/occ_metadata.r | 2 R/organizations.r | 2 R/parsenames.R | 2 R/zzz.r | 12 +-- README.md | 9 +- inst/doc/downloads.html | 4 - inst/doc/issues.Rmd | 2 inst/doc/issues.html | 6 - inst/doc/rgbif.Rmd | 2 inst/doc/rgbif.html | 6 - inst/doc/taxonomic_names.html | 4 - man/dataset_metrics.Rd | 2 man/dataset_search.Rd | 2 man/gbif_issues.Rd | 4 - man/installations.Rd | 2 man/name_lookup.Rd | 2 man/name_suggest.Rd | 2 man/networks.Rd | 2 man/nodes.Rd | 2 man/occ_count.Rd | 4 - man/occ_data.Rd | 30 +++++++-- man/occ_download.Rd | 4 - man/occ_issues.Rd | 2 man/occ_metadata.Rd | 2 man/occ_search.Rd | 10 +-- man/organizations.Rd | 2 man/parsenames.Rd | 2 tests/fixtures/occ_data_dropped_fields.yml |only tests/testthat/test-occ_data.R | 16 ++++ tests/testthat/test-occ_download_cached.R | 20 +++--- vignettes/issues.Rmd | 2 vignettes/rgbif.Rmd | 2 48 files changed, 205 insertions(+), 135 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results and where your package stands in the
CRAN submission queue in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 1.2.3 dated 2020-07-30 and 1.3.1 dated 2020-09-08
DESCRIPTION | 7 + MD5 | 31 ++++--- NAMESPACE | 1 NEWS.md | 18 ++++ R/cran_files.R | 24 +++--- R/cran_queue.R | 128 +++++++++++++++++++++------------ R/winbuilder_queue.R |only README.md | 61 +++++++-------- inst/WORDLIST | 3 inst/doc/foghorn.html | 32 +++----- man/cran_details.Rd | 4 + man/cran_incoming.Rd | 6 + man/cran_results.Rd | 4 + man/winbuilder_queue.Rd |only tests/testthat/test-foghorn.R | 15 +-- tests/testthat/test-incoming.R | 18 +++- tests/testthat/test-n_cran_platforms.R | 2 tests/testthat/test-winbuilder-queue.R |only 18 files changed, 217 insertions(+), 137 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 1.2 dated 2020-08-31 and 1.3 dated 2020-09-08
DESCRIPTION | 8 MD5 | 14 R/RcppExports.R | 606 +++++++------- R/rand_CLI.R | 2184 ++++++++++++++++++++++++++--------------------------- R/rand_evalRand.R | 8 R/test_Rfunction.R | 3 data/pats.rda |binary inst/NEWS.Rd | 8 8 files changed, 1420 insertions(+), 1411 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 0.3.0 dated 2020-09-01 and 0.3.1 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/cpp11.cpp | 23 ++++++++++++----------- src/font_registry.cpp | 7 ++++--- 5 files changed, 28 insertions(+), 22 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Blaise Melly [ctb] (Contributions to preprocessing code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Cleve Moler [ctb] (author of several linpack routines),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.61 dated 2020-07-09 and 5.65 dated 2020-09-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/quantreg.R | 4 ++-- inst/ChangeLog | 9 +++++++++ man/rq.Rd | 10 ++++++++-- man/rq.fit.lasso.Rd | 2 +- man/summary.rq.Rd | 7 ++++++- 7 files changed, 35 insertions(+), 15 deletions(-)
Title: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Description: Functions for the input/output and visualization of
medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI'
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [aut],
Karsten Tabelow [ctb],
Jon Clayden [ctb],
John Muschelli [aut]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>
Diff between oro.nifti versions 0.10.3 dated 2020-06-08 and 0.11.0 dated 2020-09-08
DESCRIPTION | 12 ++++---- MD5 | 12 ++++---- NEWS.md | 6 ++++ R/writeS4.R | 77 ++++++++++++++++++++++++++++------------------------- inst/CITATION | 2 - man/write_anlz.Rd | 2 - man/write_nifti.Rd | 8 ++--- 7 files changed, 66 insertions(+), 53 deletions(-)
Title: RUV-III-C
Description: Variations of Remove Unwanted Variation-III (RUV-III) known as RUV-III-C (RUV-III Complete). RUV-III performs normalisation using negative control variables and replication. RUV-III-C extends this method to cases where the data contains missing values, by applying RUV-III to complete subsets of the data. Originally designed for SWATH-MS proteomics datasets.
Poulos et al. (2020) <doi:10.1038/s41467-020-17641-3>.
Author: Rohan Shah [aut, cre], Sean Peters [ctb], Qing Zhong [ctb], Children's Medical Research Institute [cph]
Maintainer: Rohan Shah <rshah@cmri.org.au>
Diff between RUVIIIC versions 1.0.16 dated 2020-09-04 and 1.0.17 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ R/RUVIII_C.R | 2 ++ R/RUVIII_C_Varying.R | 2 ++ R/RcppExports.R | 8 ++++++++ R/threads.R |only man/RUVIII_C.Rd | 2 ++ man/RUVIII_C_Varying.Rd | 2 ++ man/openmp.Rd |only src/RUVIIIC_openmp.cpp |only src/RUVIIIC_openmp.h |only src/RcppExports.cpp | 23 +++++++++++++++++++++++ 13 files changed, 57 insertions(+), 12 deletions(-)
Title: Demonstration of Disease Freedom (DDF)
Description: Implements the formulae required to calculate freedom
from disease according to Cameron and Baldock (1998)
<doi:10.1016/S0167-5877(97)00081-0>. These are the
methods used at the Swedish national veterinary institute (SVA) to
evaluate the performance of our nation animal disease
surveillance programmes.
Author: Thomas Rosendal [aut, cre] (<https://orcid.org/0000-0002-6576-9668>)
Maintainer: Thomas Rosendal <trosendal@gmail.com>
Diff between freedom versions 1.0 dated 2020-09-02 and 1.0.1 dated 2020-09-08
DESCRIPTION | 8 - MD5 | 43 +++--- NEWS.md | 16 ++ R/data_gen.R | 45 +++++- R/herd_se.R | 28 ++-- R/risk.R | 12 - R/temporal_discounting.R | 8 - README.md | 1 man/EffProbInf.Rd | 6 man/hse.Rd | 4 man/hse_finite.Rd | 4 man/hse_infinite.Rd | 4 man/post_fr.Rd | 6 man/prior_fr.Rd | 2 man/sample_data.Rd | 4 man/sysse.Rd | 2 man/sysse_finite.Rd | 2 man/valid_proportions.Rd |only tests/full_test.R | 34 ++--- tests/gen_data.R | 239 +++++++++++++++++++------------------ tests/multi_risk_herd_and_animal.R | 57 +++++--- tests/multirisk_test.R | 14 +- tests/risk.R | 21 ++- 23 files changed, 316 insertions(+), 244 deletions(-)
Title: Convert Decimals to Fractions
Description: Provides functions for converting decimals to a
matrix of numerators and denominators or a character vector of
fractions. Supports mixed or improper fractions, finding common
denominators for vectors of fractions, limiting denominators to powers
of ten, and limiting denominators to a maximum value. Also includes
helper functions for finding the least common multiple and greatest
common divisor for a vector of integers. Implemented using C++ for
maximum speed.
Author: Alexander Rossell Hayes [aut, cre, cph]
(<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between fracture versions 0.1.0 dated 2020-09-03 and 0.1.2 dated 2020-09-08
DESCRIPTION | 12 +++-- MD5 | 32 +++++++------ NAMESPACE | 2 NEWS.md | 31 +++++++++++++ R/frac_mat.R | 22 ++++++++- R/frac_style.R |only R/fracture.R | 60 +++++++++++++------------- R/sysdata.rda |only R/zzz.R | 4 + README.md | 83 ++++++++++++++++++++--------------- man/frac_mat.Rd | 9 ++- man/frac_style.Rd |only man/fracture-package.Rd | 1 man/fracture.Rd | 6 +- src/RcppExports.cpp | 8 +-- src/decimal_to_fraction.cpp | 53 +++++++++------------- tests/testthat/test-frac_mat.R | 21 +++++++++ tests/testthat/test-frac_style.R |only tests/testthat/test-fracture.R | 90 +++++++++++++++++++++++++++++++++++++++ 19 files changed, 308 insertions(+), 126 deletions(-)
Title: Methods for Detecting Safety Signals in Clinical Trials Using
Body-Systems (System Organ Classes)
Description: Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class. This work was supported by the Engineering and Physical Sciences Research Council (UK) (EPSRC) [award reference 1521741] and Frontier Science (Scotland) Ltd. The package title c212 is in reference to the original Engineering and Physical Sciences Research Council (UK) funded project which was named CASE 2/12.
Author: Raymond Carragher [aut, cre] (<https://orcid.org/0000-0002-0120-625X>)
Maintainer: Raymond Carragher <rcarragh@gmail.com>
Diff between c212 versions 0.97 dated 2020-09-03 and 0.98 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/c2121a.cpp | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 1.2-1 dated 2020-07-19 and 1.2-2 dated 2020-09-08
BayesSUR-1.2-1/BayesSUR/R/example_GDSC.R |only BayesSUR-1.2-1/BayesSUR/R/example_eQTL.R |only BayesSUR-1.2-1/BayesSUR/R/get.estimator.R |only BayesSUR-1.2-1/BayesSUR/R/plot.CPO.R |only BayesSUR-1.2-1/BayesSUR/R/plot.MCMCdiag.R |only BayesSUR-1.2-1/BayesSUR/R/plot.Manhattan.R |only BayesSUR-1.2-1/BayesSUR/R/plot.estimator.R |only BayesSUR-1.2-1/BayesSUR/R/plot.network.R |only BayesSUR-1.2-1/BayesSUR/R/plot.response.graph.R |only BayesSUR-1.2-1/BayesSUR/data/example_GDSC.rda |only BayesSUR-1.2-1/BayesSUR/data/example_eQTL.rda |only BayesSUR-1.2-1/BayesSUR/man/example_GDSC.Rd |only BayesSUR-1.2-1/BayesSUR/man/example_eQTL.Rd |only BayesSUR-1.2-1/BayesSUR/man/get.estimator.Rd |only BayesSUR-1.2-1/BayesSUR/man/plot.CPO.Rd |only BayesSUR-1.2-1/BayesSUR/man/plot.MCMCdiag.Rd |only BayesSUR-1.2-1/BayesSUR/man/plot.Manhattan.Rd |only BayesSUR-1.2-1/BayesSUR/man/plot.estimator.Rd |only BayesSUR-1.2-1/BayesSUR/man/plot.network.Rd |only BayesSUR-1.2-1/BayesSUR/man/plot.response.graph.Rd |only BayesSUR-1.2-2/BayesSUR/DESCRIPTION | 10 - BayesSUR-1.2-2/BayesSUR/MD5 | 98 +++++----- BayesSUR-1.2-2/BayesSUR/NAMESPACE | 16 + BayesSUR-1.2-2/BayesSUR/R/BayesSUR.R | 188 ++++++++++----------- BayesSUR-1.2-2/BayesSUR/R/RcppExports.R | 4 BayesSUR-1.2-2/BayesSUR/R/coef.BayesSUR.R | 29 ++- BayesSUR-1.2-2/BayesSUR/R/elpd.R | 18 +- BayesSUR-1.2-2/BayesSUR/R/exampleEQTL.R |only BayesSUR-1.2-2/BayesSUR/R/exampleGDSC.R |only BayesSUR-1.2-2/BayesSUR/R/fitted.BayesSUR.R | 39 ++-- BayesSUR-1.2-2/BayesSUR/R/getEstimator.R |only BayesSUR-1.2-2/BayesSUR/R/plot.BayesSUR.R | 178 +++++++++++++------ BayesSUR-1.2-2/BayesSUR/R/plotCPO.R |only BayesSUR-1.2-2/BayesSUR/R/plotEstimator.R |only BayesSUR-1.2-2/BayesSUR/R/plotGraph.R |only BayesSUR-1.2-2/BayesSUR/R/plotMCMCdiag.R |only BayesSUR-1.2-2/BayesSUR/R/plotManhattan.R |only BayesSUR-1.2-2/BayesSUR/R/plotNetwork.R |only BayesSUR-1.2-2/BayesSUR/R/predict.BayesSUR.R | 80 ++++---- BayesSUR-1.2-2/BayesSUR/R/print.BayesSUR.R | 16 - BayesSUR-1.2-2/BayesSUR/R/summary.BayesSUR.R | 19 +- BayesSUR-1.2-2/BayesSUR/R/targetGene.R | 12 - BayesSUR-1.2-2/BayesSUR/build/vignette.rds |binary BayesSUR-1.2-2/BayesSUR/data/datalist | 4 BayesSUR-1.2-2/BayesSUR/data/exampleEQTL.rda |only BayesSUR-1.2-2/BayesSUR/data/exampleGDSC.rda |only BayesSUR-1.2-2/BayesSUR/inst/doc/BayesSUR.pdf |binary BayesSUR-1.2-2/BayesSUR/man/BayesSUR.Rd | 72 ++++---- BayesSUR-1.2-2/BayesSUR/man/coef.BayesSUR.Rd | 22 +- BayesSUR-1.2-2/BayesSUR/man/elpd.Rd | 16 - BayesSUR-1.2-2/BayesSUR/man/exampleEQTL.Rd |only BayesSUR-1.2-2/BayesSUR/man/exampleGDSC.Rd |only BayesSUR-1.2-2/BayesSUR/man/fitted.BayesSUR.Rd | 22 +- BayesSUR-1.2-2/BayesSUR/man/getEstimator.Rd |only BayesSUR-1.2-2/BayesSUR/man/plot.BayesSUR.Rd | 53 ++++- BayesSUR-1.2-2/BayesSUR/man/plotCPO.Rd |only BayesSUR-1.2-2/BayesSUR/man/plotEstimator.Rd |only BayesSUR-1.2-2/BayesSUR/man/plotGraph.Rd |only BayesSUR-1.2-2/BayesSUR/man/plotMCMCdiag.Rd |only BayesSUR-1.2-2/BayesSUR/man/plotManhattan.Rd |only BayesSUR-1.2-2/BayesSUR/man/plotNetwork.Rd |only BayesSUR-1.2-2/BayesSUR/man/predict.BayesSUR.Rd | 32 +-- BayesSUR-1.2-2/BayesSUR/man/print.BayesSUR.Rd | 16 - BayesSUR-1.2-2/BayesSUR/man/summary.BayesSUR.Rd | 16 - BayesSUR-1.2-2/BayesSUR/man/targetGene.Rd | 9 - BayesSUR-1.2-2/BayesSUR/src/BayesSUR.cpp | 4 BayesSUR-1.2-2/BayesSUR/src/RcppExports.cpp | 8 BayesSUR-1.2-2/BayesSUR/src/drive.cpp | 38 ++-- BayesSUR-1.2-2/BayesSUR/src/drive.h | 2 BayesSUR-1.2-2/BayesSUR/src/utils.h | 2 70 files changed, 572 insertions(+), 451 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrGraph versions 1.0.2 dated 2020-07-09 and 1.0.4 dated 2020-09-08
wrGraph-1.0.2/wrGraph/inst/doc/wrGraphVignette2.R |only wrGraph-1.0.2/wrGraph/inst/doc/wrGraphVignette2.Rmd |only wrGraph-1.0.2/wrGraph/inst/doc/wrGraphVignette2.html |only wrGraph-1.0.2/wrGraph/vignettes/wrGraphVignette2.Rmd |only wrGraph-1.0.4/wrGraph/DESCRIPTION | 6 - wrGraph-1.0.4/wrGraph/MD5 | 22 ++-- wrGraph-1.0.4/wrGraph/R/checkForLegLoc.R | 4 wrGraph-1.0.4/wrGraph/R/mouseOverHtmlFile.R | 28 ++--- wrGraph-1.0.4/wrGraph/R/vioplotW.R | 101 ++++++++++++------- wrGraph-1.0.4/wrGraph/build/vignette.rds |binary wrGraph-1.0.4/wrGraph/inst/doc/wrGraphVignette1.R |only wrGraph-1.0.4/wrGraph/inst/doc/wrGraphVignette1.Rmd |only wrGraph-1.0.4/wrGraph/inst/doc/wrGraphVignette1.html |only wrGraph-1.0.4/wrGraph/man/mouseOverHtmlFile.Rd | 2 wrGraph-1.0.4/wrGraph/man/vioplotW.Rd | 9 + wrGraph-1.0.4/wrGraph/vignettes/wrGraphVignette1.Rmd |only 16 files changed, 101 insertions(+), 71 deletions(-)
Title: Text Alignment with Smith-Waterman
Description: Find similarities between texts using the Smith-Waterman algorithm. The algorithm performs local sequence alignment and determines similar regions between two strings.
The Smith-Waterman algorithm is explained in the paper: "Identification of common molecular subsequences" by T.F.Smith and M.S.Waterman (1981), available at <doi:10.1016/0022-2836(81)90087-5>.
This package implements the same logic for sequences of words and letters instead of molecular sequences.
Author: Jan Wijffels [aut, cre, cph] (Rewrite of functionalities from the
textreuse R package),
Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital
Humanities [cph],
Lincoln Mullen [ctb, cph]
Maintainer: Jan Wijffels <jan.wijffels@vub.be>
Diff between text.alignment versions 0.1.1 dated 2020-04-23 and 0.1.2 dated 2020-09-08
DESCRIPTION | 11 +- MD5 | 25 +++--- NAMESPACE | 1 NEWS.md | 5 + R/smith_waterman.R | 156 +++++++++++++++++++++++++++++++++------ README.md | 2 build/vignette.rds |binary inst/doc/textalignment.R | 2 inst/doc/textalignment.Rmd | 2 inst/doc/textalignment.html | 27 +++++- man/smith_waterman.Rd | 7 + man/smith_waterman_misaligned.Rd |only man/smith_waterman_pairwise.Rd | 98 ++++++++++++------------ vignettes/textalignment.Rmd | 2 14 files changed, 239 insertions(+), 99 deletions(-)
More information about text.alignment at CRAN
Permanent link
Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with
'mlr3', e.g. Grid Search, Random Search, or Simulated Annealing.
Various termination criteria can be set and combined. The class
'AutoTuner' provides a convenient way to perform nested resampling in
combination with 'mlr3'.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Daniel Schalk [aut] (<https://orcid.org/0000-0003-0950-1947>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.2.0 dated 2020-07-28 and 0.3.0 dated 2020-09-08
DESCRIPTION | 15 +++--- MD5 | 50 +++++++++++----------- NAMESPACE | 1 NEWS.md | 27 ++++++++++++ R/ArchiveTuning.R |only R/AutoTuner.R | 4 - R/ObjectiveTuning.R | 56 +++++++++++++++---------- R/Tuner.R | 4 + R/TunerFromOptimizer.R | 2 R/TuningInstanceMulticrit.R | 19 ++++---- R/TuningInstanceSingleCrit.R | 13 +++-- R/zzz.R | 2 README.md | 2 build/partial.rdb |binary man/ArchiveTuning.Rd |only man/AutoTuner.Rd | 4 - man/ObjectiveTuning.Rd | 17 ++++--- man/Tuner.Rd | 10 ++-- man/TunerFromOptimizer.Rd | 2 man/TuningInstanceMultiCrit.Rd | 9 ++-- man/TuningInstanceSingleCrit.Rd | 13 +++-- man/mlr3tuning-package.Rd | 4 - tests/testthat/helper.R | 8 +-- tests/testthat/test_AutoTuner.R | 21 ++++----- tests/testthat/test_ObjectiveTuning.R | 16 ++++--- tests/testthat/test_TuningInstanceMultiCrit.R | 10 +++- tests/testthat/test_TuningInstanceSingleCrit.R | 47 ++++++++++++-------- 27 files changed, 215 insertions(+), 141 deletions(-)
Title: Analysis of Doubly-Truncated Data
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models.
Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and
Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>.
Parametric models from the special exponential family (SEF) are based on
Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and
Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
The parametric location-scale models are based on Dorre et al. (2020) <doi:10.1007/s00180-020-01027-6>.
Author: Takeshi Emura, Ya-Hsuan Hu, Chung-Yan Huang
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between double.truncation versions 1.6 dated 2020-08-27 and 1.7 dated 2020-09-08
DESCRIPTION | 10 +-- MD5 | 18 ++--- R/PMLE.Weibull.R | 126 ++++++++++++++++----------------------- R/PMLE.loglogistic.R | 120 +++++++++++++++---------------------- R/PMLE.lognormal.R | 126 ++++++++++++++++----------------------- man/PMLE.Weibull.Rd | 4 - man/PMLE.loglogistic.Rd | 2 man/PMLE.lognormal.Rd | 2 man/double.truncation-package.Rd | 6 - man/simu.Weibull.Rd | 10 +-- 10 files changed, 180 insertions(+), 244 deletions(-)
More information about double.truncation at CRAN
Permanent link
Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening
Services
Description: Allows using two URL shortening services, which also provide
expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth2) and 'is.gd' (no API key).
Author: John Malc [aut, cre] (@dmpe),
Andrea Dodet [ctb] (@andodet)
Maintainer: John Malc <cincenko@outlook.com>
Diff between urlshorteneR versions 1.1.2 dated 2019-09-07 and 1.3.0 dated 2020-09-08
DESCRIPTION | 27 - MD5 | 134 ++--- NAMESPACE | 3 NEWS | 7 R/ApiKey.R | 20 R/addins.R |only R/bitly_bsd.R | 8 R/bitly_camp.R | 115 ++-- R/bitly_custom_links.R | 58 +- R/bitly_groups.R | 4 R/bitly_links.R | 340 +++++++------- R/bitly_orgs.R | 24 R/bitly_user_app_info.R | 34 - R/vgd_links.R | 1 R/zzz.R | 2 build/vignette.rds |binary inst/doc/Tutorial.R | 16 inst/doc/Tutorial.html | 159 +++--- inst/rstudio |only man/bitly_add_cust_bitlink.Rd | 17 man/bitly_app_details.Rd | 9 man/bitly_auth.Rd | 7 man/bitly_bsds.Rd | 2 man/bitly_create_bitlink.Rd | 18 man/bitly_create_campaigns.Rd | 11 man/bitly_create_channel.Rd | 15 man/bitly_expand_link.Rd | 2 man/bitly_retrieve_bitlink.Rd | 2 man/bitly_retrieve_bitlinks_by_groups.Rd | 25 - man/bitly_retrieve_campaign.Rd | 2 man/bitly_retrieve_campaigns.Rd | 2 man/bitly_retrieve_channel.Rd | 2 man/bitly_retrieve_channels.Rd | 9 man/bitly_retrieve_clicks.Rd | 11 man/bitly_retrieve_clicks_summary.Rd | 13 man/bitly_retrieve_cust_bitlink.Rd | 5 man/bitly_retrieve_destination_metrics.Rd | 8 man/bitly_retrieve_group.Rd | 2 man/bitly_retrieve_group_click_metrics_by_countries.Rd | 8 man/bitly_retrieve_group_click_metrics_by_ref_networks.Rd | 8 man/bitly_retrieve_group_pref.Rd | 2 man/bitly_retrieve_group_shorten_counts.Rd | 2 man/bitly_retrieve_groups.Rd | 2 man/bitly_retrieve_links_grouped.Rd | 27 - man/bitly_retrieve_metrics_by_countries.Rd | 15 man/bitly_retrieve_metrics_by_referrers.Rd | 15 man/bitly_retrieve_metrics_by_referrers_by_domain.Rd | 15 man/bitly_retrieve_sorted_bitlinks_by_groups.Rd | 12 man/bitly_retrieve_sorted_links.Rd | 14 man/bitly_retrieve_tags.Rd | 2 man/bitly_shorten_link.Rd | 10 man/bitly_update_bitlink.Rd | 27 - man/bitly_update_campaign.Rd | 13 man/bitly_update_channel.Rd | 16 man/bitly_update_cust_bitlink.Rd | 9 man/bitly_update_group.Rd | 10 man/bitly_update_group_pref.Rd | 5 man/bitly_update_user.Rd | 5 man/bitly_user_info.Rd | 2 man/bitly_user_metrics_referring_domains.Rd | 17 man/clipExpanderAddin.Rd |only man/clipShortenerAddin.Rd |only man/isgd_LinksShorten.Rd | 8 man/shortenerAddin.Rd |only man/vgd_LinksShorten.Rd | 8 tests/testthat.R | 8 tests/testthat/test-Information.R | 1 tests/testthat/test-Links.R | 5 tests/testthat/test-UserMetrics.R | 12 tests/testthat/test-addins.R |only tests/testthat/test-grOrgBDS.R | 6 71 files changed, 795 insertions(+), 603 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Provides various features that help with creating publication-quality figures
with 'ggplot2', such as a set of themes, functions to align plots and arrange
them into complex compound figures, and functions that make it easy to annotate
plots and or mix plots with images. The package was originally written for
internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package).
It has also been used extensively in the book Fundamentals of Data
Visualization.
Author: Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 1.0.0 dated 2019-07-11 and 1.1.0 dated 2020-09-08
cowplot-1.0.0/cowplot/tests/testthat/Rplots.pdf |only cowplot-1.1.0/cowplot/DESCRIPTION | 17 - cowplot-1.1.0/cowplot/MD5 | 140 +++++----- cowplot-1.1.0/cowplot/NAMESPACE | 2 cowplot-1.1.0/cowplot/NEWS.md | 12 cowplot-1.1.0/cowplot/R/align_plots.R | 68 ++++ cowplot-1.1.0/cowplot/R/as_grob.R | 72 ++--- cowplot-1.1.0/cowplot/R/axis_canvas.R | 15 - cowplot-1.1.0/cowplot/R/cowplot.R | 10 cowplot-1.1.0/cowplot/R/draw.R | 64 +++- cowplot-1.1.0/cowplot/R/get_panel.R | 2 cowplot-1.1.0/cowplot/R/gtable.R | 2 cowplot-1.1.0/cowplot/R/plot_grid.R | 28 +- cowplot-1.1.0/cowplot/R/save.R | 15 - cowplot-1.1.0/cowplot/R/set_null_device.R | 28 +- cowplot-1.1.0/cowplot/R/setup.R | 10 cowplot-1.1.0/cowplot/README.md | 10 cowplot-1.1.0/cowplot/build/vignette.rds |binary cowplot-1.1.0/cowplot/inst/doc/introduction.R | 14 - cowplot-1.1.0/cowplot/inst/doc/introduction.Rmd | 2 cowplot-1.1.0/cowplot/inst/doc/introduction.html | 76 +++-- cowplot-1.1.0/cowplot/man/add_sub.Rd | 22 + cowplot-1.1.0/cowplot/man/align_plots.Rd | 8 cowplot-1.1.0/cowplot/man/axis_canvas.Rd | 11 cowplot-1.1.0/cowplot/man/background_grid.Rd | 14 - cowplot-1.1.0/cowplot/man/cowplot.Rd | 11 cowplot-1.1.0/cowplot/man/draw_figure_label.Rd | 9 cowplot-1.1.0/cowplot/man/draw_grob.Rd | 20 + cowplot-1.1.0/cowplot/man/draw_image.Rd | 36 ++ cowplot-1.1.0/cowplot/man/draw_label.Rd | 20 + cowplot-1.1.0/cowplot/man/draw_plot.Rd | 19 + cowplot-1.1.0/cowplot/man/draw_plot_label.Rd | 16 - cowplot-1.1.0/cowplot/man/draw_text.Rd | 3 cowplot-1.1.0/cowplot/man/get_panel.Rd | 2 cowplot-1.1.0/cowplot/man/ggsave2.Rd | 16 - cowplot-1.1.0/cowplot/man/gtable_squash_cols.Rd | 4 cowplot-1.1.0/cowplot/man/insert_xaxis_grob.Rd | 20 + cowplot-1.1.0/cowplot/man/panel_border.Rd | 3 cowplot-1.1.0/cowplot/man/plot_grid.Rd | 48 ++- cowplot-1.1.0/cowplot/man/png_null_device.Rd | 3 cowplot-1.1.0/cowplot/man/rectangle_key_glyph.Rd | 24 + cowplot-1.1.0/cowplot/man/save_plot.Rd | 33 +- cowplot-1.1.0/cowplot/man/set_null_device.Rd | 9 cowplot-1.1.0/cowplot/man/stamp.Rd | 15 - cowplot-1.1.0/cowplot/man/theme_cowplot.Rd | 20 + cowplot-1.1.0/cowplot/man/theme_map.Rd | 10 cowplot-1.1.0/cowplot/man/theme_minimal_grid.Rd | 39 ++ cowplot-1.1.0/cowplot/tests/figs/deps.txt | 2 cowplot-1.1.0/cowplot/tests/figs/draw-functions/four-corners-aligned-scaled.svg |only cowplot-1.1.0/cowplot/tests/figs/draw-functions/four-corners-centered-scaled.svg |only cowplot-1.1.0/cowplot/tests/figs/plot-grid/colwise-arranging.svg |only cowplot-1.1.0/cowplot/tests/figs/plot-grid/h-v-alignment-right-and-top-axes.svg | 6 cowplot-1.1.0/cowplot/tests/figs/plot-grid/horizontal-alignment-bottom-axis.svg | 6 cowplot-1.1.0/cowplot/tests/figs/plot-grid/horizontal-alignment-top-axis.svg | 6 cowplot-1.1.0/cowplot/tests/figs/plot-grid/vertical-alignment-left-axis.svg | 6 cowplot-1.1.0/cowplot/tests/figs/plot-grid/vertical-alignment-right-axis.svg | 6 cowplot-1.1.0/cowplot/tests/figs/themes/theme-half-open-huge.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-half-open-tiny.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-half-open.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-grid-huge.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-grid-tiny.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-grid.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-hgrid-huge.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-hgrid-tiny.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-hgrid.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-vgrid-huge.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-vgrid-tiny.svg | 30 +- cowplot-1.1.0/cowplot/tests/figs/themes/theme-minimal-vgrid.svg | 30 +- cowplot-1.1.0/cowplot/tests/testthat/test_align_plots.R | 80 +++++ cowplot-1.1.0/cowplot/tests/testthat/test_draw_.R | 54 +++ cowplot-1.1.0/cowplot/tests/testthat/test_plot_grid.R | 4 cowplot-1.1.0/cowplot/tests/testthat/test_themes.R | 6 cowplot-1.1.0/cowplot/vignettes/introduction.Rmd | 2 73 files changed, 1045 insertions(+), 515 deletions(-)
Title: Confidentiality of Spatial Point Data
Description: Provides an automatic aggregation tool to manage point data privacy,
intended to be helpful for the production of official spatial data and for researchers.
The package pursues the data accuracy at the smallest possible areas preventing
individual information disclosure. The methodology, based on hierarchical geographic
data structures performs aggregation and local suppression of point data to ensure privacy
as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>.
The data structures are created following the guidelines for grid datasets from the
European Forum for Geography and Statistics.
Author: Raymond Lagonigro [aut, cre] (<https://orcid.org/0000-0002-8091-4296>),
Ramon Oller [aut] (<https://orcid.org/0000-0002-4333-0021>),
Joan Carles Martori [aut] (<https://orcid.org/0000-0002-8400-5487>)
Maintainer: Raymond Lagonigro <raymond.lagonigro@uvic.cat>
Diff between AQuadtree versions 1.0.1 dated 2020-07-08 and 1.0.2 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- NEWS | 9 +++++---- R/createAQuadtree.R | 2 +- R/createGrid.R | 2 +- R/joinAQuadtrees.R | 8 ++++---- R/pointsToAQuadtree.R | 4 ++-- data/BarcelonaCensusTracts.rda |binary data/BarcelonaPop.rda |binary data/CharlestonCensusTracts.rda |binary data/CharlestonPop.rda |binary inst/doc/AQuadtreeUse.html | 21 ++++++++++----------- 13 files changed, 40 insertions(+), 40 deletions(-)
Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038> and Rabe, Vasishth, Hohenstein, Kliegl, and Schad (2020) <doi:10.21105/joss.02134>.
Author: Maximilian M. Rabe [aut, cre] (<https://orcid.org/0000-0002-2556-5644>),
Shravan Vasishth [aut] (<https://orcid.org/0000-0003-2027-1994>),
Sven Hohenstein [aut] (<https://orcid.org/0000-0002-9708-1593>),
Reinhold Kliegl [aut] (<https://orcid.org/0000-0002-0180-8488>),
Daniel J. Schad [aut] (<https://orcid.org/0000-0003-2586-6823>)
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between hypr versions 0.1.9 dated 2020-07-29 and 0.1.10 dated 2020-09-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/hypr.R | 12 +++++++----- README.md | 6 +++--- inst/doc/hypr-intro.html | 8 ++++---- man/ginv2.Rd | 4 +++- 6 files changed, 25 insertions(+), 21 deletions(-)
Title: Latent Class Analysis with Group Variable
Description: Fits latent class analysis (LCA) including group variable and covariates.
The group variable can be handled either by multilevel LCA described in Vermunt (2003) <DOI:10.1111/j.0081-1750.2003.t01-1-00131.x> or standard LCA at each level of group variable.
The covariates can be incorporated in the form of logistic regression (Bandeen-Roche et al. (1997) <DOI:10.1080/01621459.1997.10473658>).
Author: Youngsun Kim [aut, cre],
Hwan Chung [aut]
Maintainer: Youngsun Kim <kim0sun@korea.ac.kr>
Diff between glca versions 1.0.0 dated 2020-09-07 and 1.0.1 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/glca.R | 5 ++--- R/glca.gof.R | 2 +- R/glca_encode.R | 3 ++- build/partial.rdb |binary man/glca.Rd | 5 ++--- man/glca.gof.Rd | 2 +- 8 files changed, 19 insertions(+), 20 deletions(-)
Title: A Fast, Easy-to-Use Database Interface
Description: Provides select, insert, update, upsert, and delete database operations. Supports 'PostgreSQL', 'MySQL', 'SQLite', and more, and plays nicely with the 'DBI' package.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>
Diff between dbx versions 0.2.6 dated 2020-06-15 and 0.2.7 dated 2020-09-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ tests/testthat/helper-run-data-type-tests.R | 6 ++++++ tests/testthat/test-postgres.R | 3 +++ tests/testthat/test-postgresql.R | 3 +++ 6 files changed, 25 insertions(+), 9 deletions(-)
Title: Wildlife Sightability Modeling
Description: Uses logistic regression to model the probability of detection as a function of covariates.
This model is then used with observational survey data to estimate population size, while
accounting for uncertain detection. See Steinhorst and Samuel (1989).
Author: Fieberg John [aut],
Schwarz Carl James [aut, cre]
Maintainer: Schwarz Carl James <cschwarz.stat.sfu.ca@gmail.com>
Diff between SightabilityModel versions 1.4.0 dated 2020-07-17 and 1.4.1 dated 2020-09-08
DESCRIPTION | 8 - MD5 | 42 ++--- R/MoosePopR.r | 20 +- R/Sight.Est.R | 2 R/Sight.Est.Ratio.R | 4 R/SightabilityPopR.R | 14 + R/data.R | 2 README.md | 6 inst/CITATION | 4 inst/NEWS.Rd | 11 + inst/doc/MoosePopR-SightabilityPopR-Demo.Rmd | 2 inst/doc/MoosePopR-SightabilityPopR-Demo.html | 194 +++++++++++++++++++++++++- inst/doc/RatioEstimator.pdf.asis | 2 inst/doc/SightabilityModel.pdf |binary man/MoosePopR.Rd | 7 man/Sight.Est.Ratio.Rd | 2 man/Sight.Est.Rd | 2 man/SightabilityModel-package.Rd | 2 man/SightabilityPopR.Rd | 5 vignettes/MoosePopR-SightabilityPopR-Demo.Rmd | 2 vignettes/RatioEstimator.pdf.asis | 2 vignettes/vignette.bib | 24 +-- 22 files changed, 282 insertions(+), 75 deletions(-)
More information about SightabilityModel at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-24 2.3.0
2020-08-03 2.2.2
Title: An R Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS, see <http://nomads.ncep.noaa.gov/> for more information) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of over 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve some archived models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <danny.c.bowman@gmail.com>
Diff between rNOMADS versions 2.4.2 dated 2020-02-29 and 2.5.0 dated 2020-09-08
DESCRIPTION | 12 +++---- MD5 | 56 ++++++++++++++++++------------------ NEWS | 7 ++++ R/GetArchiveGrib.R | 16 +++++----- R/GetDODS.R | 20 +------------ R/Models.R | 69 ++++++++++----------------------------------- R/onAttach.R | 2 - man/ArchiveGribGrab.Rd | 8 +++-- man/BuildProfile.Rd | 2 - man/CheckNOMADSArchive.Rd | 10 +++--- man/CrawlModels.Rd | 2 - man/DODSGrab.Rd | 2 - man/GetClosestForecasts.Rd | 2 - man/GetDODSDates.Rd | 11 +------ man/GetDODSModelRunInfo.Rd | 2 - man/GetDODSModelRuns.Rd | 9 ----- man/GribGrab.Rd | 2 - man/GribInfo.Rd | 2 - man/LinkExtractor.Rd | 2 - man/MagnitudeAzimuth.Rd | 2 - man/ModelGrid.Rd | 2 - man/NOMADSArchiveList.Rd | 8 +---- man/NOMADSRealTimeList.Rd | 2 - man/ParseModelPage.Rd | 2 - man/PlotWindProfile.Rd | 4 +- man/ReadGrib.Rd | 2 - man/SanitizeURL.Rd | 2 - man/SubsetNOMADS.Rd | 2 - man/WebCrawler.Rd | 2 - 29 files changed, 103 insertions(+), 161 deletions(-)
Title: NEON Data Store
Description: The National Ecological Observatory Network (NEON) provides access
to its numerous data products through its REST API,
<https://data.neonscience.org/data-api/>. This package provides a
high-level user interface for downloading and storing NEON data products.
While each of NEON data products consist of hundreds or thousands of individual
files. Unlike 'neonUtilities', this package will avoid repeated downloading,
provides persistent storage, and improves performance. This package does not
provide expose interactions with the individual low-level NEON API endpoints.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Quinn Thomas [ctb],
Christine Laney [aut] (<https://orcid.org/0000-0002-4944-2083>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between neonstore versions 0.2.1 dated 2020-08-29 and 0.2.2 dated 2020-09-08
neonstore-0.2.1/neonstore/R/neon_store.R |only neonstore-0.2.1/neonstore/man/neon_store.Rd |only neonstore-0.2.2/neonstore/DESCRIPTION | 8 neonstore-0.2.2/neonstore/MD5 | 44 ++-- neonstore-0.2.2/neonstore/NAMESPACE | 6 neonstore-0.2.2/neonstore/NEWS.md | 11 + neonstore-0.2.2/neonstore/R/neon_dir.R | 4 neonstore-0.2.2/neonstore/R/neon_download.R | 36 ++- neonstore-0.2.2/neonstore/R/neon_export.R | 35 +++ neonstore-0.2.2/neonstore/R/neon_filename_parser.R | 88 ++++++--- neonstore-0.2.2/neonstore/R/neon_index.R | 25 ++ neonstore-0.2.2/neonstore/R/neon_read.R | 77 ++++++-- neonstore-0.2.2/neonstore/README.md | 120 +++++++------ neonstore-0.2.2/neonstore/inst/WORDLIST | 18 + neonstore-0.2.2/neonstore/man/neon_dir.Rd | 4 neonstore-0.2.2/neonstore/man/neon_download.Rd | 5 neonstore-0.2.2/neonstore/man/neon_download_s3.Rd | 5 neonstore-0.2.2/neonstore/man/neon_export.Rd | 15 + neonstore-0.2.2/neonstore/man/neon_filename_parser.Rd | 87 ++++++--- neonstore-0.2.2/neonstore/man/neon_import.Rd | 7 neonstore-0.2.2/neonstore/man/neon_index.Rd | 20 ++ neonstore-0.2.2/neonstore/man/neon_read.Rd | 33 +++ neonstore-0.2.2/neonstore/tests/testthat/test-additional.R | 49 +++++ neonstore-0.2.2/neonstore/tests/testthat/test-store.R | 20 -- 24 files changed, 514 insertions(+), 203 deletions(-)
Title: An Interface for Content-Based Identifiers
Description: An interface for creating, registering, and resolving content-based
identifiers for data management. Content-based identifiers rely on
the 'cryptographic' hashes to refer to the files they identify, thus,
anyone possessing the file can compute the identifier using a
well-known standard algorithm, such as 'SHA256'. By registering
a URL at which the content is accessible to a public archive, such
as <https://hash-archive.org>, the content identifier can serve
many functions typically associated with A Digital Object Identifier
('DOI'). Unlike location-based identifiers like 'DOIs', content-based
identifiers permit the same content to be registered in many locations.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Jorrit Poelen [aut] (<https://orcid.org/0000-0003-3138-4118>),
NSF OAC 1839201 [fnd]
(https://www.nsf.gov/awardsearch/showAward?AWD_ID=1839201)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between contentid versions 0.0.6 dated 2020-08-31 and 0.0.7 dated 2020-09-08
DESCRIPTION | 7 +++--- MD5 | 31 +++++++++++++++++------------ NEWS.md | 7 ++++++ R/content_id.R | 33 +++++++++++++++++++++---------- R/local_registry.R | 2 - R/resolve.R | 2 - R/retrieve.R | 33 +++++++++++++++++-------------- R/store.R | 41 ++++++++++++++++++++------------------- README.md | 2 + build |only inst/WORDLIST | 33 +++++++++++++++++++++++++++++++ inst/doc |only man/content_id.Rd | 20 +++++++++++++++---- tests/testthat/test-content_id.R | 6 ++--- tests/testthat/test-multihash.R | 4 +-- tests/testthat/test-pin.R | 4 +-- vignettes |only 17 files changed, 152 insertions(+), 73 deletions(-)
Title: A Parametric Method for Generating Synthetic Data
Description: Builds synthetic data applicable across multiple domains. This package also provides flexibility to control data distribution to make it relevant to many industry examples.
Author: Sidharth Macherla [aut, cre] (<https://orcid.org/0000-0002-4825-2026>)
Maintainer: Sidharth Macherla <msidharthrasik@gmail.com>
Diff between conjurer versions 1.1.1 dated 2020-03-21 and 1.2.0 dated 2020-09-08
DESCRIPTION | 10 - MD5 | 20 +- NAMESPACE | 1 NEWS.md | 10 - R/buildDistr.R | 22 ++- R/buildNum.R |only inst/doc/introduction_to_conjurer.R | 48 ++++-- inst/doc/introduction_to_conjurer.Rmd | 40 ++++- inst/doc/introduction_to_conjurer.html | 233 ++++++++++++++++++--------------- man/buildDistr.Rd | 4 man/buildNum.Rd |only vignettes/introduction_to_conjurer.Rmd | 40 ++++- 12 files changed, 272 insertions(+), 156 deletions(-)