Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre],
Luke Winslow [aut],
Scott Chamberlain [ctb],
Alison Appling [ctb],
Jordan Read [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between sbtools versions 1.1.21 dated 2022-11-03 and 1.2.0 dated 2023-04-30
DESCRIPTION | 12 +-- MD5 | 35 ++++----- NAMESPACE | 1 NEWS.md | 7 + R/REST_helpers.R | 5 + R/authenticate_sb.R | 12 ++- R/gql_helpers.R | 18 ++++ R/item_file_download.R | 2 R/item_list_children.R | 2 R/item_list_files.R | 6 + R/item_upload_files.R | 33 +++++++- R/sbtools-package.R | 76 ++++++++++---------- README.md | 170 +++++++++++++++++++++++++-------------------- inst/CITATION | 14 ++- man/item_list_children.Rd | 2 man/item_publish_cloud.Rd |only man/item_upload_cloud.Rd | 2 man/sbtools-package.Rd | 86 +++++++++++----------- tests/testthat/test-auth.R | 26 ++++++ 19 files changed, 312 insertions(+), 197 deletions(-)
Title: Nonparametric Failure Time Bayesian Additive Regression Trees
Description: Nonparametric Failure Time (NFT) Bayesian Additive Regression Trees (BART): Time-to-event Machine Learning with Heteroskedastic Bayesian Additive Regression Trees (HBART) and Low Information Omnibus (LIO) Dirichlet Process Mixtures (DPM). An NFT BART model is of the form Y = mu + f(x) + sd(x) E where functions f and sd have BART and HBART priors, respectively, while E is a nonparametric error distribution due to a DPM LIO prior hierarchy. See the following for a complete description of the model at <doi:10.1111/biom.13857>.
Author: Rodney Sparapani [aut, cre],
Robert McCulloch [aut],
Matthew Pratola [ctb],
Hugh Chipman [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between nftbart versions 1.5 dated 2023-01-06 and 1.6 dated 2023-04-30
nftbart-1.5/nftbart/man/nft.Rd |only nftbart-1.5/nftbart/man/predict.nft.Rd |only nftbart-1.5/nftbart/man/tsvs.Rd |only nftbart-1.6/nftbart/DESCRIPTION | 10 +-- nftbart-1.6/nftbart/MD5 | 42 +++++++--------- nftbart-1.6/nftbart/NAMESPACE | 2 nftbart-1.6/nftbart/NEWS | 11 ++++ nftbart-1.6/nftbart/R/Cindex.R | 2 nftbart-1.6/nftbart/R/concordance.R |only nftbart-1.6/nftbart/R/nft.R | 6 +- nftbart-1.6/nftbart/R/nft2.R | 54 ++++++++++++--------- nftbart-1.6/nftbart/configure | 43 +++++----------- nftbart-1.6/nftbart/configure.ac | 18 +------ nftbart-1.6/nftbart/demo/lung.R | 12 ++++ nftbart-1.6/nftbart/man/Cindex.Rd | 18 +++++-- nftbart-1.6/nftbart/man/nft2.Rd | 65 +++++++++++++++++++------ nftbart-1.6/nftbart/man/predict.nft2.Rd | 42 +++++++++++++--- nftbart-1.6/nftbart/man/tsvs2.Rd | 58 +++++++++++++++++++--- nftbart-1.6/nftbart/src/DPMLIOneal8.h | 25 +++++---- nftbart-1.6/nftbart/src/Makevars.in | 6 +- nftbart-1.6/nftbart/src/Makevars.win | 3 - nftbart-1.6/nftbart/src/brt.h | 4 - nftbart-1.6/nftbart/src/cnft2.h | 82 +++++++++++++++++++++----------- nftbart-1.6/nftbart/src/init.c | 4 - 24 files changed, 328 insertions(+), 179 deletions(-)
Title: Query Data from the 'EIA' API
Description: Provides a function to query and extract data from the 'US Energy Information Administration' ('EIA') API V2 <https://www.eia.gov/opendata/>. The 'EIA' API provides a variety of information, in a time series format, about the energy sector in the US. The API is open, free, and requires an access key and registration at <https://www.eia.gov/opendata/>.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between EIAapi versions 0.1.0 dated 2023-04-12 and 0.1.1 dated 2023-04-30
DESCRIPTION | 9 +++++---- MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS.md | 8 +++++++- R/metadata.R |only R/query.R | 22 ++++++++++++---------- README.md | 45 ++++++++++++++++++++++++++++++++++----------- man/eia_get.Rd | 7 ++++--- man/eia_metadata.Rd |only 9 files changed, 71 insertions(+), 35 deletions(-)
Title: Crops an Image to a Circle
Description: Images are cropped to a circle with a transparent background. The function takes a
vector of images, either local or from a link, and circle crops the image. Paths to the
cropped image are returned for plotting with 'ggplot2'.
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between cropcircles versions 0.2.2.1 dated 2023-04-27 and 0.2.3 dated 2023-04-30
cropcircles-0.2.2.1/cropcircles/man/circle_crop.Rd |only cropcircles-0.2.2.1/cropcircles/man/heart_crop.Rd |only cropcircles-0.2.2.1/cropcircles/man/hex_crop.Rd |only cropcircles-0.2.2.1/cropcircles/man/square_crop.Rd |only cropcircles-0.2.3/cropcircles/DESCRIPTION | 6 - cropcircles-0.2.3/cropcircles/MD5 | 11 -- cropcircles-0.2.3/cropcircles/NEWS.md | 6 + cropcircles-0.2.3/cropcircles/R/crop.R | 108 +++------------------ cropcircles-0.2.3/cropcircles/man/crop.Rd |only 9 files changed, 30 insertions(+), 101 deletions(-)
Title: Solve ODE for GUTS-RED-SD and GUTS-RED-IT Using Compiled Code
Description: Allows performing forwards prediction for the General Unified
Threshold model of Survival using compiled ode code. This package
was created to avoid dependency with the 'morse' package that requires
the installation of 'JAGS'. This package is based on functions from
the 'morse' package v3.3.1: Virgile Baudrot, Sandrine Charles,
Marie Laure Delignette-Muller, Wandrille Duchemin, Benoit Goussen,
Nils Kehrein, Guillaume Kon-Kam-King, Christelle Lopes, Philippe Ruiz,
Alexander Singer and Philippe Veber (2021) <https://CRAN.R-project.org/package=morse>.
Author: Benoit Goussen [aut, cre]
Maintainer: Benoit Goussen <benoit.goussen@ibacon.com>
Diff between odeGUTS versions 1.0.1 dated 2021-09-10 and 1.0.2 dated 2023-04-30
DESCRIPTION | 6 MD5 | 32 NAMESPACE | 32 NEWS.md | 3 R/importFromMorse.R | 1608 ++++++++++++++++++++++++------------------------- R/odeGUTS-Internal.R | 12 R/odeGUTS-package.R | 58 - R/onUnload.R | 2 R/utils-pipe.R | 28 man/fit_odeGUTS.Rd | 40 - man/odeGUTS-package.Rd | 74 +- man/pipe.Rd | 40 - man/predict.Rd | 224 +++--- man/predict_check.Rd | 102 +-- src/gutsRedIT.c | 4 src/gutsRedSD.c | 4 src/odeGUTS_init.c | 4 17 files changed, 1138 insertions(+), 1135 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
Description: Performs power and sample size calculation for non-proportional
hazards model using the Fleming-Harrington family of weighted log-rank
tests. The sequentially calculated log-rank test score statistics are
assumed to have independent increments as characterized in
Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean
and variance of log-rank test score statistics are calculated based on
Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities
are calculated using the recursive integration algorithm described in
Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168).
Author: Kaifeng Lu
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.1.11 dated 2023-02-09 and 0.1.12 dated 2023-04-30
DESCRIPTION | 8 MD5 | 22 - inst/doc/direct_approximation_vs_schoenfeld.html | 30 - inst/doc/fixed_follow-up.html | 66 ++-- inst/doc/group_sequential_multiplicity.html | 347 +++++++++++------------ inst/doc/group_sequential_simulation.html | 76 ++--- inst/doc/maxcombo.html | 116 +++---- inst/doc/non-proportional_hazards.html | 46 +-- inst/doc/stratified.html | 68 ++-- src/fseqbon.cpp | 63 ++-- src/lrstat.cpp | 143 +++++---- src/utilities.cpp | 13 12 files changed, 522 insertions(+), 476 deletions(-)
Title: Tools for Calculating Hypocycloids, Epicycloids, Hypotrochoids,
and Epitrochoids
Description: Tools for calculating coordinate representations of
hypocycloids, epicyloids, hypotrochoids, and epitrochoids
(altogether called 'cycloids' here) with different scaling
and positioning options. The cycloids can be visualised with
any appropriate graphics function in R.
Author: Peter Biber
Maintainer: Peter Biber <castor.fiber@gmx.de>
Diff between cycloids versions 1.0 dated 2013-11-29 and 1.0.1 dated 2023-04-30
cycloids-1.0.1/cycloids/DESCRIPTION | 12 +++++++----- cycloids-1.0.1/cycloids/MD5 | 6 +++--- cycloids-1.0.1/cycloids/NEWS.md |only cycloids-1.0.1/cycloids/R/ZFunktionen.r | 22 +++++++++++----------- cycloids-1.0/cycloids/man/figures/Thumbs.db |only 5 files changed, 21 insertions(+), 19 deletions(-)
Title: Bayesian Monotonic Regression Using a Marked Point Process
Construction
Description: An extended version of the nonparametric Bayesian monotonic regression procedure described in Saarela & Arjas (2011) <DOI:10.1111/j.1467-9469.2010.00716.x>, allowing for multiple additive monotonic components in the linear predictor, and time-to-event outcomes through case-base sampling. The extension and its applications, including estimation of absolute risks, are described in Saarela & Arjas (2015) <DOI:10.1111/sjos.12125>. The package also implements the nonparametric ordinal regression model described in Saarela, Rohrbeck & Arjas <DOI:10.1214/22-BA1310>.
Author: Olli Saarela, Christian Rohrbeck
Maintainer: Olli Saarela <olli.saarela@utoronto.ca>
Diff between monoreg versions 2.0 dated 2022-02-11 and 2.1 dated 2023-04-30
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/ordmonoreg.Rd | 7 ++++--- src/ordsampler.c | 16 ++++++++-------- src/sampler.c | 8 ++++---- 5 files changed, 25 insertions(+), 24 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-15 0.2.1
2018-07-01 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-27 1.1
2017-07-28 1.0
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, forthcoming).
Implements Seeded LDA (Lu et. al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> algorithms based on the GibbsLDA++ library.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 0.8.4 dated 2023-03-23 and 0.9.0 dated 2023-04-30
seededlda-0.8.4/seededlda/man/predict.textmodel_lda.Rd |only seededlda-0.9.0/seededlda/DESCRIPTION | 12 seededlda-0.9.0/seededlda/MD5 | 54 - seededlda-0.9.0/seededlda/NAMESPACE | 46 seededlda-0.9.0/seededlda/NEWS.md | 91 - seededlda-0.9.0/seededlda/R/RcppExports.R | 14 seededlda-0.9.0/seededlda/R/data.R | 22 seededlda-0.9.0/seededlda/R/lda.R | 224 ++-- seededlda-0.9.0/seededlda/R/predict.R | 40 seededlda-0.9.0/seededlda/R/seededlda.R | 460 ++++----- seededlda-0.9.0/seededlda/R/seqlda.R |only seededlda-0.9.0/seededlda/R/utils.R | 138 +- seededlda-0.9.0/seededlda/man/data_corpus_moviereviews.Rd | 30 seededlda-0.9.0/seededlda/man/divergence.Rd | 78 - seededlda-0.9.0/seededlda/man/print.textmodel_lda.Rd | 34 seededlda-0.9.0/seededlda/man/sizes.Rd | 28 seededlda-0.9.0/seededlda/man/terms.Rd | 39 seededlda-0.9.0/seededlda/man/textmodel_lda.Rd |only seededlda-0.9.0/seededlda/man/textmodel_seededlda.Rd | 233 +--- seededlda-0.9.0/seededlda/man/textmodel_seqlda.Rd |only seededlda-0.9.0/seededlda/man/topics.Rd | 48 seededlda-0.9.0/seededlda/src/RcppExports.cpp | 10 seededlda-0.9.0/seededlda/src/lda.cpp | 29 seededlda-0.9.0/seededlda/src/lda.h | 84 + seededlda-0.9.0/seededlda/tests/data/topics.yml | 10 seededlda-0.9.0/seededlda/tests/testthat.R | 6 seededlda-0.9.0/seededlda/tests/testthat/test-internal.R | 228 ++-- seededlda-0.9.0/seededlda/tests/testthat/test-textmodel_lda.R | 507 +++++----- seededlda-0.9.0/seededlda/tests/testthat/test-textmodel_seededlda.R | 369 +++---- seededlda-0.9.0/seededlda/tests/testthat/test-utils.R | 160 +-- 30 files changed, 1592 insertions(+), 1402 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (Panse C. (2018) <doi:10.18637/jss.v086.c01>).
This algorithm draws maps according to a given statistical value
(e.g., election results, population or epidemiological data).
The basic idea of the RecMap algorithm is that each map region
(e.g., different countries) is represented by a rectangle.
The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about the usage
of the recmap algorithm is provided by a vignette included in this package.
Author: Christian Panse [aut, cre]
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 1.0.14 dated 2023-04-23 and 1.0.15 dated 2023-04-30
recmap-1.0.14/recmap/README.md |only recmap-1.0.15/recmap/DESCRIPTION | 6 +++--- recmap-1.0.15/recmap/MD5 | 13 ++++++------- recmap-1.0.15/recmap/R/recmap.R | 1 - recmap-1.0.15/recmap/data/jss2711.RData |binary recmap-1.0.15/recmap/inst/doc/recmap.html | 30 +++++++++++++++--------------- recmap-1.0.15/recmap/man/recmapGA.Rd | 3 +++ recmap-1.0.15/recmap/tests/testthat.R | 2 ++ 8 files changed, 29 insertions(+), 26 deletions(-)
Title: Semi-Parametric Dimension Reduction Models Using Orthogonality
Constrained Optimization
Description: Utilize an orthogonality constrained optimization algorithm of
Wen & Yin (2013) <DOI:10.1007/s10107-012-0584-1> to solve a variety of
dimension reduction problems in the semiparametric framework, such as
Ma & Zhu (2012) <DOI:10.1080/01621459.2011.646925>, Ma & Zhu (2013)
<DOI:10.1214/12-AOS1072>, Sun, Zhu, Wang & Zeng (2019) <DOI:10.1093/biomet/asy064>
and Zhou, Zhu & Zeng (2021) <DOI:10.1093/biomet/asaa087>. The package also
implements some existing dimension reduction methods such as hMave by Xia, Zhang,
& Xu (2010) <DOI:10.1198/jasa.2009.tm09372> and partial SAVE by Feng, Wen & Zhu (2013)
<DOI:10.1080/01621459.2012.746065>. It also serves as a general purpose
optimization solver for problems with orthogonality constraints, i.e., in Stiefel
manifold. Parallel computing for approximating the gradient is enabled through 'OpenMP'.
Author: Ruilin Zhao [aut, cph],
Ruoqing Zhu [aut, cre, cph] ,
Jiyang Zhang [aut, cph],
Wenzhuo Zhou [aut, cph],
Peng Xu [aut, cph],
James Joseph Balamuta [ctb]
Maintainer: Ruoqing Zhu <teazrq@gmail.com>
Diff between orthoDr versions 0.6.5 dated 2022-07-19 and 0.6.7 dated 2023-04-30
DESCRIPTION | 62 +++++++++--------- MD5 | 18 ++--- R/orthoDr_pdose.r | 7 -- README.md | 19 +++++ build/partial.rdb |binary inst/CITATION | 168 +++++++++++++------------------------------------ man/orthoDr-package.Rd | 2 man/orthoDr_pdose.Rd | 7 -- src/Makevars | 2 src/Makevars.win | 2 10 files changed, 113 insertions(+), 174 deletions(-)
Title: R Bindings for the 'prql-compiler' Rust Library
Description: Provides a function to convert 'PRQL' strings to 'SQL' strings.
Combined with other R functions that take 'SQL' as an argument,
'PRQL' can be used on R.
Author: Tatsuya Shima [aut, cre]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>
Diff between prqlr versions 0.3.0 dated 2023-03-16 and 0.4.0 dated 2023-04-30
DESCRIPTION | 10 +- LICENSE.note | 35 +++++++++ MD5 | 42 ++++++----- NEWS.md | 21 +++++ R/knitr-engine.R | 27 ++++--- README.md | 10 +- inst/doc/knitr.R | 29 ++++++++ inst/doc/knitr.Rmd | 45 ++++++++++++ inst/doc/knitr.html | 50 ++++++++++++- inst/doc/prqlr.R | 4 - inst/doc/prqlr.Rmd | 29 ++++---- inst/doc/prqlr.html | 14 +-- src/rust/Cargo.lock | 122 ++++++++++++++++++++++++---------- src/rust/Cargo.toml | 8 +- src/rust/src/lib.rs | 1 tests/testthat/_snaps/compile.md | 30 ++++---- tests/testthat/_snaps/knitr-engine.md | 61 ++++++++++++++++- tests/testthat/files/eval-opt.Rmd |only tests/testthat/files/info-string.Rmd |only tests/testthat/test-compile.R | 2 tests/testthat/test-knitr-engine.R | 8 +- vignettes/knitr.Rmd | 45 ++++++++++++ vignettes/prqlr.Rmd | 29 ++++---- 23 files changed, 482 insertions(+), 140 deletions(-)
Title: Inference in Graphical Gaussian Models with Edge and Vertex
Symmetries
Description: Estimation, model selection and other aspects of
statistical inference in Graphical Gaussian models with edge and
vertex symmetries (Graphical Gaussian models with colours).
Documentation about 'gRc' is provided in the paper by Hojsgaard and
Lauritzen (2007, <doi:10.18637/jss.v023.i06>) and the paper by
Hojsgaard and Lauritzen (2008, <doi:10.1111/j.1467-9868.2008.00666.x>).
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>, Steffen L. Lauritzen <lauritzen@math.ku.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between gRc versions 0.4.4 dated 2021-04-03 and 0.4.5 dated 2023-04-30
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ R/fit-rcox-scoring.R | 2 +- R/set-op.R | 2 +- R/xxx2yyy.R | 2 +- inst/CITATION | 12 ++++++------ man/add1-drop1.Rd | 21 +++++++++------------ man/coerce-parm.Rd | 2 +- man/comparecc.Rd | 24 ++++++++++++------------ man/fit-doc.Rd | 4 ++-- man/fit-main.Rd | 12 ++++++------ man/generating-class.Rd | 4 ++-- man/join-split.Rd | 10 +++++----- man/rcox.Rd | 31 +++++++++++++++++-------------- man/set-op.Rd | 2 +- man/step.Rd | 4 ++-- man/update-doc.Rd | 14 +++++++------- src/RcppExports.cpp | 5 +++++ src/init.c | 2 +- 19 files changed, 101 insertions(+), 96 deletions(-)
Title: Handles Missing Dates and Data and Converts into Weekly and
Monthly from Daily
Description: Many times, you will not find data for all dates. After first January, 2011 you may have next data on 20th January, 2011 and so on. Also available dates may have zero values. Try to gather all such kinds of data in different excel sheets of a single excel file. Every sheet will contain two columns (1st one is dates and second one is the data). After loading all the sheets into different elements of a list, using this you can fill the gaps for all the sheets and mark all the corresponding values as zeros. Here I am talking about daily data. Finally, it will combine all the filled results into one data frame (first column is date and other columns will be corresponding values of your sheets) and give one combined data frame. Number of columns in the data frame will be number of sheets plus one. Then imputation will be done. Daily to monthly and weekly conversion is also possible. More details can be found in Garai and others (2023) <doi:10.13140/RG.2.2.11977.42087>.
Author: Mr. Sandip Garai [aut, cre]
Maintainer: Mr. Sandip Garai <sandipnicksandy@gmail.com>
Diff between MissingHandle versions 0.1.0 dated 2023-04-21 and 0.1.1 dated 2023-04-30
DESCRIPTION | 12 +- MD5 | 13 +- NAMESPACE | 1 R/missing_handle.R | 219 +++++++++++++++++++++++++++++++++++++++++++--- man/clean_and_combine.Rd | 27 +++++ man/impute_combined.Rd | 4 man/monthly_from_daily.Rd |only man/weekly_from_daily.Rd | 4 8 files changed, 246 insertions(+), 34 deletions(-)