Title: Times and Dates from S-PLUS
Description: A collection of classes and methods for working with
times and dates. The code was originally available in S-PLUS.
Author: Stephen Kaluzny [aut, cre],
TIBCO Software Inc. [aut, cph]
Maintainer: Stephen Kaluzny <spkaluzny@gmail.com>
Diff between splusTimeDate versions 2.5.0-142 dated 2019-04-19 and 2.5.2 dated 2021-04-27
DESCRIPTION | 25 ++++++++++++++++--------- LICENSE | 2 ++ MD5 | 10 +++++----- NAMESPACE | 4 +++- R/align.R | 2 ++ man/class.time.zone.Rd | 5 +++-- 6 files changed, 31 insertions(+), 17 deletions(-)
Title: Multiple Pairwise Comparison Tests
Description: Multiple pairwise comparison tests on tidy data for
one-way analysis of variance for both between-subjects and
within-subjects designs. Currently, it supports only the most common
types of statistical analyses and tests: parametric (Welch's and
Student's t-test), nonparametric (Durbin-Conover and Dunn test),
robust (Yuen’s trimmed means test), and Bayes Factor (Student's
t-test).
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between pairwiseComparisons versions 3.1.3 dated 2021-02-03 and 3.1.5 dated 2021-04-27
pairwiseComparisons-3.1.3/pairwiseComparisons/build |only pairwiseComparisons-3.1.3/pairwiseComparisons/data/iris_long.rdata |only pairwiseComparisons-3.1.3/pairwiseComparisons/man/iris_long.Rd |only pairwiseComparisons-3.1.3/pairwiseComparisons/tests/README.md |only pairwiseComparisons-3.1.5/pairwiseComparisons/DESCRIPTION | 12 pairwiseComparisons-3.1.5/pairwiseComparisons/LICENSE | 4 pairwiseComparisons-3.1.5/pairwiseComparisons/MD5 | 58 pairwiseComparisons-3.1.5/pairwiseComparisons/NAMESPACE | 101 pairwiseComparisons-3.1.5/pairwiseComparisons/NEWS.md | 250 +- pairwiseComparisons-3.1.5/pairwiseComparisons/R/data.R | 226 - pairwiseComparisons-3.1.5/pairwiseComparisons/R/global_vars.R | 36 pairwiseComparisons-3.1.5/pairwiseComparisons/R/helpers.R | 252 +- pairwiseComparisons-3.1.5/pairwiseComparisons/R/pairwise_comparisons.R | 684 ++---- pairwiseComparisons-3.1.5/pairwiseComparisons/R/reexports.R | 49 pairwiseComparisons-3.1.5/pairwiseComparisons/README.md | 1140 +++++----- pairwiseComparisons-3.1.5/pairwiseComparisons/inst/CITATION | 10 pairwiseComparisons-3.1.5/pairwiseComparisons/inst/WORDLIST | 93 pairwiseComparisons-3.1.5/pairwiseComparisons/man/figures/README-ggsignif-1.png |binary pairwiseComparisons-3.1.5/pairwiseComparisons/man/figures/README-ggsignif2-1.png |binary pairwiseComparisons-3.1.5/pairwiseComparisons/man/movies_long.Rd | 92 pairwiseComparisons-3.1.5/pairwiseComparisons/man/movies_wide.Rd | 96 pairwiseComparisons-3.1.5/pairwiseComparisons/man/p_adjust_text.Rd | 2 pairwiseComparisons-3.1.5/pairwiseComparisons/man/pairwise_caption.Rd | 2 pairwiseComparisons-3.1.5/pairwiseComparisons/man/pairwise_comparisons.Rd | 418 +-- pairwiseComparisons-3.1.5/pairwiseComparisons/man/reexports.Rd | 3 pairwiseComparisons-3.1.5/pairwiseComparisons/tests/spelling.R | 12 pairwiseComparisons-3.1.5/pairwiseComparisons/tests/testthat.R | 8 pairwiseComparisons-3.1.5/pairwiseComparisons/tests/testthat/_snaps |only pairwiseComparisons-3.1.5/pairwiseComparisons/tests/testthat/test-additional_args.R |only pairwiseComparisons-3.1.5/pairwiseComparisons/tests/testthat/test-pairwise_caption_helpers.R | 118 - pairwiseComparisons-3.1.5/pairwiseComparisons/tests/testthat/test-pairwise_comparisons_between.R | 771 ++---- pairwiseComparisons-3.1.5/pairwiseComparisons/tests/testthat/test-pairwise_comparisons_within.R | 614 ++--- 32 files changed, 2366 insertions(+), 2685 deletions(-)
More information about pairwiseComparisons at CRAN
Permanent link
Title: A High-Performance Local Taxonomic Database Interface
Description: Creates a local database of many commonly used taxonomic authorities
and provides functions that can quickly query this data.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Kari Norman [aut] (<https://orcid.org/0000-0002-2029-2325>),
Jorrit Poelen [aut] (<https://orcid.org/0000-0003-3138-4118>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between taxadb versions 0.1.2 dated 2021-03-15 and 0.1.3 dated 2021-04-27
DESCRIPTION | 7 +++---- MD5 | 16 ++++++++-------- inst/doc/backends.Rmd | 2 +- inst/doc/backends.html | 6 +++--- inst/doc/data-sources.html | 4 ++-- tests/testthat/test-filter_by.R | 2 +- tests/testthat/test-fuzzy_filter.R | 12 ++++++------ tests/testthat/test-get_ids.R | 6 +++--- vignettes/backends.Rmd | 2 +- 9 files changed, 28 insertions(+), 29 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see:
(i)"Stochastic model for analysis of longitudinal data on aging and mortality"
by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(ii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Zhbannikov, Liang He, K. Arbeev, I. Akushevich, A. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.7.9 dated 2020-11-28 and 1.7.10 dated 2021-04-27
DESCRIPTION | 10 MD5 | 32 R/spm_continuous.R | 7 R/spm_continuous_linear.R | 7 R/spm_continuous_quadratic_linear.R | 9 R/spm_pobs.R | 6 R/spm_projection.R | 1 R/spm_time-dependent.R | 12 build/vignette.rds |binary inst/NEWS | 4 inst/doc/stpm-vignette.html | 1544 ++++++++++++++++++------------------ man/spm_cont_lin.Rd | 1 man/spm_cont_quad_lin.Rd | 1 man/spm_continuous.Rd | 1 man/spm_projection.Rd | 1 man/spm_time_dep.Rd | 1 src/Makevars | 2 17 files changed, 838 insertions(+), 801 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. 'neonstore' can also
construct a local 'duckdb' database of stacked tables, making it possible
to work with tables that are far to big to fit into memory.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Quinn Thomas [aut] (<https://orcid.org/0000-0003-1282-7825>),
Christine Laney [aut] (<https://orcid.org/0000-0002-4944-2083>),
Claire Lunch [aut] (<https://orcid.org/0000-0001-8753-6593>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between neonstore versions 0.4.2 dated 2021-04-08 and 0.4.3 dated 2021-04-27
neonstore-0.4.2/neonstore/inst/examples/efi_download.R |only neonstore-0.4.2/neonstore/tests/testthat/test-releases.R |only neonstore-0.4.3/neonstore/DESCRIPTION | 6 ++-- neonstore-0.4.3/neonstore/MD5 | 12 +++------ neonstore-0.4.3/neonstore/NEWS.md | 5 +++ neonstore-0.4.3/neonstore/R/neon_filename_parser.R | 20 +++++++++++---- neonstore-0.4.3/neonstore/R/neon_index.R | 7 +++-- neonstore-0.4.3/neonstore/inst/examples/thelio_mirror.R | 19 ++++++++++++-- 8 files changed, 49 insertions(+), 20 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
Hash Archive) or depositing data in a scientific repository such 'Zenodo',
'DataONE' or 'SoftwareHeritage', 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 0.0.9 dated 2021-01-15 and 0.0.10 dated 2021-04-27
contentid-0.0.10/contentid/DESCRIPTION | 12 contentid-0.0.10/contentid/MD5 | 59 ++-- contentid-0.0.10/contentid/NEWS.md | 4 contentid-0.0.10/contentid/R/bagit.R | 2 contentid-0.0.10/contentid/R/content_id.R | 30 +- contentid-0.0.10/contentid/R/dataone_registry.R |only contentid-0.0.10/contentid/R/default_registries.R |only contentid-0.0.10/contentid/R/hash-archive.R | 16 + contentid-0.0.10/contentid/R/local_registry.R | 32 +- contentid-0.0.10/contentid/R/pin.R | 16 - contentid-0.0.10/contentid/R/query_history.R | 58 ++-- contentid-0.0.10/contentid/R/query_sources.R | 137 +++++----- contentid-0.0.10/contentid/R/register.R | 45 --- contentid-0.0.10/contentid/R/resolve.R | 10 contentid-0.0.10/contentid/R/retrieve.R | 11 contentid-0.0.10/contentid/R/software-heritage.R | 6 contentid-0.0.10/contentid/R/store.R | 42 ++- contentid-0.0.10/contentid/R/utils.R | 6 contentid-0.0.10/contentid/R/zenodo_registry.R |only contentid-0.0.10/contentid/README.md | 8 contentid-0.0.10/contentid/inst/doc/intro.Rmd | 6 contentid-0.0.10/contentid/inst/doc/intro.html | 15 - contentid-0.0.10/contentid/man/pin.Rd | 9 contentid-0.0.10/contentid/man/query_history.Rd | 11 contentid-0.0.10/contentid/man/resolve.Rd | 2 contentid-0.0.10/contentid/man/store.Rd | 5 contentid-0.0.10/contentid/tests/testthat/test-dataone.R |only contentid-0.0.10/contentid/tests/testthat/test-pin.R | 18 - contentid-0.0.10/contentid/tests/testthat/test-register-query.R | 2 contentid-0.0.10/contentid/tests/testthat/test-remote_api.R | 15 - contentid-0.0.10/contentid/vignettes/intro.Rmd | 6 contentid-0.0.10/contentid/vignettes/intro.Rmd-source | 4 contentid-0.0.9/contentid/inst/examples/dataone_registry.R |only 33 files changed, 355 insertions(+), 232 deletions(-)
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),
Hua Zhou [aut, ctb] (<https://orcid.org/0000-0003-1822-1306>),
Nicole Doudican [aut, ctb] (<https://orcid.org/0000-0003-3827-9644>),
John Carucci [aut, ctb] (<https://orcid.org/0000-0001-6817-9439>),
Adriana Heguy [aut, ctb],
Boris Reizis [aut, ctb] (<https://orcid.org/0000-0003-1140-7853>),
Aristotelis Tsirigos [aut, ctb]
(<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.6.1 dated 2021-03-04 and 1.6.4 dated 2021-04-27
DESCRIPTION | 6 +++--- MD5 | 44 +++++++++++++++++++++++--------------------- NAMESPACE | 1 + R/F00100.R | 8 ++++++-- R/F0021.R | 27 ++++++++++++++++++++------- R/F0022.R | 36 +++++++++++++++++++++++++++++------- R/F0028.R | 18 ++++++++++++++---- R/F0030.R | 8 +++++++- R/F0031.R | 8 +++++++- R/F0044.R | 1 + R/F0057.R | 2 +- R/F0058.R | 16 +++++++++++++++- R/F0070.R | 26 +++++++++++++++----------- R/F0072.R |only R/F008.R | 43 +++++++++++++++++++++++++++++++++++++++---- man/clust.avg.exp.Rd | 14 ++++++++++++-- man/findMarkers.Rd | 2 +- man/gene.plot.Rd | 2 +- man/heatmap.gg.plot.Rd | 2 +- man/hto.anno.Rd | 2 +- man/make.bed.Rd |only man/norm.data.Rd | 14 +++++++++++++- man/run.impute.Rd | 9 +++++++++ man/spatial.plot.Rd | 2 +- 24 files changed, 220 insertions(+), 71 deletions(-)
Title: Smooth Additive Quantile Regression Models
Description: Smooth additive quantile regression models, fitted using
the methods of Fasiolo et al. (2017) <arXiv:1707.03307>. Differently from
'quantreg', the smoothing parameters are estimated automatically by marginal
loss minimization, while the regression coefficients are estimated using either
PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian
credible intervals of the estimated effects have approximately the correct
coverage. The main function is qgam() which is similar to gam() in 'mgcv', but
fits non-parametric quantile regression models.
Author: Matteo Fasiolo [aut, cre],
Simon N. Wood [ctb],
Margaux Zaffran [ctb],
Yannig Goude [ctb],
Raphael Nedellec [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between qgam versions 1.3.2 dated 2020-02-03 and 1.3.3 dated 2021-04-27
DESCRIPTION | 12 ++-- MD5 | 57 ++++++++++---------- R/I_tuneLearnFullFits.R | 3 + R/check_learn.R | 6 +- R/check_learnFast.R | 6 +- R/check_qgam.R | 8 +- R/cqcheck.R | 4 - R/elf.R | 6 +- R/elflss.R | 93 ++++++++++++++++++++++---------- R/log1pexp.R | 5 + R/mqgam.R | 6 +- R/qgam.R | 6 +- R/tuneLearn.R | 8 ++ R/tuneLearnFast.R | 11 +++ README.md |only build/vignette.rds |binary inst/doc/qgam.R | 60 ++++++++++----------- inst/doc/qgam.Rmd | 2 inst/doc/qgam.html | 136 +++++++++++++++++++++--------------------------- man/UKload.Rd | 2 man/check.learn.Rd | 6 +- man/check.learnFast.Rd | 6 +- man/check.qgam.Rd | 6 +- man/elf.Rd | 6 +- man/elflss.Rd | 6 +- man/mqgam.Rd | 6 +- man/qgam.Rd | 6 +- man/tuneLearn.Rd | 6 +- man/tuneLearnFast.Rd | 6 +- vignettes/qgam.Rmd | 2 30 files changed, 278 insertions(+), 209 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included.
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis.
b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534.
c) Tsagris M. (2015). A novel, divergence based, regression for compositional data. Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444.
d) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Statistics, 6(2):47--57.
e) Tsagris M., Preston S. and Wood A.T.A. (2016). Improved supervised classification for compositional data using the alpha-transformation. Journal of Classification, 33(2):243--261. <doi:10.1007/s00357-016-9207-5>.
f) Tsagris M., Preston S. and Wood A.T.A. (2017). Nonparametric hypothesis testing for equality of means on the simplex. Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>.
g) Tsagris M. and Stewart C. (2018). A Dirichlet regression model for compositional data with zeros. Lobachevskii Journal of Mathematics,39(3): 398--412. <doi:10.1134/S1995080218030198>.
h) Alenazi A. (2019). Regression for compositional data with compositional data as predictor variables with or without zero values. Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>.
i) Tsagris M. and Stewart C. (2020). A folded model for compositional data analysis. Australian and New Zealand Journal of Statistics, 62(2):249--277. <doi:10.1111/anzs.12289>.
j) Tsagris M., Alenazi A. and Stewart C. (2020). The alpha-k-NN regression for compositional data. <arXiv:2002.05137>.
We further include functions for percentages (or proportions).
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 4.5 dated 2021-03-23 and 4.6 dated 2021-04-27
DESCRIPTION | 9 +++----- MD5 | 14 ++++++------ R/aknnreg.tune.R | 48 +++---------------------------------------- R/compppr.tune.R | 44 +++++++++------------------------------ R/lc.reg.R | 10 +++++--- man/Compositional-package.Rd | 4 +-- man/aknnreg.tune.Rd | 13 +---------- man/compppr.tune.Rd | 31 ++++++++------------------- 8 files changed, 46 insertions(+), 127 deletions(-)
Title: Uncertainty in Partial Credit Models
Description: Provides an extension to the Partial Credit Model and Generalized Partial Credit Models which allows for an additional person parameter that characterizes the uncertainty of the person. The method was originally proposed by Tutz and Schauberger (2020) <doi:10.1177/0146621620920932>.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between UPCM versions 0.0-2 dated 2021-04-26 and 0.0-3 dated 2021-04-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/UPCM-package.R | 8 -------- R/UPCM.R | 7 +++---- man/UPCM-package.Rd | 8 -------- man/UPCM.Rd | 7 +++---- 7 files changed, 17 insertions(+), 35 deletions(-)
Title: Analysis of Data with Measurement Error Using a Validation
Subsample
Description: Analyze data with measurement error when there is a validation subsample randomly selected from the full sample. The method assumes surrogate variables measured with error are available for the full sample, and reference variables measured with little or no error are available for this randomly selected subsample of the full sample. Measurement errors may be differential or non differential, in any or all predictors (simultaneously) as well as outcome. The "augmented" estimates derived are based upon the multivariate correlation between regression model parameter estimates for the reference variables and for the surrogate variables in the validation subset. Because the validation subsample is chosen at random whatever biases are imposed by measurement error, non-differential or differential, are reflected in this correlation and can be used to derive estimates for the reference variables using data from the whole sample. The main functions in the package are meerva.fit which calculates estimates for a dataset, and meerva.sim.block which simulates multiple datasets as described by the user, and analyzes these datasets, storing the regression coefficient estimates for inspection. This work derives from Chen Y-H, Chen H. (2000) <doi:10.1111/1467-9868.00243>, Chen Y-H. (2002) <doi:10.1111/1467-9868.00324>, Wang X, Wang Q (2015) <doi:10.1016/j.jmva.2015.05.017> and Tong J, Huang J, Chubak J, et al. (2020) <doi:10.1093/jamia/ocz180>.
Author: Walter K Kremers [aut, cre] (<https://orcid.org/0000-0001-5714-3473>)
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between meerva versions 0.1-1 dated 2021-04-19 and 0.1-2 dated 2021-04-27
meerva-0.1-1/meerva/R/meerva.sim.brn_210412.R |only meerva-0.1-1/meerva/R/meerva.sim.cox_210412.R |only meerva-0.1-1/meerva/R/meerva.sim.nrm_210412.R |only meerva-0.1-1/meerva/R/meerva.sim.tools_210414.R |only meerva-0.1-1/meerva/R/meerva_210412.R |only meerva-0.1-2/meerva/DESCRIPTION | 10 ++--- meerva-0.1-2/meerva/MD5 | 47 ++++++++++++------------ meerva-0.1-2/meerva/R/meerva.sim.brn_210424.R |only meerva-0.1-2/meerva/R/meerva.sim.cox_210424.R |only meerva-0.1-2/meerva/R/meerva.sim.nrm_210424.R |only meerva-0.1-2/meerva/R/meerva.sim.tools_210424.R |only meerva-0.1-2/meerva/R/meerva_210424.R |only meerva-0.1-2/meerva/man/compmse.Rd | 2 - meerva-0.1-2/meerva/man/coverage.Rd | 2 - meerva-0.1-2/meerva/man/coverage2.Rd | 2 - meerva-0.1-2/meerva/man/dfbetac.Rd | 2 - meerva-0.1-2/meerva/man/meerva.Rd | 4 +- meerva-0.1-2/meerva/man/meerva.fit.Rd | 9 +++- meerva-0.1-2/meerva/man/meerva.sim.block.Rd | 13 +++--- meerva-0.1-2/meerva/man/meerva.sim.brn.Rd | 2 - meerva-0.1-2/meerva/man/meerva.sim.cox.Rd | 2 - meerva-0.1-2/meerva/man/meerva.sim.nrm.Rd | 2 - meerva-0.1-2/meerva/man/myttest.Rd | 2 - meerva-0.1-2/meerva/man/plot.meerva.sim.Rd | 2 - meerva-0.1-2/meerva/man/print.meerva.Rd | 2 - meerva-0.1-2/meerva/man/reldif.Rd | 2 - meerva-0.1-2/meerva/man/subvec.Rd | 2 - meerva-0.1-2/meerva/man/summary.meerva.Rd | 2 - meerva-0.1-2/meerva/man/summary.meerva.sim.Rd | 8 ++-- meerva-0.1-2/meerva/man/ztest.Rd |only 30 files changed, 62 insertions(+), 55 deletions(-)
Title: Generate Concentration-Time Profiles from Linear PK Systems
Description: Generate concentration-time profiles from linear pharmacokinetic
(PK) systems, possibly with first-order absorption or zero-order infusion,
possibly with one or more peripheral compartments, and possibly under
steady-state conditions. Single or multiple doses may be specified. Secondary
(derived) PK parameters (e.g. Cmax, Ctrough, AUC, Tmax, half-life, etc.) are
computed.
Author: Benjamin Rich [aut, cre]
Maintainer: Benjamin Rich <mail@benjaminrich.net>
Diff between linpk versions 1.0 dated 2018-06-12 and 1.1.1 dated 2021-04-27
DESCRIPTION | 19 + MD5 | 26 +- NEWS.md | 10 R/linpk.R | 6 README.md | 9 build/vignette.rds |binary inst/doc/linpk-intro.Rmd | 13 - inst/doc/linpk-intro.html | 395 +++++++++++++------------------------- man/as.data.frame.pkprofile.Rd | 3 man/generateETA.Rd | 8 man/pkprofile.Rd | 34 ++- man/pkprofile.pkprofile.Rd | 3 vignettes/linpk-intro.Rmd | 13 - vignettes/vignette.css | 416 ++++++++++++++++++++--------------------- 14 files changed, 444 insertions(+), 511 deletions(-)
Title: Hidden Markov Models
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte <d.s.harte@gmail.com>
Diff between HiddenMarkov versions 1.8-11 dated 2017-11-01 and 1.8-13 dated 2021-04-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/partial.rdb |binary inst/doc/index.html | 22 +++++++++++----------- man/Changes.Rd | 2 ++ man/HiddenMarkov.Rd | 4 ++-- 6 files changed, 25 insertions(+), 23 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the clustering algorithms
DBSCAN (density-based spatial clustering of applications with noise)
and HDBSCAN (hierarchical DBSCAN), the ordering algorithm
OPTICS (ordering points to identify the clustering structure),
and the outlier detection algorithm LOF (local outlier factor).
The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search.
An R interface to fast kNN and fixed-radius NN search is also provided.
Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-7 dated 2021-04-22 and 1.1-8 dated 2021-04-27
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 5 R/LOF.R | 5 R/frNN.R | 2 build/partial.rdb |binary inst/doc/dbscan.pdf |binary src/R_kNN.cpp | 7 - src/R_lof.cpp | 29 ++-- src/R_regionQuery.cpp | 4 src/R_regionQuery.h | 8 - src/kd_fix_rad_search.cpp | 6 - tests/testthat/test-frNN.R | 3 tests/testthat/test-kNN.R | 2 tests/testthat/test-lof.R | 263 ++++++++++++++++++--------------------------- 15 files changed, 165 insertions(+), 205 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE), measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or
Stan's Hamiltonian Monte Carlo sampling. See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual
overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>.
Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> .
Stan based functions are not available on 32 bit Windows systems at present.
<https://cdriver.netlify.app/> contains some tutorial blog posts.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver@ibe.uzh.ch>
Diff between ctsem versions 3.4.2 dated 2021-02-24 and 3.4.3 dated 2021-04-27
ctsem-3.4.2/ctsem/man/ctStanParMatrices.Rd |only ctsem-3.4.3/ctsem/DESCRIPTION | 12 ctsem-3.4.3/ctsem/MD5 | 81 - ctsem-3.4.3/ctsem/NAMESPACE | 2 ctsem-3.4.3/ctsem/NEWS | 8 ctsem-3.4.3/ctsem/R/ctCheckFit.R | 7 ctsem-3.4.3/ctsem/R/ctDiscretePars.R | 10 ctsem-3.4.3/ctsem/R/ctFitMultiModel.R |only ctsem-3.4.3/ctsem/R/ctKalman.R | 52 - ctsem-3.4.3/ctsem/R/ctStanContinuousPars.R | 5 ctsem-3.4.3/ctsem/R/ctStanData.R | 28 ctsem-3.4.3/ctsem/R/ctStanFit.R | 13 ctsem-3.4.3/ctsem/R/ctStanModel.R | 2 ctsem-3.4.3/ctsem/R/ctStanModelWriter.R | 60 - ctsem-3.4.3/ctsem/R/ctStanParMatrices.R | 118 +- ctsem-3.4.3/ctsem/R/ctStanTIpredeffects.R | 86 - ctsem-3.4.3/ctsem/R/ctSummarise.R | 450 +++++----- ctsem-3.4.3/ctsem/R/ctsem.R | 2 ctsem-3.4.3/ctsem/R/extract.ctStanFit.R | 4 ctsem-3.4.3/ctsem/R/llsurface.R | 32 ctsem-3.4.3/ctsem/R/sdpcor2cov.R | 4 ctsem-3.4.3/ctsem/R/sgd.R | 103 -- ctsem-3.4.3/ctsem/R/stanoptimis.R | 173 ++- ctsem-3.4.3/ctsem/R/summary.ctStanFit.R | 6 ctsem-3.4.3/ctsem/build/vignette.rds |binary ctsem-3.4.3/ctsem/data/ctstantestdat.rda |binary ctsem-3.4.3/ctsem/data/ctstantestfit.rda |binary ctsem-3.4.3/ctsem/inst/doc/hierarchicalmanual.R | 25 ctsem-3.4.3/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.4.3/ctsem/inst/doc/hierarchicalmanual.rnw | 28 ctsem-3.4.3/ctsem/man/ctCheckFit.Rd | 2 ctsem-3.4.3/ctsem/man/ctFitMultiModel.Rd |only ctsem-3.4.3/ctsem/man/ctKalman.Rd | 2 ctsem-3.4.3/ctsem/man/ctStanDiscretePars.Rd | 2 ctsem-3.4.3/ctsem/man/ctStanTIpredeffects.Rd | 4 ctsem-3.4.3/ctsem/man/stanoptimis.Rd | 4 ctsem-3.4.3/ctsem/src/Makevars.win | 2 ctsem-3.4.3/ctsem/src/stan_files/ctsm.stan | 64 - ctsem-3.4.3/ctsem/src/stan_files/ctsmgen.stan | 64 - ctsem-3.4.3/ctsem/tests/testthat/test-ctRaschExampleTest.R | 4 ctsem-3.4.3/ctsem/tests/testthat/test-knownFits.R | 4 ctsem-3.4.3/ctsem/vignettes/hierarchicalmanual-concordance.tex | 6 ctsem-3.4.3/ctsem/vignettes/hierarchicalmanual.rnw | 28 43 files changed, 763 insertions(+), 734 deletions(-)
Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureGraph versions 1.2.2 dated 2021-04-06 and 1.3.0 dated 2021-04-27
DESCRIPTION | 6 - MD5 | 65 +++++++------ NAMESPACE | 3 NEWS.md | 15 +++ R/az_app.r | 16 ++- R/az_device.R | 2 R/az_dir_role.R | 13 ++ R/az_group.R | 37 +++++-- R/az_object.R | 32 ++++-- R/az_svc_principal.R | 2 R/az_user.R | 58 +++++++----- R/ms_graph.R | 144 ++++++++++++++++++++++++++---- R/ms_graph_pager.R |only R/ms_object.R | 65 ++++++++++--- R/zzz_class_directory.R | 13 ++ README.md | 8 + build/vignette.rds |binary inst/doc/batching_paging.Rmd |only inst/doc/batching_paging.html |only inst/doc/intro.Rmd | 34 +++++-- inst/doc/intro.html | 186 +++++++++++++++++++++------------------- man/az_app.Rd | 11 +- man/az_device.Rd | 2 man/az_directory_role.Rd | 8 + man/az_group.Rd | 24 +++-- man/az_object.Rd | 11 +- man/az_service_principal.Rd | 2 man/az_user.Rd | 26 ++++- man/extract_list_values.Rd |only man/find_class_generator.Rd |only man/ms_graph.Rd | 55 +++++++++-- man/ms_graph_pager.Rd |only man/ms_object.Rd | 61 +++++++++---- tests/testthat/test03_usergrp.R | 19 +++- tests/testthat/test05_pager.R |only tests/testthat/test06_filter.R |only vignettes/batching_paging.Rmd |only vignettes/intro.Rmd | 34 +++++-- 38 files changed, 668 insertions(+), 284 deletions(-)
Title: Multiple Imputation for Recurrent Events
Description: Performs reference based multiple imputation of recurrent event data
based on a negative binomial regression model, as described
by Keene et al (2014) <doi:10.1002/pst.1624>.
Author: Nikolas Burkoff [aut],
Paul Metcalfe [aut],
Jonathan Bartlett [aut, cre],
David Ruau [aut]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between dejaVu versions 0.2.1 dated 2021-01-13 and 0.3.0 dated 2021-04-27
DESCRIPTION | 7 +-- MD5 | 24 +++++------ NEWS.md | 2 R/copyRefImpute.r | 13 ++++-- R/specificImputeMechanisms.R | 12 +++-- build/vignette.rds |binary inst/doc/UserGuide.pdf |binary inst/doc/analysingExistingDatasets.Rnw | 2 inst/doc/analysingExistingDatasets.pdf |binary man/copy_reference.Rd | 8 +++ man/weighted_j2r.Rd | 7 ++- tests/testthat/test-CopyReference.R | 67 ++++++++++++++++++++++++++++++++ vignettes/analysingExistingDatasets.Rnw | 2 13 files changed, 117 insertions(+), 27 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.5.0 dated 2021-02-23 and 2.5.1 dated 2021-04-27
DESCRIPTION | 8 MD5 | 28 +-- R/BAT.R | 302 +++++++++++++++++++++--------------- man/dummy.Rd | 8 man/gdm.Rd | 2 man/kernel.alpha.Rd | 4 man/kernel.beta.Rd | 4 man/kernel.beta.evenness.Rd | 4 man/kernel.contribution.Rd | 28 ++- man/kernel.dispersion.Rd | 6 man/kernel.evenness.Rd | 4 man/kernel.evenness.contribution.Rd | 4 man/kernel.originality.Rd | 4 man/kernel.similarity.Rd | 2 man/rao.alpha.Rd | 13 - 15 files changed, 251 insertions(+), 170 deletions(-)
Title: Closed Testing Procedure (CTP)
Description: This is a package for constructing hypothesis trees for treatment comparisons based
on the closure principle and analysing the corresponding Closed Testing Procedures (CTP)
using adjusted p-values. For reference, see
Marcus, R., Peritz, E, and Gabriel, K.R. (1976) <doi:10.2307/2335748> and
Bauer, P (1991) <doi:10.1002/sim.4780100609>.
Author: Paul Jordan [aut, cre],
Matthias Herpers [aut]
Maintainer: Paul Jordan <paul.jordan@roche.com>
Diff between CTP versions 3.0 dated 2021-03-15 and 3.0.1 dated 2021-04-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/doc/Flowchart.html | 4 ++-- inst/doc/closed_testing_procedure.html | 4 ++-- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] (<https://orcid.org/0000-0003-0071-1745>),
Cory Merow [aut] (<https://orcid.org/0000-0003-0561-053X>),
Brian Maitner [aut] (<https://orcid.org/0000-0002-2118-9880>),
Jamie M. Kass [aut] (<https://orcid.org/0000-0002-9432-895X>),
Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>),
Robert P. Guralnick [aut] (<https://orcid.org/0000-0001-6682-1504>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.4.6 dated 2021-02-21 and 0.4.7 dated 2021-04-27
occCite-0.4.6/occCite/inst/doc/occCite_Vignette.R |only occCite-0.4.6/occCite/inst/doc/occCite_Vignette.Rmd |only occCite-0.4.6/occCite/inst/doc/occCite_Vignette.html |only occCite-0.4.6/occCite/man/GBIFtableCleanup.Rd |only occCite-0.4.6/occCite/man/gbifRetriever.Rd |only occCite-0.4.6/occCite/man/tabGBIF.Rd |only occCite-0.4.6/occCite/vignettes/occCite_Vignette.Rmd |only occCite-0.4.7/occCite/DESCRIPTION | 17 occCite-0.4.7/occCite/MD5 | 116 +- occCite-0.4.7/occCite/NAMESPACE | 2 occCite-0.4.7/occCite/NEWS.md | 7 occCite-0.4.7/occCite/R/GBIFLogin.R | 19 occCite-0.4.7/occCite/R/GBIFLoginManager.R | 69 - occCite-0.4.7/occCite/R/GBIFtableCleanup.R | 25 occCite-0.4.7/occCite/R/data.R | 2 occCite-0.4.7/occCite/R/gbifRetriever.R | 89 + occCite-0.4.7/occCite/R/getBIENpoints.R | 66 - occCite-0.4.7/occCite/R/getGBIFpoints.R | 96 +- occCite-0.4.7/occCite/R/occCitation.R | 194 ++-- occCite-0.4.7/occCite/R/occCiteCitation.R | 7 occCite-0.4.7/occCite/R/occCiteData.R | 16 occCite-0.4.7/occCite/R/occCitePrint.R | 208 ++-- occCite-0.4.7/occCite/R/occCite_plotting.R | 446 +++++----- occCite-0.4.7/occCite/R/occQuery.R | 187 ++-- occCite-0.4.7/occCite/R/occSum.R | 151 ++- occCite-0.4.7/occCite/R/prevGBIFdownload.R | 50 - occCite-0.4.7/occCite/R/studyTaxonList.R | 80 + occCite-0.4.7/occCite/R/tabGBIF.R | 33 occCite-0.4.7/occCite/R/taxonRectification.R | 63 - occCite-0.4.7/occCite/build/vignette.rds |binary occCite-0.4.7/occCite/inst/CITATION |only occCite-0.4.7/occCite/inst/doc/Advanced.R |only occCite-0.4.7/occCite/inst/doc/Advanced.Rmd |only occCite-0.4.7/occCite/inst/doc/Advanced.html |only occCite-0.4.7/occCite/inst/doc/Simple.R |only occCite-0.4.7/occCite/inst/doc/Simple.Rmd |only occCite-0.4.7/occCite/inst/doc/Simple.html |only occCite-0.4.7/occCite/man/GBIFLogin-class.Rd | 8 occCite-0.4.7/occCite/man/GBIFLoginManager.Rd | 16 occCite-0.4.7/occCite/man/getBIENpoints.Rd | 4 occCite-0.4.7/occCite/man/getGBIFpoints.Rd | 10 occCite-0.4.7/occCite/man/myOccCiteObject.Rd | 24 occCite-0.4.7/occCite/man/occCiteMap.Rd | 15 occCite-0.4.7/occCite/man/occQuery.Rd | 46 - occCite-0.4.7/occCite/man/plot.occCiteData.Rd | 11 occCite-0.4.7/occCite/man/prevGBIFdownload.Rd | 19 occCite-0.4.7/occCite/man/print.occCiteCitation.Rd | 1 occCite-0.4.7/occCite/man/studyTaxonList.Rd | 27 occCite-0.4.7/occCite/man/summary.occCiteData.Rd | 1 occCite-0.4.7/occCite/man/tabulate.occResults.Rd | 12 occCite-0.4.7/occCite/man/taxonRectification.Rd | 9 occCite-0.4.7/occCite/tests/testthat/test-GBIFLoginManager.R | 27 occCite-0.4.7/occCite/tests/testthat/test-GBIFtableCleanup.R | 70 - occCite-0.4.7/occCite/tests/testthat/test-gbifRetriever.R | 26 occCite-0.4.7/occCite/tests/testthat/test-getBIENpoints.R | 12 occCite-0.4.7/occCite/tests/testthat/test-getGBIFpoints.R | 133 +- occCite-0.4.7/occCite/tests/testthat/test-map.R | 44 occCite-0.4.7/occCite/tests/testthat/test-occCitation.R | 86 + occCite-0.4.7/occCite/tests/testthat/test-occSum.R | 16 occCite-0.4.7/occCite/tests/testthat/test-prevGBIFdownload.R | 70 - occCite-0.4.7/occCite/tests/testthat/test-studyTaxonList.R | 14 occCite-0.4.7/occCite/tests/testthat/test-sumFig.R | 32 occCite-0.4.7/occCite/tests/testthat/test-tabGBIF.R | 99 +- occCite-0.4.7/occCite/tests/testthat/test-tabulate.R | 12 occCite-0.4.7/occCite/tests/testthat/test-taxonRectification.R | 8 occCite-0.4.7/occCite/vignettes/Advanced.Rmd |only occCite-0.4.7/occCite/vignettes/Simple.Rmd |only 67 files changed, 1654 insertions(+), 1141 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut, ths] (<https://orcid.org/0000-0002-1444-1830>),
David Dorchies [aut] (<https://orcid.org/0000-0002-6595-7984>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb] (<https://orcid.org/0000-0002-4142-4454>),
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>),
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.6.10.4 dated 2021-01-29 and 1.6.12 dated 2021-04-27
DESCRIPTION | 19 MD5 | 117 ++--- NAMESPACE | 1 NEWS.md | 48 +- R/Calibration.R | 19 R/Calibration_Michel.R | 9 R/CreateCalibOptions.R | 16 R/CreateInputsModel.R | 109 +---- R/CreateRunOptions.R | 169 ++----- R/PE_Oudin.R | 2 R/RunModel.R | 21 R/RunModel_CemaNeige.R | 37 - R/RunModel_CemaNeigeGR4H.R | 91 ++-- R/RunModel_CemaNeigeGR4J.R | 38 - R/RunModel_CemaNeigeGR5H.R | 100 ++-- R/RunModel_CemaNeigeGR5J.R | 33 - R/RunModel_CemaNeigeGR6J.R | 91 ++-- R/RunModel_GR1A.R | 53 +- R/RunModel_GR2M.R | 90 ++-- R/RunModel_GR4H.R | 95 ++-- R/RunModel_GR4J.R | 84 +-- R/RunModel_GR5H.R | 29 - R/RunModel_GR5J.R | 33 - R/RunModel_GR6J.R | 33 - R/RunModel_Lag.R | 81 +-- R/TransfoParam_GR5H.R | 26 - R/Utils.R | 64 ++ README.md | 6 build/partial.rdb |binary inst/doc/V01_get_started.R | 2 inst/doc/V01_get_started.Rmd | 6 inst/doc/V01_get_started.html | 709 ++++++++++++++------------------ inst/doc/V02.1_param_optim.R | 9 inst/doc/V02.1_param_optim.Rmd | 35 + inst/doc/V02.1_param_optim.html | 642 ++++++++++++----------------- inst/doc/V02.2_param_mcmc.R | 17 inst/doc/V02.2_param_mcmc.Rmd | 21 inst/doc/V02.2_param_mcmc.html | 500 +++++++++-------------- inst/doc/V03_param_sets_GR4J.R | 1 inst/doc/V03_param_sets_GR4J.Rmd | 3 inst/doc/V03_param_sets_GR4J.html | 532 ++++++++++-------------- inst/doc/V04_cemaneige_hysteresis.html | 680 ++++++++++++++----------------- inst/doc/V05_sd_model.R | 46 +- inst/doc/V05_sd_model.Rmd | 53 +- inst/doc/V05_sd_model.html | 710 ++++++++++++++------------------- inst/modelsFeatures |only man/Calibration.Rd | 20 man/Calibration_Michel.Rd | 4 man/CreateInputsModel.Rd | 20 man/RunModel.Rd | 4 man/RunModel_Lag.Rd | 71 +-- man/TransfoParam.Rd | 6 man/airGR.Rd | 26 - man/plot.OutputsModel.Rd | 8 tests/testthat/test-RunModel_Lag.R | 224 +++++++--- vignettes/V01_get_started.Rmd | 6 vignettes/V02.1_param_optim.Rmd | 35 + vignettes/V02.2_param_mcmc.Rmd | 21 vignettes/V03_param_sets_GR4J.Rmd | 3 vignettes/V05_sd_model.Rmd | 53 +- 60 files changed, 2864 insertions(+), 3117 deletions(-)
Title: Geographical Detectors for Assessing Spatial Factors
Description: Geographical detectors for measuring spatial stratified heterogeneity,
as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and
Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the
optimal discretization of continuous data, four primary functions of
geographical detectors, comparison of size effects of spatial unit and
the visualizations of results.
To use the package and to refer the
descriptions of the package, methods and case datasets, please cite
Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>.
The model has been applied in factor exploration of road performance and
multi-scale spatial segmentation for network data, as described in
Yongze Song (2018) <doi:10.3390/rs10111696> and
Yongze Song (2020) <doi:10.1109/TITS.2020.3001193>, respectively.
Author: Yongze Song [aut, cre] (<https://orcid.org/0000-0003-3420-9622>)
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>
Diff between GD versions 1.9 dated 2020-06-29 and 1.10 dated 2021-04-27
DESCRIPTION | 10 - MD5 | 22 +- NAMESPACE | 1 R/gdeco.R | 19 +- R/zzz.R | 2 build/vignette.rds |binary inst/doc/GD.Rmd | 32 +-- inst/doc/GD.html | 390 +++++++++++++++++++++++++--------------------- man/H1N1.Rd | 10 - man/NDVI.Rd | 16 + vignettes/GD.Rmd | 32 +-- vignettes/fig/Figure7.png |binary 12 files changed, 291 insertions(+), 243 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut, cre],
Ian Cook [aut],
Jonathan Keane [aut],
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 3.0.0 dated 2021-01-27 and 4.0.0 dated 2021-04-27
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-16 1.1.5
2018-07-24 1.1.3
2018-05-28 1.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-10 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-20 0.1.2
2019-03-23 0.1.1
2019-03-07 0.1.0
Title: The Exterior Calculus
Description: Provides functionality for working with tensors, alternating
tensors, wedge products, Stokes's theorem, and related concepts
from the exterior calculus. Functionality for Grassman algebra
is provided. The canonical reference would be:
M. Spivak (1965, ISBN:0-8053-9021-9) "Calculus on Manifolds".
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between stokes versions 1.0-5 dated 2020-03-20 and 1.0-7 dated 2021-04-27
stokes-1.0-5/stokes/inst/examples.R |only stokes-1.0-5/stokes/inst/try.R |only stokes-1.0-7/stokes/DESCRIPTION | 21 stokes-1.0-7/stokes/MD5 | 73 +-- stokes-1.0-7/stokes/NAMESPACE | 6 stokes-1.0-7/stokes/R/mult.R | 58 ++ stokes-1.0-7/stokes/R/ops.R | 6 stokes-1.0-7/stokes/R/print.R |only stokes-1.0-7/stokes/README.md | 154 +++---- stokes-1.0-7/stokes/build/partial.rdb |binary stokes-1.0-7/stokes/build/stokes.pdf |only stokes-1.0-7/stokes/build/vignette.rds |binary stokes-1.0-7/stokes/inst/Alt.Rmd |only stokes-1.0-7/stokes/inst/doc/stokes.R | 35 + stokes-1.0-7/stokes/inst/doc/stokes.Rmd | 152 +++++-- stokes-1.0-7/stokes/inst/doc/stokes.html | 386 ++++++++++-------- stokes-1.0-7/stokes/man/Alt.Rd | 39 + stokes-1.0-7/stokes/man/Ops.Rd | 8 stokes-1.0-7/stokes/man/as.1form.Rd | 33 - stokes-1.0-7/stokes/man/consolidate.Rd | 8 stokes-1.0-7/stokes/man/contract.Rd | 16 stokes-1.0-7/stokes/man/cross.Rd | 11 stokes-1.0-7/stokes/man/inner.Rd | 33 - stokes-1.0-7/stokes/man/kform.Rd | 56 +- stokes-1.0-7/stokes/man/ktensor.Rd | 19 stokes-1.0-7/stokes/man/print.Rd |only stokes-1.0-7/stokes/man/rform.Rd | 13 stokes-1.0-7/stokes/man/symbolic.Rd | 7 stokes-1.0-7/stokes/man/transform.Rd | 38 - stokes-1.0-7/stokes/man/volume.Rd | 27 - stokes-1.0-7/stokes/man/wedge.Rd | 2 stokes-1.0-7/stokes/man/zap.Rd |only stokes-1.0-7/stokes/tests/testthat/test_ktensor.R | 1 stokes-1.0-7/stokes/tests/testthat/test_misc.R | 5 stokes-1.0-7/stokes/tests/testthat/test_mult.R | 9 stokes-1.0-7/stokes/tests/testthat/test_ops_kform.R | 2 stokes-1.0-7/stokes/tests/testthat/test_ops_ktensor.R | 2 stokes-1.0-7/stokes/tests/testthat/test_print.R |only stokes-1.0-7/stokes/tests/testthat/test_transform.R | 5 stokes-1.0-7/stokes/tests/testthat/test_wedge.R | 5 stokes-1.0-7/stokes/tests/testthat/test_zap.R |only stokes-1.0-7/stokes/vignettes/stokes.Rmd | 152 +++++-- 42 files changed, 856 insertions(+), 526 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.6.4 dated 2020-06-02 and 1.6.5 dated 2021-04-27
DESCRIPTION | 10 MD5 | 355 +- NAMESPACE | 174 - NEWS.md | 11 R/00-gconfig.R | 118 R/01-geojob-obj.R | 342 +- R/02-webgeom-obj.R | 342 +- R/03-webdata-obj.R | 380 +- R/04-webprocess-obj.R | 376 +- R/06-simplegeom-obj.R | 254 - R/07-datagroup-obj.R | 226 - R/algorithm-webprocess.R | 130 R/algorithmVersion-webprocess.R | 16 R/attribute-webgeom.R | 60 R/bufferPoint.R | 66 R/cancel-geojob.R | 78 R/check.R | 162 - R/dodsReplace.R | 26 R/download-geojob.R | 98 R/email-geojob.R | 76 R/geoknife-generic.R | 302 +- R/geoknifeUtils.R | 166 - R/geom-webgeom.R | 74 R/initializeProcessInputs.R | 132 R/inputs-webprocess.R | 250 - R/parseCategorical.R | 148 - R/parseTimeseries.R | 232 - R/processInputsToXML.R | 392 +- R/query-webdata-times.R | 124 R/query-webdata-variables.R | 110 R/query-webdata.R | 188 - R/query-webgeom.R | 60 R/query-webprocess.R | 32 R/result.R | 174 - R/setJobState.R | 82 R/setProcessInputs.R | 112 R/show-datagroup.R | 20 R/show-geojob.R | 14 R/show-simplegeom.R | 6 R/show-webdata.R | 14 R/show-webgeom.R | 14 R/show-webprocess.R | 26 R/start-geojob.R | 104 R/successful.R | 120 R/times-webdata.R | 152 - R/url-generic.R | 138 R/values-webgeom.R | 156 - R/variables-webdata.R | 80 R/version-generic.R | 66 R/waitUntilFinished.R | 126 build/vignette.rds |binary demo/00Index | 6 demo/iclus_categorical.R | 36 demo/prism_subset.R | 46 demo/prism_summary.R | 48 inst/CITATION | 28 inst/doc/custom_data_sources.R | 102 inst/doc/custom_data_sources.Rmd | 160 - inst/doc/custom_data_sources.html | 570 +--- inst/doc/geoknife.R | 508 +-- inst/doc/geoknife.Rmd | 1152 ++++---- inst/doc/geoknife.html | 1482 ++++------ inst/doc/plot_geotiff.R | 106 inst/doc/plot_geotiff.Rmd | 168 - inst/doc/plot_geotiff.html | 600 +--- inst/draw.xsd |only inst/extdata/SB_getCapabilities.xml | 776 ++--- inst/extdata/completed_request.xml | 202 - inst/extdata/csv_categorical_multifeature.csv | 24 inst/extdata/csv_linear_ring.csv | 12 inst/extdata/csv_multi_feature_stat.csv | 24 inst/extdata/csv_multi_threshold.csv | 2280 ++++++++-------- inst/extdata/csv_time_dimension_parse.csv | 736 ++--- inst/extdata/get_attribute_values.xml | 2 inst/extdata/multi_poly_post.xml | 236 - inst/extdata/state_webgeom_post.xml | 186 - inst/extdata/testjob.xml | 214 - inst/extdata/tsv_linear_ring.tsv | 12 inst/extdata/tsv_multi_feature.tsv | 16 inst/extdata/tsv_multi_feature_var.tsv | 90 inst/extdata/tsv_multi_var_feature_stat.tsv | 2208 +++++++-------- inst/templates/execute_template.xml | 142 inst/templates/getfeature_template.xml | 30 inst/templates/utility_execute_template.xml | 46 man/XML-method.Rd | 68 man/abstract-datagroup.Rd | 46 man/algorithm-webprocess.Rd | 72 man/attribute.Rd | 50 man/bufferPoint.Rd | 64 man/canStart.Rd | 30 man/cancel-methods.Rd | 86 man/check-geojob.Rd | 82 man/datagroup-class.Rd | 32 man/datagroup-methods.Rd | 82 man/defaultProcessInputs.Rd | 42 man/download.Rd | 72 man/email-method.Rd | 38 man/gconfig.Rd | 62 man/gcontent.Rd | 30 man/geojob-class.Rd | 48 man/geojob-methods.Rd | 140 man/geoknife-methods.Rd | 124 man/geom.Rd | 60 man/getJobState.Rd | 30 man/inputs-webprocess.Rd | 116 man/parseCategorical.Rd | 56 man/parseTimeseries.Rd | 66 man/query.Rd | 112 man/result-methods.Rd | 86 man/retryVERB.Rd | 42 man/setJobState.Rd | 42 man/simplegeom-class.Rd | 62 man/simplegeom-methods.Rd | 84 man/start-methods.Rd | 80 man/successful-methods.Rd | 88 man/times-webdata.Rd | 62 man/times_query-method.Rd | 38 man/url.Rd | 82 man/values.Rd | 66 man/variables-webdata.Rd | 54 man/variables_query-method.Rd | 44 man/version.Rd | 50 man/wait.Rd | 80 man/webdata-class.Rd | 40 man/webdata-methods.Rd | 116 man/webgeom-class.Rd | 84 man/webgeom-methods.Rd | 164 - man/webprocess-class.Rd | 108 man/webprocess-methods.Rd | 70 tests/testthat.R | 2 tests/testthat/00_create_test_data.R | 112 tests/testthat/data/test_XML_no_gmlid_wd.rds |binary tests/testthat/data/test_XML_no_gmlid_wg.rds |binary tests/testthat/data/test_XML_no_gmlid_xml.xml | 204 - tests/testthat/data/test_XML_sg_xml.xml | 204 - tests/testthat/data/test_XML_two_points_xml.xml | 236 - tests/testthat/data/test_XML_wg_xml.xml | 196 - tests/testthat/data/test_XML_wp_opendapsubset.rds |binary tests/testthat/data/test_email.xml | 58 tests/testthat/data/test_getgridtimerange.xml | 54 tests/testthat/data/test_listopendapgrids.xml | 42 tests/testthat/data/test_query_webdata.rds |binary tests/testthat/data/test_simplegeom_two_points.rds |binary tests/testthat/data/test_webdata_fabric.rds |binary tests/testthat/data/test_webdata_prism_year.rds |binary tests/testthat/data/test_webgeom_WI.rds |binary tests/testthat/data/test_webgeom_huc08.rds |binary tests/testthat/data/test_webprocess_algorithms.rds |binary tests/testthat/data/test_webprocess_algorithms_prod.rds |binary tests/testthat/data/test_webprocess_knife.rds |binary tests/testthat/data/test_webprocess_knife_prod.rds |binary tests/testthat/data/test_webprocess_sleep-plus-five.rds |binary tests/testthat/data/test_webprocess_tab.rds |binary tests/testthat/data/test_wfsgetfeature.xml | 40 tests/testthat/test-dodsReplace.R | 14 tests/testthat/test-download_result.R | 64 tests/testthat/test-gconfig.R | 58 tests/testthat/test-geoknife_output_parser.R | 134 tests/testthat/test-geoknife_setters.R | 182 - tests/testthat/test-geoknife_utils.R | 174 - tests/testthat/test-geoknife_xml_parser.R | 18 tests/testthat/test-knife_shorthand.R | 48 tests/testthat/test-parseCategorical.R | 50 tests/testthat/test-processErrors.R | 48 tests/testthat/test-query_webdata.R | 78 tests/testthat/test-query_webdatasets.R | 60 tests/testthat/test-query_webgeom.R | 90 tests/testthat/test-setJobState.R | 60 tests/testthat/test-show_object.R | 54 tests/testthat/test-sleep_time.R | 36 tests/testthat/test-times_webdata.R | 82 tests/testthat/test-waitUntilFinished.R | 62 tests/testthat/test-webdata_object.R | 104 tests/testthat/test-webprocess_input.R | 130 tests/testthat/test-webprocess_object.R | 147 - tests/testthat/test-whisker_templating.R | 156 - vignettes/custom_data_sources.Rmd | 160 - vignettes/geoknife.Rmd | 1152 ++++---- vignettes/plot_geotiff.Rmd | 168 - 179 files changed, 13140 insertions(+), 13649 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.15.0 dated 2021-03-28 and 1.16.0 dated 2021-04-27
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral and social sciences. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial (Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of predictions, which are easily interpretable for behavioral and social researchers. The floodlight analysis and mediation analysis based on these models are also provided. BANOVA uses 'Stan' and 'JAGS' as the computational platform. References: Dong and Wedel (2017) <doi:10.18637/jss.v081.i09>; Wedel and Dong (2020) <doi:10.1002/jcpy.1111>.
Author: Chen Dong, Michel Wedel, Anna Kopyakova
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 1.1.9 dated 2021-03-15 and 1.2.0 dated 2021-04-27
BANOVA-1.1.9/BANOVA/README.md |only BANOVA-1.2.0/BANOVA/DESCRIPTION | 8 BANOVA-1.2.0/BANOVA/MD5 | 35 BANOVA-1.2.0/BANOVA/NEWS | 4 BANOVA-1.2.0/BANOVA/build/vignette.rds |binary BANOVA-1.2.0/BANOVA/inst/doc/banova_examples.html | 819 +++++----- BANOVA-1.2.0/BANOVA/inst/stan/Bernoulli_Normal.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/Binomial_Normal.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/Multinomial_Normal.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/Multinomial_Normal_slow.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/Normal_Normal.stan | 4 BANOVA-1.2.0/BANOVA/inst/stan/Poisson_Normal.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/ordMultinomial_Normal.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/ordMultinomial_Normal_dirichlet.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/single_Normal.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/single_T.stan | 2 BANOVA-1.2.0/BANOVA/inst/stan/single_truncNormal.stan | 2 BANOVA-1.2.0/BANOVA/man/BANOVA-package.Rd | 4 BANOVA-1.2.0/BANOVA/man/BANOVA.multi.mediation.Rd | 2 19 files changed, 451 insertions(+), 445 deletions(-)