Title: Stochastic Limited Memory Quasi-Newton Optimizers
Description: Implementations of stochastic, limited-memory quasi-Newton optimizers,
similar in spirit to the LBFGS (Limited-memory Broyden-Fletcher-Goldfarb-Shanno) algorithm,
for smooth stochastic optimization. Implements the following methods:
oLBFGS (online LBFGS) (Schraudolph, N.N., Yu, J. and Guenter, S., 2007 <http://proceedings.mlr.press/v2/schraudolph07a.html>),
SQN (stochastic quasi-Newton) (Byrd, R.H., Hansen, S.L., Nocedal, J. and Singer, Y., 2016 <arXiv:1401.7020>),
adaQN (adaptive quasi-Newton) (Keskar, N.S., Berahas, A.S., 2016, <arXiv:1511.01169>).
Provides functions for easily creating R objects
with partial_fit/predict methods from some given objective/gradient/predict functions.
Includes an example stochastic logistic regression using these optimizers.
Provides header files and registered C routines for using it directly from C/C++.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between stochQN versions 0.1.0 dated 2019-08-29 and 0.1.1 dated 2019-08-29
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/optimizers_free.R | 9 ++++++--- R/optimizers_guided.R | 9 ++++++--- man/SQN.Rd | 3 ++- man/SQN_free.Rd | 3 ++- man/adaQN.Rd | 3 ++- man/adaQN_free.Rd | 3 ++- man/oLBFGS.Rd | 3 ++- man/oLBFGS_free.Rd | 3 ++- src/stochqn.c | 43 +++++++++++++++++++++++++++++++++---------- 11 files changed, 71 insertions(+), 36 deletions(-)
Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for
single-case designs, including several non-overlap measures and parametric
effect size measures, and for estimating the gradual effects model developed
by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>.
Standard errors and confidence intervals (based on the assumption that the outcome
measurements are mutually independent) are provided for the subset of effect sizes
indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre],
Daniel M. Swan [aut]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between SingleCaseES versions 0.4.2 dated 2019-06-14 and 0.4.3 dated 2019-08-29
DESCRIPTION | 8 MD5 | 18 - NEWS.md | 10 R/calculate-effect-sizes.R | 12 - R/parametric-measures.R | 72 ++++-- inst/shiny-examples/SCD-effect-sizes/markdown/LRR.html |only inst/shiny-examples/SCD-effect-sizes/markdown/LRR.md | 7 inst/shiny-examples/SCD-effect-sizes/markdown/PND-message.md |only inst/shiny-examples/SCD-effect-sizes/server.R | 69 +++-- inst/shiny-examples/SCD-effect-sizes/ui.R | 128 ++++++----- man/LRR.Rd | 28 +- 11 files changed, 234 insertions(+), 118 deletions(-)
Title: Local Control Strategy for Robust Analysis of Cross-Sectional
Data
Description: Especially when cross-sectional data are observational, effects of treatment
selection bias and confounding are revealed by using the Nonparametric and Unsupervised
"preprocessing" methods central to Local Control (LC) Strategy. The LC objective is to
estimate the "effect-size distribution" that best quantifies a potentially causal
relationship between a numeric y-Outcome variable and a t-Treatment variable. This
t-variable may be either binary {1 = "new" vs 0 = "control"} or a numeric measure of
Exposure level. LC Strategy starts by CLUSTERING experimental units (patients) on their
pre-exposure X-Covariates, forming mutually exclusive and exhaustive BLOCKS of relatively
well-matched units. The implicit statistical model for LC is thus simple one-way ANOVA.
The Within-Block measures of effect-size are Local Rank Correlations (LRCs) when Exposure
is numeric with more than two levels. Otherwise, Treatment choice is Nested within
BLOCKS, and effect-sizes are LOCAL Treatment Differences (LTDs) between within-cluster
y-Outcome Means ["new" minus "control"]. An Instrumental Variable (IV) method is also
provided so that Local Average y-Outcomes (LAOs) within BLOCKS may also contribute
information for effect-size inferences ...assuming that X-Covariates influence only
Treatment choice or Exposure level and otherwise have no direct effects on y-Outcome.
Finally, a "Most-Like-Me" function provides histograms of effect-size distributions to
aid Doctor-Patient communications about Personalized Medicine.
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between LocalControlStrategy versions 1.3.2 dated 2019-01-07 and 1.3.3 dated 2019-08-29
COPYING |only DESCRIPTION | 24 +++++++++++++----------- MD5 | 21 ++++++++++++++------- NAMESPACE | 7 +++++++ R/LCsetup.R | 4 ++-- R/mlme.R |only R/mlme.stats.R |only build/partial.rdb |binary demo/pci15k.R | 10 ++++++++++ demo/radon.R | 16 ++++++++++++++++ man/LocalControlStrategy-package.Rd | 18 +++++++++++++----- man/mlme.Rd |only man/mlme.stats.Rd |only man/plot.mlme.Rd |only man/print.mlme.Rd |only 15 files changed, 75 insertions(+), 25 deletions(-)
More information about LocalControlStrategy at CRAN
Permanent link
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly
enhanced predictive power over traditional GxE models which include only a single
genetic variant and a single environmental exposure. Although this approach was
originally made for GxE modelling, it is flexible and does not require the use of
genetic and environmental variables. It can also handle more than 2 latent variables
(rather than just G and E) and 3-way interactions or more. The LEGIT model produces
highly interpretable results and is very parameter-efficient thus it can even be
used with small sample sizes (n < 250). Tools to determine the type of interaction
(vantage sensitivity, diathesis-stress or differential susceptibility), with any
number of genetic variants or environments, are available <arXiv:1712.04058>.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.3 dated 2019-07-26 and 1.3.1 dated 2019-08-29
DESCRIPTION | 8 MD5 | 18 - NAMESPACE | 2 NEWS | 10 R/LEGIT.R | 411 +++++++++++++++++----------- build/vignette.rds |binary inst/doc/ElasticNet.html | 533 +++++++++++++++++++++++------------- inst/doc/GxE_testing.html | 475 +++++++++++++++++++++----------- inst/doc/LEGIT.html | 670 ++++++++++++++++++++++++++++++---------------- man/IMLEGIT_to_LEGIT.Rd |only man/LEGIT_to_IMLEGIT.Rd |only 11 files changed, 1382 insertions(+), 745 deletions(-)
Title: Google's S2 Library for Geometry on the Sphere
Description: R bindings for Google's s2 library for geometric calculations on
the sphere.
Author: Ege Rubak [aut, cre],
Jeroen Ooms [aut] (configure and cleanup script),
Edzer Pebesma [aut] (Interface to sf),
Google, Inc. [cph] (Original s2 source code)
Maintainer: Ege Rubak <rubak@math.aau.dk>
Diff between s2 versions 0.4-0 dated 2018-04-21 and 0.4-2 dated 2019-08-29
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/include/Rcpp_datatypes.h | 2 +- man/S2Polygon.Rd | 5 +++-- man/s2-package.Rd | 2 +- src/geometry/base/logging.cc | 4 ++++ src/geometry/s2loop.cc | 4 ++-- src/geometry/s2polyline.cc | 4 ++-- src/geometry/s2regioncoverer.cc | 2 +- 9 files changed, 26 insertions(+), 21 deletions(-)
Title: Interchange Tools for Multi-Parameter Spatiotemporal Data
Description: Formatting and structuring multi-parameter spatiotemporal data
is often a time-consuming task. This package offers functions and data structures
designed to easily organize and visualize these data for applications in geology,
paleolimnology, dendrochronology, and paleoclimate. See Dunnington and Spooner (2018)
<doi:10.1139/facets-2017-0026>.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between mudata2 versions 1.0.6 dated 2019-03-16 and 1.0.7 dated 2019-08-29
DESCRIPTION | 9 MD5 | 82 +++---- R/autoplot.R | 24 +- R/biplot.R | 16 - R/data.R | 20 - R/mudata.R | 34 +-- R/mudata.io.R | 21 - R/mudata_helpers.R | 4 R/mudata_subset.R | 50 ++-- R/package_doc.R | 12 - R/rename.R | 22 +- R/types.R | 65 +++-- R/utils.R | 10 build/vignette.rds |binary inst/doc/mudata.html | 429 +++++++++++++++++++++++++++++---------- inst/doc/mudata_create.html | 467 +++++++++++++++++++++++++++++++------------ man/alta_lake.Rd | 4 man/as_col_spec.Rd | 4 man/autoplot.mudata.Rd | 2 man/biplot.mudata.Rd | 4 man/collect.mudata.Rd | 6 man/filterers.Rd | 4 man/long_ggplot.Rd | 13 - man/long_lake.Rd | 6 man/long_pairs.Rd | 13 - man/mudata.Rd | 8 man/mudata2-package.Rd | 6 man/mudata_prepare_column.Rd | 8 man/mutate_data.Rd | 2 man/parallel_gather.Rd | 8 man/rbind.mudata.Rd | 8 man/reexports.Rd | 9 man/rename_cols_base.Rd | 5 man/rename_datasets_base.Rd | 2 man/rename_values_base.Rd | 2 man/renamers.Rd | 4 man/second_lake_temp.Rd | 6 man/selecters.Rd | 8 man/subset.mudata.Rd | 6 man/tbl_data.Rd | 3 man/write_mudata.Rd | 10 tests/testthat/Rplots.pdf |binary 42 files changed, 921 insertions(+), 495 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains many functions useful for managing 'NetCDF' files (see <http://en.wikipedia.org/wiki/NetCDF>), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 3.6 dated 2019-06-27 and 3.7 dated 2019-08-29
DESCRIPTION | 10 - MD5 | 46 ++--- NAMESPACE | 2 NEWS | 12 + R/HelpersMG-package.R | 4 R/LD50.R | 35 ++- R/LD50_fit.R | 14 - R/MHalgoGen.R | 389 +++++++++++++++++++++++-------------------- R/as.quantile.R |only R/flexit.R |only R/plot.mcmcComposite.R | 2 R/similar.R | 4 R/sysdata.rda |binary man/HelpersMG-package.Rd | 4 man/LD50.Rd | 14 - man/MHalgoGen.Rd | 29 ++- man/as.mcmc.mcmcComposite.Rd | 2 man/as.parameters.Rd | 1 man/as.quantile.Rd |only man/flexit.Rd |only man/invlogit.Rd | 2 man/logit.Rd | 2 man/merge.mcmcComposite.Rd | 2 man/plot.mcmcComposite.Rd | 2 man/similar.Rd | 4 man/summary.mcmcComposite.Rd | 2 26 files changed, 332 insertions(+), 250 deletions(-)
Title: 'CRU' 'CL' v. 2.0 Climatology Client
Description: Provides functions that automate downloading and importing
University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0
climatology data, facilitates the calculation of minimum temperature and
maximum temperature and formats the data into a tidy data frame as a
'tibble' or a list of 'raster' 'stack' objects for use. 'CRU' 'CL' v. 2.0
data are a gridded climatology of 1961-1990 monthly means released in 2002
and cover all land areas (excluding Antarctica) at 10 arcminutes
(0.1666667 degree) resolution. For more information see the description of
the data provided by the University of East Anglia Climate Research Unit,
<https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between getCRUCLdata versions 0.3.0 dated 2019-04-12 and 0.3.1 dated 2019-08-29
DESCRIPTION | 13 ++++++------- MD5 | 24 ++++++++++++------------ NEWS.md | 19 +++++++++++++++---- R/create_CRU_stack.R | 2 +- R/getCRUCLdata.R | 4 ++-- R/get_CRU_df.R | 5 ++++- R/manage_cached_files.R | 2 ++ README.md | 7 ++++--- build/vignette.rds |binary man/create_CRU_stack.Rd | 2 +- man/getCRUCLdata.Rd | 4 ++-- man/get_CRU_df.Rd | 5 ++++- man/manage_cache.Rd | 3 +++ 13 files changed, 56 insertions(+), 34 deletions(-)
Title: Platform for EDGAR Filing Management and Textual Analysis
Description: In the USA, companies file different forms with the U.S.
Securities and Exchange Commission (SEC) through EDGAR (Electronic
Data Gathering, Analysis, and Retrieval system). The EDGAR
database automated system collects all the different necessary
filings and makes it publicly available. Investors, regulators,
and researchers often require these forms for various purposes.
This package helps in bulk data gathering and textual analysis of
EDGAR filings. It downloads filings from SEC server in bulk with
a single query. Additionally, it provides various useful functions:
extracts 8-K triggering events, extract "Business (Item 1)" and
"Management's Discussion and Analysis(Item 7)" sections of annual
statements, search filings for desired words, provides sentiment
measures, parse filing header information, and provides HTML
view of SEC filings.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil
<bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 2.0.1 dated 2019-03-22 and 2.0.2 dated 2019-08-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/getBusinessDescr.R | 47 +++++++++++++++++++++++++++++++++++------------ R/getFilingHeader.R | 2 +- R/getFilingsHTML.R | 13 +++++++------ R/getMgmtDisc.R | 50 +++++++++++++++++++++++++++++++++++--------------- R/getSentiment.R | 10 +++++++--- R/searchFilings.R | 2 +- 8 files changed, 97 insertions(+), 49 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, David, 2018, <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a hierarchical
structure, and is fit through either proximal gradient or conjugate gradient instead of variational inference.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.1.1 dated 2019-08-01 and 0.1.2 dated 2019-08-29
DESCRIPTION | 8 +-- MD5 | 8 +-- R/poismf.R | 1 src/pgd.cpp | 138 ++++++++++++++++++++++++++++--------------------------- src/rwrapper.cpp | 18 +++---- 5 files changed, 89 insertions(+), 84 deletions(-)
Title: Arctic Ice Studio's Nord and Group of Seven Inspired Colour
Palettes for 'ggplot2'
Description: Provides the Arctic Ice Studio's Nord and Group of Seven inspired colour palettes for use with 'ggplot2' via custom functions.
Author: Jake Kaupp [aut, cre] (<https://orcid.org/0000-0002-3217-3294>)
Maintainer: Jake Kaupp <jkaupp@gmail.com>
Diff between nord versions 0.0.1 dated 2018-02-05 and 1.0.0 dated 2019-08-29
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/scales.R | 6 +++--- README.md | 10 ++++++++-- man/scale_fill_nord.Rd | 2 +- 6 files changed, 38 insertions(+), 21 deletions(-)
Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information returned
online by Google Trends is provided. Trends (number of hits) over the time as
well as geographic representation of the results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.4.3 dated 2019-05-02 and 1.4.4 dated 2019-08-29
DESCRIPTION | 7 +++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/zzz.R | 4 ++++ 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features
an API for extending these templates to address novel scientific research aims.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Skye Bender-deMoll [ctb],
Kevin Weiss [ctb],
Shawnee Anderson [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 1.7.2 dated 2018-12-18 and 1.7.3 dated 2019-08-29
EpiModel-1.7.2/EpiModel/man/calc_eql.Rd |only EpiModel-1.7.3/EpiModel/DESCRIPTION | 10 EpiModel-1.7.3/EpiModel/MD5 | 35 +-- EpiModel-1.7.3/EpiModel/NAMESPACE | 1 EpiModel-1.7.3/EpiModel/NEWS.md | 15 + EpiModel-1.7.3/EpiModel/R/EpiModel-package.r | 4 EpiModel-1.7.3/EpiModel/R/net.mod.simnet.R | 2 EpiModel-1.7.3/EpiModel/R/net.utils.R | 91 -------- EpiModel-1.7.3/EpiModel/R/netdx.R | 227 ++++++++++---------- EpiModel-1.7.3/EpiModel/R/plot.R | 9 EpiModel-1.7.3/EpiModel/R/print.r | 18 - EpiModel-1.7.3/EpiModel/build/vignette.rds |binary EpiModel-1.7.3/EpiModel/inst/doc/Intro.html | 48 ++-- EpiModel-1.7.3/EpiModel/man/EpiModel-package.Rd | 4 EpiModel-1.7.3/EpiModel/man/netdx.Rd | 5 EpiModel-1.7.3/EpiModel/man/plot.icm.Rd | 2 EpiModel-1.7.3/EpiModel/man/plot.netsim.Rd | 2 EpiModel-1.7.3/EpiModel/tests/testthat/test-netdx.R | 24 ++ EpiModel-1.7.3/EpiModel/tests/testthat/test-utils.R | 47 ---- 19 files changed, 232 insertions(+), 312 deletions(-)
Title: A Class for Working with Time Series Based on 'data.table' and
'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing
values, application of arbitrary aggregation as well as rolling window
functions and automatic detection of periodicity. As it is mainly based on
'data.table', it is fast and - in combination with the 'R6' package - offers
reference semantics. In addition to its native R6 interface, it provides an
S3 interface inclusive an S3 wrapper method generator for those who prefer
the latter.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <ghepp@iwag.tuwien.ac.at>
Diff between DTSg versions 0.1.2 dated 2019-03-13 and 0.1.3 dated 2019-08-29
DTSg-0.1.2/DTSg/inst/doc/advancedUsage.R |only DTSg-0.1.2/DTSg/inst/doc/advancedUsage.Rmd |only DTSg-0.1.2/DTSg/inst/doc/advancedUsage.html |only DTSg-0.1.2/DTSg/inst/doc/basicUsage.R |only DTSg-0.1.2/DTSg/inst/doc/basicUsage.Rmd |only DTSg-0.1.2/DTSg/inst/doc/basicUsage.html |only DTSg-0.1.2/DTSg/vignettes/advancedUsage.Rmd |only DTSg-0.1.2/DTSg/vignettes/basicUsage.Rmd |only DTSg-0.1.3/DTSg/DESCRIPTION | 6 ++--- DTSg-0.1.3/DTSg/MD5 | 28 +++++++++++++------------- DTSg-0.1.3/DTSg/NEWS.md | 4 +++ DTSg-0.1.3/DTSg/R/Swrappers.R | 6 ++--- DTSg-0.1.3/DTSg/README.md | 8 +++++++ DTSg-0.1.3/DTSg/build/vignette.rds |binary DTSg-0.1.3/DTSg/inst/doc/a_basicUsage.R |only DTSg-0.1.3/DTSg/inst/doc/a_basicUsage.Rmd |only DTSg-0.1.3/DTSg/inst/doc/a_basicUsage.html |only DTSg-0.1.3/DTSg/inst/doc/b_advancedUsage.R |only DTSg-0.1.3/DTSg/inst/doc/b_advancedUsage.Rmd |only DTSg-0.1.3/DTSg/inst/doc/b_advancedUsage.html |only DTSg-0.1.3/DTSg/man/aggregate.DTSg.Rd | 6 ++--- DTSg-0.1.3/DTSg/vignettes/a_basicUsage.Rmd |only DTSg-0.1.3/DTSg/vignettes/b_advancedUsage.Rmd |only 23 files changed, 35 insertions(+), 23 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.0.4-2 dated 2016-07-25 and 2.0.4-4 dated 2019-08-29
DESCRIPTION | 9 +- MD5 | 26 ++++---- R/load.module.runjags.R | 2 R/runjags.summaries.R | 13 +++- R/utilities.invisible.R | 4 - build/vignette.rds |binary cleanup | 2 configure.win |only inst/doc/UserGuide.pdf |binary inst/doc/quickjags.Rmd | 4 - inst/doc/quickjags.html | 150 +++++++++++++++++++++++++++--------------------- src/Makevars.in | 2 src/Makevars.win | 13 +++- src/init.c |only vignettes/quickjags.Rmd | 4 - 15 files changed, 133 insertions(+), 96 deletions(-)
Title: Satellite Nightlight Data Extraction
Description: Extracts raster and zonal statistics
from satellite nightlight rasters downloaded from the United States
National Oceanic and Atmospheric Administration (<http://www.noaa.gov>)
free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly
nightlight raster data are supported. Satellite nightlight raster tiles are
downloaded and cropped to the country boundaries using shapefiles from the GADM
database of Global Administrative Areas (<http://gadm.org>). Zonal statistics
are then calculated at the lowest administrative boundary for the selected
country and cached locally for future retrieval. Finally, a simple data
explorer/browser is included that allows one to visualize the cached data e.g.
graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph]
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>
Diff between Rnightlights versions 0.2.3 dated 2018-10-13 and 0.2.4 dated 2019-08-29
Rnightlights-0.2.3/Rnightlights/man/nlInit.Rd |only Rnightlights-0.2.3/Rnightlights/tests/testthat/NL_DATA_STP_ADM0_GADM-2.8.csv |only Rnightlights-0.2.3/Rnightlights/tests/testthat/STP_OLS_1992.tif |only Rnightlights-0.2.3/Rnightlights/tests/testthat/STP_VIIRS_201401.tif |only Rnightlights-0.2.3/Rnightlights/tests/testthat/helper_testutils.R |only Rnightlights-0.2.4/Rnightlights/DESCRIPTION | 20 Rnightlights-0.2.4/Rnightlights/MD5 | 221 +- Rnightlights-0.2.4/Rnightlights/NAMESPACE | 12 Rnightlights-0.2.4/Rnightlights/R/ctrycode.R | 16 Rnightlights-0.2.4/Rnightlights/R/ctrynldata.R | 560 ++++- Rnightlights-0.2.4/Rnightlights/R/datapath.R | 103 Rnightlights-0.2.4/Rnightlights/R/downloadnltiles.R | 375 ++- Rnightlights-0.2.4/Rnightlights/R/gasflares.R |only Rnightlights-0.2.4/Rnightlights/R/getnlfilename.R | 158 + Rnightlights-0.2.4/Rnightlights/R/getnlurl.R | 94 Rnightlights-0.2.4/Rnightlights/R/masq.R | 130 - Rnightlights-0.2.4/Rnightlights/R/nightlights.R | 517 +++- Rnightlights-0.2.4/Rnightlights/R/nlperiod.R | 24 Rnightlights-0.2.4/Rnightlights/R/options.R | 172 + Rnightlights-0.2.4/Rnightlights/R/polygons.R | 1076 ++++++++-- Rnightlights-0.2.4/Rnightlights/R/stats.R | 243 +- Rnightlights-0.2.4/Rnightlights/R/tiles.R | 111 - Rnightlights-0.2.4/Rnightlights/R/upgrade.R | 377 ++- Rnightlights-0.2.4/Rnightlights/R/utils.R | 426 +-- Rnightlights-0.2.4/Rnightlights/R/vignette.R |only Rnightlights-0.2.4/Rnightlights/R/zzz.R | 72 Rnightlights-0.2.4/Rnightlights/inst/application/server.R | 375 ++- Rnightlights-0.2.4/Rnightlights/inst/application/ui.R | 4 Rnightlights-0.2.4/Rnightlights/man/ZonalPipe.Rd | 13 Rnightlights-0.2.4/Rnightlights/man/addCtryPolyIdx.Rd | 4 Rnightlights-0.2.4/Rnightlights/man/allExistsCtryNlData.Rd |only Rnightlights-0.2.4/Rnightlights/man/allValid.Rd | 4 Rnightlights-0.2.4/Rnightlights/man/allValidCtryAdmLvls.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/createCtryNlDataDF.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/createCtryStruct.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/ctryShpLyrName2Num.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/deleteCtryPoly.Rd |only Rnightlights-0.2.4/Rnightlights/man/deleteNlDataCol.Rd | 21 Rnightlights-0.2.4/Rnightlights/man/dnldCtryPoly.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/dnldGADMCtryShpZip.Rd |only Rnightlights-0.2.4/Rnightlights/man/dnldGADMCtrySpRds.Rd |only Rnightlights-0.2.4/Rnightlights/man/dot-RnightlightsEnv.Rd |only Rnightlights-0.2.4/Rnightlights/man/downloadNlTiles.Rd | 8 Rnightlights-0.2.4/Rnightlights/man/downloadNlTilesOLS.Rd | 11 Rnightlights-0.2.4/Rnightlights/man/downloadNlTilesVIIRS.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/existsCtryNlData.Rd | 21 Rnightlights-0.2.4/Rnightlights/man/existsCtryNlDataFile.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/existsCtryPoly.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/existsPolyFnamePath.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/existsPolyFnameRDS.Rd |only Rnightlights-0.2.4/Rnightlights/man/existsPolyFnameZip.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/fnAggRadGdal.Rd | 21 Rnightlights-0.2.4/Rnightlights/man/fnAggRadRast.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getAllGadmPolyTypes.Rd |only Rnightlights-0.2.4/Rnightlights/man/getAllNlConfigNames.Rd |only Rnightlights-0.2.4/Rnightlights/man/getBatchBytes.Rd |only Rnightlights-0.2.4/Rnightlights/man/getCRS.Rd |only Rnightlights-0.2.4/Rnightlights/man/getCtryNlData.Rd | 21 Rnightlights-0.2.4/Rnightlights/man/getCtryNlDataColName.Rd | 12 Rnightlights-0.2.4/Rnightlights/man/getCtryNlDataFname.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getCtryNlDataFnamePath.Rd | 8 Rnightlights-0.2.4/Rnightlights/man/getCtryPolyAdmLevelNames.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getCtryPolyUrl.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getCtryRasterOutputFname.Rd | 21 Rnightlights-0.2.4/Rnightlights/man/getCtryRasterOutputFnamePath.Rd | 18 Rnightlights-0.2.4/Rnightlights/man/getCtryShpAllAdmLvls.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getCtryShpLowestLyrNames.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getCtryShpLyrNames.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getCtryStructAdmLevelNames.Rd | 12 Rnightlights-0.2.4/Rnightlights/man/getCtryStructFname.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getCtryStructFnamePath.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/getFreeRAM.Rd |only Rnightlights-0.2.4/Rnightlights/man/getNlTifLclNameOLS.Rd | 9 Rnightlights-0.2.4/Rnightlights/man/getNlTileTifLclNameOLS.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getNlTileTifLclNamePath.Rd | 8 Rnightlights-0.2.4/Rnightlights/man/getNlTileTifLclNamePathOLS.Rd | 8 Rnightlights-0.2.4/Rnightlights/man/getNlTileTifLclNamePathVIIRS.Rd | 12 Rnightlights-0.2.4/Rnightlights/man/getNlTileTifLclNameVIIRS.Rd | 10 Rnightlights-0.2.4/Rnightlights/man/getNlTileZipLclNameOLS.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getNlTileZipLclNamePath.Rd | 6 Rnightlights-0.2.4/Rnightlights/man/getNlTileZipLclNameVIIRS.Rd | 10 Rnightlights-0.2.4/Rnightlights/man/getNlUrl.Rd |only Rnightlights-0.2.4/Rnightlights/man/getNlUrlOLS.Rd | 4 Rnightlights-0.2.4/Rnightlights/man/getPolyFname.Rd | 4 Rnightlights-0.2.4/Rnightlights/man/getPolyFnamePath.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getPolyFnameRDS.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getPolyFnameZip.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/getWorldMap.Rd |only Rnightlights-0.2.4/Rnightlights/man/insertNlDataCol.Rd | 14 Rnightlights-0.2.4/Rnightlights/man/listCtryNlData.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/listCtryNlRasters.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/listNlTiles.Rd | 6 Rnightlights-0.2.4/Rnightlights/man/masqOLS.Rd | 4 Rnightlights-0.2.4/Rnightlights/man/masqVIIRS.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/myZonal.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/myfun.Rd |only Rnightlights-0.2.4/Rnightlights/man/nlCleanup.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/pkgDefaults.Rd |only Rnightlights-0.2.4/Rnightlights/man/pkgOptions.Rd | 67 Rnightlights-0.2.4/Rnightlights/man/printCredits.Rd |only Rnightlights-0.2.4/Rnightlights/man/processNLCountry.Rd | 21 Rnightlights-0.2.4/Rnightlights/man/processNlData.Rd | 16 Rnightlights-0.2.4/Rnightlights/man/readCtryPolyAdmLayer.Rd | 4 Rnightlights-0.2.4/Rnightlights/man/readCtryStruct.Rd | 7 Rnightlights-0.2.4/Rnightlights/man/removeDataPath.Rd | 8 Rnightlights-0.2.4/Rnightlights/man/saveCtryNlData.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/searchAdmLevel.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/setDataVersion.Rd |only Rnightlights-0.2.4/Rnightlights/man/validCtryAdmLvls.Rd | 5 Rnightlights-0.2.4/Rnightlights/man/validGadmPolyTypes.Rd |only Rnightlights-0.2.4/Rnightlights/man/validNlConfigName.Rd |only Rnightlights-0.2.4/Rnightlights/tests/testthat.R | 17 Rnightlights-0.2.4/Rnightlights/tests/testthat/NL_DATA_STP_ADM2_GADM-2.8-SHPZIP.csv |only Rnightlights-0.2.4/Rnightlights/tests/testthat/NL_STP_OLS.Y_1992_STABLE_LIGHTS_GADM-2.8-SHPZIP.tif |only Rnightlights-0.2.4/Rnightlights/tests/testthat/NL_STP_VIIRS.M_201401_VCMCFG_GADM-2.8-SHPZIP.tif |only Rnightlights-0.2.4/Rnightlights/tests/testthat/helper.R | 23 Rnightlights-0.2.4/Rnightlights/tests/testthat/helper_ctrynldata.R | 25 Rnightlights-0.2.4/Rnightlights/tests/testthat/helper_ctrynltiles.R | 26 Rnightlights-0.2.4/Rnightlights/tests/testthat/helper_masq.R | 6 Rnightlights-0.2.4/Rnightlights/tests/testthat/nltiles.csv | 14 Rnightlights-0.2.4/Rnightlights/tests/testthat/test-admlevels.R | 16 Rnightlights-0.2.4/Rnightlights/tests/testthat/test-ctrynldata.R | 13 Rnightlights-0.2.4/Rnightlights/tests/testthat/test-ctrynltiles.R | 58 Rnightlights-0.2.4/Rnightlights/tests/testthat/test-datapath.R | 28 Rnightlights-0.2.4/Rnightlights/tests/testthat/test-nlfilename.R | 38 Rnightlights-0.2.4/Rnightlights/tests/testthat/test-nlurl.R |only Rnightlights-0.2.4/Rnightlights/tests/testthat/test-utils.R |only 127 files changed, 4500 insertions(+), 1451 deletions(-)
Title: Decoupled Hydrological Model for Research and Education Purposes
Description: The HBV (Hydrologiska Byråns Vattenbalansavdelning) hydrological model is decoupled to allow the user
to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia
y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA
incorporates modules for precipitation and temperature interpolation, and also for clean and debris covered ice melt estimations.
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Diff between HBV.IANIGLA versions 0.1.0 dated 2019-08-24 and 0.1.1 dated 2019-08-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/RcppExports.cpp | 4 ++-- src/UH_HBV.cpp | 2 +- src/median.cpp | 4 ++-- src/median.h | 2 +- 6 files changed, 15 insertions(+), 15 deletions(-)
Title: Provides an R Interface to 'Enrichr'
Description: Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See (<http://amp.pharm.mssm.edu/Enrichr/>) for further details.
Author: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <wj241@alumni.cam.ac.uk>
Diff between enrichR versions 2.0 dated 2019-07-25 and 2.1 dated 2019-08-29
DESCRIPTION | 6 MD5 | 17 - R/functions.R | 47 +++- README.md | 85 ++++---- build/vignette.rds |binary inst/doc/enrichR.Rmd | 6 inst/doc/enrichR.html | 484 +++++++++++++++++++++++++------------------------- man/dot-onAttach.Rd |only vignettes/enrichR.Rmd | 6 vignettes/enrichr.bib | 3 10 files changed, 331 insertions(+), 323 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation. References: Bürkner (2017)
<doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>;
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 2.9.0 dated 2019-05-23 and 2.10.0 dated 2019-08-29
brms-2.10.0/brms/DESCRIPTION | 18 brms-2.10.0/brms/MD5 | 220 brms-2.10.0/brms/NAMESPACE | 15 brms-2.10.0/brms/NEWS.md | 3578 ++--- brms-2.10.0/brms/R/brm.R | 25 brms-2.10.0/brms/R/brmsfit-helpers.R | 223 brms-2.10.0/brms/R/brmsfit-methods.R | 6794 +++++----- brms-2.10.0/brms/R/brmsformula.R | 2943 ++-- brms-2.10.0/brms/R/correlations.R | 1144 - brms-2.10.0/brms/R/data-helpers.R | 1400 +- brms-2.10.0/brms/R/data-predictor.R | 2281 +-- brms-2.10.0/brms/R/distributions.R | 4068 +++-- brms-2.10.0/brms/R/exclude_pars.R | 222 brms-2.10.0/brms/R/extract_draws.R | 139 brms-2.10.0/brms/R/families.R | 3128 ++-- brms-2.10.0/brms/R/family-lists.R | 910 - brms-2.10.0/brms/R/fitted.R | 1115 - brms-2.10.0/brms/R/formula-helpers.R | 1661 +- brms-2.10.0/brms/R/generics.R | 1327 - brms-2.10.0/brms/R/hypothesis.R | 1026 - brms-2.10.0/brms/R/log_lik.R | 1521 +- brms-2.10.0/brms/R/loo-helpers.R | 2001 +- brms-2.10.0/brms/R/make_stancode.R | 49 brms-2.10.0/brms/R/marginal_effects-helpers.R | 23 brms-2.10.0/brms/R/marginal_smooths-helpers.R | 396 brms-2.10.0/brms/R/misc-methods.R | 2 brms-2.10.0/brms/R/misc.R | 37 brms-2.10.0/brms/R/predict.R | 1449 +- brms-2.10.0/brms/R/predictor.R | 22 brms-2.10.0/brms/R/priors.R | 3656 ++--- brms-2.10.0/brms/R/re-syntax-helpers.R | 2 brms-2.10.0/brms/R/rename_pars.R | 1148 - brms-2.10.0/brms/R/restructure.R | 1 brms-2.10.0/brms/R/sp-syntax-helpers.R | 712 - brms-2.10.0/brms/R/stan-helpers.R | 1697 +- brms-2.10.0/brms/R/stan-likelihood.R | 1484 +- brms-2.10.0/brms/R/stan-predictor.R | 3355 ++-- brms-2.10.0/brms/R/stan-prior.R | 834 - brms-2.10.0/brms/R/sysdata.rda |binary brms-2.10.0/brms/R/validate.R | 2477 +-- brms-2.10.0/brms/README.md | 626 brms-2.10.0/brms/build/vignette.rds |binary brms-2.10.0/brms/inst/chunks/fun_cholesky_cor_ar1.stan |only brms-2.10.0/brms/inst/chunks/fun_cholesky_cor_arma1.stan |only brms-2.10.0/brms/inst/chunks/fun_cholesky_cor_cosy.stan |only brms-2.10.0/brms/inst/chunks/fun_cholesky_cor_ma1.stan |only brms-2.10.0/brms/inst/chunks/fun_cox.stan |only brms-2.10.0/brms/inst/chunks/fun_normal_cov.stan | 79 brms-2.10.0/brms/inst/chunks/fun_normal_errorsar.stan | 11 brms-2.10.0/brms/inst/chunks/fun_normal_lagsar.stan | 11 brms-2.10.0/brms/inst/chunks/fun_scale_cov_err.stan | 9 brms-2.10.0/brms/inst/chunks/fun_student_t_cov.stan | 73 brms-2.10.0/brms/inst/chunks/fun_student_t_errorsar.stan | 13 brms-2.10.0/brms/inst/chunks/fun_student_t_lagsar.stan | 13 brms-2.10.0/brms/inst/chunks/fun_zero_inflated_asym_laplace.stan |only brms-2.10.0/brms/inst/doc/brms_customfamilies.R | 19 brms-2.10.0/brms/inst/doc/brms_customfamilies.Rmd | 194 brms-2.10.0/brms/inst/doc/brms_customfamilies.html | 107 brms-2.10.0/brms/inst/doc/brms_distreg.Rmd | 137 brms-2.10.0/brms/inst/doc/brms_distreg.html | 108 brms-2.10.0/brms/inst/doc/brms_families.html | 8 brms-2.10.0/brms/inst/doc/brms_missings.Rmd | 330 brms-2.10.0/brms/inst/doc/brms_missings.html | 65 brms-2.10.0/brms/inst/doc/brms_monotonic.Rmd | 95 brms-2.10.0/brms/inst/doc/brms_monotonic.html | 164 brms-2.10.0/brms/inst/doc/brms_multilevel.pdf |binary brms-2.10.0/brms/inst/doc/brms_multivariate.Rmd | 85 brms-2.10.0/brms/inst/doc/brms_multivariate.html | 196 brms-2.10.0/brms/inst/doc/brms_nonlinear.Rmd | 141 brms-2.10.0/brms/inst/doc/brms_nonlinear.html | 128 brms-2.10.0/brms/inst/doc/brms_overview.pdf |binary brms-2.10.0/brms/inst/doc/brms_phylogenetics.Rmd | 125 brms-2.10.0/brms/inst/doc/brms_phylogenetics.html | 146 brms-2.10.0/brms/man/addition-terms.Rd | 27 brms-2.10.0/brms/man/brm.Rd | 23 brms-2.10.0/brms/man/brm_multiple.Rd | 23 brms-2.10.0/brms/man/brmsfamily.Rd | 4 brms-2.10.0/brms/man/brmsformula.Rd | 28 brms-2.10.0/brms/man/cor_car.Rd | 12 brms-2.10.0/brms/man/cor_cosy.Rd |only brms-2.10.0/brms/man/get_prior.Rd | 3 brms-2.10.0/brms/man/horseshoe.Rd | 18 brms-2.10.0/brms/man/hypothesis.Rd | 16 brms-2.10.0/brms/man/is.cor_brms.Rd | 3 brms-2.10.0/brms/man/kfold.brmsfit.Rd | 4 brms-2.10.0/brms/man/loo.brmsfit.Rd | 4 brms-2.10.0/brms/man/loo_model_weights.brmsfit.Rd | 4 brms-2.10.0/brms/man/make_stancode.Rd | 23 brms-2.10.0/brms/man/make_standata.Rd | 20 brms-2.10.0/brms/man/model_weights.Rd | 4 brms-2.10.0/brms/man/nsamples.brmsfit.Rd |only brms-2.10.0/brms/man/post_prob.brmsfit.Rd | 4 brms-2.10.0/brms/man/posterior_average.Rd | 4 brms-2.10.0/brms/man/pp_average.Rd | 4 brms-2.10.0/brms/man/reloo.brmsfit.Rd |only brms-2.10.0/brms/man/set_prior.Rd | 13 brms-2.10.0/brms/man/summary.brmsfit.Rd | 9 brms-2.10.0/brms/man/waic.brmsfit.Rd | 4 brms-2.10.0/brms/tests/testthat/tests.brmsfit-helpers.R | 41 brms-2.10.0/brms/tests/testthat/tests.brmsfit-methods.R | 1496 +- brms-2.10.0/brms/tests/testthat/tests.fitted.R | 361 brms-2.10.0/brms/tests/testthat/tests.log_lik.R | 960 - brms-2.10.0/brms/tests/testthat/tests.make_stancode.R | 3608 ++--- brms-2.10.0/brms/tests/testthat/tests.make_standata.R | 1679 +- brms-2.10.0/brms/tests/testthat/tests.predict.R | 748 - brms-2.10.0/brms/tests/testthat/tests.rename_pars.R | 13 brms-2.10.0/brms/vignettes/brms_customfamilies.Rmd | 194 brms-2.10.0/brms/vignettes/brms_distreg.Rmd | 137 brms-2.10.0/brms/vignettes/brms_missings.Rmd | 330 brms-2.10.0/brms/vignettes/brms_monotonic.Rmd | 95 brms-2.10.0/brms/vignettes/brms_multivariate.Rmd | 85 brms-2.10.0/brms/vignettes/brms_nonlinear.Rmd | 141 brms-2.10.0/brms/vignettes/brms_phylogenetics.Rmd | 125 brms-2.9.0/brms/inst/chunks/fun_cholesky_cov_ar1.stan |only brms-2.9.0/brms/inst/chunks/fun_cholesky_cov_arma1.stan |only brms-2.9.0/brms/inst/chunks/fun_cholesky_cov_ma1.stan |only brms-2.9.0/brms/man/nsamples.Rd |only brms-2.9.0/brms/man/reloo.Rd |only 118 files changed, 34471 insertions(+), 31782 deletions(-)
Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework
including a variety of developer convenience functions with the goal of both
streamlining robust application development while assisting with creating a
consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre],
Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer),
Ger Inberg [ctb],
Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>
Diff between periscope versions 0.4.3 dated 2019-07-25 and 0.4.4 dated 2019-08-29
DESCRIPTION | 9 +++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 3 ++- R/downloadableTable.R | 14 +++++++++++--- R/generate_template.R | 7 +++++-- R/periscope.R | 2 ++ inst/doc/downloadFile-module.html | 4 ++-- inst/doc/downloadablePlot-module.html | 4 ++-- inst/doc/downloadableTable-module.html | 4 ++-- inst/doc/new-application.Rmd | 5 +++++ inst/doc/new-application.html | 6 ++++-- man/create_new_application.Rd | 7 +++++-- man/downloadableTable.Rd | 2 +- man/periscope.Rd | 3 +++ vignettes/new-application.Rmd | 5 +++++ 15 files changed, 68 insertions(+), 35 deletions(-)
Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary data.
Author: Kevin R. Coombes, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 0.8.8 dated 2019-08-02 and 0.9.5 dated 2019-08-29
DESCRIPTION | 12 - MD5 | 38 +-- NAMESPACE | 17 - NEWS | 86 +++++++ R/02-binaryMatrix.R | 2 R/04-vis.R | 120 ++++++++++ TODO | 37 +-- inst/doc/mercator.R | 31 -- inst/doc/mercator.Rmd | 35 +- inst/doc/mercator.html | 482 +++++++++++------------------------------ man/Mercator-class.Rd | 46 +++ man/coloring.Rd | 20 - man/downsample.Rd | 8 tests/test-04vis.R | 21 + tests/test-04vis.Rout.save | 28 +- tests/test-05recolor.R | 10 tests/test-05recolor.Rout.save | 19 + tests/test-06names.R | 8 tests/test-06names.Rout.save | 10 vignettes/mercator.Rmd | 35 +- 20 files changed, 530 insertions(+), 535 deletions(-)
Title: Multidimensional Penalized Splines for Survival and Net Survival
Models
Description: Fits hazard and excess hazard models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for
multidimensional penalized hazard and excess hazard models. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics.
See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.
Author: Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 1.1.0 dated 2019-05-02 and 1.2.0 dated 2019-08-29
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Title: R Interface to the 'Yacas' Computer Algebra System
Description: Interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).
Author: Mikkel Meyer Andersen [aut, cre, cph],
Rob Goedman [aut, cph],
Gabor Grothendieck [aut, cph],
Søren Højsgaard [aut, cph],
Grzegorz Mazur [aut, cph],
Ayal Pinkus [aut, cph],
Nemanja Trifunovic [cph] (UTF-8 part of yacas
(src/yacas/include/yacas/utf8*))
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
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Ryacas-1.0.0/Ryacas/src/yacas/src/lisperror.cpp | 6 Ryacas-1.0.0/Ryacas/src/yacas/src/lispeval.cpp | 557 +-- Ryacas-1.0.0/Ryacas/src/yacas/src/lispevalhash.cpp | 129 Ryacas-1.0.0/Ryacas/src/yacas/src/lisphash.cpp | 6 Ryacas-1.0.0/Ryacas/src/yacas/src/lispio.cpp | 2 Ryacas-1.0.0/Ryacas/src/yacas/src/lispobject.cpp | 21 Ryacas-1.0.0/Ryacas/src/yacas/src/lispparser.cpp | 28 Ryacas-1.0.0/Ryacas/src/yacas/src/lispuserfunc.cpp | 28 Ryacas-1.0.0/Ryacas/src/yacas/src/mathcommands.cpp | 1306 ++++----- Ryacas-1.0.0/Ryacas/src/yacas/src/mathcommands2.cpp | 66 Ryacas-1.0.0/Ryacas/src/yacas/src/mathcommands3.cpp | 912 +++--- Ryacas-1.0.0/Ryacas/src/yacas/src/mathuserfunc.cpp | 267 - Ryacas-1.0.0/Ryacas/src/yacas/src/mempool.cpp |only Ryacas-1.0.0/Ryacas/src/yacas/src/nn.cpp |only Ryacas-1.0.0/Ryacas/src/yacas/src/numbers.cpp | 25 Ryacas-1.0.0/Ryacas/src/yacas/src/patcher.cpp | 15 Ryacas-1.0.0/Ryacas/src/yacas/src/patternclass.cpp | 10 Ryacas-1.0.0/Ryacas/src/yacas/src/patterns.cpp | 204 - Ryacas-1.0.0/Ryacas/src/yacas/src/platmath.cpp | 53 Ryacas-1.0.0/Ryacas/src/yacas/src/standard.cpp | 281 -- Ryacas-1.0.0/Ryacas/src/yacas/src/stdfileio.cpp | 60 Ryacas-1.0.0/Ryacas/src/yacas/src/stringio.cpp | 10 Ryacas-1.0.0/Ryacas/src/yacas/src/substitute.cpp | 68 Ryacas-1.0.0/Ryacas/src/yacas/src/tokenizer.cpp | 976 +++--- Ryacas-1.0.0/Ryacas/src/yacas/src/xmltokenizer.cpp | 8 Ryacas-1.0.0/Ryacas/src/yacas/src/yacasapi.cpp | 145 - Ryacas-1.0.0/Ryacas/src/yacas/src/yacasnumbers.cpp | 1402 ++++------ Ryacas-1.0.0/Ryacas/src/yacas/src/zz.cpp |only Ryacas-1.0.0/Ryacas/tests/testthat/test-ryacas-init.R |only Ryacas-1.0.0/Ryacas/tests/testthat/test-smoke.R | 92 Ryacas-1.0.0/Ryacas/tests/testthat/test-symbol.R |only Ryacas-1.0.0/Ryacas/vignettes/arbitrary-precision.Rmd |only Ryacas-1.0.0/Ryacas/vignettes/getting-started.Rmd | 224 + Ryacas-1.0.0/Ryacas/vignettes/high-level.Rmd |only Ryacas-1.0.0/Ryacas/vignettes/latent-variable-model.Rmd | 27 Ryacas-1.0.0/Ryacas/vignettes/low-level.Rmd |only Ryacas-1.0.0/Ryacas/vignettes/ssm-matrix.Rmd | 45 Ryacas-1.0.0/Ryacas/vignettes/yacas-rules.Rmd |only 243 files changed, 7349 insertions(+), 6661 deletions(-)
Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics
and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'RxODE' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Yuan Xiong [aut],
Rik Schoemaker [aut] (<https://orcid.org/0000-0002-7538-3005>),
Justin Wilkins [aut] (<https://orcid.org/0000-0002-7099-9396>),
Mirjam Trame [aut],
Richard Hooijmaijers [aut],
Teun Post [aut],
Robert Leary [ctb],
Wenping Wang [aut, cre],
Hadley Wickham [ctb],
Dirk Eddelbuettel [cph],
Johannes Pfeifer [ctb],
Robert B. Schnabel [ctb],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb],
David Ardia [cph],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Katharine Mullen [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between nlmixr versions 1.1.1-1 dated 2019-08-23 and 1.1.1-2 dated 2019-08-29
nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.cmt-theo_sd-nlme-cfba27fa29748ed9c2461fb17be06e70.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-fo-ef371e68bb35059915ce3fab3344aace.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-foce-6ccf05e12bc4784008625d13075e1874.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-focei-c80161900a3a3ae78b92bdefa30d49d6.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-focei-e6381b7980734c49f1962f0247c64b7c.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-foi-c9375b45b5f04dc4ca848f5fdcc4ca0f.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-nlme-e96375306c0e3aa1f27f5e604454cac0.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-posthoc-85d33d430a7e81ef5bce1221d9496bdf.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-saem-34940a3d459170d6b6c7285d181df2ce.rds |only nlmixr-1.1.1-1/nlmixr/inst/nlmixr-one.compartment-theo_sd-saem-dfc65a1c287e7cd4d1b1f9af89c7fc37.rds |only nlmixr-1.1.1-2/nlmixr/DESCRIPTION | 6 nlmixr-1.1.1-2/nlmixr/MD5 | 46 nlmixr-1.1.1-2/nlmixr/R/RcppExports.R | 8 nlmixr-1.1.1-2/nlmixr/R/foceiFit.R | 2 nlmixr-1.1.1-2/nlmixr/R/saem_fit.R | 143 + nlmixr-1.1.1-2/nlmixr/R/saem_fit_aux.R | 36 nlmixr-1.1.1-2/nlmixr/R/vpc.saemFit.R | 11 nlmixr-1.1.1-2/nlmixr/configure | 4 nlmixr-1.1.1-2/nlmixr/configure.ac | 8 nlmixr-1.1.1-2/nlmixr/inst/doc/running_nlmixr.R | 29 nlmixr-1.1.1-2/nlmixr/inst/doc/running_nlmixr.Rmd | 54 nlmixr-1.1.1-2/nlmixr/inst/doc/running_nlmixr.html | 900 +++++----- nlmixr-1.1.1-2/nlmixr/inst/fit.rds |only nlmixr-1.1.1-2/nlmixr/inst/fit2.rds |only nlmixr-1.1.1-2/nlmixr/inst/fitF.rds |only nlmixr-1.1.1-2/nlmixr/inst/xpdb.rds |binary nlmixr-1.1.1-2/nlmixr/src/Makevars.in | 2 nlmixr-1.1.1-2/nlmixr/src/RcppExports.cpp | 30 nlmixr-1.1.1-2/nlmixr/src/init.c | 5 nlmixr-1.1.1-2/nlmixr/src/saem.cpp |only nlmixr-1.1.1-2/nlmixr/vignettes/running_nlmixr.Rmd | 54 31 files changed, 773 insertions(+), 565 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity.
Author: Kris Boudt [aut, cre],
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [ctb] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Kris Boudt
<Kris.Boudt@econ.kuleuven.be>
Diff between highfrequency versions 0.6.0 dated 2019-08-20 and 0.6.1 dated 2019-08-29
DESCRIPTION | 13 ++-- MD5 | 11 ++- NEWS.md |only R/har_model.R | 2 man/harModel.Rd | 2 tests/testthat/tests_realized_measures.R | 90 +++++++++++++++---------------- tests/testthat/tests_spotvol_and_drift.R | 4 - 7 files changed, 61 insertions(+), 61 deletions(-)
Title: Statistical Tools for Covariance Analysis
Description: Covariance is of universal prevalence across various disciplines within statistics.
We provide a rich collection of geometric and inferential tools for convenient analysis of
covariance structures, topics including distance measures, mean covariance estimator,
covariance hypothesis test for one-sample and two-sample cases, and covariance estimation.
For an introduction to covariance in multivariate statistical analysis,
see Schervish (1987) <doi:10.1214/ss/1177013111>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [ctb],
Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <ksyou496@gmail.com>
Diff between CovTools versions 0.5.1 dated 2019-01-29 and 0.5.2 dated 2019-08-29
DESCRIPTION | 12 MD5 | 28 + NAMESPACE | 4 NEWS.md |only R/CovEst.2003LW.R |only R/CovEst.2010OAS.R |only R/CovEst.2010RBLW.R |only R/RcppExports.R | 12 R/init.R | 6 R/package-CovTools.R | 42 -- README.md | 204 ++++++++++++- build/partial.rdb |binary inst/REFERENCES.bib | 752 +++++++++++++++++++++++++----------------------- man/CovEst.2003LW.Rd |only man/CovEst.2010OAS.Rd |only man/CovEst.2010RBLW.Rd |only man/package-CovTools.Rd | 43 -- src/RcppExports.cpp | 42 ++ src/rcpp_2003LW.cpp |only 19 files changed, 687 insertions(+), 458 deletions(-)
Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.2.3 dated 2019-07-26 and 0.2.5 dated 2019-08-29
DESCRIPTION | 8 MD5 | 37 - NEWS.md | 8 R/msoa_centroids.R | 7 R/uptake.R | 2 build/vignette.rds |binary inst/doc/pct-international.Rmd | 2 inst/doc/pct-international.html | 38 - inst/doc/pct.html | 34 - inst/doc/pct_training.R | 106 ++-- inst/doc/pct_training.Rmd | 169 ++++-- inst/doc/pct_training.html | 162 +++--- inst/pct-wy.R |only inst/pct_training.R |only inst/pct_training_solutions.Rmd |only inst/rmd/pct-slides.Rmd | 144 ++++- inst/rmd/pct-slides.html | 266 ++++++---- man/uptake_pct_govtarget.Rd | 2 vignettes/pct-international.Rmd | 2 vignettes/pct_training.Rmd | 169 ++++-- vignettes/refs_training.bib | 979 +++++++++++++++++++++++++++++++++++++++- 21 files changed, 1668 insertions(+), 467 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.5 dated 2019-07-28 and 0.3.6 dated 2019-08-29
anytime-0.3.5/anytime/inst/tinytest/test_gh_issue_5.R |only anytime-0.3.5/anytime/inst/tinytest/test_gh_issue_84.R |only anytime-0.3.5/anytime/inst/tinytest/test_gh_issue_96.R |only anytime-0.3.5/anytime/inst/tinytest/test_gh_issues_36_51.R |only anytime-0.3.5/anytime/inst/tinytest/test_r_format.R |only anytime-0.3.5/anytime/inst/tinytest/test_validate.R |only anytime-0.3.6/anytime/ChangeLog | 96 + anytime-0.3.6/anytime/DESCRIPTION | 10 anytime-0.3.6/anytime/MD5 | 46 anytime-0.3.6/anytime/NAMESPACE | 27 anytime-0.3.6/anytime/R/RcppExports.R | 4 anytime-0.3.6/anytime/R/anytime.R | 87 anytime-0.3.6/anytime/R/formats.R | 50 anytime-0.3.6/anytime/README.md | 29 anytime-0.3.6/anytime/build/partial.rdb |binary anytime-0.3.6/anytime/inst/NEWS.Rd | 18 anytime-0.3.6/anytime/inst/doc/anytime-introduction.pdf |binary anytime-0.3.6/anytime/inst/tinytest/hide |only anytime-0.3.6/anytime/inst/tinytest/test_all_formats.R | 215 +- anytime-0.3.6/anytime/inst/tinytest/test_bulk.R | 1221 ++++++------- anytime-0.3.6/anytime/inst/tinytest/test_simple.R | 210 +- anytime-0.3.6/anytime/src/RcppExports.cpp | 10 anytime-0.3.6/anytime/src/anytime.cpp | 112 - anytime-0.3.6/anytime/tests/tinytest.R | 15 anytime-0.3.6/anytime/vignettes/anytime-intro.pdf |binary 25 files changed, 1204 insertions(+), 946 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-35 dated 2018-06-05 and 3.1-37 dated 2019-08-29
DESCRIPTION | 8 - MD5 | 37 ++++---- NAMESPACE | 1 NEWS | 46 ++++++++++ R/ae.dotplot7.R | 6 - R/as.likert.R | 3 R/likert.R | 3 R/likert.formula.R | 15 ++- R/panel.interaction2wt.R | 4 R/useOuterScales.R |only build/partial.rdb |binary inst/shiny/PopulationPyramid/DESCRIPTION | 2 man/ae.dotplot.Rd | 3 man/ae.dotplot7.Rd | 3 man/ae.dotplot7a.Rd | 3 man/as.likert.Rd | 1 man/bivariateNormal.Rd | 3 man/hh.Rd | 4 man/likert.Rd | 133 ++++++++++++++++--------------- man/strip.useOuterStrips.first.Rd |only man/useOuterScales.Rd |only 21 files changed, 172 insertions(+), 103 deletions(-)
Title: Structural Data for Norway
Description: Provides structural data for Norway. Datasets relating to maps, population in municipalities, vaccination coverage for childhood vaccines, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2019.
Author: Richard White [aut, cre]
Maintainer: Richard White <w@rwhite.no>
Diff between fhidata versions 2019.6.24 dated 2019-06-24 and 2019.8.27 dated 2019-08-29
DESCRIPTION | 8 ++-- MD5 | 42 ++++++++++++++---------- NEWS.md | 4 ++ R/data_gen_all.r | 8 ++++ R/data_norway_population.r | 33 +++++++++++++------ R/data_norway_thredds.R |only R/days.r |only R/onAttach.R | 2 - build/vignette.rds |binary data/countries_nb_to_en.rda |binary data/datalist | 2 + data/days.rda |only data/norway_childhood_vax.rda |binary data/norway_locations_current.rda |binary data/norway_locations_long_current.rda |binary data/norway_locations_long_original.rda |binary data/norway_locations_original.rda |binary data/norway_municip_merging.rda |binary data/norway_population_current.rda |binary data/norway_population_original.rda |binary data/senorge.rda |only inst/doc/datasets.html | 54 ++++++++++++++++---------------- man/days.Rd |only man/norway_population_current.Rd | 6 +-- man/senorge.Rd |only 25 files changed, 95 insertions(+), 64 deletions(-)
More information about ExtractTrainData at CRAN
Permanent link
Title: Terribly-Simple Data Base for Time Series
Description: A terribly-simple data base for numeric
time series, written purely in R, so no external
database-software is needed. Series are stored in
plain-text files (the most-portable and enduring file
type) in CSV format. Timestamps are encoded using R's
native numeric representation for 'Date'/'POSIXct',
which makes them fast to parse, but keeps them
accessible with other software. The package provides
tools for saving and updating series in this
standardised format, for retrieving and joining data,
for summarising files and directories, and for
coercing series from and to other data types (such as
'zoo' series).
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between tsdb versions 0.7-0 dated 2019-08-27 and 0.7-1 dated 2019-08-29
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 4 ++++ inst/tinytest/test_tsdb.R | 12 ------------ man/read_ts_tables.Rd | 38 +++++++++++++++++++++++++++++--------- 6 files changed, 49 insertions(+), 30 deletions(-)
Title: Testing for Symmetry of Data and Model Residuals
Description: Implementations of a large number of tests for symmetry and their
bootstrap variants, which can be used for testing the symmetry of random
samples around a known or unknown mean. Functions are also there for testing
the symmetry of model residuals around zero. Currently, the supported models
are linear models and generalized autoregressive conditional
heteroskedasticity (GARCH) models (fitted with the 'fGarch' package). All
tests are implemented using the 'Rcpp' package which ensures great
performance of the code.
Author: Blagoje Ivanović [aut, cre]
Bojana Milošević [aut]
Marko Obradović [aut]
Maintainer: Blagoje Ivanović <blagoje_ivanovic@matf.bg.ac.rs>
Diff between symmetry versions 0.1.0 dated 2019-08-27 and 0.1.1 dated 2019-08-29
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- build/partial.rdb |binary src/BHI.cpp | 2 +- src/BHK.cpp | 2 +- src/CM.cpp | 2 +- src/K2.cpp | 1 - src/K2U.cpp | 1 - src/MGG.cpp | 2 +- src/MOI.cpp | 2 +- src/MOK.cpp | 2 +- src/NAI.cpp | 2 +- src/NAK.cpp | 2 +- src/SGN.cpp | 2 +- src/T2.cpp | 2 +- src/WCX.cpp | 5 ++--- src/bootstrap.cpp | 16 ++++++++-------- 17 files changed, 40 insertions(+), 43 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX <https://sdmx.org>) Web Services
(<https://ec.europa.eu/eurostat/web/sdmx-web-services/about-this-service>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Mátyás Mészáros [aut, cre]
Maintainer: Mátyás Mészáros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.2.3 dated 2019-07-23 and 0.3.5 dated 2019-08-29
DESCRIPTION | 10 ++-- MD5 | 58 +++++++++++++------------- NAMESPACE | 1 R/extract_data.R | 5 +- R/extract_dsd.R | 3 - R/extract_toc.R | 3 - R/get_compressed_sdmx.R |only R/get_eurostat_bulk.R | 4 + R/get_eurostat_cache.R | 2 R/get_eurostat_data.R | 16 +++---- R/get_eurostat_dsd.R | 13 ++++- R/get_eurostat_raw.R | 100 ++++++++++++++++----------------------------- R/get_eurostat_toc.R | 36 +++++++++++----- R/load_cfg.R | 22 ++++----- R/put_eurostat_cache.R | 2 R/search_eurostat_dsd.R | 2 R/search_eurostat_toc.R | 2 man/extract_data.Rd | 4 - man/extract_dsd.Rd | 2 man/extract_toc.Rd | 2 man/get_compressed_sdmx.Rd |only man/get_eurostat_bulk.Rd | 2 man/get_eurostat_cache.Rd | 2 man/get_eurostat_data.Rd | 2 man/get_eurostat_dsd.Rd | 2 man/get_eurostat_raw.Rd | 6 +- man/get_eurostat_toc.Rd | 6 +- man/put_eurostat_cache.Rd | 2 man/search_eurostat_dsd.Rd | 2 man/search_eurostat_toc.Rd | 2 tests/testthat/test-all.R | 8 +++ 31 files changed, 165 insertions(+), 156 deletions(-)
Title: A Dynamic Bipartite Latent Space Model to Analyse Irish
Companies' Boards from 2003 to 2013
Description: Provides the dataset and an implementation of the method illustrated in Friel, N., Rastelli, R., Wyse, J. and Raftery, A.E. (2016) <DOI:10.1073/pnas.1606295113>.
Author: Riccardo Rastelli [aut, cre]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between IrishDirectorates versions 0.2.0 dated 2017-08-02 and 1.4 dated 2019-08-29
IrishDirectorates-0.2.0/IrishDirectorates/data/IrishDirectorates.RData |only IrishDirectorates-0.2.0/IrishDirectorates/man/IrishDirectorates.Rd |only IrishDirectorates-1.4/IrishDirectorates/DESCRIPTION | 22 ++++---- IrishDirectorates-1.4/IrishDirectorates/MD5 | 27 ++++++++-- IrishDirectorates-1.4/IrishDirectorates/NAMESPACE | 5 + IrishDirectorates-1.4/IrishDirectorates/R |only IrishDirectorates-1.4/IrishDirectorates/build |only IrishDirectorates-1.4/IrishDirectorates/data/IrishDirectoratesData.RData |only IrishDirectorates-1.4/IrishDirectorates/data/IrishDirectoratesFit.RData |only IrishDirectorates-1.4/IrishDirectorates/man/IrishDirectorates-package.Rd |only IrishDirectorates-1.4/IrishDirectorates/man/IrishDirectoratesData.Rd |only IrishDirectorates-1.4/IrishDirectorates/man/IrishDirectoratesFit.Rd |only IrishDirectorates-1.4/IrishDirectorates/man/dblpm_mcmc.Rd |only IrishDirectorates-1.4/IrishDirectorates/man/dblpm_posterior.Rd |only IrishDirectorates-1.4/IrishDirectorates/src |only 15 files changed, 40 insertions(+), 14 deletions(-)
More information about IrishDirectorates at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-28 0.1.0
Title: Reproducible Reports in Psychology
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Knitr'/'Latex' integration within *.Rnw files.
Author: Ian G Mackenzie
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Diff between psychReport versions 0.4 dated 2018-10-29 and 0.7 dated 2019-08-29
psychReport-0.4/psychReport/inst |only psychReport-0.7/psychReport/DESCRIPTION | 12 - psychReport-0.7/psychReport/MD5 | 80 ++++------ psychReport-0.7/psychReport/R/aovDispMeans.R | 20 +- psychReport-0.7/psychReport/R/aovDispTable.R | 10 - psychReport-0.7/psychReport/R/aovEffectSize.R | 9 - psychReport-0.7/psychReport/R/aovTable.R | 16 +- psychReport-0.7/psychReport/R/ciStrT.R | 2 psychReport-0.7/psychReport/R/effectsizeValueString.R | 11 - psychReport-0.7/psychReport/R/fValueString.R | 2 psychReport-0.7/psychReport/R/mathString.R | 2 psychReport-0.7/psychReport/R/numValueString.R | 4 psychReport-0.7/psychReport/R/pValueString.R | 6 psychReport-0.7/psychReport/R/printAovMeans.R | 9 - psychReport-0.7/psychReport/R/printTable.R | 26 ++- psychReport-0.7/psychReport/R/requiredPackages.R | 29 ++- psychReport-0.7/psychReport/R/sphericityValueString.R | 2 psychReport-0.7/psychReport/R/tValueString.R | 2 psychReport-0.7/psychReport/README.md | 2 psychReport-0.7/psychReport/man/aovDispMeans.Rd | 4 psychReport-0.7/psychReport/man/aovDispTable.Rd | 4 psychReport-0.7/psychReport/man/aovEffectSize.Rd | 3 psychReport-0.7/psychReport/man/aovTable.Rd | 4 psychReport-0.7/psychReport/man/effectsizeValueString.Rd | 3 psychReport-0.7/psychReport/man/printAovMeans.Rd | 2 psychReport-0.7/psychReport/man/printTable.Rd | 3 psychReport-0.7/psychReport/man/requiredPackages.Rd | 10 - psychReport-0.7/psychReport/tests/testthat/test-aovEffectSize.R | 9 - psychReport-0.7/psychReport/tests/testthat/test-aovTable.R | 1 psychReport-0.7/psychReport/tests/testthat/test-ciStrT.R | 6 psychReport-0.7/psychReport/tests/testthat/test-effectsizeValueString.R | 12 - psychReport-0.7/psychReport/tests/testthat/test-fValueString.R | 6 psychReport-0.7/psychReport/tests/testthat/test-mathString.R | 4 psychReport-0.7/psychReport/tests/testthat/test-meanStrAov.R | 2 psychReport-0.7/psychReport/tests/testthat/test-meanStrT.R | 2 psychReport-0.7/psychReport/tests/testthat/test-numValueString.R | 4 psychReport-0.7/psychReport/tests/testthat/test-printAovMeans.R | 6 psychReport-0.7/psychReport/tests/testthat/test-sphericityValueString.R | 4 psychReport-0.7/psychReport/tests/testthat/test-statStrAov.R | 8 - psychReport-0.7/psychReport/tests/testthat/test-statStrT.R | 2 psychReport-0.7/psychReport/tests/testthat/test-tValueString.R | 4 41 files changed, 181 insertions(+), 166 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation (ODE) models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
VODE and LSODA are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Melissa Hallow [aut],
Wenping Wang [aut, cre],
Zufar Mulyukov [ctb],
Justin Wilkins [ctb] (<https://orcid.org/0000-0002-7099-9396>),
Simon Frost [ctb],
Heng Li [ctb],
Yu Feng [ctb],
Alan Hindmarsh [ctb],
Linda Petzold [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
J Colinge [ctb],
Hadley Wickham [ctb],
G Grothendieck [ctb],
Robert Gentleman [ctb],
Ross Ihaka [ctb],
R core team [cph],
odepack authors [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between RxODE versions 0.9.1-3 dated 2019-08-06 and 0.9.1-4 dated 2019-08-29
DESCRIPTION | 11 MD5 | 67 - NAMESPACE | 1 R/RcppExports.R | 102 +- R/RxODE.R | 39 + R/et.R | 3 R/rxsolve.R | 2 configure.win | 2 inst/doc/RxODE-cmt.html | 12 inst/doc/RxODE-covariates.html | 4 inst/doc/RxODE-data-frame.html | 4 inst/doc/RxODE-events.Rmd | 46 - inst/doc/RxODE-events.html | 34 inst/doc/RxODE-intro.html | 4 inst/doc/RxODE-model-types.html | 8 inst/doc/RxODE-shiny.html | 4 inst/doc/RxODE-stiff.html | 4 inst/doc/RxODE-syntax.html | 4 inst/doc/RxODE-transit-compartments.html | 4 inst/include/RxODE_RcppExports.h | 44 - man/rxDynProtect.Rd |only src/Makevars.in | 4 src/RcppExports.cpp | 106 -- src/cvPost.cpp |only src/et.cpp | 143 +++ src/etTran.cpp | 68 + src/lincmt.c | 52 - src/par_solve.c | 42 - src/rxData.cpp | 1168 ++++++++++++++----------------- tests/testthat/test-cov.R | 50 + tests/testthat/test-deSolve-events.R |only tests/testthat/test-gc.R | 53 + tests/testthat/test-issue-56.R | 1 tests/testthat/test-omega-chol.R | 2 tests/testthat/test-rxIs.R | 2 vignettes/RxODE-events.Rmd | 46 - 36 files changed, 1169 insertions(+), 967 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 6.500 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.1.15.0.1 dated 2019-05-20 and 0.1.16.0.1 dated 2019-08-29
ChangeLog | 12 DESCRIPTION | 6 MD5 | 154 +++++----- NEWS.md | 11 inst/include/ensmallen.hpp | 1 inst/include/ensmallen_bits/ada_delta/ada_delta.hpp | 10 inst/include/ensmallen_bits/ada_delta/ada_delta_impl.hpp | 6 inst/include/ensmallen_bits/ada_grad/ada_grad.hpp | 10 inst/include/ensmallen_bits/ada_grad/ada_grad_impl.hpp | 6 inst/include/ensmallen_bits/adam/adam.hpp | 10 inst/include/ensmallen_bits/adam/adam_impl.hpp | 6 inst/include/ensmallen_bits/bigbatch_sgd/adaptive_stepsize.hpp | 19 - inst/include/ensmallen_bits/bigbatch_sgd/bigbatch_sgd.hpp | 13 inst/include/ensmallen_bits/bigbatch_sgd/bigbatch_sgd_impl.hpp | 17 - inst/include/ensmallen_bits/ens_version.hpp | 4 inst/include/ensmallen_bits/eve/eve.hpp | 13 inst/include/ensmallen_bits/eve/eve_impl.hpp | 19 - inst/include/ensmallen_bits/ftml/ftml.hpp | 10 inst/include/ensmallen_bits/ftml/ftml_impl.hpp | 6 inst/include/ensmallen_bits/fw/proximal/proximal_impl.hpp | 2 inst/include/ensmallen_bits/katyusha/katyusha.hpp | 13 inst/include/ensmallen_bits/katyusha/katyusha_impl.hpp | 19 - inst/include/ensmallen_bits/padam/padam.hpp | 13 inst/include/ensmallen_bits/problems/ackley_function.hpp |only inst/include/ensmallen_bits/problems/ackley_function_impl.hpp |only inst/include/ensmallen_bits/problems/beale_function.hpp |only inst/include/ensmallen_bits/problems/beale_function_impl.hpp |only inst/include/ensmallen_bits/problems/booth_function.hpp | 14 inst/include/ensmallen_bits/problems/bukin_function.hpp | 16 - inst/include/ensmallen_bits/problems/colville_function.hpp | 14 inst/include/ensmallen_bits/problems/cross_in_tray_function.hpp |only inst/include/ensmallen_bits/problems/cross_in_tray_function_impl.hpp |only inst/include/ensmallen_bits/problems/drop_wave_function.hpp | 14 inst/include/ensmallen_bits/problems/easom_function.hpp | 14 inst/include/ensmallen_bits/problems/eggholder_function.hpp | 14 inst/include/ensmallen_bits/problems/fw_test_function.hpp | 3 inst/include/ensmallen_bits/problems/generalized_rosenbrock_function.hpp | 18 - inst/include/ensmallen_bits/problems/goldstein_price_function.hpp |only inst/include/ensmallen_bits/problems/goldstein_price_function_impl.hpp |only inst/include/ensmallen_bits/problems/himmelblau_function.hpp |only inst/include/ensmallen_bits/problems/himmelblau_function_impl.hpp |only inst/include/ensmallen_bits/problems/holder_table_function.hpp |only inst/include/ensmallen_bits/problems/holder_table_function_impl.hpp |only inst/include/ensmallen_bits/problems/levy_function_n13.hpp |only inst/include/ensmallen_bits/problems/levy_function_n13_impl.hpp |only inst/include/ensmallen_bits/problems/logistic_regression_function.hpp | 4 inst/include/ensmallen_bits/problems/matyas_function.hpp | 14 inst/include/ensmallen_bits/problems/matyas_function_impl.hpp | 2 inst/include/ensmallen_bits/problems/mc_cormick_function.hpp | 14 inst/include/ensmallen_bits/problems/problems.hpp | 10 inst/include/ensmallen_bits/problems/rastrigin_function.hpp | 16 - inst/include/ensmallen_bits/problems/rosenbrock_function.hpp | 14 inst/include/ensmallen_bits/problems/rosenbrock_wood_function.hpp | 14 inst/include/ensmallen_bits/problems/schaffer_function_n2.hpp |only inst/include/ensmallen_bits/problems/schaffer_function_n2_impl.hpp |only inst/include/ensmallen_bits/problems/schaffer_function_n4.hpp |only inst/include/ensmallen_bits/problems/schaffer_function_n4_impl.hpp |only inst/include/ensmallen_bits/problems/schwefel_function.hpp | 14 inst/include/ensmallen_bits/problems/sgd_test_function.hpp | 5 inst/include/ensmallen_bits/problems/sphere_function.hpp | 14 inst/include/ensmallen_bits/problems/styblinski_tang_function.hpp | 14 inst/include/ensmallen_bits/problems/three_hump_camel_function.hpp |only inst/include/ensmallen_bits/problems/three_hump_camel_function_impl.hpp |only inst/include/ensmallen_bits/problems/wood_function.hpp | 14 inst/include/ensmallen_bits/pso |only inst/include/ensmallen_bits/qhadam/qhadam.hpp | 10 inst/include/ensmallen_bits/qhadam/qhadam_impl.hpp | 6 inst/include/ensmallen_bits/qhadam/qhadam_update.hpp | 22 - inst/include/ensmallen_bits/rmsprop/rmsprop.hpp | 13 inst/include/ensmallen_bits/sarah/sarah.hpp | 13 inst/include/ensmallen_bits/sarah/sarah_impl.hpp | 17 - inst/include/ensmallen_bits/sgd/sgd.hpp | 13 inst/include/ensmallen_bits/sgd/sgd_impl.hpp | 17 - inst/include/ensmallen_bits/sgdr/sgdr.hpp | 10 inst/include/ensmallen_bits/sgdr/sgdr_impl.hpp | 6 inst/include/ensmallen_bits/sgdr/snapshot_sgdr.hpp | 13 inst/include/ensmallen_bits/sgdr/snapshot_sgdr_impl.hpp | 18 - inst/include/ensmallen_bits/smorms3/smorms3.hpp | 10 inst/include/ensmallen_bits/smorms3/smorms3_impl.hpp | 6 inst/include/ensmallen_bits/spalera_sgd/spalera_sgd.hpp | 13 inst/include/ensmallen_bits/spalera_sgd/spalera_sgd_impl.hpp | 17 - inst/include/ensmallen_bits/svrg/svrg.hpp | 13 inst/include/ensmallen_bits/svrg/svrg_impl.hpp | 17 - inst/include/ensmallen_bits/swats/swats.hpp | 10 inst/include/ensmallen_bits/swats/swats_impl.hpp | 6 inst/include/ensmallen_bits/wn_grad/wn_grad.hpp | 10 inst/include/ensmallen_bits/wn_grad/wn_grad_impl.hpp | 6 87 files changed, 601 insertions(+), 301 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre],
Tao Yang [aut],
Zonglin He [aut],
Adam Elder [aut],
Hyunju Son [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2019.3-12 dated 2019-03-13 and 2019.8-28 dated 2019-08-29
chngpt-2019.3-12/chngpt/src/fastgrid_binomial.cpp |only chngpt-2019.3-12/chngpt/src/fastgrid_binomial_wrapper.cpp |only chngpt-2019.8-28/chngpt/ChangeLog | 101 chngpt-2019.8-28/chngpt/DESCRIPTION | 16 chngpt-2019.8-28/chngpt/MD5 | 40 chngpt-2019.8-28/chngpt/NAMESPACE | 5 chngpt-2019.8-28/chngpt/R/chngpt.test.R | 12 chngpt-2019.8-28/chngpt/R/chngptm.R | 1026 +++++----- chngpt-2019.8-28/chngpt/R/sim.chngpt.R | 10 chngpt-2019.8-28/chngpt/build/vignette.rds |binary chngpt-2019.8-28/chngpt/inst/doc/chngpt-vignette.pdf |binary chngpt-2019.8-28/chngpt/inst/unitTests/runit.chngpt.test.R | 24 chngpt-2019.8-28/chngpt/inst/unitTests/runit.chngptm.linear.R | 28 chngpt-2019.8-28/chngpt/inst/unitTests/runit.chngptm.logistic.R | 31 chngpt-2019.8-28/chngpt/man/chngptm.Rd | 54 chngpt-2019.8-28/chngpt/man/sim.chngpt.Rd | 4 chngpt-2019.8-28/chngpt/src/Makevars | 1 chngpt-2019.8-28/chngpt/src/Makevars.win | 1 chngpt-2019.8-28/chngpt/src/fastgrid.cc | 7 chngpt-2019.8-28/chngpt/src/fastgrid2.cc | 458 +++- chngpt-2019.8-28/chngpt/src/grid.cc | 8 chngpt-2019.8-28/chngpt/src/smath.h | 5 22 files changed, 1186 insertions(+), 645 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides
C implementations of the association mining algorithms Apriori and Eclat.
See Christian Borgelt (2012) <doi:10.1002/widm.1074>.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Ian Johnson [ctb, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.6-3 dated 2019-03-07 and 1.6-4 dated 2019-08-29
DESCRIPTION | 11 ++++++----- MD5 | 31 ++++++++++++++++--------------- NEWS.md | 6 ++++++ R/apriori.R | 2 +- R/eclat.R | 2 +- R/interestMeasures.R | 4 ++-- R/is.closed.R | 37 ++++++++++++++----------------------- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/arules.pdf |binary man/APappearance-class.Rd | 2 +- man/AScontrol-class.Rd | 2 +- man/ASparameter-class.Rd | 2 +- man/apriori.Rd | 6 +++++- man/interestMeasure.Rd | 2 +- man/transactions-class.Rd | 9 +++++---- 17 files changed, 61 insertions(+), 57 deletions(-)