Title: Inverse Probability of Censoring Weights to Deal with Treatment
Switch in Randomized Clinical Trials
Description: Contains functions for formatting clinical trials data and implementing inverse probability of censoring weights to handle treatment switches when estimating causal treatment effect in randomized clinical trials.
Author: Nathalie Graffeo [aut, cre],
Aurelien Latouche [aut],
Sylvie Chevret [aut]
Maintainer: Nathalie Graffeo <nathalie.graffeo@univ-amu.fr>
Diff between ipcwswitch versions 1.0.2 dated 2019-02-16 and 1.0.3 dated 2019-05-15
DESCRIPTION | 6 - MD5 | 14 +-- R/ipcw.R | 233 ++++++++++++++++++++++++++++++++++++------------------ R/replicRows.R | 135 ++++++++++++++++++++++--------- inst/news.Rd | 7 + man/SHIdat.Rd | 36 +++++--- man/ipcw.Rd | 14 ++- man/replicRows.Rd | 30 ++++-- 8 files changed, 327 insertions(+), 148 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008> and Phillips et al. (2019) <doi:10.1002/ece3.4757>.
Author: Jarrett D. Phillips [aut, cre], Steven H. French [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.0 dated 2019-05-09 and 1.0.1 dated 2019-05-15
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/HAC.sim.R | 2 +- R/zzz.R | 4 ++-- build/partial.rdb |binary man/HAC.simrep.Rd | 16 ++++++++++++---- man/HACClass.Rd | 2 +- man/HACHypothetical.Rd | 6 +++--- man/HACReal.Rd | 6 +++--- man/HACSim-package.Rd | 2 +- man/envr.Rd | 37 +++++++++++++++++++++++++++++++++++-- 11 files changed, 73 insertions(+), 32 deletions(-)
Title: Sacramento and San Joaquin Valley Water Year Types
Description: Provides Water Year Hydrologic Classification Indices based on measured
unimpaired runoff (in million acre-feet). Data is provided by California Department of Water Resources
and subject to revision.
Author: Sadie Gill [cre, aut]
Maintainer: Sadie Gill <sgill@flowwest.com>
Diff between waterYearType versions 1.0.0 dated 2019-03-31 and 1.0.1 dated 2019-05-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- data/water_year_indices.rda |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Simultaneous Generation of Count and Continuous Data
Description: Generation of count (assuming Poisson distribution) and continuous data (using Fleishman polynomials) simultaneously.
Author: Hakan Demirtas, Yaru Shi, Rawan Allozi, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between PoisNonNor versions 1.6 dated 2019-02-28 and 1.6.1 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/PoisNonNor-package.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Data Generation with Poisson, Binary, Ordinal and Normal
Components
Description: Generation of multiple count, binary, ordinal and normal variables simultaneously given the marginal characteristics and association structure.
Author: Hakan Demirtas, Yiran Hu, Rawan Allozi, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between PoisBinOrdNor versions 1.6 dated 2019-02-28 and 1.6.1 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/PoisBinOrdNor-package.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Data Generation with Poisson, Binary and Ordinal Components
Description: Generation of multiple count, binary and ordinal variables simultaneously
given the marginal characteristics and association structure. Throughout the package,
the word 'Poisson' is used to imply count data under the assumption of Poisson distribution.
Author: Gul Inan, Hakan Demirtas, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between PoisBinOrd versions 1.4 dated 2019-03-05 and 1.4.1 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/PoisBinOrd-package.Rd | 8 ++++---- man/intermediate.corr.BO.Rd | 6 +++--- 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Non-Linear Model Fitting of Time Distribution of Biological
Phenomena
Description: Fit biologically meaningful distribution functions to
time-sequence data (phenology), estimate parameters to draw the cumulative
distribution function and probability density function and calculate standard
statistical moments and percentiles.
Author: Nathan Eastwood [cre, prg, trl],
Miguel Franco [aut],
Paul Ramsay [aut],
Nicola Steer [aut]
Maintainer: Nathan Eastwood <nathan.eastwood@icloud.com>
Diff between nlstimedist versions 1.1.3 dated 2018-10-28 and 1.1.4 dated 2019-05-15
DESCRIPTION | 25 +++++++++++++------------ MD5 | 6 +++--- NEWS.md | 5 ++--- inst/doc/nlstimedist.html | 7 +++++-- 4 files changed, 23 insertions(+), 20 deletions(-)
Title: Electrochemical Reactions Simulation
Description: Digital simulation of electrochemical processes.
Each function allows for implicit and explicit solution of the differential equation using methods like Euler, Backwards implicit, Runge Kutta 4, Crank Nicholson and Backward differentiation formula as well as different number of points for derivative approximation. Several electrochemical processes can be simulated such as: Chronoamperometry, Potential Step, Linear Sweep, Cyclic Voltammetry, Cyclic Voltammetry with electrochemical reaction followed by chemical reaction (EC mechanism) and CV with two following electrochemical reaction (EE mechanism). In update 1.1.0 has been added a general purpose CV function that allow to simulate up to 4 EE mechanism combined with chemical reaction for each species.
Bibliography regarding this methods can be found in the following texts.
Dieter Britz, Jorg Strutwolf (2016) <ISBN:978-3-319-30292-8>.
Allen J. Bard, Larry R. Faulkner (2000) <ISBN:978-0-471-04372-0>.
Author: Federico Maria Vivaldi [aut, cre]
Maintainer: Federico Maria Vivaldi <federico-vivaldi@virgilio.it>
Diff between EleChemr versions 1.0.0 dated 2019-04-14 and 1.1.0 dated 2019-05-15
DESCRIPTION | 16 MD5 | 20 NAMESPACE | 2 R/Derivative.R | 261 ++++++ R/EleChemr.R | 2322 ++++++++++++++++++++++++++++++++++++--------------------- man/CV.Rd | 2 man/CVEC.Rd | 4 man/CVEE.Rd | 4 man/Gen_CV.Rd |only man/LinSwp.Rd | 2 man/ParCall.Rd |only man/PotStep.Rd | 4 12 files changed, 1789 insertions(+), 848 deletions(-)
Title: Display Information About Nested Subsets of a Data Frame
Description: A tool for calculating and drawing "variable trees". Variable trees display information about hierarchical subsets of a data frame defined by values of categorical variables.
Author: Nick Barrowman
Maintainer: Nick Barrowman <nbarrowman@cheo.on.ca>
Diff between vtree versions 1.0.0 dated 2019-01-07 and 2.0.0 dated 2019-05-15
vtree-1.0.0/vtree/README.md |only vtree-1.0.0/vtree/tests/testthat/testthat.R |only vtree-1.0.0/vtree/vignettes/Thumbs.db |only vtree-2.0.0/vtree/DESCRIPTION | 10 vtree-2.0.0/vtree/MD5 | 28 vtree-2.0.0/vtree/NAMESPACE | 1 vtree-2.0.0/vtree/NEWS.md | 54 vtree-2.0.0/vtree/R/vtree.R | 4152 ++++++++++++++------------ vtree-2.0.0/vtree/build/vignette.rds |binary vtree-2.0.0/vtree/inst/doc/vtree.R | 388 +- vtree-2.0.0/vtree/inst/doc/vtree.Rmd | 1088 +++++- vtree-2.0.0/vtree/inst/doc/vtree.html | 945 +++-- vtree-2.0.0/vtree/man/crosstabToCases.Rd |only vtree-2.0.0/vtree/man/vtree.Rd | 199 - vtree-2.0.0/vtree/tests/testthat.R |only vtree-2.0.0/vtree/tests/testthat/test-vtree.R |only vtree-2.0.0/vtree/vignettes/vtree.Rmd | 1088 +++++- vtree-2.0.0/vtree/vignettes/vtreeVignette.css | 410 +- 18 files changed, 5240 insertions(+), 3123 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework (Albert Bifet, Geoff Holmes, Richard Kirkby, Bernhard Pfahringer (2010). MOA: Massive Online Analysis, Journal of Machine Learning Research 11: 1601-1604).
Author: Michael Hahsler [aut, cre, cph],
John Forrest [aut, cph],
Matthew Bolanos [ctb],
Matthias Carnein [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.2-1 dated 2019-03-20 and 1.2-2 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/streamMOA.pdf |binary inst/java/StreamMOA.jar |binary inst/java/moa.jar |binary java/Makefile | 4 ++-- 8 files changed, 18 insertions(+), 13 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to
make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 0.3.3 dated 2019-04-11 and 0.3.4 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/parse.R | 14 ++------------ R/selectors.R | 2 +- inst/doc/selectorgadget.html | 4 ++-- man/html.Rd | 3 --- man/html_nodes.Rd | 2 +- 9 files changed, 22 insertions(+), 32 deletions(-)
Title: Multilevel Exponential-Family Random Graph Models
Description: Estimates exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. The scope, at present, covers multilevel models where the set of nodes is nested within known blocks. The estimation method uses Monte-Carlo maximum likelihood estimation (MCMLE) methods to estimate a variety of canonical or curved exponential family models for binary random graphs. MCMLE methods for curved exponential-family random graph models can be found in Hunter and Handcock (2006) <DOI: 10.1198/106186006X133069>. The package supports parallel computing, and provides methods for assessing goodness-of-fit of models and visualization of networks.
Author: Jonathan Stewart [cre, aut],
Michael Schweinberger [ctb]
Maintainer: Jonathan Stewart <jonathan.stewart@rice.edu>
Diff between mlergm versions 0.1 dated 2018-12-03 and 0.2 dated 2019-05-15
DESCRIPTION | 13 +- MD5 | 46 ++++---- R/MCMC_sample.R | 8 - R/MCMLE.R | 8 + R/compute_initial_estimate.R | 3 R/data.R | 7 - R/gof.mlergm.R | 8 - R/helper_functions.R | 220 +++++++++++++++++++++--------------------- R/mlergm.R | 19 +++ R/mlnet.R | 2 R/plot.gof_mlergm.R | 15 +- R/plot.mlnet.R | 2 R/print.gof_mlergm.R | 3 R/print.mlergm.R | 2 R/simulate_mlnet.R | 29 +++-- R/summary.mlergm.R | 10 - build/vignette.rds |binary inst/doc/mlergm_tutorial.Rmd | 56 +++++++--- inst/doc/mlergm_tutorial.html | 79 +++++++++------ man/classes.Rd | 6 - man/mlergm.Rd | 13 ++ man/simulate_mlnet.Rd | 15 +- vignettes/mlergm_tutorial.Rmd | 56 +++++++--- vignettes/vig_data.rda |binary 24 files changed, 363 insertions(+), 257 deletions(-)
Title: Mapping Markers to the Nearest Genomic Feature
Description: Allows the user to generate a list of features (gene, pseudo, RNA,
CDS, and/or UTR) directly from NCBI database for any species with a current
build available. Option to save downloaded and formatted files is available,
and the user can prioritize the feature list based on type and assembly builds
present in the current build used. The user can then use the list of features
generated or provide a list to map a set of markers (designed for SNP markers
with a single base pair position available) to the closest feature based on
the map build. This function does require map positions of the markers to be
provided and the positions should be based on the build being queried through
NCBI.
Author: Lauren L. Hulsman Hanna and David G. Riley
Maintainer: Lauren Hanna <Lauren.Hanna@ndsu.edu>
Diff between Map2NCBI versions 1.2 dated 2019-04-17 and 1.3 dated 2019-05-15
DESCRIPTION | 8 - MD5 | 20 ++-- NAMESPACE | 2 R/GetGeneList.R | 5 - R/GetGeneList_v11.R |only R/MapMarkers.R | 206 ++++++++++++--------------------------------- man/Example10MarkerFile.Rd | 4 man/GeneList_BTA1.Rd | 2 man/GetGeneList.Rd | 27 +++-- man/GetGeneList_v11.Rd |only man/Map2NCBI-package.Rd | 17 +-- man/MapMarkers.Rd | 40 ++++---- 12 files changed, 123 insertions(+), 208 deletions(-)
Title: Bayesian Estimation of the Evolutionary Rate Matrix
Description: Estimates the evolutionary rate matrix (R) using Markov chain Monte Carlo (MCMC) as described in Caetano and Harmon (2017) <doi:10.1111/2041-210X.12826>. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
Author: Daniel Caetano [aut, cre],
Luke Harmon [aut]
Maintainer: Daniel Caetano <caetanods1@gmail.com>
Diff between ratematrix versions 1.2 dated 2019-05-06 and 1.2.1 dated 2019-05-15
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- R/continueMCMC.R | 2 - R/plotRatematrix.R | 35 +++++++++++++++++++++++++++---- R/ratematrixMCMC.R | 2 - README.md | 8 ++----- inst/doc/Making_prior_on_ratematrix.html | 20 ++++++++--------- inst/doc/Set_custom_starting_point.html | 32 ++++++++++++++-------------- src/MultRegimeMCMC.cpp | 2 - 9 files changed, 74 insertions(+), 49 deletions(-)
Title: Read 'IPUMS' Extract Files
Description: An easy way to import census, survey and geographic data provided by 'IPUMS'
into R plus tools to help use the associated metadata to make analysis easier. 'IPUMS'
data describing 1.4 billion individuals drawn from over 750 censuses and surveys is
available free of charge from our website <https://ipums.org>.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Minnesota Population Center [cph]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between ipumsr versions 0.4.0 dated 2019-03-08 and 0.4.1 dated 2019-05-15
DESCRIPTION | 20 MD5 | 85 - NAMESPACE | 5 NEWS.md | 5 R/ddi_print.r | 52 R/ddi_read.r | 120 + R/examples.r | 70 - R/import.r | 212 +-- R/lbl_pillar.r | 291 +++- R/micro_read_helpers.r | 18 R/nhgis_read.r | 514 ++++---- R/proj_config.r | 204 +-- R/shape_join.r | 688 +++++------ R/shape_read.r | 12 R/terra_read.r | 778 ++++++------ R/utils.r | 128 +- R/viewer.r | 4 R/web_url.r | 280 ++-- README.md | 43 build/vignette.rds |binary inst/WORDLIST | 224 +-- inst/doc/ipums-bigdata.html | 951 +++++++++------ inst/doc/ipums-cps.html | 714 +++++++---- inst/doc/ipums-geography.html | 719 +++++++---- inst/doc/ipums-nhgis.html | 674 +++++++---- inst/doc/ipums-terra.Rmd | 636 +++++----- inst/doc/ipums-terra.html | 554 ++++++--- inst/doc/ipums.html | 728 +++++++---- inst/doc/value-labels.html | 857 ++++++++------ inst/extdata/cps_00006.xml | 1100 ++++++++--------- inst/extdata/cps_00010.xml | 1142 +++++++++--------- inst/extdata/cps_00015.xml | 2384 +++++++++++++++++++-------------------- man/ipumsr-package.Rd | 8 tests/testthat.R | 8 tests/testthat/test_fostr.R |only tests/testthat/test_ipums_info.r | 84 - tests/testthat/test_lbls.r | 452 +++---- tests/testthat/test_list_files.r | 260 ++-- tests/testthat/test_micro.r | 32 tests/testthat/test_nhgis.r | 336 ++--- tests/testthat/test_shape_join.r | 224 +-- tests/testthat/test_terra.r | 2 tools/spellcheck.r | 2 vignettes/ipums-terra.Rmd | 636 +++++----- 44 files changed, 9089 insertions(+), 7167 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Tools for analyzing and visualizing circular data,
including scoring functions for relevant instruments and a
generalization of the bootstrapped structural summary method from
Zimmermann & Wright (2017) <doi:10.1177/1073191115621795> and
functions for creating publication-ready tables and figures from the
results. Future versions will include tools for circular fit and
reliability analyses, as well as visualization enhancements.
Author: Jeffrey Girard [aut, cre] (<https://orcid.org/0000-0002-7359-3746>),
Johannes Zimmermann [aut] (<https://orcid.org/0000-0001-6975-2356>),
Aidan Wright [aut] (<https://orcid.org/0000-0002-2369-0601>)
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 0.3.0 dated 2019-04-26 and 0.3.1 dated 2019-05-15
DESCRIPTION | 6 MD5 | 18 NEWS.md | 8 R/ssm_bootstrap.R | 2 README.md | 16 build/vignette.rds |binary inst/doc/intermediate-ssm-analysis.html | 808 +++++++++++++++++---------- inst/doc/introduction-to-ssm-analysis.html | 534 ++++++++++++------ inst/doc/using-instruments.html | 852 ++++++++++++++++++----------- man/figures/README-plot-1.png |binary 10 files changed, 1446 insertions(+), 798 deletions(-)
Title: Simulate Genotypes from the BN-PSD Admixture Model
Description: The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>),
John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between bnpsd versions 1.0.4 dated 2019-02-12 and 1.1.1 dated 2019-05-15
bnpsd-1.0.4/bnpsd/R/biasCoeff.R |only bnpsd-1.0.4/bnpsd/R/biasCoeffSolveParam.R |only bnpsd-1.0.4/bnpsd/R/coanc.R |only bnpsd-1.0.4/bnpsd/R/fst.R |only bnpsd-1.0.4/bnpsd/R/q1d.R |only bnpsd-1.0.4/bnpsd/R/q1dc.R |only bnpsd-1.0.4/bnpsd/R/qis.R |only bnpsd-1.0.4/bnpsd/R/rbnpsd.R |only bnpsd-1.0.4/bnpsd/R/rescaleF.R |only bnpsd-1.0.4/bnpsd/R/rgeno.R |only bnpsd-1.0.4/bnpsd/R/rpanc.R |only bnpsd-1.0.4/bnpsd/R/rpiaf.R |only bnpsd-1.0.4/bnpsd/R/rpint.R |only bnpsd-1.0.4/bnpsd/inst/doc/bnpsd.pdf |only bnpsd-1.0.4/bnpsd/man/coanc.Rd |only bnpsd-1.0.4/bnpsd/man/fst.Rd |only bnpsd-1.0.4/bnpsd/man/q1d.Rd |only bnpsd-1.0.4/bnpsd/man/q1dc.Rd |only bnpsd-1.0.4/bnpsd/man/qis.Rd |only bnpsd-1.0.4/bnpsd/man/rbnpsd.Rd |only bnpsd-1.0.4/bnpsd/man/rgeno.Rd |only bnpsd-1.0.4/bnpsd/man/rpanc.Rd |only bnpsd-1.0.4/bnpsd/man/rpiaf.Rd |only bnpsd-1.0.4/bnpsd/man/rpint.Rd |only bnpsd-1.1.1/bnpsd/DESCRIPTION | 26 bnpsd-1.1.1/bnpsd/MD5 | 87 + bnpsd-1.1.1/bnpsd/NAMESPACE | 11 bnpsd-1.1.1/bnpsd/NEWS.md | 55 + bnpsd-1.1.1/bnpsd/R/admix_prop_1d_circular.R |only bnpsd-1.1.1/bnpsd/R/admix_prop_1d_linear.R |only bnpsd-1.1.1/bnpsd/R/admix_prop_indep_subpops.R |only bnpsd-1.1.1/bnpsd/R/bias_coeff_admix.R |only bnpsd-1.1.1/bnpsd/R/bias_coeff_admix_fit.R |only bnpsd-1.1.1/bnpsd/R/bnpsd-deprecated.R |only bnpsd-1.1.1/bnpsd/R/bnpsd.R | 49 - bnpsd-1.1.1/bnpsd/R/coanc_admix.R |only bnpsd-1.1.1/bnpsd/R/coanc_to_kinship.R | 66 - bnpsd-1.1.1/bnpsd/R/draw_all_admix.R |only bnpsd-1.1.1/bnpsd/R/draw_genotypes_admix.R |only bnpsd-1.1.1/bnpsd/R/draw_p_anc.R |only bnpsd-1.1.1/bnpsd/R/draw_p_subpops.R |only bnpsd-1.1.1/bnpsd/R/fixed_loci.R | 21 bnpsd-1.1.1/bnpsd/R/fst_admix.R |only bnpsd-1.1.1/bnpsd/R/make_p_ind_admix.R |only bnpsd-1.1.1/bnpsd/R/rescale_coanc_subpops.R |only bnpsd-1.1.1/bnpsd/build/vignette.rds |binary bnpsd-1.1.1/bnpsd/inst/doc/bnpsd.R | 354 ++++--- bnpsd-1.1.1/bnpsd/inst/doc/bnpsd.Rmd | 416 +++++---- bnpsd-1.1.1/bnpsd/inst/doc/bnpsd.html |only bnpsd-1.1.1/bnpsd/man/admix_prop_1d_circular.Rd |only bnpsd-1.1.1/bnpsd/man/admix_prop_1d_linear.Rd |only bnpsd-1.1.1/bnpsd/man/admix_prop_indep_subpops.Rd |only bnpsd-1.1.1/bnpsd/man/bnpsd-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/bnpsd.Rd | 53 - bnpsd-1.1.1/bnpsd/man/coanc-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/coanc_admix.Rd |only bnpsd-1.1.1/bnpsd/man/coanc_to_kinship.Rd | 46 - bnpsd-1.1.1/bnpsd/man/draw_all_admix.Rd |only bnpsd-1.1.1/bnpsd/man/draw_genotypes_admix.Rd |only bnpsd-1.1.1/bnpsd/man/draw_p_anc.Rd |only bnpsd-1.1.1/bnpsd/man/draw_p_subpops.Rd |only bnpsd-1.1.1/bnpsd/man/fixed_loci.Rd | 9 bnpsd-1.1.1/bnpsd/man/fst_admix.Rd |only bnpsd-1.1.1/bnpsd/man/make_p_ind_admix.Rd |only bnpsd-1.1.1/bnpsd/man/q1d-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/q1dc-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/qis-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/rbnpsd-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/rgeno-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/rpanc-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/rpiaf-deprecated.Rd |only bnpsd-1.1.1/bnpsd/man/rpint-deprecated.Rd |only bnpsd-1.1.1/bnpsd/tests/testthat/test_bnpsd.R | 1010 ++++++++++++++-------- bnpsd-1.1.1/bnpsd/vignettes/bnpsd.Rmd | 416 +++++---- 74 files changed, 1702 insertions(+), 917 deletions(-)
Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with
'Socrata' open data portals <http://dev.socrata.com>.
Users can provide a 'Socrata' data set resource URL,
or a 'Socrata' Open Data API (SoDA) web query,
or a 'Socrata' "human-friendly" URL,
returns an R data frame. Converts dates to 'POSIX'
format and manages throttling by 'Socrata'.
Users can upload data to 'Socrata' portals directly
from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>
Diff between RSocrata versions 1.7.7-1 dated 2019-04-27 and 1.7.8-4 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-all.R | 10 +++++----- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: Effect Size Computation for Meta Analysis
Description: Implementation of the web-based 'Practical Meta-Analysis Effect Size
Calculator' from David B. Wilson (<http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php>)
in R. Based on the input, the effect size can be returned as standardized mean
difference, Cohen's f, Hedges' g, Pearson's r or Fisher's
transformation z, odds ratio or log odds, or eta squared effect size.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between esc versions 0.4.1 dated 2018-05-06 and 0.5.0 dated 2019-05-15
esc-0.4.1/esc/R/esc_d2etasq.R |only esc-0.4.1/esc/R/esc_d2f.R |only esc-0.4.1/esc/R/esc_d2logit.R |only esc-0.4.1/esc/R/esc_d2or.R |only esc-0.4.1/esc/R/esc_d2r.R |only esc-0.4.1/esc/R/esc_or2d.R |only esc-0.4.1/esc/R/esc_z2r.R |only esc-0.4.1/esc/man/esc_d2etasq.Rd |only esc-0.4.1/esc/man/esc_d2f.Rd |only esc-0.4.1/esc/man/esc_d2logit.Rd |only esc-0.4.1/esc/man/esc_d2or.Rd |only esc-0.4.1/esc/man/esc_d2r.Rd |only esc-0.4.1/esc/man/esc_or2d.Rd |only esc-0.4.1/esc/man/esc_r2z.Rd |only esc-0.4.1/esc/man/esc_z2r.Rd |only esc-0.5.0/esc/DESCRIPTION | 17 - esc-0.5.0/esc/MD5 | 101 ++++----- esc-0.5.0/esc/NAMESPACE | 18 - esc-0.5.0/esc/NEWS.md | 11 + esc-0.5.0/esc/R/Deprecated.R |only esc-0.5.0/esc/R/S3-methods.R | 2 esc-0.5.0/esc/R/combine_esc.R | 255 +++++++++++------------ esc-0.5.0/esc/R/convert_d2etasq.R |only esc-0.5.0/esc/R/convert_d2f.R |only esc-0.5.0/esc/R/convert_d2logit.R |only esc-0.5.0/esc/R/convert_d2or.R |only esc-0.5.0/esc/R/convert_d2r.R |only esc-0.5.0/esc/R/convert_or2d.R |only esc-0.5.0/esc/R/convert_z2r.R |only esc-0.5.0/esc/R/esc.R | 303 +++++++++++++-------------- esc-0.5.0/esc/R/esc_2x2.R | 182 ++++++++-------- esc-0.5.0/esc/R/esc_B.R | 92 ++++---- esc-0.5.0/esc/R/esc_beta.R | 134 ++++++------ esc-0.5.0/esc/R/esc_bin_prop.R | 96 ++++---- esc-0.5.0/esc/R/esc_chisq.R | 256 +++++++++++------------ esc-0.5.0/esc/R/esc_f.R | 72 +++--- esc-0.5.0/esc/R/esc_helper.R | 254 +++++++++++------------ esc-0.5.0/esc/R/esc_mean_gain.R | 379 ++++++++++++++++++----------------- esc-0.5.0/esc/R/esc_mean_sd.R | 299 +++++++++++++++------------ esc-0.5.0/esc/R/esc_rpb.R | 214 +++++++++---------- esc-0.5.0/esc/R/esc_t.R | 236 ++++++++++----------- esc-0.5.0/esc/R/hedges_g.R | 195 +++++++++--------- esc-0.5.0/esc/README.md | 170 ++++++++------- esc-0.5.0/esc/build/partial.rdb |binary esc-0.5.0/esc/inst/CITATION | 18 - esc-0.5.0/esc/man/convert_d2etasq.Rd |only esc-0.5.0/esc/man/convert_d2f.Rd |only esc-0.5.0/esc/man/convert_d2logit.Rd |only esc-0.5.0/esc/man/convert_d2or.Rd |only esc-0.5.0/esc/man/convert_d2r.Rd |only esc-0.5.0/esc/man/convert_or2d.Rd |only esc-0.5.0/esc/man/convert_r2z.Rd |only esc-0.5.0/esc/man/convert_z2r.Rd |only esc-0.5.0/esc/man/effect_sizes.Rd | 8 esc-0.5.0/esc/man/esc_2x2.Rd | 8 esc-0.5.0/esc/man/esc_B.Rd | 8 esc-0.5.0/esc/man/esc_beta.Rd | 8 esc-0.5.0/esc/man/esc_bin_prop.Rd | 8 esc-0.5.0/esc/man/esc_chisq.Rd | 8 esc-0.5.0/esc/man/esc_f.Rd | 8 esc-0.5.0/esc/man/esc_mean_gain.Rd | 14 - esc-0.5.0/esc/man/esc_mean_sd.Rd | 21 + esc-0.5.0/esc/man/esc_mean_se.Rd | 11 - esc-0.5.0/esc/man/esc_phi.Rd | 8 esc-0.5.0/esc/man/esc_rpb.Rd | 8 esc-0.5.0/esc/man/esc_t.Rd | 8 esc-0.5.0/esc/man/write_esc.Rd | 2 67 files changed, 1756 insertions(+), 1676 deletions(-)
Title: Flexible Phenotype Simulation from Different Genetic and Noise
Models
Description: Simulation is a critical part of method development and assessment
in quantitative genetics. 'PhenotypeSimulator' allows for the flexible
simulation of phenotypes under different models, including genetic variant
and infinitesimal genetic effects (reflecting population structure) as well
as non-genetic covariate effects, observational noise and additional
correlation effects. The different phenotype components are combined into a
final phenotype while controlling for the proportion of variance explained
by each of the components. For each effect component, the number of
variables, their distribution and the design of their effect across traits
can be customised. For the simulation of the genetic effects, external
genotype data from a number of standard software ('plink', 'hapgen2'/
'impute2', 'genome', 'bimbam', simple text files) can be imported. The final
simulated phenotypes and its components can be automatically saved into .rds
or .csv files. In addition, they can be saved in formats compatible with
commonly used genetic association software ('gemma', 'bimbam', 'plink',
'snptest', 'LiMMBo').
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>),
Konrad Rudolph [ctb] (<https://orcid.org/0000-0002-9866-7051>)
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>
Diff between PhenotypeSimulator versions 0.3.1 dated 2018-10-25 and 0.3.3 dated 2019-05-15
PhenotypeSimulator-0.3.1/PhenotypeSimulator/inst/doc/UsagePhenotypeSimulator.R |only PhenotypeSimulator-0.3.1/PhenotypeSimulator/inst/doc/UsagePhenotypeSimulator.Rmd |only PhenotypeSimulator-0.3.1/PhenotypeSimulator/inst/doc/UsagePhenotypeSimulator.pdf |only PhenotypeSimulator-0.3.1/PhenotypeSimulator/tests/testthat/test-output.r |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/DESCRIPTION | 17 PhenotypeSimulator-0.3.3/PhenotypeSimulator/MD5 | 84 + PhenotypeSimulator-0.3.3/PhenotypeSimulator/NAMESPACE | 1 PhenotypeSimulator-0.3.3/PhenotypeSimulator/NEWS.md | 19 PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/PhenotypeSimulator.R | 1 PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/commandlineFunctions.R | 9 PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/createphenotypeFunctions.R | 16 PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/genotypeFunctions.R | 484 +++++----- PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/outputFunctions.R | 2 PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/utilityFunctions.R | 6 PhenotypeSimulator-0.3.3/PhenotypeSimulator/R/variancecomponentFunctions.R | 4 PhenotypeSimulator-0.3.3/PhenotypeSimulator/README.md | 10 PhenotypeSimulator-0.3.3/PhenotypeSimulator/build/vignette.rds |binary PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/CITATION |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/PhenotypeSimulator.R | 3 PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/PhenotypeSimulator.Rmd | 3 PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/PhenotypeSimulator.pdf |binary PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Sample-scripts-external-genotype-simulation.R | 8 PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Sample-scripts-external-genotype-simulation.Rmd | 70 + PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Sample-scripts-external-genotype-simulation.pdf |binary PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/Simulation-and-LinearModel.pdf |binary PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/SimulationBasedOnExampleData.R |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/SimulationBasedOnExampleData.Rmd |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/doc/SimulationBasedOnExampleData.pdf |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/extdata/genotypes/genotypes_chr22.bimbam |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/extdata/genotypes/hapgen/genotypes_hapgen_chr22.gen |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/extdata/genotypes/hapgen/genotypes_hapgen_chr22.sample |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/inst/extdata/vignettes |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/getAlleleFrequencies.Rd | 2 PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/getCausalSNPs.Rd | 72 - PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/getKinship.Rd | 16 PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/readStandardGenotypes.Rd | 132 +- PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/read_lines.Rd | 4 PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/runSimulation.Rd | 16 PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/simulateGenotypes.Rd | 10 PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/standardiseGenotypes.Rd | 2 PhenotypeSimulator-0.3.3/PhenotypeSimulator/man/writeStandardOutput.Rd | 2 PhenotypeSimulator-0.3.3/PhenotypeSimulator/tests/testthat/test-genotype.r | 45 PhenotypeSimulator-0.3.3/PhenotypeSimulator/tests/testthat/test-output.R |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/vignettes/PhenotypeSimulator.Rmd | 3 PhenotypeSimulator-0.3.3/PhenotypeSimulator/vignettes/Sample-scripts-external-genotype-simulation.Rmd | 70 + PhenotypeSimulator-0.3.3/PhenotypeSimulator/vignettes/SimulationBasedOnExampleData.Rmd |only PhenotypeSimulator-0.3.3/PhenotypeSimulator/vignettes/Vignette-example-data.bib |only 47 files changed, 683 insertions(+), 428 deletions(-)
More information about PhenotypeSimulator at CRAN
Permanent link
Title: A Package to Visualize Linear Models Features and Play with Them
Description: Contains three shiny applications.
Two are meant to explore linear model inference feature through simulation.
The third is a game to learn interpreting diagnostic plots.
Author: Francesco Pauli (see file LICENSEMEDIA for credits on sounds and images)
Maintainer: Francesco Pauli <francesco.pauli@deams.units.it>
Diff between lmviz versions 0.1.1 dated 2018-11-18 and 0.1.2 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md |only R/BadLM.r | 16 ++++++++-------- R/QuizResidual.r | 17 +++++++++-------- inst/BadLMApp.r | 14 ++++++++++---- inst/QuizResidualApp.r | 15 ++++++++------- inst/SimpleLMApp.r | 6 +++--- 8 files changed, 49 insertions(+), 40 deletions(-)
Title: Canadian Forest Fire Danger Rating System
Description: This project provides a group of new functions to calculate the
outputs of the two main components of the Canadian Forest Fire Danger Rating
System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System and
the Fire Behaviour Prediction (FBP) System. Some functions have two versions,
table and raster based.
Author: Xianli Wang, Alan Cantin, Marc-André Parisien, Mike Wotton, Kerry
Anderson, Brett Moore, Tom Schiks, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>
Diff between cffdrs versions 1.8.5 dated 2019-04-24 and 1.8.6 dated 2019-05-15
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/FBPcalc.r | 4 ++-- man/cffdrs-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 13 deletions(-)
More information about SoftRandomForest at CRAN
Permanent link
Title: Simulations and Visualizations of Rubik's Cube (with Mods)
Description: Provides simplified methods for managing classic Rubik's cubes and many other modifications of it (such as NxNxN size cubes, void cubes and 8-coloured cubes - so called octa cubes). Includes functions of handling special syntax for managing such cubes; and different approach to plotting 3D cubes without using external libraries (for example 'OpenGL').
Author: Wojciech Rosa
Maintainer: Wojciech Rosa <w.rosa@pollub.pl>
Diff between rcube versions 0.3 dated 2018-09-27 and 0.5 dated 2019-05-15
DESCRIPTION | 10 MD5 | 41 +-- NAMESPACE | 28 +- R/createCube.R | 320 ++++++++++++------------- R/misc.R | 634 ++++++++++++++++++++++++++------------------------- R/plot.cube.R | 68 ++--- R/plot3dCube.R | 52 ++-- R/plot3dFlat.R |only R/positions.R | 32 +- R/scramble.R | 2 R/twistCube.R | 20 - README.md |only data/positions.RData |binary man/createCube.Rd | 76 +++--- man/is.solved.Rd | 72 ++--- man/plot.cube.Rd | 50 ++-- man/plot3dCube.Rd | 57 ++-- man/plot3dFlat.Rd |only man/positions.Rd | 42 +-- man/print.cube.Rd | 48 +-- man/scramble.Rd | 54 ++-- man/translate.Rd | 50 ++-- man/twistCube.Rd | 140 +++++------ 23 files changed, 909 insertions(+), 887 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2018) <arXiv:1711.05632>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated.
Author: Keefe Murphy [aut, cre],
Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between MoEClust versions 1.2.1 dated 2018-12-11 and 1.2.2 dated 2019-05-15
DESCRIPTION | 15 MD5 | 58 +-- NAMESPACE | 4 R/Functions.R | 927 ++++++++++++++++++++++++++++++------------------ R/MoEClust.R | 31 - R/Plotting_Functions.R | 270 ++++++++----- README.md | 5 build/vignette.rds |binary inst/CITATION | 18 inst/NEWS.md | 53 ++ inst/doc/MoEClust.R | 51 +- inst/doc/MoEClust.Rmd | 79 ++-- inst/doc/MoEClust.html | 196 ++++++---- man/MoEClust-package.Rd | 27 - man/MoE_clust.Rd | 36 + man/MoE_compare.Rd | 42 +- man/MoE_control.Rd | 64 +-- man/MoE_cstep.Rd | 2 man/MoE_dens.Rd | 11 man/MoE_estep.Rd | 11 man/MoE_gpairs.Rd | 41 +- man/MoE_plotGate.Rd | 8 man/MoE_plotLogLik.Rd | 2 man/as.Mclust.Rd | 13 man/drop_constants.Rd | 7 man/expert_covar.Rd | 6 man/noise_vol.Rd | 22 - man/plot.MoEClust.Rd | 6 man/predict.MoEClust.Rd | 12 vignettes/MoEClust.Rmd | 79 ++-- 30 files changed, 1288 insertions(+), 808 deletions(-)
Title: Aids in Processing and Plotting Data from a Lemna-Tec
Scananalyzer
Description: Note that 'imageData' has been superseded by 'growthPheno'.
The package 'growthPheno' incorporates all the functionality of
'imageData' and has functionality not available in 'imageData',
but some 'imageData' functions have been renamed.
The 'imageData' package is no longer maintained, but is retained
for legacy purposes.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@unisa.edu.au>
Diff between imageData versions 0.1-50 dated 2018-06-11 and 0.1-59 dated 2019-05-15
imageData-0.1-50/imageData/R/dataLongi_v7.r |only imageData-0.1-50/imageData/inst/doc/imageData-Ex.pdf |only imageData-0.1-59/imageData/DESCRIPTION | 32 +++++----- imageData-0.1-59/imageData/MD5 | 23 +++---- imageData-0.1-59/imageData/R/dataLongi_v8.r | 21 ++++++ imageData-0.1-59/imageData/R/imageDataUtilities.r | 11 +++ imageData-0.1-59/imageData/build/partial.rdb |binary imageData-0.1-59/imageData/build/vignette.rds |only imageData-0.1-59/imageData/inst/News.Rd | 30 +++++++++ imageData-0.1-59/imageData/inst/doc/imageData-manual.pdf |binary imageData-0.1-59/imageData/inst/doc/imageData-manual.pdf.asis |only imageData-0.1-59/imageData/man/fitSpline.Rd | 2 imageData-0.1-59/imageData/man/probeDF.Rd | 24 ++++++- imageData-0.1-59/imageData/man/splitSplines.Rd | 4 - imageData-0.1-59/imageData/vignettes |only 15 files changed, 113 insertions(+), 34 deletions(-)
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changes in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 1.7.2 dated 2019-04-02 and 1.7.3 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 2 +- tests/testthat/test-fnsComparison.R | 28 +++++++++++++++------------- 5 files changed, 27 insertions(+), 22 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab priors for variable selection mean/variance regression models, for univariate and multivariate response models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.0.8 dated 2018-09-27 and 2.0.9 dated 2019-05-15
BNSP-2.0.8/BNSP/ChangeLog |only BNSP-2.0.9/BNSP/DESCRIPTION | 12 BNSP-2.0.9/BNSP/MD5 | 36 +- BNSP-2.0.9/BNSP/NAMESPACE | 11 BNSP-2.0.9/BNSP/R/bnpMulti.R |only BNSP-2.0.9/BNSP/R/dpmj.R | 2 BNSP-2.0.9/BNSP/R/mvrm.R | 509 ++++++++++++++++++------------------ BNSP-2.0.9/BNSP/inst |only BNSP-2.0.9/BNSP/man/BNSP-package.Rd | 4 BNSP-2.0.9/BNSP/man/clustering.Rd |only BNSP-2.0.9/BNSP/man/continue.Rd |only BNSP-2.0.9/BNSP/man/histCorr.Rd |only BNSP-2.0.9/BNSP/man/mmvrm.Rd |only BNSP-2.0.9/BNSP/man/mmvrm2mcmc.Rd |only BNSP-2.0.9/BNSP/man/mvrm.Rd | 94 +++--- BNSP-2.0.9/BNSP/man/plot.mvrm.Rd | 2 BNSP-2.0.9/BNSP/man/plotCorr.Rd |only BNSP-2.0.9/BNSP/src/BNSP_init.c | 30 -- BNSP-2.0.9/BNSP/src/BayesMult.c |only BNSP-2.0.9/BNSP/src/BayesMultG.c |only BNSP-2.0.9/BNSP/src/BayesMultGV.c |only BNSP-2.0.9/BNSP/src/matalg.h | 16 + BNSP-2.0.9/BNSP/src/mvrmGAM.c | 161 ++++++++--- BNSP-2.0.9/BNSP/src/pdfs.h | 30 -- BNSP-2.0.9/BNSP/src/spec.BCM.h | 236 ++++++++++++++++ 25 files changed, 751 insertions(+), 392 deletions(-)
Title: Manipulate and Explore UK Biobank Data
Description: A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html),
visualize primary demographic data for a sample subset, query ICD diagnoses,
retrieve genetic metadata, read and write standard file formats for genetic analyses.
Author: Ken Hanscombe [aut, cre]
Maintainer: Ken Hanscombe <ken.hanscombe@gmail.com>
Diff between ukbtools versions 0.11.2 dated 2019-04-25 and 0.11.3 dated 2019-05-15
DESCRIPTION | 6 MD5 | 26 +- NEWS.md | 21 + R/diagnosis.R | 32 +- R/ukb_dataset.R | 5 build/vignette.rds |binary data/icd10codes.rda |binary data/icd9codes.rda |binary inst/doc/explore-ukb-data.Rmd | 6 inst/doc/explore-ukb-data.html | 441 ++++++++++++++++++++++++++++++----------- man/ukb_icd_freq_by.Rd | 2 man/ukb_icd_keyword.Rd | 4 man/ukb_icd_prevalence.Rd | 6 vignettes/explore-ukb-data.Rmd | 6 14 files changed, 394 insertions(+), 161 deletions(-)
Title: Infrastructure for Running, Cycling and Swimming Data from
GPS-Enabled Tracking Devices
Description: Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Hannah Frick [aut] (<https://orcid.org/0000-0002-6049-5258>),
Robin Hornak [aut]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between trackeR versions 1.5.1 dated 2019-04-10 and 1.5.2 dated 2019-05-15
trackeR-1.5.1/trackeR/inst/extdata/gpx/20170708-154835-Run.gpx |only trackeR-1.5.1/trackeR/inst/extdata/gpx/20170709-151453-Ride.gpx |only trackeR-1.5.1/trackeR/inst/extdata/gpx/20170714-143644-Swim.gpx |only trackeR-1.5.1/trackeR/inst/extdata/tcx/2013-06-01-183220.TCX |only trackeR-1.5.1/trackeR/inst/extdata/tcx/2013-06-08-090442.TCX |only trackeR-1.5.2/trackeR/DESCRIPTION | 6 trackeR-1.5.2/trackeR/MD5 | 48 trackeR-1.5.2/trackeR/NEWS.md | 16 trackeR-1.5.2/trackeR/R/constants.R | 2 trackeR-1.5.2/trackeR/R/reading.R | 30 trackeR-1.5.2/trackeR/R/trackeRdata.R | 2 trackeR-1.5.2/trackeR/build/vignette.rds |binary trackeR-1.5.2/trackeR/inst/doc/TourDetrackeR.R | 2 trackeR-1.5.2/trackeR/inst/doc/TourDetrackeR.Rmd | 4 trackeR-1.5.2/trackeR/inst/doc/TourDetrackeR.html | 5409 +++++++++- trackeR-1.5.2/trackeR/inst/doc/trackeR.R | 2 trackeR-1.5.2/trackeR/inst/doc/trackeR.Rnw | 2 trackeR-1.5.2/trackeR/inst/doc/trackeR.pdf |binary trackeR-1.5.2/trackeR/inst/extdata/gpx/20170708-154835-Run.gpx.gz |only trackeR-1.5.2/trackeR/inst/extdata/gpx/20170709-151453-Ride.gpx.gz |only trackeR-1.5.2/trackeR/inst/extdata/gpx/20170714-143644-Swim.gpx.gz |only trackeR-1.5.2/trackeR/inst/extdata/json |only trackeR-1.5.2/trackeR/inst/extdata/tcx/2013-06-01-183220.TCX.gz |only trackeR-1.5.2/trackeR/inst/extdata/tcx/2013-06-08-090442.TCX.gz |only trackeR-1.5.2/trackeR/man/readX.Rd | 6 trackeR-1.5.2/trackeR/man/read_container.Rd | 6 trackeR-1.5.2/trackeR/man/read_directory.Rd | 7 trackeR-1.5.2/trackeR/man/trackeRdata.Rd | 2 trackeR-1.5.2/trackeR/vignettes/TourDetrackeR.Rmd | 4 trackeR-1.5.2/trackeR/vignettes/_region_.tex |only trackeR-1.5.2/trackeR/vignettes/trackeR.Rnw | 2 31 files changed, 5112 insertions(+), 438 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
and
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.5.5 dated 2019-02-11 and 0.5.6 dated 2019-05-15
DESCRIPTION | 12 - MD5 | 144 ++++++++-------- NAMESPACE | 6 NEWS.md | 55 ++++++ R/1.R | 8 R/acf.R | 5 R/anonymize.R | 4 R/color.R | 261 +++++++++++++++++++---------- R/covm.R |only R/ctmm.R | 207 +---------------------- R/emulate.R | 337 +++++++++++++++++--------------------- R/extent.R | 30 +++ R/generic.R | 20 +- R/kalman.R | 188 +++++++++++++++++---- R/krige.R | 124 ++++++++------ R/lasso.R |only R/likelihood.R | 401 +++++++++++++++++++++------------------------- R/matrix.R | 71 ++++++-- R/mean.R | 40 +--- R/median.R | 2 R/modes.R |only R/optim.R | 82 +++++---- R/outlier.R | 5 R/overlap.R | 198 +++------------------- R/parallel.R | 6 R/parameters.R | 77 ++++---- R/periodogram.R | 8 R/plot.telemetry.R | 73 +++++--- R/plot.variogram.R | 16 + R/projection.R | 4 R/select.R | 106 +++++++++--- R/speed.R | 41 ++-- R/speeds.R | 24 ++ R/split.R |only R/stats.R | 21 +- R/summary.ctmm.R | 113 ++++++++---- R/telemetry.R | 158 +++++++++++++++--- R/uere.R | 195 +++++++++++++++++----- R/units.R | 18 -- R/variogram.R | 2 R/variogram.fit.R | 9 - R/variogram.test.R | 5 TODO | 31 ++- build/vignette.rds |binary data/buffalo.rda |binary data/coati.rda |binary data/gazelle.rda |binary data/turtle.rda |binary data/wolf.rda |binary inst/doc/akde.html | 8 inst/doc/error.R | 41 ++-- inst/doc/error.Rmd | 72 ++++---- inst/doc/error.html | 124 ++++++++------ inst/doc/periodogram.R | 20 +- inst/doc/periodogram.Rmd | 24 +- inst/doc/periodogram.html | 122 +++++++------ inst/doc/variogram.R | 2 inst/doc/variogram.Rmd | 6 inst/doc/variogram.html | 63 +++---- man/akde.Rd | 9 - man/as.telemetry.Rd | 6 man/color.Rd |only man/ctmm-FAQ.Rd | 2 man/ctmm-package.Rd | 4 man/ctmm.boot.Rd | 18 +- man/ctmm.fit.Rd | 11 - man/occurrence.Rd | 15 + man/plot.telemetry.Rd | 3 man/plot.variogram.Rd | 3 man/projection.Rd | 3 man/residuals.Rd | 12 - man/select.Rd |only man/variogram.fit.Rd | 5 vignettes/error.Rmd | 72 ++++---- vignettes/periodogram.Rmd | 24 +- vignettes/variogram.Rmd | 6 76 files changed, 2122 insertions(+), 1660 deletions(-)
Title: Supports the Analysis of RTI MicroPEM Output Files
Description: Supports the input and reproducible analysis of RTI
MicroPEM output files.
Author: Maëlle Salmon [aut, cre],
Zheng Zhou [aut] (Department of Environmental Health Sciences Mailman
School of Public Health at Columbia University, New York, USA),
ERC Grant Agreement number 336167 - the CHAI Project [fnd],
Carles Milà [ctb],
Sreekanth Vakacherla [ctb],
Cathryn Tonne [ctb],
Julian Marshall [ctb],
Lucy D'Agostino McGowan [rev] (Lucy D'Agostino McGowan reviewed the
package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/126),
Kara Woo [rev] (Kara Woo reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/126)
Maintainer: Maëlle Salmon <maelle.salmon@yahoo.se>
Diff between rtimicropem versions 1.3 dated 2017-08-02 and 1.4.0 dated 2019-05-15
rtimicropem-1.3/rtimicropem/inst/doc/vignette_ammon.R |only rtimicropem-1.3/rtimicropem/inst/doc/vignette_ammon.Rmd |only rtimicropem-1.3/rtimicropem/inst/doc/vignette_ammon.html |only rtimicropem-1.3/rtimicropem/vignettes/vignette_ammon.Rmd |only rtimicropem-1.4.0/rtimicropem/DESCRIPTION | 69 + rtimicropem-1.4.0/rtimicropem/MD5 | 58 - rtimicropem-1.4.0/rtimicropem/NAMESPACE | 20 rtimicropem-1.4.0/rtimicropem/NEWS.md | 4 rtimicropem-1.4.0/rtimicropem/R/chai_alarm.R | 8 rtimicropem-1.4.0/rtimicropem/R/convert_output.R | 6 rtimicropem-1.4.0/rtimicropem/R/micropem_class.R | 2 rtimicropem-1.4.0/rtimicropem/build/vignette.rds |binary rtimicropem-1.4.0/rtimicropem/inst/doc/chai_data_cleaning.R | 6 rtimicropem-1.4.0/rtimicropem/inst/doc/chai_data_cleaning.Rmd | 206 ++-- rtimicropem-1.4.0/rtimicropem/inst/doc/chai_data_cleaning.html | 441 +++++++--- rtimicropem-1.4.0/rtimicropem/inst/doc/rtimicropem.R |only rtimicropem-1.4.0/rtimicropem/inst/doc/rtimicropem.Rmd |only rtimicropem-1.4.0/rtimicropem/inst/doc/rtimicropem.html |only rtimicropem-1.4.0/rtimicropem/man/CHAI.Rd | 34 rtimicropem-1.4.0/rtimicropem/man/Columbia.Rd | 34 rtimicropem-1.4.0/rtimicropem/man/Columbia2.Rd | 34 rtimicropem-1.4.0/rtimicropem/man/batch_convert.Rd | 52 - rtimicropem-1.4.0/rtimicropem/man/chai_alarm.Rd | 44 rtimicropem-1.4.0/rtimicropem/man/clean_measures.Rd | 74 - rtimicropem-1.4.0/rtimicropem/man/convert_output.Rd | 44 rtimicropem-1.4.0/rtimicropem/man/identify_lags.Rd | 56 - rtimicropem-1.4.0/rtimicropem/man/micropem.Rd | 146 +-- rtimicropem-1.4.0/rtimicropem/man/micropemC1.Rd | 30 rtimicropem-1.4.0/rtimicropem/man/micropemC2.Rd | 30 rtimicropem-1.4.0/rtimicropem/man/micropemChai.Rd | 30 rtimicropem-1.4.0/rtimicropem/man/rtimicropem-package.Rd | 79 - rtimicropem-1.4.0/rtimicropem/man/run_shiny_app.Rd | 42 rtimicropem-1.4.0/rtimicropem/vignettes/chai_data_cleaning.Rmd | 206 ++-- rtimicropem-1.4.0/rtimicropem/vignettes/rtimicropem.Rmd |only 34 files changed, 984 insertions(+), 771 deletions(-)
Title: Depth Measures in Multivariate, Regression and Functional
Settings
Description: Tools to compute depth measures and implementations of related
tasks such as outlier detection, data exploration and
classification of multivariate, regression and functional data.
Author: Pieter Segaert [aut],
Mia Hubert [aut],
Peter Rousseeuw [aut],
Jakob Raymaekers [aut, cre],
Kaveh Vakili [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between mrfDepth versions 1.0.10 dated 2018-10-12 and 1.0.11 dated 2019-05-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/bagplot.R | 2 +- R/compBagplot.R | 6 +++--- inst/NEWS.Rd | 6 ++++++ src/Makevars | 2 +- src/Makevars.win | 2 +- 7 files changed, 23 insertions(+), 17 deletions(-)
Title: Read, Create and Write 'PharmML' Standard Output (so) XML Files
Description: Handle 'PharmML' (Pharmacometrics Markup Language) standard output (SO) XML files.
SO files can be created, read, manipulated and written through a
data binding from the XML structure to a tree structure of R objects.
Author: Rikard Nordgren <rikard.nordgren@farmbio.uu.se>
Maintainer: Rikard Nordgren <rikard.nordgren@farmbio.uu.se>
Diff between libsoc versions 0.6.4 dated 2018-01-28 and 0.7 dated 2019-05-15
libsoc-0.6.4/libsoc/man/Bootstrap.Rd |only libsoc-0.6.4/libsoc/man/ConditionNumber.Rd |only libsoc-0.6.4/libsoc/man/Content.Rd |only libsoc-0.6.4/libsoc/man/DataFile.Rd |only libsoc-0.6.4/libsoc/man/Design.Rd |only libsoc-0.6.4/libsoc/man/DiagnosticPlotsStructuralModel.Rd |only libsoc-0.6.4/libsoc/man/File.Rd |only libsoc-0.6.4/libsoc/man/GraphicsFile.Rd |only libsoc-0.6.4/libsoc/man/IndependentVariable.Rd |only libsoc-0.6.4/libsoc/man/IndivFits.Rd |only libsoc-0.6.4/libsoc/man/Level.Rd |only libsoc-0.6.4/libsoc/man/Likelihood.Rd |only libsoc-0.6.4/libsoc/man/ModelDefinition.Rd |only libsoc-0.6.4/libsoc/man/Name.Rd |only libsoc-0.6.4/libsoc/man/NumberChains.Rd |only libsoc-0.6.4/libsoc/man/NumberIterations.Rd |only libsoc-0.6.4/libsoc/man/OutputFilePath.Rd |only libsoc-0.6.4/libsoc/man/ParentLevel.Rd |only libsoc-0.6.4/libsoc/man/PharmML.Rd |only libsoc-0.6.4/libsoc/man/RunTime.Rd |only libsoc-0.6.4/libsoc/man/Severity.Rd |only libsoc-0.6.4/libsoc/man/SimulatedData.Rd |only libsoc-0.6.4/libsoc/man/SymbRef.Rd |only libsoc-0.6.4/libsoc/man/Toolname.Rd |only libsoc-0.6.4/libsoc/man/VariabilityModel.Rd |only libsoc-0.6.4/libsoc/src/include/so/private/Bootstrap.h |only libsoc-0.6.4/libsoc/src/include/so/private/ConditionNumber.h |only libsoc-0.6.4/libsoc/src/include/so/private/Content.h |only libsoc-0.6.4/libsoc/src/include/so/private/DataFile.h |only libsoc-0.6.4/libsoc/src/include/so/private/Design.h |only libsoc-0.6.4/libsoc/src/include/so/private/DiagnosticPlotsStructuralModel.h |only libsoc-0.6.4/libsoc/src/include/so/private/File.h |only libsoc-0.6.4/libsoc/src/include/so/private/GraphicsFile.h |only libsoc-0.6.4/libsoc/src/include/so/private/IndivFits.h |only libsoc-0.6.4/libsoc/src/include/so/private/Likelihood.h |only libsoc-0.6.4/libsoc/src/include/so/private/Name.h |only libsoc-0.6.4/libsoc/src/include/so/private/NumberChains.h |only libsoc-0.6.4/libsoc/src/include/so/private/NumberIterations.h |only libsoc-0.6.4/libsoc/src/include/so/private/OutputFilePath.h |only libsoc-0.6.4/libsoc/src/include/so/private/RunTime.h |only libsoc-0.6.4/libsoc/src/include/so/private/Severity.h |only libsoc-0.6.4/libsoc/src/include/so/private/SimulatedData.h |only libsoc-0.6.4/libsoc/src/include/so/private/Toolname.h |only libsoc-0.7/libsoc/DESCRIPTION | 10 libsoc-0.7/libsoc/MD5 | 73 libsoc-0.7/libsoc/NAMESPACE | 46 libsoc-0.7/libsoc/R/soc.R | 9 libsoc-0.7/libsoc/build/vignette.rds |binary libsoc-0.7/libsoc/inst/doc/creating_an_so.html | 521 ++- libsoc-0.7/libsoc/inst/doc/so.html | 695 ++-- libsoc-0.7/libsoc/man/dv_column.Rd | 7 libsoc-0.7/libsoc/man/dv_column_name.Rd | 7 libsoc-0.7/libsoc/man/id_column.Rd | 7 libsoc-0.7/libsoc/man/id_column_name.Rd | 7 libsoc-0.7/libsoc/man/idv_column.Rd | 7 libsoc-0.7/libsoc/man/idv_column_name.Rd | 7 libsoc-0.7/libsoc/src/Makevars.win | 1 libsoc-0.7/libsoc/src/libsoc_init.c | 1484 +++++----- libsoc-0.7/libsoc/src/static-Table.c | 4 59 files changed, 1482 insertions(+), 1403 deletions(-)
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph],
Robert Rigby [aut],
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb],
Fernanda De Bastiani [ctb],
Raydonal Ospina [ctb],
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [ctb],
Marco Enea [ctb],
Alexios Ghalanos [ctb],
Christos Argyropoulos [ctb],
Almond Stocker [ctb],
Jens Lichter [ctb],
Stanislaus Stadlmann [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 5.1-3 dated 2019-03-20 and 5.1-4 dated 2019-05-15
DESCRIPTION | 8 +- MD5 | 19 ++--- NAMESPACE | 1 R/PARETO.R | 7 + R/PARETO1.R | 12 +-- R/PARETO1_mu_fixed.R |only R/WARING_BOB.r | 6 - R/plottingDist.R | 183 +++++++++++++++++++++++++++++++++------------------ build/partial.rdb |binary man/PARETO2.Rd | 15 +++- man/count_1_31.Rd | 43 ++++++++--- 11 files changed, 196 insertions(+), 98 deletions(-)
Title: GAMLSS Data
Description: Data used as examples to demonstrate GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby, Fernanda De Bastiani
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.data versions 5.1-3 dated 2019-03-20 and 5.1-4 dated 2019-05-15
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- data/InfMort.RData |only data/datalist | 1 + man/InfMort.Rd |only 5 files changed, 9 insertions(+), 6 deletions(-)
Title: Read, Manipulate and Explore Chess PGN Files
Description: Provides functions for reading *.PGN files with more than one game, including large files without copying it into RAM (using 'ff' package or 'RSQLite' package). Handle chess data and chess aggregated data, count figure moves statistics, create player profile, plot winning chances, browse openings.
Author: Wojciech Rosa
Maintainer: Wojciech Rosa <w.rosa@pollub.pl>
Diff between bigchess versions 1.2.0 dated 2018-11-04 and 1.3.2 dated 2019-05-15
DESCRIPTION | 12 +- MD5 | 18 ++- NAMESPACE | 2 R/browse_opening.R | 12 +- R/extract_moves.R | 2 R/read.pgn.R | 242 +++++++++++++++++++++++++++-------------------------- R/read.pgn.db.R |only R/read.pgn.ff.R | 156 +++++++++++++++++----------------- man/read.pgn.Rd | 4 man/read.pgn.db.Rd |only man/read.pgn.ff.Rd | 8 + 11 files changed, 244 insertions(+), 212 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
design functions for randomizing and assessing designs available as a
vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
The package 'dae' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@unisa.edu.au>
Diff between dae versions 3.0-23 dated 2018-10-25 and 3.0-32 dated 2019-05-15
dae-3.0-23/dae/inst/doc/daeDesignNotes.pdf |only dae-3.0-32/dae/DESCRIPTION | 26 - dae-3.0-32/dae/MD5 | 45 +- dae-3.0-32/dae/NAMESPACE | 2 dae-3.0-32/dae/R/daeAttach.r | 4 dae-3.0-32/dae/R/design.r | 2 dae-3.0-32/dae/R/designPlot.v2.r | 18 dae-3.0-32/dae/R/mat.functions.r | 7 dae-3.0-32/dae/R/pstructure.v2.r | 543 +++++++++++++------------- dae-3.0-32/dae/R/twophAnatomies.r |only dae-3.0-32/dae/build/partial.rdb |binary dae-3.0-32/dae/build/vignette.rds |only dae-3.0-32/dae/inst/NEWS.Rd | 37 + dae-3.0-32/dae/inst/doc/DesignNotes.pdf |only dae-3.0-32/dae/inst/doc/DesignNotes.pdf.asis |only dae-3.0-32/dae/inst/doc/dae-manual.pdf |binary dae-3.0-32/dae/inst/doc/dae-manual.pdf.asis |only dae-3.0-32/dae/man/dae-package.Rd | 20 dae-3.0-32/dae/man/daeTips.Rd | 5 dae-3.0-32/dae/man/designAnatomy.Rd | 20 dae-3.0-32/dae/man/designPlotlabels.Rd | 5 dae-3.0-32/dae/man/designTwophaseAnatomies.Rd |only dae-3.0-32/dae/man/fac.gen.Rd | 4 dae-3.0-32/dae/man/summary.pcanon.Rd | 3 dae-3.0-32/dae/tests/testthat/testAmeasures.r | 7 dae-3.0-32/dae/tests/testthat/testCanon.r | 44 ++ dae-3.0-32/dae/vignettes |only 27 files changed, 468 insertions(+), 324 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.5.2 dated 2018-08-18 and 3.6.0 dated 2019-05-15
tergm-3.5.2/tergm/BUGS |only tergm-3.5.2/tergm/tests/dynamic_MLE.Rout |only tergm-3.6.0/tergm/DESCRIPTION | 20 - tergm-3.6.0/tergm/LICENSE | 2 tergm-3.6.0/tergm/MD5 | 146 ++++++------ tergm-3.6.0/tergm/NAMESPACE | 15 - tergm-3.6.0/tergm/R/InitConstraint.R | 6 tergm-3.6.0/tergm/R/InitErgmTerm.duration.R | 6 tergm-3.6.0/tergm/R/InitMHP.DynMLE.R | 6 tergm-3.6.0/tergm/R/InitMHP.DynMLE.blockdiag.R | 6 tergm-3.6.0/tergm/R/InitMHP.DynMoME.R | 6 tergm-3.6.0/tergm/R/coef.stergm.R | 6 tergm-3.6.0/tergm/R/combine.networks.R | 18 - tergm-3.6.0/tergm/R/control.logLik.stergm.R | 6 tergm-3.6.0/tergm/R/control.simulate.stergm.R | 11 tergm-3.6.0/tergm/R/control.stergm.R | 31 +- tergm-3.6.0/tergm/R/ergm.godfather.R | 8 tergm-3.6.0/tergm/R/gof.stergm.R | 6 tergm-3.6.0/tergm/R/impute.network.list.R | 6 tergm-3.6.0/tergm/R/is.lasttoggle.R | 6 tergm-3.6.0/tergm/R/logLik.stergm.R | 6 tergm-3.6.0/tergm/R/mcmc.diagnostics.stergm.R | 6 tergm-3.6.0/tergm/R/print.stergm.R | 6 tergm-3.6.0/tergm/R/simulate.stergm.R | 24 -- tergm-3.6.0/tergm/R/stergm.CMLE.R | 17 - tergm-3.6.0/tergm/R/stergm.EGMME.GD.R | 14 - tergm-3.6.0/tergm/R/stergm.EGMME.R | 107 +++------ tergm-3.6.0/tergm/R/stergm.EGMME.SA.R | 22 - tergm-3.6.0/tergm/R/stergm.EGMME.initialfit.R | 6 tergm-3.6.0/tergm/R/stergm.R | 14 - tergm-3.6.0/tergm/R/stergm.getMCMCsample.R | 12 - tergm-3.6.0/tergm/R/stergm.utils.R | 6 tergm-3.6.0/tergm/R/summary.statistics.networkDynamic.R | 6 tergm-3.6.0/tergm/R/summary.stergm.R | 6 tergm-3.6.0/tergm/R/tergm-deprecated.R | 38 --- tergm-3.6.0/tergm/R/zzz.R | 8 tergm-3.6.0/tergm/inst/CITATION | 4 tergm-3.6.0/tergm/inst/NEWS.Rd | 32 ++ tergm-3.6.0/tergm/inst/doc/STERGM.pdf |binary tergm-3.6.0/tergm/man/control.simulate.stergm.Rd | 6 tergm-3.6.0/tergm/man/control.stergm.Rd | 51 ++-- tergm-3.6.0/tergm/man/ergm-constraints.Rd | 6 tergm-3.6.0/tergm/man/ergm-terms.Rd | 6 tergm-3.6.0/tergm/man/stergm.Rd | 12 - tergm-3.6.0/tergm/man/tergm-internal.Rd | 6 tergm-3.6.0/tergm/man/tergm-package.Rd | 6 tergm-3.6.0/tergm/man/tergm_MH_proposals.Rd | 6 tergm-3.6.0/tergm/src/DynSA.c | 52 ++-- tergm-3.6.0/tergm/src/DynSA.h | 14 - tergm-3.6.0/tergm/src/MCMCDyn.c | 166 ++++++++------ tergm-3.6.0/tergm/src/MCMCDyn.h | 28 +- tergm-3.6.0/tergm/src/MHproposals_DynMLE.c | 46 +-- tergm-3.6.0/tergm/src/MHproposals_DynMLE.h | 12 - tergm-3.6.0/tergm/src/MHproposals_DynMLE_block.c | 46 ++- tergm-3.6.0/tergm/src/MHproposals_DynMLE_block.h | 10 tergm-3.6.0/tergm/src/MHproposals_DynMoME.c | 62 ++--- tergm-3.6.0/tergm/src/MHproposals_DynMoME.h | 14 - tergm-3.6.0/tergm/src/changestats_duration.c | 13 - tergm-3.6.0/tergm/src/changestats_duration.h | 6 tergm-3.6.0/tergm/src/godfather.c | 26 +- tergm-3.6.0/tergm/src/godfather.h | 6 tergm-3.6.0/tergm/src/include_stubs.c | 6 tergm-3.6.0/tergm/src/init.c | 6 tergm-3.6.0/tergm/tests/combine.networks.R | 6 tergm-3.6.0/tergm/tests/degree.mean.age.R | 6 tergm-3.6.0/tergm/tests/dynamic_EGMME.R | 6 tergm-3.6.0/tergm/tests/dynamic_EGMME.simple.R | 6 tergm-3.6.0/tergm/tests/dynamic_MLE.R | 40 +-- tergm-3.6.0/tergm/tests/dynamic_MLE_2.R | 42 ++- tergm-3.6.0/tergm/tests/dynamic_MLE_blockdiag.R | 40 +-- tergm-3.6.0/tergm/tests/dynamic_MLE_blockdiag.bipartite.R | 45 ++- tergm-3.6.0/tergm/tests/sim_gf_sum.R | 6 tergm-3.6.0/tergm/tests/simulate_networkDynamic.R | 6 tergm-3.6.0/tergm/tests/tergm_offset_tests.R | 6 tergm-3.6.0/tergm/tests/tergm_parallel.R | 6 75 files changed, 757 insertions(+), 715 deletions(-)
Title: User-specified Terms for the statnet Suite of Packages
Description: A template package to demonstrate the use of user-specified statistics for use in 'ergm' models as part of the Statnet suite of packages.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Martina Morris [aut]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.userterms versions 3.9.0 dated 2018-08-25 and 3.10.0 dated 2019-05-15
DESCRIPTION | 13 +++++++------ LICENSE | 2 +- MD5 | 30 +++++++++++++++--------------- R/InitErgmTerm.users.R | 6 +++--- R/zzz.R | 6 +++--- inst/CITATION | 8 ++++---- inst/doc/ergmuserterms.pdf |binary man/ergm.userterms-package.Rd | 6 +++--- man/eut-upgrade.Rd | 6 +++--- man/mindegree-term.Rd | 6 +++--- src/changestats.users.c | 6 +++--- src/changestats.users.h | 6 +++--- src/include_stubs.c | 6 +++--- src/init.c | 6 +++--- tests/examples.R | 6 +++--- tests/requireNamespaceTest.R | 10 +++++----- 16 files changed, 62 insertions(+), 61 deletions(-)
More information about ergm.userterms at CRAN
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Title: Fit, Simulate and Diagnose Exponential-Family Models for
Rank-Order Relational Data
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are ranks.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Carter T. Butts [ctb],
Mark S. Handcock [ctb],
David R. Hunter [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.rank versions 1.1.0 dated 2018-08-25 and 1.2.0 dated 2019-05-15
DESCRIPTION | 12 ++++++---- LICENSE | 12 +++++----- MD5 | 44 +++++++++++++++++++-------------------- NAMESPACE | 3 -- R/InitErgmReference.R | 6 ++--- R/InitWtErgmProposal.R | 6 ++--- R/InitWtErgmTerm_rank.R | 6 ++--- R/zzz.R | 6 ++--- build/partial.rdb |binary inst/CITATION | 14 ++++++------ inst/NEWS.Rd | 53 +++++++++++++++++++++++++++++++++++++++-------- man/ergm-references.Rd | 6 ++--- man/ergm-terms.Rd | 6 ++--- man/ergm.rank-package.Rd | 6 ++--- man/newcomb.Rd | 6 ++--- src/include_stubs.c | 6 ++--- src/init.c | 6 ++--- src/wtMHproposals.c | 13 +++-------- src/wtMHproposals.h | 8 +++---- src/wtchangestat_rank.h | 6 ++--- src/wtchangestats_rank.c | 6 ++--- src/wtchangestats_rank.h | 6 ++--- tests/termTests_rank.R | 6 ++--- 23 files changed, 138 insertions(+), 105 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [ctb],
David R. Hunter [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.count versions 3.3.0 dated 2018-08-25 and 3.4.0 dated 2019-05-15
DESCRIPTION | 12 +++--- LICENSE | 2 - MD5 | 42 +++++++++++----------- NAMESPACE | 3 - R/InitErgmReference.R | 6 +-- R/InitWtErgmProposal.R | 6 +-- R/InitWtErgmTerm.R | 6 +-- R/zzz.R | 6 +-- inst/CITATION | 8 ++-- inst/NEWS.Rd | 86 +++++++++++++++++++++++++++++++--------------- man/ergm-references.Rd | 6 +-- man/ergm-terms.Rd | 6 +-- man/ergm.count-package.Rd | 6 +-- man/zach.Rd | 6 +-- src/include_stubs.c | 6 +-- src/init.c | 6 +-- src/wtMHproposals.c | 22 +++++------ src/wtMHproposals.h | 20 +++++----- src/wtchangestats.c | 6 +-- src/wtchangestats.h | 6 +-- tests/valued_fit.R | 8 ++-- tests/valued_sim.R | 6 +-- 22 files changed, 157 insertions(+), 124 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-24 1.1
2014-12-22 1.0