Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.1.0 dated 2016-06-17 and 1.1.4 dated 2016-07-21
DESCRIPTION | 8 +- MD5 | 31 +++++++---- NAMESPACE | 13 +++- NEWS | 3 - R/PointProcessClasses.R |only R/RcppExports.R |only R/llag.R | 11 ++- R/qmle.R | 79 +++++++++++++++++++++++----- R/setHawkes.R | 91 +++++++++++++++------------------ R/setPpr.R |only R/simulateForMapsIntegralAndOperator.R | 10 ++- R/simulateForPpr.R |only R/simulateMultiProcess.R | 6 +- man/info.Ppr.Rd |only man/qmle.Rd | 9 ++- man/setHawkes.Rd |only man/setPpr.Rd |only man/yuima.Hawkes.Rd |only man/yuima.Ppr.Rd |only src/RcppExports.cpp |only src/cce_functions.c | 10 +++ src/qmlecpp.cpp |only 22 files changed, 181 insertions(+), 90 deletions(-)
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.5 dated 2016-03-07 and 1.5.6 dated 2016-07-21
DESCRIPTION | 10 ++++----- MD5 | 28 ++++++++++++------------- R/AIC.ssym.R | 6 ----- R/BIC.ssym.R | 6 ----- R/envelope.R | 12 ++++++---- R/plot.ssym.R | 4 +-- R/ssym.l.R | 8 +++++-- R/ssym.l2.R | 4 +-- R/ssym.nl.R | 3 +- man/ncs.Rd | 7 +++--- man/psp.Rd | 5 ++-- man/ssym-package.Rd | 10 +++++---- man/ssym.l.Rd | 34 ++++++++++++++++++++----------- man/ssym.l2.Rd | 18 +++++++++------- man/ssym.nl.Rd | 57 ++++++++++++++++++++++++++++++---------------------- 15 files changed, 118 insertions(+), 94 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [ctb],
Dirk Eddelbuettel [ctb] (ziggurat rnorm sources),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 1.9.0.1 dated 2016-07-10 and 1.9.16 dated 2016-07-21
DESCRIPTION | 8 - MD5 | 88 +++++++++--------- NAMESPACE | 7 - R/CanonizeRanPars.R | 8 + R/GLM.fit.R | 7 + R/HLCor.R | 3 R/HLfit.R | 48 ++++------ R/HLfit_Internals.R | 159 ++++++++++++++++++++++++++++------ R/HLframes.R | 146 ++++++++++++++++--------------- R/LR.R | 32 +++--- R/MakeCovEst.R | 8 - R/SEMbetalambda.R | 2 R/auglinmodfit.R | 8 - R/confint.R | 87 ++++++++++++------ R/corrHLfit.R | 3 R/corrMM.LRT.R | 35 ++++--- R/extractors.R | 22 ++-- R/fitme.R | 14 ++ R/mapMM.R | 12 +- R/predict.R | 33 +++++-- R/preprocess.R | 20 ++-- R/simulate.HL.R | 173 +++++++++++++++++++------------------ R/spaMM.data.R | 10 +- R/summary.HL.R | 44 +++++---- inst/NEWS.Rd | 28 +++++ man/COMPoisson.Rd | 2 man/HLfit.Rd | 4 man/fitme.Rd | 2 man/mapMM.Rd | 42 ++++---- man/options.Rd | 6 - man/predict.Rd | 25 ++++- man/seaMask.Rd | 4 man/simulate.HLCor.Rd | 10 +- man/spaMM-internal.Rd | 5 + man/spaMMcolors.Rd | 3 src/COMPoisson.cpp | 2 src/Makevars.win | 3 src/Ziggurat.h | 2 src/corMatern.cpp | 6 - src/gsl_bessel.cpp | 1 src/pMVN.cpp | 3 tests/testthat/test-CAR.R | 14 ++ tests/testthat/test-HLfit.R | 5 - tests/testthat/test-filled.mapMM.R | 8 - tests/testthat/test-predVar.R | 16 +++ 45 files changed, 718 insertions(+), 450 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to http://www.sealifebase.org data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.1.0 dated 2015-11-10 and 2.1.1 dated 2016-07-21
DESCRIPTION | 8 - MD5 | 117 ++++++++++---------- NAMESPACE | 4 NEWS | 11 + R/00-endpoint.R | 90 +++++++++++++-- R/check_and_parse.R | 10 - R/common_names.R | 2 R/distribution.R | 113 ++++++++++++++----- R/heartbeat.R | 3 R/list_fields.R | 2 R/load_taxa.R | 31 ++++- R/species.R | 7 - R/synonyms.R | 2 R/trophic_ecology.R | 6 - README.md | 155 ++++++++++++++++---------- build/vignette.rds |binary inst/CITATION |only inst/doc/tutorial.R |only inst/doc/tutorial.Rmd | 128 ++++++++++++++++++++++ inst/doc/tutorial.html | 213 +++++++++++++++++++++++++++++++++++-- man/c_code.Rd |only man/common_names.Rd | 4 man/country.Rd |only man/countrysub.Rd |only man/countrysubref.Rd |only man/diet.Rd | 8 - man/distribution.Rd | 10 + man/ecology.Rd | 8 - man/ecosystem.Rd | 8 - man/faoareas.Rd | 10 + man/fecundity.Rd | 8 - man/fooditems.Rd | 8 - man/heartbeat.Rd | 3 man/introductions.Rd | 10 + man/length_freq.Rd | 10 + man/length_length.Rd | 10 + man/length_weight.Rd | 10 + man/load_taxa.Rd | 2 man/maturity.Rd | 8 - man/morphology.Rd | 10 + man/morphometrics.Rd | 10 + man/occurrence.Rd | 27 ---- man/oxygen.Rd | 8 - man/popchar.Rd | 8 - man/popgrowth.Rd | 8 - man/popqb.Rd | 8 - man/predators.Rd | 8 - man/ration.Rd | 8 - man/reproduction.Rd | 10 + man/sci_to_common.Rd | 2 man/spawning.Rd | 8 - man/species.Rd | 8 - man/speed.Rd | 8 - man/stocks.Rd | 8 - man/swimming.Rd | 8 - man/synonyms.Rd | 6 - man/validate_names.Rd | 2 tests/testthat/test_commonnames.R | 4 tests/testthat/test_endpoint.R | 11 + tests/testthat/test_load_taxa.R | 6 - tests/testthat/test_maturity.R |only tests/testthat/test_species.R | 46 +++++++ tests/testthat/test_species_list.R | 2 63 files changed, 931 insertions(+), 312 deletions(-)
Title: Helper Functions for QCA in R
Description: Helper functions for Qualitative Comparative Analysis: evaluate and
plot Boolean formulae on fuzzy set score data, apply Boolean operations, compute
consistency and coverage measures.
Author: Jirka Lewandowski <jirka.lewandowski@wzb.eu> [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between QCAtools versions 0.2.1 dated 2016-01-13 and 0.2.2 dated 2016-07-21
DESCRIPTION | 7 ++++--- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/xyplot.R | 5 +++-- man/QCAtools.Rd | 2 +- man/boolean.Rd | 3 +-- man/consistency.Rd | 6 ++---- man/evaluate_dnf.Rd | 3 +-- man/format_dnf.Rd | 2 +- man/formula_to_function.Rd | 3 +-- man/plot.qca.Rd | 5 +++-- man/xyplot.Rd | 3 +-- 12 files changed, 30 insertions(+), 33 deletions(-)
Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for
multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>
Diff between imputeMulti versions 0.5.3 dated 2016-06-16 and 0.6.1 dated 2016-07-21
DESCRIPTION | 12 ++- MD5 | 17 ++-- NAMESPACE | 9 ++ R/class_imputeMulti.R | 134 ++++++---------------------------- R/int-count_levels.R | 4 - R/methods_imputeMulti.R |only man/imputeMulti-class.Rd | 24 ++++-- man/mod_imputeMulti-class.Rd | 48 ++++++++++-- man/summary-imputeMulti-method.Rd | 2 man/summary-mod_imputeMulti-method.Rd | 2 10 files changed, 116 insertions(+), 136 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 2.1.3 dated 2016-07-15 and 2.1.4 dated 2016-07-21
DESCRIPTION | 14 ++--- MD5 | 46 +++++++++++-------- NAMESPACE | 5 +- NEWS | 11 ++++ R/calc-tern-tlr2xy.R | 11 ++-- R/coord-tern.R | 101 ++++++++++++++++++++++--------------------- R/geom-mask.R | 101 ++++++++++++++++++++----------------------- R/gg-internal.R | 3 - R/onLoad.R | 8 ++- R/plot-build.R | 2 R/plot.R | 15 ------ R/scales-tern.R | 6 +- R/theme-defaults.R | 12 +++-- R/theme-elements.R | 2 R/theme-mesh.R |only R/utilities-help.R | 5 +- R/utilities.R | 76 +++++++++++++++++++++++--------- build/partial.rdb |binary demo |only man/coord-tern.Rd | 2 man/getBreaks.Rd |only man/ggplot.Rd | 13 ----- man/scale_tern_continuous.Rd | 6 +- man/theme_mesh.Rd |only man/undocumented.Rd | 14 ----- 25 files changed, 237 insertions(+), 216 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous data and utility functions
for manipulating data and your R environment.
Author: Stephen Turner <vustephen@gmail.com>
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.7 dated 2016-06-15 and 0.1.8 dated 2016-07-21
DESCRIPTION | 7 ++++--- MD5 | 20 ++++++++++++++------ NAMESPACE | 5 +++++ NEWS.md | 7 +++++++ R/Mode.R |only R/are_all_equal.R |only R/gg_na.R |only R/gghues.R | 5 +++-- R/jsd.R |only README.md | 2 ++ man/Mode.Rd |only man/are_all_equal.Rd |only man/gg_na.Rd |only man/gghues.Rd | 5 +++-- man/jsd.Rd |only 15 files changed, 38 insertions(+), 13 deletions(-)
Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search 'API' (http://api.plos.org/) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.5.6 dated 2016-02-15 and 0.6.0 dated 2016-07-21
DESCRIPTION | 8 - MD5 | 50 ++++---- NAMESPACE | 2 NEWS.md | 18 +++ R/citations.R | 25 +--- R/fulltext.R | 48 +++++--- R/plosviews.R | 2 R/rplos-package.R | 2 R/searchplos.R | 2 README.md | 201 ++++++++++++++++++----------------- build/vignette.rds |binary man/citations.Rd | 8 - man/full_text_urls.Rd | 11 + man/plos_fulltext.Rd | 3 man/plosabstract.Rd | 12 ++ man/plosauthor.Rd | 12 ++ man/plosfigtabcaps.Rd | 12 ++ man/plossubject.Rd | 12 ++ man/plostitle.Rd | 12 ++ man/searchplos.Rd | 12 ++ tests/testthat/test-citations.R | 5 tests/testthat/test-facetplos.R | 2 tests/testthat/test-fulltext.R | 12 ++ tests/testthat/test-highplos.R | 2 tests/testthat/test-journalnamekey.R | 2 tests/testthat/test-plosviews.R | 10 + 26 files changed, 304 insertions(+), 181 deletions(-)
Title: Easy to Use Tools for Common Forms of Random Assignment
Description: Generates random assignments for common experimental
designs: simple, complete, blocked, and clustered.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between randomizr versions 0.4.0 dated 2016-07-20 and 0.4.1 dated 2016-07-21
DESCRIPTION | 8 +++--- MD5 | 28 +++++++++++----------- R/block_and_cluster_ra_probabilities.R | 38 +++++++++++++++++------------- R/block_ra_probabilities.R | 31 +++++++++++++++--------- R/cluster_ra_probabilities.R | 34 +++++++++++++++++--------- R/complete_ra_probabilities.R | 31 +++++++++++++++++------- R/helper_functions.R | 6 ++-- R/simple_ra_probabilities.R | 27 +++++++++++++++------ inst/doc/randomizr_vignette.html | 4 +-- man/block_and_cluster_ra_probabilities.Rd | 38 +++++++++++++++++------------- man/block_ra_probabilities.Rd | 27 +++++++++++++-------- man/cluster_ra_probabilities.Rd | 34 +++++++++++++++++--------- man/complete_ra_probabilities.Rd | 31 +++++++++++++++++------- man/simple_ra_probabilities.Rd | 27 +++++++++++++++------ tests/testthat/test-complete_ra.R | 1 15 files changed, 232 insertions(+), 133 deletions(-)
Title: Optimal Designs for Estimating the Slope Divided by the
Intercept
Description: Compute optimal experimental designs
that measure the slope divided by the intercept.
Author: Adam Kapelner, Abba Krieger and William J. Blanford
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between optDesignSlopeInt versions 1.0 dated 2016-04-13 and 1.1 dated 2016-07-21
CHANGELOG | 4 ++++ DESCRIPTION | 13 ++++++------- MD5 | 10 ++++++---- R/public.R | 31 ++++++++++++++++++++++++++----- data |only man/design_bakeoff.Rd | 8 +++++--- man/napth.Rd |only 7 files changed, 47 insertions(+), 19 deletions(-)
More information about optDesignSlopeInt at CRAN
Permanent link
Title: A Parallel Simulation Framework
Description: Functions for easy and reproducible simulation.
Author: Andrew Redd
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between harvestr versions 0.6.0 dated 2014-05-27 and 0.7.0 dated 2016-07-21
harvestr-0.6.0/harvestr/build |only harvestr-0.6.0/harvestr/inst/doc |only harvestr-0.6.0/harvestr/inst/tests |only harvestr-0.6.0/harvestr/tests/testthat-package.R |only harvestr-0.6.0/harvestr/vignettes/harvestr.Rnw |only harvestr-0.7.0/harvestr/DESCRIPTION | 18 harvestr-0.7.0/harvestr/MD5 | 76 +- harvestr-0.7.0/harvestr/NAMESPACE | 14 harvestr-0.7.0/harvestr/NEWS | 7 harvestr-0.7.0/harvestr/R/Interactive.R |only harvestr-0.7.0/harvestr/R/attributes.R |only harvestr-0.7.0/harvestr/R/gather.R | 710 +++++++++++---------- harvestr-0.7.0/harvestr/R/harvestr-package.R | 163 ++-- harvestr-0.7.0/harvestr/R/option.R |only harvestr-0.7.0/harvestr/R/utils.R | 176 ++--- harvestr-0.7.0/harvestr/R/withseed.R | 332 +++++---- harvestr-0.7.0/harvestr/README.md | 10 harvestr-0.7.0/harvestr/inst/examples/use_method.R | 4 harvestr-0.7.0/harvestr/man/Interactive.Rd |only harvestr-0.7.0/harvestr/man/bale.Rd | 3 harvestr-0.7.0/harvestr/man/called_from.Rd |only harvestr-0.7.0/harvestr/man/farm.Rd | 19 harvestr-0.7.0/harvestr/man/gather.Rd | 8 harvestr-0.7.0/harvestr/man/getAttr.Rd |only harvestr-0.7.0/harvestr/man/harvest.Rd | 15 harvestr-0.7.0/harvestr/man/harvestr.Rd | 18 harvestr-0.7.0/harvestr/man/is_seeded.Rd | 3 harvestr-0.7.0/harvestr/man/noattr.Rd | 5 harvestr-0.7.0/harvestr/man/plant.Rd | 19 harvestr-0.7.0/harvestr/man/plow.Rd | 16 harvestr-0.7.0/harvestr/man/reap.Rd | 14 harvestr-0.7.0/harvestr/man/seed_funs.Rd | 13 harvestr-0.7.0/harvestr/man/sprout.Rd | 14 harvestr-0.7.0/harvestr/man/total_time.Rd | 3 harvestr-0.7.0/harvestr/man/use_method.Rd | 7 harvestr-0.7.0/harvestr/tests/testthat |only harvestr-0.7.0/harvestr/tests/testthat.R |only harvestr-0.7.0/harvestr/vignettes/harvestr.Rmd |only harvestr-0.7.0/harvestr/vignettes/workflow.png |only 39 files changed, 922 insertions(+), 745 deletions(-)
Title: Generate, Visualise, and Compare Fast and Frugal Decision Trees
Description: Fast and Frugal Trees (FFTs) are very simple decision trees for
classifying cases (i.e.; breast cancer patients) into one of two classes (e.g.;
no cancer vs. true cancer). FFTs can be preferable to more complex algorithms (such as
logistic regression) because they are easy to communicate and implement, and are
robust against noisy data. This package contains several functions that allow users
to create, visualize, and test FFts from their input their own data.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>
Diff between FFTrees versions 1.1.0 dated 2016-07-19 and 1.1.1 dated 2016-07-21
DESCRIPTION | 8 ++--- MD5 | 47 +++++++++++++++-------------- NAMESPACE | 2 + R/FFTreesguide_function.R |only R/plotfft_function.R | 6 ++- R/zzz.R |only build/vignette.rds |binary inst/doc/fft_examples.R | 3 - inst/doc/fft_examples.Rmd | 12 +++---- inst/doc/fft_examples.html | 65 ++++++----------------------------------- inst/doc/fft_function.Rmd | 2 - inst/doc/fft_function.html | 10 +++--- inst/doc/fft_overview.R | 2 - inst/doc/fft_overview.Rmd | 12 ++++--- inst/doc/fft_overview.html | 71 +++++++++++++++++++++++++++++++++++++++------ inst/doc/fft_plot.R | 36 ++++++++++++++++++---- inst/doc/fft_plot.Rmd | 66 ++++++++++++++++++++++++++++++++++------- inst/doc/fft_plot.html | 65 +++++++++++++++++++++++++++++++---------- man/FFTrees.guide.Rd |only vignettes/fft.bib | 30 +++++++++++++++++++ vignettes/fft_examples.Rmd | 12 +++---- vignettes/fft_examples.md | 65 +++-------------------------------------- vignettes/fft_function.Rmd | 2 - vignettes/fft_overview.Rmd | 12 ++++--- vignettes/fft_plot.Rmd | 66 ++++++++++++++++++++++++++++++++++------- vignettes/fft_plot.md | 70 +++++++++++++++++++++++++++++++++++--------- 26 files changed, 420 insertions(+), 244 deletions(-)
Title: Modeling Animal Movement with Continuous-Time Discrete-Space
Markov Chains
Description: Software to facilitates taking movement data in xyt format and pairing it with raster covariates within a continuous time Markov chain (CTMC) framework. As described in Hanks et al. (2015) <DOI:10.1214/14-AOAS803> , this allows flexible modeling of movement in response to covariates (or covariate gradients) with model fitting possible within a Poisson GLM framework.
Author: Ephraim Hanks
Maintainer: Ephraim Hanks <hanks@psu.edu>
Diff between ctmcmove versions 1.2.5 dated 2016-07-20 and 1.2.6 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ctmc2glm.R | 7 +++++-- 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Modeling Correlational Magnitude Transformations in
Discretization Contexts
Description: Modeling the correlation transitions under specified distributional assumptions within the realm of discretization in the context of the latency and threshold concepts.
Author: Rawan Allozi, Hakan Demirtas
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Diff between CorrToolBox versions 1.0 dated 2016-07-19 and 1.1 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/corrZ2ophi.R | 4 ++-- R/mps2cps.R | 2 +- R/ophi2corrZ.R | 4 ++-- R/ophi2poly.R | 4 ++-- R/ordY.R | 2 +- R/poly2ophi.R | 4 ++-- R/pps2ps.R | 2 +- R/ps2pps.R | 2 +- man/CorrToolBox-package.Rd | 4 ++-- 11 files changed, 28 insertions(+), 28 deletions(-)
Title: Soundscape Ecology
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera <ljvillanueva@coquipr.com>
Diff between soundecology versions 1.3.1 dated 2015-12-30 and 1.3.2 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 5 +++++ R/acoustic_complexity_index.R | 29 +++++++++++++++++++++++++++++ R/acoustic_diversity.R | 21 ++++++++++++++++++++- R/acoustic_evenness.R | 22 +++++++++++++++++++++- R/bioacoust_index.R | 21 +++++++++++++++++++++ R/ndsi.R | 32 ++++++++++++++++++++++++++++++++ R/sound_raster.R | 13 +++++++++++++ inst/doc/ACIandSeewave.html | 6 ++++++ man/soundecology.package.Rd | 4 ++-- 11 files changed, 163 insertions(+), 18 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.6-2 dated 2016-05-11 and 3.6-3 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/draw.ellipse.R | 18 +++++++++++------- R/stackpoly.R | 2 ++ man/draw.ellipse.Rd | 2 +- man/stackpoly.Rd | 3 ++- 7 files changed, 31 insertions(+), 19 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-12 dated 2016-03-03 and 1.8-13 dated 2016-07-21
ChangeLog | 90 ++++++ DESCRIPTION | 6 MD5 | 122 ++++---- NAMESPACE | 4 R/bam.r | 393 +++++----------------------- R/coxph.r | 6 R/efam.r | 2 R/fast-REML.r | 220 +++++++++++---- R/gam.fit3.r | 220 ++++++++++++++- R/gam.fit4.r | 206 +++++++++++--- R/gamlss.r | 459 ++++++++++++++++++++++++++++++++- R/gamm.r | 15 - R/jagam.r | 8 R/mgcv.r | 298 +++++++++++++++------ R/mvam.r | 7 R/plots.r | 31 +- R/smooth.r | 134 +++++++-- man/Tweedie.Rd | 5 man/anova.gam.Rd | 11 man/bam.Rd | 32 -- man/bam.update.Rd | 4 man/bug.reports.mgcv.Rd | 2 man/cSplineDes.Rd | 3 man/coxph.Rd | 5 man/family.mgcv.Rd | 5 man/formula.gam.Rd | 4 man/gam.Rd | 16 - man/gam.outer.Rd | 4 man/gamm.Rd | 2 man/gaulss.Rd | 5 man/gevlss.Rd |only man/identifiability.Rd |only man/jagam.Rd | 2 man/ldTweedie.Rd | 19 - man/mgcv-FAQ.Rd | 2 man/multinom.Rd | 7 man/mvn.Rd | 5 man/negbin.Rd | 5 man/ocat.Rd | 5 man/one.se.rule.Rd |only man/predict.gam.Rd | 6 man/random.effects.Rd | 17 + man/s.Rd | 6 man/scat.Rd | 5 man/sdiag.Rd | 6 man/smooth.construct.bs.smooth.spec.Rd | 20 + man/smooth2random.Rd |only man/smoothCon.Rd | 6 man/t2.Rd | 8 man/te.Rd | 9 man/uniquecombs.Rd | 23 + man/ziP.Rd | 5 man/ziplss.Rd | 5 src/discrete.c | 5 src/gdi.c | 12 src/init.c | 1 src/magic.c | 6 src/mat.c | 14 - src/matrix.c | 36 +- src/mgcv.c | 3 src/mgcv.h | 3 src/misc.c | 144 ++++++++++ src/soap.c | 3 src/sparse-smooth.c | 3 64 files changed, 1921 insertions(+), 789 deletions(-)
Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with spatial-temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).
Author: Jan Philipp Dietrich,
Benjamin Bodirsky,
Misko Stevanovic,
Lavinia Baumstark,
Christoph Bertram,
Markus Bonsch,
Anastasis Giannousakis,
Florian Humpenoeder,
David Klein,
Ina Neher,
Michaja Pehl,
Anselm Schultes
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between magclass versions 3.74 dated 2015-11-18 and 3.85 dated 2016-07-21
DESCRIPTION | 8 MD5 | 22 +- R/as.quitte.R | 28 +- R/calibrate_it.R | 1 R/convert.report.R | 1 R/is.quitte.R | 70 +++--- R/mbind.R | 3 R/read.magpie.R | 377 +++++++++++++++++----------------- R/read.report.R | 232 ++++++++++----------- R/write.magpie.R | 523 +++++++++++++++++++++++------------------------- man/magclass-package.Rd | 17 + man/quitte-class.Rd | 3 12 files changed, 659 insertions(+), 626 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin <davidbolin@gmail.com> and Finn Lindgren <finn.lindgren@gmail.com>
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.2.1 dated 2016-07-06 and 2.2.2 dated 2016-07-21
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Item Focused Trees for the Identification of Items in
Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of
items and variables that induce Differential Item Functioning (DIF) based on the
Rasch Model or the Logistic Regression Approach for DIF detection.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Diff between DIFtree versions 2.0.3 dated 2016-06-30 and 2.0.4 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/tree_Rasch.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Combine Multidimensional Arrays
Description: Combine multidimensional arrays into a single array.
This is a generalization of 'cbind' and 'rbind'. Works with
vectors, matrices, and higher-dimensional arrays. Also
provides functions 'adrop', 'asub', and 'afill' for manipulating,
extracting and replacing data in arrays.
Author: Tony Plate <tplate@acm.org> and Richard Heiberger
Maintainer: Tony Plate <tplate@acm.org>
Diff between abind versions 1.4-3 dated 2015-03-13 and 1.4-5 dated 2016-07-21
ChangeLog | 7 +++++ DESCRIPTION | 9 +++--- MD5 | 20 +++++++-------- NAMESPACE | 2 + R/adrop.R | 9 +++++- R/afill.R | 3 +- R/asub.R | 9 +++++- man/adrop.Rd | 4 ++- man/asub.Rd | 6 +++- tests/afill.R | 17 +++++++++++++ tests/afill.Rout.save | 65 ++++++++++++++++++++++++++++++++++++++------------ 11 files changed, 114 insertions(+), 37 deletions(-)
Title: Social Relation Model (SRM) Analyses for Single or Multiple
Groups
Description: Social Relation Model (SRM) analyses for single or multiple
round-robin groups are performed. These analyses are either based on one
manifest variable, one latent construct measured by two manifest variables,
two manifest variables and their bivariate relations, or two latent
constructs each measured by two manifest variables. Within-group t-tests
for variance components and covariances are provided for single groups.
For multiple groups two types of significance tests are provided:
between-groups t-tests (as in SOREMO) and enhanced standard errors based on
Lashley and Bond (1997) <DOI:10.1037/1082-989X.2.3.278>. Handling for missing values is provided.
Author: F. D. Schönbrodt, M. D. Back, S. C. Schmukle
Maintainer: Felix Schönbrodt <felix.schoenbrodt@psy.lmu.de>
Diff between TripleR versions 1.5.1 dated 2016-04-11 and 1.5.3 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 14 ++++++++++++++ R/RR.r | 8 +++++++- 4 files changed, 28 insertions(+), 8 deletions(-)
Title: Multi-Resolution Scanning for Cross-Sample Differences
Description: An implementation of the MRS algorithm for comparison across distributions.
The model is based on a nonparametric process taking the form of a Markov model
that transitions between a "null" and an "alternative" state
on a multi-resolution partition tree of the sample space.
MRS effectively detects and characterizes a variety of underlying differences.
These differences can be visualized using several plotting functions.
Author: Jacopo Soriano and Li Ma
Maintainer: Jacopo Soriano <jsoriano.stat@gmail.com>
Diff between MRS versions 1.2 dated 2016-07-17 and 1.2.1 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/recursion.cpp | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Bicycling Data Analysis with R
Description: Functions to facilitate cycling analysis within the R environment.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between elpatron versions 0.0.2 dated 2016-06-05 and 0.0.3 dated 2016-07-21
elpatron-0.0.2/elpatron/NEWS |only elpatron-0.0.2/elpatron/src/fit_r.cpp |only elpatron-0.0.3/elpatron/DESCRIPTION | 10 +++++----- elpatron-0.0.3/elpatron/MD5 | 26 +++++++++++++------------- elpatron-0.0.3/elpatron/NAMESPACE | 2 +- elpatron-0.0.3/elpatron/NEWS.md |only elpatron-0.0.3/elpatron/R/cleaning.R | 6 ++++-- elpatron-0.0.3/elpatron/R/elpatron-package.R | 8 +++++--- elpatron-0.0.3/elpatron/R/file_import.R | 8 ++++---- elpatron-0.0.3/elpatron/R/utils.R | 2 +- elpatron-0.0.3/elpatron/man/clean_bikedata.Rd | 6 ++++-- elpatron-0.0.3/elpatron/man/import_ride.Rd | 2 +- elpatron-0.0.3/elpatron/man/pipe.Rd | 2 +- elpatron-0.0.3/elpatron/src/fit.h | 2 +- elpatron-0.0.3/elpatron/src/fit_field.cpp | 1 - elpatron-0.0.3/elpatron/src/parse_fit_r.cpp |only 16 files changed, 40 insertions(+), 35 deletions(-)
Title: A Penalty Approach to Differential Item Functioning in Rasch
Models
Description: Performs DIFlasso, a method to detect DIF (Differential Item Functioning) in Rasch Models. It can handle settings with many variables and also metric variables.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@stat.uni-muenchen.de>
Diff between DIFlasso versions 1.0-1 dated 2014-04-22 and 1.0-2 dated 2016-07-21
DESCRIPTION | 17 ++--- MD5 | 24 +++---- NAMESPACE | 6 + R/DIFlasso.R | 148 +++++++++++++++++++++++++++++--------------- data/simul.data.rda |binary man/DIFlasso-package.Rd | 6 - man/DIFlasso.Rd | 26 +++++-- man/plot.DIFlasso.Rd | 4 - man/plot.DIFlasso.refit.Rd | 4 - man/print.DIFlasso.Rd | 4 - man/print.DIFlasso.refit.Rd | 4 - man/refitDIFlasso.Rd | 4 - man/simul.data.Rd | 27 +++----- 13 files changed, 171 insertions(+), 103 deletions(-)
Title: FLuctuation ANalysis on Mutation Models
Description: Tools for fluctuations analysis of mutant cells counts.
Author: Adrien Mazoyer [aut, cre],
Remy Drouilhet [aut],
Stephane Despreaux [aut],
Bernard Ycart [aut]
Maintainer: Adrien Mazoyer <Adrien.Mazoyer@imag.fr>
Diff between flan versions 0.1 dated 2016-06-03 and 0.2 dated 2016-07-21
DESCRIPTION | 18 ++++++++--------- MD5 | 16 +++++++-------- R/flan.R | 31 ++++++++++++++++------------- data/david.RData |binary man/mutestim.Rd | 3 +- src/FLAN_Clone.cpp | 47 ++++++++++++++++++++++----------------------- src/FLAN_MutationModel.cpp | 19 ++++++++++++++---- src/FLAN_Sim.cpp | 2 - src/MATH_Function.cpp | 5 +--- 9 files changed, 78 insertions(+), 63 deletions(-)
Title: Clinical Significance Functions
Description: Functions for calculating clinical significance.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between clinsig versions 1.1 dated 2015-10-19 and 1.2 dated 2016-07-21
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NAMESPACE | 6 +-- NEWS | 4 ++ R/clinsig.R | 37 +++++++++++++++++-- man/clinsig.Rd | 107 +++++++++++++++++++++++++++++++++++++++++---------------- 6 files changed, 127 insertions(+), 47 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.62 dated 2016-02-02 and 0.63 dated 2016-07-21
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++++-------- NAMESPACE | 3 +++ R/Rxiv.R |only R/WLVmix.R |only R/bball.R | 4 ++-- R/medde.R | 5 +++-- demo/00Index | 1 + demo/Brown.R |only inst/ChangeLog | 16 +++++++++++++++- man/Rxiv.Rd |only man/WLVmix.Rd |only man/bball.Rd | 4 ++-- man/medde.Rd | 3 ++- 14 files changed, 44 insertions(+), 19 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-6 dated 2016-03-26 and 0.7-7 dated 2016-07-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/weights.R | 6 ++---- src/bsC.c | 1 + 4 files changed, 10 insertions(+), 11 deletions(-)