Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.5 dated 2015-10-02 and 2.1.6 dated 2015-11-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/ReadGrib.R | 23 ++++++++++++++++++++--- man/PlotWindProfile.Rd | 2 +- man/ReadGrib.Rd | 9 +++++++-- 6 files changed, 40 insertions(+), 15 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data. Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison test according
to Nemenyi is also provided in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 1.3 dated 2015-11-07 and 2.0 dated 2015-11-13
DESCRIPTION | 8 +-- MD5 | 29 ++++++----- NAMESPACE | 8 ++- R/dunn.test.control.R |only R/posthoc.kruskal.dunn.test.R |only R/posthoc.kruskal.nemenyi.test.R | 2 inst/CITATION |only inst/NEWS.Rd | 15 +++++ inst/doc/PMCMR.R | 54 +++++++++++++++++---- inst/doc/PMCMR.Rnw | 89 +++++++++++++++++++++++++++++++---- inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 24 ++++++--- man/dunn.test.control.Rd |only man/posthoc.friedman.nemenyi.test.Rd | 4 + man/posthoc.kruskal.dunn.test.Rd |only man/posthoc.kruskal.nemenyi.test.Rd | 2 vignettes/PMCMR.Rnw | 89 +++++++++++++++++++++++++++++++---- vignettes/PMCMR.bib | 35 +++++++++++++ 18 files changed, 303 insertions(+), 56 deletions(-)
Title: Penalized Regression-Based Clustering Method
Description: Clustering is unsupervised and exploratory in nature. Yet, it can be performed through penalized regression with grouping pursuit. In this package, we provide two algorithms for fitting the penalized regression-based clustering (PRclust). One algorithm is based on quadratic penalty and difference convex method. Another algorithm is based on difference convex and ADMM, called DC-ADD, which is more efficient. Generalized cross validation was provided to select the tuning parameters. Rand index, adjusted Rand index and Jaccard index were provided to estimate the agreement between estimated cluster memberships and the truth.
Author: Chong Wu, Wei Pan
Maintainer: Chong Wu <wuxx0845@umn.edu>
Diff between prclust versions 1.0 dated 2015-11-06 and 1.1 dated 2015-11-13
prclust-1.0/prclust/README.md |only prclust-1.1/prclust/DESCRIPTION | 10 +++++----- prclust-1.1/prclust/MD5 | 9 ++++----- prclust-1.1/prclust/R/GCVOrignial.R | 2 +- prclust-1.1/prclust/man/PRclust.Rd | 6 ------ prclust-1.1/prclust/man/prclust-package.Rd | 4 ++-- 6 files changed, 12 insertions(+), 19 deletions(-)
Title: Bayesian Non-Parametric Dependent Models for Time-Indexed
Functional Data
Description: Estimates a collection of time-indexed functions under
either of Gaussian process (GP) or intrinsic Gaussian Markov
random field (iGMRF) prior formulations where a Dirichlet process
mixture allows sub-groupings of the functions to share the same
covariance or precision parameters. The GP and iGMRF formulations
both support any number of additive covariance or precision terms,
respectively, expressing either or both of multiple trend and
seasonality.
Author: Terrance Savitsky
Maintainer: Terrance Savitsky <tds151@gmail.com>
Diff between growfunctions versions 0.11 dated 2014-12-09 and 0.12 dated 2015-11-13
DESCRIPTION | 19 +- MD5 | 72 +++++----- NAMESPACE | 5 NEWS | 10 + R/gp_car_fit_compare_facet.R | 129 ++++++++++------- R/gp_informative_compare_plot.R | 8 - R/gpdpgrow.R | 8 - R/help.R | 219 +++++++++++++++++------------- man/MSPE.Rd | 91 ++++++------ man/cluster_plot.Rd | 43 +++-- man/cps.Rd | 19 +- man/fit_compare.Rd | 142 +++++++++++-------- man/gen_informative_sample.Rd | 55 +++---- man/gmrfdpPost.Rd | 31 ++-- man/gmrfdpgrow.Rd | 63 ++++---- man/gpBFixPost.Rd | 9 - man/gpFixPost.Rd | 9 - man/gpPost.Rd | 9 - man/gpdpPost.Rd | 11 - man/gpdpbPost.Rd | 11 - man/gpdpgrow.Rd | 107 +++++++------- man/growfunctions-package.Rd | 259 ++++++++++++++++++++---------------- man/informative_plot.Rd | 85 +++++------ man/plot_cluster.Rd | 11 - man/predict_functions.Rd | 3 man/predict_functions.gmrfdpgrow.Rd | 29 ++-- man/predict_functions.gpdpgrow.Rd | 27 +-- man/predict_plot.Rd | 55 +++---- man/samples.Rd | 3 man/samples.gmrfdpgrow.Rd | 3 src/dpmix.cpp | 4 src/gp.cpp | 2 src/gpbfix.cpp | 2 src/gpdpbmix.cpp | 6 src/gpdpmix.cpp | 6 src/gpdpmix_moves.cpp | 14 - src/gpfix.cpp | 2 37 files changed, 863 insertions(+), 718 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native binary
(ENVI) format directly into R based on the widely applied 'raster' package;
calculate monthly value composites (e.g. maximum value composites, MVC) from the
bi-monthly input data; and derive long-term monotonous trends from the
Mann-Kendall trend test, optionally featuring pre-whitening to
account for lag-1 autocorrelation.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.2.0 dated 2015-10-26 and 0.3.0 dated 2015-11-13
DESCRIPTION | 25 +- MD5 | 36 +-- NAMESPACE | 5 R/downloadGimms.R | 91 ++++++- R/gimms-package.R | 54 ++-- R/monthlyComposite.R | 180 +++++++-------- R/rasterizeGimms.R | 2 R/rearrangeFiles.R | 171 +++++++------- R/significantTau.R |only R/updateInventory.R | 19 + README.md | 562 +----------------------------------------------- man/createHeader.Rd | 3 man/downloadGimms.Rd | 36 ++- man/gimms-package.Rd | 2 man/monthlyComposite.Rd | 7 man/monthlyIndices.Rd | 5 man/rasterizeGimms.Rd | 5 man/rearrangeFiles.Rd | 10 man/significantTau.Rd |only man/updateInventory.Rd | 12 - 20 files changed, 404 insertions(+), 821 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.3.1 dated 2015-10-04 and 0.3.2 dated 2015-11-13
DESCRIPTION | 18 +- MD5 | 71 +++++----- NAMESPACE | 2 NEWS | 6 R/bf.R | 10 - R/bfse.R | 1 R/calcbf.R | 18 +- R/comparebinlinks.R | 6 R/geobayes-package.R | 6 R/geoesteb.R | 25 +-- R/mcsp2.R | 24 ++- demo/rhizoctonia5.R | 22 +-- demo/yield3.R | 6 demo/yield4.R | 6 man/bf1skel.Rd | 9 - man/bf2new.Rd | 9 - man/bf2optim.Rd | 3 man/bfse.Rd | 4 man/comparebinlinks.Rd | 3 man/ebsglmm.Rd | 11 - man/ebstrga.Rd | 3 man/geoBayes.Rd | 9 - man/linkfcn.Rd | 7 man/mcmcmake.Rd | 3 man/mcsglmm.Rd | 3 man/mcstrga.Rd | 3 man/mkpredgrid2d.Rd | 3 man/plotbf2.Rd | 3 man/rhizoctonia.Rd | 3 man/stackdata.Rd | 3 src/Makevars | 11 - src/betaprior.f90 |only src/bfsp.f90 | 29 ---- src/calcb2.f90 | 114 ++++------------ src/llik.f90 | 45 ------ src/mcsp2.f90 | 346 ++++++++++++++++++++++++------------------------- src/pdfw.f90 | 6 37 files changed, 393 insertions(+), 458 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 0.6 dated 2015-04-14 and 0.7 dated 2015-11-13
DESCRIPTION | 17 +- MD5 | 55 ++++---- NAMESPACE | 20 ++ R/custom.R | 7 - R/deriv.R | 26 ++- R/flexsurvreg.R | 119 ++++++++++------- R/spline.R | 255 ++++++++++++++++++++++++++------------ R/utils.R | 12 + build/vignette.rds |binary inst/NEWS | 39 +++++ inst/doc/flexsurv-examples.R | 12 - inst/doc/flexsurv-examples.pdf |binary inst/doc/flexsurv.R | 58 ++++---- inst/doc/flexsurv.pdf |binary man/Survspline.Rd | 13 + man/WeibullPH.Rd |only man/flexsurvreg.Rd | 9 + man/flexsurvspline.Rd | 33 +++- man/msfit.flexsurvreg.Rd | 6 man/summary.flexsurvreg.Rd | 14 +- tests/test_base.R | 5 tests/testthat/test_deriv.R | 8 - tests/testthat/test_flexsurvreg.R | 13 + tests/testthat/test_mstate.R | 6 tests/testthat/test_outputs.R | 36 +++++ tests/testthat/test_spline.R | 56 +++++--- tests/testthat/test_utils.R | 41 +++++- vignettes/flexsurv-examples.Rnw | 19 +- vignettes/flexsurv.Rnw | 64 +++++---- 29 files changed, 636 insertions(+), 307 deletions(-)
Title: Easy Analysis and Visualization of Factorial Experiments
Description: Facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. "repeated measures"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.
Author: Michael A. Lawrence <mike.lwrnc@gmail.com>
Maintainer: Michael A. Lawrence <mike.lwrnc@gmail.com>
Diff between ez versions 4.2-2 dated 2013-09-13 and 4.3 dated 2015-11-13
CHANGES | 3 ++ DESCRIPTION | 12 ++++----- MD5 | 18 +++++++------- NAMESPACE | 26 +++++++++++++-------- R/ezCor.R | 65 +++++++++++++++++++++++++++--------------------------- R/ezDesign.R | 17 ++------------ R/ezPlot.R | 4 +-- R/ezPredict.R | 2 - man/ez-package.Rd | 4 +-- man/ezPlot.Rd | 10 -------- 10 files changed, 76 insertions(+), 85 deletions(-)
Title: Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre],
David Welch [aut],
David Hunter [ctb]
Maintainer: Chris Groendyke <cgroendyke@gmail.com>
Diff between epinet versions 2.0.9 dated 2014-12-16 and 2.1.5 dated 2015-11-13
epinet-2.0.9/epinet/R/BuildDyadicCovMatrix.R |only epinet-2.0.9/epinet/R/BuildDyadicLinearERGM.R |only epinet-2.0.9/epinet/man/BuildDyadicCovMatrix.Rd |only epinet-2.0.9/epinet/man/BuildDyadicLinearERGM.Rd |only epinet-2.0.9/epinet/man/NetworkEpiBayesSEIR.Rd |only epinet-2.1.5/epinet/DESCRIPTION | 12 - epinet-2.1.5/epinet/MD5 | 45 ++- epinet-2.1.5/epinet/NAMESPACE | 9 epinet-2.1.5/epinet/R/BuildX.R |only epinet-2.1.5/epinet/R/Epinet.R |only epinet-2.1.5/epinet/R/NetworkEpiBayesSEIR.R | 64 ++--- epinet-2.1.5/epinet/R/PlotEpiTree.R | 230 ++++++++++++++------ epinet-2.1.5/epinet/R/SEIR.simulator.R | 22 - epinet-2.1.5/epinet/R/SimulateDyadicLinearERGM.R |only epinet-2.1.5/epinet/R/ess.R | 2 epinet-2.1.5/epinet/data/Hagelloch.rda |binary epinet-2.1.5/epinet/man/BuildX.Rd |only epinet-2.1.5/epinet/man/Epinet.Rd |only epinet-2.1.5/epinet/man/Hagelloch.Rd | 2 epinet-2.1.5/epinet/man/MCMCcontrol.Rd |only epinet-2.1.5/epinet/man/PlotEpiTree.Rd | 49 ++-- epinet-2.1.5/epinet/man/Priorcontrol.Rd |only epinet-2.1.5/epinet/man/SEIR.simulator.Rd | 18 - epinet-2.1.5/epinet/man/SimulateDyadicLinearERGM.Rd |only epinet-2.1.5/epinet/man/epi2newick.Rd |only epinet-2.1.5/epinet/man/epinet-internal.Rd | 3 epinet-2.1.5/epinet/man/ess.Rd | 6 epinet-2.1.5/epinet/man/print.epinet.Rd |only epinet-2.1.5/epinet/man/summary.epinet.Rd |only epinet-2.1.5/epinet/man/write.epinet.Rd |only epinet-2.1.5/epinet/src/NetworkEpiMCMCSEIR.c | 47 +--- epinet-2.1.5/epinet/src/NetworkEpiMCMCSEIR.h | 4 32 files changed, 308 insertions(+), 205 deletions(-)
Title: R Interface to the EcoData Retriever
Description: Provides an R interface to the EcoData Retriever
(http://ecodataretriever.org/) via the EcoData Retriever's
command line interface. The EcoData Retriever automates the
tasks of finding, downloading, and cleaning ecological datasets,
and then stores them in a local database.
Author: Daniel McGlinn [aut, cre],
Ethan White [aut]
Maintainer: Daniel McGlinn <danmcglinn@gmail.com>
Diff between ecoretriever versions 0.1 dated 2014-09-28 and 0.2 dated 2015-11-13
DESCRIPTION | 13 ++++---- MD5 | 19 ++++++------ NAMESPACE | 4 +- R/ecoretriever.R | 79 ++++++++++++++++++++++++++++++++++++---------------- README.md | 4 +- man/datasets.Rd | 9 +++-- man/download.Rd | 7 +++- man/ecoretriever.Rd | 3 + man/fetch.Rd | 3 + man/get_updates.Rd |only man/install.Rd | 7 ++-- 11 files changed, 97 insertions(+), 51 deletions(-)
Title: Diversity-Dependent Diversification
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 2.7 dated 2015-03-20 and 3.0 dated 2015-11-13
DDD-2.7/DDD/R/L2phylo.R |only DDD-2.7/DDD/R/bd_simplex.R |only DDD-2.7/DDD/R/brts2phylo.R |only DDD-2.7/DDD/R/conv.R |only DDD-2.7/DDD/R/dd_KI_simplex.R |only DDD-2.7/DDD/R/dd_SR_simplex.R |only DDD-2.7/DDD/R/dd_simplex.R |only DDD-2.7/DDD/R/flavec.R |only DDD-3.0/DDD/DESCRIPTION | 11 DDD-3.0/DDD/MD5 | 77 ++- DDD-3.0/DDD/NAMESPACE | 7 DDD-3.0/DDD/R/bd_ML.R | 171 ++++---- DDD-3.0/DDD/R/bd_loglik.R | 652 +++++++++++++++++---------------- DDD-3.0/DDD/R/bd_loglik_choosepar.R | 6 DDD-3.0/DDD/R/dd_KI_ML.R | 9 DDD-3.0/DDD/R/dd_KI_loglik.R | 22 - DDD-3.0/DDD/R/dd_KI_loglik_choosepar.R | 4 DDD-3.0/DDD/R/dd_KI_sim.R |only DDD-3.0/DDD/R/dd_LR.R |only DDD-3.0/DDD/R/dd_ML.R | 12 DDD-3.0/DDD/R/dd_MS_ML.R |only DDD-3.0/DDD/R/dd_MS_loglik.R |only DDD-3.0/DDD/R/dd_MS_loglik_choosepar.R |only DDD-3.0/DDD/R/dd_MS_sim.R |only DDD-3.0/DDD/R/dd_SR_ML.R | 13 DDD-3.0/DDD/R/dd_SR_loglik.R | 29 - DDD-3.0/DDD/R/dd_SR_loglik_choosepar.R | 4 DDD-3.0/DDD/R/dd_loglik.R | 18 DDD-3.0/DDD/R/dd_loglik_M.R |only DDD-3.0/DDD/R/dd_loglik_choosepar.R | 4 DDD-3.0/DDD/R/dd_logliknorm_rhs3.R |only DDD-3.0/DDD/R/dd_sim.R | 60 +-- DDD-3.0/DDD/R/dd_utils.R |only DDD-3.0/DDD/R/lamu_dd_td.R |only DDD-3.0/DDD/R/td_loglik_rhs.R | 91 +--- DDD-3.0/DDD/R/td_loglik_rhs_sim.R |only DDD-3.0/DDD/R/td_sim.R |only DDD-3.0/DDD/man/DDD-internal.Rd | 18 DDD-3.0/DDD/man/DDD-package.Rd | 20 - DDD-3.0/DDD/man/bd_ML.Rd | 10 DDD-3.0/DDD/man/bd_loglik.Rd | 8 DDD-3.0/DDD/man/dd_KI_ML.Rd | 7 DDD-3.0/DDD/man/dd_KI_loglik.Rd | 5 DDD-3.0/DDD/man/dd_KI_sim.Rd |only DDD-3.0/DDD/man/dd_LR.Rd |only DDD-3.0/DDD/man/dd_ML.Rd | 10 DDD-3.0/DDD/man/dd_MS_ML.Rd |only DDD-3.0/DDD/man/dd_MS_loglik.Rd |only DDD-3.0/DDD/man/dd_MS_sim.Rd |only DDD-3.0/DDD/man/dd_SR_ML.Rd | 15 DDD-3.0/DDD/man/dd_SR_loglik.Rd | 5 DDD-3.0/DDD/man/dd_loglik.Rd | 5 52 files changed, 685 insertions(+), 608 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full
Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.5.0 dated 2015-09-13 and 0.6.0 dated 2015-11-13
brms-0.5.0/brms/R/deprecated.R |only brms-0.5.0/brms/man/brmdata.Rd |only brms-0.5.0/brms/man/brmpars.Rd |only brms-0.5.0/brms/man/cor.brms.Rd |only brms-0.5.0/brms/tests/testthat/tests.deprecated.R |only brms-0.6.0/brms/DESCRIPTION | 21 brms-0.6.0/brms/MD5 | 135 - brms-0.6.0/brms/NAMESPACE | 35 brms-0.6.0/brms/R/brm.R | 393 ++-- brms-0.6.0/brms/R/brmsfit-helpers.R | 392 +++- brms-0.6.0/brms/R/brmsfit-methods.R | 695 ++++--- brms-0.6.0/brms/R/correlations.R | 196 +- brms-0.6.0/brms/R/data.R | 332 ++- brms-0.6.0/brms/R/distributions.R | 136 + brms-0.6.0/brms/R/families.R |only brms-0.6.0/brms/R/fitted.R |only brms-0.6.0/brms/R/generics.R | 110 - brms-0.6.0/brms/R/loglik.R | 488 +++-- brms-0.6.0/brms/R/misc.R | 123 + brms-0.6.0/brms/R/predict.R | 388 +++- brms-0.6.0/brms/R/priors.R |only brms-0.6.0/brms/R/rename.R | 28 brms-0.6.0/brms/R/stan.R | 1576 ++++++++++++----- brms-0.6.0/brms/R/validate.R | 606 +----- brms-0.6.0/brms/R/zzz-example.R |only brms-0.6.0/brms/README.md | 32 brms-0.6.0/brms/inst/NEWS.Rd |only brms-0.6.0/brms/inst/doc/brms.ltx | 156 - brms-0.6.0/brms/inst/doc/brms.pdf |binary brms-0.6.0/brms/man/LOO.Rd | 31 brms-0.6.0/brms/man/VarCorr.Rd | 19 brms-0.6.0/brms/man/WAIC.Rd | 13 brms-0.6.0/brms/man/brm.Rd | 415 ++-- brms-0.6.0/brms/man/brms-package.Rd | 2 brms-0.6.0/brms/man/brmsfamily.Rd |only brms-0.6.0/brms/man/brmsfit-class.Rd | 56 brms-0.6.0/brms/man/cor_ar.Rd | 34 brms-0.6.0/brms/man/cor_arma.Rd | 50 brms-0.6.0/brms/man/cor_arr.Rd |only brms-0.6.0/brms/man/cor_brms.Rd |only brms-0.6.0/brms/man/cor_ma.Rd | 27 brms-0.6.0/brms/man/epilepsy.Rd | 33 brms-0.6.0/brms/man/fitted.brmsfit.Rd | 31 brms-0.6.0/brms/man/fixef.Rd | 5 brms-0.6.0/brms/man/get_prior.Rd | 102 - brms-0.6.0/brms/man/hypothesis.Rd | 11 brms-0.6.0/brms/man/inhaler.Rd | 25 brms-0.6.0/brms/man/kidney.Rd | 25 brms-0.6.0/brms/man/launch_shiny.Rd | 9 brms-0.6.0/brms/man/logLik.brmsfit.Rd | 4 brms-0.6.0/brms/man/macf.Rd | 13 brms-0.6.0/brms/man/make_stancode.Rd |only brms-0.6.0/brms/man/make_standata.Rd |only brms-0.6.0/brms/man/ngrps.Rd | 2 brms-0.6.0/brms/man/parnames.Rd | 2 brms-0.6.0/brms/man/plot.brmsfit.Rd | 23 brms-0.6.0/brms/man/posterior_samples.Rd | 19 brms-0.6.0/brms/man/predict.brmsfit.Rd | 47 brms-0.6.0/brms/man/print.brmsfit.Rd | 9 brms-0.6.0/brms/man/prior_samples.Rd | 16 brms-0.6.0/brms/man/ranef.Rd | 7 brms-0.6.0/brms/man/residuals.brmsfit.Rd | 25 brms-0.6.0/brms/man/set_prior.Rd | 197 +- brms-0.6.0/brms/man/stancode.Rd | 3 brms-0.6.0/brms/man/standata.Rd | 3 brms-0.6.0/brms/man/stanplot.Rd |only brms-0.6.0/brms/man/summary.brmsfit.Rd | 7 brms-0.6.0/brms/man/update.brmsfit.Rd |only brms-0.6.0/brms/man/vcov.brmsfit.Rd | 4 brms-0.6.0/brms/tests/testthat/tests.brm.R | 110 + brms-0.6.0/brms/tests/testthat/tests.brmsfit-helpers.R | 40 brms-0.6.0/brms/tests/testthat/tests.data.R | 313 ++- brms-0.6.0/brms/tests/testthat/tests.priors.R |only brms-0.6.0/brms/tests/testthat/tests.stan.R | 260 ++ brms-0.6.0/brms/tests/testthat/tests.validate.R | 137 - brms-0.6.0/brms/vignettes/brms.ltx | 156 - brms-0.6.0/brms/vignettes/citations.bib | 250 +- brms-0.6.0/brms/vignettes/flowchart.pdf |only 78 files changed, 5486 insertions(+), 2891 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.1.0 dated 2015-07-29 and 1.2.0 dated 2015-11-13
ChangeLog | 122 ++++++++++++++ DESCRIPTION | 10 - MD5 | 74 ++++---- NAMESPACE | 3 NEWS | 41 ++++ R/checkArgClassValue.R | 8 R/constants.R |only R/cumBg.R | 11 - R/mass2vol.R | 11 - R/molMass.R | 31 +-- R/predBg.R | 105 +++++++++--- R/readFormula.R | 18 +- R/summBg.R | 10 - R/vol2mass.R | 5 R/vol2mol.R |only build/vignette.rds |binary data/comp.rda |binary data/comp2.rda |binary data/mass.rda |binary data/massw.rda |binary data/oldcomp.rda |binary data/setup.rda |binary data/setup2.rda |binary data/vol.rda |binary data/vol2.rda |binary inst/doc/biogas_quick_start.R | 56 +++--- inst/doc/biogas_quick_start.Rnw | 109 +++--------- inst/doc/biogas_quick_start.pdf |binary inst/doc/predBg.R |only inst/doc/predBg.Rnw |only inst/doc/predBg.pdf |only man/biogas-package.Rd | 2 man/cumBg.Rd | 2 man/mass2vol.Rd | 264 +++++++++++++++---------------- man/predBg.Rd | 59 +++++- man/stdVol.Rd | 10 - man/vol2mol.Rd |only tests/testthat/test.mass.csv |only tests/testthat/test_HighLevelFunctions.R | 40 +++- tests/testthat/test_LowLevelFunctions.R | 11 - vignettes/biogas_quick_start.Rnw | 109 +++--------- vignettes/predBg.Rnw |only 42 files changed, 666 insertions(+), 445 deletions(-)
Title: Inference, Aggregation and Visualization for Top-K Ranked Lists
Description: For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Author: Michael G. Schimek, Eva Budinska, Jie Ding, Karl G. Kugler, Vendula Svendova, Shili Lin
Maintainer: Michael G. Schimek <michael.schimek@medunigraz.at>
Diff between TopKLists versions 1.0.3 dated 2014-11-11 and 1.0.6 dated 2015-11-13
TopKLists-1.0.3/TopKLists/vignettes/TopKListsGUI-2-Results.png |only TopKLists-1.0.3/TopKLists/vignettes/TopKListsGUI-2-SummaryTable.png |only TopKLists-1.0.3/TopKLists/vignettes/TopKListsGUI-2-Venn.png |only TopKLists-1.0.6/TopKLists/DESCRIPTION | 17 TopKLists-1.0.6/TopKLists/MD5 | 35 TopKLists-1.0.6/TopKLists/NAMESPACE | 4 TopKLists-1.0.6/TopKLists/NEWS | 21 TopKLists-1.0.6/TopKLists/R/TopKCEMC.R | 54 TopKLists-1.0.6/TopKLists/R/TopKGraphics.R | 28 TopKLists-1.0.6/TopKLists/R/TopKInference.R | 690 +++++----- TopKLists-1.0.6/TopKLists/build/vignette.rds |binary TopKLists-1.0.6/TopKLists/data/TopKSpaceSampleInput.rda |binary TopKLists-1.0.6/TopKLists/data/breast.rda |binary TopKLists-1.0.6/TopKLists/inst/CITATION |only TopKLists-1.0.6/TopKLists/inst/doc/TopKLists.R | 20 TopKLists-1.0.6/TopKLists/inst/doc/TopKLists.Rnw | 268 +-- TopKLists-1.0.6/TopKLists/inst/doc/TopKLists.pdf |binary TopKLists-1.0.6/TopKLists/man/TopKLists-package.Rd | 4 TopKLists-1.0.6/TopKLists/vignettes/TopKLists.Rnw | 268 +-- TopKLists-1.0.6/TopKLists/vignettes/aggmap.png |only TopKLists-1.0.6/TopKLists/vignettes/summarytable.png |only TopKLists-1.0.6/TopKLists/vignettes/venndiagram.png |only 22 files changed, 726 insertions(+), 683 deletions(-)
Title: Companion Package to the Book 'R: Einführung durch angewandte
Statistik'
Description: Provides functions used in the 'R: Einführung durch angewandte Statistik' (second edition).
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier <marco.maier@wu.ac.at>
Diff between REdaS versions 0.9.2 dated 2015-01-04 and 0.9.3 dated 2015-11-13
DESCRIPTION | 17 +++++++++-------- MD5 | 8 ++++---- NAMESPACE | 3 +++ build/partial.rdb |binary inst/CITATION | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
More information about PortfolioEffectEstim at CRAN
Permanent link
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.0.9.2 dated 2015-07-26 and 1.1.0 dated 2015-11-13
DESCRIPTION | 11 MD5 | 19 - NAMESPACE | 10 NEWS |only R/borrowed.R | 243 --------------------- R/lm.R | 119 +--------- R/mixlm.R | 11 R/statistics.R | 602 ++++++++++++----------------------------------------- R/utilities.R | 31 -- man/Anova.Rd | 32 -- man/simple.glht.Rd | 3 11 files changed, 200 insertions(+), 881 deletions(-)
Title: Standard and Nonstandard Statistical Models and Methods for Test
Equating
Description: Contains functions to perform various models and
methods for test equating. It currently implements the traditional
mean, linear and equipercentile equating methods, as well as the
mean-mean, mean-sigma, Haebara and Stocking-Lord IRT linking methods.
It also supports newest methods such that local equating, kernel
equating (using Gaussian, logistic and uniform kernels) with presmoothing,
and IRT parameter linking methods based on asymmetric item characteristic
functions. Functions to obtain both standard error of equating (SEE)
and standard error of equating difference between two equating
functions (SEED) are also implemented for the kernel method of
equating.
Author: Jorge Gonzalez Burgos [cre, aut],
Daniel Acu<c3><b1>a Leon [ctb]
Maintainer: Jorge Gonzalez Burgos <jgonzale@mat.puc.cl>
Diff between SNSequate versions 1.1-1 dated 2014-08-09 and 1.2.1 dated 2015-11-13
DESCRIPTION | 24 MD5 | 17 NAMESPACE | 21 R/PREp.R | 45 - R/fitmeasures.R |only R/helperfuncs.R |only R/ker.eq.R | 1971 +++++++++++++++++++++++++++++---------------------- R/loglin.smooth.R | 371 +++++---- man/fitmeasures.Rd |only man/ker.eq.Rd | 32 man/loglin.smooth.Rd | 52 + 11 files changed, 1506 insertions(+), 1027 deletions(-)
Title: Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation.
Author: Andrew T. Karl (Adsurgo LLC), Jennifer Broatch (Arizona State University)
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mvglmmRank versions 1.1-1 dated 2015-07-19 and 1.1-2 dated 2015-11-13
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 9 +++++++++ R/NB_cre.R | 14 ++++++++++++-- R/NB_mov.r | 2 +- R/PB_cre.R | 4 ++-- R/binary_cre.R | 2 +- R/mvglmmRank.R | 1 - R/normal_cre.R | 13 +++++++++++-- R/poisson_cre.R | 4 ++-- man/mvglmmRank-package.Rd | 4 ++-- 11 files changed, 54 insertions(+), 27 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 1.0 dated 2013-09-24 and 1.1 dated 2015-11-13
DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/GetGeneList.R | 22 ++++++++++++++-------- R/MapMarkers.R | 20 ++++++++++---------- man/GetGeneList.Rd | 10 +++++----- man/Map2NCBI-package.Rd | 8 ++++---- man/MapMarkers.Rd | 2 +- 8 files changed, 56 insertions(+), 49 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.5 dated 2015-10-14 and 0.0.6 dated 2015-11-13
DESCRIPTION | 10 +++---- MD5 | 14 +++++----- NAMESPACE | 23 ++++++++++++++--- R/CheckInputs.R | 49 +++++++++++++++++++++++++------------ R/MultiPlot.R | 2 - R/SinglePlot.R | 2 - R/create_infotables.R | 6 ++-- inst/doc/Information-vignette.html | 4 +-- 8 files changed, 72 insertions(+), 38 deletions(-)
More information about listWithDefaults at CRAN
Permanent link
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Lord & Barton's four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2015).
Author: Steven Andrew Culpepper [aut, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0.1 dated 2015-10-13 and 1.0.2 dated 2015-11-13
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- NAMESPACE | 2 +- src/fourpno_101315.cpp | 12 ++++++------ 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Engle-Granger Cointegration Models
Description: An easy-to-use implementation of the Engle-Granger
two-step procedure for identifying pairs of cointegrated series. It is geared towards
the analysis of pairs of securities. Summary and plot functions are provided,
and the package is able to fetch closing prices of securities from Yahoo.
A variety of unit root tests are supported, and an improved unit root test is included.
Author: Matthew Clegg [aut, cre, cph]
Maintainer: Matthew Clegg <matthewcleggphd@gmail.com>
Diff between egcm versions 1.0.6 dated 2015-02-06 and 1.0.8 dated 2015-11-13
CHANGELOG | 1 + DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 6 +++++- R/egcm.R | 17 +++++++++-------- 5 files changed, 26 insertions(+), 19 deletions(-)