Title: Stacked Species Distribution Modelling
Description: Allows to map species richness and endemism based on stacked
species distribution models (SSDM). Individuals SDMs can be created using a
single or multiple algorithms (ensemble SDMs). For each species, an SDM can
yield a habitat suitability map, a binary map, a between-algorithm variance
map, and can assess variable importance, algorithm accuracy, and between-
algorithm correlation. Methods to stack individual SDMs include summing
individual probabilities and thresholding then summing. Thresholding can be
based on a specific evaluation metric or by drawing repeatedly from a Bernoulli
distribution. The SSDM package also provides a user-friendly interface.
Author: Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Philippe Birnbaum
Maintainer: Sylvain Schmitt <sylvain.schmitt@agroparistech.fr>
Diff between SSDM versions 0.1.1 dated 2016-02-17 and 0.2.0 dated 2017-03-17
SSDM-0.1.1/SSDM/NEWS |only SSDM-0.2.0/SSDM/DESCRIPTION | 29 SSDM-0.2.0/SSDM/MD5 | 106 ++- SSDM-0.2.0/SSDM/NAMESPACE | 11 SSDM-0.2.0/SSDM/NEWS.md |only SSDM-0.2.0/SSDM/R/Algorithm.SDM.R | 671 +---------------------- SSDM-0.2.0/SSDM/R/Ensemble.SDM.R | 18 SSDM-0.2.0/SSDM/R/Env.R | 2 SSDM-0.2.0/SSDM/R/PA.select.R |only SSDM-0.2.0/SSDM/R/SDM.R |only SSDM-0.2.0/SSDM/R/checkargs.R | 292 +++++++--- SSDM-0.2.0/SSDM/R/data.values.R |only SSDM-0.2.0/SSDM/R/ensemble.R | 447 +++++++++------ SSDM-0.2.0/SSDM/R/ensemble_modelling.R | 153 +++-- SSDM-0.2.0/SSDM/R/evaluate.R |only SSDM-0.2.0/SSDM/R/evaluate.axes.R |only SSDM-0.2.0/SSDM/R/get_PA.R |only SSDM-0.2.0/SSDM/R/get_model.R |only SSDM-0.2.0/SSDM/R/gui.R | 19 SSDM-0.2.0/SSDM/R/load_model.R | 87 +- SSDM-0.2.0/SSDM/R/load_occ.R | 143 +++- SSDM-0.2.0/SSDM/R/load_var.R | 165 +++-- SSDM-0.2.0/SSDM/R/mapDiversity.R |only SSDM-0.2.0/SSDM/R/modelling.R | 223 ++++--- SSDM-0.2.0/SSDM/R/plot.model.R | 389 +++++++------ SSDM-0.2.0/SSDM/R/project.R |only SSDM-0.2.0/SSDM/R/save.model.R | 119 ++-- SSDM-0.2.0/SSDM/R/stack_modelling.R | 349 ++++++----- SSDM-0.2.0/SSDM/R/stacking.R | 497 +++++++++-------- SSDM-0.2.0/SSDM/R/update.stack.R | 124 ++-- SSDM-0.2.0/SSDM/R/zzz.R | 6 SSDM-0.2.0/SSDM/README.md |only SSDM-0.2.0/SSDM/inst/extdata |only SSDM-0.2.0/SSDM/inst/shiny/gui/server.R | 412 ++++++++------ SSDM-0.2.0/SSDM/inst/shiny/gui/ui.R | 27 SSDM-0.2.0/SSDM/man/Algorithm.SDM-class.Rd | 6 SSDM-0.2.0/SSDM/man/Ensemble.SDM-class.Rd | 10 SSDM-0.2.0/SSDM/man/Env.Rd | 5 SSDM-0.2.0/SSDM/man/Occurrences.Rd | 3 SSDM-0.2.0/SSDM/man/SSDM.Rd | 2 SSDM-0.2.0/SSDM/man/Stacked.SDM-class.Rd | 8 SSDM-0.2.0/SSDM/man/ensemble.Rd | 30 - SSDM-0.2.0/SSDM/man/ensemble_modelling.Rd | 18 SSDM-0.2.0/SSDM/man/evaluate.Rd |only SSDM-0.2.0/SSDM/man/gui.Rd | 19 SSDM-0.2.0/SSDM/man/load.model.Rd | 7 SSDM-0.2.0/SSDM/man/load_occ.Rd | 16 SSDM-0.2.0/SSDM/man/load_var.Rd | 10 SSDM-0.2.0/SSDM/man/mapDiversity.Rd |only SSDM-0.2.0/SSDM/man/modelling.Rd | 28 SSDM-0.2.0/SSDM/man/plot.model.Rd | 9 SSDM-0.2.0/SSDM/man/save.model.Rd | 21 SSDM-0.2.0/SSDM/man/stack_modelling.Rd | 108 +-- SSDM-0.2.0/SSDM/man/stacking.Rd | 125 +--- SSDM-0.2.0/SSDM/man/update-Stacked.SDM-method.Rd | 10 SSDM-0.2.0/SSDM/tests |only 56 files changed, 2407 insertions(+), 2317 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness,
sparseness and orthogonality of eigenfunctions by using the alternating direction method of
multipliers algorithm. The method can be applied to either regularly or irregularly spaced
data (Wang and Huang, 2017).
Author: Wen-Ting Wang, Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.1.1.1 dated 2016-05-27 and 1.1.1.2 dated 2017-03-17
DESCRIPTION | 19 ++++++++++++------- MD5 | 17 ++++++++++------- NAMESPACE | 2 +- R/RcppExports.R | 2 +- R/SpatPCA.R | 42 +++++++++++++++++------------------------- README.md |only man/SpatPCA-package.Rd | 4 ++-- man/spatpca.Rd | 33 ++++++++++++++------------------- src/Makevars.win |only src/RcppExports.cpp | 26 +++++++++++++------------- src/registerDynamicSymbol.c |only 11 files changed, 70 insertions(+), 75 deletions(-)
Title: Regularized Spatial Maximum Covariance Analysis
Description: Provide regularized maximum covariance analysis incorporating smoothness,
sparseness and orthogonality of couple patterns by using the alternating direction method
of multipliers algorithm. The method can be applied to either regularly or irregularly
spaced data (Wang and Huang, 2017).
Author: Wen-Ting Wang [aut, cre], Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatMCA versions 1.0.0.1 dated 2016-06-04 and 1.0.0.2 dated 2017-03-17
DESCRIPTION | 22 +-- MD5 | 19 +- NAMESPACE | 3 R/RcppExports.R | 6 R/SpatMCA.R | 40 ++++- README.md |only man/SpatMCA-package.Rd | 4 man/SpatMCAinternal3.Rd |only man/spatmca.Rd | 21 +- src/RcppExports.cpp | 43 ++++-- src/registerDynamicSymbol.c |only src/spatmca.cpp | 310 ++++++++++++++++++++++++++++++++++++-------- 12 files changed, 368 insertions(+), 100 deletions(-)
Title: Simulation of the Forensic DNA Process
Description: Simulate the forensic DNA process: generate random or fixed DNA
profiles, create forensic samples including mixtures of diploid and haploid
cells, simulate DNA extraction, normalization, degradation, amplification
including stutters and inter-locus balance, and capillary electrophoresis.
DNA profiles are visualized as electropherograms and saved in tables.
The command pcrsim() opens up a graphical user interface which allow the user
to create projects, to enter, load, and save parameters required for the simulation.
The simulation is transparent and the parameters used in each step of the simulation
can be viewed in the result tables.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between pcrsim versions 1.0.1 dated 2016-10-03 and 1.0.2 dated 2017-03-17
DESCRIPTION | 12 +++++------ MD5 | 46 ++++++++++++++++++++++---------------------- NEWS | 7 ++++++ R/pcrsim.r | 13 +++++++++++- R/simNormalize.r | 11 ++++++++++ inst/extdata/parameters.txt | 17 ++++++++++++++++ man/calculateDegradation.Rd | 1 man/calibrateLb.Rd | 1 man/calibratePCRsim.Rd | 1 man/calibrateScaling.Rd | 1 man/compact.Rd | 1 man/compactStutter.Rd | 1 man/getParameter.Rd | 1 man/pcrsim-package.Rd | 7 ++---- man/pcrsim.Rd | 1 man/rmultinomxl.Rd | 1 man/simCE.Rd | 1 man/simDegradation.Rd | 1 man/simDilution.Rd | 1 man/simExtraction.Rd | 1 man/simNormalize.Rd | 1 man/simPCR.Rd | 1 man/simProfile.Rd | 1 man/simSample.Rd | 1 24 files changed, 79 insertions(+), 51 deletions(-)
Title: Elithorn Maze Generator
Description: A maze generator that creates the Elithorn Maze (HTML file) and the functions to calculate the associated maze parameters (i.e. Difficulty and Ability).
Author: Bao Sheng Loe (Aiden) [aut,cre,cph],
Maria Sanchez[ctb]
Maintainer: Bao Sheng Loe (Aiden) <bsl28@cam.ac.uk>
Diff between mazeGen versions 0.1.1 dated 2017-02-12 and 0.1.2 dated 2017-03-17
DESCRIPTION | 10 - MD5 | 307 ++++++++++++++++++++++---------------------- NEWS.md | 10 + R/data.R | 192 +++++++++++++++++++++++++++ R/jsTimer.R | 8 - R/mazeHTML.R | 2 data/gridEightDown.rda |binary data/gridEightLeft.rda |binary data/gridEightRight.rda |binary data/gridEightUp.rda |binary data/gridEighteenDown.rda |binary data/gridEighteenLeft.rda |binary data/gridEighteenRight.rda |binary data/gridEighteenUp.rda |binary data/gridElevenDown.rda |binary data/gridElevenLeft.rda |binary data/gridElevenRight.rda |binary data/gridElevenUp.rda |binary data/gridFifteenDown.rda |binary data/gridFifteenLeft.rda |binary data/gridFifteenRight.rda |binary data/gridFifteenUp.rda |binary data/gridFiveDown.rda |binary data/gridFiveLeft.rda |binary data/gridFiveRight.rda |binary data/gridFiveUp.rda |binary data/gridFourDown.rda |binary data/gridFourLeft.rda |binary data/gridFourRight.rda |binary data/gridFourUp.rda |binary data/gridFourteenDown.rda |binary data/gridFourteenLeft.rda |binary data/gridFourteenRight.rda |binary data/gridFourteenUp.rda |binary data/gridNineDown.rda |binary data/gridNineLeft.rda |binary data/gridNineRight.rda |binary data/gridNineUp.rda |binary data/gridNineteenDown.rda |only data/gridNineteenLeft.rda |only data/gridNineteenRight.rda |only data/gridNineteenUp.rda |only data/gridSevenDown.rda |binary data/gridSevenLeft.rda |binary data/gridSevenRight.rda |binary data/gridSevenUp.rda |binary data/gridSeventeenDown.rda |binary data/gridSeventeenLeft.rda |binary data/gridSeventeenRight.rda |binary data/gridSeventeenUp.rda |binary data/gridSixDown.rda |binary data/gridSixLeft.rda |binary data/gridSixRight.rda |binary data/gridSixUp.rda |binary data/gridSixteenDown.rda |binary data/gridSixteenLeft.rda |binary data/gridSixteenRight.rda |binary data/gridSixteenUp.rda |binary data/gridTenDown.rda |binary data/gridTenLeft.rda |binary data/gridTenRight.rda |binary data/gridTenUp.rda |binary data/gridThirteenDown.rda |binary data/gridThirteenLeft.rda |binary data/gridThirteenRight.rda |binary data/gridThirteenUp.rda |binary data/gridThreeDown.rda |binary data/gridThreeLeft.rda |binary data/gridThreeRight.rda |binary data/gridThreeUp.rda |binary data/gridTwelveDown.rda |binary data/gridTwelveLeft.rda |binary data/gridTwelveRight.rda |binary data/gridTwelveUp.rda |binary data/gridTwentyDown.rda |only data/gridTwentyLeft.rda |only data/gridTwentyRight.rda |only data/gridTwentyUp.rda |only man/genEMLseed.Rd | 7 - man/genMaze.Rd | 1 man/genPathSeed.Rd | 7 - man/gridEightDown.Rd | 1 man/gridEightLeft.Rd | 1 man/gridEightRight.Rd | 1 man/gridEightUp.Rd | 1 man/gridEighteenDown.Rd | 1 man/gridEighteenLeft.Rd | 1 man/gridEighteenRight.Rd | 1 man/gridEighteenUp.Rd | 1 man/gridElevenDown.Rd | 1 man/gridElevenLeft.Rd | 1 man/gridElevenRight.Rd | 1 man/gridElevenUp.Rd | 1 man/gridFifteenDown.Rd | 1 man/gridFifteenLeft.Rd | 1 man/gridFifteenRight.Rd | 1 man/gridFifteenUp.Rd | 1 man/gridFiveDown.Rd | 1 man/gridFiveLeft.Rd | 1 man/gridFiveRight.Rd | 1 man/gridFiveUp.Rd | 1 man/gridFourDown.Rd | 1 man/gridFourLeft.Rd | 1 man/gridFourRight.Rd | 1 man/gridFourUp.Rd | 1 man/gridFourteenDown.Rd | 1 man/gridFourteenLeft.Rd | 1 man/gridFourteenRight.Rd | 1 man/gridFourteenUp.Rd | 1 man/gridNineDown.Rd | 1 man/gridNineLeft.Rd | 1 man/gridNineRight.Rd | 1 man/gridNineUp.Rd | 1 man/gridNineteenUp.Rd |only man/gridSevenDown.Rd | 1 man/gridSevenLeft.Rd | 1 man/gridSevenRight.Rd | 1 man/gridSevenUp.Rd | 1 man/gridSeventeenDown.Rd | 1 man/gridSeventeenLeft.Rd | 1 man/gridSeventeenRight.Rd | 1 man/gridSeventeenUp.Rd | 1 man/gridSixDown.Rd | 1 man/gridSixLeft.Rd | 1 man/gridSixRight.Rd | 1 man/gridSixUp.Rd | 1 man/gridSixteenDown.Rd | 1 man/gridSixteenLeft.Rd | 1 man/gridSixteenRight.Rd | 1 man/gridSixteenUp.Rd | 1 man/gridTenDown.Rd | 1 man/gridTenLeft.Rd | 1 man/gridTenRight.Rd | 1 man/gridTenUp.Rd | 1 man/gridThirteenDown.Rd | 1 man/gridThirteenLeft.Rd | 1 man/gridThirteenRight.Rd | 1 man/gridThirteenUp.Rd | 1 man/gridThreeDown.Rd | 1 man/gridThreeLeft.Rd | 1 man/gridThreeRight.Rd | 1 man/gridThreeUp.Rd | 1 man/gridTwelveDown.Rd | 1 man/gridTwelveLeft.Rd | 1 man/gridTwelveRight.Rd | 1 man/gridTwelveUp.Rd | 1 man/gridTwentyDown.Rd |only man/gridTwentyLeft.Rd |only man/gridTwentyRight.Rd |only man/gridTwentyUp.Rd |only man/howMany.Rd | 7 - man/lowerGrid.Rd | 1 man/maxScore.Rd | 1 man/mazeAbility.Rd | 7 - man/mazeDiff.Rd | 7 - man/mazeEst.Rd | 7 - man/mazeGen.Rd | 1 man/mazeHTML.Rd | 7 - man/mazeObject.Rd | 7 - man/np.Rd | 7 - man/topNodes.Rd | 1 161 files changed, 399 insertions(+), 262 deletions(-)
Title: Estimate Directed and Undirected Graphical Models and Construct
Networks
Description: Provides an equivalent measure of partial correlation coefficients for high-dimensional Gaussian Graphical Models to learn and visualize the underlying relationships between variables from single or multiple datasets. You can refer to Liang, F., Song, Q. and Qiu, P. (2015) <doi:10.1080/01621459.2015.1012391> for more detail. Based on this method, the package also provides the method for constructing networks for Next Generation Sequencing Data, for jointly estimating multiple Gaussian Graphical Models and constructing directed acyclic graph (Bayesian Network).
Author: Bochao Jia, Faming Liang, Runmin Shi, Suwa Xu
Maintainer: Bochao Jia <jbc409@ufl.edu>
Diff between equSA versions 1.0.1 dated 2017-02-23 and 1.1.1 dated 2017-03-17
DESCRIPTION | 14 +++++++------- MD5 | 15 ++++++++++++--- NAMESPACE | 6 +++--- R/DAGsim.R |only R/p_learning.R |only R/simtoequiv.R |only data/datalist |only data/mixed3000.rda |only man/DAGsim.Rd |only man/equSA-package.Rd | 27 +++++++++++++++++++++++---- man/mixed3000.Rd |only man/p_learning.Rd |only man/simtoequiv.Rd |only 13 files changed, 45 insertions(+), 17 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <http://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and a vignette with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 1.1.0 dated 2016-12-19 and 1.2.0 dated 2017-03-17
DESCRIPTION | 14 +-- MD5 | 58 ++++++++------- NAMESPACE | 6 + NEWS.md | 9 ++ R/log_lik.R | 3 R/loo-functions.R |only R/posterior_interval.R | 5 - R/posterior_linpred.R |only R/posterior_predict.R | 5 - R/predictive_error.R | 3 R/predictive_interval.R | 4 - R/prior_summary.R | 4 - R/rstan_package_skeleton.R | 96 ++++++++++++++----------- R/rstantools-package.r | 13 +-- build/vignette.rds |binary inst/doc/developer-guidelines.R |only inst/doc/developer-guidelines.Rmd | 22 ++++- inst/doc/developer-guidelines.html | 55 +++++++++++++- man/log_lik.Rd | 23 ++++- man/loo-prediction.Rd |only man/posterior_interval.Rd | 25 ++++-- man/posterior_linpred.Rd |only man/posterior_predict.Rd | 25 ++++-- man/predictive_error.Rd | 23 ++++- man/predictive_interval.Rd | 24 ++++-- man/prior_summary.Rd | 24 ++++-- man/rstan_package_skeleton.Rd | 44 ++++++----- man/rstantools.Rd | 34 +++++--- tests/testthat/loo_pit.RDS |only tests/testthat/test-default-methods.R | 7 + tests/testthat/test-generics-with-no-methods.R | 22 +++-- tests/testthat/test-rstan_package_skeleton.R | 2 vignettes/developer-guidelines.Rmd | 22 ++++- 33 files changed, 380 insertions(+), 192 deletions(-)
Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to
H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: JJ Allaire [aut],
Erin LeDell [aut],
Michal Malohlava [aut],
Navdeep Gill [aut, cre],
Jakub Hava [aut],
RStudio [cph],
H2O.ai [cph]
Maintainer: Navdeep Gill <navdeep@h2o.ai>
Diff between rsparkling versions 0.1.1 dated 2017-02-24 and 0.2.0 dated 2017-03-17
rsparkling-0.1.1/rsparkling/NEWS |only rsparkling-0.1.1/rsparkling/tests/testthat/h2ologs |only rsparkling-0.1.1/rsparkling/tests/testthat/log4j.spark.log |only rsparkling-0.2.0/rsparkling/DESCRIPTION | 6 rsparkling-0.2.0/rsparkling/MD5 | 21 -- rsparkling-0.2.0/rsparkling/NAMESPACE | 3 rsparkling-0.2.0/rsparkling/NEWS.md |only rsparkling-0.2.0/rsparkling/R/install_h2o.R |only rsparkling-0.2.0/rsparkling/R/package.R | 103 +++++++++-- rsparkling-0.2.0/rsparkling/man/h2o_release_table.Rd |only rsparkling-0.2.0/rsparkling/tests/run-tests-local.sh |only rsparkling-0.2.0/rsparkling/tests/testthat.R | 19 +- rsparkling-0.2.0/rsparkling/tests/testthat/test_transforms.R | 16 - 13 files changed, 124 insertions(+), 44 deletions(-)
Title: Functions for Set-Theoretic Multi-Method Research and Advanced
QCA
Description: This initiated as a package companion to the book by C. Q.
Schneider and C. Wagemann "Set-Theoretic Methods for the Social
Sciences", Cambridge University Press. It grew to include functions
for performing set-theoretic multi-method research, QCA for clustered
data, theory evaluation, and Enhanced Standard Analysis. Additionally
it includes data to replicate the examples in the book and in the online
appendix.
Author: Juraj Medzihorsky [aut],
Ioana-Elena Oana [aut, cre],
Mario Quaranta [aut],
Carsten Q. Schneider [aut]
Maintainer: Ioana-Elena Oana <oana_ioana-elena@phd.ceu.edu>
Diff between SetMethods versions 2.0 dated 2016-08-14 and 2.1 dated 2017-03-17
DESCRIPTION | 10 +- MD5 | 92 ++++++++++--------- NAMESPACE | 4 NEWS |only R/QCAfit.R | 35 ++++--- R/cases.suf.dcn.R | 6 + R/cases.suf.dcv.R | 6 + R/cases.suf.typ.R | 6 + R/cases.theory.evaluation.R | 60 +++++++++++- R/cluster.eqmcc.R | 6 + R/esa.R | 121 ++++++++++++++------------ R/matches.suf.dcviir.R | 6 + R/matches.suf.typdcn.R | 6 + R/matches.suf.typiir.R | 32 ++++-- R/matches.suf.typtyp.R | 34 ++++--- R/pimdata.R | 13 ++ R/pimplot.R | 161 ++++++++++++++++++++++++++++++---- R/print.casestheoryeval.R |only R/print.matchessuf.R |only R/theory.evaluation.R | 6 + R/xy.plot.R | 19 +++- R/xy.plot.lat.R | 7 + R/zzz.R |only man/QCAfit.Rd | 97 ++++++++++---------- man/SetMethods-package.Rd | 6 - man/cases.nec.iir.Rd | 4 man/cases.suf.dcn.Rd | 4 man/cases.suf.dcv.Rd | 4 man/cases.suf.iir.Rd | 4 man/cases.suf.typ.Rd | 4 man/cases.suf.typ.most.Rd | 4 man/cases.suf.typ.unique.Rd | 6 - man/cases.theory.evaluation.Rd | 4 man/cluster.diagnostics.Rd | 4 man/cluster.eqmcc.Rd | 10 +- man/esa.Rd | 25 +++-- man/matches.suf.dcviir.Rd | 6 - man/matches.suf.typdcn.Rd | 6 - man/matches.suf.typiir.Rd | 4 man/matches.suf.typtyp.Rd | 4 man/pimdata.Rd | 8 - man/pimplot.Rd | 77 +++++++++++++--- man/print.casestheoryeval.Rd |only man/print.clusterdiagnostics.Rd | 4 man/print.clustereqmcc.Rd | 4 man/print.matchessuf.Rd |only man/theory.evaluation.Rd | 9 + man/theory.fit.Rd | 6 - man/xy.plot.Rd | 185 ++++++++++++++++++++-------------------- man/xy.plot.lat.Rd | 148 ++++++++++++++++---------------- 50 files changed, 798 insertions(+), 469 deletions(-)
Title: Stochastic Frontier Analysis
Description: Maximum Likelihood Estimation of
Stochastic Frontier Production and Cost Functions.
Two specifications are available:
the error components specification with time-varying efficiencies
(Battese and Coelli, 1992)
and a model specification in which the firm effects are directly
influenced by a number of variables (Battese and Coelli, 1995).
Author: Tim Coelli, Arne Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between frontier versions 1.1-0 dated 2013-08-20 and 1.1-2 dated 2017-03-17
DESCRIPTION | 14 MD5 | 50 - NAMESPACE | 35 - NEWS | 18 R/frontierDataTable.R |only R/frontierQuad.R | 32 - R/resettestFrontier.R |only R/sfa.R | 219 +------ R/zzz.R | 2 inst/CITATION | 4 man/efficiencies.frontier.Rd | 4 man/fitted.frontier.Rd | 2 man/front41Data.Rd | 62 +- man/front41Est.Rd | 2 man/front41ReadOutput.Rd | 2 man/front41WriteInput.Rd | 2 man/frontier.Rd | 6 man/frontierQuad.Rd | 10 man/lrtest.frontier.Rd | 2 man/resettestFrontier.Rd |only man/residuals.frontier.Rd | 2 man/riceProdPhil.Rd | 124 ++-- man/summary.frontier.Rd | 2 src/front41.f | 1321 ++++++++++++++++++++++--------------------- src/frontier_init.c |only tests/fail.R | 31 - tests/frontierTest.R | 204 ++++-- tests/nestedModels.R | 7 28 files changed, 1105 insertions(+), 1052 deletions(-)
Title: Calculate Ad Hoc Distance Thresholds for DNA Barcoding
Identification
Description: Two functions to calculate intra- and interspecific pairwise distances, evaluate DNA barcoding identification error and calculate an ad hoc distance threshold for each particular reference library of DNA barcodes. Specimen identification at this ad hoc distance threshold (using the best close match method) will produce identifications with an estimated relative error probability that can be fixed by the user (e.g. 5%).
Author: Gontran Sonet
Maintainer: Gontran Sonet <gosonet@gmail.com>
Diff between adhoc versions 1.0 dated 2013-12-13 and 1.1 dated 2017-03-17
DESCRIPTION | 16 ++++++++-------- MD5 | 17 +++++++++-------- NAMESPACE | 7 +++++-- R/adhocTHR.R | 9 +++++---- R/checkDNAbcd.R | 39 +++++++++++++++++++++++++++++++-------- inst |only man/adhoc-package.Rd | 2 +- man/adhocTHR.Rd | 2 +- man/checkDNAbcd.Rd | 22 +++++++++++++++++++--- man/tephdata.Rd | 2 +- 10 files changed, 80 insertions(+), 36 deletions(-)
Title: Group Factor Analysis
Description: Factor analysis implementation for multiple data sources, i.e., for groups of variables. The whole data analysis pipeline is provided, including functions and recommendations for data normalization and model definition, as well as missing value prediction and model visualization. The model group factor analysis (GFA) is inferred with Gibbs sampling, and it has been presented originally by Virtanen et al. (2012), and extended in Klami et al. (2015) <DOI:10.1109/TNNLS.2014.2376974> and Bunte et al. (2016) <DOI:10.1093/bioinformatics/btw207>; for details, see the citation info.
Author: Eemeli Leppaaho [aut, cre],
Seppo Virtanen [aut],
Muhammad Ammad-ud-din [ctb],
Suleiman A Khan [ctb],
Tommi Suvitaival [ctb],
Inka Saarinen [ctb],
Samuel Kaski [ctb]
Maintainer: Eemeli Leppaaho <eemeli.leppaaho@aalto.fi>
Diff between GFA versions 1.0.0 dated 2016-10-11 and 1.0.1 dated 2017-03-17
DESCRIPTION | 11 MD5 | 34 - NAMESPACE | 2 NEWS | 4 R/GFA.R | 1249 ++++++++++++++++++++--------------------- R/robustComponents.R | 138 ++-- demo/GFAexample.R | 4 demo/GFApipeline.R | 8 man/GFA-package.Rd | 4 man/getDefaultOpts.Rd | 5 man/gfa.Rd | 11 man/informativeNoisePrior.Rd | 3 man/normalizeData.Rd | 3 man/reconstruction.Rd | 5 man/robustComponents.Rd | 9 man/sequentialGfaPrediction.Rd | 3 man/undoNormalizeData.Rd | 3 man/visualizeComponents.Rd | 3 18 files changed, 748 insertions(+), 751 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut],
Yixuan Qiu [ctb],
R Core Team [cph] (Cairo code from X11 device),
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.1.3 dated 2016-11-10 and 0.1.4 dated 2017-03-17
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NEWS | 5 +++++ cleanup |only man/font_family_exists.Rd | 1 - man/match_family.Rd | 1 - man/raster_str.Rd | 1 - man/raster_write.Rd | 1 - man/set_dummy_conf.Rd | 1 - man/str_extents.Rd | 1 - man/str_metrics.Rd | 1 - man/sys_fonts.Rd | 1 - man/version_cairo.Rd | 1 - src/registerDynamicSymbol.c |only 14 files changed, 23 insertions(+), 25 deletions(-)
More information about AcousticNDLCodeR at CRAN
Permanent link
Title: Functions for Benchmarking Time Series Prediction
Description: Functions for time series prediction and accuracy assessment using automatic linear modelling. The generated linear models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Author: Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ), Eduardo Ogasawara [ths] (CEFET/RJ)
Maintainer: Rebecca Pontes Salles <rebeccapsalles@acm.org>
Diff between TSPred versions 2.0 dated 2015-04-07 and 3.0 dated 2017-03-17
DESCRIPTION | 23 +++--- MD5 | 77 ++++++++++++++-------- NAMESPACE | 7 +- R/MSE.r |only R/NMSE.r |only R/SSMpolynomial.r |only R/fittestArima.r |only R/fittestArimaKF.r |only R/fittestLM.r |only R/fittestPolyR.r |only R/fittestPolyRKF.r |only R/slidingWindows.r |only data/CATS.cont.rda |binary data/CATS.rda |binary data/EUNITE.Loads.cont.rda |binary data/EUNITE.Loads.rda |binary data/EUNITE.Reg.cont.rda |binary data/EUNITE.Reg.rda |binary data/EUNITE.Temp.cont.rda |binary data/EUNITE.Temp.rda |binary data/NN3.A.cont.rda |binary data/NN3.A.rda |binary data/NN5.A.cont.rda |binary data/NN5.A.rda |binary data/SantaFe.A.cont.rda |binary data/SantaFe.A.rda |binary data/SantaFe.D.cont.rda |binary data/SantaFe.D.rda |binary inst |only man/MAPE.Rd | 2 man/MSE.Rd |only man/NMSE.Rd |only man/SantaFe.A.Rd | 2 man/SantaFe.A.cont.Rd | 2 man/SantaFe.D.Rd | 2 man/SantaFe.D.cont.Rd | 2 man/TSPred-internal.Rd |only man/TSPred-package.Rd | 151 ++++++++++++++++++++++++++++++++++++++++++--- man/arimainterp.Rd | 2 man/arimapar.Rd | 2 man/arimapred.Rd | 4 - man/fittestArima.Rd |only man/fittestArimaKF.Rd |only man/fittestLM.Rd |only man/fittestPolyR.Rd |only man/fittestPolyRKF.Rd |only man/plotarimapred.Rd | 6 - man/sMAPE.Rd | 2 man/slidingWindows.Rd |only 49 files changed, 222 insertions(+), 62 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis, LU factorization
and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.0.1.12-1 dated 2017-03-08 and 5.0.1.12-3 dated 2017-03-17
DESCRIPTION | 8 +++---- MD5 | 29 +++++++++++++-------------- src/Makevars | 7 ++++-- src/Makevars.win | 6 ----- src/lib/MUMPS_5.0.1/Makefile | 2 - src/lib/Makefile | 2 - src/lib/Makefile.win | 2 - src/lib/scotch_6.0.4/src/Makefile | 10 ++++----- src/lib/scotch_6.0.4/src/Makefile.inc | 4 +-- src/lib/scotch_6.0.4/src/Makefile.inc.macos |only src/lib/scotch_6.0.4/src/Makefile.inc.rmumps | 4 +-- src/lib/scotch_6.0.4/src/Makefile.win | 8 +++---- src/lib/scotch_6.0.4/src/esmumps/Makefile | 2 - src/lib/scotch_6.0.4/src/libscotch/Makefile | 2 - src/lib/scotch_6.0.4/src/libscotch/graph.h | 1 src/rmumps_module.cpp | 4 +-- 16 files changed, 46 insertions(+), 45 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data for Report
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features are
1) CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Produce pdf, rtf, text report files.
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between ncar versions 0.3.3 dated 2017-03-14 and 0.3.4 dated 2017-03-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/pdfNCA.R | 2 +- R/rtfNCA.R | 3 +-- R/tabNCA.R | 3 +-- inst/NEWS.Rd | 5 +++++ inst/doc/ncar-manual.pdf |binary tests/Test.R | 3 +++ 8 files changed, 22 insertions(+), 16 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed);
- generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.8-0 dated 2017-03-12 and 4.8-1 dated 2017-03-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 18 ++++++++++++++++-- R/metacum.R | 19 +++++++++++++------ R/metainf.R | 19 +++++++++++++------ man/metacum.Rd | 5 +++++ man/metainf.Rd | 6 ++++++ 7 files changed, 63 insertions(+), 24 deletions(-)
Title: Multivariate Statistical Analysis in Chemometrics
Description: R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).
Author: Peter Filzmoser and Kurt Varmuza
Maintainer: P. Filzmoser <P.Filzmoser@tuwien.ac.at>
Diff between chemometrics versions 1.4.1 dated 2016-08-03 and 1.4.2 dated 2017-03-17
DESCRIPTION | 8 - MD5 | 22 +-- R/pcaCV.R | 129 ++++++--------------- inst/doc/chemometrics-vignette.pdf |binary vignettes/Figures/Fig-02-01-pcaCV.pdf |binary vignettes/Figures/Fig-02-03-pcaDiagplot-nipals.pdf |binary vignettes/Figures/Fig-02-04-pcaDiagplot-robust.pdf |binary vignettes/Figures/Fig-03-01-BIC.pdf |binary vignettes/Figures/Fig-03-02-lmCV.pdf |binary vignettes/Figures/Fig-03-13-plotridge.pdf |binary vignettes/Figures/Fig-04-01-knneval.pdf |binary vignettes/Figures/Fig-04-03-treeeval.pdf |binary 12 files changed, 57 insertions(+), 102 deletions(-)
Title: n-Gram Text Regression, aka Concise Comparative Summarization
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix <lmiratrix@stat.harvard.edu>
Diff between textreg versions 0.1.3 dated 2015-11-11 and 0.1.4 dated 2017-03-17
textreg-0.1.3/textreg/inst/doc/bathtub_vignette.R |only textreg-0.1.3/textreg/inst/doc/bathtub_vignette.Rnw |only textreg-0.1.3/textreg/inst/doc/bathtub_vignette.pdf |only textreg-0.1.3/textreg/inst/test-all.R |only textreg-0.1.3/textreg/vignettes/bathtub_vignette.Rnw |only textreg-0.1.4/textreg/DESCRIPTION | 13 - textreg-0.1.4/textreg/MD5 | 140 +++++++------ textreg-0.1.4/textreg/NAMESPACE | 32 ++ textreg-0.1.4/textreg/R/clean_text.R | 2 textreg-0.1.4/textreg/R/cross_validation_code.R | 8 textreg-0.1.4/textreg/R/make_word_lists.R | 4 textreg-0.1.4/textreg/R/sequenceplotter.R | 1 textreg-0.1.4/textreg/R/stempp.R | 43 ++- textreg-0.1.4/textreg/R/text_searching.R | 34 ++- textreg-0.1.4/textreg/R/textreg.R | 20 + textreg-0.1.4/textreg/R/vizualize_phrases.R | 7 textreg-0.1.4/textreg/build/vignette.rds |binary textreg-0.1.4/textreg/data/bathtub.RData |binary textreg-0.1.4/textreg/data/dirtyBathtub.RData |binary textreg-0.1.4/textreg/data/testCorpora.RData |binary textreg-0.1.4/textreg/inst/doc/bathtub-vignette.R |only textreg-0.1.4/textreg/inst/doc/bathtub-vignette.Rmd |only textreg-0.1.4/textreg/inst/doc/bathtub-vignette.html |only textreg-0.1.4/textreg/man/bathtub.Rd | 3 textreg-0.1.4/textreg/man/build.corpus.Rd | 17 - textreg-0.1.4/textreg/man/calc.loss.Rd | 3 textreg-0.1.4/textreg/man/clean.text.Rd | 7 textreg-0.1.4/textreg/man/cluster.phrases.Rd | 7 textreg-0.1.4/textreg/man/convert.tm.to.character.Rd | 9 textreg-0.1.4/textreg/man/cpp_build.corpus.Rd | 3 textreg-0.1.4/textreg/man/cpp_textreg.Rd | 3 textreg-0.1.4/textreg/man/dirtyBathtub.Rd | 3 textreg-0.1.4/textreg/man/find.CV.C.Rd | 3 textreg-0.1.4/textreg/man/find.threshold.C.Rd | 3 textreg-0.1.4/textreg/man/grab.fragments.Rd | 17 - textreg-0.1.4/textreg/man/is.fragment.sample.Rd | 7 textreg-0.1.4/textreg/man/is.textreg.corpus.Rd | 3 textreg-0.1.4/textreg/man/is.textreg.result.Rd | 6 textreg-0.1.4/textreg/man/list.table.chart.Rd | 3 textreg-0.1.4/textreg/man/make.CV.chart.Rd | 5 textreg-0.1.4/textreg/man/make.appearance.matrix.Rd | 11 - textreg-0.1.4/textreg/man/make.count.table.Rd | 9 textreg-0.1.4/textreg/man/make.list.table.Rd | 7 textreg-0.1.4/textreg/man/make.path.matrix.Rd | 9 textreg-0.1.4/textreg/man/make.phrase.correlation.chart.Rd | 7 textreg-0.1.4/textreg/man/make.phrase.matrix.Rd | 5 textreg-0.1.4/textreg/man/make.similarity.matrix.Rd | 9 textreg-0.1.4/textreg/man/make_search_phrases.Rd | 5 textreg-0.1.4/textreg/man/path.matrix.chart.Rd | 7 textreg-0.1.4/textreg/man/phrase.count.Rd | 5 textreg-0.1.4/textreg/man/phrase.matrix.Rd | 3 textreg-0.1.4/textreg/man/phrases.Rd |only textreg-0.1.4/textreg/man/plot.textreg.result.Rd | 7 textreg-0.1.4/textreg/man/predict.textreg.result.Rd | 7 textreg-0.1.4/textreg/man/print.fragment.sample.Rd | 6 textreg-0.1.4/textreg/man/print.textreg.corpus.Rd | 6 textreg-0.1.4/textreg/man/print.textreg.result.Rd | 5 textreg-0.1.4/textreg/man/reformat.textreg.model.Rd | 6 textreg-0.1.4/textreg/man/sample.fragments.Rd | 8 textreg-0.1.4/textreg/man/save.corpus.to.files.Rd | 3 textreg-0.1.4/textreg/man/stem.corpus.Rd | 22 +- textreg-0.1.4/textreg/man/testCorpora.Rd | 3 textreg-0.1.4/textreg/man/textreg-package.Rd | 9 textreg-0.1.4/textreg/man/textreg.Rd | 5 textreg-0.1.4/textreg/man/tm_gregexpr.Rd | 5 textreg-0.1.4/textreg/src/textreg.cpp | 2 textreg-0.1.4/textreg/tests |only textreg-0.1.4/textreg/vignettes/bathtub-vignette.Rmd |only 68 files changed, 321 insertions(+), 256 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.4.14 dated 2016-05-11 and 1.4.15 dated 2017-03-17
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Ruby Fore [aut],
Will Leahy [aut],
Henry Nguyen [aut],
Robin Winstanley [aut],
Alice Yang [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialUtils versions 0.4.8 dated 2016-11-18 and 0.4.9 dated 2017-03-17
MazamaSpatialUtils-0.4.8/MazamaSpatialUtils/man/initializeSpatialData.Rd |only MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/DESCRIPTION | 11 +- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/MD5 | 54 +++++----- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/NAMESPACE | 1 MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/MazamaSpatialUtils.R | 31 ----- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/convertGADM.R | 46 +++++--- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getCountry.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getCountryCode.R | 8 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getCountryName.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getHUC.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getHUCName.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getSpatialData.R | 15 ++ MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getState.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getStateCode.R | 15 +- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getStateName.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getTimezone.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getUSCounty.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/getVariable.R | 10 + MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/installSpatialData.R | 33 ++---- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/R/loadSpatialData.R | 43 +++++-- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/README.md | 28 +++++ MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/build |only MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/data/SimpleCountries.RData |binary MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/data/SimpleTimezones.RData |binary MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/inst |only MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/man/getStateCode.Rd | 4 MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/man/installSpatialData.Rd | 21 ++- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/man/loadSpatialData.Rd | 27 +++-- MazamaSpatialUtils-0.4.9/MazamaSpatialUtils/vignettes |only 29 files changed, 263 insertions(+), 164 deletions(-)
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural proprieties)
analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav
Yalamanchi [aut], Mildenberger Thoralf [ctb], Deepak Yadav [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.6.6 dated 2017-01-23 and 0.6.8.1 dated 2017-03-17
markovchain-0.6.6/markovchain/man/verifyMarkovProperty.Rd |only markovchain-0.6.6/markovchain/tests/testthat/testHigerOrder.R |only markovchain-0.6.6/markovchain/tests/testthat/testInference.R |only markovchain-0.6.6/markovchain/tests/testthat/testParallelBootstrap.R |only markovchain-0.6.8.1/markovchain/ChangeLog | 9 markovchain-0.6.8.1/markovchain/DESCRIPTION | 14 markovchain-0.6.8.1/markovchain/MD5 | 95 - markovchain-0.6.8.1/markovchain/NAMESPACE | 13 markovchain-0.6.8.1/markovchain/NEWS | 8 markovchain-0.6.8.1/markovchain/R/1_functions4Fitting.R | 87 - markovchain-0.6.8.1/markovchain/R/5_statisticalTests.R | 558 ++++++---- markovchain-0.6.8.1/markovchain/R/RcppExports.R | 12 markovchain-0.6.8.1/markovchain/R/sysdata.rda |only markovchain-0.6.8.1/markovchain/build/vignette.rds |binary markovchain-0.6.8.1/markovchain/data/kullback.rda |only markovchain-0.6.8.1/markovchain/inst/CITATION | 13 markovchain-0.6.8.1/markovchain/inst/doc/an_introduction_to_markovchain_package.R | 60 - markovchain-0.6.8.1/markovchain/inst/doc/an_introduction_to_markovchain_package.Rnw | 100 - markovchain-0.6.8.1/markovchain/inst/doc/an_introduction_to_markovchain_package.pdf |binary markovchain-0.6.8.1/markovchain/inst/doc/complicateSteadyStates.pdf |binary markovchain-0.6.8.1/markovchain/inst/doc/markovchainCrashIntro.pdf |binary markovchain-0.6.8.1/markovchain/inst/extdata |only markovchain-0.6.8.1/markovchain/man/absorbingStates.Rd | 16 markovchain-0.6.8.1/markovchain/man/conditionalDistribution.Rd | 7 markovchain-0.6.8.1/markovchain/man/firstPassage.Rd | 7 markovchain-0.6.8.1/markovchain/man/fitHighOrderMultivarMC.Rd | 7 markovchain-0.6.8.1/markovchain/man/getName.Rd | 1 markovchain-0.6.8.1/markovchain/man/hommc-class.Rd | 4 markovchain-0.6.8.1/markovchain/man/hommc-show.Rd | 1 markovchain-0.6.8.1/markovchain/man/inferHyperparam.Rd | 7 markovchain-0.6.8.1/markovchain/man/is.accessible.Rd | 7 markovchain-0.6.8.1/markovchain/man/is.irreducible.Rd | 7 markovchain-0.6.8.1/markovchain/man/kullback.Rd |only markovchain-0.6.8.1/markovchain/man/markovchainFit.Rd | 20 markovchain-0.6.8.1/markovchain/man/markovchainListFit.Rd | 4 markovchain-0.6.8.1/markovchain/man/markovchainSequence.Rd | 7 markovchain-0.6.8.1/markovchain/man/rmarkovchain.Rd | 7 markovchain-0.6.8.1/markovchain/man/sales.Rd | 1 markovchain-0.6.8.1/markovchain/man/setName.Rd | 1 markovchain-0.6.8.1/markovchain/man/states.Rd | 7 markovchain-0.6.8.1/markovchain/man/statisticalTests.Rd |only markovchain-0.6.8.1/markovchain/man/steadyStates.Rd | 7 markovchain-0.6.8.1/markovchain/man/transition2Generator.Rd | 1 markovchain-0.6.8.1/markovchain/man/transitionProbability.Rd | 7 markovchain-0.6.8.1/markovchain/src/1_ctmcFunctions4Fitting.cpp | 2 markovchain-0.6.8.1/markovchain/src/1_functions4Fitting.cpp | 121 +- markovchain-0.6.8.1/markovchain/src/RcppExports.cpp | 7 markovchain-0.6.8.1/markovchain/src/init.c |only markovchain-0.6.8.1/markovchain/src/mapFitFunctionsSAI.h | 32 markovchain-0.6.8.1/markovchain/tests/testthat/testBasic1.R | 53 markovchain-0.6.8.1/markovchain/tests/testthat/testFits.R |only markovchain-0.6.8.1/markovchain/tests/testthat/testHigherOrder.R |only markovchain-0.6.8.1/markovchain/tests/testthat/testSteadyStates.R |only markovchain-0.6.8.1/markovchain/vignettes/an_introduction_to_markovchain_package.Rnw | 100 - markovchain-0.6.8.1/markovchain/vignettes/markovchainBiblio.bib | 28 55 files changed, 865 insertions(+), 573 deletions(-)
Title: Furniture for Quantitative Scientists
Description: Contains two main functions (i.e., two pieces of furniture):
table1() which produces a well-formatted table of descriptives common as Table 1
in research articles and washer() which is helpful in cleaning up your data.
These furniture functions are designed to simplify common tasks in
quantitative analysis.
Author: Tyson Barrett [aut, cre],
Emily Brignone [aut]
Maintainer: Tyson Barrett <t.barrett@aggiemail.usu.edu>
Diff between furniture versions 1.4.1 dated 2016-12-13 and 1.5.0 dated 2017-03-17
furniture-1.4.1/furniture/data/nhanes10.rda |only furniture-1.4.1/furniture/man/nhanes10.Rd |only furniture-1.4.1/furniture/man/tableM.Rd |only furniture-1.4.1/furniture/tests/testthat/test_tableM.R |only furniture-1.4.1/furniture/vignettes/Table1 |only furniture-1.5.0/furniture/DESCRIPTION | 17 furniture-1.5.0/furniture/MD5 | 51 furniture-1.5.0/furniture/NAMESPACE | 4 furniture-1.5.0/furniture/NEWS.md |only furniture-1.5.0/furniture/R/Table1.R | 1024 ++++++-------- furniture-1.5.0/furniture/R/furniture.R | 4 furniture-1.5.0/furniture/R/nhanes_data.R | 38 furniture-1.5.0/furniture/R/zzz.R | 2 furniture-1.5.0/furniture/data/nhanes_2010.rda |only furniture-1.5.0/furniture/inst/doc/Furniture.R | 33 furniture-1.5.0/furniture/inst/doc/Furniture.Rmd | 26 furniture-1.5.0/furniture/inst/doc/Furniture.html | 184 +- furniture-1.5.0/furniture/inst/doc/Table1.R | 18 furniture-1.5.0/furniture/inst/doc/Table1.Rmd | 28 furniture-1.5.0/furniture/inst/doc/Table1.html | 358 ++-- furniture-1.5.0/furniture/man/furniture.Rd | 5 furniture-1.5.0/furniture/man/grapes-xt-grapes.Rd | 1 furniture-1.5.0/furniture/man/nhanes_2010.Rd |only furniture-1.5.0/furniture/man/table1.Rd | 53 furniture-1.5.0/furniture/man/table1_.Rd | 3 furniture-1.5.0/furniture/man/table1_format_condense.Rd |only furniture-1.5.0/furniture/man/table1_format_nocondense.Rd |only furniture-1.5.0/furniture/man/table1_summarizing.Rd |only furniture-1.5.0/furniture/man/washer.Rd | 1 furniture-1.5.0/furniture/tests/testthat/test_table1.R | 125 - furniture-1.5.0/furniture/vignettes/Furniture.Rmd | 26 furniture-1.5.0/furniture/vignettes/Table1.Rmd | 28 32 files changed, 887 insertions(+), 1142 deletions(-)
Title: Bayesian Adaptive Spline Surfaces
Description: Bayesian fitting and sensitivity analysis methods for adaptive
spline surfaces. Built to handle continuous and categorical inputs as well as
functional or scalar output. An extension of the methodology in Denison, Mallick
and Smith (1998) <doi:10.1023/A:1008824606259>.
Author: Devin Francom [aut, cre],
Bruno Sanso [ths],
Agner Fog [ctb, cph]
Maintainer: Devin Francom <devinfrancom@gmail.com>
Diff between BASS versions 0.2.0 dated 2017-01-10 and 0.2.2 dated 2017-03-17
BASS-0.2.0/BASS/inst/doc/article1-vignette.pdf |only BASS-0.2.0/BASS/inst/doc/article1-vignette.pdf.asis |only BASS-0.2.0/BASS/vignettes/article1-vignette.pdf.asis |only BASS-0.2.2/BASS/DESCRIPTION | 14 ++-- BASS-0.2.2/BASS/MD5 | 51 +++++++++++------ BASS-0.2.2/BASS/NAMESPACE | 3 + BASS-0.2.2/BASS/NEWS.md | 8 ++ BASS-0.2.2/BASS/R/bass.R | 28 +++++++-- BASS-0.2.2/BASS/R/generics.R |only BASS-0.2.2/BASS/R/mcmc_funcs.R | 25 ++++---- BASS-0.2.2/BASS/R/mcmc_update.R | 4 - BASS-0.2.2/BASS/R/misc.R | 6 ++ BASS-0.2.2/BASS/R/plot.R | 54 +++++++++++-------- BASS-0.2.2/BASS/R/predict.R | 4 - BASS-0.2.2/BASS/R/sobol.R | 27 +++++---- BASS-0.2.2/BASS/build/vignette.rds |binary BASS-0.2.2/BASS/inst/doc/article2-vignette.R |only BASS-0.2.2/BASS/inst/doc/article2-vignette.Rnw |only BASS-0.2.2/BASS/inst/doc/article2-vignette.pdf |only BASS-0.2.2/BASS/man/bass.Rd | 7 +- BASS-0.2.2/BASS/man/plot.bass.Rd | 3 - BASS-0.2.2/BASS/man/plot.bassSob.Rd | 1 BASS-0.2.2/BASS/man/predict.bass.Rd | 1 BASS-0.2.2/BASS/man/print.bass.Rd |only BASS-0.2.2/BASS/man/sobol.Rd | 1 BASS-0.2.2/BASS/man/summary.bass.Rd |only BASS-0.2.2/BASS/src/init.c |only BASS-0.2.2/BASS/vignettes/article2-vignette.Rnw |only BASS-0.2.2/BASS/vignettes/bibl.bib |only BASS-0.2.2/BASS/vignettes/child |only BASS-0.2.2/BASS/vignettes/myCommands.sty |only 31 files changed, 147 insertions(+), 90 deletions(-)
Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions
that have to be met so that errors in data used in
analysis pipelines can fail quickly. Similar to
'stopifnot()' but more powerful, friendly, and easier
for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>
Diff between assertr versions 1.0.2 dated 2016-08-02 and 2.0.0 dated 2017-03-17
DESCRIPTION | 14 - LICENSE | 2 MD5 | 66 ++--- NAMESPACE | 18 + NEWS | 18 + R/assertions.R | 379 +++++++++++++++++++---------- R/errors.R |only R/predicates.R | 91 +++++- R/row-redux.R | 57 ++++ R/utils.R | 93 +++---- README.md | 17 - build/vignette.rds |binary inst/doc/assertr.Rmd | 177 +++++++++++-- inst/doc/assertr.html | 432 ++++++++++++++++++++------------- man/assert.Rd | 28 +- man/assert_rows.Rd | 26 + man/assertr.Rd | 1 man/chaining_functions.Rd |only man/col_concat.Rd |only man/has_all_names.Rd |only man/in_set.Rd | 1 man/insist.Rd | 28 +- man/insist_rows.Rd | 25 + man/is_uniq.Rd |only man/maha_dist.Rd | 9 man/not_na.Rd | 1 man/num_row_NAs.Rd | 1 man/print.assertr_assert_error.Rd |only man/print.assertr_verify_error.Rd |only man/success_and_error_functions.Rd |only man/summary.assertr_assert_error.Rd |only man/summary.assertr_verify_error.Rd |only man/verify.Rd | 19 + man/within_bounds.Rd | 1 man/within_n_mads.Rd | 1 man/within_n_sds.Rd | 1 tests/testthat/test-assertions.R | 470 +++++++++++++++++++++--------------- tests/testthat/test-predicates.R | 89 ++++++ vignettes/assertr.Rmd | 177 +++++++++++-- 39 files changed, 1534 insertions(+), 708 deletions(-)