Title: Programming with Big Data -- Demonstrations and Examples Using
'pbdR' Packages
Description: A set of demos of 'pbdR' packages, together with a useful,
unifying vignette.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDEMO versions 0.3-0 dated 2016-01-24 and 0.3-1 dated 2016-10-25
pbdDEMO-0.3-0/pbdDEMO/COPYING |only pbdDEMO-0.3-0/pbdDEMO/INSTALL |only pbdDEMO-0.3-0/pbdDEMO/build |only pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_cov.r |only pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_lmfit.r |only pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_pca.r |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pics/Phylogeny_of_Retroviruses.jpg |only pbdDEMO-0.3-1/pbdDEMO/ChangeLog | 5 pbdDEMO-0.3-1/pbdDEMO/DESCRIPTION | 21 +- pbdDEMO-0.3-1/pbdDEMO/MD5 | 70 ++++----- pbdDEMO-0.3-1/pbdDEMO/R/load_balance.r | 2 pbdDEMO-0.3-1/pbdDEMO/README.md | 47 ++++-- pbdDEMO-0.3-1/pbdDEMO/data/TREFHT.rda |binary pbdDEMO-0.3-1/pbdDEMO/demo/00Index | 1 pbdDEMO-0.3-1/pbdDEMO/demo/balance.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/binning.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/gbd_dmat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/mcmc_rjags.r |only pbdDEMO-0.3-1/pbdDEMO/demo/monte_carlo.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/nc4_serial.r | 4 pbdDEMO-0.3-1/pbdDEMO/demo/ols.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/ols_dmat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/phyclust_bootstrap.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/quantile.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/randmat_global.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/randmat_local.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/read_csv.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/read_ncdf.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/sample_stat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/sample_stat_dmat.r | 2 pbdDEMO-0.3-1/pbdDEMO/demo/trefht.r | 2 pbdDEMO-0.3-1/pbdDEMO/inst/CITATION | 25 ++- pbdDEMO-0.3-1/pbdDEMO/inst/doc/pbdDEMO-guide.Rnw | 2 pbdDEMO-0.3-1/pbdDEMO/inst/doc/pbdDEMO-guide.pdf |binary pbdDEMO-0.3-1/pbdDEMO/man/load_balance.Rd | 2 pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-guide.Rnw | 2 pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/01-introduction.tex | 3 pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/applications/a4-Bayes.tex | 74 ++++++++-- pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/pbdDEMO.bib | 8 + pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/pics/Phylogeny_of_Retroviruses.png |only pbdDEMO-0.3-1/pbdDEMO/vignettes/pbdDEMO-include/pics/galaxy_rjags.pdf |only 41 files changed, 196 insertions(+), 100 deletions(-)
Title: Mean-Variance Regularization
Description: This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include:
(i) Normalization and/or variance stabilization of the data,
(ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow),
(iii) Generation of diverse diagnostic plots,
(iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
Author: Jean-Eudes Dazard [aut, cre], Hua Xu [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Diff between MVR versions 1.30.3 dated 2016-01-28 and 1.31.0 dated 2016-10-25
MVR-1.30.3/MVR/inst/doc/MVR_1.30.3.pdf |only MVR-1.31.0/MVR/DESCRIPTION | 12 MVR-1.31.0/MVR/MD5 | 34 MVR-1.31.0/MVR/NAMESPACE | 28 MVR-1.31.0/MVR/R/MVRr.internal.r | 763 +++++++++++------- MVR-1.31.0/MVR/R/MVRr.r | 1034 ++++++++++++++----------- MVR-1.31.0/MVR/inst/NEWS | 11 MVR-1.31.0/MVR/inst/doc/MVR_1.31.0.pdf |only MVR-1.31.0/MVR/man/MVR-package.Rd | 40 MVR-1.31.0/MVR/man/MVR.news.Rd | 12 MVR-1.31.0/MVR/man/Real-data.Rd | 12 MVR-1.31.0/MVR/man/Synthetic-data.Rd | 12 MVR-1.31.0/MVR/man/cluster.diagnostic.Rd | 53 - MVR-1.31.0/MVR/man/mvr.Rd | 71 - MVR-1.31.0/MVR/man/mvrt.test.Rd | 112 +- MVR-1.31.0/MVR/man/normalization.diagnostic.Rd | 51 - MVR-1.31.0/MVR/man/stabilization.diagnostic.Rd | 54 - MVR-1.31.0/MVR/man/target.diagnostic.Rd | 51 - MVR-1.31.0/MVR/src/MVRc.cpp | 1 19 files changed, 1285 insertions(+), 1066 deletions(-)
Title: Morphometrics using R
Description: A complete toolkit for morphometrics, from data extraction to
multivariate analyses. Most common 2D morphometrics approaches are
included: outlines, open outlines, configurations of landmarks,
traditional morphometrics, and facilities for data preparation,
manipulation and visualization with a consistent grammar throughout.
Momocs allows reproducible, complex morphometric analyses, paves the
way for a pure open-source workflow in R, and other morphometrics
approaches should be easy to plug in, or develop from, on top of this
canvas.
Author: Vincent Bonhomme [aut, cre],
Julien Claude [aut]
Maintainer: Vincent Bonhomme <bonhomme.vincent@gmail.com>
Diff between Momocs versions 1.0.0 dated 2016-03-18 and 1.1.0 dated 2016-10-25
DESCRIPTION | 26 ++-- MD5 | 189 +++++++++++++++--------------- NAMESPACE | 16 ++ R/Momocs-package.R | 8 - R/babel-import.R | 49 +++++--- R/cl-def-Ldk.R | 2 R/cl-def-Opn.R | 2 R/cl-def-Out.R | 10 - R/cl-handling.R | 42 +++++- R/cl-utilities.R | 45 +++++++ R/coo-shapedescriptors.R | 33 ++++- R/coo-utilities.R | 63 +++++++++- R/core-premodern.R | 2 R/gr-Coo.R | 10 - R/gr-LDA.R | 91 +++++++------- R/gr-PCA.R | 6 R/gr-PCA2.R | 16 +- R/gr-domesticplotters.R | 15 +- R/gr-layers.R | 11 + R/mult-Manova.R | 12 + R/mult-PCA.R | 12 + R/mult-mshapes.R | 3 build/vignette.rds |binary inst/NEWS.Rd | 7 + inst/doc/Momocs_speed_dating.R | 6 inst/doc/Momocs_speed_dating.Rmd | 26 ++-- inst/doc/Momocs_speed_dating.html | 232 ++++++++++++++++++++------------------ man/MANOVA.Rd | 12 + man/Momocs.Rd | 6 man/Out.Rd | 6 man/OutCoe.Rd | 2 man/add_ldk.Rd |only man/boxplot.PCA.Rd | 2 man/coo_align.Rd | 1 man/coo_aligncalliper.Rd | 1 man/coo_alignminradius.Rd | 1 man/coo_alignxax.Rd | 1 man/coo_baseline.Rd | 1 man/coo_bookstein.Rd | 1 man/coo_calliper.Rd | 1 man/coo_centdist.Rd | 1 man/coo_center.Rd | 1 man/coo_centpos.Rd | 1 man/coo_centsize.Rd | 1 man/coo_close.Rd | 2 man/coo_down.Rd | 1 man/coo_dxy.Rd | 1 man/coo_elongation.Rd | 2 man/coo_extract.Rd | 1 man/coo_flip.Rd | 1 man/coo_force2close.Rd | 1 man/coo_interpolate.Rd | 1 man/coo_jitter.Rd | 1 man/coo_left.Rd | 1 man/coo_listpanel.Rd | 4 man/coo_lw.Rd | 2 man/coo_nb.Rd | 1 man/coo_perim.Rd | 1 man/coo_perimcum.Rd | 1 man/coo_perimpts.Rd | 1 man/coo_rev.Rd | 1 man/coo_right.Rd | 1 man/coo_rotate.Rd | 1 man/coo_rotatecenter.Rd | 1 man/coo_sample.Rd | 1 man/coo_samplerr.Rd | 1 man/coo_scale.Rd | 1 man/coo_scalexy.Rd | 1 man/coo_shear.Rd | 1 man/coo_slice.Rd | 1 man/coo_slide.Rd | 1 man/coo_slidedirection.Rd | 3 man/coo_slidegap.Rd | 3 man/coo_smooth.Rd | 1 man/coo_smoothcurve.Rd | 3 man/coo_solidity.Rd | 2 man/coo_template.Rd | 3 man/coo_trans.Rd | 3 man/coo_trim.Rd | 6 man/coo_trimbottom.Rd |only man/coo_trimtop.Rd |only man/coo_up.Rd | 1 man/coo_width.Rd | 2 man/def_ldk.Rd | 8 - man/def_slidings.Rd | 6 man/get_ldk.Rd | 6 man/get_slidings.Rd | 6 man/import_txt.Rd | 4 man/is_closed.Rd | 1 man/lf_structure.Rd | 2 man/nef2Coe.Rd | 7 - man/panel.Coo.Rd | 2 man/plot.LDA.Rd | 6 man/plot.PCA.Rd | 6 man/plot2.PCA.Rd | 10 - man/slidings_scheme.Rd | 6 vignettes/Momocs_speed_dating.Rmd | 26 ++-- 97 files changed, 731 insertions(+), 398 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a
Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <mdramins@ipipan.waw.pl>
Diff between rmcfs versions 1.1.1 dated 2016-03-29 and 1.1.2 dated 2016-10-25
rmcfs-1.1.1/rmcfs/LICENSE |only rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/tree/parser/J48NodeParser.java |only rmcfs-1.1.1/rmcfs/java/src/dmLab/utils/cmatrix/AccuracyMeasure.java |only rmcfs-1.1.2/rmcfs/DESCRIPTION | 10 rmcfs-1.1.2/rmcfs/LICENSE.note |only rmcfs-1.1.2/rmcfs/MD5 | 127 - rmcfs-1.1.2/rmcfs/NEWS | 62 rmcfs-1.1.2/rmcfs/R/rmcfs.R | 196 +- rmcfs-1.1.2/rmcfs/R/rmcfs.plot.R | 46 rmcfs-1.1.2/rmcfs/inst/java/dmLab.jar |binary rmcfs-1.1.2/rmcfs/inst/java/weka12.jar |binary rmcfs-1.1.2/rmcfs/java/src/dmLab/DMLabInfo.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/Array.java | 13 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/FArray.java | 40 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/functions/SelectFunctions.java | 5 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/loader/fileLoader/FileLoaderADX.java | 15 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/loader/fileLoader/FileLoaderArff.java | 2 rmcfs-1.1.2/rmcfs/java/src/dmLab/array/saver/Array2ADX.java | 31 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/Classifier.java | 175 + rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/Prediction.java | 121 - rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/PredictionResult.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/WekaClassifier.java | 77 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/WekaTree.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/adx/ADXClassifier.java | 31 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/attributeIndicators/SliqNodeIndicators.java | 7 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/bayesNet/BayesNetClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/ensemble/EnsembleClassifier.java | 18 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/hyperPipes/HyperPipesClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/j48/J48Classifier.java | 299 --- rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/j48/J48Params.java | 18 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/knn/KNNClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/logistic/LogisticClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/m5 |only rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/nb/NBClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/randomForest/RandomForestClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/ripper/RipperClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/rnd/RNDClassifier.java | 19 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/sliq/SliqClassifier.java | 19 rmcfs-1.1.2/rmcfs/java/src/dmLab/classifier/svm/SVMClassifier.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/experiment/classification/ClassificationBody.java | 913 ++++------ rmcfs-1.1.2/rmcfs/java/src/dmLab/experiment/classification/ClassificationParams.java | 23 rmcfs-1.1.2/rmcfs/java/src/dmLab/experiment/ensembleOptimization/EnsembleExperiment.java | 15 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/MCFSFinalCV.java | 41 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/MCFSParams.java | 93 - rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/attributesID/AttributesID.java | 4 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/attributesID/DependencyFactors.java | 7 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/attributesRI/AttributesRI.java | 6 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/MCFSExperiment.java | 30 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/GlobalStats.java | 37 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/MCFSFramework.java | 52 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/MCFSJob.java | 38 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/modules/Projection.java | 47 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/mcfsEngine/modules/Split.java | 22 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/Tree.java | 62 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/J48Parser.java | 53 rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/M5Parser.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/TreeNodeParser.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/mcfs/tree/parser/TreeParser.java | 60 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/ArrayUtils.java | 11 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/MathUtils.java | 343 +-- rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/StringUtils.java | 3 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/cmatrix/ConfusionMatrix.java | 16 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/cmatrix/QualityMeasure.java |only rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/dataframe/DataFrame.java | 5 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/statFunctions/StatFunctions.java | 48 rmcfs-1.1.2/rmcfs/java/src/dmLab/utils/statList/StatsList.java | 37 rmcfs-1.1.2/rmcfs/man/build.idgraph.Rd | 2 rmcfs-1.1.2/rmcfs/man/mcfs.Rd | 7 rmcfs-1.1.2/rmcfs/man/plot.mcfs.Rd | 4 69 files changed, 1767 insertions(+), 1579 deletions(-)
Title: Read and Combine Multiple Data Files
Description: Combine multiple data files from a common directory.
The data files will be read into R and bound together, creating a
single large data.frame. A general function is provided along with
a specific function for data that was collected using the open-source
experiment builder 'OpenSesame' <http://osdoc.cogsci.nl/>.
Author: Pascal J. Kieslich [aut, cre],
Felix Henninger [aut]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>
Diff between readbulk versions 1.0.0 dated 2016-02-14 and 1.1.0 dated 2016-10-25
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 8 ++++---- NEWS.md |only R/read_bulk.R | 12 +++++++++--- R/read_opensesame.R | 4 +++- README.md | 7 ++++++- man/read_bulk.Rd | 7 +++++-- man/read_opensesame.Rd | 5 ++++- 9 files changed, 45 insertions(+), 25 deletions(-)
Title: Process and Analyze Mouse-Tracking Data
Description: Mouse-tracking, the analysis of mouse movements in computerized
experiments, is a method that is becoming increasingly popular in the
cognitive sciences. The mousetrap package offers functions for importing,
preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
Author: Pascal J. Kieslich [aut, cre],
Felix Henninger [aut],
Dirk U. Wulff [ctb],
Sarah Brockhaus [ctb]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>
Diff between mousetrap versions 1.2.0 dated 2016-07-09 and 2.0.0 dated 2016-10-25
mousetrap-1.2.0/mousetrap/R/variables.R |only mousetrap-1.2.0/mousetrap/man/mt_calculate_derivatives.Rd |only mousetrap-1.2.0/mousetrap/man/mt_calculate_deviations.Rd |only mousetrap-1.2.0/mousetrap/man/mt_calculate_measures.Rd |only mousetrap-1.2.0/mousetrap/man/mt_id.Rd |only mousetrap-1.2.0/mousetrap/man/mt_variable_labels.Rd |only mousetrap-2.0.0/mousetrap/DESCRIPTION | 23 mousetrap-2.0.0/mousetrap/MD5 | 105 - mousetrap-2.0.0/mousetrap/NAMESPACE | 9 mousetrap-2.0.0/mousetrap/NEWS.md | 37 mousetrap-2.0.0/mousetrap/R/aggregate.R |only mousetrap-2.0.0/mousetrap/R/bimodality.R | 6 mousetrap-2.0.0/mousetrap/R/check.R | 8 mousetrap-2.0.0/mousetrap/R/data.R | 32 mousetrap-2.0.0/mousetrap/R/derivatives.R | 250 +-- mousetrap-2.0.0/mousetrap/R/deviations.R | 150 - mousetrap-2.0.0/mousetrap/R/export.R |only mousetrap-2.0.0/mousetrap/R/import.R | 722 +++++--- mousetrap-2.0.0/mousetrap/R/measures.R | 276 +-- mousetrap-2.0.0/mousetrap/R/mousetrap.R | 25 mousetrap-2.0.0/mousetrap/R/movement_angle.R | 51 mousetrap-2.0.0/mousetrap/R/preprocess.R | 1139 +++++++------- mousetrap-2.0.0/mousetrap/R/reshape.R | 645 ++----- mousetrap-2.0.0/mousetrap/R/riverbed.R | 6 mousetrap-2.0.0/mousetrap/R/sample_entropy.R | 45 mousetrap-2.0.0/mousetrap/R/standardize.R | 16 mousetrap-2.0.0/mousetrap/R/startupmessage.R |only mousetrap-2.0.0/mousetrap/R/utils.R | 147 + mousetrap-2.0.0/mousetrap/R/visualize.R | 134 + mousetrap-2.0.0/mousetrap/README.md | 4 mousetrap-2.0.0/mousetrap/man/mousetrap.Rd | 25 mousetrap-2.0.0/mousetrap/man/mt_add_variables.Rd |only mousetrap-2.0.0/mousetrap/man/mt_aggregate.Rd | 101 - mousetrap-2.0.0/mousetrap/man/mt_aggregate_per_subject.Rd | 67 mousetrap-2.0.0/mousetrap/man/mt_align_start.Rd | 31 mousetrap-2.0.0/mousetrap/man/mt_average.Rd | 82 - mousetrap-2.0.0/mousetrap/man/mt_check_bimodality.Rd | 4 mousetrap-2.0.0/mousetrap/man/mt_check_resolution.Rd | 12 mousetrap-2.0.0/mousetrap/man/mt_derivatives.Rd |only mousetrap-2.0.0/mousetrap/man/mt_deviations.Rd |only mousetrap-2.0.0/mousetrap/man/mt_example.Rd | 32 mousetrap-2.0.0/mousetrap/man/mt_exclude_initiation.Rd | 41 mousetrap-2.0.0/mousetrap/man/mt_export_long.Rd |only mousetrap-2.0.0/mousetrap/man/mt_import_long.Rd | 88 - mousetrap-2.0.0/mousetrap/man/mt_import_mousetrap.Rd | 71 mousetrap-2.0.0/mousetrap/man/mt_import_wide.Rd | 98 - mousetrap-2.0.0/mousetrap/man/mt_measures.Rd |only mousetrap-2.0.0/mousetrap/man/mt_movement_angle.Rd | 27 mousetrap-2.0.0/mousetrap/man/mt_plot.Rd | 31 mousetrap-2.0.0/mousetrap/man/mt_plot_per_trajectory.Rd | 37 mousetrap-2.0.0/mousetrap/man/mt_plot_riverbed.Rd | 2 mousetrap-2.0.0/mousetrap/man/mt_remap_symmetric.Rd | 42 mousetrap-2.0.0/mousetrap/man/mt_resample.Rd | 47 mousetrap-2.0.0/mousetrap/man/mt_reshape.Rd | 152 + mousetrap-2.0.0/mousetrap/man/mt_sample_entropy.Rd | 26 mousetrap-2.0.0/mousetrap/man/mt_space_normalize.Rd | 57 mousetrap-2.0.0/mousetrap/man/mt_standardize.Rd | 4 mousetrap-2.0.0/mousetrap/man/mt_subset.Rd | 30 mousetrap-2.0.0/mousetrap/man/mt_time_normalize.Rd | 53 mousetrap-2.0.0/mousetrap/man/reexports.Rd |only mousetrap-2.0.0/mousetrap/man/scale_within.Rd | 8 61 files changed, 2786 insertions(+), 2212 deletions(-)
Title: Multivariate Bias Correction of Climate Model Outputs
Description: Calibrate and apply multivariate bias correction algorithms
for climate model simulations of multiple climate variables. Three methods
by Cannon (2016, submitted) are supported: MBCp, MBCr, and MBCn.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between MBC versions 0.1 dated 2016-10-13 and 0.10-1 dated 2016-10-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/MBC-QDM.R | 45 +++++++++++++++++++++++++++++++-------------- man/MBCn.Rd | 6 +++++- man/MBCp.Rd | 6 +++++- man/MBCr.Rd | 6 +++++- man/QDM.Rd | 7 ++++++- 7 files changed, 61 insertions(+), 27 deletions(-)
Title: Extractive Summarization of Text with the LexRank Algorithm
Description: An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
Author: Adam Spannbauer <spannbaueradam@gmail.com>
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Diff between lexRankr versions 0.2.0 dated 2016-09-21 and 0.3.0 dated 2016-10-25
DESCRIPTION | 12 +++++++----- MD5 | 13 ++++++++----- NAMESPACE | 2 ++ NEWS.md | 5 +++++ R/RcppExports.R |only R/sentenceSimil.R | 30 ++++++++++++++++++------------ README.md | 4 +++- src |only 8 files changed, 43 insertions(+), 23 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.7 dated 2016-03-29 and 0.8 dated 2016-10-25
DESCRIPTION | 11 +++---- MD5 | 48 ++++++++++++++++++------------- NAMESPACE | 2 - R/CoreSetOptimizer.R | 25 +++++++++------- R/CoreSetter.R | 71 ++++++++++++++++++++++++++++------------------ R/CoreSetterCombined.R | 71 +++++++++++++++++++++++++++++++++------------- R/CoreSetterPoly.R |only R/MTK.R | 2 - R/Mat.R |only R/MtkCalc.R | 2 - R/SubsetterMTK.R | 2 - build |only data/genotypes.rda |binary inst |only man/CoreSetOptimizer.Rd | 6 +-- man/CoreSetter.Rd | 8 ++--- man/CoreSetterCombined.Rd | 12 +++---- man/CoreSetterPoly.Rd |only man/GeneticSubsetter.Rd | 5 +-- man/MTK.Rd | 2 - man/Mat.Rd |only man/MtkCalc.Rd | 2 - man/PicCalc.Rd | 2 - man/SubsetterMTK.Rd | 2 - man/SubsetterPIC.Rd | 2 - man/genotypes.Rd | 5 +-- man/genotypes.poly.Rd |only vignettes |only 28 files changed, 171 insertions(+), 109 deletions(-)
More information about GeneticSubsetter at CRAN
Permanent link
Title: Bayesian Network Modeling and Analysis
Description: A 'Shiny' web application for creating interactive Bayesian Network models,
learning the structure and parameters of Bayesian networks, and utilities for classical
network analysis.
Author: Paul Govan [aut, cre]
Maintainer: Paul Govan <pgovan1@aggienetwork.com>
Diff between BayesianNetwork versions 0.1.0 dated 2016-07-20 and 0.1.1 dated 2016-10-25
DESCRIPTION | 10 MD5 | 16 - NEWS.md |only R/BayesianNetwork.R | 2 README.md | 42 +-- build |only inst/bn/rsconnect |only inst/bn/server.R | 212 +++++++++-------- inst/bn/ui.R | 629 ++++++++++++++++++++++++++++++++-------------------- inst/doc |only vignettes |only 11 files changed, 544 insertions(+), 367 deletions(-)
More information about BayesianNetwork at CRAN
Permanent link
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and in forecasting.
Currently the package includes exponential smoothing models and SARIMA in state-space
form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for
Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 1.4.5 dated 2016-10-17 and 1.4.6 dated 2016-10-25
DESCRIPTION | 8 - MD5 | 70 ++++----- NAMESPACE | 11 + NEWS | 23 +++ R/RcppExports.R | 8 - R/es.R | 70 ++++++++- R/methods.R | 284 ++++++++++++++++++++++++++++++++++---- R/simces.R |only R/simes.R | 21 ++ R/simssarima.R |only R/ssarima.R | 1 R/ssfunctions.R | 148 ++++++++++++++----- README.md | 2 build/vignette.rds |binary inst/doc/ces.html | 53 +++---- inst/doc/es.html | 93 +++++++----- inst/doc/ges.html | 28 ++- inst/doc/simulate.R | 48 +++++- inst/doc/simulate.Rmd | 82 +++++++++- inst/doc/simulate.html | 105 +++++++++++--- inst/doc/sma.html | 8 - inst/doc/smooth-Documentation.pdf |binary inst/doc/smooth.html | 4 inst/doc/ssarima.html | 35 ++-- man/AICc.Rd | 4 man/ces.Rd | 2 man/es.Rd | 11 - man/ges.Rd | 2 man/orders-lags-modelType.Rd |only man/simes.Rd | 3 man/simssarima.Rd |only man/sma.Rd | 2 man/ssarima.Rd | 4 src/RcppExports.cpp | 20 ++ src/ssgeneralfun.cpp | 48 +++--- tests/testthat/test_es.R | 6 tests/testthat/test_simulate.R | 10 + vignettes/simulate.Rmd | 82 +++++++++- 38 files changed, 993 insertions(+), 303 deletions(-)
Title: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Description: Functions for the detection of footprints of selection on
dense SNP data using Extended Homozygosity Haplotype (EHH)
based tests. The package includes computation of EHH, iHS
(within population) and Rsb or XP-EHH (across pairs of populations)
statistics. Various plotting functions are also included to
facilitate visualization and interpretation of the results.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@supagro.inra.fr>
Diff between rehh versions 2.0.0 dated 2016-08-01 and 2.0.1 dated 2016-10-25
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 36 ++++++++++++++++++------------------ R/calc_ehh.R | 6 +++++- R/calc_ehhs.R | 16 +++++++++------- R/scan_hh.R | 6 +++++- inst/doc/rehh.R | 6 +++--- inst/doc/rehh.Rmd | 14 +++++++------- inst/doc/rehh.pdf |binary man/calc_ehh.Rd | 3 ++- man/calc_ehhs.Rd | 3 ++- man/scan_hh.Rd | 3 ++- src/CALL_EHH.c | 5 +++-- src/CALL_EHHS.c | 3 ++- src/CALL_SCAN_HH.c | 7 ++++--- src/hh_utils.c | 32 ++++++++++++++++++++++++++++++++ src/hh_utils.h | 5 ++--- vignettes/rehh.Rmd | 14 +++++++------- vignettes/rehh.html | 12 ++++++------ 19 files changed, 116 insertions(+), 65 deletions(-)
Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.3-0 dated 2016-08-24 and 2.3-1 dated 2016-10-25
DESCRIPTION | 10 MD5 | 22 +- NEWS | 8 R/startup.R | 4 inst/CITATION | 28 ++ inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/de/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/eu/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 12 - po/R-ca.po | 4 po/R-de.po | 337 +++++++++++++++++++++++++------ po/R-eu.po | 406 ++++++++++++++++++++++++++++++-------- 12 files changed, 657 insertions(+), 174 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.4 dated 2016-05-08 and 0.3.5 dated 2016-10-25
ChangeLog | 64 ++++++++++++++++++ DESCRIPTION | 16 ++-- MD5 | 44 ++++++------ NAMESPACE | 1 R/RcppExports.R | 10 ++ R/bsrch.R | 8 +- R/getBars.R | 9 +- R/getTicks.R | 77 +++++++++++----------- R/portfolio.R |only README.md | 15 +++- build/vignette.rds |binary inst/NEWS.Rd | 17 ++++- inst/doc/rblpapi-intro.Rmd | 8 +- inst/doc/rblpapi-intro.html | 66 ++++++++++++------- inst/unitTests/runit.getTicks.R | 30 +++++++- man/bsrch.Rd | 2 man/getBars.Rd | 7 +- man/getMultipleTicks.Rd | 9 +- man/getPortfolio.Rd |only man/getTicks.Rd | 24 +++++-- src/RcppExports.cpp | 136 ++++++++++++++++++++++------------------ src/bds.cpp | 59 +++++++++++++++-- src/getTicks.cpp | 43 +++++------- vignettes/rblpapi-intro.Rmd | 8 +- 24 files changed, 427 insertions(+), 226 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 2.0.1 dated 2016-10-19 and 2.0.2 dated 2016-10-25
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ README.md | 1 inst/doc/oem_vignette.html | 48 ++++++++++++++++++++++---------------------- src/oem_dense.h | 8 +++---- src/oem_logistic_dense.h | 8 +++---- src/oem_logistic_sparse.cpp | 2 - src/oem_logistic_sparse.h | 9 +++----- 8 files changed, 49 insertions(+), 49 deletions(-)
Title: Loading NONMEM Output Files and Simulate with Parameter
Uncertainty
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/solutions/nonmem/> ) output files and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>
Diff between nonmem2R versions 0.1.4 dated 2016-05-10 and 0.1.5 dated 2016-10-25
DESCRIPTION | 8 - MD5 | 19 +- NAMESPACE | 5 R/LoadNonmemOutput.R | 20 ++ R/Simulation.R | 291 ++++++++++++++++++++++++++++++++----------- R/VPCs.R |only inst/extdata/vpc_results.csv |only inst/extdata/vpctab004.dat |only man/extload.Rd | 5 man/grid.sim.Rd | 29 ++-- man/grid.sim.internal1.Rd |only man/grid.sim.internal2.Rd |only man/grid.sim.internal3.Rd |only man/vpcfig.Rd |only 14 files changed, 286 insertions(+), 91 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.0.7 dated 2016-06-18 and 1.0.8 dated 2016-10-25
mvMORPH-1.0.7/mvMORPH/vignettes/How_to_use_mvMORPH.html |only mvMORPH-1.0.8/mvMORPH/DESCRIPTION | 8 +- mvMORPH-1.0.8/mvMORPH/MD5 | 33 ++++---- mvMORPH-1.0.8/mvMORPH/R/mvBM.r | 3 mvMORPH-1.0.8/mvMORPH/R/mvBMTS.r | 4 - mvMORPH-1.0.8/mvMORPH/R/mvEB.r | 21 +++-- mvMORPH-1.0.8/mvMORPH/R/mvOU.r | 3 mvMORPH-1.0.8/mvMORPH/R/mvOUTS.r | 3 mvMORPH-1.0.8/mvMORPH/R/mvSHIFT.r | 26 ++++--- mvMORPH-1.0.8/mvMORPH/R/zzz.r | 2 mvMORPH-1.0.8/mvMORPH/README.md | 16 ++-- mvMORPH-1.0.8/mvMORPH/inst/doc/How_to_use_mvMORPH.R | 48 ++++++++++++- mvMORPH-1.0.8/mvMORPH/inst/doc/How_to_use_mvMORPH.Rmd | 59 ++++++++++++++-- mvMORPH-1.0.8/mvMORPH/inst/doc/How_to_use_mvMORPH.pdf |binary mvMORPH-1.0.8/mvMORPH/inst/doc/tutorial_mvMORPH.Rmd | 2 mvMORPH-1.0.8/mvMORPH/inst/doc/tutorial_mvMORPH.pdf |binary mvMORPH-1.0.8/mvMORPH/vignettes/How_to_use_mvMORPH.Rmd | 59 ++++++++++++++-- mvMORPH-1.0.8/mvMORPH/vignettes/tutorial_mvMORPH.Rmd | 2 18 files changed, 222 insertions(+), 67 deletions(-)
Title: Multiscale Clustering of Geometrical Network
Description: Co-Expression Network Analysis by adopting network embedding technique.
Author: Won-Min Song, Bin Zhang
Maintainer: Won-Min Song <wonmin1984@gmail.com>
Diff between MEGENA versions 1.3.4-6 dated 2016-10-06 and 1.3.5-2 dated 2016-10-25
MEGENA-1.3.4-6/MEGENA/inst/doc/MEGENA_pipeline_10052016.R |only MEGENA-1.3.4-6/MEGENA/inst/doc/MEGENA_pipeline_10052016.Rmd |only MEGENA-1.3.4-6/MEGENA/inst/doc/MEGENA_pipeline_10052016.html |only MEGENA-1.3.4-6/MEGENA/vignettes/MEGENA_pipeline_10052016.Rmd |only MEGENA-1.3.5-2/MEGENA/DESCRIPTION | 6 MEGENA-1.3.5-2/MEGENA/MD5 | 31 ++-- MEGENA-1.3.5-2/MEGENA/NAMESPACE | 4 MEGENA-1.3.5-2/MEGENA/R/ClusteringPackage.R | 79 +++++++---- MEGENA-1.3.5-2/MEGENA/R/Combined_functions.R | 44 ++++-- MEGENA-1.3.5-2/MEGENA/R/ModuleHierarchyPlot.R |only MEGENA-1.3.5-2/MEGENA/R/ModulePlot.R | 16 +- MEGENA-1.3.5-2/MEGENA/R/NetworkSummary.R | 24 ++- MEGENA-1.3.5-2/MEGENA/R/PFN_Computation.R | 4 MEGENA-1.3.5-2/MEGENA/build/vignette.rds |binary MEGENA-1.3.5-2/MEGENA/inst/doc/MEGENA_pipeline_10062016.R |only MEGENA-1.3.5-2/MEGENA/inst/doc/MEGENA_pipeline_10062016.Rmd |only MEGENA-1.3.5-2/MEGENA/inst/doc/MEGENA_pipeline_10062016.html |only MEGENA-1.3.5-2/MEGENA/man/calculate.PFN.Rd | 5 MEGENA-1.3.5-2/MEGENA/man/do.MEGENA.Rd | 3 MEGENA-1.3.5-2/MEGENA/man/get.DegreeHubStatistic.Rd |only MEGENA-1.3.5-2/MEGENA/man/plot_module_hierarchy.Rd |only MEGENA-1.3.5-2/MEGENA/vignettes/MEGENA_pipeline_10062016.Rmd |only 22 files changed, 137 insertions(+), 79 deletions(-)
Title: Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre],
Pei Wang Developer [aut],
Zhidong Tu Developer [aut],
Won-min Song Developer [aut],
Adele Cutler Developer [ctb],
Leo Breiman Developer [ctb],
Andy Liaw Developer [ctb],
Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>
Diff between JRF versions 0.1-3 dated 2016-01-20 and 0.1-4 dated 2016-10-25
DESCRIPTION | 8 ++-- MD5 | 20 ++++++----- NAMESPACE | 2 + R/JRF.R | 19 +++++----- R/JRF_network.R |only R/JRF_permutation.R | 4 +- R/Run_permutation.R |only man/JRF.Rd | 4 +- man/JRF_network.Rd |only man/JRF_permutation.Rd | 6 +-- man/Run_permutation.Rd |only src/regTree.c | 8 ++++ src/regrf.c | 86 ------------------------------------------------- 13 files changed, 44 insertions(+), 113 deletions(-)
Title: Imputation for Proteomics
Description: Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
Author: Quentin Giai Gianetto
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between imp4p versions 0.1 dated 2016-08-18 and 0.2 dated 2016-10-25
imp4p-0.1/imp4p/R/delete_na_rows.R |only imp4p-0.1/imp4p/man/delete_na_rows.Rd |only imp4p-0.2/imp4p/DESCRIPTION | 6 +-- imp4p-0.2/imp4p/MD5 | 54 +++++++++++++++--------------- imp4p-0.2/imp4p/NAMESPACE | 2 - imp4p-0.2/imp4p/R/estim_bound.R | 2 + imp4p-0.2/imp4p/R/estim_mix.R | 6 +-- imp4p-0.2/imp4p/R/impute_igcda.R | 6 +-- imp4p-0.2/imp4p/R/impute_mi.R |only imp4p-0.2/imp4p/R/impute_mix.R | 7 ++- imp4p-0.2/imp4p/R/impute_pa.R | 27 +++++++++++---- imp4p-0.2/imp4p/R/impute_rand.R |only imp4p-0.2/imp4p/R/impute_slsa.R | 13 ++++++- imp4p-0.2/imp4p/R/mi_mix.R | 34 +++++++++++++++--- imp4p-0.2/imp4p/R/prob_mcar.R | 9 ++++- imp4p-0.2/imp4p/R/prob_mcar_tab.R | 6 ++- imp4p-0.2/imp4p/man/estim_mix.Rd | 53 +++++++++++++---------------- imp4p-0.2/imp4p/man/imp4p-package.Rd | 4 +- imp4p-0.2/imp4p/man/impute_igcda.Rd | 9 +---- imp4p-0.2/imp4p/man/impute_mi.Rd |only imp4p-0.2/imp4p/man/impute_mix.Rd | 29 ++++++---------- imp4p-0.2/imp4p/man/impute_pa.Rd | 13 ++++--- imp4p-0.2/imp4p/man/impute_rand.Rd |only imp4p-0.2/imp4p/man/impute_slsa.Rd | 19 +++------- imp4p-0.2/imp4p/man/mi_mix.Rd | 29 ++++++---------- imp4p-0.2/imp4p/man/miss_mcar_process.Rd | 9 +---- imp4p-0.2/imp4p/man/miss_mnar_process.Rd | 9 +---- imp4p-0.2/imp4p/man/miss_total_process.Rd | 9 +---- imp4p-0.2/imp4p/man/prob_mcar.Rd | 13 ++----- imp4p-0.2/imp4p/man/proba_mcar_tab.Rd | 11 +----- imp4p-0.2/imp4p/man/sim_data.Rd | 6 +-- 31 files changed, 203 insertions(+), 182 deletions(-)
Title: Useful Functions for Building Physics
Description: A collection of functions useful for the analysis of
building physics experiments.
Author: Neurobat AG
Maintainer: David Lindelöf <david.lindelof@neurobat.net>
Diff between homeR versions 0.2 dated 2016-06-06 and 0.3.0 dated 2016-10-25
homeR-0.2/homeR/tests/testthat/oilConsumption.RData |only homeR-0.3.0/homeR/DESCRIPTION | 12 +- homeR-0.3.0/homeR/MD5 | 17 ++- homeR-0.3.0/homeR/NAMESPACE | 5 - homeR-0.3.0/homeR/NEWS.md |only homeR-0.3.0/homeR/R/bhm.R | 69 ++++++++++----- homeR-0.3.0/homeR/man/bhm.Rd | 15 ++- homeR-0.3.0/homeR/man/logposterior.Rd |only homeR-0.3.0/homeR/man/pmv.Rd | 6 - homeR-0.3.0/homeR/tests/testthat/alv.RData |only homeR-0.3.0/homeR/tests/testthat/fakeMonthlyEnergy.RData |only homeR-0.3.0/homeR/tests/testthat/test_bhm.R | 52 +++++++++-- 12 files changed, 124 insertions(+), 52 deletions(-)
Title: Read Data from Files Readable by 'gnumeric'
Description: Read data files readable by 'gnumeric' into 'R'. Can read
whole sheet or a range, from several file formats, including
the native format of 'gnumeric'. Reading is done by using
'ssconvert' (a file converter utility included in the 'gnumeric'
distribution <http://projects.gnome.org/gnumeric/>) to convert
the requested part to CSV. From 'gnumeric' files (but not other
formats) can list sheet names and sheet sizes or read all
sheets.
Author: Karoly Antal <antalk2@gmail.com>.
Maintainer: Karoly Antal <antalk2@gmail.com>
Diff between gnumeric versions 0.7-4 dated 2015-07-03 and 0.7-6 dated 2016-10-25
DESCRIPTION | 20 ++++++------ MD5 | 6 +-- R/read.gnumeric.R | 52 ++++++++++++++++---------------- man/read.gnumeric.sheet.Rd | 72 +++++++++++++++++++++++---------------------- 4 files changed, 76 insertions(+), 74 deletions(-)
Title: A View Generator for Multidimensional Data
Description: A tool to explore wide data sets, by detecting, ranking
and plotting groups of statistically dependent columns.
Author: Thibault Sellam
Maintainer: Thibault Sellam <thibault.sellam@cwi.nl>
Diff between findviews versions 0.1.1 dated 2016-10-10 and 0.1.2 dated 2016-10-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 8 +++++++- R/findviews.R | 2 -- R/findviews_to_compare.R | 5 ++--- R/findviews_to_predict.R | 5 ++--- README.md | 2 ++ man/findviews_core.Rd | 2 -- man/findviews_to_compare_core.Rd | 2 -- man/findviews_to_predict_core.Rd | 2 -- 10 files changed, 25 insertions(+), 27 deletions(-)
Title: Read RSS/Atom Feeds from R
Description: Retrieve data from RSS/Atom feeds.
Author: Andrew Collier [aut, cre]
Maintainer: Andrew Collier <andrew@exegetic.biz>
Diff between feedeR versions 0.0.4 dated 2016-08-14 and 0.0.7 dated 2016-10-25
DESCRIPTION | 10 ++++--- MD5 | 13 +++++---- NAMESPACE | 1 R/read.R | 63 +++++++++++++++++++++++++++++++++++++-------- README.md | 7 +++++ man/feed.extract.Rd | 11 ++++++- man/parse.rdf.Rd |only tests/testthat/test_util.R | 11 +++++-- 8 files changed, 91 insertions(+), 25 deletions(-)
Title: Ensemble Partial Least Squares Regression
Description: An algorithmic framework for measuring feature importance, outlier detection, model applicability domain evaluation, and ensemble predictive modeling with (sparse) partial least squares regressions.
Author: Nan Xiao <me@nanx.me>, Dong-Sheng Cao,
Miao-Zhu Li <miaozhu.li@duke.edu>, Qing-Song Xu <qsxu@csu.edu.cn>
Maintainer: Nan Xiao <me@nanx.me>
Diff between enpls versions 4.5 dated 2016-09-15 and 5.0 dated 2016-10-25
DESCRIPTION | 12 +-- MD5 | 67 ++++++++++++-------- NAMESPACE | 11 +++ NEWS.md | 60 ++++++++++-------- R/enpls.ad.R |only R/enpls.od.R | 2 R/enspls.ad.R |only R/enspls.fit.R | 3 R/enspls.od.R | 5 - R/plot.enpls.R | 147 +++++++++++++++++++++++++++++++++++++++++---- R/plot.enspls.R | 132 +++++++++++++++++++++++++++++++++++++--- R/print.enpls.R | 60 ++++++++++++++++++ R/print.enspls.R | 69 ++++++++++++++++++++- README.md | 2 inst/doc/enpls.R | 22 ++++++ inst/doc/enpls.Rmd | 80 +++++++++++++++++++----- inst/doc/enpls.html | 63 +++++++++++++++---- man/enpls.ad.Rd |only man/enpls.ad.core.fit.Rd |only man/enpls.ad.core.pred.Rd |only man/enpls.od.Rd | 2 man/enspls.ad.Rd |only man/enspls.ad.core.fit.Rd |only man/enspls.ad.core.pred.Rd |only man/enspls.fit.Rd | 3 man/enspls.od.Rd | 3 man/plot.cv.enpls.Rd | 5 + man/plot.cv.enspls.Rd | 5 + man/plot.enpls.ad.Rd |only man/plot.enpls.od.Rd | 4 - man/plot.enspls.ad.Rd |only man/plot.enspls.od.Rd | 4 - man/print.enpls.ad.Rd |only man/print.enpls.od.Rd | 2 man/print.enspls.ad.Rd |only man/print.enspls.fit.Rd | 3 man/print.enspls.fs.Rd | 3 man/print.enspls.od.Rd | 3 man/rgb2alpha.Rd |only vignettes/enpls.Rmd | 80 +++++++++++++++++++----- vignettes/enpls.bib | 13 +++ 41 files changed, 721 insertions(+), 144 deletions(-)
Title: scrypt key derivation functions for R
Description: scrypt is an R package for working with scrypt. Scrypt is a
password-based key derivation function created by Colin Percival. The
algorithm was specifically designed to make it costly to perform
large-scale custom hardware attacks by requiring large amounts of memory.
Author: RStudio, Inc.; Colin Percival
Maintainer: ORPHANED
Diff between scrypt versions 0.1.0 dated 2014-02-25 and 0.1.1 dated 2016-10-25
DESCRIPTION | 11 +++++++---- MD5 | 6 +++--- src/Makevars.win | 2 +- src/util.cpp | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Capture the Genes and Variants Related to a Genetic Disease from
Public Databases and PubMed
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Diff between VarfromPDB versions 2.1.9 dated 2016-08-20 and 2.1.10 dated 2016-10-25
DESCRIPTION | 8 ++-- MD5 | 6 +-- R/extract_clinvar.R | 95 +++++++++++++++++++++++++++------------------------- R/extract_omim.R | 15 +++++++- 4 files changed, 71 insertions(+), 53 deletions(-)
Title: Stochastic Newton Sampler (SNS)
Description: Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability density functions (PDFs) where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A Boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the PDF (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle. Numerical differentiation is available when analytical expressions for gradient and Hessian are not available. Facilities for validation and numerical differentiation of log-density are provided.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Alireza Mahani <alireza.s.mahani@gmail.com>
Diff between sns versions 1.1.1 dated 2016-09-08 and 1.1.2 dated 2016-10-25
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- inst/CITATION |only inst/doc/SNS.pdf |binary man/plot.sns.Rd | 4 ++++ man/predict.sns.Rd | 4 ++++ man/sns.Rd | 3 +++ man/sns.check.logdensity.Rd | 6 +++--- man/sns.fghEval.numaug.Rd | 6 +++--- man/sns.part.Rd | 4 ++++ man/sns.run.Rd | 6 +++--- man/summary.sns.Rd | 4 ++++ 13 files changed, 48 insertions(+), 24 deletions(-)
Title: Quantitative Fatty Acid Signature Analysis in R
Description: An implementation of Quantitative Fatty Acid Signature
Analysis (QFASA) in R. QFASA is a method of estimating the diet
composition of predators. The fundamental unit of information in
QFASA is a fatty acid signature (signature), which is a vector of
proportions describing the composition of fatty acids within lipids.
Signature data from at least one predator and from samples of all
potential prey types are required. Calibration coefficients, which
adjust for the differential metabolism of individual fatty acids by
predators, are also required. Given those data inputs, a predator
signature is modeled as a mixture of prey signatures and its diet
estimate is obtained as the mixture that minimizes a measure of
distance between the observed and modeled signatures. A variety of
estimation options and simulation capabilities are implemented.
Please refer to the vignette for additional details and references.
Author: Jeffrey F. Bromaghin [aut, cre]
Maintainer: Jeffrey F. Bromaghin <jbromaghin@usgs.gov>
Diff between qfasar versions 1.0.0 dated 2016-08-25 and 1.1.0 dated 2016-10-25
DESCRIPTION | 12 ++-- MD5 | 60 +++++++++++++-------- R/adj_diet_fat.R | 8 +- R/cc_aug.R | 2 R/comp_chi_gamma.R | 54 ++++++++----------- R/est_diet.R | 137 ++++++++++++++++++++++++-------------------------- R/find_boot_ss.R | 24 ++++---- R/gof.R | 24 +------- R/make_diet_rand.R | 2 R/make_pred_sigs.R | 4 - R/make_prey_part.R | 8 +- build/vignette.rds |binary inst/doc/qfasar.Rmd | 56 +++++++++++--------- inst/doc/qfasar.html | 73 ++++++++++++++++++-------- man/cc_aug.Rd | 2 man/comp_chi_gamma.Rd | 12 ---- man/est_diet.Rd | 15 ++--- man/find_boot_ss.Rd | 24 ++++---- man/gof.Rd | 24 +------- man/make_diet_rand.Rd | 2 man/make_pred_sigs.Rd | 4 - man/make_prey_part.Rd | 8 +- tests |only vignettes/qfasar.Rmd | 56 +++++++++++--------- 24 files changed, 306 insertions(+), 305 deletions(-)
Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (<http://turfjs.org>) for
'geospatial' analysis. The package revolves around using 'GeoJSON'
data. Functions are included for creating 'GeoJSON' data objects,
measuring aspects of 'GeoJSON', and combining, transforming,
and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre],
Jeff Hollister [aut],
Morgan Herlocker [cph]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between lawn versions 0.1.7 dated 2016-05-03 and 0.3.0 dated 2016-10-25
lawn-0.1.7/lawn/NEWS |only lawn-0.1.7/lawn/R/aggregate.R |only lawn-0.1.7/lawn/R/jenks.R |only lawn-0.1.7/lawn/R/quantile.R |only lawn-0.1.7/lawn/R/reclass.R |only lawn-0.1.7/lawn/R/size.R |only lawn-0.1.7/lawn/inst/js/turf.js |only lawn-0.1.7/lawn/man/lawn_erase.Rd |only lawn-0.1.7/lawn/tests/testthat/test-aggregate.R |only lawn-0.1.7/lawn/tests/testthat/test-jenks.R |only lawn-0.1.7/lawn/tests/testthat/test-quantile.R |only lawn-0.1.7/lawn/tests/testthat/test-reclass.R |only lawn-0.1.7/lawn/tests/testthat/test-size.R |only lawn-0.3.0/lawn/DESCRIPTION | 16 lawn-0.3.0/lawn/MD5 | 283 ++++--- lawn-0.3.0/lawn/NAMESPACE | 27 lawn-0.3.0/lawn/NEWS.md |only lawn-0.3.0/lawn/R/as.turf.R | 22 lawn-0.3.0/lawn/R/average.R | 14 lawn-0.3.0/lawn/R/bbox_polygon.R | 6 lawn-0.3.0/lawn/R/buffer.R | 14 lawn-0.3.0/lawn/R/circle.R |only lawn-0.3.0/lawn/R/collect.R |only lawn-0.3.0/lawn/R/count.R | 21 lawn-0.3.0/lawn/R/data-types.R | 10 lawn-0.3.0/lawn/R/defunct-deprecated.R |only lawn-0.3.0/lawn/R/deviation.R | 37 lawn-0.3.0/lawn/R/erase.R | 15 lawn-0.3.0/lawn/R/extent.R | 2 lawn-0.3.0/lawn/R/featurecollection.R | 29 lawn-0.3.0/lawn/R/filter.R | 15 lawn-0.3.0/lawn/R/geometrycollection.R |only lawn-0.3.0/lawn/R/kinks.R | 14 lawn-0.3.0/lawn/R/lawn-package.R | 2 lawn-0.3.0/lawn/R/lawn_bbox.R |only lawn-0.3.0/lawn/R/lawn_feature.R |only lawn-0.3.0/lawn/R/linestring.R | 4 lawn-0.3.0/lawn/R/max.R | 13 lawn-0.3.0/lawn/R/median.R | 17 lawn-0.3.0/lawn/R/merge.R | 12 lawn-0.3.0/lawn/R/min.R | 13 lawn-0.3.0/lawn/R/multilinestring.R |only lawn-0.3.0/lawn/R/multipoint.R |only lawn-0.3.0/lawn/R/multipolygon.R |only lawn-0.3.0/lawn/R/onLoad.R | 15 lawn-0.3.0/lawn/R/point.R | 7 lawn-0.3.0/lawn/R/polygon.R | 10 lawn-0.3.0/lawn/R/print_methods.R | 35 lawn-0.3.0/lawn/R/random.R | 2 lawn-0.3.0/lawn/R/remove.R | 13 lawn-0.3.0/lawn/R/sum.R | 13 lawn-0.3.0/lawn/R/tag.R | 25 lawn-0.3.0/lawn/R/tesselate.R |only lawn-0.3.0/lawn/R/variance.R | 13 lawn-0.3.0/lawn/R/view.R | 2 lawn-0.3.0/lawn/R/zzz.R | 16 lawn-0.3.0/lawn/README.md | 49 - lawn-0.3.0/lawn/build/vignette.rds |binary lawn-0.3.0/lawn/inst/doc/lawn_vignette.R | 6 lawn-0.3.0/lawn/inst/doc/lawn_vignette.Rmd | 28 lawn-0.3.0/lawn/inst/doc/lawn_vignette.html | 596 ++++++++-------- lawn-0.3.0/lawn/inst/ignore |only lawn-0.3.0/lawn/inst/js/LICENSE-clone |only lawn-0.3.0/lawn/inst/js/LICENSE-geojson-random |only lawn-0.3.0/lawn/inst/js/LICENSE-simple-statistics |only lawn-0.3.0/lawn/inst/js/README.md |only lawn-0.3.0/lawn/inst/js/cloner.js |only lawn-0.3.0/lawn/inst/js/geojsonhint-v2beta.js |only lawn-0.3.0/lawn/inst/js/simple-statistics.js |only lawn-0.3.0/lawn/inst/js/turf352.js |only lawn-0.3.0/lawn/man/data-types.Rd | 10 lawn-0.3.0/lawn/man/lawn-defunct.Rd |only lawn-0.3.0/lawn/man/lawn-package.Rd | 3 lawn-0.3.0/lawn/man/lawn_aggregate.Rd | 54 - lawn-0.3.0/lawn/man/lawn_along.Rd | 4 lawn-0.3.0/lawn/man/lawn_area.Rd | 4 lawn-0.3.0/lawn/man/lawn_average.Rd | 11 lawn-0.3.0/lawn/man/lawn_bbox.Rd |only lawn-0.3.0/lawn/man/lawn_bbox_polygon.Rd | 7 lawn-0.3.0/lawn/man/lawn_bearing.Rd | 5 lawn-0.3.0/lawn/man/lawn_bezier.Rd | 6 lawn-0.3.0/lawn/man/lawn_buffer.Rd | 6 lawn-0.3.0/lawn/man/lawn_center.Rd | 5 lawn-0.3.0/lawn/man/lawn_centroid.Rd | 5 lawn-0.3.0/lawn/man/lawn_circle.Rd |only lawn-0.3.0/lawn/man/lawn_collect.Rd |only lawn-0.3.0/lawn/man/lawn_concave.Rd | 6 lawn-0.3.0/lawn/man/lawn_convex.Rd | 6 lawn-0.3.0/lawn/man/lawn_count.Rd | 19 lawn-0.3.0/lawn/man/lawn_destination.Rd | 9 lawn-0.3.0/lawn/man/lawn_deviation.Rd | 28 lawn-0.3.0/lawn/man/lawn_difference.Rd |only lawn-0.3.0/lawn/man/lawn_distance.Rd | 6 lawn-0.3.0/lawn/man/lawn_envelope.Rd | 6 lawn-0.3.0/lawn/man/lawn_extent.Rd | 6 lawn-0.3.0/lawn/man/lawn_feature.Rd |only lawn-0.3.0/lawn/man/lawn_featurecollection.Rd | 14 lawn-0.3.0/lawn/man/lawn_filter.Rd | 14 lawn-0.3.0/lawn/man/lawn_geometrycollection.Rd |only lawn-0.3.0/lawn/man/lawn_intersect.Rd | 2 lawn-0.3.0/lawn/man/lawn_jenks.Rd | 38 - 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Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.4-2 dated 2015-10-15 and 0.9.5 dated 2016-10-25
DESCRIPTION | 11 ++++++----- MD5 | 31 +++++++++++++++++++++---------- R/simurun.R |only build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.pdf |binary man/hamlet-package.Rd | 11 ++++------- man/match.allocate.Rd | 7 ++++--- man/match.bb.Rd | 7 ++++--- man/orxlong.Rd | 2 +- man/orxwide.Rd | 2 +- man/vcaplong.Rd | 4 +++- man/vcapwide.Rd | 4 +++- vignettes/introduction-007.pdf |only vignettes/introduction-013.pdf |only vignettes/introduction-014.pdf |only vignettes/introduction-016.pdf |only vignettes/introduction-017.pdf |only vignettes/introduction-019.pdf |only vignettes/introduction-020.pdf |only vignettes/introduction-022.pdf |only vignettes/introduction-023.pdf |only 22 files changed, 47 insertions(+), 32 deletions(-)
Title: A Companion to the e-Book "YaRrr!: The Pirate's Guide to R"
Description: Contains a mixture of functions and data sets referred to in the introductory e-book "YaRrr!: The Pirate's Guide to R". The latest version of the e-book is available for free at <https://www.thepiratesguidetor.com>.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <yarrr.book@gmail.com>
Diff between yarrr versions 0.1.1 dated 2016-10-16 and 0.1.2 dated 2016-10-25
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 6 R/pirateplot_function.R | 520 +++++++++++++++++++++++++++++++++++------------ R/zzz.R | 12 - README.md | 21 - inst/doc/guide.html | 6 inst/doc/pirateplot.R | 107 +++++---- inst/doc/pirateplot.Rmd | 147 ++++++++----- inst/doc/pirateplot.html | 163 +++++++++----- man/pirateplot.Rd | 33 +- vignettes/pirateplot.Rmd | 147 ++++++++----- 12 files changed, 790 insertions(+), 402 deletions(-)