Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.3.1 dated 2015-09-10 and 0.4.0 dated 2016-01-18
tidyr-0.3.1/tidyr/man/seq_range.Rd |only tidyr-0.3.1/tidyr/tests/testthat/test-matrixToDataFrame.R |only tidyr-0.4.0/tidyr/DESCRIPTION | 9 - tidyr-0.4.0/tidyr/MD5 | 112 +++++++------ tidyr-0.4.0/tidyr/NAMESPACE | 16 + tidyr-0.4.0/tidyr/R/RcppExports.R | 12 - tidyr-0.4.0/tidyr/R/complete.R | 18 +- tidyr-0.4.0/tidyr/R/expand.R | 113 ++++++++++---- tidyr-0.4.0/tidyr/R/extract.R | 8 tidyr-0.4.0/tidyr/R/fill.R | 28 ++- tidyr-0.4.0/tidyr/R/gather.R | 48 +++-- tidyr-0.4.0/tidyr/R/id.R |only tidyr-0.4.0/tidyr/R/nest.R | 67 ++++++-- tidyr-0.4.0/tidyr/R/separate.R | 24 ++ tidyr-0.4.0/tidyr/R/seq.R |only tidyr-0.4.0/tidyr/R/spread.R | 74 ++++++--- tidyr-0.4.0/tidyr/R/unite.R | 14 + tidyr-0.4.0/tidyr/R/unnest.R | 71 ++++++-- tidyr-0.4.0/tidyr/R/utils.R | 10 + tidyr-0.4.0/tidyr/README.md | 2 tidyr-0.4.0/tidyr/build/vignette.rds |binary tidyr-0.4.0/tidyr/inst/doc/tidy-data.html | 96 +++++------ tidyr-0.4.0/tidyr/man/complete.Rd | 25 +-- tidyr-0.4.0/tidyr/man/complete_.Rd | 4 tidyr-0.4.0/tidyr/man/expand.Rd | 54 +++++- tidyr-0.4.0/tidyr/man/expand_.Rd | 2 tidyr-0.4.0/tidyr/man/extract.Rd | 6 tidyr-0.4.0/tidyr/man/extract_.Rd | 2 tidyr-0.4.0/tidyr/man/extract_numeric.Rd | 2 tidyr-0.4.0/tidyr/man/fill.Rd | 15 + tidyr-0.4.0/tidyr/man/fill_.Rd | 7 tidyr-0.4.0/tidyr/man/full_seq.Rd |only tidyr-0.4.0/tidyr/man/gather.Rd | 13 + tidyr-0.4.0/tidyr/man/gather_.Rd | 10 - tidyr-0.4.0/tidyr/man/nest.Rd | 24 ++ tidyr-0.4.0/tidyr/man/nest_.Rd | 7 tidyr-0.4.0/tidyr/man/pipe.Rd | 2 tidyr-0.4.0/tidyr/man/replace_na.Rd | 2 tidyr-0.4.0/tidyr/man/separate.Rd | 15 + tidyr-0.4.0/tidyr/man/separate_.Rd | 9 - tidyr-0.4.0/tidyr/man/spread.Rd | 44 +++-- tidyr-0.4.0/tidyr/man/spread_.Rd | 28 +-- tidyr-0.4.0/tidyr/man/unite.Rd | 5 tidyr-0.4.0/tidyr/man/unite_.Rd | 2 tidyr-0.4.0/tidyr/man/unnest.Rd | 22 +- tidyr-0.4.0/tidyr/man/unnest_.Rd | 9 - tidyr-0.4.0/tidyr/src/RcppExports.cpp | 29 ++- tidyr-0.4.0/tidyr/src/fill.cpp | 92 +++++++++++ tidyr-0.4.0/tidyr/src/matrixToDataFrame.cpp | 3 tidyr-0.4.0/tidyr/src/melt.cpp | 33 ++-- tidyr-0.4.0/tidyr/tests/testthat/test-expand.R | 23 ++ tidyr-0.4.0/tidyr/tests/testthat/test-extract.R | 8 tidyr-0.4.0/tidyr/tests/testthat/test-fill.R | 58 ++++++- tidyr-0.4.0/tidyr/tests/testthat/test-gather.R | 19 ++ tidyr-0.4.0/tidyr/tests/testthat/test-id.R |only tidyr-0.4.0/tidyr/tests/testthat/test-nest.R | 27 +++ tidyr-0.4.0/tidyr/tests/testthat/test-separate.R | 8 tidyr-0.4.0/tidyr/tests/testthat/test-spread.R | 102 ++++++++++++ tidyr-0.4.0/tidyr/tests/testthat/test-unite.R | 18 ++ tidyr-0.4.0/tidyr/tests/testthat/test-unnest.R | 37 ++++ 60 files changed, 1118 insertions(+), 370 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.11-22 dated 2015-10-06 and 0.11-29 dated 2016-01-18
DESCRIPTION | 12 +++---- MD5 | 40 +++++++++++++------------ NAMESPACE | 2 - R/add.pedigree.r |only R/codeGeno.r | 65 +++++++++++++++++++++++++---------------- R/create.gpData.r | 1 R/create.pedigree.r | 44 ++++++++++++--------------- R/discard.markers.r | 17 ++++++++-- R/gpMod.r | 4 +- R/kinship.r | 23 ++++++++------ R/plot.genMap.r | 2 - R/plot.pedigree.r | 5 +-- R/predict.gpMod.r | 10 ++---- R/read.write.vcf.r | 4 +- R/summary.relationshipMatrix.r | 4 +- man/add.pedigree.Rd |only man/create.pedigree.Rd | 31 ++++++++++--------- man/discard.individuals.Rd | 7 +++- man/discard.markers.Rd | 5 ++- man/kinship.Rd | 12 ++++--- man/plot.pedigree.Rd | 30 +++++++++++------- man/predict.gpMod.Rd | 56 ++++++++++++++++++----------------- 22 files changed, 210 insertions(+), 164 deletions(-)
Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based 'svg' images into high-quality custom-size bitmap
arrays using 'librsvg'. The resulting bitmap can be written to e.g. 'png', 'jpeg'
or 'webp' format. In addition, the package can convert images directly to various
formats such as pdf or postscript.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between rsvg versions 0.2 dated 2016-01-15 and 0.3 dated 2016-01-18
DESCRIPTION | 17 +++++----- MD5 | 13 ++++--- NAMESPACE | 6 +++ NEWS |only R/rsvg.R | 99 +++++++++++++++++++++++++++++++++++++++++++++++++++--------- configure | 2 - man/rsvg.Rd | 41 ++++++++++++++++++++---- src/rsvg.c | 82 +++++++++++++++++++++++++++++++++++++++++++++++-- 8 files changed, 221 insertions(+), 39 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: Previously an R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/>, and from version 0.8-0 an R
interface to the 'Spectra' library <http://yixuan.cos.name/spectra/>
to solve large scale eigenvalue/vector problems.
It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.9-0 dated 2015-11-18 and 0.10-0 dated 2016-01-18
DESCRIPTION | 18 LICENSE | 2 MD5 | 31 - README.md | 8 inst/NEWS.Rd | 9 inst/include/Spectra/CompInfo.h |only inst/include/Spectra/GenEigsSolver.h | 348 ++++++++--------- inst/include/Spectra/LinAlg/DoubleShiftQR.h | 291 +++++++------- inst/include/Spectra/LinAlg/TridiagEigen.h | 120 ++++- inst/include/Spectra/LinAlg/UpperHessenbergEigen.h | 52 +- inst/include/Spectra/LinAlg/UpperHessenbergQR.h | 194 ++++----- inst/include/Spectra/MatOp/DenseGenComplexShiftSolve.h | 30 - inst/include/Spectra/MatOp/DenseGenMatProd.h | 14 inst/include/Spectra/MatOp/DenseGenRealShiftSolve.h | 22 - inst/include/Spectra/MatOp/DenseSymShiftSolve.h | 22 - inst/include/Spectra/MatOp/SparseGenMatProd.h | 14 inst/include/Spectra/SymEigsSolver.h | 331 ++++++++-------- 17 files changed, 822 insertions(+), 684 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and NIST curves P-256, P-384 and P-521.
Cryptographic signatures can either be created and verified manually or via x509
certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA
for asymmetric (public key) encryption. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.9 dated 2016-01-13 and 0.9.1 dated 2016-01-18
DESCRIPTION | 6 +++--- MD5 | 28 +++++++++++++++------------- NAMESPACE | 1 + R/askpass.R |only R/read.R | 2 +- R/rsa.R | 2 +- R/signing.R | 2 +- configure | 2 +- inst/doc/bignum.html | 24 ++++++++++++------------ inst/doc/crypto_hashing.html | 4 ++-- inst/doc/secure_rng.html | 18 +++++++++--------- man/askpass.Rd |only man/read_key.Rd | 2 +- man/rsa_encrypt.Rd | 2 +- man/signatures.Rd | 2 +- src/ssl.c | 8 +++++++- 16 files changed, 56 insertions(+), 47 deletions(-)
Title: Visualisation of Oceanographic Data and Model Output
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between OceanView versions 1.0.3 dated 2015-03-04 and 1.0.4 dated 2016-01-18
OceanView |only 1 file changed
Title: Latin Hypercube Samples
Description: Provides a number of methods for creating and augmenting Latin Hypercube Samples.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between lhs versions 0.12 dated 2016-01-15 and 0.13 dated 2016-01-18
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/unitTests/runit_augmentLHS.r | 28 ++++++++++++++++++++++++---- inst/unitTests/runit_geneticLHS.r | 23 ++++++++++++++++++----- inst/unitTests/runit_optAugmentLHS.r | 14 ++++++++++++-- inst/unitTests/runit_optSeededLHS.r | 21 ++++++++++++++++++--- inst/unitTests/runit_optimumLHS.r | 28 ++++++++++++++++++++++++---- inst/unitTests/runit_randomLHS.r | 2 +- 9 files changed, 112 insertions(+), 31 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/'LaTeX'.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.3 dated 2015-04-21 and 1.5 dated 2016-01-18
htmlTable-1.3/htmlTable/tests/visual_tests/htmlTable_markdown.Rmd |only htmlTable-1.3/htmlTable/tests/visual_tests/pandoc_v1.13_bug.md |only htmlTable-1.5/htmlTable/DESCRIPTION | 24 htmlTable-1.5/htmlTable/MD5 | 104 + htmlTable-1.5/htmlTable/NAMESPACE | 13 htmlTable-1.5/htmlTable/NEWS | 16 htmlTable-1.5/htmlTable/R/htmlTable.R | 121 +- htmlTable-1.5/htmlTable/R/htmlTable_helpers.R | 114 +- htmlTable-1.5/htmlTable/R/htmlTable_render.R | 48 htmlTable-1.5/htmlTable/R/interactiveTable.R |only htmlTable-1.5/htmlTable/R/txtFrmt.R | 33 htmlTable-1.5/htmlTable/build/vignette.rds |binary htmlTable-1.5/htmlTable/inst/doc/general.html | 196 +-- htmlTable-1.5/htmlTable/inst/doc/tables.R | 6 htmlTable-1.5/htmlTable/inst/doc/tables.html | 190 ++- htmlTable-1.5/htmlTable/inst/examples/interactiveTable_example.R |only htmlTable-1.5/htmlTable/inst/html_components |only htmlTable-1.5/htmlTable/inst/javascript |only htmlTable-1.5/htmlTable/man/SCB.Rd | 10 htmlTable-1.5/htmlTable/man/htmlTable.Rd | 570 ++++------ htmlTable-1.5/htmlTable/man/interactiveTable.Rd |only htmlTable-1.5/htmlTable/man/outputInt.Rd | 5 htmlTable-1.5/htmlTable/man/prAddCells.Rd | 65 - htmlTable-1.5/htmlTable/man/prAddSemicolon2StrEnd.Rd | 18 htmlTable-1.5/htmlTable/man/prAttr4RgroupAdd.Rd | 26 htmlTable-1.5/htmlTable/man/prConvertDfFactors.Rd |only htmlTable-1.5/htmlTable/man/prGetAlign.Rd | 20 htmlTable-1.5/htmlTable/man/prGetCgroupHeader.Rd | 122 -- htmlTable-1.5/htmlTable/man/prGetRgroupLine.Rd | 87 - htmlTable-1.5/htmlTable/man/prGetRowlabelPos.Rd | 43 htmlTable-1.5/htmlTable/man/prGetScriptString.Rd |only htmlTable-1.5/htmlTable/man/prGetStyle.Rd | 33 htmlTable-1.5/htmlTable/man/prGetThead.Rd | 175 +-- htmlTable-1.5/htmlTable/man/prMergeClr.Rd | 15 htmlTable-1.5/htmlTable/man/prPrepareAlign.Rd | 58 - htmlTable-1.5/htmlTable/man/prPrepareCgroup.Rd | 59 - htmlTable-1.5/htmlTable/man/prPrepareColors.Rd | 11 htmlTable-1.5/htmlTable/man/prPrepareCss.Rd | 30 htmlTable-1.5/htmlTable/man/prSkipRownames.Rd | 14 htmlTable-1.5/htmlTable/man/prTblNo.Rd | 31 htmlTable-1.5/htmlTable/man/pvalueFormatter.Rd | 5 htmlTable-1.5/htmlTable/man/splitLines4Table.Rd | 4 htmlTable-1.5/htmlTable/man/tblNoLast.Rd | 15 htmlTable-1.5/htmlTable/man/tblNoNext.Rd | 15 htmlTable-1.5/htmlTable/man/txtInt.Rd | 24 htmlTable-1.5/htmlTable/man/txtMergeLines.Rd | 30 htmlTable-1.5/htmlTable/man/txtPval.Rd | 52 htmlTable-1.5/htmlTable/man/txtRound.Rd | 46 htmlTable-1.5/htmlTable/tests/testInteractive.R |only htmlTable-1.5/htmlTable/tests/testthat/test-htmlTable.R | 106 - htmlTable-1.5/htmlTable/tests/testthat/test-htmlTable_cgroup.R |only htmlTable-1.5/htmlTable/tests/testthat/test-htmlTable_rgroup_tspanner.R | 80 + htmlTable-1.5/htmlTable/tests/testthat/test-interactiveTable.R |only htmlTable-1.5/htmlTable/tests/testthat/test-txtFrmt.R | 25 htmlTable-1.5/htmlTable/tests/testthat/test-txtMergeLines.R |only htmlTable-1.5/htmlTable/tests/visual_tests/htmlTable_vtests.R | 4 htmlTable-1.5/htmlTable/tests/visual_tests/pandoc_test.Rmd | 16 htmlTable-1.5/htmlTable/tests/visual_tests/word_test.Rmd |only htmlTable-1.5/htmlTable/tests/visual_tests/word_test.html |only htmlTable-1.5/htmlTable/vignettes/custom.css | 2 60 files changed, 1417 insertions(+), 1264 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.6.2 dated 2015-12-20 and 0.7.4 dated 2016-01-18
DESCRIPTION | 12 MD5 | 57 ++-- NAMESPACE | 3 R/Convert_Simulated_Networks_To_Observed_Scale.R | 90 ++++-- R/Estimate_GERGM.R | 262 +++++-------------- R/GERGM_Class.R | 15 - R/GOF.R | 20 - R/Helper_Functions.R | 12 R/Log_Likelihood_and_MPLE_Objective.R | 33 +- R/MCMCMLE.R | 302 ++++++++++++----------- R/Optimize_Proposal_Variance.R |only R/Package_Documentation.R | 22 + R/Parse_Formula_Object.R | 11 R/Prepare_Covariates.R | 2 R/Run_MPLE.R |only R/Simulate_GERGM.R | 73 +++-- R/Symmetrize_Network.R |only R/Thin_Statistic_Samples.R | 2 R/Update_Lambda_Estimates.R |only R/gergm.R | 178 ++++++------- R/hysteresis.R |only R/hysteresis_parallel.R |only R/hysteresis_plot.R |only R/parallel_gergm.R |only R/simulate_networks.R | 84 ++---- R/single_gergm_specification.R |only R/zzz.R |only README.md | 4 man/gergm.Rd | 16 + man/hysteresis.Rd |only man/hysteresis_plot.Rd |only man/parallel_gergm.Rd |only src/Metropolis_Hastings_Sampler.cpp | 80 ++---- tests/testthat/test_experimental_features.R | 86 +++--- tests/testthat/test_gergm.R | 37 +- tests/testthat/test_hysteresis.R |only tests/testthat/test_parallel_gergm.R |only 37 files changed, 693 insertions(+), 708 deletions(-)
Title: Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, K-Nearest Neighbors, Penalized Regression (L1/L2), and Bayesian Additive Regression Trees. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>
Diff between EnsembleBase versions 0.7.1 dated 2015-01-05 and 1.0.0 dated 2016-01-18
ChangeLog | 10 + DESCRIPTION | 13 - MD5 | 34 ++-- NAMESPACE | 16 +- R/aaa.R | 2 R/baselearners.R | 244 +++++++++++++++++++++++++++---- R/regression_bart.R |only R/regression_gbm.R | 6 R/regression_knn.R | 6 R/regression_nnet.R | 6 R/regression_penreg.R |only R/regression_rf.R | 6 R/regression_svm.R | 6 man/ALL.Regression.Config-class.Rd | 16 +- man/ALL.Regression.FitObj-class.Rd | 6 man/BaseLearner.CV.Batch.FitObj-class.Rd | 1 man/BaseLearner.Fit-methods.Rd | 8 + man/Regression.CV.Batch.Fit.Rd | 22 ++ man/make.configs.Rd | 14 + 19 files changed, 346 insertions(+), 70 deletions(-)
Title: Copula Based Bivariate Beta-Binomial Model for Diagnostic Test
Accuracy Studies
Description: Modelling of sensitivity and specificity on their natural scale
using copula based bivariate beta-binomial distribution to yield marginal mean sensitivity
and specificity. The intrinsic negative correlation between sensitivity and
specificity is modelled using a copula function. A forest plot can be obtained
for categorical covariates or for the model with intercept only.
Author: Victoria N Nyaga [aut, cre]
Maintainer: Victoria N Nyaga <victoria.nyaga@outlook.com>
Diff between CopulaDTA versions 0.0.1 dated 2015-12-03 and 0.0.2 dated 2016-01-18
CopulaDTA-0.0.1/CopulaDTA/man/fitcopula.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/forestplot.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/ft.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/printcopula.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/summarycopula.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/tracecopula.Rd |only CopulaDTA-0.0.2/CopulaDTA/DESCRIPTION | 14 CopulaDTA-0.0.2/CopulaDTA/MD5 | 50 - CopulaDTA-0.0.2/CopulaDTA/NAMESPACE | 20 CopulaDTA-0.0.2/CopulaDTA/R/classes.R |only CopulaDTA-0.0.2/CopulaDTA/R/data.R | 2 CopulaDTA-0.0.2/CopulaDTA/R/fit.R | 619 +++----------------- CopulaDTA-0.0.2/CopulaDTA/R/methods.R |only CopulaDTA-0.0.2/CopulaDTA/R/model.R |only CopulaDTA-0.0.2/CopulaDTA/R/plot.R | 83 +- CopulaDTA-0.0.2/CopulaDTA/R/print.R | 90 +- CopulaDTA-0.0.2/CopulaDTA/R/summary.R | 55 - CopulaDTA-0.0.2/CopulaDTA/R/traceplot.R | 26 CopulaDTA-0.0.2/CopulaDTA/R/utils.R | 57 + CopulaDTA-0.0.2/CopulaDTA/inst/CITATION | 27 CopulaDTA-0.0.2/CopulaDTA/man/ascus.Rd | 3 CopulaDTA-0.0.2/CopulaDTA/man/cdtafit-class.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/cdtamodel-class.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/cdtamodel.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/fit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/fit.cdtamodel.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/forestplot.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/omega.to.ktau.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/plot.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/prep.data.Rd | 5 CopulaDTA-0.0.2/CopulaDTA/man/print.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/show.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/summary.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/telomerase.Rd | 3 CopulaDTA-0.0.2/CopulaDTA/man/traceplot.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/traceplot.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/waic.Rd | 38 - 37 files changed, 344 insertions(+), 748 deletions(-)
Title: Calculate the Assortativity Coefficient of Weighted and Binary
Networks
Description: Functions to calculate the assortment of vertices in social networks. This can be measured on both weighted and binary networks, with discrete or continuous vertex values.
Author: Damien Farine <dfarine@orn.mpg.de>
Maintainer: Damien Farine <dfarine@orn.mpg.de>
Diff between assortnet versions 0.11 dated 2016-01-07 and 0.12 dated 2016-01-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/assortment.continuous.R | 2 +- R/assortment.discrete.R | 2 +- man/assortnet-package.Rd | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from http://www.r-inla.org. It is recommended the testing version, which can be downloaded by running: source("http://www.math.ntnu.no/inla/givemeINLA-testing.R"). A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the abn website.
Author: Fraser Ian Lewis [aut], Marta Pittavino [cre, ctb], Reinhard Furrer [ctb]
Maintainer: Marta Pittavino <marta.pittavino@math.uzh.ch>
Diff between abn versions 0.86 dated 2015-12-28 and 1.0 dated 2016-01-18
abn-0.86/abn/data/pigs1par.RData |only abn-0.86/abn/inst/doc/abn_v0.85.R |only abn-0.86/abn/inst/doc/abn_v0.85.Rnw |only abn-0.86/abn/inst/doc/abn_v0.85.pdf |only abn-0.86/abn/man/pigs.1par.rd |only abn-0.86/abn/man/var33.rd |only abn-0.86/abn/vignettes/abn_v0.85.Rnw |only abn-1.0/abn/ChangeLog | 3 abn-1.0/abn/DESCRIPTION | 8 abn-1.0/abn/MD5 | 43 abn-1.0/abn/build/vignette.rds |binary abn-1.0/abn/data/pigs.vienna.RData |only abn-1.0/abn/inst/bootstrapping_example/10KBootstrapping.R |only abn-1.0/abn/inst/bootstrapping_example/10Kbootstrapping.bash |only abn-1.0/abn/inst/bootstrapping_example/MargPlots_PigsData.pdf |only abn-1.0/abn/inst/bootstrapping_example/Pigs_PostBootPlots.pdf |only abn-1.0/abn/inst/bootstrapping_example/inits.R |only abn-1.0/abn/inst/bootstrapping_example/initsearch.bash |only abn-1.0/abn/inst/bootstrapping_example/jags_pigs_script.R |only abn-1.0/abn/inst/bootstrapping_example/pigs_model.bug |only abn-1.0/abn/inst/bootstrapping_example/pigs_post_params.R |only abn-1.0/abn/inst/doc/abn_v1.0.R |only abn-1.0/abn/inst/doc/abn_v1.0.Rnw |only abn-1.0/abn/inst/doc/abn_v1.0.pdf |only abn-1.0/abn/man/pigs.vienna.Rd |only abn-1.0/abn/man/var33.Rd |only abn-1.0/abn/vignettes/Bootstrapping.png |only abn-1.0/abn/vignettes/ComparisonOfNetworkScore.pdf |only abn-1.0/abn/vignettes/DAG_cycle.pdf |only abn-1.0/abn/vignettes/MargPlots_PigsData.pdf |only abn-1.0/abn/vignettes/PigsArea.png |only abn-1.0/abn/vignettes/Pigs_PostBootPlots.pdf |only abn-1.0/abn/vignettes/Summary.png |only abn-1.0/abn/vignettes/abn.bib | 694 +++++++++- abn-1.0/abn/vignettes/abn_v1.0.Rnw |only abn-1.0/abn/vignettes/abn_v10-newfile.pdf |only abn-1.0/abn/vignettes/map1_10var.dot |only abn-1.0/abn/vignettes/map_1par.dot |only abn-1.0/abn/vignettes/plbinaryNode.png |only abn-1.0/abn/vignettes/postbootpigs.pdf |only 40 files changed, 698 insertions(+), 50 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.1.0 dated 2016-01-16 and 1.1.1 dated 2016-01-18
cycleRtools-1.1.0/cycleRtools/java/Tests.java |only cycleRtools-1.1.0/cycleRtools/tests |only cycleRtools-1.1.1/cycleRtools/DESCRIPTION | 10 +-- cycleRtools-1.1.1/cycleRtools/MD5 | 29 ++------- cycleRtools-1.1.1/cycleRtools/NEWS | 5 + cycleRtools-1.1.1/cycleRtools/R/Wbal.R | 3 cycleRtools-1.1.1/cycleRtools/build/vignette.rds |binary cycleRtools-1.1.1/cycleRtools/inst/doc/cycling_data_analysis.R | 4 + cycleRtools-1.1.1/cycleRtools/inst/doc/cycling_data_analysis.Rmd | 20 ++++-- cycleRtools-1.1.1/cycleRtools/inst/doc/cycling_data_analysis.html | 32 ++++++++-- cycleRtools-1.1.1/cycleRtools/man/Wbal.Rd | 2 cycleRtools-1.1.1/cycleRtools/vignettes/cycling_data_analysis.Rmd | 20 ++++-- 12 files changed, 84 insertions(+), 41 deletions(-)
Title: Plotting Multi-Dimensional Data - Using 'rgl'
Description: The 'rgl' implementation of plot3D functions.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3Drgl versions 1.0 dated 2014-03-17 and 1.0.1 dated 2016-01-18
DESCRIPTION | 17 ++++----- MD5 | 23 ++++++------ NAMESPACE | 6 ++- R/arrowsrgl.R | 75 +++++++++++++++++---------------------- R/imagergl.R | 73 +++++++++++++++++++++----------------- R/plot2Drgl.R | 100 +++++++++++++++++++++++++++++++++++++++++++++-------- R/plot3Drgl.R | 53 ++++++++++++++++++++++------ R/plotrgl.R | 85 +++++++++++++++++++++++++++++---------------- R/plotrglcolkey.R |only R/scatterrgl.R | 60 ++++++++++++++++++++++--------- build/vignette.rds |binary man/imagergl.Rd | 77 +++++++++++++++++++++++++++++++--------- man/persp3Drgl.Rd | 6 +-- 13 files changed, 387 insertions(+), 188 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full
Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.6.0 dated 2015-11-13 and 0.7.0 dated 2016-01-18
brms-0.6.0/brms/man/VarCorr.Rd |only brms-0.6.0/brms/man/fixef.Rd |only brms-0.6.0/brms/man/macf.Rd |only brms-0.6.0/brms/man/ngrps.Rd |only brms-0.6.0/brms/man/ranef.Rd |only brms-0.7.0/brms/DESCRIPTION | 21 brms-0.7.0/brms/MD5 | 146 +- brms-0.7.0/brms/NAMESPACE | 20 brms-0.7.0/brms/R/brm.R | 426 ++++-- brms-0.7.0/brms/R/brmsfit-helpers.R | 500 ++++---- brms-0.7.0/brms/R/brmsfit-methods.R | 1043 +++++++++++------ brms-0.7.0/brms/R/correlations.R | 94 - brms-0.7.0/brms/R/data.R | 553 +++++---- brms-0.7.0/brms/R/datasets.R | 144 +- brms-0.7.0/brms/R/distributions.R | 96 + brms-0.7.0/brms/R/families.R | 219 +++ brms-0.7.0/brms/R/fitted.R | 70 - brms-0.7.0/brms/R/generics.R | 431 +++---- brms-0.7.0/brms/R/loglik.R | 103 + brms-0.7.0/brms/R/misc-methods.R |only brms-0.7.0/brms/R/misc.R | 156 ++ brms-0.7.0/brms/R/predict.R | 107 + brms-0.7.0/brms/R/priors.R | 272 ++-- brms-0.7.0/brms/R/rename.R | 254 ++-- brms-0.7.0/brms/R/stan.R | 676 ++++++----- brms-0.7.0/brms/R/validate.R | 437 ++++--- brms-0.7.0/brms/R/zzz-example.R | 14 brms-0.7.0/brms/README.md | 45 brms-0.7.0/brms/build/vignette.rds |binary brms-0.7.0/brms/inst/NEWS.Rd | 81 + brms-0.7.0/brms/inst/doc/brms.ltx | 6 brms-0.7.0/brms/inst/doc/brms.pdf |binary brms-0.7.0/brms/inst/doc/brms_families.R |only brms-0.7.0/brms/inst/doc/brms_families.Rmd |only brms-0.7.0/brms/inst/doc/brms_families.html |only brms-0.7.0/brms/man/LOO.Rd | 36 brms-0.7.0/brms/man/VarCorr.brmsfit.Rd |only brms-0.7.0/brms/man/WAIC.Rd | 34 brms-0.7.0/brms/man/brm.Rd | 294 ++-- brms-0.7.0/brms/man/brms-package.Rd | 28 brms-0.7.0/brms/man/brmsfamily.Rd | 24 brms-0.7.0/brms/man/brmsfit-class.Rd | 27 brms-0.7.0/brms/man/coef.brmsfit.Rd |only brms-0.7.0/brms/man/epilepsy.Rd | 52 brms-0.7.0/brms/man/fitted.brmsfit.Rd | 80 - brms-0.7.0/brms/man/fixef.brmsfit.Rd |only brms-0.7.0/brms/man/get_prior.Rd | 47 brms-0.7.0/brms/man/hypothesis.Rd | 113 + brms-0.7.0/brms/man/inhaler.Rd | 41 brms-0.7.0/brms/man/kidney.Rd | 49 brms-0.7.0/brms/man/launch_shiny.Rd | 12 brms-0.7.0/brms/man/logLik.brmsfit.Rd | 6 brms-0.7.0/brms/man/make_stancode.Rd | 57 brms-0.7.0/brms/man/make_standata.Rd | 48 brms-0.7.0/brms/man/ngrps.brmsfit.Rd |only brms-0.7.0/brms/man/pairs.brmsfit.Rd |only brms-0.7.0/brms/man/parnames.Rd | 5 brms-0.7.0/brms/man/plot.brmsfit.Rd | 37 brms-0.7.0/brms/man/posterior_samples.Rd | 41 brms-0.7.0/brms/man/predict.brmsfit.Rd | 103 + brms-0.7.0/brms/man/print.brmsfit.Rd | 3 brms-0.7.0/brms/man/prior_samples.Rd | 26 brms-0.7.0/brms/man/ranef.brmsfit.Rd |only brms-0.7.0/brms/man/residuals.brmsfit.Rd | 64 - brms-0.7.0/brms/man/set_prior.Rd | 132 +- brms-0.7.0/brms/man/stanplot.Rd | 67 - brms-0.7.0/brms/man/update.brmsfit.Rd | 13 brms-0.7.0/brms/man/vcov.brmsfit.Rd | 6 brms-0.7.0/brms/tests/testthat/tests.brm.R | 106 - brms-0.7.0/brms/tests/testthat/tests.brmsfit-helpers.R | 103 + brms-0.7.0/brms/tests/testthat/tests.brmsfit-methods.R |only brms-0.7.0/brms/tests/testthat/tests.data.R | 218 ++- brms-0.7.0/brms/tests/testthat/tests.distributions.R | 39 brms-0.7.0/brms/tests/testthat/tests.families.R |only brms-0.7.0/brms/tests/testthat/tests.fitted.R |only brms-0.7.0/brms/tests/testthat/tests.loglik.R |only brms-0.7.0/brms/tests/testthat/tests.misc.R | 46 brms-0.7.0/brms/tests/testthat/tests.plots.R |only brms-0.7.0/brms/tests/testthat/tests.predict.R |only brms-0.7.0/brms/tests/testthat/tests.priors.R | 119 + brms-0.7.0/brms/tests/testthat/tests.rename.R | 74 - brms-0.7.0/brms/tests/testthat/tests.stan.R | 258 ++-- brms-0.7.0/brms/tests/testthat/tests.validate.R | 205 ++- brms-0.7.0/brms/vignettes/brms.ltx | 6 brms-0.7.0/brms/vignettes/brms_families.Rmd |only 85 files changed, 5359 insertions(+), 3174 deletions(-)
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between strvalidator versions 1.5.2 dated 2015-08-31 and 1.6.0 dated 2016-01-18
strvalidator-1.5.2/strvalidator/R/compact.r |only strvalidator-1.5.2/strvalidator/man/compact.Rd |only strvalidator-1.5.2/strvalidator/man/strValidator-package.Rd |only strvalidator-1.6.0/strvalidator/DESCRIPTION | 16 strvalidator-1.6.0/strvalidator/MD5 | 386 strvalidator-1.6.0/strvalidator/NAMESPACE | 78 strvalidator-1.6.0/strvalidator/NEWS | 102 strvalidator-1.6.0/strvalidator/R/addColor.r | 12 strvalidator-1.6.0/strvalidator/R/addData.r | 33 strvalidator-1.6.0/strvalidator/R/addData_gui.r | 66 strvalidator-1.6.0/strvalidator/R/addDye_gui.r | 9 strvalidator-1.6.0/strvalidator/R/addMarker.r | 9 strvalidator-1.6.0/strvalidator/R/addMarker_gui.r | 10 strvalidator-1.6.0/strvalidator/R/addSize.r | 10 strvalidator-1.6.0/strvalidator/R/addSize_gui.r | 10 strvalidator-1.6.0/strvalidator/R/calculateAT.r | 119 strvalidator-1.6.0/strvalidator/R/calculateAT6.r | 39 strvalidator-1.6.0/strvalidator/R/calculateAT6_gui.r | 8 strvalidator-1.6.0/strvalidator/R/calculateAT_gui.r | 34 strvalidator-1.6.0/strvalidator/R/calculateAllele.r |only strvalidator-1.6.0/strvalidator/R/calculateBalance.r | 67 strvalidator-1.6.0/strvalidator/R/calculateBalance_gui.r | 113 strvalidator-1.6.0/strvalidator/R/calculateConcordance_gui.r | 2 strvalidator-1.6.0/strvalidator/R/calculateDropout.r | 196 strvalidator-1.6.0/strvalidator/R/calculateDropout_gui.r | 73 strvalidator-1.6.0/strvalidator/R/calculateHeight.r | 11 strvalidator-1.6.0/strvalidator/R/calculateHeight_gui.r | 21 strvalidator-1.6.0/strvalidator/R/calculateLb.r |only strvalidator-1.6.0/strvalidator/R/calculateLb_gui.r |only strvalidator-1.6.0/strvalidator/R/calculatePullup_gui.r | 2 strvalidator-1.6.0/strvalidator/R/calculateRatio.r |only strvalidator-1.6.0/strvalidator/R/calculateRatio_gui.r |only strvalidator-1.6.0/strvalidator/R/calculateResultType_gui.r | 2 strvalidator-1.6.0/strvalidator/R/calculateSpike.r |only strvalidator-1.6.0/strvalidator/R/calculateSpike_gui.r |only strvalidator-1.6.0/strvalidator/R/calculateStutter.r | 18 strvalidator-1.6.0/strvalidator/R/calculateStutter_gui.r | 15 strvalidator-1.6.0/strvalidator/R/checkSubset.r | 18 strvalidator-1.6.0/strvalidator/R/checkSubset_gui.r | 49 strvalidator-1.6.0/strvalidator/R/colConvert.r |only strvalidator-1.6.0/strvalidator/R/columns.r | 52 strvalidator-1.6.0/strvalidator/R/columns_gui.r | 50 strvalidator-1.6.0/strvalidator/R/cropData_gui.r | 68 strvalidator-1.6.0/strvalidator/R/detectKit.r | 52 strvalidator-1.6.0/strvalidator/R/editData_gui.r | 327 strvalidator-1.6.0/strvalidator/R/filterProfile.r | 185 strvalidator-1.6.0/strvalidator/R/filterProfile_gui.r | 48 strvalidator-1.6.0/strvalidator/R/filterSpike_gui.r |only strvalidator-1.6.0/strvalidator/R/generateEPG.r | 659 strvalidator-1.6.0/strvalidator/R/generateEPG_gui.r | 154 strvalidator-1.6.0/strvalidator/R/getKit.r | 5 strvalidator-1.6.0/strvalidator/R/ggsave_gui.r | 14 strvalidator-1.6.0/strvalidator/R/globals.R | 23 strvalidator-1.6.0/strvalidator/R/heightToPeak.r | 89 strvalidator-1.6.0/strvalidator/R/hooks.r | 7 strvalidator-1.6.0/strvalidator/R/import.r | 66 strvalidator-1.6.0/strvalidator/R/import_gui.r | 178 strvalidator-1.6.0/strvalidator/R/modelDropout_gui.r | 9 strvalidator-1.6.0/strvalidator/R/plotAT_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotBalance_gui.r | 355 strvalidator-1.6.0/strvalidator/R/plotCapillary_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotDistribution_gui.r | 59 strvalidator-1.6.0/strvalidator/R/plotDropout_gui.r | 8 strvalidator-1.6.0/strvalidator/R/plotKit_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotPeaks_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotPrecision_gui.r | 20 strvalidator-1.6.0/strvalidator/R/plotPullup_gui.r | 20 strvalidator-1.6.0/strvalidator/R/plotRatio_gui.r |only strvalidator-1.6.0/strvalidator/R/plotResultType_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotStutter_gui.r | 23 strvalidator-1.6.0/strvalidator/R/readPanelsFile.r | 3 strvalidator-1.6.0/strvalidator/R/scrambleAlleles.r |only strvalidator-1.6.0/strvalidator/R/slim.r | 13 strvalidator-1.6.0/strvalidator/R/slim_gui.r | 18 strvalidator-1.6.0/strvalidator/R/strvalidator-package.r | 49 strvalidator-1.6.0/strvalidator/R/strvalidator.r | 265 strvalidator-1.6.0/strvalidator/R/tableBalance.r | 10 strvalidator-1.6.0/strvalidator/R/tableBalance_gui.r | 7 strvalidator-1.6.0/strvalidator/R/tablePrecision_gui.r | 2 strvalidator-1.6.0/strvalidator/R/trim.r | 27 strvalidator-1.6.0/strvalidator/R/trim_gui.r | 28 strvalidator-1.6.0/strvalidator/inst/extdata/database.txt | 2 strvalidator-1.6.0/strvalidator/inst/extdata/database_readme.txt | 4 strvalidator-1.6.0/strvalidator/inst/extdata/kit.txt | 9518 +++++----- strvalidator-1.6.0/strvalidator/man/addColor.Rd | 4 strvalidator-1.6.0/strvalidator/man/addData.Rd | 6 strvalidator-1.6.0/strvalidator/man/addData_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/addDye_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/addMarker.Rd | 2 strvalidator-1.6.0/strvalidator/man/addMarker_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/addSize.Rd | 2 strvalidator-1.6.0/strvalidator/man/addSize_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/blockAT.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateAT.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateAT6.Rd | 11 strvalidator-1.6.0/strvalidator/man/calculateAT6_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateAT_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateAllele.Rd |only strvalidator-1.6.0/strvalidator/man/calculateBalance.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateBalance_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateCapillary.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateCapillary_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateConcordance.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateConcordance_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateDropout.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateDropout_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateHeight.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateHeight_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateHeterozygous.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateHeterozygous_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateLb.Rd |only strvalidator-1.6.0/strvalidator/man/calculateLb_gui.Rd |only strvalidator-1.6.0/strvalidator/man/calculateMixture.Rd | 10 strvalidator-1.6.0/strvalidator/man/calculateMixture_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateOL.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateOL_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateOverlap.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateOverlap_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculatePeaks.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculatePeaks_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculatePullup.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculatePullup_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateRatio.Rd |only strvalidator-1.6.0/strvalidator/man/calculateRatio_gui.Rd |only strvalidator-1.6.0/strvalidator/man/calculateResultType.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateResultType_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateSpike.Rd |only strvalidator-1.6.0/strvalidator/man/calculateSpike_gui.Rd |only strvalidator-1.6.0/strvalidator/man/calculateStutter.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateStutter_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/checkDataset.Rd | 2 strvalidator-1.6.0/strvalidator/man/checkSubset.Rd | 13 strvalidator-1.6.0/strvalidator/man/checkSubset_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/colConvert.Rd |only strvalidator-1.6.0/strvalidator/man/colNames.Rd | 2 strvalidator-1.6.0/strvalidator/man/columns.Rd | 24 strvalidator-1.6.0/strvalidator/man/columns_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/combineBinsAndPanels.Rd | 6 strvalidator-1.6.0/strvalidator/man/combine_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/cropData_gui.Rd | 6 strvalidator-1.6.0/strvalidator/man/detectKit.Rd | 6 strvalidator-1.6.0/strvalidator/man/editData_gui.Rd | 8 strvalidator-1.6.0/strvalidator/man/export.Rd | 4 strvalidator-1.6.0/strvalidator/man/export_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/filterProfile.Rd | 6 strvalidator-1.6.0/strvalidator/man/filterProfile_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/generateEPG.Rd | 19 strvalidator-1.6.0/strvalidator/man/generateEPG_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/getDb.Rd | 2 strvalidator-1.6.0/strvalidator/man/getKit.Rd | 6 strvalidator-1.6.0/strvalidator/man/ggsave_gui.Rd | 7 strvalidator-1.6.0/strvalidator/man/guessProfile.Rd | 2 strvalidator-1.6.0/strvalidator/man/guessProfile_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/heightToPeak.Rd | 2 strvalidator-1.6.0/strvalidator/man/import.Rd | 9 strvalidator-1.6.0/strvalidator/man/import_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/listObjects.Rd | 2 strvalidator-1.6.0/strvalidator/man/makeKit_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/modelDropout_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotAT_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotBalance_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotCapillary_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotDistribution_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotDropout_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/plotKit_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotPeaks_gui.Rd | 6 strvalidator-1.6.0/strvalidator/man/plotPrecision_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotPullup_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotRatio_gui.Rd |only strvalidator-1.6.0/strvalidator/man/plotResultType_gui.Rd | 6 strvalidator-1.6.0/strvalidator/man/plotStutter_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/readBinsFile.Rd | 2 strvalidator-1.6.0/strvalidator/man/readPanelsFile.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref1.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref11.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref2.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref3.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref4.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref51.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref52.Rd | 2 strvalidator-1.6.0/strvalidator/man/saveObject.Rd | 4 strvalidator-1.6.0/strvalidator/man/scrambleAlleles.Rd |only strvalidator-1.6.0/strvalidator/man/set1.Rd | 2 strvalidator-1.6.0/strvalidator/man/set2.Rd | 2 strvalidator-1.6.0/strvalidator/man/set3.Rd | 2 strvalidator-1.6.0/strvalidator/man/set4.Rd | 2 strvalidator-1.6.0/strvalidator/man/set5.Rd | 2 strvalidator-1.6.0/strvalidator/man/slim.Rd | 2 strvalidator-1.6.0/strvalidator/man/slim_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/sortMarker.Rd | 4 strvalidator-1.6.0/strvalidator/man/strvalidator-package.Rd |only strvalidator-1.6.0/strvalidator/man/strvalidator.Rd | 42 strvalidator-1.6.0/strvalidator/man/tableBalance.Rd | 2 strvalidator-1.6.0/strvalidator/man/tableBalance_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/tableCapillary.Rd | 4 strvalidator-1.6.0/strvalidator/man/tableCapillary_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/tablePrecision.Rd | 2 strvalidator-1.6.0/strvalidator/man/tablePrecision_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/tableStutter.Rd | 2 strvalidator-1.6.0/strvalidator/man/tableStutter_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/trim.Rd | 6 strvalidator-1.6.0/strvalidator/man/trim_gui.Rd | 4 strvalidator-1.6.0/strvalidator/tests/testthat/test-calculateBalance.r | 1852 + strvalidator-1.6.0/strvalidator/tests/testthat/test-calculateDropout.r | 55 strvalidator-1.6.0/strvalidator/tests/testthat/test-calculateLb.r |only strvalidator-1.6.0/strvalidator/tests/testthat/test-filterProfile.r | 154 strvalidator-1.6.0/strvalidator/tests/testthat/test-tableBalance.r | 5 207 files changed, 9787 insertions(+), 6684 deletions(-)
Title: Automatic Marking of R Assignments
Description: Automatic marking of R assignments for students and teachers based
on 'testthat' test suites.
Author: Mans Magnusson, Oscar Pettersson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between markmyassignment versions 0.3.0 dated 2015-12-28 and 0.4.0 dated 2016-01-18
markmyassignment-0.3.0/markmyassignment/man/stop_if_circular_calls.Rd |only markmyassignment-0.4.0/markmyassignment/DESCRIPTION | 12 - markmyassignment-0.4.0/markmyassignment/MD5 | 89 ++++---- markmyassignment-0.4.0/markmyassignment/R/assertion_funcions.R | 8 markmyassignment-0.4.0/markmyassignment/R/expectations.R | 20 ++ markmyassignment-0.4.0/markmyassignment/R/mark_my_assignment.R | 94 ++++++--- markmyassignment-0.4.0/markmyassignment/R/mark_my_file.R | 19 + markmyassignment-0.4.0/markmyassignment/R/reporter.R | 2 markmyassignment-0.4.0/markmyassignment/R/set_assignment.R | 53 ++++- markmyassignment-0.4.0/markmyassignment/README.md | 99 +--------- markmyassignment-0.4.0/markmyassignment/build |only markmyassignment-0.4.0/markmyassignment/inst/doc |only markmyassignment-0.4.0/markmyassignment/inst/extdata/example_assignment07_pkgs.yml |only markmyassignment-0.4.0/markmyassignment/inst/extdata/example_assignment08_bad_pkgs.yml |only markmyassignment-0.4.0/markmyassignment/inst/extdata/example_lab_file_messy.R |only markmyassignment-0.4.0/markmyassignment/man/StudentReporter-class.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/assert_function_arguments_in_API.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/assignment_yml_ok.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/cached_tasks.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/check_assignment_file.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/check_existance_tasks.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/check_installed_packages.Rd |only markmyassignment-0.4.0/markmyassignment/man/cheer.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/delete_circular_calls.Rd |only markmyassignment-0.4.0/markmyassignment/man/directories.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_function_arguments.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_function_code.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_package.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_self_contained.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_tidy_code.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/find_expr.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/function_code.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/get_file.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/get_mark_my_reporter.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/get_tests.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/has_function_arguments.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/is_self_contained.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/mark_my_dir.Rd | 5 markmyassignment-0.4.0/markmyassignment/man/mark_my_file.Rd | 6 markmyassignment-0.4.0/markmyassignment/man/path_type.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/read_assignment_yml.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/run_test_suite.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/show_tasks.Rd | 4 markmyassignment-0.4.0/markmyassignment/man/temp_folder_check_create.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/use_package.Rd | 1 markmyassignment-0.4.0/markmyassignment/tests/testthat/test-mark_my_assignment.R | 18 - markmyassignment-0.4.0/markmyassignment/tests/testthat/test-mark_my_file.R | 51 +++-- markmyassignment-0.4.0/markmyassignment/tests/testthat/test-set_assignment.R | 13 + markmyassignment-0.4.0/markmyassignment/vignettes |only 49 files changed, 311 insertions(+), 207 deletions(-)
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Title: MA Birk's Functions
Description: This is a compilation of functions that I found useful to make.
It currently includes a couple of functions to work with converting units of
measurement, and some miscellaneous wrapper functions to make R code shorter and
faster to write.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between birk versions 1.3.0 dated 2015-02-01 and 2.0.0 dated 2016-01-18
birk-1.3.0/birk/R/Q10calc.R |only birk-1.3.0/birk/man/Q10calc.Rd |only birk-2.0.0/birk/DESCRIPTION | 15 - birk-2.0.0/birk/MD5 | 34 +- birk-2.0.0/birk/NAMESPACE | 8 birk-2.0.0/birk/NEWS | 20 + birk-2.0.0/birk/R/birk.R | 6 birk-2.0.0/birk/R/conv_dim.R |only birk-2.0.0/birk/R/conv_unit.R | 369 +++++++++++++++++++++---------- birk-2.0.0/birk/R/range_seq.R | 7 birk-2.0.0/birk/R/se.R | 3 birk-2.0.0/birk/R/summ_stat.R |only birk-2.0.0/birk/R/which.closest.R |only birk-2.0.0/birk/man/birk.Rd | 6 birk-2.0.0/birk/man/conv_dim.Rd |only birk-2.0.0/birk/man/conv_unit.Rd | 62 ++--- birk-2.0.0/birk/man/conv_unit_options.Rd | 5 birk-2.0.0/birk/man/geom_mean.Rd | 3 birk-2.0.0/birk/man/range_seq.Rd | 3 birk-2.0.0/birk/man/se.Rd | 3 birk-2.0.0/birk/man/summ_stat.Rd |only birk-2.0.0/birk/man/which.closest.Rd |only 22 files changed, 360 insertions(+), 184 deletions(-)