Title: Utilities for Multi-Label Learning
Description: Multi-label learning strategies and others procedures to support multi-
label classification in R. The package provides a set of multi-label procedures such as
sampling methods, transformation strategies, threshold functions, pre-processing
techniques and evaluation metrics. A complete overview of the matter can be seen in
Zhang, M. and Zhou, Z. (2014) <doi:10.1109/TKDE.2013.39> and Gibaja, E. and
Ventura, S. (2015) <doi:10.1145/2716262>.
Author: Adriano Rivolli [aut, cre]
Maintainer: Adriano Rivolli <rivolli@utfpr.edu.br>
Diff between utiml versions 0.1.2 dated 2017-04-06 and 0.1.3 dated 2017-07-31
utiml-0.1.2/utiml/man/fill_sparce_mldata.Rd |only utiml-0.1.3/utiml/DESCRIPTION | 10 - utiml-0.1.3/utiml/MD5 | 129 ++++++++-------- utiml-0.1.3/utiml/NAMESPACE | 2 utiml-0.1.3/utiml/NEWS.md | 14 + utiml-0.1.3/utiml/R/base_learner.R | 10 - utiml-0.1.3/utiml/R/ensemble.R | 6 utiml-0.1.3/utiml/R/evaluation.R | 77 +++++++-- utiml-0.1.3/utiml/R/internal.R | 2 utiml-0.1.3/utiml/R/method_baseline.R | 7 utiml-0.1.3/utiml/R/method_brplus.R | 10 - utiml-0.1.3/utiml/R/method_cc.R | 2 utiml-0.1.3/utiml/R/method_ctrl.R | 1 utiml-0.1.3/utiml/R/method_dbr.R | 6 utiml-0.1.3/utiml/R/method_ebr.R | 4 utiml-0.1.3/utiml/R/method_ecc.R | 4 utiml-0.1.3/utiml/R/method_eps.R | 4 utiml-0.1.3/utiml/R/method_lift.R | 2 utiml-0.1.3/utiml/R/method_mbr.R | 2 utiml-0.1.3/utiml/R/method_prudent.R | 4 utiml-0.1.3/utiml/R/method_rdbr.R | 10 - utiml-0.1.3/utiml/R/mlresult.R | 13 - utiml-0.1.3/utiml/R/pre_process.R | 16 - utiml-0.1.3/utiml/R/sampling.R | 6 utiml-0.1.3/utiml/R/threshold.R | 14 - utiml-0.1.3/utiml/R/utiml.R | 2 utiml-0.1.3/utiml/build/vignette.rds |binary utiml-0.1.3/utiml/man/brplus.Rd | 2 utiml-0.1.3/utiml/man/compute_multilabel_predictions.Rd | 2 utiml-0.1.3/utiml/man/create_holdout_partition.Rd | 2 utiml-0.1.3/utiml/man/dbr.Rd | 6 utiml-0.1.3/utiml/man/ebr.Rd | 4 utiml-0.1.3/utiml/man/ecc.Rd | 4 utiml-0.1.3/utiml/man/eps.Rd | 4 utiml-0.1.3/utiml/man/fill_sparse_mldata.Rd |only utiml-0.1.3/utiml/man/fixed_threshold.Rd | 6 utiml-0.1.3/utiml/man/lift.Rd | 2 utiml-0.1.3/utiml/man/mbr.Rd | 2 utiml-0.1.3/utiml/man/mlpredict.Rd | 2 utiml-0.1.3/utiml/man/mltrain.Rd | 4 utiml-0.1.3/utiml/man/multilabel_evaluate.Rd | 15 + utiml-0.1.3/utiml/man/normalize_mldata.Rd | 2 utiml-0.1.3/utiml/man/partition_fold.Rd | 4 utiml-0.1.3/utiml/man/predict.BRPmodel.Rd | 2 utiml-0.1.3/utiml/man/predict.CCmodel.Rd | 2 utiml-0.1.3/utiml/man/prudent.Rd | 4 utiml-0.1.3/utiml/man/rdbr.Rd | 10 - utiml-0.1.3/utiml/man/remove_attributes.Rd | 4 utiml-0.1.3/utiml/man/remove_labels.Rd | 4 utiml-0.1.3/utiml/man/remove_skewness_labels.Rd | 2 utiml-0.1.3/utiml/man/remove_unique_attributes.Rd | 2 utiml-0.1.3/utiml/man/remove_unlabeled_instances.Rd | 2 utiml-0.1.3/utiml/man/replace_nominal_attributes.Rd | 2 utiml-0.1.3/utiml/man/scut_threshold.Rd | 4 utiml-0.1.3/utiml/man/sub-.mlresult.Rd | 4 utiml-0.1.3/utiml/man/subset_correction.Rd | 4 utiml-0.1.3/utiml/man/utiml.Rd | 2 utiml-0.1.3/utiml/man/utiml_ensemble_majority.Rd | 2 utiml-0.1.3/utiml/man/utiml_lapply.Rd | 2 utiml-0.1.3/utiml/man/utiml_measure_binary_balacc.Rd |only utiml-0.1.3/utiml/man/utiml_measure_ranking_error.Rd | 2 utiml-0.1.3/utiml/man/utiml_predict_binary_ensemble.Rd | 2 utiml-0.1.3/utiml/tests/testthat/test_base_learner.R | 6 utiml-0.1.3/utiml/tests/testthat/test_evaluation.R | 26 +-- utiml-0.1.3/utiml/tests/testthat/test_mlresult.R | 4 utiml-0.1.3/utiml/tests/testthat/test_preprocess.R | 6 utiml-0.1.3/utiml/vignettes/utiml-overview.html | 48 ++--- 67 files changed, 319 insertions(+), 245 deletions(-)
Title: A Constrained L1 Minimization Approach for Estimating Multiple
Sparse Gaussian or Nonparanormal Graphical Models
Description: This is an R implementation of a constrained l1 minimization approach for estimating multiple Sparse Gaussian or Nonparanormal Graphical Models (SIMULE). The SIMULE algorithm can be used to estimate multiple related precision matrices. For instance, it can identify context-specific gene networks from multi-context gene expression datasets. By performing data-driven network inference from high-dimensional and heterogenous data sets, this tool can help users effectively translate aggregated data into knowledge that take the form of graphs among entities. Please run demo(simuleDemo) to learn the basic functions provided by this package. For further details, please read the original paper: Beilun Wang, Ritambhara Singh, Yanjun Qi (2017) <DOI:10.1007/s10994-017-5635-7>.
Author: Beilun Wang [aut, cre], Yanjun Qi [aut]
Maintainer: Beilun Wang <bw4mw@virginia.edu>
Diff between simule versions 1.1.1 dated 2017-07-12 and 1.1.2 dated 2017-07-31
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ R/SIMULE.R | 7 +++++++ data/cancer.rdata |only demo/simuleDemo.R | 32 ++++++++++++++++++++++++++++++++ man/data-cancer.Rd |only man/exampleData.Rd | 2 +- man/plot.simule.Rd | 2 +- man/simule-package.Rd | 4 ++-- 9 files changed, 56 insertions(+), 15 deletions(-)
Title: EBGM Scores for Mining Large Contingency Tables
Description: An implementation of DuMouchel's (1999)
<doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the
market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and
quantile scores from the posterior distribution using the Gamma-Poisson
Shrinker (GPS) model to find unusually large cell counts in large, sparse
contingency tables. Can be used to find unusually high reporting rates of
adverse events associated with products. In general, can be used to mine any
database where the co-occurrence of two variables or items is of interest.
Also calculates relative and proportional reporting ratios. Builds on the work
of the 'PhViD' package, from which much of the code is derived. Some of the
added features include stratification to adjust for confounding variables and
data squashing to improve computational efficiency.
Author: John Ihrie [cre, aut],
Travis Canida [aut],
Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)),
Antoine Poncet [ctb] (author of 'PhViD' package (derived code))
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between openEBGM versions 0.1.0 dated 2017-05-05 and 0.2.0 dated 2017-07-31
DESCRIPTION | 6 +- MD5 | 39 +++++++++-------- NEWS |only R/f_checkInputs.R | 23 ++++++++++ R/f_classFunctions.R | 43 ++++++++++--------- R/f_createObject.R | 57 ++++++++++++++------------ R/f_hyperEstimation.R | 14 +++--- build/vignette.rds |binary inst/doc/x1_introAndDataPrepVignette.html | 4 - inst/doc/x2_rawDataProcessingVignette.html | 4 - inst/doc/x3_hyperParameterVignette.Rmd | 2 inst/doc/x3_hyperParameterVignette.html | 8 +-- inst/doc/x4_posteriorCalculationVignette.html | 4 - inst/doc/x5_openEBGMObjectVignette.R | 4 - inst/doc/x5_openEBGMObjectVignette.Rmd | 24 +++++----- inst/doc/x5_openEBGMObjectVignette.html | 36 +++++----------- man/print.openEBGM.Rd |only man/summary.openEBGM.Rd | 3 - tests/testthat/testEBGM.R | 2 tests/testthat/testObject.R |only vignettes/x3_hyperParameterVignette.Rmd | 2 vignettes/x5_openEBGMObjectVignette.Rmd | 24 +++++----- 22 files changed, 163 insertions(+), 136 deletions(-)
Title: Functions to Explore L-Systems (Lindenmayer Systems)
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can
be used to simulate biological forms and certain kinds of fractals.
Briefly, in an L-system a series of symbols in a string are replaced
iteratively according to rules to give a more complex string. Eventually,
the symbols are translated into turtle graphics for plotting. Wikipedia has
a very good introduction: en.wikipedia.org/wiki/L-system This package
provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between LindenmayeR versions 0.1.6 dated 2015-07-16 and 0.1.13 dated 2017-07-31
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- NEWS | 4 ++++ R/Lsys.R | 10 +++++++++- R/drawLsys.R | 28 ++++++++++++++++++++++------ man/LindenmayeR-package.Rd | 5 ++--- man/Lsys.Rd | 12 ++++++++++-- man/drawLsys.Rd | 30 +++++++++++++++++++++++------- 9 files changed, 84 insertions(+), 32 deletions(-)
Title: Spatial Graph-Theoretic Genetic Gravity Modelling
Description: Implementation of spatial graph-theoretic genetic gravity models.
The model framework is applicable for other types of spatial flow questions.
Includes functions for constructing spatial graphs, sampling and summarizing
associated raster variables and building unconstrained and singly constrained
gravity models.
Author: Jeffrey S. Evans [aut, cre],
Melanie Murphy [aut]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between GeNetIt versions 0.1-0 dated 2016-03-09 and 0.1-1 dated 2017-07-31
DESCRIPTION | 10 ++++---- MD5 | 36 ++++++++++++++--------------- R/gravity.R | 52 ++++++++++++++++++++++++++++++------------- R/summary.gravity.R | 3 +- inst/NEWS | 7 ++++- man/area.graph.statistics.Rd | 1 man/build.node.data.Rd | 1 man/dmatrix.df.Rd | 1 man/dps.Rd | 1 man/graph.statistics.Rd | 1 man/gravity.Rd | 46 ++++++++++++++++++++++++++------------ man/knn.graph.Rd | 7 ++--- man/plot.gravity.Rd | 7 ++--- man/predict.gravity.Rd | 1 man/print.gravity.Rd | 1 man/ralu.model.Rd | 1 man/ralu.site.Rd | 1 man/rasters.Rd | 1 man/summary.gravity.Rd | 3 -- 19 files changed, 107 insertions(+), 74 deletions(-)
Title: Downscaling Species Occupancy
Description: A set of functions that downscales species occupancy at
coarse grain sizes to predict species occupancy at fine grain sizes.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>
Diff between downscale versions 1.2-4 dated 2016-11-25 and 2.0-0 dated 2017-07-31
downscale-1.2-4/downscale/vignettes/Downscaling-downscale11.pdf |only downscale-2.0-0/downscale/DESCRIPTION | 14 - downscale-2.0-0/downscale/MD5 | 39 +-- downscale-2.0-0/downscale/NEWS | 6 downscale-2.0-0/downscale/R/HuiFunctions.R | 22 +- downscale-2.0-0/downscale/R/hui.downscale.R | 73 +++++-- downscale-2.0-0/downscale/R/upgrain.R | 102 ++++++++-- downscale-2.0-0/downscale/R/upgrain.threshold.R | 48 +++- downscale-2.0-0/downscale/build/vignette.rds |binary downscale-2.0-0/downscale/inst/doc/Downscaling.pdf |binary downscale-2.0-0/downscale/inst/doc/Upgraining.Rnw | 2 downscale-2.0-0/downscale/inst/doc/Upgraining.pdf |binary downscale-2.0-0/downscale/inst/extdata/atlas_data.txt | 2 downscale-2.0-0/downscale/man/downscale.Rd | 2 downscale-2.0-0/downscale/man/ensemble.downscale.Rd | 2 downscale-2.0-0/downscale/man/figures/Flow.png |binary downscale-2.0-0/downscale/man/hui.downscale.Rd | 4 downscale-2.0-0/downscale/man/upgrain.Rd | 8 downscale-2.0-0/downscale/man/upgrain.threshold.Rd | 8 downscale-2.0-0/downscale/vignettes/Upgraining.Rnw | 2 downscale-2.0-0/downscale/vignettes/figures/Flow.png |binary 21 files changed, 229 insertions(+), 105 deletions(-)
Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions and
use them to create shells (skeletons which must be manually completed by
the user) of test files to be tested with the 'testthat' package.
Author: Rory Nolan [aut, cre],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between exampletestr versions 1.0.0 dated 2017-07-08 and 1.0.1 dated 2017-07-31
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 6 ++++++ build/vignette.rds |binary inst/CITATION |only inst/doc/exampletestr.html | 10 +++++----- tests/testthat/test_exemplar.R | 3 +-- 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Functions for Wind Resource Assessment
Description: A collection of functions to analyse, visualize and interpret wind data
and to calculate the potential energy production of wind turbines.
Author: Christian Graul and Carsten Poppinga
Maintainer: Christian Graul <christian.graul@gmail.com>
Diff between bReeze versions 0.4-0 dated 2014-09-18 and 0.4-1 dated 2017-07-31
DESCRIPTION | 13 +- LICENSE |only MD5 | 53 ++++++------ NAMESPACE | 5 + R/day.plot.R | 2 R/map.plot.R | 2 R/pc.R | 2 R/plot.aep.R | 220 +++++++++++++++++++++++++------------------------- R/plot.availability.R | 10 +- R/plot.energy.R | 18 ++-- R/plot.frequency.R | 2 R/plot.mast.R | 20 ++-- R/plot.month.stats.R | 22 ++--- R/plot.pc.R | 20 ++-- R/plot.profile.R | 38 ++++---- R/plot.turbulence.R | 10 +- R/plot.uncertainty.R | 30 +++--- R/plot.weibull.R | 28 +++--- R/polar.plot.R | 8 - R/subset.int.R | 4 data/winddata.RData |binary inst/CITATION | 22 +---- inst/NEWS | 6 + man/aep.Rd | 3 man/bReeze-package.Rd | 2 man/energy.Rd | 2 man/frequency.Rd | 2 man/pc.Rd | 1 28 files changed, 280 insertions(+), 265 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.1.4 dated 2017-05-11 and 2.1.5 dated 2017-07-31
gjam-2.1.4/gjam/src/init.c |only gjam-2.1.5/gjam/DESCRIPTION | 8 gjam-2.1.5/gjam/MD5 | 29 gjam-2.1.5/gjam/NAMESPACE | 7 gjam-2.1.5/gjam/R/RcppExports.R | 38 gjam-2.1.5/gjam/R/gjamHfunctions.R | 526 +++-- gjam-2.1.5/gjam/build/vignette.rds |binary gjam-2.1.5/gjam/inst/doc/gjamVignette.R | 30 gjam-2.1.5/gjam/inst/doc/gjamVignette.Rmd | 36 gjam-2.1.5/gjam/inst/doc/gjamVignette.html | 2732 ++++++++++++++++------------- gjam-2.1.5/gjam/man/gjam-package.Rd | 4 gjam-2.1.5/gjam/src/Makevars | 7 gjam-2.1.5/gjam/src/Makevars.win | 6 gjam-2.1.5/gjam/src/RcppExports.cpp | 103 - gjam-2.1.5/gjam/src/cppFns.cpp | 73 gjam-2.1.5/gjam/vignettes/gjamVignette.Rmd | 36 16 files changed, 2026 insertions(+), 1609 deletions(-)
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.3 dated 2015-12-14 and 2.4 dated 2017-07-31
DESCRIPTION | 12 ++-- MD5 | 20 +++---- R/ThresholdROC-2states.R | 125 +++++++++++++++++++++++++++----------------- R/ThresholdROC-3states.R | 89 ++++++++++++++++++------------- man/ThresholdROC-package.Rd | 2 man/lines-thres2.Rd | 8 +- man/lines-thres3.Rd | 2 man/plot-thres2.Rd | 4 - man/plot-thres3.Rd | 4 - man/thres2.Rd | 18 ++++-- man/thres3.Rd | 16 ++++- 11 files changed, 185 insertions(+), 115 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.4.5 dated 2017-07-27 and 0.9.4.6 dated 2017-07-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Rstringdist.c | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals are provided for one-way experimental designs with one or many normally distributed, primary response variables (endpoints). Differences (Hasler and Hothorn, 2011) or ratios (Hasler and Hothorn, 2012) of means can be considered. Various contrasts can be chosen, unbalanced sample sizes are allowed as well as heterogeneous variances (Hasler and Hothorn, 2008) or covariance matrices (Hasler, 2014).
Author: Mario Hasler, Christof Kluss
Maintainer: Mario Hasler <hasler@email.uni-kiel.de>
Diff between SimComp versions 2.2 dated 2014-09-12 and 3.2 dated 2017-07-31
DESCRIPTION | 13 +- MD5 | 86 ++++++++++-------- NAMESPACE | 19 +++- R/DfSattDiff.R | 33 +++--- R/DfSattRat.R | 61 +++++------- R/SimCheck.R |only R/SimCiDiff.R | 101 --------------------- R/SimCiDiff.default.R |only R/SimCiDiff.formula.R |only R/SimCiDiffHet.R | 106 +++++++++++++--------- R/SimCiDiffHom.R | 107 +++++++++++----------- R/SimCiRat.R | 126 -------------------------- R/SimCiRat.default.R |only R/SimCiRat.formula.R |only R/SimCiRatHet.R | 228 ++++++++++++++++++++++++++---------------------- R/SimCiRatHom.R | 221 +++++++++++++++++++++++++--------------------- R/SimTestDiff.R | 124 -------------------------- R/SimTestDiff.default.R |only R/SimTestDiff.formula.R |only R/SimTestDiffHet.R | 77 ++++++++-------- R/SimTestDiffHom.R | 75 ++++++--------- R/SimTestDiffHomMiva.R |only R/SimTestP.R |only R/SimTestRat.R | 149 ------------------------------- R/SimTestRat.default.R |only R/SimTestRat.formula.R |only R/SimTestRatHet.R | 87 +++++++++--------- R/SimTestRatHom.R | 77 ++++++++-------- R/ermvnorm.R | 26 +---- R/plot.SimCi.R | 2 R/print.SimCi.R | 14 +- R/print.SimTest.R | 14 +- R/summary.SimCi.R | 43 +++++---- R/summary.SimTest.R | 55 +++++++---- build |only man/DfSattDiff.Rd | 44 ++++----- man/DfSattRat.Rd | 55 +++++------ man/SimCiDiff.Rd | 123 ++++++++++++++----------- man/SimCiRat.Rd | 192 +++++++++++++++++++++------------------- man/SimComp-package.Rd | 99 +++++--------------- man/SimTestDiff.Rd | 126 ++++++++++++++------------ man/SimTestRat.Rd | 182 +++++++++++++++++++------------------- man/coagulation.Rd | 2 man/ermvnorm.Rd | 14 +- man/plot.SimCi.Rd | 14 -- man/print.SimCi.Rd | 5 - man/print.SimTest.Rd | 6 - man/rcm.Rd | 2 man/summary.SimCi.Rd | 8 - man/summary.SimTest.Rd | 8 - 50 files changed, 1155 insertions(+), 1569 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) and transforms to the appropriate formats of
the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization
for the structure of RDML object and GUI for RDML editing.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut],
Andrej-Nikolai Spiess [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>
Diff between RDML versions 0.9-6 dated 2017-04-24 and 0.9-7 dated 2017-07-31
CHANGELOG | 4 DESCRIPTION | 17 - LICENSE |only MD5 | 33 +- NAMESPACE | 1 R/RDML.R | 2 R/RDML.types.R | 44 +++ README.md | 14 inst/RDMLedit/md/help.md | 2 inst/doc/CreateRDML.Rmd | 6 inst/doc/CreateRDML.html | 10 inst/doc/RDML.R | 46 +-- inst/doc/RDML.Rmd | 220 ++++++++------- inst/doc/RDML.html | 370 +++++++++++++------------- man/extractdatapoints-method.Rd |only vignettes/CreateRDML.Rmd | 6 vignettes/RDML.Rmd | 220 ++++++++------- vignettes/RDML.bib | 80 +++++ vignettes/usingRDML_with_other_R_packages.Rmd |only 19 files changed, 618 insertions(+), 457 deletions(-)
Title: Generalized Waring Regression Model for Count Data
Description: Statistical functions to fit, validate and describe a Generalized
Waring Regression Model (GWRM).
Author: Antonio Jose Saez-Castillo [aut, cre],
Silverio Vilchez-Lopez [aut],
Maria Jose Olmo-Jimenez [aut],
Jose Rodriguez-Avi [aut],
Antonio Conde-Sanchez [aut],
Ana Maria Martinez-Rodriguez [aut]
Maintainer: Antonio Jose Saez-Castillo <ajsaez@ujaen.es>
Diff between GWRM versions 2.1.0.2 dated 2016-04-13 and 2.1.0.3 dated 2017-07-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/gw.r | 16 ++++++++++++---- inst/CITATION | 2 +- 4 files changed, 20 insertions(+), 12 deletions(-)
Title: Parameterized Queries Extension for RODBC
Description: An extension for RODBC package adding support for parameterized
queries.
Author: Mateusz Zoltak [aut, cre],
Brian Ripley [aut],
Michael Lapsley [aut],
Will Beasley [ctb],
Juergen Altfeld [ctb]
Maintainer: Mateusz Zoltak <zozlak@zozlak.org>
Diff between RODBCext versions 0.3.0 dated 2017-04-10 and 0.3.1 dated 2017-07-31
DESCRIPTION | 8 MD5 | 37 - NEWS | 11 build/vignette.rds |binary inst/doc/Parameterized_SQL_queries.R | 2 inst/doc/Parameterized_SQL_queries.Rmd | 976 ++++++++++++++++---------------- inst/doc/Parameterized_SQL_queries.html | 8 man/odbcFetchRows.Rd | 1 man/odbcGetQueryTimeout.Rd | 1 man/odbcSetQueryTimeout.Rd | 1 man/sqlExecute.Rd | 1 man/sqlFetchMore.Rd | 1 man/sqlPrepare.Rd | 1 src/RODBC.c | 12 src/RODBCext.c | 13 tests/testthat.R | 10 tests/testthat/test-dates.R | 45 - tests/testthat/test-oracle.R |only tests/testthat/test-varchar.R | 35 - vignettes/Parameterized_SQL_queries.Rmd | 976 ++++++++++++++++---------------- 20 files changed, 1090 insertions(+), 1049 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing code and packages that communicate with remote servers can
be painful. Dealing with authentication, bootstrapping server state,
cleaning up objects that may get created during the test run, network
flakiness, and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three test
contexts that mock the network connection in different ways, and it offers
additional expectations to assert that HTTP requests were--or were
not--made. Using these tools, one can test that code is making the intended
requests and that it handles the expected responses correctly, all without
depending on a connection to a remote API.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 2.0.0 dated 2017-06-05 and 2.1.0 dated 2017-07-31
DESCRIPTION | 11 +++++------ MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ R/capture-requests.R | 19 +++++++++++++------ R/mock-api.R | 24 +++++++++++++++++++++--- R/without-internet.R | 4 ++-- README.md | 18 ++++++++++++++++++ inst/doc/httptest.Rmd | 2 +- inst/doc/httptest.html | 2 +- man/capture_requests.Rd | 13 ++++++++++--- tests/testthat/test-capture-requests.R | 24 ++++++++++++++++++++++-- tests/testthat/test-mock-api.R | 33 +++++++++++++++++++++++++++++++++ tests/testthat/test-without-internet.R | 4 ++++ vignettes/httptest.Rmd | 2 +- 14 files changed, 150 insertions(+), 38 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks, including
the methods 'backShift' (from package 'backShift'), 'bivariateANM' (bivariate
additive noise model), 'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'), 'hiddenICP' (invariant
causal prediction with hidden variables), 'ICP' (invariant causal prediction)
(from package 'InvariantCausalPrediction'), 'GES' (greedy equivalence
search), 'GIES' (greedy interventional equivalence search), 'LINGAM', 'PC' (PC
Algorithm), 'FCI' (fast causal inference),
'RFCI' (really fast causal inference) (all from package 'pcalg') and
regression.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.1.8 dated 2017-07-17 and 0.1.9 dated 2017-07-31
DESCRIPTION | 8 MD5 | 18 - R/checkDependencies.R | 37 ++-- R/getParents.R | 159 ++++++++--------- R/getRanking.R | 25 +- demo/simulation.R | 163 +++++++++--------- man/getParents.Rd | 159 ++++++++--------- man/getRanking.Rd | 25 +- tests/testthat.R | 8 tests/testthat/test_getParents_defaults_all_methods.R | 36 +-- 10 files changed, 331 insertions(+), 307 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Tools for Accessing the Botanical Information and Ecology
Network Database
Description: Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <http://Bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.
Author: Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between BIEN versions 1.1.0 dated 2017-03-08 and 1.2.1 dated 2017-07-31
BIEN-1.1.0/BIEN/man/BIEN_list_shapefile.Rd |only BIEN-1.1.0/BIEN/man/BIEN_occurrence_shapefile.Rd |only BIEN-1.1.0/BIEN/man/BIEN_ranges_shapefile.Rd |only BIEN-1.1.0/BIEN/man/is_char.Rd |only BIEN-1.1.0/BIEN/man/is_log.Rd |only BIEN-1.1.0/BIEN/man/is_num.Rd |only BIEN-1.2.1/BIEN/DESCRIPTION | 8 BIEN-1.2.1/BIEN/MD5 | 123 BIEN-1.2.1/BIEN/NAMESPACE | 58 BIEN-1.2.1/BIEN/NEWS | 23 BIEN-1.2.1/BIEN/R/BIEN.R | 3415 +++++-------- BIEN-1.2.1/BIEN/R/BIEN_info.R |only BIEN-1.2.1/BIEN/R/BIEN_sql.R |only BIEN-1.2.1/BIEN/R/internals.R |only BIEN-1.2.1/BIEN/build/vignette.rds |binary BIEN-1.2.1/BIEN/inst/doc/BIEN.Rmd | 4 BIEN-1.2.1/BIEN/inst/doc/BIEN.html | 15 BIEN-1.2.1/BIEN/inst/doc/BIEN_tutorial.R |only BIEN-1.2.1/BIEN/inst/doc/BIEN_tutorial.Rmd |only BIEN-1.2.1/BIEN/inst/doc/BIEN_tutorial.html |only BIEN-1.2.1/BIEN/man/BIEN.Rd | 2 BIEN-1.2.1/BIEN/man/BIEN_list_all.Rd | 2 BIEN-1.2.1/BIEN/man/BIEN_list_country.Rd | 10 BIEN-1.2.1/BIEN/man/BIEN_list_county.Rd | 21 BIEN-1.2.1/BIEN/man/BIEN_list_spatialpolygons.Rd |only BIEN-1.2.1/BIEN/man/BIEN_list_state.Rd | 15 BIEN-1.2.1/BIEN/man/BIEN_metadata_citation.Rd | 7 BIEN-1.2.1/BIEN/man/BIEN_metadata_database_version.Rd | 1 BIEN-1.2.1/BIEN/man/BIEN_metadata_list_political_names.Rd |only BIEN-1.2.1/BIEN/man/BIEN_metadata_match_data.Rd | 1 BIEN-1.2.1/BIEN/man/BIEN_occurrence_box.Rd | 14 BIEN-1.2.1/BIEN/man/BIEN_occurrence_country.Rd | 23 BIEN-1.2.1/BIEN/man/BIEN_occurrence_county.Rd | 30 BIEN-1.2.1/BIEN/man/BIEN_occurrence_family.Rd | 14 BIEN-1.2.1/BIEN/man/BIEN_occurrence_genus.Rd | 16 BIEN-1.2.1/BIEN/man/BIEN_occurrence_records_per_species.Rd | 4 BIEN-1.2.1/BIEN/man/BIEN_occurrence_spatialpolygons.Rd |only BIEN-1.2.1/BIEN/man/BIEN_occurrence_species.Rd | 14 BIEN-1.2.1/BIEN/man/BIEN_occurrence_state.Rd | 26 BIEN-1.2.1/BIEN/man/BIEN_phylogeny_complete.Rd | 3 BIEN-1.2.1/BIEN/man/BIEN_phylogeny_conservative.Rd | 3 BIEN-1.2.1/BIEN/man/BIEN_plot_country.Rd | 18 BIEN-1.2.1/BIEN/man/BIEN_plot_dataset.Rd | 14 BIEN-1.2.1/BIEN/man/BIEN_plot_datasource.Rd | 14 BIEN-1.2.1/BIEN/man/BIEN_plot_metadata.Rd | 1 BIEN-1.2.1/BIEN/man/BIEN_plot_name.Rd | 14 BIEN-1.2.1/BIEN/man/BIEN_plot_sampling_protocol.Rd | 12 BIEN-1.2.1/BIEN/man/BIEN_plot_state.Rd | 26 BIEN-1.2.1/BIEN/man/BIEN_ranges_box.Rd | 21 BIEN-1.2.1/BIEN/man/BIEN_ranges_genus.Rd | 27 BIEN-1.2.1/BIEN/man/BIEN_ranges_intersect_species.Rd | 17 BIEN-1.2.1/BIEN/man/BIEN_ranges_list.Rd | 3 BIEN-1.2.1/BIEN/man/BIEN_ranges_load_species.Rd | 6 BIEN-1.2.1/BIEN/man/BIEN_ranges_spatialpolygons.Rd |only BIEN-1.2.1/BIEN/man/BIEN_ranges_species.Rd | 24 BIEN-1.2.1/BIEN/man/BIEN_stem_datasource.Rd | 13 BIEN-1.2.1/BIEN/man/BIEN_stem_family.Rd | 11 BIEN-1.2.1/BIEN/man/BIEN_stem_genus.Rd | 11 BIEN-1.2.1/BIEN/man/BIEN_stem_species.Rd | 11 BIEN-1.2.1/BIEN/man/BIEN_trait_family.Rd | 4 BIEN-1.2.1/BIEN/man/BIEN_trait_genus.Rd | 4 BIEN-1.2.1/BIEN/man/BIEN_trait_mean.Rd | 3 BIEN-1.2.1/BIEN/man/BIEN_trait_species.Rd | 4 BIEN-1.2.1/BIEN/man/BIEN_trait_trait.Rd | 7 BIEN-1.2.1/BIEN/man/BIEN_trait_traitbyfamily.Rd | 7 BIEN-1.2.1/BIEN/man/BIEN_trait_traitbygenus.Rd | 7 BIEN-1.2.1/BIEN/man/BIEN_trait_traitbyspecies.Rd | 7 BIEN-1.2.1/BIEN/tests/testthat |only BIEN-1.2.1/BIEN/tests/testthat.R | 88 BIEN-1.2.1/BIEN/vignettes/BIEN.Rmd | 4 BIEN-1.2.1/BIEN/vignettes/BIEN.md |only BIEN-1.2.1/BIEN/vignettes/BIEN_tutorial.Rmd |only 72 files changed, 1914 insertions(+), 2316 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-28 0.4-5
2009-12-16 0.4-4
2009-10-07 0.4-3
2009-09-07 0.4-2
2009-01-14 0.3-9
2008-09-28 0.3-6
2008-05-25 0.3-3
2008-03-21 0.3-1
2008-02-11 0.2-7
2008-02-08 0.2-6
2008-01-08 0.2-5
2008-01-03 0.2-4
2007-12-18 0.1-17
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre],
Xin-Qiu Yao [aut],
Lars Skjaerven [aut],
Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@umich.edu>
Diff between bio3d versions 2.3-2 dated 2017-06-14 and 2.3-3 dated 2017-07-31
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- R/cnapath.R | 4 ++-- R/community.aln.R | 6 ++++++ man/bio3d.package.Rd | 4 ++-- man/cna.Rd | 6 +++++- man/cnapath.Rd | 6 ++++++ man/community.aln.Rd | 7 ++++++- man/community.tree.Rd | 5 +++++ man/identify.cna.Rd | 5 +++++ man/layout.cna.Rd | 5 +++++ man/mustang.Rd | 6 ++++++ man/network.amendment.Rd | 7 ++++++- man/plot.cna.Rd | 11 ++++++----- man/print.cna.Rd | 5 +++++ man/prune.cna.Rd | 5 +++++ man/vmd.cna.Rd | 5 +++++ src/read_cif.cpp | 14 +++++++------- 18 files changed, 102 insertions(+), 39 deletions(-)