Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. Alternating optimization is
an iterative process where the genetic score weights, the environmental score weights,
and the main model parameters are estimated in turn assuming the other parameters to
be constant. This approach has greatly enhanced predictive power over traditional GxE
models which include only a single genetic variant and a single environmental
exposure. Gene x gene interactions (GxG) and environment x environment interactions
(ExE) can be incorporated into the genetic and environmental scores. Any standard
model formula can be used, it doesn't have to be a two-way interaction model.
Although this approach was made for GxE modelling, the genetic score doesn't need to
contain genetic variables and the environmental score doesn't need to contain
environmental variables, therefore this approach is highly flexible.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.0.1 dated 2017-03-24 and 1.0.2 dated 2017-04-02
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- build/vignette.rds |binary inst/doc/LEGIT.R | 5 ++- inst/doc/LEGIT.Rmd | 26 +++++++++++++----- inst/doc/LEGIT.html | 72 +++++++++++++++++++++++++++++++++++++++++++++------- vignettes/LEGIT.Rmd | 26 +++++++++++++----- 7 files changed, 112 insertions(+), 35 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single PNG
image that can be played back. See <http://canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut, cre],
Connie Brett [ctb]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 0.14.7 dated 2017-03-08 and 0.15.2 dated 2017-04-02
DESCRIPTION | 6 - MD5 | 8 - NEWS.md | 3 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 98 +++++++++++++++++- 5 files changed, 104 insertions(+), 13 deletions(-)
Title: Bayesian Tensor Factorization Linked to External Data
Description: BaTFLED is a machine learning algorithm designed to make predictions and determine interactions in data that varies along three independent modes. For example BaTFLED was developed to predict the growth of cell lines when treated with drugs at different doses. The first mode corresponds to cell lines and incorporates predictors such as cell line genomics and growth conditions. The second mode corresponds to drugs and incorporates predictors indicating known targets and structural features. The third mode corresponds to dose and there are no dose-specific predictors (although the algorithm is capable of including predictors for the third mode if present). See 'BaTFLED3D_vignette.rmd' for a simulated example.
Author: Nathan Lazar [aut, cre]
Maintainer: Nathan Lazar <nathan.lazar@gmail.com>
Diff between BaTFLED3D versions 0.1.7 dated 2017-02-12 and 0.2.1 dated 2017-04-02
DESCRIPTION | 25 +++++----- MD5 | 56 +++++++++++++----------- NAMESPACE | 2 R/Tucker_model.R | 6 +- R/diagonal.R |only R/exp_var.R | 12 ++--- R/get_data_params.R | 6 +- R/get_model_params.R | 38 ++++++++-------- R/kernelize.R | 89 ++++++++++++++++++--------------------- R/lower_bnd_CP.R | 23 +++++++--- R/lower_bnd_Tucker.R | 21 ++++++--- R/nrmse.R |only R/rmse.R | 7 +-- R/test_results.R | 43 ++++++++---------- R/update_mode1_CP.R | 8 +-- R/update_mode1_Tucker.R | 6 +- R/update_mode2_CP.R | 8 +-- R/update_mode2_Tucker.R | 6 +- R/update_mode3_CP.R | 8 +-- R/update_mode3_Tucker.R | 6 +- README.md | 2 inst/doc/BaTFLED3D_vignette.R | 2 inst/doc/BaTFLED3D_vignette.html | 16 +++---- inst/doc/BaTFLED3D_vignette.rmd | 4 - man/diagonal.Rd |only man/get_data_params.Rd | 4 - man/get_model_params.Rd | 34 +++++++------- man/kernelize.Rd | 31 +++++++------ man/nrmse.Rd |only man/test_results.Rd | 5 +- vignettes/BaTFLED3D_vignette.rmd | 4 - 31 files changed, 248 insertions(+), 224 deletions(-)
Title: Extensions of Exponential Random Graph Models
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), Temporal Network Autocorrelation Models (TNAM), and Relational Event Models (REM). This package acts as a meta-package for several sub-packages on which it depends.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>
Diff between xergm versions 1.7.3 dated 2016-06-21 and 1.8.2 dated 2017-04-02
DESCRIPTION | 22 ++++++++----------- MD5 | 6 ++--- inst/CITATION | 2 - man/xergm-package.Rd | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 70 insertions(+), 17 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package
evaluates the mass and charge balance, extracts all reactants, products, orphan
metabolites, metabolite names and compartments. Also are included some options
to characterize and write models in TSV and SBML formats.
Author: Daniel Osorio [aut, cre],
Janneth Gonzalez [aut, ths],
Andres Pinzon [aut, ths]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.6 dated 2017-04-02 and 0.6-1 dated 2017-04-02
DESCRIPTION | 17 ++++++++++++----- MD5 | 10 +++++----- inst/doc/MINVALintroduction.R | 2 ++ inst/doc/MINVALintroduction.Rmd | 2 ++ inst/doc/MINVALintroduction.html | 2 ++ vignettes/MINVALintroduction.Rmd | 2 ++ 6 files changed, 25 insertions(+), 10 deletions(-)
Title: Tools for Obtaining and Cleaning Medicare Public Use Files
Description: Publicly available data from Medicare frequently requires extensive
initial effort to extract desired variables and merge them; this package
formalizes the techniques I've found work best. More information on the
Medicare program, as well as guidance for the publicly available data this package
targets, can be found on CMS's website covering publicly available data. See <https://www.cms.gov/Research-Statistics-Data-and-Systems/Research-Statistics-Data-and-Systems.html>.
Author: Robert Gambrel [aut, cre]
Maintainer: Robert Gambrel <robert.gambrel@gmail.com>
Diff between medicare versions 0.2.0 dated 2016-11-18 and 0.2.1 dated 2017-04-02
DESCRIPTION | 8 +- MD5 | 44 +++++++-------- NEWS.md | 9 ++- R/price_deflate.R | 86 ++++++++++++------------------- build/vignette.rds |binary inst/doc/cost-report-analysis.html | 6 +- inst/doc/provider_of_service_naming.html | 6 +- man/cr_alpha_names.Rd | 1 man/cr_extract.Rd | 1 man/cr_nmrc_names.Rd | 1 man/cr_rpt_names.Rd | 1 man/hospiceALPHA.Rd | 1 man/hospiceNMRC.Rd | 1 man/hospiceRPT.Rd | 1 man/medicare.Rd | 2 man/pos2010.Rd | 1 man/pos_names.Rd | 1 man/pos_names_extract.Rd | 1 man/price_deflate.Rd | 18 ++++-- man/subset_column.Rd | 1 man/subset_row.Rd | 1 man/subset_worksheet.Rd | 1 tests/testthat/test-price_deflate.R | 6 +- 23 files changed, 90 insertions(+), 108 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.3.3 dated 2017-02-09 and 1.3.4 dated 2017-04-02
DESCRIPTION | 9 ++++---- MD5 | 6 ++--- R/dunn.test.R | 59 ++++++++++++++++++++++++++++++++++++------------------- man/dunn.test.Rd | 22 ++++++++++---------- 4 files changed, 58 insertions(+), 38 deletions(-)
Title: Conover-Iman Test of Multiple Comparisons Using Rank Sums
Description: Computes the Conover-Iman test (1979) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Conover-Iman test may be understood as a test for median difference. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between conover.test versions 1.1.2 dated 2017-02-09 and 1.1.3 dated 2017-04-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/conover.test.R | 34 +++++++++++++++++++--------------- man/conover.test.Rd | 20 ++++++++++---------- 4 files changed, 36 insertions(+), 32 deletions(-)
Title: Generic Sparse Group Lasso Solver
Description: Fast generic solver for sparse group lasso optimization
problems. The loss (objective) function must be defined in a
C++ module. The optimization problem is solved using a
coordinate gradient descent algorithm. Convergence of the
algorithm is established (see reference) and the algorithm is
applicable to a broad class of loss functions. Use of parallel
computing for cross validation and subsampling is supported
through the 'foreach' and 'doParallel' packages. Development
version is on GitHub, please report package issues on GitHub.
Author: Martin Vincent
Maintainer: Martin Vincent <martin.vincent.dk@gmail.com>
Diff between sglOptim versions 1.3.5 dated 2016-12-28 and 1.3.6 dated 2017-04-02
sglOptim-1.3.5/sglOptim/tests/D_subsampling_run_tests.R |only sglOptim-1.3.6/sglOptim/DESCRIPTION | 30 +- sglOptim-1.3.6/sglOptim/MD5 | 46 +-- sglOptim-1.3.6/sglOptim/NAMESPACE | 1 sglOptim-1.3.6/sglOptim/R/prepare_args.R | 203 +++++++++----- sglOptim-1.3.6/sglOptim/R/rtools_test.R | 29 +- sglOptim-1.3.6/sglOptim/R/sgl_config.R | 2 sglOptim-1.3.6/sglOptim/R/sgl_subsampling.R | 8 sglOptim-1.3.6/sglOptim/build |only sglOptim-1.3.6/sglOptim/inst/NEWS.Rd | 6 sglOptim-1.3.6/sglOptim/inst/doc |only sglOptim-1.3.6/sglOptim/inst/include/sgl/sgl_problem.h | 129 ++++---- sglOptim-1.3.6/sglOptim/src/only_for_testing.cpp | 5 sglOptim-1.3.6/sglOptim/tests/A_lambda_run_tests.R | 4 sglOptim-1.3.6/sglOptim/tests/B_fit_run_tests_0.R | 2 sglOptim-1.3.6/sglOptim/tests/B_fit_run_tests_1.R | 2 sglOptim-1.3.6/sglOptim/tests/C_cv_run_tests_1.R | 2 sglOptim-1.3.6/sglOptim/tests/C_cv_run_tests_2.R | 4 sglOptim-1.3.6/sglOptim/tests/D_subsampling_run_tests_1.R |only sglOptim-1.3.6/sglOptim/tests/D_subsampling_run_tests_2.R |only sglOptim-1.3.6/sglOptim/tests/F_parallel_run_tests.R | 2 sglOptim-1.3.6/sglOptim/tests/H_error_tests.R | 11 sglOptim-1.3.6/sglOptim/tests/units/generate_data.R | 13 sglOptim-1.3.6/sglOptim/tests/units/subsampling_test_1.R | 5 sglOptim-1.3.6/sglOptim/tests/units/subsampling_test_2.R | 5 sglOptim-1.3.6/sglOptim/vignettes |only 26 files changed, 322 insertions(+), 187 deletions(-)
Title: High Dimensional Multiclass Classification Using Sparse Group
Lasso
Description: Multinomial logistic regression with sparse group lasso
penalty. Simultaneous feature selection and parameter
estimation for classification. Suitable for high dimensional
multiclass classification with many classes. The algorithm
computes the sparse group lasso penalized maximum likelihood
estimate. Use of parallel computing for cross validation and
subsampling is supported through the 'foreach' and 'doParallel'
packages. Development version is on GitHub, please report
package issues on GitHub.
Author: Martin Vincent
Maintainer: Martin Vincent <martin.vincent.dk@gmail.com>
Diff between msgl versions 2.3.5 dated 2016-12-28 and 2.3.6 dated 2017-04-02
msgl-2.3.5/msgl/tests/msgl_configuration_test.R |only msgl-2.3.5/msgl/tests/msgl_cv_test_1.R |only msgl-2.3.5/msgl/tests/msgl_cv_test_2.R |only msgl-2.3.5/msgl/tests/msgl_cv_test_3.R |only msgl-2.3.5/msgl/tests/msgl_cv_test_4.R |only msgl-2.3.5/msgl/tests/msgl_grouping_test_1.R |only msgl-2.3.5/msgl/tests/msgl_grouping_test_2.R |only msgl-2.3.5/msgl/tests/msgl_grouping_test_3.R |only msgl-2.3.5/msgl/tests/msgl_grouping_test_4.R |only msgl-2.3.5/msgl/tests/msgl_predict_test_1.R |only msgl-2.3.5/msgl/tests/msgl_predict_test_2.R |only msgl-2.3.5/msgl/tests/msgl_sub_test_1.R |only msgl-2.3.5/msgl/tests/msgl_test_1.R |only msgl-2.3.5/msgl/tests/msgl_test_2.R |only msgl-2.3.5/msgl/tests/msgl_test_3.R |only msgl-2.3.5/msgl/tests/msgl_test_4.R |only msgl-2.3.6/msgl/DESCRIPTION | 31 ++-- msgl-2.3.6/msgl/MD5 | 59 ++++---- msgl-2.3.6/msgl/NAMESPACE | 1 msgl-2.3.6/msgl/R/config.R | 2 msgl-2.3.6/msgl/R/fit.R | 33 ++++ msgl-2.3.6/msgl/R/process-arguments.R | 57 ++++++-- msgl-2.3.6/msgl/R/subsampling.R | 7 - msgl-2.3.6/msgl/build/vignette.rds |binary msgl-2.3.6/msgl/inst/NEWS.Rd | 6 msgl-2.3.6/msgl/inst/doc/README.R |only msgl-2.3.6/msgl/inst/doc/README.Rmd |only msgl-2.3.6/msgl/inst/doc/README.html |only msgl-2.3.6/msgl/inst/doc/quick-start.html | 133 +++++++++----------- msgl-2.3.6/msgl/src/msgl.cpp | 31 +++- msgl-2.3.6/msgl/tests/A_lambda_run_tests.R |only msgl-2.3.6/msgl/tests/B_cv_consistency_tests.R |only msgl-2.3.6/msgl/tests/B_fit_run_tests_1.R |only msgl-2.3.6/msgl/tests/B_fit_run_tests_2.R |only msgl-2.3.6/msgl/tests/B_fit_run_tests_CRAN.R |only msgl-2.3.6/msgl/tests/C_cv_run_tests_1.R |only msgl-2.3.6/msgl/tests/C_cv_run_tests_2.R |only msgl-2.3.6/msgl/tests/C_cv_run_tests_CRAN.R |only msgl-2.3.6/msgl/tests/D_subsampling_run_test_1.R |only msgl-2.3.6/msgl/tests/D_subsampling_run_test_CRAN.R |only msgl-2.3.6/msgl/tests/F_parallel_run_tests.R |only msgl-2.3.6/msgl/tests/H_error_test.R |only msgl-2.3.6/msgl/tests/I_configuration_test.R |only msgl-2.3.6/msgl/tests/units |only msgl-2.3.6/msgl/vignettes/README.Rmd |only 45 files changed, 216 insertions(+), 144 deletions(-)
Title: Linear Multiple Output Sparse Group Lasso
Description: Linear multiple output using sparse group lasso. The
algorithm finds the sparse group lasso penalized maximum
likelihood estimator. This result in feature and parameter
selection, and parameter estimation. Use of parallel computing
for cross validation and subsampling is supported through the
'foreach' and 'doParallel' packages. Development version is on
GitHub, please report package issues on GitHub.
Author: Martin Vincent
Maintainer: Martin Vincent <martin.vincent.dk@gmail.com>
Diff between lsgl versions 1.3.5 dated 2016-12-28 and 1.3.6 dated 2017-04-02
DESCRIPTION | 23 +++++----- MD5 | 29 +++++++------ NAMESPACE | 1 R/config.R | 2 R/navigate.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/README.R |only inst/doc/README.Rmd |only inst/doc/README.html |only inst/doc/quick-start.R | 4 - inst/doc/quick-start.Rmd | 4 - inst/doc/quick-start.html | 102 +++++++++++++++++++++------------------------- man/Err.lsgl.Rd | 2 src/lsgl.cpp | 40 +++++++++++------- tests/A_lsgl_fit_test_2.R |only vignettes/README.Rmd |only vignettes/quick-start.Rmd | 4 - 18 files changed, 117 insertions(+), 102 deletions(-)
Title: Hydrological Data Discovery Tools
Description: Facilitates discovery and handling of hydrological data, access to catalogues and databases.
Author: Claudia Vitolo [aut, cre],
Wouter Buytaert [ctb] (This package was developed during Claudia's PhD
at Imperial College London and Wouter was the PhD supervisor.),
Erin Le Dell [ctb] (Erin reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/73),
Michael Sumner [ctb] (Michael reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/73)
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between hddtools versions 0.6 dated 2017-03-03 and 0.7 dated 2017-04-02
hddtools-0.6/hddtools/R/TRMM.R |only hddtools-0.6/hddtools/inst/blog |only hddtools-0.6/hddtools/inst/tmp |only hddtools-0.6/hddtools/man/TRMM.Rd |only hddtools-0.6/hddtools/tests/testthat/test-TRMM.R |only hddtools-0.7/hddtools/DESCRIPTION | 6 +-- hddtools-0.7/hddtools/MD5 | 29 +++--------------- hddtools-0.7/hddtools/NAMESPACE | 1 hddtools-0.7/hddtools/README.md | 4 -- hddtools-0.7/hddtools/inst/doc/hddtools_vignette.Rmd | 5 ++- hddtools-0.7/hddtools/inst/doc/hddtools_vignette.html | 4 +- hddtools-0.7/hddtools/vignettes/hddtools_vignette.Rmd | 5 ++- 12 files changed, 21 insertions(+), 33 deletions(-)
Title: R API Datetime
Description: Access to the C-level R date and datetime code is provided for
C-level API use by other packages via registration of native functions.
Client packages simply include a single header 'RApiDatetime.h' provided
by this package, and also 'import' it. The R Core group is the original
author of the code made available with slight modifications by this package.
Author: Dirk Eddelbuettel and R Core (original code)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RApiDatetime versions 0.0.2 dated 2017-03-25 and 0.0.3 dated 2017-04-02
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 9 +++++++-- inst/NEWS.Rd | 8 ++++++++ inst/include/RApiDatetime.h | 4 ++-- 6 files changed, 44 insertions(+), 13 deletions(-)
Title: Miscellaneous Functions for the Correlation Coefficient
Description: Statistical test for the product-moment correlation coefficient based on H0: rho = rho0
including sample size computation, statistical test for comparing the product-moment
correlation coefficient in independent ad dependent samples, sequential triangular
test for the product-moment correlation coefficient, partial and semipartial correlation,
simulation of bivariate normal and non-normal distribution with a specified correlation.
Author: Takuya Yanagida [cre, aut]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between miscor versions 0.1-0 dated 2016-08-15 and 0.1-1 dated 2017-04-02
DESCRIPTION | 22 +++++------ MD5 | 74 +++++++++++++++++++++----------------- NAMESPACE | 7 +-- R/conf.cor.R | 2 - R/internal.BBsolve.R |only R/internal.Param.fleishman.R |only R/internal.RNG_P_NN.R |only R/internal.Validate.correlation.R |only R/internal.bounds.corr.R |only R/internal.count.overplot.R | 4 -- R/internal.intercor.R |only R/internal.intercor.all.R |only R/internal.is.positive.definite.R |only R/internal.print.seqtest.cor.R | 1 R/internal.sizeplot.R | 4 -- R/par.cor.R | 20 +++++----- R/print.par.cor.R | 10 ++--- R/print.sim.seqtest.cor.R | 8 ++-- R/print.test.cor.R | 12 +++--- R/seqtest.cor.R | 10 ++--- R/sim.cor.R | 17 +++++--- R/sim.seqtest.cor.R | 14 +++---- R/test.cor.R | 30 +++++++-------- man/comptest.cor.Rd | 16 ++++---- man/conf.cor.Rd | 13 +++--- man/par.cor.Rd | 17 ++++---- man/plot.seqtest.Rd | 7 +-- man/plot.sim.seqtest.cor.Rd | 9 ++-- man/print.comptest.cor.Rd | 7 +-- man/print.conf.cor.Rd | 7 +-- man/print.par.cor.Rd | 9 ++-- man/print.seqtest.Rd | 7 +-- man/print.sim.seqtest.cor.Rd | 15 +++---- man/print.size.Rd | 7 +-- man/print.test.cor.Rd | 11 ++--- man/scatterplot.Rd | 9 ++-- man/seqtest.cor.Rd | 21 +++++----- man/sim.cor.Rd | 12 +++--- man/sim.seqtest.cor.Rd | 28 +++++++------- man/size.cor.Rd | 9 ++-- man/test.cor.Rd | 19 ++++----- man/update.seqtest.Rd | 9 ++-- 42 files changed, 230 insertions(+), 237 deletions(-)
Title: Evolutionary Learning of Globally Optimal Trees
Description: Commonly used classification and regression tree methods like the CART algorithm
are recursive partitioning methods that build the model in a forward stepwise search.
Although this approach is known to be an efficient heuristic, the results of recursive
tree methods are only locally optimal, as splits are chosen to maximize homogeneity at
the next step only. An alternative way to search over the parameter space of trees is
to use global optimization methods like evolutionary algorithms. The 'evtree' package
implements an evolutionary algorithm for learning globally optimal classification and
regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while
the 'partykit' package is leveraged to represent the resulting trees in R, providing
unified infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre],
Achim Zeileis [aut],
Karl-Peter Pfeiffer [aut]
Maintainer: Thomas Grubinger <Thomas.Grubinger@scch.at>
Diff between evtree versions 1.0-3 dated 2017-03-31 and 1.0-4 dated 2017-04-02
DESCRIPTION | 13 MD5 | 26 NEWS | 13 build/vignette.rds |binary data/BBBClub.rda |binary data/ContraceptiveChoice.RData |binary data/GermanCredit.RData |binary data/MAGICGammaTelescope.RData |binary data/StatlogHeart.RData |binary inst/doc/evtree.R | 1100 ++++++++++++++++++++--------------------- inst/doc/evtree.pdf |binary src/container.cpp | 28 - src/container.h | 1 src/tree.cpp | 2 14 files changed, 594 insertions(+), 589 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package
evaluates the mass and charge balance, extracts all reactants, products, orphan
metabolites, metabolite names and compartments. Also are included some options
to characterize and write models in TSV and SBML formats.
Author: c(person("Daniel","Osorio",email="dcosorioh@unal.edu.co",role=c("aut","cre")), person("Janneth","Gonzalez",role=c("aut","ths")), person("Andres","Pinzon",role=c("aut","ths")))
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.5 dated 2016-10-04 and 0.6 dated 2017-04-02
minval-0.5/minval/NEWS |only minval-0.5/minval/R/convert2sbml.R |only minval-0.5/minval/R/convert2sbmlR.R |only minval-0.5/minval/R/getChEBI.R |only minval-0.5/minval/R/isBalanced.R |only minval-0.5/minval/R/isValidSyntax.R |only minval-0.5/minval/R/mapReactions.R |only minval-0.5/minval/R/minvalInternal.R |only minval-0.5/minval/R/orphanProducts.R |only minval-0.5/minval/R/orphanReactants.R |only minval-0.5/minval/R/xls2sbml.R |only minval-0.5/minval/inst/extdata/glycolysisKEGG.csv |only minval-0.5/minval/inst/extdata/glycolysisKEGG.xlsx |only minval-0.5/minval/inst/tests |only minval-0.5/minval/man/convert2sbml.Rd |only minval-0.5/minval/man/convert2sbmlR.Rd |only minval-0.5/minval/man/getChEBI.Rd |only minval-0.5/minval/man/isBalanced.Rd |only minval-0.5/minval/man/isValidSyntax.Rd |only minval-0.5/minval/man/mapReactions.Rd |only minval-0.5/minval/man/orphanProducts.Rd |only minval-0.5/minval/man/orphanReactants.Rd |only minval-0.5/minval/man/xls2sbml.Rd |only minval-0.5/minval/tests/doRUnit.R |only minval-0.6/minval/DESCRIPTION | 19 +- minval-0.6/minval/MD5 | 101 +++++------ minval-0.6/minval/NAMESPACE | 17 - minval-0.6/minval/NEWS.md |only minval-0.6/minval/R/characterizeReactions.R |only minval-0.6/minval/R/checkBalance.R |only minval-0.6/minval/R/compartments.R | 82 +++++---- minval-0.6/minval/R/downloadChEBI.R |only minval-0.6/minval/R/internalFunctions.R |only minval-0.6/minval/R/metabolites.R | 64 +++---- minval-0.6/minval/R/orphanMetabolites.R |only minval-0.6/minval/R/products.R | 76 ++++---- minval-0.6/minval/R/reactants.R | 71 ++++---- minval-0.6/minval/R/stoichiometricMatrix.R | 107 +++++++----- minval-0.6/minval/R/validateSyntax.R |only minval-0.6/minval/R/writeSBMLmod.R |only minval-0.6/minval/R/writeTSVmod.R | 186 +++++++++++++-------- minval-0.6/minval/README.md | 41 +--- minval-0.6/minval/build |only minval-0.6/minval/inst/doc |only minval-0.6/minval/inst/extdata/glycolysisModel.csv |only minval-0.6/minval/inst/extdata/mRECON2.csv |only minval-0.6/minval/inst/extdata/rRECON2.csv |only minval-0.6/minval/man/characterizeReactions.Rd |only minval-0.6/minval/man/checkBalance.Rd |only minval-0.6/minval/man/compartments.Rd | 59 +++--- minval-0.6/minval/man/downloadChEBI.Rd |only minval-0.6/minval/man/metabolites.Rd | 52 ++--- minval-0.6/minval/man/orphanMetabolites.Rd |only minval-0.6/minval/man/products.Rd | 46 +---- minval-0.6/minval/man/reactants.Rd | 46 +---- minval-0.6/minval/man/stoichiometricMatrix.Rd | 49 ++--- minval-0.6/minval/man/validateSyntax.Rd |only minval-0.6/minval/man/writeSBMLmod.Rd |only minval-0.6/minval/man/writeTSVmod.Rd | 76 ++++---- minval-0.6/minval/tests/testthat |only minval-0.6/minval/tests/testthat.R |only minval-0.6/minval/vignettes |only 62 files changed, 593 insertions(+), 499 deletions(-)
Title: Lightweight Biology Software Installer
Description:
Install and download massive bioinformatics analysis software and database, such as NGS analysis tools with its required database or/and reference genome, is still a complicated task. BioInstaller can be used to install that tools and database in R conveniently.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between BioInstaller versions 0.0.2 dated 2017-04-01 and 0.0.3 dated 2017-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/utils_function.R | 2 ++ 3 files changed, 7 insertions(+), 5 deletions(-)