Title: An Implementation of the TSIR Model
Description: An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different
fitting options for infectious disease time series data. The method implemented here is described by Finkenstadt and Grenfell (2000) <DOI:10.1111/1467-9876.00187>.
Author: Alexander D. Becker [aut, cre],
Sinead E. Morris [ctb]
Maintainer: Alexander D. Becker <adbecker@princeton.edu>
Diff between tsiR versions 0.1.0 dated 2017-02-17 and 0.2.0 dated 2017-05-23
DESCRIPTION | 6 ++--- MD5 | 18 +++++++-------- R/epitimes_function.R | 52 ++++++++++++++++++++++++++++++++++++++-------- R/estpars_function.R | 2 - R/mcmcestpars_function.R | 2 - R/mcmctsir_function.R | 6 ++--- R/plotbreaks_function.R | 2 - R/runtsir_function.R | 6 ++--- R/simulatetsir_function.R | 4 +-- man/epitimes.Rd | 4 ++- 10 files changed, 69 insertions(+), 33 deletions(-)
Title: Simulation Education
Description: Contains various functions to be used for simulation education,
including queueing simulation functions, variate generation functions
capable of producing independent streams and antithetic variates, functions
for illustrating random variate generation for various discrete and
continuous distributions, and functions to compute time-persistent
statistics. Also contains two queueing data sets (one fabricated, one
real-world) to facilitate input modeling.
Author: Barry Lawson, Larry Leemis
Maintainer: Barry Lawson <blawson@richmond.edu>
Diff between simEd versions 1.0.0 dated 2017-05-10 and 1.0.1 dated 2017-05-23
DESCRIPTION | 6 MD5 | 46 ++-- NEWS.md |only R/msq.R | 8 R/ssq.R | 8 R/utils.R | 498 +++++++++++++++++++++++++++--------------------------- README.md |only build/partial.rdb |binary man/ibinom.Rd | 11 - man/iexp.Rd | 3 man/igamma.Rd | 10 - man/igeom.Rd | 2 man/inorm.Rd | 3 man/iunif.Rd | 5 man/iweibull.Rd | 7 man/msq.Rd | 3 man/set.seed.Rd | 7 man/ssq.Rd | 8 man/vbinom.Rd | 7 man/vexp.Rd | 4 man/vgamma.Rd | 16 - man/vgeom.Rd | 2 man/vnorm.Rd | 3 man/vunif.Rd | 3 man/vweibull.Rd | 7 25 files changed, 346 insertions(+), 321 deletions(-)
Title: Network-Based Regularization for Generalized Linear Models
Description: Network-based regularization has achieved success in variable selections for
high-dimensional biological data, due to its ability to incorporate the correlations
among genomic features. This package provides procedures for fitting network-based
regularization, minimax concave penalty (MCP) and lasso penalty for generalized linear
models. This first version, regnet0.1.1, focuses on binary outcomes. Functions for
continuous, survival outcomes and other regularization methods will be included in the
forthcoming upgraded version.
Author: Jie Ren, Luann C. Jung, Yinhao Du, Cen Wu, Yu Jiang, Junhao Liu
Maintainer: Jie Ren <jieren@ksu.edu>
Diff between regnet versions 0.1.0 dated 2017-05-21 and 0.1.1 dated 2017-05-23
DESCRIPTION | 33 +++++++++++---------------------- MD5 | 16 ++++++++-------- R/ElasticLogistic.R | 4 ++-- R/McpLogistic.R | 4 ++-- R/NetworkLogistic.R | 6 +++--- README.md | 2 +- man/ElasLogistic.Rd | 4 ++-- man/McpLogistic.Rd | 4 ++-- man/NetLogistic.Rd | 6 +++--- 9 files changed, 34 insertions(+), 45 deletions(-)
Title: High Throughput Sequencing of Stable Isotope Probing Data
Analysis
Description: Functions for analyzing high throughput sequencing
stable isotope probing (HTS-SIP) data.
Analyses include high resolution stable isotope probing (HR-SIP),
multi-window high resolution stable isotope probing (MW-HR-SIP),
and quantitative stable isotope probing (q-SIP).
Author: Nicholas Youngblut [aut, cre],
Samuel Barnett [ctb]
Maintainer: Nicholas Youngblut <nyoungb2@gmail.com>
Diff between HTSSIP versions 1.0.3 dated 2016-11-01 and 1.1.1 dated 2017-05-23
DESCRIPTION | 27 +--- MD5 | 148 +++++++++++++------------- NEWS.md | 15 ++ R/BD_ordinations.R | 6 - R/Util.R | 2 README.md | 10 + build/vignette.rds |binary inst/doc/BD_shifts.Rmd | 6 - inst/doc/BD_shifts.html | 69 +++++++----- inst/doc/HTSSIP_intro.Rmd | 21 ++- inst/doc/HTSSIP_intro.html | 93 +++++++++------- inst/doc/HTSSIP_sim.Rmd | 6 - inst/doc/HTSSIP_sim.html | 70 +++++++----- inst/doc/MW_HR_SIP.Rmd | 6 - inst/doc/MW_HR_SIP.html | 176 +++++++++++++++++-------------- inst/doc/beta_diversity_ordinations.Rmd | 10 + inst/doc/beta_diversity_ordinations.html | 127 ++++++++++++---------- inst/doc/qSIP.Rmd | 8 + inst/doc/qSIP.html | 122 ++++++++++++--------- inst/doc/quant_incorp.Rmd | 6 - inst/doc/quant_incorp.html | 119 +++++++++++--------- man/BD_shift.Rd | 1 man/DESeq2_l2fc.Rd | 1 man/HRSIP.Rd | 1 man/HTSSIP.Rd | 1 man/HTSSIP_sim.Rd | 1 man/OTU_qPCR_trans.Rd | 1 man/SIP_betaDiv_ord.Rd | 1 man/as.Num.Rd | 1 man/calc_Gi.Rd | 1 man/calc_Mheavymax.Rd | 1 man/calc_atom_excess.Rd | 1 man/data-physeq_S2D1.Rd | 1 man/data-physeq_S2D1_l.Rd | 1 man/data-physeq_S2D2.Rd | 1 man/data-physeq_S2D2_l.Rd | 1 man/data-physeq_rep3.Rd | 1 man/data-physeq_rep3_qPCR.Rd | 1 man/delta_BD.Rd | 1 man/evaluate_matches.Rd | 1 man/expr_param_extract.Rd | 1 man/extract_expressions.Rd | 1 man/extract_formats.Rd | 1 man/filter_l2fc.Rd | 1 man/format_metadata.Rd | 1 man/fraction_overlap.Rd | 1 man/get_treatment_params.Rd | 1 man/gradient_sim.Rd | 1 man/match_brace.Rd | 1 man/match_placeholders.Rd | 1 man/max_BD_range.Rd | 1 man/overlap_wmean_dist.Rd | 1 man/parse_dist.Rd | 1 man/perc_overlap.Rd | 1 man/phyloseq2df.Rd | 1 man/phyloseq2table.Rd | 3 man/phyloseq_list_ord_dfs.Rd | 1 man/phyloseq_ord_plot.Rd | 1 man/phyloseq_subset.Rd | 1 man/physeq_format.Rd | 1 man/physeq_list_betaDiv.Rd | 1 man/physeq_list_ord.Rd | 1 man/qPCR_sim.Rd | 1 man/qSIP_atom_excess.Rd | 1 man/qSIP_atom_excess_format.Rd | 1 man/qSIP_bootstrap.Rd | 1 man/stringterpolate.Rd | 1 man/tss.Rd | 1 vignettes/BD_shifts.Rmd | 6 - vignettes/HTSSIP_intro.Rmd | 21 ++- vignettes/HTSSIP_sim.Rmd | 6 - vignettes/MW_HR_SIP.Rmd | 6 - vignettes/beta_diversity_ordinations.Rmd | 10 + vignettes/qSIP.Rmd | 8 + vignettes/quant_incorp.Rmd | 6 - 75 files changed, 641 insertions(+), 518 deletions(-)
Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, and for computing term occurrence frequencies.
Author: Patrick O. Perry [aut, cre],
Martin Porter and Richard Boulton [ctb, cph] (Snowball),
Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between corpus versions 0.4.0 dated 2017-05-16 and 0.5.0 dated 2017-05-23
corpus-0.4.0/corpus/src/corpus/src/token.c |only corpus-0.4.0/corpus/src/corpus/src/token.h |only corpus-0.4.0/corpus/src/corpus/tests/check_token.c |only corpus-0.4.0/corpus/src/text_filter.c |only corpus-0.5.0/corpus/DESCRIPTION | 11 corpus-0.5.0/corpus/MD5 | 110 ++- corpus-0.5.0/corpus/NAMESPACE | 20 corpus-0.5.0/corpus/NEWS |only corpus-0.5.0/corpus/R/jsondata.R | 29 - corpus-0.5.0/corpus/R/methods.R | 2 corpus-0.5.0/corpus/R/text-proc.R | 281 +++++++--- corpus-0.5.0/corpus/R/text.R | 23 corpus-0.5.0/corpus/man/corpus-package.Rd |only corpus-0.5.0/corpus/man/read_ndjson.Rd | 32 - corpus-0.5.0/corpus/man/stopwords.Rd |only corpus-0.5.0/corpus/man/term_counts.Rd |only corpus-0.5.0/corpus/man/term_matrix.Rd |only corpus-0.5.0/corpus/man/text.Rd | 49 + corpus-0.5.0/corpus/man/tokens.Rd | 197 +++++-- corpus-0.5.0/corpus/src/Makevars | 7 corpus-0.5.0/corpus/src/corpus/Doxyfile | 6 corpus-0.5.0/corpus/src/corpus/Makefile | 86 +-- corpus-0.5.0/corpus/src/corpus/NEWS.md | 8 corpus-0.5.0/corpus/src/corpus/corpus.xcodeproj/project.pbxproj | 56 + corpus-0.5.0/corpus/src/corpus/src/data.c | 3 corpus-0.5.0/corpus/src/corpus/src/datatype.c | 5 corpus-0.5.0/corpus/src/corpus/src/filter.c |only corpus-0.5.0/corpus/src/corpus/src/filter.h |only corpus-0.5.0/corpus/src/corpus/src/main.c | 5 corpus-0.5.0/corpus/src/corpus/src/main_get.c | 3 corpus-0.5.0/corpus/src/corpus/src/main_scan.c | 3 corpus-0.5.0/corpus/src/corpus/src/main_sentences.c | 3 corpus-0.5.0/corpus/src/corpus/src/main_tokens.c | 263 +++++++-- corpus-0.5.0/corpus/src/corpus/src/private/stopwords.h | 4 corpus-0.5.0/corpus/src/corpus/src/symtab.c | 22 corpus-0.5.0/corpus/src/corpus/src/symtab.h | 12 corpus-0.5.0/corpus/src/corpus/src/text.c | 54 + corpus-0.5.0/corpus/src/corpus/src/text.h | 34 + corpus-0.5.0/corpus/src/corpus/src/textset.c |only corpus-0.5.0/corpus/src/corpus/src/textset.h |only corpus-0.5.0/corpus/src/corpus/src/tree.c |only corpus-0.5.0/corpus/src/corpus/src/tree.h |only corpus-0.5.0/corpus/src/corpus/src/typemap.c |only corpus-0.5.0/corpus/src/corpus/src/typemap.h |only corpus-0.5.0/corpus/src/corpus/tests/check_data.c | 3 corpus-0.5.0/corpus/src/corpus/tests/check_filter.c |only corpus-0.5.0/corpus/src/corpus/tests/check_sentscan.c | 17 corpus-0.5.0/corpus/src/corpus/tests/check_symtab.c | 17 corpus-0.5.0/corpus/src/corpus/tests/check_tree.c |only corpus-0.5.0/corpus/src/corpus/tests/check_typemap.c |only corpus-0.5.0/corpus/src/corpus/tests/check_wordscan.c | 71 +- corpus-0.5.0/corpus/src/corpus/tests/testutil.h | 8 corpus-0.5.0/corpus/src/corpus/util/gen-stopwords.py | 4 corpus-0.5.0/corpus/src/filter.c |only corpus-0.5.0/corpus/src/init.c | 8 corpus-0.5.0/corpus/src/jsondata.c | 197 ++++++- corpus-0.5.0/corpus/src/rcorpus.h | 31 - corpus-0.5.0/corpus/src/schema.c | 3 corpus-0.5.0/corpus/src/stopwords.c |only corpus-0.5.0/corpus/src/term_counts.c |only corpus-0.5.0/corpus/src/term_matrix.c |only corpus-0.5.0/corpus/src/tokens.c | 185 ++---- corpus-0.5.0/corpus/src/util.c | 12 corpus-0.5.0/corpus/tests/testthat/test-jsondata_record.R | 4 corpus-0.5.0/corpus/tests/testthat/test-read_ndjson.R | 9 corpus-0.5.0/corpus/tests/testthat/test-term_counts.R |only corpus-0.5.0/corpus/tests/testthat/test-term_matrix.R |only corpus-0.5.0/corpus/tests/testthat/test-text.R | 2 corpus-0.5.0/corpus/tests/testthat/test-tokens.R | 94 +++ 69 files changed, 1461 insertions(+), 532 deletions(-)
Title: Differential RNA Methylation Analysis for Count-Based
Small-Sample Sequencing Data with a Quad-Negative Binomial
Model
Description: As a newly emerged research area, RNA epigenetics has drawn increasing
attention recently for the participation of RNA methylation and other
modifications in a number of crucial biological processes. Thanks to high
throughput sequencing techniques, such as m6A-Seq, transcriptome-wide RNA
methylation profile is now available in the form of count-based data, with
which it is often of interests to study the dynamics in epitranscriptomic
layer. However, the sample size of RNA methylation experiment is usually
very small due to its costs; and additionally, there usually exist a large
number of genes whose methylation level cannot be accurately estimated due
to their low expression level, making differential RNA methylation analysis
a difficult task.
We present QNB, a statistical approach for differential RNA methylation
analysis with count-based small-sample sequencing data. The method is based
on 4 independent negative binomial dis-tributions with their variances and
means linked by local regressions. QNB showed improved performance on
simulated and real m6A-Seq datasets when compared with competing algorithms.
And the QNB model is also applicable to other datasets related RNA
modifications, including but not limited to RNA bisulfite sequencing,
m1A-Seq, Par-CLIP, RIP-Seq, etc.Please don't hesitate to contact
<liulian19860905@163.com> if you have any questions.
Author: Lian Liu <liulian19860905@163.com>
Maintainer: Lian Liu <liulian19860905@163.com>
Diff between QNB versions 1.1.7 dated 2017-01-11 and 1.1.8 dated 2017-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/qnbtest.R | 9 +++++++++ man/QNB-package.Rd | 4 ++-- 4 files changed, 18 insertions(+), 9 deletions(-)
Title: Clustering a Data Set using Multi-SOM Algorithm
Description: Implements two versions of the algorithm namely: stochastic and batch. The package determines also the best number of clusters and offers to the user the best clustering scheme from different results.
Author: Sarra Chair and Malika Charrad
Maintainer: Sarra Chair <sarra.chair@gmail.com>
Diff between multisom versions 1.2 dated 2016-11-06 and 1.3 dated 2017-05-23
multisom-1.2/multisom/LICENSE |only multisom-1.3/multisom/DESCRIPTION | 12 ++--- multisom-1.3/multisom/MD5 | 9 +--- multisom-1.3/multisom/NAMESPACE | 5 +- multisom-1.3/multisom/R/multisom.stochastic.R | 7 ++- multisom-1.3/multisom/man/multisom.stochastic.Rd | 51 +++++++++++------------ 6 files changed, 43 insertions(+), 41 deletions(-)
Title: Implements Under/Oversampling for Probability Estimation
Description: Implements under/oversampling for probability estimation. To be
used with machine learning methods such as adaBoost, random forests, etc.
Author: Matthew Olson [aut, cre]
Maintainer: Matthew Olson <maolson@wharton.upenn.edu>
Diff between JOUSBoost versions 1.0.0 dated 2016-09-12 and 2.0.0 dated 2017-05-23
JOUSBoost-1.0.0/JOUSBoost/R/adaBoost.R |only JOUSBoost-1.0.0/JOUSBoost/man/adaBoost.Rd |only JOUSBoost-2.0.0/JOUSBoost/DESCRIPTION | 10 - JOUSBoost-2.0.0/JOUSBoost/MD5 | 44 ++--- JOUSBoost-2.0.0/JOUSBoost/NAMESPACE | 7 JOUSBoost-2.0.0/JOUSBoost/R/RcppExports.R | 1 JOUSBoost-2.0.0/JOUSBoost/R/adaboost.R |only JOUSBoost-2.0.0/JOUSBoost/R/jous.R | 169 ++++++++++++++++------ JOUSBoost-2.0.0/JOUSBoost/R/jous_utility.R | 2 JOUSBoost-2.0.0/JOUSBoost/R/simulation.R | 7 JOUSBoost-2.0.0/JOUSBoost/README.md | 8 - JOUSBoost-2.0.0/JOUSBoost/man/JOUSBoost.Rd | 1 JOUSBoost-2.0.0/JOUSBoost/man/adaboost.Rd |only JOUSBoost-2.0.0/JOUSBoost/man/circle_data.Rd | 4 JOUSBoost-2.0.0/JOUSBoost/man/friedman_data.Rd | 3 JOUSBoost-2.0.0/JOUSBoost/man/grid_probs.Rd | 1 JOUSBoost-2.0.0/JOUSBoost/man/index_over.Rd | 1 JOUSBoost-2.0.0/JOUSBoost/man/index_under.Rd | 1 JOUSBoost-2.0.0/JOUSBoost/man/jous.Rd | 63 ++++++-- JOUSBoost-2.0.0/JOUSBoost/man/predict.AdaBoost.Rd | 18 +- JOUSBoost-2.0.0/JOUSBoost/man/predict.JOUS.Rd | 13 - JOUSBoost-2.0.0/JOUSBoost/man/print.AdaBoost.Rd | 9 - JOUSBoost-2.0.0/JOUSBoost/man/print.JOUS.Rd |only JOUSBoost-2.0.0/JOUSBoost/man/sonar.Rd | 1 JOUSBoost-2.0.0/JOUSBoost/src/grid_probs.cpp | 1 JOUSBoost-2.0.0/JOUSBoost/src/init.c |only 26 files changed, 242 insertions(+), 122 deletions(-)
Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the
'IRIS DMC MUSTANG' project. The functionality in this package
builds upon the base classes of the 'IRISSeismic' package.
Metrics include basic statistics as well as higher level
'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Mary Templeton [aut],
Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISMustangMetrics versions 2.0.4 dated 2017-02-11 and 2.0.8 dated 2017-05-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 6 ++++-- R/BSSUtils.R | 7 ++++--- R/Class-Metric.R | 8 +++++--- R/ISPAQUtils.R | 2 +- R/PSDMetric.R | 22 +++++----------------- R/crossCorrelationMetric.R | 36 +++++++++++++++++++----------------- man/IRISMustangMetrics-package.Rd | 21 +++++++++++++++++++++ man/crossCorrelationMetric.Rd | 18 +++++------------- 10 files changed, 77 insertions(+), 69 deletions(-)
More information about IRISMustangMetrics at CRAN
Permanent link
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 0.3.0 dated 2017-01-22 and 0.4.0 dated 2017-05-23
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Title: Efficient Breeding by Genomic Mating
Description: Implements the genomic mating approach in the recently published article: Akdemir, D., & Sanchez, J. I. (2016). Efficient Breeding by Genomic Mating. Frontiers in Genetics, 7. <DOI:10.3389/fgene.2016.00210>.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between GenomicMating versions 1.1 dated 2017-05-22 and 1.2 dated 2017-05-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/MatingPrograms.R | 2 +- build/partial.rdb |binary 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' (Schauberger and Tutz, 2017: Subject-Specific Modelling of Paired Comparison Data - a Lasso-Type Penalty Approach), a method to include different types of variables in paired
comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and
can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used
to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between BTLLasso versions 0.1-5 dated 2017-01-16 and 0.1-6 dated 2017-05-23
BTLLasso-0.1-5/BTLLasso/R/bootstrap.R |only BTLLasso-0.1-5/BTLLasso/R/ci.BTLLasso.R |only BTLLasso-0.1-5/BTLLasso/R/singlepaths.R |only BTLLasso-0.1-5/BTLLasso/man/ci.BTLLasso.Rd |only BTLLasso-0.1-5/BTLLasso/man/singlepaths.Rd |only BTLLasso-0.1-6/BTLLasso/DESCRIPTION | 14 BTLLasso-0.1-6/BTLLasso/MD5 | 81 ++--- BTLLasso-0.1-6/BTLLasso/NAMESPACE | 25 + BTLLasso-0.1-6/BTLLasso/R/BTLLasso-package.R | 314 ++++++++++++-------- BTLLasso-0.1-6/BTLLasso/R/BTLLasso.R | 295 +++++++++++++----- BTLLasso-0.1-6/BTLLasso/R/bin.fit.Cpp.R | 3 BTLLasso-0.1-6/BTLLasso/R/boot.BTLLasso.R |only BTLLasso-0.1-6/BTLLasso/R/coef.cv.BTLLasso.R |only BTLLasso-0.1-6/BTLLasso/R/create.design.R | 19 - BTLLasso-0.1-6/BTLLasso/R/cum.fit.Cpp.R | 3 BTLLasso-0.1-6/BTLLasso/R/cv.BTLLasso.R | 174 +++++++---- BTLLasso-0.1-6/BTLLasso/R/design.BTLLasso.R | 41 +- BTLLasso-0.1-6/BTLLasso/R/df.BTLLasso.R |only BTLLasso-0.1-6/BTLLasso/R/find.lambda.R |only BTLLasso-0.1-6/BTLLasso/R/fit.cv.BTLLasso.R | 4 BTLLasso-0.1-6/BTLLasso/R/functions.R | 11 BTLLasso-0.1-6/BTLLasso/R/paths.R | 182 +++++++---- BTLLasso-0.1-6/BTLLasso/R/plot.BTLLasso.R |only BTLLasso-0.1-6/BTLLasso/R/plot.boot.BTLLasso.R |only BTLLasso-0.1-6/BTLLasso/R/predict.BTLLasso.R |only BTLLasso-0.1-6/BTLLasso/R/predict.help.R |only BTLLasso-0.1-6/BTLLasso/R/print.BTLLasso.R | 124 +++++-- BTLLasso-0.1-6/BTLLasso/R/print.boot.BTLLasso.R | 134 +++++--- BTLLasso-0.1-6/BTLLasso/R/print.cv.BTLLasso.R | 142 +++++---- BTLLasso-0.1-6/BTLLasso/R/response.BTLLasso.R | 62 +++ BTLLasso-0.1-6/BTLLasso/data/BuliResponse.RData |only BTLLasso-0.1-6/BTLLasso/data/SimData.RData |binary BTLLasso-0.1-6/BTLLasso/man/BTLLasso-package.Rd | 130 +++++--- BTLLasso-0.1-6/BTLLasso/man/BTLLasso.Rd | 139 ++++++-- BTLLasso-0.1-6/BTLLasso/man/Buli1516.Rd | 30 + BTLLasso-0.1-6/BTLLasso/man/BuliResponse.Rd |only BTLLasso-0.1-6/BTLLasso/man/GLES.Rd | 19 + BTLLasso-0.1-6/BTLLasso/man/GLESsmall.Rd | 28 - BTLLasso-0.1-6/BTLLasso/man/SimData.Rd | 83 +---- BTLLasso-0.1-6/BTLLasso/man/boot.BTLLasso.Rd | 164 ++++++---- BTLLasso-0.1-6/BTLLasso/man/ctrl.BTLLasso.Rd | 150 ++++++--- BTLLasso-0.1-6/BTLLasso/man/cv.BTLLasso.Rd | 146 ++++++--- BTLLasso-0.1-6/BTLLasso/man/paths.Rd | 143 +++++---- BTLLasso-0.1-6/BTLLasso/man/plot.BTLLasso.Rd |only BTLLasso-0.1-6/BTLLasso/man/plot.boot.BTLLasso.Rd |only BTLLasso-0.1-6/BTLLasso/man/predict.BTLLasso.Rd |only BTLLasso-0.1-6/BTLLasso/man/print.BTLLasso.Rd | 131 +++++--- BTLLasso-0.1-6/BTLLasso/man/print.boot.BTLLasso.Rd | 136 +++++--- BTLLasso-0.1-6/BTLLasso/man/print.cv.BTLLasso.Rd | 131 +++++--- BTLLasso-0.1-6/BTLLasso/man/response.BTLLasso.Rd | 50 ++- BTLLasso-0.1-6/BTLLasso/src/registerDynamicSymbol.c |only 51 files changed, 2040 insertions(+), 1068 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models
using Stan for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 1.6.1 dated 2017-04-17 and 1.7.0 dated 2017-05-23
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Title: Modeling Framework for Cellular Communities in their
Environments
Description: Can be used for simulation of organisms living in
communities. Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.
Author: Eugen Bauer [aut],
Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
Diff between BacArena versions 1.5.1 dated 2016-07-25 and 1.6 dated 2017-05-23
BacArena-1.5.1/BacArena/man/Organism-class.Rd |only BacArena-1.6/BacArena/DESCRIPTION | 12 BacArena-1.6/BacArena/MD5 | 226 ++-- BacArena-1.6/BacArena/NAMESPACE | 13 BacArena-1.6/BacArena/NEWS | 23 BacArena-1.6/BacArena/R/Arena.R | 769 ++++++++++---- BacArena-1.6/BacArena/R/BacArena.R | 7 BacArena-1.6/BacArena/R/Organism.R | 216 ++- BacArena-1.6/BacArena/R/RcppExports.R | 2 BacArena-1.6/BacArena/R/Stuff.R | 350 ++++-- BacArena-1.6/BacArena/R/Substance.R | 61 - BacArena-1.6/BacArena/README.md | 2 BacArena-1.6/BacArena/build/vignette.rds |binary BacArena-1.6/BacArena/data/colpal.rda |binary BacArena-1.6/BacArena/inst/doc/BacArena-Introduction.R | 11 BacArena-1.6/BacArena/inst/doc/BacArena-Introduction.Rmd | 16 BacArena-1.6/BacArena/inst/doc/BacArena-Introduction.pdf |binary BacArena-1.6/BacArena/man/Arena-class.Rd | 4 BacArena-1.6/BacArena/man/Arena-constructor.Rd | 8 BacArena-1.6/BacArena/man/Bac-Constructor.Rd | 3 BacArena-1.6/BacArena/man/Bac.Rd | 8 BacArena-1.6/BacArena/man/Eval-constructor.Rd | 3 BacArena-1.6/BacArena/man/Human-constructor.Rd | 5 BacArena-1.6/BacArena/man/NemptyHood.Rd | 1 BacArena-1.6/BacArena/man/Organism-constructor.Rd | 7 BacArena-1.6/BacArena/man/Organism.Rd |only BacArena-1.6/BacArena/man/Substance-constructor.Rd | 21 BacArena-1.6/BacArena/man/Substance.Rd | 6 BacArena-1.6/BacArena/man/addDefaultMed.Rd | 7 BacArena-1.6/BacArena/man/addEssentialMed.Rd | 12 BacArena-1.6/BacArena/man/addEval.Rd | 1 BacArena-1.6/BacArena/man/addOrg.Rd | 16 BacArena-1.6/BacArena/man/addSubs.Rd | 21 BacArena-1.6/BacArena/man/cellgrowth.Rd | 7 BacArena-1.6/BacArena/man/changeDiff.Rd | 1 BacArena-1.6/BacArena/man/changeFobj.Rd | 1 BacArena-1.6/BacArena/man/changeOrg.Rd | 3 BacArena-1.6/BacArena/man/changeSub.Rd | 1 BacArena-1.6/BacArena/man/checkCorr.Rd | 1 BacArena-1.6/BacArena/man/checkPhen.Rd | 1 BacArena-1.6/BacArena/man/checkPhen_par.Rd | 1 BacArena-1.6/BacArena/man/chemotaxis.Rd | 1 BacArena-1.6/BacArena/man/colpal1.Rd | 1 BacArena-1.6/BacArena/man/colpal2.Rd | 1 BacArena-1.6/BacArena/man/colpal3.Rd | 1 BacArena-1.6/BacArena/man/colpal4.Rd | 1 BacArena-1.6/BacArena/man/colpal5.Rd | 1 BacArena-1.6/BacArena/man/colpal6.Rd | 1 BacArena-1.6/BacArena/man/constrain.Rd | 14 BacArena-1.6/BacArena/man/consume.Rd | 1 BacArena-1.6/BacArena/man/createGradient.Rd | 1 BacArena-1.6/BacArena/man/dat2mat.Rd | 1 BacArena-1.6/BacArena/man/diffuse.Rd | 1 BacArena-1.6/BacArena/man/diffusePDE.Rd | 9 BacArena-1.6/BacArena/man/diffuseR.Rd | 7 BacArena-1.6/BacArena/man/diffuse_par.Rd | 1 BacArena-1.6/BacArena/man/emptyHood.Rd | 1 BacArena-1.6/BacArena/man/evalArena.Rd | 3 BacArena-1.6/BacArena/man/extractMed.Rd | 1 BacArena-1.6/BacArena/man/findFeeding.Rd | 1 BacArena-1.6/BacArena/man/findFeeding2.Rd | 1 BacArena-1.6/BacArena/man/findFeeding3.Rd | 7 BacArena-1.6/BacArena/man/findFeeding3rep.Rd |only BacArena-1.6/BacArena/man/findInArena.Rd | 1 BacArena-1.6/BacArena/man/findRxnFlux.Rd |only BacArena-1.6/BacArena/man/flushSubs.Rd | 1 BacArena-1.6/BacArena/man/fluxVarSim.Rd |only BacArena-1.6/BacArena/man/getArena.Rd | 1 BacArena-1.6/BacArena/man/getCorrM.Rd | 1 BacArena-1.6/BacArena/man/getPhenoMat.Rd | 1 BacArena-1.6/BacArena/man/getPhenotype.Rd | 1 BacArena-1.6/BacArena/man/getSubHist.Rd | 9 BacArena-1.6/BacArena/man/getSublb.Rd | 1 BacArena-1.6/BacArena/man/getVarSubs.Rd | 1 BacArena-1.6/BacArena/man/growExp.Rd | 7 BacArena-1.6/BacArena/man/growLin.Rd | 7 BacArena-1.6/BacArena/man/growth.Rd | 7 BacArena-1.6/BacArena/man/growth_par.Rd | 7 BacArena-1.6/BacArena/man/lsd.Rd | 1 BacArena-1.6/BacArena/man/lysis.Rd | 1 BacArena-1.6/BacArena/man/minePheno.Rd | 1 BacArena-1.6/BacArena/man/move.Rd | 1 BacArena-1.6/BacArena/man/openArena.Rd | 1 BacArena-1.6/BacArena/man/optimizeLP.Rd | 6 BacArena-1.6/BacArena/man/plotAbundance.Rd | 1 BacArena-1.6/BacArena/man/plotCurves.Rd | 7 BacArena-1.6/BacArena/man/plotCurves2.Rd | 1 BacArena-1.6/BacArena/man/plotFVA.Rd |only BacArena-1.6/BacArena/man/plotFluxVar.Rd | 1 BacArena-1.6/BacArena/man/plotGrowthCurve.Rd | 8 BacArena-1.6/BacArena/man/plotInterNum.Rd | 1 BacArena-1.6/BacArena/man/plotPhenCurve.Rd | 12 BacArena-1.6/BacArena/man/plotPhenNum.Rd | 1 BacArena-1.6/BacArena/man/plotReaActivity.Rd |only BacArena-1.6/BacArena/man/plotShadowCost.Rd | 1 BacArena-1.6/BacArena/man/plotSpecActivity.Rd | 1 BacArena-1.6/BacArena/man/plotSubCurve.Rd | 1 BacArena-1.6/BacArena/man/plotSubDist.Rd |only BacArena-1.6/BacArena/man/plotSubDist2.Rd |only BacArena-1.6/BacArena/man/plotSubUsage.Rd | 3 BacArena-1.6/BacArena/man/plotSubVar.Rd | 3 BacArena-1.6/BacArena/man/plotTotFlux.Rd | 1 BacArena-1.6/BacArena/man/redEval.Rd | 1 BacArena-1.6/BacArena/man/reset_screen.Rd | 1 BacArena-1.6/BacArena/man/rmSubs.Rd | 1 BacArena-1.6/BacArena/man/selPheno.Rd | 1 BacArena-1.6/BacArena/man/setKinetics.Rd | 1 BacArena-1.6/BacArena/man/sihumi_test.Rd | 1 BacArena-1.6/BacArena/man/simBac.Rd | 1 BacArena-1.6/BacArena/man/simBac_par.Rd | 1 BacArena-1.6/BacArena/man/simEnv.Rd | 11 BacArena-1.6/BacArena/man/simEnv_par.Rd | 7 BacArena-1.6/BacArena/man/simHum.Rd | 13 BacArena-1.6/BacArena/man/statPheno.Rd | 1 BacArena-1.6/BacArena/man/stirEnv.Rd | 1 BacArena-1.6/BacArena/man/unit_conversion.Rd |only BacArena-1.6/BacArena/man/usd.Rd | 1 BacArena-1.6/BacArena/src/RcppExports.cpp | 50 BacArena-1.6/BacArena/vignettes/BacArena-Introduction.Rmd | 7 119 files changed, 1367 insertions(+), 733 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous utility functions for data manipulation,
data tidying, and working with gene expression data.
Author: Stephen Turner [aut, cre]
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.15 dated 2017-05-16 and 0.1.16 dated 2017-05-23
Tmisc-0.1.15/Tmisc/R/nin.R |only Tmisc-0.1.16/Tmisc/DESCRIPTION | 10 ++++++---- Tmisc-0.1.16/Tmisc/MD5 | 21 +++++++++++++++------ Tmisc-0.1.16/Tmisc/NAMESPACE | 22 ++++++++++++++++++++++ Tmisc-0.1.16/Tmisc/NEWS.md | 23 +++++++++++++++++++++++ Tmisc-0.1.16/Tmisc/R/aliases.R |only Tmisc-0.1.16/Tmisc/R/grapes.R |only Tmisc-0.1.16/Tmisc/R/gt2refalt.R |only Tmisc-0.1.16/Tmisc/R/insertInAddin.R |only Tmisc-0.1.16/Tmisc/README.md | 4 +++- Tmisc-0.1.16/Tmisc/inst/rstudio |only Tmisc-0.1.16/Tmisc/man/aliases.Rd |only Tmisc-0.1.16/Tmisc/man/grapes-like-grapes.Rd |only Tmisc-0.1.16/Tmisc/man/grapes-nin-grapes.Rd | 8 +++----- Tmisc-0.1.16/Tmisc/man/grapes-nlike-grapes.Rd |only Tmisc-0.1.16/Tmisc/man/gt2refalt.Rd |only Tmisc-0.1.16/Tmisc/man/insertInAddin.Rd |only 17 files changed, 72 insertions(+), 16 deletions(-)
Title: Recognising Visual Charting Patterns in Time Series Data
Description: Generating visual charting patterns and noise,
smoothing to find a signal in noisy time series and enabling
users to apply their findings to real life data.
Author: Stephan Maier [aut, cre]
Maintainer: Stephan Maier <sm297@st-andrews.ac.uk>
Diff between rpatrec versions 0.9.1 dated 2017-04-20 and 1.0.1 dated 2017-05-23
DESCRIPTION | 14 - MD5 | 66 ++++---- R/Testfunction.R | 79 ++++++--- R/data.R | 2 R/datainput.R | 34 ++-- R/generator.R | 150 ++++++++++-------- R/inputchecks.R | 163 ++++++++++---------- R/interpreter.R | 358 ++++++++++++++++++++++++++------------------ R/rpatrec.R |only R/smoother1.R | 63 ++++--- R/smoother2.r | 38 +++- R/smoother3.R | 77 +++++---- R/smoother_additional.R | 52 ++++-- build/vignette.rds |binary inst/doc/Dissertation.R | 6 inst/doc/Dissertation.Rmd | 10 - inst/doc/Dissertation.html | 82 +++++----- inst/doc/Dissertation2.Rmd | 16 + inst/doc/Dissertation2.html | 15 + man/data.Rd | 2 man/generator.Rd | 7 man/interpret.Rd | 49 +++++- man/iq.Rd | 5 man/kernel.Rd | 24 ++ man/loess.rpatrec.Rd | 23 ++ man/mav.Rd | 20 ++ man/noise.Rd | 23 ++ man/rpatrec.Rd |only man/sample.pre.Rd | 12 - man/savgolay.Rd | 20 ++ man/slicer.Rd | 32 ++- man/splines.Rd | 23 ++ man/test.smoother.Rd | 21 ++ vignettes/Dissertation.Rmd | 10 - vignettes/Dissertation2.Rmd | 16 + 35 files changed, 966 insertions(+), 546 deletions(-)
More information about ROI.models.miplib at CRAN
Permanent link
Title: Individual Tree Crowns Segmentation
Description: Three methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
Author: Michele Dalponte
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>
Diff between itcSegment versions 0.4 dated 2017-04-13 and 0.5 dated 2017-05-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 2 ++ R/agb.R |only R/dbh.R |only R/itcLiDARallo.R | 5 +++-- man/agb.Rd |only man/dbh.Rd |only man/itcLiDARallo.Rd | 4 +++- 9 files changed, 20 insertions(+), 11 deletions(-)
Title: High Dimensional Locally-Linear Mapping
Description: Provides a tool for non linear mapping (non linear regression) using a mixture of regression model and an inverse regression strategy. The methods include the GLLiM model (see Deleforge et al (2015) <DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust version of GLLiM, named SLLiM (see Perthame et al (2016) <https://hal.archives-ouvertes.fr/hal-01347455>) based on a mixture of Generalized Student distributions. The methods also include BLLiM (see Devijver et al (2017) <https://arxiv.org/abs/1701.07899>) which is an extension of GLLiM with a sparse block diagonal structure for large covariance matrices (particularly interesting for transcriptomic data).
Author: Emeline Perthame (emeline.perthame@inria.fr), Florence Forbes (florence.forbes@inria.fr), Antoine Deleforge (antoine.deleforge@inria.fr), Emilie Devijver (emilie.devijver@kuleuven.be), Melina Gallopin (melina.gallopin@u-psud.fr)
Maintainer: Emeline Perthame <emeline.perthame@pasteur.fr>
Diff between xLLiM versions 2.0 dated 2017-05-16 and 2.1 dated 2017-05-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gllim.R | 2 +- R/sllim.R | 2 +- man/xLLiM-package.Rd | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Predicted Values and Discrete Changes for GLM
Description: Functions to calculate predicted values and the difference between
the two cases with confidence interval for glm(), glm.nb(), polr() and multinom().
Author: Benjamin Schlegel [aut,cre]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between glm.predict versions 2.5-0 dated 2017-05-16 and 2.5-1 dated 2017-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/nominal_discrete.change.R | 33 +++++++++++++++++++++++---------- R/predict_multinom.R | 27 +++++++++++++++++++++------ 4 files changed, 51 insertions(+), 23 deletions(-)
Title: FLuctuation ANalysis on Mutation Models
Description: Tools for fluctuations analysis of mutant cells counts.
Author: Adrien Mazoyer [aut, cre],
Remy Drouilhet [aut],
Stephane Despreaux [aut],
Bernard Ycart [aut]
Maintainer: Adrien Mazoyer <Adrien.Mazoyer@univ-grenoble-alpes.fr>
Diff between flan versions 0.4 dated 2017-03-02 and 0.5 dated 2017-05-23
DESCRIPTION | 8 MD5 | 24 +- R/flan.R | 432 ++++++++++++++++++++++++++++++--------------- man/flan-package.Rd | 6 man/flan.test.Rd | 2 man/mutestim.Rd | 2 man/rflan.Rd | 10 - src/FLAN_Clone.cpp | 302 ++++++++++++++++++++----------- src/FLAN_Clone.h | 29 +-- src/FLAN_MutationModel.cpp | 28 +- src/FLAN_MutationModel.h | 1 src/MATH_Function.cpp | 53 +++++ src/MATH_Function.h | 1 13 files changed, 597 insertions(+), 301 deletions(-)
More information about RNAstructureModuleMiner at CRAN
Permanent link
Title: Tools for Parsing, Manipulating, and Graphing Hierarchical Data
Description: A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
Author: Zachary Foster [aut, cre],
Niklaus Grunwald [ths]
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between metacoder versions 0.1.2 dated 2016-08-26 and 0.1.3 dated 2017-05-23
metacoder-0.1.2/metacoder/tests/testthat/test--plot_taxonomy.R |only metacoder-0.1.3/metacoder/DESCRIPTION | 12 metacoder-0.1.3/metacoder/MD5 | 313 ++++---- metacoder-0.1.3/metacoder/NEWS.md | 33 metacoder-0.1.3/metacoder/R/dataset_documentation.R | 6 metacoder-0.1.3/metacoder/R/extract_taxonomy--internal.R | 2 metacoder-0.1.3/metacoder/R/extract_taxonomy--parsers.R | 24 metacoder-0.1.3/metacoder/R/extract_taxonomy--wrappers.R | 2 metacoder-0.1.3/metacoder/R/extract_taxonomy.R | 114 +-- metacoder-0.1.3/metacoder/R/heat_tree--internal.R | 88 ++ metacoder-0.1.3/metacoder/R/heat_tree--layouts.R | 2 metacoder-0.1.3/metacoder/R/heat_tree--legend.R | 18 metacoder-0.1.3/metacoder/R/heat_tree--mapping.R | 19 metacoder-0.1.3/metacoder/R/heat_tree--resizing_text.R | 13 metacoder-0.1.3/metacoder/R/heat_tree--vertex_size.R | 4 metacoder-0.1.3/metacoder/R/heat_tree.R | 352 ++++------ metacoder-0.1.3/metacoder/R/in_silico_pcr.R | 6 metacoder-0.1.3/metacoder/R/internal.R | 24 metacoder-0.1.3/metacoder/R/metacoder-package.r | 4 metacoder-0.1.3/metacoder/R/mothur.R | 16 metacoder-0.1.3/metacoder/R/taxmap--internal.R | 11 metacoder-0.1.3/metacoder/R/taxmap--mutate.R | 4 metacoder-0.1.3/metacoder/R/taxmap--sample.R | 4 metacoder-0.1.3/metacoder/R/taxmap--utilities.R | 2 metacoder-0.1.3/metacoder/README.md | 29 metacoder-0.1.3/metacoder/build/vignette.rds |binary metacoder-0.1.3/metacoder/inst/CITATION |only metacoder-0.1.3/metacoder/inst/doc/introduction.html | 72 +- metacoder-0.1.3/metacoder/man/DNAbin_to_char.Rd | 1 metacoder-0.1.3/metacoder/man/add_alpha.Rd | 1 metacoder-0.1.3/metacoder/man/apply_color_scale.Rd | 1 metacoder-0.1.3/metacoder/man/arrange_obs.Rd | 1 metacoder-0.1.3/metacoder/man/arrange_taxa.Rd | 1 metacoder-0.1.3/metacoder/man/bryophytes_ex_data.Rd | 1 metacoder-0.1.3/metacoder/man/can_be_num.Rd |only metacoder-0.1.3/metacoder/man/check_element_length.Rd | 1 metacoder-0.1.3/metacoder/man/class_from_class.Rd | 5 metacoder-0.1.3/metacoder/man/class_from_name.Rd | 1 metacoder-0.1.3/metacoder/man/class_from_obs_id.Rd | 4 metacoder-0.1.3/metacoder/man/class_from_taxon_id.Rd | 1 metacoder-0.1.3/metacoder/man/class_to_taxonomy.Rd | 1 metacoder-0.1.3/metacoder/man/contains.Rd | 1 metacoder-0.1.3/metacoder/man/contaminants.Rd | 3 metacoder-0.1.3/metacoder/man/convert_numeric_cols.Rd | 1 metacoder-0.1.3/metacoder/man/count_capture_groups.Rd | 1 metacoder-0.1.3/metacoder/man/delete_vetices_and_children.Rd | 1 metacoder-0.1.3/metacoder/man/diverging_palette.Rd | 3 metacoder-0.1.3/metacoder/man/drawDetails.resizingTextGrob.Rd | 1 metacoder-0.1.3/metacoder/man/edge_list_depth.Rd | 1 metacoder-0.1.3/metacoder/man/ends_with.Rd | 1 metacoder-0.1.3/metacoder/man/everything.Rd | 1 metacoder-0.1.3/metacoder/man/extract_taxonomy.Rd | 34 metacoder-0.1.3/metacoder/man/fasta_headers.Rd | 1 metacoder-0.1.3/metacoder/man/filter_obs.Rd | 1 metacoder-0.1.3/metacoder/man/filter_taxa.Rd | 1 metacoder-0.1.3/metacoder/man/format_taxon_subset.Rd | 1 metacoder-0.1.3/metacoder/man/genbank_ex_data.Rd | 3 metacoder-0.1.3/metacoder/man/get_class_from_el.Rd | 1 metacoder-0.1.3/metacoder/man/get_edge_children.Rd | 1 metacoder-0.1.3/metacoder/man/get_edge_parents.Rd | 1 metacoder-0.1.3/metacoder/man/get_id_from_name.Rd | 1 metacoder-0.1.3/metacoder/man/get_name_from_id.Rd | 1 metacoder-0.1.3/metacoder/man/get_node_children.Rd | 1 metacoder-0.1.3/metacoder/man/get_numerics.Rd |only metacoder-0.1.3/metacoder/man/get_optimal_range.Rd | 1 metacoder-0.1.3/metacoder/man/get_taxonomy_levels.Rd | 1 metacoder-0.1.3/metacoder/man/grapes-greater-than-grapes.Rd | 1 metacoder-0.1.3/metacoder/man/heat_tree.Rd | 26 metacoder-0.1.3/metacoder/man/hierarchies.Rd | 1 metacoder-0.1.3/metacoder/man/inter_circle_gap.Rd | 1 metacoder-0.1.3/metacoder/man/inverse.Rd | 1 metacoder-0.1.3/metacoder/man/its1_ex_data.Rd | 1 metacoder-0.1.3/metacoder/man/label_bounds.Rd |only metacoder-0.1.3/metacoder/man/layout_functions.Rd | 3 metacoder-0.1.3/metacoder/man/line_coords.Rd | 1 metacoder-0.1.3/metacoder/man/make_new_ids.Rd | 1 metacoder-0.1.3/metacoder/man/make_plot_legend.Rd | 7 metacoder-0.1.3/metacoder/man/make_text_grobs.Rd | 1 metacoder-0.1.3/metacoder/man/map_unique.Rd | 1 metacoder-0.1.3/metacoder/man/matches.Rd | 1 metacoder-0.1.3/metacoder/man/metacoder.Rd | 6 metacoder-0.1.3/metacoder/man/molten_dist.Rd | 5 metacoder-0.1.3/metacoder/man/mutate_obs.Rd | 1 metacoder-0.1.3/metacoder/man/mutate_taxa.Rd | 1 metacoder-0.1.3/metacoder/man/n_obs.Rd | 1 metacoder-0.1.3/metacoder/man/n_obs_1.Rd | 1 metacoder-0.1.3/metacoder/man/n_subtaxa.Rd | 1 metacoder-0.1.3/metacoder/man/n_subtaxa_1.Rd | 1 metacoder-0.1.3/metacoder/man/n_supertaxa.Rd | 1 metacoder-0.1.3/metacoder/man/ncbi_sequence.Rd | 1 metacoder-0.1.3/metacoder/man/ncbi_taxon_sample.Rd | 1 metacoder-0.1.3/metacoder/man/num_range.Rd | 1 metacoder-0.1.3/metacoder/man/obs.Rd | 1 metacoder-0.1.3/metacoder/man/obs_data.Rd | 1 metacoder-0.1.3/metacoder/man/obs_data_colnames.Rd | 1 metacoder-0.1.3/metacoder/man/obs_data_cols_used.Rd | 1 metacoder-0.1.3/metacoder/man/one_of.Rd | 1 metacoder-0.1.3/metacoder/man/parse_hmp_qiime.Rd | 3 metacoder-0.1.3/metacoder/man/parse_mothur_summary.Rd | 7 metacoder-0.1.3/metacoder/man/parse_primersearch.Rd | 1 metacoder-0.1.3/metacoder/man/parse_summary_seqs.Rd | 1 metacoder-0.1.3/metacoder/man/parse_taxonomy_table.Rd | 9 metacoder-0.1.3/metacoder/man/plot_alignment.Rd | 1 metacoder-0.1.3/metacoder/man/polygon_coords.Rd | 1 metacoder-0.1.3/metacoder/man/postDrawDetails.resizingTextGrob.Rd | 1 metacoder-0.1.3/metacoder/man/pr2_ex_data.Rd | 1 metacoder-0.1.3/metacoder/man/preDrawDetails.resizingTextGrob.Rd | 1 metacoder-0.1.3/metacoder/man/primersearch.Rd | 4 metacoder-0.1.3/metacoder/man/primersearch_is_installed.Rd | 1 metacoder-0.1.3/metacoder/man/print.taxmap.Rd | 1 metacoder-0.1.3/metacoder/man/qualitative_palette.Rd | 3 metacoder-0.1.3/metacoder/man/quantative_palette.Rd | 3 metacoder-0.1.3/metacoder/man/rdp_ex_data.Rd | 3 metacoder-0.1.3/metacoder/man/read_fasta.Rd | 1 metacoder-0.1.3/metacoder/man/read_lines_apply.Rd | 1 metacoder-0.1.3/metacoder/man/recursive_sample.Rd | 1 metacoder-0.1.3/metacoder/man/remove_redundant_names.Rd | 5 metacoder-0.1.3/metacoder/man/rename_duplicated.Rd | 1 metacoder-0.1.3/metacoder/man/rescale.Rd | 3 metacoder-0.1.3/metacoder/man/resizingTextGrob.Rd | 1 metacoder-0.1.3/metacoder/man/roots.Rd | 1 metacoder-0.1.3/metacoder/man/run_primersearch.Rd | 1 metacoder-0.1.3/metacoder/man/sample_frac_obs.Rd | 3 metacoder-0.1.3/metacoder/man/sample_frac_taxa.Rd | 3 metacoder-0.1.3/metacoder/man/sample_n_obs.Rd | 1 metacoder-0.1.3/metacoder/man/sample_n_taxa.Rd | 1 metacoder-0.1.3/metacoder/man/scale_bar_coords.Rd | 1 metacoder-0.1.3/metacoder/man/select_labels.Rd | 1 metacoder-0.1.3/metacoder/man/select_obs.Rd | 1 metacoder-0.1.3/metacoder/man/select_taxa.Rd | 1 metacoder-0.1.3/metacoder/man/silva_ex_data.Rd | 1 metacoder-0.1.3/metacoder/man/split_by_level.Rd | 1 metacoder-0.1.3/metacoder/man/split_class_list.Rd | 1 metacoder-0.1.3/metacoder/man/starts_with.Rd | 1 metacoder-0.1.3/metacoder/man/subtaxa.Rd | 3 metacoder-0.1.3/metacoder/man/supertaxa.Rd | 1 metacoder-0.1.3/metacoder/man/taxmap.Rd | 1 metacoder-0.1.3/metacoder/man/taxon_data.Rd | 1 metacoder-0.1.3/metacoder/man/taxon_data_colnames.Rd | 1 metacoder-0.1.3/metacoder/man/taxon_data_cols_used.Rd | 1 metacoder-0.1.3/metacoder/man/taxonomic_sample.Rd | 1 metacoder-0.1.3/metacoder/man/taxonomy_ranks.Rd | 1 metacoder-0.1.3/metacoder/man/text_grob_length.Rd | 7 metacoder-0.1.3/metacoder/man/transform_data.Rd | 1 metacoder-0.1.3/metacoder/man/transmute_obs.Rd | 1 metacoder-0.1.3/metacoder/man/transmute_taxa.Rd | 1 metacoder-0.1.3/metacoder/man/unique_mapping.Rd | 1 metacoder-0.1.3/metacoder/man/unite_ex_data_1.Rd | 1 metacoder-0.1.3/metacoder/man/unite_ex_data_2.Rd | 1 metacoder-0.1.3/metacoder/man/unite_ex_data_3.Rd | 1 metacoder-0.1.3/metacoder/man/validate_regex_key_pair.Rd | 3 metacoder-0.1.3/metacoder/man/validate_regex_match.Rd | 1 metacoder-0.1.3/metacoder/man/verify_color_range.Rd | 1 metacoder-0.1.3/metacoder/man/verify_label_count.Rd | 1 metacoder-0.1.3/metacoder/man/verify_size.Rd | 1 metacoder-0.1.3/metacoder/man/verify_size_range.Rd | 1 metacoder-0.1.3/metacoder/man/verify_trans.Rd | 1 metacoder-0.1.3/metacoder/man/vigilant_report.Rd | 1 metacoder-0.1.3/metacoder/tests/testthat/Rplots.pdf |only metacoder-0.1.3/metacoder/tests/testthat/test--extract_taxonomy.R | 24 metacoder-0.1.3/metacoder/tests/testthat/test--heat_tree.R |only 161 files changed, 779 insertions(+), 679 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 0.7 dated 2017-05-23
DESCRIPTION | 18 +++++++++++++----- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/checkBalance.R | 3 +-- README.md | 2 +- build/vignette.rds |binary inst/doc/MINVALintroduction.R | 2 ++ inst/doc/MINVALintroduction.Rmd | 2 ++ inst/doc/MINVALintroduction.html | 5 +++-- inst/doc/characterizeReactions.html | 6 +++--- vignettes/MINVALintroduction.Rmd | 2 ++ 11 files changed, 41 insertions(+), 23 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: A collection of functions to help build complex HTML or 'LaTeX'
tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'.
Function 'kable()' is a light weight table generator coming from 'knitr'.
This package simplifies the way to manipulate the HTML or 'LaTeX' codes
generated by 'kable()' and allows users to construct complex tables
and customize styles using a readable syntax.
Author: Hao Zhu [aut, cre],
Will Beasley [ctb],
Yihui Xie [ctb],
Thomas Travison [ctb],
GuangChuang Yu [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 0.1.0 dated 2017-03-02 and 0.2.0 dated 2017-05-23
DESCRIPTION | 18 MD5 | 50 - NAMESPACE | 4 R/add_header_above.R | 6 R/add_indent.R |only R/group_rows.R |only R/kableExtra-package.R | 1 R/kable_styling.R | 10 R/landscape.R |only R/magic_mirror.R | 2 R/util.R | 19 README.md | 34 build/vignette.rds |binary inst/NEWS |only inst/doc/awesome_table_in_html.R | 16 inst/doc/awesome_table_in_html.Rmd | 40 - inst/doc/awesome_table_in_html.html | 605 ++++++++++++++++- inst/doc/use_kable_in_shiny.R |only inst/doc/use_kable_in_shiny.Rmd |only inst/doc/use_kable_in_shiny.html |only man/add_indent.Rd |only man/group_rows.Rd |only man/landscape.Rd |only tests/visual_tests/add_indent_and_group_rows_html.Rmd |only tests/visual_tests/add_indent_and_group_rows_html.html |only tests/visual_tests/add_indent_and_group_rows_pdf.Rmd |only tests/visual_tests/add_indent_and_group_rows_pdf.pdf |only tests/visual_tests/indent_and_row_group.Rmd |only tests/visual_tests/indent_and_row_group.pdf |only tests/visual_tests/kable_styling_pdf.pdf |binary tests/visual_tests/kable_styling_pdf.tex | 17 tests/visual_tests/landscape_table.Rmd |only tests/visual_tests/landscape_table.pdf |only tests/visual_tests/landscape_table.tex |only vignettes/awesome_table_in_html.Rmd | 40 - vignettes/use_kable_in_shiny.Rmd |only 36 files changed, 774 insertions(+), 88 deletions(-)
Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@berkeley.edu>
Diff between distances versions 0.1.1 dated 2017-05-21 and 0.1.2 dated 2017-05-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ src/Makevars | 2 +- src/libann/Makefile | 2 +- src/libann/src/kd_dump.cpp | 2 +- 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from
National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.1 dated 2017-05-19 and 2.7.2 dated 2017-05-23
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/constructNWISURL.r | 2 +- R/readNWISdata.r | 2 +- R/readNWISunit.r | 8 ++++---- R/sysdata.rda |binary R/tabbedDataRetrievals.R | 7 ++----- R/whatNWISsites.R | 3 +-- inst/doc/dataRetrieval.html | 2 +- man/constructNWISURL.Rd | 2 +- man/dataRetrieval.Rd | 2 +- man/parameterCdFile.Rd | 5 +---- man/readNWISdata.Rd | 2 +- man/readNWISmeas.Rd | 2 +- man/readNWISstat.Rd | 2 +- man/readNWISuv.Rd | 4 ++-- man/whatNWISsites.Rd | 3 +-- 17 files changed, 39 insertions(+), 47 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 0.3.4 dated 2017-03-31 and 0.3.6 dated 2017-05-23
crul-0.3.4/crul/inst/doc/async.R |only crul-0.3.4/crul/inst/doc/crul_vignette.R |only crul-0.3.4/crul/inst/doc/how-to-use-crul.R |only crul-0.3.6/crul/DESCRIPTION | 8 crul-0.3.6/crul/MD5 | 60 +++---- crul-0.3.6/crul/NAMESPACE | 3 crul-0.3.6/crul/NEWS.md | 28 +++ crul-0.3.6/crul/R/auth.R |only crul-0.3.6/crul/R/client.R | 40 +++- crul-0.3.6/crul/R/crul-package.r | 11 + crul-0.3.6/crul/R/httprequest.R | 19 +- crul-0.3.6/crul/R/mocking.R |only crul-0.3.6/crul/R/onLoad.R |only crul-0.3.6/crul/R/proxies.R | 9 - crul-0.3.6/crul/R/response.R | 19 +- crul-0.3.6/crul/R/stubbed-response.R |only crul-0.3.6/crul/R/zzz.R | 28 ++- crul-0.3.6/crul/README.md | 61 ++++--- crul-0.3.6/crul/build/vignette.rds |binary crul-0.3.6/crul/inst/doc/async.Rmd | 215 ++++++++++++++++++++------ crul-0.3.6/crul/inst/doc/async.html | 195 ++++++----------------- crul-0.3.6/crul/inst/doc/crul_vignette.Rmd | 204 +++++++++++++++++++----- crul-0.3.6/crul/inst/doc/crul_vignette.html | 200 +++++------------------- crul-0.3.6/crul/inst/doc/how-to-use-crul.Rmd | 148 +++++++++++++---- crul-0.3.6/crul/inst/doc/how-to-use-crul.html | 151 +++--------------- crul-0.3.6/crul/man/HttpClient.Rd | 2 crul-0.3.6/crul/man/HttpStubbedResponse.Rd |only crul-0.3.6/crul/man/auth.Rd |only crul-0.3.6/crul/man/crul-package.Rd | 13 + crul-0.3.6/crul/man/mock.Rd |only crul-0.3.6/crul/tests/testthat/test-auth.R |only crul-0.3.6/crul/tests/testthat/test-delete.R | 2 crul-0.3.6/crul/tests/testthat/test-headers.R | 6 crul-0.3.6/crul/tests/testthat/test-mocking.R |only crul-0.3.6/crul/vignettes/async.Rmd | 215 ++++++++++++++++++++------ crul-0.3.6/crul/vignettes/crul_vignette.Rmd | 204 +++++++++++++++++++----- crul-0.3.6/crul/vignettes/how-to-use-crul.Rmd | 148 +++++++++++++---- 37 files changed, 1246 insertions(+), 743 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-08 1.10.18
2016-09-29 1.10.17
2016-06-13 1.9.17
2016-05-25 1.9.16
2016-04-01 1.8.16
2015-11-02 1.8.15
2015-10-30 1.8.14
2015-09-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-18 0.1.0