Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data. This includes, for example, biological count data
generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
ChIP-sequencing, Methyl-Capture sequencing, and other techniques. This package
implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 3.1.1 dated 2017-11-13 and 3.1.2 dated 2017-12-14
DESCRIPTION | 6 +- MD5 | 38 +++++++++--------- NEWS.md | 9 ++++ R/propdViz.R | 38 ++++-------------- R/proprViz.R | 24 ++++------- README.md | 18 +++++++- build/vignette.rds |binary inst/CITATION | 30 ++++++++++++-- inst/doc/a_introduction.html | 12 ++--- inst/doc/b_visualization.html | 10 ++-- inst/doc/c_indexing.html | 88 +++++++++++++++++++++--------------------- inst/doc/d_advanced.html | 43 +++++++++++--------- inst/doc/e_differential.Rmd | 4 - inst/doc/e_differential.html | 44 ++++++++++----------- inst/doc/f_moderation.html | 12 ++--- inst/doc/g_questions.Rmd | 2 inst/doc/g_questions.html | 18 ++++---- man/propr.Rd | 4 - vignettes/e_differential.Rmd | 4 - vignettes/g_questions.Rmd | 2 20 files changed, 216 insertions(+), 190 deletions(-)
Title: Rapid Deployment of Machine Learning Algorithms
Description: Supervised machine learning has an increasingly important role in data
analysis. This package introduces a framework for rapidly building and deploying
supervised machine learning in a high-throughput manner. This package provides a
user-friendly interface that empowers investigators to execute state-of-the-art
binary and multi-class classification, as well as regression, with minimal
programming experience necessary.
Author: Thomas Quinn [aut, cre],
Daniel Tylee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between exprso versions 0.2.6 dated 2017-11-30 and 0.2.7 dated 2017-12-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/1.2-methods.R | 8 +++++++- inst/doc/a_introduction-vignette.html | 4 ++-- inst/doc/b_advanced-vignette.html | 4 ++-- inst/doc/c_readme.html | 4 ++-- 7 files changed, 27 insertions(+), 16 deletions(-)
Title: Efficient Score Statistics for Genome-Wide SNP Set Analysis
Description: An implementation of the use of efficient score statistics
in genome-wide SNP set analysis with complex traits. Three standard score statistics
(Cox, binomial, and Gaussian) are provided, but the package is easily extensible to
include others. Code implementing the inferential procedure is primarily written in C++ and
utilizes parallelization of the analysis to reduce runtime. A supporting function offers
simple computation of observed, permutation, and FWER and FDR adjusted p-values.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between RSNPset versions 0.5.2 dated 2017-02-21 and 0.5.3 dated 2017-12-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 4 ++++ build/vignette.rds |binary inst/doc/RSNPset.R | 7 ++++--- inst/doc/RSNPset.Rnw | 8 +++++--- inst/doc/RSNPset.pdf |binary man/RSNPset-package.Rd | 6 +++--- vignettes/RSNPset.Rnw | 8 +++++--- 9 files changed, 33 insertions(+), 24 deletions(-)
Title: A Set of RStudio Addins
Description: A set of RStudio addins that are designed to be used in
combination with user-defined RStudio keyboard shortcuts. These
addins either:
1) insert text at a cursor position (e.g. insert
operators %>%, <<-, %$%, etc.),
2) replace symbols in selected pieces of text (e.g., convert
backslashes to forward slashes which results in stings like
"c:\data\" converted into "c:/data/") or
3) enclose text with special symbols (e.g., converts "bold" into
"**bold**") which is convenient for editing R Markdown files.
Author: Vilmantas Gegzna [aut, cre, cph]
Maintainer: Vilmantas Gegzna <GegznaV@gmail.com>
Diff between spAddins versions 0.1.7 dated 2017-01-03 and 0.2.0 dated 2017-12-14
spAddins-0.1.7/spAddins/R/Arrows_insert_addins.R |only spAddins-0.1.7/spAddins/R/Replace_addins.R |only spAddins-0.1.7/spAddins/R/enclose_addins.R |only spAddins-0.1.7/spAddins/R/insert_Line_addins.R |only spAddins-0.1.7/spAddins/R/insert_addins.R |only spAddins-0.1.7/spAddins/R/magrittr_operators_insert_addins.R |only spAddins-0.1.7/spAddins/man/Back2ForwardSlash.Rd |only spAddins-0.1.7/spAddins/man/Back2doubleBackSlash.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_asterisk.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_asterisk2.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_backtick.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_dollar.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_dollar2.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_tilde.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_tilde2.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_underscore.Rd |only spAddins-0.1.7/spAddins/man/enclose_with_underscore2.Rd |only spAddins-0.1.7/spAddins/man/insertArrowLR2_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertCompAssignPipe_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertExPipe_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertIfNULL_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertIn_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertMatMuliplication_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertNotIn_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertPaste0_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertPaste_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertPipeline_Addin.Rd |only spAddins-0.1.7/spAddins/man/insertTeeOperator_Addin.Rd |only spAddins-0.1.7/spAddins/man/insert_ds_line_Addin.Rd |only spAddins-0.1.7/spAddins/man/insert_if_null_Addin.Rd |only spAddins-0.1.7/spAddins/man/insert_if_null_or_len0_Addin.Rd |only spAddins-0.1.7/spAddins/man/insert_ss_line_Addin.Rd |only spAddins-0.1.7/spAddins/man/insert_sw_line_Addin.Rd |only spAddins-0.2.0/spAddins/DESCRIPTION | 15 spAddins-0.2.0/spAddins/MD5 | 93 +-- spAddins-0.2.0/spAddins/NAMESPACE | 89 ++- spAddins-0.2.0/spAddins/R/1_spAddins-package.R | 15 spAddins-0.2.0/spAddins/R/insert_arrows.R |only spAddins-0.2.0/spAddins/R/insert_code_block.R |only spAddins-0.2.0/spAddins/R/insert_lines.R |only spAddins-0.2.0/spAddins/R/insert_operators_magrittr.R |only spAddins-0.2.0/spAddins/R/insert_operators_other.R |only spAddins-0.2.0/spAddins/R/repeat_symbol.R |only spAddins-0.2.0/spAddins/R/replace_slash.R |only spAddins-0.2.0/spAddins/R/rmd_equations.R |only spAddins-0.2.0/spAddins/R/rmd_formatting.R |only spAddins-0.2.0/spAddins/R/rmd_headings.R |only spAddins-0.2.0/spAddins/R/rmd_lists.R |only spAddins-0.2.0/spAddins/R/rs_enclose_selection_with.R |only spAddins-0.2.0/spAddins/R/rs_enclose_with_lines.R |only spAddins-0.2.0/spAddins/R/rs_get_ind_first_selected_col.R |only spAddins-0.2.0/spAddins/R/rs_insert_at_row_start.R |only spAddins-0.2.0/spAddins/R/rs_insert_symbol_seq.R |only spAddins-0.2.0/spAddins/R/rs_replace_in_selection.R |only spAddins-0.2.0/spAddins/README.md | 171 ------ spAddins-0.2.0/spAddins/build/vignette.rds |binary spAddins-0.2.0/spAddins/inst/doc/v1_workflow.R | 12 spAddins-0.2.0/spAddins/inst/doc/v1_workflow.Rmd | 182 ++++-- spAddins-0.2.0/spAddins/inst/doc/v1_workflow.html | 248 +++++--- spAddins-0.2.0/spAddins/inst/rstudio/addins.dcf | 283 ++++++---- spAddins-0.2.0/spAddins/man/format_rmd.Rd |only spAddins-0.2.0/spAddins/man/insert_arrows.Rd |only spAddins-0.2.0/spAddins/man/insert_magrittr_operators.Rd |only spAddins-0.2.0/spAddins/man/insert_symbol_sequences.Rd |only spAddins-0.2.0/spAddins/man/repeat_symbol.Rd |only spAddins-0.2.0/spAddins/man/replace_slash.Rd |only spAddins-0.2.0/spAddins/man/rmd_code_block.Rd |only spAddins-0.2.0/spAddins/man/rmd_equations.Rd |only spAddins-0.2.0/spAddins/man/rmd_headings.Rd |only spAddins-0.2.0/spAddins/man/rmd_list.Rd |only spAddins-0.2.0/spAddins/man/rs_enclose_all_with_lines.Rd |only spAddins-0.2.0/spAddins/man/rs_enclose_selection_with.Rd |only spAddins-0.2.0/spAddins/man/rs_get_ind_first_selected_col.Rd |only spAddins-0.2.0/spAddins/man/rs_get_ind_first_selected_row.Rd |only spAddins-0.2.0/spAddins/man/rs_insert_at_row_start.Rd |only spAddins-0.2.0/spAddins/man/rs_insert_infix_R.Rd |only spAddins-0.2.0/spAddins/man/rs_insert_infix_in.Rd |only spAddins-0.2.0/spAddins/man/rs_insert_infix_not_in.Rd |only spAddins-0.2.0/spAddins/man/rs_insert_matrix_multiplication.Rd |only spAddins-0.2.0/spAddins/man/rs_insert_symbol_seq.Rd |only spAddins-0.2.0/spAddins/man/rs_replace_in_selection.Rd |only spAddins-0.2.0/spAddins/man/spAddins.Rd | 13 spAddins-0.2.0/spAddins/vignettes/v1_workflow.Rmd | 187 ++++-- 83 files changed, 729 insertions(+), 579 deletions(-)
Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multispecies, trait
based and community size spectrum ecological models, focussed on the marine
environment.
Author: Finlay Scott [aut, cph],
Julia Blanchard [aut, cph],
Ken Andersen [aut, cph],
Gustav Delius [ctb, cre],
Richard Southwell [ctb]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 0.2 dated 2014-04-16 and 0.4 dated 2017-12-14
mizer-0.2/mizer/R/MizerParams-class.r |only mizer-0.2/mizer/R/MizerSim-class.r |only mizer-0.2/mizer/R/NS_species_params-data.R |only mizer-0.2/mizer/R/help.r |only mizer-0.2/mizer/R/plots.r |only mizer-0.2/mizer/R/project.r |only mizer-0.2/mizer/R/project_methods.r |only mizer-0.2/mizer/R/selectivity_funcs.r |only mizer-0.2/mizer/R/summary_methods.r |only mizer-0.2/mizer/inst/tests |only mizer-0.2/mizer/man/MizerParams-methods.Rd |only mizer-0.2/mizer/man/MizerSim-methods.Rd |only mizer-0.2/mizer/man/getBiomass-methods.Rd |only mizer-0.2/mizer/man/getCommunitySlope-methods.Rd |only mizer-0.2/mizer/man/getEGrowth-methods.Rd |only mizer-0.2/mizer/man/getEReproAndGrowth-methods.Rd |only mizer-0.2/mizer/man/getESpawning-methods.Rd |only mizer-0.2/mizer/man/getFMort-methods.Rd |only mizer-0.2/mizer/man/getFMortGear-methods.Rd |only mizer-0.2/mizer/man/getFeedingLevel-methods.Rd |only mizer-0.2/mizer/man/getM2-methods.Rd |only mizer-0.2/mizer/man/getM2Background-methods.Rd |only mizer-0.2/mizer/man/getMeanMaxWeight-methods.Rd |only mizer-0.2/mizer/man/getMeanWeight-methods.Rd |only mizer-0.2/mizer/man/getN-methods.Rd |only mizer-0.2/mizer/man/getPhiPrey-methods.Rd |only mizer-0.2/mizer/man/getPredRate-methods.Rd |only mizer-0.2/mizer/man/getProportionOfLargeFish-methods.Rd |only mizer-0.2/mizer/man/getRDD-methods.Rd |only mizer-0.2/mizer/man/getRDI-methods.Rd |only mizer-0.2/mizer/man/getSSB-methods.Rd |only mizer-0.2/mizer/man/getYield-methods.Rd |only mizer-0.2/mizer/man/getYieldGear-methods.Rd |only mizer-0.2/mizer/man/getZ-methods.Rd |only mizer-0.2/mizer/man/plot-methods.Rd |only mizer-0.2/mizer/man/plotBiomass-methods.Rd |only mizer-0.2/mizer/man/plotFMort-methods.Rd |only mizer-0.2/mizer/man/plotFeedingLevel-methods.Rd |only mizer-0.2/mizer/man/plotM2-methods.Rd |only mizer-0.2/mizer/man/plotSpectra-methods.Rd |only mizer-0.2/mizer/man/plotYield-methods.Rd |only mizer-0.2/mizer/man/plotYieldGear-methods.Rd |only mizer-0.2/mizer/man/project-methods.Rd |only mizer-0.2/mizer/man/summary-methods.Rd |only mizer-0.2/mizer/tests/run-all.r |only mizer-0.4/mizer/DESCRIPTION | 44 mizer-0.4/mizer/MD5 | 154 +- mizer-0.4/mizer/NAMESPACE | 71 - mizer-0.4/mizer/NEWS | 16 mizer-0.4/mizer/R/MizerParams-class.R |only mizer-0.4/mizer/R/MizerSim-class.R |only mizer-0.4/mizer/R/RcppExports.R |only mizer-0.4/mizer/R/data.R |only mizer-0.4/mizer/R/help.R |only mizer-0.4/mizer/R/plots.R |only mizer-0.4/mizer/R/project.R |only mizer-0.4/mizer/R/project_methods.R |only mizer-0.4/mizer/R/selectivity_funcs.R |only mizer-0.4/mizer/R/summary_methods.R |only mizer-0.4/mizer/R/wrapper_functions.R | 232 ++-- mizer-0.4/mizer/build/vignette.rds |binary mizer-0.4/mizer/inst/doc/mizer_vignette.R | 886 ++++------------ mizer-0.4/mizer/inst/doc/mizer_vignette.Rnw | 329 +++-- mizer-0.4/mizer/inst/doc/mizer_vignette.pdf |binary mizer-0.4/mizer/inst/examples/supplementary_material.R | 3 mizer-0.4/mizer/man/MizerParams-class.Rd | 150 +- mizer-0.4/mizer/man/MizerParams.Rd |only mizer-0.4/mizer/man/MizerSim-class.Rd | 43 mizer-0.4/mizer/man/MizerSim.Rd |only mizer-0.4/mizer/man/NS_species_params.Rd | 40 mizer-0.4/mizer/man/NS_species_params_gears.Rd |only mizer-0.4/mizer/man/getBiomass.Rd |only mizer-0.4/mizer/man/getCommunitySlope.Rd |only mizer-0.4/mizer/man/getEGrowth.Rd |only mizer-0.4/mizer/man/getEReproAndGrowth.Rd |only mizer-0.4/mizer/man/getESpawning.Rd |only mizer-0.4/mizer/man/getFMort.Rd |only mizer-0.4/mizer/man/getFMortGear.Rd |only mizer-0.4/mizer/man/getFeedingLevel.Rd |only mizer-0.4/mizer/man/getM2.Rd |only mizer-0.4/mizer/man/getM2Background.Rd |only mizer-0.4/mizer/man/getMeanMaxWeight.Rd |only mizer-0.4/mizer/man/getMeanWeight.Rd |only mizer-0.4/mizer/man/getN.Rd |only mizer-0.4/mizer/man/getPhiPrey.Rd |only mizer-0.4/mizer/man/getPredRate.Rd |only mizer-0.4/mizer/man/getProportionOfLargeFish.Rd |only mizer-0.4/mizer/man/getRDD.Rd |only mizer-0.4/mizer/man/getRDI.Rd |only mizer-0.4/mizer/man/getSSB.Rd |only mizer-0.4/mizer/man/getYield.Rd |only mizer-0.4/mizer/man/getYieldGear.Rd |only mizer-0.4/mizer/man/getZ.Rd |only mizer-0.4/mizer/man/get_initial_n.Rd | 26 mizer-0.4/mizer/man/inter.Rd | 30 mizer-0.4/mizer/man/knife_edge.Rd | 14 mizer-0.4/mizer/man/mizer.Rd | 37 mizer-0.4/mizer/man/plotBiomass.Rd |only mizer-0.4/mizer/man/plotFMort.Rd |only mizer-0.4/mizer/man/plotFeedingLevel.Rd |only mizer-0.4/mizer/man/plotM2.Rd |only mizer-0.4/mizer/man/plotMizerSim.Rd |only mizer-0.4/mizer/man/plotSpectra.Rd |only mizer-0.4/mizer/man/plotYield.Rd |only mizer-0.4/mizer/man/plotYieldGear.Rd |only mizer-0.4/mizer/man/project.Rd |only mizer-0.4/mizer/man/project_methods.Rd |only mizer-0.4/mizer/man/set_community_model.Rd | 162 +- mizer-0.4/mizer/man/set_trait_model.Rd | 214 +-- mizer-0.4/mizer/man/sigmoid_length.Rd | 27 mizer-0.4/mizer/man/summary-MizerParams-method.Rd |only mizer-0.4/mizer/man/summary-MizerSim-method.Rd |only mizer-0.4/mizer/src |only mizer-0.4/mizer/tests/testthat |only mizer-0.4/mizer/tests/testthat.R |only mizer-0.4/mizer/vignettes/mizer_vignette.Rnw | 329 +++-- mizer-0.4/mizer/vignettes/reflib.bib | 53 117 files changed, 1300 insertions(+), 1560 deletions(-)
Title: Wrap R Functions for Debugging and Parametric Programming
Description: Powerful tools for writing and debugging R code. Provides: 'let()' which converts non-standard evaluation interfaces to
parametric standard evaluation interface, 'DebugFnW()' to capture function context on error for
debugging, and ':=' named map builder, and lambda-abstraction.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.0.1 dated 2017-11-17 and 1.0.2 dated 2017-12-14
DESCRIPTION | 8 ++++---- MD5 | 36 +++++++++++++++++++++--------------- NAMESPACE | 4 ++++ NEWS.md | 7 +++++++ R/bpipe.R | 25 +++++++++++++++++++++++++ R/map_to_char.R |only R/namedMapBuilder.R | 3 +++ R/qae.R |only R/qc.R | 33 +++++++++++++++++++++++++++------ inst/doc/CornerCases.html | 4 ++-- inst/doc/DebugFnW.html | 6 +++--- inst/doc/SubstitutionModes.html | 4 ++-- inst/doc/dot_pipe.html | 4 ++-- inst/doc/lambda.html | 4 ++-- inst/doc/let.html | 4 ++-- inst/doc/named_map_builder.html | 4 ++-- man/grapes-.-greater-than-grapes.Rd | 1 + man/grapes-greater-than-.-grapes.Rd |only man/map_to_char.Rd |only man/qae.Rd |only man/qc.Rd | 2 ++ man/qe.Rd |only 22 files changed, 109 insertions(+), 40 deletions(-)
Title: Unicode Text Processing
Description: Processing and printing 'UTF-8' encoded international text (Unicode). Functions to input, validate, normalize, encode, format, and display.
Author: Patrick O. Perry [aut, cph, cre],
Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between utf8 versions 1.1.1 dated 2017-11-29 and 1.1.2 dated 2017-12-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 8 ++++++++ src/utf8_format.c | 3 +-- tests/testthat/test-utf8_format.R | 7 +++++++ 5 files changed, 23 insertions(+), 9 deletions(-)
Title: Evaluation of Tweedie Exponential Family Models
Description: Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
Author: Peter K. Dunn [cre, aut]
Maintainer: Peter K. Dunn <pdunn2@usc.edu.au>
Diff between tweedie versions 2.3.1 dated 2017-11-16 and 2.3.2 dated 2017-12-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ R/tweedie.R | 21 +++++++++++++++------ build/partial.rdb |binary man/tweedie-package.Rd | 4 ++-- man/tweedie.convert.Rd | 43 +++++++++++++++++++++++-------------------- man/tweedie.profile.Rd | 2 +- 8 files changed, 56 insertions(+), 40 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a 'shiny' interface which can be started from R using
treespaceServer().
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treespace versions 1.0.0 dated 2017-03-17 and 1.0.1 dated 2017-12-14
treespace-1.0.0/treespace/src/treespace_init.c |only treespace-1.0.1/treespace/DESCRIPTION | 22 treespace-1.0.1/treespace/LICENSE | 2 treespace-1.0.1/treespace/MD5 | 170 treespace-1.0.1/treespace/NAMESPACE | 122 treespace-1.0.1/treespace/R/RcppExports.R | 14 treespace-1.0.1/treespace/R/data.R | 184 treespace-1.0.1/treespace/R/findGroves.R | 200 treespace-1.0.1/treespace/R/medTree.R | 436 treespace-1.0.1/treespace/R/metrics.R | 1019 - treespace-1.0.1/treespace/R/plotGroves.R | 502 treespace-1.0.1/treespace/R/plotTreeDiff.R | 426 treespace-1.0.1/treespace/R/servers.R | 148 treespace-1.0.1/treespace/R/transmissionTrees.R | 448 treespace-1.0.1/treespace/R/treespace.R | 303 treespace-1.0.1/treespace/README.md | 316 treespace-1.0.1/treespace/build/vignette.rds |binary treespace-1.0.1/treespace/data/DengueBEASTMCC.RData |binary treespace-1.0.1/treespace/data/DengueSeqs.RData |binary treespace-1.0.1/treespace/data/DengueTrees.RData |binary treespace-1.0.1/treespace/data/fluTrees.RData |binary treespace-1.0.1/treespace/data/woodmiceTrees.RData |binary treespace-1.0.1/treespace/inst/doc/DengueVignette.R | 468 treespace-1.0.1/treespace/inst/doc/DengueVignette.Rmd | 694 treespace-1.0.1/treespace/inst/doc/DengueVignette.html | 7148 +++++----- treespace-1.0.1/treespace/inst/doc/TransmissionTreesVignette.R | 264 treespace-1.0.1/treespace/inst/doc/TransmissionTreesVignette.Rmd | 427 treespace-1.0.1/treespace/inst/doc/TransmissionTreesVignette.html | 631 treespace-1.0.1/treespace/inst/doc/introduction.R | 308 treespace-1.0.1/treespace/inst/doc/introduction.Rmd | 792 - 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Title: Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Description: Extracts sentiment and sentiment-derived plot arcs
from text using a variety of sentiment dictionaries conveniently
packaged for consumption by R users. Implemented dictionaries include
"syuzhet" (default) developed in the Nebraska Literary Lab
"afinn" developed by Finn {\AA}rup Nielsen, "bing" developed by Minqing Hu
and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D.
Applicable references are available in README.md and in the documentation
for the "get_sentiment" function. The package also provides a hack for
implementing Stanford's coreNLP sentiment parser. The package provides
several methods for plot arc normalization.
Author: Matthew Jockers [aut, cre]
Maintainer: Matthew Jockers <mjockers@gmail.com>
Diff between syuzhet versions 1.0.1 dated 2017-03-06 and 1.0.4 dated 2017-12-14
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Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Description: Tools to create a layout for figures made of multiple panels, and
to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap'
plots, grobs, and PNG, JPEG, SVG and TIFF images.
Author: Johannes Graumann [cre, aut],
Richard Cotton [ctb]
Maintainer: Johannes Graumann <jog2030@qatar-med.cornell.edu>
Diff between multipanelfigure versions 0.10.5 dated 2017-08-31 and 0.10.6 dated 2017-12-14
DESCRIPTION | 8 - MD5 | 12 - R/fill_panel.R | 23 ++- build/vignette.rds |binary inst/doc/panel-positioning.html | 231 +++++++++++++++++++++++++++++--- inst/doc/scaling-clipping-images.html | 239 ++++++++++++++++++++++++++++++---- man/fill_panel.Rd | 4 7 files changed, 452 insertions(+), 65 deletions(-)
More information about multipanelfigure at CRAN
Permanent link
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [aut],
Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.6.0 dated 2017-10-22 and 0.7.0 dated 2017-12-14
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Title: Estimation Methods for Gravity Models
Description: Gravity models are used to explain bilateral flows related to the sizes of bilateral partners, a measure of distance between them and other influences on interaction costs. The underlying idea is rather simple. The greater the masses of two bodies and the smaller the distance between them, the stronger their attraction. This concept is applied to several research topics such as trade, migration or foreign direct investment. Even though their basic idea is rather simple, gravity models can become complex regarding the choice of models or estimation methods. As especially for gravity beginners it is difficult to get an overview of the different methods and implement them in R, the package provides a wrapper of different standard estimation methods for gravity models. By considering the descriptions and codes of the estimation methods, users get a comprehensive and application-oriented overview of the different methods, see which method may be suitable for a certain research question or type of data and extend the code available to their research projects. The package contains two types of estimation methods: those estimating gravity models in their log-log form, such as Ordinary Least Squares (OLS), Fixed Effects, Double Demeaning (DDM), Bonus vetus OLS with simple averages (BVU) and with GDP-weights (BVW), Structural Iterated Least Squares (SILS), Tetrads, and different Tobit models (Tobit, ET-Tobit, EK-Tobit). These methods are partly complex to understand and program and thus a comparison of them is not straightforward, wherefore the package aims at easing an overview of the different methods combined with a direct application. A second type of estimation methods utilizes the gravity model in its multiplicative form with a log-link and different families of distributions. They are relatively easy to compute, added for completeness and contain the methods Poisson Pseudo Maximum Likelihood (PPML), Gamma Pseudo Maximum Likelihood (GPML), Negative Binomial Pseudo Maximum Likelihood (NBPML), and Nonlinear Least Squares (NLS). All functions named estimate gravity models, but they differ in whether they estimate them in their multiplicative or additive form, their requirements and assumptions with respect to data, their handling of Multilateral Resistance terms as well as their possibilities concerning the inclusion of unilateral independent variables. Therefore, they normally lead to different estimation results. We refer the user to the Gravity Cookbook website (<https://sites.google.com/site/hiegravity/>) for more information on gravity models in general. Head, K. and Mayer, T. (2014) <DOI:10.1016/B978-0-444-54314-1.00003-3> provide a comprehensive and accessible overview of the theoretical and empirical development of the gravity literature as well as the use of gravity models and the various estimation methods, especially their merits and potential problems regarding applicability as well as different datasets. In order to have a straightforward application of all methods, the package comes with two example dataset, one including and the other one excluding zero trade flows. Examples utilizing these dataset are included in the description of the methods. As the range of gravity models and their suitable estimation methods is huge and specific to data and research question at hand, the functions are kept simple such that researchers can utilize them as a starting point of their research and get familiar with them. On the Gravity Cookbook website (<https://sites.google.com/site/hiegravity/>) Keith Head and Thierry Mayer provide Stata code for most methods. Where possible, the functions are tested to lead the same results as the Stata code when choosing the option of robust variance estimation. However, compared to the Stata code available, the functions presented in this package provide users with more flexibility regarding the type of estimation, the number and type of independent variables as well as the possible data. Furthermore, additional functions are added. The functions of the package include distance as an independent variable. If a panel model is used time-invariant effects, such as geographical distance, may have to be excluded; see the respective descriptions. Therefore, it is up to the user to ensure that the functions can be applied to panel data. Depending on the panel dataset and the variables - specifically the type of fixed effects - included in the model, it may easily occur that the model is not computable. Depending on the specific model, the code of the respective function may has to be changed in order to exclude the distance variable from the estimation. For a comprehensive overview of gravity models for panel data see Egger, P., & Pfaffermayr, M. (2003) <DOI:10.1007/s001810200146>, Gomez-Herrera, E. (2013) <DOI:10.1007/s00181-012-0576-2> and Head, K., Mayer, T., & Ries, J. (2010) <DOI:10.1016/j.jinteco.2010.01.002> as well as the references therein (see also the references included in the descriptions of the different functions). At the very least, the user should take special care with respect to the meaning of the estimated coefficients and variances as well as the decision about which effects to include in the estimation. As, to our knowledge at the moment, there is no explicit literature covering the estimation of a gravity equation by Double Demeaning, Structural Iterated Least Squares or Bonus vetus OLS using panel data, we do not recommend to apply these methods in this case. Contributions, extensions and error corrections are very welcome. Please do not hesitate to contact us. We thank Martin Bresslein for valuable comments and advice on early versions of the package.
Author: Anna-Lena Woelwer <woelwer@uni-trier.de>, Jan Pablo Burgard <burgardj@uni-trier.de>
Maintainer: Anna-Lena Woelwer <woelwer@uni-trier.de>
Diff between gravity versions 0.5 dated 2017-11-14 and 0.6 dated 2017-12-14
gravity-0.5/gravity/R/Gravity_Data_Example.R |only gravity-0.5/gravity/data/Gravity.RData |only gravity-0.5/gravity/man/Gravity.Rd |only gravity-0.6/gravity/DESCRIPTION | 19 - gravity-0.6/gravity/MD5 | 65 ++-- gravity-0.6/gravity/NAMESPACE | 3 gravity-0.6/gravity/R/BVU.R | 68 ++--- gravity-0.6/gravity/R/BVW.R | 90 +++--- gravity-0.6/gravity/R/DDM.R | 100 +++---- gravity-0.6/gravity/R/EK_Tobit.R |only gravity-0.6/gravity/R/ET_Tobit.R |only gravity-0.6/gravity/R/Fixed_effects.R | 53 ++- gravity-0.6/gravity/R/GPML.R | 46 ++- gravity-0.6/gravity/R/Gravity_Data_Example_with_zero_trade.R |only gravity-0.6/gravity/R/Gravity_Data_Example_without_zero_trade.R |only gravity-0.6/gravity/R/NBPML.R | 72 +++-- gravity-0.6/gravity/R/NLS.R | 73 +++-- gravity-0.6/gravity/R/OLS.R | 81 +++--- gravity-0.6/gravity/R/PPML.R | 47 ++- gravity-0.6/gravity/R/SILS.R | 97 +++---- gravity-0.6/gravity/R/Tetrads.R | 133 ++++------ gravity-0.6/gravity/R/Tobit.R |only gravity-0.6/gravity/R/gravity-internal.R | 43 +-- gravity-0.6/gravity/data/Gravity_no_zeros.RData |only gravity-0.6/gravity/data/Gravity_zeros.RData |only gravity-0.6/gravity/man/BVU.Rd | 32 +- gravity-0.6/gravity/man/BVW.Rd | 32 +- gravity-0.6/gravity/man/DDM.Rd | 19 + gravity-0.6/gravity/man/EK_Tobit.Rd |only gravity-0.6/gravity/man/ET_Tobit.Rd |only gravity-0.6/gravity/man/Fixed_Effects.Rd | 20 + gravity-0.6/gravity/man/GPML.Rd | 22 + gravity-0.6/gravity/man/Gravity_no_zeros.Rd |only gravity-0.6/gravity/man/Gravity_zeros.Rd |only gravity-0.6/gravity/man/NBPML.Rd | 36 ++ gravity-0.6/gravity/man/NLS.Rd | 38 ++ gravity-0.6/gravity/man/OLS.Rd | 24 + gravity-0.6/gravity/man/PPML.Rd | 33 +- gravity-0.6/gravity/man/SILS.Rd | 18 + gravity-0.6/gravity/man/Tetrads.Rd | 18 + gravity-0.6/gravity/man/Tobit.Rd |only 41 files changed, 773 insertions(+), 509 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus genotype-by-environment) and
GGB (genotype plus genotype-by-block-of-environments) models.
Author: Kevin Wright [aut, cre],
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.2 dated 2017-05-25 and 1.3 dated 2017-12-14
gge-1.2/gge/R/RcppExports.R |only gge-1.2/gge/R/gge.R |only gge-1.2/gge/man/nipals.Rd |only gge-1.2/gge/man/rnipals.Rd |only gge-1.2/gge/src |only gge-1.3/gge/DESCRIPTION | 15 - gge-1.3/gge/MD5 | 28 -- gge-1.3/gge/NAMESPACE | 5 gge-1.3/gge/R/gge.r |only gge-1.3/gge/build/vignette.rds |binary gge-1.3/gge/inst/doc/gge_examples.R | 20 + gge-1.3/gge/inst/doc/gge_examples.Rmd | 62 ++++ gge-1.3/gge/inst/doc/gge_examples.html | 75 +++-- gge-1.3/gge/man/RedGrayBlue.Rd | 2 gge-1.3/gge/man/gge.Rd | 36 +- gge-1.3/gge/tests/testthat/test_gge.R | 413 ++++++++++++++++++--------------- gge-1.3/gge/vignettes/gge_examples.Rmd | 62 ++++ 17 files changed, 464 insertions(+), 254 deletions(-)
Title: Elo Ratings
Description: A flexible framework for calculating Elo ratings and resulting
rankings of any two-team-per-matchup system (chess, sports leagues, 'Go',
etc.). This implementation is capable of evaluating a variety of matchups,
Elo rating updates, and win probabilities, all based on the basic Elo
rating system.
Author: Ethan Heinzen [aut, cre]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between elo versions 1.0.0 dated 2017-11-20 and 1.0.1 dated 2017-12-14
DESCRIPTION | 8 MD5 | 26 - NEWS.md | 8 R/RcppExports.R | 4 R/elo.model.frame.R | 13 R/elo.run.R | 2 R/internal.functions.R | 1 inst/doc/elo.html | 584 +++++++++------------------- man/elo.model.frame.Rd | 7 src/RcppExports.cpp | 9 src/asMatrix.cpp | 4 src/elo.cpp | 11 tests/testthat/test_elo.run.R | 6 tests/testthat/test_elo.run_regress_group.R | 24 - 14 files changed, 272 insertions(+), 435 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R
language objects, as well as a function 'hmac()' to create hash-based
message authentication code. Please note that this package is not meant to
be deployed for cryptographic purposes for which more comprehensive (and
widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang and Viliam Simko.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.12 dated 2017-01-27 and 0.6.13 dated 2017-12-14
ChangeLog | 34 ++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- R/digest.R | 30 +++++++++++++++++++----------- R/init.R |only build/vignette.rds |binary inst/doc/sha1.Rmd | 2 +- inst/doc/sha1.html | 52 ++++++++++++++++++++++++++-------------------------- man/digest.Rd | 27 ++++++++++++++++++++++----- src/aes.c | 10 +++++----- src/md5.c | 2 +- src/pmurhash.c | 2 +- src/sha1.c | 2 +- src/sha256.c | 2 +- vignettes/sha1.Rmd | 2 +- 15 files changed, 130 insertions(+), 70 deletions(-)
Title: Antares Results Processing
Description: Process results generated by Antares, a powerful software developed by
RTE to simulate and study electric power systems (more information about
Antares here: <https://antares.rte-france.com>). This package provides
functions to create new columns like net load, load factors, upward and
downward margins or to compute aggregated statistics like economic surpluses
of consumers, producers and sectors.
Author: Jalal-Edine ZAWAM [aut, cre],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Diff between antaresProcessing versions 0.12 dated 2017-12-07 and 0.13 dated 2017-12-14
antaresProcessing-0.12/antaresProcessing/man/thermalGeneration.Rd |only antaresProcessing-0.12/antaresProcessing/tests/testthat/test-thermalGeneration.R |only antaresProcessing-0.13/antaresProcessing/DESCRIPTION | 8 ++-- antaresProcessing-0.13/antaresProcessing/MD5 | 18 +++++----- antaresProcessing-0.13/antaresProcessing/NAMESPACE | 2 - antaresProcessing-0.13/antaresProcessing/NEWS | 4 ++ antaresProcessing-0.13/antaresProcessing/R/thermalGeneration.R | 6 +-- antaresProcessing-0.13/antaresProcessing/inst/doc/antaresProcessing.html | 4 +- antaresProcessing-0.13/antaresProcessing/man/thermalGroupCapacities.Rd |only antaresProcessing-0.13/antaresProcessing/tests/testthat/helper_init.R | 1 antaresProcessing-0.13/antaresProcessing/tests/testthat/test-h5_processing.R | 11 +++--- antaresProcessing-0.13/antaresProcessing/tests/testthat/test-thermalGroupCapacities.R |only 12 files changed, 30 insertions(+), 24 deletions(-)
More information about antaresProcessing at CRAN
Permanent link
Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.3.0 dated 2017-12-13 and 2.3.1 dated 2017-12-14
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- R/Bacon.R | 5 ++--- src/cal.h | 7 ++++--- src/hist2.cpp | 4 ++-- 5 files changed, 21 insertions(+), 21 deletions(-)
Title: Multilingual Stopword Lists
Description: Provides multiple sources of stopwords, for use in text analysis and natural language processing.
Author: Kenneth Benoit [aut],
David Muhr [aut, cre],
Kohei Watanabe [aut]
Maintainer: David Muhr <muhrdavid+github@gmail.com>
Diff between stopwords versions 0.1.0 dated 2017-11-12 and 0.9.0 dated 2017-12-14
stopwords-0.1.0/stopwords/data/stopwords.rda |only stopwords-0.9.0/stopwords/DESCRIPTION | 23 - stopwords-0.9.0/stopwords/MD5 | 34 + stopwords-0.9.0/stopwords/NAMESPACE | 5 stopwords-0.9.0/stopwords/NEWS | 10 stopwords-0.9.0/stopwords/R/data.r | 128 +++---- stopwords-0.9.0/stopwords/R/stopwords-options.R |only stopwords-0.9.0/stopwords/R/stopwords-package.R |only stopwords-0.9.0/stopwords/R/stopwords.R |only stopwords-0.9.0/stopwords/README.md | 179 +++++----- stopwords-0.9.0/stopwords/data/data_stopwords_misc.rda |only stopwords-0.9.0/stopwords/data/data_stopwords_smart.rda |only stopwords-0.9.0/stopwords/data/data_stopwords_snowball.rda |only stopwords-0.9.0/stopwords/data/data_stopwords_stopwordsiso.rda |only stopwords-0.9.0/stopwords/man/data_stopwords_misc.Rd |only stopwords-0.9.0/stopwords/man/data_stopwords_smart.Rd |only stopwords-0.9.0/stopwords/man/data_stopwords_snowball.Rd |only stopwords-0.9.0/stopwords/man/data_stopwords_stopwordsiso.Rd |only stopwords-0.9.0/stopwords/man/lookup_iso_639_1.Rd |only stopwords-0.9.0/stopwords/man/stopwords-package.Rd |only stopwords-0.9.0/stopwords/man/stopwords.Rd | 98 +---- stopwords-0.9.0/stopwords/man/stopwords_getlanguages.Rd |only stopwords-0.9.0/stopwords/man/stopwords_getsources.Rd |only stopwords-0.9.0/stopwords/man/stopwords_options.Rd |only stopwords-0.9.0/stopwords/tests |only 25 files changed, 245 insertions(+), 232 deletions(-)
Title: Recursive Partitioning for Structural Equation Models
Description: SEM Trees and SEM Forests -- an extension of model-based decision
trees and forests to Structural Equation Models (SEM). SEM trees hierarchically
split empirical data into homogeneous groups sharing similar data patterns
with respect to a SEM by recursively selecting optimal predictors of these
differences. SEM forests are an extension of SEM trees. They are ensembles of
SEM trees each built on a random sample of the original data. By aggregating
over a forest, we obtain measures of variable importance that are more robust
than measures from single trees.
Author: Andreas M. Brandmaier [aut, cre],
John J. Prindle [aut]
Maintainer: Andreas M. Brandmaier <andy@brandmaier.de>
Diff between semtree versions 0.9.10 dated 2017-04-05 and 0.9.11 dated 2017-12-14
semtree-0.9.10/semtree/man/toLatex.Rd |only semtree-0.9.11/semtree/DESCRIPTION | 22 semtree-0.9.11/semtree/MD5 | 48 - semtree-0.9.11/semtree/NAMESPACE | 50 - semtree-0.9.11/semtree/NEWS.md | 9 semtree-0.9.11/semtree/R/diversityMatrix.R |only semtree-0.9.11/semtree/R/evaluateDataLikelihood.R | 16 semtree-0.9.11/semtree/R/evaluateTreeConditional.R |only semtree-0.9.11/semtree/R/fitSubmodels.R | 62 + semtree-0.9.11/semtree/R/getExpectedCov.R |only semtree-0.9.11/semtree/R/getExpectedMean.R |only semtree-0.9.11/semtree/R/hellinger.R |only semtree-0.9.11/semtree/R/kl.R |only semtree-0.9.11/semtree/R/partialDependencePlot.R | 16 semtree-0.9.11/semtree/R/plot.diversityMatrix.R |only semtree-0.9.11/semtree/R/plot.semtree.R | 2 semtree-0.9.11/semtree/R/toLatex.R | 4 semtree-0.9.11/semtree/R/traverseConditional.R |only semtree-0.9.11/semtree/R/treeDivergence.R |only semtree-0.9.11/semtree/R/varimp.R | 345 ++++++---- semtree-0.9.11/semtree/README.md | 59 + semtree-0.9.11/semtree/demo/00Index | 2 semtree-0.9.11/semtree/demo/semforestLGCModelOpenMx.R | 6 semtree-0.9.11/semtree/demo/semforestLGCModellavaan.R |only semtree-0.9.11/semtree/demo/semtreeLGCModelOpenMxInvariance.R |only semtree-0.9.11/semtree/man/distances.Rd |only semtree-0.9.11/semtree/man/diversityMatrix.Rd |only semtree-0.9.11/semtree/man/semtree.Rd | 1 semtree-0.9.11/semtree/man/varimp.Rd | 8 semtree-0.9.11/semtree/tests/invariance.R |only semtree-0.9.11/semtree/tests/lavaan.R | 8 semtree-0.9.11/semtree/tests/tree.R | 3 semtree-0.9.11/semtree/tests/vim.R |only 33 files changed, 433 insertions(+), 228 deletions(-)
More information about PooledMeanGroup at CRAN
Permanent link
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 3.2.1 dated 2017-07-08 and 3.3.0 dated 2017-12-14
DESCRIPTION | 8 MD5 | 9 NAMESPACE | 2 R/CMplot.r | 919 +++++++++++++++++++++++++++++++++++--------------- R/zzz.R |only man/CMplot-package.Rd | 42 +- 6 files changed, 683 insertions(+), 297 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a preprint manuscript of Bourke et al. (2017) <doi:10.1101/228817>.
Author: Peter Bourke [aut, cre],
Geert van Geest [aut]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.0.11 dated 2017-12-05 and 1.0.12 dated 2017-12-14
DESCRIPTION | 13 MD5 | 28 R/exported_functions.R | 2125 ++++++++++++++++++------------------ inst/doc/Vignette_polymapR.html | 48 man/MDSMap_from_list.Rd | 6 man/cluster_per_LG.Rd | 2 man/createTetraOriginInput.Rd | 2 man/create_phased_maplist.Rd | 21 man/finish_linkage_analysis.Rd | 4 man/linkage.Rd | 2 man/marker_data_summary.Rd | 6 man/overviewSNlinks.Rd | 2 man/plot_map.Rd | 2 man/screen_for_duplicate_markers.Rd | 4 man/write.mct.Rd | 4 15 files changed, 1174 insertions(+), 1095 deletions(-)
Title: Permutation Based Non-Parametric Analysis of CRISPR Screen Data
Description: Permutation based
non-parametric analysis of CRISPR screen data. Details about this algorithm are published in the following paper published on BMC genomics, Jia et al. (2017) <doi:10.1186/s12864-017-3938-5>: A permutation-based non-parametric analysis of CRISPR screen data. Please cite this paper if you use this algorithm for your paper.
Author: Gaoxiang Jia [aut, cre]
Maintainer: Gaoxiang Jia <GJia@SMU.edu>
Diff between PBNPA versions 0.0.1 dated 2016-12-20 and 0.0.2 dated 2017-12-14
DESCRIPTION | 21 MD5 | 14 NAMESPACE | 8 R/PBNPA.R | 328 +++++------ inst/extdata/simdata_20per_off48.csv | 1001 ---------------------------------- inst/extdata/simdata_20per_off49.csv | 1002 ----------------------------------- inst/extdata/simdata_20per_off50.csv | 1001 ---------------------------------- man/PBNPA.Rd | 112 +-- 8 files changed, 232 insertions(+), 3255 deletions(-)
More information about childhoodmortality at CRAN
Permanent link
Title: Graph Edge Computations for Spatial Point Patterns
Description: Graphs (or networks) and graph component
calculations for spatial locations in 1D, 2D, 3D etc.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between spatgraphs versions 3.1-3 dated 2017-10-06 and 3.2-1 dated 2017-12-14
spatgraphs-3.1-3/spatgraphs/man/plot3.sg.Rd |only spatgraphs-3.1-3/spatgraphs/man/prune.sg.Rd |only spatgraphs-3.1-3/spatgraphs/man/spectral.sg.Rd |only spatgraphs-3.1-3/spatgraphs/man/weight.sg.Rd |only spatgraphs-3.2-1/spatgraphs/DESCRIPTION | 8 ++-- spatgraphs-3.2-1/spatgraphs/MD5 | 34 ++++++++++----------- spatgraphs-3.2-1/spatgraphs/NAMESPACE | 12 ++++--- spatgraphs-3.2-1/spatgraphs/R/adjacency_matrix.R | 17 +--------- spatgraphs-3.2-1/spatgraphs/R/class_sgc.R | 1 spatgraphs-3.2-1/spatgraphs/R/plot_sg.R | 4 +- spatgraphs-3.2-1/spatgraphs/R/prune_sg.R | 11 ++++++ spatgraphs-3.2-1/spatgraphs/R/set_weights.R | 4 +- spatgraphs-3.2-1/spatgraphs/R/spatgraph.R | 6 +-- spatgraphs-3.2-1/spatgraphs/R/spectral_sg.R | 9 +++-- spatgraphs-3.2-1/spatgraphs/man/plot.sgspectral.Rd | 2 - spatgraphs-3.2-1/spatgraphs/man/plot3_sg.Rd |only spatgraphs-3.2-1/spatgraphs/man/prune_sg.Rd |only spatgraphs-3.2-1/spatgraphs/man/spatgraph.Rd | 5 +-- spatgraphs-3.2-1/spatgraphs/man/spectral_sg.Rd |only spatgraphs-3.2-1/spatgraphs/man/weight_sg.Rd |only spatgraphs-3.2-1/spatgraphs/src/Graph.cpp | 2 - spatgraphs-3.2-1/spatgraphs/src/remove_nodes.cpp | 5 +-- 22 files changed, 61 insertions(+), 59 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz, Theo van Kraay
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.2.1 dated 2017-05-18 and 1.3.0 dated 2017-12-14
clickstream-1.2.1/clickstream/man/absorbingStates-methods.Rd |only clickstream-1.2.1/clickstream/man/hmPlot-methods.Rd |only clickstream-1.2.1/clickstream/man/predict-methods.Rd |only clickstream-1.2.1/clickstream/man/randomClicks-methods.Rd |only clickstream-1.2.1/clickstream/man/show-methods.Rd |only clickstream-1.2.1/clickstream/man/states-methods.Rd |only clickstream-1.2.1/clickstream/man/summary-methods.Rd |only clickstream-1.2.1/clickstream/man/transientStates-methods.Rd |only clickstream-1.3.0/clickstream/DESCRIPTION | 14 +- clickstream-1.3.0/clickstream/MD5 | 56 +++++--- clickstream-1.3.0/clickstream/NAMESPACE | 14 ++ clickstream-1.3.0/clickstream/NEWS | 12 + clickstream-1.3.0/clickstream/R/Clickstream.r | 10 + clickstream-1.3.0/clickstream/R/ClusterOptimization.r |only clickstream-1.3.0/clickstream/R/Evaluation.r |only clickstream-1.3.0/clickstream/R/Fitting.r | 5 clickstream-1.3.0/clickstream/R/MarkovChain.r | 63 ++++++---- clickstream-1.3.0/clickstream/R/Pattern.r | 41 +++++- clickstream-1.3.0/clickstream/R/clickstream-package.R | 8 - clickstream-1.3.0/clickstream/man/EvaluationResult-class.Rd |only clickstream-1.3.0/clickstream/man/EvaluationResult-method.Rd |only clickstream-1.3.0/clickstream/man/MarkovChain-class.Rd | 7 - clickstream-1.3.0/clickstream/man/MarkovChain-method.Rd |only clickstream-1.3.0/clickstream/man/Pattern-class.Rd | 6 clickstream-1.3.0/clickstream/man/Pattern-method.Rd |only clickstream-1.3.0/clickstream/man/absorbingStates-method.Rd |only clickstream-1.3.0/clickstream/man/chiSquareTest.Rd |only clickstream-1.3.0/clickstream/man/clickstream-package.Rd | 4 clickstream-1.3.0/clickstream/man/fitMarkovChains.Rd |only clickstream-1.3.0/clickstream/man/getConsensusClusters.Rd |only clickstream-1.3.0/clickstream/man/getConsensusClustersParallel.Rd |only clickstream-1.3.0/clickstream/man/getOptimalMarkovChain.Rd |only clickstream-1.3.0/clickstream/man/hmPlot-method.Rd |only clickstream-1.3.0/clickstream/man/initialize-method.Rd |only clickstream-1.3.0/clickstream/man/mcEvaluate.Rd |only clickstream-1.3.0/clickstream/man/mcEvaluateAll.Rd |only clickstream-1.3.0/clickstream/man/mcEvaluateAllClusters.Rd |only clickstream-1.3.0/clickstream/man/plot-method.Rd |only clickstream-1.3.0/clickstream/man/plus-method.Rd |only clickstream-1.3.0/clickstream/man/predict-method.Rd |only clickstream-1.3.0/clickstream/man/randomClicks-method.Rd |only clickstream-1.3.0/clickstream/man/readClickstreams.Rd | 2 clickstream-1.3.0/clickstream/man/states-method.Rd |only clickstream-1.3.0/clickstream/man/summary-method.Rd |only clickstream-1.3.0/clickstream/man/transientStates-method.Rd |only 45 files changed, 168 insertions(+), 74 deletions(-)