Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.6.7 dated 2017-12-10 and 3.7.0 dated 2018-01-05
lessR-3.6.7/lessR/R/details.brief.R |only lessR-3.7.0/lessR/DESCRIPTION | 10 - lessR-3.7.0/lessR/MD5 | 84 ++++++------ lessR-3.7.0/lessR/NAMESPACE | 8 - lessR-3.7.0/lessR/NEWS | 57 ++++++++ lessR-3.7.0/lessR/R/BoxPlot.R | 23 --- lessR-3.7.0/lessR/R/Histogram.R | 6 lessR-3.7.0/lessR/R/Plot.R | 2 lessR-3.7.0/lessR/R/Read.R | 156 ++++++++++++----------- lessR-3.7.0/lessR/R/Sort.R | 4 lessR-3.7.0/lessR/R/VariableLabels.R | 186 +++++++++++++--------------- lessR-3.7.0/lessR/R/bar.zlattice.R | 3 lessR-3.7.0/lessR/R/bc.zmain.R | 84 +++++++----- lessR-3.7.0/lessR/R/bx.R | 2 lessR-3.7.0/lessR/R/db.R |only lessR-3.7.0/lessR/R/details.R | 31 ++-- lessR-3.7.0/lessR/R/dn.zmain.R | 1 lessR-3.7.0/lessR/R/hst.zmain.R | 1 lessR-3.7.0/lessR/R/pc.zmain.R | 21 ++- lessR-3.7.0/lessR/R/plt.zVBS.R | 36 +++-- lessR-3.7.0/lessR/R/plt.ztxt.R | 5 lessR-3.7.0/lessR/R/reg.z5Plot.R | 11 + lessR-3.7.0/lessR/R/zzz.R | 96 +++++++++----- lessR-3.7.0/lessR/data/dataCars93.rda |binary lessR-3.7.0/lessR/data/dataEmployee.rda |binary lessR-3.7.0/lessR/data/dataEmployee_lbl.rda |only lessR-3.7.0/lessR/data/dataJackets.rda |binary lessR-3.7.0/lessR/data/dataLearn.rda |binary lessR-3.7.0/lessR/data/dataMach4.rda |binary lessR-3.7.0/lessR/data/dataMach4_lbl.rda |only lessR-3.7.0/lessR/data/dataStockPrice.rda |binary lessR-3.7.0/lessR/man/BarChart.Rd | 29 +--- lessR-3.7.0/lessR/man/Plot.Rd | 28 ++-- lessR-3.7.0/lessR/man/Read.Rd | 46 ++---- lessR-3.7.0/lessR/man/Recode.Rd | 1 lessR-3.7.0/lessR/man/Regression.Rd | 64 +++++---- lessR-3.7.0/lessR/man/Transform.Rd | 6 lessR-3.7.0/lessR/man/VariableLabels.Rd | 52 ++++--- lessR-3.7.0/lessR/man/corCFA.Rd | 2 lessR-3.7.0/lessR/man/dataEmployee_lbl.Rd |only lessR-3.7.0/lessR/man/dataMach4.Rd | 25 --- lessR-3.7.0/lessR/man/dataMach4_lbl.Rd |only lessR-3.7.0/lessR/man/dataStockPrice.Rd | 4 lessR-3.7.0/lessR/man/details.Rd | 8 - lessR-3.7.0/lessR/man/label.Rd | 18 +- lessR-3.7.0/lessR/man/xRow.Rd | 2 46 files changed, 617 insertions(+), 495 deletions(-)
Title: Financial Market Building Blocks
Description: Implements basic financial market objects like currencies, currency
pairs, interest rates and interest rate indices. You will be able to use
Benchmark instances of these objects which have been defined using their most
common conventions or those defined by International Swap Dealer Association
(ISDA, <https://www.isda.org>) legal documentation.
Author: Imanuel Costigan [aut, cre]
Maintainer: Imanuel Costigan <i.costigan@me.com>
Diff between fmbasics versions 0.2.0 dated 2017-04-30 and 0.3.0 dated 2018-01-05
fmbasics-0.2.0/fmbasics/R/zero-curve.R |only fmbasics-0.2.0/fmbasics/man/fmdata_example.Rd |only fmbasics-0.3.0/fmbasics/DESCRIPTION | 29 +-- fmbasics-0.3.0/fmbasics/MD5 | 80 ++++---- fmbasics-0.3.0/fmbasics/NAMESPACE | 27 ++ fmbasics-0.3.0/fmbasics/NEWS | 18 + fmbasics-0.3.0/fmbasics/R/cash-flow-class.R |only fmbasics-0.3.0/fmbasics/R/currency-class.R | 53 +---- fmbasics-0.3.0/fmbasics/R/currency-pair-class.R | 55 +++-- fmbasics-0.3.0/fmbasics/R/generic-methods.R |only fmbasics-0.3.0/fmbasics/R/indices-class.R | 135 +++++--------- fmbasics-0.3.0/fmbasics/R/interest-rate-classes.R | 54 ++++- fmbasics-0.3.0/fmbasics/R/interest-rate-ops.R | 29 +-- fmbasics-0.3.0/fmbasics/R/money-class.R |only fmbasics-0.3.0/fmbasics/R/utils.R | 40 +--- fmbasics-0.3.0/fmbasics/R/zero-curve-class.R |only fmbasics-0.3.0/fmbasics/README.md | 44 ++-- fmbasics-0.3.0/fmbasics/build/vignette.rds |binary fmbasics-0.3.0/fmbasics/inst/README-unnamed-chunk-7-1.png |binary fmbasics-0.3.0/fmbasics/inst/doc/basics.html | 24 +- fmbasics-0.3.0/fmbasics/inst/doc/rates.R | 12 - fmbasics-0.3.0/fmbasics/inst/doc/rates.Rmd | 22 -- fmbasics-0.3.0/fmbasics/inst/doc/rates.html | 39 +--- fmbasics-0.3.0/fmbasics/man/CashFlow.Rd |only fmbasics-0.3.0/fmbasics/man/CurrencyPairMethods.Rd | 5 fmbasics-0.3.0/fmbasics/man/DiscountFactor-operators.Rd | 2 fmbasics-0.3.0/fmbasics/man/DiscountFactor.Rd | 3 fmbasics-0.3.0/fmbasics/man/InterestRate-operators.Rd | 2 fmbasics-0.3.0/fmbasics/man/Interpolation.Rd | 2 fmbasics-0.3.0/fmbasics/man/MultiCurrencyMoney.Rd |only fmbasics-0.3.0/fmbasics/man/SingleCurrencyMoney.Rd |only fmbasics-0.3.0/fmbasics/man/ZeroCurve.Rd | 10 - fmbasics-0.3.0/fmbasics/man/as_tibble.ZeroCurve.Rd | 2 fmbasics-0.3.0/fmbasics/man/build_zero_curve.Rd | 6 fmbasics-0.3.0/fmbasics/man/indexshifters.Rd | 2 fmbasics-0.3.0/fmbasics/man/interpolate.Rd | 7 fmbasics-0.3.0/fmbasics/man/interpolate.ZeroCurve.Rd | 13 - fmbasics-0.3.0/fmbasics/man/interpolate_dfs.Rd |only fmbasics-0.3.0/fmbasics/man/interpolate_zeros.Rd |only fmbasics-0.3.0/fmbasics/man/is.CashFlow.Rd |only fmbasics-0.3.0/fmbasics/man/is.CurrencyPair.Rd |only fmbasics-0.3.0/fmbasics/man/is.Interpolation.Rd | 2 fmbasics-0.3.0/fmbasics/man/is.MultiCurrencyMoney.Rd |only fmbasics-0.3.0/fmbasics/man/is.SingleCurrencyMoney.Rd |only fmbasics-0.3.0/fmbasics/man/is.ZeroCurve.Rd |only fmbasics-0.3.0/fmbasics/man/iso.Rd | 22 +- fmbasics-0.3.0/fmbasics/tests/testthat/test-cash-flows.R |only fmbasics-0.3.0/fmbasics/tests/testthat/test-interpolate.R | 17 + fmbasics-0.3.0/fmbasics/tests/testthat/test-money.R |only fmbasics-0.3.0/fmbasics/vignettes/rates.Rmd | 22 -- 50 files changed, 384 insertions(+), 394 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.4-0 dated 2017-11-20 and 1.4-1 dated 2018-01-05
DESCRIPTION | 8 MD5 | 41 +-- NAMESPACE | 12 - NEWS | 37 ++- R/compare.syn.r | 124 +++++----- R/functions.syn.r | 8 R/methods.syn.r | 368 ++++++++++++++++++------------ R/syn.r | 11 R/utility.syn.r | 559 ++++++++++++++++++++++++++++------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/inference.pdf |binary inst/doc/synthpop.pdf |binary man/glm.synds.Rd | 7 man/multi.compare.Rd | 8 man/multinom.synds.Rd |only man/summary.fit.synds.Rd | 2 man/syn.Rd | 2 man/syn.cart.Rd | 4 man/synthpop-package.Rd | 4 man/utility.gen.Rd | 112 +++++---- man/utility.tab.Rd | 11 22 files changed, 784 insertions(+), 534 deletions(-)
Title: Processing Data for Quantitative Language Comparison (QLC)
Description: This is a collection of functions to read, recode, and transcode data for QLC.
Author: Michael Cysouw
Maintainer: Michael Cysouw <cysouw@mac.com>
Diff between qlcData versions 0.2.0 dated 2018-01-02 and 0.2.1 dated 2018-01-05
DESCRIPTION | 8 - MD5 | 16 +-- R/tokenize.R | 9 +- inst/doc/orthography_processing.R | 2 inst/doc/orthography_processing.Rmd | 6 - inst/doc/orthography_processing.html | 156 +++++++++++++++++------------------ inst/doc/recoding_nominal_data.html | 8 - man/qlcData-package.Rd | 4 vignettes/orthography_processing.Rmd | 6 - 9 files changed, 110 insertions(+), 105 deletions(-)
Title: Kernel for 'Jupyter'
Description: Provides a full implementation of the 'Jupyter' <http://jupyter.org/> messaging protocol in C++ by leveraging 'Rcpp' and 'Xeus' <https://github.com/QuantStack/xeus>.
'Jupyter' supplies an interactive computing environment and a messaging protocol defined over 'ZeroMQ' for multiple programming languages. This package implements
the 'Jupyter' kernel interface so that 'R' is exposed to this interactive computing environment. 'ZeroMQ' functionality is provided by the 'pbdZMQ' package.
'Xeus' is a C++ library that facilitates the implementation of kernels for 'Jupyter'. Additionally, 'Xeus' provides an interface to libraries that exist in the 'Jupyter' ecosystem for building widgets,
plotting, and more <https://blog.jupyter.org/interactive-workflows-for-c-with-jupyter-fe9b54227d92>. 'JuniperKernel' uses 'Xeus' as a library for the 'Jupyter' messaging protocol.
Author: Spencer Aiello [aut, cre, cph],
Wei-Chen Chen [ctb],
Stephan Brumme [cph],
Jake Luciani [cph],
Tony Plate [cph],
Matthieu Decorde [cph],
RStudio (Hadley Wickham) [cph],
Sylvain Corlay [cph],
Johan Mabille [cph],
Niels Lohmann [cph]
Maintainer: Spencer Aiello <spnrpa@gmail.com>
Diff between JuniperKernel versions 1.2.0.0 dated 2018-01-04 and 1.2.1.0 dated 2018-01-05
JuniperKernel-1.2.0.0/JuniperKernel/tests |only JuniperKernel-1.2.1.0/JuniperKernel/DESCRIPTION | 8 +++---- JuniperKernel-1.2.1.0/JuniperKernel/MD5 | 11 ++++++---- JuniperKernel-1.2.1.0/JuniperKernel/NEWS.md | 9 ++++++++ JuniperKernel-1.2.1.0/JuniperKernel/configure | 8 +++++-- JuniperKernel-1.2.1.0/JuniperKernel/inst/include/zmq.h |only JuniperKernel-1.2.1.0/JuniperKernel/inst/include/zmq.hpp |only JuniperKernel-1.2.1.0/JuniperKernel/inst/include/zmq_addon.hpp |only JuniperKernel-1.2.1.0/JuniperKernel/inst/include/zmq_utils.h |only 9 files changed, 26 insertions(+), 10 deletions(-)
Title: Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance 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 0.1.3 dated 2017-05-23 and 0.2.0 dated 2018-01-05
metacoder-0.1.3/metacoder/R/extract_taxonomy--internal.R |only metacoder-0.1.3/metacoder/R/extract_taxonomy--parsers.R |only metacoder-0.1.3/metacoder/R/extract_taxonomy--wrappers.R |only metacoder-0.1.3/metacoder/R/extract_taxonomy.R |only metacoder-0.1.3/metacoder/R/in_silico_pcr.R |only metacoder-0.1.3/metacoder/R/metacoder-package.r |only metacoder-0.1.3/metacoder/R/old_code.R |only metacoder-0.1.3/metacoder/R/plot_alignment.R |only metacoder-0.1.3/metacoder/R/reading_files.R |only metacoder-0.1.3/metacoder/R/taxmap--arrange.R |only metacoder-0.1.3/metacoder/R/taxmap--class.R |only metacoder-0.1.3/metacoder/R/taxmap--column_generators.R |only metacoder-0.1.3/metacoder/R/taxmap--filter.R |only metacoder-0.1.3/metacoder/R/taxmap--internal.R |only metacoder-0.1.3/metacoder/R/taxmap--mutate.R |only metacoder-0.1.3/metacoder/R/taxmap--sample.R |only metacoder-0.1.3/metacoder/R/taxmap--select.R |only metacoder-0.1.3/metacoder/R/taxmap--utilities.R |only metacoder-0.1.3/metacoder/R/taxonomic_sample.R |only metacoder-0.1.3/metacoder/R/taxonomy.R |only metacoder-0.1.3/metacoder/data/bryophytes_ex_data.rda |only metacoder-0.1.3/metacoder/data/contaminants.rda |only metacoder-0.1.3/metacoder/data/genbank_ex_data.rda |only metacoder-0.1.3/metacoder/data/its1_ex_data.rda |only metacoder-0.1.3/metacoder/data/pr2_ex_data.rda |only metacoder-0.1.3/metacoder/data/rdp_ex_data.rda |only metacoder-0.1.3/metacoder/data/silva_ex_data.rda |only metacoder-0.1.3/metacoder/data/unite_ex_data_1.rda |only metacoder-0.1.3/metacoder/data/unite_ex_data_2.rda |only metacoder-0.1.3/metacoder/data/unite_ex_data_3.rda |only metacoder-0.1.3/metacoder/inst/extdata/its1_chytridiomycota_hmm.fasta |only metacoder-0.1.3/metacoder/inst/extdata/mothur_16S_training_subset.fasta.gz |only metacoder-0.1.3/metacoder/inst/extdata/ncbi_basidiomycetes.fasta |only metacoder-0.1.3/metacoder/inst/extdata/pr2_stramenopiles_gb203.fasta |only metacoder-0.1.3/metacoder/inst/extdata/rdp_current_Archaea_unaligned.fa |only metacoder-0.1.3/metacoder/inst/extdata/silva_nr99.fasta |only metacoder-0.1.3/metacoder/inst/extdata/unite_general_release.fasta |only metacoder-0.1.3/metacoder/man/arrange_obs.Rd |only metacoder-0.1.3/metacoder/man/arrange_taxa.Rd |only metacoder-0.1.3/metacoder/man/bryophytes_ex_data.Rd |only metacoder-0.1.3/metacoder/man/class_from_class.Rd |only metacoder-0.1.3/metacoder/man/class_from_name.Rd |only metacoder-0.1.3/metacoder/man/class_from_obs_id.Rd |only metacoder-0.1.3/metacoder/man/class_from_taxon_id.Rd |only metacoder-0.1.3/metacoder/man/class_to_taxonomy.Rd |only metacoder-0.1.3/metacoder/man/contaminants.Rd |only metacoder-0.1.3/metacoder/man/convert_numeric_cols.Rd |only metacoder-0.1.3/metacoder/man/count_capture_groups.Rd |only metacoder-0.1.3/metacoder/man/delete_vetices_and_children.Rd |only metacoder-0.1.3/metacoder/man/drawDetails.resizingTextGrob.Rd |only metacoder-0.1.3/metacoder/man/extract_taxonomy.Rd |only metacoder-0.1.3/metacoder/man/filter_obs.Rd |only metacoder-0.1.3/metacoder/man/filter_taxa.Rd |only metacoder-0.1.3/metacoder/man/format_taxon_subset.Rd |only metacoder-0.1.3/metacoder/man/genbank_ex_data.Rd |only metacoder-0.1.3/metacoder/man/get_id_from_name.Rd |only metacoder-0.1.3/metacoder/man/get_name_from_id.Rd |only metacoder-0.1.3/metacoder/man/hierarchies.Rd |only metacoder-0.1.3/metacoder/man/its1_ex_data.Rd |only metacoder-0.1.3/metacoder/man/make_new_ids.Rd |only metacoder-0.1.3/metacoder/man/make_text_grobs.Rd |only metacoder-0.1.3/metacoder/man/mutate_obs.Rd |only metacoder-0.1.3/metacoder/man/mutate_taxa.Rd |only metacoder-0.1.3/metacoder/man/n_obs.Rd |only metacoder-0.1.3/metacoder/man/n_obs_1.Rd |only metacoder-0.1.3/metacoder/man/n_subtaxa.Rd |only metacoder-0.1.3/metacoder/man/n_subtaxa_1.Rd |only metacoder-0.1.3/metacoder/man/n_supertaxa.Rd |only metacoder-0.1.3/metacoder/man/obs.Rd |only metacoder-0.1.3/metacoder/man/obs_data.Rd |only metacoder-0.1.3/metacoder/man/obs_data_colnames.Rd |only metacoder-0.1.3/metacoder/man/obs_data_cols_used.Rd |only metacoder-0.1.3/metacoder/man/parse_hmp_qiime.Rd |only metacoder-0.1.3/metacoder/man/parse_mothur_summary.Rd |only metacoder-0.1.3/metacoder/man/parse_taxonomy_table.Rd |only metacoder-0.1.3/metacoder/man/plot_alignment.Rd |only metacoder-0.1.3/metacoder/man/postDrawDetails.resizingTextGrob.Rd |only metacoder-0.1.3/metacoder/man/pr2_ex_data.Rd |only metacoder-0.1.3/metacoder/man/preDrawDetails.resizingTextGrob.Rd |only metacoder-0.1.3/metacoder/man/print.taxmap.Rd |only metacoder-0.1.3/metacoder/man/rdp_ex_data.Rd |only metacoder-0.1.3/metacoder/man/recursive_sample.Rd |only metacoder-0.1.3/metacoder/man/remove_redundant_names.Rd |only metacoder-0.1.3/metacoder/man/rename_duplicated.Rd |only metacoder-0.1.3/metacoder/man/resizingTextGrob.Rd |only metacoder-0.1.3/metacoder/man/roots.Rd |only metacoder-0.1.3/metacoder/man/sample_frac_obs.Rd |only metacoder-0.1.3/metacoder/man/sample_frac_taxa.Rd |only metacoder-0.1.3/metacoder/man/sample_n_obs.Rd |only metacoder-0.1.3/metacoder/man/sample_n_taxa.Rd |only metacoder-0.1.3/metacoder/man/select_obs.Rd |only metacoder-0.1.3/metacoder/man/select_taxa.Rd |only metacoder-0.1.3/metacoder/man/silva_ex_data.Rd |only metacoder-0.1.3/metacoder/man/split_class_list.Rd |only metacoder-0.1.3/metacoder/man/subtaxa.Rd |only metacoder-0.1.3/metacoder/man/supertaxa.Rd |only metacoder-0.1.3/metacoder/man/taxmap.Rd |only metacoder-0.1.3/metacoder/man/taxon_data.Rd |only metacoder-0.1.3/metacoder/man/taxon_data_colnames.Rd |only metacoder-0.1.3/metacoder/man/taxon_data_cols_used.Rd |only metacoder-0.1.3/metacoder/man/taxonomic_sample.Rd |only metacoder-0.1.3/metacoder/man/taxonomy_ranks.Rd |only metacoder-0.1.3/metacoder/man/transmute_obs.Rd |only metacoder-0.1.3/metacoder/man/transmute_taxa.Rd |only metacoder-0.1.3/metacoder/man/unite_ex_data_1.Rd |only metacoder-0.1.3/metacoder/man/unite_ex_data_2.Rd |only metacoder-0.1.3/metacoder/man/unite_ex_data_3.Rd |only metacoder-0.1.3/metacoder/man/validate_regex_key_pair.Rd |only metacoder-0.1.3/metacoder/man/validate_regex_match.Rd |only metacoder-0.1.3/metacoder/man/vigilant_report.Rd |only metacoder-0.1.3/metacoder/tests/testthat/test--extract_taxonomy.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap--arrange.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap--filter.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap--mutate.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap--sample.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap--select.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap--utilities.R |only metacoder-0.1.3/metacoder/tests/testthat/test--taxmap.R |only metacoder-0.2.0/metacoder/DESCRIPTION | 26 metacoder-0.2.0/metacoder/MD5 | 275 ++-- metacoder-0.2.0/metacoder/NAMESPACE | 78 - metacoder-0.2.0/metacoder/NEWS.md | 38 metacoder-0.2.0/metacoder/R/RcppExports.R |only metacoder-0.2.0/metacoder/R/calculations--internal.R |only metacoder-0.2.0/metacoder/R/calculations.R |only metacoder-0.2.0/metacoder/R/dataset_documentation.R | 260 ---- metacoder-0.2.0/metacoder/R/heat_tree--internal.R | 87 + metacoder-0.2.0/metacoder/R/heat_tree--legend.R | 25 metacoder-0.2.0/metacoder/R/heat_tree--resizing_text.R | 157 -- metacoder-0.2.0/metacoder/R/heat_tree--shape_generators.R | 2 metacoder-0.2.0/metacoder/R/heat_tree--vertex_size.R | 4 metacoder-0.2.0/metacoder/R/heat_tree.R | 424 +++++-- metacoder-0.2.0/metacoder/R/heat_tree_matrix.R |only metacoder-0.2.0/metacoder/R/internal.R | 180 +++ metacoder-0.2.0/metacoder/R/metacoder-package.R |only metacoder-0.2.0/metacoder/R/mothur.R | 59 - metacoder-0.2.0/metacoder/R/option_parsers.R |only metacoder-0.2.0/metacoder/R/parsers.R |only metacoder-0.2.0/metacoder/R/primersearch.R |only metacoder-0.2.0/metacoder/R/read_fasta.R |only metacoder-0.2.0/metacoder/R/remove_ambiguous.R |only metacoder-0.2.0/metacoder/R/sequence_download.R | 72 - metacoder-0.2.0/metacoder/R/tools.R |only metacoder-0.2.0/metacoder/R/writers.R |only metacoder-0.2.0/metacoder/README.md | 515 ++++++++- metacoder-0.2.0/metacoder/build/vignette.rds |binary metacoder-0.2.0/metacoder/data/hmp_otus.rda |only metacoder-0.2.0/metacoder/data/hmp_samples.rda |only metacoder-0.2.0/metacoder/inst/doc/introduction.R | 146 +- metacoder-0.2.0/metacoder/inst/doc/introduction.Rmd | 296 +++-- metacoder-0.2.0/metacoder/inst/doc/introduction.html | 555 +++++++--- metacoder-0.2.0/metacoder/inst/extdata/silva_subset.fa |only metacoder-0.2.0/metacoder/man/ambiguous_patterns.Rd |only metacoder-0.2.0/metacoder/man/calc_n_samples.Rd |only metacoder-0.2.0/metacoder/man/calc_obs_props.Rd |only metacoder-0.2.0/metacoder/man/calc_taxon_abund.Rd |only metacoder-0.2.0/metacoder/man/check_for_pkg.Rd |only metacoder-0.2.0/metacoder/man/compare_groups.Rd |only metacoder-0.2.0/metacoder/man/complement.Rd |only metacoder-0.2.0/metacoder/man/convert_base.Rd |only metacoder-0.2.0/metacoder/man/do_calc_on_num_cols.Rd |only metacoder-0.2.0/metacoder/man/edge_list_depth.Rd | 2 metacoder-0.2.0/metacoder/man/fasta_headers.Rd | 2 metacoder-0.2.0/metacoder/man/figures |only metacoder-0.2.0/metacoder/man/filter_ambiguous_taxa.Rd |only metacoder-0.2.0/metacoder/man/get_class_from_el.Rd | 2 metacoder-0.2.0/metacoder/man/get_numeric_cols.Rd |only metacoder-0.2.0/metacoder/man/get_optimal_range.Rd | 4 metacoder-0.2.0/metacoder/man/get_taxmap_cols.Rd |only metacoder-0.2.0/metacoder/man/get_taxmap_data.Rd |only metacoder-0.2.0/metacoder/man/get_taxmap_other_cols.Rd |only metacoder-0.2.0/metacoder/man/get_taxmap_table.Rd |only metacoder-0.2.0/metacoder/man/get_taxonomy_levels.Rd | 2 metacoder-0.2.0/metacoder/man/heat_tree.Rd | 136 ++ metacoder-0.2.0/metacoder/man/heat_tree_matrix.Rd |only 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metacoder-0.2.0/metacoder/man/parse_seq_input.Rd |only metacoder-0.2.0/metacoder/man/parse_silva_fasta.Rd |only metacoder-0.2.0/metacoder/man/parse_summary_seqs.Rd | 2 metacoder-0.2.0/metacoder/man/parse_unite_general.Rd |only metacoder-0.2.0/metacoder/man/polygon_coords.Rd | 2 metacoder-0.2.0/metacoder/man/primersearch.Rd | 158 ++ metacoder-0.2.0/metacoder/man/primersearch_is_installed.Rd | 2 metacoder-0.2.0/metacoder/man/rarefy_obs.Rd |only metacoder-0.2.0/metacoder/man/read_fasta.Rd | 25 metacoder-0.2.0/metacoder/man/read_lines_apply.Rd | 2 metacoder-0.2.0/metacoder/man/rev_comp.Rd |only metacoder-0.2.0/metacoder/man/reverse.Rd |only metacoder-0.2.0/metacoder/man/run_primersearch.Rd | 12 metacoder-0.2.0/metacoder/man/split_by_level.Rd | 2 metacoder-0.2.0/metacoder/man/transform_data.Rd | 2 metacoder-0.2.0/metacoder/man/verify_taxmap.Rd |only metacoder-0.2.0/metacoder/man/write_greengenes.Rd |only metacoder-0.2.0/metacoder/man/write_mothur_taxonomy.Rd |only metacoder-0.2.0/metacoder/man/write_rdp.Rd |only metacoder-0.2.0/metacoder/man/write_silva_fasta.Rd |only metacoder-0.2.0/metacoder/man/write_unite_general.Rd |only metacoder-0.2.0/metacoder/man/zero_low_counts.Rd |only metacoder-0.2.0/metacoder/src |only metacoder-0.2.0/metacoder/tests/testthat/Rplots.pdf |binary metacoder-0.2.0/metacoder/tests/testthat/example_data |only metacoder-0.2.0/metacoder/tests/testthat/test--calculations.R |only metacoder-0.2.0/metacoder/tests/testthat/test--heat_tree.R | 34 metacoder-0.2.0/metacoder/tests/testthat/test--parsers_and_writers.R |only metacoder-0.2.0/metacoder/tests/testthat/test--simulated_pcr.R |only metacoder-0.2.0/metacoder/vignettes/introduction.Rmd | 296 +++-- 223 files changed, 2639 insertions(+), 1397 deletions(-)
Title: False Discovery Rate Procedures Under Discrete and Heterogeneous
Null Distributions
Description: It is known that current false discovery rate (FDR) procedures can be very conservative when applied to multiple testing in the discrete paradigm where p-values (and test statistics) have discrete and heterogeneous null distributions. This package implements more powerful weighted or adaptive FDR procedures for FDR control and estimation in the discrete paradigm. The package takes in the original data set rather than just the p-values in order to carry out the adjustments for discreteness and heterogeneity of p-value distributions. The package implements methods for two types of test statistics and their p-values: (a) binomial test on if two independent Poisson distributions have the same means, (b) Fisher's exact test on if the conditional distribution is the same as the marginal distribution for two binomial distributions, or on if two independent binomial distributions have the same probabilities of success.
Author: Xiongzhi Chen and Rebecca W. Doerge <rwdoerge@andrew.cmu.edu>
Maintainer: Xiongzhi Chen <xiongzhi.chen@wsu.edu>
Diff between fdrDiscreteNull versions 1.2 dated 2017-10-10 and 1.3 dated 2018-01-05
DESCRIPTION | 10 MD5 | 14 - NAMESPACE | 3 R/Generalized_FDR_Estimators.r | 90 ++++--- R/MultipleTesting_HeteroDist.r | 95 ++----- R/MultipleTesting_HeteroDist_ModFuncs.r | 388 +++++++++++++++++--------------- man/GeneralizedEstimatorsGrouped.Rd | 31 +- man/GeneralizedFDREstimators.Rd | 22 + 8 files changed, 346 insertions(+), 307 deletions(-)
More information about fdrDiscreteNull at CRAN
Permanent link
Title: Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
Description: Contains various routines for drawing
ellipses and ellipse-like confidence regions, implementing the plots
described in Murdoch and Chow (1996), A graphical display of large
correlation matrices, The American Statistician 50, 178-180. There are
also routines implementing the profile plots described in Bates and
Watts (1988), Nonlinear Regression Analysis and its Applications.
Author: Duncan Murdoch <murdoch@stats.uwo.ca> and E. D. Chow
(porting to R by Jesus M. Frias Celayeta <iosu@bureau.ucc.ie>)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between ellipse versions 0.3-8 dated 2013-04-13 and 0.4.1 dated 2018-01-05
DESCRIPTION | 28 +++---- MD5 | 15 ++-- NAMESPACE | 9 ++ R/pairs.profile.R | 21 +++++ README | 9 ++ man/ellipse.profile.nls.Rd | 5 - man/pairs.Rd |only man/pairs.profile.Rd | 30 +++++++- man/plotcorr.Rd | 165 ++++++++++++++++++++++----------------------- 9 files changed, 174 insertions(+), 108 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi.org/10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Luedeling and Gassner (2012) <doi.org/10.1016/j.agrformet.2011.10.020>).
As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses. Since version 0.70, 'chillR' contains a function for interpolating
hourly temperature records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.70.0 dated 2018-01-04 and 0.70.1 dated 2018-01-05
DESCRIPTION | 17 ++++++++++------- MD5 | 10 +++++----- R/chillR-package.R | 30 ++++++++++++++++++------------ R/handle_cimis.R | 11 ++++++++++- inst/doc/hourly_temperatures.html | 4 ++-- man/chillR-package.Rd | 30 ++++++++++++++++++------------ 6 files changed, 63 insertions(+), 39 deletions(-)
Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly minimizing the negative log likelihood function using the gradient descent algorithm. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu, Ana-Maria Staicu, Eric Laber
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>
Diff between ziphsmm versions 1.0.8 dated 2017-10-23 and 2.0.1 dated 2018-01-05
DESCRIPTION | 8 MD5 | 44 + NAMESPACE | 5 R/RcppExports.R | 40 + R/data.R | 4 R/dist_learn.R | 709 ++++++++++++++++++++--------- R/dist_learn2.R | 820 +++++++++++++++++++++++++--------- R/hmmsmooth.cont.R |only R/hmmsmooth.cont2.R |only R/hmmviterbi.cont.R | 2 R/hsmmfit_exp.R |only R/hsmmsim2.R | 3 R/hsmmsim2_exp.R |only R/hsmmviterbi_exp.R |only R/package.R | 4 man/CAT.Rd | 4 man/dist_learn.Rd | 80 ++- man/dist_learn2.Rd | 86 ++- man/hmmsmooth.cont.Rd |only man/hmmsmooth.cont2.Rd |only man/hmmviterbi.cont.Rd | 4 man/hsmmfit_exp.Rd |only man/hsmmsim2.Rd | 3 man/hsmmsim2_exp.Rd |only man/hsmmviterbi_exp.Rd |only man/package-ziphsmm.Rd | 4 src/RcppExports.cpp | 189 +++++++ src/rcpparma_hello_world.cpp | 1031 ++++++++++++++++++++++++++++++++++++++++++- 28 files changed, 2530 insertions(+), 510 deletions(-)
Title: Constrained Triangulation for Simple Features
Description: Build a constrained 'Delaunay' triangulation from simple features
objects, applying constraints based on input line segments, and triangle
properties including maximum area, minimum internal angle.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between sfdct versions 0.0.4 dated 2017-08-29 and 0.0.5 dated 2018-01-05
DESCRIPTION | 12 - MD5 | 15 - NEWS.md | 4 README.md | 22 - build/vignette.rds |binary inst/doc/sfdct.html | 452 ++++++++++++----------------------------- inst/examples |only tests/testthat/test-basic-ct.R | 14 - 8 files changed, 180 insertions(+), 339 deletions(-)
Title: Tidy Data Validation Reports
Description: Tools for creating data validation pipelines and tidy reports. This
package offers a framework for exploring and validating data frame like
objects using 'dplyr' grammar of data manipulation.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between ruler versions 0.1.0 dated 2017-11-26 and 0.1.1 dated 2018-01-05
DESCRIPTION | 6 +- MD5 | 22 +++++----- NEWS.md | 4 + R/actions.R | 2 README.md | 66 +++++++++++++++++-------------- build/vignette.rds |binary inst/doc/design-and-format.html | 4 - inst/doc/rule-packs.html | 43 +++++++++----------- inst/doc/validation.html | 76 ++++++++++++++++++------------------ man/act_after_exposure.Rd | 2 tests/testthat/helper-expose-data.R | 6 +- tests/testthat/test-exposure.R | 65 +++++++++++++++++++++++++++--- 12 files changed, 177 insertions(+), 119 deletions(-)
Title: Estimation and Inference in Random Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agents do not pay full attention to all available choices, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures documented in Cattaneo, Ma, Masatlioglu and Suleymanov (2017) <arXiv:1712.03448>, which utilizes standard choice data to partially identify and estimate decision maker's preference. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <xinweima@umich.edu>
Diff between ramchoice versions 0.1 dated 2017-11-20 and 0.2 dated 2018-01-05
DESCRIPTION | 8 MD5 | 20 - R/rAtte.R | 598 +++++++++++++++++++++++++++++++++-------------- R/rAtte_fun.R | 35 +- R/ramchoice-package.R | 6 R/ramdata.R | 4 man/genMat.Rd | 11 man/rAtte.Rd | 40 +-- man/ramchoice-package.Rd | 6 man/ramdata.Rd | 4 man/sumData.Rd | 22 - 11 files changed, 507 insertions(+), 247 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Michael T. Brannick [ctb],
Jack Kostal [ctb],
Sean Potter [ctb],
Yuejia (Mandy) Teng [ctb]
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>
Diff between psychmeta versions 0.1.3 dated 2017-12-13 and 0.2.0 dated 2018-01-05
psychmeta-0.1.3/psychmeta/man/ma_r_generic.Rd |only psychmeta-0.2.0/psychmeta/DESCRIPTION | 11 psychmeta-0.2.0/psychmeta/MD5 | 76 - psychmeta-0.2.0/psychmeta/NAMESPACE | 9 psychmeta-0.2.0/psychmeta/NEWS | 6 psychmeta-0.2.0/psychmeta/R/composites.R | 26 psychmeta-0.2.0/psychmeta/R/convert_es.R | 314 +++++ psychmeta-0.2.0/psychmeta/R/convert_ma.R | 10 psychmeta-0.2.0/psychmeta/R/create_ad_wrappers.R | 103 - psychmeta-0.2.0/psychmeta/R/data_wrangling.R | 6 psychmeta-0.2.0/psychmeta/R/intervals.R | 4 psychmeta-0.2.0/psychmeta/R/itemize_scales.R |only psychmeta-0.2.0/psychmeta/R/ma_d.R | 74 + psychmeta-0.2.0/psychmeta/R/ma_generic.R | 6 psychmeta-0.2.0/psychmeta/R/ma_r.R | 21 psychmeta-0.2.0/psychmeta/R/metabulate.R |only psychmeta-0.2.0/psychmeta/R/print_methods.R | 4 psychmeta-0.2.0/psychmeta/R/psychmeta.R | 1 psychmeta-0.2.0/psychmeta/R/reshape.R | 5 psychmeta-0.2.0/psychmeta/R/simulate.R |only psychmeta-0.2.0/psychmeta/R/simulate_d.R | 1012 ++++++++++--------- psychmeta-0.2.0/psychmeta/R/simulate_r.R | 799 +++++++++------ psychmeta-0.2.0/psychmeta/R/summarize_ads.R |only psychmeta-0.2.0/psychmeta/R/var_error.R | 57 + psychmeta-0.2.0/psychmeta/R/zzz.R | 3 psychmeta-0.2.0/psychmeta/README.md | 2 psychmeta-0.2.0/psychmeta/man/add_commas.Rd |only psychmeta-0.2.0/psychmeta/man/convert_es.Rd | 22 psychmeta-0.2.0/psychmeta/man/generate_directory.Rd | 6 psychmeta-0.2.0/psychmeta/man/ma_d.Rd | 32 psychmeta-0.2.0/psychmeta/man/ma_generic.Rd |only psychmeta-0.2.0/psychmeta/man/ma_r.Rd | 15 psychmeta-0.2.0/psychmeta/man/metabulate.Rd |only psychmeta-0.2.0/psychmeta/man/psychmeta-package.Rd | 1 psychmeta-0.2.0/psychmeta/man/reshape_wide2long.Rd | 5 psychmeta-0.2.0/psychmeta/man/round2char.Rd | 4 psychmeta-0.2.0/psychmeta/man/simulate_alpha.Rd | 2 psychmeta-0.2.0/psychmeta/man/simulate_d_database.Rd | 10 psychmeta-0.2.0/psychmeta/man/simulate_d_sample.Rd | 11 psychmeta-0.2.0/psychmeta/man/simulate_matrix.Rd | 2 psychmeta-0.2.0/psychmeta/man/simulate_r_database.Rd | 15 psychmeta-0.2.0/psychmeta/man/simulate_r_sample.Rd | 7 psychmeta-0.2.0/psychmeta/man/summarize_ads.Rd |only psychmeta-0.2.0/psychmeta/man/var_error_A.Rd |only 44 files changed, 1752 insertions(+), 929 deletions(-)
Title: Bayesian Modeling via Goodness of Fit
Description: Non-parametric method for learning prior distribution starting with parametric (subjective) prior. It performs four interconnected tasks: (i) characterizes the uncertainty of the elicited prior; (ii) exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) performs macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. (2017, Technical Report).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>
Diff between BayesGOF versions 1.3 dated 2017-11-16 and 1.4 dated 2018-01-05
BayesGOF-1.3/BayesGOF/R/PP.prt.2.R |only BayesGOF-1.4/BayesGOF/DESCRIPTION | 10 ++++-- BayesGOF-1.4/BayesGOF/MD5 | 35 +++++++++++++----------- BayesGOF-1.4/BayesGOF/R/ConMean.prt.2.R |only BayesGOF-1.4/BayesGOF/R/DS.PostMean.R | 22 +++------------ BayesGOF-1.4/BayesGOF/R/DS.PostMean.reduce.R | 2 - BayesGOF-1.4/BayesGOF/R/DS.micro.inf.R | 33 ++++++++++------------ BayesGOF-1.4/BayesGOF/R/DS.mode.map.R | 3 -- BayesGOF-1.4/BayesGOF/R/DS.prior.R | 8 +++-- BayesGOF-1.4/BayesGOF/R/EXP.score.R | 2 - BayesGOF-1.4/BayesGOF/R/plot.DS_GF.R | 20 ++++++------- BayesGOF-1.4/BayesGOF/R/plot.DS_GF_macro_mean.R | 4 +- BayesGOF-1.4/BayesGOF/R/plot.DS_GF_macro_mode.R | 10 +++--- BayesGOF-1.4/BayesGOF/R/plot.DS_GF_micro.R | 7 ++-- BayesGOF-1.4/BayesGOF/build/partial.rdb |binary BayesGOF-1.4/BayesGOF/build/vignette.rds |only BayesGOF-1.4/BayesGOF/inst |only BayesGOF-1.4/BayesGOF/man/DS.PostMean.Rd | 10 ++---- BayesGOF-1.4/BayesGOF/man/DS.prior.Rd | 2 - BayesGOF-1.4/BayesGOF/vignettes |only 20 files changed, 78 insertions(+), 90 deletions(-)
Title: Unsupervised Multivariate Outlier Probabilities for Large
Datasets
Description: Estimates unsupervised outlier probabilities for multivariate numeric data with many observations from a nonparametric outlier statistic.
Author: Chris Fraley [aut, cre]
Maintainer: Chris Fraley <cfraley@tableau.com>
Diff between probout versions 1.0 dated 2017-11-06 and 1.1.1 dated 2018-01-05
CHANGELOG |only DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- inst/doc/probout.Rmd | 43 ++++++++++++++++++++++++++++++++++++------- inst/doc/probout.html | 26 ++++++++++++++++++-------- man/OutlierStatistic.Rd | 4 ++-- vignettes/probout.Rmd | 43 ++++++++++++++++++++++++++++++++++++------- 7 files changed, 103 insertions(+), 34 deletions(-)
Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.0.4 dated 2017-11-03 and 0.0.5 dated 2018-01-05
ChangeLog | 13 ++++++++++ DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++ inst/doc/tintHTML.R | 15 +++++------- inst/doc/tintHTML.Rmd | 19 ++++++++------- inst/doc/tintHTML.html | 59 +++++++++++++++++++++++-------------------------- inst/doc/tintPDF.R | 13 ++++------ inst/doc/tintPDF.Rmd | 15 ++++++------ inst/doc/tintPDF.pdf |binary tests/simple.R | 9 ++++--- vignettes/tintHTML.Rmd | 19 ++++++++------- vignettes/tintPDF.Rmd | 15 ++++++------ 14 files changed, 122 insertions(+), 98 deletions(-)
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented in the summary-methods.
Author: Miguel Alvarez <kamapu78@gmail.com>
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.1.2 dated 2017-08-06 and 0.1.3 dated 2018-01-05
DESCRIPTION | 18 - MD5 | 49 +-- NAMESPACE | 2 R/add_concept.R | 2 R/add_trait.R |only R/backup_object.R | 3 R/clean.R | 18 + R/merge_taxa.R | 37 ++ R/summary.R | 4 R/supporting_functions.R |only R/tax2traits.R |only R/taxlist-class.R | 31 +- build/vignette.rds |binary data/Easplist.rda |binary inst/ChangeLog | 8 inst/doc/taxlist-intro.R | 9 inst/doc/taxlist-intro.Rmd | 18 - inst/doc/taxlist-intro.html | 517 +++++++++++++++++++++++++------------- man/add_parent.Rd | 2 man/add_trait.Rd |only man/add_view.Rd | 2 man/df2taxlist.Rd | 5 man/merge_taxa.Rd | 18 - man/tax2traits.Rd |only man/taxon_traits.Rd | 2 tests/extras/0_before_building.R | 5 tests/extras/building_vignettes.R | 2 vignettes/taxlist-intro.Rmd | 18 - 28 files changed, 529 insertions(+), 241 deletions(-)
Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Author: Mathieu Ribatet [aut, cre],
Richard Singleton [ctb],
R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@umontpellier.fr>
Diff between SpatialExtremes versions 2.0-5 dated 2017-09-17 and 2.0-6 dated 2018-01-05
DESCRIPTION | 8 +- MD5 | 31 +++++----- NAMESPACE | 6 +- NEWS | 7 ++ R/methods.R | 2 R/predict.R | 68 +++++++++++------------ R/psplines.R | 40 ++++++------- R/selection.R | 4 - R/smith.R | 2 inst/doc/SpatialExtremesGuide.R | 106 ++++++++++++++++--------------------- inst/doc/SpatialExtremesGuide.Rnw | 58 ++++++++++---------- inst/doc/SpatialExtremesGuide.pdf |binary man/predict.Rd | 6 +- man/print.Rd | 6 +- vignettes/SpatialExtremes.sty | 19 +++++- vignettes/SpatialExtremesGuide.Rnw | 58 ++++++++++---------- vignettes/auto |only 17 files changed, 217 insertions(+), 204 deletions(-)
More information about SpatialExtremes at CRAN
Permanent link
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze randomized response
(RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A
survey technique for eliminating evasive answer bias. Journal of the
American Statistical Association, 60, 63–69). <doi:10.2307/2283137>
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression (with or
without random effects), as predictors in a linear regression, or as
dependent variable in a beta-binomial ANOVA. For simulation and bootstrap
purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <heck@uni-mannheim.de>
Diff between RRreg versions 0.6.2 dated 2017-03-08 and 0.6.4 dated 2018-01-05
DESCRIPTION | 20 ++- MD5 | 46 ++++---- NAMESPACE | 1 NEWS | 14 ++ R/RRcor.R | 32 +++-- R/RRlin.R | 2 R/RRlog.R | 19 ++- R/RRmixed.R | 92 ++++++++++++---- R/RRreg-package.R | 7 - R/RRuni.R | 22 ++- R/RRuni.models.R | 110 ++++++++++++------- R/RRuni_ll.R | 12 +- build/vignette.rds |binary inst/CITATION | 13 +- inst/doc/RRreg.R | 59 +++++++--- inst/doc/RRreg.Rmd | 67 +++++++----- inst/doc/RRreg.html | 283 ++++++++++++++++++++++++--------------------------- man/RRcor.Rd | 2 man/RRlin.Rd | 2 man/RRlog.Rd | 2 man/RRmixed.Rd | 16 ++ man/RRreg-package.Rd | 5 man/RRuni.Rd | 10 + vignettes/RRreg.Rmd | 67 +++++++----- 24 files changed, 546 insertions(+), 357 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: PORD, METIS, SCOTCH.
MUMPS method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [ctb],
Jean-Yves L'Excellent [ctb],
Stephane Pralet [ctb],
Chiara Puglisi [ctb],
Francois-Henry Rouet [ctb],
Wissam Sid-Lakhdar [ctb],
Tzvetomila Slavova [ctb],
Bora Ucar [ctb],
Clement Weisbecker [ctb],
Juergen Schulze [ctb],
George Karypis [ctb],
Douglas C. Schmidt [ctb],
Isamu Hasegawa [ctb],
Alexander Chemeris [ctb],
Makoto Matsumoto [ctb],
Takuji Nishimura [ctb],
Francois Pellegrini [ctb],
David Goudin [ctb],
Pascal Henon [ctb],
Pierre Ramet [ctb],
Sebastien Fourestier [ctb],
Jun-Ho Her [ctb],
Cedric Chevalier [ctb],
Timothy A. Davis [ctb],
Iain S. Duff [ctb],
John K. Reid [ctb],
Richard Stallman [ctb],
Samuel Thibault [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.1.2-2 dated 2017-12-18 and 5.1.2-4 dated 2018-01-05
DESCRIPTION | 24 ++++++++++-------- MD5 | 16 ++++++------ NEWS | 14 ++++++++++ man/rmumps-package.Rd | 31 +++++++++++------------ src/lib/scotch_6.0.4/src/Makefile.inc | 2 - src/lib/scotch_6.0.4/src/Makefile.inc.macos | 2 - src/lib/scotch_6.0.4/src/Makefile.inc.rmumps | 2 - tests/testthat.R | 5 +++ tests/testthat/test_rmumps.R | 35 ++++++++++++++------------- 9 files changed, 76 insertions(+), 55 deletions(-)
Title: Parametric Linkage and Other Pedigree Analysis in R
Description: A suite of tools for analysing pedigrees with marker data, including parametric linkage analysis, forensic computations, relatedness analysis and marker simulations. The core of the package is an implementation of the Elston-Stewart algorithm for pedigree likelihoods, extended to allow mutations as well as complex inbreeding. Features for linkage analysis include singlepoint LOD scores, power analysis, and multipoint analysis (the latter through a wrapper to the 'MERLIN' software). Forensic applications include exclusion probabilities, genotype distributions and conditional simulations. Data from the 'Familias' software can be imported and analysed in 'paramlink'. Finally, 'paramlink' offers many utility functions for creating, manipulating and plotting pedigrees with or without marker data (the actual plotting is done by the 'kinship2' package).
Author: Magnus Dehli Vigeland [aut, cre],
Thore Egeland [ctb],
Guro Doerum [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between paramlink versions 1.1-1 dated 2017-08-14 and 1.1-2 dated 2018-01-05
DESCRIPTION | 8 - MD5 | 40 ++--- NAMESPACE | 4 NEWS | 9 + R/IBDest_getAlleleData.R |only R/IBDestimate.R | 353 +++++++++++++---------------------------------- R/IBDtriangle.R | 45 +++++ R/LR.R |only R/as.matrix.linkdat.R | 3 R/examineKinships.R | 132 +++++++++-------- R/familias2linkdat.R | 37 ++-- R/markerSim.R | 10 - R/markers.R | 40 ++++- R/paramlink.R | 1 R/pedParts.R | 25 +-- man/Familias2linkdat.Rd | 3 man/IBDestimate.Rd | 73 ++++----- man/IBDtriangle.Rd | 13 + man/LR.Rd |only man/examineKinships.Rd | 29 +-- man/markerSim.Rd | 9 - man/pedParts.Rd | 2 man/showInTriangle.Rd |only 23 files changed, 379 insertions(+), 457 deletions(-)
Title: Clustering of Genomic Regions Analysis Method
Description: Provides a new method for identification of clusters of genomic
regions within chromosomes. Primarily, it is used for calling clusters of
cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions
in the tissue or cell type of interest, such as those generated from chromatin-based
assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements
within chromosomes of a given sample to identify COREs in the following steps:
1) It identifies window size or the maximum allowed distance between the elements
within each CORE, 2) It identifies number of elements which should be clustered
as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which
does not pass the threshold considered in the approach.
Author: Seyed Ali Madani Tonekaboni [aut],
Victor Kofia [aut],
Mathieu Lupien [aut],
Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Diff between CREAM versions 1.0.0 dated 2017-10-27 and 1.1.0 dated 2018-01-05
DESCRIPTION | 6 +-- MD5 | 14 ++++----- R/CREAM.R | 31 +++++++++++++------- R/ElementRecog.R | 28 +++++++++--------- R/PeakMinFilt.R | 12 ++----- R/WindowSizeRecog.R | 80 ++++++++++++++++++++-------------------------------- R/WindowVec.R | 11 +++---- README.md | 7 +++- 8 files changed, 91 insertions(+), 98 deletions(-)
Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>
Diff between PracTools versions 0.7 dated 2017-11-23 and 0.8 dated 2018-01-05
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/BW2stagePPSe.R | 6 ++++-- data/Domainy1y2.RData |binary data/MDarea.pop.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary 13 files changed, 20 insertions(+), 18 deletions(-)
Title: Detection and Control of Tree-Ring Widths on Scanned Image
Sections
Description: Identification of ring borders on scanned image sections from dendrochronological samples. Processing of image reflectances to produce gray matrices and time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders, or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical device, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values.
Author: Wilson Lara, Carlos Sierra, Felipe Bravo
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between measuRing versions 0.4 dated 2017-05-11 and 0.4.1 dated 2018-01-05
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS | 16 ++++ R/crossRings.R | 168 +++++++++++++++++------------------------------ R/multiDetect.R | 11 ++- R/reduceList.R | 3 R/ringDetect.R | 2 build/partial.rdb |binary inst/P105_b.tif |binary inst/P105_c.tif |binary man/crossRings.Rd | 51 +++++--------- man/measuRing-package.Rd | 5 + man/multiDetect.Rd | 65 +++++++++--------- man/reduceList.Rd | 33 ++++----- man/ringDetect.Rd | 2 15 files changed, 186 insertions(+), 206 deletions(-)
Title: Access the 'languagelayer' API
Description: Improve your text analysis with languagelayer
<https://languagelayer.com>, a powerful language detection
API.
Author: Colin FAY [aut, cre]
Maintainer: Colin FAY <contact@colinfay.me>
Diff between languagelayeR versions 1.1.0 dated 2017-07-18 and 1.2.1 dated 2018-01-05
languagelayeR-1.1.0/languagelayeR/R/setApiKey.R |only languagelayeR-1.1.0/languagelayeR/man/getLanguage.Rd |only languagelayeR-1.1.0/languagelayeR/man/getSupportedLanguage.Rd |only languagelayeR-1.1.0/languagelayeR/man/setApiKey.Rd |only languagelayeR-1.2.1/languagelayeR/DESCRIPTION | 14 languagelayeR-1.2.1/languagelayeR/LICENSE |only languagelayeR-1.2.1/languagelayeR/MD5 | 43 - languagelayeR-1.2.1/languagelayeR/NAMESPACE | 6 languagelayeR-1.2.1/languagelayeR/R/get_lang.R | 30 languagelayeR-1.2.1/languagelayeR/R/get_supported_lang.R | 26 languagelayeR-1.2.1/languagelayeR/R/utils.R | 1 languagelayeR-1.2.1/languagelayeR/build/vignette.rds |binary languagelayeR-1.2.1/languagelayeR/inst/articles |only languagelayeR-1.2.1/languagelayeR/inst/authors.html |only languagelayeR-1.2.1/languagelayeR/inst/doc/Introduction.Rmd | 1 languagelayeR-1.2.1/languagelayeR/inst/doc/Introduction.html | 333 ++++++++-- languagelayeR-1.2.1/languagelayeR/inst/index.html |only languagelayeR-1.2.1/languagelayeR/inst/jquery.sticky-kit.min.js |only languagelayeR-1.2.1/languagelayeR/inst/link.svg |only languagelayeR-1.2.1/languagelayeR/inst/news |only languagelayeR-1.2.1/languagelayeR/inst/pkgdown.css |only languagelayeR-1.2.1/languagelayeR/inst/pkgdown.js |only languagelayeR-1.2.1/languagelayeR/inst/reference |only languagelayeR-1.2.1/languagelayeR/man/get_lang.Rd | 2 languagelayeR-1.2.1/languagelayeR/man/get_supported_lang.Rd | 2 languagelayeR-1.2.1/languagelayeR/vignettes/Introduction.Rmd | 1 26 files changed, 327 insertions(+), 132 deletions(-)
Title: Simplifies Plotting Data Inside Databases
Description: Leverages 'dplyr' to process the calculations of a plot inside a database.
This package provides helper functions that abstract the work at three levels:
outputs a 'ggplot', outputs the calculations, outputs the formula
needed to calculate bins.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between dbplot versions 0.1.1 dated 2017-11-27 and 0.2.0 dated 2018-01-05
DESCRIPTION | 10 MD5 | 73 ++-- NAMESPACE | 30 - NEWS.md | 20 - R/boxplot.R | 217 ++++++------- R/discrete.R | 295 +++++++++-------- R/histogram.R | 215 ++++++------ R/raster.R | 301 +++++++++--------- R/utils.R | 97 ++--- README.md | 597 ++++++++++++++++-------------------- man/db_bin.Rd | 72 ++-- man/db_compute_bins.Rd | 76 ++-- man/db_compute_boxplot.Rd | 52 +-- man/db_compute_count.Rd | 64 +-- man/db_compute_raster.Rd | 103 +++--- man/dbplot_bar.Rd | 78 ++-- man/dbplot_boxplot.Rd | 60 +-- man/dbplot_histogram.Rd | 82 ++-- man/dbplot_line.Rd | 78 ++-- man/dbplot_raster.Rd | 116 +++--- tests/testthat.R | 10 tests/testthat/test-dbbin.R | 51 +-- tests/testthat/test-dbplots.R |only tools/readme/logo.png |only tools/readme/unnamed-chunk-10-1.png |binary tools/readme/unnamed-chunk-11-1.png |binary tools/readme/unnamed-chunk-12-1.png |binary tools/readme/unnamed-chunk-13-1.png |binary tools/readme/unnamed-chunk-14-1.png |only tools/readme/unnamed-chunk-15-1.png |binary tools/readme/unnamed-chunk-16-1.png |only tools/readme/unnamed-chunk-18-1.png |binary tools/readme/unnamed-chunk-19-1.png |only tools/readme/unnamed-chunk-3-1.png |binary tools/readme/unnamed-chunk-4-1.png |binary tools/readme/unnamed-chunk-5-1.png |binary tools/readme/unnamed-chunk-6-1.png |binary tools/readme/unnamed-chunk-7-1.png |binary tools/readme/unnamed-chunk-8-1.png |binary tools/readme/unnamed-chunk-9-1.png |binary 40 files changed, 1350 insertions(+), 1347 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.2-5 dated 2017-06-29 and 1.2-6 dated 2018-01-05
DESCRIPTION | 6 ++--- MD5 | 42 +++++++++++++++++++------------------- R/CRS-methods.R | 12 ++++++++-- R/SpatialGrid-methods.R | 2 + build/vignette.rds |binary inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 2 - inst/include/sp_xports.c | 32 ++++++++++++++-------------- man/00sp.Rd | 2 - man/CRS-class.Rd | 2 - man/SpatialGrid.Rd | 2 - man/SpatialGridDataFrame-class.Rd | 4 +-- man/meuse.Rd | 2 - man/over.Rd | 2 - man/spsample.Rd | 2 - man/zerodist.Rd | 2 - src/pip.c | 8 +++---- src/pip2.c | 12 +++++----- src/sp.h | 2 - src/sp_xports.c | 32 ++++++++++++++-------------- 22 files changed, 88 insertions(+), 80 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Hervé
Maintainer: Maxime Hervé <maxime.herve@univ-rennes1.fr>
Diff between RVAideMemoire versions 0.9-68 dated 2017-08-21 and 0.9-69 dated 2018-01-05
RVAideMemoire-0.9-68/RVAideMemoire/R/back.lsmeans.R |only RVAideMemoire-0.9-68/RVAideMemoire/R/rating.lsmeans.R |only RVAideMemoire-0.9-68/RVAideMemoire/man/back.lsmeans.Rd |only RVAideMemoire-0.9-68/RVAideMemoire/man/rating.lsmeans.Rd |only RVAideMemoire-0.9-69/RVAideMemoire/DESCRIPTION | 12 +- RVAideMemoire-0.9-69/RVAideMemoire/MD5 | 38 +++--- RVAideMemoire-0.9-69/RVAideMemoire/NAMESPACE | 8 - RVAideMemoire-0.9-69/RVAideMemoire/NEWS | 5 RVAideMemoire-0.9-69/RVAideMemoire/R/OR.multinom.R | 57 +++++++--- RVAideMemoire-0.9-69/RVAideMemoire/R/back.emmeans.R |only RVAideMemoire-0.9-69/RVAideMemoire/R/deprecated.R | 8 + RVAideMemoire-0.9-69/RVAideMemoire/R/plotresid.R | 12 ++ RVAideMemoire-0.9-69/RVAideMemoire/R/rating.emmeans.R |only RVAideMemoire-0.9-69/RVAideMemoire/R/test.multinom.R | 57 +++++++--- RVAideMemoire-0.9-69/RVAideMemoire/R/user.cont.R | 4 RVAideMemoire-0.9-69/RVAideMemoire/R/zzz.R | 2 RVAideMemoire-0.9-69/RVAideMemoire/man/OR.multinom.Rd | 2 RVAideMemoire-0.9-69/RVAideMemoire/man/RVAideMemoire-package.Rd | 6 - RVAideMemoire-0.9-69/RVAideMemoire/man/back.emmeans.Rd |only RVAideMemoire-0.9-69/RVAideMemoire/man/deprecated.Rd | 6 + RVAideMemoire-0.9-69/RVAideMemoire/man/plotresid.Rd | 4 RVAideMemoire-0.9-69/RVAideMemoire/man/rating.emmeans.Rd |only RVAideMemoire-0.9-69/RVAideMemoire/man/test.multinom.Rd | 2 RVAideMemoire-0.9-69/RVAideMemoire/man/user.cont.Rd | 23 ++-- 24 files changed, 167 insertions(+), 79 deletions(-)
Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for
feature selection in high-dimensional regressions proposed in
Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>,
with support for multi-step adaptive MCP-net (MSAMNet) and
multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre] (0000-0002-0250-5673),
Qing-Song Xu [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between msaenet versions 2.7 dated 2017-09-24 and 2.8 dated 2018-01-05
DESCRIPTION | 18 +- MD5 | 28 +-- NAMESPACE | 3 NEWS.md | 6 R/msaenet-package.R | 4 R/plot-msaenet.R | 88 +++++++++- README.md | 4 build/vignette.rds |binary inst/doc/msaenet.R | 3 inst/doc/msaenet.Rmd | 10 + inst/doc/msaenet.html | 425 +++++++++++++++++++++++++++++++++---------------- man/msaenet-package.Rd | 4 man/plot.msaenet.Rd | 28 ++- vignettes/msaenet.Rmd | 10 + vignettes/msaenet.css | 4 15 files changed, 459 insertions(+), 176 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local and Zellner priors. Bayes factors, marginal densities and variable selection in regression setups. Routines to sample, evaluate prior densities, distribution functions and quantiles are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.9.5 dated 2017-05-26 and 1.9.6 dated 2018-01-05
ChangeLog | 3 DESCRIPTION | 16 +- MD5 | 17 +-- R/gam.R |only build/vignette.rds |binary data/hald.rda |binary inst/doc/mombf.pdf |binary src/cstat.cpp | 300 +++++++++++++++++++++++------------------------------ src/do_mombf.h | 3 src/modelSel.cpp | 19 +++ 10 files changed, 176 insertions(+), 182 deletions(-)
Title: Multiple Aggregation Prediction Algorithm
Description: Functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts time series at multiple temporal aggregation levels, thus strengthening and attenuating the various time series components for better holistic estimation of its structure. For details see Kourentzes et al. (2014) <doi:10.1016/j.ijforecast.2013.09.006>.
Author: Nikolaos Kourentzes [aut, cre],
Fotios Petropoulos [aut]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Diff between MAPA versions 2.0.2 dated 2017-06-05 and 2.0.4 dated 2018-01-05
DESCRIPTION | 17 ++++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 9 +++++++++ R/mapa.R | 10 +++++----- R/mapa.estim.R | 25 +++++++++++++++++++++---- R/mapa.forecast.R | 15 +++++++-------- man/mapa.Rd | 4 ++-- man/mapacalc.Rd | 2 +- man/mapafor.Rd | 4 ++-- man/mapasimple.Rd | 4 ++-- 10 files changed, 68 insertions(+), 40 deletions(-)
Title: Handy File and String Manipulation
Description: Convenient functions for moving files, deleting directories,
and a variety of string operations that facilitate manipulating files
and extracting information from strings.
Author: Rory Nolan [aut, cre, cph],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 2.0.1 dated 2017-12-12 and 2.0.2 dated 2018-01-05
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/utils.R | 9 ++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/files.html | 4 ++-- inst/doc/strings.html | 8 ++++---- man/all_equal.Rd | 7 ++++++- tests/testthat/test_utils.R | 2 ++ 10 files changed, 40 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-18 2.43
2017-11-06 2.42
2017-10-16 2.41
2017-08-14 2.40
2017-06-21 2.39
2017-06-20 2.38
2017-05-24 2.37
2017-04-28 2.36
2017-04-15 2.35
2017-04-14 2.34
2017-02-12 2.33
2017-01-09 2.32
2016-12-20 2.31
2016-11-15 2.30
2016-10-11 2.29
2016-10-03 2.28
2016-04-22 2.27
2015-12-21 2.26
2015-11-19 2.25
2015-11-18 2.24
2015-09-30 2.23
2015-08-31 2.22
2015-08-23 2.21
2015-08-21 2.20
2015-06-16 2.19
2015-04-19 2.18
2015-03-10 2.17
2015-02-27 2.16
2015-01-23 2.15
2014-12-19 2.14
2014-11-17 2.13
2014-09-24 2.12
2014-09-23 2.11
2014-07-11 2.10
2014-07-02 2.9
2014-05-29 2.8
2013-12-20 2.7
2013-05-06 2.6
2013-04-29 2.5
2013-04-22 2.4
2013-04-08 2.3
2013-03-24 2.2
2013-03-17 2.1
2013-02-05 2.0
2012-10-24 1.2
2012-10-08 1.1
2012-09-26 1.0
Title: Assessment and Evaluation of Formations in United
Description: United is a software tool which can be downloaded at the following
website <http://www.schroepl.net/pbm/software/united/>. In general, it is
a virtual manager game for football teams. This package contains helpful
functions for determining an optimal formation for a virtual match in
United. E.g. knowing that the opponent has a strong defensive it is
advisable to beat him in the midfield. Furthermore, this package contains
functions for computing the optimal usage of hardness in a game.
Author: David Schindler [aut, cre]
Maintainer: David Schindler <dv.schindler@gmail.com>
Diff between unitedR versions 0.3 dated 2018-01-03 and 0.3.1 dated 2018-01-05
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- R/unitedRPackage.R | 2 - R/unitedSimResults.R | 70 ++++++++++++++++++++++++------------------------- inst/doc/unitedR.Rnw | 8 ++--- inst/doc/unitedR.pdf |binary man/unitedR-package.Rd | 2 - vignettes/unitedR.Rnw | 8 ++--- 8 files changed, 55 insertions(+), 55 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including BLACS, PBLAS, and ScaLAPACK in double precision via
pbdMPI based on ScaLAPACK version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.2-2 dated 2016-09-25 and 0.2-3 dated 2018-01-05
ChangeLog | 4 +++ DESCRIPTION | 10 ++++----- MD5 | 34 ++++++++++++++++--------------- README.md | 2 + inst/doc/pbdSLAP-guide.Rnw | 12 +++-------- inst/doc/pbdSLAP-guide.pdf |binary man/00_pbdSLAP-package.Rd | 2 - man/slap_gridinfo.Rd | 2 - src/Makevars.in | 9 ++++++-- src/Makevars.win | 5 ++++ src/SLmake.inc.org | 2 - src/SLmake.inc.win | 2 - src/ScaLAPACK/pdlaqr5.f | 48 +++++++++++++++++++++++++++++--------------- src/ScaLAPACK/pdtrord.f | 3 +- src/ScaLAPACK/pdtrsen.f | 3 +- src/TOOLS/Makefile | 4 +-- src/zzz.c |only src/zzz.h |only vignettes/pbdSLAP-guide.Rnw | 12 +++-------- 19 files changed, 91 insertions(+), 63 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al.
(2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan H Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.8.1 dated 2017-11-18 and 0.8.2 dated 2018-01-05
mplot-0.8.1/mplot/build |only mplot-0.8.1/mplot/inst/doc |only mplot-0.8.1/mplot/vignettes |only mplot-0.8.2/mplot/DESCRIPTION | 9 mplot-0.8.2/mplot/MD5 | 49 --- mplot-0.8.2/mplot/NEWS | 8 mplot-0.8.2/mplot/R/bglmnet.R | 480 +++++++++++++++++++++++++--------- mplot-0.8.2/mplot/R/mplot-package.R | 3 mplot-0.8.2/mplot/R/vis.R | 14 mplot-0.8.2/mplot/man/bglmnet.Rd | 31 ++ mplot-0.8.2/mplot/man/plot.bglmnet.Rd | 24 + mplot-0.8.2/mplot/man/plot.vis.Rd | 4 12 files changed, 445 insertions(+), 177 deletions(-)
Title: Matrix Clustering with Gaussian and Manly Mixture Models
Description: Matrix clustering with finite mixture models.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between MatManlyMix versions 0.1.2 dated 2017-08-05 and 1.1.1 dated 2018-01-05
MatManlyMix-0.1.2/MatManlyMix/R/libMatManlySelect.R |only MatManlyMix-0.1.2/MatManlyMix/src/crosen.c |only MatManlyMix-0.1.2/MatManlyMix/src/crosenAR.c |only MatManlyMix-0.1.2/MatManlyMix/src/crosenReg.c |only MatManlyMix-0.1.2/MatManlyMix/src/libMatManlyAR1.c |only MatManlyMix-0.1.2/MatManlyMix/src/libMatManlyAR1reg.c |only MatManlyMix-0.1.2/MatManlyMix/src/libMatManlyFull.c |only MatManlyMix-0.1.2/MatManlyMix/src/libMatManlydiag.c |only MatManlyMix-0.1.2/MatManlyMix/src/runMatManlyAR.c |only MatManlyMix-0.1.2/MatManlyMix/src/runMatManlyFull.c |only MatManlyMix-0.1.2/MatManlyMix/src/runMatManlydiag.c |only MatManlyMix-1.1.1/MatManlyMix/DESCRIPTION | 8 MatManlyMix-1.1.1/MatManlyMix/MD5 | 52 MatManlyMix-1.1.1/MatManlyMix/NEWS | 9 MatManlyMix-1.1.1/MatManlyMix/R/libMatManlyFull.R | 2028 +++----------- MatManlyMix-1.1.1/MatManlyMix/data/IMDb.RData |only MatManlyMix-1.1.1/MatManlyMix/data/Satellite.RData |only MatManlyMix-1.1.1/MatManlyMix/data/crime.RData |binary MatManlyMix-1.1.1/MatManlyMix/demo |only MatManlyMix-1.1.1/MatManlyMix/man/IMDb.Rd |only MatManlyMix-1.1.1/MatManlyMix/man/MatManly.EM.Rd | 38 MatManlyMix-1.1.1/MatManlyMix/man/MatManly.init.Rd | 37 MatManlyMix-1.1.1/MatManlyMix/man/MatManlyMix-package.Rd | 2 MatManlyMix-1.1.1/MatManlyMix/man/Satellite.Rd |only MatManlyMix-1.1.1/MatManlyMix/man/crime.Rd | 2 MatManlyMix-1.1.1/MatManlyMix/src/MatManlyMix.h | 97 MatManlyMix-1.1.1/MatManlyMix/src/crosen1.c |only MatManlyMix-1.1.1/MatManlyMix/src/crosen1Reg.c |only MatManlyMix-1.1.1/MatManlyMix/src/crosen2.c |only MatManlyMix-1.1.1/MatManlyMix/src/crosen2Reg.c |only MatManlyMix-1.1.1/MatManlyMix/src/crosenAR1.c |only MatManlyMix-1.1.1/MatManlyMix/src/crosenAR1Reg.c |only MatManlyMix-1.1.1/MatManlyMix/src/libAR1.c |only MatManlyMix-1.1.1/MatManlyMix/src/libAR1reg.c |only MatManlyMix-1.1.1/MatManlyMix/src/libFull.c |only MatManlyMix-1.1.1/MatManlyMix/src/libFullReg.c |only MatManlyMix-1.1.1/MatManlyMix/src/libMatrix.c | 17 MatManlyMix-1.1.1/MatManlyMix/src/registerDynamicSymbol.c | 1 MatManlyMix-1.1.1/MatManlyMix/src/runAR.c |only MatManlyMix-1.1.1/MatManlyMix/src/runFull.c |only 40 files changed, 642 insertions(+), 1649 deletions(-)
Title: Learning Plane Geometry
Description: Contains some functions to learn and teach basic plane Geometry at undergraduate level with the aim of being helpful to young students with little programming skills.
Author: Alvaro Briz-Redon, Angel Serrano-Aroca
Maintainer: Alvaro Briz-Redon <albrizre@gmail.com>
Diff between LearnGeom versions 1.2 dated 2017-12-03 and 1.3 dated 2018-01-05
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++++-------------- NAMESPACE | 2 ++ R/AddPointPoly.R |only R/CreateArcPointsDist.R | 4 ++-- R/CreatePolygon.R | 18 ++++++++++++++++++ R/ReflectedPolygon.R | 2 +- R/RemovePointPoly.R |only R/ShearedPolygon.R | 2 +- R/SimilarPolygon.R | 2 +- inst/doc/my-vignette.Rmd | 2 +- inst/doc/my-vignette.pdf |binary man/AddPointPoly.Rd |only man/CreateArcPointsDist.Rd | 2 +- man/ReflectedPolygon.Rd | 2 +- man/RemovePointPoly.Rd |only man/ShearedPolygon.Rd | 2 +- man/SimilarPolygon.Rd | 2 +- vignettes/my-vignette.Rmd | 2 +- 19 files changed, 52 insertions(+), 28 deletions(-)
Title: Hierarchical Multiple Imputation
Description: Runs single level and multilevel imputation models. The user just has to pass the data to the main function and, optionally, his analysis model. Basically the package then translates this analysis model into commands to impute the data according to it with functions from 'mice', 'MCMCglmm' or routines build for this package.
Author: Matthias Speidel [aut, cre] (Institute for Employment Research,
Nuremberg, Germany),
Joerg Drechsler [aut] (Institute for Employment Research, Nuremberg,
Germany),
Shahab Jolani [aut] (Maastricht University, Maastricht, The
Netherlands)
Maintainer: Matthias Speidel <matthias.speidel@googlemail.com>
Diff between hmi versions 0.8.1 dated 2017-11-18 and 0.8.2 dated 2018-01-05
hmi-0.8.1/hmi/R/hmi_imp_roundedcont_2017-10-18.R |only hmi-0.8.1/hmi/R/hmi_smallfunctions_2017-11-14.R |only hmi-0.8.1/hmi/R/hmi_wrapper_2017-10-12.R |only hmi-0.8.1/hmi/man/components.Rd |only hmi-0.8.1/hmi/man/negloglik2.Rd |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-11_dffb77ed681fbadf70a14ba46ee4c6fa.RData |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-11_dffb77ed681fbadf70a14ba46ee4c6fa.rdb |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-11_dffb77ed681fbadf70a14ba46ee4c6fa.rdx |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-14_e851ed0eed73b79bdf7bd634e4ce47ae.RData |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-14_e851ed0eed73b79bdf7bd634e4ce47ae.rdb |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-14_e851ed0eed73b79bdf7bd634e4ce47ae.rdx |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-3_2fd14409fb8e79d599e9f676a57c85c6.RData |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-3_2fd14409fb8e79d599e9f676a57c85c6.rdb |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-3_2fd14409fb8e79d599e9f676a57c85c6.rdx |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-8_e95d99b5a8aed1eb89410b1838e4f2d3.RData |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-8_e95d99b5a8aed1eb89410b1838e4f2d3.rdb |only hmi-0.8.1/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-8_e95d99b5a8aed1eb89410b1838e4f2d3.rdx |only hmi-0.8.2/hmi/DESCRIPTION | 6 hmi-0.8.2/hmi/MD5 | 201 ++++------ hmi-0.8.2/hmi/R/hmi_imp_binary_multi_2017-10-12.R | 8 hmi-0.8.2/hmi/R/hmi_imp_binary_single_2017-04-11.R | 6 hmi-0.8.2/hmi/R/hmi_imp_cat_multi_2017-11-17.R | 10 hmi-0.8.2/hmi/R/hmi_imp_cat_single_2017-04-13.R | 6 hmi-0.8.2/hmi/R/hmi_imp_catordered_multi_2017-11-13.R | 12 hmi-0.8.2/hmi/R/hmi_imp_catordered_single_2017-08-02.R | 5 hmi-0.8.2/hmi/R/hmi_imp_cont_multi_2017-10-25.R | 11 hmi-0.8.2/hmi/R/hmi_imp_cont_single_2017-04-11.R | 6 hmi-0.8.2/hmi/R/hmi_imp_count_multi_2017-10-12.R | 10 hmi-0.8.2/hmi/R/hmi_imp_count_single_2017-10-12.R | 8 hmi-0.8.2/hmi/R/hmi_imp_interval_2017-10-17.R | 6 hmi-0.8.2/hmi/R/hmi_imp_roundedcont_2017-12-27.R |only hmi-0.8.2/hmi/R/hmi_imp_semicont_multi_2017-10-12.R | 12 hmi-0.8.2/hmi/R/hmi_imp_semicont_single_2017-04-11.R | 11 hmi-0.8.2/hmi/R/hmi_smallfunctions_2017-12-28.R |only hmi-0.8.2/hmi/R/hmi_wrapper_2017-12-20.R |only hmi-0.8.2/hmi/build/vignette.rds |binary hmi-0.8.2/hmi/inst/doc/my-vignette.R | 10 hmi-0.8.2/hmi/inst/doc/my-vignette.Rmd | 12 hmi-0.8.2/hmi/inst/doc/my-vignette.html | 8 hmi-0.8.2/hmi/man/as.data.frame.interval.Rd | 2 hmi-0.8.2/hmi/man/as.interval.Rd | 2 hmi-0.8.2/hmi/man/center.interval.Rd | 2 hmi-0.8.2/hmi/man/chaincheck.Rd | 2 hmi-0.8.2/hmi/man/cleanup.Rd | 2 hmi-0.8.2/hmi/man/contributions4intervals.Rd | 2 hmi-0.8.2/hmi/man/decompose_interval.Rd | 2 hmi-0.8.2/hmi/man/doubleintegral.Rd | 2 hmi-0.8.2/hmi/man/extract_varnames.Rd | 2 hmi-0.8.2/hmi/man/fixed_intercept_check.Rd | 2 hmi-0.8.2/hmi/man/generate_interval.Rd | 2 hmi-0.8.2/hmi/man/get_type.Rd | 6 hmi-0.8.2/hmi/man/hmi.Rd | 15 hmi-0.8.2/hmi/man/hmi_pool.Rd | 2 hmi-0.8.2/hmi/man/idf2interval.Rd | 2 hmi-0.8.2/hmi/man/imp_binary_multi.Rd | 4 hmi-0.8.2/hmi/man/imp_binary_single.Rd | 4 hmi-0.8.2/hmi/man/imp_cat_multi.Rd | 4 hmi-0.8.2/hmi/man/imp_cat_single.Rd | 4 hmi-0.8.2/hmi/man/imp_cont_multi.Rd | 6 hmi-0.8.2/hmi/man/imp_cont_single.Rd | 4 hmi-0.8.2/hmi/man/imp_count_multi.Rd | 6 hmi-0.8.2/hmi/man/imp_count_single.Rd | 7 hmi-0.8.2/hmi/man/imp_interval.Rd | 4 hmi-0.8.2/hmi/man/imp_orderedcat_multi.Rd | 6 hmi-0.8.2/hmi/man/imp_orderedcat_single.Rd | 4 hmi-0.8.2/hmi/man/imp_roundedcont.Rd | 10 hmi-0.8.2/hmi/man/imp_semicont_multi.Rd | 6 hmi-0.8.2/hmi/man/imp_semicont_single.Rd | 5 hmi-0.8.2/hmi/man/imputationcycle.Rd | 7 hmi-0.8.2/hmi/man/interval-add.Rd | 2 hmi-0.8.2/hmi/man/interval-divide.Rd | 2 hmi-0.8.2/hmi/man/interval-multiply.Rd | 2 hmi-0.8.2/hmi/man/interval-subtract.Rd | 2 hmi-0.8.2/hmi/man/interval2idf.Rd | 2 hmi-0.8.2/hmi/man/is.na.interval.Rd | 2 hmi-0.8.2/hmi/man/is_interval.Rd | 2 hmi-0.8.2/hmi/man/list_of_types_maker.Rd | 6 hmi-0.8.2/hmi/man/negloglik.Rd |only hmi-0.8.2/hmi/man/negloglik2_intervalsonly.Rd | 2 hmi-0.8.2/hmi/man/pbivnormX.Rd | 2 hmi-0.8.2/hmi/man/plot.interval.Rd | 2 hmi-0.8.2/hmi/man/random_intercept_check.Rd | 2 hmi-0.8.2/hmi/man/resetPar.Rd | 2 hmi-0.8.2/hmi/man/sample_imp.Rd | 2 hmi-0.8.2/hmi/man/sampler.Rd | 2 hmi-0.8.2/hmi/man/sna_interval.Rd | 2 hmi-0.8.2/hmi/man/split_interval.Rd | 2 hmi-0.8.2/hmi/man/stand.Rd | 6 hmi-0.8.2/hmi/vignettes/my-vignette.Rmd | 12 hmi-0.8.2/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-10_489a2f29f6f9f692ab9f48055578184f.RData |binary hmi-0.8.2/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-10_489a2f29f6f9f692ab9f48055578184f.rdx |binary 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insertions(+), 228 deletions(-)
Title: Functions for Wind Resource Assessment
Description: A collection of functions to analyse, visualize and interpret wind data
and to calculate the potential energy production of wind turbines.
Author: Christian Graul and Carsten Poppinga
Maintainer: Christian Graul <christian.graul@gmail.com>
Diff between bReeze versions 0.4-1 dated 2017-07-31 and 0.4-2 dated 2018-01-05
bReeze-0.4-1/bReeze/man/profile.Rd |only bReeze-0.4-2/bReeze/DESCRIPTION | 8 ++++---- bReeze-0.4-2/bReeze/LICENSE | 2 +- bReeze-0.4-2/bReeze/MD5 | 24 ++++++++++++------------ bReeze-0.4-2/bReeze/NAMESPACE | 6 +++--- bReeze-0.4-2/bReeze/R/plot.profile.R | 2 +- bReeze-0.4-2/bReeze/R/print.profile.R | 2 +- bReeze-0.4-2/bReeze/R/profile.R | 2 +- bReeze-0.4-2/bReeze/R/zzz.R | 2 +- bReeze-0.4-2/bReeze/data/winddata.RData |binary bReeze-0.4-2/bReeze/inst/CITATION | 6 +++--- bReeze-0.4-2/bReeze/inst/NEWS | 6 ++++++ bReeze-0.4-2/bReeze/man/bReeze-package.Rd | 2 +- bReeze-0.4-2/bReeze/man/windprofile.Rd |only 14 files changed, 34 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-27 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-08 1.4
2015-10-14 1.2
2015-10-14 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-20 1.2
2016-05-19 1.1
2016-05-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-09 0.2.4
2013-04-14 0.2.3
2011-05-26 0.2.2
2011-04-26 0.2.1
2010-11-01 0.2.0
2010-10-23 0.1.9
2010-09-01 0.1.8
2010-08-17 0.1.7
2010-03-05 0.1.6
2010-01-20 0.1.5
2010-01-19 0.1.4
2010-01-11 0.1.3
2009-09-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-19 0.1.1
2017-10-12 0.1.0
Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran <j.curran@auckland.ac.nz>
Diff between relSim versions 0.2-0 dated 2015-04-03 and 0.2-9 dated 2018-01-05
DESCRIPTION | 14 + MD5 | 153 ++++++++++-------- NAMESPACE | 74 +++++--- R/IBS.R | 29 +++ R/ISweights.R |only R/RcppExports.R | 67 ++++++-- R/as.npmresult.R |only R/blockSim.R | 224 ++++++++++++++++++--------- R/breedFst.R | 129 ++++++++++----- R/calcFst.R | 28 +++ R/checkFreqs.R | 24 ++ R/data-description.R |only R/errorRate.R | 46 +++++ R/estimateQuantile.R | 380 +++++++++++++++++++++++----------------------- R/exclusionPower.R | 45 ++++- R/fetchBMdata.R | 32 +++ R/locusIBS.R | 21 ++ R/lrMix.R | 30 +++ R/lrPC.R | 38 ++++ R/lrSib.R | 39 ++++ R/lrSibDebug.R | 38 ++++ R/maximizeLRPC.R | 78 ++++----- R/normalizeFreqs.R | 26 +++ R/plot.npmresult.R |only R/print.npmresult.R |only R/print.population.R | 17 ++ R/print.profile.R | 20 ++ R/randomChild.R | 34 ++++ R/randomPCPairs.R | 27 +++ R/randomProfile.R | 21 ++ R/randomProfilePairs.R | 29 +++ R/randomProfiles.R |only R/randomSample.R | 26 +++ R/randomSib.R | 34 ++++ R/randomSibPairs.R | 27 +++ R/readFreqs.R | 43 +++++ R/readProfiles.R |only R/readResults.R | 39 ++++ R/relSim-package.R |only R/sim.R | 51 ++++++ R/simNpersonMixture.R |only R/sysdata.rda |only R/testIS.R |only R/toNexus.R | 134 +++++++++------- R/writeCSV.R |only R/writePop.R |only R/xtable.npmresult.R |only data/USCaucs.rda |binary data/fbiCaucs.rda |binary man/IBS.Rd | 29 ++- man/USCaucs.Rd | 43 ++--- man/blockSim.Rd | 185 +++++++++++----------- man/breedFst.Rd | 81 +++++---- man/calcFst.Rd | 47 +++-- man/checkFreqs.Rd | 34 ++-- man/errorRate.Rd | 83 +++++----- man/exclusionPower.Rd | 35 ++-- man/famSearch.Rd |only man/fbiCaucs.Rd | 40 ++-- man/fetchBMdata.Rd | 51 +++--- man/locusIBS.Rd | 29 ++- man/lrMix.Rd | 51 +++--- man/lrPC.Rd | 67 ++++---- man/lrSib.Rd | 67 ++++---- man/lrSibDebug.Rd | 63 ++++--- man/normalizeFreqs.Rd | 39 ++-- man/print.population.Rd | 29 ++- man/print.profile.Rd | 29 ++- man/randomChild.Rd | 58 +++---- man/randomPCPairs.Rd | 42 ++--- man/randomProfile.Rd | 37 ++-- man/randomProfilePairs.Rd | 43 ++--- man/randomSample.Rd | 45 +++-- man/randomSib.Rd | 61 +++---- man/randomSibPairs.Rd | 43 ++--- man/readFreqs.Rd | 87 +++++----- man/readProfiles.Rd |only man/readResults.Rd | 64 ++++--- man/relSim.Rd |only man/sim.Rd | 90 ++++++---- man/simNpersonMixture.Rd |only man/toNexus.Rd | 40 ++-- man/writeCSV.Rd |only man/writePop.Rd |only src/RcppExports.cpp | 216 +++++++++++++++++--------- src/calcFst.cpp | 26 +-- src/importance.cpp |only src/relSim.cpp | 219 ++++++++++++++++++++++++++ 88 files changed, 2766 insertions(+), 1324 deletions(-)
Title: Remote R: Control a Remote R Session from a Local One
Description: A set of utilities for client/server computing with R, controlling
a remote R session (the server) from a local one (the client). Simply set
up a server (see package vignette for more details) and connect to it from
your local R session ('RStudio', terminal, etc). The client/server
framework is a custom 'REPL' and runs entirely in your R session without the
need for installing a custom environment on your system. Network
communication is handled by the 'ZeroMQ' library by way of the 'pbdZMQ'
package.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between remoter versions 0.3-2 dated 2016-04-29 and 0.4-0 dated 2018-01-05
remoter-0.3-2/remoter/R/000_globalVariables.r |only remoter-0.3-2/remoter/R/00_internals.r |only remoter-0.3-2/remoter/build |only remoter-0.3-2/remoter/inst/doc/remoter.Rmd |only remoter-0.3-2/remoter/inst/doc/remoter.html |only remoter-0.3-2/remoter/man/internals.Rd |only remoter-0.3-2/remoter/vignettes/include/custom.css |only remoter-0.3-2/remoter/vignettes/include/header.html |only remoter-0.3-2/remoter/vignettes/include/headers.js |only remoter-0.3-2/remoter/vignettes/include/ieee.csl |only remoter-0.3-2/remoter/vignettes/rebuild |only remoter-0.3-2/remoter/vignettes/remoter.Rmd |only remoter-0.4-0/remoter/ChangeLog | 98 +++- remoter-0.4-0/remoter/DESCRIPTION | 40 +- remoter-0.4-0/remoter/LICENSE | 2 remoter-0.4-0/remoter/MD5 | 103 ++--- remoter-0.4-0/remoter/NAMESPACE | 40 +- remoter-0.4-0/remoter/R/00_globalVariables.r |only remoter-0.4-0/remoter/R/batch.r |only remoter-0.4-0/remoter/R/c2s.r | 6 remoter-0.4-0/remoter/R/checks.r | 19 remoter-0.4-0/remoter/R/client.r | 172 ++++++-- remoter-0.4-0/remoter/R/crypto.r | 17 remoter-0.4-0/remoter/R/exit.r | 45 ++ remoter-0.4-0/remoter/R/logging.r | 18 remoter-0.4-0/remoter/R/printing.r | 11 remoter-0.4-0/remoter/R/reactor.r |only remoter-0.4-0/remoter/R/relay.r | 8 remoter-0.4-0/remoter/R/remoter-package.r | 23 - remoter-0.4-0/remoter/R/s2c.r | 24 - remoter-0.4-0/remoter/R/server.r | 200 ++++++++-- remoter-0.4-0/remoter/R/state.r | 51 +- remoter-0.4-0/remoter/R/utils.r | 38 + remoter-0.4-0/remoter/R/wcc_addhistory.r |only remoter-0.4-0/remoter/R/wcc_client_device.r |only remoter-0.4-0/remoter/R/wcc_rhelp.r |only remoter-0.4-0/remoter/R/wcc_rpng.r |only remoter-0.4-0/remoter/R/wcc_rpng_utils.r |only remoter-0.4-0/remoter/README.md | 62 +-- remoter-0.4-0/remoter/inst/CITATION | 16 remoter-0.4-0/remoter/inst/doc/remote_machines.Rnw |only remoter-0.4-0/remoter/inst/doc/remote_machines.pdf |only remoter-0.4-0/remoter/inst/doc/remoter.Rnw |only remoter-0.4-0/remoter/inst/doc/remoter.pdf |only remoter-0.4-0/remoter/man/batch.Rd |only remoter-0.4-0/remoter/man/c2s.Rd | 7 remoter-0.4-0/remoter/man/client.Rd | 10 remoter-0.4-0/remoter/man/evalc.Rd | 1 remoter-0.4-0/remoter/man/exit.Rd | 18 remoter-0.4-0/remoter/man/has.sodium.Rd | 1 remoter-0.4-0/remoter/man/is.secure.Rd | 1 remoter-0.4-0/remoter/man/lsc.Rd | 1 remoter-0.4-0/remoter/man/rDevices.Rd |only remoter-0.4-0/remoter/man/rDevices_rpng.Rd |only remoter-0.4-0/remoter/man/relay.Rd | 1 remoter-0.4-0/remoter/man/remoter-package.Rd | 18 remoter-0.4-0/remoter/man/rhelp.Rd |only remoter-0.4-0/remoter/man/rmc.Rd | 1 remoter-0.4-0/remoter/man/s2c.Rd | 21 - remoter-0.4-0/remoter/man/server.Rd | 16 remoter-0.4-0/remoter/man/showlog.Rd | 1 remoter-0.4-0/remoter/vignettes/build_pdf.sh |only remoter-0.4-0/remoter/vignettes/cover |only remoter-0.4-0/remoter/vignettes/include/00-acknowledgement.tex |only remoter-0.4-0/remoter/vignettes/include/remoter.bib | 55 ++ remoter-0.4-0/remoter/vignettes/include/settings.tex |only remoter-0.4-0/remoter/vignettes/include/uch_small.png |only remoter-0.4-0/remoter/vignettes/remote_machines.Rnw |only remoter-0.4-0/remoter/vignettes/remoter.Rnw |only 69 files changed, 855 insertions(+), 290 deletions(-)
Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written
for the purpose of more efficiently understanding and sharing the results of
(primarily) regression analyses. There are a number of functions focused
specifically on the interpretation and presentation of interactions in linear
models. Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre] (0000-0002-1582-6214)
Maintainer: Jacob A. Long <long.1377@osu.edu>
Diff between jtools versions 0.9.0 dated 2017-11-12 and 0.9.1 dated 2018-01-05
DESCRIPTION | 6 MD5 | 46 ++-- NEWS.md | 23 ++ R/export_summ.R | 2 R/interact_plot.R | 94 +++++--- R/internal.R | 54 ++++ R/summ.R | 24 -- README.md | 90 +++---- build/vignette.rds |binary inst/doc/categorical.html | 22 - inst/doc/interactions.html | 66 ++--- inst/doc/summ.html | 240 ++++++++++----------- inst/doc/svycor.html | 4 man/cat_plot.Rd | 3 man/interact_plot.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test-misc.R | 116 ++++++---- tools/README-interact_plot_continuous-1.png |binary tools/README-interact_plot_continuous_points-1.png |binary tools/README-interact_plot_factor-1.png |binary tools/README-j-n-plot-1.png |binary tools/README-theme_apa_ex-1.png |binary tools/README-unnamed-chunk-7-1.png |binary tools/README-unnamed-chunk-8-1.png |binary 24 files changed, 467 insertions(+), 329 deletions(-)
Title: Generalized Correlations and Initial Causal Path
Description: Since causal paths from data are important for all sciences, the
package provides sophisticated functions. The idea is simply
that if X causes Y (path: X to Y) then non-deterministic variation in X
is more "original or independent" than similar variation in Y. We compare
two flipped kernel regressions: X=f(Y, Z) and Y=g(X,Z), where Z are control
variables. Our first two criteria compare absolute cross products
of regressor values and residuals (Cr1) and
absolute residuals (Cr2), are both quantified by stochastic dominance of four
orders (SD1 to SD4). Our third criterion (Cr3) expects X to be better able
to predict Y than the other way around using generalized partial correlation
If |r*(x|y)|> |r*(y|x)| it suggests that y is more likely
the "kernel cause" of x. The usual partial correlations are generalized with
a new non-symmetric matrix developed here.
Partial correlations help asses effect of x on y after removing the effect of a
set of variables.
The package provides additional tools for causal assessment,
for printing the causal directions in a clear, comprehensive compact summary form,
for matrix algebra, for "outlier detection", and for numerical integration by the
trapezoidal rule, stochastic dominance, etc.
The package has functions for bootstrap-based statistical inference and one
for a heuristic t-test.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.0.9 dated 2017-10-03 and 1.1.0 dated 2018-01-05
DESCRIPTION | 17 +++++------ MD5 | 56 +++++++++++++++++++++++-------------- NAMESPACE | 8 +++++ NEWS | 4 ++ R/abs_stdapdC.R | 2 - R/abs_stdrhserC.R |only R/abs_stdrhserr.R |only R/causeSummary.R | 7 ++-- R/causeSummary0.R |only R/comp_portfo2.R | 2 - R/kern_ctrl.R | 2 - R/parcorMany.R | 3 + R/silentMtx0.R |only R/silentPairs.R | 18 +++++------ R/silentPairs0.R |only R/someCPairs.R | 5 +-- R/someCPairs2.R |only R/somePairs2.R |only R/stdres.R |only build/vignette.rds |binary inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary man/abs_stdapdC.Rd | 2 - man/abs_stdrhserC.Rd |only man/abs_stdrhserr.Rd |only man/causeSummary.Rd | 7 ++-- man/causeSummary0.Rd |only man/comp_portfo2.Rd | 2 - man/parcorMany.Rd | 3 + man/silentMtx0.Rd |only man/silentPairs.Rd | 6 +-- man/silentPairs0.Rd |only man/someCPairs.Rd | 5 +-- man/someCPairs2.Rd |only man/somePairs2.Rd |only man/stdres.Rd |only 37 files changed, 90 insertions(+), 59 deletions(-)