Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed
Data
Description: Semi-parametric approach for sparse canonical correlation analysis
which can handle mixed data types: continuous, binary and truncated continuous.
Bridge functions are provided to connect Kendall's tau to latent correlation
under the Gaussian copula model. The methods are described in
Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and
Yoon, Müller and Gaynanova (2020) <arXiv:2006.13875>.
Author: Grace Yoon [aut, cre] (<https://orcid.org/0000-0003-3263-1352>),
Irina Gaynanova [aut] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: Grace Yoon <gyoon6067@gmail.com>
Diff between mixedCCA versions 1.3.1 dated 2020-08-27 and 1.4.3 dated 2020-10-11
mixedCCA-1.3.1/mixedCCA/R/fromKtoR_ipol.R |only mixedCCA-1.4.3/mixedCCA/DESCRIPTION | 17 - mixedCCA-1.4.3/mixedCCA/MD5 | 16 - mixedCCA-1.4.3/mixedCCA/R/GenerateData.R | 4 mixedCCA-1.4.3/mixedCCA/R/KendallTau.R | 59 ++--- mixedCCA-1.4.3/mixedCCA/R/bridgeInv.R | 88 ++----- mixedCCA-1.4.3/mixedCCA/R/estimateR.R | 318 ++++++++++------------------ mixedCCA-1.4.3/mixedCCA/R/fromKtoR.R | 71 ++---- mixedCCA-1.4.3/mixedCCA/R/fromKtoR_ml.R |only mixedCCA-1.4.3/mixedCCA/man/GenerateData.Rd | 4 10 files changed, 227 insertions(+), 350 deletions(-)
Title: Two-Steps Benchmarks for Time Series Disaggregation
Description: The twoStepsBenchmark() function and its wrappers allow you to disaggregate a low frequency time serie with time series of higher frequency, using the French National Accounts methodology.
The aggregated sum of the resulting time-serie is strictly equal to the low-frequency serie within the benchmarking window.
Typically, the low frequency serie is an annual one, unknown for the last year, and the high frequency is either quarterly or mensual.
See "Methodology of quarterly national accounts", Insee Méthodes N°126, by Insee (2012, ISBN:978-2-11-068613-8).
Author: Arnaud Feldmann
Maintainer: Arnaud Feldmann <arnaud.feldmann@gmail.com>
Diff between disaggR versions 0.1.8 dated 2020-10-10 and 0.1.9 dated 2020-10-11
DESCRIPTION | 6 - MD5 | 10 - NEWS.md | 3 R/twoStepsBenchmark.R | 9 - tests/testthat/test-twoStepsBenchmark.R | 2 tests/testthat/test-utils.R | 180 ++++++++++++++++---------------- 6 files changed, 108 insertions(+), 102 deletions(-)
Title: Calculates Demographic Indicators
Description: Calculates key indicators such as fertility rates (Total Fertility Rate (TFR), General Fertility Rate (GFR),
and Age Specific Fertility Rate (ASFR)) using Demographic and Health Survey (DHS) women/individual data,
childhood mortality probabilities and rates such as Neonatal Mortality Rate (NNMR), Post-neonatal Mortality Rate (PNNMR),
Infant Mortality Rate (IMR), Child Mortality Rate (CMR), and Under-five Mortality Rate (U5MR), and adult mortality indicators
such as the Age Specific Mortality Rate (ASMR), Age Adjusted Mortality Rate (AAMR), Age Specific Maternal Mortality Rate (ASMMR),
Age Adjusted Maternal Mortality Rate (AAMMR), Age Specific Pregnancy Related Mortality Rate (ASPRMR),
Age Adjusted Pregnancy Related Mortality Rate (AAPRMR), Maternal Mortality Ratio (MMR) and Pregnancy Related Mortality Ratio (PRMR).
In addition to the indicators, the 'DHS.rates' package estimates sampling errors indicators such as Standard Error (SE),
Design Effect (DEFT), Relative Standard Error (RSE) and Confidence Interval (CI).
The package is developed according to the DHS methodology of calculating the fertility indicators and
the childhood mortality rates outlined in the
"Guide to DHS Statistics" (Croft, Trevor N., Aileen M. J. Marshall, Courtney K. Allen, et al. 2018, <https://dhsprogram.com/Data/Guide-to-DHS-Statistics/index.cfm>)
and the DHS methodology of estimating the sampling errors indicators outlined in
the "DHS Sampling and Household Listing Manual" (ICF International 2012, <https://dhsprogram.com/pubs/pdf/DHSM4/DHS6_Sampling_Manual_Sept2012_DHSM4.pdf>).
Author: Mahmoud Elkasabi
Maintainer: Mahmoud Elkasabi <mahmoud.elkasabi@icf.com>
Diff between DHS.rates versions 0.7.1 dated 2020-05-18 and 0.8.0 dated 2020-10-11
DESCRIPTION | 20 ++++++++----- MD5 | 37 +++++++++++++++++-------- NAMESPACE | 3 ++ R/AAGFR.R |only R/AAMMR.R |only R/AAMR.R |only R/AAPRMR.R |only R/ASFR.R | 3 ++ R/ASMMR.R |only R/ASMR.R |only R/ASPRMR.R |only R/CHMORT5.R | 2 + R/DataPrepareM.R |only R/DataPrepareM_GFR.R |only R/GFR.R | 3 ++ R/MMR.R |only R/PRMR.R |only R/TFR.R | 3 ++ R/admort.R |only R/chmort.R | 2 - R/fert.R | 4 -- build/vignette.rds |binary inst/doc/DHS.rates.html | 70 ++++++++++++++++++++++++------------------------ man/admort.Rd |only man/chmort.Rd | 2 - man/fert.Rd | 2 - 26 files changed, 91 insertions(+), 60 deletions(-)
Title: Biterm Topic Models for Short Text
Description: Biterm Topic Models find topics in collections of short texts.
It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms.
This in contrast to traditional topic models like Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis
which are word-document co-occurrence topic models.
A biterm consists of two words co-occurring in the same short text window.
This context window can for example be a twitter message, a short answer on a survey, a sentence of a text or a document identifier.
The techniques are explained in detail in the paper 'A Biterm Topic Model For Short Text' by Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) <https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/BTM-WWW13.pdf>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Xiaohui Yan [ctb, cph] (BTM C++ library)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between BTM versions 0.3.3 dated 2020-10-10 and 0.3.4 dated 2020-10-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/rcpp_BTM.cpp | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal, or
conservative). The objective of this package is to make it as simple as
possible to identify global objects for the purpose of exporting them in
parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph],
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.13.0 dated 2020-09-17 and 0.13.1 dated 2020-10-11
DESCRIPTION | 23 ++++++++------ MD5 | 16 ++++----- NEWS | 22 +++++++++++++ R/findGlobals.R | 87 ++++++++++++++++++++++++++++++++++++++++++------------ R/utils.R | 1 inst/WORDLIST | 20 ++++++++++++ tests/dotdotdot.R | 9 +++++ tests/formulas.R | 23 ++++++++++++++ tests/utils.R | 8 ++++ 9 files changed, 172 insertions(+), 37 deletions(-)
Title: Statistical Models for Word Frequency Distributions
Description: Statistical models and utilities for the analysis of word frequency distributions.
The utilities include functions for loading, manipulating and visualizing word frequency
data and vocabulary growth curves. The package also implements several statistical
models for the distribution of word frequencies in a population. (The name of this package
derives from the most famous word frequency distribution, Zipf's law.)
Author: Stefan Evert <stefan.evert@fau.de>, Marco Baroni <marco.baroni@unitn.it>
Maintainer: Stefan Evert <stefan.evert@fau.de>
Diff between zipfR versions 0.6-66 dated 2019-10-01 and 0.6-70 dated 2020-10-11
DESCRIPTION | 12 +- MD5 | 158 +++++++++++++++--------------- NAMESPACE | 5 NEWS | 29 +++-- R/VV_vgc.R | 2 R/VVm_vgc.R | 2 R/V_vgc.R | 2 R/Vm_vgc.R | 2 R/bootstrap_confint.R | 9 + R/lnre.R | 29 +++-- R/lnre_bootstrap.R | 102 +++++++++++++------ R/lnre_fzm.R | 8 + R/lnre_gigp.R | 4 R/lnre_productivity_measures.R |only R/lnre_spc.R | 2 R/lnre_zm.R | 9 + R/plot_lnre.R |only R/plot_spc.R | 33 +++--- R/plot_tfl.R | 135 +++++++++++++++++-------- R/plot_vgc.R | 49 ++++----- R/productivity_measures.R | 2 R/productivity_measures_default.R | 4 R/productivity_measures_spc.R | 52 ++++++--- R/productivity_measures_tfl.R | 4 R/productivity_measures_vgc.R | 35 +++--- R/spc.R | 1 R/tfl2spc.R | 4 R/zipfR_par.R | 24 ++-- TODO | 32 +++--- build/vignette.rds |binary data/Baayen2001.rda |binary data/Brown.emp.vgc.rda |binary data/Brown.spc.rda |binary data/Brown100k.spc.rda |binary data/BrownAdj.emp.vgc.rda |binary data/BrownAdj.spc.rda |binary data/BrownImag.emp.vgc.rda |binary data/BrownImag.spc.rda |binary data/BrownInform.emp.vgc.rda |binary data/BrownInform.spc.rda |binary data/BrownNoun.emp.vgc.rda |binary data/BrownNoun.spc.rda |binary data/BrownVer.emp.vgc.rda |binary data/BrownVer.spc.rda |binary data/Dickens.emp.vgc.rda |binary data/Dickens.spc.rda |binary data/DickensGreatExpectations.emp.vgc.rda |binary data/DickensGreatExpectations.spc.rda |binary data/DickensOliverTwist.emp.vgc.rda |binary data/DickensOliverTwist.spc.rda |binary data/DickensOurMutualFriend.emp.vgc.rda |binary data/DickensOurMutualFriend.spc.rda |binary data/EvertLuedeling2001.rda |binary data/ItaRi.emp.vgc.rda |binary data/ItaRi.spc.rda |binary data/ItaUltra.emp.vgc.rda |binary data/ItaUltra.spc.rda |binary data/TigerNP.emp.vgc.rda |binary data/TigerNP.spc.rda |binary data/TigerNP.tfl.rda |binary data/TigerPP.emp.vgc.rda |binary data/TigerPP.spc.rda |binary data/TigerPP.tfl.rda |binary inst/doc/zipfr-tutorial.R | 1 inst/doc/zipfr-tutorial.Rnw | 4 inst/doc/zipfr-tutorial.pdf |binary man/Dickens.Rd | 4 man/N_V_Vm_vgc.Rd | 2 man/Tiger.Rd | 2 man/beta_gamma.Rd | 4 man/bootstrap_confint.Rd | 25 ++-- man/lnre.Rd | 27 ++++- man/lnre_bootstrap.Rd | 83 +++++++++++++-- man/lnre_productivity_measures.Rd |only man/lnre_technical_details.Rd | 6 - man/plot_lnre.Rd |only man/plot_spc.Rd | 24 ++-- man/plot_tfl.Rd | 109 +++++++++++++++----- man/plot_vgc.Rd | 28 +++-- man/productivity_measures.Rd | 139 ++++++++++++++++++-------- man/zipfR_package.Rd | 11 +- vignettes/zipfr-tutorial.Rnw | 4 82 files changed, 802 insertions(+), 421 deletions(-)
Title: Named Entity Recognition in Texts using 'NameTag'
Description: Wraps the 'nametag' library <https://github.com/ufal/nametag>, allowing users to find and extract entities (names, persons, locations, addresses, ...) in raw text and build your own entity recognition models.
Based on a maximum entropy Markov model which is described in Strakova J., Straka M. and Hajic J. (2013) <http://ufal.mff.cuni.cz/~straka/papers/2013-tsd_ner.pdf>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between nametagger versions 0.1.0 dated 2020-06-04 and 0.1.1 dated 2020-10-11
DESCRIPTION | 12 ++++---- MD5 | 20 +++++++------- NAMESPACE | 3 -- NEWS.md | 5 +++ R/datasets.R | 3 ++ R/nametagger.R | 54 +++++++++++++++++++++++++++++++-------- R/pkg.R | 1 man/europeana_read.Rd | 3 ++ man/nametagger.Rd | 5 ++- man/nametagger_download_model.Rd | 2 - man/nametagger_options.Rd | 4 +- 11 files changed, 77 insertions(+), 35 deletions(-)
Title: Optimal Designs for Nonlinear Statistical Models by Imperialist
Competitive Algorithm (ICA)
Description: Finds optimal designs for nonlinear models using a metaheuristic algorithm called Imperialist Competitive Algorithm (ICA). See, for details, Masoudi et al. (2017) <doi:10.1016/j.csda.2016.06.014> and Masoudi et al. (2019) <doi:10.1080/10618600.2019.1601097>.
Author: Ehsan Masoudi [aut, cre],
Heinz Holling [aut],
Weng Kee Wong [aut],
Seongho Kim [ctb]
Maintainer: Ehsan Masoudi <esn_mud@yahoo.com>
Diff between ICAOD versions 1.0.0 dated 2020-08-02 and 1.0.1 dated 2020-10-11
ICAOD-1.0.0/ICAOD/build |only ICAOD-1.0.0/ICAOD/inst/doc |only ICAOD-1.0.0/ICAOD/vignettes |only ICAOD-1.0.1/ICAOD/DESCRIPTION | 12 ++++++------ ICAOD-1.0.1/ICAOD/MD5 | 6 +----- 5 files changed, 7 insertions(+), 11 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines" <doi:10.1214/aos/1176347963>.
(The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 5.2.0 dated 2020-09-16 and 5.3.0 dated 2020-10-11
earth-5.2.0/earth/inst/slowtests/test.earthc.bat |only earth-5.2.0/earth/inst/slowtests/test.earthc.mak |only earth-5.2.0/earth/inst/slowtests/test.earthmain.vc.bat |only earth-5.3.0/earth/DESCRIPTION | 8 earth-5.3.0/earth/MD5 | 107 earth-5.3.0/earth/NEWS | 24 earth-5.3.0/earth/build/partial.rdb |binary earth-5.3.0/earth/inst/doc/earth-notes.pdf |binary earth-5.3.0/earth/inst/doc/earth-varmod.pdf |binary earth-5.3.0/earth/inst/doc/index.html | 2 earth-5.3.0/earth/inst/slowtests/earth.times.bat | 2 earth-5.3.0/earth/inst/slowtests/make.bat | 21 earth-5.3.0/earth/inst/slowtests/makeclean.bat |only earth-5.3.0/earth/inst/slowtests/test.allowedfunc.bat | 2 earth-5.3.0/earth/inst/slowtests/test.big.bat | 2 earth-5.3.0/earth/inst/slowtests/test.bpairs.bat | 2 earth-5.3.0/earth/inst/slowtests/test.cv.bat | 2 earth-5.3.0/earth/inst/slowtests/test.earthc.c | 183 earth-5.3.0/earth/inst/slowtests/test.earthc.clang.bat |only earth-5.3.0/earth/inst/slowtests/test.earthc.gcc.bat |only earth-5.3.0/earth/inst/slowtests/test.earthc.msc.bat |only earth-5.3.0/earth/inst/slowtests/test.earthc.msc.mak |only earth-5.3.0/earth/inst/slowtests/test.earthc.out.save | 5327 +++++----- earth-5.3.0/earth/inst/slowtests/test.earthmain.clang.bat | 24 earth-5.3.0/earth/inst/slowtests/test.earthmain.gcc.bat | 42 earth-5.3.0/earth/inst/slowtests/test.earthmain.gcc64.bat | 21 earth-5.3.0/earth/inst/slowtests/test.earthmain.msc.bat |only earth-5.3.0/earth/inst/slowtests/test.emma.Rout.save | 2 earth-5.3.0/earth/inst/slowtests/test.emma.bat | 2 earth-5.3.0/earth/inst/slowtests/test.expand.bpairs.bat | 2 earth-5.3.0/earth/inst/slowtests/test.full.R | 88 earth-5.3.0/earth/inst/slowtests/test.full.Rout.save | 524 earth-5.3.0/earth/inst/slowtests/test.full.bat | 2 earth-5.3.0/earth/inst/slowtests/test.glm.R | 4 earth-5.3.0/earth/inst/slowtests/test.glm.Rout.save | 56 earth-5.3.0/earth/inst/slowtests/test.glm.bat | 2 earth-5.3.0/earth/inst/slowtests/test.incorrect.bat | 2 earth-5.3.0/earth/inst/slowtests/test.mem.Rout.save | 143 earth-5.3.0/earth/inst/slowtests/test.mem.bat | 2 earth-5.3.0/earth/inst/slowtests/test.mods.R | 6 earth-5.3.0/earth/inst/slowtests/test.mods.Rout.save | 228 earth-5.3.0/earth/inst/slowtests/test.mods.bat | 2 earth-5.3.0/earth/inst/slowtests/test.multresp.bat | 2 earth-5.3.0/earth/inst/slowtests/test.numstab-mfpmath-387.Rout.save |only earth-5.3.0/earth/inst/slowtests/test.numstab.R |only earth-5.3.0/earth/inst/slowtests/test.numstab.Rout.save |only earth-5.3.0/earth/inst/slowtests/test.numstab.bat |only earth-5.3.0/earth/inst/slowtests/test.offset.bat | 2 earth-5.3.0/earth/inst/slowtests/test.ordinal.bat | 2 earth-5.3.0/earth/inst/slowtests/test.plotd.bat | 2 earth-5.3.0/earth/inst/slowtests/test.pmethod.cv.bat | 2 earth-5.3.0/earth/inst/slowtests/test.varmod.bat | 2 earth-5.3.0/earth/inst/slowtests/test.varmod.mgcv.bat | 2 earth-5.3.0/earth/inst/slowtests/test.weights.R | 5 earth-5.3.0/earth/inst/slowtests/test.weights.Rout.save | 53 earth-5.3.0/earth/inst/slowtests/test.weights.bat | 2 earth-5.3.0/earth/man/earth.object.Rd | 11 earth-5.3.0/earth/man/mars.to.earth.Rd | 2 earth-5.3.0/earth/src/allowed.c | 15 earth-5.3.0/earth/src/earth.c | 93 earth-5.3.0/earth/src/rentries.c | 7 61 files changed, 3799 insertions(+), 3237 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016) <https://learning-analytics.info/index.php/JLA/article/view/4329>.
Author: Cody L Marquart [aut, cre] (<https://orcid.org/0000-0002-3387-6792>),
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rENA versions 0.2.1.1 dated 2020-10-02 and 0.2.1.2 dated 2020-10-11
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- NEWS.md | 7 ++++- inst/CITATION | 2 - inst/doc/getting-started.html | 34 ++++++++++++------------- inst/doc/means-rotation.html | 8 ++--- src/ena.cpp | 2 - tests/testthat/test.ena.accumulate.data.file.R | 5 ++- 8 files changed, 43 insertions(+), 35 deletions(-)
Title: A Poor Man's Dependency Free Recreation of 'dplyr'
Description: A replication of key functionality from 'dplyr' and the wider 'tidyverse' using only 'base'.
Author: Nathan Eastwood [aut, cre]
Maintainer: Nathan Eastwood <nathan.eastwood@icloud.com>
Diff between poorman versions 0.2.1 dated 2020-07-01 and 0.2.2 dated 2020-10-11
poorman-0.2.1/poorman/R/reexports.R |only poorman-0.2.1/poorman/man/joins.Rd |only poorman-0.2.2/poorman/DESCRIPTION | 20 +- poorman-0.2.2/poorman/MD5 | 90 +++++++----- poorman-0.2.2/poorman/NAMESPACE | 12 + poorman-0.2.2/poorman/NEWS.md | 62 ++++++-- poorman-0.2.2/poorman/R/bind.R |only poorman-0.2.2/poorman/R/case_when.R |only poorman-0.2.2/poorman/R/coalesce.R | 5 poorman-0.2.2/poorman/R/context.R | 8 + poorman-0.2.2/poorman/R/count-tally.R | 6 poorman-0.2.2/poorman/R/group_cols.R |only poorman-0.2.2/poorman/R/joins.R | 22 ++- poorman-0.2.2/poorman/R/joins_filtering.R | 2 poorman-0.2.2/poorman/R/na_if.R | 4 poorman-0.2.2/poorman/R/nest_by.R |only poorman-0.2.2/poorman/R/pipe.R | 63 +++++++- poorman-0.2.2/poorman/R/pull.R | 14 - poorman-0.2.2/poorman/R/recode.R | 3 poorman-0.2.2/poorman/R/relocate.R | 3 poorman-0.2.2/poorman/R/rename.R | 39 +++++ poorman-0.2.2/poorman/R/replace_na.R | 5 poorman-0.2.2/poorman/R/select_helpers.R | 4 poorman-0.2.2/poorman/R/select_positions.R | 11 - poorman-0.2.2/poorman/R/slice.R | 18 +- poorman-0.2.2/poorman/R/unite.R |only poorman-0.2.2/poorman/R/utils.R | 33 +--- poorman-0.2.2/poorman/R/where.R | 2 poorman-0.2.2/poorman/README.md | 100 +++++++------- poorman-0.2.2/poorman/build |only poorman-0.2.2/poorman/inst/doc |only poorman-0.2.2/poorman/inst/tinytest/test_bind.R |only poorman-0.2.2/poorman/inst/tinytest/test_case_when.R |only poorman-0.2.2/poorman/inst/tinytest/test_joins_filter.R | 18 ++ poorman-0.2.2/poorman/inst/tinytest/test_nest_by.R |only poorman-0.2.2/poorman/inst/tinytest/test_pipe.R |only poorman-0.2.2/poorman/inst/tinytest/test_relocate.R | 12 + poorman-0.2.2/poorman/inst/tinytest/test_rename_with.R |only poorman-0.2.2/poorman/inst/tinytest/test_select_helpers.R | 17 ++ poorman-0.2.2/poorman/inst/tinytest/test_unite.R |only poorman-0.2.2/poorman/man/bind.Rd |only poorman-0.2.2/poorman/man/case_when.Rd |only poorman-0.2.2/poorman/man/coalesce.Rd | 5 poorman-0.2.2/poorman/man/context.Rd | 7 poorman-0.2.2/poorman/man/group_cols.Rd |only poorman-0.2.2/poorman/man/mutate_joins.Rd |only poorman-0.2.2/poorman/man/na_if.Rd | 4 poorman-0.2.2/poorman/man/nest_by.Rd |only poorman-0.2.2/poorman/man/pipe.Rd | 38 ++++- poorman-0.2.2/poorman/man/poorman.Rd | 5 poorman-0.2.2/poorman/man/recode.Rd | 3 poorman-0.2.2/poorman/man/rename.Rd | 24 +++ poorman-0.2.2/poorman/man/replace_na.Rd | 5 poorman-0.2.2/poorman/man/select_helpers.Rd | 2 poorman-0.2.2/poorman/man/unite.Rd |only poorman-0.2.2/poorman/vignettes |only 56 files changed, 478 insertions(+), 188 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-23 1.0-1
2014-07-17 1.0
Title: Taxonomic Monographs Tools
Description: Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology charts and distributional and diversity maps are also available.
Author: Marcelo Reginato
Maintainer: Marcelo Reginato <reginatobio@yahoo.com.br>
Diff between monographaR versions 1.2.0 dated 2016-07-13 and 1.2.1 dated 2020-10-11
monographaR-1.2.0/monographaR/R/monographaR-internal.R |only monographaR-1.2.1/monographaR/DESCRIPTION | 10 monographaR-1.2.1/monographaR/MD5 | 37 monographaR-1.2.1/monographaR/R/buildMonograph.R | 15 monographaR-1.2.1/monographaR/R/collectorList.R | 15 monographaR-1.2.1/monographaR/R/collectorList2.R | 9 monographaR-1.2.1/monographaR/R/mapBatch.R | 5 monographaR-1.2.1/monographaR/R/mapPhenology.R | 4 monographaR-1.2.1/monographaR/R/mapTable.R | 24 monographaR-1.2.1/monographaR/R/tableToDescription.R | 5 monographaR-1.2.1/monographaR/R/tableToDescription2.R | 1 monographaR-1.2.1/monographaR/build/vignette.rds |binary monographaR-1.2.1/monographaR/data/monographaR_examples.rda |binary monographaR-1.2.1/monographaR/inst/doc/tutorial.R | 78 - monographaR-1.2.1/monographaR/inst/doc/tutorial.Rmd | 2 monographaR-1.2.1/monographaR/inst/doc/tutorial.html | 868 ++++++++---- monographaR-1.2.1/monographaR/man/buildMonograph.Rd | 6 monographaR-1.2.1/monographaR/man/mapTable.Rd | 14 monographaR-1.2.1/monographaR/man/monographaR-package.Rd | 8 monographaR-1.2.1/monographaR/vignettes/tutorial.Rmd | 2 20 files changed, 743 insertions(+), 360 deletions(-)
Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of
isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>),
SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
and fair-cut forest (Cortes (2019) <arXiv:1911.06646>),
for isolation-based outlier detection, clustered outlier detection, distance or similarity
approximation (Cortes (2019) <arXiv:1910.12362>),
and imputation of missing values (Cortes (2019) <arXiv:1911.06646>),
based on random or guided decision tree splitting. Provides simple heuristics for fitting the model to
categorical columns and handling missing data, and offers options for varying between random and guided
splits, and for using different splitting criteria.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between isotree versions 0.1.18 dated 2020-07-29 and 0.1.19 dated 2020-10-11
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/helpers.R | 17 +++++++++++++---- R/isoforest.R | 33 ++++++++++++++++++++------------- man/export.isotree.model.Rd | 2 +- man/isolation.forest.Rd | 2 +- man/predict.isolation_forest.Rd | 23 +++++++++++++++-------- src/Rwrapper.cpp | 3 +++ src/dist.cpp | 6 +++--- src/fit_model.cpp | 11 +++++++++++ src/merge_models.cpp | 2 +- src/predict.cpp | 2 +- 12 files changed, 85 insertions(+), 48 deletions(-)
Title: Cache 'CRAN'-Like Metadata and R Packages
Description: Metadata and package cache for CRAN-like repositories.
This is a utility package to be used by package management tools
that want to take advantage of caching.
Author: Gábor Csárdi [aut, cre]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between pkgcache versions 1.1.0 dated 2020-07-07 and 1.1.1 dated 2020-10-11
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 13 ++++++++++++- R/aaa-async.R | 14 +++++++------- R/async-http.R | 16 ++++++++-------- R/progress-bar.R | 19 ++++++++++++++----- README.md | 12 ++++++++---- man/pkgcache-package.Rd | 3 +++ tests/test-async.R | 20 +++++--------------- tests/testthat.R | 2 +- tests/testthat/test-4-async-http.R | 1 + 11 files changed, 72 insertions(+), 54 deletions(-)
Title: Time Zone Database Updater
Description: Download and compile any version of the
IANA Time Zone Database (also known as Olson database)
and make it current in your R session.
Beware: on Windows 'Cygwin' is required!
Author: Sebastien Thonnard
Maintainer: Sebastien Thonnard <sebastien.thonnard@icloud.com>
Diff between tzupdater versions 0.1.1 dated 2020-08-12 and 0.1.2 dated 2020-10-11
DESCRIPTION | 8 - MD5 | 6 R/hidden.R | 17 ++ R/tzupdater.R | 393 +++++++++++++++++++++++++++++++++++++--------------------- 4 files changed, 273 insertions(+), 151 deletions(-)
Title: Visualizes a Matrix as Heatmap
Description: Visualizes a matrix object plainly as heatmap. It provides S3 functions to plot simple matrices and loading matrices.
Author: Sigbert Klinke [aut, cre],
Frédéric Chevalier [ctb]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between plot.matrix versions 1.4 dated 2019-12-09 and 1.5.1 dated 2020-10-11
DESCRIPTION | 10 MD5 | 46 +-- R/data.R | 10 R/plot.assoc.R | 3 R/plot.cor.R | 3 R/plot.loadings.R | 3 R/plot.matrix.R | 43 ++- R/plot.pvalue.R | 1 README.md | 3 build/vignette.rds |binary data/air.pvalue.rda |binary inst/doc/plot.matrix.R | 88 ++++-- inst/doc/plot.matrix.Rmd | 34 ++ inst/doc/plot.matrix.html | 586 +++++++++++++++++++++++++++++++++------------- man/Titanic.cramer.Rd | 6 man/air.pvalue.Rd | 6 man/bfi.2.Rd | 14 - man/ind.Rd | 6 man/plot.assoc.Rd | 3 man/plot.cor.Rd | 3 man/plot.loadings.Rd | 3 man/plot.matrix.Rd | 51 +++- man/plot.pvalue.Rd | 3 vignettes/plot.matrix.Rmd | 34 ++ 24 files changed, 682 insertions(+), 277 deletions(-)
Title: Conditional Binary Quantile Models
Description: Estimates conditional binary quantile models developed by Lu (2020) <doi:10.1017/pan.2019.29>. The estimation procedure is implemented based on Markov chain Monte Carlo methods.
Author: Xiao Lu
Maintainer: Xiao LU <xiao.lu.research@gmail.com>
Diff between cbq versions 0.2.0.1 dated 2020-05-27 and 0.2.0.2 dated 2020-10-11
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + R/cbq-package.R | 3 ++- R/cbq.R | 2 +- README.md | 5 +++-- man/cbq-package.Rd | 2 +- man/cbq.Rd | 2 +- 8 files changed, 22 insertions(+), 18 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports
the static site generator 'Hugo' (<https://gohugo.io>) best, and it also
supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Beilei Bian [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
JJ Allaire [ctb],
Kevin Ushey [ctb],
Leonardo Collado-Torres [ctb],
Xianying Tan [ctb],
Raniere Silva [ctb],
Jozef Hajnala [ctb],
RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 0.20 dated 2020-06-23 and 0.21 dated 2020-10-11
DESCRIPTION | 18 +- MD5 | 46 +++--- NAMESPACE | 8 + NEWS.md | 42 ++++++ R/format.R | 5 R/hugo.R | 162 ++++++++++++++++++++--- R/install.R | 4 R/package.R | 10 + R/render.R | 99 +++++++++----- R/serve.R | 278 ++++++++++++++++++++++++++++------------ R/site.R | 43 ++++-- R/utils.R | 217 +++++++++++++++++++++++++------ README.md | 4 inst/scripts/child_pids.sh |only inst/scripts/render_page.R | 4 inst/scripts/render_rmarkdown.R | 2 man/build_site.Rd | 54 +++++-- man/bundle_site.Rd |only man/html_page.Rd | 3 man/hugo_cmd.Rd | 14 +- man/install_theme.Rd | 2 man/md5sum_filter.Rd |only man/read_toml.Rd |only man/serve_site.Rd | 53 +++++-- tests/testit/test-list.R | 2 tests/testit/test-utils.R | 6 26 files changed, 804 insertions(+), 272 deletions(-)
Title: Matrix Bending
Description: Bending non-positive-definite (symmetric) matrices to positive-definite, using weighted and unweighted methods.
Jorjani, H., et al. (2003) <doi:10.3168/jds.S0022-0302(03)73646-7>.
Schaeffer, L. R. (2014) <http://animalbiosciences.uoguelph.ca/~lrs/ELARES/PDforce.pdf>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between mbend versions 1.3.0 dated 2020-06-05 and 1.3.1 dated 2020-10-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 - NEWS.md | 5 +++++ R/bend.R | 2 +- build/vignette.rds |binary 6 files changed, 15 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-21 1.5.1
2016-08-26 1.5
2016-04-04 1.2.1
2016-03-30 1.2
2016-03-16 1.0
2016-01-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-13 0.1.2
2017-02-09 0.1.1
Title: Data Visualization for IP Addresses and Networks
Description: A 'ggplot2' extension that enables visualization of
IP (Internet Protocol) addresses and networks. The address space is
mapped onto the Cartesian coordinate system using a space-filling
curve. Offers full support for both IPv4 and IPv6 (Internet Protocol
versions 4 and 6) address spaces.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ggip versions 0.1.0 dated 2020-09-25 and 0.2.0 dated 2020-10-11
DESCRIPTION | 11 +-- MD5 | 32 +++++---- NAMESPACE | 7 ++ NEWS.md |only R/geom-hilbert-outline.R |only R/ggip-package.R | 1 R/stat-summary-address.R | 12 ++- R/vctrs-coords.R | 26 +++++++ README.md | 19 ++++- inst/doc/ggip.html | 2 inst/doc/visualizing-ip-data.R | 30 +++++++- inst/doc/visualizing-ip-data.Rmd | 40 ++++++++++- inst/doc/visualizing-ip-data.html | 98 +++++++++++++++++++++++++++++ man/figures/README-ipv4-heatmap-1.png |binary man/geom_hilbert_outline.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/test-geom-hilbert-outline.R |only tests/testthat/test-stat-summary-address.R | 13 +++ tests/testthat/test-theme-ip.R |only vignettes/visualizing-ip-data.Rmd | 40 ++++++++++- 20 files changed, 292 insertions(+), 39 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [aut] (<https://orcid.org/0000-0001-8008-2787>),
John Hickey [aut] (<https://orcid.org/0000-0001-5675-3974>),
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 0.12.2 dated 2020-05-19 and 0.13.0 dated 2020-10-11
AlphaSimR-0.12.2/AlphaSimR/man/AlphaSimR.Rd |only AlphaSimR-0.13.0/AlphaSimR/DESCRIPTION | 21 AlphaSimR-0.13.0/AlphaSimR/LICENSE | 2 AlphaSimR-0.13.0/AlphaSimR/MD5 | 280 AlphaSimR-0.13.0/AlphaSimR/NAMESPACE | 240 AlphaSimR-0.13.0/AlphaSimR/NEWS | 340 - AlphaSimR-0.13.0/AlphaSimR/R/AlphaSimR.R | 63 AlphaSimR-0.13.0/AlphaSimR/R/Class-HybridPop.R | 248 AlphaSimR-0.13.0/AlphaSimR/R/Class-LociMap.R | 616 - AlphaSimR-0.13.0/AlphaSimR/R/Class-Pop.R | 1156 +-- AlphaSimR-0.13.0/AlphaSimR/R/Class-RRsol.R | 44 AlphaSimR-0.13.0/AlphaSimR/R/Class-SimParam.R | 3723 +++++------ AlphaSimR-0.13.0/AlphaSimR/R/GS.R | 2726 ++++---- AlphaSimR-0.13.0/AlphaSimR/R/RcppExports.R | 360 - AlphaSimR-0.13.0/AlphaSimR/R/crossing.R | 1614 ++-- AlphaSimR-0.13.0/AlphaSimR/R/founderPop.R | 818 +- AlphaSimR-0.13.0/AlphaSimR/R/hybrids.R | 624 - AlphaSimR-0.13.0/AlphaSimR/R/mergePops.R | 267 AlphaSimR-0.13.0/AlphaSimR/R/misc.R | 1136 +-- AlphaSimR-0.13.0/AlphaSimR/R/phenotypes.R | 292 AlphaSimR-0.13.0/AlphaSimR/R/polyploids.R | 562 - AlphaSimR-0.13.0/AlphaSimR/R/popSummary.R | 1204 +-- AlphaSimR-0.13.0/AlphaSimR/R/pullGeno.R | 1574 ++-- AlphaSimR-0.13.0/AlphaSimR/R/selection.R | 818 +- AlphaSimR-0.13.0/AlphaSimR/R/writeRecords.R | 214 AlphaSimR-0.13.0/AlphaSimR/README.md | 18 AlphaSimR-0.13.0/AlphaSimR/build/vignette.rds |binary AlphaSimR-0.13.0/AlphaSimR/inst/doc/intro.R | 100 AlphaSimR-0.13.0/AlphaSimR/inst/doc/intro.Rmd | 264 AlphaSimR-0.13.0/AlphaSimR/inst/doc/intro.html | 909 +- AlphaSimR-0.13.0/AlphaSimR/inst/doc/traits.Rmd | 372 - AlphaSimR-0.13.0/AlphaSimR/inst/doc/traits.pdf |binary AlphaSimR-0.13.0/AlphaSimR/man/AlphaSimR-package.Rd |only AlphaSimR-0.13.0/AlphaSimR/man/HybridPop-class.Rd | 106 AlphaSimR-0.13.0/AlphaSimR/man/LociMap-class.Rd | 38 AlphaSimR-0.13.0/AlphaSimR/man/MapPop-class.Rd | 82 AlphaSimR-0.13.0/AlphaSimR/man/Pop-class.Rd | 144 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP.Rd | 138 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP2.Rd | 230 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUPMemUse.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP_D.Rd | 140 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP_D2.Rd | 184 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP_GCA.Rd | 142 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP_GCA2.Rd | 182 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP_SCA.Rd | 140 AlphaSimR-0.13.0/AlphaSimR/man/RRBLUP_SCA2.Rd | 190 AlphaSimR-0.13.0/AlphaSimR/man/RRsol-class.Rd | 52 AlphaSimR-0.13.0/AlphaSimR/man/RawPop-class.Rd | 106 AlphaSimR-0.13.0/AlphaSimR/man/SimParam.Rd | 3172 ++++----- AlphaSimR-0.13.0/AlphaSimR/man/TraitA-class.Rd | 36 AlphaSimR-0.13.0/AlphaSimR/man/TraitA2-class.Rd | 34 AlphaSimR-0.13.0/AlphaSimR/man/TraitA2D-class.Rd | 32 AlphaSimR-0.13.0/AlphaSimR/man/TraitAD-class.Rd | 32 AlphaSimR-0.13.0/AlphaSimR/man/TraitADE-class.Rd | 32 AlphaSimR-0.13.0/AlphaSimR/man/TraitADEG-class.Rd | 40 AlphaSimR-0.13.0/AlphaSimR/man/TraitADG-class.Rd | 40 AlphaSimR-0.13.0/AlphaSimR/man/TraitAE-class.Rd | 32 AlphaSimR-0.13.0/AlphaSimR/man/TraitAEG-class.Rd | 40 AlphaSimR-0.13.0/AlphaSimR/man/TraitAG-class.Rd | 40 AlphaSimR-0.13.0/AlphaSimR/man/aa.Rd | 62 AlphaSimR-0.13.0/AlphaSimR/man/bv.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/cChr.Rd | 50 AlphaSimR-0.13.0/AlphaSimR/man/calcGCA.Rd | 72 AlphaSimR-0.13.0/AlphaSimR/man/dd.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/doubleGenome.Rd | 78 AlphaSimR-0.13.0/AlphaSimR/man/ebv.Rd | 58 AlphaSimR-0.13.0/AlphaSimR/man/editGenome.Rd | 96 AlphaSimR-0.13.0/AlphaSimR/man/editGenomeTopQtl.Rd | 88 AlphaSimR-0.13.0/AlphaSimR/man/fastRRBLUP.Rd | 154 AlphaSimR-0.13.0/AlphaSimR/man/genParam.Rd | 128 AlphaSimR-0.13.0/AlphaSimR/man/genicVarA.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/genicVarAA.Rd | 62 AlphaSimR-0.13.0/AlphaSimR/man/genicVarD.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/genicVarG.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/getQtlMap.Rd | 80 AlphaSimR-0.13.0/AlphaSimR/man/getSnpMap.Rd | 82 AlphaSimR-0.13.0/AlphaSimR/man/gv.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/hybridCross.Rd | 100 AlphaSimR-0.13.0/AlphaSimR/man/makeCross.Rd | 82 AlphaSimR-0.13.0/AlphaSimR/man/makeCross2.Rd | 86 AlphaSimR-0.13.0/AlphaSimR/man/makeDH.Rd | 84 AlphaSimR-0.13.0/AlphaSimR/man/meanG.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/meanP.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/mergeGenome.Rd | 84 AlphaSimR-0.13.0/AlphaSimR/man/mergePops.Rd | 62 AlphaSimR-0.13.0/AlphaSimR/man/mutate.Rd | 92 AlphaSimR-0.13.0/AlphaSimR/man/nInd.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/newMapPop.Rd | 100 AlphaSimR-0.13.0/AlphaSimR/man/newPop.Rd | 112 AlphaSimR-0.13.0/AlphaSimR/man/pedigreeCross.Rd | 158 AlphaSimR-0.13.0/AlphaSimR/man/pheno.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/popVar.Rd | 40 AlphaSimR-0.13.0/AlphaSimR/man/pullIbdHaplo.Rd | 118 AlphaSimR-0.13.0/AlphaSimR/man/pullQtlGeno.Rd | 188 AlphaSimR-0.13.0/AlphaSimR/man/pullQtlHaplo.Rd | 254 AlphaSimR-0.13.0/AlphaSimR/man/pullSegSiteGeno.Rd | 74 AlphaSimR-0.13.0/AlphaSimR/man/pullSegSiteHaplo.Rd | 82 AlphaSimR-0.13.0/AlphaSimR/man/pullSnpGeno.Rd | 78 AlphaSimR-0.13.0/AlphaSimR/man/pullSnpHaplo.Rd | 86 AlphaSimR-0.13.0/AlphaSimR/man/quickHaplo.Rd | 70 AlphaSimR-0.13.0/AlphaSimR/man/randCross.Rd | 106 AlphaSimR-0.13.0/AlphaSimR/man/randCross2.Rd | 124 AlphaSimR-0.13.0/AlphaSimR/man/reduceGenome.Rd | 108 AlphaSimR-0.13.0/AlphaSimR/man/resetPop.Rd | 72 AlphaSimR-0.13.0/AlphaSimR/man/runMacs.Rd | 124 AlphaSimR-0.13.0/AlphaSimR/man/runMacs2.Rd | 154 AlphaSimR-0.13.0/AlphaSimR/man/sampleHaplo.Rd | 66 AlphaSimR-0.13.0/AlphaSimR/man/selIndex.Rd | 90 AlphaSimR-0.13.0/AlphaSimR/man/selInt.Rd | 36 AlphaSimR-0.13.0/AlphaSimR/man/selectCross.Rd | 174 AlphaSimR-0.13.0/AlphaSimR/man/selectFam.Rd | 164 AlphaSimR-0.13.0/AlphaSimR/man/selectInd.Rd | 148 AlphaSimR-0.13.0/AlphaSimR/man/selectOP.Rd | 150 AlphaSimR-0.13.0/AlphaSimR/man/selectWithinFam.Rd | 166 AlphaSimR-0.13.0/AlphaSimR/man/self.Rd | 82 AlphaSimR-0.13.0/AlphaSimR/man/setEBV.Rd | 132 AlphaSimR-0.13.0/AlphaSimR/man/setPheno.Rd | 163 AlphaSimR-0.13.0/AlphaSimR/man/setPhenoGCA.Rd | 152 AlphaSimR-0.13.0/AlphaSimR/man/smithHazel.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/usefulness.Rd | 122 AlphaSimR-0.13.0/AlphaSimR/man/varA.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/varAA.Rd | 62 AlphaSimR-0.13.0/AlphaSimR/man/varD.Rd | 60 AlphaSimR-0.13.0/AlphaSimR/man/varG.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/varP.Rd | 56 AlphaSimR-0.13.0/AlphaSimR/man/writePlink.Rd | 130 AlphaSimR-0.13.0/AlphaSimR/man/writeRecords.Rd | 80 AlphaSimR-0.13.0/AlphaSimR/src/algorithm.cpp | 184 AlphaSimR-0.13.0/AlphaSimR/src/datastructures.cpp | 267 AlphaSimR-0.13.0/AlphaSimR/src/plink.cpp | 4 AlphaSimR-0.13.0/AlphaSimR/src/simulator.cpp | 245 AlphaSimR-0.13.0/AlphaSimR/src/simulator.h | 38 AlphaSimR-0.13.0/AlphaSimR/tests/testthat.R | 8 AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-addTrait.R | 132 AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-crossing.R | 256 AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-editGenome.R | 30 AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-hybrids.R | 128 AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-ibdRecHaplo.R | 1468 ++-- AlphaSimR-0.13.0/AlphaSimR/tests/testthat/test-statistics.R | 60 AlphaSimR-0.13.0/AlphaSimR/vignettes/AlphaSimR.bib | 288 AlphaSimR-0.13.0/AlphaSimR/vignettes/intro.Rmd | 264 AlphaSimR-0.13.0/AlphaSimR/vignettes/traits.Rmd | 372 - 142 files changed, 17887 insertions(+), 18359 deletions(-)