Files in TGuillerme/Inapp
Reconstruction of Inapplicable Discrete Characters on Phylogenetic Trees

.Rbuildignore
.gitignore
.travis.yml
Analysis/Data/Chains.bib
Analysis/Data/Counting/Baker2009.nex.tre.orig
Analysis/Data/Matrices/Asher2005.nex
Analysis/Data/Matrices/Baker2009.nex
Analysis/Data/Matrices/Bouchenak2010.nex
Analysis/Data/Matrices/Dikow2009.nex
Analysis/Data/Matrices/Geisler2001.nex
Analysis/Data/Matrices/Giles2015.nex
Analysis/Data/Matrices/Griswold1999.nex
Analysis/Data/Matrices/Liljeblad2008.nex
Analysis/Data/Matrices/Loconte1991.nex
Analysis/Data/Matrices/Longrich2010.nex
Analysis/Data/Matrices/Sharkey2011.nex
Analysis/Data/Matrices/Sundue2010.nex
Analysis/Data/Matrices/Wiens2010.nex
Analysis/Data/Matrices/Wilson2003.nex
Analysis/Data/Matrices/Wortley2006.nex
Analysis/Data/Matrices/Zanol2012.nex
Analysis/Data/PAWM
Analysis/Data/Trees/move.trees.sh
Analysis/Data/count.morphy.sh
Analysis/Data/set.job.paup.sh
Analysis/Data/solving.polytomies.sh
Analysis/Functions/count.morphy.sh
Analysis/Functions/plot.scores.R Analysis/Functions/read.tree.score.R
Analysis/Functions/set.job.paup.sh
Analysis/Functions/solving.polytomies.sh
Analysis/Functions/standardise.score.R Analysis/Functions/test.R Analysis/Pipeline_description.md Analysis/algorithm_effect.Rmd
Analysis/algorithm_effect.html
Analysis/algorithm_effect_old.Rmd
Analysis/algorithm_effect_old.html
Analysis/count_difference.tex
Analysis/pipeline.R
DESCRIPTION
NAMESPACE
R/Fitch.reconstruction.R R/Inapp-package.R R/NA.reconstruction.R R/NA.utilities.R R/apply.reconstruction.R R/output.results.R R/output.results_fun.R R/plot.algorithm.R R/runInapp.R R/svg.R R/vignettePlots.R README.md Writing/algorithm_description.pdf
Writing/algorithm_description.tex
codecov.yml
helpers.R
inst/REFERENCES.bib
inst/gitbook/01_Fitch.Rmd inst/gitbook/02_problems.Rmd inst/gitbook/03_ourSolution.Rmd inst/gitbook/04_codingData.Rmd inst/gitbook/05_ambiguousData.Rmd inst/gitbook/06_globalOptima.Rmd inst/gitbook/07_examples.Rmd inst/gitbook/08_references.Rmd inst/gitbook/Inapplicable_data.Rmd inst/gitbook/Inapplicable_data.pdf
inst/gitbook/Inapplicable_data.tex
inst/gitbook/_book/Inapplicable_data.epub
inst/gitbook/_book/Inapplicable_data.pdf
inst/gitbook/_book/Inapplicable_data.tex
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inst/gitbook/_book/ambiguity.html
inst/gitbook/_book/coding.html
inst/gitbook/_book/examples.html
inst/gitbook/_book/fitch.html
inst/gitbook/_book/global.html
inst/gitbook/_book/index.html
inst/gitbook/_book/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
inst/gitbook/_book/libs/gitbook-2.6.7/css/plugin-bookdown.css
inst/gitbook/_book/libs/gitbook-2.6.7/css/plugin-fontsettings.css
inst/gitbook/_book/libs/gitbook-2.6.7/css/plugin-highlight.css
inst/gitbook/_book/libs/gitbook-2.6.7/css/plugin-search.css
inst/gitbook/_book/libs/gitbook-2.6.7/css/style.css
inst/gitbook/_book/libs/gitbook-2.6.7/js/app.min.js
inst/gitbook/_book/libs/gitbook-2.6.7/js/jquery.highlight.js
inst/gitbook/_book/libs/gitbook-2.6.7/js/lunr.js
inst/gitbook/_book/libs/gitbook-2.6.7/js/plugin-bookdown.js
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inst/gitbook/_book/libs/gitbook-2.6.7/js/plugin-sharing.js
inst/gitbook/_book/libs/jquery-2.2.3/jquery.min.js
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inst/gitbook/_bookdown.yml
inst/gitbook/_bookdown_files/Inapplicable_data_files/figure-latex/unnamed-chunk-73-1.pdf
inst/gitbook/_output.yml
inst/gitbook/compiling_gitbook.sh
inst/gitbook/index.Rmd
inst/gitbook/packages.bib
inst/gitbook/preamble.tex
inst/gitbook/sortReferences.html
inst/gitbook/style.css
inst/gitbook/sysbio.bst
inst/gitbook/vancouver.bst
man-roxygen/canvasParam.R man-roxygen/outgroupTipsParam.R man-roxygen/treeNamesParam.R man/Inapp-package.Rd man/PlotCharacterMapping.Rd man/PrintJavascript.Rd man/PrintSwitcher.Rd man/SVGCanvas.Rd man/SVGTree.Rd man/apply.reconstruction.Rd man/convert.char.Rd man/first.downpass.Rd man/first.uppass.Rd man/fitch.downpass.Rd man/fitch.uppass.Rd man/make.states.matrix.Rd man/output.states.matrix.Rd man/plot.states.matrix.Rd man/print.states.matrix.Rd man/runInapp.Rd man/second.downpass.Rd man/second.uppass.Rd man/vignettePlot.Rd patch_notes.md server.R
support/Data/MartinTree.tre
support/Data/Matrix1.txt
support/Data/Matrix2.txt
support/Data/Matrix3.txt
support/Data/Matrix4.txt
support/Data/Matrix5.txt
support/Data/combined.nex
support/Data/matrix.nex
support/Data/tree.nex
support/Data/tree2.nex
support/Doc/plotting.inapplicable.Rmd
support/Doc/plotting.inapplicable.html
support/TestingAlgo.xlsx
support/Writing/Abstract.fls
support/Writing/Abstract.pdf
support/Writing/Abstract.tex
support/desiderata.md support/errors.md tests/testthat.R tests/testthat/test-Fitch.reconstruction.R tests/testthat/test-NA.counting.R tests/testthat/test-NA.reconstruction.R tests/testthat/test-NA.utilities.R tests/testthat/test-apply.reconstruction.R tests/testthat/test-output.results.R tests/testthat/test-plot.algorithm.R ui.R
www/slimline.css
TGuillerme/Inapp documentation built on Sept. 7, 2018, 7:48 a.m.