nLTT: Calculate the NLTT Statistic

Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.

Install the latest version of this package by entering the following in R:
install.packages("nLTT")
AuthorThijs Janzen [aut, cre], Richel Bilderbeek [aut]
Date of publication2016-10-12 00:10:19
MaintainerThijs Janzen <thijsjanzen@gmail.com>
LicenseGPL-2
Version1.3.1
https://github.com/richelbilderbeek/nLTT

View on CRAN

Functions

abc_smc_nltt Man page
calculate_weight Man page
exampleTrees Man page
get_average_nltt_matrix Man page
get_nltt_values Man page
get_phylogeny_nltt_matrix Man page
mcmc_nltt Man page
nLTT Man page
nltt_diff Man page
nltt_diff_exact Man page
nltt_lines Man page
nLTT-package Man page
nltt_plot Man page
nltts_plot Man page
nLTTstat Man page
nLTTstat_exact Man page
stretch_nltt_matrix Man page

Files

inst
inst/doc
inst/doc/vignette_nltts_plot.Rmd
inst/doc/vignette_get_nltt_values.Rmd
inst/doc/walkthrough.R
inst/doc/vignette_stretch_nltt_matrix.Rmd
inst/doc/trees_with_root_edge.R inst/doc/vignette_stretch_nltt_matrix.R inst/doc/vignette_get_nltt_values.R
inst/doc/trees_with_root_edge.html
inst/doc/vignette_stretch_nltt_matrix.html
inst/doc/vignette_get_nltt_values.html
inst/doc/walkthrough.Rmd
inst/doc/trees_with_root_edge.Rmd
inst/doc/walkthrough.html
inst/doc/vignette_nltts_plot.html
inst/doc/vignette_nltts_plot.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test_mcmc_nltt.R tests/testthat/test-nLTTstat.R tests/testthat/test_get_nltt_values.R tests/testthat/test_stretch_nltt_matrix.R tests/testthat/test-nLTTstat_exact.R tests/testthat/test_abc_smc_nltt.R tests/testthat/test_get_phylogeny_nltt_matrix.R tests/testthat/test_get_average_nltt.R tests/testthat/test-nltt_plot.R tests/testthat/test_get_average_nltt_matrix.R tests/testthat/test_calculate_weight.R
NAMESPACE
data
data/exampleTrees.rda
R
R/stretch_nltt_matrix.R R/nLTTDiff.R R/get_phylogeny_nltt_matrix.R R/plot_nLTT.R R/ABC_SMC.R R/get_average_nltt_matrix.R R/get_nltt_values.R R/nltts_plot.R
vignettes
vignettes/vignette_nltts_plot.Rmd
vignettes/vignette_get_nltt_values.Rmd
vignettes/vignette_stretch_nltt_matrix.Rmd
vignettes/walkthrough.Rmd
vignettes/trees_with_root_edge.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/stretch_nltt_matrix.Rd man/get_nltt_values.Rd man/nLTTstat.Rd man/abc_smc_nltt.Rd man/nLTTstat_exact.Rd man/nltt_diff_exact.Rd man/exampleTrees.Rd man/nltt_diff.Rd man/get_average_nltt_matrix.Rd man/MCMC_nLTT.Rd man/nLTT-internal.Rd man/nltt_lines.Rd man/nLTT-package.Rd man/nltt_plot.Rd man/nltts_plot.Rd man/get_phylogeny_nltt_matrix.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.