nLTT: Calculate the NLTT Statistic

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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.

Author
Thijs Janzen [aut, cre], Richel Bilderbeek [aut]
Date of publication
2016-10-12 00:10:19
Maintainer
Thijs Janzen <thijsjanzen@gmail.com>
License
GPL-2
Version
1.3.1
URLs

View on CRAN

Man pages

abc_smc_nltt
A function to perform Approximate Bayesian Computation within...
exampleTrees
example trees to test the functionality of the package
get_average_nltt_matrix
Get the average nLTT from a collection of phylogenies
get_nltt_values
Collects the nLTT values of all phylogenies in the...
get_phylogeny_nltt_matrix
Extract the nLTT matrix from a phylogeny
MCMC_nLTT
Code to perform Metropolis-Hastings MCMC for a...
nltt_diff
Calculates the exact difference between the lineage through...
nltt_diff_exact
Calculates the exact, difference between the lineage through...
nLTT-internal
Internal nLTT functions
nltt_lines
Normalized version of the ape function ltt.lines.
nLTT-package
Package providing functions to visualize the normalized...
nltt_plot
Normalized version of the ape function ltt.plot
nltts_plot
Get the average nLTT from a collection of phylogenies
nLTTstat
Calculate the difference between two normalized...
nLTTstat_exact
Calculate the exact difference between two normalized...
stretch_nltt_matrix
Stretch matrix 'm' with a timestep resolution of 'dt'

Files in this package

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