Package: nLTT 1.4.10

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.

Authors:Thijs Janzen [aut, cre], Richèl J.C. Bilderbeek [aut], Pedro Neves [ctb]

nLTT_1.4.10.tar.gz
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nLTT_1.4.10.tgz(r-4.6-any)nLTT_1.4.10.tgz(r-4.5-any)
nLTT_1.4.10.tar.gz(r-4.7-any)nLTT_1.4.10.tar.gz(r-4.6-any)
nLTT_1.4.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
nLTT/json (API)

# Install 'nLTT' in R:
install.packages('nLTT', repos = c('https://thijsjanzen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thijsjanzen/nltt/issues

Datasets:
  • exampleTrees - Example trees to test the functionality of the package

On CRAN:

Conda:

nlttnltt-statisticphylogenetic-treesphylogenetics

7.00 score 6 stars 70 scripts 779 downloads 2 mentions 26 exports 7 dependencies

Last updated from:a70bad0bc1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK152
source / vignettesOK209
linux-release-x86_64OK150
macos-release-arm64OK127
macos-oldrel-arm64OK95
windows-develOK106
windows-releaseOK105
windows-oldrelOK111
wasm-releaseOK133

Exports:abc_smc_nlttcheck_input_event_timescheck_phylogeniescheck_step_typecheck_time_unitget_average_nltt_matrixget_branching_timesget_n_lineagesget_nltt_valuesget_norm_brtsget_norm_nget_phylogeny_nltt_matrixmcmc_nlttnltt_diffnltt_diff_exactnltt_diff_exact_brtsnltt_diff_exact_calc_extinctnltt_diff_exact_extinctnltt_diff_exact_norm_brtsnltt_linesnltt_plotnltts_diffnltts_plotnLTTstatnLTTstat_exactstretch_nltt_matrix

Dependencies:apecodadigestlatticenlmeRcpptestit

How to stretch an nLTT timepoints matrix
Examples | Example: Easy tree | Example: Tree that has two branching events at the same time | Example: Complex tree
Rendered fromstretch_nltt_matrix.Rmdusingknitr::rmarkdown

Last update: 2022-05-23
Started: 2017-01-24

How to visualize nLTT values distributions
Example: Easy trees | Example: Harder trees | Example: Five random trees
Rendered fromget_nltt_values.Rmdusingknitr::rmarkdown

Last update: 2022-05-23
Started: 2017-01-24

Walkthrough using the nLTT package
nLTT statistic & nLTT plot | Average nLTT matrix & Average nLTT plot
Rendered fromwalkthrough.Rmdusingknitr::rmarkdown

Last update: 2022-05-13
Started: 2016-10-06

nltt_diff functions
Close to polytomies, easier to eyeball | Two pylogenies | Two LTT plots | Two nLTT plots
Rendered fromnltt_diff.Rmdusingknitr::rmarkdown

Last update: 2022-05-08
Started: 2017-01-23

Trees with a root edge
Rendered fromtrees_with_root_edge.Rmdusingknitr::rmarkdown

Last update: 2018-04-13
Started: 2016-08-03

How to plot multiple nLTTs and their average
Example: Easy trees | Example: Harder trees
Rendered fromnltts_plot.Rmdusingknitr::rmarkdown

Last update: 2017-01-24
Started: 2017-01-24

Readme and manuals

Help Manual

Help pageTopics
Package providing functions to visualize the normalized Lineage-Through-Time statistic, and calculate the difference between two nLTT curvesnLTT-package nLTT
A function to perform Approximate Bayesian Computation within a Sequential Markov Chain (ABC-SMC), for diversification analysis of phylogenetic trees.abc_smc_nltt
Checks that event times are correctcheck_input_event_times
Check if the input is a valid collection of one or more phylogeniescheck_phylogenies
Check if the step type is validcheck_step_type
Check if the time unit is validcheck_time_unit
This function does nothing. It is intended to inherit is parameters' documentation.default_params_doc
example trees to test the functionality of the packageexampleTrees
Get the average nLTT from a collection of phylogeniesget_average_nltt_matrix
Collect the branching times from the stem ageget_branching_times
Collect the number of lineages from the stem ageget_n_lineages
Get the nLTT values in timeget_nltt_values
Collect the normalized branching times from the stem ageget_norm_brts
Collect the normalized number of lineages from the stem ageget_norm_n
Extract the nLTT matrix from a phylogenyget_phylogeny_nltt_matrix
function, using a Monte Carlo Markov Chainmcmc_nltt
Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)nltt_diff
Calculates the exact, difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)nltt_diff_exact
Calculates the exact difference between the nLTT curves of the branching timesnltt_diff_exact_brts
Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.nltt_diff_exact_calc_extinct
Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.nltt_diff_exact_extinct
Calculates the exact difference between the nLTT curves of the branching timesnltt_diff_exact_norm_brts
Normalized version of the ape function ltt.lines.nltt_lines
Normalized version of the ape function ltt.plotnltt_plot
Calculates the nLTT statistic between each phylogeny in a collection compared to a same focal/reference treenltts_diff
Get the average nLTT from a collection of phylogeniesnltts_plot
Calculate the difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.nLTTstat
Calculate the exact difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.nLTTstat_exact
Stretch matrix 'm' with a timestep resolution of 'dt'.stretch_nltt_matrix