This package is considered a duplicate. The official version of this package is found at:https://thijsjanzen.r-universe.dev/nodeSub

Package: nodeSub 1.2.8

Thijs Janzen

nodeSub: Simulate DNA Alignments Using Node Substitutions

Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.

Authors:Thijs Janzen

nodeSub_1.2.8.tar.gz
nodeSub_1.2.8.tar.gz(r-4.5-noble)nodeSub_1.2.8.tar.gz(r-4.4-noble)
nodeSub_1.2.8.tgz(r-4.4-emscripten)nodeSub_1.2.8.tgz(r-4.3-emscripten)
nodeSub.pdf |nodeSub.html✨
nodeSub/json (API)

# Install 'nodeSub' in R:

install.packages('nodeSub', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

Uses libs:

c++– GNU Standard C++ Library v3
openjdk– OpenJDK Java runtime, using Hotspot JIT

2.70 score 3 scripts 228 downloads 18 exports 98 dependencies

Last updated 1 years agofrom:8c128f140e. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-linux-x86_64	OK	Nov 09 2024

Exports:calc_expected_hidden_nodes calc_fraction calc_required_node_time calc_sum_stats count_hidden create_balanced_tree create_equal_alignment create_equal_alignment_explicit create_unbalanced_tree estimate_marginal_models infer_phylogeny reduce_tree sim_linked sim_normal sim_normal_explicit sim_unlinked sim_unlinked_explicit slow_matrix

Dependencies:ade4 ape askpass beastier beautier BH bit bit64 cli clipr clusterGeneration coda codetools colorspace combinat cpp11 crayon curl DDD DEoptim deSolve digest doParallel dplyr expm fansi fastmatch foreach geiger generics glue gmp hms httr igraph iterators jsonlite lattice lifecycle magrittr maps MASS Matrix mime mnormt mvtnorm ncbit nlme numDeriv openssl optimParallel pbapply phangorn phylobase phytools pillar pixmap pkgconfig plyr prettyunits progress purrr quadprog R6 rappdirs Rcpp RcppArmadillo RcppEigen readr reshape2 rJava rlang Rmpfr rncl RNeXML scatterplot3d segmented seqinr sessioninfo sp SparseM stringi stringr subplex sys testit tibble tidyr tidyselect tracerer tzdb utf8 uuid vctrs vroom withr XML xml2

substitution_models

Thijs Janzen

Rendered fromsubstitution_models.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2023-11-15
Started: 2021-09-30

Citation

Readme and manuals

Help Manual

Help page	Topics
Package providing functions to simulate sequences under different DNA evolution models	nodeSub-package nodeSub
Calculate the number of expected hidden nodes in a phylogenetic tree	calc_expected_hidden_nodes
Calculate the expected fraction of substitutions at the nodes, relative to the fraction at the branches	calc_fraction
Calculate the required node time to obtain a desired fraction of substitutions at the node	calc_required_node_time
calculate summary statistics of a phylogenetic tree, compared with a reference tree. The following statistics are calculated: the beta statistic, gamma statistic, crown age, mean branch length, number of tips, the nLTT statistic and the laplacian difference, given by RPANDA's JSDtree. Because JSDtree can sometimes cause issues, some additional checks are performed to ensure that is possible to run this function.	calc_sum_stats
Function to calculate the number of hidden speciation events, e.g. speciation events that have lead to an extinct species. Thus, these hidden speciation events can only be detected in complete trees (as opposed to reconstructed trees).	count_hidden
create a balanced tree out of branching times	create_balanced_tree
function create an alignment with identical information content	create_equal_alignment
function create an alignment with identical information content, using the explicit method to simulate substitutions	create_equal_alignment_explicit
create an unbalanced tree out of branching times	create_unbalanced_tree
estimate the marginal likelihood of the relaxed and strict clock model for a provided alignment	estimate_marginal_models
calculate p matrix	get_p_matrix
infer the time calibrated phylogeny associated with the provided alignment. This function uses the R package babette to infer the phylogeny using BEAST2.	infer_phylogeny
Function to remove speciation events occuring after an extinction event. Extinct species are pruned randomly, such that only a single extinct species per branching event (if any extinct species) remains.	reduce_tree
simulate a sequence assuming conditional substitutions on the node.	sim_linked
Simulate sequences for a given evolutionary tree, using a standard model of sequence evolution along the branches. Code for this function was heavily inspired by the function 'simSeq' from the phangorn package.	sim_normal
simulate a sequence assuming substitutions are only accumulated along the branches, using the explicit simulation method (e.g. reverse substitutions are modeled explicitly)	sim_normal_explicit
Simulate a sequence assuming node substitutions are not shared amongst offspring, given two substitution matrices: one for substitutions occuring on the nodes, and one for substitutions occuring along the branches.	sim_unlinked
Simulate a sequence assuming node substitutions are not shared amongst offspring, using the explicit simulation method (e.g. reverse substitutions are modeled explicitly)	sim_unlinked_explicit
this function calculates the p matrix within R this is slower than the C++ implementation in 'get_p_matrix' but provides a way to debug and verify	slow_matrix