Package: nodeSub 1.2.8
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:
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nodeSub.pdf |nodeSub.html✨
nodeSub/json (API)
# Install 'nodeSub' in R: |
install.packages('nodeSub', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thijsjanzen/nodesub/issues
Last updated 10 months agofrom:4602a937a0. Checks:OK: 1 NOTE: 1 WARNING: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 06 2024 |
R-4.5-win-x86_64 | WARNING | Sep 06 2024 |
R-4.5-linux-x86_64 | NOTE | Sep 06 2024 |
R-4.4-win-x86_64 | WARNING | Sep 06 2024 |
R-4.4-mac-x86_64 | WARNING | Sep 06 2024 |
R-4.4-mac-aarch64 | WARNING | Sep 06 2024 |
R-4.3-win-x86_64 | WARNING | Sep 06 2024 |
R-4.3-mac-x86_64 | WARNING | Sep 06 2024 |
R-4.3-mac-aarch64 | WARNING | Sep 06 2024 |
Exports:calc_expected_hidden_nodescalc_fractioncalc_required_node_timecalc_sum_statscount_hiddencreate_balanced_treecreate_equal_alignmentcreate_equal_alignment_explicitcreate_unbalanced_treeestimate_marginal_modelsinfer_phylogenyreduce_treesim_linkedsim_normalsim_normal_explicitsim_unlinkedsim_unlinked_explicitslow_matrix
Dependencies:ade4apeaskpassbeastierbeautierBHbitbit64clicliprclusterGenerationcodacodetoolscolorspacecombinatcpp11crayoncurlDDDDEoptimdeSolvedigestdoParalleldplyrexpmfansifarverfastmatchforeachgeigergenericsggplot2ggseqlogogluegmpgtablehmshttrigraphisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmimemnormtmunsellmvtnormncbitnlmenumDerivopenssloptimParallelpbapplyphangornphylobasephytoolspillarpixmappkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreshape2rJavarlangRmpfrrnclRNeXMLscalesscatterplot3dsegmentedseqinrsessioninfospSparseMstringistringrsubplexsystestittibbletidyrtidyselecttracerertzdbutf8uuidvctrsviridisLitevroomwithrXMLxml2