Package: FossilSim 2.4.0

Joelle Barido-Sottani

FossilSim: Simulation and Plots for Fossil and Taxonomy Data

Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.

Authors:Rachel Warnock [aut, cph], Joelle Barido-Sottani [aut, cre, cph], Walker Pett [aut, cph], O'Reilly Joseph [aut, cph], Ugnė Stolz [aut, cph]

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FossilSim.pdf |FossilSim.html✨
FossilSim/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/fossilsim/fossilsim/issues

On CRAN:

49 exports 9 stars 1.95 score 51 dependencies 1 dependents 64 scripts 1.1k downloads

Last updated 3 days agofrom:1e26ef2084. Checks:OK: 3 ERROR: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 05 2024
R-4.5-winERRORSep 05 2024
R-4.5-linuxERRORSep 05 2024
R-4.4-winERRORSep 05 2024
R-4.4-macERRORSep 05 2024
R-4.3-winOKSep 05 2024
R-4.3-macOKSep 05 2024

Exports:as.fossilsas.taxonomybeast.fbd.formatcount.fossilscount.fossils.binnedfbdrangefossilsfossils.to.BEAST.constraintsfossils.to.BEAST.start.treefossils.to.paleotree.recordfossils.to.pyrateget_fbdrange_from_fileget.tip.descsis.fossilsis.taxonomypaleotree.record.to.fossilsplace.fossilsprune.fossil.tipsprune.fossilsrangeplot.asymmetricreconcile.fossils.taxonomyreconstructed.tree.fossils.objectsremove.stem.fossilsremove.stem.lineagessampled.tree.from.combinedSAtreeSAtree.from.fossilssim.anagenetic.speciessim.cryptic.speciessim.extant.samplessim.fbd.agesim.fbd.rateshift.taxasim.fbd.taxasim.fossils.environmentsim.fossils.intervalssim.fossils.poissonsim.gradientsim.interval.agessim.taxonomysim.tip.samplessim.trait.valuesspecies.endspecies.startsubsample.fossils.oldestsubsample.fossils.oldest.and.youngestsubsample.fossils.uniformsubsample.fossils.youngesttaxonomytree.max

Dependencies:apeaplotclicolorspacecpp11digestdplyrfansifarverfsgenericsggfunggplot2ggplotifyggtreegluegridGraphicsgtableisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkpillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils

Converting from and to paleotree format

Joelle Barido-Sottani

Rendered frompaleotree.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2018-09-17
Started: 2018-06-15

Exporting sampled ancestor trees

Joelle Barido-Sottani

Rendered fromSAtree.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2021-04-20
Started: 2018-06-15

The FossilSim package

Joelle Barido-Sottani, Rachel C. M. Warnock

Rendered fromintro.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2021-04-05
Started: 2018-06-29

Simulating fossils

Rachel C. M. Warnock

Rendered fromfossils.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2018-10-04
Started: 2018-06-29

Simulating taxonomy

Joelle Barido-Sottani, Rachel C. M. Warnock

Rendered fromtaxonomy.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2018-09-18
Started: 2018-06-29

Simulating trees from the fossilized birth-death process

Walker Pett

Rendered fromsimfbd.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2019-09-26
Started: 2018-06-30

Readme and manuals

Help Manual

Help pageTopics
Transforms a tree and fossils into a sampled tree in beast-usable format and writes it in Newick format. Designed to work with FBD.beast.fbd.format
Count the total number of fossilscount.fossils
Count the total number of fossils per intervalcount.fossils.binned
Creates an fbdrange object from provided tree and datafbdrange
Fossils objectas.fossils fossils is.fossils
Create a set of BEAST2 constraints to construct a DPPDIV style fixed extant topology FBD analysisfossils.to.BEAST.constraints
Create a suitable starting tree for a DPPDIV style FBD analysis in BEAST2fossils.to.BEAST.start.tree
Transforms a fossils dataframe and either taxonomy or tree into a fossilRecordSimulation object from package paleotree.fossils.to.paleotree.record
Generate output in the format used by the program PyRatefossils.to.pyrate
FossilSim: A package for simulating and plotting fossil and taxonomy dataFossilSim-package FossilSim
Import fbdrange object from fileget_fbdrange_from_file
Obtain the tips that define each node in a treeget.tip.descs
Transforms a fossilRecordSimulation object from package paleotree to a tree and taxonomy and fossils objects.paleotree.record.to.fossils
Place fossil samples from one tree in another tree, or find the ancestral node for each fossil sample in one tree.place.fossils
Plot oriented tree with stratigraphic rangesplot.fbdrange
Plot simulated fossilsplot.fossils
Plot simulated taxonomyplot.taxonomy
Remove fossil lineages from a treeprune.fossil.tips
Removes all intermediate fossils from a combined tree and labels the first and last fossils of each lineage. Can be used with sampled or complete trees. If only one fossil is present for a particular species it is labelled as first.prune.fossils
Make an asymmetric stratigraphic range plot from a tree object of class phylorangeplot.asymmetric
Reconcile existing fossil and taxonomy objectsreconcile.fossils.taxonomy
Returns tree and fossil objects that you can use to plot the reconstructed tree.reconstructed.tree.fossils.objects
Remove fossil samples that occur in the stemremove.stem.fossils
Remove stem lineages from a tree.remove.stem.lineages
Removes all unsampled lineages from a combined tree. Extinct tips are only sampled if they are fossils. With default settings all extant tips are sampled.sampled.tree.from.combined
Tree with sampled ancestors represented as zero-length edgesSAtree
Transforms a tree and fossils dataframe to a combined SA tree. Sampled ancestors are represented as tips on zero-length edges to maintain compatibility with the ape format. Tip labels are set to "species id"_"index", where the most recent tip of a given species receives index 1 and indices increase towards the past.SAtree.from.fossils
Simulate anagenetic species on a taxonomy objectsim.anagenetic.species
Simulate cryptic species on a taxonomy objectsim.cryptic.species
Include extant samples in the fossil object, with optional rho sampling.sim.extant.samples
sim.fbd.age: Simulating fossilized birth-death trees of a fixed age.sim.fbd.age
sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorporating rate shifts.sim.fbd.rateshift.taxa
sim.fbd.taxa: Simulating fossilized birth-death trees on a fixed number of extant taxa.sim.fbd.taxa
Simulate fossils under an environment-dependent model of preservation (Holland, 1995)sim.fossils.environment
Simulate fossils under a non-uniform model of preservation for a given set of consecutive time intervalssim.fossils.intervals
Simulate fossils under a Poisson sampling modelsim.fossils.poisson
Simulate an environmental gradientsim.gradient
Reassign fossil ages to user-specified stratigraphic intervalssim.interval.ages
Simulate taxonomysim.taxonomy
Include extant and extinct tip samples in the fossil object, with optional rho sampling.sim.tip.samples
Simulate trait values with variation across lineagessim.trait.values
Find a species' end (i.e extinction) time from a taxonomy objectspecies.end
Find a species' start (i.e speciation) time from a taxonomy objectspecies.start
Obtain a subsample of fossil occurrences containing the oldest fossil sample in each node of the tree.subsample.fossils.oldest
Obtain a subsample of fossil occurrences containing the oldest and youngest fossil sample found at each node of the tree.subsample.fossils.oldest.and.youngest
Obtain a uniform random sample of fossil occurrences.subsample.fossils.uniform
Obtain a subsample of fossil occurrences containing the youngest fossil sample in each node of the tree.subsample.fossils.youngest
Display taxonomy objectsummary.taxonomy
Taxonomy objectas.taxonomy is.taxonomy taxonomy
Find the maximum age in a phylo object (root age or origin time)tree.max