R: Construct a Fully Formatted NEXUS Script for Performing...

createMrBayesTipDatingNexus {paleotree}

R Documentation

Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayes

Description

This function is meant to expedite the creation of NEXUS files formatted for performing tip-dating analyses in the popular phylogenetics software MrBayes, particularly clock-less tip-dating analyses executed with 'empty' morphological matrices (i.e. where all taxa are coded for a single missing character), although a pre-existing morphological matrix can also be input by the user (see argument origNexusFile). Under some options, this pre-existing matrix may be edited by this function. The resulting full NEXUS script is output as a set of character strings either printed to the R console, or output to file which is then overwritten.

Usage

createMrBayesTipDatingNexus(
  tipTimes,
  outgroupTaxa = NULL,
  treeConstraints = NULL,
  ageCalibrationType,
  whichAppearance = "first",
  treeAgeOffset,
  minTreeAge = NULL,
  collapseUniform = TRUE,
  anchorTaxon = TRUE,
  newFile = NULL,
  origNexusFile = NULL,
  parseOriginalNexus = TRUE,
  createEmptyMorphMat = TRUE,
  orderedChars = NULL,
  morphModel = "strong",
  morphFiltered = "parsInf",
  runName = NULL,
  ngen = "100000000",
  doNotRun = FALSE,
  autoCloseMrB = FALSE,
  cleanNames = TRUE,
  printExecute = TRUE
)

Arguments

`tipTimes`	This input may be either: (a) a `timeList` object, consisting of a `list` of `length = 2`, composed of a table of interval upper and lower time boundaries (i.e., the earlier and latter bounds of the intervals) and a table of first and last intervals for taxa, or (b) a matrix with row names corresponding to taxon names, matching those names listed in the MrBayes block, with either one, two or four columns containing ages (respectively) for point occurrences with precise dates (for a single column), uncertainty bounds on a point occurrence (for two columns), or uncertainty bounds on the first and last occurrence (for four columns). Note that precise first and last occurrence dates should not be entered as a two column matrix, as this will instead be interpreted as uncertainty bounds on a single occurrence. Instead, either select which you want to use for tip-dates and give a one-column matrix, or repeat (and collate) the columns, so that the first and last appearances has uncertainty bounds of zero.
`outgroupTaxa`	A vector of type 'character', containing taxon names designating the outgroup. All taxa not listed in the outgroup will be constrained to be a monophyletic ingroup, for sake of rooting the resulting dated tree. Either `treeConstraints` or `outgroupTaxa` must be defined, but not both. If the outgroup-ingroup split is not present on the supplied `treeConstraints`, add that split to `treeConstraints` manually.
`treeConstraints`	An object of class `phylo`, from which (if `treeConstraints` is supplied) the set topological constraints are derived, as as described for argument `tree` for function `createMrBayesConstraints`. Either `treeConstraints` or `outgroupTaxa` must be defined, but not both. If the outgroup-ingroup split is not present on the supplied `treeConstraints`, add that split to `treeConstraints` manually.
`ageCalibrationType`	This argument decides how age calibrations are defined, and currently allows for four options: `"fixedDateEarlier"` which fixes tip ages at the earlier (lower) bound for the selected age of appearance (see argument `whichAppearance` for how that selection is made), `"fixedDateLatter"` which fixes the date to the latter (upper) bound of the selected age of appearance, `"fixedDateRandom"` which fixes tips to a date that is randomly drawn from a uniform distribution bounded by the upper and lower bounds on the selected age of appearance, or (the recommended option) `"uniformRange"` which places a uniform prior on the age of the tip, bounded by the latest and earliest (upper and lower) bounds on the the selected age.
`whichAppearance`	Which appearance date of the taxa should be used: their `'first'` or their `'last'` appearance date? The default option is to use the 'first' appearance date. Note that use of the last appearance date means that tips will be constrained to occur before their last occurrence, and thus could occur long after their first occurrence (!). In addition, `createMrBayesTipDatingNexus` allows for two options for this argument that are in addition to those offered by `createMrBayesTipCalibrations`. Both of these options will duplicate the taxa in the inputs multiple times, modifying their OTU labels, thus allowing multiple occurrences of long-lived morphotaxa to be listed as multiple OTUs arrayed across their stratigraphic duration. If `whichAppearance = "firstLast"`, taxa will be duplicated so each taxon is listed as occurring twice: once at their first appearance, and a second time at their last appearance. Note that if a taxon first and last appears in the same interval, and `ageCalibrationType = "uniformRange"`, then the resulting posterior trees may place the OTU assigned to the last occurrence before the first occurrence in temporal order (but the assignment, in that case, was entirely arbitrary). When `whichAppearance = "rangeThrough"`, each taxon will be duplicated into as many OTUs as each interval that a taxon ranges through (in a `timeList` format, see other `paleotree` functions), with the corresponding age uncertainties for those intervals. If the input `tipTimes` is not a list of `length = 2`, however, the function will return an error under this option.
`treeAgeOffset`	A parameter given by the user controlling the offset between the minimum and expected tree age prior. mean tree age for the offset exponential prior on tree age will be set to the minimum tree age, plus this offset value. Thus, an offset of 10 million years would equate to a prior assuming that the expected tree age is around 10 million years before the minimum age.
`minTreeAge`	if `NULL` (the default), then `minTreeAge` will be set as the oldest date among the tip age used (those used being determine by user choices (or oldest bound on a tip age). Otherwise, the user can supply their own minimum tree, which must be greater than whatever the oldest tip age used is.
`collapseUniform`	MrBayes won't accept uniform age priors where the maximum and minimum age are identical (i.e. its actually a fixed age). Thus, if this argument is `TRUE` (the default), this function will treat any taxon ages where the maximum and minimum are identical as a fixed age, and will override setting `ageCalibrationType = "uniformRange"` for those dates. All taxa with their ages set to fixed by the behavior of `anchorTaxon` or `collapseUniform` are returned as a list within a commented line of the returned MrBayes block.
`anchorTaxon`	This argument may be a logical (default is `TRUE`, or a character string of length = 1. This argument has no effect if `ageCalibrationType` is not set to `"uniformRange"`, but the argument may still be evaluated. If `ageCalibrationType = "uniformRange"`, MrBayes will do a tip-dating analysis with uniform age uncertainties on all taxa (if such uncertainties exist; see `collapseUniform`). However, MrBayes does not record how each tree sits on an absolute time-scale, so if the placement of every tip is uncertain, lining up multiple dated trees sampled from the posterior (where each tip's true age might differ) could be a nightmare to back-calculate, if not impossible. Thus, if `ageCalibrationType = "uniformRange"`, and there are no tip taxa given fixed dates due to `collapseUniform` (i.e. all of the tip ages have a range of uncertainty on them), then a particular taxon will be selected and given a fixed date equal to its earliest appearance time for its respective `whichAppearance`. This taxon can either be indicated by the user or instead the first taxon listed in `tipTimes` will be arbitrary selected. All taxa with their ages set to fixed by the behavior of `anchorTaxon` or `collapseUniform` are returned as a list within a commented line of the returned MrBayes block.
`newFile`	Filename (possibly with path) as a character string leading to a file which will be overwritten with the output tip age calibrations. If `NULL`, tip calibration commands are output to the console.
`origNexusFile`	Filename (possibly with path) as a character string leading to a NEXUS text file, presumably containing a matrix of character date formated for MrBayes. If supplied (it does not need to be supplied), the listed file is read as a text file, and concatenated with the MrBayes script produced by this function, so as to reproduce the original NEXUS matrix for executing in MrBayes. Note that the taxa in this NEXUS file are NOT checked against the user input `tipTimes` and `treeConstraints`, so it is up to the user to ensure the taxa are the same across the three data sources.
`parseOriginalNexus`	If `TRUE` (the default), the original NEXUS file is parsed and the taxon names listed within in the matrix are compared against the other inputs for matching (completely, across all inputs that include taxon names). Thus, it is up to the user to ensure the same taxa are found in all inputs. However, some NEXUS files may not parse correctly (particularly if character data for taxa stretches across more than a single line in the matrix). This may necessitate setting this argument to `FALSE`, which will instead do a straight scan of the NEXUS matrix without parsing it, and without checking the taxon names against other outputs. Some options for `whichAppearance` will not be available, however.
`createEmptyMorphMat`	If `origNexusFile` is not specified (implying there is no pre-existing morphological character matrix for this dataset), then an 'empty' NEXUS-formatted matrix will be appended to the set of MrBayes commands if this command is `TRUE` (the default). This 'empty' matrix will have each taxon in `tipTimes` coded for a single missing character (i.e., '?'). This allows tip-dating analyses with hard topological constraints, and ages determined entirely by the fossilized birth-death prior, with no impact from a presupposed morphological clock (thus a 'clock-less analysis').
`orderedChars`	Should be a vector of numbers, indicating which characters should have their character-type in MrBayes changed to 'ordered'. If `NULL`, the default, then all characters will be treated as essentially unordered. No character ID should be listed that is higher than the number of characters in the matrix provided in `origNexusFile`. If `origNexusFile` is not provided, while `orderedChars` is defined, then an error will be returned.
`morphModel`	This argument can be used to switch between two end-member models of morphological evolution in MrBayes, here named 'strong' and 'relaxed', for the 'strong assumptions' and 'relaxed assumptions' models described by Bapst et al. (2018, Syst. Biol.). The default is a model which makes very 'strong' assumptions about the process of morphological evolution, while the 'relaxed' alternative allows for considerably more heterogeneity in the rate of morphological evolution across characters, and in the forward and reverse transition rates between states. Also see argument `morphFiltered`.
`morphFiltered`	This argument controls what type of filtering the input morphological data is assumed to have been collected under. The likelihood of the character data will be modified to take into account the apparent filtering (Lewis, 2001; Allman et al., 2010). The default value, `"parsInf"`, forces characters to be treated as if they were collected as part of a parsimony-based study, with constant characters and autapomorphies (characters that only differ in state in a single taxon unit) ignored or otherwise filtered out, and any such characters in the presented matrix will be ignored. `morphFiltered = "variable"` assumes that while constant characters are still filtered out (e.g. it is difficult or impossible to count the number of morphological characters that show no variation across a group), the autapomorphies were intentionally collected and included in the presented matrix. Thus, constant characters in the included matrix will be ignored, but autapomorphies will be considered.
`runName`	The name of the run, used for naming the log files and MCMC output files. If not set, the name will be taken from the name given for outputting the NEXUS script (`newFile`). If `newFile` is not given, and `runName` is not set by the user, the default run name will be "new_run_paleotree".
`ngen`	Number of generations to set the MCMCMC to run for. Default (`ngen = 100000000`) is very high.
`doNotRun`	If `TRUE`, the commands that cause a script to automatically begin running in MrBayes will be left out. Useful for troubleshooting initial runs of scripts for non-fatal errors and warnings (such as ignored constraints). Default for this argument is `FALSE`.
`autoCloseMrB`	If `TRUE`, the MrBayes script created by this function will 'autoclose', so that when an MCMC run finishes the specified number of generations, it does not interactively check whether to continue the MCMC. This is often necessary for batch analyses.
`cleanNames`	If `TRUE` (the default), then special characters (currently, this only contains the forward-slashes: '/') are removed from taxon names before construction of the NEXUS file.
`printExecute`	If `TRUE` (the default) and if output is directed to a `newFile` (i.e. a `newFile` is specified), a line for pasting into MrBayes for executing the newly created file will be messaged to the terminal.

Details

Users must supply a data set of tip ages (in various formats), which are used to construct age calibrations commands on the tip taxa (via paleotree function createMrBayesTipCalibrations). The user must also supply some topological constraint: either a set of taxa designated as the outgroup, which is then converted into a command constraining the monophyly on the ingroup taxa, which is presumed to be all taxa not listed in the outgroup. Alternatively, a user may supply a tree which is then converted into a series of hard topological constraints (via function createMrBayesConstraints. Both types of topological constraints cannot be applied.

Many of the options available with createMrBayesTipCalibrations are available with this function, allowing users to choose between fixed calibrations or uniform priors that approximate stratigraphic uncertainty. In addition, the user may also supply a path to a text file presumed to be a NEXUS file containing character data formatted for use with MrBayes.

The taxa listed in tipTimes must match the taxa in treeConstraints, if such is supplied. If supplied, the taxa in outgroupTaxa must be contained within this same set of taxa. These all must have matches in the set of taxa in origNexusFile, if provided and if parseOriginalNexus is TRUE.

Note that because the same set of taxa must be contained in all inputs, relationships are constrained as 'hard' constraints, rather than 'partial' constraints, which allows some taxa to float across a partially fixed topology. See the documentation for createMrBayesConstraints, for more details.

Value

If argument newFile is NULL, then the text of the generated NEXUS script is output to the console as a series of character strings.

Note

This function allows a user to take an undated phylogenetic tree in R, and a set of age estimates for the taxa on that tree, and produce a posterior sample of dated trees using the MCMCMC in MrBayes, while treating an 'empty' morphological matrix as an uninformative set of missing characters. This 'clock-less tip-dating' approach is essentially an alternative to the cal3 method in paleotree, sharing the same fundamental theoretical model (a version of the fossilized birth-death model), but with a better algorithm that considers the whole tree simultaneously, rather than evaluating each node individually, from the root up to the tips (as cal3 does it, and which may cause artifacts). That said, cal3 still has a few advantages: tip-dating as of April 2017 still only treats OTUs as point observations, contained in a single time-point, while cal3 can consider taxa as having durations with first and last occurrences. This means it may be more straightforward to assess the extent of budding cladogenesis patterns of ancestor-descendant relationships in cal3, than in tip-dating.

Author(s)

David W. Bapst. This code was produced as part of a project funded by National Science Foundation grant EAR-1147537 to S. J. Carlson.

The basic MrBayes commands utilized in the output script are a collection of best practices taken from studying NEXUS files supplied by April Wright, William Gearty, Graham Slater, Davey Wright, and guided by the recommendations of Matzke and Wright, 2016 in Biology Letters.

References

The basic fundamentals of tip-dating, and tip-dating with the fossilized birth-death model are introduced in these two papers:

Ronquist, F., S. Klopfstein, L. Vilhelmsen, S. Schulmeister, D. L. Murray, and A. P. Rasnitsyn. 2012. A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera. Systematic Biology 61(6):973-999.

Zhang, C., T. Stadler, S. Klopfstein, T. A. Heath, and F. Ronquist. 2016. Total-Evidence Dating under the Fossilized Birth-Death Process. Systematic Biology 65(2):228-249.

For recommended best practices in tip-dating analyses, please see:

Matzke, N. J., and A. Wright. 2016. Inferring node dates from tip dates in fossil Canidae: the importance of tree priors. Biology Letters 12(8).

The rationale behind the two alternative morphological models are described in more detail here:

Bapst, D. W., H. A. Schreiber, and S. J. Carlson. 2018. Combined Analysis of Extant Rhynchonellida (Brachiopoda) using Morphological and Molecular Data. Systematic Biology 67(1):32-48.

Examples


# load retiolitid dataset
data(retiolitinae)

# let's try making a NEXUS file!

# Use a uniform prior, with a 10 million year offset for
	 # the expected tree age from the earliest first appearance

# Also set average tree age to be 10 Ma earlier than first FAD

outgroupRetio <- "Rotaretiolites" 
# this taxon will now be sister to all other included taxa

# the following will create a NEXUS file 
  # with an 'empty' morph matrix
	 # where the only topological constraint is on ingroup monophyly
	 # Probably shouldn't do this: leaves too much to the FBD prior
 
# with doNotRun set to TRUE for troubleshooting

createMrBayesTipDatingNexus(
tipTimes = retioRanges,
		outgroupTaxa = outgroupRetio,
		treeConstraints = NULL,
		ageCalibrationType = "uniformRange",
		whichAppearance = "first",
		treeAgeOffset = 10,	
		newFile = NULL,	
		origNexusFile = NULL,
		createEmptyMorphMat = TRUE,
		runName = "retio_dating",
		doNotRun = TRUE
		)

# let's try it with a tree for topological constraints
     # this requires setting outgroupTaxa to NULL
# let's also set doNotRun to FALSE

createMrBayesTipDatingNexus(
   tipTimes = retioRanges,
		outgroupTaxa = NULL,
		treeConstraints = retioTree,
		ageCalibrationType = "uniformRange",
		whichAppearance = "first",
		treeAgeOffset = 10,	
		newFile = NULL,	
		origNexusFile = NULL,
		createEmptyMorphMat = TRUE,
		runName = "retio_dating",
		doNotRun = FALSE
		)

# the above is essentially cal3 with a better algorithm,
		# and no need for a priori rate estimates
# just need a tree and age estimates for the tips!

####################################################
# some more variations for testing purposes

# no morph matrix supplied or generated
	# you'll need to manually append to an existing NEXUS file
	
createMrBayesTipDatingNexus(
   tipTimes = retioRanges,
		outgroupTaxa = NULL,
		treeConstraints = retioTree,
		ageCalibrationType = "uniformRange",
		whichAppearance = "first",
		treeAgeOffset = 10,
		newFile = NULL,	
		origNexusFile = NULL,
		createEmptyMorphMat = FALSE,
		runName = "retio_dating",
		doNotRun = TRUE
		)

## Not run: 

# let's actually try writing an example with topological constraints
	# to file and see what happens

# here's my super secret MrBayes directory
file <- "D:\\dave\\workspace\\mrbayes\\exampleRetio.nex"

createMrBayesTipDatingNexus(
   tipTimes = retioRanges,
		outgroupTaxa = NULL,
		treeConstraints = retioTree,
		ageCalibrationType = "uniformRange",
		whichAppearance = "first",
		treeAgeOffset = 10,	
		newFile = file,	
		origNexusFile = NULL,
		createEmptyMorphMat = TRUE,
		runName = "retio_dating",
		doNotRun = FALSE
		)


## End(Not run)

[Package paleotree version 3.4.7 Index]