Description Usage Arguments Details Value See Also Examples

Calculates multiple diversity curves from a list of datasets of taxic ranges and/or phylogenetic trees, for the same intervals, for all the individual datasets. A median curve with 95 percent quantile bounds is also calculated and plotted for each interval.

1 2 3 4 5 6 7 8 9 | ```
multiDiv(data, int.length = 1, plot = TRUE, split.int = TRUE,
drop.ZLB = TRUE, drop.cryptic = FALSE, extant.adjust = 0.01,
plotLogRich = FALSE, yAxisLims = NULL, timelims = NULL,
int.times = NULL, plotMultCurves = FALSE, multRainbow = TRUE,
divPalette = NULL, divLineType = 1, main = NULL)
plotMultiDiv(results, plotLogRich = FALSE, timelims = NULL,
yAxisLims = NULL, plotMultCurves = FALSE, multRainbow = TRUE,
divPalette = NULL, divLineType = 1, main = NULL)
``` |

`data` |
A list where each element is a dataset, formatted to be input in
one of the diversity curve functions listed in |

`int.length` |
The length of intervals used to make the diversity curve. Ignored if int.times is given. |

`plot` |
If |

`split.int` |
For discrete time data, should calculated/input intervals be split at discrete time interval boundaries? If FALSE, can create apparent artifacts in calculating the diversity curve. See below. |

`drop.ZLB` |
If true, zero-length terminal branches are dropped from the input tree for phylogenetic datasets, before calculating standing diversity. |

`drop.cryptic` |
If TRUE, cryptic taxa are merged to form one taxon for
estimating taxon curves. Only works for objects from |

`extant.adjust` |
Amount of time to be added to extend start time for (0,0) bins for extant taxa, so that the that 'time interval' does not appear to have an infinitely small width. |

`plotLogRich` |
If TRUE, taxic diversity is plotted on log scale. |

`yAxisLims` |
Limits for the y (i.e. richness) axis on the plotted diversity curves. Only
affects plotting. Given as either NULL (the default) or as a vector of
length two as for |

`timelims` |
Limits for the x (time) axis for diversity curve plots. Only
affects plotting. Given as either NULL (the default) or as a vector of
length two as for |

`int.times` |
An optional two-column matrix of the interval start and end times for calculating the diversity curve. If NULL, calculated internally. If given, the argument split.int and int.length are ignored. |

`plotMultCurves` |
If |

`multRainbow` |
If |

`divPalette` |
Can be used so users can pass a vector of chosen color identifiers for each diversity curve in 'data' which will take precedence over multRainbow. Must be the same length as the number of diversity curves supplied. |

`divLineType` |
Used to determine line type ( |

`main` |
The main label for the figure. |

`results` |
The output of a previous run of multiDiv for replotting. |

This function is essentially a wrapper for the individual diversity curve
functions included in paleotree. multiDiv will intuitively decide whether
input datasets are continuous-time taxic ranges, discrete-time (binned
interval) taxic ranges or phylogenetic trees, as long as they are formatted
as required by the respective diversity curve functions. A list that
contains a mix of data types is entirely acceptable. A list of matrices
output from `fossilRecord2fossilTaxa`

, via simulation with `simFossilRecord`

is allowable, and treated as input for `taxicDivCont`

.
Data of an unknown type gives back an error.

The argument split.int splits intervals, if and only if discrete interval
time data is included among the datasets. See the help file for taxicDivDisc
to see an explanation of why `split.int = TRUE`

by default is probably a good
thing.

As with many functions in the paleotree library, absolute time is always decreasing, i.e. the present day is zero.

The 'averaged' curve is actually the median rather than the mean as diversity counts are often highly skewed (in this author's experience).

The shaded certainty region around the median curve is the two-tailed 95 percent lower and upper quantiles, calculated from the observed data. It is not a true probabilisitic confidence interval, as it has no relationship to the standard error.

A list composed of three elements will be invisibly returned:

`int.times` |
A two column matrix giving interval start and end times |

`div` |
A matrix of measured diversities in particular intervals by rows, with each column representing a different dataset included in the input |

`median.curve` |
A three column matrix, where the first column is the calculated median curve and the second and third columns are the 95 percent quantile upper and lower bounds |

The diversity curve functions used include: `phyloDiv`

,
`taxicDivCont`

and `taxicDivDisc`

.

Also see the function LTT.average.root in the package TreeSim, which calculates an average LTT curve for multiple phylogenies, the functions codemltt.plot in ape and codeltt in phytools.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | ```
set.seed(444)
record<-simFossilRecord(p=0.1, q=0.1, nruns=1,
nTotalTaxa=c(30,40), nExtant=0)
taxa<-fossilRecord2fossilTaxa(record)
rangesCont <- sampleRanges(taxa, r=0.5)
rangesDisc <- binTimeData(rangesCont, int.length=1)
cladogram<-taxa2cladogram(taxa, plot=TRUE)
#using multiDiv with very different data types
ttree <- timePaleoPhy(cladogram, rangesCont, type="basic", add.term=TRUE, plot=FALSE)
input <- list(rangesCont, rangesDisc, ttree)
multiDiv(input, plot=TRUE)
#using fixed interval times
multiDiv(input, int.times=rangesDisc[[1]], plot=TRUE)
#using multiDiv with samples of trees
ttrees <- timePaleoPhy(cladogram, rangesCont, type="basic",
randres=TRUE, ntrees=10, add.term=TRUE)
multiDiv(ttrees)
#uncertainty in diversity history is solely due to
#the random resolution of polytomies
#multiDiv can also take output from simFossilRecord, via fossilRecord2fossilTaxa
#what do many simulations run under some set of conditions 'look' like on average?
set.seed(444)
records<-simFossilRecord(p=0.1, q=0.1, nruns=10,
totalTime=30, plot=TRUE)
taxa<-sapply(records,fossilRecord2fossilTaxa)
multiDiv(taxa)
#increasing cone of diversity!
#Even better on a log scale:
multiDiv(taxa, plotLogRich=TRUE)
#pure-birth example with simFossilRecord
#note that conditioning is tricky
set.seed(444)
recordsPB<-simFossilRecord(p=0.1, q=0, nruns=10,
totalTime=30,plot=TRUE)
taxaPB<-sapply(recordsPB,fossilRecord2fossilTaxa)
multiDiv(taxaPB,plotLogRich=TRUE)
#compare many discrete diversity curves
discreteRanges<-lapply(taxa,function(x)
binTimeData(sampleRanges(x, r=0.5,
min.taxa=1), int.length=7))
multiDiv(discreteRanges)
layout(1)
``` |

paleotree documentation built on Nov. 17, 2017, 5:11 a.m.

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