Description Usage Arguments Details Examples
View source: R/diversityDynamics.r
This function calculates various metrics from occurrence datasets in the form of time series.
1 2 3 
x 

tax 

bin 

age 

revtime 

breaks 

coll 

ref 

om 

noNAStart 
(logical) Useful when the entries in the 
data.frame 

filterNA 

The following variables are produced:
bin
: Bin number, or the numeric identifier of the bin.
tThrough
: Number of throughranging taxa, taxa that have first occurrences before, and last occurrences after the focal bin.
tOri
: Number of originating taxa, taxa that have first occurrences in the focal bin, and last occurrences after it.
tExt
: Number of taxa getting extinct. These are taxa that have first occurrences before the focal bin, and last occurrences in it.
tSing
: Number of stratigraphic singleton (singleinterval) taxa, taxa that only occur in the focal bin.
t2d
: Number of lower two timers (Alroy, 2008; 2014), taxa that are present in the i1th and the ith bin (focal bin).
t2u
: Number of upper two timers (Alroy, 2008; 2014), taxa that are present in the ith (focal) and the i+1th bin. (Alroy, 2008; 2014)
tGFu
: Number of upper gapfillers (Alroy, 2014), taxa that occurr in bin i+2 and i1, but were not found in i+1. (Alroy, 2014)
tGFd
: Number of lower gapfillers (Alroy, 2014), taxa that occurr in bin i2 and i+1, but were not found in i1. (Alroy, 2014)
t3
: Number of three timer taxa (Alroy, 2008; 2014), present in bin i1, i, and i+1. (Alroy, 2008; 2014)
tPart
: Part timer taxa (Alroy, 2008; 2014), present in bin i1,and i+1, but not in bin i.
extProp
: Proportional extinctions including singleinterval taxa: (tExt + tSing) / (tThrough + tOri + tExt + tSing).
oriProp
: Proportional originations including singleinterval taxa: (tOri + tSing) / (tThrough + tOri + tExt + tSing).
extPC
: Per capita extinction rates of Foote (1999). log(tExt/(tExt + tThrough)). Values are not normalized with bin lengths. Similar equations were used by Alroy (1996) but without taking the logarithm.
oriPC
: Per capita origination rates of Foote (1999). log(tOri/(tOri + tThrough)). Values are not normalized with bin lengths. Similar equations were used by Alroy (1996) but without taking the logarithm.
ext3t
: Threetimer extinction rates of Alroy (2008). log(t2d/t3).
ori3t
: Threetimer origination rates of Alroy (2008). log(t2u/t3).
extC3t
: Corrected threetimer extinction rates of Alroy (2008). ext3t[i] + log(samp3t[i+1]).
oriC3t
: Corrected threetimer origination rates of Alroy (2008). ori3t[i] + log(samp3t[i1]).
divSIB
: Sampledinbin diversity (richness), the number of genera sampled in the focal bin.
divCSIB
: Corrected sampledinbin diversity (richness). divSIB/samp3t*totSamp3t, where totSamp3t is total threetimer sampling completeness of the dataset (Alroy, 2008).
divBC
: Boundarycrosser diversity (richness), the number of taxa with ranges crossing the boundaries of the interval. tExt + tOri + tThrough.
divRT
: Rangethrough diversity (richness), all taxa in the interval, based on the rangethrough assumption. (tSing + tOri + tExt + tThrough).
sampRange
: Rangebased sampling probability, without observed range endpoints (Foote), (divSIB  tExt  tOri tSing)/tThrough
samp3t
: Threetimer sampling completeness of Alroy (2008). t3/(t3+tPart)
extGF
: Gapfiller extinction rates of Alroy(2014). log((t2d + tPart)/(t3+tPart+tGFd))
oriGF
: Gapfiller origination rates of Alroy(2014). log((t2u + tPart)/(t3+tPart+tGFd))
E2f3
: Secondforthird extinction propotions of Alroy (2015). As these metrics are based on an algorithmic approach, for the equations please refer to the Alroy (2015, p. 634, right column and Eq. 4)). See source code (http://www.github.com/adamkocsis/divDyn) for the exact implementation, found in the Metrics
function in the diversityDynamics.R file.
O2f3
: Secondforthird origination propotions of Alroy (2015). Please see E2f3
.
ext2f3
: Secondforthird extinction rates (based on Alroy, 2015). Transformed to the usual rate form with log(1/(1E2f3)).
ori2f3
: Secondforthird origination rates (based on Alroy, 2015). Transformed to the usual rate form with log(1/(1O2f3)).
References:
Foote, M. (1999) Morphological Diversity In The Evolutionary Radiation Of Paleozoic and PostPaleozoic Crinoids. Paleobiology 25, 1–115. doi:10.1017/S0094837300020236.
Alroy, J. (2008) Dynamics of origination and extinction in the marine fossil record. Proceedings of the National Academy of Science 105, 1153611542. doi: 10.1073/pnas.0802597105
Alroy, J. (2014) Accurate and precise estimates of origination and extinction rates. Paleobiology 40, 374397. doi: 10.1666/13036
Alroy, J. (2015) A more precise speciation and extinction rate estimator. Paleobiology 41, 633639. doi: 10.1017/pab.2015.26
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  # import data
data(corals)
data(stages)
# calculate metrics of diversity dynamics
dd < divDyn(corals, tax="genus", bin="stg")
# plotting
tsplot(stages, shading="series", boxes="sys", xlim=c(260,0),
ylab="rangethrough diversity (genera)", ylim=c(0,230))
lines(stages$mid, dd$divRT, lwd=2)
# with omission of single reference taxa
ddNoSing < divDyn(corals, tax="genus", bin="stg", om="ref", ref="reference_no")
lines(stages$mid, ddNoSing$divRT, lwd=2, col="red")
# using the estimated ages (less robust)  10 million years
# mean ages
corals$me_ma < apply(corals[, c("max_ma", "min_ma")], 1, mean)
# ages reverse the direction of time! set ages to TRUE in this case
ddRadio10 < divDyn(corals, tax="genus", age="me_ma",
breaks=seq(250,0,10))
lines(ddRadio10$me_ma, ddRadio10$divRT, lwd=2, col="green")
# legend
legend("topleft", legend=c("all", "no singleref. taxa", "all, estimated ages"),
col=c("black", "red", "green"), lwd=c(2,2,2), bg="white")

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.