ranges | R Documentation |
Visualization of occurrence data
ranges( dat, bin = NULL, tax = NULL, xlim = NULL, ylim = c(0, 1), total = "", filt = "include", occs = FALSE, labs = FALSE, decreasing = TRUE, group = NULL, gap = 0, labels.args = NULL, ranges.args = NULL, occs.args = NULL, total.args = NULL )
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bin |
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tax |
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xlim |
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ylim |
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total |
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filt |
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occs |
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labs |
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decreasing |
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group |
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gap |
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labels.args |
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ranges.args |
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occs.args |
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total.args |
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This function will draw a visual representation of the occurrence dataset. The interpolated ranges will be drawn, as well as the occurrence points.
The function has no return value.
# import data(stages) data(corals) # all ranges - using the age uncertainties of the occurrences tsplot(stages, boxes="sys", xlim=c(250,0)) ranges(corals, bin=c("max_ma", "min_ma"), tax="genus", occs=FALSE) # or use single estimates: assign age esimates to the occurrences corals$est<-stages$mid[corals$stg] # all ranges (including the recent!!) tsplot(stages, boxes="sys", xlim=c(250,0)) ranges(corals, bin="est", tax="genus", occs=FALSE) # closing on the Cretaceous, with occurrences tsplot(stages, boxes="series", xlim=c(145,65), shading="short") ranges(corals, bin="est", tax="genus", occs=TRUE, ranges.args=list(lwd=0.1)) # z and az separately tsplot(stages, boxes="series", xlim=c(145,65), shading="short") ranges(corals, bin="est", tax="genus", occs=FALSE, group="ecology", ranges.args=list(lwd=0.1)) # same, show only taxa that originate within the interval tsplot(stages, boxes="series", xlim=c(105,60), shading="short") ranges(corals, bin="est", tax="genus", occs=TRUE, group="ecology", filt="orig" , labs=TRUE, labels.args=list(cex=0.5)) # same using the age uncertainties of the occurrence age estimates tsplot(stages, boxes="series", xlim=c(105,60), shading="short") ranges(corals, bin=c("max_ma", "min_ma"), tax="genus", occs=TRUE, group="ecology", filt="orig" , labs=TRUE, labels.args=list(cex=0.5)) # fully customized/ annotated tsplot(stages, boxes="series", xlim=c(105,60), shading="short") ranges( corals, # dataset bin="est", # bin column tax="genus", # taxon column occs=TRUE, # occurrence points will be plotted group="growth", # separate ranges based on growth types filt="orig" , # show only taxa that originate in the interval ranges.args=list( lwd=1, # set range width to 1 col=c("darkgreen", "darkred") # set color of the ranges (by groups) ), total.args=list( cex=2, # set the size of the group identifier lablels col=c("darkgreen", "darkred") # set the color of the group identifier labels ), occs.args=list( col=c("darkgreen", "darkred"), pch=3 ), labs=TRUE, # taxon labels will be plotted labels.args=list( cex=0.4, # the sizes of the taxon labels col=c("darkgreen", "darkred") # set the color of the taxon labels by group ) )
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