Offline Reconstruction Part I

This is an example of how to use the chronosphere package to reconstruct the paleogeography across the Late Paleozoic Ice Age (LPIA), 360 to 260 Ma. Occurrence data from the Paleobiology Database (paleobiodb.org) is downloaded and prepared using the divDyn package and then plotted onto these maps.

library(chronosphere) #load chronosphere package
## Loading required package: raster
## Loading required package: sp

Part One: Paleogeographic maps

I chose six time slices across the time interval of the LPIA.

lpia <- c(360,340,320,300,280,260) #six time intervals during LPIA, 360-260 Ma
pm <- fetch("paleomap","model") #download and install paleomap rotation model from GPlates (GPlates was downloaded and installed locally)
maps <- reconstruct("plates", age=lpia, model=pm) #plate reconstruction
map360<-maps[[1]] #accessing the different elements corresponding to each age separately
map340<-maps[[2]]
map320<-maps[[3]]
map300<-maps[[4]]
map280<-maps[[5]]
map260<-maps[[6]]

This is what one of those plots looks like.

plot(map280, col="lightgreen") #paleogeographic reconstruction at 280 Ma

Now I want to reconstruct the coastlines.

coast <- reconstruct("coastlines", age=lpia) #reconstruction of coastlines
coast360<-coast[[1]] #accessing the different elements corresponding to each age separately
coast340<-coast[[2]]
coast320<-coast[[3]]
coast300<-coast[[4]]
coast280<-coast[[5]]
coast260<-coast[[6]] 

This is the same plot but without the borders:

plot(map280, col="lightgreen",border=NA) #example for paleogeographic reconstruction at 280 Ma without borders

Now add the coastlines:

{plot(map280, col="lightgreen",border=NA) #example for paleogeographic reconstruction at 280 Ma without borders
  lines(coast280, col="grey28")} #adding coastlines

Use the paleomap dataset:

pr <- fetch(dat="paleomap", var="paleoatlas", res=0.5) #download and install paleomap dataset
## If you use the data in publications, please cite its
## reference, as well as that of the 'chronosphere' package.
## - Scotese, C. R. (2016) Tutorial: PALEOMAP PaleoAtlas for GPlates and the PaleoData Plotter Program. URL: https://www.earthbyte.org/paleomap-paleoatlas-for-gplates/
pa360 <- pr["360", ]  #accessing the different elements corresponding to each age separately
pa340 <- pr["340", ]
pa320 <- pr["320", ]
pa300 <- pr["300", ]
pa280 <- pr["280", ]
pa260 <- pr["260", ]

This is the reconstruction at 280 Ma:

mapplot(pa280)  #example for 280 Ma maps for each of the RGB channels

I want to plot all six paleogeographic maps in one figure:

op <- par(mfrow=c(3,2))
mapplot(pa360, rgb=TRUE)
mapplot(pa340, rgb=TRUE)
mapplot(pa320, rgb=TRUE)
mapplot(pa300, rgb=TRUE)
mapplot(pa280, rgb=TRUE)
mapplot(pa260, rgb=TRUE)

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