tabs (version 0.2.0)

get_tree: get_tree

Description

get the tree based on a tabs object or recvect object

Usage

get_tree(
  filename,
  extant = TRUE,
  recname = NULL,
  ultrametric = FALSE,
  verbose = FALSE
)

Value

list of dendrogram objects

Arguments

filename

path where files or qs2/rds was exported, reconstruct object of class tabs or recvect object

extant

boolean, only for currently existing shapes (TRUE) or all shapes (FALSE)

recname

recname, default NULL will create a tree for every merged polygon

ultrametric

boolean, if TRUE, all the tips (leaves) are the same distance from the root

verbose

boolean, print messages

Author

Johannes De Groeve

Examples

if (FALSE) {
# load data samples
sporades <- sporades()
topo <- sporades$topo
labs <- sporades$labs
curve <- sporades$curve


# change duplicated names 
duplicates <- labs[labs$name == 'UNKNOWN',]$name
labs[labs$name == 'UNKNOWN',]$name <- paste0(duplicates,' ',toupper(letters[1:length(duplicates)]))

# reconstruct
rec <- reconstruct(topo=topo,
                   region=labs,
                   curve=curve,
                   reclabs='name'
                   )

# present day shapes only
trees_e <- get_tree(rec,
                    extant=TRUE,
                    ultrametric=FALSE)
trees_e_u <- get_tree(rec,
                      extant=TRUE,
                      ultrametric=TRUE)
                      
par(mar=c(4,4,2,8),mfrow=c(1,2), oma = c(0, 0, 4, 0))
plot(trees_e[[2]], horiz = TRUE, 
     main = "Observed tree", xlab = "Years BP")
plot(trees_e_u[[2]], horiz = TRUE, 
     main = "Ultrametric tree", xlab = "Years BP")                  
mtext("Connectivity change over time", outer = TRUE, cex = 1.5, line = 1) 
mtext("present-day islands", outer = TRUE, cex = 1, line = -0.2) 
            
# present and past shapes               
trees_a <- get_tree(rec,
                    extant=FALSE,
                    ultrametric=FALSE)
trees_a_u <- get_tree(rec,
                      extant=FALSE,
                      ultrametric=TRUE)
         
par(mar=c(4,0,2,8),mfrow=c(1,2), oma = c(0, 0, 4, 0))
plot(trees_a[[2]], 
     horiz = TRUE, 
     main = "Observed tree", 
     xlab = "Years BP")
plot(trees_a_u[[2]], 
     horiz = TRUE, 
     main = "Ultrametric tree", 
     xlab = "Years BP")
mtext("Connectivity change over time", outer = TRUE, cex = 1.5, line = 1) 
mtext("present and past islands", outer = TRUE, cex = 1, line = -0.2) 
                     
# select specific shape for which the connectivity change is plotted
tree <- get_tree(rec,
                 recname=rec$recvect$AP0000000$recname[6],
                 extant=FALSE)
par(mar=c(4,0,2,8),mfrow=c(1,1), oma = c(0, 0, 0, 0))
plot(tree$`Nisí Peristéra`, 
     horiz = TRUE, 
     main = "Observed tree", 
     xlab = "Years BP")
}