[R] Average skyline plot from newick trees stored

Dear all, Does anyone know how can one loop through the newick phylogenetic trees stored in a nexus file and generate an average skyline plot with coalescent intervals? I have managed to generate the plot with one tree, but is it possible to create that consensus/average plot in R?

[R] plot error bars on skyline plot

Hi, I have generated a skyline plot of a tree in newick format using ape. How can I plot the error bars for this graph? I only have the the tree data. un-8.1:0, 20.1:0):0, 6.1:3):123, (35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0,

[R] Skyline plots from several trees in newick format

Dear all, I am trying to create a consensus skyline plot using the ape package(newbie). I have a nexus file that looks like the one from above containing many trees. (my_file.trees) #NEXUS begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)] tree true_tree_1 =

[R] plot probabilities of occurrence of values in a vector using connected points

Hi all, I have been struggling with some plotting issues (maybe not that difficult but I am stuck). If I have 2 vectors : 1st with average values of the columns of a data frame, which, looks similar to : v: (1.4,3,3,3,4.5,0,0,0,0,0,0,0,25.5,6,6,4.2) 2nd with