The fossilbm from dsilvestro

According to the script and example data, it seems that it cannot run normally.

Dear Professor:
Thank you very much for developing the FossilBM package, which has been of great help to my biogeographic research. However, there are some problems recently when using the script in github to run example data. I would like to ask you:
run_FBD.r

>fbm_obj <- read_and_transform_data(treefile, datafile, log_trait_data=10)
Warning messages:
1: In treedata(t, trait) :
  The following tips were not found in 'data' and were dropped from 'phy':
	Aotus_infulatus
	Callicebus_coimbrai
	Callicebus_nigrifrons
	Chiropotes_israelita
	Saguinus_graellsi
	Saguinus_martinsi
	Saguinus_melanoleucus
	Saguinus_tripartitus
	Sapajus_robustus
2: In treedata(t, trait) :
  The following tips were not found in 'phy' and were dropped from 'data':
	Aotus_brumbacki
	Aotus_zonalis
	Callicebus_discolor
	Callicebus_medemi
	Callicebus_ornatus
	Callithrix_flaviceps
	Cebus_aequatorialis
	Chiropotes_albinasus
	Lagothris_poeppigii
	Lagothrix_flavicauda
	Lagothrix_lugens
	Leontopithecus_caissara
	Mico_melanurus
	Mico_nigriceps
	Pithecia_aequatorialis
	Pithecia_albicans
	Saguinus_inustus
	Saguinus_leucopus
	Saimiri_vanzolinii
	Sapajus_nigritus

So, I deleted the unmatched samples in platyrrhine_FBD.trees and platyrrhine_bodymass.txt so that the samples in both files were the same. Ultimately, this step was successful.

Then, drawing failed

>plot_time_varying_trend(fbm_obj, output_file, resfile="trends.pdf")
Error in plot.window(...) : need finite 'ylim' values
6. plot.window(...)
5. localWindow(xlim, ylim, log, asp, ...)
4. plot.default(time_axis, res[1, ], ylab = ylab, xlab = "Time", type = "n", ylim = c(min(res), max(res)), main = main)
3. plot(time_axis, res[1, ], ylab = ylab, xlab = "Time", type = "n", ylim = c(min(res), max(res)), main = main) at fossilBM_lib.R#1325
2. plot_res_trend(res, time_axis, ylab = "Change in expected phenotype (y_t)",
main = paste0("Partition ", i)) at fossilBM_lib.R#1369

Then I saved the file as platyrrhine_bodymass_img.rda (although there is no such command in the code) and tried extract_ancestral_state_time.R, but many problems occurred:

These environments at the beginning of the script are not given in the example data:

#setwd("/Volumes/DSILVESTRO/data/fossilizedBM/EMPIRICAL_ANALYSIS/FBM20170316/latitude/")
#setwd("/Volumes/DSILVESTRO 1/platy_log_files/bodymass")
setwd("/Users/danielesilvestro/Desktop/platy_log_files/bodymass")
setwd("/Users/danielesilvestro/Desktop/platy_log_files/latitude")
setwd("/Users/danielesilvestro/Desktop/platy_log_files/bodymass_nofoss")
setwd("/Users/danielesilvestro/Desktop/platy_log_files/latitude_nofoss")

Error：

[1] "platyrrhine_bodymass_img.rda"
Error: object 'tree' not found

I changed the phy=tree in the script to phy=fbm_obj$tree, but the error continued:

[1] "platyrrhine_bodymass_img.rda"
Error in sample.int(x, size, replace, prob) : 
  cannot take a sample larger than the population when 'replace = FALSE'

………………

According to the script and example data, it seems that it cannot run properly. Looking forward to your reply, thank you very much！

dsilvestro / fossilbm Goto Github PK

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add phylogenetic imputation to output files

According to the script and example data, it seems that it cannot run normally.

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