View source: R/prepare_badirate.R
prepare_badirate | R Documentation |
Create BadiRate setup table and corresponding scripts for PBS job arrays
prepare_badirate(og_path, tree, branch_models = c(gr = "GR", fr = "FR", sp = "15->16"), rate_model = "GD", estimation = "ML", out_dir = "./raw_outputs", script_dir = "./scripts", replicates = 2, ancestral = TRUE, outlier = TRUE, seed = 20180808, start_value = 1, pbs_q = "smps", badirate_path = "", create_scripts = "pbs")
og_path |
Path to single-file orthogroup folder, created with 'split_orthogroups()' |
tree |
Path to ultrametric species tree file. Leaf names have to match to orthogroup header names. |
branch_models |
Vector of named branch models. Name should be a 2-letter abbreviation of choice (except gr and fr, which are specific). Value should be either "GR", "FR" or a specific branch model in the syntax of badirate (e.g. "13->14:13->15_18->21"). *CAUTION: More complex models can increase running time drastically.* |
rate_model |
Rate model. Deafult is GD. |
estimation |
Estimation method used for BadiRate. Default is ML. |
out_dir |
Output directory for the future runs. |
script_dir |
Directory which the script files should be saved. |
replicates |
How many replications per model. Default is 2. *CAUTION: Big number of replicates can drastically extend runtime* |
ancestral |
Logical. See BadiRate -anc option. |
outlier |
Logical. See BadiRate -outlier option. |
seed |
Initial seed value to set. |
start_value |
0 or 1. 0 will start parameter search from Maximum Parsimony, 1 will choose a random number. |
pbs_q |
Queue of PBS. Default is smps. |
badirate_path |
Path to BadiRate.pl executabe if not in $PATH. |
create_scripts |
Logical. Create pbs job scripts if TRUE, which is the default. |
Set up table of experimetns. Also writes out script files.
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