Comments (7)
Requested for use case on simple data. I have only inexact ideas what combined chains are.
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@thijsjanzen will try to create a simple usecase 👍
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I have a simple user case here.
Surprisingly, it appears to work as intended, no problems here. Darn. That means that in my previous analysis, I did something wrong, rather than blaming poor babette!
`#devtools::install_github("richelbilderbeek/babette")
library(babette)
library(beastier)
#beastier::install_beast2()
setwd("/Users/janzen/MEGAsync/CARL/test_beast/")
all_chains <- c()
found_ESS <- c()
for(i in 1:5) {
cat(i, "\n")
bbt_run(
fasta_filenames = get_babette_path("anthus_aco.fas"),
mcmc = create_mcmc(chain_length = 2000000, store_every = 5000),
rng_seed = i,
beast2_output_log_filename = paste0("log_",i,".log"),
cleanup = FALSE
)
beast_log_full <- parse_beast_log(paste0(getwd(),"/log_",i,".log"))
beast_log <- remove_burn_ins(beast_log_full,
burn_in_fraction = 0.1)
found_ESS[i] <- calc_ess(beast_log$posterior, sample_interval = 5000)
all_chains <- c(all_chains, beast_log$posterior)
}
this should be (following tracer on the log files)
1362, 1285, 1618, 1345, 1546
found_ESS
and this should be:
7502
calc_ess(all_chains, sample_interval = 5000)
`
from babette.
Happy to hear. I do test babette
to have exactly the same results as Tracer, but not on combined chains. But well, if it all works correctly, there is no need to add a test.
Thanks for confirming babette
also works as intended on combined chains!
from babette.
Will close this Issue, unless @thijsjanzen has some concluding words of wisdom 🌈 ?
from babette.
Always provide a solid user case!
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👍
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