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)
`

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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!

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Will close this Issue, unless @thijsjanzen has some concluding words of wisdom 🌈 ?

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Always provide a solid user case!

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👍

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