babette is an R package to work with BEAST2
Home Page: https://docs.ropensci.org/babette
License: GNU General Public License v3.0
This repository has been archived. The former README is now in README-NOT.md.
bbt_run <- function(
site_model, # Was 'site_models' (plural)
# rest as-is
)
Follow guidelines at https://ropensci.github.io/dev_guide/evolution.html
From here:
Approved! Thanks @bjoelle and @dwinter for your thorough reviews and follow-ups, and @richelbilderbeek for your diligent work. It's been a long road and a lot of code to go through and I'm glad to have this suite as part of rOpenSci.
To-dos:
Wrap up richelbilderbeek/babette#38
Transfer the repos to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
Add the rOpenSci badge to top and footer to the bottom of your READMEs
" [](https://github.com/ropensci/onboarding/issues/209)"
" [](https://ropensci.org)"
Fix any links in badges for CI and coverage to point to the ropensci URL. We no longer transfer Appveyor projects to ropensci Appveyor account so after transfer of your repo to rOpenSci's "ropensci" GitHub organization the badge should be [](https://ci.appveyor.com/project/individualaccount/pkgname).
We're starting to roll out software metadata files to all ropensci packages via the Codemeta initiative, see https://github.com/ropensci/codemetar/#codemetar for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.
Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent). More info on this here.
Welcome aboard! We'd also love a blog post about your packages, either a short-form intro to it (https://ropensci.org/tech-notes/) or long-form post with more narrative about its development. (https://ropensci.org/blog/). If you are interested, @stefaniebutland will be in touch about content and timing.
We've started putting together a gitbook with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding. Please tell us what could be improved, the corresponding repo is here.
bbt_run <- function(
fasta_filename, # Was 'fasta_filenames' (plural)
# rest as-is
)
Follow guidelines at https://ropensci.github.io/dev_guide/evolution.html
From @dwinter:
I don't think it possible to set a shifted gamma distribution (i.e. a gamma distribution with an additional "offset" value) yet. I didn't check others, but these shifted distributions are often helpful for setting node dates
From dwright I found here the best way to thank rOpenSci reviewers:
Example:
person("Bea", "Hernández", role = "rev",
comment = "Bea reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/116")
# babette
library(devtools)
#devtools::install_github("richelbilderbeek/beautier")
#devtools::install_github("richelbilderbeek/tracerer")
#devtools::install_github("richelbilderbeek/beastier")
#devtools::install_github("richelbilderbeek/mauricer")
#devtools::install_github("richelbilderbeek/babette")
library(beautier)
library(tracerer)
library(beastier)
install_beast2()
library(mauricer)
library(babette)
session_info()
#Session info --------------------------------------------------------------------------------------------------------------
#setting value
#version R version 3.4.1 (2017-06-30)
#system x86_64, linux-gnu
#ui RStudio (1.1.419)
#language (EN)
#collate de_DE.UTF-8
#tz Europe/Berlin
#date 2018-12-24
#Packages ------------------------------------------------------------------------------------------------------------------
# package * version date source
#babette * 1.3 2018-12-24 Github (richelbilderbeek/babette@4d28d36)
#base * 3.4.1 2017-07-08 local
#beastier * 1.5.2 2018-12-24 Github (richelbilderbeek/beastier@bfcd6ef)
#beautier * 1.15 2018-12-24 Github (richelbilderbeek/beautier@949c01a)
#compiler 3.4.1 2017-07-08 local
#curl 3.2 2018-03-28 cran (@3.2)
#datasets * 3.4.1 2017-07-08 local
#devtools * 1.13.3 2017-08-02 CRAN (R 3.4.1)
#digest 0.6.18 2018-10-10 cran (@0.6.18)
#git2r 0.19.0 2017-07-19 CRAN (R 3.4.1)
#graphics * 3.4.1 2017-07-08 local
#grDevices * 3.4.1 2017-07-08 local
#httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
#knitr 1.17 2017-08-10 CRAN (R 3.4.1)
#mauricer * 1.1.1 2018-12-24 Github (richelbilderbeek/mauricer@3cd6bd7)
#memoise 1.1.0 2017-04-21 CRAN (R 3.4.1)
#methods * 3.4.1 2017-07-08 local
#R.cache 0.13.0 2018-01-04 CRAN (R 3.4.1)
#R.methodsS3 1.7.1 2016-02-16 cran (@1.7.1)
#R.oo 1.21.0 2016-11-01 cran (@1.21.0)
#R.rsp 0.42.0 2018-01-10 CRAN (R 3.4.1)
#R.utils 2.6.0 2017-11-05 cran (@2.6.0)
#R6 2.3.0 2018-10-04 cran (@2.3.0)
#rappdirs 0.3.1 2016-03-28 cran (@0.3.1)
#Rcpp 1.0.0 2018-11-07 cran (@1.0.0)
#rstudioapi 0.6 2016-06-27 CRAN (R 3.4.1)
#stats * 3.4.1 2017-07-08 local
#testit 0.9 2018-12-05 cran (@0.9)
#tools 3.4.1 2017-07-08 local
#tracerer * 1.5.2 2018-12-24 Github (richelbilderbeek/tracerer@f345fc3)
#utils * 3.4.1 2017-07-08 local
#withr 2.1.2 2018-03-15 CRAN (R 3.4.1)
#yaml 2.1.16 2017-12-12 cran (@2.1.16)
#https://github.com/richelbilderbeek/babette/blob/master/vignettes/tutorial.R
require(babette)
## ------------------------------------------------------------------------
fasta_filename <- get_babette_path("anthus_aco.fas")
testit::assert(file.exists(fasta_filename))
## ------------------------------------------------------------------------
mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)
## ------------------------------------------------------------------------
site_model <- create_site_model_jc69()
site_model <- create_jc69_site_model()
## ------------------------------------------------------------------------
clock_model <- create_clock_model_strict()
clock_model <- create_strict_clock_model()
## ------------------------------------------------------------------------
tree_prior <- create_tree_prior_yule()
tree_prior <- create_yule_tree_prior()
## ------------------------------------------------------------------------
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = fasta_filename),
taxa_names = get_taxa_names(filename = fasta_filename)[1:2],
is_monophyletic = TRUE
)
## ------------------------------------------------------------------------
mrca_distr <- create_normal_distr(
mean = 15.0,
sigma = 1.0
)
## ------------------------------------------------------------------------
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = fasta_filename),
taxa_names = get_taxa_names(filename = fasta_filename),
mrca_distr = mrca_distr
)
## ------------------------------------------------------------------------
if (1 == 2) {
beast2_input_filename <- "beast_input.xml"
beast2_output_log_filename <- "beast_ouput.log"
beast2_output_trees_filenames <- "beast_output.trees"
beast2_output_state_filename <- "beast_state.xml.state"
all_files <- c(
beast2_input_filename,
beast2_output_log_filename,
beast2_output_trees_filenames,
beast2_output_state_filename
)
out <- bbt_run(
fasta_filename = fasta_filename,
mcmc = mcmc,
beast2_input_filename = beast2_input_filename,
beast2_output_log_filename = beast2_output_log_filename,
beast2_output_trees_filenames = beast2_output_trees_filenames,
beast2_output_state_filename = beast2_output_state_filename
)
testit::assert(all(file.exists(all_files)))
file.remove(all_files)
}
## ------------------------------------------------------------------------
beast2_path <- beastier::get_default_beast2_path()
print(beast2_path)
## ------------------------------------------------------------------------
if (file.exists(beast2_path)) {
out <- bbt_run(
fasta_filename = fasta_filename,
mcmc = mcmc,
beast2_path = beast2_path
)
}
#Fehler in check_input_filename_validity(input_filename = input_filename, :
#'input_filename' must be a valid BEAST2 XML file. File '/tmp/RtmpAYPTAj/beast2_2eaf0e5f70.xml' is not a valid BEAST2 file. FALSE
#Zusätzlich: Warnmeldungen:
#1: Ausführung von Kommando ''/usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java' -jar "/home/axel/.local/share/beast/lib/beast.jar" -validate "/tmp/RtmpAYPTAj/beast2_2eaf0e5f70.xml" 2>&1' ergab Status 1
#2: Ausführung von Kommando ''/usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java' -jar "/home/axel/.local/share/beast/lib/beast.jar" -validate "/tmp/RtmpAYPTAj/beast2_2eaf0e5f70.xml" 2>&1' ergab Status 1
Model f(a) f(c) f(g) f(t) kappa titv Ra Rb Rc Rd Re Rf pInv gamma
----------------------------------------------------------------------------------------------------------------------------------------
AIC TPM2uf+I+G 0.41 0.20 0.13 0.25 0.00 0.00 0.488 7.746 0.488 1.000 7.746 1.000 0.61 3.08
Nu zou ik dus graag een TPM2uf+I+G model willen gebruiken voor mijn COI alignment.
Ik kende dit model nog niet (eerder gebruikte ik gewoon een algemeen GTR model), maar vond dit erover http://www.iqtree.org/doc/Substitution-Models.
Typisch aan dit model is, dat bepaalde frequenties gelijk worden gesteld aan elkaar: AC=AT, AG=CT, CG=GT and equal base freq.
Is het mogelijk om dit te doen mbv babette? Of uberhaupt in BEAUti, dat jij weet?
Begin ik met "create_gtr_site_model()" om dan vervolgens daar details op te geven van frequenties van substituties?
Ik neem aan dat als ik dat doe door de waarden uit de vet gedrukte rij hierboven simpelweg over te nemen, dit alleen startwaarden zijn voor de MCMC run?
Suggested by reviewer of [1]
Bilderbeek, Richel JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST2 and Tracer for R." bioRxiv (2018): 271866.
bbt_run <- function(
mrca_prior, # Was 'mrca_priors' (plural)
# rest as-is
)
Follow guidelines at https://ropensci.github.io/dev_guide/evolution.html
From @thijsjanzen:
Babette is echt superhandig om de ESS te berekenen, en lijkt ook wel sneller te zijn dan tracer. Wat me wel opviel is dat de ESS waarden exact overeenkomen met tracer, behalve voor 'combined'.
Ik run vaak 10 onafhankelijke BEAST chains, en plak deze dan aan elkaar om 1 grote chain te krijgen. Zo weet je zekerder dat je niet in een lokaal optimum zit. Om te checken dat de chains allemaal naar hetzelfde convergeren, is het handig om de ESS van de gecombineerde chain te checken. Nu zag ik alleen dat deze ESS waarden niet overeenkomen met die van tracer.
Het mooiste zou nu natuurlijk zijn als ik een user-case zou meegeven, maar de log files zijn wat groot om te demonstreren hier. Ik vermoed dat je deze situatie ook makkelijk zelf kan repliceren.
Moved from there:
As far as I can tell it is not possible to estimate one tree from multiple alignments. (i.e. one tree prior, multiple alignments possibly each with its own site model). I suspect this is a common use-case (either specified this way or through a concatenated alignment with partitions). If I have this wrong then a partitioned dataset should be added to the examples vignette. If this is not currently possible it should be a priority for future development
test_that("use, one alignment, plot with nLTT", {
skip("Expose bug")
out <- run(
fasta_filenames = get_babette_path("anthus_aco.fas"),
mcmc = create_mcmc(chain_length = 1000, store_every = 1000)
)
testit::assert(
all(grepl(pattern = "STATE_", x = names(out$anthus_aco_trees)) == FALSE)
)
testthat::expect_silent(
nLTT::nltts_plot(out$anthus_aco_trees)
)
})
Instead, the names should be stripped to have a pure multiPhylo.
From Huw Ogilvie, one of the article reviewers:
Continuing the grand tradition of picking alliterative puns for BEAST program names, the authors have gone with "babette". I guess that this is in reference to one of the maids that cleans up after The Beast in the famous fairy tale. I think the name is logical and clever. However in the older Disney animated versions of the fairy tale the maid is a "sexy maid" stereotype, and the authors seem to have directly copied the babette logo from the animation. The authors should reconsider this, not only because of the notorious litigousness of Disney lawyers, but also because the optics of using a "sexy maid" logo for scientific software is bad, especially in 2018, especially from two male authors. Sorry if this point gets interpreted as not having a sense of humor, but I think it should be addressed.
Will change logo, sent out email to research group for contributions.
babette has its interface simplified, due to many deprecations. Let beautier follow.
[65] "Error 110 parsing the xml input file"
[66] ""
[67] "validate and intialize error: standard deviation must be positive (-4.554)"
[68] ""
[69] "Error detected about here:"
[70] " <beast>"
[71] " <run id='mcmc' spec='MCMC'>"
[72] " <distribution id='posterior' spec='util.CompoundDistribution'>"
[73] " <distribution id='prior' spec='util.CompoundDistribution'>"
[74] " <prior id='GammaShapePrior.s:anthus_aco' name='distribution'>"
[75] " <LogNormal id='LogNormalDistributionModel.0' name='distr'>"
bbt_run <- function(
# posterior_crown_age = NA, # Remove
# rest as-is
)
Follow guidelines at https://ropensci.github.io/dev_guide/evolution.html
bbt_run <- function(
tree_prior, # Was 'tree_priors' (plural)
# rest as-is
)
Follow guidelines at https://ropensci.github.io/dev_guide/evolution.html
Relaxed lognormal clock model does not work properly
# Reproduce the bug
# Load data
fasta_filename <- paste0("primates_long.fas")
testit::assert(file.exists(fasta_filename))
# Create MCMC chain
sample_interval <- 1000
mcmc <- create_mcmc(chain_length = 2000, store_every = sample_interval)
# Other priors
site_model <- create_site_model_jc69()
clock_model <- create_clock_model_rln()
tree_prior <- create_tree_prior_yule()
# Set MRCA prior
mrca_distr <- create_normal_distr(mean = 15.0, sigma = 1.0)
mrca_prior <- mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = fasta_filename),
taxa_names = get_taxa_names(filename = fasta_filename),
mrca_distr = mrca_distr
)
# Run babette
out <- bbt_run(
fasta_filenames = fasta_filename,
mcmc = mcmc,
site_models = site_model,
clock_models = clock_model,
tree_priors = tree_prior,
mrca_priors = mrca_prior,
verbose = F
)
I misunderstood the software machinery of how the Nested-Sampling marginal likelihood estimation worked:
This should be separated in the documentation and code.
Put Issues at this tracerer Project
TECE voted with 7 pro and 2 con for babette over rbeast2
Dear Richel,
I created a BEAST2 input file as follows:
create_beast2_input_file(input_filenames = c(input_Plectostoma_COI,input_Plectostoma_ITS1),
output_filename = output_Plectostoma_all_markers_combined)
No error message.
When I open in BEAUti I get this error message, suggesting a duplicate sequence name. But this 'duplicate' is from two different alignments.
What can I have done wrong?
Thanks!
Some Linux distro's (e.g. Lubuntu) allow the option to have an encrypted home folder. babette will fail when running from such a setup, as the temporary files are different.
It would help out the users to warn them.
bbt_run <- function(
clock_model, # Was 'clock_models' (plural)
# rest as-is
)
Follow guidelines at https://ropensci.github.io/dev_guide/evolution.html
[65] "Error 110 parsing the xml input file"
[66] ""
[67] "validate and intialize error: beta must be positive (-87.108)"
[68] ""
[69] "Error detected about here:"
[70] " <beast>"
[71] " <run id='mcmc' spec='MCMC'>"
[72] " <distribution id='posterior' spec='util.CompoundDistribution'>"
[73] " <distribution id='prior' spec='util.CompoundDistribution'>"
[74] " <prior id='GammaShapePrior.s:anthus_aco' name='distribution'>"
[75] " <Gamma id='Gamma.0' name='distr'>"
[65] "Error 110 parsing the xml input file"
[66] ""
[67] "validate and intialize error: alpha must be positive (-9.486)"
[68] ""
[69] "Error detected about here:"
[70] " <beast>"
[71] " <run id='mcmc' spec='MCMC'>"
[72] " <distribution id='posterior' spec='util.CompoundDistribution'>"
[73] " <distribution id='prior' spec='util.CompoundDistribution'>"
[74] " <prior id='GammaShapePrior.s:anthus_aco' name='distribution'>"
[75] " <Gamma id='Gamma.0' name='distr'>"
Question from an email:
[...]I want to install the script babette but does not recognize the R version 3.4.2 ,
in which R version should I install it?Warning in install.packages :
package ‘babette’ is not available (for R version 3.4.2)
From here:
One additional thing I would suggest would be to include the overwrite parameter in babette::bbt_run (it's only present in beastier::run_beast2 at present), and to set it to FALSE by default (as it is in BEAST2).
Described and done at #9
From @ksw9 at this Issue:
Great resource! Do you have plans for a function to import tip dates?
Thank you!
From #48:
Transfer the repos to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
Add the rOpenSci badge to top and footer to the bottom of your READMEs
" [](https://github.com/ropensci/onboarding/issues/209)"
" [](https://ropensci.org)"
Fix any links in badges for CI and coverage to point to the ropensci URL. We no longer transfer Appveyor projects to ropensci Appveyor account so after transfer of your repo to rOpenSci's "ropensci" GitHub organization the badge should be [](https://ci.appveyor.com/project/individualaccount/pkgname).
We're starting to roll out software metadata files to all ropensci packages via the Codemeta initiative, see https://github.com/ropensci/codemetar/#codemetar for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.
Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent). More info on this here.
As mauricer has not been reviewed, I cannot add names to DESCRIPTION,
Hi,
Thank you for your effort, it is a great initiative. I would love to try how babette can fit in some automated pipeline.
I was just trying out babette with some example data, but I got the following issue:
library(babette)
fasta_name <- "anthus_aco.fasta"
mrca_priors <- create_mrca_prior(
taxa_names = get_taxa_names(fasta_name),
alignment_id = get_alignment_id(fasta_name),
mrca_distr = create_normal_distr(mean = 15.0, sigma = 0.025)
)
mcmc = create_mcmc(chain_length=2000, store_every = 1000)
out <- bbt_run(fasta_name, mcmc = mcmc, mrca_priors = mrca_priors)
Error: file.exists(output_log_filename) is not TRUE
In addition: Warning messages:
1: In file.rename(from = from, to = output_log_filename) :
cannot rename file 'anthus_aco.log' to '/tmp/RtmpI5Egd6/beast2_258b458753999log', reason 'Invalid cross-device link'
2: In file.rename(from = from, to = to) :
cannot rename file 'anthus_aco.trees' to '/tmp/RtmpI5Egd6/beast2_anthus_aco_258b42309a56a.trees', reason 'Invalid cross-device link'
I could not find any workaround for this issue. Do you have any idea how to solve?
Thank you in advance!
Best,
Gergo
This is a problem with CentOS and the temporary files babette creates, as reported in #31. AFAIK, there is no continuous integration system to create a CentOS environment. As long as I cannot support CentOS, it would be helpful if the users would know there will be problems.
Oops, incorrect repo. Closing this Issue.
Suggested by reviewer of [1]
Bilderbeek, Richel JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST2 and Tracer for R." bioRxiv (2018): 271866.
Reproduce:
out <- bbt_run(
"anthus_aco.fas",
site_models = create_hky_site_model(),
clock_models = create_rln_clock_model(),
tree_priors = create_bd_tree_prior(),
mcmc = mcmc
)
From Axel Hille:
I have another issue, it is more informal concerning the use of babette. How can I use alignments which are split into various subsets == partitions, for example split genes into introns and exons? In BEAST you have the possibility to load a nexus-file, where the partitions are defined in the "BEGIN CODONS;" - block. I wonder if the "deprecated two and more alignments" solution in babette was for this issue?
Any hints are appreciated.
How does it work exactly?
When you use a Nested Sampling setup and the BEAST2 jar file, one gets this error:
'input_filename' must be a valid BEAST2 XML file. File '/tmp/RtmpfHeHcJ/beast2_138222bbda78.xml' is not a valid BEAST2 file. FALSE
Execution halted
It should be something like:
When using Nested Sampling, one must use the binary BEAST2 executable
[65] "Error 110 parsing the xml input file"
[66] ""
[67] "validate and intialize error: Upper value should be higher than lower value"
[68] ""
[69] "Error detected about here:"
[70] " <beast>"
[71] " <run id='mcmc' spec='MCMC'>"
[72] " <distribution id='posterior' spec='util.CompoundDistribution'>"
[73] " <distribution id='prior' spec='util.CompoundDistribution'>"
[74] " <prior id='GammaShapePrior.s:anthus_aco' name='distribution'>"
[75] " <Uniform id='Uniform.0' name='distr'>"
Attached is a file that has this:
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