Newest versions at top.
DESCRIPTION
, thanks Kurt Hornikusethis::use_package_doc()
check_empty_beastier_folder
works under Windowsbeastier_report
check_can_create_file
creates folder if neededinstall_beast2
, upgrade_beast2
, uninstall_beast2
are deprecated,
as these violated CRAN policy. Thanks to Brian Ripley for sharing!
The deprecation message will point users to the non-official
beastierinstall
package at https://github.com/richelbilderbeek/beastierinstall
update_beastier
continue_beast2
to continue a BEAST2 runis_on_github_actions
to detect the GitHub Actions environmentis_on_ci
detects the GitHub Actions environmentupdate_beastier
: gives deprecation messageget_default_beast2_jar_path
allows for a custom folder nameinstall_beast2
is silent by defaultinstall_beast2
and uninstall_beast2
give more information when
verbosetestthat
tests in code examplesrename_beast2_options_filenames
get_beast2_options_filenames
~/beast2.xml
beastier_report
to help create a bug reportinstall_beast2
for a specific versionbeautier
v2.3 interfacebeast2_output_log_filename
and beast2_output_trees_filename
have become obsolete. Use
create_tracelog()$filename
and create_treelog()$filename
as
part of an MCMC insteadbeast2_working_dir
is obsoleted, because it
no longer served a purpose. Use setwd
to set the working directoryget_beast2_example_filenames
to get the
full paths of all the BEAST2 example filesget_beast2_example_filename
to get the
full path of a BEAST2 example fileget_default_beast2_working_dir
to get the full path of
the default BEAST2 working directoryclear_beast2_working_dir
to clear the BEAST2 working directorybeast2_path
still/already exists in check_beast2_options
update_beastier
to update the beastier
dependenciescreate_beast2_options
checks that the filenames are not in the same
folder as the BEAST2 working directoryget_beast2_options_filenames
to obtain the filenames in a
beast2_options
check_beast2_options
checks for duplicate filenamesv2.6.0
, instead of v2.5.2
are_identical_alignments
is_alignment
This version never had a formal release.
This version never had a formal release.
run_beast2
run_beast2
/home/username
,
thanks to Brian RipleySystemRequirements
field to DESCRIPTION
v2.5.2
, instead of v2.5.1
run_beast2
/run_beast2_from_options
in parallelget_default_beast2_bin_path
is silent if BEAST2 is absent'R'
for programsGPL-3
instead of also adding the file LICENSE
ropensci
beautier
.jar
path
(using the argument beast2_jar_path
), one
can now also supply the BEAST2 binary path.beast2_jar_path
are now called beast2_path
run_beast2
had a parameter called overwrite_state_file
, which is renamed
to overwrite
and states if the .log
file and .trees
files will be overwritten,
like BEAST2 does. This is a bug fix, as the obsolete parameter name did not
prevent the state file being overwritten.run_beast2
with a parameter called overwrite_state_file
is obsolete.
Use the parameter overwrite
instead.babette
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