Newest versions at top.
usethis::use_package_doc()
create_strict_clock_model
can also create a strict model from
only a string (conversion from a double was already supported)create_mean_param
can also create a mean parameter from
only a string (conversion from a double was already supported)get_default_beast_namespace_v2_4
and get_default_beast_namespace_v2_6
,
to work well with create_beauti_options_v2_4
and create_beauti_options_v2_6
respectivelycreate_freq_param
/create_param_freq
for the GTR, HKY and TN93 site modelscreate_kappa_param
/create_param_kappa
for the HKY site modelis_freq_param
for the GTR, HKY and TN93 site modelsis_kappa_param
for the HKY site modelcreate_hky_site_model
does not have kappa
as an argument anymore:
use kappa_param
instead. Using kappa
gives a proper deprecation messagecheck_empty_beautier_folder
works correctly on Windowscheck_empty_beautier_folder
to make sure
no temporary files are createdclock_model_to_xml_prior_distr
,
tipdate_taxa_to_xml_tree
, tree_priors_to_xml_operators
work with infererence_model
,
deprecated other argumentsclock_models_to_xml_prior_distr
,
redirect user to clock_model_to_xml_prior_distr
tree_priors_to_xml_operators
,
redirect user to tree_prior_to_xml_operators
clock_models_to_xml_state
,
redirect user to clock_model_to_xml_state
clock_models_to_xml_operators
,
redirect user to clock_model_to_xml_operators
clock_models_to_xml_tracelog
,
redirect user to clock_model_to_xml_tracelog
mrca_priors_to_xml_tracelog
,
redirect user to mrca_prior_to_xml_tracelog
tree_models_to_xml_tracelog
,
redirect user to tree_model_to_tracelog_xml
~/.cache
, fix #129LazyData: true
from DESCRIPTIONsystem2
phylo_to_xml_state
removedsite_models_to_xml_state
gives a deprecation messagetree_priors_to_xml_state
gives a deprecation messagemrca_priors_to_xml_state
has the arguments mrca_prior
and has_non_strict_clock_model
replaced by inference_model
inference_models
vignettecreate_ns_inference_model
testthat
tests in examplesinference_model
(instead of
multiple elements of it)get_mcmc_filenames
and get_inference_model_filenames
rename_mcmc_filenames
and rename_inference_model_filenames
get_remove_dir_fun
, get_remove_hex_fun
and get_replace_dir_fun
geiger
packagefasta_to_phylo
and fastas_to_phylos
to repository at
https://github.com/richelbilderbeek/ribir
to lose dependency on
orphaned geiger
packagetestthat
in documentation, instead of the less known testit
create_tracelog
, create_screenlog
, create_treelog
, that
indicate where BEAST2 will store its output filecreate_mcmc
has all elements that BEAUti hascreate_test_mcmc
, create_test_tracelog
,
create_test_screenlog
, create_test_treelog
and create_test_inference_model
create_beast2_input_from_model
functioncheck_mcmc_nested_sampling
functionis_
functionscheck_file_exists
functionis_one_int
and is_one_double
functionsbeautier
has passed rOpenSci peer reviewbeautier
is on CRANis_x
and check_x
functions# Old
distr <- create_distr_poisson(id = 1, lambda = create_lambda_param(value = 1.2))
# Added
distr <- create_distr_poisson(id = 1, lambda = 1.2)
.xml
files.xml
would be incompletebabette
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