ropensci beautier issues

ropensci / beautier

R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2

https://docs.ropensci.org/beautier

GNU General Public License v3.0

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issues

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Do different NS MCMCs created different BEAST2 input files?

#93 richelbilderbeek closed 5 years ago
1
Use Beasy?

#92 richelbilderbeek opened 5 years ago
0
Make sure NEWS.md is up to date and use release notes

#91 sckott closed 5 years ago
3
Measure an NS ESS

#90 richelbilderbeek closed 5 years ago
1
Second line must start a new doc paragraph

#89 richelbilderbeek closed 5 years ago
0
Use check_mcmc and is_mcmc better

#88 richelbilderbeek closed 5 years ago
1
Add @seealso to doc

#87 richelbilderbeek closed 5 years ago
0
Deprecate get_has_non_strict_clock_model

#86 richelbilderbeek closed 5 years ago
1
Check doc for examples

#85 richelbilderbeek closed 5 years ago
1
Check doc for author

#84 richelbilderbeek closed 5 years ago
0
Check doc for return

#83 richelbilderbeek closed 5 years ago
0
Remove old interface

#82 richelbilderbeek closed 5 years ago
0
clock_prior_distr_id is not checked throughly

#81 richelbilderbeek closed 5 years ago
0
Check if vignette works

#80 richelbilderbeek closed 5 years ago
1
Check if citation works

#79 richelbilderbeek closed 5 years ago
1
Rename misc_options to beauti_options

#78 richelbilderbeek closed 5 years ago
0
Add 'check_misc_options'

#77 richelbilderbeek closed 5 years ago
0
Add 'create_inference_model'

#76 richelbilderbeek closed 5 years ago
0
Let beautier set an MRCA prior's alignment ID and taxon names

#75 richelbilderbeek closed 5 years ago
0
Creating and MRCA prior that is non-/monophyletic

#74 richelbilderbeek closed 6 years ago
1
Improve interfacte of create_tn93_site_model

#73 richelbilderbeek closed 6 years ago
4
Do not modify globals

#72 richelbilderbeek closed 6 years ago
0
Simplify API or add narrative explanation

#71 richelbilderbeek closed 6 years ago
4
Support shifted gamma distribution

#70 richelbilderbeek closed 6 years ago
1
Support multiple alignments for one tree

#69 richelbilderbeek closed 6 years ago
1
Improve doc create_beast2_input_run

#68 richelbilderbeek closed 6 years ago
0
has_xml_short_closing_tag doc

#67 richelbilderbeek closed 6 years ago
0
Confusing descriptions

#66 richelbilderbeek closed 6 years ago
0
init_gamma_site_model takes one site model

#65 richelbilderbeek closed 6 years ago
0
has_xml_closing_tag doc

#64 richelbilderbeek closed 6 years ago
0
clock_model_to_xml_tracelog links to itself

#63 richelbilderbeek closed 6 years ago
0
remove_multiline doc typo

#62 richelbilderbeek closed 6 years ago
0
remove_first_brm_clock_rate misses doc

#61 richelbilderbeek closed 6 years ago
0
is_in_patterns mismatched documentation

#60 richelbilderbeek closed 6 years ago
0
get_site_model_n_params returns number of parameters

#59 richelbilderbeek closed 6 years ago
0
Wrong doc

#58 richelbilderbeek closed 6 years ago
0
fastas_to_phylos does not return a random phylo

#57 richelbilderbeek closed 6 years ago
0
Remove empty file to_do.R

#56 richelbilderbeek closed 6 years ago
1
Refactor clock_models_to_xml to avoid duplication

#55 richelbilderbeek closed 6 years ago
1
Document the purpose of get_id better

#54 richelbilderbeek closed 6 years ago
0
Document that fasta_file_to_sequences uses one file as input

#53 richelbilderbeek closed 6 years ago
0
Document that clock_model_to_xml_lh_distr builds the branchRateModel

#52 richelbilderbeek closed 6 years ago
0
Document that kappa_1, kappa_2 and tree prior parameters are always estimated

#51 richelbilderbeek closed 6 years ago
5
get_site_model_n_params and get_site_model_n_distrs assume gamma rate categories

#50 richelbilderbeek closed 6 years ago
1
Mismatch between is_distr and documentation

#49 richelbilderbeek closed 6 years ago
0
Mismatch between is_index_of_first_shared_clock_model and its documentation

#48 richelbilderbeek closed 6 years ago
0
get_phylo_crown_age only works on ultrametric trees

#47 richelbilderbeek closed 6 years ago
0
Interaction kappa1, kappa2 and S in TN93

#46 richelbilderbeek closed 6 years ago
0
Hyper parameters are not estimated

#45 richelbilderbeek closed 6 years ago
5
XML should be added on monophyly instead of a strict clock

#44 richelbilderbeek closed 6 years ago
0

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