Issues

• Requesting support with simulating under the host repertoire model

  treeppl/treepplr#32 · Filter by author alexreiss1 opened on Sep 17, 2026

• tp_compile() silently returns a phantom model when tpplc fails with exit code != 1

  treeppl/treepplr#28 · Filter by author maribraga opened on Jul 29, 2026

• tp_run() fails at large particle counts: R character strings are limited to 2^31-1 bytes

  treeppl/treepplr#27 · Filter by author maribraga opened on Jul 28, 2026

• tp_run() has no n_runs/n_processes argument; multiple independent runs go through the sweeps runtime option

  treeppl/treepplr#26 · Filter by author maribraga opened on Jul 28, 2026

• align=TRUE is rejected for smc-bpf/smc-apf; no guidance toward --resample align

  treeppl/treepplr#25 · Filter by author maribraga opened on Jul 28, 2026

• tp_compile() gives no guidance when a method name has been renamed across tpplc versions

  treeppl/treepplr#24 · Filter by author maribraga opened on Jul 28, 2026

• tp_compile_options() throws on tpplc 0.4's --help output (stale "Options:" header assumption)

  treeppl/treepplr#23 · Filter by author maribraga opened on Jul 28, 2026

• Feature request: tidy parser for importance-sampling/SMC output (samples + weights + normConst)

  treeppl/treepplr#22 · Filter by author maribraga opened on Jul 28, 2026

• tp_parse_mcmc() output is hard to consume: long format, __data__.-prefixed names, junk __constructor__ rows, string-typed samples

  treeppl/treepplr#21 · Filter by author maribraga opened on Jul 28, 2026

• Inf/-Inf/NaN returned as {"__float__": ...} break unlist() and aren't handled by tp_parse_mcmc()/tp_parse_smc()

  treeppl/treepplr#20 · Filter by author maribraga opened on Jul 28, 2026

• tp_parse_smc() reports log_weight/norm_constant that don't match the actual particle weights

  treeppl/treepplr#19 · Filter by author maribraga opened on Jul 28, 2026

• tree_age_cumul() / tp_phylo_to_tpjson() default age="" fails with a cryptic data.frame error

  treeppl/treepplr#18 · Filter by author maribraga opened on Jul 28, 2026

• options_to_string() corrupts boolean compile flags when mixed with non-logical options

  treeppl/treepplr#17 · Filter by author maribraga opened on Jul 28, 2026

• JSON to phylo

  enhancement
  Task

  treeppl/treepplr#16 · Filter by author maribraga opened on Jul 28, 2026

• Functions in wrong .R file

  enhancement
  Task

  treeppl/treepplr#15 · Filter by author maribraga opened on Jul 28, 2026