Write explicit recruitment and population-weight metadata
write_spm_metadata.RdVersion 2 metadata is embedded in comments in each species input file by default. An explicitly named JSON file supports older workflows. Split-sex species files contain `wt_M` immediately after `wt_F`; pooled-sex files use `wt_F` for both internal sex groups. Recruitment must be identified as total across sexes or per sex. Population weights are distinct from fishery and spawning weights. Version-2 projections use `TAC_ABC = 1` and do not read `tacpar.dat`. Inputs are validated before replacing metadata. Work in a copy of the assessment inputs to retain the original export.
Usage
write_spm_metadata(dirname, species, metadata = NULL, strict = TRUE)
validate_spm_inputs(dirname, metadata = NULL, strict = TRUE)Arguments
- dirname
Directory containing `spm.dat` and species files.
- species
A list of species records. Each record contains `file`, `recruitment_basis` (`"total"` or `"per_sex"`), consecutive integer `ages`, `units`, and `population_weights`. Units contain `abundance` (`"fish"`, `"thousand_fish"`, or `"million_fish"`), `weight` (`"kg"`), and matching `biomass` (`"kg"`, `"t"`, or `"thousand_t"`). Each population-weight record contains `ages` and `values`. Female population weights are required. Split-sex male weights are required unless `male_population_substitute` explicitly specifies `"female_population"` or `"mean_male_fishery"`. Pooled-sex models can use the female population vector for both internal sex groups; that assumption is recorded and reported.
- metadata
`NULL` embeds metadata when writing and discovers embedded metadata when validating. Validation falls back to `spm_metadata.json` when no species file has embedded metadata. Supply a relative `.json` filename to explicitly write or read JSON instead. Embedded declarations take precedence over an old JSON file during automatic discovery.
- strict
Logical. If `TRUE`, reject unknown metadata fields; otherwise report them as warnings. Required fields and scientific checks always apply.