Add standalone documentation for sr_model class#195
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Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/6530ae68-4931-43a9-afe7-d3a8fad022b6 Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>
Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/6530ae68-4931-43a9-afe7-d3a8fad022b6 Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com>
sr_model class
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📖 https://ucd-serg.github.io/serodynamics/preview/pr195 |
Kwan-Jenny
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Kwan-Jenny
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Thanks @sschildhauer ! The new standalone ?sr_model page
is going to be really helpful for users — having all the columns and
attributes in one place is great.
I left a few suggestions inline:
population_paramsdocumentation depends on PR #141 not yet
being merged.Iso_type↔biomarker_var— a cross-reference would help
users trace the data pipeline.@examplesblock — would be a nice addition.
| #' sampling.} | ||
| #' \item{nThin}{[integer] thinning interval (ratio of total iterations to | ||
| #' retained samples, i.e., `niter / nmc`).} | ||
| #' \item{population_params}{(optional) a [tibble::tbl_df] of modeled |
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Since population_params attribute is being introduced in PR #141 (not yet merged into main), I think we should either:
(a) wait to merge this PR until #141 is merged, or
(b) add a note in the documentation like (available when run_mod() is called with with_pop_params = TRUE in package versions ≥ X.X.X.XXXX)
Otherwise users reading ?sr_model may get confused when they don't see this attribute on their sr_model object.
| #' \item `shape` -- shape parameter | ||
| #' \item `alpha` -- decay rate | ||
| #' }} | ||
| #' \item{Iso_type}{[character] antibody/antigen isotype combination being |
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Quick clarifying question — is Iso_type in sr_model the same conceptual variable as biomarker_var in as_case_data()?
| #' | ||
| #' @name sr_model-class | ||
| #' @aliases sr_model | ||
| NULL |
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Would it be possible to add a small @examples block showing how to inspect an sr_model object? Even something like:
| NULL | |
| #' @examples | |
| #' \dontrun{ | |
| #' data(nepal_sees_jags_output) | |
| #' class(nepal_sees_jags_output) | |
| #' attributes(nepal_sees_jags_output) | |
| #' head(nepal_sees_jags_output) | |
| #' } |
The
sr_modelclass had no dedicated help page — its structure was only documented inline inrun_mod()'s@returnssection.Changes
R/sr_model-class.R— New roxygen2 documentation page covering all data columns, custom attributes (including thepopulation_paramsattribute from PR Adding population parameters as attributes #141), class inheritance, and construction notespkgdown/_pkgdown.yml— Registersr_model-classin the "Model seroresponse" reference section[dplyr::tbl_df]→[tibble::tbl_df]cross-references inRun_Mod.R,nepal_sees_jags_output.R,plot_predicted_curve.R,use_att_names.R— these were resolving todplyr::defunctsincetbl_dfmoved to tibbleinst/WORDLIST— Added "precisions"Usage
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