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clarify jags code #144

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clarify jags code #144

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3af1715
Increment version number to 0.0.0.9045
d-morrison Jan 5, 2026
6035c21
Merge branch 'main' into clarify-jags
d-morrison Jan 5, 2026
c6e1f95
Merge branch 'main' into clarify-jags
d-morrison Jan 5, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: serodynamics
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9044
Version: 0.0.0.9045
Authors@R: c(
person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
comment = "Author of the method and original code."),
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12 changes: 7 additions & 5 deletions inst/extdata/model.jags
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Expand Up @@ -55,11 +55,13 @@ model {
}

# these are random effects
y0[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,1])
y1[subj,cur_antigen_iso] <- y0[subj,cur_antigen_iso] + exp(par[subj,cur_antigen_iso,2]) # par[,,2] must be log(y1-y0)
t1[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,3])
alpha[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,4]) # `nu` in the paper
shape[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,5]) + 1 # `r` in the paper
y0[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,1])
# par[,,2] is log(y1-y0):
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Copilot AI Jan 5, 2026

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The comment "par[,,2] is log(y1-y0)" is technically imprecise. Based on the code, par[,,2] represents log(y1-y0), and when exponentiated it gives change_y = y1 - y0.

Consider revising the comment to be more explicit, such as: "par[,,2] represents log(change in y from baseline to peak)"

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# par[,,2] is log(y1-y0):
# par[,,2] represents log(change in y from baseline (y0) to peak (y1)):

Copilot uses AI. Check for mistakes.
change_y[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,2])
y1[subj,cur_antigen_iso] <- y0[subj,cur_antigen_iso] + change_y[subj,cur_antigen_iso]
t1[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,3])
alpha[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,4]) # `nu` in the paper
shape[subj,cur_antigen_iso] <- exp(par[subj,cur_antigen_iso,5]) + 1 # `r` in the paper

# `n_params` is the number of model parameters; y0, y1, t1, alpha (aka nu), and r
# this is the prior distribution
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