check for selpar inits outside bounds, fixes #31

timjmiller · Dec 2, 2020 · 4ed394b · 4ed394b
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diff --git a/NEWS.md b/NEWS.md
@@ -4,7 +4,11 @@ wham 1.0.1.9000
 ### Minor improvements
 
 * add `1e-15` to predicted proportions to make age composition likelihoods robust to 0 predictions when selAA is fixed at 0. This affects the multinomial, Dirichlet, and Dirichlet-multinomial (options 1-3), since the logistic normal (options 4-7) already did this. [88f15d4](https://github.com/timjmiller/wham/commit/88f15d4a51f69a3d649d76bcac0a8cf299c3135e)
-* can now specify age composition model using `age_comp` argument to `prepare_wham_input`
+* can now specify age composition model using `age_comp` argument to `prepare_wham_input`. See [`?prepare_wham_input`](https://timjmiller.github.io/wham/reference/prepare_wham_input.html) for details. [fd94b3d](https://github.com/timjmiller/wham/commit/fd94b3dcaf189482e10a6750c2f1b8350837fd48)
+
+### Bug fixes
+
+* check for sel par inits outside lower/upper bounds
 
 wham 1.0.1 (2020-11-12)
 =========================

diff --git a/R/prepare_wham_input.R b/R/prepare_wham_input.R
@@ -935,6 +935,8 @@ Ex: ",ecov$label[i]," in ",years[1]," affects ", c('recruitment','M')[data$Ecov_
   map$log_NAA = factor(tmp)
 
   # selectivity pars
+  selpars_ini[selpars_ini > selpars_hi] <- selpars_hi[selpars_ini > selpars_hi]
+  selpars_ini[selpars_ini < selpars_lo] <- selpars_lo[selpars_ini < selpars_lo]
   par$logit_selpars = log(selpars_ini-selpars_lo) - log(selpars_hi - selpars_ini)
   par$logit_selpars[!is.na(map$logit_selpars) & is.infinite(par$logit_selpars) & par$logit_selpars<0] = -10
   par$logit_selpars[!is.na(map$logit_selpars) & is.infinite(par$logit_selpars) & par$logit_selpars>0] = 10