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error handling / factors and chars #208

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May 11, 2023
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error handling / factors and chars #208

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error handling / factors and chars
ericward-noaa May 10, 2023
855e25a
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ericward-noaa May 11, 2023
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13 changes: 13 additions & 0 deletions R/fit.R
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Original file line number Diff line number Diff line change
Expand Up @@ -907,7 +907,17 @@ sdmTMB <- function(
if (identical(family$family[1], "binomial") && !delta) {
## call this to catch the factor / matrix cases
y_i <- model.response(mf[[1]], type = "any")
## allow character
if (is.character(y_i)) {
y_i <- model.response(mf[[1]], type = "factor")
if(nlevels(y_i) > 2) {
cli_abort("More than 2 levels detected for response")
}
}
if (is.factor(y_i)) {
if(nlevels(y_i) > 2) {
cli_abort("More than 2 levels detected for response")
}
## following glm, ‘success’ is interpreted as the factor not
## having the first level (and hence usually of having the
## second level).
Expand Down Expand Up @@ -1119,6 +1129,9 @@ sdmTMB <- function(
no_spatial = no_spatial
)

if(is.na(sum(nobs_RE))) {
cli_abort("One of the groups used in the factor levels is NA - please remove")
}
b_thresh <- matrix(0, 2L, n_m)
if (thresh[[1]]$threshold_func == 2L) b_thresh <- matrix(0, 3L, n_m) # logistic #TODO: change hard coding on index of thresh[[1]]

Expand Down