Temporary hack to fix #261 and #261

If keeping, need to fix licensing
pbs-assess · Oct 10, 2023 · 3396683 · 3396683
1 parent af49635
commit 3396683
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Showing 6 changed files with 560 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.3.1.9000
+Version: 0.3.1.9001
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),
@@ -71,6 +71,7 @@ Imports:
     glmmTMB,
     graphics,
     lifecycle,
+    lme4,
     Matrix,
     methods,
     mgcv,
@@ -92,7 +93,6 @@ Suggests:
     INLA,
     inlabru,
     knitr,
-    lme4,
     rgdal,
     rmarkdown,
     sf,

diff --git a/NAMESPACE b/NAMESPACE
@@ -92,6 +92,7 @@ importFrom(lifecycle,deprecate_stop)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
 importFrom(lifecycle,is_present)
+importFrom(lme4,nobars)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(mgcv,s)

diff --git a/R/fit.R b/R/fit.R
@@ -824,8 +824,7 @@ sdmTMB <- function(
     contains_offset <- check_offset(formula[[ii]])
 
     # anything in a list here needs to be saved for tmb data
-    formula_no_sm <- remove_s_and_t2(formula[[ii]])
-    split_formula[[ii]] <- glmmTMB::splitForm(formula_no_sm)
+    split_formula[[ii]] <- splitForm(formula[ii][[1]])
     RE_names <- barnames(split_formula[[ii]]$reTrmFormulas)
 
     fct_check <- vapply(RE_names, function(x) check_valid_factor_levels(data[[x]], .name = x), TRUE)
@@ -835,8 +834,9 @@ sdmTMB <- function(
     formula[[ii]] <- split_formula[[ii]]$fixedFormula
     ln_tau_G_index[[ii]] <- unlist(lapply(seq_along(nobs_RE[[ii]]), function(i) rep(i, each = nobs_RE[[ii]][i]))) - 1L
 
-    X_ij[[ii]] <- model.matrix(split_formula[[ii]]$fixedFormula, data)
-    mf[[ii]] <- model.frame(split_formula[[ii]]$fixedFormula, data)
+    formula_no_sm <- remove_s_and_t2(formula[[ii]])
+    X_ij[[ii]] <- model.matrix(formula_no_sm, data)
+    mf[[ii]] <- model.frame(formula_no_sm, data)
     # Check for random slopes:
     if (length(split_formula[[ii]]$reTrmFormulas)) {
       termsfun <- function(x) {

diff --git a/R/mesh.R b/R/mesh.R
@@ -25,8 +25,7 @@
 #'
 #' @export
 #'
-#' mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 30, type = "cutoff")
-#' plot(mesh)
+#' @examples
 #'
 #' \donttest{
 #' mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 5, type = "cutoff")
@@ -38,6 +37,7 @@
 #' mesh <- make_mesh(pcod, c("X", "Y"), n_knots = 50, type = "kmeans")
 #' plot(mesh)
 #'
+#'}
 # # Defining a mesh directly with fmesher (formerly in INLA):
 # bnd <- fmesher::fm_nonconvex_hull(cbind(pcod$X, pcod$Y), convex = -0.05)
 # inla_mesh <- fmesher::fm_mesh_2d_inla(
@@ -49,6 +49,7 @@
 # )
 # mesh <- make_mesh(pcod, c("X", "Y"), mesh = inla_mesh)
 # plot(mesh)
+
 make_mesh <- function(data, xy_cols,
                       type = c("kmeans", "cutoff", "cutoff_search"),
                       cutoff, n_knots,