Fix R CMD check and tests

pbs-assess · Oct 11, 2023 · 08325b4 · 08325b4
1 parent 3e775ad
commit 08325b4
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/R/mesh.R b/R/mesh.R
@@ -128,11 +128,11 @@ make_mesh <- function(data, xy_cols,
     loc_centers <- NA
   }
   # TODO:
-  spde <- INLA::inla.spde2.matern(mesh)
+  # spde <- INLA::inla.spde2.matern(mesh)
   # mesh_inla <- INLA::inla.mesh.create(loc_xy, refine = TRUE, cutoff = cutoff)
   # names(spde_inla$param.inla)
 
-  # spde <- fmesher::fm_matern_precision(mesh, alpha = 2)
+  spde <- fmesher::fm_matern_precision(mesh, alpha = 2)
   # A_inla <- INLA::inla.spde.make.A(mesh, loc = loc_xy)
   A <- fmesher::fm_basis(mesh, loc = loc_xy)
 

diff --git a/tests/testthat/test-3-spatial-varying.R b/tests/testthat/test-3-spatial-varying.R
@@ -106,7 +106,7 @@ test_that("Delta model with spatially varying factor predictor and no spatiotemp
     spatial = "off", # since spatially varying predictor is a factor
     spatial_varying = ~0 + quarter,
     time = "year",
-    control = sdmTMBcontrol(newton_loops = 0L)
+    control = sdmTMBcontrol(newton_loops = 1L)
   )
   expect_s3_class(m, "sdmTMB")
   expect_true(sum(is.na(m$sd_report$sd)) == 0L)

diff --git a/tests/testthat/test-cross-validation.R b/tests/testthat/test-cross-validation.R
@@ -88,8 +88,8 @@ test_that("Cross validation with offsets works", {
   d <- pcod_2011
   d$log_effort <- rnorm(nrow(d))
 
-  library(future)
-  future::plan(future::multisession)
+  # library(future)
+  # future::plan(future::multisession)
 
   expect_error(
     fit_cv_off1 <- sdmTMB_cv(
@@ -213,7 +213,7 @@ test_that("Cross validation with offsets works", {
   expect_equal(round(fit_cv_off5$models[[1]]$model$par, 4), round(fit_cv_off7$models[[1]]$model$par, 4))
   expect_equal(round(fit_cv_off5$models[[1]]$model$par, 4), round(fit_cv_off8$models[[1]]$model$par, 4))
 
-  future::plan(future::sequential)
+  # future::plan(future::sequential)
 })
 
 test_that("Delta model cross validation works", {