Set get_index(..., bias_correct = TRUE) as default #456

Author: seananderson

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.7.2.9004
+Version: 0.7.2.9005
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),

NEWS.md

@@ -2,6 +2,10 @@
 
 ## Minor improvements and fixes
 
+* Change default in `get_index()` etc. to `bias_correct = TRUE`. This is the
+  recommended setting for final inference and speed improvements within TMB
+  have made it more viable to include the bias correction by default. #456
+
 * Only retain Newton update parameters if they improve the objective function.
   #455
 

R/index.R

@@ -5,6 +5,9 @@
 #'   Alternatively, if [sdmTMB()] was called with `do_index = TRUE` or if using
 #'   the helper function [get_index_split()], an object from [sdmTMB()].
 #' @param bias_correct Should bias correction be implemented [TMB::sdreport()]?
+#'   This is recommended to be `TRUE` for any final analyses, but one may wish
+#'   to set this to `FALSE` for slightly faster calculations while experimenting
+#'   with models.
 #' @param level The confidence level.
 #' @param area Grid cell area. A vector of length `newdata` from
 #'   [predict.sdmTMB()] *or* a value of length 1 which will be repeated
@@ -115,7 +118,7 @@
 #'   ylim(0, NA)
 #' }
 #' @export
-get_index <- function(obj, bias_correct = FALSE, level = 0.95, area = 1, silent = TRUE, ...)  {
+get_index <- function(obj, bias_correct = TRUE, level = 0.95, area = 1, silent = TRUE, ...)  {
   # if offset is a character vector, use the value in the dataframe
   if (is.character(area)) {
     area <- obj$data[[area]]

man/get_index.Rd

@@ -11,11 +11,11 @@ test_that("get_index works", {
   )
   nd <- replicate_df(qcs_grid, "year", unique(pcod$year))
   predictions <- predict(m, newdata = nd, return_tmb_object = TRUE)
-  ind <- get_index(predictions)
+  ind <- get_index(predictions, bias_correct = FALSE)
   ind
   expect_s3_class(ind, "data.frame")
 
-  indsp <- get_index_split(m, nd, nsplit = 2)
+  indsp <- get_index_split(m, nd, nsplit = 2, bias_correct = FALSE)
   expect_equal(ind, indsp)
   expect_identical(chunk_time(c(1, 2, 3), 2), list(`1` = c(1, 2), `2` = 3))
   expect_error(chunk_time(c(1, 2), 0))
@@ -40,8 +40,8 @@ test_that("get_index works", {
   # splits work with areas:
   set.seed(1)
   areas <- rlnorm(nrow(nd), meanlog = 0, sdlog = 0.1)
-  ind <- get_index(predictions, area = areas)
-  indsp <- get_index_split(m, nd, nsplit = 2, area = areas)
+  ind <- get_index(predictions, area = areas, bias_correct = FALSE)
+  indsp <- get_index_split(m, nd, nsplit = 2, area = areas, bias_correct = FALSE)
   expect_equal(ind, indsp)
 
   # splits work with offsets:
@@ -57,8 +57,8 @@ test_that("get_index works", {
   set.seed(1)
   fake_offset <- rnorm(nrow(nd2), 0, 0.1)
   predictions2 <- predict(m2, newdata = nd2, return_tmb_object = TRUE, offset = fake_offset)
-  ind <- get_index(predictions2)
-  indsp <- get_index_split(m2, nd2, nsplit = 2, predict_args = list(offset = fake_offset))
+  ind <- get_index(predictions2, bias_correct = FALSE)
+  indsp <- get_index_split(m2, nd2, nsplit = 2, predict_args = list(offset = fake_offset), bias_correct = FALSE)
   expect_equal(ind, indsp)
 })
 
@@ -130,13 +130,13 @@ test_that("Index integration with area vector works with extra time and possibly
   nd <- replicate_df(qcs_grid, "year", seq(2011, 2017))
   nd$area <- 4
   p <- predict(fit, newdata = nd, return_tmb_object = TRUE)
-  ind0 <- get_index(p, area = nd$area)
+  ind0 <- get_index(p, area = nd$area, bias_correct = FALSE)
 
   # newdata doesn't have all fitted years:
   nd <- replicate_df(qcs_grid, "year", unique(pcod_2011$year))
   nd$area <- 4
   p <- predict(fit, newdata = nd, return_tmb_object = TRUE)
-  ind <- get_index(p, area = nd$area)
+  ind <- get_index(p, area = nd$area, bias_correct = FALSE)
   if (FALSE) {
     library(ggplot2)
     ggplot(ind, aes(year, est, ymin = lwr, ymax = upr)) + geom_pointrange() +
@@ -165,9 +165,9 @@ test_that("get_index works", {
   predictions <- predict(m, newdata = nd, return_tmb_object = TRUE)
 
   # get predictions with area passed as vector
-  ind <- get_index(predictions, area = nd$area)
+  ind <- get_index(predictions, area = nd$area, bias_correct = FALSE)
   # get predictions with area as a named column
-  ind2 <- get_index(predictions, area = "area")
+  ind2 <- get_index(predictions, area = "area", bias_correct = FALSE)
   expect_equal(ind, ind2)
 
   # get predictions with area passed as vector