Harbour seals - add tests and update documentation, document(), #38.

R/data.R

@@ -979,6 +979,8 @@
 ##' Report. 2022/034.
 ##' https://www.dfo-mpo.gc.ca/csas-sccs/Publications/SAR-AS/2022/2022_034-eng.html
 ##'
+##' See also: `harbour_seals_data_final_year` for the year of the final data for
+##'   each region.
 ##' @format A tibble also of class `pacea_harbour_seals` with columns:
 ##' \describe{
 ##'   \item{date:}{Date of the GAM estimate of abundance; there is a time step
@@ -1009,7 +1011,7 @@
 
 ##' Final year of Pacific Harbour Seals survey in each of seven regions
 ##'
-##' Used for colouring the plots of the estimates contained in `harbour_seals`
+##' Used for understanding the final year of data for the estimates contained in `harbour_seals`
 ##' (since some are projections beyond the data). Also see `?harbour_seals`.
 ##'
 ##' @format A tibble with columns:

R/plot-pacea-harbour-seals.R

@@ -29,7 +29,6 @@
 ##' @param median_line_col col for median
 ##' @param median_line_lty lty for median
 ##' @param median_line_lwd lwd for median
-##' @param ... further options passed onto `plot.default()`
 ##' @inherit plot.pacea_index
 ##' @return plot of the time series as median with bars showing uncertainty (if
 ##'   `low` and `high` are columns of `obj) to the current device; returns nothing.
@@ -59,9 +58,7 @@ plot.pacea_harbour_seals <- function(obj,
                                      median_pch = 16,
                                      median_line_col = "black",
                                      median_line_lty = 1,
-                                     median_line_lwd = 2,
-                                     ...   # pass onto default plot
-                                     ){
+                                     median_line_lwd = 2){
 
   stopifnot("value must be a column of the object in the first argument" =
             value %in% names(obj))

tests/testthat/test-plot-time-series.R

@@ -1,4 +1,5 @@
-# These are on plotting functions for pacea_index and then pacea_recruitment and pacea_biomass objects.
+# These are on plotting functions for pacea_index and then pacea_recruitment,
+# pacea_biomass, pacea_buoy, and pacea_harbour_seals objects.
 
 test_that("index plotting: the stopifnot commands are working", {
   expect_error(plot(oni,
@@ -91,3 +92,20 @@ test_that("buoy SST plotting  works with various options", {
                       years = 2010:2020))
   expect_error(plot(buoy_sst, stn_id = c("C46004", "C46036")))
 })
+
+# plot.pacea_harbour_seals()
+test_that("harbour seals plotting  works with various options", {
+  expect_visible(plot(harbour_seals))
+  expect_invisible(plot(harbour_seals,
+                      region = "SOG"))
+  expect_error(plot(harbour_seals,
+                    region = "nonsense"))
+  expect_error(plot(harbour_seals,
+                    value = "nonsense"))
+  # Doesn't pass, even though figures do look the same
+  #expect_equal(plot(dplyr::filter(harbour_seals,
+  #                                region != "Coastwide")),
+  #             plot(harbour_seals,
+  #                  include_coastwide = FALSE))
+
+})