Remove uncertainties from hake age-1 biomass so that plotting functio…

…ns are automatic, but had to adapt tickmarks to not do too many, ended up doing for several functions; add test, document().

NAMESPACE

@@ -117,6 +117,7 @@ export(pacea_installed)
 export(pacea_long)
 export(pacea_wide)
 export(plot_buoy_sst_single)
+export(plot_with_uncertainty_discrete)
 export(standardise)
 importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)

R/add-tickmarks.R

@@ -18,6 +18,7 @@ add_tickmarks <- function(obj_lub,
                           y_tick_by,
                           y_tick_start,
                           y_tick_end,
+                          y_tick_max_number = 50,
                           x_tick_extra_years,
                           start_decade_ticks){
   min <- min(lubridate::floor_date(obj_lub$date,
@@ -58,6 +59,16 @@ add_tickmarks <- function(obj_lub,
   # that nothing got messed up. Though if they look funny people should just
   # change y_tick_by, which has default 0.25 for indices, which likely just works
   # as they are standardised.
+  # For plot.pacea_biomass() default y_tick_by is 1 which has worked fine,
+  # except for age-1 hake since max is about 1200 (x1000 tons). So tweaking
+  # here with a new argument y_tick_max_number.
+
+  while(length(seq(y_tick_start,
+                   y_tick_end,
+                   by = y_tick_by)) > y_tick_max_number){
+    y_tick_by <- y_tick_by*10
+  }
+
   axis(2,
        seq(y_tick_start,
            y_tick_end,

R/plot-pacea-biomass.R

@@ -45,6 +45,7 @@ plot.pacea_biomass <- function(obj,
                                                                    truncated = 2),
                                style = "no_uncertainty",
                                y_max = NULL,
+                               y_tick_max_number = 50,
                                uncertainty_shade_col = rgb(0, 0, 1, .1),
                                uncertainty_line_col = "blue",
                                uncertainty_line_lty = 3,
@@ -101,10 +102,17 @@ plot.pacea_biomass <- function(obj,
                  ...)
   }
 
+  if(attr(obj_lub, "axis_name") == "Pacific Hake spawning biomass (million t)"){
+    if(y_tick_by == 1){
+      y_tick_by <- 0.25
+    }
+  }
+
   add_tickmarks(obj_lub,
                 y_tick_by = y_tick_by,
                 y_tick_start = 0,
                 y_tick_end = ceiling(par("usr")[4]),
+                y_tick_max_number = y_tick_max_number,
                 x_tick_extra_years = x_tick_extra_years,
                 start_decade_ticks = start_decade_ticks)
 }

R/plot-pacea-index.R

@@ -24,10 +24,14 @@
 ##'   Report style plots}
 ##'   \item{"plain":}{just a plain line}
 ##' }
-##' @param y_tick_by increment for y-axis ticks
+##' @param y_tick_by increment for y-axis ticks; gets
+##'   overwritten in `add_tickmarks()` if this yields more than
+##'   `y_tick_max_number` tickmarks. If using [plot.pacea_biomass()] the default
+##'   of 1 gets automatically changed to 0.25 for `plot(hake_biomass)`.
 ##' @param y_tick_start where to start y-axis tickmarks, set automatically if not
 ##'   specified (may need to occasionally specify)
 ##' @param y_tick_end where to end y-axis tickmars, as for `y_tick_start`
+##' @param y_tick_max_number maximum number of y tickmarks.
 ##' @param x_tick_extra_years number of extra years to expand around the range
 ##'   of data for which to add annual tick marks (does not expand the axis); in
 ##'   hindsight could have simplified this in `add_tickmarks()`, but just made
@@ -92,6 +96,7 @@ plot.pacea_index <- function(obj,
                              y_tick_by = 0.25,
                              y_tick_start = NULL,
                              y_tick_end = NULL,
+                             y_tick_max_number = 50,
                              x_tick_extra_years = 200,
                              start_decade_ticks = lubridate::ymd("1800-01-01",
                                                                  truncated = 2),
@@ -146,6 +151,7 @@ plot.pacea_index <- function(obj,
                 y_tick_by = y_tick_by,
                 y_tick_start = y_tick_start,
                 y_tick_end = y_tick_end,
+                y_tick_max_number = y_tick_max_number,
                 x_tick_extra_years = x_tick_extra_years,
                 start_decade_ticks = start_decade_ticks)
 

data-raw/groundfish/hake.R

@@ -217,6 +217,15 @@ hake_total_biomass_age_1_new <- readRDS(paste0(hake_dir,
                                                assess_yr,
                                                ".rds"))
 
+if(!is.na(hake_total_biomass_age_1_new[1, "low"])){
+  stop("Can remove the next lines it seems as now have uncertainties")
+}
+
+# Removing these makes plot(hake_total_biomass_age_1) automatically work
+hake_total_biomass_age_1_new <- dplyr::select(hake_total_biomass_age_1_new,
+                                              -c("low",
+                                                 "high"))
+
 class(hake_total_biomass_age_1_new) <- c("pacea_biomass",
                                          class(hake_total_biomass_age_1_new))
 

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

@@ -68,6 +68,7 @@ test_that("recruitment plotting works with various options", {
                         y_max = 100))
   expect_invisible(plot(hake_recruitment_over_2010))
   expect_invisible(plot(hake_recruitment_over_R0))
+  expect_invisible(plot(hake_recruitment_deviations))
 })
 
 # Adapting some of that for hake_biomass