In pbs-assess/PACea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 6
)

Zooplankton anomalies in the Strait of Georgia

library(pacea)
library(dplyr)

Pacea now includes anomalies of zooplankton biomass in the Strait of Georgia, BC, provided by Kelly Young (Institute of Ocean Sciences, DFO). These update the calculations presented by Perry et al. (2021) and in the annual State of the Pacific Ocean report (Young et al., 2023); see ?zooplankton for full details and latest citations. Here we explain what is included, and update the figures presented by Perry et al. (2021) for total biomass and 20 species groups.

The data are stored as a tibble in pacea, as simply:

zooplankton_sog

with the final years being

tail(zooplankton_sog)

The first three columns are year (the year of the calculated anomalies), number_samples (total number of samples used for the annual anomalies), and volume_filtered (total volume of water filtered for all tows, in m$^3$). The number_samples column matches the Total column in Table 3 of Perry et al. (2021), though only up to 2013; from 2014-2018 the numbers here are higher due to further samples being processed. Data from 2019 onwards were not available for the Perry at al. (2021) study.

The remaining columns correspond to anomalies for total_biomass (the total biomass of all zooplankton) or various species groups, given as annual anomalies in units of $\log10~\mbox{g m}^{-2}$. See ?zooplankton_sog for more details, and Perry et al. (2021) for the full calculations. (As ever in pacea, please read through the help files for any data objects you are using).

The full available species groups (plus the first three columns) are:

names(zooplankton_sog)

The descriptions are fairly self explanatory, and are explained in more detail in Perry et al. (2021).

pacea has a built-in plotting function, so users can simply plot the total biomass (the default) with

plot(zooplankton_sog)

where the bars are automatically coloured red/blue for positive/negative anomalies. The plot defaults to showing the total biomass anomaly, and so updates Figure 2D of Perry et al. (2021), which included data only to 2018. Note that anomalies are now calculated compared to a climatology for the full time series (Young et al. 2023), whereas Perry et al. (2021) used the years 1996-2010 for their climatology, and extra historical samples have been processed (see ?zooplankton_sog). Hence, numbers can differ when comparing new plots to older ones.

So, to plot one of the other species groups (total_biomass is the default, and so was plotted above):

plot(zooplankton_sog,
     species_group = "cladocera")

Supplementary Figure S1 of Perry et al. (2021) showed the anomalies for 20 species groups (almost all those in our data). We produce an updated version here, arranging the plots in the same way as Perry et al. (2021) for ease of comparison. For simplicity we have included a column in_perry_fig_s1 in the data object zooplankton_sog_axis_names, which we an use to filter the required species names.

sp_groups <- filter(zooplankton_sog_axis_names,
                    in_perry_fig_s1)$species_group_name
lwd_val <- 7      # Thickness of the bars, tweak depending on output

Now plot in three panels:

par(mfrow = c(4, 2))
for(i in 1:8){
  plot(zooplankton_sog,
       species_group = sp_groups[i],
       lwd = lwd_val)
}

par(mfrow = c(4, 2))
for(i in 9:16){
  plot(zooplankton_sog,
       species_group = sp_groups[i],
       lwd = lwd_val)
}

par(mfrow = c(2, 2))
for(i in 17:20){
  plot(zooplankton_sog,
       species_group = sp_groups[i],
       lwd = lwd_val)
}

All species groups show positive anomalies in recent years, continuing the pattern shown in Figure S1 of Perry et al. (2021). The only group in that figure that ended with a negative anomaly (in 2018) was Chaetognatha; the run of negative anomalies from 2016-2018 show up here, but are followed ever since by positive anomalies.

The remaining species groups not shown (including Total biomass, even though it was already shown above), are:

sp_groups_not <- filter(zooplankton_sog_axis_names,
                        !in_perry_fig_s1)$species_group_name
par(mfrow = c(3, 2))
for(i in 1:5){
  plot(zooplankton_sog,
       species_group = sp_groups_not[i],
       lwd = lwd_val)
}

These also show recent positive anomalies, except for Scyphozoa.

Technial notes

Note that the zooplankton_sog object has class pacea_zooplankton:

class(hake_biomass)

such that the above command plot(zooplankton_sog) first looks to use our tailored function plot.pacea_zooplankton(), which in turn calls plot.pacea_index(), to give the style of plot shown above. The lwd argument may need to be tailored to control the widths of the bars, as in the final plots here, depending on how big your plot is (see ?plot.pacea_zooplankton).

Also note how the y-axis labels are automatically created with sensible text, including the anomaly units. Users should not need to worry too much, but this is done internally by plot.pacea_zooplankton(); see example in ?zooplankton_sog_axis_names to adapt one of the existing ones, or just define your own and specify it as the usual ylab argument.

pbs-assess/PACea documentation built on April 17, 2025, 11:36 p.m.