stock_env: Compile ECSA Data.

In NOAA-EDAB/ECSA: Ecosystem Context for Stock Advice

Description

This function aggregates data for stock-specific ecosystem context reporting. Data that can be accessed include surface and bottom temperature and salinity, chlorophyll concentration, zooplankton abundance, and occupancy probability for the US Northeast Shelf.

Usage

stock_env(variable, type = NULL, season, genus = NULL, svspp,
  mask_type, xlab, interpo = F, ylab, ylim = NULL, plt = F)

Arguments

variable	Can be "chlorophyll", "temperature", "salinity", "zooplankton", "occupancy hab", or "occupancy prob".
type	Specific to temperature and salinity variables. Either "bottom" or "surface".
season	Either "spring" or "fall".
genus	Specific to zooplankton. Can be one of "centropages", "temora", or "pseudocalanus".
svspp	Input svspp code for species of interest.
mask_type	Specifies raster masking behavior. Can be one of "nes", "gom", "gbk", "sne", or "unit". If mask is "unit", then returned time series reflect stock boundaries drawn from depth strata.
xlab	Plot labels if plt = T.
interpo	Logical. If missing values should be interpolated linearly. Current not functional.
ylab	Plot y label if plt = T.
ylim	Vector in the form of c(min,max) to specifiy y limits if plt = T.
plt	Plots output rather than returning a data frame of results.

Details

Data for this function are currently limited to american lobster (svspp = 301), summer flounder (svspp = 103), and jonah crab (svspp = 312). Occupancy habitat is limited to summer flounder only.

Value

If plt = F, a data frame containing time series of compiled data is returned.

Examples

#USAGE --------------------------------------------------------------------------

sf1 <- stock_env(variable = "salinity",type = "surface",
                  season = "spring", svspp = 103, mask_type = "unit")
ss1 <- stock_env(variable = "salinity",type = "surface",
                 season = "fall", svspp = 103, mask_type = "unit")

bf1 <- stock_env(variable = "salinity",type = "bottom",
                 season = "spring", svspp = 103, mask_type = "unit")
bs1 <- stock_env(variable = "salinity",type = "bottom",
                 season = "fall", svspp = 103, mask_type = "unit")
                 
#Plotting example ---------------------------------------------------------------
surface <- rbind(sf1, ss1)
bottom <- rbind(bf1, bs1)

xmin <- rbind(min(surface$Time),min(bottom$Time))
xmin <- min(xmin)

#Y scales can be adjusted by adding 'scales' argument to facet_wrap.
library(ggplot2);library(gridExtra)
s_plt <- ggplot(data = surface, aes(x = Time, y = Value)) +
  ylab("Surface Salinity (PSU)") +
  xlab("") +
  xlim(xmin, NA) +
  geom_line() +
  geom_point() +
  facet_wrap(Season ~., nrow = 1, scale = 'free_y') +
  theme_bw() +
  theme(plot.title = element_blank(),
        strip.background = element_blank(),
        strip.text.x = element_blank()) +
  annotate("text", label = c("A","B"), x = xmin, y = Inf, vjust = 1.5, size = 5)

b_plt <- ggplot(data = bottom, aes(x = Time, y = Value)) +
  ylab("Bottom Salinity (PSU)") +
  xlab("Year") +
  xlim(xmin, NA) +
  geom_line() +
  geom_point() +
  facet_wrap(Season ~., nrow = 1, scale = 'free_y') +
  theme_bw() +
  theme(plot.title = element_blank(),
        strip.background = element_blank(),
        strip.text.x = element_blank()) +
  annotate("text", label = c("C","D"), x = xmin, y = Inf, vjust = 1.5, size = 5)

grid.arrange(s_plt, b_plt, nrow = 2)

#Do not include "type" when calling CHL, zooplankton, or occupancy:
#CHL-----------------------------------------------------------------------------
cs1 <- stock_env(variable = "chlorophyll",
                 season = "spring", svspp = svspp, mask_type = "unit")
cf1 <- stock_env(variable = "chlorophyll",
                 season = "fall", svspp = svspp, mask_type = "unit")
chl <- rbind(cs1, cf1)
xmin <- rbind(min(chl$Time),min(chl$Time))
xmin <- min(xmin)
ggplot(data = chl, aes(x = Time, y = Value)) +
    ylab("Chlorophyll mg m^-3") +
    xlab("") +
    xlim(xmin, NA) +
    geom_line() +
    geom_point() +
    facet_wrap(Season ~., nrow = 1, scale = 'free_y') +
    theme_bw() +
    theme(plot.title = element_blank(),
        strip.background = element_blank(),
        strip.text.x = element_blank()) +
    annotate("text", label = c("A","B"), x = xmin, y = Inf, vjust = 1.5, size = 5)
    
#Zooplankton --------------------------------------------------------------------
ct1 <- stock_env(variable = "zooplankton", genus = "centropages",
                 season = "spring", svspp = 103, mask_type = "unit")

ct2 <- stock_env(variable = "zooplankton", genus = "centropages",
                 season = "fall", svspp = 103, mask_type = "unit")

t1 <- stock_env(variable = "zooplankton", genus = "temora",
                 season = "spring", svspp = 103, mask_type = "unit")

t2 <- stock_env(variable = "zooplankton", genus = "temora",
                 season = "fall", svspp = 103, mask_type = "unit")

ps1 <- stock_env(variable = "zooplankton", genus = "pseudocalanus",
                season = "spring", svspp = 103, mask_type = "unit")

ps2 <- stock_env(variable = "zooplankton", genus = "pseudocalanus",
                season = "fall", svspp = 103, mask_type = "unit")

NOAA-EDAB/ECSA documentation built on Oct. 24, 2020, 2:21 p.m.