Grow macroalgae

This space will be used to detail how to use the main model function, grow_macroalgae().

library(macrogrow)
library(magrittr)

## Warning: package 'magrittr' was built under R version 4.4.3

library(units)

## Warning: package 'units' was built under R version 4.4.3

## udunits database from C:/Program Files/R/R-4.4.2/library/units/share/udunits/udunits2.xml

library(lubridate)

## Warning: package 'lubridate' was built under R version 4.4.3

## 
## Attaching package: 'lubridate'

## The following objects are masked from 'package:base':
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##     date, intersect, setdiff, union

library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.4.3

library(cowplot)

## Warning: package 'cowplot' was built under R version 4.4.3

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## Attaching package: 'cowplot'

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library(dplyr)

## Warning: package 'dplyr' was built under R version 4.4.3

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## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
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##     filter, lag

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library(tidyr)

## Warning: package 'tidyr' was built under R version 4.4.3

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## Attaching package: 'tidyr'

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##     extract

remove_unit("gN")
remove_unit("molN")
install_unit(name = "gN")
install_unit(name = "molN", def = "14.067 gN")

dir.create("pngs")

## Warning in dir.create("pngs"): 'pngs' already exists

Load datasets

Within this package, there are three default datasets:

env is a datafrae of default environmental variables
a_armata is a named vector of parameters for Asparagopsis armata
site_params is a named vector of site-specific parameters (culture conditions)

env$nitrate_uM <- env$nitrate %>% set_units("mgN m-3") %>% set_units("umolN L-1") %>% drop_units()
env$ammonium_uM <- env$ammonium %>% set_units("mgN m-3") %>% set_units("umolN L-1") %>% drop_units()

my_species <- a_armata

Check environmental data

First let’s check to make sure our environmental inputs look reasonable. You should also check that they are within the species tolerance limits or the macroalgae will not grow (or maybe that’s what you want).

p_temperature <- ggplot(env, aes(x = t, y = temperature)) +
     geom_line(linewidth = 0.75) +
     theme_classic() +
     labs(x = "Day of year", y = "Temperature (°C)") +
     ggtitle("Surface temperature")

p_light <- ggplot(env, aes(x = t, y = (light*exp(-(kW*site_params['d_top']))))) +
     geom_line(linewidth = 0.75) +
     theme_classic() +
     labs(x = "Day of year", y = "Light (μmol m⁻² s⁻¹)") +
     ggtitle("Light at top of canopy")

p_salinity <- ggplot(env, aes(x = t, y = salinity)) +
     geom_line(linewidth = 0.75) +
     theme_classic() +
     labs(x = "Day of year", y = "Salinity (g L⁻¹)") +
     ggtitle("Salinity")

p_velocity <- ggplot(env, aes(x = t, y = velocity)) +
     geom_line(linewidth = 0.75) +   
     theme_classic() +
     labs(x = "Day of year", y = "Velocity (m s⁻¹)") +
     ggtitle("Water Velocity")

p_nitrate <- ggplot(env, aes(x = t, y = nitrate)) +
     geom_line(linewidth = 0.75) +   
     theme_classic() +
     labs(x = "Day of year", y = "Nitrate (mg m⁻³)") +
     ggtitle("Ambient nitrate concentration")

p_ammonium <- ggplot(env, aes(x = t, y = ammonium)) +
     geom_line(linewidth = 0.75) +   
     theme_classic() +
     labs(x = "Day of year", y = "Ammonium (mg m⁻³)") +
     ggtitle("Ambient ammonium concentration")

p_nitrate_2 <- ggplot(env, aes(x = t, y = nitrate_uM)) +
     geom_line(linewidth = 0.75) +   
     theme_classic() +
     labs(x = "Day of year", y = expression("Nitrate ("*mu*"M)")) +
     ggtitle("Ambient nitrate concentration (uM)")

p_ammonium_2 <- ggplot(env, aes(x = t, y = ammonium_uM)) +
     geom_line(linewidth = 0.75) +   
     theme_classic() +
     labs(x = "Day of year", y = expression("Ammonium ("*mu*"M)")) +
     ggtitle("Ambient ammonium concentration (uM)")

plot_grid(
     p_temperature + theme(axis.title.x = element_blank(), axis.text.x = element_blank()), 
     p_light + theme(axis.title.x = element_blank(), axis.text.x = element_blank()), 
     p_salinity + theme(axis.title.x = element_blank(), axis.text.x = element_blank()), 
     p_velocity + theme(axis.title.x = element_blank(), axis.text.x = element_blank()), 
     p_nitrate + theme(axis.title.x = element_blank(), axis.text.x = element_blank()), 
     p_ammonium + theme(axis.title.x = element_blank(), axis.text.x = element_blank()),
     p_nitrate_2,
     p_ammonium_2,
     ncol = 2
)

Get initial macroalgae stat

Three values are required for macroalgae initialisation: \(N_f\), \(N_s\), and \(Q_{rel}\). \(N_f\), \(N_s\) must be in mg m\(^{-3}\) and can be calculated from an initial biomass using biomass_to_Nf().

init_biomass <- 0.005 %>% set_units("g L-1") %>% set_units("mg m-3") %>% drop_units()

init_NfNs <- biomass_to_Nf(
     biomass = init_biomass, 
     Q_rel = 0.5, 
     spec_params = my_species,
     dry = T
)

init_state <- c(init_NfNs, Q_rel = 0.5)

Check all inputs

Since the grow_macroalgae() function has so many inputs with very specific requirements, the check_grow() function is designed to take the exact same inputs as grow_macroalgae() and provide a report.

check_grow(
    t = 1:60,
    temperature = env$temperature[1:60],
    salinity = env$salinity[1:60],
    light = env$light[1:60],
    kW = env$kW[1:60],
    velocity = env$velocity[1:60],
    nitrate = env$nitrate[1:60],
    ammonium = env$ammonium[1:60],
    ni_uptake = NA,
    am_uptake = NA,
    site_params = site_params,
    spec_params = my_species,
    initials = init_state,
    # sparse_output = T,
    # other_constants = c(s = 0.0045, gam = 1.13, a2 = 0.2^2, Cb = 0.0025)
  )

## Starting all checks...
## ✔ Timeseries looks good.
## ✔ Variable 'temperature' looks good.
## ✔ Variable 'salinity' looks good.
## ✔ Variable 'light' looks good.
## ✔ Variable 'kW' looks good.
## ✔ Variable 'light' looks good.
## ✔ Variable 'velocity' looks good.
## ✔ Variable 'nitrate' looks good.
## ✔ Variable 'ammonium' looks good.
## ✔ Site params looks good.
## ✔ Variable Nf in initials looks good.
## ✔ Variable Q_int/Q_rel in initials looks good.
## → spec_params has provided linear parameters for nitrate. Uptake will use linear kinetics.
## → spec_params has provided parameters for both Michaelis-Menton and linear uptake for ammonium. Uptake will default to Michaelis-Menton kinetics.

gro <- grow_macroalgae(
    t = 1:60,
    temperature = env$temperature[1:60],
    salinity = env$salinity[1:60],
    light = env$light[1:60],
    kW = env$kW[1:60],
    velocity = env$velocity[1:60],
    nitrate = env$nitrate[1:60],
    ammonium = env$ammonium[1:60],
    ni_uptake = NA,
    am_uptake = NA,
    site_params = c(site_params, turbulence = NA),
    spec_params = my_species,
    initials = init_state,
    # sparse_output = T,
    # other_constants = c(s = 0.0045, gam = 1.13, a2 = 0.2^2, Cb = 0.0025)
  )

gro <- as.data.frame(gro)

Biomass, Nf and Ns outputs

ggplot(gro, aes(t, B_dw.mg * hm)) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Dry biomass (mg m"^-2*")"))

ggsave("pngs/biomass.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, (Nf * Ns))) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Total macroalgae nitrogen (mg m"^-3*")"))

ggsave("pngs/nitrogen.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, hm)) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Macroalgae height (m)"))

ggsave("pngs/height.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, up_Ni)) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Nitrate taken up (mg m-3)"))

ggsave("pngs/nitrate_uptake.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, up_Am)) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Ammonium taken up (mg m-3)"))

ggsave("pngs/ammonium_uptake.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, Q_lim)) +
  geom_line(linewidth = 0.75) +
  scale_y_continuous(limits = c(0,1)) +
  theme_classic() +
  ggtitle(expression("Q limitation"))

ggsave("pngs/Q_lim.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, T_lim)) +
  geom_line(linewidth = 0.75) +
  scale_y_continuous(limits = c(0,1)) +
  theme_classic() +
  ggtitle(expression("Temperature limitation"))

ggsave("pngs/T_lim.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, I_lim)) +
  geom_line(linewidth = 0.75) +
  scale_y_continuous(limits = c(0,1)) +
  theme_classic() +
  ggtitle(expression("Light limitation"))

ggsave("pngs/I_lim.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, S_lim)) +
  geom_line(linewidth = 0.75) +
  scale_y_continuous(limits = c(0,1)) +
  theme_classic() +
  ggtitle(expression("Salinity limitation"))

ggsave("pngs/S_lim.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, u_c)) +
  geom_line(linewidth = 0.75) +
  scale_y_continuous(limits = c(0,1)) +
  theme_classic() +
  ggtitle(expression("Water attenuation"))

ggsave("pngs/u_c.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, growth_rate)) +
  geom_line(linewidth = 0.75) +
  geom_hline(yintercept = my_species["mu"], linetype = "dashed") +
  theme_classic() +
  ggtitle(expression("Growth rate (d-1)"))

ggsave("pngs/growth_rate.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, Nf_loss)) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Nf loss (mg m-3)"))

ggsave("pngs/Nf_loss.png")

## Saving 7.29 x 4.51 in image

ggplot(gro, aes(t, Ns_loss)) +
  geom_line(linewidth = 0.75) +
  theme_classic() +
  ggtitle(expression("Ns loss (mg m-3)"))

ggsave("pngs/Ns_loss.png")

## Saving 7.29 x 4.51 in image

Sensitivity to parameter changes

params <- names(my_species)
params <- params[!params %in% c("M_am", "C_am", "V_ni", "K_ni", "D_lo", "D_mi", "D_hi", "T_opt", "T_min", "T_max", "S_opt", "S_min", "S_max")]
factors <- c(0.9, 1, 1.1)

res <- data.frame(
  param = rep(params, each = length(factors)),
  factor = rep(factors, times = length(params))
)

params_adj <- purrr::map(1:nrow(res), function(r) {
  my_species_adj <- my_species
  my_species_adj[res$param[r]] <- my_species_adj[res$param[r]] * res$factor[r]
  my_species_adj
})

res_1 <- purrr::map(params_adj, function(pa) {
  gro <- grow_macroalgae(
    t = 1:60,
    temperature = env$temperature[1:60],
    salinity = env$salinity[1:60],
    light = env$light[1:60],
    kW = env$kW[1:60],
    velocity = env$velocity[1:60],
    nitrate = env$nitrate[1:60],
    ammonium = env$ammonium[1:60],
    ni_uptake = NA,
    am_uptake = NA,
    site_params = c(site_params, turbulence = NA),
    spec_params = pa,
    initials = init_state
  )
  data.frame(
    B_dw = unname(gro[nrow(gro),"B_dw.mg"]),
    total_N = unname((gro[nrow(gro),"Nf"] + gro[nrow(gro),"Ns"])*gro[nrow(gro),"hm"])
  )
})

res_2 <- res_1 %>% 
  bind_rows() %>% 
  cbind(res) %>% 
  pivot_wider(
    names_from = factor,
    values_from = c(B_dw, total_N)
  ) %>% 
  mutate(sens.total_N = (total_N_1.1-total_N_0.9)/(0.2*total_N_1),
         sens.B_dw = (B_dw_1.1-B_dw_0.9)/(0.2*B_dw_1)) %>% 
  dplyr::select(c(param, contains("sens")))

ggplot(res_2, aes(x = param, y = sens.total_N)) +
  geom_col() +
  coord_flip()

Grow macroalgae

Tormey Reimer

2025-10-30

Load datasets

Check environmental data

Get initial macroalgae stat

Check all inputs

Grow macroalgae

Biomass, Nf and Ns outputs

Sensitivity to parameter changes