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Initiate subsoil_c_densities.R to calculate data ranges of carbon den…
…sity in 80 - 100 cm depth range
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# Calculate carbon density between 80 and 100 cm | ||
# _________________________________________ | ||
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# This script calculates an average value for the carbon density (t C ha-1 cm-1) | ||
# to be used to gap-fill carbon densities between 80 and 100 cm | ||
# in the carbon stock calculation function ("get_stocks") | ||
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# Script initiation date: 2024-03-24 | ||
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# Import data ---- | ||
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# Layer 1 data | ||
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source("./src/functions/read_processed.R") | ||
read_processed(save_to_env = TRUE) | ||
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# Data Denmark | ||
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denmark_stocks <- | ||
openxlsx::read.xlsx(paste0("data/additional_data/", | ||
"national_coauthor_carbon_stocks/Denmark/", | ||
"Denmark_BIOSOIL Level I soil C data from 2007 ", | ||
"and 20187Mar2024.xlsx"), | ||
sheet = 1) %>% | ||
mutate(plot_id = paste0("8_", Plot)) %>% | ||
rename(c_layer_stock = "C.(Mg.C.ha-1)") %>% | ||
filter(Layer == "80-100 cm") %>% | ||
mutate(c_density = c_layer_stock / 20) %>% | ||
select(plot_id, c_density) | ||
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# Combine data ---- | ||
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subsoil_c_densities <- bind_rows( | ||
s1_som %>% | ||
select(plot_id, profile_id, | ||
layer_limit_superior, layer_limit_inferior, | ||
bulk_density, coarse_fragment_vol, organic_carbon_total), | ||
s1_pfh %>% | ||
rename(layer_limit_superior = horizon_limit_up) %>% | ||
rename(layer_limit_inferior = horizon_limit_low) %>% | ||
rename(organic_carbon_total = horizon_c_organic_total) %>% | ||
select(plot_id, profile_id, | ||
layer_limit_superior, layer_limit_inferior, | ||
bulk_density, coarse_fragment_vol, organic_carbon_total), | ||
so_som %>% | ||
select(plot_id, profile_id, | ||
layer_limit_superior, layer_limit_inferior, | ||
bulk_density, coarse_fragment_vol, organic_carbon_total), | ||
so_pfh %>% | ||
rename(layer_limit_superior = horizon_limit_up) %>% | ||
rename(layer_limit_inferior = horizon_limit_low) %>% | ||
rename(organic_carbon_total = horizon_c_organic_total) %>% | ||
select(plot_id, profile_id, | ||
layer_limit_superior, layer_limit_inferior, | ||
bulk_density, coarse_fragment_vol, organic_carbon_total)) %>% | ||
# Filter for the wanted depths | ||
filter(!is.na(layer_limit_superior) & | ||
!is.na(layer_limit_inferior) & | ||
layer_limit_superior >= 70 & | ||
layer_limit_superior < 90 & | ||
layer_limit_inferior <= 110 & | ||
layer_limit_inferior > 90) %>% | ||
mutate(coarse_fragment_vol_frac = | ||
ifelse(is.na(.data$coarse_fragment_vol), | ||
0, | ||
.data$coarse_fragment_vol / 100)) %>% | ||
mutate(layer_thickness = ifelse(!is.na(.data$layer_limit_superior) & | ||
!is.na(.data$layer_limit_inferior) & | ||
(.data$layer_limit_superior != | ||
.data$layer_limit_inferior), | ||
abs(.data$layer_limit_superior - | ||
.data$layer_limit_inferior), | ||
NA_real_)) %>% | ||
# Carbon stock per layer (t C ha-1 (per layer)) | ||
mutate(c_stock_layer = | ||
(.data$organic_carbon_total * .data$bulk_density * | ||
(1 - .data$coarse_fragment_vol_frac) * .data$layer_thickness) / | ||
10000) %>% | ||
filter(!is.na(c_stock_layer)) %>% | ||
group_by(profile_id, plot_id) %>% | ||
reframe(c_stock_layer = sum(c_stock_layer, na.rm = TRUE), | ||
layer_thickness = sum(layer_thickness)) %>% | ||
ungroup() %>% | ||
# Calculate carbon density per cm (t C ha-1 cm-1) | ||
mutate(c_density = c_stock_layer / layer_thickness) %>% | ||
group_by(plot_id) %>% | ||
reframe(c_density = mean(c_density)) %>% | ||
ungroup %>% | ||
bind_rows(denmark_stocks) %>% | ||
arrange(c_density) %>% | ||
pull(c_density) | ||
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summary(subsoil_c_densities) | ||
median(subsoil_c_densities) | ||
quantile(subsoil_c_densities, c(0.05, 0.95)) | ||
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# Min. 1st Qu. Median Mean 3rd Qu. Max. | ||
# 0.009834 0.098497 0.306272 0.730857 0.616370 12.661800 | ||
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# 5% 95% | ||
# 0.05784099 2.23027130 | ||
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