Create teros-variability.R

pipeline/utils/teros-variability.R

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+library(compasstools)
+library(dplyr)
+library(ggplot2)
+theme_set(theme_bw())
+library(lubridate)
+
+set.seed(123)
+
+# Nick asks:
+# I wonder if you or someone has already done an analysis of how much we
+# gain by having so much replication of Teros 12’s at TEMPEST? E.g., if we
+# had 50% less sensors how much of the total variability would we not see?
+
+# variable <- "soil-EC-15cm"
+# variable <- "soil-temp-15cm"
+variable <- "soil-vwc-15cm"
+site <- "TMP"
+dat <- read_L2_variable(variable, path = "~/sensor_data/Level2/v2-1/", site = site)
+
+dat %>%
+    filter(!is.na(Value)) %>%
+    mutate(Year = year(TIMESTAMP),
+           Day = yday(TIMESTAMP),
+           Hour = hour(TIMESTAMP)) %>%
+    filter(Year == 2024) %>%
+    select(-Instrument, -Location, -N_avg, -N_drop, -Value_MAC) ->
+    dat
+
+# Figure out how many distinct sensors we have in each plot
+dat %>%
+    group_by(Plot) %>%
+    summarise(n = n_distinct(Sensor_ID)) %>%
+    summarise(min(n)) %>%
+    pull() ->
+    sensors_per_plot
+
+sizes <- as.integer(seq(from = 2, to = sensors_per_plot, length.out = 10))
+
+# Run through various sample sizes and then, for each plot,
+# repeatedly sample that many sensors and compute the CV
+results_list <- list()
+for(sample_size in sizes) {
+    for(p in unique(dat$Plot)) {
+        dat %>% filter(Plot == p) -> dat_p
+        message(sample_size)
+        for(i in 1:10) {
+            sensors_to_sample <- sample(unique(dat_p$Sensor_ID),
+                                        sample_size,
+                                        replace = FALSE)
+            dat_p %>%
+                filter(Sensor_ID %in% sensors_to_sample) %>%
+                group_by(Plot, Day, Hour, research_name) %>%
+                summarise(CV = sd(Value) / mean(Value), .groups = "drop") %>%
+                mutate(n_sensors = sample_size) ->
+                results_list[[paste(p, sample_size, i)]]
+        }
+    }
+}
+
+# Summarise and plot
+bind_rows(results_list) %>%
+    group_by(Plot, Day, research_name, n_sensors) %>%
+    summarise(CV = mean(CV), .groups = "drop") ->
+    results
+
+p1 <- ggplot(results, aes(Day, CV, color = n_sensors)) +
+    geom_point(na.rm = TRUE) +
+    facet_grid(Plot ~ ., scales = "free") +
+    ylab("Hourly CV of sensors") +
+    ggtitle(paste(site, results$research_name[1]))
+
+print(p1)
+ggsave(paste(site, variable, "doy-var.png", sep = "_"), width = 8, height = 6)
+
+p2 <- results %>%
+    group_by(Plot, n_sensors) %>%
+    summarise(CV = mean(CV, na.rm = TRUE), .groups = "drop") %>%
+    ggplot(aes(n_sensors, CV, color = Plot)) + geom_line() +
+    ylab("Hourly CV of sensors") +
+    ggtitle(paste(site, results$research_name[1]))
+
+print(p2)
+ggsave(paste(site, variable, "n-var.png", sep = "_"), width = 8, height = 6)
+
+message("All done")