Merge pull request #12 from stineb/main

Added Ch 7 and Exercises in Ch 6 and 7

analysis/plot_radiation_sites_biomes.R

@@ -0,0 +1,307 @@
+library(dplyr)
+library(tidyr)
+library(purrr)
+library(readr)
+library(lubridate)
+library(hms)
+library(khroma)
+library(ggplot2)
+library(cowplot)
+
+source(here::here("R/read_fdk.R"))
+
+# Reading -----------
+# read from file
+# df_sites <- read_rds(here::here("data/df_sites.rds"))
+df_sites <- read_csv(here::here("data/fdk_site_info.csv"))
+
+# chose representative sites
+use_sites <- c(
+  "FI-Hyy", # Boreal Forests/Taiga
+  "DE-Hai", # Temperate Broadleaf & Mixed Forests
+  "DE-Tha", # Temperate Coniferous
+  "DE-Gri", # Grassland just next to DE-Tha
+  "BR-Sa3", # Tropical
+  "US-ICh"  # Tundra
+)
+
+# subset sites
+df_sites_sub <- df_sites |> 
+  filter(sitename %in% use_sites)
+
+# saveRDS(df_sites_sub, file = here::here("data/df_sites_sub.rds"))
+
+## Half-hourly data --------------
+# read hourly flux data for each site
+hdf <- df_sites_sub |> 
+  dplyr::select(sitename, lon, lat, elv) |> 
+  mutate(data = purrr::map(
+    sitename, ~read_fdk(
+      ., 
+      path = "~/data/FluxDataKit/v3.1/fluxnet/",
+      # path = "~/data/FluxDataKit/FLUXDATAKIT_FLUXNET",
+      pattern = "HH"
+    ))) |> 
+  unnest(data) |> 
+  group_by(sitename) |> 
+  nest()
+
+## Daily data --------------
+# read daily flux data for each site
+ddf <- df_sites_sub |> 
+  select(sitename, lon, lat, elv) |> 
+  mutate(data = purrr::map(
+    sitename, ~read_fdk(
+      ., 
+      path = "~/data/FluxDataKit/v3.1/fluxnet/",
+      # path = "~/data/FluxDataKit/FLUXDATAKIT_FLUXNET",
+      pattern = "DD"
+      ))) |> 
+  unnest(data) |> 
+  group_by(sitename) |> 
+  nest()
+
+# Aggregate -----------
+## Hourly -----------
+# aggregate to hours for mid-summer
+hdf_sub <- hdf |> 
+  unnest(data) |> 
+  mutate(TIMESTAMP_START = ymd_hm(TIMESTAMP_START),
+         TIMESTAMP_END = ymd_hm(TIMESTAMP_END)) |> 
+  mutate(year = lubridate::year(TIMESTAMP_START),
+         month = lubridate::month(TIMESTAMP_START),
+         day = lubridate::mday(TIMESTAMP_START)) |> 
+  filter(month == 7) |> 
+  mutate(hm = as_hms(TIMESTAMP_START)) |> 
+  group_by(sitename, hm) |> 
+  summarise(
+    # latent heat flux
+    le = mean(LE_F_MDS, na.rm = TRUE),
+
+    # sensible heat flux
+    heat = mean(H_F_MDS, na.rm = TRUE), 
+
+    # net radiation
+    netrad = mean(NETRAD, na.rm = TRUE),
+
+    # shortwave radiation
+    sw = mean(SW_IN_F_MDS, na.rm = TRUE),
+
+    # longwave radiation
+    lw = mean(LW_IN_F_MDS, na.rm = TRUE)
+    )
+
+## Daily to mean season -----------
+# aggregate to mean seasonal cycle
+ddf_sub <- ddf |> 
+  unnest(data) |> 
+  mutate(TIMESTAMP = ymd(TIMESTAMP)) |> 
+  mutate(year = year(TIMESTAMP),
+         doy = yday(TIMESTAMP)) |> 
+  group_by(sitename, doy) |> 
+  summarise(
+    # latent heat flux
+    le = mean(LE_F_MDS, na.rm = TRUE),
+
+    # sensible heat flux
+    heat = mean(H_F_MDS, na.rm = TRUE), 
+
+    # net radiation
+    netrad = mean(NETRAD, na.rm = TRUE),
+
+    # shortwave radiation
+    sw = mean(SW_IN_F_MDS, na.rm = TRUE),
+
+    # longwave radiation
+    lw = mean(LW_IN_F_MDS, na.rm = TRUE)
+  ) |> 
+  mutate(date = ymd("2023-01-01") + doy - 1)
+
+
+# Plot -----------
+## Diurnal cycle in July  -----------
+### Components ----------------
+hdf_sub |> 
+  mutate(res = heat + le - netrad) |> 
+  pivot_longer(cols = c(netrad, heat, le)) |>  # , res
+  mutate(sitename = factor(
+    sitename, 
+    levels = c(
+      "US-ICh",  # Tundra
+      "FI-Hyy", # Boreal Forests/Taiga
+      "BR-Sa3", # Tropical
+      "DE-Hai", # Temperate Broadleaf & Mixed Forests
+      "DE-Tha", # Temperate Coniferous
+      "DE-Gri"  # Grassland just next to DE-Tha
+      )
+    )
+    # name = factor(name, levels = c("netrad", "heat", "le", "res"))
+    ) |> 
+  ggplot(aes(hm, value, color = name)) +
+  geom_hline(yintercept = 0, linetype = "dotted") +
+  geom_line() +
+  scale_x_time() +
+  # scale_x_datetime(date_breaks= "2 hours", date_labels = "%H:%M") +
+  scale_color_manual(
+    name = "",
+    labels = c(
+      heat = expression(paste(italic("H"))),
+      le = expression(paste(lambda, italic("E"))),
+      netrad = expression(paste(italic("R")[net]))
+      # res = "Residual"
+      ),
+    values = c(
+      heat = "#E69F00",
+      le = "#56B4E9",
+      netrad = "black"
+      # res = "grey70"
+    )
+    ) +
+  # scale_linetype_manual(
+  #   name = "",
+  #   labels = c(
+  #     heat = expression(paste(italic("H"))),
+  #     le = expression(paste(lambda, italic("E"))),
+  #     netrad = expression(paste(italic("R")[net])),
+  #     res = "Residual"
+  #   ),
+  #   values = c(
+  #     heat = "solid",
+  #     le = "solid",
+  #     netrad = "solid",
+  #     res = "dashed"
+  #   )
+  # ) +
+  theme_classic() +
+  labs(
+    x = "Time of day",
+    y = expression(paste("Energy flux (W m"^-2, ")"))
+  ) +
+  facet_wrap(~sitename)
+
+ggsave(
+  here::here("book/images/diurnal_cycle_radiation.png"),
+  width = 12, 
+  height = 7
+)
+
+### Residual (ground heat flux) -----------
+hdf_sub |> 
+  mutate(res = heat + le - netrad) |> 
+  mutate(sitename = factor(
+    sitename, 
+    levels = c(
+      "US-ICh",  # Tundra
+      "FI-Hyy", # Boreal Forests/Taiga
+      "BR-Sa3", # Tropical
+      "DE-Hai", # Temperate Broadleaf & Mixed Forests
+      "DE-Tha", # Temperate Coniferous
+      "DE-Gri"  # Grassland just next to DE-Tha
+    )
+  )) |> 
+  ggplot(aes(hm, res)) +
+  geom_hline(yintercept = 0, linetype = "dotted") +
+  geom_line() +
+  scale_x_time() +
+  theme_classic() +
+  labs(
+    x = "Time of day",
+    y = expression(paste("Energy flux (W m"^-2, ")"))
+  ) +
+  facet_wrap(~sitename)
+
+## Mean seasonal cycle  -----------
+### Components ----------
+ddf_sub |> 
+  # mutate(res = heat + le - netrad) |> 
+  pivot_longer(cols = c(netrad, heat, le)) |>  # , res
+  mutate(sitename = factor(
+    sitename, 
+    levels = c(
+      "US-ICh",  # Tundra
+      "FI-Hyy", # Boreal Forests/Taiga
+      "BR-Sa3", # Tropical
+      "DE-Hai", # Temperate Broadleaf & Mixed Forests
+      "DE-Tha", # Temperate Coniferous
+      "DE-Gri"  # Grassland just next to DE-Tha
+    )
+  )) |> 
+  ggplot(aes(date, value, color = name)) +
+  geom_hline(yintercept = 0, linetype = "dotted") +
+  geom_line() +
+  scale_x_date(date_breaks = "1 month", date_labels = "%b") +
+  scale_color_manual(
+    name = "",
+    labels = c(
+      heat = expression(paste(italic("H"))),
+      le = expression(paste(lambda, italic("E"))),
+      netrad = expression(paste(italic("R")[net]))
+      # res = "Residual"
+    ),
+    values = c(
+      heat = "#E69F00",
+      le = "#56B4E9",
+      netrad = "black"
+      # res = "grey70"
+    )
+  ) +
+  theme_classic() +
+  labs(
+    x = "",
+    y = expression(paste("Energy flux (W m"^-2, ")"))
+  ) +
+  facet_wrap(~sitename)
+
+ggsave(
+  here::here("book/images/seasonal_cycle_radiation.png"),
+  width = 12, 
+  height = 7
+)
+
+# # annual values: GPP vs PPFD
+# adf_mean <- ddf |> 
+#   unnest(data) |> 
+#   mutate(year = year(TIMESTAMP)) |> 
+#   group_by(sitename, year) |> 
+#   summarise(
+#     gpp = sum(GPP_NT_VUT_REF),
+#     sw = sum(SW_IN_F_MDS)
+#     ) |> 
+#   ungroup() |> 
+#   group_by(sitename) |> 
+#   summarise(
+#     gpp = mean(gpp),
+#     sw = mean(sw)
+#   )
+# 
+# adf_mean |> 
+#   ggplot(aes(sw, gpp)) +
+#   geom_point()
+
+
+### Residual (ground heat flux) --------
+# ground heat flux
+ddf_sub |> 
+  mutate(res = heat + le - netrad) |> 
+  mutate(sitename = factor(
+    sitename, 
+    levels = c(
+      "US-ICh",  # Tundra
+      "FI-Hyy", # Boreal Forests/Taiga
+      "BR-Sa3", # Tropical
+      "DE-Hai", # Temperate Broadleaf & Mixed Forests
+      "DE-Tha", # Temperate Coniferous
+      "DE-Gri"  # Grassland just next to DE-Tha
+    )
+  )) |> 
+  ggplot(aes(date, res)) +
+  geom_hline(yintercept = 0, linetype = "dotted") +
+  geom_line() +
+  scale_x_date(date_breaks = "1 month", date_labels = "%b") +
+  theme_classic() +
+  labs(
+    x = "",
+    y = expression(paste("Energy flux (W m"^-2, ")"))
+  ) +
+  facet_wrap(~sitename)
+

book/ecohydrology.qmd

@@ -2,3 +2,9 @@
 
 Coming soon.
 
+- Forests sustain the hydrologic cycle through evapotranspiration, which cools climate through feedbacks with clouds and precipitation
+- Tropical forests:
+  - "Observations show that forest transpiration is sustained during the dry season (11); this is seen also in CO2 fluxes (12) and satellite monitoring of vegetation (13, 14), to a greater extent than represented in many models."  (Bonan 2008)
+- Material from trial lecture: lecture_et_giub.key
+- Geographic patterns of evapotranspira- tion are explained by Budyko’s analysis of the control of evapotranspiration by net radiation and precipitation.
+- 3.4 Hydrologic Cycle (Bonan)