In stineb/ingestr: Environmental point data ingest

library(ingestr)
library(dplyr)
library(tidyr)
library(readr)
library(ggplot2)

Define sites

use_sites <- c("CH-Dav", "AT-Neu", "US-MMS", "AU-Tum")

Define settings

• Data product: "modis_fpar": MODIS collection 6, MCD15A3H, band Fpar_500m
• Interpolation methods: LOESS spline (method_interpol = "loess")

settings_modis <- get_settings_modis(
  bundle            = "modis_fpar",
  data_path         = "~/data/modis_subsets/",
  method_interpol   = "loess",
  keep              = TRUE,
  overwrite_raw     = FALSE,
  overwrite_interpol= TRUE,
  n_focal           = 0,
  network           = "FLUXNET"
  )

Get data

df_modis_fpar <- ingest(
  siteinfo_fluxnet2015 %>% 
    filter(sitename %in% use_sites), 
  source = "modis",
  settings = settings_modis,
  parallel = FALSE
  )

Plot

Define a function to plot the data.

plot_fapar_ingestr_bysite <- function(df, settings, sitename = NULL){

  if (is.null(sitename)) sitename <- df$sitename[[1]]

  ddf <- df %>%
    pivot_longer(cols = c(linear, spline, loess, sgfilter), 
                 names_to = "method", 
                 values_to = "modisvar_interpol")

  gg <- ggplot() +
    geom_point(  data = df, aes(x = date, y = modisvar), color = "red") +
    # geom_point(  data = df, aes(x = date, y = modisvar_filled), col = 'blue') +
    geom_point(  data = df, aes(x = date, y = modisvar_filtered), color = "black") +
    # geom_line(  data = ddf, aes(x = date, y = modisvar_interpol, color = method)) +
    # geom_line(  data = df, aes(x = date, y = linear, color = "linear")) +
    geom_line(  data = df, aes(x = date, y = spline, color = "Spline")) +
    geom_line(  data = df, aes(x = date, y = loess, color = "LOESS")) +
    # geom_line(  data = df, aes(x = date, y = sgfilter), col = 'green') +

    labs(x = "Date", y = settings$varnam, 
         title = sitename, subtitle = paste(settings$prod, settings$band_var)) +

    scale_color_manual(name = "Interpolation",
                       breaks = c("LOESS", "Spline"),
                       # breaks = c("linear", "spline", "loess"),
                       # values = c("linear" = "red", "spline" = "cyan", "loess" = "blue") )
                       values = c("LOESS" = "springgreen3", "Spline" = "royalblue") )

    ylim(0, max(df$modisvar, na.rm = TRUE))

  return(gg)
}

AT-Neu

plot_fapar_ingestr_bysite(
  df_modis_fpar$data[[1]], 
  settings_modis
  ) + 
  labs(title = df_modis_fpar$sitename[[1]]) +
  ylim(-0.5, 1.5)

AU-Tum

plot_fapar_ingestr_bysite(
  df_modis_fpar$data[[2]], 
  settings_modis
  ) + 
  labs(title = df_modis_fpar$sitename[[2]]) +
  ylim(-0.5, 1.5)

CH-Dav

plot_fapar_ingestr_bysite(
  df_modis_fpar$data[[3]], 
  settings_modis
  ) + 
  labs(title = df_modis_fpar$sitename[[3]]) +
  ylim(-0.5, 1.5)

US-MMS

plot_fapar_ingestr_bysite(
  df_modis_fpar$data[[4]], 
  settings_modis
  ) + 
  labs(title = df_modis_fpar$sitename[[4]]) +
  ylim(-0.5, 1.5)

stineb/ingestr documentation built on July 21, 2024, 6:39 p.m.