modis_interpolation.Rmd

---
title: "Interpolation of MODIS data"
author: "Beni Stocker"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Interpolation of MODIS data}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}
---

```{r setup, include=FALSE}
library(ingestr)
library(dplyr)
library(tidyr)
library(readr)
library(ggplot2)
```

## Define sites

```{r}
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"`)

```{r eval=FALSE}
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
```{r warning=FALSE, eval=FALSE}
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.
```{r eval=FALSE}
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
```{r warning=FALSE, eval=FALSE}
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

```{r warning=FALSE, eval=FALSE}
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

```{r warning=FALSE, eval=FALSE}
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 

```{r warning=FALSE, eval=FALSE}
plot_fapar_ingestr_bysite(
  df_modis_fpar$data[[4]], 
  settings_modis
  ) + 
  labs(title = df_modis_fpar$sitename[[4]]) +
  ylim(-0.5, 1.5)
```