From 3baed70c44bfb73c4c8dbab51b9acf1710c4396c Mon Sep 17 00:00:00 2001
From: Koen Hufkens <koen.hufkens@gmail.com>
Date: Fri, 16 Feb 2024 15:02:39 +0100
Subject: [PATCH] batch calculate VI

---
 R/calc_VI.R | 73 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 R/calc_VI.R

diff --git a/R/calc_VI.R b/R/calc_VI.R
new file mode 100644
index 0000000..ba8074e
--- /dev/null
+++ b/R/calc_VI.R
@@ -0,0 +1,73 @@
+#' Batch calculate VI
+#'
+#' Calculate VI for the machine learning input
+#' data frame based on the spectral indices table
+#' (in csv format).
+#'
+#' @param df the machine learning data frame including the 7 MODIS NBAR bands
+#' @param indices path to the spectral indices file
+#'
+#' @return select spectral indices for all values in the data frame
+#' @export
+
+calc_VI <- function(
+    df,
+    indices = "data/spectral-indices-table.csv"
+  ){
+
+  # read in spectral indices file
+  vi <- readr::read_csv(indices) |>
+    dplyr::filter(
+      application_domain == "vegetation",
+      #grepl("drought|water", tolower(long_name)),
+      short_name != "MNLI",
+      !grepl("nexp|sla|slb|gamma|epsilon|alpha|beta|omega|A|fdelta|cexp|G1|RE1|RE2|PAR|lambda*",formula)
+    )
+
+  # read data and rename columns
+  df <- df |>
+    dplyr::rename(
+      R = Nadir_Reflectance_Band1,
+      N = Nadir_Reflectance_Band2,
+      B = Nadir_Reflectance_Band3,
+      G = Nadir_Reflectance_Band4,
+      S1 = Nadir_Reflectance_Band6,
+      S2 = Nadir_Reflectance_Band7
+    ) |>
+    dplyr::select(
+      site, date, year, doy,
+      flue, is_flue_drought, cluster,
+      R, N, B, G, S1, S2, LST_Day_1km
+    )
+
+  # loop over all indices
+  df_vi <- lapply(1:nrow(vi), function(i){
+
+    # create temporary object
+    tmp <- df
+
+    # set constants dynamically
+    if(grepl("EVI",vi$short_name[i])){
+      tmp$L <- 1
+      tmp$C1 <- 6
+      tmp$C2 <- 7.5
+      tmp$g <- 2.5
+    }
+
+    if(grepl("SAVI|SARVI",vi$short_name[i])){
+      tmp$L <- 0.5
+    }
+
+    # calculate and return index
+    tmp |>
+      mutate(
+        !!vi$short_name[i] := eval(rlang::parse_expr(vi$formula[i]))
+      ) |>
+      select(
+        !!vi$short_name[i]
+      )
+  }) |>
+    bind_cols()
+
+  return(df_vi)
+}