From dc586fbff06f484096c13a82dfadc95b2c78a89c Mon Sep 17 00:00:00 2001
From: Koen Hufkens <koen.hufkens@gmail.com>
Date: Wed, 7 Feb 2024 15:42:52 +0100
Subject: [PATCH] new functions

---
 NAMESPACE                           |  2 +
 R/merge_normalized_differences.R    | 57 +++++++++++++++++++++++++++++
 R/normalized_difference.R           | 16 ++++++++
 man/merge_normalized_differences.Rd | 19 ++++++++++
 man/normalized_difference.Rd        | 20 ++++++++++
 5 files changed, 114 insertions(+)
 create mode 100644 R/merge_normalized_differences.R
 create mode 100644 R/normalized_difference.R
 create mode 100644 man/merge_normalized_differences.Rd
 create mode 100644 man/normalized_difference.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 562ed4a..8e66561 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(align_events)
+export(merge_normalized_differences)
+export(normalized_difference)
 export(read_appeears)
 export(read_ml_data)
diff --git a/R/merge_normalized_differences.R b/R/merge_normalized_differences.R
new file mode 100644
index 0000000..0d7b57a
--- /dev/null
+++ b/R/merge_normalized_differences.R
@@ -0,0 +1,57 @@
+
+#' Merge / calculate difference ratios
+#'
+#' Calculate normalized difference ratios
+#' for all possible "sur_refl" band combinations
+#'
+#' @param ml_df a machine learning data frame with "sur_refl" prefix column
+#'  names apply the band ratios to
+#'
+#' @return A machine learning data frame with normalized band ratios appended
+#' @export
+
+merge_normalized_differences <- function(ml_df){
+
+  # split out surface reflectance values
+  sur_refl <- ml_df |>
+    dplyr::select(
+      starts_with("sur_refl")
+    )
+
+  # calculate all normalized difference ratios
+  ndr <- lapply(names(sur_refl), function(band){
+
+    # split out reference band
+    band_1 <- sur_refl |>
+      dplyr::select(
+        all_of(band)
+      )
+
+    # mutate over all other collumns
+    df <- sur_refl |>
+      dplyr::select(
+        !all_of(band)
+      )
+
+    # wrangle all column names
+    cols <- gsub("sur_refl_", "", names(df))
+    ref_col <- gsub("sur_refl_", "", names(band_1))
+
+    df <- df |>
+      dplyr::transmute_all(
+        function(x){as.vector(normalized_difference(band_1, x))}
+      )
+
+    # add clean column names
+    colnames(df) <- paste(ref_col, cols, sep = "_")
+    return(df)
+  })
+
+  # bind columns in one big tibble
+  ndr <- dplyr::bind_cols(ndr)
+
+  # merge with original data
+  ml_df <- bind_cols(ml_df, ndr)
+}
+
+
diff --git a/R/normalized_difference.R b/R/normalized_difference.R
new file mode 100644
index 0000000..39e53f0
--- /dev/null
+++ b/R/normalized_difference.R
@@ -0,0 +1,16 @@
+
+#' Normalized difference
+#'
+#' Calculates normalized difference for two (arbitrary) bands. The difference
+#' is taken as band 1 - band 2
+#'
+#' @param band_1 first band
+#' @param band_2 second band
+#'
+#' @return normalized difference index for two bands
+#' @export
+
+normalized_difference <- function(band_1, band_2){
+  ndr <- (band_1 - band_2)/(band_1 + band_2)
+  as.matrix(ndr)
+}
diff --git a/man/merge_normalized_differences.Rd b/man/merge_normalized_differences.Rd
new file mode 100644
index 0000000..fa0980c
--- /dev/null
+++ b/man/merge_normalized_differences.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/merge_normalized_differences.R
+\name{merge_normalized_differences}
+\alias{merge_normalized_differences}
+\title{Merge / calculate difference ratios}
+\usage{
+merge_normalized_differences(ml_df)
+}
+\arguments{
+\item{ml_df}{a machine learning data frame with "sur_refl" prefix column
+names apply the band ratios to}
+}
+\value{
+A machine learning data frame with normalized band ratios appended
+}
+\description{
+Calculate normalized difference ratios
+for all possible "sur_refl" band combinations
+}
diff --git a/man/normalized_difference.Rd b/man/normalized_difference.Rd
new file mode 100644
index 0000000..b6ac13e
--- /dev/null
+++ b/man/normalized_difference.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/normalized_difference.R
+\name{normalized_difference}
+\alias{normalized_difference}
+\title{Normalized difference}
+\usage{
+normalized_difference(band_1, band_2)
+}
+\arguments{
+\item{band_1}{first band}
+
+\item{band_2}{second band}
+}
+\value{
+normalized difference index for two bands
+}
+\description{
+Calculates normalized difference for two (arbitrary) bands. The difference
+is taken as band 1 - band 2
+}