ndvi anomaly calculations with historical date ranges

ecohealthalliance · Nov 6, 2023 · 2688c34 · 2688c34
1 parent 939d64f
commit 2688c34
Show file tree

Hide file tree

Showing 3 changed files with 45 additions and 14 deletions.
diff --git a/R/calculate_ndvi_anomalies.R b/R/calculate_ndvi_anomalies.R
@@ -14,7 +14,7 @@
 #' @author Emma Mendelsohn
 #' @export
 calculate_ndvi_anomalies <- function(ndvi_date_lookup, ndvi_historical_means,
-                                     ndvi_anomalies_directory, model_dates,
+                                     ndvi_anomalies_directory,
                                      model_dates_selected, lag_intervals,
                                      overwrite = FALSE) {
 
@@ -30,25 +30,33 @@ calculate_ndvi_anomalies <- function(ndvi_date_lookup, ndvi_historical_means,
     return(file.path(ndvi_anomalies_directory, save_filename))
   }
 
-  # Get historical means for DOY
-  doy <- model_dates |> filter(date == date_selected) |> pull(day_of_year)
-  doy_frmt <- str_pad(doy,width = 3, side = "left", pad = "0")
-  historical_means <- read_parquet(ndvi_historical_means[str_detect(ndvi_historical_means, doy_frmt)]) |> 
-    select(-day_of_year)
-
   # Get the lagged anomalies for selected dates, mapping over the lag intervals
-  row_select <- which(model_dates$date == date_selected)
-
-  lag_intervals_start <- c(1 , 1+lag_intervals[-length(lag_intervals)])
-  lag_intervals_end <- lag_intervals
+  lag_intervals_start <- c(1 , 1+lag_intervals[-length(lag_intervals)]) # 1 to start with previous day
+  lag_intervals_end <- lag_intervals # 30 days total including end day
 
   anomalies <- map2(lag_intervals_start, lag_intervals_end, function(start, end){
 
-    lag_dates <- model_dates |> slice((row_select - start):(row_select - end))
+    # get lag dates, removing doy 366
+    lag_dates <- seq(date_selected - end, date_selected - start, by = "day")
+    lag_doys <- yday(lag_dates)
+    if(366 %in% lag_doys){
+      lag_doys <- lag_doys[lag_doys!=366]
+      lag_doys <- c(head(lag_doys, 1) - 1, lag_doys)
+    }
+
+    # Get historical means for lag period
+    doy_start <- head(lag_doys, 1)
+    doy_end <- tail(lag_doys, 1)
+    doy_start_frmt <- str_pad(doy_start, width = 3, side = "left", pad = "0")
+    doy_end_frmt <- str_pad(doy_end, width = 3, side = "left", pad = "0")
+    doy_range <- glue::glue("{doy_start_frmt}_to_{doy_end_frmt}")
 
+    historical_means <- read_parquet(ndvi_historical_means[str_detect(ndvi_historical_means, doy_range)]) 
+    assertthat::assert_that(nrow(historical_means) > 0)
+
     # get files and weights for the calculations
     weights <- ndvi_date_lookup |> 
-      mutate(lag_date = map(lookup_dates, ~. %in% lag_dates$date)) |> 
+      mutate(lag_date = map(lookup_dates, ~. %in% lag_dates)) |> 
       mutate(weight = unlist(map(lag_date, sum))) |> 
       filter(weight > 0) |> 
       select(start_date, filename, weight)

diff --git a/_targets.R b/_targets.R
@@ -424,7 +424,6 @@ data_targets <- tar_plan(
   tar_target(ndvi_anomalies, calculate_ndvi_anomalies(ndvi_date_lookup,
                                                       ndvi_historical_means,
                                                       ndvi_anomalies_directory,
-                                                      model_dates,
                                                       model_dates_selected,
                                                       lag_intervals,
                                                       overwrite = FALSE),

diff --git a/renv.lock b/renv.lock
@@ -252,6 +252,12 @@
       "Version": "1.3.2",
       "Repository": "CRAN"
     },
+    "crew": {
+      "Source": "Repository",
+      "Package": "crew",
+      "Version": "0.4.0",
+      "Repository": "CRAN"
+    },
     "crul": {
       "Source": "Repository",
       "Package": "crul",
@@ -425,6 +431,12 @@
       "Version": "0.2-2",
       "Repository": "CRAN"
     },
+    "getip": {
+      "Source": "Repository",
+      "Package": "getip",
+      "Version": "0.1-3",
+      "Repository": "CRAN"
+    },
     "ggforce": {
       "Source": "Repository",
       "Package": "ggforce",
@@ -641,6 +653,12 @@
       "Version": "0.12",
       "Repository": "CRAN"
     },
+    "mirai": {
+      "Source": "Repository",
+      "Package": "mirai",
+      "Version": "0.9.1",
+      "Repository": "CRAN"
+    },
     "modelr": {
       "Source": "Repository",
       "Package": "modelr",
@@ -653,6 +671,12 @@
       "Version": "0.5.0",
       "Repository": "CRAN"
     },
+    "nanonext": {
+      "Source": "Repository",
+      "Package": "nanonext",
+      "Version": "0.9.1",
+      "Repository": "CRAN"
+    },
     "nasapower": {
       "Source": "Repository",
       "Package": "nasapower",