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calculate anomalies for NDVI - partial run
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#' .. content for \description{} (no empty lines) .. | ||
#' | ||
#' .. content for \details{} .. | ||
#' | ||
#' @title | ||
#' @param ndvi_date_lookup | ||
#' @param ndvi_historical_means | ||
#' @param ndvi_anomalies_directory | ||
#' @param model_dates | ||
#' @param model_dates_selected | ||
#' @param lag_intervals | ||
#' @param overwrite | ||
#' @return | ||
#' @author Emma Mendelsohn | ||
#' @export | ||
calculate_ndvi_anomalies <- function(ndvi_date_lookup, ndvi_historical_means, | ||
ndvi_anomalies_directory, model_dates, | ||
model_dates_selected, lag_intervals, | ||
overwrite = FALSE) { | ||
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# Set filename | ||
date_selected <- model_dates_selected | ||
save_filename <- glue::glue("ndvi_anomaly_{date_selected}.gz.parquet") | ||
message(paste0("Calculating NDVI anomalies for ", date_selected)) | ||
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# Check if file already exists | ||
existing_files <- list.files(ndvi_anomalies_directory) | ||
if(save_filename %in% existing_files & !overwrite) { | ||
message("file already exists, skipping download") | ||
return(file.path(ndvi_anomalies_directory, save_filename)) | ||
} | ||
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# 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) | ||
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# Get the lagged anomalies for selected dates, mapping over the lag intervals | ||
row_select <- which(model_dates$date == date_selected) | ||
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lag_intervals_start <- c(1 , 1+lag_intervals[-length(lag_intervals)]) | ||
lag_intervals_end <- lag_intervals | ||
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anomalies <- map2(lag_intervals_start, lag_intervals_end, function(start, end){ | ||
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lag_dates <- model_dates |> slice((row_select - start):(row_select - end)) | ||
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# get files and weights for the calculations | ||
weights <- ndvi_date_lookup |> | ||
mutate(lag_date = map(lookup_dates, ~. %in% lag_dates$date)) |> | ||
mutate(weight = unlist(map(lag_date, sum))) |> | ||
filter(weight > 0) |> | ||
select(start_date, filename, weight) | ||
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ndvi_dataset <- open_dataset(weights$filename) | ||
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# Lag: calculate mean by pixel for the preceding x days | ||
lagged_means <- ndvi_dataset |> | ||
left_join(weights |> select(-filename)) |> | ||
group_by(x, y) |> | ||
summarize(lag_ndvi_mean = sum(ndvi * weight)/ sum(weight)) |> | ||
ungroup() | ||
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# Join in historical means to calculate anomalies raw and scaled | ||
full_join(lagged_means, historical_means, by = c("x", "y")) |> | ||
mutate(!!paste0("anomaly_ndvi_", end) := lag_ndvi_mean - historical_ndvi_mean, | ||
!!paste0("anomaly_ndvi_scaled_", end) := (lag_ndvi_mean - historical_ndvi_mean)/historical_ndvi_sd) |> | ||
select(-starts_with("lag"), -starts_with("historical")) | ||
}) |> | ||
reduce(left_join, by = c("x", "y")) |> | ||
mutate(date = date_selected) |> | ||
relocate(date) | ||
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# Save as parquet | ||
write_parquet(anomalies, here::here(ndvi_anomalies_directory, save_filename), compression = "gzip", compression_level = 5) | ||
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return(file.path(ndvi_anomalies_directory, save_filename)) | ||
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} | ||
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