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adding benthic temperature pressure and adjusting layer files
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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| title: "Benthic temperature" | ||
| format: html | ||
| editor: visual | ||
| --- | ||
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| ## Benthic temperature | ||
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| The Ocean temperature data are bio-oracle data from here: | ||
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| https://bio-oracle.org/downloads-to-email.php | ||
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| units: degrees C | ||
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| average of a given decade, and long-term average of the yearly monthly maxima and minima of a given decade (e.g., the average temperature of the warmest month in the period 2000-2010). | ||
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| Resolution: 0.05 degree resolution | ||
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| For benthic: because focal cells at 0.05 degree resolution comprise a wide range of depth values, the benthic layers were developed for the minimum, average and maximum depth within focal cells. | ||
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| Downloaded September 30 2024. | ||
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| ```{r} | ||
| library(tidyverse) | ||
| library(terra) | ||
| library(ncdf4) | ||
| library(biooracler) | ||
| library(here) | ||
| # devtools::install_github("bio-oracle/biooracler") | ||
| ``` | ||
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| Downloading the data (https://github.com/bio-oracle/biooracler): | ||
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| ```{r} | ||
| list_layers("Temperature")$dataset_id | ||
| dataset_id <- "thetao_ssp245_2020_2100_depthmean" | ||
| info_layer(dataset_id) | ||
| # make a function to download the data from site | ||
| # (called by getdata function after this) | ||
| layer_download <- function(time, latitude, longitude, dataset_id, statistic){ | ||
| constraints = list(time, latitude, longitude) | ||
| names(constraints) = c("time", "latitude", "longitude") | ||
| variables = paste0(variable, "_", statistic) | ||
| layers <- download_layers(dataset_id, variables, constraints) | ||
| return(layers) | ||
| } | ||
| # make a function to get oxygen and depth data for each time period. | ||
| getdata <- function(variable = "thetao", depth = "depthmean", statistic = "mean"){ | ||
| latitude = c(-89.975, 89.975) | ||
| longitude = c(-179.975, 179.975) | ||
| scenarios = c("ssp119", "ssp126", "ssp245", "ssp370", "ssp460", "ssp585") | ||
| #historical | ||
| dataset_id <- paste0(variable, "_baseline_2000_2019_", depth) | ||
| time = c('2000-01-01T00:00:00Z', '2000-01-01T00:00:00Z') | ||
| layers <- layer_download(time=time, latitude=latitude, longitude = longitude, dataset_id = dataset_id, statistic = statistic) | ||
| writeRaster(layers, filename = file.path("//home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature", paste0(variable, "-", depth, "_", statistic, "_hist_hist.tif")), overwrite=TRUE) | ||
| #current | ||
| dataset_id <- paste0(variable, "_baseline_2000_2019_", depth) | ||
| time = c('2010-01-01T00:00:00Z', '2010-01-01T00:00:00Z') | ||
| layers <- layer_download(time=time, latitude=latitude, longitude = longitude, dataset_id = dataset_id, statistic=statistic) | ||
| writeRaster(layers, filename = file.path("/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature", paste0(variable, "-", depth, "_", statistic, "_current_current.tif")), overwrite=TRUE) | ||
| # scenarios | ||
| for(scenario in scenarios){ # scenario=scenarios[3] | ||
| dataset_id <- paste0(variable, "_", scenario, "_2020_2100_", depth) | ||
| ##near | ||
| time = c('2020-01-01T00:00:00Z', '2030-01-01T00:00:00Z') | ||
| layers <- layer_download(time=time, latitude=latitude, longitude = longitude, dataset_id = dataset_id, statistic=statistic) | ||
| rmean <- app(layers, mean) | ||
| writeRaster(rmean, filename = file.path("/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature", paste0(variable, "-", depth, "_", statistic, "_", scenario, "_near-term.tif")), overwrite=TRUE) | ||
| ##medium | ||
| time = c('2040-01-01T00:00:00Z', '2050-01-01T00:00:00Z') | ||
| layers <- layer_download(time=time, latitude=latitude, longitude = longitude, dataset_id = dataset_id, statistic=statistic) | ||
| rmean <- app(layers, mean) | ||
| writeRaster(rmean, filename = file.path("/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature", paste0(variable, "-", depth, "_", statistic, "_", scenario, "_medium-term.tif")), overwrite=TRUE) | ||
| ##long | ||
| time = c('2080-01-01T00:00:00Z', '2090-01-01T00:00:00Z') | ||
| layers <- layer_download(time=time, latitude=latitude, longitude = longitude, dataset_id = dataset_id, statistic=statistic) | ||
| rmean <- app(layers, mean) | ||
| writeRaster(rmean, filename = file.path("/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature", paste0(variable, "-", depth, "_", statistic, "_", scenario, "_long-term.tif")), overwrite=TRUE) | ||
| } | ||
| } | ||
| #### This will update the data in the folder! | ||
| # benthic (average depth) data | ||
| # mean temperature | ||
| #getdata(variable = "thetao", depth="depthmean", statistic="mean") | ||
| # average yearly range (based on average monthly high and low) | ||
| #getdata(variable = "thetao", depth="depthmean", statistic="range") | ||
| ``` | ||
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| # Rescaling | ||
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| ```{r} | ||
| rescale_files <- expand.grid( | ||
| scenario = c("ssp119", "ssp126", "ssp245", "ssp370", "ssp460", "ssp585"), | ||
| time_frame =c("near-term", "medium-term", "long-term")) | ||
| current <- data.frame(scenario = "current", time_frame = "current") | ||
| rescale_files <- rbind(rescale_files, current) | ||
| rescale_temp <- function(scenario = "ssp585", | ||
| time_frame = "medium-term", | ||
| historic_range = "/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature/thetao-depthmean_range_hist_hist.tif", | ||
| historic_mean = "/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature/thetao-depthmean_mean_hist_hist.tif"){ | ||
| hist_mean <- rast(historic_mean) | ||
| hist_range <- rast(historic_range) | ||
| future <- rast(sprintf("/home/shares/ohi/stressors_2021/_raw_data/biooracle_temperature/thetao-depthmean_mean_%s_%s.tif", scenario, time_frame)) | ||
| change <- future - hist_mean | ||
| rescale <- change/hist_range | ||
| rescale <- ifel(rescale > 1, 1, rescale) | ||
| rescale <- ifel(rescale<=0, 0, rescale) | ||
| writeRaster(rescale, sprintf("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled/benthic-temp_%s_%s.tif", scenario, time_frame), overwrite=TRUE) | ||
| } | ||
| for(i in 1:dim(rescale_files)[1]){ # i=1 | ||
| tmp_scenario = rescale_files[i,"scenario"] | ||
| tmp_time = rescale_files[i,"time_frame"] | ||
| rescale_temp(scenario = tmp_scenario, | ||
| time_frame = tmp_time) | ||
| } | ||
| # delete the aux files | ||
| delete_files <- list.files("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled", full=TRUE, pattern=".aux") | ||
| file.remove(delete_files) | ||
| # expand the current ones | ||
| scenarios <- c("ssp119", "ssp126", "ssp245", "ssp370", "ssp460", "ssp585") | ||
| current_files <- list.files("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled", full=TRUE, pattern="current") | ||
| for(current_file in current_files){ #current_file <- current_files[1] | ||
| tmp <- rast(current_file) | ||
| for(scenario in scenarios){ # scenario = scenarios[1] | ||
| saveName <- basename(current_file) | ||
| saveName <- gsub("_current_", sprintf("_%s_", scenario), saveName) | ||
| writeRaster(tmp, sprintf("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled/%s", saveName)) | ||
| }} | ||
| # delete the current ones | ||
| delete_files <- list.files("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled", full=TRUE, pattern="current_current") | ||
| file.remove(delete_files) | ||
| ``` | ||
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| Final formatting | ||
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| ```{r} | ||
| rast_base_10km_file <- terra::rast(here('_spatial/rast_base_mol_10km.tif')) | ||
| ocean_template <- terra::rast(here('_spatial/ocean_area_mol.tif')) | ||
| ocean_template[ocean_template>0] <- 1 | ||
| plot(ocean_template) | ||
| T_paths <- list.files("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled", full=TRUE) | ||
| for(T_path in T_paths){ # T_path = T_paths[1] | ||
| T_rast <- terra::rast(T_path) | ||
| mol_rast <- terra::project(T_rast, rast_base_10km_file, method="bilinear", over=TRUE) | ||
| #plot(mol_rast) | ||
| ## gapfill | ||
| gf_raster <- function(x){raster::focal(x, w = matrix(1,3,3), fun = mean, na.rm=TRUE, na.policy="only")} | ||
| r = mol_rast | ||
| ## Repeat 50 times (most is immediately gapfilled but the antarctic area was persistent) | ||
| i <- 0 | ||
| while (i <= 50){ | ||
| r <- gf_raster(r) | ||
| i <- i + 1 | ||
| print(i) | ||
| } | ||
| # plot(r) | ||
| r <- r*ocean_template | ||
| # diff_rast <- r - mol_rast | ||
| #plot(diff_rast) # should be 0 | ||
| saveName <- basename(T_path) | ||
| writeRaster(r, filename = file.path("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled_mol", saveName), overwrite = TRUE) | ||
| } | ||
| ``` | ||
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| Quick look at some! | ||
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| ```{r} | ||
| raws <- list.files("/home/shares/ohi/stressors_2021/_dataprep/T_benthic/rescaled_mol", full=TRUE) | ||
| tmp <- rast(raws[10]) - rast(raws[1]) | ||
| plot(tmp) | ||
| ``` |