Update documentation and site

.gitignore

@@ -54,3 +54,7 @@ codes/drafts/
 data/
 
 functions/drafts/
+
+*.zip
+
+temp/

README.md

@@ -24,8 +24,25 @@ Oxygen data download proceeded the same way as temperature (use the code with th
 
 ### Data processing
 
+__Marine heat waves and Cold spells__
+
 Data analysis for Marine Heat Waves and Cold Spells was done using the package [`heatwaveR`](https://robwschlegel.github.io/heatwaveR/). More details to be added after the workshop.
 
+__Temperature by species__
+
+- `get_edna_marinespecies.R`: aggregate species list from the eDNA project downloaded from the repository https://github.com/iobis/edna-species-lists
+- `temperature_database.R`: aggregate temperature/environmental layers to the OBIS/GBIF database (see details for the database here https://github.com/iobis/protectedseas-statistics)
+- `get_sst_marinespecies.R`: extract temperature information for all species listed on the sites
+- `plot_sst_marinespecies.R`: plot temperature information for a selected species
+
+There is also a function on the `functions` folder, `query_sst_marinespecies.R`, that can be used to query full data or summaries of temperature for a species (using the database).
+
+__Others__
+
+- `get_depthprofiles.R`: see which is the actual depth that was used when obtaining the data from Copernicus
+- `generate_quarto_sites.R`: generate quarto pages by site
+
+
 ----
 
 <img src="https://obis.org/images/logo.png" width="200">

codes/download_oxygen_toolbox.R

@@ -126,11 +126,21 @@ proc <- job::job({
              cat("File already processed, skipping.\n")
            } else {
              r <- rast(fname)
-             r_dat <- as.data.frame(r, xy = TRUE, time = TRUE, wide = FALSE)
-             r_dat <- subset(r_dat, select = -layer)
+             r_dat <- as.data.frame(r, xy = TRUE, time = TRUE)
+             r_dat <- r_dat %>%
+               pivot_longer(3:length(.), names_to = "time", values_to = "values") %>%
+               mutate(layer = gsub("\\..*", "", names(r))[1])
              arrow::write_parquet(r_dat, outfile, compression = "gzip")
            }
 
            return(invisible(NULL))
          })
+
+  lf <- list.files(outfolder, full.name = T, pattern = "\\.parquet")
+  base <- list.files(outfolder, full.name = T, pattern = "\\.nc")[1]
+
+  zip("oxygen_dayly.zip", c(lf, base))
+
+  job::export("none")
 })
+

codes/download_temperature_toolbox.R

@@ -126,11 +126,23 @@ proc <- job::job({
              cat("File already processed, skipping.\n")
            } else {
              r <- rast(fname)
-             r_dat <- as.data.frame(r, xy = TRUE, time = TRUE, wide = FALSE)
-             r_dat <- subset(r_dat, select = -layer)
+             r_dat <- as.data.frame(r, xy = TRUE, time = TRUE)
+             r_dat <- r_dat %>%
+               pivot_longer(3:length(.), names_to = "time", values_to = "values") %>%
+               mutate(layer = gsub("\\..*", "", names(r))[1])
              arrow::write_parquet(r_dat, outfile, compression = "gzip")
            }
 
            return(invisible(NULL))
          })
+
+  lf <- list.files(outfolder, full.name = T, pattern = "\\.parquet")
+  base <- list.files(outfolder, full.name = T, pattern = "\\.nc")[1]
+
+  zip("temperature_dayly.zip", c(lf, base))
+
+  job::export("none")
 })
+
+
+