Salinity data at depth not pulling

[dancrear]

Hi,

Your package has been great and I really appreciate you developing it! When I use the code below, I end up only downloading the top layer of salinity when I wish to download surface and subsurface data. I’m pretty sure salinity data at depth is available because in the Copernicus Marine Data Store form I can adjust the depth range I want. I've noticed the same issue for other variables from the same product. I have tried to follow the example here. I have also tried switching the values around and using negatives, but no matter what I try the data pull only has one layer (valid_min: 0.494024991989136, valid_max: 0.494024991989136). I can't tell if there's something wrong with the request on my end or the database end.

cms_download_subset( destination = destination, product = “GLOBAL_ANALYSISFORECAST_PHY_001_024”, layer = "cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m", variable = "so", region = c(-150,-40,-70,40), timerange = c("2021-03-01 UTC", "2021-04-01 UTC"), verticalrange = c(0, 10), overwrite = TRUE)

Thanks, Dan

[pepijn-devries]

Hi @dancrear,

Thanks for your report. I've scaled down your subset and created the following reprex which does reproduce your issue:

library(CopernicusMarine)
library(stars)

destination <- tempfile("copernicus", fileext = ".nc")
cms_download_subset(
  destination   = destination,
  product       = "GLOBAL_ANALYSISFORECAST_PHY_001_024",
  layer         = "cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m",
  variable      = "so",
  region        = c(-150,-40,-140,-35),
  timerange     = c("2021-03-01 UTC", "2021-04-01 UTC"),
  verticalrange = c(0, 10),
  overwrite     = TRUE)

sal <- read_stars(destination)
print(sal)

Which produces:

stars object with 4 dimensions and 1 attribute
attribute(s):
                               Min. 1st Qu.   Median     Mean 3rd Qu.     Max.
copernicus456838124d5d.nc  33.90225 34.5031 34.68702 34.74365 34.9466 35.74508
dimension(s):
      from  to                  offset    delta  refsys x/y
x        1 121                    -150  0.08333      NA [x]
y        1  61                  -34.96 -0.08333      NA [y]
depth    1   1               0.494 [m]       NA      NA    
time     1  31 2021-03-01 12:00:00 UTC   1 days POSIXct    

Where I can see that indeed only 1 depth layer is downloaded whereas the product specification lists multiple depth layers. I will look into this and hoop to fix this soon. I will post my findings/fixes here.

Cheers,

Pepijn

[pepijn-devries]

Hi @dancrear,

After some testing it would appear that the verticalrange range needs to be specified as negative numbers, as it is below the sea surface. So if you use verticalrange = c(0,-10), you should get multiple depth layers. I will update the documentation to make this more clear, it took me a while to figure this out as well...

[pepijn-devries]

This is taken care of in commit https://github.com/pepijn-devries/CopernicusMarine/pull/32/commits/e5d46f215c2bc4f5c7b2efc4e50289b8f338053f

[dancrear]

Awesome! I really appreciate you figuring this out. Using your advice I was able to download the correct data as well. Again, thank you for developing a package that is so easy for ecologists like myself to use.

[dancrear]

Hi @pepijn-devries

One more question. I'm wondering if there is a size limit for downloaded file. Using the code below I was able to download salinity data from surface to 55m depth, but beyond that I receive the error:

Failed to collect information from job-check. HTTP 400 Bad Request.

I was hoping to pull data from the surface down to 500m. It looks like they have data available to +5000m so I'm wondering if there is file size limit given the volume of the area I need.

cms_download_subset( destination = destination, product = “GLOBAL_ANALYSISFORECAST_PHY_001_024”, layer = "cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m", variable = "so", region = c(-150,-40,-70,40), timerange = c("2021-03-01 UTC", "2021-04-01 UTC"), verticalrange = c(0, -500), overwrite = TRUE)

Thanks, Dan

[pepijn-devries]

Hi @dancrear,

Yes, for subsetting data Copernicus has set a file size limit on their server. So you need to split up your request and stitch them together afterwards. You can also download the complete set with cms_download_stac.

The error message that you get isn't very helpful. I will see if I can generate a more informative error message.

Cheers,

Pepijn