Changes in list_layers() and download_dataset()

[salvafern]

Changes:

New helper function to get the default URL of ERDDAP.

biooracler/R/utils.R

Line 9 in 29013dc

erddap.bio_oracle.org <- function(){

Can be overriden via options('ERDDAP.BIO-ORACLE.URL') for testing

list_layers()

• Allows now free text search, e.g. list_layers('Ocean Temperature')
• Provides a simplified version by default with only the dataset ID, title and summary.

list_layers("Ocean Temperature", simplify = TRUE)
#> # A tibble: 28 × 3
#> dataset_id                          title                       summary
#> <chr>                               <chr>                       <chr>  
#> 1 thetao_baseline_2000_2019_depthmax  Bio-Oracle OceanTemperatur… "Uses …
#> 2 thetao_ssp119_2020_2100_depthmax    Bio-Oracle OceanTemperatur… "Uses …
#> 3 thetao_ssp126_2020_2100_depthmax    Bio-Oracle OceanTemperatur… "Uses …
#> 4 thetao_ssp245_2020_2100_depthmax    Bio-Oracle OceanTemperatur… "Uses …
#> 5 thetao_ssp370_2020_2100_depthmax    Bio-Oracle OceanTemperatur… "Uses …
#> 6 thetao_ssp460_2020_2100_depthmax    Bio-Oracle OceanTemperatur… "Uses …
#> 7 thetao_ssp585_2020_2100_depthmax    Bio-Oracle OceanTemperatur… "Uses …
#> 8 thetao_baseline_2000_2019_depthmean Bio-Oracle OceanTemperatur… "Uses …
#> 9 thetao_ssp119_2020_2100_depthmean   Bio-Oracle OceanTemperatur… "Uses …
#> 10 thetao_ssp126_2020_2100_depthmean   Bio-Oracle OceanTemperatur… "Uses …
#> # … with 18 more rows

• It is also memoised to reduce unnecessary calls.

  biooracler/R/main.R

  Line 151 in 29013dc

  list_layers <- memoise::memoise(.list_layers)

download_dataset()

• ERDDAP url passed by default
• Method to transform into SpatRaster class from terra package (See Consider different output types #5 (comment))

# Example dataset
dataset_id = "tas_baseline_2000_2020_depthsurf"
time = c('2001-01-01T00:00:00Z', '2010-01-01T00:00:00Z')
latitude = c(10, 20)
longitude = c(120, 130)
variables = c("tas_mean")
constraints = list(time, latitude, longitude)
names(constraints) = c("time", "latitude", "longitude")

# Perform
download_dataset(dataset_id, variables, constraints, fmt = "raster")
#> Selected dataset tas_baseline_2000_2020_depthsurf.
#> Dataset info available at: http://erddap.bio-oracle.org/erddap/griddap/tas_baseline_2000_2020_depthsurf.html
#> Selected 1 variables: tas_mean
#> info() output passed to x; setting base url to: http://erddap.bio-oracle.org/erddap
#> class       : SpatRaster 
#> dimensions  : 201, 201, 4  (nrow, ncol, nlyr)
#> resolution  : 0.05000694, 0.0500139  (x, y)
#> extent      : 119.9667, 130.0181, 9.952765, 20.00556  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 
#> sources     : f9db8428abb69301c6f80584b16feaf5.nc:tas_max  (2 layers) 
#> f9db8428abb69301c6f80584b16feaf5.nc:tas_min  (2 layers) 
#> varnames    : tas_max (Maximum AirTemperature) 
#> tas_min (Minimum AirTemperature) 
#> names       : tas_max_1, tas_max_2, tas_min_1, tas_min_2 
#> unit        :         K,         K,         K,         K 
#> time        : 2000-01-01 to 2010-01-01 UTC 

[vinisalazar]

LGTM, nice job @salvafern. I will try to add the text search, simplify and memoisation features to the Python counterpart.

[jorgeassis]

👌🏻

…

On 25 Jun 2023, at 15:10, Vini Salazar ***@***.***> wrote: @vinisalazar approved this pull request. LGTM, nice job @salvafern <https://github.com/salvafern>. I will try to add the text search, simplify and memoisation features to the Python counterpart. — Reply to this email directly, view it on GitHub <#9 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAK7E4EVYDR7ZH3PJ4NXBPDXNBBEPANCNFSM6AAAAAAZRT4UKI>. You are receiving this because your review was requested.