enRichment

data enrichment from an OPeNDAP dataset

Description

This process take in parameter a spatio-temporal dataset and an OPeNDAP dataset URL and try to enrich the input dataset with OPeNDAP data. Input dataset must be point only geometry (actually).

Use

require(IRDTunaAtlas)
df <- readData(dataType="WFS", 
               url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/dbTaggingRTTP?REQUEST=getFeature&SERVICE=WFS&VERSION=2.0.0&typeNames=query_all_schools_biological_datasampling")

enriched.df <- enRichment(data=df, 
                          opendapUrl="http://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/PH/sstd/1day", 
                          varName="sea_surface_temperature", 
                          timeName="bio_timestamp", 
                          verbose=TRUE)

Output examples

> names(enriched.df)[! names(enriched.df) %in% names(df)]
[1] "sea_surface_temperature"           "sea_surface_temperature_longitude" "sea_surface_temperature_latitude"  "sea_surface_temperature_time"
> enriched.df$sea_surface_temperature[smp]
 [1] 28.2   NA   NA   NA   NA   NA   NA   NA   NA   NA
> enriched.df$time <- strptime(enriched.df$bio_timestamp, format="%Y-%m-%dT%H:%M:%OSZ")
> smp <- sample(1:nrow(enriched.df), 10)

> data.frame(obs.time=enriched.df$time, sst.time=enriched.df$sea_surface_temperature_time, diff.time=enriched.df$time - enriched.df$sea_surface_temperature_time)[smp,]
                obs.time            sst.time diff.time
272  2006-04-18 22:00:00 2006-04-18 13:00:00   9 hours
1808 2006-10-08 22:00:00 2006-10-08 13:00:00   9 hours
2426 2006-04-26 22:00:00 2006-04-26 13:00:00   9 hours
2553 2007-07-11 22:00:00 2007-07-11 13:00:00   9 hours
1212 2005-08-16 22:00:00 2005-08-16 13:00:00   9 hours
2214 2006-10-08 22:00:00 2006-10-08 13:00:00   9 hours
1761 2006-10-20 22:00:00 2006-10-20 13:00:00   9 hours
3209 2007-04-25 22:00:00 2007-04-25 13:00:00   9 hours
1018 2006-04-24 22:00:00 2006-04-24 13:00:00   9 hours
3150 2007-02-25 23:00:00 2007-02-25 12:00:00  11 hours

> myDistFun <- function(x) 
+ {
+   return(spDistsN1( matrix(c(x[1],x[2]), ncol=2), c(x[3],x[4]), longlat=TRUE))
+ }
> res <- apply(cbind(coordinates(enriched.df)[,1], coordinates(enriched.df)[,2], enriched.df$sea_surface_temperature_longitude, enriched.df$sea_surface_temperature_latitude), c(1), myDistFun)
> res[smp]
 [1] 1.4150088 1.1159907 1.4378368 2.0110477 1.2079209 2.4496984 0.9213724 2.1955204 0.2455549 1.3299811