[R-sig-Geo] Automate the extraction of climate variable at different time depths from netcdf in r

[Barnabas Daru]

Dear all,
I write to seek help with extracting climate data at various times and
depth from NETCDF in R.
The climate data is sea surface temperature monthly means from 1854 to
2014.
My goal is to automate the extraction of SST climate data for a set of
points with different time depths.

I have successfully used the 'brick' function in the raster package to get
climate data at various time depths as follows:

b <- brick("~sst.mnmean.nc", varname="sst")

mydate <- b[["X1869.09.01"]] # SST for September in 1869

mydata <- read.csv("~Species one.csv")

mydataSPDF <- SpatialPointsDataFrame(mydata[,5:6],data.frame(mydata))

extract.mydata <- extract(mydate, mydataSPDF, sp=TRUE)

extract.mydata <- data.frame(extract.mydata)

write.csv(extract.mydata, file = "Species_one_extracted.csv")

My major challenge is that I have to keep extracting manually for each time
depth, then copy and paste in the main dataframe and the data has about
3000 observations, meaning I have to keep copying and pasting ~3000 times
for one species!
Is there a way I can iterate the process in R to loop through each month's
climate and extract the data for each point and time depth rather than to
do it manually?

Here's how my data frame looks like:
  Date year month day lon lat SST  1855-01-01 1855 1 1 11.6861 57.7254
3.440000057  1859-07-26 1859 7 26 25.46122 60.26766 13.25  1860-01-01 1860 1
1 10.9154 53.9484 15.10999966  1861-07-10 1861 7 10 7.79588 58.08673
15.71000004  1861-07-26 1861 7 26 -2.84072 54.0778  1861-08-17 1861 8 17
11.9792 57.51298  1862-01-01 1862 1 1 22.20467 60.27955  1862-08-05 1862 8 5
11.78316 57.61649  1862-08-23 1862 8 23 11.9792 57.51298  1863-08-26 1863 8
26 10.72237 59.97258  1863-08-28 1863 8 28 15.53721 56.20091  1863-09-22
1863 9 22 16.37849 56.84255  1864-07-05 1864 7 5 -4.07097 51.09542
1864-07-18 1864 7 18 -4.21368 51.0928  1864-08-26 1864 8 26 -4.07097
51.09542  1865-09-07 1865 9 7 10.76144 59.91271  1865-09-27 1865 9 27
10.53107 60.43395  1867-08-28 1867 8 28 12.82669 55.86822  1868-01-01 1868 1
1 12.8944 56.6897  1868-01-01 1868 1 1 4.82685 53.13793
Thanks and kind regards
Barnabas Daru

-- 

  \-/
   /\
  /--|
 /---/ *Daru, Barnabas Haruna*
 |--/  PhD Candidate,
 \-/   African Centre for DNA Barcoding,
 /\    University of Johannesburg,
/--\   PO BOX 524 Auckland Park, 2006,
|---\  South Africa
 \---\ Lab: +27 11 559 3477
  \--| Mobile: +27 7381 89 583
   \-/
   /\  My homepage: http://barnabasdaru.com
<http://acdb.co.za/index.php?page=mr-barnabas-h-daru>
  /--\

	[[alternative HTML version deleted]]