Compiling source code of netcdf4 on linux

First obtain szip libraries (from the link at http://www.hdfgroup.org/HDF5/release/obtain5.html)
wget http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz
tar -xzvf szip-2.1.tar.gz
cd szip-2.1

./configure --prefix=/home/acizmeli/opt

make 

make test

make install

Then obtain the hd5 source code  (again from http://www.hdfgroup.org/HDF5/release/obtain5.html)

wget http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz

tar -xzvf hdf5-1.8.8.tar.gz 

cd hdf5-1.8.8

./configure --prefix=/home/acizmeli/opt  --with-szlib=/home/acizmeli/opt/

(make sure that ./configure has recognized the szip libraries)

make

(or for parallel compilation : ) make -j -16

make install

Then obtain the netcdf4 source :

wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.2.tar.gz

tar -xzvf netcdf-4.2.tar.gz

cd netcdf-4.2

CPPFLAGS=-I/home/acizmeli/opt/include/ LDFLAGS=-L/home/acizmeli/opt/lib ./configure --prefix=/home/acizmeli/opt/

make

make install

If there is a doxygen error, try adding --disable-doxygen

Find nearest neighbours in a point cloud

From http://rwiki.sciviews.org/doku.php?id=tips:spatial-data:overlapping

library(spdep)
data(columbus)
#Extract coordinates from a data frame
coords <- columbus[,c("X", "Y")]
#For each point, determine the four closest points based on great circle distances:
knn.col <- knearneigh(as.matrix(coords), k=4, longlat=T)
knn.nb <- knn2nb(knn.col)
#What are the indices of the four nearest neighbours to point number 5?
knn.col$nn[5,]
#Equivalently:
knn.nb[[5]]
#Plot all points, then mark point number 5 by red, and its four nearest neighbours by blue:
plot(coords)
points(coords[5,], col="red", pch=19)
points(coords[knn.nb[[5]],], col="blue", pch=19)

Some beginner tricks with git

#################################################
Problem : error: Your local changes to the following files would be overwritten by merge: rfiles/BiOpticaR/Various/spacetime_ISIN.R
Please, commit your changes or stash them before you can merge.Aborting
#################################################
$ git pull
remote: Counting objects: 38, done.
remote: Compressing objects: 100% (19/19), done.
remote: Total 25 (delta 13), reused 1 (delta 0)
Unpacking objects: 100% (25/25), done.
From ssh://ekumen/home/acizmeli/GIT
   d63ba8f..cea6b9e  master     -> origin/master
Updating d63ba8f..cea6b9e
error: Your local changes to the following files would be overwritten by merge:
    rfiles/BiOpticaR/Various/spacetime_ISIN.R
Please, commit your changes or stash them before you can merge.
Aborting

Solution:
$ git reset --hard HEAD
HEAD is now at d63ba8f Moved all netcdf imagery functions in the fil......
$ git pull

#################################################
Problem :  Push rejected
! [rejected]        master -> master (non-fast forward)
error: failed to push some refs to.....
#################################################
Solution:
(From http://rip747.wordpress.com/2009/04/20/git-push-rejected-non-fast-forward/)

When trying to do a push to a repo, you might encounter the following error:

$ git push github master
To git@gitproxy:rip747/cfwheels.git
! [rejected]        master -> master (non-fast forward)
error: failed to push some refs to ‘git@gitproxy:rip747/cfwheels.git’

Don’t panic, this is extremely easy to fix. All you have to do is issue a pull and your branch will be fast-forward:

$ git pull github master
From git@gitproxy:rip747/cfwheels
* branch            master     -> FETCH_HEAD
Already uptodate!
Merge made by recursive.

Then retry your push and everything should be fine:
$ git push github master

#################################################
Problem : Automatic merge failed; fix conflicts and then commit the result.
#################################################
use :
git mergetool

Some time conversions in R

Form a "POSIXlt" object from a string :

tt = strptime("20100101","%Y%m%d", tz="GMT")

Compute the seconds since 1970 ((Internal storage format of the "POSIXlt" class)

as.double(tt)

Compute the days since 1970 (Internal storage format of the "Date class)

as.double(as.Date(tt))

or

unclass(as.Date(tt)) 

Convert an xts object into seconds since 1970

xx = xts(111, tt)
as.double(time(xx))

Convert an xts object into days since 1970

floor(as.double(time(xx))/60/60/24)

Construct a time object from different numeric components

ISOdatetime(year, month, day, hour, min, sec, tz = "")

Extract from a POSIXlt object the Year, month, day  etc information in numeric format :

class(a)
[1] "POSIXlt" "POSIXt"

a
[1] "2009-07-06 20:00:28"

c(a$year+1900, a$mon+1, a$mday, a$hour, a$min, a$sec)
[1] 2009    7    6   20    0   28

Convert a ESRI shapefile into GMT vector format

Use ogr2ogr to convert the shapefile into GMT vector format :

ogr2ogr -f "GMT" Hudson_bounds.gmt  Hudson_bounds.shp