How to perform precipitation data analysis? I want to make precipitation data analysis for the Latvian territory.
I only have meteorological stations and reanalysis  data. 
My data from meteorological stations are in the format:

year  month  day    time      station1 station2 station3
2013    1     1    03.00        0                 0.1
2013    1     1    06.00        0.1               0.2
2013    1     1    15.00        0       0.1         0
2013    1     1    18.00        0.2     0         0.3
2013    1     2     03.00        0                 0.4
                  ...  


I also have a file with coordinates for meteorological stations.
And data from reanalysis is in format 

&gt; head(data)
  longitude latitude   time value
1     -27.0      -27 990555     0
2     -25.5      -27 990555     0
3     -24.0      -27 990555     0
4     -22.5      -27 990555     0
5     -21.0      -27 990555     0
6     -19.5      -27 990555     0


Edited: My main questions are:
1) What can tell me if these data are similar, should I look their summary and compare, or it is better to use some tests. Could you advice methods how to compare different data.
2) If there are missing values, should I just get them out and then analyse data?
3) Maybe someone can advice some tutorial with R code? Can someone tell me how to decode time values from format like 990555 (I need formula or function for R)?
Date/timestamps are tricky to convert without further information; are the values you show days (unlikely, if 990555 is your date/time value), hours, seconds? See if you can figure out the system used (either by knowing which date your timestamp is supposed to represent, or looking at the step sizes for the data); this will generally give you an idea of what is being represented, and how to convert to an actual date.
Coordinate and long/lat are basically the same thing, only built up from decimals or hours/minutes (e.g. 0.5 representing 30 minutes). Conversion can be found http://transition.fcc.gov/mb/audio/bickel/DDDMMSS-decimal.html, for instance. Mind that other coordinate systems are also possible, which will make the conversion different; again, this is important to figure out before you can convert your data.
Comparison options will depend on: 1) whether your data corresponds (do you have measurements on the same date/time, as well as the same location?), 2) what you are interested in.