Lab #3: Fitting a nonstationary spatial covariance model
using the MCMCdeform program.
The MCMCdeform.exe program and all R
code and data files described here are available in this zip
file:
Rcode.and.data.zip
You want to put all these things on your desktop (don't worry about the
executable file, it is already there).
1. The folder
Output on your
desktop contains output from MCMCdeform from a run of 400,000 MCMC
iterations, with every 200
th iteration saved. To get
a feeling for what you can do with the output, you want to examine it
using the R code in
MCMC.read.R.
Before you use that code, you need to change the address where the
files are kept (replace "peter" by "studentxx"). You will also need the
R functions
dist2full,
Fdrawtps,
Flamb2,
FLmatrix,
Fseval, and
Flink.cor.
Fairly detailed explanations of the program are provided in the
manual. See the end of that document for an
explanation of the input and output.
2. To develop an understanding of the MCMC program for fitting a
spatial deformation model, run the MCMCdeform program on the spatial
covariance matrix derived from 124 2-week average NOx concentration
data at 28 monitoring sites in southern California. Time series
plots of the raw data from which these covariances were computed are
provided in the file
CA.2wkmeanlog.trendfits.jpg. You will want to run
relatively few MCMC iterations in
order to obtain a result in a reasonable amount of time. The program
estimates how long it will take to run, so you may want to stop it and
change the input if it looks unreasonable.
The executable
file,
MCMCdeform.exe, should sit in the same folder as the input files
listed here. On the virtual machine they are all on the Desktop.
You will need to have the text files below (ca28.nox.*.txt) on the
desktop of the virtual machine. The program will ask for:
-
a name for the
output folder: (you choose)
-
an input file: ca28.nox.input.txt
-
Do you want to
use geographic coordinates as initial configuration for the D-space? y
-
a file name for
Coordinates:
ca28.nox.lamb100.txt [the coordinates will be printed out]
-
a file name for
the sample Covariance matrix:
ca28.nox.cov.txt
-
initial
variance field vector:
ca28.nox.nu0.txt
You want to modify the number of MCMC iterations, and play some with
the other parameters in the input file to get some feel for how they
affect the results.
3. Look at the
results of your runs, compare them to the run used in question 1, and
discuss the outcome. As usual, a report is due in a week, but we will
see how long things take, and may use the following Thursday as a lab
session if needed. In that case the report will be due two weeks from
today.
Here are a couple of GIS maps of the LA area:
011306_LA.jpg
011306_population.jpg
R
code for visualizing MCMC output from deformation program.
California NOx data input files
