Adjusting Prior Ranges

BRAINS sets default prior ranges for parameters in MCMC sampling. In some cases, these default prior ranges might be inapproprite. BRAINS allows to adjust prior ranges as follows.

First, generate the default prior ranges adopted in BRAINS with the command

./brains param -n

This will output the prior ranges to a file named data/para_names_xx.txt. The content looks like:

# Par                                 Min        Max Prior  Fix             Val       Mean(Gau)        Std(Gau)
0 BLR_model_ln(Rblr)            -2.302585   2.504504    2    0  -1.797693e+308    0.000000e+00    0.000000e+00
1 BLR_model_beta                 0.001000   2.000000    2    0  -1.797693e+308    0.000000e+00    0.000000e+00
2 BLR_model_F                    0.000000   1.000000    2    0  -1.797693e+308    0.000000e+00    0.000000e+00
3 BLR_model_Inc                  0.000000   1.000000    2    0  -1.797693e+308    0.000000e+00    0.000000e+00
4 BLR_model_Opn                  0.000000  90.000000    2    0  -1.797693e+308    0.000000e+00    0.000000e+00

Here, Min and Max columns represent the lower and upper limits. For Prior column, 1 means Gaussian prior and 2 means uniform prior. For Fix column, 0 means not fixed and 1 means fixed. When the parameter is fixed, the Val columns represent the fixed value. When the prior is Gaussian, the Mean(Gau) and Std(Gau) represent the mean and standard deviation of the Gaussian, respectively. The lines starting with “#” will be neglected.

Note that do not change the format the file, otherwise, there will be an error when reading in it.

If the prior range of some parameters needs to change, just adjust the corresponding Min and Max columns. Then save the edited file to a new file, e.g., say, data/new_prior.txt. Note that for the sake of brevity, one can only keep those lines for the parameters to be adjusted. The rest lines can be removed. However, it is still fine to keep all lines. For example, one can edit the 1st and 3rd parameters (counting from 0) as:

1 BLR_model_beta                 0.001000   2.000000    2    0  -1.797693e+308    0.000000e+00    0.000000e+00
3 BLR_model_Inc                  0.000000   1.000000    2    0  -1.797693e+308    0.000000e+00    0.000000e+00

Afterwards, pass this new prior file to BRAINS as

mpiexec -n 6 ./brains param -l data/new_prior.txt

BRAINS will read in the prior ranges and use them for MCMC sampling.