Description Usage Arguments Author(s) See Also Examples
Makes four panel plot showing trace plots, moving average, autocorrelations, and densities for chosen parameters from MCMC output.
1 2 3 4 5 6 | mcmc.out(directory = "c:/mydirectory/", run = "mymodel/",
file = "keyposteriors.csv", namefile = "postplotnames.sso",
names = FALSE, headernames = TRUE, numparams = 1, closeall = TRUE,
burn = 0, thin = 1, scatter = FALSE, surface = FALSE, surf1 = 1,
surf2 = 2, stats = FALSE, plots = TRUE, header = TRUE, sep = ",",
print = FALSE, new = T, colNames = NULL)
|
directory |
Directory where all results are located, one level above directory for particular run. |
run |
Directory with files from a particular run. |
file |
File containing posterior samples for key parameters. This could
be written by the function |
namefile |
The (optional) file name of the dimension and names of posteriors. |
names |
Read in names file (T) or use generic naming (F). |
headernames |
Use the names in the header of |
numparams |
The number of parameters to analyze. |
closeall |
By default close all open devices. |
burn |
Optional burn-in value to apply on top of the option in the
starter file and |
thin |
Optional thinning value to apply on top of the option in the
starter file, in the |
scatter |
Can add a scatter-plot of all params at end, default is none. |
surface |
Add a surface plot of 2-way correlations. |
surf1 |
The first parameter for the surface plot. |
surf2 |
The second parameter for the surface plot. |
stats |
Print stats if desired. |
plots |
Show plots or not. |
header |
Data file with header? |
sep |
Separator for data file passed to the |
print |
Send to screen unless asked to print. |
new |
Logical whether or not to open a new plot window before plotting |
colNames |
Specific names of the |
Ian Stewart, Allan Hicks (modifications)
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
mcmc.df <- SSgetMCMC(dir="mcmcRun", writecsv=T,
keystrings = c("NatM", "R0", "steep", "Q_extraSD"),
nuisancestrings = c("Objective_function", "SPB_", "InitAge", "RecrDev"))
mcmc.out("mcmcRun",run="",numparams=4,closeall=F)
#Or for more control
par(mar=c(5,3.5,0,0.5),oma=c(0,2.5,0.2,0))
mcmc.out("mcmcRun",run="",numparams=1,closeall=F,new=F,colNames=c("NatM_p_1_Fem_GP_1"))
mtext("M (natural mortality)",side=2,outer=T,line=1.5,cex=1.1)
## End(Not run)
|
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