From b10cde66e13785d5cdaf6b64faef4bea3bc3bd97 Mon Sep 17 00:00:00 2001
From: Wjgatt <williamjgatt@gmail.com>
Date: Thu, 16 Mar 2023 19:17:32 +0100
Subject: [PATCH] Variable number of parameter MCMC plots
This change allows the user to change the number of parameters for which the MCMC convergence diagnostics are shown. The user needs to set a value for options_.nparMCMCdisp for an aribitrary number of parameters to be shown, but defaulting to 3 if no input is supplied. This change also defaults to 3 if the user for some reason enters the value 0, as otherwise the code gets stuck in an infinite loop that keeps on opening new figure objects.
---
.../convergence_diagnostics/McMCDiagnostics.m | 25 ++++++++++++++++---
1 file changed, 22 insertions(+), 3 deletions(-)
diff --git a/matlab/convergence_diagnostics/McMCDiagnostics.m b/matlab/convergence_diagnostics/McMCDiagnostics.m
index 18887db3b4..20e906992f 100644
--- a/matlab/convergence_diagnostics/McMCDiagnostics.m
+++ b/matlab/convergence_diagnostics/McMCDiagnostics.m
@@ -49,6 +49,19 @@ MAX_nruns = ceil(options_.MaxNumberOfBytes/(npar+2)/8);
load_last_mh_history_file(MetropolisFolder, ModelName);
NumberOfMcFilesPerBlock = record.LastFileNumber;
+% Check whether umber of parameters displayed in MCMC convergence
+% diagnostics figures has been declared. If not, default to 3.
+if isfield(options_,'nparMCMCdisp')
+ if options_.nparMCMCdisp == 0
+ warning('Cannot plot 0 variables, reseting options_.nparMCMCdisp to 3 [default]');
+ options_.nparMCMCdisp = 3;
+ end
+ npardisp = options_.nparMCMCdisp;
+else
+ npardisp = 3;
+end
+%------------------
+
% Check that the declared number of blocks is consistent with informations saved in mh-history files.
if ~isequal(nblck,record.Nblck)
disp(['Estimation::mcmc::diagnostics: The number of MCMC chains you declared (' num2str(nblck) ') is inconsistent with the information available in the mh-history files (' num2str(record.Nblck) ' chains)!'])
@@ -284,12 +297,14 @@ end
UDIAG(:,[2 4 6],:) = UDIAG(:,[2 4 6],:)/nblck;
skipline()
clear pmet temp moyenne CSUP CINF csup cinf n linea iter tmp;
-pages = floor(npar/3);
+% pages = floor(npar/3);
+pages = floor(npar/npardisp); % changed from 3 to npardisp
k = 0;
for i = 1:pages
h=dyn_figure(options_.nodisplay,'Name','MCMC univariate convergence diagnostic (Brooks and Gelman,1998)');
boxplot = 1;
- for j = 1:3 % Loop over parameters
+% for j = 1:3 % Loop over parameters
+ for j = 1:npardisp % Loop over parameters %npardisp instead of 3
k = k+1;
[nam,namtex] = get_the_name(k,TeX,M_,estim_params_,options_);
for crit = 1:3% Loop over criteria
@@ -306,7 +321,8 @@ for i = 1:pages
plt2 = UDIAG(:,6,k);
namnam = [nam , ' (m3)'];
end
- subplot(3,3,boxplot);
+% subplot(3,3,boxplot);
+ subplot(npardisp,3,boxplot); %Added more rows to display more variables
plot(xx,plt1,'-b'); % Pooled
hold on;
plot(xx,plt2,'-r'); % Within (mean)
@@ -342,6 +358,9 @@ if reste
elseif reste == 2
nr = 2;
nc = 3;
+ else % Conditional for additional rows (variables) when not towards the end of the loop
+ nr = npardisp;
+ nc = 3;
end
h = dyn_figure(options_.nodisplay,'Name','MCMC univariate convergence diagnostic (Brooks and Gelman, 1998)');
boxplot = 1;
--
GitLab