Remove reliance on the stats toolbox and simplify install procedure.

README.md

@@ -28,8 +28,9 @@ A: Most modifications can be done using the function handles. See the function h
 
 ## Included functions
 - notBoxPlot.m - generates plots as shown in screenshot
-- SEM_calc.m - calculate standard error of the mean. Provided as a separate function file so that it can be used for other purposes.
-- tInterval_calc.m - calculate a t-interval. For small sample sizes, the t-interval is larger than the SEM. Provided as a separate function file so that it can be used for other purposes.
+- NBP.SEM_calc.m - calculate standard error of the mean. Provided as a separate function file so that it can be used for other purposes.
+- NBP.tInterval_calc.m - calculate a t-interval. For small sample sizes, the t-interval is larger than the SEM. Provided as a separate function file so that it can be used for other purposes.
+- NBP.example - makes a nice example plot
 
-## Note
-The MATLAB statistics toolbox is not required if you install the nantoolbox from here: http://pub.ist.ac.at/~schloegl/matlab/NaN/ Otherwise you will need the statistics toolbox for nan-handling.
+## Installation
+Add the ``code`` directory to your MATLAB path. Does not rely on any toolboxes. 

code/plotting/NBP_example.m → code/+NBP/example.m

@@ -1,8 +1,14 @@
-function NBP_example
+function example
 % Pretty example use of notBoxPlot
 
-clf 
-set(gcf,'PaperPosition',[0,0,12,9]) %Just to make save to disk consistent
+disp('Running example')
+
+hFig=figure(1984);
+
+set(hFig,...
+	'Name','notBoxPlot example',...
+	'PaperPosition',[0,0,12,9]) %Just to make save to disk consistent)
+clf
 
 W=0.45; %image width
 

code/plotting/notBoxPlot.m → code/notBoxPlot.m

@@ -138,7 +138,7 @@
 %
 % Rob Campbell - August 2016
 %
-% Also see: boxplot, NBP_example
+% Also see: boxplot, NBP.example
 
 
 
@@ -188,7 +188,7 @@
 
     %TODO: the following will be removed, along with other references to legacy calling, in the next release
     varargin={'jitter',jitter,'style',style,'interval','SEM'}; %define varargin so we feed the new-form inputs to the recursive call, below.
-    intervalFun = @SEM_calc; 
+    intervalFun = @NBP.SEM_calc; 
     interval= 'SEM';
     markMedian = false;
 end
@@ -219,9 +219,9 @@
     %Set interval function
     switch interval
         case 'SEM'
-            intervalFun = @SEM_calc;
+            intervalFun = @NBP.SEM_calc;
         case 'tInterval'
-            intervalFun = @tInterval_calc;
+            intervalFun = @NBP.tInterval_calc;
         otherwise
             error('Interval %s is unknown',interval)
     end
@@ -325,10 +325,10 @@
 function [h,statsOut]=myPlotter(X,Y)
 
  SEM=intervalFun(Y); %Supplied external function
- SD=nanstd(Y);  %Requires the stats toolbox 
- mu=nanmean(Y); %Requires the stats toolbox 
+ SD=std(Y,'omitnan');  %Requires the stats toolbox 
+ mu=mean(Y,'omitnan'); %Requires the stats toolbox 
  if markMedian
-    med = nanmedian(Y);
+    med = median(Y,'omitnan');
  end
 
 

tests/core_tests.m

@@ -107,8 +107,8 @@ function checkInputParameters(testCase)
 			h=notBoxPlot(y,x,'style','line','markMedian',true);
 			testCase.verifyTrue(isfield(h,'med'))
 
-			clf 
-			NBP_example
+			%Check that the example runs
+			NBP.example
 
  			close(gcf)
 		end