function mean_and_error_matrix=analyze_and_plot_mean_responses(beflive,aflive,critz,array_of_values,casecolor,x_offset,figaddon)
%description: takes uploaded psc values from pscmat or charge values from careful charge calculator, finds the mean and confidence interval before and after induction, plots the mean and error bar in the style instructed
%called by: analyze_across_sd_stdp_expts
%calls: agresti_coull_binomial_confidence_interval, generalized_rung_plotter or double_errorbar_plotter, standard_err
%notes:
%code confirmed date:

do_rungs_plot_not_double_errobar_plot=0;
use_first_val_only=1;
    strip_zeros_from_group_psccharge_data=1;    %only applies if ~use_first_value_only

if use_first_val_only   %only the first value, value_o, is considered from each trial
    preinduction_criteria=critz(1,beflive);postinduction_criteria=critz(1,aflive);
	values_antes=array_of_values(1,beflive);values_despues=array_of_values(1,aflive);
	values_succ_antes=values_antes(find(preinduction_criteria));values_succ_despues=values_despues(find(postinduction_criteria));
	values_fail_antes=values_antes(find(~preinduction_criteria));;values_fail_despues=values_despues(find(~postinduction_criteria));
    
	%proportion of successes of event_o with binomial confidence interval
	numsuccantes=length(values_succ_antes);      numtrialsantes=length(beflive);
	numsuccdespues=length(values_succ_despues);     numtrialsdespues=length(aflive);
	succpropantes=numsuccantes/numtrialsantes;succpropdespues=numsuccdespues/numtrialsdespues;
	[upperlimbefore,lowerlimbefore]=agresti_coull_binomial_confidence_interval(numsuccantes,numtrialsantes);
	[upperlimafter,lowerlimafter]=agresti_coull_binomial_confidence_interval(numsuccdespues,numtrialsdespues);

else        %modification oct 5 2007 to use pot of all trials and reliability rather than pr_o
	num_APs=size(critz,1)
    successes_per_trial=sum(critz);
    reliability=successes_per_trial/num_APs;
	mean_values=sum(array_of_values)/num_APs;
    array_for_potency=array_of_values;
	array_for_potency(find(~critz))=0;
	potency_numerator=sum(array_for_potency);
	mean_potency=potency_numerator./successes_per_trial;
	mean_potency(isnan(mean_potency))=0;
	    %mean_potency=replace_zeros(mean_potency);
    array_for_failure=array_of_values;
    array_for_failure(find(critz))=0;
    failure_numerator=sum(array_for_failure);
    mean_failure=failure_numerator./(num_APs-successes_per_trial);
    mean_failure(isnan(mean_failure))=0;
     
    values_antes=mean_values(beflive);values_despues=mean_values(aflive);    
    values_succ_antes=mean_potency(beflive);values_succ_despues=mean_potency(aflive);
    values_fail_antes=mean_failure(beflive);values_fail_despues=mean_failure(aflive);
    if strip_zeros_from_group_psccharge_data
        values_succ_antes(find(~values_succ_antes))=[];values_succ_despues(find(~values_succ_despues))=[];
        values_fail_antes(find(~values_fail_antes))=[];values_fail_despues(find(~values_fail_despues))=[];
    end
        
    succpropantes=mean(reliability(beflive));
    upperlimbefore=succpropantes+standard_err(reliability(beflive));
    lowerlimbefore=succpropantes-standard_err(reliability(beflive));
    succpropdespues=mean(reliability(aflive));
    upperlimafter=succpropdespues+standard_err(reliability(aflive));
    lowerlimafter=succpropdespues-standard_err(reliability(aflive));
end

%mean of all value_o (success and failure) with SEM
meanbefore=mean(values_antes);stdbefore=std(values_antes);sembefore=stdbefore/sqrt(length(values_antes));
meanafter=mean(values_despues);stdafter=std(values_despues);semafter=stdafter/sqrt(length(values_despues));

%mean of value_o success only with SEM
meansuccbefore=mean(values_succ_antes);stdsuccbefore=std(values_succ_antes);semsuccbefore=stdsuccbefore/sqrt(length(values_succ_antes));
meansuccafter=mean(values_succ_despues);stdsuccafter=std(values_succ_despues);semsuccafter=stdsuccafter/sqrt(length(values_succ_despues));

%mean of value_o failure only with SEM
meanfailbefore=mean(values_fail_antes);stdfailbefore=std(values_fail_antes);semfailbefore=stdfailbefore/sqrt(length(values_fail_antes));
meanfailafter=mean(values_fail_despues);stdfailafter=std(values_fail_despues);semfailafter=stdfailafter/sqrt(length(values_fail_despues));

figure(1+figaddon),hold on, title('value_o')
if do_rungs_plot_not_double_errobar_plot
    subplot(3,3,[2 5 8]),set(gcf,'position',[145   120   278   707]);generalized_rung_plotter([meanbefore meanafter],[meanbefore+sembefore meanafter+semafter],[meanbefore-sembefore meanafter-semafter],casecolor,x_offset)
else
    double_errorbar_plotter_dwn([meanbefore,sembefore,meanafter,semafter],casecolor)
end

figure(2+figaddon),hold on, title('value_o, success trials')
if do_rungs_plot_not_double_errobar_plot
    subplot(3,3,[2 5 8]),set(gcf,'position',[445   120   278   707]);generalized_rung_plotter([meansuccbefore meansuccafter],[meansuccbefore+semsuccbefore meansuccafter+semsuccafter],[meansuccbefore-semsuccbefore meansuccafter-semsuccafter],casecolor,x_offset)
else
    double_errorbar_plotter_dwn([meansuccbefore,semsuccbefore,meansuccafter,semsuccafter],casecolor)
end

figure(3+figaddon),hold on, title('proportion successes')
if do_rungs_plot_not_double_errobar_plot
    subplot(3,3,[2 5 8]),set(gcf,'position',[745   120   278   707]),generalized_rung_plotter([succpropantes succpropdespues],[upperlimbefore upperlimafter],[lowerlimbefore lowerlimafter],casecolor,x_offset);
else
    double_errorbar_plotter_dwn([succpropantes,upperlimbefore,lowerlimbefore,succpropdespues,upperlimafter,lowerlimafter],casecolor)
end
    
figure(4+figaddon),hold on, title('value_o, failure trials')
if do_rungs_plot_not_double_errobar_plot
    subplot(3,3,[2 5 8]),set(gcf,'position',[1045   120   278   707]),generalized_rung_plotter([meanfailbefore meanfailafter],[meanfailbefore+semfailbefore meanfailafter+semfailafter],[meanfailbefore-semfailbefore meanfailafter-semfailafter],casecolor,x_offset)
else
    double_errorbar_plotter_dwn([meanfailbefore,semfailbefore,meanfailafter,semfailafter],casecolor)
end

mean_and_error_matrix=[meanbefore,sembefore,meanafter,semafter,meansuccbefore,semsuccbefore,meansuccafter,semsuccafter,succpropantes,upperlimbefore,lowerlimbefore,succpropdespues,upperlimafter,lowerlimafter,meanfailbefore,semfailbefore,meanfailafter,semfailafter]';