forked from LIMO-EEG-Toolbox/limo_tools
-
Notifications
You must be signed in to change notification settings - Fork 1
/
limo_compute_H0.m
157 lines (140 loc) · 6.37 KB
/
limo_compute_H0.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
function varargout=limo_compute_H0(varargin)
% this function allows comnputing the null distribution of any of the
% LIMO EEG 2nd level statistical tests using bootstrap
%
% FORMAT [H0_data,boot_table] = limo_compute_H0(0,data,nboot,test);
% status = limo_compute_H0(type,data,label,nboot)
%
% -------------------------------------------------------------------------
% [H0_data,boot_table] = limo_compute_H0(0,data,nboot,test)
% the generic case to compute H0 using limo stat functions
%
% INPUTS: 0 stands for type = 0 and indicates the generic case
% data this is a 4D or 3D matrix of data
% nboot is the number of boostrap to use (recommended at least 800)
% test is one of limo statistical test: 'limo_trimci' 'limo_yuen'
% 'limo_yuend' 'limo_glm'
% 'limo_'
%
% OUTPUTS: H0_data is the matrix of statistical values (t/F and p) needed
% to do a correction for multiple comparisons
% boot_table is the resampling table used
%
% -------------------------------------------------------------------------
% status = limo_compute_H0(type,data,label,boot_table)
% this is the format used by LIMO EEG, and in this case it creates data on
% the drive using dedicated names and format - see limo_random_robust for
% details of inputs and outputs
%
% -------------------------------------------------------------------------
% see also limo_create_boot_table
%
%
type = varargin(1);
% get the data and boot_table
if type == 0
test = varargin(end);
if strcmpi(test,'limo_yuen_ttest') || strcmpi(test,'limo_yuend_ttest')
data1 = varagin(2);
data2 = varagin(3);
nboot = varargin(4);
else
data = varagin(2);
nboot = varargin(3);
end
elseif type == 1 || type > 3
data = varagin(2);
nboot = varargin(3);
else
data1 = varagin(2);
data2 = varagin(3);
nboot = varargin(4);
end
clear varargin
% -------------------------------------------------------------------------
switch type
case {1}
% one sample t-test
% -----------------
bootex = 1;
boot_name = sprintf('H0_one_sample_ttest_parameter_%g',parameter);
if exist(['H0', filesep, boot_name, '.mat'], 'file')
answer = questdlg('a boostrap file already exist - overwrite?','data check','Yes','No','Yes');
if strcmp(answer,'Yes');
bootex = 1;
else
bootex = 0;
end
end
if bootex == 1;
mkdir H0
% create a boot one_sample file to store data under H0 and H1
H0_one_sample = NaN(size(data,1), size(data,2),2,nboot); % stores T and p values for each boot under H0
% create centered data to estimate H0
centered_data = data - repmat(limo_trimmed_mean(data),[1 1 size(data,3)]);
% centered_data = data - repmat(nanmean(data,3),[1 1 size(data,3)]);
% get boot table
disp('making boot table ...')
boot_table = limo_create_boot_table(data,nboot);
save(['H0', filesep, 'boot_table'], 'boot_table')
% get results under H0
for electrode = 1:size(data,1)
fprintf('bootstrap: electrode %g parameter %g \n',electrode,parameter);
tmp = centered_data(electrode,:,:); Y = tmp(1,:,find(~isnan(tmp(1,1,:))));
if exist('parfor','file') ~=0
parfor b=1:nboot
[t{b},~,~,~,p{b},~,~]=limo_trimci(Y(1,:,boot_table{electrode}(:,b)));
end
for b=1:nboot
H0_one_sample(electrode,:,1,b) = t{b};
H0_one_sample(electrode,:,2,b) = p{b};
end
else
for b=1:nboot
[H0_one_sample(electrode,:,1,b),tmdata,trimci,se,H0_one_sample(electrode,:,2,b),tcrit,df]=limo_trimci(Y(1,:,boot_table{electrode}(:,b)));
% [m,dfe,ci,sd,n,H0_one_sample(electrode,:,1,b),H0_one_sample(electrode,:,2,b)] = limo_ttest(1,Y(1,:,boot_table{electrode}(:,b)),0,5/100);
end
end
clear tmp Y
end % closes for electrode
if strcmp(LIMO.Analysis,'Time-Frequency') || strcmp(LIMO.Analysis,'ITC')
H0_one_sample = limo_tf_5d_reshape(H0_one_sample);
end
save (['H0', filesep, boot_name],'H0_one_sample','-v7.3');
end
% ----------------------------------------------------------------------
% ----------------------------------------------------------------------
% THIS IS TYPE 0 - GENRERIC CASE
% ----------------------------------------------------------------------
% ----------------------------------------------------------------------
case {0}
% one sample t-test
% -----------------
if strcmpi(test,'limo_trimci')
reshape = 0;
if numel(size(data)) == 4
reshape = 1; [elect,freq,time,obs]=size(data);
data = limo_tf_4d_reshape(data,[elect,freq*time,obs]);
end
H0 = NaN(size(data,1), size(data,2),2,nboot); % stores T and p values for each boot under H0
centered_data = data - repmat(limo_trimmed_mean(data),[1 1 size(data,3)]);
disp('making boot table ...'); boot_table = limo_create_boot_table(data,nboot);
for electrode = 1:size(data,1)
fprintf('bootstrap: electrode %g parameter %g \n',electrode,parameter);
tmp = centered_data(electrode,:,:); Y = tmp(1,:,find(~isnan(tmp(1,1,:))));
parfor b=1:nboot
[t{b},~,~,~,p{b},~,~]=limo_trimci(Y(1,:,boot_table{electrode}(:,b)));
end
for b=1:nboot
H0(electrode,:,1,b) = t{b};
H0(electrode,:,2,b) = p{b};
end
clear tmp Y
end % closes for electrode
if reshape == 1
H0 = limo_tf_5d_reshape(H0,[elect,freq,time,nboot]);
end
end
clear data; varargout{2} = boot_table; cleaer boot_table
varargout{1} = H0; clear H0;
end