/
sas_two_way_anova_with_grouping.m
146 lines (128 loc) · 5.17 KB
/
sas_two_way_anova_with_grouping.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
function out = sas_two_way_anova_with_grouping(varargin)
% Parse params
p = inputParser;
addOptional(p,'excel_file_string','');
addOptional(p,'excel_sheet','Sheet1');
addOptional(p,'factor_1','');
addOptional(p,'factor_2','');
addOptional(p,'grouping','tag');
addOptional(p,'test_variable','');
addOptional(p,'results_file_string','');
addOptional(p,'results_type','html');
addOptional(p,'treat_f2_numbers_as_strings',1);
addOptional(p,'f2_numbers_as_strings_decimal_places',8);
addOptional(p,'calling_path_string','');
addOptional(p,'tidy_low_concentrations_in_SAS',0);
parse(p,varargin{:});
% Test type
test_type = 'two_way_with_grouping';
% Code
% Deduce the calling function to help with paths
% Deduce the calling function to help with paths
if (isempty(p.Results.calling_path_string))
st=dbstack('-completenames');
calling_function=st(2).file;
calling_path_string=fileparts(calling_function);
else
calling_path_string = p.Results.calling_path_string;
end
% Code
out = run_sas_model( ...
'excel_file_string',p.Results.excel_file_string, ...
'excel_sheet',p.Results.excel_sheet, ...
'test_type',test_type, ...
'factor_1',p.Results.factor_1, ...
'factor_2',p.Results.factor_2, ...
'grouping',p.Results.grouping, ...
'test_variable',p.Results.test_variable, ...
'results_file_string',p.Results.results_file_string, ...
'results_type',p.Results.results_type, ...
'calling_path_string',calling_path_string);
if (p.Results.tidy_low_concentrations_in_SAS)
tidy_low_concentrations_in_SAS_output( ...
sprintf('%s.%s', ...
p.Results.results_file_string, ...
p.Results.results_type));
end
% Scrape html for p values
if (strcmp(p.Results.results_type,'html'))
% First get main effects
tag_string = 'Type III Tests of Fixed Effects';
table_strings = pull_table_strings_from_html( ...
out.results_file_string,tag_string,21);
out.p_table.tests{1}=table_strings{7};
out.p_table.p(1)=convert_p_string_to_number(table_strings{11});
out.p_table.tests{2}=table_strings{12};
out.p_table.p(2)=convert_p_string_to_number(table_strings{16});
out.p_table.tests{3}=table_strings{17};
out.p_table.p(3)=convert_p_string_to_number(table_strings{21});
% Pull post-hoc tests
% First look for factor_1 and factor_2 entries
d = readtable(p.Results.excel_file_string, ...
'Sheet', p.Results.excel_sheet);
% d = read_structure_from_excel( ...
% 'filename',p.Results.excel_file_string, ...
% 'sheet',p.Results.excel_sheet, ...
% 'debug_mode',1);
f1_strings = unique(d.(p.Results.factor_1))
f2_strings = unique(d.(p.Results.factor_2));
if (p.Results.treat_f2_numbers_as_strings)
if (isnumeric(f2_strings))
for i=1:numel(f2_strings)
switch f2_strings(i)
case 1e-8
temp{i}='1E-8';
case 1e-7
temp{i}='1E-7';
case 1e-6
temp{i}='1E-6';
case 1e-5
temp{i}='0.00001';
case 5e-5
temp{i}='0.00005';
otherwise
format_string = sprintf('%%.%.0ff', ...
p.Results.f2_numbers_as_strings_decimal_places);
temp{i}=sprintf(format_string,f2_strings(i));
end
end
f2_strings = temp
end
end
counter=numel(out.p_table.tests);
for f1=1:numel(f1_strings)
tag_string = sprintf('%s %s',p.Results.factor_1,f1_strings{f1});
temp_strings = pull_table_strings_from_html( ...
out.results_file_string,tag_string, ...
[8 nchoosek(numel(f2_strings),2)]);
for f2=1:nchoosek(numel(f2_strings),2)
counter=counter+1;
out.p_table.tests{counter} = sprintf('%s %s %s %s', ...
p.Results.factor_1,f1_strings{f1}, ...
temp_strings{f2,1},temp_strings{f2,2});
out.p_table.p(counter) = convert_p_string_to_number( ...
temp_strings{f2,8});
end
end
counter=numel(out.p_table.tests);
for f2=1:numel(f2_strings)
tag_string = sprintf('%s %s',p.Results.factor_2,f2_strings{f2});
temp_strings = pull_table_strings_from_html( ...
out.results_file_string,tag_string, ...
[8 nchoosek(numel(f1_strings),2)]);
for f1=1:nchoosek(numel(f1_strings),2)
counter=counter+1;
out.p_table.tests{counter} = sprintf('%s %s %s %s', ...
p.Results.factor_2,f2_strings{f2}, ...
temp_strings{f1,1},temp_strings{f1,2});
out.p_table.p(counter) = convert_p_string_to_number( ...
temp_strings{f1,8});
end
end
% Transpose structure
out.p_table.tests = out.p_table.tests';
out.p_table.p = out.p_table.p';
out.p_table = struct2table(out.p_table);
out.f1_strings = f1_strings;
out.f2_strings = f2_strings;
end