From 730de861fd12cf0824594939c0df97db5ff15a0d Mon Sep 17 00:00:00 2001 From: Hyatt Moore IV Date: Tue, 18 Feb 2014 10:33:17 -0800 Subject: [PATCH 1/5] miscellaneous updates --- sample_data.xls | Bin 182272 -> 182272 bytes softROC_settings.plist | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/sample_data.xls b/sample_data.xls index b090f61a8243ff6554a1a173732103c6ada38342..21c0c2a896869ee631e86d48528c1d4bd4f4f370 100755 GIT binary patch delta 30 mcmZpez}+x`dqWNjJ7>tkS=V&VHy5+C7qc*KFJ@utJq!S@;R`?j delta 30 mcmZpez}+x`dqWNjyI$);rkQ+an~Pc6i&+@A7qc++9tHrVq6(n^ diff --git a/softROC_settings.plist b/softROC_settings.plist index 0b21ccb..f6af176 100644 --- a/softROC_settings.plist +++ b/softROC_settings.plist @@ -31,7 +31,7 @@ plot_se_vs_sp 1.000000 current_pathname - /Users/hyattmoore/Google Drive/work/softROC requests/ + /Users/hyatt4/Google Drive/work/softROC requests/ pfile softROC_settings.plist log_filename From 089cb8e16a08c91a87236595b3f903c40a4c98f3 Mon Sep 17 00:00:00 2001 From: Hyatt Moore IV Date: Tue, 18 Feb 2014 10:47:52 -0800 Subject: [PATCH 2/5] update warning message when file does not have a gold standard column File must have at least one column of data which contains two, and only two unique values that can be utilized as the gold standard. --- softROC.m | 9 +++++++-- softROC_settings.plist | 2 +- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/softROC.m b/softROC.m index 7669782..10c2371 100644 --- a/softROC.m +++ b/softROC.m @@ -314,8 +314,13 @@ function push_select_file_Callback(hObject, eventdata, handles) catch ME disp(ME.message); - disp('There was an error loading the file. Verify its integrity and Excel format.'); - disp('If error invovles ''biffparse'' try saving the XLS file using Microsoft Excel 95 format.'); + if(isempty(handles.controls.indices)) + disp('There was an error loading the file. At least one column must contain two, and only two unique indices to represent the gold standard evaluation'); + else + disp('There was an error loading the file. Verify its integrity and Excel format.'); + disp('If error invovles ''biffparse'' try saving the XLS file using Microsoft Excel 95 format.'); + + end set(handles.text_filename,'string','The file could not be loaded - please verify its format','enable','inactive'); end diff --git a/softROC_settings.plist b/softROC_settings.plist index f6af176..f65d01c 100644 --- a/softROC_settings.plist +++ b/softROC_settings.plist @@ -31,7 +31,7 @@ plot_se_vs_sp 1.000000 current_pathname - /Users/hyatt4/Google Drive/work/softROC requests/ + /Users/hyatt4/git/softroc/ pfile softROC_settings.plist log_filename From 228f58d3438a9a199f80c708680909bdfc01531f Mon Sep 17 00:00:00 2001 From: Hyatt Moore IV Date: Wed, 26 Feb 2014 17:17:28 -0800 Subject: [PATCH 3/5] Prefilter categories and recognize case when no gold standard exists --- softROC.m | 26 ++++++++++++++++++++++++++ softROC_file_log.txt | 8 ++++++++ softROC_settings.plist | 6 +++--- 3 files changed, 37 insertions(+), 3 deletions(-) diff --git a/softROC.m b/softROC.m index 10c2371..b76408b 100644 --- a/softROC.m +++ b/softROC.m @@ -241,8 +241,34 @@ function push_select_file_Callback(hObject, eventdata, handles) try [number,txt,raw]=xlsread(full_filename,1,'','basic'); + + settings = handles.user.settings; + + + %exclude bad rows on launch? + if(settings.exclude_number_data) + numRows = size(raw,1)-1; + numCols = size(raw,2); + bad_rows = false(numRows,1); + for k=1:numCols + data = raw(2:end,k); + if(iscellstr(data)) + + else + bad_rows = bad_rows | feval(settings.binop_number,cell2mat(data),settings.exclude_number_value); + end + + end + + bad_rows = [false;bad_rows]; + raw(bad_rows,:) = []; + end + handles.user.filename = filename; + + + numCols = size(raw,2); unique_ind = false(1,numCols); unique_vals = cell(1,numCols); diff --git a/softROC_file_log.txt b/softROC_file_log.txt index 0b91a03..af63746 100644 --- a/softROC_file_log.txt +++ b/softROC_file_log.txt @@ -8,3 +8,11 @@ Gold Standard = Dx Positivity Value = 1.00 HCRT_5_6_-_6_8 >= [1.00 : 100.00] AND HCRT_8_7_-_9_9 >= [1.00 : 100.00] + +18-Feb-2014 11:53:09 /Users/hyatt4/Google Drive/work/softROC requests/result - alberto.txt + Gold Standard = IsIt0 Positivity Value = 1.00 + Prediction < [0.00 : 20000.00] + +18-Feb-2014 12:07:58 /Users/hyatt4/Google Drive/work/softROC requests/result - alberto_strong vs weak or not.txt + Gold Standard = IsIt2 Positivity Value = 1.00 + Prediction < [0.00 : 20000.00] diff --git a/softROC_settings.plist b/softROC_settings.plist index f65d01c..48e3609 100644 --- a/softROC_settings.plist +++ b/softROC_settings.plist @@ -9,11 +9,11 @@ se_vs_sp_alpha 0.500000 plot_option - Optimal ROC results + All ROC results decimal_places 2.000000 exclude_number_data - 1.000000 + 0.000000 binop_number lt exclude_number_value @@ -31,7 +31,7 @@ plot_se_vs_sp 1.000000 current_pathname - /Users/hyatt4/git/softroc/ + /Users/hyatt4/Google Drive/work/softROC requests/ pfile softROC_settings.plist log_filename From 78669098577c3dd1b7cb3b124f2761240e1c14c1 Mon Sep 17 00:00:00 2001 From: informaton Date: Sat, 13 Sep 2014 03:15:45 -0700 Subject: [PATCH 4/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 697578c..a813f34 100644 --- a/README.md +++ b/README.md @@ -9,4 +9,4 @@ Released under the Creative Commons License 3.0 Attribution (CC BY 3.0) http://creativecommons.org/licenses/by/3.0/ Attribution text: -softROC program initially written by Hyatt Moore, IV \ No newline at end of file +Moore IV, Hyatt E., Olivier Andlauer, Noah Simon, and Emmanuel Mignot. "Exploring medical diagnostic performance using interactive, multi-parameter sourced receiver operating characteristic scatter plots." Computers in biology and medicine 47 (2014): 120-129. From 46551c15faa196a2df2dfb9e22670b5e9975e169 Mon Sep 17 00:00:00 2001 From: informaton Date: Sat, 13 Sep 2014 03:16:09 -0700 Subject: [PATCH 5/5] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index a813f34..ddac7fc 100644 --- a/README.md +++ b/README.md @@ -9,4 +9,5 @@ Released under the Creative Commons License 3.0 Attribution (CC BY 3.0) http://creativecommons.org/licenses/by/3.0/ Attribution text: + Moore IV, Hyatt E., Olivier Andlauer, Noah Simon, and Emmanuel Mignot. "Exploring medical diagnostic performance using interactive, multi-parameter sourced receiver operating characteristic scatter plots." Computers in biology and medicine 47 (2014): 120-129.