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name: <unnamed>
log: /Users/RJCC/Documents/rjcc3/pwin/pwin.smcl
log type: smcl
opened on: 3 Mar 2016, 08:41:16
. * insheet using dddd.csv, delimiter(";") clear
. import excel "`dirname'/pwin_lungca.xlsx", sheet("pce_pri") firstrow case(lower) clear
. * Hypothesis: PCE window had better survival if lung ca=0
. * Variables:
. * id age dob d_adm d_mbd F die_mbd op d_op lca lungca die2 d_last dxi
. * Plans:
. * Baseline (overall, lungca=0,1): age sex(F) dxi
. * Outcome die_mbd die2 los fu_die
. * K-M curve (die_mbd, los) for lungca=0 vs 1, log-rank test
. * K-M curve (die2, fu_die) for lungca=0 vs 1, log-rank test
.
. co lungca age
Summary for variables: age
by categories of: lungca (lungca)
lungca | N mean sd p50 iqr min max
-------+----------------------------------------------------------------------
N | 22 59.97727 10.07515 60.875 14.91667 43.16667 77.08333
Y | 30 63.06944 13.50023 62.95833 15.83333 31.16667 86.5
-------+----------------------------------------------------------------------
Total | 52 61.76122 12.15784 62.45833 18.33333 31.16667 86.5
------------------------------------------------------------------------------
Two-sample Wilcoxon rank-sum (Mann-Whitney) test
lungca | obs rank sum expected
-------------+---------------------------------
N | 22 526 583
Y | 30 852 795
-------------+---------------------------------
combined | 52 1378 1378
unadjusted variance 2915.00
adjustment for ties -0.25
----------
adjusted variance 2914.75
Ho: age(lungca==N) = age(lungca==Y)
z = -1.056
Prob > |z| = 0.2911
. ca lungca f
+-------------------+
| Key |
|-------------------|
| frequency |
| row percentage |
| column percentage |
+-------------------+
| f
lungca | 0 1 | Total
-----------+----------------------+----------
N | 11 11 | 22
| 50.00 50.00 | 100.00
| 34.38 55.00 | 42.31
-----------+----------------------+----------
Y | 21 9 | 30
| 70.00 30.00 | 100.00
| 65.62 45.00 | 57.69
-----------+----------------------+----------
Total | 32 20 | 52
| 61.54 38.46 | 100.00
| 100.00 100.00 | 100.00
Fisher's exact = 0.162
1-sided Fisher's exact = 0.120
. forvalues i = 1(1)12 {
2. icd9 gen dx`i'a = dx`i', des
3. }
. list dx1a dx2a dx3a dx4a
+------------------------------------------------------------------------------------------------------------+
| dx1a dx2a dx3a dx4a |
|------------------------------------------------------------------------------------------------------------|
1. | mal neo middle lobe lung enlargement lymph nodes sciatica pleural effusion nos |
2. | cardiogenic shock mal neo upper lobe lung |
3. | mal neo nasopharynx nos pericardial disease nos secondary malig neo lung mal neo lymph-axilla/arm |
4. | mal neo upper lobe lung empyema w/o fistula pericardial disease nos acute kidney failure nos |
5. | secondary malig neo nec pericardial disease nos cardiogenic shock |
|------------------------------------------------------------------------------------------------------------|
6. | post-proc states nec hepatitis b carrier |
7. | mal neo soft tissue leg |
8. | second malig neo adrenal pericardial disease nos hypopotassemia |
9. | cardiogenic shock mal neo bronch/lung nos hypertension nos |
10. | shock nos pericardial disease nos chr airway obstruct nec cachexia |
|------------------------------------------------------------------------------------------------------------|
11. | mal neo lymph-axilla/arm second malig neo pleura pericardial disease nos cachexia |
12. | accidental op laceration ventricular flutter vocal paral unilat part mononeuritis arm nec |
13. | mal neo lower lobe lung secondary malig neo bone acute respiratry failure |
14. | pericardial disease nos obs chr bronc w(ac) exac pleural effusion nos esophageal reflux |
15. | malign neopl breast nos secondary malig neo bone secondary malig neo lung cachexia |
|------------------------------------------------------------------------------------------------------------|
16. | acute respiratry failure pneumonia, organism nos pleural effusion nos pericardial disease nos |
17. | mal neo cervix uteri nos secondary malig neo lung insomnia nos constipation* |
18. | secondary malig neo bone second malig neo liver secondary malig neo nec pericardial disease nos |
19. | mal neo lymph-head/neck pericardial disease nos pleural effusion nos |
20. | pleural effusion nos malig neopl stomach nos sec mal neo peritoneum hx of breast malignancy |
|------------------------------------------------------------------------------------------------------------|
21. | pleural effusion nos |
22. | pleural effusion nos react-oth vasc dev/graft mal neo lower lobe lung |
23. | secondary malig neo nec septicemia nos second malig neo pleura thrush |
24. | mal neo upper lobe lung second malig neo pleura chr airway obstruct nec allergic rhinitis nos |
25. | mal neo lymph-intrathor secondary malig neo nec pericardial disease nos pleural effusion nos |
|------------------------------------------------------------------------------------------------------------|
26. | mal neo lower lobe lung k. pneumoniae pneumonia secondary malig neo nec second malig neo pleura |
27. | pleural effusion nos chf nos atrial fibrillation mal neo esophagus nos |
28. | secondary malig neo nec dmii wo cmp nt st uncntr |
29. | myasthenia gravis# atrial fibrillation mononeuritis arm nec traum subcutan emphysema |
30. | sec mal neo brain/spine pericardial disease nos neurofibromatosis type i endocarditis nos |
|------------------------------------------------------------------------------------------------------------|
31. | pericardial disease nos pleural effus nec not tb# chr peptic ulcer w hem hyperpotassemia |
32. | secondary malig neo lung secondary malig neo bone pericardial disease nos |
33. | pleural effusion nos acute kidney failure nos renal & ureteral dis nos |
34. | pericardial disease nos |
35. | pleural effusion nos benign neo esophagus |
|------------------------------------------------------------------------------------------------------------|
36. | pericardial disease nos |
37. | radiotherapy encounter mal neo middle 3rd esoph pericardial disease nos pleural effusion nos |
38. | secondary malig neo lung pericardial disease nos pleural effusion nos pneumonia, organism nos |
39. | secondary malig neo nec secondary malig neo lung pericardial disease nos mal neo nasopharynx nos |
40. | mal neo cervix uteri nos mal neo lymph-head/neck mal neo lymph-inguin/leg pericardial disease nos |
|------------------------------------------------------------------------------------------------------------|
41. | secondary malig neo nec secondary malig neo bone asthma nos hx-oral/pharynx malg nec |
42. | pericardial disease nos pleural effusion nos |
43. | |
44. | benign neoplasm heart cirrhosis of liver nos ascites# pleural effusion nos |
45. | chf nos hyperlipidemia nec/nos hypertrophy of prostate# chr airway obstruct nec |
|------------------------------------------------------------------------------------------------------------|
46. | chronic sinusitis nos |
47. | mal neo lower lobe lung pericardial disease nos atrial fibrillation |
48. | asthma nos w (ac) exac mal neo bronch/lung nos |
49. | secondary malig neo bone pericardial disease nos |
50. | secondary malig neo nec secondary malig neo bone stomach ulcer nos vocal cord paralysis nos |
|------------------------------------------------------------------------------------------------------------|
51. | malignant neoplasm nos pericardial disease nos hypertension nos |
52. | pericardial disease nos pneumonia, organism nos mal neo upper lobe lung secondary malig neo bone |
+------------------------------------------------------------------------------------------------------------+
. list dx5a dx6a dx7a dx8a
+----------------------------------------------------------------------------------------------------------+
| dx5a dx6a dx7a dx8a |
|----------------------------------------------------------------------------------------------------------|
1. | dis plas protein met nec dis urea cycle metabol anemia nos dmii wo cmp nt st uncntr |
2. | |
3. | |
4. | oliguria & anuria other dsrders esophagus ulcer of esophagus# oth spf gstrt w/o hmrhg |
5. | |
|----------------------------------------------------------------------------------------------------------|
6. | |
7. | |
8. | |
9. | |
10. | dmii wo cmp nt st uncntr |
|----------------------------------------------------------------------------------------------------------|
11. | |
12. | |
13. | |
14. | |
15. | |
|----------------------------------------------------------------------------------------------------------|
16. | septicemia nos hyperosmolality hypopotassemia hypovolemia# |
17. | heart failure nos |
18. | |
19. | |
20. | |
|----------------------------------------------------------------------------------------------------------|
21. | |
22. | |
23. | |
24. | constipation* hypertension nos hepatitis b carrier |
25. | |
|----------------------------------------------------------------------------------------------------------|
26. | |
27. | |
28. | |
29. | |
30. | hepatitis b carrier |
|----------------------------------------------------------------------------------------------------------|
31. | hyposmolality |
32. | |
33. | |
34. | |
35. | |
|----------------------------------------------------------------------------------------------------------|
36. | |
37. | |
38. | |
39. | |
40. | gram-neg septicemia nec cardiomegaly anemia nos dis plas protein met nec |
|----------------------------------------------------------------------------------------------------------|
41. | |
42. | |
43. | |
44. | |
45. | mal neo lower lobe lung mal neo lymph-intrathor dmii wo cmp nt st uncntr secondary malig neo nec |
|----------------------------------------------------------------------------------------------------------|
46. | |
47. | |
48. | |
49. | |
50. | |
|----------------------------------------------------------------------------------------------------------|
51. | |
52. | secondary malig neo lung chf nos panhypopituitarism diabetes insipidus |
+----------------------------------------------------------------------------------------------------------+
. list dx9a dx10a dx11a dx12a
+-----------------------------------------------------------------------------------------------------------+
| dx9a dx10a dx11a dx12a |
|-----------------------------------------------------------------------------------------------------------|
1. | hypertrophy of prostate# diarrhea |
2. | |
3. | |
4. | vocal paral unilat part alcoh dep nec/nos-unspec |
5. | |
|-----------------------------------------------------------------------------------------------------------|
6. | |
7. | |
8. | |
9. | |
10. | |
|-----------------------------------------------------------------------------------------------------------|
11. | |
12. | |
13. | |
14. | |
15. | |
|-----------------------------------------------------------------------------------------------------------|
16. | obs chr bronc w(ac) exac constipation* |
17. | |
18. | |
19. | |
20. | |
|-----------------------------------------------------------------------------------------------------------|
21. | |
22. | |
23. | |
24. | |
25. | |
|-----------------------------------------------------------------------------------------------------------|
26. | |
27. | |
28. | |
29. | |
30. | |
|-----------------------------------------------------------------------------------------------------------|
31. | |
32. | |
33. | |
34. | |
35. | |
|-----------------------------------------------------------------------------------------------------------|
36. | |
37. | |
38. | |
39. | |
40. | pleural effusion nos |
|-----------------------------------------------------------------------------------------------------------|
41. | |
42. | |
43. | |
44. | |
45. | malig neo parotid hx of colonic malignancy |
|-----------------------------------------------------------------------------------------------------------|
46. | |
47. | |
48. | |
49. | |
50. | |
|-----------------------------------------------------------------------------------------------------------|
51. | |
52. | hypothyroidism nos endocrine/nerv neo nos corticoadrenal insuffic# dis plas protein met nec |
+-----------------------------------------------------------------------------------------------------------+
.
. ca lungca die_mbd
+-------------------+
| Key |
|-------------------|
| frequency |
| row percentage |
| column percentage |
+-------------------+
| die_mbd
lungca | 0 1 | Total
-----------+----------------------+----------
N | 19 3 | 22
| 86.36 13.64 | 100.00
| 44.19 33.33 | 42.31
-----------+----------------------+----------
Y | 24 6 | 30
| 80.00 20.00 | 100.00
| 55.81 66.67 | 57.69
-----------+----------------------+----------
Total | 43 9 | 52
| 82.69 17.31 | 100.00
| 100.00 100.00 | 100.00
Fisher's exact = 0.717
1-sided Fisher's exact = 0.415
. ca lungca die2
+-------------------+
| Key |
|-------------------|
| frequency |
| row percentage |
| column percentage |
+-------------------+
| die2
lungca | 0 1 | Total
-----------+----------------------+----------
N | 16 6 | 22
| 72.73 27.27 | 100.00
| 72.73 20.00 | 42.31
-----------+----------------------+----------
Y | 6 24 | 30
| 20.00 80.00 | 100.00
| 27.27 80.00 | 57.69
-----------+----------------------+----------
Total | 22 30 | 52
| 42.31 57.69 | 100.00
| 100.00 100.00 | 100.00
Fisher's exact = 0.000
1-sided Fisher's exact = 0.000
. co lungca los
Summary for variables: los
by categories of: lungca (lungca)
lungca | N mean sd p50 iqr min max
-------+----------------------------------------------------------------------
N | 22 10.95455 7.319103 8.5 10 1 27
Y | 30 13.93333 12.61617 10 8 2 65
-------+----------------------------------------------------------------------
Total | 52 12.67308 10.71323 10 8 1 65
------------------------------------------------------------------------------
Two-sample Wilcoxon rank-sum (Mann-Whitney) test
lungca | obs rank sum expected
-------------+---------------------------------
N | 22 535.5 583
Y | 30 842.5 795
-------------+---------------------------------
combined | 52 1378 1378
unadjusted variance 2915.00
adjustment for ties -13.19
----------
adjusted variance 2901.81
Ho: los(lungca==N) = los(lungca==Y)
z = -0.882
Prob > |z| = 0.3779
. co lungca fu_die
Summary for variables: fu_die
by categories of: lungca (lungca)
lungca | N mean sd p50 iqr min max
-------+----------------------------------------------------------------------
N | 22 1750.727 1527.314 1427.5 3102 3 4078
Y | 30 627.1 1086.225 83 549 2 3741
-------+----------------------------------------------------------------------
Total | 52 1102.481 1394.862 382 2224 2 4078
------------------------------------------------------------------------------
Two-sample Wilcoxon rank-sum (Mann-Whitney) test
lungca | obs rank sum expected
-------------+---------------------------------
N | 22 756 583
Y | 30 622 795
-------------+---------------------------------
combined | 52 1378 1378
unadjusted variance 2915.00
adjustment for ties -0.25
----------
adjusted variance 2914.75
Ho: fu_die(lungca==N) = fu_die(lungca==Y)
z = 3.204
Prob > |z| = 0.0014
.
. stset los, failure(die_mbd) scale(7)
failure event: die_mbd != 0 & die_mbd < .
obs. time interval: (0, los]
exit on or before: failure
t for analysis: time/7
------------------------------------------------------------------------------
52 total observations
0 exclusions
------------------------------------------------------------------------------
52 observations remaining, representing
9 failures in single-record/single-failure data
94.14286 total analysis time at risk and under observation
at risk from t = 0
earliest observed entry t = 0
last observed exit t = 9.285714
. sts graph, ytitle(Proportion of Survival) ///
> ylabel(, angle(horizontal)) ///
> risktable censored(single) ///
> by(lungca) title(Kaplan-Meier Curves (Survival on Discharge)) ///
> xtitle(Week) xlabel(0(1)10) caption(Log-rank test p=0.9736)
failure _d: die_mbd
analysis time _t: los/7
. sts test lungca
failure _d: die_mbd
analysis time _t: los/7
Log-rank test for equality of survivor functions
| Events Events
lungca | observed expected
-------+-------------------------
N | 3 3.05
Y | 6 5.95
-------+-------------------------
Total | 9 9.00
chi2(1) = 0.00
Pr>chi2 = 0.9736
. graph export km_die_mbd.pdf, replace
(file /Users/RJCC/Documents/rjcc3/pwin/km_die_mbd.pdf written in PDF format)
.
. stset fu_die, failure(die2) scale(30.5)
failure event: die2 != 0 & die2 < .
obs. time interval: (0, fu_die]
exit on or before: failure
t for analysis: time/30.5
------------------------------------------------------------------------------
52 total observations
0 exclusions
------------------------------------------------------------------------------
52 observations remaining, representing
30 failures in single-record/single-failure data
1879.639 total analysis time at risk and under observation
at risk from t = 0
earliest observed entry t = 0
last observed exit t = 133.7049
. sts graph, ytitle(Proportion of Survival) ///
> ylabel(, angle(horizontal)) ///
> risktable censored(single) ///
> by(lungca) title(Kaplan-Meier Curves (Overall Survival)) ///
> xlabel(0(12)134) xtitle(Month) caption(Log-rank test p=0.0002)
failure _d: die2
analysis time _t: fu_die/30.5
. sts test lungca
failure _d: die2
analysis time _t: fu_die/30.5
Log-rank test for equality of survivor functions
| Events Events
lungca | observed expected
-------+-------------------------
N | 6 15.96
Y | 24 14.04
-------+-------------------------
Total | 30 30.00
chi2(1) = 13.66
Pr>chi2 = 0.0002
. graph export km_die2.pdf, replace
(file /Users/RJCC/Documents/rjcc3/pwin/km_die2.pdf written in PDF format)
.
. log close
name: <unnamed>
log: /Users/RJCC/Documents/rjcc3/pwin/pwin.smcl
log type: smcl
closed on: 3 Mar 2016, 08:41:20
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