/*

filename:  KS-fish_4-15-02__pre-post-delta_.txt
directory:  C:\Documents and Settings\John Bailer\My Documents\baileraj\Classes\Fall 2003\SAS-programs

Swim test data generated by S. Roark – pgm from B. Noble and K. See

*/ 
options ls=78 formdlim='-' nodate pageno=1 ps=2000;
title KS-fish 3-8swim 3-8-02;
data swim1;
  input prebm postbm fish gpif gpis pgmf pgms ldhs hlwi Ucrit0 Ucrit1 TTF0 TTF1 delta supp sex;
  if ttf1=0 then ttf1=0.001;
  *velocity1=Ucrit1; *velocity0=Ucrit0;
  cards;
2	2.4	1	22	22	13	33	12	0.4	46.02	35.74	124.08	82.96	41.12	1	1
2.7	2.3	2	22	22	13	23	11	0.4	34.38	15	77.52	0	77.52	1	1
2	2	3	22	22	12	33	11	0.2	42.56	35.84	110.24	83.36	26.88	1	1
1.9	2.2	4	22	22	13	13	11	0.4	35.8	25.74	83.2	42.96	40.24	1	1
1.8	1.6	5	23	33	22	33	12	0.4	40.43	36.7	101.72	86.8	14.92	1	1
2.5	2.6	6	22	22	13	13	11	0.4	40.9	20.12	103.6	20.48	83.12	1	1
1.9	2.1	7	23	22	23	33	11	0.4	40.95	41.24	103.8	104.96	-1.16	1	1
2	1.6	8	23	22	23	33	12	0.6	35.74	31.44	82.96	65.76	17.2	1	1
1.4	1.9	9	23	22	13	33	13	0.6	35.91	16.98	83.64	7.92	75.72	1	1
1.9	1.8	10	23	22	13	23	12	0.8	35.64	40.94	82.56	103.76	-21.2	1	1
1.6	1.6	11	22	22	23	33	11	0.2	41.13	40.76	104.52	103.04	1.48	1	1
2.2	1.9	12	22	22	13	23	12	0.6	37.4	30.35	89.6	61.4	28.2	1	1
2	1.9	13	23	22	12	33	12	0.6	39.95	36.46	99.8	85.84	13.96	1	1
1.6	1.7	14	33	23	13	13	12	0.8	31.26	29.75	65.04	59	6.04	1	1
1.7	1.7	15	22	23	12	33	12	0.6	31.18	35.96	64.72	83.84	-19.12	1	1
2.4	2.4	16	12	22	23	33	11	0.4	38.3	39.98	93.2	99.92	-6.72	1	1
1.3	1.1	17	22	22	22	23	11	0.2	37.42	30.53	89.68	62.12	27.56	2	1
1.5	1.8	18	22	23	11	33	11	0.2	36.68	31.53	86.72	66.12	20.6	2	1
1.7	1.8	19	22	22	23	33	11	0.2	30.58	26.65	62.32	46.6	15.72	2	1
2.1	2.1	20	22	23	22	13	11	0.4	40.71	32.31	102.84	69.24	33.6	2	1
1.9	2.1	21	22	12	12	33	12	0.6	45.66	15.24	122.64	0.96	121.68	2	1
1.4	1.8	22	23	23	11	13	12	0.8	40.46	41.13	101.84	104.52	-2.68	2	1
1.5	1.8	23	22	33	22	13	12	0.4	40.39	32.26	101.56	69.04	32.52	2	1
1.4	1.5	24	22	22	23	23	11	0.4	41.04	38.5	104.16	94	10.16	2	1
1.3	1.1	25	22	22	13	33	11	0.2	40.75	31.05	103	64.2	38.8	2	1
1.6	1.7	26	22	23	13	33	11	0.4	37.41	31.87	89.64	67.48	22.16	2	1
2.4	2.2	27	22	23	22	12	11	0.4	34.38	31.67	77.52	66.68	10.84	3	1
2.2	2.5	28	23	22	22	12	11	0.4	41.95	26.38	107.8	45.52	62.28	3	1
2.2	2.2	29	22	22	22	13	12	0.4	41.89	40.4	107.56	101.6	5.96	3	1
1.9	2.2	30	22	22	23	33	11	0.2	40.95	40.28	103.8	101.12	2.68	3	1
2.1	2	31	22	22	13	33	11	0.2	42	36.81	108	87.24	20.76	3	1
2.3	2.1	32	22	22	12	33	11	0.2	37.54	29.5	90.16	58	32.16	3	1
1.8	1.9	33	33	12	23	13	11	0.6	38.76	41.67	95.04	106.68	-11.64	3	1
2.3	2.3	34	33	22	23	13	11	0.4	45.68	36.96	122.72	87.84	34.88	3	1
1.5	1.5	35	23	22	12	11	12	0.6	40.73	35.31	102.92	81.24	21.68	3	1
1.8	1.7	36	23	12	23	13	11	0.8	41.03	17.55	104.12	10.2	93.92	3	1
1.8	1.9	37	22	23	12	11	11	0.4	41.21	35.84	104.84	83.36	21.48	3	1
2.1	2	38	22	22	22	33	11	0	40.71	37.55	102.84	90.2	12.64	3	1
1.7	1.7	39	33	23	23	13	11	0.6	40.25	26.21	101	44.84	56.16	3	1
1.8	1.8	40	22	22	13	33	11	0.2	41.02	40.33	104.08	101.32	2.76	3	1
2.1	2.2	41	22	23	23	11	11	0.4	41	35.3	104	81.2	22.8	3	1
1.6	2	42	22	22	22	13	11	0.2	42.25	51.04	109	144.16	-35.16	3	1
1.4	1.2	43	22	22	23	33	12	0.4	35.55	15	82.2	0	82.2	1	0
1.8	1.7	44	22	22	33	33	11	0	35.74	40.45	82.96	101.8	-18.84	1	0
1.6	1.4	45	23	22	23	33	12	0.6	32.12	37.49	68.48	89.96	-21.48	1	0
1.5	1.4	46	22	22	13	13	11	0.4	32.15	31.66	68.6	66.64	1.96	1	0
1.5	1.4	47	22	22	12	33	13	0.4	30.03	27.5	60.12	50	10.12	1	0
1.7	1.5	48	33	23	23	33	12	0.6	38.06	31.68	92.24	66.72	25.52	1	0
1.5	1.3	49	22	22	23	33	11	0.2	45.68	35.56	122.72	82.24	40.48	1	0
1.4	1.4	50	22	22	23	33	12	0.4	37.25	23.43	89	33.72	55.28	1	0
1.6	1.6	51	23	23	13	33	12	0.8	30.58	15.2	62.32	0.8	61.52	1	0
1.4	1.2	52	23	22	33	33	12	0.4	35.58	22.25	82.32	29	53.32	1	0
1.6	1.4	53	22	22	13	33	12	0.4	35.5	28.14	82	52.56	29.44	1	0
1.3	1.4	54	22	22	11	23	11	0.2	36.2	37.25	84.8	89	-4.2	1	0
1.4	1.6	55	22	22	11	23	12	0.4	32.4	15	69.6	0	69.6	1	0
1.2	1.6	56	23	22	13	13	12	0.8	35.55	36.19	82.2	84.76	-2.56	1	0
1.4	1.3	57	22	23	22	33	11	0.2	35.84	27.21	83.36	48.84	34.52	1	0
1.4	1.4	58	22	22	12	13	11	0.4	40.4	32.93	101.6	71.72	29.88	2	0
2.1	1.7	59	22	22	23	23	12	0.6	31.6	30.85	66.4	63.4	3	2	0
2	1.4	60	22	22	12	33	11	0.2	36.3	30.99	85.2	63.96	21.24	2	0
1.6	1.6	61	22	22	12	33	11	0.2	36.26	35.42	85.04	81.68	3.36	2	0
1.4	1.9	62	23	22	22	12	12	0.6	32.42	32.17	69.68	68.68	1	2	0
1.7	1.1	63	23	23	23	23	11	0.8	31.82	38.5	67.28	94	-26.72	2	0
1.7	1.3	64	22	22	12	33	12	0.4	30.38	31.13	61.52	64.52	-3	2	0
2.1	1.8	65	23	22	12	13	12	0.8	35.63	28.54	82.52	54.16	28.36	2	0
1.4	1.5	66	22	22	22	33	11	0	37.53	31.38	90.12	65.52	24.6	2	0
1.6	1.5	67	23	22	22	13	11	0.4	36.78	41.15	87.12	104.6	-17.48	2	0
1.8	1.9	68	23	22	12	23	11	0.6	41.18	35.67	104.72	82.68	22.04	2	0
1.6	1.5	69	22	22	12	33	12	0.4	36.21	31.73	84.84	66.92	17.92	2	0
1.5	1.4	70	22	22	22	33	11	0	35.63	35.31	82.52	81.24	1.28	2	0
1.7	1.5	71	22	22	23	23	12	0.6	40.7	36	102.8	84	18.8	2	0
1.7	1.8	72	22	22	23	12	11	0.4	29.63	35.7	58.52	82.8	-24.28	2	0
1.7	1.4	73	23	22	12	11	12	0.6	41.43	37.49	105.72	89.96	15.76	3	0
1.8	1.7	74	22	22	23	11	11	0.2	43.05	34.04	112.2	76.16	36.04	3	0
1.8	1.8	75	33	22	13	33	11	0.2	42.25	25.79	109	43.16	65.84	3	0
1.5	1.6	76	22	22	23	13	11	0.4	38.93	20.74	95.72	22.96	72.76	3	0
1.3	1.4	77	23	22	12	13	12	0.8	40.53	29.88	102.12	59.52	42.6	3	0
1.6	1.7	78	22	22	23	11	11	0.2	35.79	25.88	83.16	43.52	39.64	3	0
1.3	1.4	79	22	22	22	11	12	0.2	40.7	32.24	102.8	68.96	33.84	3	0
1.4	1.3	80	33	22	22	13	12	0.4	38.52	35.75	94.08	83	11.08	3	0
1.5	1.9	81	22	22	13	11	11	0.2	36.18	31.62	84.72	66.48	18.24	3	0
1.6	1.7	82	33	22	23	13	12	0.6	41.63	33	106.52	72	34.52	3	0
1.6	1.6	83	22	22	23	33	11	0.2	36.42	37.01	85.68	88.04	-2.36	3	0
1.5	1.5	84	22	22	12	13	11	0.4	39.21	31.07	96.84	64.28	32.56	3	0
1.3	1.3	85	12	22	12	13	11	0.6	39.42	31.05	97.68	64.2	33.48	3	0
;
run;
*proc print;
data swim2; set swim1; event=1; time=7;
title swim2 data - convert into LB values; 
  if 0<=TTF1<20 then tinterval=1; if tinterval=1 then t=20;
  if 20<=TTF1<40 then tinterval=2; if tinterval=2 then t=40;
  if 40<=TTF1<60 then tinterval=3; if tinterval=3 then t=60; 
  if 60<=TTF1<80 then tinterval=4; if tinterval=4 then t=80; 
  if 80<=TTF1<100 then tinterval=5; if tinterval=5 then t=100;
  if 100<=TTF1<120 then tinterval=6; if tinterval=6 then t=120; 
  if TTF1>120 then tinterval=7; if tinterval=7 then t=140;
 * if TTF1>=140 then timeinterval=8 and t=160;

  if 15<=Ucrit1<20 then velocity1=15;  *Post velocity;
  if 20<=Ucrit1<25 then velocity1=20;
  if 25<=Ucrit1<30 then velocity1=25;
  if 30<=Ucrit1<35 then velocity1=30;
  if 35<=Ucrit1<40 then velocity1=35;
  if 40<=Ucrit1<45 then velocity1=40;
  if 45<=Ucrit1<50 then velocity1=45;
  if Ucrit1>= 50 then velocity1=50;

  if 15<=Ucrit0<20 then velocity0=15;  *Pre velocity;
  if 20<=Ucrit0<25 then velocity0=20;
  if 25<=Ucrit0<30 then velocity0=25;
  if 30<=Ucrit0<35 then velocity0=30;
  if 35<=Ucrit0<40 then velocity0=35;
  if 40<=Ucrit0<45 then velocity0=40;
  if 45<=Ucrit0<50 then velocity0=45;
  if Ucrit0>= 50 then velocity0=50;

proc print data=swim2(obs=10); 
  var fish event velocity1 TTF1 tinterval t;
run;
proc lifetest data=swim2 method=life plots=(s,h) intervals=20 40 60 80 100 120; 
title lifereg - survival function and hazard function;
	  time TTF1*event(0);
title LIFETEST - plot of survival and hazard vs time;
run;

/*
data swim3; set swim2; 
  period=7; * ceil(TTF1/20)?; 
   do j=1 to period; 
     time=7; outevent =0;
     if j=period and event=1 then do;
	   outevent=1;
	   time=t; /*TTF1-20*(period-1)?;*/;
	 *  LTIME=log(time); ** for GENMOD part below; /*
	 end;
	 output;
  end;
run;
*/

data swim3;
  set swim2; bodymass_d=prebm-postbm;velocity_d=velocity0-velocity1;
  j = tinterval;
  event=12;
run; 
proc print data=swim3(obs=15); 
proc lifereg data=swim3;
title Lifereg: ttf1 velocity 1 - post;
  class gpif gpis pgmf pgms ldhs supp sex;
  model ttf1=gpif gpis pgmf pgms ldhs hlwi supp sex velocity1
                         /dist=exponential;
run;
/*proc lifereg data=swim3;
title ttf0 velocity 0 - pre;
  class gpif gpis pgmf pgms ldhs supp sex;
  model ttf0=gpif gpis pgmf pgms ldhs hlwi supp sex velocity0
                         /dist=exponential;
run;*/
proc genmod data=swim3;
  title Genmode: ttf1 velocity 1 - post;
  class gpif gpis pgmf pgms ldhs supp sex velocity1;
  model ttf1 =  velocity1 gpif gpis pgmf pgms ldhs supp sex postbm
                         / dist=gamma link=log type3; *exponential not working in GENMOD?;
  lsmeans gpif  / diff;
  lsmeans gpis / diff; 
  lsmeans ldhs / diff;
run;

proc genmod data=swim3;
  title Genmode: ttf0 velocity 0 - pre;
  class gpif gpis pgmf pgms ldhs supp sex velocity0;
  model ttf0 =  velocity0 gpif gpis pgmf pgms ldhs supp sex prebm
                         / dist=gamma link=log type3; *exponential not working in GENMOD?;
  lsmeans ldhs / diff;
run;

proc genmod data=swim3;
  title Genmode: delta=pre-post;
  class gpif gpis pgmf pgms ldhs supp sex velocity0 velocity1;
  model delta =  velocity_d gpif gpis pgmf pgms ldhs supp sex bodymass_d
                         / dist=normal link=identity type3; *exponential not working in GENMOD?;
  lsmeans pgms / diff;
run;

proc genmod data=swim3;
  title HLWI: post;
  class supp sex hlwi;
  model ttf1 = supp sex hlwi / dist=gamma link=log type3;
run;

proc genmod data=swim3;
  title HLWI pre;
  class supp sex hlwi;
  model ttf0 =  supp sex hlwi / dist=gamma link=log type3; *exponential not working in GENMOD?;
run;

proc genmod data=swim3;
  title HLWI delta=pre-post;
  class supp sex hlwi;
  model delta =  supp sex hlwi / dist=normal link=identity type3; *exponential not working in GENMOD?;
run;