-
Notifications
You must be signed in to change notification settings - Fork 0
/
test_asis.R
161 lines (134 loc) · 5.5 KB
/
test_asis.R
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
156
157
158
159
160
161
cat("# asis test\n")
library("qgcomp")
# does the checknames correctly intuit which are linear/non-linear models for common specifications
set.seed(50)
N=50
dat <- data.frame(time=(tmg <- pmin(.1,rweibull(N, 10, 0.1))),
d=1.0*(tmg<0.1), x1=runif(N), x2=runif(N), z=runif(N))
expnms=paste0("x", 1:2)
##### non additive
f0 = survival::Surv(time, d)~ x1 + x2
f1 = survival::Surv(time, d)~ x1*x2
f2 = survival::Surv(time, d)~ x1 + x2 + I(x1*x2)
f3 = survival::Surv(time, d)~x1 + x2 + x1:x2
set.seed(12321)
#res = try(qgcomp(f0, expnms = expnms, data = dat, B=2, MCsize=50))
#stopifnot(class(res)=="try-error")
res = try(obj0 <- qgcomp(f0, expnms = expnms, data = dat))
stopifnot(inherits(res, "qgcompfit"))
set.seed(12321)
res = try(obj1 <- qgcomp(f1, expnms = expnms, data = dat, B=2, MCsize=50))
stopifnot(inherits(res, "qgcompfit"))
set.seed(12321)
res = try(obj2 <- qgcomp(f2, expnms = expnms, data = dat, B=2, MCsize=50))
stopifnot(inherits(res, "qgcompfit"))
set.seed(12321)
res = try(obj3 <- qgcomp(f3, expnms = expnms, data = dat, B=2, MCsize=50))
stopifnot(inherits(res, "qgcompfit"))
stopifnot(all.equal(
obj0$fit$coefficients,
obj1$fit$coefficients, check.names=FALSE
)=="Numeric: lengths (2, 3) differ")
stopifnot(all.equal(
obj1$fit$coefficients,
obj3$fit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj1$fit$coefficients,
obj2$fit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj1$msmfit$coefficients,
obj3$msmfit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj1$msmfit$coefficients,
obj2$msmfit$coefficients, check.names=FALSE))
f0b = d ~ x1 + x2
f4 = d ~ x1*x2
f5 = d ~ x1 + x2 + I(x1*x2)
f6 = d ~ x1 + x2 + x1:x2
res = try(obj0b <- qgcomp(f0b, expnms = expnms, data = dat, B=2, family=binomial()))
stopifnot(inherits(res,"qgcompfit"))
res = try(obj4 <- qgcomp(f4, expnms = expnms, data = dat, B=2, family=binomial()))
stopifnot(inherits(res,"qgcompfit"))
res = try(obj5 <- qgcomp(f5, expnms = expnms, data = dat, B=2, family=binomial()))
stopifnot(inherits(res,"qgcompfit"))
res = try(obj6 <- qgcomp(f6, expnms = expnms, data = dat, B=2, family=binomial()))
stopifnot(inherits(res,"qgcompfit"))
stopifnot(all.equal(
obj0b$fit$coefficients,
obj4$fit$coefficients, check.names=FALSE
)=="Numeric: lengths (3, 4) differ")
stopifnot(all.equal(
obj4$fit$coefficients,
obj6$fit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj4$msmfit$coefficients,
obj6$msmfit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj4$fit$coefficients,
obj5$fit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj4$msmfit$coefficients,
obj5$msmfit$coefficients, check.names=FALSE))
##### non linear
# behavior changes when considering self interactions!
f0c = survival::Surv(time, d)~ x1 + x1:x1
f1c = survival::Surv(time, d)~ x1^2
f3c = survival::Surv(time, d)~ x1 + I(x1*x1)
f4c = survival::Surv(time, d)~ x1 + I(x1^2)
stopifnot(all.equal(
survival::coxph(f0c, data=dat)$coefficients,
survival::coxph(f1c, data=dat)$coefficients, check.names=FALSE))
stopifnot(all.equal(
survival::coxph(f3c, data=dat)$coefficients,
survival::coxph(f4c, data=dat)$coefficients, check.names=FALSE))
stopifnot(all.equal(
survival::coxph(f0c, data=dat)$coefficients,
survival::coxph(f3c, data=dat)$coefficients, check.names=FALSE)=="Numeric: lengths (1, 2) differ")
f0 = d~ x1 + x1:x1
f1 = d~ x1^2
f3 = d~ x1 + I(x1*x1)
f4 = d~ x1 + I(x1^2)
glm(f0, data=dat, family=binomial())$coefficients
glm(f1, data=dat, family=binomial())$coefficients
glm(f3, data=dat, family=binomial())$coefficients
glm(f4, data=dat, family=binomial())$coefficients
stopifnot(all.equal(
glm(f0, data=dat, family=binomial())$coefficients,
glm(f1, data=dat, family=binomial())$coefficients, check.names=FALSE))
stopifnot(all.equal(
glm(f3, data=dat, family=binomial())$coefficients,
glm(f4, data=dat, family=binomial())$coefficients, check.names=FALSE))
stopifnot(all.equal(
glm(f0, data=dat, family=binomial())$coefficients,
glm(f3, data=dat, family=binomial())$coefficients, check.names=FALSE)=="Numeric: lengths (2, 3) differ")
res = try(obj0 <- qgcomp(f0, expnms = expnms,
data = dat, B=2, family=binomial())) # defaults to RR
stopifnot(inherits(res,"qgcompfit"))
#res = try(obj0 <- qgcomp(f0, expnms = expnms,
# data = dat, B=2, family=gaussian())) # gives error due to B
res = try(obj1 <- qgcomp(f1, expnms = expnms, data = dat, B=2, family=binomial()))
#res = try(obj1 <- qgcomp(f1, expnms = expnms,
# data = dat, B=2, family=gaussian())) # gives error due to B
res = try(obj3 <- qgcomp(f3, expnms = expnms,
data = dat, B=2, family=binomial())) # defaults to RR
stopifnot(inherits(res,"qgcompfit"))
#res = try(obj0 <- qgcomp(f0, expnms = expnms,
# data = dat, B=2, family=gaussian())) # gives error due to B
res = try(obj4 <- qgcomp(f4, expnms = expnms, data = dat, B=2, family=binomial()))
#res = try(obj1 <- qgcomp(f1, expnms = expnms,
# data = dat, B=2, family=gaussian())) # gives error due to B
stopifnot(inherits(res,"qgcompfit"))
stopifnot(all.equal(
obj0$fit$coefficients,
obj1$fit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj3$fit$coefficients,
obj4$fit$coefficients, check.names=FALSE))
stopifnot(all.equal(
obj0$fit$coefficients,
obj3$fit$coefficients, check.names=FALSE)=="Numeric: lengths (2, 3) differ")
# should result in different MSMs
stopifnot(substr(all.equal(
obj0$msmfit$coefficients,
obj3$msmfit$coefficients, check.names=FALSE), 1, 10)=="Mean relat")
cat("done")