R Under development (unstable) (2023-08-08 r84908 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> cat("# asis test\n")
# asis test
> 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())$coefficients
(Intercept)          x1 
  0.7031927  -0.7495068 
> glm(f1, data=dat, family=binomial())$coefficients
(Intercept)          x1 
  0.7031927  -0.7495068 
> glm(f3, data=dat, family=binomial())$coefficients
(Intercept)          x1  I(x1 * x1) 
  0.2239853   2.5594880  -3.4638440 
> glm(f4, data=dat, family=binomial())$coefficients
(Intercept)          x1     I(x1^2) 
  0.2239853   2.5594880  -3.4638440 
> 
> 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")
done> 
> proc.time()
   user  system elapsed 
   3.15    0.45    3.54