R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
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> cat("# factors test\n")
# factors test
> library("qgcomp")
> library("survival")
> library('pscl')
Classes and Methods for R originally developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University (2002-2015),
by and under the direction of Simon Jackman.
hurdle and zeroinfl functions by Achim Zeileis.
> # are results at a given seed numerically stable across versions?
> 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), 
+                 z2 = as.factor(sample(c(1,2,3), size=N, replace=TRUE)))
> expnms=paste0("x", 1:2)
> 
> 
> 
> ##### binomial
> set.seed(123123)
> f0 = d ~ x1 + x2 + z2
> obj0a <- qgcomp.noboot(f0, expnms = expnms, data = dat, family=binomial())
> print(obj0a)
Scaled effect size (positive direction, sum of positive coefficients = 0.31)
x2 
 1 

Scaled effect size (negative direction, sum of negative coefficients = -0.0979)
x1 
 1 

Mixture log(OR) (delta method CI):

            Estimate Std. Error Lower CI Upper CI Z value Pr(>|z|)
(Intercept)  0.57991    0.83304  -1.0528  2.21264  0.6961   0.4863
psi1         0.21192    0.39481  -0.5619  0.98574  0.5368   0.5914
> pointwisebound.noboot(obj0a)
  quantile quantile.midpoint   linpred       or   se.lnor     ll.or     ul.or
1        0             0.125 0.5799074 1.000000 0.0000000 1.0000000  1.000000
2        1             0.375 0.7918281 1.236050 0.3948143 0.5701242  2.679801
3        2             0.625 1.0037488 1.527819 0.7896285 0.3250416  7.181332
4        3             0.875 1.2156695 1.888461 1.1844428 0.1853141 19.244538
   ll.linpred ul.linpred
1  0.57990737  0.5799074
2  0.01800634  1.5656498
3 -0.54389468  2.5513922
4 -1.10579571  3.5371347
> 
> ##### survival
> f1 = survival::Surv(time, d)~ x1 + x2 + z2
> obj0b <- qgcomp.cox.noboot(f1, expnms = expnms, data = dat)
> print(obj0b)
Scaled effect size (positive direction, sum of positive coefficients = 0.176)
x2 
 1 

Scaled effect size (negative direction, sum of negative coefficients = -0.0998)
x1 
 1 

Mixture log(hazard ratio) (delta method CI):

     Estimate Std. Error Lower CI Upper CI Z value Pr(>|z|)
psi1 0.076072   0.245428 -0.40496   0.5571    0.31   0.7566
> 
> res = try(pointwisebound.noboot(obj0b), silent=TRUE)
> stopifnot(class(res)=="try-error")
> 
> ##### zi
> f2 = d ~ x1 + x2 + z2 | x1 + x2 + z2
> pp = pscl::zeroinfl(formula = f2, data = dat)
> obj0c <- qgcomp.zi.noboot(f2, expnms = expnms, data = dat)
Warning messages:
1: In Ops.factor(x1 + x2, z2) : '+' not meaningful for factors
2: In Ops.factor(x1 + x2, z2) : '+' not meaningful for factors
> res = try(pointwisebound.noboot(obj0c), silent=TRUE)
> stopifnot(class(res)=="try-error")
> 
> 
> proc.time()
   user  system elapsed 
   2.23    0.31    2.53