R Under development (unstable) (2023-09-10 r85120 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #--------------------------------------------------------------------------------------------------------------------------
> # test code for survPen package
> #--------------------------------------------------------------------------------------------------------------------------
> 
> 
>  library(survPen)
>  library(splines)
>  data(datCancer) # simulated dataset with 2000 individuals diagnosed with cervical cancer
>  
>  
>  cat("\n","______________________________________________________________________________________________","\n")

 ______________________________________________________________________________________________ 
>  cat("\n","survPen test code","\n")

 survPen test code 
>  cat("\n","______________________________________________________________________________________________","\n")

 ______________________________________________________________________________________________ 
> 
>  
>  #-------------------------------------------------------- example 0
>  # Comparison between restricted cubic splines and penalized restricted cubic splines
>  cat("\n","______________________________________________________________________________________________","\n")

 ______________________________________________________________________________________________ 
>  cat("\n","example 0","\n")

 example 0 
>  cat("\n","Comparison between restricted cubic splines and penalized restricted cubic splines","\n")

 Comparison between restricted cubic splines and penalized restricted cubic splines 
>  
> 
> 
>  # unpenalized
>  f <- ~ns(fu,knots=c(0.25, 0.5, 1, 2, 4),Boundary.knots=c(0,5))
> 
>  mod <- survPen(f,data=datCancer,t1=fu,event=dead)
> 
>  cat("\n","--------------------------------","\n")

 -------------------------------- 
>  cat("\n","summary of the unpenalized model","\n")

 summary of the unpenalized model 
>  print(summary(mod))
hazard model 
 
Call:
survPen(formula = f, data = datCancer, t1 = fu, event = dead)

Parametric coefficients:
                                                                  Estimate
(Intercept)                                                      -1.880242
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))1 -0.029509
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))2  0.012000
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))3 -0.726988
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))4 -0.612175
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))5 -1.876409
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))6 -1.644222
                                                                 Std. Error
(Intercept)                                                        0.229846
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))1   0.256168
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))2   0.301039
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))3   0.314238
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))4   0.312224
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))5   0.558958
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))6   0.321442
                                                                 z value
(Intercept)                                                      -8.1804
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))1 -0.1152
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))2  0.0399
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))3 -2.3135
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))4 -1.9607
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))5 -3.3570
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))6 -5.1151
                                                                  Pr(>|z|)    
(Intercept)                                                      2.828e-16 ***
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))1  0.908291    
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))2  0.968204    
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))3  0.020696 *  
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))4  0.049915 *  
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))5  0.000788 ***
ns(fu, knots = c(0.25, 0.5, 1, 2, 4), Boundary.knots = c(0, 5))6 3.135e-07 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

likelihood = -2319
Number of parameters = 7
converged= TRUE
>  
>  # penalized
>  f.pen <- ~ smf(fu,knots=c(0,0.25, 0.5, 1, 2, 4,5)) # careful here: the boundary knots are included
> 
>  mod.pen <- survPen(f.pen,data=datCancer,t1=fu,event=dead)
> 
>  cat("\n","--------------------------------","\n")

 -------------------------------- 
>  cat("\n","summary of the penalized model","\n")

 summary of the penalized model 
>  print(summary(mod.pen))
penalized hazard model 
 
Call:
survPen(formula = f.pen, data = datCancer, t1 = fu, event = dead)

Parametric coefficients:
            Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -3.04226    0.12344 -24.645 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2320.8, penalized log-likelihood = -2321.7
Number of parameters = 7, effective degrees of freedom = 3.6549
LAML = 2326.3 
 
Smoothing parameter(s):
smf(fu) 
 1690.5 

edf of smooth terms:
smf(fu) 
 2.6549 

converged= TRUE
>  
>  
>  # predictions
> 
>  new.time <- seq(0,5,length=50)
>  pred <- predict(mod,data.frame(fu=new.time))
>  pred.pen <- predict(mod.pen,data.frame(fu=new.time))
> 
>  pdf("compar_unpen_pen.pdf",height=5,width=6)
>  par(mfrow=c(1,1))
>  plot(new.time,pred$haz,type="l",ylim=c(0,0.2),main="hazard vs time",
+  xlab="time since diagnosis (years)",ylab="hazard",col="red")
>  lines(new.time,pred.pen$haz,col="blue3")
>  legend("topright",legend=c("unpenalized","penalized"),
+  col=c("red","blue3"),lty=rep(1,2))
> 
>  dev.off()
null device 
          1 
>  
> 
>  #-------------------------------------------------------- example 1
>  # hazard models with unpenalized formulas compared to a penalized tensor product smooth
>  cat("\n","______________________________________________________________________________________________","\n")

 ______________________________________________________________________________________________ 
>  cat("\n","example 1","\n")

 example 1 
>  cat("\n","hazard models with unpenalized formulas compared to a penalized tensor product smooth","\n")

 hazard models with unpenalized formulas compared to a penalized tensor product smooth 
>  
> 
>  # constant hazard model
>  f.cst <- ~1
>  mod.cst <- survPen(f.cst,data=datCancer,t1=fu,event=dead)
> 
>  # piecewise constant hazard model
>  f.pwcst <- ~cut(fu,breaks=seq(0,5,by=0.5),include.lowest=TRUE)
>  mod.pwcst <- survPen(f.pwcst,data=datCancer,t1=fu,event=dead,n.legendre=200)
>  # we increase the number of points for Gauss-Legendre quadrature to make sure that the cumulative
>  # hazard is properly approximated
> 
>  # linear effect of time
>  f.lin <- ~fu
>  mod.lin <- survPen(f.lin,data=datCancer,t1=fu,event=dead)
> 
>  # linear effect of time and age with proportional effect of age
>  f.lin.age <- ~fu+age
>  mod.lin.age <- survPen(f.lin.age,data=datCancer,t1=fu,event=dead)
> 
>  # linear effect of time and age with time-dependent effect of age (linear)
>  f.lin.inter.age <- ~fu*age
>  mod.lin.inter.age <- survPen(f.lin.inter.age,data=datCancer,t1=fu,event=dead)
> 
>  # cubic B-spline of time with a knot at 1 year, linear effect of age and time-dependent effect
>  # of age with a quadratic B-spline of time with a knot at 1 year
>  f.spline.inter.age <- ~bs(fu,knots=c(1),Boundary.knots=c(0,5))+age+
+  age:bs(fu,knots=c(1),Boundary.knots=c(0,5),degree=2)
>  # here, bs indicates an unpenalized cubic spline
> 
>  mod.spline.inter.age <- survPen(f.spline.inter.age,data=datCancer,t1=fu,event=dead)
> 
> 
>  # tensor of time and age
>  f.tensor <- ~tensor(fu,age)
>  mod.tensor <- survPen(f.tensor,data=datCancer,t1=fu,event=dead)
> 
> 
>  # predictions of the models at age 60
> 
>  new.time <- seq(0,5,length=50)
>  pred.cst <- predict(mod.cst,data.frame(fu=new.time))
>  pred.pwcst <- predict(mod.pwcst,data.frame(fu=new.time))
>  pred.lin <- predict(mod.lin,data.frame(fu=new.time))
>  pred.lin.age <- predict(mod.lin.age,data.frame(fu=new.time,age=60))
>  pred.lin.inter.age <- predict(mod.lin.inter.age,data.frame(fu=new.time,age=60))
>  pred.spline.inter.age <- predict(mod.spline.inter.age,data.frame(fu=new.time,age=60))
>  pred.tensor <- predict(mod.tensor,data.frame(fu=new.time,age=60))
>  
>  lwd1 <- 2
>  
>  pdf("compar_several_mods.pdf",height=5,width=6)
>  par(mfrow=c(1,1))
>  plot(new.time,pred.cst$haz,type="l",ylim=c(0,0.2),main="hazard vs time",
+  xlab="years since diagnosis",ylab="hazard",col="blue3",lwd=lwd1)
>  segments(x0=new.time[1:49],x1=new.time[2:50],y0=pred.pwcst$haz[1:49],col="lightblue2",lwd=lwd1)
>  lines(new.time,pred.lin$haz,col="green3",lwd=lwd1)
>  lines(new.time,pred.lin.age$haz,col="yellow",lwd=lwd1)
>  lines(new.time,pred.lin.inter.age$haz,col="orange",lwd=lwd1)
>  lines(new.time,pred.spline.inter.age$haz,col="red",lwd=lwd1)
>  lines(new.time,pred.tensor$haz,col="black",lwd=lwd1)
>  legend("topright",
+  legend=c("cst","pwcst","lin","lin.age","lin.inter.age","spline.inter.age","tensor"),
+  col=c("blue3","lightblue2","green3","yellow","orange","red","black"),
+  lty=rep(1,7),lwd=rep(lwd1,7))
>  
>  dev.off()
null device 
          1 
>  
>  # you can also calculate the hazard yourself with the lpmatrix option.
>  # For example, compare the following predictions:
>  haz.tensor <- pred.tensor$haz
> 
>  X.tensor <- predict(mod.tensor,data.frame(fu=new.time,age=60),type="lpmatrix")
>  haz.tensor.lpmatrix <- exp(X.tensor%*%mod.tensor$coefficients)
> 
>  cat("\n","--------------------------------","\n")

 -------------------------------- 
>  cat("\n","difference between standard and lpmatrix predictions","\n")

 difference between standard and lpmatrix predictions 
>  print(summary(as.numeric(haz.tensor.lpmatrix - haz.tensor)))
      Min.    1st Qu.     Median       Mean    3rd Qu.       Max. 
-1.665e-16 -5.551e-17  0.000e+00 -4.163e-19  5.378e-17  2.498e-16 
> 
>  #---------------- The 95% confidence intervals can be calculated like this:
>  
>  # standard errors from the Bayesian covariance matrix Vp
>  std <- sqrt(rowSums((X.tensor%*%mod.tensor$Vp)*X.tensor))
>  
>  qt.norm <- stats::qnorm(1-(1-0.95)/2)
>  haz.inf <- as.vector(exp(X.tensor%*%mod.tensor$coefficients-qt.norm*std))
>  haz.sup <- as.vector(exp(X.tensor%*%mod.tensor$coefficients+qt.norm*std))
>  
>  # checking that they are similar to the ones given by the predict function
>  cat("\n","--------------------------------","\n")

 -------------------------------- 
>  cat("\n","difference between standard and lpmatrix confidence intervals","\n")

 difference between standard and lpmatrix confidence intervals 
>  summary(haz.inf - pred.tensor$haz.inf)
      Min.    1st Qu.     Median       Mean    3rd Qu.       Max. 
-1.527e-16 -4.163e-17  0.000e+00  1.249e-18  4.163e-17  2.220e-16 
>  summary(haz.sup - pred.tensor$haz.sup)
      Min.    1st Qu.     Median       Mean    3rd Qu.       Max. 
-2.220e-16 -8.327e-17  0.000e+00 -4.302e-18  6.939e-17  2.776e-16 
>  
> 
>  
>  
>  #-------------------------------------------------------- example 2
>  cat("\n","______________________________________________________________________________________________","\n")

 ______________________________________________________________________________________________ 
>  cat("\n","example 2","\n")

 example 2 
>  cat("\n","smoothing parameter estimation, excess hazard and left truncation","\n")

 smoothing parameter estimation, excess hazard and left truncation 
>  
>  # model : unidimensional penalized spline for time since diagnosis with 5 knots
>  f1 <- ~smf(fu,df=5)
>  # when knots are not specified, quantiles are used. For example, for the term "smf(x,df=df1)",
>  # the vector of knots will be: quantile(unique(x),seq(0,1,length=df1)) 
> 
>  # you can specify your own knots if you want
>  # f1 <- ~smf(fu,knots=c(0,1,3,6,8))
>  
>  # hazard model
>  mod1 <- survPen(f1,data=datCancer,t1=fu,event=dead,expected=NULL,method="LAML")
>  cat("\n","--------------------------------","\n")

 -------------------------------- 
>  cat("\n","summary of the LAML model","\n")

 summary of the LAML model 
>  print(summary(mod1))
penalized hazard model 
 
Call:
survPen(formula = f1, data = datCancer, t1 = fu, event = dead, 
    expected = NULL, method = "LAML")

Parametric coefficients:
            Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -3.02234    0.11124  -27.17 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2321.3, penalized log-likelihood = -2322
Number of parameters = 5, effective degrees of freedom = 3.4489
LAML = 2326.6 
 
Smoothing parameter(s):
smf(fu) 
 133.54 

edf of smooth terms:
smf(fu) 
 2.4489 

converged= TRUE
>  
>  # to see where the knots were placed
>  cat("\n","--------------------------------","\n") 

 -------------------------------- 
>  cat("\n","default knots location","\n")

 default knots location 
>  print(mod1$list.smf)
[[1]]
$term
[1] "fu"

$dim
[1] 1

$knots
$knots$fu
         0%         25%         50%         75%        100% 
0.001455958 0.732075578 1.425060350 2.570586727 5.000000000 


$df
[1] 5

$by
[1] "NULL"

$same.rho
[1] FALSE

$name
[1] "smf(fu)"

attr(,"class")
[1] "smf.smooth.spec"

>  
>  # with LCV instead of LAML
>  mod1bis <- survPen(f1,data=datCancer,t1=fu,event=dead,expected=NULL,method="LCV")
>  cat("\n","--------------------------------","\n") 

 -------------------------------- 
>  cat("\n","summary of the LCV model","\n")

 summary of the LCV model 
>  print(summary(mod1bis))
penalized hazard model 
 
Call:
survPen(formula = f1, data = datCancer, t1 = fu, event = dead, 
    expected = NULL, method = "LCV")

Parametric coefficients:
            Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -3.01983    0.10967 -27.535 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2321.3, penalized log-likelihood = -2322.1
Number of parameters = 5, effective degrees of freedom = 3.3722
LCV = 2324.7 
 
Smoothing parameter(s):
smf(fu) 
 157.76 

edf of smooth terms:
smf(fu) 
 2.3722 

converged= TRUE
>  
>  # hazard model taking into account left truncation (not representative of cancer data, 
>  # the begin variable was simulated for illustration purposes only)
>  mod2 <- survPen(f1,data=datCancer,t0=begin,t1=fu,event=dead,expected=NULL,method="LAML")
>  cat("\n","--------------------------------","\n") 

 -------------------------------- 
>  cat("\n","summary of the left-truncated model","\n")

 summary of the left-truncated model 
>  print(summary(mod2))
penalized hazard model 
 
Call:
survPen(formula = f1, data = datCancer, t1 = fu, t0 = begin, 
    event = dead, expected = NULL, method = "LAML")

Parametric coefficients:
             Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -2.917629   0.073679 -39.599 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2274.3, penalized log-likelihood = -2274.3
Number of parameters = 5, effective degrees of freedom = 2.0817
LAML = 2277.6 
 
Smoothing parameter(s):
smf(fu) 
  11775 

edf of smooth terms:
smf(fu) 
 1.0817 

converged= TRUE
>  
>  # excess hazard model
>  mod3 <- survPen(f1,data=datCancer,t1=fu,event=dead,expected=rate,method="LAML")
>  cat("\n","--------------------------------","\n") 

 -------------------------------- 
>  cat("\n","summary of the excess hazard model","\n")

 summary of the excess hazard model 
>  print(summary(mod3))
penalized excess hazard model 
 
Call:
survPen(formula = f1, data = datCancer, t1 = fu, event = dead, 
    expected = rate, method = "LAML")

Parametric coefficients:
            Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -3.44113    0.16832 -20.444 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2169.3, penalized log-likelihood = -2170.3
Number of parameters = 5, effective degrees of freedom = 4.0414
LAML = 2175.5 
 
Smoothing parameter(s):
smf(fu) 
 24.923 

edf of smooth terms:
smf(fu) 
 3.0414 

converged= TRUE
>  
>  # compare the predictions of the models
>  new.time <- seq(0,5,length=50)
>  pred1 <- predict(mod1,data.frame(fu=new.time))
>  pred1bis <- predict(mod1bis,data.frame(fu=new.time))
>  pred2 <- predict(mod2,data.frame(fu=new.time))
>  pred3 <- predict(mod3,data.frame(fu=new.time))
>  
>  # LAML vs LCV
>  pdf("compar_LAML_LCV.pdf",height=5,width=10)
>  par(mfrow=c(1,2))
>  plot(new.time,pred1$haz,type="l",ylim=c(0,0.2),main="LCV vs LAML",
+  xlab="years since diagnosis",ylab="hazard")
>  lines(new.time,pred1bis$haz,col="blue3",lty=2)
>  legend("topright",legend=c("LAML","LCV"),col=c("black","blue3"),lty=c(1,2))
>  
>  plot(new.time,pred1$surv,type="l",ylim=c(0,1),main="LCV vs LAML",
+  xlab="years since diagnosis",ylab="survival")
>  lines(new.time,pred1bis$surv,col="blue3",lty=2)
>  
>  dev.off()
null device 
          1 
>  
>  # hazard vs excess hazard
>  pdf("compar_total_excess.pdf",height=5,width=10)
>  par(mfrow=c(1,2))
>  plot(new.time,pred1$haz,type="l",ylim=c(0,0.2),main="hazard vs excess hazard",
+  xlab="years since diagnosis",ylab="hazard")
>  lines(new.time,pred3$haz,col="green3")
>  legend("topright",legend=c("overall","excess"),col=c("black","green3"),lty=c(1,1))
>  
>  plot(new.time,pred1$surv,type="l",ylim=c(0,1),main="survival vs net survival",
+  xlab="time",ylab="survival")
>  lines(new.time,pred3$surv,col="green3")
>  legend("topright",legend=c("overall survival","net survival"), col=c("black","green3"), lty=c(1,1)) 
> 
>  dev.off()
null device 
          1 
>  
>  
>  # hazard vs excess hazard with 95% Bayesian confidence intervals (based on Vp matrix, 
>  # see predict.survPen)
>  pdf("compar_total_excess_CI.pdf",height=5,width=6)
>  
>  par(mfrow=c(1,1))
>  plot(new.time,pred1$haz,type="l",ylim=c(0,0.2),main="hazard vs excess hazard",
+  xlab="years since diagnosis",ylab="hazard")
>  lines(new.time,pred3$haz,col="green3")
>  legend("topright",legend=c("overall","excess"),col=c("black","green3"),lty=c(1,1))
>  
>  lines(new.time,pred1$haz.inf,lty=2)
>  lines(new.time,pred1$haz.sup,lty=2)
>  
>  lines(new.time,pred3$haz.inf,lty=2,col="green3")
>  lines(new.time,pred3$haz.sup,lty=2,col="green3")
>  
>  dev.off()
null device 
          1 
> 
> 
>  #-------------------------------------------------------- example 3
>  # models: tensor product smooth vs tensor product interaction of time since diagnosis and 
>  # age at diagnosis. Smoothing parameters are estimated via LAML maximization
>  cat("\n","______________________________________________________________________________________________","\n")

 ______________________________________________________________________________________________ 
>  cat("\n","example 3","\n")

 example 3 
>  cat("\n","tensor product smooth vs tensor product interaction","\n")

 tensor product smooth vs tensor product interaction 
>  
> 
>  f2 <- ~tensor(fu,age,df=c(5,5))
>  
>  f3 <- ~tint(fu,df=5)+tint(age,df=5)+tint(fu,age,df=c(5,5))
>  
>  # hazard model
>  mod4 <- survPen(f2,data=datCancer,t1=fu,event=dead)
>  cat("\n","--------------------------------","\n") 

 -------------------------------- 
>  cat("\n","summary of the tensor model","\n")

 summary of the tensor model 
>  print(summary(mod4))
penalized hazard model 
 
Call:
survPen(formula = f2, data = datCancer, t1 = fu, event = dead)

Parametric coefficients:
            Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -3.31334    0.17612 -18.813 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2106.2, penalized log-likelihood = -2110
Number of parameters = 25, effective degrees of freedom = 11.69
LAML = 2121.7 
 
Smoothing parameter(s):
tensor(fu,age).1 tensor(fu,age).2 
         0.77927         21.67000 

edf of smooth terms:
tensor(fu,age) 
         10.69 

converged= TRUE
>  
>  mod5 <- survPen(f3,data=datCancer,t1=fu,event=dead)
>  cat("\n","--------------------------------","\n") 

 -------------------------------- 
>  cat("\n","summary of the tint model","\n")

 summary of the tint model 
>  print(summary(mod5))
penalized hazard model 
 
Call:
survPen(formula = f3, data = datCancer, t1 = fu, event = dead)

Parametric coefficients:
            Estimate Std. Error z value  Pr(>|z|)    
(Intercept) -3.23237    0.15164 -21.316 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

log-likelihood = -2106.4, penalized log-likelihood = -2109.6
Number of parameters = 25, effective degrees of freedom = 10.462
LAML = 2122.7 
 
Smoothing parameter(s):
      tint(fu)      tint(age) tint(fu,age).1 tint(fu,age).2 
    9.4054e-01     6.4517e+00     1.8307e-01     1.2800e+05 

edf of smooth terms:
    tint(fu)    tint(age) tint(fu,age) 
      3.5664       2.5192       3.3764 

converged= TRUE
>  
>  # predictions
>  new.age <- seq(50,90,length=50)
>  new.time <- seq(0,7,length=50)
>  
>  Z4 <- outer(new.time,new.age,function(t,a) predict(mod4,data.frame(fu=t,age=a))$haz)
>  Z5 <- outer(new.time,new.age,function(t,a) predict(mod5,data.frame(fu=t,age=a))$haz)
>  
>  # color settings
>  col.pal <- colorRampPalette(c("white", "red"))
>  colors <- col.pal(100)
>  
>  facet <- function(z){
+  
+  	facet.center <- (z[-1, -1] + z[-1, -ncol(z)] + z[-nrow(z), -1] + z[-nrow(z), -ncol(z)])/4
+  	cut(facet.center, 100)
+  	
+  }
>  
>  # plot the hazard surfaces for both models
>  pdf("compar_tensor_tint.pdf",height=5,width=10)
>  par(mfrow=c(1,2))
>  persp(new.time,new.age,Z4,col=colors[facet(Z4)],main="tensor",theta=30,
+  xlab="years since diagnosis",ylab="age at diagnosis",zlab="excess hazard",ticktype="detailed")
>  persp(new.time,new.age,Z5,col=colors[facet(Z5)],main="tint",theta=30,
+  xlab="years since diagnosis",ylab="age at diagnosis",zlab="excess hazard",ticktype="detailed")
>  dev.off()
null device 
          1 
>  
> 
>  
> 
> #################################################################################################################
> 
> 
> proc.time()
   user  system elapsed 
  10.12    2.14   12.25