whitespaces

tests/testthat/generate_test_data_gamma.R

@@ -33,5 +33,3 @@ gamma.dataset <- data.frame(Id=1:N,
 
 #save(gamma.dataset,file="gamma_test.rda")
 #must move file into testthat directory
-
-

tests/testthat/test-internalGamma.R

@@ -15,170 +15,170 @@ test_that(".CoxMImpute",{
     answer=min(subset(hazard_boot, hazard>=quant)$time)
     mytime+answer
   }
-  
+
   check.same <- function(my.time,beta,basehaz,seed){
     set.seed(seed)
     Jans <- Jackson.snippet(my.time,beta,basehaz,runif(1))
-    
+
     set.seed(seed)
     myans <- .CoxMImpute(my.time,beta,basehaz)
-    
+
     expect_equal(Jans,myans)
   }
-  
-  
+
+
    basehaz <- data.frame(hazard=c(0.1,0.5,1.0,1.5,2.5,4),
                          time=c(1,2,3,4,5,6))
-   
+
    check.same(my.time=3,beta=0.4,basehaz,seed=10)
    check.same(my.time=8,beta=0.8,basehaz,seed=23)
    check.same(my.time=5,beta=-0.8,basehaz,seed=123)
    check.same(my.time=5.3,beta=1,basehaz,seed=1323)
    check.same(my.time=0.5,beta=1,basehaz,seed=1323)
-   
-   
+
+
 })
 
 test_that(".SetupStrataBaseHaz.no.strata",{
-  
+
   data <- data.frame(id=1:5,
                      time=1:5,
                      event=c(0,1,1,0,1),
                      x=c(1,0,1,1,0),
                      y=c(1,1,1,0,0))
-  
+
   formula <- formula(Surv(time,event)~x)
-  
+
   basehaz <- data.frame(hazard=c(1,2.2,4.5,8),
                         time=c(1:4))
-  
+
   stratas <- character(0)
   ans <- .SetupStrataBaseHaz(data,formula,stratas,basehaz)
-  
+
   expect_equal(rep("all",5),ans$index)
   expect_equal("all",names(ans$base.hazard))
-  
+
 })
 
 
 test_that(".SetupStrataBaseHaz.strata.error",{
-  
+
   data <- data.frame(id=1:5,
                      time=1:5,
                      event=c(0,1,1,0,1),
                      x=c(1,0,1,1,0),
                      y=c(1,1,1,0,0))
-  
+
   formula <- formula(Surv(time,event)~strata(x))
-  
+
   basehaz <- data.frame(hazard=c(1,2.2,4.5,2,4,7,11),
                         time=c(1:3,1:4),
                         strata=c(rep("x=1",3),rep("x=2",4)))
-  
+
   stratas <- "strata(x)"
-  
+
   expect_error(.SetupStrataBaseHaz(data,formula,stratas,basehaz))
-  
+
 })
 
 
 test_that(".SetupStrataBaseHaz.one.strata",{
-  
+
   data <- data.frame(id=1:5,
                      time=1:5,
                      event=c(0,1,1,0,1),
                      x=c(1,0,1,1,0),
                      y=c(1,1,1,0,0))
-  
+
   formula <- formula(Surv(time,event)~strata(x))
   basehaz <- data.frame(hazard=c(1,2.2,4.5,2,4,7,11),
                         time=c(1:3,1:4),
                         strata=c(rep("x=0",3),rep("x=1",4)))
-  
+
   stratas <- "strata(x)"
-  
+
   ans <- .SetupStrataBaseHaz(data,formula,stratas,basehaz)
   expect_equal(c("x=1","x=0","x=1","x=1","x=0"),ans$index)
   expect_equal(c("x=0","x=1"),names(ans$base.hazard))
-  
+
   expect_equal(ans$base.hazard$`x=0`,basehaz[basehaz$strata=="x=0",])
-  
-  
+
+
   #Now redo with x as factor
   data$x <- factor(data$x)
   basehaz$strata <- c(rep(0,3),rep(1,4))
   ans <- .SetupStrataBaseHaz(data,formula,stratas,basehaz)
   expect_equal(c("1","0","1","1","0"),ans$index)
   expect_equal(c("0","1"),names(ans$base.hazard))
-  
+
   expect_equal(ans$base.hazard$`1`,basehaz[basehaz$strata=="1",])
-  
-  #Now check strata(x*y) works 
+
+  #Now check strata(x*y) works
   data$x <- c(1,0,1,1,0)
   formula <- formula(Surv(time,event)~strata(x*y))
   stratas <- "strata(x * y)"
   basehaz$strata <- c(rep("x * y=0",3),rep("x * y=1",4))
   ans <- .SetupStrataBaseHaz(data,formula,stratas,basehaz)
   expect_equal(c("x * y=1","x * y=0","x * y=1","x * y=0","x * y=0"),ans$index)
   expect_equal(c("x * y=0","x * y=1"),names(ans$base.hazard))
-})  
+})
 
 test_that(".SetupStrataBaseHaz.two.strata",{
   data <- data.frame(id=1:5,
                      time=1:5,
                      event=c(0,1,1,0,1),
                      x=c(1,0,1,1,0),
                      y=c(1,1,1,0,0))
-  
+
   data$x <- factor(data$x)
   formula <- formula(Surv(time,event)~strata(x)+strata(y))
   stratas <- c("strata(x)","strata(y)")
-  
+
   basehaz <- data.frame(hazard=c(1,3,2,1),
                         time=1:4,
                         strata=c("0, y=0","0, y=1","1, y=0","1, y=1"))
-  
+
   ans <- .SetupStrataBaseHaz(data,formula,stratas,basehaz)
   expect_equal(c("1, y=1","0, y=1","1, y=1","1, y=0","0, y=0"),ans$index)
   expect_equal(c("0, y=0","0, y=1","1, y=0","1, y=1"),names(ans$base.hazard))
   expect_equal(ans$base.hazard$`0, y=1`,basehaz[basehaz$strata=="0, y=1",])
 })
 
 test_that("untangle.specials.behaves.as.expected",{
-  
+
   data <- data.frame(id=1:9,
                      time=1:9,
                      event=c(0,1,1,0,1,1,0,1,1),
                      x=c(1,0,1,1,0,1,1,0,1),
                      y=c(1,1,1,0,0,1,1,0,1))
-  
+
   formula <- formula(Surv(time,event)~x)
   m <- coxph(formula,data)
   expect_equal(character(0),untangle.specials(m$terms,"strata")$var)
-  
-  
+
+
   formula <- formula(Surv(time,event)~x+strata(y))
   expect_warning(m <- coxph(formula,data)) #not interested in lack of convergence
   expect_equal("strata(y)",untangle.specials(m$terms,"strata")$var)
 
   formula <- formula(Surv(time,event)~x*strata(y))
   expect_warning(m <- coxph(formula,data)) #not interested in lack of convergence
   expect_equal("strata(y)",untangle.specials(m$terms,"strata")$var)
-  
+
   formula <- formula(Surv(time,event)~strata(x)*strata(y))
   expect_warning(m <- coxph(formula,data)) #not interested in lack of convergence
   expect_equal(c("strata(x)","strata(y)"),untangle.specials(m$terms,"strata")$var)
-  
+
   formula <- formula(Surv(time,event)~strata(x*y))
-  m <- coxph(formula,data) 
+  m <- coxph(formula,data)
   expect_equal("strata(x * y)",untangle.specials(m$terms,"strata")$var)
-  
+
   formula <- formula(Surv(time,event)~strata(x, y))
-  m <- coxph(formula,data) 
+  m <- coxph(formula,data)
   expect_equal("strata(x, y)",untangle.specials(m$terms,"strata")$var)
-  
+
   formula <- formula(Surv(time,event)~strata(y) + strata( x))
-  m <- coxph(formula,data) 
+  m <- coxph(formula,data)
   expect_equal(c("strata(y)","strata(x)"),untangle.specials(m$terms,"strata")$var)
-  
-})
+
+})