podatki <- read.table("/cloud/project/Poglavje 4/Naloga 1/Zdravilo.csv", header=TRUE, sep=";", dec=",")
head(podatki)
##   ID Dnevi Dogodek Zdravilo Starost Oteklina Bilirubin Albumin
## 1  1  2055       2        1      54        0       0.3    4.08
## 2  2  2466       2        2      53        0       0.3    4.00
## 3  3  3611       0        2      56        0       0.3    3.39
## 4  4   994       0        2      58        0       0.4    2.75
## 5  5  1153       0        1      61        0       0.4    3.58
## 6  6  1831       0        1      56        0       0.4    3.72
##   Strjevanje
## 1        9.9
## 2       11.0
## 3       10.6
## 4       10.8
## 5       10.4
## 6       10.1

Opis spremenljivk:

podatki$Status <- ifelse(podatki$Dogodek==2, yes=1, no=0)

podatki$ZdraviloF <- factor(podatki$Zdravilo, 
                            levels = c(2, 1), 
                            labels = c("Placebo", "D-Penic."))

podatki$OteklinaF <- factor(podatki$Oteklina, 
                            levels = c(0, 0.5, 1), 
                            labels = c("Brez", "Zmerna", "Večja"))
summary(podatki[c(-1, -3, -4, -6)])
##      Dnevi         Starost        Bilirubin         Albumin    
##  Min.   :  41   Min.   :26.00   Min.   : 0.300   Min.   :1.96  
##  1st Qu.:1191   1st Qu.:42.00   1st Qu.: 0.800   1st Qu.:3.31  
##  Median :1840   Median :50.00   Median : 1.350   Median :3.55  
##  Mean   :2006   Mean   :50.06   Mean   : 3.256   Mean   :3.52  
##  3rd Qu.:2697   3rd Qu.:57.00   3rd Qu.: 3.425   3rd Qu.:3.80  
##  Max.   :4556   Max.   :78.00   Max.   :28.000   Max.   :4.64  
##    Strjevanje        Status          ZdraviloF    OteklinaF  
##  Min.   : 9.00   Min.   :0.0000   Placebo :154   Brez  :263  
##  1st Qu.:10.00   1st Qu.:0.0000   D-Penic.:158   Zmerna: 29  
##  Median :10.60   Median :0.0000                  Večja : 20  
##  Mean   :10.73   Mean   :0.4006                              
##  3rd Qu.:11.10   3rd Qu.:1.0000                              
##  Max.   :17.10   Max.   :1.0000
library(survival)
prež_obj <- Surv(podatki$Dnevi, podatki$Status)

KM_fit <- survfit(prež_obj ~ 1)

summary(KM_fit, times = c(0, 365*(1:12)))
## Call: survfit(formula = prež_obj ~ 1)
## 
##  time n.risk n.event survival std.err lower 95% CI upper 95% CI
##     0    312       0    1.000  0.0000        1.000        1.000
##   365    290      22    0.929  0.0145        0.902        0.958
##   730    278      11    0.894  0.0174        0.861        0.929
##  1095    240      26    0.809  0.0224        0.766        0.854
##  1460    194      16    0.752  0.0250        0.704        0.802
##  1825    159      10    0.711  0.0268        0.660        0.765
##  2190    130       7    0.677  0.0283        0.624        0.735
##  2555     95      10    0.619  0.0314        0.560        0.683
##  2920     67       6    0.573  0.0342        0.510        0.644
##  3285     47       6    0.511  0.0387        0.441        0.593
##  3650     32       6    0.439  0.0432        0.362        0.532
##  4015     21       3    0.392  0.0463        0.311        0.494
##  4380      8       2    0.341  0.0528        0.251        0.461
KM_fit
## Call: survfit(formula = prež_obj ~ 1)
## 
##        n events median 0.95LCL 0.95UCL
## [1,] 312    125   3395    3086    3853
library(ggplot2)
library(ggfortify)
autoplot(KM_fit, 
         ylab="Stopnja preživetja", 
         xlab="Čas v dnevih", 
         main="Funkcija preživetja") +
         theme_linedraw()

library(survival)
fit <- coxph(prež_obj ~ Starost + OteklinaF + Bilirubin + Albumin + Strjevanje + ZdraviloF, 
             data = podatki)

summary(fit)
## Call:
## coxph(formula = prež_obj ~ Starost + OteklinaF + Bilirubin + 
##     Albumin + Strjevanje + ZdraviloF, data = podatki)
## 
##   n= 312, number of events= 125 
## 
##                        coef exp(coef)  se(coef)      z Pr(>|z|)    
## Starost            0.034044  1.034630  0.009467  3.596 0.000323 ***
## OteklinaFZmerna   -0.020937  0.979280  0.287959 -0.073 0.942037    
## OteklinaFVečja     1.015548  2.760875  0.315480  3.219 0.001286 ** 
## Bilirubin          0.120515  1.128078  0.015672  7.690 1.47e-14 ***
## Albumin           -1.198893  0.301528  0.236062 -5.079 3.80e-07 ***
## Strjevanje         0.262154  1.299727  0.075530  3.471 0.000519 ***
## ZdraviloFD-Penic.  0.108034  1.114086  0.191368  0.565 0.572390    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                   exp(coef) exp(-coef) lower .95 upper .95
## Starost              1.0346     0.9665    1.0156    1.0540
## OteklinaFZmerna      0.9793     1.0212    0.5569    1.7219
## OteklinaFVečja       2.7609     0.3622    1.4877    5.1237
## Bilirubin            1.1281     0.8865    1.0940    1.1633
## Albumin              0.3015     3.3164    0.1898    0.4789
## Strjevanje           1.2997     0.7694    1.1209    1.5071
## ZdraviloFD-Penic.    1.1141     0.8976    0.7656    1.6211
## 
## Concordance= 0.827  (se = 0.02 )
## Likelihood ratio test= 167  on 7 df,   p=<2e-16
## Wald test            = 189.2  on 7 df,   p=<2e-16
## Score (logrank) test = 309.9  on 7 df,   p=<2e-16