gistfile1.txt

try2<-total%>%dplyr::filter(!Patientnr%in%8 & !Patientnr%in%20)
try2$meds  <- c(0,0,1,0,1,0,0,0,0,1,0,0,0,1,0,0,0,0,1,1,0,0,1,0,0,0,0,0) 
try2$RT <- recode(try2$Total_dose_spec, "1:2=1; 3=2")
table(try2$RT)
class(try2$RT)
fitLME <- lme(Severity ~ ns(time,3) + 
              Gender + 
              NRS_WorstPain_at_consultation + 
              Age_at_consultation + 
              Opioid_spec + 
              Total_dose_spec,
              random = ~ time | Patientnr, 
              data=try2,
              control=lmeControl(maxIter = 10000),
              na.action=na.exclude)

## Check assumptions
plot(fitLME)
qqnorm(fitLME)
plot(fitLME, Gender ~ resid(.), abline = 0 )
plot(fitLME, NRS_WorstPain_at_consultation ~ resid(.), abline = 0 )
plot(fitLME, Age_at_consultation ~ resid(.), abline = 0 )
plot(fitLME, as.factor(Patientnr) ~ resid(.), abline = 0 )
plot(fitLME, as.factor(Surgery_prior_to_consultation) ~ resid(.), abline = 0 )
plot(fitLME, as.factor(Disease_stage_at_consultation) ~ resid(.), abline = 0 )
plot(fitLME, as.factor(Tumorsite_in_pancreas) ~ resid(.), abline = 0 )
plot(fitLME, as.factor(Non_opioid_spec) ~ resid(.), abline = 0 )
plot(fitLME, as.factor(Opioid_spec) ~ resid(.), abline = 0 )
plot(fitLME, as.factor(RT) ~ resid(.), abline = 0 )

coef(fitLME)  #BELANDRIJK! ALLE INTERCEPTS PER PATIENT!
pairs(fitLME)
summary(fitLME)

plot_model(fitLME, grid=T, sort.est="sort.all", y.offset=1.0)  # Plot showing coefficients and their confidence interval
plot_model(fitLME, grid=T, type="diag")                        # Diagnostics plots
plot_model(fitLME, type="eff")
plot_model(fitLME, show.values = TRUE, value.offset = .3)
plot_model(fitLME, type="re") ##!!ERROR
plot_model(fitLME, type="std") 
plot_model(fitLME, type="slope") 
plot_model(fitLME, type="resid") ##!!ERROR
plot_model(fitLME, type="pred", grid=T, terms=c("time [all]")) ##!! ALLEEN MET TIME WERKT!!
plot_model(fitLME, type="pred", pred.type = "re", grid=T, terms=c("time [all]"))    ##!!ERROR
plot_model(fitLME, type="pred", show.data = TRUE, pred.type = "fe", grid=T, terms=c("time [all]")) ##!! ALLEEN MET TIME WERKT!!
tab_model(fitLME,        #BELANGRIJK!!!!!!!
          show.std=T, 
          show.r2=T, 
          show.aic=T, 
          show.aicc = T, 
          show.dev=T, 
          show.re.var=T)