Comparison revBayes - compoGM - Jags

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setwd("/home/boussau/Programming/CompoGM/compoGM")
library(coda)

read data

compo<-read.table("scripts/tmp0.dat", h=T)
revb<-read.table("scripts/Output/M2_out.log", h=T)
jag <- read.table("scripts/Jags_Output/trace.1.tsv", h=T)
# Only looking at log10alpha parameters
#revb_sel<-revb[6]
#compo_sel<-compo[1]
#jag_sel <- jag[1]
revb_sel<-revb[15:24]
compo_sel<-compo[1:10]
jag_sel <- jag[1:10]
a<-autocorr.plot(revb_sel, auto.layout = F)

read data

a<-autocorr.plot(compo_sel, auto.layout = F)

a<-autocorr.plot(jag_sel, auto.layout = F)

effectiveSize(compo_sel[,1])

    var1 
4650.184 

effectiveSize(revb_sel[,1])

var1 
5001 

effectiveSize(jag_sel[,1])

    var1 
2136.863 

effectiveSize(compo_sel[,2])

    var1 
30.25024 

effectiveSize(revb_sel[,2])

    var1 
2599.953 

effectiveSize(jag_sel[,2])

    var1 
2242.251 

comp_ess <- effectiveSize(compo_sel)
revb_ess <- effectiveSize(revb_sel)
jag_ess <- effectiveSize(jag_sel)

plot(comp_ess, revb_ess)
points(comp_ess, jag_ess, col="red")

summary(comp_ess)

    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
   4.941   35.193 1280.597 1786.846 3181.462 4650.184 

summary(revb_ess)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  385.7  1041.9  3597.7  3151.7  5001.0  5668.9 

summary(jag_ess)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  25.77  624.21 1745.70 1485.22 2215.90 2773.26 

boxplot(comp_ess, revb_ess, jag_ess, names=c("Compo_GM", "RevBayes", "RJags"), ylab = "ESS")

par(mfrow=c(3,1))
plot(compo_sel$log10.alpha.__HRA1, t="l" )
plot(revb_sel$log10_alpha.3., t='l' )

plot(jag_sel$log10_alpha.3.  , t="l" )