change in figures

R/analysis/lmer.output.figs.R

@@ -50,14 +50,14 @@ DF.temp2$trait <- NULL
 DF.results$id2 <- paste(DF.results$id,DF.results$trait)
 DF.results <- merge(DF.results,DF.temp2,by='id2',all.y=FALSE)
 
-### save 
+### save
 saveRDS(DF.results,file='output/lmer/DF.results.merged.rds')
 
 DF.results <- readRDS(file='output/lmer/DF.results.merged.rds')
 
 ### DO THE ACTUAL ANALYSIS OF THE RESULTS
-DF.results <-  DF.results[! DF.results$model %in% c('lmer.LOGLIN.AD.Tf','lmer.LOGLIN.E.Tf','lmer.LOGLIN.R.Tf',
-   'lmer.LOGLIN.ER.Tf','lmer.LOGLIN.nocomp.Tf','lmer.LOGLIN.simplecomp.Tf'),] #,'lmer.LOGLIN.E','lmer.LOGLIN.R'
+## DF.results <-  DF.results[! DF.results$model %in% c('lmer.LOGLIN.AD.Tf','lmer.LOGLIN.E.Tf','lmer.LOGLIN.R.Tf',
+##    'lmer.LOGLIN.ER.Tf','lmer.LOGLIN.nocomp.Tf','lmer.LOGLIN.simplecomp.Tf'),] #,'lmer.LOGLIN.E','lmer.LOGLIN.R'
 
 
 fun.compute.criteria.diff <- function(i,DF.results,criteria.selected){
@@ -88,8 +88,8 @@ diff.criteria.no.compet.t <- DF.results[[criteria.selected]][i] -
 diff.criteria.simple.compet.t <- DF.results[[criteria.selected]][i] - DF.results[[criteria.selected]][
                                                                                 select.simple.compet]
 R2.ratio <- (diff.criteria.simple.compet.t/diff.criteria.no.compet.t)
-if(diff.criteria.no.compet.t<0) R2.ratio <- NA
-if(diff.criteria.simple.compet.t<0) R2.ratio <- NA
+## if(diff.criteria.no.compet.t<0) R2.ratio <- NA
+## if(diff.criteria.simple.compet.t<0) R2.ratio <- NA
 }else{
 R2.ratio <- NA
 }
@@ -162,7 +162,7 @@ best <- DF$model[DF$id2==i][DF$delta.AIC[DF$id2==i]==0]
 if(best %in% c('lmer.LOGLIN.E','lmer.LOGLIN.R'))  {
     d.AIC[ DF$model[DF$id2==i]=='lmer.LOGLIN.ER'] <- 0}
 return(d.AIC)
-}    
+}
 d.AIC <- do.call('c',lapply(unique(DF.results$id2),FUN=f,DF.results))
 DF.results$delta.AIC <- d.AIC
 
@@ -560,7 +560,7 @@ models <- c('lmer.LOGLIN.ER.Tf','lmer.LOGLIN.E.Tf','lmer.LOGLIN.R.Tf','lmer.LOGL
 names(models) <- c('Effect/response','Effect','Response','Absolute distance')
 list.params <- list(c(Response='sumTfBn',Effect='sumTnBn'),
                     c('sumTnBn'),
-                    c('sumTfBn'),                    
+                    c('sumTfBn'),
                     c('sumTnTfBn.abs'))
 
 pdf('figs/parameters.MAP.4models.pdf',width=9,height=9)