start to solve issue with lmer for all

R/analysis/lmer.run.nolog.all.R

@@ -49,6 +49,7 @@ fun.call.lmer <- function(formula,df.lmer){
 
 
 fun.call.lmer.and.save <- function(formula,df.lmer,path.out){
+    browser()
    lmer.output <- lmer(formula=formula,data=df.lmer,REML = FALSE)
    print(summary(lmer.output))
   saveRDS(lmer.output,file=file.path(path.out, "results.nolog.all.rds"))

R/find.trait/BCI.R

@@ -89,9 +89,9 @@ data.cat.extract <- merge(data.cat.extract,
                           by="Latin_name",all.x=TRUE,all.y=FALSE)
 write.csv(data.cat.extract,file="output/pheno.comparison.bci.joe.csv",row.names = FALSE)
 
-data.cat.extract$deciduous[data.cat.extract$deciduous %in% c('DB','DF','D-NOVEMBER') &
+data.cat.extract$deciduous[data.cat.extract$deciduous %in% c('DB','D-NOVEMBER') &
                            !is.na(data.cat.extract$deciduous)] <- 'D_EV'
-data.cat.extract$deciduous[data.cat.extract$deciduous %in% c('DO') &
+data.cat.extract$deciduous[data.cat.extract$deciduous %in% c('DO','DF') &
                            !is.na(data.cat.extract$deciduous)] <- 'D'
 data.cat.extract$deciduous[data.cat.extract$deciduous %in% c('E') &
                            !is.na(data.cat.extract$deciduous)] <- 'EV'
@@ -102,7 +102,7 @@ data.traits <- merge(data.traits,data.cat.extract[,c("sp","Phylo.group","Pheno.T
 
 
 
-### 
+###
 write.csv(data.traits,file="output/formatted/BCI/traits.csv",row.names = FALSE)