diff --git a/02_Mesobromion_ExamineOutput.R b/02_Mesobromion_ExamineOutput.R index 1dfd91fa9efaed94084b7a1913050fe1427ec78d..25a76f5b575ad23dcd617b912fd484291ca9fbda 100644 --- a/02_Mesobromion_ExamineOutput.R +++ b/02_Mesobromion_ExamineOutput.R @@ -25,6 +25,9 @@ get.best <- function(x, N, labs){ ####1. Reimport data ################################ traits <- read_delim("_data/Mesobromion/traits.v2.10perc.txt", delim="\t") + +traits <- traits %>% + rename(Schlerophylly=Leaf_Scleroph) #traits.sign.cov <- read_delim("_data/Mesobromion/traits.v2.10perc.cov.sign.txt", delim="\t") #traits.sign.pa <- read_delim("_data/Mesobromion/traits.v2.10perc.pa.sign.txt", delim="\t") trait.labs <- data.frame(trait.name=colnames(traits)[-1]) %>% @@ -38,7 +41,7 @@ species.cov <- read_delim("_data/Mesobromion/species.v2.10perc.cov.txt", delim=" traits <- traits %>% as.data.frame() %>% - mutate_at(.vars=vars(Leaf_Scleroph, LifeSpan, Rosette), + mutate_at(.vars=vars(Schlerophylly, LifeSpan, Rosette), .funs=~as.ordered(.)) %>% # filter(species0 %in% colnames(species)) %>% mutate_if(~is.character(.), .funs=~as.factor(.)) %>% @@ -111,7 +114,9 @@ trait.recap <- trait.recap %>% mutate(Variable=ifelse(Code %in% c("SeedLength","DispUnitLength"), paste0(Variable, " (mm)"), Variable)) %>% mutate(Variable=ifelse(Code=="LeafNarea", paste0(Variable, " (g m-2)"), Variable)) %>% mutate(Variable=ifelse(Code=="Leaf.delta.15N", paste0(Variable, " (ppm)"), Variable)) %>% - mutate(Variable=ifelse(Code=="LeafFreshMass", paste0(Variable, " (g)"), Variable)) + mutate(Variable=ifelse(Code=="LeafFreshMass", paste0(Variable, " (g)"), Variable)) %>% + rename(`Short name`=Code, `Long name`=Variable) %>% + rownames_to_column("Code") @@ -142,7 +147,7 @@ trait.coverage <- species.cov %>% trait.recap <- trait.recap %>% - left_join(trait.coverage, by=c("Code"="trait")) + left_join(trait.coverage, by=c("Short name"="trait")) write_csv(trait.recap, path="_output/S3_Traits.recap.csv") @@ -213,7 +218,7 @@ mydata.byone <- corXY.ci %>% filter(ntraits==1)%>% arrange(Coef.obs) %>% mutate(seq=1:n()) %>% - left_join(trait.labs, by=c("trait1"="trait.name")) + left_join(trait.labs %>% dplyr::select(trait.name, Long_English_name), by=c("trait1"="trait.name")) write_csv(mydata.byone %>% dplyr::select(Trait.comb:sign_plus) %>%