From 18c0251c620f55e93662dfc9497e4b2bf4684f6d Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Mon, 17 Aug 2020 11:28:59 +0200
Subject: [PATCH] Temporary change - exclude nas
---
01b_MesobromionCluster.R | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/01b_MesobromionCluster.R b/01b_MesobromionCluster.R
index 79bf597..223f6cd 100644
--- a/01b_MesobromionCluster.R
+++ b/01b_MesobromionCluster.R
@@ -80,11 +80,20 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
traits <- traits %>%
- column_to_rownames("species0") %>%
rename_all(.funs=~gsub(pattern=".mean$", replacement="", x=.)) %>%
- mutate_if(~is.character(.), .funs=~as.factor(.))
+ mutate_if(~is.character(.), .funs=~as.factor(.)) %>%
+ column_to_rownames("species0")
+
#temporary ### Use only a subset of traits
#dplyr::select(LeafArea:Disp.unit.leng)
+ print("TEMPORARY - delete species with any NA in traits")
+ traits <- traits %>%
+ filter(complete.cases(.))
+ species <- species %>%
+ dplyr::select(rownames(traits))
+
+ print("TEMPORARY - revert back species to pa")
+ species <- (species>0)*1
if(combinations=="all") {
## create list of indices for each combination of traits up to a max number of interactions
--
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