From a289afd8fc705ff856a53562742c7631e5f258eb Mon Sep 17 00:00:00 2001
From: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Date: Sun, 17 Oct 2021 08:17:41 +0200
Subject: [PATCH] fix leftjoin row order

---
 Project.toml                   | 2 +-
 docs/src/examples/nodebased.md | 4 ++--
 src/GetandSetdata.jl           | 6 ++++++
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/Project.toml b/Project.toml
index 1675ba3..c5bd961 100644
--- a/Project.toml
+++ b/Project.toml
@@ -20,7 +20,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [compat]
-DataFrames = "~1.0, ~1.1"
+DataFrames = "1.0, 1.1, 1.2"
 DataFramesMeta = "0.5, 0.6, 0.7, 0.8, 0.9"
 Distances = "0.8, 0.9, 0.10"
 EcoBase = "0.1"
diff --git a/docs/src/examples/nodebased.md b/docs/src/examples/nodebased.md
index 5ac37f1..35f8e9e 100644
--- a/docs/src/examples/nodebased.md
+++ b/docs/src/examples/nodebased.md
@@ -271,12 +271,12 @@ the [nodiv](https://github.com/mkborregaard/nodiv) R package
 ```@example nodebased
 using ProgressLogging
 function node_based_analysis(assemblage::Assemblage, tree::AbstractTree)
-   nodevec = collect(nodenamefilter(!isleaf, tree))
+   nodevec = traversal(tree, preorder) # collect(nodenamefilter(!isleaf, tree))
    SOSs = Matrix{Float64}(undef, nsites(tyrants), length(nodevec))
    GNDs = Vector{Float64}(undef, length(nodevec))
    @progress for (i, node) in enumerate(nodevec)
         println(i)
-       SOSs[:,i], GNDs[i] = process_node(tyrants, tree, node)
+       SOSs[:,i], GNDs[i] = process_node(tyrants, tree, getnodename(tree, node))
    end
    SOSs, GNDs
 end
diff --git a/src/GetandSetdata.jl b/src/GetandSetdata.jl
index fab9f1a..f021633 100644
--- a/src/GetandSetdata.jl
+++ b/src/GetandSetdata.jl
@@ -67,7 +67,10 @@ function addtraits!(asm::Assemblage, newtraits::DataFrames.DataFrame, species::S
 
     nm = propertynames(newtraits)
     rename!(newtraits, species => :name)
+    asm.occ.traits.__run_number = 1:nrow(asm.occ.traits)
     asm.occ.traits = leftjoin(asm.occ.traits, newtraits, on = :name, makeunique = makeunique)
+    sort!(asm.occ.traits, :__run_number)
+    select!(asm.occ.traits, Not(:__run_number))
     rename!(newtraits, nm)
     #assemblagejoin!(asm.occ.traits, newtraits, :name, species)
     nothing
@@ -94,7 +97,10 @@ function addsitestats!(asm::Assemblage, newsites::DataFrames.DataFrame, sites::S
     #assemblagejoin!(asm.site.sitestats, newsites, :sites, sites) #TODO this should instead be on the sitenames of the objects and adjusted below
     nm = propertynames(newsites)
     rename!(newsites, sites => :sites)
+    asm.site.sitestats.__run_number = 1:nrow(asm.site.sitestats)
     asm.site.sitestats = leftjoin(asm.site.sitestats, newsites, on = :sites, makeunique = makeunique)
+    sort!(asm.site.sitestats, :__run_number)
+    select!(asm.site.sitestats, Not(:__run_number))
     rename!(newsites, nm)
     nothing
 end