Merge branch 'main' of https://github.com/viralemergence/clover into …

…main
viralemergence · Jun 14, 2021 · f33300c · f33300c
2 parents 1bb3d4d + fe308a4
commit f33300c
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diff --git a/clover/clover_0.1_mammalviruses/phylogenies/make_translation_table.R b/clover/clover_0.1_mammalviruses/phylogenies/make_translation_table.R
@@ -2,24 +2,23 @@
 
 require(ape)
 
-clover <- read.csv("./clover/clover_0.1_mammalviruses/CLOVER_0.1_MammalViruses_AssociationsFlatFile.csv")
+clover <- read.csv("../CLOVER_0.1_MammalViruses_AssociationsFlatFile.csv")
 
 # subset to mammals
 clover <- clover[clover$HostClass=="mammalia",]
 
-
 # Import the Upham et al. node-dated phylogeny for mammals
 # Use a single tree for now
 # tree_upham <- read.nexus("./vertlife_mammals_node_dated.nex")[[666]]
 # write.nexus(tree_upham, file="./upham_tree_666.nex")
-tree_upham <- read.nexus("./clover/clover_0.1_mammalviruses/phylogenies/upham_tree_666.nex")
+tree_upham <- read.nexus("./upham_tree_666.nex")
 
 tree_upham$tip.label <- gsub("_"," ", tree_upham$tip.label)
 
 clover$Host_Upham <- Hmisc::capitalize(clover$Host)
 
 # % match
-length(intersect(tree_upham$tip.label, clover$Host_Upham))/length(unique(clover$Host_Upham))# 95.8%
+length(intersect(tree_upham$tip.label, clover$Host_Upham))/length(unique(clover$Host_Upham))# 94%
 setdiff(clover$Host_Upham, tree_upham$tip.label)
 
 # Collapsing subspecies (removes everything after second " ")
@@ -33,7 +32,7 @@ length(intersect(tree_upham$tip.label, clover$Host_Upham))/length(unique(clover$
 setdiff(clover$Host_Upham, tree_upham$tip.label)
 
 # Using Upham Master Taxonomy to translate NCBI names to IUCN / Upham
-IUCN_2_NCBI <- read.csv("./clover/clover_0.1_mammalviruses/phylogenies/Upham_S1_Data/Upham_IUCN_to_NCBI.csv")
+IUCN_2_NCBI <- read.csv("./Upham_S1_Data/Upham_IUCN_to_NCBI.csv")
 
 IUCN_2_NCBI$NCBI_SciName <- gsub("_"," ", IUCN_2_NCBI$NCBI_SciName)
 IUCN_2_NCBI$MasterTax_SciName <- gsub("_"," ", IUCN_2_NCBI$MasterTax_SciName)
@@ -47,7 +46,7 @@ length(intersect(tree_upham$tip.label, clover$Host_Upham))/length(unique(clover$
 setdiff(clover$Host_Upham, tree_upham$tip.label)
 
 # Using ASM Mammal Diversity Database Taxonomy v1.3 (https://www.mammaldiversity.org/)
-MDD <- read.csv("./clover/clover_0.1_mammalviruses/phylogenies/MDD_taxonomy/MDD_v1.3_6513species.csv")
+MDD <- read.csv("./MDD_taxonomy/MDD_v1.3_6513species.csv")
 
 # First pass mapping from MSW3
 MDD$MSW3_sciName <- gsub("_"," ", MDD$MSW3_sciName)
@@ -61,21 +60,31 @@ clover$Host_Upham=plyr::revalue(clover$Host_Upham, to_swap)
 length(intersect(tree_upham$tip.label, clover$Host_Upham))/length(unique(clover$Host_Upham))# 98.7%
 setdiff(clover$Host_Upham, tree_upham$tip.label)
 
-# six manual changes
-unique(clover[!clover$Host_Upham %in% tree_upham$tip.label, c("Host_Upham")])
+# 14 manual changes
+sort(unique(clover[!clover$Host_Upham %in% tree_upham$tip.label, c("Host_Upham")]))
 # looking at synonyms and manually searching notes in MDD and Upham MasterTaxonomy
 
 clover$Host_Upham=plyr::revalue(clover$Host_Upham,
-                           c("Bubalus carabanensis"="Bubalus arnee", ## B. carabensis is B. bubalis, which is the domestic form of B. arnee
-                           	 "Dermanura cinerea"="Dermanura cinereus",
-                             "Dermanura tolteca"="Dermanura toltecus",
-                             "Lissonycteris angolensis"="Myonycteris angolensis",
+                           c("Aeorestes cinereus"="Lasiurus cinereus",
+                           	 "Aeorestes egregius"="Lasiurus egregius",
+                           	 "Bubalus carabanensis"="Bubalus arnee", ## B. carabensis is B. bubalis, which is the domestic form of B. arnee
+                           	 "Coendou rothschildi"="Coendou quichua",
+                           	 "Dasypterus ega"="Lasiurus xanthinus",
+                           	 "Dasypterus intermedius"="Lasiurus intermedius",
+                           	 "Dasypterus xanthinus"="Lasiurus xanthinus",
+                           	 "Dobsonia andersoni"="Dobsonia anderseni", # looks like different sources name this with o or e, but no source has both (seems to be typo / discrepancy)	                           
+                           	 "Lissonycteris angolensis"="Myonycteris angolensis",
+                             "Macaca balantak"="Macaca tonkeana", # According to WR05: "According to Froehlich et al. (1998), the macaques of the Balantak Mtns on the E peninsula of Sulawesi constitute a separate species from those of the main part of the range; in this case, the name tonkeana would apply to the Balantak form"
                              "Macronycteris commersoni"="Hipposideros commersoni",
-                             "Piliocolobus semlikiensis"="Procolobus badius"))# CLOVER synonym is Colobus badius semlikiensis, 
+                             "Piliocolobus semlikiensis"="Procolobus badius", # CLOVER synonym is Colobus badius semlikiensis, 
 								# MDD reports some Piliocolobus were Colobus,
 								# and Upham reports Procolobus badius as extinct MSW3 synonym of Piliocolobus badius
+							 "Rattus flavipectus"="Rattus tanezumi", # From WR05: "Verneau et al. (1997), for example, split Vietnamese R. flavipectus from R. tanezumi because of a difference in Fundamental Numbers of karyotypes."
+							 "Terricola subterraneus"="Microtus subterraneus" #WR05 indicates Terricola is a subgenus of Microtus
+							 ))
+
 
 length(intersect(tree_upham$tip.label, clover$Host_Upham))/length(unique(clover$Host_Upham))# 100%
 
 upham_translation_table <- data.frame(Host=clover$Host, Host_Upham=clover$Host_Upham)
-write.csv(upham_translation_table,"./data/phylogenies/mammal_phylo_translations.csv")
+write.csv(upham_translation_table,"./mammal_phylo_translations.csv")