Add Code Not Data

viralemergence · Dec 3, 2019 · 4ada013 · 4ada013
1 parent b028535
commit 4ada013
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Showing 68 changed files with 13,835 additions and 255 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.data
+.Iceberg December Saves
diff --git a/Data for dispersal_Corrected.csv b/Data for dispersal_Corrected.csv
diff --git a/Greg GAM Code/0_Master Iceberg.R b/Greg GAM Code/0_Master Iceberg.R
@@ -15,7 +15,7 @@
 #source("02_Iceberg ENM Futures.R")
 
 print("Spatial!")
-source("Final Iceberg Code/1_Iceberg Spatial.R")
+# source("Final Iceberg Code/1_Iceberg Spatial.R")
 
 print("Data Import!")
 source("Final Iceberg Code/2_Iceberg Data Import.R")

diff --git a/Greg GAM Code/2_Iceberg Data Import.R b/Greg GAM Code/2_Iceberg Data Import.R
@@ -180,7 +180,7 @@ NonEutherianSp <- Panth1[Panth1$hOrder%in%NonEutherians,"Sp"]
 
 tFullSTMatrix <- 1 - 
   (FullSTMatrix[!rownames(FullSTMatrix)%in%NonEutherianSp,!rownames(FullSTMatrix)%in%NonEutherianSp] - 
-     min(FullSTMatrix[!rownames(FullSTMatrix)%in%NonEutherianSp,!rownames(FullSTMatrix)%in%NonEutherianSp]))/
+                        min(FullSTMatrix[!rownames(FullSTMatrix)%in%NonEutherianSp,!rownames(FullSTMatrix)%in%NonEutherianSp]))/
   max(FullSTMatrix[!rownames(FullSTMatrix)%in%NonEutherianSp,!rownames(FullSTMatrix)%in%NonEutherianSp])
 
 tSTMatrix <- tFullSTMatrix

diff --git a/Greg GAM Code/3_Iceberg GAMs.R b/Greg GAM Code/3_Iceberg GAMs.R
@@ -167,7 +167,7 @@ if(Output){
 
   plot_grid(FitList[[Pipeline]] %>% 
               filter(!is.na(SpaceQuantile)) %>%
-              ggplot(aes(Phylo, Fit, colour = SpaceQuantile)) + 
+              ggplot(aes(Phylo, Fit, colour = SpaceQuantile)) + theme_cowplot() + 
               geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = SpaceQuantile), alpha = 0.2, colour = NA) +
               geom_line(aes(group = as.factor(Space))) +
               labs(y = "Viral sharing probability", x = "Phylogenetic similarity", 
@@ -183,7 +183,7 @@ if(Output){
 
             FitList[[Pipeline]] %>% 
               filter(!is.na(PhyloQuantile)) %>%
-              ggplot(aes(Space, Fit, colour = PhyloQuantile)) + 
+              ggplot(aes(Space, Fit, colour = PhyloQuantile)) +  theme_cowplot() + 
               geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = PhyloQuantile), alpha = 0.2, colour = NA) +
               geom_line(aes(group = as.factor(Phylo))) +
               labs(y = "Viral sharing probability", x = "Geographic overlap", 
@@ -200,7 +200,7 @@ if(Output){
             FitList[[Pipeline]] %>% 
               filter(!Phylo == last(unique(Phylo)),
                      !Space == last(unique(Space))) %>%
-              ggplot(aes(Space, Phylo)) + 
+              ggplot(aes(Space, Phylo)) +  theme_cowplot() + 
               geom_tile(aes(fill = Fit)) + 
               labs(x = "Geographic overlap", 
                    y = "Phylogenetic similarity",
@@ -217,7 +217,7 @@ if(Output){
                                                breaks = c(0,0.5,1)),
 
             DataList[[Pipeline]] %>%
-              ggplot(aes(Space, Phylo)) + 
+              ggplot(aes(Space, Phylo)) +  theme_cowplot() + 
               labs(x = "Geographic overlap", 
                    y = "Phylogenetic similarity") +
               #ggtitle("Data Distribution") +

diff --git a/Greg GAM Code/4_Iceberg Prediction.R b/Greg GAM Code/4_Iceberg Prediction.R
@@ -64,14 +64,6 @@ AllMammalMatrix[,SpaceVars] <-
 
   }) %>% bind_cols
 
-for(i in 1:length(PipelineReps)){
-
-  AllMammalMatrix[, paste0("Delta", SpaceVars[1:4 + (i-1)*4])] <-
-
-    apply(AllMammalMatrix[, SpaceVars[1:4 + (i-1)*4]], 2, function(a) a - AllMammalMatrix[ , paste0("Space.Currents", PipelineReps[i])])
-
-}
-
 UpperMammals <- which(upper.tri(tFullSTMatrix[AllMammals, AllMammals], diag = T))
 
 AllMammaldf <- AllMammalMatrix[-UpperMammals,]
@@ -153,16 +145,12 @@ for(Pipeline in PipelineReps){
 
     AllMammaldf2 <- AllMammaldf %>% dplyr::select(-Spp)
 
-    saveRDS(AllMammaldf2, file = "Iceberg Output Files/AllMammaldf.rds")
-
   }
 
 }
 
 AllMammaldf <- AllMammaldf %>% dplyr::select(-Spp)
 
-save(AllMammaldf, file = paste0("Iceberg Output Files/AllMammaldf.Rdata"))
-
 for(i in 1:length(PipelineReps)){
 
   AllMammaldf[, paste0("Delta", SpaceVars[2:5 + (i-1)*5])] <-
@@ -206,16 +194,16 @@ NewEncountersList <-
 
 names(NewEncountersList) <- PipelineReps
 
-# Making new encounters ####
+# Making old encounters ####
 
-NewEncountersList <- 
+OldEncountersList <- 
 
   lapply(PipelineReps, function(b){
 
     l1 <- lapply(PredReps[2:5], function(a){
 
-      AllMammaldf[AllMammaldf[,paste0("Space.Currents",b)]==0&
-                    AllMammaldf[,paste0("Space.", a, b)]>0,]
+      AllMammaldf[AllMammaldf[,paste0("Space.Currents",b)]>0&
+                    AllMammaldf[,paste0("Space.", a, b)]==0,]
 
     })
 
@@ -225,11 +213,8 @@ NewEncountersList <-
 
   })
 
-names(NewEncountersList) <- PipelineReps
-
-save(AllMammaldf, file = paste0("Iceberg Output Files/AllMammaldf.Rdata"))
-save(NewEncountersList, file = paste0("Iceberg Output Files/NewEncounters.Rdata"))
-
-??pivot_wider
-
+names(OldEncountersList) <- PipelineReps
 
+saveRDS(AllMammaldf, file = "Iceberg Output Files/AllMammaldf.rds")
+saveRDS(NewEncountersList, file = paste0("Iceberg Output Files/NewEncounters.rds"))
+saveRDS(OldEncountersList, file = paste0("Iceberg Output Files/OldEncounters.rds"))