Code for interpretting results and table with results

Author: Sean Lucey

R/table_for_plotting.R

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+library(data.table); library(here)
+
+files <- as.data.table(dir(here::here('WSS28model', 'data neutrals')))
+#only use .RData
+files <- files[V1 %like% '.RData']
+
+all.results <- c()
+for(isim in 1:nrow(files)){
+    load(here::here('WSS28model', 'data neutrals', files[isim, ]))
+    
+    #Create output data.tablereg
+    model <- gsub(".*neu(.*)\\..*", "\\1", files[isim, ])
+    groups <- dimnames(results)[[1]]
+    neg <- results[, 1]
+    neu <- results[, 2]
+    pos <- results[, 3]
+    out <- data.table(Model_name = model,
+                      Group = groups,
+                      Neg = neg,
+                      Neu = neu,
+                      Pos = pos)
+    
+    #Assign Negative, Neutral, Positive, or Mixed result
+    out[Neg > 600, Symbol := 'Neg']
+    out[Neu > 600, Symbol := 'Neu']
+    out[Pos > 600, Symbol := 'Pos']
+    out[is.na(Symbol), Symbol := 'Mix']
+    
+    #Assign Strength of dominant direction
+    out[Symbol == 'Neg', Size := Neg + 0.5*Neu]
+    out[Symbol == 'Pos', Size := Pos + 0.5*Neu]
+    out[Symbol == 'Neu', Size := (-1 * Neg) + Pos]
+    out[Symbol == 'Mix', Size := 701]
+    
+    out[Size > 599 & Size <= 700, Strength := 'Weak']
+    out[Size > 700 & Size <= 900, Strength := 'Moderate']
+    out[Size > 900, Strength := 'Strong']
+    
+    #Drop extra columns
+    out[, c('Neg', 'Neu', 'Pos', 'Size') := NULL]
+    
+    #join
+    all.results <- rbindlist(list(all.results, out))
+
+}
+
+
+
+
+
+
+#Jamie's code
+
+library(reshape2)
+library(ggplot2)
+library(gridExtra)
+require(tidyverse)
+
+WSS28_results_ecosQNM <- readRDS(here::here("data/WSS28_results_ecosQNM.RDS"))
+
+
+ecoQNMresults<-WSS28_results_ecosQNM %>%
+    unite("scenario", Group:Direction, remove=FALSE ) %>%
+    unite("Model_name", Model:model_links, remove=FALSE)
+
+ecoQNMresults_long<-ecoQNMresults %>%
+    pivot_longer (cols= 8:35, names_to="node" ) %>%
+    mutate(sign=value) %>%
+    mutate(sign=case_when(sign >= 600 ~ "positive",
+                          sign <600 & sign >=400~ "zero",
+                          sign <400 ~ "negative")) %>%
+    # mutate(fill=value) %>%
+    mutate(scaled_value= (abs(value-500)))
+
+# Plot up responses as bubble plots 
+dat_fishplus<- ecoQNMresults_long %>% 
+    filter(scenario=="Fishery_plus")
+
+
+p_fishplus<- ggplot(dat_fishplus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black", "white"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black", "white")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+
+
+
+dat_fishminus<- ecoQNMresults_long %>% 
+    filter(scenario=="Fishery_minus")
+
+p_fishminus<- ggplot(dat_fishminus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+
+
+dat_sealminus<- ecoQNMresults_long %>% 
+    filter(scenario=="Seal_minus")
+
+p_sealminus<- ggplot(dat_sealminus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+
+dat_sealplus<- ecoQNMresults_long %>% 
+    filter(scenario=="Seal_plus")
+
+p_sealplus<- ggplot(dat_sealplus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+
+dat_smallpelagicsminus<- ecoQNMresults_long %>% 
+    filter(scenario=="Small pelagics_minus")
+
+p_smallpelagicsminus<- ggplot(dat_smallpelagicsminus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+
+dat_smallpelagicsplus<- ecoQNMresults_long %>% 
+    filter(scenario=="Small pelagics_plus")
+
+p_smallpelagicsplus<- ggplot(dat_smallpelagicsplus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+
+dat_phytoplanktonminus<- ecoQNMresults_long %>% 
+    filter(scenario=="Phytoplankton_minus")
+
+p_phytoplanktonminus<- ggplot(dat_phytoplanktonminus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )
+dat_phytoplanktonplus<- ecoQNMresults_long %>% 
+    filter(scenario=="Phytoplankton_plus")
+
+p_phytoplanktonplus<- ggplot(dat_phytoplanktonplus)+
+    geom_point(aes(y=node, x=Model_name,cex=scaled_value, 
+                   pch=sign, color=sign, fill=sign)) + 
+    # pch=sign, color=sign, fill=fill)) + 
+    scale_color_manual( values=c("paleturquoise4","goldenrod3","black"))+
+    scale_shape_manual(values=c(25,24,4)) + 
+    scale_fill_manual(values=c("paleturquoise4","goldenrod3", "black")) + 
+    
+    theme_bw() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          panel.background = element_blank(),
+          
+          axis.title.x=element_blank(),
+          axis.title.y=element_blank(),
+          axis.text.x=element_text (angle=-90, hjust=0) 
+    )