Merge branch 'career-2023' of https://github.com/anyaevostinar/Symbul…

…ationEmp into career-2023

Analysis/04-25-22-ParaSpatial/TaskComp.R

@@ -0,0 +1,60 @@
+require(ggplot2)
+#install.packages("viridis")
+library(viridis)
+library(scales)
+
+#Set your working directory to the Analysis folder for your project
+
+#Read in the data
+initial_data <- read.table("04-25-22-ParaSpatial/munged_basic.dat", h=T)
+initial_data$task <- factor(initial_data$task, levels=c("NOT", "NAND", "AND", "ORN", "OR", "ANDN", "NOR", "XOR", "EQU"))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid0", "Well-mixed", x)}))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid1", "Structured", x)}))
+final_update <- subset(initial_data, update == "40000")
+
+host_data <- subset(final_update, partner == "Host")
+
+#Plot the host task counts at final update
+
+#violin plot?
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_violin() + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free") + geom_boxplot(alpha=0.5, outlier.size=0, width=0.1) 
+
+#regular box plot
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_boxplot(alpha=0.5, outlier.size=1) + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free")
+
+
+
+wilcox.test(subset(host_data, treatment=="Absent" & task=="NOT")$count, subset(host_data, treatment=="Present" & task=="NOT")$count)
+median(subset(host_data, treatment=="Absent" & task=="NOT")$count)
+median(subset(host_data, treatment=="Present" & task=="NOT")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="NAND")$count, subset(host_data, treatment=="Present" & task=="NAND")$count)
+median(subset(host_data, treatment=="Absent" & task=="NAND")$count)
+median(subset(host_data, treatment=="Present" & task=="NAND")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="AND")$count, subset(host_data, treatment=="Present" & task=="AND")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="ANDN")$count, subset(host_data, treatment=="Present" & task=="ANDN")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="OR")$count, subset(host_data, treatment=="Present" & task=="OR")$count)
+median(subset(host_data, treatment=="Absent" & task=="OR")$count)
+median(subset(host_data, treatment=="Present" & task=="OR")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="ORN")$count, subset(host_data, treatment=="Present" & task=="ORN")$count)
+
+#All tasks over time
+ggplot(data=initial_data, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ partner, scales='free')
+
+# Specific host tasks over time
+host_over_time <- subset(initial_data, partner=="Host")
+limited_tasks <- subset(host_over_time, task=="NOT" | task=="NAND" | task=="AND" | task=="ORN" | task=="OR" | task=="ANDN")
+
+ggplot(data=limited_tasks, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(name = "Parasites", values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ ., scales='free')
+
+# Specific parasite tasks over time
+parasite_over_time <- subset(initial_data, partner=="Parasite")
+para_limited_tasks <- subset(parasite_over_time, task=="NOT" | task=="NAND" | task=="AND" | task=="ORN" | task=="OR")
+
+ggplot(data=para_limited_tasks, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(name = "Parasites", values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ ., scales='free')
+
+#Tasks over time by replicate
+NAND <- subset(initial_data, task=="NAND")
+NOT <- subset(initial_data, task=="NOT")
+AND <- subset(initial_data, task=="AND")
+
+ggplot(data=NOT, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(partner~rep, scales='free')

Analysis/04-25-22-SpatialNoPara/TaskComp.R

@@ -0,0 +1,58 @@
+require(ggplot2)
+#install.packages("viridis")
+library(viridis)
+library(scales)
+
+#Set your working directory to the Analysis folder for your project
+
+#Read in the data
+initial_data <- read.table("04-25-22-SpatialNoPara/munged_basic.dat", h=T)
+initial_data$task <- factor(initial_data$task, levels=c("NOT", "NAND", "AND", "ORN", "OR", "ANDN", "NOR", "XOR", "EQU"))
+final_update <- subset(initial_data, update == "40000")
+
+host_data <- subset(final_update, partner == "Host")
+
+#Plot the host task counts at final update
+
+#violin plot?
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_violin() + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free") + geom_boxplot(alpha=0.5, outlier.size=0, width=0.1) 
+
+#regular box plot
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_boxplot(alpha=0.5, outlier.size=1) + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free")
+
+
+
+wilcox.test(subset(host_data, treatment=="Absent" & task=="NOT")$count, subset(host_data, treatment=="Present" & task=="NOT")$count)
+median(subset(host_data, treatment=="Absent" & task=="NOT")$count)
+median(subset(host_data, treatment=="Present" & task=="NOT")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="NAND")$count, subset(host_data, treatment=="Present" & task=="NAND")$count)
+median(subset(host_data, treatment=="Absent" & task=="NAND")$count)
+median(subset(host_data, treatment=="Present" & task=="NAND")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="AND")$count, subset(host_data, treatment=="Present" & task=="AND")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="ANDN")$count, subset(host_data, treatment=="Present" & task=="ANDN")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="OR")$count, subset(host_data, treatment=="Present" & task=="OR")$count)
+median(subset(host_data, treatment=="Absent" & task=="OR")$count)
+median(subset(host_data, treatment=="Present" & task=="OR")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="ORN")$count, subset(host_data, treatment=="Present" & task=="ORN")$count)
+
+#All tasks over time
+ggplot(data=initial_data, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ partner, scales='free')
+
+# Specific host tasks over time
+host_over_time <- subset(initial_data, partner=="Host")
+limited_tasks <- subset(host_over_time, task=="NOT" | task=="NAND" | task=="AND" | task=="ORN" | task=="OR" | task=="ANDN")
+
+ggplot(data=limited_tasks, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(name = "Parasites", values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ ., scales='free')
+
+# Specific parasite tasks over time
+parasite_over_time <- subset(initial_data, partner=="Parasite")
+para_limited_tasks <- subset(parasite_over_time, task=="NOT" | task=="NAND" | task=="AND" | task=="ORN" | task=="OR")
+
+ggplot(data=para_limited_tasks, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(name = "Parasites", values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ ., scales='free')
+
+#Tasks over time by replicate
+NAND <- subset(initial_data, task=="NAND")
+NOT <- subset(initial_data, task=="NOT")
+AND <- subset(initial_data, task=="AND")
+
+ggplot(data=NOT, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(partner~rep, scales='free')

Analysis/SpatialComp.R

@@ -0,0 +1,60 @@
+require(ggplot2)
+#install.packages("viridis")
+library(viridis)
+library(scales)
+
+#Set your working directory to the Analysis folder for your project
+
+#Read in the data
+initial_data <- read.table("04-25-22-ParaSpatial/munged_basic.dat", h=T)
+initial_data$task <- factor(initial_data$task, levels=c("NOT", "NAND", "AND", "ORN", "OR", "ANDN", "NOR", "XOR", "EQU"))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid0", "Well-mixed", x)}))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid1", "Structured", x)}))
+final_update <- subset(initial_data, update == "40000")
+
+host_data <- subset(final_update, partner == "Host")
+
+#Plot the host task counts at final update
+
+#violin plot?
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_violin() + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free") + geom_boxplot(alpha=0.5, outlier.size=0, width=0.1) 
+
+#regular box plot
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_boxplot(alpha=0.5, outlier.size=1) + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free")
+
+
+
+wilcox.test(subset(host_data, treatment=="Absent" & task=="NOT")$count, subset(host_data, treatment=="Present" & task=="NOT")$count)
+median(subset(host_data, treatment=="Absent" & task=="NOT")$count)
+median(subset(host_data, treatment=="Present" & task=="NOT")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="NAND")$count, subset(host_data, treatment=="Present" & task=="NAND")$count)
+median(subset(host_data, treatment=="Absent" & task=="NAND")$count)
+median(subset(host_data, treatment=="Present" & task=="NAND")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="AND")$count, subset(host_data, treatment=="Present" & task=="AND")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="ANDN")$count, subset(host_data, treatment=="Present" & task=="ANDN")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="OR")$count, subset(host_data, treatment=="Present" & task=="OR")$count)
+median(subset(host_data, treatment=="Absent" & task=="OR")$count)
+median(subset(host_data, treatment=="Present" & task=="OR")$count)
+wilcox.test(subset(host_data, treatment=="Absent" & task=="ORN")$count, subset(host_data, treatment=="Present" & task=="ORN")$count)
+
+#All tasks over time
+ggplot(data=initial_data, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ partner, scales='free')
+
+# Specific host tasks over time
+host_over_time <- subset(initial_data, partner=="Host")
+limited_tasks <- subset(host_over_time, task=="NOT" | task=="NAND" | task=="AND" | task=="ORN" | task=="OR" | task=="ANDN")
+
+ggplot(data=limited_tasks, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(name = "Parasites", values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ ., scales='free')
+
+# Specific parasite tasks over time
+parasite_over_time <- subset(initial_data, partner=="Parasite")
+para_limited_tasks <- subset(parasite_over_time, task=="NOT" | task=="NAND" | task=="AND" | task=="ORN" | task=="OR")
+
+ggplot(data=para_limited_tasks, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(name = "Parasites", values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ ., scales='free')
+
+#Tasks over time by replicate
+NAND <- subset(initial_data, task=="NAND")
+NOT <- subset(initial_data, task=="NOT")
+AND <- subset(initial_data, task=="AND")
+
+ggplot(data=NOT, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(partner~rep, scales='free')

Data/04-25-22-SpatialNoPara/simple_repeat.py

@@ -41,8 +41,8 @@ def silent_cmd(command):
 print("Using seeds", start_range, "through", end_range-1)
 
 for a in seeds:
-    command_str = './symbulation_parasite -SEED '+str(a)+ ' -FILE_NAME _Grid0_Para0'
-    settings_filename = "Output_Grid0_Para0"+"_SEED"+str(a)+".data"
+    command_str = './symbulation_parasite -SEED '+str(a)+ ' -FILE_NAME _Grid1_Para0'
+    settings_filename = "Output_Grid1_Para0"+"_SEED"+str(a)+".data"
 
     print(command_str)
     cmd(command_str+" > "+settings_filename)