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430 lines (369 loc) · 15.3 KB
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library(ggplot2)
library(plyr)
library(cowplot)
library(ggsignif)
library(ggthemes)
library(RColorBrewer)
dexp1<-read.csv("exp1.csv")
dexp2<-read.csv("exp2.csv")
dexp3<-read.csv("exp3.csv")
#standard errors
se<-function(x){sd(x)/sqrt(length(x))}
#data summary function
data_summary <- function(x) {
m <- mean(x, na.rm=TRUE)
sem <-sd(x, na.rm=TRUE)/sqrt(sum(!is.na(x)))
ymin<-m-1.96*sem
ymax<-m+1.96*sem
return(c(y=m,ymin=ymin,ymax=ymax))
}
#position dodge
pd<-position_dodge(0.1)
#my palette
mypalette<-brewer.pal(7,"Dark2")
#standard errors
se<-function(x){sd(x)/sqrt(length(x))}
#data summary function
data_summary <- function(x) {
m <- mean(x, na.rm=TRUE)
sem <-sd(x, na.rm=TRUE)/sqrt(sum(!is.na(x)))
ymin<-m-1.96*sem
ymax<-m+1.96*sem
return(c(y=m,ymin=ymin,ymax=ymax))
}
#binomial function
mybinomfunc<-function(x, mark){
b1<-binom.test(sum(x==mark), length(x), p=1/2, conf.level=0.95)
dout<-data.frame(state=mark, p=as.numeric(b1$estimate), clow=b1$conf.int[1], cup=b1$conf.int[2])
return(dout)
}
#position dodge
pd1<-position_dodge(0.1)
pd2<-position_dodge(0.01)
#my palette
mypalette<-brewer.pal(2,"Dark2")
#point data frame
dpoint<-data.frame(Condition=dexp1$condition, doors=dexp1$ndoors)
#mark conditions
dpoint$Condition<-factor(dpoint$Condition, levels=c("1-animal", "8-animals"))
#summarized points
dm<-ddply(dpoint, ~Condition, summarize, m=mean(doors), se=se(doors))
#reshape summary data frame
dsum<-data.frame(m=dm$m,Conditionl=dm$Condition,ymin=dm$m-dm$se, ymax=dm$m+dm$se)
#let's plot it
p1<-ggplot(dpoint, aes(x =Condition, y = doors, fill=Condition, color=Condition))+
#dot plots
geom_dotplot(binaxis='y', stackdir='center',stackratio=1.5, dotsize=4, binwidth=0.5, position=pd1, alpha=0.5) +
#summary function
stat_summary(fun.data=data_summary, color="grey30", size=1, alpha=0.75)+
#minimal theme
theme_minimal()+
#change text
theme(text = element_text(size=20, family="sans"))+
#colors and fill
scale_fill_manual(values =mypalette)+
scale_color_manual(values = mypalette)+
#write Bayes Factor on top
geom_signif(comparisons=list(c("1-animal", "8-animals")), annotations="BF=50.8",
y_position = 50, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#label axes
xlab("Condition")+ylab("Doors opened")+
#scale of ticks
scale_y_continuous(breaks=c(0,10,20,30,40,50), limits = c(0,58))+
#no legend
theme(legend.position="none", strip.background=element_blank(), legend.key=element_rect(color=NA))+
#title
ggtitle("Persistence")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1),
plot.title=element_text(face="italic"))
p1
#point data frame
dpoint<-data.frame(Condition=dexp1$condition, latency=dexp1$latency)
#mark conditions
dpoint$Condition<-factor(dpoint$Condition, levels=c("1-animal", "8-animals"))
#summarized points
dm<-ddply(dpoint, ~Condition, summarize, m=mean(latency), se=se(latency))
#reshape summary data frame
dsum<-data.frame(m=dm$m,Conditionl=dm$Condition,ymin=dm$m-dm$se, ymax=dm$m+dm$se)
p2<-ggplot(dpoint, aes(x =Condition, y = latency, fill=Condition, color=Condition))+
#dot plot
geom_dotplot(binaxis='y', stackdir='center',stackratio=2, dotsize=4, binwidth=2, position=pd2, alpha=0.5) +
#limits
ylim(c(0, 230))+
#summary function
stat_summary(fun.data=data_summary, color="grey30", size=1, alpha=0.75)+
#theme and fonts
theme_minimal()+ theme(text = element_text(size=20, family="sans"))+
#colors and fill
scale_fill_manual(values =mypalette)+
scale_color_manual(values = mypalette)+
#add Bayes Factor on top
geom_signif(comparisons=list(c("1-animal", "8-animals")), annotations="BF=55.1",
y_position = 200, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#label axes
xlab("Condition")+ylab("Latency in s")+
#no legend
theme(legend.position="none", strip.background=element_blank(), legend.key=element_rect(color=NA))+
#title
ggtitle("First signs of leaving")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1),
plot.title=element_text(face="italic"))
p2
#subset of data
dc1<-subset(dexp1, condition=="1-animal")
dc2<-subset(dexp1, condition=="8-animals")
#apply binomial function
dp<-rbind(mybinomfunc(dc1$completion, 1), mybinomfunc(dc2$completion, 1))
#labels state
dp$state<-c("1-animal", "8-animals")
#let's plot it
p3 <- ggplot(dp, aes(y=p, x=as.factor(state), fill=as.factor(state))) +
#summarize as a bar
stat_summary(fun.y = mean, geom = "bar", position = "dodge", color='black', width=0.6) +
#points
geom_point()+
#error bars
geom_errorbar(aes(ymin=clow, ymax=cup),color='black', width = .33, position=position_dodge((width=0.9))) +
#label axes
ylab("Proportion")+ xlab("Condition")+
#theme and font change
theme_minimal()+ theme(text = element_text(size=20, family="sans"))+
#change color
scale_fill_manual(values = mypalette)+
#now legend
theme(strip.background=element_blank(), legend.key=element_rect(color=NA), legend.position="none")+
guides(color=FALSE, shape=FALSE)+
#add Bayes Factor above
geom_signif(comparisons=list(c("1-animal", "8-animals")), annotations="BF=207.9",
y_position = 0.91, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#change y limits
scale_y_continuous(expand = c(0,0),
limits = c(0,1.08)) +
#change title
ggtitle("Completion")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1),
plot.title=element_text(face="italic"))
p3
#point data frame
dpoint<-data.frame(Condition=dexp2$condition, doors=dexp2$ndoors)
#mark conditions
dpoint$Condition<-factor(dpoint$Condition, levels=c("2-animals", "8-animals"))
#summarized points
dm<-ddply(dpoint, ~Condition, summarize, m=mean(doors), se=se(doors))
#reshape summary data frame
dsum<-data.frame(m=dm$m,Conditionl=dm$Condition,ymin=dm$m-dm$se, ymax=dm$m+dm$se)
#let's plot it
p4<-ggplot(dpoint, aes(x =Condition, y = doors, fill=Condition, color=Condition))+
#dot plots
geom_dotplot(binaxis='y', stackdir='center',stackratio=1.5, dotsize=4, binwidth=0.5, position=pd1, alpha=0.5) +
#summary function
stat_summary(fun.data=data_summary, color="grey30", size=1, alpha=0.75)+
#minimal theme
theme_minimal()+
#change text
theme(text = element_text(size=20, family="sans"))+
#colors and fill
scale_fill_manual(values =mypalette)+
scale_color_manual(values = mypalette)+
#write Bayes Factor on top
geom_signif(comparisons=list(c("2-animals", "8-animals")), annotations="BF=89.5",
y_position = 50, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#label axes
xlab("Condition")+ylab("Doors opened")+
#scale of ticks
scale_y_continuous(breaks=c(0,10,20,30,40,50), limits = c(0,58))+
#no legend
theme(legend.position="none", strip.background=element_blank(), legend.key=element_rect(color=NA))+
#title
ggtitle(" ")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1))
p4
#point data frame
dpoint<-data.frame(Condition=dexp2$condition, latency=dexp2$latency)
#mark conditions
dpoint$Condition<-factor(dpoint$Condition, levels=c("2-animals", "8-animals"))
#summarized points
dm<-ddply(dpoint, ~Condition, summarize, m=mean(latency), se=se(latency))
#reshape summary data frame
dsum<-data.frame(m=dm$m,Conditionl=dm$Condition,ymin=dm$m-dm$se, ymax=dm$m+dm$se)
p5<-ggplot(dpoint, aes(x =Condition, y = latency, fill=Condition, color=Condition))+
#dot plot
geom_dotplot(binaxis='y', stackdir='center',stackratio=2, dotsize=4, binwidth=2, position=pd2, alpha=0.5) +
#limits
scale_y_continuous(limits = c(0,265), breaks = seq(0, 200, by = 50)) + #summary function
stat_summary(fun.data=data_summary, color="grey30", size=1, alpha=0.75)+
#theme and fonts
theme_minimal()+ theme(text = element_text(size=20, family="sans"))+
#colors and fill
scale_fill_manual(values =mypalette)+
scale_color_manual(values = mypalette)+
#add Bayes Factor on top
geom_signif(comparisons=list(c("2-animals", "8-animals")), annotations="BF=6.4",
y_position = 235, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#label axes
xlab("Condition")+ylab("Latency in s")+
#no legend
theme(legend.position="none", strip.background=element_blank(), legend.key=element_rect(color=NA))+
#title
ggtitle(" ")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1))
p5
#subset of data
dc1<-subset(dexp2, condition=="2-animals")
dc2<-subset(dexp2, condition=="8-animals")
#apply binomial function
dp<-rbind(mybinomfunc(dc1$completion, 1), mybinomfunc(dc2$completion, 1))
#labels state
dp$state<-c("2-animals", "8-animals")
#let's plot it
p6 <- ggplot(dp, aes(y=p, x=as.factor(state), fill=as.factor(state))) +
#summarize as a bar
stat_summary(fun.y = mean, geom = "bar", position = "dodge", color='black', width=0.6) +
#points
geom_point()+
#error bars
geom_errorbar(aes(ymin=clow, ymax=cup),color='black', width = .33, position=position_dodge((width=0.9))) +
#label axes
ylab("Proportion")+ xlab("Condition")+
#theme and font change
theme_minimal()+ theme(text = element_text(size=20, family="sans"))+
#change color
scale_fill_manual(values = mypalette)+
#now legend
theme(strip.background=element_blank(), legend.key=element_rect(color=NA), legend.position="none")+
guides(color=FALSE, shape=FALSE)+
#add Bayes Factor above
geom_signif(comparisons=list(c("2-animals", "8-animals")), annotations="BF=5.7",
y_position = 1.01, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#change y limits
scale_y_continuous(expand = c(0,0),
limits = c(0,1.18), breaks = seq(0, 1, by = 0.25)) +
#change title
ggtitle(" ")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1))
p6
#point data frame
dpoint<-data.frame(Condition=dexp3$condition, doors=dexp3$ndoors)
#mark conditions
dpoint$Condition<-factor(dpoint$Condition, levels=c("1-animal", "8-animals"))
#summarized points
dm<-ddply(dpoint, ~Condition, summarize, m=mean(doors), se=se(doors))
#reshape summary data frame
dsum<-data.frame(m=dm$m,Conditionl=dm$Condition,ymin=dm$m-dm$se, ymax=dm$m+dm$se)
#let's plot it
p7<-ggplot(dpoint, aes(x =Condition, y = doors, fill=Condition, color=Condition))+
#dot plots
geom_dotplot(binaxis='y', stackdir='center',stackratio=1.5, dotsize=4, binwidth=0.5, position=pd1, alpha=0.5) +
#summary function
stat_summary(fun.data=data_summary, color="grey30", size=1, alpha=0.75)+
#minimal theme
theme_minimal()+
#change text
theme(text = element_text(size=20, family="sans"))+
#colors and fill
scale_fill_manual(values =mypalette)+
scale_color_manual(values = mypalette)+
#write Bayes Factor on top
geom_signif(comparisons=list(c("1-animal", "8-animals")), annotations="BF=34.9",
y_position = 45, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#label axes
xlab("Condition")+ylab("Doors opened")+
#scale of ticks
scale_y_continuous(breaks=c(0,10,20,30,40,50), limits = c(0,50))+
#no legend
theme(legend.position="none", strip.background=element_blank(), legend.key=element_rect(color=NA))+
#title
ggtitle(" ")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1))
p7
dpoint<-data.frame(Condition=dexp3$condition, latency=dexp3$latency)
#mark conditions
dpoint$Condition<-factor(dpoint$Condition, levels=c("1-animal", "8-animals"))
#summarized points
dm<-ddply(dpoint, ~Condition, summarize, m=mean(latency), se=se(latency))
#reshape summary data frame
dsum<-data.frame(m=dm$m,Conditionl=dm$Condition,ymin=dm$m-dm$se, ymax=dm$m+dm$se)
p8<-ggplot(dpoint, aes(x =Condition, y = latency, fill=Condition, color=Condition))+
#dot plot
geom_dotplot(binaxis='y', stackdir='center',stackratio=2, dotsize=4, binwidth=2, position=pd2, alpha=0.5) +
#limits
ylim(c(0, 225))+
#summary function
stat_summary(fun.data=data_summary, color="grey30", size=1, alpha=0.75)+
#theme and fonts
theme_minimal()+ theme(text = element_text(size=20, family="sans"))+
#colors and fill
scale_fill_manual(values =mypalette)+
scale_color_manual(values = mypalette)+
#add Bayes Factor on top
geom_signif(comparisons=list(c("1-animal", "8-animals")), annotations="BF=13.0",
y_position = 200, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#label axes
xlab("Condition")+ylab("Latency in s")+
#no legend
theme(legend.position="none", strip.background=element_blank(), legend.key=element_rect(color=NA))+
#title
ggtitle(" ")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1))
p8
#subset of data
dc1<-subset(dexp3, condition=="1-animal")
dc2<-subset(dexp3, condition=="8-animals")
#apply binomial function
dp<-rbind(mybinomfunc(dc1$completion, 1), mybinomfunc(dc2$completion, 1))
#labels state
dp$state<-c("1-animal", "8-animals")
#let's plot it
p9 <- ggplot(dp, aes(y=p, x=as.factor(state), fill=as.factor(state))) +
#summarize as a bar
stat_summary(fun.y = mean, geom = "bar", position = "dodge", color='black', width=0.6) +
#points
geom_point()+
#error bars
geom_errorbar(aes(ymin=clow, ymax=cup),color='black', width = .33, position=position_dodge((width=0.9))) +
#label axes
ylab("Proportion")+ xlab("Condition")+
#theme and font change
theme_minimal()+ theme(text = element_text(size=20, family="sans"))+
#change color
scale_fill_manual(values = mypalette)+
#now legend
theme(strip.background=element_blank(), legend.key=element_rect(color=NA), legend.position="none")+
guides(color=FALSE, shape=FALSE)+
#add Bayes Factor above
geom_signif(comparisons=list(c("1-animal", "8-animals")), annotations="BF=124.9",
y_position = 0.91, tip_length = 0, vjust=-0.1, col="black", size=1.1, textsize=6) +
#change y limits
scale_y_continuous(expand = c(0,0),
limits = c(0,1.05)) +
#change title
ggtitle(" ")+
#various theme changes including reducing white space and adding axes
theme(axis.line.x = element_line(color="grey20", size = 1),
axis.line.y = element_line(color="grey20", size = 1))
p9
library(gridExtra)
pdf('doors.pdf', width=13, height=10)
grid.arrange( arrangeGrob(p1, p2, p3, top=textGrob("Study 1",gp=gpar(fontsize=24))),
arrangeGrob(p4, p5, p6, top=textGrob("Study 2",gp=gpar(fontsize=24))),
arrangeGrob(p7, p8, p9, top=textGrob("Study 3",gp=gpar(fontsize=24))),
ncol=3)
dev.off()
library(grid)
library(gridExtra)