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@darwinanddavis
darwinanddavis authored Jun 21, 2018
1 parent 371b97c commit 43721fa
Showing 1 changed file with 43 additions and 35 deletions.
78 changes: 43 additions & 35 deletions snail_mesocosm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,8 @@ boxplot(Diameter~Week, data=meso1,
ylim=c(0,max(meso1$Diameter+(meso1$Diameter*buffer))),
col = "light blue",
notch = T,xlab="Week",ylab="Diameter (mm)",
main=paste0("Shell diameter (mm) over ",max(meso1$Week)," weeks")
main=paste0("Shell diameter (mm) over ",max(meso1$Week)," weeks"),
xaxs = "i", yaxs = "i"
)
abline(h=mean(meso1$Diameter),col="pink",lty=3)
par(new=T)
Expand All @@ -133,7 +134,6 @@ abline(h=mean(meso1$Diameter),col="pink",lty=3)
with(meso1,t.test(Diameter,Tank)) # t.test

### Snail size and number of cercariae produced
### ~1000 eggs inoculated at 0,2,4,6 weeks
# Point size by cercariae number
col <- "lightblue"
with(meso1,plot(Diameter,Cercariae,pch=20,
Expand Down Expand Up @@ -178,33 +178,31 @@ title(ylab="Density",line=3.5)
### Individual cercariae production over time
# Cercariae shed over 90 mins per week
### ~1000 eggs inoculated at 0,2,4,6 weeks
tank <- 2 # max 48
tank <- 21 # max 48
cer_total <- 0 # set ylim either to max for tank or max across all tanks (6100)

snail <- subset(meso1,subset=Cercariae>0);snail # get only cercariae
snail <- subset(snail,subset=Tank==tank);snail # get tank level indiviudals
buffer <- 0.25 # axis buffer
cer_total <- 0 # set ylim either to max for tank or max across all tanks (6100)
xlim <- max(meso1$Week) # uses total num of weeks
ifelse(cer_total==1,ylim <- round_any(max(meso1$Cercariae),100),ylim <- max(snail$Cercariae))
col <- "lightblue"
with(snail,plot(Cercariae~Week,
col=adjustcolor(col,alpha=0.5),
type="p",
xlim=c(0,xlim),ylim=c(0,ylim+(ylim*buffer)),
xlab="",ylab="",main=""
))
abline(h=mean(snail$Cercariae),col=col,lty=3,ylim=c(0,ylim+(ylim*buffer))) # get mean
title(main=paste0("Cercariae production for tank ",tank," over ",max(meso1$Week)," weeks"),
xlab="Week")
title(ylab="Number of cercariae shed in 90 mins",line=3.5)
par(new=T)
points(x=c(0,2,4,6),y=rep(50,4),type="h",col="red")# add inoculation points
if(length(snail$Cercariae)>0){
with(snail,plot(Cercariae~Week,
col=adjustcolor(col,alpha=0.5),
type="h",
lwd=5,
xlim=c(0,xlim),ylim=c(0,ylim+(ylim*buffer)),
xlab="",ylab="",main=""
))
abline(h=mean(snail$Cercariae),col=col,lty=3,ylim=c(0,ylim+(ylim*buffer))) # get mean
title(main=paste0("Cercariae production for tank ",tank," over ",max(meso1$Week)," weeks"),
xlab="Week")
title(ylab="Number of cercariae shed in 90 mins",line=3.5)
par(new=T)
points(x=c(0,2,4,6),y=rep(30,4),pch="~",cex=1.5,col="red")# add inoculation points
}else{print("No cercariae in this tank")}

with(snail,barplot(Cercariae,
col=adjustcolor(col,alpha=0.5),
xlim=c(0,xlim),ylim=c(0,ylim+(ylim*buffer)),
xlab="",ylab="",main=""
))
?barplot
############################################################################################################

# Mesocosm 2 data sheet
Expand Down Expand Up @@ -270,7 +268,7 @@ with(meso2,stripchart(Phyto_F~NP,
abline(h=mean(meso2$Eggs),col="pink",lty=3)
title(main=paste0("Phytoplankton concentration for high and low N/P \n levels over ",max(meso1$Week)," weeks"),
xlab="N/P level")
title(,ylab="Phytoplankton concentration",line=3.5)
title(ylab="Phytoplankton concentration",line=3.5)

# N/P concentration v peri
with(meso2,stripchart(Peri_F~NP,
Expand All @@ -286,36 +284,44 @@ with(meso2,stripchart(Peri_F~NP,
abline(h=mean(meso2$Eggs),col="pink",lty=3)

# make phyto and peri vs NP into grouped bargraph
col1 <- "lightblue"
col2 <- "orange"
buffer <- 0.3
den <- density(meso2$Phyto_F)
xlim <- max(den$x);xlim
ylim <- max(den$y);ylim
plot(den,
col=adjustcolor("light blue",alpha=0.5),
col=adjustcolor(col1,alpha=0.5),
xlim=c(0,xlim+(xlim*buffer)),
ylim=c(0,ylim+(ylim*buffer)),
xlab="",
ylab="",
main=""
)
polygon(den, col=adjustcolor("light blue",alpha=0.5),border="light blue") # fill AUC
abline(v=mean(meso2$Phyto_F),col="light blue",lty=3,ylim=c(0,ylim+(ylim*buffer))) # get mean
polygon(den, col=adjustcolor(col1,alpha=0.5),border=col1) # fill AUC
abline(v=mean(meso2$Phyto_F),col=col1,lty=3,ylim=c(0,ylim+(ylim*buffer))) # get mean
par(new=T) # add periphyton concentration
den2 <- density(meso2$Peri_F)
plot(den2,
col=adjustcolor("orange",alpha=0.5),
col=adjustcolor(col2,alpha=0.5),
xlim=c(0,xlim+(xlim*buffer)), # uses xy lims from phyto
ylim=c(0,ylim+(ylim*buffer)),
xlab="",
ylab="",
main=""
)
polygon(den2, col=adjustcolor("orange",alpha=0.5),border="orange") # fill AUC
abline(v=mean(meso2$Peri_F),col="orange",lty=3,ylim=c(0,ylim+(ylim*buffer))) # get mean
polygon(den2, col=adjustcolor(col2,alpha=0.5),border=col2) # fill AUC
abline(v=mean(meso2$Peri_F),col=col2,lty=3,ylim=c(0,ylim+(ylim*buffer))) # get mean
title(main=paste0("Resource concentration over ",max(meso1$Week)," weeks"),
xlab="Resource concentration")
title(ylab="Density",line=3.5)

legend("topright",legend=c("Phytoplankton","Periphyton"),title="Resource type",
border="white",pch=19,ncol=1,bty="n",
cex=0.75,
xjust=0.5,yjust=0.5,x.intersp = 0.5,y.intersp = 0.5,
col=c(col1,col2)
)

# N/P concentration v presence of schisto
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails
Expand All @@ -325,29 +331,28 @@ head(meso2)
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails

par(new=T)
points(x=c(0,2,4,6),y=rep(30,4),pch="~",cex=1.5,col="red")# add inoculation points


# egg mass v phyto
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails

# egg mass v peri
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails

# diameter dists for different NP levels
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails
# https://www.statmethods.net/graphs/density.html

# diameter vs phyto
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails

# diameter vs peri
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails

# Diameter vs egg mass (with schisto)
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails
plot(meso2$Eggs~meso1$Diameter)
length(meso1$Diameter)/length(meso2$Eggs)
Expand All @@ -357,6 +362,9 @@ head(meso2)
### ~1000 eggs inoculated at 0,2,4,6 weeks
# _______________________________________________ compare un/infected snails

par(new=T)
points(x=c(0,2,4,6),y=rep(30,4),pch="~",cex=1.5,col="red")# add inoculation points


###########################################################################################

Expand Down

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