"Streamlining" an R code for population models - r

Question

I was wondering if it would be possible to get help streamlining some code I have made for a class at uni. I have essentially been thrown into the deep end with R in the past week (so know very little), and wanted to know if there is a really obvious way I could streamline this so it isn't as clunky!
I am calculating the settlement rate of a population of barnacles on the rocky shore (As per Hines 1979). I have my script up and running for my three species at four different settlement rates no problem, I just wanted to know how I could neaten it up a bit. The script is as follows:
# Roughgarden et al 1985
# Six age classes. Data from Roughgardenetal1985_1Species.xls
# Population projection matrix
############################### C.FISSUS #####################################
#1.0
A <- matrix(c(0.8609, 1.4062, 1.9515, 2.4957, 2.6825, 2.8339,
0.1522, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000,
0.0000, 0.2378, 0.0000, 0.0000, 0.0000, 0.0000,
0.0000, 0.0000, 0.1000, 0.0000, 0.0000, 0.0000,
0.0000, 0.0000, 0.0000, 0.1000, 0.0000, 0.0000,
0.0000, 0.0000, 0.0000, 0.0000, 0.1000, 0.0000
), nrow=6, byrow=TRUE)
par(mfrow=c(2,4))
# Starting population vector
N0 <- matrix(c(0, 0, 0, 0, 0, 0), nrow=6, byrow=TRUE)
# Settlement per unit free space (per cm2 / 100 = per mm2), for each species use: 1.0, 0.1, 0.01, and 0.001
s <-1.0
# Area occupied by age classes (mm2)
Ax <- matrix(c(2.33,9.45,15.15,18.78,20.92,22.14), nrow=6, byrow=TRUE)
# Set up matrix to store population stage (rows) structure over time (cols)
Nt<-matrix(data=0, ncol=50, nrow=6) # Create a vector to store results
Nt[,1]<-N0 # Make the first element (col 1) equal to N0
for (step in 1:49) { # Step through time, calculating Nt+1 each time
Nt[,step+1]<- A %*% Nt[,step] # Apply mortality
AreaOfBarnacles <- Ax * Nt[,step+1] # Calculate area occupied by surviving barnacles
Ft <- max(100 - sum(AreaOfBarnacles),0) # Calculate free space
print(sum(AreaOfBarnacles))
Nt[1,step+1] <- s * Ft # Number of new recruits
}
#Nt
# Transpose Nt for plotting
TNt <- t(Nt)
matplot(TNt, xlab = "Time, t", ylab = "Population Size, Nt", type="l", main = "Chthamalus fissus")
title(main="s = 1.0", line = 0.5)
I essentially need to run this part of script a total of 12 times. Four times for each of the three species (with a changing s value each time (1, 0.1, 0.01, and 0.001). I wanted to try and make it so I could add a bit where it would kind of be like "run this script under these four different settlement rates and produce four graphs of it each time" so I would just have this section of script repeated three times (once for each species). However, I can't seem to get it to work and ended up doing it the long way!
Thank you so much for taking the time to read this lengthy question, like I said, I'm VERY new to R (and coding in general) so I do apologise if anything I am asking is stupid!
P.S. (bonus round?)
How would I add a legend to these graphs without it getting in the way? Is there a way I can make a legend that is its own image so it doesn't overlay my graphs?

Answer 1

You can wrap your operations into a function:
## Defining the function
population.projection <- function(settlement, matrix_A, area_occupied) {
# Starting population vector
N0 <- matrix(c(0, 0, 0, 0, 0, 0), nrow=6, byrow=TRUE)
# Set up matrix to store population stage (rows) structure over time (cols)
Nt<-matrix(data=0, ncol=50, nrow=6) # Create a vector to store results
Nt[,1]<-N0 # Make the first element (col 1) equal to N0
for (step in 1:49) { # Step through time, calculating Nt+1 each time
Nt[,step+1]<- matrix_A %*% Nt[,step] # Apply mortality
AreaOfBarnacles <- area_occupied * Nt[,step+1] # Calculate area occupied by surviving barnacles
Ft <- max(100 - sum(AreaOfBarnacles),0) # Calculate free space
# print(sum(AreaOfBarnacles))
Nt[1,step+1] <- settlement * Ft # Number of new recruits
}
# Transpose Nt for plotting
return(t(Nt))
}
This function intakes your s variable and the two matrices A and Ax renamed settlement, matrix_A and area_occupied to be more self-explanatory.
You can then input your data:
## matrix_A input
matrix_A<- matrix(c(0.8609, 1.4062, 1.9515, 2.4957, 2.6825, 2.8339,
0.1522, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000,
0.0000, 0.2378, 0.0000, 0.0000, 0.0000, 0.0000,
0.0000, 0.0000, 0.1000, 0.0000, 0.0000, 0.0000,
0.0000, 0.0000, 0.0000, 0.1000, 0.0000, 0.0000,
0.0000, 0.0000, 0.0000, 0.0000, 0.1000, 0.0000
), nrow=6, byrow=TRUE)
## Area occupied by age classes (mm2)
area_occupied <- matrix(c(2.33,9.45,15.15,18.78,20.92,22.14), nrow=6, byrow=TRUE)
## Setting the s values
my_settlement_values <- c(1, 0.1, 0.01, 0.001)
And loop through your settlement values for plotting the results:
## Setting the graphic parameters
par(mfrow=c(2,2))
## Looping through the s values
for(one_settlement in my_settlement_values) {
## Plotting the results
matplot(population.projection(settlement = one_settlement, matrix_A, area_occupied), xlab = "Time, t", ylab = "Population Size, Nt", type="l", main = "Chthamalus fissus")
## Adding the title
title(main = paste("s =", one_settlement), line = 0.5)
}