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Last week I spent some time reminiscing about my PhD and looking through some old R code. This trip down memory lane led to some of my old R scripts that amazingly still run. My R scripts were fairly simple and just created a few graphs. However now that I’ve been programming in R for a while, with hindsight (and also things have changed), my original R code could be improved.
I wrote this code around April 2000. To put this into perspective,
- R mailing list was started in 1997
- R version 1.0 was released in Feb 29, 2000
- The initial release of Git was in 2005
- Twitter started in 2006
- StackOverflow was launched in 2008
Basically, sharing code and getting help was much more tricky than today – so cut me some slack!
The Original Code
My original code was fairly simple – a collection of
scan() commands with some
lines() function calls.
## Bad code, don't copy! ## Seriously, don't copy par(cex=2) a<-scan("data/time10.out",list(x=0)) c<-seq(0,120) plot(c,a$x,type='l',xlab="Counts",ylim=c(0,0.08),ylab="Probability",lwd=2.5) a<-scan("data/time15.out",list(x=0)) lines(c,a$x,col=2,lwd=2.5) a<-scan("data/time20.out",list(x=0)) lines(c,a$x,col=3,lwd=2.5) a<-scan("data/time25.out",list(x=0)) lines(c,a$x,col=4,lwd=2.5) a<-scan("data/time30.out",list(x=0)) lines(c,a$x,col=6,lwd=2.5) abline(h=0) legend(90,0.08,lty=c(1,1,1,1,1),lwd=2.5,col=c(1,2,3,4,6), c("t=10","t=15","t=20","t=25","t=30"))
The resulting graph ended up in my thesis and a black and white version in a resulting paper. Notice that it took over eight years to get published! A combination of focusing on my thesis, very long review times (over a year) and that we sent the paper via snail mail to journals.
How I should have written the code
Within the code, there are a number of obvious improvements that could be made.
In 2000, it appears that I didn’t really see the need for formatting code. A few spaces around assignment arrows would be nice.
I could have been cleverer with my
par()settings. See our recent blog post on styling base graphics.
My file extensions for the data sets weren’t great. For some reason, I used
scan()to read in the data. It would be much nicer using
My variable names could be more informative, for example, avoiding
Generating some of the vectors could be more succinct. For example
rep.int(1, 5) # instead of c(1, 1, 1, 1, 1)
0:120 # instead of seq(0, 120)
Overall, other than my use of
scan(), the actual code would be remarkably similar.
A tidyverse version
An interesting experiment is how the code structure differs using a tidyverse. The first step is to load the necessary packages
library("fs") # Overkill here library("purrr") # Fancy for loops library("readr") # Reading in csv files library("dplyr") # Manipulation of data frames library("ggplot2") # Plotting
The actual tidyverse inspired code consists of three main section
- Read the data into a single data frame/tibble using
- Cleaning up the data frame using
- Plotting the data using gplot2
The amount of code is similar in length
dir_ls(path = "data") %>% # list files map_df(read_csv, .id = "filename", col_names = FALSE) %>% # read & combine files mutate(Time = rep(0:120, 5)) %>% # Create Time column rename("Counts" = "X1") %>% # Rename column ggplot(aes(Time, Counts)) + geom_line(aes(colour = filename)) + theme_minimal() + # Nicer theme scale_colour_viridis_d(labels = paste0("t = ", seq(10, 30, 5)), name = NULL) # Change colours
and gives a similar (but nicer) looking graph.
I lied about my code working
Everyone who uses R knows that there are two assignment operators:
=. These operators are (more or less, but not quite) equivalent. However, when R was first created, there was another assignment operator, the underscore
_. My original code actually used the
_ as the assignment operator, i.e.
I can’t find
_ operator was finally removed from R, I seem to recall around 2005.