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Could you please recommend more good examples?
Dear Thibault and Ben,
Thank you so much for the excellent talk on Monday and for developing this repo! I am currently a first-year PhD student at Oxford and previously I was trained in medicine and public health. I am quite new to programming and I learned quite a lot from your materials. However, I wonder, could you please recommend more good codes examples? Programming is a language and I feel most of my day when I was coding by myself I was just checking R/Python libraries--- this feels I was more like learning how to use vocabularies. However, usually when we learn a new language, we also want to learn from good articles so that to learn how other people organize their articles and use different vocabularies. so I wonder, have you noticed any good open-source code project in health data science field? I know nowadays more infectious disease modellers shared their codes, but sometimes I found some of them are so hard to read/understand!
In addition, do you by any chance know any research coding community within Oxford? It would be nice to learn from and help with each other!
Many thanks,
Code snippets for nested if/else statements
Code snippets for long parameter lists
This is a method that runs a simulation. How can we make it better?
model <- function(start, stop, stoc,
spec, dens,
b,
i_mat, i_dur,
ntype, ncov) {
# do stuff
}Change the names to convey meaning
simulate <- function(time_start, time_stop,
is_stochastic, mosquito_species,
mosquito_density,
mosquito_to_human_prob,
immunity_maternal, immunity_duration,
net_type, net_coverage) {
# do stuff
}What are the problems with this?
- We're passing a long list of things that could easily be mixed up; especially if we don't always pass in named arguments
- It's not clear what types things are expected to be
- If we add more parameters, the thing can quickly get unwieldy
How can we make it better?
SimulationParameters <- setClass("SimulationParameters",
slots=list(time_start="numeric",
time_stop="numeric",
is_stochastic="logical"))
# doesn't work
simulation_parameters <- SimulationParameters(
time_start=1990,
time_stop=2018,
is_stochastic=2)
# works
simulation_parameters <- SimulationParameters(
time_start=1990,
time_stop=2018,
is_stochastic=FALSE)Other parameter classes
check <-function(object) {
if(!object@net_type %in% c("net 1", "net 2"))
return("A net must of type `net 1` or `net 2`.")
coverage <- object@net_coverage
if(coverage < 0 | coverage > 1)
return("Net coverage must not be outside [0, 1].")
}
BednetParameters <- setClass("BednetParameters",
slots=list(net_type="character",
net_coverage="numeric"),
validity = check)
# fails
bednet_parameters <- BednetParameters(net_type = "net 3",
net_coverage = 0.3)
# fails
bednet_parameters <- BednetParameters(net_type = "net 2",
net_coverage = 100)Simulation object
Simulation <- setClass("Simulation",
slots=list(simulation_parameters="SimulationParameters",
bednet_parameters="BednetParameters",
immunity_parameters="ImmunityParameters",
mosquito_parameters="MosquitoParameters"))
# ...don't show how to do but could create a "run" method
simulation <- Simulation(simulation_parameters=....)
result <- run(simulation)
# what parameters did I use to run my simulation?
simulation@simulation_parametersMost useful tips for epidemiological coders
I've been going through the various links (thanks @tlestang!) and, to my mind, the following is an ordering representing the prevalence of various code smells in epidemiological code. Note, this partly reflects that most epidemiological people code in R (there are people that also code in C++ but I don't know the language as well) and don't tend to use classes.
- Long parameter lists (I liked the refactoring guru heuristic here ">3/4 parameters?")
- Long methods
- Highly nested if/else loops (Jenny Bryan's presentation had a good example of this)
- Comments within methods
- Abstract or unhelpful variable or function names
What are your thoughts @tlestang ? Any clangers I've missed off? I don't think we'll want to go into the detail of too many.
Snippet for long method -> short functions
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