Bio 708/theobio style guide

Follow Hadley Wickham’s style guide, adapted from Google’s style guide (HW’s link to Google is broken). Some of the differences between Google and HW are:

HW prefers snake_case for identifiers, Google likes kebab or camel (variable.name (or variableName), FunctionName, kConstantName)
HW uses Roxygen
See “Code Smells and Feels.”, Jenny Bryan (2018), for some more advanced suggestions.

Additions from BMB and JD:

DRY = “don’t repeat yourself”. Encapsulate common stuff in functions, or use tidyverse magic (across)
never use absolute paths
don’t use file names with spaces or parens
use stopifnot() for assertions
don’t mask built-in R objects (t, c, data, …)
don’t depend on case sensitivity
don’t put rm(list=ls()) at the top of your code (see commentary by Jenny Bryan)
use TRUE and FALSE rather than T/F (is this in the other style guides already???)
surround multi-line expressions with parentheses instead of relying on R’s rule that statements should be carried on to the next line when the line ends with a binary operator (usually +, %>%). For example,

thing <- (thing %>%
          mutate(foo=x^2)
)

rather than

thing <- thing %>%
    mutate(foo=x^2)

for complicated multi-argument expressions, put the comma on the following line to make commenting/deleting arguments easier (JD)

thing <- (thing 
    %>% mutate(foo=x^2
           , bar=x^3
           , bletch=x^4
    )
)

rather than

thing <- thing %>%
    mutate(foo=x^2,
           bar=x^3,
           bletch=x^4)

use explicit print() statements rather than relying on objects to self-print
use explicit return() statements rather than relying on R’s implicit “return value is the last statement in the function” rule
use ESS conventions of # for end-of-line comments, ## for comments on a line by themselves
omit unnecessary c() (e.g. c(1:30)). Lean toward seq() and seq_along(), but OK (?) to use :