flexible_argument: Flexible Variable Usage in 'popEpi' Functions

In WetRobot/popEpi: Functions for Epidemiological Analysis using Population Data

Flexible Variable Usage in popEpi Functions

Description

Certain arguments in popEpi can be passed in multiple ways. This document shows the usage and a pitfall in the usage of such flexible arguments.

Details

Flexible arguments in popEpi are used to pass variables existing in your data or in the environment where the function is used (for everyday users this is the global environment - in simple terms, where your data is / your work space). The flexible arguments are modelled after the by argument in data.tables - see ?data.table. There are many ways to supply the same information to certain functions in popEpi, but the possible ways listed below may be limited in some of them to only allow for using only a part of them.

Everyday usage

Most commonly you may pass variable names as character strings, e.g.

FUN(arg = c("V1", "V2"), data = x)

which may be stored in advance:

vars <- c("V1", "V2")

FUN(arg = vars, data = x)

where x contains those variables. You may also supply variable names as symbols:

FUN(arg = V1, data = x)

Or as a list of symbols (similarly to as in aggregate):

FUN(arg = list(V1, V2), data = x)

Or as a list of expressions:

FUN(arg = list(V1 + 1, factor(V2)), data = x)

A formula without a left-hand-side specified is sometimes allowed as well:

FUN(arg = ~ I(V1 + 1) + factor(V2), data = x)

Using a symbol or a list of symbols/expressions typically causes the function to look for the variable(s) first in the supplied data (if any) and then where the function was called. For everyday users this means you might define e.g.

V3 <- factor(letters)

and do e.g.

FUN(arg = list(V1 + 1, factor(V2), V3), data = x)

provided V1 and V2 exist in x or in the function calling environment.

A pitfall

There is one way to use flexible arguments incorrectly: By supplying the name of a variable which exists both in the supplied data and the calling environment, and intending the latter to be used. E.g.

vars <- c("V2")

FUN(arg = V3, data = x)

where x has a column named vars. This causes the function to use x$vars and NOT x$V2.

Advanced

Function programmers are advised to pass character strings whenever possible. To fool-proof against conflicts as described in the section above, refer to the calling environment explicitly when passing the variable containing the character strings:

TF <- environment() ## current env to refer to

vars <- c("V1", "V2")

FUN(arg = TF$vars, data = x)

Even if x has columns named vars and TF, using TF$vars does not use those columns but only evaluates TF$vars in the calling environment. This is made possible by the fact that data is always passed as a data.frame, within which evaluation of expressions using the dollar operator is not possible. Therefore it is safe to assume the data should not be used. However, lists of expressions will not be checked for dollar use and will fail in conflict situations:

TF <- environment() ## current env to refer to

vars <- letters[1:5]

x <- data.frame(vars = 1:5, TF = 5:1, V1 = 10:6)

FUN(arg = list(TF$vars, V1), data = x)

On the other hand you may typically also pass quoted (quote) or substituted substitute expressions etc., where the env$object trick will work as well:

q <- quote(list(vars, V1))

FUN(arg = TF$q, data = x)

This works even with

a <- 1:5

V1 <- quote(TF$a)

FUN(arg = TF$V1, data = x)

So no conflicts should occur.

Author(s)

Joonas Miettinen

See Also

Other popEpi argument evaluation docs: direct_standardization

Examples

data(sire)
## prepare data for e.g. 5-year "period analysis" for 2008-2012
## note: sire is a simulated cohort integrated into popEpi.
BL <- list(fot=seq(0, 5, by = 1/12))
x <- lexpand(sire, birth = bi_date, entry = dg_date, exit = ex_date,
             status = status %in% 1:2,
             breaks = BL)
              
x <- aggre(x, by = fot)

## silly example of referring to pyrs data by fixed character string;
## its possible that the real name wont be fixed in a real-life application.
pyrs <- "actual_pyrs"  
TF <- environment()
x$actual_pyrs <- as.numeric(x$pyrs)
x$pyrs <- 1
             
## this works (uses actual_pyrs eventually)
st <- survtab_ag(fot ~ 1, data = x, surv.type = "surv.obs",
                 pyrs = TF$pyrs, d = from0to1, 
                 surv.method = "hazard")
## this would be wrong (sees expression 'pyrs' and uses that column,
## which is not what is intended here)
st <- survtab_ag(fot ~ 1, data = x, surv.type = "surv.obs",
                 pyrs = pyrs, d = from0to1,
                 surv.method = "hazard")

WetRobot/popEpi documentation built on Aug. 29, 2023, 3:53 a.m.