Hi Freek,
the helper_function() is not defined in the main function, but only
called there. I decided to pass a named list of parameters, from which
each helper function grabs those it needs. I also thought about defining
the function in the main function, but decided that this neither helps
the readability nor is particularly useful (I could just do what the
helper function does in the main function directly...).
It would rather have the ability to define for the lapply (or the helper
function itself) that the locale environment of the main function should
be used, but this is at least a workable solution.
But many thanks for your suggestion nonetheless :)
Best
Severin
On 19.04.21 11:14, Manders-2, F.M. wrote:
Hi Severin,
I'm not sure what the best practice is, but since your anonymous function is
defined inside your main function, you don't need to supply it with all those
arguments.
This should also work, because R has lexical scoping:
main_function <- function(alot, of, paramters) {
var01 <- foo
...
varXX <- bar
data_list <- list(data01, data02, data03, ... , dataYY)
lapply(
seq_along(data_list),
function(i) {
stuff
helper_function(var01, ... , varXX)
}
}
This is already a bit shorter.
I hope this helps,
Freek
On 16/04/2021, 13:45, "Bioc-devel on behalf of Severin Bang"
<bioc-devel-boun...@r-project.org on behalf of severin.b...@physik.uni-freiburg.de> wrote:
Dear community,
I am writing my first package with the aim to publish it on
Bioconductor. To structure the code and make it (human) readable I have
defined some helper functions, that will not be exported.
The main function (which will be user available) makes some data
structuring, defines some variables and will then call a helper function
in a lapply-call on a list of data.frames.
Now I find myself passing >>10 arguments (basically everything that was
defined in the main function before the lapply call) to the helper
function when executed by lapply. All arguments (except the index of the
current data.frame from the list which is lapplyd over) are static for
all the runs.
My question is now: What is considered best practice in this case?
should I put all parameters in a list? Is there a way to pass the whole
"parent" environment (the locale of the main function) to lapply, or
should I keep all the single parameters?
Maybe a "pseudo code" example is useful; this is how my problem is
structured:
main_function <- function(alot, of, paramters) {
var01 <- foo
...
varXX <- bar
data_list <- list(data01, data02, data03, ... , dataYY)
lapply(
seq_along(data_list),
function(
i,
var01,
...
varXX
) {
stuff
helper_function(var01, ... , varXX)
},
var01 = var01,
...
varXX = varXX
)
}
Thank you very much!
Best,
Severin
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