Hi Martin,
thank you for this approach. I will check my code and see where I can
use it.
Tobias
Am 12.02.19 um 14:58 schrieb Martin Morgan:
use `globalVariables()` to declare these symbols and quieten warnings, at the
expense of quietening warnings about undefined variables in _all_ code and
potentially silencing true positives. Avoid non-standard evaluation (this is
what ddply is doing, using special rules to resolve symbols like `name`) by
using base R functionality; note also that non-standard evaluation is prone to
typos, e.g., looking for the typo `hpx` in the calling environment rather than
the data frame
hpx = 1
ddply(mtcars, "cyl", "summarize", value = mean(hpx)). ## oops, meant
`mean(hp)`.
cyl summarize
1 4 1
2 6 1
3 8 1
Marginally better is
aggregate(hp ~ cyl, mtcars, mean)
cyl hp
1 4 82.63636
2 6 122.28571
3 8 209.21429
where R recognizes symbols in the formula ~ as intentionally unresolved. The
wizards on the list might point to constructs in the rlang package.
Martin
On 2/12/19, 2:35 AM, "Bioc-devel on behalf of web working"
<bioc-devel-boun...@r-project.org on behalf of webwork...@posteo.de> wrote:
Hi,
I am developing a Bioconductor package and can not get rid of some
warning messages. During devtools::check() I get the following warning
messages:
...
summarizeDataFrame: no visible binding for global variable ‘name’
summarizeDataFrame: no visible binding for global variable ‘gene’
summarizeDataFrame: no visible binding for global variable ‘value’
...
Here a short version of the function:
#' Collapse rows with duplicated name column
#'
#' @param dat a \cite{tibble} with the columns name, gene and value
#' @importFrom plyr ddply
#' @import tibble
#' @return a \cite{tibble}
#' @export
#'
#' @examples
#' dat <- tibble(name = c(paste0("position", 1:5), paste0("position",
c(1:3))), gene = paste0("gene", 1:8), value = 1:8)
#' summarizeDataFrame(dat)
summarizeDataFrame <- function(dat){
ddply(dat, "name", "summarize",
name=unique(name),
gene=paste(unique(gene), collapse = ","),
value=mean(value))
}
R interprets the "name", "gene" and "value" column names as variables
during the check. Does anyone has an idea how to change the syntax of
ddply or how to get rid of the warning message?
Thanks in advance!
Tobias
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