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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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30
R/join_microorganisms.R
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@ -42,21 +42,22 @@
#' left_join_microorganisms(as.mo("K. pneumoniae"))
#' left_join_microorganisms("B_KLBSL_PNMN")
#'
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
#' to = as.Date("2018-01-07"),
#' by = 1),
#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
#' "E. coli", "E. coli", "E. coli")),
#' stringsAsFactors = FALSE)
#' colnames(df)
#'
#' df_joined <- left_join_microorganisms(df, "bacteria")
#' colnames(df_joined)
#'
#' \donttest{
#' if (require("dplyr")) {
#' example_isolates %>%
#' left_join_microorganisms() %>%
#' colnames()
#'
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
#' to = as.Date("2018-01-07"),
#' by = 1),
#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
#' "E. coli", "E. coli", "E. coli")),
#' stringsAsFactors = FALSE)
#' colnames(df)
#' df_joined <- left_join_microorganisms(df, "bacteria")
#' colnames(df_joined)
#' }
#' }
inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
@ -119,9 +120,14 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
check_dataset_integrity()
if (!is.data.frame(x)) {
x <- data.frame(mo = x, stringsAsFactors = FALSE)
if (pkg_is_available("tibble", also_load = FALSE)) {
x <- import_fn("tibble", "tibble")(mo = x)
} else {
x <- data.frame(mo = x, stringsAsFactors = FALSE)
}
by <- "mo"
}
x.bak <- x
if (is.null(by)) {
by <- search_type_in_df(x, "mo", info = FALSE)
if (is.null(by) && NCOL(x) == 1) {
@ -171,5 +177,5 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
warning_("in `", type, "_join()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
}
joined
as_original_data_class(joined, class(x.bak))
}