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update to septic_patients, speed improvements

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dr. M.S. (Matthijs) Berends
2018-07-25 14:17:04 +02:00
parent 03a3cb397b
commit d9e204031d
26 changed files with 273 additions and 233 deletions
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24
R/join_microorganisms.R
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@ -26,8 +26,8 @@
#' df2 <- left_join_microorganisms(df, "bacteria_id")
#' colnames(df2)
inner_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
if (!any(class(x) %in% c("data.frame", "matrix"))) {
x <- data.frame(bactid = as.character(x), stringsAsFactors = FALSE)
}
# no name set to `by` parameter
if (is.null(names(by))) {
@ -48,8 +48,8 @@ inner_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...
#' @rdname join
#' @export
left_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
if (!any(class(x) %in% c("data.frame", "matrix"))) {
x <- data.frame(bactid = as.character(x), stringsAsFactors = FALSE)
}
# no name set to `by` parameter
if (is.null(names(by))) {
@ -70,8 +70,8 @@ left_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
#' @rdname join
#' @export
right_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
if (!any(class(x) %in% c("data.frame", "matrix"))) {
x <- data.frame(bactid = as.character(x), stringsAsFactors = FALSE)
}
# no name set to `by` parameter
if (is.null(names(by))) {
@ -92,8 +92,8 @@ right_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...
#' @rdname join
#' @export
full_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
if (!any(class(x) %in% c("data.frame", "matrix"))) {
x <- data.frame(bactid = as.character(x), stringsAsFactors = FALSE)
}
# no name set to `by` parameter
if (is.null(names(by))) {
@ -114,8 +114,8 @@ full_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
#' @rdname join
#' @export
semi_join_microorganisms <- function(x, by = 'bactid', ...) {
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
if (!any(class(x) %in% c("data.frame", "matrix"))) {
x <- data.frame(bactid = as.character(x), stringsAsFactors = FALSE)
}
# no name set to `by` parameter
if (is.null(names(by))) {
@ -132,8 +132,8 @@ semi_join_microorganisms <- function(x, by = 'bactid', ...) {
#' @rdname join
#' @export
anti_join_microorganisms <- function(x, by = 'bactid', ...) {
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
if (!any(class(x) %in% c("data.frame", "matrix"))) {
x <- data.frame(bactid = as.character(x), stringsAsFactors = FALSE)
}
# no name set to `by` parameter
if (is.null(names(by))) {