mirror of https://github.com/msberends/AMR.git
(v1.2.0.9002) fix for joins
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Package: AMR
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Package: AMR
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Version: 1.2.0.9001
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Version: 1.2.0.9002
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Date: 2020-06-03
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Date: 2020-06-03
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.2.0.9001
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# AMR 1.2.0.9002
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## <small>Last updated: 03-Jun-2020</small>
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## <small>Last updated: 03-Jun-2020</small>
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### Changed
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### Changed
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@ -57,7 +57,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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check_dataset_integrity()
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check_dataset_integrity()
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check_groups_before_join(x, "inner_join_microorganisms")
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check_groups_before_join(x, "inner_join_microorganisms")
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checked <- joins_check_df(x, by)
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checked <- joins_check_df(x, by)
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x_class <- class(x)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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x <- checked$x
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by <- checked$by
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by <- checked$by
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join <- suppressWarnings(
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join <- suppressWarnings(
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@ -76,7 +76,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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check_dataset_integrity()
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check_dataset_integrity()
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check_groups_before_join(x, "left_join_microorganisms")
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check_groups_before_join(x, "left_join_microorganisms")
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checked <- joins_check_df(x, by)
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checked <- joins_check_df(x, by)
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x_class <- class(x)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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x <- checked$x
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by <- checked$by
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by <- checked$by
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join <- suppressWarnings(
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join <- suppressWarnings(
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@ -95,7 +95,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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check_dataset_integrity()
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check_dataset_integrity()
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check_groups_before_join(x, "right_join_microorganisms")
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check_groups_before_join(x, "right_join_microorganisms")
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checked <- joins_check_df(x, by)
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checked <- joins_check_df(x, by)
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x_class <- class(x)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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x <- checked$x
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by <- checked$by
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by <- checked$by
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join <- suppressWarnings(
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join <- suppressWarnings(
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@ -114,7 +114,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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check_dataset_integrity()
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check_dataset_integrity()
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check_groups_before_join(x, "full_join_microorganisms")
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check_groups_before_join(x, "full_join_microorganisms")
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checked <- joins_check_df(x, by)
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checked <- joins_check_df(x, by)
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x_class <- class(x)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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x <- checked$x
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by <- checked$by
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by <- checked$by
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join <- suppressWarnings(
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join <- suppressWarnings(
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@ -132,7 +132,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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semi_join_microorganisms <- function(x, by = NULL, ...) {
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semi_join_microorganisms <- function(x, by = NULL, ...) {
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check_dataset_integrity()
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check_dataset_integrity()
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check_groups_before_join(x, "semi_join_microorganisms")
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check_groups_before_join(x, "semi_join_microorganisms")
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x_class <- class(x)
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x_class <- get_prejoined_class(x)
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checked <- joins_check_df(x, by)
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checked <- joins_check_df(x, by)
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x <- checked$x
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x <- checked$x
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by <- checked$by
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by <- checked$by
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@ -149,7 +149,7 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
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check_dataset_integrity()
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check_dataset_integrity()
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check_groups_before_join(x, "anti_join_microorganisms")
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check_groups_before_join(x, "anti_join_microorganisms")
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checked <- joins_check_df(x, by)
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checked <- joins_check_df(x, by)
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x_class <- class(x)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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x <- checked$x
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by <- checked$by
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by <- checked$by
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join <- suppressWarnings(
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join <- suppressWarnings(
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@ -190,6 +190,14 @@ joins_check_df <- function(x, by) {
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by = joinby)
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by = joinby)
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}
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}
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get_prejoined_class <- function(x) {
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if (is.data.frame(x)) {
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class(x)
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} else {
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"data.frame"
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}
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}
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check_groups_before_join <- function(x, fn) {
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check_groups_before_join <- function(x, fn) {
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if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
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if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
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warning("Groups are dropped, since the ", fn, "() function relies on merge() from base R, not on join() from dplyr.", call. = FALSE)
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warning("Groups are dropped, since the ", fn, "() function relies on merge() from base R, not on join() from dplyr.", call. = FALSE)
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -43,7 +43,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -229,9 +229,9 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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</div>
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<div id="amr-1209001" class="section level1">
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<div id="amr-1209002" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9001">
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<h1 class="page-header" data-toc-text="1.2.0.9002">
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<a href="#amr-1209001" class="anchor"></a>AMR 1.2.0.9001<small> Unreleased </small>
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<a href="#amr-1209002" class="anchor"></a>AMR 1.2.0.9002<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-03-jun-2020" class="section level2">
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<div id="last-updated-03-jun-2020" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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last_built: 2020-06-03T09:44Z
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last_built: 2020-06-03T12:33Z
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urls:
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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article: https://msberends.gitlab.io/AMR/articles
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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