From fc269e667d5fd374084fcb05e95f44ce61209a8a Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Mon, 20 May 2024 18:58:35 +0200 Subject: [PATCH] unit test fix --- .github/workflows/check-old.yaml | 1 + .github/workflows/check-recent.yaml | 4 ++-- DESCRIPTION | 2 +- NEWS.md | 2 +- R/bug_drug_combinations.R | 14 +++++++++----- R/plot.R | 4 ++-- R/sir.R | 2 +- 7 files changed, 17 insertions(+), 12 deletions(-) diff --git a/.github/workflows/check-old.yaml b/.github/workflows/check-old.yaml index 01adad0d..13ce2b80 100644 --- a/.github/workflows/check-old.yaml +++ b/.github/workflows/check-old.yaml @@ -49,6 +49,7 @@ jobs: # Test all old versions of R >= 3.0, we support them all! # For these old versions, dependencies and vignettes will not be checked. # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases). + - {os: ubuntu-latest, r: '3.6', allowfail: false} # - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8 - {os: ubuntu-latest, r: '3.4', allowfail: false} - {os: ubuntu-latest, r: '3.3', allowfail: false} diff --git a/.github/workflows/check-recent.yaml b/.github/workflows/check-recent.yaml index c102ee6f..298b42dd 100644 --- a/.github/workflows/check-recent.yaml +++ b/.github/workflows/check-recent.yaml @@ -63,10 +63,10 @@ jobs: - {os: ubuntu-latest, r: 'release', allowfail: false} # older versions (see also check-old.yaml for even older versions): + - {os: ubuntu-latest, r: '4.3', allowfail: false} - {os: ubuntu-latest, r: '4.2', allowfail: false} - {os: ubuntu-latest, r: '4.1', allowfail: false} - - {os: ubuntu-latest, r: '4.0', allowfail: false} - - {os: ubuntu-latest, r: '3.6', allowfail: false} # when a new R releases, this one has to move to check-old.yaml + - {os: ubuntu-latest, r: '4.0', allowfail: false} # when a new R releases, this one has to move to check-old.yaml env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index 53c19e7c..93a2c9f7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9030 +Version: 2.1.1.9031 Date: 2024-05-20 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index ae01943d..52848c78 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9030 +# AMR 2.1.1.9031 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)* diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index d0f0f543..6b02fdf8 100755 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -108,6 +108,7 @@ bug_drug_combinations <- function(x, SDD = integer(0), I = integer(0), R = integer(0), + N = integer(0), total = integer(0), stringsAsFactors = FALSE ) @@ -122,18 +123,19 @@ bug_drug_combinations <- function(x, x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.sir))), drop = FALSE] # turn and merge everything pivot <- lapply(x_mo_filter, function(x) { - m <- as.matrix(table(x)) - data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE) + m <- as.matrix(table(as.sir(x))) + data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], N = m["N", ], stringsAsFactors = FALSE) }) merged <- do.call(rbind_AMR, pivot) out_group <- data.frame( mo = rep(unique_mo[i], NROW(merged)), ab = rownames(merged), S = merged$S, - SDD = merged$SSD, + SDD = merged$SDD, I = merged$I, R = merged$R, - total = merged$S + merged$I + merged$R, + N = merged$N, + total = merged$S + merged$SDD + merged$I + merged$R + merged$N, stringsAsFactors = FALSE ) if (data_has_groups) { @@ -208,11 +210,13 @@ format.bug_drug_combinations <- function(x, SDD = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$SDD[i], na.rm = TRUE)), I = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$I[i], na.rm = TRUE)), R = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)), + N = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)), total = vapply(FUN.VALUE = double(1), idx, function(i) { sum(x$S[i], na.rm = TRUE) + sum(x$SDD[i], na.rm = TRUE) + sum(x$I[i], na.rm = TRUE) + - sum(x$R[i], na.rm = TRUE) + sum(x$R[i], na.rm = TRUE) + + sum(x$N[i], na.rm = TRUE) }), stringsAsFactors = FALSE ) diff --git a/R/plot.R b/R/plot.R index 5ae31ac7..d4727df3 100755 --- a/R/plot.R +++ b/R/plot.R @@ -713,12 +713,12 @@ barplot.sir <- function(height, if (length(colours_SIR) == 1) { colours_SIR <- rep(colours_SIR, 3) } - # add SSD and N to colours + # add SDD and N to colours colours_SIR <- c(colours_SIR[1:2], colours_SIR[2], colours_SIR[3], "#888888") main <- gsub(" +", " ", paste0(main, collapse = " ")) x <- table(height) - # remove missing I, SSD, and N + # remove missing I, SDD, and N colours_SIR <- colours_SIR[!(names(x) %in% c("SDD", "I", "N") & x == 0)] x <- x[!(names(x) %in% c("SDD", "I", "N") & x == 0)] # plot it diff --git a/R/sir.R b/R/sir.R index c36ee8a7..1f314635 100755 --- a/R/sir.R +++ b/R/sir.R @@ -327,7 +327,7 @@ is_sir_eligible <- function(x, threshold = 0.05) { # extra param: warn (logical, to never throw a warning) as.sir.default <- function(x, S = "^(S|U)+$", I = "^(I|H)+$", R = "^(R)+$", N = "^(N|V)+$", SDD = "^(SDD|D)+$", ...) { if (inherits(x, "sir")) { - return(x) + return(as_sir_structure(x)) } x.bak <- x