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random() fix

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dr. M.S. (Matthijs) Berends
2023-07-08 21:00:49 +02:00
parent acb534102b
commit 3829311dd3
4 changed files with 11 additions and 9 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 2.0.0.9027 Version: 2.0.0.9028
Date: 2023-07-08 Date: 2023-07-08
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 2.0.0.9027 # AMR 2.0.0.9028
## New ## New
* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations * Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

13
R/random.R
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@@ -94,12 +94,13 @@ random_sir <- function(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...) {
sample(as.sir(c("S", "I", "R")), size = size, replace = TRUE, prob = prob_SIR) sample(as.sir(c("S", "I", "R")), size = size, replace = TRUE, prob = prob_SIR)
} }
random_exec <- function(type, size, mo = NULL, ab = NULL) { random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
df <- AMR::clinical_breakpoints %pm>% df <- AMR::clinical_breakpoints %pm>%
pm_filter(guideline %like% "EUCAST") %pm>% pm_filter(guideline %like% "EUCAST") %pm>%
pm_arrange(pm_desc(guideline)) %pm>% pm_arrange(pm_desc(guideline)) %pm>%
subset(guideline == max(guideline) & subset(guideline == max(guideline) &
method == type) method == method_type &
type == "human")
if (!is.null(mo)) { if (!is.null(mo)) {
mo_coerced <- as.mo(mo) mo_coerced <- as.mo(mo)
@@ -114,7 +115,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
if (nrow(df_new) > 0) { if (nrow(df_new) > 0) {
df <- df_new df <- df_new
} else { } else {
warning_("in `random_", tolower(type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`") warning_("in `random_", tolower(method_type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
} }
} }
@@ -125,11 +126,11 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
if (nrow(df_new) > 0) { if (nrow(df_new) > 0) {
df <- df_new df <- df_new
} else { } else {
warning_("in `random_", tolower(type), "()`: no rows found that match ab '", ab, "', ignoring argument `ab`") warning_("in `random_", tolower(method_type), "()`: no rows found that match ab '", ab, "' (", ab_name(ab_coerced, tolower = TRUE, language = NULL), "), ignoring argument `ab`")
} }
} }
if (type == "MIC") { if (method_type == "MIC") {
# set range # set range
mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256) mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256)
@@ -156,7 +157,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
out[out == max(out)] <- paste0(">=", out[out == max(out)]) out[out == max(out)] <- paste0(">=", out[out == max(out)])
} }
return(out) return(out)
} else if (type == "DISK") { } else if (method_type == "DISK") {
set_range <- seq( set_range <- seq(
from = as.integer(min(df$breakpoint_R, na.rm = TRUE) / 1.25), from = as.integer(min(df$breakpoint_R, na.rm = TRUE) / 1.25),
to = as.integer(max(df$breakpoint_S, na.rm = TRUE) * 1.25), to = as.integer(max(df$breakpoint_S, na.rm = TRUE) * 1.25),

1
_pkgdown.yml
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@@ -233,6 +233,7 @@ reference:
- "`example_isolates`" - "`example_isolates`"
- "`microorganisms`" - "`microorganisms`"
- "`microorganisms.codes`" - "`microorganisms.codes`"
- "`microorganisms.groups`"
- "`antibiotics`" - "`antibiotics`"
- "`intrinsic_resistant`" - "`intrinsic_resistant`"
- "`dosage`" - "`dosage`"