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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 18:46:11 +01:00
This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-10-23 14:59:36 +02:00
parent 0062a3facb
commit 707aa20a37
6 changed files with 12 additions and 25 deletions

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@ -1,6 +1,10 @@
image: jangorecki/r-base-dev
# from https://stackoverflow.com/questions/51866926
image: rocker/r-base
test:
script:
script:
- apt-get update
- apt-get install --yes --no-install-recommends r-cran-testthat r-cran-devtools
- R -e "devtools::install_deps()"
- R CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual

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@ -58,6 +58,7 @@ globalVariables(c(".",
"Pasted",
"patient_id",
"prevalence",
"psae",
"R",
"ref",
"real_first_isolate",

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@ -329,11 +329,6 @@ MDRO <- function(tbl,
& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
& rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
), 'MDRO'] <- 4
a <<- tbl[which(
tbl$family == 'Enterobacteriaceae'
& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
& rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
), ]
tbl[which(
tbl$family == 'Enterobacteriaceae'
& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1

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@ -67,13 +67,7 @@
#' # get bacteria properties like genus and species
#' left_join_microorganisms("mo") %>%
#' # calculate first isolates
#' mutate(first_isolate =
#' first_isolate(.,
#' "date",
#' "patient_id",
#' "mo",
#' col_specimen = NA,
#' col_icu = NA)) %>%
#' mutate(first_isolate = first_isolate(.)) %>%
#' # filter on first E. coli isolates
#' filter(genus == "Escherichia",
#' species == "coli",

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@ -7,7 +7,7 @@
\alias{EUCAST_exceptional_phenotypes}
\title{Determine multidrug-resistant organisms (MDRO)}
\usage{
MDRO(tbl, country = NULL, col_mo = "mo", info = TRUE,
MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
@ -22,8 +22,7 @@ MDRO(tbl, country = NULL, col_mo = "mo", info = TRUE,
peni = "peni", pita = "pita", poly = "poly", qida = "qida",
rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
trim = "trim", trsu = "trsu", vanc = "vanc",
col_bactid = "bactid")
trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
BRMO(tbl, country = "nl", ...)

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@ -73,13 +73,7 @@ septic_patients \%>\%
# get bacteria properties like genus and species
left_join_microorganisms("mo") \%>\%
# calculate first isolates
mutate(first_isolate =
first_isolate(.,
"date",
"patient_id",
"mo",
col_specimen = NA,
col_icu = NA)) \%>\%
mutate(first_isolate = first_isolate(.)) \%>\%
# filter on first E. coli isolates
filter(genus == "Escherichia",
species == "coli",