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scientific notation for MICs

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dr. M.S. (Matthijs) Berends
2023-10-20 15:45:00 +02:00
parent bcab4bc9ba
commit ca72a646d0
8 changed files with 23 additions and 7 deletions
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3
R/aa_globals.R
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@ -102,7 +102,7 @@ TAXONOMY_VERSION <- list(
),
SNOMED = list(
accessed_date = as.Date("2021-07-01"),
citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
url = "https://phinvads.cdc.gov"
),
LOINC = list(
@ -113,6 +113,7 @@ TAXONOMY_VERSION <- list(
)
globalVariables(c(
".GenericCallEnv",
".mo",
".rowid",
".syndromic_group",

2
R/mic.R
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@ -184,6 +184,8 @@ as.mic <- function(x, na.rm = FALSE) {
# comma to period
x <- gsub(",", ".", x, fixed = TRUE)
# transform scientific notation
x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"] <- as.double(x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"])
# transform Unicode for >= and <=
x <- gsub("\u2264", "<=", x, fixed = TRUE)
x <- gsub("\u2265", ">=", x, fixed = TRUE)