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prelim fix for g.test

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dr. M.S. (Matthijs) Berends
2023-01-30 12:26:48 +01:00
parent 126afb01a4
commit 89a577805f
5 changed files with 10 additions and 5 deletions
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2
R/g.test.R
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@ -179,7 +179,7 @@ g.test <- function(x,
V <- outer(sr, sc, v, n)
dimnames(E) <- dimnames(x)
STATISTIC <- 2 * sum(x * log(x / E)) # sum((abs(x - E) - YATES)^2/E) for chisq.test
STATISTIC <- 2 * sum(x * log(x / E), na.rm = TRUE) # sum((abs(x - E) - YATES)^2/E) for chisq.test
PARAMETER <- (nr - 1L) * (nc - 1L)
PVAL <- pchisq(STATISTIC, PARAMETER, lower.tail = FALSE)
} else {

2
R/mo.R
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@ -210,7 +210,7 @@ as.mo <- function(x,
# From known codes ----
out[is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code] <- AMR::microorganisms.codes$mo[match(toupper(x)[is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code], AMR::microorganisms.codes$code)]
# From SNOMED ----
if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(microorganisms$snomed), na.rm = TRUE)) {
if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed), na.rm = TRUE)) {
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
out[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)] <- AMR_env$MO_lookup$mo[rep(seq_along(AMR_env$MO_lookup$snomed), vapply(FUN.VALUE = double(1), AMR_env$MO_lookup$snomed, length))[match(x[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)], unlist(AMR_env$MO_lookup$snomed))]]
}