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prelim fix for g.test

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dr. M.S. (Matthijs) Berends committed 2023-01-30 12:26:48 +01:00
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.8.2.9103 Version: 1.8.2.9104
Date: 2023-01-24 Date: 2023-01-30
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)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
NEWS.md
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# AMR 1.8.2.9103 # AMR 1.8.2.9104
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
R/g.test.R
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@@ -179,7 +179,7 @@ g.test <- function(x,
V <- outer(sr, sc, v, n) V <- outer(sr, sc, v, n)
dimnames(E) <- dimnames(x) 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) PARAMETER <- (nr - 1L) * (nc - 1L)
PVAL <- pchisq(STATISTIC, PARAMETER, lower.tail = FALSE) PVAL <- pchisq(STATISTIC, PARAMETER, lower.tail = FALSE)
} else { } else {
R/mo.R
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@@ -210,7 +210,7 @@ as.mo <- function(x,
# From known codes ---- # 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)] 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 ---- # 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$snomed), na.rm = TRUE)) {
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331 # found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
out[is.na(out) & x %in% unlist(AMR_env$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$snomed))]] out[is.na(out) & x %in% unlist(AMR_env$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))]]
} }
pkgdown/extra.css
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content: 'Maintainers'; content: 'Maintainers';
} }
/* marked words for after using the search box */
mark, .mark {
background: rgba(17, 143, 118, 0.25) !important;
}
/* SYNTAX */ /* SYNTAX */
/* These are simple changes for the syntax highlighting */ /* These are simple changes for the syntax highlighting */