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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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4
DESCRIPTION
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@ -1,6 +1,6 @@
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

2
NEWS.md
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@ -1,4 +1,4 @@
# 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!)*

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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 {

2
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))]]
} }

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pkgdown/extra.css
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@ -49,6 +49,11 @@
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 */