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Fix refs to mirixdb and NAMESPACE
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@Ulthran
Ulthran committed Jun 26, 2024
1 parent 168ebdc commit 64832b0
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Showing 6 changed files with 33 additions and 33 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ Suggests:
rmarkdown,
covr,
testthat
Depends:
Depends:
R (>= 2.10)
Imports:
whatbacteria
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2 changes: 1 addition & 1 deletion NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -14,4 +14,4 @@ export(mirix_metronidazole)
export(mirix_vancomycin)
export(phenotype_susceptibility)
export(predict_abundance)
import(mirixdb)
import(whatbacteria)
18 changes: 9 additions & 9 deletions R/abx_index.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ NULL
mirix_vancomycin <- function(abundance,
lineage,
replace_zero = 1e-4,
antibiotic_db = mirixdb::taxon_susceptibility,
phenotype_db = mirixdb::taxon_phenotypes) {
antibiotic_db = whatbacteria::taxon_susceptibility,
phenotype_db = whatbacteria::taxon_phenotypes) {
susceptibility <- antibiotic_susceptibility_vancomycin(
lineage, antibiotic_db, phenotype_db)
mirix(abundance, susceptibility, replace_zero)
Expand All @@ -36,7 +36,7 @@ mirix_vancomycin <- function(abundance,
mirix_doxycycline <- function(abundance,
lineage,
replace_zero = 1e-4,
antibiotic_db = mirixdb::taxon_susceptibility) {
antibiotic_db = whatbacteria::taxon_susceptibility) {
susceptibility <- antibiotic_susceptibility_tetracycline(
lineage, antibiotic_db)
mirix(abundance, susceptibility, replace_zero)
Expand All @@ -47,7 +47,7 @@ mirix_doxycycline <- function(abundance,
mirix_amoxicillin <- function(abundance,
lineage,
replace_zero = 1e-4,
antibiotic_db = mirixdb::taxon_susceptibility) {
antibiotic_db = whatbacteria::taxon_susceptibility) {
susceptibility <- antibiotic_susceptibility_penicillin(
lineage, antibiotic_db)
mirix(abundance, susceptibility, replace_zero)
Expand All @@ -58,7 +58,7 @@ mirix_amoxicillin <- function(abundance,
mirix_metronidazole <- function(abundance,
lineage,
replace_zero = 1e-4,
phenotype_db = mirixdb::taxon_phenotypes) {
phenotype_db = whatbacteria::taxon_phenotypes) {
susceptibility <- phenotype_susceptibility(
lineage = lineage,
phenotype = "aerobic_status",
Expand All @@ -75,7 +75,7 @@ mirix_metronidazole <- function(abundance,
mirix_ciprofloxacin <- function(abundance,
lineage,
replace_zero = 1e-4,
phenotype_db = mirixdb::taxon_phenotypes) {
phenotype_db = whatbacteria::taxon_phenotypes) {
susceptibility <- phenotype_susceptibility(
lineage = lineage,
phenotype = "aerobic_status",
Expand All @@ -92,8 +92,8 @@ mirix_ciprofloxacin <- function(abundance,
mirix_gentamicin <- function(abundance,
lineage,
replace_zero = 1e-4,
antibiotic_db = mirixdb::taxon_susceptibility,
phenotype_db = mirixdb::taxon_phenotypes) {
antibiotic_db = whatbacteria::taxon_susceptibility,
phenotype_db = whatbacteria::taxon_phenotypes) {
susceptibility <- antibiotic_susceptibility_aminoglycoside(
lineage, antibiotic_db, phenotype_db)
mirix(abundance, susceptibility, replace_zero)
Expand All @@ -111,7 +111,7 @@ mirix_gentamicin <- function(abundance,
#' 0.5 is typical. For relative abundances, a number that is slightly lower
#' than the lowest relative abundance will work.
#'
#' @import mirixdb
#' @import whatbacteria
#' @return The MiRIx value
#' @export
mirix <- function (abundance, susceptibility, replace_zero = 1e-4) {
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16 changes: 8 additions & 8 deletions R/susceptibility.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@ NULL
#' @rdname antibiotic_specific_susceptibility
#' @export
antibiotic_susceptibility_vancomycin <- function (lineage,
antibiotic_db = mirixdb::taxon_susceptibility,
phenotype_db = mirixdb::taxon_phenotypes) {
antibiotic_db = whatbacteria::taxon_susceptibility,
phenotype_db = whatbacteria::taxon_phenotypes) {
# Gram-positive organisms are susceptible to vancomycin
ph_sus <- phenotype_susceptibility(
lineage = lineage,
Expand All @@ -33,7 +33,7 @@ antibiotic_susceptibility_vancomycin <- function (lineage,
#' @rdname antibiotic_specific_susceptibility
#' @export
antibiotic_susceptibility_tetracycline <- function (lineage,
antibiotic_db = mirixdb::taxon_susceptibility) {
antibiotic_db = whatbacteria::taxon_susceptibility) {
intrinsic_sus <- rep("susceptible", length(lineage))
abx_sus <- antibiotic_susceptibility(
lineage = lineage,
Expand All @@ -45,7 +45,7 @@ antibiotic_susceptibility_tetracycline <- function (lineage,
#' @rdname antibiotic_specific_susceptibility
#' @export
antibiotic_susceptibility_penicillin <- function(lineage,
antibiotic_db = mirixdb::taxon_susceptibility) {
antibiotic_db = whatbacteria::taxon_susceptibility) {
intrinsic_sus <- rep("susceptible", length(lineage))
abx_sus <- antibiotic_susceptibility(
lineage = lineage,
Expand All @@ -57,13 +57,13 @@ antibiotic_susceptibility_penicillin <- function(lineage,
#' @rdname antibiotic_specific_susceptibility
#' @export
antibiotic_susceptibility_aminoglycoside <- function (lineage,
antibiotic_db = mirixdb::taxon_susceptibility,
phenotype_db = mirixdb::taxon_phenotypes) {
gram_stain_db <- mirixdb::taxon_phenotypes[,c("taxon", "rank", "gram_stain")]
antibiotic_db = whatbacteria::taxon_susceptibility,
phenotype_db = whatbacteria::taxon_phenotypes) {
gram_stain_db <- whatbacteria::taxon_phenotypes[,c("taxon", "rank", "gram_stain")]
colnames(gram_stain_db)[3] <- "value"
gram_stain_phenotype <- match_annotation(lineage, gram_stain_db)

aerobic_status_db <- mirixdb::taxon_phenotypes[,c("taxon", "rank", "aerobic_status")]
aerobic_status_db <- whatbacteria::taxon_phenotypes[,c("taxon", "rank", "aerobic_status")]
colnames(aerobic_status_db)[3] <- "value"
aerobic_status_phenotype <- match_annotation(lineage, aerobic_status_db)

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12 changes: 6 additions & 6 deletions man/antibiotic_specific_susceptibility.Rd
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16 changes: 8 additions & 8 deletions man/mirix_antibiotic.Rd
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