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mirror of https://github.com/msberends/AMR.git synced 2025-07-09 02:03:04 +02:00

New mo algorithm, prepare for 2.0

This commit is contained in:
Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
committed by GitHub
parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -31,11 +35,15 @@ expect_equal(AMR:::percentage(0.1234), "12.3%")
expect_equal(AMR:::percentage(0.0054), "0.5%")
expect_equal(AMR:::percentage(0.0055), "0.6%")
expect_equal(AMR:::strrep("A", 5), "AAAAA")
expect_equal(AMR:::strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
expect_equal(AMR:::trimws(" test "), "test")
expect_equal(AMR:::trimws(" test ", "l"), "test ")
expect_equal(AMR:::trimws(" test ", "r"), " test")
# test functions on all R versions - R < 3.3 did not contain these
expect_equal(strrep("A", 5), "AAAAA")
expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
expect_equal(trimws(" test "), "test")
expect_equal(trimws(" test ", "l"), "test ")
expect_equal(trimws(" test ", "r"), " test")
expect_equal(AMR:::trimws2(" test "), "test")
expect_equal(AMR:::trimws2(" test ", "l"), "test ")
expect_equal(AMR:::trimws2(" test ", "r"), " test")
expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -23,8 +27,6 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_true(AMR:::check_dataset_integrity()) # in misc.R
# IDs should always be unique
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
expect_identical(class(microorganisms$mo), c("mo", "character"))
@ -66,26 +68,14 @@ df <- AMR:::MO_lookup
expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
expect_true(all(c(
"mo", "fullname",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "ref", "species_id", "source", "prevalence", "snomed",
"kingdom_index", "fullname_lower", "g_species"
"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies", "rank", "ref", "source",
"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
"snomed", "kingdom_index", "fullname_lower", "full_first", "species_first"
) %in% colnames(df)))
expect_true(all(c(
"fullname", "fullname_new", "ref", "prevalence",
"fullname_lower", "g_species"
) %in% colnames(AMR:::MO.old_lookup)))
expect_inherits(AMR:::MO_CONS, "mo")
expect_identical(
class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list")
)
expect_stdout(print(catalogue_of_life_version()))
uncategorised <- subset(
microorganisms,
genus == "Staphylococcus" &
@ -97,7 +87,8 @@ expect_true(NROW(uncategorised) == 0,
"All staphylococcal species categorised as CoNS/CoPS.",
paste0(
"Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")"
uncategorised$species, " (", uncategorised$mo, ")",
collapse = "\n"
)
)
)

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@ -5,8 +5,12 @@
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -42,11 +46,11 @@ pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.disk(c(10, 20, 40))), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_stdout(print(as.disk(12)))

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -36,8 +40,8 @@ expect_equal(
)
)
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
MOs_mentioned <- sort(AMR:::trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned, keep_synonyms = TRUE, language = NULL)))
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))

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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -57,11 +61,11 @@ pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8))), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_stdout(print(as.mic(c(1, 2, 4, 8))))

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -27,7 +31,7 @@ MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
expect_identical(
as.character(as.mo(c("E. coli", "H. influenzae"))),
as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
c("B_ESCHR_COLI", "B_HMPHL_INFL")
)
@ -36,12 +40,12 @@ expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
expect_equal(as.character(as.mo("Eschr spp.")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
@ -49,9 +53,8 @@ expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
@ -86,14 +89,13 @@ expect_identical(
"staaur",
"S. aureus",
"S aureus",
"Sthafilokkockus aureeuzz",
"Sthafilokkockus aureus",
"Staphylococcus aureus",
"MRSA",
"VISA",
"meth.-resis. S. aureus (MRSA)"
))
"VISA"
), minimum_matching_score = 0)
)),
rep("B_STPHY_AURS", 10)
rep("B_STPHY_AURS", 9)
)
expect_identical(
as.character(
@ -144,8 +146,8 @@ expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
@ -209,34 +211,23 @@ expect_equal(
# check empty values
expect_equal(
as.character(suppressWarnings(as.mo(""))),
as.character(as.mo("")),
NA_character_
)
# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
print(mo_renamed())
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
# check uncertain names
expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
expect_equal(suppressMessages(as.character(as.mo(c("s aure THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_AURS", "B_STPHY_AURS_AURS"))
# predefined reference_df
expect_equal(
as.character(as.mo("TestingOwnID",
@ -255,7 +246,7 @@ expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))
# combination of existing mo and other code
expect_identical(
as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
c("B_ESCHR_COLI", "B_ESCHR_COLI")
)
@ -279,18 +270,18 @@ expect_equal(
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")
)
expect_stdout(print(mo_uncertainties()))
x <- as.mo("S. aur")
x <- as.mo("Sta. aur")
# many hits
expect_stdout(print(mo_uncertainties()))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"), keep_synonyms = FALSE)),
as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
)
# no viruses
expect_equal(as.character(as.mo("Virus")), NA_character_)
expect_equal(as.mo("Virus"), as.mo("UNKNOWN"))
# summary
expect_equal(length(summary(example_isolates$mo)), 6)
@ -308,13 +299,6 @@ expect_equal(
rep("UNKNOWN", 3)
)
expect_null(mo_failures())
expect_error(translate_allow_uncertain(5))
# debug mode
expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
# ..coccus
expect_equal(
as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -25,7 +29,7 @@
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
@ -55,7 +59,7 @@ expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
expect_equal(names(mo_info("Escherichia coli")), c(
"kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"synonyms", "gramstain", "url", "ref",
"status", "synonyms", "gramstain", "url", "ref",
"snomed"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
@ -64,31 +68,29 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
expect_equal(mo_year("Escherichia coli"), 1919)
expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
expect_true(mo_url("Candida albicans") %like% "gbif.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity
MOs <- microorganisms
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en", keep_synonyms = TRUE))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
expect_stdout(print(mo_gramstain("Escherichia coli", language = "en")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "de")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "nl")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "es")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "pt")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "it")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
gr <- mo_gramstain("Escherichia coli", language = NULL)
for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l))
}
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE) # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL, keep_synonyms = TRUE),
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names
# manual property function
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
expect_identical(
mo_property("Escherichia coli", property = "fullname"),
@ -103,12 +105,16 @@ expect_identical(
mo_species("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "species_id"),
mo_property("Escherichia coli", property = "lpsn"),
mo_lpsn("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "gbif"),
mo_gbif("Escherichia coli")
)
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
expect_true(112283007 %in% mo_snomed("Escherichia coli"))
# old codes must throw a warning in mo_* family

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -28,7 +32,9 @@
# functions used by import_fn()
import_functions <- c(
"%chin%" = "data.table",
"anti_join" = "dplyr",
"chmatch" = "data.table",
"cur_column" = "dplyr",
"full_join" = "dplyr",
"has_internet" = "curl",