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(v2.1.1.9054) fix examples

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dr. M.S. (Matthijs) Berends
2024-06-17 13:52:02 +02:00
parent 2dee1d71dc
commit 13baf8d7be
4 changed files with 156 additions and 62 deletions
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105
R/sir.R
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@ -158,33 +158,89 @@
#' summary(example_isolates) # see all SIR results at a glance
#'
#' # For INTERPRETING disk diffusion and MIC values -----------------------
#'
#' # example data sets, with combined MIC values and disk zones
#' df_wide <- data.frame(
#' microorganism = "Escherichia coli",
#' AMP = as.mic(8),
#' CIP = as.mic(0.256),
#' GEN = as.disk(18),
#' TOB = as.disk(16),
#' ERY = "R"
#' )
#' df_long <- data.frame(
#' bacteria = rep("Escherichia coli", 3),
#' antibiotic = c("amoxicillin", "cipro", "tobra", "genta"),
#' mics = as.mic(c(0.01, 1, 4, 8)),
#' disks = as.disk(c(6, 10, 14, 18))
#' )
#'
#' \donttest{
#' ## Using dplyr -------------------------------------------------
#' if (require("dplyr")) {
#' # approaches that all work without additional arguments:
#' df %>% mutate_if(is.mic, as.sir)
#' df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
#' df %>% mutate(across(where(is.mic), as.sir))
#' df %>% mutate_at(vars(AMP:TOB), as.sir)
#' df %>% mutate(across(AMP:TOB, as.sir))
#' df_wide %>% mutate_if(is.mic, as.sir)
#' df_wide %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
#' df_wide %>% mutate(across(where(is.mic), as.sir))
#' df_wide %>% mutate_at(vars(AMP:TOB), as.sir)
#' df_wide %>% mutate(across(AMP:TOB, as.sir))
#'
#' # approaches that all work with additional arguments:
#' df %>% mutate_if(is.mic, as.sir, mo = "column1", guideline = "CLSI")
#' df %>% mutate(across(where(is.mic),
#' function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
#' df %>% mutate_at(vars(AMP:TOB), as.sir, mo = "column1", guideline = "CLSI")
#' df %>% mutate(across(AMP:TOB,
#' function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
#' df_long %>%
#' # given a certain data type, e.g. MIC values
#' mutate_if(is.mic, as.sir,
#' mo = "bacteria",
#' ab = "antibiotic",
#' guideline = "CLSI")
#' df_long %>%
#' mutate(across(where(is.mic),
#' function(x) as.sir(x,
#' mo = "bacteria",
#' ab = "antibiotic",
#' guideline = "CLSI")))
#' df_long %>%
#' # given certain columns, e.g. from AMP to TOB
#' mutate_at(vars(AMP:TOB), as.sir,
#' mo = "bacteria",
#' ab = "antibiotic",
#' guideline = "CLSI")
#' df_long %>%
#' mutate(across(AMP:TOB,
#' function(x) as.sir(x,
#' mo = "bacteria",
#' ab = "antibiotic",
#' guideline = "CLSI")))
#'
#' # for veterinary breakpoints, add 'host':
#' df %>% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "species_column")
#' df %>% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "horse")
#' df %>% mutate(across(where(is.mic),
#' function(x) as.sir(x, guideline = "CLSI", host = "species_column")))
#' df %>% mutate_at(vars(AMP:TOB), as.sir, guideline = "CLSI", host = "species_column")
#' df %>% mutate(across(AMP:TOB,
#' function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
#' df_long$animal_species <- c("cats", "dogs", "horses", "cattle")
#' df_long %>%
#' # given a certain data type, e.g. MIC values
#' mutate_if(is.mic, as.sir,
#' mo = "bacteria",
#' ab = "antibiotic",
#' host = "animal_species",
#' guideline = "CLSI")
#' df_long %>%
#' mutate(across(where(is.mic),
#' function(x) as.sir(x,
#' mo = "bacteria",
#' ab = "antibiotic",
#' host = "animal_species",
#' guideline = "CLSI")))
#' df_long %>%
#' # given certain columns, e.g. from AMP to TOB
#' mutate_at(vars(AMP:TOB), as.sir,
#' mo = "bacteria",
#' ab = "antibiotic",
#' host = "animal_species",
#' guideline = "CLSI")
#' df_long %>%
#' mutate(across(AMP:TOB,
#' function(x) as.sir(x,
#' mo = "bacteria",
#' ab = "antibiotic",
#' host = "animal_species",
#' guideline = "CLSI")))
#'
#' # to include information about urinary tract infections (UTI)
#' data.frame(mo = "E. coli",
@ -197,23 +253,14 @@
#' specimen = c("urine", "blood")) %>%
#' as.sir() # automatically determines urine isolates
#'
#' df %>%
#' df_wide %>%
#' mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
#' }
#'
#'
#' ## Using base R ------------------------------------------------
#'
#' # a whole data set, even with combined MIC values and disk zones
#' df <- data.frame(
#' microorganism = "Escherichia coli",
#' AMP = as.mic(8),
#' CIP = as.mic(0.256),
#' GEN = as.disk(18),
#' TOB = as.disk(16),
#' ERY = "R"
#' )
#' as.sir(df)
#' as.sir(df_wide)
#'
#' # return a 'logbook' about the results:
#' sir_interpretation_history()