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(v2.1.1.9054) fix examples
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105
R/sir.R
105
R/sir.R
@ -158,33 +158,89 @@
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#' summary(example_isolates) # see all SIR results at a glance
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#'
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#' # For INTERPRETING disk diffusion and MIC values -----------------------
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#'
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#' # example data sets, with combined MIC values and disk zones
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#' df_wide <- data.frame(
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#' microorganism = "Escherichia coli",
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#' AMP = as.mic(8),
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#' CIP = as.mic(0.256),
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#' GEN = as.disk(18),
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#' TOB = as.disk(16),
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#' ERY = "R"
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#' )
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#' df_long <- data.frame(
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#' bacteria = rep("Escherichia coli", 3),
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#' antibiotic = c("amoxicillin", "cipro", "tobra", "genta"),
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#' mics = as.mic(c(0.01, 1, 4, 8)),
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#' disks = as.disk(c(6, 10, 14, 18))
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#' )
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#'
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#' \donttest{
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#' ## Using dplyr -------------------------------------------------
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#' if (require("dplyr")) {
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#' # approaches that all work without additional arguments:
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#' df %>% mutate_if(is.mic, as.sir)
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#' df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
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#' df %>% mutate(across(where(is.mic), as.sir))
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#' df %>% mutate_at(vars(AMP:TOB), as.sir)
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#' df %>% mutate(across(AMP:TOB, as.sir))
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#' df_wide %>% mutate_if(is.mic, as.sir)
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#' df_wide %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
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#' df_wide %>% mutate(across(where(is.mic), as.sir))
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#' df_wide %>% mutate_at(vars(AMP:TOB), as.sir)
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#' df_wide %>% mutate(across(AMP:TOB, as.sir))
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#'
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#' # approaches that all work with additional arguments:
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#' df %>% mutate_if(is.mic, as.sir, mo = "column1", guideline = "CLSI")
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#' df %>% mutate(across(where(is.mic),
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#' function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
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#' df %>% mutate_at(vars(AMP:TOB), as.sir, mo = "column1", guideline = "CLSI")
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#' df %>% mutate(across(AMP:TOB,
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#' function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
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#' df_long %>%
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#' # given a certain data type, e.g. MIC values
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#' mutate_if(is.mic, as.sir,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' guideline = "CLSI")
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#' df_long %>%
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#' mutate(across(where(is.mic),
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#' function(x) as.sir(x,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' guideline = "CLSI")))
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#' df_long %>%
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#' # given certain columns, e.g. from AMP to TOB
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#' mutate_at(vars(AMP:TOB), as.sir,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' guideline = "CLSI")
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#' df_long %>%
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#' mutate(across(AMP:TOB,
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#' function(x) as.sir(x,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' guideline = "CLSI")))
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#'
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#' # for veterinary breakpoints, add 'host':
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#' df %>% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "species_column")
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#' df %>% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "horse")
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#' df %>% mutate(across(where(is.mic),
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#' function(x) as.sir(x, guideline = "CLSI", host = "species_column")))
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#' df %>% mutate_at(vars(AMP:TOB), as.sir, guideline = "CLSI", host = "species_column")
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#' df %>% mutate(across(AMP:TOB,
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#' function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
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#' df_long$animal_species <- c("cats", "dogs", "horses", "cattle")
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#' df_long %>%
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#' # given a certain data type, e.g. MIC values
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#' mutate_if(is.mic, as.sir,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' host = "animal_species",
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#' guideline = "CLSI")
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#' df_long %>%
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#' mutate(across(where(is.mic),
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#' function(x) as.sir(x,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' host = "animal_species",
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#' guideline = "CLSI")))
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#' df_long %>%
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#' # given certain columns, e.g. from AMP to TOB
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#' mutate_at(vars(AMP:TOB), as.sir,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' host = "animal_species",
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#' guideline = "CLSI")
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#' df_long %>%
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#' mutate(across(AMP:TOB,
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#' function(x) as.sir(x,
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#' mo = "bacteria",
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#' ab = "antibiotic",
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#' host = "animal_species",
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#' guideline = "CLSI")))
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#'
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#' # to include information about urinary tract infections (UTI)
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#' data.frame(mo = "E. coli",
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@ -197,23 +253,14 @@
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#' specimen = c("urine", "blood")) %>%
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#' as.sir() # automatically determines urine isolates
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#'
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#' df %>%
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#' df_wide %>%
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#' mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
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#' }
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#'
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#'
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#' ## Using base R ------------------------------------------------
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#'
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#' # a whole data set, even with combined MIC values and disk zones
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#' df <- data.frame(
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#' microorganism = "Escherichia coli",
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#' AMP = as.mic(8),
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#' CIP = as.mic(0.256),
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#' GEN = as.disk(18),
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#' TOB = as.disk(16),
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#' ERY = "R"
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#' )
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#' as.sir(df)
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#' as.sir(df_wide)
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#'
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#' # return a 'logbook' about the results:
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#' sir_interpretation_history()
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