Arguments
@@ -577,10 +578,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
# 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),
+
amoxicillin = as.mic(8),
+
cipro = as.mic(0.256),
+
tobra = as.disk(16),
+
genta = as.disk(18),
ERY = "R"
)
df_long <- data.frame(
@@ -597,8 +598,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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))
+
df_wide %>% mutate_at(vars(amoxicillin:tobra), as.sir)
+
df_wide %>% mutate(across(amoxicillin:tobra, as.sir))
# approaches that all work with additional arguments:
df_long %>%
@@ -613,17 +614,15 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")))
-
df_long %>%
+
df_wide %>%
# given certain columns, e.g. from 'cipro' to 'genta'
mutate_at(vars(cipro:genta), as.sir,
mo = "bacteria",
-
ab = "antibiotic",
guideline = "CLSI")
-
df_long %>%
+
df_wide %>%
mutate(across(cipro:genta,
function(x) as.sir(x,
mo = "bacteria",
-
ab = "antibiotic",
guideline = "CLSI")))
# for veterinary breakpoints, add 'host':
@@ -642,18 +641,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")))
-
df_long %>%
-
# given certain columns, e.g. from AMP to TOB
+
df_wide %>%
mutate_at(vars(cipro:genta), as.sir,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")
-
df_long %>%
+
df_wide %>%
mutate(across(cipro:genta,
function(x) as.sir(x,
mo = "bacteria",
-
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")))
@@ -673,66 +670,60 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
}
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
-
#> Interpreting MIC values: 'AMP' (ampicillin) based on column
+
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
#> 'microorganism', EUCAST 2024...
#> OK
-
#> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
#> 'microorganism', EUCAST 2024...
-
#> NOTES
+
#> NOTE
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
-
#> Interpreting MIC values: 'AMP' (ampicillin) based on column
+
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
#> 'microorganism', EUCAST 2024...
#> OK
-
#> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
#> 'microorganism', EUCAST 2024...
-
#> NOTES
+
#> NOTE
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column
-
#> 'microorganism', EUCAST 2024...
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on
+
#> column 'microorganism', EUCAST 2024...
#> OK
-
#> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column
-
#> 'microorganism', EUCAST 2024...
+
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin) based on
+
#> column 'microorganism', EUCAST 2024...
#> OK
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
-
#> Interpreting MIC values: 'AMP' (ampicillin) based on column
+
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
#> 'microorganism', EUCAST 2024...
#> OK
-
#> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
#> 'microorganism', EUCAST 2024...
-
#> NOTES
+
#> NOTE
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
-
#> Interpreting MIC values: 'AMP' (ampicillin) based on column
+
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
#> 'microorganism', EUCAST 2024...
#> OK
-
#> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
#> 'microorganism', EUCAST 2024...
-
#> NOTES
+
#> NOTE
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column
-
#> 'microorganism', EUCAST 2024...
-
#> OK
-
#> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column
-
#> 'microorganism', EUCAST 2024...
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on
+
#> column 'microorganism', EUCAST 2024...
#> OK
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
-
#> Interpreting MIC values: 'AMP' (ampicillin) based on column
+
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
#> 'microorganism', EUCAST 2024...
#> OK
-
#> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
#> 'microorganism', EUCAST 2024...
-
#> NOTES
+
#> NOTE
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column
-
#> 'microorganism', EUCAST 2024...
-
#> OK
-
#> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column
-
#> 'microorganism', EUCAST 2024...
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on
+
#> column 'microorganism', EUCAST 2024...
#> OK
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
@@ -745,9 +736,104 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
#> 'bacteria', CLSI 2024...
+
#> WARNING
+
#> • Returned an empty result, which is unexpected. Are all of mo, ab, and host set and available?
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2024...
#> OK
-
#> Error in tbl_at_vars(tbl, vars, .include_group_vars = .include_group_vars, error_call = error_call): Can't select columns that don't exist.
-
#> ✖ Column `cipro` doesn't exist.
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...
+
#> OK
+
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2024...
+
#> OK
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2024...
+
#> OK
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...
+
#> OK
+
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2024...
+
#> OK
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> ℹ Assuming breakpoint_type = "animal", since host is set.
+
#> ℹ Please note that in the absence of specific veterinary breakpoints for
+
#> certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,
+
#> aquatic, and poultry, in that order, are used as substitutes.
+
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
+
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
+
#> 'bacteria', CLSI 2024...
+
#> NOTE
+
#> • Using dogs breakpoints since cattle for gentamicin (GEN) in Escherichia coli are not available.
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> ℹ Assuming breakpoint_type = "animal", since host is set.
+
#> ℹ Please note that in the absence of specific veterinary breakpoints for
+
#> certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,
+
#> aquatic, and poultry, in that order, are used as substitutes.
+
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
+
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
+
#> 'bacteria', CLSI 2024...
+
#> NOTE
+
#> • Using dogs breakpoints since cattle for gentamicin (GEN) in Escherichia coli are not available.
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> ℹ Assuming breakpoint_type = "animal", since host is set.
+
#> ℹ Please note that in the absence of specific veterinary breakpoints for
+
#> certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,
+
#> aquatic, and poultry, in that order, are used as substitutes.
+
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI
+
#> 2024...
+
#> WARNING
+
#> • No CLSI 2024 MIC breakpoints available for test Antibiotic (TESTAB).
+
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),
+
#> CLSI 2024...
+
#> WARNING
+
#> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).
+
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),
+
#> CLSI 2024...
+
#> WARNING
+
#> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> ℹ Assuming breakpoint_type = "animal", since host is set.
+
#> ℹ Please note that in the absence of specific veterinary breakpoints for
+
#> certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,
+
#> aquatic, and poultry, in that order, are used as substitutes.
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2024...
+
#> WARNING
+
#> • No CLSI 2024 MIC breakpoints available for ciprofloxacin (CIP).
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...
+
#> OK
+
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2024...
+
#> OK
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),
+
#> EUCAST 2024...
+
#> NOTE
+
#> • Breakpoints for nitrofurantoin (NIT) in Escherichia coli are only available for (uncomplicated) urinary tract infections (UTI); assuming uti = TRUE.
+
#> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract
+
#> infection.
+
#> Use as.sir(uti = FALSE) to prevent this.
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),
+
#> EUCAST 2024...
+
#> NOTE
+
#> • Breakpoints for nitrofurantoin (NIT) in Escherichia coli are only available for (uncomplicated) urinary tract infections (UTI); assuming uti = TRUE.
+
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+
#> all the details of the breakpoint interpretations.
+
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), EUCAST 2024...
+
#> OK
+
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), EUCAST
+
#> 2024...
+
#> OK
+
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), EUCAST
+
#> 2024...
+
#> OK
+
#> microorganism amoxicillin cipro tobra genta ERY
+
#> 1 Escherichia coli 8 <NA> S S R
## Using base R ------------------------------------------------
@@ -755,38 +841,39 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
as.sir(df_wide)
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
-
#> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2024...
+
#> Interpreting MIC values: column 'amoxicillin' (AMX), EUCAST 2024...
#> OK
-
#> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2024...
-
#> NOTES
+
#> Interpreting MIC values: column 'cipro' (CIP, ciprofloxacin), EUCAST
+
#> 2024...
+
#> NOTE
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST
+
#> Interpreting disk diffusion zones: column 'tobra' (TOB, tobramycin), EUCAST
#> 2024...
#> OK
-
#> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST
+
#> Interpreting disk diffusion zones: column 'genta' (GEN, gentamicin), EUCAST
#> 2024...
#> OK
#> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...
#> OK
-
#> microorganism AMP CIP GEN TOB ERY
-
#> 1 Escherichia coli S I S S R
+
#> microorganism amoxicillin cipro tobra genta ERY
+
#> 1 Escherichia coli S I S S R
# return a 'logbook' about the results:
sir_interpretation_history()
-
#> # A tibble: 37 × 16
+
#> # A tibble: 55 × 16
#> datetime index ab_given mo_given host_given ab mo
#> * <dttm> <int> <chr> <chr> <chr> <ab> <mo>
-
#> 1 2024-06-17 12:56:05 4 AMX B_STRPT… human AMX B_STRPT_PNMN
-
#> 2 2024-06-17 12:56:11 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR
-
#> 3 2024-06-17 12:56:11 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR
-
#> 4 2024-06-17 12:56:05 3 AMX B_STRPT… human AMX B_STRPT_PNMN
-
#> 5 2024-06-17 12:56:11 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR
-
#> 6 2024-06-17 12:56:11 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR
-
#> 7 2024-06-17 12:56:05 2 AMX B_STRPT… human AMX B_STRPT_PNMN
-
#> 8 2024-06-17 12:56:11 2 cipro Escheri… human CIP B_[ORD]_ENTRBCTR
-
#> 9 2024-06-17 12:56:11 2 cipro Escheri… human CIP B_[ORD]_ENTRBCTR
-
#> 10 2024-06-17 12:56:04 1 ampicil… Strep p… human AMP B_STRPT_PNMN
-
#> # ℹ 27 more rows
+
#> 1 2024-06-17 14:56:02 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR
+
#> 2 2024-06-17 14:56:02 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR
+
#> 3 2024-06-17 14:56:02 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR
+
#> 4 2024-06-17 14:56:01 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR
+
#> 5 2024-06-17 14:56:02 3 tobra Escheri… horse TOB B_ESCHR_COLI
+
#> 6 2024-06-17 14:56:02 3 tobra Escheri… horse TOB B_ESCHR_COLI
+
#> 7 2024-06-17 14:56:01 2 cipro Escheri… human CIP B_[ORD]_ENTRBCTR
+
#> 8 2024-06-17 14:56:02 2 cipro Escheri… dogs CIP B_ESCHR_COLI
+
#> 9 2024-06-17 14:56:02 2 cipro Escheri… dogs CIP B_ESCHR_COLI
+
#> 10 2024-06-17 14:56:03 2 nitrofu… E. coli human NIT B_ESCHR_COLI
+
#> # ℹ 45 more rows
#> # ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,
#> # notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>
@@ -801,7 +888,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
#> all the details of the breakpoint interpretations.
#> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...
-
#> NOTES
+
#> NOTE
#> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus pneumoniae - assuming body site 'Non-meningitis'.
#> Class 'sir'
#> [1] R
diff --git a/reference/atc_online.html b/reference/atc_online.html
index ef69c47f..0c143761 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -10,7 +10,7 @@
AMR (for R)
-
2.1.1.9056
+
2.1.1.9057
Response from CLSI and EUCAST
-
The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this AMR package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the AMR package.
+
The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this AMR package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this AMR package.
diff --git a/reference/count.html b/reference/count.html
index 8ba50071..c60a65bd 100644
--- a/reference/count.html
+++ b/reference/count.html
@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
AMR (for R)
-
2.1.1.9056
+
2.1.1.9057