R/validate_data.R
validate_microbiology.Rd
Validate microbial isolates & susceptibility records
validate_microbiology(specimens, isolates, susceptibilities)
a data frame with one row per specimen sent to laboratory (see details)
a data frame with one row per microorganism isolated from the laboratory specimen (see details)
a data frame with one row per susceptibility (see details)
TRUE if the validation is passed
The following fields are mandatory:
specimen_id
a unique specimen identifier with no missing value
patient_id
a patient identifier with no missing value
status
one value from the following FHIR R4 reference set:
"available"
: The physical specimen is present and
in good condition.
"unavailable"
: There is no physical specimen because it is either
lost, destroyed or consumed.
"unsatisfactory"
: The specimen cannot be used because of a
quality issue such as a broken container, contamination, or too old.
"entered-in-error"
: The specimen was entered in error and
therefore nullified.
specimen_datetime
datetime when specimen was sampled or received for processing.
specimen_type_code
character vector of descendants of
the SNOMED CT concept 123038009 | Specimen (specimen) |
. Admissible
values are listed in reference_specimen_type
specimen_type_name
character vector of the SNOMED CT
preferred terms for specimen_type_code
specimen_type_display
character vector of custom specimen types for display in user interfaces
The following fields are optional:
encounter_id
a hospital encounter identifier (if the specimen was sampled during admission)
test_display
free text description of test requested for display in user interfaces. For instance: "Mycobacteria culture" or "Microbial culture, anaerobic, initial isolation". Coded concepts should be stored in other custom columns.
reason_display
free text reason for a procedure for display in user interfaces. For instance, "Suspected urinary tract infection", or "Surgical site microbiological sample". Coded concepts should be stored in other custom columns.
The following fields are mandatory:
isolate_id
a unique isolated organism identifier with no missing value
specimen_id
a specimen identifier with no missing value
patient_id
a patient identifier with no missing value
organism_code
a character vector containing either:
a microorganism code validated using as.mo()
NA_character_
if no microorganism was isolated, for instance
due to no growth or mixed heavy growth
organism_name
a microorganism name provided by
mo_name()
, or NA
if no microorganism was isolated
organism_display_name
microorganism name as labelled by the laboratory, for display in user interfaces. No growth/mixed heavy growth should be referenced here
isolation_datetime
datetime when the organism was first isolated (or reported) by the laboratory
The following field is optional:
mdr_classification
character vector of classifications produced by
mdro()
. Admissible values are:
NA_character_
when susceptibilities are not available/conclusive
"Negative"
for isolate presenting no wide resistance phenotype
other character codes dependent on the guideline
parameter
provided to mdro()
The following fields are mandatory:
isolate_id
an isolated organism identifier with no missing value
specimen_id
a specimen identifier with no missing value
patient_id
a patient identifier with no missing value
organism_code
a microorganism code validated using
as.mo()
, with no missing values
organism_name
a microorganism name provided by
mo_name()
, with no missing values
organism_display_name
microorganism name as labelled by the laboratory, for display in user interfaces, with no missing values
agent_code
code of the antimicrobial tested as provided by
as.ab()
agent_name
name of the antimicrobial tested as provided by
ab_name()
agent_display_name
name of the antimicrobial tested,
with no missing values, for display in reports and user interfaces
(can be the same as drug_name
)
rsi_code
"R"
(resistant), "S"
(susceptible),
or "I"
(intermediate exposure), as determined by the laboratory or by
as.sir()
on the basis of minimum inhibitory concentrations
or disk diffusion diameters