Coinfection Species Count
Deduplicate reported parasite species and flag multiple-species detections.
Description
A specimen report can list the same species more than once.
A specimen report can list the same species more than once. Counting distinct detected labels separates repeated reporting from detections of multiple species.
The tool returns uniqueSpecies (unique species); speciesCount (species count); mixedDetection (mixed detection). Input measurements and model parameters are supplied by the caller; the tool computes the stated summary rather than acquiring those measurements.
When to use Coinfection Species Count
Use Coinfection Species Count when you already have detectedSpecies and want uniqueSpecies, speciesCount, mixedDetection. This is useful for checking a supplied calculation, documenting a measurement convention, or comparing observations prepared on the same basis.
How to use Coinfection Species Count and understand its results
- Enter detectedSpecies using the field table below. Match the units, ordering and data boundaries described in the calculation.
- Run the tool after checking the stated bounds and matching paired observations or categories. A malformed request gives a tool error rather than a usable measurement.
- Read uniqueSpecies, speciesCount, mixedDetection. Use the calculation and interpretation below to distinguish amounts, ratios, signs and decision flags where applicable.
- Review the supplied parameters and assumptions before using the result in a report or comparing it with another observation.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| detectedSpecies | Detected species | list of string | Required |
Deduplicate exact nonblank labels in first-observed order. An empty list produces zero species and a false mixed flag.
species count = size(unique detected labels); mixed = species count > 1 The symbols refer to the supplied quantities or generated values described above; unit conversions and comparison boundaries follow the stated implementation.
{
"input": {
"detectedSpecies": [
"A",
"A",
"B"
]
},
"output": {
"uniqueSpecies": [
"A",
"B"
],
"speciesCount": 2,
"mixedDetection": true
}
}Limitations and assumptions
No taxonomy normalization, sequencing or organism-load interpretation is performed. No detections does not prove absence of infection.
Numerical inputs must be finite. The tool checks its declared input shape and calculation constraints; those checks do not verify the quality, calibration or representativeness of the supplied observations.
Alternative or Complementary methods
Multiplex Target Decode: Decode multiplex target detections while preserving the supplied assay-control validity flag. Morbidity Register Summary: Deduplicate a morbidity register and tally unique patients by reported condition code.
Methodological background: DPDx: diagnostic procedures.1
References
-
DPDx: diagnostic procedures — Centers for Disease Control and Prevention
Similar or alternative tools
- Multiplex Target Decode
Decode multiplex target detections while preserving the supplied assay-control validity flag.
- Morbidity Register Summary
Deduplicate a morbidity register and tally unique patients by reported condition code.