1Load your extraction data
SynthVahti reads one extraction.csv, the file ExtractVahti exports, one row per study × cutoff. Load it below, or start from the worked example to see the format.
FORMATWhat each column means — and the two ways to give SynthVahti a study
Header row required. Give either a full 2×2 count (tp,fp,fn,tn) or a precomputed proportion with its denominator (opa + n). The 2×2 is preferred — it lets SynthVahti pool positive and negative agreement too, not just overall agreement.
| column | meaning | required? |
|---|---|---|
| record_id | study label shown on the forest plot (e.g. a PMID or first-author-year) | recommended |
| cutoff | the positivity threshold; rows are pooled within each cutoff (e.g. >=1%, >=50%) | recommended |
| tp fp fn tn | the 2×2 agreement table vs the reference standard (true/false positives & negatives) | one of these two |
| opa n | overall percent agreement (0–1) and the total N it was computed on | …or these two |
| kappa_linear | per-study weighted κ, shown descriptively in the table (not pooled) | optional |
Reads as agreement against an imperfect reference, not accuracy — a ≥2-pathologist consensus shares error with the comparator. That framing carries through every figure and export.
Minimal valid file:
2Results — exploratory agreement synthesis
READWhat the results mean
- Overall agreement is the proportion of all classifications that agree.
- Positive agreement is the proportion of reference-positive cases the index assessment classifies as positive.
- Negative agreement is the proportion of reference-negative cases the index assessment classifies as negative.
- The bivariate model (in R) estimates positive and negative agreement jointly across studies, because changing the threshold can raise one while lowering the other; pooling them independently here is for inspection only.
- The SROC curve (in R) summarizes their relationship across studies and thresholds.
These results describe comparative classification performance against the declared reference. They do not establish biological truth, clinical utility, or freedom from reference-standard bias.