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Update "get started" vignette. Minor fixes.
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sdgamboa committed Mar 12, 2024
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6 changes: 3 additions & 3 deletions vignettes/bugphyzz.Rmd
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Expand Up @@ -85,7 +85,7 @@ Metadata associated with the attribute values:
on the curator’s knowledge or results of ASR or IBD.
* Validation. Score of the [10-fold cross-validation analysis](https://github.com/waldronlab/taxPProValidation).
Matthews correlation coefficient (MCC) for discrete attributes and
R-squared for numeric attributes. Default values is 0.5 and above.
R-squared for numeric attributes. Default threshold value is 0.5 and above.
* NSTI. Nearest sequence taxon index as described in
[PICRUSt](https://doi.org/10.1038/nbt.2676) or the
[castor](https://cran.r-project.org/web/packages/castor/index.html) package.
Expand All @@ -97,7 +97,7 @@ Metadata associated with the attribute values:
value of a source based on three criteria: 1) it has a source, 2) it has valid
references, and 3) the curation was peer-reviewed.
Valid options: high, medium, or low, used when a source satisfied three, two,
or one or less of these criteria.
or one of these criteria.

**More information**

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Compare the column names with the data schema described above.

## Creating signatures
## Create signatures

After the attributes have been imported, we can use the `makeSignatures`
function to create a list of signatures. `makeSignatures` accepts a few
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