IBI calculation - potential data QC checks

[leppott]

Is your feature request related to a problem? Please describe. Potential checks:

1. Strata spellings. Make sure all are of the correct convention (i.e., spelling).
2. Exclude column. TRUE/FALSE vs. other formats.
3. Add a master taxa list check. User provides and the master taxa list and reports back non-matches. a. Can do for fish and bugs. Just need the lists. If posted online much easier to update/distribute to the users but can put in a current version.
4. Ensure samples with 0 organisms get an IBI of 1.

Describe the solution you'd like A clear and concise description of what you want to happen.

Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered.

Additional context Add any other context or screenshots about the feature request here.

[leppott]

Potentially could create a report of the number of taxa that do / do not have autecological information. Concentrate on what is needed for IBI calculations.

• Phylo information
• habits
• FFG
• tolval (urban)
• fish groups

[leppott]

Could run a routine on Excluded taxa as defined by user vs. automated.

BioMonTools::markExcluded.

Could import routine so don't rely on another package.

https://github.com/leppott/BioMonTools/blob/master/man/markExcluded.Rd

https://github.com/leppott/BioMonTools/blob/master/doc/ExcludedTaxaDecisionCrit.pdf

[leppott]

Count vs. Non-Count taxa per MBSS protocols.

For example, MBSS does not include Acari (water mites) in its samples.

[leppott]

Min/Max individuals.

Min = 60 Max = __

Already have the QC value in the output.

And if less than Min was the sample 100% sorted.

[leppott]

Should check contents of FFG and Habit columns for accepted values.

[leppott]

Added QC check for 0 organisms. Metric Scores and IBI are now "1".

Added one new sample to the example data to ensure catch the error.

Modified Code in metric.values().

Warning message to user.

[ashtonmj]

Erik, I don’t think the 0 individuals = IBI of 1 holds true for bugs as it is for fish. Again, I don’t know why there are so many basic inconsistencies between them, but there are nevertheless. There are no 0 organisms benthic samples in the database; either we don’t calculate it or maybe a sample was re-taken?

Sent from my iPhone

On May 20, 2020, at 7:58 AM, Erik Leppo notifications@github.com wrote:



Added QC check for 0 organisms. Metric Scores and IBI are now "1".

Modified Code in metric.values(). [image: image] https://user-images.githubusercontent.com/24276278/82443563-b6f86180-9a6f-11ea-9b68-dbd2aedac549.png

Warning message to user. [image: image] https://user-images.githubusercontent.com/24276278/82443496-9af4c000-9a6f-11ea-9d7b-75a20db0f8c6.png

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[leppott]

Commented out the BUGS section.

For bugs have a post calculation set of code in the example to test for "large" and "small" samples.

[leppott]

Master taxa (species) is a new function qc_taxa(). Issue #13

[leppott]

Example console output:

[leppott]

Added "NA", "-", "DV", and "SK" as valid values for Habit.

Otherwise returns error.

[leppott]

FFG valid values converted to upper case to avoid showing errors in case:

[leppott]

FFG and Habit check all parts of multi-entry records against the valid values.

For example, ""SW, CN, SP" becomes separate entries for SW, CN, and SP and each is checked against the valid values. This allows for any combination of valid values to be checked.

[leppott]

Added check for fish strata as well.