leppott / biomontools

Tools for biomonitoring and bioassessment; metric calculation for benthic macroinvertebrates, fish, and periphyton.

README-BioMonTools

#> Last Update: 2024-05-13 19:40:31.237479

BioMonTools

Functions to aid the data analysis of bioassessment and biomonitoring data. Suite of functions and tools for metric calculation and scoring for mult-metric indices and related data manipulation.

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Installation

To install the current version use the code below to install from GitHub. The use of “force = TRUE” ensures the package is installed even if already present. If the package remotes is missing the code below will install it.

if(!require(remotes)){install.packages("remotes")}  #install if needed
install_github("leppott/BioMonTools", force=TRUE)

Vignettes are not installed by default. If you want the additional documentation (recommended) then use this version of the code.

if(!require(remotes)){install.packages("remotes")}  #install if needed
install_github("leppott/BioMonTools", force=TRUE, build_vignettes=TRUE)

If having issues with install (e.g., ‘cannot open URL’) it could be a latency issue with GitHub.

Use the code below before retrying the above install commands.

options(timeout=400)

Status

In development.

Usage

By those using involved with bioassessment and biomonitoring and the need for data manipulation.

A common set of tools will standardize outputs across entities. No longer need to use the same database or spreadsheet. Only need to format data for use with these tools.

Documentation

Vignette and install guide updates are planned for the future.

Issues

https://github.com/leppott/BioMonTools/issues

Planned Updates

• None at this time.

Future Possible Updates

• Periphyton metrics.
• Coral and Fish metrics (Puerto Rico and US Virgin Islands)
• TaxaList Check
• Map taxon observations

biomontools's Issues

Metric.Values - add periphyton metrics.

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

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
NA

Metrics - bugs - add UFC (taxonomic uncertainty frequency class)

Is your feature request related to a problem? Please describe.
Add UFC metric for benthic macroinvertebrates.
https://doi.org/10.1371/journal.pone.0241933

Describe the solution you'd like
Add to metric_values.R

• calculation (similar to HBI, add at end after BCG)
• Add UFC as required field
• Add to function help file
• Update input example data with UFC field

Describe alternatives you've considered
Only way to add is to require the field.

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

Error: 'pivot_longer' is not an exported object from 'namespace:tidyr'

Describe the bug
Error message:

Error: 'pivot_longer' is not an exported object from 'namespace:tidyr'

To Reproduce
v0.4.0.9013
metric.stats() or metric.stats2()

Expected behavior
Should not get an error.

Screenshots
NA

Additional context
tidyr not listed in DESCRIPTION.

Add it to avoid this error on systems without tidyr installed.

Failed install - R v3.6.0 - staged install

Describe the bug
Staged install implemented in R v.3.6.0 is causing the package to not install.

StagedInstall: no in DESCRIPTION is a quick (temporary) fix.

Due to use of system.file(package="BioMonTools"). Probably save to a variable.

Staged install installs to temp directory and fails.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html

Metric - Request List

Is your feature request related to a problem? Please describe.
Want to be able to calculate any and all metrics for biological programs (bugs, fish, and algae).

Describe the solution you'd like
Add to this issue any metrics that are not in the package but want in the package.

Describe alternatives you've considered
NA

Additional context
Add here and will try to get in the package.

pi_EPT accidentally removes Family Cheumatopsyche

pi_EPT accidentally removes Family Cheumatopsyche:

pi_EPT = 100*sum(N_TAXA[ORDER == "Ephemeroptera" |
ORDER == "Trichoptera" | ORDER == "Plecoptera" &
(is.na(FAMILY)==TRUE | FAMILY != "Cheumatopsyche")], na.rm=TRUE)/ni_total
I will change on my end but I just wanted to bring this up as you may wonder why I made the change!

BioMonTools/R/metric.values.R

Line 796 in 5539f4a

, pi_EPT = 100*sum(N_TAXA[ORDER == "Ephemeroptera" |

README - install command quotes not working

Describe the bug
Using the install command from the README file as displayed on GitHub website fails. It fails due to smart quotes. Double or single doesn't matter as both fail.

To Reproduce

Expected behavior
Should not have to convert quotes.

Screenshots
See above.

Desktop (please complete the following information):

• Win 7
  

• Firefox or Chrome

Additional context
NA

MapTaxaObs - Percent text is 0-1 instead of 0-100

Is your feature request related to a problem? Please describe.
Taxa maps have percent as 0-1. Convert to 0-100 to be consistent throughout the package.

Describe the solution you'd like
Change text in bottom left of the maps.

Describe alternatives you've considered
NA

Additional context
Related to issue #8

#8

metric.values - sort metrics

Is your feature request related to a problem? Please describe.
Sort output columns by metric name.

Describe the solution you'd like
see above

Describe alternatives you've considered
Can use fun.MetricNames to get any groupings but need to specify all names. Want a quicker method for sorting alphabetical.

Additional context
NA

metric.values - stalls when use in Shiny

Describe the bug
The QC check for columns is a prompt to the user in the console. In Shiny don't get the console so the app will stall.

To Reproduce
Run metric.values() when in Shiny.

Expected behavior
Need to skip.

Screenshots
NA

Additional context
The function use interactive() but Shiny counts as TRUE.

metric.values - pi_EphemNoCaeBae

Describe the bug
Metric pi_EphemNoCaeBae is not working. Is counting nearly all Ephemeroptera.

To Reproduce
Run example code from BioMonTools::metric.values

Sample "03013CSR_Bug_2003-07-01_0".

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots

Additional context
Add any other context about the problem here.

"Error" Failed to install..." R (3.6.1)

A clear and concise description of what the bug is.

BioMonTools fails to install in V3.6.1

To Reproduce

1. Go to '...'

library(devtools) #install if needed
Sys.setenv("TAR" = "internal") # needed for R v3.6.0
install_github("leppott/BioMonTools", force=TRUE, build_vignettes=TRUE)

2. See error

Expected behavior

Expected BioMonTools to load.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Windows 10
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

metric.values - error when run all metrics

Describe the bug
When run all metrics (as in example) get error:

df_metric_values_bugs <- metric.values(df_samps_bugs, "bugs", fun.cols2keep=myCols)
Error in !(names(met.val %in% MetricNames_Marine)) :
invalid argument type

To Reproduce
Steps to reproduce the behavior:
Use the example

# Example data

library(readxl)
library(reshape2)

df_samps_bugs <- read_excel(system.file("extdata/Data_Benthos.xlsx"
                                       , package="BioMonTools")
                            , guess_max = 10^6)

# Columns to keep
myCols <- c("Area_mi2", "SurfaceArea", "Density_m2", "Density_ft2")

# Run Function
df_metric_values_bugs <- metric.values(df_samps_bugs, "bugs", fun.cols2keep=myCols)

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
Must be related to recent metric additions for coastal data.

metric.values - nt_natinsctcypr - error - not checking for native

Describe the bug
metric.values - nt_natinsctcypr - error - not checking for native

To Reproduce
GA DNR 2020 index

Expected behavior
Only checking for insectivorous and cyprinidae. Not checking for Native.

Additional context

Index Scoring

Is your feature request related to a problem? Please describe.
Add index scoring.

Describe the solution you'd like
Use framework from MMIcalc and MBSStools.

Describe alternatives you've considered
Need a table as input.

Additional context
Test case use MBSStools data to QC results.

Need multiple scoring regimes.

• Categorical, 1,3,5
• Categorical, 0,2,4,6
• Continuous, 0-1 (or 0-100)

metric.scores - add factor levels to narrative output

Is your feature request related to a problem? Please describe.
The index narrative is returned as text.

Would be good to have it as a factor with levels specified. Then can plot immediately and the order is Poor, Fair, Good and not Fair, Good, Poor (alphabetical or in the order of appearance in the file).

Describe the solution you'd like
See above.

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

Additional context
Example code used after getting result back from metric.scores.

# add factor levels (in order) to narrative

lev_nar <- c("Very Poor", "Poor", "Fair", "Good", "very Good", "Exceptional")
df_metsc_sort$Index_Nar <- factor(df_metsc_sort$Index_Nar, levels=lev_nar)

Vignette - taxa check

Is your feature request related to a problem? Please describe.
Add a vignette for checking taxa lists.

Describe the solution you'd like
BioData, taxize, etc.

Need examples. Don't need functions in the package.

Metric.Score - New Scoring Regimes

Is your feature request related to a problem? Please describe.
GA Fish Index has the original Karr hand drawn lines. AND has inflection points. AND has one metric where if above a certain value then -4 is added to the summed metric scores. AND has a normal distribution (scored as 5 in the center, 3 outside of the center, and scored as 1 on the tails).

Describe the solution you'd like
Add new metric scoring regimes will need changes in metric.scores.R and in MetricScores.xlsx.

New scoring regimes:

• CatGrad_135 (includes inflection point to change to regular Cat_135 scoring regime).

• SingleValue_Add

• Norm_Dist_135

Will need to add extra columns to the Excel file.

And then will have to QC check for those columns.

And will need new scoring regimes.

Describe alternatives you've considered
NA

Additional context
NA

CRAN - prep

Is your feature request related to a problem? Please describe.
Want to eventually post package to CRAN.

Describe the solution you'd like
Need to ensure the package it good to go.

Describe alternatives you've considered
NA

Additional context
Run Check and ensure no issues and adhere to other CRAN guidelines.

Add metric stats for MMI development

Is your feature request related to a problem? Please describe.
Add metric statistics for when developing an MMI.

Describe the solution you'd like
Basic stats (n, min, max, mean, median, quantiles [05, 10, 25, 75, 90, 95], cv]) for each metric.

Subset by ref/str/oth and by dev/cal

Describe alternatives you've considered
New function. metric.stats() matches with metric.values() and metric.scores().

Additional context
Need to output a single dataframe and let the user save it to file.

metric.scores() 2nd example not working (MBSS)

Describe the bug
Using example code in 2nd example (MBSS) of metric.scores() get an error.

To Reproduce
See above.

Expected behavior
Should not get errors.

Screenshots
NA

Additional context
NA

Update parmeters and functions from "." to "_".

Is your feature request related to a problem? Please describe.
Use "_" instead of "." in parameter and function names. Better practice.

Describe the solution you'd like
Will need to add in "deprecated" statements and such.

1. New function names to redirect to old names.
2. Include warnings.
3. Parameters; rename old ones.
4. Add existing "dot" parameters to end of parameter list.
5. Within functions redirect "dot" to "underscore" parameters.
6. Ensure within functions using "_" not ".".

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.

Vignette - Data Prep - fix cases

Describe the bug

from user SH using BCGcalc

And here are my notes of issues I came across:

1. The vignette lists variables to include, in the “Data Prep” section. They are all caps. Yet the data tables had a mixed result of matching cases to what is in the vignette. I made it work on my end, but would expect this could drive some folks batty.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
Add any other context about the problem here.

Add periphyton metrics

Is your feature request related to a problem? Please describe.
Add periphyton metrics to metric.values()

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.

Metric Scoring - imported values "off"

Describe the bug
Some values in MetricScoring.xlsx import with extra decimal places or are off just slightly.

To Reproduce
import the file and check

col2keep <- c("INDEX_REGION", "METRIC_NAME", "Direction", "Thresh_Lo", "Thresh_Hi")
dir <- "C:\\Users\\Erik.Leppo\\OneDrive - Tetra Tech, Inc\\MyDocs_OneDrive\\GitHub\\BioMonTools\\inst\\extdata"
fn <- file.path(dir, "MetricScoring.xlsx")
df <- read_excel(fn, sheet="metric.scoring")
df_MA <- df[df[, "INDEX_NAME"]=="MassDEP.2019.Bugs", c(col2keep, "Scoring_Formula")]
df_MA

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots

Additional context
Due to floating point precision errors in rounding between what is saved and what is shown in Excel.

Test - MS DEQ - MBISQ

Is your feature request related to a problem? Please describe.
Add test for MS DEQ MBISQ.

Describe the solution you'd like
Tested with phase 2018 data and things worked.
Use that data and code as "test".

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.

MapTaxaObs - output_dir is not used.

Describe the bug
if use the example code and change the directory to something other than the working directory it is ignored.

Also, the example does not include nay of the "output" parameters.

To Reproduce
Steps to reproduce the behavior:

df_obs <- data_Taxa_MA
SampID <- "estuary"
TaxaID <- "TaxaName"
TaxaCount <- "Count"
Lat <- "Latitude"
Long <- "Longitude"
output_dir <- getwd()
output_prefix <- "maps.taxa."
output_type <- "pdf"

myDB <- "state"
myRegion <- "massachusetts"
myXlim     <- c(-(73+(30/60)), -(69+(56/60)))
myYlim     <- c((41+(14/60)),(42+(53/60)))

# Run function with extra arguments for map
## Not run: 
MapTaxaObs(df_obs, SampID, TaxaID, TaxaCount, Lat, Long
           , database="state", regions="massachusetts", xlim=myXlim, ylim=myYlim)

Expected behavior
Should accept the output_dir parameter and use the provided folder to save the output file.

Screenshots
NA

Additional context
NA

metric.scores - error when INDEX_REGION doesn't match

Describe the bug
If INDEX_REGION is NA for any records then the function quits.

To Reproduce
Run the metric.scores function with at least one INDEX_REGION as "NA".

Expected behavior
Should skip those records and give a warning.

Screenshots

Additional context
Probably the same for mismatched ones as well.

Need to check.

metric.scores, Cont0100, errors

Describe the bug
Use of median function returning only 1 value for each column.

So only 1st row getting values returned. But is the median of the entire column so values not correct.

To Reproduce
Run metric.scores with an index with 0-100 continuous scoring. For example, GADNR.2006.

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots

Additional context
Use median within sapply to keep the vector of results intact and properly calculated.

metric.values not working - error N_TAXA not found.

Describe the bug
Get an error about N_TAXA not being found when try to calculate metrics.

To Reproduce
Use the example in the function metric.scores.

# Example data

library(readxl)
library(reshape2)

df_samps_bugs <- read_excel(system.file("extdata/Data_Benthos.xlsx"
                                       , package="BioMonTools")
                            , guess_max = 10^6)

# Columns to keep
myCols <- c("Area_mi2", "SurfaceArea", "Density_m2", "Density_ft2")

# Run Function
df_metric_values_bugs <- metric.values(df_samps_bugs, "bugs", fun.cols2keep=myCols)

Expected behavior
Should calculate without error.

Screenshots

Additional context
NA

Metrics - habit/ffg/etc - primary vs. any

Is your feature request related to a problem? Please describe.
Code is set up for any CN to be included in Clinger metrics.
Some programs use only primary. So CN and CN, CB would be included but CB, CN would not.

Describe the solution you'd like
Guess another set of metric output. Maybe "1" for "primary" and "8" for "multiple". In Access use infinity sign for "many" side of relationships.

Describe alternatives you've considered
Haven't thought all the way through yet.

Maybe keep current calculations for "many" and only add in "1" for primary only. (Like this solution better).

Additional context
Will need to generate some new columns for calculation of these metrics.

metric.values - speed up

Adding 11 dominant metrics slowed up metric.values() considerably. Try to speed up.

DESCRIPTION - remove MBSStools

Is your feature request related to a problem? Please describe.
Should not need MBSStools listed in DESCRIPTION.

Describe the solution you'd like
May have to modify some examples.

Describe alternatives you've considered
Don't want the need for another non-CRAN package.

Additional context
NA

dplyr warning - group_by

Describe the bug
With an update to dplyr now get a warning about group_by_(). Should be using group_by().

To Reproduce
Run the example code for metric.values in R v3.6.0.

MBSStools, v0.3.0.9018

Expected behavior
Still works so non-critical.

Screenshots

Additional context
Still works so non-critical.

MapTaxaObs - adding grouping variable for color

Is your feature request related to a problem? Please describe.
Add grouping variable so maps can be color coded.

Describe the solution you'd like
Add "map_grp" to identify a column in the data to be used for plotting by color.

Describe alternatives you've considered
NA

Additional context
If use map_grp = NULL in function call the map does not produce any errors.

Migrate qc.checks function to BioMonTools from BCGcalc.

Is your feature request related to a problem? Please describe.
qc.checks goes with metric.values so have in only this package.

Describe the solution you'd like
Keep base files in both since could change.

Describe alternatives you've considered
NA

Additional context
NA

Metric - Oligochaeta

Is your feature request related to a problem? Please describe.
Oligochaeta has changed from Class to Subclass.

Only using Class in function metric.values()

Describe the solution you'd like
Allow for use of Class or Subclass.

Describe alternatives you've considered
Add a "worms" column. This is fraught with issues. For example, not getting populated, populated in error, or being incomplete. If keep to the phylogenetic columns should not have this problem.

Additional context
Will need to add Subclass as a required field.

Add a statement to the help file to inform users.

markExcluded - Fails if phylo column logical

Describe the bug
Fails when checking phylo levels when all values are NA and R assigns class "logical" instead of "character".

To Reproduce
Add a new column, e.g., SuperFamily, but don't populate with data. So all values are NA and read_excel imports as logical.

Expected behavior
Create check so skips field and/or warns the user.

Screenshots
NA

Additional context
Also happens if use dplyr::filter to get a smaller data set and that doesn't include any values for a phylo level.

markExcluded - dplyr deprecation messages

Describe the bug
dplyr deprecated functions give warning.

To Reproduce
Steps to reproduce the behavior:

1. Use markExcluded example.

Expected behavior
Should have not messages.

Screenshots

Additional context
summarise_() and group_by_()

Help file for package.

Is your feature request related to a problem? Please describe.
Add help file for the package.

Describe the solution you'd like
Easier if have it so can request help at the package level.

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.

metric.values - Index Region - output not the same as input

Describe the bug
The output of the metric.values function for Index_Region is lower case when the input is mixed case.

To Reproduce
See image below.

Expected behavior
Should get back the same case. Values not being used in metric calculation so should be unaffected.

Screenshots

Additional context
Add any other context about the problem here.

Warning messages - clean up

Is your feature request related to a problem? Please describe.
Clean up warning messages when have missing columns for metrics. The first warning is ok. The 2nd is a product of the first (All NA fields go to logical class). The 2nd is an issue with classes of columns and reshape2::melt.

Describe the solution you'd like
Probably check for an "logical" fields and convert to numeric before use reshape2::melt in metric.values function.

Describe alternatives you've considered
NA

Additional context

MetricNames.xlsx - add fish metrics

Is your feature request related to a problem? Please describe.
Fish metrics are in the script metric.values but not declared in meta-data file MetricNames.xlsx.

Describe the solution you'd like
Add them

Describe alternatives you've considered
NA

Additional context
NA

Flags -

Describe the bug
In the MetricFlags table (BCGCalc). For the ni_total metrics, you have two different thresholds entered for Hi vs. Lo sites (one says 400, the other 450). Both should be 450.

Email, from user 2019-04-10.

To Reproduce
File inst/extdata/MetricFlags.xlsx

Expected behavior

Screenshots
NA

Additional context
NA

Vignette - metric.values - SiteType vs. Index_Region

Describe the bug
The function metric.values uses Index_Region.

Previously used Site_Type and this is still in the vignette.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
Function Help

Vignette

Additional context
Add any other context about the problem here.

BCG metrics all zero, metric.values()

Describe the bug
BCG metrics all zero in metric.values().

To Reproduce
Doesn't happen all the time. Does not happen with example dataset.

Expected behavior
Should calculate.

Screenshots
NA

Additional context
Need example data set.

metric.values - not removing non-target taxa

Describe the bug
Metric.values function not removing non-target taxa for benthic macroinvertebrates.

To Reproduce
Use example file below.
NonTargetMiscount.xlsx

Expected behavior
Example file has 15 taxa but should be 14 when remove nontarget = TRUE.

Screenshots
NA

Additional context
NA

metric.values - percent metrics 0-1 or 0-100

Is your feature request related to a problem? Please describe.
From user SH.

Metrics: “pi_XXXXX” represents percent individuals. Yet, the values are <= 1. I believe these are proportions, correct?

Describe the solution you'd like
Will add sentence to help file for metric.values that values are 0-1 (i.e., 0.5 equals 50%).

Describe alternatives you've considered
NA

Additional context
Not sure of any other places this should be mentioned.

markExcluded - dplyr - deprecated functions - summarize_() and group_by_()

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Use example code.

Warning only shows up every 8 hours. Restart R to show the warning.

# Packages
library(readxl)
library(dplyr)
library(lazyeval)
library(knitr)

# Data
df_samps_bugs <- read_excel(system.file("./extdata/Data_Benthos.xlsx"
                                        , package="BioMonTools")
                           , guess_max=10^6)

# Variables
SampID     <- "SampleID"
TaxaID     <- "TaxaID"
TaxaCount  <- "N_Taxa"
Exclude    <- "Exclude_New"
TaxaLevels <- c("Kingdom"
                , "Phylum"
                , "SubPhylum"
                , "Class"
                , "SubClass"
                , "Order"
                , "SubOrder"
                , "SuperFamily"
                , "Family"
                , "SubFamily"
                , "Tribe"
                , "Genus"
                , "SubGenus"
                , "Species"
                , "Variety")
# Taxa that should be treated as equivalent
Exceptions <- data.frame("TaxaID"=c("Sphaeriidae")
                                    , "PhyloID"=c("Pisidiidae"))

# Filter Data
# df_samptax <- filter(df_samps_bugs, !!as.name(SampID) ==
#                                                  "08BEA3478__2013-08-21_0")
# df_tst_small <- markExcluded(df_samptax, SampID, TaxaID, TaxaCount
#                              , TaxaLevels, Exceptions, Exclude)

# EXAMPLE 1
df_tst <- markExcluded(df_samps_bugs
                       , SampID="SampleID"
                       , TaxaID="TaxaID"
                       , TaxaCount = "N_Taxa"
                       , Exclude="Exclude_New"
                       , TaxaLevels=TaxaLevels
                       , Exceptions=Exceptions)

Expected behavior
Shouldn't have any warnings.

Screenshots

Additional context
Replace "_" functions without the "_". Should work fine when change.

Add "ExcludedTaxa" function

Is your feature request related to a problem? Please describe.
Add ExcludedTaxa function.

Describe the solution you'd like
Mark excluded taxa to then be used by metric.values function.

Describe alternatives you've considered
Don't want to rely on user to always populate correctly.

Additional context
Some refer to ExcludedTaxa as ambiguous taxa, non-distinct taxa, or non-unique taxa.