Started in v0.0.0.9005.

Describe the bug
License tag not showing properly.

To Reproduce
https://leppott.github.io/MBSStools/

Expected behavior
License should be clear.
Make sure everything agrees.

Screenshots

Describe the bug
Fails with non-standard files.

To Reproduce
Load files in Shiny app.

Expected behavior
Should handle files that worked a week ago.

Screenshots
NA

Additional context
Sample files being tested.

Add required packages to each function description and vignette.

Example code fails.

Metrics, MBSS Index, Fish

myIndex <- "MBSS.2005.Fish"

Thresholds

thresh <- metrics_scoring

get metric names for myIndex

(myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"]))))

Taxa Data

myDF.Fish <- taxa_fish
myMetric.Values.Fish <- metric.values(myDF.Fish, "SampleID", "fish", myMetrics.Fish)
View(myMetric.Values.Fish)

Move packages from "Suggests:" to "Imports:" in DESCRIPTION.

Is your feature request related to a problem? Please describe.
Add a Shiny app for metric calculation.

Describe the solution you'd like

• upload a file
• choose MMI
• calculate
• download results as zip file

Describe alternatives you've considered
NA

Additional context
May need to include

• instructions on file input
• MMI basics
• Review / qc file input structure / content
• Review results (table and plot - use dygraphs or plotly)

Is your feature request related to a problem? Please describe.
Warning and error messages in metric.scores don't always space and/or paste correctly.

Describe the solution you'd like
See BioMonTools package for updates.

Describe alternatives you've considered
NA

Additional context
Non-critical.

Describe the bug
QC message about samples with 0 individuals and scoring a 1 is always showing. Even if count is zero.

To Reproduce
Calc FIBI.

Expected behavior
Should only show when count is greater than 0.

Screenshots

Additional context
Add if/then to code is metric.scores().

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

To Reproduce
See images below from the code and the help file.

Expected behavior
NA

Screenshots

Fish

Bugs

Additional context
Checked both bugs and fish and missing 3 required fields from fish index; NATIVE_MBSS, SILT, and TOTBIOM.

data.PHI <- MBSS.PHI
PHI <- PHIcalc(data.PHI)
Error in fun.df[, name.Remote_020][boo.BioRegion == TRUE]/20 :
non-numeric argument to binary operator

Describe the bug
There are two invertebrates in MD with the FFG characteristic "Piercer". If this designation is included in the dataset, it fails to run. Please add this to the valid inputs list.

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
NA

Additional context
Add any other context about the problem here.

Describe the bug
Calculating metrics for fish results in error and no calculation.

To Reproduce
Run example code in metric.values and get error.

# Metrics, MBSS Index, Fish
myIndex <- "MBSS.2005.Fish"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,
"Index.Name"]==myIndex,"MetricName.Other"]))))
# Taxa Data
myDF.Fish <- taxa_fish
myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish)
View(myMetric.Values.Fish)

Expected behavior
Should run without error.

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

Additional context
Did not test other R versions.

Sessioninfo below.

Describe the bug
I get an error code if I have "build_vignettes = TRUE" that says "failed re-building". If I dont put that in there, it works fine.

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
NA

Additional context
Add any other context about the problem here.

Describe the bug
Zip file not created on some computers.

Works on ShinyApps.io and most test machines.

To Reproduce
Run the shiny app but the zip file never gets created so cannot download data.

Expected behavior
Zip file should always get created.

Screenshots
NA

Additional context
utils::zip is the command.

Describe the bug
The sp, rgdal, and maptools packages are to be deprecated at the end of 2023.

To Reproduce
Replace packages with some combination of functions from sf, GEOS, GDAL, or PROJ.

Expected behavior
NA

Additional context
https://www.r-bloggers.com/2022/04/r-spatial-evolution-retirement-of-rgdal-rgeos-and-maptools/

Is your feature request related to a problem? Please describe.
Update GitHub Actions to current standards.

Describe the solution you'd like
See baytrends package.

Describe alternatives you've considered
Not good to leave "as is" since not all actions working.

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

Is your feature request related to a problem? Please describe.
Per email from Matt, 20190221.

Matt sent revised file.

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.

Email from DNR staff on 2017-10-26

Hi Erik,

I am attempting to calculate a FIBI using the package you developed and I found an issue in the metric.scores function, specifically line 181 of the scrip https://github.com/leppott/MBSStools/blob/master/R/metric.scores.R t:

myTF <- DF_Metrics[,IndexName]=="MBSS.2005.Fish" & DF_Metrics[,IndexRegion]=="WARM"

Basically, there is no "WARM" stratum, but rather a warmwater highland stratum, which we designate as "HIGHLAND". I think that changing that in the package script would fix the issues I'm having calculating a FIBI. Let me know what you think.

Thanks,

Jonathan

Add feature; fish maps

Is your feature request related to a problem? Please describe.
Most users won't know the strata for a given site but should have GIS coordinates. Keep users in the R environment instead of requiring GIS (of which most may not have access).

Describe the solution you'd like
Build function to determine strata based on input coordinates.

Describe alternatives you've considered
Access to GIS software is a high bar for most. Keep it simple and stay in R.

Additional context
Use the absolute coordinates. Not checking for location on a blue line (stream). May add distance to blue line and/or edge of strata polygon.

Run Check and make the package CRAN ready.

Describe the bug
The exclude column does not seem to be working. I have tried using the Y/N and TRUE/FALSE designations, but all taxa are being counted in the metrics. This was not a problem when I ran these data in the Fall. Regardless of how this column is formatted, the code does run. Invalid input in this column should trigger a fatal error.

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
NA

Additional context
Add any other context about the problem here.

Is your feature request related to a problem? Please describe.
Benthic macroinvertebrate sample database populates a factor to identify non-unique taxon (EXCLUDE) with levels "TRUE" and "FALSE". MBSStools metric.values.R sets levels of Exclude as "Y" and null. This has created problems reading data in this column when there are long strings of null values and currently requires additional tidying that is not required.

Describe the solution you'd like
Change factor for EXCLUDE from "Y" to "TRUE" when the row is a non-unique taxon to establish consistency with level used in the benthic sample database. This change should be applied in the following lines of metric.values.R

212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 226, 245, 246, 247, 255, 256, 257, 258, 259, 277, 278, 279, 280, 281, 289, 290, 291, 295, 296, 297 (twice), 313, and 439

Describe alternatives you've considered
We have currently made these changes with additional, personal lines of code or directly in flat files, which is not desired.

Describe the bug
Check for and ensure consistency of variable names and examples between functions. For example, Highland vs. Highlands.

To Reproduce
Steps to reproduce the behavior:

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

Expected behavior
Should be the same across datasets and functions.

Screenshots
NA

Additional context
Add any other context about the problem here.

Add feature for calculating MBSS fish and bug MMI (Southerland et al. 2006).

Extra QC checks on taxa data before calculating metrics. And report back to the user.

In Vignette for Taxa maps add "messages=FALSE" to code chunk.

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.

Describe the bug
Ran example code from PHIcalc? on 10/18/2018 in R 3.4.0 and see many NA in raw values for PHI data table. Referenced a handful of sites in database and see they should have data.

To Reproduce
Steps to reproduce the behavior:

1. Go to PHIcalc? http://127.0.0.1:11817/library/MBSStools/html/PHIcalc.html
2. Copy and paste example code into R console and run
3. Visually examine InStrmHab_020 for StationID 1:10
4. See NA
5. Those sites have Instream Habitat scores

Expected behavior
Function ran as expected, but View(PHI) returns table of suspect data

Screenshots

Desktop (please complete the following information):

• OS: Windows 7 Enterprise
• Browser Chrome
• Version Unknown

Describe the bug
If running SHINY on your local machine using the function in R, when you click "download data" you get an extensionless filename suggestion, that gives the error "failed-no file" when you try to save it.

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
NA

Additional context
Add any other context about the problem here.

Is your feature request related to a problem? Please describe.
Want users to be able to use the official MBSS master taxa list in calculations.

Describe the solution you'd like
Shiny App: Add ability to merge the standard master taxa lists (taxa characteristics) with uploaded sample data.

Describe alternatives you've considered
Need in the Shiny app.

Additional context
NA

Error when running MapTaxObs function when loading the county boundary shapefile from GIT.

First ran the function with the directories that already existed in my wd. After the error I deleted the GIS and Maps directories and re-ran the function pulling the GIS data from GIT, but got the same error.

library(MBSStools)

Set Working Directory

wd <- getwd()

Create Example Data if Needed

Create Directories

myDir.create <- file.path(wd,"Data")
ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
[1] "Directory already exists"
myDir.create <- file.path(wd,"GIS")
ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
[1] TRUE
myDir.create <- file.path(wd,"Maps")
ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists")
[1] TRUE

Create Data

Taxa Data

myFiles <- c("AllFish_95to16.xls", "TaxaMapsCrossWalk20170731.xlsx")
file.copy(file.path(path.package("MBSStools"),"extdata",myFiles),file.path(wd,"Data",myFiles))
[1] FALSE FALSE

GIS

unzip(file.path(path.package("MBSStools"),"extdata","MD_GIS.zip"),exdir=file.path(wd,"GIS"))

Inputs

Obs <- "AllFish_95to16.xls"
XWalk <- "TaxaMapsCrossWalk20170731.xlsx"
wd <- getwd()

Create maps

MapTaxaObs(Obs, XWalk, wd)
C:/Users/mashton/Documents
OGR data source with driver: ESRI Shapefile
Source: "C:\Users\mashton\Documents\GIS", layer: "MD_State_Boundary"
with 2 features
It has 9 fields
Integer64 fields read as strings: OBJECTID
OGR data source with driver: ESRI Shapefile
Source: "C:\Users\mashton\Documents\GIS", layer: "MD_Coast_Hydrology"
with 1117 features
It has 9 fields
Integer64 fields read as strings: OBJECTID
OGR data source with driver: ESRI Shapefile
Source: "C:\Users\mashton\Documents\GIS", layer: "MD_Boundary_County_Detailed"
with 24 features
It has 7 fields
Integer64 fields read as strings: OBJECTID DISTRICT COUNTY_FIP COUNTYNUM
Error in as.double(y) :
cannot coerce type 'S4' to vector of type 'double'

Is your feature request related to a problem? Please describe.
Preparing for release to a wider audience. Need more background/explanation in descriptions.

Describe the solution you'd like
Update help documentation, R vignette, and possibly develop a user manual.

Describe alternatives you've considered
NA

Additional context
NA

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

StagedInstall = FALSE in DESCRIPTION is a quick (temporary) fix.

Due to use system.file(package="ContDataQC").

Staged install installs to temp directory and fails.

To Reproduce
Fails on devtools::install_github("leppott/MBSStools")

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

MBSS.Ion.Data and MBSS.Ion.Ref not loading unless use data().

v0.0.0.9006.

Add feature for manipulating CORE data.

add feature for ion matrix.

Describe the bug
Unlike genus BIBI the Family BIBI uses "greater than" instead of "greater than or equal" for its thresholds. The values entered in to the rules table did not adjust for this and values at the upper threshold are being scored a "5" instead of a "3".

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

Metric thresholds from report.

Additional context
Revised threshold values provided by MBSS staff.

Unlike the BioMonTools package that uses an Excel file the extdata folder the MBSStools package has the values in the package as an internal data file. Revise the .tab file and process data script in "data-raw" folder.

Matt, email 20170623.

Still get an error message (below) even when the excel sheet being read in only has one site's (ANTI-101-S-2015) worth of data. All other command lines work up until I request results.

Error in model.frame.default(formula = data.calc[, name.DisCell] ~ data.calc[, :
invalid type (list) for variable 'data.calc[, name.DisCell]'

If I do it with two sites worth (ANTI-101-S and ANTI-101-X) I get the same error message as before multiple zero values per channel.

Error in try(if (sum(tbl.zero$Freq) != nrow(tbl.zero)) stop(msg.dupChan)) :

More than one zero value for Lateral Distance ('Lat. Loc (m)').

This indicates more than one channel ('SumFlowChannelNum') per sample ('SITEYR'). Or an error in the data.

Please correct then retry. Sample and Channel IDs are presented below:

Is your feature request related to a problem? Please describe.
Provide examples for getting data from a database (or Excel) and then calculating the BIBI and FIBI.

Describe the solution you'd like
Another Vignette but also include in the README.

Describe alternatives you've considered
Work with a flat table as well as get from a database query.

Additional context
Need to include the required fields.

Is your feature request related to a problem? Please describe.
Add IBI Narrative

Describe the solution you'd like
Put into example for metric.scores.

Describe alternatives you've considered
It could be in the function but the factor doesn't always translate outside of the function.

Additional context
Added to BioMonTools inside the function but have returned as text.

v0.0.0.9002.
Example data had 2 errors. One sample with repeat single line of all zeros (no affect on results). 2nd sample had 2 channels but both identified as channel 1. Incorrect calculation of total discharge due to 'diff' command not know it was a new channel.