NEWS.md
In BioMonTools: Biomonitoring and Bioassessment Calculations

NEWS

#> Last Update: 2025-10-06 14:15:45.452906

Version History

refactor: Bump version number for CRAN

refactor: Remove or edit examples with errors, warnings, or long run times
taxa_translate
- Non-ASCII character in translation file

refactor: Remove or edit examples with errors, warnings, or long run times
metric.scores
metric.values

fix: Remove non-portable command from example
rarify

fix: Fix typo in example
rarify

refactor: Remove print to console for function defaults
rarify.R
MapTaxaObs.R
markExcluded.R
fix: Fix typo in example
markExcluded

style: Use commas at end of wrap lines instead of start of next line
Examples
- assign_indexclass.R
- markExcluded.R
- metric_scores.R
- metric_stats.R
- metric_stats2.R
- metric_values_excel.R
- metric_values.R
- qc_checks.R
- qc_taxa.R
- rarify.R
- taxa_translate.R
refactor: Remove write example in vignette example

docs: Update title and description per CRAN review
refactor: Uncomment or remove lines of code in examples
markExcluded
metric_values_excel
metric.values
qc.checks
refactor: Replace dontrun with donttest in examples
metric.scores
metrics.stats
qc.taxa
MapTaxaObs
style: Format function inputs with ending commas and separate lines for each input
fix: Remove a write location that wasn’t tempdir from vignette
refactor: Reduce records and runtime for MapTaxaObs
fix: Add error condition in qc_taxa for when required field is missing
fix: Update example for qc_taxa to avoid error with missing column name

refactor: Create smaller data set for data_mmi_dev_small
refactor: Use smaller data set for metric.stats and metric.stats2

docs: Bump version for CRAN submission

refactor: Add entire example for metric.stats to don’t run
Fails (\< 5 seconds) on Debian when submit to CRAN

docs: Bump version for CRAN submission

refactor: Update example for metric.stats for speed
Reduce number of rows input rather than reduce the file size

docs: Bump version number for submission to CRAN

refactor: Reduce size of example file in metric.stats
Failed time check (\< 5 seconds) for one OS
docs: Update cran-comments
docs: Add cran-comments.md to .Rbuildignore

docs: Bump version number for submission to CRAN, Issue #49
docs: Update README for install from CRAN

docs: Update authors in DESCRIPTION, per CRAN check, Issue #49
docs: Update URLS in README, per CRAN check, Issue #49
docs: Add cran-comments file

style: Convert = to \<- in metric_values_excel.R
docs: Don’t run examples for taxa.translate to avoid issues with pkgdown

docs: Update license file, Issue #49
Split files per SO article
- https://stackoverflow.com/questions/43550479/how-to-satisfy-both-cran-and-github-license-file-naming-requirements
refactor: Update example data for shorter run times, Issue #49
ext/Data_Benthos.xlsx
docs: Update columns for some datasets in data.R
docs: Add missing dataset documentation to data.R
docs: Update a few missing imports and global bindings
refactor: Modify seq statement in metric.stats per CodeFactor

refactor: Remove large file, Issue #49

breaking: Move Shiny app to a different repo, BioMonTools_Shiny
breaking: Remove run shiny function
version: Bump minor version number to reflect change in Shiny app location

refactor: Add missing package references to function calls, Issue #49
refactor: Add missing global variable bindings, Issue #49
assign_IndexClass
metric.values.bugs
metric.values.fish
metric.values.coral
taxa_translate
refactor: Change if/then statement for checking class in metric.values, Issue #49

tests: Update metric.calc, Issue #113
PA
Algae, Issue #108
- disable until update QC data
Coral
- Fix syntax of test
tests: Update taxa_translate, Issue #113
tests: Update metric_stats, Issue #113
tests: Update metric_names, Issue #113
Algae
fix: Update assign_indexclass, Issue #113
Add TYPE for multi and single
tests: Update assign_indexclass, Issue #113
tests: Update taxa_translate, Issue #113
tests: Remove coral test from metric.values, Issue #113
refactor: Suppress filter warning in metric.scores, Issue #122

fix: Add extra columns to example fish data
docs: Update documentation for example fish data
fix: Update examples
metric.values()
metric.stats(), Issue #122
metric.stats2(), Issue #122
refactor: Update group_by .dots statements in metric.values(), Issue #84

refactor: Update metric.values() for global variables, Issue #49

refactor: Add new metrics for ORWA, Issue #121

refactor: Add new metrics for ORWA, Issue #120
refactor: Convert required logical columns to logical in metric.values
bugs, fish, and coral
no logical required columns for algae

refactor: Add new metrics for GP, Issue #118

refactor: Update MetricScoring.xlsx to fix metric scoring directionality for MIEGLE

refactor: Update Shiny
Make button enable/disable consistent
Make results folder cleand up consistent
- Could lead to errors if don’t refresh app between files and operations
Make selection box defaults consistent
Metric Calculation
- Create select boxes
- Modify columns for metric.values() input

feature: Added Exclude feature to metric calculation in Shiny

refactor: Add parameters to BioMonTools::taxa_translation in Shiny
trim_ws = TRUE
match_caps = TRUE

refactor: Shiny updates
Add shinyalerts to Shiny app for taxa translation
- From MNcalc
disable taxa trans button on startup and enable on upload file
- From MNcalc

refactor: Add taxa translation for RMN to Shiny
docs: Add shinyalert to DESCRIPTION Suggests

refactor: Add metrics, bugs
MS, Issue #116
habit and habitat, Issue #117

refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2
MetricNames.xlsx
metric_values.R

refactor: Add fish metric permutations of non-native
MetricNames.xlsx
metric_values.R

fix: Modify fish metrics BCG_ATTR2 to convert to upper case
metric_values.R
fix: Update fish metrics BCG2_att1234b (nt_, pi_, and pt_)
metric_values.R

refactor: Add new fish metric (pi_BCG2_att1234b)
MetricNames.xlsx
metric_values.R

docs: Update comment about NATIVE in metric.values help

refactor: Add new fish metrics (BCG_att4w5); same as bugs
MetricNames.xlsx
metric_values.R
docs: Start to populate values column in MetricNames.xlsx

refactor: Update MetricNames.xlsx for test
New field is mostly blank so imports as logical and causes error

refactor: Add new fish metrics (nt_, pi_, and pt_) for invertivore
MetricNames.xlsx
metric_values.R

refactor: Update search patterns for some fish trophic metrics
IV
TC

refactor: Add new fish metric for Idaho, trophic invertivore top carnivore
metric_values.R
- Add “IV_TC”
- Modify “IV” to check for specific cases
MetricNames.xlsx

refactor: Add new metric for MN, nt_total_ExclSchool
metric_values.R
MetricNames.xlsx

refactor: Modify code for schooling fish in TYPE for MN metrics
SCHOOLING to SCH
refactor: Modify code for brook trout fish in TYPE for MN metrics
BROOKTROUT to BKT
docs: Update notes for MN metrics above in MetricNames.xlsx
docs: Add date to version number in NEWS
Current entry only

docs: Update Excel files for MN_IBI_Fish Index_Class 1
pi_piscivore_ExclSchool to nt_piscivore

refactor: Add new metrics for MN_IBI_Bugs
nfam_Baetidae
nt_POETNoBae
nt_POETfamBae
docs: Update Excel files for new metrics for MN_IBI_Bugs
MetricNames
MetricScoring

refactor: Update MetricScoring.xlsx
MN, pi_TrichNoHydro scoring formula text

fix: Update MetricScoring.xlsx
MN, narratives

fix: Update MetricScoring.xlsx (MN)

refactor: Update MetricScoring.xlsx
MN_IBI_Fish and MN_IBI_Bugs, index numeric and narrative

style: Clean up new additions to metric_values.R
Move new metrics for GP to alongside previous GP metrics
Move munging for new metrics to alongside previous munging for TYPE

refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT)

refactor: MetricScoring.xlsx change MN IBI classes
Flip Bugs and Fish for 8/9 and 10/11

refactor: Update MN IBI (bugs and fish), Issue #92
Drop “modified” narrative
MetricScoring.xlsx

refactor: Update MN Fish and Bug IBI index scoring, Issue #92

refactor: Update MN fish metric ni_m2_notoler to ni_m_notoler, Issue #92
Length (m) not area (m2)
metric.values.R
MetricScoring.xlsx
MetricNames.xlsx

refactor: Change MN Bugs Index_Class from 8 and 9 to 10 and 11, Issue #92
MetricScoring.xlsx

fix: Update fish metrics brook trout code, Issue #92
Change for MN to replace space invalidated code
Added TYPE_BROOKTROUT to make metric simpler

docs: Add “demo only” language to ORWA example data

BREAKING: Deprecate sum_n_taxa in taxa_translate
Leave in code so if fix can re-enable
Doesn’t work all the time with match_caps and non-ascii character code

refactor: Update zeroind scoring for MN Bugs and Fish IBI, Issue #111
MetricScoring.xlsx

refactor: Update taxa_translate columns for unique taxa output

refactor: Update match_caps code in taxa_translate

refactor: Add default value for match_caps in taxa_translate

refactor: Update MN_Fish_IBI metrics, Issue #111
pi_wetland_notoler_ExclSchool to nt_wetland_notoler
- MetricScoring.xlsx
- MetricNames.xlsx
- metric.values

refactor: Add pi_OligoHiru to metric.values

refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #111

refactor: Update taxa_translate taxatrax_unique ouput
Add match with CAPS

fix: Add TolVal2 as required field for fish metrics in metric.values

test: Add taxa.translate triws test
Add white space (leading, trailing, both) and internal nbsp to test data

feature: Update taxa.translate trimws feature to replace internal

feature: Update metric.scores() to account for MN_IBI_Fish, Issue #111
If another metric is below a threshold then score as zero
refactor: Add hooks in metric.scores() for score zero modifications, Issue #111
refactor: Update help example for metric.scores()

refactor: Update MetricNames.xlsx to mark bug metrics to use for Large Rare metric calculations
refactor: Add remove spaces to columns for metric calculation
Bugs
- HABIT, FFG, LIFE_CYCLE, FFG2, THERMAL_INDICATOR, HABSTRUCT , ELEVATION_ATTR, GRADIENT_ATTR, WSAREA_ATTR
Fish
- TROPHIC, THERMAL_INDICATOR, REPRODUCTION, HABITAT, ELEVATION_ATTR , GRADIENT_ATTR, WSAREA_ATTR
refactor: Add new fish metrics for MN_Fish_IBI, Issue #111
metric.values
MetricNames.xlsx
MetricScoring.xlsx
style: Reorder some metrics in fish section of metric.values
Organize Munge section by column name
tests: metric.values() move time inside verbose to avoid warning message

refactor: Remove match_caps parameter from taxa_translate function, Issue #111
tests: Remove taxa_translate match_caps test, Issue #111

tests: Add tests for removing white space, Issue #111
feature: Update taxa_translate with clean parameters, Issue #111

refactor: Update for MN_Fish_IBI, Issue #92
MetricNames.xlsx
metric_values.R
- Updates to data munging prior to metric calculation

refactor: Update MetricScoring.xlsx for MN_Bug_IBI, Issue #92

refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #92
refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue #92

refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #92
refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue #92
docs: Edit README for timeout issue

refactor: Update pi_Cheu text in MetricNames.xlsx

refactor: Update MetricNames.xlsx for Great Plains BCG

refactor: Merge pull request 114
Add metrics (bugs and fish) for Great Plains BCG

feature: Options added to taxa_translate, Issue #111
Match on ALL CAPS
Clean input names
Not fully implemented

refactor: Post merge updates
Reconcile names for same calculation but different programs and columns
- benthicInvertivore in merge to habitat_beninvert
- MetricNames.xlsx
- metric_values.R
tests: Update fish metric names for new metrics
refactor: Add MN_IBI_Fish metrics to MetricNames.xlsx, Issue #92

refactor: Merge pull request 110
New metrics for NM BCG Fish
- MetricNames.xlsx
- metric_values.R

refactor: New index scoring regimes, Issue #92
MetricScoring.xlsx
AVERAGE_100_M10_R2 for MN_IBI_Bugs
AVERAGE_100_M10_R3 for MN_IBI_Fish

refactor: Modify scoring regime (AVERAGE_100_M10), Issue #92
Round scaling to 2 decimals
Modify MetricScoring.xlsx
metric.scores
refactor: Add new scoring regime (CAT_0510) to metric.scores, Issue #92
fix: Update MN_IBI_Fish thresholds, MetricScoring.xlsx, Issue #92

refactor: Update MetricScoring.xlsx, Issue #92
New scoring regime, AVERAGE_100_M10
Change MN_Bug_IBI scoring regime
refactor: Add new scoring regime calculation to metric.scores , Issue #92

fix: Update MN IBI Fish thresholds in MetricScoring.xlsx, Issue #92
test: Update thresholds for extra digits in MetricScoring.xlsx, Issue #101
Adjust from 11 to 13 digits for one index (WY)

fix: Update MN IBI Bugs thresholds in MetricScoring.xlsx, Issue #92

refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92

refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92

refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92

fix: Update metric.values pi_dom01_BCG* metrics
Add zero to max function to avoid max returning -Inf
refactor: Update metric.values debug steps for fish
Was 10 and changed to 12

refactor: Update MetricScoring.xlsx for WY, Issue #101
fix: After testing add 4 metrics for WY from scoring, Issue #101
Add to MetricNames.xlsx
Add to metric.values.R

fix: Update MetricNames.xlsx for missing coral metric per tests

refactor: Update Excel files for MN IBI
MetricFlags.xlsx
MetricNames.xlsx
MetricScoring.xlsx

refactor: Update GitHub Actions with usethis::use_github_action()
check-standard
test-coverage
pkgdown
docs: Update check badge in ReadMe

fix: Remove uneeded concatenate in tests per CodeFactor
test_metric_names

fix: Update to minor version number 1.0.2
Incorrect version numbers from pull request

pull request 107
refactor: Coral metrics from Blocktt

fix: made changes to coral metrics
added test for Florida BCG

update: Added coral metrics, specifically for FL BCG
metric_values.R
MetricNames.xlsx

refactor: Additional metrics for Great Plains BCG, Issue #106
metric_values.R
MetricNames.xlsx

fix: Update MetricScoring.xlsx
Change MN_IBI_Bugs INDEX_CLASS from 5 IBI classes to 9 site classes, Issue #92
Update all ScoreRegime from Cont_010 to Cont_0010
Added Modify_Value and Modify_Code to adjust values before scoring
- not implemented
style: Update spacing in metric.values

fix: Update MetricScoring.xlsx, ScoreRegime for MN_IBI_bugs, Issue #92
Cont_010 to Cont_0010 to match code

fix: Update metric.values metric, nt_COETNoBraBaeHydTri, Issue #101
Replace Hydropsyche with Hydropsychidae
Metric not calculating properly
Update MetricNames.xlsx
tests: Wrote test for nt_COETNoBraBaeHydTri, Issue #101

fix: Modify metric.values() benthic metric nt_tv_toler8, Issue #104
Was using 6 instead of 8 as minimum

refactor: Add metrics for WY bug MMI, Issue #101
MetricNames.xlsx
MetricScoring.xlsx
metric.values()
fix: Correct metric.values nt_PolyNoSpion, Issue #102
Was not calculating number of taxa
fix: Update metric.values fun.cols2keep to ignore required cols, Issue #100
fix: Change input parameter in metric.scores function, Issue #103
Replace col_IndexRegion with col_IndexClass
Add col_IndexRegion at end of parameters to avoid breaking existing code

refactor: Add ni_total flags (small and large) for MN_IBI_Bugs, Issue #92
MetricFlags.xlsx

feat: Add new issue template for metric and index requests, Issue #99
refactor: Add metrics and index for MN IBI (bugs and fish), Issue #92
MetricNames.xlsx
MetricScoring.xlsx
metric.values()
tests: Run tests for new metrics
Tweak data and tests as needed

refactor: Add metrics for NM BCG, Issue #97
Pull request not able to easily merge, make changes by hand

refactor: Add testing (QC) to metric.values fish calc section

refactor: Add EXCLUDE taxa to fish metrics
nt_*
Error checking to ensure column is included
refactor: Added QC check to fish calc in metric.values
fix: Change QC sub function name for fish in metric.values
refactor: Add “EXCLUDE” column to example fish data
docs: Update description of data_fish_MBSS

refactor: Remove interactive TRUE from algae in metric.values
Same issue with the fish but being proactive
Not included on bugs

refactor: Edits to metric.values fish calc for error in Red Lakes Shiny app
N_ANOMALIES NA to 0
Change “interactive” part of require column check

refactor: More edits to metric.values fish calc for error in Red Lakes Shiny app

refactor: Edit metric.values fish calc for error in Red Lakes Shiny app

refactor: Modify verbose statements in metric.values
Change terminology in code so more generic
Add verbose statements to fish sub function

refactor: Update MetricNames.xlsx with recent name changes

refactor: Change names of trout metrics in metric.values
Better reflects contents of metrics

refactor: Add pi_trout to metric.values

refactor: Update MetricNames.xlsx to match function, fish metrics
refactor: Update metric.values to match MetricNames.xlsx, fish metrics
Added “nt_BCG_att12346”
Left “nt_BCG_att1236sp” to be added later as unsure of definition
tests: Update taxa_translate test for file name change

fix: metric.values boo.shiny code updated to match bugs and algae

refactor: metric.values specify parameters for subfunctions

fix: Update metric, nt_BCG_att55a6, Issue #92
add ‘na.rm = TRUE’

fix: Add missing metric, nt_BCG_att55a6, Issue #92

refactor: Fix BCG_att1236sp fish metrics, pi and pt
Remove nt

feature: Add MN BCG fish metrics, Issue #92
BCG_att1236sp fish metrics (n=3) as NA until better defined
refactor: Update MetricNames.xlsx with new metrics, Issue #92

fix: Cheumatopsyche metrics, Issue #93
Search term updated; Cheumatopsyche to CHEUMATOPSYCHE
Add missing equal sign
Move so alphabetical in output

feature: Add taxaid_dni parameter to metric.values, Issue #96

refactor: Modify output of taxa_translate function, Issue #94
taxatrans\$taxatrans_unique

feat: Add new metric, ni_totalNoDeca, Issue #94
style: Add spaces to code for readability

fix: Update Cheumatopsyche metrics in MetricNames.xlsx, Issue #93
pi_Cheu
pi_EPTNoCheu

fix: Update code for Cheumatopsyche metrics, metric_values.R, Issue #93
pi_Cheu
pi_EPTNoCheu

fix: BioMonTools vignette change reference to metric names
corecold changed to stenocold

fix: Fill in missing Vignette Builder for vignette_NewIndex

fix: Add line for “changed” taxa in taxa_translate

fix: Update domX calculations to combine taxa before calculate in metric_values
bugs and fish

refactor: Update metrics for MN BCG, Issue #92
In myDF remove NA for specialized dom01 calculations

refactor: Update metrics for MN BCG, Issue #92

refactor: Add percent Cheumatopsyche metric

refactor: Additional metrics for MN BCG, Issue #92

refactor: Add bug metrics for MN BCG, Issue #92
style: Update spacing in test file metric_names

refactor: Update MetricFlags.xlsx for MTTI index

refactor: Update metric.values MTTI subset metrics, Issue #90

refactor: Update MetricFlags.xlsx for MTTI index

feature: New parameter in metric.values to run only subset, Issue #90
style: Style changes in metric_values.R

docs: Add vignette for adding a new index, Issue #87
incomplete
refactor: Add CO MMI (bugs)
Draft 2006, verify with report and EDAS database

fix: Update metric.values thermal NA metrics
Add blank (““) to NA as a condition
test: Additional assign_indexclass tests

refactor: Update assign_indexclass to account or NA and ““, Issue #85
fix: Update assign_indexclass to account non standard column names, Isue #85
tests: Add tests for assign_indexclass, Issue #85
refactor: Update assign_indexclass to not fail if index_class in input data, Issue #85

refactor: Update MetricNames.xlsx groupings
Added “Experimental”

feature: Add unique taxa crosswalk to output of taxa_translate

test: Add test for multiple stages for taxa_translate

fix: Turn off QC testing in function assign_indexclass
Was using test data instead of user input

docs: Update taxa_translate example files

refactor: Update taxa_translate to drop a particular ID after translation , Issue #81
Added input paramter
Updated example
Updated test

data: Update extdata for taxa_translate example, Issue #81
Revised PacNW_ORWA data file (2022-12-19)
tests: Revise taxa_translate test for revised data

tests: Create tests for taxa_translate, Issue #81

fix: Update taxa_translaste
Update nonmatch to data frame with count and sum of occurrence, Issue #81
Refine matching
Include summed taxa properly
Drop non-matching taxa (NA and DNI)
Update example

fix: Update taxa_translate for when sum taxa, Issue #81
update: Revise taxa_translate files in extdata

refactor: Tweak debug code in taxa_translate, Issue #81
fix: Update taxa_translate for col_drop_project
Should be debug only

refactor: Change internal workings of taxa_translate, Issue #81
If summarize retain the official taxa columns
Reorder columns in the merged output

refactor: Change internal parameter boo_DEBUG to boo_DEBUG_tt in taxa_translate, Issue #81

refactor: Make taxa_translate as an export object, Issue #81

fix: Updated taxa_translate function to include metadata as parameter, Issue #81

feature: Add taxa_translate function, Issue #81
More general than qc_taxa

fix: Update markExclude to avoid dplyr deprecation warnings, Issue #51

breaking change: Site_Type and Index_Region to Index_Class
refactor: Update rarify function to save example to tempdir

feat: New function assign_IndexClass, Issue #82
Add IndexClass.xlsx to ext folder

refactor: Additional benthic metrics
metric_values.R
MetricNames.xlsx
refactor: Additional column for benthic metrics; AirBreather
modify metric_values for required column
Add to data_benthos_PacNW

fix: Update and add some metrics
metric_values.R
MetricNames.xlsx

fix: Tweak secondary metric name in MetricScoring.xlsx
GA_DNR_Fish_2020

refactor: Modify default term for markExcl from Excluded to Exclude
Ensure is consistent in function, example, vignette
refactor: markExcl warning don’t trigger for 0 levels missing, Issue #80
refcator: markExcl add default of NA to Exceptions parameter, Issue #80

docs: Typo in MetricNames.xlsx (Isoptera instead of Isopoda)
fix: Change logic in metric.values for insertion of missing column names
Was not working in server environment (interacive == FALSE)
docs: Update error message in metric.values for complex columns, Issue #71
Add code needed to error message (base R and tidyverse)
refactor: Change logic for Shiny on server when encounter complex, Issue #71
BCG_ATTR column only, interactive FALSE or boo.Shiny TRUE

feat: Additional BCG metrics, Issue #79
style: Surround operators with space
metric_values
test: Add sum of parts tests for new BCG metrics

fix: Update bug thermal metrics, Issue #78

feature: Additional algae metrics, Issue #75
style: Add outlining to algae metrics
style: Add spaces before and after operators in algae calculations
refactor: Add missing values in MetricNames.xlsx based on tests
refactor: Add missing algae metric pt_BC_12_adj as NA

fix: Hemiptera metrics (nt and pt) not working, Issue #74
Fix spelling

refactor: Additional metrics, Issue #74
fix: Change metric HabitatStruct from RW to RM, Issue #73

refactor: Additional bug and fish metrics, Issue #73
refactor: Add BCG_ATTR as upper case for fish metrics
Update fish BCG metrics to use upper case letters for BCG metrics
style: Add spacing and outlining to metric_values.R
refactor: Updates to MetricNames.xlsx to pass tests

refactor: Change variable classes in metric.scores()
Avoid errors in import via read_excel

refactor: Rename one misspelled bug thermal metrics, Issue #72
‘pt_ti_cool_warm_stenowarm’ should be ‘pt_ti_warm_stenowarm’

refactor: Add and modify bug thermal metrics, Issue #72
metric_values()
extdata.xlsx
style: Add extra spaces to some lines in metric_values()

refactor: Add metrics and scoring for So Cal Marine Bays
extdata.xlsx
extdata.xlsx
tests: Add tests for So Cal Marine Bays
Incomplete

fix: Restore extdata.xlsx
Deleted in v0.5.0.9109, last mod was v0.5.0.9100

docs: Update required fields text in metric.values()
refactor: Copy (as comments) required fields code from bugs to other communities in metric.values()

refactor: Additional output messages to screen in metric.values()

tests: Update metric_stats test for new metrics
fix: Update metric.values() for 1i and 1m metrics, use upper case
Recent change to have all columns to upper case make 1i into 1I

fix: metric.values() remove some fields from conversion to upper case, Issue #69
SAMPLEID, INDEX_NAME, INDEX_REGION
fixes issue with vignettes flag example, Issue #70
fix: Update metvalgrpxl() NOTES, Issue #69
Input File Name to Input Data Frame
Convert text to formula for Description of Work
- Moved from column 1 (text) to column 2 (formulas) in v0.5.0.9101
fix: Shiny, BCG_Attr importing as complex, Issue #71
Specify colClasses as character

refactor: Tweak error checking for bugs in metric.values()
fix: metric.values() columns to upper case for calculation
Error introduced in v0.5.0.9093 (2022-02-03)
refactor: Change reference to some files in BioMonTools vignette
flag section
rebuild without vignettes

refactor: Tweak error checking for bugs in metric.values()

refactor: Tweak error checking for bugs in metric.values()

refactor: Tweak error checking for bugs in metric.values()

refactor: Update shiny app to use metric.values(…, verbose = TRUE)
refactor: Update number of steps in verbose for metric.values()
refactor: Update fill missing columns metric.values()
NA to NA_character_

refactor: Refine message output of metric.values() for use in Shiny
refactor: Add verbose paramters to metric.values()
refactor: Tweak Notes worksheet for metric Excel output

refactor: Add new metric to MetricNames.xlsx

refactor: Shiny add ‘tab’ as acceptable text file upload format.
refactor: Add new bug metric to metric.values()
pi_SphaerCorb

refactor: Modify debugging messages to metric.values() for Shiny log

refactor: Add debugging messages to metric.values()

fix: Update metric.values() for input data missing Index_Name and Index_Region

fix: Update metric.values() with more error checking for missing columns
At start for minimal required fields before community specific sections
After metric values calculated in bug section for NA to 0

refactor: Update metvalgrpxl() for blank cells hiding text to left

fix: Update to changes in metric.values()

fix: Remove redundant code in metric.values()
Causing failures on Shiny.io with missing required columns

refactor: Update metvalgrpxl() to use input parameter for groupings

refactor: Small edits to Shiny app
Text edits to help pages
Update links for TaxaMaps
refactor: Update metvalgrpxl() to use formulas in output

refactor: Edits to help pages in Shiny app
Update links to download files

refactor: Shiny app updates
Calculate Metrics
Update help/notes for each function
- RMD in data-raw
Add download files to www folder
refactor: Define global variables in functions
metric.values
refactor: Define imported function
MapTaxaObs
markExcluded
metric.stats2
feature: Update MetricNames.xlsx with Sort_Group
feature: Add new function, metvalgrpxl(), Issue #68

fix: Correct spelling of file name in global.R
ShinyApps.io is Linux and is case-sensitive

refactor: Reorganize -raw folder with subfolders
Keep only the scripts to be run at the root
Will have to update scripts at later date to use the new structure
feature: Added HTML creation scripts for text in shiny app to -raw
feature: Updates to Shiny app to include help text for each function
feature: Add runShiny() to launch shiny app from console
docs: Removed XLConnect from DESCRIPTION Suggests package list
Not used
docs: Added writexl package to DESCRIPTIOn Suggest for upcoming change , Issue # 68

docs: Update GitHub default branch from “master” to “main”

refactor: Added global variable bindings to fish metrics metric.values()
Only BCG_Attr
fix: metric.values() example 4 (fish) view statement incorrect

feature: Add new fish metrics to metric.values()
pi_BCG_att23_SCC
nt_BCG_att23_SCC
pt_BCG_att23_SCC

feature: Add new fish metrics to metric.values()
pi_Lepomis
pt_Lepomis
nt_BCG_attNA
pi_BCG_attNA
pt_BCG_attNA

refactor: Modify shiny mark excluded default new column name
EXCLUDED to Exclude to match required column for metric calc
refactor: Add package version number to shiny About page
docs: Add DT package to DESCRIPTION

feature: Update Shiny app, all functions working, Issue #67

feature: Add Shiny app, basic outline only, Issue #67

refactor: Allow for mixed case in bug metric phylo metrics, Issue #65

fix: Update metric.values(), was returning 0 records
length_m was commented out and caused error in met.val

tests: Update tests to ensure MetricNames.xlsx is complete
refactor: Update metric.valus() with metrics used in MetricScoring.xlsx

docs: Create documentation for data_fish_MBSS dataset
docs: Update MetricNames.xlsx and MetricScoring.xlsx for any new metrics, Issue #64

feature: New fish metrics, Issue #64
feature: Add fish example data
refactor: Add .groups = “drop_last” to each subfunction in metric_values(), Issue #20
refactor: Fish metric names
nt_natcent to nt_natCent_sunfish
- GADNR_Fish_2020
- Includes sunfish and had to add a Centrarchidae only metric
- Fixed in metric.values() and MetricScoring.xlsx
lepomis to Lepomis

refactor: Update thermal metric default values, Core-Cold to CoreC
metric.values()
data_benthos_PacNW

fix: metric.values() thermal indicator metric not correct
nt_ti_corecold_cold
pt_ti_corecold_cold

fix: metric.values() thermal indicator NA metric not correct
Using wrong column (Habitat) to find NA

fix: metric.values() not working for new metrics, Issue #62
Elevation, Gradient, and WSArea

refactor: Update MetricScoring.xlsx for IEPA, Issue #63
tests: Update test_threshold_numdigits to show rows with issues

feature: Add more benthic metrics, Issue #62
Adds new required fields
- GRADIENT
- ELEVATION
- WSAREA
Update data with new columns
- data_benthos_PacNW
- Data_Benthos.xlsx
Update data.R with changes to data_benthos_PacNW
refactor: Update Vignettes for changes in metrics
refactor: Update tests for changes in metrics
break: Rename thermal benthic metrics, Issue #62
tests: Update metric test names

tests: Update tests for benthos for UFC column
refactor: Update diatom mmi dev data for tests, add Phylum
ProcessData
data description
refactor: Update MetricNames to match MetricScores
Failed test after addition of algal metrics
Add metrics “pi_BCG_att5extra” and “x_UFC”
Add notes
tests: Update metric name tests
tests: Update metric stats test

refactor: Update MetricScoring.xlsx from dev_periphyton merge

fix: Remove unneeded concatenation, markExcluded, Issue #61

fix: Update NEWS after merging of pull request
Add items below from branch NEWS
- Some updates missing filled in from Branch info
dev_metric_periphyton, Version 0.5.0.9066 (2021-06-23)
refactor: added diatom example dataset to package
- Added diatom metric value dataset for internal QC
dev_metric_periphyton, Version 0.5.0.9065 (2021-06-23)
refactor: Added example taxa data and example metric value data to package
refactor: Added testthat script (test_metric_calc.R) to test metric calculation.
dev_metric_periphyton, Version 0.5.0.9064 (2021-06-23)
refactor: Updated MetricNames.xlsx according to Ben Jessup’s metric descriptions for Indiana
dev_metric_periphyton, Version 0.5.0.9063 (2021-06-22)
refactor: metric.values
- Added 52 new diatom metrics (added from EDAS)
refactor: MetricNames.xlsx
- Update for new diatom metrics, but missing descriptions
refactor: Added scoring formulae for IDEM Diatom IBIs
dev_metric_periphyton, Version 0.5.0.9062 (2021-06-22)
refactor: Added *_RefIndicators metrics
dev_metric_periphyton, Version 0.5.0.9061 (2021-06-15)
Fix: grepl issues in algae metrics
dev_metric_periphyton, Version 0.5.0.9060 (2021-06-11)
refactor: metric.values
- Added over 150 diatom metrics
- Almost all were USGS diatom metrics
refactor: MetricNames.xlsx
- Update for new diatom metrics
dev_metric_periphyton, Version 0.5.0.9059 (2021-06-10)
refactor: metric.values added periphyton/diatom metric functionality
- Added metrics for Indiana diatoms IBIs
refactor: MetricNames.xlsx
- Update for new diatom metrics

feature: Add qc_taxa function from MBSStools package
Update example
feature: Add Shiny app folders and files
docs: Add shiny related packages to DESCRIPTION Suggests
refactor: Started adding NJ fish IBI 2005 to MetricScoring.xlsx

feature: Add taxonomic uncertainty frequency class metric for bugs, Issue #57
refactor: Update example data with UFC field, Issue #57
extdata_Benthos.xlsx
data_benthos_PacNW
Update data.R

feature: Add pi_BCG_att5extra to metric.values() for bugs
5 and 5.5

feature: Add more fish metrics to metric.values()
refactor: For fish community for metric.values() convert to upper case

refactor: Move legend to the right margin, MapTaxaObs, Issue #52
docs: README, update install code to use remotes instead of devtools

refactor: Update MapTaxaObs
subset function not working as intended
refactor: MapTaxaObs, percent 0-100, Issue #28
refactor: MapTaxaObs, add output directory path, Issue #27
refactor: MapTaxaObs, add grouping variable to color points, Issue #52
Add colors and legend
Add new parameters to function
Update example

refactor: Convert messages to warnings in markExcluded
cat() and flush.console() to message()

refactor: Update scoring to allow for scaling from metric to index scores
MetricScoring.xlsx, add ScoreScaling column
metric_scores.R, add AVERAGESCALE_100 as new index scoring option

refactor: Incorporate pull request #50
metric.stats2, fix group_by with change in dplyr

refactor: Metric.Scoring.xlsx, updates for FFXCOVA_2018 metrics
Coastal Plain, x_HBI, Cont_0100 to Cont_0010
Floating point errors, n = 7
refactor: Add new metric, pi_EPTNoHydro to MetricNames.xlsx

refactor: Metric.Scoring.xlsx, update to remove NA from index scoring
Both numeric and narrative.
Caused an issue with scoring FFXCOVA_2018

refactor: metric.values, update new metric, pi_EPTNoHydro

docs: Add Ben Block as contributor.
refactor: metric.values, add new metric, pi_EPTNoHydro
refactor: Metric.Scoring.xlsx, updates for FFXCOVA_2018

refactor: metric.values, fix nt_ECT
Had nt_ECP

refactor: metric.values add new metric if IL EPA lakes, Issue #3
nt, pi, pt
- Ephemeroptera, Coleoptera, Trichoptera
Add global variable bindings
refactor: MetricNames.xlsx
Update for new metrics
refactor: Update MetricScoring.xlsx
MassIBI Low Gradient
- Update narrative thresholds
IL EPA Lakes
- Add new indices
docs: markExcluded example missing a comment line
Causing examples to fail

refactor: metric.values, add 3 new FFG metrics, Issue #3
nt, pi, pt
- omnivore (OM)
- parasite (PA)
refactor: metric.values, Add global variable binding
FFG metrics new here and from v0.5.0.9444
refactor: MetricNames.xlsx
Update for new metrics
refactor: Modify ffg_filt metrics to use CF or FC
metric.values
- nt, pi, pt
MetricNames.xlsx
refactor: Modify ffg_col metrics to use CG or GC
metric.values
- nt, pi, pt
MetricNames.xlsx

feature: Add logo from RBP 2nd edition
docs: Update README with logo

style: Fix items, goodpractice::gp()
Replace ‘=’ with ‘\<-’
- metric_stats.R
- metric_stats2.R
Trim lines to 80 characters
- test_qc_checks.R
- test_metric_names.R
- test_metric_calc.R
- test_markExcluded.R
- rarify.R
- qc_checks.R
- metric_values.R (partial)
- metric_stats2.R
- metric_stats.R
- metric_scores.R (partial)
- markExcluded.R
style: Fix spelling, devtools::spell_check()
ReadMe
NEWS
metric_stats.R

refactor: metric.values, add 3 new FFG metrics, Issue #3
nt, pi, pt
- macrophyte herbivore (MAH)
- xylophage (XYL)
- piercer-herbivore (PIH)
refactor: MetricNames.xlsx
Update for new metrics
refactor: MetricScores.xlsx
GADNR_fish_2005, ensure consistent index_region between metric and index scoring
Test was failing. Passes now

refactor: metric.values, add pi_DiptNonIns metric
style: metric.values, start to trim lines to 80 characters

refactor: metric.values, modify GA fish metric pi_natinsctcypr, Issue #48
Was not checking for Native

refactor: metric.values, modify fish metrics for TROPHIC to account for multiple values

refactor: MetricScoring.xlsx
GA DNR Fish, standardize 2005 index regions to all CAPS the same as 2020.
Breaking change for scripts based on 2005 fish index

docs: Move updates from NEWS to README
refactor: Update MetricScoring.xlsx for MA

docs: Update README install section, Issue #11

tests: Activate tests
rarify

test: Add blank testing file for any function without a test
MapTaxaObs
refactor: Update MapTaxaObs example
Direct to tempdir() instead of getwd()
Comment out 2nd non-working example
style: Update MapTaxaObs for readability

fix: Replace instances of deprecated functions
Change dplyr::group_by_ to dplyr::group_by
- metric.stats2
test: Add tests
metric.stats2
test: Comment out failing tests so package builds
Tests ok in console but not passing after build
markExcluded
qc_checks
metric.stats2
rarify

fix: Replace instances of deprecated functions
Change dplyr::group_by_ to dplyr::group_by
- metric.values
test: Add tests
qc_checks
markExcluded
metric.stats

test: Add metric.values and metrics.scores for MA kick/logradient IBI
docs: Update data.R for missing columns
data_benthos_MBSS
data_mmi_dev
refactor: document internal functions of metric.values()
fix: Remove non-ASCII character from data_mmi_dev

refactor: Add global variable binding
metric.stats
metric.scores
test: qc.check test not working, comment out
docs: Document undocumented argument
metric.stats2
fix: Rebuild data_benthos_MBSS with missing columns so no warnings in example
chore: Add to .Rbuildignore
NEWS.rmd
README.rmd
data-raw folder

docs: DESCRIPTION, move packages from Imports to Suggests
knitr
rmarkdown
docs: DESCRIPTION, set license
refactor: Add foo:: to missing functions
metric.stats
metric.stats2
refactor: Add global variable binding
markExcluded
metric.scores
metric.stats
metric.stats2
metric.values
qc.checks

doc: Delete docso will rebuild.
style: Remove undesireable function, replace library(foo) with foo::bar()
vignette_MapTaxaObs
style: Trim to 80 character lines
vignette_MapTaxaObs

test: Add tests + rarify + qc_checks (gives warning but passes)

refactor: Remove unneeded concatenations
metric_stats
vignette_BioMonTools
refactor: Remove undesireable function, replace library(foo) with foo::bar()
vignette_BioMonTools
style: Trim to 80 character lines
vignette_BioMonTools
NEWS

refactor: Add foo:: to missing functions
ProcessData_TaxaMater_Ben_BCG_PacNW.R
test_metric_calc.R
refactor: Trim lines to 80 characters

refactor: Add foo:: to missing functions

ci: Add code coverage GitHub Action

refactor: change 1:foo() to seq_len(foo())
test_metric_calc
metric_stats
qc_checks

style: rarify, remove trailing ;

docs: Change to pkgdown from manual (docs in main branch) to GitHub Action (gh-pages branch)

docs: ReadMe, add badges for codefactor and codecov

docs: ReadMe, knit with updates from previous commit

ci: Change from TravisCI to GitHub Actions
docs: ReadMe, Add CI badge
docs: ReadMe, add lifecycle badge

MetricScoring.xlsx
Fix two index threshold values with floating point errors; GBI_MS_2013
Update Test
test_thresholds_numdigits
Test for any values with more than 11 digits.

MetricScoring.xlsx
Modify MassDEP metrics and index scoring.
Update Test
test_metric_names
Update test for AVERAGE_10 and AVERAGE_20 to AVERAGE_100.

Change index scoring regimes.
Replace AVERAGE_10 and AVERAGE_20 with AVERAGE_100
- Use number of metrics for the scaling to 100.
- metric_scores.R
- MetricScoring.xlsx, FFXCOVA indices.

Check
Shorten lines longer than 100 characters.
- markExcluded.R
- metric_scores.R
Add stats to DESCRIPTION, IMPORTS

metric_scores.R
Add CONT_0010 scoring regime.
Modify CONT_0100 to match CONT_0010 with score_max variable.
Add index scoring regimes.
- AVERAGE_10
- AVERAGE_20
MetricScoring.xlsx
FFXCOVA_2018, INDEX_REGION
- Triassic to Triassic Basin

MetricScoring.xlsx, Issue #3
Add Fairfax County, VA
MetricNames.xlsx
Add 2 new metrics for Fairfax Co.
Rename pi_TricNoHydro to pi_TrichNoHydro
metric_values.R
Add x_HBI2
Add pi_habit_cling_PlecoNoCling
Rename pi_TricNoHydro to pi_TrichNoHydro
Update Test for number metric names for scoring index.

MetricScoring.xlsx, Issue #3
Update MassDEP and SNEP index scoring
Replace “.” with “_“; MBSS_2005_Bugs, MSW_1999_Bugs, MBSS_2005_Fish , BCG_PacNW_L1
Remove NMSCI_2006 as had index scoring but not metric scroing.
Update tests.
Rename “test” files.
Update tests to pass.
Rename R function files with “_” rather than “.”.
metric_scores.R
Update examples from “.” to “_“.
Change MBSStools::taxa_bugs_genus to internal data taxa_benthos_MBSS.
Add new data taxa_benthos_MBSS from MBSStools::taxa_bugs_genus, Issue #32
Add ProcessData_benthos_MBSS.R to data-raw.
Add to data.R
MetricFlags.xlsx
MBSS.2005.Bugs to MBSS_2005_Bugs

MetricScoring.xlsx
Add MA indices, Issue #3.
test-metric_calc.R
Update for MA indices.

MetricScoring.xlsx
Update GADNR_Fish_2020, Issue #3.

MetricScoring.xlsx
Update GADNR_Fish_2020, Issue #3.

MetricScoring.xlsx
Update GADNR_Fish_2020, Issue #3.

MetricScoring.xlsx
Update MassDEP_2019_Bugs, Issue #3.

MetricScoring.xlsx
Update MassDEP_2019_Bugs, Issue #3.

Tweaks to tests.

Update NEWS for pull request.
Update notes in MetricScoring.xlsx

Merged Pull Request #44 (0.5.0.9001 and 9002)

MetricScoring.xlsx
Updated MI narratives.

MetricScoring.xlsx
Changed MI narratives and fixed NumMetrics error for MI - East.

Update to new version number.
Rebuild package down website.
Create new release on GitHub.

Remove extra file (metric.values.tsv) from root folder of package.

Updates for MI index; Issue #3
metric.values.R
- Add pi_IsopGastHiru
- Add pi_EPTNoBaeHydro
- Add pi_tv_toler6
- Modified intol4 metrics from \<= to \<.
- Modified toler6 metrics from >= to >.
MetricNames.xlsx
- Add missing metrics.
- Community name bmi to bugs.
- Modified text on intol4 and toler6 metrics.
MetricScoring.xlsx
- Community names to bugs and fish on both tabs.
Add test to for metric names, Community = bugs.
metric.values and MetricNames.xlsx.
MetricScoring.xlsx and MetricNames.xlsx
MetricScroing.xlsx and metric.values()
Resolved issues.
Update dataset “data_benthos_PacNW”.
Index_Name had a number and was different on each line (Excel autofill error).
Last updated 0.4.0.9008 (2020-04-28).
Update tests for metric.values calc.
metric.values.R
Modify NonTarget check for is.na() in cases where the column is missing; Issue #39

metric.values; Issue #3, Issue #41
Fix pi_EPT and pi_EPTNoCheu
- swamped when created in v0.4.0.9019 (2020-07-06).

metric.values, Skip column QC check in Shiny; Issue #40

metric.values, NonTarget still counted; Issue #39
Inadvertently removed in v0.3.3.9017 (2020-02-24)

WV GLIMPSS, Issue #3
Narrative categories are: Very good, Good, Degraded, Severely degraded
- Pond et al. 2012
- MetricScoring.xlsx

WV GLIMPSS, Issue #3
MetricScoring.xlsx
MetricNames.xlsx
metric.values.R
testthat
Update pkgdown website.

metric.values.R
Correct nt_intol4_EPT to nt_tv_intol4_EPT
Add x_Becks3
MetricScoring.xlsx
Add PADEP Freestone IBI (metrics and scoring).
MetricNames.xlsx
Add new metrics.
Use testthat
Set up tests for PA Freestone IBI (values and scores).
Passes both but test incomplete.

Referenced wrong issue in last update.

metric.values.R, Issue #3
Add new metrics for PA and WV BIBIs.
- nt_tv_intol4
- nt_tv_intol4_EPT
- pi_Ortho
- pi_Chiro_Anne
Need to document.

DESCRIPTION
Add package tidyr to support metric.stats2(); Issue # 37

metric.stats2.R, Issue #36
Add DE and z-scores based on metric.stats and metric.values.

Update pkgdown website documentation.

metric.stats.R, Issue #36
Add new function to calculate statistics for developing multi-metric index
data_mmi_dev
Example data for metric.stats()
data.R
Update for new data.

metric.values.R, Issue #35
Modify Oligochaete metrics to use Class or Subclass.
Add Subclass as a required field.

metric.values.R
More new metrics.
- nt, pt, pi - ET (Trichoptera, and Ephemeroptera)
- nt, pt, pi - EOT (Odonata, Trichoptera, and Ephemeroptera)
- nt, pt, pi - COTE (Coleoptera, Odonata, Trichoptera, and Ephemeroptera)
- % Individs Amphipoda + Isopoda

Start using R v4.0.0.
metric.values.R
Additional metrics, Issue #3.
- nt_BCG_attNA
- pi_BCG_attNA
- pt_BCG_attNA
- Habitat metrics, 8 values, nt, pi, pt.
MetricNames.xlsx
Add new metrics.
New data set to utilize new metrics.
data_benthos_PacNW

metric.values.R
Additional metrics, Issue #3.
- nt_BCG_att1
- pi_BCG_att1
- pt_BCG_att1

metric.values.R
QC on line 371 did not declare package. Issue #33.
Define pipe in subfunctions.
metric.scores.R
Modify example. Issue #34.
- Only one occurence of Index_Name and Index_Region in the data.frame.
- Purge tibble error by converting to drop = TRUE.

Tweak for SelMet.
metric.scores.R

Change DepMet to SelMet.
Better terminology as selecting a metric to use.
metric.scores.R
MetricScoring.xlsx

Add ability to score index when have zero individuals.
metric.scores.R
MetricScoring.xlsx

metric.score.R
Account for “no organisms collected”.
- TAXAID needs to be “NONE”.
- N_TAXA needs to be zero.
- Both bugs and fish will exclude all other N_TAXA = 0 but keep if TAXAID == “NONE”.
- nt_total metric has condition for N_TAXA > 0.
- All other metrics will calculate but receive values of 0, NA, or NaN as appropriate.

Tweak for GA Fish IBI, Issue #3
Modify ni_natnonhybrid and ni_natnonhybridnonlepomis to also exclude mosquitofish.
- MetricScoring.xlsx
- metric.score.R
Add nt_nativenonhybrid
- MetricScoring.xlsx
- metric.score.R
metric.score.R
Update ni_natnonhybridnonlepomis.

Changes to fish metric significant enough for a minor version update.
Some previous calculations may not work. Function made more generic.

MetricScoring.xlsx, Issue #3
Tweak scoring for GA Fish IBI
Add metric value calculation for GA Fish IBI metrics.
New Scoring Regimes and associated columns.
Remove MBSStools from Suggests in DESCRIPTION.
metric.values
Modifications for GA Fish IBI.
- All columns to upper case.
Default values to NA rather than zero.
Use toupper rater than tolower.
metric.scores
Modifications for GA Fish IBI.
- Additional Scoring Regimes.
- Additional fish metrics.
All columns to upper case using toupper.
Default values to NA rather than zero.
vignette_BioMonTools.Rmd
Added library(dplyr) to one of the examples.

MetricScoring.xlsx, Issue #3
Tweak values for GA Fish IBI.
- ACF, 6b, inflection point is 2 not 1.

metric.values.R
Minor edits.
MetricScoring.xlsx, Issue #3
Tweak values for GA Fish IBI.
- Convert some values to text.

metric.values.R
Tweak index NormDist_135.
MetricScoring.xlsx, Issue #3
Tweak values for GA Fish IBI.
- Convert some values to text.

metric.values.R
Tweak index sum to account for NA.
MetricScoring.xlsx, Issue #3
Tweak values for GA Fish IBI.

metric.values.R
Error in excluding marine metrics when no metric list given (i.e., want all metrics).
- Misplaced “)”. Issue # 31.

MetricScoring.xlsx, Issue #3, Issue #30
Added more columns for new scoring regimes for GA Fish IBI.
MetricNames.xlsx
Added new fish metric names.
metric.scores.R
Added more scoring regimes (GA Fish IBI).

MetricScoring.xlsx, Issue #3
Numeric to text.

MetricScoring.xlsx, Issue #3
Updates for GBI_MS_2013

MetricScoring.xlsx, Issue #3
Updates for GBI_MS_2013
Numeric to text.

MetricScoring.xlsx, Issue #3
Updates for GBI_MS_2013
Numeric to text.

MetricScoring.xlsx, Issue #3
Updates for GBI_MS_2013

MetricScoring.xlsx, Issue #3
Updates for GBI_MS_2013

Additional scoring and index. Issue #3
Gulf Biotic Index, 2011
Mississippi Gulf Biotic Index, 2013

metric.values, Issue #3
Additional estuary/marine metrics
- Gulf Biotic Index, 2011
- Mississippi Gulf Biotic Index, 2013
Additional input parameter, boo.Marine
Data_Benthos.xlsx
- Add “InfraOrder” column.
- Require in metric.values

metric.values, Issue #3
Add placeholders for marine/estuarine metrics
- Not yet in MetricScoring.xlsx or MetricNames.xlsx

metric.values
Update Beck’s Biotic Index cutoff signs.
- \< 1.5 and >= 1.5 to \<= 1.5 and > 1.5.
- Only affects tolerance values of exactly 1.5.

New release version.

metric.scoring.xlsx
Update “scoring formula” column for 2 MA WestHighlands metrics.
Actual thresholds not affected.

New release version.

MetricScoring.xlsx, issue #22
New metric misspelled.
Add capability for 6 narrative categories.
MetricScoring.xlsx
metric.scores.R
- Minor edit for number of columns.

New release version.

MetricScoring.xlsx, issue #22
Some numbers to character with ’ prefix.
These numbers not importing correctly from Excel.
- Floating point errors in rounding.

MetricNames.xlsx
Add fish metric names, Issue #21
Demonstration only. Not final format in function.
MetricScoring.xlsx
Update date on Notes worksheet.
metric.values.R
Update demonstration fish metrics, Issue #21.

Check
DESCRIPTION
- rmarkdown listed under imports and suggests. Remove from suggests.
- Add to suggests; ggplot2 and reshape2.
- Add MBSStools to suggests. May import the data later and remove.
Example, move “View” to dontrun.
- metric.scores.R
- metric.values.R
- qc.checks.R
- rarify.R
Fix line widths greater than 100 characters:
- markExcluded.R
- metric.scores.R
Properly declare functions from other packages:
- “grDevices”, “dev.off”, “jpeg”, “pdf”
- “graphics”, “mtext”, “points”
- “stats”, “median”, “runif”
- “utils”, “flush.console”
MapTaxaObs.R
- Document the “…” argument.

Updated metric names for MA index, Issue #3
MetricScoring.xlsx
Added “to do” and “references” to metricscoring.xlsx, Issue #3

Updated metric names for MBISQ index, Issue #3
MetricScoring.xlsx

Added metrics, Issue #3
metric.values
- x_NCBI, x_D_Mg, x_D_G
- Additional QC for TolVal2 as numeric (same as TolVal).
MetricNames.xlsx

Fixes for R v3.6.0, Issue #18
DESCRIPTION
- Remove StagedInstall: no
README
- Add directions for fix for devtools.
README
Update badges.

Metric names, fix those added in previous update, Issue #3
Files
- metric.values.R
- MetricNames.xlsx
- MetricScoring.xlsx
metric.scores, Issue #19
Continuous 0-100 scoring only reporting 1 value per column.
Fixed so reports all values.
- Was taking median of column not per row.

Temp fix for staged install with R v3.6.0, Issue #18
DESCRIPTION, StagedInstall: no
Add additional metrics (GA DNR). Issue #3.
Files
- metric.values.R
- MetricNames.xlsx
- MetricScoring.xlsx
Metrics
- pi_Hydro2EPT
- pi_Hydro2Trich
- pi_Ortho2Chi
- pi_Tanyp2Chi
- pi_ChCr2Chi

inst/extdata/MetricFlags.xlsx
Update ni_total for Hi to match Lo (both 450), Issue #16

metric.values, Issue #15
Fix metric pi_EphemNoCaeBae
- Was calculating the same as pi_Ephem.
Checked all other “No” metrics.
- All ok.

metric.values
Fix Trombidiformes metric.
- Mispelled search term so wasn’t working.
Added Megaloptera metrics (nt, pi, and pt).

metric.values
Remove metric sorting. Rely on fun.MetricNames to request and sort metrics.
Modify TolVal character check for NA.
Add example keeping only some metrics.
extdata/MetricScoring.xlsx
Modify percent metric thresholds (from 0-1 to 0-100).
extdata/MetricFlags.xlsx
Modify percent metric thresholds (from 0-1 to 0-100).

docs/ExcludedTaxaDecisionCrit.pdf
Recreate. Wasn’t opening.

extdata/MetricNames.xlsx
move “0-100” from notes to description.

metric.values
Mistyped “FAMILY” as “Family” when added pi_Baet.

docs
Added ExcludedTaxaDecisionCrit.docx

Remove metric names PDF
metric.scores
Add pi_Baet
Percent metrics to 0-100 from 0-1.
Add pi_Baet to extdata/MetricNames.xlsx
input TolVal “NA” (character) to NA.

metric.scores
Additional metrics.
Metric name sort variable. Issue #13
Organize metrics ni, nt, pi, pt for each section.
Update extdata/MetricNames.xlsx
MapTaxaObs
Set up for ability to sort taxa but not active.

DESCRIPTION
maps package missing from Imports.
- Used in MapTaxaObs function.

README
Update install example to force vignettes.
metric.scores
pt_habit metrics (n=5) used ni_total instead of nt_total in denominator.

MapTaxaObs
Account for tibbles as input.
- Convert to a data frame inside the function. Otherwise fails.
Subset function not working in every case. Update line 128.
Add map inputs database and regions and funcion inputs.
extdata/Data_Benthos.xlsx
Update with TolVal2 for example in Vignette to avoid warning.
Vignette
SITE_TYPE to INDEX_REGION
qc.checks
- Update example chunk to match example in function; package BCGcalc to BioMonTools.

Vignette
kable used without library(knitr) in rarify chunk.

Update QC flags input.
Add metric names to Excel file.
MetricName to METRIC_NAME in input files.

New release version.

Metric scoring function, Issue #12.

README.rmd, Issue #11.
install_github command comes out as smart quotes if copy and paste from GitHub website.
Looks ok in RStudio but fixed to test if that is the issue.

Added MapTaxaObs.

Percent metrics as 0-1. Issue #9.

Add qc.checks function from BCGcalc package. Issue #9
qc.checks.R
Vignette
extdata.xlsx
Update read_excel with guess_max=10^6 for bio data file.

Update SuperFamily Tipuloidea.
Update data and examples in function and vignette

Add Travis CI.

Initial release version.

Add SuperFamily
function
vignette
example data file
Add metric names files to extdata and doc

markExcluded
Add function with examples
extdata_Benthos.xlsx
Updated bad Excluded entries.
- FALSE to TRUE, n=6
- TRUE to FALSE, n=1
DESCRIPTION
Update Imports and Suggests
NEWS
Update Planned and Future Updates
README
Tweak language in Usage section.
Update icons.
Add Travis CI.
Vignette

extdata_Benthos.xlsx
OneDrive messed up version included in package.

Added basic package structure.
Folders (data, data-raw, inst/doc, inst/extdata, man, R, vignettes)
NEWS, README, LICENSE
Update DESCRIPTION, NEWS, and README
Add functions and data
rarify
metric.values

Initial commit on GitHub.

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BioMonTools documentation built on Nov. 5, 2025, 7:18 p.m.

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BioMonTools Biomonitoring and Bioassessment Calculations

NEWS.md In BioMonTools: Biomonitoring and Bioassessment Calculations

NEWS

Version History

Changes in version 1.2.4 (2025-10-06)

Changes in version 1.2.3.9008 (2025-10-06)

Changes in version 1.2.3.9007 (2025-10-06)

Changes in version 1.2.3.9006 (2025-10-03)

Changes in version 1.2.3.9005 (2025-10-03)

Changes in version 1.2.3.9004 (2025-10-03)

Changes in version 1.2.3.9003 (2025-10-03)

Changes in version 1.2.3.9002 (2025-09-22)

Changes in version 1.2.3.9001 (2025-09-11)

Changes in version 1.2.3 (2025-09-10)

Changes in version 1.2.2.9001 (2025-09-10)

Changes in version 1.2.2 (2025-09-10)

Changes in version 1.2.1.9001 (2025-09-10)

Changes in version 1.2.1 (2025-09-10)

Changes in version 1.2.0.9001 (2025-09-10)

Changes in version 1.2.0 (2025-09-10)

Changes in version 1.1.0.9005 (2025-09-10)

Changes in version 1.1.0.9004 (2025-09-09)

Changes in version 1.1.0.9003 (2025-09-09)

Changes in version 1.1.0.9002 (2025-09-09)

Changes in version 1.1.0.9001 (2025-09-09)

Changes in version 1.0.2.9081 (2025-09-09)

Changes in version 1.0.2.9080 (2025-09-08)

Changes in version 1.0.2.9079 (2025-09-05)

Changes in version 1.0.2.9078 (2025-09-05)

Changes in version 1.0.2.9077 (2025-06-19)

Changes in version 1.0.2.9076 (2025-06-13)

Changes in version 1.0.2.9075 (2025-06-12)

Changes in version 1.0.2.9074 (2025-06-05)

Changes in version 1.0.2.9073 (2025-04-04)

Changes in version 1.0.2.9072 (2025-04-04)

Changes in version 1.0.2.9071 (2025-02-26)

Changes in version 1.0.2.9070 (2025-02-26)

Changes in version 1.0.2.9069 (2025-02-25)

Changes in version 1.0.2.9068 (2025-02-10)

Changes in version 1.0.2.9067 (2024-11-20)

Changes in version 1.0.2.9066 (2024-11-07)

Changes in version 1.0.2.9065 (2024-11-06)

Changes in version 1.0.2.9064 (2024-11-06)

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Changes in version 1.0.2.9062 (2024-11-06)

Changes in version 1.0.2.9061 (2024-11-05)

Changes in version 1.0.2.9060 (2024-11-05)

Changes in version 1.0.2.9059 (2024-11-01)

Changes in version 1.0.2.9058 (2024-11-01)

Changes in version 1.0.2.9057 (2024-10-30)

Changes in version 1.0.2.9056 (2024-10-29)

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BioMonTools
Biomonitoring and Bioassessment Calculations

NEWS.md
In BioMonTools: Biomonitoring and Bioassessment Calculations