NEWS

---

BCGcalc 2.3.1.9007

• refactor: Update GP (MO) Bug Rules, Issue #103
  • Rules.xlsx

BCGcalc 2.3.1.9006

• refactor: Update GP Bug Rules, Issue #102
  • Rules.xlsx

BCGcalc 2.3.1.9005

• fix: Update MetricFlags.xlsx symbols
  • “==” not “=” for new rules

BCGcalc 2.3.1.9004

• refactor: Update MetricFlags.xlsx
  • LBR_Fish_BCG_v1
    • Remove existing Main_Eckert before adding updated flags

BCGcalc 2.3.1.9003

• refactor: Add secret token in code coverage YAML

BCGcalc 2.3.1.9002

• refactor: Update code coverage YAML and badge in README

BCGcalc 2.3.1.9001

• tests: Add tests for code coverage
  • metric.membership
    • shape
    • missing metrics
• refactor: Modify metric.membership error for missing metrics
  • Allow for test to check class so it is generic
• docs: Add rlang to DESCRIPTION as Suggests
• tests: Split test file into function_calculations and rules_flags
• refactor: Add error for level.membership for missing metrics in data, Issue #54

BCGcalc 2.3.1 (2026-08-08)

• refactor: Bump version number for resubmittal to CRAN, Issue #100

BCGcalc 2.3.0.9004

• refactor: Move Shiny example files to BCGcalc_ORWA, Issue #100

BCGcalc 2.3.0.9003

• refactor: Move large files to BCGcalc_ORWA, Issue #100
  • Data_BCG_PugLowWilVal.csv
  • _Input_HiGradHiElev_noExclude_20220108.csv
• refactor: Make smaller versions (1000 records) of example files, Issue #100
  • Data_BCG_PugLowWilVal.xlsx
  • ExampleMunge_UnformattedData.xlsx

BCGcalc 2.3.0.9002

• docs: Update package description with more detail and references per CRAN fix, Issue #100

BCGcalc 2.3.0.9001

• refactor: Remove example BDVI data as not used in package
  • CRAN fix, Issue #100
  • Moved to BCGcalc_ORWA
• docs: Update package description per CRAN fix, Issue #100

BCGcalc 2.3

• docs: Increase version for CRAN release

BCGcalc 2.2.0.9013

• refactor: Updates for CRAN, Issue #100
• docs: Add cran comments to _test
• refactor: Add cran comments to buildignore
• docs: Update title of package to Title Case
• docs: Remove Remotes line from DESCRIPTION
• docs: Update URLs in README
  • CodeCov
  • lifecycle
• refactor: Trim number of records in example for BCG.Metric.Membership

BCGcalc 2.2.0.9012

• refactor: Update Rules.xlsx
  • Remove metric nt_ti_stenocold_cold_cool from BCG_ORWA_v1_Bugs500ct, Foothills_Multihab

BCGcalc 2.2.0.9011

• tests: Update duplicate metric test
  • Add Symbol and Increase columns

BCGcalc 2.2.0.9010

• fix: Update Boise BCG Fish Level nt_total Level 4 duplicate to Level 5
• tests: Add test for duplicate metrics
  • Index_Name, INDEX_CLASS, Level, Rule_Type
  • Keep disabled as may not be always true

BCGcalc 2.2.0.9009

• refactor: Make example run time shorter, Issue #100
  • BCG.Level.Assignment

BCGcalc 2.2.0.9008

• refactor: Update documentation for metrics_values, Issue #100
• refactor: Make examples run times shorter, Issue #100

BCGcalc 2.2.0.9007

• refactor: Remove unused GIS data files, Issue #100
  • Move to BCGcalc_ORWA repo

BCGcalc 2.2.0.9006

• docs: Update README, Issue #99

BCGcalc 2.2.0.9005

• refactor: Update OK_Bugs_BCG rules for pi_COEPT_BCG_att1i234b4m
  • Rules.xlsx

BCGcalc 2.2.0.9004

• refactor: Update rules and flags for ORWA
  • 6 to 6m6t
• refactor: Modify deprecated input col_SITE_TYPE message with global binding
  • BCG.Metric.Membership
  • BCG.Level.Membership

BCGcalc 2.2.0.9003

• fix: Remove runShiny

BCGcalc 2.2.0.9002

• refactor: Replace Boise NotusParma rules with updated rules
  • Rules.xlsx

BCGcalc 2.2.0.9001

• refactor: Add missing global bindings
  • BCG.Level.Membership
• docs: Update help file for TaxaMaster_Ben_BCG_PugLowWilVal
• docs: Add help files for those missing help files
  • data_GIS_BCGclass
  • data_GIS_eco3_orwa
  • data_GIS_eco3_orwa_bcg
• refactor: Update BCGcalc_Map vignette
  • Still has issues

BCGcalc 2.2.0

• refactor: Move Shiny app out of BCGcalc into its own package
• docs: Remove Shiny-centric packages from DESCRIPTION

BCGcalc 2.1.0.9042

• fix: Remove browser command from Shiny app

BCGcalc 2.1.0.9041

• fix: Change Shiny import routine for BCG_Attr and BCG_Attr2
  • Certain conditions the imported file had all values on each row
• fix: Update MetricFlags.xlsx
  • ORWA flags from 2.1.0.9035 file symbols to be R compliant
• docs: Update NEWS file for undocumented updates.
• tests: Add nt_largeriver as a non BioMonTools metric for testing for MetricFlags.xlsx

BCGcalc 2.1.0.9040

• docs: Originally added as 2.1.0.9035
• refactor: Comment out user file columns for statewide model in Shiny app
• refactor: Add check for existing column for Exclude taxa in statewide model

BCGcalc 2.1.0.9039

• Updated rules to fix Kansas rules

BCGcalc 2.1.0.9038

• Updated rules to replace pi_COEPT_BCG_att234b4m with pi_COEPT_BCG_att1i234b4m.

BCGcalc 2.1.0.9037

• Added rules for Oklahoma associated with GP BCG

BCGcalc 2.1.0.9036

• Updated OWRA and Kansas bug BCG rules

BCGcalc 2.1.0.9035

• Updated OWRA rules and metric flags per Jen’s updates on 06/23

BCGcalc 2.1.0.9034

• refactor: Add ORWA Statewide BCG classes (20260603) to Shiny data folder
  • In preparation for addition of ORWA index assign class to Shiny app calculator
• refactor: Remove older ORWA rules (Hi/Lo-Grad/Elev) from Rules.xlsx
• refactor: Update MetricFlags.xlsx for ORWA
• style: Update tests with package name for each test

BCGcalc 2.1.0.9033

• refactor: Update Rules.xlsx for BCG_ORWA_v1_Bugs500ct

BCGcalc 2.1.0.9032

• refactor: Update Rules.xlsx for Metric_Sort column spelling

BCGcalc 2.1.0.9031

• refactor: Update Rules.xlsx with Metric_Sort column
  • LBR Bugs and Fish

BCGcalc 2.1.0.9030

• fix: Remove draft rules (2.0.1.9027, 2025-12-26)
  • BCG, Boise, Fish, Main_Eckert, Issue #97

BCGcalc 2.1.0.9029

• refactor: Add flags, Boise BCG, Bugs
  • sum_density_m2
• refactor: Add rules, Boise BCG, Fish
• tests: Write rule for symbols for Rules.xlsx

BCGcalc 2.1.0.9028

• refactor: Add rules, Boise BCG, Bugs
• refactor: Add flags, Boise BCG, Bugs
• refactor: Update Vignette due to m2 fields from new metrics
  • BCGcalc_Map.Rmd
  • vignette_BCGcalc.Rmd

BCGcalc 2.1.0.9027

• refactor: Add additional rules, Boise BCG, Issue #97
• refactor: Add additional flags, Boise BCG, Issue #97

BCGcalc 2.1.0.9025

• docs: Update LICENSE files and reference in DESCRIPTION
• docs: Move BioMonTools from Imports to Suggests in DESCRIPTION

BCGcalc 2.1.0.9024

• refactor: Replace old and non-working GitHub Actions
  • Add from BioMonTools package

BCGcalc 2.1.0.9023

• fix: Update BCG.ContLevel example to not fail
• fix: Update example code in Vignettes to avoid failures
• docs: Remove reshape2 from suggests in DESCRIPTION
• fix: Add files in root directory to .Rbuildignore
  • NEWS.rmd
  • README.rmd
  • _test/
  • data-raw/
• refactor: Add missing package references to functions in code
  • BCG.Level.Membership
  • BCG.ContLevel

BCGcalc 2.1.0.9022

• refactor: Shiny app, MariNW,
  • Exclude taxa, add new levels
    • SpeciesGroup, SpeciesSubGroup, and SpeciesComplex
  • Add ‘required’ to section E for column names
  • Add example for Ecoregion (e.g., 2, 3, or 4)

BCGcalc 2.1.0.9021

• refactor: Add new Flags for GP BCG, Issue #96

BCGcalc 2.1.0.9020

• fix: Update server for columns for BCG Attr
• refactor: Update NE_Bugs_BCG rules, Issue #95
• fix: Update Rules, failed test
  • pi_SCC to pi_scc
• fix: Update test, Flags, Metrics, BioMonTools

BCGcalc 2.1.0.9019

• refactor: Update Generate BCG Class parameters to include watershed area
  • Re-enable and then rename all caps to match model
• fix: Update BCG for statewide and marine northwest
  • Rename objects by model
  • Reference correct objects within each model
  • Remove “out of experience” from statewide model pop up

BCGcalc 2.1.0.9018

• fix: Update calls to StreamCatTools for Shiny getClassParam function, Issue #93
  • Changes to StreamCatTools functions due to changes in API

BCGcalc 2.1.0.9017

• refactor: Update Shiny app references to taxa file on BioMonTools_SupportFiles

BCGcalc 2.1.0.9016

• refactor: Update MetricFlags.xlsx
  • New ORWA move ni_total flags to top of list for each Index_Class

BCGcalc 2.1.0.9015

• refactor: Add BCG_ORWA_v1_Bugs500ct to Rules.xlsx
• refactor: Add BCG_ORWA_v1_Bugs500ct to MetricFlags.xlsx

BCGcalc 2.1.0.9014

• fix: Modify BCG.Level.Membership
  • Update for exception rules
    • Edit FLIPMINMAX to flip min and max
    • Add MIN012MAX, MIN of Rules 0, 1, 2 then MAX
• refactor: Update Rules.xlsx
  • Populate missing INCREASE values
  • Add metadata worksheet for EXC_RULE
  • Add MN_BCG for EXC_RULE MIN012MAX
• refactor: Add error message for NA in INCREASE column for BCG.Metric.Membership

BCGcalc 2.1.0.9013

• fix: Modify BCG.Level.Membership to flip min and max as an exception rule
• refactor: Update Rules.xlsx for MN_BCG for EXC_RULE FLIPMINMAX

BCGcalc 2.1.0.9012

• fix: Modify BCG.Level.Membership to avoid duplication in output for level assigment
  • Modify INDEX_CLASS_ORIG
  • Modify Exception calculations (i.e., median, small2, small2A, small2B, and small3)

BCGcalc 2.1.0.9011

• refactor: Add Great Plains BCG metric flags

BCGcalc 2.1.0.9010

• refactor: Add summation of duplicate taxa in taxa translate in Shiny

BCGcalc 2.1.0.9009

• refactor: Merge Pull Request 92

BCGcalc 2.1.0.9008

• refactor: Update Rules.xlsx for MN_BCG metric descriptions and index regions

BCGcalc 2.1.0.9007

• refactor: Update Rules.xlsx for MN_BCG fish10a and fish10b

BCGcalc 2.1.0.9006

• refactor: Add Shiny calculation Fish Thermal Class to menu and a page
• refactor: Add Shiny troubleshooting menu option
• refactor: Update Shiny MTTI citation
• refactor: Update Shiny Thermal Preference Metrics citation

BCGcalc 2.1.0.9005

• fix: Update MTTI shiny code to avoid name conflict
  • TolVal2 vs. TOLVAL2

BCGcalc 2.1.0.9004

• docs: Update help on ORWA taxa list to reinforce is demo only

BCGcalc 2.1.0.9003

• refactor: Update functions to retain original case for INDEX_CLASS, Issue #91
  • BCG.Metric.Membership
  • BCG.Level.Membership

BCGcalc 2.1.0.9002

• refactor: Define pipe in BCG.Level.Membership

BCGcalc 2.1.0.9001

• refactor: Update rules for SMALL2 and SMALL3
  • Sort ascending
  • Add rules for SMALL2A and SMALL2B

BCGcalc 2.1.0.9000

• break: Fix Rules for SMALL2 and SMALL3
  • Sort descending and take row 2 or 3
  • This could be a breaking change
    • Updating version number

BCGcalc 2.0.0.9146

• refactor: Update ‘GP_BCG_Fish’ to ‘GP_Fish_BCG’ to match GP Bug models
  • Rules.xlsx

BCGcalc 2.0.0.9145

• refactor: Update Rules.xlsx for Great Plains BCG

BCGcalc 2.0.0.9144

• refactor: Modify language on Shiny app pop up for assign class

BCGcalc 2.0.0.9143

• fix: Update MetricFlags.xlsx for FL Coral BCG

BCGcalc 2.0.0.9142

• fix: Update Rules.xlsx for FL Coral BCG

BCGcalc 2.0.0.9141

• docs: Update BCG.Metric.Membership language for col_INCREASE
• refactor: Update Rules.xlsx for FL Coral BCG

BCGcalc 2.0.0.9140

• feature: Add new template for new metrics, models, and rules
• fix: Update package documenation per roxygen2

BCGcalc 2.0.0.9139

• refactor: Shiny app file builder generate class parameters, Issue #89
  • Add shinyalert for more than 500 records
  • nhdplustools and StreamCatTools timeout issues with too many records
• fix: Shiny app calculation of BioMonTools::metric.scores, leppott/BioMonTools#103
  • Affected BDI calculation, checked and no other instances
• fix: Update package documenation per roxygen2 (since 7.0.0)

BCGcalc 2.0.0.9138

• fix: Shiny app fuzzy model not working, change community reference
  • Also fixed thermal metrics for status message

BCGcalc 2.0.0.9137

• fix: Update naming scheme for BCG calculation in Shiny app, Issue #87
  • Add “_” prefix to Results.

BCGcalc 2.0.0.9136

• fix: Update naming scheme for BCG calculation in Shiny app, Issue #87
• refactor: Update text on BCG calculation pop up in Shiny app, Issue #88

BCGcalc 2.0.0.9135

• refactor: Update NM BCG, drop percent max ffg from L2 and L4 per documentation

BCGcalc 2.0.0.9134

• refactor: Update NM BCG Index_Name and Index_Class in Rules.xlsx

BCGcalc 2.0.0.9133

• fix: Add shiny::validate(msg) back to shiny alert for when no file uploaded
  • Avoid the app crashing by preventing rest of code from running
• refactor: update shiny alert message for upload to account for file upload not complete
• fix: Update order of conditional formatting for nt_ti_stenocold

BCGcalc 2.0.0.9132

• fix: Remove testing line in Report server code
  • Caused ShinyApps.io to crash trying to open Excel

BCGcalc 2.0.0.9131

• refactor: Update Report
  • Add conditional formatting for summary worksheet for data columns
    • MTTI
    • Thermal Metrics
  • Add error checking if thermal metrics not present

BCGcalc 2.0.0.9130

• docs: Add tag to roxygen chunk to allow for table in BCG.Level.Membership
• refactor: Update BCG.Level.Membership for new exception rules (NM bugs)
  • Added routines for Exception Rules Small2 and Small3
• refactor: Update Rules.xlsx (NM bugs)

BCGcalc 2.0.0.9129

• refactor: Modify Shiny single report
  • Properly filter for singe station for every worksheet
  • Modify freeze panes for summary wide
• refactor: Calculation community buttons to default to NA
  • calc_BCG
  • calc_thermalfuzzy
  • calc_thermalmetrics

BCGcalc 2.0.0.9128

• refactor: Modify Shiny single report
  • Add taxatrans table
  • Verify sorting of tables by user selections
  • Add summary color thresholds
  • Color summary color thresholds
  • Set column widths
  • update formulas on NOTES

BCGcalc 2.0.0.9127

• refactor: Modify Shiny single report
  • Zip file download

BCGcalc 2.0.0.9126

• fix: Update app BCG calculation for cases where have no flags

BCGcalc 2.0.0.9125

• fix: Update MN fish metric names (trout) to be more specific

BCGcalc 2.0.0.9124

• tests: Update tests for name changes in 2.0.0.9004
• fix: Update metric name in Rules.xlsx to match BioMonTools
  • pi_Trout to pi_trout

BCGcalc 2.0.0.9123

• fix: Modify taxatrans hack for noteworthy to only trigger if present

BCGcalc 2.0.0.9122

• refactor: BCG calculation user column select to lower case
  • elev_m
  • pslope_nhd
• refactor: Rename BCG calculation flag output (previously model experience)

BCGcalc 2.0.0.9121

• feature: Add ecoregion L3 to generate index class parameters

BCGcalc 2.0.0.9120

• refactor: Modify QC check on BCG model experience to BCG calculate
  • Change text on pop-up
  • Modify structure of output file
  • Add checks for slope and elevation
• refactor: Result files remove leading “_”

BCGcalc 2.0.0.9119

• fix: Modify QC check on BCG model experience to BCG calculate
  • total flags

BCGcalc 2.0.0.9118

• refactor: Modify QC check on BCG model experience to BCG calculate

BCGcalc 2.0.0.9117

• feature: Add QC check on BCG model experience to BCG calculate
• fix: Comment out all other instances of validate(msg) to avoid potential issues

BCGcalc 2.0.0.9116

• fix: File builder taxa translate remove validate statement from pop up
  • Was causing the server to pause and not continue

BCGcalc 2.0.0.9115

• feature: Add pop-up for taxa translate with mismatch taxa

BCGcalc 2.0.0.9114

• refactor: Modify output file names
  • Shorten names by dropping user input file name
• style: Add package names to a functions, Global.R
  • write_disk was missing httr:: prefix

BCGcalc 2.0.0.9113

• refactor: Add MN BCG Fish rules, Rules.xlsx

BCGcalc 2.0.0.9112

• feature: Added single site report
  • Formatting incomplete but function working in Shiny

BCGcalc 2.0.0.9111

• fix: Change order of operations to allow multiple uses of single import
  • For example, taxa translate now generates only the current results
• refactor: Create helper functions for re-used code
  • clean_results
  • copy_import_file

BCGcalc 2.0.0.9110

• fix: Create workaround for Generate Class Param
  • If reused an output as input duplicate fields are created
  • Then crashes when tries to join results
  • Rename existing fields as _OLD

BCGcalc 2.0.0.9109

• fix: Updates TaxaTranslate file output (names and folders)

BCGcalc 2.0.0.9108

• refactor: Updates to Shiny interface

BCGcalc 2.0.0.9107

• refactor: Implement result folder changes
• refactor: Add subfolder for user import file
• refactor: Implement changes for new source files in taxa translator
• refactor: Implement file name changes

BCGcalc 2.0.0.9106

• refactor: Implement result file name changes using global abbreviations

BCGcalc 2.0.0.9105

• refactor: Remove toner lite base layer from Shiny maps
  • no longer supporter after 2023-10-31
• refactor: Sidebar menu updates
  • Label calculations as ‘Draft’ (non-BCG)
  • Tweak ‘Taxa Translate’ language
• refactor: Update Shiny map clustering options
• refactor: Reports to only multi and single
• refactor: Add result file and folder abbreviations to global

BCGcalc 2.0.0.9104

• feature: Add report to Shiny
  • Still under construction
• refactor: Update Shiny import to remove empty directories as well as files
  • Change from file.remove to unlink
• docs: Add openxlsx to DESCRIPTION for report creation in Shiny

BCGcalc 2.0.0.9103

• fix: Shiny, taxatrans_late_0filesversion.csv, swap 2 columns

BCGcalc 2.0.0.9102

• refactor: Leaflet map Fuzzy Thermal changes
  • Create multiple TIEs for legend so don’t count as NA
    • TIE_A_B same as TIE_B_A
  • Remove Continuous_Thermal as a required field
    • Was used for size but size no longer being used

BCGcalc 2.0.0.9101

• refactor: For leaflet map change to addCircleMarkers
  • Replaced addCircles

BCGcalc 2.0.0.9100

• fix: Change leaflet map proxy to redraw legend
  • Prevents thermal metric legends from having multiple on screen
• refactor: Add “DRAFT” to BDI

BCGcalc 2.0.0.9099

• refactor: Remove base layers too large to use
  • NorWeST
  • NHD+ catchment
  • NDD+ flowlines
• fix: Change Fuzzy Thermal legend
  • Move first ties up 1 slot each
  • Change legend colors
• refactor: Change jitter on map from jitter function to custom
  • jitter didn’t always work with large data sets

BCGcalc 2.0.0.9098

• feat: Update Shiny map
  • Add Imagery as baselayer to Shiny map
  • Add legend title variable to Shiny map legend
  • Add jitter to map plot to avoid overlap of multiple samples per location
  • Change legend and colors
    • BDI
    • BCG
    • MTTI
    • Thermal Metrics

BCGcalc 2.0.0.9097

• refactor: Add download links to KMZ files
• refactor: Update map legends coding, Issue #67

BCGcalc 2.0.0.9096

• feature: Add KMZ downloads to Shiny app
  • NorWeST_ORWA
  • PNMR_BCGclasses
• feature: Updated maps in Shiny, Issue #67

BCGcalc 2.0.0.9095

• feat: Add example script for MTTI

BCGcalc 2.0.0.9094

• feat: Add example data for MTTI to external folder

BCGcalc 2.0.0.9093

• feat: Add maps for each index, Issue #67

BCGcalc 2.0.0.9092

• fix: BDI, if no Index_Class was not adding proper variable name, Issue #66
  • Caused samples to not be scored

BCGcalc 2.0.0.9091

• fix: Typo on “Covert OTU” on MTTI and BDI shiny tabs
• refactor: Adjust Excl taxa triggers and QC in code, Issue #66

BCGcalc 2.0.0.9090

• fix: Removed browser() statement from QC of last update, Issue #84

BCGcalc 2.0.0.9089

• feature: Automate Index Name and Class for fuzzy set calculation, Issue #84
  • Shiny

BCGcalc 2.0.0.9088

• feature: Add BDI calculation to Shiny, Issue #66
  • COMPLETE
• refactor: Shiny required fields type for TRUE/FALSE changed text to logical

BCGcalc 2.0.0.9087

• refactor: Update MN BCG (bugs) in Rules.xlsx, Issue #82

BCGcalc 2.0.0.9086

• refactor: Add MN BCG (bugs) to Rules.xlsx, Issue #82

BCGcalc 2.0.0.9085

• refactor: Updates to BDI calculation, Issue #66
  • INCOMPLETE, completed in 2.0.0.988

BCGcalc 2.0.0.9084

• fix: Update complex number import code (BCG_ATTR), Issue #77
  • Should work in all cases and not cause issues with other fields
• feature: Enable BDI calculation in Shiny app, Issue #66
  • PARTIAL

BCGcalc 2.0.0.9083

• refactor: Modify code for import and merge files, Issue #77
  • Only specify BCG_ATTR column
  • Undoes some edits in v2.0.0.9081
• fix: Adjust import function to allow for user selection of tab or comma
  • Comma was hard coded even though gave user the choice of separators

BCGcalc 2.0.0.9082

• refactor: Updates to Shiny map, Issue #67
  • INCOMPLETE
• refactor: Change taxa translator to no default

BCGcalc 2.0.0.9081

• fix: Modify code for complex number (BCG_ATTR), Issue #77
  • Other logical fields could cause issues with older import method

BCGcalc 2.0.0.9080

• fix: Change links to files in Shiny from “" to”/”
• refactor: Update Index Class Parameter, Issue #73
• refactor: Update to text for Fuzzy Set Input File, Issue #70

BCGcalc 2.0.0.9079

• refactor: Update Index Class Parameter, Issue #73

• refactor: Update Shiny Fuzzy Set

BCGcalc 2.0.0.9078

• feature: Add upset plot to MTTI results report
• docs: Add ComplexUpset to DESCRIPTION Suggests and Shiny global

BCGcalc 2.0.0.9077

• refactor: Update Shiny MTTI, Issue #74
  • Onscreen text
  • Example files
• style: Move MTTI model file location

BCGcalc 2.0.0.9076

• fix: MetricFlags.xlsx ‘pctSLOPE’ to ‘pslope_nhd’
  • Align with index class assignment
  • Add PRECIP8110CAT for BCG_MariNW_Bugs500ct (all classes)
• refactor: Add more StreamCat variables to get index parameters, Issue #75
  • PRECIP8110CAT
  • ICI
  • IWI

BCGcalc 2.0.0.9075

fix: Update MTTI routine for user SampleID, Issue #74 + One instance was hard-coded

BCGcalc 2.0.0.9074

refactor: Update MTTI output, Issue #74

BCGcalc 2.0.0.9073

style: Code coverage updates

BCGcalc 2.0.0.9072

• refactor: Change order of columns for Fuzzy Thermal, Issue #70
  • modtherm_5levassign.csv

BCGcalc 2.0.0.9071

• fix: Update overlapping Fuzzy Thermal CheckNames in MetricFlags.xlsx, Issue #72

BCGcalc 2.0.0.9070

• refactor: Add columns and classifications to Fuzzy Thermal model, Issue #70

BCGcalc 2.0.0.9069

• fix: MetricFlags.xlsx ‘pcSLOPE’ to ‘pctSLOPE’ (typo)
• fix: MetricFlags.xlsx ‘DrArea_mi2’ to ‘WSAREASQKM’ (and values)

BCGcalc 2.0.0.9068

• fix: Remove browser call in fuzzy thermal model

BCGcalc 2.0.0.9067

• refactor: Additional flags for fuzzy thermal model

BCGcalc 2.0.0.9066

• refactor: Updates to fuzzy thermal model output

BCGcalc 2.0.0.9065

• fix: BCG.Level.Membership account for less than 5 rules, Issue #68
• fix: Update examples so don’t get duplicate columns kept in output
  • Can cause successive examples to fail
  • BCG.Metric.Membership
  • BCG.Level.Membership

BCGcalc 2.0.0.9064

• refactor: Error checking for missing variables, Shiny
  • Fuzzy Thermal Model
  • Index Class Param, Issue #42

BCGcalc 2.0.0.9063

• refactor: Update Index Class Param onscreen help in Shiny, Issue #42

BCGcalc 2.0.0.9062

• refactor: Shiny get Index Class Params, Issue #42
  • Allow for user defined column
    • Default is NAD83 North America, EPSG = 4269
  • Trim output

BCGcalc 2.0.0.9061

• refactor: Update Shiny MTTI calculation and flags calculation and output

BCGcalc 2.0.0.9060

• refactor: Update Shiny MTTI calculation to include flags
• style: Modify some lines based on lintr suggestions
  • Add nolint to Shiny library calls

BCGcalc 2.0.0.9059

• fix: Update Shiny app import to better handle BCG_ATTR (complex)
  • Added exception for only integer values

BCGcalc 2.0.0.9058

• fix: Ensure all Shiny buttons use same terminology
  • b_calc_x
  • b_download_x

BCGcalc 2.0.0.9057

• fix: Update names of assign indec class buttons
  • calc and download
• style: Modify outlining in server.R
• refactor: Modify Shiny Generate Index Class Param
  • Add column names to match Shiny Assign Index Class
    • Allows user to upload file with no modifications

BCGcalc 2.0.0.9056

• docs: Update DESCRIPTION R >= 2.1 to >= 3.5.0 due to code dependency
  • Loading of MTTI model file in Shiny app
• refactor: Add data-raw Process Data script for nhdplusTools vaa file
  • Only VPUID 16, 17, and 18 for use with OR and WA.
  • Add fst package to Suggests in DESCRIPTION
  • Unable to upload full file to GitHub

BCGcalc 2.0.0.9055

• refactor: Shiny index class parameter generation, Issue #42
• docs: Add packages used in Shiny app to DESCRTION Suggests
  • StreamCatTools
  • nhdplusTools

BCGcalc 2.0.0.9054

• fix: Shiny index class parameter generation, Issue #42
• refactor: Shiny MTTI change language
  • ‘Pacific Northwest’ to ‘Oregon/Washington’
• fix: Change utils::zip to zip::zip in Shiny
  • Not working locally or on ShinyApps.io
• docs: Add zips to DESCRIPTION Suggests

BCGcalc 2.0.0.9053

• refactor: Update Shiny MTTI calculation (was placeholder)

BCGcalc 2.0.0.9052

• feat: Add Shiny tab for generating index class parameters, Issue #42
  • Placeholder only

BCGcalc 2.0.0.9051

• refactor: Add map column select and base map, Issue #67
  • Not complete

BCGcalc 2.0.0.9050

• feat: Add placeholder for map, Issue #67

BCGcalc 2.0.0.9049

• fix: Remove example file link in fuzzy thermal about page
  • No fuzzy thermal examples
• feat: Add fuzzy thermal calculation and associated pages to Shiny, Issue #65

BCGcalc 2.0.0.9048

• refactor: Add link for example scripts to fuzzy thermal about page

BCGcalc 2.0.0.9047

• docs: Update BCG.Level.Assignment example code
• refactor: Update example script (BCG calc)

BCGcalc 2.0.0.9046

• refactor: Create ‘process’ file in data-raw for creating zip file of examples for Shiny app (‘www’)
• refactor: Update example scripts
• refactor: Add link to download example zip file in Shiny app

BCGcalc 2.0.0.9045

• refactor: Create Shiny Merge Files Output tab

BCGcalc 2.0.0.9044

• refactor: Update Shiny output tabs

BCGcalc 2.0.0.9043

• refactor: Update taxa translate 0fileversion output
  • Shiny, server.R
  • example code, taxa translate

BCGcalc 2.0.0.9042

• feature: Add example scripts and data for Shiny File Builder functions
  • Taxa Translate
  • Assign Index_Class
  • Merge Files
• feature: Add Fuzzy Thermal narrative to Shiny operation

BCGcalc 2.0.0.9041

• refactor: Update Shiny onscreen text, inputs BCG calc
• refactor: Update Shiny onscreen text, inputs thermal metrics

BCGcalc 2.0.0.9040

• refactor: Update Shiny onscreen text, thermal preference metrics
  • Add metadata file to calculation thermal metrics results

BCGcalc 2.0.0.9039

• refactor: Update Shiny onscreen text, BCG calc

BCGcalc 2.0.0.9038

• docs: Update readme install section with quick code
• refactor: Update Shiny onscreen text, Assign Index_Class

BCGcalc 2.0.0.9037

• refactor: Update Shiny onscreen text, Merge Files

BCGcalc 2.0.0.9036

• refactor: Change Shiny merge files order (x and y)
  • Samples should be the main file (x) and keep all records and info

BCGcalc 2.0.0.9035

• refactor: Update Shiny app text

BCGcalc 2.0.0.9034

• refactor: Update Shiny to include change in BioMonTools package

BCGcalc 2.0.0.9033

• fix: Update file import routine
  • Account for multiple permutations of BCG_Attr
  • Add “” to na.strings

BCGcalc 2.0.0.9032

• fix: Adjust QC routine in Shiny app assign index class

BCGcalc 2.0.0.9031

• refactor: Finish updates to Shiny app merge files tab

BCGcalc 2.0.0.9030

• refactor: Add error checking for Index_Class in Shiny

BCGcalc 2.0.0.9029

• docs: Add Shiny link to README
• refactor: Layout changes to taxa translate section of Shiny app

BCGcalc 2.0.0.9028

• refactor: Add Shiny merge files tab placeholder
  • proof of concept, not complete

BCGcalc 2.0.0.9027

• refactor: Update onscreen text for Shiny assign index class

BCGcalc 2.0.0.9026

• refactor: Remove uneeded QC steps in Shiny assign_indexclass routine

BCGcalc 2.0.0.9025

• refactor: Add excluded taxa subroutine to thermal metrics in Shiny

BCGcalc 2.0.0.9024

• refactor: BioMonTools MetricNames.xlsx from GitHub instead of package in Shiny

BCGcalc 2.0.0.9023

• refactor: Add taxa translate unique crosswalk to output of taxatranslate in Shiny

BCGcalc 2.0.0.9022

• fix: Modify code in Shiny for assign_indexclass so won’t fail if field not provided.

BCGcalc 2.0.0.9021

• feature: Add thermal metric calculation to Shiny app

BCGcalc 2.0.0.9020

• feature: Add assign index class to Shiny
• refactor: Update Shiny tabs to not include numbered steps (all were step 2)
• fix: Update shiny taxa translate to combine duplicate taxa by default

BCGcalc 2.0.0.9019

• refactor: Update Shiny taxa trans to drop translator columns if have an attributes table

BCGcalc 2.0.0.9018

• refactor: Update Shiny taxa trans to use default names
  • SampleID, TaxaID, and N_Taxa

BCGcalc 2.0.0.9017

• refactor: Update Shiny taxa trans to include filenames in MERGED output

BCGcalc 2.0.0.9016

• refactor: Update Shiny, split file builder in to taxa trans and assign index class

BCGcalc 2.0.0.9015

• refactor: Update Shiny app MTTI tab

BCGcalc 2.0.0.9014

• refactor: Update Shiny app for taxaid_drop parameter in BioMonTools::taxa_translate

BCGcalc 2.0.0.9013

• refactor: Sort columns and order output of taxa translator

BCGcalc 2.0.0.9012

• feature: Add INDEX_NAME and INDEX_CLASS as input parameters to BCG.Level.Assignment

BCGcalc 2.0.0.9011

• refactor: Shiny app, filebuilder
  • save version of files in download
  • reorganize the required fields requested of user
  • change some text on screen

BCGcalc 2.0.0.9010

• refactor: Shiny app, filebuilder
  • Ensure consistency of BCGcalc and BioMonTools columns names (all caps)
  • Add about and output tabs to taxa translator
  • Update for consistency pick list file names in file and in code
  • Update routine for translating then adding attributes
    • Leave some projects with one file but add ability for two files (PacNW)

BCGcalc 2.0.0.9009

• refactor: Update filebuilder tab in Shiny app
  • Use “user file” less often
  • Change summary default to TRUE
  • Modified output files to include “taxatrans”
  • Renamed RESULTS to MERGED in output file
  • Add link to Taxa Translate Official files on GitHub
  • Fix non-match output

BCGcalc 2.0.0.9008

• refactor: Change BCG.ContLevelText status from x/y tie to x.5, Issue #64

BCGcalc 2.0.0.9007

• feature: Add taxa translator tab and functionality to Shiny

BCGcalc 2.0.0.9006

• feature: Add new function to calculate BCG Status
  • Uses continuous value to get Integer or PlusMinus text

BCGcalc 2.0.0.9005

• refactor: Additional Shiny outputs
  • 6metflags; flag metrics, values, thresholds
  • 3metrules; rules table
• refactor: Update Shiny text for additional outputs

BCGcalc 2.0.0.9004

• refactor: Update Shiny app text for slim to BCG file name for BCG output
• refactor: Change order and names of columns in BCG.Level.Assignment output
  • Memb.Total to Membership_Total
  • Memb.QC to Membership_Total_QC
  • Lev.1.Memb to Primary_Membership
  • Lev.1.Name to Primary_BCG_Level
  • Lev.2.Memb to Secondary_Membership
  • Lev.2.Name to Secondary_BCG_Level
  • Lev.Memb.Diff to Membership_Diff
  • Lev.Memb.close to Membership_Close
  • Lev.Prop.Num to Continuous_BCG_Level
  • Lev.Prop.Nar to BCG_Status

BCGcalc 2.0.0.9003

• refactor: Change Shiny output 2metval_slim.csv to 2metval_BCG.csv

BCGcalc 2.0.0.9002

• fix: Update Rules.xlsx for non-ASCII characters

BCGcalc 2.0.0.9001

• breaking change: Site_Type and Index_Region to INDEX_CLASS, Issue #63
  • Deprecate in functions (allow for ‘…’) and shiny
    • BCG.Level.Membership
    • BCG.Metric.Membership
    • Include warning for old code
• refactor: Update reference Excel files for updated field, Issue #63
  • Rules.xlsx
  • MetricFlags.xlsx

BCGcalc 1.3.5.9018

• refactor: Shiny, change menu item name

BCGcalc 1.3.5.9017

• fix: Shiny app ‘slim’ output, Issue #62

BCGcalc 1.3.5.9016

• fix: Shiny app, markExcl, EXCLUDED to EXCLUDE

BCGcalc 1.3.5.9015

• update: Change name of PacNW model, Issue #61
  • Rules.xlsx
  • MetricFlags.xlsx
  • Example files (file name, data, sheet names)
  • Update examples in functions
  • Vignettes

BCGcalc 1.3.5.9014

• update: Update BCG style temperature model thresholds
  • Rules.xlsx

BCGcalc 1.3.5.9013

• refactor: Upgrades to Shiny app

BCGcalc 1.3.5.9012

• refactor: Upgrades to Shiny app

BCGcalc 1.3.5.9011

• refactor: Upgrades to Shiny app
  • Rework tab order and names
  • Update About
  • Other

BCGcalc 1.3.5.9010

• refactor: Upgrades to Shiny app
  • Added summary report
  • Added packages needed for report
  • Minor edits to main menu
  • Minor edits to About
• update: Add ‘Therm_ORWA_Bugs500ct’ model to Excel files

BCGcalc 1.3.5.9009

• refactor: Upgrades to Shiny app
  • Mark Excluded taxa
  • Minor updates
  • Added footer to app with shinydashboardPlus
    • Added package to DESCRIPTION
  • Update About
  • Add placeholder tabs for future updates

BCGcalc 1.3.5.9008

• refactor: Upgrades to Shiny app
  • Second version of results/metval with only those for the model
  • Ensure result files removed from previous imports

BCGcalc 1.3.5.9007

• refactor: Upgrades to Shiny app

BCGcalc 1.3.5.9006

• docs: Update examples for missing columns in sample data for all functions
• fix: Update MetricFlags.xlsx for one flag

BCGcalc 1.3.5.9005

• docs: Update packages in DESCRIPTION and global.R in Shiny app

BCGcalc 1.3.5.9004

• feat: Redesign shiny app
• docs: Add packages needed by Shiny app to DESCRIPTION

BCGcalc 1.3.5.9003

• style: Perform updates from lintr and goodpractice
• fix: Update Font Awesome icons, some were deprecated
• fix: Shiny About links update so open in new tab

BCGcalc 1.3.5.9002

• docs: Update format of NEWS

BCGcalc 1.3.5.9001

• feature: Add Shiny app skeleton and function to run it, Issue #58

BCGcalc 1.3.5

• refactor: Bump version number.

BCGcalc 1.3.4.9047

• fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9046

• fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9045

• fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9044

• fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9043

• fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9042

• refactor: Update metric.values()
  • Failed when rules table included more than 1 region and metrics uneven

BCGcalc 1.3.4.9041

• refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9040

• refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

BCGcalc 1.3.4.9039

• refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
• tests: Add tests for flags and metric names

BCGcalc 1.3.4.9038

• refactor: Update BCG.Level.Membership() for new median rule type, Issue #55
• refactor: Update Rules.xlsx to handle new median rule type, Issue #55

BCGcalc 1.3.4.9037

• refactor: Update MetricFlags.xlsx
  • Match metric names to BioMonTools::metric.values()
  • Add BioMonTools_MetNam column for future test (some not metrics)
  • Change symbols from = to ==
  • Write test to check for Flag symbols
• fix: One entry in Rules.xlsx was “[” instead of “>=”.

BCGcalc 1.3.4.9036

• fix: BCG.Level.Membership fails test
  • Missing EXC_RULE in merge statement
• refactor: Update “Notes” to “Note_Rules” in Rules.xlsx
• tests: Update test for revised sheet name in Rules.xlsx

BCGcalc 1.3.4.9035

• fix: Renamed master branch to main
• docs: Move wishlist from NEWS to GitHub Issue #56
• refactor: Updated Rules.xlsx for PacNW BCG, Issue #55
• refactor: Updated Flags.xlsx for PacNW BCG, Issue #55
• tests: Add test for floating point error
  • Rules.xlsx
  • Flags.xlsx
• docs: Update example for additional required columns in BioMonTools::metric.values()
  • BCG.Metric.Membership()
  • BCG.Level.Membership()

BCGcalc 1.3.4.9034

• feat: Update BCG.Level.Membership() to account for special conditions
  • Use Index_Name and Site_Type to allow for individual model exceptions to the typical rules for level membership
• feat: Update Rules.xlsx for exceptions in level membership in BCG.Level.Membership()

BCGcalc 1.3.4.9033

• fix: Update BCG.Metric.Membership() to use <= and >= when checking for values below and above limits rather than < and > due to rules in CT BCG using 0 as a lower AND upper limit

BCGcalc 1.3.4.9032

• fix: Update Rules.xlsx for CT BCG model, Issue #48
  • Removed double entries for fish01, fish02, and fish03 SiteType

BCGcalc 1.3.4.9031

• fix: Update Rules.xlsx for CT BCG model, Issue #48
  • Removed double entries for bug01 SiteType

BCGcalc 1.3.4.9030

• refactor: Update BCG.Metric.Membership() for lower and upper bounds
  • Per CT Access db (2013-08-09) use <= and >= instead of < and >
• style: Wrap some lines more than 80 characters, BCG.Level.Assignment()

BCGcalc 1.3.4.9029

• fix: Update BCG.Metric.Membership() for calculating membership for more than one Site_Type at a time, Issue #53
  • Allows for NA for metrics not common to all included Site Types

BCGcalc 1.3.4.9028

• refactor: Update Rules.xlsx for CT BCG benthos
  • pi_BCG_att5 to pi_BCG_att5extra

BCGcalc 1.3.4.9027

• refactor: Update BCG.Level.Membership with stop message if unable to merge data frames

BCGcalc 1.3.4.9026

• refactor: Update Rules.xlsx to match BioMonTools::metric.values()
  • rename brook trout wild

BCGcalc 1.3.4.9025

• refactor: Update Rules.xlsx to match BioMonTools::metric.values()
  • Add “BCG” to BCG attribute metric names

BCGcalc 1.3.4.9024

• refactor: Update BCG.Level.Assignment()
  • Add column name inputs and defaults
  • Update code to use inputs
  • Add tempdir() to save example
  • Update example to not have warning for BioMonTools::metric.values()
  • Apply fixes for changes in dplyr
• refactor: Update BCG.Level.Membership()
  • Add column name inputs and defaults
  • Update code to use inputs
  • Add tempdir() to save example
  • Add QC in function to retain only the input columns
  • Update example to not have warning for BioMonTools::metric.values()
  • Apply fixes for changes in dplyr
• refactor: Update BCG.Metric.Membership()
  • Add column name inputs and defaults
  • Update code to use inputs
  • Add tempdir() to save example
  • Update example to not have warning for BioMonTools::metric.values()
  • Apply fixes for changes in dplyr
• style: Trim lines to 80 characters (partial)
  • BCG.Level.Assignment()
  • BCG.Level.Membership()
  • BCG.Metric.Membership()
• style: Update function examples to use “_” instead of “.” in object names
  • BCG.Level.Assignment()
  • BCG.Level.Membership()
  • BCG.Metric.Membership()
• style: Update function examples to use foo::fun() instead of library(foo)
  • BCG.Level.Assignment()
  • BCG.Level.Membership()
  • BCG.Metric.Membership()

BCGcalc 1.3.4.9023

• refactor: Update Rules.xlsx, Issue #48
  • Change Index_Name, Site_Type, and Index_Region

BCGcalc 1.3.4.9022

• docs: Update DESCRIPTION remotes to proper url
• refactor: Update metric.membership() example to use updated Rules.xlsx, Issue #48
• refactor: Update Rules.xlsx file, Issue #48
• refactor: Update level.membership() example to use updated Rules.xlsx, Issue #48
• refactor: Update level.assignment() example to use updated Rules.xlsx, Issue #48

BCGcalc 1.3.4.9021

• refactor: Merge pull request with updated rules, Issue #52

BCGcalc 1.3.4.9020

• refactor: Update model rules, Rules.xlsx, Issue #48

BCGcalc 1.3.4.9019

• docs: Add sticker to README

BCGcalc 1.3.4.9018

• feature: Add sticker
  • Create with hexSticker

BCGcalc 1.3.4.9017

• style: Fix devtools::spell_check() issues
  • NEWS
  • README
  • vignette_BCGcalc.Rmd
• refactor: README
  • Update example, change devtools::install_github to remotes::install_github
  • Rebuild README

BCGcalc 1.3.4.9016

• docs: Remove date from DESCRIPTION
• tests: Add tests
  • metric_membership
  • level_membership
  • level_assignment
• feature: Create metrics_values dataset to use in tests
• docs: Document metrics_values dataset
• refactor: Replace undesirable function, library
  • ProcessData_TaxaMaster_Ben_BCG_PacNW

BCGcalc 1.3.4.9015

• test: set up test folder

BCGcalc 1.3.4.9014

• ci: Add GitHub Action test coverage
• ci: Add GitHub Action pkgdown
• docs: ReadMe, add codecov badge
• docs: ReadMe, add lifecycle badge
• docs: ReadMe, add codefactor badge
• docs: Remove docs folder from main branch for pkgdown
• docs: Redirect GitHub repo for pkgdown to gh-pages branch

BCGcalc 1.3.4.9013

• ci: Add GitHub Actions, continuous integration
• ci: Remove TravisCI
• docs: ReadMe, remove TravisCI badge
• docs: ReadMe, Add GitHub Actions CMD check badge

BCGcalc 1.3.4.9012

• Add pkgdown website.
  • Need to fix vignettes/BCGcalc_Map.Rmd.
    • INFRAORDER missing.

BCGcalc 1.3.4.9011

• Build Check fixes.
  • Move “View” in example to “do not run”.
    • BCG.Level.Assignment
    • BCG.Level.Membership
    • BCG.Metric.Membership
  • Column names of TaxaMaster_Ben_BCG_PacNW
    • Data.R
  • Depends on R >= 2.10
    • DESCRIPTION
  • Add .github to .Rbuildignore
  • Remove unused data (data folder and data.R)
    • taxa_fish
    • taxa_bugs_family
    • taxa_bugs_genus

BCGcalc 1.3.4.9010

• Update for R v3.6.0, Issue #46
  • README
    • Add extra line for devtools::install_github to work properly
• Added badges to README
• Map Vignette
  • Update title.

BCGcalc 1.3.4.9009

• BCG.Level.Assignment
  • Proportional BCG final scores, Issue #43.
    • Add “tie” to narrative.

BCGcalc 1.3.4.9008

• BCG.Level.Assignment
  • Proportional BCG final scores, Issue #43
    • Turn on features from v1.3.4.9004.
    • Add proportional narrative (+/-).

BCGcalc 1.3.4.9007

• extdata.xlsx
  • ni_total, Hi, to 450 from 400.
    • Matches file in BioMonTools package.

BCGcalc 1.3.4.9006

• Remove format Hoboware file from extdata folder.
  • From another package under development.

BCGcalc 1.3.4.9005

• MetricFlags.xlsx
  • Percent metrics to 0-100. Issues #45.
  • Add field Index_Region
• Data_BCG_PacNW.xlsx
  • Add fields: Issue #33.
    • Index_Region
    • LongLived
    • NoteWorthy
    • FFG2
    • TolVal2
• Rules.xlsx
  • Add field Index_Region Issue #33.
  • Update percent metrics to 0-100. Issue #45.
• Vignette, modify for Site_Type to Index_Region
  • BCGcalc_Map.RMD
  • vignette_BCGcalc.RMD
    • Add “Site_Type”” to columns to keep
• Modify example for Site_Type to Index_Region Issue #33.
  • BCG.Level.Assignment.R
  • BCG.Level.Membership.R
  • BCG.Metric.Membership.R

BCGcalc 1.3.4.9004

• Proportional Level Assignment. Issue #43.
  • Needs more polish for different conditions.
  • Assign all to NA.

BCGcalc 1.3.4.9003

• Last update not complete before uploaded.

BCGcalc 1.3.4.9002

• Move qc.checks to BioMonTools package. Issue #44
  • Remove qc.checks.R
  • Update Vignette.
• Update read_excel with guess_max=10^6 for bio data file.

BCGcalc 1.3.4.9001

• Add proportional Level Assignment. Issue #43.
  • BCG.Level.Assignment

BCGcalc 1.3.4

• Update release version with Remote”s”” fix.

BCGcalc 1.3.3.9005

• BioMonTools dependency not installing.
  • Move Remote up in listing in DESCRIPTION.
  • Renamed Remote to Remotes.

BCGcalc 1.3.3.9004

• Add BioMonTools to Imports so will auto install.
  • Had removed at some point since don’t use the functions in any BCGcalc functions.

BCGcalc 1.3.3.9003

• Update SuperFamily Tipuloidea
  • /extdata/Data_BCG_PacNW.xlsx
  • /extdata/TaxaMaster_Bug_BCG_PacNW_v1.xlsx

BCGcalc 1.3.3.9002

• /extdata/Data_BCG_PacNW.xlsx
  • Update Exclude column after QC with BioMonTools::markExcluded
    • Change 6 FALSE to TRUE
    • Change 1 TRUE to FALSE

BCGcalc 1.3.3.9001

• Update ReadMe for BioMonTools::metric.values. Issue #41.

BCGcalc 1.3.3

• Update version have changes related to moving functions to the BioMonTools package.

BCGcalc 1.3.2.9012

• metric.values, move to another package, Issue #40
  • Moved to separate package. _ https://github.com/leppott/BioMonTools
    • BioMonTools is for bioassessment and biomonitoring.
    • ContDataQC should stay focused on continuous data.
  • Vignette
    • Updated each section with metric.values
    • BCGcalc_Map.rmd
    • vignette_BCGcalc.rmd
  • R/data.R
    • Keep example data since specific to BCG project
  • Remove
    • R/metric.values.R
  • Update function examples.
    • Add library(BioMonTools)
    • qc.checks.R
    • BCG.Metric.Membership.R
    • BCG.Level.Membership.R
    • BCG.Level.Assignment.R
• Update map colors, Issue #35.
• BCG.Metric.Membership.R
  • Update details.
• BCG.Level.Assignment.R
  • Add don’t run to simple example for write.csv.

BCGcalc 1.3.2.9011

• rarify, move to another package, Issue #40
  • Moved to separate package.
    _ https://github.com/leppott/BioMonTools
    • BioMonTools is for bioassessment and biomonitoring.
    • BCGcalc should stay focused on BCG models.
  • DESCRIPTION
    • Add Remote: leppott/BioMonTools
    • Remove Jon van Sickles as contributor since removed rarify function.
  • Vignette
    • rarify section updated.
  • R/data.R
    • Remove reference to data_bio2rarify
  • Remove
    • R/rarify.R
    • data-raw/ProcessData_rarify.R
    • data-raw/ 3 data files
    • data/data_bio2rarify.rda

BCGcalc 1.3.2.9010

• Metric calculations, additional metrics.
  • metric.values.R
    • nt_Ephemerellidae
    • nt_Heptageniidae
    • nt_Nemouridae
    • nt_Perlidae
    • nt_Rhyacophila
    • nt_Tipulidae
  • MetricNames.xlsx
• Fix error with habit metric names.
  • metric.values.R
  • MetricNames.xlsx

BCGcalc 1.3.2.9009

• Metric calculation;
  • x_HBI. Issue #37
    • calculation use TOLVAL>=0 rather than TOLVAL>0 in denominator.
  • Consistent naming. Issue #38
    • habit_clmbrs to habit_climb
    • habit_clngrs to habit_cling
    • habit_swmmrs to habit_swim

BCGcalc 1.3.2.9008

• Metric calculation;
  • Tolerance metrics
    • nt_tv_intol
    • nt_tv_toler
    • pt_tv_intol
    • pt_tv_toler
    • Added lower and upper limits for intol and toler

BCGcalc 1.3.2.9007

• Metric calculation;
  • pi_Colesen
    • Change is.na(FAMILY) from FALSE to TRUE.

BCGcalc 1.3.2.9006

• Metric calculation;
  • pi_Hydro
    • Equal sign missing in equation (“=” instead of “==”).

BCGcalc 1.3.2.9005

• Metric calculation;
  • pi_Tanyp
    • Misspelled Tanypodinae

BCGcalc 1.3.2.9004

• Metric calculations;
  • x_HBI
    • Remove negative sign. Issue #37
  • x_Shan_e, x_Shan_2, x_Shan_10
    • Fix equation. Not properly calculating proportions.
    • Drop use of x_Shan_Num. Use x_Shan_e then convert for other log bases.
  • x_D
    • Fix equation.

BCGcalc 1.3.2.9003

• Fix metric calculation; na.rm=TRUE for sum. Issue #37
  • x_HBI _ If had any NA values for TolVal the final value was NA.
    • Added na.rm=TRUE to sum function for numerator.
    • Denominator already included na.rm=TRUE.
  • x_D
    • No effect as no records should be NA for count
  • dominant calculation intermediate columns
    • No effect as no records should be NA for count
  • ni_total
    • No effect as no records should be NA for count
  • All fish metrics (with “sum”)

BCGcalc 1.3.2.9002

• Add 8 additional metrics to metric.values
  • MS DEQ, MBISQ 2015 _ pi_Hydro
    • nt_NonIns
    • pt_NonIns
    • pi_Tanyp
    • pt_tv_intol
    • pt_tv_toler
    • pi_Colesens
    • pi_COC2Chi

BCGcalc 1.3.2.9001

• Mapping Vignette. Issue #34.
  • DESCRIPTION
    • Add ggplot2 to Suggests
  • extdata_BCG_PacNW.xlsx
    • Add Latitude, Longitude, and COMID
  • Create Vignette for mapping

BCGcalc 1.3.2

• Release version.

BCGcalc 1.3.1.9001

• Master Taxa List
  • Turbellaria BCG Attribute.
    • Change from “x” to “4” to match its synonym Trepaxonemata.

BCGcalc 1.3.1

• Release version.

BCGcalc 1.3.0.9001

• Rules.xlsx
  • Fix typos in “Numeric_Rules” field.
    • No impact on calculations.

BCGcalc 1.3.0

• Release version.

BCGcalc 1.2.2.9033

• Update Vignette.
  • Rarify section to 600.

BCGcalc 1.2.2.9032

• Update Vignette.
  • Fix a few typos.

BCGcalc 1.2.2.9031

• Update Rules.xlsx.
  • 300 count model edits.

BCGcalc 1.2.2.9030

• Vignette updates.

BCGcalc 1.2.2.9029

• Updated rarify data; data_bio2rarify
  • Replace fully qualified 500 count data with 3 column 600 count.
  • Update data.R entry.
  • Update rarify function example.
  • Update vignette example.

BCGcalc 1.2.2.9028

• Updated docs.
  • extdata/ExampleDataFile.xlsx
  • docs/BCGcalc_README_20180919.pdf

BCGcalc 1.2.2.9027

• Updated Rules.xlsx file in extdata.

BCGcalc 1.2.2.9026

• Finish updates to Vignette.

BCGcalc 1.2.2.9025

• Level.Assignment. Issue #11
  • Update example so don’t calculate metrics twice.

BCGcalc 1.2.2.9024

• Vignette updates (incomplete).
• Metric.Membership. Issue #11
  • Non numeric extra columns caused errors. Fixed.

BCGcalc 1.2.2.9023

• extdata
  • TaxaMaster_Bug_BCG_PacNW_v1.xlsx; rename worksheet to match previous version.
• data-raw
  • Remove data_bio2rarify.txt
  • Recreate TaxaMaster_Ben_BCG_PacNW using revised XLSX file.
  • Update 500count.tsv thermal column name.
• data.R
  • Update entries for TaxaMaster_Ben_BCG_PacNW and data_bio2rarify
• Vignette
  • Start on updates.

BCGcalc 1.2.2.9022

• Update Data_BCG_PacNW.xlsx. Issue #32
  • Remove unnecessary worksheets.
  • Rename single remaining worksheet.
  • Update phylogenetic columns.
  • Rearrange columns into required and optional.
• Add master taxa list file to external docs.
• Add thermal indicators file to external docs.

BCGcalc 1.2.2.9021

• update ReadMe. Issue #31

BCGcalc 1.2.2.9020

• Ensure reshape2 package references are consistent. Issue #30
  • Ensure functions use reshape2::melt (or dcast)
  • Ensure examples (and vignette) use library(reshape) and melt or dcast.

BCGcalc 1.2.2.9019

• File formats. Issue #28
  • Add statement about file formats to Vignette.

BCGcalc 1.2.2.9018

• rarify data. Issue #19
  • Use USGS 500 to 300 count data instead of MS 200 count.
  • Change raw data process script.
  • Replace data_bio2rarify.
  • Modify rarify example.
  • Modified rarify example in Vignette.

BCGcalc 1.2.2.9017

• BCG PacNW primer. Issue #29
  • BCGcalc_README_20180918.pdf to so shows up in package help.
• MetricFlags.xlsx
  • Last line, Index_Name updated for 300 count model.

BCGcalc 1.2.2.9016

• Example “write” statements as “dontrun”. Issue #27
  • BCG.Level.Assignment; also moved write statement to end
  • BCG.Level.Membership
  • BCG.Metric.Membership
  • metric.values; included write and DataExplorer
  • qc.checks; no write statement.
  • rarify; Changed from commented out to donotrun
  • Vignette; leave “as is”. Write statements all commented out.
• BCG.Level.Assignment
  • Change write.table(tsv) to write.csv. Issue #28

BCGcalc 1.2.2.9015

• extdata.xlsx. Issue #26
  • Added NOTES worksheet.
  • Added MetricMetadata from MetricNames.xlsx.
  • Added NOTES worksheet to MetricNames.xlsx.
  • Renamed worksheet “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
  • Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
  • Added worksheet “BCG_PacNW_v1_300ct”.
• Revised code references to Rules.xlsx (worksheet and Index_Name). Mostly examples.
• extdata_BCG_PacNW.xlsx
  • Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
• extdata.xlsx
  • Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
  • Added Index_Name “BCG_PacNW_v1_300ct”. Adjust some flags based on 500 vs. 300 count.

BCGcalc 1.2.2.9014

• qc.checks. Issue #25.
  • Update Description.
  • Add View for imported checks file.
  • Vignette. Change section title from QC Checks to Flags.
  • Update Level Assignment example in Vignette with real data and append flags.

BCGcalc 1.2.2.9013

• Function rarify. Issue #19
  • Remove keywords.

BCGcalc 1.2.2.9012

• Function rafify. Issue #19
  • Fix typo in @param mySeed. Remove extra period.

BCGcalc 1.2.2.9011

• Metric Names metadata Issue #18
  • Update extdata.xlsx
  • Add PDF version to docs.

BCGcalc 1.2.2.9010

• More Indiana files. Issue #24
  • extdata_IN_BCG_Bugs_20170203.xlsm
  • extdata_Metrics_Bugs_IN.xlsx

BCGcalc 1.2.2.9009

• Remove Indiana references. Issue #24.
  • Delete extdata Indiana file (Data_BCG_Indiana.xlsx).
  • Delete data-raw Indiana database (BCG_Model_Calc (IN 20170301).mdb. Already excluded from package build.
  • Delete example in metric.values function.

BCGcalc 1.2.2.9008

• DESCRIPTION
  • Add date.
  • Add Jen Stamp as contributor
• Citation still gives error but is more complete now. Issue #23

BCGcalc 1.2.2.9007

• metric.values
  • Fixed included metrics (fun.MetricNames)

BCGcalc 1.2.2.9006

• metric.values
  • Added QC check for NonTarget==FALSE.
  • Give a warning if have zero FALSE values.

BCGcalc 1.2.2.9005

• metric.values
  • Added QC check for Exclude==TRUE.
  • Give a warning if have zero TRUE values.

BCGcalc 1.2.2.9004

• Update Vignette.
  • Add data munging example. Issue #14
  • Update metric.values section for required fields. Issue #13.
  • Added section demonstrating saving only select metrics. Issue #15
• Update text in metric.values.

BCGcalc 1.2.2.9003

• metric.values. Issue #16
  • Added QC worksheet to extdata_BCG_PacNW.xlsx

BCGcalc 1.2.2.9002

• metric.values. Issue #13
  • Add required fields (columns) to help file.
  • Add QC check in function. Prompt user to continue or stop.

BCGcalc 1.2.2.9001

• metric.values
  • Added metric Percent Baetis tricaudatus complex + Simuliidae individuals (pi_SimBtri). Issue #16.

BCGcalc 1.2.2

• New release version.

BCGcalc 1.2.1.9001

• qc.checks.R
  • Modification to use metric names as lower case. Issue #12.
  • Example table; useNA=“ifany”.

BCGcalc 1.2.1

• New release version.

BCGcalc 1.2.0.9001

• BCG.Level.Assignment.R
  • Membership QC (sum===1) add “round” 8 to avoid too many samples being flagged as “FAIL”.
  • Example changes:
  • Changed terminology from PASS/FAIL to NA/flag in flag fields.
  • Changed “NumFlagFAIL” to “NumFlags”.
  • Reordered columns so “NumFlags” is before the flag fields.

BCGcalc 1.2.0

• Release version for Pacific Northwest BCG workgroup with updated model.

BCGcalc 1.1.0.9010

• BCG.Level.Assignment.R
  • Example code to match up with qc.checks output.
  • Includes export to file.
• qc.checks.R
  • Remove example modifying column names.

BCGcalc 1.1.0.9009

• BCG.Level.Membership.R
  • Added “round” to 8 places when determining level membership.
  • Floating point error resulted in the occassional value of 1.1E-16 when the previous level was “1”.
  • This resulted in the sample getting a split level assignment, e.g., 3:4 when it was 100% 3.

BCGcalc 1.1.0.9008

• metric.values.R
  • Add additional metrics
  • nt; BCG_att; 1i, 1m, 3
  • pt; BCG_att; 1i, 1m, 3
  • pi; BCG_att; 1i, 1m, 2, 3
  • thermal indicator metrics
  • modify grepl to == because COLD was matching COLD and COLD_COOL. Only want exact match.

BCGcalc 1.1.0.9007

• Update Rules.xlsx.
  • Level 3 (Hi and Lo), pi_BCG_att56 changed to pt_BCG_att1i23.
  • Change involved both direction and thresholds.

BCGcalc 1.1.0.9006

• Update metric.values.
  • Add “cols2keep” to allow for extra fields in output.
  • Need extra fields for qc.checks
• Update qc.checks.
  • Update example with cols2keep from metric.values example.

BCGcalc 1.1.0.9005

• Update bio data to be used for the model; Issue #7
  • Collapse mites to Order.

BCGcalc 1.1.0.9004

• Update extdata/Rules.xlsx; Issue #7

BCGcalc 1.1.0.9003

• metric.values dd nt, pi, and pt metrics; Issue #7
  • NonIns_BCG_attr456
  • NonInsJugaRiss_BCG_attr456

BCGcalc 1.1.0.9002

• QC Flags, Add pi_dom02. Issue #7
• Update format of NEWS.
• metric.values, row_number to dplyr::row_number for dominant metrics.

BCGcalc 1.1.0.9001

• metric.values, Issue #7
  • Update metrics from NonClump to NoJugaRiss.

BCGcalc 1.1.0.0000

• Release new and fully QCed version.

BCGcalc 1.0.0.9002

• Metric.values
  • Fix metrics with not equal functions.
  • Ensure use is.na(x)==TRUE rather than x==NA
  • When have more than one condition for a data column need to be in the same statement.
  • Better define clumpy taxa for 2 metrics.
• BCG.Level.Membership
  • Fixed combination of rules by level. Missed a column and was getting duplicates for alt rules that changed the outcome.
• BCG.Level.Assignment
  • Replace For loop with apply.
  • Add special conditions for ties (2 levels with 0.5) and primary level is 1 (no 2nd level).

BCGcalc 1.0.0.9001

• Metric.values
  • Fix non-clumpy metrics.
  • Remove extra data frames for dominance metrics. Slight speed improvement. Issue #5.
• Fix version numbers in NEWS.
• Updated ReadMe with only the relevant packages. Issue #4.

BCGcalc 1.0.0.0000

• Only metric value issues left to resolve with test data set. Rest of the calculations are ok.

BCGcalc 0.1.0.9019

• Rules.xlsx
  • Fill in missing cells.
• metric.values.R
  • Update FFG abbreviations to match example data.
  • Dominant N and special Dominant N metrics.
  • Define pipe as referencing dplyr. Slows down the functions but keeps dplyr from needing to be loaded.
• SiteType values to lowercase.
  • metric.values.R
  • BCG.Metric.Membership.R
  • BCG.Level.Membership.R
  • BCG.Level.Assignment.R
• Consistent terminology; don’t mix “.”, ” “, and”“. Use””.
  • METRIC_NAMES
  • METRIC_VALUES
  • SITE_TYPE (and change from REGION)
  • RULE_TYPE
  • NUMERIC_RULES
  • LIFE_CYCLE
  • LONG_LIVED
  • THERMAL_INDICATOR
  • NAME_WIDE
• Rebuild PacNW master taxa list with changes.
  • Consistent names (columns and categories).
• Example PacNW data.
  • Consistent names (columns).
• QC Checks
• Update Vignette.
• All functions and examples seem to be generating the proper outputs. When QC only a few metrics are off. But enough that no final results are correct (that is, all levels, site types, and samples are affected but the remaining QC issues). Non-Insect and modified dominant 2 metrics are the 4 that have issues.

BCGcalc 0.1.0.9018

• BCG.Level.Membership.R
  • Correct function to consider preceding levels when assigning membership scores.

BCGcalc 0.1.0.9017

• metric.values.R
  • Added Thermal Indicator (TI) metrics.
• Updates to PacNW bug data and rules files (xlsx).

BCGcalc 0.1.0.9016

• metric.values.R
  • Update pt_BCG_att1i2 and 1i23 metrics (numerator not capturing “i” taxa).
• Update Rules.xlsx

BCGcalc 0.1.0.9015

• Vignette didn’t update in previous version.

BCGcalc 0.1.0.9014

• Tweak “data.R”. Not complete!
  • Added example save code for master taxa list.
• Update BCG.Metric.Membership.
  • Add some error checking.
  • Colnames to upper case.
• Updated Rules.xlsx
  • Percent metrics converted to 0-1 values to match metric.values calculations.
  • Fixed Index Name for some records.
• metric.values.R
  • Updated examples, details, and description.
• Update BCGcalc Vignette.
• Update Readme.
• Update BCG.Level.Membership

BCGcalc 0.1.0.9013

• Added PacNW benthic master taxa list to data.
• Created “data.R”. Not complete!

BCGcalc 0.1.0.9012

• Update PacNW example data to use TRUE/FALSE for Excluded and NonTarget fields.
• Updated metric.values
  • Moved common data munging to earlier in function so applies to all communities.
  • Enabled NonTarget exclusion. NonTarget column now required.

BCGcalc 0.1.0.9011

• Completed lingering edits for “Tier” to “Level”.
• Completed BCG.Level.Membership function.

BCGcalc 0.1.0.9010

• Remove “Tier” wording in package and rename some functions to better reflect usage.
• Include example code for saving results for each function.
• Change Region to SiteType in code and example data files.

BCGcalc 0.1.0.9009

• Dom02 special metric placeholder.
• Update Rule table for Level assignments.
• BCG.Levels function.
• Fixed error in sequencing in BCG.Membership function.

BCGcalc 0.1.0.9008

• Add last of the PacNW specific metrics to metric.values.
• Added Vignette.

BCGcalc 0.1.0.9007

• Check clean up.
• Convert data imports from development folder to pacakge folder with system.file.
• Add data for rarify function.

BCGcalc 0.1.0.9006

• BCG.Tiers function.

BCGcalc 0.1.0.9005

• Add BCG.Membership function. Return is in long format.
  • Not QCed but has some known issues.

BCGcalc 0.1.0.9004

• Add subtitles, date, author to YAML header to NEWS and README.
• Add “flags” Excel file to raw-data for QC checks. Used in qc.checks function (new).
• Added 4 new ni metrics to metric values to be used for QC checks (flags).
• qc.checks.R (incomplete but works).
• Add BCGcalc.R to describe the package.
• Update documentation headers in R files.

BCGcalc 0.1.0.9003

• metric.values.R, benthos
  • Added BCG attribute metrics.
  • Added outlining for readability in code.
  • More metrics and clean up of file.
  • Prepare example data for metric calculation.
  • Added na.rm=TRUE to n_distinct and sum in summarise.

Changes in Version 0.1.0.9002 (2018-02-16)

• Add parts without any modification from MBSStools package.
  • rarify function
  • metric.values function
  • included data folder and files
  • added Excel file to extdata with metric naming explanation

BCGcalc 0.1.0.9001

• Updated files for package.
  • Readme, NEWS, DESCRIPTION
  • Not complete.

BCGcalc 0.1.0

• Created GitHub repository