NEWS.rmd

---
title: "BCGcalc-NEWS"
author: "Erik.Leppo@tetratech.com"
date: "`r Sys.time()`"
output: github_document
  #md_document:
   # variant: markdown_github
---

<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "NEWS-"
)
```

```{r, echo = FALSE}
cat(paste0("Last Update: ",Sys.time()))
```

# BCGcalc 2.1.0.9014 (2024-10-08)

* 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 (2024-10-08)

* 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 (2024-08-08)

* 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 (2024-08-06)

* refactor: Add Great Plains BCG metric flags

# BCGcalc 2.1.0.9010 (2024-08-06)

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

# BCGcalc 2.1.0.9009 (2024-07-30)

* refactor: Merge Pull Request 92

# BCGcalc 2.1.0.9008 (2024-07-29)

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

# BCGcalc 2.1.0.9007 (2024-07-24)

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

# BCGcalc 2.1.0.9006 (2024-07-03)

* 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 (2024-06-19)

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

# BCGcalc 2.1.0.9004 (2024-06-19)

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

# BCGcalc 2.1.0.9003 (2024-06-07)

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

# BCGcalc 2.1.0.9002 (2024-06-07)

* refactor: Define pipe in `BCG.Level.Membership`

# BCGcalc 2.1.0.9001 (2024-06-07)

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

# BCGcalc 2.1.0.9000 (2024-06-06)

* 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 (2024-05-14)

* refactor: Update 'GP_BCG_Fish' to 'GP_Fish_BCG' to match GP Bug models
    + Rules.xlsx

# BCGcalc 2.0.0.9145 (2024-05-14)

* refactor: Update Rules.xlsx for Great Plains BCG

# BCGcalc 2.0.0.9144 (2024-05-09)

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

# BCGcalc 2.0.0.9143 (2024-04-11)

* fix: Update MetricFlags.xlsx for FL Coral BCG

# BCGcalc 2.0.0.9142 (2024-03-29)

* fix: Update Rules.xlsx for FL Coral BCG

# BCGcalc 2.0.0.9141 (2024-03-28)

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

# BCGcalc 2.0.0.9140 (2024-02-27)

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

# BCGcalc 2.0.0.9139 (2024-02-06)

* 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 (2024-02-01)

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

# BCGcalc 2.0.0.9137 (2024-02-01)

* fix: Update naming scheme for BCG calculation in Shiny app, Issue #87
    + Add "_" prefix to Results.

# BCGcalc 2.0.0.9136 (2024-02-01)

* 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 (2024-01-11)

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

# BCGcalc 2.0.0.9134 (2024-01-11)

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

# BCGcalc 2.0.0.9133 (2024-01-09)

* 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 (2024-01-08)

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

# BCGcalc 2.0.0.9131 (2024-01-08)

* 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 (2024-01-02)

* 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 (2023-12-21)

* 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 (2023-12-20)

* 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 (2023-12-19)

* refactor: Modify Shiny single report
    + Zip file download

# BCGcalc 2.0.0.9126 (2023-12-07)

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

# BCGcalc 2.0.0.9125 (2023-12-06)

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

# BCGcalc 2.0.0.9124 (2023-12-06)

* 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 (2023-12-01)

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

# BCGcalc 2.0.0.9122 (2023-12-01)

* 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 (2023-11-30)

* feature: Add ecoregion L3 to generate index class parameters

# BCGcalc 2.0.0.9120 (2023-11-30)

* 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 (2023-11-29)

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

# BCGcalc 2.0.0.9118 (2023-11-29)

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

# BCGcalc 2.0.0.9117 (2023-11-29)

* 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 (2023-11-28)

* 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 (2023-11-21)

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

# BCGcalc 2.0.0.9114 (2023-11-21)

* 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 (2023-11-20)

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

# BCGcalc 2.0.0.9112 (2023-11-13)

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

# BCGcalc 2.0.0.9111 (2023-11-06)

* 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 (2023-11-04)

* 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 (2023-11-04)

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

# BCGcalc 2.0.0.9108 (2023-11-03)

* refactor: Updates to Shiny interface

# BCGcalc 2.0.0.9107 (2023-11-03)

* 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 (2023-10-31)

* refactor: Implement result file name changes using global abbreviations

# BCGcalc 2.0.0.9105 (2023-10-31)

* 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 (2023-10-27)

* 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 (2023-10-20)

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

# BCGcalc 2.0.0.9102 (2023-10-17)

* 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 (2023-10-03)

* refactor: For leaflet map change to addCircleMarkers
    + Replaced addCircles

# BCGcalc 2.0.0.9100 (2023-10-02)

* 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 (2023-09-29)

* 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 (2023-09-28)

* 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 (2023-09-27)

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

# BCGcalc 2.0.0.9096 (2023-09-26)

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

# BCGcalc 2.0.0.9095 (2023-09-07)

* feat: Add example script for MTTI

# BCGcalc 2.0.0.9094 (2023-09-07)

* feat: Add example data for MTTI to external folder

# BCGcalc 2.0.0.9093 (2023-08-29)

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

# BCGcalc 2.0.0.9092 (2023-08-25)

* 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 (2023-08-25)

* 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 (2023-08-24)

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

# BCGcalc 2.0.0.9089 (2023-08-24)

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

# BCGcalc 2.0.0.9088 (2023-08-17)

* 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 (2023-07-13)

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

# BCGcalc 2.0.0.9086 (2023-07-12)

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

# BCGcalc 2.0.0.9085 (2023-07-11)

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

# BCGcalc 2.0.0.9084 (2023-06-19)

* 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 (2023-06-13)

* 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 (2023-06-12)

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

# BCGcalc 2.0.0.9081 (2023-06-08)

* 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 (2023-06-08)

* 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 (2023-06-07)

* refactor: Update Index Class Parameter, Issue #73

# BCGcalc 2.0.0.9079 (2023-06-07)

* refactor: Update Shiny Fuzzy Set

# BCGcalc 2.0.0.9078 (2023-06-07)

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

# BCGcalc 2.0.0.9077 (2023-06-06)

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

# BCGcalc 2.0.0.9076 (2023-06-06)

* 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 (2023-06-06)

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

# BCGcalc 2.0.0.9074 (2023-06-06)

refactor: Update MTTI output, Issue #74

# BCGcalc 2.0.0.9073 (2023-06-06)

style: Code coverage updates

# BCGcalc 2.0.0.9072 (2023-06-05)

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

# BCGcalc 2.0.0.9071 (2023-06-05)

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

# BCGcalc 2.0.0.9070 (2023-06-05)

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

# BCGcalc 2.0.0.9069 (2023-06-05)

* fix: MetricFlags.xlsx 'pcSLOPE' to 'pctSLOPE' (typo)
* fix: MetricFlags.xlsx 'DrArea_mi2' to 'WSAREASQKM' (and values)

# BCGcalc 2.0.0.9068 (2023-06-05)

* fix: Remove `browser` call in fuzzy thermal model

# BCGcalc 2.0.0.9067 (2023-06-05)

* refactor: Additional flags for fuzzy thermal model

# BCGcalc 2.0.0.9066 (2023-06-02)

* refactor: Updates to fuzzy thermal model output

# BCGcalc 2.0.0.9065 (2023-06-02)

* 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 (2023-06-01)

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

# BCGcalc 2.0.0.9063 (2023-06-01)

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

# BCGcalc 2.0.0.9062 (2023-06-01)

* 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 (2023-05-26)

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

# BCGcalc 2.0.0.9060 (2023-05-26)

* 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 (2023-05-23)

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

# BCGcalc 2.0.0.9058 (2023-05-23)

* fix: Ensure all Shiny buttons use same terminology
    + b_calc_x
    + b_download_x

# BCGcalc 2.0.0.9057 (2023-05-23)

* 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 (2023-05-23)

* 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 (2023-05-19)

* 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 (2023-05-19)

* 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 (2023-05-17)

* refactor: Update Shiny MTTI calculation (was placeholder)

# BCGcalc 2.0.0.9052 (2023-05-16)

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

# BCGcalc 2.0.0.9051 (2023-03-20)

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

# BCGcalc 2.0.0.9050 (2023-03-17)

* feat: Add placeholder for map, Issue #67

# BCGcalc 2.0.0.9049 (2023-03-17)

* 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 (2023-03-17)

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

# BCGcalc 2.0.0.9047 (2023-02-10)

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

# BCGcalc 2.0.0.9046 (2023-02-08)

* 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 (2023-02-08)

* refactor: Create Shiny Merge Files Output tab

# BCGcalc 2.0.0.9044 (2023-02-08)

* refactor: Update Shiny output tabs

# BCGcalc 2.0.0.9043 (2023-02-07)

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

# BCGcalc 2.0.0.9042 (2023-02-07)

* 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 (2023-02-03)

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

# BCGcalc 2.0.0.9040 (2023-02-03)

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

# BCGcalc 2.0.0.9039 (2023-02-03)

* refactor: Update Shiny onscreen text, BCG calc

# BCGcalc 2.0.0.9038 (2023-02-03)

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

# BCGcalc 2.0.0.9037 (2023-02-03)

* refactor: Update Shiny onscreen text, Merge Files

# BCGcalc 2.0.0.9036 (2023-02-03)

* 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 (2023-02-02)

* refactor: Update Shiny app text

# BCGcalc 2.0.0.9034 (2023-02-02)

* refactor: Update Shiny to include change in BioMonTools package

# BCGcalc 2.0.0.9033 (2023-02-02)

* fix: Update file import routine
    + Account for multiple permutations of BCG_Attr
    + Add "" to na.strings 

# BCGcalc 2.0.0.9032 (2023-01-31)

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

# BCGcalc 2.0.0.9031 (2023-01-31)

* refactor: Finish updates to Shiny app merge files tab

# BCGcalc 2.0.0.9030 (2023-01-30)

* refactor: Add error checking for Index_Class in Shiny

# BCGcalc 2.0.0.9029 (2023-01-27)

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

# BCGcalc 2.0.0.9028 (2023-01-27)

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

# BCGcalc 2.0.0.9027 (2023-01-24)

* refactor: Update onscreen text for Shiny assign index class

# BCGcalc 2.0.0.9026 (2023-01-23)

* refactor: Remove uneeded QC steps in Shiny assign_indexclass routine

# BCGcalc 2.0.0.9025 (2023-01-20)

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

# BCGcalc 2.0.0.9024 (2023-01-20)

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

# BCGcalc 2.0.0.9023 (2023-01-20)

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

# BCGcalc 2.0.0.9022 (2023-01-19)

* fix: Modify code in Shiny for `assign_indexclass` so won't fail if field not
provided.

# BCGcalc 2.0.0.9021 (2023-01-19)

* feature: Add thermal metric calculation to Shiny app

# BCGcalc 2.0.0.9020 (2023-01-16)

* 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 (2023-01-02)

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

# BCGcalc 2.0.0.9018 (2023-01-02)

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

# BCGcalc 2.0.0.9017 (2022-12-23)

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

# BCGcalc 2.0.0.9016 (2022-12-23)

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

# BCGcalc 2.0.0.9015 (2022-12-23)

* refactor: Update Shiny app MTTI tab

# BCGcalc 2.0.0.9014 (2022-12-20)

* refactor: Update Shiny app for taxaid_drop parameter in 
`BioMonTools::taxa_translate`

# BCGcalc 2.0.0.9013 (2022-12-15)

* refactor: Sort columns and order output of taxa translator

# BCGcalc 2.0.0.9012 (2022-12-15)

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

# BCGcalc 2.0.0.9011 (2022-12-15)

* 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 (2022-12-14)

* 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 (2022-12-13)

* 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 (2022-12-13)

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


# BCGcalc 2.0.0.9007 (2022-12-12)

* feature: Add taxa translator tab and functionality to Shiny

# BCGcalc 2.0.0.9006 (2022-11-29)

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

# BCGcalc 2.0.0.9005 (2022-11-18)

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

# BCGcalc 2.0.0.9004 (2022-11-18)

* 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 (2022-11-17)

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

# BCGcalc 2.0.0.9002 (2022-11-17)

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

# BCGcalc 2.0.0.9001 (2022-11-16)

* 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 (2022-11-16)

* refactor: Shiny, change menu item name

# BCGcalc 1.3.5.9017 (2022-11-11)

* fix: Shiny app 'slim' output, Issue #62

# BCGcalc 1.3.5.9016 (2022-11-03)

* fix: Shiny app, markExcl, EXCLUDED to EXCLUDE

# BCGcalc 1.3.5.9015 (2022-11-01)

* 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 (2022-10-21)

* update: Update BCG style temperature model thresholds
    + Rules.xlsx

# BCGcalc 1.3.5.9013 (2022-10-14)

* refactor: Upgrades to Shiny app

# BCGcalc 1.3.5.9012 (2022-10-14)

* refactor: Upgrades to Shiny app

# BCGcalc 1.3.5.9011 (2022-10-13)

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

# BCGcalc 1.3.5.9010 (2022-10-11)

* 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 (2022-10-11)

* 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 (2022-09-30)

* 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 (2022-09-29)

* refactor: Upgrades to Shiny app

# BCGcalc 1.3.5.9006 (2022-09-28)

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

# BCGcalc 1.3.5.9005 (2022-09-28)

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

# BCGcalc 1.3.5.9004 (2022-09-28)

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

# BCGcalc 1.3.5.9003 (2022-09-23)

* 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 (2022-08-19)

* docs: Update format of NEWS

# BCGcalc 1.3.5.9001 (2022-08-18)

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

# BCGcalc 1.3.5 (2022-08-18)

* refactor: Bump version number.

# BCGcalc 1.3.4.9047 (2022-03-31)

* fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9046 (2022-02-14)

* fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9045 (2022-02-14)

* fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9044 (2022-02-14)

* fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9043 (2022-02-14)

* fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9042 (2022-02-14)

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

# BCGcalc 1.3.4.9041 (2022-02-11)

* refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9040 (2022-02-11)

* refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models

# BCGcalc 1.3.4.9039 (2022-02-11)

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

# BCGcalc 1.3.4.9038 (2021-12-03)

* 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 (2021-12-02)

* 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 (2021-12-01)

* 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 (2021-12-01)

* 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 (2021-08-09)

* 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 (2021-08-06)

* 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 (2021-08-04)

* fix: Update Rules.xlsx for CT BCG model, Issue #48
    + Removed double entries for fish01, fish02, and fish03 SiteType
    
# BCGcalc 1.3.4.9031 (2021-08-04)

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

# BCGcalc 1.3.4.9030 (2021-08-04)

* 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 (2021-08-03)

* 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 (2021-07-30)

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

# BCGcalc 1.3.4.9027 (2021-07-30)

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

# BCGcalc 1.3.4.9026 (2021-07-30)

* refactor: Update Rules.xlsx to match BioMonTools::metric.values()
    + rename brook trout wild
    
# BCGcalc 1.3.4.9025 (2021-07-29)

* refactor: Update Rules.xlsx to match BioMonTools::metric.values()
    + Add "BCG" to BCG attribute metric names

# BCGcalc 1.3.4.9024 (2021-07-28)

* 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 (2021-07-23)

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

# BCGcalc 1.3.4.9022 (2021-07-01)

* 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 (2021-07-01)

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

# BCGcalc 1.3.4.9020 (2021-06-22)

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

# BCGcalc 1.3.4.9019 (2021-04-04)

* docs: Add sticker to README

# BCGcalc 1.3.4.9018 (2021-04-04)

* feature: Add sticker
    + Create with hexSticker

# BCGcalc 1.3.4.9017 (2021-04-04)

* 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 (2021-01-18)

* 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 (2020-12-27)

* test: set up test folder

# BCGcalc 1.3.4.9014 (2020-12-27)

* 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 (2020-12-27)

* 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 (2019-11-07)

* Add pkgdown website.
    + Need to fix vignettes/BCGcalc_Map.Rmd.
        - INFRAORDER missing.

# BCGcalc 1.3.4.9011 (2019-06-26)

* 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 (2019-05-17)

* 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 (2019-04-18)

* BCG.Level.Assignment
    + Proportional BCG final scores, Issue #43.
        - Add "tie" to narrative.

# BCGcalc 1.3.4.9008 (2019-04-17)

* 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 (2019-04-17)

* extdata\MetricFlags.xlsx
    + ni_total, Hi, to 450 from 400.
        - Matches file in BioMonTools package.

# BCGcalc 1.3.4.9006 (2019-04-17)

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

# BCGcalc 1.3.4.9005 (2019-03-15)

* 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 (2018-11-26)

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

# BCGcalc 1.3.4.9003 (2018-11-26)

* Last update not complete before uploaded.

# BCGcalc 1.3.4.9002 (2018-11-26)

* 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 (2018-11-26)

* Add proportional Level Assignment.  Issue #43.
    + BCG.Level.Assignment

# BCGcalc 1.3.4 (2018-11-21)

* Update release version with Remote"s"" fix.

# BCGcalc 1.3.3.9005 (2018-11-21)

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

# BCGcalc 1.3.3.9004 (2018-11-21)

* 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 (2018-11-20)

* Update SuperFamily Tipuloidea
    + /extdata/Data_BCG_PacNW.xlsx
    + /extdata/TaxaMaster_Bug_BCG_PacNW_v1.xlsx

# BCGcalc 1.3.3.9002 (2018-11-19)

* /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 (2018-11-19)

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

# BCGcalc 1.3.3 (2018-11-19)

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

# BCGcalc 1.3.2.9012 (2018-11-19)

* 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 (2018-11-15)

* 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 (2018-11-07)

* 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 (2018-10-23)

* 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 (2018-10-22)

* 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 (2018-10-22)

* Metric calculation;
    + pi_Colesen
        - Change is.na(FAMILY) from FALSE to TRUE.

# BCGcalc 1.3.2.9006 (2018-10-22)

* Metric calculation;
    + pi_Hydro
        - Equal sign missing in equation ("=" instead of "==").

# BCGcalc 1.3.2.9005 (2018-10-22)

* Metric calculation;
    + pi_Tanyp
        - Misspelled Tanypodinae

# BCGcalc 1.3.2.9004 (2018-10-22)

* 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 (2018-10-22)

* 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 (2018-10-12)

* 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 (2018-10-12)

* Mapping Vignette.  Issue #34.
    + DESCRIPTION
        - Add ggplot2 to Suggests
    + extdata\Data_BCG_PacNW.xlsx
        - Add Latitude, Longitude, and COMID
    + Create Vignette for mapping

# BCGcalc 1.3.2 (2018-10-11)

* Release version.

# BCGcalc 1.3.1.9001 (2018-10-11)

* Master Taxa List
    + Turbellaria BCG Attribute.
        - Change from "x" to "4" to match its synonym Trepaxonemata.

# BCGcalc 1.3.1 (2018-10-10)

* Release version.

# BCGcalc 1.3.0.9001 (2018-10-10)

* Rules.xlsx
    + Fix typos in "Numeric_Rules" field.  
        - No impact on calculations.

# BCGcalc 1.3.0 (2018-10-09)

* Release version.

# BCGcalc 1.2.2.9033 (2018-10-09)

* Update Vignette.
    + Rarify section to 600.

# BCGcalc 1.2.2.9032 (2018-10-09)

* Update Vignette.
    + Fix a few typos.

# BCGcalc 1.2.2.9031 (2018-10-09)

* Update Rules.xlsx.
    + 300 count model edits.

# BCGcalc 1.2.2.9030 (2018-10-09)

* Vignette updates.

# BCGcalc 1.2.2.9029 (2018-10-05)

* 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 (2018-10-05)

* Updated docs.
    + extdata/ExampleDataFile.xlsx
    + docs/BCGcalc_README_20180919.pdf

# BCGcalc 1.2.2.9027 (2018-10-05)

* Updated Rules.xlsx file in extdata.

# BCGcalc 1.2.2.9026 (2018-09-28)

* Finish updates to Vignette.

# BCGcalc 1.2.2.9025 (2018-09-28)

* Level.Assignment.  Issue #11
    + Update example so don't calculate metrics twice.

# BCGcalc 1.2.2.9024 (2018-09-28)

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

# BCGcalc 1.2.2.9023 (2018-09-27)

* 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 (2018-09-27)

* 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 (2018-09-27)

* update ReadMe.  Issue #31

# BCGcalc 1.2.2.9020 (2018-09-27)

* 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 (2018-09-26)

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

# BCGcalc 1.2.2.9018 (2018-09-26)

* 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 (2018-09-26)

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

# BCGcalc 1.2.2.9016 (2018-09-26)

* 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 (2018-09-26)

* extdata\Rules.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\Data_BCG_PacNW.xlsx 
    + Renamed Index_Name from "BCG_PacNW_2018" to "BCG_PacNW_v1_500ct".
* extdata\MetricFlags.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 (2018-09-25)

* 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 (2018-09-25)

* Function rarify.  Issue #19
    + Remove keywords.

# BCGcalc 1.2.2.9012 (2018-09-25)

* Function rafify.  Issue #19
    + Fix typo in @param mySeed.  Remove extra period.
    
# BCGcalc 1.2.2.9011 (2018-09-20)

* Metric Names metadata  Issue #18
    + Update extdata\MetricNames.xlsx
    + Add PDF version to docs.

# BCGcalc 1.2.2.9010 (2018-09-20)

* More Indiana files.  Issue #24
    + extdata\QC_IN_BCG_Bugs_20170203.xlsm
    + extdata\QC_Metrics_Bugs_IN.xlsx

# BCGcalc 1.2.2.9009 (2018-09-20)

* 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 (2018-09-12)

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

# BCGcalc 1.2.2.9007 (2018-09-07)

* metric.values
    + Fixed included metrics (fun.MetricNames)

# BCGcalc 1.2.2.9006 (2018-09-07)

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

# BCGcalc 1.2.2.9005 (2018-09-07)

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

# BCGcalc 1.2.2.9004 (2018-09-05)

* 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 (2018-09-04)

* metric.values.  Issue #16
    + Added QC worksheet to extdata\Data_BCG_PacNW.xlsx

# BCGcalc 1.2.2.9002 (2018-08-28)

* 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 (2018-08-15)

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

# BCGcalc 1.2.2 (2018-06-14)

* New release version.

# BCGcalc 1.2.1.9001 (2018-06-14)

* qc.checks.R
    + Modification to use metric names as lower case.  Issue #12.
    + Example table; useNA="ifany".

# BCGcalc 1.2.1 (2018-06-13)

* New release version.

# BCGcalc 1.2.0.9001 (2018-06-13)

* 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 (2018-06-13)

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

# BCGcalc 1.1.0.9010 (2018-06-13)

* 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 (2018-06-13)

* 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 (2018-06-13)

* 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 (2018-06-12)

* 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 (2018-06-12)

* 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 (2018-06-11)

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

# BCGcalc 1.1.0.9004 (2018-06-08)

* Update extdata/Rules.xlsx; Issue #7

# BCGcalc 1.1.0.9003 (2018-06-08)

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

# BCGcalc 1.1.0.9002 (2018-06-08)

* 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 (2018-06-08)

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


# BCGcalc 1.1.0.0000 (2018-03-19)

* Release new and fully QCed version.

# BCGcalc 1.0.0.9002 (2018-03-19)

* 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 (2018-03-18)

* 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 (2018-03-18)

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

# BCGcalc 0.1.0.9019 (2018-03-18)

* 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 (2018-03-17)

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

# BCGcalc 0.1.0.9017 (2018-03-16)

* metric.values.R
    + Added Thermal Indicator (TI) metrics.
* Updates to PacNW bug data and rules files (xlsx).
    
# BCGcalc 0.1.0.9016 (2018-03-16)

* metric.values.R
    + Update pt_BCG_att1i2 and 1i23 metrics (numerator not capturing "i" taxa).
* Update Rules.xlsx
    
# BCGcalc 0.1.0.9015 (2018-03-16)

* Vignette didn't update in previous version.

# BCGcalc 0.1.0.9014 (2018-03-15)

* 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 (2018-03-14)

* Added PacNW benthic master taxa list to data.
* Created "data.R".  Not complete!

# BCGcalc 0.1.0.9012 (2018-03-08)

* 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 (2018-03-08)

* Completed lingering edits for "Tier" to "Level".
* Completed BCG.Level.Membership function.

# BCGcalc 0.1.0.9010 (2018-03-07)

* 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 (2018-03-05)

* 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 (2018-03-05)

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

# BCGcalc 0.1.0.9007 (2018-03-05)

* 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 (2018-03-04)

* BCG.Tiers function.

# BCGcalc 0.1.0.9005 (2018-03-04)

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

# BCGcalc 0.1.0.9004 (2018-03-03)

* 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 (2018-02-20)

* 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 (2018-02-16)

* Updated files for package.
    + Readme, NEWS, DESCRIPTION
    + Not complete.

# BCGcalc 0.1.0 (2018-02-16)

* Created GitHub repository