• refactor: Add additional rules, Boise BCG, Issue #97
  • refactor: Add additional flags, Boise BCG, Issue #97
  • docs: Update LICENSE files and reference in DESCRIPTION
  • docs: Move BioMonTools from Imports to Suggests in DESCRIPTION
  • refactor: Replace old and non-working GitHub Actions
    • Add from BioMonTools package
  • 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
  • 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)
  • refactor: Add new Flags for GP BCG, Issue #96
  • 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
  • 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
  • fix: Update calls to StreamCatTools for Shiny getClassParam function, Issue #93
    • Changes to StreamCatTools functions due to changes in API
  • refactor: Update Shiny app references to taxa file on BioMonTools_SupportFiles
  • refactor: Update MetricFlags.xlsx
    • New ORWA move ni_total flags to top of list for each Index_Class
  • refactor: Add BCG_ORWA_v1_Bugs500ct to Rules.xlsx
  • refactor: Add BCG_ORWA_v1_Bugs500ct to MetricFlags.xlsx
  • 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
  • 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
  • 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)
  • refactor: Add Great Plains BCG metric flags
  • refactor: Add summation of duplicate taxa in taxa translate in Shiny
  • refactor: Merge Pull Request 92
  • refactor: Update Rules.xlsx for MN_BCG metric descriptions and index regions
  • refactor: Update Rules.xlsx for MN_BCG fish10a and fish10b
  • 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
  • fix: Update MTTI shiny code to avoid name conflict
    • TolVal2 vs. TOLVAL2
  • docs: Update help on ORWA taxa list to reinforce is demo only
  • refactor: Update functions to retain original case for INDEX_CLASS, Issue #91
    • BCG.Metric.Membership
    • BCG.Level.Membership
  • refactor: Define pipe in BCG.Level.Membership
  • refactor: Update rules for SMALL2 and SMALL3
    • Sort ascending
    • Add rules for SMALL2A and SMALL2B
  • break: Fix Rules for SMALL2 and SMALL3
    • Sort descending and take row 2 or 3
    • This could be a breaking change
      • Updating version number
  • refactor: Update ‘GP_BCG_Fish’ to ‘GP_Fish_BCG’ to match GP Bug models
    • Rules.xlsx
  • refactor: Update Rules.xlsx for Great Plains BCG
  • refactor: Modify language on Shiny app pop up for assign class
  • fix: Update MetricFlags.xlsx for FL Coral BCG
  • fix: Update Rules.xlsx for FL Coral BCG
  • docs: Update BCG.Metric.Membership language for col_INCREASE
  • refactor: Update Rules.xlsx for FL Coral BCG
  • feature: Add new template for new metrics, models, and rules
  • fix: Update package documenation per roxygen2
  • 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)
  • fix: Shiny app fuzzy model not working, change community reference
    • Also fixed thermal metrics for status message
  • fix: Update naming scheme for BCG calculation in Shiny app, Issue #87
    • Add “_” prefix to Results.
  • 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
  • refactor: Update NM BCG, drop percent max ffg from L2 and L4 per documentation
  • refactor: Update NM BCG Index_Name and Index_Class in Rules.xlsx
  • 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
  • fix: Remove testing line in Report server code
    • Caused ShinyApps.io to crash trying to open Excel
  • refactor: Update Report
    • Add conditional formatting for summary worksheet for data columns
      • MTTI
      • Thermal Metrics
    • Add error checking if thermal metrics not present
  • 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)
  • 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
  • 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
  • refactor: Modify Shiny single report
    • Zip file download
  • fix: Update app BCG calculation for cases where have no flags
  • fix: Update MN fish metric names (trout) to be more specific
  • 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
  • fix: Modify taxatrans hack for noteworthy to only trigger if present
  • refactor: BCG calculation user column select to lower case
    • elev_m
    • pslope_nhd
  • refactor: Rename BCG calculation flag output (previously model experience)
  • feature: Add ecoregion L3 to generate index class parameters
  • 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 “_”
  • fix: Modify QC check on BCG model experience to BCG calculate
    • total flags
  • refactor: Modify QC check on BCG model experience to BCG calculate
  • feature: Add QC check on BCG model experience to BCG calculate
  • fix: Comment out all other instances of validate(msg) to avoid potential issues
  • fix: File builder taxa translate remove validate statement from pop up
    • Was causing the server to pause and not continue
  • feature: Add pop-up for taxa translate with mismatch taxa
  • 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
  • refactor: Add MN BCG Fish rules, Rules.xlsx
  • feature: Added single site report
    • Formatting incomplete but function working in Shiny
  • 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
  • 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
  • fix: Updates TaxaTranslate file output (names and folders)
  • refactor: Updates to Shiny interface
  • 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
  • refactor: Implement result file name changes using global abbreviations
  • 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
  • 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
  • fix: Shiny, taxatrans_late_0filesversion.csv, swap 2 columns
  • 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
  • refactor: For leaflet map change to addCircleMarkers
    • Replaced addCircles
  • fix: Change leaflet map proxy to redraw legend
    • Prevents thermal metric legends from having multiple on screen
  • refactor: Add “DRAFT” to BDI
  • 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
  • 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
  • refactor: Add download links to KMZ files
  • refactor: Update map legends coding, Issue #67
  • feature: Add KMZ downloads to Shiny app
    • NorWeST_ORWA
    • PNMR_BCGclasses
  • feature: Updated maps in Shiny, Issue #67
  • feat: Add example script for MTTI
  • feat: Add example data for MTTI to external folder
  • feat: Add maps for each index, Issue #67
  • fix: BDI, if no Index_Class was not adding proper variable name, Issue #66
    • Caused samples to not be scored
  • fix: Typo on “Covert OTU” on MTTI and BDI shiny tabs
  • refactor: Adjust Excl taxa triggers and QC in code, Issue #66
  • fix: Removed browser() statement from QC of last update, Issue #84
  • feature: Automate Index Name and Class for fuzzy set calculation, Issue #84
    • Shiny
  • feature: Add BDI calculation to Shiny, Issue #66
    • COMPLETE
  • refactor: Shiny required fields type for TRUE/FALSE changed text to logical
  • refactor: Update MN BCG (bugs) in Rules.xlsx, Issue #82
  • refactor: Add MN BCG (bugs) to Rules.xlsx, Issue #82
  • refactor: Updates to BDI calculation, Issue #66
    • INCOMPLETE, completed in 2.0.0.988
  • 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
  • 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
  • refactor: Updates to Shiny map, Issue #67
    • INCOMPLETE
  • refactor: Change taxa translator to no default
  • fix: Modify code for complex number (BCG_ATTR), Issue #77
    • Other logical fields could cause issues with older import method
  • 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
  • refactor: Update Index Class Parameter, Issue #73
  • refactor: Update Shiny Fuzzy Set
  • feature: Add upset plot to MTTI results report
  • docs: Add ComplexUpset to DESCRIPTION Suggests and Shiny global
  • refactor: Update Shiny MTTI, Issue #74
    • Onscreen text
    • Example files
  • style: Move MTTI model file location
  • 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

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

refactor: Update MTTI output, Issue #74

style: Code coverage updates

  • refactor: Change order of columns for Fuzzy Thermal, Issue #70
    • modtherm_5levassign.csv
  • fix: Update overlapping Fuzzy Thermal CheckNames in MetricFlags.xlsx, Issue #72
  • refactor: Add columns and classifications to Fuzzy Thermal model, Issue #70
  • fix: MetricFlags.xlsx ‘pcSLOPE’ to ‘pctSLOPE’ (typo)
  • fix: MetricFlags.xlsx ‘DrArea_mi2’ to ‘WSAREASQKM’ (and values)
  • fix: Remove browser call in fuzzy thermal model
  • refactor: Additional flags for fuzzy thermal model
  • refactor: Updates to fuzzy thermal model output
  • 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
  • refactor: Error checking for missing variables, Shiny
    • Fuzzy Thermal Model
    • Index Class Param, Issue #42
  • refactor: Update Index Class Param onscreen help in Shiny, Issue #42
  • refactor: Shiny get Index Class Params, Issue #42
    • Allow for user defined column
      • Default is NAD83 North America, EPSG = 4269
    • Trim output
  • refactor: Update Shiny MTTI calculation and flags calculation and output
  • refactor: Update Shiny MTTI calculation to include flags
  • style: Modify some lines based on lintr suggestions
    • Add nolint to Shiny library calls
  • fix: Update Shiny app import to better handle BCG_ATTR (complex)
    • Added exception for only integer values
  • fix: Ensure all Shiny buttons use same terminology
    • b_calc_x
    • b_download_x
  • 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
  • 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
  • refactor: Shiny index class parameter generation, Issue #42
  • docs: Add packages used in Shiny app to DESCRTION Suggests
    • StreamCatTools
    • nhdplusTools
  • 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
  • refactor: Update Shiny MTTI calculation (was placeholder)
  • feat: Add Shiny tab for generating index class parameters, Issue #42
    • Placeholder only
  • refactor: Add map column select and base map, Issue #67
    • Not complete
  • feat: Add placeholder for map, Issue #67
  • 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
  • refactor: Add link for example scripts to fuzzy thermal about page
  • docs: Update BCG.Level.Assignment example code
  • refactor: Update example script (BCG calc)
  • 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
  • refactor: Create Shiny Merge Files Output tab
  • refactor: Update Shiny output tabs
  • refactor: Update taxa translate 0fileversion output
    • Shiny, server.R
    • example code, taxa translate
  • 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
  • refactor: Update Shiny onscreen text, inputs BCG calc
  • refactor: Update Shiny onscreen text, inputs thermal metrics
  • refactor: Update Shiny onscreen text, thermal preference metrics
    • Add metadata file to calculation thermal metrics results
  • refactor: Update Shiny onscreen text, BCG calc
  • docs: Update readme install section with quick code
  • refactor: Update Shiny onscreen text, Assign Index_Class
  • refactor: Update Shiny onscreen text, Merge Files
  • refactor: Change Shiny merge files order (x and y)
    • Samples should be the main file (x) and keep all records and info
  • refactor: Update Shiny app text
  • refactor: Update Shiny to include change in BioMonTools package
  • fix: Update file import routine
    • Account for multiple permutations of BCG_Attr
    • Add “” to na.strings
  • fix: Adjust QC routine in Shiny app assign index class
  • refactor: Finish updates to Shiny app merge files tab
  • refactor: Add error checking for Index_Class in Shiny
  • docs: Add Shiny link to README
  • refactor: Layout changes to taxa translate section of Shiny app
  • refactor: Add Shiny merge files tab placeholder
    • proof of concept, not complete
  • refactor: Update onscreen text for Shiny assign index class
  • refactor: Remove uneeded QC steps in Shiny assign_indexclass routine
  • refactor: Add excluded taxa subroutine to thermal metrics in Shiny
  • refactor: BioMonTools MetricNames.xlsx from GitHub instead of package in Shiny
  • refactor: Add taxa translate unique crosswalk to output of taxatranslate in Shiny
  • fix: Modify code in Shiny for assign_indexclass so won’t fail if field not provided.
  • feature: Add thermal metric calculation to Shiny app
  • 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
  • refactor: Update Shiny taxa trans to drop translator columns if have an attributes table
  • refactor: Update Shiny taxa trans to use default names
    • SampleID, TaxaID, and N_Taxa
  • refactor: Update Shiny taxa trans to include filenames in MERGED output
  • refactor: Update Shiny, split file builder in to taxa trans and assign index class
  • refactor: Update Shiny app MTTI tab
  • refactor: Sort columns and order output of taxa translator
  • feature: Add INDEX_NAME and INDEX_CLASS as input parameters to BCG.Level.Assignment
  • refactor: Shiny app, filebuilder
    • save version of files in download
    • reorganize the required fields requested of user
    • change some text on screen
  • 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)
  • 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
  • refactor: Change BCG.ContLevelText status from x/y tie to x.5, Issue #64
  • feature: Add taxa translator tab and functionality to Shiny
  • feature: Add new function to calculate BCG Status
    • Uses continuous value to get Integer or PlusMinus text
  • refactor: Additional Shiny outputs
    • 6metflags; flag metrics, values, thresholds
    • 3metrules; rules table
  • refactor: Update Shiny text for additional outputs
  • 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
  • refactor: Change Shiny output 2metval_slim.csv to 2metval_BCG.csv
  • fix: Update Rules.xlsx for non-ASCII characters
  • 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
  • refactor: Shiny, change menu item name
  • fix: Shiny app ‘slim’ output, Issue #62
  • fix: Shiny app, markExcl, EXCLUDED to EXCLUDE
  • update: Change name of PacNW model, Issue #61
    • Rules.xlsx
    • MetricFlags.xlsx
    • Example files (file name, data, sheet names)
    • Update examples in functions
    • Vignettes
  • update: Update BCG style temperature model thresholds
    • Rules.xlsx
  • refactor: Upgrades to Shiny app
  • refactor: Upgrades to Shiny app
  • refactor: Upgrades to Shiny app
    • Rework tab order and names
    • Update About
    • Other
  • 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
  • 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
  • refactor: Upgrades to Shiny app
    • Second version of results/metval with only those for the model
    • Ensure result files removed from previous imports
  • refactor: Upgrades to Shiny app
  • docs: Update examples for missing columns in sample data for all functions
  • fix: Update MetricFlags.xlsx for one flag
  • docs: Update packages in DESCRIPTION and global.R in Shiny app
  • feat: Redesign shiny app
  • docs: Add packages needed by Shiny app to DESCRIPTION
  • 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
  • docs: Update format of NEWS
  • feature: Add Shiny app skeleton and function to run it, Issue #58
  • refactor: Bump version number.
  • fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • refactor: Update metric.values()
    • Failed when rules table included more than 1 region and metrics uneven
  • refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
  • tests: Add tests for flags and metric names
  • refactor: Update BCG.Level.Membership() for new median rule type, Issue #55
  • refactor: Update Rules.xlsx to handle new median rule type, Issue #55
  • 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 “>=”.
  • 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
  • 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()
  • 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()
  • 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
  • fix: Update Rules.xlsx for CT BCG model, Issue #48
    • Removed double entries for fish01, fish02, and fish03 SiteType
  • fix: Update Rules.xlsx for CT BCG model, Issue #48
    • Removed double entries for bug01 SiteType
  • 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()
  • 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
  • refactor: Update Rules.xlsx for CT BCG benthos
    • pi_BCG_att5 to pi_BCG_att5extra
  • refactor: Update BCG.Level.Membership with stop message if unable to merge data frames
  • refactor: Update Rules.xlsx to match BioMonTools::metric.values()
    • rename brook trout wild
  • refactor: Update Rules.xlsx to match BioMonTools::metric.values()
    • Add “BCG” to BCG attribute metric names
  • 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()
  • refactor: Update Rules.xlsx, Issue #48
    • Change Index_Name, Site_Type, and Index_Region
  • 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
  • refactor: Merge pull request with updated rules, Issue #52
  • refactor: Update model rules, Rules.xlsx, Issue #48
  • docs: Add sticker to README
  • feature: Add sticker
    • Create with hexSticker
  • 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
  • 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
  • test: set up test folder
  • 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
  • ci: Add GitHub Actions, continuous integration
  • ci: Remove TravisCI
  • docs: ReadMe, remove TravisCI badge
  • docs: ReadMe, Add GitHub Actions CMD check badge
  • Add pkgdown website.
    • Need to fix vignettes/BCGcalc_Map.Rmd.
      • INFRAORDER missing.
  • 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
  • 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.
  • BCG.Level.Assignment
    • Proportional BCG final scores, Issue #43.
      • Add “tie” to narrative.
  • BCG.Level.Assignment
    • Proportional BCG final scores, Issue #43
      • Turn on features from v1.3.4.9004.
      • Add proportional narrative (+/-).
  • extdata.xlsx
    • ni_total, Hi, to 450 from 400.
      • Matches file in BioMonTools package.
  • Remove format Hoboware file from extdata folder.
    • From another package under development.
  • 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
  • Proportional Level Assignment. Issue #43.
    • Needs more polish for different conditions.
    • Assign all to NA.
  • Last update not complete before uploaded.
  • 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.
  • Add proportional Level Assignment. Issue #43.
    • BCG.Level.Assignment
  • Update release version with Remote”s”” fix.
  • BioMonTools dependency not installing.
    • Move Remote up in listing in DESCRIPTION.
    • Renamed Remote to Remotes.
  • Add BioMonTools to Imports so will auto install.
    • Had removed at some point since don’t use the functions in any BCGcalc functions.
  • Update SuperFamily Tipuloidea
    • /extdata/Data_BCG_PacNW.xlsx
    • /extdata/TaxaMaster_Bug_BCG_PacNW_v1.xlsx
  • /extdata/Data_BCG_PacNW.xlsx
    • Update Exclude column after QC with BioMonTools::markExcluded
      • Change 6 FALSE to TRUE
      • Change 1 TRUE to FALSE
  • Update ReadMe for BioMonTools::metric.values. Issue #41.
  • Update version have changes related to moving functions to the BioMonTools package.
  • 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.
  • 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
  • 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
  • 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
  • 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
  • Metric calculation;
    • pi_Colesen
      • Change is.na(FAMILY) from FALSE to TRUE.
  • Metric calculation;
    • pi_Hydro
      • Equal sign missing in equation (“=” instead of “==”).
  • Metric calculation;
    • pi_Tanyp
      • Misspelled Tanypodinae
  • 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.
  • 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”)
  • 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
  • Mapping Vignette. Issue #34.
    • DESCRIPTION
      • Add ggplot2 to Suggests
    • extdata_BCG_PacNW.xlsx
      • Add Latitude, Longitude, and COMID
    • Create Vignette for mapping
  • Release version.
  • Master Taxa List
    • Turbellaria BCG Attribute.
      • Change from “x” to “4” to match its synonym Trepaxonemata.
  • Release version.
  • Rules.xlsx
    • Fix typos in “Numeric_Rules” field.
      • No impact on calculations.
  • Release version.
  • Update Vignette.
    • Rarify section to 600.
  • Update Vignette.
    • Fix a few typos.
  • Update Rules.xlsx.
    • 300 count model edits.
  • Vignette updates.
  • 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.
  • Updated docs.
    • extdata/ExampleDataFile.xlsx
    • docs/BCGcalc_README_20180919.pdf
  • Updated Rules.xlsx file in extdata.
  • Finish updates to Vignette.
  • Level.Assignment. Issue #11
    • Update example so don’t calculate metrics twice.
  • Vignette updates (incomplete).
  • Metric.Membership. Issue #11
    • Non numeric extra columns caused errors. Fixed.
  • 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.
  • 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.
  • update ReadMe. Issue #31
  • 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.
  • File formats. Issue #28
    • Add statement about file formats to Vignette.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • Function rarify. Issue #19
    • Remove keywords.
  • Function rafify. Issue #19
    • Fix typo in @param mySeed. Remove extra period.
  • Metric Names metadata Issue #18
    • Update extdata.xlsx
    • Add PDF version to docs.
  • More Indiana files. Issue #24
    • extdata_IN_BCG_Bugs_20170203.xlsm
    • extdata_Metrics_Bugs_IN.xlsx
  • 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.
  • DESCRIPTION
    • Add date.
    • Add Jen Stamp as contributor
  • Citation still gives error but is more complete now. Issue #23
  • metric.values
    • Fixed included metrics (fun.MetricNames)
  • metric.values
    • Added QC check for NonTarget==FALSE.
    • Give a warning if have zero FALSE values.
  • metric.values
    • Added QC check for Exclude==TRUE.
    • Give a warning if have zero TRUE values.
  • 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.
  • metric.values. Issue #16
    • Added QC worksheet to extdata_BCG_PacNW.xlsx
  • metric.values. Issue #13
    • Add required fields (columns) to help file.
    • Add QC check in function. Prompt user to continue or stop.
  • metric.values
    • Added metric Percent Baetis tricaudatus complex + Simuliidae individuals (pi_SimBtri). Issue #16.
  • New release version.
  • qc.checks.R
    • Modification to use metric names as lower case. Issue #12.
    • Example table; useNA=“ifany”.
  • New release version.
  • 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.
  • Release version for Pacific Northwest BCG workgroup with updated model.
  • 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.
  • 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.
  • 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.
  • Update Rules.xlsx.
    • Level 3 (Hi and Lo), pi_BCG_att56 changed to pt_BCG_att1i23.
    • Change involved both direction and thresholds.
  • 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.
  • Update bio data to be used for the model; Issue #7
    • Collapse mites to Order.
  • Update extdata/Rules.xlsx; Issue #7
  • metric.values dd nt, pi, and pt metrics; Issue #7
    • NonIns_BCG_attr456
    • NonInsJugaRiss_BCG_attr456
  • QC Flags, Add pi_dom02. Issue #7
  • Update format of NEWS.
  • metric.values, row_number to dplyr::row_number for dominant metrics.
  • metric.values, Issue #7
    • Update metrics from NonClump to NoJugaRiss.
  • Release new and fully QCed version.
  • 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).
  • 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.
  • Only metric value issues left to resolve with test data set. Rest of the calculations are ok.
  • 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.
  • BCG.Level.Membership.R
    • Correct function to consider preceding levels when assigning membership scores.
  • metric.values.R
    • Added Thermal Indicator (TI) metrics.
  • Updates to PacNW bug data and rules files (xlsx).
  • metric.values.R
    • Update pt_BCG_att1i2 and 1i23 metrics (numerator not capturing “i” taxa).
  • Update Rules.xlsx
  • Vignette didn’t update in previous version.
  • 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
  • Added PacNW benthic master taxa list to data.
  • Created “data.R”. Not complete!
  • 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.
  • Completed lingering edits for “Tier” to “Level”.
  • Completed BCG.Level.Membership function.
  • 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.
  • Dom02 special metric placeholder.
  • Update Rule table for Level assignments.
  • BCG.Levels function.
  • Fixed error in sequencing in BCG.Membership function.
  • Add last of the PacNW specific metrics to metric.values.
  • Added Vignette.
  • Check clean up.
  • Convert data imports from development folder to pacakge folder with system.file.
  • Add data for rarify function.
  • BCG.Tiers function.
  • Add BCG.Membership function. Return is in long format.
    • Not QCed but has some known issues.
  • 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.
  • 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
  • Updated files for package.
    • Readme, NEWS, DESCRIPTION
    • Not complete.
  • Created GitHub repository