Changes in version 2.3.1.9007 - refactor: Update GP (MO) Bug Rules, Issue #103 - Rules.xlsx Changes in version 2.3.1.9006 - refactor: Update GP Bug Rules, Issue #102 - Rules.xlsx Changes in version 2.3.1.9005 - fix: Update MetricFlags.xlsx symbols - “==” not “=” for new rules Changes in version 2.3.1.9004 - refactor: Update MetricFlags.xlsx - LBR_Fish_BCG_v1 - Remove existing Main_Eckert before adding updated flags Changes in version 2.3.1.9003 - refactor: Add secret token in code coverage YAML Changes in version 2.3.1.9002 - refactor: Update code coverage YAML and badge in README Changes in version 2.3.1.9001 - tests: Add tests for code coverage - metric.membership - shape - missing metrics - refactor: Modify metric.membership error for missing metrics - Allow for test to check class so it is generic - docs: Add rlang to DESCRIPTION as Suggests - tests: Split test file into function_calculations and rules_flags - refactor: Add error for level.membership for missing metrics in data, Issue #54 Changes in version 2.3.1 (2026-08-08) - refactor: Bump version number for resubmittal to CRAN, Issue #100 Changes in version 2.3.0.9004 - refactor: Move Shiny example files to BCGcalc_ORWA, Issue #100 Changes in version 2.3.0.9003 - refactor: Move large files to BCGcalc_ORWA, Issue #100 - Data_BCG_PugLowWilVal.csv - _Input_HiGradHiElev_noExclude_20220108.csv - refactor: Make smaller versions (1000 records) of example files, Issue #100 - Data_BCG_PugLowWilVal.xlsx - ExampleMunge_UnformattedData.xlsx Changes in version 2.3.0.9002 - docs: Update package description with more detail and references per CRAN fix, Issue #100 Changes in version 2.3.0.9001 - refactor: Remove example BDVI data as not used in package - CRAN fix, Issue #100 - Moved to BCGcalc_ORWA - docs: Update package description per CRAN fix, Issue #100 Changes in version 2.3 - docs: Increase version for CRAN release Changes in version 2.2.0.9013 - refactor: Updates for CRAN, Issue #100 - docs: Add cran comments to _test - refactor: Add cran comments to buildignore - docs: Update title of package to Title Case - docs: Remove Remotes line from DESCRIPTION - docs: Update URLs in README - CodeCov - lifecycle - refactor: Trim number of records in example for BCG.Metric.Membership Changes in version 2.2.0.9012 - refactor: Update Rules.xlsx - Remove metric nt_ti_stenocold_cold_cool from BCG_ORWA_v1_Bugs500ct, Foothills_Multihab Changes in version 2.2.0.9011 - tests: Update duplicate metric test - Add Symbol and Increase columns Changes in version 2.2.0.9010 - fix: Update Boise BCG Fish Level nt_total Level 4 duplicate to Level 5 - tests: Add test for duplicate metrics - Index_Name, INDEX_CLASS, Level, Rule_Type - Keep disabled as may not be always true Changes in version 2.2.0.9009 - refactor: Make example run time shorter, Issue #100 - BCG.Level.Assignment Changes in version 2.2.0.9008 - refactor: Update documentation for metrics_values, Issue #100 - refactor: Make examples run times shorter, Issue #100 Changes in version 2.2.0.9007 - refactor: Remove unused GIS data files, Issue #100 - Move to BCGcalc_ORWA repo Changes in version 2.2.0.9006 - docs: Update README, Issue #99 Changes in version 2.2.0.9005 - refactor: Update OK_Bugs_BCG rules for pi_COEPT_BCG_att1i234b4m - Rules.xlsx Changes in version 2.2.0.9004 - refactor: Update rules and flags for ORWA - 6 to 6m6t - refactor: Modify deprecated input col_SITE_TYPE message with global binding - BCG.Metric.Membership - BCG.Level.Membership Changes in version 2.2.0.9003 - fix: Remove runShiny Changes in version 2.2.0.9002 - refactor: Replace Boise NotusParma rules with updated rules - Rules.xlsx Changes in version 2.2.0.9001 - refactor: Add missing global bindings - BCG.Level.Membership - docs: Update help file for TaxaMaster_Ben_BCG_PugLowWilVal - docs: Add help files for those missing help files - data_GIS_BCGclass - data_GIS_eco3_orwa - data_GIS_eco3_orwa_bcg - refactor: Update BCGcalc_Map vignette - Still has issues Changes in version 2.2.0 - refactor: Move Shiny app out of BCGcalc into its own package - docs: Remove Shiny-centric packages from DESCRIPTION Changes in version 2.1.0.9042 - fix: Remove browser command from Shiny app Changes in version 2.1.0.9041 - fix: Change Shiny import routine for BCG_Attr and BCG_Attr2 - Certain conditions the imported file had all values on each row - fix: Update MetricFlags.xlsx - ORWA flags from 2.1.0.9035 file symbols to be R compliant - docs: Update NEWS file for undocumented updates. - tests: Add nt_largeriver as a non BioMonTools metric for testing for MetricFlags.xlsx Changes in version 2.1.0.9040 - docs: Originally added as 2.1.0.9035 - refactor: Comment out user file columns for statewide model in Shiny app - refactor: Add check for existing column for Exclude taxa in statewide model Changes in version 2.1.0.9039 - Updated rules to fix Kansas rules Changes in version 2.1.0.9038 - Updated rules to replace pi_COEPT_BCG_att234b4m with pi_COEPT_BCG_att1i234b4m. Changes in version 2.1.0.9037 - Added rules for Oklahoma associated with GP BCG Changes in version 2.1.0.9036 - Updated OWRA and Kansas bug BCG rules Changes in version 2.1.0.9035 - Updated OWRA rules and metric flags per Jen’s updates on 06/23 Changes in version 2.1.0.9034 - refactor: Add ORWA Statewide BCG classes (20260603) to Shiny data folder - In preparation for addition of ORWA index assign class to Shiny app calculator - refactor: Remove older ORWA rules (Hi/Lo-Grad/Elev) from Rules.xlsx - refactor: Update MetricFlags.xlsx for ORWA - style: Update tests with package name for each test Changes in version 2.1.0.9033 - refactor: Update Rules.xlsx for BCG_ORWA_v1_Bugs500ct Changes in version 2.1.0.9032 - refactor: Update Rules.xlsx for Metric_Sort column spelling Changes in version 2.1.0.9031 - refactor: Update Rules.xlsx with Metric_Sort column - LBR Bugs and Fish Changes in version 2.1.0.9030 - fix: Remove draft rules (2.0.1.9027, 2025-12-26) - BCG, Boise, Fish, Main_Eckert, Issue #97 Changes in version 2.1.0.9029 - refactor: Add flags, Boise BCG, Bugs - sum_density_m2 - refactor: Add rules, Boise BCG, Fish - tests: Write rule for symbols for Rules.xlsx Changes in version 2.1.0.9028 - refactor: Add rules, Boise BCG, Bugs - refactor: Add flags, Boise BCG, Bugs - refactor: Update Vignette due to m2 fields from new metrics - BCGcalc_Map.Rmd - vignette_BCGcalc.Rmd Changes in version 2.1.0.9027 - refactor: Add additional rules, Boise BCG, Issue #97 - refactor: Add additional flags, Boise BCG, Issue #97 Changes in version 2.1.0.9025 - docs: Update LICENSE files and reference in DESCRIPTION - docs: Move BioMonTools from Imports to Suggests in DESCRIPTION Changes in version 2.1.0.9024 - refactor: Replace old and non-working GitHub Actions - Add from BioMonTools package Changes in version 2.1.0.9023 - fix: Update BCG.ContLevel example to not fail - fix: Update example code in Vignettes to avoid failures - docs: Remove reshape2 from suggests in DESCRIPTION - fix: Add files in root directory to .Rbuildignore - NEWS.rmd - README.rmd - _test/ - data-raw/ - refactor: Add missing package references to functions in code - BCG.Level.Membership - BCG.ContLevel Changes in version 2.1.0.9022 - refactor: Shiny app, MariNW, - Exclude taxa, add new levels - SpeciesGroup, SpeciesSubGroup, and SpeciesComplex - Add ‘required’ to section E for column names - Add example for Ecoregion (e.g., 2, 3, or 4) Changes in version 2.1.0.9021 - refactor: Add new Flags for GP BCG, Issue #96 Changes in version 2.1.0.9020 - fix: Update server for columns for BCG Attr - refactor: Update NE_Bugs_BCG rules, Issue #95 - fix: Update Rules, failed test - pi_SCC to pi_scc - fix: Update test, Flags, Metrics, BioMonTools Changes in version 2.1.0.9019 - refactor: Update Generate BCG Class parameters to include watershed area - Re-enable and then rename all caps to match model - fix: Update BCG for statewide and marine northwest - Rename objects by model - Reference correct objects within each model - Remove “out of experience” from statewide model pop up Changes in version 2.1.0.9018 - fix: Update calls to StreamCatTools for Shiny getClassParam function, Issue #93 - Changes to StreamCatTools functions due to changes in API Changes in version 2.1.0.9017 - refactor: Update Shiny app references to taxa file on BioMonTools_SupportFiles Changes in version 2.1.0.9016 - refactor: Update MetricFlags.xlsx - New ORWA move ni_total flags to top of list for each Index_Class Changes in version 2.1.0.9015 - refactor: Add BCG_ORWA_v1_Bugs500ct to Rules.xlsx - refactor: Add BCG_ORWA_v1_Bugs500ct to MetricFlags.xlsx Changes in version 2.1.0.9014 - fix: Modify BCG.Level.Membership - Update for exception rules - Edit FLIPMINMAX to flip min and max - Add MIN012MAX, MIN of Rules 0, 1, 2 then MAX - refactor: Update Rules.xlsx - Populate missing INCREASE values - Add metadata worksheet for EXC_RULE - Add MN_BCG for EXC_RULE MIN012MAX - refactor: Add error message for NA in INCREASE column for BCG.Metric.Membership Changes in version 2.1.0.9013 - fix: Modify BCG.Level.Membership to flip min and max as an exception rule - refactor: Update Rules.xlsx for MN_BCG for EXC_RULE FLIPMINMAX Changes in version 2.1.0.9012 - fix: Modify BCG.Level.Membership to avoid duplication in output for level assigment - Modify INDEX_CLASS_ORIG - Modify Exception calculations (i.e., median, small2, small2A, small2B, and small3) Changes in version 2.1.0.9011 - refactor: Add Great Plains BCG metric flags Changes in version 2.1.0.9010 - refactor: Add summation of duplicate taxa in taxa translate in Shiny Changes in version 2.1.0.9009 - refactor: Merge Pull Request 92 Changes in version 2.1.0.9008 - refactor: Update Rules.xlsx for MN_BCG metric descriptions and index regions Changes in version 2.1.0.9007 - refactor: Update Rules.xlsx for MN_BCG fish10a and fish10b Changes in version 2.1.0.9006 - refactor: Add Shiny calculation Fish Thermal Class to menu and a page - refactor: Add Shiny troubleshooting menu option - refactor: Update Shiny MTTI citation - refactor: Update Shiny Thermal Preference Metrics citation Changes in version 2.1.0.9005 - fix: Update MTTI shiny code to avoid name conflict - TolVal2 vs. TOLVAL2 Changes in version 2.1.0.9004 - docs: Update help on ORWA taxa list to reinforce is demo only Changes in version 2.1.0.9003 - refactor: Update functions to retain original case for INDEX_CLASS, Issue #91 - BCG.Metric.Membership - BCG.Level.Membership Changes in version 2.1.0.9002 - refactor: Define pipe in BCG.Level.Membership Changes in version 2.1.0.9001 - refactor: Update rules for SMALL2 and SMALL3 - Sort ascending - Add rules for SMALL2A and SMALL2B Changes in version 2.1.0.9000 - break: Fix Rules for SMALL2 and SMALL3 - Sort descending and take row 2 or 3 - This could be a breaking change - Updating version number Changes in version 2.0.0.9146 - refactor: Update ‘GP_BCG_Fish’ to ‘GP_Fish_BCG’ to match GP Bug models - Rules.xlsx Changes in version 2.0.0.9145 - refactor: Update Rules.xlsx for Great Plains BCG Changes in version 2.0.0.9144 - refactor: Modify language on Shiny app pop up for assign class Changes in version 2.0.0.9143 - fix: Update MetricFlags.xlsx for FL Coral BCG Changes in version 2.0.0.9142 - fix: Update Rules.xlsx for FL Coral BCG Changes in version 2.0.0.9141 - docs: Update BCG.Metric.Membership language for col_INCREASE - refactor: Update Rules.xlsx for FL Coral BCG Changes in version 2.0.0.9140 - feature: Add new template for new metrics, models, and rules - fix: Update package documenation per roxygen2 Changes in version 2.0.0.9139 - refactor: Shiny app file builder generate class parameters, Issue #89 - Add shinyalert for more than 500 records - nhdplustools and StreamCatTools timeout issues with too many records - fix: Shiny app calculation of BioMonTools::metric.scores, leppott/BioMonTools#103 - Affected BDI calculation, checked and no other instances - fix: Update package documenation per roxygen2 (since 7.0.0) Changes in version 2.0.0.9138 - fix: Shiny app fuzzy model not working, change community reference - Also fixed thermal metrics for status message Changes in version 2.0.0.9137 - fix: Update naming scheme for BCG calculation in Shiny app, Issue #87 - Add “_” prefix to Results. Changes in version 2.0.0.9136 - fix: Update naming scheme for BCG calculation in Shiny app, Issue #87 - refactor: Update text on BCG calculation pop up in Shiny app, Issue #88 Changes in version 2.0.0.9135 - refactor: Update NM BCG, drop percent max ffg from L2 and L4 per documentation Changes in version 2.0.0.9134 - refactor: Update NM BCG Index_Name and Index_Class in Rules.xlsx Changes in version 2.0.0.9133 - fix: Add shiny::validate(msg) back to shiny alert for when no file uploaded - Avoid the app crashing by preventing rest of code from running - refactor: update shiny alert message for upload to account for file upload not complete - fix: Update order of conditional formatting for nt_ti_stenocold Changes in version 2.0.0.9132 - fix: Remove testing line in Report server code - Caused ShinyApps.io to crash trying to open Excel Changes in version 2.0.0.9131 - refactor: Update Report - Add conditional formatting for summary worksheet for data columns - MTTI - Thermal Metrics - Add error checking if thermal metrics not present Changes in version 2.0.0.9130 - docs: Add tag to roxygen chunk to allow for table in BCG.Level.Membership - refactor: Update BCG.Level.Membership for new exception rules (NM bugs) - Added routines for Exception Rules Small2 and Small3 - refactor: Update Rules.xlsx (NM bugs) Changes in version 2.0.0.9129 - refactor: Modify Shiny single report - Properly filter for singe station for every worksheet - Modify freeze panes for summary wide - refactor: Calculation community buttons to default to NA - calc_BCG - calc_thermalfuzzy - calc_thermalmetrics Changes in version 2.0.0.9128 - refactor: Modify Shiny single report - Add taxatrans table - Verify sorting of tables by user selections - Add summary color thresholds - Color summary color thresholds - Set column widths - update formulas on NOTES Changes in version 2.0.0.9127 - refactor: Modify Shiny single report - Zip file download Changes in version 2.0.0.9126 - fix: Update app BCG calculation for cases where have no flags Changes in version 2.0.0.9125 - fix: Update MN fish metric names (trout) to be more specific Changes in version 2.0.0.9124 - tests: Update tests for name changes in 2.0.0.9004 - fix: Update metric name in Rules.xlsx to match BioMonTools - pi_Trout to pi_trout Changes in version 2.0.0.9123 - fix: Modify taxatrans hack for noteworthy to only trigger if present Changes in version 2.0.0.9122 - refactor: BCG calculation user column select to lower case - elev_m - pslope_nhd - refactor: Rename BCG calculation flag output (previously model experience) Changes in version 2.0.0.9121 - feature: Add ecoregion L3 to generate index class parameters Changes in version 2.0.0.9120 - refactor: Modify QC check on BCG model experience to BCG calculate - Change text on pop-up - Modify structure of output file - Add checks for slope and elevation - refactor: Result files remove leading “_” Changes in version 2.0.0.9119 - fix: Modify QC check on BCG model experience to BCG calculate - total flags Changes in version 2.0.0.9118 - refactor: Modify QC check on BCG model experience to BCG calculate Changes in version 2.0.0.9117 - feature: Add QC check on BCG model experience to BCG calculate - fix: Comment out all other instances of validate(msg) to avoid potential issues Changes in version 2.0.0.9116 - fix: File builder taxa translate remove validate statement from pop up - Was causing the server to pause and not continue Changes in version 2.0.0.9115 - feature: Add pop-up for taxa translate with mismatch taxa Changes in version 2.0.0.9114 - refactor: Modify output file names - Shorten names by dropping user input file name - style: Add package names to a functions, Global.R - write_disk was missing httr:: prefix Changes in version 2.0.0.9113 - refactor: Add MN BCG Fish rules, Rules.xlsx Changes in version 2.0.0.9112 - feature: Added single site report - Formatting incomplete but function working in Shiny Changes in version 2.0.0.9111 - fix: Change order of operations to allow multiple uses of single import - For example, taxa translate now generates only the current results - refactor: Create helper functions for re-used code - clean_results - copy_import_file Changes in version 2.0.0.9110 - fix: Create workaround for Generate Class Param - If reused an output as input duplicate fields are created - Then crashes when tries to join results - Rename existing fields as _OLD Changes in version 2.0.0.9109 - fix: Updates TaxaTranslate file output (names and folders) Changes in version 2.0.0.9108 - refactor: Updates to Shiny interface Changes in version 2.0.0.9107 - refactor: Implement result folder changes - refactor: Add subfolder for user import file - refactor: Implement changes for new source files in taxa translator - refactor: Implement file name changes Changes in version 2.0.0.9106 - refactor: Implement result file name changes using global abbreviations Changes in version 2.0.0.9105 - refactor: Remove toner lite base layer from Shiny maps - no longer supporter after 2023-10-31 - refactor: Sidebar menu updates - Label calculations as ‘Draft’ (non-BCG) - Tweak ‘Taxa Translate’ language - refactor: Update Shiny map clustering options - refactor: Reports to only multi and single - refactor: Add result file and folder abbreviations to global Changes in version 2.0.0.9104 - feature: Add report to Shiny - Still under construction - refactor: Update Shiny import to remove empty directories as well as files - Change from file.remove to unlink - docs: Add openxlsx to DESCRIPTION for report creation in Shiny Changes in version 2.0.0.9103 - fix: Shiny, taxatrans_late_0filesversion.csv, swap 2 columns Changes in version 2.0.0.9102 - refactor: Leaflet map Fuzzy Thermal changes - Create multiple TIEs for legend so don’t count as NA - TIE_A_B same as TIE_B_A - Remove Continuous_Thermal as a required field - Was used for size but size no longer being used Changes in version 2.0.0.9101 - refactor: For leaflet map change to addCircleMarkers - Replaced addCircles Changes in version 2.0.0.9100 - fix: Change leaflet map proxy to redraw legend - Prevents thermal metric legends from having multiple on screen - refactor: Add “DRAFT” to BDI Changes in version 2.0.0.9099 - refactor: Remove base layers too large to use - NorWeST - NHD+ catchment - NDD+ flowlines - fix: Change Fuzzy Thermal legend - Move first ties up 1 slot each - Change legend colors - refactor: Change jitter on map from jitter function to custom - jitter didn’t always work with large data sets Changes in version 2.0.0.9098 - feat: Update Shiny map - Add Imagery as baselayer to Shiny map - Add legend title variable to Shiny map legend - Add jitter to map plot to avoid overlap of multiple samples per location - Change legend and colors - BDI - BCG - MTTI - Thermal Metrics Changes in version 2.0.0.9097 - refactor: Add download links to KMZ files - refactor: Update map legends coding, Issue #67 Changes in version 2.0.0.9096 - feature: Add KMZ downloads to Shiny app - NorWeST_ORWA - PNMR_BCGclasses - feature: Updated maps in Shiny, Issue #67 Changes in version 2.0.0.9095 - feat: Add example script for MTTI Changes in version 2.0.0.9094 - feat: Add example data for MTTI to external folder Changes in version 2.0.0.9093 - feat: Add maps for each index, Issue #67 Changes in version 2.0.0.9092 - fix: BDI, if no Index_Class was not adding proper variable name, Issue #66 - Caused samples to not be scored Changes in version 2.0.0.9091 - fix: Typo on “Covert OTU” on MTTI and BDI shiny tabs - refactor: Adjust Excl taxa triggers and QC in code, Issue #66 Changes in version 2.0.0.9090 - fix: Removed browser() statement from QC of last update, Issue #84 Changes in version 2.0.0.9089 - feature: Automate Index Name and Class for fuzzy set calculation, Issue #84 - Shiny Changes in version 2.0.0.9088 - feature: Add BDI calculation to Shiny, Issue #66 - COMPLETE - refactor: Shiny required fields type for TRUE/FALSE changed text to logical Changes in version 2.0.0.9087 - refactor: Update MN BCG (bugs) in Rules.xlsx, Issue #82 Changes in version 2.0.0.9086 - refactor: Add MN BCG (bugs) to Rules.xlsx, Issue #82 Changes in version 2.0.0.9085 - refactor: Updates to BDI calculation, Issue #66 - INCOMPLETE, completed in 2.0.0.988 Changes in version 2.0.0.9084 - fix: Update complex number import code (BCG_ATTR), Issue #77 - Should work in all cases and not cause issues with other fields - feature: Enable BDI calculation in Shiny app, Issue #66 - PARTIAL Changes in version 2.0.0.9083 - refactor: Modify code for import and merge files, Issue #77 - Only specify BCG_ATTR column - Undoes some edits in v2.0.0.9081 - fix: Adjust import function to allow for user selection of tab or comma - Comma was hard coded even though gave user the choice of separators Changes in version 2.0.0.9082 - refactor: Updates to Shiny map, Issue #67 - INCOMPLETE - refactor: Change taxa translator to no default Changes in version 2.0.0.9081 - fix: Modify code for complex number (BCG_ATTR), Issue #77 - Other logical fields could cause issues with older import method Changes in version 2.0.0.9080 - fix: Change links to files in Shiny from “" to”/” - refactor: Update Index Class Parameter, Issue #73 - refactor: Update to text for Fuzzy Set Input File, Issue #70 Changes in version 2.0.0.9079 - refactor: Update Index Class Parameter, Issue #73 - refactor: Update Shiny Fuzzy Set Changes in version 2.0.0.9078 - feature: Add upset plot to MTTI results report - docs: Add ComplexUpset to DESCRIPTION Suggests and Shiny global Changes in version 2.0.0.9077 - refactor: Update Shiny MTTI, Issue #74 - Onscreen text - Example files - style: Move MTTI model file location Changes in version 2.0.0.9076 - fix: MetricFlags.xlsx ‘pctSLOPE’ to ‘pslope_nhd’ - Align with index class assignment - Add PRECIP8110CAT for BCG_MariNW_Bugs500ct (all classes) - refactor: Add more StreamCat variables to get index parameters, Issue #75 - PRECIP8110CAT - ICI - IWI Changes in version 2.0.0.9075 fix: Update MTTI routine for user SampleID, Issue #74 + One instance was hard-coded Changes in version 2.0.0.9074 refactor: Update MTTI output, Issue #74 Changes in version 2.0.0.9073 style: Code coverage updates Changes in version 2.0.0.9072 - refactor: Change order of columns for Fuzzy Thermal, Issue #70 - modtherm_5levassign.csv Changes in version 2.0.0.9071 - fix: Update overlapping Fuzzy Thermal CheckNames in MetricFlags.xlsx, Issue #72 Changes in version 2.0.0.9070 - refactor: Add columns and classifications to Fuzzy Thermal model, Issue #70 Changes in version 2.0.0.9069 - fix: MetricFlags.xlsx ‘pcSLOPE’ to ‘pctSLOPE’ (typo) - fix: MetricFlags.xlsx ‘DrArea_mi2’ to ‘WSAREASQKM’ (and values) Changes in version 2.0.0.9068 - fix: Remove browser call in fuzzy thermal model Changes in version 2.0.0.9067 - refactor: Additional flags for fuzzy thermal model Changes in version 2.0.0.9066 - refactor: Updates to fuzzy thermal model output Changes in version 2.0.0.9065 - fix: BCG.Level.Membership account for less than 5 rules, Issue #68 - fix: Update examples so don’t get duplicate columns kept in output - Can cause successive examples to fail - BCG.Metric.Membership - BCG.Level.Membership Changes in version 2.0.0.9064 - refactor: Error checking for missing variables, Shiny - Fuzzy Thermal Model - Index Class Param, Issue #42 Changes in version 2.0.0.9063 - refactor: Update Index Class Param onscreen help in Shiny, Issue #42 Changes in version 2.0.0.9062 - refactor: Shiny get Index Class Params, Issue #42 - Allow for user defined column - Default is NAD83 North America, EPSG = 4269 - Trim output Changes in version 2.0.0.9061 - refactor: Update Shiny MTTI calculation and flags calculation and output Changes in version 2.0.0.9060 - refactor: Update Shiny MTTI calculation to include flags - style: Modify some lines based on lintr suggestions - Add nolint to Shiny library calls Changes in version 2.0.0.9059 - fix: Update Shiny app import to better handle BCG_ATTR (complex) - Added exception for only integer values Changes in version 2.0.0.9058 - fix: Ensure all Shiny buttons use same terminology - b_calc_x - b_download_x Changes in version 2.0.0.9057 - fix: Update names of assign indec class buttons - calc and download - style: Modify outlining in server.R - refactor: Modify Shiny Generate Index Class Param - Add column names to match Shiny Assign Index Class - Allows user to upload file with no modifications Changes in version 2.0.0.9056 - docs: Update DESCRIPTION R >= 2.1 to >= 3.5.0 due to code dependency - Loading of MTTI model file in Shiny app - refactor: Add data-raw Process Data script for nhdplusTools vaa file - Only VPUID 16, 17, and 18 for use with OR and WA. - Add fst package to Suggests in DESCRIPTION - Unable to upload full file to GitHub Changes in version 2.0.0.9055 - refactor: Shiny index class parameter generation, Issue #42 - docs: Add packages used in Shiny app to DESCRTION Suggests - StreamCatTools - nhdplusTools Changes in version 2.0.0.9054 - fix: Shiny index class parameter generation, Issue #42 - refactor: Shiny MTTI change language - ‘Pacific Northwest’ to ‘Oregon/Washington’ - fix: Change utils::zip to zip::zip in Shiny - Not working locally or on ShinyApps.io - docs: Add zips to DESCRIPTION Suggests Changes in version 2.0.0.9053 - refactor: Update Shiny MTTI calculation (was placeholder) Changes in version 2.0.0.9052 - feat: Add Shiny tab for generating index class parameters, Issue #42 - Placeholder only Changes in version 2.0.0.9051 - refactor: Add map column select and base map, Issue #67 - Not complete Changes in version 2.0.0.9050 - feat: Add placeholder for map, Issue #67 Changes in version 2.0.0.9049 - fix: Remove example file link in fuzzy thermal about page - No fuzzy thermal examples - feat: Add fuzzy thermal calculation and associated pages to Shiny, Issue #65 Changes in version 2.0.0.9048 - refactor: Add link for example scripts to fuzzy thermal about page Changes in version 2.0.0.9047 - docs: Update BCG.Level.Assignment example code - refactor: Update example script (BCG calc) Changes in version 2.0.0.9046 - refactor: Create ‘process’ file in data-raw for creating zip file of examples for Shiny app (‘www’) - refactor: Update example scripts - refactor: Add link to download example zip file in Shiny app Changes in version 2.0.0.9045 - refactor: Create Shiny Merge Files Output tab Changes in version 2.0.0.9044 - refactor: Update Shiny output tabs Changes in version 2.0.0.9043 - refactor: Update taxa translate 0fileversion output - Shiny, server.R - example code, taxa translate Changes in version 2.0.0.9042 - feature: Add example scripts and data for Shiny File Builder functions - Taxa Translate - Assign Index_Class - Merge Files - feature: Add Fuzzy Thermal narrative to Shiny operation Changes in version 2.0.0.9041 - refactor: Update Shiny onscreen text, inputs BCG calc - refactor: Update Shiny onscreen text, inputs thermal metrics Changes in version 2.0.0.9040 - refactor: Update Shiny onscreen text, thermal preference metrics - Add metadata file to calculation thermal metrics results Changes in version 2.0.0.9039 - refactor: Update Shiny onscreen text, BCG calc Changes in version 2.0.0.9038 - docs: Update readme install section with quick code - refactor: Update Shiny onscreen text, Assign Index_Class Changes in version 2.0.0.9037 - refactor: Update Shiny onscreen text, Merge Files Changes in version 2.0.0.9036 - refactor: Change Shiny merge files order (x and y) - Samples should be the main file (x) and keep all records and info Changes in version 2.0.0.9035 - refactor: Update Shiny app text Changes in version 2.0.0.9034 - refactor: Update Shiny to include change in BioMonTools package Changes in version 2.0.0.9033 - fix: Update file import routine - Account for multiple permutations of BCG_Attr - Add “” to na.strings Changes in version 2.0.0.9032 - fix: Adjust QC routine in Shiny app assign index class Changes in version 2.0.0.9031 - refactor: Finish updates to Shiny app merge files tab Changes in version 2.0.0.9030 - refactor: Add error checking for Index_Class in Shiny Changes in version 2.0.0.9029 - docs: Add Shiny link to README - refactor: Layout changes to taxa translate section of Shiny app Changes in version 2.0.0.9028 - refactor: Add Shiny merge files tab placeholder - proof of concept, not complete Changes in version 2.0.0.9027 - refactor: Update onscreen text for Shiny assign index class Changes in version 2.0.0.9026 - refactor: Remove uneeded QC steps in Shiny assign_indexclass routine Changes in version 2.0.0.9025 - refactor: Add excluded taxa subroutine to thermal metrics in Shiny Changes in version 2.0.0.9024 - refactor: BioMonTools MetricNames.xlsx from GitHub instead of package in Shiny Changes in version 2.0.0.9023 - refactor: Add taxa translate unique crosswalk to output of taxatranslate in Shiny Changes in version 2.0.0.9022 - fix: Modify code in Shiny for assign_indexclass so won’t fail if field not provided. Changes in version 2.0.0.9021 - feature: Add thermal metric calculation to Shiny app Changes in version 2.0.0.9020 - feature: Add assign index class to Shiny - refactor: Update Shiny tabs to not include numbered steps (all were step 2) - fix: Update shiny taxa translate to combine duplicate taxa by default Changes in version 2.0.0.9019 - refactor: Update Shiny taxa trans to drop translator columns if have an attributes table Changes in version 2.0.0.9018 - refactor: Update Shiny taxa trans to use default names - SampleID, TaxaID, and N_Taxa Changes in version 2.0.0.9017 - refactor: Update Shiny taxa trans to include filenames in MERGED output Changes in version 2.0.0.9016 - refactor: Update Shiny, split file builder in to taxa trans and assign index class Changes in version 2.0.0.9015 - refactor: Update Shiny app MTTI tab Changes in version 2.0.0.9014 - refactor: Update Shiny app for taxaid_drop parameter in BioMonTools::taxa_translate Changes in version 2.0.0.9013 - refactor: Sort columns and order output of taxa translator Changes in version 2.0.0.9012 - feature: Add INDEX_NAME and INDEX_CLASS as input parameters to BCG.Level.Assignment Changes in version 2.0.0.9011 - refactor: Shiny app, filebuilder - save version of files in download - reorganize the required fields requested of user - change some text on screen Changes in version 2.0.0.9010 - refactor: Shiny app, filebuilder - Ensure consistency of BCGcalc and BioMonTools columns names (all caps) - Add about and output tabs to taxa translator - Update for consistency pick list file names in file and in code - Update routine for translating then adding attributes - Leave some projects with one file but add ability for two files (PacNW) Changes in version 2.0.0.9009 - refactor: Update filebuilder tab in Shiny app - Use “user file” less often - Change summary default to TRUE - Modified output files to include “taxatrans” - Renamed RESULTS to MERGED in output file - Add link to Taxa Translate Official files on GitHub - Fix non-match output Changes in version 2.0.0.9008 - refactor: Change BCG.ContLevelText status from x/y tie to x.5, Issue #64 Changes in version 2.0.0.9007 - feature: Add taxa translator tab and functionality to Shiny Changes in version 2.0.0.9006 - feature: Add new function to calculate BCG Status - Uses continuous value to get Integer or PlusMinus text Changes in version 2.0.0.9005 - refactor: Additional Shiny outputs - 6metflags; flag metrics, values, thresholds - 3metrules; rules table - refactor: Update Shiny text for additional outputs Changes in version 2.0.0.9004 - refactor: Update Shiny app text for slim to BCG file name for BCG output - refactor: Change order and names of columns in BCG.Level.Assignment output - Memb.Total to Membership_Total - Memb.QC to Membership_Total_QC - Lev.1.Memb to Primary_Membership - Lev.1.Name to Primary_BCG_Level - Lev.2.Memb to Secondary_Membership - Lev.2.Name to Secondary_BCG_Level - Lev.Memb.Diff to Membership_Diff - Lev.Memb.close to Membership_Close - Lev.Prop.Num to Continuous_BCG_Level - Lev.Prop.Nar to BCG_Status Changes in version 2.0.0.9003 - refactor: Change Shiny output 2metval_slim.csv to 2metval_BCG.csv Changes in version 2.0.0.9002 - fix: Update Rules.xlsx for non-ASCII characters Changes in version 2.0.0.9001 - breaking change: Site_Type and Index_Region to INDEX_CLASS, Issue #63 - Deprecate in functions (allow for ‘…’) and shiny - BCG.Level.Membership - BCG.Metric.Membership - Include warning for old code - refactor: Update reference Excel files for updated field, Issue #63 - Rules.xlsx - MetricFlags.xlsx Changes in version 1.3.5.9018 - refactor: Shiny, change menu item name Changes in version 1.3.5.9017 - fix: Shiny app ‘slim’ output, Issue #62 Changes in version 1.3.5.9016 - fix: Shiny app, markExcl, EXCLUDED to EXCLUDE Changes in version 1.3.5.9015 - update: Change name of PacNW model, Issue #61 - Rules.xlsx - MetricFlags.xlsx - Example files (file name, data, sheet names) - Update examples in functions - Vignettes Changes in version 1.3.5.9014 - update: Update BCG style temperature model thresholds - Rules.xlsx Changes in version 1.3.5.9013 - refactor: Upgrades to Shiny app Changes in version 1.3.5.9012 - refactor: Upgrades to Shiny app Changes in version 1.3.5.9011 - refactor: Upgrades to Shiny app - Rework tab order and names - Update About - Other Changes in version 1.3.5.9010 - refactor: Upgrades to Shiny app - Added summary report - Added packages needed for report - Minor edits to main menu - Minor edits to About - update: Add ‘Therm_ORWA_Bugs500ct’ model to Excel files Changes in version 1.3.5.9009 - refactor: Upgrades to Shiny app - Mark Excluded taxa - Minor updates - Added footer to app with shinydashboardPlus - Added package to DESCRIPTION - Update About - Add placeholder tabs for future updates Changes in version 1.3.5.9008 - refactor: Upgrades to Shiny app - Second version of results/metval with only those for the model - Ensure result files removed from previous imports Changes in version 1.3.5.9007 - refactor: Upgrades to Shiny app Changes in version 1.3.5.9006 - docs: Update examples for missing columns in sample data for all functions - fix: Update MetricFlags.xlsx for one flag Changes in version 1.3.5.9005 - docs: Update packages in DESCRIPTION and global.R in Shiny app Changes in version 1.3.5.9004 - feat: Redesign shiny app - docs: Add packages needed by Shiny app to DESCRIPTION Changes in version 1.3.5.9003 - style: Perform updates from lintr and goodpractice - fix: Update Font Awesome icons, some were deprecated - fix: Shiny About links update so open in new tab Changes in version 1.3.5.9002 - docs: Update format of NEWS Changes in version 1.3.5.9001 - feature: Add Shiny app skeleton and function to run it, Issue #58 Changes in version 1.3.5 - refactor: Bump version number. Changes in version 1.3.4.9047 - fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9046 - fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9045 - fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9044 - fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9043 - fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9042 - refactor: Update metric.values() - Failed when rules table included more than 1 region and metrics uneven Changes in version 1.3.4.9041 - refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9040 - refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models Changes in version 1.3.4.9039 - refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models - tests: Add tests for flags and metric names Changes in version 1.3.4.9038 - refactor: Update BCG.Level.Membership() for new median rule type, Issue #55 - refactor: Update Rules.xlsx to handle new median rule type, Issue #55 Changes in version 1.3.4.9037 - refactor: Update MetricFlags.xlsx - Match metric names to BioMonTools::metric.values() - Add BioMonTools_MetNam column for future test (some not metrics) - Change symbols from = to == - Write test to check for Flag symbols - fix: One entry in Rules.xlsx was “[” instead of “>=”. Changes in version 1.3.4.9036 - fix: BCG.Level.Membership fails test - Missing EXC_RULE in merge statement - refactor: Update “Notes” to “Note_Rules” in Rules.xlsx - tests: Update test for revised sheet name in Rules.xlsx Changes in version 1.3.4.9035 - fix: Renamed master branch to main - docs: Move wishlist from NEWS to GitHub Issue #56 - refactor: Updated Rules.xlsx for PacNW BCG, Issue #55 - refactor: Updated Flags.xlsx for PacNW BCG, Issue #55 - tests: Add test for floating point error - Rules.xlsx - Flags.xlsx - docs: Update example for additional required columns in BioMonTools::metric.values() - BCG.Metric.Membership() - BCG.Level.Membership() Changes in version 1.3.4.9034 - feat: Update BCG.Level.Membership() to account for special conditions - Use Index_Name and Site_Type to allow for individual model exceptions to the typical rules for level membership - feat: Update Rules.xlsx for exceptions in level membership in BCG.Level.Membership() Changes in version 1.3.4.9033 - fix: Update BCG.Metric.Membership() to use <= and >= when checking for values below and above limits rather than < and > due to rules in CT BCG using 0 as a lower AND upper limit Changes in version 1.3.4.9032 - fix: Update Rules.xlsx for CT BCG model, Issue #48 - Removed double entries for fish01, fish02, and fish03 SiteType Changes in version 1.3.4.9031 - fix: Update Rules.xlsx for CT BCG model, Issue #48 - Removed double entries for bug01 SiteType Changes in version 1.3.4.9030 - refactor: Update BCG.Metric.Membership() for lower and upper bounds - Per CT Access db (2013-08-09) use <= and >= instead of < and > - style: Wrap some lines more than 80 characters, BCG.Level.Assignment() Changes in version 1.3.4.9029 - fix: Update BCG.Metric.Membership() for calculating membership for more than one Site_Type at a time, Issue #53 - Allows for NA for metrics not common to all included Site Types Changes in version 1.3.4.9028 - refactor: Update Rules.xlsx for CT BCG benthos - pi_BCG_att5 to pi_BCG_att5extra Changes in version 1.3.4.9027 - refactor: Update BCG.Level.Membership with stop message if unable to merge data frames Changes in version 1.3.4.9026 - refactor: Update Rules.xlsx to match BioMonTools::metric.values() - rename brook trout wild Changes in version 1.3.4.9025 - refactor: Update Rules.xlsx to match BioMonTools::metric.values() - Add “BCG” to BCG attribute metric names Changes in version 1.3.4.9024 - refactor: Update BCG.Level.Assignment() - Add column name inputs and defaults - Update code to use inputs - Add tempdir() to save example - Update example to not have warning for BioMonTools::metric.values() - Apply fixes for changes in dplyr - refactor: Update BCG.Level.Membership() - Add column name inputs and defaults - Update code to use inputs - Add tempdir() to save example - Add QC in function to retain only the input columns - Update example to not have warning for BioMonTools::metric.values() - Apply fixes for changes in dplyr - refactor: Update BCG.Metric.Membership() - Add column name inputs and defaults - Update code to use inputs - Add tempdir() to save example - Update example to not have warning for BioMonTools::metric.values() - Apply fixes for changes in dplyr - style: Trim lines to 80 characters (partial) - BCG.Level.Assignment() - BCG.Level.Membership() - BCG.Metric.Membership() - style: Update function examples to use “_” instead of “.” in object names - BCG.Level.Assignment() - BCG.Level.Membership() - BCG.Metric.Membership() - style: Update function examples to use foo::fun() instead of library(foo) - BCG.Level.Assignment() - BCG.Level.Membership() - BCG.Metric.Membership() Changes in version 1.3.4.9023 - refactor: Update Rules.xlsx, Issue #48 - Change Index_Name, Site_Type, and Index_Region Changes in version 1.3.4.9022 - docs: Update DESCRIPTION remotes to proper url - refactor: Update metric.membership() example to use updated Rules.xlsx, Issue #48 - refactor: Update Rules.xlsx file, Issue #48 - refactor: Update level.membership() example to use updated Rules.xlsx, Issue #48 - refactor: Update level.assignment() example to use updated Rules.xlsx, Issue #48 Changes in version 1.3.4.9021 - refactor: Merge pull request with updated rules, Issue #52 Changes in version 1.3.4.9020 - refactor: Update model rules, Rules.xlsx, Issue #48 Changes in version 1.3.4.9019 - docs: Add sticker to README Changes in version 1.3.4.9018 - feature: Add sticker - Create with hexSticker Changes in version 1.3.4.9017 - style: Fix devtools::spell_check() issues - NEWS - README - vignette_BCGcalc.Rmd - refactor: README - Update example, change devtools::install_github to remotes::install_github - Rebuild README Changes in version 1.3.4.9016 - docs: Remove date from DESCRIPTION - tests: Add tests - metric_membership - level_membership - level_assignment - feature: Create metrics_values dataset to use in tests - docs: Document metrics_values dataset - refactor: Replace undesirable function, library - ProcessData_TaxaMaster_Ben_BCG_PacNW Changes in version 1.3.4.9015 - test: set up test folder Changes in version 1.3.4.9014 - ci: Add GitHub Action test coverage - ci: Add GitHub Action pkgdown - docs: ReadMe, add codecov badge - docs: ReadMe, add lifecycle badge - docs: ReadMe, add codefactor badge - docs: Remove docs folder from main branch for pkgdown - docs: Redirect GitHub repo for pkgdown to gh-pages branch Changes in version 1.3.4.9013 - ci: Add GitHub Actions, continuous integration - ci: Remove TravisCI - docs: ReadMe, remove TravisCI badge - docs: ReadMe, Add GitHub Actions CMD check badge Changes in version 1.3.4.9012 - Add pkgdown website. - Need to fix vignettes/BCGcalc_Map.Rmd. - INFRAORDER missing. Changes in version 1.3.4.9011 - Build Check fixes. - Move “View” in example to “do not run”. - BCG.Level.Assignment - BCG.Level.Membership - BCG.Metric.Membership - Column names of TaxaMaster_Ben_BCG_PacNW - Data.R - Depends on R >= 2.10 - DESCRIPTION - Add .github to .Rbuildignore - Remove unused data (data folder and data.R) - taxa_fish - taxa_bugs_family - taxa_bugs_genus Changes in version 1.3.4.9010 - Update for R v3.6.0, Issue #46 - README - Add extra line for devtools::install_github to work properly - Added badges to README - Map Vignette - Update title. Changes in version 1.3.4.9009 - BCG.Level.Assignment - Proportional BCG final scores, Issue #43. - Add “tie” to narrative. Changes in version 1.3.4.9008 - BCG.Level.Assignment - Proportional BCG final scores, Issue #43 - Turn on features from v1.3.4.9004. - Add proportional narrative (+/-). Changes in version 1.3.4.9007 - extdata.xlsx - ni_total, Hi, to 450 from 400. - Matches file in BioMonTools package. Changes in version 1.3.4.9006 - Remove format Hoboware file from extdata folder. - From another package under development. Changes in version 1.3.4.9005 - MetricFlags.xlsx - Percent metrics to 0-100. Issues #45. - Add field Index_Region - Data_BCG_PacNW.xlsx - Add fields: Issue #33. - Index_Region - LongLived - NoteWorthy - FFG2 - TolVal2 - Rules.xlsx - Add field Index_Region Issue #33. - Update percent metrics to 0-100. Issue #45. - Vignette, modify for Site_Type to Index_Region - BCGcalc_Map.RMD - vignette_BCGcalc.RMD - Add “Site_Type”” to columns to keep - Modify example for Site_Type to Index_Region Issue #33. - BCG.Level.Assignment.R - BCG.Level.Membership.R - BCG.Metric.Membership.R Changes in version 1.3.4.9004 - Proportional Level Assignment. Issue #43. - Needs more polish for different conditions. - Assign all to NA. Changes in version 1.3.4.9003 - Last update not complete before uploaded. Changes in version 1.3.4.9002 - Move qc.checks to BioMonTools package. Issue #44 - Remove qc.checks.R - Update Vignette. - Update read_excel with guess_max=10^6 for bio data file. Changes in version 1.3.4.9001 - Add proportional Level Assignment. Issue #43. - BCG.Level.Assignment Changes in version 1.3.4 - Update release version with Remote”s”” fix. Changes in version 1.3.3.9005 - BioMonTools dependency not installing. - Move Remote up in listing in DESCRIPTION. - Renamed Remote to Remotes. Changes in version 1.3.3.9004 - Add BioMonTools to Imports so will auto install. - Had removed at some point since don’t use the functions in any BCGcalc functions. Changes in version 1.3.3.9003 - Update SuperFamily Tipuloidea - /extdata/Data_BCG_PacNW.xlsx - /extdata/TaxaMaster_Bug_BCG_PacNW_v1.xlsx Changes in version 1.3.3.9002 - /extdata/Data_BCG_PacNW.xlsx - Update Exclude column after QC with BioMonTools::markExcluded - Change 6 FALSE to TRUE - Change 1 TRUE to FALSE Changes in version 1.3.3.9001 - Update ReadMe for BioMonTools::metric.values. Issue #41. Changes in version 1.3.3 - Update version have changes related to moving functions to the BioMonTools package. Changes in version 1.3.2.9012 - metric.values, move to another package, Issue #40 - Moved to separate package. _ https://github.com/leppott/BioMonTools - BioMonTools is for bioassessment and biomonitoring. - ContDataQC should stay focused on continuous data. - Vignette - Updated each section with metric.values - BCGcalc_Map.rmd - vignette_BCGcalc.rmd - R/data.R - Keep example data since specific to BCG project - Remove - R/metric.values.R - Update function examples. - Add library(BioMonTools) - qc.checks.R - BCG.Metric.Membership.R - BCG.Level.Membership.R - BCG.Level.Assignment.R - Update map colors, Issue #35. - BCG.Metric.Membership.R - Update details. - BCG.Level.Assignment.R - Add don’t run to simple example for write.csv. Changes in version 1.3.2.9011 - rarify, move to another package, Issue #40 - Moved to separate package. _ https://github.com/leppott/BioMonTools - BioMonTools is for bioassessment and biomonitoring. - BCGcalc should stay focused on BCG models. - DESCRIPTION - Add Remote: leppott/BioMonTools - Remove Jon van Sickles as contributor since removed rarify function. - Vignette - rarify section updated. - R/data.R - Remove reference to data_bio2rarify - Remove - R/rarify.R - data-raw/ProcessData_rarify.R - data-raw/ 3 data files - data/data_bio2rarify.rda Changes in version 1.3.2.9010 - Metric calculations, additional metrics. - metric.values.R - nt_Ephemerellidae - nt_Heptageniidae - nt_Nemouridae - nt_Perlidae - nt_Rhyacophila - nt_Tipulidae - MetricNames.xlsx - Fix error with habit metric names. - metric.values.R - MetricNames.xlsx Changes in version 1.3.2.9009 - Metric calculation; - x_HBI. Issue #37 - calculation use TOLVAL>=0 rather than TOLVAL>0 in denominator. - Consistent naming. Issue #38 - habit_clmbrs to habit_climb - habit_clngrs to habit_cling - habit_swmmrs to habit_swim Changes in version 1.3.2.9008 - Metric calculation; - Tolerance metrics - nt_tv_intol - nt_tv_toler - pt_tv_intol - pt_tv_toler - Added lower and upper limits for intol and toler Changes in version 1.3.2.9007 - Metric calculation; - pi_Colesen - Change is.na(FAMILY) from FALSE to TRUE. Changes in version 1.3.2.9006 - Metric calculation; - pi_Hydro - Equal sign missing in equation (“=” instead of “==”). Changes in version 1.3.2.9005 - Metric calculation; - pi_Tanyp - Misspelled Tanypodinae Changes in version 1.3.2.9004 - Metric calculations; - x_HBI - Remove negative sign. Issue #37 - x_Shan_e, x_Shan_2, x_Shan_10 - Fix equation. Not properly calculating proportions. - Drop use of x_Shan_Num. Use x_Shan_e then convert for other log bases. - x_D - Fix equation. Changes in version 1.3.2.9003 - Fix metric calculation; na.rm=TRUE for sum. Issue #37 - x_HBI _ If had any NA values for TolVal the final value was NA. - Added na.rm=TRUE to sum function for numerator. - Denominator already included na.rm=TRUE. - x_D - No effect as no records should be NA for count - dominant calculation intermediate columns - No effect as no records should be NA for count - ni_total - No effect as no records should be NA for count - All fish metrics (with “sum”) Changes in version 1.3.2.9002 - Add 8 additional metrics to metric.values - MS DEQ, MBISQ 2015 _ pi_Hydro - nt_NonIns - pt_NonIns - pi_Tanyp - pt_tv_intol - pt_tv_toler - pi_Colesens - pi_COC2Chi Changes in version 1.3.2.9001 - Mapping Vignette. Issue #34. - DESCRIPTION - Add ggplot2 to Suggests - extdata_BCG_PacNW.xlsx - Add Latitude, Longitude, and COMID - Create Vignette for mapping Changes in version 1.3.2 - Release version. Changes in version 1.3.1.9001 - Master Taxa List - Turbellaria BCG Attribute. - Change from “x” to “4” to match its synonym Trepaxonemata. Changes in version 1.3.1 - Release version. Changes in version 1.3.0.9001 - Rules.xlsx - Fix typos in “Numeric_Rules” field. - No impact on calculations. Changes in version 1.3.0 - Release version. Changes in version 1.2.2.9033 - Update Vignette. - Rarify section to 600. Changes in version 1.2.2.9032 - Update Vignette. - Fix a few typos. Changes in version 1.2.2.9031 - Update Rules.xlsx. - 300 count model edits. Changes in version 1.2.2.9030 - Vignette updates. Changes in version 1.2.2.9029 - Updated rarify data; data_bio2rarify - Replace fully qualified 500 count data with 3 column 600 count. - Update data.R entry. - Update rarify function example. - Update vignette example. Changes in version 1.2.2.9028 - Updated docs. - extdata/ExampleDataFile.xlsx - docs/BCGcalc_README_20180919.pdf Changes in version 1.2.2.9027 - Updated Rules.xlsx file in extdata. Changes in version 1.2.2.9026 - Finish updates to Vignette. Changes in version 1.2.2.9025 - Level.Assignment. Issue #11 - Update example so don’t calculate metrics twice. Changes in version 1.2.2.9024 - Vignette updates (incomplete). - Metric.Membership. Issue #11 - Non numeric extra columns caused errors. Fixed. Changes in version 1.2.2.9023 - extdata - TaxaMaster_Bug_BCG_PacNW_v1.xlsx; rename worksheet to match previous version. - data-raw - Remove data_bio2rarify.txt - Recreate TaxaMaster_Ben_BCG_PacNW using revised XLSX file. - Update 500count.tsv thermal column name. - data.R - Update entries for TaxaMaster_Ben_BCG_PacNW and data_bio2rarify - Vignette - Start on updates. Changes in version 1.2.2.9022 - Update Data_BCG_PacNW.xlsx. Issue #32 - Remove unnecessary worksheets. - Rename single remaining worksheet. - Update phylogenetic columns. - Rearrange columns into required and optional. - Add master taxa list file to external docs. - Add thermal indicators file to external docs. Changes in version 1.2.2.9021 - update ReadMe. Issue #31 Changes in version 1.2.2.9020 - Ensure reshape2 package references are consistent. Issue #30 - Ensure functions use reshape2::melt (or dcast) - Ensure examples (and vignette) use library(reshape) and melt or dcast. Changes in version 1.2.2.9019 - File formats. Issue #28 - Add statement about file formats to Vignette. Changes in version 1.2.2.9018 - rarify data. Issue #19 - Use USGS 500 to 300 count data instead of MS 200 count. - Change raw data process script. - Replace data_bio2rarify. - Modify rarify example. - Modified rarify example in Vignette. Changes in version 1.2.2.9017 - BCG PacNW primer. Issue #29 - BCGcalc_README_20180918.pdf to so shows up in package help. - MetricFlags.xlsx - Last line, Index_Name updated for 300 count model. Changes in version 1.2.2.9016 - Example “write” statements as “dontrun”. Issue #27 - BCG.Level.Assignment; also moved write statement to end - BCG.Level.Membership - BCG.Metric.Membership - metric.values; included write and DataExplorer - qc.checks; no write statement. - rarify; Changed from commented out to donotrun - Vignette; leave “as is”. Write statements all commented out. - BCG.Level.Assignment - Change write.table(tsv) to write.csv. Issue #28 Changes in version 1.2.2.9015 - extdata.xlsx. Issue #26 - Added NOTES worksheet. - Added MetricMetadata from MetricNames.xlsx. - Added NOTES worksheet to MetricNames.xlsx. - Renamed worksheet “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”. - Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”. - Added worksheet “BCG_PacNW_v1_300ct”. - Revised code references to Rules.xlsx (worksheet and Index_Name). Mostly examples. - extdata_BCG_PacNW.xlsx - Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”. - extdata.xlsx - Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”. - Added Index_Name “BCG_PacNW_v1_300ct”. Adjust some flags based on 500 vs. 300 count. Changes in version 1.2.2.9014 - qc.checks. Issue #25. - Update Description. - Add View for imported checks file. - Vignette. Change section title from QC Checks to Flags. - Update Level Assignment example in Vignette with real data and append flags. Changes in version 1.2.2.9013 - Function rarify. Issue #19 - Remove keywords. Changes in version 1.2.2.9012 - Function rafify. Issue #19 - Fix typo in @param mySeed. Remove extra period. Changes in version 1.2.2.9011 - Metric Names metadata Issue #18 - Update extdata.xlsx - Add PDF version to docs. Changes in version 1.2.2.9010 - More Indiana files. Issue #24 - extdata_IN_BCG_Bugs_20170203.xlsm - extdata_Metrics_Bugs_IN.xlsx Changes in version 1.2.2.9009 - Remove Indiana references. Issue #24. - Delete extdata Indiana file (Data_BCG_Indiana.xlsx). - Delete data-raw Indiana database (BCG_Model_Calc (IN 20170301).mdb. Already excluded from package build. - Delete example in metric.values function. Changes in version 1.2.2.9008 - DESCRIPTION - Add date. - Add Jen Stamp as contributor - Citation still gives error but is more complete now. Issue #23 Changes in version 1.2.2.9007 - metric.values - Fixed included metrics (fun.MetricNames) Changes in version 1.2.2.9006 - metric.values - Added QC check for NonTarget==FALSE. - Give a warning if have zero FALSE values. Changes in version 1.2.2.9005 - metric.values - Added QC check for Exclude==TRUE. - Give a warning if have zero TRUE values. Changes in version 1.2.2.9004 - Update Vignette. - Add data munging example. Issue #14 - Update metric.values section for required fields. Issue #13. - Added section demonstrating saving only select metrics. Issue #15 - Update text in metric.values. Changes in version 1.2.2.9003 - metric.values. Issue #16 - Added QC worksheet to extdata_BCG_PacNW.xlsx Changes in version 1.2.2.9002 - metric.values. Issue #13 - Add required fields (columns) to help file. - Add QC check in function. Prompt user to continue or stop. Changes in version 1.2.2.9001 - metric.values - Added metric Percent Baetis tricaudatus complex + Simuliidae individuals (pi_SimBtri). Issue #16. Changes in version 1.2.2 - New release version. Changes in version 1.2.1.9001 - qc.checks.R - Modification to use metric names as lower case. Issue #12. - Example table; useNA=“ifany”. Changes in version 1.2.1 - New release version. Changes in version 1.2.0.9001 - BCG.Level.Assignment.R - Membership QC (sum===1) add “round” 8 to avoid too many samples being flagged as “FAIL”. - Example changes: - Changed terminology from PASS/FAIL to NA/flag in flag fields. - Changed “NumFlagFAIL” to “NumFlags”. - Reordered columns so “NumFlags” is before the flag fields. Changes in version 1.2.0 - Release version for Pacific Northwest BCG workgroup with updated model. Changes in version 1.1.0.9010 - BCG.Level.Assignment.R - Example code to match up with qc.checks output. - Includes export to file. - qc.checks.R - Remove example modifying column names. Changes in version 1.1.0.9009 - BCG.Level.Membership.R - Added “round” to 8 places when determining level membership. - Floating point error resulted in the occassional value of 1.1E-16 when the previous level was “1”. - This resulted in the sample getting a split level assignment, e.g., 3:4 when it was 100% 3. Changes in version 1.1.0.9008 - metric.values.R - Add additional metrics - nt; BCG_att; 1i, 1m, 3 - pt; BCG_att; 1i, 1m, 3 - pi; BCG_att; 1i, 1m, 2, 3 - thermal indicator metrics - modify grepl to == because COLD was matching COLD and COLD_COOL. Only want exact match. Changes in version 1.1.0.9007 - Update Rules.xlsx. - Level 3 (Hi and Lo), pi_BCG_att56 changed to pt_BCG_att1i23. - Change involved both direction and thresholds. Changes in version 1.1.0.9006 - Update metric.values. - Add “cols2keep” to allow for extra fields in output. - Need extra fields for qc.checks - Update qc.checks. - Update example with cols2keep from metric.values example. Changes in version 1.1.0.9005 - Update bio data to be used for the model; Issue #7 - Collapse mites to Order. Changes in version 1.1.0.9004 - Update extdata/Rules.xlsx; Issue #7 Changes in version 1.1.0.9003 - metric.values dd nt, pi, and pt metrics; Issue #7 - NonIns_BCG_attr456 - NonInsJugaRiss_BCG_attr456 Changes in version 1.1.0.9002 - QC Flags, Add pi_dom02. Issue #7 - Update format of NEWS. - metric.values, row_number to dplyr::row_number for dominant metrics. Changes in version 1.1.0.9001 - metric.values, Issue #7 - Update metrics from NonClump to NoJugaRiss. Changes in version 1.1.0.0000 - Release new and fully QCed version. Changes in version 1.0.0.9002 - Metric.values - Fix metrics with not equal functions. - Ensure use is.na(x)==TRUE rather than x==NA - When have more than one condition for a data column need to be in the same statement. - Better define clumpy taxa for 2 metrics. - BCG.Level.Membership - Fixed combination of rules by level. Missed a column and was getting duplicates for alt rules that changed the outcome. - BCG.Level.Assignment - Replace For loop with apply. - Add special conditions for ties (2 levels with 0.5) and primary level is 1 (no 2nd level). Changes in version 1.0.0.9001 - Metric.values - Fix non-clumpy metrics. - Remove extra data frames for dominance metrics. Slight speed improvement. Issue #5. - Fix version numbers in NEWS. - Updated ReadMe with only the relevant packages. Issue #4. Changes in version 1.0.0.0000 - Only metric value issues left to resolve with test data set. Rest of the calculations are ok. Changes in version 0.1.0.9019 - Rules.xlsx - Fill in missing cells. - metric.values.R - Update FFG abbreviations to match example data. - Dominant N and special Dominant N metrics. - Define pipe as referencing dplyr. Slows down the functions but keeps dplyr from needing to be loaded. - SiteType values to lowercase. - metric.values.R - BCG.Metric.Membership.R - BCG.Level.Membership.R - BCG.Level.Assignment.R - Consistent terminology; don’t mix “.”, ” “, and”“. Use””. - METRIC_NAMES - METRIC_VALUES - SITE_TYPE (and change from REGION) - RULE_TYPE - NUMERIC_RULES - LIFE_CYCLE - LONG_LIVED - THERMAL_INDICATOR - NAME_WIDE - Rebuild PacNW master taxa list with changes. - Consistent names (columns and categories). - Example PacNW data. - Consistent names (columns). - QC Checks - Update Vignette. - All functions and examples seem to be generating the proper outputs. When QC only a few metrics are off. But enough that no final results are correct (that is, all levels, site types, and samples are affected but the remaining QC issues). Non-Insect and modified dominant 2 metrics are the 4 that have issues. Changes in version 0.1.0.9018 - BCG.Level.Membership.R - Correct function to consider preceding levels when assigning membership scores. Changes in version 0.1.0.9017 - metric.values.R - Added Thermal Indicator (TI) metrics. - Updates to PacNW bug data and rules files (xlsx). Changes in version 0.1.0.9016 - metric.values.R - Update pt_BCG_att1i2 and 1i23 metrics (numerator not capturing “i” taxa). - Update Rules.xlsx Changes in version 0.1.0.9015 - Vignette didn’t update in previous version. Changes in version 0.1.0.9014 - Tweak “data.R”. Not complete! - Added example save code for master taxa list. - Update BCG.Metric.Membership. - Add some error checking. - Colnames to upper case. - Updated Rules.xlsx - Percent metrics converted to 0-1 values to match metric.values calculations. - Fixed Index Name for some records. - metric.values.R - Updated examples, details, and description. - Update BCGcalc Vignette. - Update Readme. - Update BCG.Level.Membership Changes in version 0.1.0.9013 - Added PacNW benthic master taxa list to data. - Created “data.R”. Not complete! Changes in version 0.1.0.9012 - Update PacNW example data to use TRUE/FALSE for Excluded and NonTarget fields. - Updated metric.values - Moved common data munging to earlier in function so applies to all communities. - Enabled NonTarget exclusion. NonTarget column now required. Changes in version 0.1.0.9011 - Completed lingering edits for “Tier” to “Level”. - Completed BCG.Level.Membership function. Changes in version 0.1.0.9010 - Remove “Tier” wording in package and rename some functions to better reflect usage. - Include example code for saving results for each function. - Change Region to SiteType in code and example data files. Changes in version 0.1.0.9009 - Dom02 special metric placeholder. - Update Rule table for Level assignments. - BCG.Levels function. - Fixed error in sequencing in BCG.Membership function. Changes in version 0.1.0.9008 - Add last of the PacNW specific metrics to metric.values. - Added Vignette. Changes in version 0.1.0.9007 - Check clean up. - Convert data imports from development folder to pacakge folder with system.file. - Add data for rarify function. Changes in version 0.1.0.9006 - BCG.Tiers function. Changes in version 0.1.0.9005 - Add BCG.Membership function. Return is in long format. - Not QCed but has some known issues. Changes in version 0.1.0.9004 - Add subtitles, date, author to YAML header to NEWS and README. - Add “flags” Excel file to raw-data for QC checks. Used in qc.checks function (new). - Added 4 new ni metrics to metric values to be used for QC checks (flags). - qc.checks.R (incomplete but works). - Add BCGcalc.R to describe the package. - Update documentation headers in R files. Changes in version 0.1.0.9003 - metric.values.R, benthos - Added BCG attribute metrics. - Added outlining for readability in code. - More metrics and clean up of file. - Prepare example data for metric calculation. - Added na.rm=TRUE to n_distinct and sum in summarise. Changes in Version 0.1.0.9002 (2018-02-16) - Add parts without any modification from MBSStools package. - rarify function - metric.values function - included data folder and files - added Excel file to extdata with metric naming explanation Changes in version 0.1.0.9001 - Updated files for package. - Readme, NEWS, DESCRIPTION - Not complete. Changes in version 0.1.0 - Created GitHub repository