Changes in version 1.2.4.9024 - refactor: Add nord_EPT to MetricNames.xlsx Changes in version 1.2.4.9023 - refactor: Add nord_EPT to metric.values Changes in version 1.2.4.9022 - style: Updates per good practice package - Replace stray “=” with “<-” - Long code lines - refactor: Update help text for qc functions Changes in version 1.2.4.9021 - data: Update data_diatom_mmi_dev columns for new metrics, Issue #142 - Mertens, 7 new categorical columns Changes in version 1.2.4.9020 - refactor: Add metrics to metric.values and MetricNames.xlsx, Issue #142 - Algae, BCG versions of bug BCG, n = 86 Changes in version 1.2.4.9019 - style: Replace pounds with dashes for outline in metric.values - refactor: Add metrics to metric.values and MetricNames.xlsx, Issue #142 - Benthos, n = 7 Changes in version 1.2.4.9018 - fix: Update metric.values pi_dom01_BCG_att456t - 6t wasn’t being captured Changes in version 1.2.4.9017 - fix: Rename metric n_ac_wmf to n_ac_mwf - MetricNames.xlsx - metric.values Changes in version 1.2.4.9016 - refactor: Additional metrics, Issue #140 - fix: Reconcile differences between Metric.Names.xlsx and metric.calc() - Add metrics to both - data: Update PacNW and MBSS benthos datasets for area metrics Changes in version 1.2.4.9015 - refactor: Replace migrittr pipe with native pipe, Issue #130 - Tests Changes in version 1.2.4.9014 - refactor: Additional metrics, Issue #140 - refactor: Update metricnames.xlsx and metricscoring.xlsx for missing/extra values Changes in version 1.2.4.9013 - refactor: Rename qc_taxa_match_official to qc_taxa_names_match - feature: Add qc_taxa_names_proof function - Check for spelling issues - feature: Add qc_taxa_phylo for checking master taxa list names - refactor: Change names from distinct to parent in qc_taxa_phylo$unique_parent output - data: Create example final id issues dataset - docs: Document finalid_issues data - fix: Fix metric x_Obs_CatoRhin in metric.values, Issue #138 Changes in version 1.2.4.9012 - feature: Add qc_taxa_values_tolval function Changes in version 1.2.4.9011 - refactor: Add default column name to qc_taxa_values_ffg - feature: Add qc_taxa_values_habit function Changes in version 1.2.4.9010 - feature: Add qc_taxa_values_ffg function Changes in version 1.2.4.9009 - deprecate: Change qc_taxa to qc_taxa_match_official - Will be removed in a future version - refactor: Add qc_taxa_match_official and update with new name Changes in version 1.2.4.9008 - test: Add test for metric.values for collapsing, bugs and fish, Issue #131 Changes in version 1.2.4.9007 - refactor: Add new fish metrics Changes in version 1.2.4.9006 - fix: Update dominance metrics (fish and bugs), Issue #131 - Dom01 used max original data not dom dataset - Other dom numbers unaffected Changes in version 1.2.4.9005 - docs: Update README, Issue #127 - Citation - Badges, add - Project status - CRAN release - CRAN downloads - Badges, remove - GitHub release - GitHub downloads - docs: Add help file for package, Issue #128 Changes in version 1.2.4.9004 - refactor: Add new fish ageclass metrics, Issue #129 - tests: Update fish tests with new column, ageclass Changes in version 1.2.4.9003 - refactor: Update MetricScoring.xlsx for EGLE_2025 (MI) Changes in version 1.2.4.9002 - style: Updates to code style, metric.values - fix: Correct for missing EXCLUDE column to all FALSE, Issue #126 - Bugs and Fish metrics - tests: Add tests for metric.values for NA values in EXCLUDE column, Issues #126 - Bugs and Fish - Missing column and any NA values Changes in version 1.2.4.9001 - fix: Convert input to dataframe in rarify, Issue #123 Changes in version 1.2.4 (2025-10-09) - refactor: Bump version number for CRAN Changes in version 1.2.3.9008 - refactor: Remove or edit examples with errors, warnings, or long run times - taxa_translate - Non-ASCII character in translation file Changes in version 1.2.3.9007 - refactor: Remove or edit examples with errors, warnings, or long run times - metric.scores - metric.values Changes in version 1.2.3.9006 - fix: Remove non-portable command from example - rarify Changes in version 1.2.3.9005 - fix: Fix typo in example - rarify Changes in version 1.2.3.9004 - refactor: Remove print to console for function defaults - rarify.R - MapTaxaObs.R - markExcluded.R - fix: Fix typo in example - markExcluded Changes in version 1.2.3.9003 - style: Use commas at end of wrap lines instead of start of next line - Examples - assign_indexclass.R - markExcluded.R - metric_scores.R - metric_stats.R - metric_stats2.R - metric_values_excel.R - metric_values.R - qc_checks.R - qc_taxa.R - rarify.R - taxa_translate.R - refactor: Remove write example in vignette example Changes in version 1.2.3.9002 - docs: Update title and description per CRAN review - refactor: Uncomment or remove lines of code in examples - markExcluded - metric_values_excel - metric.values - qc.checks - refactor: Replace dontrun with donttest in examples - metric.scores - metrics.stats - qc.taxa - MapTaxaObs - style: Format function inputs with ending commas and separate lines for each input - fix: Remove a write location that wasn’t tempdir from vignette - refactor: Reduce records and runtime for MapTaxaObs - fix: Add error condition in qc_taxa for when required field is missing - fix: Update example for qc_taxa to avoid error with missing column name Changes in version 1.2.3.9001 - refactor: Create smaller data set for data_mmi_dev_small - refactor: Use smaller data set for metric.stats and metric.stats2 Changes in version 1.2.3 - docs: Bump version for CRAN submission Changes in version 1.2.2.9001 - refactor: Add entire example for metric.stats to don’t run - Fails (< 5 seconds) on Debian when submit to CRAN Changes in version 1.2.2 - docs: Bump version for CRAN submission Changes in version 1.2.1.9001 - refactor: Update example for metric.stats for speed - Reduce number of rows input rather than reduce the file size Changes in version 1.2.1 - docs: Bump version number for submission to CRAN Changes in version 1.2.0.9001 - refactor: Reduce size of example file in metric.stats - Failed time check (< 5 seconds) for one OS - docs: Update cran-comments - docs: Add cran-comments.md to .Rbuildignore Changes in version 1.2.0 - docs: Bump version number for submission to CRAN, Issue #49 - docs: Update README for install from CRAN Changes in version 1.1.0.9005 - docs: Update authors in DESCRIPTION, per CRAN check, Issue #49 - docs: Update URLS in README, per CRAN check, Issue #49 - docs: Add cran-comments file Changes in version 1.1.0.9004 - style: Convert = to <- in metric_values_excel.R - docs: Don’t run examples for taxa.translate to avoid issues with pkgdown Changes in version 1.1.0.9003 - docs: Update license file, Issue #49 - Split files per SO article - https://stackoverflow.com/questions/43550479/how-to-satisfy-both-cran-and-github-license-file-naming-requirements - refactor: Update example data for shorter run times, Issue #49 - ext/Data_Benthos.xlsx - docs: Update columns for some datasets in data.R - docs: Add missing dataset documentation to data.R - docs: Update a few missing imports and global bindings - refactor: Modify seq statement in metric.stats per CodeFactor Changes in version 1.1.0.9002 - refactor: Remove large file, Issue #49 Changes in version 1.1.0.9001 - breaking: Move Shiny app to a different repo, BioMonTools_Shiny - breaking: Remove run shiny function - version: Bump minor version number to reflect change in Shiny app location Changes in version 1.0.2.9081 - refactor: Add missing package references to function calls, Issue #49 - refactor: Add missing global variable bindings, Issue #49 - assign_IndexClass - metric.values.bugs - metric.values.fish - metric.values.coral - taxa_translate - refactor: Change if/then statement for checking class in metric.values, Issue #49 Changes in version 1.0.2.9080 - tests: Update metric.calc, Issue #113 - PA - Algae, Issue #108 - disable until update QC data - Coral - Fix syntax of test - tests: Update taxa_translate, Issue #113 - tests: Update metric_stats, Issue #113 - tests: Update metric_names, Issue #113 - Algae - fix: Update assign_indexclass, Issue #113 - Add TYPE for multi and single - tests: Update assign_indexclass, Issue #113 - tests: Update taxa_translate, Issue #113 - tests: Remove coral test from metric.values, Issue #113 - refactor: Suppress filter warning in metric.scores, Issue #122 Changes in version 1.0.2.9079 - fix: Add extra columns to example fish data - docs: Update documentation for example fish data - fix: Update examples - metric.values() - metric.stats(), Issue #122 - metric.stats2(), Issue #122 - refactor: Update group_by .dots statements in metric.values(), Issue #84 Changes in version 1.0.2.9078 - refactor: Update metric.values() for global variables, Issue #49 Changes in version 1.0.2.9077 - refactor: Add new metrics for ORWA, Issue #121 Changes in version 1.0.2.9076 - refactor: Add new metrics for ORWA, Issue #120 - refactor: Convert required logical columns to logical in metric.values - bugs, fish, and coral - no logical required columns for algae Changes in version 1.0.2.9075 - refactor: Add new metrics for GP, Issue #118 Changes in version 1.0.2.9074 - refactor: Update MetricScoring.xlsx to fix metric scoring directionality for MIEGLE Changes in version 1.0.2.9073 - refactor: Update Shiny - Make button enable/disable consistent - Make results folder cleand up consistent - Could lead to errors if don’t refresh app between files and operations - Make selection box defaults consistent - Metric Calculation - Create select boxes - Modify columns for metric.values() input Changes in version 1.0.2.9072 - feature: Added Exclude feature to metric calculation in Shiny Changes in version 1.0.2.9071 - refactor: Add parameters to BioMonTools::taxa_translation in Shiny - trim_ws = TRUE - match_caps = TRUE Changes in version 1.0.2.9070 - refactor: Shiny updates - Add shinyalerts to Shiny app for taxa translation - From MNcalc - disable taxa trans button on startup and enable on upload file - From MNcalc Changes in version 1.0.2.9069 - refactor: Add taxa translation for RMN to Shiny - docs: Add shinyalert to DESCRIPTION Suggests Changes in version 1.0.2.9068 - refactor: Add metrics, bugs - MS, Issue #116 - habit and habitat, Issue #117 Changes in version 1.0.2.9067 - refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2 - MetricNames.xlsx - metric_values.R Changes in version 1.0.2.9066 - refactor: Add fish metric permutations of non-native - MetricNames.xlsx - metric_values.R Changes in version 1.0.2.9065 - fix: Modify fish metrics BCG_ATTR2 to convert to upper case - metric_values.R - fix: Update fish metrics BCG2_att1234b (nt_, pi_, and pt_) - metric_values.R Changes in version 1.0.2.9064 - refactor: Add new fish metric (pi_BCG2_att1234b) - MetricNames.xlsx - metric_values.R Changes in version 1.0.2.9063 - docs: Update comment about NATIVE in metric.values help Changes in version 1.0.2.9062 - refactor: Add new fish metrics (BCG_att4w5); same as bugs - MetricNames.xlsx - metric_values.R - docs: Start to populate values column in MetricNames.xlsx Changes in version 1.0.2.9061 - refactor: Update MetricNames.xlsx for test - New field is mostly blank so imports as logical and causes error Changes in version 1.0.2.9060 - refactor: Add new fish metrics (nt_, pi_, and pt_) for invertivore - MetricNames.xlsx - metric_values.R Changes in version 1.0.2.9059 - refactor: Update search patterns for some fish trophic metrics - IV - TC Changes in version 1.0.2.9058 - refactor: Add new fish metric for Idaho, trophic invertivore top carnivore - metric_values.R - Add “IV_TC” - Modify “IV” to check for specific cases - MetricNames.xlsx Changes in version 1.0.2.9057 - refactor: Add new metric for MN, nt_total_ExclSchool - metric_values.R - MetricNames.xlsx Changes in version 1.0.2.9056 - refactor: Modify code for schooling fish in TYPE for MN metrics - SCHOOLING to SCH - refactor: Modify code for brook trout fish in TYPE for MN metrics - BROOKTROUT to BKT - docs: Update notes for MN metrics above in MetricNames.xlsx - docs: Add date to version number in NEWS - Current entry only Changes in version 1.0.2.9055 - docs: Update Excel files for MN_IBI_Fish Index_Class 1 - pi_piscivore_ExclSchool to nt_piscivore Changes in version 1.0.2.9054 - refactor: Add new metrics for MN_IBI_Bugs - nfam_Baetidae - nt_POETNoBae - nt_POETfamBae - docs: Update Excel files for new metrics for MN_IBI_Bugs - MetricNames - MetricScoring Changes in version 1.0.2.9053 - refactor: Update MetricScoring.xlsx - MN, pi_TrichNoHydro scoring formula text Changes in version 1.0.2.9052 - fix: Update MetricScoring.xlsx - MN, narratives Changes in version 1.0.2.9051 - fix: Update MetricScoring.xlsx (MN) Changes in version 1.0.2.9050 - refactor: Update MetricScoring.xlsx - MN_IBI_Fish and MN_IBI_Bugs, index numeric and narrative Changes in version 1.0.2.9049 - style: Clean up new additions to metric_values.R - Move new metrics for GP to alongside previous GP metrics - Move munging for new metrics to alongside previous munging for TYPE Changes in version 1.0.2.9048 - refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT) Changes in version 1.0.2.9047 - refactor: MetricScoring.xlsx change MN IBI classes - Flip Bugs and Fish for 8/9 and 10/11 Changes in version 1.0.2.9046 - refactor: Update MN IBI (bugs and fish), Issue #92 - Drop “modified” narrative - MetricScoring.xlsx Changes in version 1.0.2.9045 - refactor: Update MN Fish and Bug IBI index scoring, Issue #92 Changes in version 1.0.2.9044 - refactor: Update MN fish metric ni_m2_notoler to ni_m_notoler, Issue #92 - Length (m) not area (m2) - metric.values.R - MetricScoring.xlsx - MetricNames.xlsx Changes in version 1.0.2.9043 - refactor: Change MN Bugs Index_Class from 8 and 9 to 10 and 11, Issue #92 - MetricScoring.xlsx Changes in version 1.0.2.9042 - fix: Update fish metrics brook trout code, Issue #92 - Change for MN to replace space invalidated code - Added TYPE_BROOKTROUT to make metric simpler Changes in version 1.0.2.9041 - docs: Add “demo only” language to ORWA example data Changes in version 1.0.2.9040 - BREAKING: Deprecate sum_n_taxa in taxa_translate - Leave in code so if fix can re-enable - Doesn’t work all the time with match_caps and non-ascii character code Changes in version 1.0.2.9039 - refactor: Update zeroind scoring for MN Bugs and Fish IBI, Issue #111 - MetricScoring.xlsx Changes in version 1.0.2.9038 - refactor: Update taxa_translate columns for unique taxa output Changes in version 1.0.2.9037 - refactor: Update match_caps code in taxa_translate Changes in version 1.0.2.9036 - refactor: Add default value for match_caps in taxa_translate Changes in version 1.0.2.9035 - refactor: Update MN_Fish_IBI metrics, Issue #111 - pi_wetland_notoler_ExclSchool to nt_wetland_notoler - MetricScoring.xlsx - MetricNames.xlsx - metric.values Changes in version 1.0.2.9034 - refactor: Add pi_OligoHiru to metric.values Changes in version 1.0.2.9033 - refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #111 Changes in version 1.0.2.9032 - refactor: Update taxa_translate taxatrax_unique ouput - Add match with CAPS Changes in version 1.0.2.9031 - fix: Add TolVal2 as required field for fish metrics in metric.values Changes in version 1.0.2.9030 - test: Add taxa.translate triws test - Add white space (leading, trailing, both) and internal nbsp to test data Changes in version 1.0.2.9029 - feature: Update taxa.translate trimws feature to replace internal Changes in version 1.0.2.9028 - feature: Update metric.scores() to account for MN_IBI_Fish, Issue #111 - If another metric is below a threshold then score as zero - refactor: Add hooks in metric.scores() for score zero modifications, Issue #111 - refactor: Update help example for metric.scores() Changes in version 1.0.2.9027 - refactor: Update MetricNames.xlsx to mark bug metrics to use for Large Rare metric calculations - refactor: Add remove spaces to columns for metric calculation - Bugs - HABIT, FFG, LIFE_CYCLE, FFG2, THERMAL_INDICATOR, HABSTRUCT , ELEVATION_ATTR, GRADIENT_ATTR, WSAREA_ATTR - Fish - TROPHIC, THERMAL_INDICATOR, REPRODUCTION, HABITAT, ELEVATION_ATTR , GRADIENT_ATTR, WSAREA_ATTR - refactor: Add new fish metrics for MN_Fish_IBI, Issue #111 - metric.values - MetricNames.xlsx - MetricScoring.xlsx - style: Reorder some metrics in fish section of metric.values - Organize Munge section by column name - tests: metric.values() move time inside verbose to avoid warning message Changes in version 1.0.2.9026 - refactor: Remove match_caps parameter from taxa_translate function, Issue #111 - tests: Remove taxa_translate match_caps test, Issue #111 Changes in version 1.0.2.9025 - tests: Add tests for removing white space, Issue #111 - feature: Update taxa_translate with clean parameters, Issue #111 Changes in version 1.0.2.9024 - refactor: Update for MN_Fish_IBI, Issue #92 - MetricNames.xlsx - metric_values.R - Updates to data munging prior to metric calculation Changes in version 1.0.2.9023 - refactor: Update MetricScoring.xlsx for MN_Bug_IBI, Issue #92 Changes in version 1.0.2.9022 - refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #92 - refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue #92 Changes in version 1.0.2.9021 - refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #92 - refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue #92 - docs: Edit README for timeout issue Changes in version 1.0.2.9020 - refactor: Update pi_Cheu text in MetricNames.xlsx Changes in version 1.0.2.9019 - refactor: Update MetricNames.xlsx for Great Plains BCG Changes in version 1.0.2.9018 - refactor: Merge pull request 114 - Add metrics (bugs and fish) for Great Plains BCG Changes in version 1.0.2.9017 - feature: Options added to taxa_translate, Issue #111 - Match on ALL CAPS - Clean input names - Not fully implemented Changes in version 1.0.2.9016 - refactor: Post merge updates - Reconcile names for same calculation but different programs and columns - benthicInvertivore in merge to habitat_beninvert - MetricNames.xlsx - metric_values.R - tests: Update fish metric names for new metrics - refactor: Add MN_IBI_Fish metrics to MetricNames.xlsx, Issue #92 Changes in version 1.0.2.9015 - refactor: Merge pull request 110 - New metrics for NM BCG Fish - MetricNames.xlsx - metric_values.R Changes in version 1.0.2.9014 - refactor: New index scoring regimes, Issue #92 - MetricScoring.xlsx - AVERAGE_100_M10_R2 for MN_IBI_Bugs - AVERAGE_100_M10_R3 for MN_IBI_Fish Changes in version 1.0.2.9013 - refactor: Modify scoring regime (AVERAGE_100_M10), Issue #92 - Round scaling to 2 decimals - Modify MetricScoring.xlsx - metric.scores - refactor: Add new scoring regime (CAT_0510) to metric.scores, Issue #92 - fix: Update MN_IBI_Fish thresholds, MetricScoring.xlsx, Issue #92 Changes in version 1.0.2.9012 - refactor: Update MetricScoring.xlsx, Issue #92 - New scoring regime, AVERAGE_100_M10 - Change MN_Bug_IBI scoring regime - refactor: Add new scoring regime calculation to metric.scores , Issue #92 Changes in version 1.0.2.9011 - fix: Update MN IBI Fish thresholds in MetricScoring.xlsx, Issue #92 - test: Update thresholds for extra digits in MetricScoring.xlsx, Issue #101 - Adjust from 11 to 13 digits for one index (WY) Changes in version 1.0.2.9010 - fix: Update MN IBI Bugs thresholds in MetricScoring.xlsx, Issue #92 Changes in version 1.0.2.9009 - refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92 Changes in version 1.0.2.9008 - refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92 Changes in version 1.0.2.9007 - refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92 Changes in version 1.0.2.9006 - fix: Update metric.values pi_dom01_BCG* metrics - Add zero to max function to avoid max returning -Inf - refactor: Update metric.values debug steps for fish - Was 10 and changed to 12 Changes in version 1.0.2.9005 - refactor: Update MetricScoring.xlsx for WY, Issue #101 - fix: After testing add 4 metrics for WY from scoring, Issue #101 - Add to MetricNames.xlsx - Add to metric.values.R Changes in version 1.0.2.9004 - fix: Update MetricNames.xlsx for missing coral metric per tests Changes in version 1.0.2.9003 - refactor: Update Excel files for MN IBI - MetricFlags.xlsx - MetricNames.xlsx - MetricScoring.xlsx Changes in version 1.0.2.9002 - refactor: Update GitHub Actions with usethis::use_github_action() - check-standard - test-coverage - pkgdown - docs: Update check badge in ReadMe Changes in version 1.0.2.9001 - fix: Remove uneeded concatenate in tests per CodeFactor - test_metric_names Changes in version 1.0.2 - fix: Update to minor version number 1.0.2 - Incorrect version numbers from pull request Changes in version 1.0.1.9551 - pull request 107 - refactor: Coral metrics from Blocktt Changes in version 1.0.1.9550 - fix: made changes to coral metrics - added test for Florida BCG Changes in version 1.0.1.9501 - update: Added coral metrics, specifically for FL BCG - metric_values.R - MetricNames.xlsx Changes in version 1.0.0.9066 - refactor: Additional metrics for Great Plains BCG, Issue #106 - metric_values.R - MetricNames.xlsx Changes in version 1.0.0.9065 - fix: Update MetricScoring.xlsx - Change MN_IBI_Bugs INDEX_CLASS from 5 IBI classes to 9 site classes, Issue #92 - Update all ScoreRegime from Cont_010 to Cont_0010 - Added Modify_Value and Modify_Code to adjust values before scoring - not implemented - style: Update spacing in metric.values Changes in version 1.0.0.9064 - fix: Update MetricScoring.xlsx, ScoreRegime for MN_IBI_bugs, Issue #92 - Cont_010 to Cont_0010 to match code Changes in version 1.0.0.9063 - fix: Update metric.values metric, nt_COETNoBraBaeHydTri, Issue #101 - Replace Hydropsyche with Hydropsychidae - Metric not calculating properly - Update MetricNames.xlsx - tests: Wrote test for nt_COETNoBraBaeHydTri, Issue #101 Changes in version 1.0.0.9062 - fix: Modify metric.values() benthic metric nt_tv_toler8, Issue #104 - Was using 6 instead of 8 as minimum Changes in version 1.0.0.9061 - refactor: Add metrics for WY bug MMI, Issue #101 - MetricNames.xlsx - MetricScoring.xlsx - metric.values() - fix: Correct metric.values nt_PolyNoSpion, Issue #102 - Was not calculating number of taxa - fix: Update metric.values fun.cols2keep to ignore required cols, Issue #100 - fix: Change input parameter in metric.scores function, Issue #103 - Replace col_IndexRegion with col_IndexClass - Add col_IndexRegion at end of parameters to avoid breaking existing code Changes in version 1.0.0.9060 - refactor: Add ni_total flags (small and large) for MN_IBI_Bugs, Issue #92 - MetricFlags.xlsx Changes in version 1.0.0.9059 - feat: Add new issue template for metric and index requests, Issue #99 - refactor: Add metrics and index for MN IBI (bugs and fish), Issue #92 - MetricNames.xlsx - MetricScoring.xlsx - metric.values() - tests: Run tests for new metrics - Tweak data and tests as needed Changes in version 1.0.0.9058 - refactor: Add metrics for NM BCG, Issue #97 - Pull request not able to easily merge, make changes by hand Changes in version 1.0.0.9057 - refactor: Add testing (QC) to metric.values fish calc section Changes in version 1.0.0.9056 - refactor: Add EXCLUDE taxa to fish metrics - nt_* - Error checking to ensure column is included - refactor: Added QC check to fish calc in metric.values - fix: Change QC sub function name for fish in metric.values - refactor: Add “EXCLUDE” column to example fish data - docs: Update description of data_fish_MBSS Changes in version 1.0.0.9055 - refactor: Remove interactive TRUE from algae in metric.values - Same issue with the fish but being proactive - Not included on bugs Changes in version 1.0.0.9054 - refactor: Edits to metric.values fish calc for error in Red Lakes Shiny app - N_ANOMALIES NA to 0 - Change “interactive” part of require column check Changes in version 1.0.0.9053 - refactor: More edits to metric.values fish calc for error in Red Lakes Shiny app Changes in version 1.0.0.9052 - refactor: Edit metric.values fish calc for error in Red Lakes Shiny app Changes in version 1.0.0.9051 - refactor: Modify verbose statements in metric.values - Change terminology in code so more generic - Add verbose statements to fish sub function Changes in version 1.0.0.9050 - refactor: Update MetricNames.xlsx with recent name changes Changes in version 1.0.0.9049 - refactor: Change names of trout metrics in metric.values - Better reflects contents of metrics Changes in version 1.0.0.9048 - refactor: Add pi_trout to metric.values Changes in version 1.0.0.9047 - refactor: Update MetricNames.xlsx to match function, fish metrics - refactor: Update metric.values to match MetricNames.xlsx, fish metrics - Added “nt_BCG_att12346” - Left “nt_BCG_att1236sp” to be added later as unsure of definition - tests: Update taxa_translate test for file name change Changes in version 1.0.0.9046 - fix: metric.values boo.shiny code updated to match bugs and algae Changes in version 1.0.0.9045 - refactor: metric.values specify parameters for subfunctions Changes in version 1.0.0.9044 - fix: Update metric, nt_BCG_att55a6, Issue #92 - add ‘na.rm = TRUE’ Changes in version 1.0.0.9043 - fix: Add missing metric, nt_BCG_att55a6, Issue #92 Changes in version 1.0.0.9042 - refactor: Fix BCG_att1236sp fish metrics, pi and pt - Remove nt Changes in version 1.0.0.9041 - feature: Add MN BCG fish metrics, Issue #92 - BCG_att1236sp fish metrics (n=3) as NA until better defined - refactor: Update MetricNames.xlsx with new metrics, Issue #92 Changes in version 1.0.0.9040 - fix: Cheumatopsyche metrics, Issue #93 - Search term updated; Cheumatopsyche to CHEUMATOPSYCHE - Add missing equal sign - Move so alphabetical in output Changes in version 1.0.0.9039 - feature: Add taxaid_dni parameter to metric.values, Issue #96 Changes in version 1.0.0.9038 - refactor: Modify output of taxa_translate function, Issue #94 - taxatrans$taxatrans_unique Changes in version 1.0.0.9037 - feat: Add new metric, ni_totalNoDeca, Issue #94 - style: Add spaces to code for readability Changes in version 1.0.0.9036 - fix: Update Cheumatopsyche metrics in MetricNames.xlsx, Issue #93 - pi_Cheu - pi_EPTNoCheu Changes in version 1.0.0.9035 - fix: Update code for Cheumatopsyche metrics, metric_values.R, Issue #93 - pi_Cheu - pi_EPTNoCheu Changes in version 1.0.0.9034 - fix: BioMonTools vignette change reference to metric names - corecold changed to stenocold Changes in version 1.0.0.9033 - fix: Fill in missing Vignette Builder for vignette_NewIndex Changes in version 1.0.0.9032 - fix: Add line for “changed” taxa in taxa_translate Changes in version 1.0.0.9031 - fix: Update domX calculations to combine taxa before calculate in metric_values - bugs and fish Changes in version 1.0.0.9030 - refactor: Update metrics for MN BCG, Issue #92 - In myDF remove NA for specialized dom01 calculations Changes in version 1.0.0.9029 - refactor: Update metrics for MN BCG, Issue #92 Changes in version 1.0.0.9028 - refactor: Add percent Cheumatopsyche metric Changes in version 1.0.0.9027 - refactor: Additional metrics for MN BCG, Issue #92 Changes in version 1.0.0.9026 - refactor: Add bug metrics for MN BCG, Issue #92 - style: Update spacing in test file metric_names Changes in version 1.0.0.9025 - refactor: Update MetricFlags.xlsx for MTTI index Changes in version 1.0.0.9024 - refactor: Update metric.values MTTI subset metrics, Issue #90 Changes in version 1.0.0.9023 - refactor: Update MetricFlags.xlsx for MTTI index Changes in version 1.0.0.9022 - feature: New parameter in metric.values to run only subset, Issue #90 - style: Style changes in metric_values.R Changes in version 1.0.0.9021 - docs: Add vignette for adding a new index, Issue #87 - incomplete - refactor: Add CO MMI (bugs) - Draft 2006, verify with report and EDAS database Changes in version 1.0.0.9020 - fix: Update metric.values thermal NA metrics - Add blank (““) to NA as a condition - test: Additional assign_indexclass tests Changes in version 1.0.0.9019 - refactor: Update assign_indexclass to account or NA and ““, Issue #85 - fix: Update assign_indexclass to account non standard column names, Isue #85 - tests: Add tests for assign_indexclass, Issue #85 - refactor: Update assign_indexclass to not fail if index_class in input data, Issue #85 Changes in version 1.0.0.9018 - refactor: Update MetricNames.xlsx groupings - Added “Experimental” Changes in version 1.0.0.9017 - feature: Add unique taxa crosswalk to output of taxa_translate Changes in version 1.0.0.9016 - test: Add test for multiple stages for taxa_translate Changes in version 1.0.0.9015 - fix: Turn off QC testing in function assign_indexclass - Was using test data instead of user input Changes in version 1.0.0.9014 - docs: Update taxa_translate example files Changes in version 1.0.0.9013 - refactor: Update taxa_translate to drop a particular ID after translation , Issue #81 - Added input paramter - Updated example - Updated test Changes in version 1.0.0.9012 - data: Update extdata for taxa_translate example, Issue #81 - Revised PacNW_ORWA data file (2022-12-19) - tests: Revise taxa_translate test for revised data Changes in version 1.0.0.9011 - tests: Create tests for taxa_translate, Issue #81 Changes in version 1.0.0.9010 - fix: Update taxa_translaste - Update nonmatch to data frame with count and sum of occurrence, Issue #81 - Refine matching - Include summed taxa properly - Drop non-matching taxa (NA and DNI) - Update example Changes in version 1.0.0.9009 - fix: Update taxa_translate for when sum taxa, Issue #81 - update: Revise taxa_translate files in extdata Changes in version 1.0.0.9008 - refactor: Tweak debug code in taxa_translate, Issue #81 - fix: Update taxa_translate for col_drop_project - Should be debug only Changes in version 1.0.0.9007 - refactor: Change internal workings of taxa_translate, Issue #81 - If summarize retain the official taxa columns - Reorder columns in the merged output Changes in version 1.0.0.9006 - refactor: Change internal parameter boo_DEBUG to boo_DEBUG_tt in taxa_translate, Issue #81 Changes in version 1.0.0.9005 - refactor: Make taxa_translate as an export object, Issue #81 Changes in version 1.0.0.9004 - fix: Updated taxa_translate function to include metadata as parameter, Issue #81 Changes in version 1.0.0.9003 - feature: Add taxa_translate function, Issue #81 - More general than qc_taxa Changes in version 1.0.0.9002 - fix: Update markExclude to avoid dplyr deprecation warnings, Issue #51 Changes in version 1.0.0.9001 - breaking change: Site_Type and Index_Region to Index_Class - refactor: Update rarify function to save example to tempdir Changes in version 0.5.0.9127 - feat: New function assign_IndexClass, Issue #82 - Add IndexClass.xlsx to ext folder Changes in version 0.5.0.9126 - refactor: Additional benthic metrics - metric_values.R - MetricNames.xlsx - refactor: Additional column for benthic metrics; AirBreather - modify metric_values for required column - Add to data_benthos_PacNW Changes in version 0.5.0.9125 - fix: Update and add some metrics - metric_values.R - MetricNames.xlsx Changes in version 0.5.0.9124 - fix: Tweak secondary metric name in MetricScoring.xlsx - GA_DNR_Fish_2020 Changes in version 0.5.0.9123 - refactor: Modify default term for markExcl from Excluded to Exclude - Ensure is consistent in function, example, vignette - refactor: markExcl warning don’t trigger for 0 levels missing, Issue #80 - refcator: markExcl add default of NA to Exceptions parameter, Issue #80 Changes in version 0.5.0.9122 - docs: Typo in MetricNames.xlsx (Isoptera instead of Isopoda) - fix: Change logic in metric.values for insertion of missing column names - Was not working in server environment (interacive == FALSE) - docs: Update error message in metric.values for complex columns, Issue #71 - Add code needed to error message (base R and tidyverse) - refactor: Change logic for Shiny on server when encounter complex, Issue #71 - BCG_ATTR column only, interactive FALSE or boo.Shiny TRUE Changes in version 0.5.0.9121 - feat: Additional BCG metrics, Issue #79 - style: Surround operators with space - metric_values - test: Add sum of parts tests for new BCG metrics Changes in version 0.5.0.9120 - fix: Update bug thermal metrics, Issue #78 Changes in version 0.5.0.9119 - feature: Additional algae metrics, Issue #75 - style: Add outlining to algae metrics - style: Add spaces before and after operators in algae calculations - refactor: Add missing values in MetricNames.xlsx based on tests - refactor: Add missing algae metric pt_BC_12_adj as NA Changes in version 0.5.0.9118 - fix: Hemiptera metrics (nt and pt) not working, Issue #74 - Fix spelling Changes in version 0.5.0.9117 - refactor: Additional metrics, Issue #74 - fix: Change metric HabitatStruct from RW to RM, Issue #73 Changes in version 0.5.0.9116 - refactor: Additional bug and fish metrics, Issue #73 - refactor: Add BCG_ATTR as upper case for fish metrics - Update fish BCG metrics to use upper case letters for BCG metrics - style: Add spacing and outlining to metric_values.R - refactor: Updates to MetricNames.xlsx to pass tests Changes in version 0.5.0.9115 - refactor: Change variable classes in metric.scores() - Avoid errors in import via read_excel Changes in version 0.5.0.9114 - refactor: Rename one misspelled bug thermal metrics, Issue #72 - ‘pt_ti_cool_warm_stenowarm’ should be ‘pt_ti_warm_stenowarm’ Changes in version 0.5.0.9113 - refactor: Add and modify bug thermal metrics, Issue #72 - metric_values() - extdata.xlsx - style: Add extra spaces to some lines in metric_values() Changes in version 0.5.0.9112 - refactor: Add metrics and scoring for So Cal Marine Bays - extdata.xlsx - extdata.xlsx - tests: Add tests for So Cal Marine Bays - Incomplete Changes in version 0.5.0.9111 - fix: Restore extdata.xlsx - Deleted in v0.5.0.9109, last mod was v0.5.0.9100 Changes in version 0.5.0.9110 - docs: Update required fields text in metric.values() - refactor: Copy (as comments) required fields code from bugs to other communities in metric.values() Changes in version 0.5.0.9109 - refactor: Additional output messages to screen in metric.values() Changes in version 0.5.0.9108 - tests: Update metric_stats test for new metrics - fix: Update metric.values() for 1i and 1m metrics, use upper case - Recent change to have all columns to upper case make 1i into 1I Changes in version 0.5.0.9107 - fix: metric.values() remove some fields from conversion to upper case, Issue #69 - SAMPLEID, INDEX_NAME, INDEX_REGION - fixes issue with vignettes flag example, Issue #70 - fix: Update metvalgrpxl() NOTES, Issue #69 - Input File Name to Input Data Frame - Convert text to formula for Description of Work - Moved from column 1 (text) to column 2 (formulas) in v0.5.0.9101 - fix: Shiny, BCG_Attr importing as complex, Issue #71 - Specify colClasses as character Changes in version 0.5.0.9106 - refactor: Tweak error checking for bugs in metric.values() - fix: metric.values() columns to upper case for calculation - Error introduced in v0.5.0.9093 (2022-02-03) - refactor: Change reference to some files in BioMonTools vignette - flag section - rebuild without vignettes Changes in version 0.5.0.9105 - refactor: Tweak error checking for bugs in metric.values() Changes in version 0.5.0.9104 - refactor: Tweak error checking for bugs in metric.values() Changes in version 0.5.0.9103 - refactor: Tweak error checking for bugs in metric.values() Changes in version 0.5.0.9102 - refactor: Update shiny app to use metric.values(…, verbose = TRUE) - refactor: Update number of steps in verbose for metric.values() - refactor: Update fill missing columns metric.values() - NA to NA_character_ Changes in version 0.5.0.9101 - refactor: Refine message output of metric.values() for use in Shiny - refactor: Add verbose paramters to metric.values() - refactor: Tweak Notes worksheet for metric Excel output Changes in version 0.5.0.9100 - refactor: Add new metric to MetricNames.xlsx Changes in version 0.5.0.9099 - refactor: Shiny add ‘tab’ as acceptable text file upload format. - refactor: Add new bug metric to metric.values() - pi_SphaerCorb Changes in version 0.5.0.9098 - refactor: Modify debugging messages to metric.values() for Shiny log Changes in version 0.5.0.9097 - refactor: Add debugging messages to metric.values() Changes in version 0.5.0.9096 - fix: Update metric.values() for input data missing Index_Name and Index_Region Changes in version 0.5.0.9095 - fix: Update metric.values() with more error checking for missing columns - At start for minimal required fields before community specific sections - After metric values calculated in bug section for NA to 0 Changes in version 0.5.0.9094 - refactor: Update metvalgrpxl() for blank cells hiding text to left Changes in version 0.5.0.9093 - fix: Update to changes in metric.values() Changes in version 0.5.0.9092 - fix: Remove redundant code in metric.values() - Causing failures on Shiny.io with missing required columns Changes in version 0.5.0.9091 - refactor: Update metvalgrpxl() to use input parameter for groupings Changes in version 0.5.0.9090 - refactor: Small edits to Shiny app - Text edits to help pages - Update links for TaxaMaps - refactor: Update metvalgrpxl() to use formulas in output Changes in version 0.5.0.9089 - refactor: Edits to help pages in Shiny app - Update links to download files Changes in version 0.5.0.9088 - refactor: Shiny app updates - Calculate Metrics - Update help/notes for each function - RMD in data-raw - Add download files to www folder - refactor: Define global variables in functions - metric.values - refactor: Define imported function - MapTaxaObs - markExcluded - metric.stats2 - feature: Update MetricNames.xlsx with Sort_Group - feature: Add new function, metvalgrpxl(), Issue #68 Changes in version 0.5.0.9087 - fix: Correct spelling of file name in global.R - ShinyApps.io is Linux and is case-sensitive Changes in version 0.5.0.9086 - refactor: Reorganize -raw folder with subfolders - Keep only the scripts to be run at the root - Will have to update scripts at later date to use the new structure - feature: Added HTML creation scripts for text in shiny app to -raw - feature: Updates to Shiny app to include help text for each function - feature: Add runShiny() to launch shiny app from console - docs: Removed XLConnect from DESCRIPTION Suggests package list - Not used - docs: Added writexl package to DESCRIPTIOn Suggest for upcoming change , Issue # 68 Changes in version 0.5.0.9085 - docs: Update GitHub default branch from “master” to “main” Changes in version 0.5.0.9083 - refactor: Added global variable bindings to fish metrics metric.values() - Only BCG_Attr - fix: metric.values() example 4 (fish) view statement incorrect Changes in version 0.5.0.9082 - feature: Add new fish metrics to metric.values() - pi_BCG_att23_SCC - nt_BCG_att23_SCC - pt_BCG_att23_SCC Changes in version 0.5.0.9081 - feature: Add new fish metrics to metric.values() - pi_Lepomis - pt_Lepomis - nt_BCG_attNA - pi_BCG_attNA - pt_BCG_attNA Changes in version 0.5.0.9080 - refactor: Modify shiny mark excluded default new column name - EXCLUDED to Exclude to match required column for metric calc - refactor: Add package version number to shiny About page - docs: Add DT package to DESCRIPTION Changes in version 0.5.0.9079 - feature: Update Shiny app, all functions working, Issue #67 Changes in version 0.5.0.9078 - feature: Add Shiny app, basic outline only, Issue #67 Changes in version 0.5.0.9077 - refactor: Allow for mixed case in bug metric phylo metrics, Issue #65 Changes in version 0.5.0.9076 - fix: Update metric.values(), was returning 0 records - length_m was commented out and caused error in met.val Changes in version 0.5.0.9075 - tests: Update tests to ensure MetricNames.xlsx is complete - refactor: Update metric.valus() with metrics used in MetricScoring.xlsx Changes in version 0.5.0.9074 - docs: Create documentation for data_fish_MBSS dataset - docs: Update MetricNames.xlsx and MetricScoring.xlsx for any new metrics, Issue #64 Changes in version 0.5.0.9073 - feature: New fish metrics, Issue #64 - feature: Add fish example data - refactor: Add .groups = “drop_last” to each subfunction in metric_values(), Issue #20 - refactor: Fish metric names - nt_natcent to nt_natCent_sunfish - GADNR_Fish_2020 - Includes sunfish and had to add a Centrarchidae only metric - Fixed in metric.values() and MetricScoring.xlsx - lepomis to Lepomis Changes in version 0.5.0.9072 - refactor: Update thermal metric default values, Core-Cold to CoreC - metric.values() - data_benthos_PacNW Changes in version 0.5.0.9071 - fix: metric.values() thermal indicator metric not correct - nt_ti_corecold_cold - pt_ti_corecold_cold Changes in version 0.5.0.9070 - fix: metric.values() thermal indicator NA metric not correct - Using wrong column (Habitat) to find NA Changes in version 0.5.0.9069 - fix: metric.values() not working for new metrics, Issue #62 - Elevation, Gradient, and WSArea Changes in version 0.5.0.9068 - refactor: Update MetricScoring.xlsx for IEPA, Issue #63 - tests: Update test_threshold_numdigits to show rows with issues Changes in version 0.5.0.9067 - feature: Add more benthic metrics, Issue #62 - Adds new required fields - GRADIENT - ELEVATION - WSAREA - Update data with new columns - data_benthos_PacNW - Data_Benthos.xlsx - Update data.R with changes to data_benthos_PacNW - refactor: Update Vignettes for changes in metrics - refactor: Update tests for changes in metrics - break: Rename thermal benthic metrics, Issue #62 - tests: Update metric test names Changes in version 0.5.0.9066 - tests: Update tests for benthos for UFC column - refactor: Update diatom mmi dev data for tests, add Phylum - ProcessData - data description - refactor: Update MetricNames to match MetricScores - Failed test after addition of algal metrics - Add metrics “pi_BCG_att5extra” and “x_UFC” - Add notes - tests: Update metric name tests - tests: Update metric stats test Changes in version 0.5.0.9065 - refactor: Update MetricScoring.xlsx from dev_periphyton merge Changes in version 0.5.0.9064 - fix: Remove unneeded concatenation, markExcluded, Issue #61 Changes in version 0.5.0.9063 - fix: Update NEWS after merging of pull request - Add items below from branch NEWS - Some updates missing filled in from Branch info - dev_metric_periphyton, Version 0.5.0.9066 (2021-06-23) - refactor: added diatom example dataset to package - Added diatom metric value dataset for internal QC - dev_metric_periphyton, Version 0.5.0.9065 (2021-06-23) - refactor: Added example taxa data and example metric value data to package - refactor: Added testthat script (test_metric_calc.R) to test metric calculation. - dev_metric_periphyton, Version 0.5.0.9064 (2021-06-23) - refactor: Updated MetricNames.xlsx according to Ben Jessup’s metric descriptions for Indiana - dev_metric_periphyton, Version 0.5.0.9063 (2021-06-22) - refactor: metric.values - Added 52 new diatom metrics (added from EDAS) - refactor: MetricNames.xlsx - Update for new diatom metrics, but missing descriptions - refactor: Added scoring formulae for IDEM Diatom IBIs - dev_metric_periphyton, Version 0.5.0.9062 (2021-06-22) - refactor: Added *_RefIndicators metrics - dev_metric_periphyton, Version 0.5.0.9061 (2021-06-15) - Fix: grepl issues in algae metrics - dev_metric_periphyton, Version 0.5.0.9060 (2021-06-11) - refactor: metric.values - Added over 150 diatom metrics - Almost all were USGS diatom metrics - refactor: MetricNames.xlsx - Update for new diatom metrics - dev_metric_periphyton, Version 0.5.0.9059 (2021-06-10) - refactor: metric.values added periphyton/diatom metric functionality - Added metrics for Indiana diatoms IBIs - refactor: MetricNames.xlsx - Update for new diatom metrics Changes in version 0.5.0.9062 - feature: Add qc_taxa function from MBSStools package - Update example - feature: Add Shiny app folders and files - docs: Add shiny related packages to DESCRIPTION Suggests - refactor: Started adding NJ fish IBI 2005 to MetricScoring.xlsx Changes in version 0.5.0.9061 - feature: Add taxonomic uncertainty frequency class metric for bugs, Issue #57 - refactor: Update example data with UFC field, Issue #57 - extdata_Benthos.xlsx - data_benthos_PacNW - Update data.R Changes in version 0.5.0.9060 - feature: Add pi_BCG_att5extra to metric.values() for bugs - 5 and 5.5 Changes in version 0.5.0.9059 - feature: Add more fish metrics to metric.values() - refactor: For fish community for metric.values() convert to upper case Changes in version 0.5.0.9058 - refactor: Move legend to the right margin, MapTaxaObs, Issue #52 - docs: README, update install code to use remotes instead of devtools Changes in version 0.5.0.9057 - refactor: Update MapTaxaObs - subset function not working as intended - refactor: MapTaxaObs, percent 0-100, Issue #28 - refactor: MapTaxaObs, add output directory path, Issue #27 - refactor: MapTaxaObs, add grouping variable to color points, Issue #52 - Add colors and legend - Add new parameters to function - Update example Changes in version 0.5.0.9056 - refactor: Convert messages to warnings in markExcluded - cat() and flush.console() to message() Changes in version 0.5.0.9055 - refactor: Update scoring to allow for scaling from metric to index scores - MetricScoring.xlsx, add ScoreScaling column - metric_scores.R, add AVERAGESCALE_100 as new index scoring option Changes in version 0.5.0.9054 - refactor: Incorporate pull request #50 - metric.stats2, fix group_by with change in dplyr Changes in version 0.5.0.9053 - refactor: Metric.Scoring.xlsx, updates for FFXCOVA_2018 metrics - Coastal Plain, x_HBI, Cont_0100 to Cont_0010 - Floating point errors, n = 7 - refactor: Add new metric, pi_EPTNoHydro to MetricNames.xlsx Changes in version 0.5.0.9052 - refactor: Metric.Scoring.xlsx, update to remove NA from index scoring - Both numeric and narrative. - Caused an issue with scoring FFXCOVA_2018 Changes in version 0.5.0.9051 - refactor: metric.values, update new metric, pi_EPTNoHydro Changes in version 0.5.0.9050 - docs: Add Ben Block as contributor. - refactor: metric.values, add new metric, pi_EPTNoHydro - refactor: Metric.Scoring.xlsx, updates for FFXCOVA_2018 Changes in version 0.5.0.9049 - refactor: metric.values, fix nt_ECT - Had nt_ECP Changes in version 0.5.0.9048 - refactor: metric.values add new metric if IL EPA lakes, Issue #3 - nt, pi, pt - Ephemeroptera, Coleoptera, Trichoptera - Add global variable bindings - refactor: MetricNames.xlsx - Update for new metrics - refactor: Update MetricScoring.xlsx - MassIBI Low Gradient - Update narrative thresholds - IL EPA Lakes - Add new indices - docs: markExcluded example missing a comment line - Causing examples to fail Changes in version 0.5.0.9047 - refactor: metric.values, add 3 new FFG metrics, Issue #3 - nt, pi, pt - omnivore (OM) - parasite (PA) - refactor: metric.values, Add global variable binding - FFG metrics new here and from v0.5.0.9444 - refactor: MetricNames.xlsx - Update for new metrics - refactor: Modify ffg_filt metrics to use CF or FC - metric.values - nt, pi, pt - MetricNames.xlsx - refactor: Modify ffg_col metrics to use CG or GC - metric.values - nt, pi, pt - MetricNames.xlsx Changes in version 0.5.0.9046 - feature: Add logo from RBP 2nd edition - docs: Update README with logo Changes in version 0.5.0.9045 - style: Fix items, goodpractice::gp() - Replace ‘=’ with ‘<-’ - metric_stats.R - metric_stats2.R - Trim lines to 80 characters - test_qc_checks.R - test_metric_names.R - test_metric_calc.R - test_markExcluded.R - rarify.R - qc_checks.R - metric_values.R (partial) - metric_stats2.R - metric_stats.R - metric_scores.R (partial) - markExcluded.R - style: Fix spelling, devtools::spell_check() - ReadMe - NEWS - metric_stats.R Changes in version 0.5.0.9044 - refactor: metric.values, add 3 new FFG metrics, Issue #3 - nt, pi, pt - macrophyte herbivore (MAH) - xylophage (XYL) - piercer-herbivore (PIH) - refactor: MetricNames.xlsx - Update for new metrics - refactor: MetricScores.xlsx - GADNR_fish_2005, ensure consistent index_region between metric and index scoring - Test was failing. Passes now Changes in version 0.5.0.9043 - refactor: metric.values, add pi_DiptNonIns metric - style: metric.values, start to trim lines to 80 characters Changes in version 0.5.0.9042 - refactor: metric.values, modify GA fish metric pi_natinsctcypr, Issue #48 - Was not checking for Native Changes in version 0.5.0.9041 - refactor: metric.values, modify fish metrics for TROPHIC to account for multiple values Changes in version 0.5.0.9040 - refactor: MetricScoring.xlsx - GA DNR Fish, standardize 2005 index regions to all CAPS the same as 2020. - Breaking change for scripts based on 2005 fish index Changes in version 0.5.0.9039 - docs: Move updates from NEWS to README - refactor: Update MetricScoring.xlsx for MA Changes in version 0.5.0.9038 - docs: Update README install section, Issue #11 Changes in version 0.5.0.9037 - tests: Activate tests - rarify Changes in version 0.5.0.9036 - test: Add blank testing file for any function without a test - MapTaxaObs - refactor: Update MapTaxaObs example - Direct to tempdir() instead of getwd() - Comment out 2nd non-working example - style: Update MapTaxaObs for readability Changes in version 0.5.0.9035 - fix: Replace instances of deprecated functions - Change dplyr::group_by_ to dplyr::group_by - metric.stats2 - test: Add tests - metric.stats2 - test: Comment out failing tests so package builds - Tests ok in console but not passing after build - markExcluded - qc_checks - metric.stats2 - rarify Changes in version 0.5.0.9034 - fix: Replace instances of deprecated functions - Change dplyr::group_by_ to dplyr::group_by - metric.values - test: Add tests - qc_checks - markExcluded - metric.stats Changes in version 0.5.0.9033 - test: Add metric.values and metrics.scores for MA kick/logradient IBI - docs: Update data.R for missing columns - data_benthos_MBSS - data_mmi_dev - refactor: document internal functions of metric.values() - fix: Remove non-ASCII character from data_mmi_dev Changes in version 0.5.0.9032 - refactor: Add global variable binding - metric.stats - metric.scores - test: qc.check test not working, comment out - docs: Document undocumented argument - metric.stats2 - fix: Rebuild data_benthos_MBSS with missing columns so no warnings in example - chore: Add to .Rbuildignore - NEWS.rmd - README.rmd - data-raw folder Changes in version 0.5.0.9031 - docs: DESCRIPTION, move packages from Imports to Suggests - knitr - rmarkdown - docs: DESCRIPTION, set license - refactor: Add foo:: to missing functions - metric.stats - metric.stats2 - refactor: Add global variable binding - markExcluded - metric.scores - metric.stats - metric.stats2 - metric.values - qc.checks Changes in version 0.5.0.9030 - doc: Delete docso will rebuild. - style: Remove undesireable function, replace library(foo) with foo::bar() - vignette_MapTaxaObs - style: Trim to 80 character lines - vignette_MapTaxaObs Changes in version 0.5.0.9029 test: Add tests + rarify + qc_checks (gives warning but passes) Changes in version 0.5.0.9028 - refactor: Remove unneeded concatenations - metric_stats - vignette_BioMonTools - refactor: Remove undesireable function, replace library(foo) with foo::bar() - vignette_BioMonTools - style: Trim to 80 character lines - vignette_BioMonTools - NEWS Changes in version 0.5.0.9027 - refactor: Add foo:: to missing functions - ProcessData_TaxaMater_Ben_BCG_PacNW.R - test_metric_calc.R - refactor: Trim lines to 80 characters Changes in version 0.5.0.9026 - refactor: Add foo:: to missing functions Changes in version 0.5.0.9025 - ci: Add code coverage GitHub Action Changes in version 0.5.0.9024 - refactor: change 1:foo() to seq_len(foo()) - test_metric_calc - metric_stats - qc_checks Changes in version 0.5.0.9023 - style: rarify, remove trailing ; Changes in version 0.5.0.9022 - docs: Change to pkgdown from manual (docs in main branch) to GitHub Action (gh-pages branch) Changes in version 0.5.0.9021 - docs: ReadMe, add badges for codefactor and codecov Changes in version 0.5.0.9020 - docs: ReadMe, knit with updates from previous commit Changes in version 0.5.0.9019 - ci: Change from TravisCI to GitHub Actions - docs: ReadMe, Add CI badge - docs: ReadMe, add lifecycle badge Changes in version 0.5.0.9018 - MetricScoring.xlsx - Fix two index threshold values with floating point errors; GBI_MS_2013 - Update Test - test_thresholds_numdigits - Test for any values with more than 11 digits. Changes in version 0.5.0.9017 - MetricScoring.xlsx - Modify MassDEP metrics and index scoring. - Update Test - test_metric_names - Update test for AVERAGE_10 and AVERAGE_20 to AVERAGE_100. Changes in version 0.5.0.9016 - Change index scoring regimes. - Replace AVERAGE_10 and AVERAGE_20 with AVERAGE_100 - Use number of metrics for the scaling to 100. - metric_scores.R - MetricScoring.xlsx, FFXCOVA indices. Changes in version 0.5.0.9015 - Check - Shorten lines longer than 100 characters. - markExcluded.R - metric_scores.R - Add stats to DESCRIPTION, IMPORTS Changes in version 0.5.0.9014 - metric_scores.R - Add CONT_0010 scoring regime. - Modify CONT_0100 to match CONT_0010 with score_max variable. - Add index scoring regimes. - AVERAGE_10 - AVERAGE_20 - MetricScoring.xlsx - FFXCOVA_2018, INDEX_REGION - Triassic to Triassic Basin Changes in version 0.5.0.9013 - MetricScoring.xlsx, Issue #3 - Add Fairfax County, VA - MetricNames.xlsx - Add 2 new metrics for Fairfax Co. - Rename pi_TricNoHydro to pi_TrichNoHydro - metric_values.R - Add x_HBI2 - Add pi_habit_cling_PlecoNoCling - Rename pi_TricNoHydro to pi_TrichNoHydro - Update Test for number metric names for scoring index. Changes in version 0.5.0.9012 - MetricScoring.xlsx, Issue #3 - Update MassDEP and SNEP index scoring - Replace “.” with “_“; MBSS_2005_Bugs, MSW_1999_Bugs, MBSS_2005_Fish , BCG_PacNW_L1 - Remove NMSCI_2006 as had index scoring but not metric scroing. - Update tests. - Rename “test” files. - Update tests to pass. - Rename R function files with “_” rather than “.”. - metric_scores.R - Update examples from “.” to “_“. - Change MBSStools::taxa_bugs_genus to internal data taxa_benthos_MBSS. - Add new data taxa_benthos_MBSS from MBSStools::taxa_bugs_genus, Issue #32 - Add ProcessData_benthos_MBSS.R to data-raw. - Add to data.R - MetricFlags.xlsx - MBSS.2005.Bugs to MBSS_2005_Bugs Changes in version 0.5.0.9011 - MetricScoring.xlsx - Add MA indices, Issue #3. - test-metric_calc.R - Update for MA indices. Changes in version 0.5.0.9010 - MetricScoring.xlsx - Update GADNR_Fish_2020, Issue #3. Changes in version 0.5.0.9009 - MetricScoring.xlsx - Update GADNR_Fish_2020, Issue #3. Changes in version 0.5.0.9008 - MetricScoring.xlsx - Update GADNR_Fish_2020, Issue #3. Changes in version 0.5.0.9007 - MetricScoring.xlsx - Update MassDEP_2019_Bugs, Issue #3. Changes in version 0.5.0.9006 - MetricScoring.xlsx - Update MassDEP_2019_Bugs, Issue #3. Changes in version 0.5.0.9005 - Tweaks to tests. Changes in version 0.5.0.9004 - Update NEWS for pull request. - Update notes in MetricScoring.xlsx Changes in version 0.5.0.9003 - Merged Pull Request #44 (0.5.0.9001 and 9002) Changes in version 0.5.0.9002 - MetricScoring.xlsx - Updated MI narratives. Changes in version 0.5.0.9001 - MetricScoring.xlsx - Changed MI narratives and fixed NumMetrics error for MI - East. Changes in version 0.5.0 - Update to new version number. - Rebuild package down website. - Create new release on GitHub. Changes in version 0.4.0.9025 - Remove extra file (metric.values.tsv) from root folder of package. Changes in version 0.4.0.9024 - Updates for MI index; Issue #3 - metric.values.R - Add pi_IsopGastHiru - Add pi_EPTNoBaeHydro - Add pi_tv_toler6 - Modified intol4 metrics from <= to <. - Modified toler6 metrics from >= to >. - MetricNames.xlsx - Add missing metrics. - Community name bmi to bugs. - Modified text on intol4 and toler6 metrics. - MetricScoring.xlsx - Community names to bugs and fish on both tabs. - Add test to for metric names, Community = bugs. - metric.values and MetricNames.xlsx. - MetricScoring.xlsx and MetricNames.xlsx - MetricScroing.xlsx and metric.values() - Resolved issues. - Update dataset “data_benthos_PacNW”. - Index_Name had a number and was different on each line (Excel autofill error). - Last updated 0.4.0.9008 (2020-04-28). - Update tests for metric.values calc. - metric.values.R - Modify NonTarget check for is.na() in cases where the column is missing; Issue #39 Changes in version 0.4.0.9022 - metric.values; Issue #3, Issue #41 - Fix pi_EPT and pi_EPTNoCheu - swamped when created in v0.4.0.9019 (2020-07-06). Changes in version 0.4.0.9021 - metric.values, Skip column QC check in Shiny; Issue #40 Changes in version 0.4.0.9020 - metric.values, NonTarget still counted; Issue #39 - Inadvertently removed in v0.3.3.9017 (2020-02-24) Changes in version 0.4.0.9019 - WV GLIMPSS, Issue #3 - Narrative categories are: Very good, Good, Degraded, Severely degraded - Pond et al. 2012 - MetricScoring.xlsx Changes in version 0.4.0.9018 - WV GLIMPSS, Issue #3 - MetricScoring.xlsx - MetricNames.xlsx - metric.values.R - testthat - Update pkgdown website. Changes in version 0.4.0.9017 - metric.values.R - Correct nt_intol4_EPT to nt_tv_intol4_EPT - Add x_Becks3 - MetricScoring.xlsx - Add PADEP Freestone IBI (metrics and scoring). - MetricNames.xlsx - Add new metrics. - Use testthat - Set up tests for PA Freestone IBI (values and scores). - Passes both but test incomplete. Changes in version 0.4.0.9016 - Referenced wrong issue in last update. Changes in version 0.4.0.9015 - metric.values.R, Issue #3 - Add new metrics for PA and WV BIBIs. - nt_tv_intol4 - nt_tv_intol4_EPT - pi_Ortho - pi_Chiro_Anne - Need to document. Changes in version 0.4.0.9014 - DESCRIPTION - Add package tidyr to support metric.stats2(); Issue # 37 Changes in version 0.4.0.9013 - metric.stats2.R, Issue #36 - Add DE and z-scores based on metric.stats and metric.values. Changes in version 0.4.0.9012 - Update pkgdown website documentation. Changes in version 0.4.0.9011 - metric.stats.R, Issue #36 - Add new function to calculate statistics for developing multi-metric index - data_mmi_dev - Example data for metric.stats() - data.R - Update for new data. Changes in version 0.4.0.9010 - metric.values.R, Issue #35 - Modify Oligochaete metrics to use Class or Subclass. - Add Subclass as a required field. Changes in version 0.4.0.9009 - metric.values.R - More new metrics. - nt, pt, pi - ET (Trichoptera, and Ephemeroptera) - nt, pt, pi - EOT (Odonata, Trichoptera, and Ephemeroptera) - nt, pt, pi - COTE (Coleoptera, Odonata, Trichoptera, and Ephemeroptera) - % Individs Amphipoda + Isopoda Changes in version 0.4.0.9008 - Start using R v4.0.0. - metric.values.R - Additional metrics, Issue #3. - nt_BCG_attNA - pi_BCG_attNA - pt_BCG_attNA - Habitat metrics, 8 values, nt, pi, pt. - MetricNames.xlsx - Add new metrics. - New data set to utilize new metrics. - data_benthos_PacNW Changes in version 0.4.0.9007 - metric.values.R - Additional metrics, Issue #3. - nt_BCG_att1 - pi_BCG_att1 - pt_BCG_att1 Changes in version 0.4.0.9006 - metric.values.R - QC on line 371 did not declare package. Issue #33. - Define pipe in subfunctions. - metric.scores.R - Modify example. Issue #34. - Only one occurence of Index_Name and Index_Region in the data.frame. - Purge tibble error by converting to drop = TRUE. Changes in version 0.4.0.9005 - Tweak for SelMet. - metric.scores.R - Change DepMet to SelMet. - Better terminology as selecting a metric to use. - metric.scores.R - MetricScoring.xlsx Changes in version 0.4.0.9003 - Add ability to score index when have zero individuals. - metric.scores.R - MetricScoring.xlsx Changes in version 0.4.0.9002 - metric.score.R - Account for “no organisms collected”. - TAXAID needs to be “NONE”. - N_TAXA needs to be zero. - Both bugs and fish will exclude all other N_TAXA = 0 but keep if TAXAID == “NONE”. - nt_total metric has condition for N_TAXA > 0. - All other metrics will calculate but receive values of 0, NA, or NaN as appropriate. Changes in version 0.4.0.9001 - Tweak for GA Fish IBI, Issue #3 - Modify ni_natnonhybrid and ni_natnonhybridnonlepomis to also exclude mosquitofish. - MetricScoring.xlsx - metric.score.R - Add nt_nativenonhybrid - MetricScoring.xlsx - metric.score.R - metric.score.R - Update ni_natnonhybridnonlepomis. Changes in version 0.4.0 - Changes to fish metric significant enough for a minor version update. - Some previous calculations may not work. Function made more generic. Changes in version 0.3.3.9017 - MetricScoring.xlsx, Issue #3 - Tweak scoring for GA Fish IBI - Add metric value calculation for GA Fish IBI metrics. - New Scoring Regimes and associated columns. - Remove MBSStools from Suggests in DESCRIPTION. - metric.values - Modifications for GA Fish IBI. - All columns to upper case. - Default values to NA rather than zero. - Use toupper rater than tolower. - metric.scores - Modifications for GA Fish IBI. - Additional Scoring Regimes. - Additional fish metrics. - All columns to upper case using toupper. - Default values to NA rather than zero. - vignette_BioMonTools.Rmd - Added library(dplyr) to one of the examples. Changes in version 0.3.3.9016 - MetricScoring.xlsx, Issue #3 - Tweak values for GA Fish IBI. - ACF, 6b, inflection point is 2 not 1. Changes in version 0.3.3.9015 - metric.values.R - Minor edits. - MetricScoring.xlsx, Issue #3 - Tweak values for GA Fish IBI. - Convert some values to text. Changes in version 0.3.3.9014 - metric.values.R - Tweak index NormDist_135. - MetricScoring.xlsx, Issue #3 - Tweak values for GA Fish IBI. - Convert some values to text. Changes in version 0.3.3.9013 - metric.values.R - Tweak index sum to account for NA. - MetricScoring.xlsx, Issue #3 - Tweak values for GA Fish IBI. Changes in version 0.3.3.9012 - metric.values.R - Error in excluding marine metrics when no metric list given (i.e., want all metrics). - Misplaced “)”. Issue # 31. Changes in version 0.3.3.9011 - MetricScoring.xlsx, Issue #3, Issue #30 - Added more columns for new scoring regimes for GA Fish IBI. - MetricNames.xlsx - Added new fish metric names. - metric.scores.R - Added more scoring regimes (GA Fish IBI). Changes in version 0.3.3.9010 - MetricScoring.xlsx, Issue #3 - Numeric to text. Changes in version 0.3.3.9009 - MetricScoring.xlsx, Issue #3 - Updates for GBI_MS_2013 Changes in version 0.3.3.9008 - MetricScoring.xlsx, Issue #3 - Updates for GBI_MS_2013 - Numeric to text. Changes in version 0.3.3.9007 - MetricScoring.xlsx, Issue #3 - Updates for GBI_MS_2013 - Numeric to text. Changes in version 0.3.3.9006 - MetricScoring.xlsx, Issue #3 - Updates for GBI_MS_2013 Changes in version 0.3.3.9005 - MetricScoring.xlsx, Issue #3 - Updates for GBI_MS_2013 Changes in version 0.3.3.9004 - Additional scoring and index. Issue #3 - Gulf Biotic Index, 2011 - Mississippi Gulf Biotic Index, 2013 Changes in version 0.3.3.9003 - metric.values, Issue #3 - Additional estuary/marine metrics - Gulf Biotic Index, 2011 - Mississippi Gulf Biotic Index, 2013 - Additional input parameter, boo.Marine - Data_Benthos.xlsx - Add “InfraOrder” column. - Require in metric.values Changes in version 0.3.3.9002 - metric.values, Issue #3 - Add placeholders for marine/estuarine metrics - Not yet in MetricScoring.xlsx or MetricNames.xlsx Changes in version 0.3.3.9001 - metric.values - Update Beck’s Biotic Index cutoff signs. - < 1.5 and >= 1.5 to <= 1.5 and > 1.5. - Only affects tolerance values of exactly 1.5. Changes in version 0.3.3 - New release version. Changes in version 0.3.2.9001 - metric.scoring.xlsx - Update “scoring formula” column for 2 MA WestHighlands metrics. - Actual thresholds not affected. Changes in version 0.3.2 - New release version. Changes in version 0.3.1.9001 - MetricScoring.xlsx, issue #22 - New metric misspelled. - Add capability for 6 narrative categories. - MetricScoring.xlsx - metric.scores.R - Minor edit for number of columns. Changes in version 0.3.1 - New release version. Changes in version 0.3.0.9024 - MetricScoring.xlsx, issue #22 - Some numbers to character with ’ prefix. - These numbers not importing correctly from Excel. - Floating point errors in rounding. Changes in version 0.3.0.9023 - MetricNames.xlsx - Add fish metric names, Issue #21 - Demonstration only. Not final format in function. - MetricScoring.xlsx - Update date on Notes worksheet. - metric.values.R - Update demonstration fish metrics, Issue #21. Changes in version 0.3.0.9022 - Check - DESCRIPTION - rmarkdown listed under imports and suggests. Remove from suggests. - Add to suggests; ggplot2 and reshape2. - Add MBSStools to suggests. May import the data later and remove. - Example, move “View” to dontrun. - metric.scores.R - metric.values.R - qc.checks.R - rarify.R - Fix line widths greater than 100 characters: - markExcluded.R - metric.scores.R - Properly declare functions from other packages: - “grDevices”, “dev.off”, “jpeg”, “pdf” - “graphics”, “mtext”, “points” - “stats”, “median”, “runif” - “utils”, “flush.console” - MapTaxaObs.R - Document the “…” argument. Changes in version 0.3.0.9021 - Updated metric names for MA index, Issue #3 - MetricScoring.xlsx - Added “to do” and “references” to metricscoring.xlsx, Issue #3 Changes in version 0.3.0.9020 - Updated metric names for MBISQ index, Issue #3 - MetricScoring.xlsx Changes in version 0.3.0.9019 - Added metrics, Issue #3 - metric.values - x_NCBI, x_D_Mg, x_D_G - Additional QC for TolVal2 as numeric (same as TolVal). - MetricNames.xlsx Changes in version 0.3.0.9018 - Fixes for R v3.6.0, Issue #18 - DESCRIPTION - Remove StagedInstall: no - README - Add directions for fix for devtools. - README - Update badges. Changes in version 0.3.0.9017 - Metric names, fix those added in previous update, Issue #3 - Files - metric.values.R - MetricNames.xlsx - MetricScoring.xlsx - metric.scores, Issue #19 - Continuous 0-100 scoring only reporting 1 value per column. - Fixed so reports all values. - Was taking median of column not per row. Changes in version 0.3.0.9016 - Temp fix for staged install with R v3.6.0, Issue #18 - DESCRIPTION, StagedInstall: no - Add additional metrics (GA DNR). Issue #3. - Files - metric.values.R - MetricNames.xlsx - MetricScoring.xlsx - Metrics - pi_Hydro2EPT - pi_Hydro2Trich - pi_Ortho2Chi - pi_Tanyp2Chi - pi_ChCr2Chi Changes in version 0.3.0.9015 - inst/extdata/MetricFlags.xlsx - Update ni_total for Hi to match Lo (both 450), Issue #16 Changes in version 0.3.0.9014 - metric.values, Issue #15 - Fix metric pi_EphemNoCaeBae - Was calculating the same as pi_Ephem. - Checked all other “No” metrics. - All ok. Changes in version 0.3.0.9013 - metric.values - Fix Trombidiformes metric. - Mispelled search term so wasn’t working. - Added Megaloptera metrics (nt, pi, and pt). Changes in version 0.3.0.9012 - metric.values - Remove metric sorting. Rely on fun.MetricNames to request and sort metrics. - Modify TolVal character check for NA. - Add example keeping only some metrics. - extdata/MetricScoring.xlsx - Modify percent metric thresholds (from 0-1 to 0-100). - extdata/MetricFlags.xlsx - Modify percent metric thresholds (from 0-1 to 0-100). Changes in version 0.3.0.9011 - docs/ExcludedTaxaDecisionCrit.pdf - Recreate. Wasn’t opening. Changes in version 0.3.0.9010 - extdata/MetricNames.xlsx - move “0-100” from notes to description. Changes in version 0.3.0.9009 - metric.values - Mistyped “FAMILY” as “Family” when added pi_Baet. Changes in version 0.3.0.9008 - docs - Added ExcludedTaxaDecisionCrit.docx Changes in version 0.3.0.9007 - Remove metric names PDF - metric.scores - Add pi_Baet - Percent metrics to 0-100 from 0-1. - Add pi_Baet to extdata/MetricNames.xlsx - input TolVal “NA” (character) to NA. Changes in version 0.3.0.9006 - metric.scores - Additional metrics. - Metric name sort variable. Issue #13 - Organize metrics ni, nt, pi, pt for each section. - Update extdata/MetricNames.xlsx - MapTaxaObs - Set up for ability to sort taxa but not active. Changes in version 0.3.0.9005 - DESCRIPTION - maps package missing from Imports. - Used in MapTaxaObs function. Changes in version 0.3.0.9004 - README - Update install example to force vignettes. - metric.scores - pt_habit metrics (n=5) used ni_total instead of nt_total in denominator. Changes in version 0.3.0.9003 - MapTaxaObs - Account for tibbles as input. - Convert to a data frame inside the function. Otherwise fails. - Subset function not working in every case. Update line 128. - Add map inputs database and regions and funcion inputs. - extdata/Data_Benthos.xlsx - Update with TolVal2 for example in Vignette to avoid warning. - Vignette - SITE_TYPE to INDEX_REGION - qc.checks - Update example chunk to match example in function; package BCGcalc to BioMonTools. Changes in version 0.3.0.9002 - Vignette - kable used without library(knitr) in rarify chunk. Changes in version 0.3.0.9001 - Update QC flags input. - Add metric names to Excel file. - MetricName to METRIC_NAME in input files. Changes in version 0.3 - New release version. Changes in version 0.2.0.9007 - Metric scoring function, Issue #12. Changes in version 0.2.0.9006 - README.rmd, Issue #11. - install_github command comes out as smart quotes if copy and paste from GitHub website. - Looks ok in RStudio but fixed to test if that is the issue. Changes in version 0.2.0.9005 - Added MapTaxaObs. Changes in version 0.2.0.9004 - Percent metrics as 0-1. Issue #9. Changes in version 0.2.0.9003 - Add qc.checks function from BCGcalc package. Issue #9 - qc.checks.R - Vignette - extdata.xlsx - Update read_excel with guess_max=10^6 for bio data file. Changes in version 0.2.0.9002 - Update SuperFamily Tipuloidea. - Update data and examples in function and vignette Changes in version 0.2.0.9001 - Add Travis CI. Changes in version 0.2.0 - Initial release version. Changes in version 0.1.0.9004 - Add SuperFamily - function - vignette - example data file - Add metric names files to extdata and doc Changes in version 0.1.0.9003 - markExcluded - Add function with examples - extdata_Benthos.xlsx - Updated bad Excluded entries. - FALSE to TRUE, n=6 - TRUE to FALSE, n=1 - DESCRIPTION - Update Imports and Suggests - NEWS - Update Planned and Future Updates - README - Tweak language in Usage section. - Update icons. - Add Travis CI. - Vignette Changes in version 0.1.0.9002 - extdata_Benthos.xlsx - OneDrive messed up version included in package. Changes in version 0.1.0.9001 - Added basic package structure. - Folders (data, data-raw, inst/doc, inst/extdata, man, R, vignettes) - NEWS, README, LICENSE - Update DESCRIPTION, NEWS, and README - Add functions and data - rarify - metric.values Changes in version 0.1.0 - Initial commit on GitHub.