NEWS

Erik.Leppo@tetratech.com

#> Last Update: 2025-10-06 14:15:45.452906

Version History

Changes in version 1.2.4 (2025-10-06)

• refactor: Bump version number for CRAN

Changes in version 1.2.3.9008 (2025-10-06)

• 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 (2025-10-06)

• refactor: Remove or edit examples with errors, warnings, or long run times
  • metric.scores
  • metric.values

Changes in version 1.2.3.9006 (2025-10-03)

• fix: Remove non-portable command from example
  • rarify

Changes in version 1.2.3.9005 (2025-10-03)

• fix: Fix typo in example
  • rarify

Changes in version 1.2.3.9004 (2025-10-03)

• 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 (2025-10-03)

• 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 (2025-09-22)

• 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 (2025-09-11)

• 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 (2025-09-10)

• docs: Bump version for CRAN submission

Changes in version 1.2.2.9001 (2025-09-10)

• 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 (2025-09-10)

• docs: Bump version for CRAN submission

Changes in version 1.2.1.9001 (2025-09-10)

• 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 (2025-09-10)

• docs: Bump version number for submission to CRAN

Changes in version 1.2.0.9001 (2025-09-10)

• 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 (2025-09-10)

• docs: Bump version number for submission to CRAN, Issue #49
• docs: Update README for install from CRAN

Changes in version 1.1.0.9005 (2025-09-10)

• 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 (2025-09-09)

• 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 (2025-09-09)

• 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 (2025-09-09)

• refactor: Remove large file, Issue #49

Changes in version 1.1.0.9001 (2025-09-09)

• 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 (2025-09-09)

• 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 (2025-09-08)

• 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 (2025-09-05)

• 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 (2025-09-05)

• refactor: Update metric.values() for global variables, Issue #49

Changes in version 1.0.2.9077 (2025-06-19)

• refactor: Add new metrics for ORWA, Issue #121

Changes in version 1.0.2.9076 (2025-06-13)

• 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 (2025-06-12)

• refactor: Add new metrics for GP, Issue #118

Changes in version 1.0.2.9074 (2025-06-05)

• refactor: Update MetricScoring.xlsx to fix metric scoring directionality for MIEGLE

Changes in version 1.0.2.9073 (2025-04-04)

• 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 (2025-04-04)

• feature: Added Exclude feature to metric calculation in Shiny

Changes in version 1.0.2.9071 (2025-02-26)

• refactor: Add parameters to BioMonTools::taxa_translation in Shiny
  • trim_ws = TRUE
  • match_caps = TRUE

Changes in version 1.0.2.9070 (2025-02-26)

• 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 (2025-02-25)

• refactor: Add taxa translation for RMN to Shiny
• docs: Add shinyalert to DESCRIPTION Suggests

Changes in version 1.0.2.9068 (2025-02-10)

• refactor: Add metrics, bugs
  • MS, Issue #116
  • habit and habitat, Issue #117

Changes in version 1.0.2.9067 (2024-11-20)

• refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2
  • MetricNames.xlsx
  • metric_values.R

Changes in version 1.0.2.9066 (2024-11-07)

• refactor: Add fish metric permutations of non-native
  • MetricNames.xlsx
  • metric_values.R

Changes in version 1.0.2.9065 (2024-11-06)

• 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 (2024-11-06)

• refactor: Add new fish metric (pi_BCG2_att1234b)
  • MetricNames.xlsx
  • metric_values.R

Changes in version 1.0.2.9063 (2024-11-06)

• docs: Update comment about NATIVE in metric.values help

Changes in version 1.0.2.9062 (2024-11-06)

• 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 (2024-11-05)

• 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 (2024-11-05)

• refactor: Add new fish metrics (nt_, pi_, and pt_) for invertivore
  • MetricNames.xlsx
  • metric_values.R

Changes in version 1.0.2.9059 (2024-11-01)

• refactor: Update search patterns for some fish trophic metrics
  • IV
  • TC

Changes in version 1.0.2.9058 (2024-11-01)

• 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 (2024-10-30)

• refactor: Add new metric for MN, nt_total_ExclSchool
  • metric_values.R
  • MetricNames.xlsx

Changes in version 1.0.2.9056 (2024-10-29)

• 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 (2024-03-18)

• fix: made changes to coral metrics
  • added test for Florida BCG

Changes in version 1.0.1.9501 (2024-03-07)

• update: Added coral metrics, specifically for FL BCG
  • metric_values.R
  • MetricNames.xlsx

Changes in version 1.0.0.9066 (2024-03-05)

• refactor: Additional metrics for Great Plains BCG, Issue #106
  • metric_values.R
  • MetricNames.xlsx

Changes in version 1.0.0.9065 (2024-02-22)

• 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 (2024-02-21)

• 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 (2024-02-15)

• 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 (2024-01-26)

• 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 (2024-01-26)

• 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 (2024-01-10)

• refactor: Add ni_total flags (small and large) for MN_IBI_Bugs, Issue #92
  • MetricFlags.xlsx

Changes in version 1.0.0.9059 (2024-01-09)

• 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 (2023-12-14)

• 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 (2023-12-12)

• refactor: Add testing (QC) to metric.values fish calc section

Changes in version 1.0.0.9056 (2023-12-11)

• 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 (2023-12-08)

• 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 (2023-12-08)

• 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 (2023-12-08)

• refactor: More edits to metric.values fish calc for error in Red Lakes Shiny app

Changes in version 1.0.0.9052 (2023-12-08)

• refactor: Edit metric.values fish calc for error in Red Lakes Shiny app

Changes in version 1.0.0.9051 (2023-12-08)

• 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 (2023-12-06)

• refactor: Update MetricNames.xlsx with recent name changes

Changes in version 1.0.0.9049 (2023-12-06)

• refactor: Change names of trout metrics in metric.values
  • Better reflects contents of metrics

Changes in version 1.0.0.9048 (2023-12-06)

• refactor: Add pi_trout to metric.values

Changes in version 1.0.0.9047 (2023-12-06)

• 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 (2023-12-05)

• fix: metric.values boo.shiny code updated to match bugs and algae

Changes in version 1.0.0.9045 (2023-12-05)

• refactor: metric.values specify parameters for subfunctions

Changes in version 1.0.0.9044 (2023-12-05)

• fix: Update metric, nt_BCG_att55a6, Issue #92
  • add ‘na.rm = TRUE’

Changes in version 1.0.0.9043 (2023-11-21)

• fix: Add missing metric, nt_BCG_att55a6, Issue #92

Changes in version 1.0.0.9042 (2023-11-20)

• refactor: Fix BCG_att1236sp fish metrics, pi and pt
  • Remove nt

Changes in version 1.0.0.9041 (2023-11-20)

• 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 (2023-11-20)

• 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 (2023-10-24)

• feature: Add taxaid_dni parameter to metric.values, Issue #96

Changes in version 1.0.0.9038 (2023-10-20)

• refactor: Modify output of taxa_translate function, Issue #94
  • taxatrans$taxatrans_unique

Changes in version 1.0.0.9037 (2023-10-20)

• feat: Add new metric, ni_totalNoDeca, Issue #94
• style: Add spaces to code for readability

Changes in version 1.0.0.9036 (2023-09-25)

• fix: Update Cheumatopsyche metrics in MetricNames.xlsx, Issue #93
  • pi_Cheu
  • pi_EPTNoCheu

Changes in version 1.0.0.9035 (2023-09-25)

• fix: Update code for Cheumatopsyche metrics, metric_values.R, Issue #93
  • pi_Cheu
  • pi_EPTNoCheu

Changes in version 1.0.0.9034 (2023-08-11)

• fix: BioMonTools vignette change reference to metric names
  • corecold changed to stenocold

Changes in version 1.0.0.9033 (2023-08-11)

• fix: Fill in missing Vignette Builder for vignette_NewIndex

Changes in version 1.0.0.9032 (2023-08-10)

• fix: Add line for “changed” taxa in taxa_translate

Changes in version 1.0.0.9031 (2023-07-28)

• fix: Update domX calculations to combine taxa before calculate in metric_values
  • bugs and fish

Changes in version 1.0.0.9030 (2023-07-28)

• refactor: Update metrics for MN BCG, Issue #92
  • In myDF remove NA for specialized dom01 calculations

Changes in version 1.0.0.9029 (2023-07-28)

• refactor: Update metrics for MN BCG, Issue #92

Changes in version 1.0.0.9028 (2023-07-26)

• refactor: Add percent Cheumatopsyche metric

Changes in version 1.0.0.9027 (2023-07-12)

• refactor: Additional metrics for MN BCG, Issue #92

Changes in version 1.0.0.9026 (2023-07-12)

• refactor: Add bug metrics for MN BCG, Issue #92
• style: Update spacing in test file metric_names

Changes in version 1.0.0.9025 (2023-05-26)

• refactor: Update MetricFlags.xlsx for MTTI index

Changes in version 1.0.0.9024 (2023-05-26)

• refactor: Update metric.values MTTI subset metrics, Issue #90

Changes in version 1.0.0.9023 (2023-05-26)

• refactor: Update MetricFlags.xlsx for MTTI index

Changes in version 1.0.0.9022 (2023-05-25)

• 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 (2023-02-02)

• 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 (2023-02-02)

• 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 (2023-01-23)

• 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 (2023-01-20)

• refactor: Update MetricNames.xlsx groupings
  • Added “Experimental”

Changes in version 1.0.0.9017 (2023-01-20)

• feature: Add unique taxa crosswalk to output of taxa_translate

Changes in version 1.0.0.9016 (2023-01-16)

• test: Add test for multiple stages for taxa_translate

Changes in version 1.0.0.9015 (2023-01-09)

• fix: Turn off QC testing in function assign_indexclass
  • Was using test data instead of user input

Changes in version 1.0.0.9014 (2022-12-23)

• docs: Update taxa_translate example files

Changes in version 1.0.0.9013 (2022-12-20)

• 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 (2022-12-20)

• 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 (2022-12-19)

• tests: Create tests for taxa_translate, Issue #81

Changes in version 1.0.0.9010 (2022-12-16)

• 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 (2022-12-13)

• fix: Update taxa_translate for when sum taxa, Issue #81
• update: Revise taxa_translate files in extdata

Changes in version 1.0.0.9008 (2022-12-13)

• 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 (2022-12-13)

• 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 (2022-12-12)

• refactor: Change internal parameter boo_DEBUG to boo_DEBUG_tt in taxa_translate, Issue #81

Changes in version 1.0.0.9005 (2022-12-12)

• refactor: Make taxa_translate as an export object, Issue #81

Changes in version 1.0.0.9004 (2022-12-02)

• fix: Updated taxa_translate function to include metadata as parameter, Issue #81

Changes in version 1.0.0.9003 (2022-12-01)

• feature: Add taxa_translate function, Issue #81
  • More general than qc_taxa

Changes in version 1.0.0.9002 (2022-11-17)

• fix: Update markExclude to avoid dplyr deprecation warnings, Issue #51

Changes in version 1.0.0.9001 (2022-11-16)

• 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 (2022-11-15)

• feat: New function assign_IndexClass, Issue #82
  • Add IndexClass.xlsx to ext folder

Changes in version 0.5.0.9126 (2022-11-11)

• 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 (2022-11-10)

• fix: Update and add some metrics
  • metric_values.R
  • MetricNames.xlsx

Changes in version 0.5.0.9124 (2022-11-08)

• fix: Tweak secondary metric name in MetricScoring.xlsx
  • GA_DNR_Fish_2020

Changes in version 0.5.0.9123 (2022-11-03)

• 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 (2022-09-29)

• 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 (2022-09-27)

• 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 (2022-09-22)

• fix: Update bug thermal metrics, Issue #78

Changes in version 0.5.0.9119 (2022-06-09)

• 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 (2022-06-03)

• fix: Hemiptera metrics (nt and pt) not working, Issue #74
  • Fix spelling

Changes in Version 0.5.0.9117 (2022-05-31)

• refactor: Additional metrics, Issue #74
• fix: Change metric HabitatStruct from RW to RM, Issue #73

Changes in Version 0.5.0.9116 (2022-05-18)

• 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 (2022-04-08)

• refactor: Change variable classes in metric.scores()
  • Avoid errors in import via read_excel

Changes in Version 0.5.0.9114 (2022-03-30)

• 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 (2022-03-28)

• 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 (2022-03-22)

• 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 (2022-03-04)

• fix: Restore extdata.xlsx
  • Deleted in v0.5.0.9109, last mod was v0.5.0.9100

Changes in Version 0.5.0.9110 (2022-03-02)

• 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 (2022-02-22)

• refactor: Additional output messages to screen in metric.values()

Changes in Version 0.5.0.9108 (2022-02-22)

• 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 (2022-02-21)

• 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 (2022-02-21)

• 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 (2022-02-18)

• refactor: Tweak error checking for bugs in metric.values()

Changes in Version 0.5.0.9104 (2022-02-18)

• refactor: Tweak error checking for bugs in metric.values()

Changes in Version 0.5.0.9103 (2022-02-18)

• refactor: Tweak error checking for bugs in metric.values()

Changes in Version 0.5.0.9102 (2022-02-18)

• 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 (2022-02-18)

• 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 (2022-02-11)

• refactor: Add new metric to MetricNames.xlsx

Changes in Version 0.5.0.9099 (2022-02-11)

• 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 (2022-02-07)

• refactor: Modify debugging messages to metric.values() for Shiny log

Changes in Version 0.5.0.9097 (2022-02-07)

• refactor: Add debugging messages to metric.values()

Changes in Version 0.5.0.9096 (2022-02-07)

• fix: Update metric.values() for input data missing Index_Name and Index_Region

Changes in Version 0.5.0.9095 (2022-02-04)

• 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 (2022-02-03)

• refactor: Update metvalgrpxl() for blank cells hiding text to left

Changes in Version 0.5.0.9093 (2022-02-03)

• fix: Update to changes in metric.values()

Changes in Version 0.5.0.9092 (2022-02-03)

• fix: Remove redundant code in metric.values()
  • Causing failures on Shiny.io with missing required columns

Changes in Version 0.5.0.9091 (2022-02-03)

• refactor: Update metvalgrpxl() to use input parameter for groupings

Changes in Version 0.5.0.9090 (2022-02-02)

• 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 (2022-02-01)

• refactor: Edits to help pages in Shiny app
  • Update links to download files

Changes in Version 0.5.0.9088 (2022-02-01)

• 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 (2022-01-12)

• fix: Correct spelling of file name in global.R
  • ShinyApps.io is Linux and is case-sensitive

Changes in Version 0.5.0.9086 (2022-01-12)

• 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 (2022-01-10)

• docs: Update GitHub default branch from “master” to “main”

Changes in Version 0.5.0.9083 (2022-01-10)

• 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 (2022-01-03)

• 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 (2021-12-22)

• 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 (2021-12-22)

• 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 (2021-12-22)

• feature: Update Shiny app, all functions working, Issue #67

Changes in Version 0.5.0.9078 (2021-12-21)

• feature: Add Shiny app, basic outline only, Issue #67

Changes in Version 0.5.0.9077 (2021-12-16)

• refactor: Allow for mixed case in bug metric phylo metrics, Issue #65

Changes in Version 0.5.0.9076 (2021-12-15)

• 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 (2021-12-13)

• 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 (2021-12-10)

• 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 (2021-12-10)

• 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 (2021-12-09)

• refactor: Update thermal metric default values, Core-Cold to CoreC
  • metric.values()
  • data_benthos_PacNW

Changes in Version 0.5.0.9071 (2021-12-09)

• fix: metric.values() thermal indicator metric not correct
  • nt_ti_corecold_cold
  • pt_ti_corecold_cold

Changes in Version 0.5.0.9070 (2021-12-09)

• fix: metric.values() thermal indicator NA metric not correct
  • Using wrong column (Habitat) to find NA

Changes in Version 0.5.0.9069 (2021-11-19)

• fix: metric.values() not working for new metrics, Issue #62
  • Elevation, Gradient, and WSArea

Changes in Version 0.5.0.9068 (2021-11-18)

• 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 (2021-11-18)

• 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 (2021-11-02)

• 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 (2021-11-01)

• refactor: Update MetricScoring.xlsx from dev_periphyton merge

Changes in Version 0.5.0.9064 (2021-11-01)

• fix: Remove unneeded concatenation, markExcluded, Issue #61

Changes in Version 0.5.0.9063 (2021-11-01)

• 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 (2021-09-23)

• 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 (2021-09-09)

• 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 (2021-07-30)

• feature: Add pi_BCG_att5extra to metric.values() for bugs
  • 5 and 5.5

Changes in Version 0.5.0.9059 (2021-07-30)

• 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 (2021-05-21)

• 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 (2021-05-19)

• 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 (2021-05-18)

• refactor: Convert messages to warnings in markExcluded
  • cat() and flush.console() to message()

Changes in Version 0.5.0.9055 (2021-05-14)

• 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 (2021-05-13)

• refactor: Incorporate pull request #50
  • metric.stats2, fix group_by with change in dplyr

Changes in Version 0.5.0.9053 (2021-05-10)

• 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 (2021-05-10)

• 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 (2021-05-10)

• refactor: metric.values, update new metric, pi_EPTNoHydro

Changes in Version 0.5.0.9050 (2021-05-10)

• 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 (2021-04-15)

• refactor: metric.values, fix nt_ECT
  • Had nt_ECP

Changes in Version 0.5.0.9048 (2021-04-14)

• 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 (2021-04-08)

• 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 (2021-04-06)

• feature: Add logo from RBP 2nd edition
• docs: Update README with logo

Changes in Version 0.5.0.9045 (2021-04-01)

• 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 (2021-03-31)

• 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 (2021-03-22)

• refactor: metric.values, add pi_DiptNonIns metric
• style: metric.values, start to trim lines to 80 characters

Changes in Version 0.5.0.9042 (2021-03-14)

• refactor: metric.values, modify GA fish metric pi_natinsctcypr, Issue #48
  • Was not checking for Native

Changes in Version 0.5.0.9041 (2021-02-26)

• refactor: metric.values, modify fish metrics for TROPHIC to account for multiple values

Changes in Version 0.5.0.9040 (2021-02-26)

• refactor: MetricScoring.xlsx
  • GA DNR Fish, standardize 2005 index regions to all CAPS the same as
  • Breaking change for scripts based on 2005 fish index

Changes in Version 0.5.0.9039 (2021-02-23)

• docs: Move updates from NEWS to README
• refactor: Update MetricScoring.xlsx for MA

Changes in Version 0.5.0.9038 (2021-02-22)

• docs: Update README install section, Issue #11

Changes in Version 0.5.0.9037 (2021-01-19)

• tests: Activate tests
  • rarify

Changes in Version 0.5.0.9036 (2021-01-13)

• 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 (2021-01-12)

• 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 (2021-01-12)

• 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 (2021-01-06)

• 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 (2021-01-03)

• 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 (2021-01-03)

• 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 (2021-01-03)

• 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 (2021-01-02)

test: Add tests + rarify + qc_checks (gives warning but passes)

Changes in Version 0.5.0.9028 (2021-01-02)

• 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 (2020-12-29)

• 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 (2020-12-27)

• refactor: Add foo:: to missing functions

Changes in Version 0.5.0.9025 (2020-12-25)

• ci: Add code coverage GitHub Action

Changes in Version 0.5.0.9024 (2020-12-25)

• refactor: change 1:foo() to seq_len(foo())
  • test_metric_calc
  • metric_stats
  • qc_checks

Changes in Version 0.5.0.9023 (2020-12-25)

• style: rarify, remove trailing ;

Changes in Version 0.5.0.9022 (2020-12-25)

• docs: Change to pkgdown from manual (docs in main branch) to GitHub Action (gh-pages branch)

Changes in Version 0.5.0.9021 (2020-12-25)

• docs: ReadMe, add badges for codefactor and codecov

Changes in Version 0.5.0.9020 (2020-12-25)

• docs: ReadMe, knit with updates from previous commit

Changes in Version 0.5.0.9019 (2020-12-25)

• ci: Change from TravisCI to GitHub Actions
• docs: ReadMe, Add CI badge
• docs: ReadMe, add lifecycle badge

Changes in Version 0.5.0.9018 (2020-12-07)

• 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 (2020-12-07)

• 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 (2020-11-30)

• 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 (2020-11-24)

• Check
  • Shorten lines longer than 100 characters.
    • markExcluded.R
    • metric_scores.R
  • Add stats to DESCRIPTION, IMPORTS

Changes in Version 0.5.0.9014 (2020-11-24)

• 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 (2020-11-24)

• 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 (2020-10-28)

• 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 (2020-10-26)

• MetricScoring.xlsx
  • Add MA indices, Issue #3.
• test-metric_calc.R
  • Update for MA indices.

Changes in Version 0.5.0.9010 (2020-10-06)

• MetricScoring.xlsx
  • Update GADNR_Fish_2020, Issue #3.

Changes in Version 0.5.0.9009 (2020-10-06)

• MetricScoring.xlsx
  • Update GADNR_Fish_2020, Issue #3.

Changes in Version 0.5.0.9008 (2020-10-05)

• MetricScoring.xlsx
  • Update GADNR_Fish_2020, Issue #3.

Changes in Version 0.5.0.9007 (2020-09-04)

• MetricScoring.xlsx
  • Update MassDEP_2019_Bugs, Issue #3.

Changes in Version 0.5.0.9006 (2020-09-04)

• MetricScoring.xlsx
  • Update MassDEP_2019_Bugs, Issue #3.

Changes in Version 0.5.0.9005 (2020-08-11)

• Tweaks to tests.

Changes in Version 0.5.0.9004 (2020-08-11)

• Update NEWS for pull request.
• Update notes in MetricScoring.xlsx

Changes in Version 0.5.0.9003 (2020-08-11)

• Merged Pull Request #44 (0.5.0.9001 and 9002)

Changes in Version 0.5.0.9002 (2020-08-10)

• MetricScoring.xlsx
  • Updated MI narratives.

Changes in Version 0.5.0.9001 (2020-08-03)

• MetricScoring.xlsx
  • Changed MI narratives and fixed NumMetrics error for MI - East.

Changes in Version 0.5.0 (2020-07-24)

• Update to new version number.
• Rebuild package down website.
• Create new release on GitHub.

Changes in Version 0.4.0.9025 (2020-07-24)

• Remove extra file (metric.values.tsv) from root folder of package.

Changes in Version 0.4.0.9024 (2020-07-24)

• 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 (2020-07-23)

• 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 (2020-07-06)

• metric.values, Skip column QC check in Shiny; Issue #40

Changes in Version 0.4.0.9020 (2020-07-06)

• metric.values, NonTarget still counted; Issue #39
  • Inadvertently removed in v0.3.3.9017 (2020-02-24)

Changes in Version 0.4.0.9019 (2020-07-06)

• 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 (2020-07-06)

• WV GLIMPSS, Issue #3
  • MetricScoring.xlsx
  • MetricNames.xlsx
  • metric.values.R
  • testthat
• Update pkgdown website.

Changes in Version 0.4.0.9017 (2020-06-25)

• 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 (2020-06-19)

• Referenced wrong issue in last update.

Changes in Version 0.4.0.9015 (2020-06-19)

• 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 (2020-06-18)

• DESCRIPTION
  • Add package tidyr to support metric.stats2(); Issue # 37

Changes in Version 0.4.0.9013 (2020-06-03)

• metric.stats2.R, Issue #36
  • Add DE and z-scores based on metric.stats and metric.values.

Changes in Version 0.4.0.9012 (2020-06-01)

• Update pkgdown website documentation.

Changes in Version 0.4.0.9011 (2020-06-01)

• 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 (2020-05-11)

• 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 (2020-05-07)

• 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 (2020-04-28)

• 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 (2020-04-27)

• metric.values.R
  • Additional metrics, Issue #3.
    • nt_BCG_att1
    • pi_BCG_att1
    • pt_BCG_att1

Changes in Version 0.4.0.9006 (2020-04-24)

• 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 (2020-02-28)

• Tweak for SelMet.
  • metric.scores.R

Changes in Version 0.4.0.9005 (2020-02-28)

• Change DepMet to SelMet.
  • Better terminology as selecting a metric to use.
  • metric.scores.R
  • MetricScoring.xlsx

Changes in Version 0.4.0.9003 (2020-02-27)

• Add ability to score index when have zero individuals.
  • metric.scores.R
  • MetricScoring.xlsx

Changes in Version 0.4.0.9002 (2020-02-27)

• 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 (2020-02-27)

• 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 (2020-02-24)

• 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 (2020-02-24)

• 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 (2020-01-31)

• 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 (2020-01-08)

• 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 (2020-01-07)

• 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 (2020-01-07)

• 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 (2020-01-02)

• 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 (2019-12-18)

• 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 (2019-10-17)

• MetricScoring.xlsx, Issue #3
  • Numeric to text.

Changes in Version 0.3.3.9009 (2019-10-17)

• MetricScoring.xlsx, Issue #3
  • Updates for GBI_MS_2013

Changes in Version 0.3.3.9008 (2019-10-16)

• MetricScoring.xlsx, Issue #3
  • Updates for GBI_MS_2013
  • Numeric to text.

Changes in Version 0.3.3.9007 (2019-10-16)

• MetricScoring.xlsx, Issue #3
  • Updates for GBI_MS_2013
  • Numeric to text.

Changes in Version 0.3.3.9006 (2019-10-15)

• MetricScoring.xlsx, Issue #3
  • Updates for GBI_MS_2013

Changes in Version 0.3.3.9005 (2019-10-15)

• MetricScoring.xlsx, Issue #3
  • Updates for GBI_MS_2013

Changes in Version 0.3.3.9004 (2019-10-15)

• Additional scoring and index. Issue #3
  • Gulf Biotic Index, 2011
  • Mississippi Gulf Biotic Index, 2013

Changes in Version 0.3.3.9003 (2019-09-15)

• 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 (2019-07-03)

• 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 (2019-07-02)

• 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 (2019-07-02)

• New release version.

Changes in Version 0.3.2.9001 (2019-07-02)

• metric.scoring.xlsx
  • Update “scoring formula” column for 2 MA WestHighlands metrics.
  • Actual thresholds not affected.

Changes in Version 0.3.2 (2019-06-28)

• New release version.

Changes in Version 0.3.1.9001 (2019-06-27)

• 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 (2019-06-27)

• New release version.

Changes in Version 0.3.0.9024 (2019-06-27)

• 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 (2019-06-27)

• 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 (2019-06-27)

• 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 (2019-06-27)

• 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 (2019-05-24)

• Updated metric names for MBISQ index, Issue #3
  • MetricScoring.xlsx

Changes in Version 0.3.0.9019 (2019-05-24)

• 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 (2019-05-17)

• 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 (2019-05-08)

• 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 (2019-05-07)

• 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 (2019-04-11)

• inst/extdata/MetricFlags.xlsx
  • Update ni_total for Hi to match Lo (both 450), Issue #16

Changes in Version 0.3.0.9014 (2019-04-02)

• 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 (2019-01-25)

• 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 (2019-01-17)

• 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 (2019-01-17)

• docs/ExcludedTaxaDecisionCrit.pdf
  • Recreate. Wasn’t opening.

Changes in Version 0.3.0.9010 (2019-01-17)

• extdata/MetricNames.xlsx
  • move “0-100” from notes to description.

Changes in Version 0.3.0.9009 (2019-01-17)

• metric.values
  • Mistyped “FAMILY” as “Family” when added pi_Baet.

Changes in Version 0.3.0.9008 (2019-01-17)

• docs
  • Added ExcludedTaxaDecisionCrit.docx

Changes in Version 0.3.0.9007 (2019-01-17)

• 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 (2019-01-17)

• 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 (2019-01-14)

• DESCRIPTION
  • maps package missing from Imports.
    • Used in MapTaxaObs function.

Changes in Version 0.3.0.9004 (2019-01-14)

• 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 (2019-01-14)

• 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 (2019-01-14)

• Vignette
  • kable used without library(knitr) in rarify chunk.

Changes in Version 0.3.0.9001 (2018-12-21)

• Update QC flags input.
• Add metric names to Excel file.
• MetricName to METRIC_NAME in input files.

Changes in Version 0.3 (2018-12-20)

• New release version.

Changes in Version 0.2.0.9007 (2018-12-20)

• Metric scoring function, Issue #12.

Changes in Version 0.2.0.9006 (2018-12-03)

• 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 (2018-11-26)

• Added MapTaxaObs.

Changes in Version 0.2.0.9004 (2018-11-26)

• Percent metrics as 0-1. Issue #9.

Changes in Version 0.2.0.9003 (2018-11-26)

• 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 (2018-11-20)

• Update SuperFamily Tipuloidea.
  • Update data and examples in function and vignette

Changes in Version 0.2.0.9001 (2018-11-20)

• Add Travis CI.

Changes in Version 0.2.0 (2018-11-20)

• Initial release version.

Changes in Version 0.1.0.9004 (2018-11-20)

• Add SuperFamily
  • function
  • vignette
  • example data file
• Add metric names files to extdata and doc

Changes in Version 0.1.0.9003 (2018-11-20)

• 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 (2018-11-16)

• extdata_Benthos.xlsx
  • OneDrive messed up version included in package.

Changes in Version 0.1.0.9001 (2018-11-16)

• 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 (2018-11-16)

• Initial commit on GitHub.