The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.