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NEWS
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NEWS
================
<Erik.Leppo@tetratech.com>
<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
#> Last Update: 2024-11-20 08:24:14.42573
# Version History
## 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 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