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---
title: "NEWS"
author: Erik.Leppo@tetratech.com
output: github_document
#md_document:
# variant: markdown_github
---
<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
```{r Options, echo = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.path = "NEWS-")
```
```{r LastUpdate, echo = FALSE}
cat(paste0("Last Update: ",Sys.time()))
```
# Version History
## 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\MetricNames.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\MetricNames.xlsx
+ extdata\MetricScoring.xlsx
* tests: Add tests for So Cal Marine Bays
+ Incomplete
## Changes in Version 0.5.0.9111 (2022-03-04)
* fix: Restore extdata\MetricNames.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 \data-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 \data-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