#> Last Update: 2024-11-20 08:24:14.42573
- refactor: Add fish metrics; nt/pi/pt BCG_att4 b/m/2
- MetricNames.xlsx
- metric_values.R
- refactor: Add fish metric permutations of non-native
- MetricNames.xlsx
- metric_values.R
- 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
- refactor: Add new fish metric (pi_BCG2_att1234b)
- MetricNames.xlsx
- metric_values.R
- docs: Update comment about NATIVE in metric.values help
- refactor: Add new fish metrics (BCG_att4w5); same as bugs
- MetricNames.xlsx
- metric_values.R
- docs: Start to populate values column in MetricNames.xlsx
- refactor: Update MetricNames.xlsx for test
- New field is mostly blank so imports as logical and causes error
- refactor: Add new fish metrics (nt_, pi_, and pt_) for invertivore
- MetricNames.xlsx
- metric_values.R
- refactor: Update search patterns for some fish trophic metrics
- IV
- TC
- 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
- metric_values.R
- refactor: Add new metric for MN, nt_total_ExclSchool
- metric_values.R
- MetricNames.xlsx
- 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
- docs: Update Excel files for MN_IBI_Fish Index_Class 1
- pi_piscivore_ExclSchool to nt_piscivore
- 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
- refactor: Update MetricScoring.xlsx
- MN, pi_TrichNoHydro scoring formula text
- fix: Update MetricScoring.xlsx
- MN, narratives
- fix: Update MetricScoring.xlsx (MN)
- refactor: Update MetricScoring.xlsx
- MN_IBI_Fish and MN_IBI_Bugs, index numeric and narrative
- 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
- refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT)
- refactor: MetricScoring.xlsx change MN IBI classes
- Flip Bugs and Fish for 8/9 and 10/11
- refactor: Update MN IBI (bugs and fish), Issue #92
- Drop “modified” narrative
- MetricScoring.xlsx
- refactor: Update MN Fish and Bug IBI index scoring, Issue #92
- 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
- refactor: Change MN Bugs Index_Class from 8 and 9 to 10 and 11, Issue
#92
- MetricScoring.xlsx
- fix: Update fish metrics brook trout code, Issue #92
- Change for MN to replace space invalidated code
- Added TYPE_BROOKTROUT to make metric simpler
- docs: Add “demo only” language to ORWA example data
- 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
- refactor: Update zeroind scoring for MN Bugs and Fish IBI, Issue #111
- MetricScoring.xlsx
- refactor: Update
taxa_translatecolumns for unique taxa output
- refactor: Update match_caps code in
taxa_translate
- refactor: Add default value for match_caps in
taxa_translate
- refactor: Update MN_Fish_IBI metrics, Issue #111
- pi_wetland_notoler_ExclSchool to nt_wetland_notoler
- MetricScoring.xlsx
- MetricNames.xlsx
metric.values
- pi_wetland_notoler_ExclSchool to nt_wetland_notoler
- refactor: Add pi_OligoHiru to
metric.values
- refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #111
- refactor: Update taxa_translate taxatrax_unique ouput
- Add match with CAPS
- fix: Add TolVal2 as required field for fish metrics in
metric.values
- test: Add taxa.translate triws test
- Add white space (leading, trailing, both) and internal nbsp to test data
- feature: Update taxa.translate trimws feature to replace internal
- 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()
- 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
- Bugs
- 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
- refactor: Remove match_caps parameter from taxa_translate function, Issue #111
- tests: Remove taxa_translate match_caps test, Issue #111
- tests: Add tests for removing white space, Issue #111
- feature: Update taxa_translate with clean parameters, Issue #111
- refactor: Update for MN_Fish_IBI, Issue #92
- MetricNames.xlsx
- metric_values.R
- Updates to data munging prior to metric calculation
- refactor: Update MetricScoring.xlsx for MN_Bug_IBI, Issue #92
- refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue #92
- refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue #92
- 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
- refactor: Update pi_Cheu text in MetricNames.xlsx
- refactor: Update MetricNames.xlsx for Great Plains BCG
- refactor: Merge pull request 114
- Add metrics (bugs and fish) for Great Plains BCG
- feature: Options added to taxa_translate, Issue #111
- Match on ALL CAPS
- Clean input names
- Not fully implemented
- 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
- Reconcile names for same calculation but different programs and
columns
- tests: Update fish metric names for new metrics
- refactor: Add MN_IBI_Fish metrics to MetricNames.xlsx, Issue #92
- refactor: Merge pull request 110
- New metrics for NM BCG Fish
- MetricNames.xlsx
- metric_values.R
- New metrics for NM BCG Fish
- 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
- 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
- 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
- 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)
- fix: Update MN IBI Bugs thresholds in MetricScoring.xlsx, Issue #92
- refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92
- refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92
- refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue #92
- fix: Update
metric.valuespi_dom01_BCG* metrics- Add zero to max function to avoid max returning -Inf
- refactor: Update
metric.valuesdebug steps for fish- Was 10 and changed to 12
- 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
- fix: Update MetricNames.xlsx for missing coral metric per tests
- refactor: Update Excel files for MN IBI
- MetricFlags.xlsx
- MetricNames.xlsx
- MetricScoring.xlsx
- refactor: Update GitHub Actions with usethis::use_github_action()
- check-standard
- test-coverage
- pkgdown
- docs: Update check badge in ReadMe
- fix: Remove uneeded concatenate in tests per CodeFactor
- test_metric_names
- fix: Update to minor version number 1.0.2
- Incorrect version numbers from pull request
- refactor: Coral metrics from Blocktt
- fix: made changes to coral metrics
- added test for Florida BCG
- update: Added coral metrics, specifically for FL BCG
- metric_values.R
- MetricNames.xlsx
- refactor: Additional metrics for Great Plains BCG, Issue #106
- metric_values.R
- MetricNames.xlsx
- 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
- fix: Update MetricScoring.xlsx, ScoreRegime for MN_IBI_bugs, Issue
#92
- Cont_010 to Cont_0010 to match code
- 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
- fix: Modify metric.values() benthic metric nt_tv_toler8, Issue #104
- Was using 6 instead of 8 as minimum
- 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
- refactor: Add ni_total flags (small and large) for MN_IBI_Bugs, Issue
#92
- MetricFlags.xlsx
- 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
- refactor: Add metrics for NM BCG, Issue #97
- Pull request not able to easily merge, make changes by hand
- refactor: Add testing (QC) to
metric.valuesfish calc section
- 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
- refactor: Remove interactive TRUE from algae in
metric.values- Same issue with the fish but being proactive
- Not included on bugs
- refactor: Edits to
metric.valuesfish calc for error in Red Lakes Shiny app- N_ANOMALIES NA to 0
- Change “interactive” part of require column check
- refactor: More edits to
metric.valuesfish calc for error in Red Lakes Shiny app
- refactor: Edit
metric.valuesfish calc for error in Red Lakes Shiny app
- refactor: Modify verbose statements in
metric.values- Change terminology in code so more generic
- Add verbose statements to fish sub function
- refactor: Update MetricNames.xlsx with recent name changes
- refactor: Change names of trout metrics in
metric.values- Better reflects contents of metrics
- refactor: Add pi_trout to
metric.values
- refactor: Update MetricNames.xlsx to match function, fish metrics
- refactor: Update
metric.valuesto 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
- fix: metric.values boo.shiny code updated to match bugs and algae
- refactor: metric.values specify parameters for subfunctions
- fix: Update metric, nt_BCG_att55a6, Issue #92
- add ‘na.rm = TRUE’
- fix: Add missing metric, nt_BCG_att55a6, Issue #92
- refactor: Fix BCG_att1236sp fish metrics, pi and pt
- Remove nt
- 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
- fix: Cheumatopsyche metrics, Issue #93
- Search term updated; Cheumatopsyche to CHEUMATOPSYCHE
- Add missing equal sign
- Move so alphabetical in output
- feature: Add taxaid_dni parameter to metric.values, Issue #96
- refactor: Modify output of
taxa_translatefunction, Issue #94- taxatrans$taxatrans_unique
- feat: Add new metric, ni_totalNoDeca, Issue #94
- style: Add spaces to code for readability
- fix: Update Cheumatopsyche metrics in MetricNames.xlsx, Issue #93
- pi_Cheu
- pi_EPTNoCheu
- fix: Update code for Cheumatopsyche metrics, metric_values.R, Issue
#93
- pi_Cheu
- pi_EPTNoCheu
- fix: BioMonTools vignette change reference to metric names
- corecold changed to stenocold
- fix: Fill in missing Vignette Builder for vignette_NewIndex
- fix: Add line for “changed” taxa in
taxa_translate
- fix: Update domX calculations to combine taxa before calculate in
metric_values
- bugs and fish
- refactor: Update metrics for MN BCG, Issue #92
- In myDF remove NA for specialized dom01 calculations
- refactor: Update metrics for MN BCG, Issue #92
- refactor: Add percent Cheumatopsyche metric
- refactor: Additional metrics for MN BCG, Issue #92
- refactor: Add bug metrics for MN BCG, Issue #92
- style: Update spacing in test file metric_names
- refactor: Update MetricFlags.xlsx for MTTI index
- refactor: Update metric.values MTTI subset metrics, Issue #90
- refactor: Update MetricFlags.xlsx for MTTI index
- feature: New parameter in
metric.valuesto run only subset, Issue #90 - style: Style changes in metric_values.R
- docs: Add vignette for adding a new index, Issue #87
- incomplete
- refactor: Add CO MMI (bugs)
- Draft 2006, verify with report and EDAS database
- fix: Update
metric.valuesthermal NA metrics- Add blank (““) to NA as a condition
- test: Additional
assign_indexclasstests
- refactor: Update
assign_indexclassto account or NA and ““, Issue #85 - fix: Update
assign_indexclassto account non standard column names, Isue #85 - tests: Add tests for
assign_indexclass, Issue #85 - refactor: Update
assign_indexclassto not fail if index_class in input data, Issue #85
- refactor: Update MetricNames.xlsx groupings
- Added “Experimental”
- feature: Add unique taxa crosswalk to output of
taxa_translate
- test: Add test for multiple stages for
taxa_translate
- fix: Turn off QC testing in function
assign_indexclass- Was using test data instead of user input
- docs: Update
taxa_translateexample files
- refactor: Update
taxa_translateto drop a particular ID after translation , Issue #81- Added input paramter
- Updated example
- Updated test
- data: Update extdata for
taxa_translateexample, Issue #81- Revised PacNW_ORWA data file (2022-12-19)
- tests: Revise
taxa_translatetest for revised data
- tests: Create tests for
taxa_translate, Issue #81
- 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
- fix: Update
taxa_translatefor when sum taxa, Issue #81 - update: Revise taxa_translate files in extdata
- refactor: Tweak debug code in
taxa_translate, Issue #81 - fix: Update
taxa_translatefor col_drop_project- Should be debug only
- refactor: Change internal workings of
taxa_translate, Issue #81- If summarize retain the official taxa columns
- Reorder columns in the merged output
- refactor: Change internal parameter boo_DEBUG to boo_DEBUG_tt in
taxa_translate, Issue #81
- refactor: Make
taxa_translateas an export object, Issue #81
- fix: Updated
taxa_translatefunction to include metadata as parameter, Issue #81
- feature: Add
taxa_translatefunction, Issue #81- More general than qc_taxa
- fix: Update
markExcludeto avoid dplyr deprecation warnings, Issue #51
- breaking change: Site_Type and Index_Region to Index_Class
- refactor: Update rarify function to save example to tempdir
- feat: New function
assign_IndexClass, Issue #82- Add IndexClass.xlsx to ext folder
- 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
- fix: Update and add some metrics
- metric_values.R
- MetricNames.xlsx
- fix: Tweak secondary metric name in MetricScoring.xlsx
- GA_DNR_Fish_2020
- 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
- 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
- feat: Additional BCG metrics, Issue #79
- style: Surround operators with space
- metric_values
- test: Add sum of parts tests for new BCG metrics
- fix: Update bug thermal metrics, Issue #78
- 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
- fix: Hemiptera metrics (nt and pt) not working, Issue #74
- Fix spelling
- refactor: Additional metrics, Issue #74
- fix: Change metric HabitatStruct from RW to RM, Issue #73
- 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
- refactor: Change variable classes in metric.scores()
- Avoid errors in import via read_excel
- refactor: Rename one misspelled bug thermal metrics, Issue #72
- ‘pt_ti_cool_warm_stenowarm’ should be ‘pt_ti_warm_stenowarm’
- refactor: Add and modify bug thermal metrics, Issue #72
- metric_values()
- extdata.xlsx
- style: Add extra spaces to some lines in metric_values()
- refactor: Add metrics and scoring for So Cal Marine Bays
- extdata.xlsx
- extdata.xlsx
- tests: Add tests for So Cal Marine Bays
- Incomplete
- fix: Restore extdata.xlsx
- Deleted in v0.5.0.9109, last mod was v0.5.0.9100
- docs: Update required fields text in metric.values()
- refactor: Copy (as comments) required fields code from bugs to other communities in metric.values()
- refactor: Additional output messages to screen in metric.values()
- 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
- 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
- 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
- refactor: Tweak error checking for bugs in metric.values()
- refactor: Tweak error checking for bugs in metric.values()
- refactor: Tweak error checking for bugs in metric.values()
- 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_
- 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
- refactor: Add new metric to MetricNames.xlsx
- refactor: Shiny add ‘tab’ as acceptable text file upload format.
- refactor: Add new bug metric to metric.values()
- pi_SphaerCorb
- refactor: Modify debugging messages to metric.values() for Shiny log
- refactor: Add debugging messages to metric.values()
- fix: Update metric.values() for input data missing Index_Name and Index_Region
- 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
- refactor: Update metvalgrpxl() for blank cells hiding text to left
- fix: Update to changes in metric.values()
- fix: Remove redundant code in metric.values()
- Causing failures on Shiny.io with missing required columns
- refactor: Update metvalgrpxl() to use input parameter for groupings
- refactor: Small edits to Shiny app
- Text edits to help pages
- Update links for TaxaMaps
- refactor: Update metvalgrpxl() to use formulas in output
- refactor: Edits to help pages in Shiny app
- Update links to download files
- 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
- fix: Correct spelling of file name in global.R
- ShinyApps.io is Linux and is case-sensitive
- 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
- docs: Update GitHub default branch from “master” to “main”
- refactor: Added global variable bindings to fish metrics
metric.values()
- Only BCG_Attr
- fix: metric.values() example 4 (fish) view statement incorrect
- feature: Add new fish metrics to metric.values()
- pi_BCG_att23_SCC
- nt_BCG_att23_SCC
- pt_BCG_att23_SCC
- feature: Add new fish metrics to metric.values()
- pi_Lepomis
- pt_Lepomis
- nt_BCG_attNA
- pi_BCG_attNA
- pt_BCG_attNA
- 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
- feature: Update Shiny app, all functions working, Issue #67
- feature: Add Shiny app, basic outline only, Issue #67
- refactor: Allow for mixed case in bug metric phylo metrics, Issue #65
- fix: Update metric.values(), was returning 0 records
- length_m was commented out and caused error in met.val
- tests: Update tests to ensure MetricNames.xlsx is complete
- refactor: Update metric.valus() with metrics used in MetricScoring.xlsx
- docs: Create documentation for data_fish_MBSS dataset
- docs: Update MetricNames.xlsx and MetricScoring.xlsx for any new metrics, Issue #64
- 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
- nt_natcent to nt_natCent_sunfish
- refactor: Update thermal metric default values, Core-Cold to CoreC
- metric.values()
- data_benthos_PacNW
- fix: metric.values() thermal indicator metric not correct
- nt_ti_corecold_cold
- pt_ti_corecold_cold
- fix: metric.values() thermal indicator NA metric not correct
- Using wrong column (Habitat) to find NA
- fix: metric.values() not working for new metrics, Issue #62
- Elevation, Gradient, and WSArea
- refactor: Update MetricScoring.xlsx for IEPA, Issue #63
- tests: Update test_threshold_numdigits to show rows with issues
- 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
- Adds new required fields
- 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
- 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
- refactor: Update MetricScoring.xlsx from dev_periphyton merge
- fix: Remove unneeded concatenation, markExcluded, Issue #61
- fix: Update NEWS after merging of pull request
- Add items below from branch NEWS
- Some updates missing filled in from Branch info
- Add items below from branch NEWS
- 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
- refactor: added diatom example dataset to package
- 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
- refactor: metric.values
- 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
- refactor: metric.values
- 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
- refactor: metric.values added periphyton/diatom metric functionality
- 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
- 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
- feature: Add pi_BCG_att5extra to metric.values() for bugs
- 5 and 5.5
- feature: Add more fish metrics to metric.values()
- refactor: For fish community for metric.values() convert to upper case
- refactor: Move legend to the right margin, MapTaxaObs, Issue #52
- docs: README, update install code to use remotes instead of devtools
- 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
- refactor: Convert messages to warnings in markExcluded
- cat() and flush.console() to message()
- 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
- refactor: Incorporate pull request #50
- metric.stats2, fix group_by with change in dplyr
- 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
- refactor: Metric.Scoring.xlsx, update to remove NA from index scoring
- Both numeric and narrative.
- Caused an issue with scoring FFXCOVA_2018
- refactor: metric.values, update new metric, pi_EPTNoHydro
- docs: Add Ben Block as contributor.
- refactor: metric.values, add new metric, pi_EPTNoHydro
- refactor: Metric.Scoring.xlsx, updates for FFXCOVA_2018
- refactor: metric.values, fix nt_ECT
- Had nt_ECP
- refactor: metric.values add new metric if IL EPA lakes, Issue #3
- nt, pi, pt
- Ephemeroptera, Coleoptera, Trichoptera
- Add global variable bindings
- nt, pi, pt
- refactor: MetricNames.xlsx
- Update for new metrics
- refactor: Update MetricScoring.xlsx
- MassIBI Low Gradient
- Update narrative thresholds
- IL EPA Lakes
- Add new indices
- MassIBI Low Gradient
- docs: markExcluded example missing a comment line
- Causing examples to fail
- refactor: metric.values, add 3 new FFG metrics, Issue #3
- nt, pi, pt
- omnivore (OM)
- parasite (PA)
- nt, pi, pt
- 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
- metric.values
- refactor: Modify ffg_col metrics to use CG or GC
- metric.values
- nt, pi, pt
- MetricNames.xlsx
- metric.values
- feature: Add logo from RBP 2nd edition
- docs: Update README with logo
- 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
- Replace ‘=’ with ‘<-’
- style: Fix spelling, devtools::spell_check()
- ReadMe
- NEWS
- metric_stats.R
- refactor: metric.values, add 3 new FFG metrics, Issue #3
- nt, pi, pt
- macrophyte herbivore (MAH)
- xylophage (XYL)
- piercer-herbivore (PIH)
- nt, pi, pt
- 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
- refactor: metric.values, add pi_DiptNonIns metric
- style: metric.values, start to trim lines to 80 characters
- refactor: metric.values, modify GA fish metric pi_natinsctcypr, Issue
#48
- Was not checking for Native
- refactor: metric.values, modify fish metrics for TROPHIC to account for multiple values
- refactor: MetricScoring.xlsx
- GA DNR Fish, standardize 2005 index regions to all CAPS the same as 2020.
- Breaking change for scripts based on 2005 fish index
- docs: Move updates from NEWS to README
- refactor: Update MetricScoring.xlsx for MA
- docs: Update README install section, Issue #11
- tests: Activate tests
- rarify
- 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
- fix: Replace instances of deprecated functions
- Change dplyr::group_by_ to dplyr::group_by
- metric.stats2
- Change dplyr::group_by_ to dplyr::group_by
- 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
- fix: Replace instances of deprecated functions
- Change dplyr::group_by_ to dplyr::group_by
- metric.values
- Change dplyr::group_by_ to dplyr::group_by
- test: Add tests
- qc_checks
- markExcluded
- metric.stats
- 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
- 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
- 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
- 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
test: Add tests + rarify + qc_checks (gives warning but passes)
- 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
- refactor: Add foo:: to missing functions
- ProcessData_TaxaMater_Ben_BCG_PacNW.R
- test_metric_calc.R
- refactor: Trim lines to 80 characters
- refactor: Add foo:: to missing functions
- ci: Add code coverage GitHub Action
- refactor: change 1:foo() to seq_len(foo())
- test_metric_calc
- metric_stats
- qc_checks
- style: rarify, remove trailing ;
- docs: Change to pkgdown from manual (docs in main branch) to GitHub Action (gh-pages branch)
- docs: ReadMe, add badges for codefactor and codecov
- docs: ReadMe, knit with updates from previous commit
- ci: Change from TravisCI to GitHub Actions
- docs: ReadMe, Add CI badge
- docs: ReadMe, add lifecycle badge
- 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.
- MetricScoring.xlsx
- Modify MassDEP metrics and index scoring.
- Update Test
- test_metric_names
- Update test for AVERAGE_10 and AVERAGE_20 to AVERAGE_100.
- 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.
- Replace AVERAGE_10 and AVERAGE_20 with AVERAGE_100
- Check
- Shorten lines longer than 100 characters.
- markExcluded.R
- metric_scores.R
- Add stats to DESCRIPTION, IMPORTS
- Shorten lines longer than 100 characters.
- 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
- FFXCOVA_2018, INDEX_REGION
- 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.
- 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
- MetricScoring.xlsx
- Add MA indices, Issue #3.
- test-metric_calc.R
- Update for MA indices.
- MetricScoring.xlsx
- Update GADNR_Fish_2020, Issue #3.
- MetricScoring.xlsx
- Update GADNR_Fish_2020, Issue #3.
- MetricScoring.xlsx
- Update GADNR_Fish_2020, Issue #3.
- MetricScoring.xlsx
- Update MassDEP_2019_Bugs, Issue #3.
- MetricScoring.xlsx
- Update MassDEP_2019_Bugs, Issue #3.
- Tweaks to tests.
- Update NEWS for pull request.
- Update notes in MetricScoring.xlsx
- Merged Pull Request #44 (0.5.0.9001 and 9002)
- MetricScoring.xlsx
- Updated MI narratives.
- MetricScoring.xlsx
- Changed MI narratives and fixed NumMetrics error for MI - East.
- Update to new version number.
- Rebuild package down website.
- Create new release on GitHub.
- Remove extra file (metric.values.tsv) from root folder of package.
- 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.
- metric.values.R
- 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
- metric.values; Issue #3, Issue #41
- Fix pi_EPT and pi_EPTNoCheu
- swamped when created in v0.4.0.9019 (2020-07-06).
- Fix pi_EPT and pi_EPTNoCheu
- metric.values, Skip column QC check in Shiny; Issue #40
- metric.values, NonTarget still counted; Issue #39
- Inadvertently removed in v0.3.3.9017 (2020-02-24)
- WV GLIMPSS, Issue #3
- Narrative categories are: Very good, Good, Degraded, Severely
degraded
- Pond et al. 2012
- MetricScoring.xlsx
- Narrative categories are: Very good, Good, Degraded, Severely
degraded
- WV GLIMPSS, Issue #3
- MetricScoring.xlsx
- MetricNames.xlsx
- metric.values.R
- testthat
- Update pkgdown website.
- 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.
- Referenced wrong issue in last update.
- 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.
- Add new metrics for PA and WV BIBIs.
- DESCRIPTION
- Add package tidyr to support metric.stats2(); Issue # 37
- metric.stats2.R, Issue #36
- Add DE and z-scores based on metric.stats and metric.values.
- Update pkgdown website documentation.
- 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.
- metric.values.R, Issue #35
- Modify Oligochaete metrics to use Class or Subclass.
- Add Subclass as a required field.
- 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
- More new metrics.
- 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.
- Additional metrics, Issue #3.
- MetricNames.xlsx
- Add new metrics.
- New data set to utilize new metrics.
- data_benthos_PacNW
- metric.values.R
- Additional metrics, Issue #3.
- nt_BCG_att1
- pi_BCG_att1
- pt_BCG_att1
- Additional metrics, Issue #3.
- 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.
- Modify example. Issue #34.
- Tweak for SelMet.
- metric.scores.R
- Change DepMet to SelMet.
- Better terminology as selecting a metric to use.
- metric.scores.R
- MetricScoring.xlsx
- Add ability to score index when have zero individuals.
- metric.scores.R
- MetricScoring.xlsx
- 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.
- Account for “no organisms collected”.
- 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
- Modify ni_natnonhybrid and ni_natnonhybridnonlepomis to also exclude
mosquitofish.
- metric.score.R
- Update ni_natnonhybridnonlepomis.
- Changes to fish metric significant enough for a minor version update.
- Some previous calculations may not work. Function made more generic.
- 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.
- Modifications for GA Fish IBI.
- 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.
- Modifications for GA Fish IBI.
- vignette_BioMonTools.Rmd
- Added library(dplyr) to one of the examples.
- MetricScoring.xlsx, Issue #3
- Tweak values for GA Fish IBI.
- ACF, 6b, inflection point is 2 not 1.
- Tweak values for GA Fish IBI.
- metric.values.R
- Minor edits.
- MetricScoring.xlsx, Issue #3
- Tweak values for GA Fish IBI.
- Convert some values to text.
- Tweak values for GA Fish IBI.
- metric.values.R
- Tweak index NormDist_135.
- MetricScoring.xlsx, Issue #3
- Tweak values for GA Fish IBI.
- Convert some values to text.
- Tweak values for GA Fish IBI.
- metric.values.R
- Tweak index sum to account for NA.
- MetricScoring.xlsx, Issue #3
- Tweak values for GA Fish IBI.
- metric.values.R
- Error in excluding marine metrics when no metric list given (i.e.,
want all metrics).
- Misplaced “)”. Issue # 31.
- Error in excluding marine metrics when no metric list given (i.e.,
want all metrics).
- 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).
- MetricScoring.xlsx, Issue #3
- Numeric to text.
- MetricScoring.xlsx, Issue #3
- Updates for GBI_MS_2013
- MetricScoring.xlsx, Issue #3
- Updates for GBI_MS_2013
- Numeric to text.
- MetricScoring.xlsx, Issue #3
- Updates for GBI_MS_2013
- Numeric to text.
- MetricScoring.xlsx, Issue #3
- Updates for GBI_MS_2013
- MetricScoring.xlsx, Issue #3
- Updates for GBI_MS_2013
- Additional scoring and index. Issue #3
- Gulf Biotic Index, 2011
- Mississippi Gulf Biotic Index, 2013
- 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
- Additional estuary/marine metrics
- metric.values, Issue #3
- Add placeholders for marine/estuarine metrics
- Not yet in MetricScoring.xlsx or MetricNames.xlsx
- Add placeholders for marine/estuarine metrics
- 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.
- Update Beck’s Biotic Index cutoff signs.
- New release version.
- metric.scoring.xlsx
- Update “scoring formula” column for 2 MA WestHighlands metrics.
- Actual thresholds not affected.
- New release version.
- MetricScoring.xlsx, issue #22
- New metric misspelled.
- Add capability for 6 narrative categories.
- MetricScoring.xlsx
- metric.scores.R
- Minor edit for number of columns.
- New release version.
- MetricScoring.xlsx, issue #22
- Some numbers to character with ’ prefix.
- These numbers not importing correctly from Excel.
- Floating point errors in rounding.
- 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.
- 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.
- DESCRIPTION
- Updated metric names for MA index, Issue #3
- MetricScoring.xlsx
- Added “to do” and “references” to metricscoring.xlsx, Issue #3
- Updated metric names for MBISQ index, Issue #3
- MetricScoring.xlsx
- 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
- metric.values
- Fixes for R v3.6.0, Issue #18
- DESCRIPTION
- Remove StagedInstall: no
- README
- Add directions for fix for devtools.
- DESCRIPTION
- README
- Update badges.
- Metric names, fix those added in previous update, Issue #3
- Files
- metric.values.R
- MetricNames.xlsx
- MetricScoring.xlsx
- Files
- 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.
- 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
- Files
- inst/extdata/MetricFlags.xlsx
- Update ni_total for Hi to match Lo (both 450), Issue #16
- metric.values, Issue #15
- Fix metric pi_EphemNoCaeBae
- Was calculating the same as pi_Ephem.
- Checked all other “No” metrics.
- All ok.
- Fix metric pi_EphemNoCaeBae
- metric.values
- Fix Trombidiformes metric.
- Mispelled search term so wasn’t working.
- Added Megaloptera metrics (nt, pi, and pt).
- Fix Trombidiformes metric.
- 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).
- docs/ExcludedTaxaDecisionCrit.pdf
- Recreate. Wasn’t opening.
- extdata/MetricNames.xlsx
- move “0-100” from notes to description.
- metric.values
- Mistyped “FAMILY” as “Family” when added pi_Baet.
- docs
- Added ExcludedTaxaDecisionCrit.docx
- 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.
- 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.
- DESCRIPTION
- maps package missing from Imports.
- Used in MapTaxaObs function.
- maps package missing from Imports.
- README
- Update install example to force vignettes.
- metric.scores
- pt_habit metrics (n=5) used ni_total instead of nt_total in denominator.
- 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.
- Account for tibbles as input.
- 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.
- Vignette
- kable used without library(knitr) in rarify chunk.
- Update QC flags input.
- Add metric names to Excel file.
- MetricName to METRIC_NAME in input files.
- New release version.
- Metric scoring function, Issue #12.
- 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.
- Added MapTaxaObs.
- Percent metrics as 0-1. Issue #9.
- 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.
- Update SuperFamily Tipuloidea.
- Update data and examples in function and vignette
- Add Travis CI.
- Initial release version.
- Add SuperFamily
- function
- vignette
- example data file
- Add metric names files to extdata and doc
- markExcluded
- Add function with examples
- extdata_Benthos.xlsx
- Updated bad Excluded entries.
- FALSE to TRUE, n=6
- TRUE to FALSE, n=1
- Updated bad Excluded entries.
- DESCRIPTION
- Update Imports and Suggests
- NEWS
- Update Planned and Future Updates
- README
- Tweak language in Usage section.
- Update icons.
- Add Travis CI.
- Vignette
- extdata_Benthos.xlsx
- OneDrive messed up version included in package.
- 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
- Initial commit on GitHub.