Erik.Leppo@tetratech.com 2024-10-08 21:43:53.732261
#> Last Update: 2024-10-08 21:43:53.756255
- fix: Modify BCG.Level.Membership
- Update for exception rules
- Edit FLIPMINMAX to flip min and max
- Add MIN012MAX, MIN of Rules 0, 1, 2 then MAX
- Update for exception rules
- refactor: Update Rules.xlsx
- Populate missing INCREASE values
- Add metadata worksheet for EXC_RULE
- Add MN_BCG for EXC_RULE MIN012MAX
- refactor: Add error message for NA in INCREASE column for BCG.Metric.Membership
- fix: Modify BCG.Level.Membership to flip min and max as an exception rule
- refactor: Update Rules.xlsx for MN_BCG for EXC_RULE FLIPMINMAX
- fix: Modify BCG.Level.Membership to avoid duplication in output for
level assigment
- Modify INDEX_CLASS_ORIG
- Modify Exception calculations (i.e., median, small2, small2A, small2B, and small3)
- refactor: Add Great Plains BCG metric flags
- refactor: Add summation of duplicate taxa in taxa translate in Shiny
- refactor: Merge Pull Request 92
- refactor: Update Rules.xlsx for MN_BCG metric descriptions and index regions
- refactor: Update Rules.xlsx for MN_BCG fish10a and fish10b
- refactor: Add Shiny calculation Fish Thermal Class to menu and a page
- refactor: Add Shiny troubleshooting menu option
- refactor: Update Shiny MTTI citation
- refactor: Update Shiny Thermal Preference Metrics citation
- fix: Update MTTI shiny code to avoid name conflict
- TolVal2 vs. TOLVAL2
- docs: Update help on ORWA taxa list to reinforce is demo only
- refactor: Update functions to retain original case for INDEX_CLASS,
Issue #91
BCG.Metric.MembershipBCG.Level.Membership
- refactor: Define pipe in
BCG.Level.Membership
- refactor: Update rules for SMALL2 and SMALL3
- Sort ascending
- Add rules for SMALL2A and SMALL2B
- break: Fix Rules for SMALL2 and SMALL3
- Sort descending and take row 2 or 3
- This could be a breaking change
- Updating version number
- refactor: Update ‘GP_BCG_Fish’ to ‘GP_Fish_BCG’ to match GP Bug models
- Rules.xlsx
- refactor: Update Rules.xlsx for Great Plains BCG
- refactor: Modify language on Shiny app pop up for assign class
- fix: Update MetricFlags.xlsx for FL Coral BCG
- fix: Update Rules.xlsx for FL Coral BCG
- docs: Update BCG.Metric.Membership language for col_INCREASE
- refactor: Update Rules.xlsx for FL Coral BCG
- feature: Add new template for new metrics, models, and rules
- fix: Update package documenation per roxygen2
- refactor: Shiny app file builder generate class parameters, Issue #89
- Add shinyalert for more than 500 records
nhdplustoolsandStreamCatToolstimeout issues with too many records
- fix: Shiny app calculation of BioMonTools::metric.scores,
leppott/BioMonTools#103
- Affected BDI calculation, checked and no other instances
- fix: Update package documenation per roxygen2 (since 7.0.0)
- fix: Shiny app fuzzy model not working, change community reference
- Also fixed thermal metrics for status message
- fix: Update naming scheme for BCG calculation in Shiny app, Issue #87
- Add “_” prefix to Results.
- fix: Update naming scheme for BCG calculation in Shiny app, Issue #87
- refactor: Update text on BCG calculation pop up in Shiny app, Issue #88
- refactor: Update NM BCG, drop percent max ffg from L2 and L4 per documentation
- refactor: Update NM BCG Index_Name and Index_Class in Rules.xlsx
- fix: Add shiny::validate(msg) back to shiny alert for when no file
uploaded
- Avoid the app crashing by preventing rest of code from running
- refactor: update shiny alert message for upload to account for file upload not complete
- fix: Update order of conditional formatting for nt_ti_stenocold
- fix: Remove testing line in Report server code
- Caused ShinyApps.io to crash trying to open Excel
- refactor: Update Report
- Add conditional formatting for summary worksheet for data columns
- MTTI
- Thermal Metrics
- Add error checking if thermal metrics not present
- Add conditional formatting for summary worksheet for data columns
- docs: Add tag to roxygen chunk to allow for table in
BCG.Level.Membership - refactor: Update
BCG.Level.Membershipfor new exception rules (NM bugs)- Added routines for Exception Rules Small2 and Small3
- refactor: Update Rules.xlsx (NM bugs)
- refactor: Modify Shiny single report
- Properly filter for singe station for every worksheet
- Modify freeze panes for summary wide
- refactor: Calculation community buttons to default to NA
- calc_BCG
- calc_thermalfuzzy
- calc_thermalmetrics
- refactor: Modify Shiny single report
- Add taxatrans table
- Verify sorting of tables by user selections
- Add summary color thresholds
- Color summary color thresholds
- Set column widths
- update formulas on NOTES
- refactor: Modify Shiny single report
- Zip file download
- fix: Update app BCG calculation for cases where have no flags
- fix: Update MN fish metric names (trout) to be more specific
- tests: Update tests for name changes in 2.0.0.9004
- fix: Update metric name in Rules.xlsx to match BioMonTools
- pi_Trout to pi_trout
- fix: Modify taxatrans hack for noteworthy to only trigger if present
- refactor: BCG calculation user column select to lower case
- elev_m
- pslope_nhd
- refactor: Rename BCG calculation flag output (previously model experience)
- feature: Add ecoregion L3 to generate index class parameters
- refactor: Modify QC check on BCG model experience to BCG calculate
- Change text on pop-up
- Modify structure of output file
- Add checks for slope and elevation
- refactor: Result files remove leading “_”
- fix: Modify QC check on BCG model experience to BCG calculate
- total flags
- refactor: Modify QC check on BCG model experience to BCG calculate
- feature: Add QC check on BCG model experience to BCG calculate
- fix: Comment out all other instances of validate(msg) to avoid potential issues
- fix: File builder taxa translate remove validate statement from pop up
- Was causing the server to pause and not continue
- feature: Add pop-up for taxa translate with mismatch taxa
- refactor: Modify output file names
- Shorten names by dropping user input file name
- style: Add package names to a functions, Global.R
- write_disk was missing httr:: prefix
- refactor: Add MN BCG Fish rules, Rules.xlsx
- feature: Added single site report
- Formatting incomplete but function working in Shiny
- fix: Change order of operations to allow multiple uses of single
import
- For example, taxa translate now generates only the current results
- refactor: Create helper functions for re-used code
- clean_results
- copy_import_file
- fix: Create workaround for Generate Class Param
- If reused an output as input duplicate fields are created
- Then crashes when tries to join results
- Rename existing fields as _OLD
- fix: Updates TaxaTranslate file output (names and folders)
- refactor: Updates to Shiny interface
- refactor: Implement result folder changes
- refactor: Add subfolder for user import file
- refactor: Implement changes for new source files in taxa translator
- refactor: Implement file name changes
- refactor: Implement result file name changes using global abbreviations
- refactor: Remove toner lite base layer from Shiny maps
- no longer supporter after 2023-10-31
- refactor: Sidebar menu updates
- Label calculations as ‘Draft’ (non-BCG)
- Tweak ‘Taxa Translate’ language
- refactor: Update Shiny map clustering options
- refactor: Reports to only multi and single
- refactor: Add result file and folder abbreviations to global
- feature: Add report to Shiny
- Still under construction
- refactor: Update Shiny import to remove empty directories as well as
files
- Change from
file.removetounlink
- Change from
- docs: Add openxlsx to DESCRIPTION for report creation in Shiny
- fix: Shiny, taxatrans_late_0filesversion.csv, swap 2 columns
- refactor: Leaflet map Fuzzy Thermal changes
- Create multiple TIEs for legend so don’t count as NA
- TIE_A_B same as TIE_B_A
- Remove Continuous_Thermal as a required field
- Was used for size but size no longer being used
- Create multiple TIEs for legend so don’t count as NA
- refactor: For leaflet map change to addCircleMarkers
- Replaced addCircles
- fix: Change leaflet map proxy to redraw legend
- Prevents thermal metric legends from having multiple on screen
- refactor: Add “DRAFT” to BDI
- refactor: Remove base layers too large to use
- NorWeST
- NHD+ catchment
- NDD+ flowlines
- fix: Change Fuzzy Thermal legend
- Move first ties up 1 slot each
- Change legend colors
- refactor: Change jitter on map from jitter function to custom
- jitter didn’t always work with large data sets
- feat: Update Shiny map
- Add Imagery as baselayer to Shiny map
- Add legend title variable to Shiny map legend
- Add jitter to map plot to avoid overlap of multiple samples per location
- Change legend and colors
- BDI
- BCG
- MTTI
- Thermal Metrics
- refactor: Add download links to KMZ files
- refactor: Update map legends coding, Issue #67
- feature: Add KMZ downloads to Shiny app
- NorWeST_ORWA
- PNMR_BCGclasses
- feature: Updated maps in Shiny, Issue #67
- feat: Add example script for MTTI
- feat: Add example data for MTTI to external folder
- feat: Add maps for each index, Issue #67
- fix: BDI, if no Index_Class was not adding proper variable name, Issue
#66
- Caused samples to not be scored
- fix: Typo on “Covert OTU” on MTTI and BDI shiny tabs
- refactor: Adjust Excl taxa triggers and QC in code, Issue #66
- fix: Removed browser() statement from QC of last update, Issue #84
- feature: Automate Index Name and Class for fuzzy set calculation,
Issue #84
- Shiny
- feature: Add BDI calculation to Shiny, Issue #66
- COMPLETE
- refactor: Shiny required fields type for TRUE/FALSE changed text to logical
- refactor: Update MN BCG (bugs) in Rules.xlsx, Issue #82
- refactor: Add MN BCG (bugs) to Rules.xlsx, Issue #82
- refactor: Updates to BDI calculation, Issue #66
- INCOMPLETE, completed in 2.0.0.988
- fix: Update complex number import code (BCG_ATTR), Issue #77
- Should work in all cases and not cause issues with other fields
- feature: Enable BDI calculation in Shiny app, Issue #66
- PARTIAL
- refactor: Modify code for import and merge files, Issue #77
- Only specify BCG_ATTR column
- Undoes some edits in v2.0.0.9081
- fix: Adjust import function to allow for user selection of tab or
comma
- Comma was hard coded even though gave user the choice of separators
- refactor: Updates to Shiny map, Issue #67
- INCOMPLETE
- refactor: Change taxa translator to no default
- fix: Modify code for complex number (BCG_ATTR), Issue #77
- Other logical fields could cause issues with older import method
- fix: Change links to files in Shiny from “" to”/”
- refactor: Update Index Class Parameter, Issue #73
- refactor: Update to text for Fuzzy Set Input File, Issue #70
- refactor: Update Index Class Parameter, Issue #73
- refactor: Update Shiny Fuzzy Set
- feature: Add upset plot to MTTI results report
- docs: Add
ComplexUpsetto DESCRIPTION Suggests and Shiny global
- refactor: Update Shiny MTTI, Issue #74
- Onscreen text
- Example files
- style: Move MTTI model file location
- fix: MetricFlags.xlsx ‘pctSLOPE’ to ‘pslope_nhd’
- Align with index class assignment
- Add PRECIP8110CAT for BCG_MariNW_Bugs500ct (all classes)
- refactor: Add more StreamCat variables to get index parameters, Issue
#75
- PRECIP8110CAT
- ICI
- IWI
fix: Update MTTI routine for user SampleID, Issue #74 + One instance was hard-coded
refactor: Update MTTI output, Issue #74
style: Code coverage updates
- refactor: Change order of columns for Fuzzy Thermal, Issue #70
- modtherm_5levassign.csv
- fix: Update overlapping Fuzzy Thermal CheckNames in MetricFlags.xlsx, Issue #72
- refactor: Add columns and classifications to Fuzzy Thermal model, Issue #70
- fix: MetricFlags.xlsx ‘pcSLOPE’ to ‘pctSLOPE’ (typo)
- fix: MetricFlags.xlsx ‘DrArea_mi2’ to ‘WSAREASQKM’ (and values)
- fix: Remove
browsercall in fuzzy thermal model
- refactor: Additional flags for fuzzy thermal model
- refactor: Updates to fuzzy thermal model output
- fix: BCG.Level.Membership account for less than 5 rules, Issue #68
- fix: Update examples so don’t get duplicate columns kept in output
- Can cause successive examples to fail
- BCG.Metric.Membership
- BCG.Level.Membership
- refactor: Error checking for missing variables, Shiny
- Fuzzy Thermal Model
- Index Class Param, Issue #42
- refactor: Update Index Class Param onscreen help in Shiny, Issue #42
- refactor: Shiny get Index Class Params, Issue #42
- Allow for user defined column
- Default is NAD83 North America, EPSG = 4269
- Trim output
- Allow for user defined column
- refactor: Update Shiny MTTI calculation and flags calculation and output
- refactor: Update Shiny MTTI calculation to include flags
- style: Modify some lines based on lintr suggestions
- Add nolint to Shiny library calls
- fix: Update Shiny app import to better handle BCG_ATTR (complex)
- Added exception for only integer values
- fix: Ensure all Shiny buttons use same terminology
- b_calc_x
- b_download_x
- fix: Update names of assign indec class buttons
- calc and download
- style: Modify outlining in server.R
- refactor: Modify Shiny Generate Index Class Param
- Add column names to match Shiny Assign Index Class
- Allows user to upload file with no modifications
- Add column names to match Shiny Assign Index Class
- docs: Update DESCRIPTION R >= 2.1 to >= 3.5.0 due to code dependency
- Loading of MTTI model file in Shiny app
- refactor: Add data-raw Process Data script for nhdplusTools vaa file
- Only VPUID 16, 17, and 18 for use with OR and WA.
- Add fst package to Suggests in DESCRIPTION
- Unable to upload full file to GitHub
- refactor: Shiny index class parameter generation, Issue #42
- docs: Add packages used in Shiny app to DESCRTION Suggests
- StreamCatTools
- nhdplusTools
- fix: Shiny index class parameter generation, Issue #42
- refactor: Shiny MTTI change language
- ‘Pacific Northwest’ to ‘Oregon/Washington’
- fix: Change utils::zip to zip::zip in Shiny
- Not working locally or on ShinyApps.io
- docs: Add zips to DESCRIPTION Suggests
- refactor: Update Shiny MTTI calculation (was placeholder)
- feat: Add Shiny tab for generating index class parameters, Issue #42
- Placeholder only
- refactor: Add map column select and base map, Issue #67
- Not complete
- feat: Add placeholder for map, Issue #67
- fix: Remove example file link in fuzzy thermal about page
- No fuzzy thermal examples
- feat: Add fuzzy thermal calculation and associated pages to Shiny, Issue #65
- refactor: Add link for example scripts to fuzzy thermal about page
- docs: Update
BCG.Level.Assignmentexample code - refactor: Update example script (BCG calc)
- refactor: Create ‘process’ file in data-raw for creating zip file of examples for Shiny app (‘www’)
- refactor: Update example scripts
- refactor: Add link to download example zip file in Shiny app
- refactor: Create Shiny Merge Files Output tab
- refactor: Update Shiny output tabs
- refactor: Update taxa translate 0fileversion output
- Shiny, server.R
- example code, taxa translate
- feature: Add example scripts and data for Shiny File Builder functions
- Taxa Translate
- Assign Index_Class
- Merge Files
- feature: Add Fuzzy Thermal narrative to Shiny operation
- refactor: Update Shiny onscreen text, inputs BCG calc
- refactor: Update Shiny onscreen text, inputs thermal metrics
- refactor: Update Shiny onscreen text, thermal preference metrics
- Add metadata file to calculation thermal metrics results
- refactor: Update Shiny onscreen text, BCG calc
- docs: Update readme install section with quick code
- refactor: Update Shiny onscreen text, Assign Index_Class
- refactor: Update Shiny onscreen text, Merge Files
- refactor: Change Shiny merge files order (x and y)
- Samples should be the main file (x) and keep all records and info
- refactor: Update Shiny app text
- refactor: Update Shiny to include change in BioMonTools package
- fix: Update file import routine
- Account for multiple permutations of BCG_Attr
- Add “” to na.strings
- fix: Adjust QC routine in Shiny app assign index class
- refactor: Finish updates to Shiny app merge files tab
- refactor: Add error checking for Index_Class in Shiny
- docs: Add Shiny link to README
- refactor: Layout changes to taxa translate section of Shiny app
- refactor: Add Shiny merge files tab placeholder
- proof of concept, not complete
- refactor: Update onscreen text for Shiny assign index class
- refactor: Remove uneeded QC steps in Shiny assign_indexclass routine
- refactor: Add excluded taxa subroutine to thermal metrics in Shiny
- refactor: BioMonTools MetricNames.xlsx from GitHub instead of package in Shiny
- refactor: Add taxa translate unique crosswalk to output of taxatranslate in Shiny
- fix: Modify code in Shiny for
assign_indexclassso won’t fail if field not provided.
- feature: Add thermal metric calculation to Shiny app
- feature: Add assign index class to Shiny
- refactor: Update Shiny tabs to not include numbered steps (all were step 2)
- fix: Update shiny taxa translate to combine duplicate taxa by default
- refactor: Update Shiny taxa trans to drop translator columns if have an attributes table
- refactor: Update Shiny taxa trans to use default names
- SampleID, TaxaID, and N_Taxa
- refactor: Update Shiny taxa trans to include filenames in MERGED output
- refactor: Update Shiny, split file builder in to taxa trans and assign index class
- refactor: Update Shiny app MTTI tab
- refactor: Update Shiny app for taxaid_drop parameter in
BioMonTools::taxa_translate
- refactor: Sort columns and order output of taxa translator
- feature: Add INDEX_NAME and INDEX_CLASS as input parameters to
BCG.Level.Assignment
- refactor: Shiny app, filebuilder
- save version of files in download
- reorganize the required fields requested of user
- change some text on screen
- refactor: Shiny app, filebuilder
- Ensure consistency of BCGcalc and BioMonTools columns names (all caps)
- Add about and output tabs to taxa translator
- Update for consistency pick list file names in file and in code
- Update routine for translating then adding attributes
- Leave some projects with one file but add ability for two files (PacNW)
- refactor: Update filebuilder tab in Shiny app
- Use “user file” less often
- Change summary default to TRUE
- Modified output files to include “taxatrans”
- Renamed RESULTS to MERGED in output file
- Add link to Taxa Translate Official files on GitHub
- Fix non-match output
- refactor: Change BCG.ContLevelText status from x/y tie to x.5, Issue #64
- feature: Add taxa translator tab and functionality to Shiny
- feature: Add new function to calculate BCG Status
- Uses continuous value to get Integer or PlusMinus text
- refactor: Additional Shiny outputs
- 6metflags; flag metrics, values, thresholds
- 3metrules; rules table
- refactor: Update Shiny text for additional outputs
- refactor: Update Shiny app text for slim to BCG file name for BCG output
- refactor: Change order and names of columns in BCG.Level.Assignment
output
- Memb.Total to Membership_Total
- Memb.QC to Membership_Total_QC
- Lev.1.Memb to Primary_Membership
- Lev.1.Name to Primary_BCG_Level
- Lev.2.Memb to Secondary_Membership
- Lev.2.Name to Secondary_BCG_Level
- Lev.Memb.Diff to Membership_Diff
- Lev.Memb.close to Membership_Close
- Lev.Prop.Num to Continuous_BCG_Level
- Lev.Prop.Nar to BCG_Status
- refactor: Change Shiny output 2metval_slim.csv to 2metval_BCG.csv
- fix: Update Rules.xlsx for non-ASCII characters
- breaking change: Site_Type and Index_Region to INDEX_CLASS, Issue #63
- Deprecate in functions (allow for ‘…’) and shiny
- BCG.Level.Membership
- BCG.Metric.Membership
- Include warning for old code
- Deprecate in functions (allow for ‘…’) and shiny
- refactor: Update reference Excel files for updated field, Issue #63
- Rules.xlsx
- MetricFlags.xlsx
- refactor: Shiny, change menu item name
- fix: Shiny app ‘slim’ output, Issue #62
- fix: Shiny app, markExcl, EXCLUDED to EXCLUDE
- update: Change name of PacNW model, Issue #61
- Rules.xlsx
- MetricFlags.xlsx
- Example files (file name, data, sheet names)
- Update examples in functions
- Vignettes
- update: Update BCG style temperature model thresholds
- Rules.xlsx
- refactor: Upgrades to Shiny app
- refactor: Upgrades to Shiny app
- refactor: Upgrades to Shiny app
- Rework tab order and names
- Update About
- Other
- refactor: Upgrades to Shiny app
- Added summary report
- Added packages needed for report
- Minor edits to main menu
- Minor edits to About
- update: Add ‘Therm_ORWA_Bugs500ct’ model to Excel files
- refactor: Upgrades to Shiny app
- Mark Excluded taxa
- Minor updates
- Added footer to app with shinydashboardPlus
- Added package to DESCRIPTION
- Update About
- Add placeholder tabs for future updates
- refactor: Upgrades to Shiny app
- Second version of results/metval with only those for the model
- Ensure result files removed from previous imports
- refactor: Upgrades to Shiny app
- docs: Update examples for missing columns in sample data for all functions
- fix: Update MetricFlags.xlsx for one flag
- docs: Update packages in DESCRIPTION and global.R in Shiny app
- feat: Redesign shiny app
- docs: Add packages needed by Shiny app to DESCRIPTION
- style: Perform updates from lintr and goodpractice
- fix: Update Font Awesome icons, some were deprecated
- fix: Shiny About links update so open in new tab
- docs: Update format of NEWS
- feature: Add Shiny app skeleton and function to run it, Issue #58
- refactor: Bump version number.
- fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- fix: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- refactor: Update metric.values()
- Failed when rules table included more than 1 region and metrics uneven
- refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- refactor: Update MetricFlags.xlsx for BCG_MariNW_Bugs500ct models
- tests: Add tests for flags and metric names
- refactor: Update BCG.Level.Membership() for new median rule type, Issue #55
- refactor: Update Rules.xlsx to handle new median rule type, Issue #55
- refactor: Update MetricFlags.xlsx
- Match metric names to BioMonTools::metric.values()
- Add BioMonTools_MetNam column for future test (some not metrics)
- Change symbols from = to ==
- Write test to check for Flag symbols
- fix: One entry in Rules.xlsx was “[” instead of “>=”.
- fix: BCG.Level.Membership fails test
- Missing EXC_RULE in merge statement
- refactor: Update “Notes” to “Note_Rules” in Rules.xlsx
- tests: Update test for revised sheet name in Rules.xlsx
- fix: Renamed master branch to main
- docs: Move wishlist from NEWS to GitHub Issue #56
- refactor: Updated Rules.xlsx for PacNW BCG, Issue #55
- refactor: Updated Flags.xlsx for PacNW BCG, Issue #55
- tests: Add test for floating point error
- Rules.xlsx
- Flags.xlsx
- docs: Update example for additional required columns in
BioMonTools::metric.values()
- BCG.Metric.Membership()
- BCG.Level.Membership()
- feat: Update BCG.Level.Membership() to account for special conditions
- Use Index_Name and Site_Type to allow for individual model exceptions to the typical rules for level membership
- feat: Update Rules.xlsx for exceptions in level membership in BCG.Level.Membership()
- fix: Update BCG.Metric.Membership() to use <= and >= when checking for values below and above limits rather than < and > due to rules in CT BCG using 0 as a lower AND upper limit
- fix: Update Rules.xlsx for CT BCG model, Issue #48
- Removed double entries for fish01, fish02, and fish03 SiteType
- fix: Update Rules.xlsx for CT BCG model, Issue #48
- Removed double entries for bug01 SiteType
- refactor: Update BCG.Metric.Membership() for lower and upper bounds
- Per CT Access db (2013-08-09) use <= and >= instead of < and >
- style: Wrap some lines more than 80 characters, BCG.Level.Assignment()
- fix: Update BCG.Metric.Membership() for calculating membership for
more than one Site_Type at a time, Issue #53
- Allows for NA for metrics not common to all included Site Types
- refactor: Update Rules.xlsx for CT BCG benthos
- pi_BCG_att5 to pi_BCG_att5extra
- refactor: Update BCG.Level.Membership with stop message if unable to merge data frames
- refactor: Update Rules.xlsx to match BioMonTools::metric.values()
- rename brook trout wild
- refactor: Update Rules.xlsx to match BioMonTools::metric.values()
- Add “BCG” to BCG attribute metric names
- refactor: Update BCG.Level.Assignment()
- Add column name inputs and defaults
- Update code to use inputs
- Add tempdir() to save example
- Update example to not have warning for BioMonTools::metric.values()
- Apply fixes for changes in dplyr
- refactor: Update BCG.Level.Membership()
- Add column name inputs and defaults
- Update code to use inputs
- Add tempdir() to save example
- Add QC in function to retain only the input columns
- Update example to not have warning for BioMonTools::metric.values()
- Apply fixes for changes in dplyr
- refactor: Update BCG.Metric.Membership()
- Add column name inputs and defaults
- Update code to use inputs
- Add tempdir() to save example
- Update example to not have warning for BioMonTools::metric.values()
- Apply fixes for changes in dplyr
- style: Trim lines to 80 characters (partial)
- BCG.Level.Assignment()
- BCG.Level.Membership()
- BCG.Metric.Membership()
- style: Update function examples to use “_” instead of “.” in object
names
- BCG.Level.Assignment()
- BCG.Level.Membership()
- BCG.Metric.Membership()
- style: Update function examples to use foo::fun() instead of
library(foo)
- BCG.Level.Assignment()
- BCG.Level.Membership()
- BCG.Metric.Membership()
- refactor: Update Rules.xlsx, Issue #48
- Change Index_Name, Site_Type, and Index_Region
- docs: Update DESCRIPTION remotes to proper url
- refactor: Update
metric.membership()example to use updated Rules.xlsx, Issue #48 - refactor: Update Rules.xlsx file, Issue #48
- refactor: Update
level.membership()example to use updated Rules.xlsx, Issue #48 - refactor: Update
level.assignment()example to use updated Rules.xlsx, Issue #48
- refactor: Merge pull request with updated rules, Issue #52
- refactor: Update model rules, Rules.xlsx, Issue #48
- docs: Add sticker to README
- feature: Add sticker
- Create with hexSticker
- style: Fix devtools::spell_check() issues
- NEWS
- README
- vignette_BCGcalc.Rmd
- refactor: README
- Update example, change devtools::install_github to remotes::install_github
- Rebuild README
- docs: Remove date from DESCRIPTION
- tests: Add tests
- metric_membership
- level_membership
- level_assignment
- feature: Create metrics_values dataset to use in tests
- docs: Document metrics_values dataset
- refactor: Replace undesirable function, library
- ProcessData_TaxaMaster_Ben_BCG_PacNW
- test: set up test folder
- ci: Add GitHub Action test coverage
- ci: Add GitHub Action pkgdown
- docs: ReadMe, add codecov badge
- docs: ReadMe, add lifecycle badge
- docs: ReadMe, add codefactor badge
- docs: Remove docs folder from main branch for pkgdown
- docs: Redirect GitHub repo for pkgdown to gh-pages branch
- ci: Add GitHub Actions, continuous integration
- ci: Remove TravisCI
- docs: ReadMe, remove TravisCI badge
- docs: ReadMe, Add GitHub Actions CMD check badge
- Add pkgdown website.
- Need to fix vignettes/BCGcalc_Map.Rmd.
- INFRAORDER missing.
- Need to fix vignettes/BCGcalc_Map.Rmd.
- Build Check fixes.
- Move “View” in example to “do not run”.
- BCG.Level.Assignment
- BCG.Level.Membership
- BCG.Metric.Membership
- Column names of TaxaMaster_Ben_BCG_PacNW
- Data.R
- Depends on R >= 2.10
- DESCRIPTION
- Add .github to .Rbuildignore
- Remove unused data (data folder and data.R)
- taxa_fish
- taxa_bugs_family
- taxa_bugs_genus
- Move “View” in example to “do not run”.
- Update for R v3.6.0, Issue #46
- README
- Add extra line for devtools::install_github to work properly
- README
- Added badges to README
- Map Vignette
- Update title.
- BCG.Level.Assignment
- Proportional BCG final scores, Issue #43.
- Add “tie” to narrative.
- Proportional BCG final scores, Issue #43.
- BCG.Level.Assignment
- Proportional BCG final scores, Issue #43
- Turn on features from v1.3.4.9004.
- Add proportional narrative (+/-).
- Proportional BCG final scores, Issue #43
- extdata.xlsx
- ni_total, Hi, to 450 from 400.
- Matches file in BioMonTools package.
- ni_total, Hi, to 450 from 400.
- Remove format Hoboware file from extdata folder.
- From another package under development.
- MetricFlags.xlsx
- Percent metrics to 0-100. Issues #45.
- Add field Index_Region
- Data_BCG_PacNW.xlsx
- Add fields: Issue #33.
- Index_Region
- LongLived
- NoteWorthy
- FFG2
- TolVal2
- Add fields: Issue #33.
- Rules.xlsx
- Add field Index_Region Issue #33.
- Update percent metrics to 0-100. Issue #45.
- Vignette, modify for Site_Type to Index_Region
- BCGcalc_Map.RMD
- vignette_BCGcalc.RMD
- Add “Site_Type”” to columns to keep
- Modify example for Site_Type to Index_Region Issue #33.
- BCG.Level.Assignment.R
- BCG.Level.Membership.R
- BCG.Metric.Membership.R
- Proportional Level Assignment. Issue #43.
- Needs more polish for different conditions.
- Assign all to NA.
- Last update not complete before uploaded.
- Move qc.checks to BioMonTools package. Issue #44
- Remove qc.checks.R
- Update Vignette.
- Update read_excel with guess_max=10^6 for bio data file.
- Add proportional Level Assignment. Issue #43.
- BCG.Level.Assignment
- Update release version with Remote”s”” fix.
- BioMonTools dependency not installing.
- Move Remote up in listing in DESCRIPTION.
- Renamed Remote to Remotes.
- Add BioMonTools to Imports so will auto install.
- Had removed at some point since don’t use the functions in any BCGcalc functions.
- Update SuperFamily Tipuloidea
- /extdata/Data_BCG_PacNW.xlsx
- /extdata/TaxaMaster_Bug_BCG_PacNW_v1.xlsx
- /extdata/Data_BCG_PacNW.xlsx
- Update Exclude column after QC with BioMonTools::markExcluded
- Change 6 FALSE to TRUE
- Change 1 TRUE to FALSE
- Update Exclude column after QC with BioMonTools::markExcluded
- Update ReadMe for BioMonTools::metric.values. Issue #41.
- Update version have changes related to moving functions to the BioMonTools package.
- metric.values, move to another package, Issue #40
- Moved to separate package. _
https://github.com/leppott/BioMonTools
- BioMonTools is for bioassessment and biomonitoring.
- ContDataQC should stay focused on continuous data.
- Vignette
- Updated each section with metric.values
- BCGcalc_Map.rmd
- vignette_BCGcalc.rmd
- R/data.R
- Keep example data since specific to BCG project
- Remove
- R/metric.values.R
- Update function examples.
- Add library(BioMonTools)
- qc.checks.R
- BCG.Metric.Membership.R
- BCG.Level.Membership.R
- BCG.Level.Assignment.R
- Moved to separate package. _
https://github.com/leppott/BioMonTools
- Update map colors, Issue #35.
- BCG.Metric.Membership.R
- Update details.
- BCG.Level.Assignment.R
- Add don’t run to simple example for write.csv.
- rarify, move to another package, Issue #40
- Moved to separate package.
_ https://github.com/leppott/BioMonTools- BioMonTools is for bioassessment and biomonitoring.
- BCGcalc should stay focused on BCG models.
- DESCRIPTION
- Add Remote: leppott/BioMonTools
- Remove Jon van Sickles as contributor since removed rarify function.
- Vignette
- rarify section updated.
- R/data.R
- Remove reference to data_bio2rarify
- Remove
- R/rarify.R
- data-raw/ProcessData_rarify.R
- data-raw/ 3 data files
- data/data_bio2rarify.rda
- Moved to separate package.
- Metric calculations, additional metrics.
- metric.values.R
- nt_Ephemerellidae
- nt_Heptageniidae
- nt_Nemouridae
- nt_Perlidae
- nt_Rhyacophila
- nt_Tipulidae
- MetricNames.xlsx
- metric.values.R
- Fix error with habit metric names.
- metric.values.R
- MetricNames.xlsx
- Metric calculation;
- x_HBI. Issue #37
- calculation use TOLVAL>=0 rather than TOLVAL>0 in denominator.
- Consistent naming. Issue #38
- habit_clmbrs to habit_climb
- habit_clngrs to habit_cling
- habit_swmmrs to habit_swim
- x_HBI. Issue #37
- Metric calculation;
- Tolerance metrics
- nt_tv_intol
- nt_tv_toler
- pt_tv_intol
- pt_tv_toler
- Added lower and upper limits for intol and toler
- Tolerance metrics
- Metric calculation;
- pi_Colesen
- Change is.na(FAMILY) from FALSE to TRUE.
- pi_Colesen
- Metric calculation;
- pi_Hydro
- Equal sign missing in equation (“=” instead of “==”).
- pi_Hydro
- Metric calculation;
- pi_Tanyp
- Misspelled Tanypodinae
- pi_Tanyp
- Metric calculations;
- x_HBI
- Remove negative sign. Issue #37
- x_Shan_e, x_Shan_2, x_Shan_10
- Fix equation. Not properly calculating proportions.
- Drop use of x_Shan_Num. Use x_Shan_e then convert for other log bases.
- x_D
- Fix equation.
- x_HBI
- Fix metric calculation; na.rm=TRUE for sum. Issue #37
- x_HBI _ If had any NA values for TolVal the final value was NA.
- Added na.rm=TRUE to sum function for numerator.
- Denominator already included na.rm=TRUE.
- x_D
- No effect as no records should be NA for count
- dominant calculation intermediate columns
- No effect as no records should be NA for count
- ni_total
- No effect as no records should be NA for count
- All fish metrics (with “sum”)
- x_HBI _ If had any NA values for TolVal the final value was NA.
- Add 8 additional metrics to metric.values
- MS DEQ, MBISQ 2015 _ pi_Hydro
- nt_NonIns
- pt_NonIns
- pi_Tanyp
- pt_tv_intol
- pt_tv_toler
- pi_Colesens
- pi_COC2Chi
- MS DEQ, MBISQ 2015 _ pi_Hydro
- Mapping Vignette. Issue #34.
- DESCRIPTION
- Add ggplot2 to Suggests
- extdata_BCG_PacNW.xlsx
- Add Latitude, Longitude, and COMID
- Create Vignette for mapping
- DESCRIPTION
- Release version.
- Master Taxa List
- Turbellaria BCG Attribute.
- Change from “x” to “4” to match its synonym Trepaxonemata.
- Turbellaria BCG Attribute.
- Release version.
- Rules.xlsx
- Fix typos in “Numeric_Rules” field.
- No impact on calculations.
- Fix typos in “Numeric_Rules” field.
- Release version.
- Update Vignette.
- Rarify section to 600.
- Update Vignette.
- Fix a few typos.
- Update Rules.xlsx.
- 300 count model edits.
- Vignette updates.
- Updated rarify data; data_bio2rarify
- Replace fully qualified 500 count data with 3 column 600 count.
- Update data.R entry.
- Update rarify function example.
- Update vignette example.
- Updated docs.
- extdata/ExampleDataFile.xlsx
- docs/BCGcalc_README_20180919.pdf
- Updated Rules.xlsx file in extdata.
- Finish updates to Vignette.
- Level.Assignment. Issue #11
- Update example so don’t calculate metrics twice.
- Vignette updates (incomplete).
- Metric.Membership. Issue #11
- Non numeric extra columns caused errors. Fixed.
- extdata
- TaxaMaster_Bug_BCG_PacNW_v1.xlsx; rename worksheet to match previous version.
- data-raw
- Remove data_bio2rarify.txt
- Recreate TaxaMaster_Ben_BCG_PacNW using revised XLSX file.
- Update 500count.tsv thermal column name.
- data.R
- Update entries for TaxaMaster_Ben_BCG_PacNW and data_bio2rarify
- Vignette
- Start on updates.
- Update Data_BCG_PacNW.xlsx. Issue #32
- Remove unnecessary worksheets.
- Rename single remaining worksheet.
- Update phylogenetic columns.
- Rearrange columns into required and optional.
- Add master taxa list file to external docs.
- Add thermal indicators file to external docs.
- update ReadMe. Issue #31
- Ensure reshape2 package references are consistent. Issue #30
- Ensure functions use reshape2::melt (or dcast)
- Ensure examples (and vignette) use library(reshape) and melt or dcast.
- File formats. Issue #28
- Add statement about file formats to Vignette.
- rarify data. Issue #19
- Use USGS 500 to 300 count data instead of MS 200 count.
- Change raw data process script.
- Replace data_bio2rarify.
- Modify rarify example.
- Modified rarify example in Vignette.
- BCG PacNW primer. Issue #29
- BCGcalc_README_20180918.pdf to so shows up in package help.
- MetricFlags.xlsx
- Last line, Index_Name updated for 300 count model.
- Example “write” statements as “dontrun”. Issue #27
- BCG.Level.Assignment; also moved write statement to end
- BCG.Level.Membership
- BCG.Metric.Membership
- metric.values; included write and DataExplorer
- qc.checks; no write statement.
- rarify; Changed from commented out to donotrun
- Vignette; leave “as is”. Write statements all commented out.
- BCG.Level.Assignment
- Change write.table(tsv) to write.csv. Issue #28
- extdata.xlsx. Issue #26
- Added NOTES worksheet.
- Added MetricMetadata from MetricNames.xlsx.
- Added NOTES worksheet to MetricNames.xlsx.
- Renamed worksheet “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
- Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
- Added worksheet “BCG_PacNW_v1_300ct”.
- Revised code references to Rules.xlsx (worksheet and Index_Name). Mostly examples.
- extdata_BCG_PacNW.xlsx
- Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
- extdata.xlsx
- Renamed Index_Name from “BCG_PacNW_2018” to “BCG_PacNW_v1_500ct”.
- Added Index_Name “BCG_PacNW_v1_300ct”. Adjust some flags based on 500 vs. 300 count.
- qc.checks. Issue #25.
- Update Description.
- Add View for imported checks file.
- Vignette. Change section title from QC Checks to Flags.
- Update Level Assignment example in Vignette with real data and append flags.
- Function rarify. Issue #19
- Remove keywords.
- Function rafify. Issue #19
- Fix typo in @param mySeed. Remove extra period.
- Metric Names metadata Issue #18
- Update extdata.xlsx
- Add PDF version to docs.
- More Indiana files. Issue #24
- extdata_IN_BCG_Bugs_20170203.xlsm
- extdata_Metrics_Bugs_IN.xlsx
- Remove Indiana references. Issue #24.
- Delete extdata Indiana file (Data_BCG_Indiana.xlsx).
- Delete data-raw Indiana database (BCG_Model_Calc (IN 20170301).mdb. Already excluded from package build.
- Delete example in metric.values function.
- DESCRIPTION
- Add date.
- Add Jen Stamp as contributor
- Citation still gives error but is more complete now. Issue #23
- metric.values
- Fixed included metrics (fun.MetricNames)
- metric.values
- Added QC check for NonTarget==FALSE.
- Give a warning if have zero FALSE values.
- metric.values
- Added QC check for Exclude==TRUE.
- Give a warning if have zero TRUE values.
- Update Vignette.
- Add data munging example. Issue #14
- Update metric.values section for required fields. Issue #13.
- Added section demonstrating saving only select metrics. Issue #15
- Update text in metric.values.
- metric.values. Issue #16
- Added QC worksheet to extdata_BCG_PacNW.xlsx
- metric.values. Issue #13
- Add required fields (columns) to help file.
- Add QC check in function. Prompt user to continue or stop.
- metric.values
- Added metric Percent Baetis tricaudatus complex + Simuliidae individuals (pi_SimBtri). Issue #16.
- New release version.
- qc.checks.R
- Modification to use metric names as lower case. Issue #12.
- Example table; useNA=“ifany”.
- New release version.
- BCG.Level.Assignment.R
- Membership QC (sum===1) add “round” 8 to avoid too many samples being flagged as “FAIL”.
- Example changes:
- Changed terminology from PASS/FAIL to NA/flag in flag fields.
- Changed “NumFlagFAIL” to “NumFlags”.
- Reordered columns so “NumFlags” is before the flag fields.
- Release version for Pacific Northwest BCG workgroup with updated model.
- BCG.Level.Assignment.R
- Example code to match up with qc.checks output.
- Includes export to file.
- qc.checks.R
- Remove example modifying column names.
- BCG.Level.Membership.R
- Added “round” to 8 places when determining level membership.
- Floating point error resulted in the occassional value of 1.1E-16 when the previous level was “1”.
- This resulted in the sample getting a split level assignment, e.g., 3:4 when it was 100% 3.
- metric.values.R
- Add additional metrics
- nt; BCG_att; 1i, 1m, 3
- pt; BCG_att; 1i, 1m, 3
- pi; BCG_att; 1i, 1m, 2, 3
- thermal indicator metrics
- modify grepl to == because COLD was matching COLD and COLD_COOL. Only want exact match.
- Update Rules.xlsx.
- Level 3 (Hi and Lo), pi_BCG_att56 changed to pt_BCG_att1i23.
- Change involved both direction and thresholds.
- Update metric.values.
- Add “cols2keep” to allow for extra fields in output.
- Need extra fields for qc.checks
- Update qc.checks.
- Update example with cols2keep from metric.values example.
- Update bio data to be used for the model; Issue #7
- Collapse mites to Order.
- Update extdata/Rules.xlsx; Issue #7
- metric.values dd nt, pi, and pt metrics; Issue #7
- NonIns_BCG_attr456
- NonInsJugaRiss_BCG_attr456
- QC Flags, Add pi_dom02. Issue #7
- Update format of NEWS.
- metric.values, row_number to dplyr::row_number for dominant metrics.
- metric.values, Issue #7
- Update metrics from NonClump to NoJugaRiss.
- Release new and fully QCed version.
- Metric.values
- Fix metrics with not equal functions.
- Ensure use is.na(x)==TRUE rather than x==NA
- When have more than one condition for a data column need to be in the same statement.
- Better define clumpy taxa for 2 metrics.
- BCG.Level.Membership
- Fixed combination of rules by level. Missed a column and was getting duplicates for alt rules that changed the outcome.
- BCG.Level.Assignment
- Replace For loop with apply.
- Add special conditions for ties (2 levels with 0.5) and primary level is 1 (no 2nd level).
- Metric.values
- Fix non-clumpy metrics.
- Remove extra data frames for dominance metrics. Slight speed improvement. Issue #5.
- Fix version numbers in NEWS.
- Updated ReadMe with only the relevant packages. Issue #4.
- Only metric value issues left to resolve with test data set. Rest of the calculations are ok.
- Rules.xlsx
- Fill in missing cells.
- metric.values.R
- Update FFG abbreviations to match example data.
- Dominant N and special Dominant N metrics.
- Define pipe as referencing dplyr. Slows down the functions but keeps dplyr from needing to be loaded.
- SiteType values to lowercase.
- metric.values.R
- BCG.Metric.Membership.R
- BCG.Level.Membership.R
- BCG.Level.Assignment.R
- Consistent terminology; don’t mix “.”, ” “, and”“. Use””.
- METRIC_NAMES
- METRIC_VALUES
- SITE_TYPE (and change from REGION)
- RULE_TYPE
- NUMERIC_RULES
- LIFE_CYCLE
- LONG_LIVED
- THERMAL_INDICATOR
- NAME_WIDE
- Rebuild PacNW master taxa list with changes.
- Consistent names (columns and categories).
- Example PacNW data.
- Consistent names (columns).
- QC Checks
- Update Vignette.
- All functions and examples seem to be generating the proper outputs. When QC only a few metrics are off. But enough that no final results are correct (that is, all levels, site types, and samples are affected but the remaining QC issues). Non-Insect and modified dominant 2 metrics are the 4 that have issues.
- BCG.Level.Membership.R
- Correct function to consider preceding levels when assigning membership scores.
- metric.values.R
- Added Thermal Indicator (TI) metrics.
- Updates to PacNW bug data and rules files (xlsx).
- metric.values.R
- Update pt_BCG_att1i2 and 1i23 metrics (numerator not capturing “i” taxa).
- Update Rules.xlsx
- Vignette didn’t update in previous version.
- Tweak “data.R”. Not complete!
- Added example save code for master taxa list.
- Update BCG.Metric.Membership.
- Add some error checking.
- Colnames to upper case.
- Updated Rules.xlsx
- Percent metrics converted to 0-1 values to match metric.values calculations.
- Fixed Index Name for some records.
- metric.values.R
- Updated examples, details, and description.
- Update BCGcalc Vignette.
- Update Readme.
- Update BCG.Level.Membership
- Added PacNW benthic master taxa list to data.
- Created “data.R”. Not complete!
- Update PacNW example data to use TRUE/FALSE for Excluded and NonTarget fields.
- Updated metric.values
- Moved common data munging to earlier in function so applies to all communities.
- Enabled NonTarget exclusion. NonTarget column now required.
- Completed lingering edits for “Tier” to “Level”.
- Completed BCG.Level.Membership function.
- Remove “Tier” wording in package and rename some functions to better reflect usage.
- Include example code for saving results for each function.
- Change Region to SiteType in code and example data files.
- Dom02 special metric placeholder.
- Update Rule table for Level assignments.
- BCG.Levels function.
- Fixed error in sequencing in BCG.Membership function.
- Add last of the PacNW specific metrics to metric.values.
- Added Vignette.
- Check clean up.
- Convert data imports from development folder to pacakge folder with system.file.
- Add data for rarify function.
- BCG.Tiers function.
- Add BCG.Membership function. Return is in long format.
- Not QCed but has some known issues.
- Add subtitles, date, author to YAML header to NEWS and README.
- Add “flags” Excel file to raw-data for QC checks. Used in qc.checks function (new).
- Added 4 new ni metrics to metric values to be used for QC checks (flags).
- qc.checks.R (incomplete but works).
- Add BCGcalc.R to describe the package.
- Update documentation headers in R files.
- metric.values.R, benthos
- Added BCG attribute metrics.
- Added outlining for readability in code.
- More metrics and clean up of file.
- Prepare example data for metric calculation.
- Added na.rm=TRUE to n_distinct and sum in summarise.
- Add parts without any modification from
MBSStoolspackage.- rarify function
- metric.values function
- included data folder and files
- added Excel file to extdata with metric naming explanation
- Updated files for package.
- Readme, NEWS, DESCRIPTION
- Not complete.
- Created GitHub repository