#> Last Update: 2024-04-08 12:38:08.080495
- fix: Update examples and vignette to not use droplevels()
- Revised thresholds no longer has levels
- refactor: Bump version number for fix in previous commit
- docs: Create release on GitHub using new version number
- fix: Revise family BIBI scoring thresholds, Issue #45
- test: Added test for extra digits for scoring thresholds
- refactor: Update vignette for IBI calculations, Issue #45
- StringAsFactors default now FALSE so don’t have to remove in Vignette
- refactor: Update GitHub repo default branch from ‘master’ to ‘main’
- docs: Update runShiny() documentation with updated URL
- docs: Add sf to MapTaxaObs example in vignette
- refactor: Modify
metric.values()calculations to use na.rm=TRUE- All
sum()andmax()metrics
- All
- refactor: Update example in MapTaxaObs
- Swap
path.package()forfind.package()
- Swap
- refactor: Shiny app make download button disabled when click
‘calculate’
- Issue #32
- refactor: Tweak Exclude column QC in
metric.values(), Issue #31
- refactor: Add markdown to DESCRIPTION Suggests to avoid build failure on GitHub Actions
- refactor: Tweak vignette so GitHub Action doesn’t fail
- refactor: Update ‘add_new’ case in
qc_taxa() - tests: Update testcases for qc_taxa to match recent changes
- refactor: Add package to referenced function in MapTaxaObs
- refactor: Add global variable bindings
- MapTaxaObs
- metric.scores
- refactor: Update map example in Vignette from rgdal to sf
- refactor: Update FlowSum to convert input from tibble to data frame
- Example was failing
- refactor: Update IonContrib ion.ref default to NULL
- is.na() was causing issues when doing QC check within the function
- fix: Fix combining of files in qc_taxa
- Change order of data frames in merge
- Convert input data frame to taxanames in all caps prior to matching
- refactor: Shiny UI, remove semicolon for file delimiter
- refactor: Update MapTaxaObs function, Issue #17
- Issues with state shapefile and rgdal, switch to sf package
- docs: Add sf package to DESCRIPTION
- refactor: Update GIS files for use with strata for consistency, Issue
#36
- Highlands to Highland
- Piedmont to EPiedmont
- refactor: Update PHIcalc for consistency, Issue #36
- Highlands to Highland
- Piedmont to EPiedmont
- CoastalPlain to Coastal
- BioRegion paramater to Strata
- Add QC check to use uppercase for strata
- refactor: Update MBSS.PHI data strata for consistency, Issue #36
- refactor: Add fibi and msw GIS base files to strata(), Issue #39
- Update ProcessData script
- Add shape files to extdata_GIS_strata.zip
- Update data.R
- Update strata function for the new layers
- docs: Tweak help file for strata function, Issue #39
- feat: Add strata function to assign strata based on lat-long, Issue
#39
- Add function strata
- Add data _GIS_strata.zip
- Add internal data shp_strata_bugs and shp_strata_fish
- Create ProcessData in data-raw for shapefiles
- style: Trim to 80 characters, NEWS
- docs: Add packages to DESCRIPTION Suggests for strata function, Issue
#39
- sp
- MazamaSpatialUtils
- refactor: Update license file and README badge, Issue #41
- refactor: Add binding for global variable, metric.scores.R
- docs: Rename example inputs to match MapTaxaObs function call, Issue
#36
- Issue #17
- style: Edit style of MapTaxaObs code
- refactor: Rework filepath within MapTaxaObs, Issue #17
- refactor: Edits to MBSStools_vignette.Rmd
- Move files to proper folder (vignettes)
- Fix code blocks so run properly
- Comment out write.csv()
- Convert View() to kable(head()) where eval=TRUE
- refactor: Edits to MBSStools_vignette.Rmd
- Merge pull request 42
- refactor: Update install code example
- README
- MBSStools_vignette.Rmd
- refactor: Update example, MapTaxaObs
- Change getwd() to tempdir()
- docs: Update spelling and language in MBSStools_vignette.Rmd
- style: Fix items from goodpractice::gp()
- Trim lines to 80 characters
- IonContrib
- test-qc_taxa
- qc_taxa
- data
- MapTaxaObs
- server
- global
- Replace ‘=’ with ‘<-’
- IonContrib
- Trim lines to 80 characters
- style: Fix typos
- chore: Rename files in instwith non-portable names
- chore: Fix comment line without leading comment symbol
- chore: Document subfunctions of metric.values()
- chore: Rename files in instwith non-portable names
- chore: Add bindings for global variables
- MapTaxaObs
- metric.scores
- metric.values
- style: Trim lines to 80 characters
- metric.scores
- runShiny
- PHIcalc
- chore: Remove View() from examples
- metric.scores
- metric.values
- PHIcalc
- IonContrib
- FlowSum
- chore: Remove Excel files from data folder
- AllFish_95to16.xls
- TaxaMapsCrossWalk20170731.xlsx
- style: Trim to 80 character lines
- FlowSum.R
- chore: Remove orphaned package from DESCRIPTION
- plotly in Suggests
- chore: Add non standard files to .Rbuildignore
- NEWS.rmd
- README.Rmd
- chore: Change default for ion.ref parameter in IonContrib to NA
- Use MBSS.Ion.Ref if NA
- docs: DESCRIPTION, add Bug Reports entry
- tests: qc_taxa, replace = with <-
- refactor: Add foo:: to missing functions.
- docs: Readme, add codecov badge
- docs: Readme, add gh R-CMD-check badge
- docs: Readme, sort badges
- docs: Add test-coverage gh Action, codecov.io
refactor: CodeFactor change 1:foo() to seq_len(foo()) + MapTaxaObs.R
- docs: Remove docs folder for pkgdown in main branch
- pkgdown now handled by GitHub Action and is stored in the gh-pages branch
- docs: Add pkgdown github action
- ci: Remove travis.yml (free service shutting down)
- docs: ReadMe, add lifecycle badge
- docs: ReadMe, not all changes updated from previous update
-
docs: ReadMe, add CodeFactor badge
-
docs: ReadMe, Remove TravisCI badge as service is shutting down free accounts
-
ci: Remove TravisCI yaml and switch to GitHub Actions CI
- Rebuild vignette with taxa distribution map as image; Issue #33
-
Shiny app, ensure download button is not active until create zip file; Issue #32
- Add shinyjs to DESCRIPTION
-
metric.values; Issue #30 and #31
- Modify Exclude column QC check.
-
metric.values; Issue #34
- Added Piercer as valid FFG entry.
-
UI.R
- Added version number to title of Shiny app.
- metric.values; Issue #30
- Add basic QC fixes for non-standard bug files.
- qc_taxa
- Fix typo in example.
- metric.scores; Issue #29
- Fish message about 0 individuals always showing.
- Added condition so prints only if relevant.
- Fish message about 0 individuals always showing.
- Update taxa_fish data without an extra column.
- Remove SiteID from _95to16.xls.
- Replace example data files in shiny app (munged Site IDs).
- Update Vignette.
- Modify Site IDs in bug (genus and family) and fish data.
- Update Vignette.
- Vignette not rebuilding.
- Replace XLConnect with readxl.
- Java issue.
- Replace XLConnect with readxl.
- Update Shiny app to use qc_taxa(); Issue #26
- Update pkgdown website.
- metric.values
- QC checks on valid values; Issue #26
- qc_taxa
- New function; Issue #13 and #26
- tests
- Add tests for qc_taxa
- taxa_fish
- Update 2 Species name errors so passes QC check.
- Add testing
- DESCRIPTION, add testthat to Suggests
- test PHIcalc, Issue #19
- metric.scores.R, Issue #20
- Update column name checking for user input data frame.
- Edit error message to user.
- Update column name checking for user input data frame.
- metric.scores.R
- Fix error in assigning final IBI due to changes in behavior of Tibbles.
- Shiny App, Issue #22.
- File upload size increased from 10 to 25 MB.
- Output file format, tsv to csv.
- Zip file download.
- Remove input file (original and transformed).
- Keep only the “results_” files (values, scores, and plot).
- Update fish metric scoring for no taxa obsevered, Issue #26
- taxa_fish.rda
- data.r
- metric.scores.r
- Update metric.values.
- Error when using R v4.0. Issue #28.
- Add pkgdown website.
- Examples failed for FlowSum and IonContrib.
- Shiny release version
- Shiny app, Issue #22
- Remove link to package vignette (doesn’t work on Shiny.io)
- Additional packages to Suggests for the Shiny app, Issue #22
- Complete Shiny app, Issue #22
- README
- Update install example to ensure vignettes are installed.
- Update for R v3.6.0, Issue #27
- README
- Added extra line to make work devtools::install_github()
- DESCRIPTION
- Remove StagedInstall: no
- README
- README
- Update badges.
- Shiny app development, Issue #22
- Not complete.
- Revise for staged install for R v3.6.0, Issue #27
- DESCRIPTION
- StagedInstall: no
- Temporary fix. Still needs to be installed from a local file.
- DESCRIPTION
- Edits to Shiny App. Issue #22.
- Incomplete.
- Revise “EXCLUDE” column in benthic data from “Y” and “” to TRUE and
FALSE.
Issue #25.- data
- taxa_bugs_family
- taxa_bugs_genus, ProcessData had additional issues that weren’t present in prior versions.
- function; metric.values
- Function help text
- Example use “MetricName.Other” rather than “Metric” to get pertinent metrics.
- Replace EXCLUDE!=“Y” with EXCLUDE!=TRUE
- data
- Vignette
- Example for installing a package (line 51) had a typo.
- droplevels update for MetricName.Other (line 110, 161, and 187).
- Shiny example code, eval=FALSE
- Revised scoring thresholds table, per MBSS. Issue #23.
- metric.scores.R
- Update example code to match the MBSS metric names.
- Slight tweaking of QC check for column names.
- Shiny app, Issue #22
- Include function to launch the Shiny app.
- runShiny
- Add to Vignette.
- metric.scores
- Add example of adding narrative to IBI scores. Issue #21.
- DESCRIPTION
- Suggests; XLConnect (MBSStools_vignette.Rmd)
- Maintainer; Erik.Leppo@tetratech.com (Needed if submit to CRAN)
- Description; make more verbose. (Needed if submit to CRAN)
- Title; remove ending period.
- NEWS
- Restructure. Still not right but has all info now.
- Remove planned updates.
- Shorten long lines.
- FlowSum.R
- IonContrib.R
- MapTaxaObs.R
- metric.scores.R
- metric.values.R
- PHIcalc.R
- Remove “keywords” (incorrect usage).
- FlowSum.R
- IonContrib.R
- MapTaxaObs.R
- metric.scores.R
- metric.values.R
- PHIcalc.R
- .travis.yml
- Add TravisCI yml to GitHub directory.
- Add TravisCI yml to Rbuildignore.
- Add continuous integration (TravisCI) badge to ReadMe.
- DESCRIPTION
- Move dplyr and rgdal from Suggests to Imports
- Packages not always loading. Issue #15 and Issue #17
- Modify minimum version of R from 3.3.2 to 3.4.0.
- MapTaxaObs did not work in earlier version of R.
Updated to v3.4.0 and no issue. Issue #17.
- MapTaxaObs did not work in earlier version of R.
- Issue #17 with MapTaxaObs
- Removed extra file in vignette folder.
- Update Vignette as doesn’t build in check; commented out MapTaxaObs.
- Corrected metric.score() [line 181] for fish for “HIGHLANDS” was incorrectly designated. These sites were not getting a final FIBI score.
-
Update each function’s description and vignette with the packages needed for that function to work properly.
-
Update Vignette for a few typos and so shows in final package. Also messages=FALSE for XLConnect example.
-
DESCRIPTION. Move rgdal from Depends to Suggests.
-
Fish metric example not working in metric.values(). Issue #14.
Extra parameter. Removed and works.
- Release version 1.
-
Add install guide notebook.
-
Tweak vignette.
-
Update Readme.
-
Final version before going to v1.0.0.
-
IonContrib, ensure data input is a data frame.
-
PHI, ensure data input is a data frame.
-
Update vignette.
-
Fixed example for fish metrics in metric.values(). 20170920.
- IonContrib() added barplot example. 20170919.
- Fix typo in example for metric.scores(); “Metrics.Bugs.Scores” to “Metrics.Bugs.Scores.MBSS”. 20170913.
- Added MSW (family) data, values, and scores. 20170909.
- Added BIBI.
- Updated metric names to match those used by MBSS.
- Updated metric.values() and metric.scores().
- Updated genus level bug data file.
- Add FIBI. 2017-09-05.
- metric.values.R
- metric.score.R
- example data files
- -raw.scoring.tab and metric adjustment
- Added dplyr to DESCRIPTION. Needed for metric values and scores. 20170908
- Modified -raw.scoring.tab to resolve QC issues with 2016 data. 20170908.
- Updated taxa map data for typo in “no fish observed”. 20170822.
- Updated fish data and crosswalk table examples so have more matched
data.
Also update help to remind that data has to be on the first worksheet for the Excel file. 20170731.
- Updated DESCRIPTION. “Erik” to “Erik W.” and added Matt Ashton as data contributor. 20170728.
-
Added TaxaMapsObs(). Issue #2. 20170720.
-
Libraries readxl (suggested) and rgdal (required) added to DESCRIPTION.
Maps won’t generate without rgdal loaded. 20170720. -
Added example data and GIS files (zipped). 20170721.
- Added “LazyData: true” to DESCRIPTION. Data was not being loaded
properly.
Issue #9. 20170623.
-
Modified vignette.
-
Modified data-raw Process data R files (wd).
-
Added IonContrib.R
- Added vignette for documentation of each function and the library as a whole.
- Address issues with PHIcalc from testing. Removed extra rows from Excel import for data MBSS.PHI. Added line to convert values to numeric inside MBSS.PHI. (not complete)
- FlowSum(). Added Error Handling for misidentified Channels.
Updated data MBSS.flow.
-
Flow sum calculation completed. Included Channel Number as grouping variable but sum across channels to get the total site flow.
-
PHI, edit script for outlining in RStudio.
-
PHI.calc() to PHIcalc().
-
Data.R and folder “data-raw”.
-
PHI, tweak for created data. Using Excel to build rda rather than txt file from the Excel.
- Completed PHI calculation.
-
Created GitHub repository.
-
Added ReadME.RMD and NEWS.RMD
-
PHI calculation started.