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Update main branch for tcpl v3.2 CRAN release #300
Commits on Sep 28, 2023
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Commits on Oct 2, 2023
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Commits on Oct 5, 2023
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Merge pull request #153 from USEPA/142-add-flags-in-tcplPlot-output
142 added level 6 flags to tcplPlot output by boolean flag
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Commits on Oct 11, 2023
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Merge pull request #157 from USEPA/147-clean-up-mc6-flag-descriptions
147 cleaned up mc6 flag descriptions
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Merge pull request #139 from USEPA/128-subset-chid-export_ready-false
128 changed export_ready parameter default to FALSE
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Commits on Oct 12, 2023
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Merge pull request #159 from USEPA/149-remove-lvl-paramter-tcplPlot
149 removed lvl parameter from tcplPlot, assigned by type now
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Commits on Oct 13, 2023
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Merge pull request #158 from USEPA/60-update-processing-for-control-d…
…ata-inclusion 60 remove subset by wllt in mc4.R
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Merge pull request #160 from USEPA/148-add-y-axis-scaling
148 add y axis scaling
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Commits on Oct 16, 2023
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Commits on Oct 17, 2023
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151 cran 310 release (#152) (#156)
* updated docs * added github to buildignore * added documentation for invitrodb_dd data file * updated version number * fixes variable binding note * moved vdiffr from imports to suggests since it is only used in tests and not required to use the package normally * added default multi for old style plots * accepted and resolved minor snapshot test difference based on testing environment * updated news and cran-comments * added additional rhub to cran comments
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Merge branch '92-update-tcplPlot-sc-plotting' of https://github.com/U…
…SEPA/CompTox-ToxCast-tcpl into 92-update-tcplPlot-sc-plotting
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Commits on Nov 1, 2023
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Commits on Nov 20, 2023
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Merge pull request #143 from USEPA/5-padilla-phase-iii-sc-mthds
5 add padilla phase iii sc2 mthds and fix spid character string call This is an outstanding pull request that could have been merged since data has been processed successfully
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Commits on Nov 22, 2023
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Merge pull request #167 from USEPA/165-update-model-types-for-ow-bidi…
…r-mthds 165 update the model types in ow mc5 methods for plotting
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Commits on Nov 27, 2023
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Merge pull request #168 from USEPA/92-update-tcplPlot-sc-plotting
92 update tcpl plot sc plotting
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Commits on Nov 28, 2023
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Merge pull request #171 from USEPA/165-update-model-types-for-ow-bidi…
…r-mthds 165 fix for = error on build
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Commits on Nov 29, 2023
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Commits on Dec 1, 2023
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Revert "Revert "Merge branch 'main' into dev""
This reverts commit f91399b.
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Commits on Dec 6, 2023
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Merge pull request #174 from USEPA/57-add-tcplPlot-compare-parameter
Merge compare feature into main plotting branch
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Commits on Dec 7, 2023
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* removed logging at level 3 and unlogging at levels 4 and 5 * resoliving merge conflict * removed unlogging from plotting * updated logc to conc for pipelining through level 5 * updated logc to conc in plotting * updated mc3_methods to use conc instead of logc * updated load * updated mc5 for logc_min to conc_min * updated level 6 files for conc compatibility * removed null concs from level 4 and added warning
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Commits on Dec 12, 2023
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Commits on Dec 14, 2023
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set all b and n wells to 0 conc and after check for any remaining nul…
…ls and throw error (#181)
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Commits on Dec 20, 2023
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* changed tcplloaddata for sc1 from logc to conc * specify sc1.conc in load data
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Commits on Dec 21, 2023
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Merge pull request #146 from USEPA/92-update-tcplPlot-sc-plotting
Update tcpl plot - 7 tickets
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Commits on Jan 30, 2024
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173 overhaul tcpl load data for backwards compatibility (#191)
* 173 start new load scheme * 173 improved tcplLoadData to be flexible to any version of invitrodb * 173 added schema check for lvls 4+5 add.fld
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196 overwrite osd during hitcalling (#199)
* created overwrite method for osd so that bmr == coff and removed unnecessary sql statement from mc5 * removed ow from mc5 method as that is only applied after hitcalling * added if statement to check for osd_coff_bmr method and to overwrite osd right before hitcalling * removed bug where loec.coff copied code was left in osd codeblock * changed osd value to all_onesd to match what is loaded during tcplloaddata * pivot mc4 dat to long format to fit how tcplfit2 nesting is required * initialize overwrite_osd value
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Commits on Feb 22, 2024
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Merge pull request #205 from USEPA/204-plotting-error-in-sc-related-t…
…o-tcplLoadData-update 204 fixed tcplLoadData space bug and tcplPlot order bug
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Commits on Mar 1, 2024
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207 added saving errfun to mc4 params and including the saved value i…
…n mc5 hitcalling
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207 Added default for mc4 errfun if tcplfit2_core does not return an …
…errfun Could not assume that errfun would be returned (ie using the main/CRAN version of tcplfit2 before errfun updates are released)
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Merge pull request #195 from USEPA/163-create-single-direction-sc-met…
…hods 163 create single direction sc methods
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Merge pull request #209 from USEPA/207-investigate-level-5-mutate-pro…
…cessing-error 207 solve mutate error, added errfun to params
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Commits on Mar 20, 2024
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202 reworked tcplQueryAPI to pull from all assays or just by aeid
pulls from all assays if supplied 'fld' is not 'aeid'
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Commits on Mar 29, 2024
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220 update mc6 methods to use model_type, update descs, remove no.med…
….single.dir.gt.3bmad
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Commits on Apr 2, 2024
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Merge pull request #201 from USEPA/17-add-toxref-toxcast-aed-vignette
Add ToxRefDB-AED comparison section to data retrieval vignette
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Commits on Apr 8, 2024
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Merge pull request #221 from USEPA/202-integrate-ccdR-into-tcplLoadData
202 integrate ccdR into tcpl load data
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Merge pull request #225 from USEPA/216-backwards-compatibility-checks…
…-fixes 216 backwards compatibility checks fixes
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161/82 investigate combined sc-mc output: tcplVarMat() overhaul
rebasing varmat branch with dev after updates to subsetChid and loadData
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Merge pull request #222 from USEPA/220-update-mc6_methods.R-to-accoun…
…t-for-model_type 220 update mc6 methods to use model_type, update descs, remove no.med.single.dir.gt.3bmad
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Commits on Apr 12, 2024
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Merge pull request #229 from USEPA/226-tcplPlot-fails-when-winning-mo…
…del-is-none 226/172 tcpl plot fails when winning model is none/unregistered chemicals do not show NA
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Added description and plot of biphasic poly2 to table 7 and figure 2;…
… Added explanations of new poly2 function and default error function.
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Commits on Apr 15, 2024
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check for rmysql and unload if in namespace (#214)
* check for rmysql and unload if in namespace * added warning
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Commits on Apr 18, 2024
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- Added descriptions for method fc0.25 and pc40
- Removed redundant method descriptions that were incorrectly grouped under other (previous merge issue? - Cleaned up indentation/alignment issues and removed unnecessary white spaces - Added method fc0.25 and pc50
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Merge branch 'dev' of https://github.com/USEPA/CompTox-ToxCast-tcpl i…
…nto 227-tcpl-data-processing-vignette-updates-accounting-for-updates-to-tcplfit2
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Merge pull request #239 from USEPA/211-add-fc025-mc5-cutoff-method-fo…
…r-tshr-processing 211 add fc025 mc5 cutoff method for tshr processing
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Merge pull request #186 from USEPA/161-investigate-combined-sc-mc-out…
…put-varmat 161/82 investigate combined sc-mc output: tcplVarMat() overhaul
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Standalone Plotting (and comparison between versions of invitrodb) (#242
) * first pass standalone data * first refactor with ability to supply standalone dat * moved code so ordering is preserved * added tcplPlotValidate function as a function that lets us validate the variables that user supplied. Then add those validated parameters back into the function environment * if dat is provided by user, still create a compare column * readded compare == FALSE because rbind adds compare data back in * added type to tcplPlotSetYRange * length check needs to check that compare.val length = to dat nrows now because val COULD be null, but regardless dat will be filled by then * added rbind into else clause so it is before y range * minor changes from meeting with carter * add lvl to tcplPlotValidate list * move length check to be after loading - now can use aeid/spid to compare * use fld instead of join_condition, works for all flds not just m4id and s2id * changed order set to be compatible with multiple length fld put the field that dictates the order first in your list like: fld = c("spid", "aeid") --------- Co-authored-by: cthunes <[email protected]>
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243 update blineshift and related methods (#245)
* 243 removed well type filtering from blineshift methods * 243 updated blineShift csub to be log10(conc)
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233 expand ccd r integration into tcpl load funcs (#246)
* 233 integrated tcplQueryAPI into 4 tcplLoadAxxx funcs * 233 integrate tcplLoadUnit and fix small tcplQueryAPI bug * 233 integrated into tcplLoadConcUnit, small tcplQueryAPI bug fix * 234 integrated into tcplLoadChem, small tcplQueryAPI update * update tcplPrepOtpt to make compatible with API plotting
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Merge branch '231-add-data-retrieval-via-API-vignette' of https://git…
…hub.com/USEPA/CompTox-ToxCast-tcpl into 231-add-data-retrieval-via-API-vignette
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fixed order bug, now with use in list or non-list 'val'
for hopefully the last time...
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Merge pull request #257 from USEPA/235-247-248-206-API-plotting-and-b…
…ug-fixes 235 247 248 206 api plotting and bug fixes
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Merge pull request #261 from USEPA/258-add-sc1-method-for-bval-by-wllt
Added sc1 method bval.nwlls.med
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Merge branch '231-add-data-retrieval-via-API-vignette' of https://git…
…hub.com/USEPA/CompTox-ToxCast-tcpl into 231-add-data-retrieval-via-API-vignette merge rebase from dev
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Merge pull request #260 from USEPA/231-add-data-retrieval-via-API-vig…
…nette 231 add data retrieval via api vignette
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Merge pull request #240 from USEPA/227-tcpl-data-processing-vignette-…
…updates-accounting-for-updates-to-tcplfit2 227 tcpl data processing vignette updates accounting for updates to tcplfit2
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Merge pull request #264 from USEPA/230-update-tcplVarMat-docs
230 update tcpl var mat docs
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Merge pull request #269 from USEPA/48-tox-485-chemical-not-populated-…
…in-cytotox-table-even-though-there-is-data-at-mc4 removed gnls filter
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changed load clib to chemlist (#270)
* changed load clib to chemlist * removed clib function * 251 ran devtools::document() to add exported function to NAMESPACE * 251 cleaned up some clib -> chemlist changes in code and docs --------- Co-authored-by: Carter Thunes <[email protected]>
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Merge pull request #273 from USEPA/268-update-ccdR-dependency-to-ctxR
268 update references to ccdR to use ctxR instead
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Merge pull request #274 from USEPA/267-export-tcplPlotLoadData-as-sep…
…arate-file 267 created separate tcplPlotLoadData function to export and refactored related code
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Merge pull request #277 from USEPA/276-add-mc7-to-tcplLoadData
276 added mc7 to tcplLoadData, only for MySQL connections
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Merge pull request #279 from USEPA/278-require-nhit-=-2-for-tcplcytop…
…t-calculations New logic stipulates that if either of those conditions is not met, we would report the default tcplCytoPt. This has been updated in invitrodb and v4.2.
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First pass vignette updates for v3.2 release (#271)
* 210 intro vignette conc -> logc change * 210 new mc4 cols added to intro vignette mc4 table * 210 updated titles and removed data retrieval v2 vignette * 210 added link to URL line in DESCRIPTION * 210 updated tcplVarMat appendix section to reflect updates * 210 updated tcplConf section * 210 remove level 6 processing not possible * 210 added sections in data retrieval vignette covering new 'ow' mthds * 210 update data retrieval title * 210 remove line about removing well types * 210 update summary values list in processing vignette * 210 update existing tcplPlot text and examples with updated parameters * 210 added new tcplPlot examples showing new parameters and use-cases * 210 added single conc plotting examples to data retrieval vignette * 210 data retrieval add tcplConf, backwards compatibility, fix headers * 210 update tcplLoadClib to tcplLoadChemList in data retrieval vignette * clean up mc4 and mc6 mthd documentation * Reformat Rmds style, add hex, edits throughout * fix model_type in mc5 table * fix cytotox * Update Data_interpretation.Rmd I edited text throughout in minor ways to clarify. * Update Introduction_Appendices.Rmd Minor textual changes * Update Data_processing.Rmd Minor edits throughout - tcplfit2 (case sensitive), POD to potency estimates (so as not to confused with in vivo PODs), and some other textual edits. * Update Data_processing.Rmd More minor text updates on flag filtering. * Update Data_retrieval.Rmd Minor typos fixed * Update Data_retrieval_via_API.Rmd Minor grammatical changes * minor vignette updates, clean up README and DESC * update readme as Rmd for badges * add DOI and hex * additional badges * update hex for better alignment * fix badges * final badge update * hyperlink hex to CRAN * Update Data_interpretation.Rmd delete "provided for the Hill and Gain Loss models" from ac50 explanation * update hit call, ac50, and cutoff paragraphs Clarified some text around definitions of hit call, ac50, and cutoff * Update Data_interpretation.Rmd minor grammar edits * Changes to activity concentration text Updates to text for activity concentration at specified response and cutoff for read-ability. * Update representative sample and tcplVarMat sections text updates for clarity. * Updates to burst cytotox text Minor updates to burst cytotox text * text edits to potency metric section * cytotox burst edits * Update Data_interpretation.Rmd Updated cytotox burst text, see lines 304-309 * combine vignettes into 1 * fix some typos and remove orig JSON file * final edits before handing off to Ashley to review * Corrected in text links, cleaned up code spacing for consistancy, other small formatting changes corrected to text for consistancy, added better description of nmed_gtbl_pos/neg and related level 6 flags. * Corrected in text links, cleaned up code spacing for consistancy, other small formatting changes corrected to text for consistancy, added better description of nmed_gtbl_pos/neg and related level 6 flags. * Removed extra spaces and aligned lists. * Repaired broken link * Updated data.table requirements to reflect new 1.15.0 requirement * Removing extra space from version requirement to data.table * Update Introduction_Appendices.Rmd Switching package load from devtools to library(tcpl) * switch to new hex that includes link and EPA logo --------- Co-authored-by: Feshuk <[email protected]> Co-authored-by: kpaulfriedman <[email protected]> Co-authored-by: Ko <[email protected]> Co-authored-by: Madison Feshuk <[email protected]>
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Merge pull request #282 from USEPA/198-update-github-actions-to-inclu…
…de-dev-branch Large update to unit test suite including mocking invitrodb and CTX API data
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259 remove tcpl lite and add api throughout package (#283)
* 259 remove tcplLite and add API throughout package * 259 remove tcplLite and add API throughout package * 259 fix test after removal of 'tcplLite' in error message * 259 deleted tcplConfExample, removed config related lines in examples also wrapped examples in \dontrun{} * 259 ran devtools::document * 259 remove inst/csv and inst/example, used by tcplLite, tests passing * 259 fix build error with example in tcplListFlds * 259 removed chdat, replaced it in vignette with static version * 259 removed chdat docs * added rmdformats to suggests
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286 technical review comments (#287)
* technical reviewer KB * technical review JDR * additional edits * address bugs from #284 --------- Co-authored-by: Feshuk <[email protected]>
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Merge pull request #289 from USEPA/286-technical-review-comments
286 technical review comments
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* updated package links for data.table and reran documentation * Add NEWS.md * change from NEWS to NEWS.md * removed old NEWS file * updated news * Add GitHub links to DESCRIPTION * updated links in readme and vignettes to match cran guidelines * removed references to clib function that is no longer used * Increment version number to 3.2.0 * added params to docs for tcplQueryAPI * exported load units so they can be used and removed unneccessary devtools load_all from vignette * removed more clib references * variable binding * change .. data.table select notation to dplyr select notation * build readme * updated readme links * changed links to doi * removed offending zscore equation * added default mthdlist information for when there is no db connection and no api functionality * reference tcpl when calling data * updated cran comments * replace with default * add all_of to select to resolve 41 test warnings * resolve varmat warning, update docs * add validation to tcplMthdList --------- Co-authored-by: Carter Thunes <[email protected]>
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added greek encoding to pdf options and revert on exit so tests pass …
…on debian environment (#295)
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added quotes to tcpl and invitrodb and think I fixed the URIs (#298)
* added quotes to tcpl and invitrodb and think I fixed the URIs * updated winbuilder check results
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