Update main branch for tcpl v3.2 CRAN release #300
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142 added level 6 flags to tcplPlot output by boolean flag
147 cleaned up mc6 flag descriptions
128 changed export_ready parameter default to FALSE
149 removed lvl parameter from tcplPlot, assigned by type now
* 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]>
…de-dev-branch Large update to unit test suite including mocking invitrodb and CTX API data
* 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
* technical reviewer KB * technical review JDR * additional edits * address bugs from #284 --------- Co-authored-by: Feshuk <[email protected]>
286 technical review comments
* 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]>
…on debian environment (#295)
* added quotes to tcpl and invitrodb and think I fixed the URIs * updated winbuilder check results
brown-jason
approved these changes
Oct 10, 2024
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Will draft release notes after this is merged