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]>

Author: 4 people

Diff for: .Rbuildignore

@@ -6,7 +6,7 @@
 ^inst/sql/create_sql_files\.R$
 man-roxygen
 tcpl.Rcheck
-README.md
+^README\.Rmd$
 CONTRIBUTING.md
 cran-comments.md
 ^CRAN-RELEASE$

Diff for: DESCRIPTION

@@ -2,30 +2,28 @@ Package: tcpl
 Title: ToxCast Data Analysis Pipeline
 Version: 3.1.0
 Authors@R: c(
-    person("Richard S", "Judson",role = c("ctb","ths"), email = "[email protected]"),
-    person("Dayne L", "Filer", role = "aut",email = "[email protected]"),
-    person("Jason","Brown",role = "cre", email = "[email protected]"),
-    person("Sarah E","Davidson-Fritz",role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-2891-9380")),
+    person("Richard S", "Judson",role = c("ctb","ths"), comment = c(ORCID = "0000-0002-2348-9633")),
+    person("Dayne L", "Filer", role = "aut"),
+    person("Jason","Brown", role = "cre", email = "[email protected]", comment = c(ORCID = "0009-0000-2294-641X")),
+    person("Sarah E","Davidson-Fritz", role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-2891-9380")),
     person("Madison","Feshuk",role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-1390-6405")),
-    person("Lori","Kolaczkowski",role = "ctb",email = "[email protected]"),
-    person("Kurt", "Dunham", role = "ctb", email = "[email protected]"),
     person("Carter", "Thunes", role = "ctb", email = "[email protected]"),
     person("Ashley", "Ko", role = "ctb", email = "[email protected]"),
-    person("Todd", "Zurlinden", role="ctb"),
+    person("Kelly", "Carstens", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-1746-5379")),
+    person("Todd", "Zurlinden", role="ctb", comment = c(ORCID = "0000-0003-1372-3913")),
+    person("Lori","Kolaczkowski",role = "ctb"),
+    person("Kurt", "Dunham", role = "ctb"),
     person("Parth", "Kothiya", role = "ctb"),
     person("Woodrow R", "Setzer", role = "ctb"),
     person("Matthew T", "Martin", role = c("ctb", "ths")),
     person("Katie", "Paul Friedman", role=c("ctb"), email = "[email protected]", comment = c(ORCID = "0000-0002-2710-1691"))
     )
-Description: A set of tools for processing and modeling high-throughput and
-    high-content chemical screening data. The package was developed for the
-    the chemical screening data generated by the US EPA ToxCast program, but
-    can be used for diverse chemical screening efforts.
-URL: https://github.com/USEPA/CompTox-ToxCast-tcpl
+Description: The ToxCast Data Analysis Pipeline (tcpl) is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, invitrodb. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but tcpl can be used to support diverse chemical screening efforts.
+URL: https://github.com/USEPA/CompTox-ToxCast-tcpl, https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast
 Depends:
     R (>= 3.5.0)
 Imports:
-    data.table (>= 1.9.4),
+    data.table (>= 1.15.0),
     DBI,
     RMariaDB,
     numDeriv,

Diff for: R/mc4_mthds.R

@@ -35,23 +35,22 @@
 #' 
 #'   \describe{
 #'     \item{bmad.aeid.lowconc.twells}{Calculate the baseline median absolute value (bmad) as the 
-#'     median absolute deviation of normalized response values (rep) for test compound wells 
-#'     (wllt = t) with concentration index (cndx) equal to 1 or 2.}
+#'     median absolute deviation of normalized response values (rep) for test compound wells (wllt = t) 
+#'     with concentration index (cndx) equal to 1 or 2. Calculate one standard deviation of the normalized 
+#'     response for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2; 
+#'     onesd = sqrt(sum((resp - mean resp)^2)/sample size - 1). Onesd is used to establish BMR and therefore required for tcplfit2 processing.}
 #'     \item{bmad.aeid.lowconc.nwells}{Calculate the baseline median absolute value (bmad) as the 
-#'     median absolute deviation of normalized response values (resp) for neutral control wells 
-#'     (wllt = n).}
-#'     \item{onesd.aeid.lowconc.twells}{Calculate one standard deviation of the normalized response 
-#'     for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2; 
-#'      \eqn{onesd=\sqrt{\sum{(resp-mean(resp))^{2}}/(n-1)}}{onesd = sqrt(sum((resp - mean 
-#'      resp)^2)/sample size - 1)}. Used to establish BMR and therefore required for tcplfit2 
-#'      processing.}
+#'     median absolute deviation of normalized response values (resp) for neutral control wells (wllt = n).
+#'     Calculate one standard deviation of the normalized response for neutral control wells (wllt = n);
+#'     onesd = sqrt(sum((resp - mean resp)^2)/sample size - 1). Onesd is used to establish BMR and therefore required for tcplfit2 processing.}
 #'     \item{bidirectional.false}{Limits bidirectional fitting and processes data in positive 
 #'     analysis direction only. Use for gain-of-signal or inverted data.}
 #'     \item{bmad5.onesd16.static}{Replace baseline median absolute deviation
 #'     (bmad) with 5 and one standard deviation (osd) of the normalized response
 #'     for test compound wells (wllt = t) with a concentration index (cndx) of 1
 #'     or 2 with 16. Typically used for binary data where values would otherwise
 #'     be 0; non-zero values are required for tcplfit2 processing.}
+#'     \item{no.unbounded.models}{Exclude unbounded models and only fit data to bounded models (hill, gnls, exp4 and exp5).}
 #'   }
 #' 
 #' @note

Diff for: R/mc6_mthds.R

@@ -67,11 +67,6 @@
 #'   defined by 3 times the baseline median absolute deviation (bmad); nmed_gtbl_pos and
 #'   nmed_gtbl_neg both = 0, where nmed_gtbl_pos/_neg is the number of medians greater than 3 * 
 #'   bmad/less than -3 * bmad.}
-#'   \item{no.med.single.dir.gt.3bmad}{Flag series where no median response values in the intended
-#'   fit direction are greater than baseline as defined by 3 times the baseline median absolute
-#'   deviation (bmad); Depending on intended direction, either nmed_gtbl_pos or nmed_gtbl_neg are
-#'   = 0, where nmed_gtbl_pos/_neg is the number of medians greater than 3 * bmad/less than -3 
-#'   * bmad.}
 #' }
 #' 
 #' @note

Diff for: R/tcplSubsetChid.R

@@ -23,7 +23,7 @@
 #' To select a single sample, first a "consensus hit-call" is made by majority
 #' rule, with ties defaulting to active. After the chemical-wise hit call is
 #' made, the samples corresponding to to chemical-wise hit call are logically
-#' ordered using the fit category, the number of the flags, and the modl_ga,
+#' ordered using the fit category, the number of the flags, and AC50 (or modl_ga),
 #' then the first sample for every chemical is selected.
 #'
 #' The \code{flag} param can be used to specify a subset of flags to be used in

Diff for: README.Rmd

@@ -0,0 +1,38 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# tcpl: The ToxCast Data Analysis Pipeline Supporting Accessible Bioactivity Data for Toxicology
+
+<!-- badges: start -->
+
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/tcpl)](https://cran.r-project.org/package=tcpl)
+[![Active](http://img.shields.io/badge/Status-Active-green.svg)](https://cran.r-project.org/package=tcpl) 
+[![Monthly Downloads](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)
+[![DOI](https://zenodo.org/badge/doi/	10.32614/CRAN.package.tcpl.svg)](http://dx.doi.org/10.32614/CRAN.package.tcpl)
+
+<!-- badges: end -->
+
+## Welcome to the GitHub repository for the tcpl package.
+
+<a href="https://cran.r-project.org/web/packages/tcpl/index.html"><img src="vignettes/img/tcpl_hex.png" width="200" align="right" /></a>
+
+The ToxCast Data Analysis Pipeline (tcpl) is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, invitrodb. The package was developed for the chemical screening data generated by the [US EPA's Toxicity Forecaster (ToxCast) program](https://www.epa.gov/chemical-research/toxicity-forecasting). tcpl can be used to support diverse chemical screening efforts.
+
+If you are interested in contributing or want to report a bug, please submit a issue or start a discussion. See [CONTRIBUTING](CONTRIBUTING.md) for more information. 
+
+To install the current development version, run the following command: 
+
+    devtools::install_github("USEPA/CompTox-ToxCast-tcpl")
+

Diff for: README.md

@@ -1,11 +1,33 @@
-### tcpl: An R package for processing high-throughput chemical screening data
 
-Welcome to the GitHub repository for the tcpl package.
+<!-- README.md is generated from README.Rmd. Please edit that file -->
 
-The tcpl package provides a set of tools for processing and modeling high-throughput and high-content chemical screening data. The package was developed for the chemical screening data generated by the US EPA [ToxCast program](https://www.epa.gov/chemical-research/toxicity-forecasting), but can be used for diverse chemical screening efforts.
+# tcpl: The ToxCast Data Analysis Pipeline Supporting Accessible Bioactivity Data for Toxicology
 
-If you are interested in contributing or want to report a bug, please see [CONTRIBUTING](CONTRIBUTING.md) for more information. 
+<!-- badges: start -->
 
-To install the current development version run the following command: 
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/tcpl)](https://cran.r-project.org/package=tcpl)
+[![Active](http://img.shields.io/badge/Status-Active-green.svg)](https://cran.r-project.org/package=tcpl)
+[![Monthly
+Downloads](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)
+[![DOI](https://zenodo.org/badge/doi/%2010.32614/CRAN.package.tcpl.svg)](http://dx.doi.org/10.32614/CRAN.package.tcpl)
+
+<!-- badges: end -->
+
+## Welcome to the GitHub repository for the tcpl package.
+
+<a href="https://cran.r-project.org/web/packages/tcpl/index.html"><img src="vignettes/img/tcpl_hex.png" width="200" align="right" /></a>
+
+The ToxCast Data Analysis Pipeline (tcpl) is an R package that manages,
+curve-fits, plots, and stores ToxCast data to populate its linked MySQL
+database, invitrodb. The package was developed for the chemical
+screening data generated by the [US EPA’s Toxicity Forecaster (ToxCast)
+program](https://www.epa.gov/chemical-research/toxicity-forecasting).
+tcpl can be used to support diverse chemical screening efforts.
+
+If you are interested in contributing or want to report a bug, please
+submit a issue or start a discussion. See
+[CONTRIBUTING](CONTRIBUTING.md) for more information.
+
+To install the current development version, run the following command:
 
     devtools::install_github("USEPA/CompTox-ToxCast-tcpl")