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added quotes to tcpl and invitrodb and think I fixed the URIs #298

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Oct 9, 2024
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added quotes to tcpl and invitrodb and think I fixed the URIs #298

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48540d5
added quotes to tcpl and invitrodb and think I fixed the URIs
brown-jason Oct 9, 2024
fc9ef49
updated winbuilder check results
brown-jason Oct 9, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -18,7 +18,7 @@ Authors@R: c(
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: 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.
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)
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -30,7 +30,7 @@ knitr::opts_chunk$set(

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/comptox-tools/toxicity-forecasting-toxcast). 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.
If you are interested in contributing or want to report a bug, please submit a issue or start a discussion. See [CONTRIBUTING](https://github.com/USEPA/CompTox-ToxCast-tcpl/blob/dev/CONTRIBUTING.md) for more information.

To install the current development version, run the following command:

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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -26,7 +26,8 @@ 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.
[CONTRIBUTING](https://github.com/USEPA/CompTox-ToxCast-tcpl/blob/dev/CONTRIBUTING.md)
for more information.

To install the current development version, run the following command:

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21 changes: 7 additions & 14 deletions cran-comments.md
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@@ -1,3 +1,6 @@
* added single quotes to invitrodb and tcpl in DESCRIPTION
* fixed aeds URI

## Changes from last version
* To resolve current cran check results: added package anchors to links
* Updated docs and vignette
Expand All @@ -10,21 +13,11 @@
* R Under development (unstable) (2024-10-04 r87208 ucrt)

## winbuilder check results
* The note below references misspelled words and invalid file URIs but the words are correctly spelled and the URIs point to the correct location within the respective documents.

NOTE
Maintainer: 'Jason Brown <[email protected]>'
Installation time in seconds: 13
Check time in seconds: 183
Status: OK
R Under development (unstable) (2024-10-08 r87214 ucrt)

Possibly misspelled words in DESCRIPTION:
invitrodb (21:168)
tcpl (21:50, 21:304)

Found the following (possibly) invalid file URIs:
URI: aeds
From: inst/doc/Introduction_Appendices.html
URI: CONTRIBUTING.md
From: README.md


## local R CMD check results

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2 changes: 1 addition & 1 deletion vignettes/Introduction_Appendices.Rmd
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Expand Up @@ -3264,7 +3264,7 @@ toxcast_mc5_liver_summary <- toxcast_mc5_liver[,list(
mean.ac50uM = mean(ac50_uM, na.rm = T))]
```

[Administered Equivalent Doses](aeds) can be accessed from Level 7, or calculated *ad hoc* using the [High-throughput Toxicokinetics R package (httk)](https://CRAN.R-project.org/package=httk). Potency estimates and model options can be adjusted based on use case. In this example, modeling assumptions when estimating the AEDs with httk were:
[Administered Equivalent Doses](#aed) can be accessed from Level 7, or calculated *ad hoc* using the [High-throughput Toxicokinetics R package (httk)](https://CRAN.R-project.org/package=httk). Potency estimates and model options can be adjusted based on use case. In this example, modeling assumptions when estimating the AEDs with httk were:

- Species options include ‘Rat’, ‘Rabbit’, ’Dog’, ’Mouse’ or default ‘Human'
- Which quantile from Monte Carlo steady-state simulation (for Css)? The scaling factor is the inverse of the steady state plasma concentration (Css) predicted for a 1 mg/kg/day exposure dose rate. This simulates variability and propagates uncertainty to calculate an upper 95th percentile Css,95 for individuals who get higher plasma concentrations from the same exposure, i.e. 95th concentration quantile produces the 5th dose quantile (most sensitive measure).;
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