### Install Development Version of tcplfit2

Source: https://github.com/usepa/comptox-toxcast-tcplfit2/blob/dev/README.md

To install the current development version of the tcplfit2 package, use the devtools::install_github function. This command fetches the latest code directly from the GitHub repository.

```r
devtools::install_github("USEPA/CompTox-ToxCast-tcplfit2")
```

--------------------------------

### Run Concentration-Response Models for Multiple Samples

Source: https://github.com/usepa/comptox-toxcast-tcplfit2/blob/dev/tcplfit2-vignette.md

This R code snippet demonstrates how to load assay data, preprocess it, and run a series of concentration-response models for selected samples. It includes determining background variation and plotting the results for each sample.

```r
  # read in the data
  file <- "data/mc3.RData"
  load(file=file)
  print(dim(mc3))

  # set up a 3 x 2 grid for the plots
  oldpar <- par(no.readonly = TRUE)
  on.exit(par(oldpar))            
  par(mfrow=c(3,2),mar=c(4,4,2,2))

  # determine the background variation
  temp <- mc3[mc3$logc<= -2,"resp"]
  bmad <- mad(temp)
  onesd <- sd(temp)
  cutoff <- 3*bmad

  # select six samples. Note that there may be more than one sample processed for a given chemical
  spid.list <- unique(mc3$spid)
  spid.list <- spid.list[1:6]

  for(spid in spid.list) {
    # select the data for just this sample
    temp <- mc3[is.element(mc3$spid,spid),]

    # The data file has stored concentration in log10 form, so fix that
    conc <- 10**temp$logc
    resp <- temp$resp

    # pull out all of the chemical identifiers and the name of the assay
    dtxsid <- temp[1,"dtxsid"]
    casrn <- temp[1,"casrn"]
    name <- temp[1,"name"]
    assay <- temp[1,"assay"]

    # create the row object
    row <- list(conc = conc, resp = resp, bmed = 0, cutoff = cutoff, onesd = onesd,assay=assay,dtxsid=dtxsid,casrn=casrn,name=name)

    # run the concentration-response modeling for a single sample
    res <- concRespCore(row,fitmodels = c("cnst", "hill", "gnls", "poly1", "poly2", "pow", "exp2", "exp3",
                                          "exp4", "exp5"),conthits = T, aicc = F,bidirectional=F)

    # plot the results
    concRespPlot(res$summary,ymin=-10,ymax=100)
  }

```

--------------------------------

### Load tcplfit2 Package

Source: https://github.com/usepa/comptox-toxcast-tcplfit2/blob/dev/tcplfit2-vignette.md

Loads the tcplfit2 package for use in subsequent operations.

```r
library(tcplfit2)
```

--------------------------------

### Run Single Concentration-Response Calculation

Source: https://github.com/usepa/comptox-toxcast-tcplfit2/blob/dev/tcplfit2-vignette.md

Performs a single concentration-response calculation using the concRespCore function with specified parameters and models. The output includes a summary of the winning model and detailed results for all run models.

```r
  conc <- list(.03,.1,.3,1,3,10,30,100)
  resp <- list(0,.2,.1,.4,.7,.9,.6, 1.2)
  row <- list(conc = conc, resp = resp, bmed = 0, cutoff = 1, onesd = .5)
  res <- concRespCore(row,fitmodels = c("cnst", "hill", "gnls", "poly1", "poly2", "pow", "exp2", "exp3",
                                        "exp4", "exp5"),conthits = T, do.plot=T)
  res$summary
```

=== COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.