concRespCore {tcplfit2}

Concentration Response Core

Description

Core of concentration response curve fitting for pvalue based cutoff. This function calls tcplfit2_core to get curve fits, and then tcplhit2_core to perform the hitcalling.

Usage

concRespCore(
  row,
  fitmodels = c("cnst", "hill", "gnls", "poly1", "poly2", "pow", "exp2", "exp3", "exp4",
    "exp5"),
  conthits = TRUE,
  aicc = FALSE,
  force.fit = FALSE,
  bidirectional = TRUE,
  verbose = FALSE,
  do.plot = FALSE,
  return.details = FALSE,
  bmr_scale = 1.349,
  bmd_low_bnd = NULL,
  bmd_up_bnd = NULL
)

Arguments

row

A named list that must include:

• conc - list of concentrations (not in log units)

• resp - list of corresponding responses

• bmed - median of noise estimate.

• cutoff - noise cutoff

• onesd - 1 standard deviation of the noise (for bmd calculation)

Other elements (usually identifiers, like casrn) of row will be attached to the final output.

fitmodels

Vector of model names to use.

conthits

conthits = TRUE uses continuous hitcalls, otherwise they're discrete.

aicc

aicc = TRUE uses corrected AIC to choose winning method; otherwise regular AIC.

force.fit

If TRUE force the fitting to proceed even if there are no points outside of the bounds (default FALSE)

bidirectional

If TRUE allow fitting to happen in both directions (default TRUE)

verbose

If TRUE, write extra output from tcplfit2_core (default FALSE)

do.plot

If TRUE, create a plot in the tcplfit2_core function (default FALSE)

return.details

If TRUE, return the hitcalling details and the summary, if FALSE (default), just return the summary

bmr_scale

- bmr scaling factor (for bmd calculation) default = 1.349

bmd_low_bnd

Multiplier for bmd lower bound. A value of .1 would require the bmd to be no lower than 1/10th of the lowest concentration tested.

bmd_up_bnd

Multiplier for the bmd upper bound. A value of 10 would require the bmd to be no lower than 10 times the highest concentration tested.

Value

A list of two elements. The first (summary) is the output from tcplhit2_core. The second, params is the output from tcplfit2_core a dataframe of one row containing

Examples

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,
            name = "some chemical",
            assay = "some assay")
concRespCore(row, conthits = TRUE)
concRespCore(row, aicc = TRUE)