tcplhit2_core {tcplfit2}R Documentation

Hitcalling Function

Description

Core of hitcalling function. This method chooses the winning model from tcplfit2_core, extracts the top and ac50, computes the hitcall, and calculates bmd/bmdl/bmdu among other statistics. Nested model selection is used to choose between poly1/poly2, then the model with the lowest AIC (or AICc) is declared the winner. Continuous hitcalls requires tcplfit2_core to be run with force.fit = TRUE and "cnst" never to be chosen as the winner.

Usage

tcplhit2_core(
  params,
  conc,
  resp,
  cutoff,
  onesd,
  bmr_scale = 1.349,
  bmed = 0,
  conthits = TRUE,
  aicc = FALSE,
  identifiers = NULL,
  bmd_low_bnd = NULL,
  bmd_up_bnd = NULL,
  poly2.biphasic = TRUE,
  verbose = FALSE
)

Arguments

params

The output from tcplfit2_core

conc

list of concentrations (not in log units)

resp

list of corresponding responses

cutoff

noise cutoff

onesd

1 standard deviation of the noise (for bmd calculation)

bmr_scale

bmr scaling factor. Default = 1.349

bmed

median of noise estimate. Default 0

conthits

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

aicc

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

identifiers

A one-row data frame containing identifiers of the concentration-response profile, such as the chemical name or other identifiers, and any assay identifiers. The column names identify the type of value. This can be NULL. The values will be included in the output summary data frame

bmd_low_bnd

Multiplier for bmd lower bound, must be between 0 and 1 (excluding 0). A value of 0.1 would require the bmd is no lower than a of 1/10th of the lowest tested concentration (i.e. lower threshold). If the bmd is less than the threshold, the bmd and its confidence interval will be censored and shifted right.

bmd_up_bnd

Multiplier for the bmd upper bound, must be greater than or equal to 1. A value of 10 would require the bmd is no larger than 10 times the highest tested concentration (i.e. upper threshold). If the bmd is greater than the threshold, the bmd and its confidence interval will be censored and shifted left.

poly2.biphasic

If poly2.biphasic = TRUE, allows for biphasic polynomial 2 model fits (i.e. both monotonic and non-monotonic). (Defaults to TRUE.)

verbose

If verbose = TRUE, will print status of empirical calculations. (Defaults to FALSE.)

Value

A list of with the detailed results from all of the different model fits. The elements of summary are:


[Package tcplfit2 version 0.1.8 Index]