tcplhit2_core {tcplfit2}

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
)

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

• any elements of the identifiers input

• n_gt_cutoff - number of data points above the cutoff

• cutoff - noise cutoff

• fit_method - curve fit method

• top_over_cutoff - top divided by cutoff

• rmse - RMSE of the data points around the best model curve

• a - fitting parameter methods: exp2, exp3, poly1, poly2, pow

• b - fitting parameter methods: exp2, exp3, ploy2

• p - fitting parameter methods: exp3, exp5, gnls, hill, pow

• q - fitting parameter methods: gnls,

• tp - top of the curve

• ga - ac50 for the rising curve in a gnls model or the Hill model

• la - ac50 for the falling curve in a gnls model

• er - fitted error term for plotting error bars

• bmr - benchmark response; level at which bmd is calculated = onesd*bmr_scale default bmr_scale is 1.349

• bmd - benchmark dose, curve value at bmr

• bmdl - lower limit on the bmd

• bmdu - upper limit on the bmd

• caikwt - one factor used in calculating the continuous hitcall. It is calcalated from the formula = exp(-aic(cnst)/2)/(exp(-aic(cnst)/2) + exp(-aic(fit_method)/2)) and measures how much lower the selected method AIC is than that for the constant model

• mll - another factor used in calcualting the continuous hitcall = length(modpars) - aic(fit_method)/2

• hitcall - the final hitcall, a value ranging from 0 to 1

• top - curve top

• ac50 - curve value at 50% of top, curve value at cutoff

• lc50 - curve value at 50% of top corresponding to the loss side of the gain-loss curve

• ac5 - curve value at 5% of top

• ac10 - curve value at 10% of top

• ac20 - curve value at 20% of top

• acc - curve value at cutoff

• ac1sd - curve value at 1 standard deviation

• conc - conc string separated by |'s

• resp - response string separated by |'s