fitUrsaModel: URSA Response Surface Fitting

In braidrm: Fitting Combined Action with the BRAID Response Surface Model

URSA Response Surface Fitting

Description

Fits the universal response surface approach (URSA) model to the given data (Greco, Park, and Rustum 1990)

Usage

fitUrsaModel(
  formula,
  data,
  weights = NULL,
  direction = 0,
  lower = NULL,
  upper = NULL
)

## S3 method for class 'formula'
fitUrsaModel(
  formula,
  data,
  weights = NULL,
  direction = 0,
  lower = NULL,
  upper = NULL
)

## Default S3 method:
fitUrsaModel(
  formula,
  data,
  weights = NULL,
  direction = 0,
  lower = NULL,
  upper = NULL
)

Arguments

formula	Either an object of class formula such as would be provided to a modeling function like stats::lm(), or a width-2 numeric array vector of concentration pairs (including 0 or Inf). A formula should specify a single output as a function of two inputs, eg. activity ~ conc1 + conc2.
data	If forumula is a symbolic formula, a data frame containing the specified values. If formula is a numeric array of concentrations, a numeric vector of response values, the same length as the number of rows of formula.
weights	A vector of weights (between 0 and 1) the same length as the data which determines the weight with which each measurement will impact the the sum of squared errors. Weights will be multiplied by errors before squaring. If NULL (the default) all weights will be set to 1. Can be a numeric vector, or the name of a column in data if formula is a symbolic formula
direction	Determines the possible directionality of the BRAID model. If 0 (the default) no additional constraints are placed on the parameters. If greater than 0, the fitting will require that the maximal effects are all greater than or equal to the minimal effect. If less than 0, the fitting will require that all maximal effect is less than or equal to the minimal effect.
lower	An optional set of lower bounds on the seven URSA response parameters. Any values set to NA will be filled with default calculated bounds.
upper	An optional set of upper bounds on the seven URSA response parameters. Any values set to NA will be filled with default calculated bounds.

Value

An object of class braidAltFit with the following values:

• concs: The array of concentrations passed to the functions

• act: The vector of measurements associated with the given dose pairs

• weights: The vector of weights for the given measurements, set to 1 for all measurements by default

• method: Specifying the alternate surface model being used (in this case "URSA")

• coefficients: A length-seven parameter vector specifying the URSA response surface

• fitted.values: The predicted response surface value for the given dose pairs and best-fit response surface

• residuals: The difference between the predicted and measured values for the given dose pairs, always equal to "measured minus predicted"

• direction: The direction value passed to the function

• pbounds': A 2-by-7 array of bounds on the URSA parameters used in the parameter optimization

References

Greco, William R, Hyoung Sook Park, and Youcef M Rustum. 1990. “Application of a New Approach for the Quantitation of Drug Synergism to the Combination of Cis-Diamminedichloroplatinum and 1-b-d-Arabinofuranosylcytosine.” Cancer Research 50 (17): 5318–27.

Examples

ufit1 <- fitUrsaModel(measure ~ concA + concB, additiveExample)
coef(ufit1)

ufit2 <- fitUrsaModel(measure ~ concA + concB, synergisticExample,
                      direction = 1, lower=c(NA, NA, NA, NA, NA, 0, 0))
coef(ufit2)

braidrm documentation built on Sept. 30, 2024, 9:40 a.m.