runBraidAnalysis {braidReports} | R Documentation |
BRAID Surface Analysis
Description
Performs a convenient pre-built set of BRAID and dose-response analysis tasks
Usage
runBraidAnalysis(
formula,
data,
defaults,
weights = NULL,
start = NULL,
direction = 0,
lower = NULL,
upper = NULL,
useBIC = TRUE,
...
)
## S3 method for class 'formula'
runBraidAnalysis(
formula,
data,
defaults,
weights = NULL,
start = NULL,
direction = 0,
lower = NULL,
upper = NULL,
useBIC = TRUE,
...
)
## Default S3 method:
runBraidAnalysis(
formula,
data,
defaults,
weights = NULL,
start = NULL,
direction = 0,
lower = NULL,
upper = NULL,
useBIC = TRUE,
...
)
Arguments
formula |
Either an object of class |
data |
If |
defaults |
Default minimal and maximal effect values used to fix effect parameters during model selection. |
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 |
start |
A BRAID parameter vector specifying the first guess where the
non-linear optimization should begin. May be a length 7, 8, or 9 vector,
though a full length vector is always preferable. If |
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 |
A numeric vector of lower bounds on the fitted parameter values.
May be the same length as the number of fitted parameters, or a full,
length-9 vector. Missing or unspecified lower bounds may be included as |
upper |
A numeric vector of upper bounds on the fitted parameter values.
Used in the same way as |
useBIC |
If |
... |
Additional parameters to be passed to |
Value
An object of class braidAnalysis
, containing the following values:
-
concs
: a width-two array containing the two tested doses for each measurement -
act
: a numeric vector with as many values asconcs
has rows, containing the measured values for each measurement -
weights
: a numeric vector of weights, the same length asact
, specifying the weight given to each measurement in fitting. All weights are 1 by default -
braidFit
: a fit object of classbraidrm
containing the best-fit BRAID surface according to the given constraints -
hillFit1
: If the given data contains measurements of the first drug in isolation, those measurements are fit using basicdrm::findBestHillModel; the results of this analysis are stored as an object of classhillrm
ashillFit1
. If no such measurements are found, this will beNULL
-
hillFit2
: the corresponding fit for measurements of the second drug alone, if they are included;NULL
otherwise
Examples
surface <- synergisticExample
analysis <- runBraidAnalysis(measure~concA+concB, surface, defaults=c(0,1))
names(analysis)