doNls {mixlow} | R Documentation |
Organizes input and calls the nls
function to estimate the
parameters of sigmoidal concentration-response curves. Users can supply
starting values for parameters or can use default values that are based
on the data.
doNls(mixlowData, parameterDefaults, lambdaThreshold=0.05, numRandomTries=10, verbose=FALSE)
mixlowData |
A list obtained from prepareData . |
parameterDefaults |
A list obtained from
getNlsParameterDefaults . The default values can be edited
as desired before sending to the doNls function. |
lambdaThreshold |
A scalar designating any lower boundary for lambda. If a model estimates a lambda value less than the threshold, that model will be discarded and a model that does not use a lambda parameter will be used instead. |
numRandomTries |
A scalar designating the number of attempts that should be made to reach convergence for each model. For each attempt, starting values are randomly selected from a normal distribution with mean equal to the given parameter starting value and a standard deviation equal to the given standard deviation. |
verbose |
An optional logical value. If TRUE , information
from intermediate steps in the doNls analysis is printed.
Default is FALSE . |
See doNlme
for a description of the parameters estimated.
See getNlsParameterDefaults
for a description of default
parameter values. Parameter values of NaN indicate the following default
values will be used: param.g=0, param.g.std=1, param.p = the closest tested
log concentration corresponding to 1/2 the mean response of control wells,
and param.p.std = the absolute value of param.p/2. The default for
param.lambda is NaN, which indicates that a lambda term will not be used.
If a lambda term is used, its value should be between zero and 0.5.
A list of type nlsData
of length equal to the number of trays with
the following components:
nlsEstimates |
Data frame containing parameter estimates |
nlsGraphing |
List used by plotNlsData for making graphs:
|
Adjusted responses take into account responses in optical control wells
(see prepareData
). In the adjusted concentrations, values of zero
are replaced by concentrations of 1/1000th of the lowest nonzero
concentration (for log-plot graphing purposes only).
John Boik jcboik@stanford.edu
Boik J.C., Newman R.A., Boik R.J. (2008) Quantifying synergism/antagonism using nonlinear mixed-effects modeling: a simulation study. Statistics in Medicine 27(7), 1040-61
# mixlowData data object is obtained using the prepareData function data(mixlowData) trays <- getTrays(mixlowData) parameterDefaults <- getNlsParameterDefaults(trays=trays[1:9]) nlsData <- doNls(mixlowData=mixlowData, parameterDefaults)