grofit (version 1.1.1-1)

drFit: Function to run the dose-response curve fit and EC50 estimation

Description

The function serves to estimate several dose-response curves at once. The function calls the functions drFitSpline and drBootSpline to generate a table with estimates for EC50 and respecting statistics.

Usage

drFit(gcFitData, control = grofit.control())

Arguments

gcFitData

Data frame containing the data for the dose-response curve estimation. It must follow the convention: 1. column: string, naming the experiment for which a dose-response curve shall be estimated; 2. column: string, additional information about the experiment; 3. column: numeric, concentration of substrate; 4. column: logical, reliability flag, 5. column: string, naming a parametric model, 6. column: logical, indicating wether a logarithmic transformation was applied to the time points of the growth data; 7. column: logical, indicating wether a logarithmic transformation was applied to the growth values of the growth data; 8.-55. characteristic growth parameters obtained from growth curve fit.

control

Object of class grofit.control containing a list of options generated by the function grofit.control.

Value

Generates an object of class drFit

raw.data

Data that passed to the function as gcFitData.

drTable

Data frame, 1. column: string, naming the experiment; 2. column: logical, indicating wether a logarithmic transformation was applied to concentration data; 3. column, logical, indicating wether a logarithmic transformation was applied to growth parameter; 4. column, numeric, number of bootstrap samples used; 5.-8. column: numeric, estimated EC50 value and respecting reponse value (5.-6.), also in original scale if a transformation is applied (7.-8.); 9.-10. column: numeric, mean and standard dev. from bootstrap sample; 11.-14. column: 90 and 95 percent confidence interval from bootstrap sample; 15. column: mean EC50 of bootstrap sample in original scale; 16.-19. 90 and 95 percent confidence interval in original scale.

drBootSplines

List of all drBootSpline objects generated by the call of drBootSpline for each distinct experiments. Note: access to each object via double brace: LIST[[1]], LIST[[2]]...

drFittedSplines

list of all drFitSpline objects generated by the call of drFitSpline for each distinct experiments. Note: access to each object via double brace: LIST[[1]], LIST[[2]]...

control

Object of class grofit.control containing list of options passed to the function as control.

Details

The function is meant to process the result from the fit of several growth curves performed by gcFit. It therefore expects a certain input format. For each of the distinct experiments specified by the names in the first column, the function relates the concentration (3. column) to a characteristic growth parameter (8.-55. columns). The choice of the parameter depends on the option parameter specified by the grofit.control function. The concentration and parameter are passed to drFitSpline and drBootSpline, which perform the dose-response curve estimation and bootstrapping.

See Also

drFitSpline, drBootSpline, drBootSpline, summary.drFit, plot.drFit

Examples

# generate random growth curve data set
foo <- ran.data(100, 25)
time <- foo$time
data <- foo$data
# fit dose response curves
drData <- gcFit(time, data, control = grofit.control(interactive = FALSE))
# use the output of gcFit as an input for drFit
drFit.result <- drFit(summary(drData))
print(summary(drFit.result))
plot(drFit.result)