grofit (version 1.1.1-1)

gcFit: Function to run growth curve fitting on several data sets containing growth data.

Description

The function serves to estimate several growth curves at once. The function calls the functions gcFitSpline, gcFitModel and gcBootSpline to generate estimates for growth parameters and respecting statistics.

Usage

gcFit(time, data, control = grofit.control())

Arguments

time

Numeric matrix, consisting of n columns for the time points and m rows for the different experiments.

data

Data frame consisting of 3+n columns, containing three coulumns of additional information and n columns of growth data corresponding to time. Format convention: 1. column, character as an experiment identifier; 2. column: character, additional information about respecting experiment; 3. column: concentration of substrate of a compound under which the experiment is obtained; 4.-(n+3). column: growth data corresponding to the time points in time.

control

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

Value

Generates an object of class gcFit

raw.time

Raw time passed to the function as time.

raw.data

Raw time passed to the function as data.

gcTable

Table with characteristic growth values and related statistics related for each growth curve data provided to the function. This table, which is also returned by the generic summary.gcFit method applied to an gcFit object, is used as an input for drFit. 1. column: character, 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.

gcFittedModels

All gcFitModel objects, generated by the call of gcFitModel. Note: access to each object via double brace: gcFittedModels[[#n]].

gcFittedSplines

All gcFitSpline objects, generated by the call of gcFitSpline. Note: access to each object via double brace: gcFittedSplines[[#n]].

gcBootSplines

All gcFitSpline objects, generated by the call of gcFitSpline. Note: access to each object via double brace: gcFittedSplines[[#n]].

control

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

See Also

grofit, grofit.time, grofit.data, ran.data , summary.gcFit, plot.gcFit

Examples

# generate random growth curve data sets,
# fulfilling the conventions described in arguments
foo <- ran.data(100, 25)
time <- foo$time
data <- foo$data
# fit dose response curves
result <- gcFit(time,data, control=grofit.control(fit.opt="b"))
print(summary(result))
plot(result)