Description Usage Arguments Details Author(s) See Also Examples
Compute generalized additive model for lethal dose finding and corresponding confidence intervals using parametric bootstrap approaches
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## S3 method for class 'formula'
LD(formula, groups = NULL, experiment = NULL,
lethal.dose = c(50, 10),
dose_trafo = c("sqrt", "log", "none"),
data, family = nb(), ...)
## S3 method for class 'LD'
LD(object, lethal.dose = NULL, group = NULL, ...)
## S3 method for class 'LD'
confint(object, level = 0.95, lethal.dose = NULL,
B1 = 20, B2 = 100, newdata = NULL,
myapply = mclapply, ...)
### just wrappers to LD functions as defined above
### (i.e., with same arguments)
## S3 method for class 'formula'
lethal.dose(...)
## S3 method for class 'LD'
lethal.dose(...)
|
formula |
Specify the main dose-response model in the form
|
groups |
(optional) define the name of the grouping factor (if available in the data set). This could be for example the species, the strain, or any other factor (with two or more groups). |
experiment |
(optional) define the name of the experiment variable if multiple replicates (biological or technical) are used. This variable is included as randondom effect in the lethal dose model. |
lethal.dose |
vector of LDXX values. Per default, |
dose_trafo |
define a character string for the transformation that is used to stabilize the estimation of the dose effect. Note that this does not influence the form of the dose-response relation ship as we use a smooth function of dose (or a smooth function of the transformation of dose) in the model. This is really more a technical option. |
data |
data set with an outcome variable (i.e., number of surviving cells/bacteria/...), a dose variable and optionally a grouping variable (with two or more groups) that is used to comparte the groups. Further more, the data set can optionally contain an indicator for the experiment, which is used to model possible experiment effects. |
family |
distributional assumption. Currently only |
object |
Lethal dose model fitted using function |
group |
(optional) specify a factor level of |
level |
coverage probability of confidence interval |
newdata |
(optional) list of data frames, one per strain, with a fine grid for dose. Only for expert users. Usually this data set is built internally. |
B1 |
number of new sampled data sets. |
B2 |
number of draws from the distribution of the fitted coefficients. |
myapply |
either |
... |
further arguments. |
Explain the model that is used to derive the lethal doses here...
Benjamin Hofner <benjamin.hofner@fau.de>
methods for fitted LD
models:
predict.LD
, summary.LD
, etc.
1 2 3 4 5 6 | ## model survival fractions for UV radiation experiment
data("geoderm.uv")
mod.uv <- LD(value ~ time, groups = "strain", experiment = "replicate",
dose_trafo = "sqrt", data = geoderm.uv)
## for more examples see ?summary.LD
|
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