S3 method to use to make prediction using fitted results from lifelihood().
Usage
prediction(
object,
parameter_name,
newdata = NULL,
type = c("link", "response"),
se.fit = FALSE
)Arguments
- object
output of
lifelihood()- parameter_name
A string specifying the name of the parameter for which to make the prediction. Must be one of
unique(lifelihoodResults$effects$parameter).- newdata
Data for prediction. If absent, predictions are for the subjects used in the original fit.
- type
The type of the predicted value: if "response," it is on the original data scale; if "link," it is on the lifelihood scale.
- se.fit
Whether or not to include standard errors in the prediction.
Examples
df <- fakesample |>
mutate(
geno = as.factor(geno),
type = as.factor(type)
)
clutchs <- c(
"clutch_start1", "clutch_end1", "clutch_size1",
"clutch_start2", "clutch_end2", "clutch_size2"
)
dataLFH <- lifelihoodData(
df = df,
sex = "sex",
sex_start = "sex_start",
sex_end = "sex_end",
maturity_start = "mat_start",
maturity_end = "mat_end",
clutchs = clutchs,
death_start = "death_start",
death_end = "death_end",
covariates = c("geno", "type"),
model_specs = c("gam", "lgn", "wei")
)
results <- lifelihood(
lifelihoodData = dataLFH,
path_config = get_config_path("config2"),
seeds = c(1, 2, 3, 4),
raise_estimation_warning = FALSE
)
predict(results, "expt_death")
#> Error in UseMethod("predict"): no applicable method for 'predict' applied to an object of class "lifelihoodResults"
predict(results, "expt_death", type = "response")
#> Error in UseMethod("predict"): no applicable method for 'predict' applied to an object of class "lifelihoodResults"
# predict on new data
newdata <- data.frame(
type = c(1, 2, 0, 1, 2, 0),
geno = c(0, 1, 0, 1, 0, 1)
)
newdata$type <- factor(newdata$type)
newdata$geno <- factor(newdata$geno)
predict(results, "expt_death", newdata)
#> Error in UseMethod("predict"): no applicable method for 'predict' applied to an object of class "lifelihoodResults"
predict(results, "expt_death", newdata, type = "response")
#> Error in UseMethod("predict"): no applicable method for 'predict' applied to an object of class "lifelihoodResults"