fit_surv.RdCreates a survfit object for day and status, then fits a survival curve by condition.
fit_surv(
df_isurv,
formula = "Surv(day, status) ~ condition",
as_data_frame = FALSE
)A data.frame object of survival data with one individual per
row. If starting with bulk survival data (multiple observations per row), run get_indiv_surv() first.
A character string passed to a survival::survfit.formula.
Default: "Surv(day, status) ~ condition"
If FALSE, returns a survfit object from the survival
package. If TRUE, returns it in a data.frame format. Default: FALSE
A survival::survfit() object. If as_data_frame = TRUE,
returns it in a data.frame format. Default: FALSE
Call: survival::survfit(Surv(day, status) ~ condition, data = df_isurv)}
# Convert bulk survival to individual survival
df_isurv <- get_indiv_surv(sample_data, sample_order = c("WT", "Drug1", "Drug2"))
#> Joining with `by = join_by(x, condition, day, sex, status)`
# Fit survival object with the default call (condition)
surv_fit <- fit_surv(df_isurv)
#>
#> call: formula = Surv(day, status) ~ condition
surv_fit
#> Call: survfit(formula = Surv(day, status) ~ condition, data = df_isurv)
#>
#> n events median 0.95LCL 0.95UCL
#> condition=WT 50 47 20.0 19 21
#> condition=Drug1 50 46 4.5 4 6
#> condition=Drug2 50 42 33.0 32 35
# Fit survival object with custom call (condition + sex)
surv_fit <- fit_surv(df_isurv, formula = "Surv(day, status) ~ sex + condition")
#>
#> call: formula = Surv(day, status) ~ sex + condition
surv_fit
#> Call: survfit(formula = Surv(day, status) ~ sex + condition, data = df_isurv)
#>
#> n events median 0.95LCL 0.95UCL
#> sex=F, condition=WT 38 38 20.5 20 22
#> sex=F, condition=Drug1 3 2 13.0 11 NA
#> sex=F, condition=Drug2 33 32 35.0 33 36
#> sex=M, condition=WT 12 9 4.0 3 NA
#> sex=M, condition=Drug1 47 44 4.0 3 6
#> sex=M, condition=Drug2 17 10 28.0 27 NA