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Error in ggsurvplot when using as.formula() #624

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rchemist0123 opened this issue Apr 12, 2023 · 0 comments
Open

Error in ggsurvplot when using as.formula() #624

rchemist0123 opened this issue Apr 12, 2023 · 0 comments

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@rchemist0123
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I'm trying to solve a problem from stackoverflow.

Here's the code I've tried.

df <- lung %>%
  transmute(time,
            status,  # censoring status 1=censored, 2=dead
            Age = age,
            Sex = factor(sex, labels = c("Male", "Female")),
            ECOG = factor(lung$ph.ecog),
            `Meal Cal` = as.numeric(meal.cal))
vars <- c("ECOG", "Sex")
surv_plot_func <- function(df, vars, time, status) {
  # fit_list <- list()
  for(var in vars) {
    form <- paste0("Surv(", time, ", ", status,") ~ ",var)
    fit <- survfit(as.formula(form), data=df)
    ggsurvplot(fit)
    # plot(fit)
    # fit_list[[var]] <- fit
  }
surv_plot_func(df, vars, "time", "status")

However, error Error in as.formula(form) : object 'form' not found is printed. I guess error keeps occurring in ggsurvplot().
How could I handle this error?

Below is the traceback() of the code.

16: as.formula(form)
15: eval(x)
14: eval(x)
13: formula.default(object, env = baseenv())
12: formula(object, env = baseenv())
11: stats::as.formula(.)
10: fit$call$formula %>% stats::as.formula()
9: .extract.survfit(fit, data)
8: .pvalue(fit, data = data, method = method, pval = pval, pval.coord = pval.coord, 
       pval.method.coord = pval.method.coord, get_coord = get_coord, 
       test.for.trend = test.for.trend)
7: dplyr::select(., variable, dplyr::everything())
6: .pvalue(fit, data = data, method = method, pval = pval, pval.coord = pval.coord, 
       pval.method.coord = pval.method.coord, get_coord = get_coord, 
       test.for.trend = test.for.trend) %>% dplyr::select(variable, 
       dplyr::everything())
5: surv_pvalue(fit, method = log.rank.weights, data = data, pval = pval, 
       pval.coord = pval.coord, pval.method.coord = pval.method.coord, 
       test.for.trend = test.for.trend)
4: (function (fit, data = NULL, fun = NULL, color = NULL, palette = NULL, 
       linetype = 1, break.x.by = NULL, break.y.by = NULL, break.time.by = NULL, 
       surv.scale = c("default", "percent"), xscale = 1, conf.int = FALSE, 
       conf.int.fill = "gray", conf.int.style = "ribbon", conf.int.alpha = 0.3, 
       censor = TRUE, censor.shape = "+", censor.size = 4.5, pval = FALSE, 
       pval.size = 5, pval.coord = c(NULL, NULL), test.for.trend = FALSE, 
       pval.method = FALSE, pval.method.size = pval.size, pval.method.coord = c(NULL, 
           NULL), log.rank.weights = c("survdiff", "1", "n", "sqrtN", 
           "S1", "S2", "FH_p=1_q=1"), title = NULL, xlab = "Time", 
       ylab = "Survival probability", xlim = NULL, ylim = NULL, 
       axes.offset = TRUE, legend = c("top", "bottom", "left", "right", 
           "none"), legend.title = "Strata", legend.labs = NULL, 
       fontsize = 4.5, font.family = "", tables.height = 0.25, tables.y.text = TRUE, 
       tables.col = "black", tables.y.text.col = TRUE, risk.table = FALSE, 
       risk.table.pos = c("out", "in"), risk.table.title = NULL, 
       risk.table.col = tables.col, risk.table.fontsize = fontsize, 
       risk.table.y.text = tables.y.text, risk.table.y.text.col = tables.y.text.col, 
       risk.table.height = tables.height, surv.plot.height = 0.75, 
       ncensor.plot.height = tables.height, cumevents.height = tables.height, 
       cumcensor.height = tables.height, ncensor.plot = FALSE, ncensor.plot.title = NULL, 
    ...
3: do.call(ggsurvplot_core, opts)
2: ggsurvplot(fit) at #6
1: surv_plot_func(df, vars, "time", "status")

session_info()

─ Session info ────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Ventura 13.2.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Asia/Seoul
 date     2023-04-12
 rstudio  2023.03.0+386 Cherry Blossom (desktop)
 pandoc   2.19.2 @ /private/var/folders/fk/0srf_1114xdc8lfw3trytk340000gn/T/AppTranslocation/47FE72EE-7A9F-42E7-A5C8-FE44251CB14E/d/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ────────────────────────────────
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