RATET01

Event Rate Summary for Recurrent Events

Output

This example will focus on data from a single visit “WEEK 1 DAY 8” and a single endpoint “FKSI-FWB”. Only evaluable populations will be analyzed.

Code
lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM", ref_group = "B: Placebo", split_fun = ref_group_position("first")) %>%
  analyze_vars(
    "AVAL_f",
    var_labels = "Number of exacerbations per patient",
    .stats = c("count_fraction"),
    .formats = c("count_fraction" = "xx (xx.xx%)"),
    .labels = c("Number of exacerbations per patient")
  ) %>%
  summarize_glm_count(
    vars = "AVAL",
    variables = list(arm = "ARM", offset = "lgTMATRSK", covariates = NULL),
    conf_level = 0.95,
    distribution = "poisson",
    rate_mean_method = "emmeans",
    var_labels = "Unadjusted exacerbation rate (per year)",
    table_names = "unadj",
    .stats = c("rate"),
    .labels = c(rate = "Rate")
  ) %>%
  summarize_glm_count(
    vars = "AVAL",
    variables = list(arm = "ARM", offset = "lgTMATRSK", covariates = c("REGION1")),
    conf_level = 0.95,
    distribution = "quasipoisson",
    rate_mean_method = "ppmeans",
    var_labels = "Adjusted (QP) exacerbation rate (per year)",
    table_names = "adj-qp",
    .stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
    .labels = c(
      rate = "Rate", rate_ci = "Rate CI", rate_ratio = "Rate Ratio",
      rate_ratio_ci = "Rate Ratio CI", pval = "p-value"
    )
  ) %>%
  summarize_glm_count(
    vars = "AVAL",
    variables = list(arm = "ARM", offset = "lgTMATRSK", covariates = c("REGION1")),
    conf_level = 0.95,
    distribution = "negbin",
    rate_mean_method = "emmeans",
    var_labels = "Adjusted (NB) exacerbation rate (per year)",
    table_names = "adj-nb",
    .stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
    .labels = c(
      rate = "Rate", rate_ci = "Rate CI", rate_ratio = "Rate Ratio",
      rate_ratio_ci = "Rate Ratio CI", pval = "p-value"
    )
  )
result <- build_table(
  lyt = lyt,
  df = anl
)
result
                                                B: Placebo         A: Drug X        C: Combination 
                                                 (N=134)            (N=134)            (N=132)     
———————————————————————————————————————————————————————————————————————————————————————————————————
Number of exacerbations per patient                                                                
  0                                             10 (7.46%)         6 (4.48%)          11 (8.33%)   
  1                                            25 (18.66%)        21 (15.67%)        14 (10.61%)   
  2                                            38 (28.36%)        41 (30.60%)        33 (25.00%)   
  3                                            22 (16.42%)        26 (19.40%)        21 (15.91%)   
  4                                             13 (9.70%)        18 (13.43%)        30 (22.73%)   
  5                                             11 (8.21%)         10 (7.46%)         12 (9.09%)   
  6                                             10 (7.46%)         7 (5.22%)          7 (5.30%)    
  7                                             3 (2.24%)          4 (2.99%)          3 (2.27%)    
  8                                             1 (0.75%)          1 (0.75%)          1 (0.76%)    
  9                                             1 (0.75%)          0 (0.00%)          0 (0.00%)    
Unadjusted exacerbation rate (per year)                                                            
  Rate                                            7.2364             8.2148             9.8131     
Adjusted (QP) exacerbation rate (per year)                                                         
  Rate                                            2.4550             2.8514             3.4304     
    Rate CI                                  (1.6194, 3.7219)   (1.8974, 4.2850)   (2.2946, 5.1284)
  Rate Ratio                                                         1.1615             1.3973     
    Rate Ratio CI                                               (0.6462, 2.0877)   (0.7789, 2.5067)
    p-value                                                          0.6169             0.2619     
Adjusted (NB) exacerbation rate (per year)                                                         
  Rate                                            2.7374             2.8150             2.9789     
    Rate CI                                  (2.3932, 3.1311)   (2.4681, 3.2106)   (2.6152, 3.3932)
  Rate Ratio                                                         1.0283             1.0882     
    Rate Ratio CI                                               (0.8856, 1.1941)   (0.9381, 1.2624)
    p-value                                                          0.7140             0.2643

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Code
library(tern)
library(dplyr)

anl <- random.cdisc.data::cadtte %>%
  filter(PARAMCD == "TNE")

# Ensure number of exacerbation is a factor and NAs are explicit missing levels.
anl$AVAL_f <- as.factor(anl$AVAL)
anl <- df_explicit_na(anl)

Reproducibility

Timestamp

[1] "2024-11-20 17:47:09 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-11-20
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version     date (UTC) lib source
 backports           1.5.0       2024-05-23 [1] RSPM
 brio                1.1.5       2024-04-24 [1] RSPM
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 cli                 3.6.3       2024-06-21 [1] RSPM
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 codetools           0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
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 emmeans             1.10.5      2024-10-14 [1] RSPM
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 yaml                2.3.10      2024-07-26 [1] RSPM
 zoo                 1.8-12      2023-04-13 [1] CRAN (R 4.4.1)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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