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                                            18.4450              28.0582              23.9304      
    Rate CI                                  (13.9015, 24.4736)   (21.3288, 36.9108)   (18.1382, 31.5722)
  Rate Ratio                                                            1.5212               1.2974      
    Rate Ratio CI                                                  (1.1166, 2.0724)     (0.9505, 1.7708) 
    p-value                                                             0.0078               0.1009

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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] "2024-12-21 17:42:12 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     2024-12-21
 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
 broom               1.0.7       2024-09-26 [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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 estimability        1.5.1       2024-05-12 [1] RSPM
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 random.cdisc.data   0.3.16.9001 2024-12-21 [1] https://p~
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 stringr             1.5.1       2023-11-14 [1] RSPM
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 TH.data             1.1-2       2023-04-17 [1] CRAN (R 4.4.1)
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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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