# Table Gallery

Gallery showing various tables possible with the {gtsummary} package. If you have created an interesting table using {gtsummary}, please submit it to the gallery via a pull request to the GitHub repository.

    library(gtsummary); library(gt); library(survival)
    #> Warning: package 'gt' was built under R version 4.0.2
    #> Warning: package 'survival' was built under R version 4.0.2
    library(dplyr); library(stringr); library(purrr); library(forcats)
    #> Warning: package 'dplyr' was built under R version 4.0.2

## Summary Tables

Add a spanning header over the group columns for increased clarity, reporting the number of non-missing observations, and modifying column headers.

    trial[c("trt", "age", "grade")] %>%
      tbl_summary(
        by = trt,
        missing = "no",
        statistic = all_continuous() ~ "{median} ({p25}, {p75}) [N = {N_nonmiss}]"
      ) %>%
      modify_header(stat_by = md("**{level}**<br>N =  {n} ({style_percent(p)}%)")) %>%
      add_n() %>%
      bold_labels() %>%
      modify_spanning_header(starts_with("stat_") ~ "**Chemotherapy Treatment**")

Characteristic | N | Chemotherapy Treatment
--- | --- | ---
Drug A N = 98 (49%)1 | Drug B N = 102 (51%)1
Age | 189 | 46 (37, 59) [N = 91] | 48 (39, 56) [N = 98]
Grade | 200 |  |
I |  | 35 (36%) | 33 (32%)
II |  | 32 (33%) | 36 (35%)
III |  | 31 (32%) | 33 (32%)
1 Statistics presented: median (IQR) [N = N]; n (%)

Modify the function that formats the p-values, change variable labels, updating tumor response header, and add a correction for multiple testing.

    trial[!is.na(trial$response), c("response", "age", "grade")] %>%
      mutate(response = factor(response, labels = c("No Tumor Response", "Tumor Responded"))) %>%
      tbl_summary(
        by = response,
        missing = "no",
        label = list(age ~ "Patient Age", grade ~ "Tumor Grade")
      ) %>%
      add_p(pvalue_fun = partial(style_pvalue, digits = 2)) %>%
      add_q()
    #> Adjusting p-values with
    #> `stats::p.adjust(x$table_body$p.value, method = "fdr")`

Characteristic | No Tumor Response, N = 1321 | Tumor Responded, N = 611 | p-value2 | q-value3
--- | --- | --- | --- | ---
Patient Age | 46 (36, 55) | 49 (43, 59) | 0.091 | 0.18
Tumor Grade |  |  | 0.93 | 0.93
I | 46 (35%) | 21 (34%) |  |
II | 44 (33%) | 19 (31%) |  |
III | 42 (32%) | 21 (34%) |  |
1 Statistics presented: median (IQR); n (%) 2 Statistical tests performed: Wilcoxon rank-sum test; chi-square test of independence 3 False discovery rate correction for multiple testing

Include missing tumor response as column using `fct_explicit_na()`.

    trial[c("response", "age", "grade")] %>%
      mutate(
        response = factor(response, labels = c("No Tumor Response", "Tumor Responded")) %>%
          fct_explicit_na(na_level = "Missing Response Status")
      ) %>%
      tbl_summary(
        by = response,
        label = list(age ~ "Patient Age", grade ~ "Tumor Grade")
      )

Characteristic | No Tumor Response, N = 1321 | Tumor Responded, N = 611 | Missing Response Status, N = 71
--- | --- | --- | ---
Patient Age | 46 (36, 55) | 49 (43, 59) | 52 (44, 57)
Unknown | 7 | 3 | 1
Tumor Grade |  |  |
I | 46 (35%) | 21 (34%) | 1 (14%)
II | 44 (33%) | 19 (31%) | 5 (71%)
III | 42 (32%) | 21 (34%) | 1 (14%)
1 Statistics presented: median (IQR); n (%)

Include p-values comparing all groups to a single reference group.

    # table summarizing data with no p-values
    t0 <- trial %>%
      select(grade, age, response) %>%
      tbl_summary(by = grade, missing = "no") %>%
      modify_header(stat_by = md("**{level}**"))

    # table comparing grade I and II
    t1 <- trial %>%
      select(grade, age, response) %>%
      filter(grade %in% c("I", "II")) %>%
      tbl_summary(by = grade, missing = "no") %>%
      add_p() %>%
      modify_header(p.value ~ md("**I vs. II**"))

    # table comparing grade I and II
    t2 <- trial %>%
      select(grade, age, response) %>%
      filter(grade %in% c("I", "III")) %>%
      tbl_summary(by = grade, missing = "no") %>%
      add_p()  %>%
      modify_header(p.value ~ md("**I vs. III**"))

    # merging the 3 tables together, and adding additional gt formatting
    tbl_merge(list(t0, t1, t2)) %>%
      modify_spanning_header(
        list(
          starts_with("stat_") ~ "**Tumor Grade**",
          starts_with("p.value") ~ "**p-value**"
        )
      ) %>%
      as_gt(include = -tab_spanner) %>%
      # hiding repeated summary columns
      cols_hide(columns = vars(stat_1_2, stat_2_2, stat_3_2, stat_1_3, stat_2_3, stat_3_3))

Characteristic | I1 | II1 | III1 | I vs. II2 | I vs. III2
--- | --- | --- | --- | --- | ---
Age | 47 (37, 56) | 48 (37, 57) | 47 (38, 58) | 0.7 | 0.5
Tumor Response | 21 (31%) | 19 (30%) | 21 (33%) | >0.9 | 0.9
1 Statistics presented: median (IQR); n (%) 2 Statistical tests performed: Wilcoxon rank-sum test; Fisher's exact test

Add additional statistics as additional columns.

    # define function for lower and upper bounds of the mean CI
    ll <- function(x) t.test(x)$conf.int[1]
    ul <- function(x) t.test(x)$conf.int[2]

    t1 <-
      trial %>%
      select(age, marker) %>%
      tbl_summary(statistic = all_continuous() ~ "{mean} ({sd})", missing = "no") %>%
      modify_header(stat_0 ~ "**Mean (SD)**")

    t2 <-
      trial %>%
      select(age, marker) %>%
      tbl_summary(statistic = all_continuous() ~ "{ll}, {ul}", missing = "no") %>%
      modify_header(stat_0 ~ "**95% CI for Mean**")

    tbl_merge(list(t1, t2)) %>%
      modify_footnote(everything() ~ NA_character_) %>%
      modify_spanning_header(everything() ~ NA_character_)

Characteristic | Mean (SD) | 95% CI for Mean
--- | --- | ---
Age | 47 (14) | 45, 49
Marker Level (ng/mL) | 0.92 (0.86) | 0.79, 1.04

## Regression Tables

Include number of observations and the number of events in a univariate regression table.

    trial[c("response", "age", "grade")] %>%
      tbl_uvregression(
        method = glm,
        y = response,
        method.args = list(family = binomial),
        exponentiate = TRUE
      ) %>%
      add_nevent()

Characteristic | N | Event N | OR1 | 95% CI1 | p-value
--- | --- | --- | --- | --- | ---
Age | 183 | 58 | 1.02 | 1.00, 1.04 | 0.10
Grade | 193 | 61 |  |  |
I |  |  | — | — |
II |  |  | 0.95 | 0.45, 2.00 | 0.9
III |  |  | 1.10 | 0.52, 2.29 | 0.8
1 OR = Odds Ratio, CI = Confidence Interval

Include two related models side-by-side with descriptive statistics.

    gt_r1 <- glm(response ~ age + trt, trial, family = binomial) %>%
      tbl_regression(exponentiate = TRUE)
    gt_r2 <- coxph(Surv(ttdeath, death) ~ age + trt, trial) %>%
      tbl_regression(exponentiate = TRUE)
    gt_t1 <- trial[c("age", "trt")] %>% tbl_summary(missing = "no") %>% add_n()

    tbl_merge(
      list(gt_t1, gt_r1, gt_r2),
      tab_spanner = c("**Summary Statistics**", "**Tumor Response**", "**Time to Death**")
    )

Characteristic | Summary Statistics | Tumor Response | Time to Death
--- | --- | --- | ---
N | N = 2001 | OR2 | 95% CI2 | p-value | HR2 | 95% CI2 | p-value
Age | 189 | 47 (38, 57) | 1.02 | 1.00, 1.04 | 0.095 | 1.01 | 0.99, 1.02 | 0.4
Chemotherapy Treatment | 200 |  |  |  |  |  |  |
Drug A |  | 98 (49%) | — | — |  | — | — |
Drug B |  | 102 (51%) | 1.13 | 0.60, 2.13 | 0.7 | 1.31 | 0.89, 1.93 | 0.2
1 Statistics presented: median (IQR); n (%) 2 OR = Odds Ratio, CI = Confidence Interval, HR = Hazard Ratio

Include the number of events at each level of a categorical predictor.

    gt_model <-
      trial[c("ttdeath", "death", "stage", "grade")] %>%
      tbl_uvregression(
        method = coxph,
        y = Surv(ttdeath, death),
        exponentiate = TRUE,
        hide_n = TRUE
      )

    gt_eventn <-
      trial %>%
      filter(death ==  1) %>%
      select(stage, grade) %>%
      tbl_summary(
        statistic = all_categorical() ~ "{n}",
        label = list(stage ~ "T Stage", grade ~ "Grade")
      ) %>%
      modify_header(stat_0 ~ "**Event N**") %>%
      modify_footnote(everything() ~ NA_character_)

    tbl_merge(list(gt_eventn, gt_model)) %>%
      bold_labels() %>%
      italicize_levels() %>%
      modify_spanning_header(everything() ~ NA_character_)

Characteristic | Event N | HR1 | 95% CI1 | p-value
--- | --- | --- | --- | ---
T Stage |  |  |  |
T1 | 24 | — | — |
T2 | 27 | 1.18 | 0.68, 2.04 | 0.6
T3 | 22 | 1.23 | 0.69, 2.20 | 0.5
T4 | 39 | 2.48 | 1.49, 4.14 | <0.001
Grade |  |  |  |
I | 33 | — | — |
II | 36 | 1.28 | 0.80, 2.05 | 0.3
III | 43 | 1.69 | 1.07, 2.66 | 0.024
1 HR = Hazard Ratio, CI = Confidence Interval

Regression model where the covariate remains the same, and the outcome changes.

    tbl_reg <-
      trial[c("age", "marker", "trt")] %>%
      tbl_uvregression(
        method = lm,
        x = trt,
        show_single_row = "trt",
        hide_n = TRUE
      ) %>%
      modify_header(list(
        label ~"**Model Outcome**",
        estimate ~ "**Treatment Coef.**"
      ))

    tbl_reg %>%
      modify_footnote(estimate ~ "Values larger than 0 indicate larger values in the Drug group.")

Model Outcome | Treatment Coef.1 | 95% CI2 | p-value
--- | --- | --- | ---
Age | 0.44 | -3.7, 4.6 | 0.8
Marker Level (ng/mL) | -0.20 | -0.44, 0.05 | 0.12
1 Values larger than 0 indicate larger values in the Drug group. 2 CI = Confidence Interval

Add descriptive statistics by treatment group to the table above to produce a table often reported two group comparisons.

    gt_sum <-
      trial[c("age", "marker", "trt")] %>%
      mutate(trt = fct_rev(trt)) %>%
      tbl_summary(by = trt,
                  statistic = all_continuous() ~ "{mean} ({sd})",
                  missing = "no") %>%
      add_n() %>%
      modify_header(stat_by = md("**{level}**"))

    tbl_merge(list(gt_sum, tbl_reg))  %>%
      modify_header(estimate_2 ~ "**Difference**") %>%
      modify_spanning_header(everything() ~ NA_character_)

Characteristic | N | Drug B1 | Drug A1 | Difference | 95% CI2 | p-value
--- | --- | --- | --- | --- | --- | ---
Age | 189 | 47 (14) | 47 (15) | 0.44 | -3.7, 4.6 | 0.8
Marker Level (ng/mL) | 190 | 0.82 (0.83) | 1.02 (0.89) | -0.20 | -0.44, 0.05 | 0.12
1 Statistics presented: mean (SD) 2 CI = Confidence Interval

Implement a custom tidier to report Wald confidence intervals. The Wald confidence intervals are calculated using `confint.default()`.

    my_tidy <- function(x, exponentiate =  FALSE, conf.level = 0.95, ...) {
      dplyr::bind_cols(
        broom::tidy(x, exponentiate = exponentiate, conf.int = FALSE),
        # calculate the confidence intervals, and save them in a tibble
        stats::confint.default(x) %>%
          tibble::as_tibble() %>%
          rlang::set_names(c("conf.low", "conf.high"))  )
    }

    lm(age ~ grade + marker, trial) %>%
      tbl_regression(tidy_fun = my_tidy)

Characteristic | Beta | 95% CI1 | p-value
--- | --- | --- | ---
Grade |  |  |
I | — | — |
II | 0.64 | -4.6, 5.9 | 0.8
III | 2.4 | -2.8, 7.6 | 0.4
Marker Level (ng/mL) | -0.04 | -2.6, 2.5 | >0.9
1 CI = Confidence Interval