Fix kable duplicating table headings

.github/workflows/deploy_bookdown.yml

@@ -13,7 +13,7 @@ jobs:
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
-      GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       EMAIL: ${{ secrets.EMAIL }}
     steps:
       # Checkout repository
@@ -54,7 +54,7 @@ jobs:
               install.packages(c("tidyverse", "bookdown"));
             }'
         env:
-          GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       # Install and cache TinyTeX only if needed
       - name: Install TinyTeX if Needed

02-visualization.Rmd

@@ -109,7 +109,7 @@ In February 2006, a Swedish physician and data advocate named Hans Rosling gave
 ```{r gapminder-2007, echo=FALSE, purl=FALSE}
 gapminder_2007 %>%
   head(3) %>%
-  kable(
+  kbl(
     digits = 2,
     caption = "Gapminder 2007 Data: First 3 of 142 countries" # ,
   ) %>%
@@ -166,7 +166,7 @@ tibble(
   aes = c("x", "y", "size", "color"),
   geom = c("point", "point", "point", "point")
 ) %>%
-  kable(
+  kbl(
     caption = "Summary of the grammar of graphics for this plot",
     booktabs = TRUE,
     linesep = ""
@@ -881,7 +881,7 @@ Observe in Figure \@ref(fig:flightsbar) that United Airlines (UA), JetBlue Airwa
 flights_counted <- flights %>%
   group_by(carrier) %>%
   summarize(number = n())
-kable(flights_counted,
+kbl(flights_counted,
   digits = 3,
   caption = "Number of flights pre-counted for each carrier",
   booktabs = TRUE,
@@ -1151,7 +1151,7 @@ if (is_latex_output()) {
   summary_table_ch2 %>%
     # Weird tick marks show up in PDF:
     mutate(`Geometric object` = str_replace_all(`Geometric object`, "`", "")) %>%
-    kable(
+    kbl(
       caption = "Summary of Five Named Graphs",
       booktabs = TRUE,
       format = "latex",
@@ -1163,7 +1163,7 @@ if (is_latex_output()) {
     column_spec(5, width = "1.6in")
 } else {
   summary_table_ch2 %>%
-    kable(
+    kbl(
       caption = "Summary of Five Named Graphs",
       booktabs = TRUE,
       format = "html"

03-wrangling.Rmd

@@ -485,7 +485,7 @@ Let's take a look at only the `dep_delay`, `arr_delay`, and the resulting `gain`
 flights %>% 
   select(dep_delay, arr_delay, gain) %>% 
   slice(1:5) %>% 
-  kable(
+  kbl(
     caption = "First five rows of departure/arrival delay and gain variables"
   ) %>%
   kable_styling(position = "center", latex_options = "hold_position")
@@ -872,7 +872,7 @@ if (is_latex_output()) {
       Verb = str_replace_all(Verb, "`", ""),
       `Data wrangling operation` = str_replace_all(`Data wrangling operation`, "`", ""),
     ) %>%
-    kable(
+    kbl(
       caption = "Summary of data wrangling verbs",
       booktabs = TRUE,
       linesep = "",

04-tidy.Rmd

@@ -225,7 +225,7 @@ stocks <- tibble(
 ) %>%
   slice(1:2)
 stocks %>%
-  kable(
+  kbl(
     digits = 2,
     caption = "Stock prices (non-tidy format)",
     booktabs = TRUE,
@@ -253,7 +253,7 @@ stocks_tidy <- stocks %>%
     values_to = "Stock Price"
   )
 stocks_tidy %>%
-  kable(
+  kbl(
     digits = 2,
     caption = "Stock prices (tidy format)",
     booktabs = TRUE,
@@ -275,7 +275,7 @@ stocks <- tibble(
 ) %>%
   slice(1:2)
 stocks %>%
-  kable(
+  kbl(
     digits = 2,
     caption = "Example of tidy data" # ,
     #    booktabs = TRUE

05-regression.Rmd

@@ -178,7 +178,7 @@ evals_ch5 %>%
 ```{r five-random-courses, echo=FALSE, purl=FALSE}
 evals_ch5 %>%
   sample_n(5) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "A random sample of 5 out of the 463 courses at UT Austin",
     booktabs = TRUE,
@@ -429,7 +429,7 @@ evals_line <- score_model %>%
 ```
 ```{r regtable, echo=FALSE, purl=FALSE}
 get_regression_table(score_model) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Linear regression table",
     booktabs = TRUE,
@@ -516,7 +516,7 @@ y_hat <- target_point$score_hat
 resid <- target_point$residual
 evals_ch5 %>%
   slice(index) %>%
-  kable(
+  kbl(
     digits = 4,
     caption = "Data for the 21st course out of 463",
     booktabs = TRUE,
@@ -694,7 +694,7 @@ gapminder2007 %>% sample_n(size = 5)
 ```{r model2-data-preview, echo=FALSE, purl=FALSE}
 gapminder2007 %>%
   sample_n(5) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Random sample of 5 out of 142 countries",
     booktabs = TRUE,
@@ -872,7 +872,7 @@ gapminder2007 %>%
   group_by(continent) %>%
   summarize(mean = mean(lifeExp)) %>%
   mutate(`Difference versus Africa` = mean - mean_africa) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Mean life expectancy by continent and relative differences from mean for Africa",
     booktabs = TRUE,
@@ -916,7 +916,7 @@ lifeExp_model <- lm(lifeExp ~ continent, data = gapminder2007)
 ```
 ```{r catxplot4b, echo=FALSE, purl=FALSE}
 get_regression_table(lifeExp_model) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Linear regression table",
     booktabs = TRUE,
@@ -1059,7 +1059,7 @@ regression_points
 regression_points <- get_regression_points(lifeExp_model, ID = "country")
 regression_points %>%
   slice(1:10) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression points (First 10 out of 142 countries)",
     booktabs = TRUE,
@@ -1302,7 +1302,7 @@ get_regression_table(score_model)
 ```{r recall-table, echo=FALSE, purl=FALSE}
 score_model <- lm(score ~ bty_avg, data = evals_ch5)
 get_regression_table(score_model) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression table",
     booktabs = TRUE,
@@ -1341,7 +1341,7 @@ score_model %>%
     lower_ci = conf_low,
     upper_ci = conf_high
   ) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression table using tidy() from broom package",
     booktabs = TRUE,
@@ -1375,7 +1375,7 @@ score_model %>%
   clean_names() %>%
   select(-c("std_resid", "hat", "sigma", "cooksd", "std_resid")) %>%
   slice(1:10) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression points using augment() from broom package",
     booktabs = TRUE,

06-multiple-regression.Rmd

@@ -130,7 +130,7 @@ evals_ch6 %>% sample_n(size = 5)
 ```{r model4-data-preview, echo=FALSE, purl=FALSE}
 evals_ch6 %>%
   sample_n(5) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "A random sample of 5 out of the 463 courses at UT Austin",
     booktabs = TRUE,
@@ -221,7 +221,7 @@ lifeExp_model <- lm(lifeExp ~ continent, data = gapminder2007)
 
 # Get regression table and kable output
 get_regression_table(lifeExp_model) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression table for life expectancy as a function of continent",
     booktabs = TRUE,
@@ -267,7 +267,7 @@ get_regression_table(score_model_interaction)
 ```{r regtable-interaction, echo=FALSE, purl=FALSE}
 score_model_interaction <- lm(score ~ age * gender, data = evals_ch6)
 get_regression_table(score_model_interaction) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression table for interaction model",
     booktabs = TRUE,
@@ -312,7 +312,7 @@ tibble(
   Intercept = c(intercept_female, intercept_male),
   `Slope for age` = c(slope_female, slope_male)
 ) %>%
-  kable(
+  kbl(
     digits = 4,
     caption = "Comparison of intercepts and slopes for interaction model",
     booktabs = TRUE,
@@ -429,7 +429,7 @@ get_regression_table(score_model_parallel_slopes)
 ```{r regtable-parallel-slopes, echo=FALSE, purl=FALSE}
 score_model_parallel_slopes <- lm(score ~ age + gender, data = evals_ch6)
 get_regression_table(score_model_parallel_slopes) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression table for parallel slopes model",
     booktabs = TRUE,
@@ -469,7 +469,7 @@ tibble(
   Intercept = c(intercept_female_parallel, intercept_male_parallel),
   `Slope for age` = c(age_coef, age_coef)
 ) %>%
-  kable(
+  kbl(
     digits = 4,
     caption = "Comparison of intercepts and slope for parallel slopes model",
     booktabs = TRUE,
@@ -595,7 +595,7 @@ regression_points
 regression_points <- get_regression_points(score_model_interaction)
 regression_points %>%
   slice(1:10) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression points (First 10 out of 463 courses)" # ,
     #    booktabs = TRUE
@@ -668,7 +668,7 @@ credit_ch6 %>% sample_n(size = 5)
 ```{r model3-data-preview, echo=FALSE, purl=FALSE}
 credit_ch6 %>%
   sample_n(5) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Random sample of 5 credit card holders",
     booktabs = TRUE,
@@ -720,7 +720,7 @@ credit_ch6 %>%
 credit_ch6 %>%
   select(debt, credit_limit, income) %>%
   cor() %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Correlation coefficients between credit card debt, credit limit, and income",
     booktabs = TRUE,
@@ -874,7 +874,7 @@ debt_model <- lm(debt ~ credit_limit + income, data = credit_ch6)
 credit_line <- get_regression_table(debt_model) %>%
   pull(estimate)
 get_regression_table(debt_model) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Multiple regression table",
     booktabs = TRUE,
@@ -941,7 +941,7 @@ set.seed(76)
 regression_points <- get_regression_points(debt_model)
 regression_points %>%
   slice(1:10) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Regression points (First 10 credit card holders out of 400)",
     booktabs = TRUE,
@@ -1062,7 +1062,7 @@ model_2_interaction <- lm(average_sat_math ~ perc_disadvan * size,
   data = MA_schools
 )
 get_regression_table(model_2_interaction) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Interaction model regression table",
     booktabs = TRUE,
@@ -1083,7 +1083,7 @@ model_2_parallel_slopes <- lm(average_sat_math ~ perc_disadvan + size,
   data = MA_schools
 )
 get_regression_table(model_2_parallel_slopes) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Parallel slopes regression table",
     booktabs = TRUE,
@@ -1178,7 +1178,7 @@ bind_rows(
   variances_parallel_slopes
 ) %>% 
   select(model, var_y, var_y_hat, var_residual, r_squared) %>% 
-  knitr::kable(
+  kbl(
     digits = 3,
     caption = "Comparing variances from interaction and parallel slopes models for MA school data", 
     booktabs = TRUE,
@@ -1205,7 +1205,7 @@ bind_rows(
   variances_parallel_slopes
 ) %>% 
   select(model, var_y, var_y_hat, var_residual, r_squared) %>% 
-  knitr::kable(
+  kbl(
     digits = 3,
     caption = "Comparing variances from interaction and parallel slopes models for UT Austin data", 
     booktabs = TRUE,
@@ -1244,7 +1244,7 @@ credit_ch6 %>%
   select(debt, income) %>%
   mutate(income = income * 1000) %>%
   cor() %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Correlation between income (in dollars) and credit card debt",
     booktabs = TRUE,
@@ -1274,7 +1274,7 @@ debt_model <- lm(debt ~ credit_limit + income, data = credit_ch6)
 credit_line <- get_regression_table(debt_model) %>%
   pull(estimate)
 get_regression_table(debt_model) %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Multiple regression results",
     booktabs = TRUE,

07-sampling.Rmd

@@ -621,7 +621,7 @@ comparing_n_table <- virtual_prop %>%
   rename(`Number of slots in shovel` = n, `Standard deviation of proportions red` = sd)
 
 comparing_n_table %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Comparing standard deviations of proportions red for three different shovels",
     booktabs = TRUE,
@@ -817,7 +817,7 @@ comparing_n_table <- virtual_prop %>%
   rename(`Number of slots in shovel` = n, `Standard deviation of proportions red` = sd)
 
 comparing_n_table %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Previously seen comparing standard deviations of proportions red for three different shovels",
     booktabs = TRUE,
@@ -873,7 +873,7 @@ comparing_n_table <- virtual_prop %>%
   rename(`Sample size (n)` = n, `Standard error of $\\widehat{p}$` = sd)
 
 comparing_n_table %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Standard errors of the sample proportion based on sample sizes of 25, 50, and 100",
     booktabs = TRUE,
@@ -985,7 +985,7 @@ comparing_n_table <- virtual_prop %>%
   sample_frac(1)
 
 comparing_n_table %>%
-  kable(
+  kbl(
     digits = 3,
     caption = "Standard errors of $\\widehat{p}$ based on n = 25, 50, 100",
     booktabs = TRUE,
@@ -1177,7 +1177,7 @@ if (!file.exists("rds/sampling_scenarios.rds")) {
 }
 
 sampling_scenarios %>%
-  kable(
+  kbl(
     caption = "\\label{tab:summarytable-ch8}Scenarios of sampling for inference",
     booktabs = TRUE,
     escape = FALSE,