Table of contents not showing for flextable captions in Word

[jwe4ec]

First, thank you to all of the contributors for this extremely helpful package!

I am having trouble adding a table of contents based on the captions for about 50 flextables that I am writing to a single Word doc and would be very grateful for any advice. Details and code are below.

Details

When I set the caption with set_caption(), I use the argument word_stylename = "heading 1". Then when I try adding the table of contents with body_add_toc(), I use the argument style = "heading 1".

The captions and tables write to full_tbls.docx just fine, but when I try opening this doc in Word (Version 2302), I get this window:

After I click Yes, I get this window:

After I click OK, the line "No table of contents entries found" is at the top of the doc:

I have also tried using "Table Caption" instead of "heading 1", but I get the same result. I tried using "heading 1" given Word's instruction above to "start by applying a heading style from the Styles gallery to the selected text." Any suggestions?

Code

My code is below, with the sections likely to be more important surrounded by separators likes this:

# ---------------------------------------------------------------------------- #
MORE IMPORTANT CODE SECTION
# ---------------------------------------------------------------------------- #

Load packages

library(flextable) # Using Version 0.8.6 in R 4.1.2
library(officer)   # Using Version 0.6.0

Set flextable defaults and define section and text properties

# Set defaults for "flextable" package (mimic those of MS Word)

set_flextable_defaults(font.size = 12, font.family = "Times New Roman", font.color = "black", 
                       border.width = 0.5, border.color = "black",
                       padding.bottom = 0, padding.top = 0, 
                       padding.left = 0.08, padding.right = 0.08,
                       line_spacing = 1)

# Define section and text properties

psect_prop <- prop_section(page_size(orient = "portrait", width = 8.5, height = 11),
                           type = "nextPage")
lsect_prop <- prop_section(page_size(orient = "landscape", width = 8.5, height = 11),
                           type = "nextPage")
text_prop <- fp_text_lite(color = "black", font.size = 12, font.family = "Times New Roman")

Create flextables

# Define function to format full tables

format_full_tbl <- function(results_trim, a_contrast_type, gen_note) {
  # Extract model info and full table
  
  analysis_type   <- results_trim$model_info$analysis_type
  analysis_sample <- results_trim$model_info$analysis_sample
  y_var           <- results_trim$model_info$y_var
  a_contrast      <- results_trim$model_info$a_contrast
  
  full_tbl <- results_trim$full_tbl
  
  # Create labels for title
  
  if (analysis_type == "efficacy") {
    analysis_type_label <- "Efficacy"
  } else if (analysis_type == "dropout") {
    analysis_type_label <- "Dropout"
  }
  
  if (a_contrast_type == "a1") {
    stage_number <- "1"
  } else if (a_contrast_type == "a2") {
    stage_number <- "2"
  }
  
  if (analysis_sample == "c1_corr_itt_2000") {
    analysis_sample_label <- "Intent-To-Treat"
  } else if (analysis_sample == "c2_4_class_meas_compl") {
    analysis_sample_label <- "Classif. Measure Compl."
  } else if (analysis_sample %in% c("c1_corr_s5_train_compl_2000", "c2_4_s5_train_compl")) {
    analysis_sample_label <- "Session 5 Training Compl."
  }
  
  if (y_var == "rr_pos_threat_m") {
    y_var_label <- "Positive Bias (RR)"
  } else if (y_var == "rr_neg_threat_m") {
    y_var_label <- "Negative Bias (RR)"
  } else if (y_var == "bbsiq_ben_m") {
    y_var_label <- "Benign Bias (BBSIQ)"
  } else if (y_var == "bbsiq_neg_m") {
    y_var_label <- "Negative Bias (BBSIQ)"
  } else if (y_var == "oa_m") {
    y_var_label <- "Anxiety (OASIS)"
  } else if (y_var == "dass21_as_m") {
    y_var_label <- "Anxiety (DASS-21-AS)"
  }
  
  if (a_contrast == "a1") {
    a_contrast_label <- "CBM-I vs. Psychoed."
  } else if (a_contrast == "a2_1") {
    a_contrast_label <- "CBM-I HR Coaching vs. No Coaching"
  } else if (a_contrast == "a2_2") {
    a_contrast_label <- "CBM-I HR Coaching vs. CBM-I LR"
  } else if (a_contrast == "a2_3") {
    a_contrast_label <- "CBM-I HR No Coaching vs. CBM-I LR"
  }
  
  # Create title
  
  if (analysis_type == "efficacy") {
    title <- paste0("Stage ", stage_number, " (", a_contrast_label, ") ",
                    analysis_type_label, " Results for ", y_var_label, 
                    " for ", analysis_sample_label, " Sample")
  } else if (analysis_type == "dropout") {
    title <- paste0("Full Stage ", stage_number, " (", a_contrast_label, ") ",
                    analysis_type_label, " Results for ", 
                    analysis_sample_label, " Sample")
  }
  
  # Format table
  
  left_align_body_cols <- c("param", "label")

  if (a_contrast_type == "a1") {
    target_cols <- c("model", "param", "label", "mean", "emp_sd", "avg_sd",
                     "pctl_bs_ci", "num_converge_all")
    col_to_bold <- "pctl_bs_ci"
  } else if (a_contrast_type == "a2") {
    target_cols <- c("model", "param", "label", "mean", "emp_sd",
                     "hpd_ci", "geweke_z")
    col_to_bold <- "hpd_ci"
  }
  
  # Restructure data as grouped data for table spanners based on "model"
  
  full_tbl <- as_grouped_data(full_tbl[, target_cols], groups = "model",
                              columns = target_cols[!(target_cols %in% "model")])
  
  full_tbl_ft <- as_flextable(full_tbl) |>
    set_table_properties(align = "left") |>

# ---------------------------------------------------------------------------- #
    set_caption(as_paragraph(as_i(title)), word_stylename = "heading 1",
                fp_p = fp_par(padding.left = 0, padding.right = 0),
                align_with_table = FALSE) |>
# ---------------------------------------------------------------------------- #
    
    align(align = "center", part = "header") |>
    align(align = "center", part = "body") |>
    align(j = left_align_body_cols, align = "left", part = "body") |>
    align(align = "left", part = "footer") |>
    
    align(j = 1, i = ~ !is.na(model), align = "center", part = "body") |>
    hline(j = 1, i = ~ !is.na(model), part = "body") |>
    bold(j = 1, i = ~ !is.na(model), part = "body") |>
  
    bold(which(full_tbl$sig == 1), col_to_bold) |>
    
    set_header_labels(param                = "Parameter",
                      label                = "Description") |>
    compose(j = "mean", part = "header",
            value = as_paragraph("Emp. ", as_i("M"))) |>
    compose(j = "emp_sd", part = "header",
            value = as_paragraph("Emp. ", as_i("SD"))) |>
    
    add_footer_lines(as_paragraph(as_i("Note."), gen_note))
  
  if (a_contrast_type == "a1") {
    full_tbl_ft <- full_tbl_ft |>
      set_header_labels(pctl_bs_ci         = "95% PB CI",
                        num_converge_all   = "No. Samples") |>
      compose(j = "avg_sd", part = "header",
              value = as_paragraph("Avg. ", as_i("SD"))) |>
    
    footnote(j = "num_converge_all", part = "header",
             value = as_paragraph(" Results were pooled across this number of samples (out of 2,000), for which all parameters converged (i.e., Geweke's ",
                                  as_i("z"), " in [-1.96, 1.96])."),
             ref_symbols = " a")
  } else if (a_contrast_type == "a2") {
    full_tbl_ft <- full_tbl_ft |>
      set_header_labels(hpd_ci             = "95% HPD CI") |>
      compose(j = "geweke_z", part = "header",
              value = as_paragraph("Geweke's ", as_i("z")))
  }
  
  full_tbl_ft <- full_tbl_ft |>
    autofit()
  
  # Add to list
  
  results_trim$full_tbl_ft <- full_tbl_ft
  
  return(results_trim)
}

# Define general notes

gen_note_drp_a1 <- " Significant parameters are in boldface (only para[1] and para[3] were interpreted). The latter level of the contrast is the reference group. CBM-I = cognitive bias modification for interpretation; PB CI = percentile bootstrap confidence interval."
gen_note_eff_a1 <- " Significant parameters are in boldface (only para[1] through para[4] were interpreted). The latter level of the contrast is the reference group. CBM-I = cognitive bias modification for interpretation; PB CI = percentile bootstrap confidence interval."

gen_note_drp_a2 <- " Significant parameters are in boldface (only para[1] and para[3] were interpreted). The latter level of the contrast is the reference group. CBM-I = cognitive bias modification for interpretation; HR = High Risk; LR = Low Risk; HPD CI = Highest Posterior Density Credible Interval."
gen_note_eff_a2 <- " Significant parameters are in boldface (only para[1] through para[4] were interpreted). The latter level of the contrast is the reference group. CBM-I = cognitive bias modification for interpretation; HR = High Risk; LR = Low Risk; HPD CI = Highest Posterior Density Credible Interval."

# Run function

res_trm_drp_c1_2000bs <- lapply(res_trm_drp_c1_2000bs, format_full_tbl, "a1", gen_note_drp_a1)
res_trm_eff_c1_2000bs <- lapply(res_trm_eff_c1_2000bs, format_full_tbl, "a1", gen_note_eff_a1)

res_trm_drp_c2_4_1000000iter <- lapply(res_trm_drp_c2_4_1000000iter, format_full_tbl, "a2", gen_note_drp_a2)
res_trm_eff_c2_4_1000000iter <- lapply(res_trm_eff_c2_4_1000000iter, format_full_tbl, "a2", gen_note_eff_a2)

Write flextables to Word

# Write full tables (note: for some reason a blank page shows at end of doc)

# Order list so full tables match the order of summary tables below

analysis_type_order   <- c("efficacy", "dropout")
analysis_sample_order <- c("c1_corr_itt_2000", "c2_4_class_meas_compl", 
                           "c1_corr_s5_train_compl_2000", "c2_4_s5_train_compl")
y_var_order           <- c("rr_pos_threat_m", "rr_neg_threat_m", "bbsiq_ben_m",
                           "bbsiq_neg_m", "oa_m", "dass21_as_m")
a_contrast_order      <- c("a1", "a2_1", "a2_2", "a2_3")

res_trm_all <- c(res_trm_eff_c1_2000bs,
                 res_trm_eff_c2_4_1000000iter,
                 res_trm_drp_c1_2000bs,
                 res_trm_drp_c2_4_1000000iter)

res_trm_all <- res_trm_all[order(sapply(res_trm_all, function(x) match(x$model_info$analysis_type,
                                                                       analysis_type_order)),
                                 sapply(res_trm_all, function(x) match(x$model_info$analysis_sample,
                                                                       analysis_sample_order)),
                                 sapply(res_trm_all, function(x) match(x$model_info$y_var,
                                                                       y_var_order)),
                                 sapply(res_trm_all, function(x) match(x$model_info$a_contrast,
                                                                       a_contrast_order)))]

full_tbl_ft_list <- lapply(res_trm_all, function(x) x$full_tbl_ft)

# Write tables

full_tbl_orientations <- rep("l", length(full_tbl_ft_list))
full_tbl_numbers <- paste0("SB", 1:length(full_tbl_ft_list))

# ---------------------------------------------------------------------------- #
doc <- read_docx()
doc <- body_set_default_section(doc, psect_prop)

doc <- body_add_toc(doc, style = "heading 1")

for (i in 1:length(full_tbl_ft_list)) {
  doc <- body_add_fpar(doc, fpar(ftext(paste0("Table ", full_tbl_numbers[[i]]),
                                       prop = update(text_prop, bold = TRUE))))
  doc <- body_add_par(doc, "")
  
  doc <- body_add_flextable(doc, full_tbl_ft_list[[i]], align = "left")

  doc <- body_end_block_section(doc, block_section(lsect_prop))
}

full_tbl_path <- "./results/bayesian/tables/full/"

dir.create(full_tbl_path, recursive = TRUE)

print(doc, target = paste0(full_tbl_path, "full_tbls.docx"))
# ---------------------------------------------------------------------------- #

[davidgohel]

I don't think we can build a TOC for tables with a protected style such as 'heading 1'.

I don't understand why it did not work with style "Table Caption" that works on my computer.

library(officer)
library(flextable)
doc <- read_docx()

doc <- body_add_toc(doc, style = "Table Caption")

zz <- as_flextable(airquality) |>
  set_caption(as_paragraph(as_i("title")),
    word_stylename = "Table Caption"
  )
doc <- body_add_flextable(doc, zz, align = "left")

print(doc, target = "toot.docx")

[davidgohel]

Did you update the TOC? The TOC (and all word computed fields) must be refreshed (with F9).

[davidgohel]

Could you post the file you produced?

[jwe4ec]

I hadn't tried F9, but I just tried it and nothing happened. I'm attaching the toot.docx file here. Thanks!

toot.docx

[davidgohel]

I opened your file and this is the result - I can see the TOC!

[jwe4ec]

So odd! I just downloaded the file I posted, opened it, and still don't see the TOC. I will send the file to some colleagues likely using the same Office 365 I have and see if they can see the TOC.

[davidgohel]

I think you need to refresh your document with F9, this is about Word not flextable nor officer

[jwe4ec]

Thanks. When I press F9 or right click on the TOC field and click "Update Field", I still get this message. (This is what originally led me to try using the "heading 1" style instead of "Table Caption".)

[davidgohel]

I tried on my mac and on a computer of a customer. It worked

[jwe4ec]

Very confusing! I had three people open the file (two on Mac, one on PC) and update the TOC by right-clicking and choosing Update Field and by pressing F9, and all of them said they still saw "No table of contents entries found."

I'm not sure what else to do so may have to just create the TOC manually. Thanks for your help!