## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", warning = FALSE, message = FALSE ) library(TernTables) options(tibble.width = Inf) # show all columns in printed tibbles # Output directory for exported .docx files. # Override by setting options(TernTables.vignette_outdir = "/your/path") before rendering. out_dir <- getOption("TernTables.vignette_outdir", default = tempdir()) ## ----load-data---------------------------------------------------------------- data(tern_colon) ## ----ternP-run, eval = FALSE-------------------------------------------------- # # Load a messy CSV shipped with the package # path <- system.file("extdata/csv", "tern_colon_messy.csv", # package = "TernTables") # raw <- readr::read_csv(path, show_col_types = FALSE) # result <- ternP(raw) # # The print method fires automatically, summarising every transformation applied. ## ----ternP-access, eval = FALSE----------------------------------------------- # result$clean_data # Cleaned, analysis-ready tibble # result$sparse_rows # Rows with >50% NA (retained, not removed — review these) # result$feedback # Named list; NULL elements mean no action was taken ## ----ternP-doc, eval = FALSE-------------------------------------------------- # write_cleaning_doc(result, # filename = file.path(out_dir, "cleaning_summary.docx")) ## ----ternP-handoff, eval = FALSE---------------------------------------------- # tbl <- ternG(result$clean_data, # exclude_vars = c("ID"), # group_var = "Recurrence") ## ----ternD-example, results = "hide"------------------------------------------ tbl_descriptive <- ternD( data = tern_colon, exclude_vars = c("ID"), output_docx = file.path(out_dir, "Tern_descriptive.docx"), methods_filename = file.path(out_dir, "TernTables_methods.docx"), open_doc = FALSE, category_start = c( "Patient Demographics" = "Age (yr)", "Surgical Findings" = "Colonic Obstruction", "Tumor Characteristics" = "Positive Lymph Nodes (n)", "Outcomes" = "Recurrence" ) ) tbl_descriptive ## ----ternD-figure, echo=FALSE, fig.align="center", out.width="45%"------------ knitr::include_graphics("figures/tern_descriptive.png") ## ----ternG-2group, results = "hide"------------------------------------------- tbl_2group <- ternG( data = tern_colon, exclude_vars = c("ID"), group_var = "Recurrence", output_docx = file.path(out_dir, "Tern_2_group.docx"), methods_filename = file.path(out_dir, "TernTables_methods.docx"), open_doc = FALSE, OR_col = TRUE, insert_subheads = TRUE, category_start = c( "Patient Demographics" = "Age (yr)", "Surgical Findings" = "Colonic Obstruction", "Tumor Characteristics" = "Positive Lymph Nodes (n)", "Treatment Details" = "Treatment Arm" ) ) tbl_2group ## ----ternG-3group, results = "hide"------------------------------------------- tbl_3group <- ternG( data = tern_colon, exclude_vars = c("ID"), group_var = "Treatment_Arm", group_order = c("Observation", "Levamisole", "Levamisole + 5FU"), output_docx = file.path(out_dir, "Tern_3_group.docx"), methods_filename = file.path(out_dir, "TernTables_methods.docx"), open_doc = FALSE, consider_normality = "ROBUST", post_hoc = TRUE, category_start = c( "Patient Demographics" = "Age (yr)", "Surgical Findings" = "Colonic Obstruction", "Tumor Characteristics" = "Positive Lymph Nodes (n)", "Outcomes" = "Recurrence" ) ) tbl_3group ## ----ternG-fdr, eval = FALSE-------------------------------------------------- # tbl_fdr <- ternG( # data = tern_colon, # exclude_vars = c("ID"), # group_var = "Recurrence", # p_adjust = TRUE, # p_adjust_display = "both", # show raw AND FDR-corrected P values # methods_doc = FALSE # ) ## ----row-pct-example, eval = FALSE-------------------------------------------- # tbl_rowpct <- ternG( # data = tern_colon, # vars = c("Tumor_Differentiation", "Extent_of_Local_Spread", # "Colonic_Obstruction"), # group_var = "Recurrence", # percentage_compute = "row", # output_docx = file.path(out_dir, "Tern_row_pct.docx"), # open_doc = FALSE, # citation = FALSE # ) ## ----show-p-example, eval = FALSE--------------------------------------------- # tbl_desc_grouped <- ternG( # data = tern_colon, # exclude_vars = c("ID"), # group_var = "Treatment_Arm", # show_p = FALSE, # output_docx = file.path(out_dir, "Tern_no_pval.docx"), # open_doc = FALSE, # citation = FALSE # ) ## ----show-missing-example, eval = FALSE--------------------------------------- # tbl_with_missing <- ternG( # data = tern_colon, # exclude_vars = c("ID"), # group_var = "Recurrence", # show_missing = TRUE, # output_docx = file.path(out_dir, "Tern_missing.docx"), # open_doc = FALSE, # citation = FALSE # ) ## ----caption-example, eval = FALSE-------------------------------------------- # tbl_descriptive <- ternD( # data = tern_colon, # exclude_vars = c("ID"), # output_docx = file.path(out_dir, "Tern_descriptive.docx"), # table_caption = "Table 1. Baseline patient characteristics." # ) ## ----footnote-example, eval = FALSE------------------------------------------- # tbl_2group <- ternG( # data = tern_colon, # exclude_vars = c("ID"), # group_var = "Recurrence", # OR_col = TRUE, # output_docx = file.path(out_dir, "Tern_2_group.docx"), # table_caption = "Table 2. Characteristics by recurrence status.", # table_footnote = c( # "Abbreviations: OR, odds ratio; CI, confidence interval.", # "\u2020 P values from chi-square or Wilcoxon rank-sum test.", # "\u2021 ORs from unadjusted logistic regression." # ) # ) ## ----font-example, eval = FALSE----------------------------------------------- # options(TernTables.font_family = "Times New Roman") # # All subsequent ternG/ternD/word_export calls use Times New Roman ## ----variable-footnote-example, eval = FALSE---------------------------------- # tbl <- ternG( # data = tern_colon, # vars = c("Age_Years", "Sex", "Colonic_Obstruction"), # group_var = "Recurrence", # variable_footnote = c( # "Age (yr)" = "Age at registration.", # "Colonic Obstruction" = "Defined as complete mechanical obstruction on imaging." # ), # open_doc = FALSE, # citation = FALSE # ) ## ----classify-normality-example, eval = FALSE--------------------------------- # norm_tbl <- classify_normality(tern_colon, group_var = "Recurrence") # print(norm_tbl) ## ----methods-doc, eval = FALSE------------------------------------------------ # write_methods_doc( # tbl = tbl_2group, # filename = file.path(out_dir, "Tern_methods.docx") # ) ## ----ternStyle-example, eval = FALSE------------------------------------------ # custom <- tibble::tibble( # Variable = c("Institution", "Study period", # "N enrolled", "Median follow-up (months)"), # Value = c("Single centre", "2010 \u2013 2022", # "47", "28.3 [18.1, 40.2]") # ) # ternStyle( # tbl = custom, # table_caption = "Table S1. Study overview.", # filename = file.path(out_dir, "Tern_custom.docx"), # open_doc = FALSE, # citation = FALSE # ) ## ----ternStyle-spanner, eval = FALSE------------------------------------------ # results <- tibble::tibble( # Variable = c("Age (yr)", "BMI"), # `Uni HR (95% CI)` = c("1.02 [0.98\u20131.06]", "1.11 [1.03\u20131.19]"), # `Uni p` = c("0.31", "0.006"), # `Multi HR (95% CI)` = c("1.01 [0.97\u20131.05]", "1.08 [1.00\u20131.17]"), # `Multi p` = c("0.64", "0.047") # ) # ternStyle( # tbl = results, # filename = file.path(out_dir, "Tern_regression.docx"), # spanner = list( # "Univariate" = c("Uni HR (95% CI)", "Uni p"), # "Multivariate" = c("Multi HR (95% CI)", "Multi p") # ), # open_doc = FALSE, # citation = FALSE # ) ## ----ternStyle-spanner-named, eval = FALSE------------------------------------ # cor_tbl <- tibble::tibble( # Variable = c("Gene A", "Gene B", "Gene C"), # `SLAM r` = c("0.42", "-0.18", "0.67"), # `SLAM p` = c("0.031", "0.214", "< 0.001"), # `Control r` = c("0.11", "0.05", "0.38"), # `Control p` = c("0.401", "0.712", "0.044") # ) # ternStyle( # tbl = cor_tbl, # filename = file.path(out_dir, "Tern_correlation.docx"), # col1_header = "Gene", # spanner = list( # "SLAM" = c("r" = "SLAM r", "p" = "SLAM p"), # "Control" = c("r" = "Control r", "p" = "Control p") # ), # open_doc = FALSE, # citation = FALSE # ) # # Spanner row: SLAM | Control # # Column-names row: r p | r p