knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(tfrmt) library(dplyr) library(tidyr)
AE Mocks
Reusable tfrmt base layer:
ae_mock_table <- function(tfrmt_obj){ tfrmt( title = "Table Name", subtitle = "Study ID: GSK12345", body_plan = body_plan( frmt_structure(group_val = ".default", label_val = ".default", frmt_combine( "{count} {percent}", count = frmt("XXX"), percent = frmt_when("==100"~ frmt(""), "==0"~ "", "TRUE" ~ frmt("(XX.X%)")))), frmt_structure(group_val = ".default", label_val = ".default", frmt_combine( "{num} ({lower}, {upper})", num = frmt("XX.X"), lower = frmt_when("==100"~ frmt(""), "==0"~ "", "TRUE" ~ frmt("XX.X%")), upper = frmt_when("==100"~ frmt(""), "==0"~ "", "TRUE" ~ frmt("XX.X%")))) ), col_plan = col_plan( T1, T2, `T1&T2`, PL, everything(), -starts_with("ord") ) ) }
Example 1: mock table with no groups
df <- bind_rows( crossing(label = c("label 1", "label 2", "label 3"), column = c("T1", "T2", "T1&T2", "PL"), param = c("count", "percent")) %>% mutate(ord1 = rep(seq(1:length(unique(.$label))), each = nrow(.)/length(unique(.$label)) )), crossing(label = c("label 1", "label 2", "label 3"), column = c("risk T1-PL", "risk T2-PL", "risk T1&T2-PL"), param = c("num", "lower", "upper")) %>% mutate(ord1 = rep(seq(1:length(unique(.$label))), each = nrow(.)/length(unique(.$label)) )) ) %>% arrange_all() ae_mock_table() %>% tfrmt( label = "label", param = "param", column = "column", value = value, sorting_cols = vars(ord1) ) %>% print_mock_gt(df)
Example 2: mock table with one level of grouping, indented labels
df <- bind_rows( crossing(group = c("grp1", "grp2"), label = c("label 1", "label 2", "label 3"), column = c("T1", "T2", "T1&T2", "PL"), param = c("count", "percent")), crossing(group = c("grp1", "grp2"), label = c("label 1", "label 2", "label 3"), column = c("risk T1-PL", "risk T2-PL", "risk T1&T2-PL"), param = c("num", "lower", "upper")) ) %>% arrange_all() ae_mock_table() %>% tfrmt( group = group, label = "label", param = "param", column = "column", value = value, row_grp_plan = row_grp_plan( row_grp_structure(group_val = ".default", element_block(post_space = " ")) ), col_plan = col_plan( T1, T2, `T1&T2`, PL, `risk T1-PL`, `risk T2-PL`, `risk T1&T2-PL`, everything(), -starts_with("ord")) ) %>% print_mock_gt(df)
Example 3: mock table with two levels of grouping, indented labels
df <- bind_rows( crossing(grp1 = c("group 1.1", "group 1.2"), grp2 = c("group 2.1", "group 2.2"), label = c("label 1", "label 2"), column = c("T1", "T2", "T1&T2", "PL"), param = c("count", "percent")), crossing(grp1 = c("group 1.1", "group 1.2"), grp2 = c("group 2.1", "group 2.2"), label = c("label 1", "label 2"), column = c("risk T1-PL", "risk T2-PL", "risk T1&T2-PL"), param = c("num", "lower", "upper")) ) %>% arrange_all() ae_mock_table() %>% tfrmt( group = c(grp1, grp2), label = "label", param = "param", column = "column", value = value, row_grp_plan = row_grp_plan( row_grp_structure(group_val = ".default", element_block(post_space = " ")) ), col_plan = col_plan( T1, T2, `T1&T2`, PL, `risk T1-PL`, `risk T2-PL`, `risk T1&T2-PL`, everything(), -starts_with("ord")) ) %>% print_mock_gt(df)
Example 4: mock table with two levels of grouping, column separated labels
ae_mock_table() %>% tfrmt( group = c(grp1, grp2), label = "label", param = "param", column = "column", value = value, row_grp_plan = row_grp_plan(label_loc = element_row_grp_loc(location = "column")), col_plan = col_plan( T1, T2, `T1&T2`, PL, `risk T1-PL`, `risk T2-PL`, `risk T1&T2-PL`, everything(), -starts_with("ord")) ) %>% print_mock_gt(df)
Example 5: mock table with combined columns, using data_ae
fmt_spec <- tfrmt( group = AEBODSYS, label = AETERM, param = param, column = c(col2, col1), value = value, row_grp_plan = row_grp_plan(), body_plan = body_plan( frmt_structure(group_val = ".default", label_val = ".default", frmt_combine("{n} {pct}", n = frmt("XXX"), pct = frmt_when( "==100" ~ "", "==0" ~ "", TRUE ~ frmt("(xx.x %)")))), frmt_structure(group_val = ".default", label_val = ".default", AEs = frmt("[XXX]")), frmt_structure(group_val = ".default", label_val = ".default", pval = frmt_when(">0.99" ~ ">0.99", "<0.001" ~ "<0.001", "<0.05" ~ frmt("x.xxx*"), TRUE ~ frmt("x.xxx", missing = "--"))) ), col_plan = col_plan(-starts_with("ord"))) # data_ae2 <- data_ae %>% group_by(AEBODSYS, AETERM) %>% mutate(pct_high = value[col2=="Xanomeline High Dose" & param=="pct"]) %>% ungroup %>% filter(pct_high >10) %>% select(-pct_high) data_ae2 %>% select(-value) %>% arrange(ord1, ord2 ) %>% print_mock_gt(fmt_spec, . )
Demography Mocks
tfrmt( # specify columns in the data group = c(rowlbl1,grp), label = rowlbl2, column = column, param = param, value = value, sorting_cols = c(ord1, ord2), # Specify body plan body_plan = body_plan( frmt_structure(group_val = ".default", label_val = ".default", frmt_combine("{n} {pct}", n = frmt("xxx"), pct = frmt_when("==100" ~ "", "==0" ~ "", TRUE ~ frmt("(xx.x %)")))), frmt_structure(group_val = ".default", label_val = "n", frmt("xxx")), frmt_structure(group_val = ".default", label_val = c("Mean", "Median", "Min","Max"), frmt("xxx.x")), frmt_structure(group_val = ".default", label_val = "SD", frmt("xxx.xx")), frmt_structure(group_val = ".default", label_val = ".default", p = frmt("")), frmt_structure(group_val = ".default", label_val = c("n","<65 yrs","<12 months","<25"), p = frmt_when(">0.99" ~ ">0.99", "<0.001" ~ "<0.001", TRUE ~ frmt("x.xxx", missing = ""))) ), # Specify row group plan row_grp_plan = row_grp_plan( row_grp_structure(group_val = ".default", element_block(post_space = " ")), label_loc = element_row_grp_loc(location = "column") ), # Specify column styling plan col_style_plan = col_style_plan( col_style_structure(align = c(".",","," "), col = vars(everything())) ), # remove extra cols col_plan = col_plan(-grp, -starts_with("ord") ) ) %>% print_mock_gt(data_demog %>% select(-value))
Efficacy Mocks
tfrmt( group = group, label = label, column = column, param = param, value = value, sorting_cols = c(ord1, ord2), row_grp_plan = row_grp_plan( row_grp_structure(group_val = list(group="Change from Baseline"), element_block(post_space = " ")), row_grp_structure(group_val = list(group="p-value (Dose Response)"), element_block(post_space = " ")), row_grp_structure(group_val = list(group="p-value (Xan - Placebo)"), element_block(post_space = " ")) ), body_plan = body_plan( frmt_structure(group_val = ".default", label_val = "n", frmt("xx")), frmt_structure(group_val = ".default", label_val = "Median (Range)", frmt_combine("{median} ({min};{max})", median = frmt("xx.x"), min = frmt("xx"), max = frmt("xx"), missing = " ")), frmt_structure(group_val = ".default", label_val = "Mean (SD)", frmt_combine("{mean} ({sd})", mean = frmt("xx.x"), sd = frmt("xx.xx"), missing = " ")), frmt_structure(group_val = ".default", label_val = "Diff of LS Means (SE)", frmt_combine("{diff} ({diff_se})", diff = frmt("xx.x"), diff_se = frmt("xx.xx"), missing = " ")), frmt_structure(group_val = ".default", label_val = "95% CI", frmt_combine("({diff_lcl};{diff_ucl})", diff_lcl = frmt("xx.x"), diff_ucl = frmt("xx.x"), missing = " ")), frmt_structure(group_val = ".default", label_val = ".default", p.value = frmt_when("<0.001" ~ "<0.001", ">0.99" ~ ">0.99", TRUE ~ frmt("x.xxx", missing = " "))) ), col_plan = col_plan( group, label, contains("Placebo"), contains("Low"), contains("High") ) ) %>% print_mock_gt(data_efficacy %>% select(-value))
