In metrumresearchgroup/pmtables: Tables for Pharmacometrics

library(dplyr)
library(purrr)
library(yspec)
library(pmtables)

spec <- ys_help$spec()

units <- ys_get_unit(spec, parens = TRUE)

\clearpage

Basic table

out <- stable(pmt_summarized)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "basic-table.tex", dir = params$dir)   
}

\clearpage

Bold cols

out <- stable(pmt_summarized, cols_bold = TRUE)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "basic-table-bold.tex", dir = params$dir)   
}

\clearpage

File names

out <- stable(pmt_summarized, r_file = "validate.Rmd", output_file = "file-names.tex")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, dir = params$dir)   
}
file.exists("file-names.tex")

\clearpage

Notes tpt

out <- stable(pmt_summarized, notes = c("WT: weight", "ALB: albumin"))

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "notes-tpt.tex", dir = params$dir)   
}

\clearpage

Notes minipage

conf <- noteconf(type = 'minipage')

out <- stable(pmt_summarized, notes = c("WT: weight", "ALB: albumin"), note_config = conf)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "notes-mini.tex", dir = params$dir)   
}

\clearpage

Panel basic

out <- stable(pmt_summarized, panel = "STUDY")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "panel-basic.tex", dir = params$dir)   
}

\clearpage

Panel prefix

out <- stable(pmt_summarized, panel = as.panel("STUDY", prefix = "Study: "))

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "panel-prefix.tex", dir = params$dir)   
}

\clearpage

Clear reps

out <- stable(pmt_summarized, clear_reps = "STUDY")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "clear-reps.tex", dir = params$dir)   
}

\clearpage

Clear grouped reps

out <- stable(pmt_summarized, clear_grouped_reps = "STUDY,DOSE")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "clear-grouped-reps.tex", dir = params$dir)   
}

\clearpage

hline at

out <- stable(pmt_summarized, hline_at = c(2,4,6))

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "hline-at.tex", dir = params$dir)   
}

\clearpage

hline from

out <- stable(pmt_summarized, hline_from = "STUDY")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "hline-from.tex", dir = params$dir)   
}

\clearpage

hline from with clear

out <- stable(pmt_summarized, hline_from = "STUDY", clear_reps = "STUDY")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "hline-from-clear.tex", dir = params$dir)   
}

\clearpage

Align

align <- cols_center(.outer = 'lr', DOSE = 'r')

out <- stable(pmt_summarized, align = align)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "align.tex", dir = params$dir)   
}

\clearpage

rename

out <- stable(pmt_summarized, cols_rename = c(Weight = "WT", Dose = "DOSE"))

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "col-rename.tex", dir = params$dir)   
}

\clearpage

blank

out <- stable(pmt_summarized, cols_blank = "WT,ALB")

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "col-blank.tex", dir = params$dir)   
}

\clearpage

multi-line

out <- stable(pmt_summarized, cols_rename = c("Protocol...Number" = "STUDY", Weight = "WT"))

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "col-multi-line.tex", dir = params$dir)   
}

\clearpage

multi-line units

out <- stable(
  pmt_summarized, 
  cols_rename = c("Protocol...Number" = "STUDY", Weight = "WT"), 
  units = units
)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "col-multi-line-units.tex", dir = params$dir)   
}

\clearpage

span

out <- stable(
  pmt_summarized, 
  span = colgroup("Final model", AGE:CRCL)
)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "span.tex", dir = params$dir)   
}

\clearpage

span levels

out <- stable(
  pmt_summarized, 
  span = list(
    colgroup("All covariates", WT:SCR, level = 2), 
    colgroup("Final model", AGE:CRCL)
  )
)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "span-levels.tex", dir = params$dir)   
}

\clearpage

Row spacing

out <- stable(
  pmt_summarized, 
  sizes = tab_size(row = 0.8)
)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "row-space.tex", dir = params$dir)   
}

\clearpage

Col spacing

out <- stable(
  pmt_summarized, 
  sizes = tab_size(col = 15)
)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "col-space.tex", dir = params$dir)   
}

\clearpage

Header spacing

• Extra space between table rows
• Tight space betwen header rows

out <- stable(
  pmt_summarized, 
  cols_rename = c("Clinical ... Study ... Number" = "STUDY"),
  sizes = tab_size(row = 2.4, header_row = -1.4)
)

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "header-space.tex", dir = params$dir)   
}

\clearpage

Continuous long panel

out <- pt_cont_long(
  pmt_first, cols = "WT,CRCL,ALB", panel = "STUDYf", 
  units = units
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "continuous-long-panel.tex", dir = params$dir)   
}

\clearpage

Continuous wide by

out <- pt_cont_wide(
  pmt_first, 
  cols = "WT,CRCL,ALB", by = "STUDYf", 
  units = units
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "continuous-wide-by.tex", dir = params$dir)   
}

\clearpage

Categorical long by

out <- pt_cat_long(
  pmt_first, 
  cols = "SEXf,RFf,FORMf", 
  span = "STUDYf"
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "cat-long-span.tex", dir = params$dir)   
}

\clearpage

Categorical wide by panel

out <- pt_cat_wide(
  pmt_first, 
  cols = "SEXf,RFf",
  by = "FORMf",
  panel = "STUDYf"
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "cat-wide-by-panel.tex", dir = params$dir)   
}

\clearpage

Inventory by

out <- pt_data_inventory(
  pmt_pk, 
  by = "STUDYf"
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "inventory-by.tex", dir = params$dir)   
}

\clearpage

Inventory panel by

out <- pt_data_inventory(
  pmt_pk, 
  panel = "FORMf",
  by = "STUDYf"
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "inventory-panel-by.tex", dir = params$dir)   
}

\clearpage

Inventory stacked

out <- pt_data_inventory(
  pmt_obs, 
  by = "STUDYf", 
  panel = "SEQf",
  stacked = TRUE
) %>% as_stable()

pt_wrap(out, con = stdout()) 

if(params$save) {
  stable_save(out, file = "inventory-stacked.tex", dir = params$dir)   
}

metrumresearchgroup/pmtables documentation built on Oct. 27, 2024, 5:16 p.m.