reportifyr New User Guide

Welcome to the reportifyr New User Guide!

Getting Started with reportifyr

Are you ready to write your first report draft with reportifyr?

Please follow this step-by-step guide to get started:

Step 1

Run the following to load reportifyr:

library(reportifyr)

Step 2

Next, initialize a report project at the project root directory by running:

initialize_report_project(project_dir = here::here())

Step 3

Run the following to retrieve meta_abbrevs and meta_type parameters to standardize footnotes:

meta_abbrevs <- get_meta_abbrevs(path_to_footnotes_yaml = here::here("report", "standard_footnotes.yaml"))
meta_type <- get_meta_type(path_to_footnotes_yaml = here::here("report", "standard_footnotes.yaml"))

Step 4

We can now run the following to generate a pharmacokinetic parameter summary table and a linear regression of area under the concentration-time curve (AUC) vs. subject weight:

library(dplyr)
library(ggplot2)

data <- Theoph

calc_auc_linear_log <- function(time, conc) {
  auc <- 0

  cmax_index <- which.max(conc)

  for (i in 1:(length(time) - 1)) {
    delta_t <- time[i + 1] - time[i]

    if (i < cmax_index) {

      auc <- auc + delta_t * (conc[i + 1] + conc[i]) / 2
    } else if (i >= cmax_index && conc[i + 1] > 0 && conc[i] > 0) {

      auc <- auc + delta_t * (conc[i] - conc[i + 1]) / log(conc[i] / conc[i + 1])
    } else {

      auc <- auc + delta_t * (conc[i + 1] + conc[i]) / 2
    }
  }

  return(auc)
}

pk_params <- data %>%
  mutate(Subject = as.numeric(Subject)) %>%
  group_by(Subject) %>%
  summarise(
    cmax = max(conc, na.rm = TRUE),
    tmax = Time[which.max(conc)],
    auc = calc_auc_linear_log(Time, conc),
    wt = Wt %>% unique()
  )

lr <- pk_params %>%
  ggplot(aes(x = wt, y = auc)) +
  geom_point() +
  geom_smooth(method = "lm", formula = y ~ x, se = TRUE, color = "blue") +
  theme_bw() +
  labs(x = "Subject weight (kg)", y = "AUC (hr*mg/L)")

Step 5

Now run the following to save the table and plot to .csv and .png, respectively:

tables_path <- here::here("OUTPUTS", "tables")
outfile_name <- "theoph-pk-parameters.csv"

write_csv_with_metadata(
  object = pk_params,
  file = file.path(tables_path, outfile_name),
  meta_abbrevs = c(meta_abbrevs$AUC),
  row.names = FALSE
)

figures_path <- here::here("OUTPUTS", "figures")
plot_file_name <- "theoph-pk-exposure.png"

ggsave_with_metadata(
  filename = file.path(figures_path, plot_file_name),
  meta_abbrevs = c(meta_abbrevs$AUC),
  meta_type = meta_type$`linear-regression-plot`,
  plot = lr,
  height = 4,
  width = 6
)

Step 6

Ensure that initial document requirements are satisified before uploading to the appropriate directory:

• each figure or table (artifact) has a caption
• each caption is accompanied by a reportifyr magic string

As depicted here:

Step 7

Run the following to build a report:

docx_in <- here::here("report", "shell", "template.docx")
docx_out <- here::here("report", "draft", "template-draft.docx")
tables_path <- here::here("OUTPUTS", "tables")
figures_path <- here::here("OUTPUTS", "figures")
standard_footnotes_yaml <- here::here("report", "standard_footnotes.yaml")

build_report(
  docx_in = docx_in,
  docx_out = docx_out,
  figures_path = figures_path,
  tables_path = tables_path,
  standard_footnotes_yaml = standard_footnotes_yaml
)

Step 8

Lastly, run the following to finalize the document:

finalize_document(
  docx_in = here::here("report", "draft", "template-draft.docx"),
  docx_out = here::here("report", "final", "template-final.docx")
)

An important note, this step-by-step guide is an abbreviated form of the guides on Initializing Reportifyr, Performing Analyses, and Drafting Reports.