Structure into a pipeline with targets.

Multiple formats, customised options.

_targets.R

+library(targets)
+library(tarchetypes)
+source("src/functions.R")
+options(tidyverse.quiet = TRUE)
+
+## Uncomment below to use local multicore computing
+## when running tar_make_clustermq().
+# options(clustermq.scheduler = "multicore")
+
+# Uncomment below to deploy targets to parallel jobs
+# on a Sun Grid Engine cluster when running tar_make_clustermq().
+# options(clustermq.scheduler = "sge", clustermq.template = "sge.tmpl")
+
+
+tar_option_set(
+  packages = c(
+    "boot",
+    "furrr",
+    "here",
+    "hrbrthemes",
+    "janitor",
+    "kableExtra",
+    "knitr",
+    "readxl",
+    "tidyverse"
+  )
+)
+
+## Interactive workflow
+# pacman::p_load(char = tar_option_get("packages"))
+# tar_load(everything())
+
+
+## Define the pipeline. A pipeline is just a list of targets.
+list(
+
+  # SOURCE FILES ------------------------------------------------------------
+
+  tar_target(
+    data_file,
+    "data/HumanDogRatioData.xlsx",
+    format = "file"
+  )
+  ,
+
+
+  # SOURCE DATA ---------------------------------------------------
+
+  tar_target(
+  	raw_data,
+	  read_excel(data_file)
+  )
+  ,
+
+
+  tar_target(
+    sim_pars,
+    tribble(
+      ~param, ~value,
+      "N", 334,
+      "b0", -2,
+      "b1", -.2
+    )
+  )
+  ,
+
+  tar_target(
+    sim_data,
+    do.call(
+      simulate_household_data,
+      as.list(pull(sim_pars, value, name = param))
+    )
+  )
+  ,
+
+
+  # DERIVED DATA --------------------------------------------------
+
+  tar_target(
+  	clean_data,
+  	raw_data %>% cleanup()
+  )
+  ,
+
+
+  # PARAMETERS ----------------------------------------------------
+
+
+  # DESCRIPTION ---------------------------------------------------
+
+
+  # MODELS --------------------------------------------------------
+
+
+  # DIAGNOSIS -----------------------------------------------------
+
+
+  # REPORTS -------------------------------------------------------
+
+  tar_render(
+  	report_html,
+    "src/confint_ratio.Rmd",
+    output_dir = "public",  # https://github.com/ropensci/drake/issues/742
+    output_format =
+      rmdformats::readthedown(
+        dev = "CairoPNG",
+        toc_depth = 3,
+        lightbox = T,
+        gallery = T,
+        use_bookdown = T,
+        number_sections = T),
+    output_file =
+      "public/confint_ratio.html",
+      quiet = FALSE
+  )
+  ,
+
+  tar_render(
+  	report_pdf,
+  	"src/confint_ratio.Rmd",
+    output_dir = "reports",  # https://github.com/ropensci/drake/issues/742
+    output_format =
+      bookdown::pdf_document2(
+        dev = "pdf",
+        includes = list(
+          in_header = "preamble.tex",
+          before_body = "before_body.tex"
+        ),
+        toc = T,
+        toc_depth = 3,
+        number_sections = T,
+        latex_engine = "xelatex"
+      ),
+    output_file = "reports/confint_ratio.pdf",
+    quiet = FALSE
+  )
+
+)
+

src/before_body.tex

+%\newpage

src/confint_ratio.Rmd

@@ -12,19 +12,10 @@ editor_options:
     wrap: 72
 ---
 
-
-```{r packages, include = FALSE}
-pacman::p_load(
-  "boot",
-  "furrr",
-  "here",
-  "hrbrthemes",
-  "janitor",
-  "kableExtra",
-  "knitr",
-  "readxl",
-  "tidyverse"
-)
+```{r eval = interactive(), cache = FALSE, include = FALSE}
+source("src/packages.R")
+source("src/functions.R")
+message("Assuming interactive session")
 ```
 
 ```{r setup, include=FALSE, cache = FALSE}
@@ -38,35 +29,19 @@ knitr::opts_chunk$set(
 theme_set(theme_ipsum(grid = "Y"))
 ```
 
-```{r functions}
-source("src/functions.R")
-```
-
-```{r parameters}
-sim_pars <- tribble(
-  ~param, ~value,
-  "N", 334,
-  "b0", -2,
-  "b1", -.2
-)
-
-```
-
-```{r data}
-data_file <- here::here("data/HumanDogRatioData.xlsx")
-
-raw_data <- read_excel(data_file)
+# Introduction
 
-sim_data <- do.call(
-  simulate_household_data,
-  as.list(pull(sim_pars, value, name = param))
+```{r load, include = FALSE}
+tar_load(
+  c(
+    clean_data,
+    sim_data,
+    sim_pars,
+    raw_data
+  )
 )
-
-clean_data <- cleanup(raw_data)
 ```
 
-# Introduction
-
 We surveyed 2 variables ($X$ and $Y$ counts) from a population and we
 are interested in their ratio $Y/X$. We want to make inference on the
 **average ratio** in the population.
@@ -126,6 +101,16 @@ confint_ratio_normal <- function(x, alpha = 0.05) {
 ```
 
 ```{r res-normal}
+# res_normal <- 
+#   bind_rows(
+#     clean_data |>
+#       select(zone, y = dh_ratio) |> 
+#       add_column(dataset = "Real", .before = 1),
+#     sim_data |>
+#       select(zone, y = r) |> 
+#       add_column(dataset = "Simulated", .before = 1)
+#   ) |> 
+#   group_by(dataset, zone) |> 
 res_normal <- 
   clean_data |>
   select(zone, y = dh_ratio) |> 
@@ -267,35 +252,35 @@ Note that we no longer talk of differences but of relative factor, as a conseque
 Computing confidence intervals here would involve the use of the Bootstrap again, but using the model estimates instead of empirical averages.
 However, there is evidence of over-dispersion in the data, so a more appropriate model should be first developed in order to continue the analysis.
 
-\clearpage
+<!-- \clearpage -->
 
-# Simulation study
+<!-- # Simulation study -->
 
 
-```{r sim-pars}
-cap <- "Parameters used for simulating data."
-sim_pars |>
-  kbl(
-    booktabs = TRUE,
-    caption = cap
-  )
-```
+<!-- ```{r sim-pars} -->
+<!-- cap <- "Parameters used for simulating data." -->
+<!-- sim_pars |>  -->
+<!--   kbl( -->
+<!--     booktabs = TRUE, -->
+<!--     caption = cap -->
+<!--   ) -->
+<!-- ``` -->
 
-In order to evaluate the accuracy of the alternative methods, I simulated data from model \@ref(eq:model) with parameters (Table \@ref(tab:sim-pars)) that mimic the real observed data (Figure \@ref(fig:sim-data-description)).
+<!-- In order to evaluate the accuracy of the alternative methods, I simulated data from model \@ref(eq:model) with parameters (Table \@ref(tab:sim-pars)) that mimic the real observed data (Figure \@ref(fig:sim-data-description)).  -->
 
 
-```{r sim-data-description, fig.cap = cap}
-cap <- "Sample distributions of __simulated__ survey data (dog-human ratio (r), number of humans (x) and number of dogs (y)) by zone."
-sim_data |>
-  pivot_longer(
-    x:r,
-    names_to = "variable",
-    values_to = "value"
-  ) |>
-  ggplot(aes(value)) +
-  geom_histogram(bins = 15) +
-  facet_grid(zone ~ variable, scales = "free")
-```
+<!-- ```{r sim-data-description, fig.cap = cap} -->
+<!-- cap <- "Sample distributions of __simulated__ survey data (dog-human ratio (r), number of humans (x) and number of dogs (y)) by zone." -->
+<!-- sim_data |>  -->
+<!--   pivot_longer( -->
+<!--     x:r, -->
+<!--     names_to = "variable", -->
+<!--     values_to = "value" -->
+<!--   ) |>  -->
+<!--   ggplot(aes(value)) + -->
+<!--   geom_histogram(bins = 15) + -->
+<!--   facet_grid(zone ~ variable, scales = "free") -->
+<!-- ``` -->
 
 
 

src/preamble.tex

+\usepackage{fontspec}  % Handle fonts with XeLaTeX
+\defaultfontfeatures{Ligatures=TeX}  % Use LaTeX font ligatures
+\setmainfont{Palatino}
+
+%\usepackage{palatino}  % Unnecessary
+%\renewcommand{\familydefault}{\sfdefault} % sans serif
+%\fontfamily{ppl}\selectfont  % LaTeX
+% \usepackage[utf8]{inputenc}
+% \usepackage[T1]{fontenc}
+% \usepackage{newpxtext,newpxmath}
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+\usepackage[document]{ragged2e}
+
+\usepackage{array}
+\usepackage{longtable}
+\usepackage{booktabs}
+\usepackage{multirow}
+% \usepackage{mathtools}
+