Draft make_project paper (gits) files

inst/gists/analysis_1_0_2_9001.Rmd

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+---
+title: "your_title_goes_here"
+author: "your_name_goes_here"
+date: "`r Sys.Date()`"
+output:
+  bookdown::html_document2:
+    number_sections: false
+---
+
+```{r setup, echo=FALSE}
+knitr::opts_chunk$set(
+                     ########## set global options ############
+    echo = FALSE,    # don't show code
+    collapse = TRUE, # keep code from blocks together (if shown)
+    message = TRUE,  # show messages
+    warning = TRUE,  # show warnings
+    error = TRUE,    # show error messages
+    comment = ""     # don't show ## with printed output
+)
+
+# R's default rounding is to show 7 digits. This rounds results to 3 digits.
+options(digits = 3)
+```
+
+```{r tidyverse-tidymodels, echo=FALSE}
+library(conflicted)
+suppressPackageStartupMessages(library(tidymodels))
+tidymodels_prefer()
+suppressPackageStartupMessages(library(tidyverse))
+
+# suppress "`summarise()` has grouped output by " messages
+options(dplyr.summarise.inform = FALSE)
+```
+
+```{r other-packages}
+library(glue)  # for glue()
+library(rUM)  # needed for the bibliography
+library(rio)  # for import() 
+# library(table1)  # for table1()
+
+# gtsummary for tbl_summary(), add_n(), add_p(), modify_header(), bold_labels()
+suppressPackageStartupMessages(library(gtsummary)) 
+```
+
+```{r load-data}
+# raw_data <- import("")  # your data file goes inside the ""
+```
+
+```{r analysis-1}
+# preprocess your data and ultimately make a dataset called analysis
+analysis <- mtcars |> 
+  mutate(auto_man = if_else(am == 0, "Automatic", "Manual")) |> 
+  select(mpg, auto_man)
+```
+
+# Abstract
+
+# Introduction
+
+# Methods
+Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `table1` (`r packageVersion("table1")`) packages used to preprocess and summarize data.[@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-table1]
+
+# Results
+
+```{r table-1}
+
+# The table1::table1 does quick pretty descriptive tables but they don't support
+#   hyperlinks/cross-references in the paper
+#
+# analysis |> 
+#  select(everything()) |> # choose your variables here
+#  table1(
+#    # change auto_man to the name of your column variable or delete | auto_man
+#    ~ . | auto_man, 
+#    data = _
+#  ) 
+
+analysis |> 
+  tbl_summary(
+    include = c(everything()), # choose your variables here
+    # change auto_man to the name of your column variable or delete by = auto_man
+    by = auto_man, # split table by group
+    missing = "no" # don't list missing data separately
+  ) %>%
+  # add_n() %>% # add column with total number of non-missing observations
+  # add_p() %>% # test for a difference between groups
+  modify_header(label = "") %>% # update the column header to be blank
+  bold_labels() |> 
+  modify_caption(
+    "Cross references to tables start with tab: then the code chunk label."
+  ) 
+```
+
+As can be seen in Table \@ref(tab:table-1) or [Table 1](#tab:table-1)
+
+```{r}
+#| label: figure1
+#| fig.cap: "Remember figure references begin with #fig:"
+
+analysis |> 
+  ggplot(aes(x=mpg)) + 
+  geom_histogram(bins = 5) + 
+  facet_wrap(vars(auto_man), ncol = 1)
+```
+
+See Figure \@ref(fig:figure1) or [Figure 1](#fig:figure1)
+
+
+# Discussion
+
+# References {-}
+
+```{r include=FALSE}
+# automatically create a bib database for loaded R packages & rUM
+knitr::write_bib(
+  c(
+    .packages(),
+    "rUM"
+  ),
+  "packages.bib"
+)
+```

inst/gists/analysis_1_0_2_9001.qmd

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+---
+title: "your_title_goes_here"
+author: "your_name_goes_here"
+date: "`r Sys.Date()`"
+format:
+  html:
+    self-contained: true
+knitr:
+  opts_chunk:      ########## set global options ############
+    collapse: true # keep code from blocks together (if shown)
+    echo: false    # don't show code
+    message: true  # show messages
+    warning: true  # show warnings
+    error: true    # show error messages
+    comment: ""    # don't show ## with printed output
+    R.options:    
+      digits: 3    # round to three digits
+editor: visual
+---
+
+```{r tidyverse-tidymodels, echo=FALSE}
+library(conflicted)
+suppressPackageStartupMessages(library(tidymodels))
+tidymodels_prefer()
+suppressPackageStartupMessages(library(tidyverse))
+
+# suppress "`summarise()` has grouped output by " messages
+options(dplyr.summarise.inform = FALSE)
+```
+
+```{r other-packages}
+library(glue)  # for glue()
+library(rUM)  # needed for the bibliography
+library(rio)  # for import() 
+# library(table1)  # for table1()
+
+# gtsummary for tbl_summary(), add_n(), add_p(), modify_header(), bold_labels()
+suppressPackageStartupMessages(library(gtsummary)) 
+```
+
+```{r load-data}
+# raw_data <- import("")  # your data file goes inside the ""
+```
+
+```{r analysis-1}
+# preprocess your data and ultimately make a dataset called analysis
+analysis <- mtcars |> 
+  mutate(auto_man = if_else(am == 0, "Automatic", "Manual")) |> 
+  select(mpg, auto_man)
+```
+
+# Abstract
+
+# Introduction
+
+# Methods
+
+Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `table1` (`r packageVersion("table1")`) packages used to preprocess and summarize data.[@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-table1]
+
+# Results
+
+```{r}
+#| label: tbl-table1
+#| tbl-cap: "Cross references to tables use labels for the code chunk starting with tbl-."
+
+# The table1::table1 does quick pretty descriptive tables but they don't support
+#   hyperlinks/cross-references in the paper
+#
+# analysis |> 
+#  select(everything()) |> # choose your variables here
+#  table1(
+#    # change auto_man to the name of your column variable or delete | auto_man
+#    ~ . | auto_man, 
+#    data = _
+#  ) 
+
+analysis |> 
+  tbl_summary(
+    include = c(everything()), # choose your variables here
+    # change auto_man to the name of your column variable or delete by = auto_man
+    by = auto_man, # split table by group
+    missing = "no" # don't list missing data separately
+  ) %>%
+  # add_n() %>% # add column with total number of non-missing observations
+  # add_p() %>% # test for a difference between groups
+  modify_header(label = "") %>% # update the column header to be blank
+  bold_labels()
+```
+
+As can be seen in @tbl-table1 ....
+
+```{r}
+#| label: fig-figure-1
+#| fig-cap: "Remember figure labels begin with fig-"
+
+analysis |> 
+  ggplot(aes(x=mpg)) + 
+  geom_histogram(bins = 5) + 
+  facet_wrap(vars(auto_man), ncol = 1)
+```
+
+As can be seen in @fig-figure-1 ...
+
+# Discussion
+
+# References {.unnumbered}
+
+```{r}
+#| include: false
+
+# automatically create a bib database for loaded R packages & rUM
+knitr::write_bib(
+  c(
+    .packages(),
+    "rUM"
+  ),
+  "packages.bib"
+)
+```