From d946b9d77c67681fce61962b5e33deec8dc9a93e Mon Sep 17 00:00:00 2001 From: "Raymond R. Balise" Date: Mon, 1 Jan 2024 09:57:43 -0500 Subject: [PATCH] Draft make_project paper (gits) files --- inst/gists/analysis_1_0_2_9001.Rmd | 122 +++++++++++++++++++++++++++++ inst/gists/analysis_1_0_2_9001.qmd | 119 ++++++++++++++++++++++++++++ 2 files changed, 241 insertions(+) create mode 100644 inst/gists/analysis_1_0_2_9001.Rmd create mode 100644 inst/gists/analysis_1_0_2_9001.qmd diff --git a/inst/gists/analysis_1_0_2_9001.Rmd b/inst/gists/analysis_1_0_2_9001.Rmd new file mode 100644 index 00000000..9de6cf99 --- /dev/null +++ b/inst/gists/analysis_1_0_2_9001.Rmd @@ -0,0 +1,122 @@ +--- +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" +) +``` diff --git a/inst/gists/analysis_1_0_2_9001.qmd b/inst/gists/analysis_1_0_2_9001.qmd new file mode 100644 index 00000000..417b30be --- /dev/null +++ b/inst/gists/analysis_1_0_2_9001.qmd @@ -0,0 +1,119 @@ +--- +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" +) +```