rmd.snippets

snippet meta
---
title: "${1:}"
author: "${2:Albert Lee}"
date: "\`r Sys.Date()\`"
output:
  rmdformats::readthedown:
    code_folding: hide
    lightbox: true
    gallery: true
    fig_caption: true
    fig_width: 14
    fig_height: 8
    df_print: kable
    number_sections: true
params:
  data: "NO_INPUT"
---

# Meta

**Author**: Albert Lee (alee@counsyl.com) <br/>
**Date Created**: `date +%Y-%m-%d` <br/>
**Date Updated**: \`r Sys.Date()\` </br>
**Tags**: #has_tag </br>
**TLDR**: </br>
**Environment** : </br>

* __Report Root Directory__: \`r getwd()\`

\`\`\`{r setup, include=FALSE}
REPORT_OUTPUT_DIR <- getwd()
if(exists("params")) {
 if(!is.null(params$report_outputdir)) {
    REPORT_OUTPUT_DIR <- params$report_outputdir
  }
}
PROJECT_ROOT_DIR <- rprojroot::find_rstudio_root_file()
knitr::opts_knit\$set(root.dir = PROJECT_ROOT_DIR)
knitr::opts_chunk\$set(fig.align='center')

cache_fig_dir <- glue::glue("{REPORT_OUTPUT_DIR}/_cache_and_figs/")
dir.create(cache_fig_dir, showWarnings=FALSE)
knitr::opts_chunk\$set(fig.path=cache_fig_dir)
knitr::opts_chunk\$set(cache.path=cache_fig_dir)
knitr::opts_chunk\$set(cache = TRUE)

options(rlang_trace_top_env = rlang::current_env())
options(error = function() {
  sink()
  print(rlang::trace_back(bottom = sys.frame(-1)), simplify = "none")
})
\`\`\`

\`\`\`{r result='asis', echo=FALSE, include=FALSE, cache=FALSE}
git_repo <- "NOT_GIT_REPO"
git_hash <- "NA"

res <- suppressWarnings(system("[ -d .git ] || git rev-parse --git-dir > /dev/null 2>&1", intern=TRUE))
if(is.null(attr(res, "status"))) {
  git_repo <- basename(system("git rev-parse --show-toplevel", intern = TRUE))
  git_hash <- system("git rev-parse --short HEAD", intern = TRUE)
}
\`\`\`


* __Execution Root Directory__: \`r getwd()\`

* __Git__: \`r git_repo\` (\`r git_hash\`)

\`\`\`{r echo=FALSE, results='asis'}
cat("**Input(s) / Output(s)**: \n\n")
for(i in seq_along(params)) {
  if(length(params[[i]]) == 1) {
    cat(paste0("* __", names(params)[[i]], "__ : ", params[[i]] , "(", class(params[[i]]) ,")", "\n"))
  } else {
    collapsed_values <- paste0(params[[i]], collapse=", ")
    cat(paste0("* __", names(params)[[i]], "__ : ", collapsed_values, " (", class(params[[i]]) ,")", "\n"))
  }
}
\`\`\`

endsnippet

snippet supp "suppressPackageStartupMessages" b
suppressPackageStartupMessages(${VISUAL})
endsnippet

snippet libt
library(tidyverse)
library(glue)
endsnippet

snippet lib

\`\`\`\{r libs, cache=FALSE, echo=FALSE\}
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(glue))
suppressPackageStartupMessages(library(kableExtra))
suppressPackageStartupMessages(library(prequel))
suppressPackageStartupMessages(library(nexusr))
suppressPackageStartupMessages(library(here))
library(tictoc)
library(counsylthemes)
theme_set(theme_counsyl())
COLORS <- counsylthemes::get_colors()

if(file.exists("src/shared.R")) {
  shared <- new.env()
  source("src/shared.R", local=shared)
}



library(tictoc)
tic("Knitting the document")
\`\`\`

\`\`\`\{r funcs\}
display_graphics <- function(path) {
	knitr::include_graphics(normalizePath(path))
}

display_text <- function(raw_text) {
  text <- glue::glue(raw_text)
  cat(text, sep="\n")
}
\`\`\`

# Introduction

## Data {#data}

\`\`\`\{r data\}
df <- read_csv("${1}")
\`\`\`


# Conclusion

# Session Information

\`\`\`\{r session_info, echo=FALSE\}
sessionInfo()
\`\`\`

# Time to Knit

\`\`\`\{r time_to_knit, echo=FALSE, cache=FALSE\}
toc()
\`\`\`


\`\`\`{css echo=FALSE}
#main .nav-pills > li.active > a,
#main .nav-pills > li.active > a:hover,
#main .nav-pills > li.active > a:focus {
   background-color: #084B85;
}

#main .nav-pills > li > a:hover {
   background-color: #084B85;
}

h1,h2,h3,h4,h5,h6,legend{
    color: #084B85;
}


#nav-top span.glyphicon {
	color: #084B85;
}

#table-of-contents header{
	color: #084B85;
}

#table-of-contents h2{
    background-color: #084B85
}

#main a {
    background-image: linear-gradient(180deg,#E0833B,#E0833B);
    color: #E0833B;
}

a:hover{
    color:#3d1308
}

a:visited{
    color:#3d1308
}
\`\`\`
endsnippet



snippet ccc
\`\`\`\{r ${1}\}
${0}
\`\`\`
endsnippet

snippet ppp "split chunk"
\`\`\`

\`\`\`\{r ${1}\}
endsnippet

snippet "```" "chunk" rbA
\`\`\`\{r ${1}${2:, dependson=c(-1)}\}
${3}
\`\`\`
endsnippet

snippet info

# Session Information

\`\`\`\{r session_info\}
sessionInfo()
\`\`\`

endsnippet

snippet doc "add roxygen2 snippet" b
#' ${1:Title}
#'
#' @param env
#'
#' @return
#' @export
endsnippet
snippet docopt
"usage: ${1:SCRIPT_NAME} [ --input-df INPUT_DF]

options:
--input-df INPUT_DF  ${2:input csv file}]
" -> doc

library(methods)
library(docopt)
opts <- docopt(doc)
endsnippet


snippet f "function"
function() {
  ${1}
}
endsnippet

snippet func "func"
function() {
  ${1}
}
endsnippet

snippet function "function"
function() {
  ${1}
}
endsnippet

snippet eq

\$\$
\begin{aligned}

${0:x = }

\end{aligned}
\$\$
endsnippet


snippet "\\frac" "latex_frac" rA
\frac{$1}{$2}
endsnippet

snippet "file\." "file_path" rA
file.path(${2:REPORT_OUTPUT_DIR}, "${1}")
endsnippet


snippet gbox "boxplot"
ggplot(aes(x=$1, y=$2)) +
  geom_boxplot() +
  labs(title=glue("${3:untitled}"))
endsnippet

snippet gscat "scatter plot"
ggplot(aes(x=$1, y=$2)) +
  geom_point() +
  labs(title=glue("${3:untitled}"))
endsnippet

snippet memoise "Description" b
suppressPackageStartupMessages(library(memoise))
memcache <- memoise::cache_filesystem("~/.r.cache")
endsnippet


snippet minimal "Minimal Yaml Template" b
---
title: "Check if a pickle is Lasso or Ridge"
author: "Albert Lee"
date: "`r Sys.Date()`"
---

```{r setup, include=FALSE}
PROJECT_ROOT_DIR <- rprojroot::find_rstudio_root_file()
knitr::opts_knit$set(root.dir = PROJECT_ROOT_DIR)
```
endsnippet

snippet !vig "Vignette Analysis" b
---
title: "${1:Untitled}"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{blog}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
params:
  data: "hi"
---

\`\`\`{r, include = FALSE}
knitr::opts_chunk\$set(
  collapse = TRUE,
  comment = "#>"
)
knitr::opts_chunk\$set(cache = TRUE)
\`\`\`

\`\`\`{r setup}
library(tidyverse)
library(glue)
library(tidylog, warn.conflicts = FALSE)

library(tictoc)
library(counsylthemes)
theme_set(theme_counsyl())

library(testpac)
library(nexusr)
\`\`\`
endsnippet


snippet !debug "Description" b
options(rlang_trace_top_env = rlang::current_env())
options(error = function() {
  sink()
  print(rlang::trace_back(bottom = sys.frame(-1)), simplify = "none")
})
endsnippet

snippet !debug2 "Description" b
# run this in a interactive mode
options(error = function() {
  sink()
  recover()
})
endsnippet

snippet geom_his "Description"
geom_histogram($1)
endsnippet
snippet geom_hist "Description"
geom_histogram($1)
endsnippet

snippet !reload "Reload a library" b
devtools::reload(devtools::inst("$1"))
endsnippet


snippet !vector "Description" b
$0 <- `!p
x = snip.v.text
x = x.strip("\n")
x = x.split("\n")
x = ['"' + i + '"' for i in x if x is not "\n"]
snip.rv = "c(" + ",".join(x) + ")"
`
endsnippet


snippet !lib "Basic libraries" b
library <- function(...) {
  suppressPackageStartupMessages(base::library(...))
}
library(tidyverse)
library(glue)
library(here)
library(prequel)
library(nexusr)
library(fs)
library(usethis)
library(counsylthemes)
theme_set(theme_counsyl())
endsnippet


snippet !cache "Description" b
knitr::opts_chunk\$set(cache = TRUE)
endsnippet


snippet !p3 "Param to list"
`!p
x = snip.v.text
x = x.replace("params:", "params = list(")
x = x.replace(":", "=")
x = x + ")"
snip.rv = x`
endsnippet

snippet p4 "Description"
hi
endsnippet


snippet labt "lab title" b
labs(title="$1") ${0:+}
endsnippet

snippet labx "lab title" b
labs(x="$1") ${0:+}
endsnippet


snippet meta2 "Description" b
---
title: "${1:}"
author: "${2:Albert Lee}"
date: "\`r Sys.Date()\`"
output:
  rmdformats::readthedown:
    code_folding: hide
    lightbox: true
    gallery: true
    fig_caption: true
    fig_width: 14
    fig_height: 8
params:
  data: "NO_INPUT"
---
\`\`\`{r setup, include=FALSE}
REPORT_OUTPUT_DIR <- getwd()
if(exists("params")) {
 if(!is.null(params$report_outputdir)) {
    REPORT_OUTPUT_DIR <- params$report_outputdir
  }
}
PROJECT_ROOT_DIR <- rprojroot::find_rstudio_root_file()
knitr::opts_knit\$set(root.dir = PROJECT_ROOT_DIR)
knitr::opts_chunk\$set(fig.align='center')

cache_fig_dir <- glue::glue("{REPORT_OUTPUT_DIR}/_cache_and_figs/")
dir.create(cache_fig_dir, showWarnings=FALSE)
knitr::opts_chunk\$set(fig.path=cache_fig_dir)
knitr::opts_chunk\$set(cache.path=cache_fig_dir)
knitr::opts_chunk\$set(cache = TRUE)

options(rlang_trace_top_env = rlang::current_env())
options(error = function() {
  sink()
  print(rlang::trace_back(bottom = sys.frame(-1)), simplify = "none")
})
knitr::opts_chunk$set(warning = FALSE)
knitr::opts_chunk$set(message = FALSE)
\`\`\`
endsnippet

snippet !!sep "Description" b
`!p
SEP_DEFAULT_SIZE = 70
x = snip.v.text
x = x.strip()
text_len = len(x)
if text_len > 0:
   remainder = SEP_DEFAULT_SIZE - (text_len + 2)
   sep = "-" * remainder
   snip.rv = f"# {x} {sep}"
`
endsnippet


snippet !exec "Executive summary" b
# Executive Summary

<style>
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
</style>
<div class = "blue">

- First conclusion
- Second conclusion

</div>

endsnippet


snippet meta3 "Description" b
---
title: "${1:}"
author: "${2:Albert Lee}"
date: "\`r Sys.Date()\`"
output:
  rmdformats::readthedown:
    code_folding: hide
    lightbox: true
    gallery: true
    fig_caption: true
    fig_width: 14
    fig_height: 8
    df_print: kable
    number_sections: true
params:
  data: "NO_INPUT"
---

<!--

# Settings {.exclude}

-->
$0
endsnippet


snippet !opt "Description" b
\`\`\`{r include=FALSE}
knitr::opts_chunk$set(eval = FALSE)
knitr::opts_chunk$set(cache = TRUE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)
\`\`\`
endsnippet