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r.snippets
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# ============================================================================ #
#
# ---- Personal Snippets ----
#
# ============================================================================ #
# This document is all the snippets I may or may not use.
# Modify snippets: `usethis::edit_rstudio_snippets()`
# List of Snippets:
# General
# lib
# libr - recommended
# req
# src - source
# src2
# src_env
# src_env2
# ret
# ret_list
# ret_list2
# mat - matrix
# sg - setGeneric
# sm - setMethod
# sc - setClass
# shinyapp
# shinymod
# hh
# aa
# qq
# aq
# prettydate
# tts - time to string
# dateprnt
# mm
# a_eq
# shrtcut - create a shortcut
# quick_tip - create a tip
# maxima
# debug_mode
# para_proc - parallel processing
# bench_snip - benchmarking
#
# Control Flow:
# if - if
# el - else
# ei - else if
# ie - if else
# for
# while
# switch
# tryc - try catch
# TODO: tryc_r - try catch with restart
#
# Apply Family
# apply
# lapply
# sapply
# mapply
# tapply
# vapply
# rapply
#
# Standard Libraries
# tidyverse
# tidyverse2 - recommended using librarian
#
# Operators
# op_default
# zz
# op_notnull
# op_notnullish
#
# Section Headers
# comm_time - comment with time
# d_line - dashed line
# hdr_main
# hdr1
# hdr2
# hdr3
# hdr4
#
# ggplot2
# gg "ggplot generic"
# ggl "ggplot line"
# ggp "ggplot point"
# ggs "ggsave()"
# gge "geom_*"
# ggeb "element_blank"
# gger "element_rect"
# gget "element_text"
# ggel "element_line"
# ggt "themes"
# gg_cam
#
# dplyr, purrr:
# br "bind_rows()"
# bc "bind_cols()"
# jo "*_join"
# pm "purrr::map()"
# pmc "purrr::map_chr()"
# pmi "purrr::map_int()"
# pmb "purrr::map_lgl()"
# pmdb "purrr::map_dbl()"
# plonger
# pwider
# fun_map
# lam_fun
#
# Rmarkdown/Quarto
# r
# r2
# qmd_start
# save_loc_data
# dt
# auth
#
# Functions:
# fun
# lilbox
# fn_doc - use `docthis` to document a function
# fun_author
#
# Saving Shorcuts
# hfile - save a file with a header
# filen - file name skeleton, not used as much
# save_gg
# save_walk
# save_csv
# save_bin
#
# Opening Files, Folders, or Browser:
# open_path
# open_proj
# open_folder
# open_file
# open_edge
# open_chrome
# ------------------------------------------------------------
#
# General
#
# ------------------------------------------------------------
snippet lib
library("${1:package}")
# Dec 13, 2023
snippet libr
librarian::shelf(
quiet = TRUE,
librarian,
${1:package}
)
snippet req
require("${1:package}")
# ------------------------------------------------------------
# Shortcut: Sourcing Functions
# ------------------------------------------------------------
# below: `src2` is a better version
snippet src
source("${1:file.R}")
# updates the `src` snippet to source a file in the `scripts` folder
# update: Dec 13, 2023
# source script
snippet src2
source(here::here("scripts", "${1:file}.R"))
# allows sourcing scripts to an environment
snippet src_env
{
# attach functions to environment
${1:proj_functions} <- new.env()
source(here::here("scripts", "${2:file}.R"), local = ${1:proj_functions})
attach(${1:proj_functions})
rm(${1:proj_functions})
# functions available in `${1:proj_functions}` environment
cli::cli_alert_info(
c(
"These are custom functions avaiable for this project!\n",
"Documentations is location in {.path {here(\"scripts\")}}")
)
cli::cat_bullet(paste0(ls("${1:proj_functions}"), "()"))
}
# allows sourcing multiple scripts to an environment
snippet src_env2
{
# attach functions to environment
${1:proj_functions} <- new.env()
here::here("scripts", c("${2:file}.R")) |>
purrr::walk(~ source(.x, local = ${1:proj_functions}))
attach(${1:proj_functions})
rm(${1:proj_functions})
# functions available in `${1:proj_functions}` environment
cli::cli_alert_info(
c(
"These are custom functions avaiable for this project!\n",
"Documentations is location in {.path {here(\"scripts\")}}")
)
cli::cat_bullet(paste0(ls("${1:proj_functions}"), "()"))
}
snippet ret
return(${1:code})
# Dec 13, 2023
snippet ret_list
return(
list(
${1:var_name} = ${2:var}
)
)
# Dec 13, 2023
snippet ret_list2
${1:results} <-
list(
${2:var_name} = ${3:var}
)
return(${1:results})
snippet mat
matrix(${1:data}, nrow = ${2:rows}, ncol = ${3:cols})
snippet sg
setGeneric("${1:generic}", function(${2:x, ...}) {
standardGeneric("${1:generic}")
})
snippet sm
setMethod("${1:generic}", ${2:class}, function(${2:x, ...}) {
${0}
})
snippet sc
setClass("${1:Class}", slots = c(${2:name = "type"}))
snippet shinyapp
library(shiny)
ui <- fluidPage(
${0}
)
server <- function(input, output, session) {
}
shinyApp(ui, server)
snippet shinymod
${1:name}_UI <- function(id) {
ns <- NS(id)
tagList(
${0}
)
}
${1:name} <- function(input, output, session) {
}
snippet hh
here::here("${1:path}")
snippet aa
${1:var} <- ${1:var} %>%
${0}
snippet qq
${1:var} %>%
${0}
snippet aq
${1:newvar} <- ${2:df} %>%
${0}
snippet prettydate
strftime(Sys.time(), "%A, %b %d, %Y")
snippet tts
strftime(Sys.time(), "${1:%F %T}")
snippet dateprnt
`r paste("# ${1:Author}", strftime(Sys.time(), "%A, %b %d, %Y"))`
# snippet a= # didnt work
snippet a_eq
${1:opt} = ${1:opt}
# ------------------------------------------------------------
# Shortcut: For new shortcuts
# ------------------------------------------------------------
# Nov 3, 2023
# shortcut to creating a new shortcut.
snippet shrtcut
# `r paste0(rep("-", 60), collapse = "")`
# Shortcut: ${1:shortcut purpose}
# `r paste0(rep("-", 60), collapse = "")`
# `r format(Sys.Date(), "%b %d, %Y")`
#
snippet ${2:shortcut_name}
${3:shortcut_code}
usethis::edit_rstudio_snippets() # delete after adding
# ------------------------------------------------------------
# Shortcut: Quick Tip
# ------------------------------------------------------------
# Nov 03, 2023
# snippet quick_tip
# # ============================================================================ #
# # ---- ${1:Name of Tip} ----
# # ============================================================================ #
# # `r format(Sys.Date(), "%b %d, %Y")`
# #
#
# # ============================================================================ #
# update: Dec 13, 2023
snippet quick_tip
# `r paste0(rep("=", 76), collapse = "")` #
# ---- ${1:Name of Tip} ----
# `r paste0(rep("=", 76), collapse = "")` #
# `r format(Sys.Date(), "%b %d, %Y")`
# `r paste0(rep("=", 76), collapse = "")` #
# ------------------------------------------------------------
# Shortcut: Maximima Program
# ------------------------------------------------------------
# Oct 2023
snippet maxima
```{maxima}`r ''`
L: sqrt(1 - 1/R^2);
assume(R > 0)$
'integrate(x, x, 0, L) = integrate(x, x, 0, L);
```
# ------------------------------------------------------------
# Shortcut: Set Debug Options
# ------------------------------------------------------------
# Dec 13, 2023
# This is useful when wanting to debug a function. Temporalily set the debug
# options to `recover` to stop when an error hits. Then, you can inspect the
# environment and see what is going on.
snippet debug_mode
{
options(error = recover)
# add code here
}
# ------------------------------------------------------------
# Shortcut: Debug One Time
# ------------------------------------------------------------
# Dec 19, 2023
#
snippet debug_1
debugonce(${1:fun})
# ------------------------------------------------------------
# Shortcut: Parallel Processing Template
# ------------------------------------------------------------
# Dec 14, 2023
#
snippet para_proc
# look for `furrr` and `progressr` package, and will skip is not downloaded.
parallel_pkgs <- c("furrr", "progressr", "future")
if (all(map_lgl(parallel_pkgs, ~ nzchar(system.file(package = .x))))) {
librarian::shelf(parallel_pkgs)
handlers("cli")
tictoc::tic() # <-- start clock
plan(multisession, workers = 5)
with_progress({
p <- progressor(steps = nrow(${1:data_frame}))
${1:data_frame} %>%
mutate(
# ${5:data_manipulation}
${2:new_var} = future_map(${3:col}, ~ ${4:func}, .progress = TRUE)
)
})
plan(sequential)
tictoc::toc() # <-- end clock
unshelf(parallel_pkgs)
} else {
cli_alert_warning(
c(
"The packages {.pkg {parallel_pkgs}} ",
"{col_red(\"were not found\")} in your search path.\n\n",
"If you want to do parallel processing, try:\n\n",
"\t{.code librarian::shelf({parallel_pkgs[1]}, {parallel_pkgs[2]})}"
)
)
}
rm(parallel_pkgs)
# ------------------------------------------------------------
# Shortcut: Benchmark
# ------------------------------------------------------------
# Dec 15, 2023
#
snippet bench_snip
bench <- microbenchmark::microbenchmark(
times = ${1:100},
control = list(order = "inorder"),
# check = "equal", # uncomment for equal
${2:one} = {
${3}
},
${4:two} = {
${5}
}
)
boxplot(bench)
# ------------------------------------------------------------
#
# Control Flow
#
# ------------------------------------------------------------
snippet if
if (${1:condition}) {
${0}
}
snippet el
else {
${0}
}
snippet ei
else if (${1:condition}) {
${0}
}
snippet ie
if (${1:cond}) {
${2:true}
} else {
${3:false}
}
snippet for
for (${1:variable} in ${2:vector}) {
${0}
}
snippet while
while (${1:condition}) {
${0}
}
snippet switch
switch(${1:object},
${2:case} = ${3:action}
)
snippet tryc
${1:variable} <-
tryCatch({
# main code
${2}
}, warning = function(w) {
# catch warning
message(sprintf("Warning in %s: %s", deparse(w[["call"]]), w[["message"]]))
${3}
}, error = function(e) {
# catch error
message(sprintf("Error in %s: %s", deparse(e[["call"]]), e[["message"]]))
${4}
}, finally = { # expression to be evaluated before returning or exiting
# end code to run after main code if no errors, remove if not needed
${5}
})
# ------------------------------------------------------------
# Shortcut: TODO: trycatch with restart
# ------------------------------------------------------------
# Dec 18, 2023
# add a snippet for a trycatch with restart
# snippet tryc_r
# ------------------------------------------------------------
#
# Apply Family
#
# ------------------------------------------------------------
snippet apply
apply(${1:array}, ${2:margin}, ${3:...})
snippet lapply
lapply(${1:list}, ${2:function})
snippet sapply
sapply(${1:list}, ${2:function})
snippet mapply
mapply(${1:function}, ${2:...})
snippet tapply
tapply(${1:vector}, ${2:index}, ${3:function})
snippet vapply
vapply(${1:list}, ${2:function}, FUN.VALUE = ${3:type}, ${4:...})
snippet rapply
rapply(${1:list}, ${2:function})
# ------------------------------------------------------------
#
# Standard Libraries
#
# ------------------------------------------------------------
# Snippets below inspired from https://github.com/gadenbuie/snippets
# updated with comment April 16, 2023
# - this snippet not used anymore in favor of `tidyvers2` with
# with `librarian` package
snippet tidyverse
library("ggplot2")
library("tibble")
library("tidyr")
library("readr")
library("purrr")
library("dplyr")
library("stringr")
library("forcats")
library("lubridate")
library("glue")
library("fs")
library("magrittr")
library("here")
# added Nov 26, 2022 by Sebastian Di Geronimo
# ---- updated Apil 16th, 2023
# - using if statement at top in case giving to someone else they will
# have less issues if they don't have `librarian`
# - also will help with downloading from github if they specify the
# user
# - changed because `conflicted` seems to work if included in `shelf()`
# - `conflicts_prefer()` adds multiple functions to the conflicted
snippet tidyverse2
if (!nzchar(system.file(package = "librarian")))
install.packages("librarian")
librarian::shelf(
quiet = TRUE,
librarian, conflicted, ggplot2, tibble, tidyr, readr, purrr, dplyr, stringr,
forcats, lubridate, glue, fs, magrittr, here,
# additional packages, if from GitHub, include username
)
conflicts_prefer(
dplyr::filter,
dplyr::select
)
# removed Apil 16th, 2023
# library("conflicted")
# conflict_prefer("filter", "dplyr")
# conflict_prefer("select", "dplyr")
# ------------------------------------------------------------
#
# Operators:
#
# ------------------------------------------------------------
#snippet op:default
snippet op_default
# use y if x is.null
`%||%` <- function(x, y) if (is.null(x)) y else x
snippet zz
${1:var} <- ${1:var} %||% ${0}
# snippet op:notnull
snippet op_notnull
# use y if x is not null (otherwise NULL)
`%??%` <- function(x, y) if (!is.null(x)) y
# snippet op:notnullish
snippet op_notnullish
# use y if x is not null(ish) (otherwise NULL)
`%??%` <- function(x, y) if (!is.null(x) && x != "") y
# ------------------------------------------------------------
# Shortcut: Matrix Multiplication
# ------------------------------------------------------------
snippet mm
%*%
# ------------------------------------------------------------
#
# Section Headers
#
# ------------------------------------------------------------
# comment time
# update: Dec 18, 2023
snippet comm_time
`r paste("#", date(), " ") |>
stringr::str_pad(width = 78, side = "right", pad = "-") |>
paste("#")`
# `r paste("#", date(), "------------------------------ # \n")`
# dashed line
# update: Dec 18, 2023
snippet d_line
`r paste("#", stringr::str_dup("-", times = 76), "#")`
# `r paste("# ------------------------------ # \n")`
# Sebastian D.
# Nov 12, 2022
# updated: Dec 13, 2023
snippet hdr_main
# `r paste0(rep("=", 76), collapse = "")` #
#
# ---- ${1:header} ----
#
# `r paste0(rep("=", 76), collapse = "")` #
# snippet hdr1
# # ============================================================================ #
# # ---- ${1:header} ----
# # ============================================================================ #
snippet hdr1
# `r paste0(rep("=", 76), collapse = "")` #
# ---- ${1:header} ----
# `r paste0(rep("=", 76), collapse = "")` #
snippet hdr2
# ---- ${1:header} ---- #
snippet hdr3
# ---- ${1:header}
snippet hdr4
# ---- ${1:header} ----
# ------------------------------------------------------------
#
# ggplot2
#
# ------------------------------------------------------------
snippet gg "ggplot generic"
ggplot(${1:data}, aes(${2:aes})) + ${0}
snippet ggl "ggplot line"
ggplot(${1:data}, aes(${2:x}, ${3:y})) +
geom_line()${0}
snippet ggp "ggplot point"
ggplot(${1:data}, aes(${2:x}, ${3:y})) +
geom_point()${0}
snippet ggs "ggsave()"
ggsave("${1:filename}.pdf", width = ${2:6}, height = ${3:6})${0}
snippet gge "geom_*"
geom_${1:point}(${0})
snippet ggeb "element_blank"
element_blank($0)
snippet gger "element_rect"
element_rect($0)
snippet gget "element_text"
element_text($0)
snippet ggel "element_line"
element_line($0)
# Dec 13, 2023
# ggthemes (default: calc)
snippet ggt "themes"
ggthemes::theme_${1:calc}(base_size = 12, base_family = "serif")
# ------------------------------------------------------------
# Shortcut: Add Camcorder When Testing Plots
# ------------------------------------------------------------
# Feb 15, 2024
# this will add code to use camcorder with typical values for saving. Once
# completed the adjustments, then save as normal using save_gg
snippet gg_cam
shelf(camcorder)
# camcorder::gg_record(
# dir = here::here("data", "cam_test", "${1:fig_name}"),
# device = "png",
# width = 90,
# height = 90 * 0.5625,
# dpi = 600,
# units = "mm"
# )
# shell.exec(here::here("data", "cam_test", "${1:fig_name}"))
# gg_stop_recording()
# ------------------------------------------------------------
#
# dplyr, purrr
#
# ------------------------------------------------------------
snippet br "bind_rows()"
bind_rows(${0})
snippet bc "bind_cols()"
bind_cols(${0})
snippet jo "*_join"
${1:inner}_join(${0})
# superseded: use map |> list_rbind
# removed: Dec 13, 2023
# snippet pmd "purrr::map_dfr()"
# purrr::map_dfr(${0})
#
# superseded: use map |> list_cbind
# snippet pmdc "purrr::map_dfc()"
# purrr::map_dfc(${0})
snippet pm "purrr::map()"
purrr::map(${0})
snippet pmc "purrr::map_chr()"
purrr::map_chr(${0})
snippet pmi "purrr::map_int()"
purrr::map_int(${0})
snippet pmb "purrr::map_lgl()"
purrr::map_lgl(${0})
snippet pmdb "purrr::map_dbl()"
purrr::map_dbl(${0})
# ------------------------------------------------------------
# Pivoting Shortcuts (August 23, 2022)
# ------------------------------------------------------------
# from https://www.infoworld.com/article/3637083/never-look-up-tidyrs-pivotwider-or-pivotlonger-again.html
#snippet plonger
# pivot_longer(${1:mydf},
# cols = ${2:columns to pivot long},
# names_to = "${3:desired name for category column}",
# values_to = "${4:desired name for value column}"
# )
#snippet pwider
# pivot_wider(${1:mydf},
# # id_cols = ${2:optional vector of unaffected columns},
# names_from = c(${3:category column(s) to pivot wide}),
# values_from = c(${4:value column(s) that hold data for each category column}),
# names_sep = "_"
# )
# update plonger (Janurary 30, 2023)
snippet plonger
pivot_longer(
data = .,
cols = c(), # columns to pivot long,
names_to = "name", # desired name for category column
values_to = "value", # desired name for value column
)
# update pwider (Feburary 02, 2023)
snippet pwider
pivot_wider(
data = .,
id_cols = c(), # *optional* vector of unaffected columns,
names_from = c(), # category column(s) to pivot wide
values_from = c(), # value column(s) that hold data for each category column
names_sep = "_",
names_repair = janitor::make_clean_names
)
# ------------------------------------------------------------
# Shortcut: Function Use within `map()` function
# ------------------------------------------------------------
# May 9, 2023
snippet fun_map
function(${1:input}) {
${2:}
}
# ------------------------------------------------------------
# Shortcut: Lambda Function
# ------------------------------------------------------------
# Mar 16, 2023
# update: Dec 13, 2023
# Anonymous functions using lambda notation instead of `function()` or `~`
# ex (\(x) x + 1)(3)
snippet lam_fun
\(${1:inputs}) {
${2:fun}
}
# ------------------------------------------------------------
#
# Rmarkdown/Quarto
#
# ------------------------------------------------------------
# note: not necessary anymore
snippet r
```{r ${1:label}, ${2:options}}
${0}
```
# not needed anymore
# separate two chunks
snippet r2
```
```{r ${1:label}}
# ------------------------------------------------------------
# Shortcut: Start `qmd_start` function (Oct 2023)
# ------------------------------------------------------------
# since creating a template qmd file is hard, this is the header code
# I want to use
# date: "`r Sys.Date()`"
# update Dec 17, 2023
snippet qmd_start
if (!nzchar(system.file(package = "librarian")))
install.packages("librarian")
librarian::shelf(
quiet = TRUE,
librarian, conflicted, ggplot2, tibble, tidyr, readr, purrr, dplyr, stringr,
forcats, lubridate, glue, fs, magrittr, here,
# additional
)
conflicts_prefer(
dplyr::filter(),
dplyr::select()
)
(function() {
context <- rstudioapi::getActiveDocumentContext()
lign <- min(grep("format", context\$contents))
lign <- 1
rstudioapi::modifyRange(
location = rstudioapi::document_range(
rstudioapi::document_position(lign, 1),
rstudioapi::document_position(lign, 77777)
),
#text = paste0("author: \"Sebastian Di Geronimo\"\ndate: \"", Sys.Date(), "\"\n"),
text =
paste0(
"---\n",
"title: \"${1:title}\"\n",
"author: \"Sebastian Di Geronimo\"\ndate: \"", Sys.Date(),
"\"\nformat: html",
"\neditor: source",
"\n---\n\n",
"# 1.0 ---- Summary of Document ----\n\n\n\n",
"# 2.0 ---- Setup ----\n\n\n",
"## 2.1 Load Libraries\n\n",
"```{r setup, include=FALSE}"),
id = context\$id
)
context <- rstudioapi::getActiveDocumentContext()
lign_start <- (grep("\\\(function\\\(\\\) \\\{", context\$contents))
lign_end <- (grep("\\\}\\\)\\\(\\\)", context\$contents))
rstudioapi::modifyRange(
location = rstudioapi::document_range(
rstudioapi::document_position(lign_start, 1),
rstudioapi::document_position(lign_end, 777777)
),
text = "",
id = context\$id
)
})()${2:}
```
## 2.2 Load Dataset
```{r load-data}
# run snippet after saving file
save_loc_data
# ------------------------------------------------------------
# Shortcut: Set Location and Save Data
# ------------------------------------------------------------
# Dec 15, 2023
# update: Dec 17, 2023
# - changed `stringr::str_remove("\\.qmd|\\.Rmd")`
# to `tools::file_path_sans_ext()`")`
snippet save_loc_data
# set location to save data and plots
dir_data_save <- here("data", "processed", "`r basename(rstudioapi::getActiveDocumentContext()$path) |>
tools::file_path_sans_ext()`")
dir_plt_save <- here("data", "plots", "`r basename(rstudioapi::getActiveDocumentContext()$path) |>
tools::file_path_sans_ext()`")
# ------------------------------------------------------------
# Shortcut: Print Date
# ------------------------------------------------------------
# Mar 22, 2023
# Used in qmd yaml header
# Not super useful now
snippet dt
date: "`r Sys.Date()`"
# ------------------------------------------------------------
# Shortcut: Add Author to YAML Header
# ------------------------------------------------------------
# Dec 18, 2023
# Will need to edit author name if different
snippet auth
(function() {
context <- rstudioapi::getActiveDocumentContext()
lign <- min(grep("format", context\$contents))
rstudioapi::modifyRange(
location = rstudioapi::document_range(
rstudioapi::document_position(lign, 1),
rstudioapi::document_position(lign, 1)
),
text = paste0("author: \"Sebastian Di Geronimo\"\ndate: \"", Sys.Date(), "\"\n"),
id = context\$id
)
context <- rstudioapi::getActiveDocumentContext()
lign_start <- min(grep("\\\(function\\\(\\\) \\\{", context\$contents))
lign_end <- min(grep("\\\}\\\)\\\(\\\)", context\$contents))
rstudioapi::modifyRange(
location = rstudioapi::document_range(
rstudioapi::document_position(lign_start, 1),
rstudioapi::document_position(lign_end, 777777)
),
text = "",
id = context\$id
)
})()
# ------------------------------------------------------------
#
# Functions
#
# ------------------------------------------------------------
# edit June 2, 2023 to include `end of function`
snippet fun
${1:name} <- function(${2:variables}) {
${0}
# ---- end of function ${1:name}
}
# ------------------------------------------------------------
# Shortcut: Function Box
# ------------------------------------------------------------
# Dec 17, 2023
# Create a box around a function name and document with the current variables
# This takes inspiration from:
# - https://github.com/VincentGuyader/littleboxes
# - https://github.com/mdlincoln/docthis/tree/master
#
# This is to help to use as a shortcut instead using the addin buttom