Package prep
Timothee Bonnet
22 June 2020
Why create your own R-packages?
- Increases reproducibility
- Forces you to clean, check and document your code; which removes many mistakes and problems.
- Simple to do but looks so cool.
- Opens the door to putting packages along publications, Github, CRAN and be recognized and cited for your programming work.
Packages you will need to create packages easily
Install if you do not have them already.
library(devtools)## Loading required package: usethislibrary(roxygen2)Note: there are several pipelines to create packages, some using directly RStudio tools. I chose to demonstrate using a pipeline that relies mostly on code and little on clicking buttons, because the former is more reproducible.
Getting started
Start a R session from a parent directory in which you want to create your package. The package will be initialized inside a new directory. This new directory will also be a new RStudio project.
We will create a package that contains a few functions to handle temperature data. Our package will simply be called “temperature”.
Let’s initialize the package:
create("temperature")Check the content of the new directory “temperature”:
- A folder “R”, currently empty. We will store our R-functions in there.
- A file DESCRIPTION. Meta-data about your package.
- A file NAMESPACE. Handle relationships with other packages. Do not modify by hand. Not that important if you’re only developing packages for yourself; very important if you plan to share.
- An RStudio project file “temperature.Rproj”. Don’t worry about it.
Let’s add some R-functions to the R-folder. Create a R-file called “functions.R” and containing the following two functions that form the base of our package:
fahr_to_kelvin <- function(temp) {
stopifnot(is.numeric(temp))
kelvin <- ((temp - 32) * (5 / 9)) + 273.15
return(kelvin)
}
kelvin_to_celsius <- function(temp) {
celsius <- temp - 273.15
return(celsius)
}
celsius_to_kelvin <- function(temp) {
kelvin <- temp + 273.15
return(kelvin)
}You can create this file by hand or use some code:
sink(file = "R/Functions.R")
cat("fahr_to_kelvin <- function(temp) {
stopifnot(is.numeric(temp))
kelvin <- ((temp - 32) * (5 / 9)) + 273.15
return(kelvin)
}
kelvin_to_celsius <- function(temp) {
celsius <- temp - 273.15
return(celsius)
}
celsius_to_kelvin <- function(temp) {
kelvin <- temp + 273.15
return(kelvin)
}
")
sink()Now we can load the functions and get ready to install your package:
load_all(".")## Loading temperaturedocument(".")For now document() only created the empty directory man/ and nothing else. That is because there was nothing to document yet.
Now we can install the package from the parent directory:
install("../temperature")Your package already appears in R-Studio Package tab and can be used. However, there is not much information about the package and its functions.
Our functions are not accessible in R:
fahr_to_kelvin(10)And there is no information about them:
?fahr_to_kelvinLet’s add more information to our package using Roxygen syntax. First for the fahr_to_kelvin function:
#' Fahrenheit to Kelvin conversion
#'
#' This function takes a temperature expressed in Fahrenheit and convert it to Kelvin.
#' @param temp A temperature expressed in Fahrenheit
#'
#' @export
fahr_to_kelvin <- function(temp) {
stopifnot(is.numeric(temp))
kelvin <- ((temp - 32) * (5 / 9)) + 273.15
return(kelvin)
}The @export line is critical. This tells Roxygen2 to add this function to the NAMESPACE file, so that it will be accessible to users. For your first R package, you’ll probably want to include @export for each of your functions (in large packages it is sometimes a good idea to hide some functions that are used only internally by other functions).
Now let’s repeat the process:
load_all(".")
document(".")Notice that the NAMESPACE file has changed.
This time a file has been created in /man
install("../temperature")And we can reach our function help page and run the function:
?fahr_to_kelvin
fahr_to_kelvin(10)You can see that it is still missing some usual components that are for instance on the mean() help page: Value, References, See Also, Examples…
#' Fahrenheit to Kelvin conversion
#'
#' This function takes a temperature expressed in Fahrenheit and convert it to Kelvin.
#' @param temp A temperature expressed in Fahrenheit
#'
#' @return A temperature in Kelvin
#'
#' @examples
#' fahr_to_kelvin(32)
#'
#' @export
fahr_to_kelvin <- function(temp) {
stopifnot(is.numeric(temp))
kelvin <- ((temp - 32) * (5 / 9)) + 273.15
return(kelvin)
}load_all(".", reset = TRUE)
document(".")
install("../temperature", reload = TRUE)library(temperature)
?fahr_to_kelvin
fahr_to_kelvin(temp = )By the way, sometimes you need to restart your R-session between installations for RStudio to be able to find help pages.
Now create documentation for
kelvin_to_celsius(), re-install the package and check you can access the new help page.
#' Kelvin to Celsius conversion
#'
#' This function takes a temperature expressed in Kelvin and convert it to Celsius.
#'
#' @param temp A temperature expressed in Kelvin
#'
#' @return A temperature in Celsius.
#'
#' @examples
#' kelvin_to_celsius(300)
#'
#' @export
kelvin_to_celsius <- function(temp) {
celsius <- temp - 273.15
return(celsius)
}Initial fill of the DESCRIPTION
Package: temperature
Title: Utilities to handle temperature data
Version: 0.0.1
Authors@R:
person(given = "Timothée",
family = "Bonnet",
role = c("aut", "cre"),
email = "timotheebonnetc@gmail.com",
comment = c(ORCID = "0000-0001-7186-5288"))
Description: What the package does (one paragraph).
License: GPL-3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.0More complete build
#roxygenise(".", clean = TRUE)
load_all(".")
document(".")
build(pkg = ".", manual = TRUE)
check(".", manual = TRUE )
install("../temperature", reload = TRUE)Check is very useful. Always try to get 0 errors, 0 warnings, 0 notes.
More complete documentation:
build_manual()
build_readme()
build_site()At a later stage consider creating vignettes (i.e. tutorials, examples…)
build_vignettes()Add data
Temperature data from Tuggeranong 1997-2019 http://www.bom.gov.au/climate/data/
download.file("https://timotheenivalis.github.io/data/tuggeranong.csv",
destfile = "tuggeranong.csv")
tuggeranong <- read.csv("tuggeranong.csv")Initialize the dataset
use_data(tuggeranong, overwrite = TRUE)We need to document the dataset. The documentation goes into the /R folder in a file called data.R.
sink("R/data.R")
cat("
#' Mean maximum temperature (monthly average) at Tuggeranong
#'
#' A dataset containing the average mean maximum temperature per month from 1997 to 2019.
#'
#' @format A data frame with 23 rows and 13 variables:
#' \\describe{
#' \\item{Year}{Year}
#' \\item{Jan}{January mean maximum temperature}
#' \\item{Feb}{February mean maximum temperature}
#' \\item{Mar}{March mean maximum temperature}
#' \\item{Apr}{April mean maximum temperature}
#' \\item{May}{May mean maximum temperature}
#' \\item{Jun}{June mean maximum temperature}
#' \\item{Jul}{July mean maximum temperature}
#' \\item{Aug}{August mean maximum temperature}
#' \\item{Sep}{September mean maximum temperature}
#' \\item{Oct}{October mean maximum temperature}
#' \\item{Nov}{November mean maximum temperature}
#' \\item{Dec}{December mean maximum temperature}
#' ...
#' }
#' @source \\url{http://www.bom.gov.au/climate/data/}
\"tuggeranong\"
")
sink()Don’t use @export for a dataset. The export is automatic.
#roxygenise(".", clean = TRUE)
load_all(".")
document(".")
build(pkg = ".", manual = TRUE)
check(".", manual = TRUE )
install("../temperature", reload = TRUE)library(temperature)
data("tuggeranong")
tuggeranong## Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
## 1 1997 27.2 30.4 24.8 23.0 16.7 12.8 12.2 13.9 16.1 21.7 26.9 29.9
## 2 1998 29.5 30.5 27.8 21.4 16.2 12.8 11.2 13.7 17.7 18.7 21.4 27.8
## 3 1999 29.5 27.1 25.1 19.0 17.8 12.6 13.3 14.9 18.1 20.2 20.9 24.9
## 4 2000 25.1 29.2 25.7 20.4 15.1 12.6 11.9 13.5 18.2 19.5 22.8 28.0
## 5 2001 31.2 29.0 23.7 21.3 16.6 14.3 12.6 13.7 18.8 18.9 22.4 26.5
## 6 2002 28.7 24.5 25.5 22.6 16.2 13.4 12.8 14.9 17.9 21.7 27.7 28.4
## 7 2003 30.6 29.2 23.9 20.1 17.2 13.2 12.5 13.3 16.8 17.9 24.4 27.6
## 8 2004 29.5 30.5 27.0 22.1 16.5 13.1 12.1 14.6 17.5 20.3 23.7 26.4
## 9 2005 28.8 27.0 24.5 24.3 18.3 13.9 12.7 14.5 16.4 20.4 22.9 28.8
## 10 2006 30.6 30.5 27.0 19.6 16.1 11.8 12.5 15.4 19.3 24.0 26.4 27.7
## 11 2007 30.8 28.3 25.8 22.0 17.9 11.6 11.4 15.2 17.4 23.0 24.8 25.1
## 12 2008 29.2 24.5 26.0 19.6 17.2 14.5 11.6 13.0 18.3 23.1 23.1 24.9
## 13 2009 31.3 28.9 26.6 19.6 16.4 12.4 12.6 14.7 17.6 18.8 28.8 29.0
## 14 2010 31.6 27.2 24.9 21.4 16.6 13.3 12.8 12.5 16.7 19.7 22.5 24.9
## 15 2011 28.7 26.5 23.3 19.4 15.3 13.4 12.2 15.8 17.9 20.3 25.0 23.4
## 16 2012 26.8 24.7 22.1 20.2 15.5 12.7 12.7 13.5 18.0 20.9 25.3 27.2
## 17 2013 32.0 26.8 25.1 21.8 16.8 13.4 12.7 14.3 19.7 21.9 23.7 28.5
## 18 2014 31.2 28.9 24.1 19.3 17.4 13.0 12.1 13.9 17.8 22.7 27.3 27.3
## 19 2015 26.9 27.1 25.6 18.5 16.0 13.3 10.9 13.4 17.2 24.8 24.4 28.6
## 20 2016 27.7 29.1 26.8 23.4 17.2 12.8 12.6 14.2 15.7 18.5 25.0 28.1
## 21 2017 31.9 29.6 25.5 19.6 16.2 13.4 12.7 13.6 17.8 22.6 23.8 27.4
## 22 2018 31.0 28.3 26.3 24.9 17.3 13.0 13.3 13.7 17.9 22.4 24.1 29.1
## 23 2019 34.1 28.9 25.6 22.5 16.4 13.7 13.6 14.1 18.6 23.3 26.2 31.2image(as.matrix(tuggeranong[,-1]))
At least two reasons to include data in your package:
- Give realistic input to examples in your function documentation
- Share data along your analyses so that analyses can be reproduced and improved
Connect to other packages
So far our package only uses R-base code. However we could write fancier functions if we used code already available in other packages.
Let’s try to include this function in the package:
Wide_To_Long_Temperature <- function(dat, id.vars="Year",
variable.name = "Month",
value.name = "Temperature"){
require(reshape2)
stopifnot(expr={is.data.frame(dat)
id.vars %in% colnames(dat)
})
melttemp <- melt(dat, id.vars = id.vars,
variable.name = variable.name,
value.name = value.name)
return(melttemp)
}
Wide_To_Long_Temperature(tuggeranong)## Loading required package: reshape2## Year Month Temperature
## 1 1997 Jan 27.2
## 2 1998 Jan 29.5
## 3 1999 Jan 29.5
## 4 2000 Jan 25.1
## 5 2001 Jan 31.2
## 6 2002 Jan 28.7
## 7 2003 Jan 30.6
## 8 2004 Jan 29.5
## 9 2005 Jan 28.8
## 10 2006 Jan 30.6
## 11 2007 Jan 30.8
## 12 2008 Jan 29.2
## 13 2009 Jan 31.3
## 14 2010 Jan 31.6
## 15 2011 Jan 28.7
## 16 2012 Jan 26.8
## 17 2013 Jan 32.0
## 18 2014 Jan 31.2
## 19 2015 Jan 26.9
## 20 2016 Jan 27.7
## 21 2017 Jan 31.9
## 22 2018 Jan 31.0
## 23 2019 Jan 34.1
## 24 1997 Feb 30.4
## 25 1998 Feb 30.5
## 26 1999 Feb 27.1
## 27 2000 Feb 29.2
## 28 2001 Feb 29.0
## 29 2002 Feb 24.5
## 30 2003 Feb 29.2
## 31 2004 Feb 30.5
## 32 2005 Feb 27.0
## 33 2006 Feb 30.5
## 34 2007 Feb 28.3
## 35 2008 Feb 24.5
## 36 2009 Feb 28.9
## 37 2010 Feb 27.2
## 38 2011 Feb 26.5
## 39 2012 Feb 24.7
## 40 2013 Feb 26.8
## 41 2014 Feb 28.9
## 42 2015 Feb 27.1
## 43 2016 Feb 29.1
## 44 2017 Feb 29.6
## 45 2018 Feb 28.3
## 46 2019 Feb 28.9
## 47 1997 Mar 24.8
## 48 1998 Mar 27.8
## 49 1999 Mar 25.1
## 50 2000 Mar 25.7
## 51 2001 Mar 23.7
## 52 2002 Mar 25.5
## 53 2003 Mar 23.9
## 54 2004 Mar 27.0
## 55 2005 Mar 24.5
## 56 2006 Mar 27.0
## 57 2007 Mar 25.8
## 58 2008 Mar 26.0
## 59 2009 Mar 26.6
## 60 2010 Mar 24.9
## 61 2011 Mar 23.3
## 62 2012 Mar 22.1
## 63 2013 Mar 25.1
## 64 2014 Mar 24.1
## 65 2015 Mar 25.6
## 66 2016 Mar 26.8
## 67 2017 Mar 25.5
## 68 2018 Mar 26.3
## 69 2019 Mar 25.6
## 70 1997 Apr 23.0
## 71 1998 Apr 21.4
## 72 1999 Apr 19.0
## 73 2000 Apr 20.4
## 74 2001 Apr 21.3
## 75 2002 Apr 22.6
## 76 2003 Apr 20.1
## 77 2004 Apr 22.1
## 78 2005 Apr 24.3
## 79 2006 Apr 19.6
## 80 2007 Apr 22.0
## 81 2008 Apr 19.6
## 82 2009 Apr 19.6
## 83 2010 Apr 21.4
## 84 2011 Apr 19.4
## 85 2012 Apr 20.2
## 86 2013 Apr 21.8
## 87 2014 Apr 19.3
## 88 2015 Apr 18.5
## 89 2016 Apr 23.4
## 90 2017 Apr 19.6
## 91 2018 Apr 24.9
## 92 2019 Apr 22.5
## 93 1997 May 16.7
## 94 1998 May 16.2
## 95 1999 May 17.8
## 96 2000 May 15.1
## 97 2001 May 16.6
## 98 2002 May 16.2
## 99 2003 May 17.2
## 100 2004 May 16.5
## 101 2005 May 18.3
## 102 2006 May 16.1
## 103 2007 May 17.9
## 104 2008 May 17.2
## 105 2009 May 16.4
## 106 2010 May 16.6
## 107 2011 May 15.3
## 108 2012 May 15.5
## 109 2013 May 16.8
## 110 2014 May 17.4
## 111 2015 May 16.0
## 112 2016 May 17.2
## 113 2017 May 16.2
## 114 2018 May 17.3
## 115 2019 May 16.4
## 116 1997 Jun 12.8
## 117 1998 Jun 12.8
## 118 1999 Jun 12.6
## 119 2000 Jun 12.6
## 120 2001 Jun 14.3
## 121 2002 Jun 13.4
## 122 2003 Jun 13.2
## 123 2004 Jun 13.1
## 124 2005 Jun 13.9
## 125 2006 Jun 11.8
## 126 2007 Jun 11.6
## 127 2008 Jun 14.5
## 128 2009 Jun 12.4
## 129 2010 Jun 13.3
## 130 2011 Jun 13.4
## 131 2012 Jun 12.7
## 132 2013 Jun 13.4
## 133 2014 Jun 13.0
## 134 2015 Jun 13.3
## 135 2016 Jun 12.8
## 136 2017 Jun 13.4
## 137 2018 Jun 13.0
## 138 2019 Jun 13.7
## 139 1997 Jul 12.2
## 140 1998 Jul 11.2
## 141 1999 Jul 13.3
## 142 2000 Jul 11.9
## 143 2001 Jul 12.6
## 144 2002 Jul 12.8
## 145 2003 Jul 12.5
## 146 2004 Jul 12.1
## 147 2005 Jul 12.7
## 148 2006 Jul 12.5
## 149 2007 Jul 11.4
## 150 2008 Jul 11.6
## 151 2009 Jul 12.6
## 152 2010 Jul 12.8
## 153 2011 Jul 12.2
## 154 2012 Jul 12.7
## 155 2013 Jul 12.7
## 156 2014 Jul 12.1
## 157 2015 Jul 10.9
## 158 2016 Jul 12.6
## 159 2017 Jul 12.7
## 160 2018 Jul 13.3
## 161 2019 Jul 13.6
## 162 1997 Aug 13.9
## 163 1998 Aug 13.7
## 164 1999 Aug 14.9
## 165 2000 Aug 13.5
## 166 2001 Aug 13.7
## 167 2002 Aug 14.9
## 168 2003 Aug 13.3
## 169 2004 Aug 14.6
## 170 2005 Aug 14.5
## 171 2006 Aug 15.4
## 172 2007 Aug 15.2
## 173 2008 Aug 13.0
## 174 2009 Aug 14.7
## 175 2010 Aug 12.5
## 176 2011 Aug 15.8
## 177 2012 Aug 13.5
## 178 2013 Aug 14.3
## 179 2014 Aug 13.9
## 180 2015 Aug 13.4
## 181 2016 Aug 14.2
## 182 2017 Aug 13.6
## 183 2018 Aug 13.7
## 184 2019 Aug 14.1
## 185 1997 Sep 16.1
## 186 1998 Sep 17.7
## 187 1999 Sep 18.1
## 188 2000 Sep 18.2
## 189 2001 Sep 18.8
## 190 2002 Sep 17.9
## 191 2003 Sep 16.8
## 192 2004 Sep 17.5
## 193 2005 Sep 16.4
## 194 2006 Sep 19.3
## 195 2007 Sep 17.4
## 196 2008 Sep 18.3
## 197 2009 Sep 17.6
## 198 2010 Sep 16.7
## 199 2011 Sep 17.9
## 200 2012 Sep 18.0
## 201 2013 Sep 19.7
## 202 2014 Sep 17.8
## 203 2015 Sep 17.2
## 204 2016 Sep 15.7
## 205 2017 Sep 17.8
## 206 2018 Sep 17.9
## 207 2019 Sep 18.6
## 208 1997 Oct 21.7
## 209 1998 Oct 18.7
## 210 1999 Oct 20.2
## 211 2000 Oct 19.5
## 212 2001 Oct 18.9
## 213 2002 Oct 21.7
## 214 2003 Oct 17.9
## 215 2004 Oct 20.3
## 216 2005 Oct 20.4
## 217 2006 Oct 24.0
## 218 2007 Oct 23.0
## 219 2008 Oct 23.1
## 220 2009 Oct 18.8
## 221 2010 Oct 19.7
## 222 2011 Oct 20.3
## 223 2012 Oct 20.9
## 224 2013 Oct 21.9
## 225 2014 Oct 22.7
## 226 2015 Oct 24.8
## 227 2016 Oct 18.5
## 228 2017 Oct 22.6
## 229 2018 Oct 22.4
## 230 2019 Oct 23.3
## 231 1997 Nov 26.9
## 232 1998 Nov 21.4
## 233 1999 Nov 20.9
## 234 2000 Nov 22.8
## 235 2001 Nov 22.4
## 236 2002 Nov 27.7
## 237 2003 Nov 24.4
## 238 2004 Nov 23.7
## 239 2005 Nov 22.9
## 240 2006 Nov 26.4
## 241 2007 Nov 24.8
## 242 2008 Nov 23.1
## 243 2009 Nov 28.8
## 244 2010 Nov 22.5
## 245 2011 Nov 25.0
## 246 2012 Nov 25.3
## 247 2013 Nov 23.7
## 248 2014 Nov 27.3
## 249 2015 Nov 24.4
## 250 2016 Nov 25.0
## 251 2017 Nov 23.8
## 252 2018 Nov 24.1
## 253 2019 Nov 26.2
## 254 1997 Dec 29.9
## 255 1998 Dec 27.8
## 256 1999 Dec 24.9
## 257 2000 Dec 28.0
## 258 2001 Dec 26.5
## 259 2002 Dec 28.4
## 260 2003 Dec 27.6
## 261 2004 Dec 26.4
## 262 2005 Dec 28.8
## 263 2006 Dec 27.7
## 264 2007 Dec 25.1
## 265 2008 Dec 24.9
## 266 2009 Dec 29.0
## 267 2010 Dec 24.9
## 268 2011 Dec 23.4
## 269 2012 Dec 27.2
## 270 2013 Dec 28.5
## 271 2014 Dec 27.3
## 272 2015 Dec 28.6
## 273 2016 Dec 28.1
## 274 2017 Dec 27.4
## 275 2018 Dec 29.1
## 276 2019 Dec 31.2#' Wide to long conversion for standard monthly temperature
#'
#' This function takes a standard monthly temperature dataframe in wide format to long format.
#'
#' @param dat A temperature dataframe
#' @param id.vars Character string. vector of id variables. Can be integer (variable position) or string (variable name). If blank, will use all non-measured variables.
#' @param variable.name Character string. Nname of variable used to store measured variable names
#' @param value.name Character string. Name of variable used to store values
#'
#' @return A dataframe
#'
#' @examples
#' data("tuggeranong")
#' Wide_To_Long_Temperature(tuggeranong)
#'
#' @export
Wide_To_Long_Temperature <- function(dat, id.vars="Year",
variable.name = "Month",
value.name = "Temperature"){
require(reshape2)
stopifnot(expr={is.data.frame(dat)
id.vars %in% colnames(dat)
})
melttemp <- melt(dat, id.vars = id.vars,
variable.name = variable.name,
value.name = value.name)
return(melttemp)
}load_all()
document()
check()We get a warning message. Never use library() or require() in a R package!
Two things to do:
In DESCRIPTION add:
Imports: reshape2In your function change
melttoreshape2::melt
load_all()## Loading temperature## Warning:
## ── Conflicts ──────────────────────────────────────────────────────────────────────────── temperature conflicts ──
## x Wide_To_Long_Temperature() masks temperature::Wide_To_Long_Temperature()
##
## Did you accidentally source a file rather than using `load_all()`?
## Run `rm(list = c("Wide_To_Long_Temperature"))` to remove the conflicts.document()## Updating temperature documentation
## Loading temperature## Warning:
## ── Conflicts ──────────────────────────────────────────────────────────────────────────── temperature conflicts ──
## x Wide_To_Long_Temperature() masks temperature::Wide_To_Long_Temperature()
##
## Did you accidentally source a file rather than using `load_all()`?
## Run `rm(list = c("Wide_To_Long_Temperature"))` to remove the conflicts.## Writing NAMESPACE
## Writing NAMESPACEcheck()## Updating temperature documentation
## Loading temperature## Warning:
## ── Conflicts ──────────────────────────────────────────────────────────────────────────── temperature conflicts ──
## x Wide_To_Long_Temperature() masks temperature::Wide_To_Long_Temperature()
##
## Did you accidentally source a file rather than using `load_all()`?
## Run `rm(list = c("Wide_To_Long_Temperature"))` to remove the conflicts.## Writing NAMESPACE
## Writing NAMESPACE
## ── Building ─────────────────────────────────────────────────────────────────────────────────────── temperature ──
## Setting env vars:
## ● CFLAGS : -Wall -pedantic
## ● CXXFLAGS : -Wall -pedantic
## ● CXX11FLAGS: -Wall -pedantic
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
##
checking for file ‘/home/timothee/Documents/CanberraPostDoc/teaching/RStats2020/Rpackages/temperature/DESCRIPTION’ ...
✓ checking for file ‘/home/timothee/Documents/CanberraPostDoc/teaching/RStats2020/Rpackages/temperature/DESCRIPTION’
##
─ preparing ‘temperature’:
## checking DESCRIPTION meta-information ...
✓ checking DESCRIPTION meta-information
##
─ checking for LF line-endings in source and make files and shell scripts
##
─ checking for empty or unneeded directories
## ─ looking to see if a ‘data/datalist’ file should be added
##
─ building ‘temperature_0.0.1.tar.gz’
##
##
── Checking ─────────────────────────────────────────────────────────────────────────────────────── temperature ──
## Setting env vars:
## ● _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
## ● _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
## ● _R_CHECK_CRAN_INCOMING_ : FALSE
## ● _R_CHECK_FORCE_SUGGESTS_ : FALSE
## ● NOT_CRAN : true
## ── R CMD check ─────────────────────────────────────────────────────────────────
## * using log directory ‘/tmp/RtmpoR7D94/temperature.Rcheck’
## * using R version 3.6.3 (2020-02-29)
## * using platform: x86_64-pc-linux-gnu (64-bit)
## * using session charset: UTF-8
## * using options ‘--no-manual --as-cran’
## * checking for file ‘temperature/DESCRIPTION’ ... OK
## * this is package ‘temperature’ version ‘0.0.1’
## * package encoding: UTF-8
## * checking package namespace information ... OK
## * checking package dependencies ... OK
## * checking if this is a source package ... OK
## * checking if there is a namespace ... OK
## * checking for executable files ... OK
## * checking for hidden files and directories ... OK
## * checking for portable file names ... OK
## * checking for sufficient/correct file permissions ... OK
## * checking serialization versions ... OK
## * checking whether package ‘temperature’ can be installed ... OK
## * checking installed package size ... OK
## * checking package directory ... OK
## * checking for future file timestamps ... OK
## * checking DESCRIPTION meta-information ... OK
## * checking top-level files ... NOTE
## Non-standard file/directory found at top level:
## ‘preparation_files’
## * checking for left-over files ... OK
## * checking index information ... OK
## * checking package subdirectories ... OK
## * checking R files for non-ASCII characters ... OK
## * checking R files for syntax errors ... OK
## * checking whether the package can be loaded ... OK
## * checking whether the package can be loaded with stated dependencies ... OK
## * checking whether the package can be unloaded cleanly ... OK
## * checking whether the namespace can be loaded with stated dependencies ... OK
## * checking whether the namespace can be unloaded cleanly ... OK
## * checking loading without being on the library search path ... OK
## * checking dependencies in R code ... OK
## * checking S3 generic/method consistency ... OK
## * checking replacement functions ... OK
## * checking foreign function calls ... OK
## * checking R code for possible problems ... OK
## * checking Rd files ... OK
## * checking Rd metadata ... OK
## * checking Rd line widths ... OK
## * checking Rd cross-references ... OK
## * checking for missing documentation entries ... OK
## * checking for code/documentation mismatches ... OK
## * checking Rd \usage sections ... OK
## * checking Rd contents ... OK
## * checking for unstated dependencies in examples ... OK
## * checking contents of ‘data’ directory ... OK
## * checking data for non-ASCII characters ... OK
## * checking data for ASCII and uncompressed saves ... OK
## * checking examples ... OK
## * checking for detritus in the temp directory ... OK
## * DONE
##
## Status: 1 NOTE
## See
## ‘/tmp/RtmpoR7D94/temperature.Rcheck/00check.log’
## for details.## ── R CMD check results ────────────────────────────────── temperature 0.0.1 ────
## Duration: 9.8s
##
## > checking top-level files ... NOTE
## Non-standard file/directory found at top level:
## ‘preparation_files’
##
## 0 errors ✓ | 0 warnings ✓ | 1 note xNo more warnings!
Now practice by adding the function below to your package:
plot_trend <- function(dat=tuggeranong){
melttemp <- Wide_To_Long_Temperature(dat)
model <- summary(lm(Temperature ~ Year + Month, data = melttemp))
year_effect <- round(model$coefficients["Year",],3)
library(ggplot2)
ggplot(data=melttemp,
aes(x=Year,y=Temperature, color=Month))+
geom_point() + geom_smooth(alpha=0.2) +
annotate("label", x = mean(melttemp$Year),
y = max(melttemp$Temperature),
label = paste0(ifelse(year_effect[1]>=0, "+", "-"),
year_effect[1], "°C/year, p=",year_effect[4]))
}Make the package a GitHub repository and install from github
If you already have a Github account create a new repo for your package. You can leave the repository completely empty during initialization.
echo "# temperature" >> README.md
git init
git add README.md
git commit -m "first commit"
git remote add origin https://github.com/timotheenivalis/temperature.git
git push -u origin mastergit add data/ man/ R/ NAMESPACE DESCRIPTION .gitignore .Rbuildignore
git commit -m "load all package files"
git pushNow people can install your package from github. If you want to see my final code, it is there!
install_github("timotheenivalis/temperature")## Downloading GitHub repo timotheenivalis/temperature@master##
##
checking for file ‘/tmp/RtmpoR7D94/remotes32a3272eb708/timotheenivalis-temperature-3c7f1ce/DESCRIPTION’ ...
✓ checking for file ‘/tmp/RtmpoR7D94/remotes32a3272eb708/timotheenivalis-temperature-3c7f1ce/DESCRIPTION’
##
─ preparing ‘temperature’:
##
checking DESCRIPTION meta-information ...
✓ checking DESCRIPTION meta-information
##
─ checking for LF line-endings in source and make files and shell scripts
##
─ checking for empty or unneeded directories
## ─ looking to see if a ‘data/datalist’ file should be added
##
─ building ‘temperature_0.0.1.tar.gz’
##
## ## Installing package into '/home/timothee/R/x86_64-pc-linux-gnu-library/3.6'
## (as 'lib' is unspecified)More information
R packages book by Hadley Wickham: http://r-pkgs.had.co.nz/intro.html