diff --git a/.Rprofile b/.Rprofile index 0756325bb..95d762fd9 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,4 +1,5 @@ source("renv/activate.R") + # in .Rprofile of the website project if (file.exists("~/.Rprofile")) { base::sys.source("~/.Rprofile", envir = environment()) diff --git a/config/_default/hugo.toml b/config/_default/hugo.toml index f2338eef0..2d5d955c5 100644 --- a/config/_default/hugo.toml +++ b/config/_default/hugo.toml @@ -42,7 +42,7 @@ ignoreFiles = ["\\.Rmd$", "\\.Rmarkdown$", "_cache$", "index\\.html", "about\\.h # All possible themes can # be found at: https://highlightjs.org/examples - highightStyle = "foundation" + highightStyle = "night-owl" # Or set your own custom colours primary = "#198c8c" diff --git a/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-10.svg b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-10.svg new file mode 100644 index 000000000..fc1c061f8 --- /dev/null +++ b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-10.svg @@ -0,0 +1 @@ +RunningundermacOSSonoma14.5Systemtimeis2024-06-0111:50:22.921649Librarypathssetto•/Users/athanasm/Library/Caches/org.R-project.R/R/renv/library/profiles/readme/renv/drmowinckels-45df6871/R-4.3/aarch64-apple-darwin20•/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/libraryHeyMo!Youarepraiseworthy! 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\ No newline at end of file diff --git a/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-5.svg b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-5.svg new file mode 100644 index 000000000..030c7df9d --- /dev/null +++ b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-5.svg @@ -0,0 +1 @@ +Rversion4.3.3(2024-02-29)RunningundermacOSSonoma14.5Systemtimeis2024-06-0111:50:21.932735 \ No newline at end of file diff --git a/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-7.svg b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-7.svg new file mode 100644 index 000000000..b340b18df --- /dev/null +++ b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-7.svg @@ -0,0 +1 @@ +nv/drmowinckels-45df6871/R-4.3/aarch64-apple-darwin20/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library \ No newline at end of file diff --git a/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-9.svg b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-9.svg new file mode 100644 index 000000000..06c8a8587 --- /dev/null +++ b/content/blog/2024/06-01_rprofile/index.markdown_strict_files/figure-markdown_strict/unnamed-chunk-9.svg @@ -0,0 +1 @@ +renv/drmowinckels-45df6871/R-4.3/aarch64-apple-darwin20•/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library \ No newline at end of file diff --git a/content/blog/2024/06-01_rprofile/index.md b/content/blog/2024/06-01_rprofile/index.md new file mode 100644 index 000000000..2d0de483a --- /dev/null +++ b/content/blog/2024/06-01_rprofile/index.md @@ -0,0 +1,559 @@ +--- +title: Customise your R startup message +author: Dr. Mowinckel +date: '2024-06-01' +categories: [] +tags: + - R + - startup + - pride +slug: "rproject" +image: "startup.png" +format: hugo-md +summary: | + We all know the R startup message. It tells us the version + of R we are running, the date, the platform we are running + on, and some informative tips on using R. + When you've been using R a while, though, it get old. + Let me show you how you can customise your startup message! +--- + +I love customizing things. +I seem to never let anything I work with that can be customized, not be customized. +Colours of the software, websites I work on. +I just like having things the way *I* like having things. + +This ofcourse, also extends to R. +The R startup message is just, so much! +And when you have been working with it so long, it's just noise. + +I mean, look at this: + +``` r +R version 4.3.3 (2024-02-29) -- "Angel Food Cake" +Copyright (C) 2024 The R Foundation for Statistical Computing +Platform: aarch64-apple-darwin20 (64-bit) + +R is free software and comes with ABSOLUTELY NO WARRANTY. +You are welcome to redistribute it under certain conditions. +Type 'license()' or 'licence()' for distribution details. + + Natural language support but running in an English locale + +R is a collaborative project with many contributors. +Type 'contributors()' for more information and +'citation()' on how to cite R or R packages in publications. + +Type 'demo()' for some demos, 'help()' for on-line help, or +'help.start()' for an HTML browser interface to help. +Type 'q()' to quit R. +``` + +Ok, it's all informative and meaningful information. +You just don't need that information every time, and wouldn't it be fun if we could make it more personal? + +I had wanted to do this for a while, but never really got around to it. +Mostly because I tried finding ways of clearing the startup message, but just couldn't figure it out. + +Enter Danielle Navarro and her amazingness. +Danielle is amazing in a multitude of ways, I respect and look up to her for so many reasons, coding and not. +She had a post on mastodon with a custom startup message, and I was like, "I need to do that!". + +{{% toot server="fosstodon.org" user="djnavarro" toot="110541882131342960" %}} + +## The user `.Rprofile` + +The way to customise this is through the `.Rprofile` file. This file is a script that is run every time you start R. +It can be used to set up your environment, load packages, and do whatever you want to do every time you start R. + +> Be cautious! +> Don't load packages in the `.Rprofile` if you want to work reproducibly. +> It's better to load packages in your script, so it's transparent to anyone wanting to run it what it need. + +If you've used R a while, you have likely already tampered a little with this file. +Most commonly, we use it to set the default CRAN mirror, or to set the default options for R with the `options()` function. + +There are two `.Rprofile` files you can use. +One is in your home directory, and one is in the R project directory. +The one in your home directory is the one you should use for anything you want to always apply to your R session. +The project `.Rprofile` is for things you want to apply only to that project. + +> Note! If you have a project Rprofile, the home Rprofile will not be executed. +> This is to avoid conflicts between the two. +> There are ways around this, but I'm not going to recommend them here. +> Mostly because it's an advanced thing and you aught to have a good reason for doing it. + +You can access these files easily with the {usethis} package. + +``` r +# default opens user profile +usethis::edit_r_profile() + +# opens the project profile +usethis::edit_r_profile(scope = "project") +``` + +## The common problem - CRAN mirror + +For instance, in my `.Rprofile` I set not only CRAN mirror, but also the `ggseg` and `lcbc` repositories, from the [R-universe](https://ggseg.r-universe.dev/builds) which contain important packages for me that don't exist on CRAN. +Those settings can be set with the `options` function in R, in the `repos` argument. + +``` r +# Set the default CRAN mirror +options( + repos = c( + ggseg = 'https://ggseg.r-universe.dev', + lcbc = 'https://lcbc-uio.r-universe.dev', + CRAN = "https://cloud.r-project.org/" + ) +) +``` + +Having this set means I don't have to set the repositories every time I install a package. +I can just use `install.packages` and it will know where to look. +It will look for the package I ask for in the order the repositories are listed. +Which is super convenient, and saves me a lot of time. + +## Your daily praise. + +But that was not the fun customisation I was talking about. That was just a useful customisation. + +Let us maybe have a little praise every time we start R! +Days can be long and hard, and a little praise can go a long way. + +We can do this with the {praise} package. +The {praise} package contains a list of praises that you can use to get a random praise every time you run the function `praise()`. + +``` r +praise::praise() +``` + + [1] "You are perfect!" + +See? Isn't that nice? And it will be a different phrase every time you start R, it's a nice little boost. + +To make this happen, we can add the following code to our `.Rprofile` file. + +``` r +if("paise" %in% utils::installed.packages()){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) +} +``` + +There is a little to unpack in this code. +Firstly, we check if the package `praise` is installed. +I do this because R will error on startup if it is not and we don't want that. +So if you are doing this on a new computer etc, you will need to install the package first to actually get your little piece of daily praise. + +We then use the `cat` function to print out the praise. +Because we want it to print in the console, not be returned as a value `## [1] "praise"`. +We use the `sep` argument to separate the praise from the "Hey Mo!" string, and we want it to be a new line, which is indicated with the `\n` character. + +That is our first piece of fun customisation! +But that will still print the normal startup message, and then append our own praise at the end. + +``` r +R version 4.3.3 (2024-02-29) -- "Angel Food Cake" +Copyright (C) 2024 The R Foundation for Statistical Computing +Platform: aarch64-apple-darwin20 (64-bit) + +R is free software and comes with ABSOLUTELY NO WARRANTY. +You are welcome to redistribute it under certain conditions. +Type 'license()' or 'licence()' for distribution details. + + Natural language support but running in an English locale + +R is a collaborative project with many contributors. +Type 'contributors()' for more information and +'citation()' on how to cite R or R packages in publications. + +Type 'demo()' for some demos, 'help()' for on-line help, or +'help.start()' for an HTML browser interface to help. +Type 'q()' to quit R. + +Hey Mo! +You are awesome! +``` + +## Clearing the console + +We need a bit of code that clears the console before we print our praise. +This will remove the old message before printing the new one. + +``` r +# Clear if running in terminal +system2("clear") +# Clear if running in RStudio +cat("\014") +``` + +Here we have two different ways to clear the console, because I interact with R in several ways. +I use RStudio, but I also use the terminal (and vscode), and I want the console to be cleared in both cases. +These two lines of code will clear the console in both cases. + +## Print some system information + +Now that we have cleared the console, we can print some system information. +This information is useful to have, and it's nice to see it every time you start R. +It can be useful to know what version of R you are running, what operating system you are on, and what time it is. +This can be useful for debugging, and it's just nice to know. + +To do this, I'm going to use the {cli} package, which can print nice colours, bullet points and all sorts of fun things! + +``` r +if("cli" %in% utils::installed.packages()){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") +} +``` + + + +As with praise, we start with checking if the package is installed. +Just to be sure we don't get an error on startup. + +Then we'll print the R version, the operating system version, and the system time. + +Now that we have some meaningful system information, I also like to print my library paths as shown in the `.libPaths()` function. +This is useful to know where your packages are installed. +In particular, this will also help expose if you are in an {renv} project, as the library paths will be different. + +``` r +# Exposes where library paths are set to +.libPaths() +``` + + [1] "/Users/athanasm/Library/Caches/org.R-project.R/R/renv/library/profiles/readme/renv/drmowinckels-45df6871/R-4.3/aarch64-apple-darwin20" + [2] "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library" + +Now that we know where out libraries are set to, we can print this information in a nice way using the {cli} package, with `cli_bullets`. + +``` r +cli::cli_bullets(.libPaths()) +``` + + + +Now, I can keep it to that, but I'm gonna over-think it. +I want my bullets to actually start with bullets! +In {cli} we can accomplish this having each element in the vector have an asterisk as its name. +This will make the bullets appear as bullets in the console. +To accomplish this, I'm going to use the `setNames` function from the {stats} package. + +``` r +stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + )) +``` + + * + "/Users/athanasm/Library/Caches/org.R-project.R/R/renv/library/profiles/readme/renv/drmowinckels-45df6871/R-4.3/aarch64-apple-darwin20" + * + "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library" + +Now that we have all the pieces, we can feed them to cli_bullets. + +``` r +cli::cli_bullets( + stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + ))) +``` + + + +Now we have a nice list of library paths, with bullets, in the console. +Let's put all we have for now together in our `.Rprofile` file. + +``` r +system2("clear") +cat("\014") +``` + +``` r +instl <- utils::installed.packages() +if("cli" %in% instl){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") + cli::cli_text("Library paths set to") + cli::cli_bullets( + stats::setNames( + .libPaths(), + rep("*", length(.libPaths()) + ))) +} # end if cli installed + +cat("\n") +if("praise" %in% instl){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) +} # end if praise installed +``` + + + +## A colour bar, because we can! + +The last bits of magic in my profile are a colour bar. +My colourbar is R-Ladies purple, except for June, when its rainbow pride colours. +It just makes my Pride month happier to see a rainbow in my console. + +But getting there is a little chore! +Let us start with the single colour purple bar, then expand to the pride bar later. +We first make a vector of 10 purple colours. + +``` r +colour <- rep("#88398a", 10) +colour +``` + + [1] "#88398a" "#88398a" "#88398a" "#88398a" "#88398a" "#88398a" "#88398a" + [8] "#88398a" "#88398a" "#88398a" + +Now, we have to do some fancy work to make this into a colour bar. +We have to convert the hex colours to ANSI colours. +This is done using the `cli::make_ansi_style` function. +We can use `sapply` to apply this function to each element in the vector. +If you don't know about the `apply` functions, then [I have a post on that](blog/2022/lets-get-applying). +In short, its a type of loop, that applies the same function to all values of a vector. + +``` r +colour <- rep("#88398a", 10) +lapply(colour, cli::make_ansi_style) +``` + + + +Now we have a vector of ANSI colours, next we need to apply them to a character. +To make a colourbar, I'm going to use the ANSI character for 'LOWER THREE EIGHTHS BLOCK', which is a thick underscore, and I'm going to make it 6 characters long for each colour. + +``` r +rep("\u2583", 6) +``` + + [1] "▃" "▃" "▃" "▃" "▃" "▃" + +To make a single line colour bar, we can use `paste0` to paste the colour and the block together. +We can use `collapse = ""` to make it a single string. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +thick_bar +``` + + [1] "▃▃▃▃▃▃" + +Here is the true tricky part. +The ansi-colour style we have is actually a list of functions that can be applied to a string. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +style <- cli::make_ansi_style("#88398a") +style(thick_bar) +``` + + + +Lastly, we need to `cat` this again, to print it nicely to the console. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +style <- cli::make_ansi_style("#88398a") +cat(style(thick_bar)) +``` + + + +Now, since we want a longer bar, we need to apply across all the 10 colours specified. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- rep("#88398a", 10) +lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +``` + + + +The colourbar looks great. But all those NULLs, Ack! +We can use `invisible` to suppress the output of the `cat` function. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- rep("#88398a", 10) + +invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +) +``` + + + +Now we have a nice purple colour bar. +We are going to make the pride bar now. +We need to make a vector of the pride colours. +I'm going to use the hex codes for the pride flag colours. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") +invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +) +``` + + + +Now, we need something that will detect that we are in the month of June, so we can toggle the pride colours rather than the purple. + +The `Sys.Date()` function will give us the current date, and we can discern that its June by looking for "-06-" in the date. +We can use this logic in the `grepl` function, which will return `TRUE` if the pattern is found in the string. + +``` r +Sys.Date() +``` + + [1] "2024-06-01" + +``` r +grepl("-06-", Sys.Date() ) +``` + + [1] TRUE + +Putting it all together as chunk together, we get a piece of code that will create our custom colourbar. + +``` r +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- rep("#88398a", 10) +if(grepl("-06-", Sys.Date() )){ + colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") +} +invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +) +``` + + + +Alrighty! +We now have can make a file that: + +1. Clears the console +2. Prints system info in a nice consise way +3. Prints a fun colourbar +4. Gives a random praise + +``` r +if(interactive()){ + system2("clear") + cat("\014") + instl <- utils::installed.packages() + if("cli" %in% instl){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") + cli::cli_text("Library paths set to") + cli::cli_bullets( + stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + ))) + thick_bar <- paste0(rep("\u2583", 6), collapse = "") + (function(){ + colour <- rep("#88398a", 10) + if(grepl("-06-", Sys.Date() )){ + colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") + } + invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) + ) + })() + } + cat("\n") + if("praise" %in% instl){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) + } + rm(instl, thick_bar, colour) +} +``` + +``` r +instl <- utils::installed.packages() +if("cli" %in% instl){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") + cli::cli_text("Library paths set to") + cli::cli_bullets( + stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + ))) + thick_bar <- paste0(rep("\u2583", 6), collapse = "") + (function(){ + colour <- rep("#88398a", 10) + if(grepl("-06-", Sys.Date() )){ + colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") + } + invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) + ) + })() +} +cat("\n") +if("praise" %in% instl){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) +} +``` + + + +There you have it! +The piece of (rather long) code that customised my R startup to something shorter, more informative and also that makes me smile every time. + +Do you customise your startup in any way, or put anything in particular in your `.Rprofile`? diff --git a/content/blog/2024/06-01_rprofile/index.qmd b/content/blog/2024/06-01_rprofile/index.qmd new file mode 100644 index 000000000..75b6860a0 --- /dev/null +++ b/content/blog/2024/06-01_rprofile/index.qmd @@ -0,0 +1,527 @@ +--- +title: Customise your R startup message +author: Dr. Mowinckel +date: '2024-06-01' +categories: [] +tags: + - R + - startup + - pride +slug: "rproject" +image: "startup.png" +format: hugo-md +summary: | + We all know the R startup message. It tells us the version + of R we are running, the date, the platform we are running + on, and some informative tips on using R. + When you've been using R a while, though, it get old. + Let me show you how you can customise your startup message! +--- + +```{r, include = FALSE, cache = FALSE} +Sys.setenv(CLI_TICK_TIME = "100") +asciicast::init_knitr_engine( + startup = quote({ + library(cli) + set.seed(1) }), + echo = TRUE, + echo_input = FALSE +) +``` + +I love customizing things. +I seem to never let anything I work with that can be customized, not be customized. +Colours of the software, websites I work on. +I just like having things the way *I* like having things. + +This ofcourse, also extends to R. +The R startup message is just, so much! +And when you have been working with it so long, it's just noise. + +I mean, look at this: + +``` r +R version 4.3.3 (2024-02-29) -- "Angel Food Cake" +Copyright (C) 2024 The R Foundation for Statistical Computing +Platform: aarch64-apple-darwin20 (64-bit) + +R is free software and comes with ABSOLUTELY NO WARRANTY. +You are welcome to redistribute it under certain conditions. +Type 'license()' or 'licence()' for distribution details. + + Natural language support but running in an English locale + +R is a collaborative project with many contributors. +Type 'contributors()' for more information and +'citation()' on how to cite R or R packages in publications. + +Type 'demo()' for some demos, 'help()' for on-line help, or +'help.start()' for an HTML browser interface to help. +Type 'q()' to quit R. +``` + +Ok, it's all informative and meaningful information. +You just don't need that information every time, and wouldn't it be fun if we could make it more personal? + +I had wanted to do this for a while, but never really got around to it. +Mostly because I tried finding ways of clearing the startup message, but just couldn't figure it out. + +Enter Danielle Navarro and her amazingness. +Danielle is amazing in a multitude of ways, I respect and look up to her for so many reasons, coding and not. +She had a post on mastodon with a custom startup message, and I was like, "I need to do that!". + +{{% toot server="fosstodon.org" user="djnavarro" toot="110541882131342960" %}} + +## The user `.Rprofile` + +The way to customise this is through the `.Rprofile` file. This file is a script that is run every time you start R. +It can be used to set up your environment, load packages, and do whatever you want to do every time you start R. + +> Be cautious! +> Don't load packages in the `.Rprofile` if you want to work reproducibly. +> It's better to load packages in your script, so it's transparent to anyone wanting to run it what it need. + +If you've used R a while, you have likely already tampered a little with this file. +Most commonly, we use it to set the default CRAN mirror, or to set the default options for R with the `options()` function. + +There are two `.Rprofile` files you can use. +One is in your home directory, and one is in the R project directory. +The one in your home directory is the one you should use for anything you want to always apply to your R session. +The project `.Rprofile` is for things you want to apply only to that project. + +> Note! If you have a project Rprofile, the home Rprofile will not be executed. +> This is to avoid conflicts between the two. +> There are ways around this, but I'm not going to recommend them here. +> Mostly because it's an advanced thing and you aught to have a good reason for doing it. + +You can access these files easily with the {usethis} package. + +``` r +# default opens user profile +usethis::edit_r_profile() + +# opens the project profile +usethis::edit_r_profile(scope = "project") +``` + +## The common problem - CRAN mirror + +For instance, in my `.Rprofile` I set not only CRAN mirror, but also the `ggseg` and `lcbc` repositories, from the [R-universe](https://ggseg.r-universe.dev/builds) which contain important packages for me that don't exist on CRAN. +Those settings can be set with the `options` function in R, in the `repos` argument. + +```{r} +# Set the default CRAN mirror +options( + repos = c( + ggseg = 'https://ggseg.r-universe.dev', + lcbc = 'https://lcbc-uio.r-universe.dev', + CRAN = "https://cloud.r-project.org/" + ) +) +``` + +Having this set means I don't have to set the repositories every time I install a package. +I can just use `install.packages` and it will know where to look. +It will look for the package I ask for in the order the repositories are listed. +Which is super convenient, and saves me a lot of time. + +## Your daily praise. + +But that was not the fun customisation I was talking about. That was just a useful customisation. + +Let us maybe have a little praise every time we start R! +Days can be long and hard, and a little praise can go a long way. + +We can do this with the {praise} package. +The {praise} package contains a list of praises that you can use to get a random praise every time you run the function `praise()`. + +```{r} +praise::praise() +``` + +See? Isn't that nice? And it will be a different phrase every time you start R, it's a nice little boost. + +To make this happen, we can add the following code to our `.Rprofile` file. + +```{r} +if("paise" %in% utils::installed.packages()){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) +} +``` + +There is a little to unpack in this code. +Firstly, we check if the package `praise` is installed. +I do this because R will error on startup if it is not and we don't want that. +So if you are doing this on a new computer etc, you will need to install the package first to actually get your little piece of daily praise. + +We then use the `cat` function to print out the praise. +Because we want it to print in the console, not be returned as a value `## [1] "praise"`. +We use the `sep` argument to separate the praise from the "Hey Mo!" string, and we want it to be a new line, which is indicated with the `\n` character. + +That is our first piece of fun customisation! +But that will still print the normal startup message, and then append our own praise at the end. + +``` r +R version 4.3.3 (2024-02-29) -- "Angel Food Cake" +Copyright (C) 2024 The R Foundation for Statistical Computing +Platform: aarch64-apple-darwin20 (64-bit) + +R is free software and comes with ABSOLUTELY NO WARRANTY. +You are welcome to redistribute it under certain conditions. +Type 'license()' or 'licence()' for distribution details. + + Natural language support but running in an English locale + +R is a collaborative project with many contributors. +Type 'contributors()' for more information and +'citation()' on how to cite R or R packages in publications. + +Type 'demo()' for some demos, 'help()' for on-line help, or +'help.start()' for an HTML browser interface to help. +Type 'q()' to quit R. + +Hey Mo! +You are awesome! +``` + +## Clearing the console + +We need a bit of code that clears the console before we print our praise. +This will remove the old message before printing the new one. + +``` r +# Clear if running in terminal +system2("clear") +# Clear if running in RStudio +cat("\014") +``` + +Here we have two different ways to clear the console, because I interact with R in several ways. +I use RStudio, but I also use the terminal (and vscode), and I want the console to be cleared in both cases. +These two lines of code will clear the console in both cases. + +## Print some system information + +Now that we have cleared the console, we can print some system information. +This information is useful to have, and it's nice to see it every time you start R. +It can be useful to know what version of R you are running, what operating system you are on, and what time it is. +This can be useful for debugging, and it's just nice to know. + +To do this, I'm going to use the {cli} package, which can print nice colours, bullet points and all sorts of fun things! + +```{asciicast} +if("cli" %in% utils::installed.packages()){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") +} +``` + +As with praise, we start with checking if the package is installed. +Just to be sure we don't get an error on startup. + +Then we'll print the R version, the operating system version, and the system time. + +Now that we have some meaningful system information, I also like to print my library paths as shown in the `.libPaths()` function. +This is useful to know where your packages are installed. +In particular, this will also help expose if you are in an {renv} project, as the library paths will be different. + +```{r} +# Exposes where library paths are set to +.libPaths() +``` + +Now that we know where out libraries are set to, we can print this information in a nice way using the {cli} package, with `cli_bullets`. + +```{asciicast} +cli::cli_bullets(.libPaths()) +``` + +Now, I can keep it to that, but I'm gonna over-think it. +I want my bullets to actually start with bullets! +In {cli} we can accomplish this having each element in the vector have an asterisk as its name. +This will make the bullets appear as bullets in the console. +To accomplish this, I'm going to use the `setNames` function from the {stats} package. + +```{r} +stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + )) +``` + +Now that we have all the pieces, we can feed them to cli_bullets. + +```{asciicast} +cli::cli_bullets( + stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + ))) +``` + +Now we have a nice list of library paths, with bullets, in the console. +Let's put all we have for now together in our `.Rprofile` file. + +``` r +system2("clear") +cat("\014") +``` + +```{asciicast} +instl <- utils::installed.packages() +if("cli" %in% instl){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") + cli::cli_text("Library paths set to") + cli::cli_bullets( + stats::setNames( + .libPaths(), + rep("*", length(.libPaths()) + ))) +} # end if cli installed + +cat("\n") +if("praise" %in% instl){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) +} # end if praise installed +``` + +## A colour bar, because we can! + +The last bits of magic in my profile are a colour bar. +My colourbar is R-Ladies purple, except for June, when its rainbow pride colours. +It just makes my Pride month happier to see a rainbow in my console. + +But getting there is a little chore! +Let us start with the single colour purple bar, then expand to the pride bar later. +We first make a vector of 10 purple colours. + +```{r} +colour <- rep("#88398a", 10) +colour +``` + +Now, we have to do some fancy work to make this into a colour bar. +We have to convert the hex colours to ANSI colours. +This is done using the `cli::make_ansi_style` function. +We can use `sapply` to apply this function to each element in the vector. +If you don't know about the `apply` functions, then [I have a post on that](blog/2022/lets-get-applying). +In short, its a type of loop, that applies the same function to all values of a vector. + +```{asciicast} +colour <- rep("#88398a", 10) +lapply(colour, cli::make_ansi_style) +``` + +Now we have a vector of ANSI colours, next we need to apply them to a character. +To make a colourbar, I'm going to use the ANSI character for 'LOWER THREE EIGHTHS BLOCK', which is a thick underscore, and I'm going to make it 6 characters long for each colour. + +```{r} +rep("\u2583", 6) +``` + +To make a single line colour bar, we can use `paste0` to paste the colour and the block together. +We can use `collapse = ""` to make it a single string. + +```{r} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +thick_bar +``` + +Here is the true tricky part. +The ansi-colour style we have is actually a list of functions that can be applied to a string. + +```{asciicast} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +style <- cli::make_ansi_style("#88398a") +style(thick_bar) +``` + +Lastly, we need to `cat` this again, to print it nicely to the console. + +```{asciicast} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +style <- cli::make_ansi_style("#88398a") +cat(style(thick_bar)) +``` + +Now, since we want a longer bar, we need to apply across all the 10 colours specified. + +```{asciicast} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- rep("#88398a", 10) +lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +``` + +The colourbar looks great. But all those NULLs, Ack! +We can use `invisible` to suppress the output of the `cat` function. + +```{asciicast} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- rep("#88398a", 10) + +invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +) +``` + +Now we have a nice purple colour bar. +We are going to make the pride bar now. +We need to make a vector of the pride colours. +I'm going to use the hex codes for the pride flag colours. + +```{asciicast} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") +invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +) +``` + +Now, we need something that will detect that we are in the month of June, so we can toggle the pride colours rather than the purple. + +The `Sys.Date()` function will give us the current date, and we can discern that its June by looking for "-06-" in the date. +We can use this logic in the `grepl` function, which will return `TRUE` if the pattern is found in the string. + +```{r} +Sys.Date() +grepl("-06-", Sys.Date() ) +``` + +Putting it all together as chunk together, we get a piece of code that will create our custom colourbar. + +```{asciicast} +thick_bar <- paste0(rep("\u2583", 6), collapse = "") +colour <- rep("#88398a", 10) +if(grepl("-06-", Sys.Date() )){ + colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") +} +invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) +) +``` + +Alrighty! +We now have can make a file that: + +1. Clears the console +1. Prints system info in a nice consise way +1. Prints a fun colourbar +1. Gives a random praise + + +```{r} + +if(interactive()){ + system2("clear") + cat("\014") + instl <- utils::installed.packages() + if("cli" %in% instl){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") + cli::cli_text("Library paths set to") + cli::cli_bullets( + stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + ))) + thick_bar <- paste0(rep("\u2583", 6), collapse = "") + (function(){ + colour <- rep("#88398a", 10) + if(grepl("-06-", Sys.Date() )){ + colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") + } + invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) + ) + })() + } + cat("\n") + if("praise" %in% instl){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) + } + rm(instl, thick_bar, colour) +} + +``` + +```{asciicast, verbose=FALSE} +instl <- utils::installed.packages() +if("cli" %in% instl){ + cli::cli_text(R.version.string) + cli::cli_text("Running under {utils::osVersion}") + cli::cli_text("System time is {Sys.time()}") + cli::cli_text("Library paths set to") + cli::cli_bullets( + stats::setNames(.libPaths(), + rep("*", length(.libPaths()) + ))) + thick_bar <- paste0(rep("\u2583", 6), collapse = "") + (function(){ + colour <- rep("#88398a", 10) + if(grepl("-06-", Sys.Date() )){ + colour <- c("#e50000", "#ff8d00", "#ffee00", + "#028121", "#004cff", "#770088", + "#ffffff", "#ffafc7", "#73D7EE", + "#613915", "#000000") + } + invisible( + lapply(colour, cli::make_ansi_style) |> + lapply(\(x){ + cat(x(thick_bar)) + }) + ) + })() +} +cat("\n") +if("praise" %in% instl){ + cat( + "\nHey Mo!", + praise::praise(), + sep = "\n" + ) +} +``` + + + +There you have it! +The piece of (rather long) code that customised my R startup to something shorter, more informative and also that makes me smile every time. + +Do you customise your startup in any way, or put anything in particular in your `.Rprofile`? diff --git a/content/blog/2024/06-01_rprofile/startup.png b/content/blog/2024/06-01_rprofile/startup.png new file mode 100644 index 000000000..2fe527460 Binary files /dev/null and b/content/blog/2024/06-01_rprofile/startup.png differ diff --git a/content/blog/_index.md b/content/blog/_index.md index 9a92dcd9e..aa6ca823c 100644 --- a/content/blog/_index.md +++ b/content/blog/_index.md @@ -1,9 +1,9 @@ --- title: "Blog" weight: 30 -type: grid +type: blog home: true -n_posts: 4 +n_posts: 1 --- I blog mainly about R, with some neuroimaging in there. Most posts are set up as tutorials or walk-through's, so I hope they are of value. diff --git a/content/r-paks/_index.md b/content/r-paks/_index.md index 7c3060662..f0118769c 100644 --- a/content/r-paks/_index.md +++ b/content/r-paks/_index.md @@ -2,11 +2,9 @@ title: "R-paks" subtitle: "Projects featured here are R-package development. Project summaries, links to source code and demos can be found by clicking each." weight: 2 -type: slider +type: grid home: true -height: - slider: "250" - image: "500" +n_posts: 4 --- While I am a scientist and have lost of research projects ongoing, here I'd rather showcase the wonderful world of development I have started exploring. diff --git a/content/r-paks/ggseg/index.md b/content/r-paks/ggseg/index.md index 531560154..f781080a2 100644 --- a/content/r-paks/ggseg/index.md +++ b/content/r-paks/ggseg/index.md @@ -3,9 +3,6 @@ title: ggseg subtitle: "polygon visualisation of brain segmentations" image: "logo.png" type: slider -output: - html_document: - keep_md: yes external_link: "" weight: 1 color: "#333333" diff --git a/content/r-paks/ggseg3d/index.md b/content/r-paks/ggseg3d/index.md index 176a0ca6d..d1a03c8ec 100644 --- a/content/r-paks/ggseg3d/index.md +++ b/content/r-paks/ggseg3d/index.md @@ -3,9 +3,6 @@ title: "ggseg3d" subtitle: "3d mesh visualisation of brain segmentations" type: slider image: "logo.png" -output: - html_document: - keep_md: yes weight: 1 draft: false color: "#222222" diff --git a/drmowinckels.code-workspace b/drmowinckels.code-workspace new file mode 100644 index 000000000..876a1499c --- /dev/null +++ b/drmowinckels.code-workspace @@ -0,0 +1,8 @@ +{ + "folders": [ + { + "path": "." + } + ], + "settings": {} +} \ No newline at end of file diff --git a/themes/hugo-igloo b/themes/hugo-igloo index 390211260..f53eb4cda 160000 --- a/themes/hugo-igloo +++ b/themes/hugo-igloo @@ -1 +1 @@ -Subproject commit 390211260ac62e4bfeb0b99d46f6c6ae826a4310 +Subproject commit f53eb4cda3262552e48531884d8bf3d453e441be