From 3c56f2314d7902c589bf834db4f87034e5d25607 Mon Sep 17 00:00:00 2001 From: Daniel Date: Sat, 13 Jul 2024 20:40:43 +0200 Subject: [PATCH 1/3] Fix CRAN errors --- vignettes/tidyverse_translation.Rmd | 105 ++++++++++++++-------------- 1 file changed, 53 insertions(+), 52 deletions(-) diff --git a/vignettes/tidyverse_translation.Rmd b/vignettes/tidyverse_translation.Rmd index 11e6097d2..b4cac0a50 100644 --- a/vignettes/tidyverse_translation.Rmd +++ b/vignettes/tidyverse_translation.Rmd @@ -1,6 +1,6 @@ --- title: "Coming from 'tidyverse'" -output: +output: rmarkdown::html_vignette: toc: true vignette: > @@ -22,7 +22,8 @@ knitr::opts_chunk$set( pkgs <- c( "dplyr", "datawizard", - "tidyr" + "tidyr", + "htmltools" ) # since we explicitely put eval = TRUE for some chunks, we can't rely on @@ -35,7 +36,7 @@ if (!all(vapply(pkgs, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1L)) } row <- function(...) { - div( + htmltools::div( class = "custom_note", ... ) @@ -63,19 +64,19 @@ Patil et al., (2022). datawizard: An R Package for Easy Data Preparation and Sta # Introduction -`{datawizard}` package aims to make basic data wrangling easier than +`{datawizard}` package aims to make basic data wrangling easier than with base R. The data wrangling workflow it supports is similar to the one supported by the tidyverse package combination of `{dplyr}` and `{tidyr}`. However, one of its main features is that it has a very few dependencies: `{stats}` and `{utils}` -(included in base R) and `{insight}`, which is the core package of the _easystats_ -ecosystem. This package grew organically to simultaneously satisfy the +(included in base R) and `{insight}`, which is the core package of the _easystats_ +ecosystem. This package grew organically to simultaneously satisfy the "0 non-base hard dependency" principle of _easystats_ and the data wrangling needs -of the constituent packages in this ecosystem. It is also -important to note that `{datawizard}` was designed to avoid namespace collisions +of the constituent packages in this ecosystem. It is also +important to note that `{datawizard}` was designed to avoid namespace collisions with `{tidyverse}` packages. -In this article, we will see how to go through basic data wrangling steps with -`{datawizard}`. We will also compare it to the `{tidyverse}` syntax for achieving the same. +In this article, we will see how to go through basic data wrangling steps with +`{datawizard}`. We will also compare it to the `{tidyverse}` syntax for achieving the same. This way, if you decide to make the switch, you can easily find the translations here. This vignette is largely inspired from `{dplyr}`'s [Getting started vignette](https://dplyr.tidyverse.org/articles/dplyr.html). @@ -94,7 +95,7 @@ efc <- head(efc) # Workhorses -Before we look at their *tidyverse* equivalents, we can first have a look at +Before we look at their *tidyverse* equivalents, we can first have a look at `{datawizard}`'s key functions for data wrangling: | Function | Operation | @@ -187,9 +188,9 @@ starwars <- head(starwars) ## Selecting {#selecting} -`data_select()` is the equivalent of `dplyr::select()`. +`data_select()` is the equivalent of `dplyr::select()`. The main difference between these two functions is that `data_select()` uses two -arguments (`select` and `exclude`) and requires quoted column names if we want to +arguments (`select` and `exclude`) and requires quoted column names if we want to select several variables, while `dplyr::select()` accepts any unquoted column names. :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -327,8 +328,8 @@ You can find a list of all the select helpers with `?data_select`. ## Modifying {#modifying} -`data_modify()` is a wrapper around `base::transform()` but has several additional -benefits: +`data_modify()` is a wrapper around `base::transform()` but has several additional +benefits: * it allows us to use newly created variables in the following expressions; * it works with grouped data; @@ -336,8 +337,8 @@ benefits: * it accepts expressions as character vectors so that it is easy to program with it -This last point is also the main difference between `data_modify()` and -`dplyr::mutate()`. +This last point is also the main difference between `data_modify()` and +`dplyr::mutate()`. :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -430,7 +431,7 @@ starwars |> ```{r arrange1, eval = evaluate_chunk, echo = FALSE} ``` -You can also sort variables in descending order by putting a `"-"` in front of +You can also sort variables in descending order by putting a `"-"` in front of their name, like below: :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -459,8 +460,8 @@ starwars |> ## Extracting {#extracting} -Although we mostly work on data frames, it is sometimes useful to extract a single -column as a vector. This can be done with `data_extract()`, which reproduces the +Although we mostly work on data frames, it is sometimes useful to extract a single +column as a vector. This can be done with `data_extract()`, which reproduces the behavior of `dplyr::pull()`: :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -499,9 +500,9 @@ starwars |> ## Renaming {#renaming} -`data_rename()` is the equivalent of `dplyr::rename()` but the syntax between the +`data_rename()` is the equivalent of `dplyr::rename()` but the syntax between the two is different. While `dplyr::rename()` takes new-old pairs of column -names, `data_rename()` requires a vector of column names to rename, and then +names, `data_rename()` requires a vector of column names to rename, and then a vector of new names for these columns that must be of the same length. :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -535,8 +536,8 @@ starwars |> ```{r rename1, eval = evaluate_chunk, echo = FALSE} ``` -The way `data_rename()` is designed makes it easy to apply the same modifications -to a vector of column names. For example, we can remove underscores and use +The way `data_rename()` is designed makes it easy to apply the same modifications +to a vector of column names. For example, we can remove underscores and use TitleCase with the following code: ```{r rename2} @@ -552,8 +553,8 @@ starwars |> ```{r rename2, eval = evaluate_chunk, echo = FALSE} ``` -It is also possible to add a prefix or a suffix to all or a subset of variables -with `data_addprefix()` and `data_addsuffix()`. The argument `select` accepts +It is also possible to add a prefix or a suffix to all or a subset of variables +with `data_addprefix()` and `data_addsuffix()`. The argument `select` accepts all select helpers that we saw above with `data_select()`: ```{r rename3} @@ -577,7 +578,7 @@ Sometimes, we want to relocate one or a small subset of columns in the dataset. Rather than typing many names in `data_select()`, we can use `data_relocate()`, which is the equivalent of `dplyr::relocate()`. Just like `data_select()`, we can specify a list of variables we want to relocate with `select` and `exclude`. -Then, the arguments `before` and `after`^[Note that we use `before` and `after` +Then, the arguments `before` and `after`^[Note that we use `before` and `after` whereas `dplyr::relocate()` uses `.before` and `.after`.] specify where the selected columns should be relocated: @@ -591,7 +592,7 @@ starwars |> data_relocate(sex:homeworld, before = "height") ``` ::: - + ::: {} ```{r, class.source = "tidyverse"} @@ -600,14 +601,14 @@ starwars |> relocate(sex:homeworld, .before = height) ``` ::: - + :::: ```{r relocate1, eval = evaluate_chunk, echo = FALSE} ``` In addition to column names, `before` and `after` accept column indices. Finally, -one can use `before = -1` to relocate the selected columns just before the last +one can use `before = -1` to relocate the selected columns just before the last column, or `after = -1` to relocate them after the last column. ```{r eval = evaluate_chunk} @@ -622,10 +623,10 @@ starwars |> ### Longer Reshaping data from wide to long or from long to wide format can be done with -`data_to_long()` and `data_to_wide()`. These functions were designed to match -`tidyr::pivot_longer()` and `tidyr::pivot_wider()` arguments, so that the only -thing to do is to change the function name. However, not all of -`tidyr::pivot_longer()` and `tidyr::pivot_wider()` features are available yet. +`data_to_long()` and `data_to_wide()`. These functions were designed to match +`tidyr::pivot_longer()` and `tidyr::pivot_wider()` arguments, so that the only +thing to do is to change the function name. However, not all of +`tidyr::pivot_longer()` and `tidyr::pivot_wider()` features are available yet. We will use the `relig_income` dataset, as in the [`{tidyr}` vignette](https://tidyr.tidyverse.org/articles/pivot.html). @@ -634,11 +635,11 @@ relig_income ``` -We would like to reshape this dataset to have 3 columns: religion, count, and -income. The column "religion" doesn't need to change, so we exclude it with -`-religion`. Then, each remaining column corresponds to an income category. -Therefore, we want to move all these column names to a single column called -"income". Finally, the values corresponding to each of these columns will be +We would like to reshape this dataset to have 3 columns: religion, count, and +income. The column "religion" doesn't need to change, so we exclude it with +`-religion`. Then, each remaining column corresponds to an income category. +Therefore, we want to move all these column names to a single column called +"income". Finally, the values corresponding to each of these columns will be reshaped to be in a single new column, called "count". :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -765,12 +766,12 @@ fish_encounters |> -In `{datawizard}`, joining datasets is done with `data_join()` (or its alias -`data_merge()`). Contrary to `{dplyr}`, this unique function takes care of all +In `{datawizard}`, joining datasets is done with `data_join()` (or its alias +`data_merge()`). Contrary to `{dplyr}`, this unique function takes care of all types of join, which are then specified inside the function with the argument `join` (by default, `join = "left"`). -Below, we show how to perform the four most common joins: full, left, right and +Below, we show how to perform the four most common joins: full, left, right and inner. We will use the datasets `band_members`and `band_instruments` provided by `{dplyr}`: :::: {style="display: grid; grid-template-columns: 50% 50%; grid-column-gap: 10px;"} @@ -935,7 +936,7 @@ test |> ) ``` ::: - + ::: {} ```{r, class.source = "tidyverse"} @@ -948,7 +949,7 @@ test |> ) ``` ::: - + :::: ```{r unite1, eval = evaluate_chunk, echo = FALSE} @@ -969,7 +970,7 @@ test |> ) ``` ::: - + ::: {} ```{r, class.source = "tidyverse"} @@ -983,7 +984,7 @@ test |> ) ``` ::: - + :::: ```{r unite2, eval = evaluate_chunk, echo = FALSE} @@ -1017,7 +1018,7 @@ test |> ) ``` ::: - + ::: {} ```{r, class.source = "tidyverse"} @@ -1029,7 +1030,7 @@ test |> ) ``` ::: - + :::: ```{r separate1, eval = evaluate_chunk, echo = FALSE} @@ -1051,9 +1052,9 @@ test |> # Other useful functions -`{datawizard}` contains other functions that are not necessarily included in -`{dplyr}` or `{tidyr}` or do not directly modify the data. Some of them are -inspired from the package `janitor`. +`{datawizard}` contains other functions that are not necessarily included in +`{dplyr}` or `{tidyr}` or do not directly modify the data. Some of them are +inspired from the package `janitor`. ## Work with rownames @@ -1079,7 +1080,7 @@ mtcars2 |> The main difference is when we use it with grouped data. While `tibble::rowid_to_column()` uses one distinct rowid for every row in the dataset, `rowid_as_column()` creates one id for every row *in each group*. Therefore, two rows in different groups -can have the same row id. +can have the same row id. This means that `rowid_as_column()` is closer to using `n()` in `mutate()`, like the following: From 8511d4388dd30c1b6991fd2af2f8e0878fb54845 Mon Sep 17 00:00:00 2001 From: Daniel Date: Sat, 13 Jul 2024 20:41:23 +0200 Subject: [PATCH 2/3] version --- DESCRIPTION | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 24d744094..f062fc912 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: datawizard Title: Easy Data Wrangling and Statistical Transformations -Version: 0.12.0 +Version: 0.12.0.1 Authors@R: c( person("Indrajeet", "Patil", , "patilindrajeet.science@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-1995-6531", Twitter = "@patilindrajeets")), @@ -21,10 +21,10 @@ Authors@R: c( person("Robert", "Garrett", , "rcg4@illinois.edu", role = "rev") ) Maintainer: Etienne Bacher -Description: A lightweight package to assist in key steps involved in any data - analysis workflow: (1) wrangling the raw data to get it in the needed form, - (2) applying preprocessing steps and statistical transformations, and - (3) compute statistical summaries of data properties and distributions. +Description: A lightweight package to assist in key steps involved in any data + analysis workflow: (1) wrangling the raw data to get it in the needed form, + (2) applying preprocessing steps and statistical transformations, and + (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) . License: MIT + file LICENSE @@ -36,7 +36,7 @@ Imports: insight (>= 0.20.1), stats, utils -Suggests: +Suggests: bayestestR, boot, brms, @@ -68,7 +68,7 @@ Suggests: tibble, tidyr, withr -VignetteBuilder: +VignetteBuilder: knitr Encoding: UTF-8 Language: en-US From 9ca8a05bee5423fc417a177884e76006a223c39a Mon Sep 17 00:00:00 2001 From: Daniel Date: Sat, 13 Jul 2024 20:43:16 +0200 Subject: [PATCH 3/3] load conditional --- vignettes/tidyverse_translation.Rmd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/vignettes/tidyverse_translation.Rmd b/vignettes/tidyverse_translation.Rmd index b4cac0a50..6197341d1 100644 --- a/vignettes/tidyverse_translation.Rmd +++ b/vignettes/tidyverse_translation.Rmd @@ -34,7 +34,9 @@ evaluate_chunk <- TRUE if (!all(vapply(pkgs, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1L))) || getRversion() < "4.1.0") { evaluate_chunk <- FALSE } +``` +```{r echo=FALSE, message=FALSE, eval=evaluate_chunk} row <- function(...) { htmltools::div( class = "custom_note",