class: center, middle, inverse, title-slide # Tidy work in Tidyverse ## R Programming Foundation for Life Scientists ### 06-Nov-2020 ### NBIS --- exclude: true count: false <link href="https://fonts.googleapis.com/css?family=Roboto|Source+Sans+Pro:300,400,600|Ubuntu+Mono&amp;subset=latin-ext" rel="stylesheet"> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous"> <!-- ----------------- Only edit title & author above this ----------------- --> ## Tidyverse -- What is it all About? * [Tidyverse](http://www.tidyverse.org) is a collection of packages. * Created by [Hadley Wickham](http://hadley.nz). * Gains popularity, on the way to become a *de facto* standard in data analyses. * Knowing how to use it can increase your salary :-) * A philosophy of programming or a programing paradigm. * Everything is about the flow of *tidy data*. .center[ <img src="data/slide_tidyverse/hex-tidyverse.png", style="height:200px;"> <img src="data/slide_tidyverse/Hadley-wickham2016-02-04.jpeg", style="height:200px;"> <img src="data/slide_tidyverse/RforDataScience.jpeg", style="height:200px;"> ] .vsmall[sources of images: www.tidyverse.org, Wikipedia, www.tidyverse.org] --- name: tidyverse_workflow ## Typical Tidyverse Workflow The tidyverse curse? -- > Navigating the balance between base R and the tidyverse is a challenge to learn. [-Robert A. Muenchen](http://r4stats.com/articles/why-r-is-hard-to-learn/) -- .center[<img src="data/slide_tidyverse/tidyverse-flow.png", style="height:400px;">] .vsmall[source: http://www.storybench.org/getting-started-with-tidyverse-in-r/] --- name: intro_to_pipes ## Introduction to Pipes .pull-left-50[ .center[<img src="data/slide_tidyverse/pipe_magritte.jpg", style="width:300px;">] .vsmall[Rene Magritt, *La trahison des images*, [Wikimedia Commons](https://en.wikipedia.org/wiki/The_Treachery_of_Images#/media/File:MagrittePipe.jpg)] .center[<img src="data/slide_tidyverse/magrittr.png", style="width:150px;">] ] -- .pull-right-50[ * Let the data flow. * *Ceci n'est pas une pipe* -- `magrittr` * The `%>%` pipe: + `x %>% f` `\(\equiv\)` `f(x)` + `x %>% f(y)` `\(\equiv\)` `f(x, y)` + `x %>% f %>% g %>% h` `\(\equiv\)` `h(g(f(x)))` ] -- .pull-right-50[ instead of writing this: ```r data <- iris data <- head(data, n=3) ``` ] -- .pull-right-50[ write this: ```r iris %>% head(n=3) ``` ``` ## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## 1 5.1 3.5 1.4 0.2 setosa ## 2 4.9 3.0 1.4 0.2 setosa ## 3 4.7 3.2 1.3 0.2 setosa ``` ] --- name: tibble_intro ## Tibbles .pull-left-50[ .center[<img src="data/slide_tidyverse/hex-tibble.png">] ```r as_tibble(iris) ``` ``` ## # A tibble: 150 x 5 ## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## <dbl> <dbl> <dbl> <dbl> <fct> ## 1 5.1 3.5 1.4 0.2 setosa ## 2 4.9 3 1.4 0.2 setosa ## 3 4.7 3.2 1.3 0.2 setosa ## 4 4.6 3.1 1.5 0.2 setosa ## 5 5 3.6 1.4 0.2 setosa ## 6 5.4 3.9 1.7 0.4 setosa ## 7 4.6 3.4 1.4 0.3 setosa ## 8 5 3.4 1.5 0.2 setosa ## 9 4.4 2.9 1.4 0.2 setosa ## 10 4.9 3.1 1.5 0.1 setosa ## 11 5.4 3.7 1.5 0.2 setosa ## 12 4.8 3.4 1.6 0.2 setosa ## 13 4.8 3 1.4 0.1 setosa ## 14 4.3 3 1.1 0.1 setosa ## 15 5.8 4 1.2 0.2 setosa ## # … with 135 more rows ``` ] .pull-right-50[ * `tibble` is one of the unifying features of tidyverse, * it is a *better* `data.frame` realization, * objects `data.frame` can be coerced to `tibble` using `as_tibble()` ```r tibble( x = 1, # recycling y = runif(8), z = x + y^2, outcome = rnorm(8) ) ``` ``` ## # A tibble: 8 x 4 ## x y z outcome ## <dbl> <dbl> <dbl> <dbl> ## 1 1 0.598 1.36 -0.741 ## 2 1 0.924 1.85 0.963 ## 3 1 0.767 1.59 -2.24 ## 4 1 0.0402 1.00 -0.873 ## 5 1 0.338 1.11 -0.210 ## 6 1 0.922 1.85 -0.296 ## 7 1 0.490 1.24 1.16 ## 8 1 0.0561 1.00 1.83 ``` ] --- name: tibble2 ## More on Tibbles * When you print a `tibble`: + all columns that fit the screen are shown, + first 10 rows are shown, + data type for each column is shown. ```r as_tibble(cars) %>% print(n = 5) ``` ``` ## # A tibble: 5 x 2 ## speed dist ## <dbl> <dbl> ## 1 4 2 ## 2 4 10 ## 3 7 4 ## 4 7 22 ## 5 8 16 ``` * `my_tibble %>% print(n = 50, width = Inf)`, * `options(tibble.print_min = 15, tibble.print_max = 25)`, * `options(dplyr.print_min = Inf)`, * `options(tibble.width = Inf)` --- name: tibble2 ## Subsetting Tibbles ```r vehicles <- as_tibble(cars[1:5,]) vehicles[['speed']] vehicles[[1]] vehicles$speed # Using placeholders vehicles %>% .$dist vehicles %>% .[['dist']] vehicles %>% .[[2]] ``` ``` ## [1] 4 4 7 7 8 ## [1] 4 4 7 7 8 ## [1] 4 4 7 7 8 ## [1] 2 10 4 22 16 ## [1] 2 10 4 22 16 ## [1] 2 10 4 22 16 ``` -- **Note!** Not all old R functions work with tibbles, than you have to use `as.data.frame(my_tibble)`. --- name: tibbles_partial_matching ## Tibbles are Stricter than `data.frames` ```r cars <- cars[1:5,] ``` ```r cars$spe # partial matching ``` ``` ## [1] 4 4 7 7 8 ``` ```r vehicles$spe # no partial matching ``` ``` ## Warning: Unknown or uninitialised column: `spe`. ``` ``` ## NULL ``` ```r cars$gear ``` ``` ## NULL ``` ```r vehicles$gear ``` ``` ## Warning: Unknown or uninitialised column: `gear`. ``` ``` ## NULL ``` --- name: loading_data ## Loading Data In `tidyverse` you import data using `readr` package that provides a number of useful data import functions: * `read_delim()` a generic function for reading *-delimited files. There are a number of convenience wrappers: + `read_csv()` used to read comma-delimited files, + `read_csv2()` reads semicolon-delimited files, `read_tsv()` that reads tab-delimited files. * `read_fwf` for reading fixed-width files with its wrappers: + fwf_widths() for width-based reading, + fwf_positions() for positions-based reading and + read_table() for reading white space-delimited fixed-width files. * `read_log()` for reading Apache-style logs. -- The most commonly used `read_csv()` has some familiar arguments like: * `skip` -- to specify the number of rows to skip (headers), * `col_names` -- to supply a vector of column names, * `comment` -- to specify what character designates a comment, * `na` -- to specify how missing values are represented. --- name: readr ## Importing Data Using `readr` When reading and parsing a file, `readr` attempts to guess proper parser for each column by looking at the 1000 first rows. ```r tricky_dataset <- read_csv(readr_example('challenge.csv')) ``` ``` ## ## ── Column specification ──────────────────────────────────────────────────────── ## cols( ## x = col_double(), ## y = col_logical() ## ) ``` ``` ## Warning: 1000 parsing failures. ## row col expected actual file ## 1001 y 1/0/T/F/TRUE/FALSE 2015-01-16 '/home/runner/work/_temp/Library/readr/extdata/challenge.csv' ## 1002 y 1/0/T/F/TRUE/FALSE 2018-05-18 '/home/runner/work/_temp/Library/readr/extdata/challenge.csv' ## 1003 y 1/0/T/F/TRUE/FALSE 2015-09-05 '/home/runner/work/_temp/Library/readr/extdata/challenge.csv' ## 1004 y 1/0/T/F/TRUE/FALSE 2012-11-28 '/home/runner/work/_temp/Library/readr/extdata/challenge.csv' ## 1005 y 1/0/T/F/TRUE/FALSE 2020-01-13 '/home/runner/work/_temp/Library/readr/extdata/challenge.csv' ## .... ... .................. .......... ............................................................. ## See problems(...) for more details. ``` OK, so there are some parsing failures. We can examine them more closely using `problems()` as suggested in the above output. --- name: readr_problems ## Looking at Problematic Columns ```r (p <- problems(tricky_dataset)) ``` ``` ## # A tibble: 1,000 x 5 ## row col expected actual file ## <int> <chr> <chr> <chr> <chr> ## 1 1001 y 1/0/T/F/TRUE/F… 2015-01… '/home/runner/work/_temp/Library/readr/… ## 2 1002 y 1/0/T/F/TRUE/F… 2018-05… '/home/runner/work/_temp/Library/readr/… ## 3 1003 y 1/0/T/F/TRUE/F… 2015-09… '/home/runner/work/_temp/Library/readr/… ## 4 1004 y 1/0/T/F/TRUE/F… 2012-11… '/home/runner/work/_temp/Library/readr/… ## 5 1005 y 1/0/T/F/TRUE/F… 2020-01… '/home/runner/work/_temp/Library/readr/… ## 6 1006 y 1/0/T/F/TRUE/F… 2016-04… '/home/runner/work/_temp/Library/readr/… ## 7 1007 y 1/0/T/F/TRUE/F… 2011-05… '/home/runner/work/_temp/Library/readr/… ## 8 1008 y 1/0/T/F/TRUE/F… 2020-07… '/home/runner/work/_temp/Library/readr/… ## 9 1009 y 1/0/T/F/TRUE/F… 2011-04… '/home/runner/work/_temp/Library/readr/… ## 10 1010 y 1/0/T/F/TRUE/F… 2010-05… '/home/runner/work/_temp/Library/readr/… ## 11 1011 y 1/0/T/F/TRUE/F… 2014-11… '/home/runner/work/_temp/Library/readr/… ## 12 1012 y 1/0/T/F/TRUE/F… 2014-06… '/home/runner/work/_temp/Library/readr/… ## 13 1013 y 1/0/T/F/TRUE/F… 2017-05… '/home/runner/work/_temp/Library/readr/… ## 14 1014 y 1/0/T/F/TRUE/F… 2017-11… '/home/runner/work/_temp/Library/readr/… ## 15 1015 y 1/0/T/F/TRUE/F… 2013-04… '/home/runner/work/_temp/Library/readr/… ## # … with 985 more rows ``` OK, let's see which columns cause trouble: ```r p %$% table(col) ``` ``` ## col ## y ## 1000 ``` Looks like the problem occurs only in the `x` column. --- name: readr_problems_fixing ## Fixing Problematic Columns So, how can we fix the problematic columns? 1. We can explicitely tell what parser to use: ```r tricky_dataset <- read_csv(readr_example('challenge.csv'), col_types = cols(x = col_double(), y = col_character())) tricky_dataset %>% tail(n = 5) ``` ``` ## # A tibble: 5 x 2 ## x y ## <dbl> <chr> ## 1 0.164 2018-03-29 ## 2 0.472 2014-08-04 ## 3 0.718 2015-08-16 ## 4 0.270 2020-02-04 ## 5 0.608 2019-01-06 ``` As you can see, we can still do better by parsing the `y` column as *date*, not as *character*. --- name: readr_problems_fixing2 ## Fixing Problematic Columns cted. But knowing that the parser is guessed based on the first 1000 lines, we can see what sits past the 1000-th line in the data: ```r tricky_dataset %>% head(n = 1002) %>% tail(n = 4) ``` ``` ## # A tibble: 4 x 2 ## x y ## <dbl> <chr> ## 1 4569 <NA> ## 2 4548 <NA> ## 3 0.238 2015-01-16 ## 4 0.412 2018-05-18 ``` It seems, we were very unlucky, because up till 1000-th line there are only integers in the x column and `NA`s in the y column so the parser cannot be guessed correctly. To fix this: ```r tricky_dataset <- read_csv(readr_example('challenge.csv'), guess_max = 1001) ``` ``` ## ## ── Column specification ──────────────────────────────────────────────────────── ## cols( ## x = col_double(), ## y = col_date(format = "") ## ) ``` --- name: readr_writing ## Writing to a File The `readr` package also provides functions useful for writing tibbled data into a file: * `write_csv()` * `write_tsv()` * `write_excel_csv()` They **always** save: * text in UTF-8, * dates in ISO8601 But saving in csv (or tsv) does mean you loose information about the type of data in particular columns. You can avoid this by using: * `write_rds()` and `read_rds()` to read/write objects in R binary rds format, * use `write_feather()` and `read_feather()` from package `feather` to read/write objects in a fast binary format that other programming languages can access. --- name: basic_data_transformations ## Basic Data Transformations with `dplyr` Let us create a tibble: ```r (bijou <- as_tibble(diamonds) %>% head(n = 100)) ``` ``` ## # A tibble: 100 x 10 ## carat cut color clarity depth table price x y z ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> ## 1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43 ## 2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31 ## 3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31 ## 4 0.290 Premium I VS2 62.4 58 334 4.2 4.23 2.63 ## 5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75 ## 6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48 ## 7 0.24 Very Good I VVS1 62.3 57 336 3.95 3.98 2.47 ## 8 0.26 Very Good H SI1 61.9 55 337 4.07 4.11 2.53 ## 9 0.22 Fair E VS2 65.1 61 337 3.87 3.78 2.49 ## 10 0.23 Very Good H VS1 59.4 61 338 4 4.05 2.39 ## 11 0.3 Good J SI1 64 55 339 4.25 4.28 2.73 ## 12 0.23 Ideal J VS1 62.8 56 340 3.93 3.9 2.46 ## 13 0.22 Premium F SI1 60.4 61 342 3.88 3.84 2.33 ## 14 0.31 Ideal J SI2 62.2 54 344 4.35 4.37 2.71 ## 15 0.2 Premium E SI2 60.2 62 345 3.79 3.75 2.27 ## # … with 85 more rows ``` .center[<img src="data/slide_tidyverse/diamonds.png", style="height:200px">] --- name: filter ## Picking Observations using `filter()` ```r bijou %>% filter(cut == 'Ideal' | cut == 'Premium', carat >= 0.23) %>% head(n = 5) ``` ``` ## # A tibble: 5 x 10 ## carat cut color clarity depth table price x y z ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> ## 1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43 ## 2 0.290 Premium I VS2 62.4 58 334 4.2 4.23 2.63 ## 3 0.23 Ideal J VS1 62.8 56 340 3.93 3.9 2.46 ## 4 0.31 Ideal J SI2 62.2 54 344 4.35 4.37 2.71 ## 5 0.32 Premium E I1 60.9 58 345 4.38 4.42 2.68 ``` Be careful with floating point comparisons! Also, rows with comparison resulting in `NA` are skipped by default! ```r bijou %>% filter(near(0.23, carat) | is.na(carat)) %>% head(n = 5) ``` ``` ## # A tibble: 5 x 10 ## carat cut color clarity depth table price x y z ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> ## 1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43 ## 2 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31 ## 3 0.23 Very Good H VS1 59.4 61 338 4 4.05 2.39 ## 4 0.23 Ideal J VS1 62.8 56 340 3.93 3.9 2.46 ## 5 0.23 Very Good E VS2 63.8 55 352 3.85 3.92 2.48 ``` --- name: arrange ## Rearranging Observations using `arrange()` ```r bijou %>% arrange(cut, carat, desc(price)) ``` ``` ## # A tibble: 100 x 10 ## carat cut color clarity depth table price x y z ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> ## 1 0.22 Fair E VS2 65.1 61 337 3.87 3.78 2.49 ## 2 0.86 Fair E SI2 55.1 69 2757 6.45 6.33 3.52 ## 3 0.96 Fair F SI2 66.3 62 2759 6.27 5.95 4.07 ## 4 0.23 Good F VS1 58.2 59 402 4.06 4.08 2.37 ## 5 0.23 Good E VS1 64.1 59 402 3.83 3.85 2.46 ## 6 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31 ## 7 0.26 Good E VVS1 57.9 60 554 4.22 4.25 2.45 ## 8 0.26 Good D VS2 65.2 56 403 3.99 4.02 2.61 ## 9 0.26 Good D VS1 58.4 63 403 4.19 4.24 2.46 ## 10 0.3 Good H SI1 63.7 57 554 4.28 4.26 2.72 ## 11 0.3 Good I SI1 63.2 55 405 4.25 4.29 2.7 ## 12 0.3 Good J SI1 63.4 54 351 4.23 4.29 2.7 ## 13 0.3 Good J SI1 63.8 56 351 4.23 4.26 2.71 ## 14 0.3 Good I SI2 63.3 56 351 4.26 4.3 2.71 ## 15 0.3 Good J SI1 64 55 339 4.25 4.28 2.73 ## # … with 85 more rows ``` The `NA`s always end up at the end of the rearranged tibble. --- name: select ## Selecting Variables with `select()` Simple `select` with a range: ```r bijou %>% select(color, clarity, x:z) %>% head(n = 4) ``` ``` ## # A tibble: 4 x 5 ## color clarity x y z ## <ord> <ord> <dbl> <dbl> <dbl> ## 1 E SI2 3.95 3.98 2.43 ## 2 E SI1 3.89 3.84 2.31 ## 3 E VS1 4.05 4.07 2.31 ## 4 I VS2 4.2 4.23 2.63 ``` -- Exclusive `select`: ```r bijou %>% select(-(x:z)) %>% head(n = 4) ``` ``` ## # A tibble: 4 x 7 ## carat cut color clarity depth table price ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> ## 1 0.23 Ideal E SI2 61.5 55 326 ## 2 0.21 Premium E SI1 59.8 61 326 ## 3 0.23 Good E VS1 56.9 65 327 ## 4 0.290 Premium I VS2 62.4 58 334 ``` --- name: select2 ## Selecting Variables with `select()` cted. `rename` is a variant of `select`, here used with `everything()` to move `x` to the beginning and rename it to `var_x` ```r bijou %>% rename(var_x = x) %>% head(n = 5) ``` ``` ## # A tibble: 5 x 10 ## carat cut color clarity depth table price var_x y z ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> ## 1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43 ## 2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31 ## 3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31 ## 4 0.290 Premium I VS2 62.4 58 334 4.2 4.23 2.63 ## 5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75 ``` -- use `everything()` to bring some columns to the front: ```r bijou %>% select(x:z, everything()) %>% head(n = 4) ``` ``` ## # A tibble: 4 x 10 ## x y z carat cut color clarity depth table price ## <dbl> <dbl> <dbl> <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> ## 1 3.95 3.98 2.43 0.23 Ideal E SI2 61.5 55 326 ## 2 3.89 3.84 2.31 0.21 Premium E SI1 59.8 61 326 ## 3 4.05 4.07 2.31 0.23 Good E VS1 56.9 65 327 ## 4 4.2 4.23 2.63 0.290 Premium I VS2 62.4 58 334 ``` --- name: mutate ## Create/alter new Variables with `mutate` ```r bijou %>% mutate(p = x + z, q = p + y) %>% select(-(depth:price)) %>% head(n = 5) ``` ``` ## # A tibble: 5 x 9 ## carat cut color clarity x y z p q ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 0.23 Ideal E SI2 3.95 3.98 2.43 6.38 10.4 ## 2 0.21 Premium E SI1 3.89 3.84 2.31 6.2 10.0 ## 3 0.23 Good E VS1 4.05 4.07 2.31 6.36 10.4 ## 4 0.290 Premium I VS2 4.2 4.23 2.63 6.83 11.1 ## 5 0.31 Good J SI2 4.34 4.35 2.75 7.09 11.4 ``` -- or with `transmute` (only the transformed variables will be retained) ```r bijou %>% transmute(carat, cut, sum = x + y + z) %>% head(n = 5) ``` ``` ## # A tibble: 5 x 3 ## carat cut sum ## <dbl> <ord> <dbl> ## 1 0.23 Ideal 10.4 ## 2 0.21 Premium 10.0 ## 3 0.23 Good 10.4 ## 4 0.290 Premium 11.1 ## 5 0.31 Good 11.4 ``` --- name: grouped_summaries ## Group and Summarize ```r bijou %>% group_by(cut) %>% summarize(max_price = max(price), mean_price = mean(price), min_price = min(price)) ``` ``` ## # A tibble: 5 x 4 ## cut max_price mean_price min_price ## <ord> <int> <dbl> <int> ## 1 Fair 2759 1951 337 ## 2 Good 2759 661. 327 ## 3 Very Good 2760 610. 336 ## 4 Premium 2760 569. 326 ## 5 Ideal 2757 693. 326 ``` -- ```r bijou %>% group_by(cut, color) %>% summarize(max_price = max(price), mean_price = mean(price), min_price = min(price)) %>% head(n = 4) ``` ``` ## # A tibble: 4 x 5 ## # Groups: cut [2] ## cut color max_price mean_price min_price ## <ord> <ord> <int> <dbl> <int> ## 1 Fair E 2757 1547 337 ## 2 Fair F 2759 2759 2759 ## 3 Good D 403 403 403 ## 4 Good E 2759 1010. 327 ``` --- name: other_data_manipulations ## Other data manipulation tips ```r bijou %>% group_by(cut) %>% summarize(count = n()) ``` ``` ## # A tibble: 5 x 2 ## cut count ## <ord> <int> ## 1 Fair 3 ## 2 Good 18 ## 3 Very Good 38 ## 4 Premium 22 ## 5 Ideal 19 ``` -- When you need to regroup within the same pipe, use `ungroup()`. --- name: concept_of_tidy_data ## The Concept of Tidy Data Data are tidy *sensu Wickham* if: * each and every observation is represented as exactly one row, * each and every variable is represented by exactly one column, * thus each data table cell contains only one value. <img src="data/slide_tidyverse/tidy_data.png" width="2560" style="display: block; margin: auto auto auto 0;" /> Usually data are untidy in only one way. However, if you are unlucky, they are really untidy and thus a pain to work with... --- name: tidy_data ## Tidy Data <img src="data/slide_tidyverse/tidy_data.png" style="height:100px"> -- .center[**Are these data tidy?**] .pull-left-70[ <table class="table table-striped table-hover table-responsive table-condensed" style=""> <thead> <tr> <th style="text-align:center;"> Sepal.Length </th> <th style="text-align:center;"> Sepal.Width </th> <th style="text-align:center;"> Petal.Length </th> <th style="text-align:center;"> Petal.Width </th> <th style="text-align:center;"> Species </th> </tr> </thead> <tbody> <tr> <td style="text-align:center;"> 5.1 </td> <td style="text-align:center;"> 3.5 </td> <td style="text-align:center;"> 1.4 </td> <td style="text-align:center;"> 0.2 </td> <td style="text-align:center;"> setosa </td> </tr> <tr> <td style="text-align:center;"> 4.9 </td> <td style="text-align:center;"> 3.0 </td> <td style="text-align:center;"> 1.4 </td> <td style="text-align:center;"> 0.2 </td> <td style="text-align:center;"> setosa </td> </tr> <tr> <td style="text-align:center;"> 4.7 </td> <td style="text-align:center;"> 3.2 </td> <td style="text-align:center;"> 1.3 </td> <td style="text-align:center;"> 0.2 </td> <td style="text-align:center;"> setosa </td> </tr> </tbody> </table> ] -- .pull-right-30[ <table class="table table-striped table-hover table-responsive table-condensed" style=""> <thead> <tr> <th style="text-align:center;"> Species </th> <th style="text-align:center;"> variable </th> <th style="text-align:center;"> value </th> </tr> </thead> <tbody> <tr> <td style="text-align:center;"> setosa </td> <td style="text-align:center;"> Sepal.Length </td> <td style="text-align:center;"> 5.1 </td> </tr> <tr> <td style="text-align:center;"> setosa </td> <td style="text-align:center;"> Sepal.Length </td> <td style="text-align:center;"> 4.9 </td> </tr> <tr> <td style="text-align:center;"> setosa </td> <td style="text-align:center;"> Sepal.Length </td> <td style="text-align:center;"> 4.7 </td> </tr> </tbody> </table> ] <br>&nbsp;<hr><br> -- .pull-left-50[ <table class="table table-striped table-hover table-responsive table-condensed" style=""> <thead> <tr> <th style="text-align:center;"> Sepal.L.W </th> <th style="text-align:center;"> Petal.L.W </th> <th style="text-align:center;"> Species </th> </tr> </thead> <tbody> <tr> <td style="text-align:center;"> 5.1/3.5 </td> <td style="text-align:center;"> 1.4/0.2 </td> <td style="text-align:center;"> setosa </td> </tr> <tr> <td style="text-align:center;"> 4.9/3 </td> <td style="text-align:center;"> 1.4/0.2 </td> <td style="text-align:center;"> setosa </td> </tr> <tr> <td style="text-align:center;"> 4.7/3.2 </td> <td style="text-align:center;"> 1.3/0.2 </td> <td style="text-align:center;"> setosa </td> </tr> </tbody> </table> ] -- .pull-right-50[ <table class="table table-striped table-hover table-responsive table-condensed" style=""> <tbody> <tr> <td style="text-align:left;"> Sepal.Length </td> <td style="text-align:center;"> 5.1 </td> <td style="text-align:center;"> 4.9 </td> <td style="text-align:center;"> 4.7 </td> <td style="text-align:center;"> 4.6 </td> </tr> <tr> <td style="text-align:left;"> Sepal.Width </td> <td style="text-align:center;"> 3.5 </td> <td style="text-align:center;"> 3.0 </td> <td style="text-align:center;"> 3.2 </td> <td style="text-align:center;"> 3.1 </td> </tr> <tr> <td style="text-align:left;"> Petal.Length </td> <td style="text-align:center;"> 1.4 </td> <td style="text-align:center;"> 1.4 </td> <td style="text-align:center;"> 1.3 </td> <td style="text-align:center;"> 1.5 </td> </tr> <tr> <td style="text-align:left;"> Petal.Width </td> <td style="text-align:center;"> 0.2 </td> <td style="text-align:center;"> 0.2 </td> <td style="text-align:center;"> 0.2 </td> <td style="text-align:center;"> 0.2 </td> </tr> <tr> <td style="text-align:left;"> Species </td> <td style="text-align:center;"> setosa </td> <td style="text-align:center;"> setosa </td> <td style="text-align:center;"> setosa </td> <td style="text-align:center;"> setosa </td> </tr> </tbody> </table> ] --- name: tidying_data_pivot_longer ## Tidying Data with `tidyr::pivot_longer` If some of your column names are actually values of a variable, use `pivot_longer` (replaces `gather`): ```r bijou2 %>% head(n = 5) ``` ``` ## # A tibble: 5 x 3 ## cut `2008` `2009` ## <ord> <int> <dbl> ## 1 Ideal 326 333. ## 2 Premium 326 333. ## 3 Good 327 334. ## 4 Premium 334 341. ## 5 Good 335 342. ``` ```r bijou2 %>% pivot_longer(c(`2008`, `2009`), names_to = 'year', values_to = 'price') %>% head(n = 5) ``` ``` ## # A tibble: 5 x 3 ## cut year price ## <ord> <chr> <dbl> ## 1 Ideal 2008 326 ## 2 Ideal 2009 333. ## 3 Premium 2008 326 ## 4 Premium 2009 333. ## 5 Good 2008 327 ``` --- name: tidying_data_pivot_wider ## Tidying Data with `tidyr::pivot_wider` If some of your observations are scattered across many rows, use `pivot_wider` (replaces `gather`): ```r bijou3 ``` ``` ## # A tibble: 9 x 5 ## cut price clarity dimension measurement ## <ord> <int> <ord> <chr> <dbl> ## 1 Ideal 326 SI2 x 3.95 ## 2 Premium 326 SI1 x 3.89 ## 3 Good 327 VS1 x 4.05 ## 4 Ideal 326 SI2 y 3.98 ## 5 Premium 326 SI1 y 3.84 ## 6 Good 327 VS1 y 4.07 ## 7 Ideal 326 SI2 z 2.43 ## 8 Premium 326 SI1 z 2.31 ## 9 Good 327 VS1 z 2.31 ``` ```r bijou3 %>% pivot_wider(names_from=dimension, values_from=measurement) %>% head(n = 4) ``` ``` ## # A tibble: 3 x 6 ## cut price clarity x y z ## <ord> <int> <ord> <dbl> <dbl> <dbl> ## 1 Ideal 326 SI2 3.95 3.98 2.43 ## 2 Premium 326 SI1 3.89 3.84 2.31 ## 3 Good 327 VS1 4.05 4.07 2.31 ``` --- name: tidying_data_separate ## Tidying Data with `separate` If some of your columns contain more than one value, use `separate`: ```r bijou4 ``` ``` ## # A tibble: 5 x 4 ## cut price clarity dim ## <ord> <int> <ord> <chr> ## 1 Ideal 326 SI2 3.95/3.98/2.43 ## 2 Premium 326 SI1 3.89/3.84/2.31 ## 3 Good 327 VS1 4.05/4.07/2.31 ## 4 Premium 334 VS2 4.2/4.23/2.63 ## 5 Good 335 SI2 4.34/4.35/2.75 ``` ```r bijou4 %>% separate(dim, into = c("x", "y", "z"), sep = "/", convert = T) ``` ``` ## # A tibble: 5 x 6 ## cut price clarity x y z ## <ord> <int> <ord> <dbl> <dbl> <dbl> ## 1 Ideal 326 SI2 3.95 3.98 2.43 ## 2 Premium 326 SI1 3.89 3.84 2.31 ## 3 Good 327 VS1 4.05 4.07 2.31 ## 4 Premium 334 VS2 4.2 4.23 2.63 ## 5 Good 335 SI2 4.34 4.35 2.75 ``` --- name: tidying_data_separate ## Tidying Data with `unite` If some of your columns contain more than one value, use `separate`: ```r bijou5 ``` ``` ## # A tibble: 5 x 7 ## cut price clarity_prefix clarity_suffix x y z ## <ord> <int> <chr> <chr> <dbl> <dbl> <dbl> ## 1 Ideal 326 SI 2 3.95 3.98 2.43 ## 2 Premium 326 SI 1 3.89 3.84 2.31 ## 3 Good 327 VS 1 4.05 4.07 2.31 ## 4 Premium 334 VS 2 4.2 4.23 2.63 ## 5 Good 335 SI 2 4.34 4.35 2.75 ``` ```r bijou5 %>% unite(clarity, clarity_prefix, clarity_suffix, sep='') ``` ``` ## # A tibble: 5 x 6 ## cut price clarity x y z ## <ord> <int> <chr> <dbl> <dbl> <dbl> ## 1 Ideal 326 SI2 3.95 3.98 2.43 ## 2 Premium 326 SI1 3.89 3.84 2.31 ## 3 Good 327 VS1 4.05 4.07 2.31 ## 4 Premium 334 VS2 4.2 4.23 2.63 ## 5 Good 335 SI2 4.34 4.35 2.75 ``` **Note:** that `sep` is here interpreted as the position to split on. It can also be a *regular expression* or a delimiting string/character. Pretty flexible approach! --- name: missing_complete ## Completing Missing Values Using `complete` ```r bijou %>% head(n = 10) %>% select(cut, clarity, price) %>% mutate(continent = sample(c('AusOce', 'Eur'), size = 10, replace = T)) -> missing_stones ``` ```r missing_stones %>% complete(cut, continent) ``` ``` ## # A tibble: 14 x 4 ## cut continent clarity price ## <ord> <chr> <ord> <int> ## 1 Fair AusOce VS2 337 ## 2 Fair Eur <NA> NA ## 3 Good AusOce <NA> NA ## 4 Good Eur VS1 327 ## 5 Good Eur SI2 335 ## 6 Very Good AusOce VVS2 336 ## 7 Very Good AusOce VVS1 336 ## 8 Very Good AusOce SI1 337 ## 9 Very Good Eur VS1 338 ## 10 Premium AusOce SI1 326 ## 11 Premium AusOce VS2 334 ## 12 Premium Eur <NA> NA ## 13 Ideal AusOce SI2 326 ## 14 Ideal Eur <NA> NA ``` --- name: more_tidyverse ## Some Other Friends * `stringr` for string manipulation and regular expressions, * `forcats` for working with factors, * `lubridate` for working with dates. --- name: end-slide class: end-slide # Thank you. Questions? .end-text[ <p>R version 4.0.3 (2020-10-10)<br><p>Platform: x86_64-pc-linux-gnu (64-bit)</p><p>OS: Ubuntu 18.04.5 LTS</p><br> <hr> <span class="small">Built on : <i class='fa fa-calendar' aria-hidden='true'></i> 06-Nov-2020 at <i class='fa fa-clock-o' aria-hidden='true'></i> 22:21:03</span> <b>2020</b> • [SciLifeLab](https://www.scilifelab.se/) • [NBIS](https://nbis.se/) ]