class: center, middle, inverse, title-slide # Data Wrangling II ## <br><br> Introduction to Global Health Data Science ### <a href="https://sta198f2021.github.io/website/">Back to Website</a> ### <br> Prof. Amy Herring --- layout: true <div class="my-footer"> <span> <a href="https://sta198f2021.github.io/website/" target="_blank">Back to website</a> </span> </div> --- class: middle # .hand[We...] .huge[.green[have]] .hand[multiple data frames] .huge[.pink[want]] .hand[to bring them together] This slide deck adapted from Data Science in a Box! --- ## Data: Women in Science Information on 10 women in science who changed the world .small[ |name | |:------------------| |Ada Lovelace | |Marie Curie | |Janaki Ammal | |Chien-Shiung Wu | |Katherine Johnson | |Rosalind Franklin | |Vera Rubin | |Gladys West | |Flossie Wong-Staal | |Jennifer Doudna | ] .footnote[ Source: [Discover Magazine](https://www.discovermagazine.com/the-sciences/meet-10-women-in-science-who-changed-the-world) ] --- ## Inputs .panelset[ .panel[.panel-name[professions] ```r professions ``` ``` ## # A tibble: 10 × 2 ## name profession ## <chr> <chr> ## 1 Ada Lovelace Mathematician ## 2 Marie Curie Physicist and Chemist ## 3 Janaki Ammal Botanist ## 4 Chien-Shiung Wu Physicist ## 5 Katherine Johnson Mathematician ## 6 Rosalind Franklin Chemist ## 7 Vera Rubin Astronomer ## 8 Gladys West Mathematician ## 9 Flossie Wong-Staal Virologist and Molecular Biologist ## 10 Jennifer Doudna Biochemist ``` ] .panel[.panel-name[dates] ```r dates ``` ``` ## # A tibble: 8 × 3 ## name birth_year death_year ## <chr> <dbl> <dbl> ## 1 Janaki Ammal 1897 1984 ## 2 Chien-Shiung Wu 1912 1997 ## 3 Katherine Johnson 1918 2020 ## 4 Rosalind Franklin 1920 1958 ## 5 Vera Rubin 1928 2016 ## 6 Gladys West 1930 NA ## 7 Flossie Wong-Staal 1947 2020 ## 8 Jennifer Doudna 1964 NA ``` ] .panel[.panel-name[works] ```r works ``` ``` ## # A tibble: 9 × 2 ## name known_for ## <chr> <chr> ## 1 Ada Lovelace first computer algorithm ## 2 Marie Curie theory of radioactivity, discovery of elem… ## 3 Janaki Ammal hybrid species, biodiversity protection ## 4 Chien-Shiung Wu confim and refine theory of radioactive bet… ## 5 Katherine Johnson calculations of orbital mechanics critical … ## 6 Vera Rubin existence of dark matter ## 7 Gladys West mathematical modeling of the shape of the E… ## 8 Flossie Wong-Staal first scientist to clone HIV and create a m… ## 9 Jennifer Doudna one of the primary developers of CRISPR, a … ``` ] ] --- ## Desired output ``` ## # A tibble: 10 × 5 ## name profession birth_year death_year known_for ## <chr> <chr> <dbl> <dbl> <chr> ## 1 Ada Lovelace Mathematic… NA NA first co… ## 2 Marie Curie Physicist … NA NA theory o… ## 3 Janaki Ammal Botanist 1897 1984 hybrid s… ## 4 Chien-Shiung Wu Physicist 1912 1997 confim a… ## 5 Katherine Johnson Mathematic… 1918 2020 calculat… ## 6 Rosalind Franklin Chemist 1920 1958 <NA> ## 7 Vera Rubin Astronomer 1928 2016 existenc… ## 8 Gladys West Mathematic… 1930 NA mathemat… ## 9 Flossie Wong-Staal Virologist… 1947 2020 first sc… ## 10 Jennifer Doudna Biochemist 1964 NA one of t… ``` --- ## Inputs, reminder .pull-left[ ```r names(professions) ``` ``` ## [1] "name" "profession" ``` ```r names(dates) ``` ``` ## [1] "name" "birth_year" "death_year" ``` ```r names(works) ``` ``` ## [1] "name" "known_for" ``` ] .pull-right[ ```r nrow(professions) ``` ``` ## [1] 10 ``` ```r nrow(dates) ``` ``` ## [1] 8 ``` ```r nrow(works) ``` ``` ## [1] 9 ``` ] --- class: middle # Joining data frames --- ## Joining data frames ```r something_join(x, y) ``` - `left_join()`: all rows from x - `right_join()`: all rows from y - `full_join()`: all rows from both x and y - `semi_join()`: all rows from x where there are matching values in y, keeping just columns from x - `inner_join()`: all rows from x where there are matching values in y, return all combination of multiple matches in the case of multiple matches - `anti_join()`: return all rows from x where there are not matching values in y, never duplicate rows of x - ... --- ## Setup For the next few slides... .pull-left[ ```r x ``` ``` ## # A tibble: 3 × 2 ## id value_x ## <dbl> <chr> ## 1 1 x1 ## 2 2 x2 ## 3 3 x3 ``` ] .pull-right[ ```r y ``` ``` ## # A tibble: 3 × 2 ## id value_y ## <dbl> <chr> ## 1 1 y1 ## 2 2 y2 ## 3 4 y4 ``` ] --- ## `left_join()` .pull-left[ <img src="img/left-join.gif" width="80%" style="background-color: #FDF6E3" style="display: block; margin: auto;" /> ] .pull-right[ ```r left_join(x, y) ``` ``` ## # A tibble: 3 × 3 ## id value_x value_y ## <dbl> <chr> <chr> ## 1 1 x1 y1 ## 2 2 x2 y2 ## 3 3 x3 <NA> ``` ] --- ## `left_join()` ```r professions %>% * left_join(dates) ``` ``` ## # A tibble: 10 × 4 ## name profession birth_year death_year ## <chr> <chr> <dbl> <dbl> ## 1 Ada Lovelace Mathematician NA NA ## 2 Marie Curie Physicist and Chemist NA NA ## 3 Janaki Ammal Botanist 1897 1984 ## 4 Chien-Shiung Wu Physicist 1912 1997 ## 5 Katherine Johnson Mathematician 1918 2020 ## 6 Rosalind Franklin Chemist 1920 1958 ## 7 Vera Rubin Astronomer 1928 2016 ## 8 Gladys West Mathematician 1930 NA ## 9 Flossie Wong-Staal Virologist and Molec… 1947 2020 ## 10 Jennifer Doudna Biochemist 1964 NA ``` --- ## `right_join()` .pull-left[ <img src="img/right-join.gif" width="80%" style="background-color: #FDF6E3" style="display: block; margin: auto;" /> ] .pull-right[ ```r right_join(x, y) ``` ``` ## # A tibble: 3 × 3 ## id value_x value_y ## <dbl> <chr> <chr> ## 1 1 x1 y1 ## 2 2 x2 y2 ## 3 4 <NA> y4 ``` ] --- ## `right_join()` ```r professions %>% * right_join(dates) ``` ``` ## # A tibble: 8 × 4 ## name profession birth_year death_year ## <chr> <chr> <dbl> <dbl> ## 1 Janaki Ammal Botanist 1897 1984 ## 2 Chien-Shiung Wu Physicist 1912 1997 ## 3 Katherine Johnson Mathematician 1918 2020 ## 4 Rosalind Franklin Chemist 1920 1958 ## 5 Vera Rubin Astronomer 1928 2016 ## 6 Gladys West Mathematician 1930 NA ## 7 Flossie Wong-Staal Virologist and Molecu… 1947 2020 ## 8 Jennifer Doudna Biochemist 1964 NA ``` --- ## `full_join()` .pull-left[ <img src="img/full-join.gif" width="80%" style="background-color: #FDF6E3" style="display: block; margin: auto;" /> ] .pull-right[ ```r full_join(x, y) ``` ``` ## # A tibble: 4 × 3 ## id value_x value_y ## <dbl> <chr> <chr> ## 1 1 x1 y1 ## 2 2 x2 y2 ## 3 3 x3 <NA> ## 4 4 <NA> y4 ``` ] --- ## `full_join()` ```r dates %>% * full_join(works) ``` ``` ## # A tibble: 10 × 4 ## name birth_year death_year known_for ## <chr> <dbl> <dbl> <chr> ## 1 Janaki Ammal 1897 1984 hybrid species, biod… ## 2 Chien-Shiung Wu 1912 1997 confim and refine th… ## 3 Katherine Johnson 1918 2020 calculations of orbi… ## 4 Rosalind Franklin 1920 1958 <NA> ## 5 Vera Rubin 1928 2016 existence of dark ma… ## 6 Gladys West 1930 NA mathematical modelin… ## 7 Flossie Wong-Staal 1947 2020 first scientist to c… ## 8 Jennifer Doudna 1964 NA one of the primary d… ## 9 Ada Lovelace NA NA first computer algor… ## 10 Marie Curie NA NA theory of radioactiv… ``` --- ## `inner_join()` .pull-left[ <img src="img/inner-join.gif" width="80%" style="background-color: #FDF6E3" style="display: block; margin: auto;" /> ] .pull-right[ ```r inner_join(x, y) ``` ``` ## # A tibble: 2 × 3 ## id value_x value_y ## <dbl> <chr> <chr> ## 1 1 x1 y1 ## 2 2 x2 y2 ``` ] --- ## `inner_join()` ```r dates %>% * inner_join(works) ``` ``` ## # A tibble: 7 × 4 ## name birth_year death_year known_for ## <chr> <dbl> <dbl> <chr> ## 1 Janaki Ammal 1897 1984 hybrid species, biodi… ## 2 Chien-Shiung Wu 1912 1997 confim and refine the… ## 3 Katherine Johnson 1918 2020 calculations of orbit… ## 4 Vera Rubin 1928 2016 existence of dark mat… ## 5 Gladys West 1930 NA mathematical modeling… ## 6 Flossie Wong-Staal 1947 2020 first scientist to cl… ## 7 Jennifer Doudna 1964 NA one of the primary de… ``` --- ## `semi_join()` .pull-left[ <img src="img/semi-join.gif" width="80%" style="background-color: #FDF6E3" style="display: block; margin: auto;" /> ] .pull-right[ ```r semi_join(x, y) ``` ``` ## # A tibble: 2 × 2 ## id value_x ## <dbl> <chr> ## 1 1 x1 ## 2 2 x2 ``` ] --- ## `semi_join()` ```r dates %>% * semi_join(works) ``` ``` ## # A tibble: 7 × 3 ## name birth_year death_year ## <chr> <dbl> <dbl> ## 1 Janaki Ammal 1897 1984 ## 2 Chien-Shiung Wu 1912 1997 ## 3 Katherine Johnson 1918 2020 ## 4 Vera Rubin 1928 2016 ## 5 Gladys West 1930 NA ## 6 Flossie Wong-Staal 1947 2020 ## 7 Jennifer Doudna 1964 NA ``` --- ## `anti_join()` .pull-left[ <img src="img/anti-join.gif" width="80%" style="background-color: #FDF6E3" style="display: block; margin: auto;" /> ] .pull-right[ ```r anti_join(x, y) ``` ``` ## # A tibble: 1 × 2 ## id value_x ## <dbl> <chr> ## 1 3 x3 ``` ] --- ## `anti_join()` ```r dates %>% * anti_join(works) ``` ``` ## # A tibble: 1 × 3 ## name birth_year death_year ## <chr> <dbl> <dbl> ## 1 Rosalind Franklin 1920 1958 ``` --- ## Putting it all together ```r professions %>% left_join(dates) %>% left_join(works) ``` ``` ## # A tibble: 10 × 5 ## name profession birth_year death_year known_for ## <chr> <chr> <dbl> <dbl> <chr> ## 1 Ada Lovelace Mathematic… NA NA first co… ## 2 Marie Curie Physicist … NA NA theory o… ## 3 Janaki Ammal Botanist 1897 1984 hybrid s… ## 4 Chien-Shiung Wu Physicist 1912 1997 confim a… ## 5 Katherine Johnson Mathematic… 1918 2020 calculat… ## 6 Rosalind Franklin Chemist 1920 1958 <NA> ## 7 Vera Rubin Astronomer 1928 2016 existenc… ## 8 Gladys West Mathematic… 1930 NA mathemat… ## 9 Flossie Wong-Staal Virologist… 1947 2020 first sc… ## 10 Jennifer Doudna Biochemist 1964 NA one of t… ``` --- class: middle # Case study: Medical records --- ## Medical Records - Have: - Enrolled: officially enrolled in Duke MyChart - Survey: completed by those seen in hospital clinics over past year - Want: Survey info for all officially enrolled in Duke MyChart --- .pull-left[ ```r enrollment ``` ``` ## # A tibble: 3 × 2 ## id name ## <dbl> <chr> ## 1 1 Cruella de Vil ## 2 2 Shere Khan ## 3 3 Shan Yu ``` ] .pull-right[ ```r survey ``` ``` ## # A tibble: 4 × 3 ## id name clinic ## <dbl> <chr> <chr> ## 1 2 Cruella de Vil Plastic and Reconstructive Surgery ## 2 3 Shere Khan Urology ## 3 4 Scar Cognitive Behavioral Therapy ## 4 5 Maleficent Oncology ``` ] --- ## Medical records .panelset[ .panel[.panel-name[In MyChart] ```r enrollment %>% * left_join(survey, by = "id") ``` ``` ## # A tibble: 3 × 4 ## id name.x name.y clinic ## <dbl> <chr> <chr> <chr> ## 1 1 Cruella de Vil <NA> <NA> ## 2 2 Shere Khan Cruella de Vil Plastic and Reconstructive… ## 3 3 Shan Yu Shere Khan Urology ``` ] .panel[.panel-name[Survey missing] ```r enrollment %>% * anti_join(survey, by = "id") ``` ``` ## # A tibble: 1 × 2 ## id name ## <dbl> <chr> ## 1 1 Cruella de Vil ``` ] .panel[.panel-name[MyChart not activated] ```r survey %>% * anti_join(enrollment, by = "id") ``` ``` ## # A tibble: 2 × 3 ## id name clinic ## <dbl> <chr> <chr> ## 1 4 Scar Cognitive Behavioral Therapy ## 2 5 Maleficent Oncology ``` ] ]