2020-03-31 09:42:04
Preliminaries
Check-in
Announcements
Today’s topics
- Managing resources from afar via APIs
Managing resources from afar via APIs
What are APIs
- Application Program Interface (API)
- Talk to computer services
Why use APIs
- Reduce human manipulation of data files
- Reduce errors
- Reduce security/privacy breaches
- Improve reproducibility
](https://www.nature.com/article-assets/npg/nathumbehav/2017/s41562-016-0021/images_hires/w926/s41562-016-0021-f1.jpg)
Some useful APIs
- Box
- Google Drive
- OSF
- Databrary
Box.com
Google Drive
Open Science Framework (OSF)
Databrary
What can you do with these APIs?
- Move data to/from cloud storage
- Leave data on cloud storage; clean, visualize locally
- Produce reproducible workflows from the get-go
- Reduce the likelihood that data can “leak”
- Access & visualize data shared by others
What’s involved?
- Downloading package
- Configuring authentication
- Testing the connection
- Writing code to do what you want
Example 1: databraryapi
- Summarize demographics of specific study
Tamis-LeMonda, C. (2013). Language, cognitive, and socio-emotional skills from 9 months until their transition to first grade in U.S. children from African-American, Dominican, Mexican, and Chinese backgrounds. Databrary. Retrieved March 29, 2020 from http://doi.org/10.17910/B7CC74.
- Login
databraryapi::login_db()
## Please enter your Databrary user ID (email).
## Email:
## [1] FALSE
- Download demographic data
demog <- databraryapi::download_session_csv(8)
str(demog)
## 'data.frame': 1351 obs. of 36 variables: ## $ session_id : int 190 191 192 193 194 195 196 197 198 199 ... ## $ session_name : logi NA NA NA NA NA NA ... ## $ session_date : chr "2006-XX-XX" "2006-XX-XX" "2006-XX-XX" "2006-XX-XX" ... ## $ session_release : chr "EXCERPTS" "PRIVATE" "EXCERPTS" "PRIVATE" ... ## $ participant.ID : int 3814 3811 3808 3806 3804 3803 3801 3800 3797 3796 ... ## $ participant.birthdate: logi NA NA NA NA NA NA ... ## $ participant.gender : chr "Male" "Female" "Female" "Male" ... ## $ participant.race : chr "Black or African American" "Black or African American" "Black or African American" "Black or African American" ... ## $ participant.ethnicity: chr "Dominican" "Dominican" "Dominican" "Unknown or not reported" ... ## $ participant.language : chr "English" "English" "English" "English" ... ## $ group.name : chr "14 month" "14 month" "14 month" "14 month" ... ## $ task1.name : chr "Novel toy: string with beads" "Novel toy: string with beads" "Novel toy: string with beads" "Novel toy: string with beads" ... ## $ task1.description : chr "Mother-child play with beads and string\nMother-child dyads played with beads and string." "Mother-child play with beads and string\nMother-child dyads played with beads and string." "Mother-child play with beads and string\nMother-child dyads played with beads and string." "Mother-child play with beads and string\nMother-child dyads played with beads and string." ... ## $ task2.name : chr "Mother-child free play" "Mother-child free play" "Mother-child free play" "Mother-child free play" ... ## $ task2.description : chr "Child alone play with standard set of toys\nMother-child dyads played with a set of toys for 8 minutes. Toys pr"| __truncated__ "Child alone play with standard set of toys\nMother-child dyads played with a set of toys for 8 minutes. Toys pr"| __truncated__ "Child alone play with standard set of toys\nMother-child dyads played with a set of toys for 8 minutes. Toys pr"| __truncated__ "Child alone play with standard set of toys\nMother-child dyads played with a set of toys for 8 minutes. Toys pr"| __truncated__ ... ## $ task3.name : chr "Numeracy book" "Numeracy book" "Numeracy book" "Numeracy book" ... ## $ task3.description : chr "Mother-child booksharing wordless number book\nMothers shared a wordless number book with their children." "Mother-child booksharing wordless number book\nMothers shared a wordless number book with their children." "Mother-child booksharing wordless number book\nMothers shared a wordless number book with their children." "Mother-child booksharing wordless number book\nMothers shared a wordless number book with their children." ... ## $ task4.name : chr "Emotion book" "Emotion book" "Emotion book" "Emotion book" ... ## $ task4.description : chr "Mother-child booksharing wordless book of baby faces expressing emotions\nMother-child dyads shared a wordless "| __truncated__ "Mother-child booksharing wordless book of baby faces expressing emotions\nMother-child dyads shared a wordless "| __truncated__ "Mother-child booksharing wordless book of baby faces expressing emotions\nMother-child dyads shared a wordless "| __truncated__ "Mother-child booksharing wordless book of baby faces expressing emotions\nMother-child dyads shared a wordless "| __truncated__ ... ## $ task5.name : chr "Familiar toy" "Familiar toy" "Familiar toy" "Familiar toy" ... ## $ task5.description : chr "Mother-child play interaction with child favorite toy\nMother-child dyads played with the child's favorite toy." "Mother-child play interaction with child favorite toy\nMother-child dyads played with the child's favorite toy." "Mother-child play interaction with child favorite toy\nMother-child dyads played with the child's favorite toy." "Mother-child play interaction with child favorite toy\nMother-child dyads played with the child's favorite toy." ... ## $ task6.name : chr "" "" "" "" ... ## $ task6.description : chr "" "" "" "" ... ## $ task7.name : chr "" "" "" "" ... ## $ task7.description : chr "" "" "" "" ... ## $ task8.name : chr "" "" "" "" ... ## $ task8.description : chr "" "" "" "" ... ## $ task9.name : chr "" "" "" "" ... ## $ task9.description : chr "" "" "" "" ... ## $ task10.name : chr "" "" "" "" ... ## $ task10.description : chr "" "" "" "" ... ## $ task11.name : chr "" "" "" "" ... ## $ task11.description : chr "" "" "" "" ... ## $ context.setting : chr "Home" "Home" "Home" "Home" ... ## $ context.state : chr "NY" "NY" "NY" "NY" ... ## $ vol_id : num 8 8 8 8 8 8 8 8 8 8 ...
- Clean and visualize
sex_race <- demog %>%
dplyr::select(., sex = participant.gender,
race = participant.race)
xtabs(formula = ~ sex + race, sex_race)
## race ## sex Asian Black or African American Unknown or not reported White ## 7 0 0 0 0 ## Female 0 112 341 4 209 ## Male 0 111 410 2 155
Other working examples
- Quality Assurance (QA) on PLAY
- Databrary weekly report
Example 2: NY Times data on COVID-19
- Data: https://github.com/nytimes/covid-19-data
- NY tracking page: https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
# Note the URL uses raw.githubusercontent.com
cv19 <- readr::read_csv("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv")
## Parsed with column specification: ## cols( ## date = col_date(format = ""), ## state = col_character(), ## fips = col_character(), ## cases = col_double(), ## deaths = col_double() ## )
str(cv19)
## tibble [1,499 × 5] (S3: spec_tbl_df/tbl_df/tbl/data.frame) ## $ date : Date[1:1499], format: "2020-01-21" "2020-01-22" ... ## $ state : chr [1:1499] "Washington" "Washington" "Washington" "Illinois" ... ## $ fips : chr [1:1499] "53" "53" "53" "17" ... ## $ cases : num [1:1499] 1 1 1 1 1 1 1 1 1 2 ... ## $ deaths: num [1:1499] 0 0 0 0 0 0 0 0 0 0 ... ## - attr(*, "spec")= ## .. cols( ## .. date = col_date(format = ""), ## .. state = col_character(), ## .. fips = col_character(), ## .. cases = col_double(), ## .. deaths = col_double() ## .. )
cv19 %>%
dplyr::filter(., state %in% c("Pennsylvania", "New York", "New Jersey", "Maryland", "Ohio", "West Virginia", "Delaware")) %>%
ggplot(.) +
aes(date, cases, color = state) +
geom_point() +
geom_line()
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This talk was produced on 2020-03-31 in RStudio using R Markdown. The code and materials used to generate the slides may be found at https://github.com/psu-psychology/psy-525-reproducible-research-2020. Information about the R Session that produced the code is as follows:
## R version 3.6.2 (2019-12-12) ## Platform: x86_64-apple-darwin15.6.0 (64-bit) ## Running under: macOS Mojave 10.14.6 ## ## Matrix products: default ## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib ## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib ## ## locale: ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.3 ## [5] readr_1.3.1 tidyr_1.0.2 tibble_3.0.0 ggplot2_3.3.0 ## [9] tidyverse_1.3.0 ## ## loaded via a namespace (and not attached): ## [1] tidyselect_1.0.0 xfun_0.12 haven_2.2.0 lattice_0.20-40 ## [5] colorspace_1.4-1 vctrs_0.2.4 generics_0.0.2 htmltools_0.4.0 ## [9] yaml_2.2.1 rlang_0.4.5 pillar_1.4.3 withr_2.1.2 ## [13] glue_1.3.2 DBI_1.1.0 dbplyr_1.4.2 modelr_0.1.6 ## [17] readxl_1.3.1 lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0 ## [21] cellranger_1.1.0 rvest_0.3.5 evaluate_0.14 labeling_0.3 ## [25] knitr_1.28 curl_4.3 fansi_0.4.1 highr_0.8 ## [29] broom_0.5.5 Rcpp_1.0.4 backports_1.1.5 scales_1.1.0 ## [33] jsonlite_1.6.1 farver_2.0.3 databraryapi_0.1.9 fs_1.3.2 ## [37] hms_0.5.3 digest_0.6.25 stringi_1.4.6 keyring_1.1.0 ## [41] grid_3.6.2 cli_2.0.2 tools_3.6.2 magrittr_1.5 ## [45] crayon_1.3.4 pkgconfig_2.0.3 ellipsis_0.3.0 xml2_1.2.5 ## [49] reprex_0.3.0 lubridate_1.7.4 assertthat_0.2.1 rmarkdown_2.1 ## [53] httr_1.4.1 rstudioapi_0.11 R6_2.4.1 nlme_3.1-145 ## [57] compiler_3.6.2