ruODK is a great package for interacting with ODK Central via R. Full details of how to use it are here.
To connect your ODK Central account to R, you’ll need to set up your passwords in the r.environ file so they’re not exposed in scripts. Your passwords will be stored in plain text on your r.environ so be cautious about which machines you work with this way. There’s also options to add you password manually each time, but we’ll assume you’re on a secure machine when you do this.
Run this command to open the r.environ file
usethis::edit_r_environ(scope = “user”)
Inside renviron file, be careful not to delete anything, but add these lines (substituting your ODK central URL and email address in the appropriate places.
ODKC_URL=“https://central.xxx.com”
ODKC_UN=“mustafa.orbach@xxx.com”
On a new line, add the password you use to log in to the system. Substitute xxx for your password
ODKC_PW=“xxx”
On a new line, add your password for decryption (if you use project level encryption). Substitute xxx for your password
ODKC_PP=“xxx”
Finally, save the r.environ file and restart R to load it in to R.
library(ruODK)
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.1 ✔ purrr 1.0.1
✔ tibble 3.2.1 ✔ dplyr 1.1.0
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.4 ✔ forcats 1.0.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()library(knitr)My servers are at central.lshtm.ac.uk. You need to change this to yours. Sys.getenv() pulls the passwords from the r.environ file in a way that is more secure than just adding to the script.
#connect to server
ruODK::ru_setup(
url = "https://central.lshtm.ac.uk",
un = Sys.getenv("ODKC_UN"),
pw = Sys.getenv("ODKC_PW"),
tz = "Europe/London",
verbose = TRUE
)<ruODK settings>
Default ODK Central Project ID:
Default ODK Central Form ID:
Default ODK Central URL: https://central.lshtm.ac.uk
Default ODK Central Username: chrissy.roberts@lshtm.ac.uk
Default ODK Central Password: run ruODK::get_default_pw() to show
Default ODK Central Passphrase: run ruODK::get_default_pp() to show
Default Time Zone: Europe/London
Default ODK Central Version: 1.1
Default HTTP GET retries: 3
Verbose messages: TRUE
Test ODK Central Project ID:
Test ODK Central Form ID:
Test ODK Central Form ID (ZIP tests):
Test ODK Central Form ID (Attachment tests):
Test ODK Central Form ID (Parsing tests):
Test ODK Central Form ID (WKT tests):
Test ODK Central URL:
Test ODK Central Username:
Test ODK Central Password: run ruODK::get_test_pw() to show
Test ODK Central Passphrase: run ruODK::get_test_pp() to show
Test ODK Central Version: 1.1 You’ll want to know the pid number, given here as id
kable(ruODK::project_list()[1:2,-9])| id | name | description | archived | key_id | created_at | updated_at | deleted_at | forms | app_users | datasets | last_submission |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 37 | 000_Scratch_Project__Chrissy | NA | FALSE | NA | 2021-06-10 12:43:13 | 2022-10-21 11:38:39 | NA | 10 | 1 | 0 | 2022-10-21 11:48:21 |
| 18 | 000_Scratch_project__Chrissy_Sham | NA | FALSE | 466 | 2021-01-27 19:27:38 | 2022-05-02 12:21:00 | NA | 19 | 2 | 0 | 2022-09-24 13:18:49 |
kable(ruODK::form_list(pid = 37))Warning: Automatic coercion from integer to character was deprecated in purrr 1.0.0.
ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
ℹ The deprecated feature was likely used in the ruODK package.
Please report the issue at <https://github.com/ropensci/ruODK/issues>.| name | fid | version | state | submissions | created_at | created_by_id | created_by | updated_at | published_at | last_submission | hash |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Eureka Study | Consent_Online | 1 | open | 2 | 2022-10-21 11:25:43 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:58:58 | 2022-10-21 11:58:58 | 2022-10-21 11:48:21 | cf910d1d93c659fe238c0a5d51d0e695 |
| geopoint_map | geopoint_map | open | 3 | 2022-07-21 11:00:49 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | 2022-07-21 13:09:42 | 2022-07-21 13:13:51 | f0b34efc38940a990396576f4643a008 | |
| geopoint_test | geopoint_test | open | 0 | 2022-06-16 12:19:45 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | 2022-06-16 12:20:55 | NA | dacea051c12f44b2241eb51b83157c4c | |
| Guinée questionnaire sur l’implémentation 22 Septembre 2022 V5 | Guinée questionnaire sur l’implémentation 22 Septembre 2022 V5 | open | 0 | 2022-09-22 11:42:24 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | NA | NA | 15bfaa3400d9aefe5cc72171abe2a035 | |
| indexed_repeat_with_internal_cascading_select | indexed_repeat_with_internal_cascading_select | open | 3 | 2022-06-09 08:35:34 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | 2022-06-09 08:36:48 | 2022-06-09 08:38:12 | e61dbda049489bcff50d5d21603a34f0 | |
| period.diary | period.diary | open | 0 | 2022-06-14 22:40:55 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | NA | NA | d4ce754877a34b1ab1c66f4c0ece4f03 | |
| prepopulate.example | prepopulate.example | 1 | open | 13 | 2021-06-10 13:26:35 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | 2021-06-10 13:27:20 | 2021-06-10 13:53:25 | 9518e5bc127b144b11fd469684b3ac80 |
| Social_Contact_Survey | socialcontact | 20192310 | open | 0 | 2022-07-20 11:36:55 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | NA | NA | 0a4bc27525b822f379a5522423107270 |
| V2_02_Test_de_grossesse | V2_02_Test_de_grossesse | 1907081903 | open | 0 | 2022-09-07 11:41:10 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | NA | NA | 25d707ef9c7a4ea257bec37627426f60 |
| Zim_Photos | Zim_Photos | open | 0 | 2022-09-09 10:48:36 | 19 | Chrissy h. Roberts (SA) | 2022-10-21 11:38:39 | 2022-09-09 10:48:54 | NA | 118c629659e9e59d18bcbdf248019d16 |
kable(ruODK::form_detail(pid = 37,fid = "geopoint_map"))| name | fid | version | state | submissions | created_at | created_by_id | created_by | updated_at | published_at | last_submission | hash |
|---|---|---|---|---|---|---|---|---|---|---|---|
| geopoint_map | geopoint_map | open | 3 | 2022-07-21T10:00:49.605Z | 19 | Chrissy h. Roberts (SA) | 2022-10-21T10:38:39.291Z | 2022-07-21T12:09:42.248Z | 2022-07-21T12:13:51.306Z | f0b34efc38940a990396576f4643a008 |
kable(ruODK::submission_list(pid = 37,fid = "geopoint_map"))| instance_id | submitter_id | device_id | created_at | updated_at | review_state | submitter_id_2 | submitter_type | submitter_display_name | submitter_created_at | submitter_updated_at | submitter_deleted_at |
|---|---|---|---|---|---|---|---|---|---|---|---|
| uuid:0a671884-27ed-4eb8-9102-310149899678 | 1094 | collect:v2m4bt3bE9ZfeMfi | 2022-07-21 13:13:51 | 2022-09-15 11:08:57 | NA | 1094 | field_key | chrissy | 2021-11-03 12:44:28 | NA | NA |
| uuid:9f6a1fd4-3394-4e5a-b013-e344272cdf70 | 1094 | collect:v2m4bt3bE9ZfeMfi | 2022-07-21 13:13:24 | NA | NA | 1094 | field_key | chrissy | 2021-11-03 12:44:28 | NA | NA |
| uuid:0a65e09e-18e5-4fd3-bbe8-4c57529ccc89 | 1094 | collect:v2m4bt3bE9ZfeMfi | 2022-07-21 13:11:19 | NA | NA | 1094 | field_key | chrissy | 2021-11-03 12:44:28 | NA | NA |
ruODK is very powerful and can get quite complicated. The most basic thing you need is a dataframe with your submissions. Here’s how to get one.
df<-ruODK::odata_submission_get(pid = "37",fid="geopoint_map")kable(df[,1:4])| geopoint_longitude | geopoint_latitude | geopoint_altitude | geopoint_accuracy |
|---|---|---|---|
| -0.054687 | 52.07809 | 0 | 0 |
| 152.504487 | -32.18187 | 0 | 0 |
| 152.526883 | -32.20085 | 0 | 0 |