Connect to the DHIS2 instance using Dhis2r$new()
In this vignette I used a Personal Access Token (PAT) as a more secure alternative to HTTP Basic Authentication, and should be your preferred choice when creating a new app/script etc.
dhis2_play_connection <- Dhis2r$new(base_url = "https://play.im.dhis2.org/dev",
username = "admin",
password = "district")dhis2_play_connection <- Dhis2r$new(base_url = "https://play.im.dhis2.org/stable-2-40-5",
api_token = "d2pat_2EkxmqdxtwAGDGe1hXzpWEixYdvHGRw71587176066")# [Ways of keeping your user credentials safe](https://solutions.posit.co/connections/db/best-practices/managing-credentials/)
dhis2_play_connection$get_user_info()
#> https://play.im.dhis2.org/dev/api/me
#> name email
#> "John Traore" "[email protected]"Get information about the account
Get access rights information about the account
Get all resources on which you can get metadata on.
dhis2_play_connection$get_metadata()
#> https://play.im.dhis2.org/dev/api/resources
#> # A tibble: 86 × 4
#> displayName singular plural href
#> <chr> <chr> <chr> <chr>
#> 1 Option Group Sets optionGroupSet optionGrou… http…
#> 2 Data Element Group Sets dataElementGroupSet dataElemen… http…
#> 3 Icons icon icons http…
#> 4 Data Element Operands dataElementOperand dataElemen… http…
#> 5 Categories category categories http…
#> 6 Category Option Group Sets categoryOptionGroupSet categoryOp… http…
#> 7 Dashboard Items dashboardItem dashboardI… http…
#> 8 Program Sections programSection programSec… http…
#> 9 Tracked Entity Instance Filters trackedEntityInstanceFilter trackedEnt… http…
#> 10 Validation Rule Groups validationRuleGroup validation… http…
#> # ℹ 76 more rowsGet metadata on Data Elements using the plural name
dataElements.
dhis2_play_connection$get_metadata(endpoint = "dataElements")
#> https://play.im.dhis2.org/dev/api/dataElements?fields=name%2Cid
#> # A tibble: 50 × 2
#> name id
#> <chr> <chr>
#> 1 Accute Flaccid Paralysis (Deaths < 5 yrs) FTRrcoaog83
#> 2 Acute Flaccid Paralysis (AFP) follow-up P3jJH5Tu5VC
#> 3 Acute Flaccid Paralysis (AFP) new FQ2o8UBlcrS
#> 4 Acute Flaccid Paralysis (AFP) referrals M62VHgYT2n0
#> 5 Additional medication WO8yRIZb7nb
#> 6 Additional notes related to facility uF1DLnZNlWe
#> 7 Admission Date eMyVanycQSC
#> 8 Age in years qrur9Dvnyt5
#> 9 Age of LLINs JuTpJ2Ywq5b
#> 10 Albendazole given at ANC (2nd trimester) hCVSHjcml9g
#> # ℹ 40 more rowsThe code above only returns it’s name and code/ID used on DHIS2, we shall use the code to get analytics.
You can get more fields beyond ID and name
NOTE All resources have different fields
dhis2_play_connection$get_metadata_fields(endpoint = "dataElements")
#> https://play.im.dhis2.org/dev/api/dataElements?fields=%3Aall&paging=true&pageSize=1
#> [1] "access" "aggregationLevels" "aggregationType"
#> [4] "attributeValues" "categoryCombo" "code"
#> [7] "created" "createdBy" "dataElementGroups"
#> [10] "dataSetElements" "dimensionItem" "dimensionItemType"
#> [13] "displayFormName" "displayName" "displayShortName"
#> [16] "domainType" "favorite" "favorites"
#> [19] "href" "id" "lastUpdated"
#> [22] "legendSets" "name" "optionSetValue"
#> [25] "sharing" "shortName" "translations"
#> [28] "url" "user" "valueType"
#> [31] "zeroIsSignificant" dhis2_play_connection$get_metadata_fields(endpoint = "organisationUnits")
#> https://play.im.dhis2.org/dev/api/organisationUnits?fields=%3Aall&paging=true&pageSize=1
#> [1] "access" "ancestors" "attributeValues"
#> [4] "children" "code" "created"
#> [7] "dataSets" "dimensionItem" "dimensionItemType"
#> [10] "displayFormName" "displayName" "displayShortName"
#> [13] "favorite" "favorites" "href"
#> [16] "id" "lastUpdated" "leaf"
#> [19] "legendSets" "level" "name"
#> [22] "openingDate" "organisationUnitGroups" "parent"
#> [25] "path" "programs" "sharing"
#> [28] "shortName" "translations" "users" dhis2_play_connection$get_metadata_fields(endpoint = "indicators")
#> https://play.im.dhis2.org/dev/api/indicators?fields=%3Aall&paging=true&pageSize=1
#> [1] "access" "annualized"
#> [3] "attributeValues" "code"
#> [5] "created" "createdBy"
#> [7] "dataSets" "denominator"
#> [9] "denominatorDescription" "description"
#> [11] "dimensionItem" "dimensionItemType"
#> [13] "displayDenominatorDescription" "displayDescription"
#> [15] "displayFormName" "displayName"
#> [17] "displayNumeratorDescription" "displayShortName"
#> [19] "favorite" "favorites"
#> [21] "href" "id"
#> [23] "indicatorGroups" "indicatorType"
#> [25] "lastUpdated" "legendSets"
#> [27] "name" "numerator"
#> [29] "numeratorDescription" "sharing"
#> [31] "shortName" "translations"
#> [33] "url" "user"dataElements
dhis2_play_connection$get_metadata(endpoint = "dataElements", fields = c("name","id","aggregationType"))
#> https://play.im.dhis2.org/dev/api/dataElements?fields=name%2Cid%2CaggregationType
#> # A tibble: 50 × 3
#> name aggregationType id
#> <chr> <chr> <chr>
#> 1 Accute Flaccid Paralysis (Deaths < 5 yrs) SUM FTRrcoaog83
#> 2 Acute Flaccid Paralysis (AFP) follow-up SUM P3jJH5Tu5VC
#> 3 Acute Flaccid Paralysis (AFP) new SUM FQ2o8UBlcrS
#> 4 Acute Flaccid Paralysis (AFP) referrals SUM M62VHgYT2n0
#> 5 Additional medication NONE WO8yRIZb7nb
#> 6 Additional notes related to facility SUM uF1DLnZNlWe
#> 7 Admission Date AVERAGE eMyVanycQSC
#> 8 Age in years AVERAGE qrur9Dvnyt5
#> 9 Age of LLINs SUM JuTpJ2Ywq5b
#> 10 Albendazole given at ANC (2nd trimester) SUM hCVSHjcml9g
#> # ℹ 40 more rowsorganisationUnits
dhis2_play_connection$get_metadata(endpoint = "organisationUnits",
fields = c("name","id", "level"))
#> https://play.im.dhis2.org/dev/api/organisationUnits?fields=name%2Cid%2Clevel
#> # A tibble: 50 × 3
#> name id level
#> <chr> <chr> <int>
#> 1 Adonkia CHP Rp268JB6Ne4 4
#> 2 Afro Arab Clinic cDw53Ej8rju 4
#> 3 Agape CHP GvFqTavdpGE 4
#> 4 Ahamadyya Mission Cl plnHVbJR6p4 4
#> 5 Ahmadiyya Muslim Hospital BV4IomHvri4 4
#> 6 Air Port Centre, Lungi qjboFI0irVu 4
#> 7 Alkalia CHP dWOAzMcK2Wt 4
#> 8 Allen Town Health Post kbGqmM6ZWWV 4
#> 9 Approved School CHP eoYV2p74eVz 4
#> 10 Arab Clinic nq7F0t1Pz6t 4
#> # ℹ 40 more rowsYou can use ":all" in the fields to get all fields of
metadata associated with a resources
periodTypes
dhis2_play_connection$get_metadata(endpoint = "periodTypes", fields = ":all")
#> https://play.im.dhis2.org/dev/api/periodTypes?fields=%3Aall
#> # A tibble: 20 × 4
#> name isoDuration isoFormat frequencyOrder
#> <chr> <chr> <chr> <int>
#> 1 Daily P1D yyyyMMdd 1
#> 2 Weekly P7D yyyyWn 7
#> 3 WeeklyWednesday P7D yyyyWedWn 7
#> 4 WeeklyThursday P7D yyyyThuWn 7
#> 5 WeeklySaturday P7D yyyySatWn 7
#> 6 WeeklySunday P7D yyyySunWn 7
#> 7 BiWeekly P14D yyyyBiWn 14
#> 8 Monthly P1M yyyyMM 30
#> 9 BiMonthly P2M yyyyMMB 61
#> 10 Quarterly P3M yyyyQn 91
#> 11 QuarterlyNov P3M yyyyNovQn 91
#> 12 SixMonthly P6M yyyySn 182
#> 13 SixMonthlyApril P6M yyyyAprilSn 182
#> 14 SixMonthlyNov P6M yyyyNovSn 182
#> 15 Yearly P1Y yyyy 365
#> 16 FinancialApril P1Y yyyyApril 365
#> 17 FinancialJuly P1Y yyyyJuly 365
#> 18 FinancialSep P1Y yyyySep 365
#> 19 FinancialOct P1Y yyyyOct 365
#> 20 FinancialNov P1Y yyyyNov 365dhis2_play_connection$get_metadata(endpoint = "indicators")
#> https://play.im.dhis2.org/dev/api/indicators?fields=name%2Cid
#> # A tibble: 50 × 2
#> name id
#> <chr> <chr>
#> 1 ANC 1-3 Dropout Rate ReUHfIn0pTQ
#> 2 ANC 1 Coverage Uvn6LCg7dVU
#> 3 ANC 2 Coverage OdiHJayrsKo
#> 4 ANC 3 Coverage sB79w2hiLp8
#> 5 ANC => 4 Coverage AUqdhY4mpvp
#> 6 ANC IPT 1 Coverage dwEq7wi6nXV
#> 7 ANC IPT 2 Coverage c8fABiNpT0B
#> 8 ANC LLITN coverage Tt5TAvdfdVK
#> 9 ANC TT2 coverage puykO1tbcdi
#> 10 ANC visits per clinical professional Lzg9LtG1xg3
#> # ℹ 40 more rowsdhis2_play_connection$get_analytics(analytic = "s46m5MS0hxu",
org_unit = c("O6uvpzGd5pu", "fdc6uOvgoji"),
period = "202101",
output_scheme = "NAME")
#> https://play.im.dhis2.org/dev/api/analytics?dimension=dx%3As46m5MS0hxu&dimension=ou%3AO6uvpzGd5pu%3Bfdc6uOvgoji&dimension=pe%3A202101&outputIdScheme=NAME
#> # A tibble: 2 × 4
#> analytic org_unit period value
#> <fct> <fct> <chr> <dbl>
#> 1 BCG doses given Bombali January 2021 608
#> 2 BCG doses given Bo January 2021 710dhis2_play_connection$get_analytics(analytic = "FTRrcoaog83", #Accute Flaccid Paralysis (Deaths < 5 yrs)
org_unit = c("ImspTQPwCqd"), #Sierra Leone (National level)
period = "LAST_12_MONTHS",
output_scheme = "NAME")
#> https://play.im.dhis2.org/dev/api/analytics?dimension=dx%3AFTRrcoaog83&dimension=ou%3AImspTQPwCqd&dimension=pe%3ALAST_12_MONTHS&outputIdScheme=NAME
#> # A tibble: 2 × 4
#> analytic org_unit period value
#> <fct> <fct> <chr> <dbl>
#> 1 Accute Flaccid Paralysis (Deaths < 5 yrs) Sierra Leone February 2024 34
#> 2 Accute Flaccid Paralysis (Deaths < 5 yrs) Sierra Leone January 2024 12