Fix/after/merging

episodes/clean-data.Rmd

@@ -353,7 +353,7 @@
 
 :::::::::
 
 ::::::::::::::::: checkpoint
 
 At this point, we removed a number of columns and rows. Compare the dimensions of `raw_ebola_data` and `sim_ebola_data`.
 
@@ -570,7 +570,8 @@
   dplyr::select(
     study_id,
     date_of_birth,
-    age_in_years
+    age_in_years,
+    remainder_months
   )
 ```
 
@@ -693,7 +694,6 @@
     target_columns = "case_id",
     range = c(1, 15000)
   ) %>%
-  cleanepi::convert_to_numeric(target_columns = "age") %>%
   # epidemiological operations ------------------------------
   cleanepi::standardize_dates(
     target_columns = c("date_onset", "date_sample")
@@ -707,7 +707,8 @@
     span_unit = "days",
     span_column_name = "reporting_delay"
   ) %>%
-  cleanepi::clean_using_dictionary(dictionary = test_dict)
+  cleanepi::clean_using_dictionary(dictionary = test_dict) %>%
+  cleanepi::convert_to_numeric(target_columns = "age")
 ```
 
 ```{r, echo=FALSE, eval=TRUE}

episodes/read-cases.Rmd

@@ -316,16 +316,33 @@ dhis2_login <- readepi::login(
   user_name = "admin",
   password = "district"
 )
+```
+
+::::::: caution
 
+Avoid publishing your USER NAME and PASSWORD. You could use `{rstudioapi}`:
+
+```{r, eval = FALSE}
+dhis2_login <- readepi::login(
+  type = "dhis2",
+  from = "https://play.im.dhis2.org/stable-2-41-8-1",
+  user_name = rstudioapi::askForPassword("Database username"),
+  password = rstudioapi::askForPassword("Database password")
+)
+```
+
+Your can read further from this blogpost on [How to Avoid Publishing Credentials in Your Code](https://rviews.rstudio.com/2019/03/21/how-to-avoid-publishing-credentials-in-your-code/)
+
+:::::::
+
+```{r}
 # get the names and IDs of the programs
 programs <- readepi::get_programs(login = dhis2_login)
 
 # print tables
 tibble::as_tibble(programs)
 ```
 
-
-
 ```{r}
 # get the names and IDs of the organisation units
 org_units <- readepi::get_organisation_units(login = dhis2_login)
@@ -337,58 +354,68 @@ tibble::as_tibble(org_units)
 After retrieving organization units and program names from the DHIS2 database, we can import data using either names or coded IDs, as demonstrated in the code chunk below
 
 ```{r,message=FALSE}
-data <- readepi::read_dhis2(
+# import data from DHIS2 using names
+data_name <- readepi::read_dhis2(
   login = dhis2_login,
-  org_unit = "Keneba",
-  program = "Child Registration & Treatment "
+  org_unit = "Bucksal Clinic",
+  program = "Child Programme"
 )
 
-tibble::as_tibble(data)
+tibble::as_tibble(data_name)
 ```
 
 ```{r,eval=TRUE,message=FALSE}
-# import data from DHIS2 using names
 # import data from DHIS2 using IDs
-data <- readepi::read_dhis2(
+data_id <- readepi::read_dhis2(
   login = dhis2_login,
-  org_unit = "GcLhRNAFppR",
-  program = "E5IUQuHg3Mg"
+  org_unit = "vRC0stJ5y9Q",
+  program = "IpHINAT79UW"
 )
 
-tibble::as_tibble(data)
+identical(data_id, data_name)
 ```
 
 Note that not all organization units are registered for a specific program. To find which organization units are running a particular program, use the `get_program_org_units()` function as shown below:
 
 ```{r}
-# get the list of organisation units that run the program "E5IUQuHg3Mg"
+# get the list of organisation units that run the program "IpHINAT79UW"
 target_org_units <- readepi::get_program_org_units(
   login = dhis2_login,
-  program = "E5IUQuHg3Mg",
+  program = "IpHINAT79UW",
   org_units = org_units
 )
 
 tibble::as_tibble(target_org_units)
 ```
 
-:::::::::::::::: callout
+<!-- :::::::::::::::: callout
 
 Note: This example uses a DHIS2 system provided by the Ministry of Health of The Gambia for testing and development purposes. In practice, you should customize the parameters for your own DHIS2 instance. 
 
-::::::::::::::::
-
+:::::::::::::::: -->
 
 :::::::::::::::::::::: challenge
 
-### Reading from your DHIS2 sever
+### Reading from a DHIS2 sever
+
+<!-- The DHIS2 organization provides demo servers for development and testing. One of these is called **stable-2-41-8-1**, from many other available in a list of [DHIS2 Demo Instances](https://im.dhis2.org/public/instances), and accessible with username `"admin"` and password `"district"`.  -->
+
+Test `{readepi}` by accessing to a DHIS2 server with your credentials.
+
+Do the following:
+
+- Log into a different server,
+- List all available programs and organization units, 
+- Read data from one of these programs,
+- Optional: Reproduce one descriptive figure.
+
+::::::::: hint
+
+Try using `rstudioapi::askForPassword()` for `user_name` and `password`.
 
-If you have your credentials, try accessing to a DHIS2 server.
+If you get errors, please fill an issue in the [`readepi` GitHub repository](https://github.com/epiverse-trace/readepi/issues/).
 
-<!--
-The DHIS2 organization provides demo servers for development and testing. One of
-these is called **stable-242-4**, available at the link
-("https://play.im.dhis2.org/stable-2-41-8-1"), and accessible with username "admin" and password "district". Log into this server, list all available programs and organization units, and read data from one of these programs.
--->
+:::::::::
 
 ::::::::::::::::::::::