Reading from databases

episodes/read-cases.Rmd

@@ -70,9 +70,33 @@ rio::import("/path_name/file_name.zip")
 
 ## Reading from databases
 
+The [DBI](https://dbi.r-dbi.org/) package serves as a versatile interface for interacting with database management systems (DBMS) across different back-ends or servers. It offers a uniform method for accessing and retrieving data from various database systems.
+
+
+The following code chunk demonstrates how to create a temporary SQLite database in memory, store the `case_data` dataframe as a table within it, and subsequently read from it:
+
+```{r,warning=FALSE,message=FALSE}
+library(DBI)
+library(RSQLite)
+# Create a temporary SQLite database in memory
+db_con <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")
+# Store the 'case_data' dataframe as a table named 'cases' in the SQLite database
+DBI::dbWriteTable(db_con, "cases", case_data)
+# Read data from the 'cases' table
+result <- DBI::dbReadTable(db_con, "cases")
+# Close the database connection
+DBI::dbDisconnect(db_con)
+# View the result
+base::print(utils::head(result))
+```
+
+This code first establishes a connection to an SQLite database created in memory using `dbConnect` function. Then, it writes the `case_data` dataframe into a table named 'cases' within the database using `dbWriteTable` function. Subsequently, it reads the data from the 'cases' table using `dbReadTable` function. Finally, it closes the database connection with `dbDisconnect` function.
+
+More examples about SQL databases and R can be found [here](https://datacarpentry.org/R-ecology-lesson/05-r-and-databases.html).
 
 ## Reading from HIS APIs
 
+Coming soon with {readepi}
 
 ::::::::::::::::::::::::::::::::::::: keypoints 
 - Use `{rio}, {io}, {readr}` and `{ImportExport}` to read data from individual files.

renv/profiles/lesson-requirements/renv.lock

@@ -177,6 +177,25 @@
       ],
       "Hash": "45f0398006e83a5b10b72a90663d8d8c"
     },
+    "RSQLite": {
+      "Package": "RSQLite",
+      "Version": "2.3.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "DBI",
+        "R",
+        "bit64",
+        "blob",
+        "cpp11",
+        "memoise",
+        "methods",
+        "pkgconfig",
+        "plogr",
+        "rlang"
+      ],
+      "Hash": "f5a75d57e0a3014a6ef537ac04a80fc6"
+    },
     "Rcpp": {
       "Package": "Rcpp",
       "Version": "1.0.12",
@@ -1431,6 +1450,13 @@
       ],
       "Hash": "01f28d4278f15c76cddbea05899c5d6f"
     },
+    "plogr": {
+      "Package": "plogr",
+      "Version": "0.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "09eb987710984fc2905c7129c7d85e65"
+    },
     "plyr": {
       "Package": "plyr",
       "Version": "1.8.9",