update readme and vignette

DESCRIPTION

@@ -39,6 +39,7 @@ Imports:
 Suggests: 
     bookdown,
     httptest,
+    kableExtra,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)

README.Rmd

@@ -1,5 +1,8 @@
 ---
 output: github_document
+editor_options: 
+  markdown: 
+    wrap: 72
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file. -->

vignettes/readepi.Rmd

@@ -1,17 +1,21 @@
 ---
 title: "readepi: Reading data from health information systems"
-output:
-  bookdown::html_vignette2:
-    fig_caption: yes
-    code_folding: show
-pkgdown:
-  as_is: false
+output: 
+  rmarkdown::html_vignette:
+    df_print: "kable"
 vignette: >
   %\VignetteIndexEntry{Reading data from health information systems}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 
+```{r, include = FALSE} 
+knitr::opts_chunk[["set"]](collapse = TRUE, comment = "#>", eval = FALSE,
+                           fig.width = 7L, fig.height = 7L, message = FALSE,
+                           fig.align = "center", warning = FALSE, dpi = 300L)
+row_id <- group_id <- NULL
+```
+
 # Overview 
 
 Health-related data in general, and epidemiological data in particular, are stored in files, relation database management systems (RDBMS), or health information systems (HIS). Each category includes numerous options, such as various file formats, RDBMS types, and HIS APIs. Import data from such repositories involve the usage of different format-specific functions or API-specific packages, which is an exhausting task for end users. 
@@ -20,18 +24,7 @@ The main objective of **{readepi}** package is to simplify the process of readin
 
 The current implementation of **{readepi}** provides a function for reading data from three common HIS: ([REDCap](https://www.project-redcap.org/), [DHIS2](https://dhis2.org/), and [Fingertips](https://fingertips.phe.org.uk/)), and RDBMS such as MS SQL, MySQL, and PostgreSQL. Other utility functions for processing and manipulating the imported data, such as row or column/row sub-setting, are also included in this package.
 
-
-```{r, include = FALSE}
-knitr::opts_chunk[["set"]](
-  collapse = TRUE,
-  comment = "#>",
-  message = FALSE,
-  warning = FALSE,
-  dpi = 300L
-)
-```
-
-```{r setup}
+```{r setup, eval=TRUE}
 # LOAD readepi
 library("readepi") # nolint
 ```
@@ -144,7 +137,7 @@ This credential (tab-delimited) file must contain the following columns:
 
 To see the structure of a toy credentials file used as a template in the **{readepi}** package, use the `show_example_file()` function as shown below.
 
-```{r eval=FALSE}
+```{r eval=TRUE}
 # DISPLAY THE STRUCTURE OF THE TEMPLATE CREDENTIALS FILE
 show_example_file()
 ```
@@ -153,7 +146,7 @@ show_example_file()
 
 This section contains various examples demonstrating how **{readepi}** imports data from databases. We assume that the credentials are stored in a file as explained above. Furthermore, these examples are based on a MySQL server that does not need the user to supply the `driver name`. 
 
-```{r eval=FALSE}
+```{r eval=TRUE}
 # DEFINING THE PATH TO THE TEMPLATE CREDENTIALS FILE
 credentials_file <- system.file("extdata", "test.ini", package = "readepi")
 ```
@@ -162,7 +155,7 @@ credentials_file <- system.file("extdata", "test.ini", package = "readepi")
 
 To display  list of tables from a database of interest, use:  
 
-```{r eval=FALSE}
+```{r eval=TRUE}
 show_tables(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
@@ -179,7 +172,7 @@ When importing data from **MS SQL, MySQL and PostgreSQL servers**, the user need
 - `driver_name`: the name of the MS driver (only for MS SQL servers).
 - `from`: the name of the table from which the data will be fetched. This can also be the SQL query to be used for fetching data from the system.
 
-```{r eval=FALSE}
+```{r eval=TRUE}
 # VISUALIZING THE FIRST 5 ROWS OF THE TABLE 'author'
 visualise_table(
   data_source      = "mysql-rfam-public.ebi.ac.uk",