# install.packages("devtools")
# devtools::install_github("epiverse-trace/readepi@develop", build_vignettes = TRUE)
library(readepi)

# READING DATA FROM JSON file
file <- system.file("extdata", "test.json", package = "readepi")
data <- readepi(file_path = file)

# IMPORTING DATA FROM THE SECOND EXCEL SHEET
file <- system.file("extdata", "test.xlsx", package = "readepi")
data <- readepi(file_path = file, which = "Sheet2")

# IMPORTING DATA FROM THE FIRST AND SECOND EXCEL SHEETS
file <- system.file("extdata", "test.xlsx", package = "readepi")
data <- readepi(file_path = file, which = c("Sheet2", "Sheet1"))

# READING ALL FILES IN A GIVEN DIRECTORY
dir_path <- system.file("extdata", package = "readepi")
data <- readepi(file_path = dir_path)

# READING ONLY '.txt' FILES
data <- readepi(file_path = dir_path, pattern = ".txt")

# READING '.txt' and '.xlsx' FILES
data <- readepi(file_path = dir_path, pattern = c(".txt", ".xlsx"))

# DISPLAY THE STRUCTURE OF THE CREDENTIALS FILE
show_example_file()

# DEFINING THE CREDENTIALS FILE
credentials_file <- system.file("extdata", "test.ini", package = "readepi")

# READING ALL FIELDS AND RECORDS FROM A REDCap PROJECT
data <- readepi(
  credentials_file = credentials_file,
  project_id = "SD_DATA"
)
project_data <- data$data
project_metadeta <- data$metadata

# DISPLAY THE LIST OF ALL TABLES IN A DATABASE HOSTED IN A MySQL SERVER
# for the test MySQL server, the driver name does not need to be specified
show_tables(
  credentials_file = credentials_file,
  project_id = "Rfam",
  driver_name = ""
)

# VISUALIZE THE FIRST 5 ROWS OF THE TABLE 'author'
visualise_table(
  credentials_file = credentials_file,
  source = "author", # this is the table name
  project_id = "Rfam", # this is the database name
  driver_name = ""
)

# READING ALL FIELDS AND ALL RECORDS FROM A DATABASE HOSTED BY A MS SQL SERVER
data <- readepi(
  credentials_file = credentials_file,
  project_id = "Rfam", # this is the database name
  driver_name = "",
  source = "author"
)

# READING DATA FROM DHIS2
data <- readepi(
  credentials_file = credentials_file,
  project_id = "DHIS2_DEMO",
  dataset = "pBOMPrpg1QX",
  organisation_unit = "DiszpKrYNg8",
  data_element_group = NULL,
  start_date = "2014",
  end_date = "2023"
)

# READING FROM FINFERTIPS
data <- readepi(
  indicator_id = 90362,
  area_type_id = 202,
  parent_area_type_id = 6 # optional
)

# OPEN THE VIGNETTE WITHIN RSTUDIO
vignette("readepi")

# OPEN THE VIGNETTE IN YOUR WEB BROWSER. 
browseVignettes("readepi")