fix-issue-16

epiverse-trace · Sep 10, 2023 · eb55928 · eb55928
1 parent a273574
commit eb55928
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Showing 3 changed files with 44 additions and 44 deletions.
diff --git a/README.Rmd b/README.Rmd
@@ -72,12 +72,12 @@ show_example_file()
 credentials_file <- system.file("extdata", "test.ini", package = "readepi")
 
 # READING FILE FROM A PROJECT IN A REDCap DATABASE
-data <- readepi(
+dat <- readepi(
   data_source      = "https://bbmc.ouhsc.edu/redcap/api/",
   credentials_file = credentials_file
 )
-project_data     <- data$data # accessing the actual data
-project_metadeta <- data$metadata # accessing the metadata associated with project
+project_data     <- dat$data # accessing the actual data
+project_metadeta <- dat$metadata # accessing the metadata associated with project
 
 # VIEWING THE LIST OF ALL TABLES IN A MySQL DATABASE
 show_tables(
@@ -95,15 +95,15 @@ visualise_table(
 )
 
 # READING ALL FILEDS AND RECORDS FROM A MySQL SERVER
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "author", # this is the table name
   driver_name      = ""
 )
 
 # READING DATA FROM DHIS2
-data <- readepi(
+dat <- readepi(
   data_source        = "https://play.dhis2.org/dev",
   credentials_file   = credentials_file,
   dataset            = "pBOMPrpg1QX",
@@ -114,7 +114,7 @@ data <- readepi(
 )
 
 # READING DATA FROM THE FINGERTIPS REPOSITORY
-data <- readepi(
+dat <- readepi(
   indicator_id        = 90362,
   area_type_id        = 202,
   parent_area_type_id = 6 # optional

diff --git a/README.md b/README.md
@@ -91,12 +91,12 @@ show_example_file()
 credentials_file <- system.file("extdata", "test.ini", package = "readepi")
 
 # READING FILE FROM A PROJECT IN A REDCap DATABASE
-data <- readepi(
+dat <- readepi(
   data_source      = "https://bbmc.ouhsc.edu/redcap/api/",
   credentials_file = credentials_file
 )
-project_data     <- data$data # accessing the actual data
-project_metadeta <- data$metadata # accessing the metadata associated with project
+project_data     <- dat$data # accessing the actual data
+project_metadeta <- dat$metadata # accessing the metadata associated with project
 
 # VIEWING THE LIST OF ALL TABLES IN A MySQL DATABASE
 show_tables(
@@ -114,15 +114,15 @@ visualise_table(
 )
 
 # READING ALL FILEDS AND RECORDS FROM A MySQL SERVER
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "author", # this is the table name
   driver_name      = ""
 )
 
 # READING DATA FROM DHIS2
-data <- readepi(
+dat <- readepi(
   data_source        = "https://play.dhis2.org/dev",
   credentials_file   = credentials_file,
   dataset            = "pBOMPrpg1QX",
@@ -133,7 +133,7 @@ data <- readepi(
 )
 
 # READING DATA FROM THE FINGERTIPS REPOSITORY
-data <- readepi(
+dat <- readepi(
   indicator_id        = 90362,
   area_type_id        = 202,
   parent_area_type_id = 6 # optional

diff --git a/vignettes/readepi.Rmd b/vignettes/readepi.Rmd
@@ -183,7 +183,7 @@ visualise_table(
 )
 
 # READING ALL FIELDS AND ALL RECORDS FROM ONE TABLE (`author`)
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "author", # this is the table name
@@ -192,7 +192,7 @@ data <- readepi(
 
 # READING SPECIFIED FIELDS AND ALL RECORDS FROM ONE TABLE
 fields <- "author_id,name,last_name,initials"
-data <- readepi(
+dat    <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "author", # this is the table name
@@ -202,7 +202,7 @@ data <- readepi(
 
 # READING SPECIFIED RECORDS AND ALL FIELDS FROM ONE TABLE
 records <- "1, 34, 15, 70, 118, 20"
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "author", # this is the table name
@@ -212,7 +212,7 @@ data <- readepi(
 )
 
 # READING SPECIFIED FIELDS AND RECORDS ONE THE TABLE
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "author", # this is the table name
@@ -224,7 +224,7 @@ data <- readepi(
 
 # READING DATA FROM SEVERAL TABLES
 table_names <- c("author", "family_author")
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = table_names, # this is the table name
@@ -239,7 +239,7 @@ fields <- c(
 # the first string in the field vector corresponds to the name of the
 # columns of interest from the first table specified in the `table_names`
 # argument and so on...
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = table_names, # this is the table name
@@ -256,7 +256,7 @@ records <- c(
 # interest from the first table specified in the `table_name` argument and so
 # on... when the id column is not the first column in a table,
 # use the `id_position`"
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = table_names, # this is the table name
@@ -267,7 +267,7 @@ data <- readepi(
 
 # READING DATA FROM SEVERAL TABLES AND SUBSETTING RECORDS AND FIELDS ACROSS
 # TABLES
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = table_names, # this is the table name
@@ -282,7 +282,7 @@ data <- readepi(
 
 ```{r eval=FALSE}
 # SELECT FEW COLUMNS FROM ONE TABLE AND LEFT JOIN WITH ANOTHER TABLE
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "select author.author_id, author.name,
@@ -292,31 +292,31 @@ data <- readepi(
 )
 
 # SELECT ALL DATA FROM THE author TABLE
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "select * from author",
   driver_name      = ""
 )
 
 # SELECT FEW COLUMNS FROM THE author TABLE
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "select author_id, name, last_name from author",
   driver_name      = ""
 )
 
 # SELECT FEW RECORDS FROM THE author TABLE
-data <- readepi(
+dat <- readepi(
   data_source = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   source = "select * from author where author_id in ('1','20','50')",
   driver_name = ""
 )
 
 # SELECT FEW RECORDS AND FIELDS FROM THE author TABLE
-data <- readepi(
+dat <- readepi(
   data_source      = "mysql-rfam-public.ebi.ac.uk",
   credentials_file = credentials_file,
   from             = "select author_id, name, last_name from author where
@@ -343,40 +343,40 @@ Both the data and its associated metadata will be returned after a successful im
 
 ```{r eval=FALSE}
 # READING ALL FIELDS AND RECORDS FROM A REDCap PROJECT
-data <- readepi(
+dat <- readepi(
   data_source      = "https://bbmc.ouhsc.edu/redcap/api/",
   credentials_file = credentials_file
 )
-project_data <- data[["data"]]
-project_metadeta <- data[["metadata"]]
+project_data <- dat[["data"]]
+project_metadeta <- dat[["metadata"]]
 
 # READING SPECIFIC FIELDS AND ALL RECORDS FROM THE PROJECT
 fields <- c("record_id", "name_first", "age", "bmi")
-data <- readepi(
+dat <- readepi(
   data_source      = "https://bbmc.ouhsc.edu/redcap/api/",
   credentials_file = credentials_file,
   fields           = fields
 )
 
 # READING SPECIFIC RECORDS AND ALL FIELDS FROM THE PROJECT
 records <- c("1", "3", "5")
-data <- readepi(
+dat <- readepi(
   data_source      = "https://bbmc.ouhsc.edu/redcap/api/",
   credentials_file = credentials_file,
   records          = records,
   id_col_name      = "record_id"
 )
 
 # READING SPECIFIC RECORDS AND FIELDS FROM THE PROJECT
-data <- readepi(
+dat <- readepi(
   data_source      = "https://bbmc.ouhsc.edu/redcap/api/",
   credentials_file = credentials_file,
   records          = records,
   fields           = fields,
   id_col_name      = "record_id"
 )
-project_data <- data[["data"]]
-project_metadeta <- data[["metadata"]]
+project_data <- dat[["data"]]
+project_metadeta <- dat[["metadata"]]
 ```
 
 
@@ -429,7 +429,7 @@ data_element_groups <- get_dhis2_attributes(
 )
 
 # READING THE DATASET ID `pBOMPrpg1QX`
-data <- readepi(
+dat <- readepi(
   data_source        = "https://play.dhis2.org/dev",
   credentials_file   = credentials_file,
   dataset            = "pBOMPrpg1QX",
@@ -440,7 +440,7 @@ data <- readepi(
 )
 
 # READING DATA FROM 2 DATASETS `pBOMPrpg1QX`
-data <- readepi(
+dat <- readepi(
   data_source        = "https://play.dhis2.org/dev",
   credentials_file   = credentials_file,
   dataset            = "pBOMPrpg1QX,BfMAe6Itzgt",
@@ -452,7 +452,7 @@ data <- readepi(
 
 # READING SPECIFIC DATA ELEMENTS FROM THE DATASET ID `pBOMPrpg1QX`
 data_elts <- c("FTRrcoaog83", "eY5ehpbEsB7", "Ix2HsbDMLea")
-data <- readepi(
+dat <- readepi(
   data_source        = "https://play.dhis2.org/dev",
   credentials_file   = credentials_file,
   dataset            = "pBOMPrpg1QX",
@@ -465,7 +465,7 @@ data <- readepi(
 )
 
 # READING SPECIFIC COLUMNS FROM A DATASET
-data <- readepi(
+dat <- readepi(
   data_source        = "https://play.dhis2.org/dev",
   credentials_file   = credentials_file,
   dataset            = "pBOMPrpg1QX,BfMAe6Itzgt",
@@ -509,37 +509,37 @@ head(metadata[["indicator_ids_names"]])
 head(metadata[["area_type"]])
 
 # IMPORTING DATA USING THE INDICATOR ID
-data <- readepi(
+dat <- readepi(
   indicator_id = 90362L,
   area_type_id = 202L
 )
 
 # IMPORTING DATA USING THE INDICATOR NAME
-data <- readepi(
+dat <- readepi(
   indicator_name = "Healthy life expectancy at birth",
   area_type_id   = 202L
 )
 
 # IMPORTING DATA USING THE DOMAIN NAME
-data <- readepi(
+dat <- readepi(
   domain_name  = "A. Overarching indicators",
   area_type_id = 202L
 )
 
-data <- readepi(
+dat <- readepi(
   indicator_name = "Healthy life expectancy at birth",
   area_type_id   = 202L,
   domain_name    = "A. Overarching indicators"
 )
 
 # IMPORTING DATA USING THE PROFILE ID
-data <- readepi(
+dat <- readepi(
   profile_id   = 19L,
   area_type_id = 202L
 )
 
 # IMPORTING DATA FROM SPECIFIC INDICATOR, DOMAIN, PROFILE, AREA TYPE
-data <- readepi(
+dat <- readepi(
   indicator_id        = 90362L,
   indicator_name      = "Healthy life expectancy at birth",
   area_type_id        = 202L,
@@ -555,7 +555,7 @@ data <- readepi(
 )
 
 # IMPORTING DATA AND SUBSETTING SPECIFIC RECORDS AND FIELDS
-data <- readepi(
+dat <- readepi(
   indicator_id = 90362L,
   area_type_id = 202L,
   fields       = c("IndicatorID", "AreaCode", "Age", "Value"),