edbRead.RODBC_MySQL: Read all or part of a table in a MySQL database (referenced...
In easyrodbcmysql: Simple Database Interface for MySQL

Description Usage Arguments Value Author(s) See Also Examples

Read all or part of a table in a MySQL database (referenced by 'edb').

## S3 method for class 'RODBC_MySQL'
edbRead(edb, tableName, sRow = NULL, sCol = NULL, 


    sRowOp = c("AND", "OR")[1], formatCol = NULL, distinct = FALSE, 


    orderBy = NULL, testFiles = TRUE, verbose = FALSE, 


    ...)

`edb`	An object of class 'edb', such as returned by `edb`.
`tableName`	Single character string. Name of the table to read in 'edb'.
`sRow`	A list of named items. List of contrains/criterion to be applied on `tableName` to retrieve a subset of rows. Each item in `rowC` must be named after the columns on which the constrain apply. The (vector of) value(s) of each items are the possible values that can be retrieved. Values can be character or numeric. If NULL (the default), all values are returned.
`sCol`	Either (1) a vector of character strings with the name of the columns to retrieve or (2) a vector of logical of the same length as the number of columns or (3) a vector of indexes / integers giving the indexes of the column to retrieve. If negative, then it indicates the indexes of the column to leave out.
`sRowOp`	A single character string. Operator to be used to combine multiple constrains in sRow. Possible values are "OR" or "AND". Default value is "AND".
`formatCol`	If not NULL, a named list of functions to be applied to certain columns after the data has been extracted from the database. The name of each list item gives the column to process, and the value of each item gives the function that must be applied. For instance formatCol = list("DATE"=as.Date) will apply the function as.Date to the column "DATE".
`distinct`	Single logical. If TRUE, unique values in the result table will be returned, using the `SELECT DISTINCT` SQL statement. This is equivalent to applying `unique` to the data.frame returned by the function, except that the action is performed inside the database (not in R).
`orderBy`	Vector of character strings, or NULL (the default). If non NULL, vector of column names that must be used to sort the result table. Column names may be followed by a space and 'DESC' if the column must be sorted in a descending order ('ASC', ascending, is the default). This operation is performed in the database with SQL ORDER BY statement and is equivalent to ordering the data in R with `order`. You may write the column names between “ delimiters if they contain spaces.
`testFiles`	Single logical. Should the function test for the presence (file.exist()) of the needed files in the folder before trying to fetch information from the database?
`verbose`	Single logical. If TRUE, information on what is done are output on screen.
`...`	Additional parameters to be passed to `dbGetQuery`.

The function returns the requested table.

Julien MOEYS <Julien.Moeys@mark.slu.se>

edb, edbWrite.RODBC_MySQL,

edbNames.RODBC_MySQL,

edbColnames.RODBC_MySQL.

library( "easyrodbcmysql" ) 











testMySQL <- FALSE # Set to TRUE to run some tests


                   # after modifying the edb() part below 


                   # with your own database setting











### Windows only:


if( (Sys.info()[[ "sysname" ]] == "Windows") & testMySQL ){ 


    


    ### Describe the database (NB: this is not a connection)


    myDb <- edb( 


        dbType       = "RODBC_MySQL", 


        dbSourceName = "nameOfODBCSource", # or any name you like


        dbName       = "nameOfDatabase", 


        dbLogin      = "yourUserName", 


        dbPwd        = "yourPassword", 


        dbHost       = "127.0.0.1", 


        dbPort       = 3306 


    )   #    


    


    


    


    ### Register the data source in ODBC 


    edbDataSource( myDb, verbose = TRUE ) 


    


    


    


    ### Use the database:


    


    ## Read data in a table in the database


    


    # Retrieve a table (data.frame style subsetting):


    myDb[ "WRB_SOIL_GROUP" ] 


    


    # Same operation, but with edbRead()


    edbRead( edb = myDb, tableName = "WRB_SOIL_GROUP" ) 


    


    # Retrieve part of a table (with row constrains)


    myDb[ "WRB_SOIL_GROUP", list("ABBREV" = c("AC","CR","PL")) ] 


    


    # Same operation, but with edbRead()


    edbRead( 


        edb       = myDb, 


        tableName = "WRB_SOIL_GROUP", 


        sRow      = list("ABBREV" = c("AC","CR","PL")) 


    )   


    


    # Retrieve part of a table (row constrains + select only some columns)


    myDb[ 


        "WRB_SOIL_GROUP", 


        list("ABBREV" = c("AC","CR","PL")), 


        c("ID_WRB_SOIL_GROUP","NAME") 


    ]   


    


    # Same operation, but with edbRead()


    edbRead( 


        edb       = myDb, 


        tableName = "WRB_SOIL_GROUP", 


        sRow      = list("ABBREV" = c("AC","CR","PL")), 


        sCol      = c("ID_WRB_SOIL_GROUP","NAME") 


    )   


    


    # Use some SQL constrains


    myDb[ 


        "WRB_SOIL_GROUP", 


        list( 


            "ABBREV" = c("AC","AB","AL","AN","AT"), 


            "SQL" = "NAME LIKE 'Al%'"


        )   


    ]   


    


    # NB: the different elements in the list are separated by 


    # "AND" statement


    


    # Multiple row constrains, alternative (constrain 1 OR constrin 2) 


    myDb[ 


        "WRB_SOIL_GROUP", 


        list( 


            "ABBREV" = c("AC","AB"), 


            "ID_WRB_SOIL_GROUP" = 25:30


        ),  


        sRowOp = "OR" 


    ]   


    


    


    


    # Check the dimension of a table


    # - Number of columns:


    edbNCol( edb = myDb, tableName = "WRB_SOIL_GROUP" ) 


    # - Number of rows:


    edbNRow( edb = myDb, tableName = "WRB_SOIL_GROUP" ) 


    # - Number of rows, with constrains: 


    edbNRow( edb = myDb, tableName = "WRB_SOIL_GROUP", 


        sRow = list("ABBREV" = c("AC","AB")) ) 


    # - Dimensions:


    edbDim( edb = myDb, tableName = "WRB_SOIL_GROUP" ) 


    


    


    


    # More ways to select columns:


    


    # - Indexes


    myDb[ "WRB_SOIL_GROUP", sCol = 2:3 ] 


    


    # - Logicals


    myDb[ "WRB_SOIL_GROUP", sCol = c(FALSE,TRUE,TRUE) ] 


    


    


    # It may be useful to transform some columns 'on-the-fly', after 


    # they have been read from the database. In the example below we 


    # have some dates and times values, as well as some boolean stored 


    # as integers (seconds or days since 1970-01-01 or 0/1 values, 


    # respectively). We want to transform them into dates or boolean.


    


    myDb[ "MISCFORMAT" ]


    # NB: although Yes/No format, the last column is read as integer too...


    


    # So date variables stored as integers have to be converted.


    # The code below show how to do that.


    


    # Function to convert POSIX integer "seconds from 1970-01-01" into 


    # R POSIXct date format.


    formatDT <- function( x, tz = "GMT" ){ 


        res <- ISOdatetime( year = 1970, month = 1, day = 1, 


            hour = 0, min = 0, sec = 0, tz = tz ) 


        res <- res + x 


        return( res ) } 


            


    


    # Function to convert integer "days from 1970-01-01" into 


    # R Date format.


    formatD <- function( x, tz = "GMT" ){ 


        res <- ISOdate( year = 1970, month = 1, day = 1, tz = tz ) 


        res <- res + (x * 24 * 60 * 60 ) 


        res <- as.Date( res ) 


        return( res ) } 


    


    # Now we can convert the columns on-the-fly


    myDb[ "MISCFORMAT", formatCol = list( "DAT_TIM_SEC" = formatDT, 


        "DAT_DAY" = formatD, "TEST_BOOL" = as.logical ) ] 


    


    


    


    # SQL SELECT DISTINCT, equivalent of R unique().


    # To select unique / distinct values in a (group of) columns, 


    # set 'distinct' to TRUE:


    myDb[ "PROFILE", sCol = "COMMENTS", distinct = TRUE ] 


    


    


    


    # SQL ORDER BY, equivalent of R order(). 


    # To sort the table according to some columns (ascending or 


    # descending), use 'orderBy':


    myDb[ "WRB_SOIL_GROUP", orderBy = "ABBREV DESC" ] 


    


    


    


    ### Un-register the data source in ODBC (windows only)


    edbDataSource( myDb, trash = TRUE ) 


}   #