Understanding RODBC and Reading Excel Files with R

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Introduction

In this article, we will delve into the world of data extraction using R’s ODBC (Open Database Connectivity) driver, RODBC. Specifically, we will explore how to read .xls files with RODBC without relying on colnames, which often causes issues when dealing with non-standard column names in Excel spreadsheets.

Background

RODBC is an R extension that provides a standardized interface for accessing relational databases using the ODBC API. While it’s primarily designed for SQL databases like MySQL, PostgreSQL, and Oracle, it also supports reading Excel files (.xls) through the Microsoft Access database engine (also known as the “Microsoft Jet” engine).

The Problem with Colnames

When using RODBC to read an .xls file, the colnames argument in the sqlFetch() function is used to specify whether the returned data frame should have column names. However, when colnames=FALSE, RODBC defaults to assigning the first row of the Excel sheet as the column names. This can lead to issues if the data is not in a standard format.

A Closer Look at sqlFetch

To understand why this happens, let’s take a closer look at the sqlFetch() function in the source code. Specifically, we’ll examine how it handles the case when there are no explicit column names specified.

## Step 1: Check if SQL table has column name sequence
if (is.null(as.character(sqlGetColNames()))) {
    # If no column name sequence is found,
    # assume first row contains field names
}

As shown above, the sqlGetColNames() function checks if a SQL table has an explicit column name sequence. If it doesn’t, RODBC assumes that the first row of the Excel sheet contains the field names.

The Solution: Using strsplit

One possible solution to this issue is to use the strsplit() function to extract the field names from the first row of the data frame. Here’s an updated version of the read.info.default function:

## Step 1: Connect to Excel file using ODBC
fc <- odbcConnectExcel(file)

## Step 2: Fetch data from Excel sheet without column names
tryCatch({
    x <- sqlFetch(fc,
                  sqtable=sheet,
                  as.is=TRUE,
                  rownames=FALSE)
}, 
error = function(e) {stop(e)},
finally=close(fc))

## Step 3: Extract field names from first row
field_names <- strsplit(as.character(x[1,]), ",")[[1]]

## Step 4: Assign field names to data frame
colnames(x) <- field_names

return(x)

In this updated version, we use strsplit() to extract the field names from the first row of the data frame. We then assign these field names to the x data frame using the colnames() function.

Alternative Solution: Using gdata Package

Another possible solution is to use the gdata package, which provides a Perl-based interface for reading Excel files. This package can be used with R without relying on ODBC or Perl.

To use gdata, you’ll need to install it first using the following command:

install.packages("gdata")

Then, you can use the readxl package from the same developers as gdata, which is a faster and more convenient way of reading Excel files with R.

Here’s an example code snippet that demonstrates how to read an .xls file using the gdata package:

library(gdata)

# Read Excel file
file <- "example.xls"
df <- xlsReadWrite::readXL(file, sheet = 1)

# Extract field names from first row
field_names <- colnames(df)[1]

# Assign field names to data frame
colnames(df) <- field_names

return(df)

Note that the gdata package provides a more convenient and efficient way of reading Excel files than RODBC.

Conclusion

In this article, we’ve explored how to read .xls files with RODBC without relying on colnames. We’ve examined the source code of sqlFetch() and discovered why RODBC defaults to assigning the first row as column names when colnames=FALSE. We’ve also provided a solution using strsplit(), which extracts field names from the first row of the data frame.

Additionally, we’ve introduced an alternative solution using the gdata package, which provides a Perl-based interface for reading Excel files. This package can be used with R without relying on ODBC or Perl.

Whether you choose to use RODBC or gdata, this article has provided you with the knowledge and tools necessary to read .xls files with ease.

Last modified on 2023-06-21