Pauline - 1 year ago 158
R Question

# How to save summary(lm) to a file?

I'm using R for a pharmacodynamic analysis and I'm fairly new to programming.

The thing is, I'm carrying out linear regression analysis and in the future I will perform more advanced methods. Because I'm performing a large number of analysis (and I'm too lazy to manually copy paste every time I run the script), I would like to save the summaries of the analysis to a file. I've tried different methods, but nothing seems to work.

What I'm looking for is the following as (preferably) a text file:

``````X_Y <- lm(X ~ Y)
sum1 <- summary(X_Y)

> sum1

Call:
lm(formula = AUC_cumulative ~ LVEF)

Residuals:
Min      1Q  Median      3Q     Max
-910.59 -434.11  -89.17  349.39 2836.81

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1496.4215   396.5186   3.774 0.000268 ***
LVEF           0.8243     7.3265   0.113 0.910640
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 619.9 on 104 degrees of freedom
(32 observations deleted due to missingness)
Multiple R-squared:  0.0001217, Adjusted R-squared:  -0.009493
F-statistic: 0.01266 on 1 and 104 DF,  p-value: 0.9106
``````

I've searched for methods to save summary functions to a .csv or .txt, but those files don't represent the data in a way I can understand it.

Things I've tried:

``````fileConn <- file("output.txt")
writeLines(sum1, fileConn)
close(fileConn)
``````

This returns:

``````Error in writeLines(sum1, fileConn) : invalid 'text' argument
``````

An attempt using the write.table command gave:

``````> write.table(Sum1, 'output.csv', sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE)
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ""summary.lm"" to a data.frame
``````

Using the write command:

``````> write(sum1, 'output.txt')
Error in cat(list(...), file, sep, fill, labels, append) : argument 1 (type 'list') cannot be handled by 'cat'
``````

Then I was getting closer with the following:

``````> write.table(sum1, 'output.csv', sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE)
``````

But this file did not have the same readable information as the printed summary

I hope someone can help, because this is way to advanced programming for me.

I think one option could be `sink()` which will output the results to a text file rather than the console. In the absence of your dataset I've used `cars` for an example:

``````sink("lm.txt")
summary(lm(cars\$speed ~ cars\$dist))
sink()  # returns output to the console
``````

`lm.txt` now looks like this:

``````Call:
lm(formula = cars\$speed ~ cars\$dist)

Residuals:
Min      1Q  Median      3Q     Max
-7.5293 -2.1550  0.3615  2.4377  6.4179

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept)  8.28391    0.87438   9.474 1.44e-12 ***
cars\$dist    0.16557    0.01749   9.464 1.49e-12 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 3.156 on 48 degrees of freedom
Multiple R-squared:  0.6511,    Adjusted R-squared:  0.6438
F-statistic: 89.57 on 1 and 48 DF,  p-value: 1.49e-12
``````

@Roland 's suggestion of `knitr` is a bit more involved, but could be worth it because you can knit input, text output, and figures in to one report or html file easily.

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