export R output to .txt file

[Soulhog]

Hi!

I am somewhat new to R, and I don't know how to export the results of a statistical test that I conducted to a text file. I would like to save these results on my desktop so I don't have to go back and run the tests all over again to see the results! This is what my console looks like:

> summary(AtTotal_Model)

Call:
lm(formula = Total_amino_acids ~ Genotype * Timepoint, data = AtAAdata)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.7262 -1.3018 -0.1063  0.6585  3.5841 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)    
(Intercept)             18.2507     1.1737  15.549 2.57e-09 ***
GenotypeWT              -0.7114     1.6599  -0.429   0.6758    
TimepointEN              0.4763     1.6599   0.287   0.7790    
TimepointXN              3.0512     1.6599   1.838   0.0909 .  
GenotypeWT:TimepointEN  -5.4021     2.3474  -2.301   0.0401 *  
GenotypeWT:TimepointXN  -6.8777     2.3474  -2.930   0.0126 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 2.033 on 12 degrees of freedom
Multiple R-squared:  0.7636,	Adjusted R-squared:  0.665 
F-statistic: 7.751 on 5 and 12 DF,  p-value: 0.001825

> TukeyHSD(aov(AtTotal_Model))
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = AtTotal_Model)

$Genotype
            diff      lwr       upr     p adj
WT-pgm -4.804637 -6.89268 -2.716595 0.0003024

$Timepoint
            diff       lwr       upr     p adj
EN-ED -2.2247282 -5.356057 0.9066003 0.1822890
XN-ED -0.3876198 -3.518948 2.7437088 0.9419387
XN-EN  1.8371084 -1.294220 4.9684370 0.2973240

$`Genotype:Timepoint`
                    diff        lwr         upr     p adj
WT:ED-pgm:ED  -0.7113773  -6.286825  4.86407077 0.9976703
pgm:EN-pgm:ED  0.4763289  -5.099119  6.05177699 0.9996611
WT:EN-pgm:ED  -5.6371626 -11.212611 -0.06171456 0.0469793
pgm:XN-pgm:ED  3.0512134  -2.524235  8.62666144 0.4792415
WT:XN-pgm:ED  -4.5378302 -10.113278  1.03761788 0.1386769
pgm:EN-WT:ED   1.1877062  -4.387742  6.76315427 0.9762591
WT:EN-WT:ED   -4.9257853 -10.501233  0.64966271 0.0954621
pgm:XN-WT:ED   3.7625907  -1.812857  9.33803871 0.2780518
WT:XN-WT:ED   -3.8264529  -9.401901  1.74899516 0.2634488
WT:EN-pgm:EN  -6.1134916 -11.688940 -0.53804351 0.0289673
pgm:XN-pgm:EN  2.5748844  -3.000564  8.15033249 0.6414669
WT:XN-pgm:EN  -5.0141591 -10.589607  0.56128893 0.0875370
pgm:XN-WT:EN   8.6883760   3.112928 14.26382405 0.0022231
WT:XN-WT:EN    1.0993324  -4.476116  6.67478049 0.9829996
WT:XN-pgm:XN  -7.5890436 -13.164492 -2.01359551 0.0065118

I just want to export this from the R console to a text file!

Thanks,

Erik

[Soulhog]

Wow, that copy and paste went horribly wrong..... sorry about that haha

[siddharthprabhu]

You can use the sink() function in R. It will divert all R console output between the first and second call of sink() to a file that you specify. Here is an example using a linear model fitted to the iris data set.

fit <- lm(Petal.Length ~ Sepal.Length, data = iris)

sink(file = "lm_output.txt")
summary(fit)
sink(file = NULL)

This will create a file lm_output.txt in your working directory containing the output of summary(fit).

[francisko.rezende]

Hi Erik!

Have you considered using RMarkdown to make a word/pdf file with your results? I think in your case you'd only need a few code chunks with your model summary and your tukey results.

It isn't exactly what you asked but I hope it is somewhat helpful anyway

[Soulhog]

Hi Sid-

Thanks so much for the suggestion. It worked perfectly. However, how do I switch back to the output appearing in the console? Right now when I give the summary() command it doesn't appear in the console.

[ashap222]

If all you need is to save your output for reference sink is a good option. I think this is a good place to introduce the package: broom. The broom package takes the messy output of built-in functions in R, such as lm , nls , or t.test , and turns them into tidy data frames. This is super useful if you want to use your coefficients or standard errors in further analyses.

https://cran.r-project.org/web/packages/broom/vignettes/broom.html

[nirgrahamuk]

@Soulhog

Right now when I give the summary() command it doesn't appear in the console.

had you done this part ?

@siddharthprabhu

sink(file = NULL)

[Soulhog]

Yes I have, and it ran in my console.

Thanks,

Erik

[siddharthprabhu]

Can you please run sink.number() and see if there are a non-zero number of connections? If there, are, please call sink(file = NULL) until the number of reported connections are zero.

[Soulhog]

Hi-

Sorry, I ran the sink.number() code and nothing happened...

[siddharthprabhu]

You should see output like this in the console.

> sink.number()
[1] 0
> 

[Soulhog]

yes, I see that now. Thanks! I think it has been fixed.

[siddharthprabhu]

Great! If I solved your problem, please consider marking my post as a solution.

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[e_vlasov]

I guess sink() will work as well instead of `sink(file=NULL).