CODEWITHSUNDEEP
rknitrr-markdown
Dominik
Dominik

Reputation: 792

remove messages from sourced script

I am trying to source a script that uses raster::extract(raster,spatialpolygons) so it prints the message about which polygon it is using for extracting. The final output from the file is a ggplot which I want to show, but I don't want any messages from R to show.

```{r percent of avg, echo=FALSE,message=FALSE,warning=FALSE,fig.width=15}
source('src/analysis/extract_huc4_elev.R') 
```

none of the chunk options echo, message or warning seem to suppress this output. if I use include=F then the plot doesn't show.

EDIT: I had a print statement so that explains some of it :-/ and some additional sleuthing discovered it was actually this line:

> huc4=readOGR('data/gis','UpperCRB')

## OGR data source with driver: ESRI Shapefile 
## Source: "data/gis", layer: "UpperCRB"
## with 8 features
## It has 9 fields

and you can hide the message in the script with:

> huc4=readOGR('data/gis','UpperCRB',verbose=F)

I do still wish there were a way to hide all script messages in the markdown output, e.g. in this case I'm sourcing an R file because I think it'll be more maintainable (this is my first reproducible report)- meaning I still would like to see those messages (print statements, verbose output, etc) when I'm working on the script itself.

also, here is the sessionInfo() just in case:

## R version 3.2.2 (2015-08-14)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.9.5 (Mavericks)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] ncdf4_1.13      gstat_1.0-26    doMC_1.3.3      iterators_1.0.7
##  [5] foreach_1.4.2   ipred_0.9-5     MASS_7.3-44     rgdal_1.0-7    
##  [9] readr_0.1.1     dplyr_0.4.3     plyr_1.8.3      tidyr_0.3.1    
## [13] raster_2.4-20   sp_1.2-0        ggplot2_1.0.1  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.1      formatR_1.2.1    xts_0.9-7        class_7.3-13    
##  [5] tools_3.2.2      rpart_4.1-10     digest_0.6.8     evaluate_0.8    
##  [9] gtable_0.1.2     lattice_0.20-33  DBI_0.3.1        yaml_2.1.13     
## [13] prodlim_1.5.5    proto_0.3-10     stringr_1.0.0    knitr_1.11      
## [17] grid_3.2.2       nnet_7.3-11      spacetime_1.1-4  R6_2.1.1        
## [21] survival_2.38-3  rmarkdown_0.8    lava_1.4.1       reshape2_1.4.1  
## [25] magrittr_1.5     intervals_0.15.1 codetools_0.2-14 scales_0.3.0    
## [29] htmltools_0.2.6  splines_3.2.2    assertthat_0.1   colorspace_1.2-6
## [33] stringi_0.5-5    lazyeval_0.1.10  munsell_0.4.2    FNN_1.1         
## [37] zoo_1.7-12

Upvotes: 2

Views: 453

Answers (2)

Dominik
Dominik

Reputation: 792

After messing with this some more, I realized another way to do it was use include=F and save the plot to disk in the R script and then outside the r chunk use ![Figure](/path/to/fig.png)

Upvotes: 0

Dominik
Dominik

Reputation: 792

Based on the link that @RobertH commented http://yihui.name/knitr/demo/output, I tested and found that you can use results='hide',fig.keep='high',fig.show='asis' and text output such as print() and cat() statements don't get printed in the html but the graph still comes through!

Upvotes: 0

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