makefile.Rmd

---
title: "Space average makefile, compilation notes"
author: "Daniel Reuman, Shyamolina Ghosh"
date: ""
output: pdf_document
params: 
  mf : MT_spatial_avg.Rmd
  sf : SI_spatial_avg.Rmd
---

<!--checkpoint package-->
```{r checkpoint_chunk, echo=F, warning=F, message=F, results="hide"}
library(checkpoint)
if (!dir.exists("./.checkpoint/")){
  dir.create("./.checkpoint/")
}
checkpoint("2018-07-23",R.version=getRversion(),checkpointLocation=getwd(),scanForPackages = FALSE) #mine is R-3.4.4
```

```{r}
library(stringr)
mfile.Rmd<-params$mf
sfile.Rmd<-params$sf
ym<-str_sub(mfile.Rmd,start=1,end=-5)
mfile.tex<-paste(ym,".tex",sep="")
ys<-str_sub(sfile.Rmd,start=1,end=-5)
sfile.tex<-paste(ys,".tex",sep="")
```

# Get tex files and pdf files for the supp mat, but the pdf files 
#are missing the external references 

```{r tex_for_supp_mat}
library(rmarkdown)
rmarkdown::render(input=sfile.Rmd) 
```

# Get tex files and pdf files for the main text, but the pdf files 
#are missing the external references 

```{r tex_for_main_text}
rmarkdown::render(input=mfile.Rmd) 
```

# Now recompile the latex

```{r recompile_latex}
#do it once
system2(command="pdflatex",args=sfile.tex,stdout=TRUE,stderr=TRUE)
system2(command="pdflatex",args=mfile.tex,stdout=TRUE,stderr=TRUE)

#do it again to make sure to get the external references right
system2(command="pdflatex",args=sfile.tex,stdout=TRUE,stderr=TRUE)
system2(command="pdflatex",args=mfile.tex,stdout=TRUE,stderr=TRUE)
```