Errors in including dependencies in models section

[pmabee]

> ## Right now this is done manually, we are working on making it work for the graphs we created above, but lets do it one by one for each module. 
> M <- list() # Stores our matrices
> G.mental.barbel <- induced_subgraph(G1, which(con.comp$membership==3))
> bin_mats <- init_binary_matrix(G.mental.barbel) # Start with independent models for each trait
Error in init_binary_matrix(G.mental.barbel) : 
  could not find function "init_binary_matrix"
> gtraits <- names(bin_mats) # Pull out the names of the traits we're working with
Error: object 'bin_mats' not found

```and more errors after this for both Wasila and I

[pmabee]

downstream errors:

> data(td.comb)
> dir <- "../revbayes/" #Location to store revbayes scripts
> dirD <- "../revbayes/data/" #Location to store data
> dirW <- "../revbayes/Discr_maps/" #Location to store maps
> dirR <- "../revbayes/output/" #Location to store output
> write.nexus(td.comb$phy, file="../revbayes/data/fishtree.tre") #This will be provided to you, but if you run your own analysis, you will want to put a tree in place that you can use in RevBayes
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '../revbayes/data/fishtree.tre': No such file or directory
> 
> data(ParamoRevTemplate) # This reads in our template Rev file that we will modify
> 
> writeRevOntologyModels(td, M, dir, dirW, dirR, dirD)
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '../revbayes/data/vomer.char': No such file or directory
> setwd(dir)
Error in setwd(dir) : cannot change working directory
> # Load these packages if you have access to multiple cores and want to run in parallel
> library(foreach) # Optional
Error in library(foreach) : there is no package called ‘foreach’
> library(doParallel) # Optional
Error in library(doParallel) : there is no package called ‘doParallel’
> registerDoParallel(cores=1) # Optional, if you are running on a server and have many cores!
Error in registerDoParallel(cores = 1) : 
  could not find function "registerDoParallel"
> res <- foreach(i=1:ncol(MT)) %dopar% {
+   cmd <- paste("./rb07 ", colnames(MT)[i], ".Rev &", sep="") #./rb07 is Revbayes 1.07, which works well with this script. 
+   #system(cmd) #Don't actually run!!
+ }
Error in foreach(i = 1:ncol(MT)) %dopar% { : 
  could not find function "%dopar%"