MAS Demo Notebook

Here we present an example of how a modular stock assessment software architecture may be implemented using Rcpp.

Setup

Before running this notebook, you will need to ensure you have a C++ compiler and Rcpp installed. Then, try to install the r4MAS package from Github and load it. If you have trouble, it could be because of a problem with your C++ compiler - see the Readme for a potential fix.

require(Rcpp)

## Loading required package: Rcpp

remotes::install_github("nmfs-fish-tools/r4MAS")

## Downloading GitHub repo nmfs-fish-tools/r4MAS@HEAD

## Rcpp (1.0.7 -> 1.0.8) [CRAN]

## Installing 1 packages: Rcpp

## Warning: package 'Rcpp' is in use and will not be installed

##   
  
  
   checking for file 'C:\Users\bai.li\AppData\Local\Temp\RtmpKq7gWg\remotes35c016e91c59\nmfs-fish-tools-r4MAS-a3fdf46/DESCRIPTION' ...
  
   checking for file 'C:\Users\bai.li\AppData\Local\Temp\RtmpKq7gWg\remotes35c016e91c59\nmfs-fish-tools-r4MAS-a3fdf46/DESCRIPTION' ... 
  
 [32mv [39m   [38;5;247mchecking for file 'C:\Users\bai.li\AppData\Local\Temp\RtmpKq7gWg\remotes35c016e91c59\nmfs-fish-tools-r4MAS-a3fdf46/DESCRIPTION' [39m [36m [36m (609ms) [36m [39m
## 
  
  
  
 [38;5;247m- [39m [38;5;247m   [39m [38;5;247mpreparing 'r4MAS': [39m [36m [36m (2.3s) [36m [39m
##    checking DESCRIPTION meta-information ...
  
   checking DESCRIPTION meta-information ... 
  
 [32mv [39m   [38;5;247mchecking DESCRIPTION meta-information [39m [36m [39m
##  [38;5;247m- [39m [38;5;247m   [39m [38;5;247mcleaning src [39m [36m [39m
## 
  
  
  
 [38;5;247m- [39m [38;5;247m   [39m [38;5;247mchecking for LF line-endings in source and make files and shell scripts [39m [36m [36m (755ms) [36m [39m
## 
  
  
  
   
  
   checking for empty or unneeded directories
  
 [38;5;247m- [39m [38;5;247m   [39m [38;5;247mchecking for empty or unneeded directories [39m [36m [36m (1.7s) [36m [39m
## 
  
Removed empty directory 
  
   Removed empty directory 'r4MAS/src/mas/third_party/ATL/docs/html'
##    Removed empty directory 'r4MAS/src/mas/third_party/ATL/docs/latex'
## 
  
   Omitted 'LazyData' from DESCRIPTION
## 
  
  
  
 [38;5;247m- [39m [38;5;247m   [39m [38;5;247mbuilding 'r4MAS_0.1.0.tar.gz' [39m [36m [39m
## 
  
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
##      storing paths of more than 100 bytes is not portable:
##      'r4MAS/src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/array-hash/array_growth_policy.h'
## 
  
   
##

## Installing package into 'C:/Users/bai.li/AppData/Local/Temp/RtmpI3qN8m/temp_libpath2bbc5c4c1486'
## (as 'lib' is unspecified)

## Warning in i.p(...): installation of package 'C:/Users/bai.li/AppData/Local/
## Temp/RtmpKq7gWg/file35c0771149e4/r4MAS_0.1.0.tar.gz' had non-zero exit status

Setup

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