BIAD

Big Interdisciplinary Archaeological Database

This github repository supports the BIAD wiki biadwiki.org by providing a single collaborative repository to develop R code ONLY for maintaining the wiki.

Installation

To use the BIADwiki repository you may need to install some of the following packages, depending on which scripts you wish to run:

install.package(
    c("ADMUR", #to automatically compute date based on C14 sample and phases proximities
      "httr",#to send  files to wiki.js
      "gridExtra",
      "rnaturalearth",
      "DiagrammeRsvg",
      "DiagrammeR",  # exports some nice data trees 
      "ggplot2",
      "svglite",
      "maps",
      "mapdata",
      "terra", #this is for rnaturalearth
      "sf",
      "gt", # to export tables
      "rsvg"
     )
)

!!! note that I (simon) had to install some as sudo (thus doing sudo R, before install) because weirdly admin can't write in /tmp/ or whatever ; I don't understand anyway I couldn't compile stuff for SF so it failed, and same for TERRA, and same for FS & SASS, both some frontend stuff used by gt. very annoying this tmp problem, no time to solve it atm

These package needs some system wide dependencies:

 apt install libcurl4-openssl-dev \ #for diagrammeRsvg; god knows why they use that... 
             librsvg2 \  #for rsvg (I personnally vote to rewrite auto.make... to NOT USE diagrammeRsvg 
             libudunits2-dev  \ # for units, used by sf
             libgdal-dev libgeos-dev libproj-dev \ #these are also used by sf ;
             libmysqlclient-dev # needed that for libgdal-dev to install, why throwing conflict with mariadb

R scripts run only by the server

Various internal consistency checks, summary statistics and images are generated automatically from BIAD and used to populate the BIADwiki. These R scripts are prefaced 'auto.make.xxxxxx.R and run on the hosting server daily. A single bash script BIADwiki.sh is run by the server's crontab schedule. BIADwiki.sh invokes R to run a single R script controller.R. The R script controller.R runs the auto.make.xxx.R scripts. Login credentials for the local server are stored in the .Rprofile and therefore are automatically invoked when the server runs R in admin. These scripts will not work if you want to run them externally from the server as a standard user. To fix this issue it is necessary to first load the functions source("https://raw.githubusercontent.com/BIADwiki/BIADwiki/main/R/functions.R") and to replace the "query.database" function with "run.server.query(query.database(sql.command)".