/Scriptbox

Scripts which will be useful for CMEP / RBGE work

Primary LanguageR

SCRIPTBOX

Flic Anderson 1st July 2014

Aim: To hold scripts which will be useful for CMEP / RBGE work & manage these through Git version control associated with (currently private) GitHub repository @ https://github.com/FlicAnderson/Scriptbox

More Details: Containing scripts & documentation for Padme/R read/writes and eventually will contain analysis scripts.

Folder System:

  • data_*/ folders:
    These contain scripts for dealing with data from various sources (such as GBIF, IUCN redlist, etc)

  • database_analysis:
    Analysis & summary stats for database output

  • database_connections:
    Connection scripts to databases such as Padme Arabia

  • database_export:
    Scripts dealing with exporting datasets such as ethnographic data or specimen data from databases such as Padme Arabia

  • database_importing:
    Functions & scripts for welding ethnographic annotations into Padme, checking & matching latin names against Padme's Latin Names tables, pulling in endemic annotations

  • database_output:
    Pulling data out of databases; datagrab scripts for specific queries or general regions or groups (herbarium = E, field observation counts, socotra specimens only, etc)

  • database_updating:
    Scripts for updating database directly: USE WITH CAUTION!! Ideally, don't re-use these since they've been written often as one-time-only problem solvers & will screw up the database if they run at all now... But allow tagging particular subsets such as expeditions, record fixes to the Socotra data etc

  • function_template:
    "function_format.R" contains the template layout for function scripts, including function title, date created/author details, aim of function, call info, code. Follow this for all functions added to Scriptbox.

  • general_utilities:
    Contain various snippets of old stuff & generally useful functions or scripts such as function padmeNameMatch.R which will check strings against Padme's Latin Names table & suggest fuzzy matches if it's not a direct match. Also function getFamilies.R which pulls out & attaches families from Padme's Latin Names table to taxa

  • mapping:
    Scripts pertaining to mapping data & records; may include leaflet stuff, other mapping

  • script_template:
    "script_format.R" contains the template layout for script files, including project/title, date created/author details, aim of script, code. Follow this for all files added to Scriptbox.

  • web_reactiveApps:
    Things like Shiny apps; to continue & develop

  • web_xml-processing:
    Example xml-processing script, not fully developed or continued