README.md

In SOLV-Code/sdsynopsis: Salmon data extraction and summary

sdsynopsis-Package

Package with functions for extracting, merging, and summarizing salmon data from various databases

Important Note

THIS IS AN EARLY PROTOTYPE. This package is under development. Functions will change rapidly and substantially. Do not use these if you are not part of the development team!

Install

To install this package directly from github, use

install.packages("devtools") # Install the devtools package
library(devtools) # Load the devtools package.
install_github("sdsynopsis", 
                dependencies = TRUE,
                build_vignettes = FALSE)
library(sdsynopsis)             

Overview

Focus on 3 database sources:

• nuSEDS: salmon escapement by site
• EPAD: hatchery broodstock takes and releases
• MRP: mark-recapture data

Functions

Function | Description -- | -- xls2csv() | read in an excel file using the readxl package, and produce a cleaned csv. Options for "nuSEDS", "EPAD", or "MRP" csv2rds() | read in a csv file and produce a cleaned data frame stored in an R data file in rds format. Options for "nuSEDS", "EPAD", or "MRP" mergeData() | combine records from the 3 databases into 2 separate R data objects (.rds), one at the population/site level and one at the CU level summarizeData() | produce various summaries by population/site and by CU, and generate flat csv files as outputs. *reportData() | for now, generate a series of pdf summary plots. Once the plot design is finalized, turn this into a full markdown report.

SOLV-Code/sdsynopsis documentation built on April 29, 2020, 5:20 p.m.