README.md

In pbsag/swimr: Functions for Looking at Swim

swimr

Visualizations and Reports for SWIM

User's Guide

See https://github.com/tlumip/tlumip/wiki/Visualizing-Outputs

Dependent Libraries

This package uses some dependencies that are not on CRAN. Devtools should find most of these, but the following code will ensure you have all of them.

CRAN Dependencies

if("devtools" %in% rownames(installed.packages()) == FALSE) {install.packages("devtools")}
if("tidyverse" %in% rownames(installed.packages()) == FALSE) {install.packages("tidyverse")}
if("RSQLite" %in% rownames(installed.packages()) == FALSE) {install.packages("RSQLite")}
if("plotly" %in% rownames(installed.packages()) == FALSE) {install.packages("plotly")}
if("kfigr" %in% rownames(installed.packages()) == FALSE) {install.packages("kfigr")}
if("zoo" %in% rownames(installed.packages()) == FALSE) {install.packages("zoo")}
if("leaflet" %in% rownames(installed.packages()) == FALSE) {install.packages("leaflet")}
if("digest" %in% rownames(installed.packages()) == FALSE) {install.packages("digest")}
if("DT" %in% rownames(installed.packages()) == FALSE) {install.packages("DT")}
if("sf" %in% rownames(installed.packages()) == FALSE) {install.packages("sf")}

Bioconductor dependency for omxr

if("rhdf5" %in% rownames(installed.packages()) == FALSE) {
  source("http://bioconductor.org/biocLite.R")
  biocLite("rhdf5")
}

Github libraries

if("omxr" %in% rownames(installed.packages()) == FALSE) {
  devtools::install_github("gregmacfarlane/omxr")
}
if("dplyrExtras" %in% rownames(installed.packages()) == FALSE) {
  devtools::install_github("skranz/dplyrExtras")
}
if("outviz" %in% rownames(installed.packages()) == FALSE) {
  devtools::install_github("pbsag/outviz")
}
if("swimr" %in% rownames(installed.packages()) == FALSE) {
  devtools::install_github("tlumip/swimr", dependencies=FALSE)
}

Developer's Guide

• Getting Started
  • Make sure you have a SWIM reporting database (*.db SQLite file)
  • Clone this repo
  • Open swimr.Rproj in RStudio
  • Open the vignettes\pop_and_emp.Rmd Rmarkdown file
  • Update the input reporting datatbase file name - db_path
  • Render the Rmd as html with knitr via the Knit button
  • swimR contains four template Rmd files:
  • assignment validation
  • compare scenarios
  • population analysis
  • reference scenario
  • The template Rmd files are available via File + New File + R Markdown + From Template
  • After loading a template Rmd, update any required settings such as the input databases, and then knit it
• Static Package Data
  • swimr contains static package data sets in the data folder
  • To update these files, do the following:
  • Open swimr.Rproj in RStudio
  • Find the relevant R script and/or data in data-raw folder
  • Update the relevant raw data and re-run the script to update the version in the data folder
• Zone polygons
  • The zone polygons are now stored in the SWIM reporting SQLite database, in the table ALLZONES, in the column WKTSURFACE
  • The leaflet functions in SWIMR now extract the zones from the database automatically
  • To update the zone polygons, do the following:
  • Run the VISUM data export Python script to export the zone WKT strings
  • Read the zone WKT strings into the SQLite db using build_Viz_DB.R.

pbsag/swimr documentation built on Dec. 12, 2020, 3:08 a.m.