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---
title: "BCGcalc-README"
author: "Erik.Leppo@tetratech.com"
date: "`r Sys.time()`"
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE
, collapse = TRUE
, comment = "#>"
, fig.path = "README-")
```
```{r, echo = FALSE}
cat(paste0("Last Update: ",Sys.time()))
```
# BCGcalc <a href='https://github.com/leppott/BCGcalc'><img src='inst/figures/logo.png' align="right" height="139" /></a>
Biological Condition Gradient (BCG) calculator. Perform basic functions needed
for metric calculation and model (level) assignments.
Badges
-----------
[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/leppott/BCGcalc/graphs/commit-activity)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://www.tidyverse.org/lifecycle/#stable)
[![GitHub license](https://img.shields.io/github/license/leppott/BCGcalc.svg)](https://github.com/leppott/BCGcalc/blob/master/LICENSE)
[![CodeFactor](https://www.codefactor.io/repository/github/leppott/BCGcalc/badge)](https://www.codefactor.io/repository/github/leppott/BCGcalc)
[![codecov](https://codecov.io/gh/leppott/BCGcalc/branch/master/graph/badge.svg)](https://codecov.io/gh/leppott/BCGcalc)
[![R-CMD-check](https://github.com/leppott/BCGcalc/workflows/R-CMD-check/badge.svg)](https://github.com/leppott/BCGcalc/actions)
[![GitHub issues](https://img.shields.io/github/issues/leppott/BCGcalc.svg)](https://GitHub.com/leppott/BCGcalc/issues/)
[![GitHub release](https://img.shields.io/github/release/leppott/BCGcalc.svg)](https://GitHub.com/leppott/BCGcalc/releases/)
[![Github all releases](https://img.shields.io/github/downloads/leppott/BCGcalc/total.svg)](https://GitHub.com/leppott/BCGcalc/releases/)
Installation
-----------------
To install the current version use the code below to install from GitHub. The
use of “force = TRUE” ensures the package is installed even if already present.
If the package `remotes` is missing the code below will install it.
```{r Install, eval=FALSE}
if(!require(remotes)){install.packages("remotes")} #install if needed
install_github("leppott/BCGcalc", force=TRUE)
```
The vignette (big help file) isn't created when installing from GitHub with the
basic `install_github` command. If you want the vignette install with the
code below.
```{r Install_Vignette, eval=FALSE}
if(!require(remotes)){install.packages("remotes")} #install if needed
install_github("leppott/BCGcalc", force=TRUE, build_vignettes=TRUE)
```
All dependent libraries should install with the install_github command but
occassionally they do not. If you encounter issues the dependent libraries can
be installed separately with the command below.
```{r Install_Libraries, eval=FALSE}
# Choose a CRAN mirror (dowload site) first (can change number)
chooseCRANmirror(ind=21)
# libraries to be installed
data.packages = c(
"devtools" # install helper for non CRAN libraries
,"installr" # install helper
,"knitr" # create documents in other formats (e.g., PDF or Word)
,"dplyr" # summary stats
,"reshape2" # convert wide to long format
,"rmarkdown" # a dependency that is sometimes missed.
,"readxl" # for importing Excel data
)
lapply(data.packages,function(x) install.packages(x))
```
Additionally Pandoc is required for creating the reports and (sometimes) needs
to be installed separately. Pandoc is installed with RStudio so if you have
RStudio you already have Pandoc on your computer. Install directions are
included below.
```{r Install_Pandoc, eval=FALSE}
## pandoc
#install.packages("installr")
library(installr)
install.pandoc()
```
Purpose
--------------
To aid users in data tasks related to the Biological Condition Gradient for the
Pacific Northwest.
Usage
------------
Everytime R is launched the `BCGcalc` package needs to be loaded.
```{r LoadLibrary, eval=FALSE}
# load library and dependant libraries
library("BCGcalc")
```
The default working directory is based on how R was installed but is typically
the user's 'MyDocuments' folder. You can change it through the menu bar in R
(File - Change dir) or RStudio (Session - Set Working Directory). You can also
change it from the command line.
```{r Directory, eval=FALSE}
# if specify directory use "/" not "\" (as used in Windows) and leave off final "/" (example below).
#myDir.BASE <- "C:/Users/Erik.Leppo/Documents/ProjectName"
myDir.BASE <- getwd()
setwd(myDir.BASE)
```
Shiny
------------
The Shiny app code is included in the package but is also on the web.
https://tetratech-wtr-wne.shinyapps.io/BCGcalc/
Help
------------
Every function has a help file with a working example. There is also a vignette
with descriptions and examples of all functions in the `BCGcalc` library.
```{r Help_Function, eval=FALSE}
# To get help on a function
# library(BCGcalc) # the library must be loaded before accessing help
?BCGcalc
```
To see all available functions in the package use the command below.
```{r Help_Index, eval=FALSE}
# To get index of help on all functions
# library(BCGcalc) # the library must be loaded before accessing help
help(package="BCGcalc")
```
The vignette file is located in the “doc” directory of the library in the R
install folder. Below is the path to the file on my PC. But it is much easier
to use the code below to call the vignette by name. There is also be a link to
the vignette at the top of the help index for the package.
"C:\\Programs\\R\\R-3.4.3\\library\\BCGcalc\\doc\\vignette_BCGcalc.html"
```{r Help_Vignette, eval=FALSE}
vignette("vignette_BCGcalc", package="BCGcalc")
```
If the vignette fails to show on your computer. Run the code below to reinstall
the package and specify the creation of the vignette.
```{r Install_Vignette2, eval=FALSE}
library(remotes)
remotes::install_github("leppott/BCGcalc", force=TRUE, build_vignettes=TRUE)
```
Example
------------
A quick example showing the calculation of metrics on a dataset but returning
only a select few (e.g., the 12 metrics used in the BCG model for the Pacific
NW). This functionality is built into the `metric.values` function as an
optional parameter.
```{r Metric_Select, eval=FALSE, echo=TRUE}
library(BCGcalc)
library(readxl)
library(reshape2)
library(knitr)
library(BioMonTools)
df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_PacNW.xlsx"
, package="BCGcalc"))
myDF <- df.samps.bugs
# Columns to keep
myCols <- c("Area_mi2", "SurfaceArea", "Density_m2", "Density_ft2")
# Metrics to Keep
met2keep <- c("ni_total", "nt_total", "nt_BCG_att1i2", "pt_BCG_att1i23"
, "pi_BCG_att1i23", "pt_BCG_att56", "pi_BCG_att56"
, "nt_EPT_BCG_att1i23", "pi_NonInsJugaRiss_BCG_att456"
, "pt_NonIns_BCG_att456", "pi_NonIns_BCG_att456", "nt_EPT")
# Run Function
df.metric.values.bugs <- metric.values(myDF, "bugs", fun.MetricNames=met2keep
, fun.cols2keep=myCols)
# View Results
#View(df.metric.values.bugs)
kable(head(df.metric.values.bugs), caption="Selected metric results")
```