README.md

In luismurao/nichetoolbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment

For more stable version of nichetoolbox go to ntbox repo

NicheToolBox

nichetoolbox is an R package with a friendly Graphical User Interface (GUI) developed using shiny framework. The package aims to facilitate the process of building niche models and estimate the species distributions.

Alternatively you can install a more stable version of nichetoolbox, ntbox package.

Installation

if (!require('devtools')) install.packages('devtools')
devtools::install_github('luismurao/nichetoolbox')

Warning

There is a bug in install_github function of the devtools package. Because of this sometimes you will have troubles while installing nichetoolbox package (see #issue 3). In order to install it you will first have to install some of the dependencies of the package:

Example

If you see an error like this:

installing source package 'nichetoolbox' ...
Warning in .write_description(db, file.path(outDir, "DESCRIPTION")) :
Unknown encoding with non-ASCII data: converting to ASCII
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called 'ridigbio'
Error : package 'spocc' could not be loaded
ERROR: lazy loading failed for package 'nichetoolbox'

Note that the error is generated because there is no package called 'ridigbio'.

Just run the following code:

ntbox_pkgs <- c("devtools", "shiny", "rgeos", "rgdal", "sp", "raster", "maptools", "dismo", 
                 "rgl", "dygraphs", "png", "rmarkdown", "knitr", "stringr", "MASS",
                 "animation", "mgcv", "googleVis","rasterVis", "shinyBS","shinyjs",
                 "rglwidget", "car", "maps", "corrplot", "dplyr", "cluster", "sqldf",
                 "fields", "devtools", "psych", "shinythemes", "grid", "RColorBrewer",
                 "ade4", "spocc")

#missing_pkgs <- ntbox_pkgs[which(!ntbox_pkgs %in% installed.packages())]

#if(length(missing_pkgs))
#  install.packages(ntbox_pkgs)
install.packages(ntbox_pkgs)
devtools::install_github("luismurao/leaflet")
devtools::install_github("AnalytixWare/ShinySky")
devtools::install_github("ENMGadgets", "narayanibarve")

and then try to install nichetoolbox again

devtools::install_github('luismurao/nichetoolbox')

Usage

library(nichetoolbox)
run_nichetoolbox()

Tutorial

nichetoolbox

luismurao/nichetoolbox documentation built on May 21, 2019, 8:56 a.m.