In FranzKrah/rMyCoPortal: rMyCoPortal - An R package to interface with the Mycology Collections Portal

Requirements

Under the new MacOS Mojave there have been problems with the sf and raster package. This vignette works fine under Sierra and Windows10. However, the vignette application example might create errors.

R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6

The MyCoPortal

The Mycology Collections data Portal (MyCoPortal) is a database of fungal diversity with records mainly from North America. For more - and detailled - information, please visit http://mycoportal.org/portal/index.php.

The rMyCoPortal R package is an interface to the content stored on the MyCoPoral website. It allows to download records from the database readily in R for further analysis. It further provides some basic plotting functions. Below I will show the basic usability and some further possibilites of using the data.

Install rMyCoPortal

install.packages("devtools")
devtools::install_github("FranzKrah/rMyCoPortal")

Docker

Before we start using rMyCoPortal, we need to install docker (https://docs.docker.com/install/). Docker performs virtualization, also known as "containerization". rMyCoPortal interally uses the R package RSelenium to create a Selenium Server from which the MyCoPortal website is addressed. Docker needs to run before using the rMyCoPortal.

Download records for Amanita muscaria, the fly agaric

## Load library
library("rMyCoPortal")

## Download records

am.rec <- mycoportal(taxon = "Amanita muscaria")
am.rec

head(am.rec@records)

Visualization

We can now use several plotting methods to visualize the data.

x <- am.rec

## plot_recordstreemap can be used to visualize relative importance of aspects of the data
plot_recordstreemap(x = x, groupvar = "country", log = FALSE) # e.g., the country distribution

## plot_distmap can be used to plot interactive and static distribution maps
p1 <- plot_distmap(x = x, mapdatabase = "world", interactive = FALSE, plot = FALSE) # the default is interactive

# same for states
p2 <- plot_distmap(x = x, mapdatabase = "state", interactive = FALSE, plot = FALSE)

cowplot::plot_grid(p1, p2, ncol = 1, align = T)

## plot_datamap can be used to plot heatmaps for either records or species richness (index = "rich")
p3 <- plot_datamap(x = x, mapdatabase = "world", index = "rec", plot = FALSE)

## the same but cropped to Europe
p4 <- plot_datamap(x = x, mapdatabase = "state", index = "rec", plot = FALSE)

cowplot::plot_grid(p3, p4, ncol = 1, align = TRUE)

## And we can look up details for specific specimens
library(magick)
det <- details(x@records$Symbiota.ID[1])
length(det$urls)
par(mfrow = c(1,2), mar = c(0,0,0,0))
plot(image_read(det$urls[1]))
plot(image_read(det$urls[3]))

FranzKrah/rMyCoPortal documentation built on May 14, 2019, 11:11 a.m.