dev/vignettes/introduction.R

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

## ----setup, include=TRUE, eval=FALSE-------------------------------------
#  
#  install.packages("devtools")
#  devtools::install_github("FranzKrah/rMyCoPortal")
#  

## ----example1, include=TRUE, eval=TRUE, echo=TRUE------------------------
## Load library
library("rMyCoPortal")

## Download records

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

head(am.rec@records)

## ----plots, include=TRUE, eval=TRUE, echo=TRUE---------------------------

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]))