rvanmazijk

# Import your raster, e.g.:
GCFR_QDS_richness <- raster("GCFR_QDS_richness.tif")

# Let `ggplot2` figure out what to do with it...
gplot(GCFR_QDS_richness) +  # NB: Not a typo! Use `gplot` not `ggplot` for this!
  # Then tell it to use the raster cell values to colour the tiles
  geom_tile(aes(fill = value)) +
  # Then the rest of your regular `ggplot2` code can go here, e.g.:
  labs(title = "QDS-richness (GCFR)", x = "Longitude(º)", y = "Latitude (º)") +
  scale_x_continuous(breaks = c(18, 22, 26)) +

rvanmazijk

1. Go to /Library/Application Support/McAfee/MSS/Applications/
2. Rename Menulet.app to something else
   • Can't just delete as is always running, and un-quittable
3. Optional: copy Menulet*.app to somewhere else, for safety's sake
4. Delete Menulet*.app
   • Can do this now as new filename is not blocked from deletion

rvanmazijk

cd /Library/LaunchAgents
sudo mv com.cisco.anyconnect.gui.plist com.cisco.anyconnect.gui.plist.bak
sudo mv com.cisco.anyconnect.notification.plist com.cisco.anyconnect.notification.gui.plist.bak

rvanmazijk

Open ~/Library/QuickLook/QLStephen.qlgenerator/Contents/Info.plist and add the following within the <key>CFBundleTypeName</key> section:

<string>net.daringfireball.markdown</string>

Then, reset and restart QuickLook:

$ qlmanage -r

rvanmazijk

# List processes using external hard drive /RUAN/
sudo lsof | grep /Volumes/RUAN

# (Usually mds and/or mds_store processes are to blame...)
# (Kill like this:)
sudo killall mds

rvanmazijk

defaults write com.apple.dock tilesize -integer 40
defaults write com.apple.dock largesize -integer 40
killall Dock

rvanmazijk

# This function plots two phylogenetic trees with the same tip-names,
# but differing topologies, by rotating branches so as to minimise the amount of times
# the lines connecting the same species on each tree cross (using phytools::cophylo()).

# Note, this does **NOT** mean that crossed lines show incongruence, 
# or that parallel lines show congruence, but it does help you check it manually
# much faster than just looking at each tree individually.

library(phytools)  # Needed for cophylo()

rvanmazijk

library(xfun)  # ::file_ext()
library(stringr)
library(magrittr)  # %<>%

add_missing_ext <- function(x, ext) {
  missing_ext <- file_ext(x) == ""
  x[missing_ext] <- paste0(x[missing_ext], ext)
  x
}

rvanmazijk

snippet lib
	library(${1:package})

snippet req
	require(${1:package})

snippet src
	source("${1:file.R}")

snippet ret

rvanmazijk

pretty_table <- function(x) {
  # Remove column contents after first mention in table
  for (column in columns) {
    for (group in unique(x[[column]])) {
      to_remove <- which(x[[column]] == group)[-1]
      x[to_remove, column] <- " "
    }
  }
  x
}