code

A growing list of R code files for various tasks

Code is only included in this list if it's well-formed enough to be worth sharing, and if the author decides it can go here. Most of the code is as nice html with code chunks, but some may be R source, or un-rendered R markdown.

mapping and spatial analysis

• basic tile-based maps with data overlays in R
  • based on the sf package, and includes coordinate conversion
• georeferenced jpeg images for map backgrounds in R
  • based on the stars package, using images from NearMap
• Save kml from Google Earth and use the saved coordinates in R
  • uses the sf package, which has the st_read() function which can convert kml to class sf objects in R
• Reading and uisng ESRI shapefiles in R
  • also uses st_read() from sf to convert shapefiles to sf objects
• Geostatistics and spatial interpolation
  • based on a few spatial packages including sf, lctools, and gstat

 

exploratory data analysis

• How to boxplot
• For exploratory data analysis I draw a lot of boxplots, . . . [for] mainly positively skewed variables . . .
• Function to show the colour palette
• I tend to change palettes often for different plot of map types, so it's good to get a quick visual reminder . . .
• Summary Tables showing sample counts exceeding environmental trigger values
• In environmental reporting it's common to produce tables containing statistical summaries of variables which also show if any samples have concentrations of contaminants that exceed environmental thresholds . . .

 

soil science

• different ways to plot soil depth profiles
• plotting the change in a variable vs. depth is a common task in soil science. This code will plot depth profiles at continuous or discrete depths
• solute transport animation using gganimate
• a simple demonstration of solute dispersion during transport, and a way to learn gganimate

 

file conversions

• convert xrdml XRD output file(s) to R data frame or csv
• converts a widely-used format for X-Ray Diffraction output
• read Hydrus-1D Nod_Inf.out files, convert to R data frame
• useful to make use of the plotting capabilities in R (Hydrus-1D in-built plots are not report- or publication-quality)
• Using the imager package to resize multiple images in a batch
• not really a file conversion, but useful nevertheless!

 

environmental biology

• using vegan for environmental DNA data analysis
• trying to emulate the procedures we have been teaching using Primer software

 

compositional data analysis

• introduction to compositional data analysis
• the basic ideas of analysing data with fixed-sum closure

• principal components analysis for compositional data
• an example of multivariate analysis for data with fixed-sum closure

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