Authoring

Citation Software

• Zotero: Your personal research assistant. Entering grad studies and beginning many weeks of reading this has revolutionized my life.
• Better Bibtex for Zotero keep an always up to date .bib file for integration with LaTeX or Rmarkdown citation.

LaTeX

I’m not totally convinced that I want to commit to LaTeX as Rmarkdown and bookdown do such nice jobs of it. That being said it is a great fallback. Escape GUI document writing and get using this typesetting system that has you focus on your words not on your formatting.

• MikTeX the engine of LaTeX
• TeXStudio that don’e call it this but essentially it is an IDE for LaTeX.

GIS and Remote Sensing

• QGIS: On MS Windows I recommend using OSGEO4W installer to ensure that you get all the goodies and plugins.
• SAGA GIS: Although often bundled with the QGIS a newer version is available via https://sourceforge.net/projects/saga-gis/
• LASTools: Very powerful set of tools for manipulating, using, and extracting additional data products from LiDAR. I have the privellage of using this through our lab’s accademic license.
• Quick Terrain Reader. Freeware - Great for displaying LAS data

Stats

• R
• RStudio
• Rtools – essential if using packages that are in development (e.g. on GitHub)

Essential Packages for R

## Stats and the tidyverse
pk <- c("tidyverse", "psych", "lme4", "caret")

## Geo-spatial analysis
pk <- append(pk, c("sf", "sp", "raster", "stars", "lwgeom",
         "mapview","tmap", "lidR", "gdalcubes"))

## Creating documents and interactive documents
pk <- append(pk, c("rmarkdown", "bookdown", "rmdformats",
                   "blogdown", "rticles"))

## Install the packages if this has not been done already
new.packages <- pk[!(pk %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

someday I may get around to documenting how to make the above packages portable … mostly

Utilities

• ConEmu: essential replacement of the windows CMD.exe shell. OK it’s more of an integration of that shell… but bettter.
• Kinesics Text Editor: like nano but for windows – great to have this coupled with ConEmu.
• Atom - excellent text editor! Really what does a text editor do… This one seems to be able to do anything you want! Syntax highlighting, Markdown preview. Integration with gitHub, ….
• GIT
• GitHub GUI a nice little program for viewing git changes – note can be used in git folders that are not uploaded to github. _Caution!! – I think it is actually better practice to use the commandline then to make changes with the GUI … It is very easy to get yourself in trouble with the GUI
• FreeCommander a replacement for windows file explorer. Allows 2 panes and some great file sync utilities.
• 7-zip A great file compression utility. When in windows don’t forget to install the commandline portion