Category Archives: Open Source

Dealing with Factors in R

What is the deal with the data type “Factor” in R?  It has a purpose and I know that a number of packages use this format, however, I often find that (1) my data somehow ends up in the format and (2) it’s not what I want.

My goal for this post: to write down what I’ve learned (this time, again!) before I forget and have to learn it all over again next time (just like all the other times).  If you found this, I hope it’s helpful and that you came here before you started tearing your hair out, yelling at the computer, or banging your head on the desk.

So here we go.  Add your ways to deal with factors in the comments and I’ll update the page as needed.

Avoid Creating Factors

Number 1 best way to deal with factors (when you don’t need them) is to not create them in the first place!  When you import a csv or other similar data, use the option stringsAsFactors = FALSE (or similar… read the docs for find the options for the command you’re using) to make sure your string data isn’t converted automatically to a factor.  R will sometimes also convert what seems to clearly be numerical data to a factor as well, so even if you only have numbers, you may still need this option.

MyData<-read.csv(file="SomeData.csv", header=TRUE, stringsAsFactors = FALSE)

Convert Data

Ok, but what if creating a factor is unavoidable?  You can convert it.  It’s not intuitive so I keep forgetting.  Wrap your factor in an as.character() to just get the data.  It’s now in string format, so if you need numbers, wrap all of that in as.numeric().

#Convert from a factor to a list

#Convert from a factor to numerical data


What’s Missing?

Do you have any other tricks to working with data that ends up as a Factor?  Let me know in the comments!

Inkscape for Applique Sewing Patterns

Inkscape is a vector illustration program so most people think of it as an art program for producing slick graphics.  But it’s a really useful tool for planning an preparing for other art forms.  For example, I’ve been using it for sewing.  What?  Yes, sewing.  It’s incredibly useful for drawing patterns.  Recently I’ve been working on a needle turn applique quilt based on the work of Charley Harper, but for the past few years I’ve made felt Christmas ornaments for friends and family, for all of which I used Inkscape to draw the patterns.

If you’re familiar with Inkscape already, making applique patterns will be pretty straight forward. If you’re new to the program, I highly recommend working through a couple of tutorials.  Here’s my general workflow (yours may differ):

  1. Start with an image.  On Pinterest, great projects abound, but sometimes the post links to costly instructions, or no pattern at all.  I’ve also found things that I like the look of, but are a different scale – too big or too small.  Or, as with my latest project, I’m creating my own pattern pieces from an image.  Look for images with distinct polygons of colors.  Blended or faded areas are going to be harder to duplicate with applique unless you can find fabric with the right fade or you dye your own.
  2. Put the image into an Inkscape file and resize it to the size you want your final project to be.
  3. Draw polygons around each of the colors you see in your image.  You’ll want to think about how you’ll put the whole thing together as you trace, so think about how the layers will work together.  For example, if you have polka-dots, you’ll want to place the circles on top of a larger background color, not have a section of background color with holes cut out like Swiss cheese.


    Start by tracing out all of the sections you’ll need to cut from various colors of fabric.

  4. Start a new Inkscape file and make the size of the page whatever size you plan to print.  For those in the US, you’ll probably want US Letter Size.
  5. Copy your polygons from the first file and past them into the second.  (I find keeping both files is helpful later for placement of the pieces.)  Arrange all your polygons on the page so that none overlap.  For larger projects, I’ve made several files. If the same shape shows up multiple times in your pattern, for example maybe eyes or ears, you only need to include that shape once.


    One of 3 pages of pattern pieces for a larger work with many pieces.

  6. On each piece, I like to print the color of the fabric I plan to use and how many of this piece I need to cut out.
  7. If you have a really big pattern piece that’s bigger than your printable page size, there’s a solution.  Put the big pieces into one Inkscape file, then size the page to the content, giving it a reasonable margin for your printer.  Then save the file as a PDF.  Open the PDF and in the print options, pick Poster (or similar setting).  It will divide up the pattern into printable pages.  Then you can tape the pages together before you cut out the pattern.


    My printer settings have an option to print large PDFs in pieces.  Yours probably has something similar.  Super useful for printing larger pattern pieces.

Bonus! Now when you’re placing your pieces, some stuff you can just eyeball and it will be fine.  In some situations though you might need to be more precise.  Because you have your original pattern tracing in Inkscape, you can go back to that file and measure the distance between items.  I set my units to inches and draw a line, then see how long my line is.  Super simple, but very effective.


The red line measures how long the vertical eye whisker is.

See the finished piece on a previous blog post.

Limp on a Limb: Another Charley Harper Inspired Quilt Block

This second block in my Charley Harper Quilt is inspired by the piece Limp on a Limb.  If you compare the original and the block, you’ll see that I’ve made some edits.  Most notably, I have decided (for now at least) to not include the leaf pattern in the background.  Repeated shapes are a hallmark of Harper’s work, so including the pattern would be more true to the work, but in reality, it would require extensive embroidery and I’m afraid that won’t hold up long-term, especially given the light weight of the fabric I’ve chosen for the background.  That being said, the fabric I chose is mottled green and I hope it at least gives the piece some more depth.


Example diagram from placing the cat’s eye wiskers.

For this block, I thought I would show some of the detail of how I transfer lines from the pattern to the piece.  All my patterns are digital svg files, which means I can measure the size of each object in Inkscape.  (I promise to write a post about this with more detail and hopefully convert some quilters to Inkscape quilt designers… but later.  Ok, it’s later. See the post here.)  I make measurements from a reference point, draw out a diagram, then transfer the measurements to the fabric using a chalk pencil (either white or blue depending on the color of the fabric).  Then I embroider.  It’s important to mark as little as possible on the fabric with the calk pencils, because the marks are hard to get out.


Faint chalk pencil marks show where to embroider the eye whiskers.

When placing any object in a piece, whether it’s embroidery or a layer of fabric, I’ve found that it’s important to figure out what feature the new object needs to be inline with. For placing the eye whiskers, at first I was going to reference the corner of the eye. It seemed logical. Then I found that in the original piece, the left eye and whiskers don’t line up. What? But there’s always such precision in Harper’s work! But after some staring at the piece, I realized that the vertical line of both sets of eye whiskers intersects the point where the ear meets the head. Bingo! Now my whiskers are in the right spot.


The finished piece.

Designing The Charley Harper Quilt

I’ve been a big fan of modern artists Charley Harper’s work since 2012 when I taught may Science to Art course at University of California Davis.  In that class, students were tasked with communicating science concepts through art.  At the suggestion of the Wildlife Museum staff who sponsored the course, we chose to emulate Charley Harper’s style of simplifying species down to their most simple yet still recognizable forms.  We learned how Harper repeated forms – leaves and mice in one image are the same teardrop shape, for example – and simplified bodies down to their most elemental form.  The work was all completed in Inkscape and eventually printed on large banners that hang in Academic Surge.  The results were magical.

Fast forward a few years and I saw a post on the Charley Harper Studios’ Facebook page asking people to post images of quilts they had made using Harper’s images or their line of fabrics.  The quilts were charming and it made me think about how those simplified forms would easily translate into quilt blocks.

So, I set out to figure out how I could make one.  I have made one traditional quilt and one comforter more than ten years ago, but I regularly sew and do felt applique for Christmas ornaments, so the skills are there.  I learned about applique for quilting (particularly with woven fabrics that can fray, unlike felt) and decided that needleturn applique sounded like the least fussy option.  I found this video on YouTube to be an excellent quick tutorial:

Next, I needed a plan so I found a bunch of images I liked and arranged them in an Inkscape file with a page size set to the size of the finished product that I could later turn into vector lines for pattern pieces.  More on that later.  This is my plan (please note that the artwork is copyrighted by the artist):


I’ll update my progress as I go.

Making of a Moon Tree Map


I’m presenting a workflow for finishing maps in Inkscape at FOSS4G North America this year (2016). To really show the process effectively, I made a map and took screenshots along the way.

The Data

I decided to work with Moon Tree location data.  It’s quirky and interesting… and given that this is a geek conference I figured the space reference would be appreciated.  A few months ago I learned about Moon Trees watching an episode of Huell Howser on KVIE Public Television and then visited the one on the California State Capitol grounds.  I later learned from my aunt that my grandfather was a part of the telemetry crew that retrieved the Apollo 14 mission that carried the seeds that would become the Moon Trees, so there’s something of a connection to this idea.  Followers of my research also know that I’m a plant person, particularly plant geography.  So this seemed like the perfect dataset.  I was fortunate to find that Heather Archuletta had already digitized the locations of public trees and made them available in KML format.

Data Processing

The KML format is great for some applications (particularly Google maps, for which it was designed) but it poses some challenges.  I spent several hours… maybe more than I want to admit… formatting the .dbf to make the shapefile more useful for my purposes.  I created columns and standardized the content.  The map does not present all the data available (um… duh.).  It was challenge enough getting all this onto one page.

Yes, Inkscape is Necessary

You can’t make this map in QGIS completely.  I mean, normally you can make some fantastic maps in QGIS, but this one is actually not possible.  Right now, QGIS can’t handle having map frames with different projections.  I tried, but I found that even when the map composer looked right, the export in all three export options changed the projection and center of each frame to match that of the last active frame.  So I ended up with a layout with three zoom levels centered on Brazil… interesting, but not what I had in mind.  So I exported an .svg file three times from the map composer – one for each map frame – and put them together in Inkscape.

Sneaky Cartography

One of the methods I often use in my maps is to create subtle blurred halos behind text or icons that might otherwise get lost on a busy background.  I don’t like when the viewer sees the halos (maybe it’s from teaching ArcMap far too many years at universities).  It’s not quite a pet peeve, but I think there’s often better ways to handle busy backgrounds and readability.  My blog, my soapbox.  Can you spot them?  There are a couple in the map and in the final slide of the pitch video.  It doesn’t look like much, but I promise the text is easier to read.

The texture on the continents is the moon.  I clipped a photo of the moon using the continent outlines.  I liked the idea of trees on the moon.


The icons are special to me.  I’ve been really wanting to make a map using images from Phylopic and I thought this was the perfect opportunity… but… but… no one had uploaded outlines for any of the species I needed.  So I made them and uploaded them.  So if you want an .svg of these, help yourself.  If, however, you need dinosaurs, they’ve got you covered.

Watch it happen:

My pitch video captures the process from start to finish:

 Want more open source cartography?

Come to FOSS4G North America and see my and several other talks focused on cartography.  I’ll cover methods and tools in Inkscape common for cartography.

Spatially Enabled Zotero Database

As a geographer, I’m a visual person.  I like to see distributions on a map and where things are matters to me.  A few years ago, while I was writing a paper I became overwhelmed with trying to remember the locations for the studies I had read (for coastal plants, latitude matters), so I started marking the locations of studies on a map and eventually turned it into a printed map.


But adding new studies and sharing the results is a cumbersome and the spatial data is largely separate from the citation information.  So I set out to find a way to store spatial information in my citation database and access the spatial information for mapping purposes.  The end result (which is still a work in progress at press time) is a web map of coastal vegetation literature that updates when new citations are added to my Zotero database online.


How I Did It:

Key ingredients: Zotero, QGIS, Spatialite, Zotero Online Account

I started working with the Zotero database I already have populated with literature relevant to my research on coastal vegetation.  I moved citations that I wanted to map into a separate folder just to make the API queries easier later.  I made a point in a shapefile for the location of each study using QGIS.  I gave the attribute table fields for the in-text citation and a text description of the location for human-readability, but the most important field is the ZoteroKey.  This is the item key that uniquely identifies each record in the Zotero database.  To find the key for each citation, in your local version of Zotero, right click on the record and pick “generate report”.  The text for the key is after the underscore in the URL for the report.  In the online version, click the citation in your list.  The key is at the end of the URL in the page that opens.


My map only has point geometries right now, but that will change in the coming weeks.

The spatial information was then to be added to the Zotero database (specific queries can be found on GitHub) in Spatialite.  The Zotero schema is quite large but not impossible to navigate.  Currently, there is no option to add your own fields to Zotero (I tried… I failed… they tell me the option is coming soon) so I put my geometries into the “Extra” field.  Using Spatialite, I opened the Zotero database and imported my shapefile of citation locations (having new tables doesn’t break the database, thank goodness).  Then I removed any existing information in the “Extra” field and filled it in with geometry information in the style of geoJSON.  The string looks like this:

{"type": "Point", "coordinates": [-123.069403678033, 38.3159528822055]}

After updating the citation records to house the geometries, I synced the changes to my online Zotero repository from my desktop program.  Now it’s ready to go into a web map using the Zotero API.  My webmap code can be found in my GitHub Repository.

What’s Next?

I would like to develop a plug-in for QGIS that makes adding the geometries to the Zotero database easier because not everyone wants to run SQL queries on their active citation database that has been years in the making (I backed mine up first!).  The interface would show the citations you want to map, then users would pick a citation, then click the location on their QGIS project where the citations should be located.  The plug-in would insert the corresponding geometry for them.

Getting Started with LaTeX

I’ve been thinking for a while that I would like to learn how to use LaTeX.  Aside from being something that geeky types seem to love, it makes documents that look beautiful.  It actually looks easier than getting Word or LibreOffice to behave in predictable ways beyond simple text.  So why am I finally learning how to use this?  I want to submit an article to a journal and they require all submissions be in LaTeX format.  (As an aside, why did they have to make the capitalization of LaTeX so odd?  It’s hard to type!)  I thought I would post some notes on tools I found useful for learning.


You need both a LaTeX engine and an editor.  I installed MikTex as the engine and TexMaker for the editor.


Michelle Krummel has a multi-part video tutorial on YouTube that moves at a good pace (not too fast or slow).  She teaches all the basics you need to understand how to set up a document and how formatting works.  Even though it’s specifically geared towards mathematics, the concepts all apply to what you would need for other sciences as well.

Cheat Sheets

Winston Chang wrote an excellent cheat sheet to remind you of the basic formatting you’ll need.