Blog Archives

Open Science Challenge

January 8, 2013
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Open Science Challenge

Open Science Science is becoming more open in many areas: publishing, data sharing, lab notebooks, and software. There are many benefits to open science. For example, sharing research data alongside your publications leads to increased citation ra...

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Open Science Challenge

January 8, 2013
By
Open Science Challenge

Open Science Science is becoming more open in many areas: publishing, data sharing, lab notebooks, and software. There are many benefits to open science. For example, sharing research data alongside your publications leads to increased citation ra...

Read more »

Is invasive?

December 13, 2012
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Is invasive?

The Global Invasive Species Database (GISD) (see their website for more info here) has data on the invasiveness status of many species. From taxize you can now query the GISD database. Introducing the function gisd_isinvasive. This function was contributed to taxize by Ignasi Bartomeus, a postdoc at the Swedish University Agricultural Sciences. There are two possible outputs from using...

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Is invasive?

December 13, 2012
By
Is invasive?

The Global Invasive Species Database (GISD) (see their website for more info here) has data on the invasiveness status of many species. From taxize you can now query the GISD database. Introducing the function gisd_isinvasive. This function was contributed to taxize by Ignasi Bartomeus, a postdoc at the Swedish University Agricultural Sciences. There are two possible outputs from using...

Read more »

Shiny apps are awesome

December 10, 2012
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Shiny apps are awesome

RStudio has a new product called Shiny that, quoting from their website, "makes it super simple for R users like you to turn analyses into interactive web applications that anyone can use". See here for more information. A Shiny basically consists of two files: a ui.r file and a server.r file. The ui.r file, as it says, provides...

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Shiny apps are awesome

December 10, 2012
By
Shiny apps are awesome

RStudio has a new product called Shiny that, quoting from their website, "makes it super simple for R users like you to turn analyses into interactive web applications that anyone can use". See here for more information. A Shiny basically consists of two files: a ui.r file and a server.r file. The ui.r file, as it says, provides...

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One R package for all your taxonomic needs

December 6, 2012
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UPDATE: there were some errors in the tests for taxize, so the binaries aren't avaiable yet. You can install from source though, see below. Getting taxonomic information for the set of species you are studying can be a pain in the ass. You have to manually type, or paste in, your species one-by-one. Or, if you are lucky, there is...

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One R package for all your taxonomic needs

December 6, 2012
By

UPDATE: there were some errors in the tests for taxize, so the binaries aren't avaiable yet. You can install from source though, see below. Getting taxonomic information for the set of species you are studying can be a pain in the ass. You have to manually type, or paste in, your species one-by-one. Or, if you are lucky, there is...

Read more »

Displaying Your Data in Google Earth Using R2G2

October 24, 2012
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Displaying Your Data in Google Earth Using R2G2

Have you ever wanted to easily visualize your ecology data in Google Earth? R2G2 is a new package for R, available via R CRAN and formally described in this Molecular Ecology Resources article, which provides a user-friendly bridge between R and the Google Earth interface. Here, we will provide a brief introduction to...

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Getting taxonomic names downstream

October 16, 2012
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It can be a pain in the ass to get taxonomic names. For example, I sometimes need to get all the Class names for a set of species. This is a relatively easy problem using the ITIS API (example below). The much harder problem is getting all the taxono...

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