442 search results for "knitr"

FillIn: a function for filling in missing data in one data frame with info from another

February 15, 2013
By

Sometimes I want to use R to fill in values that are missing in one data frame with values from another. For example, I have data from the World Bank on government deficits. However, there are some country-years with missing data. I gathered data from ...

Read more »

Getting a simple tree via NCBI

February 14, 2013
By
Getting a simple tree via NCBI

I was just at the Phylotastic hackathon in Tucson, AZ at the iPlant facilities at the UofA. A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant phylogenies (at least 250 or so papers...

Read more »

Getting a simple tree via NCBI

February 14, 2013
By
Getting a simple tree via NCBI

I was just at the Phylotastic hackathon in Tucson, AZ at the iPlant facilities at the UofA. A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant phylogenies (at least 250 or so papers...

Read more »

Sharing my work for “Advanced Methods III”

February 13, 2013
By
Sharing my work for “Advanced Methods III”

This semester I’m taking the live version of the Data Analysis class by Jeff Leek. His more popular version of the course is available through Coursera.  One of the things that Jeff promotes is reproducibility and sharing code. I share that tendency and thus created a Git repository for my homework and code for the class: lcollado753. I’m...

Read more »

R package building automation

February 11, 2013
By

Title: R package building automationInspired by the post at http://giventhedata.blogspot.tw/2013/02/my-r-package-development-cheat-sheet.html. I have decided to publish my cheat script for package development as well. Building package used to be a nightmare, filling in all those Rdfiles manually can cause some serious brain...

Read more »

Slideshows in R

February 7, 2013
By

A while ago I was asked to give a presentation at my job about using R to create statistical graphics. I had also just read some reviews of the Slidify package in R and I thought it would be extremely appropriate to create my presentation about visuali...

Read more »

Tables from R into Word

February 5, 2013
By
Tables from R into Word

A good looking table matters! This tutorial is on how to create a neat table in Word by combining knitr and R Markdown. I'll be using my own function, htmlTable, from the Gmisc package. Background: Because most journals that I submit to want...

Read more »

Data Visualization for Education

February 3, 2013
By

Recently I was invited to give a talk to two cohorts of Strategic Data Project fellows. I was asked to speak about using data visualization to help inform decision-making of policy makers. At the same time, the group had a lot of variation in their int...

Read more »

repmis: misc. tools for reproducible research in R

January 30, 2013
By

I've started to put together an R package called repmis. It has miscellaneous tools for reproducible research with R. The idea behind the package is to collate commands that simplify some of the common R code used within knitr-type reproducible research papers. It's still very much in the early stages of development and has two commands: LoadandCite:...

Read more »

Waiting for an API request to complete

January 26, 2013
By

Dealing with API tokens in R In my previous post I showed an example of calling the Phylotastic taxonomic name resolution API Taxosaurus here. When you query their API they give you a token which you use later to retrieve the result (see examples on their page above). However, you don't know when the query will be...

Read more »