Gleon Fellowship - User contributions [en]

Looping a Function Over Multiple Data Files - Mindy Morales

2015-01-26T19:41:47Z

Morales:

=== Usefulness of skill ===
* DOM fluorescence spectroscopy generates many large matrix files
* Files require multiple corrections, calculations, and extraction of wavelength regions to provide useful information about DOM pool
* Usually done in MATLAB; open source code has not been developed for R
* Technique is not exclusive to EEM data and can be applied to any analysis that requires applying the same operation to multiple files.

=== Challenges ===
Working directory should only contain files of specified extension that you want to analyze

=== Sample code ===
In this example, a humification index (HIX, with corrections from Ohno 2008) is calculated from multiple .csv files

;Define function
: <code>HIX<-function(low,high){sum(high)/(sum(high)+sum(low))}</code>

;Batch import csv files from wd
: <code>hixfiles <- list.files(pattern = "csv")</code>

;Create NULL vector to drop data into
: <code>hix_o <- NULL</code>

;Loop calculates HIX across all files in wd
: <code>for (i in 1:length(hixfiles)){
tmp <- read.csv(hixfiles[i])
hix_o[i] = HIX(tmp$low, tmp$high)
}</code>

;Define vector to store results
: <code>results = data.frame(hixfiles, hix_o)</code>
: <code>print(results)</code>

;Export to wd
: <code>write.csv(hix_o,file="hix.csv")</code>



{{#set:
Expertise=R_programming|
Owner=Mindy|
Progress=100|
StartDate=2015-01-26|
TargetDate=2015-01-26|
Type=Low}}

Looping a Function Over Multiple Data Files - Mindy Morales

2015-01-26T19:37:45Z

Morales: /* Sample code */

Looping a Function Over Multiple Data Files - Mindy Morales

2015-01-26T19:36:56Z

Morales: Created page with "=== Usefulness of skill === * DOM fluorescence spectroscopy generates many large matrix files * Files require multiple corrections, calculations, and extraction of wavelength..."

=== Usefulness of skill ===
* DOM fluorescence spectroscopy generates many large matrix files
* Files require multiple corrections, calculations, and extraction of wavelength regions to provide useful information about DOM pool
* Usually done in MATLAB; open source code has not been developed for R
* Technique is not exclusive to EEM data and can be applied to any analysis that requires applying the same operation to multiple files.

=== Challenges ===
Working directory should only contain files of specified extension that you want to analyze

=== Sample code ===
In this example, a humification index (HIX, with corrections from Ohno 2008) is calculated from multiple .csv files

;Define function
: <code>HIX<-function(low,high){ sum(high)/(sum(high)+sum(low))}</code>

;Batch import csv files from wd
: <code>hixfiles <- list.files(pattern = "csv")</code>

;Create NULL vector to drop data into
: <code>hix_o <- NULL</code>

;Loop calculates HIX across all files in wd
: <code>for (i in 1:length(hixfiles)){
tmp <- read.csv(hixfiles[i])
hix_o[i] = HIX(tmp$low, tmp$high)
}</code>

;Define vector to store results
: <code>results = data.frame(hixfiles, hix_o)</code>
: <code>print(results)</code>

;Export to wd
: <code>write.csv(hix_o,file="hix.csv")</code>

Skills Sharing Activity

2015-01-26T17:55:28Z

Morales:

[[Category:Task]]

==Introduction to R coding==

The first workshop began with an R Skills Sharing activity. All fellows presented on their chosen skill.

The general instructions were:
Identify a skill, tool technique you currently do not know how to implement, and learn how to carry it out. Explain the skill’s relevance to you (why did you choose it?) and to others (how can others use it?), and visualize results in a plot, if appropriate. Overall, you should aim to stretch a bit outside of your current knowledge ‘comfort zone’.

The presentations are included here.



{{#set:
Owner=Hilary|
StartDate=2015-01-12|
SubTask=Downloading_and_Processing_Radiation_Data|
SubTask=Batch_Files_-_Hilary_Dugan|
SubTask=Importing_Google_Maps_to_Plot_Data-_Kait_Farrell|
SubTask=Filling_Time-Series_Data_Gaps_-_Derek_Roberts|
SubTask=Creating_Maps_and_Assessing_Spatial_Autocorrelation|
SubTask=Zonal_Statistics_or_Extracting_Raster_Data|
SubTask=Looping_a_Function_Over_Multiple_Data_Files_-_Mindy_Morales|
TargetDate=2015-01-23|
Type=Medium}}

Participants

2015-01-23T20:29:24Z

Morales: /* Fellows */

[[Category:Task]]

===Leadership Team===
{| class="wikitable"
! Name
! Institution
|-
| Paul Hanson
| University of Wisconsin-Madison
|-
| Kathleen Weathers
| Cary Institute
|-
| Grace Hong
| University of Wisconsin-Madison
|-
| Hilary Dugan
| University of Wisconsin-Madison
|}

===Fellows===
{| class="wikitable"
! Name
! Institution
|-
|Kait Farrell
|University of Georgia
|-
|Flora Krivak-Tetley
| Dartmouth College
|-
| Ian McCullough
| University of California, Santa Barbara
|-
| Mindy Morales
| Iowa State
|-
| Derek Roberts
| University of California, Davis
|-
| Nick Skaff
| Michigan State University
|}



{{#set:
Owner=Hilary|
Progress=50|
StartDate=2015-01-11|
TargetDate=2015-01-16|
Type=Low}}