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POLooping and storing results over many data frames
 

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    <p>I want to to perform at least six looping steps in R. My data sets are <a href="https://drive.google.com/folderview?id=0B90n5RdIvP6qbkNaUG1rTXN5OFE&amp;usp=sharing" rel="nofollow">28 files</a> stored in one folder. Each file has 22 rows (21 individual cases and one row for column names) and columns as follows: Id, id, PC1, PC2….PC20.</p> <p>I intend to: </p> <ol> <li>read each file into R as a data frame</li> <li>delete first column named “Id” in the each data frame </li> <li><p>arrange each data frame as follows:</p> <ul> <li><p>first column should be “id” and </p></li> <li><p>next ten columns should be first ten PCs (PC1, PC2, …PC10)</p></li> </ul></li> <li>sort each data frame according to “id” (data frames should have the same order of individuals and their respective PC’s scores)</li> <li>perform pairwise comparison by <strong>protest function</strong> in the <em>vegan</em> package among all possible pair’s combinations (378 combinations)</li> <li>store result of each pair’s comparison in a symmetric (28*28) matrix which will be used in further analysis</li> </ol> <p>At the moment I am able to do it manually for each pair of data (code is below):</p> <pre><code>## 1. step ## read files into R as a data frame c_2d_hand_1a&lt;-read.table("https://googledrive.com/host/0B90n5RdIvP6qbkNaUG1rTXN5OFE/PC scores, c_2d_hand-1a, Symmetric component.txt",header=T) c_2d_hand_1b&lt;-read.table("https://googledrive.com/host/0B90n5RdIvP6qbkNaUG1rTXN5OFE/PC scores, c_2d_hand-1b, Symmetric component.txt",header=T) ## 2. step ## delete first column named “Id” in the each data frame c_2d_hand_1a[,1]&lt;-NULL c_2d_hand_1b[,1]&lt;-NULL ## 3. step ## arrange each data frame that have 21 rows and 11 columns (id,PC1,PC2..PC10) c_2d_hand_1a&lt;-c_2d_hand_1a[,1:11] c_2d_hand_1b&lt;-c_2d_hand_1b[,1:11] ## 4. step ## sort each data frame according to “id” c_2d_hand_1a&lt;-c_2d_hand_1a[order(c_2d_hand_1a$id),] c_2d_hand_1b&lt;-c_2d_hand_1b[order(c_2d_hand_1b$id),] ## 5. step ## perform pairwise comparison by protest function library(permute) library(vegan) c_2d_hand_1a_c_2d_hand_1b&lt;-protest(c_2d_hand_1a[,2:ncol(c_2d_hand_1a)],c_2d_hand_1b[,2:ncol(c_2d_hand_1b)],permutations=10000) summary(c_2d_hand_1a_c_2d_hand_1b)[2] ## or c_2d_hand_1a_c_2d_hand_1b[3] </code></pre> <p>Since I am a newbie in data handling/manipulation in R, my self-learning skills are suitable to perform respective steps manually, typing codes for each data set and perform each pairwise comparisons at the time. Since I need to perform those six steps 378 times, manual typing would be exhaustive and time consuming. </p> <p>I tried to import files as a list and tried several operations, but I was unsuccessful. Specifically, using list.files(), I made the list, called “probe”. I was able to select certain data frame using e.g. probe[2]. Also I could assess column “Id” by e.g. probe&#91;2]&#91;1], and deleted it by probe&#91;2]&#91;1]&lt;-NULL. But when I tried to work with for loop, I was stuck. </p>
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    1. COYou should use lists anad `lapply`/`sapply`, along with `list.files`.
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      1. USRoman Luštrik
    2. COTnx Roman, I tried it prior to my post. However, I had a struggle with handling of those function because of inexperience.
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