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POR KNN imputation - function returning erroneous results & missing help page
 

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  1. POR KNN imputation - function returning erroneous results & missing help page
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    <p>I'm trying to impute some missing values in <code>R</code> using <code>library(imputation)</code> and <code>kNNImpute()</code>. The input data frame is 44 rows of 13 variables. There are 30 complete observations and 14 observations with missing values in 2 columns.</p> <p>The code is saying it's imputing all the missing values; however, it's imputing the last 4 values as <code>0</code>. From my reading of the code, this appears to be a flaw based on using <code>0</code> as a default for errors. My code:</p> <pre><code># impute data library(imputation) knn_data &lt;- kNNImpute(x, k= 5) # examine kNNImpute code kNNImpute </code></pre> <p><code>kNNImpute</code>'s code: See lines 4, 8 the function starting on line 24 and the 2nd line from the bottom (line 48):</p> <pre><code>[4] prelim = impute.prelim(x) [8] x.missing = prelim$x.missing [24] x.missing.imputed = t(apply(x.missing, 1, function(i) {...} [48] x[missing.matrix2] = 0 </code></pre> <p><code>??impute.prelim</code> returns no results (the help page is missing). So, I can't examine this code. </p> <p>However, the program flow for <code>kNNImpute</code> appears to be </p> <pre><code>[4] # run a (seemingly undefined) screening function [8] # pull in the missing rows for later imputation [24] # run imputation function [48] # based on line [4] output, impute all "error rows" == 0 </code></pre> <p>Can anyone explain why this is happening and/or how to solve this problem? </p> <p><strong>FYI</strong>- I have emailed the package author a link to this page.</p>
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    1. USAlex W
    1. USAlex W
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    1. CO`impute.prelim` is perfectly well defined, it's just not exported. Try `imputation:::impute.prelim`. I agree, though, that setting all values not successfully imputed to 0 should at least be documented (which I don't see).
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      1. USjoran
    2. COTry `Amelia` or other `mi` packages?
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      1. USagstudy
    3. COI also can't find the documentation for these two internal functions required for the function on line [24]: `pdist` (line 40) and `.dist.2dto1d` (line 36)
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      1. USAlex W
 

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