Home/ Questions/Error in do_one(nmeth) : na/nan/inf in foreign function call (arg 1) - Simple way to solve it
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Agathe Couturier
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Asked: 2022-05-12T07:36:19+00:00 In:

Error in do_one(nmeth) : na/nan/inf in foreign function call (arg 1) – Simple way to solve it

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I have the following r code, but I do not know how to find the correct result. Why has this problem occurred, and how can it be solved? This is the code I am running:

#create data frame df 

<- data.frame(var1=c(2, 4, 4, 6, 7, 8, 8, 9, 9, 12), 
              
              var2=c(12, 14, 14, 8, 8, 15, 16, 9, 9, 11), 
              
              var3=c(22, NA, 23, 24, 28, 23, 19, 16, 12, 15)) 


row.names(df) <- LETTERS[1:10] 


#view data frame 

df 


 
 var1 var2 var3 

A   2   12   22 

B   4   14   NA 

C   4   14   23 

D   6    8   24 

E   7    8   28 

F   8   15   23 

G   8   16   19 

H   9    9   16 

I   9    9   12 

J  12   11   15

This is the error text I receive:

#attempt to perform k-means clustering with k = 3 clusters
km <- kmeans(df, centers = 3)

Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
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2 Answers

  1. Best Answer
    Expert

    The cause: The reason is that when you attempt to perform k-means clustering in R but the data frame you’re using misses one or more values.

    Solution: The simpliest way to fix this error is to use the na.omit() function to remove rows with missing values from the data frame:

    #remove rows with NA values
df <- na.omit(df)

#perform k-means clustering with k = 3 clusters
km <- kmeans(df, centers = 3)

#view results
km

K-means clustering with 3 clusters of sizes 4, 3, 2

Cluster means:
  var1      var2     var3
1  5.5 14.250000 21.75000
2 10.0  9.666667 14.33333
3  6.5  8.000000 26.00000

Clustering vector:
A C D E F G H I J 
1 1 3 3 1 1 2 2 2 

Within cluster sum of squares by cluster:
[1] 46.50000 17.33333  8.50000
 (between_SS / total_SS =  79.5 %)

Available components:

[1] "cluster"      "centers"      "totss"        "withinss"     "tot.withinss"
[6] "betweenss"    "size"         "iter"         "ifault"
    • 18

  2. Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)

    This error can also be caused by non-numerical values in the table.

    • 17

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