mean calculation with data.frame in R

Question

I am a beginner in R. I am trying to calculate the between group variance using the following code.

calcBetweenGroupsVariance <- function(variable,groupvariable)
{
 # find out how many values the group variable can take
 groupvariable2 <- as.factor(groupvariable[[1]])
 levels <- levels(groupvariable2)
 numlevels <- length(levels)
 # calculate the overall grand mean:
 grandmean <- mean(variable)
 # get the mean and standard deviation for each group:
 numtotal <- 0
 denomtotal <- 0
 for (i in 1:numlevels)
 {
    leveli <- levels[i]
    levelidata <- variable[groupvariable==leveli,]
    levelilength <- length(levelidata)
    # get the mean and standard deviation for group i:
    meani <- mean(levelidata)
    sdi <- sd(levelidata)
    numi <- levelilength * ((meani - grandmean)^2)
    denomi <- levelilength
    numtotal <- numtotal + numi
    denomtotal <- denomtotal + denomi
 }
 # calculate the between-groups variance
 Vb <- numtotal / (numlevels - 1)
 Vb <- Vb[[1]]
 return(Vb)
}

However, I am getting the following error while using this function,

calcBetweenGroupsVariance (data[3],data[2])

Warning message: In mean.default(variable) : argument is not numeric or logical: returning NA

I understand something is going wrong while using the mean function.

Here is the output of str(data)

'data.frame':   45 obs. of  11 variables:
 $ V1 : int  2 3 3 2 3 2 2 2 3 2 ...
 $ V2 : num  1.3243 -2.4546 0.1352 0.0676 -1.1901 ...
 $ V3 : num  0.913 -2.644 0.663 1.217 -0.409 ...  
 $ V4 : num  -1.863 1.965 -0.698 -0.945 0.617 ...
 $ V5 : num  -0.574 1.031 -0.308 -0.574 0.354 ...
 $ V6 : num  -0.8963 2.5702 0.0736 -1.3671 0.9045 ...
 $ V7 : num  0.2276 0.0624 0.5945 0.6194 0.5473 ...
 $ V8 : num  1.304 -1.624 0.408 0.368 -0.559 ...
 $ V9 : num  -0.1827 -0.9748 -0.5158 -0.0191 -0.3053 ...  
 $ V10: num  -0.964 0.67 -0.12 0.789 0.711 ...  
 $ V11: num  -0.833 -0.833 -0.833 -0.0539 -0.0539 ...

Kindly suggest how to get rid of this error.

Thanks and regards

Answer 1

There are mutliple errors in your script related to dimensions of the arrays and the difference bewteen a vector and a list

Let's assume the arguments variable, groupvariable of your function should be vectors / 1d-arrays.

• The line groupvariable2 <- as.factor(groupvariable[[1]]) should be groupvariable2 <- as.factor(groupvariable) because groupvariable is not a list and youa re not just interested in the first element but in all.

• The line levelidata <- variable[groupvariable==leveli,] should be levelidata <- variable[groupvariable==leveli] because variable has only one dimension (it is not a matrix)

• The call to your function should be calcBetweenGroupsVariance(data[[3]], data[[2]]) (with double brackets [[]] )) or alternatively calcBetweenGroupsVariance(data[, 3],data[, 2]) or you will pass a list instead of a vector to the function.