Imputation of missing data in life-history trait datasets: which approach performs the best?

Penone, Caterina, Davidson, Ana D., Shoemaker, Kevin T., Di Marco, Moreno, Rondinini, Carlo, Brooks, Thomas M., Young, Bruce E., Graham, Catherine H. and Costa, Gabriel C. (2014) Imputation of missing data in life-history trait datasets: which approach performs the best?. Methods in Ecology and Evolution, 5 9: 1-10. doi:10.1111/2041-210X.12232


Author Penone, Caterina
Davidson, Ana D.
Shoemaker, Kevin T.
Di Marco, Moreno
Rondinini, Carlo
Brooks, Thomas M.
Young, Bruce E.
Graham, Catherine H.
Costa, Gabriel C.
Title Imputation of missing data in life-history trait datasets: which approach performs the best?
Journal name Methods in Ecology and Evolution   Check publisher's open access policy
ISSN 2041-210X
Publication date 2014-09
Sub-type Article (original research)
DOI 10.1111/2041-210X.12232
Open Access Status Not yet assessed
Volume 5
Issue 9
Start page 1
End page 10
Total pages 10
Place of publication Chichester, West Sussex United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Formatted abstract
1. Despite efforts in data collection, missing values are commonplace in life-history trait databases. Because these values typically are not missing randomly, the common practice of removing missing data not only reduces sample size, but also introduces bias that can lead to incorrect conclusions. Imputing missing values is a potential solution to this problem. Here, we evaluate the performance of four approaches for estimating missing values in trait databases (K-nearest neighbour (kNN), multivariate imputation by chained equations (mice), missForest and Phylopars), and test whether imputed datasets retain underlying allometric relationships among traits.

2. Starting with a nearly complete trait dataset on the mammalian order Carnivora (using four traits), we artificially removed values so that the percent of missing values ranged from 10% to 80%. Using the original values as a reference, we assessed imputation performance using normalized root mean squared error. We also evaluated whether including phylogenetic information improved imputation performance in kNN, mice, and missForest (it is a required input in Phylopars). Finally, we evaluated the extent to which the allometric relationship between two traits (body mass and longevity) was conserved for imputed datasets by looking at the difference (bias) between the slope of the original and the imputed datasets or datasets with missing values removed.

3. Three of the tested approaches (mice, missForest and Phylopars), resulted in qualitatively equivalent imputation performance, and all had significantly lower errors than kNN. Adding phylogenetic information into the imputation algorithms improved estimation of missing values for all tested traits. The allometric relationship between body mass and longevity was conserved when up to 60% of data were missing, either with or without phylogenetic information, depending on the approach. This relationship was less biased in imputed datasets compared to datasets with missing values removed, especially when more than 30% of values were missing.

4. Imputations provide valuable alternatives to removing missing observations in trait databases as they produce low errors and retain relationships among traits. Although we must continue to prioritize data collection on species traits, imputations can provide a valuable solution for conducting macroecological and evolutionary studies using life-history trait databases.
Keyword Body mass
Carnivores
KNN
Longevity
MissForest
Multivariate imputation by chained equations
Phylogeny
Phylopars
Rootmean squared error
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Biological Sciences Publications
 
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