DOI: 10.5061/dryad.crjdfn37m
title: Data from: A real data-driven simulation strategy to select an imputation method for mixed-type trait data

description: Missing observations in trait datasets pose an obstacle for analyses in
 myriad biological disciplines. Considering the mixed results of
 imputation, the wide variety of available methods, and the varied
 structure of real trait datasets, a framework for selecting a suitable
 imputation method is advantageous. We invoked a real data-driven
 simulation strategy to select an imputation method for a given mixed-type
 (categorical, count, continuous) target dataset. Candidate methods
 included mean/mode imputation, k-nearest neighbour, random
 forests, and multivariate imputation by chained equations (MICE). Using a
 trait dataset of squamates (lizards and amphisbaenians; order: Squamata)
 as a target dataset, a complete-case dataset consisting of species with
 nearly completed information was formed for the imputation method
 selection. Missing data were induced by removing values from this dataset
 under different missingness mechanisms: missing completely at random
 (MCAR), missing at random (MAR), and missing not at random (MNAR). For
 each method, combinations with and without phylogenetic information from
 single gene (nuclear and mitochondrial) or multigene trees were used to
 impute the missing values for five numerical and two categorical traits.
 The performances of the methods were evaluated under each missing
 mechanism by determining the mean squared error and proportion falsely
 classified rates for numerical and categorical traits, respectively. A
 random forest method supplemented with a nuclear-derived phylogeny
 resulted in the lowest error rates for the majority of traits, and this
 method was used to impute missing values in the original dataset. Data
 with imputed values better reflected the characteristics and distributions
 of the original data compared to complete-case data. However, caution
 should be taken when imputing trait data as phylogeny did not always
 improve performance for every trait and in every scenario. Ultimately,
 these results support the use of a real data-driven simulation strategy
 for selecting a suitable imputation method for a given mixed-type trait
 dataset.
description: Cytochrome <em>c</em> oxidase subunit I (COI)
 sequence records were originally downloaded from The Barcode of Life Data
 System (BOLD) (Ratnasingham & Hebert, 2007) (sequence data
 available at dx.doi.org/10.5883/DS-IMPMIX2). Data were filtered for
 records that have been identified to the species level. Additional quality
 control checks on the sequence data included trimming N and gap content
 from sequence ends and removing sequences with greater than 1% of internal
 N and/or gap content across their entire sequence
 length. The <em>AlignTranslation</em> function from the R
 package “DECIPHER” v. 2.18.1 (Wright, 2015, 2020) was used to perform a
 multiple sequence alignment on the COI sequences.
 Phylogenetic trees were built using RAxML v. 8 (Stamatakis,
 2014). The model GTRGAMMAI was specified (option -m), and the alignments
 were partitioned based on codon position (option -q). Nuclear sequence
 data used for building the c-mos, RAG1 and multigene trees were obtained
 from a multigene alignment published in Pyron et al. (2013) available
 at https://doi.org/10.5061/dryad.82h0m. GenBank accession numbers for the sequence records used to build the tree in S2 File. Citations/data sources: Pyron RA, Burbrink FT, Wiens JJ. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol. 2013 Apr 29;13(1):93. Pyron RA, Burbrink FT, Wiens JJ. Data from: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. Dryad Dataset [Internet]. 2013; Available from: https://doi.org/10.5061/dryad.82h0m Ratnasingham S, Hebert PDN. bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes. 2007 May 1;7(3):355–64. Data from: Barcode of Life Data System: DS-IMPMIX2: Squamata cytochrome c oxidase subunit I (COI) dataset. [Internet]. 2020. Available from: dx.doi.org/10.5883/DS-IMPMIX2 Sayers EW, Cavanaugh M, Clark K, Ostell J, Pruitt KD, Karsch-Mizrachi, I. GenBank. Nucleic Acids Research. 2020;48:D84-D86. Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.  Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics. 2015 Oct 6;16(1):322. Wright ES. RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. RNA. 2020 May 1;26(5):531–40.
description: Alignment and phylogenetic trees may be opened and visualized by
 software capable of handling Newick and FASTA file formats.