scholarly journals fullfact: an R package for the analysis of genetic and maternal variance components from full factorial mating designs

2016 ◽  
Vol 6 (6) ◽  
pp. 1656-1665 ◽  
Author(s):  
Aimee Lee S. Houde ◽  
Trevor E. Pitcher
Author(s):  
Jose J. Marulanda ◽  
Xuefei Mi ◽  
H. Friedrich Utz ◽  
Albrecht E. Melchinger ◽  
Tobias Würschum ◽  
...  

Abstract Key message A breeding strategy combining genomic with one-stage phenotypic selection maximizes annual selection gain for net merit. Choice of the selection index strongly affects the selection gain expected in individual traits. Abstract Selection indices using genomic information have been proposed in crop-specific scenarios. Routine use of genomic selection (GS) for simultaneous improvement of multiple traits requires information about the impact of the available economic and logistic resources and genetic properties (variances, trait correlations, and prediction accuracies) of the breeding population on the expected selection gain. We extended the R package “selectiongain” from single trait to index selection to optimize and compare breeding strategies for simultaneous improvement of two traits. We focused on the expected annual selection gain (ΔGa) for traits differing in their genetic correlation, economic weights, variance components, and prediction accuracies of GS. For all scenarios considered, breeding strategy GSrapid (one-stage GS followed by one-stage phenotypic selection) achieved higher ΔGa than classical two-stage phenotypic selection, regardless of the index chosen to combine the two traits and the prediction accuracy of GS. The Smith–Hazel or base index delivered higher ΔGa for net merit and individual traits compared to selection by independent culling levels, whereas the restricted index led to lower ΔGa in net merit and divergent results for selection gain of individual traits. The differences among the indices depended strongly on the correlation of traits, their variance components, and economic weights, underpinning the importance of choosing the selection indices according to the goal of the breeding program. We demonstrate our theoretical derivations and extensions of the R package “selectiongain” with an example from hybrid wheat by designing indices to simultaneously improve grain yield and grain protein content or sedimentation volume.


2021 ◽  
Author(s):  
Donald Ray Williams ◽  
Josue E. Rodriguez ◽  
Paul - Christian Bürkner

We shed much needed light upon a critical assumption that is oft-overlooked---or not considered at all---in random-effects meta-analysis.Namely, that between-study variance is constant across \emph{all} studies which implies they are from the \emph{same} population. Yet it is not hard to imagine a situation where there are several and not merely one population of studies, perhaps differing in their between-study variance (i.e., heteroskedasticity). The objective is to then make inference, given that there are variations in heterogeneity. There is an immediate problem, however, in that modeling heterogeneous variance components is not straightforward to do in a general way. To this end, we propose novel methodology, termed Bayesian location-scale meta-analysis, that can accommodate moderators for both the overall effect (location) and the between-study variance (scale). After introducing the model, we then extend heterogeneity statistics, prediction intervals, and hierarchical shrinkage, all of which customarily assume constant heterogeneity, to include variations therein. With these new tools in hand, we go to work demonstrating that quite literally \emph{everything} changes when between-study variance is not constant across studies. The changes were not small and easily passed the interocular trauma test---the importance hits right between the eyes. Such examples include (but are not limited to) inference on the overall effect, a compromised predictive distribution, and improper shrinkage of the study-specific effects. Further, we provide an illustrative example where heterogeneity was not considered a mere nuisance to show that modeling variance for its own sake can provide unique inferences, in this case into discrimination across nine countries. The discussion includes several ideas for future research. We have implemented the proposed methodology in the {\tt R} package \textbf{blsmeta}.


2020 ◽  
Author(s):  
Donald Ray Williams

In mixed-effects (a.k.a, hierarchical or multilevel) models, intraclass correlation coefficients (ICC) are commonly computed, with applications spanning from characterizing group-level homogeneity to measurement reliability. While there are a wide spectrum of applications, an underlying assumption of each is that the variance components used in their computation are fixed and non-varying. The methodology in the R package \textbf{vICC} was specifically designedto quantify variation in the ICC. This can be used to identify groups that are more (or less) homogeneous, as well as which groups are adequately described by the non-varying ICC. I end with future directions.


2009 ◽  
Vol 39 (2) ◽  
pp. 495-514 ◽  
Author(s):  
Hassine Belhadj ◽  
Vincent Goulet ◽  
Tommy Ouellet

AbstractOne can find in the literature three main sets of estimators for the variance components in the hierarchical credibility model. This paper presents these estimators in a unified notation, studies some of their properties important for numerical evaluation and compares their relative performance by simulation. The paper also demonstrates how function cm of the R package actuar can be used to fit hierarchical models to insurance data.


2021 ◽  
Author(s):  
Weihua Zhang ◽  
Ruiyan Wei ◽  
Yan Liu ◽  
Yuanzhen Lin

Progeny tests play important roles in plant and animal breeding programs, and mixed linear models are usually performed to estimate variance components of random effects, estimate the fixed effects (Best Linear Unbiased Estimates, BLUEs) and predict the random effects (Best Linear Unbiased Predictions, BLUPs) via restricted maximum likehood (REML) methods in progeny test datasets. The current pioneer software for genetic assessment is ASReml, but it is commercial and expensive. Although there is free software such as Echidna or the R package sommer, the Echidna syntax is complex and the R package functionality is limited. Therefore, this study aims to develop a R package named AFEchidna based on Echidna software. The mixed linear models are conveniently implemented for users through the AFEchidna package to solve variance components, genetic parameters and the BLUP values of random effects, and the batch analysis of multiple traits, multiple variance structures and multiple genetic parameters can be also performed, as well as comparison between different models and genomic BLUP analysis. The AFEchidna package is free, please email us ([email protected]) to get a copy if one is interested for it. The AFEchidna package is developed to expand free genetic assessment software with the expectation that its efficiency could be close to the commercial software.


Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
C Roullier ◽  
Y Guitton ◽  
S Prado ◽  
O Grovel ◽  
YF Pouchus

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.


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