Advances in methodology for random regression analyses

2005 ◽  
Vol 45 (8) ◽  
pp. 847 ◽  
Author(s):  
K. Meyer
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Full Rank ◽  
Random Regression ◽  
Regression Analyses ◽  
Rank Estimation ◽  
Reduced Rank ◽  
Combined Application ◽  
Spline Basis ◽  
Small Set

Random regression analyses have become standard methodology for the analysis of traits with repeated records that are thought of as representing points on a trajectory. Modelling curves as a regression on functions of a continuous covariable, such as time, for each individual, random regression models are readily implemented in standard, linear mixed model analyses. Early applications have made extensive use of regressions on orthogonal polynomials. Recently, spline functions have been considered as an alternative. The use of a particular type of spline function, the so-called B-splines, as basis functions for random regression analyses is outlined, emphasising the local influence of individual observations and low degree of polynomials employed. While such analyses are likely to involve more regression coefficients than polynomial models, it is demonstrated that reduced rank estimation via the leading principal components is feasible and likely to yield more parsimonious models and more stable estimates than full rank analyses. The combined application of B-spline basis function and reduced rank estimation is illustrated for a small set of data for beef cattle.

scholarly journals A Novel Approach to the Design and Analysis of Field Experiments to Study Variation in the Tolerance and Resistance of Cultivars to Root Lesion Nematodes (Pratylenchus spp.)

2020 ◽  
Vol 110 (10) ◽  
pp. 1623-1631
Author(s):  
Karyn L. Reeves ◽  
Clayton R. Forknall ◽  
Alison M. Kelly ◽  
Kirsty J. Owen ◽  
Joshua Fanning ◽  
...  
Keyword(s):  
Mixed Model ◽  
Field Experiments ◽  
Linear Mixed Model ◽  
Random Regression ◽  
Yield Response ◽  
Response Curves ◽  
Model Framework ◽  
Management Options ◽  
Nematode Reproduction ◽  
Yield Response Curves

The root lesion nematode (RLN) species Pratylenchus thornei and P. neglectus are widely distributed within cropping regions of Australia and have been shown to limit grain production. Field experiments conducted to compare the performance of cultivars in the presence of RLNs investigate management options for growers by identifying cultivars with resistance, by limiting nematode reproduction, and tolerance, by yielding well in the presence of nematodes. A novel experimental design approach for RLN experiments is proposed where the observed RLN density, measured prior to sowing, is used to condition the randomization of cultivars to field plots. This approach ensured that all cultivars were exposed to consistent ranges of RLN in order to derive valid assessments of relative cultivar tolerance and resistance. Using data from a field experiment designed using the conditioned randomization approach and conducted in Formartin, Australia, the analysis of tolerance and resistance was undertaken in a linear mixed model framework. Yield response curves were derived using a random regression approach and curves modeling change in RLN densities between sowing and harvest were derived using splines to account for nonlinearity. Groups of cultivars sharing similar resistance levels could be identified. A comparison of slopes of yield response curves of cultivars belonging to the same resistance class identified differing tolerance levels for cultivars with equivalent exposures to both presowing and postharvest RLN densities. As such, the proposed design and analysis approach allowed tolerance to be assessed independently of resistance.

scholarly journals The association between circulating levels of vitamin D and inflammatory markers in the first 2 years after colorectal cancer diagnosis

2020 ◽  
Vol 13 ◽  
pp. 175628482092392 ◽  
Author(s):  
Evertine Wesselink ◽  
Michiel Balvers ◽  
Martijn J. L. Bours ◽  
Johannes H. W. de Wilt ◽  
Renger F. Witkamp ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Vitamin D ◽  
Cancer Progression ◽  
Inflammatory Markers ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Active Form ◽  
Inverse Association ◽  
Z Score ◽  
Regression Analyses

Background: Calcitriol, the active form of vitamin D, may inhibit colorectal cancer (CRC) progression, which has been mechanistically linked to an attenuation of a pro-inflammatory state. The present study investigated the associations between circulating 25 hydroxy vitamin D3 (25(OH)D3) levels and inflammatory markers (IL10, IL8, IL6, TNFα and hsCRP) in the 2 years following CRC diagnosis. Methods: Circulating 25(OH)D3 levels and inflammatory markers were assessed at diagnosis, after 6, 12 and 24 months from 798 patients with sporadic CRC participating in two prospective cohort studies. Associations between 25(OH)D3 levels and individual inflammatory markers as well as a summary inflammatory z-score were assessed at each time point by multiple linear regression analyses. To assess the association between 25(OH)D3 and inflammatory markers over the course of 2 years, linear mixed model regression analyses were conducted. Results: Higher 25(OH)D3 levels were associated with lower IL6 levels at diagnosis, at 6 months after diagnosis and over the course of 2 years (β −0.06, 95% CI −0.08 to −0.04). In addition, 25(OH)D3 levels were inversely associated with the summary inflammatory z-score at diagnosis and over the course of 2 years (β −0.17, 95% CI −0.25 to −0.08). In addition, a significant inverse association between 25(OH)D3 levels and IL10 was found over the course of 2 years. Intra-individual analyses showed an inverse association between 25(OH)D3 and IL10, IL6 and TNFα. No statistically significant associations between 25(OH)D3 and IL8 and hsCRP levels were observed. Conclusions: Serum 25(OH)D3 levels were inversely associated with the summary inflammatory z-score and in particular with IL6 in the years following CRC diagnosis. This is of potential clinical relevance as IL6 has an important role in chronic inflammation and is also suggested to stimulate cancer progression. Further observational studies should investigate whether a possible 25(OH)D3-associated reduction of inflammatory mediators influences treatment efficacy and CRC recurrence.

scholarly journals MTG2: An efficient algorithm for multivariate linear mixed model analysis based on genomic information

2015 ◽  
Author(s):  
Sang Hong Lee ◽  
Julius van der Werf
Keyword(s):  
Complex Traits ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Covariance Structure ◽  
Random Regression ◽  
Current Standard ◽  
Model Framework ◽  
Genetic Covariance ◽  
Mixed Model Analysis ◽  
Mixed Model Equation

We have developed an algorithm for genetic analysis of complex traits using genome-wide SNPs in a linear mixed model framework. Compared to current standard REML software based on the mixed model equation, our method could be more than 1000 times faster. The advantage is largest when there is only a single genetic covariance structure. The method is particularly useful for multivariate analysis, including multi-trait models and random regression models for studying reaction norms. We applied our proposed method to publicly available mice and human data and discuss advantages and limitations.

scholarly journals Up hill, down dale: quantitative genetics of curvaceous traits

2005 ◽  
Vol 360 (1459) ◽  
pp. 1443-1455 ◽  
Author(s):  
Karin Meyer ◽  
Mark Kirkpatrick
Keyword(s):  
Quantitative Genetics ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Selection Response ◽  
Repeated Measurements ◽  
Random Regression ◽  
Model Framework ◽  
Covariance Functions ◽  
Continuous Scale ◽  
Estimated Breeding Values

‘Repeated’ measurements for a trait and individual, taken along some continuous scale such as time, can be thought of as representing points on a curve, where both means and covariances along the trajectory can change, gradually and continually. Such traits are commonly referred to as ‘function-valued’ (FV) traits. This review shows that standard quantitative genetic concepts extend readily to FV traits, with individual statistics, such as estimated breeding values and selection response, replaced by corresponding curves, modelled by respective functions. Covariance functions are introduced as the FV equivalent to matrices of covariances. Considering the class of functions represented by a regression on the continuous covariable, FV traits can be analysed within the linear mixed model framework commonly employed in quantitative genetics, giving rise to the so-called random regression model. Estimation of covariance functions, either indirectly from estimated covariances or directly from the data using restricted maximum likelihood or Bayesian analysis, is considered. It is shown that direct estimation of the leading principal components of covariance functions is feasible and advantageous. Extensions to multi-dimensional analyses are discussed.

Analyzing discontinuities in longitudinal count data: A multilevel generalized linear mixed model.

2020 ◽  
Author(s):  
James L. Peugh ◽  
Sarah J. Beal ◽  
Meghan E. McGrady ◽  
Michael D. Toland ◽  
Constance Mara
Keyword(s):  
Count Data ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Longitudinal Count Data

Predicting bycatch hotspots based on suitable habitat derived from fishery-independent data

2020 ◽  
Vol 641 ◽  
pp. 159-175
Author(s):  
J Runnebaum ◽  
KR Tanaka ◽  
L Guan ◽  
J Cao ◽  
L O’Brien ◽  
...  
Keyword(s):  
Habitat Suitability ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Homarus Americanus ◽  
Management Tool ◽  
American Lobster ◽  
Suitable Habitat ◽  
Climate Conditions ◽  
Suitability Index

Bycatch remains a global problem in managing sustainable fisheries. A critical aspect of management is understanding the timing and spatial extent of bycatch. Fisheries management often relies on observed bycatch data, which are not always available due to a lack of reporting or observer coverage. Alternatively, analyzing the overlap in suitable habitat for the target and non-target species can provide a spatial management tool to understand where bycatch interactions are likely to occur. Potential bycatch hotspots based on suitable habitat were predicted for cusk Brosme brosme incidentally caught in the Gulf of Maine American lobster Homarus americanus fishery. Data from multiple fisheries-independent surveys were combined in a delta-generalized linear mixed model to generate spatially explicit density estimates for use in an independent habitat suitability index. The habitat suitability indices for American lobster and cusk were then compared to predict potential bycatch hotspot locations. Suitable habitat for American lobster has increased between 1980 and 2013 while suitable habitat for cusk decreased throughout most of the Gulf of Maine, except for Georges Basin and the Great South Channel. The proportion of overlap in suitable habitat varied interannually but decreased slightly in the spring and remained relatively stable in the fall over the time series. As Gulf of Maine temperatures continue to increase, the interactions between American lobster and cusk are predicted to decline as cusk habitat continues to constrict. This framework can contribute to fisheries managers’ understanding of changes in habitat overlap as climate conditions continue to change and alter where bycatch interactions could occur.

Long-term seizure outcomes after pediatric temporal lobectomy: does brain MRI lesion matter?

2019 ◽  
Vol 24 (2) ◽  
pp. 200-208
Author(s):  
Ravindra Arya ◽  
Francesco T. Mangano ◽  
Paul S. Horn ◽  
Sabrina K. Kaul ◽  
Serena K. Kaul ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Hippocampal Sclerosis ◽  
Brain Mri ◽  
Temporal Lobectomy ◽  
Seizure Freedom ◽  
Seizure Onset

OBJECTIVEThere is emerging data that adults with temporal lobe epilepsy (TLE) without a discrete lesion on brain MRI have surgical outcomes comparable to those with hippocampal sclerosis (HS). However, pediatric TLE is different from its adult counterpart. In this study, the authors investigated if the presence of a potentially epileptogenic lesion on presurgical brain MRI influences the long-term seizure outcomes after pediatric temporal lobectomy.METHODSChildren who underwent temporal lobectomy between 2007 and 2015 and had at least 1 year of seizure outcomes data were identified. These were classified into lesional and MRI-negative groups based on whether an epilepsy-protocol brain MRI showed a lesion sufficiently specific to guide surgical decisions. These patients were also categorized into pure TLE and temporal plus epilepsies based on the neurophysiological localization of the seizure-onset zone. Seizure outcomes at each follow-up visit were incorporated into a repeated-measures generalized linear mixed model (GLMM) with MRI status as a grouping variable. Clinical variables were incorporated into GLMM as covariates.RESULTSOne hundred nine patients (44 females) were included, aged 5 to 21 years, and were classified as lesional (73%), MRI negative (27%), pure TLE (56%), and temporal plus (44%). After a mean follow-up of 3.2 years (range 1.2–8.8 years), 66% of the patients were seizure free for ≥ 1 year at last follow-up. GLMM analysis revealed that lesional patients were more likely to be seizure free over the long term compared to MRI-negative patients for the overall cohort (OR 2.58, p < 0.0001) and for temporal plus epilepsies (OR 1.85, p = 0.0052). The effect of MRI lesion was not significant for pure TLE (OR 2.64, p = 0.0635). Concordance of ictal electroencephalography (OR 3.46, p < 0.0001), magnetoencephalography (OR 4.26, p < 0.0001), and later age of seizure onset (OR 1.05, p = 0.0091) were associated with a higher likelihood of seizure freedom. The most common histological findings included cortical dysplasia types 1B and 2A, HS (40% with dual pathology), and tuberous sclerosis.CONCLUSIONSA lesion on presurgical brain MRI is an important determinant of long-term seizure freedom after pediatric temporal lobectomy. Pediatric TLE is heterogeneous regarding etiologies and organization of seizure-onset zones with many patients qualifying for temporal plus nosology. The presence of an MRI lesion determined seizure outcomes in patients with temporal plus epilepsies. However, pure TLE had comparable surgical seizure outcomes for lesional and MRI-negative groups.

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