scholarly journals Deletion diagnostics for the generalised linear mixed model with independent random effects

2015 ◽  
Vol 35 (9) ◽  
pp. 1488-1501 ◽  
Author(s):  
B. Ganguli ◽  
S. Sen Roy ◽  
M. Naskar ◽  
E. J. Malloy ◽  
E. A. Eisen
Keyword(s):  
Random Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalised Linear Mixed Model ◽  
Deletion Diagnostics

scholarly journals Bayesian spatial and spatio-temporal approaches to modelling dengue fever: a systematic review

2018 ◽  
Vol 147 ◽  
Author(s):  
A. Aswi ◽  
S. M. Cramb ◽  
P. Moraga ◽  
K. Mengersen
Keyword(s):  
Dengue Fever ◽  
Random Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Assessment Tool ◽  
Temporal Dynamics ◽  
Random Effect ◽  
Temperature And Precipitation ◽  
Generalised Linear Mixed Model ◽  
Spatio Temporal

AbstractDengue fever (DF) is one of the world's most disabling mosquito-borne diseases, with a variety of approaches available to model its spatial and temporal dynamics. This paper aims to identify and compare the different spatial and spatio-temporal Bayesian modelling methods that have been applied to DF and examine influential covariates that have been reportedly associated with the risk of DF. A systematic search was performed in December 2017, using Web of Science, Scopus, ScienceDirect, PubMed, ProQuest and Medline (via Ebscohost) electronic databases. The search was restricted to refereed journal articles published in English from January 2000 to November 2017. Thirty-one articles met the inclusion criteria. Using a modified quality assessment tool, the median quality score across studies was 14/16. The most popular Bayesian statistical approach to dengue modelling was a generalised linear mixed model with spatial random effects described by a conditional autoregressive prior. A limited number of studies included spatio-temporal random effects. Temperature and precipitation were shown to often influence the risk of dengue. Developing spatio-temporal random-effect models, considering other priors, using a dataset that covers an extended time period, and investigating other covariates would help to better understand and control DF transmission.

scholarly journals The generalizability crisis

2020 ◽  
pp. 1-37
Author(s):  
Tal Yarkoni
Keyword(s):  
Quantitative Analysis ◽  
Statistical Inference ◽  
Random Effects ◽  
False Positive ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Random Effect ◽  
Statistical Procedures ◽  
Subject Variability ◽  
Replication Crisis

Abstract Most theories and hypotheses in psychology are verbal in nature, yet their evaluation overwhelmingly relies on inferential statistical procedures. The validity of the move from qualitative to quantitative analysis depends on the verbal and statistical expressions of a hypothesis being closely aligned—that is, that the two must refer to roughly the same set of hypothetical observations. Here I argue that many applications of statistical inference in psychology fail to meet this basic condition. Focusing on the most widely used class of model in psychology—the linear mixed model—I explore the consequences of failing to statistically operationalize verbal hypotheses in a way that respects researchers' actual generalization intentions. I demonstrate that whereas the "random effect" formalism is used pervasively in psychology to model inter-subject variability, few researchers accord the same treatment to other variables they clearly intend to generalize over (e.g., stimuli, tasks, or research sites). The under-specification of random effects imposes far stronger constraints on the generalizability of results than most researchers appreciate. Ignoring these constraints can dramatically inflate false positive rates, and often leads researchers to draw sweeping verbal generalizations that lack a meaningful connection to the statistical quantities they are putatively based on. I argue that failure to take the alignment between verbal and statistical expressions seriously lies at the heart of many of psychology's ongoing problems (e.g., the replication crisis), and conclude with a discussion of several potential avenues for improvement.

scholarly journals 103 Periodontal Health and Sarcopenia: Cross-Sectional Evidence From A Cohort of 2040 Twin Volunteers

2021 ◽  
Vol 50 (Supplement_1) ◽  
pp. i12-i42
Author(s):  
M B Zazzara ◽  
P M Wells ◽  
R C E Bowyer ◽  
M N Lochlainn ◽  
E J Thompson ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Frailty Index ◽  
Muscle Quality ◽  
Low Grade ◽  
Periodontal Health ◽  
Cross Sectional ◽  
Age Related ◽  
European Working ◽  
Generalised Linear Mixed Model

Abstract Introduction Periodontitis is a chronic inflammatory disease affecting the periodontium, ultimately leading to looseness and/or loss of teeth. Sarcopenia refers to age-related reduction in muscle mass and strength. Similar to periodontitis, chronic low-grade inflammation is thought to play a key role in its development. In addition, both increase in prevalence with advancing age. Despite known associations with other diseases involving a dysregulated inflammatory response, for example rheumatoid arthritis,, the relationship between periodontitis and sarcopenia, and whether they could be driven by similar processes, remains uncertain. The aim of this study was to explore the association between periodontitis and sarcopenia. Methods Observational study of 2040 adult volunteers [age 67.18 (12.17)] enrolled in the TwinsUK cohort study. Presence of tooth mobility and number of teeth lost were used to assess periodontal health. A binary variable was created to define periodontitis. Measurements of muscle strength, muscle quality/quantity and physical performance were used to assess sarcopenia. A categorical variable was created according to the European Working Group on Sarcopenia in Older People (EWGSOP2) consensus, to define sarcopenia (1: probable; 2: positive; 3: severe). Generalised linear mixed model analysis used on complete cases and age-matched (n = 1,288) samples to ascertain associations between periodontitis and sarcopenia. Results No significant association was found between periodontitis and sarcopenia in both the complete cases analysis and age-matched analysis. Results were consistent when analysis was adjusted for potential confounders including body mass index, frailty index, Mini Mental State Examination smoking, nutritional status and educational level. Conclusions This study found no significant association between periodontitis and sarcopenia in a cohort of 2040 adults. Although both periodontitis and sarcopenia have been linked to a dysregulated immune response and demonstrate an increase in prevalence with increasing age, our work is inconclusive due to the plethora of possible aetiopathogenetic pathways.

scholarly journals Response transformations for random effect and variance component models

2020 ◽  
pp. 1471082X2096691
Author(s):  
Amani Almohaimeed ◽  
Jochen Einbeck
Keyword(s):  
Maximum Likelihood ◽  
Random Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Random Effect ◽  
Statistical Technique ◽  
Response Distribution ◽  
Level Data ◽  
Variance Component Models ◽  
Response Transformation

Random effect models have been popularly used as a mainstream statistical technique over several decades; and the same can be said for response transformation models such as the Box–Cox transformation. The latter aims at ensuring that the assumptions of normality and of homoscedasticity of the response distribution are fulfilled, which are essential conditions for inference based on a linear model or a linear mixed model. However, methodology for response transformation and simultaneous inclusion of random effects has been developed and implemented only scarcely, and is so far restricted to Gaussian random effects. We develop such methodology, thereby not requiring parametric assumptions on the distribution of the random effects. This is achieved by extending the ‘Nonparametric Maximum Likelihood’ towards a ‘Nonparametric profile maximum likelihood’ technique, allowing to deal with overdispersion as well as two-level data scenarios.

Factors influencing the occurrence of high ultimate pH in three muscles of lamb carcasses in Australia

2014 ◽  
Vol 54 (10) ◽  
pp. 1853 ◽  
Author(s):  
N. G. McPhail ◽  
J. L. Stark ◽  
A. J. Ball ◽  
R. D. Warner
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Rectus Femoris ◽  
Carcass Weight ◽  
Mixed Model Analysis ◽  
Factors Influencing ◽  
South Wales ◽  
Generalised Linear Mixed Model ◽  
Processing Plants ◽  
Few Data

Chilled lamb meat exported from Australia has, on occasions, been rejected by importing countries due to greening, after only 6 weeks of storage time. Greening is known to be more prevalent in high ultimate pH (pHu) beef meat (>5.9). There are few data available for lamb carcasses in Australia on the occurrence of high pHu meat, which may have an impact on the understanding and control of quality and greening during storage. The aim of this project was to determine the prevalence of, and influencing factors for, high pHu meat in a range of muscle types in lamb carcasses in Australia. Muscle pHu data were collected from a total of 1614 carcasses from 78 lots at four lamb processing plants in Victoria and New South Wales in autumn and spring of 2013. The pHu of the knuckle (rectus femoris), rack (longissimus) and blade (infraspinatus) was measured and data on carcass and lot characteristics were recorded. Data were subjected to restricted maximum likelihood and generalised linear mixed model analysis. The mean pHu of the knuckle, rack and shoulder were 6.06, 5.79 and 6.12 respectively, and the main factors influencing muscle pHu and occurrence of dark-cutting were breed, season, electrical stimulation and carcass weight. Merino lambs had a higher pHu in the blade and knuckle than did other breeds (P < 0.05, P < 0.01 respectively). Lambs processed in autumn had a higher predicted pHu in the blade and knuckle and a higher percentage dark-cutting (DC; pHu >6.0) for those muscles, than did those processed in spring (P < 0.05). Carcasses that had been electrically stimulated had a higher %DC and a higher pHu in all three muscles (P < 0.05). Carcass weight had a significant effect on the pHu of all three muscles (P < 0.001), with heavier carcasses having a lower pHu and lower %DC. The pHu of the rack was not a reliable predictor for the pHu in other muscles of the lamb carcass. In conclusion, the high occurrence of DC in the muscles, particularly the blade and knuckle, suggests that these muscles may be at risk for producing greening in the vacuum bag during storage.

scholarly journals Thalamic white matter macrostructure and subnuclei volumes in Parkinson’s disease depression

2022 ◽  
Vol 8 (1) ◽  
Author(s):  
R. Bhome ◽  
A. Zarkali ◽  
G. E. C. Thomas ◽  
J. E. Iglesias ◽  
J. H. Cole ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
White Matter ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Neural Structure ◽  
Generalised Linear Mixed Model ◽  
Antidepressant Use ◽  
The Relationship

AbstractDepression is a common non-motor feature of Parkinson’s disease (PD) which confers significant morbidity and is challenging to treat. The thalamus is a key component in the basal ganglia-thalamocortical network critical to the pathogenesis of PD and depression but the precise thalamic subnuclei involved in PD depression have not been identified. We performed structural and diffusion-weighted imaging (DWI) on 76 participants with PD to evaluate the relationship between PD depression and grey and white matter thalamic subnuclear changes. We used a thalamic segmentation method to divide the thalamus into its 50 constituent subnuclei (25 each hemisphere). Fixel-based analysis was used to calculate mean fibre cross-section (FC) for white matter tracts connected to each subnucleus. We assessed volume and FC at baseline and 14–20 months follow-up. A generalised linear mixed model was used to evaluate the relationship between depression, subnuclei volume and mean FC for each thalamic subnucleus. We found that depression scores in PD were associated with lower right pulvinar anterior (PuA) subnucleus volume. Antidepressant use was associated with higher right PuA volume suggesting a possible protective effect of treatment. After follow-up, depression scores were associated with reduced white matter tract macrostructure across almost all tracts connected to thalamic subnuclei. In conclusion, our work implicates the right PuA as a relevant neural structure in PD depression and future work should evaluate its potential as a therapeutic target for PD depression.

scholarly journals The SARS-CoV-2 Alpha variant is associated with increased clinical severity of disease

2021 ◽  
Author(s):  
David J Pascall ◽  
Guy Mollett ◽  
Rachel Blacow ◽  
Naomi Bulteel ◽  
Robyn Campbell ◽  
...  
Keyword(s):  
Growth Rate ◽  
Cohort Study ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Transmission Rate ◽  
Severe Disease ◽  
Positive Association ◽  
Clinical Severity ◽  
Generalised Linear Mixed Model ◽  
The Impact

Background The Alpha (B.1.1.7) SARS-CoV-2 variant of concern has been associated with increased transmission and increased 28-day mortality. We aimed to investigate the impact of infection on clinical severity of illness, including the need for oxygen or ventilation in a national cohort study. Methods In this prospective clinical cohort study, 1475 SARS-CoV-2 sequences were obtained from patients infected in Scotland, UK between the 1st November 2020 and 30th January 2021 and matched to clinical outcomes as the lineage became dominant in Scotland. We modelled the association between B.1.1.7 infection and severe disease using a cumulative generalised linear mixed model employing a 4-point scale of maximum severity based on requirement of respiratory support at 28 days. We also estimated the growth rate of B.1.1.7-associated infections as it emerged in Scotland using a phylogenetic exponential growth rate population model. Results The B.1.1.7 lineage was responsible for a third wave of SARS-CoV-2 infection in Scotland in association with a transmission rate 5-fold higher than the preceding second wave B.1.177 lineage. Of 1475 patients, 364 were infected with B.1.1.7, 1030 with B.1.177 and 81 with other lineages. Our analysis found a positive association between increased clinical severity and lineage (B.1.1.7 versus non-B.1.1.7; cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93). Viral load was higher in B.1.1.7 samples than in non-B.1.1.7 samples, as measured by cycle threshold (Ct) value (mean Ct change: -2.46, 95% CI: -4.22, -0.70). Conclusions The B.1.1.7 lineage was associated with more severe clinical disease in Scottish patients than co-circulating lineages.

Analysis of aggregation, a worked example: numbers of ticks on red grouse chicks

Parasitology ◽  
2001 ◽  
Vol 122 (5) ◽  
pp. 563-569 ◽  
Author(s):  
D. A. ELSTON ◽  
R. MOSS ◽  
T. BOULINIER ◽  
C. ARROWSMITH ◽  
X. LAMBIN
Keyword(s):  
Random Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Negative Binomial ◽  
Generalized Linear Mixed Model ◽  
Red Grouse ◽  
Worked Example ◽  
Fixed And Random Effects ◽  
Individual Effects ◽  
Lagopus Lagopus Scoticus

The statistical aggregation of parasites among hosts is often described empirically by the negative binomial (Poisson-gamma) distribution. Alternatively, the Poisson-lognormal model can be used. This has the advantage that it can be fitted as a generalized linear mixed model, thereby quantifying the sources of aggregation in terms of both fixed and random effects. We give a worked example, assigning aggregation in the distribution of sheep ticksIxodes ricinuson red grouseLagopus lagopus scoticuschicks to temporal (year), spatial (altitude and location), brood and individual effects. Apparent aggregation among random individuals in random broods fell 8-fold when spatial and temporal effects had been accounted for.

Symptomatic Relief is Related to Serum Free Triiodothyronine Concentrations during Follow-up in Levothyroxine-Treated Patients with Differentiated Thyroid Cancer

2018 ◽  
Vol 126 (09) ◽  
pp. 546-552 ◽  
Author(s):  
Rolf Larisch ◽  
John Midgley ◽  
Johannes Dietrich ◽  
Rudolf Hoermann
Keyword(s):  
Mixed Model ◽  
Clinical Decision Making ◽  
Linear Mixed Model ◽  
Reference Range ◽  
Symptomatic Relief ◽  
Symptom Relief ◽  
Multivariable Analysis ◽  
Free Triiodothyronine ◽  
Generalised Linear Mixed Model

Abstract Aim Patients on levothyroxine-treatment frequently have complaints although TSH is within the reference range. Moreover, FT3 is often low in these patients. The clinical significance of this disequilibrium is studied here. Patients, methods We conducted a retrospective longitudinal study including 319 patients with differentiated thyroid carcinoma on LT4-medication (1.8 [1.6,2.1] µg/kg body weight). Patients were followed at 2309 visits for at median 63 [46,81] months. Association of reported complaints during follow-up with changes in thyroid parameters were analysed using a generalised linear mixed model accounting for within-variability and intra-subject correlations. Results 26% of patients expressed hypothyroid and 9.7% hyperthyroid complaints at any one visit, rates per visit being 6.5% and 2%, respectively. During follow-up, median changes in spans were as follows, LT4-dose 0.49 [IQR 0.29,0.72] µg/kg, FT3 1.77 [1.25,2.32] pmol/l, FT4 9.80 [6.70,12.8] pmol/l and TSH 1.25 [0.42,2.36] mIU/l. While rates of both hypothyroid or hyperthyroid symptoms were significantly related to all three thyroid parameters, the relationship of hypothyroid symptoms with FT3 extended to a below reference TSH range. Hypothyroid symptom relief was associated with both a T4 dose giving TSH-suppression below the lower reference limit and FT3 elevated further into the upper half of its reference range. In multivariable analysis, relationships between complaints and FT3 concentrations remained significant after adjusting for gender, age and BMI. Conclusion Residual hypothyroid complaints in LT4-treated patients are specifically related to low FT3 concentrations. This supports an important role of FT3 for clinical decision making on dose adequacy, particularly in symptomatic athyreotic patients.

Commercial cane sugar trends in the Tully sugar district

2000 ◽  
Vol 40 (7) ◽  
pp. 969 ◽  
Author(s):  
R. A. Lawes ◽  
M. K. Wegener ◽  
K. E. Basford ◽  
R. J. Lawn
Keyword(s):  
Random Effects ◽  
Transport Process ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Cane Sugar ◽  
Commercial Cane Sugar ◽  
Mixed Model Analysis ◽  
Sugar Mills ◽  
Wet Tropics ◽  
Model Year

Commercial cane sugar (CCS), as measured by sugar mills, is in decline in the wet tropics of Australia. One of these mills, Tully Sugar Ltd, has measured CCS in the factory as required by legislation and also measured whole clean stalk CCS through a small mill, which is free of contaminants. ‘Factory CCS’ measures the CCS of cane entering the mill, after it has been harvested. The harvesting and transport process delivers to the mill cane that is contaminated by extraneous matter such as leaf material and soil. Beween 1988 and 1998, 1516 blocks were sampled for ‘small mill CCS’. These data were combined with block productivity information to determine the trends in small mill CCS and factory CCS using a linear mixed model analysis as the data were unbalanced. Other data, including the date of harvest for factory CCS, date of sampling for small mill CCS, farm of origin and cane variety were available and fitted as random effects in the mixed model. Year was fixed to determine time related trends in the 2 measures of CCS. Small mill CCS was higher than factory CCS and remained constant from 1988 to 1998. Predicted factory CCS declined from 12.76 units in 1988 to 10.91 units in 1998. We conclude that the CCS levels in whole clean stalks were actually stable, since small mill CCS remained constant over the 10-year period. Possible reasons for the differences in the trends for the 2 CCS measures are discussed.

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