scholarly journals Using mixed models to combine smooth size-selection and catch-comparison curves over hauls

2003 ◽  
Vol 60 (4) ◽  
pp. 448-459 ◽  
Author(s):  
R J Fryer ◽  
A F Zuur ◽  
N Graham
Keyword(s):  
Mixed Models ◽  
Fixed Effects ◽  
Mixed Model ◽  
Random Effect ◽  
Categorical Variable ◽  
Size Selection ◽  
Research Survey ◽  
Different Levels ◽  
Selection Of ◽  
Comparison Data

Parametric size-selection curves are often combined over hauls to estimate a mean selection curve using a mixed model in which between-haul variation in selection is treated as a random effect. This paper shows how the mixed model can be extended to estimate a mean selection curve when smooth nonparametric size-selection curves are used. The method also estimates the between-haul variation in selection at each length and can model fixed effects in the form of the different levels of a categorical variable. Data obtained to estimate the size-selection of dab by a Nordmøre grid are used for illustration. The method can also be used to provide a length-based analysis of catch-comparison data, either to compare a test net with a standard net or to calibrate two research survey vessels. Haddock data from an intercalibration exercise are used for illustration.

scholarly journals The Impact of Misspecified Random Effect Distribution in a Weibull Regression Mixed Model

Stats ◽  
2018 ◽  
Vol 1 (1) ◽  
pp. 48-76
Author(s):  
Freddy Hernández ◽  
Viviana Giampaoli
Keyword(s):  
Weibull Distribution ◽  
Random Effects ◽  
Mixed Models ◽  
Fixed Effects ◽  
Mixed Model ◽  
Random Effect ◽  
Estimation Procedure ◽  
Weibull Regression ◽  
Two Parameters ◽  
The Impact

Mixed models are useful tools for analyzing clustered and longitudinal data. These models assume that random effects are normally distributed. However, this may be unrealistic or restrictive when representing information of the data. Several papers have been published to quantify the impacts of misspecification of the shape of the random effects in mixed models. Notably, these studies primarily concentrated their efforts on models with response variables that have normal, logistic and Poisson distributions, and the results were not conclusive. As such, we investigated the misspecification of the shape of the random effects in a Weibull regression mixed model with random intercepts in the two parameters of the Weibull distribution. Through an extensive simulation study considering six random effect distributions and assuming normality for the random effects in the estimation procedure, we found an impact of misspecification on the estimations of the fixed effects associated with the second parameter σ of the Weibull distribution. Additionally, the variance components of the model were also affected by the misspecification.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P < 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

scholarly journals Goats Given Transdermal Flunixin Meglumine Displayed Less Pain Behavior After Castration

2020 ◽  
Author(s):  
Amanda Lee ◽  
Meggan Graves ◽  
Andrea Lear ◽  
Sherry Cox ◽  
Marc Caldwell ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Body Position ◽  
Random Effect ◽  
Pain Behavior ◽  
Bout Duration ◽  
Flunixin Meglumine ◽  
Meat Goats ◽  
Transdermal Application

AbstractPain management should be utilized with castration to reduce physiological and behavioral changes. Transdermal application of drugs require less animal management and fewer labor risks, which can occur with oral administration or injections. The objective was to determine the effects of transdermal flunixin meglumine on meat goats’ behavior post-castration. Male goats (N = 18; mean body weight ± standard deviation: 26.4 ± 1.6 kg) were housed individually in pens and randomly assigned to 1 of 3 treatments: (1) castrated, dosed with transdermal flunixin meglumine; (2) castrated, dosed with transdermal placebo; and (3) sham castrated, dosed with transdermal flunixin meglumine. Body position, rumination, and head- pressing were observed for 1 h ± 10 minutes twice daily on days −1, 0, 1, 2, and 5 around castration. Each goat was observed once every 5-minutes (scan samples) and reported as percentage of observations. Accelerometers were used to measure standing, lying, and laterality (total time, bouts, and bout duration). A linear mixed model was conducted using GLIMMIX. Fixed effects of treatment, day relative to castration, and treatment*day relative to castration and random effect of date and goat nested within treatment were included. Treatment 1 goats (32.7 ± 2.8%) and treatment 2 goats (32.5 ± 2.8%) ruminated less than treatment 3 goats (47.4 ± 2.8%, P = 0.0012). Head pressing was greater on day of castration in treatment 2 goats (P < 0.001). Standing bout duration was greatest in treatment 2 goats on day 1 post-castration (P < 0.001). Lying bout duration was greatest in treatment 2 goats on day 1 post-castration compared to treatment 1 and treatment 3 goats(P < 0.001). Transdermal flunixin meglumine improved goats’ fluidity of movement post-castration and decreased head pressing, indicating a mitigation of pain behavior.

scholarly journals PSXI-32 Potential improvements in milk production of mid lactating Holstein cows through changes in the defoliation intensity on a mixed pasture

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 384-385
Author(s):  
Oliver Fast Hinz ◽  
Pablo Chilibroste ◽  
Gabriel Menegazzi ◽  
Matías Oborsky ◽  
Pablo Soca ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Festuca Arundinacea ◽  
Fixed Effects ◽  
Mixed Model ◽  
Body Condition Score ◽  
Random Effect ◽  
Milk Composition ◽  
Control Treatment ◽  
Condition Score

Abstract An experiment was performed to study the effect of two contrasting defoliation intensities of a fescue based pasture on milk production of 24 mid lactating multiparous cows. The animals were blocked according to parity, body weight (587 ± 42 kg), body condition score (2.77 ± 0.16) and calving date, and were randomly allocated to one of these two treatments: lax treatment (TL) 12 cm and control treatment (TC) 6 cm, with four replications. It was used a second-year pasture of Festuca arundinacea and Lotus corniculatus (2530 ± 180 kgDM/ha), divided into eight plots of 0.3 ha. Each plot was grazed by three cows during as many days as necessary until the defoliation height of each treatment was achieved. This would be determined by daily measures of the pasture height. Animals had one grazing session from 8:00 to 16:00 h. Both treatments received 7.5 kgDM of supplementation (17% Crude Protein; 2.81 Mcal/kgDM) in individual troughs. The cows were milked twice a day (05:00 and 17:00 h). Milk production was registered daily while milk composition was measured at the beginning and at the end of the experiment (samples from two consecutive milking). For milk yield results, a mixed model was used (Glimmix procedure, SAS 9.2, 2010) to analyse with treatment, day and their interaction as fixed effects and block as a random effect. While milk composition was analysed with only treatment as fixed effect. Milk yield was greater for TL than TC, while there was no difference in milk composition between treatments (Table 1). There is a significant effect of the day and an interaction between treatment and day (Figure 1), as difference was greater for TL to the end of the grazing period. This leads to the conclusion that it is possible to improve the milk production through less defoliation intensity.

Generalized linear mixed models for multi-reader multi-case studies of diagnostic tests

2015 ◽  
Vol 26 (3) ◽  
pp. 1373-1388 ◽  
Author(s):  
Wei Liu ◽  
Norberto Pantoja-Galicia ◽  
Bo Zhang ◽  
Richard M Kotz ◽  
Gene Pennello ◽  
...  
Keyword(s):  
Mixed Models ◽  
Diagnostic Tests ◽  
Fixed Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Models ◽  
Characteristic Curve ◽  
Linear Mixed Models ◽  
Parametric Bootstrap ◽  
Pseudo Likelihood

Diagnostic tests are often compared in multi-reader multi-case (MRMC) studies in which a number of cases (subjects with or without the disease in question) are examined by several readers using all tests to be compared. One of the commonly used methods for analyzing MRMC data is the Obuchowski–Rockette (OR) method, which assumes that the true area under the receiver operating characteristic curve (AUC) for each combination of reader and test follows a linear mixed model with fixed effects for test and random effects for reader and the reader–test interaction. This article proposes generalized linear mixed models which generalize the OR model by incorporating a range-appropriate link function that constrains the true AUCs to the unit interval. The proposed models can be estimated by maximizing a pseudo-likelihood based on the approximate normality of AUC estimates. A Monte Carlo expectation-maximization algorithm can be used to maximize the pseudo-likelihood, and a non-parametric bootstrap procedure can be used for inference. The proposed method is evaluated in a simulation study and applied to an MRMC study of breast cancer detection.

Dorsiflexion But Not Plantarflexion Force Declines At Lower Foot Skin Temperatures

2019 ◽  
Vol 26 (6) ◽  
pp. 13-13
Author(s):  
Julie S Bieles ◽  
Stuart A Bruce ◽  
Di J Newham ◽  
David A Green
Keyword(s):  
Skin Temperature ◽  
Fixed Effects ◽  
Mixed Model ◽  
Random Effect ◽  
Length Relationship ◽  
Muscle Cooling ◽  
Maximum Voluntary Force ◽  
Skin Temperatures ◽  
Large Muscle ◽  
Condition Interaction

Background/Aims Muscle maximum voluntary force declines at skin temperature <20°C, attributed to cold muscle, however large muscle deep fibres remain at >20°C. Large muscle maximum voluntary force decline is comparable to that in small superficial muscle where muscle temperature remains close to skin temperature. Therefore, factors in addition to temperature may contribute to large muscle maximum voluntary force decline. This study compares the effects of foot and/or shank skin temperature on dorsiflexion and plantarflexion maximum voluntary force with the hypotheses that: dorsiflexion maximum voluntary force>plantarflexion maximum voluntary force decline at lower skin temperature; and, plantarflexion and dorsiflexion maximum voluntary force will decline at lower shank skin temperature independent of foot skin temperature. Methods A total of 24 adults (15 females, 9 males, 29 ± 11.8 years, 170.1 ± 8.0 cm, 66.9 ± 9.3 kg [mean ± standard deviation]) gave informed consent to participate on three visits – cooling/warming of: foot only; foot and shank; and shank only. Foot and/or shank temperature was adjusted using Cryocuff™ sleeves filled with ~45°C or ~4°C water. Temperature, taken before each maximum voluntary force set, was monitored through thermocouples placed on the limb. Plantarflexion and dorsiflexion maximum voluntary force were measured with a KinCom isokinetic dynamometer, with subjects seated on a plinth with knee fully extended and neutral ankle. A general mixed model was used to evaluate the effects of skin temperature on maximum voluntary force. Fixed effects were skin temperature and condition, with subject as a random effect. The skin temperature*condition interaction was also modelled. P-values were obtained by likelihood ratio tests. Results Foot skin temperature <18.5°C resulted in a 10% (χ2(1)=5.479, P=0.019) dorsiflexion maximum voluntary force decline, with a skin temperature*condition interaction (χ2(2)=11.031, P=0.004), this decline was 12% (χ2(1)=13.18, P=0.0003) in foot only and 8% (χ2(1)=4.675, P=0.031) in foot and shank. Leg skin temperature did not affect (χ2(1)=2.849, P=0.091) dorsiflexion maximum voluntary force. Plantarflexion maximum voluntary force did not change with foot skin temperature (χ2(1)=0.04, P=0.841) or leg skin temperature (χ2(1)=0.082, P=0.929). Conclusions Dorsiflexion maximum voluntary force declines at lower foot skin temperature independently of shank skin temperature, whereas plantarflexion maximum voluntary force is unaffected by skin temperature, possibly because in this protocol the shank was insufficiently cooled. Therefore factors other than direct muscle cooling must contribute to dorsiflexion maximum voluntary force decline. One theory is a rightward shift in the force-length relationship, due to stiffer tendon, could result in dorsiflexions operating in the descending limb of the force-length relationship. This warrants further investigation.

scholarly journals Factors associated with the weight of individual primal cuts and their inter-relationship in cattle

2019 ◽  
Vol 3 (4) ◽  
pp. 1593-1605 ◽  
Author(s):  
Michelle M Judge ◽  
Thierry Pabiou ◽  
Stephen Conroy ◽  
Rory Fanning ◽  
Martin Kinsella ◽  
...  
Keyword(s):  
Decision Support ◽  
Fixed Effects ◽  
Mixed Model ◽  
Random Effect ◽  
Carcass Weight ◽  
Holstein Friesian ◽  
Support Tools ◽  
Beef Herd ◽  
Fat Score ◽  
The Individual

Abstract Input parameters for decision support tools are comprised of, amongst others, knowledge of the associated factors and the extent of those associations with the animal-level feature of interest. The objective of the present study was to quantify the association between animal-level factors with primal cut yields in cattle and to understand the extent of the variability in primal cut yields independent carcass weight. The data used consisted of the weight of 14 primal carcass cuts (as well as carcass weight, conformation, and fat score) on up to 54,250 young cattle slaughtered between the years 2013 and 2017. Linear mixed models, with contemporary group of herd-sex-season of slaughter as a random effect, were used to quantify the associations between a range of model fixed effects with each primal cut separately. Fixed effects in the model were dam parity, heterosis coefficient, recombination loss, a covariate per breed representing the proportion of Angus, Belgian Blue, Charolais, Jersey, Hereford, Limousin, Simmental, and Holstein–Friesian and a three-way interaction between whether the animal was born in a dairy or beef herd, sex, and age at slaughter, with or without carcass weight as a covariate in the mixed model. The raw correlations among all cuts were all positive varying from 0.33 (between the bavette and the striploin) to 0.93 (between the topside and knuckle). The partial correlation among cuts, following adjustment for differences in carcass weight, varied from −0.36 to 0.74. Age at slaughter, sex, dam parity, and breed were all associated (P &lt; 0.05) with the primal cut weight. Knowledge of the relationship between the individual primal cuts, and the solutions from the models developed in the study, could prove useful inputs for decision support systems to increase performance.

Misspecification of the random effect structure: Implications for the linear mixed model

2020 ◽  
Author(s):  
Brandon LeBeau
Keyword(s):  
Fixed Effects ◽  
Serial Correlation ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Type I Error ◽  
Random Effect ◽  
Correlated Data ◽  
Unbiased Estimation ◽  
Type I ◽  
Nested Data

<p>The linear mixed model is a commonly used model for longitudinal or nested data due to its ability to account for the dependency of nested data. Researchers typically rely on the random effects to adequately account for the dependency due to correlated data, however serial correlation can also be used. If the random effect structure is misspecified (perhaps due to convergence problems), can the addition of serial correlation overcome this misspecification and allow for unbiased estimation and accurate inferences? This study explored this question with a simulation. Simulation results show that the fixed effects are unbiased, however inflation of the empirical type I error rate occurs when a random effect is missing from the model. Implications for applied researchers are discussed.</p>

The Evaluation of Bivariate Mixed Models in Meta-analyses of Diagnostic Accuracy Studies with SAS, Stata and R

2018 ◽  
Vol 57 (03) ◽  
pp. 111-119 ◽  
Author(s):  
Felicitas Vogelgesang ◽  
Marc Dewey ◽  
Peter Schlattmann
Keyword(s):  
Diagnostic Accuracy ◽  
Sensitivity And Specificity ◽  
Mixed Models ◽  
Mixed Model ◽  
Mean Squared Error ◽  
Random Effect ◽  
Model Specification ◽  
Bivariate Model ◽  
Statistical Point ◽  
Meta Analyses

Summary Background: Meta-analyses require a thoroughly planned procedure to obtain unbiased overall estimates. From a statistical point of view not only model selection but also model implementation in the software affects the results. Objectives: The present simulation study investigates the accuracy of different implementations of general and generalized bivariate mixed models in SAS (using proc mixed, proc glimmix and proc nlmixed), Stata (using gllamm, xtmelogit and midas) and R (using reitsma from package mada and glmer from package lme4). Both models incorporate the relationship between sensitivity and specificity – the two outcomes of interest in meta-analyses of diagnostic accuracy studies – utilizing random effects. Methods: Model performance is compared in nine meta-analytic scenarios reflecting the combination of three sizes for meta-analyses (89, 30 and 10 studies) with three pairs of sensitivity/specificity values (97%/87%; 85%/75%; 90%/93%). Results: The evaluation of accuracy in terms of bias, standard error and mean squared error reveals that all implementations of the generalized bivariate model calculate sensitivity and specificity estimates with deviations less than two percentage points. proc mixed which together with reitsma implements the general bivariate mixed model proposed by Reitsma rather shows convergence problems. The random effect parameters are in general underestimated. Conclusions: This study shows that flexibility and simplicity of model specification together with convergence robustness should influence implementation recommendations, as the accuracy in terms of bias was acceptable in all implementations using the generalized approach.

scholarly journals Exercise-induced hypoalgesia in women with varying levels of menstrual pain

2018 ◽  
Vol 18 (2) ◽  
pp. 303-310 ◽  
Author(s):  
Mervyn Travers ◽  
Penny Moss ◽  
William Gibson ◽  
Dana Hince ◽  
Sheree Yorke ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Random Effect ◽  
Activity Levels ◽  
Menstrual Pain ◽  
Isometric Handgrip ◽  
Pressure Pain Thresholds ◽  
Significant Difference ◽  
Exercise Induced

Abstract Background and aims: Exercise-induced hypoalgesia (EIH) is a well-established phenomenon in pain-free individuals that describes a decrease in pain sensitivity after an acute bout of exercise. The EIH response has been demonstrated to be sub-optimal in the presence of persisting pain. Menstrual pain is a common recurrent painful problem with many women experiencing high levels of pain each cycle. However, the EIH response has not been examined in a cohort of women with high levels of menstrual pain. This research aimed to examine whether EIH manifests differently in women with varying levels of menstrual pain. The primary hypothesis was that women with high levels of menstrual pain would demonstrate compromised EIH. Secondary aims were to explore relationships between EIH and emotional state, sleep quality, body mass index (BMI) or physical activity levels. Methods: Pressure pain thresholds (PPT) were measured in 64 participants using a digital handheld algometer before and after a submaximal isometric-handgrip exercise. EIH index was compared between low (VAS 0–3), moderate (VAS 4–7) and high (VAS 8–10) pain groups, using a linear mixed model analysis with participant as a random effect, and site, menstrual pain category and the interaction between the two, as fixed effects. Results: EIH was consistently induced in all groups. However, there was no statistically significant difference between the pain groups for EIH index (p=0.835) or for any co-variates (p>0.05). Conclusions: EIH was not found to differ between women who report regular low, moderate or high levels of menstrual pain, when measured at a point in their menstrual cycle when they are pain free. Implications: This study provides insight that EIH does not vary in women with differing levels of menstrual pain when they are not currently experiencing pain. The current findings indicate that, although menstrual pain can involve regular episodes of high pain levels, it may not be associated with the same central nervous system dysfunctions as seen in sustained chronic pain conditions.

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