Proc glimmix

Manufactured by SAS Institute

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PROC GLIMMIX is a procedure in the SAS software suite that fits generalized linear mixed models. It can handle a wide variety of distribution types and link functions, and allows for the modeling of correlated data structures.

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Lab products found in correlation

74 protocols using proc glimmix

Impacts of Fungus and Wolbachia on qPCR

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For qPCR data and PO data, outliers were identified via GraphPad statistical software and removed from the analysis. A total of 25 out of 1407 data points were identified as outliers in Ae. albopictus and 45 out of 1393 data points in Cx. pipiens. A 2-way ANOVA was performed within gene targets for each species using a generalized linear model (PROC GLIMMIX, SAS 9.4) with a Gamma distribution of error and a log link function. The SAS ILINK option was used to express least squares means and confidence intervals on the original scale. Significant effects were further analyzed by pairwise comparisons of the gamma distributed estimates for the main effects of fungal treatment (F), with 3 levels (B. bassiana, B. brongniartii, uninfected control) Wolbachia treatment (W) with 2 levels (W+, W-) and their interaction (F*W) with a Tukey adjustment for multiple comparisons. Graphical representation of the data was done using Graph-Pad Prism 9 (GraphPad). Analyses for fungal effects on Wolbachia load were done using only the Wolbachia infected groups in a one-way ANOVA, with the same 3 levels (B. bassiana, B. brongniartii, uninfected control), using a generalized linear model (PROC GLIMMIX, SAS 9.4) with a Gamma distribution of error and a log link function. Pairwise comparisons among means also used a Tukey adjustment.

Ramirez J.L., Schumacher M.K., Ower G., Palmquist D.E, & Juliano S.A. (2021). Impacts of fungal entomopathogens on survival and immune responses of Aedes albopictus and Culex pipiens mosquitoes in the context of native Wolbachia infections. PLoS Neglected Tropical Diseases, 15(11), e0009984.

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Assessing Cultivar Susceptibility and Pathogen Virulence

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The relative susceptibility of cultivars and pathogenicity of isolates were analyzed as the final lesion diameter on wound-inoculated fruits. The wound size (5 mm) was deducted from the final lesion size before data analysis. The cultivars' and isolates' main effect or their interaction on the final lesion diameter was subjected to analysis of variance using a generalized linear mixed model analysis (PROC GLIMMIX, SAS, ver. 9.4, SAS Institute, Cary, NC). The isolates' aggressiveness was measured as the area under the disease progress curve (AUDPC) for every experimental unit (cultivar × isolate × replication) using the formula:
where x i is the lesion size at every measurement day after inoculation and (t i -t i-1 ) is the time between evaluations. The AUDPC values were subjected to analysis of variance using a generalized linear mixed model analysis (PROC GLIMMIX, SAS, ver. 9.4, SAS Institute, Cary, NC) with replication as a random effect. The treatment effects were analyzed as main effects of cultivars and isolates within each Alternaria section using Fisher's protected least significant difference test (α = 0.05). The disease incidence on spray-inoculated fruits was calculated as the number of fruits with Alternaria rot divided by the total number of inoculated fruits expressed as a percentage.

DeShields J.B, & Kc A.N. (2021). Morphological and Molecular Characterization of Alternaria spp. Isolated from European Pears. Plant disease, 105(9).

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Randomized Sperm and Fecundity Analysis

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All experiments, but sperm viability, were performed under a completely randomized design. Sperm viability was performed in triplicate, with each time considered a block using different cohort. The values for live, dead, and total sperm recorded from five pictures (pseudo replicates) were averaged to produce one value for each individual adult. Means of adult and larval head capsule width and dry weight, weekly and cumulative number of eggs (female fecundity, when females are exposed to dsRNAs or unexposed females are mated with exposed males), and sperm count were compared by analysis of variance or pairwise comparison (two means) using least square means in a generalized linear mixed model (PROC GLIMMIX) in SAS 9.4 (SAS Institute, Cary, SC) at α = 0.05. Percentage data such as egg hatch, larval recovery, and larval instar had binomial distributions with all response variables considered as random effects. Number of larvae that were recovered from larval development bioassays were unbalanced and presented different degrees of freedom for each treatment. The data were compared with analysis of variance using least square means in generalized linear mixed model (PROC GLIMMIX) in SAS 9.4 (SAS Institute, Cary, SC) at α = 0.05.

Pereira A.E., Vélez A.M., Meinke L.J, & Siegfried B.D. (2017). Sublethal Effects of vATPase-A and Snf7 dsRNAs on Biology of Southern Corn Rootworm, Diabrotica undecimpunctata howardi Barber. Journal of economic entomology, 110(6).

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Dietary Impact on Gut Microbiome Dynamics

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The effect of diet and sampling time on the seminal and fecal microbial community structure was assessed using Bray-Curtis dissimilarities and PERMANOVA (adonis2 function). Pairwise comparisons of the Bray-Curtis dissimilarities among different sampling time points and treatment groups were done using the R package pairwise Adonis v. 0.01 with the Benjamini-Hochberg procedure used to correct for multiple comparisons. The number of ASVs (richness), alpha diversity indices, and relative abundance of the most relatively abundant phyla and genera between treatment groups within a sampling time point and between different sampling time points were compared using the generalized linear mixed-model estimation procedure (PROC GLIMMIX) in SAS (ver. 9.4, SAS Institute Inc., Cary, NC, USA). The model included the main effects rate of gain (high or moderate), sampling time, and the respective interactions. Means among different sampling times or treatment groups within each sample type were compared using the lsmeans statement, and significance was declared at a P value of <0.05.

Webb E.M., Holman D.B., Schmidt K.N., Crouse M.S., Dahlen C.R., Cushman R.A., Snider A.P., McCarthy K.L, & Amat S. (2023). A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain. Microbiology Spectrum, 11(2), e05180-22.

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Salmonella Infection and Pig Physiology

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Prior to analysis, intraperitoneal temperature (TEMP) was averaged into 1-h intervals. Intraperitoneal temperature, serum cortisol, and CBC data were analyzed using the MIXED procedure of SAS specific for repeated measures (SAS Inst. Inc., Cary, NC). Sex, time and their interaction were included as fixed effects with pig within sex as the experimental unit. Specific treatment comparisons were made using the PDIFF option in SAS, with P ≤ 0.05 considered significant and P ≤ 0.10 considered a tendency. Salmonella tissue and fecal count data were analyzed in SAS using Proc Glimmix of SAS at an ɑ = 0.05 utilizing the Tukey option for mean separation. Positive/negative binomial data to indicate the presence or absence of Salmonella in a tissue were analyzed using logistics regression in Proc Glimmix. All data are presented as the LSM ± SEM.

Burdick Sanchez N.C., Broadway P.R., Carroll J.A., Gart E.V., Bryan L.K, & Lawhon S.D. (2017). Weaned pigs experimentally infected with Salmonella display sexually dimorphic innate immune responses without affecting pathogen colonization patterns,,. Translational Animal Science, 1(1), 69-76.

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Assessing Bone Fracture Risk from PM2.5 Exposure

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We estimated the association of 1-year PM_2.5 average with annual rates of bone fracture hospital admissions using generalized linear mixed models (PROC GLIMMIX, SAS Institute, Cary, NC) with Poisson distribution and random intercepts for zip code. We considered the Akaike information criterion (AIC) and residuals’ plots to evaluate goodness-of-fit. We adjusted the final model for the multiple zip code-level confounders described in Supplementary Table 2. We used Medicare data on age that provides per each zip code the percent of the population between 65 to 74 years old and the percent >75 years. We also adjusted for number of days below 0°C to minimize the potential impact of fall risk due to freezing weather. Urban and rural areas were classified according to the Rural-Urban commuting area from the U.S. Department of Agriculture, which classify U.S. census tracts using measures of population density, urbanization and daily commuting. In separate models, we tested interaction terms between zip-code characteristics and PM_2.5 levels. Findings at p<0.05 were considered significant.

Prada D., Zhong J., Colicino E., Zanobetti A., Schwartz J., Dagincourt N., Fang S.C., Kloog I., Zmuda J.M., Holick M., Herrera L.A., Hou L., Dominici F., Bartali B, & Baccarelli A.A. (2017). Association of air particulate pollution with bone loss over time and bone fracture risk: analysis of data from two independent studies. The Lancet. Planetary health, 1(8), e337-e347.

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Bioassays for Larval and Adult Bee Mortality

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Results from larval rearing bioassays were analyzed with a generalized linear mixed model in SAS (PROC GLIMMIX, version 9.4; SAS Institute Inc. Cary, NC, USA). A binomial distribution was used as the response variable was binary; live or dead. Treatment was used as the fixed effect and grafting day as random effect. Post hoc pairwise comparisons of survival between treatments were performed using the Least Squares Means difference.
Mortality data from adult bee dose response bioassays was analyzed using generalized linear models (GLMs) with a log-probit transformation to calculate LD₅₀ values and 95% confidence intervals [38 (link),53 ]. Pairwise tests were used to compare treatments and assess interactive effects between test chemical combinations. A test of parallelism was used to assess differences in the slope of the dose-response. A test of equality was used to assess differences between dose-response in one treatment relative to another. Statistical analysis of the results from adult assays was performed in R (version 3.4.2, R Foundation for Statistical Computing, Vienna, Austria).

Wade A., Lin C.H., Kurkul C., Regan E.R, & Johnson R.M. (2019). Combined Toxicity of Insecticides and Fungicides Applied to California Almond Orchards to Honey Bee Larvae and Adults. Insects, 10(1), 20.

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Multivariate Analysis of Insect Ecology

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Data were evaluated with ANOVA and regression analyses (Proc Glimmix, SAS 9.3, SAS 2012 ). A negative binomial distribution with a log link function was used for number of pupae, a lognormal distribution for ammonium, a normal distribution for pupal weight, pH, and conductivity and a binomial distribution with a logit link function was used for sex ratio and emergence. All experiments were replicated three times.

Friesen K., Berkebile D.R., Zhu J.J, & Taylor D.B. (2017). Augmenting Laboratory Rearing of Stable Fly (Diptera: Muscidae) Larvae With Ammoniacal Salts. Journal of Insect Science, 17(1), 21.

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Cultivar Growth CO2 Effects Analysis

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Gas exchange and biochemical data were analyzed for each year as a randomized complete block split-plot design using a generalized linear mixed model and three-way (cultivar × growth [CO₂] × growth stage) analysis of variance (PROC GLIMMIX, SAS 9.3, SAS Inc.) to examine overall treatment effects, as well as a two-way (cultivar × growth [CO₂]) analysis of variance at each growth stage to identify treatment mean differences. The FACE treatment was treated as a whole-plot effect, and the cultivars were subplots.

Chen C.P., Sakai H., Tokida T., Usui Y., Nakamura H, & Hasegawa T. (2014). Do the Rich Always Become Richer? Characterizing the Leaf Physiological Response of the High-Yielding Rice Cultivar Takanari to Free-Air CO2 Enrichment. Plant and Cell Physiology, 55(2), 381-391.

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Prevalence of STEC and Campylobacter spp.

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Prevalence of STEC or Campylobacter spp. among sample types collected and animal species were compared with generalized linear mixed models (Proc Glimmix, SAS 9.3, SAS Institute Inc., Ottawa, ON, Canada) using a binomial distribution. Model adjusted means (back-transformed to original scale) were reported and deemed significant at p < 0.05.

Conrad C.C., Stanford K., Narvaez-Bravo C., Neumann N.F., Munns K., Tymensen L., Jokinen C, & McAllister T.A. (2018). Zoonotic Fecal Pathogens and Antimicrobial Resistance in Canadian Petting Zoos. Microorganisms, 6(3), 70.

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