Tag: lme4

ios – How to install package “marked” on RStudio?

I’ve tried installing packages specific to my studies ( BayesFactor and marked ) but each time it ask fro a “sub”package ( Matrix and lme4 ) and it always give me a code line where I can seems to use the sub package. the end line is always : ‘/private/var/folders/6n/5bhjfv893xggr98bhctym2sr0000gn/T/Rtmp7wjqtG/downloaded_packages’…

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Rstudio crashes just before producing a brms model – General

Hello, I am trying to run a brms model with 20000 iterations. After many hours of simulations, and just before being done, Rstudio crashes without any warning. The model compiles successfully with 1000 iterations and, sometimes, with 10000 iterations but several attempts to run the model with 20000 iterations or…

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Is it appropriate to apply linear mixed models to Voom transformed data?

Is it appropriate to apply linear mixed models to Voom transformed data? 1 @4b83ad99 Last seen 18 hours ago Canada Hello, I have some gene expression data for different tissue types with multiple replicates. My species has undergone a historical duplication event and and I am looking to compare the…

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Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish

Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article  PubMed  Google Scholar  Gartland, L. A., Firth, J. A., Laskowski,…

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Bioconductor – dreamlet

DOI: 10.18129/B9.bioc.dreamlet   Cohort-scale differential expression analysis of single cell data using linear (mixed) models Bioconductor version: Release (3.18) Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of…

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A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

Animal models All procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) at Washington University in St. Louis, MO. Veterinary care and housing was provided by the veterinarians and veterinary technicians of Washington University School of Medicine under Dougherty lab’s approved IACUC protocol. All protocols…

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Fatal error – Running lmer – General

Hi! I am a beginner trying to model microbiome alpha diversity in Rstudio, and have been stuck, as every time I try to run the lmer function in Rstudio, R aborts and terminates my session. I have tried updating R, updating packages, removing and re-installing packages, and detaching packages that…

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Why is R-Studio Only Showing Comments from Some Package Functions, but not all? – RStudio IDE

I’ve noticed that there may be a new feature on the latest version of R Studio on Ubuntu 22.04, but I can’t seem to find any news about it and I don’t know what to search on Google to understand it more. Here is my R Studio Version RStudio 2023.09.1+494…

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Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data

Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…

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Assignment 6 – In RStudio you can create an R markdown (.Rmd) file that can be knit to Word or PDF

Assignment Due by 3pm 19 May 2023 STAT201 Assignment 6 Your assignment should contain: answers to the questions below including graphs, R output, and code. In RStudio you can create an R markdown (.Rmd) file that can be knit to Word or PDF document with your answers, code, R output,…

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What is the difference between R and SPSS in estimating random effects? – rstudio

Hello,I need to estimate a generalized linear mixed model (GLMM).When using R, I need to choose a specific fixed effect (one of the independent variables in the model) to have a random slope according to a random variable such as subject ID.But when using SPSS, I can’t choose a specific…

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Software Compatibility Issue Between phyloseq and lme4 Packages

Hi, I’ve encountered a rather peculiar software issue involving the phyloseq package and the lme4 package when analyzing longitudinal microbiome data. Below, please find a reproducible example that triggers the error: First, when I run the mixed effects model code provided by lme4, it works perfectly: data(“sleepstudy”, package = “lme4”)…

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ggplot2 – How to remove the square surrounding legend keys in a plot made by plot_model (ggplot) in R

I’m currently working on creating some complex visualizations using the plot_model function from the sjPlot package in R. Specifically, I’m dealing with interaction plots of linear models, and I’m facing an issue related to customizing the legend. When I plot it, the keys of the legend appear inside squares, and…

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Gut microbial carbohydrate metabolism contributes to insulin resistance

Study participants and data collection The study participants were recruited from 2014 to 2016 during their annual health check-ups at the University of Tokyo Hospital. The individuals included both male and female Japanese individuals aged from 20 to 75 years. The exclusion criteria were as follows: established diagnosis of diabetes,…

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How to visualize a mixed effects model using ggplot2 in R

I have a dataset with two groups (p and c) where I measured the volume 2-3 times in several samples (ID). Volume and Time correlate very well with each other and my hypothesis would be, that the slope between the groups is different. I now have the following mixed-effect model…

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DNA methylation analysis for paired samples using random effects model

DNA methylation analysis for paired samples using random effects model 1 I am very new to bioinformatics. I am currently examining the differences between DNA methylation in blood and synovial tissue. The DNA methylation data was generated using Illumina EPIC array. I have paired data for 50 patients i.e. each…

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Merging Methylation data (M-values) with phenotypic data

Merging Methylation data (M-values) with phenotypic data 0 Hi Members, I am relatively new to R and am having an issue with lme4. I want to use my methylation (m-values) and my phenotypic datasets. However, when I run my code I get an error about different variable lengths. I believe…

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Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants

Klepzig KD, Adams AS, Handelsman J, Raffa KF. Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans. Environ Entomol. 2009;38:67–77. CAS  PubMed  Google Scholar  Dale C, Moran NA. Molecular interactions between bacterial symbionts and their hosts. Cell. 2006;126:453–65. CAS  PubMed  Google Scholar  Salem…

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Bioconductor – autonomics

DOI: 10.18129/B9.bioc.autonomics   Generifying and intuifying cross-platform omics analysis Bioconductor version: Release (3.17) This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm. Author: Aditya Bhagwat…

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Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population | BMC Genomics

Oikonomou EK, Antoniades C. The role of adipose tissue in cardiovascular health and disease. Nat Rev Cardiol. 2019;16(2):83–99. Article  PubMed  Google Scholar  Sakers A, De Siqueira MK, Seale P, Villanueva CJ. Adipose-tissue plasticity in health and disease. Cell. 2022;185(3):419–46. Article  CAS  PubMed  Google Scholar  Sun W, von Meyenn F, Peleg-Raibstein…

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Molecular features driving cellular complexity of human brain evolution

King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975). Article  ADS  CAS  PubMed  Google Scholar  Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601–617 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Liu, X. et al….

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missing values and NaN’s not allowed if ‘na.rm’ is FALSE

I’m using lme4 (v.1.1-33) in R v.4.3.1 to create a generalized linear mixed model with a couple random effects and several fixed effects. I get no errors or warnings from this line. fit<-glmer(formula= Response ~ (1|random1) + (1|random2) + fixed1*fixed2 + fixed3, family= Gamma(link=”log”), data=df, na.action=na.omit, control = glmerControl(optimizer =…

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Course on Generalised Linear Mixed Models in R

Dear all, We are excited to announce our upcoming course on (GENERALISED) LINEAR MIXED MODELS IN R, taking place from October 9th to 13th, 2023. To ensure global accessibility, this course will be conducted online, allowing participants from all over the world to benefit from the invaluable knowledge shared. COURSE…

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Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16:410–22. doi.org/10.1038/s41579-018-0029-9. Article  CAS  PubMed  Google Scholar  Blaxter M. Counting angels with DNA. Nature. 2003;421:122–3. doi.org/10.1038/421122a. Article  CAS  PubMed  Google Scholar  Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas…

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Bioconductor – sparsenetgls

DOI: 10.18129/B9.bioc.sparsenetgls     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see sparsenetgls. Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression Bioconductor version: 3.13 The package provides methods of combining the graph structure learning and generalized…

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ggplot2 – adding a trend line in ggplot as well as ascertain its significance

I need help with finding and adding a trend line into my ggplot generated from an lmer model. My objective is to determine whether there is a significant trend within my exposure group, as well as to ascertain its significance. library(lme4) # linear mixed-effects models library(lmerTest) # test for linear…

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Handling NA’s in Deseq2

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

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r – How to Resolve Warning Message in lme4 mixed effects model?

I am having an issue with running a linear mixed effects model. I’m constantly presented with the same warning message and I’m unsure how to go about tackling this issue. The code: model_CRP <- lmer(mem ~ binding*time_years + AGE + GENDER + EDU_VERHAGE_YEARS + (1 | famnr) + (1+time_years|famnr:EMI), data=df_long_final,…

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Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species

Introduction Tropical rainforests in the Amazon basin harbor the highest tree diversity on earth (Ter Steege et al., 2020). Most of this diversity is concentrated in a relatively small number of plant families, including Chrysobalanaceae, Fabaceae, Lauraceae, Lecythidaceae, Malvaceae (sensu lato), Myrtaceae, Rubiaceae, and Sapotaceae, that can comprise > 60%…

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statistical comparison between accession based on their origins

statistical comparison between accession based on their origins 0 I have about 50 accession and their origins are divided in 2 centuries (20 accession from American, 30 accession from European) and there are 10,000 gene for each accession so the dataframe looks like this … Now, I have to check…

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r – Error in UseMethod(“droplevels”) when using ggpredict to plot a daily diary study

This isn’t hard to replicate. You can’t use a Date-type object in a regression model (or at least you can’t rely on it working for everything you want to do). library(lme4) ## `sleepstudy` is a built-in object in the lme4 package. ## Days is numeric, make a date out of…

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Lake Sinai virus is a diverse, globally distributed but not emerging multi-strain honeybee virus

doi: 10.1111/mec.16987. Online ahead of print. Affiliations Expand Affiliations 1 Chinese Academy of Agricultural Sciences, Institute of Bast Fiber Crops and Center of Southern Economic Crops, Changsha, China. 2 Beijing Academy of Agriculture and Forestry Sciences, National Engineering Research Center for Vegetables (Institute of Vegetable Science), Beijing, China. 3 Key…

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r – How to add equation and R2 for a facetted plot in ggplot R2?

The data has two factors. I ran a simple lmer for the model. I want to plot the data using facet_plot in ggplot. I want to display the equation and R2. Here is my attempt. I don’t know to facet within the lm_eqn and then display correspond to the plots….

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Weather anomalies more important than climate means in driving insect phenology

Cohen, J. M., Lajeunesse, M. J. & Rohr, J. R. A global synthesis of animal phenological responses to climate change. Nat. Clim. Chang. 8, 224–228 (2018). Park, D. S., Newman, E. A. & Breckheimer, I. K. Scale gaps in landscape phenology: challenges and opportunities. Trends Ecol. Evol. 36, 709–721 (2021)….

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ggplot2 – plot estimates with 95%CI from lmer model

I need help in plotting the estimates and 95% CI from Lmer model, i am using plot_model from sjplot function. library(lme4) # linear mixed-effects models library(lmerTest) # test for linear mixed-effects models library(gtsummary) library(sjPlot) library(ggplot2) names(trajectories) library(tidyverse) str(trajectories$yr_qun) trajectories <- trajectories %>% mutate(yr_qun = yr_qun %>% fct_relevel(“2001_low”,”2001_medium”, “2001_high”, “2002_low”,”2002_medium”, “2002_high”,…

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Bioconductor – IMAS

DOI: 10.18129/B9.bioc.IMAS     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IMAS. Integrative analysis of Multi-omics data for Alternative Splicing Bioconductor version: 3.12 Integrative analysis of Multi-omics data for Alternative splicing. Author: Seonggyun Han, Younghee Lee Maintainer: Seonggyun Han <hangost at ssu.ac.kr>…

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ggplot2 – Illustrate interaction between main variable and interaction variable in R

library(ggplot2) library(lme4) library(lmerTest) library(jtools) set.seed(123) # create data frame with 1000 rows for 100 participants with 2-5 visits n_participants <- 100 n_visits <- sample(2:5, n_participants, replace = TRUE) n_rows <- sum(n_visits) df <- data.frame( subnum = rep(1:n_participants, times = n_visits), visit = unlist(lapply(n_visits, seq_len)), zatt_new = rnorm(n_rows, mean = 0,…

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lme4 nlme – RStudio: Help on Linear Mixed Models

I am a beginner in linear mixed models on RStudio and would like some advice on what I would like to do with my data. I work in the field of cognitive neuroscience and my research focuses on understanding face processing in adults. We measure face processing using eye-tracking measures…

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r – Desperate for help, MLB model crash and burn

Closed. This question needs to be more focused. It is not currently accepting answers. Want to improve this question? Update the question so it focuses on one problem only by editing this post. This post was edited and submitted for review 14 hours ago. I…

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Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters

Ethics statement In vitro and animal work were conducted under appropriate biosafety conditions in a BSL-3 facility at the Institut für Virologie, Freie Universität Berlin, Germany. All animal experiments were performed in compliance with relevant institutional, national and international guidelines for the care and humane use of animals and approved…

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Gene duplicate

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

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Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome

Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article  Google Scholar  Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…

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The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater

Falkowski, P. G., Barber, R. T. & Smetacek, V. Biogeochemical controls and feedbacks on ocean primary production. Science (1979) 281, 200–206 (1998). CAS  Google Scholar  Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013). Article  PubMed  PubMed Central  Google Scholar …

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Evolutionary differentiation of androgen receptor is responsible for sexual characteristic development in a teleost fish

Animals All the procedures and protocols were approved by the Institutional Animal Care and Use Committee of the National Institute for Basic Biology (15A005, 14A003, 13A023, 12A020, 11A028) and Kyushu University (A21-043-0, A19-137-0, A19-137-1, A19-137-2, A29-088-0, A29-088-1, A29-088-2). Japanese medaka (Oryzias latipes) were bred and maintained under artificial reproductive conditions…

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Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem

Proctor, L. Priorities for the next 10 years of human microbiome research. Nature 569(7758), 623–625 (2019). Article  ADS  CAS  PubMed  Google Scholar  Bahl, M. I., Bergström, A. & Licht, T. R. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis….

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Impact of microbial genome completeness on metagenomic functional inference

Genome retrieval, annotation and distillation We browsed the GTDB database [9], which contains complete and draft bacterial genomes with associated CheckM completeness scores, for Bacterial phyla with at least 100 genomes in each of the 1% windows ranging 70–100% of genome completeness with <10% contamination. These criteria were met by…

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Unable to install clusterProfiler on Mac M1

Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…

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Bioconductor – MSstats

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MSstats. Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments Bioconductor version: 3.4 A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA…

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Mixed model analysis using lme4

Mixed model analysis using lme4 0 Hi all, I am a novice in using mixed models. I am not sure how to set up the fixed and random effects in mixed model. Your expertise would be much appreciated. My experimental set up is as follows: Three years of experiment (Experiment),…

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