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Since, in this study, a single-SNP regression was performed using the LM model and all lower-density SNPs were included in the higher-density dataset, all significant SNPs that were identified with LMMD were also detected with LMHD, and all significant SNPs that were identified with LMHD were also detected with LMSEQ if the same significance threshold was used.
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Figure 1 shows the associations of SNPs with mastitis using the LM and BVS models.
In a protein-by-protein analysis, we performed linear fits of ω R 4 S with either MSF (Flexibility Model) or MLmS (Stress Model) using the lm function of the base package of R for each protein.
Protein properties were analyzed by implementing a multiple regression model using the "lm" function.
We fit an ordinary least squares (OLS) linear model (using the lm function in R) to the log2 transformed fold change of the significantly differentially expressed genes for each pairwise comparison of the evolved lines with the ancestor.
Association between expression data and storage time was assessed through linear modeling using the lm function in R. Significance threshold was set at nominal P < 0.001.
Unless otherwise noted, all P values were generated by fitting linear models using the "lm" package of R (http://www.R-project.org) and testing for significant terms using analysis of variance.
Effects of population on pre-reproductive vegetative diameter were tested for all plants in the study with linear models using the lm function in R, and were log transformed to improve homoscedasticity.
Then, significance of environmental fixed effects was assessed (using a statistical significance threshold of P < 0.05) by fitting linear regression models using the lm function for TKC, EPG and weight traits, and the glm function for IBK binary in the R software package [ 24].
The regression analysis was performed using the lm function in R. The linear model used was: leafout ~ phylogeny + bio1 + bio7 + bio10 + bio11 + bio12 + bio15 + bio18 + bio19 + elevation + photoperiod.
The model was fitted using the lm function of R (version 2.6.1) [53].
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