The LMMsolver package | Introduction | Linear Regression | Fitting a non-linear function. | Smoothing combining two experiments | Smooth trends in two dimensions | US precipitation example | Sea Surface Temperatures | Generalized Linear Mixed Models. | Modelling count data using Poisson model. | Binomial distribution | Multinomial distribution | Examples in Quantitative Genetics and Agriculture | Linear Variance model oats data | Generalized Heritability | Modelling longitudinal data | QTL mapping using IBDs | References

The douconca package | Double constained correspondence analysis | Example data and questions | Basic analysis | Statistical testing | Fitted values and predictions | Which set of traits is most closely related to abundance and to the environment? | Do the morphological traits contribute after accounting for the ecological traits? | One trait: CWM regression without inflated type I error. | Introduction | Testing the relationship between LDMC and the environmental variables | The coefficients of a CWM-regression are proportional to those of dc-CA | Restrictions on names of variables and levels of factors | References

The statgenHTP Package | Data description | Example 1: photosystem efficiency in Arabidopsis | Data preparation | Data visualization | Layout plot | Raw data plot | Boxplot | Correlation plot | Outlier detection for single observations | Correction for spatial trends | Spatial model using SpATS | Model plots | Extracting model results | Outlier detection for series of observations | Modeling the genetic signal | Model fitting | Model prediction | Model plot | Estimation of parameters from time courses | References

The statgenIBD package | Population types | Examples | Steptoe Morex | Visualizing results | Pedigree plot | Genetic map plot | Single genotype plot | Plot of IBD probabilities for all genotypes. | Plot the coverage of each parent across the genome. | Plot the total coverage of each parent | Evaluation positions | Extracting value for markers of interest | Write and read tab-delimited *.txt files | Write results to Flapjack format | Simulated data | F4 | C4S3 | Multi-cross | Importing IBD probabilities computed using RABBIT | References

The statgenGxE package | Data preparation | Coloring of genotypes and trials | Mixed model analysis of GxE table of means | Model fitted with all terms as fixed | Model fitted with all terms as random | Mixed model | Finlay-Wilkinson Analysis | AMMI Analysis | GGE Analysis | Identifying mega environments | Stability measures | Modeling of heterogeneity of genetic variances and correlations | Fitted values and residuals | Reporting | References

The statgenMPP package | Example simulated data | Example maize | Example barley | Parallel computing | Summary | References

The statgenSTA Package | Data preparation | Creating a TD object | Example | Metadata | Add extra data to a TD object | Summarizing a TD object | Plotting a TD object | Layout plot | Map plot | Box plot | Correlation plot | Scatter plot matrix | Modeling | Model types | Spatial models | Model summary | Model plots | Base plots | Spatial plots | Outlier detection | Model reports | Extracting model results | Adding extra variables | Prepare data for GxE analysis | References

The statgenGWAS package | Theoretical background | Application in the package | The class gData | Marker map | Marker matrix | Phenotypic data | Kinship matrix | Further covariates | Worked example | Load data | Create gData object | Recoding and cleaning of markers | Single trait GWAS | GWAS Summary | GWAS Plots | QQ-plots | Manhattan plots | QTL plots | Kinship matrices | Further options | Multiple trials and traits | Significance thresholds | Controlling false discovery rate | Variance covariance matrix | Genomic control correction | Covariates | Minor Allele Frequency | SNPs close to significant SNPs | References

Multi-Trait GWAS | Theoretical background | Hypotheses for the SNP-effects | Models for the genetic and residual covariance | The class gData | Worked example 1: multiple traits in one trial | Create gData object | Recoding and cleaning of markers | Running Multi-trait GWAS | GWAS Summary | GWAS Plots | QQ plots | Manhattan plots | QTL plots | Kinship matrices | Worked example 2: one trait measured in multiple trials | Multi-trial GWAS | Further options | Significance thresholds | Variance components | Covariates | Minor Allele Frequency | Estimation of common SNP effects and QTL×E effects. | References

File format | Examples | Writing IBD probabilities to a file | Reading IBD probabilities from file

The isatabr package | The ISA tab structure | The Investigation file | The Study file | The Assay file | Example data | Reading files in the ISA-Tab format | Accessing and updating ISA objects. | Processing assay files | Mass spectrometry assay files | Microarray assay files | Writing files in the ISA-Tab format. | References