Variance Components

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Last updated: 2026-04-08

Checks: 6 1

Knit directory: Integrating-nir-genomic-kernel/

This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20250829)

The command set.seed(20250829) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 7a97272

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 7a97272. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

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Rmd	f18937a	WevertonGomesCosta	2025-11-04	chance components_variance to variance_components

---

The document starts by setting knitting options so that tables, code, and figures are displayed consistently throughout the tutorial.

This chunk initializes the session and standard document options for the variance-component module. It ensures that the following analyses start from a controlled and reproducible environment.

Language / Idioma: English | Português

1. Introduction

This tutorial summarizes variance components for the predictive models used in this study. In the current workflow, this file is used mainly to consolidate and interpret results that were already estimated previously, although it still keeps the code structure needed to fit the models when that step must be rerun.

The goal is to quantify how much of the total phenotypic variance is attributed to the main effects and interaction terms included in each model. In practical terms, this script helps answer questions such as:

• How much variance is associated with the categorical environment effect (E)?
• How much is captured by the genomic kernels?
• How much is captured by the phenomic/NIRS kernels (P)?
• How much is associated with the weather kernel (W), which is used mainly in models Eta10-Eta18?
• How relevant are the interaction terms such as G × E, G × W, P × E, and P × W?

This script is organized into four stages:

1. Load kernels and phenotypic data produced in matrizes.Rmd.
2. Define the 18 variance-component models.
3. Read or rerun the BGLR outputs, depending on whether the saved posterior summaries already exist.
4. Process and visualize the variance decomposition for Grain Yield (GY) and Kernel Weight (KW).

A high variance share for a given source should not be interpreted automatically as evidence of biological complementarity or better predictive performance. This point is especially important for P, because NIRS-based similarity may reflect strong physiological response to the environment in addition to any stable biological signal, and for W, because the weather kernel complements but does not replace the categorical environment effect.

Inputs, outputs and next step

Inputs of this step - matrices and kernels generated by matrizes.Rmd - the reduced catalog of 18 models used in the project

Outputs of this step - raw variance-component results - processed variance-component summaries - percentage tables and diagnostic figures

Next step - this stage complements the structural interpretation of the models and should be read together with the predictive results generated later in analysis_prediction.Rmd.

2. R Environment and Required Inputs

First, we load the packages used to manipulate the data, fit the Bayesian models, and generate the final article-quality figures.

The next step loads the packages needed for reading the saved artifacts, reshaping the results, plotting summaries, and running the heavy estimation stage when required.

This chunk loads the packages used for model fitting, data manipulation, tabulation, and plotting. Bringing them together here makes the structure of the module easier to understand.

library(dplyr)
library(tidyr)
library(readr)
library(stringr)
library(tibble)
library(ggplot2)
library(BGLR)
library(parallel)
library(doParallel)
library(foreach)
library(ggthemes)
library(scales)
library(fs)
library(grid)
library(knitr)
library(kableExtra)

2.1. File paths

All kernels and phenotypic objects are expected to be available in output/Matrizes/, which is the output directory created in matrizes.Rmd. The variance-component results generated here are stored in output/variance_components/.

The following lines define the project directories used to find matrices, store outputs, and organize the saved variance-component files.

This chunk defines the folders used to read the matrices and to save the variance-component outputs. Making the paths explicit clarifies where the module receives inputs and where it writes results.

kernel_dir <- "output/Matrizes"
results_dir <- "output/variance_components"
figure_dir <- file.path(results_dir, "figures")
bglr_runs_dir <- file.path(results_dir, "bglr_runs")

dir.create(results_dir, recursive = TRUE, showWarnings = FALSE)
dir.create(bglr_runs_dir, recursive = TRUE, showWarnings = FALSE)
dir.create(figure_dir, recursive = TRUE, showWarnings = FALSE)

2.2. Input checks

Before reading the files, we check whether the expected .rds objects are present in the matrices output folder. This makes the tutorial easier to follow because the script stops immediately if a required object is missing.

Before moving into model definition or result processing, the script checks that the required input files and directories are available.

This chunk verifies that all required matrices and supporting files are available. The goal is to stop early if the upstream modules have not produced the objects needed for this stage.

required_files <- c(
  "ZG.rds", "ZP.rds", "ZE.rds", "ZEZE.rds", "ZW.rds",
  "ZGZE.rds", "ZPZE.rds", "ZGZW.rds", "ZPZW.rds",
  "GGK.rds", "PGK.rds", "GAK.rds", "PAK.rds",
  "GGKE.rds", "PGKE.rds", "GGKW.rds", "PGKW.rds",
  "GAKE.rds", "PAKE.rds", "GAKW.rds", "PAKW.rds",
  "Pheno.rds", "Pedigree.rds"
)

missing_files <- required_files[!file.exists(file.path(kernel_dir, required_files))]

if (length(missing_files) > 0) {
  stop(
    "The following required files were not found in output/Matrizes/: ",
    paste(missing_files, collapse = ", "),
    ". Run matrizes.Rmd first."
  )
}

2.3. Labels used in the final tables and figures

These vectors define how the variance components will appear in the final outputs. Keeping these labels visible in the main script helps the reader understand how internal model names are translated into article-ready labels.

Here the script defines the labels and naming conventions that will be reused in tables, output files, and figures.

This chunk defines the labels used to translate model components into readable output names. These labels are important because they make the saved variance summaries easier to interpret.

component_display <- c(
  E = "Environment (E)",
  G = "Genomic linear (G)",
  P = "Phenomic linear (P)",
  W = "Weather kernel (W)",
  GE = "G × E",
  PE = "P × E",
  GW = "G × W",
  PW = "P × W",
  GGK = "Genomic Gaussian (GGK)",
  PGK = "Phenomic Gaussian (PGK)",
  GAK = "Genomic arc-cosine (GAK)",
  PAK = "Phenomic arc-cosine (PAK)",
  GGKE = "GGK × E",
  PGKE = "PGK × E",
  GAKE = "GAK × E",
  PAKE = "PAK × E",
  GGKW = "GGK × W",
  PGKW = "PGK × W",
  GAKW = "GAK × W",
  PAKW = "PAK × W",
  Residual = "Residual"
)

component_order <- c(
  "Environment (E)",
  "Genomic linear (G)",
  "Phenomic linear (P)",
  "Weather kernel (W)",
  "G × E",
  "P × E",
  "G × W",
  "P × W",
  "Genomic Gaussian (GGK)",
  "Phenomic Gaussian (PGK)",
  "Genomic arc-cosine (GAK)",
  "Phenomic arc-cosine (PAK)",
  "GGK × E",
  "PGK × E",
  "GAK × E",
  "PAK × E",
  "GGK × W",
  "PGK × W",
  "GAK × W",
  "PAKW × W",
  "Residual"
)

component_order[component_order == "PAKW × W"] <- "PAK × W"

3. Loading the Kernels and Phenotypic Objects

This section loads the matrices generated in matrizes.Rmd. These objects are the core inputs for the variance-component analysis.

At this point, the script reads the matrices and kernels generated in the previous module so the variance-component models use the same aligned inputs as the prediction stage.

This chunk restores the matrices and kernels that enter the variance-component models. Once loaded, these objects provide the full set of sources whose contributions will be summarized.

ZG    <- readRDS(file.path(kernel_dir, "ZG.rds"))
ZP    <- readRDS(file.path(kernel_dir, "ZP.rds"))
ZE    <- readRDS(file.path(kernel_dir, "ZE.rds"))
ZEZE  <- readRDS(file.path(kernel_dir, "ZEZE.rds"))
ZW    <- readRDS(file.path(kernel_dir, "ZW.rds"))

ZGZE  <- readRDS(file.path(kernel_dir, "ZGZE.rds"))
ZPZE  <- readRDS(file.path(kernel_dir, "ZPZE.rds"))
ZGZW  <- readRDS(file.path(kernel_dir, "ZGZW.rds"))
ZPZW  <- readRDS(file.path(kernel_dir, "ZPZW.rds"))

GGK   <- readRDS(file.path(kernel_dir, "GGK.rds"))
PGK   <- readRDS(file.path(kernel_dir, "PGK.rds"))
GAK   <- readRDS(file.path(kernel_dir, "GAK.rds"))
PAK   <- readRDS(file.path(kernel_dir, "PAK.rds"))

GGKE  <- readRDS(file.path(kernel_dir, "GGKE.rds"))
PGKE  <- readRDS(file.path(kernel_dir, "PGKE.rds"))
GGKW  <- readRDS(file.path(kernel_dir, "GGKW.rds"))
PGKW  <- readRDS(file.path(kernel_dir, "PGKW.rds"))

GAKE  <- readRDS(file.path(kernel_dir, "GAKE.rds"))
PAKE  <- readRDS(file.path(kernel_dir, "PAKE.rds"))
GAKW  <- readRDS(file.path(kernel_dir, "GAKW.rds"))
PAKW  <- readRDS(file.path(kernel_dir, "PAKW.rds"))

Pheno    <- readRDS(file.path(kernel_dir, "Pheno.rds"))
Pedigree <- readRDS(file.path(kernel_dir, "Pedigree.rds"))

n_obs <- nrow(Pheno)
cat("Number of phenotypic observations:", n_obs, "\n")

Number of phenotypic observations: 982 

cat("Number of pedigrees:", length(Pedigree), "\n")

Number of pedigrees: 329 

3.1. Alignment diagnostics

Before fitting the models, it is important to verify that the kernels are square and aligned to the same observation order used in Pheno. In a tutorial context, this is an important check because many downstream errors are caused by mismatched row and column orders.

The loaded kernels are then checked for compatibility in dimension and ordering before they are combined in the Bayesian models.

This chunk performs structural checks to confirm that the loaded matrices are dimensionally aligned. These checks help ensure that the model components can be combined without hidden indexing problems.

reference_ids <- Pheno$ObsID

ZE <- ZE[match(reference_ids, rownames(ZE)), , drop = FALSE]

ZG   <- ZG[reference_ids, reference_ids, drop = FALSE]
ZP   <- ZP[reference_ids, reference_ids, drop = FALSE]
ZEZE <- ZEZE[reference_ids, reference_ids, drop = FALSE]
ZW   <- ZW[reference_ids, reference_ids, drop = FALSE]
ZGZE <- ZGZE[reference_ids, reference_ids, drop = FALSE]
ZPZE <- ZPZE[reference_ids, reference_ids, drop = FALSE]
ZGZW <- ZGZW[reference_ids, reference_ids, drop = FALSE]
ZPZW <- ZPZW[reference_ids, reference_ids, drop = FALSE]
GGK  <- GGK[reference_ids, reference_ids, drop = FALSE]
PGK  <- PGK[reference_ids, reference_ids, drop = FALSE]
GAK  <- GAK[reference_ids, reference_ids, drop = FALSE]
PAK  <- PAK[reference_ids, reference_ids, drop = FALSE]
GGKE <- GGKE[reference_ids, reference_ids, drop = FALSE]
PGKE <- PGKE[reference_ids, reference_ids, drop = FALSE]
GGKW <- GGKW[reference_ids, reference_ids, drop = FALSE]
PGKW <- PGKW[reference_ids, reference_ids, drop = FALSE]
GAKE <- GAKE[reference_ids, reference_ids, drop = FALSE]
PAKE <- PAKE[reference_ids, reference_ids, drop = FALSE]
GAKW <- GAKW[reference_ids, reference_ids, drop = FALSE]
PAKW <- PAKW[reference_ids, reference_ids, drop = FALSE]

kernel_inventory <- tibble(
  kernel = c("ZG", "ZP", "ZEZE", "ZW", "GGK", "PGK", "GAK", "PAK"),
  n_rows = c(nrow(ZG), nrow(ZP), nrow(ZEZE), nrow(ZW), nrow(GGK), nrow(PGK), nrow(GAK), nrow(PAK)),
  n_cols = c(ncol(ZG), ncol(ZP), ncol(ZEZE), ncol(ZW), ncol(GGK), ncol(PGK), ncol(GAK), ncol(PAK)),
  is_square = c(
    nrow(ZG) == ncol(ZG),
    nrow(ZP) == ncol(ZP),
    nrow(ZEZE) == ncol(ZEZE),
    nrow(ZW) == ncol(ZW),
    nrow(GGK) == ncol(GGK),
    nrow(PGK) == ncol(PGK),
    nrow(GAK) == ncol(GAK),
    nrow(PAK) == ncol(PAK)
  ),
  symmetric_names = c(
    identical(rownames(ZG), colnames(ZG)),
    identical(rownames(ZP), colnames(ZP)),
    identical(rownames(ZEZE), colnames(ZEZE)),
    identical(rownames(ZW), colnames(ZW)),
    identical(rownames(GGK), colnames(GGK)),
    identical(rownames(PGK), colnames(PGK)),
    identical(rownames(GAK), colnames(GAK)),
    identical(rownames(PAK), colnames(PAK))
  ),
  aligned_with_reference = c(
    identical(rownames(ZG), reference_ids),
    identical(rownames(ZP), reference_ids),
    identical(rownames(ZEZE), reference_ids),
    identical(rownames(ZW), reference_ids),
    identical(rownames(GGK), reference_ids),
    identical(rownames(PGK), reference_ids),
    identical(rownames(GAK), reference_ids),
    identical(rownames(PAK), reference_ids)
  )
)

kernel_inventory %>%
  dplyr::mutate(
    n_rows = format(n_rows, big.mark = ","),
    n_cols = format(n_cols, big.mark = ",")
  ) %>%
  knitr::kable(
    caption = "Diagnostic summary of the main kernels used in the variance-component analysis after explicit alignment to the phenotypic observation order.",
    align = "lcccccc"
  ) %>%
  kableExtra::kable_styling(
    bootstrap_options = c("striped", "hover", "condensed", "responsive"),
    full_width = FALSE,
    position = "left"
  ) %>%
  kableExtra::scroll_box(width = "100%", height = "260px")

Diagnostic summary of the main kernels used in the variance-component analysis after explicit alignment to the phenotypic observation order.

kernel	n_rows	n_cols	is_square	symmetric_names	aligned_with_reference
ZG	982	982	TRUE	TRUE	TRUE
ZP	982	982	TRUE	TRUE	TRUE
ZEZE	982	982	TRUE	TRUE	TRUE
ZW	982	982	TRUE	TRUE	TRUE
GGK	982	982	TRUE	TRUE	TRUE
PGK	982	982	TRUE	TRUE	TRUE
GAK	982	982	TRUE	TRUE	TRUE
PAK	982	982	TRUE	TRUE	TRUE

4. Definition of the 18 Predictive Models

Each model is defined as a list in the format required by the ETA argument of BGLR. The environment term (E) is included as a fixed-effect design matrix with model = "BRR", while the kernels are fitted as random effects with model = "RKHS".

The reduced set of 18 Bayesian multi-kernel models is defined below in the form required for the variance-component workflow.

This chunk defines the 18 model structures used for variance decomposition. It mirrors the model catalog used in prediction so that the interpretation of components remains consistent across modules.

models <- list()

models[[1]] <- list(
  E  = list(X = ZE, model = "BRR"),
  G  = list(K = ZG, model = "RKHS"),
  GE = list(K = ZGZE, model = "RKHS")
)

models[[2]] <- list(
  E  = list(X = ZE, model = "BRR"),
  P  = list(K = ZP, model = "RKHS"),
  PE = list(K = ZPZE, model = "RKHS")
)

models[[3]] <- list(
  E    = list(X = ZE, model = "BRR"),
  GGK  = list(K = GGK, model = "RKHS"),
  GGKE = list(K = GGKE, model = "RKHS")
)

models[[4]] <- list(
  E    = list(X = ZE, model = "BRR"),
  PGK  = list(K = PGK, model = "RKHS"),
  PGKE = list(K = PGKE, model = "RKHS")
)

models[[5]] <- list(
  E    = list(X = ZE, model = "BRR"),
  GAK  = list(K = GAK, model = "RKHS"),
  GAKE = list(K = GAKE, model = "RKHS")
)

models[[6]] <- list(
  E    = list(X = ZE, model = "BRR"),
  PAK  = list(K = PAK, model = "RKHS"),
  PAKE = list(K = PAKE, model = "RKHS")
)

models[[7]] <- list(
  E  = list(X = ZE, model = "BRR"),
  G  = list(K = ZG, model = "RKHS"),
  P  = list(K = ZP, model = "RKHS"),
  GE = list(K = ZGZE, model = "RKHS"),
  PE = list(K = ZPZE, model = "RKHS")
)

models[[8]] <- list(
  E    = list(X = ZE, model = "BRR"),
  GGK  = list(K = GGK, model = "RKHS"),
  PGK  = list(K = PGK, model = "RKHS"),
  GGKE = list(K = GGKE, model = "RKHS"),
  PGKE = list(K = PGKE, model = "RKHS")
)

models[[9]] <- list(
  E    = list(X = ZE, model = "BRR"),
  GAK  = list(K = GAK, model = "RKHS"),
  PAK  = list(K = PAK, model = "RKHS"),
  GAKE = list(K = GAKE, model = "RKHS"),
  PAKE = list(K = PAKE, model = "RKHS")
)

models[[10]] <- list(
  E  = list(X = ZE, model = "BRR"),
  W  = list(K = ZW, model = "RKHS"),
  G  = list(K = ZG, model = "RKHS"),
  GE = list(K = ZGZE, model = "RKHS"),
  GW = list(K = ZGZW, model = "RKHS")
)

models[[11]] <- list(
  E  = list(X = ZE, model = "BRR"),
  W  = list(K = ZW, model = "RKHS"),
  P  = list(K = ZP, model = "RKHS"),
  PE = list(K = ZPZE, model = "RKHS"),
  PW = list(K = ZPZW, model = "RKHS")
)

models[[12]] <- list(
  E  = list(X = ZE, model = "BRR"),
  W  = list(K = ZW, model = "RKHS"),
  G  = list(K = ZG, model = "RKHS"),
  P  = list(K = ZP, model = "RKHS"),
  GE = list(K = ZGZE, model = "RKHS"),
  PE = list(K = ZPZE, model = "RKHS"),
  GW = list(K = ZGZW, model = "RKHS"),
  PW = list(K = ZPZW, model = "RKHS")
)

models[[13]] <- list(
  E    = list(X = ZE, model = "BRR"),
  W    = list(K = ZW, model = "RKHS"),
  GGK  = list(K = GGK, model = "RKHS"),
  GGKE = list(K = GGKE, model = "RKHS"),
  GGKW = list(K = GGKW, model = "RKHS")
)

models[[14]] <- list(
  E    = list(X = ZE, model = "BRR"),
  W    = list(K = ZW, model = "RKHS"),
  PGK  = list(K = PGK, model = "RKHS"),
  PGKE = list(K = PGKE, model = "RKHS"),
  PGKW = list(K = PGKW, model = "RKHS")
)

models[[15]] <- list(
  E    = list(X = ZE, model = "BRR"),
  W    = list(K = ZW, model = "RKHS"),
  GGK  = list(K = GGK, model = "RKHS"),
  PGK  = list(K = PGK, model = "RKHS"),
  GGKE = list(K = GGKE, model = "RKHS"),
  PGKE = list(K = PGKE, model = "RKHS"),
  GGKW = list(K = GGKW, model = "RKHS"),
  PGKW = list(K = PGKW, model = "RKHS")
)

models[[16]] <- list(
  E    = list(X = ZE, model = "BRR"),
  W    = list(K = ZW, model = "RKHS"),
  GAK  = list(K = GAK, model = "RKHS"),
  GAKE = list(K = GAKE, model = "RKHS"),
  GAKW = list(K = GAKW, model = "RKHS")
)

models[[17]] <- list(
  E    = list(X = ZE, model = "BRR"),
  W    = list(K = ZW, model = "RKHS"),
  PAK  = list(K = PAK, model = "RKHS"),
  PAKE = list(K = PAKE, model = "RKHS"),
  PAKW = list(K = PAKW, model = "RKHS")
)

models[[18]] <- list(
  E    = list(X = ZE, model = "BRR"),
  W    = list(K = ZW, model = "RKHS"),
  GAK  = list(K = GAK, model = "RKHS"),
  PAK  = list(K = PAK, model = "RKHS"),
  GAKE = list(K = GAKE, model = "RKHS"),
  PAKE = list(K = PAKE, model = "RKHS"),
  GAKW = list(K = GAKW, model = "RKHS"),
  PAKW = list(K = PAKW, model = "RKHS")
)

names(models) <- paste0("Eta", seq_along(models))

model_component_lookup <- bind_rows(
  lapply(seq_along(models), function(i) {
    tibble(
      ModelID = i,
      EtaIndex = seq_along(models[[i]]),
      ComponentBase = names(models[[i]])
    )
  })
)

4.1. Model catalog

This table is useful both for internal checks and for linking figure labels to the formal description of each model.

The code below builds a compact model catalog linking each model identifier to its category and descriptive label for later summaries.

This chunk builds a tabular description of the model catalog used in the variance analysis. The table serves as a guide when reading the summaries and figures produced later.

model_info <- tibble(
  ModelID = 1:18,
  Model = paste0("Eta", 1:18),
  ETA = names(models),
  Category = c(
    rep("Single-source + E", 6),
    rep("Integrated G/P + E", 3),
    rep("Weather-augmented", 9)
  ),
  Description = c(
    "E + G + GE",
    "E + P + PE",
    "E + GGK + GGKE",
    "E + PGK + PGKE",
    "E + GAK + GAKE",
    "E + PAK + PAKE",
    "E + G + P + GE + PE",
    "E + GGK + PGK + GGKE + PGKE",
    "E + GAK + PAK + GAKE + PAKE",
    "E + W + G + GE + GW",
    "E + W + P + PE + PW",
    "E + W + G + P + GE + PE + GW + PW",
    "E + W + GGK + GGKE + GGKW",
    "E + W + PGK + PGKE + PGKW",
    "E + W + GGK + PGK + GGKE + PGKE + GGKW + PGKW",
    "E + W + GAK + GAKE + GAKW",
    "E + W + PAK + PAKE + PAKW",
    "E + W + GAK + PAK + GAKE + PAKE + GAKW + PAKW"
  )
)

readr::write_csv(model_info, file.path(results_dir, "model_catalog.csv"))

model_info %>%
  knitr::kable(
    caption = "Catalog of the 18 models evaluated in the variance-component analysis.",
    align = "cll"
  ) %>%
  kableExtra::kable_styling(
    bootstrap_options = c("striped", "hover", "condensed", "responsive"),
    full_width = FALSE,
    position = "left"
  ) %>%
  kableExtra::scroll_box(width = "100%", height = "340px")

Catalog of the 18 models evaluated in the variance-component analysis.

ModelID	Model	ETA	Category	Description
1	Eta1	Eta1	Single-source + E	E + G + GE
2	Eta2	Eta2	Single-source + E	E + P + PE
3	Eta3	Eta3	Single-source + E	E + GGK + GGKE
4	Eta4	Eta4	Single-source + E	E + PGK + PGKE
5	Eta5	Eta5	Single-source + E	E + GAK + GAKE
6	Eta6	Eta6	Single-source + E	E + PAK + PAKE
7	Eta7	Eta7	Integrated G/P + E	E + G + P + GE + PE
8	Eta8	Eta8	Integrated G/P + E	E + GGK + PGK + GGKE + PGKE
9	Eta9	Eta9	Integrated G/P + E	E + GAK + PAK + GAKE + PAKE
10	Eta10	Eta10	Weather-augmented	E + W + G + GE + GW
11	Eta11	Eta11	Weather-augmented	E + W + P + PE + PW
12	Eta12	Eta12	Weather-augmented	E + W + G + P + GE + PE + GW + PW
13	Eta13	Eta13	Weather-augmented	E + W + GGK + GGKE + GGKW
14	Eta14	Eta14	Weather-augmented	E + W + PGK + PGKE + PGKW
15	Eta15	Eta15	Weather-augmented	E + W + GGK + PGK + GGKE + PGKE + GGKW + PGKW
16	Eta16	Eta16	Weather-augmented	E + W + GAK + GAKE + GAKW
17	Eta17	Eta17	Weather-augmented	E + W + PAK + PAKE + PAKW
18	Eta18	Eta18	Weather-augmented	E + W + GAK + PAK + GAKE + PAKE + GAKW + PAKW

5. MCMC Settings

These values define the Gibbs sampler used by BGLR. Adjust them here if a longer chain is required for convergence diagnostics or sensitivity analyses.

This section defines the MCMC settings and execution controls that regulate the estimation stage when the heavy computation is turned on.

This chunk records the MCMC settings and repetition controls used in the variance-component fits. These values define the computational plan for the decomposition stage.

nIter   <- 5000
burnIn  <- 1000
thin    <- 10
num_rep <- 10
traits  <- c("GY", "KW")

6. Running BGLR for Each Model

This is the computationally expensive step of the workflow.

The next block contains the parallel estimation stage that fits the variance-component models, preserves the iterative BGLR artifacts in persistent folders, and saves the raw posterior summaries.

This chunk fits the variance-component models and saves the raw BGLR artifacts needed for later consolidation. It is the computational core of the module.

numCores <- parallel::detectCores()
useCores <- max(1, numCores - 1)
cl <- parallel::makeCluster(useCores)
doParallel::registerDoParallel(cl)

combos <- expand.grid(
  Model = 1:18,
  REP = 1:num_rep,
  Trait = traits,
  stringsAsFactors = FALSE
)

results_list <- foreach(
  i = 1:nrow(combos),
  .packages = c("BGLR", "dplyr", "tibble")
) %dopar% {
  Model <- combos$Model[i]
  rep_num <- combos$REP[i]
  Trait <- combos$Trait[i]
  rep_label <- sprintf("rep%02d", rep_num)
  eta_label <- paste0("Eta", Model)

  pheno <- data.frame(Pheno)
  y_data <- as.numeric(pheno[[Trait]])

  out_dir <- file.path(bglr_runs_dir, Trait, rep_label, eta_label)
  dir.create(out_dir, recursive = TRUE, showWarnings = FALSE)

  save_prefix <- file.path(
    out_dir,
    paste0("VC_", Trait, "_", eta_label, "_", rep_label, "_")
  )

  start_time <- Sys.time()
  fit <- BGLR(
    y = y_data,
    ETA = models[[Model]],
    nIter = nIter,
    burnIn = burnIn,
    thin = thin,
    saveAt = save_prefix
  )
  end_time <- Sys.time()

  effect_names <- names(models[[Model]])
  effect_models <- vapply(models[[Model]], function(x) x$model, character(1))
  effect_labels <- paste0(effect_names, "_", effect_models)

  generated_files <- list.files(
    out_dir,
    pattern = paste0("^", basename(save_prefix)),
    full.names = TRUE
  )

  if (length(generated_files) > 0) {
    for (current_file in generated_files) {
      current_name <- basename(current_file)
      renamed_name <- current_name

      for (j in seq_along(effect_labels)) {
        renamed_name <- sub(
          paste0("ETA_", j),
          effect_labels[j],
          renamed_name,
          fixed = TRUE
        )
      }

      if (!identical(current_name, renamed_name)) {
        file.rename(current_file, file.path(out_dir, renamed_name))
      }
    }
  }

  variance_samples <- list()

  if (!is.null(fit$ETA)) {
    if (is.null(effect_names)) {
      effect_names <- paste0("Effect_", seq_along(fit$ETA))
    }

    for (j in seq_along(fit$ETA)) {
      parameter_names <- names(fit$ETA[[j]])
      var_parameter <- parameter_names[grepl("^var", parameter_names)]

      if (length(var_parameter) > 0) {
        variance_samples[[effect_names[j]]] <- fit$ETA[[j]][[var_parameter[1]]]
      }
    }
  }

  metrics_object <- list(
    varE_samples = fit$varE,
    variances_samples = variance_samples,
    DIC = fit$fit$DIC,
    runtime_sec = as.numeric(difftime(end_time, start_time, units = "secs"))
  )

  saveRDS(metrics_object, file.path(out_dir, "variance_metrics.rds"))

  result_table <- tibble(
    Component = "Residual",
    MeanVar = mean(metrics_object$varE_samples, na.rm = TRUE)
  )

  if (length(metrics_object$variances_samples) > 0) {
    for (nm in names(metrics_object$variances_samples)) {
      result_table <- bind_rows(
        result_table,
        tibble(
          Component = nm,
          MeanVar = mean(metrics_object$variances_samples[[nm]], na.rm = TRUE)
        )
      )
    }
  }

  rm(fit)
  gc()

  result_table %>%
    mutate(Model = Model, Rep = rep_num, Trait = Trait)
}

stopCluster(cl)

all_variance <- bind_rows(results_list)
write_csv(all_variance, file.path(results_dir, "variance_components_raw.csv"))
saveRDS(all_variance, file.path(results_dir, "variance_components_raw.rds"))

7. Consolidating Saved Posterior Summaries

In the current version of the workflow, this is the section used most often. Instead of refitting all models every time, the script reads the previously saved variance_metrics.rds files from output/variance_components/bglr_runs/ and consolidates them into one object. This keeps the tutorial practical and reproducible, while making it clear that this page is mainly a result-consolidation step unless the user intentionally reruns the full BGLR estimation stage.

The saved outputs produced by the estimation stage are consolidated below into a single structure that can be processed more easily later.

This chunk gathers the saved outputs produced during model fitting and reorganizes them into analysis-ready tables. The purpose is to bridge the raw artifacts and the final summaries.

rds_files <- list.files(
  path = bglr_runs_dir,
  pattern = "(variance_metrics|_(metrics|metricas))\\.rds$",
  recursive = TRUE,
  full.names = TRUE
)

if (length(rds_files) > 0) {
  all_tables <- vector("list", length(rds_files))

  for (i in seq_along(rds_files)) {
    current_file <- normalizePath(rds_files[i], winslash = "/", mustWork = FALSE)
    path_parts <- str_split(current_file, "/")[[1]]

    rep_part <- path_parts[str_detect(path_parts, "^rep[0-9]+$|^rep_[0-9]+$")][1]
    eta_part <- path_parts[str_detect(path_parts, "^Eta")][1]
    trait_part <- path_parts[path_parts %in% traits][1]

    rep_value <- as.integer(str_remove(rep_part, "^rep_?0*"))
    model_value <- as.integer(str_remove(eta_part, "^Eta0*"))
    trait_value <- trait_part

    current_object <- readRDS(current_file)

    current_table <- tibble(
      Rep = rep_value,
      Model = model_value,
      Trait = trait_value,
      Component = "Residual",
      MeanVar = mean(current_object$varE_samples, na.rm = TRUE),
      DIC = current_object$DIC,
      runtime_sec = current_object$runtime_sec
    )

    if (length(current_object$variances_samples) > 0) {
      for (nm in names(current_object$variances_samples)) {
        current_table <- bind_rows(
          current_table,
          tibble(
            Rep = rep_value,
            Model = model_value,
            Trait = trait_value,
            Component = {
              current_component <- nm
              if (grepl("^ETA_[0-9]+$", current_component)) {
                current_eta_index <- suppressWarnings(as.integer(sub("^ETA_", "", current_component)))
                current_match <- which(
                  model_component_lookup$ModelID == model_value &
                    model_component_lookup$EtaIndex == current_eta_index
                )
                if (length(current_match) == 1) {
                  current_component <- model_component_lookup$ComponentBase[current_match]
                }
              }
              current_component <- sub("_(BRR|RKHS)$", "", current_component)
              current_component
            },
            MeanVar = mean(current_object$variances_samples[[nm]], na.rm = TRUE),
            DIC = current_object$DIC,
            runtime_sec = current_object$runtime_sec
          )
        )
      }
    }

    all_tables[[i]] <- current_table
  }

  all_variance <- bind_rows(all_tables)

  saveRDS(all_variance, file.path(results_dir, "variance_components_all.rds"))
  write_csv(all_variance, file.path(results_dir, "variance_components_raw.csv"))
}

8. Loading the Consolidated Variance-Component Object

This section loads the consolidated results and prepares them for summarization. If the file does not exist, the script stops and instructs the user to execute the model-fitting stage first.

The document now loads the already consolidated variance-component results so that it can summarize and visualize them without repeating the expensive estimation.

This chunk restores the consolidated variance results so the remaining sections can focus on processing and interpretation. This keeps the explanatory part of the document centered on the final outputs.

raw_file <- file.path(results_dir, "variance_components_all.rds")

if (!file.exists(raw_file)) {
  stop(
    "The file '", raw_file, "' was not found. ",
    "Run the Bayesian fitting stage first or keep the previously saved _metrics.rds files in output/variance_components/."
  )
}

all_variance <- readRDS(raw_file)

all_variance <- all_variance %>%
  mutate(
    Trait = str_extract(Trait, "GY|KW"),
    Trait = ifelse(is.na(Trait), Trait, Trait),
    Model = as.integer(Model)
  )

cat("Number of rows in consolidated variance object:", nrow(all_variance), "\n")

Number of rows in consolidated variance object: 2100 

9. Summarizing the Variance Components

Now we average the posterior means across repetitions for each model, trait, and component. Then we convert the results to percentages of total variance, which makes the models directly comparable.

The loaded results are then reshaped and annotated so that posterior means can be compared across traits, models, and component categories.

This chunk calculates the processed summaries that express how much variance is attributed to each model component. These summaries turn the raw saved quantities into interpretable decomposition results.

variance_summary <- all_variance %>%
  group_by(Model, Trait, Component) %>%
  summarise(
    AvgVar = mean(MeanVar, na.rm = TRUE),
    MeanDIC = mean(DIC, na.rm = TRUE),
    MeanRuntimeSec = mean(runtime_sec, na.rm = TRUE),
    .groups = "drop"
  ) %>%
  filter(!is.na(AvgVar), AvgVar > 0) %>%
  group_by(Model, Trait) %>%
  mutate(
    TotalVar = sum(AvgVar),
    Percentage = AvgVar / TotalVar
  ) %>%
  ungroup() %>%
  left_join(model_info, by = c("Model" = "ModelID")) %>%
  mutate(
    ModelNumber = Model,
    EtaIndex = ifelse(grepl("^ETA_[0-9]+$", Component),
                      suppressWarnings(as.integer(sub("^ETA_", "", Component))),
                      NA_integer_),
    Component = ifelse(
      !is.na(EtaIndex),
      model_component_lookup$ComponentBase[
        match(
          paste(ModelNumber, EtaIndex),
          paste(model_component_lookup$ModelID, model_component_lookup$EtaIndex)
        )
      ],
      Component
    ),
    Component = sub("_(BRR|RKHS)$", "", Component),
    Model = factor(paste0("Eta", ModelNumber), levels = paste0("Eta", 1:18)),
    ComponentLabel = dplyr::recode(Component, !!!component_display),
    ComponentLabel = factor(ComponentLabel, levels = component_order),
    Trait = factor(Trait, levels = c("GY", "KW"))
  ) %>%
  dplyr::select(-ModelNumber, -EtaIndex)

readr::write_csv(variance_summary, file.path(results_dir, "variance_components_processed.csv"))

9.1. Wide-format summary table

This table is helpful when you need a compact numerical summary for the manuscript or supplementary material.

The next table summarizes the relative contribution of each variance component across models.

This chunk assembles the main tabular summary of the variance decomposition. The table provides a compact numerical view of the component contributions across models.

variance_table <- variance_summary %>%
  dplyr::select(Model, Trait, ComponentLabel, Percentage) %>%
  dplyr::mutate(Percentage = round(100 * Percentage, 2)) %>%
  tidyr::pivot_wider(names_from = ComponentLabel, values_from = Percentage)

readr::write_csv(variance_table, file.path(results_dir, "variance_components_table_percent.csv"))

head(variance_table, 12) %>%
  knitr::kable(
    caption = "Preview of the processed variance-component table (percent of total variance).",
    align = "lcccccccccccc"
  ) %>%
  kableExtra::kable_styling(
    bootstrap_options = c("striped", "hover", "condensed", "responsive"),
    full_width = FALSE,
    position = "left"
  ) %>%
  kableExtra::scroll_box(width = "100%", height = "320px")

Preview of the processed variance-component table (percent of total variance).

Model	Trait	Environment (E)	Genomic linear (G)	G × E	Residual	Phenomic linear (P)	P × E	Genomic Gaussian (GGK)	GGK × E	Phenomic Gaussian (PGK)	PGK × E	Genomic arc-cosine (GAK)	GAK × E	Phenomic arc-cosine (PAK)	PAK × E	G × W	Weather kernel (W)	P × W	GGK × W	PGK × W	GAK × W	PAK × W
Eta1	GY	83.59	11.96	1.70	2.75	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta1	KW	75.42	20.80	1.46	2.33	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta2	GY	0.00	NA	NA	0.00	100	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta2	KW	0.00	NA	NA	0.00	100	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta3	GY	49.52	NA	NA	1.92	NA	NA	45.13	3.43	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta3	KW	35.42	NA	NA	1.26	NA	NA	61.28	2.04	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta4	GY	78.05	NA	NA	10.87	NA	NA	NA	NA	7.54	3.53	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta4	KW	73.38	NA	NA	11.51	NA	NA	NA	NA	11.07	4.04	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta5	GY	5.49	NA	NA	0.26	NA	NA	NA	NA	NA	NA	92.52	1.72	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta5	KW	3.38	NA	NA	0.16	NA	NA	NA	NA	NA	NA	95.71	0.75	NA	NA	NA	NA	NA	NA	NA	NA	NA
Eta6	GY	18.38	NA	NA	3.26	NA	NA	NA	NA	NA	NA	NA	NA	77.06	1.30	NA	NA	NA	NA	NA	NA	NA
Eta6	KW	10.60	NA	NA	2.14	NA	NA	NA	NA	NA	NA	NA	NA	86.37	0.89	NA	NA	NA	NA	NA	NA	NA

10. Figure for the Article

The next figure summarizes the percentage contribution of each variance component across the 18 models for both traits. To keep the x-axis readable, the models are displayed as Eta1 to Eta18, and the detailed descriptions remain available in the model catalog saved above.

This figure should be read as a structural summary of the fitted models, not as direct proof that combining more data sources automatically leads to stronger biological complementarity or better predictive performance.

The final figure turns the processed table into a compact visual summary for interpretation.

This chunk builds the final figure that compares variance contributions across models and traits. The graphic helps interpret how the structure of each model redistributes the explained variance.

trait_labels <- c(
  GY = "A. Grain yield (GY)",
  KW = "B. Kernel weight (KW)"
)

variance_plot <- variance_summary %>%
  ggplot(aes(x = Model, y = Percentage, fill = ComponentLabel)) +
  geom_col(color = "white", linewidth = 0.15, width = 0.82) +
  facet_wrap(~ Trait, ncol = 1, labeller = as_labeller(trait_labels)) +
  ggthemes::scale_fill_gdocs(name = "Variance component", drop = FALSE) +
  scale_y_continuous(
    labels = scales::percent_format(accuracy = 1),
    expand = expansion(mult = c(0, 0.02))
  ) +
  labs(
    x = "Model ID",
    y = "Proportion of total variance"
  ) +
  theme_minimal(base_size = 11) +
  theme(
    plot.title = element_text(face = "bold", size = 13, hjust = 0.5),
    strip.text = element_text(face = "bold", size = 11),
    axis.title = element_text(face = "bold"),
    axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1, size = 8),
    axis.text.y = element_text(size = 9),
    legend.position = "right",
    legend.box = "vertical",
    legend.title = element_text(face = "bold", size = 10),
    legend.text = element_text(size = 8),
    legend.key.height = unit(0.45, "cm"),
    legend.key.width = unit(0.55, "cm"),
    panel.grid.major.x = element_blank(),
    panel.grid.minor = element_blank()
  ) +
  guides(fill = guide_legend(ncol = 2, byrow = TRUE))

print(variance_plot)

Figure 3. Posterior mean percentage of total variance attributed to each model component across the 18 predictive models for grain yield (GY) and kernel weight (KW). Each stacked bar represents one model (Eta1-Eta18), averaged across repetitions, and colors identify the variance components included in the model structure. The weather kernel (W) and its associated interaction terms appear mainly in models Eta10-Eta18. Variance decomposition should be interpreted as a description of model structure and not automatically as evidence of stronger biological complementarity among information sources.

Past versions of variance-figure-1.png

Version	Author	Date
0b2db18	WevertonGomesCosta	2026-04-07
4fb14e1	WevertonGomesCosta	2026-04-06
d1beaba	WevertonGomesCosta	2026-04-06
d54afd7	WevertonGomesCosta	2026-04-01
00ef3ef	WevertonGomesCosta	2026-04-01
4e5af9a	WevertonGomesCosta	2026-03-27

ggsave(
  filename = file.path(figure_dir, "variance_components_article.tiff"),
  plot = variance_plot,
  width = 14,
  height = 10,
  dpi = 300,
  compression = "lzw",
  bg = "white"
)

11. Interpretation Guide

This final section clarifies how the figure should be interpreted.

• A large Environment (E) segment indicates that the categorical macro-environment effect dominates the variance partition.
• Large genomic terms such as G, GGK, or GAK indicate that genomic similarity captures an important share of the trait variability.
• Large phenomic terms such as P, PGK, or PAK indicate stronger contribution of the NIRS-derived similarity, but these terms should be interpreted with caution because NIRS may also reflect strong physiological response to the environment.
• Large weather-related terms such as W, G × W, or P × W indicate that weather-derived covariates explain additional structure. These terms appear mainly in models Eta10-Eta18 and should be interpreted as complementary to the categorical environment effect, not as a replacement for E.
• A large Residual segment indicates that important sources of variability remain unexplained by the fitted model.

In the context of this article, these variance decompositions complement the predictive analyses by showing which information sources contribute to model structure. However, a large variance share for a component should not be read automatically as evidence of stronger biological complementarity or of better predictive ability.

Stage navigation

Previous stage: Matrices
Next stage: Prediction — Part I

Session information

sessionInfo()

R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8  LC_CTYPE=Portuguese_Brazil.utf8   
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.utf8    

time zone: America/Sao_Paulo
tzcode source: internal

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] kableExtra_1.4.0  knitr_1.50        fs_1.6.6          scales_1.4.0     
 [5] ggthemes_5.2.0    doParallel_1.0.17 iterators_1.0.14  foreach_1.5.2    
 [9] BGLR_1.1.4        ggplot2_4.0.2     tibble_3.3.1      stringr_1.6.0    
[13] readr_2.2.0       tidyr_1.3.2       dplyr_1.2.0      

loaded via a namespace (and not attached):
 [1] gtable_0.3.6       xfun_0.54          bslib_0.9.0        tzdb_0.5.0        
 [5] vctrs_0.7.1        tools_4.5.1        generics_0.1.4     pkgconfig_2.0.3   
 [9] RColorBrewer_1.1-3 S7_0.2.1           lifecycle_1.0.5    truncnorm_1.0-9   
[13] compiler_4.5.1     farver_2.1.2       git2r_0.36.2       textshaping_1.0.4 
[17] codetools_0.2-20   httpuv_1.6.16      htmltools_0.5.9    sass_0.4.10       
[21] yaml_2.3.12        later_1.4.4        pillar_1.11.1      crayon_1.5.3      
[25] jquerylib_0.1.4    whisker_0.4.1      MASS_7.3-65        cachem_1.1.0      
[29] tidyselect_1.2.1   digest_0.6.39      stringi_1.8.7      purrr_1.2.1       
[33] labeling_0.4.3     rprojroot_2.1.1    fastmap_1.2.0      cli_3.6.5         
[37] magrittr_2.0.4     withr_3.0.2        promises_1.5.0     bit64_4.6.0-1     
[41] rmarkdown_2.30     bit_4.6.0          otel_0.2.0         workflowr_1.7.2   
[45] ragg_1.5.0         hms_1.1.4          evaluate_1.0.5     viridisLite_0.4.2 
[49] rlang_1.1.7        Rcpp_1.1.1         glue_1.8.0         xml2_1.5.1        
[53] svglite_2.2.2      rstudioapi_0.17.1  vroom_1.7.0        jsonlite_2.0.0    
[57] R6_2.6.1           systemfonts_1.3.1