17 Function Reference Quick Guide

17.1 Core Functions

Function	Purpose
`creating.diploid()`	Create founder population
`breeding.diploid()`	Simulate breeding actions
`creating.trait()`	Add traits to population

17.2 Extraction Functions (get.*)

Function	Returns
`get.bv()`	True breeding values
`get.bve()`	Estimated breeding values
`get.pheno()`	Phenotypes
`get.geno()`	Genotypes (0/1/2 matrix)
`get.haplo()`	Haplotypes
`get.pedigree()`	Pedigree (ID, Sire, Dam)
`get.map()`	Genetic map
`get.qtl()`	QTL positions

17.3 Analysis Functions

Function	Purpose
`kinship.emp()`	Genomic kinship matrix
`kinship.exp()`	Pedigree kinship matrix
`inbreeding.emp()`	Genomic inbreeding
`inbreeding.exp()`	Pedigree inbreeding
`get.pca()`	PCA plot
`get.admixture()`	Admixture analysis
`bv.development()`	Genetic trend plot
`analyze.bv()`	Prediction accuracy

17.4 Utility Functions

Function	Purpose
`summary()`	Population summary
`get.size()`	Number of individuals
`set.class()`	Assign class to individuals
`clean.up()`	Free memory
`new.base.generation()`	Reset generation numbering

17.5 Export Functions

Function	Purpose
`get.vcf()`	Export VCF file
`get.plink()`	Export PLINK files
`get.pedmap()`	Export ped/map files

17.6 For Full Documentation

# Function help
?creating.diploid
?breeding.diploid

# Package help
help(package = "MoBPS")

17.7 Summary

Quick reference for common MoBPS functions. See the full manual for complete parameter lists and details.

# Function Reference Quick Guide {#sec-function-reference}

## Core Functions

| Function | Purpose |
|----------|---------|
| `creating.diploid()` | Create founder population |
| `breeding.diploid()` | Simulate breeding actions |
| `creating.trait()` | Add traits to population |

## Extraction Functions (get.*)

| Function | Returns |
|----------|---------|
| `get.bv()` | True breeding values |
| `get.bve()` | Estimated breeding values |
| `get.pheno()` | Phenotypes |
| `get.geno()` | Genotypes (0/1/2 matrix) |
| `get.haplo()` | Haplotypes |
| `get.pedigree()` | Pedigree (ID, Sire, Dam) |
| `get.map()` | Genetic map |
| `get.qtl()` | QTL positions |

## Analysis Functions

| Function | Purpose |
|----------|---------|
| `kinship.emp()` | Genomic kinship matrix |
| `kinship.exp()` | Pedigree kinship matrix |
| `inbreeding.emp()` | Genomic inbreeding |
| `inbreeding.exp()` | Pedigree inbreeding |
| `get.pca()` | PCA plot |
| `get.admixture()` | Admixture analysis |
| `bv.development()` | Genetic trend plot |
| `analyze.bv()` | Prediction accuracy |

## Utility Functions

| Function | Purpose |
|----------|---------|
| `summary()` | Population summary |
| `get.size()` | Number of individuals |
| `set.class()` | Assign class to individuals |
| `clean.up()` | Free memory |
| `new.base.generation()` | Reset generation numbering |

## Export Functions

| Function | Purpose |
|----------|---------|
| `get.vcf()` | Export VCF file |
| `get.plink()` | Export PLINK files |
| `get.pedmap()` | Export ped/map files |

## For Full Documentation

```{r}
#| eval: false

# Function help
?creating.diploid
?breeding.diploid

# Package help
help(package = "MoBPS")
```

## Summary

Quick reference for common MoBPS functions. See the full manual for complete parameter lists and details.