bv.development {MoBPS}

Development of genetic/breeding value

Description

Function to plot genetic/breeding values for multiple generation/cohorts

Usage

bv.development(
  population,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  confidence = c(1, 2, 3),
  development = c(1, 2, 3),
  quantile = 0.95,
  bvrow = "all",
  ignore.zero = TRUE,
  json = FALSE,
  display.time.point = FALSE,
  display.creating.type = FALSE,
  display.cohort.name = FALSE,
  display.sex = FALSE,
  equal.spacing = FALSE,
  time_reorder = FALSE,
  display.line = TRUE,
  ylim = NULL,
  fix_mfrow = FALSE
)

Arguments

population

population list

database

Groups of individuals to consider for the export

gen

Quick-insert for database (vector of all generations to export)

cohorts

Quick-insert for database (vector of names of cohorts to export)

confidence

Draw confidence intervals for (1- bv, 2- bve, 3- pheno; default: c(1,2,3))

development

Include development of (1- bv, 2- bve, 3- pheno; default: c(1,2,3))

quantile

Quantile of the confidence interval to draw (default: 0.05)

bvrow

Which traits to display (for multiple traits separate plots (par(mfrow)))

ignore.zero

Cohorts with only 0 individuals are not displayed (default: TRUE)

json

If TRUE extract which cohorts to plot according to the json-file used in json.simulation

display.time.point

Set TRUE to use time point of generated to sort groups

display.creating.type

Set TRUE to show Breedingtype used in generation (web-interface)

display.cohort.name

Set TRUE to display the name of the cohort in the x-axis

display.sex

Set TRUE to display the creating.type (Shape of Points - web-based-application)

equal.spacing

Equal distance between groups (independent of time.point)

time_reorder

Set TRUE to order cohorts according to the time point of generation

display.line

Set FALSE to not display the line connecting cohorts

ylim

Set this to fix the y-axis of the plot

fix_mfrow

Set TRUE to not use mfrow - use for custom plots

Value

Genomic values of selected gen/database/cohort

Examples

data(ex_pop)
bv.development(ex_pop, gen=1:5)