revdep/checks/AquaBPsim/old/AquaBPsim.Rcheck/AquaBPsim-Ex.R
In friendly/matlib: Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics
pkgname <- "AquaBPsim"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
options(pager = "console")
library('AquaBPsim')
base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
cleanEx()
nameEx("avail_selection")
### * avail_selection
flush(stderr()); flush(stdout())
### Name: avail_selection
### Title: Available as selection candidates
### Aliases: avail_selection
### ** Examples
cleanEx()
nameEx("breeding_values")
### * breeding_values
flush(stderr()); flush(stdout())
### Name: breeding_values
### Title: Simulating estimated breeding values
### Aliases: breeding_values
### ** Examples
cleanEx()
nameEx("cor_var")
### * cor_var
flush(stderr()); flush(stdout())
### Name: cor_var
### Title: simulating correlated variable
### Aliases: cor_var
### ** Examples
cor_var(c(2,4,2,2,6,7,5,6,6,7,9,4,5), 0.5)
cleanEx()
nameEx("deltaG_F")
### * deltaG_F
flush(stderr()); flush(stdout())
### Name: deltaG_F
### Title: Calculating genetic gain and rate of inbreeding
### Aliases: deltaG_F
### ** Examples
## Not run:
##D deltaG_F()
## End(Not run)
cleanEx()
nameEx("founderpopfam")
### * founderpopfam
flush(stderr()); flush(stdout())
### Name: founderpopfam
### Title: Founder population family design
### Aliases: founderpopfam
### ** Examples
ped <- founderpopfam(Nm=60, Nm2=0,
Nf=60, Nf2=0,
batch = c(0,1,2),
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0.5,
0.5 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(150,1000),
e_var= c(250,12000))
ped <- founderpopfam(Nm=60,
Nf=60,
Nm2=120,
Nf2=120,
Nbatch = 4,
batch2 = c(-3,-2,-1,0),
Ntraits=2,
TraitsIndex = c(1,2),
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000),
est_EBV = TRUE,
EBV= c("pheno", "EBV"),
accuracy= c(NA,0.78),
indexweight= c(1,5))
cleanEx()
nameEx("founderpopgroup")
### * founderpopgroup
flush(stderr()); flush(stdout())
### Name: founderpopgroup
### Title: Founder population group mating design
### Aliases: founderpopgroup
### ** Examples
ped <- founderpopgroup(Nm=60, Nm2=0,
Nf=60, Nf2 = 0,
batch = c(0,1,2),
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000))
ped <- founderpopgroup(Nm=60,
Nf=60,
Nm2=120,
Nf2=120,
Nbatch = 4,
batch2 = c(-3,-2,-1,0),
Ntraits=2,
TraitsIndex = c(1,2),
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000),
est_EBV = TRUE,
EBV= c("pheno", "EBV"),
accuracy= c(NA,0.78),
indexweight= c(1,5))
cleanEx()
nameEx("gen_param")
### * gen_param
flush(stderr()); flush(stdout())
### Name: gen_param
### Title: Importing genetic parameters from excel file
### Aliases: gen_param
### ** Examples
## Not run:
##D BPdata <- gen_param("example.xlsx")
## End(Not run)
cleanEx()
nameEx("groupmating")
### * groupmating
flush(stderr()); flush(stdout())
### Name: groupmating
### Title: Group mating
### Aliases: groupmating
### ** Examples
{ped <- founderpopgroup(Nm=60,
Nf=60,
Nm2=120,
Nf2=120,
Nbatch = 4,
batch2 = c(-3,-2,-1,0),
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000))
Mating <- groupmating(gen = 0,
batch=-3,
No=1000,
contr_m = 0.5,
contr_f = 0.5)
}
cleanEx()
nameEx("offspringFSfam")
### * offspringFSfam
flush(stderr()); flush(stdout())
### Name: offspringFSfam
### Title: Creating offspring for family design
### Aliases: offspringFSfam
### ** Examples
cleanEx()
nameEx("offspringFSgroup")
### * offspringFSgroup
flush(stderr()); flush(stdout())
### Name: offspringFSgroup
### Title: Creating offspring for a group mating design
### Aliases: offspringFSgroup
### ** Examples
cleanEx()
nameEx("preselphen")
### * preselphen
flush(stderr()); flush(stdout())
### Name: preselphen
### Title: Preselecting offspring based on phenotype
### Aliases: preselphen
### ** Examples
cleanEx()
nameEx("preselrandom")
### * preselrandom
flush(stderr()); flush(stdout())
### Name: preselrandom
### Title: Randomly preselecting offspring
### Aliases: preselrandom
### ** Examples
cleanEx()
nameEx("preselselcand")
### * preselselcand
flush(stderr()); flush(stdout())
### Name: preselselcand
### Title: Preselection of selection candidates
### Aliases: preselselcand
### ** Examples
cleanEx()
nameEx("randommating")
### * randommating
flush(stderr()); flush(stdout())
### Name: randommating
### Title: Random mating family design
### Aliases: randommating
### ** Examples
{ ped <- founderpopfam(Nm=60,
Nf=60,
Nm2=0,
Nf2=0,
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0.5,
0.5 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(150,1000),
e_var= c(250,12000))
Mating <- randommating(gen = 0,
Nfam_FS = 120)
}
cleanEx()
nameEx("select")
### * select
flush(stderr()); flush(stdout())
### Name: select
### Title: Selection
### Aliases: select
### ** Examples
cleanEx()
nameEx("survive")
### * survive
flush(stderr()); flush(stdout())
### Name: survive
### Title: Survive
### Aliases: survive
### ** Examples
### * <FOOTER>
###
cleanEx()
options(digits = 7L)
base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')
friendly/matlib documentation built on March 3, 2024, 12:18 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
pkgname <- "AquaBPsim"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
options(pager = "console")
library('AquaBPsim')
base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
cleanEx()
nameEx("avail_selection")
### * avail_selection
flush(stderr()); flush(stdout())
### Name: avail_selection
### Title: Available as selection candidates
### Aliases: avail_selection
### ** Examples
cleanEx()
nameEx("breeding_values")
### * breeding_values
flush(stderr()); flush(stdout())
### Name: breeding_values
### Title: Simulating estimated breeding values
### Aliases: breeding_values
### ** Examples
cleanEx()
nameEx("cor_var")
### * cor_var
flush(stderr()); flush(stdout())
### Name: cor_var
### Title: simulating correlated variable
### Aliases: cor_var
### ** Examples
cor_var(c(2,4,2,2,6,7,5,6,6,7,9,4,5), 0.5)
cleanEx()
nameEx("deltaG_F")
### * deltaG_F
flush(stderr()); flush(stdout())
### Name: deltaG_F
### Title: Calculating genetic gain and rate of inbreeding
### Aliases: deltaG_F
### ** Examples
## Not run:
##D deltaG_F()
## End(Not run)
cleanEx()
nameEx("founderpopfam")
### * founderpopfam
flush(stderr()); flush(stdout())
### Name: founderpopfam
### Title: Founder population family design
### Aliases: founderpopfam
### ** Examples
ped <- founderpopfam(Nm=60, Nm2=0,
Nf=60, Nf2=0,
batch = c(0,1,2),
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0.5,
0.5 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(150,1000),
e_var= c(250,12000))
ped <- founderpopfam(Nm=60,
Nf=60,
Nm2=120,
Nf2=120,
Nbatch = 4,
batch2 = c(-3,-2,-1,0),
Ntraits=2,
TraitsIndex = c(1,2),
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000),
est_EBV = TRUE,
EBV= c("pheno", "EBV"),
accuracy= c(NA,0.78),
indexweight= c(1,5))
cleanEx()
nameEx("founderpopgroup")
### * founderpopgroup
flush(stderr()); flush(stdout())
### Name: founderpopgroup
### Title: Founder population group mating design
### Aliases: founderpopgroup
### ** Examples
ped <- founderpopgroup(Nm=60, Nm2=0,
Nf=60, Nf2 = 0,
batch = c(0,1,2),
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000))
ped <- founderpopgroup(Nm=60,
Nf=60,
Nm2=120,
Nf2=120,
Nbatch = 4,
batch2 = c(-3,-2,-1,0),
Ntraits=2,
TraitsIndex = c(1,2),
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000),
est_EBV = TRUE,
EBV= c("pheno", "EBV"),
accuracy= c(NA,0.78),
indexweight= c(1,5))
cleanEx()
nameEx("gen_param")
### * gen_param
flush(stderr()); flush(stdout())
### Name: gen_param
### Title: Importing genetic parameters from excel file
### Aliases: gen_param
### ** Examples
## Not run:
##D BPdata <- gen_param("example.xlsx")
## End(Not run)
cleanEx()
nameEx("groupmating")
### * groupmating
flush(stderr()); flush(stdout())
### Name: groupmating
### Title: Group mating
### Aliases: groupmating
### ** Examples
{ped <- founderpopgroup(Nm=60,
Nf=60,
Nm2=120,
Nf2=120,
Nbatch = 4,
batch2 = c(-3,-2,-1,0),
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0,
0 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(0,0),
e_var= c(250,12000))
Mating <- groupmating(gen = 0,
batch=-3,
No=1000,
contr_m = 0.5,
contr_f = 0.5)
}
cleanEx()
nameEx("offspringFSfam")
### * offspringFSfam
flush(stderr()); flush(stdout())
### Name: offspringFSfam
### Title: Creating offspring for family design
### Aliases: offspringFSfam
### ** Examples
cleanEx()
nameEx("offspringFSgroup")
### * offspringFSgroup
flush(stderr()); flush(stdout())
### Name: offspringFSgroup
### Title: Creating offspring for a group mating design
### Aliases: offspringFSgroup
### ** Examples
cleanEx()
nameEx("preselphen")
### * preselphen
flush(stderr()); flush(stdout())
### Name: preselphen
### Title: Preselecting offspring based on phenotype
### Aliases: preselphen
### ** Examples
cleanEx()
nameEx("preselrandom")
### * preselrandom
flush(stderr()); flush(stdout())
### Name: preselrandom
### Title: Randomly preselecting offspring
### Aliases: preselrandom
### ** Examples
cleanEx()
nameEx("preselselcand")
### * preselselcand
flush(stderr()); flush(stdout())
### Name: preselselcand
### Title: Preselection of selection candidates
### Aliases: preselselcand
### ** Examples
cleanEx()
nameEx("randommating")
### * randommating
flush(stderr()); flush(stdout())
### Name: randommating
### Title: Random mating family design
### Aliases: randommating
### ** Examples
{ ped <- founderpopfam(Nm=60,
Nf=60,
Nm2=0,
Nf2=0,
Ntraits=2,
TraitsIndex = 2,
Rgen= matrix(c(1.00 , 0.48,
0.48 , 1.00),
nrow = 2),
Rcom= matrix(c(1.00 , 0.5,
0.5 , 1.00),
nrow = 2),
Rres= matrix(c(1.00 , 0.32,
0.32 , 1.00),
nrow = 2),
mean=c(50,500),
a_var=c(200,8000),
c_var=c(150,1000),
e_var= c(250,12000))
Mating <- randommating(gen = 0,
Nfam_FS = 120)
}
cleanEx()
nameEx("select")
### * select
flush(stderr()); flush(stdout())
### Name: select
### Title: Selection
### Aliases: select
### ** Examples
cleanEx()
nameEx("survive")
### * survive
flush(stderr()); flush(stdout())
### Name: survive
### Title: Survive
### Aliases: survive
### ** Examples
### * <FOOTER>
###
cleanEx()
options(digits = 7L)
base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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