after selects(SP) ,how to simer(SP)

[quanhw]

hello,when i finsh my simulation and selections, how can i simer(SP)

library(simer)

Generate genotype simulation parameters

SP <- param.annot(pop.marker = 1e4,species='pig', qtn.num = list(tr1 = 10, tr2 = 10))

Generate annotation simulation parameters

SP <- param.geno(SP = SP, pop.ind = 1e2)

Generate phenotype simulation parameters

SP <- param.pheno(
SP = SP,

phe.var = list(tr1 = 100, tr2 = 100),

phe.model = list(
tr1 = "T1 = A + E",
tr2 = "T2 = A + E"
)
)

Generate selection parameters

！！！！！********** SP <- param.sel(SP = SP, sel.multi = "indcul") ***********！！！！！

index.wt=c(0.6,0.4),sel.multi = "index"

sel.multi = "indcul"

sel.multi = "tdm"

Run annotation simulation

SP <- annotation(SP)

Run genotype simulation

SP <- genotype(SP)

Run phenotype simulation

SP <- phenotype(SP)

Run selection

SP <- selects(SP)

I want to simulate the effect of comparing different sel.multi，but different sel.multi have same mean(SP[["pheno"]][["pop"]][["gen1"]][["T2"]])
what can i do about this

and the error is

SP <- simer(SP)
错误于if (verbose) {: 参数长度为零

[Foredawnbio]

Thank you for using SIMER, you can use following code to compare different selection methods.

# If you want to test three different multiple trait selection methods, 
# you should first use the same random number seeds to generate the same base population, 
# and then use different multiple trait selection methods for selection.
# Three selection methods need to be simulated respectively.

# Tandem selection
# Set the same random number seed to generate the same phenotype
set.seed(1)
SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10))
SP <- param.geno(SP = SP, pop.ind = 1e2)
SP <- param.pheno(
  SP = SP, 
  phe.var = list(tr1 = 100, tr2 = 100),
  phe.model = list(
    tr1 = "T1 = A + E",
    tr2 = "T2 = A + E"
  )
)
SP <- param.sel(SP = SP, sel.multi = "tdm")
# When pop.gen >= 2, simer starts running selection
SP$global$pop.gen = 2

SP <- annotation(SP)
SP <- genotype(SP)
SP <- phenotype(SP)
SP <- selects(SP)

# They are selected sires and dams
str(SP$sel$pop.sel$gen1)

# Independent culling selection
# Set the same random number seed to generate the same phenotype
set.seed(1)
SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10))
SP <- param.geno(SP = SP, pop.ind = 1e2)
SP <- param.pheno(
  SP = SP, 
  phe.var = list(tr1 = 100, tr2 = 100),
  phe.model = list(
    tr1 = "T1 = A + E",
    tr2 = "T2 = A + E"
  )
)
SP <- param.sel(SP = SP, sel.multi = "indcul")
# When pop.gen >= 2, simer starts running selection
SP$global$pop.gen = 2

SP <- annotation(SP)
SP <- genotype(SP)
SP <- phenotype(SP)
SP <- selects(SP)

# They are selected sires and dams
str(SP$sel$pop.sel$gen1)

# Index selection
# Set the same random number seed to generate the same phenotype
set.seed(1)
SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10))
SP <- param.geno(SP = SP, pop.ind = 1e2)
SP <- param.pheno(
  SP = SP, 
  phe.var = list(tr1 = 100, tr2 = 100),
  phe.model = list(
    tr1 = "T1 = A + E",
    tr2 = "T2 = A + E"
  )
)
SP <- param.sel(SP = SP, sel.multi = "index", index.wt = c(0.6, 0.4))
# When pop.gen >= 2, simer starts running selection
SP$global$pop.gen = 2

SP <- annotation(SP)
SP <- genotype(SP)
SP <- phenotype(SP)
SP <- selects(SP)

# They are selected sires and dams
str(SP$sel$pop.sel$gen1)

[quanhw]

Thank you very much for your reply, it was very helpful, thanks, I hope we can talk more in the future, thanks again! 。 ***@***.*** &nbsp;

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "xiaolei-lab/SIMER" ***@***.***&gt;; 发送时间:&nbsp;2025年3月11日(星期二) 上午10:27 ***@***.***&gt;; ***@***.******@***.***&gt;; 主题:&nbsp;Re: [xiaolei-lab/SIMER] after selects(SP) ,how to simer(SP) (Issue #7) Thank you for using SIMER, you can use following code to compare different selection methods. # If you want to test three different multiple trait selection methods, # you should first use the same random number seeds to generate the same base population, # and then use different multiple trait selection methods for selection. # Three selection methods need to be simulated respectively. # Tandem selection # Set the same random number seed to generate the same phenotype set.seed(1) SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10)) SP <- param.geno(SP = SP, pop.ind = 1e2) SP <- param.pheno( SP = SP, phe.var = list(tr1 = 100, tr2 = 100), phe.model = list( tr1 = "T1 = A + E", tr2 = "T2 = A + E" ) ) SP <- param.sel(SP = SP, sel.multi = "tdm") # When pop.gen &gt;= 2, simer starts running selection SP$global$pop.gen = 2 SP <- annotation(SP) SP <- genotype(SP) SP <- phenotype(SP) SP <- selects(SP) # They are selected sires and dams str(SP$sel$pop.sel$gen1) # Independent culling selection # Set the same random number seed to generate the same phenotype set.seed(1) SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10)) SP <- param.geno(SP = SP, pop.ind = 1e2) SP <- param.pheno( SP = SP, phe.var = list(tr1 = 100, tr2 = 100), phe.model = list( tr1 = "T1 = A + E", tr2 = "T2 = A + E" ) ) SP <- param.sel(SP = SP, sel.multi = "indcul") # When pop.gen &gt;= 2, simer starts running selection SP$global$pop.gen = 2 SP <- annotation(SP) SP <- genotype(SP) SP <- phenotype(SP) SP <- selects(SP) # They are selected sires and dams str(SP$sel$pop.sel$gen1) # Index selection # Set the same random number seed to generate the same phenotype set.seed(1) SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10)) SP <- param.geno(SP = SP, pop.ind = 1e2) SP <- param.pheno( SP = SP, phe.var = list(tr1 = 100, tr2 = 100), phe.model = list( tr1 = "T1 = A + E", tr2 = "T2 = A + E" ) ) SP <- param.sel(SP = SP, sel.multi = "index", index.wt = c(0.6, 0.4)) # When pop.gen &gt;= 2, simer starts running selection SP$global$pop.gen = 2 SP <- annotation(SP) SP <- genotype(SP) SP <- phenotype(SP) SP <- selects(SP) # They are selected sires and dams str(SP$sel$pop.sel$gen1) — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt; Foredawnbio left a comment (xiaolei-lab/SIMER#7) Thank you for using SIMER, you can use following code to compare different selection methods. # If you want to test three different multiple trait selection methods, # you should first use the same random number seeds to generate the same base population, # and then use different multiple trait selection methods for selection. # Three selection methods need to be simulated respectively. # Tandem selection # Set the same random number seed to generate the same phenotype set.seed(1) SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10)) SP <- param.geno(SP = SP, pop.ind = 1e2) SP <- param.pheno( SP = SP, phe.var = list(tr1 = 100, tr2 = 100), phe.model = list( tr1 = "T1 = A + E", tr2 = "T2 = A + E" ) ) SP <- param.sel(SP = SP, sel.multi = "tdm") # When pop.gen &gt;= 2, simer starts running selection SP$global$pop.gen = 2 SP <- annotation(SP) SP <- genotype(SP) SP <- phenotype(SP) SP <- selects(SP) # They are selected sires and dams str(SP$sel$pop.sel$gen1) # Independent culling selection # Set the same random number seed to generate the same phenotype set.seed(1) SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10)) SP <- param.geno(SP = SP, pop.ind = 1e2) SP <- param.pheno( SP = SP, phe.var = list(tr1 = 100, tr2 = 100), phe.model = list( tr1 = "T1 = A + E", tr2 = "T2 = A + E" ) ) SP <- param.sel(SP = SP, sel.multi = "indcul") # When pop.gen &gt;= 2, simer starts running selection SP$global$pop.gen = 2 SP <- annotation(SP) SP <- genotype(SP) SP <- phenotype(SP) SP <- selects(SP) # They are selected sires and dams str(SP$sel$pop.sel$gen1) # Index selection # Set the same random number seed to generate the same phenotype set.seed(1) SP <- param.annot(pop.marker = 1e4, qtn.num = list(tr1 = 10, tr2 = 10)) SP <- param.geno(SP = SP, pop.ind = 1e2) SP <- param.pheno( SP = SP, phe.var = list(tr1 = 100, tr2 = 100), phe.model = list( tr1 = "T1 = A + E", tr2 = "T2 = A + E" ) ) SP <- param.sel(SP = SP, sel.multi = "index", index.wt = c(0.6, 0.4)) # When pop.gen &gt;= 2, simer starts running selection SP$global$pop.gen = 2 SP <- annotation(SP) SP <- genotype(SP) SP <- phenotype(SP) SP <- selects(SP) # They are selected sires and dams str(SP$sel$pop.sel$gen1) — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;

[Foredawnbio]

I hope SIMER can help you, and I also hope we can communicate more in the future！