SIMER | Data Simulation for Life Science and Breeding

After installed successfully, SIMER can be loaded by typing. Typing ?simer could get the details of all parameters.
After obtaining genotypic map data and genotype data, we can start our simulation. num.gen, number of generations in simulation replication, replication index of simulation verbose, whether to print detail mrk.dense, whether markers are dense, it is TRUE when sequencing data out, prefix of output file name outpath, path of output files out.format, format of output, "numeric" or "plink" seed.geno, random seed of a simulation process seed.map, random seed of map file out.geno.gen, indice of generations of output genotype out.pheno.gen, indice of generations of output phenotype rawgeno1, extrinsic genotype matrix1 rawgeno2, extrinsic genotype matrix2 rawgeno3, extrinsic genotype matrix3 rawgeno4, extrinsic genotype matrix4 num.ind, population size of base population prob, weight of "0" and "1" in genotype matrix, the sum of elements in vector equal to 1 input.map, map that should be input, the marker number should be consistent in both map file and genotype data len.block, length of every blocks range.hot, range of exchages in hot spot block range.cold, range of exchages in cold spot block rate.mut, mutation rate between 1e-8 and 1e-6 cal.model, phenotype model with "A", "AD", "ADI" FR, list of fixed effects, random effects, and their combination h2.tr1, heritability vector of a single trait, every element are corresponding to a, d, aXa, aXd, dXa, dXd respectively num.qtn.tr1, integer or integer vector, the number of QTN in a single trait sd.tr1, standard deviation of different effects, the last 5 vector elements are corresponding to d, aXa, aXd, dXa, dXd respectively and the rest elements are corresponding to a dist.qtn.tr1, distribution of QTN's effects with options: "normal", "geometry" and "gamma", vector elements are corresponding to a, d, aXa, aXd, dXa, dXd respectively eff.unit.tr1, unit effect of geometric distribution of a single trait, vector elements are corresponding to a, d, aXa, aXd, dXa, dXd respectively shape.tr1, shape of gamma distribution of a single trait, vector elements are corresponding to a, d, aXa, aXd, dXa, dXd respectively scale.tr1, scale of gamma distribution of a single trait, vector elements are corresponding to a, d, aXa, aXd, dXa, dXd respectively multrait, whether applying pair traits with overlapping, TRUE represents applying, FALSE represents not num.qtn.trn, QTN distribution matrix, diagnal elements are total QTN number of the trait, non-diagnal are QTN number of overlop qtn eff.sd, a matrix with the standard deviation of QTN effects gnt.cov, genetic covariance matrix among all traits env.cov, environment covariance matrix among all traits qtn.spot, QTN probability in every blocks maf, Minor Allele Frequency, markers selection range is from maf to 0.5 sel.crit, selection criteria with options: "TGV", "TBV", "pEBVs", "gEBVs", "ssEBVs", "pheno" sel.on, whether to add selection mtd.reprod, different reproduction methods with options: "clone", "dh", "selfpol", "singcro", "tricro", "doubcro", "backcro","randmate", "randexself" and "userped" userped, user-designed pedigree to control mating process num.prog, litter size of dams ratio, ratio of males in all individuals prog.tri, litter size of the first single cross process in trible cross process prog.doub, litter size of the first two single cross process in double cross process prog.back, a vector with litter size in every generation of back-cross ps, fraction selected in selection decr, whether to sort by decreasing sel.multi, selection method of multiple traits with options: "tdm", "indcul" and "index" index.wt, economic weights of selection index method, its length should equals to the number of traits index.tdm, index represents which trait is being selected goal.perc, percentage of goal more than mean of scores of individuals pass.perc, percentage of expected excellent individuals sel.sing, selection method of single trait with options: "ind", "fam", "infam" and "comb".