Function reference • CKMRsim

All functions
`CKMRsim`	My package documentation
`Qij_class()`	Constructor function for the class Qij
`brook_trout_genos`	Microsatellite data from brook trout
`ckmr2colony()`	make a rudimentary colony input file
`ckmr_class()`	constructor function for the ckmr class
`ckmr_relats()`	return a vector of the relationships in a ckmr_class object
`combine_miscalls_and_dropouts()`	implements the generalized miscall + dropout model
`comp_ind_pairwise()`	Compute pairwise relationship measures between all individuals in source and one individual in target
`create_ckmr()`	prepare to simulate pairwise relationships from locus data
`create_integer_genotype_matrix()`	turns long format genotypes into a matrix of integer-code genotypes
`example_L_biallelic`	An example biallelic locus
`example_L_microhap`	An example microhaplotype locus
`example_L_microsat`	An example microsatellite locus
`extract_logls()`	Extract log-likelihood ratios and associated values from a Qij object
`find_close_matching_genotypes()`	Return every pair of individuals that mismatch at no more than max_miss loci
`flatten_ckmr()`	flatten a from/to pair from a ckmr object (see `ckmr_class`into a long vector of probabilities
`format(<Qij>)`	format method for Qij class (to print)
`format(<ckmr>)`	format method for ckmr class (to print)
`ge_model_TGIE()`	implements a simple true-genotype-independent genotyping error model
`ge_model_microhap1()`	create matrix C for probability of observed genotypes from microhaplotype data
`ge_model_microsat1()`	a simple "length-aware" genotyping error model for microsatellites
`general_allele_based_geno_err_model()`	implements the generalized Allele-Based genotyping error model
`geometric_chromo_lengths()`	simulate a distribution of fake chromosome lengths
`hap_obs_prob()`	a simple helper function
`id_prepend()`	prepend an ID to a mendel input or output file
`index_ab()`	a function to compute the genotype index from alleles a and b
`insert_C_l_matrices()`	insert the matrix C_l into each element of the list of X_l matrices
`insert_Y_l_matrices()`	compute the Y_l matrices for each locus in a list
`install_mendel()`	Download the mendel binary and install it where CKMRpop expects it
`kappas`	A matrix of Cotterman coefficients for a variety of pairwise relationships
`labrador_salar_ngs_msats`	Next-generation-sequencing-genotyped microsatellites from Labrador Atlantic salmon
`linked_mhaps`	Microhaplotype data from kelp rockfish Sebastes atrovirens with pretend linkage positions
`locus_specific_pairwise()`	Return locus-specific pairwise relationship measures between desired pairs of individuals
`loggy_reweight()`	reweight logs without underflow
`long_markers`	A long format way of specifying markers.
`long_markers_to_X_l_list()`	convert a long data frame of marker allele frequencies to a list of X_l matrices
`make_matrix_X_l()`	compute the matrix X_l given allele frequencies and kappa
`markers40`	40 dinucleotide markers for a quick test data set
`markers_on_map`	An example of how to specify markers mapped onto chromosomes
`mc_sample_simple()`	sample Q values to get and analyze a sample of Lambdas with simple (non-mixture) hypotheses
`mendelBin()`	Given the operating system, check for mendel program in the typical location
`mendel_control_list()`	return a list of values for a Mendel definitions file for gene dropping
`microhaps`	100 microhaplotype markers for a quick test data set
`pairwise_geno_id()`	Return every pair of individuals that mismatch at no more than max_miss loci
`pairwise_kin_logl_ratios()`	compute pairwise log likelihood ratios between two sets of individuals
`pedigrees`	A list of pedigrees specifying different pairwise relationships for MORGAN's genedrop program.
`print(<Qij>)`	print a Qij object nicely
`print(<ckmr>)`	print method for ckmr class
`read_mendel_outped()`	pick the genotypes out of the Mendel output pedigree file to use to compute Q
`reindex_markers()`	re-index loci and or alleles given a data frame of markers
`run_mendel()`	Run the mendel binary in directory Dir using control file Control
`samp_from_mat()`	Sample 1 observation from cell probabilities that are columns of a matrix
`sample_linked_genotype_pairs()`	simulate genotype-pairs from linked markers using Mendel
`sebastes`	Microhaplotype data from kelp rockfish Sebastes atrovirens
`simulate_Qij()`	compute the all-locus genotype pair probs for pairs simulated given specified relationships
`simulate_and_calc_Q()`	compute all-locus genotype pair probs for pairs simulated given specified relationships
`sprinkle_markers_into_genome()`	Randomly distribute markers along the chromosomes of a genome
`tag_mendelian_incompatibilities()`	Identify loci in PO pairs that are Mendelian incompatible

Reference

All functions