Man pages for eriqande/CKMRsim
Inference of Pairwise Relationships Using Likelihood Ratios
| afreq_str | prints out the integer allele names and their freqs into... |
| 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 |
| CKMRsim | My package documentation |
| combine_miscalls_and_dropouts | implements the generalized miscall + dropout model |
| comp_ind_pairwise | Compute pairwise relationship measures between all... |
| create_ckmr | prepare to simulate pairwise relationships from locus data |
| create_integer_genotype_matrix | turns long format genotypes into a matrix of integer-code... |
| 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... |
| find_close_matching_genotypes | Return every pair of individuals that mismatch at no more... |
| flatten_ckmr | flatten a from/to pair from a ckmr object (see... |
| format.ckmr | format method for ckmr class (to print) |
| format.Qij | format method for Qij class (to print) |
| ge_model_microhap1 | create matrix C for probability of observed genotypes from... |
| ge_model_microsat1 | a simple "length-aware" genotyping error model for... |
| ge_model_TGIE | implements a simple true-genotype-independent genotyping... |
| general_allele_based_geno_err_model | implements the generalized Allele-Based genotyping error... |
| 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... |
| 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... |
| kappas | A matrix of Cotterman coefficients for a variety of pairwise... |
| labrador_salar_ngs_msats | Next-generation-sequencing-genotyped microsatellites from... |
| linked_mhaps | Microhaplotype data from kelp rockfish _Sebastes atrovirens_... |
| locus_specific_pairwise | Return locus-specific pairwise relationship measures between... |
| 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... |
| make_matrix_X_l | compute the matrix X_l given allele frequencies and kappa |
| markers2mendel_def_lines | convert a long-format data frame of loci into a vector of... |
| markers2mendel_map_lines | create a vector of Mendel formatted map file strings |
| 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... |
| mendelBin | Given the operating system, check for mendel program in the... |
| mendel_control_list | return a list of values for a Mendel definitions file for... |
| microhaplotype_geno_err_matrix | create matrix C for probability of observed genotypes from... |
| microhaps | 100 microhaplotype markers for a quick test data set |
| pairwise_geno_id | Return every pair of individuals that mismatch at no more... |
| pairwise_kin_logl_ratios | compute pairwise log likelihood ratios between two sets of... |
| pedigree2mendel_ped_file | for making a pedigree file with no observed genotypes on it |
| pedigrees | A list of pedigrees specifying different pairwise... |
| pipe | Pipe operator |
| print.ckmr | print method for ckmr class |
| print.Qij | print a Qij object nicely |
| Qij_class | Constructor function for the class Qij |
| read_mendel_outped | pick the genotypes out of the Mendel output pedigree file to... |
| 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... |
| samp_from_mat | Sample 1 observation from cell probabilities that are columns... |
| sample_linked_genotype_pairs | simulate genotype-pairs from linked markers using Mendel |
| sebastes | Microhaplotype data from kelp rockfish _Sebastes atrovirens_ |
| simulate_and_calc_Q | compute all-locus genotype pair probs for pairs simulated... |
| simulate_Qij | compute the all-locus genotype pair probs for pairs simulated... |
| 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 |
| top_index | return indices of the top n elements of a large vector |
| write_all_mendel_files | Write all necessary files for Mendel to do a gene-dropping... |
