add_pmap                Add physical map contents to tibble
boot_pvl                Perform bootstrap sampling and calculate test
                        statistic for each bootstrap sample
calc_Bhat               Calculate estimated allele effects, B matrix
calc_Sigma              Calculate the phenotypes covariance matrix
                        Sigma
calc_covs               Calculate Vg and Ve from d-variate phenotype
                        and kinship
calc_invsqrt_mat        Calculate matrix inverse square root for a
                        covariance matrix
calc_lrt_tib            Calculate a likelihood ratio test statistic
                        from the output of scan_pvl()
calc_profile_lods       Calculate profile lods for all traits
calc_sqrt_mat           Calculate matrix square root for a covariance
                        matrix
check_identical         Check whether a vector, x, has all its entries
                        equal to its first entry
check_missingness       Check for missingness in phenotypes or
                        covariates
convert_to_scan1_output
                        Convert 'scan_multi_oneqtl' output of
                        'qtl2::scan1' output
find_pleio_peak_tib     Find the marker index corresponding to the peak
                        of the pleiotropy trace in a tibble where the
                        last column contains log likelihood values and
                        the first d columns contain marker ids
fit1_pvl                Fit a model for a specified d-tuple of markers
get_effects             Extract founder allele effects at a single
                        marker from output of qtl2::scan1coef
make_id2keep            Identify shared subject ids among all inputs:
                        covariates, allele probabilities array,
                        kinship, and phenotypes
plot_pvl                Plot tidied results of a pvl scan
prep_X_list             Create a list of component X matrices for input
                        to stagger_mats, to ultimately create design
                        matrix
prep_mytab              Prepare mytab object for use within scan_pvl R
                        code
process_inputs          Process inputs to scan functions
qtl2pleio-package       qtl2pleio.
rcpp_calc_Bhat          Estimate allele effects matrix, B hat, with
                        Rcpp functions
rcpp_calc_Bhat2         Estimate allele effects matrix, B hat, with
                        Rcpp functions
rcpp_log_dmvnorm2       Calculate log likelihood for a multivariate
                        normal
scan_multi_onechr       Perform multivariate, one-QTL model fitting for
                        markers on one chromosome
scan_multi_oneqtl       Perform multivariate, one-QTL model fitting for
                        markers on all chromosomes
scan_multi_oneqtl_perm
                        Permute the phenotypes matrix and then scan the
                        genome. Record the genomewide greatest LOD
                        score for each permuted data set.
scan_pvl                Perform model fitting for all ordered pairs of
                        markers in a genomic region of interest
sim1                    Simulate a single multivariate data set
                        consisting of n subjects and d phenotypes for
                        each
subset_input            Subset an input object - allele probabilities
                        array or phenotypes matrix or covariates
                        matrix. Kinship has its own subset function
subset_kinship          Subset a kinship matrix to include only those
                        subjects present in all inputs
