Allows other functions in the package to call the c++ function passing arguments more succinctly and by name.
call_cpp(
samples_per_chain,
y,
block_starts,
block_ends,
cases,
counts,
min_ac,
tau_shape,
pi_shape,
omega_shape,
temperatures,
z0_matrix,
estimate_omega,
logit_omegas,
logit_omega_proposal_sds,
variant_weights,
estimate_phi,
log_phis,
log_phi_mean,
log_phi_sd,
log_phi_proposal_sds,
chain_swaps_per_cycle,
annealing,
tandem_variant_updates,
comphet_variant_block_starts,
comphet_variant_block_ends,
comphet_variants,
return_z_trace,
return_x_trace,
vec_sums = FALSE,
burn = 0,
check = TRUE
)Object of class BeviMed_raw, containing the output of the MCMC sampling.
Number of samples to draw from each chain.
Logical vector of subject affectedness status.
Integer vector of k 0-indexed start positions (with respect to cases and counts) for contiguous blocks relating to the k variants.
Integer vector of (exclusive) k 0-indexed end positions.
0 based vector of case indices with respect to y.
Vector of variant counts.
Integer vector with a length equalling the number of individuals or length 1 (in which case the given value is used for all individuals) giving the minimum number of alleles at pathogenic variant sites each individual requires in order to classify as having a `pathogenic allele configuration'. Thus, this parameter encodes the mode of inheritance. For instance, setting this parameter to 1 corresponds to dominant inheritance. If there are differences in ploidy between individuals in the locus, it is necessary to set it on an sample level basis - e.g. to ensure sex is accounted for if the locus lies on the X chromosome.
Beta distribution parameterisation of benign variant configuration rate of affection, q.
Beta distribution parameterisation of pathogenic variant configuration rate of affection, p.
Beta distribution of global rate of pathogenicty of variants in gene given pathogenicity of gene, omega.
Numeric vector of temperatures of power posteriors. One chain will be created for each element of the vector at the corresponding temperature.
Matrix of logicals, where the rows are used as an initial zs for the chains.
Logical value determining whether to estimate the parameter omega.
Numeric vector of logit omega values, one value per chain.
Numeric vector of proposal standard deviations for Metropolis-Hastings sampling of logit omega parameter, one value per chain.
Vector of log-odds off-sets for rates of pathogenicity of individual variants relative to the global rate, omega.
Logical value determining whether to estimate a scaling factor of variant_weights.
Numeric vector of log phi values, one value per chain.
Mean for normal prior on scaling factor phi.
SD for normal prior on scaling factor phi.
Numeric vector of proposal standard deviations for Metropolis-Hastings sampling of log phi parameter, one value per chain.
Number of chain swaps to propose per update cycle.
Logical value determining whether to anneal the chains, e.g. for optimisation.
Number of tandem variant updates to make per update cycle.
0-indexed start positions for contiguous blocks of variants in comphet_variants.
As comphet_variant_block_starts for (exclusive) stop positions.
Integer vector giving variant numbers (0-based, i.e. between 0 and k-1). Used to pick pairs of variants for tandem updates from.
Logical value determining whether to store the z-vectors for each chain, which uses alot of memory, particularly if samples_per_chain, k and length(temperatures) are large.
Logical value determining whether to store the x variable determined by success samples of z. Potentially uses alot of memory, particularly if samples_per_chain, k and length(temperatures) are large.
Logical value determining whether to calculate vector summary statistics.
Number of samples to drop from the start of the chain.
Logical value indicating whether to perform validation on the arguments before calling the c++ function.