strainspy-package	strainspy-package
abundanceFit	abundanceFit
ani_distance	ani_distance
auto_coerce_metadata_types	auto_coerce_metadata_types
caseControlFit	caseControlFit
compute_eb_priors	compute_eb_priors
comp_ani_diff_and_posthoc_test	comp_ani_diff_and_posthoc_test
define_priors	define_priors
estimate_beta_diversity	estimate_beta_diversity
estimate_sample_richness	estimate_sample_richness
extract_fixef_priors	extract_fixef_priors
extract_fixef_priors,strainspy_priors-method	extract_fixef_priors
extract_strainspy	extract_strainspy
filter_by_presence	filter_by_presence
getCoefficients	strainspy_fit-accessors
getCoefficients,strainspy_fit-method	strainspy_fit-accessors
getContigNames	getContigNames
getContigNames,strainspy_fit-method	getContigNames
getConvergence	strainspy_fit-accessors
getConvergence,strainspy_fit-method	strainspy_fit-accessors
getDesign	strainspy_fit-accessors
getDesign,strainspy_fit-method	strainspy_fit-accessors
getFamily	strainspy_fit-accessors
getFamily,strainspy_fit-method	strainspy_fit-accessors
getFitCall	strainspy_fit-accessors
getFitCall,strainspy_fit-method	strainspy_fit-accessors
getGenomes	getGenomes
getGenomes,strainspy_fit-method	getGenomes
getPriorsDf	getPriorsDf
getPriorsDf,strainspy_priors-method	getPriorsDf
getPValues	strainspy_fit-accessors
getPValues,strainspy_fit-method	strainspy_fit-accessors
getResiduals	getResiduals
getResiduals,strainspy_fit-method	getResiduals
getRowData	strainspy_fit-accessors
getRowData,strainspy_fit-method	strainspy_fit-accessors
getSamples	getSamples
getSamples,strainspy_fit-method	getSamples
getStdErrors	strainspy_fit-accessors
getStdErrors,strainspy_fit-method	strainspy_fit-accessors
getVcov	strainspy_fit-accessors
getVcov,strainspy_fit-method	strainspy_fit-accessors
getZICoefficients	getZICoefficients
getZICoefficients,strainspy_fit-method	getZICoefficients
getZIPValues	strainspy_fit-accessors
getZIPValues,strainspy_fit-method	strainspy_fit-accessors
getZIStdErrors	strainspy_fit-accessors
getZIStdErrors,strainspy_fit-method	strainspy_fit-accessors
getZIVcov	strainspy_fit-accessors
getZIVcov,strainspy_fit-method	strainspy_fit-accessors
glmObFit	glmObFit
glmQBFit	glmQBFit
glmZiBFit	glmZiBFit
hadjust	hadjust
isScaleContinuous	strainspy_fit-accessors
isScaleContinuous,strainspy_fit-method	strainspy_fit-accessors
merge_metaphlan_files	merge_metaphlan_files
merge_sourmash_files	merge_sourmash_files
merge_sylph_files	merge_sylph_files
modify_metadata	modify_metadata
plot_ani_dist	plot_ani_dist
plot_histogram	plot_histogram
plot_manhattan	plot_manhattan
plot_mds	plot_mds
plot_pca_biplot	plot_pca_biplot
plot_prior_bootstrap	plot_prior_bootstrap
plot_prior_bootstrap,strainspy_priors-method	plot_prior_bootstrap
plot_volcano	plot_volcano
prep_for_prediction	prep_for_prediction
read_metaphlan	read_metaphlan
read_sourmash	read_sourmash
read_sylph	read_sylph
read_taxonomy	read_taxonomy
show,strainspy_fit-method	show-strainspy_fit-method
show,strainspy_priors-method	show-strainspy_priors-method
strainspy	strainspy
strainspy_fit-accessors	strainspy_fit-accessors
strainspy_fit-class	strainspy_fit-class
strainspy_priors-class	strainspy_priors-class
summary,strainspy_fit-method	summary-strainspy_fit-method
top_hits	top_hits
