# Generated by roxygen2: do not edit by hand

S3method(plot,mappoly.data)
S3method(plot,mappoly.geno.ord)
S3method(plot,mappoly.group)
S3method(plot,mappoly.homoprob)
S3method(plot,mappoly.map)
S3method(plot,mappoly.pcmap)
S3method(plot,mappoly.pcmap3d)
S3method(plot,mappoly.prefpair.profiles)
S3method(plot,mappoly.rf.matrix)
S3method(plot,mappoly.sequence)
S3method(plot,mappoly.twopt)
S3method(plot,mappoly.unique.seq)
S3method(plot,two.pts.linkage.phases)
S3method(print,cache.info)
S3method(print,mappoly.data)
S3method(print,mappoly.geno.ord)
S3method(print,mappoly.genoprob)
S3method(print,mappoly.group)
S3method(print,mappoly.homoprob)
S3method(print,mappoly.map)
S3method(print,mappoly.pcmap)
S3method(print,mappoly.pcmap3d)
S3method(print,mappoly.prefpair.profiles)
S3method(print,mappoly.rf.matrix)
S3method(print,mappoly.sequence)
S3method(print,mappoly.twopt)
S3method(print,mappoly.unique.seq)
S3method(print,two.pts.linkage.phases)
export(add_marker)
export(cache_counts_twopt)
export(calc_genoprob)
export(calc_genoprob_dist)
export(calc_genoprob_error)
export(calc_genoprob_single_parent)
export(calc_homologprob)
export(calc_prefpair_profiles)
export(check_data_sanity)
export(compare_haplotypes)
export(compare_maps)
export(cross_simulate)
export(detect_info_par)
export(dist_prob_to_class)
export(drop_marker)
export(edit_order)
export(elim_redundant)
export(est_full_hmm_with_global_error)
export(est_full_hmm_with_prior_prob)
export(est_pairwise_rf)
export(est_pairwise_rf2)
export(est_rf_hmm)
export(est_rf_hmm_sequential)
export(export_data_to_polymapR)
export(export_map_list)
export(export_qtlpoly)
export(extract_map)
export(filter_aneuploid)
export(filter_individuals)
export(filter_map_at_hmm_thres)
export(filter_missing)
export(filter_segregation)
export(find_blocks)
export(framework_map)
export(generate_all_link_phases_elim_equivalent_haplo)
export(get_LOD)
export(get_dosage_type)
export(get_genomic_order)
export(get_submap)
export(group_mappoly)
export(import_data_from_polymapR)
export(import_from_updog)
export(import_phased_maplist_from_polymapR)
export(is.prob.data)
export(loglike_hmm)
export(ls_linkage_phases)
export(make_mat_mappoly)
export(make_pairs_mappoly)
export(make_seq_mappoly)
export(mds_mappoly)
export(merge_datasets)
export(merge_maps)
export(mf_k)
export(mp_pallet1)
export(mp_pallet2)
export(mp_pallet3)
export(paralell_pairwise_discrete)
export(paralell_pairwise_probability)
export(parallel_block)
export(ph_list_to_matrix)
export(ph_matrix_to_list)
export(plot_GIC)
export(plot_compare_haplotypes)
export(plot_genome_vs_map)
export(plot_map_list)
export(plot_mappoly.map2)
export(plot_mrk_info)
export(plot_progeny_dosage_change)
export(print_mrk)
export(read_fitpoly)
export(read_geno)
export(read_geno_csv)
export(read_geno_prob)
export(read_vcf)
export(reest_rf)
export(rev_map)
export(rf_list_to_matrix)
export(rf_snp_filter)
export(sample_data)
export(segreg_poly)
export(sim_homologous)
export(split_and_rephase)
export(summary_maps)
export(update_framework_map)
export(update_map)
import(RCurl)
import(Rcpp)
import(fields)
import(ggplot2)
import(parallel)
import(reshape2)
importFrom(Rcpp,sourceCpp)
importFrom(RcppParallel,RcppParallelLibs)
importFrom(cli,rule)
importFrom(crayon,black)
importFrom(crayon,white)
importFrom(dendextend,color_branches)
importFrom(dplyr,`%>%`)
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_discrete)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,vars)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggpubr,font)
importFrom(ggpubr,ggarrange)
importFrom(ggsci,pal_d3)
importFrom(ggsci,scale_color_d3)
importFrom(grDevices,blues9)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,hsv)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(grDevices,rgb2hsv)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,pie)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(magrittr,"%>%")
importFrom(parallel,clusterEvalQ)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(plot3D,scatter3D)
importFrom(plotly,ggplotly)
importFrom(princurve,principal.curve)
importFrom(reshape2,acast)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rstudioapi,getThemeInfo)
importFrom(rstudioapi,hasFun)
importFrom(rstudioapi,isAvailable)
importFrom(smacof,smacofSym)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,chisq.test)
importFrom(stats,cutree)
importFrom(stats,dhyper)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,rect.hclust)
importFrom(stats,runif)
importFrom(utils,capture.output)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(zoo,na.approx)
useDynLib(mappoly)
