flz<-list.files(path = "~/repos/MAPpoly/man", full.names = T)
names(flz) <- list.files(path = "~/repos/MAPpoly/man/", full.names = F)
require(mappoly)
require(stringr)
#> Loading required package: stringr
sentinel0 <- yz <- NULL
for(iz in 1:length(flz)){
  tools::Rd2ex(Rd = flz[iz], out = "~/temp.R", commentDonttest = F)
  sentinel1 <- scan(file = "~/temp.R", what = "character")
  if(identical(sentinel0, sentinel1)){
    yz <- rbind(yz, data.frame(func = str_remove(string = names(flz[iz]), pattern = ".Rd"), 
                               time = 0, row.names = NULL, example = "no", donttest = NA, 
                               passed = NA))
    next()
  }
  tz <- grepl(pattern = "No test:",  paste(sentinel1, collapse = " "))
  if(grepl(pattern = "inter",  paste(sentinel1, collapse = " ")))
    system(paste("sed -i 's|inter = TRUE|inter = FALSE|g'", "~/temp.R"))
  if(grepl(pattern = "inter",  paste(sentinel1, collapse = " ")))
    system(paste("sed -i 's|inter=TRUE|inter = FALSE|g'", "~/temp.R"))
  xe <- tryCatch(xz <- system.time(source("~/temp.R")), error = function(e) e)
  if(inherits(xe, "error"))
  {
    yz <- rbind(yz, data.frame(func = str_remove(string = names(flz[iz]), pattern = ".Rd"), 
                               time = xz[3], row.names = NULL, example = "yes", donttest = tz, 
                               passed = FALSE))
  }
  yz <- rbind(yz, data.frame(func = str_remove(string = names(flz[iz]), pattern = ".Rd"), 
                             time = xz[3], row.names = NULL, example = "yes", donttest = tz,  
                             passed = TRUE))
  print(yz)
  sentinel0 <- sentinel1
}
#> 
#>     You selected: reestimate.rf = FALSE
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> 
#>     INFO:
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> 
#>     INFO:
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> `geom_smooth()` using method = 'loess' and formula 'y ~ x'
#> 
#>     You selected: reestimate.rf = FALSE
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> 
#>     INFO:
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> ════════════════════════════════════════════════════════════════════════════════════════════ Initial sequence ══
#> ══════════════════════════════════════════════════════════════════════════════════ Done with initial sequence ══
#> ══════════════════════════════════════════════════════════════════ Reestimating final recombination fractions ══
#> ════════════════════════════════════════════════════════════════════════════════════════════════════════════════
#> Loading required package: polymapR
#> ════════════════════════════════════════════════════════════════════════════════════════════ Initial sequence ══
#> ══════════════════════════════════════════════════════════════════════════════════ Done with initial sequence ══
#> ══════════════════════════════════════════════════════════════════ Reestimating final recombination fractions ══
#> ════════════════════════════════════════════════════════════════════════════════════════════════════════════════
#> 
#>     You selected: reestimate.rf = FALSE
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> Registered S3 method overwritten by 'vegan':
#>   method     from      
#>   rev.hclust dendextend
#> 
#>     You selected: reestimate.rf = FALSE
#>     -----------------------------------------
#>     The recombination fractions provided were
#>     obtained using the marker positions in the 
#>     input map; For accurate values, plese 
#>     reestimate the map using functions 'reest_rf', 
#>     'est_full_hmm_with_global_error' or 
#>     'est_full_hmm_with_prior_prob'
#> 
#> Your dataset contains removed (redundant) markers. Once finished the map, remember to add them back with the function 'update_map'.
#> 
#> Your dataset contains removed (redundant) markers. Once finished the map, remember to add them back with the function 'update_map'.
#> 
#> 
#> Your dataset contains removed (redundant) markers. Once finished the map, remember to add them back with the function 'update_map'.
yz<-yz[order(yz$time, decreasing = T), ]
colnames(yz) <- c("func","time","example","donttest","passed" )
yz <- rbind(yz, data.frame(func = "Total", time = sum(yz$time), row.names = NULL, 
                           example = "--", donttest = tz, passed = all(yz$passed, na.rm = T)))

file	context	test	user	system	real
test-2pt.R	Two point estimates	estimate two-points rf correctly	4.577	0.315	8.525
test-cahe_twopts.R	Compute genotype counts	compute genotype counts correctly	0.459	0.112	0.745
test-calc_genoprobs.R	Conditional probabilities	computes genotype probabilities correctly	1.096	0.307	1.287
test-est_hmm_map.R	Estimate HMM map	map contructed correctly	1.270	0.327	1.504
test-est_hmm_map.R	Estimate HMM map	sequential map contructed correctly	0.808	0.149	0.895
test-est_with_probs.R	Estimate map with probabilities	map estimated correctly	0.761	0.154	0.865
test-export_map_list.R	Export map list	export map list correctly	0.017	0.004	0.021
test-filters.R	Filter functions	test filter functions	0.480	0.084	0.531
test-get_submap.R	Get submap	sub-map extracted correctly	0.053	0.020	0.068
test-group.R	Groupping	assemble linkage groups correctly	0.667	0.000	0.664
test-homolog_prob.R	Homolog probability	computes homolog probabilities correctly	0.640	0.075	0.694
test-merge_maps.R	Merge maps	merging maps correctly	1.128	0.122	1.204
test-preferential_pairing.R	Preferential Pairing	computes pairing probabilities correctly	0.696	0.064	0.743
test-read_data.R	Read data	read data from VCF file correctly	0.851	0.094	1.316
test-read_data.R	Read data	read data from dosage file correctly	7.519	0.449	8.062
test-read_data.R	Read data	read data from probability file correctly	0.195	0.024	0.368
test-read_data.R	Read data	read data from CSV file correctly	7.332	0.543	8.286
test-reestmap.R	Map reestimation	reestimate genetic maps correctly correctly	0.423	0.061	0.465
test-simulation.R	Simulate datasets	simulate datasets correctly	0.308	0.060	0.353
test-split_and_rephase.R	Split and rephase	split and rephase the map correctly	0.768	0.094	0.829
test-utility_func.R	Utility functions	test several utility functions	2.257	0.333	2.473

Timing MAPpoly examples and tests

Timing examples

Timing tests

	func	time	example	donttest	passed
32	est_rf_hmm_sequential	16.542	yes	TRUE	TRUE
131	update_missing	11.865	yes	TRUE	TRUE
20	dist_prob_to_class	11.404	yes	TRUE	TRUE
8	calc_homoprob	10.693	yes	TRUE	TRUE
33	est_rf_hmm_single	9.599	yes	TRUE	TRUE
76	loglike_hmm	8.968	yes	TRUE	TRUE
35	export_data_to_polymapR	8.848	yes	TRUE	TRUE
110	read_geno	8.817	yes	TRUE	TRUE
108	read_geno_csv	8.028	yes	TRUE	TRUE
9	calc_prefpair_profiles	7.946	yes	TRUE	TRUE
1	add_marker	7.490	yes	TRUE	TRUE
5	calc_genoprob_error	5.796	yes	TRUE	TRUE
62	get_submap	5.667	yes	TRUE	TRUE
73	import_from_updog	4.997	yes	TRUE	TRUE
79	make_pairs_mappoly	2.775	yes	FALSE	TRUE
83	merge_datasets	2.726	yes	TRUE	TRUE
84	merge_maps	2.709	yes	TRUE	TRUE
34	est_rf_hmm	2.666	yes	FALSE	TRUE
4	calc_genoprob_dist	1.620	yes	FALSE	TRUE
67	hexafake.geno.dist	1.619	yes	FALSE	TRUE
27	est_full_hmm_with_global_error	1.608	yes	FALSE	TRUE
111	read_vcf	1.606	yes	TRUE	TRUE
66	group_mappoly	1.605	yes	FALSE	TRUE
74	import_phased_maplist_from_polymapR	1.449	yes	FALSE	TRUE
77	ls_linkage_phases	1.302	yes	FALSE	TRUE
3	cache_counts_twopt	1.036	yes	FALSE	TRUE
28	est_full_hmm_with_prior_prob	0.837	yes	FALSE	TRUE
109	read_geno_prob	0.682	yes	TRUE	TRUE
82	mds_mappoly	0.681	yes	FALSE	TRUE
72	import_data_from_polymapR	0.672	yes	FALSE	TRUE
31	est_pairwise_rf	0.631	yes	FALSE	TRUE
78	make_mat_mappoly	0.616	yes	FALSE	TRUE
126	split_and_rephase	0.600	yes	FALSE	TRUE
115	rf_snp_filter	0.486	yes	FALSE	TRUE
114	rf_list_to_matrix	0.468	yes	FALSE	TRUE
102	poly_cross_simulate	0.452	yes	FALSE	TRUE
97	plot_map_list	0.448	yes	FALSE	TRUE
98	plot_mrk_info	0.413	yes	FALSE	TRUE
41	filter_missing	0.291	yes	FALSE	TRUE
42	filter_non_conforming_classes	0.287	yes	FALSE	TRUE
26	elim_redundant	0.252	yes	FALSE	TRUE
7	calc_genoprob	0.242	yes	FALSE	TRUE
130	update_map	0.202	yes	FALSE	TRUE
80	make_seq_mappoly	0.102	yes	FALSE	TRUE
96	plot_genome_vs_map	0.097	yes	FALSE	TRUE
23	drop_marker	0.076	yes	FALSE	TRUE
127	summary_maps	0.042	yes	FALSE	TRUE
37	extract_map	0.029	yes	FALSE	TRUE
13	check_data_sanity	0.022	yes	FALSE	TRUE
113	rev_map	0.018	yes	FALSE	TRUE
117	segreg_poly	0.016	yes	FALSE	TRUE
36	export_map_list	0.012	yes	FALSE	TRUE
106	print_mrk	0.012	yes	FALSE	TRUE
43	filter_segregation	0.004	yes	FALSE	TRUE
121	sim_homologous	0.003	yes	FALSE	TRUE
44	format_rf	0.002	yes	FALSE	TRUE
54	get_genomic_order	0.002	yes	FALSE	TRUE
2	add_mrk_at_tail_ph_list	0.000	no	NA	NA
6	calc_genoprob_haplo	0.000	no	NA	NA
10	cat_phase	0.000	no	NA	NA
11	check_data_dist_sanity	0.000	no	NA	NA
12	check_data_dose_sanity	0.000	no	NA	NA
14	check_ls_phase	0.000	no	NA	NA
15	check_pairwise	0.000	no	NA	NA
16	compare_haplotypes	0.000	no	NA	NA
17	concatenate_new_marker	0.000	no	NA	NA
18	concatenate_ph_list	0.000	no	NA	NA
19	create_map	0.000	no	NA	NA
21	draw_cross	0.000	no	NA	NA
22	draw_phases	0.000	no	NA	NA
24	elim_conf_using_two_pts	0.000	no	NA	NA
25	elim_equiv	0.000	no	NA	NA
29	est_haplo_hmm	0.000	no	NA	NA
30	est_map_haplo_given_genoprob	0.000	no	NA	NA
38	filter_map_at_hmm_thres	0.000	no	NA	NA
39	filter_missing_ind	0.000	no	NA	NA
40	filter_missing_mrk	0.000	no	NA	NA
45	generate_all_link_phase_elim_equivalent	0.000	no	NA	NA
46	generate_all_link_phases_elim_equivalent_haplo	0.000	no	NA	NA
47	genotyping_global_error	0.000	no	NA	NA
48	get_cache_two_pts_from_web	0.000	no	NA	NA
49	get_counts_all_phases	0.000	no	NA	NA
50	get_counts_one_parent	0.000	no	NA	NA
51	get_counts_two_parents	0.000	no	NA	NA
52	get_counts	0.000	no	NA	NA
53	get_full_info_tail	0.000	no	NA	NA
55	get_ij	0.000	no	NA	NA
56	get_indices_from_selected_phases	0.000	no	NA	NA
57	get_LOD	0.000	no	NA	NA
58	get_ph_conf_ret_sh	0.000	no	NA	NA
59	get_ph_list_subset	0.000	no	NA	NA
60	get_rf_from_list	0.000	no	NA	NA
61	get_rf_from_mat	0.000	no	NA	NA
63	get_tab_mrks	0.000	no	NA	NA
64	get_w_m	0.000	no	NA	NA
65	gg_color_hue	0.000	no	NA	NA
68	hexafake	0.000	no	NA	NA
69	imf_h	0.000	no	NA	NA
70	imf_k	0.000	no	NA	NA
71	imf_m	0.000	no	NA	NA
75	is.prob.data	0.000	no	NA	NA
81	maps.hexafake	0.000	no	NA	NA
85	mf_h	0.000	no	NA	NA
86	mf_k	0.000	no	NA	NA
87	mf_m	0.000	no	NA	NA
88	mrk_chisq_test	0.000	no	NA	NA
89	msg	0.000	no	NA	NA
90	paralell_pairwise	0.000	no	NA	NA
91	perm_pars	0.000	no	NA	NA
92	perm_tot	0.000	no	NA	NA
93	ph_list_to_matrix	0.000	no	NA	NA
94	ph_matrix_to_list	0.000	no	NA	NA
95	plot_compare_haplotypes	0.000	no	NA	NA
99	plot_one_map	0.000	no	NA	NA
100	plot.mappoly.homoprob	0.000	no	NA	NA
101	plot.mappoly.prefpair.profiles	0.000	no	NA	NA
103	poly_hmm_est	0.000	no	NA	NA
104	pos_twopt_est	0.000	no	NA	NA
105	prepare_map	0.000	no	NA	NA
107	print_ph	0.000	no	NA	NA
112	reest_rf	0.000	no	NA	NA
116	sample_data	0.000	no	NA	NA
118	select_rf	0.000	no	NA	NA
119	sim_cross_one_informative_parent	0.000	no	NA	NA
120	sim_cross_two_informative_parents	0.000	no	NA	NA
122	solcap.dose.map	0.000	no	NA	NA
123	solcap.err.map	0.000	no	NA	NA
124	solcap.mds.map	0.000	no	NA	NA
125	solcap.prior.map	0.000	no	NA	NA
128	tetra.solcap.geno.dist	0.000	no	NA	NA
129	tetra.solcap	0.000	no	NA	NA
132	update_ph_list_at_hmm_thres	0.000	no	NA	NA
133	Total	158.078	–	TRUE	TRUE