miga-base 1.2.15.2 → 1.2.15.3

data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec

@@ -1,233 +0,0 @@
-8528	8627	97.03	169	2
-4500	4599	94.00	152	3
-554	653	96.00	161	6
-5564	5663	93.07	147	9
-1542	1641	95.00	158	12
-4743	4842	94.00	152	14
-2565	2664	94.12	154	17
-7723	7822	96.00	161	18
-2461	2560	94.12	154	19
-7817	7913	96.94	163	23
-8553	8649	96.91	163	25
-214	310	96.91	163	28
-2602	2701	94.12	154	33
-2086	2185	97.00	169	34
-3397	3496	94.00	150	35
-1333	1430	93.94	148	40
-6501	6600	97.03	169	44
-673	772	96.00	163	46
-6090	6189	95.05	158	47
-316	415	96.00	163	48
-4830	4929	97.00	169	49
-3925	4024	95.00	156	50
-6472	6571	95.05	158	51
-5396	5495	95.00	158	52
-958	1057	96.00	163	55
-6744	6841	93.94	148	56
-5974	6073	96.04	163	58
-5867	5966	94.06	152	60
-5438	5536	96.97	167	63
-7137	7236	97.03	169	65
-5002	5101	96.04	163	66
-8509	8606	94.90	154	68
-7966	8064	97.98	171	70
-1900	1999	93.14	148	71
-7554	7653	93.07	147	72
-7408	7507	94.06	152	73
-9071	9170	96.00	163	75
-2	85	95.24	134	75
-3295	3394	96.00	161	76
-68	167	94.12	152	79
-2903	3002	94.00	150	81
-7980	8079	94.00	150	85
-3125	3222	96.00	161	86
-8312	8411	94.06	152	87
-3810	3905	97.92	167	91
-8816	8915	95.00	156	97
-3465	3564	95.00	158	100
-6573	6672	96.04	163	109
-7433	7533	93.20	148	110
-8530	8629	95.00	156	112
-1002	1097	94.85	150	113
-109	208	95.00	156	114
-4311	4409	95.96	161	116
-2592	2688	96.91	161	117
-4431	4530	94.06	152	122
-6772	6868	96.91	163	123
-869	968	94.00	150	125
-8525	8624	98.00	174	126
-4762	4859	93.88	148	127
-3092	3191	97.00	169	128
-2768	2865	97.96	171	132
-3781	3880	94.00	150	138
-390	486	95.88	158	143
-7602	7699	94.90	154	147
-4126	4225	93.00	145	148
-6974	7073	97.00	169	151
-872	968	97.94	169	152
-6321	6420	95.00	158	153
-7890	7989	96.00	163	157
-7250	7348	97.98	172	159
-6863	6962	93.14	148	164
-4252	4351	96.00	161	165
-5421	5520	94.00	152	166
-1997	2096	94.00	150	167
-6221	6320	95.00	156	168
-4212	4311	99.00	178	169
-161	259	95.05	158	170
-1836	1935	96.00	161	172
-4646	4745	93.00	147	173
-2246	2345	95.00	156	175
-4141	4240	92.08	141	177
-7714	7813	94.12	152	181
-2761	2860	95.00	156	185
-2329	2428	96.00	161	189
-951	1050	94.00	152	191
-6926	7025	95.00	158	193
-3092	3190	92.00	139	195
-7058	7157	94.00	150	196
-8895	8994	95.00	156	198
-5428	5527	95.05	156	199
-6003	6102	94.00	150	200
-704	800	96.91	163	205
-6180	6279	96.08	165	206
-1441	1540	96.00	163	207
-4364	4462	94.00	150	210
-3275	3374	95.05	158	211
-2430	2529	97.00	169	213
-2594	2693	95.05	158	215
-3876	3975	97.00	167	217
-1203	1302	96.00	161	219
-2220	2319	98.00	174	221
-9053	9152	95.00	156	223
-2	67	93.94	99.0	223
-5239	5338	95.00	158	225
-2780	2879	94.06	152	228
-423	521	92.93	145	230
-273	372	95.00	158	231
-4097	4196	95.00	158	233
-7224	7323	93.00	147	234
-8474	8573	97.00	169	237
-5615	5714	96.00	163	238
-8804	8900	95.88	158	239
-6719	6818	95.05	158	240
-5362	5458	94.85	150	242
-866	965	94.06	152	251
-8442	8541	92.00	139	253
-7073	7172	94.06	152	254
-1580	1679	91.00	135	255
-4603	4700	95.92	158	256
-519	618	97.00	167	260
-3213	3312	97.00	169	261
-8968	9067	96.00	163	264
-6509	6605	97.94	169	270
-7649	7748	96.00	161	271
-8332	8431	93.27	150	273
-7708	7807	94.06	152	274
-6755	6854	97.00	167	275
-8704	8803	97.00	169	277
-4942	5041	96.00	161	278
-926	1025	96.00	161	280
-213	312	94.06	152	284
-5883	5980	96.94	165	285
-3427	3526	93.07	147	287
-6898	6997	97.03	169	288
-493	592	95.00	158	290
-5247	5344	94.95	154	295
-1142	1241	96.04	163	297
-837	935	97.00	167	298
-5087	5186	93.00	145	301
-9019	9115	94.90	152	302
-8527	8621	96.88	159	303
-9067	9166	95.00	156	305
-2	81	95.00	124	305
-3165	3264	94.00	152	307
-2303	2402	95.05	158	313
-6553	6652	94.00	150	315
-4703	4802	96.00	163	316
-5364	5463	96.00	163	319
-4306	4404	97.98	172	320
-2971	3070	95.05	158	321
-3652	3751	97.03	169	322
-8972	9071	93.00	145	323
-7302	7401	96.00	161	325
-1543	1642	94.06	150	326
-6034	6133	98.00	174	332
-4963	5054	93.48	135	333
-5103	5202	94.06	152	335
-1002	1097	92.71	139	336
-3007	3106	93.14	148	338
-5658	5755	95.92	158	339
-830	929	94.06	152	342
-6979	7078	93.07	147	343
-3926	4025	94.06	152	344
-2047	2145	95.96	159	345
-7952	8051	95.00	158	353
-9018	9111	96.81	158	354
-5508	5607	91.09	135	355
-5710	5809	93.07	147	362
-6296	6395	94.00	152	363
-6554	6653	97.00	169	368
-7297	7396	98.00	174	369
-31	129	96.00	161	370
-9116	9182	95.59	108	370
-6688	6787	93.00	147	371
-5769	5868	96.04	163	372
-5461	5560	96.00	163	376
-1438	1537	96.00	161	377
-3870	3969	97.00	167	380
-6937	7036	95.00	158	385
-1765	1861	96.94	163	387
-7150	7249	95.00	158	388
-6866	6962	97.94	169	389
-678	777	94.06	152	393
-2441	2540	95.00	156	396
-5634	5733	95.00	156	404
-5456	5555	96.00	161	405
-6463	6562	95.00	158	407
-122	221	95.05	158	408
-4519	4618	94.00	152	412
-3679	3778	95.00	158	413
-8626	8725	94.00	152	416
-6577	6676	93.00	147	417
-8543	8639	95.88	156	418
-8753	8852	96.00	161	420
-2224	2323	93.07	147	421
-6645	6744	93.00	145	422
-3892	3991	92.00	139	425
-3599	3698	97.00	169	426
-1408	1508	96.04	165	428
-3341	3440	97.00	167	429
-8316	8415	95.00	156	436
-1809	1908	96.00	163	438
-7770	7869	97.00	169	439
-7250	7349	97.00	169	440
-5590	5688	93.94	150	441
-8475	8574	98.02	174	443
-2139	2237	95.96	161	446
-4074	4173	95.00	158	448
-5269	5367	95.00	156	450
-7237	7336	96.00	161	451
-2461	2559	94.06	152	454
-1168	1267	95.05	158	455
-3083	3178	95.88	156	457
-5129	5228	99.00	180	463
-8590	8684	96.84	159	464
-2677	2776	93.20	148	465
-8332	8431	95.00	156	466
-7692	7791	96.04	163	470
-51	150	95.00	158	471
-1397	1496	98.00	172	472
-42	141	94.00	152	475
-2117	2216	96.00	161	476
-5481	5579	93.94	147	482
-7809	7908	95.00	158	485
-4991	5089	94.00	148	486
-9059	9158	97.00	167	487
-2	73	95.83	115	487
-133	232	95.10	158	488
-6966	7065	95.10	159	490
-6296	6390	96.84	158	492
-4728	4827	97.00	169	495
-4205	4304	96.08	165	498
-6833	6932	98.00	172	499

data/utils/enveomics/Tests/phyla_counts.tsv

@@ -1,10 +0,0 @@
-OTU	Site A	Site B	Site C	Site D
-Actinobacteria	22	1	2	22
-Dehalococcoidia	44	3	2	44
-Fusobacteria	1	4	2	32
-Nitrospirae	32	3	6	1
-Planctomycetes	11	2	1	11
-Proteobacteria	77	25	38	7
-Spirochaetes	4	11	7	3
-Thermotogae	2	11	1	2
-unclassified	1	1	1	1

data/utils/enveomics/Tests/primate_lentivirus.ogs

@@ -1,11 +0,0 @@
-hiv1	hiv2	siv
-lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001549.1_prot_NP_054369.1_2
-lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001549.1_prot_NP_687035.1_1
-lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001549.1_prot_NP_054370.1_3
-lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001549.1_prot_NP_054371.1_4
-lcl|AF033819.3_prot_AAC82591.1_5	lcl|NC_001722.1_prot_NP_056842.1_6	-
-lcl|AF033819.3_prot_AAC82592.1_6	lcl|NC_001722.1_prot_NP_056843.1_7	-
-lcl|AF033819.3_prot_AAD20388.1_7	-	-
-lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001549.1_prot_NP_054372.1_5
-lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001549.1_prot_NP_054373.1_6
--	lcl|NC_001722.1_prot_NP_056840.1_4	-

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm

@@ -1,9 +0,0 @@
-lcl|AF033819.3_prot_AAC82593.1_1	lcl|AF033819.3_prot_AAC82593.1_1	100.00	500	0	0	1	500	1	500	0.0	1044	500	500
-lcl|AF033819.3_prot_AAC82598.2_2	lcl|AF033819.3_prot_AAC82598.2_2	100.00	1003	0	0	1	1003	1	1003	0.0	2062	1003	1003
-lcl|AF033819.3_prot_AAC82594.1_3	lcl|AF033819.3_prot_AAC82594.1_3	100.00	192	0	0	1	192	1	192	6e-147	400	192	192
-lcl|AF033819.3_prot_AAC82595.1_4	lcl|AF033819.3_prot_AAC82595.1_4	100.00	78	0	0	1	78	1	78	4e-56	161	78	78
-lcl|AF033819.3_prot_AAC82591.1_5	lcl|AF033819.3_prot_AAC82591.1_5	100.00	86	0	0	1	86	1	86	6e-63	179	86	86
-lcl|AF033819.3_prot_AAC82592.1_6	lcl|AF033819.3_prot_AAC82592.1_6	100.00	116	0	0	1	116	1	116	1e-82	231	116	116
-lcl|AF033819.3_prot_AAD20388.1_7	lcl|AF033819.3_prot_AAD20388.1_7	100.00	82	0	0	1	82	1	82	2e-54	157	82	82
-lcl|AF033819.3_prot_AAC82596.1_8	lcl|AF033819.3_prot_AAC82596.1_8	100.00	856	0	0	1	856	1	856	0.0	1770	856	856
-lcl|AF033819.3_prot_AAC82597.1_9	lcl|AF033819.3_prot_AAC82597.1_9	100.00	123	0	0	1	123	1	123	1e-92	257	123	123

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm

@@ -1,8 +0,0 @@
-lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001722.1_prot_NP_056837.1_2	58.19	452	178	7	1	448	1	445	0.0	526	500	521
-lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001722.1_prot_NP_663784.1_1	58.24	953	397	1	42	994	498	1449	0.0	1169	1003	1550
-lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	33.75	160	91	6	2	153	4	156	2e-20	75.9	192	215
-lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001722.1_prot_NP_056841.1_5	40.79	76	45	0	2	77	7	82	1e-18	65.9	78	87
-lcl|AF033819.3_prot_AAC82591.1_5	lcl|NC_001722.1_prot_NP_056842.1_6	67.74	31	9	1	18	47	46	76	9e-12	47.8	86	130
-lcl|AF033819.3_prot_AAC82592.1_6	lcl|NC_001722.1_prot_NP_056843.1_7	46.43	28	14	1	8	34	5	32	0.004	25.0	116	103
-lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	34.47	879	492	22	25	856	19	860	3e-146	447	856	860
-lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	56.90	58	25	0	66	123	98	155	2e-22	80.1	123	257

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm

@@ -1,6 +0,0 @@
-lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001549.1_prot_NP_054369.1_2	52.67	524	208	9	1	496	1	512	0.0	518	500	513
-lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001549.1_prot_NP_687035.1_1	60.25	966	373	6	36	994	487	1448	0.0	1196	1003	1472
-lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	38.71	155	87	7	2	152	4	154	1e-25	90.9	192	219
-lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001549.1_prot_NP_054371.1_4	30.43	69	40	3	11	73	21	87	4e-07	34.3	78	118
-lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001549.1_prot_NP_054372.1_5	36.16	874	464	26	34	855	22	853	5e-154	467	856	854
-lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001549.1_prot_NP_054373.1_6	60.34	58	23	0	66	123	82	139	5e-21	75.9	123	223

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm

@@ -1,9 +0,0 @@
-lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001722.1_prot_NP_663784.1_1	100.00	1550	0	0	1	1550	1	1550	0.0	3210	1550	1550
-lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001722.1_prot_NP_056837.1_2	100.00	521	0	0	1	521	1	521	0.0	1077	521	521
-lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	100.00	215	0	0	1	215	1	215	5e-164	446	215	215
-lcl|NC_001722.1_prot_NP_056840.1_4	lcl|NC_001722.1_prot_NP_056840.1_4	100.00	113	0	0	1	113	1	113	6e-85	237	113	113
-lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001722.1_prot_NP_056841.1_5	100.00	87	0	0	1	87	1	87	5e-63	179	87	87
-lcl|NC_001722.1_prot_NP_056842.1_6	lcl|NC_001722.1_prot_NP_056842.1_6	100.00	130	0	0	1	130	1	130	4e-94	262	130	130
-lcl|NC_001722.1_prot_NP_056843.1_7	lcl|NC_001722.1_prot_NP_056843.1_7	100.00	103	0	0	1	103	1	103	2e-72	204	103	103
-lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	100.00	860	0	0	1	860	1	860	0.0	1799	860	860
-lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	100.00	257	0	0	1	257	1	257	0.0	536	257	257

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm

@@ -1,6 +0,0 @@
-lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001549.1_prot_NP_687035.1_1	56.99	1474	601	10	1	1458	1	1457	0.0	1697	1550	1472
-lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001549.1_prot_NP_054369.1_2	57.39	528	203	7	1	521	1	513	0.0	593	521	513
-lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	44.97	169	88	5	1	167	1	166	6e-41	132	215	219
-lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001549.1_prot_NP_054371.1_4	35.21	71	42	2	17	83	22	92	3e-11	46.2	87	118
-lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001549.1_prot_NP_054372.1_5	44.90	873	401	14	25	859	23	853	0.0	714	860	854
-lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001549.1_prot_NP_054373.1_6	41.74	230	108	5	1	224	1	210	2e-50	158	257	223

data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm

@@ -1,6 +0,0 @@
-lcl|NC_001549.1_prot_NP_687035.1_1	lcl|NC_001549.1_prot_NP_687035.1_1	100.00	1472	0	0	1	1472	1	1472	0.0	3045	1472	1472
-lcl|NC_001549.1_prot_NP_054369.1_2	lcl|NC_001549.1_prot_NP_054369.1_2	100.00	513	0	0	1	513	1	513	0.0	1067	513	513
-lcl|NC_001549.1_prot_NP_054370.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	100.00	219	0	0	1	219	1	219	7e-169	459	219	219
-lcl|NC_001549.1_prot_NP_054371.1_4	lcl|NC_001549.1_prot_NP_054371.1_4	100.00	118	0	0	1	118	1	118	3e-87	243	118	118
-lcl|NC_001549.1_prot_NP_054372.1_5	lcl|NC_001549.1_prot_NP_054372.1_5	100.00	854	0	0	1	854	1	854	0.0	1776	854	854
-lcl|NC_001549.1_prot_NP_054373.1_6	lcl|NC_001549.1_prot_NP_054373.1_6	100.00	223	0	0	1	223	1	223	5e-170	462	223	223

data/utils/enveomics/build_enveomics_r.bash

@@ -1,45 +0,0 @@
-#!/bin/bash
-
-cd $(dirname -- $0)/enveomics.R
-rm man/*
-echo '
-\name{phyla.counts}
-\docType{data}
-\alias{phyla.counts}
-\title{Counts of microbial phyla in four sites}
-\description{
-  This data set gives the counts of phyla in three different
-  sites.
-}
-\usage{phyla.counts}
-\format{A data frame with 9 rows (phyla) and 4 rows (sites).}
-\keyword{datasets}
-' > man/phyla.counts.Rd
-echo '
-\name{growth.curves}
-\docType{data}
-\alias{growth.curves}
-\title{Bacterial growth curves for three Escherichia coli mutants}
-\description{
-  This data set provides time (first column) and three triplicated growth
-  curves as optical density at 600nm (OD_600nm) for different mutants of E.
-  coli.
-}
-\usage{growth.curves}
-\format{A data frame with 16 rows (times) and 10 rows (times and OD_600nm).}
-\keyword{datasets}
-' > man/growth.curves.Rd
-echo 'roxygen2::roxygenise();' | R --vanilla
-#echo "
-#library(inlinedocs)
-#package.skeleton.dx('./');
-#" | R --vanilla
-#cat man/enveomics.R-package.Rd | tr -d '\r' \
-#  | grep -v '^}$' | grep -v '^\\author{' \
-#  | grep -v '^Maintainer' \
-#  | perl -pe 's/^\\keyword/}\n\\author{Luis M. Rodriguez-R <lmrodriguezr\@gmail.com> [aut, cre]}\n\n\\keyword/' \
-#  | perl -lwe '$/=\0; $_=<>; s/^\\details{\n+([^}].*\n+)*}\n+//mg; print' \
-#  > o && mv o man/enveomics.R-package.Rd
-#[[ ! -d inst/doc ]] && mkdir -p inst/doc
-#pandoc -o inst/doc/enveomics.R.pdf -f markdown_github README.md
-

data/utils/enveomics/enveomics.R/DESCRIPTION

@@ -1,31 +0,0 @@
-Package: enveomics.R
-Version: 1.8.0
-Authors@R: c(person("Luis M.","Rodriguez-R",role=c("aut","cre"),
-	   email="lmrodriguezr@gmail.com"))
-Title: Various Utilities for Microbial Genomics and Metagenomics
-Description: A collection of functions for microbial ecology and other
-   applications of genomics and metagenomics. Companion package for the
-   Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
-   <DOI:10.7287/peerj.preprints.1900v1>).
-Author: Luis M. Rodriguez-R [aut, cre]
-Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
-URL: http://enve-omics.ce.gatech.edu/enveomics
-Depends:
-   R (>= 2.9),
-   stats,
-   methods,
-   parallel,
-   fitdistrplus,
-   sn,
-   investr
-Suggests:
-   tools,
-   vegan,
-   ape,
-   picante,
-   gplots,
-   optparse
-License: Artistic-2.0
-LazyData: yes
-Encoding: UTF-8
-RoxygenNote: 7.0.2

data/utils/enveomics/enveomics.R/NAMESPACE

@@ -1,39 +0,0 @@
-import(methods)
-import(parallel)
-import(fitdistrplus)
-import(sn)
-importFrom("investr", "predFit")
-importFrom("grDevices", "boxplot.stats", "col2rgb", "grey", "rainbow",
-  "rgb")
-importFrom("graphics", "abline", "axis", "barplot", "hist", "image",
-  "layout", "legend", "lines", "par", "points", "polygon",
-  "rect", "text")
-importFrom("stats", "as.dist", "cophenetic", "cor", "median",
-  "quantile", "runif", "smooth.spline", "nls", "nls.control", "qnorm",
-  "dnorm", "kmeans")
-importFrom("utils", "head", "read.table", "setTxtProgressBar", "tail",
-  "txtProgressBar")
-exportClasses(enve.RecPlot2, enve.RecPlot2.Peak, enve.TRIBS, enve.TRIBStest,
-  enve.GrowthCurve)
-S3method(plot, enve.RecPlot2)
-S3method(plot, enve.TRIBS)
-S3method(plot, enve.TRIBStest)
-S3method(plot, enve.GrowthCurve)
-S3method(summary, enve.TRIBS)
-S3method(summary, enve.TRIBStest)
-S3method(summary, enve.GrowthCurve)
-export(
-  enve.cliopts, enve.col.alpha,
-  enve.barplot, enve.recplot, enve.prune.dist,
-  enve.tribs, plot.enve.TRIBS, summary.enve.TRIBS, enve.tribs.test,
-  plot.enve.TRIBStest, summary.enve.TRIBStest,
-  enve.df2dist, enve.df2dist.group, enve.df2dist.list,
-  enve.recplot2, plot.enve.RecPlot2, enve.recplot2.findPeaks,
-  enve.recplot2.findPeaks.emauto, enve.recplot2.findPeaks.em,
-  enve.recplot2.findPeaks.mower,
-  enve.recplot2.corePeak, enve.recplot2.changeCutoff,
-  enve.recplot2.windowDepthThreshold, enve.recplot2.extractWindows,
-  enve.recplot2.compareIdentities,
-  enve.recplot2.coordinates, enve.recplot2.seqdepth, enve.recplot2.ANIr,
-  enve.growthcurve, plot.enve.GrowthCurve, summary.enve.GrowthCurve,
-  enve.col2alpha, enve.truncate, enve.selvector, enve.prefscore)

data/utils/enveomics/enveomics.R/R/autoprune.R

@@ -1,155 +0,0 @@
-#' Enveomics: Prune Dist
-#' 
-#' Automatically prunes a tree, to keep representatives of each clade.
-#'
-#' @param t A \strong{phylo} object or a path to the Newick file.
-#' @param dist.quantile The quantile of edge lengths.
-#' @param min_dist The minimum distance to allow between two tips.
-#' If not set, \code{dist.quantile} is used instead to calculate it.
-#' @param quiet Boolean indicating if the function must run without output.
-#' @param max_iters Maximum number of iterations.
-#' @param min_nodes_random 
-#' Minimum number of nodes to trigger \emph{tip-pairs} nodes sampling. 
-#' This sampling is less reproducible and more computationally expensive,
-#' but it's the only solution if the cophenetic matrix exceeds \code{2^31-1} 
-#' entries; above that, it cannot be represented in R.
-#' @param random_nodes_frx 
-#' Fraction of the nodes to be sampled if more than \code{min_nodes_random}.
-#'
-#' @return Returns a pruned \strong{phylo} object.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.prune.dist <- function
-(t,
- dist.quantile=0.25,
- min_dist,
- quiet=FALSE,
- max_iters=100,
- min_nodes_random=4e4,
- random_nodes_frx=1
-){
-  if(!requireNamespace("ape", quietly=TRUE))
-    stop('Unavailable ape library.');
-  if(is.character(t)) t <- ape::read.tree(t)
-  if(missing(min_dist)){
-    if(dist.quantile>0){
-      min_dist <- as.numeric(quantile(t$edge.length, dist.quantile));
-    }else{
-      min_dist <- as.numeric(min(t$edge.length[t$edge.length>0]));
-    }
-  }
-  if(!quiet) cat('\nObjective minimum distance: ',min_dist,', initial tips: ',length(t$tip.label),'\n', sep='');
-  round=1;
-  while(round <= max_iters){
-    if(length(t$tip.label) > min_nodes_random){
-      if(!quiet) cat('  | Iter: ',round-1,', Tips: ', length(t$tip.label),
-                     ', reducing tip-pairs.\n', sep='');
-      rnd.nodes <- sample(t$tip.label, length(t$tip.label)*random_nodes_frx);
-      t <- enve.__prune.reduce(t, rnd.nodes, min_dist, quiet);
-    }else{
-      if(!quiet) cat(' Gathering distances...\r');
-      d <- cophenetic(t);
-      diag(d) <- NA;
-      if(!quiet) cat('  | Iter: ',round-1,', Tips: ', length(t$tip.label),
-                     ', Median distance: ', median(d, na.rm=TRUE),
-                     ', Minimum distance: ', min(d, na.rm=TRUE),
-                     '\n', sep='');
-      # Run iteration
-      if(min(d, na.rm=TRUE) < min_dist){
-        t <- enve.__prune.iter(t, d, min_dist, quiet);
-      }else{
-        break;
-      }
-    }
-    round <- round + 1;
-  }
-  return(t);
-}
-
-#' Enveomics: Prune Reduce (Internal Function)
-#' 
-#' Internal function for \code{\link{enve.prune.dist}}.
-#'
-#' @param t A \strong{phylo} object
-#' @param nodes Vector of nodes
-#' @param min_dist Minimum distance
-#' @param quiet If running quietly
-#' 
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.__prune.reduce <- function
-(t, nodes, min_dist, quiet){
-  if(!quiet) pb <- txtProgressBar(1, length(nodes), style=3);
-  for(i in 1:length(nodes)){
-    node.name <- nodes[i];
-    if(!quiet) setTxtProgressBar(pb, i);
-    # Get node ID
-    node <- which(t$tip.label==node.name);
-    if(length(node)==0) next;
-    # Get parent and distance to parent
-    parent.node <- t$edge[ t$edge[,2]==node, 1];
-    # Get edges to parent
-    parent.edges <- which(t$edge[,1]==parent.node);
-    stopit <- FALSE;
-    for(j in parent.edges){
-      for(k in parent.edges){
-        if(j != k & t$edge[j,2]<length(t$tip.label) & t$edge[k,2]<length(t$tip.label) & sum(t$edge.length[c(j,k)]) < min_dist){
-          t <- ape::drop.tip(t, t$edge[k,2]);
-          stopit <- TRUE;
-          break;
-        }
-      }
-      if(stopit) break;
-    }
-  }
-  if(!quiet) cat('\n');
-  return(t);
-}
-
-#' Enveomics: Prune Iter (Internal Function)
-#' 
-#' Internal function for \code{\link{enve.prune.dist}}.
-#'
-#' @param t A \strong{phylo} object
-#' @param dist Cophenetic distance matrix
-#' @param min_dist Minimum distance
-#' @param quiet If running quietly
-#' 
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.__prune.iter <- function
-(t,
- dist,
- min_dist,
- quiet){
-  ori_len <- length(t$tip.label);
-  # Prune
-  if(!quiet) pb <- txtProgressBar(1, ncol(dist)-1, style=3);
-  ignore <- c();
-  for(i in 1:(ncol(dist)-1)){
-    if(i %in% ignore) next;
-    for(j in (i+1):nrow(dist)){
-      if(dist[j, i]<min_dist){
-        t <- ape::drop.tip(t, rownames(dist)[j]);
-        ignore <- c(ignore, j);
-        break;
-      }
-    }
-    if(!quiet) setTxtProgressBar(pb, i);
-  }
-  if(!quiet) cat('\n');
-  # Check if it droped tips
-  cur_len <- length(t$tip.label);
-  if(cur_len == ori_len){
-    stop("Internal error: small edge found in tree, with no equivalent in distance matrix.\n");
-  }
-  return(t);
-}
-