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V-Z · Jan 4, 2016 · f4daa20 · f4daa20
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diff --git a/LICENSE b/LICENSE
diff --git a/README b/README
@@ -0,0 +1 @@
+
diff --git a/data/amara_aflp.txt b/data/amara_aflp.txt
@@ -0,0 +1,21 @@
+	r62	r65	r69	r76	r81	r82	r86	r91	r96	r97	r100	r119	r121	r127	r129	r153	r154	r162	r177	r180	r186	r189	r193	r195	r198	r201	r207	r213	r221
+amara-7568-1	0	0	1	1	1	0	0	0	1	0	0	1	1	0	0	1	0	0	1	0	1	1	1	1	0	0	0	0	0
+amara-7568-2	0	0	1	1	0	0	0	0	0	0	0	1	1	0	0	1	0	0	1	0	0	1	0	0	0	0	0	0	1
+amara-7568-3	0	0	1	1	0	0	0	0	1	0	0	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1
+amara-7568-4	0	0	1	1	1	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	1	1	0	1	0	0	0	0	0
+amara-7568-5	0	0	1	1	0	0	0	0	0	0	0	1	1	0	0	1	0	0	1	0	0	1	0	0	0	0	0	0	1
+amara-7568-6	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	0	0	1	0	1	1	0	1	0	0	0	1	1
+amara-7868-1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0
+amara-7868-2	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0
+amara-7868-3	0	0	1	1	0	0	0	0	1	0	0	1	1	0	0	1	0	0	1	0	0	1	0	0	0	0	0	0	0
+amara-7046-1	1	0	1	1	0	0	1	0	0	0	0	1	0	1	0	0	0	0	1	0	1	1	1	0	0	0	0	1	0
+amara-6345-1	1	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	1	0	0	0	0	0	1	0
+amara-6345-2	1	0	1	1	0	0	0	0	0	1	0	1	1	0	0	0	0	1	1	0	1	0	1	0	0	0	0	1	0
+amara-6345-3	1	0	1	1	0	0	1	0	0	1	0	1	1	0	0	1	0	1	1	0	1	1	1	0	0	0	0	1	0
+amara-6345-4	1	0	1	1	0	0	0	0	0	1	0	1	1	0	0	0	0	1	1	0	1	0	1	0	0	0	0	1	0
+amara-6345-5	1	0	1	1	0	0	0	0	0	0	0	1	1	0	0	1	0	0	1	1	0	1	0	0	0	0	0	1	0
+amara-6249-1	1	0	1	1	0	0	1	1	0	1	0	1	0	0	0	1	1	0	1	0	1	1	1	0	0	0	0	1	0
+amara-6249-2	1	0	1	1	0	0	1	1	0	1	0	1	0	0	0	1	0	0	1	0	1	1	1	0	0	0	0	1	0
+amara-6249-3	1	0	1	1	0	0	1	1	0	1	0	1	0	0	0	1	1	0	1	0	1	1	1	0	0	0	0	1	0
+amara-6249-4	1	0	1	1	0	0	1	1	0	1	0	1	0	1	0	1	1	0	1	0	1	1	1	0	0	0	0	1	0
+amara-6249-5	1	0	1	1	0	0	1	1	0	1	0	1	0	0	0	1	1	0	1	0	1	1	1	0	0	0	0	1	0
diff --git a/data/amara_pop.txt b/data/amara_pop.txt
@@ -0,0 +1,21 @@
+pop
+pop75681
+pop75682
+pop75683
+pop75684
+pop75685
+pop75686
+pop78681
+pop78682
+pop78683
+pop70461
+pop63451
+pop63452
+pop63453
+pop63454
+pop63455
+pop62491
+pop62492
+pop62493
+pop62494
+pop62495
diff --git a/data/boot_phylo_nj_pop.r b/data/boot_phylo_nj_pop.r
@@ -0,0 +1,49 @@
+## Bootstrap of NJ tree of populations. As input takes bootstraped tree, source data in geneind format and number of permutations.
+
+boot.phylo.nj.pop <- function(origtree, genindata, nperm) {
+
+# Custom variant of function sample to correct its behaviour when number of individuals within respective population is 1.
+  mysample <- function(x){
+    if (length(x) == 1) {out <- x}
+      else {out <- sample(x, replace=TRUE)}
+      return(out)
+    }
+
+# Construction of NJ tree from bootstraped dataset for further comparison with original tree.
+## Here it is possible to adjust type and/or parameters of distance matrix and/or tree constructioning.
+  treemaker <- function (ind, listgenpopobj) {
+    OpravaMatice <- dist.genpop(listgenpopobj[[ind]], method=1, diag=TRUE, upper=TRUE)
+    OpravaMatice[OpravaMatice == "Inf"] <- 10
+    nj(OpravaMatice)
+    }
+
+# Extraction of needed information from orginal data and preparation of temporal variables.
+  genindata2 <- genindata
+  data <- genindata@tab
+  pop <- genindata@pop
+  indiv <- 1:nrow(genindata@tab)
+  res <- vector(mode="list", length=nperm)
+
+# In every step (from 1 to number of permutations) sample within respective populations of source data and write it into list of geneind objects.
+  for (index in 1:nperm) {
+    struct <- unlist(tapply(indiv, pop, mysample))
+    new.tab <- data[struct,]
+    genindata2@tab <- new.tab
+# For correct writing of modified data to the list.
+    res[[index]] <- genindata2
+    }
+
+# Conversion of all genind objects in the list to genpop objects.
+  population <- lapply(res, genind2genpop)
+# Construction of trees and saving of them into the list of trees.
+  trees <- vector("list", nperm)
+  trees <- lapply(1:nperm, treemaker, population)
+# Compare every bootstraped tree with original one and return vector of bootstrap support values.
+  for (i in 1:nperm) storage.mode(trees[[i]]$Nnode) <- "integer"
+  storage.mode(origtree$Nnode) <- "integer"
+  pp <- prop.part(trees)
+  pp <- postprocess.prop.part(pp)
+  ans <- prop.clades(origtree, part=pp, rooted=FALSE)
+  return(ans)
+
+  }
diff --git a/data/course_commands.html b/data/course_commands.html
diff --git a/data/course_commands.r b/data/course_commands.r
diff --git a/data/hauss_stru.in b/data/hauss_stru.in
@@ -0,0 +1,95 @@
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diff --git a/data/haussknechtii_coordinates.csv b/data/haussknechtii_coordinates.csv
@@ -0,0 +1,48 @@
+Ind	lon	lat
+H01	21.3333	41.1
+H02	21.3333	41.1
+H03	21.3333	41.1
+H04	21.3333	41.1
+H05	21.3333	41.1
+H06	21.3333	41.1
+H07	21.3333	41.1
+H08	21.3333	41.1
+H09	21.3333	41.1
+H10	21.3333	41.1
+H11	21.3333	41.1
+H12	21.3333	41.1
+H13	21.3333	41.1
+H14	20.8	41.1333
+H15	20.8	41.1333
+H16	20.8	41.1333
+H17	20.8	41.1333
+H18	20.8	41.1333
+H19	20.8	41.1333
+H20	20.8	41.1333
+H21	20.8	41.1333
+H22	20.8	41.1333
+H23	20.8	41.1333
+H24	20.8	41.1333
+H25	20.8	41.1333
+H26	20.8	41.1333
+H27	20.8	41.1333
+H28	20.8	41.1333
+H29	20.8	41.1333
+H30	20.8	41.1333
+H31	21.55	41.3333
+H32	21.55	41.3333
+H33	22.0667	41.4833
+H34	22.0667	41.4833
+H35	22.0667	41.4833
+H36	22.0667	41.4833
+H37	22.0667	41.4833
+H38	22.0667	41.4833
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+H45	21.5167	41.9167
+H46	21.5167	41.9167
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diff --git a/data/haussknechtii_geneland.txt b/data/haussknechtii_geneland.txt
@@ -0,0 +1,47 @@
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+269	297	198	198	211	211	403	419	201	201	190	192	251	251	163	163	213	213	136	138	279	293	150	152
+273	273	180	180	221	221	397	419	199	199	168	192	261	261	165	181	219	221	136	138	263	295	150	152
+273	273	198	198	221	221	403	415	211	211	190	192	253	253	165	183	219	229	134	136	297	297	150	150
+267	271	198	180	221	221	403	415	209	209	192	192	245	255	165	183	215	227	128	134	269	295	150	150
+273	273	198	198	221	221	415	419	209	211	190	192	249	249	165	165	213	219	134	144	275	279	150	152
+273	273	198	198	221	221	403	415	211	211	190	192	253	253	165	183	219	227	134	136	293	295	150	150
+267	271	198	180	221	221	403	415	209	209	192	192	245	255	165	183	215	227	128	134	269	295	150	150
+339	341	198	180	211	211	397	399	191	209	194	194	251	251	165	187	219	221	132	138	279	279	150	152
+273	273	198	198	221	223	401	401	187	187	168	192	245	249	191	191	213	221	126	134	279	287	150	152
+325	341	198	198	211	221	399	409	197	197	168	192	261	261	181	185	219	219	130	136	277	303	152	152
+341	343	198	198	221	221	401	409	197	192	192	245	251	187	191	219	221	130	132	275	277	150	156	152
+341	343	198	198	221	221	399	409	197	192	192	245	251	187	191	219	221	130	132	275	277	150	156	152
+275	283	198	198	221	223	415	419	197	197	198	198	237	251	165	183	211	219	114	130	283	293	150	150
+283	283	198	180	221	221	403	419	197	168	168	237	251	165	165	211	211	128	132	279	283	152	152	152
+275	275	198	198	221	221	419	419	193	193	168	196	243	251	165	165	215	215	128	136	277	293	150	152
+275	275	198	198	221	221	419	419	193	193	168	196	243	251	165	165	215	215	128	136	277	293	150	152
diff --git a/data/haussknechtii_ssrs.txt b/data/haussknechtii_ssrs.txt
@@ -0,0 +1,48 @@
+	pop	msta93	msta101	msta102	msta103	msta105	msta131	msta143	msta44B	msta53	msta61	msta73	msta78
+H01	He	269/269	198/198	221/223	419/419	197/197	196/196	237/251	163/163	211/233	132/136	279/291	150/152
+H02	He	275/283	198/198	221/223	419/419	193/193	168/190	243/251	163/163	211/215	128/136	293/293	150/152
+H03	He	275/299	198/198	221/223	419/419	193/197	190/196	237/243	163/163	215/233	132/136	279/293	150/152
+H04	He	275/275	198/198	221/221	419/419	193/193	168/196	243/251	163/163	215/215	128/136	279/293	150/152
+H05	He	275/275	198/198	221/221	419/419	193/193	168/196	243/251	163/163	215/215	128/136	279/293	150/152
+H06	He	275/293	198/198	221/223	419/421	193/193	190/196	243/243	163/195	215/215	128/130	283/291	150/152
+H07	He	275/299	198/198	211/211	419/419	197/197	168/196	243/251	163/163	211/215	128/136	279/291	150/150
+H08	He	275/275	198/180	211/211	419/419	193/193	168/190	237/243	163/163	215/215	130/136	277/291	150/150
+H09	He	283/283	198/180	211/221	399/419	193/193	190/196	237/243	163/163	219/227	132/136	279/291	152/152
+H10	He	275/275	198/180	221/223	419/419	193/193	168/190	237/243	163/163	215/215	130/136	277/293	150/150
+H11	He	275/299	198/198	211/221	419/419	193/197	190/196	237/243	163/163	215/233	132/136	279/293	150/152
+H12	He	275/299	198/198	221/223	419/419	193/197	190/196	237/243	163/163	215/233	132/136	279/293	150/152
+H13	He	275/283	198/198	221/223	419/419	193/193	168/190	243/251	163/163	209/215	128/136	293/293	150/152
+H14	Oh	227/227	198/198	221/231	397/415	NA	182/182	237/237	195/187	201/201	122/128	293/293	152/192
+H15	Oh	299/327	198/180	221/223	399/419	193/195	168/190	237/247	163/163	209/213	126/128	263/277	150/152
+H16	Oh	299/327	198/180	221/223	399/419	193/195	168/190	237/247	163/163	211/213	126/128	263/277	150/152
+H17	Oh	273/307	198/180	211/211	397/405	185/195	166/192	251/251	163/163	215/219	130/146	279/281	150/150
+H18	Oh	273/309	198/180	209/209	397/419	195/207	168/168	253/253	163/163	207/219	136/142	287/295	150/150
+H19	Oh	273/309	198/180	211/211	397/419	195/207	168/168	253/253	163/163	207/219	136/142	289/297	150/150
+H20	Oh	271/271	198/180	221/223	397/397	185/209	190/192	249/249	163/163	215/215	130/134	279/281	150/152
+H21	Oh	337/339	198/198	211/211	403/407	209/209	168/190	243/243	163/181	215/219	126/126	261/261	152/152
+H22	Oh	273/309	198/198	209/209	397/401	185/205	190/180	243/249	163/163	207/207	130/130	253/253	148/150
+H23	Oh	273/309	198/198	211/211	397/401	185/205	190/180	243/249	163/163	207/207	130/130	253/297	148/150
+H24	Oh	337/339	198/198	211/211	403/407	187/187	168/190	261/261	163/181	215/219	126/126	261/261	152/152
+H25	Oh	273/309	198/180	221/221	397/407	185/195	166/192	251/251	165/165	219/221	130/146	279/281	150/150
+H26	Oh	273/311	198/180	211/211	397/419	195/207	168/168	253/253	165/165	209/219	136/142	289/297	150/150
+H27	Oh	273/311	198/180	221/221	397/407	195/207	168/168	253/253	165/165	209/219	136/142	287/295	150/150
+H28	Oh	271/273	198/180	221/221	397/397	185/195	166/180	249/249	165/165	209/219	128/130	253/253	150/152
+H29	Oh	273/311	198/198	221/221	397/397	185/205	166/180	249/251	165/165	209/219	130/134	253/281	150/150
+H30	Oh	271/271	198/198	221/221	397/419	193/195	166/168	241/253	165/165	219/219	126/136	253/289	150/150
+H31	Pr	269/315	198/198	211/211	399/399	193/193	198/198	255/255	163/163	213/215	128/134	257/305	150/150
+H32	Pr	269/297	198/198	211/211	403/419	201/201	190/192	251/251	163/163	213/213	136/138	279/293	150/152
+H33	Ne	273/273	180/180	221/221	397/419	199/199	168/192	261/261	165/181	219/221	136/138	263/295	150/152
+H34	Ne	273/273	198/198	221/221	403/415	211/211	190/192	253/253	165/183	219/229	134/136	297/297	150/150
+H35	Ne	267/271	198/180	221/221	403/415	209/209	192/192	245/255	165/183	215/227	128/134	269/295	150/150
+H36	Ne	273/273	198/198	221/221	415/419	209/211	190/192	249/249	165/165	213/219	134/144	275/279	150/152
+H37	Ne	273/273	198/198	221/221	403/415	211/211	190/192	253/253	165/183	219/227	134/136	293/295	150/150
+H38	Ne	267/271	198/180	221/221	403/415	209/209	192/192	245/255	165/183	215/227	128/134	269/295	150/150
+H39	Sk	339/341	198/180	211/211	397/399	191/209	194/194	251/251	165/187	219/221	132/138	279/279	150/152
+H40	Sk	273/273	198/198	221/223	401/401	187/187	168/192	245/249	191/191	213/221	126/134	279/287	150/152
+H41	Sk	325/341	198/198	211/221	399/409	197/197	168/192	261/261	181/185	219/219	130/136	277/303	152/152
+H42	Sk	341/343	198/198	221/221	401/409	NA	192/192	245/251	187/191	219/221	130/132	275/277	150/156
+H43	Sk	341/343	198/198	221/221	399/409	NA	192/192	245/251	187/191	219/221	130/132	275/277	150/156
+H44	Sk	275/283	198/198	221/223	415/419	197/197	198/198	237/251	165/183	211/219	114/130	283/293	150/150
+H45	Sk	283/283	198/180	221/221	403/419	NA	168/168	237/251	165/165	211/211	128/132	279/283	152/152
+H46	Sk	275/275	198/198	221/221	419/419	193/193	168/196	243/251	165/165	215/215	128/136	277/293	150/152
+H47	Sk	275/275	198/198	221/221	419/419	193/193	168/196	243/251	165/165	215/215	128/136	277/293	150/152