tree.合并工具
tree.合并基础
功能树.合并是为了融合系统发育从不同的系统发育中获得的信息整合到一棵超级树中。给了一个脊梁骨(骨干)和一个来源(源目录树)树木，树.合并滴状枝根据数据集对象中提供的信息数据.个人可以在中指示要添加的提示数据也。一旦组装超级树，根据用户特定的值。
输入树和数据
这个骨干系统发育作为定位的参考其中单个尖端或整个分支从源目录树必须连接。这个骨干假定已正确校准，以便节点和尖端老化（包括树根的年龄）保持不变，除非用户另有规定。这个源目录树是种系发生要添加的分支是从中提取的。对于连接到骨干，最近常用的分支的祖先及其后代节点保持固定，除非这些节点中任何一个的年龄都由用户指示。所有新的添加到的提示骨干，无论他们是否作为一个分支或单独的尖端连接，最大限度地放置距树根的距离，除非校准年龄由用户。这个数据对象是包含信息的数据帧关于“附加内容”、位置和方式。数据必须进行共三列：
如果提供了不同的列名，树.合并假设它们按描述排序，如果出现以下情况，则最终会失败未满足要求。类似地，使用复制绑定提供的函数停止并抛出错误消息。或者是一个分支要绑定或作为引用，必须通过排序属于它的两个进化史上最远的尖端的名字，用“-”符号分隔。或者，如果主干$node.label/source.tree$node.label是不无效的，一个绑定/参考可以指示分支适当时，称为“覆层NAMEOFTHECLADE”。类似地，整个属在两个骨干和源目录树可以标记为“NAMEOFTHEGENUS属”。不管怎么说附加，任何“绑定”提示都可以用作另一个提示的参考（单独或作为层识别的元素，即“种1种2”形式）。分支和提示的顺序提供附件并不重要。
提示和节点在树.合并通过功能的手段scaleTree（缩放树）.为此，尖端和节点的命名向量年龄，即时间必须提供与系统发育史中最年轻尖端的距离。至于数据对象，要校准的节点应通过对这两个物种的名称进行系统进化排序来进行鉴定它指向的最远的尖端，用“-”隔开。
将单个提示附加到主干树
如果只附加了单个提示源目录树可以未指定。要附加的提示集参考具有poly=假是被认为代表一种多元论。提示设置为绑定已经在主干树上的数据将从主干树中删除根据参考.在示例中下面，提示“genusE_1a”和“genusE1b”被设置为附加到相同的引用“genusE_1”，创建了一个多胞体。物种“genusC_4”和“genusC_5”都被设置为绑定到整个“Genus genusC”（包括“genusC_1”、“genusC2”和“genusC3”），但仅限于后者明确表示要创建多模分支（“poly=TRUE”）。一次附加了“genusC_5”，它是与MRCA有关的整个genusC更改骨干，因此确定了“genusC_6”的引用通过在“新”中选择两个系统发育上最远的尖端genusC，即“genusC_1-genusC_5”。属于主干被指示移动，并且“genusH_1”被添加到树中从而改变树的总高度。
|
达托
|
| 绑定 |
参考 |
聚 |
| 发电机E_1a |
属_1 |
错误的 |
| 发电机C_3a |
发电机C_3 |
错误的 |
| B_1a类 |
类别B_1 |
错误的 |
| 属_4 |
属genusC |
真的 |
| 第F_1代 |
包层直流 |
错误的 |
| 发电机G_1 |
genusF_1-genusB_2类 |
真的 |
| 发电机H_1 |
genusE_1a-genusC_3 |
错误的 |
| 发电机C_5 |
属genusC |
错误的 |
| 发电机C_6 |
发电机C_5-发电机C_1 |
错误的 |
| 第B_3代 |
第B_2代第B_1代 |
错误的 |
| 发电E_1b |
属_1 |
错误的 |
树.合并(主干=树背，数据=达托，绘图=错误的)
#>tree.merge中出现警告（backbone=tree.back，data=dato，plot=FALSE）：genusB_3已从主干树中删除
#>doTryCatch（return（expr），name，parentenv，handler）中的警告：未指示根年龄：树根任意设置在
#> 3.32
作为否小费提供给树.合并,所有新的树梢都被放置在离树根的最大距离处。由于没有指明合并树根的年龄，因此函数任意放置并生成警告以通知用户其相对于系统发育史上最年轻的尖端的位置。
校准合并中的尖端或节点的年龄树，参数小费和节点.年龄必须注明。
年龄提示
#>发电机H_1发电机E_1a发电机E_1发电机E_1b发电机F_1发电机C_5发电机C_3a发电机G_1
#> 1.0 2.0 1.7 1.5 0.8 1.5 0.3 1.2
#>B_1a类
#> 0.2
年龄.node
#>第B_1代F_1代E_1a-属E_1b代H_1代B_1
#> 2.2 2.9 3.5
树.合并(主干=树背，数据=达托，第页提示=年龄提示，节点.年龄=ages.node，绘图=错误的)
#>tree.merge中的警告（backbone=tree.back，data=dato，tip.ages=ages.tip，：genusB_3已从主干树中删除
将分支连接到主干树
当连接分支时，对向它的节点位于源目录树识别为尖端对的MRCA“Genus”，或中所示的“Clade”绑定。在下面的示例中，源中的“Genus genusA”被添加为主干内的“genusA_1”。然后，“genusL_1”绑定到新的创建了由属于“genusA”的所有提示组成的分支，位于它的两个进化上最远的尖端。
|
椰壳
|
| 绑定 |
参考 |
聚 |
| 属genusA |
A_1代 |
错误的 |
| 基因G_1-genusF_2 |
包层直流 |
错误的 |
| 克拉德HI |
属genusB |
错误的 |
| 发电机L_1 |
基因A_1-genusA_4 |
错误的 |
树.合并(主干=树背，数据=达托克拉德，源目录树=树资源，绘图=错误的)
指导性示例
###加载包含鲸目树的RRphylo示例数据集
数据(“数据鲸类”)
数据鲸类$树冠->树冠#系统发育树
树冠$节点标签[(131-Ntip公司（treecet））]<-“神秘皇冠” #指定节点标签
###选择两个分支和一些要移除的物种
提示（特雷塞特，131)->皇冠。须鲸亚目
提示（特雷塞特，193)->海豚科
c（c）(“Aetiocetus_weltoni”,“Saghacetus_osiris”,
“Zygorhiza_kochii”,“Ambulocetus_natans”,
“肯特里奥登_珀尼”,“肯特里奥登·施奈德利”,“Kentriodon_obcurus”,
“Eurhinodelphis_cristatus”,“Eurhinodelphis_bosi”)->已灭绝的
情节（特雷塞特，显示.tip.label= 错误的,无保证金=真的)
诺德拉贝尔(框架=“n”,科尔=“蓝色”,字体=2,节点=c（c）(131,193),文本=c（c）(“皇冠\n个神秘主义者“,“飞燕草”))
小费标签(框架=“圆形”,背景=“红色”,cex公司=.三,文本=代表("",长度(c（c）（王冠。神秘人，海豚科，灭绝）），
尖端=哪一个（特雷塞特$提示标签%单位：%c（c）（王冠。神秘人，海豚科，灭绝））
###创建主干树和源树
滴落.tip（特雷塞特，c（c）（王冠.蒙脱石[-哪一个(提示（特雷塞特，131)%单位：%
c（c）(“Caperea_精氨酸”,“Eubalaena_australis”))],
翠雀亚科[-哪一个(提示（特雷塞特，193)==“Tursiops_aduncus”)]，已灭绝）->后树
keep.tip公司（特雷塞特，c（c）（王冠。神秘人，海豚科，灭绝）->资源树
|
达托
|
| 绑定 |
参考 |
聚 |
| 克拉德皇冠（Mysticeti） |
福卡亚_巴埃利-埃托塞图斯_韦尔顿 |
错误的 |
| 埃蒂奥塞图斯_韦尔顿 |
致病性大肠杆菌 |
错误的 |
| Saghacetus_osiris公司 |
福卡亚_贝利-图西奥普斯_特鲁卡特斯（Fucaia_buelli-Tursiops_truncatus） |
错误的 |
| Zygorhiza_kochii公司 |
萨哈塞图斯_西里斯-福卡亚_布埃利（Saghacetus_osiris-Fucaia_buelli） |
错误的 |
| Ambulocetus_natans公司 |
达拉斯人_阿梅迪·福卡亚_布埃利 |
错误的 |
| Kentriodon属 |
Phocoena_Phocoena-海豚_delphis |
错误的 |
| Sousa_chinensis-delphis海豚队 |
Sotalia_fluviatilis水飞蓟 |
错误的 |
| 科吉亚_西马 |
Kogia_审校 |
错误的 |
| 真犀牛 |
真犀牛_长嘴犀牛 |
错误的 |
| 革兰氏菌 |
球头蚴-假rca_crassidens |
错误的 |
| Eurhinodelphis_bossi（幼犀牛） |
真犀牛_长嘴犀牛 |
错误的 |
###根据数据合并主干树和源树，无需校准尖端和节点年龄
树.合并(主干=后树，数据=达托，源目录树=资源树，绘图=错误的)
#>树中的警告。merger（主干=backtree，数据=dato，源.tree=源树，：Kogia\sima，Grampus_griseus已从主干树中删除
#>tree.merge中出现警告（backbone=backtree，data=dato，source.tree=sourcetree，：Eubalaena_australis，Caperea_marginata，Tursiops_aduncus已在源树上：已从主干树中删除
#>doTryCatch（return（expr），name，parentenv，handler）中的警告：未指示根年龄：树根任意设置在
#> 45.06
###设置提示和节点校准时间
c（c）(Aetiocetus_weltoni感染=28,
Saghacetus_osiris公司=33.9,
Zygorhiza_kochii公司=34,
Ambulocetus_natans公司=40.4,
肯特里奥登_珀尼=15.9,
肯特里奥登_施奈德里=11.61,
肯特里奥登·布斯库鲁斯=13.65,
Eurhinodelphis_bossi（幼犀牛）=13.65,
真犀牛=5.33)->酒水
c（c）(“Ambulocetus_natans-Fucaia_buelli”=52.6,
“Balaena_mysticetus-Caperea_arginata”=21.5)->节点数
###合并主干树和源树，并校准提示和节点年龄
树.合并(主干=后树，数据=达托，源目录树=资源树，
第页提示=酒水，节点.年龄=节点面积，绘图=错误的)
#>树中的警告。merger（主干=backtree，数据=dato，源.tree=源树，：Kogia\sima，Grampus_griseus已从主干树中删除
#>tree.merge中出现警告（backbone=backtree，data=dato，source.tree=sourcetree，：Eubalaena_australis，Caperea_marginata，Tursiops_aduncus已在源树上：已从主干树中删除
scaleTree工具
功能scaleTree（缩放树）是一个有用的处理工具围绕Gene Hunt的尺度Phylo编写的系统发育年龄校准函数(https://naturalhistory.si.edu/staff/gene-hunt). 它根据树种和/或节点校准年龄（指距最年轻尖端的距离树）。
如果只提供了物种年龄（参数小费),该函数更改树叶长度，留下节点年龄和内部分支长度不变。提供节点年龄时（参数节点.年龄)，该函数将节点位置沿其拥有分支，同时保持其他节点和物种位置保持不变。
#>t9 t73 t11 t43 t78 t46 t52 t26#> 1.250 1.205 0.000 2.430 3.150 1.050 0.000 1.550scaleTree（树，tip.ages=sp.ages）->树S1#> | | | 0%| | | 1%| |= | 1%| |= | 2%| |== | 2%| |== | 3%| |=== | 4%| |===|5%| |==== | 5%| |==== | 6%| |====|7%| |====== | 8%| |====== | 9%| |======= | 10%| |======== | 11%| |======== | 12%| |========= | 12%| |========= | 13%| |========== | 14%| |========== | 15%| |=========== | 15%| |=========== | 16%| |============ | 16%| |============ | 17%| |============ | 18%| |============= | 18%| |============= | 19%| |============== | 20%| |=============== | 21%| |===================|22%| |================ | 23%| |================= | 24%| |================== | 25%| |================== | 26%| |=================== | 27%| |==================== | 28%| |==================== | 29%| |===================== | 30%| |====================== | 31%| |====================== | 32%| |======================= | 32%| |======================= | 33%| |======================= | 34%| 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可能会出现需要校准的物种和/或节点年龄比他们祖先的年龄大。在这种情况下，移动物种（节点）到其目标年龄，功能重新组合系统发育通过指定相同的分支长度（通过参数设置最小支路)沿着物种的所有分支（节点）路径，以便树是一致的和祖先-后代关系保持不变。以这种方式更改为原始树拓扑只适用于沿“校准”物种的路径。
c（c）（sp.ages、nod.ages）
#>第1页96
#> 20.5 15.6
#scaleTree（tree，tip.ages=sp.ages，node.ages=nod.ages、min.branch=1）->树
#>
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指导性示例
#加载包含Felids树的RRphylo示例数据集
数据(“DataFelids”)
DataFelids公司$树叶->树
#获取物种和节点年龄
#（意思是与最年轻的物种的距离，在这种情况下是最近的）
最大值(节点高度（树）->H（H）
H（H）-dist.节点（树）[(Ntip公司（树）+1),(Ntip公司（树）+1):(Ntip公司（树）+N节点（树）]->年龄编号
H（H）-诊断(真空断路器（树）->年龄.tips
#应用Pagel的lambda转换仅更改节点年龄
重新标记RR（树，λ=0.8)->树1
#通过设置
#节点处的原始年龄为node.ages
scaleTree（缩放树）（树1，节点.年龄=年龄节点）->树S1
#>
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#10个物种叶片长度的变化
树->树2
设置种子(14)
样品（树2$提示标签，10)->萨姆斯普
年龄提示->年龄.上午
年龄.上午[哪一个（年龄.上午>0.1)]<-年龄.上午[哪一个（年龄.上午>0.1)]-1.5
年龄.上午[哪一个（年龄.上午<0.1)]<-年龄.上午[哪一个（年龄.上午<0.1)]+0.2
树2$边缘长度[比赛(比赛（sam.sp，树$tip.label），树$边缘[，2])]<-年龄.上午
#通过设置
#采样尖端的原始年龄作为tip.ages
scaleTree（缩放树）（树2，第页提示=年龄提示[sam.sp]）->树S2
#>
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#应用Pagel的kappa变换来改变物种和节点年龄，
#包括树根的年龄
重新标记RR（树，卡帕=0.5)->树3
#通过设置
#节点处的原始年龄为node.ages
scaleTree（缩放树）（树1，小费=年龄提示，节点.年龄=年龄节点）->树S3
#>
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cutPhylo工具
功能剪切Phylo意在切断系统发育树删除所有比引用年轻的提示和节点（用户特定的）年龄，也可以与特定节点一致。什么时候？整个分支被切割，用户可以选择（通过参数保持血统)保持树枝的长度作为新的尖端树，或将其完全移除。
剪切Phylo（树，年龄=5,保持血统= 真的)
剪切Phylo（树，年龄=5,保持血统= 错误的)
剪切Phylo（树，节点=129,保持血统= 真的)
剪切Phylo（树，节点=129,保持血统= 错误的)
固定多边形工具
功能固定聚乙烯随机分解多胞胎在指定节点或通过树（Castiglione etal.2020）。后一个功能类似于猿的多2di.然而，与后者相反，多面体被解析为非零长度分支，以提供进化时间的可靠划分从二分法节点下降的节点中。这可能是有助于在应用时获得实际的进化速率估计RRphylo公司。在type=塌陷用户需要指出的规范节点/秒必须转化为多毛类分支。
###加载包含鲸目树的RRphylo示例数据集
数据(“数据鲸类”)
数据鲸类$树冠->树冠
###解决鲸目动物系统发育中的所有多体型
固定聚乙烯（特雷塞特，类型=“解决”)->固定树
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##设置分支颜色
未列出的(愚蠢的(姓名(哪一个(桌子（特雷塞特$边缘[，1])>2)),功能（x）
c（c）（x，获取后代（特雷塞特，as.数字（x） ）））->托科洛
未列出的(愚蠢的(姓名(哪一个(桌子（特雷塞特$边缘[，1])>2)),功能（x）
c（c）(获取MRCA（树固定，提示（treecet，x）），
获取后代（树固定，as.数字(获取MRCA（树固定，提示（treecet，x）））->tocolo2公司
科罗<-代表(“灰色60”,nrow公司（特雷塞特$边缘））
姓名（科罗拉多州）<-树冠$边缘[，2]
二氧化碳<-代表(“灰色60”,nrow公司（树固定$边缘））
姓名（二氧化碳）<-固定树$边缘[，2]
科罗[比赛（托科洛，姓名（科罗）]<-“红色”
二氧化碳[比赛（tocolo2、，姓名（二氧化碳）]<-“红色”
标准(mfrow公司=c（c）(1,2))
情节（特雷塞特，无保证金=真的,显示.tip.label=错误的,边缘.颜色=科罗，边缘.宽度=1.3)
情节（树固定，无保证金=真的,显示.tip.label=错误的,边缘.颜色=二氧化碳，边缘.宽度=1.3)
###解决肯特里翁属的多胞体
固定聚乙烯（特雷塞特，类型=“解决”,节点=221)->固定树2
#>
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##设置分支颜色
c（c）(221,获取后代（特雷塞特，as.数字(221)))->托科洛
c（c）(获取MRCA（树固定2，提示（特雷塞特，221)),
获取后代（树固定2，as.数字(获取MRCA（树固定2，提示（特雷塞特，221)))))->tocolo2公司
科罗<-代表(“灰色60”,nrow公司（特雷塞特$边缘））
姓名（科罗拉多州）<-树冠$边缘[，2]
二氧化碳<-代表(“灰色60”,nrow公司（树固定2$边缘））
姓名（二氧化碳）<-固定树2$边缘[，2]
科罗[比赛（托科洛，姓名（科罗）]<-“红色”
二氧化碳[比赛（tocolo2、，姓名（二氧化碳）]<-“红色”
标准(mfrow公司=c（c）(1,2))
情节（特雷塞特，无保证金=真的,显示.tip.label=错误的,边缘.颜色=科罗，边缘.宽度=1.3)
情节（树固定2，无保证金=真的,显示.tip.label=错误的,边缘.颜色=二氧化碳，边缘.宽度=1.3)
###将海豚科折叠成多体分支
固定聚乙烯（特雷塞特，类型=“崩溃”,节点=179)->树cet.collapsed
#>
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#设置分支颜色
c（c）(179,获取后代（特雷塞特，as.数字(179)))->托科洛
c（c）(获取MRCA（树木倒塌，提示（特雷塞特，179)),
获取后代（树木倒塌，as.数字(获取MRCA（树木倒塌，提示（特雷塞特，179)))))->tocolo2公司
科罗<-代表(“灰色60”,nrow公司（特雷塞特$边缘））
姓名（科罗拉多州）<-树冠$边缘[，2]
二氧化碳<-代表(“灰色60”,nrow公司（树倒塌$边缘））
姓名（二氧化碳）<-树cet.collapsed$边缘[，2]
科罗[比赛（托科洛，姓名（科罗）]<-“红色”
二氧化碳[比赛（tocolo2、，姓名（二氧化碳）]<-“红色”
标准(mfrow公司=c（c）(1,2))
情节（特雷塞特，无保证金=真的,显示.tip.label=错误的,边缘.颜色=科罗，边缘.宽度=1.3)
情节（树木倒塌，无保证金=真的,显示.tip.label=错误的,边缘.颜色=二氧化碳，边缘.宽度=1.3)
