set.rate.matrix.tm(rphast)
set.rate.matrix.tm()所属R语言包：rphast
Set the rate matrix of a tree model using model-specific parameters.
设置率矩阵的树模型，使用模型的具体参数。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Set the rate matrix of a tree model using model-specific parameters.
设置率矩阵的树模型，使用模型的具体参数。
用法----------Usage----------
参数----------Arguments----------
参数：x
An object of type tm.
的对象类型tm。
参数：params
Parameters specific to the substitution model. Should be a numeric vector of length appropriate for the model. See details below.
特定的替代模型的参数。应该是一个数值向量的长度适当的模型。详见下文。
参数：scale
A logical value. If TRUE, scale the matrix so that the expected number of mutations per unit time is one per base pair.
逻辑值。如果TRUE，缩放矩阵，单位时间内的预期数量的突变是每一个碱基对。
Details
详细信息----------Details----------
The params argument is a numeric vector with the parameters specific to the model being used. Here is the meaning of params for each model:
params参数是一个数值向量的参数，具体到正在使用的模型。这里的意思是每个模型参数数量：
"JC69","F81": These models have no parameters; params should be NULL.
“JC69”，“F81”：这些模型没有参数，的PARAMS应该是NULL。
"K80","HKY85": params should be a single value representing the transition-transversion ratio (kappa).
“K80”，“HKY85”：的PARAMS应该是一个单一的值，转换颠换比（KAPPA）。
"HKY85+Gap": params should be a numeric vector of length 2; the first element represents the transition/transversion ratio (kappa), and the second is the "gap parameter", the factor by which substitution rates are multiplied if they involve an indel event.
“HKY85 +峡”：PARAMS应该是一个数值向量的长度为2的第一个元素表示的转换/颠换比（κ），而第二个是“差距参数”，替代率的因子相乘，如果它们涉及插入缺失事件。
"REV": params should be a numeric vector of length 6 (assuming a model with 4 states). With n states the vector should be of length n*(n-1)/2. The first parameter applies to the entry in the 1st row, 2nd column; the next to the 1st row, 3rd column, etc until the end of the first row; the next parameter applies to the 2nd row, 3rd column; etc.
“REV”：的PARAMS应该是一个数字矢量长度为6（假设一个模型4个州）。具有n个状态的向量应该是长度为n *（n-1个）/ 2。第一个参数，适用于第1行，第2列中的条目;下一个的第1行，第3列，等等，直到第一行的结束，下一个参数适用于第2行，第3列，等等
"SSREV": params should be a numeric vector of length 4. Assuming an alphabet "ACGT", the first parameter is the substitution rate from A->C, C->A, T->G, and G->T. The second is the rate from A->G, G->A, T->C, and C->T, The third is the rate from A->T and T->A, and the last is C->G and G->C.
“SSREV”：PARAMS应该是一个长度为4的数值向量。假设一个字母“ACGT”，第一个参数是替代率从A-> C，C-> A，T-> G，G-> T二是从A-> G，G-> A，T-> C，C->Ţ率，第三是速度从A-> T和T-> A，最后是C-> G和G-> C。
"UNREST": params should be a numeric vector of length n*n-n (where n is the number of states. params fills in the rate matrix starting at the first row going across, skipping diagonals.
“动荡”：的PARAMS应该是一个数值向量的长度为N * NN（其中n是状态的数量。PARAMS填充的速度矩阵的第一行开始，持续跨越，跳过对角线。
"R2": Parameters should be a numeric vector of length 48. There are 16 states in order AA, AC, AG, AT, CA, ..., TT (assuming alphabet order ACGT). Parameters are filled in starting row 1, column 2, going across and then down, filling in the matrix above the diagonal, and reflecting into the matrix below the diagonal. Only cells which represent a substitution which requires exactly one mutation are filled in; cells requiring greater than 1 mutation have rate 0.
“R2”：参数应该是一个数字矢量长度为48。有16个州为了AA，AC，AG，AT，CA，...，TT（假设字母顺序ACGT）。参数填充起始行1，列2，去跨越，然后向下，填充在上面的矩阵的对角线，并反射到下面的对角线矩阵。只有代表的替代，这需要一个突变的单元都充满在单元需要大于1的突变率为0。
"U2": Similar to R2, except parameters are a numeric vector of length 96. Parameters are filled in starting row 1, column to, going across and then down, filling entire matrix (rather than refelcting across the diagonal)
“U2”：R2类似，但参数是一个数字向量长度96。参数在开始行第1列，去跨越，再向下填充，填充整个矩阵（而不是refelcting的对角线）
"R2S": Similar to R2, but with strand symmetry. params should be a vector of length 24. Parameters are filled in a similar fashion as R2, except the same parameter applies to substitutions which are strand symmetric.
“R2S”：R2类似，但与链的对称性。 PARAMS应是长度为24的矢量。填充参数为R2以类似的方式，除了相同的参数，适用于取代的链对称。
"U2S": Similar to U2, but with strand symmetry. params should be a vector of length 48. Parameters are filled in a similar fashion as U2, except the same parameter applies to substitutions which are strand symmetric.
“U2S”：U2类似，但与链的对称性。的PARAMS应该是一个矢量的长度为48。填充参数为U2以类似的方式，除了相同的参数，适用于取代的链对称。
"R3","R3S","U3","U3S": Similar to R2, R2S, U2, and U2S, except there are 64 states instead of 16. params should be numeric vector of length 288, 148, 576, or 288, for models R3, R3S, U3, and U3S respectively.</ul>
“R3”，“R3S”，“U3”，“U3S”类似，R2，R2S，U2，U2S，除了有64个国家，而不是16。 PARAMS应该是数值向量的长度为288，148，576，或288，模型R3，R3S，U3，和U3S分别</微升>
值----------Value----------
An object of type tm with a rate matrix set according
对象类型tm设定的速度矩阵
（作者）----------Author(s)----------
Melissa J. Hubisz and Adam Siepel
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-9-28 00:05:12
