getFit(CellNOptR)
getFit()所属R语言包：CellNOptR
Compute the score of a model
模型计算的得分
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function computes the value of the objective function for a model and an associated data set, as a sum of a term that computes the fit of model to data, a term that penalises the NA values produced by the model, and a term that penalises increasing size of the model.
此函数计算模型的目标函数值和相关的数据集，作为一个术语，计算模型拟合数据，一个术语，惩罚模型所产生的NA值的总和，和术语的惩罚该模型的规模日益扩大。
用法----------Usage----------
getFit(SimResults, CNOlist, Model, indexList, timePoint = c("t1", "t2"), sizeFac = 1e-04, NAFac = 1)
参数----------Arguments----------
参数：SimResults
matrix of simulated results (the full one as output by the simulator)
矩阵模拟结果（全用模拟器的输出）
参数：CNOlist
a CNOlist to compare the simulated results with
比较模拟结果与1 CNOlist
参数：Model
a model that has already been cut to contain only the reactions in the optimal bitstring
一个模型，它已经削减到只包含在最佳位串的反应
参数：indexList
list of indexes as produced by indexFinder
作为由indexFinder产生索引列表
参数：timePoint
"t1" or "t2" tells which time point we are looking at. If timePoint=t1 then we will compare the SimResults to the results stored in CNOlist$valueSignals[[2]]. If timePoint=t1 then we will compare the SimResults to the results stored in CNOlist$valueSignals[[2]]
“T1”或“T2”告诉我们正在寻找的时间点。如果时间点= T1，然后我们将比较的结果存储在CNOlist美元valueSignals SimResults [2]。如果时间点= T1，然后我们将的SimResults进行比较的结果存储在CNOlist美元valueSignals [2]
参数：sizeFac
weights the penalty for the size of the model, default=0.0001
权重的刑罚为模型的大小，默认= 0.0001
参数：NAFac
weights the penalty for the number of NAs
NAS的数量权重的刑罚
Details
详情----------Details----------
BE AWARE: contrary to what is done in the Matlab version of CellNOpt, here the simulation results are computed beforehand and the Model that is input into this function is a model that has already been cut i.e. that only contains the reactions present in the optimised model (i.e.should be the same model as the one that you input into the simulator). Also, the SimResults matrix is the full one as output by the simulator, i.e. it contains results for all species in the model, not only the signals
注意：MATLAB版本的CellNOpt相反，这里的模拟结果预先计算，即投入此功能的模型是一个已经被切断的模式，即只包含在优化模型的反应（ieshould是一个相同的模式，你输入到模拟器）。此外，SimResults矩阵是一个模拟器输出，也就是说，它包含了模型中的所有物种的结果，不仅信号
值----------Value----------
This function returns a single number, the value of the objective function.
这个函数返回一个单数，目标函数值。
作者（S）----------Author(s)----------
C. Terfve
参考文献----------References----------
mammalian signal transduction, Molecular Systems Biology, 5:331, 2009.
参见----------See Also----------
gabinaryT1, indexFinder, simulatorT1
gabinaryT1，indexFinder，simulatorT1
举例----------Examples----------
#Here we will evaluate the fit of the full initial model, [在这里，我们将评估合适的完整的初始模型，]
#without pre-processing or any optimisation[无需预先处理或任何优化]
data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")
indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=FALSE)
ToyFields4Sim<-prep4Sim(ToyModel)
SimResults<-simulatorT1(
CNOlist=CNOlistToy,
Model=ToyModel,
SimList=ToyFields4Sim,
indexList=indicesToy)
Score<-getFit(
SimResults=SimResults,
CNOlist=CNOlistToy,
Model=ToyModel,
indexList=indicesToy,
timePoint="t1")
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。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-2-25 14:24:26
