StatFingerprints(StatFingerprints)
StatFingerprints()所属R语言包：StatFingerprints
Graphical user interface of StatFingerprints package
图形用户界面的StatFingerprints包
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A Tcl/Tk GUI to use functions of the StatFingerprints package.
一个Tcl / Tk的GUI StatFingerprints包的使用功能。
菜单栏----------Menu bar----------
The menu bar at the top of the window is used to launch all the functions of the package.<br>
在窗口顶部的菜单栏是用来发射的包的所有功能。<BR>
The Files menu is used to create, save and load a new project, and to quit R:
Files菜单用于创建，保存和加载一个新的项目，并退出ŕ：
- New project... is composed of two submenus: the first Import fingerprint profiles to import fingerprint profiles, and the second Import variables (quantitative or qualitative) to import tables of external variables. The fingerprint profiles can be imported in four different ways: i) from a folder containing FSA files obtained with an ABI Prism 310 or 3100 sequencer (choose Convert FSA files and import), ii) from a folder containing ASCII files (choose Import ASCII files), iii) from an ecological table with fingerprint profiles in rows or columns (choose Import an ecological table). These last two can read all ASCII formats, iv) from R objects already loaded in the environment (choose Import R objects).
- New project...由两个子菜单：第一Import fingerprint profiles导入指纹图谱，第二Import variables (quantitative or qualitative)导入表的外部变量。指纹图谱可以导入四种不同的方法：i）由FSA获得一个ABI PRISM 310或3100的音序器（选择Convert FSA files and import），II）的文件从一个文件夹，其中包含ASCII文件（选择一个文件夹，其中包含<X >），三）从生态的表行或列中的指纹图谱（选择Import ASCII files“）。最后两个可以读取所有ASCII格式，IV）从R对象已经加载的环境中（选择Import an ecological table）。
- Load project is used to import a StatFingerprints project previously saved as an Rdata file.
- Load project·是用来导入一个StatFingerprints项目以前保存为一个RDATA文件。
- Save project as... is used to save a StatFingerprints project in a specific directory. The project is saved as an Rdata file.
- Save project as...·是用来保存一个StatFingerprints项目在一个特定的目录。该项目保存的的RDATA文件的。
- Quit R opens a dialog window asking whether the environment should be saved before quitting R.
- Quit R·打开一个对话窗口，询问环境是否应该被保存在退出之前R.
The Edit menu is used to rename, add or delete fingerprint profiles of the project:
Edit菜单是用来重命名，添加或删除指纹图谱的项目：
- Change names of fingerprint profiles renames the name of the fingerprint profiles in the current project.
- Change names of fingerprint profiles的名称重命名在当前项目中的指纹图谱。
- Add fingerprint profiles to the project adds new fingerprint profiles within the current project. The new fingerprint profiles must be first processed in another new project and then this new project is merged with the current project.
- Add fingerprint profiles to the project·在当前项目中增加了新的指纹图谱。在另一个新项目，新的指纹图谱必须先处理，然后这个新项目的合并与当前项目。
- Delete fingerprint profiles in the project deletes fingerprint profiles in the current project.
- Delete fingerprint profiles in the project在当前项目中删除指纹图谱。
- Select fingerprint profiles using levels of factors offers the possibility of selecting several fingerprint profiles in the current project corresponding to one or more levels of a factor.<br>
- Select fingerprint profiles using levels of factors·提供当前项目中的相应的一个或多个级别的一个因素选择多个指纹图谱的可能性。<br>物理化学学报
The Fingerprint profiles processing menu includes all functionalities required to process the fingerprint profiles. The fingerprint profiles must be processed before statistical analyses to make them comparable.
Fingerprint profiles processing菜单包括处理指纹图谱所需的所有功能。指纹图谱的统计分析之前，必须处理，使它们相媲美。
- Step 1: define standard is needed to define the peaks of the reference standard on which fingerprint profiles will be aligned together using the Align fingerprint profiles one by one function. The x-values of each peak of the reference standard can be either manually entered using Define peaks of your own standard or automatically selected from a file named Rox.ref and located in the StatFingerprints library folder with the Use peaks of ROX define in the Rox.ref filefunction.
- Step 1: define standard·峰的参考标准指纹图谱将被排列在一起，使用Align fingerprint profiles one by one功能的定义。 X值各峰的参考标准可以是手动输入使用Define peaks of your own standard或自动选择从一个命名Rox.ref的文件和库文件夹在StatFingerprintsUse peaks of ROX define in the Rox.ref file功能。
- Step 2: align fingerprint profiles to the standard firstly allows the fingerprint profiles to be aligned one by one using the Align fingerprint profiles one by one function and secondly to check the alignment using Option: Check quality of alignment.
- Step 2: align fingerprint profiles to the standard首先允许的指纹图谱，以检查是否对齐，使用Align fingerprint profiles one by oneOption: Check quality of alignment函数和第二一致的。
- Step 3: define a common baseline for all fingerprint profiles is used to homogenise and reorientate the baseline between fingerprint profiles on a horizontal axis.
- Step 3: define a common baseline for all fingerprint profiles·是用于均质化和重新定位的基线之间的水平轴线上的指纹图谱。
- Step 4: define the range of the fingerprint profiles allows just the section where the community appears to be selected by deleting extremities of the fingerprint profiles.
- Step 4: define the range of the fingerprint profiles·仅允许部分社会选择删除的指纹图谱四肢。
- Option: Rebuild peaks of fingerprint profiles presenting defects is used to redesign a peak presenting a defect into a fingerprint profile.
- Option: Rebuild peaks of fingerprint profiles presenting defects·使用重新设计的缺陷的一个指纹图谱的高峰。
- Step 5: normalise area under fingerprint profiles is used to normalise the area under each fingerprint profile so that the area under a signal is equal to one. Three different algorithms are available to deal with minimum and negative values.
- Step 5: normalise area under fingerprint profiles被用于每个指纹档案标准化下的面积，使得该区域的信号下，等于一。三种不同的算法可用来处理，与极小值和负值。
- Option: Delete backgrounds under fingerprint profiles can be used to deletebackground under fingerprint profile.
- Option: Delete backgrounds under fingerprint profiles·可以使用来deletebackground的指纹图谱。
- Option: Transform profiles into presence/absence profiles allows quantitative fingerprint profiles to be transformed into binary fingerprint profiles so that areas with and without peaks are respectively equal to one and zero.<br>
- Option: Transform profiles into presence/absence profiles允许定量指纹图谱二进制指纹图谱，使转化的区域与无峰分别等于1和零。<br>物理化学学报
The Plot menu includes all functionalities to plot the fingerprint profiles of the project and the ordination graphs:
Plot菜单中包含的所有功能指纹图谱绘制的项目和统筹图：
- Plot fingerprint profiles is used to plot one or several fingerprint profiles in two dimensions or the entire set of fingerprint profiles in three dimensions for any processing step of the fingerprint profiles.
- Plot fingerprint profiles·用来绘制在两个维度或整个组的指纹的档案指纹图谱的处理步骤，在三维空间中的任何一个或几个的指纹公司。
- Plot saved nMDS/PCA: advanced tools plots previously calculated non-Metric Multidimensional Scaling (nMDS) and Principal Components Analysis (PCA) in a 2- or 3-dimensional display. PCA and nMDS are plotted with coloured points according to a factor and/or with contour lines coming from a quantitative variable.<br>
- Plot saved nMDS/PCA: advanced tools图2 - 或3维显示先前计算的非度量多维标度（NMDS）和主成分分析（PCA）。 PCA和NMDS绘制根据的因素和/或与来自一个定量变量的轮廓线与彩色点。<br>物理化学学报
- Two-way factor plot is used to plot one quantitative variable against one or two qualitative variables. Four kind of plot are available: points, points and line, boxplot and histogram.
- Two-way factor plot是用来绘制一个定量变量对一个或两个定性变量。四种图有：点，点，线，箱线图和柱状图。
The Univariate statistic: diversity index menu can be used both to estimate diversity indexes and to compute basic univariate statistics. It illustrates the effect of factors or external parameters on the diversity of the community.
Univariate statistic: diversity index菜单可用于估计多样性指数和计算基础的单变量统计。它说明了社会的多样性的因素或外部参数的影响。
- Compute diversity index allows various diversity indexes to be estimated.
- Compute diversity index·允许的各种多样性指数估计。
- Descriptive statistic calculates the arithmetic mean and standard deviation of diversity indexes or imported quantitative variables.
- Descriptive statistic·计算的算术平均值和标准偏差的多样性指数或进口定量变量。
- Multifactor ANOVA displays summary results of multifactor ANOVA using a diversity index or imported quantitative variables as the variable to be explained and one or more imported qualitative variables as explanatory variables.
- Multifactor ANOVA多样性指数或进口定量变量的变量来解释和一个或更多的进口定性变量作为解释变量多因素方差分析结果显示摘要。
- Simple correlation computes a simple correlation using a Pearson algorithm between two quantitative variables (diversity index or imported quantitative variable). This function returns the Pearson R-squared, its associated p value and the first degree regression coefficient.<br>
- Simple correlation·计算一个简单的相关性使用皮尔逊算法的两个定量变量（多样性指数或进口定量变量）之间。这个函数返回的Pearson R-平方，其相关的p值和的第一学位回归系数。<BR>
The Multivariate statistic: structure menu is composed of exploratory statistical methods and multivariate statistical tests. It allows the similarity between fingerprint profiles to be explored, to test the effect of a factor along the fingerprint profiles and to assess the relationship between the structure of the community and external parameters.
Multivariate statistic: structure菜单是由探索性的统计方法和多元统计检验。它允许指纹图谱之间的相似性进行探讨，以测试效果的一个因素，沿指纹图谱，并评估社会的结构和外部参数之间的关系。
- Non-Metric multiDimensional Scaling (nMDS) computes iterative nMDS and keeps the best one, i.e. that with the lowest value of the Kruskal stress.
- Non-Metric multiDimensional Scaling (nMDS)计算迭代的基本数据，并保持最好的一个，即：克鲁斯卡尔压力的最低值。
- Principal Components Analysis (PCA) computes PCA, optionally centred and or scaled.
- Principal Components Analysis (PCA)·计算PCA，可以选择中心或缩放。
- Compare PCA vs nMDS compares PCA and nMDS by calculating the Pearson R squared between the initial distances and the new distances computed by the two ordination methods.
- Compare PCA vs nMDS·比较PCA和NMDS计算的Pearson R平方之间的初始距离和新的协调方法计算距离。
- Hierarchical clustering displays a dendrogram. Several proximity indexes and dendrogram algorithms are proposed.
- Hierarchical clustering·显示一个树状图。几个的接近指标和聚类分析算法被提出。
- Heatmap displays a coloured heatmap based on hierarchical clustering.
- Heatmap·显示基于层次聚类的彩色热图。
- Multivariate ANOVA (50 50 F test and rotation) computes general linear modelling of one or more qualitative variables with the fingerprint profile set.
- Multivariate ANOVA (50 50 F test and rotation)·计算一般线性模型的一个或多个定性变量的指纹图谱集。
- ANalysis Of SIMilarity (ANOSIM) tests whether there is a significant difference between two or more groups of fingerprint profiles. Groups of fingerprint profiles are designed according to the levels of a qualitative variable with the Global ANOSIM: test effect of factor function or to each pair of levels within a factor with the Pairwise ANOSIM: test effect of levels within factor function.
- ANalysis Of SIMilarity (ANOSIM)测试是否有显着区别两个或两个以上的基团的指纹图谱。根据水平的定性变量与Global ANOSIM: test effect of factor函数或内因子水平与Pairwise ANOSIM: test effect of levels within factor函数到每个对设计组指纹图谱。
- Within group variability calculates within each group the variability between all fingerprint profiles and tests whether these variabilities are significantly different. Groups are designed according to the levels of a factor.
- Within group variability计算各组内的所有指纹图谱和测试之间的变异，这些变异是显着不同的。组的设计根据的一个因素的水平。
- SIMilarity PERcentages procedure (SIMPER) calculates the relative contribution of each variable of the fingerprint profiles to the total dissimilarity (measure by a proximity index) between two groups of fingerprint profiles. The two groups are designed according to the levels of a factor. It is a simple method for assessing which areas along the fingerprint profiles are primarily responsible for an observed difference between the two groups.
- SIMilarity PERcentages procedure (SIMPER)·计算每一个变量的指纹图谱的两组指纹图谱的的总差异性（接近指数衡量）之间的相对贡献。这两个群体设计的水平的一个因素。这是一个简单的方法来评估哪些区域沿指纹图谱主要是负责观察到两组之间的差异。
- Iterative tests (ANOVA,Mann Whitney,Fisher s exact) tests the significant differences of each variable along the fingerprint profile between two groups. The test used is the t test, the Mann Whitney test or the Fisher s exact test. The two groups are designed according to the levels of a factor. Consequently it allows assessing which areas of the fingerprint profiles are significantly responsible for the difference observed between the two groups.
- Iterative tests (ANOVA,Mann Whitney,Fisher s exact)·测试每个变量的显着差异，两组间的指纹图谱。测试使用的是经t检验，Mann Whitney检验或费舍尔的确切的测试。这两个群体设计的水平的一个因素。因此，可以评估哪些领域的指纹图谱是两组之间的差异显着负责。
- Multivariate correlation (50 50 F test and rotation) is used to test the relationship between the structure of the fingerprint profile set and an imported quantitative variable.
- Multivariate correlation (50 50 F test and rotation)·是用来测试的指纹图谱集和导入的定量变量的结构之间的关系。
- Redundancy analysis (RDA) is related to principal component analysis. It is based on Euclidean distances and perform linear mapping.
- Redundancy analysis (RDA)·主成分分析。它是基于欧几里德距离，并进行线性映射。
- Constrained Correspondance Analysis (cca) is related to correspondance analysis. It is based on Chi-squared distances and performs weighted linear mapping.
- Constrained Correspondance Analysis (cca)·相关的信函分析。它是基于卡方距离，并进行加权的线性映射。
- Constrained Analysis of Proximities (cap) is related to metric scaling (cmdscale). It can handle any dissimilarity measures and performs a linear mapping.
- Constrained Analysis of Proximities (cap)·有关为公制的的缩放（cmdscale）。它可以处理任何的相异措施和执行的线性映射。
The Help menu contains the user guide manual, an on line help, the most recent version of the present program and the bugs report.
Help菜单包含用户指南手册，在线帮助，本程序的错误报告的最新版本。
（作者）----------Author(s)----------
Rory Michelland <a href="mailto:rory.michelland@gmail.com">rory.michelland@gmail.com</a><br>
Laurent Cauquil <a href="mailto:laurent.cauquil@toulouse.inra.fr">laurent.cauquil@toulouse.inra.fr</a>
实例----------Examples----------
## Not run: [＃不运行：]
## One of these lines allows the StatFingerprints program to be started[这些线之一允许的StatFingerprints程序要启动]
StatFingerprints()
sf()
## End(Not run)[＃（不执行）]
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。
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发表于 2012-9-30 17:17:49
