mark(RMark)
mark()所属R语言包：RMark
Interface to MARK for fitting capture-recapture models
接口大关，配件捕获 - 再捕获模型
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Fits user specified models to various types of capture-recapture data by creating input file and running MARK software and retrieving output
适合用户指定的模式来捕获 - 再捕获数据的不同类型的创建输入文件并运行MARK软件和检索输出
用法----------Usage----------
mark(data, ddl = NULL, begin.time = 1, model.name = NULL,
model = "CJS", title = "", model.parameters = list(),
initial = NULL, design.parameters = list(),
right = TRUE, groups = NULL, age.var = NULL,
initial.ages = 0, age.unit = 1, time.intervals = NULL,
nocc = NULL, output = TRUE, invisible = TRUE,
adjust = TRUE, mixtures = 1, se = FALSE,
filename = NULL, prefix = "mark", default.fixed = TRUE,
silent = FALSE, retry = 0, options = NULL,
brief = FALSE, realvcv = FALSE, delete = FALSE,
external = FALSE, profile.int = FALSE, chat = NULL,
reverse = FALSE, run = TRUE, input.links = NULL,
parm.specific = FALSE, mlogit0 = FALSE, threads = -1,
hessian = FALSE)
参数----------Arguments----------
参数：data
Either the raw data which is a dataframe with at least one column named ch (a character field containing the capture history) or a processed dataframe
无论是原始数据，这是一个与至少一个列的数据框名为通道（一个字符字段包含捕获历史）或处理的数据框
参数：ddl
Design data list which contains a list element for each parameter type; if NULL it is created
设计数据列表，其中包含的每个参数类型的列表元素;创建它，如果NULL
参数：begin.time
Time of first capture(release) occasion
时间第一次捕捉（释放）的场合
参数：model.name
Optional name for the model
可选的名称为模型
参数：model
Type of c-r model (eg CJS, Burnham, Barker)
类型C-R模型（如CJS，伯纳姆，巴克）
参数：title
Optional title for the MARK analysis output
可选的标题的MARK分析的输出
参数：model.parameters
List of model parameter specifications
的模型参数规格列表
参数：initial
Optional vector of named or unnamed initial values for beta parameters or previously run model object
可选向量的有名或无名的测试参数的初始值或以前运行的模型对象
参数：design.parameters
Specification of any grouping variables for design data for each parameter
每个参数的任何设计数据分组变量规范
参数：right
if TRUE, any intervals created in design.parameters are closed on the right and open on left and vice-versa if FALSE
如果是TRUE，任何的时间间隔中创建design.parameters的关闭和开放的左，反之亦然，如果为FALSE
参数：groups
Vector of names factor variables for creating groups
创建组的名字因子变量的向量
参数：age.var
Optional index in groups vector of a variable that represents age
向量的一个变量，代表年龄组的可选指数
参数：initial.ages
Optional vector of initial ages for each age level
可选向量的初始年龄为各个年龄层
参数：age.unit
Increment of age for each increment of time
对每个增量的时间增量的年龄
参数：time.intervals
Intervals of time between the capture occasions
之间的时间间隔捕获的场合
参数：nocc
number of occasions for Nest model; either time.intervals or nocc must be specified for this model
这种模式必须指定的鸟巢模型的场合，无论是time.intervals或NOCC
参数：output
If TRUE produces summary of model input and model output
如果是TRUE模型输入和输出模式生成汇总
参数：invisible
If TRUE, window for running MARK is hidden
如果是TRUE，窗口运行MARK隐藏
参数：adjust
If TRUE, adjusts npar to number of cols in design matrix, modifies AIC and records both
如果是TRUE，调整的Npar设计矩阵的列数，修改AIC，并同时记录
参数：mixtures
number of mixtures for heterogeneity model
的异质性模型的混合物
参数：se
if TRUE, se and confidence intervals are shown in summary sent to screen
如果为TRUE，SE和置信区间是在总结发送到屏幕
参数：filename
base filename for files created by MARK.EXE. Files are named filename.*.
碱基的MARK.EXE创建的文件的文件名。被命名文件的文件名。*。
参数：prefix
base filename prefix for files created by MARK.EXE; for example if prefix="SpeciesZ" files are named "SpeciesZnnn.*"
碱基的MARK.EXE创建的文件的文件名前缀，例如，如果前缀=“SpeciesZ”的文件被命名为“SpeciesZnnn。”
参数：default.fixed
if TRUE, real parameters for which the design data have been deleted are fixed to default values
如果为TRUE，该设计数据已被删除的实参数被固定为默认值
参数：silent
if TRUE, errors that are encountered are suppressed
如果为TRUE，所遇到的错误被抑制
参数：retry
number of reanalyses to perform with new starting values when one or more parameters are singular
执行新的起点值时，一个或多个参数奇异的再分析
参数：options
character string of options for Proc Estimate statement in MARK .inp file
MARK。inp文件中的：PROC估计声明的字符串
参数：brief
if TRUE and output=TRUE then a brief summary line is given instead of a full summary for the model
如果为true，输出= TRUE，那么一个简短的摘要行是给定的，而不是一个完整的模型总结
参数：realvcv
if TRUE the vcv matrix of the real parameters is extracted and stored in the model results
如果为TRUE VCV的真实参数的矩阵模型的结果中提取并存储在
参数：delete
if TRUE the output files are deleted after the results are extracted
如果为true，输出文件被删除后的结果中提取
参数：external
if TRUE the mark object is saved externally rather than in the workspace; the filename is kept in its place
如果为true，标记对象被保存在外部，而不是在工作区中的文件名保持在其位置
参数：profile.int
if TRUE will compute profile intervals for each real parameter; or you can specify a vector of real parameter indices
如果为TRUE将计算的实际参数为每个配置文件的时间间隔;或者您也可以指定一个向量的实际参数指标
参数：chat
value of chat used for profile intervals
使用配置文件的时间间隔值的聊天
参数：reverse
if set to TRUE, will reverse timing of transition (Psi) and survival (S) in Multistratum models
如果设置为TRUE，将扭转时间的过渡（PSI）和存活率（S），多段模型
参数：run
if FALSE does not run model after creation
如果为FALSE模型创建后不运行
参数：input.links
specifies set of link functions for parameters with non-simplified structure
指定的链接功能设置的参数与非简化结构
参数：parm.specific
if TRUE, forces a link to be specified for each parameter
如果为真，为每个参数指定的链接
参数：mlogit0
if TRUE, any real parameter that is fixed to 0 and has an mlogit link will have its link changed to logit so it can be simplified
如果为TRUE，任何真正的参数，该参数被固定为0，并具有一个mlogit链路将其链接改为罗吉特，以便它可以简化
参数：threads
number of cpus to use with mark.exe if positive or number of cpus to remain idle if negative
数量的CPU使用与mark.exe，如为正数或CPU的数量保持空闲状态，如果负
参数：hessian
if TRUE specifies to MARK to use hessian rather than second partial matrix
如果是TRUE指定标志的使用麻袋，而不是第二部分矩阵
Details
详细信息----------Details----------
This function acts as an interface to the FORTRAN program MARK written by Gary White (http://www.cnr.colostate.edu/~gwhite/mark/mark.htm). It creates the input file for MARK based on user-specified sub-models (model.parameters) for each of the parameters in the capture-recapture model being fitted to the data. It runs MARK.EXE (see note below) and then imports the text output file and binary variance-covariance file that were created. It extracts output values from the text file and creates a list of results that is returned as part of the list (of class mark) which is the return value for this function.
此功能作为一个接口，FORTRAN程序MARK，写，加里·白“（http://www.cnr.colostate.edu/~gwhite /标记/ mark.htm的）。它创建的输入文件MARK根据用户指定的子模型（model.parameters）中的每一个参数的捕获 - 再捕获模型的拟合数据。它运行MARK.EXE（看到下面的注释），然后输入输出的文本文件和二进制文件，方差 - 协方差。从文本文件中提取的输出值，并创建一个（标志类），这个函数的返回值的列表的一部分返回的结果列表。
The following are the MARK capture-recapture models that are currently supported for argument model:
以下是MARK捕获 - 再捕获模式，目前支持的参数model：
The function mark is a shell that calls 5 other functions in the following order as needed: 1) process.data, 2) make.design.data, 3) make.mark.model, 4) run.mark.model, and 5) summary.mark. A MARK model can be fitted with this function (mark) or by calling the individual functions that it uses. The calling arguments for mark are a compilation of the calling arguments for each of the functions it calls (with some arguments renamed to avoid conflicts). If data is a processed dataframe (see process.data) then it expects to find a value for ddl. Likewise, if the data have not been processed, then ddl should be NULL. This dual calling structure allows either a single call approach for each model or alternatively for the data to be processed and the design data (ddl) to be created once and then a whole series of models can be analyzed without repeating those steps.
功能标记是一个shell，它需要调用其他5个功能按以下顺序：1）process.data，2）make.design.data的，3）make.mark.model的，4）run.mark.model的，和5）summary.mark。可以安装此功能（mark）或通过调用单独的功能，它使用一个标记模式。调用参数为mark是一个汇编调用参数的功能调用一些参数改名为避免冲突。如果数据是一个处理数据框（见process.data），然后它希望找到一个值ddl。同样地，如果数据没有被处理，然后ddl应该是NULL。这种双重致电结构允许一个呼叫的方法为每个模型，或者为要被处理的数据和设计数据（ddl）来创建一次，然后不重复这些步骤的情况下，可以分析整个系列的车型。
For descriptions of the arguments data, begin.time, groups, age.var, initial.ages, age.unit, time.intervals and mixtures see process.data.
有关的参数说明data，begin.time，groups，age.var，initial.ages，age.unit，time.intervals和<X >看mixtures。
For descriptions of ddl, design.parameters=parameters, and right, see make.design.data.
的说明，ddl，design.parameters=parameters，right，看到make.design.data。
For descriptions of model.name , model, title,model.parameters=parameters , default.fixed , initial, options, see make.mark.model.
描述model.name，model，title，model.parameters=parameters，default.fixed，initial，options ，请参阅make.mark.model。
And finally, for descriptions of arguments invisible, filename and adjust,see run.mark.model.
最后的参数的描述invisible，filename和adjust，看到run.mark.model。
output,silent, and retry are the only arguments specific to mark. output controls whether a summary of the model input and output are given(if output=TRUE). silent controls whether errors are shown when fitting a model. retry controls the number of times a model will be refitted with new starting values (uses 0) when some parameters are determined to be non-estimable or at a boundary. The latter is the only time it makes sense to retry with new starting values but MARK cannot discern between these two instances. The indices of the beta parameters that are "singular" are stored in results$singular.
output，silent和retry是特定标志的唯一参数。如果output控制是否总结了模型的输入和输出（output=TRUE）。 silent控制是否有错误时显示拟合模型。 retry控制模型将被改装的一些参数被确定为非可估计或的边界处时，与新的起点值（使用0）的次数。后者是唯一的一次，是有意义的重试，使用新的起点值，但的MARK无法辨别这两个实例之间。该指数的“奇异”的测试参数，这些参数都存储在results$singular。
值----------Value----------
model: a MARK object containing output and extracted results. It is a list with the following elements
产品型号：A MARK对象包含输出和提取的结果。这是一个包含下列元素的列表
参数：data
name of the processed data frame
所处理的数据框的名称
参数：model
type of analysis model (see list above)
类型分析模型（见上面的列表）
参数：title
title used for analysis
标题用于分析
参数：model.name
descriptive name of model
模型的描述性名称
参数：links
vector of link function(s) used for parameters, one for each row in design matrix or only one if all parameters use the same function
一个设计矩阵中的每一行或只有一个参数，如果使用的所有参数使用相同的功能向量的连接功能（S）
参数：mixtures
number of mixtures in Pledger-style closed capture-recapture models <tr valign="top"><td>call</td>
质风格的混合物在封闭的捕获 - 再捕获模型<tr valign="top"> <TD> call</ TD>
call to make.mark.model used to construct the model
打检测给make.mark.model用于构建模型
参数：parameters
a list of parameter descriptions including the formula, pim.type, link etc.
的的公式，pim.type，链接等的列表的参数的描述，包括
参数：model.parameters
the list of parameter descriptions used in the call to mark; this is used only by rerun.mark <tr valign="top"><td>time.intervals</td>
的列表，在调用中使用的参数说明，以纪念这仅用于rerun.mark<tr valign="top"> <TD> time.intervals</ TD>
Intervals of time between the capture occasions
之间的时间间隔捕获的场合
参数：number.of.groups
number of groups defined in the data <tr valign="top"><td>group.labels</td>
组数中定义的数据<tr valign="top"> <TD> group.labels</ TD>
vector of labels for the groups <tr valign="top"><td>nocc</td>
矢量标签的组<tr valign="top"> <TD> nocc</ TD>
number of capture occasions
数捕获的场合
参数：begin.time
single time of vector of times (if different for groups) for the first capture occasion
单次的矢量次（如果不同的团体）第一次捕捉机会
参数：covariates
vector of covariate names (as strings) used in the model <tr valign="top"><td>fixed</td>
矢量模型中的协变量的名称（字符串）<tr valign="top"> <TD>fixed</ TD>
dataframe of parameters set at fixed values; index is the parameter index in the full parameter structure and value is the fixed value for the real parameter
数据框设置为固定值的参数，“index是完整的参数结构和参数指标value是真正的参数的固定值
参数：design.matrix
design matrix used in the input to MARK.EXE <tr valign="top"><td>pims</td>
设计矩阵的输入MARK.EXE <tr valign="top"> <TD>pims</ TD>
list of pims used for each parameter including any group or strata designations; each parameter in list is denoted by name and within each parameter one or more sub-lists represent groups and strata if any <tr valign="top"><td>design.data</td>
PIMS用于包括任何一组或地层指定每个参数的列表，在列表中的每个参数的名称和表示每个参数的一个或多个子列表内如果任何<tr valign="top"> <TD>代表群体和阶层design.data</ TD>
design data used to construct the design matrix <tr valign="top"><td>strata.labels</td>
设计数据用于构造设计矩阵<tr valign="top"> <TD>strata.labels</ TD>
labels for strata if any <tr valign="top"><td>mlogit.list</td>
层标签，如果任何<tr valign="top"> <TD> mlogit.list</ TD>
structure used to simplify parameters that use mlogit links
简化的参数使用mlogit链接结构来
参数：simplify
list containing pim.translation which translate between all different and simplified pims, real.labels which are labels for real parameters for full (non-simplified) pim structure and links the link function names for the full parameter structure <tr valign="top"><td>output</td>
列表，其中包含pim.translation之间的转换各种不同的和简化的PIMS，real.labels完整（非简化的实际参数标签）PIM结构和links的链接功能名称的所有参数结构<tr valign="top"> <TD> output</ TD>
base portion of filenames for input,output, vc and residual files output from MARK.EXE <tr valign="top"><td>results</td>
底座部分的文件名，输入，输出，VC和残留文件输出MARK.EXE <tr valign="top"> <TD>results</ TD>
List of values extracted from MARK ouput </table>
列表中提取的值MARK输出功率</ TABLE>
参数：chat
over-dispersion constant; if not present assumed to be 1
过度分散常数，如果不存在，假定为1
注意----------Note----------
It is assumed that MARK.EXE is located in directory "C:/Program Files/Mark". If it is in a different location set the variable MarkPath to the directory location. For example, seting MarkPath="C:/Mark/" at the R prompt will assign run "c:/mark/mark.exe" to do the analysis. If you have chosen a non-default path for Mark.exe, MarkPath needs to be defined for each R session. It is easiest to do this assignment automatically by putting the MarkPath assignment into your .First function which is run each time an R session is initiated. In addition to MarkPath, the variable MarkViewer can be assigned to a program other than notepad.exe (see print.mark).
据推测，的MARK.EXE位于在目录“C :/ Program Files文件/标记”。如果它是在一个不同的位置设置的可变MarkPath的目录位置。例如，SETING MarkPath =“C :/马克/”在R提示符下将分配运行“C :/标记/ mark.exe的”做了分析。如果你已经选择了非默认路径Mark.exe的，MarkPath需要定义每个R会话。这是最简单的自动做这个作业，到您把MarkPath分配。每次运行R会话启动的第一个功能。在除了MarkPath，可变MarkViewer可以被分配到的程序以外的notepad.exe（见print.mark）。
（作者）----------Author(s)----------
Jeff Laake
参见----------See Also----------
make.mark.model, run.mark.model, make.design.data, process.data, summary.mark
make.mark.model，run.mark.model，make.design.data，process.data，summary.mark
实例----------Examples----------
data(dipper)
dipper.Phidot.pdot=mark(dipper)
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。
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发表于 2012-9-26 23:44:05
