sim.capthist(secr)
sim.capthist()所属R语言包：secr
Simulate Detection Histories
模拟检测历史
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Create a set of capture or marking-and-resighting histories by simulated sampling of a 2-D population using an array of detectors.
创建组捕捉或标记和resighting历史的人口的2-D的模拟采样使用一个探测器阵列。
用法----------Usage----------
sim.capthist(traps, popn = list(D = 5, buffer = 100,
Ndist = "poisson"), detectfn = 0, detectpar = list(),
noccasions = 5, nsessions = 1, binomN = NULL,
p.available = 1, renumber = TRUE, seed = NULL,
maxperpoly = 100)
sim.resight(traps, ..., q = 1, pID = 1, unmarked = TRUE,
nonID = TRUE)
参数----------Arguments----------
参数：traps
traps object with the locations and other attributes of detectors
traps对象的位置和其他属性探测器
参数：popn
locations of individuals in the population to be sampled, either as a popn object or a list with named components "D" (density) and "buffer"
个人在人群中的位置进行采样，无论是作为一个popn对象或列表的命名组件D（密度）和“缓冲”
参数：detectfn
integer code or character string for shape of detection function 0 = halfnormal etc. – see detectfn
的整数代码或字符串检测功能0 = halfnormal等形状 - detectfn
参数：detectpar
list of values for named parameters of detection function
检测功能命名参数的值列表
参数：noccasions
number of occasions to simulate
先后多次模拟
参数：nsessions
number of sessions to simulate
的会话数来模拟
参数：binomN
integer code for distribution of counts (see Details)
分布计数的整数代码（见详情）
参数：p.available
vector of one or two probabilities (see Details)
向量中的一个或两个的概率（见详情）
参数：renumber
logical for whether output rows should labeled sequentially (TRUE) or retain the numbering of the population from which they were drawn (FALSE)
逻辑输出行应否顺序标记（TRUE）或保留编号的人口，他们被画（FALSE）
参数：seed
an object specifying if and how the random number generator should be initialized ("seeded")
对象确定是否以及如何应被初始化随机数发生器（种子）
参数：maxperpoly
integer maximum number of detections of an individual in one polygon or transect on any occasion
一个人在一个多边形或在任何场合样的检测整数的最大数量
参数：...
arguments to pass to sim.capthist
参数传递给sim.capthist
参数：q
number of marking occasions
一些标记的场合
参数：pID
probability of individual identification for marked animals
有标记的动物个体识别概率
参数：unmarked
logical, if true unmarked individuals are not recorded during "sighting"
逻辑，如果真正的无人盯防的个人不会被记录在“瞄准”
参数：nonID
logical, if true then unidentified marked individuals are not recorded during "sighting"
的逻辑，如果属实，则身份不明的标记不会被记录在个人“瞄准”
Details
详细信息----------Details----------
If popn is not of class "popn" then a homogeneous Poisson population with the desired density (animals/ha) is first simulated over the rectangular area of the bounding box of traps plus a buffer of the requested width (metres). The detection algorithm depends on the detector type of traps. For "proximity" detectors, the actual detection probability of animal i at detector j is the naive probability given by the detection function. For "single" and "multi" detectors the naive probability is modified by competition between detectors and, in the case of "single" detectors, between animals. See Efford (2004) and other papers below for details.
如果popn是不是类的popn“，然后在矩形区域的边界框的traps加的缓冲区所需要的密度（动物/公顷）是一个齐次泊松人口的模拟，要求宽度（米）。的检测算法依赖于检测器类型的traps。 “接近性”探测器的检测功能，实际检测的动物，我在探测器Ĵ的概率是天真的概率。对于“单”和“多”探测器天真的概率被修改在探测器之间的竞争，在箱子“单”探测器，动物之间。 Efford（2004）和其他文件，下面的细节。
Detection parameters in detectpar are specific to the detection function, which is indicated by a numeric code (detectfn). Parameters may vary with time - for this provide a vector of length noccasions. The default detection parameters are list(g0 = 0.2, sigma = 25, z = 1).
检测参数在detectpar特定的检测功能，这是一个数字代码（detectfn）表示。参数可能会随时间而改变 - 这提供了一个矢量的长度noccasions。默认的检测参数list(g0 = 0.2, sigma = 25, z = 1)。
The default is to simulate a single session. This may be overridden by providing a list of populations to sample (argument popn) or by specifying nsessions > 1 (if both then the number of sessions must match). Using nsessions > 1 results in replicate samples of populations with the same density etc. as specified directly in the popn argument.
默认值是模拟一个会话。这可能是所覆盖的人群提供一个列表来样（参数popn）或通过指定nsessions> 1（如果两者的会话数必须匹配）。使用nsessions> 1的结果在复制的样品具有相同的人口密度等，直接指定popn参数。
binomN determines the statistical distribution of the number of detections of an individual at a particular "count" detector or polygon on a particular occasion. A Poisson distribution is indicated by binomN = 0; see secr.fit for more. The distribution is always Bernoulli (binary) for "proximity" and "signal" detectors.
p.available specifies temporary non-availability for detection in multi-session simulations. If a single probability is specified then temporary non-availability is random (independent from session to session). If two probabilities are given then non-availability is Markovian (dependent on previous state) and the two values are for animals available and not available at the preceding session. In the Markovian case, availability in the first session is assigned at random according to the equilibrium probability p2 / (1 - p1 + p2). Incomplete availability is not implemented for sampling lists of populations.
p.available非可指定临时在多届模拟检测。如果指定一个单一的概率，则暂时不可用性是随机的（独立的会话中）。如果两个概率给出，那么不可用性是马尔可夫（依赖于先前的状态），这两个值是在前述会议的可用和不可用的动物。在马氏的情况下，第一届会议的情况在随机分配的平衡概率P2 /（1 - P1 + P2）。不完整的情况不实施人口抽样列表。
detectpar may include a component "truncate" for the distance beyond which detection probability is set to zero. By default this value is NULL (no specific limit).
detectpar可以包括一个组件的截断超出检测概率的距离被设置为零。默认情况下，这个值是NULL（无特定限制）。
If popn is specified by an object of class "popn" then any individual covariates will be passed on; the covariates attribute of the output is otherwise set to NULL.
如果popn指定的对象类的POPN“，那么任何个人的协变量将通过对covariates属性的输出，否则设置为NULL。
The random number seed is managed as in simulate.
随机数种子管理作为在simulate。
sim.resight generates mark-resight data for "q" marking occasions followed by "noccasions – q" sighting occasions. sim.capthist is first called with the arguments "traps" and .... The detector type must be "proximity". The "usage" attribute of traps is ignored at present, so the same detectors are operated on all occasions. Any detection-parameter vector of length 2 in ... is interpreted as providing differing constant values for the marking and sighting phases.
sim.resight产生的标记resight数据为“Q”标识的场合，其次是“noccasions - Q瞄准场合。 sim.capthist是第一个被称为与参数“陷阱”，...该探测器的类型必须是“接近性”。 使用属性traps目前被忽略，所以同样的探测器运行在所有场合。任何检测参数矢量的长度为2 ...被解释为提供不同的常数值的标记和瞄准阶段。
值----------Value----------
For sim.capthist, an object of class capthist, a matrix or 3-dimensional array with additional attributes. Rows represent individuals and columns represent occasions; the third dimension, used when detector type = "proximity", codes presence or absence at each detector. For trap detectors ("single", "multi") each entry in capthist is either zero (no detection) or the sequence number of the trap.
对于sim.capthist，类的一个对象capthist，具有附加属性的矩阵或三维阵列。行代表个人和列代表的场合;第三个层面，使用=“接近”，代码存在或不存在于每个探测器时，探测器类型。对于的陷阱探测器（单，多）中的每个条目capthist要么是零（没有检测）或序列号的陷阱。
The initial state of the R random number generator is stored in the "seed" attribute.
的R的随机数发生器的初始状态被存储在“种子”的属性。
For sim.resight, an object of class capthist, always a 3-dimensional array, with additional attributes Tu and Tm containing counts of "unmarked" and "marked, not identified" sightings.
对于sim.resight，类的一个对象capthist，总是一个3维的数组，附加属性涂和Tm计数的“无标记的”和“显着的，没有确定的踪迹。
注意----------Note----------
External code is called to speed the simulations. The present version assumes a null model, i.e., naive detection probability is constant except for effects of distance and possibly time (using vector-valued detection parameters from 1.2.10). You can, however, use rbind.capthist to combine detections of population subclasses (e.g. males and females) simulated with different parameter values. This is not valid for detector type "single" because it fails to allow for competition for traps between subclasses. Future versions may allow more complex models.
调用外部代码，以加快模拟。本版本假定一个空的模式，即，天真的检测概率是恒定的距离，并可能影响时间（采用矢量值检测参数1.2.10）除外。但是，您可以使用rbind.capthist结合模拟不同的参数值检测的的人口子类（如男性和女性）。检测器的类型“单一”，这是无效的，因为它并没有允许子类之间竞争的陷阱。未来的版本可能会允许更复杂的模型。
truncate has no effect (i) when using a uniform detection function with radius (sigma) <= truncate and (ii) with signal strength detection (detectfn 10, 11). Note that truncated detection functions are provided for de novo simulation, but are not available when fitting models with in secr.fit or simulating from a fitted model with sim.secr.
truncate没有任何效果（i）当使用均匀的检测功能，半径为（sigma）<=truncate及（ii）与信号强度检测（detectfn 10，11）。需要注意的是截断检测功能，提供为从头模拟，但不适用于拟合模型时，在secr.fit或模拟一个合适的模型与sim.secr。
maxperpoly limits the size of the array allocated for detections in C code; an error results if the is number is exceeded.
maxperpoly检测的C代码分配的数组的大小限制，是一个错误的结果，如果数量超出。
参考文献----------References----------
likelihood methods for capture–recapture studies. Biometrics 64, 377–385.
Oikos 106, 598–610.
by spatially explicit capture-recapture: likelihood-based methods. In: D. L. Thomson, E. G. Cooch and M. J. Conroy (eds) Modeling Demographic Processes in Marked Populations. Springer, New York. Pp. 255–269.
density estimated from locations of individuals on a passive detector array. Ecology 90, 2676–2682.
参见----------See Also----------
sim.popn, capthist, traps, popn, detection functions, simulate
sim.popn，capthist，traps，popn，detection functions，simulate
实例----------Examples----------
## simple example[＃简单的例子]
## detector = "multi" (default)[＃探测器“多”（默认值）]
temptrap <- make.grid(nx = 6, ny = 6, spacing = 20)
sim.capthist (temptrap, detectpar = list(g0 = 0.2, sigma = 20))
## with detector = "proximity", there may be more than one[探测器=“近水楼台”，可能有一个以上的]
## detection per individual per occasion[＃每个人每一次的检测]
temptrap <- make.grid(nx = 6, ny = 6, spacing = 20, detector =
"proximity")
summary(sim.capthist (temptrap, detectpar =
list(g0 = 0.2, sigma = 20)))
## multiple sessions[＃多个会话]
grid4 <- make.grid(nx = 2, ny = 2)
temp <- sim.capthist (grid4, popn = list(D = 1), nsessions = 20)
summary(temp, terse = TRUE)
## unmarked or presence types[＃标记或标记存在的类型]
grid <- make.grid(nx = 10, ny = 10, detector = "unmarked")
CH <- sim.capthist (grid, noccasions = 5)
CH
## "presence" and "unmarked" data are stored as "count" data[＃“存在”和“无标记的”数据被存储为“计数”数据]
## behaviour is controlled by detector type, e.g.[＃的行为是由检测器类型，例如]
detector(traps(CH)) <- "presence"
CH
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 00:04:56
