Fits user specified models to various types of capture-recapture data by creating input file and running MARK software and retrieving output
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 = TRUE,
threads = -1,
hessian = FALSE,
accumulate = TRUE,
allgroups = FALSE,
strata.labels = NULL,
counts = NULL,
icvalues = NULL,
wrap = TRUE,
events = NULL,
nodes = 101,
useddl = FALSE,
check.model = FALSE
)model: a MARK object containing output and extracted results. It is a list with the following elements
name of the processed data frame
type of analysis model (see list above)
title used for analysis
descriptive name of model
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
number of mixtures in Pledger-style closed capture-recapture models
call to make.mark.model used to construct the model
a list of parameter descriptions including the formula, pim.type, link etc.
the list
of parameter descriptions used in the call to mark; this is used only by
rerun.mark
Intervals of time between the capture occasions
number of groups defined in the data
vector of labels for the groups
number of capture occasions
single time of vector of times (if different for groups) for the first capture occasion
vector of covariate names (as strings) used in the model
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
design matrix used in the input to MARK.EXE
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
design data used to construct the design matrix
labels for strata if any
structure used to simplify parameters that use mlogit links
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
List of values extracted from MARK ouput
lnl | -2xLog Likelihood value | |
npar | Number of parameters (always the number of columns in design matrix) | |
npar.unadjusted | number of estimated parameters from MARK if different than npar | |
n | effective sample size | |
AICc | Small sample corrected AIC using npar | |
AICc.unadjusted | Small sample corrected AIC using npar.unadjusted | |
beta | data frame of beta parameters with estimate, se, lcl, ucl | |
real | data frame of real parameters with estimate, se, lcl, ucl and fixed | |
beta.vcv | variance-covariance matrix for beta | |
derived | dataframe of derived parameters if any | |
derived.vcv | variance-covariance matrix for derived parameters if any | |
covariate.values | dataframe with fields Variable and
Value | |
| which are the covariate names and value used for real parameter | ||
| estimates in the MARK output | ||
singular | indices of beta parameters that are non-estimable or at a boundary | |
real.vcv | variance-covariance matrix for real parameters (simplified) if realvcv=TRUE |
over-dispersion constant; if not present assumed to be 1
base portion of filenames for input,output, vc and residual files output from MARK.EXE
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
Design data list which contains a list element for each parameter type; if NULL it is created
Time of first capture(release) occasion
Optional name for the model
Type of c-r model (eg CJS, Burnham, Barker)
Optional title for the MARK analysis output
List of model parameter specifications
Optional vector of named or unnamed initial values for beta parameters or previously run model object
Specification of any grouping variables for design data for each parameter
if TRUE, any intervals created in design.parameters are closed on the right and open on left and vice-versa if FALSE
Vector of names factor variables for creating groups
Optional index in groups vector of a variable that represents age
Optional vector of initial ages for each age level
Increment of age for each increment of time
Intervals of time between the capture occasions
number of occasions for Nest model; either time.intervals or nocc must be specified for this model
If TRUE produces summary of model input and model output
If TRUE, window for running MARK is hidden
If TRUE, adjusts npar to number of cols in design matrix, modifies AIC and records both
number of mixtures for heterogeneity model or number of secondary samples for MultScaleOcc model
if TRUE, se and confidence intervals are shown in summary sent to screen
base filename for files created by MARK.EXE. Files are named filename.*.
base filename prefix for files created by MARK.EXE; for example if prefix="SpeciesZ" files are named "SpeciesZnnn.*"
if TRUE, real parameters for which the design data have been deleted are fixed to default values
if TRUE, errors that are encountered are suppressed
number of reanalyses to perform with new starting values when one or more parameters are singular
character string of options for Proc Estimate statement in MARK .inp file
if TRUE and output=TRUE then a brief summary line is given instead of a full summary for the model
if TRUE the vcv matrix of the real parameters is extracted and stored in the model results
if TRUE the output files are deleted after the results are extracted
if TRUE the mark object is saved externally rather than in the workspace; the filename is kept in its place
if TRUE will compute profile intervals for each real parameter; or you can specify a vector of real parameter indices
value of chat used for profile intervals
if set to TRUE, will reverse timing of transition (Psi) and survival (S) in Multistratum models(starting with version 3.0.0 setting reverse=TRUE is not allowed)
if FALSE does not run model after creation
specifies set of link functions for parameters with non-simplified structure
if TRUE, forces a link to be specified for each parameter
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
number of cpus to use with mark.exe if positive or number of cpus to remain idle if negative
if TRUE specifies to MARK to use hessian rather than second partial matrix
if TRUE accumulate like data values into frequencies
Logical variable; if TRUE, all groups are created from
factors defined in groups even if there are no observations in the
group
vector of single character values used in capture history(ch) for ORDMS, CRDMS, RDMSOccRepro models; it can contain one more value beyond what is in ch for an unobservable state except for RDMSOccRepro which is used to specify strata ordering (eg 0 not-occupied, 1 occupied no repro, 2 occupied with repro.
named list of numeric vectors (one group) or matrices (>1 group) containing counts for mark-resight models
numeric vector of individual covariate values for computation of real values
if TRUE, data lines are wrapped to be length 80; if length of a row is not a problem set to FALSE and it will run faster
vector of character events for Hidden Markov models
number of integration nodes for individual random effects (min 15, max 505, default 101)
if TRUE and no rows of ddl are missing (deleted) then it will use ddl in place of full.ddl that is created internally.
if TRUE, code does an internal consistency check between PIMs and design data when making model.
Jeff Laake
This function acts as an interface to the FORTRAN program MARK written by
Gary White (http://www.phidot.org/software/mark/). 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.
The models that are currently supported are listed in MarkModels.pdf which you can find in the RMark sub-directory of your R Library. Also, they are listed under Help/Data Types in the MARK interface.
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.
For descriptions of the arguments data, begin.time,
groups, age.var, initial.ages, age.unit,
time.intervals and mixtures see process.data.
For descriptions of ddl, design.parameters=parameters,
and right, see make.design.data.
For descriptions of model.name , model,
title,model.parameters=parameters ,
default.fixed , initial, options, see
make.mark.model.
And finally, for descriptions of arguments invisible, filename
and adjust,see 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.
make.mark.model, run.mark.model,
make.design.data, process.data,
summary.mark
data(dipper)
dipper.Phidot.pdot=mark(dipper,threads=1,delete=TRUE)
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