Rd files package anchors

man/AIC.openCR.Rd

@@ -117,7 +117,7 @@ overdispersion has yet to be addressed (cf QAIC in MARK).
 
 \seealso{
   \code{\link[stats]{AIC}}, \code{\link{openCR.fit}},
-  \code{\link{print.openCR}}, \code{\link{LR.test}}
+  \code{\link{print.openCR}}, \code{\link[secr]{LR.test}}
 }
 
 \examples{

man/LLsurface.Rd

@@ -76,7 +76,7 @@ grid point
   parameters not beta parameters.
   
   Handling of multiple threads was changed in version 1.5.0 to align 
-  with \code{\link{LLsurface.secr}}.
+  with \code{\link[secr]{LLsurface.secr}}.
 
   The contours are approximate because they rely on interpolation. 
   

man/cumMove.Rd

@@ -64,7 +64,8 @@ For proportionInPolygon - vector of the summed weights (probabilities) for cells
 
 \seealso{
 
-\code{\link{make.kernel}}, \code{\link{pointsInPolygon}}
+\code{\link{make.kernel}}, 
+\code{\link[secr]{pointsInPolygon}}
 
 }
 

man/kernel.Rd

@@ -48,7 +48,7 @@ make.kernel(movementmodel = c("BVN", "BVE", "BVC", "BVT","RDE", "RDG", "RDL", "U
   \item{add}{logical; if TRUE a line is added to an existing plot (types "gr", "fr", "Fr")}
   \item{xscale}{numeric multiplier for distance axis (0.001 for distances in km)}
   \item{\dots}{other arguments passed to \code{\link{predict.openCR}} (\code{make.kernel}) or
-      \code{\link{plot.mask}} (plot type "kernel") or \code{\link{lines}} ( plot types "gr", "fr", "Fr") (not used by summary method)}
+      \code{\link[secr]{plot.mask}} (plot type "kernel") or \code{\link{lines}} ( plot types "gr", "fr", "Fr") (not used by summary method)}
 
   \item{object}{kernel object from \code{make.kernel}}
 
@@ -147,7 +147,7 @@ Nathan, R., Klein, E., Robledo-Arnuncio, J. J. and Revilla, E. (2012) Dispersal
 
 \seealso{
 
-\link{Movement models}, \code{\link{mask}}, \code{\link{matchscale}}, \code{\link{dkernel}}, \code{\link{pkernel}}, \code{\link{qkernel}}
+\link{Movement models}, \code{\link[secr]{mask}}, \code{\link{matchscale}}, \code{\link{dkernel}}, \code{\link{pkernel}}, \code{\link{qkernel}}
 
 }
 

man/openCR-defunct.Rd

@@ -1,5 +1,7 @@
 \name{openCR-defunct}
 \alias{openCR-defunct}
+\alias{openCR.make.newdata}
+\alias{plotkernel}
 
 \title{Defunct Functions in Package \pkg{openCR}}
 

man/openCR-internal.Rd

@@ -76,7 +76,7 @@ cyclic.fit (..., maxcycle = 10, tol = 1e-5, trace = FALSE)
   \item{nc}{number of capture histories}
   \item{kk}{number of detectors}
   \item{mm}{number of points on habitat mask}
-  \item{binomN}{code for distribution of counts (see \code{\link{secr.fit}})}
+  \item{binomN}{code for distribution of counts (see \code{\link[secr]{secr.fit}})}
 
   \item{\dots}{named arguments passed to \code{\link{openCR.fit}} or \code{predict} (see extractFocal)}
   \item{maxcycle}{integer maximum number of cycles (maximizations of a given parameter)}

man/openCR-package.Rd

@@ -27,8 +27,8 @@
 \tabular{ll}{
 Package: \tab openCR\cr
 Type: \tab Package\cr
-Version: \tab 2.2.6\cr
-Date: \tab 2023-11-28\cr
+Version: \tab 2.2.7\cr
+Date: \tab 2024-10-23\cr
 License: \tab GNU General Public License Version 2 or later\cr
 }
 
@@ -90,7 +90,7 @@ See \href{../doc/openCR-vignette.pdf}{openCR-vignette.pdf} for more.
 
 \seealso{
 
-  \code{\link{openCR.fit}}, \code{\link[secr]{capthist}}, \code{\link{ovenCH}}
+  \code{\link{openCR.fit}}, \code{\link[secr]{capthist}}, \code{\link[secr]{ovenCH}}
 
 }
 \examples{

man/openCR.fit.Rd

@@ -43,7 +43,7 @@ openCR.fit (capthist, type = "CJS", model = list(p~1, phi~1, sigma~1),
 
   \item{distribution}{character distribution of number of individuals detected}
 
-  \item{mask}{ single-session \code{\link{mask}} object; required for spatial (secr) models }
+  \item{mask}{ single-session \code{\link[secr]{mask}} object; required for spatial (secr) models }
 
   \item{detectfn}{character code}
 
@@ -125,7 +125,7 @@ Data are provided as \pkg{secr} `capthist' objects, with some
 restrictions. For nonspatial analyses, `capthist' may be
 single-session or multi-session, with any of the main detector types. For
 spatial analyses `capthist' should be a single-session dataset of a point 
-\link{detector} type (`multi', `proximity' or `count') (see also
+\link[secr]{detector} type (`multi', `proximity' or `count') (see also
 details$distribution below). In openCR the occasions of a single-session
 dataset are treated as open-population temporal samples except that occasions 
 separated by an interval of zero (0) are from the same primary session (multi-session
@@ -163,10 +163,10 @@ Movement models are list at \link{Movement models}. Their use is described in th
 The mlogit link function is used for the JSSA (POPAN) entry parameter 
 `b' (PENT in MARK) and for mixture proportions, regardless of \code{link}.
 
-Spatial models use one of the hazard-based detection functions (see \code{\link{detectfn}}) and require data
+Spatial models use one of the hazard-based detection functions (see \code{\link[secr]{detectfn}}) and require data
 from independent point detectors (\pkg{secr} detector types `multi', `proximity' or `count').
 
-Code is executed in multiple threads unless the user specifies \code{ncores = 1} or there is only one core available or \code{details$R == TRUE}. Setting \code{ncores = NULL} uses the existing value from the environment variable RCPP_PARALLEL_NUM_THREADS (see \code{\link{setNumThreads}}) or 2 if that has not been set. 
+Code is executed in multiple threads unless the user specifies \code{ncores = 1} or there is only one core available or \code{details$R == TRUE}. Setting \code{ncores = NULL} uses the existing value from the environment variable RCPP_PARALLEL_NUM_THREADS (see \code{\link[secr]{setNumThreads}}) or 2 if that has not been set. 
 
 Optional stratification was introduced in \pkg{openCR} 2.0.0. See \href{../doc/openCR-vignette.pdf}{openCR-vignette.pdf} for details.
 
@@ -379,7 +379,7 @@ probabilities for each individual in finite mixture models and saved them in
 component `posterior'. Now see \code{\link{classMembership}} for that functionality.
 
 From 1.5.0 onwards the number of threads uses the environment variable 
-RCPP_PARALLEL_NUM_THREADS, as in \code{\link{secr.fit}}. This may be set once
+RCPP_PARALLEL_NUM_THREADS, as in \code{\link[secr]{secr.fit}}. This may be set once
 in a session with \code{secr::setNumThreads}.
 
 The default movement arguments changed in \pkg{openCR} 2.1.1. Now 

man/par.openCR.fit.Rd

@@ -35,7 +35,7 @@ par.openCR.fit (arglist, ncores = 1, seed = 123, trace = FALSE, logfile = NULL,
 
 \details{
 
-In openCR >= 1.5.0, setting ncores > 1 is deprecated and triggers a warning: multithreading makes it faster to set ncores = 1 in par.secr.fit.
+In openCR >= 1.5.0, setting ncores > 1 is deprecated and triggers a warning: multithreading makes it faster to set ncores = 1 in par.openCR.fit.
 
 \code{trace} overrides any settings in \code{arglist}.
 
@@ -65,7 +65,7 @@ execution time and finish time are displayed.
 
 \seealso{
   \code{\link{openCR.fit}},
-  \link{Parallel},
+  \link[secr]{Parallel},
   \code{\link{make.table}},
   \code{\link{openCRlist}}
 }

man/read.inp.Rd

@@ -42,7 +42,7 @@ If \code{grouplevels} is specified then \code{ngroups} is taken from the number
 
 \seealso{
 
-\code{\link{RMarkInput}}, \code{\link{unRMarkInput}}
+\code{\link[secr]{RMarkInput}}, \code{\link[secr]{unRMarkInput}}
 
 }
 

man/simulate.Rd

@@ -41,9 +41,9 @@ runsim.RMark (nrepl = 100, model = "CJS", model.parameters = NULL, extractfn,
   \item{intervals}{intervals between primary sessions (see Details)}
 \item{recapfactor}{numeric multiplier for capture probability after
   first capture}
-  \item{seed}{random number seed see \link{random numbers}}
+  \item{seed}{random number seed see \link[secr]{random numbers}}
   \item{savepopn}{logical; if TRUE the generated population is saved as an attribute of the capthist object}
-  \item{\dots}{other arguments passed to \code{\link{sim.popn}} (sim.nonspatial) or \code{\link{sim.nonspatial}} (runsims)}
+  \item{\dots}{other arguments passed to \code{\link[secr]{sim.popn}} (sim.nonspatial) or \code{\link{sim.nonspatial}} (runsims)}
 
   \item{nrepl}{number of replicates}
   \item{ncores}{ integer number of cores to be used for parallel processing (see Details)}
@@ -69,7 +69,7 @@ runsim.RMark (nrepl = 100, model = "CJS", model.parameters = NULL, extractfn,
 
 For \code{sim.nonspatial} -- If \code{intervals} is specified then the number of primary and secondary sessions is inferred from \code{intervals} and \code{nsessions} and \code{noccasions} are ignored. If \code{N} and \code{p} are vectors of length 2 then subpopulations of the given initial size are sampled with the differing capture probabilities and the resulting capture histories are combined.
 
-\code{runsim.spatial} is a relatively simple wrapper for \code{\link{sim.popn}}, \code{\link{sim.capthist}}, and \code{\link{openCR.fit}}. Some arguments are set automatically: the \code{sim.capthist} argument 'renumber' is always FALSE; argument 'seed' is ignored within 'popargs' and 'detargs'; if no 'traps' argument is provided in 'detargs' then 'core' from 'popargs' will be used; detargs$popn and fitargs$capthist are derived from the preceding step. The 'type' specified in fitargs may refer to a non-spatial or spatial open-population model ('CJS', 'JSSAsecrfCL' etc.). If the \code{intervals} argument is specified it is used to set the intervals attribute of the simulated capthist object; turnover parameters in \code{sim.popn} are not scaled by \code{intervals}.
+\code{runsim.spatial} is a relatively simple wrapper for \code{\link[secr]{sim.popn}}, \code{\link[secr]{sim.capthist}}, and \code{\link{openCR.fit}}. Some arguments are set automatically: the \code{sim.capthist} argument 'renumber' is always FALSE; argument 'seed' is ignored within 'popargs' and 'detargs'; if no 'traps' argument is provided in 'detargs' then 'core' from 'popargs' will be used; detargs$popn and fitargs$capthist are derived from the preceding step. The 'type' specified in fitargs may refer to a non-spatial or spatial open-population model ('CJS', 'JSSAsecrfCL' etc.). If the \code{intervals} argument is specified it is used to set the intervals attribute of the simulated capthist object; turnover parameters in \code{sim.popn} are not scaled by \code{intervals}.
 
 Control of parallel processing changed in \pkg{openCR} 1.5.0 to conform to \pkg{secr}. In \code{runsim.nonspatial} and \code{runsim.spatial}, if \code{ncores} is NULL (the default) then the number of cores used for multithreading by \code{openCR.fit} is controlled by the environment variable RCPP_PARALLEL_NUM_THREADS. Use the secr function \code{setNumThreads} to set RCPP_PARALLEL_NUM_THREADS to a value greater than the default (2, from \pkg{openCR} 1.5 onwards).
 
@@ -99,7 +99,7 @@ Data.frame with rows `estimate', `SE.estimate', `lcl', `ucl', `RSE', `CI.length'
 
 \seealso{
 
-\code{\link{sim.popn}}, \code{\link{sim.capthist}}
+\code{\link[secr]{sim.popn}}, \code{\link[secr]{sim.capthist}}
 
 }
 

man/strata.Rd

@@ -53,7 +53,7 @@ primary sessions and concatenated as usual with \code{join()}.
 
 \seealso{ 
 
-  \code{\link{openCR.fit}}, \code{\link{session}}, \code{\link{stratify}}
+  \code{\link{openCR.fit}}, \code{\link[secr]{session}}, \code{\link{stratify}}
 
 }
 

man/stratify.Rd

@@ -16,7 +16,7 @@ stratify(..., intervals = NULL, MoreArgs = list(), covariate = NULL, bytraps = F
 \arguments{
   \item{\dots}{one or more multi-session capthist objects, or a list of such objects}
   \item{intervals}{list of intervals vectors, one for each multi-session capthist in \dots}
-  \item{MoreArgs}{list of other arguments passed to \code{\link{join}}}
+  \item{MoreArgs}{list of other arguments passed to \code{\link[secr]{join}}}
   \item{covariate}{character; name of individual or trap covariate to stratify by}
   \item{bytraps}{logical; if TRUE then covariate is interpreted as the name of a detector covariate}
 }
@@ -39,7 +39,7 @@ The result in Case 1 is identical to \code{MS.capthist(\dots)}.
 The argument \code{intervals} refers to the intervals between primary sessions 
 before joining (Cases 2,4 only) (see Examples).
 
-MoreArgs may include the arguments remove.dupl.sites, tol, sites.by.name or drop.sites of \code{\link{join}}; these otherwise take their default values.
+MoreArgs may include the arguments remove.dupl.sites, tol, sites.by.name or drop.sites of \code{\link[secr]{join}}; these otherwise take their default values.
 
 }
 
@@ -51,8 +51,8 @@ Multi-stratum (multi-session) capthist object for which each component has been
 
 \seealso{
 
-\code{\link{join}}, 
-\code{\link{MS.capthist}}, 
+\code{\link[secr]{join}}, 
+\code{\link[secr]{MS.capthist}}, 
 \code{\link{openCR.fit}}, 
 \code{\link{strata}}
 

man/ucare.Rd

@@ -22,7 +22,7 @@ ucare.cjs(CH, tests = "all", by = NULL, verbose = TRUE, rounding = 3, ...)
   \item{by}{character name of covariate in CH used to split rows of CH into separate groups }
   \item{verbose}{logical; if TRUE then additional details are tabulated}
   \item{rounding}{integer number of decimal places in output}
-  \item{\dots}{other arguments passed to \code{\link{split.capthist}} if needed }
+  \item{\dots}{other arguments passed to \code{\link[secr]{split.capthist}} if needed }
   
 }
 

man/utility.Rd

@@ -35,7 +35,7 @@ bd.array(beta, phi)
 
 The input is a capthist object representing a multi-session capture--recapture study. This may be (i) a single-session capthist in which occasions are understood to represent primary sessions, or (ii) a multi-session capthist object that is automatically converted to a single session object with \code{\link[secr]{join}} (any secondary sessions (occasions) are first collapsed with \code{reduce(object, by = 'all')}*, or (iii) a multi-session capthist object in which sessions are interpreted as strata.
 
-The argument \code{primary.only} applies for single-session input with a robust-design structure defined by the \code{\link{intervals}}. \code{last.session} results in a final row with no recaptures.
+The argument \code{primary.only} applies for single-session input with a robust-design structure defined by the \code{\link[secr]{intervals}}. \code{last.session} results in a final row with no recaptures.
 
 If the covariates attribute of \code{object} includes a column named `freq' then this is used to expand the capture histories.