added package names to \link

.#Extra/Local CI/Mhat.Rd

@@ -58,7 +58,7 @@ Mhat(X, r = NULL, ReferenceType, NeighborType = ReferenceType,
   If \emph{Individual} is \code{TRUE}, then the individual values \emph{M} in the neighborhood of each point are returned. If \emph{ReferencePoint} is also specified, then \emph{only} the individual value of M around the reference point is returned.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 
   If \code{Individual} is set to \code{TRUE}, the object also contains the value of the function around each individual \emph{ReferenceType} point taken as the only reference point. The column names of the \code{fv} are "M_" followed by the point names, i.e. the row names of the marks of the point pattern.
 }

.#Extra/kwmppp/kwmppp.Rd

@@ -18,7 +18,7 @@
     A point pattern (\code{\link{wmppp.object}}).
   }
   \item{fvind}{
-    An object of class \code{fv}, see \code{\link{fv.object}}, obtained a distance-based method, such as \code{\link{Mhat}} with individual values (argument \code{Individual = TRUE}). 
+    An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, obtained a distance-based method, such as \code{\link{Mhat}} with individual values (argument \code{Individual = TRUE}). 
   }
   \item{ReferenceType}{
     The point type used to calculate the function values.
@@ -62,7 +62,7 @@
   }
 }
 \value{
-  \code{kmppp()} produces an object of class "kwmppp" that is also an \code{\link{autoKrige}} object that can be used to produce alternative maps.
+  \code{kmppp()} produces an object of class "kwmppp" that is also an \code{\link[automap]{autoKrige}} object that can be used to produce alternative maps.
   It can be plotted.
 }
 \examples{

man/DEnvelope.Rd

@@ -48,7 +48,7 @@ DEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05,
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/Dhat.Rd

@@ -32,7 +32,7 @@ Dhat(X, r = NULL, Cases, Controls = NULL, Intertype = FALSE, CheckArguments = TR
   The \emph{Di} function allows comparing the structure of the cases to that of the controls around cases, that is to say the comparison is made around the same points. This has been advocated by Arbia et al. (2008) and formalized by Marcon and Puech (2012).
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \references{
   Arbia, G., Espa, G. and Quah, D. (2008). A class of spatial econometric methods in the empirical analysis of clusters of firms in the space. \emph{Empirical Economics} 34(1): 81-103.
@@ -42,10 +42,10 @@ Dhat(X, r = NULL, Cases, Controls = NULL, Intertype = FALSE, CheckArguments = TR
   Marcon, E. and F. Puech (2017). A typology of distance-based measures of spatial concentration. \emph{Regional Science and Urban Economics}. 62:56-67.
 }
 \note{
-  The computation of \code{Dhat} relies on spatstat functions \code{\link{Kest}} and \code{\link{Kcross}}.
+  The computation of \code{Dhat} relies on spatstat functions \code{\link[spatstat.explore]{Kest}} and \code{\link[spatstat.explore]{Kcross}}.
 }
 \seealso{
-  \code{\link{Khat}}, \code{\link{DEnvelope}}, \code{\link{Kest}}, \code{\link{Kcross}}
+  \code{\link{Khat}}, \code{\link{DEnvelope}}, \code{\link[spatstat.explore]{Kest}}, \code{\link[spatstat.explore]{Kcross}}
 }
 \examples{
 data(paracou16)

man/FillEnvelope.Rd

@@ -4,14 +4,14 @@
   Transform simulation values to an fv
 }
 \description{
-  This function is used internally to calculate envelope values and store them into an \code{\link{fv.object}}.
+  This function is used internally to calculate envelope values and store them into an \code{\link[spatstat.explore]{fv.object}}.
 }
 \usage{
 FillEnvelope(Envelope, Alpha, Global)
 }
 \arguments{
   \item{Envelope}{
-  An envelope object (\code{\link{envelope}}) containing all the simulated function values.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}) containing all the simulated function values.
   }
   \item{Alpha}{
   The risk level.
@@ -21,6 +21,6 @@ FillEnvelope(Envelope, Alpha, Global)
   }
 }
 \value{
-  Returns the envelope object (\code{\link{envelope}}) with \code{hi} and \code{lo} values calculated from the simlations.
+  Returns the envelope object (\code{\link[spatstat.explore]{envelope}}) with \code{hi} and \code{lo} values calculated from the simlations.
 }
 \keyword{internal}

man/GlobalEnvelope.Rd

@@ -11,7 +11,7 @@ GlobalEnvelope(Simulations, Alpha)
 }
 \arguments{
   \item{Simulations}{
-  An object of class \code{fv}, see \code{\link{fv.object}}, containing the simulated values.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, containing the simulated values.
   }
   \item{Alpha}{
   The risk level.

man/GoFtest.Rd

@@ -11,7 +11,7 @@ GoFtest(Envelope)
 }
 \arguments{
   \item{Envelope}{
-  An envelope object (\code{\link{envelope}}) containing simulations in its \code{simfuns} attribute. It may be the result of any estimation function of the dbmss package or obtained by the \code{\link{envelope}} function with argument \code{savefuns=TRUE}.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}) containing simulations in its \code{simfuns} attribute. It may be the result of any estimation function of the dbmss package or obtained by the \code{\link[spatstat.explore]{envelope}} function with argument \code{savefuns=TRUE}.
   }
 }
 \details{

man/KEnvelope.Rd

@@ -53,7 +53,7 @@ KEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05,
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/KdEnvelope.Rd

@@ -74,7 +74,7 @@ KdEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05, ReferenceType,
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/Kdhat.Rd

@@ -58,7 +58,7 @@
   If \code{X} is not a \code{\link{Dtable}} object, the maximum value of \code{r} is obtained from the geometry of the window rather than caculating the median distance between points as suggested by Duranton and Overman (2005) to save (a lot of) calculation time.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \note{
   Estimating \emph{Kd} relies on calculating distances, exactly or approximately (if \code{Approximate} is not 0).

man/Khat.Rd

@@ -30,15 +30,15 @@ Khat(X, r = NULL, ReferenceType = "", NeighborType = ReferenceType, CheckArgumen
   \emph{K} is a cumulative, topographic measure of a point pattern structure.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \references{
   Ripley, B. D. (1976). The Foundations of Stochastic Geometry. \emph{Annals of Probability} 4(6): 995-998.
 
   Ripley, B. D. (1977). Modelling Spatial Patterns. \emph{Journal of the Royal Statistical Society B} 39(2): 172-212.
 }
 \note{
-  The computation of \code{Khat} relies on spatstat functions \code{\link{Kest}} and \code{\link{Kcross}}.
+  The computation of \code{Khat} relies on spatstat functions \code{\link[spatstat.explore]{Kest}} and \code{\link[spatstat.explore]{Kcross}}.
 }
 \seealso{
   \code{\link{Lhat}}, \code{\link{KEnvelope}}, \code{\link{Ktest}}

man/KinhomEnvelope.Rd

@@ -28,7 +28,7 @@ KinhomEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05,
   One of the point types. Default is all point types.
   }
   \item{lambda}{
-  An estimation of the point pattern density, obtained by the \code{\link{density.ppp}} function.
+  An estimation of the point pattern density, obtained by the \code{\link[spatstat.explore]{density.ppp}} function.
   }
   \item{SimulationType}{
   A string describing the null hypothesis to simulate. The null hypothesis, may be 
@@ -57,7 +57,7 @@ KinhomEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05,
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/Kinhomhat.Rd

@@ -20,7 +20,7 @@ Kinhomhat(X, r = NULL, ReferenceType = "", lambda = NULL, CheckArguments = TRUE)
   One of the point types. Default is all point types.
   }
   \item{lambda}{
-  An estimation of the point pattern density, obtained by the \code{\link{density.ppp}} function.
+  An estimation of the point pattern density, obtained by the \code{\link[spatstat.explore]{density.ppp}} function.
   }
   \item{CheckArguments}{
   Logical; if \code{TRUE}, the function arguments are verified. Should be set to \code{FALSE} to save time in simulations for example, when the arguments have been checked elsewhere.
@@ -29,21 +29,21 @@ Kinhomhat(X, r = NULL, ReferenceType = "", lambda = NULL, CheckArguments = TRUE)
 \details{
   \emph{Kinhom} is a cumulative, topographic measure of an inhomogenous point pattern structure.
 
-  By default, density estimation is performed at points by \code{\link{density.ppp}} using the optimal bandwith (\code{\link{bw.diggle}}). It can be calculated separately (see example), including at pixels if the point pattern is too large for the default estimation to succeed, and provided as the argument \code{lambda}:
+  By default, density estimation is performed at points by \code{\link[spatstat.explore]{density.ppp}} using the optimal bandwith (\code{\link[spatstat.explore]{bw.diggle}}). It can be calculated separately (see example), including at pixels if the point pattern is too large for the default estimation to succeed, and provided as the argument \code{lambda}:
   Arbia et al. (2012) for example use another point pattern as a reference to estimate density.
 
   Bivariate \emph{Kinhom} is not currently supported.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \references{
   Baddeley, A. J., J. Moller, et al. (2000). Non- and semi-parametric estimation of interaction in inhomogeneous point patterns. \emph{Statistica Neerlandica} 54(3): 329-350.
 
   Arbia, G., G. Espa, et al. (2012). Clusters of firms in an inhomogeneous space: The high-tech industries in Milan. \emph{Economic Modelling} 29(1): 3-11.
 }
 \note{
-  The computation of \code{Kinhomhat} relies on spatstat functions \code{\link{Kinhom}}, \code{\link{density.ppp}} and \code{\link{bw.diggle}}.
+  The computation of \code{Kinhomhat} relies on spatstat functions \code{\link[spatstat.explore]{Kinhom}}, \code{\link[spatstat.explore]{density.ppp}} and \code{\link[spatstat.explore]{bw.diggle}}.
 }
 \seealso{
   \code{\link{KinhomEnvelope}}, \code{\link{Kinhom}}

man/KmmEnvelope.Rd

@@ -39,7 +39,7 @@ KmmEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05, ReferenceType
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/Kmmhat.Rd

@@ -27,18 +27,18 @@ Kmmhat(X, r = NULL, ReferenceType = "", CheckArguments = TRUE)
   The \emph{Kmm} function is used to test the independence of marks.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \references{
   Penttinen, A., Stoyan, D. and Henttonen, H. M. (1992). Marked Point Processes in Forest Statistics. \emph{Forest Science} 38(4): 806-824.
 
   Penttinen, A. (2006). Statistics for Marked Point Patterns. in \emph{The Yearbook of the Finnish Statistical Society}. The Finnish Statistical Society, Helsinki: 70-91.
 }
 \note{
-  The function is computed using \code{\link{markcorrint}} in spatstat.
+  The function is computed using \code{\link[spatstat.explore]{markcorrint}} in spatstat.
 }
 \seealso{
-  \code{\link{Lmmhat}}, \code{\link{LmmEnvelope}}, \code{\link{markcorrint}}
+  \code{\link{Lmmhat}}, \code{\link{LmmEnvelope}}, \code{\link[spatstat.explore]{markcorrint}}
 }
 \examples{
 data(paracou16)

man/Ktest.Rd

@@ -11,7 +11,7 @@ Ktest(X, r)
 }
 \arguments{
   \item{X}{
-  A point pattern (\code{\link{ppp.object}}). Marks are ignored. The window must be a rectangle sensu spatstat (tested by \code{\link{is.rectangle}}).
+  A point pattern (\code{\link[spatstat.geom]{ppp.object}}). Marks are ignored. The window must be a rectangle sensu spatstat (tested by \code{\link[spatstat.geom]{is.rectangle}}).
   }
   \item{r}{
   A vector of distances.

man/LEnvelope.Rd

@@ -49,7 +49,7 @@ LEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05,
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/Lhat.Rd

@@ -30,7 +30,7 @@ Lhat(X, r = NULL, ReferenceType = "", NeighborType = "", CheckArguments = TRUE)
   \emph{L} is the normalized version of \emph{K}: \eqn{L(r)=\sqrt{\frac{K}{\pi}}-r}.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \references{
   Besag, J. E. (1977). Comments on Ripley's paper. \emph{Journal of the Royal Statistical Society B} 39(2): 193-195.

man/LmmEnvelope.Rd

@@ -39,7 +39,7 @@ LmmEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05, ReferenceType
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }

man/Lmmhat.Rd

@@ -27,7 +27,7 @@ Lmmhat(X, r = NULL, ReferenceType = "", CheckArguments = TRUE)
   \emph{Lmm} is the normalized version of \emph{Kmm}: \eqn{Lmm(r)=\sqrt{\frac{Kmm}{\pi}}-r}.
 }
 \value{
-  An object of class \code{fv}, see \code{\link{fv.object}}, which can be plotted directly using \code{\link{plot.fv}}.
+  An object of class \code{fv}, see \code{\link[spatstat.explore]{fv.object}}, which can be plotted directly using \code{\link[spatstat.explore]{plot.fv}}.
 }
 \references{
   Penttinen, A., Stoyan, D. and Henttonen, H. M. (1992). Marked Point Processes in Forest Statistics. \emph{Forest Science} 38(4): 806-824.

man/MEnvelope.Rd

@@ -53,7 +53,7 @@ MEnvelope(X, r = NULL, NumberOfSimulations = 100, Alpha = 0.05,
   The global envelope is calculated by iteration: the simulations reaching one of the upper or lower values at any distance are eliminated at each step. The process is repeated until \emph{Alpha / Number of simulations} simulations are dropped. The remaining upper and lower bounds at all distances constitute the global envelope. Interpolation is used if the exact ratio cannot be reached.
 }
 \value{
-  An envelope object (\code{\link{envelope}}). There are methods for print and plot for this class.
+  An envelope object (\code{\link[spatstat.explore]{envelope}}). There are methods for print and plot for this class.
 
   The \code{fv} contains the observed value of the function, its average simulated value and the confidence envelope.
 }