tidy links

inst/ChangeLog

@@ -1,3 +1,71 @@
+2024-06-19  edzer <[email protected]>
+
+	* .github/workflows/rcmdcheck.yml: update tlmgr
+
+2024-06-19  edzer <[email protected]>
+
+	* R/panel.pointPairs.R, R/predict.gstat.R, R/variogram.gstat.R,
+	R/variogramST.R: along -> along.with
+
+2024-03-26  edzer <[email protected]>
+
+	* tests/unproj.R, tests/unproj.Rout.save: clean test noise output
+
+2024-03-21  edzer <[email protected]>
+
+	* : commit c8be3e8e2c5adc18c0834fee62ebaaf2cbe63112 Author: edzer
+	<[email protected]> Date:   Thu Mar 21 19:32:27 2024
+	+0100
+
+2024-03-14  Edzer Pebesma <[email protected]>
+
+	* : Merge pull request #139 from AMBarbosa/main vgm: state that 'model' can be a chr vector
+
+2024-02-21  Edzer Pebesma <[email protected]>
+
+	* : Merge pull request #138 from kadyb/main fix URL in README
+
+2024-02-21  Edzer Pebesma <[email protected]>
+
+	* : Merge pull request #136 from kadyb/main Create new rcmdcheck workflow
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .travis.yml: Delete .travis.yml
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* tic.R: Delete tic.R
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .github/workflows/tic.yml: Delete .github/workflows/tic.yml
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .github/workflows/rcmdcheck.yml: add LaTeX package
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .github/workflows/rcmdcheck.yml: add LaTeX package
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .github/workflows/rcmdcheck.yml: install LaTeX packages
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .github/workflows/rcmdcheck.yml: add TinyTeX
+
+2024-02-17  Krzysztof Dyba <[email protected]>
+
+	* .github/workflows/rcmdcheck.yml: create rcmdcheck workflow
+
+2024-01-21  edzer <[email protected]>
+
+	* .Rbuildignore, R/variogramST.R, inst/ChangeLog: allow non-POSIXct
+	and non-Date times; #135
+
 2024-01-17  edzer <[email protected]>
 
 	* .github/workflows/tic.yml: update

man/krigeST.Rd

@@ -73,7 +73,7 @@ krigeSTTg(formula, data, newdata, modelList, y, nmax=Inf, stAni=NULL,
 
 \value{
  An object of the same class as \code{newdata} (deriving from 
- \code{\linkS4class{ST}}). Attributes columns contain prediction and prediction 
+ \code{\link[spacetime:ST-class]{ST}}). Attributes columns contain prediction and prediction 
  variance.
 }
 
@@ -88,8 +88,7 @@ Wiley.
 \url{http://www.gstat.org/}
 
 Pebesma, E.J., 2004. Multivariable geostatistics in S: the gstat package.
-Computers and Geosciences, 30: 683-691.
-}
+Computers and Geosciences, 30: 683-691.  }
 \author{ Edzer Pebesma, Benedikt Graeler }
 
 \seealso{ \code{\link{krige0}}, \code{\link{gstat}}, \code{\link[gstat]{predict}}, \code{\link{krigeTg}} }

man/krigeTg.Rd

@@ -45,7 +45,7 @@ krigeTg(formula, locations, newdata, model = NULL, ...,
 }
 \details{
 Function \code{krigeTg} uses transGaussian kriging as explained in
-\url{http://www.math.umd.edu/~bnk/bak/Splus/kriging.html}. 
+\url{https://www.math.umd.edu/~bnk/bak/Splus/kriging.html}. 
 
 As it uses the R/gstat krige function to derive everything, it needs in
 addition to ordinary kriging on the transformed scale a simple kriging

man/plot.gstatVariogram.Rd

@@ -41,15 +41,15 @@ graph, using color, colored lines and symbols to distinguish them }
 each plotted semivariance symbol, if FALSE these are omitted. 
 If numeric, TRUE is assumed and the value is passed as the relative distance to be used between symbols
 and numeric text values (default 0.03). }
-\item{scales}{ optional argument that will be passed to \code{xyplot} in
+\item{scales}{ optional argument that will be passed to \code{\link[lattice]{xyplot}} in
 case of the plotting of variograms and cross variograms; use the value
 \code{list(relation = "same")} if y-axes need to share scales }
 \item{ids}{ ids of the data variables and variable pairs }
 \item{group.id}{ logical; control for directional multivariate variograms:
 if TRUE, panels divide direction and colors indicate variables
 (ids), if FALSE panels divide variables/variable pairs and colors
 indicate direction}
-\item{skip}{ logical; can be used to arrange panels, see \code{xyplot}}
+\item{skip}{ logical; can be used to arrange panels, see \code{\link[lattice]{xyplot}}}
 \item{layout}{ integer vector; can be used to set panel layout: c(ncol,nrow) }
 \item{np}{ logical (only for plotting variogram maps); if TRUE, plot number of point pairs, if FALSE plot
 semivariances }
@@ -62,7 +62,7 @@ than threshold will not be plotted}
 \item{convertMonths}{logical; if TRUE, \code{yearmon} time lags will
 be unit converted and plotted as (integer) months, and no longer match the
 numeric representation of \code{yearmon}, which has years as unit }
-\item{as.table}{controls the plotting order for multiple panels, see \code{\link{xyplot}} for details.}
+\item{as.table}{controls the plotting order for multiple panels, see \code{\link[lattice]{xyplot}} for details.}
 \item{wireframe}{logical; if TRUE, produce a wireframe plot}
 \item{diff}{logical; if TRUE, plot difference between model and sample variogram; ignores \code{all}.}
 \item{all}{logical; if TRUE, plot sample and model variogram(s) in single wireframes.}

man/variogramST.Rd

@@ -15,10 +15,10 @@ variogramST(formula, locations, data, ..., tlags = 0:15,  cutoff,
 \item{locations}{A STFDF or STSDF containing the variable; kept for 
   compatibility reasons with variogram, either \code{locations} or \code{data} 
   must be provided.}
-\item{data}{A \code{\linkS4class{STFDF}}, \code{\linkS4class{STSDF}} or \code{\linkS4class{STIDF}} containing the variable.}
+\item{data}{A \code{\link[spacetime:STFDF-class]{STFDF}}, \code{\link[spacetime:STSDF-class]{STSDF}} or \code{\link[spacetime:STIDF]{STIDF}} containing the variable.}
 \item{...}{any other arguments that will be passed to the underlying 
-  \code{\link{variogram}} function. In case of using data of type \code{\linkS4class{STIDF}}, the argument \code{tunit} is recommended (and only used in the case of STIDF) to set the temporal unit of the \code{tlags}. Additionally, \code{twindow} can be passed to control the temporal window used for temporal distance calculations. This builds on the property of xts being ordered and only the next \code{twindow} instances are considered. This avoids the need of huge temporal distance matrices. The default uses twice the number as the average difference goes into the temporal cutoff.}
-\item{tlags}{ integer; time lags to consider or in case \code{data} is of class \code{\linkS4class{STIDF}} the actual temporal boundaries with time unit given by \code{tunit} otherwise the same unit as \code{\link{diff}} on the index of the time slot will generate is assumed.}
+  \code{\link{variogram}} function. In case of using data of type \code{\link[spacetime:STIDF-class]{STIDF}}, the argument \code{tunit} is recommended (and only used in the case of STIDF) to set the temporal unit of the \code{tlags}. Additionally, \code{twindow} can be passed to control the temporal window used for temporal distance calculations. This builds on the property of xts being ordered and only the next \code{twindow} instances are considered. This avoids the need of huge temporal distance matrices. The default uses twice the number as the average difference goes into the temporal cutoff.}
+\item{tlags}{ integer; time lags to consider or in case \code{data} is of class \code{\link[spacetime:STIDF-class]{STIDF}} the actual temporal boundaries with time unit given by \code{tunit} otherwise the same unit as \code{\link{diff}} on the index of the time slot will generate is assumed.}
 \item{cutoff}{ spatial separation distance up to which point pairs
 are included in semivariance estimates; as a default, the
 length of the diagonal of the box spanning the data is divided by three. }

man/vgm.panel.Rd

@@ -39,7 +39,7 @@ panel.pointPairs(x, y, type = "p", pch = plot.symbol$pch, col, col.line =
 \item{line.pch}{ symbol type to be used for point of selected point pairs, e.g.
 to highlight point pairs with distance close to zero }
 \item{pairs}{ two-column matrix with pair indexes to be highlighted }
-\item{...}{ parameters that get passed to \link{lpoints} }
+\item{...}{ parameters that get passed to \link[lattice]{lpoints} }
 }
 \value{
 ignored; the enclosing function returns a plot of class \code{trellis}