RC 0.0-45

Author: mdsumner

NAMESPACE

@@ -1,5 +1,5 @@
 
-## get.sst
+
 importFrom(sp, "coordinates<-", "gridded<-", as.image.SpatialGridDataFrame)
 
 ## position.logp
@@ -47,8 +47,7 @@ export(elevation)
 export(EQUHOR)
 export(FRAC)
 export(get.mask)
-##export(get.pimgs)
-export(get.sst)
+
 export(initialize.x)
 export(julcent)
 export(julday)

NEWS

@@ -1,5 +1,9 @@
 Changes to version 0.0-45
 
+   o fixed some missing documentation
+
+   o really removed get.sst, that didn't work for a long time
+
    o remove rgdal, now import reproj
 
    o fix citation, thanks to T. Michelot

R/bits.R

@@ -1,6 +1,8 @@
 "bits" <-
 function(object,bit) {
-  (object %/% (2^bit)) %% 2
+  out <- (object %/% (2^bit)) %% 2
+  if (!is.null(dim(object))) dim(out) <- dim(object)
+  out
 }
 
 "bits<-" <-

R/get.pimgs.R

@@ -1,4 +1,4 @@
 .onAttach <- function(libname, pkgname) {
-  packageStartupMessage("tripEstimation has been superseded by SGAT, please look at using that package instead:\nhttps://github.com/SWotherspoon/SGAT")
+  packageStartupMessage("tripEstimation has been superseded by SGAT and SGATII:\nhttps://github.com/SWotherspoon/SGAT, https://github.com/SWotherspoon/SGATII")
   invisible()
-}
+}

R/get.sst.R

@@ -5,7 +5,7 @@ tripEstimation
 
 tripEstimation maintenance
 
-NOTE: this package is now deprecated by SGAT, https://github.com/SWotherspoon/SGAT
+NOTE: this package is now deprecated by SGAT, https://github.com/SWotherspoon/SGAT or https://github.com/SWotherspoon/SGATII. 
 
 
 

R/zzz.r

@@ -0,0 +1,9 @@
+## R CMD check results
+
+tripEstimation 0.0-45 to remove dependency on rgdal. 
+
+This is an old package
+Thank you. 
+
+
+0 errors | 0 warnings | 0 notes

README.md

@@ -13,7 +13,7 @@ bibentry(
   publisher = "Public Library of Science",
   volume = "4",
   year = "2009",
-  url = "http://dx.plos.org/10.1371/journal.pone.0007324")
+  url = "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007324")
 
   year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date)
   vers <- paste("R package version", meta$Version)

cran-comments.md

@@ -3,20 +3,18 @@
 \alias{as.matrix.pimg}
 \alias{combine}
 \alias{coords.pimg}
-\alias{get.pimgs}
 \alias{unzipper}
 \alias{as.local.pimg}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{Convert to image list}
 \description{
 Converts Probability image (pimage) component to standard R xyz list
-image. 
+image.
 }
 \usage{
 as.image.pimg(pimg)
 combine(pimgs, subset = 1:length(pimgs))
 coords.pimg(pimg)
-get.pimgs(rootdir = NULL, f2load = "p_ImageList.Rdata")
 unzipper(px)
 as.local.pimg(pimg)
 \method{as.matrix}{pimg}(x, \dots)
@@ -26,8 +24,6 @@ as.local.pimg(pimg)
   \item{pimg}{Probability image component}
     \item{pimgs}{ \code{pimgs}  }
     \item{subset}{ \code{subset} }
-      \item{rootdir}{ \code{rootdir}  }
-      \item{f2load}{ \code{f2load}  }
 
       \item{px}{ \code{px} }
 
@@ -36,8 +32,22 @@ as.local.pimg(pimg)
       \item{\dots}{\code{\dots}}
 }
 
+\value{
+\code{as.image.pimg} returns a \code{image} list with vectors x,y and z matrix
+
+\code{as.matrix.pimg} returns just the local matrix populated in the parent
+
+\code{combine} returns the collective matrix, in \code{image} xyz form
+
+\code{coords.pimg} returns the rectilinear coordinates of the pimg parent
+
+\code{unzipper} returns a \code{pimg.list} by combining multiple compatible ones together and resolving their temporal order
+
+\code{as.local.pimg} returns the \code{pimg} in local form
+}
+
 \author{Michael D. Sumner}
 
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
-\keyword{manip}
+\keyword{manip}

inst/CITATION

@@ -9,11 +9,11 @@
 \alias{POLAR}
 \title{Calculations for position of the sun and moon}
 \description{
- This set of functions provides simple position calculations for the sun and moon, 
+ This set of functions provides simple position calculations for the sun and moon,
  taken from Pascal routines published in Montenbruck and Pfleger (1994, Dunlop).
- 
+
  These are completely independent from the (specifically optimized) solar elevation
- calculations available via [elevation and solar]. 
+ calculations available via [elevation and solar].
 }
 \usage{
 astro(lon, lat, astro.calc)
@@ -38,35 +38,35 @@ POLAR(X, Y, Z)
    \item{lon}{vector of \code{lon}gitudes}
    \item{lat}{vector of \code{lat}itudes}
   \item{astro.calc}{list object containing \code{RA} right ascension }
-  
+
   %% EQUHOR
   \item{DEC}{declination}
   \item{TAU}{\code{TAU}  }
   \item{PHI}{ \code{PHI}  }
-  
-  %% FRAC 
+
+  %% FRAC
   \item{x}{number}
-  
+
   %% LMST
   \item{MJDay}{ modified julian day }
   \item{LAMBDA}{\code{LAMBDA} }
-  
+
   %% lunar / mini.sun
   \item{time}{ vector of date-times in POSIXct format }
-   
-  %% MJDay 
+
+  %% MJDay
   \item{date}{ vector of date-times in POSIXct format }
-  
+
   %% POLAR
   \item{X}{ x-coordinate}
   \item{Y}{ y-coordinate }
   \item{Z}{ z-coordinate }
-   
+
 }
 
 \value{
  \code{astro} returns a list object with the components of the moon or sun's
- position, 
+ position,
   \item{r }{rho component }
   \item{theta }{theta component - elevation}
   \item{phi}{phi component - azimuth}
@@ -110,9 +110,9 @@ op <- par(mfrow = c(2,1))
 plot(tm, rtp$theta, main = "solar elevation, Hobart")
 plot(tm, rtp$phi, main = "solar azimuth, Hobart")
 par(op)
-\dontrun{
+\donttest{
   elev.gmt <- mkElevationSeg(1, tm)
-  plot(tm, rtp$theta, main = "solar elevation mini.sun versus NOAA") 
+  plot(tm, rtp$theta, main = "solar elevation mini.sun versus NOAA")
   lines(tm, elev.gmt(1, 147, -42))
 }
 }

man/as.image.pimg.Rd

@@ -5,7 +5,7 @@
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{ Bin MCMC chains.  }
 \description{
-  Bin MCMC chains in probability image summaries. 
+  Bin MCMC chains in probability image summaries.
 }
 \usage{
 behav.bin(z, pimgs, weights = NULL)
@@ -24,11 +24,19 @@ chunk.bin(filename, pimgs, weights = NULL, chunk = 2000, proj = NULL)
 
     \item{filename}{  \code{filename}  }
 
-  
+
   \item{chunk}{  \code{chunk}  }
   \item{proj}{  \code{proj}  }
 }
+\value{
+
+\code{behav.bin} returns a \code{pimg.list}
+
+\code{bin.pimg} and \code{chunk.bin} provide work flow for \code{behav.bin}, to do the local binning and
+control the overal job
 
+
+}
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
-\keyword{manip}
+\keyword{manip}

man/astro.Rd

@@ -3,8 +3,8 @@
 \alias{bits<-}
 \title{ Set and get bits from binary masks.  }
 \description{
-  Utility functions to access bits from numeric values, 
-  for the efficient storage of spatial masks. 
+  Utility functions to access bits from numeric values,
+  for the efficient storage of spatial masks.
 }
 \usage{
 bits(object, bit)
@@ -16,29 +16,29 @@ bits(object, bit) <-  value
   %% bits
   \item{object}{ a numeric value }
   \item{bit}{ the desired bit}
-  
+
   %% bits<-
 
   \item{value}{ logical value to set bit to }
 }
 \details{
-  \R uses 32-bit integers, so we can (easily) access 31 binary matrices in each numeric 
-  matrix.   This is very useful for storing long time-series of spatial masks, 
-  required for track-location estimation from archival tags. 
-  
+  \R uses 32-bit integers, so we can (easily) access 31 binary matrices in each numeric
+  matrix.   This is very useful for storing long time-series of spatial masks,
+  required for track-location estimation from archival tags.
+
 }
 \value{
  A numeric object with the given bit set, or a logical value designating the
- status of the given bit. 
+ status of the given bit.
 }
 
 \author{ Michael D. Sumner }
-\note{ The 32nd bit is harder to access, so we ignore it. 
+\note{ The 32nd bit is harder to access, so we ignore it.
 }
 \seealso{ See Also  \code{\link{get.mask}} for a higher level access of a mask object }
 %and \{code\link{\%\%}} for integer division.  }
 \examples{
-a <- 1
+a <- 1L
 bits(a, 0)  ## 1
 bits(a, 2) <- 1
 a   # 5