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Roxygenized documentation #38

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0393ddf
Roxygenized documentation in R files
iagomosqueira Mar 15, 2021
8e33f03
Added flag to use markdown in roxygen documentation
iagomosqueira Mar 15, 2021
7553498
Deleted non-Latin1 character, roxygen chokes on it
iagomosqueira Mar 15, 2021
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1 change: 1 addition & 0 deletions vmstools/DESCRIPTION
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Expand Up @@ -11,3 +11,4 @@ Imports: cluster, data.table, doBy, maps, mapdata, maptools, PBSmapping, sp, seg
Suggests: lattice, raster, shapefiles, tcltk
Repository: CRAN
LazyLoad: Yes
Roxygen: list(markdown = TRUE)
116 changes: 70 additions & 46 deletions vmstools/R/CSquare.r
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@@ -1,46 +1,70 @@
CSquare <- function(lon,lat,degrees){

if(length(lon) != length(lat)) stop("length of longitude not equal to length of latitude")
if(!degrees %in% c(10,5,1,0.5,0.1,0.05,0.01)) stop("degrees specified not in range: c(10,5,1,0.5,0.1,0.05,0.01)")

dims <- length(lon)

quadrants <- array(NA,dim=c(4,6,dims),dimnames=list(c("globalQuadrant","intmQuadrant1","intmQuadrant2","intmQuadrant3"),c("quadrantDigit","latDigit","lonDigit","latRemain","lonRemain","code"),seq(1,dims,1)))

quadrants["globalQuadrant","quadrantDigit",] <- 4-(((2*floor(1+(lon/200)))-1)*((2*floor(1+(lat/200)))+1))
quadrants["globalQuadrant","latDigit",] <- floor(abs(lat)/10)
quadrants["globalQuadrant","lonDigit",] <- floor(abs(lon)/10)
quadrants["globalQuadrant","latRemain",] <- round(abs(lat)-(quadrants["globalQuadrant","latDigit",]*10),7)
quadrants["globalQuadrant","lonRemain",] <- round(abs(lon)-(quadrants["globalQuadrant","lonDigit",]*10),7)
quadrants["globalQuadrant","code",] <- quadrants["globalQuadrant","quadrantDigit",]*1000+quadrants["globalQuadrant","latDigit",]*100+quadrants["globalQuadrant","lonDigit",]

quadrants["intmQuadrant1","quadrantDigit",] <- (2*floor(quadrants["globalQuadrant","latRemain",]*0.2))+floor(quadrants["globalQuadrant","lonRemain",]*0.2)+1
quadrants["intmQuadrant1","latDigit",] <- floor(quadrants["globalQuadrant","latRemain",])
quadrants["intmQuadrant1","lonDigit",] <- floor(quadrants["globalQuadrant","lonRemain",])
quadrants["intmQuadrant1","latRemain",] <- round((quadrants["globalQuadrant","latRemain",]-quadrants["intmQuadrant1","latDigit",])*10,7)
quadrants["intmQuadrant1","lonRemain",] <- round((quadrants["globalQuadrant","lonRemain",]-quadrants["intmQuadrant1","lonDigit",])*10,7)
quadrants["intmQuadrant1","code",] <- quadrants["intmQuadrant1","quadrantDigit",]*100+quadrants["intmQuadrant1","latDigit",]*10+quadrants["intmQuadrant1","lonDigit",]

quadrants["intmQuadrant2","quadrantDigit",] <- (2*floor(quadrants["intmQuadrant1","latRemain",]*0.2))+floor(quadrants["intmQuadrant1","lonRemain",]*0.2)+1
quadrants["intmQuadrant2","latDigit",] <- floor(quadrants["intmQuadrant1","latRemain",])
quadrants["intmQuadrant2","lonDigit",] <- floor(quadrants["intmQuadrant1","lonRemain",])
quadrants["intmQuadrant2","latRemain",] <- round((quadrants["intmQuadrant1","latRemain",]-quadrants["intmQuadrant2","latDigit",])*10,7)
quadrants["intmQuadrant2","lonRemain",] <- round((quadrants["intmQuadrant1","lonRemain",]-quadrants["intmQuadrant2","lonDigit",])*10,7)
quadrants["intmQuadrant2","code",] <- quadrants["intmQuadrant2","quadrantDigit",]*100+quadrants["intmQuadrant2","latDigit",]*10+quadrants["intmQuadrant2","lonDigit",]

quadrants["intmQuadrant3","quadrantDigit",] <- (2*floor(quadrants["intmQuadrant2","latRemain",]*0.2))+floor(quadrants["intmQuadrant2","lonRemain",]*0.2)+1
quadrants["intmQuadrant3","latDigit",] <- floor(quadrants["intmQuadrant2","latRemain",])
quadrants["intmQuadrant3","lonDigit",] <- floor(quadrants["intmQuadrant2","lonRemain",])
quadrants["intmQuadrant3","latRemain",] <- round((quadrants["intmQuadrant2","latRemain",]-quadrants["intmQuadrant3","latDigit",])*10,7)
quadrants["intmQuadrant3","lonRemain",] <- round((quadrants["intmQuadrant2","lonRemain",]-quadrants["intmQuadrant3","lonDigit",])*10,7)
quadrants["intmQuadrant3","code",] <- quadrants["intmQuadrant3","quadrantDigit",]*100+quadrants["intmQuadrant3","latDigit",]*10+quadrants["intmQuadrant3","lonDigit",]

if(degrees == 10) CSquareCodes <- quadrants["globalQuadrant","code",]
if(degrees == 5) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","quadrantDigit",],sep="")
if(degrees == 1) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],sep="")
if(degrees == 0.5) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","quadrantDigit",],sep="")
if(degrees == 0.1) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","code",],sep="")
if(degrees == 0.05) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","code",],":",quadrants["intmQuadrant3","quadrantDigit",],sep="")
if(degrees == 0.01) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","code",],":",quadrants["intmQuadrant3","code",],sep="")

return(CSquareCodes)}
#' Calculate the CSquare notation from the GPS locations
#'
#' Compute the CSquare notation from the GPS location where you can define what
#' resolution you want the CSquare notation to be.
#'
#'
#' @param lon Longitudes of points
#' @param lat Latitudes of points
#' @param degrees Resolution of CSquare notation: 10, 5, 1, 0.5, 0.1, 0.05,
#' 0.01
#' @author Niels T. Hintzen
#' @seealso \code{\link{km2Degree}}, \code{\link{degree2Km}},
#' \code{\link{lonLatRatio}}, \code{\link{distance}}
#' @references EU Lot 2 project, based on CSquare:
#' http://www.marine.csiro.au/csquares/
#' @examples
#'
#' lon <- -4
#' lat <- 50
#' degrees <- 0.01
#'
#' CSquare(lon,lat,degrees) # "7500:104:100:100"
#'
#' @export CSquare
CSquare <- function(lon,lat,degrees){

if(length(lon) != length(lat)) stop("length of longitude not equal to length of latitude")
if(!degrees %in% c(10,5,1,0.5,0.1,0.05,0.01)) stop("degrees specified not in range: c(10,5,1,0.5,0.1,0.05,0.01)")

dims <- length(lon)

quadrants <- array(NA,dim=c(4,6,dims),dimnames=list(c("globalQuadrant","intmQuadrant1","intmQuadrant2","intmQuadrant3"),c("quadrantDigit","latDigit","lonDigit","latRemain","lonRemain","code"),seq(1,dims,1)))

quadrants["globalQuadrant","quadrantDigit",] <- 4-(((2*floor(1+(lon/200)))-1)*((2*floor(1+(lat/200)))+1))
quadrants["globalQuadrant","latDigit",] <- floor(abs(lat)/10)
quadrants["globalQuadrant","lonDigit",] <- floor(abs(lon)/10)
quadrants["globalQuadrant","latRemain",] <- round(abs(lat)-(quadrants["globalQuadrant","latDigit",]*10),7)
quadrants["globalQuadrant","lonRemain",] <- round(abs(lon)-(quadrants["globalQuadrant","lonDigit",]*10),7)
quadrants["globalQuadrant","code",] <- quadrants["globalQuadrant","quadrantDigit",]*1000+quadrants["globalQuadrant","latDigit",]*100+quadrants["globalQuadrant","lonDigit",]

quadrants["intmQuadrant1","quadrantDigit",] <- (2*floor(quadrants["globalQuadrant","latRemain",]*0.2))+floor(quadrants["globalQuadrant","lonRemain",]*0.2)+1
quadrants["intmQuadrant1","latDigit",] <- floor(quadrants["globalQuadrant","latRemain",])
quadrants["intmQuadrant1","lonDigit",] <- floor(quadrants["globalQuadrant","lonRemain",])
quadrants["intmQuadrant1","latRemain",] <- round((quadrants["globalQuadrant","latRemain",]-quadrants["intmQuadrant1","latDigit",])*10,7)
quadrants["intmQuadrant1","lonRemain",] <- round((quadrants["globalQuadrant","lonRemain",]-quadrants["intmQuadrant1","lonDigit",])*10,7)
quadrants["intmQuadrant1","code",] <- quadrants["intmQuadrant1","quadrantDigit",]*100+quadrants["intmQuadrant1","latDigit",]*10+quadrants["intmQuadrant1","lonDigit",]

quadrants["intmQuadrant2","quadrantDigit",] <- (2*floor(quadrants["intmQuadrant1","latRemain",]*0.2))+floor(quadrants["intmQuadrant1","lonRemain",]*0.2)+1
quadrants["intmQuadrant2","latDigit",] <- floor(quadrants["intmQuadrant1","latRemain",])
quadrants["intmQuadrant2","lonDigit",] <- floor(quadrants["intmQuadrant1","lonRemain",])
quadrants["intmQuadrant2","latRemain",] <- round((quadrants["intmQuadrant1","latRemain",]-quadrants["intmQuadrant2","latDigit",])*10,7)
quadrants["intmQuadrant2","lonRemain",] <- round((quadrants["intmQuadrant1","lonRemain",]-quadrants["intmQuadrant2","lonDigit",])*10,7)
quadrants["intmQuadrant2","code",] <- quadrants["intmQuadrant2","quadrantDigit",]*100+quadrants["intmQuadrant2","latDigit",]*10+quadrants["intmQuadrant2","lonDigit",]

quadrants["intmQuadrant3","quadrantDigit",] <- (2*floor(quadrants["intmQuadrant2","latRemain",]*0.2))+floor(quadrants["intmQuadrant2","lonRemain",]*0.2)+1
quadrants["intmQuadrant3","latDigit",] <- floor(quadrants["intmQuadrant2","latRemain",])
quadrants["intmQuadrant3","lonDigit",] <- floor(quadrants["intmQuadrant2","lonRemain",])
quadrants["intmQuadrant3","latRemain",] <- round((quadrants["intmQuadrant2","latRemain",]-quadrants["intmQuadrant3","latDigit",])*10,7)
quadrants["intmQuadrant3","lonRemain",] <- round((quadrants["intmQuadrant2","lonRemain",]-quadrants["intmQuadrant3","lonDigit",])*10,7)
quadrants["intmQuadrant3","code",] <- quadrants["intmQuadrant3","quadrantDigit",]*100+quadrants["intmQuadrant3","latDigit",]*10+quadrants["intmQuadrant3","lonDigit",]

if(degrees == 10) CSquareCodes <- quadrants["globalQuadrant","code",]
if(degrees == 5) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","quadrantDigit",],sep="")
if(degrees == 1) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],sep="")
if(degrees == 0.5) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","quadrantDigit",],sep="")
if(degrees == 0.1) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","code",],sep="")
if(degrees == 0.05) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","code",],":",quadrants["intmQuadrant3","quadrantDigit",],sep="")
if(degrees == 0.01) CSquareCodes <- paste(quadrants["globalQuadrant","code",],":",quadrants["intmQuadrant1","code",],":",quadrants["intmQuadrant2","code",],":",quadrants["intmQuadrant3","code",],sep="")

return(CSquareCodes)}
120 changes: 72 additions & 48 deletions vmstools/R/CSquare2LonLat.r
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CSquare2LonLat <- function(csqr,degrees){

ra <- 1e-6 #Artificial number to add for rounding of 5'ves (round(0.5) = 0, but in Excel (where conversion comes from, it is 1)
chars <- an(nchar(csqr))
tensqd <- an(substr(csqr,1,1))+ra; gqlat <- (round(abs(tensqd-4)*2/10)*10/5)-1
tenslatd <- an(substr(csqr,2,2))+ra; gqlon <- (2*round(tensqd/10)-1)*-1
tenslond <- an(substr(csqr,3,4))+ra
unitsqd <- an(substr(csqr,6,6))+ra; iqulat <- round(unitsqd*2/10)
unitslatd <- an(substr(csqr,7,7))+ra; iqulon <- (round((unitsqd-1)/2,1) - floor((unitsqd-1)/2))*2
unitslond <- an(substr(csqr,8,8))+ra
tenthsqd <- an(substr(csqr,10,10))+ra; iqtlat <- round(tenthsqd*2/10)
tenthslatd <- an(substr(csqr,11,11))+ra; iqtlon <- (round((tenthsqd-1)/2,1) - floor((tenthsqd-1)/2))*2
tenthslond <- an(substr(csqr,12,12))+ra
hundqd <- an(substr(csqr,14,14))+ra; iqhlat <- round(hundqd*2/10)
hundlatd <- an(substr(csqr,15,15))+ra; iqhlon <- (round((hundqd-1)/2,1) - floor((hundqd-1)/2))*2
hundlond <- an(substr(csqr,16,16))+ra
reso <- 10^(1-floor((chars-4)/4))-((round((chars-4)/4,1)-floor((chars-4)/4))*10^(1-floor((chars-4)/4)))

if(degrees < reso[1]) stop("Returning degrees is smaller than format of C-square")
if(degrees == 10){
lat <- ((tenslatd*10)+5)*gqlat-ra
lon <- ((tenslond*10)+5)*gqlon-ra
}
if(degrees == 5){
lat <- ((tenslatd*10)+(iqulat*5)+2.5)*gqlat-ra
lon <- ((tenslond*10)+(iqulon*5)+2.5)*gqlon-ra
}
if(degrees == 1){
lat <- ((tenslatd*10)+ unitslatd+0.5)*gqlat-ra
lon <- ((tenslond*10)+ unitslond+0.5)*gqlon-ra
}
if(degrees == 0.5){
lat <- ((tenslatd*10)+ unitslatd + (iqtlat*0.5)+0.25)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (iqtlon*0.5)+0.25)*gqlon-ra
}
if(degrees == 0.1){
lat <- ((tenslatd*10)+ unitslatd + (tenthslatd*0.1)+0.05)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (tenthslond*0.1)+0.05)*gqlon-ra
}
if(degrees == 0.05){
lat <- ((tenslatd*10)+ unitslatd + (tenthslatd*0.1)+(iqhlat*0.05)+0.025)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (tenthslond*0.1)+(iqhlon*0.05)+0.025)*gqlon-ra
}
if(degrees == 0.01){
lat <- ((tenslatd*10)+ unitslatd + (tenthslatd*0.1)+(hundlatd*0.01)+0.005)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (tenthslond*0.1)+(hundlond*0.01)+0.005)*gqlon-ra
}
return(data.frame(SI_LATI=lat,SI_LONG=lon))}
#' Calculate the GPS notation from the CSquare notation
#'
#' Convert the CSquare notation to GPS location where you can define what
#' resolution you want the GPS notation to be.
#'
#'
#' @param csqr CSquare notation like: 1400:134:120:356
#' @param degrees Degrees resolution of returned GPS notation : 10, 5, 1, 0.5,
#' 0.1, 0.05, 0.01
#' @author Niels T. Hintzen
#' @seealso \code{\link{km2Degree}}, \code{\link{degree2Km}},
#' \code{\link{lonLatRatio}}, \code{\link{distance}}
#' @references EU Lot 2 project, based on CSquare:
#' http://www.marine.csiro.au/csquares/
#' @examples
#'
#' data(tacsat)
#' tacsat$CSquare <- CSquare(tacsat$SI_LONG,tacsat$SI_LATI,0.05)
#' tacsat$SI_LONG2 <- CSquare2LonLat(tacsat$CSquare,0.5)$SI_LONG
#' tacsat$SI_LATI2 <- CSquare2LonLat(tacsat$CSquare,0.5)$SI_LATI
#' tacsat$CSquare2 <- CSquare(tacsat$SI_LONG2,tacsat$SI_LATI2,1)
#' head(tacsat[which(tacsat$CSquare != tacsat$CSquare2),])
#'
#' @export CSquare2LonLat
CSquare2LonLat <- function(csqr,degrees){

ra <- 1e-6 #Artificial number to add for rounding of 5'ves (round(0.5) = 0, but in Excel (where conversion comes from, it is 1)
chars <- an(nchar(csqr))
tensqd <- an(substr(csqr,1,1))+ra; gqlat <- (round(abs(tensqd-4)*2/10)*10/5)-1
tenslatd <- an(substr(csqr,2,2))+ra; gqlon <- (2*round(tensqd/10)-1)*-1
tenslond <- an(substr(csqr,3,4))+ra
unitsqd <- an(substr(csqr,6,6))+ra; iqulat <- round(unitsqd*2/10)
unitslatd <- an(substr(csqr,7,7))+ra; iqulon <- (round((unitsqd-1)/2,1) - floor((unitsqd-1)/2))*2
unitslond <- an(substr(csqr,8,8))+ra
tenthsqd <- an(substr(csqr,10,10))+ra; iqtlat <- round(tenthsqd*2/10)
tenthslatd <- an(substr(csqr,11,11))+ra; iqtlon <- (round((tenthsqd-1)/2,1) - floor((tenthsqd-1)/2))*2
tenthslond <- an(substr(csqr,12,12))+ra
hundqd <- an(substr(csqr,14,14))+ra; iqhlat <- round(hundqd*2/10)
hundlatd <- an(substr(csqr,15,15))+ra; iqhlon <- (round((hundqd-1)/2,1) - floor((hundqd-1)/2))*2
hundlond <- an(substr(csqr,16,16))+ra
reso <- 10^(1-floor((chars-4)/4))-((round((chars-4)/4,1)-floor((chars-4)/4))*10^(1-floor((chars-4)/4)))

if(degrees < reso[1]) stop("Returning degrees is smaller than format of C-square")
if(degrees == 10){
lat <- ((tenslatd*10)+5)*gqlat-ra
lon <- ((tenslond*10)+5)*gqlon-ra
}
if(degrees == 5){
lat <- ((tenslatd*10)+(iqulat*5)+2.5)*gqlat-ra
lon <- ((tenslond*10)+(iqulon*5)+2.5)*gqlon-ra
}
if(degrees == 1){
lat <- ((tenslatd*10)+ unitslatd+0.5)*gqlat-ra
lon <- ((tenslond*10)+ unitslond+0.5)*gqlon-ra
}
if(degrees == 0.5){
lat <- ((tenslatd*10)+ unitslatd + (iqtlat*0.5)+0.25)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (iqtlon*0.5)+0.25)*gqlon-ra
}
if(degrees == 0.1){
lat <- ((tenslatd*10)+ unitslatd + (tenthslatd*0.1)+0.05)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (tenthslond*0.1)+0.05)*gqlon-ra
}
if(degrees == 0.05){
lat <- ((tenslatd*10)+ unitslatd + (tenthslatd*0.1)+(iqhlat*0.05)+0.025)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (tenthslond*0.1)+(iqhlon*0.05)+0.025)*gqlon-ra
}
if(degrees == 0.01){
lat <- ((tenslatd*10)+ unitslatd + (tenthslatd*0.1)+(hundlatd*0.01)+0.005)*gqlat-ra
lon <- ((tenslond*10)+ unitslond + (tenthslond*0.1)+(hundlond*0.01)+0.005)*gqlon-ra
}
return(data.frame(SI_LATI=lat,SI_LONG=lon))}
24 changes: 24 additions & 0 deletions vmstools/R/ICESarea.r
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@@ -1,3 +1,27 @@
#' Get ICES area from coordinates
#'
#' Get the ICES area from any lon,lat position, given that this position is
#' within the ICES region.
#'
#'
#' @param tacsat dataframe given that they have 'SI_LONG' and 'SI_LATI' columns
#' (either tacsat format or other dataset with SI_LONG and SI_LATI columns)
#' @param areas ICES areas as SpatialPolygons
#' @param proj4string Projection string, default to NULL.
#' @param fast If memory allocation is not a problem, a faster version can be
#' switched on
#' @return Returns the areas as a vector
#' @author Niels T. Hintzen
#' @seealso \code{\link{ICESrectangle}}, \code{\link{ICESrectangle2LonLat}}
#' @references EU Lot 2 project
#' @examples
#'
#' data(ICESareas)
#' res <- data.frame(SI_LONG = c(1,2,2,4,2),
#' SI_LATI = c(53,53.2,54,56.7,55.2))
#' areas <- ICESarea(res,ICESareas)
#'
#' @export ICESarea
ICESarea <- function(tacsat,areas,proj4string=NULL,fast=FALSE){
require(sp)
if(!class(areas) %in% c("SpatialPolygons","SpatialPolygonsDataFrame")) stop("'areas' must be specified as class 'SpatialPolygons' or 'SpatialPolygonsDataFrame'")
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