R/internal_utility_functions.R

In MikkoVihtakari/SuitableHabitat: Estimate Habitat Spaces for Geographic Suitable Habitat Models

#' @title Round to multiple of any number
#' @param x numeric vector to round
#' @param accuracy number to round to; for POSIXct objects, a number of seconds
#' @param f rounding function: \code{\link{floor}}, \code{\link{ceiling}} or
#'  \code{\link{round}}
#' @keywords internal  
#' @author Hadley Wickham

round_any <- function(x, accuracy, f = round) {
  f(x / accuracy) * accuracy
}


#' @title Wrapper to \code{\link[smoothr]{smooth_ksmooth}} SpatialPolygons and SpatialPolygonsDataFrames
#' @param x SpatialPolygonsDataFrame
#' @param k The \code{smoothness} parameter in \code{\link[smoothr]{smooth_ksmooth}}
#' @param N The \code{n} parameter in \code{\link[smoothr]{smooth_ksmooth}}
#' @import smoothr sp
#' @importFrom stats na.omit
#' @keywords internal
#' @export

# Test parameters
# x = pol; k = 12; N = 5L
ksmooth_polys <- function(x, k, N) {
  
  total <- length(x@polygons)
  #pb <- txtProgressBar(min = 1, max = total, style = 3)
  
  tp <- lapply(1:total, function(i) {
    #setTxtProgressBar(pb, i)
    
    for(j in 1:length(x@polygons[[i]]@Polygons)) {
      x@polygons[[i]]@Polygons[[j]]@coords <- stats::na.omit(smoothr::smooth_ksmooth(x@polygons[[i]]@Polygons[[j]]@coords, smoothness = k, wrap = TRUE, n = N))
    }
    
    x@polygons[[i]]
    
  })
  
  out <- sp::SpatialPolygons(tp)
  suppressWarnings(sp::proj4string(out) <- sp::proj4string(x))
  
  if("SpatialPolygons" %in% class(x)) {
    out
  } else if("SpatialPolygonsDataFrame" %in% class(x)) {
    sp::SpatialPolygonsDataFrame(out, x@data)
  } else {
    stop("x is neither SpatialPolygons nor SpatialPolygonsDataFrame in ksmooth_polys,")
  }
  
}


#' @title Standard error of mean
#' @param x numeric vector

se <- function(x) {
  sd(x, na.rm = T)/sqrt(sum(!is.na(x)))
}

# Define lobal variables
utils::globalVariables(c("lon", "lat", "habitat", "long", "group", "km", "count_bin2", "level", "lon_cut", "mod.ext", "robustness", "sal", "temp", "depth", "value", "NEMOdata"))