- Added element_blank as an import from ggplot2

- Improved modelHD documentation
- Update NAMESPACE

NAMESPACE

@@ -42,16 +42,23 @@ importFrom(data.table,tstrsplit)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,arrow)
 importFrom(ggplot2,coord_equal)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_polygon)
 importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,geom_smooth)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_shape_manual)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
+importFrom(ggplot2,unit)
 importFrom(grDevices,terrain.colors)
 importFrom(graphics,axis)
 importFrom(graphics,grid)

R/checkPlotCoord.R

@@ -34,7 +34,7 @@
 #'
 #' @importFrom data.table data.table := setnames
 #' @importFrom sf st_multipoint st_polygon st_sfc
-#' @importFrom ggplot2 ggplot aes geom_point geom_segment geom_polygon geom_text scale_shape_manual scale_color_manual ggtitle theme_minimal theme coord_equal arrow unit
+#' @importFrom ggplot2 ggplot aes geom_point geom_segment geom_polygon geom_text scale_shape_manual scale_color_manual ggtitle theme_minimal theme coord_equal arrow unit element_blank
 #'
 #' @author Arthur PERE, Maxime REJOU-MECHAIN, Arthur BAILLY
 #'
@@ -78,7 +78,7 @@
 #'
 checkPlotCoord <- function(projCoord = NULL, longlat = NULL, relCoord, trustGPScorners, cornerID=NULL, maxDist = 15, rmOutliers = TRUE,  drawPlot = TRUE, treeCoord = NULL) {
 
-  # parameters verification -------------------------------------------------
+  # Checking arguments -------------------------------------------------
 
   if (is.null(longlat) && is.null(projCoord)) {
     stop("Give at least one set of coordinates: longlat or projCoord")

R/cutPlot.R

@@ -4,7 +4,7 @@ if (getRversion() >= "2.15.1") {
   ))
 }
 
-#' Divides a plot in subplots
+#' Divides one ore more plots into subplots
 #'
 #' This function divides a plot (or several plots) in subplots and returns the coordinates of the grid.
 #' This function uses a procrust analysis to fit the rectangle you gave to the plot you have.

R/modelHD.R

@@ -44,7 +44,6 @@
 #' If the parameter model is null, the function return a plot with all the methods for
 #' comparison, the function also returns a data.frame with:
 #'   - `method`: The method that had been used to construct the plot
-#'   - `color`: The color of the curve in the plot
 #'   - `RSE`: Residual Standard Error of the model
 #'   - `RSElog`: Residual Standard Error of the log model (`NULL` if other model)
 #'   - `Average_bias`: The average bias for the model
@@ -61,29 +60,36 @@
 #' # Load a data set
 #' data(NouraguesHD)
 #'
-#' # To model the height from a dataset
+#' # Fit H-D models for the Nouragues dataset
 #' \donttest{
 #' HDmodel <- modelHD(D = NouraguesHD$D, H = NouraguesHD$H, drawGraph = TRUE)
 #' }
 #'
-#' # If the method needed is known
-#' HDmodel <- modelHD(D = NouraguesHD$D, H = NouraguesHD$H, method = "weibull", drawGraph = TRUE)
-#' HDmodel <- modelHD(D = NouraguesHD$D, H = NouraguesHD$H, method = "log1", drawGraph = TRUE)
+#' # For a chosen model
+#' HDmodel <- modelHD(D = NouraguesHD$D, H = NouraguesHD$H,
+#' method = "log2", drawGraph = TRUE)
 #'
 #' # Using weights
 #' HDmodel <- modelHD(
-#'   D = NouraguesHD$D, H = NouraguesHD$H, method = "weibull", useWeight = TRUE,
-#'   drawGraph = TRUE
-#' )
+#'   D = NouraguesHD$D, H = NouraguesHD$H,
+#'   method = "log2", useWeight = TRUE,
+#'   drawGraph = TRUE)
+#' 
+#' # With multiple stands (plots)
+#' HDmodel <- modelHD(
+#'   D = NouraguesHD$D, H = NouraguesHD$H,
+#'   method = "log2", useWeight = TRUE, 
+#'   plot = NouraguesHD$plotId, drawGraph = TRUE)
+#' 
 #' @importFrom graphics legend lines par plot grid axis
 #' @importFrom stats SSmicmen lm median na.omit quantile rnorm sd predict coef
 #' @importFrom utils data
 #' @importFrom data.table data.table
-#' @importFrom ggplot2 ggplot aes geom_point geom_smooth labs theme_minimal theme scale_x_continuous scale_y_continuous
+#' @importFrom ggplot2 ggplot aes geom_point geom_smooth labs theme_minimal theme scale_x_continuous scale_y_continuous element_text 
 
 modelHD <- function(D, H, method = NULL, useWeight = FALSE, drawGraph = FALSE, plot = NULL) {
 
-  # parameters verification -------------------------------------------------
+  # Checking arguments -------------------------------------------------
 
   # Check if there is enough data to compute an accurate model
   nbNonNA <- sum(!is.na(H))

tests/testthat/test_00_modelHD.R

@@ -1,4 +1,4 @@
-require(data.table)
+#require(data.table)
 
 D <- NouraguesHD$D
 H <- NouraguesHD$H
@@ -58,13 +58,13 @@ test_that("Without parameters", {
   Res <- expect_message(modelHD(D, H, useWeight = TRUE), "build a HD model")
 
   expect_is(Res, "data.frame")
-  expect_equal(ncol(Res), 5)
+  expect_equal(ncol(Res),4)
 
-  res <- "method  color      RSE    RSElog Average_bias
-log1   blue 4.305060 0.2231136  0.004227454
-log2  green 4.222718 0.2215495  0.003121671
-weibull orange 4.307951        NA  0.002823978
-michaelis purple 4.294488        NA  0.014564152
+  res <- "method  RSE    RSElog Average_bias
+log1 4.305060 0.2231136  0.004227454
+log2  4.222718 0.2215495  0.003121671
+weibull 4.307951        NA  0.002823978
+michaelis 4.294488        NA  0.014564152
 "
 
 

tests/testthat/test_01_correctCoordGPS.R

@@ -71,26 +71,26 @@ test_that("correct coord GPS in UTM", {
 })
 
 test_that("correct coord GPS error", {
-  expect_error(correctCoordGPS(), "Give at least one set of coordinates")
+  expect_error(suppressWarnings(correctCoordGPS()), "Give at least one set of coordinates")
   expect_error(
-    correctCoordGPS(projCoord = projCoord, coordRel = coordRel, rangeX = 52, rangeY = 53,rmOutliers = FALSE),
+    suppressWarnings(correctCoordGPS(projCoord = projCoord, coordRel = coordRel, rangeX = 52, rangeY = 53,rmOutliers = FALSE)),
     "must be of length 2"
   )
   expect_error(
-    correctCoordGPS(projCoord = projCoord, coordRel = coordRel, rangeX = c(0, 100), rangeY = c(0, 100), maxDist = c(15, 0),rmOutliers = FALSE),
+    suppressWarnings(correctCoordGPS(projCoord = projCoord, coordRel = coordRel, rangeX = c(0, 100), rangeY = c(0, 100), maxDist = c(15, 0),rmOutliers = FALSE)),
     "Your argument maxDist must be of length 1"
   )
   expect_error(
-    correctCoordGPS(projCoord = projCoord, coordRel = coordRel, rangeX = c(0, 40), rangeY = c(0, 40),rmOutliers = FALSE),
+    suppressWarnings(correctCoordGPS(projCoord = projCoord, coordRel = coordRel, rangeX = c(0, 40), rangeY = c(0, 40),rmOutliers = FALSE)),
     "coordRel must be inside the X and Y ranges"
   )
   expect_error(
-    correctCoordGPS(projCoord = projCoord, coordRel = rbind(coordRel, c(40, 40)), rangeX = c(0, 100), rangeY = c(0, 100),rmOutliers = FALSE),
+    suppressWarnings(correctCoordGPS(projCoord = projCoord, coordRel = rbind(coordRel, c(40, 40)), rangeX = c(0, 100), rangeY = c(0, 100),rmOutliers = FALSE)),
     "same dimension"
   )
   skip_if_not_installed("proj4")
   expect_error(
-    correctCoordGPS(longlat = c(15, 12), projCoord = projCoord,rmOutliers = FALSE),
+    suppressWarnings(correctCoordGPS(longlat = c(15, 12), projCoord = projCoord,rmOutliers = FALSE)),
     "Give only one set of coordinates"
   )
 })