From d580ce080dad20332fc7ca1250887703a6e132f4 Mon Sep 17 00:00:00 2001
From: Cecilia Nilsson <cecilia.nilsson@biol.lu.se>
Date: Thu, 16 Apr 2020 17:30:25 +0200
Subject: [PATCH 01/35] change from stopifnot to assert_that

---
 R/get_param.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/get_param.R b/R/get_param.R
index 00d83319c..9405bb444 100644
--- a/R/get_param.R
+++ b/R/get_param.R
@@ -14,7 +14,7 @@
 #' my_param <- get_param(example_scan, "VRADH")
 #' my_param
 get_param <- function(x, param) {
-  stopifnot(inherits(x, "scan"))
-  if (!(param %in% names(x$params))) stop(paste("scan parameter", param, "not found"))
+  assert_that(class(x) == "scan", msg = "`x` must be a scan object.")
+  if (!(param %in% names(x$params))) stop(paste("Scan parameter", param, "not found in `x`."))
   x$params[[param]]
 }

From af5c919129360965d9e38bd52d5dfd3066cd0039 Mon Sep 17 00:00:00 2001
From: Cecilia Nilsson <cecilia.nilsson@biol.lu.se>
Date: Thu, 16 Apr 2020 17:30:44 +0200
Subject: [PATCH 02/35] documentation updates

---
 R/get_param.R    | 8 ++++----
 man/get_param.Rd | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/get_param.R b/R/get_param.R
index 9405bb444..5b494ab05 100644
--- a/R/get_param.R
+++ b/R/get_param.R
@@ -1,9 +1,9 @@
-#' Get a scan parameter (\code{param}) from a scan (\code{scan})
+#' Get a scan parameter `param` from a scan `scan`
 #'
-#' @param x An object of class \code{scan}.
-#' @param param a scan parameter
+#' @param x An object of class `scan`.
+#' @param param A scan parameter.
 #'
-#' @return An object of class '\link[=summary.param]{param}'.
+#' @return An object of class [param][summary.param].
 #'
 #' @export
 #' @examples
diff --git a/man/get_param.Rd b/man/get_param.Rd
index 1e37f2fc2..4c5b10813 100644
--- a/man/get_param.Rd
+++ b/man/get_param.Rd
@@ -2,20 +2,20 @@
 % Please edit documentation in R/get_param.R
 \name{get_param}
 \alias{get_param}
-\title{Get a scan parameter (\code{param}) from a scan (\code{scan})}
+\title{Get a scan parameter \code{param} from a scan \code{scan}}
 \usage{
 get_param(x, param)
 }
 \arguments{
 \item{x}{An object of class \code{scan}.}
 
-\item{param}{a scan parameter}
+\item{param}{A scan parameter.}
 }
 \value{
-An object of class '\link[=summary.param]{param}'.
+An object of class \link[=summary.param]{param}.
 }
 \description{
-Get a scan parameter (\code{param}) from a scan (\code{scan})
+Get a scan parameter \code{param} from a scan \code{scan}
 }
 \examples{
 # we will extract a scan parameter from the example scan object:

From cc4ad27b3e9f1ef4394090cd690f280f7d783b83 Mon Sep 17 00:00:00 2001
From: Cecilia Nilsson <cecilia.nilsson@biol.lu.se>
Date: Thu, 16 Apr 2020 17:31:06 +0200
Subject: [PATCH 03/35] Unit tests for get_parm

---
 tests/testthat/test-get_param.R | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/tests/testthat/test-get_param.R b/tests/testthat/test-get_param.R
index 1d86f1072..feb6358cc 100644
--- a/tests/testthat/test-get_param.R
+++ b/tests/testthat/test-get_param.R
@@ -1,3 +1,17 @@
+pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
+pvol <- read_pvolfile(pvolfile)
+scan <- pvol$scans[[1]]
+
 test_that("returns error on incorrect parameters", {
+  expect_error(get_param("not_a_scan"), "`x` must be a scan object.")
+  expect_error(get_param(vp),"`x` must be a scan object.")
+  expect_error(get_param(pvol),"`x` must be a scan object.")
+  expect_error(get_param(scan))
+  expect_error(get_param(scan, "not_a_param"), "Scan parameter not_a_param not found in `x`.")
+})
 
+test_that("get_param returns correct parameters", {
+  expect_equal(get_param(scan, names(scan$params[1])), scan$params[[1]])
+  expect_equal(get_param(scan, names(scan$params[2])), scan$params[[2]])
 })
+

From fe7c7d6c700ed793a7e2fe8e5357475c60c2dbf4 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Fri, 24 Apr 2020 13:29:11 +0200
Subject: [PATCH 04/35] Move code for as.data.frame to own file

Move test as well
---
 R/as.data.frame.R                   | 240 ++++++++++++++++++++++++++++
 R/vp.R                              | 117 --------------
 R/vpts.R                            | 124 --------------
 man/as.data.frame.vp.Rd             |   2 +-
 man/as.data.frame.vpts.Rd           |   2 +-
 tests/testthat/test-as.data.frame.R | 129 +++++++++++++++
 tests/testthat/test-vp.R            | 128 +--------------
 7 files changed, 372 insertions(+), 370 deletions(-)
 create mode 100644 R/as.data.frame.R
 create mode 100644 tests/testthat/test-as.data.frame.R

diff --git a/R/as.data.frame.R b/R/as.data.frame.R
new file mode 100644
index 000000000..2e70851d3
--- /dev/null
+++ b/R/as.data.frame.R
@@ -0,0 +1,240 @@
+#' Convert a vertical profile (\code{vp}) to a Data Frame
+#'
+#' Converts a vertical profile to a Data Frame, and optionally adds information
+#' on sunrise/sunset, day/night and derived quantities like migration
+#' traffic rates.
+#'
+#' @param x An object of class \code{vp}.
+#' @param row.names \code{NULL} or a character vector giving the row names for
+#' the data frame. Missing values are not allowed. See [base::as.data.frame()].
+#' @param optional If \code{FALSE} then the names of the variables in the data
+#' frame are checked to ensure that they are syntactically valid variable names
+#' and are not duplicated.
+#' @param quantities An optional character vector with the names of the
+#' quantities to include as columns in the data frame.
+#' @param elev Sun elevation in degrees, see \link{sunrise}/\link{sunset}.
+#' @param lat Radar latitude in decimal degrees. When set, overrides the
+#' latitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations
+#' @param lon Radar longitude in decimal degrees. When set, overrides the
+#' longitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations.
+#' @param suntime Logical, when \code{TRUE}, adds sunrise/sunset and day/night
+#' information to each row.
+#' @param geo Logical, when \code{TRUE}, adds latitude, longitude and antenna
+#' height of the radar to each row.
+#' @param ... Additional arguments to be passed to or from methods.
+#'
+#' @return An object of class \code{data.frame}.
+#'
+#' @export
+#'
+#' @details
+#' Note that only the "dens" quantity is thresholded for radial velocity
+#' standard deviation by \link{sd_vvp_threshold}. Note that this is different from the
+#' default \link{plot.vp}, \link{plot.vpts} and \link{get_quantity.vp}
+#' functions, where quantities "eta", "dbz", "ff", "u", "v", "w", "dd" are
+#' all thresholded by \link{sd_vvp_threshold}
+#'
+#' @examples
+#' # Load the example vertical profile
+#' vp <- example_vp
+#'
+#' # Convert to a data.frame
+#' vp_df <- as.data.frame(vp)
+#'
+#' # Print data.frame
+#' vp_df
+#'
+#' # Do not compute sunrise/sunset information
+#' vp_df <- as.data.frame(vp, suntime = FALSE)
+#'
+#' # Override the latitude/longitude information stored in the object when
+#' # calculating sunrise/sunset information
+#' vp_df <- as.data.frame(vp, suntime = TRUE, lat = 50, lon = 4)
+as.data.frame.vp <- function(x, row.names = NULL, optional = FALSE,
+                             quantities = names(x$data), suntime = TRUE,
+                             geo = TRUE, elev = -0.268, lat = NULL,
+                             lon = NULL, ...) {
+  stopifnot(inherits(x, "vp"))
+  if (!is.null(row.names)) {
+    if (is.character(row.names) & length(row.names) ==
+        length(x$datetime) * length(x$height)) {
+      rownames(output) <- row.names
+    } else {
+      stop(paste(
+        "`row.names` is not a character vector of length",
+        length(x$datetime) * length(x$height)
+      ))
+    }
+  }
+  if (is.null(lat)) {
+    lat <- x$attributes$where$lat
+  }
+  if (is.null(lon)) {
+    lon <- x$attributes$where$lon
+  }
+  missing <- which(!(quantities %in% names(x$data)))
+  if (length(missing) > 0) {
+    stop(paste(
+      paste(quantities[missing], collapse = " "),
+      "not an available quantity, select one or more of",
+      paste(names(x$data), collapse = ",")
+    ))
+  }
+  # coerce data to a data frame
+  output <- as.data.frame(x$data, optional = optional, ...)
+  # add height and datetime as a column
+  output <- cbind(datetime = x$datetime, height = output$height, output)
+  output$height <- NULL
+  # add radar name
+  output <- cbind(radar = x$radar, output, stringsAsFactors = FALSE)
+  # add location information
+  if (geo) {
+    output$lat <- lat
+    output$lon <- lon
+    output$height_antenna <- x$attributes$where$height
+  }
+  # override the lat,lon attributes in case of user-provided values
+  x$attributes$where$lat <- lat
+  x$attributes$where$lon <- lon
+  # add day
+  if (suntime) {
+    dayQ <- !check_night(x, elev = elev)
+    dayQ <- c(t(replicate(nrow(x), dayQ)))
+    output <- cbind(output, day = dayQ)
+    sunrise <- sunrise(x$datetime, lat = lat, lon = lon)
+    sunset <- sunset(x$datetime, lat = lat, lon = lon)
+    output$sunrise <- as.POSIXct(
+      c(t(replicate(nrow(x), sunrise))),
+      origin = "1970-1-1", tz = "UTC"
+    )
+    output$sunset <- as.POSIXct(
+      c(t(replicate(nrow(x), sunset))),
+      origin = "1970-1-1", tz = "UTC"
+    )
+  }
+  output
+}
+
+#' Convert a time series of vertical profiles (\code{vpts}) to a data frame
+#'
+#' Converts vertical profile time series (objects of class \code{vpts}) to a
+#' data Frame, and optionally adds information on sunrise/sunset, day/night
+#' and derived quantities like migration traffic rates.
+#'
+#' @param x An object of class \code{vpts}.
+#' @param row.names \code{NULL} or a character vector giving the row names for
+#' the data frame. Missing values are not allowed.
+#' @param optional If \code{FALSE} then the names of the variables in the data
+#' frame are checked to ensure that they are syntactically valid variable names
+#' and are not duplicated.
+#' @param quantities An optional character vector with the names of the
+#' quantities to include as columns in the data frame.
+#' @param elev Sun elevation in degrees, see \link{sunrise}/\link{sunset}.
+#' @param lat Radar latitude in decimal degrees. When set, overrides the
+#' latitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations.
+#' @param lon Radar longitude in decimal degrees. When set, overrides the
+#' longitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations.
+#' @param suntime Logical, when TRUE, adds sunrise/sunset and day/night
+#' information to each row.
+#' @param geo Logical, when TRUE, adds latitude, longitude and antenna height
+#' of the radar to each row.
+#' @param ... Additional arguments to be passed to or from methods.
+#'
+#' @return An object of class data.frame.
+#'
+#' @export
+#'
+#' @details
+#' Note that only the 'dens' quantity is thresholded for radial velocity
+#' standard deviation by \link{sd_vvp_threshold}. Note that this is different from the
+#' default \link{plot.vp}, \link{plot.vpts} and \link{get_quantity.vp}
+#' functions, where quantities "eta", "dbz", "ff", "u", "v", "w", "dd" are all
+#' thresholded by \link{sd_vvp_threshold}.
+#'
+#' @examples
+#' # Load the example time series of vertical profiles
+#' vpts <- example_vpts
+#'
+#' # Convert to a data.frame
+#' vpts_df <- as.data.frame(vpts)
+#'
+#' # Print the first 10 rows of the data.frame
+#' vpts_df[1:10, ]
+#'
+#' # Do not compute sunrise/sunset information
+#' vpts_df <- as.data.frame(vpts, suntime = FALSE)
+#'
+#' # Override the latitude/longitude information stored in the object when
+#' # calculating sunrise/sunset information
+#' vpts_df <- as.data.frame(vpts, suntime = TRUE, lat = 50, lon = 4)
+as.data.frame.vpts <- function(x, row.names = NULL, optional = FALSE,
+                               quantities = names(x$data), suntime = TRUE,
+                               geo = TRUE, elev = -0.268, lat = NULL,
+                               lon = NULL, ...) {
+  stopifnot(inherits(x, "vpts"))
+  if (!is.null(row.names)) {
+    if (is.character(row.names) & length(row.names) ==
+        length(x$datetime) * length(x$height)) {
+      rownames(output) <- row.names
+    } else {
+      stop(paste(
+        "'row.names' is not a character vector of length",
+        length(x$datetime) * length(x$height)
+      ))
+    }
+  }
+  if (is.null(lat)) {
+    lat <- x$attributes$where$lat
+  }
+  if (is.null(lon)) {
+    lon <- x$attributes$where$lon
+  }
+  missing <- which(!(quantities %in% names(x$data)))
+  if (length(missing) > 0) {
+    stop(paste(
+      paste(quantities[missing], collapse = " "),
+      "not an available quantity, select one or more of",
+      paste(names(x$data), collapse = ",")
+    ))
+  }
+  # coerce data to a data frame
+  output <- as.data.frame(lapply(x$data[quantities], c),
+                          optional = optional, ...
+  )
+  # add height and datetime as a column
+  output <- cbind(
+    datetime = as.POSIXct(
+      c(t(replicate(length(x$height), x$datetime))),
+      origin = "1970-1-1", tz = "UTC"
+    ),
+    height = rep(x$height, length(x$datetime)), output
+  )
+  # add radar name
+  output <- cbind(radar = x$radar, output, stringsAsFactors = FALSE)
+  # add location information
+  if (geo) {
+    output$lat <- lat
+    output$lon <- lon
+    output$height_antenna <- x$attributes$where$height
+  }
+  # override the lat,lon attributes in case of user-provided values
+  x$attributes$where$lat <- lat
+  x$attributes$where$lon <- lon
+  # add day
+  if (suntime) {
+    dayQ <- !check_night(x, elev = elev)
+    dayQ <- c(t(replicate(length(x$height), dayQ)))
+    output <- cbind(output, day = dayQ)
+    sunrise <- sunrise(x$datetime, lat = lat, lon = lon)
+    sunset <- sunset(x$datetime, lat = lat, lon = lon)
+    output$sunrise <- as.POSIXct(
+      c(t(replicate(length(x$height), sunrise))),
+      origin = "1970-1-1", tz = "UTC"
+    )
+    output$sunset <- as.POSIXct(
+      c(t(replicate(length(x$height), sunset))),
+      origin = "1970-1-1", tz = "UTC"
+    )
+  }
+  output
+}
diff --git a/R/vp.R b/R/vp.R
index 1bf9f2ba2..029437774 100644
--- a/R/vp.R
+++ b/R/vp.R
@@ -136,123 +136,6 @@ dim.vp <- function(x) {
   dim(x$data)
 }
 
-#' Convert a vertical profile (\code{vp}) to a Data Frame
-#'
-#' Converts a vertical profile to a Data Frame, and optionally adds information
-#' on sunrise/sunset, day/night and derived quantities like migration
-#' traffic rates.
-#'
-#' @param x An object of class \code{vp}.
-#' @param row.names \code{NULL} or a character vector giving the row names for
-#' the data frame. Missing values are not allowed. See [base::as.data.frame()].
-#' @param optional If \code{FALSE} then the names of the variables in the data
-#' frame are checked to ensure that they are syntactically valid variable names
-#' and are not duplicated.
-#' @param quantities An optional character vector with the names of the
-#' quantities to include as columns in the data frame.
-#' @param elev Sun elevation in degrees, see \link{sunrise}/\link{sunset}.
-#' @param lat Radar latitude in decimal degrees. When set, overrides the
-#' latitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations
-#' @param lon Radar longitude in decimal degrees. When set, overrides the
-#' longitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations.
-#' @param suntime Logical, when \code{TRUE}, adds sunrise/sunset and day/night
-#' information to each row.
-#' @param geo Logical, when \code{TRUE}, adds latitude, longitude and antenna
-#' height of the radar to each row.
-#' @param ... Additional arguments to be passed to or from methods.
-#'
-#' @return An object of class \code{data.frame}.
-#'
-#' @export
-#'
-#' @details
-#' Note that only the "dens" quantity is thresholded for radial velocity
-#' standard deviation by \link{sd_vvp_threshold}. Note that this is different from the
-#' default \link{plot.vp}, \link{plot.vpts} and \link{get_quantity.vp}
-#' functions, where quantities "eta", "dbz", "ff", "u", "v", "w", "dd" are
-#' all thresholded by \link{sd_vvp_threshold}
-#'
-#' @examples
-#' # Load the example vertical profile
-#' vp <- example_vp
-#'
-#' # Convert to a data.frame
-#' vp_df <- as.data.frame(vp)
-#'
-#' # Print data.frame
-#' vp_df
-#'
-#' # Do not compute sunrise/sunset information
-#' vp_df <- as.data.frame(vp, suntime = FALSE)
-#'
-#' # Override the latitude/longitude information stored in the object when
-#' # calculating sunrise/sunset information
-#' vp_df <- as.data.frame(vp, suntime = TRUE, lat = 50, lon = 4)
-as.data.frame.vp <- function(x, row.names = NULL, optional = FALSE,
-                             quantities = names(x$data), suntime = TRUE,
-                             geo = TRUE, elev = -0.268, lat = NULL,
-                             lon = NULL, ...) {
-  stopifnot(inherits(x, "vp"))
-  if (!is.null(row.names)) {
-    if (is.character(row.names) & length(row.names) ==
-      length(x$datetime) * length(x$height)) {
-      rownames(output) <- row.names
-    } else {
-      stop(paste(
-        "`row.names` is not a character vector of length",
-        length(x$datetime) * length(x$height)
-      ))
-    }
-  }
-  if (is.null(lat)) {
-    lat <- x$attributes$where$lat
-  }
-  if (is.null(lon)) {
-    lon <- x$attributes$where$lon
-  }
-  missing <- which(!(quantities %in% names(x$data)))
-  if (length(missing) > 0) {
-    stop(paste(
-      paste(quantities[missing], collapse = " "),
-      "not an available quantity, select one or more of",
-      paste(names(x$data), collapse = ",")
-    ))
-  }
-  # coerce data to a data frame
-  output <- as.data.frame(x$data, optional = optional, ...)
-  # add height and datetime as a column
-  output <- cbind(datetime = x$datetime, height = output$height, output)
-  output$height <- NULL
-  # add radar name
-  output <- cbind(radar = x$radar, output, stringsAsFactors = FALSE)
-  # add location information
-  if (geo) {
-    output$lat <- lat
-    output$lon <- lon
-    output$height_antenna <- x$attributes$where$height
-  }
-  # override the lat,lon attributes in case of user-provided values
-  x$attributes$where$lat <- lat
-  x$attributes$where$lon <- lon
-  # add day
-  if (suntime) {
-    dayQ <- !check_night(x, elev = elev)
-    dayQ <- c(t(replicate(nrow(x), dayQ)))
-    output <- cbind(output, day = dayQ)
-    sunrise <- sunrise(x$datetime, lat = lat, lon = lon)
-    sunset <- sunset(x$datetime, lat = lat, lon = lon)
-    output$sunrise <- as.POSIXct(
-      c(t(replicate(nrow(x), sunrise))),
-      origin = "1970-1-1", tz = "UTC"
-    )
-    output$sunset <- as.POSIXct(
-      c(t(replicate(nrow(x), sunset))),
-      origin = "1970-1-1", tz = "UTC"
-    )
-  }
-  output
-}
-
 #' Concatenate vertical profiles (`vp`) into a list of vertical profiles
 #'
 #' Concatenates vertical profiles (`vp`) into a list of vertical profiles
diff --git a/R/vpts.R b/R/vpts.R
index 3553c0fc6..39221ca55 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -202,130 +202,6 @@ dim.vpts <- function(x) {
   return(x)
 }
 
-#' Convert a time series of vertical profiles (\code{vpts}) to a data frame
-#'
-#' Converts vertical profile time series (objects of class \code{vpts}) to a
-#' data Frame, and optionally adds information on sunrise/sunset, day/night
-#' and derived quantities like migration traffic rates.
-#'
-#' @param x An object of class \code{vpts}.
-#' @param row.names \code{NULL} or a character vector giving the row names for
-#' the data frame. Missing values are not allowed.
-#' @param optional If \code{FALSE} then the names of the variables in the data
-#' frame are checked to ensure that they are syntactically valid variable names
-#' and are not duplicated.
-#' @param quantities An optional character vector with the names of the
-#' quantities to include as columns in the data frame.
-#' @param elev Sun elevation in degrees, see \link{sunrise}/\link{sunset}.
-#' @param lat Radar latitude in decimal degrees. When set, overrides the
-#' latitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations.
-#' @param lon Radar longitude in decimal degrees. When set, overrides the
-#' longitude stored in \code{x} in \link{sunrise}/\link{sunset} calculations.
-#' @param suntime Logical, when TRUE, adds sunrise/sunset and day/night
-#' information to each row.
-#' @param geo Logical, when TRUE, adds latitude, longitude and antenna height
-#' of the radar to each row.
-#' @param ... Additional arguments to be passed to or from methods.
-#'
-#' @return An object of class data.frame.
-#'
-#' @export
-#'
-#' @details
-#' Note that only the 'dens' quantity is thresholded for radial velocity
-#' standard deviation by \link{sd_vvp_threshold}. Note that this is different from the
-#' default \link{plot.vp}, \link{plot.vpts} and \link{get_quantity.vp}
-#' functions, where quantities "eta", "dbz", "ff", "u", "v", "w", "dd" are all
-#' thresholded by \link{sd_vvp_threshold}.
-#'
-#' @examples
-#' # Load the example time series of vertical profiles
-#' vpts <- example_vpts
-#'
-#' # Convert to a data.frame
-#' vpts_df <- as.data.frame(vpts)
-#'
-#' # Print the first 10 rows of the data.frame
-#' vpts_df[1:10, ]
-#'
-#' # Do not compute sunrise/sunset information
-#' vpts_df <- as.data.frame(vpts, suntime = FALSE)
-#'
-#' # Override the latitude/longitude information stored in the object when
-#' # calculating sunrise/sunset information
-#' vpts_df <- as.data.frame(vpts, suntime = TRUE, lat = 50, lon = 4)
-as.data.frame.vpts <- function(x, row.names = NULL, optional = FALSE,
-                               quantities = names(x$data), suntime = TRUE,
-                               geo = TRUE, elev = -0.268, lat = NULL,
-                               lon = NULL, ...) {
-  stopifnot(inherits(x, "vpts"))
-  if (!is.null(row.names)) {
-    if (is.character(row.names) & length(row.names) ==
-      length(x$datetime) * length(x$height)) {
-      rownames(output) <- row.names
-    } else {
-      stop(paste(
-        "'row.names' is not a character vector of length",
-        length(x$datetime) * length(x$height)
-      ))
-    }
-  }
-  if (is.null(lat)) {
-    lat <- x$attributes$where$lat
-  }
-  if (is.null(lon)) {
-    lon <- x$attributes$where$lon
-  }
-  missing <- which(!(quantities %in% names(x$data)))
-  if (length(missing) > 0) {
-    stop(paste(
-      paste(quantities[missing], collapse = " "),
-      "not an available quantity, select one or more of",
-      paste(names(x$data), collapse = ",")
-    ))
-  }
-  # coerce data to a data frame
-  output <- as.data.frame(lapply(x$data[quantities], c),
-    optional = optional, ...
-  )
-  # add height and datetime as a column
-  output <- cbind(
-    datetime = as.POSIXct(
-      c(t(replicate(length(x$height), x$datetime))),
-      origin = "1970-1-1", tz = "UTC"
-    ),
-    height = rep(x$height, length(x$datetime)), output
-  )
-  # add radar name
-  output <- cbind(radar = x$radar, output, stringsAsFactors = FALSE)
-  # add location information
-  if (geo) {
-    output$lat <- lat
-    output$lon <- lon
-    output$height_antenna <- x$attributes$where$height
-  }
-  # override the lat,lon attributes in case of user-provided values
-  x$attributes$where$lat <- lat
-  x$attributes$where$lon <- lon
-  # add day
-  if (suntime) {
-    dayQ <- !check_night(x, elev = elev)
-    dayQ <- c(t(replicate(length(x$height), dayQ)))
-    output <- cbind(output, day = dayQ)
-    sunrise <- sunrise(x$datetime, lat = lat, lon = lon)
-    sunset <- sunset(x$datetime, lat = lat, lon = lon)
-    output$sunrise <- as.POSIXct(
-      c(t(replicate(length(x$height), sunrise))),
-      origin = "1970-1-1", tz = "UTC"
-    )
-    output$sunset <- as.POSIXct(
-      c(t(replicate(length(x$height), sunset))),
-      origin = "1970-1-1", tz = "UTC"
-    )
-  }
-  output
-}
-
 vpts_to_vp <- function(x, i) {
   stopifnot(inherits(x, "vpts"))
   nvp <- dim(x)[2]
diff --git a/man/as.data.frame.vp.Rd b/man/as.data.frame.vp.Rd
index fbff1fba7..396dd8cfd 100644
--- a/man/as.data.frame.vp.Rd
+++ b/man/as.data.frame.vp.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/vp.R
+% Please edit documentation in R/as.data.frame.R
 \name{as.data.frame.vp}
 \alias{as.data.frame.vp}
 \title{Convert a vertical profile (\code{vp}) to a Data Frame}
diff --git a/man/as.data.frame.vpts.Rd b/man/as.data.frame.vpts.Rd
index 87dad7fa2..6f607d0ef 100644
--- a/man/as.data.frame.vpts.Rd
+++ b/man/as.data.frame.vpts.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/vpts.R
+% Please edit documentation in R/as.data.frame.R
 \name{as.data.frame.vpts}
 \alias{as.data.frame.vpts}
 \title{Convert a time series of vertical profiles (\code{vpts}) to a data frame}
diff --git a/tests/testthat/test-as.data.frame.R b/tests/testthat/test-as.data.frame.R
new file mode 100644
index 000000000..527305d0a
--- /dev/null
+++ b/tests/testthat/test-as.data.frame.R
@@ -0,0 +1,129 @@
+vp <- example_vp
+
+test_that("as.data.frame() returns error on incorrect parameters", {
+  expect_error(as.data.frame(vp, row.names = "not_a_vector"))
+  expect_error(
+    as.data.frame(vp, quantities = c("not_a_quantity")),
+    "select one or more of ff,dbz" # Full message is a list of all quantities
+  )
+  expect_error(as.data.frame(vp, suntime = "not_a_logical"))
+  expect_error(as.data.frame(vp, geo = "not_a_logical"))
+  expect_error(as.data.frame(vp, elev = "not_a_double"))
+  expect_error(as.data.frame(vp, lat = "not_a_double"))
+  expect_error(as.data.frame(vp, lon = "not_a_double"))
+})
+
+test_that("as.data.frame() returns a data frame", {
+  expect_is(as.data.frame(vp), "data.frame")
+})
+
+test_that("as.data.frame() returns correct number of rows/cols", {
+  df <- as.data.frame(vp)
+  expect_equal(nrow(df), 25) # 25 rows in nrow(vp$data)
+  expect_gte(ncol(df), 16) # 16 cols in ncol(vp$data), but extra added by bioRad
+})
+
+test_that("as.data.frame() returns the expected column names", {
+  expected_col_names <- c(
+    "radar", "datetime", "ff", "dbz", "dens", "u", "v", "gap", "w", "n_dbz",
+    "dd", "n", "DBZH", "height", "n_dbz_all", "eta", "sd_vvp", "n_all", "lat",
+    "lon", "height_antenna", "day", "sunrise", "sunset"
+  )
+  expect_equal(names(as.data.frame(vp)), expected_col_names)
+})
+
+test_that("as.data.frame() returns the correct data", {
+  df <- as.data.frame(example_vp)
+
+  expect_equal(unique(df[["radar"]]), "seang") # One unique radar
+  expect_equal(as.character(unique(df[["datetime"]])), "2015-10-18 18:00:00") # One unique timestamp
+
+  # Check a few randomly selected values (coming directly from the source data):
+  expect_equal(df$height[1], 0)
+  expect_equal(df$height[8], 1400)
+  expect_equal(df$ff[4], 13.77482, tolerance = 0.001)
+  expect_equal(df$dens[10], 17.3985100, tolerance = 0.001)
+  expect_equal(is.na(df$sd_vvp[1]), TRUE)
+  expect_equal(df$sd_vvp[13], 2.994742, tolerance = 0.001)
+})
+
+test_that("as.data.frame() includes lat/lon/height_antenna and can be assigned, unless geo = FALSE", {
+  # lat/lon/height_antenna columns are added by default and taken from metadata
+  df <- as.data.frame(example_vp)
+  expect_equal(unique(df[["lat"]]), example_vp$attributes$where$lat)
+  expect_equal(unique(df[["lon"]]), example_vp$attributes$where$lon)
+  expect_equal(unique(df[["height_antenna"]]), example_vp$attributes$where$height)
+
+  # lat/lon/height_antenna columns are missing if geo = FALSE
+  df_geo_false <- as.data.frame(example_vp, geo = FALSE)
+  expect_null(df_geo_false$lat)
+  expect_null(df_geo_false$lon)
+  expect_null(df_geo_false$height_antenna)
+
+  # lat/lon can be set explicitly
+  df_latlong <- as.data.frame(example_vp, lat = 50.6472, lon = 4.3603)
+  expect_equal(unique(df_latlong[["lat"]]), 50.6472)
+  expect_equal(unique(df_latlong[["lon"]]), 4.3603)
+})
+
+
+test_that("as.data.frame() includes sunset/sunrise/day cols, unless suntime = FALSE", {
+    # sunset/sunrise/day columns are added by default
+    df <- as.data.frame(example_vp)
+    expect_is(df$sunset, "POSIXct")
+    expect_is(df$sunrise, "POSIXct")
+    expect_is(df$day, "logical")
+
+    # sunset/sunrise/day columns are missing if suntime = FALSE
+    df_suntime_false <- as.data.frame(example_vp, suntime = FALSE)
+    expect_null(df_suntime_false$sunset)
+    expect_null(df_suntime_false$sunrise)
+    expect_null(df_suntime_false$day)
+  }
+)
+
+test_that("as.data.frame() values in suntime/sunset/day cols are correct and updated with lat/lon", {
+  # Note: timestamp for example_vp is 2015-10-18 18:00:00 UTC
+
+  # 1. Check for lat/long contained in example_vp: 56.3675, 12.8517
+  df <- as.data.frame(example_vp)
+
+  # Manual data check on: https://www.suncalc.org/#/56.3675,12.8517,12/2015.10.18/09:00/1/3
+  expected_sunrise <- as.POSIXlt("2015-10-18 05:45:26", tz = "UTC") # 07:45:26 UTC+2
+  expected_sunset <- as.POSIXlt("2015-10-18 16:01:13", tz = "UTC") # 18:01:13 UTC+2
+
+  expect_equal(as.POSIXlt(df$sunrise[1]), expected_sunrise, tolerance = 5) # Tolerance: minutes
+  expect_equal(as.POSIXlt(df$sunset[1]), expected_sunset, tolerance = 5)
+  expect_false(df$day[1]) # At the 18:00:00 UTC timestamp, it is night
+
+  # 2. Set lat/lon to other values and check if it's still correct
+  df <- as.data.frame(example_vp, lat = 50.6472, lon = 4.3603)
+
+  # Manual data check on: https://www.suncalc.org/#/50.6472,4.3603,12/2015.10.18/09:00/1/3
+  expected_sunrise <- as.POSIXlt("2015-10-18 06:09:09", tz = "UTC") # 08:09:09 UTC+2
+  expected_sunset <- as.POSIXlt("2015-10-18 16:45:35", tz = "UTC") # 18:45:35 UTC+2
+
+  expect_equal(as.POSIXlt(df$sunrise[1]), expected_sunrise, tolerance = 5)
+  expect_equal(as.POSIXlt(df$sunset[1]), expected_sunset, tolerance = 5)
+  expect_false(df$day[1]) # At the 18:00:00 UTC timestamp, it is night
+
+  # 3. Let's go to Antartica, it should be day there
+  df <- as.data.frame(example_vp, lat = -74.2486, lon = -1.2497)
+  expect_true(df$day[1])
+})
+
+test_that("as.data.frame() allows to select quantities", {
+  df <- as.data.frame(example_vp, quantities = c("dens", "ff"))
+  expect_is(df$dens, "numeric")
+  expect_is(df$ff, "numeric")
+
+  # FIXME: If we only request "dens", shouldn't "dd" be missing?
+  # expect_null(df$dd)
+
+  # We get a proper error message if requesting a nonexistent quantity
+
+})
+
+# TODO: test "row.names" parameter
+# TODO: test "optional" parameter
+# TODO: test "elev" parameter
diff --git a/tests/testthat/test-vp.R b/tests/testthat/test-vp.R
index 527305d0a..9a07aa619 100644
--- a/tests/testthat/test-vp.R
+++ b/tests/testthat/test-vp.R
@@ -1,129 +1,3 @@
-vp <- example_vp
+test_that("... returns error on incorrect parameters", {
 
-test_that("as.data.frame() returns error on incorrect parameters", {
-  expect_error(as.data.frame(vp, row.names = "not_a_vector"))
-  expect_error(
-    as.data.frame(vp, quantities = c("not_a_quantity")),
-    "select one or more of ff,dbz" # Full message is a list of all quantities
-  )
-  expect_error(as.data.frame(vp, suntime = "not_a_logical"))
-  expect_error(as.data.frame(vp, geo = "not_a_logical"))
-  expect_error(as.data.frame(vp, elev = "not_a_double"))
-  expect_error(as.data.frame(vp, lat = "not_a_double"))
-  expect_error(as.data.frame(vp, lon = "not_a_double"))
 })
-
-test_that("as.data.frame() returns a data frame", {
-  expect_is(as.data.frame(vp), "data.frame")
-})
-
-test_that("as.data.frame() returns correct number of rows/cols", {
-  df <- as.data.frame(vp)
-  expect_equal(nrow(df), 25) # 25 rows in nrow(vp$data)
-  expect_gte(ncol(df), 16) # 16 cols in ncol(vp$data), but extra added by bioRad
-})
-
-test_that("as.data.frame() returns the expected column names", {
-  expected_col_names <- c(
-    "radar", "datetime", "ff", "dbz", "dens", "u", "v", "gap", "w", "n_dbz",
-    "dd", "n", "DBZH", "height", "n_dbz_all", "eta", "sd_vvp", "n_all", "lat",
-    "lon", "height_antenna", "day", "sunrise", "sunset"
-  )
-  expect_equal(names(as.data.frame(vp)), expected_col_names)
-})
-
-test_that("as.data.frame() returns the correct data", {
-  df <- as.data.frame(example_vp)
-
-  expect_equal(unique(df[["radar"]]), "seang") # One unique radar
-  expect_equal(as.character(unique(df[["datetime"]])), "2015-10-18 18:00:00") # One unique timestamp
-
-  # Check a few randomly selected values (coming directly from the source data):
-  expect_equal(df$height[1], 0)
-  expect_equal(df$height[8], 1400)
-  expect_equal(df$ff[4], 13.77482, tolerance = 0.001)
-  expect_equal(df$dens[10], 17.3985100, tolerance = 0.001)
-  expect_equal(is.na(df$sd_vvp[1]), TRUE)
-  expect_equal(df$sd_vvp[13], 2.994742, tolerance = 0.001)
-})
-
-test_that("as.data.frame() includes lat/lon/height_antenna and can be assigned, unless geo = FALSE", {
-  # lat/lon/height_antenna columns are added by default and taken from metadata
-  df <- as.data.frame(example_vp)
-  expect_equal(unique(df[["lat"]]), example_vp$attributes$where$lat)
-  expect_equal(unique(df[["lon"]]), example_vp$attributes$where$lon)
-  expect_equal(unique(df[["height_antenna"]]), example_vp$attributes$where$height)
-
-  # lat/lon/height_antenna columns are missing if geo = FALSE
-  df_geo_false <- as.data.frame(example_vp, geo = FALSE)
-  expect_null(df_geo_false$lat)
-  expect_null(df_geo_false$lon)
-  expect_null(df_geo_false$height_antenna)
-
-  # lat/lon can be set explicitly
-  df_latlong <- as.data.frame(example_vp, lat = 50.6472, lon = 4.3603)
-  expect_equal(unique(df_latlong[["lat"]]), 50.6472)
-  expect_equal(unique(df_latlong[["lon"]]), 4.3603)
-})
-
-
-test_that("as.data.frame() includes sunset/sunrise/day cols, unless suntime = FALSE", {
-    # sunset/sunrise/day columns are added by default
-    df <- as.data.frame(example_vp)
-    expect_is(df$sunset, "POSIXct")
-    expect_is(df$sunrise, "POSIXct")
-    expect_is(df$day, "logical")
-
-    # sunset/sunrise/day columns are missing if suntime = FALSE
-    df_suntime_false <- as.data.frame(example_vp, suntime = FALSE)
-    expect_null(df_suntime_false$sunset)
-    expect_null(df_suntime_false$sunrise)
-    expect_null(df_suntime_false$day)
-  }
-)
-
-test_that("as.data.frame() values in suntime/sunset/day cols are correct and updated with lat/lon", {
-  # Note: timestamp for example_vp is 2015-10-18 18:00:00 UTC
-
-  # 1. Check for lat/long contained in example_vp: 56.3675, 12.8517
-  df <- as.data.frame(example_vp)
-
-  # Manual data check on: https://www.suncalc.org/#/56.3675,12.8517,12/2015.10.18/09:00/1/3
-  expected_sunrise <- as.POSIXlt("2015-10-18 05:45:26", tz = "UTC") # 07:45:26 UTC+2
-  expected_sunset <- as.POSIXlt("2015-10-18 16:01:13", tz = "UTC") # 18:01:13 UTC+2
-
-  expect_equal(as.POSIXlt(df$sunrise[1]), expected_sunrise, tolerance = 5) # Tolerance: minutes
-  expect_equal(as.POSIXlt(df$sunset[1]), expected_sunset, tolerance = 5)
-  expect_false(df$day[1]) # At the 18:00:00 UTC timestamp, it is night
-
-  # 2. Set lat/lon to other values and check if it's still correct
-  df <- as.data.frame(example_vp, lat = 50.6472, lon = 4.3603)
-
-  # Manual data check on: https://www.suncalc.org/#/50.6472,4.3603,12/2015.10.18/09:00/1/3
-  expected_sunrise <- as.POSIXlt("2015-10-18 06:09:09", tz = "UTC") # 08:09:09 UTC+2
-  expected_sunset <- as.POSIXlt("2015-10-18 16:45:35", tz = "UTC") # 18:45:35 UTC+2
-
-  expect_equal(as.POSIXlt(df$sunrise[1]), expected_sunrise, tolerance = 5)
-  expect_equal(as.POSIXlt(df$sunset[1]), expected_sunset, tolerance = 5)
-  expect_false(df$day[1]) # At the 18:00:00 UTC timestamp, it is night
-
-  # 3. Let's go to Antartica, it should be day there
-  df <- as.data.frame(example_vp, lat = -74.2486, lon = -1.2497)
-  expect_true(df$day[1])
-})
-
-test_that("as.data.frame() allows to select quantities", {
-  df <- as.data.frame(example_vp, quantities = c("dens", "ff"))
-  expect_is(df$dens, "numeric")
-  expect_is(df$ff, "numeric")
-
-  # FIXME: If we only request "dens", shouldn't "dd" be missing?
-  # expect_null(df$dd)
-
-  # We get a proper error message if requesting a nonexistent quantity
-
-})
-
-# TODO: test "row.names" parameter
-# TODO: test "optional" parameter
-# TODO: test "elev" parameter

From 186b73d76c71a143e50086d01754e32251d82a4a Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 11:38:56 +0200
Subject: [PATCH 05/35] Write summary.pvol, print.pvol, is.pvol tests

---
 tests/testthat/test-pvol.R | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-pvol.R b/tests/testthat/test-pvol.R
index 9a07aa619..aae7b1d93 100644
--- a/tests/testthat/test-pvol.R
+++ b/tests/testthat/test-pvol.R
@@ -1,3 +1,24 @@
-test_that("... returns error on incorrect parameters", {
+pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
+pvol <- read_pvolfile(pvolfile)
+vp <- example_vp
 
+# No tests for error on incorrect parameters:
+# summary(), print() are generic and work for every input
+# is.pvol() returns TRUE/FALSE and works for every input
+
+# print.pvol() is not tested as it is the same as and called from summary.pvol()
+
+test_that("summary.pvol() prints metadata to the console", {
+  expect_output(summary(pvol), "Polar volume (class pvol)", fixed = TRUE)
+  expect_output(summary(pvol), "# scans:", fixed = TRUE)
+  expect_output(summary(pvol), "radar:", fixed = TRUE)
+  expect_output(summary(pvol), "source:", fixed = TRUE)
+  expect_output(summary(pvol), "nominal time:", fixed = TRUE)
+
+})
+
+test_that("is.pvol() returns TRUE/FALSE correctly", {
+  expect_true(is.pvol(pvol))
+  expect_false(is.pvol("not_a_pvol"))
+  expect_false(is.pvol(vp))
 })

From 9638e1f5c33c15d164543c537db2d3c208a20fdd Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 12:22:35 +0200
Subject: [PATCH 06/35] Write tests for summary.scan, print.scan, is.scan,
 dim.scan

---
 tests/testthat/test-pvol.R |  3 +--
 tests/testthat/test-scan.R | 25 ++++++++++++++++++++++++-
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-pvol.R b/tests/testthat/test-pvol.R
index aae7b1d93..0a6a9e59a 100644
--- a/tests/testthat/test-pvol.R
+++ b/tests/testthat/test-pvol.R
@@ -6,9 +6,8 @@ vp <- example_vp
 # summary(), print() are generic and work for every input
 # is.pvol() returns TRUE/FALSE and works for every input
 
-# print.pvol() is not tested as it is the same as and called from summary.pvol()
-
 test_that("summary.pvol() prints metadata to the console", {
+  # print.pvol() is not tested as it is the same as and called from summary.pvol()
   expect_output(summary(pvol), "Polar volume (class pvol)", fixed = TRUE)
   expect_output(summary(pvol), "# scans:", fixed = TRUE)
   expect_output(summary(pvol), "radar:", fixed = TRUE)
diff --git a/tests/testthat/test-scan.R b/tests/testthat/test-scan.R
index 9a07aa619..955eb90e0 100644
--- a/tests/testthat/test-scan.R
+++ b/tests/testthat/test-scan.R
@@ -1,3 +1,26 @@
-test_that("... returns error on incorrect parameters", {
+scan <- example_scan
+vp <- example_vp
 
+# No tests for error on incorrect parameters:
+# summary(), print(), dim() are generic and work for every input
+# is.scan() returns TRUE/FALSE and works for every input
+
+test_that("summary.scan() prints metadata to the console", {
+  # print.scan() is not tested as it is the same as and called from summary.scan()
+  expect_output(summary(scan), "Polar scan (class scan)", fixed = TRUE)
+  expect_output(summary(scan), "parameters:", fixed = TRUE)
+  expect_output(summary(scan), "elevation angle:", fixed = TRUE)
+  expect_output(summary(scan), "dims:", fixed = TRUE)
+
+})
+
+test_that("is.scan() returns TRUE/FALSE correctly", {
+  expect_true(is.scan(scan))
+  expect_false(is.scan("not_a_scan"))
+  expect_false(is.scan(vp))
+})
+
+test_that("dim.scan() returns dimensions", {
+  expect_vector(dim(scan))
+  expect_equal(dim(scan), c(5, 480, 360)) # 5 param, 480 bins, 360 rays in example_scan
 })

From 822f68e15eaedb885fece049d7ceb2579196fc97 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 12:23:10 +0200
Subject: [PATCH 07/35] Write tests for summary.param, print.param, is.param

---
 tests/testthat/test-param.R | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-param.R b/tests/testthat/test-param.R
index 9a07aa619..b60e05d01 100644
--- a/tests/testthat/test-param.R
+++ b/tests/testthat/test-param.R
@@ -1,3 +1,19 @@
-test_that("... returns error on incorrect parameters", {
+param <- get_param(example_scan, "DBZH")
+vp <- example_vp
 
+# No tests for error on incorrect parameters:
+# summary(), print() are generic and work for every input
+# is.param() returns TRUE/FALSE and works for every input
+
+test_that("summary.param() prints metadata to the console", {
+  # print.param() is not tested as it is the same as and called from summary.param()
+  expect_output(summary(param), "Polar scan parameter (class param)", fixed = TRUE)
+  expect_output(summary(param), "quantity:", fixed = TRUE)
+  expect_output(summary(param), "dims:", fixed = TRUE)
+})
+
+test_that("is.param() returns TRUE/FALSE correctly", {
+  expect_true(is.param(param))
+  expect_false(is.param("not_a_param"))
+  expect_false(is.param(vp))
 })

From ff2576b294bfcec58bd0113873e30c85fdc6e56b Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 12:23:42 +0200
Subject: [PATCH 08/35] Write tests for summary.ppi, print.ppi, is.ppi,
 dim.ppi, subset.ppi

---
 tests/testthat/test-ppi.R | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-ppi.R b/tests/testthat/test-ppi.R
index 9a07aa619..5c75db6d0 100644
--- a/tests/testthat/test-ppi.R
+++ b/tests/testthat/test-ppi.R
@@ -1,3 +1,30 @@
-test_that("... returns error on incorrect parameters", {
+ppi <- project_as_ppi(example_scan)
+vp <- example_vp
 
+# No tests for error on incorrect parameters:
+# summary(), print(), dim() are generic and work for every input
+# is.ppi() returns TRUE/FALSE and works for every input
+
+test_that("summary.ppi() prints metadata to the console", {
+  # print.ppi() is not tested as it is the same as and called from summary.ppi()
+  expect_output(summary(ppi), "Plan position indicator (class ppi)", fixed = TRUE)
+  expect_output(summary(ppi), "parameters:", fixed = TRUE)
+  expect_output(summary(ppi), "dims:", fixed = TRUE)
+})
+
+test_that("is.ppi() returns TRUE/FALSE correctly", {
+  expect_true(is.ppi(ppi))
+  expect_false(is.ppi("not_a_ppi"))
+  expect_false(is.ppi(vp))
+})
+
+test_that("dim.ppi() returns dimensions", {
+  expect_vector(dim(ppi))
+  expect_equal(dim(ppi), c(5, 200, 200)) # 5 param, 200 x pixels, 200 y pixels for default range_max
+})
+
+test_that("[.ppi subsets by param", {
+  # parameters:  VRADH DBZH ZDR RHOHV PHIDP
+  expect_equal(names(ppi[1]$data), c("VRADH"))
+  expect_equal(names(ppi[2:4]$data), c("DBZH", "ZDR", "RHOHV"))
 })

From 218fdae0f296b95de27b0344e6bde7dbb6393d28 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 15:11:25 +0200
Subject: [PATCH 09/35] Fix #370

Ping @adokter @cecilianilsson709

- Shorten warning message and reference convert_legacy()
- Rather than testing for legacy column (HGHT, dates), it checks if the expected column (height, datetime) is there
- It uses convert_legacy() to be able to print, but doesn't change the object
---
 R/vp.R   |  8 +++-----
 R/vpts.R | 14 ++++++--------
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/R/vp.R b/R/vp.R
index 57c8a8617..fe4461d79 100644
--- a/R/vp.R
+++ b/R/vp.R
@@ -88,11 +88,9 @@ summary.vp <- function(object, ...) {
 #' @export
 print.vp <- function(x, digits = max(3L, getOption("digits") - 3L), ...) {
   stopifnot(inherits(x, "vp"))
-  if (!is.null(x$data$HGHT)) {
-    warning("vp object is an obsolete one generated with bioRad version < 0.5.0.
-      vp objects should contain a column `height` (rather than `HGHT`) in the
-      `data` element."
-    )
+  if (is.null(x$data$height)) {
+    warning("`x` is a legacy vp object without a column `height`. Use convert_legacy() to avoid errors.")
+    x <- convert_legacy(x)
   }
   cat("               Vertical profile (class vp)\n\n")
   cat("       radar: ", x$radar, "\n")
diff --git a/R/vpts.R b/R/vpts.R
index 8cf4e69d3..116f42d87 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -65,15 +65,13 @@ summary.vpts <- function(object, ...) {
 #' @export
 print.vpts <- function(x, digits = max(3L, getOption("digits") - 3L), ...) {
   stopifnot(inherits(x, "vpts"))
-  # check if we are dealing with a deprecated vpts class structure
-  if (!is.null(x$heights)) {
-    warning("obsolete vtps object generated with bioRad version < 0.5.0.
-    vpts objects should contain a list element 'height' (instead of obsolete 'heights')")
+  if (is.null(x$height)) {
+    warning("`x` is a legacy vpts object without a column `height`. Use convert_legacy() to avoid errors.")
+    x <- convert_legacy(x)
   }
-  if (!is.null(x$dates)) {
-    warning("obsolete vtps object generated with bioRad version < 0.4.0.
-    vpts objects should contain a list element 'datetime' (instead of obsolete 'dates')")
-    x$datetime <- x$dates
+  if (is.null(x$datetime)) {
+    warning("`x` is a legacy vpts object without a column `datetime`. Use convert_legacy() to avoid errors.")
+    x <- convert_legacy(x)
   }
   cat(
     "                  ",

From 4eac9cedeee915b9577bfb183ff63bf02d733414 Mon Sep 17 00:00:00 2001
From: Cecilia Nilsson <cecilia.nilsson@biol.lu.se>
Date: Mon, 27 Apr 2020 15:11:58 +0200
Subject: [PATCH 10/35] Update regularize_vpts() to remove duplicate timestamps

regularize_vpts() also fails on profiles with duplicate timestamps, see #235 . As a suggestion I just copied the code from plot.vpts() to drop duplicate timestamps.
---
 R/regularize_vpts.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/regularize_vpts.R b/R/regularize_vpts.R
index f46bf0bad..51564e701 100644
--- a/R/regularize_vpts.R
+++ b/R/regularize_vpts.R
@@ -60,6 +60,13 @@ regularize_vpts <- function(ts, interval = "auto", date_min, date_max,
     stop("Fill argument should be a logical value.")
   }
 
+  # remove profiles with duplicate timestamps:
+  index_duplicates <- which(ts$timesteps == 0) + 1
+  if (length(index_duplicates) > 0) {
+    warning(paste("Dropped", length(index_duplicates), "profiles with duplicate datetime values"))
+    ts <- ts[-index_duplicates]
+  }
+
   if (interval == "auto") {
     dt <- as.difftime(median(ts$timesteps), units = "secs")
     if (verbose) {

From f062ddffb1d8576120bd0467ebb158665621fd9d Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 16:20:17 +0200
Subject: [PATCH 11/35] Test for incorrect parameters for subset ppi

---
 tests/testthat/test-ppi.R  | 4 ++++
 tests/testthat/test-pvol.R | 1 -
 tests/testthat/test-scan.R | 1 -
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-ppi.R b/tests/testthat/test-ppi.R
index 5c75db6d0..6d76751e7 100644
--- a/tests/testthat/test-ppi.R
+++ b/tests/testthat/test-ppi.R
@@ -5,6 +5,10 @@ vp <- example_vp
 # summary(), print(), dim() are generic and work for every input
 # is.ppi() returns TRUE/FALSE and works for every input
 
+test_that("[.ppi returns error on incorrect parameters", {
+  expect_error(ppi["not_numeric"])
+})
+
 test_that("summary.ppi() prints metadata to the console", {
   # print.ppi() is not tested as it is the same as and called from summary.ppi()
   expect_output(summary(ppi), "Plan position indicator (class ppi)", fixed = TRUE)
diff --git a/tests/testthat/test-pvol.R b/tests/testthat/test-pvol.R
index 0a6a9e59a..0a9dd55c5 100644
--- a/tests/testthat/test-pvol.R
+++ b/tests/testthat/test-pvol.R
@@ -13,7 +13,6 @@ test_that("summary.pvol() prints metadata to the console", {
   expect_output(summary(pvol), "radar:", fixed = TRUE)
   expect_output(summary(pvol), "source:", fixed = TRUE)
   expect_output(summary(pvol), "nominal time:", fixed = TRUE)
-
 })
 
 test_that("is.pvol() returns TRUE/FALSE correctly", {
diff --git a/tests/testthat/test-scan.R b/tests/testthat/test-scan.R
index 955eb90e0..c975ecb72 100644
--- a/tests/testthat/test-scan.R
+++ b/tests/testthat/test-scan.R
@@ -11,7 +11,6 @@ test_that("summary.scan() prints metadata to the console", {
   expect_output(summary(scan), "parameters:", fixed = TRUE)
   expect_output(summary(scan), "elevation angle:", fixed = TRUE)
   expect_output(summary(scan), "dims:", fixed = TRUE)
-
 })
 
 test_that("is.scan() returns TRUE/FALSE correctly", {

From 81b9f3d4237a36e4cce2f4f6166ab06477ef3771 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 16:43:59 +0200
Subject: [PATCH 12/35] Use x[["height"]] since data$height tries to match
 magically

---
 R/vp.R   | 2 +-
 R/vpts.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/vp.R b/R/vp.R
index fe4461d79..6c029bf7a 100644
--- a/R/vp.R
+++ b/R/vp.R
@@ -88,7 +88,7 @@ summary.vp <- function(object, ...) {
 #' @export
 print.vp <- function(x, digits = max(3L, getOption("digits") - 3L), ...) {
   stopifnot(inherits(x, "vp"))
-  if (is.null(x$data$height)) {
+  if (is.null(x$data[["height"]])) {
     warning("`x` is a legacy vp object without a column `height`. Use convert_legacy() to avoid errors.")
     x <- convert_legacy(x)
   }
diff --git a/R/vpts.R b/R/vpts.R
index 116f42d87..4414d43d7 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -65,11 +65,11 @@ summary.vpts <- function(object, ...) {
 #' @export
 print.vpts <- function(x, digits = max(3L, getOption("digits") - 3L), ...) {
   stopifnot(inherits(x, "vpts"))
-  if (is.null(x$height)) {
+  if (is.null(x[["height"]])) {
     warning("`x` is a legacy vpts object without a column `height`. Use convert_legacy() to avoid errors.")
     x <- convert_legacy(x)
   }
-  if (is.null(x$datetime)) {
+  if (is.null(x[["datetime"]])) {
     warning("`x` is a legacy vpts object without a column `datetime`. Use convert_legacy() to avoid errors.")
     x <- convert_legacy(x)
   }

From 47a698b6ce303643da80b450d2615816bb27de9e Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 16:48:18 +0200
Subject: [PATCH 13/35] Add minimal doc to helper function vpts_to_vp

---
 R/vpts.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/vpts.R b/R/vpts.R
index 4414d43d7..52954a02d 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -195,6 +195,9 @@ dim.vpts <- function(x) {
   return(x)
 }
 
+#' Helper function to convert a vpts[i] to a vp object
+#'
+#' @noRd
 vpts_to_vp <- function(x, i) {
   stopifnot(inherits(x, "vpts"))
   nvp <- dim(x)[2]

From 7f13f866906380ca7d2676c6b0a1a74f8c0de4d3 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 16:59:55 +0200
Subject: [PATCH 14/35] Write tests for summary.vp, print.vp, is.vp, dim.vp,
 c.vp

---
 tests/testthat/test-vp.R | 40 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-vp.R b/tests/testthat/test-vp.R
index 9a07aa619..1dd05a792 100644
--- a/tests/testthat/test-vp.R
+++ b/tests/testthat/test-vp.R
@@ -1,3 +1,41 @@
-test_that("... returns error on incorrect parameters", {
+vp <- example_vp
+scan <- example_scan
 
+# No tests for error on incorrect parameters:
+# summary(), print(), dim() are generic and work for every input
+# is.vp() returns TRUE/FALSE and works for every input
+
+test_that("c.vp() returns error on incorrect parameters", {
+  expect_error(c(vp, "not_a_vp"), "Each element must be a vp object.")
+})
+
+test_that("summary.vp() prints metadata to the console", {
+  # print.vp() is not tested as it is the same as and called from summary.vp()
+  expect_output(summary(vp), "Vertical profile (class vp)", fixed = TRUE)
+  expect_output(summary(vp), "radar:", fixed = TRUE)
+  expect_output(summary(vp), "source:", fixed = TRUE)
+  expect_output(summary(vp), "nominal time:", fixed = TRUE)
+  expect_output(summary(vp), "generated by:", fixed = TRUE)
+})
+
+test_that("summary.vp() warns for legacy objects", {
+  names(vp$data) <- sub("height", "HGHT", names(vp$data)) # Rename to legacy "HGHT"
+  expect_warning(summary(vp), "`x` is a legacy vp object without a column `height`.", fixed = TRUE)
+})
+
+test_that("is.vp() returns TRUE/FALSE correctly", {
+  expect_true(is.vp(vp))
+  expect_false(is.vp("not_a_vp"))
+  expect_false(is.vp(scan))
+})
+
+test_that("dim.vp() returns dimensions", {
+  expect_vector(dim(vp))
+  expect_equal(dim(vp), c(25, 16)) # 25 heights, 17 quantities in example_vp
+})
+
+test_that("c.vp() warns if vp are not of same radar", {
+  vp_other_radar <- vp
+  vp_other_radar$radar <- "test"
+  expect_warning(c(vp, vp_other_radar), "Vertical profiles are not from a single radar.")
 })

From 2d06e24decb46a9f2716f96b047a8c1021976952 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 17:00:45 +0200
Subject: [PATCH 15/35] Write tests for summary.vpts, print.vpts, is.vpts,
 dim.vpts, subset.vpts

---
 tests/testthat/test-vpts.R | 40 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-vpts.R b/tests/testthat/test-vpts.R
index 9a07aa619..37f3d5ea6 100644
--- a/tests/testthat/test-vpts.R
+++ b/tests/testthat/test-vpts.R
@@ -1,3 +1,41 @@
-test_that("... returns error on incorrect parameters", {
+vpts <- example_vpts
+vp <- example_vp
 
+# No tests for error on incorrect parameters:
+# summary(), print(), dim() are generic and work for every input
+# is.vpts() returns TRUE/FALSE and works for every input
+# vpts["not_numeric] will return NA
+
+test_that("summary.vpts() prints metadata to the console", {
+  # print.vpts() is not tested as it is the same as and called from summary.vpts()
+  expect_output(summary(vpts), "Irregular time series of vertical profiles (class vpts)", fixed = TRUE)
+  expect_output(summary(vpts), "radar:", fixed = TRUE)
+  expect_output(summary(vpts), "# profiles:", fixed = TRUE)
+  expect_output(summary(vpts), "time range (UTC):", fixed = TRUE)
+  expect_output(summary(vpts), "time step (s):", fixed = TRUE)
+})
+
+test_that("summary.vpts() warns for legacy objects", {
+  names(vpts) <- sub("height", "heights", names(vpts)) # Rename to legacy "heights"
+  expect_warning(summary(vpts), "`x` is a legacy vpts object without a column `height`.", fixed = TRUE)
+  vpts <- convert_legacy(vpts) # Reset
+  names(vpts) <- sub("datetime", "dates", names(vpts)) # Rename to legacy "dates"
+  expect_warning(summary(vpts), "`x` is a legacy vpts object without a column `datetime`.", fixed = TRUE)
+})
+
+test_that("is.vpts() returns TRUE/FALSE correctly", {
+  expect_true(is.vpts(vpts))
+  expect_false(is.vpts("not_a_vpts"))
+  expect_false(is.vpts(vp))
+})
+
+test_that("dim.vpts() returns dimensions", {
+  expect_vector(dim(vpts))
+  expect_equal(dim(vpts), c(25, 1934, 15)) # 25 heights, 1934 datetimes, 15 quantities
+})
+
+test_that("[.vpts subsets by profiles and returns a vp object for single selection", {
+  expect_s3_class(vpts[10], "vp") # Done with internal function vpts_to_vp()
+  expect_s3_class(vpts[10:20], "vpts")
+  expect_equal(dim(vpts[10:20]), c(25, 11, 15)) # 11 datetimes selected
 })

From 143c3f32fb3f4d3ee3962d2cf3dbba914665eb7f Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 17:02:28 +0200
Subject: [PATCH 16/35] Remove error message for subsetting

@adokter dropped this error, because it seems pretty edge case to generate it. Would almost have to do vpts[c()], but maybe I am missing something? This error catch is also not there for ppi[]
---
 R/vpts.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/R/vpts.R b/R/vpts.R
index 52954a02d..afb73a6ac 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -157,9 +157,6 @@ dim.vpts <- function(x) {
 #' vpts[20:100]
 `[.vpts` <- function(x, i) {
   stopifnot(inherits(x, "vpts"))
-  if (length(i) < 1) {
-    stop("Time series should contain more than one profile.")
-  }
   if (length(i) == 1) {
     if (i > 0) {
       return(vpts_to_vp(x, i))

From f33e45b94fbe0138c370b11e65e356f98a556132 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 17:30:36 +0200
Subject: [PATCH 17/35] Correct test + add test for regular_vpts

---
 tests/testthat/test-vpts.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-vpts.R b/tests/testthat/test-vpts.R
index 37f3d5ea6..6e315a580 100644
--- a/tests/testthat/test-vpts.R
+++ b/tests/testthat/test-vpts.R
@@ -13,6 +13,9 @@ test_that("summary.vpts() prints metadata to the console", {
   expect_output(summary(vpts), "# profiles:", fixed = TRUE)
   expect_output(summary(vpts), "time range (UTC):", fixed = TRUE)
   expect_output(summary(vpts), "time step (s):", fixed = TRUE)
+
+  regular_vpts <- regularize_vpts(vpts)
+  expect_output(summary(regular_vpts), "Regular time series of vertical profiles (class vpts)", fixed = TRUE)
 })
 
 test_that("summary.vpts() warns for legacy objects", {
@@ -37,5 +40,5 @@ test_that("dim.vpts() returns dimensions", {
 test_that("[.vpts subsets by profiles and returns a vp object for single selection", {
   expect_s3_class(vpts[10], "vp") # Done with internal function vpts_to_vp()
   expect_s3_class(vpts[10:20], "vpts")
-  expect_equal(dim(vpts[10:20]), c(25, 11, 15)) # 11 datetimes selected
+  expect_equal(length(vpts[10:20]$datetime), 11) # 11 selected
 })

From 7a6c0354d0b0ce335c770ffa0529ff63fc03e8c5 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 17:55:02 +0200
Subject: [PATCH 18/35] Add dim.pvol(), see #355

---
 NAMESPACE                  |  1 +
 R/pvol.R                   | 16 ++++++++++++++++
 man/summary.pvol.Rd        |  9 +++++++++
 tests/testthat/test-pvol.R |  7 ++++++-
 4 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index b0b45a1d7..8112fed4a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,6 +26,7 @@ S3method(check_night,vpts)
 S3method(convert_legacy,vp)
 S3method(convert_legacy,vpts)
 S3method(dim,ppi)
+S3method(dim,pvol)
 S3method(dim,scan)
 S3method(dim,vp)
 S3method(dim,vpts)
diff --git a/R/pvol.R b/R/pvol.R
index f6400fe51..f1785dbed 100644
--- a/R/pvol.R
+++ b/R/pvol.R
@@ -39,6 +39,9 @@
 #' # Get summary info
 #' pvol # Same as summary(pvol) or print(pvol)
 #'
+#' # Get dimensions
+#' dim(pvol)
+#'
 #' # Get summary info for the scans in the polar volume
 #' pvol$scans
 summary.pvol <- function(object, ...) {
@@ -72,3 +75,16 @@ print.pvol <- function(x, digits = max(3L, getOption("digits") - 3L), ...) {
 is.pvol <- function(x) {
   inherits(x, "pvol")
 }
+
+#' Get dimensions for an object of class `pvol`
+#'
+#' @return For [dim.pvol()]: number of scans (`scan`) in a polar volume
+#'   (`pvol`).
+#'
+#' @rdname summary.pvol
+#'
+#' @export
+dim.pvol <- function(x) {
+  stopifnot(inherits(x, "pvol"))
+  c(length(x$scans))
+}
diff --git a/man/summary.pvol.Rd b/man/summary.pvol.Rd
index e6d105163..642388f05 100644
--- a/man/summary.pvol.Rd
+++ b/man/summary.pvol.Rd
@@ -3,11 +3,14 @@
 \name{summary.pvol}
 \alias{summary.pvol}
 \alias{is.pvol}
+\alias{dim.pvol}
 \title{Inspect a polar volume (\code{pvol})}
 \usage{
 \method{summary}{pvol}(object, ...)
 
 is.pvol(x)
+
+\method{dim}{pvol}(x)
 }
 \arguments{
 \item{object}{A \code{pvol} object.}
@@ -19,6 +22,9 @@ is.pvol(x)
 \value{
 For \code{\link[=is.pvol]{is.pvol()}}: \code{TRUE} for an object of class \code{pvol}, otherwise
 \code{FALSE}.
+
+For \code{\link[=dim.pvol]{dim.pvol()}}: number of scans (\code{scan}) in a polar volume
+(\code{pvol}).
 }
 \description{
 R base functions for inspecting a polar volume (\code{pvol}) object.
@@ -52,6 +58,9 @@ is.pvol(pvol)
 # Get summary info
 pvol # Same as summary(pvol) or print(pvol)
 
+# Get dimensions
+dim(pvol)
+
 # Get summary info for the scans in the polar volume
 pvol$scans
 }
diff --git a/tests/testthat/test-pvol.R b/tests/testthat/test-pvol.R
index 0a9dd55c5..e8b8eb393 100644
--- a/tests/testthat/test-pvol.R
+++ b/tests/testthat/test-pvol.R
@@ -3,7 +3,7 @@ pvol <- read_pvolfile(pvolfile)
 vp <- example_vp
 
 # No tests for error on incorrect parameters:
-# summary(), print() are generic and work for every input
+# summary(), print(), dim() are generic and work for every input
 # is.pvol() returns TRUE/FALSE and works for every input
 
 test_that("summary.pvol() prints metadata to the console", {
@@ -20,3 +20,8 @@ test_that("is.pvol() returns TRUE/FALSE correctly", {
   expect_false(is.pvol("not_a_pvol"))
   expect_false(is.pvol(vp))
 })
+
+test_that("dim.pvol() returns number of scans", {
+  expect_vector(dim(pvol))
+  expect_equal(dim(pvol), c(3)) # 3 scans in example_pvol
+})

From 76d562f533dbba43c25a010e83cf493ff22e3ad6 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 17:55:17 +0200
Subject: [PATCH 19/35] Be explicit about what dim should return in tests

---
 tests/testthat/test-ppi.R  | 4 ++--
 tests/testthat/test-scan.R | 2 +-
 tests/testthat/test-vp.R   | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-ppi.R b/tests/testthat/test-ppi.R
index 6d76751e7..772eb3c51 100644
--- a/tests/testthat/test-ppi.R
+++ b/tests/testthat/test-ppi.R
@@ -22,9 +22,9 @@ test_that("is.ppi() returns TRUE/FALSE correctly", {
   expect_false(is.ppi(vp))
 })
 
-test_that("dim.ppi() returns dimensions", {
+test_that("dim.ppi() returns number of params, x, y", {
   expect_vector(dim(ppi))
-  expect_equal(dim(ppi), c(5, 200, 200)) # 5 param, 200 x pixels, 200 y pixels for default range_max
+  expect_equal(dim(ppi), c(5, 200, 200)) # 5 param, 200 x, 200 y
 })
 
 test_that("[.ppi subsets by param", {
diff --git a/tests/testthat/test-scan.R b/tests/testthat/test-scan.R
index c975ecb72..77ed2a15c 100644
--- a/tests/testthat/test-scan.R
+++ b/tests/testthat/test-scan.R
@@ -19,7 +19,7 @@ test_that("is.scan() returns TRUE/FALSE correctly", {
   expect_false(is.scan(vp))
 })
 
-test_that("dim.scan() returns dimensions", {
+test_that("dim.scan() returns number of params, bins, rays", {
   expect_vector(dim(scan))
   expect_equal(dim(scan), c(5, 480, 360)) # 5 param, 480 bins, 360 rays in example_scan
 })
diff --git a/tests/testthat/test-vp.R b/tests/testthat/test-vp.R
index 1dd05a792..282f3dc48 100644
--- a/tests/testthat/test-vp.R
+++ b/tests/testthat/test-vp.R
@@ -29,7 +29,7 @@ test_that("is.vp() returns TRUE/FALSE correctly", {
   expect_false(is.vp(scan))
 })
 
-test_that("dim.vp() returns dimensions", {
+test_that("dim.vp() returns number of heights, quantities", {
   expect_vector(dim(vp))
   expect_equal(dim(vp), c(25, 16)) # 25 heights, 17 quantities in example_vp
 })

From 07a239129dd0ee5ff88f8f4b5170dbd9aeb2a1b1 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 17:56:22 +0200
Subject: [PATCH 20/35] Update dim.vpts() to datetimes, heights, quantities

Fix #355
---
 R/vpts.R                   | 7 ++++---
 tests/testthat/test-vpts.R | 4 ++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/vpts.R b/R/vpts.R
index afb73a6ac..6ab651a3c 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -117,7 +117,7 @@ is.vpts <- function(x) {
 
 #' Get dimensions for an object of class `vpts`
 #'
-#' @return For [dim.vpts()]: number of heights, datetimes and quantities in a
+#' @return For [dim.vpts()]: number of datetimes, heights and quantities in a
 #'   time series of vertical profiles (`vpts`).
 #'
 #' @rdname summary.vpts
@@ -125,8 +125,9 @@ is.vpts <- function(x) {
 #' @export
 dim.vpts <- function(x) {
   stopifnot(inherits(x, "vpts"))
-  data.dim <- dim(x$data[[1]])
-  c(data.dim, length(x$data))
+  heights <- nrow(x$data[[1]])
+  datetimes <- ncol(x$data[[1]])
+  c(datetimes, heights, length(x$data))
 }
 
 #' Subset a time series of vertical profiles (`vpts`)
diff --git a/tests/testthat/test-vpts.R b/tests/testthat/test-vpts.R
index 6e315a580..808d53ec2 100644
--- a/tests/testthat/test-vpts.R
+++ b/tests/testthat/test-vpts.R
@@ -32,9 +32,9 @@ test_that("is.vpts() returns TRUE/FALSE correctly", {
   expect_false(is.vpts(vp))
 })
 
-test_that("dim.vpts() returns dimensions", {
+test_that("dim.vpts() returns number of datetimes, heights, quantities", {
   expect_vector(dim(vpts))
-  expect_equal(dim(vpts), c(25, 1934, 15)) # 25 heights, 1934 datetimes, 15 quantities
+  expect_equal(dim(vpts), c(1934, 25, 15)) # 1934 datetimes, 25 heights, 15 quantities
 })
 
 test_that("[.vpts subsets by profiles and returns a vp object for single selection", {

From 8534b0add6d8f4c25c18a38bfa0b4ba50e0839a1 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Mon, 27 Apr 2020 18:09:02 +0200
Subject: [PATCH 21/35] Update style and documentation for convert_legacy()

---
 R/convert_legacy.R    | 16 ++++++++--------
 man/convert_legacy.Rd | 10 +++++-----
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/convert_legacy.R b/R/convert_legacy.R
index 258ac677b..a829a3ca1 100644
--- a/R/convert_legacy.R
+++ b/R/convert_legacy.R
@@ -1,19 +1,19 @@
 #' Convert legacy bioRad objects to current version
 #'
-#' Convert legacy bioRad objects (vp, vpts) that have become
-#' obsolete and make them compatible with the current bioRad version.
+#' Convert legacy bioRad objects (`vp`, `vpts`) that have become obsolete
+#' compatible with the current bioRad version.
 #'
-#' @param x A `vp`, or `vpts` object.
+#' @param x A `vp` or `vpts` object.
 #'
 #' @return An updated object of the same class as the input.
 #'
 #' @export
 #'
 #' @examples
-#' # convert a vp object:
+#' # Convert a vp object
 #' convert_legacy(example_vp)
 #'
-#' # convert a vpts object:
+#' # Convert a vpts object
 #' convert_legacy(example_vpts)
 convert_legacy <- function(x) {
   UseMethod("convert_legacy", x)
@@ -24,7 +24,7 @@ convert_legacy <- function(x) {
 #' @export
 convert_legacy.vp <- function(x) {
   assert_that(inherits(x, "vp"))
-  names(x$data)=sub("HGHT","height",names(x$data))
+  names(x$data) <- sub("HGHT", "height", names(x$data))
   x
 }
 
@@ -33,7 +33,7 @@ convert_legacy.vp <- function(x) {
 #' @export
 convert_legacy.vpts <- function(x) {
   assert_that(inherits(x, "vpts"))
-  names(x)=sub("heights","height",names(x))
-  names(x)=sub("dates","datetime",names(x))
+  names(x) <- sub("heights", "height", names(x))
+  names(x) <- sub("dates", "datetime", names(x))
   x
 }
diff --git a/man/convert_legacy.Rd b/man/convert_legacy.Rd
index 83e01f457..795577d58 100644
--- a/man/convert_legacy.Rd
+++ b/man/convert_legacy.Rd
@@ -13,19 +13,19 @@ convert_legacy(x)
 \method{convert_legacy}{vpts}(x)
 }
 \arguments{
-\item{x}{A \code{vp}, or \code{vpts} object.}
+\item{x}{A \code{vp} or \code{vpts} object.}
 }
 \value{
 An updated object of the same class as the input.
 }
 \description{
-Convert legacy bioRad objects (vp, vpts) that have become
-obsolete and make them compatible with the current bioRad version.
+Convert legacy bioRad objects (\code{vp}, \code{vpts}) that have become obsolete
+compatible with the current bioRad version.
 }
 \examples{
-# convert a vp object:
+# Convert a vp object
 convert_legacy(example_vp)
 
-# convert a vpts object:
+# Convert a vpts object
 convert_legacy(example_vpts)
 }

From 3967dae50299c1b962f1569886cc1af86416c71e Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 15:41:38 +0200
Subject: [PATCH 22/35] Add negative subsetting examples + tests

---
 R/ppi.R                    |  3 +++
 R/vpts.R                   | 11 +++++++----
 man/example_vpts.Rd        |  2 +-
 man/sub-.ppi.Rd            |  3 +++
 man/sub-.vpts.Rd           | 11 +++++++----
 man/summary.vpts.Rd        |  2 +-
 tests/testthat/test-ppi.R  |  1 +
 tests/testthat/test-vpts.R | 15 ++++++++++++---
 8 files changed, 35 insertions(+), 13 deletions(-)

diff --git a/R/ppi.R b/R/ppi.R
index b6b6907d5..4a566eaa9 100644
--- a/R/ppi.R
+++ b/R/ppi.R
@@ -117,6 +117,9 @@ dim.ppi <- function(x) {
 #'
 #' # Subset ppi to one containing the first three parameters (VRADH, DBZH, ZDR)
 #' ppi[1:3]
+#'
+#' # Subset ppi to one without the first 2 parameters (ZDR RHOHV PHIDP)
+#' ppi[-1:-2]
 `[.ppi` <- function(x, i) {
   stopifnot(inherits(x, "ppi"))
   my_ppi <- list(
diff --git a/R/vpts.R b/R/vpts.R
index 6ab651a3c..02085fc7c 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -151,11 +151,14 @@ dim.vpts <- function(x) {
 #' # This vpts contains 1934 profiles (i.e. datetimes)
 #' dim(vpts)
 #'
-#' # Subset vpts to extract 10th profile (returns a vp object)
-#' vpts[10]
+#' # Subset vpts to extract 10th profile
+#' vpts[10] # A vp object
 #'
-#' # Subset vpts to extract the 20th to 100th profile (returns a vpts object)
-#' vpts[20:100]
+#' # Subset vpts to extract the 20th to 100th profile
+#' vpts[20:100] # A vpts object with 81 profiles
+#'
+#' # Subset vpts to remove the first 10 profiles
+#' vpts[-1:-10] # A vpts object with 10 less profiles
 `[.vpts` <- function(x, i) {
   stopifnot(inherits(x, "vpts"))
   if (length(i) == 1) {
diff --git a/man/example_vpts.Rd b/man/example_vpts.Rd
index 4b7ddb3fe..373a54a1d 100644
--- a/man/example_vpts.Rd
+++ b/man/example_vpts.Rd
@@ -5,7 +5,7 @@
 \alias{example_vpts}
 \title{Example object of class \code{vpts}}
 \format{
-An object of class \code{vpts} of dimension 25 x 1934 x 15.
+An object of class \code{vpts} of dimension 1934 x 25 x 15.
 }
 \usage{
 example_vpts
diff --git a/man/sub-.ppi.Rd b/man/sub-.ppi.Rd
index 0edce4d97..a625931db 100644
--- a/man/sub-.ppi.Rd
+++ b/man/sub-.ppi.Rd
@@ -31,4 +31,7 @@ ppi[1]
 
 # Subset ppi to one containing the first three parameters (VRADH, DBZH, ZDR)
 ppi[1:3]
+
+# Subset ppi to one without the first 2 parameters (ZDR RHOHV PHIDP)
+ppi[-1:-2]
 }
diff --git a/man/sub-.vpts.Rd b/man/sub-.vpts.Rd
index 14461cc2f..ec1ee11bb 100644
--- a/man/sub-.vpts.Rd
+++ b/man/sub-.vpts.Rd
@@ -27,9 +27,12 @@ vpts <- example_vpts
 # This vpts contains 1934 profiles (i.e. datetimes)
 dim(vpts)
 
-# Subset vpts to extract 10th profile (returns a vp object)
-vpts[10]
+# Subset vpts to extract 10th profile
+vpts[10] # A vp object
 
-# Subset vpts to extract the 20th to 100th profile (returns a vpts object)
-vpts[20:100]
+# Subset vpts to extract the 20th to 100th profile
+vpts[20:100] # A vpts object with 81 profiles
+
+# Subset vpts to remove the first 10 profiles
+vpts[-1:-10] # A vpts object with 10 less profiles
 }
diff --git a/man/summary.vpts.Rd b/man/summary.vpts.Rd
index ac79cf19f..2ce5c6029 100644
--- a/man/summary.vpts.Rd
+++ b/man/summary.vpts.Rd
@@ -23,7 +23,7 @@ is.vpts(x)
 For \code{\link[=is.vpts]{is.vpts()}}: \code{TRUE} for an object of class \code{vpts}, otherwise
 \code{FALSE}.
 
-For \code{\link[=dim.vpts]{dim.vpts()}}: number of heights, datetimes and quantities in a
+For \code{\link[=dim.vpts]{dim.vpts()}}: number of datetimes, heights and quantities in a
 time series of vertical profiles (\code{vpts}).
 }
 \description{
diff --git a/tests/testthat/test-ppi.R b/tests/testthat/test-ppi.R
index 772eb3c51..ec7fe59ab 100644
--- a/tests/testthat/test-ppi.R
+++ b/tests/testthat/test-ppi.R
@@ -31,4 +31,5 @@ test_that("[.ppi subsets by param", {
   # parameters:  VRADH DBZH ZDR RHOHV PHIDP
   expect_equal(names(ppi[1]$data), c("VRADH"))
   expect_equal(names(ppi[2:4]$data), c("DBZH", "ZDR", "RHOHV"))
+  expect_equal(names(ppi[-2:-4]$data), c("VRADH", "PHIDP")) # All except 2 to 4
 })
diff --git a/tests/testthat/test-vpts.R b/tests/testthat/test-vpts.R
index 808d53ec2..f156836c4 100644
--- a/tests/testthat/test-vpts.R
+++ b/tests/testthat/test-vpts.R
@@ -37,8 +37,17 @@ test_that("dim.vpts() returns number of datetimes, heights, quantities", {
   expect_equal(dim(vpts), c(1934, 25, 15)) # 1934 datetimes, 25 heights, 15 quantities
 })
 
-test_that("[.vpts subsets by profiles and returns a vp object for single selection", {
-  expect_s3_class(vpts[10], "vp") # Done with internal function vpts_to_vp()
+test_that("[.vpts subsets by profiles", {
+  # 1934 profiles in total
+  expect_equal(length(vpts[10]$datetime), 1) # Select 10th => 1 profile
+  expect_equal(length(vpts[10:20]$datetime), 11) # Select 10:20 => 11 profiles
+  expect_equal(length(vpts[-1:-1900]$datetime), 34) # Remove 1:1900 => 34 profiles left
+})
+
+test_that("[.vpts returns a vp object for single selection", {
   expect_s3_class(vpts[10:20], "vpts")
-  expect_equal(length(vpts[10:20]$datetime), 11) # 11 selected
+  expect_s3_class(vpts[10], "vp") # Select 10th => 1 profile
+  vpts_of_2 <- vpts[1:2]
+  expect_s3_class(vpts_of_2[-1], "vp") # Remove 1st => 1 profile left
+  expect_s3_class(vpts_of_2[-2], "vp") # Remove 2nd => 1 profile left
 })

From aac4639f58f521ad41ab3c23e8cebcecf2765464 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 15:42:55 +0200
Subject: [PATCH 23/35] Simplify vpts_to_vp: only if vpts has single profile

Include test that otherwise fails
---
 R/vpts.R                   | 35 +++++++++++++----------------------
 tests/testthat/test-vpts.R |  1 +
 2 files changed, 14 insertions(+), 22 deletions(-)

diff --git a/R/vpts.R b/R/vpts.R
index 02085fc7c..1a33d3a7f 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -161,20 +161,7 @@ dim.vpts <- function(x) {
 #' vpts[-1:-10] # A vpts object with 10 less profiles
 `[.vpts` <- function(x, i) {
   stopifnot(inherits(x, "vpts"))
-  if (length(i) == 1) {
-    if (i > 0) {
-      return(vpts_to_vp(x, i))
-    } else {
-      if (dim(x)[2] == 2) {
-        if (i == -1) {
-          return(vpts_to_vp(x, 2))
-        }
-        if (i == -2) {
-          return(vpts_to_vp(x, 1))
-        }
-      }
-    }
-  }
+
   x$datetime <- x$datetime[i]
   x$daterange <- .POSIXct(c(min(x$datetime), max(x$datetime)), tz = "UTC")
   x$timesteps <- difftime(x$datetime[-1], x$datetime[-length(x$datetime)],
@@ -193,25 +180,29 @@ dim.vpts <- function(x) {
     }
   )
   names(x$data) <- quantity.names
+
+  # Convert to vp if only 1 profile
+  if(length(x$datetime) == 1) {
+    x <- vpts_to_vp(x)
+  }
+
   return(x)
 }
 
-#' Helper function to convert a vpts[i] to a vp object
+#' Helper function to convert a vpts[1] to a vp object
 #'
 #' @noRd
-vpts_to_vp <- function(x, i) {
+vpts_to_vp <- function(x) {
   stopifnot(inherits(x, "vpts"))
-  nvp <- dim(x)[2]
-  if (i < 1 || i > nvp) {
-    return(NA)
-  }
+  stopifnot(length(x$datetime) == 1)
+
   vpout <- list()
   vpout$radar <- x$radar
-  vpout$datetime <- x$datetime[i]
+  vpout$datetime <- x$datetime[1]
   vpout$data <- as.data.frame(lapply(
     names(x$data),
     function(y) {
-      x$data[y][[1]][, i]
+      x$data[y][[1]]
     }
   ))
   names(vpout$data) <- names(x$data)
diff --git a/tests/testthat/test-vpts.R b/tests/testthat/test-vpts.R
index f156836c4..6b4a12545 100644
--- a/tests/testthat/test-vpts.R
+++ b/tests/testthat/test-vpts.R
@@ -47,6 +47,7 @@ test_that("[.vpts subsets by profiles", {
 test_that("[.vpts returns a vp object for single selection", {
   expect_s3_class(vpts[10:20], "vpts")
   expect_s3_class(vpts[10], "vp") # Select 10th => 1 profile
+  expect_s3_class(vpts[-1:-1933], "vp") # Remove 1933 => 1 profile left
   vpts_of_2 <- vpts[1:2]
   expect_s3_class(vpts_of_2[-1], "vp") # Remove 1st => 1 profile left
   expect_s3_class(vpts_of_2[-2], "vp") # Remove 2nd => 1 profile left

From f485dd15532cc203441f28fa1e612fe55b5d0f3d Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 15:44:57 +0200
Subject: [PATCH 24/35] Fix updated dim

---
 R/vpts.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/vpts.R b/R/vpts.R
index 02085fc7c..477dd069f 100644
--- a/R/vpts.R
+++ b/R/vpts.R
@@ -165,7 +165,7 @@ dim.vpts <- function(x) {
     if (i > 0) {
       return(vpts_to_vp(x, i))
     } else {
-      if (dim(x)[2] == 2) {
+      if (dim(x)[1] == 2) {
         if (i == -1) {
           return(vpts_to_vp(x, 2))
         }
@@ -201,7 +201,7 @@ dim.vpts <- function(x) {
 #' @noRd
 vpts_to_vp <- function(x, i) {
   stopifnot(inherits(x, "vpts"))
-  nvp <- dim(x)[2]
+  nvp <- dim(x)[1]
   if (i < 1 || i > nvp) {
     return(NA)
   }

From 5973634dd140811a233d7d4c6a40b4c30bc49be2 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 16:52:06 +0200
Subject: [PATCH 25/35] Mention pvol in get_scan

---
 R/get_scan.R    | 3 ++-
 man/get_scan.Rd | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/get_scan.R b/R/get_scan.R
index e5e32cb57..9ffeb5f98 100644
--- a/R/get_scan.R
+++ b/R/get_scan.R
@@ -1,6 +1,7 @@
 #' Get a scan (`scan`) from a polar volume (`pvol`)
 #'
-#' Returns the scan with elevation angle closest to `elev`.
+#' Returns the scan (`scan`) from a polar volume (`pvol`) with elevation angle
+#' closest to `elev`.
 #'
 #' @param x A `pvol` object.
 #' @param elev Numeric. Elevation angle.
diff --git a/man/get_scan.Rd b/man/get_scan.Rd
index 3eaad13b3..2c26d9831 100644
--- a/man/get_scan.Rd
+++ b/man/get_scan.Rd
@@ -15,7 +15,8 @@ get_scan(x, elev)
 A \code{scan} object.
 }
 \description{
-Returns the scan with elevation angle closest to \code{elev}.
+Returns the scan (\code{scan}) from a polar volume (\code{pvol}) with elevation angle
+closest to \code{elev}.
 }
 \examples{
 # Locate and read the polar volume example file

From dd33ffa0c22d0ecf13324da34718d707760ee5ec Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 16:58:48 +0200
Subject: [PATCH 26/35] Use fixed = TRUE for error message testing

---
 tests/testthat/test-get_scan.R         | 4 ++--
 tests/testthat/test-rcs.R              | 4 ++--
 tests/testthat/test-sd_vvp_threshold.R | 4 ++--
 tests/testthat/test-vp.R               | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test-get_scan.R b/tests/testthat/test-get_scan.R
index d2c9d79cd..f94901da7 100644
--- a/tests/testthat/test-get_scan.R
+++ b/tests/testthat/test-get_scan.R
@@ -2,8 +2,8 @@ pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
 pvol <- read_pvolfile(pvolfile)
 
 test_that("get_scan() returns error on incorrect parameters", {
-  expect_error(get_scan("not_a_pvol", 5), "`x` must be a pvol object.")
-  expect_error(get_scan(pvol, "not_numeric"), "`elev` must be numeric.")
+  expect_error(get_scan("not_a_pvol", 5), "`x` must be a pvol object.", fixed = TRUE)
+  expect_error(get_scan(pvol, "not_numeric"), "`elev` must be numeric.", fixed = TRUE)
 })
 
 test_that("get_scan() returns a object of class scan", {
diff --git a/tests/testthat/test-rcs.R b/tests/testthat/test-rcs.R
index b3e1814c6..651f54960 100644
--- a/tests/testthat/test-rcs.R
+++ b/tests/testthat/test-rcs.R
@@ -6,7 +6,7 @@ vpi <- integrate_profile(example_vpts)
 
 test_that("rcs() returns error on incorrect parameters", {
   expect_error(rcs("not_a_vp"))
-  expect_error(rcs(vp_list_mixed), "`x` must be list of vp objects.")
+  expect_error(rcs(vp_list_mixed), "`x` must be list of vp objects.", fixed = TRUE)
 })
 
 test_that("rcs()<- returns error on incorrect parameters", {
@@ -14,7 +14,7 @@ test_that("rcs()<- returns error on incorrect parameters", {
   expect_error(rcs(vp) <- NULL)
   expect_error(rcs(vp) <- c(2, 2))
   expect_error(rcs("not_a_vp") <- 5)
-  expect_error(rcs(vp_list_mixed) <- 5, "`x` must be list of vp objects.")
+  expect_error(rcs(vp_list_mixed) <- 5, "`x` must be list of vp objects.", fixed = TRUE)
   expect_error(rcs(vp) <- -11)
 })
 
diff --git a/tests/testthat/test-sd_vvp_threshold.R b/tests/testthat/test-sd_vvp_threshold.R
index f6db8f27f..f393017da 100644
--- a/tests/testthat/test-sd_vvp_threshold.R
+++ b/tests/testthat/test-sd_vvp_threshold.R
@@ -5,7 +5,7 @@ vpts <- example_vpts
 
 test_that("sd_vvp_threshold() returns error on incorrect parameters", {
   expect_error(sd_vvp_threshold("not_a_vp"))
-  expect_error(sd_vvp_threshold(vp_list_mixed), "`x` must be list of vp objects.")
+  expect_error(sd_vvp_threshold(vp_list_mixed), "`x` must be list of vp objects.", fixed = TRUE)
 })
 
 test_that("sd_vvp_threshold()<- returns error on incorrect parameters", {
@@ -13,7 +13,7 @@ test_that("sd_vvp_threshold()<- returns error on incorrect parameters", {
   expect_error(sd_vvp_threshold(vp) <- NULL)
   expect_error(sd_vvp_threshold(vp) <- c(2, 2))
   expect_error(sd_vvp_threshold("not_a_vp") <- 2)
-  expect_error(sd_vvp_threshold(vp_list_mixed) <- 2, "`x` must be list of vp objects.")
+  expect_error(sd_vvp_threshold(vp_list_mixed) <- 2, "`x` must be list of vp objects.", fixed = TRUE)
 })
 
 test_that("sd_vvp_threshold() returns the correct sd_vvp_thresh", {
diff --git a/tests/testthat/test-vp.R b/tests/testthat/test-vp.R
index 282f3dc48..fb60fe2f7 100644
--- a/tests/testthat/test-vp.R
+++ b/tests/testthat/test-vp.R
@@ -6,7 +6,7 @@ scan <- example_scan
 # is.vp() returns TRUE/FALSE and works for every input
 
 test_that("c.vp() returns error on incorrect parameters", {
-  expect_error(c(vp, "not_a_vp"), "Each element must be a vp object.")
+  expect_error(c(vp, "not_a_vp"), "Each element must be a vp object.", fixed = TRUE)
 })
 
 test_that("summary.vp() prints metadata to the console", {

From ef16be11bb629542d6e7659281797371bd8683f5 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 16:59:06 +0200
Subject: [PATCH 27/35] Use get_ in get_elevation_angle tests

---
 tests/testthat/test-get_elevation_angles.R | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-get_elevation_angles.R b/tests/testthat/test-get_elevation_angles.R
index 125e0e8fb..842dc9cd9 100644
--- a/tests/testthat/test-get_elevation_angles.R
+++ b/tests/testthat/test-get_elevation_angles.R
@@ -1,12 +1,10 @@
 pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
 pvol <- read_pvolfile(pvolfile)
-scan <- pvol$scans[[1]]
-param <- scan$params$DBZH
+scan <- get_scan(pvol, 0.5)
+param <- get_param(scan, "DBZH")
 
 test_that("get_elevation_angles() returns error on incorrect parameters", {
   expect_error(get_elevation_angles("not_a_vp"))
-  expect_error(get_elevation_angles(1))
-  expect_error(get_elevation_angles(NULL))
 })
 
 test_that("get_elevation_angles() returns the correct elangle", {

From d13ffd9dddd2c8f7bf596c7d15dcf4aefea37b4f Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 16:59:48 +0200
Subject: [PATCH 28/35] Update doc and reference summary.param()

---
 R/get_param.R    | 29 ++++++++++++++++++++---------
 man/get_param.Rd | 29 +++++++++++++++++++----------
 2 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/R/get_param.R b/R/get_param.R
index 5b494ab05..e3a79f6e8 100644
--- a/R/get_param.R
+++ b/R/get_param.R
@@ -1,18 +1,29 @@
-#' Get a scan parameter `param` from a scan `scan`
+#' Get a parameter `param` from a scan (`scan`)
 #'
-#' @param x An object of class `scan`.
-#' @param param A scan parameter.
+#' Returns the selected parameter (`param`) from a scan (`scan`).
 #'
-#' @return An object of class [param][summary.param].
+#' @param x A `scan` object.
+#' @param param Character. A scan parameter, such as `DBZH` or `VRADH`. See
+#'   [summary.param()] for commonly available parameters.
+#'
+#' @return A `param` object.
 #'
 #' @export
+#'
+#' @seealso [summary.param()]
+#'
 #' @examples
-#' # we will extract a scan parameter from the example scan object:
-#' example_scan
+#' # Load the example scan
+#' scan <- example_scan
+#'
+#' # Get summary info (including parameters)
+#' scan
+#'
+#' # Extact the VRADH scan parameter
+#' param <- get_param(scan, "VRADH")
 #'
-#' # extract the VRADH scan parameter
-#' my_param <- get_param(example_scan, "VRADH")
-#' my_param
+#' # Get summary info for this parameter
+#' param
 get_param <- function(x, param) {
   assert_that(class(x) == "scan", msg = "`x` must be a scan object.")
   if (!(param %in% names(x$params))) stop(paste("Scan parameter", param, "not found in `x`."))
diff --git a/man/get_param.Rd b/man/get_param.Rd
index 4c5b10813..745048100 100644
--- a/man/get_param.Rd
+++ b/man/get_param.Rd
@@ -2,26 +2,35 @@
 % Please edit documentation in R/get_param.R
 \name{get_param}
 \alias{get_param}
-\title{Get a scan parameter \code{param} from a scan \code{scan}}
+\title{Get a parameter \code{param} from a scan (\code{scan})}
 \usage{
 get_param(x, param)
 }
 \arguments{
-\item{x}{An object of class \code{scan}.}
+\item{x}{A \code{scan} object.}
 
-\item{param}{A scan parameter.}
+\item{param}{Character. A scan parameter, such as \code{DBZH} or \code{VRADH}. See
+\code{\link[=summary.param]{summary.param()}} for commonly available parameters.}
 }
 \value{
-An object of class \link[=summary.param]{param}.
+A \code{param} object.
 }
 \description{
-Get a scan parameter \code{param} from a scan \code{scan}
+Returns the selected parameter (\code{param}) from a scan (\code{scan}).
 }
 \examples{
-# we will extract a scan parameter from the example scan object:
-example_scan
+# Load the example scan
+scan <- example_scan
 
-# extract the VRADH scan parameter
-my_param <- get_param(example_scan, "VRADH")
-my_param
+# Get summary info (including parameters)
+scan
+
+# Extact the VRADH scan parameter
+param <- get_param(scan, "VRADH")
+
+# Get summary info for this parameter
+param
+}
+\seealso{
+\code{\link[=summary.param]{summary.param()}}
 }

From 68e9d47a6dc9f7a0602d2eac7d6d0c4e6abb379a Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:00:13 +0200
Subject: [PATCH 29/35] Update error message

---
 R/get_param.R                   |  2 +-
 tests/testthat/test-get_param.R | 10 ++++------
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/R/get_param.R b/R/get_param.R
index e3a79f6e8..8e7cee984 100644
--- a/R/get_param.R
+++ b/R/get_param.R
@@ -26,6 +26,6 @@
 #' param
 get_param <- function(x, param) {
   assert_that(class(x) == "scan", msg = "`x` must be a scan object.")
-  if (!(param %in% names(x$params))) stop(paste("Scan parameter", param, "not found in `x`."))
+  if (!(param %in% names(x$params))) stop(paste0("Can't find parameter `", param, "` in `x`."))
   x$params[[param]]
 }
diff --git a/tests/testthat/test-get_param.R b/tests/testthat/test-get_param.R
index 0384827ec..28bb33f27 100644
--- a/tests/testthat/test-get_param.R
+++ b/tests/testthat/test-get_param.R
@@ -3,15 +3,13 @@ pvol <- read_pvolfile(pvolfile)
 scan <- pvol$scans[[1]]
 
 test_that("get_param() returns error on incorrect parameters", {
-  expect_error(get_param("not_a_scan"), "`x` must be a scan object.")
-  expect_error(get_param(vp),"`x` must be a scan object.")
-  expect_error(get_param(pvol),"`x` must be a scan object.")
-  expect_error(get_param(scan))
-  expect_error(get_param(scan, "not_a_param"), "Scan parameter not_a_param not found in `x`.")
+  expect_error(get_param("not_a_scan", "DBZH"), "`x` must be a scan object.", fixed = TRUE)
+  expect_error(get_param(pvol, "DBZH"),"`x` must be a scan object.", fixed = TRUE)
+  expect_error(get_param(scan)) # Parameter "param" missing
+  expect_error(get_param(scan, "not_a_param"), "Can't find parameter `not_a_param` in `x`", fixed = TRUE)
 })
 
 test_that("get_param() returns correct parameters", {
   expect_equal(get_param(scan, names(scan$params[1])), scan$params[[1]])
   expect_equal(get_param(scan, names(scan$params[2])), scan$params[[2]])
 })
-

From 6b1e179df852868006006fd2ad47076c8766f3f4 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:03:27 +0200
Subject: [PATCH 30/35] Use parenthesis

---
 R/get_param.R    | 2 +-
 man/get_param.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/get_param.R b/R/get_param.R
index 8e7cee984..267ed0e2a 100644
--- a/R/get_param.R
+++ b/R/get_param.R
@@ -1,4 +1,4 @@
-#' Get a parameter `param` from a scan (`scan`)
+#' Get a parameter (`param`) from a scan (`scan`)
 #'
 #' Returns the selected parameter (`param`) from a scan (`scan`).
 #'
diff --git a/man/get_param.Rd b/man/get_param.Rd
index 745048100..22fc17527 100644
--- a/man/get_param.Rd
+++ b/man/get_param.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/get_param.R
 \name{get_param}
 \alias{get_param}
-\title{Get a parameter \code{param} from a scan (\code{scan})}
+\title{Get a parameter (\code{param}) from a scan (\code{scan})}
 \usage{
 get_param(x, param)
 }

From 807fa8546743ae7abcf76d15bacc05983378baf3 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:03:34 +0200
Subject: [PATCH 31/35] Test for literal parameters + test class

---
 tests/testthat/test-get_param.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-get_param.R b/tests/testthat/test-get_param.R
index 28bb33f27..8d145a6d5 100644
--- a/tests/testthat/test-get_param.R
+++ b/tests/testthat/test-get_param.R
@@ -1,6 +1,6 @@
 pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
 pvol <- read_pvolfile(pvolfile)
-scan <- pvol$scans[[1]]
+scan <- example_scan
 
 test_that("get_param() returns error on incorrect parameters", {
   expect_error(get_param("not_a_scan", "DBZH"), "`x` must be a scan object.", fixed = TRUE)
@@ -9,7 +9,9 @@ test_that("get_param() returns error on incorrect parameters", {
   expect_error(get_param(scan, "not_a_param"), "Can't find parameter `not_a_param` in `x`", fixed = TRUE)
 })
 
-test_that("get_param() returns correct parameters", {
-  expect_equal(get_param(scan, names(scan$params[1])), scan$params[[1]])
-  expect_equal(get_param(scan, names(scan$params[2])), scan$params[[2]])
+test_that("get_param() returns correct parameter", {
+  # Parameters: VRADH DBZH ZDR RHOHV PHIDP
+  expect_equal(get_param(scan, "DBZH"), scan$params[["DBZH"]])
+  expect_equal(get_param(scan, "PHIDP"), scan$params[["PHIDP"]])
+  expect_s3_class(get_param(scan, "RHOHV"), "param")
 })

From 9118ae5dce0fd58e94877d67891d9a42d388ba61 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:39:02 +0200
Subject: [PATCH 32/35] Use markdown + extend examples

---
 R/data.R            | 61 ++++++++++++++++++++++++++-------------------
 man/example_scan.Rd | 21 ++++++++++------
 man/example_vp.Rd   | 22 +++++++++-------
 man/example_vpts.Rd | 21 ++++++++++------
 4 files changed, 75 insertions(+), 50 deletions(-)

diff --git a/R/data.R b/R/data.R
index 271e68b7e..bfb78f3c2 100644
--- a/R/data.R
+++ b/R/data.R
@@ -1,64 +1,75 @@
-#' Example object of class \code{vp}
+#' Vertical profile (`vp`) example
 #'
-#' Example of a \code{\link[=summary.vp]{vp}} object with name
-#' \code{example_vp}. Can be created with \code{\link{calculate_vp}} or read
-#' from file with \code{\link{read_vpfiles}}.
+#' Example object of class [`vp`][summary.vp()] with name `example_vp`.
 #'
 #' @rdname example_vp
 #'
+#' @seealso [summary.vp]
+#'
 #' @examples
-#' # get summary of example vp:
-#' summary(example_vp)
+#' # Reload example_vp from package (e.g. in case it was altered)
+#' data(example_vp)
+#'
+#' # Get summary info
+#' example_vp
 #'
-#' # example_vp was created with:
+#' # example_vp was created with
+#' \dontrun{
 #' vpfile <- system.file("extdata", "profile.h5", package = "bioRad")
 #' example_vp <- read_vpfiles(vpfile)
-#' \dontrun{
-#' # save(example_vp, file = "data/example_vp.rda")
+#' save(example_vp, file = "data/example_vp.rda")
 #' }
 "example_vp"
 
-#' Example object of class \code{scan}
+#' Scan (`scan`) example
 #'
-#' Example of a \code{\link[=summary.scan]{scan}} object with name
-#' \code{example_scan}.
+#' Example object of class [`scan`][summary.scan()] with name `example_scan`.
 #'
 #' @rdname example_scan
 #'
+#' @seealso [summary.scan]
+#'
 #' @examples
-#' # get summary of example scan:
-#' summary(example_scan)
+#' # Reload example_scan from package (e.g. in case it was altered)
+#' data(example_scan)
 #'
-#' # example_scan was created with:
+#' # Get summary info
+#' example_scan
+#'
+#' # example_scan was created with
+#' \dontrun{
 #' pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
 #' pvol <- read_pvolfile(pvolfile)
 #' example_scan <- pvol$scans[[1]]
-#' \dontrun{
-#' # save(example_scan, file = "data/example_scan.rda")
+#' save(example_scan, file = "data/example_scan.rda")
 #' }
 "example_scan"
 
-#' Example object of class \code{vpts}
+#' Time series of vertical profiles (`vpts`) example
 #'
-#' Example of a \code{\link[=summary.vpts]{vpts}} object (a time series of
-#' vertical profiles) with name \code{example_vpts}.
+#' Example object of class [`vpts`](summary.vpts()] with name `example_vpts`.
 #'
 #' @rdname example_vpts
 #'
+#' @seealso [summary.vpts]
+#'
 #' @examples
-#' # get summary of example vpts:
-#' summary(example_vpts)
+#' # Reload example_vpts from package (e.g. in case it was altered)
+#' data(example_vpts)
+#'
+#' # Get summary info
+#' example_vpts
 #'
-#' # example_vpts was created with:
+#' # example_vpts was created with
 #' \dontrun{
 #' vptsfile <- system.file("extdata", "vpts.txt.zip", package = "bioRad")
-#' unzip(vptsfile, exdir = (dirname(vptsfile)), junkpaths = T)
+#' unzip(vptsfile, exdir = (dirname(vptsfile)), junkpaths = TRUE)
 #' vptsfile <- substr(vptsfile, 1, nchar(vptsfile) - 4)
 #' example_vpts <- read_vpts(vptsfile, radar = "KBGM", wavelength = "S")
 #' rcs(example_vpts) <- 11
 #' sd_vvp_threshold(example_vpts) <- 2
 #' example_vpts$attributes$where$lat <- 42.2
 #' example_vpts$attributes$where$lon <- -75.98
-#' # save(example_vpts, file = "data/example_vpts.rda", compress = "xz")
+#' save(example_vpts, file = "data/example_vpts.rda", compress = "xz")
 #' }
 "example_vpts"
diff --git a/man/example_scan.Rd b/man/example_scan.Rd
index 9d9e9caf5..ba18c7506 100644
--- a/man/example_scan.Rd
+++ b/man/example_scan.Rd
@@ -3,7 +3,7 @@
 \docType{data}
 \name{example_scan}
 \alias{example_scan}
-\title{Example object of class \code{scan}}
+\title{Scan (\code{scan}) example}
 \format{
 An object of class \code{scan} of dimension 5 x 480 x 360.
 }
@@ -11,19 +11,24 @@ An object of class \code{scan} of dimension 5 x 480 x 360.
 example_scan
 }
 \description{
-Example of a \code{\link[=summary.scan]{scan}} object with name
-\code{example_scan}.
+Example object of class \code{\link[=summary.scan]{scan}} with name \code{example_scan}.
 }
 \examples{
-# get summary of example scan:
-summary(example_scan)
+# Reload example_scan from package (e.g. in case it was altered)
+data(example_scan)
 
-# example_scan was created with:
+# Get summary info
+example_scan
+
+# example_scan was created with
+\dontrun{
 pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
 pvol <- read_pvolfile(pvolfile)
 example_scan <- pvol$scans[[1]]
-\dontrun{
-# save(example_scan, file = "data/example_scan.rda")
+save(example_scan, file = "data/example_scan.rda")
+}
 }
+\seealso{
+\link{summary.scan}
 }
 \keyword{datasets}
diff --git a/man/example_vp.Rd b/man/example_vp.Rd
index 5f42e0274..9de20461b 100644
--- a/man/example_vp.Rd
+++ b/man/example_vp.Rd
@@ -3,7 +3,7 @@
 \docType{data}
 \name{example_vp}
 \alias{example_vp}
-\title{Example object of class \code{vp}}
+\title{Vertical profile (\code{vp}) example}
 \format{
 An object of class \code{vp} with 25 rows and 16 columns.
 }
@@ -11,19 +11,23 @@ An object of class \code{vp} with 25 rows and 16 columns.
 example_vp
 }
 \description{
-Example of a \code{\link[=summary.vp]{vp}} object with name
-\code{example_vp}. Can be created with \code{\link{calculate_vp}} or read
-from file with \code{\link{read_vpfiles}}.
+Example object of class \code{\link[=summary.vp]{vp}} with name \code{example_vp}.
 }
 \examples{
-# get summary of example vp:
-summary(example_vp)
+# Reload example_vp from package (e.g. in case it was altered)
+data(example_vp)
 
-# example_vp was created with:
+# Get summary info
+example_vp
+
+# example_vp was created with
+\dontrun{
 vpfile <- system.file("extdata", "profile.h5", package = "bioRad")
 example_vp <- read_vpfiles(vpfile)
-\dontrun{
-# save(example_vp, file = "data/example_vp.rda")
+save(example_vp, file = "data/example_vp.rda")
+}
 }
+\seealso{
+\link{summary.vp}
 }
 \keyword{datasets}
diff --git a/man/example_vpts.Rd b/man/example_vpts.Rd
index 373a54a1d..1478b2607 100644
--- a/man/example_vpts.Rd
+++ b/man/example_vpts.Rd
@@ -3,7 +3,7 @@
 \docType{data}
 \name{example_vpts}
 \alias{example_vpts}
-\title{Example object of class \code{vpts}}
+\title{Time series of vertical profiles (\code{vpts}) example}
 \format{
 An object of class \code{vpts} of dimension 1934 x 25 x 15.
 }
@@ -11,24 +11,29 @@ An object of class \code{vpts} of dimension 1934 x 25 x 15.
 example_vpts
 }
 \description{
-Example of a \code{\link[=summary.vpts]{vpts}} object (a time series of
-vertical profiles) with name \code{example_vpts}.
+Example object of class \code{\link{vpts}}(summary.vpts()] with name \code{example_vpts}.
 }
 \examples{
-# get summary of example vpts:
-summary(example_vpts)
+# Reload example_vpts from package (e.g. in case it was altered)
+data(example_vpts)
 
-# example_vpts was created with:
+# Get summary info
+example_vpts
+
+# example_vpts was created with
 \dontrun{
 vptsfile <- system.file("extdata", "vpts.txt.zip", package = "bioRad")
-unzip(vptsfile, exdir = (dirname(vptsfile)), junkpaths = T)
+unzip(vptsfile, exdir = (dirname(vptsfile)), junkpaths = TRUE)
 vptsfile <- substr(vptsfile, 1, nchar(vptsfile) - 4)
 example_vpts <- read_vpts(vptsfile, radar = "KBGM", wavelength = "S")
 rcs(example_vpts) <- 11
 sd_vvp_threshold(example_vpts) <- 2
 example_vpts$attributes$where$lat <- 42.2
 example_vpts$attributes$where$lon <- -75.98
-# save(example_vpts, file = "data/example_vpts.rda", compress = "xz")
+save(example_vpts, file = "data/example_vpts.rda", compress = "xz")
+}
 }
+\seealso{
+\link{summary.vpts}
 }
 \keyword{datasets}

From 10e6ee2fd6243874076de70328f4bc98ea0255f0 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:45:10 +0200
Subject: [PATCH 33/35] Change order to scan, vp, vpts

---
 R/data.R | 44 +++++++++++++++++++++-----------------------
 1 file changed, 21 insertions(+), 23 deletions(-)

diff --git a/R/data.R b/R/data.R
index bfb78f3c2..6e96da95f 100644
--- a/R/data.R
+++ b/R/data.R
@@ -1,26 +1,3 @@
-#' Vertical profile (`vp`) example
-#'
-#' Example object of class [`vp`][summary.vp()] with name `example_vp`.
-#'
-#' @rdname example_vp
-#'
-#' @seealso [summary.vp]
-#'
-#' @examples
-#' # Reload example_vp from package (e.g. in case it was altered)
-#' data(example_vp)
-#'
-#' # Get summary info
-#' example_vp
-#'
-#' # example_vp was created with
-#' \dontrun{
-#' vpfile <- system.file("extdata", "profile.h5", package = "bioRad")
-#' example_vp <- read_vpfiles(vpfile)
-#' save(example_vp, file = "data/example_vp.rda")
-#' }
-"example_vp"
-
 #' Scan (`scan`) example
 #'
 #' Example object of class [`scan`][summary.scan()] with name `example_scan`.
@@ -45,6 +22,27 @@
 #' }
 "example_scan"
 
+#' Vertical profile (`vp`) example
+#'
+#' Example object of class [`vp`][summary.vp()] with name `example_vp`.
+#'
+#' @rdname example_vp
+#'
+#' @examples
+#' # Reload example_vp from package (e.g. in case it was altered)
+#' data(example_vp)
+#'
+#' # Get summary info
+#' example_vp
+#'
+#' # example_vp was created with
+#' \dontrun{
+#' vpfile <- system.file("extdata", "profile.h5", package = "bioRad")
+#' example_vp <- read_vpfiles(vpfile)
+#' save(example_vp, file = "data/example_vp.rda")
+#' }
+"example_vp"
+
 #' Time series of vertical profiles (`vpts`) example
 #'
 #' Example object of class [`vpts`](summary.vpts()] with name `example_vpts`.

From c858b5ecc59dbcbc984816f15a589b52286a85e9 Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:45:26 +0200
Subject: [PATCH 34/35] Correct typo and remove see also

---
 R/data.R            | 6 +-----
 man/example_scan.Rd | 3 ---
 man/example_vp.Rd   | 3 ---
 man/example_vpts.Rd | 5 +----
 4 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/R/data.R b/R/data.R
index 6e96da95f..356c72b8f 100644
--- a/R/data.R
+++ b/R/data.R
@@ -4,8 +4,6 @@
 #'
 #' @rdname example_scan
 #'
-#' @seealso [summary.scan]
-#'
 #' @examples
 #' # Reload example_scan from package (e.g. in case it was altered)
 #' data(example_scan)
@@ -45,12 +43,10 @@
 
 #' Time series of vertical profiles (`vpts`) example
 #'
-#' Example object of class [`vpts`](summary.vpts()] with name `example_vpts`.
+#' Example object of class [`vpts`][summary.vpts()] with name `example_vpts`.
 #'
 #' @rdname example_vpts
 #'
-#' @seealso [summary.vpts]
-#'
 #' @examples
 #' # Reload example_vpts from package (e.g. in case it was altered)
 #' data(example_vpts)
diff --git a/man/example_scan.Rd b/man/example_scan.Rd
index ba18c7506..494f646df 100644
--- a/man/example_scan.Rd
+++ b/man/example_scan.Rd
@@ -28,7 +28,4 @@ example_scan <- pvol$scans[[1]]
 save(example_scan, file = "data/example_scan.rda")
 }
 }
-\seealso{
-\link{summary.scan}
-}
 \keyword{datasets}
diff --git a/man/example_vp.Rd b/man/example_vp.Rd
index 9de20461b..bfb877ab7 100644
--- a/man/example_vp.Rd
+++ b/man/example_vp.Rd
@@ -27,7 +27,4 @@ example_vp <- read_vpfiles(vpfile)
 save(example_vp, file = "data/example_vp.rda")
 }
 }
-\seealso{
-\link{summary.vp}
-}
 \keyword{datasets}
diff --git a/man/example_vpts.Rd b/man/example_vpts.Rd
index 1478b2607..826860429 100644
--- a/man/example_vpts.Rd
+++ b/man/example_vpts.Rd
@@ -11,7 +11,7 @@ An object of class \code{vpts} of dimension 1934 x 25 x 15.
 example_vpts
 }
 \description{
-Example object of class \code{\link{vpts}}(summary.vpts()] with name \code{example_vpts}.
+Example object of class \code{\link[=summary.vpts]{vpts}} with name \code{example_vpts}.
 }
 \examples{
 # Reload example_vpts from package (e.g. in case it was altered)
@@ -33,7 +33,4 @@ example_vpts$attributes$where$lon <- -75.98
 save(example_vpts, file = "data/example_vpts.rda", compress = "xz")
 }
 }
-\seealso{
-\link{summary.vpts}
-}
 \keyword{datasets}

From fee92a71cf763520b9e558f94b2ced7466d1a75e Mon Sep 17 00:00:00 2001
From: peterdesmet <peter.desmet@inbo.be>
Date: Tue, 28 Apr 2020 17:47:47 +0200
Subject: [PATCH 35/35] Add simple test for example objects

Could be extended with more tests if need be, but is not part of coverage
---
 tests/testthat/test-data.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
index 9a07aa619..10e61f403 100644
--- a/tests/testthat/test-data.R
+++ b/tests/testthat/test-data.R
@@ -1,3 +1,5 @@
-test_that("... returns error on incorrect parameters", {
-
+test_that("Example objects are of the correct class", {
+  expect_s3_class(example_scan, "scan")
+  expect_s3_class(example_vp, "vp")
+  expect_s3_class(example_vpts, "vpts")
 })