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improve altitude bin validation read_vpts() and as.vpts() #684

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improve altitude bin validation read_vpts() and as.vpts() #684

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80c2177
check for altitude bin spacing and number of bins, retain most common…
adokter Nov 4, 2024
72ac0cf
fix variable name
adokter Nov 4, 2024
5fdf406
fix test for as.vpts()
adokter Nov 4, 2024
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27 changes: 22 additions & 5 deletions R/as.vpts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,28 @@
height <- datetime <- source_file <- radar <- NULL

# Throw error if nrows per height are not identical

assertthat::assert_that(
remainder_is_zero(dim(data)[1], length(unique(data$height))) > 0,
msg = "Number of rows per height variable must be identical"
)
# FIXME: first if statement is a weak check that could fail, could be improved.
# retaining for now because of speed
if(!remainder_is_zero(dim(data)[1], length(unique(data$height)))){
data %>%
dplyr::group_by(radar, datetime) %>%
dplyr::mutate(bioRad_internal_interval = height-lag(height)) %>%
dplyr::add_count(name="bioRad_internal_levels") -> data
interval_median <- median(data$bioRad_internal_interval, na.rm=TRUE)
interval_unique <- unique(data$bioRad_internal_interval)
interval_unique <- interval_unique[!is.na(interval_unique)]
if(length(interval_unique)>1){
warning(paste("profiles found with different altitude interval:",paste(sort(interval_unique),collapse=" ")), ", retaining ",interval_median, " only.")
data <- dplyr::filter(data, bioRad_internal_interval == interval_median)

Check warning on line 37 in R/as.vpts.R

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Added lines #L36 - L37 were not covered by tests
}
levels_median <- median(data$bioRad_internal_levels)
levels_unique <- unique(data$bioRad_internal_levels)
if(length(levels_unique)>1){
warning(paste("profiles found with different number of height layers:",paste(sort(levels_unique),collapse=" ")), ", retaining ",levels_median, " only.")
data <- dplyr::filter(data, bioRad_internal_levels == levels_median)
}
data <- dplyr::select(data, -c(bioRad_internal_interval, bioRad_internal_levels))
}

radar <- unique(data[["radar"]])

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4 changes: 2 additions & 2 deletions tests/testthat/test-as.vpts.R
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
test_that("as.vpts() returns error message for incorrect data", {
test_that("as.vpts() returns warning message for incorrect data", {
df <- read.csv(system.file("extdata", "example_vpts.csv", package = "bioRad"))

#randomly remove row
randomIndex <- sample(nrow(df), 1)
df <- df[-randomIndex, ]

expect_error(as.vpts(df),"identical")
expect_warning(as.vpts(df),"profiles found with different")
})

test_that("as.vpts() handles multiple unique attribute values correctly", {
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