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Edit rescaled columns and add unit tests #337

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merged 3 commits into from
Mar 13, 2023
Merged

Edit rescaled columns and add unit tests #337

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b59c4dc
add unit tests to verify rescale calculations
lkoenig-usgs Mar 9, 2023
51b0b5d
update cols used for rescaling attributes
lkoenig-usgs Mar 9, 2023
997549c
make minor documentation edits in rescale_catchment_characteristics
lkoenig-usgs Mar 9, 2023
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15 changes: 12 additions & 3 deletions R/rescale_catchments.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,15 @@ rescale_characteristics <- function(vars, lookup_table) {
cols_min <- vars$characteristic_id[vars$summary_statistic == "min"]
cols_max <- vars$characteristic_id[vars$summary_statistic == "max"]

# adjust certain column names to use rescaled values for split catchments (if applicable)
if(!all(lookup_table$comid == lookup_table$member_comid)){
cols_area_wtd_mean <- paste0(cols_area_wtd_mean, "_rescaled")
cols_sum <- paste0(cols_sum, "_rescaled")
}

# adjust column names to include percent_nodata columns
vars_nodata <- names(select(lookup_table, starts_with("percent_nodata")))
vars_nodata <- grep("[0-9]+$", vars_nodata, value = TRUE, invert = TRUE)
if(length(vars_nodata) > 0) {
cols_area_wtd_mean <- c(cols_area_wtd_mean, vars_nodata)
}
Expand All @@ -24,7 +32,8 @@ rescale_characteristics <- function(vars, lookup_table) {
across(any_of(cols_min), \(x) min(x, na.rm = TRUE), .names = "{col}_min"),
across(any_of(cols_max), \(x) max(x, na.rm = TRUE), .names = "{col}_max")
) |>
ungroup()
ungroup() |>
rename_with(~gsub("_rescaled", "", .), contains("_rescaled"))
}

#' @description
Expand All @@ -38,7 +47,6 @@ rescale_characteristics <- function(vars, lookup_table) {
#' "areasqkm." Used to retrieve adjusted catchment areas in the case of split
#' catchments.
#'
#' @importFrom sf st_drop_geometry
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I don't see sf::st_drop_geometry used in get_catchment_areas() which is why I suggested omitting this line from the documentation.

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I have a utility function in hydroloom called "drop_geometry"

nhdplusTools/R/A_nhdplusTools.R

Line 395 in a7446dd

drop_geometry <- function(x) {

#' @importFrom dplyr mutate select right_join left_join filter rename bind_rows
#' @noRd
#'
Expand Down Expand Up @@ -212,7 +220,8 @@ rescale_catchment_characteristics <- function(vars, lookup_table,

# rescale the nldi characteristics if needed (i.e., for split catchments)
if(!all(lookup_table$comid == lookup_table$member_comid)){
lookup_table <- mutate(lookup_table, across(any_of(var_names), ~.x*.data$split_area_prop))
lookup_table <- mutate(lookup_table,
across(any_of(var_names), ~.x*.data$split_area_prop, .names = "{col}_rescaled"))
}

return(rescale_characteristics(vars, lookup_table))
Expand Down
Binary file modified tests/testthat/data/rescale_data.rds
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40 changes: 38 additions & 2 deletions tests/testthat/test_rescale_catchments.R
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Expand Up @@ -2,8 +2,8 @@
test_that("rescale", {
skip_on_cran()

vars <- data.frame(characteristic_id = c("CAT_EWT", "CAT_EWT", "CAT_EWT"),
summary_statistic = c("area_weighted_mean", "min","sum"))
vars <- data.frame(characteristic_id = c("CAT_EWT", "CAT_EWT", "CAT_EWT", "CAT_EWT", "CAT_BASIN_AREA"),
summary_statistic = c("area_weighted_mean", "min", "sum", "max", "sum"))

# file_name <- "refactor_02.gpkg"
# file_path <- file.path(tempdir(), file_name)
Expand Down Expand Up @@ -46,6 +46,42 @@ test_that("rescale", {

expect_equal(rescale, rescale_2)

expect_equal(round(rescale$areasqkm_sum,0), round(rescale$CAT_BASIN_AREA_sum,0))

test_id1 <- 10012268
comids1 <- filter(d$lookup_table, id == test_id1)
vars_comids1 <- left_join(x = left_join(x = comids1,
y = filter(d$catchment_characteristic,
comid %in% comids1$comid,
characteristic_id == "CAT_EWT"),
by = "comid"),
y = select(d$catchment_areas, c("member_comid","split_catchment_areasqkm","split_area_prop")),
by = "member_comid")
vars_comids1 <- mutate(vars_comids1, area_rescaled = split_catchment_areasqkm*split_area_prop)
rescale_test1 <- filter(rescale, id == test_id1)
expect_equal(min(vars_comids1$characteristic_value),rescale_test1$CAT_EWT_min)
expect_equal(sum(vars_comids1$characteristic_value),rescale_test1$CAT_EWT_sum)
expect_equal(max(vars_comids1$characteristic_value),rescale_test1$CAT_EWT_max)
expect_equal(weighted.mean(vars_comids1$characteristic_value, vars_comids1$area_rescaled),
rescale_test1$CAT_EWT_area_wtd)

test_id2 <- 10024048
comids2 <- filter(d$lookup_table, id == test_id2)
vars_comids2 <- left_join(x = left_join(x = comids2,
y = filter(d$catchment_characteristic,
comid %in% comids2$comid,
characteristic_id == "CAT_EWT"),
by = "comid"),
y = select(d$catchment_areas, c("member_comid","split_catchment_areasqkm","split_area_prop")),
by = "member_comid")
vars_comids2 <- mutate(vars_comids2, area_rescaled = split_catchment_areasqkm*split_area_prop)
rescale_test2 <- filter(rescale, id == test_id2)
expect_equal(min(vars_comids2$characteristic_value),rescale_test2$CAT_EWT_min)
expect_equal(sum(vars_comids2$characteristic_value*vars_comids2$split_area_prop),rescale_test2$CAT_EWT_sum)
expect_equal(max(vars_comids2$characteristic_value),rescale_test2$CAT_EWT_max)
expect_equal(weighted.mean(vars_comids2$characteristic_value*vars_comids2$split_area_prop, vars_comids2$area_rescaled),
rescale_test2$CAT_EWT_area_wtd)

borked <- dplyr::rename(d$lookup_table, borked = "member_comid")

expect_error(rescale_catchment_characteristics(vars, borked, d$split_divides),
Expand Down