fix more bugs!

ncx-co · Feb 27, 2024 · b36a579 · b36a579
1 parent 77e4190
commit b36a579
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 33 deletions.
diff --git a/R/query_FIADB.R b/R/query_FIADB.R
@@ -45,12 +45,12 @@ query_table <- function(table_name, plt_cns, con) {
     dbplyr::in_schema(dbplyr::sql("public"), dbplyr::sql(table_name))
   )
 
-  plt_cn_field <- dplyr::case_when(
-    "plt_cn" %in% colnames(tab) ~ "plt_cn",
-    !"plt_cn" %in% colnames(tab) ~ "cn"
-  )
-
-  tab |>
-    dplyr::filter(.data[[plt_cn_field]] %in% !!plt_cns) |>
-    dplyr::collect()
+  if ("plt_cn" %in% colnames(tab)) {
+    tab <- dplyr::filter(
+      tab,
+      .data$plt_cn %in% !!plt_cns
+    )
+  }
+
+  dplyr::collect(tab)
 }
diff --git a/tests/testthat/test-tidy_FIA.R b/tests/testthat/test-tidy_FIA.R
@@ -54,10 +54,6 @@ test_that("tidy_fia produces expected output when postgis = TRUE", {
   expect_true(
     all(fia_data[["cond"]][["plt_cn"]] %in% fia_data[["plot"]][["cn"]])
   )
-
-  expect_true(
-    all(fia_data[["survey"]][["cn"]] %in% fia_data[["plot"]][["cn"]])
-  )
 })
 
 test_that("tidy_fia produces expected output when postgis = FALSE", {
@@ -111,10 +107,6 @@ test_that("tidy_fia produces expected output when postgis = FALSE", {
   expect_true(
     all(fia_data[["cond"]][["plt_cn"]] %in% fia_data[["plot"]][["cn"]])
   )
-
-  expect_true(
-    all(fia_data[["survey"]][["cn"]] %in% fia_data[["plot"]][["cn"]])
-  )
 })
 
 test_that("tidy_fia produces expected output when aoi is NULL and postgis = TRUE", {
@@ -170,10 +162,6 @@ test_that("tidy_fia produces expected output when aoi is NULL and postgis = TRUE
   expect_true(
     all(fia_data[["cond"]][["plt_cn"]] %in% fia_data[["plot"]][["cn"]])
   )
-
-  expect_true(
-    all(fia_data[["survey"]][["cn"]] %in% fia_data[["plot"]][["cn"]])
-  )
 })
 
 test_that("tidy_fia produces expected output when aoi is NULL and postgis = FALSE", {
@@ -230,8 +218,4 @@ test_that("tidy_fia produces expected output when aoi is NULL and postgis = FALS
   expect_true(
     all(fia_data[["cond"]][["plt_cn"]] %in% fia_data[["plot"]][["cn"]])
   )
-
-  expect_true(
-    all(fia_data[["survey"]][["cn"]] %in% fia_data[["plot"]][["cn"]])
-  )
 })
diff --git a/vignettes/white_spruce.Rmd b/vignettes/white_spruce.Rmd
@@ -109,7 +109,7 @@ aoi <- northern_counties |>
 
 fia_data <- tidy_fia(
   aoi = aoi,
-  table_names = c("plot", "tree"),
+  table_names = c("plot", "tree", "county"),
   postgis = TRUE
 )
 ```
@@ -120,11 +120,6 @@ ref_species <- read_ref_table("REF_SPECIES") |>
   select(spcd, common_name, sftwd_hrdwd)
 ```
 
-The tree table has codes for state and county but the readable names are stored in a separate table ("COUNTY") which is stored at the state-level but is also available for the entire US.
-```{r}
-# ref_county <- read_ref_table("COUNTY") |>
-#   select(statecd, countycd, county = countynm)
-```
 
 ## Analysis
 
@@ -164,8 +159,8 @@ white_spruce <- fia_data[["tree"]] |>
     common_name == "white spruce",
     statuscd == 1, !is.na(dia), !is.na(ht)
   ) |>
-  left_join(plot_stats, by = "plt_cn") #|>
-# left_join(ref_county, by = c("statecd", "countycd"))
+  left_join(plot_stats, by = "plt_cn") |>
+  left_join(fia_data[["county"]], by = c("statecd", "countycd"))
 ```
 
 To get a sense for height/diameter relationships in white spruce I will make a graph that shows the trend by forest type and county.
@@ -185,7 +180,7 @@ white_spruce |>
 That graph is somewhat hard to read and does not show any obvious differences in height:diameter relationships so I will try one graph with a separate line for each county.
 ```{r county_plot}
 white_spruce |>
-  ggplot(aes(x = dia, y = ht, group = countycd, color = factor(countycd))) +
+  ggplot(aes(x = dia, y = ht, group = countynm, color = countynm)) +
   geom_smooth() +
   labs(
     x = "DBH (in)",