Fix a bug in qc(), improve tests, and cleanup .gitlab-ci.yml

ConorIA · Feb 7, 2019 · 7e253db · 7e253db
1 parent 3290e14
commit 7e253db
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Showing 5 changed files with 29 additions and 18 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,8 +1,4 @@
-before_script:
-  - export _R_CHECK_CRAN_INCOMING_=FALSE
-  - export _R_CHECK_FORCE_SUGGESTS_=TRUE
-
-r-base:
+test:
   stage: test
   image: r-base
   script:

diff --git a/R/qc.R b/R/qc.R
@@ -34,8 +34,8 @@ qc <- function(dat) {
     stop("You've passed a one-year table. We need (many) additional years of data for context.")
   }
 
-  if (grepl("Observations", colnames(dat)[15])) {
-    observations <- select(dat, 15) %>% unlist()
+  if (grepl("Observations", colnames(dat)[ncol(dat)])) {
+    observations <- select(dat, ncol(dat)) %>% unlist()
   } else {
     observations <- rep(NA, nrow(dat))
   }
@@ -139,8 +139,8 @@ qc <- function(dat) {
 
 
     if (any(grepl("Nivel Medio", names(dat)))) {
-      Observations <- rep('', nrow(dat))
-      Observations[!is.na(dat$`Nivel Medio (m)`) &
+      observations <- rep('', nrow(dat))
+      observations[!is.na(dat$`Nivel Medio (m)`) &
                             dat$`Nivel Medio (m)` < 0] <- paste(
                               "Level err:",
                               dat$`Nivel Medio (m)`[!is.na(dat$`Nivel Medio (m)`) &
@@ -149,7 +149,7 @@ qc <- function(dat) {
       dat$`Nivel Medio (m)`[dat$`Nivel Medio (m)` < 0] <- NA
       while (any(dat$`Nivel Medio (m)` > 10 * mean(dat$`Nivel Medio (m)`, na.rm = TRUE), na.rm = TRUE)) {
         co <- which.max(dat$`Nivel Medio (m)`)
-        Observations[co] <- paste("Level err:",
+        observations[co] <- paste("Level err:",
                                   dat$`Nivel Medio (m)`[co],
                                   "-> NA")
         dat$`Nivel Medio (m)`[co] <- NA

diff --git a/tests/testthat/test-map_stations.R b/tests/testthat/test-map_stations.R
@@ -1,6 +1,6 @@
 library("testthat")
 library("senamhiR")
-df <- station_search("Lima")
+df <- station_search(target = "000401")
 
 context("Test `map_stations()`")
 

diff --git a/tests/testthat/test-qc.R b/tests/testthat/test-qc.R
@@ -1,21 +1,36 @@
 library("testthat")
 library("senamhiR")
-indat <- senamhiR("000280")
+indat <- senamhiR(c("000280", "230715", "47270400"))
 
 context("Test `qc()`")
 
-##FIXME, make more interesting tests
 ## test qc corrections
-test_that("qc can fix errors", {
-  out <- qc(indat)
+test_that("qc can fix temperature errors", {
+  out <- qc(indat[[1]])
   expect_identical(names(out)[15], "Observations")
   expect_that(out, is_a("tbl_df"))
   expect_output(str(out), "15 variables")
   expect_equal(out$`Tmin (C)`[19660], 23.2)
-  expect_identical(out$Observations[19660], "Tmin dps: 232 -> 23.2 (1.03)")
+  expect_identical(out$Observations[19558], "Tmin err: 221.2 -> NA")
+})
+
+test_that("qc can fix CON level errors", {
+  out <- qc(indat[[2]])
+  expect_identical(names(out)[7], "Observations")
+  expect_that(out, is_a("tbl_df"))
+  expect_output(str(out), "7 variables")
+  expect_identical(out$Observations[3262], "Level err: 1.83 -> NA")
+})
+
+test_that("qc can fix SUT level errors", {
+  out <- qc(indat[[3]])
+  expect_identical(names(out)[11], "Observations")
+  expect_that(out, is_a("tbl_df"))
+  expect_output(str(out), "11 variables")
+  expect_identical(out$Observations[1255], "Level err: -123.51 -> NA")
 })
 
 ## should fail if not enough context
 test_that("qc fails if the data set is just one year", {
-  expect_error(qc(indat[format(indat$Fecha, format = "%Y") == 2013,]), "You've passed a one-year table. We need (many) additional years of data for context.", fixed=TRUE)
+  expect_error(qc(indat[[1]][format(indat[[1]]$Fecha, format = "%Y") == 2013,]), "You've passed a one-year table. We need (many) additional years of data for context.", fixed=TRUE)
 })
diff --git a/tests/testthat/test-station_search.R b/tests/testthat/test-station_search.R
@@ -23,7 +23,7 @@ test_that("station_search() can locate a station by period", {
 test_that("station_search() can locate a station by period (years)", {
   df <- station_search(period = 55)
   expect_that(df, is_a("tbl_df"))
-  expect_output(str(df), "335 obs")
+  expect_output(str(df), "3[0-9]{2} obs")
   expect_output(str(df), "14 variables")
 })