reduce package size

R/meta.R

@@ -40,9 +40,7 @@ faers_meta_cache_read <- function(internal = FALSE) {
         faers_cache_env[[".faers_meta_data"]] <- out$data
     } else {
         if (internal) {
-            out <- readRDS(system.file("extdata", "faers_meta_data.rds",
-                package = "faers"
-            ))
+            out <- readRDS(internal_file("extdata", "faers_meta_data.rds"))
             msg <- "Using internal FAERS metadata"
         } else {
             return(NULL)

R/utils.R

@@ -130,7 +130,7 @@ internal_file <- function(...) {
 }
 
 pkg_nm <- function() {
-    packageName(topenv(environment()))
+    utils::packageName(topenv(environment()))
 }
 
 assert_internet <- function(call = rlang::caller_env()) {

data-raw/DATASET.R

@@ -4,3 +4,6 @@ saveRDS(
     list(data = meta, date = Sys.time()),
     "inst/extdata/faers_meta_data.rds"
 )
+
+faers_sample(2004, "q1", dir = "inst/extdata")
+faers_sample(2017, "q2", dir = "inst/extdata")

tests/testthat/test_class.R

@@ -1,10 +1,8 @@
 testthat::test_that("FAERS object and extractor works well", {
-    data <- suppressWarnings(faers(
-        c(2004, 2004, 2011, 2012),
-        c("q1", "q2", "q4", "q1"), "ascii",
-        dir = testthat::test_path("testdata"),
+    data <- faers_parse(
+        internal_file("extdata", "aers_ascii_2004q1.zip"),
         compress_dir = tempdir()
-    ))
+    )
     data_list <- faers_data(data)
     testthat::expect_true(is.list(data_list))
     lapply(data_list, function(x) {

tests/testthat/test_combine.R

@@ -1,11 +1,14 @@
 testthat::test_that("combine FAERS ojbect works as expected", {
-    testthat::expect_no_error(data1 <- faers(2004, "q1", "ascii",
-        dir = testthat::test_path("testdata"), compress_dir = tempdir()
-    ))
-    testthat::expect_no_error(data2 <- faers(2004, "q2", "ascii",
-        dir = testthat::test_path("testdata"), compress_dir = tempdir()
-    ))
-    data3 <- faers_combine(list(data1, data2))
+    data1 <- faers_parse(
+        internal_file("extdata", "aers_ascii_2004q1.zip"),
+        compress_dir = tempdir()
+    )
+    data2 <- faers_parse(
+        internal_file("extdata", "faers_ascii_2017q2.zip"),
+        compress_dir = tempdir()
+    )
+    testthat::expect_no_error(data3 <- faers_combine(list(data1, data2)))
+    testthat::expect_warning(faers_combine(list(data1, data1)))
     testthat::expect_s4_class(data3, "FAERSascii")
     testthat::expect_false(data3@deduplication)
     testthat::expect_false(data3@standardization)

tests/testthat/test_faers.R

@@ -1,12 +1,16 @@
 testthat::test_that("faers() function works as expected", {
     testthat::expect_no_error(data1 <- faers(2004, "q1", "ascii",
-        dir = testthat::test_path("testdata"), compress_dir = tempdir()
+        dir = internal_file("extdata"),
+        compress_dir = tempdir()
     ))
-    testthat::expect_no_error(data2 <- faers(2004, "q2", "ascii",
-        dir = testthat::test_path("testdata"), compress_dir = tempdir()
+    testthat::expect_no_error(data2 <- faers(2017, "q2", "ascii",
+        dir = internal_file("extdata"),
+        compress_dir = tempdir()
     ))
-    testthat::expect_no_error(data3 <- faers(2004, c("q1", "q2"), "ascii",
-        dir = testthat::test_path("testdata"), compress_dir = tempdir()
+    testthat::expect_no_error(data3 <- faers(c(2004, 2017),
+        c("q1", "q2"), "ascii",
+        dir = internal_file("extdata"),
+        compress_dir = tempdir()
     ))
     testthat::expect_s4_class(data3, "FAERSascii")
     testthat::expect_false(data3@deduplication)

tests/testthat/test_merge.R

@@ -1,12 +1,9 @@
-data <- suppressWarnings(faers(
-    c(2004, 2004, 2011, 2012),
-    c("q1", "q2", "q4", "q1"), "ascii",
-    dir = testthat::test_path("testdata"),
-    compress_dir = tempdir()
-))
-
 testthat::test_that("`faers_merge` for FAERS ascii data works well", {
-
+    data <- faers(c(2004, 2017),
+        c("q1", "q2"), "ascii",
+        dir = internal_file("extdata"),
+        compress_dir = tempdir()
+    )
     # internal don't modify data by reference and drug_seq match well
     raw_indi <- data.table::copy(data$indi)
     raw_ther <- data.table::copy(data$ther)

tests/testthat/test_methods.R

@@ -1,9 +1,8 @@
-data <- suppressWarnings(faers(
-    c(2004, 2004, 2011, 2012),
-    c("q1", "q2", "q4", "q1"), "ascii",
-    dir = testthat::test_path("testdata"),
+data <- faers(c(2004, 2017),
+    c("q1", "q2"), "ascii",
+    dir = internal_file("extdata"),
     compress_dir = tempdir()
-))
+)
 
 testthat::test_that("faers_get works well", {
     testthat::expect_s3_class(faers_get(data, "drug"), "data.table")
@@ -81,21 +80,23 @@ testthat::test_that("`$` works well", {
 })
 
 testthat::test_that("faers_keep works well", {
-    data1 <- faers_keep(data, "4204616")
-    testthat::expect_setequal(data1$drug$primaryid, "4204616")
-    testthat::expect_setequal(data1$indi$primaryid, "4204616")
-    testthat::expect_setequal(data1$reac$primaryid, "4204616")
-    testthat::expect_setequal(data1$demo$primaryid, "4204616")
-    testthat::expect_setequal(data1$ther$primaryid, "4204616")
-    testthat::expect_setequal(data1$rpsr$primaryid, "4204616")
-    testthat::expect_setequal(data1$outc$primaryid, "4204616")
+    ids1 <- sample(faers_primaryid(data), 1L)
+    data1 <- faers_keep(data, ids1)
+    testthat::expect_setequal(data1$drug$primaryid, ids1)
+    testthat::expect_in(data1$indi$primaryid, ids1)
+    testthat::expect_in(data1$reac$primaryid, ids1)
+    testthat::expect_in(data1$demo$primaryid, ids1)
+    testthat::expect_in(data1$ther$primaryid, ids1)
+    testthat::expect_in(data1$rpsr$primaryid, ids1)
+    testthat::expect_in(data1$outc$primaryid, ids1)
 
-    data <- faers_keep(data, c("4204616", "4261678"))
-    testthat::expect_setequal(data$demo$primaryid, c("4204616", "4261678"))
-    testthat::expect_setequal(data$drug$primaryid, c("4204616", "4261678"))
-    testthat::expect_setequal(data$indi$primaryid, c("4204616", "4261678"))
-    testthat::expect_setequal(data$reac$primaryid, c("4204616", "4261678"))
-    testthat::expect_setequal(data$ther$primaryid, c("4204616", "4261678"))
-    testthat::expect_setequal(data$rpsr$primaryid, c("4204616", "4261678"))
-    testthat::expect_setequal(data$outc$primaryid, c("4204616", "4261678"))
+    ids2 <- sample(faers_primaryid(data), 2L)
+    data2 <- faers_keep(data, ids2)
+    testthat::expect_setequal(data2$demo$primaryid, ids2)
+    testthat::expect_in(data2$drug$primaryid, ids2)
+    testthat::expect_in(data2$indi$primaryid, ids2)
+    testthat::expect_in(data2$reac$primaryid, ids2)
+    testthat::expect_in(data2$ther$primaryid, ids2)
+    testthat::expect_in(data2$rpsr$primaryid, ids2)
+    testthat::expect_in(data2$outc$primaryid, ids2)
 })

tests/testthat/test_parse.R

@@ -1,8 +1,8 @@
 testthat::test_that("Parsing FAERS ascii data works well", {
-    suppressWarnings(data <- faers_parse(
-        testthat::test_path("testdata", "aers_ascii_2011q4.zip"),
+    data <- faers_parse(
+        internal_file("extdata", "aers_ascii_2004q1.zip"),
         compress_dir = tempdir()
-    ))
+    )
     testthat::expect_s4_class(data, "FAERSascii")
     testthat::expect_null(data@meddra)
     testthat::expect_false(data@deduplication)
@@ -17,28 +17,13 @@ testthat::test_that("Parsing FAERS ascii data works well", {
     testthat::expect_false(anyNA(data@data$rpsr$primaryid))
     testthat::expect_false(anyNA(data@data$outc$primaryid))
 
-    testthat::expect_equal(nrow(data@data$drug), 734093)
-    testthat::expect_equal(nrow(data@data$demo), 208489)
-    testthat::expect_equal(nrow(data@data$indi), 362256)
-    testthat::expect_equal(nrow(data@data$reac), 773537)
-    testthat::expect_equal(nrow(data@data$ther), 321898)
-    testthat::expect_equal(nrow(data@data$rpsr), 35032)
-    testthat::expect_equal(nrow(data@data$outc), 182057)
 
-    suppressWarnings(data2 <- faers_parse(
-        testthat::test_path("testdata", "aers_ascii_2012q1.zip"),
+    data2 <- faers_parse(internal_file("extdata", "aers_ascii_2004q1.zip"),
         compress_dir = tempdir()
-    ))
+    )
     testthat::expect_s4_class(data2, "FAERSascii")
     testthat::expect_null(data2@meddra)
     testthat::expect_false(data2@deduplication)
     testthat::expect_false(data2@standardization)
     testthat::expect_equal(data2@format, "ascii")
-    testthat::expect_equal(nrow(data2@data$drug), 860983)
-    testthat::expect_equal(nrow(data2@data$demo), 231737)
-    testthat::expect_equal(nrow(data2@data$indi), 453398)
-    testthat::expect_equal(nrow(data2@data$reac), 838238)
-    testthat::expect_equal(nrow(data2@data$ther), 351431)
-    testthat::expect_equal(nrow(data2@data$rpsr), 44313)
-    testthat::expect_equal(nrow(data2@data$outc), 202719)
 })

tests/testthat/test_standardize.R

@@ -1,12 +1,10 @@
 testthat::skip_on_ci()
 
-data <- suppressWarnings(faers(
-    c(2004, 2004, 2011, 2012),
-    c("q1", "q2", "q4", "q1"), "ascii",
-    dir = testthat::test_path("testdata"),
+data <- faers(c(2004, 2017),
+    c("q1", "q2"), "ascii",
+    dir = internal_file("extdata"),
     compress_dir = tempdir()
-))
-
+)
 data_std <- faers_standardize(data, "~/Data/MedDRA/MedDRA_26_1_English")
 
 testthat::test_that("standardize FAERS ascii data works well", {