library(testthat)
test_that("abra report works", {
f <- report(abra, view = FALSE)
expect_true(file.exists(f))
expect_gt(file.size(f), 10000)
})
test_that("Testing several issues related to reporting and QC in general for large files", {
testthat::skip("Skip very slow test related to very large files reporting")
library(readr)
library(digest)
FED_Rockfish_Event_0ce4_4095_ea03 <- read_csv("https://www.sciencebase.gov/catalog/file/get/59417e4fe4b0764e6c64a5cf?f=__disk__f5%2Fe8%2Ffa%2Ff5e8fa79a077338d6ecb994359353f49003768c6")
FED_Rockfish_Event_0ce4_4095_ea03 <- FED_Rockfish_Event_0ce4_4095_ea03[-1,]
FED_Rockfish_Occurrence_f448_b903_e664 <- read_csv("https://www.sciencebase.gov/catalog/file/get/59417e4fe4b0764e6c64a5cf?f=__disk__d4%2Fb7%2Fdc%2Fd4b7dcef5125d43784d4c54e9515ea1395b96be0")
FED_Rockfish_Occurrence_f448_b903_e664 <- FED_Rockfish_Occurrence_f448_b903_e664[-1,]
FED_Rockfish_Occurrence_f448_b903_e664 <- FED_Rockfish_Occurrence_f448_b903_e664[-1:-11]
# Make a few changes to the class of data and values for occurrenceStatus, remove occurrences where individualCount = NA
# FED_Rockfish_Event_0ce4_4095_ea03$eventDate <- FED_Rockfish_Event_0ce4_4095_ea03$time
check_onland(FED_Rockfish_Event_0ce4_4095_ea03)
FED_Rockfish_Event_0ce4_4095_ea03$decimalLatitude <- FED_Rockfish_Event_0ce4_4095_ea03$latitude
FED_Rockfish_Event_0ce4_4095_ea03$decimalLongitude <- FED_Rockfish_Event_0ce4_4095_ea03$longitude
check_onland(FED_Rockfish_Event_0ce4_4095_ea03)
# FED_Rockfish_Occurrence_f448_b903_e664$occurrenceStatus <- ifelse(FED_Rockfish_Occurrence_f448_b903_e664$individualCount > 0, "present", "absent")
# FED_Rockfish_Occurrence_f448_b903_e664 <- FED_Rockfish_Occurrence_f448_b903_e664[which(!is.na(FED_Rockfish_Occurrence_f448_b903_e664$individualCount)),]
# Check data using OBIS tools
FED_Rockfish_Event_0ce4_4095_ea03$decimalLatitude <- as.numeric(FED_Rockfish_Event_0ce4_4095_ea03$latitude)
FED_Rockfish_Event_0ce4_4095_ea03$decimalLongitude <- as.numeric(FED_Rockfish_Event_0ce4_4095_ea03$longitude)
fullRockfish <- merge(FED_Rockfish_Event_0ce4_4095_ea03, FED_Rockfish_Occurrence_f448_b903_e664, by = "eventID", all.x = T, all.y = T)
# check_eventdate(FED_Rockfish_Event_0ce4_4095_ea03)
check_fields(fullRockfish)
report(fullRockfish)
check_onland(FED_Rockfish_Event_0ce4_4095_ea03)
check_depth(fullRockfish)
# write.table(FED_Rockfish_Event_0ce4_4095_ea03, file="RockfishRecruitmentAndEcosystemAssessmentSurveyCatchData_event.csv", sep = "|", dec = ".", qmethod = "double",
# col.names = TRUE, row.names=FALSE, fileEncoding="UTF-8", quote=TRUE)
# write.table(FED_Rockfish_Occurrence_f448_b903_e664, file="RockfishRecruitmentAndEcosystemAssessmentSurveyCatchData_occurrence.csv", sep = "|", dec = ".", qmethod = "double",
# col.names = TRUE, row.names=FALSE, fileEncoding="UTF-8", quote=TRUE)
# head(fullRockfish)
})
test_that('Deep sea', {
skip("Skip deep sea file checking")
library(openxlsx)
library(obistools)
path <- "/Users/samuel/Downloads/OBIS-ENV-DATA_BENEFICIAL_deepsea.xlsx"
events <- read.xlsx(path, sheet = 1)
occurrences <- read.xlsx(path, sheet = 2)
emof <- read.xlsx(path, sheet = 3)
issues <- check_eventids(events)
View(issues)
flat_events <- flatten_event(events)
issues <- check_extension_eventids(events, occurrences)
data <- flatten_occurrence(events, occurrences)
report(data)
download_all <- function(url) {
data <- data.frame(stringsAsFactors = FALSE)
v <- jsonlite::fromJSON(url)
while(!is.null(v$odata.nextLink) && NROW(v$value) > 0) {
v <- jsonlite::fromJSON(v$odata.nextLink)
data <- rbind(data, v$value)
}
data
}
events <- download_all('http://testbed.ymparisto.fi/api/Pohjaelainrajapinta/1.0/odata/Event/')
})
test_that('issue with NA long/lat', {
skip("Skip issue with NA long/lat")
require(obistools)
require(finch)
dwca_cache$delete_all()
out <- dwca_read('http://www.dassh.ac.uk/ipt/archive?r=emodnet_07_cefas_mcz_improved', read = TRUE)
Event <- out$data[["event.txt"]]
Event$parentEventID <- NA
Occurrence <- out$data[["occurrence.txt"]]
eMoF <- out$data[["extendedmeasurementorfact.txt"]]
flat <- flatten_occurrence(Event, Occurrence)
report(flat)
# Quitting from lines 12-14 (report.Rmd)
# Error in if (zero_range(range)) { : missing value where TRUE/FALSE needed
# In addition: Warning message:
# distinct() does not fully support columns of type `list`.
# List elements are compared by reference, see ?distinct for details.
# This affects the following columns:
# - `extra`
#
# Volgende werkt wel
# report(flatten_occurrence(Event,Occurrence) %>% filter (!is.na(decimalLatitude), !is.na(decimalLongitude)) , view = FALSE)
})
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