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Merge pull request #37 from pepijn-devries/work-in-progress
Added test to compare online search with results from local search
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| Package: ECOTOXr | ||
| Type: Package | ||
| Title: Download and Extract Data from US EPA's ECOTOX Database | ||
| Version: 1.0.9 | ||
| Date: 2024-01-07 | ||
| Version: 1.1.0 | ||
| Date: 2024-02-10 | ||
| Authors@R: c(person("Pepijn", "de Vries", role = c("aut", "cre", "dtc"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0002-7961-6646"))) | ||
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| library(dplyr) | ||
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| check_db <- function() { | ||
| if (!check_ecotox_availability()) { | ||
| skip("ECOTOX database not available") | ||
| } | ||
| } | ||
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| test_that("Online and local search yield the same results", { | ||
| check_db() | ||
| skip_if_offline() | ||
| expect_true({ | ||
| load(file.path(testthat::test_path(), "test_data", "insecticides.rdata")) | ||
| insecticides$cas <- format(as.cas(insecticides$cas), hyphenate = FALSE) | ||
| unit_conversion <- | ||
| data.frame(what = c(rep("mass", 8), rep("volume", 2)), | ||
| unit = c("pg", "ng", "ug", "mg", "g", "nmol", "umol", "mmol", "L", "m3"), | ||
| conversion = 10^c(-12, -9, -6, -3, 0, -9, -6, -3, 0, 3)) | ||
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| insecticedes_search <- search_ecotox( | ||
| list( | ||
| test_cas = list(terms = insecticides$cas, method = "exact"), | ||
| endpoint = list(terms = c("EC50", "LC50"), method = "contains"), | ||
| latin_name = list(terms = "Daphnia magna", method = "exact"), | ||
| effect = list(terms = c("ITX", "MOR"), method = "contains") | ||
| ), | ||
| c(list_ecotox_fields(), "results.obs_duration_mean", "results.obs_duration_unit", | ||
| "results.result_id")) |> | ||
| mutate( | ||
| duration_corr = case_match( | ||
| obs_duration_unit, "d" ~ 1, "h" ~ 1/24, "mi" ~ 1/(60*24), "NR" ~ NA, "wk" ~ 7), | ||
| duration_corr = suppressWarnings(as.numeric(obs_duration_mean)*duration_corr), | ||
| test_cas = as.character(ECOTOXr::as.cas(test_cas)), | ||
| conc1_mean = suppressWarnings({as.numeric(gsub("[*]", "", conc1_mean))}) | ||
| ) |> | ||
| filter(duration_corr == 2 & conc1_mean != "NR" & !grepl("org", conc1_unit)) |> | ||
| left_join(insecticides |> distinct(), c(test_cas = "cas")) |> | ||
| mutate( | ||
| conc1_unit_fix = trimws(gsub("AI", "", conc1_unit)), | ||
| conc1_unit_fix = | ||
| case_match( | ||
| conc1_unit_fix, | ||
| "mM" ~ "mmol/L", | ||
| "uM" ~ "umol/L", | ||
| "nM" ~ "nmol/L", | ||
| "mg/kg" ~ "mg/L", | ||
| "ppm" ~ "mg/L", | ||
| "ppb" ~ "ug/L", | ||
| "ppt" ~ "ng/L", | ||
| .default = conc1_unit_fix), | ||
| conc1_conversion_factor = { | ||
| do.call(rbind, strsplit(conc1_unit_fix, "/")) |> | ||
| as.data.frame() |> | ||
| rename_with(~c("mass", "volume")) |> | ||
| left_join(unit_conversion, c(mass = "unit")) |> | ||
| rename(mass_conversion = "conversion") |> | ||
| mutate( | ||
| ## If mass is reported as volume (1 case) use specific gravity to convert to actual mass | ||
| mass_conversion = ifelse(mass == "ul" & test_cas == "333-41-5", 1.117e-6, mass_conversion) | ||
| ) |> | ||
| left_join(unit_conversion, c(volume = "unit")) |> | ||
| rename(volume_conversion = "conversion") |> | ||
| mutate(molar_conversion = ifelse(grepl("mol", mass), molweight, 1), | ||
| total_conversion = molar_conversion*mass_conversion/volume_conversion) |> | ||
| pull(total_conversion) | ||
| }, | ||
| conc1_ug_l = 1e6*conc1_mean*conc1_conversion_factor | ||
| ) |> | ||
| suppressWarnings() |> | ||
| suppressMessages() | ||
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| websearch <- list_ecotox_web_fields( | ||
| txAdvancedChemicalEntries = paste(insecticides$cas, | ||
| collapse = "\r\n"), | ||
| RBCHEMSEARCHTYPE = "EXACT", | ||
| txAdvancedSpecEntries = "daphnia magna", | ||
| RBSPECSEARCHTYPE = "EXACT", | ||
| cbResultsGroup12a = "LC50", | ||
| cbResultsGroup13a = "EC50", | ||
| cbResultsGroup6 = "MOR", | ||
| cbResultsGroup7c = "ITX", | ||
| txExposureDurationStd = "2", | ||
| cbResult_number = "Result Number") | ||
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| websearch <- suppressWarnings(websearch_ecotox(websearch)) | ||
| websearch <- websearch$`Aquatic-Export` |> | ||
| dplyr::filter(!is.na(`Conc 1 Mean (Standardized)`) & | ||
| `Conc 1 Units (Standardized)` == "AI mg/L") |> | ||
| select(result_id = "Result Number", | ||
| conc1_ug_l = "Conc 1 Mean (Standardized)", | ||
| test_cas = "CAS Number") |> | ||
| mutate(test_cas = as.character(as.cas(test_cas)), ## hyphenate the CAS numbers | ||
| conc1_ug_l = 1e3*conc1_ug_l) | ||
| conc_check <- | ||
| full_join( | ||
| websearch |> | ||
| select(web_conc = "conc1_ug_l", "result_id"), | ||
| insecticedes_search |> | ||
| select(local_conc = "conc1_ug_l", "result_id"), | ||
| by = "result_id" | ||
| ) |> | ||
| mutate( | ||
| diff = 1 - web_conc/local_conc, | ||
| check = diff < 1e-3 | ||
| ) | ||
| result <- | ||
| ## Number of records differ no more than 2 | ||
| (abs(nrow(websearch) - nrow(insecticedes_search)) <= 2) && | ||
| ## Retrieved websearch cas numbers are also in local cas numbers | ||
| all(websearch$test_cas %in% insecticedes_search$test_cas) && | ||
| ## Retrieved local cas numbers are also in websearch cas numbers | ||
| all(insecticedes_search$test_cas %in% websearch$test_cas) && | ||
| ## concentrations are identical | ||
| all(na.omit(conc_check$check)) | ||
| result | ||
| }) | ||
| }) |