tests/testthat/test-pmc_scrape.R
In fsingletonthorn/EffectSizeScraping: Effect size extractor
context("test pmc_scrape")
test_that("scrapePMC extracts files with correctly labeled sections", {
# pmcID <- 4710337
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4710337&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/bd/41/PMC4710337.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "unlabelled"],
"Prompt diagnosis is important as urgent")
)
expect_true(is.na( output$statisticalTests ) )
})
test_that("scrapePMC doesn't extract from PDFs when it is not necessary", {
# pmcID <- 5393010
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5393010&metadataPrefix=pmc"
ftpCall <-"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/a2/4e/PMC5393010.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Discussion"],
"BEI-PSY is the first study to investigate the prevalence")
)
expect_true(all(
output$statisticalTests$statistic == "chi" | output$statisticalTests$statistic == "OR"
))
})
test_that("scrapePMC process excracts stats correctly from pmc5504157", {
# pmcID <- 5504157
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5504157&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/4a/be/PMC5504157.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(all(as.numeric(output$statisticalTests$value[
output$statisticalTests$statistic == "r"
]) %in%
c(0.10,0.30,0.71,0.69,0.63,0.61,0.59,0.56,0.86,0.32,0.75,0.67,0.51,
0.45,0.39,0.41,0.30,0.31,0.31,0.59,0.56,0.48,0.52,0.38,0.63,0.41)))
expect_true(all(
as.numeric(output$statisticalTests$value[output$statisticalTests$statistic == "d"]) %in%
c(0.07,
0.44,
0.20)
))
# concatinatedText <- concatPlus(output$text$text)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Results"],
"ranged from")
)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Results"],
"in the cross-sectional design\\.\\s?$")
)
})
test_that("scrapePMC extracts the pdf when text is not otherwise avaliable", {
# pmcID <- 4710337
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5393010&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/a2/4e/PMC5393010.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Discussion"],
"The findings of this study must be")
)
})
test_that("scrapePMC extracts the pdf when text is not otherwise avaliable", {
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4311551&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/26/85/PMC4311551.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "unlabelled"],
"The increased interest in the sense of touch over the last decades will hopefully continue as much still remains to be explored\\.$")
)
})
test_that("test pmc extracts statistical test correctly", {
pmcID <- "PMC5504157"
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5504157&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/4a/be/PMC5504157.tar.gz"
output <- scrapePMC(call, ftpCall)
expect_true(output$metadata$PMCID == pmcID)
expect_identical(as.numeric(output$statisticalTests$value[output$statisticalTests$statistic == "d"]), c(.07, .44, .20))
})
test_that("initial test set gives accurate information", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4311551&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/26/85/PMC4311551.tar.gz", statcheck = F)
expect_equal(output$metadata$title, "Body in mind")
expect_equal(output$metadata$doi, "10.3389/fpsyg.2015.00056")
expect_true(all(is.na(output$sampleSizes)))
expect_true(all(is.na(output$statisticalTests)))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5572533&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/b1/cd/PMC5572533.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species")
expect_equal(output$metadata$doi, "10.7717/peerj.3640")
expect_equal(output$sampleSizes$n, c("20", "422", "422", "3445", "2944"))
expect_true(all(output$keywords$keywords %in% c("Phenotypic plasticity", "Local adaptation", "Parasitoid wasps", "Transcriptome", "Aphid pest control")) &
all(c("Phenotypic plasticity", "Local adaptation", "Parasitoid wasps", "Transcriptome", "Aphid pest control") %in% output$keywords$keywords))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5106936&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/fe/62/PMC5106936.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Mental Defectiveness")
expect_true(output$metadata$pPub == as.Date("1928-04-15 UTC"))
expect_true(is.na(output$metadata$doi))
expect_true(is.na(output$sampleSizes$n))
expect_equal(dim(output$keywords)[1], 0)
expect_true(all(is.na(output$statisticalTests)))
expect_false(any(output$CIs$CIBinary))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3704508&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/ea/88/PMC3704508.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Modeling ripple oscillations in the hippocampus")
expect_true(output$metadata$ePub == as.Date("2013-07-08 UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_equal(dim(output$keywords)[1], 0)
expect_true(is.na(output$statisticalTests)[1])
expect_false(any(output$CIs$CIBinary))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5414266&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/3c/98/PMC5414266.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Multiple phase transitions in an agent-based evolutionary model with neutral fitness")
expect_equal(output$metadata$doi, "10.1098/rsos.170005")
expect_true(is.na(output$sampleSizes$n[1]))
expect_equal(output$keywords$keywords, c("phase transition", "extinction", "agent-based model", "neutral theory", "clustering", "speciation"))
expect_true(is.na(output$sampleSizes$n[1]))
expect_false(any(output$CIs$CIBinary))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4901434&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/d3/78/PMC4901434.tar.gz", statcheck = T)
expect_equal(output$authors$surname, c("Azale", "Fekadu", "Hanlon"))
expect_equal(output$authors$firstname, c("Telake", "Abebaw", "Charlotte"))
expect_equal(output$metadata$PMCID, "PMC4901434")
expect_equal(output$metadata$doi, "10.1186/s12888-016-0892-8")
expect_equal(output$metadata$journalID, "BMC Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "BMC Psychiatry")
expect_equal(output$metadata$title, "Treatment gap and help-seeking for postpartum depression in a rural African setting")
expect_true(is.na(output$metadata$issue))
expect_equal(output$metadata$volume, "16")
expect_equal(output$metadata$ePub, as.POSIXlt.character("2016-06-10", tz = "UTC"))
expect_equal(max(as.numeric(output$sampleSizes$n)), 3147)
expect_true(all(as.numeric(output$sampleSizes$n) %in% c(385, 3147, 16, 49, 231, 374, 363, 271, 365, 353, 385, 196, 171, 104, 95,
16, 236, 12, 385, 239, 293, 257, 216, 194, 385, 15, 2))
)
expect_true(is.na(output$keywords$keywords[1]))
expect_true(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "Conclusion"], "Creating public awareness about PPD, its causes and consequences, and the need for help seeking are necessary steps to support the integration of mental health into primary care-based maternal health care."))
expect_true(stringr::str_detect(output$text$text[output$text$names == "Discussion"], "In this population-based survey of postpartum women"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "abstract"], "Postpartum depression"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "abstract"], "care services within primary care"))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3172542&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/64/34/PMC3172542.tar.gz", statcheck = T)
expect_equal(output$authors$surname, "Channabasavanna")
expect_equal(output$authors$firstname, "S.M.")
expect_equal(output$metadata$PMCID, "PMC3172542")
expect_true(is.na(output$metadata$doi))
expect_equal(output$metadata$journalID, "Indian Journal of Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "Indian J Psychiatry")
expect_equal(output$metadata$title, "THE NARCOTIC DRUGS ACT AND THE PSYCHIATRIST")
expect_equal(output$metadata$issue, "2")
expect_equal(output$metadata$volume, "28")
expect_equal(output$metadata$pPub, as.POSIXlt.character("1986-01-01", tz = "UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_true(is.na(output$keywords$keywords[1]))
expect_false(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "The legislation to make stringent provision"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "hether any difficulties arise out of enforcing the Act"))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3172542&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/64/34/PMC3172542.tar.gz", statcheck = T)
expect_equal(output$authors$surname, "Channabasavanna")
expect_equal(output$authors$firstname, "S.M.")
expect_equal(output$metadata$PMCID, "PMC3172542")
expect_true(is.na(output$metadata$doi))
expect_equal(output$metadata$journalID, "Indian Journal of Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "Indian J Psychiatry")
expect_equal(output$metadata$title, "THE NARCOTIC DRUGS ACT AND THE PSYCHIATRIST")
expect_equal(output$metadata$issue, "2")
expect_equal(output$metadata$volume, "28")
expect_equal(output$metadata$pPub, as.POSIXlt.character("1986-01-01", tz = "UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_true(is.na(output$keywords$keywords[1]))
expect_false(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "The legislation to make stringent provision"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "hether any difficulties arise out of enforcing the Act"))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3172542&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/64/34/PMC3172542.tar.gz", statcheck = T)
expect_equal(output$authors$surname, "Channabasavanna")
expect_equal(output$authors$firstname, "S.M.")
expect_equal(output$metadata$PMCID, "PMC3172542")
expect_true(is.na(output$metadata$doi))
expect_equal(output$metadata$journalID, "Indian Journal of Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "Indian J Psychiatry")
expect_equal(output$metadata$title, "THE NARCOTIC DRUGS ACT AND THE PSYCHIATRIST")
expect_equal(output$metadata$issue, "2")
expect_equal(output$metadata$volume, "28")
expect_equal(output$metadata$pPub, as.POSIXlt.character("1986-01-01", tz = "UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_true(is.na(output$keywords$keywords[1]))
expect_false(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "The legislation to make stringent provision"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "hether any difficulties arise out of enforcing the Act"))
})
test_that("PMCSCrape doesn't break when fed results with statcheck results", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5650980&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/15/30/PMC5650980.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "The Orienting Response in Healthy Aging: Novelty P3 Indicates No General Decline but Reduced Efficacy for Fast Stimulation Rates")
expect_equal(output$statcheck$Statistic, c("F", "F", "F", "F", "F", "F", "t", "t", "t", "F", "F", "F", "F", "F"))
expect_true(all(as.numeric(output$statcheck$Value) %in% as.numeric(output$statisticalTests$value)))
expect_equal(max(as.numeric(output$sampleSizes$n)), 43)
expect_true(any(output$CIs$CIBinary))
}
)
test_that("PMCSCrape can find F tests where the dfs are not separated by spaces", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3659440&metadataPrefix=pmc", ftpCall = "", statcheck = T)
expect_equal(output$metadata$title, "Healing Pathways: A Program for Women with Physical Disabilities and Depression")
expect_equal(output$statcheck$Statistic, c("F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F"))
expect_true(all(as.numeric(output$statcheck$Value) %in% as.numeric(output$statisticalTests$value)))
}
)
test_that("Testing scraper", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:166140&metadataPrefix=pmc", ftpCall = "", statcheck = F)
expect_equal(output$metadata$title, "Adaptation of the MacNew quality of life questionnaire after myocardial infarction in an Iranian population")
expect_true(output$statisticalTests$statistic == "r" &
output$statisticalTests$value == .07
)
}
)
fsingletonthorn/EffectSizeScraping documentation built on April 1, 2020, 2:52 p.m.
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context("test pmc_scrape")
test_that("scrapePMC extracts files with correctly labeled sections", {
# pmcID <- 4710337
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4710337&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/bd/41/PMC4710337.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "unlabelled"],
"Prompt diagnosis is important as urgent")
)
expect_true(is.na( output$statisticalTests ) )
})
test_that("scrapePMC doesn't extract from PDFs when it is not necessary", {
# pmcID <- 5393010
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5393010&metadataPrefix=pmc"
ftpCall <-"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/a2/4e/PMC5393010.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Discussion"],
"BEI-PSY is the first study to investigate the prevalence")
)
expect_true(all(
output$statisticalTests$statistic == "chi" | output$statisticalTests$statistic == "OR"
))
})
test_that("scrapePMC process excracts stats correctly from pmc5504157", {
# pmcID <- 5504157
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5504157&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/4a/be/PMC5504157.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(all(as.numeric(output$statisticalTests$value[
output$statisticalTests$statistic == "r"
]) %in%
c(0.10,0.30,0.71,0.69,0.63,0.61,0.59,0.56,0.86,0.32,0.75,0.67,0.51,
0.45,0.39,0.41,0.30,0.31,0.31,0.59,0.56,0.48,0.52,0.38,0.63,0.41)))
expect_true(all(
as.numeric(output$statisticalTests$value[output$statisticalTests$statistic == "d"]) %in%
c(0.07,
0.44,
0.20)
))
# concatinatedText <- concatPlus(output$text$text)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Results"],
"ranged from")
)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Results"],
"in the cross-sectional design\\.\\s?$")
)
})
test_that("scrapePMC extracts the pdf when text is not otherwise avaliable", {
# pmcID <- 4710337
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5393010&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/a2/4e/PMC5393010.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "Discussion"],
"The findings of this study must be")
)
})
test_that("scrapePMC extracts the pdf when text is not otherwise avaliable", {
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4311551&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/26/85/PMC4311551.tar.gz"
output <- scrapePMC(call, ftpCall, statcheck = F)
expect_true(
stringr::str_detect(output$text$text[output$text$names == "unlabelled"],
"The increased interest in the sense of touch over the last decades will hopefully continue as much still remains to be explored\\.$")
)
})
test_that("test pmc extracts statistical test correctly", {
pmcID <- "PMC5504157"
call <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5504157&metadataPrefix=pmc"
ftpCall <- "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/4a/be/PMC5504157.tar.gz"
output <- scrapePMC(call, ftpCall)
expect_true(output$metadata$PMCID == pmcID)
expect_identical(as.numeric(output$statisticalTests$value[output$statisticalTests$statistic == "d"]), c(.07, .44, .20))
})
test_that("initial test set gives accurate information", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4311551&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/26/85/PMC4311551.tar.gz", statcheck = F)
expect_equal(output$metadata$title, "Body in mind")
expect_equal(output$metadata$doi, "10.3389/fpsyg.2015.00056")
expect_true(all(is.na(output$sampleSizes)))
expect_true(all(is.na(output$statisticalTests)))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5572533&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/b1/cd/PMC5572533.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species")
expect_equal(output$metadata$doi, "10.7717/peerj.3640")
expect_equal(output$sampleSizes$n, c("20", "422", "422", "3445", "2944"))
expect_true(all(output$keywords$keywords %in% c("Phenotypic plasticity", "Local adaptation", "Parasitoid wasps", "Transcriptome", "Aphid pest control")) &
all(c("Phenotypic plasticity", "Local adaptation", "Parasitoid wasps", "Transcriptome", "Aphid pest control") %in% output$keywords$keywords))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5106936&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/fe/62/PMC5106936.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Mental Defectiveness")
expect_true(output$metadata$pPub == as.Date("1928-04-15 UTC"))
expect_true(is.na(output$metadata$doi))
expect_true(is.na(output$sampleSizes$n))
expect_equal(dim(output$keywords)[1], 0)
expect_true(all(is.na(output$statisticalTests)))
expect_false(any(output$CIs$CIBinary))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3704508&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/ea/88/PMC3704508.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Modeling ripple oscillations in the hippocampus")
expect_true(output$metadata$ePub == as.Date("2013-07-08 UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_equal(dim(output$keywords)[1], 0)
expect_true(is.na(output$statisticalTests)[1])
expect_false(any(output$CIs$CIBinary))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5414266&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/3c/98/PMC5414266.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "Multiple phase transitions in an agent-based evolutionary model with neutral fitness")
expect_equal(output$metadata$doi, "10.1098/rsos.170005")
expect_true(is.na(output$sampleSizes$n[1]))
expect_equal(output$keywords$keywords, c("phase transition", "extinction", "agent-based model", "neutral theory", "clustering", "speciation"))
expect_true(is.na(output$sampleSizes$n[1]))
expect_false(any(output$CIs$CIBinary))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:4901434&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/d3/78/PMC4901434.tar.gz", statcheck = T)
expect_equal(output$authors$surname, c("Azale", "Fekadu", "Hanlon"))
expect_equal(output$authors$firstname, c("Telake", "Abebaw", "Charlotte"))
expect_equal(output$metadata$PMCID, "PMC4901434")
expect_equal(output$metadata$doi, "10.1186/s12888-016-0892-8")
expect_equal(output$metadata$journalID, "BMC Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "BMC Psychiatry")
expect_equal(output$metadata$title, "Treatment gap and help-seeking for postpartum depression in a rural African setting")
expect_true(is.na(output$metadata$issue))
expect_equal(output$metadata$volume, "16")
expect_equal(output$metadata$ePub, as.POSIXlt.character("2016-06-10", tz = "UTC"))
expect_equal(max(as.numeric(output$sampleSizes$n)), 3147)
expect_true(all(as.numeric(output$sampleSizes$n) %in% c(385, 3147, 16, 49, 231, 374, 363, 271, 365, 353, 385, 196, 171, 104, 95,
16, 236, 12, 385, 239, 293, 257, 216, 194, 385, 15, 2))
)
expect_true(is.na(output$keywords$keywords[1]))
expect_true(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "Conclusion"], "Creating public awareness about PPD, its causes and consequences, and the need for help seeking are necessary steps to support the integration of mental health into primary care-based maternal health care."))
expect_true(stringr::str_detect(output$text$text[output$text$names == "Discussion"], "In this population-based survey of postpartum women"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "abstract"], "Postpartum depression"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "abstract"], "care services within primary care"))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3172542&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/64/34/PMC3172542.tar.gz", statcheck = T)
expect_equal(output$authors$surname, "Channabasavanna")
expect_equal(output$authors$firstname, "S.M.")
expect_equal(output$metadata$PMCID, "PMC3172542")
expect_true(is.na(output$metadata$doi))
expect_equal(output$metadata$journalID, "Indian Journal of Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "Indian J Psychiatry")
expect_equal(output$metadata$title, "THE NARCOTIC DRUGS ACT AND THE PSYCHIATRIST")
expect_equal(output$metadata$issue, "2")
expect_equal(output$metadata$volume, "28")
expect_equal(output$metadata$pPub, as.POSIXlt.character("1986-01-01", tz = "UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_true(is.na(output$keywords$keywords[1]))
expect_false(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "The legislation to make stringent provision"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "hether any difficulties arise out of enforcing the Act"))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3172542&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/64/34/PMC3172542.tar.gz", statcheck = T)
expect_equal(output$authors$surname, "Channabasavanna")
expect_equal(output$authors$firstname, "S.M.")
expect_equal(output$metadata$PMCID, "PMC3172542")
expect_true(is.na(output$metadata$doi))
expect_equal(output$metadata$journalID, "Indian Journal of Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "Indian J Psychiatry")
expect_equal(output$metadata$title, "THE NARCOTIC DRUGS ACT AND THE PSYCHIATRIST")
expect_equal(output$metadata$issue, "2")
expect_equal(output$metadata$volume, "28")
expect_equal(output$metadata$pPub, as.POSIXlt.character("1986-01-01", tz = "UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_true(is.na(output$keywords$keywords[1]))
expect_false(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "The legislation to make stringent provision"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "hether any difficulties arise out of enforcing the Act"))
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3172542&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/64/34/PMC3172542.tar.gz", statcheck = T)
expect_equal(output$authors$surname, "Channabasavanna")
expect_equal(output$authors$firstname, "S.M.")
expect_equal(output$metadata$PMCID, "PMC3172542")
expect_true(is.na(output$metadata$doi))
expect_equal(output$metadata$journalID, "Indian Journal of Psychiatry")
expect_equal(output$metadata$journalIDAbrev, "Indian J Psychiatry")
expect_equal(output$metadata$title, "THE NARCOTIC DRUGS ACT AND THE PSYCHIATRIST")
expect_equal(output$metadata$issue, "2")
expect_equal(output$metadata$volume, "28")
expect_equal(output$metadata$pPub, as.POSIXlt.character("1986-01-01", tz = "UTC"))
expect_true(is.na(output$sampleSizes$n))
expect_true(is.na(output$keywords$keywords[1]))
expect_false(any(output$CIs$CIBinary))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "The legislation to make stringent provision"))
expect_true(stringr::str_detect(output$text$text[output$text$names == "unlabelled"], "hether any difficulties arise out of enforcing the Act"))
})
test_that("PMCSCrape doesn't break when fed results with statcheck results", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:5650980&metadataPrefix=pmc",
ftpCall = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/15/30/PMC5650980.tar.gz", statcheck = T)
expect_equal(output$metadata$title, "The Orienting Response in Healthy Aging: Novelty P3 Indicates No General Decline but Reduced Efficacy for Fast Stimulation Rates")
expect_equal(output$statcheck$Statistic, c("F", "F", "F", "F", "F", "F", "t", "t", "t", "F", "F", "F", "F", "F"))
expect_true(all(as.numeric(output$statcheck$Value) %in% as.numeric(output$statisticalTests$value)))
expect_equal(max(as.numeric(output$sampleSizes$n)), 43)
expect_true(any(output$CIs$CIBinary))
}
)
test_that("PMCSCrape can find F tests where the dfs are not separated by spaces", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3659440&metadataPrefix=pmc", ftpCall = "", statcheck = T)
expect_equal(output$metadata$title, "Healing Pathways: A Program for Women with Physical Disabilities and Depression")
expect_equal(output$statcheck$Statistic, c("F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F"))
expect_true(all(as.numeric(output$statcheck$Value) %in% as.numeric(output$statisticalTests$value)))
}
)
test_that("Testing scraper", {
output <- scrapePMC(call = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:166140&metadataPrefix=pmc", ftpCall = "", statcheck = F)
expect_equal(output$metadata$title, "Adaptation of the MacNew quality of life questionnaire after myocardial infarction in an Iranian population")
expect_true(output$statisticalTests$statistic == "r" &
output$statisticalTests$value == .07
)
}
)
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