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Travis fixes
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- added ds_store to gitignore
- added stats::setNames
- updated extdata name
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@isteves
isteves committed Jun 28, 2018
1 parent 638c19c commit f29ce86
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1 change: 1 addition & 0 deletions .gitignore
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.Ruserdata
.httr-oauth
inst/doc
.DS_Store
4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -8,10 +8,10 @@ Authors@R: c(
person("Irene", "Steves", comment = "https://github.com/isteves", role = "aut"),
person("Mitchell", "Maier", email = "[email protected]", role = "aut"))
Maintainer: Julien Brun <[email protected]>
Description: Tools to download data and metadata from DataONE (https://www.dataone.org) and load this information in R
Description: Tools to download data and metadata from DataONE (https://www.dataone.org) and load this information in R.
License: CC0
RoxygenNote: 6.0.1.9000
Imports: dataone, dplyr, eml2, emld, lubridate, purrr, stringr, tibble, tidyr, readr
Imports: dataone, dplyr, eml2, emld, lubridate, purrr, readr, stats, stringr, tibble, tidyr
Remotes: cboettig/eml2,
cboettig/emld,
DataONEorg/rdataone
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -15,4 +15,5 @@ importFrom(dataone,CNode)
importFrom(dataone,getSystemMetadata)
importFrom(emld,as_emld)
importFrom(lubridate,ymd_hms)
importFrom(stats,setNames)
importFrom(tibble,enframe)
3 changes: 2 additions & 1 deletion R/read_d1_files.R
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Expand Up @@ -7,6 +7,7 @@
#' @import purrr
#' @import readr
#' @import stringr
#' @importFrom stats setNames
#'
#' @return (list) named list containing data and metadata as data frames
#' @export
Expand Down Expand Up @@ -43,7 +44,7 @@ read_d1_files <- function(folder_path, fnc = "read_csv", ...) {
"data"
}
})
data_meta <- setNames(data_meta, data_meta_names) %>%
data_meta <- stats::setNames(data_meta, data_meta_names) %>%
purrr::compact()
return(data_meta)
}
24 changes: 12 additions & 12 deletions ...EC] Data sets listing - Searched data.csv → ...LTER-SEC_DatasetsListing_SearchedData.csv
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@@ -1,12 +1,12 @@
LTER site abbreviation,Short Data Description,DOI,Package ID,Data Repository (PASTA) URL to Archive/Metadata,Date Accessed,Data Repository (PASTA) Filename,Data Repository (PASTA) URL to File,Primary Creator/Curator,Primary Contact Email,Working Group Participant who collected the data,Working Group Participant's Email,Used in your analysis?,Template filename,Google Drive link
AND,Stream chemistry concentrations and fluxes,doi:10.6073/pasta/22cd44c4d8f970fd290371b0604d3d16,knb-lter-and.4021.21,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-and&identifier=4021,06/06/2018,CF00201.csv,https://pasta.lternet.edu/package/data/eml/knb-lter-and/4021/21/1d31b3fa3d35cefc35cc42f35c3b3a8d,,,Sherri Johnson,[email protected],Y,Site_Data_Template_V4_AND.xlsx,
BNZ,"Stream water chemistry of CPCRW, 2002-2010",doi:10.6073/pasta/257da36f3edb8df2976696f98a219b7d,knb-lter-bnz.152.20,https://portal.lternet.edu/nis/mapbrowse?packageid=knb-lter-bnz.152.20 ,06/06/2018,152_CPCRW_Chemistry_2002-2010.txt,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-bnz.152.20&entityid=6fcb1675b162d2c8b2908bcdbe577ec9,,,Jay Johnson,[email protected],Y,Site_Data_Template_V4_BNZ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2967,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/07/2018,RioMameyesPuenteRoto.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=acb18d969cf36e7efda2604a1449e816,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2968,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/08/2018,QuebradaCuenca1-Bisley.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=6e00fe7811c8fa5ea3919e6ae02775f1,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2969,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/09/2018,QuebradaGuaba.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=50e936c844f695818a9616534f2dfccd,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2970,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/10/2018,QuebradaPrieta.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=317744e66a9ab8f48105d1436e3abfd2,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2971,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/11/2018,QuebradaPrieta-A.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=7635c4ba775bd23f134e46b2129d7c07,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2972,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/12/2018,QuebradaPrieta-B.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=266905bbeebf3bb59caeee45222eec18,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2973,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/13/2018,QuebradaSonadora.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=a05bda0a0af888cc037ff5dd00dafd7e,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2974,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/14/2018,RioIcacos.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=2cb48616b931ea4e821648759e9808f0,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
,,,, ,,,,,,,,,,
LTER site abbreviation,Short Data Description,DOI,Package ID,Data Repository (PASTA) URL to Archive/Metadata,Date Accessed,Data Repository (PASTA) Filename,Data Repository (PASTA) URL to File,Primary Creator/Curator,Primary Contact Email,Working Group Participant who collected the data,Working Group Participant's Email,Used in your analysis?,Template filename,Google Drive link
AND,Stream chemistry concentrations and fluxes,doi:10.6073/pasta/22cd44c4d8f970fd290371b0604d3d16,knb-lter-and.4021.21,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-and&identifier=4021,06/06/2018,CF00201.csv,https://pasta.lternet.edu/package/data/eml/knb-lter-and/4021/21/1d31b3fa3d35cefc35cc42f35c3b3a8d,,,Sherri Johnson,[email protected],Y,Site_Data_Template_V4_AND.xlsx,
BNZ,"Stream water chemistry of CPCRW, 2002-2010",doi:10.6073/pasta/257da36f3edb8df2976696f98a219b7d,knb-lter-bnz.152.20,https://portal.lternet.edu/nis/mapbrowse?packageid=knb-lter-bnz.152.20 ,06/06/2018,152_CPCRW_Chemistry_2002-2010.txt,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-bnz.152.20&entityid=6fcb1675b162d2c8b2908bcdbe577ec9,,,Jay Johnson,[email protected],Y,Site_Data_Template_V4_BNZ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2967,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/07/2018,RioMameyesPuenteRoto.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=acb18d969cf36e7efda2604a1449e816,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2968,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/08/2018,QuebradaCuenca1-Bisley.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=6e00fe7811c8fa5ea3919e6ae02775f1,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2969,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/09/2018,QuebradaGuaba.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=50e936c844f695818a9616534f2dfccd,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2970,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/10/2018,QuebradaPrieta.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=317744e66a9ab8f48105d1436e3abfd2,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2971,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/11/2018,QuebradaPrieta-A.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=7635c4ba775bd23f134e46b2129d7c07,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2972,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/12/2018,QuebradaPrieta-B.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=266905bbeebf3bb59caeee45222eec18,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2973,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/13/2018,QuebradaSonadora.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=a05bda0a0af888cc037ff5dd00dafd7e,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
LUQ,Chemistry of stream water from the Luquillo Mountains,doi:10.6073/pasta/f9df56348f510da0113b1e6012fa2974,knb-lter-luq.20.4923051,https://portal.lternet.edu/nis/mapbrowse?scope=knb-lter-luq&identifier=20,06/14/2018,RioIcacos.csv,https://portal.lternet.edu/nis/dataviewer?packageid=knb-lter-luq.20.4923051&entityid=2cb48616b931ea4e821648759e9808f0,,,,[email protected],Y,Site_Data_Template_V4_LUQ.xlsx,
,,,, ,,,,,,,,,,
4 changes: 2 additions & 2 deletions man/download_d1_data.Rd
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2 changes: 1 addition & 1 deletion vignettes/lter-luq-stream-chem.Rmd
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Expand Up @@ -57,7 +57,7 @@ coeff_conv_NH4_to_NH4N <- 0.7764676534
dir.create(data_folder, showWarnings = FALSE)
# Get the datasets unique identifiers
test_datasets_listing <- read_csv(system.file("extdata", "[LTER - SEC] Data sets listing - Searched data.csv",
test_datasets_listing <- read_csv(system.file("extdata", "LTER-SEC_DatasetsListing_SearchedData.csv",
package = "metajam"))
# Keep only the LUQ related datasets
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