diff --git a/.gitignore b/.gitignore index 3eb10af..baa29a2 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ .Ruserdata .httr-oauth inst/doc +.DS_Store \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 5c753a9..d7d5b1e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,10 +8,10 @@ Authors@R: c( person("Irene", "Steves", comment = "https://github.com/isteves", role = "aut"), person("Mitchell", "Maier", email = "mitchell.maier@gmail.com", role = "aut")) Maintainer: Julien Brun -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 diff --git a/NAMESPACE b/NAMESPACE index 0d18632..e8aebed 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -15,4 +15,5 @@ importFrom(dataone,CNode) importFrom(dataone,getSystemMetadata) importFrom(emld,as_emld) importFrom(lubridate,ymd_hms) +importFrom(stats,setNames) importFrom(tibble,enframe) diff --git a/R/read_d1_files.R b/R/read_d1_files.R index 4ca0cbb..292b7bd 100644 --- a/R/read_d1_files.R +++ b/R/read_d1_files.R @@ -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 @@ -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) } diff --git a/inst/extdata/[LTER - SEC] Data sets listing - Searched data.csv b/inst/extdata/LTER-SEC_DatasetsListing_SearchedData.csv similarity index 99% rename from inst/extdata/[LTER - SEC] Data sets listing - Searched data.csv rename to inst/extdata/LTER-SEC_DatasetsListing_SearchedData.csv index 7e7f4bd..7fb4fd7 100644 --- a/inst/extdata/[LTER - SEC] Data sets listing - Searched data.csv +++ b/inst/extdata/LTER-SEC_DatasetsListing_SearchedData.csv @@ -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,sherri.johnson@oregonstate.edu,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,jay.jones@alaska.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,sherri.johnson@oregonstate.edu,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,jay.jones@alaska.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,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,,,,emelendez@lternet.edu,Y,Site_Data_Template_V4_LUQ.xlsx, +,,,, ,,,,,,,,,, diff --git a/man/download_d1_data.Rd b/man/download_d1_data.Rd index 95a6d53..47ec19f 100644 --- a/man/download_d1_data.Rd +++ b/man/download_d1_data.Rd @@ -4,10 +4,10 @@ \alias{download_d1_data} \title{Downloads data from DataOne along with metadata} \usage{ -download_d1_data(data_obj, path) +download_d1_data(data_url, path) } \arguments{ -\item{data_obj}{(character) An identifier or url for a DataONE object to download.} +\item{data_url}{(character) An identifier or url for a DataONE object to download.} \item{path}{(character) Path to a directory to download data to} } diff --git a/vignettes/lter-luq-stream-chem.Rmd b/vignettes/lter-luq-stream-chem.Rmd index 621f6e7..dec9c82 100644 --- a/vignettes/lter-luq-stream-chem.Rmd +++ b/vignettes/lter-luq-stream-chem.Rmd @@ -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