Read scheme data from Excel file into dmdScheme_raw object
Source: R/read_excel_raw.R
read_excel_raw.RdReads the data from an Excel file as is and no validation. Only validation of
the scheme version and scheme name is done (when checkVersion = TRUE).
Arguments
- file
the name of the Excel file (.xls or .xlsx) containing the data to be read.
- verbose
give verbose progress info. Useful for debugging.
- checkVersion
if
TRUE, check for version or scheme conflicts between the package scheme version and the scheme version of the file. Aborts with an error if there is a conflict.
Examples
read_excel_raw( scheme_path_xlsx() )
#> $MdBibliometric
#> propertySet valueProperty type
#> 1 MdBibliometric uploadType character
#> 2 <NA> doi character
#> 3 <NA> publicationDate character
#> 4 <NA> title character
#> 5 <NA> description character
#> 6 <NA> version character
#> 7 <NA> language character
#> 8 <NA> keywords character
#> 9 <NA> additionalNotes character
#> 10 <NA> accessRights character
#> 11 <NA> accessRightsInfo character
#> 12 <NA> license character
#> suggestedValues
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#> 12 Creative Commons Attribution 4.0 International
#> allowedValues
#> 1 Dataset, Image - Photo, Video / Audio
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 Open, Embargoed, Restricted, Closed
#> 11 <NA>
#> 12 <NA>
#> Description
#> 1 The type of the data. Needs tobe one as specified in the allowedValues
#> 2 The DOI of the dataset. Usually the reserved DOI.
#> 3 Date of publication of the data package in the format YYYY-MM-DD
#> 4 Title of the data package
#> 5 Short description of the data deposited
#> 6 The version of the dataset. Usually empty, but the version should be specified if the dataset is augmented or corrected.
#> 7 The language of the dataset. E.g. "eng", "fr", …
#> 8 Keywords describing the dataset
#> 9 Some additional info, which does not fit in any category.
#> 10 Access rights to the data, normally Open or Embargoed.
#> 11 if Embargoed, the date until embargoed (YYYY-MM-DD), if Restricted, conditions under which access is granted to the data
#> 12 Should normally be "Creative Commons Attribution 4.0 International" (CCA4)
#> DATA
#> 1 Dataset
#> 2 110.1234/ffoo.bar
#> 3 2020-05-26
#> 4 Microbes under Pressure
#> 5 The dataset was generated by putting microbes under pressure through temperatue and oxygen changes and their changes ion abundance were observed.
#> 6 <NA>
#> 7 eng
#> 8 microbes, temperatur change, oxygen changes, abundance
#> 9 <NA>
#> 10 Open
#> 11 <NA>
#> 12 Creative Commons Attribution 4.0 International
#>
#> $MdAuthors
#> propertySet MdAuthors ...3
#> 1 valueProperty authorID familyName
#> 2 unit <NA> <NA>
#> 3 type character character
#> 4 suggestedValues <NA> <NA>
#> 5 allowedValues <NA> <NA>
#> 6 Description Just an id - can be a number Family name of the author
#> 7 DATA 1 Petchey
#> 8 MULTIPLE ROWS 2 Krug
#> ...4 ...5
#> 1 givenName affiliation
#> 2 <NA> <NA>
#> 3 character character
#> 4 <NA> <NA>
#> 5 <NA> <NA>
#> 6 Given name(s) of the authors Affiliation of the author
#> 7 Owen L. University of Zurich, Switzerland
#> 8 Rainer M. University of Zurich, Switzerland
#> ...6
#> 1 orcid
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 ORCID (Open Researcher and Contributor ID, as issued by https://orcid.org)
#> 7 <NA>
#> 8 <NA>
#> ...7
#> 1 role
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing
#> 6 Role of the author, using the CRediT – Contributor Roles Taxonomy at https://casrai.org/credit/. Can be more than one.
#> 7 Conceptualization, Investigation
#> 8 Data curation
#>
#> $Experiment
#> propertySet valueProperty unit type
#> 1 Experiment name <NA> character
#> 2 <NA> temperature <NA> character
#> 3 <NA> light <NA> character
#> 4 <NA> humidity <NA> character
#> 5 <NA> incubator <NA> character
#> 6 <NA> container <NA> character
#> 7 <NA> microcosmVolume ml numeric
#> 8 <NA> mediaType <NA> character
#> 9 <NA> mediaConcentration g/l numeric
#> 10 <NA> cultureConditions <NA> character
#> 11 <NA> comunityType <NA> character
#> 12 <NA> mediaAdditions <NA> character
#> 13 <NA> duration days integer
#> 14 <NA> comment <NA> character
#> suggestedValues
#> 1 <NA>
#> 2 treatment, in degrees celsius, measurement
#> 3 treatment,light, dark, cycle , e.g. 16:8 LD
#> 4 treatment, relative humidity in %
#> 5 none, bench
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 axenic, dirty, clean
#> 11 treatment, single trophic level, multiple trophic level
#> 12 <NA>
#> 13 <NA>
#> 14 <NA>
#> Description
#> 1 The name of the experiment.
#> 2 Temperature used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet.
#> 3 Light used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet.
#> 4 Humidity used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet.
#> 5 What type of incubator is used.
#> 6 What type of container is used.
#> 7 Volume of the microcosm container. Not the volume of the culture medium!
#> 8 <NA>
#> 9 <NA>
#> 10 Conditions of the cultures for all treatments.
#> 11 Characterisation of the microbe community.
#> 12 <NA>
#> 13 Length of the experiment in days. This should only include the time in which the measurements were taken!
#> 14 Additional features of the Experiment you want to provide
#> DATA dmdScheme v0.9.9
#> 1 ASR-expt1
#> 2 20
#> 3 semi-ambient
#> 4 ambient
#> 5 not given here
#> 6 Duran type bottle, red lids, 250ml
#> 7 100
#> 8 PPM
#> 9 0.55
#> 10 dirty
#> 11 initially unknown
#> 12 Wheat seeds added on specific dates, see file wheat_seed_additions.csv
#> 13 100
#> 14 <NA>
#>
#> $Genus
#> propertySet
#> 1 valueProperty
#> 2 unit
#> 3 type
#> 4 suggestedValues
#> 5 allowedValues
#> 6 Description
#> 7 DATA
#> 8 MULTIPLE ROWS
#> Genus
#> 1 speciesID
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 Id of the species and strain. Each speciesId has to be unique.
#> 7 tt_1
#> 8 unknown
#> ...3
#> 1 colour
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 Where the species was obtained from.
#> 7 ATCC
#> 8 unknown
#> ...4
#> 1 density
#> 2 cells / ml
#> 3 character
#> 4 treatment
#> 5 <NA>
#> 6 Initial density used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet.
#> 7 1
#> 8 <NA>
#> ...5
#> 1 functionalGroup
#> 2 <NA>
#> 3 character
#> 4 bacteria, bacterivore, predator, phototroph
#> 5 <NA>
#> 6 Functional group of the species.
#> 7 bacterivore
#> 8 unknown
#> ...6
#> 1 comment
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 http://www.lgcstandards-atcc.org/products/all/30007.aspx
#> 8 <NA>
#>
#> $Treatments
#> propertySet
#> 1 valueProperty
#> 2 unit
#> 3 type
#> 4 suggestedValues
#> 5 allowedValues
#> 6 Description
#> 7 DATA
#> 8 MULTIPLE ROWS
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#> Treatments
#> 1 treatmentID
#> 2 <NA>
#> 3 character
#> 4 species, temperatur, light, initial density, comunity composition, densities, dispersal, viscosity, disturbance, communityType
#> 5 <NA>
#> 6 ID of the the treatment decribed in this a row. Each treatmentId can occur multiple times as it can contain multiple treatment levels.
#> 7 Lid_treatment
#> 8 Lid_treatment
#> 9 species_1
#> 10 species_2
#> 11 species_3
#> ...3
#> 1 treatmentLevelHeight
#> 2 <NA>
#> 3 character
#> 4 value, variable: freetext
#> 5 <NA>
#> 6 The value of the parameter if the parameter is constant over time, or a description of the variability. If unit is speciesId, comma separated list of all species in the treatment.
#> 7 Loose
#> 8 Tight
#> 9 tt_1, unknown
#> 10 unknown
#> 11 tt_1
#> ...4
#> 1 comment
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#>
#> $Measurement
#> propertySet
#> 1 valueProperty
#> 2 unit
#> 3 type
#> 4 suggestedValues
#> 5 allowedValues
#> 6 Description
#> 7 DATA
#> 8 MULTIPLE ROWS
#> 9 <NA>
#> 10 <NA>
#> Measurement
#> 1 measurementID
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 Id of the Measurement process. This includes methodology, variables . Each measurementId specifies one Measurement process and must be unique in this column. Should be in the mapping column in the DataFileMetaData tab.
#> 7 oxygen concentration
#> 8 abundance
#> 9 smell
#> 10 sequenceData
#> ...3
#> 1 variable
#> 2 <NA>
#> 3 character
#> 4 O2 concentration, video, manual count, abundance, DNA
#> 5 <NA>
#> 6 The variable measured.
#> 7 DO
#> 8 abundance
#> 9 smell
#> 10 DNA
#> ...4 ...5
#> 1 method unit
#> 2 <NA> <NA>
#> 3 character character
#> 4 presens Optode, microscopy %, mmol, count
#> 5 <NA> <NA>
#> 6 Name of the method used. Unit of the measured variable
#> 7 presens Optode %
#> 8 molecular count
#> 9 nose rotten eggs or not
#> 10 NGS Nucleotide
#> ...6
#> 1 object
#> 2 <NA>
#> 3 character
#> 4 species, OUT, gene, community, particles
#> 5 <NA>
#> 6 The object measured. E.g. species in the case of manual count, gene for genetic analysis, particle for particle counters.
#> 7 community
#> 8 species
#> 9 community
#> 10 DNA fragment
#> ...7
#> 1 noOfSamplesInTimeSeries
#> 2 <NA>
#> 3 integer
#> 4 <NA>
#> 5 <NA>
#> 6 Total number of all samples in the time series.
#> 7 50
#> 8 6
#> 9 6
#> 10 6
#> ...8
#> 1 samplingVolume
#> 2 ml
#> 3 numeric
#> 4 <NA>
#> 5 <NA>
#> 6 The sampling volumne. If e.g. atmosphere in container is sampled (oxygen measurements), than enter 0.\r\nPlease use NA if sampling volumne is variable.
#> 7 0
#> 8 0.5
#> 9 0
#> 10 0
#> ...9
#> 1 dataExtractionID
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 as used in the sheet DataExtraction, column dataExtractionID
#> 7 none
#> 8 Mol_Analy_pipeline1
#> 9 none
#> 10 none
#> ...10
#> 1 measuredFrom
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 if measured from the experiment, raw, else the measurementId (first column) of the Measurement it is based on.
#> 7 raw
#> 8 sequenceData
#> 9 raw
#> 10 raw
#> ...11
#> 1 comment
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#>
#> $DataExtraction
#> propertySet
#> 1 valueProperty
#> 2 unit
#> 3 type
#> 4 suggestedValues
#> 5 allowedValues
#> 6 Description
#> 7 DATA
#> 8 MULTIPLE ROWS
#> DataExtraction
#> 1 dataExtractionID
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 Name of the DataExtraction process. This includes methodology, variables . Each name specifies one extraction process and can occur multiple times in the case of multiple parameters in the analysis.
#> 7 Mol_Analy_pipeline1
#> 8 <NA>
#> ...3
#> 1 method
#> 2 <NA>
#> 3 character
#> 4 bemovi x.y.z
#> 5 <NA>
#> 6 Method used for the DataExtraction process. If possible including version (in the case of R packages).
#> 7 <NA>
#> 8 <NA>
#> ...4
#> 1 parameter
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 parameter in the analysis. Only needs to be specified if it varies from the default.
#> 7 <NA>
#> 8 <NA>
#> ...5
#> 1 value
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 value of the parameter (you can enter a number or a word)
#> 7 <NA>
#> 8 <NA>
#> ...6
#> 1 comment
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 See description in file xxx.yyy
#> 8 <NA>
#>
#> $DataFileMetaData
#> propertySet DataFileMetaData
#> 1 valueProperty dataFileName
#> 2 unit <NA>
#> 3 type character
#> 4 suggestedValues <NA>
#> 5 allowedValues <NA>
#> 6 Description the name of the data set.
#> 7 DATA dissolved_oxygen_measures.csv
#> 8 MULTIPLE ROWS dissolved_oxygen_measures.csv
#> 9 <NA> dissolved_oxygen_measures.csv
#> 10 <NA> dissolved_oxygen_measures.csv
#> 11 <NA> dissolved_oxygen_measures.csv
#> 12 <NA> dissolved_oxygen_measures.csv
#> 13 <NA> dissolved_oxygen_measures.csv
#> 14 <NA> dissolved_oxygen_measures.csv
#> 15 <NA> dissolved_oxygen_measures.csv
#> 16 <NA> smell.csv
#> 17 <NA> smell.csv
#> 18 <NA> smell.csv
#> 19 <NA> smell.csv
#> 20 <NA> smell.csv
#> 21 <NA> abundances.csv
#> 22 <NA> abundances.csv
#> 23 <NA> abundances.csv
#> 24 <NA> abundances.csv
#> 25 <NA> abundances.csv
#> 26 <NA> abundances.csv
#> ...3
#> 1 columnName
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 Name of column in the data file. \r\nEach column in the data file needs to be documented!\r\nor NA\r\nif it is for the whole data file and not specified in the dataFileName
#> 7 Jar_ID
#> 8 DO
#> 9 Unit_1
#> 10 Mode
#> 11 Location
#> 12 Date_time
#> 13 Lid_treatment
#> 14 Jar_type
#> 15 Jar_ID
#> 16 <NA>
#> 17 smell
#> 18 Date
#> 19 Lid_treatment
#> 20 Jar_type
#> 21 <NA>
#> 22 Jar_ID
#> 23 Date_time
#> 24 Lid_treatment
#> 25 Jar_type
#> 26 count_number
#> ...4
#> 1 columnData
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 ID, Treatment, Measurement, Species, other
#> 6 The type of the data in the column.\r\nID: ID field (unique ID of unit of replication);\r\nTreatment: specifies treatment; \r\nMeasurement: contains measurements; \r\nSpecies: contains species; \r\nother: other type of data
#> 7 ID
#> 8 Measurement
#> 9 other
#> 10 other
#> 11 other
#> 12 other
#> 13 Treatment
#> 14 other
#> 15 ID
#> 16 Species
#> 17 Measurement
#> 18 other
#> 19 Treatment
#> 20 other
#> 21 Species
#> 22 ID
#> 23 other
#> 24 Treatment
#> 25 other
#> 26 Measurement
#> ...5
#> 1 mappingColumn
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 columnData = Treatment: \r\ntreatmentID as in the Treatment tab; \r\ncolumnData = Species: \r\ntreatmentID refering to species composition as in the Treatment tab\r\ncolumnData = Measurement: \r\nmeasurementID as in the Measurement tab; \r\notherwise:\r\nNA
#> 7 <NA>
#> 8 oxygen concentration
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#> 12 <NA>
#> 13 Lid_treatment
#> 14 <NA>
#> 15 <NA>
#> 16 species_1
#> 17 smell
#> 18 <NA>
#> 19 Lid_treatment
#> 20 <NA>
#> 21 species_3
#> 22 <NA>
#> 23 <NA>
#> 24 Lid_treatment
#> 25 <NA>
#> 26 abundance
#> ...6
#> 1 type
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 integer, numeric, character, logical, datetime, date, time
#> 6 Type of the column.
#> 7 character
#> 8 numeric
#> 9 character
#> 10 character
#> 11 character
#> 12 datetime
#> 13 character
#> 14 character
#> 15 character
#> 16 character
#> 17 character
#> 18 datetime
#> 19 character
#> 20 character
#> 21 character
#> 22 character
#> 23 datetime
#> 24 character
#> 25 character
#> 26 numeric
#> ...7
#> 1 description
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 if column contains measurement: General description. If type is datatime, date, or time, give the order of year month day hour minute second as e.g. ymdhms, ymd, or hms. (Do not give any other information, e.g. give nothing about how months are entered (e.g. number or name), or how years, months, day, etc are separated.
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#> 12 ymdhms
#> 13 <NA>
#> 14 <NA>
#> 15 <NA>
#> 16 <NA>
#> 17 <NA>
#> 18 ymdhms
#> 19 <NA>
#> 20 <NA>
#> 21 <NA>
#> 22 <NA>
#> 23 ymdhms
#> 24 <NA>
#> 25 <NA>
#> 26 <NA>
#> ...8
#> 1 comment
#> 2 <NA>
#> 3 character
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#> 12 <NA>
#> 13 <NA>
#> 14 <NA>
#> 15 <NA>
#> 16 <NA>
#> 17 <NA>
#> 18 <NA>
#> 19 <NA>
#> 20 <NA>
#> 21 <NA>
#> 22 <NA>
#> 23 <NA>
#> 24 <NA>
#> 25 <NA>
#> 26 <NA>
#>
#> attr(,"dmdSchemeName")
#> [1] "dmdScheme"
#> attr(,"dmdSchemeVersion")
#> [1] "0.9.9"
#> attr(,"propertyName")
#> [1] "dmdScheme"
#> attr(,"fileName")
#> [1] "dmdScheme_0.9.9.xlsx"
#> attr(,"class")
#> [1] "dmdSchemeSet_raw" "list"