The R Package
The Definition of the dmdScheme is done in an R package, which gives all the tools to enter the meatada and to export it into xml.
Installation
The package is not yet on CRAN. Therefore it needs to be installed from github. This will install the last verion on github.
For a list of releases see here
## install the devtools package if not installed yet
# install.packages("devtools")
## install the last version of dmdScheme from github
devtools::install_github("Exp-Micro-Ecol-Hub/dmdScheme", build_opts = c("--no-resave-data"))
## install a specific release, e.g. v0.8, of dmdScheme from github
devtools::install_github("Exp-Micro-Ecol-Hub/dmdScheme", ref = "v0.8", build_opts = c("--no-resave-data"))Entering new Metadata
To enter new data to the dmdScheme, you have to
This should open Excel and the file should look similar to this:
- The file is saved in a temporary directory. It needs to be saved at a different location, if you want to keep the changes.
- Data can only be entered in the green cells with. All other cells are write protected.
After entering the data, save it to a location for further processing.
Importing Data from Excel Sheet
Next, you have to import the data entered in the Excel sheet int R:
x <- read_from_excel(
file = "PATH/WHERE/THE/FILE/IS/file.xlsx",
keepData = TRUE,
verbose = TRUE,
raw = FALSE
)For convenience, we use the exapmle data included in the package by using
#> New names:
#> * `` -> ...1
#> * `` -> ...2
#> * `` -> ...3
#> * `` -> ...4
#> * `` -> ...5
#> * … and 9 more problems
#> propertySet : valueProperty
#> Transposing...
#> New names:
#> * `` -> ...1
#> * `` -> ...2
#> * `` -> ...3
#> * `` -> ...4
#> * `` -> ...5
#> * … and 9 more problems
#> Set names...
#> Set attributes...
#> Apply types...
#> Apply type 'character' to 'name'...
#> Apply type 'character' to 'temperature'...
#> Apply type 'character' to 'light'...
#> Apply type 'character' to 'humidity'...
#> Apply type 'character' to 'incubator'...
#> Apply type 'character' to 'container'...
#> Apply type 'numeric' to 'microcosmVolume'...
#> Apply type 'character' to 'mediaType'...
#> Apply type 'numeric' to 'mediaConcentration'...
#> Apply type 'character' to 'cultureConditions'...
#> Apply type 'character' to 'comunityType'...
#> Apply type 'character' to 'mediaAdditions'...
#> Apply type 'integer' to 'duration'...
#> Apply type 'character' to 'comment'...
#> Set class...
#> Done
#> propertySet : Genus
#> Set names...
#> Set attributes...
#> Apply types...
#> Apply type 'character' to 'speciesID'...
#> Apply type 'character' to 'colour'...
#> Apply type 'character' to 'density'...
#> Apply type 'character' to 'functionalGroup'...
#> Apply type 'character' to 'comment'...
#> Set class...
#> Done
#> propertySet : Treatments
#> Set names...
#> Set attributes...
#> Apply types...
#> Apply type 'character' to 'treatmentID'...
#> Apply type 'character' to 'treatmentLevelHeight'...
#> Apply type 'character' to 'comment'...
#> Set class...
#> Done
#> propertySet : Measurement
#> Set names...
#> Set attributes...
#> Apply types...
#> Apply type 'character' to 'measurementID'...
#> Apply type 'character' to 'variable'...
#> Apply type 'character' to 'method'...
#> Apply type 'character' to 'unit'...
#> Apply type 'character' to 'object'...
#> Apply type 'integer' to 'noOfSamplesInTimeSeries'...
#> Apply type 'numeric' to 'samplingVolume'...
#> Apply type 'character' to 'dataExtractionID'...
#> Apply type 'character' to 'measuredFrom'...
#> Apply type 'character' to 'comment'...
#> Set class...
#> Done
#> propertySet : DataExtraction
#> Set names...
#> Set attributes...
#> Apply types...
#> Apply type 'character' to 'dataExtractionID'...
#> Apply type 'character' to 'method'...
#> Apply type 'character' to 'parameter'...
#> Apply type 'character' to 'value'...
#> Apply type 'character' to 'comment'...
#> Set class...
#> Done
#> propertySet : DataFileMetaData
#> Set names...
#> Set attributes...
#> Apply types...
#> Apply type 'character' to 'dataFileName'...
#> Apply type 'character' to 'columnName'...
#> Apply type 'character' to 'columnData'...
#> Apply type 'character' to 'mappingColumn'...
#> Apply type 'character' to 'type'...
#> Apply type 'character' to 'description'...
#> Apply type 'character' to 'comment'...
#> Set class...
#> DonePrint dmdScheme Data
dmdScheme Data can be printed by using the print() function. The function has three arguments which control the printout:
printAttr: ifTRUE(default) print the basic attributes prefixed withAprintExAttr: ifTRUEprint the all attributes prefixed withXprintData: ifTRUE(default) print the data prefixed withD
print(
x,
printAttr = FALSE,
printExtAttr = FALSE,
printData = FALSE
)
#> dmdScheme - dmdSchemeSet
#> Experiment - dmdSchemeData
#> Genus - dmdSchemeData
#> Treatments - dmdSchemeData
#> Measurement - dmdSchemeData
#> DataExtraction - dmdSchemeData
#> DataFileMetaData - dmdSchemeDataprint(
x,
printAttr = TRUE,
printExtAttr = FALSE,
printData = FALSE
)
#> dmdScheme - dmdSchemeSet
#> Experiment - dmdSchemeData
#> A Names : name | temperature | light | humidity | incubator | container | microcosmVolume | mediaType | mediaConcentration | cultureConditions | comunityType | mediaAdditions | duration | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | g/l | NA | NA | NA | days | NA
#> A Type : character | character | character | character | character | character | numeric | character | numeric | character | character | character | integer | character
#>
#> Genus - dmdSchemeData
#> A Names : speciesID | colour | density | functionalGroup | comment
#> A Units : NA | NA | cells / ml | NA | NA
#> A Type : character | character | character | character | character
#>
#> Treatments - dmdSchemeData
#> A Names : treatmentID | treatmentLevelHeight | comment
#> A Units : NA | NA | NA
#> A Type : character | character | character
#>
#> Measurement - dmdSchemeData
#> A Names : measurementID | variable | method | unit | object | noOfSamplesInTimeSeries | samplingVolume | dataExtractionID | measuredFrom | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | NA | NA
#> A Type : character | character | character | character | character | integer | numeric | character | character | character
#>
#> DataExtraction - dmdSchemeData
#> A Names : dataExtractionID | method | parameter | value | comment
#> A Units : NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character
#>
#> DataFileMetaData - dmdSchemeData
#> A Names : dataFileName | columnName | columnData | mappingColumn | type | description | comment
#> A Units : NA | NA | NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character | character | characterprint(
x,
printAttr = TRUE,
printExtAttr = TRUE,
printData = FALSE
)
#> dmdScheme - dmdSchemeSet
#> Experiment - dmdSchemeData
#> A Names : name | temperature | light | humidity | incubator | container | microcosmVolume | mediaType | mediaConcentration | cultureConditions | comunityType | mediaAdditions | duration | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | g/l | NA | NA | NA | days | NA
#> A Type : character | character | character | character | character | character | numeric | character | numeric | character | character | character | integer | character
#>
#> XA row.names: 1
#> XA propertyName: Experiment
#> XA suggestedValues: NA | treatment, in degrees celsius, measurement | treatment,light, dark, cycle , e.g. 16:8 LD | treatment, relative humidity in % | none, bench | NA | NA | NA | NA | axenic, dirty, clean | treatment, single trophic level, multiple trophic level | NA | NA | NA
#> XA Description: The name of the experiment. | Temperature used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | Light used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | Humidity used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | What type of incubator is used. | What type of container is used. | Volume of the microcosm container. Not the volume of the culture medium! | NA | NA | Conditions of the cultures for all treatments. | Characterisation of the microbe community. | NA | Length of the experiment in days. This should only include the time in which the measurements were taken! | Additional features of the Experiment you want to provide
#> XA class: dmdSchemeData | tbl_df | tbl | data.frame
#>
#> Genus - dmdSchemeData
#> A Names : speciesID | colour | density | functionalGroup | comment
#> A Units : NA | NA | cells / ml | NA | NA
#> A Type : character | character | character | character | character
#>
#> XA row.names: 1 | 2
#> XA propertyName: Genus
#> XA suggestedValues: NA | NA | treatment | bacteria, bacterivore, predator, phototroph | NA
#> XA Description: Id of the species and strain. Each speciesId has to be unique. | Where the species was obtained from. | Initial density used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | Functional group of the species. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> Treatments - dmdSchemeData
#> A Names : treatmentID | treatmentLevelHeight | comment
#> A Units : NA | NA | NA
#> A Type : character | character | character
#>
#> XA row.names: 1 | 2 | 3 | 4 | 5
#> XA propertyName: Treatments
#> XA suggestedValues: species, temperatur, light, initial density, comunity composition, densities, dispersal, viscosity, disturbance, communityType | value, variable: freetext | NA
#> XA Description: ID of the the treatment decribed in this a row. Each treatmentId can occur multiple times as it can contain multiple treatment levels. | 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. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> Measurement - dmdSchemeData
#> A Names : measurementID | variable | method | unit | object | noOfSamplesInTimeSeries | samplingVolume | dataExtractionID | measuredFrom | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | NA | NA
#> A Type : character | character | character | character | character | integer | numeric | character | character | character
#>
#> XA row.names: 1 | 2 | 3 | 4
#> XA propertyName: Measurement
#> XA suggestedValues: NA | O2 concentration, video, manual count, abundance, DNA | presens Optode, microscopy | %, mmol, count | species, OUT, gene, community, particles | NA | NA | NA | NA | NA
#> XA Description: 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. | The variable measured. | Name of the method used. | Unit of the measured variable | The object measured. E.g. species in the case of manual count, gene for genetic analysis, particle for particle counters. | Total number of all samples in the time series. | The sampling volumne. If e.g. atmosphere in container is sampled (oxygen measurements), than enter 0.
#> Please use NA if sampling volumne is variable. | as used in the sheet DataExtraction, column dataExtractionID | if measured from the experiment, raw, else the measurementId (first column) of the Measurement it is based on. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> DataExtraction - dmdSchemeData
#> A Names : dataExtractionID | method | parameter | value | comment
#> A Units : NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character
#>
#> XA row.names: 1
#> XA propertyName: DataExtraction
#> XA suggestedValues: NA | bemovi x.y.z | NA | NA | NA
#> XA Description: 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. | Method used for the DataExtraction process. If possible including version (in the case of R packages). | parameter in the analysis. Only needs to be specified if it varies from the default. | value of the parameter (you can enter a number or a word) | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> DataFileMetaData - dmdSchemeData
#> A Names : dataFileName | columnName | columnData | mappingColumn | type | description | comment
#> A Units : NA | NA | NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character | character | character
#>
#> XA row.names: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20
#> XA propertyName: DataFileMetaData
#> XA allowedValues: NA | NA | ID, Treatment, Measurement, Species, other | NA | integer, numeric, character, logical, datetime, date, time | NA | NA
#> XA Description: the name of the data set. | Name of column in the data file.
#> Each column in the data file needs to be documented!
#> or NA
#> if it is for the whole data file and not specified in the dataFileName | The type of the data in the column.
#> ID: ID field (unique ID of unit of replication);
#> Treatment: specifies treatment;
#> Measurement: contains measurements;
#> Species: contains species;
#> other: other type of data | columnData = Treatment:
#> treatmentID as in the Treatment tab;
#> columnData = Species:
#> treatmentID refering to species composition as in the Treatment tab
#> columnData = Measurement:
#> measurementID as in the Measurement tab;
#> otherwise:
#> NA | Type of the column. | 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. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frameprint(
x,
printAttr = TRUE,
printExtAttr = TRUE,
printData = TRUE
)
#> dmdScheme - dmdSchemeSet
#> Experiment - dmdSchemeData
#> A Names : name | temperature | light | humidity | incubator | container | microcosmVolume | mediaType | mediaConcentration | cultureConditions | comunityType | mediaAdditions | duration | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | g/l | NA | NA | NA | days | NA
#> A Type : character | character | character | character | character | character | numeric | character | numeric | character | character | character | integer | character
#>
#> XA row.names: 1
#> XA propertyName: Experiment
#> XA suggestedValues: NA | treatment, in degrees celsius, measurement | treatment,light, dark, cycle , e.g. 16:8 LD | treatment, relative humidity in % | none, bench | NA | NA | NA | NA | axenic, dirty, clean | treatment, single trophic level, multiple trophic level | NA | NA | NA
#> XA Description: The name of the experiment. | Temperature used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | Light used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | Humidity used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | What type of incubator is used. | What type of container is used. | Volume of the microcosm container. Not the volume of the culture medium! | NA | NA | Conditions of the cultures for all treatments. | Characterisation of the microbe community. | NA | Length of the experiment in days. This should only include the time in which the measurements were taken! | Additional features of the Experiment you want to provide
#> XA class: dmdSchemeData | tbl_df | tbl | data.frame
#>
#> name temperature light humidity incubator
#> D 1 ASR-expt1 20 semi-ambient ambient not given here
#> container microcosmVolume mediaType
#> D 1 Duran type bottle, red lids, 250ml 100 PPM
#> mediaConcentration cultureConditions comunityType
#> D 1 0.55 dirty initially unknown
#> mediaAdditions
#> D 1 Wheat seeds added on specific dates, see file wheat_seed_additions.csv
#> duration comment
#> D 1 100 <NA>
#>
#> Genus - dmdSchemeData
#> A Names : speciesID | colour | density | functionalGroup | comment
#> A Units : NA | NA | cells / ml | NA | NA
#> A Type : character | character | character | character | character
#>
#> XA row.names: 1 | 2
#> XA propertyName: Genus
#> XA suggestedValues: NA | NA | treatment | bacteria, bacterivore, predator, phototroph | NA
#> XA Description: Id of the species and strain. Each speciesId has to be unique. | Where the species was obtained from. | Initial density used for all treatments. If different between treatments, use "treatment" and specify in the Treatment sheet. | Functional group of the species. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> speciesID colour density functionalGroup
#> D 1 tt_1 ATCC 1 bacterivore
#> D 2 unknown unknown <NA> unknown
#> comment
#> D 1 http://www.lgcstandards-atcc.org/products/all/30007.aspx
#> D 2 <NA>
#>
#> Treatments - dmdSchemeData
#> A Names : treatmentID | treatmentLevelHeight | comment
#> A Units : NA | NA | NA
#> A Type : character | character | character
#>
#> XA row.names: 1 | 2 | 3 | 4 | 5
#> XA propertyName: Treatments
#> XA suggestedValues: species, temperatur, light, initial density, comunity composition, densities, dispersal, viscosity, disturbance, communityType | value, variable: freetext | NA
#> XA Description: ID of the the treatment decribed in this a row. Each treatmentId can occur multiple times as it can contain multiple treatment levels. | 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. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> treatmentID treatmentLevelHeight comment
#> D 1 Lid_treatment Loose <NA>
#> D 2 Lid_treatment Tight <NA>
#> D 3 species_1 tt_1, unknown <NA>
#> D 4 species_2 unknown <NA>
#> D 5 species_3 tt_1 <NA>
#>
#> Measurement - dmdSchemeData
#> A Names : measurementID | variable | method | unit | object | noOfSamplesInTimeSeries | samplingVolume | dataExtractionID | measuredFrom | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | NA | NA
#> A Type : character | character | character | character | character | integer | numeric | character | character | character
#>
#> XA row.names: 1 | 2 | 3 | 4
#> XA propertyName: Measurement
#> XA suggestedValues: NA | O2 concentration, video, manual count, abundance, DNA | presens Optode, microscopy | %, mmol, count | species, OUT, gene, community, particles | NA | NA | NA | NA | NA
#> XA Description: 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. | The variable measured. | Name of the method used. | Unit of the measured variable | The object measured. E.g. species in the case of manual count, gene for genetic analysis, particle for particle counters. | Total number of all samples in the time series. | The sampling volumne. If e.g. atmosphere in container is sampled (oxygen measurements), than enter 0.
#> Please use NA if sampling volumne is variable. | as used in the sheet DataExtraction, column dataExtractionID | if measured from the experiment, raw, else the measurementId (first column) of the Measurement it is based on. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> measurementID variable method unit
#> D 1 oxygen concentration DO presens Optode %
#> D 2 abundance abundance molecular count
#> D 3 smell smell nose rotten eggs or not
#> D 4 sequenceData DNA NGS Nucleotide
#> object noOfSamplesInTimeSeries samplingVolume
#> D 1 community 50 0.0
#> D 2 species 6 0.5
#> D 3 community 6 0.0
#> D 4 DNA fragment 6 0.0
#> dataExtractionID measuredFrom comment
#> D 1 none raw <NA>
#> D 2 Mol_Analy_pipeline1 sequenceData <NA>
#> D 3 none raw <NA>
#> D 4 none raw <NA>
#>
#> DataExtraction - dmdSchemeData
#> A Names : dataExtractionID | method | parameter | value | comment
#> A Units : NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character
#>
#> XA row.names: 1
#> XA propertyName: DataExtraction
#> XA suggestedValues: NA | bemovi x.y.z | NA | NA | NA
#> XA Description: 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. | Method used for the DataExtraction process. If possible including version (in the case of R packages). | parameter in the analysis. Only needs to be specified if it varies from the default. | value of the parameter (you can enter a number or a word) | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> dataExtractionID method parameter value
#> D 1 Mol_Analy_pipeline1 <NA> <NA> <NA>
#> comment
#> D 1 See description in file xxx.yyy
#>
#> DataFileMetaData - dmdSchemeData
#> A Names : dataFileName | columnName | columnData | mappingColumn | type | description | comment
#> A Units : NA | NA | NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character | character | character
#>
#> XA row.names: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20
#> XA propertyName: DataFileMetaData
#> XA allowedValues: NA | NA | ID, Treatment, Measurement, Species, other | NA | integer, numeric, character, logical, datetime, date, time | NA | NA
#> XA Description: the name of the data set. | Name of column in the data file.
#> Each column in the data file needs to be documented!
#> or NA
#> if it is for the whole data file and not specified in the dataFileName | The type of the data in the column.
#> ID: ID field (unique ID of unit of replication);
#> Treatment: specifies treatment;
#> Measurement: contains measurements;
#> Species: contains species;
#> other: other type of data | columnData = Treatment:
#> treatmentID as in the Treatment tab;
#> columnData = Species:
#> treatmentID refering to species composition as in the Treatment tab
#> columnData = Measurement:
#> measurementID as in the Measurement tab;
#> otherwise:
#> NA | Type of the column. | 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. | NA
#> XA class: dmdSchemeData | dmdSchemeData_raw | tbl_df | tbl | data.frame
#>
#> dataFileName columnName columnData
#> D 1 dissolved_oxygen_measures.csv Jar_ID ID
#> D 2 dissolved_oxygen_measures.csv DO Measurement
#> D 3 dissolved_oxygen_measures.csv Unit_1 other
#> D 4 dissolved_oxygen_measures.csv Mode other
#> D 5 dissolved_oxygen_measures.csv Location other
#> D 6 dissolved_oxygen_measures.csv Date_time other
#> D 7 dissolved_oxygen_measures.csv Lid_treatment Treatment
#> D 8 dissolved_oxygen_measures.csv Jar_type other
#> D 9 dissolved_oxygen_measures.csv Jar_ID ID
#> D 10 smell.csv <NA> Species
#> D 11 smell.csv smell Measurement
#> D 12 smell.csv Date other
#> D 13 smell.csv Lid_treatment Treatment
#> D 14 smell.csv Jar_type other
#> D 15 abundances.csv <NA> Species
#> D 16 abundances.csv Jar_ID ID
#> D 17 abundances.csv Date_time other
#> D 18 abundances.csv Lid_treatment Treatment
#> D 19 abundances.csv Jar_type other
#> D 20 abundances.csv count_number Measurement
#> mappingColumn type description comment
#> D 1 <NA> character <NA> <NA>
#> D 2 oxygen concentration numeric <NA> <NA>
#> D 3 <NA> character <NA> <NA>
#> D 4 <NA> character <NA> <NA>
#> D 5 <NA> character <NA> <NA>
#> D 6 <NA> datetime ymdhms <NA>
#> D 7 Lid_treatment character <NA> <NA>
#> D 8 <NA> character <NA> <NA>
#> D 9 <NA> character <NA> <NA>
#> D 10 species_1 character <NA> <NA>
#> D 11 smell character <NA> <NA>
#> D 12 <NA> datetime ymdhms <NA>
#> D 13 Lid_treatment character <NA> <NA>
#> D 14 <NA> character <NA> <NA>
#> D 15 species_3 character <NA> <NA>
#> D 16 <NA> character <NA> <NA>
#> D 17 <NA> datetime ymdhms <NA>
#> D 18 Lid_treatment character <NA> <NA>
#> D 19 <NA> character <NA> <NA>
#> D 20 abundance numeric <NA> <NA>Converting Metadata to xml
You can export the data to an an xml file:
When you specify the argument file, the xml will be saved:
Validation
dmdSchemeSet_raw against dmdScheme
When running read_from_excel(), the dafault is to validate the raw data before conversion to an dmdScheme object to guarantee a valid dmdScheme is returned. If the validation fails, an error is raised.
xml against xsd
Not incorporated yet but planned.
General things
The dmdScheme data in R can be also saved, loaded, and edited using the standard R commands.