Metadata tables

The following sections describes the variables used in the different metadata tables. All tables should be machine-readable. Having key variables consistently named across tables make it possible to automatically bring them together

Code
library(knitr)
library(dplyr)
library(kableExtra)

# find files with codebooks
dirinput <- file.path('..','templates','templates_for_experiments','Facility_YYYY_month','metadata_tables')
files <- dir(dirinput,pattern = '*codebook*')


# gather codebooks
for (i in 1:length(files)){
  
  table <- read.csv(file.path(dirinput,files[i]), header = TRUE, sep = ",")
  #make it markdown
  markdown_table <- knitr::kable(table) %>% 
                  kable_styling(bootstrap_options = c("striped", "hover"))

  
  # print it 
  cat("\n")
  cat("\n")
  cat(paste0("## ",files[i]))
  cat("\n")
  print(markdown_table)  

}

Mouse_list_Facility_YYYY_month_codebook.csv

Variable Description
SubjectID “Mice unique identifier”
Research_group_University University affiliation of the group who collected the data (e.g., UZH; see glossary)
Research_group_Abbreviation Abbreviation describing the group who collected the data (e.g., TIG; see glossary)
Year “Year of collection YYYY”
Month Month of collection (Jan, Feb, Mar, etc)
Date_of_acquisition “DD/MM/YYYY”
Data_type Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)
Dataproject_ID (optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF
Facility_proposal_ID (optional) Number of the proposal for facility usage e.g., the beamline numbers
Facility_institution “Name or acronym of the institution hosting the main facility (it can be the same as University)”
Facility_country Country where the facility is located
Facility_name Name or acronym of the main facility (e.g., CLS, SPring-8,etc)
Facility_subunit (optional) Additional facility information (e.g., beamline)

Scan_list_Facility_month_YYYY_codebook.csv

Variable Description
SubjectID “Mice unique identifier”
University University affiliation of the group who collected the data (e.g., UZH; see glossary)
Research_group Abbreviation describing the group who collected the data (e.g., TIG; see glossary)
Year “Year of collection YYYY”
Month Month of collection (Jan, Feb, Mar, etc)
Date_acquisition “DD/MM/YYYY”
Data_type Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)
Dataproject_ID (optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF
Facility_proposal_ID (optional) Number of the proposal for facility usage e.g., the beamline numbers
Facility_institution “Name or acronym of the institution hosting the main facility (it can be the same as University)”
Facility_country Country where the facility is located
Facility_name Name or acronym of the main facility (e.g., CLS, SPring-8,etc)
Facility_sub (optional) Additional facility information (e.g., beamline)
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