tabshiftr

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Overview

Data are stored in many different ways in tables or spreadsheets because no strict semantic or topographic standards for the organisation of tables are commonly accepted. In the R environment the tidy paradigm is a first step towards interoperability of data, in that it requires a certain arrangement of tables, where variables are recorded in columns and observations in rows (see https://tidyr.tidyverse.org/). Tables can be tidied (i.e., brought into a tidy arrangement) via packages such as tidyr, however, all functions that deal with reshaping tables to date require data that are already organised into topologically coherent, rectangular tables. This is often violated in practice, especially in data that are scraped off of the internet.

tabshiftr fills this gap in the toolchain towards more interoperable data via schema descriptions and a reorganise() function that is largely based on tidyr.

Installation

  1. Install the official version from CRAN:
install.packages("tabshiftr")

or the latest development version from github:

devtools::install_github("EhrmannS/tabshiftr")
  1. The vignette gives an introduction, provides an instruction on how to set up schema descriptions by going step by step through certain dimensions of disorganisation to show which table arrangements can be reorganised and how that works.

Examples

A disorganised table may look like the following table:

library(tabshiftr)
library(knitr)

# a rather disorganised table with messy clusters and a distinct variable
input <- tabs2shift$clusters_messy
kable(input)
X1 X2 X3 X4 X5 X6 X7
commodities harvested production . . . .
unit 1 . . . . . .
soybean 1111 1112 year 1 . . .
maize 1121 1122 year 1 . . .
soybean 1211 1212 year 2 . . .
maize 1221 1222 year 2 . . .
. . . . . . .
commodities harvested production commodities harvested production .
unit 2 . . unit 3 . . .
soybean 2111 2112 soybean 3111 3112 year 1
maize 2121 2122 maize 3121 3122 year 1
soybean 2211 2212 soybean 3211 3212 year 2
maize 2221 2222 maize 3221 3222 year 2

If we were to transform this data into tidy data by merely using the functions in tidyr (or the extended tidyverse in general), we’d potentially end up with a massive algorithm, especially for such complicated table arrangements. For other tables that may or may not be as complicated, we’d have to set up yet more algorithms and while a pipeline of tidy functions is relatively easy to set up, it would still become very laborious to repeat this for the dozens of potential table arrangements. In tabshiftr we solve that by describing the schema of the input table and providing this schema description to the reorganise() function. This requires us to use a vastly smaller set of code and makes it thus a lot more efficient to bring multiple heterogeneous data into an interoperable format.

# put together schema description by ...
# ... identifying cluster positions
schema <- setCluster(id = "territories", left = c(1, 1, 4), top = c(1, 8, 8))

# ... specifying the cluster ID as id variable (obligatory for when we deal with clusters)
schema <- schema %>%
   setIDVar(name = "territories", columns = c(1, 1, 4), rows = c(2, 9, 9))

# ... specifying a distinct variable (explicit position)
schema <- schema %>%
   setIDVar(name = "year", columns = 4, rows = c(3:6), distinct = TRUE)

# ... specifying a tidy variable (by giving the column values)
schema <- schema %>%
   setIDVar(name = "commodities", columns = c(1, 1, 4))

# ... identifying the (tidy) observed variables
schema <- schema %>%
   setObsVar(name = "harvested", columns = c(2, 2, 5)) %>%
   setObsVar(name = "production", columns = c(3, 3, 6))

# to potentially debug the schema description, first validate the schema ...
schema_valid <- validateSchema(schema = schema, input = input)

# ... and extract parts of it
getIDVars(schema = schema_valid, input = input)
#> [[1]]
#> [[1]]$year
#> # A tibble: 4 x 1
#>   X4    
#>   <chr> 
#> 1 year 1
#> 2 year 1
#> 3 year 2
#> 4 year 2
#> 
#> [[1]]$commodities
#> # A tibble: 4 x 1
#>   X1     
#>   <chr>  
#> 1 soybean
#> 2 maize  
#> 3 soybean
#> 4 maize  
#> 
#> 
#> [[2]]
#> [[2]]$year
#> # A tibble: 4 x 1
#>   X4    
#>   <chr> 
#> 1 year 1
#> 2 year 1
#> 3 year 2
#> 4 year 2
#> 
#> [[2]]$commodities
#> # A tibble: 4 x 1
#>   X1     
#>   <chr>  
#> 1 soybean
#> 2 maize  
#> 3 soybean
#> 4 maize  
#> 
#> 
#> [[3]]
#> [[3]]$year
#> # A tibble: 4 x 1
#>   X4    
#>   <chr> 
#> 1 year 1
#> 2 year 1
#> 3 year 2
#> 4 year 2
#> 
#> [[3]]$commodities
#> # A tibble: 4 x 1
#>   X4     
#>   <chr>  
#> 1 soybean
#> 2 maize  
#> 3 soybean
#> 4 maize
getObsVars(schema = schema_valid, input = input)
#> [[1]]
#> [[1]]$harvested
#> # A tibble: 4 x 1
#>   X2   
#>   <chr>
#> 1 1111 
#> 2 1121 
#> 3 1211 
#> 4 1221 
#> 
#> [[1]]$production
#> # A tibble: 4 x 1
#>   X3   
#>   <chr>
#> 1 1112 
#> 2 1122 
#> 3 1212 
#> 4 1222 
#> 
#> 
#> [[2]]
#> [[2]]$harvested
#> # A tibble: 4 x 1
#>   X2   
#>   <chr>
#> 1 2111 
#> 2 2121 
#> 3 2211 
#> 4 2221 
#> 
#> [[2]]$production
#> # A tibble: 4 x 1
#>   X3   
#>   <chr>
#> 1 2112 
#> 2 2122 
#> 3 2212 
#> 4 2222 
#> 
#> 
#> [[3]]
#> [[3]]$harvested
#> # A tibble: 4 x 1
#>   X5   
#>   <chr>
#> 1 3111 
#> 2 3121 
#> 3 3211 
#> 4 3221 
#> 
#> [[3]]$production
#> # A tibble: 4 x 1
#>   X6   
#>   <chr>
#> 1 3112 
#> 2 3122 
#> 3 3212 
#> 4 3222

# alternatively, relative values starting from the cluster origin could be set
schema_alt <- setCluster(id = "territories",
                         left = c(1, 1, 4), top = c(1, 8, 8)) %>%
  setIDVar(name = "territories", columns = 1, rows = 2, relative = TRUE) %>%
  setIDVar(name = "year", columns = 4, rows = c(3:6), distinct = TRUE) %>%
  setIDVar(name = "commodities", columns = 1, relative = TRUE) %>%
  setObsVar(name = "harvested", columns = 2, relative = TRUE) %>%
  setObsVar(name = "production", columns = 3, relative = TRUE)

The reorganise() function carries out the steps of validating, extracting the variables, pivoting the tentative output and putting the final table together automatically, so it merely requires the finalised schema and the input table.

schema # has a pretty print function
#>   3 clusters
#>     origin : 1|1, 8|1, 8|4  (row|col)
#>     id     : territories
#> 
#>    variable      type       row    col    dist 
#>   ------------- ---------- ------ ------ ------  
#>    territories   id         2, 9   1, 4   F  
#>    year          id         3:6    4      T  
#>    commodities   id                1, 4   F  
#>    harvested     observed          2, 5   F  
#>    production    observed          3, 6   F

output <- reorganise(input = input, schema = schema)
kable(output)
territories year commodities harvested production
unit 1 year 1 maize 1121 1122
unit 1 year 1 soybean 1111 1112
unit 1 year 2 maize 1221 1222
unit 1 year 2 soybean 1211 1212
unit 2 year 1 maize 2121 2122
unit 2 year 1 soybean 2111 2112
unit 2 year 2 maize 2221 2222
unit 2 year 2 soybean 2211 2212
unit 3 year 1 maize 3121 3122
unit 3 year 1 soybean 3111 3112
unit 3 year 2 maize 3221 3222
unit 3 year 2 soybean 3211 3212

Contributions

Acknowledgement

This work was supported by funding to Carsten Meyer through the Flexpool mechanism of the German Centre for Integrative Biodiversity Research (Div) (FZT-118, DFG).