getGADS: Using a relational eatGADS data base

Benjamin Becker

2021-10-06

This vignette illustrates how a relational eatGADS data base can be accessed and used. Therefore, the vignette is targeted at users who make use of an existing data base.

For illustrative purposes we use a small example data base based on the campus files of the German PISA Plus assessment. The complete campus files and the original data set can be accessed here and here. The data base is installed alongside eatGADS and the path can be accessed via the system.file() function.

library(eatGADS)
db_path <- system.file("extdata", "pisa.db", package = "eatGADS")
db_path
#> [1] "C:/Users/beckerbz/AppData/Local/Temp/RtmpMZIJta/Rinst520351267e3/eatGADS/extdata/pisa.db"

Why?

Relational data bases created by eatGADS provide an alternative way of storing hierarchically structured data (e.g. from educational large-scale assessments). Compared to conventional approaches (one big or multiple .sav/.Rdata files) this yields the following advantages:

Inspecting the data base

We can inspect the data base structure with the namesGADS() function. The function returns a named list. Every list element represents a hierarchy level. The corresponding character vector contains all variable names on this hierarchy level.

nam <- namesGADS(db_path)
nam
#> $noImp
#>   [1] "idstud"       "idschool"     "idclass"      "schtype"      "sameteach"   
#>   [6] "g8g9"         "ganztag"      "classsize"    "repeated"     "gender"      
#>  [11] "age"          "language"     "migration"    "hisced"       "hisei"       
#>  [16] "homepos"      "books"        "pared"        "computer_age" "internet_age"
#>  [21] "int_use_a"    "int_use_b"    "truancy_a"    "truancy_b"    "truancy_c"   
#>  [26] "int_a"        "int_b"        "int_c"        "int_d"        "instmot_a"   
#>  [31] "instmot_b"    "instmot_c"    "instmot_d"    "norms_a"      "norms_b"     
#>  [36] "norms_c"      "norms_d"      "norms_e"      "norms_f"      "anxiety_a"   
#>  [41] "anxiety_b"    "anxiety_c"    "anxiety_d"    "anxiety_e"    "selfcon_a"   
#>  [46] "selfcon_b"    "selfcon_c"    "selfcon_d"    "selfcon_e"    "worketh_a"   
#>  [51] "worketh_b"    "worketh_c"    "worketh_d"    "worketh_e"    "worketh_f"   
#>  [56] "worketh_g"    "worketh_h"    "worketh_i"    "intent_a"     "intent_b"    
#>  [61] "intent_c"     "intent_d"     "intent_e"     "behav_a"      "behav_b"     
#>  [66] "behav_c"      "behav_d"      "behav_e"      "behav_f"      "behav_g"     
#>  [71] "behav_h"      "teach_a"      "teach_b"      "teach_c"      "teach_d"     
#>  [76] "teach_e"      "cognact_a"    "cognact_b"    "cognact_c"    "cognact_d"   
#>  [81] "cognact_e"    "cognact_f"    "cognact_g"    "cognact_h"    "cognact_i"   
#>  [86] "discpline_a"  "discpline_b"  "discpline_c"  "discpline_d"  "discpline_e" 
#>  [91] "relation_a"   "relation_b"   "relation_c"   "relation_d"   "relation_e"  
#>  [96] "belong_a"     "belong_b"     "belong_c"     "belong_d"     "belong_e"    
#> [101] "belong_f"     "belong_g"     "belong_h"     "belong_i"     "attitud_a"   
#> [106] "attitud_b"    "attitud_c"    "attitud_d"    "attitud_e"    "attitud_f"   
#> [111] "attitud_g"    "attitud_h"    "grade_de"     "grade_ma"     "grade_bio"   
#> [116] "grade_che"    "grade_phy"    "grade_sci"   
#> 
#> $PVs
#> [1] "idstud"    "dimension" "imp"       "value"

The example data base contains two hierarchy levels: A student level (noImp) and a plausible value level (PVs). On the student level, each row represents an individual student. On the plausible value level, each row represents an imputation number of a specific domain of an individual student.

We can access meta information of the variables in the data set using the extractMeta() function.

# Meta data for one variable
extractMeta(db_path, "age")
#>   varName             varLabel format display_width labeled value valLabel
#> 1     age Age of student at T1   F8.2            NA      no    NA     <NA>
#>   missings data_table
#> 1     <NA>      noImp

To supply variables names we can also use the named list nam extracted earlier. This way, we can extract all meta information available for a hierarchy level.

extractMeta(db_path, nam$PVs)
#>       varName                                       varLabel format
#> 236    idstud                                     Student-ID   F8.0
#> 451    idstud                                     Student-ID   F8.0
#> 452 dimension Achievement dimension (math, reading, science)   <NA>
#> 453 dimension Achievement dimension (math, reading, science)   <NA>
#> 454 dimension Achievement dimension (math, reading, science)   <NA>
#> 455       imp       Number of imputation of plausible values   <NA>
#> 456     value                                Plausible Value   <NA>
#>     display_width labeled value valLabel missings data_table
#> 236            NA      no    NA     <NA>     <NA>      noImp
#> 451            NA      no    NA     <NA>     <NA>        PVs
#> 452            NA     yes     1       ma    valid        PVs
#> 453            NA     yes     2      rea    valid        PVs
#> 454            NA     yes     3      sci    valid        PVs
#> 455            NA      no    NA     <NA>     <NA>        PVs
#> 456            NA      no    NA     <NA>     <NA>        PVs

Commonly the most informative columns are varLabel (containing variable labels), value (referencing labeled values), valLabel (containing value labels) and missings (is a labeled value a missing value ("miss") or not ("valid")).

# Meta data for manually chosen multiple variables
extractMeta(db_path, c("idstud", "schtype"))
#>     varName     varLabel format display_width labeled value
#> 236  idstud   Student-ID   F8.0            NA      no    NA
#> 360 schtype School track   F8.0            NA     yes     1
#> 361 schtype School track   F8.0            NA     yes     2
#> 362 schtype School track   F8.0            NA     yes     3
#> 451  idstud   Student-ID   F8.0            NA      no    NA
#>                                      valLabel missings data_table
#> 236                                      <NA>     <NA>      noImp
#> 360                Gymnasium (academic track)    valid      noImp
#> 361                                Realschule    valid      noImp
#> 362 schools with several courses of education    valid      noImp
#> 451                                      <NA>     <NA>        PVs

Extract data from data base

To extract a data set from the data base, we can use the function getGADS(). If the data base is stored on a server drive, getGADS_fast() provides identical functionality but substantially increases the performance. With the vSelect argument we specify our variable selection. It is important to note that getGADS() returns a so called GADSdat object. This object type contains complex meta information (that is for example also available in a SPSS data set), and is therefore not directly usable for data analysis. We can, however, use the extractMeta() function on it to access the meta data.

gads1 <- getGADS(filePath = db_path, vSelect = c("idstud", "schtype"))
class(gads1)
#> [1] "GADSdat" "list"
extractMeta(gads1)
#>     varName     varLabel format display_width labeled value
#> 236  idstud   Student-ID   F8.0            NA      no    NA
#> 360 schtype School track   F8.0            NA     yes     1
#> 361 schtype School track   F8.0            NA     yes     2
#> 362 schtype School track   F8.0            NA     yes     3
#>                                      valLabel missings
#> 236                                      <NA>     <NA>
#> 360                Gymnasium (academic track)    valid
#> 361                                Realschule    valid
#> 362 schools with several courses of education    valid

Extract data from GADSdat

If we want to use the data for analyses in R we have to extract it from the GADSdat object via the function extractData(). In doing so, we have to make two important decisions: (a) how should values marked as missing values be treated (convertMiss)? And (b) how should labeled values in general be treated (convertLabels, dropPartialLabels, convertVariables)? See ?extractData for more details.

## convert labeled variables to characters
dat1 <- extractData(gads1, convertLabels = "character")
head(dat1)
#>   idstud                                   schtype
#> 1      1                                Realschule
#> 2      2 schools with several courses of education
#> 3      3                Gymnasium (academic track)
#> 4      4 schools with several courses of education
#> 5      5                                Realschule
#> 6      6 schools with several courses of education

## leave labeled variables as numeric
dat2 <- extractData(gads1, convertLabels = "numeric")
head(dat2)
#>   idstud schtype
#> 1      1       2
#> 2      2       3
#> 3      3       1
#> 4      4       3
#> 5      5       2
#> 6      6       3

In general, we recommend leaving labeled variables as numeric and converting values with missing codes to NA. The latter is the default behavior for the argument checkMissings. If required, values labels can always be accessed via using extractMeta() on the GADSdat object or the data base.

Selecting different hierarchy levels

An important feature of eatGADS relational data bases are that data sets are automatically returned on the correct hierarchy level. For an overview of different data structures, see “Tidy Data” or this article explaining long and wide format using repeated measures. In educational large-scale assessments, data usually contain multiple imputations or plausible values. Packages that enable us analyzing these types of data (like eatRep) often require these data in the long format.

The function getGADS() extracts data automatically in the appropriate structure, depending on our variable selection. If we select only variables from the student level, the data returned is on the student level. Each student is represented in a single row.

gads1 <- getGADS(db_path, vSelect = c("schtype", "g8g9"))
dat1 <- extractData(gads1)
dim(dat1)
#> [1] 500   3
head(dat1)
#>   idstud                                   schtype                   g8g9
#> 1      1                                Realschule                   <NA>
#> 2      2 schools with several courses of education                   <NA>
#> 3      3                Gymnasium (academic track) G8 - 8 years to abitur
#> 4      4 schools with several courses of education                   <NA>
#> 5      5                                Realschule                   <NA>
#> 6      6 schools with several courses of education                   <NA>

If additionally variables from the plausible Value data table are extracted, the returned data structure changes. In the PVs data table, data is stored on the “student x dimension x plausible value number” level. The returned data has exactly this structure.

gads2 <- getGADS(db_path, vSelect = c("schtype", "value"))
dat2 <- extractData(gads2)
dim(dat2)
#> [1] 7500    5
head(dat2)
#>   idstud    schtype dimension imp       value
#> 1      1 Realschule        ma   1  0.15372011
#> 2      1 Realschule       rea   1  0.43914365
#> 3      1 Realschule       sci   1  0.13177617
#> 4      1 Realschule        ma   2 -0.04119330
#> 5      1 Realschule       rea   2  0.01991714
#> 6      1 Realschule       sci   2  0.67830064

These two examples highlight another feature of getGADS(): Only variables of substantial interest have to be selected for extraction. The correct ID variables are added automatically.

Trend data bases

In educational large-scale assessments, a common challenge is reporting longitudinal developments (trends). getTrendGADS allows extracting data from two data bases with identical variables in it. Linking errors can be automatically merged via the lePath argument.

Currently, no trend data set is available within eatGADS. However, an exemplary example function call looks like this:

gads_trend <- getTrendGADS(filePath1 = db_path, 
                           filePath2 = db_path2, 
                           lePath = le_path,
                           vSelect = c("idstud", "schtype"), 
                           years = c(2012, 2013), fast = FALSE)
dat_trend <- extractData(gads_trend)