This function takes data from a json source, optionally validates the
contents against a JSON validation schema, perform checks, calculates
the D-score, calculates Z-scores and stores the data in an list with
elements psn and xyz.
read_bds(
txt = NULL,
auto_format = TRUE,
format = "1.0",
schema = NULL,
validate = FALSE,
append_ddi = FALSE,
intermediate = FALSE,
verbose = FALSE,
...
)A JSON string, URL or file
Logical. Should the format be read from the data? Default
is TRUE.
String. JSON data schema version number. There are currently
three schemas supported: "1.0", "1.1", "2.0" and "3.0".
Formats "1.0" and "1.1" are included for backward compatibility only.
Use format = "3.0" for new applications.
A file name (optionally including the path) with the JSON
validation schema.
The schema argument overrides format. The function extracts the
version number for the basename, and overwrites the
format argument by version number.
Logical. Should the JSON-input be validated against the
JSON-schema? The default (FALSE) bypasses checking. Set validate = TRUE
to obtain diagnostic information from the jsonvalidate::json_validate()
function.
Should the DDI responses be appended? (only used for JSON schema V1.0 and V2.0)
Logical. If TRUE the function writes JSON files
with intermediate result to the working directory.
input.json: the JSON input data;
bds.json: a data frame with info per BDS;
ddi.json: result of recoding BDS into GSED item names;
psn.json: known fixed child covariates;
xy.json: time-varying variables.
Show verbose output for centile::y2z()
Ignored
A list with elements named "psn" and "xyz".
If txt is unspecified or NULL, then the return component will "xyz"
have zero rows.
The format and schema arguments specify the format of the JSON input
data argument txt. The default format = "1.0" expects that the JSON
input data conform to the schema specified in
system.file("schemas/bds_v1.0.json", package = "bdsreader"). This is only
supported for legacy. We recommend format "3.0", which expects data
coded according to
system.file("schemas/bds_v3.0.json", package = "bdsreader").
The format can be specified in the JSON data file with an entry
named Format. For auto_format == TRUE, the data specification overrides
any format and schema arguments to the read_bds() function.
Schema bds_v3.0.json requires the Format field, so the correct format
is automatically set by the data.
Legacy note: If you erroneously read a JSON file of format "1.0" using
format "2.0" you may see an error:
Error ...: incorrect number of dimensions.
In that make sure that you are reading with the format = "1.0" argument.
Reversely, if you erroneously read a JSON file of format "2.0" using format
"1.0" you may see messages .ClientGegevens should be object and
Missing 'ClientGegevens$Groepen'. In that case, specify format = "2.0".
fn <- system.file("examples/maria1.json", package = "bdsreader")
m <- read_bds(fn)
fn <- system.file("examples/test.json", package = "bdsreader")
m <- read_bds(fn)
# Assume that jamesdemodata is installed locally.
# If not use remotes::install_github("growthcharts/jamesdemodata")
# Read file with input data according to format "3.0"
data2 <- system.file("extdata/bds_v3.0/smocc/Laura_S.json",
package = "jamesdemodata")
q <- read_bds(data2)
q
#> $psn
#> # A tibble: 1 × 22
#> id name dob dobm dobf src dnr sex gad ga
#> <int> <chr> <date> <date> <date> <chr> <chr> <chr> <dbl> <dbl>
#> 1 -1 Laura S 1989-01-21 1961-07-22 NA 0 NA female 276 39
#> # ℹ 12 more variables: smo <dbl>, bw <dbl>, hgtm <dbl>, hgtf <dbl>, agem <dbl>,
#> # etn <chr>, pc4 <chr>, blbf <int>, blbm <int>, eduf <int>, edum <int>,
#> # par <int>
#>
#> $xyz
#> # A tibble: 58 × 8
#> age xname yname zname zref x y z
#> <dbl> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 0 age hgt hgt_z nl_1997_hgt_female_nl 0 48 -1.52
#> 2 0.101 age hgt hgt_z nl_1997_hgt_female_nl 0.101 53.5 -0.499
#> 3 0.159 age hgt hgt_z nl_1997_hgt_female_nl 0.159 56 -0.261
#> 4 0.236 age hgt hgt_z nl_1997_hgt_female_nl 0.236 59.5 0.163
#> 5 0.485 age hgt hgt_z nl_1997_hgt_female_nl 0.485 65.5 -0.259
#> 6 0.753 age hgt hgt_z nl_1997_hgt_female_nl 0.753 71.5 0.131
#> 7 1.02 age hgt hgt_z nl_1997_hgt_female_nl 1.02 75 -0.18
#> 8 1.25 age hgt hgt_z nl_1997_hgt_female_nl 1.25 80 0.421
#> 9 1.54 age hgt hgt_z nl_1997_hgt_female_nl 1.54 84 0.527
#> 10 2.04 age hgt hgt_z nl_1997_hgt_female_nl 2.04 90 0.67
#> # ℹ 48 more rows
#>
# Equivalent, but specifying the built-in schema file bds_v3.0.json
schema2 <- system.file("schemas/bds_v3.0.json", package = "bdsreader")
r <- read_bds(data2, schema = schema2)
identical(q, r)
#> [1] TRUE
# Automatic detection of format 3.0
# s <- read_bds(data2)
# identical(q, s)
# Reading data with older format (bds_v1.0)
data1 <- system.file("extdata/bds_v1.0/smocc/Laura_S.json",
package = "jamesdemodata")
t <- read_bds(data1)
t
#> $psn
#> # A tibble: 1 × 16
#> id name dob dobf dobm src dnr sex gad ga
#> <int> <chr> <date> <date> <date> <chr> <chr> <chr> <dbl> <dbl>
#> 1 -1 Laura S 1989-01-21 NA 1961-07-22 0 NA female 276 39
#> # ℹ 6 more variables: smo <int>, bw <dbl>, hgtm <dbl>, hgtf <dbl>, agem <dbl>,
#> # etn <chr>
#>
#> $xyz
#> # A tibble: 58 × 8
#> age xname yname zname zref x y z
#> <dbl> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 0 age hgt hgt_z nl_1997_hgt_female_nl 0 48 -1.52
#> 2 0.101 age hgt hgt_z nl_1997_hgt_female_nl 0.101 53.5 -0.499
#> 3 0.159 age hgt hgt_z nl_1997_hgt_female_nl 0.159 56 -0.261
#> 4 0.236 age hgt hgt_z nl_1997_hgt_female_nl 0.236 59.5 0.163
#> 5 0.485 age hgt hgt_z nl_1997_hgt_female_nl 0.485 65.5 -0.259
#> 6 0.753 age hgt hgt_z nl_1997_hgt_female_nl 0.753 71.5 0.131
#> 7 1.02 age hgt hgt_z nl_1997_hgt_female_nl 1.02 75 -0.18
#> 8 1.25 age hgt hgt_z nl_1997_hgt_female_nl 1.25 80 0.421
#> 9 1.54 age hgt hgt_z nl_1997_hgt_female_nl 1.54 84 0.527
#> 10 2.04 age hgt hgt_z nl_1997_hgt_female_nl 2.04 90 0.67
#> # ℹ 48 more rows
#>
# same, but using a built-in schema file
schema1 <- system.file("schemas/bds_v1.0.json", package = "bdsreader")
u <- read_bds(data1, schema = schema1)
identical(t, u)
#> [1] TRUE