knitr::opts_chunk$set(comment = '.')
. Error in get(paste0(generic, ".", class), envir = get_method_env()) :
. object 'type_sum.accel' not found
We’ll use the examples provided in the package
data <- ys_help$data()
spec <- ys_help$spec()
The data
as_tibble(data)
.
[38;5;246m# A tibble: 4,360 × 29
[39m
. C NUM ID SUBJ TIME SEQ CMT EVID AMT DV AGE WT CRCL
.
[3m
[38;5;246m<lgl>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
.
[38;5;250m 1
[39m
[31mNA
[39m 1 1 1 0 0 1 1 5 0 28.0 55.2 114.
.
[38;5;250m 2
[39m
[31mNA
[39m 2 1 1 0.61 1 2 0
[31mNA
[39m 61.0 28.0 55.2 114.
.
[38;5;250m 3
[39m
[31mNA
[39m 3 1 1 1.15 1 2 0
[31mNA
[39m 91.0 28.0 55.2 114.
.
[38;5;250m 4
[39m
[31mNA
[39m 4 1 1 1.73 1 2 0
[31mNA
[39m 122. 28.0 55.2 114.
.
[38;5;250m 5
[39m
[31mNA
[39m 5 1 1 2.15 1 2 0
[31mNA
[39m 126. 28.0 55.2 114.
.
[38;5;250m 6
[39m
[31mNA
[39m 6 1 1 3.19 1 2 0
[31mNA
[39m 84.7 28.0 55.2 114.
.
[38;5;250m 7
[39m
[31mNA
[39m 7 1 1 4.21 1 2 0
[31mNA
[39m 62.1 28.0 55.2 114.
.
[38;5;250m 8
[39m
[31mNA
[39m 8 1 1 5.09 1 2 0
[31mNA
[39m 49.1 28.0 55.2 114.
.
[38;5;250m 9
[39m
[31mNA
[39m 9 1 1 6.22 1 2 0
[31mNA
[39m 64.2 28.0 55.2 114.
.
[38;5;250m10
[39m
[31mNA
[39m 10 1 1 8.09 1 2 0
[31mNA
[39m 59.6 28.0 55.2 114.
.
[38;5;246m# ℹ 4,350 more rows
[39m
.
[38;5;246m# ℹ 16 more variables: ALB <dbl>, BMI <dbl>, AAG <dbl>, SCR <dbl>, AST <dbl>,
[39m
.
[38;5;246m# ALT <dbl>, HT <dbl>, CP <int>, TAFD <dbl>, TAD <dbl>, LDOS <int>,
[39m
.
[38;5;246m# MDV <int>, BLQ <int>, PHASE <int>, STUDY <int>, RF <chr>
[39m
The spec
spec
. name info unit short source
. C cd- . comment character ysdb_internal
. NUM --- . record number ysdb_internal
. ID --- . subject identifier ysdb_internal
. SUBJ c-- . subject identifier ysdb_internal
. TIME --- hour TIME look
. SEQ -d- . SEQ .
. CMT --- . compartment number ysdb_internal
. EVID -d- . event ID ysdb_internal
. AMT --- mg dose amount ysdb_internal
. DV --- micrograms/L dependent variable ysdb_internal
. AGE --- years age ysdb_internal
. WT --- kg weight ysdb_internal
. CRCL --- ml/min CRCL .
. ALB --- g/dL albumin ysdb_internal
. BMI --- m2/kg BMI ysdb_internal
. AAG --- mg/dL alpha-1-acid glycoprotein .
. SCR --- mg/dL serum creatinine .
. AST --- . aspartate aminotransferase .
. ALT --- . alanine aminotransferase .
. HT --- cm height ysdb_internal
. CP -d- . Child-Pugh score look
. TAFD --- hours time after first dose .
. TAD --- hours time after dose .
. LDOS --- mg last dose amount .
. MDV -d- . MDV ysdb_internal
. BLQ -d- . below limit of quantification .
. PHASE --- . study phase indicator .
. STUDY -d- . study number .
. RF cd- . renal function stage .
data <- ys_add_labels(data,spec)
It isn’t obvious that anything was done here
as_tibble(data)
.
[38;5;246m# A tibble: 4,360 × 29
[39m
. C NUM ID SUBJ TIME SEQ CMT EVID AMT DV AGE WT CRCL
.
[3m
[38;5;246m<lgl>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<int>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
.
[38;5;250m 1
[39m
[31mNA
[39m 1 1 1 0 0 1 1 5 0 28.0 55.2 114.
.
[38;5;250m 2
[39m
[31mNA
[39m 2 1 1 0.61 1 2 0
[31mNA
[39m 61.0 28.0 55.2 114.
.
[38;5;250m 3
[39m
[31mNA
[39m 3 1 1 1.15 1 2 0
[31mNA
[39m 91.0 28.0 55.2 114.
.
[38;5;250m 4
[39m
[31mNA
[39m 4 1 1 1.73 1 2 0
[31mNA
[39m 122. 28.0 55.2 114.
.
[38;5;250m 5
[39m
[31mNA
[39m 5 1 1 2.15 1 2 0
[31mNA
[39m 126. 28.0 55.2 114.
.
[38;5;250m 6
[39m
[31mNA
[39m 6 1 1 3.19 1 2 0
[31mNA
[39m 84.7 28.0 55.2 114.
.
[38;5;250m 7
[39m
[31mNA
[39m 7 1 1 4.21 1 2 0
[31mNA
[39m 62.1 28.0 55.2 114.
.
[38;5;250m 8
[39m
[31mNA
[39m 8 1 1 5.09 1 2 0
[31mNA
[39m 49.1 28.0 55.2 114.
.
[38;5;250m 9
[39m
[31mNA
[39m 9 1 1 6.22 1 2 0
[31mNA
[39m 64.2 28.0 55.2 114.
.
[38;5;250m10
[39m
[31mNA
[39m 10 1 1 8.09 1 2 0
[31mNA
[39m 59.6 28.0 55.2 114.
.
[38;5;246m# ℹ 4,350 more rows
[39m
.
[38;5;246m# ℹ 16 more variables: ALB <dbl>, BMI <dbl>, AAG <dbl>, SCR <dbl>, AST <dbl>,
[39m
.
[38;5;246m# ALT <dbl>, HT <dbl>, CP <int>, TAFD <dbl>, TAD <dbl>, LDOS <int>,
[39m
.
[38;5;246m# MDV <int>, BLQ <int>, PHASE <int>, STUDY <int>, RF <chr>
[39m
How can you tell that the labels were added?
labs <- map(data, attr, "label")
labs[1:5]
. $C
. [1] "comment character"
.
. $NUM
. [1] "record number"
.
. $ID
. [1] "subject identifier"
.
. $SUBJ
. [1] "subject identifier"
.
. $TIME
. [1] "time after first dose"
Or do this
str(data)
Ideally, we’d like to be writing in a label
entry for
every column in the data set. You can set the
ys.require.label
option to TRUE
to require
this when loading the spec (an error will be generated).
But yspec has a function called ys_get_label
that will
form a label for you. Here are the rules:
label
exists for a column, it will be usedlong
is found and it is
<=
40 characters, it be usedshort
will be used; reminder that
short
defaults to the column name (col
)
tooLet’s look at some examples:
ys_get_label(spec)[1:3]
. $C
. [1] "comment character"
.
. $NUM
. [1] "record number"
.
. $ID
. [1] "subject identifier"
ys_get_label(spec$NUM)
. [1] "record number"
spec$NUM$label
. NULL
spec$C$label
. NULL
Just as an example, we can add a custom labeling function. For example, I want the label to be the column name.
Set up a function that takes the column data as the first argument
label_fun <- function(x,...) x[["col"]]
Now, pass that function into ys_add_labels
data <- ys_add_labels(data, spec, fun = label_fun)
And check the output
map(data, attr, "label")[1:5]
. $C
. [1] "C"
.
. $NUM
. [1] "NUM"
.
. $ID
. [1] "ID"
.
. $SUBJ
. [1] "SUBJ"
.
. $TIME
. [1] "TIME"
Recall that the yspec object is just a list. We can always map across that list and grab the label field:s
map(spec, "label")[1:5]
. $C
. NULL
.
. $NUM
. NULL
.
. $ID
. NULL
.
. $SUBJ
. NULL
.
. $TIME
. [1] "time after first dose"