Description Usage Arguments Details Value Data coding Column name rules Names examples tidy data column removal See Also Examples
blink
summarizes your data tailored to the need of
ophthalmic research: It looks for VA and IOP columns and summarises those
with common statistics. In order to make it work, it requires specific
column naming - please see section "column names" and "data coding".
For more details how blink works, see vignette("eye")
1 |
x |
data frame |
va_to |
to which VA notation (passed to |
va_cols |
if specified, overruling automatic VA columns selection. tidyselection supported |
iop_cols |
if specified, overruling automatic IOP columns selection. tidyselection supported |
fct_level |
Remove columns for Summarizing when all unique values
fall into range. character or numeric vector, default |
blink
is basically a wrapper around myop, eyes and reveal:
Duplicate rows are always removed
Column names are prepared for myopization (see myop)
VA will always be converted to logmar
object of class blink
and list
. Class blink contains the
myopized data, count of patients and eyes,
and summaries for visual acuities and intraocular pressure.
Only common codes supported:
eyes: "r", "re", "od", "right" - or numeric coding r:l = 0:1 or 1:2
Visual acuity: "VA", "BCVA", "Acuity"
Intraocular pressure: "IOP", "GAT", "NCT", "pressure"
No spaces!
Do not use numeric coding for eyes in column names
Separate eye and VA and IOP codes with underscores ("bcva_l_preop", "VA_r", "left_va", "IOP_re")
Avoid separate VA or IOP codes if this is not actually containing VA/ IOP data (e.g. "stableVA" instead of "stable_va", ChangeIOP instead of "change_IOP")
Keep names short
Don't use underscores when you don't have to. Consider each section divided by an underscore as a relevant characteristic of your variable. ("preop" instead of "pre_op", "VA" instead of "VA_ETDRS_Letters")
Use common codes for your patient column (see eyes, section Guessing) (e.g., "pat", "patient" or "ID", ideally both: "patientID" or "patID")
Don't be too creative with your names!
Good names:
-c("patid", "surgery_right", "iop_r_preop", "va_r_preop", "iop_r", "iop_l")
OK names
-c("Id", "Eye", "BaselineAge", "VA_ETDRS_Letters", "InjectionNumber")
:
Names are long and there are two unnecessary underscore in the VA column.
Better just "VA"
-c("id", "r", "l")
: All names are commonly used (good!),
but which dimension of "r"/"l" are we exactly looking at?
Bad names (eye
will fail)
c("id", "iopr", "iopl", "VAr", "VAl")
:
eye
won't be able to recognize IOP and VA columns
c("id", "iop_r", "iop_l", "stable_iop_r", "stable_iop_l")
:
eye
may wrongly identify the (probably logical) columns "stable_iop"
as columns containing IOP data. Better maybe: "stableIOP_l"
c("person", "goldmann", "vision")
: eye
will not recognize that at all
blink and myop work more reliably with clean data (any package will, really!). clean data.
Done with remCols: Removes columns that only contain values defined in fct_levels or logicals from selected columns (currently for both automatically and manually selected columns). fct_levels are removed because they are likely categorical codes.
How to rename your columns (two threads on stackoverflow.com):
1 2 3 4 5 6 7 8 9 10 | library(eyedata)
blink(amd2)
messy_df <- data.frame( id = letters[1:3],
iop_r_preop = sample(21:23), iop_r_postop = sample(11:13),
iop_l_postop = sample(11:13), iop_l_preop = sample(31:33),
va_r_preop = sample(41:43), va_l_preop = sample(41:43),
va_r_postop = sample(51:53), va_l_postop = sample(45:47)
)
blink(messy_df)
|
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