cm_code.overlap function

Find Co-occurrence Between Codes

Combine co-occurrences of codes into a new code.

cm_code.overlap(x2long.obj, overlap.code.list, rm.var = NULL)

Arguments

• x2long.obj: An object from cm_range2long, cm_time2long or cm_df2long.
• overlap.code.list: A list of named character vectors of at least two code column names to aggregate co-occurrences.
• rm.var: Name of the repeated measures column.

Returns

Returns a dataframe with co-occurrences of supplied overlapping codes added.

Note

The code column must be named code and your start and end columns must be named "start" and "end".

Examples

## Not run:

foo <- list(
    AA = qcv(terms="1:10"),
    BB = qcv(terms="1:2, 3:10, 19"),
    CC = qcv(terms="1:3, 5:6")
)

foo2  <- list(
    AA = qcv(terms="4:8"),
    BB = qcv(terms="1:4, 10:12"),
    CC = qcv(terms="1, 11, 15:20"),
    DD = qcv(terms="")
)

(x <- cm_range2long(foo))
(z <- cm_range2long(foo, foo2, v.name="time"))
cm_code.overlap(x, list(AB=qcv(AA, BB)))
cm_code.overlap(x, list(ALL=qcv(AA, BB, CC)))
combines <- list(AB=qcv(AA, BB), ABC=qcv(AA, BB, CC))
(a <- cm_code.overlap(z, combines, "time"))
plot(a)

#WITH cm_time2long
x <- list(
    transcript_time_span = qcv(00:00 - 1:12:00),
    A = qcv(terms = "2.40:3.00, 5.01, 6.02:7.00, 9.00"),
    B = qcv(terms = "2.40, 3.01:3.02, 5.01, 6.02:7.00, 9.00, 
        1.12.00:1.19.01"),
    C = qcv(terms = "2.40:3.00, 5.01, 6.02:7.00, 9.00, 17.01")
)

y <- list(
    transcript_time_span = qcv(00:00 - 1:12:00),
    A = qcv(terms = "2.40:3.00, 5.01, 6.02:7.00, 9.00"),
    B = qcv(terms = "2.40, 3.01:3.02, 5.01, 6.02:7.00, 9.00, 
        1.12.00:1.19.01"),
    C = qcv(terms = "2.40:3.00, 5.01, 6.02:7.00, 9.00, 17.01")
)

dat <- cm_time2long(x, y)
head(dat, 10)
out <- cm_code.overlap(dat, list(P=qcv(A, B), Q=qcv(B, C), R=qcv(A, B, C)), 
    rm.var="variable")
head(out, 10)
## End(Not run)

See Also

cm_range2long, cm_time2long, cm_df2long, cm_code.combine, cm_code.transform