Peter Meissner
01 February 2016
Status: experimental, for own education only, possibly subject to change, still quite slow
Author: Peter Meißner
Licence: GPL-2
Description:
Merging time span data used for survival analysis via building new spans out of overlapping spans. For each context change (id1 data changes | id2 data changes) a new span is formed. Spans neither covered within dataset 1 nor 2 are put into separate spans.
Installation and start - development version
devtools::install_github("petermeissner/spanmatcher")
library(spanmatcher)
Usage
Loading the package and making up some data
library(spanmatcher)
df1 = data.frame(
id1 = letters[1:5],
from2 = as.Date(c(1,3,4,7,8), origin = "1970-01-01"),
to2 = as.Date(c(2,4,5,9,10), origin = "1970-01-01")
)
df2 = data.frame(
id2 = LETTERS[11:13],
from2 = as.Date(c(2,7,7), origin = "1970-01-01"),
to2 = as.Date(c(5,9,11), origin = "1970-01-01")
)
df1## id1 from2 to2
## 1 a 1970-01-02 1970-01-03
## 2 b 1970-01-04 1970-01-05
## 3 c 1970-01-05 1970-01-06
## 4 d 1970-01-08 1970-01-10
## 5 e 1970-01-09 1970-01-11
df2## id2 from2 to2
## 1 K 1970-01-03 1970-01-06
## 2 L 1970-01-08 1970-01-10
## 3 M 1970-01-08 1970-01-12
Mergin/joining the data
span_matcher(df1, df2)## span_id id1 id2 start end
## 1 1 a <NA> 1970-01-02 1970-01-02
## 2 2 a K 1970-01-03 1970-01-03
## 3 3 b K 1970-01-04 1970-01-05
## 4 4 c K 1970-01-05 1970-01-06
## 5 5 <NA> <NA> 1970-01-07 1970-01-07
## 6 6 d L 1970-01-08 1970-01-10
## 7 7 d M 1970-01-08 1970-01-10
## 8 8 e L 1970-01-09 1970-01-10
## 9 9 e M 1970-01-09 1970-01-11
## 10 10 <NA> M 1970-01-12 1970-01-12
Splitting spans
span_matcher(df1,df2, split_after = c(4))## span_id id1 id2 start end
## 1 1 a <NA> 1970-01-02 1970-01-02
## 2 2 a K 1970-01-03 1970-01-03
## 3 3 b K 1970-01-04 1970-01-05
## 4 4 c K 1970-01-05 1970-01-05
## 5 5 c K 1970-01-06 1970-01-06
## 6 6 <NA> <NA> 1970-01-07 1970-01-07
## 7 7 d L 1970-01-08 1970-01-10
## 8 8 d M 1970-01-08 1970-01-10
## 9 9 e L 1970-01-09 1970-01-10
## 10 10 e M 1970-01-09 1970-01-11
## 11 11 <NA> M 1970-01-12 1970-01-12
span_matcher(df1,df2, split_before = c(10))## span_id id1 id2 start end
## 1 1 a <NA> 1970-01-02 1970-01-02
## 2 2 a K 1970-01-03 1970-01-03
## 3 3 b K 1970-01-04 1970-01-05
## 4 4 c K 1970-01-05 1970-01-06
## 5 5 <NA> <NA> 1970-01-07 1970-01-07
## 6 6 d L 1970-01-08 1970-01-10
## 7 7 d M 1970-01-08 1970-01-10
## 8 8 e L 1970-01-09 1970-01-10
## 9 9 e M 1970-01-09 1970-01-10
## 10 10 e M 1970-01-11 1970-01-11
## 11 11 <NA> M 1970-01-12 1970-01-12
Contribution
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms:
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This Code of Conduct is adapted from the Contributor Covenant (http:contributor-covenant.org), version 1.0.0, available at http://contributor-covenant.org/version/1/0/0/