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

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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/