Sliding Windows for a ts_inter object
patchify_df.RdThis creates sliding windows of intervention and community composition
features for all. subjects in a ts_inter object. It returns a list giving
the "patchified" data. The first component, x, gives the microbiome and
intervention features immediately preceding the values in the second
component, y. This is constructed by running patchify_single_df over all
subjects in the dataset.
Arguments
- ts_inter
An object of class
ts_interover which to generate sliding windows.- p
The number of time lags to. use in the sliding window for the microbiome features.
- q
The number of time lags to use in the sliding window for interventions.
Examples
data(sim_ts)
result <- patchify_df(sim_ts)
lapply(result, head)
#> $x
#> taxon1_lag2 taxon2_lag2 taxon3_lag2 taxon4_lag2 taxon5_lag2 taxon6_lag2
#> [1,] 5 23 17 30 3 115
#> [2,] 7 43 40 12 2 20
#> [3,] 5 19 42 15 3 23
#> [4,] 3 3 25 7 13 1
#> [5,] 6 7 8 23 7 15
#> [6,] 2 14 13 13 4 2
#> taxon7_lag2 taxon8_lag2 taxon9_lag2 taxon10_lag2 taxon11_lag2 taxon12_lag2
#> [1,] 8 2 14 42 21 7
#> [2,] 42 3 8 9 5 53
#> [3,] 22 12 4 13 8 47
#> [4,] 6 19 14 15 21 22
#> [5,] 27 13 15 33 11 14
#> [6,] 9 14 22 19 13 14
#> taxon13_lag2 taxon14_lag2 taxon15_lag2 taxon16_lag2 taxon17_lag2
#> [1,] 12 2 10 12 4
#> [2,] 8 4 18 6 7
#> [3,] 2 23 18 2 7
#> [4,] 21 5 18 8 6
#> [5,] 12 7 13 1 11
#> [6,] 4 6 7 3 11
#> taxon18_lag2 taxon19_lag2 taxon20_lag2 taxon21_lag2 taxon22_lag2
#> [1,] 20 5 1 3 0
#> [2,] 5 2 27 3 2
#> [3,] 9 9 21 5 48
#> [4,] 4 10 0 4 13
#> [5,] 7 9 5 8 1
#> [6,] 5 24 7 1 6
#> taxon23_lag2 taxon24_lag2 taxon25_lag2 taxon26_lag2 taxon27_lag2
#> [1,] 22 1 5 35 10
#> [2,] 1 7 8 5 2
#> [3,] 3 29 2 12 8
#> [4,] 21 1 7 7 6
#> [5,] 3 4 4 4 22
#> [6,] 12 6 21 8 5
#> taxon28_lag2 taxon29_lag2 taxon30_lag2 taxon31_lag2 taxon32_lag2
#> [1,] 7 29 3 14 5
#> [2,] 13 4 5 1 0
#> [3,] 6 4 14 7 1
#> [4,] 5 0 5 4 8
#> [5,] 12 0 6 14 0
#> [6,] 10 10 6 2 2
#> taxon33_lag2 taxon34_lag2 taxon35_lag2 taxon36_lag2 taxon37_lag2
#> [1,] 6 3 7 10 48
#> [2,] 5 2 13 1 14
#> [3,] 2 8 5 9 8
#> [4,] 10 10 1 11 4
#> [5,] 2 13 14 17 14
#> [6,] 7 15 4 5 21
#> taxon38_lag2 taxon39_lag2 taxon40_lag2 taxon41_lag2 taxon42_lag2
#> [1,] 6 8 10 6 19
#> [2,] 9 4 11 8 56
#> [3,] 7 13 4 4 5
#> [4,] 7 1 7 8 7
#> [5,] 4 2 7 10 16
#> [6,] 4 7 6 2 8
#> taxon43_lag2 taxon44_lag2 taxon45_lag2 taxon46_lag2 taxon47_lag2
#> [1,] 18 13 44 23 2
#> [2,] 30 22 13 79 1
#> [3,] 26 36 10 11 2
#> [4,] 2 9 7 6 7
#> [5,] 10 32 21 6 5
#> [6,] 3 0 8 30 9
#> taxon48_lag2 taxon49_lag2 taxon50_lag2 taxon51_lag2 taxon52_lag2
#> [1,] 4 8 17 0 4
#> [2,] 7 9 6 0 2
#> [3,] 23 3 16 12 1
#> [4,] 24 17 19 11 3
#> [5,] 8 12 19 4 19
#> [6,] 14 17 22 5 2
#> taxon53_lag2 taxon54_lag2 taxon55_lag2 taxon56_lag2 taxon57_lag2
#> [1,] 15 78 17 0 1
#> [2,] 12 10 4 3 25
#> [3,] 19 19 8 3 14
#> [4,] 10 32 8 5 17
#> [5,] 5 26 16 17 8
#> [6,] 13 10 3 9 6
#> taxon58_lag2 taxon59_lag2 taxon60_lag2 taxon61_lag2 taxon62_lag2
#> [1,] 12 5 14 14 21
#> [2,] 8 3 21 56 10
#> [3,] 6 1 5 40 12
#> [4,] 8 14 9 17 12
#> [5,] 3 17 26 9 7
#> [6,] 8 9 10 52 4
#> taxon63_lag2 taxon64_lag2 taxon65_lag2 taxon66_lag2 taxon67_lag2
#> [1,] 26 28 13 16 2
#> [2,] 2 15 7 29 1
#> [3,] 25 21 10 32 9
#> [4,] 2 13 9 11 21
#> [5,] 4 25 11 6 4
#> [6,] 6 29 4 8 6
#> taxon68_lag2 taxon69_lag2 taxon70_lag2 taxon71_lag2 taxon72_lag2
#> [1,] 12 13 29 6 13
#> [2,] 0 8 40 5 1
#> [3,] 31 3 31 7 1
#> [4,] 9 3 10 4 5
#> [5,] 11 2 7 31 13
#> [6,] 15 26 13 6 4
#> taxon73_lag2 taxon74_lag2 taxon75_lag2 taxon76_lag2 taxon77_lag2
#> [1,] 5 17 6 4 7
#> [2,] 7 22 1 0 2
#> [3,] 13 12 6 5 18
#> [4,] 16 2 3 4 16
#> [5,] 18 16 5 21 2
#> [6,] 17 9 8 0 5
#> taxon78_lag2 taxon79_lag2 taxon80_lag2 taxon81_lag2 taxon82_lag2
#> [1,] 2 6 14 5 16
#> [2,] 6 0 4 7 4
#> [3,] 13 3 7 19 3
#> [4,] 3 8 0 12 5
#> [5,] 22 14 11 9 11
#> [6,] 7 11 15 4 5
#> taxon83_lag2 taxon84_lag2 taxon85_lag2 taxon86_lag2 taxon87_lag2
#> [1,] 5 5 10 18 7
#> [2,] 12 3 6 6 15
#> [3,] 36 10 7 24 1
#> [4,] 16 12 2 6 11
#> [5,] 9 10 0 12 6
#> [6,] 13 28 0 18 9
#> taxon88_lag2 taxon89_lag2 taxon90_lag2 taxon91_lag2 taxon92_lag2
#> [1,] 37 6 26 21 7
#> [2,] 10 7 12 18 13
#> [3,] 13 14 5 3 9
#> [4,] 5 3 1 13 8
#> [5,] 12 8 17 4 25
#> [6,] 11 4 6 6 20
#> taxon93_lag2 taxon94_lag2 taxon95_lag2 taxon96_lag2 taxon97_lag2
#> [1,] 10 10 3 58 10
#> [2,] 4 23 32 23 41
#> [3,] 0 9 13 15 8
#> [4,] 31 6 31 20 16
#> [5,] 14 8 9 4 15
#> [6,] 4 6 31 9 13
#> taxon98_lag2 taxon99_lag2 taxon100_lag2 taxon1_lag1 taxon2_lag1
#> [1,] 10 12 5 7 43
#> [2,] 17 4 0 5 19
#> [3,] 14 9 9 3 3
#> [4,] 0 10 1 6 7
#> [5,] 12 7 16 2 14
#> [6,] 1 18 8 7 2
#> taxon3_lag1 taxon4_lag1 taxon5_lag1 taxon6_lag1 taxon7_lag1 taxon8_lag1
#> [1,] 40 12 2 20 42 3
#> [2,] 42 15 3 23 22 12
#> [3,] 25 7 13 1 6 19
#> [4,] 8 23 7 15 27 13
#> [5,] 13 13 4 2 9 14
#> [6,] 29 13 6 11 14 13
#> taxon9_lag1 taxon10_lag1 taxon11_lag1 taxon12_lag1 taxon13_lag1
#> [1,] 8 9 5 53 8
#> [2,] 4 13 8 47 2
#> [3,] 14 15 21 22 21
#> [4,] 15 33 11 14 12
#> [5,] 22 19 13 14 4
#> [6,] 11 2 15 1 2
#> taxon14_lag1 taxon15_lag1 taxon16_lag1 taxon17_lag1 taxon18_lag1
#> [1,] 4 18 6 7 5
#> [2,] 23 18 2 7 9
#> [3,] 5 18 8 6 4
#> [4,] 7 13 1 11 7
#> [5,] 6 7 3 11 5
#> [6,] 14 2 19 3 3
#> taxon19_lag1 taxon20_lag1 taxon21_lag1 taxon22_lag1 taxon23_lag1
#> [1,] 2 27 3 2 1
#> [2,] 9 21 5 48 3
#> [3,] 10 0 4 13 21
#> [4,] 9 5 8 1 3
#> [5,] 24 7 1 6 12
#> [6,] 7 23 29 36 13
#> taxon24_lag1 taxon25_lag1 taxon26_lag1 taxon27_lag1 taxon28_lag1
#> [1,] 7 8 5 2 13
#> [2,] 29 2 12 8 6
#> [3,] 1 7 7 6 5
#> [4,] 4 4 4 22 12
#> [5,] 6 21 8 5 10
#> [6,] 5 21 14 14 4
#> taxon29_lag1 taxon30_lag1 taxon31_lag1 taxon32_lag1 taxon33_lag1
#> [1,] 4 5 1 0 5
#> [2,] 4 14 7 1 2
#> [3,] 0 5 4 8 10
#> [4,] 0 6 14 0 2
#> [5,] 10 6 2 2 7
#> [6,] 15 8 0 15 8
#> taxon34_lag1 taxon35_lag1 taxon36_lag1 taxon37_lag1 taxon38_lag1
#> [1,] 2 13 1 14 9
#> [2,] 8 5 9 8 7
#> [3,] 10 1 11 4 7
#> [4,] 13 14 17 14 4
#> [5,] 15 4 5 21 4
#> [6,] 9 3 7 8 9
#> taxon39_lag1 taxon40_lag1 taxon41_lag1 taxon42_lag1 taxon43_lag1
#> [1,] 4 11 8 56 30
#> [2,] 13 4 4 5 26
#> [3,] 1 7 8 7 2
#> [4,] 2 7 10 16 10
#> [5,] 7 6 2 8 3
#> [6,] 4 10 3 9 16
#> taxon44_lag1 taxon45_lag1 taxon46_lag1 taxon47_lag1 taxon48_lag1
#> [1,] 22 13 79 1 7
#> [2,] 36 10 11 2 23
#> [3,] 9 7 6 7 24
#> [4,] 32 21 6 5 8
#> [5,] 0 8 30 9 14
#> [6,] 12 7 3 4 6
#> taxon49_lag1 taxon50_lag1 taxon51_lag1 taxon52_lag1 taxon53_lag1
#> [1,] 9 6 0 2 12
#> [2,] 3 16 12 1 19
#> [3,] 17 19 11 3 10
#> [4,] 12 19 4 19 5
#> [5,] 17 22 5 2 13
#> [6,] 18 4 6 2 7
#> taxon54_lag1 taxon55_lag1 taxon56_lag1 taxon57_lag1 taxon58_lag1
#> [1,] 10 4 3 25 8
#> [2,] 19 8 3 14 6
#> [3,] 32 8 5 17 8
#> [4,] 26 16 17 8 3
#> [5,] 10 3 9 6 8
#> [6,] 12 9 3 0 3
#> taxon59_lag1 taxon60_lag1 taxon61_lag1 taxon62_lag1 taxon63_lag1
#> [1,] 3 21 56 10 2
#> [2,] 1 5 40 12 25
#> [3,] 14 9 17 12 2
#> [4,] 17 26 9 7 4
#> [5,] 9 10 52 4 6
#> [6,] 8 13 0 5 6
#> taxon64_lag1 taxon65_lag1 taxon66_lag1 taxon67_lag1 taxon68_lag1
#> [1,] 15 7 29 1 0
#> [2,] 21 10 32 9 31
#> [3,] 13 9 11 21 9
#> [4,] 25 11 6 4 11
#> [5,] 29 4 8 6 15
#> [6,] 8 10 3 6 9
#> taxon69_lag1 taxon70_lag1 taxon71_lag1 taxon72_lag1 taxon73_lag1
#> [1,] 8 40 5 1 7
#> [2,] 3 31 7 1 13
#> [3,] 3 10 4 5 16
#> [4,] 2 7 31 13 18
#> [5,] 26 13 6 4 17
#> [6,] 14 7 4 7 3
#> taxon74_lag1 taxon75_lag1 taxon76_lag1 taxon77_lag1 taxon78_lag1
#> [1,] 22 1 0 2 6
#> [2,] 12 6 5 18 13
#> [3,] 2 3 4 16 3
#> [4,] 16 5 21 2 22
#> [5,] 9 8 0 5 7
#> [6,] 30 25 29 4 6
#> taxon79_lag1 taxon80_lag1 taxon81_lag1 taxon82_lag1 taxon83_lag1
#> [1,] 0 4 7 4 12
#> [2,] 3 7 19 3 36
#> [3,] 8 0 12 5 16
#> [4,] 14 11 9 11 9
#> [5,] 11 15 4 5 13
#> [6,] 14 14 12 6 28
#> taxon84_lag1 taxon85_lag1 taxon86_lag1 taxon87_lag1 taxon88_lag1
#> [1,] 3 6 6 15 10
#> [2,] 10 7 24 1 13
#> [3,] 12 2 6 11 5
#> [4,] 10 0 12 6 12
#> [5,] 28 0 18 9 11
#> [6,] 6 7 7 16 13
#> taxon89_lag1 taxon90_lag1 taxon91_lag1 taxon92_lag1 taxon93_lag1
#> [1,] 7 12 18 13 4
#> [2,] 14 5 3 9 0
#> [3,] 3 1 13 8 31
#> [4,] 8 17 4 25 14
#> [5,] 4 6 6 20 4
#> [6,] 26 12 2 10 15
#> taxon94_lag1 taxon95_lag1 taxon96_lag1 taxon97_lag1 taxon98_lag1
#> [1,] 23 32 23 41 17
#> [2,] 9 13 15 8 14
#> [3,] 6 31 20 16 0
#> [4,] 8 9 4 15 12
#> [5,] 6 31 9 13 1
#> [6,] 3 15 17 4 0
#> taxon99_lag1 taxon100_lag1 intervention1_lag2 intervention1_lag1
#> [1,] 4 0 0 0
#> [2,] 9 9 0 0
#> [3,] 10 1 0 0
#> [4,] 7 16 0 0
#> [5,] 18 8 0 0
#> [6,] 11 11 0 0
#> intervention1_lag0 V1
#> [1,] 0 0.3295958
#> [2,] 0 0.3295958
#> [3,] 0 0.3295958
#> [4,] 0 0.3295958
#> [5,] 0 0.3295958
#> [6,] 0 0.3295958
#>
#> $y
#> # A tibble: 6 × 100
#> taxon1 taxon2 taxon3 taxon4 taxon5 taxon6 taxon7 taxon8 taxon9 taxon10 taxon11
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 3 3 25 7 13 1 6 19 14 15 21
#> 2 6 7 8 23 7 15 27 13 15 33 11
#> 3 2 14 13 13 4 2 9 14 22 19 13
#> 4 7 2 29 13 6 11 14 13 11 2 15
#> 5 11 18 10 7 12 22 16 9 5 19 3
#> 6 6 6 5 8 15 35 2 11 24 24 4
#> # ℹ 89 more variables: taxon12 <dbl>, taxon13 <dbl>, taxon14 <dbl>,
#> # taxon15 <dbl>, taxon16 <dbl>, taxon17 <dbl>, taxon18 <dbl>, taxon19 <dbl>,
#> # taxon20 <dbl>, taxon21 <dbl>, taxon22 <dbl>, taxon23 <dbl>, taxon24 <dbl>,
#> # taxon25 <dbl>, taxon26 <dbl>, taxon27 <dbl>, taxon28 <dbl>, taxon29 <dbl>,
#> # taxon30 <dbl>, taxon31 <dbl>, taxon32 <dbl>, taxon33 <dbl>, taxon34 <dbl>,
#> # taxon35 <dbl>, taxon36 <dbl>, taxon37 <dbl>, taxon38 <dbl>, taxon39 <dbl>,
#> # taxon40 <dbl>, taxon41 <dbl>, taxon42 <dbl>, taxon43 <dbl>, …
#>
#> $interactions
#> NULL
#>