Counterfactual Partial Dependence Effects
pd_effects.RdOur selection algorithm, select_taxa depends on estimates for
counterfactual partial dependence effects across all taxa and time lags. This
supports estimation of these effects for a single random data split pair.
Arguments
- fit
An object of class
mbtransfer_model, as generated using thembtransferfunction. This includes trained boosting models for every taxon, stored within the@parametersslot.- ts
An object of class
ts_intercontaining the time-varying microbiome community, environmental interventions, and static host features data. The columns for each element of thevaluesmatrix are expected to be consecutive timepoints in an changing community.ts_from_dfs()is a helper to create these objects fromdata.frameswith the relevant information.- w0
One of the counterfactuals with which to compute partial dependence profiles. See
stepsorpulsesfor helpers in generating these counterfactuals. The procedure concatenates these counterfactuals to the end of the series and computes the difference in the forecasts.- w1
One of the counterfactuals with which to compute partial dependence profiles. See
stepsorpulsesfor helpers in generating these counterfactuals. The procedure concatenates these counterfactuals to the end of the series and computes the difference in the forecasts.
Examples
data(sim_ts)
w0 <- cbind(sim_ts[[1]]@interventions, matrix(0, nrow = 1, ncol = 3))
w1 <- cbind(sim_ts[[1]]@interventions, matrix(1, nrow = 1, ncol = 3))
fit <- mbtransfer(sim_ts, 1, 1, nrounds = 10)
pd_effects(fit, sim_ts, w0, w1)
#> S8_S1_T1 S8_S1_T2 S8_S1_T3 S8_S1_T4 S8_S1_T5 S8_S1_T6 S8_S1_T7 S8_S1_T8
#> tax1 0 0 0 0 0 0 0 0
#> tax2 0 0 0 0 0 0 0 0
#> tax3 0 0 0 0 0 0 0 0
#> tax4 0 0 0 0 0 0 0 0
#> tax5 0 0 0 0 0 0 0 0
#> tax6 0 0 0 0 0 0 0 0
#> tax7 0 0 0 0 0 0 0 0
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#> tax11 0 0 0 0 0 0 0 0
#> tax12 0 0 0 0 0 0 0 0
#> tax13 0 0 0 0 0 0 0 0
#> tax14 0 0 0 0 0 0 0 0
#> tax15 0 0 0 0 0 0 0 0
#> tax16 0 0 0 0 0 0 0 0
#> tax17 0 0 0 0 0 0 0 0
#> tax18 0 0 0 0 0 0 0 0
#> tax19 0 0 0 0 0 0 0 0
#> tax20 0 0 0 0 0 0 0 0
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#> tax22 0 0 0 0 0 0 0 0
#> tax23 0 0 0 0 0 0 0 0
#> tax24 0 0 0 0 0 0 0 0
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#> tax27 0 0 0 0 0 0 0 0
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#> tax98 0 0 0 0 0 0 0 0
#> tax99 0 0 0 0 0 0 0 0
#> tax100 0 0 0 0 0 0 0 0
#> S8_S1_T9 S8_S1_T10 S8_S1_T11 S8_S1_T12 S8_S1_T13 S8_S1_T14 S8_S1_T15
#> tax1 0 0 0 0 0 0 0
#> tax2 0 0 0 0 0 0 0
#> tax3 0 0 0 0 0 0 0
#> tax4 0 0 0 0 0 0 0
#> tax5 0 0 0 0 0 0 0
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#> tax99 0 0 0 0 0 0 0
#> tax100 0 0 0 0 0 0 0
#> S8_S1_T16 S8_S1_T17 S8_S1_T18 S8_S1_T19 S8_S1_T20 S8_S1_T21 S8_S1_T22
#> tax1 0 0 0 0 0 0 0
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#> tax99 0 0 0 0 0 0 0
#> tax100 0 0 0 0 0 0 0
#> S8_S1_T23 S8_S1_T24 S8_S1_T25 S8_S1_T26 S8_S1_T27 S8_
#> tax1 0 0 0 0 0 -0.6328802222
#> tax2 0 0 0 0 0 -8.8437741257
#> tax3 0 0 0 0 0 0.4410572052
#> tax4 0 0 0 0 0 0.0174821445
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#> tax100 0 0 0 0 0 0.0845527649
#> S8_ S8_
#> tax1 -0.841968565 -0.8615373997
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#> tax3 0.535736538 0.5505777654
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#> tax92 0.255244800 0.2551714806
#> tax93 -0.097639220 -0.0872822489
#> tax94 0.241217755 0.2475347178
#> tax95 -0.178711517 -0.1803448995
#> tax96 -0.036196606 -0.0305729821
#> tax97 0.359314657 0.3695857979
#> tax98 0.075919185 0.0639193058
#> tax99 0.182476418 0.1737608001
#> tax100 0.145250786 0.1461371921