D_05_Figure_S12a.R

Libraries

Code

suppressPackageStartupMessages({
library(hstats)
library(here)
library(dplyr)
library(tidymodels)
library(ranger)
library(ggplot2)
library(ggthemes)
})

Interactions & their partial dependencies

Code

data <- 
  readRDS(
    here::here("Data/output/B_models/",
               "B_01_list_all_results_rf.rds"))

fit_1 <- 
  data$res[[1]] %>% 
  extract_fit_parsnip()

train <- 
  data$list_split_data[[1]]$train

pdp_J_interactions <- 
  list()

All 20 interactions from Jaccard:

Pairwise Interactions

1

Code

pdp_J_interactions[[1]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("mean_lnLac", "joincount_delta"),
    BY = "datasetID",
    grid_size = 100L
  ) %>%
  plot() +
  ggtitle("lac ~ jc ~ dataset")+
  ggthemes::theme_few()

2

Code

pdp_J_interactions[[2]] <- 
  partial_dep(
    object = fit_1,
  X = train,
  v = c("AOO", "joincount_delta"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("AOO ~ jc ~ dataset")+
  ggthemes::theme_few()

3

Code

pdp_J_interactions[[3]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("D_AOO_a", "AOO"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("D ~ AOO ~ dataset")+
  ggthemes::theme_few()

4

Code

pdp_J_interactions[[4]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("D_AOO_a", "joincount_delta"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("D ~ jc ~ dataset")+
  ggthemes::theme_few()

5

Code

pdp_J_interactions[[5]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("D_AOO_a", "circNorm"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("D ~ circ ~ dataset")+
  ggthemes::theme_few()

6

Code

pdp_J_interactions[[6]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("mean_lnLac", "AOO"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("lac ~ AOO ~ dataset")+
  ggthemes::theme_few()

7

Code

pdp_J_interactions[[7]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("AOO", "circNorm"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("AOO ~ circ ~ dataset")+
  ggthemes::theme_few()

8

Code

pdp_J_interactions[[8]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("joincount_delta", "circNorm"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("jc ~ circ ~ dataset")+
  ggthemes::theme_few()

9

Code

pdp_J_interactions[[9]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("mean_lnLac", "circNorm"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("lac ~ circ ~ dataset")+
  ggthemes::theme_few()

10

Code

pdp_J_interactions[[10]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("D_AOO_a", "mean_lnLac"),
  BY = "datasetID",
  grid_size = 100L
) %>%
  plot() +
  ggtitle("D ~ lac ~ dataset")+
  ggthemes::theme_few()

Threeway Interactions

11

Code

pdp_J_interactions[[11]] <- 
  partial_dep(
  object = fit_1,
  X = train,
  v = c("D_AOO_a", "AOO"),
  BY = "circNorm",
  grid_size = 100L,
  strategy = "uniform"
) %>%
  plot() +
  ggtitle("D ~ AOO ~ circ")+
  ggthemes::theme_few()

12

Code

pdp_J_interactions[[12]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("D_AOO_a", "mean_lnLac"),
    BY = "joincount_delta",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("D ~ lac ~ jc")+
  ggthemes::theme_few()

13

Code

pdp_J_interactions[[13]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("D_AOO_a", "AOO"),
    BY = "joincount_delta",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("D ~ AOO ~ jc")+
  ggthemes::theme_few()

14

Code

pdp_J_interactions[[14]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("mean_lnLac", "AOO"),
    BY = "joincount_delta",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("lac ~ AOO ~ jc")+
  ggthemes::theme_few()

15

Code

pdp_J_interactions[[15]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("AOO", "joincount_delta"),
    BY = "circNorm",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("AOO ~ jc ~ circ")+
  ggthemes::theme_few()

16

Code

pdp_J_interactions[[16]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("D_AOO_a", "mean_lnLac"),
    BY = "AOO",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("D ~ lac ~ AOO")+
  ggthemes::theme_few()

17

Code

pdp_J_interactions[[17]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("D_AOO_a", "joincount_delta"),
    BY = "circNorm",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("D ~ jc ~ circ")+
  ggthemes::theme_few()

18

Code

pdp_J_interactions[[18]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("mean_lnLac", "joincount_delta"),
    BY = "circNorm",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("lac ~ jc ~ circ")+
  ggthemes::theme_few()

19

Code

pdp_J_interactions[[19]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("mean_lnLac", "AOO"),
    BY = "circNorm",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("lac ~ AOO ~ circ")+
  ggthemes::theme_few()

20

Code

pdp_J_interactions[[20]] <- 
  partial_dep(
    object = fit_1,
    X = train,
    v = c("D_AOO_a", "mean_lnLac"),
    BY = "circNorm",
    grid_size = 100L,
    strategy = "uniform"
  ) %>%
  plot() +
  ggtitle("D ~ lac ~ circ")+
  ggthemes::theme_few()

Code

saveRDS(pdp_J_interactions, here("Data/output/temp/D_05_J_pdp_all.rds"))

Code

lapply(pdp_J_interactions, plot)

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