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topepo/discrim_animate.R

Created October 11, 2019 14:30
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animating a classification boundary
Raw
discrim_animate.R
library(tidymodels)
library(tune)
library(discrim)
library(klaR)
library(gganimate)
options(width = 100)
theme_set(theme_bw())
data("parabolic", package = "rsample")
set.seed(115)
data_split <- initial_split(parabolic, prop = 2 / 3)
data_tr <- training(data_split)
data_te <- testing(data_split)
pred_grid <-
expand.grid(X1 = seq(-5, 5, length = 100),
X2 = seq(-5, 5, length = 100))
p <-
ggplot(data_te, aes(x = X1, y = X2)) +
geom_point(aes(col = class), alpha = .3) +
coord_equal() +
theme(legend.position = "top")
rda_mod <-
discrim_regularized(frac_common_cov = tune(), frac_identity = tune()) %>%
set_engine("klaR")
set.seed(20014)
folds <- vfold_cv(data_tr, repeats = 5)
roc_values <- metric_set(roc_auc)
set.seed(57854)
rda_search <-
tune_Bayes(
class ~ X1 + X2,
model = rda_mod,
rs = folds,
initial = 10,
iter = 25,
perf = roc_values,
control = Bayes_control(verbose = TRUE, no_improve = Inf)
)
models <-
rda_search %>%
collect_metrics() %>%
distinct(.iter, frac_common_cov, frac_identity) %>%
dplyr::filter(.iter > 0) %>%
dplyr::select(-.iter)
for (i in 1:nrow(models)) {
new_res <-
rda_mod %>%
merge(models %>% slice(i)) %>%
pull(x) %>%
pluck(1) %>%
fit(class ~ X1 + X2, data = data_tr) %>%
predict(pred_grid, type = "prob") %>%
dplyr::select(.pred_Class1) %>%
bind_cols(pred_grid) %>%
mutate(model = i)
if (i == 1) {
grid_res <- new_res
} else {
grid_res <- bind_rows(grid_res, new_res)
}
}
contour_plot <-
ggplot(grid_res, aes(x = X1, y = X2)) +
geom_point(data = data_te, aes(col = class), alpha = .3) +
geom_contour(aes(z = .pred_Class1), breaks = .5, col = "black") +
transition_states(model) +
labs(title = 'Test set data and contours at search iteration {closest_state}') +
coord_equal() +
theme(legend.position = "top")
anim <- animate(contour_plot, width = 680, height = 680, res = 72*1.2)
anim_save("~/tmp/discrim.gif")
# > sessioninfo::session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.1 (2019-07-05)
# os macOS Mojave 10.14.6
# system x86_64, darwin15.6.0
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/New_York
# date 2019-10-11
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
# backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0)
# base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.0)
# bayesplot 1.7.0 2019-05-23 [1] CRAN (R 3.6.0)
# boot 1.3-22 2019-04-02 [1] CRAN (R 3.6.1)
# broom * 0.5.2 2019-04-07 [1] CRAN (R 3.6.0)
# callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.0)
# class 7.3-15 2019-01-01 [1] CRAN (R 3.6.1)
# classInt 0.4-1 2019-08-06 [1] CRAN (R 3.6.0)
# cli 1.9.9.9000 2019-10-04 [1] Github (r-lib/cli@ad6410a)
# codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.1)
# colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
# colourpicker 1.0 2017-09-27 [1] CRAN (R 3.6.0)
# combinat 0.0-8 2012-10-29 [1] CRAN (R 3.6.0)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
# crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.6.0)
# DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.0)
# dials * 0.0.3 2019-10-01 [1] CRAN (R 3.6.0)
# DiceDesign 1.8-1 2019-07-31 [1] CRAN (R 3.6.0)
# digest 0.6.21 2019-09-20 [1] CRAN (R 3.6.0)
# discrim * 0.0.1 2019-10-10 [1] local
# dplyr * 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
# DT 0.9 2019-09-17 [1] CRAN (R 3.6.0)
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# e1071 1.7-2 2019-06-05 [1] CRAN (R 3.6.0)
# fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
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# furrr 0.1.0 2018-05-16 [1] CRAN (R 3.6.0)
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# ggridges 0.5.1 2018-09-27 [1] CRAN (R 3.6.0)
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# globals 0.12.4 2018-10-11 [1] CRAN (R 3.6.0)
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# gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0)
# highr 0.8 2019-03-20 [1] CRAN (R 3.6.0)
# hms 0.5.1 2019-08-23 [1] CRAN (R 3.6.0)
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# htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.0)
# httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.0)
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# ipred 0.9-9 2019-04-28 [1] CRAN (R 3.6.0)
# iterators 1.0.12 2019-07-26 [1] CRAN (R 3.6.0)
# janeaustenr 0.1.5 2017-06-10 [1] CRAN (R 3.6.0)
# KernSmooth 2.23-15 2015-06-29 [1] CRAN (R 3.6.1)
# klaR * 0.6-14 2018-03-19 [1] CRAN (R 3.6.0)
# knitr 1.25 2019-09-18 [1] CRAN (R 3.6.0)
# labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
# later 1.0.0 2019-10-04 [1] CRAN (R 3.6.1)
# lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.1)
# lava 1.6.6 2019-08-01 [1] CRAN (R 3.6.0)
# lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
# lhs 1.0.1 2019-02-03 [1] CRAN (R 3.6.0)
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# listenv 0.7.0 2018-01-21 [1] CRAN (R 3.6.0)
# lme4 1.1-21 2019-03-05 [1] CRAN (R 3.6.0)
# loo 2.1.0 2019-03-13 [1] CRAN (R 3.6.0)
# lpSolve 5.6.13.3 2019-08-19 [1] CRAN (R 3.6.0)
# lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.0)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
# markdown 1.1 2019-08-07 [1] CRAN (R 3.6.0)
# MASS * 7.3-51.4 2019-03-31 [1] CRAN (R 3.6.1)
# Matrix 1.2-17 2019-03-22 [1] CRAN (R 3.6.1)
# matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.0)
# mime 0.7 2019-06-11 [1] CRAN (R 3.6.0)
# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 3.6.0)
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# parsnip * 0.0.3.9001 2019-10-11 [1] Github (tidymodels/parsnip@ae42617)
# pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
# pkgbuild 1.0.5 2019-08-26 [1] CRAN (R 3.6.0)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0)
# plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0)
# png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0)
# prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
# pROC 1.15.3 2019-07-21 [1] CRAN (R 3.6.0)
# processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
# prodlim 2018.04.18 2018-04-18 [1] CRAN (R 3.6.0)
# progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.0)
# promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.0)
# ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
# purrr * 0.3.2 2019-03-15 [1] CRAN (R 3.6.0)
# questionr 0.7.0 2018-11-26 [1] CRAN (R 3.6.0)
# R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
# Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
# recipes * 0.1.7 2019-09-15 [1] CRAN (R 3.6.0)
# reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0)
# rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
# rpart 4.1-15 2019-04-12 [1] CRAN (R 3.6.1)
# rsample * 0.0.5 2019-07-12 [1] CRAN (R 3.6.0)
# rsconnect 0.8.15 2019-07-22 [1] CRAN (R 3.6.0)
# rstan 2.19.2 2019-07-09 [1] CRAN (R 3.6.0)
# rstanarm 2.19.2 2019-10-03 [1] CRAN (R 3.6.1)
# rstantools 2.0.0 2019-09-15 [1] CRAN (R 3.6.0)
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# scales * 1.0.0 2018-08-09 [1] CRAN (R 3.6.0)
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# sf 0.8-0 2019-09-17 [1] CRAN (R 3.6.0)
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# transformr 0.1.1 2018-12-09 [1] CRAN (R 3.6.0)
# tune * 0.0.0.9002 2019-10-10 [1] local
# tweenr 1.0.1 2018-12-14 [1] CRAN (R 3.6.0)
# units 0.6-4 2019-08-22 [1] CRAN (R 3.6.0)
# vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.0)
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# zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.0)
# zoo 1.8-6 2019-05-28 [1] CRAN (R 3.6.0)
#
# [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
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