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profiling_script.R
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profiling_script.R
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library(fisheR)
library(profvis)
small_test_df <- data.frame(time = 1:100,
v1 = rnorm(100),
v2 = rnorm(100, 1),
v3 = rnorm(100,2,2),
v4 = rnorm(100),
v5 = rnorm(100,1,2))
medium_test_df <- data.frame(time = 1:1000,
v1 = rnorm(1000),
v2 = rnorm(1000, 1),
v3 = rnorm(1000,2,2),
v4 = rnorm(1000),
v5 = rnorm(1000),
v6 = rnorm(1000, 1),
v7 = rnorm(1000,2,2),
v8 = rnorm(1000),
v9 = rnorm(1000,1,2))
#####################################################################################
#####################################################################################
################################### plotting ###################################
#####################################################################################
#### To plot the time DECREASE using larger window increments
timing_function2 <- mapply(
fisher,
w_incre = c(1:5),
MoreArgs = list(small_test_df),
SIMPLIFY = F
)
# taking timing manually from printed output
time_df <- data.frame(time = c(14.82, 7.60, 4.14, 2.77, 2.13),
run = 1:5)
plot(x = time_df$run, y = time_df$time)
###################################
#### To plot the time INCREASE using larger window sizes
timing_function2 <- mapply(
fisher,
w_size = c(8:12),
MoreArgs = list(small_test_df),
SIMPLIFY = F
)
# taking timing manually from printed output
time_df2 <- data.frame(time = c(13.49, 13.38, 14.08, 15.74, 16.96),
run = 1:5)
plot(x = time_df2$run, y = time_df2$time)
#####################################################################################
################################### profiling ###################################
#####################################################################################
small_prof <- profvis::profvis({
small_test_fi <- fisheR::fisher(small_test_df, w_size = 8, w_incre = 1)
})
medium_prof <- profvis::profvis({
medium_test_fi <- fisheR::fisher(medium_test_df, w_size = 8, w_incre = 1)
})
#####################################################################################
################################### testing ###################################
#####################################################################################
medium_test_df_even <- data.frame(time = 1:1000,
v1 = rnorm(1000),
v2 = rnorm(1000, 1),
v3 = rnorm(1000,2,2),
v4 = rnorm(1000),
v5 = rnorm(1000),
v6 = rnorm(1000, 1),
v7 = rnorm(1000,2,2),
v8 = rnorm(1000),
v9 = rnorm(1000,1,2))
medium_test_df_999 <- data.frame(time = 1:999,
v1 = rnorm(999),
v2 = rnorm(999, 1),
v3 = rnorm(999,2,2),
v4 = rnorm(999),
v5 = rnorm(999),
v6 = rnorm(999, 1),
v7 = rnorm(999,2,2),
v8 = rnorm(999),
v9 = rnorm(999,1,2))
medium_test_df_333 <- data.frame(time = 1:333,
v1 = rnorm(333),
v2 = rnorm(333, 1),
v3 = rnorm(333,2,2),
v4 = rnorm(333),
v5 = rnorm(333),
v6 = rnorm(333, 1),
v7 = rnorm(333,2,2),
v8 = rnorm(333),
v9 = rnorm(333,1,2))
for (i in 1:20) {
for (j in 8:20) {
fisheR::fisher(medium_test_df_even,
w_size = j,
w_incre = i)
}
}
for (i in 1:20) {
for (j in 8:20) {
fisheR::fisher(medium_test_df_333,
w_size = j,
w_incre = i)
}
}
for (i in 1:20) {
for (j in 8:20) {
fisheR::fisher(medium_test_df_999,
w_size = j,
w_incre = i)
}
}
#####################################################################################
################################## version testing ##################################
#####################################################################################
# THIS SCRIPT IS AN ATTEMPT TO TEST TWO VERSIONS OF fisheR
# THE SCRIPT IS NOT WORKING YET, DESPITE SPECIFYING THE COMMIT CODE, PACKAGE VERSION IS NOT CHANGING
# library(testthat)
#
# set.seed(1984)
# x <- data.frame(time = 1:1000,
# v1 = c(rnorm(500, 1, 0.1), rnorm(200, 10, 1), rnorm(100, 100, 50), rnorm(200, 1, 0.1)),
# v2 = c(rnorm(500, 1, 0.1), rnorm(200, 10, 1), rnorm(100, 100, 50), rnorm(200, 1, 0.1)),
# v3 = c(rnorm(500, 1, 0.1), rnorm(200, 10, 1), rnorm(100, 100, 50), rnorm(200, 1, 0.1)),
# v4 = c(rnorm(500, 1, 0.1), rnorm(200, 10, 1), rnorm(100, 100, 50), rnorm(200, 1, 0.1)),
# v5 = c(rnorm(500, 1, 0.1), rnorm(200, 10, 1), rnorm(100, 100, 50), rnorm(200, 1, 0.1)),
# v6 = c(rnorm(500, 1, 0.1), rnorm(200, 10, 1), rnorm(100, 100, 50), rnorm(200, 1, 0.1))
# )
#
# test_that("string required?", {
#
# devtools::install_github("UoA-eResearch/fisheR@09f9324460f9797114a6a8e37b1248a90af82277", force = T)
# fish_x_old <- fisheR::fisher(x, w_size = 8)
#
# devtools::install_github("UoA-eResearch/fisheR@d7ca554576f6947c3c819744d6f0082430e7c088", force = T)
# fish_x_new <- fisheR::fisher(x, w_size = 8)
#
# expect_identical(fish_x_old, fish_x_new)
# expect_equal(fish_x_old, fish_x_new)
# })