tests/testthat/test-logAdjustment.R
In bcgov/BCForestGroundSample: BC forest ground sample compilation
test_that("logAdjustment.R: log length is not correctly adjusted.", {
library(data.table)
library(testthat)
## 1.
testtreedata <- data.table(BTOP = c(NA, NA, "D"),
MEAS_INTENSE = c("FULL", "FULL", "ENHANCED"),
HEIGHT = c(NA, NA, 7),
HT = c(NA, NA, 10),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(NA, 2, 2),
LOG_L_1 = c(NA, 5, NA),
LOG_L_2 = c(NA, 7, NA))
testtreedata[, paste("LOG_L_", 3:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
# print(testtreedata[,.(BTOP, HEIGHT, HT, NO_LOGS, LOG_L_1, LOG_L_2)])
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2
# 1: NA NA NA NA NA NA ## for testing log length and tree height information is not available
# 2: NA NA NA 2 5 7 ## for testing log is available and height is not
# 3: D 7 10 2 NA NA ## for log is not available and height is
treedata_adjusted <- logAdjustment(treeData = testtreedata)
expect_equal(treedata_adjusted[,.(BTOP, HEIGHT, HT, NO_LOGS, LOG_L_1, LOG_L_2,
LOGADJUST, LOG_L_0)],
data.table(BTOP = c(NA, NA, "D"),
HEIGHT = c(NA, NA, 7),
HT = c(NA, 12, 10),
NO_LOGS = c(NA, 2, 2),
LOG_L_1 = c(NA, 4.7, 6.7),
LOG_L_2 = c(NA, 7, 3),
LOGADJUST = c("FAIL", "PASS", "PASS"),
LOG_L_0 = c(NA, 0.3, 0.3)))
rm(testtreedata, treedata_adjusted)
## nonbroken top trees
testtreedata <- data.table(uniObs = 1:6,
BTOP = c(NA, NA, NA, NA, NA, NA),
MEAS_INTENSE = c(rep("FULL", 3), rep("ENHANCED", 3)),
HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(30, 30, 30, 50, 50, 50),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(1, 1, 1, 3, 3, 3),
LOG_L_1 = c(30, 25, 35, 30, 30, 30),
LOG_L_2 = c(NA, NA, NA, 10, 10, 10),
LOG_L_3 = c(NA, NA, NA, 10, 5, 15))
## print(testtreedata)
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: NA 30 30 1 30 NA NA ## exact match
# 2: NA 30 30 1 25 NA NA ## total log length less than tree height
# 3: NA 30 30 1 35 NA NA ## total log length more than tree height
# 4: NA 50 50 3 30 10 10 ## exact match
# 5: NA 50 50 3 30 10 5 ## total log length less than tree height
# 6: NA 50 50 3 30 10 15 ## total log length more than tree height
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
# print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
# LOG_L_2, LOG_L_3)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 30 30 1 0.3 29.7 NA NA ## GOOD
# 2: 2 30 30 1 0.3 29.7 NA NA ## GOOD
# 3: 3 30 30 1 0.3 29.7 NA NA ## GOOD
# 4: 4 50 50 3 0.3 29.7 10 10 ## GOOD
# 5: 5 50 50 2 0.3 29.7 10 0 ## DO NOT MAKE SENSE NEED CONFIRM WITH RENE OR GETA
# 6: 6 50 50 3 0.3 29.7 10 10 ## GOOD
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3)],
data.table(HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(30, 30, 30, 50, 50, 50),
NO_LOGS = c(1, 1, 1, 3, 2, 3),
LOG_L_0 = rep(0.3, 6),
LOG_L_1 = rep(29.7, 6),
LOG_L_2 = c(NA, NA, NA, 10, 10, 10),
LOG_L_3 = c(NA, NA, NA, 10, 0, 10)))
rm(testtreedata, treedata_adjusted)
## broken top trees
testtreedata <- data.table(uniObs = 1:6,
BTOP = c("D", "H", "D", "H", "D", "H"),
MEAS_INTENSE = c(rep("FULL", 3), rep("ENHANCED", 3)),
HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(35, 36, 37, 55, 56, 57),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(2, 2, 2, 4, 4, 4),
LOG_L_1 = c(30, 25, 32, 30, 25, 12),
LOG_L_2 = c(NA, NA, NA, 10, 10, 20),
LOG_L_3 = c(NA, NA, NA, 10, 10, 20))
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
## print(testtreedata)
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: D 30 35 2 30 NA NA ## exact match between broken height and log length
# 2: H 30 36 2 25 NA NA ## log 1 length less than tree broken height
# 3: D 30 37 2 32 NA NA ## log 1 length more than tree broken height (currently not be implemented)
# 4: H 50 55 4 30 10 10 ## exact match between broken height and log length
# 5: D 50 56 4 25 10 10 ## total log1-3 length less than tree broken height
# 6: H 50 57 4 12 20 20 ## total log1-3 length more than tree broken height
treedata_adjusted <- logAdjustment(treeData = testtreedata)
# print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
# LOG_L_2, LOG_L_3, LOG_L_4)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3 LOG_L_4
# 1: 1 30 35 2 0.3 29.7 5 NA NA # good
# 2: 2 30 36 2 0.3 29.7 6 NA NA # good
# 3: 3 30 37 2 0.3 29.7 7 NA NA # good
# 4: 4 50 55 4 0.3 29.7 10 10 5 # good
# 5: 5 50 56 4 0.3 24.7 10 15 6 # good
# 6: 6 50 57 4 0.3 11.7 20 18 7 # good
expect_equal(treedata_adjusted[order(uniObs),.(BTOP, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3, LOG_L_4)],
data.table(BTOP = c("D", "H", "D", "H", "D", "H"),
HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(35, 36, 37, 55, 56, 57),
NO_LOGS = c(2, 2, 2, 4, 4, 4),
LOG_L_0 = rep(0.3, 6),
LOG_L_1 = c(rep(29.7, 4), 24.7, 11.7),
LOG_L_2 = c(5:7, 10, 10, 20),
LOG_L_3 = c(NA, NA, NA, 10, 15, 18),
LOG_L_4 = c(NA, NA, NA, 5:7)))
rm(testtreedata, treedata_adjusted)
## similar to nonbroken top trees, test for a special case where the difference is same as length
## of last log
testtreedata <- data.table(uniObs = 1:2,
BTOP = c("D", "H"),
MEAS_INTENSE = c("FULL", "ENHANCED"),
HEIGHT = c(30, 30),
HT = c(35, 36),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(2, 3),
LOG_L_1 = c(15, 20),
LOG_L_2 = c(NA, 5),
LOG_L_3 = c(NA, NA))
# print(testtreedata)
# uniObs BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 D 30 35 2 15 NA NA # diff = 30-15 == 15 (length of last log)
# 2: 2 H 30 36 3 20 5 NA # diff = 30-25 == 5 (length of last log)
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
# print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
# LOG_L_2, LOG_L_3)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 30 35 1 0.3 4.7 NA NA ## does not make sense
# 2: 2 30 36 2 0.3 19.7 6 NA ## does not make sense
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3)],
data.table(HEIGHT = c(30, 30),
HT = c(35, 36),
NO_LOGS = 1:2,
LOG_L_0 = 0.3,
LOG_L_1 = c(4.7, 19.7),
LOG_L_2 = c(NA, 6),
LOG_L_3 = as.numeric(NA)))
rm(testtreedata, treedata_adjusted)
## comprehensive testing
testtreedata <- data.table(uniObs = 1:6,
BTOP = c(NA, NA, NA, NA, "D", "H"),
MEAS_INTENSE = c(rep("FULL", 3), rep("ENHANCED", 3)),
HEIGHT = c(NA, 30, 30, 30, 30, 30),
HT = c(NA, 30, 30, 30, 35, 36),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(NA, 2, 3, 3, 2, 3),
LOG_L_1 = c(NA, 15, 0.2, 5, 10, 20),
LOG_L_2 = c(NA, 15, 19.8, 7, NA, 6),
LOG_L_3 = c(NA, NA, 10, 16, NA, NA))
# uniObs BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 NA NA NA NA NA NA NA
# 2: 2 NA 30 30 2 15.0 15.0 NA
# 3: 3 NA 30 30 3 0.2 19.8 10
# 4: 4 NA 30 30 3 5.0 7.0 16
# 5: 5 D 30 35 2 10.0 NA NA
# 6: 6 H 30 36 3 20.0 6.0 NA
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3, LOGADJUST)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3 LOGADJUST
# 1: 1 NA NA NA NA NA NA NA FAIL
# 2: 2 30 30 2 0.3 14.7 15.0 NA PASS
# 3: 3 30 30 3 NA 0.2 19.8 10 SMALLFIRSTLOG
# 4: 4 30 30 3 0.3 4.7 7.0 18 PASS
# 5: 5 30 35 2 0.3 29.7 5.0 NA PASS
# 6: 6 30 36 3 0.3 19.7 10.0 6 PASS
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3, LOGADJUST)],
data.table(HEIGHT = c(NA, 30, 30, 30, 30, 30),
HT = c(NA, 30, 30, 30, 35, 36),
NO_LOGS = c(NA, 2, 3, 3, 2, 3),
LOG_L_0 = c(NA, 0.3, NA, 0.3, 0.3, 0.3),
LOG_L_1 = c(NA, 14.7, 0.2, 4.7, 29.7, 19.7),
LOG_L_2 = c(NA, 15, 19.8, 7, 5, 10),
LOG_L_3 = c(NA, NA, 10, 18, NA, 6),
LOGADJUST = c("FAIL", "PASS", "SMALLFIRSTLOG", "PASS",
"PASS", "PASS")))
## for H enhanced trees, those trees theoritically do not need to adjust,
## however, the function allows to do so to make all trees that at entrance to
## volume have same data formats
testtreedata <- data.table(uniObs = 1:6,
BTOP = c(NA, NA, NA, NA, NA, NA),
MEAS_INTENSE = c(rep("H-ENHANCED", 3)),
HEIGHT = seq(10, 50, length = 6),
HT = NA,
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(1, 1, 1, 3, 3, 3),
LOG_L_1 = c(30, 25, 35, 30, 30, 30),
LOG_L_2 = c(NA, NA, NA, 10, 10, 10),
LOG_L_3 = c(NA, NA, NA, 10, 5, 15))
## print(testtreedata)
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: NA 10 NA 1 30 NA NA ## exact match
# 2: NA 18 NA 1 25 NA NA ## total log length less than tree height
# 3: NA 26 NA 1 35 NA NA ## total log length more than tree height
# 4: NA 34 NA 3 30 10 10 ## exact match
# 5: NA 42 NA 3 30 10 5 ## total log length less than tree height
# 6: NA 50 NA 3 30 10 15 ## total log length more than tree height
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3)],
data.table(HEIGHT = seq(10, 50, length = 6),
HT = NA,
NO_LOGS = 1,
LOG_L_0 = rep(0.3, 6),
LOG_L_1 = seq(9.7, 49.7, length.out = 6),
LOG_L_2 = as.numeric(NA),
LOG_L_3 = as.numeric(NA)))
rm(testtreedata, treedata_adjusted)
})
bcgov/BCForestGroundSample documentation built on May 25, 2019, 3:21 p.m.
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test_that("logAdjustment.R: log length is not correctly adjusted.", {
library(data.table)
library(testthat)
## 1.
testtreedata <- data.table(BTOP = c(NA, NA, "D"),
MEAS_INTENSE = c("FULL", "FULL", "ENHANCED"),
HEIGHT = c(NA, NA, 7),
HT = c(NA, NA, 10),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(NA, 2, 2),
LOG_L_1 = c(NA, 5, NA),
LOG_L_2 = c(NA, 7, NA))
testtreedata[, paste("LOG_L_", 3:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
# print(testtreedata[,.(BTOP, HEIGHT, HT, NO_LOGS, LOG_L_1, LOG_L_2)])
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2
# 1: NA NA NA NA NA NA ## for testing log length and tree height information is not available
# 2: NA NA NA 2 5 7 ## for testing log is available and height is not
# 3: D 7 10 2 NA NA ## for log is not available and height is
treedata_adjusted <- logAdjustment(treeData = testtreedata)
expect_equal(treedata_adjusted[,.(BTOP, HEIGHT, HT, NO_LOGS, LOG_L_1, LOG_L_2,
LOGADJUST, LOG_L_0)],
data.table(BTOP = c(NA, NA, "D"),
HEIGHT = c(NA, NA, 7),
HT = c(NA, 12, 10),
NO_LOGS = c(NA, 2, 2),
LOG_L_1 = c(NA, 4.7, 6.7),
LOG_L_2 = c(NA, 7, 3),
LOGADJUST = c("FAIL", "PASS", "PASS"),
LOG_L_0 = c(NA, 0.3, 0.3)))
rm(testtreedata, treedata_adjusted)
## nonbroken top trees
testtreedata <- data.table(uniObs = 1:6,
BTOP = c(NA, NA, NA, NA, NA, NA),
MEAS_INTENSE = c(rep("FULL", 3), rep("ENHANCED", 3)),
HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(30, 30, 30, 50, 50, 50),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(1, 1, 1, 3, 3, 3),
LOG_L_1 = c(30, 25, 35, 30, 30, 30),
LOG_L_2 = c(NA, NA, NA, 10, 10, 10),
LOG_L_3 = c(NA, NA, NA, 10, 5, 15))
## print(testtreedata)
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: NA 30 30 1 30 NA NA ## exact match
# 2: NA 30 30 1 25 NA NA ## total log length less than tree height
# 3: NA 30 30 1 35 NA NA ## total log length more than tree height
# 4: NA 50 50 3 30 10 10 ## exact match
# 5: NA 50 50 3 30 10 5 ## total log length less than tree height
# 6: NA 50 50 3 30 10 15 ## total log length more than tree height
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
# print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
# LOG_L_2, LOG_L_3)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 30 30 1 0.3 29.7 NA NA ## GOOD
# 2: 2 30 30 1 0.3 29.7 NA NA ## GOOD
# 3: 3 30 30 1 0.3 29.7 NA NA ## GOOD
# 4: 4 50 50 3 0.3 29.7 10 10 ## GOOD
# 5: 5 50 50 2 0.3 29.7 10 0 ## DO NOT MAKE SENSE NEED CONFIRM WITH RENE OR GETA
# 6: 6 50 50 3 0.3 29.7 10 10 ## GOOD
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3)],
data.table(HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(30, 30, 30, 50, 50, 50),
NO_LOGS = c(1, 1, 1, 3, 2, 3),
LOG_L_0 = rep(0.3, 6),
LOG_L_1 = rep(29.7, 6),
LOG_L_2 = c(NA, NA, NA, 10, 10, 10),
LOG_L_3 = c(NA, NA, NA, 10, 0, 10)))
rm(testtreedata, treedata_adjusted)
## broken top trees
testtreedata <- data.table(uniObs = 1:6,
BTOP = c("D", "H", "D", "H", "D", "H"),
MEAS_INTENSE = c(rep("FULL", 3), rep("ENHANCED", 3)),
HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(35, 36, 37, 55, 56, 57),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(2, 2, 2, 4, 4, 4),
LOG_L_1 = c(30, 25, 32, 30, 25, 12),
LOG_L_2 = c(NA, NA, NA, 10, 10, 20),
LOG_L_3 = c(NA, NA, NA, 10, 10, 20))
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
## print(testtreedata)
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: D 30 35 2 30 NA NA ## exact match between broken height and log length
# 2: H 30 36 2 25 NA NA ## log 1 length less than tree broken height
# 3: D 30 37 2 32 NA NA ## log 1 length more than tree broken height (currently not be implemented)
# 4: H 50 55 4 30 10 10 ## exact match between broken height and log length
# 5: D 50 56 4 25 10 10 ## total log1-3 length less than tree broken height
# 6: H 50 57 4 12 20 20 ## total log1-3 length more than tree broken height
treedata_adjusted <- logAdjustment(treeData = testtreedata)
# print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
# LOG_L_2, LOG_L_3, LOG_L_4)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3 LOG_L_4
# 1: 1 30 35 2 0.3 29.7 5 NA NA # good
# 2: 2 30 36 2 0.3 29.7 6 NA NA # good
# 3: 3 30 37 2 0.3 29.7 7 NA NA # good
# 4: 4 50 55 4 0.3 29.7 10 10 5 # good
# 5: 5 50 56 4 0.3 24.7 10 15 6 # good
# 6: 6 50 57 4 0.3 11.7 20 18 7 # good
expect_equal(treedata_adjusted[order(uniObs),.(BTOP, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3, LOG_L_4)],
data.table(BTOP = c("D", "H", "D", "H", "D", "H"),
HEIGHT = c(30, 30, 30, 50, 50, 50),
HT = c(35, 36, 37, 55, 56, 57),
NO_LOGS = c(2, 2, 2, 4, 4, 4),
LOG_L_0 = rep(0.3, 6),
LOG_L_1 = c(rep(29.7, 4), 24.7, 11.7),
LOG_L_2 = c(5:7, 10, 10, 20),
LOG_L_3 = c(NA, NA, NA, 10, 15, 18),
LOG_L_4 = c(NA, NA, NA, 5:7)))
rm(testtreedata, treedata_adjusted)
## similar to nonbroken top trees, test for a special case where the difference is same as length
## of last log
testtreedata <- data.table(uniObs = 1:2,
BTOP = c("D", "H"),
MEAS_INTENSE = c("FULL", "ENHANCED"),
HEIGHT = c(30, 30),
HT = c(35, 36),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(2, 3),
LOG_L_1 = c(15, 20),
LOG_L_2 = c(NA, 5),
LOG_L_3 = c(NA, NA))
# print(testtreedata)
# uniObs BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 D 30 35 2 15 NA NA # diff = 30-15 == 15 (length of last log)
# 2: 2 H 30 36 3 20 5 NA # diff = 30-25 == 5 (length of last log)
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
# print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
# LOG_L_2, LOG_L_3)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 30 35 1 0.3 4.7 NA NA ## does not make sense
# 2: 2 30 36 2 0.3 19.7 6 NA ## does not make sense
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3)],
data.table(HEIGHT = c(30, 30),
HT = c(35, 36),
NO_LOGS = 1:2,
LOG_L_0 = 0.3,
LOG_L_1 = c(4.7, 19.7),
LOG_L_2 = c(NA, 6),
LOG_L_3 = as.numeric(NA)))
rm(testtreedata, treedata_adjusted)
## comprehensive testing
testtreedata <- data.table(uniObs = 1:6,
BTOP = c(NA, NA, NA, NA, "D", "H"),
MEAS_INTENSE = c(rep("FULL", 3), rep("ENHANCED", 3)),
HEIGHT = c(NA, 30, 30, 30, 30, 30),
HT = c(NA, 30, 30, 30, 35, 36),
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(NA, 2, 3, 3, 2, 3),
LOG_L_1 = c(NA, 15, 0.2, 5, 10, 20),
LOG_L_2 = c(NA, 15, 19.8, 7, NA, 6),
LOG_L_3 = c(NA, NA, 10, 16, NA, NA))
# uniObs BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: 1 NA NA NA NA NA NA NA
# 2: 2 NA 30 30 2 15.0 15.0 NA
# 3: 3 NA 30 30 3 0.2 19.8 10
# 4: 4 NA 30 30 3 5.0 7.0 16
# 5: 5 D 30 35 2 10.0 NA NA
# 6: 6 H 30 36 3 20.0 6.0 NA
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
print(treedata_adjusted[order(uniObs),.(uniObs, HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3, LOGADJUST)])
# uniObs HEIGHT HT NO_LOGS LOG_L_0 LOG_L_1 LOG_L_2 LOG_L_3 LOGADJUST
# 1: 1 NA NA NA NA NA NA NA FAIL
# 2: 2 30 30 2 0.3 14.7 15.0 NA PASS
# 3: 3 30 30 3 NA 0.2 19.8 10 SMALLFIRSTLOG
# 4: 4 30 30 3 0.3 4.7 7.0 18 PASS
# 5: 5 30 35 2 0.3 29.7 5.0 NA PASS
# 6: 6 30 36 3 0.3 19.7 10.0 6 PASS
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3, LOGADJUST)],
data.table(HEIGHT = c(NA, 30, 30, 30, 30, 30),
HT = c(NA, 30, 30, 30, 35, 36),
NO_LOGS = c(NA, 2, 3, 3, 2, 3),
LOG_L_0 = c(NA, 0.3, NA, 0.3, 0.3, 0.3),
LOG_L_1 = c(NA, 14.7, 0.2, 4.7, 29.7, 19.7),
LOG_L_2 = c(NA, 15, 19.8, 7, 5, 10),
LOG_L_3 = c(NA, NA, 10, 18, NA, 6),
LOGADJUST = c("FAIL", "PASS", "SMALLFIRSTLOG", "PASS",
"PASS", "PASS")))
## for H enhanced trees, those trees theoritically do not need to adjust,
## however, the function allows to do so to make all trees that at entrance to
## volume have same data formats
testtreedata <- data.table(uniObs = 1:6,
BTOP = c(NA, NA, NA, NA, NA, NA),
MEAS_INTENSE = c(rep("H-ENHANCED", 3)),
HEIGHT = seq(10, 50, length = 6),
HT = NA,
# HT_BTOP = c(NA, NA, 7),
NO_LOGS = c(1, 1, 1, 3, 3, 3),
LOG_L_1 = c(30, 25, 35, 30, 30, 30),
LOG_L_2 = c(NA, NA, NA, 10, 10, 10),
LOG_L_3 = c(NA, NA, NA, 10, 5, 15))
## print(testtreedata)
# BTOP HEIGHT HT NO_LOGS LOG_L_1 LOG_L_2 LOG_L_3
# 1: NA 10 NA 1 30 NA NA ## exact match
# 2: NA 18 NA 1 25 NA NA ## total log length less than tree height
# 3: NA 26 NA 1 35 NA NA ## total log length more than tree height
# 4: NA 34 NA 3 30 10 10 ## exact match
# 5: NA 42 NA 3 30 10 5 ## total log length less than tree height
# 6: NA 50 NA 3 30 10 15 ## total log length more than tree height
testtreedata[, paste("LOG_L_", 4:9, sep = "") := NA]
testtreedata[, paste("LOG_G_", 1:9, sep = "") := as.character(NA)]
testtreedata[, paste("LOG_S_", 1:9, sep = "") := as.numeric(NA)]
treedata_adjusted <- logAdjustment(treeData = testtreedata)
expect_equal(treedata_adjusted[order(uniObs),.(HEIGHT, HT, NO_LOGS, LOG_L_0, LOG_L_1,
LOG_L_2, LOG_L_3)],
data.table(HEIGHT = seq(10, 50, length = 6),
HT = NA,
NO_LOGS = 1,
LOG_L_0 = rep(0.3, 6),
LOG_L_1 = seq(9.7, 49.7, length.out = 6),
LOG_L_2 = as.numeric(NA),
LOG_L_3 = as.numeric(NA)))
rm(testtreedata, treedata_adjusted)
})
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