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-rw-r--r--tests/testthat/setup_script.R75
-rw-r--r--tests/testthat/slow/test_roundtrip_error_parameters.R45
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D.txt125
-rw-r--r--tests/testthat/test_CAKE_export.R8
-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R6
-rw-r--r--tests/testthat/test_SFORB.R32
-rw-r--r--tests/testthat/test_confidence.R15
-rw-r--r--tests/testthat/test_error_models.R31
-rw-r--r--tests/testthat/test_plots_summary_twa.R27
9 files changed, 292 insertions, 72 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
new file mode 100644
index 00000000..c1d46dcb
--- /dev/null
+++ b/tests/testthat/setup_script.R
@@ -0,0 +1,75 @@
+# Copyright (C) 2016-2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+require(mkin)
+require(testthat)
+
+# Per default (on my box where I set NOT_CRAN) use all cores minus one
+if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+ n_cores <- parallel::detectCores() - 1
+} else {
+ n_cores <- 1
+}
+
+# We are only allowed one core on travis, but they also set NOT_CRAN=true
+if (Sys.getenv("TRAVIS") != "") n_cores = 1
+
+# On Windows we would need to make a cluster first
+if (Sys.info()["sysname"] == "Windows") n_cores = 1
+
+# mmkin object of parent fits for tests
+models <- c("SFO", "FOMC", "DFOP", "HS")
+fits <- mmkin(models,
+ list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+ quiet = TRUE, cores = n_cores)
+
+# One metabolite
+SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"), quiet = TRUE)
+SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"),
+ use_of_ff = "max", quiet = TRUE)
+
+f_sfo_sfo <- mkinfit(SFO_SFO,
+ subset(FOCUS_2006_D, value != 0),
+ quiet = TRUE)
+
+f_sfo_sfo.ff <- mkinfit(SFO_SFO.ff,
+ subset(FOCUS_2006_D, value != 0),
+ quiet = TRUE)
+
+# Two metabolites
+SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
+
+DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
+
+m_synth_SFO_lin <- mkinmod(
+ parent = mkinsub("SFO", "M1"),
+ M1 = mkinsub("SFO", "M2"),
+ M2 = mkinsub("SFO"),
+ use_of_ff = "max", quiet = TRUE)
+
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+ M1 = mkinsub("SFO"),
+ M2 = mkinsub("SFO"),
+ use_of_ff = "max", quiet = TRUE)
+
+f_SFO_lin_mkin_OLS <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
+f_SFO_lin_mkin_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
+ error_model = "const", error_model_algorithm = "direct")
+
diff --git a/tests/testthat/slow/test_roundtrip_error_parameters.R b/tests/testthat/slow/test_roundtrip_error_parameters.R
index 97510563..7fa6c4e1 100644
--- a/tests/testthat/slow/test_roundtrip_error_parameters.R
+++ b/tests/testthat/slow/test_roundtrip_error_parameters.R
@@ -1,3 +1,36 @@
+# Copyright (C) 2018,2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+context("Roundtripping error model parameters")
+
+# Per default (on my box where I set NOT_CRAN) use all cores minus one
+if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+ n_cores <- parallel::detectCores() - 1
+} else {
+ n_cores <- 1
+}
+
+# We are only allowed one core on travis, but they also set NOT_CRAN=true
+if (Sys.getenv("TRAVIS") != "") n_cores = 1
+
+# On Windows we would need to make a cluster first
+if (Sys.info()["sysname"] == "Windows") n_cores = 1
+
test_that("Reweighting method 'tc' produces reasonable variance estimates", {
# Check if we can approximately obtain the parameters and the error model
@@ -19,18 +52,6 @@ test_that("Reweighting method 'tc' produces reasonable variance estimates", {
sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
n = 1, reps = 100, digits = 5, LOD = -Inf, seed = 123456)
- # Per default (on my box where I set NOT_CRAN) use all cores minus one
- if (identical(Sys.getenv("NOT_CRAN"), "true")) {
- n_cores <- parallel::detectCores() - 1
- } else {
- n_cores <- 1
- }
-
- # We are only allowed one core on travis, but they also set NOT_CRAN=true
- if (Sys.getenv("TRAVIS") != "") n_cores = 1
-
- # On Windows we would need to make a cluster first
- if (Sys.info()["sysname"] == "Windows") n_cores = 1
# Unweighted fits
f_2_10 <- mmkin("DFOP", d_2_10, error_model = "const", quiet = TRUE,
diff --git a/tests/testthat/summary_DFOP_FOCUS_D.txt b/tests/testthat/summary_DFOP_FOCUS_D.txt
new file mode 100644
index 00000000..8abc15e7
--- /dev/null
+++ b/tests/testthat/summary_DFOP_FOCUS_D.txt
@@ -0,0 +1,125 @@
+mkin version used for fitting: Dummy 0.0 for testing
+R version used for fitting: Dummy R version for testing
+Date of fit: Dummy date for testing
+Date of summary: Dummy date for testing
+
+Equations:
+d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+
+Model predictions using solution type deSolve
+
+Fitted using test 0 model solutions performed in test time 0 s
+
+Error model: Constant variance
+
+Error model algorithm: OLS
+
+Starting values for parameters to be optimised:
+ value type
+parent_0 100.7500 state
+k_parent_sink 0.1000 deparm
+k_parent_m1 0.1001 deparm
+k_m1_sink 0.1002 deparm
+
+Starting values for the transformed parameters actually optimised:
+ value lower upper
+parent_0 100.750000 -Inf Inf
+log_k_parent_sink -2.302585 -Inf Inf
+log_k_parent_m1 -2.301586 -Inf Inf
+log_k_m1_sink -2.300587 -Inf Inf
+
+Fixed parameter values:
+ value type
+m1_0 0 state
+
+Optimised, transformed parameters with symmetric confidence intervals:
+ Estimate Std. Error Lower Upper
+parent_0 99.600 1.57000 96.400 102.800
+log_k_parent_sink -3.038 0.07626 -3.193 -2.883
+log_k_parent_m1 -2.980 0.04033 -3.062 -2.898
+log_k_m1_sink -5.248 0.13320 -5.518 -4.977
+sigma 3.126 0.35850 2.396 3.855
+
+Parameter correlation:
+ parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+parent_0 1e+00 6e-01 -6e-02 -2e-01
+log_k_parent_sink 6e-01 1e+00 -9e-02 -6e-01
+log_k_parent_m1 -6e-02 -9e-02 1e+00 5e-01
+log_k_m1_sink -2e-01 -6e-01 5e-01 1e+00
+sigma 1e-09 -9e-10 2e-08 -1e-10
+ sigma
+parent_0 1e-09
+log_k_parent_sink -9e-10
+log_k_parent_m1 2e-08
+log_k_m1_sink -1e-10
+sigma 1e+00
+
+Backtransformed parameters:
+Confidence intervals for internally transformed parameters are asymmetric.
+t-test (unrealistically) based on the assumption of normal distribution
+for estimators of untransformed parameters.
+ Estimate t value Pr(>t) Lower Upper
+parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02
+k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02
+k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
+
+FOCUS Chi2 error levels in percent:
+ err.min n.optim df
+All data 6.398 4 15
+parent 6.827 3 6
+m1 4.490 1 9
+
+Resulting formation fractions:
+ ff
+parent_sink 0.4855
+parent_m1 0.5145
+m1_sink 1.0000
+
+Estimated disappearance times:
+ DT50 DT90
+parent 7.023 23.33
+m1 131.761 437.70
+
+Data:
+ time variable observed predicted residual
+ 0 parent 99.46 99.59848 -1.385e-01
+ 0 parent 102.04 99.59848 2.442e+00
+ 1 parent 93.50 90.23787 3.262e+00
+ 1 parent 92.50 90.23787 2.262e+00
+ 3 parent 63.23 74.07320 -1.084e+01
+ 3 parent 68.99 74.07320 -5.083e+00
+ 7 parent 52.32 49.91207 2.408e+00
+ 7 parent 55.13 49.91207 5.218e+00
+ 14 parent 27.27 25.01257 2.257e+00
+ 14 parent 26.64 25.01257 1.627e+00
+ 21 parent 11.50 12.53462 -1.035e+00
+ 21 parent 11.64 12.53462 -8.946e-01
+ 35 parent 2.85 3.14787 -2.979e-01
+ 35 parent 2.91 3.14787 -2.379e-01
+ 50 parent 0.69 0.71624 -2.624e-02
+ 50 parent 0.63 0.71624 -8.624e-02
+ 75 parent 0.05 0.06074 -1.074e-02
+ 75 parent 0.06 0.06074 -7.382e-04
+ 1 m1 4.84 4.80296 3.704e-02
+ 1 m1 5.64 4.80296 8.370e-01
+ 3 m1 12.91 13.02400 -1.140e-01
+ 3 m1 12.96 13.02400 -6.400e-02
+ 7 m1 22.97 25.04476 -2.075e+00
+ 7 m1 24.47 25.04476 -5.748e-01
+ 14 m1 41.69 36.69002 5.000e+00
+ 14 m1 33.21 36.69002 -3.480e+00
+ 21 m1 44.37 41.65310 2.717e+00
+ 21 m1 46.44 41.65310 4.787e+00
+ 35 m1 41.22 43.31312 -2.093e+00
+ 35 m1 37.95 43.31312 -5.363e+00
+ 50 m1 41.19 41.21831 -2.831e-02
+ 50 m1 40.01 41.21831 -1.208e+00
+ 75 m1 40.09 36.44703 3.643e+00
+ 75 m1 33.85 36.44703 -2.597e+00
+ 100 m1 31.04 31.98163 -9.416e-01
+ 100 m1 33.13 31.98163 1.148e+00
+ 120 m1 25.15 28.78984 -3.640e+00
+ 120 m1 33.31 28.78984 4.520e+00
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
index 23b424fc..a95a27ee 100644
--- a/tests/testthat/test_CAKE_export.R
+++ b/tests/testthat/test_CAKE_export.R
@@ -19,8 +19,9 @@
context("Export dataset for reading into CAKE")
test_that("Exporting is reproducible", {
- CAKE_export(list("FOCUS C" = FOCUS_2006_C,
- "FOCUS D" = FOCUS_2006_D),
+ CAKE_export(
+ ds = list("FOCUS C" = FOCUS_2006_C,
+ "FOCUS D" = FOCUS_2006_D),
map = c(parent = "Parent", m1 = "M1"),
links = c(parent = "m1"),
filename = "FOCUS_2006_D.csf", overwrite = TRUE,
@@ -28,4 +29,7 @@ test_that("Exporting is reproducible", {
csf <- readLines(con = "FOCUS_2006_D.csf")
csf[8] <- "Date: Dummy date 0000-00-00"
expect_known_value(csf, file = "FOCUS_2006_D.rds")
+ expect_error(CAKE_export(ds = list("FOCUS C" = FOCUS_2006_C),
+ filename = "FOCUS_2006_D.csf", overwrite = FALSE),
+ "already exists")
})
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index a282f5e7..614305b1 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -19,12 +19,6 @@
context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
# Results are from p. 40
-SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"), quiet = TRUE)
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"),
- use_of_ff = "max", quiet = TRUE)
-
test_that("Fits without formation fractions are correct for FOCUS D", {
fit.default <- expect_warning(mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE), "value of zero")
diff --git a/tests/testthat/test_SFORB.R b/tests/testthat/test_SFORB.R
new file mode 100644
index 00000000..49b3beed
--- /dev/null
+++ b/tests/testthat/test_SFORB.R
@@ -0,0 +1,32 @@
+# Copyright (C) 2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+context("Fitting the SFORB model")
+
+logistic <- mkinmod(parent = mkinsub("logistic"))
+
+test_that("Fitting the SFORB model is equivalent to fitting DFOP", {
+ f_sforb <- mkinfit("SFORB", FOCUS_2006_C, quiet = TRUE)
+ f_dfop <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
+ expect_equivalent(endpoints(f_sforb)$distimes, endpoints(f_dfop)$distimes,
+ tolerance = 1e-6)
+ s_sforb <- capture_output(print(summary(f_sforb)))
+ expect_match(s_sforb, "Estimated Eigenvalues of SFORB model\\(s\\):")
+ expect_match(s_sforb, "parent_b1 parent_b2")
+ expect_match(s_sforb, "0.45956 *0.01785")
+})
diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R
index e5cc1954..0423302b 100644
--- a/tests/testthat/test_confidence.R
+++ b/tests/testthat/test_confidence.R
@@ -18,20 +18,8 @@
context("Confidence intervals and p-values")
-m_synth_SFO_lin <- mkinmod(
- parent = mkinsub("SFO", "M1"),
- M1 = mkinsub("SFO", "M2"),
- M2 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
-
-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
test_that("Confidence intervals are stable", {
- f_1_mkin_OLS <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
- f_1_mkin_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
- error_model = "const", error_model_algorithm = "direct")
-
- bpar_1 <- summary(f_1_mkin_ML)$bpar[, c("Estimate", "Lower", "Upper")]
+ bpar_1 <- summary(f_SFO_lin_mkin_ML)$bpar[, c("Estimate", "Lower", "Upper")]
# The reference used here is mkin 0.9.48.1
bpar_1_mkin_0.9 <- read.table(text =
"parent_0 102.0000 98.6000 106.0000
@@ -47,5 +35,6 @@ col.names = c("parameter", "estimate", "lower", "upper"))
# Relative difference of lower bound of the confidence interval is < 0.02
expect_equivalent(bpar_1[1:6, "Lower"], bpar_1_mkin_0.9$lower,
scale = bpar_1_mkin_0.9$lower, tolerance = 0.02)
+ expect_equivalent(f_SFO_lin_mkin_OLS$bpar, f_SFO_lin_mkin_ML$bpar)
})
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index f4015e00..ba40bae6 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -18,37 +18,6 @@
context("Error model fitting")
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
- M1 = mkinsub("SFO", "M2"),
- M2 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
-
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
- M1 = mkinsub("SFO"),
- M2 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
-
-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-
-test_that("Error model 'const' works", {
- skip_on_cran()
- fit_const_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "const", quiet = TRUE)
- bpar_1 <- fit_const_1$bparms.optim
- # The reference used here is mkin 0.9.48.1
- bpar_1_mkin_0.9 <- read.table(text =
-"parent_0 102.0000
-k_parent 0.7390
-k_M1 0.2990
-k_M2 0.0202
-f_parent_to_M1 0.7690
-f_M1_to_M2 0.7230",
-col.names = c("parameter", "estimate"))
-
- expect_equivalent(signif(bpar_1, 3), bpar_1_mkin_0.9$estimate)
-})
-
test_that("Error model 'obs' works", {
skip_on_cran()
fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TRUE)
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 43036f1a..1dcf49ac 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -16,11 +16,6 @@
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
-models <- c("SFO", "FOMC", "DFOP", "HS")
-fits <- mmkin(models,
- list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
- quiet = TRUE, cores = 1)
-
context("Calculation of maximum time weighted average concentrations (TWAs)")
test_that("Time weighted average concentrations are correct", {
@@ -49,7 +44,7 @@ test_that("Time weighted average concentrations are correct", {
context("Summary")
-test_that("The summary is reproducible", {
+test_that("Summaries are reproducible", {
fit <- fits[["DFOP", "FOCUS_C"]]
test_summary <- summary(fit)
test_summary$fit_version <- "Dummy 0.0 for testing"
@@ -63,6 +58,19 @@ test_that("The summary is reproducible", {
# and between Travis and my own Linux system
test_summary$Corr <- signif(test_summary$Corr, 1)
expect_known_output(print(test_summary), "summary_DFOP_FOCUS_C.txt")
+
+ test_summary_2 <- summary(f_sfo_sfo,)
+ test_summary_2$fit_version <- "Dummy 0.0 for testing"
+ test_summary_2$fit_Rversion <- "Dummy R version for testing"
+ test_summary_2$date.fit <- "Dummy date for testing"
+ test_summary_2$date.summary <- "Dummy date for testing"
+ test_summary_2$calls <- "test 0"
+ test_summary_2$time <- c(elapsed = "test time 0")
+ # The correlation matrix is quite platform dependent
+ # It differs between i386 and amd64 on Windows
+ # and between Travis and my own Linux system
+ test_summary_2$Corr <- signif(test_summary_2$Corr, 1)
+ expect_known_output(print(test_summary_2), "summary_DFOP_FOCUS_D.txt")
})
context("Plotting")
@@ -71,11 +79,13 @@ test_that("Plotting mmkin objects is reproducible", {
skip_on_cran()
plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[["SFO", "FOCUS_C"]])
mkinparplot_FOCUS_C_SFO <- function() mkinparplot(fits[["SFO", "FOCUS_C"]])
+ mkinerrplot_FOCUS_C_SFO <- function() mkinerrplot(fits[["SFO", "FOCUS_C"]])
mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
mmkin_SFO <- function() plot(fits["SFO",])
vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
vdiffr::expect_doppelganger("mkinparplot for FOCUS C SFO", mkinparplot_FOCUS_C_SFO)
+ vdiffr::expect_doppelganger("mkinerrplot for FOCUS C SFO", mkinerrplot_FOCUS_C_SFO)
vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
})
@@ -84,7 +94,8 @@ context("AIC calculation")
test_that("The AIC is reproducible", {
expect_equivalent(AIC(fits[["SFO", "FOCUS_C"]]), 59.3, scale = 1, tolerance = 0.1)
- expect_equivalent(AIC(fits[, "FOCUS_C"]),
- data.frame(df = c(3, 4, 5, 5), AIC = c(59.3, 44.7, 29.0, 39.2)),
+ expect_equivalent(AIC(fits[, "FOCUS_C"]),
+ data.frame(df = c(3, 4, 5, 5), AIC = c(59.3, 44.7, 29.0, 39.2)),
scale = 1, tolerance = 0.1)
+ expect_error(AIC(fits["SFO", ]), "column object")
})

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