Prepare for v1.0.0v1.0.0

- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest

4 files changed, 0 insertions, 237 deletions

diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 2071e05c..547b2d6c 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -178,10 +178,6 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
 })
 
 # Mixed model fits
-saemix_available <- FALSE
-if (requireNamespace("saemix", quietly = TRUE)) {
-  if(packageVersion("saemix") > "3.1.9000") saemix_available <- TRUE
-}
 mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores)
 mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores)
 mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores)
@@ -190,16 +186,6 @@ mmkin_biphasic_mixed <- mixed(mmkin_biphasic)
 dfop_nlme_1 <- nlme(mmkin_dfop_1)
 nlme_biphasic <- nlme(mmkin_biphasic)
 
-if (saemix_available) {
-  sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix")
-
-  dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin")
-  dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
-
-  saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
-  saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
-}
-
 ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
   function(x) subset(x$data[c("name", "time", "value")]))
 names(ds_uba) <- paste("Dataset", 6:10)
@@ -211,7 +197,3 @@ f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
   ds_uba, quiet = TRUE, cores = n_cores)
 f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ])
 
-if (saemix_available) {
-  f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix")
-  f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
-}
diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt
deleted file mode 100644
index b5777ce1..00000000
--- a/tests/testthat/summary_saem_biphasic_s.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-saemix version used for fitting:      Dummy 0.0 for testing 
-mkin version used for pre-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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-           time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-           * parent
-d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
-           * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
-           exp(-k2 * time))) * parent - k_m1 * m1
-
-Data:
-509 observations of 2 variable(s) grouped in 15 datasets
-
-Model predictions using solution type analytical 
-
-Fitted in test time 0 s using 300, 100 iterations
-
-Variance model: Constant variance 
-
-Mean of starting values for individual parameters:
-      parent_0           k_m1 f_parent_to_m1             k1             k2 
-       1.0e+02        1.8e-03        4.8e-01        4.5e-02        1.9e-02 
-             g 
-       5.1e-01 
-
-Fixed degradation parameter values:
-None
-
-Results:
-
-Likelihood computed by importance sampling
-   AIC  BIC logLik
-  2692 2702  -1333
-
-Optimised parameters:
-                  est.   lower   upper
-parent_0       1.0e+02 99.3030 1.0e+02
-k_m1           2.2e-03  0.0016 2.8e-03
-f_parent_to_m1 4.9e-01  0.4477 5.3e-01
-k1             4.0e-02  0.0239 5.6e-02
-k2             1.5e-02  0.0085 2.2e-02
-g              5.0e-01  0.3805 6.2e-01
-
-Correlation: 
-               prnt_0 k_m1   f_p__1 k1     k2    
-k_m1           -0.152                            
-f_parent_to_m1 -0.138  0.396                     
-k1              0.085 -0.036 -0.026              
-k2              0.005  0.067  0.018 -0.043       
-g              -0.075 -0.113 -0.029 -0.248 -0.263
-
-Random effects:
-                  est. lower upper
-SD.parent_0       1.23  0.39  2.07
-SD.k_m1           0.14 -0.48  0.75
-SD.f_parent_to_m1 0.28  0.17  0.39
-SD.k1             0.71  0.42  1.00
-SD.k2             0.78  0.47  1.09
-SD.g              0.27 -0.33  0.86
-
-Variance model:
-    est. lower upper
-a.1  2.7   2.6   2.9
-
-Resulting formation fractions:
-              ff
-parent_m1   0.49
-parent_sink 0.51
-
-Estimated disappearance times:
-       DT50 DT90 DT50back DT50_k1 DT50_k2
-parent   27  110       33      17      46
-m1      318 1055       NA      NA      NA
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index e9af10e6..ca0072ef 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,98 +1,9 @@
 context("Nonlinear mixed-effects models")
 
-test_that("Parent fits using saemix are correctly implemented", {
-  skip_if(!saemix_available)
-
-  expect_error(saem(fits), "Only row objects")
-  # Some fits were done in the setup script
-  mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
-  expect_error(update(mmkin_sfo_1, models = c("SFOOO")), "Please supply models.*")
-
-  sfo_saem_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin")
-  sfo_saem_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
-  s_sfo_s1 <- summary(sfo_saem_1)
-  s_sfo_s2 <- summary(sfo_saem_2)
-
-  sfo_nlme_1 <- expect_warning(nlme(mmkin_sfo_1), "not converge")
-  s_sfo_n <- summary(sfo_nlme_1)
-
-  # Compare with input
-  expect_equal(round(s_sfo_s2$confint_ranef["SD.log_k_parent", "est."], 1), 0.3)
-  # k_parent is a bit different from input 0.03 here
-  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), 0.035)
-  expect_equal(round(s_sfo_s2$confint_back["k_parent", "est."], 3), 0.035)
-
-  # But the result is pretty unanimous between methods
-  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
-    round(s_sfo_s2$confint_back["k_parent", "est."], 3))
-  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
-    round(s_sfo_n$confint_back["k_parent", "est."], 3))
-
-  mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores)
-  fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE)
-  ci_fomc_s1 <- summary(fomc_saem_1)$confint_back
-
-  fomc_pop <- as.numeric(fomc_pop)
-  expect_true(all(ci_fomc_s1[, "lower"] < fomc_pop))
-  expect_true(all(ci_fomc_s1[, "upper"] > fomc_pop))
-
-  mmkin_fomc_2 <- update(mmkin_fomc_1, state.ini = 100, fixed_initials = "parent")
-  fomc_saem_2 <- saem(mmkin_fomc_2, quiet = TRUE, transformations = "mkin")
-  ci_fomc_s2 <- summary(fomc_saem_2)$confint_back
-
-  expect_true(all(ci_fomc_s2[, "lower"] < fomc_pop[2:3]))
-  expect_true(all(ci_fomc_s2[, "upper"] > fomc_pop[2:3]))
-
-  s_dfop_s1 <- summary(dfop_saemix_1)
-  s_dfop_s2 <- summary(dfop_saemix_2)
-  s_dfop_n <- summary(dfop_nlme_1)
-
-  dfop_pop <- as.numeric(dfop_pop)
-  expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop))
-  expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop))
-  expect_true(all(s_dfop_s2$confint_back[, "lower"] < dfop_pop))
-  expect_true(all(s_dfop_s2$confint_back[, "upper"] > dfop_pop))
-
-  dfop_mmkin_means_trans <- apply(parms(mmkin_dfop_1, transformed = TRUE), 1, mean)
-  dfop_mmkin_means <- backtransform_odeparms(dfop_mmkin_means_trans, mmkin_dfop_1$mkinmod)
-
-  # We get < 22% deviations by averaging the transformed parameters
-  rel_diff_mmkin <- (dfop_mmkin_means - dfop_pop) / dfop_pop
-  expect_true(all(rel_diff_mmkin < 0.22))
-
-  # We get < 50% deviations with transformations made in mkin
-  rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop
-  expect_true(all(rel_diff_1 < 0.5))
-
-  # We get < 12% deviations with transformations made in saemix
-  rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
-  expect_true(all(rel_diff_2 < 0.12))
-
-  mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores)
-  hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE)
-  ci_hs_s1 <- summary(hs_saem_1)$confint_back
-
-  hs_pop <- as.numeric(hs_pop)
-  # expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated
-  expect_true(all(ci_hs_s1[, "upper"] > hs_pop))
-
-  mmkin_hs_2 <- update(mmkin_hs_1, state.ini = 100, fixed_initials = "parent")
-  hs_saem_2 <- saem(mmkin_hs_2, quiet = TRUE)
-  ci_hs_s2 <- summary(hs_saem_2)$confint_back
-
-  #expect_true(all(ci_hs_s2[, "lower"] < hs_pop[2:4])) # k1 again overestimated
-  expect_true(all(ci_hs_s2[, "upper"] > hs_pop[2:4]))
-
-  # HS would likely benefit from implemenation of transformations = "saemix"
-})
-
 test_that("Print methods work", {
   expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt")
   expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
   expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt")
-
-  skip_if(!saemix_available)
-  expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt")
 })
 
 test_that("nlme results are reproducible to some degree", {
@@ -112,45 +23,3 @@ test_that("nlme results are reproducible to some degree", {
   # expect_true(all(ci_dfop_sfo_n[, "lower"] < dfop_sfo_pop)) # k2 is overestimated
   expect_true(all(ci_dfop_sfo_n[, "upper"] > dfop_sfo_pop))
 })
-
-test_that("saem results are reproducible for biphasic fits", {
-
-  skip_if(!saemix_available)
-  test_summary <- summary(saem_biphasic_s)
-  test_summary$saemixversion <- "Dummy 0.0 for testing"
-  test_summary$mkinversion <- "Dummy 0.0 for testing"
-  test_summary$Rversion <- "Dummy R version for testing"
-  test_summary$date.fit <- "Dummy date for testing"
-  test_summary$date.summary <- "Dummy date for testing"
-  test_summary$time <- c(elapsed = "test time 0")
-
-  expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt")
-
-  dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
-  no_k1 <- c(1, 2, 3, 5, 6)
-  no_k2 <- c(1, 2, 3, 4, 6)
-
-  ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
-  expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
-  expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
-
-  # k1 and k2 are not fitted well
-  ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
-  expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2]))
-  expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1]))
-
-  # I tried to only do few iterations in routine tests as this is so slow
-  # but then deSolve fails at some point (presumably at the switch between
-  # the two types of iterations)
-  #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve",
-  # control = list(nbiter.saemix = c(10, 5), nbiter.burn = 5), quiet = TRUE)
-
-  skip("Fitting with saemix takes around 10 minutes when using deSolve")
-  saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)
-
-  # As with the analytical solution, k1 and k2 are not fitted well
-  ci_dfop_sfo_s_d <- summary(saem_biphasic_2)$confint_back
-  expect_true(all(ci_dfop_sfo_s_d[no_k2, "lower"] < dfop_sfo_pop[no_k2]))
-  expect_true(all(ci_dfop_sfo_s_d[no_k1, "upper"] > dfop_sfo_pop[no_k1]))
-})
-
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index 1c95d069..0bf3ee66 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -35,11 +35,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed)
   vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin)
 
-  if (saemix_available) {
-    plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem)
-    vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s)
-  }
-
   skip_on_travis()
 
   plot_biphasic_nlme <- function() plot(dfop_nlme_1)
@@ -48,12 +43,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   #plot_biphasic_mmkin <- function() plot(mixed(mmkin_biphasic))
   # Biphasic fits with lots of data and fits have lots of potential for differences
   plot_biphasic_nlme <- function() plot(nlme_biphasic)
-  if (saemix_available) {
-    #plot_biphasic_saem_s <- function() plot(saem_biphasic_s)
-    plot_biphasic_saem_m <- function() plot(saem_biphasic_m)
-
-    vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m)
-  }
 
   # different results when working with eigenvalues
   plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE)