diff options
Diffstat (limited to 'tests/testthat/test_confidence.R')
| -rw-r--r-- | tests/testthat/test_confidence.R | 47 |
1 files changed, 12 insertions, 35 deletions
diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R index 5f76c344..2443fa66 100644 --- a/tests/testthat/test_confidence.R +++ b/tests/testthat/test_confidence.R @@ -1,44 +1,21 @@ -# We set up some models and fits with nls for comparisons -SFO_trans <- function(t, parent_0, log_k_parent_sink) { - parent_0 * exp(- exp(log_k_parent_sink) * t) -} -SFO_notrans <- function(t, parent_0, k_parent_sink) { - parent_0 * exp(- k_parent_sink * t) -} -f_1_nls_trans <- nls(value ~ SFO_trans(time, parent_0, log_k_parent_sink), - data = FOCUS_2006_A, - start = list(parent_0 = 100, log_k_parent_sink = log(0.1))) -f_1_nls_notrans <- nls(value ~ SFO_notrans(time, parent_0, k_parent_sink), - data = FOCUS_2006_A, - start = list(parent_0 = 100, k_parent_sink = 0.1)) - -f_1_mkin_OLS <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE) -f_1_mkin_OLS_notrans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE, - transform_rates = FALSE) - - -f_2_mkin <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE) -f_2_nls <- nls(value ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = FOCUS_2006_C) - context("Confidence intervals and p-values") test_that("The confint method 'quadratic' is consistent with the summary", { expect_equivalent( - confint(f_SFO_lin_mkin_ML, method = "quadratic"), - summary(f_SFO_lin_mkin_ML)$bpar[, c("Lower", "Upper")]) + confint(fit_nw_1, method = "quadratic"), + summary(fit_nw_1)$bpar[, c("Lower", "Upper")]) expect_equivalent( - confint(f_SFO_lin_mkin_ML, method = "quadratic", backtransform = FALSE), - summary(f_SFO_lin_mkin_ML)$par[, c("Lower", "Upper")]) + confint(fit_nw_1, method = "quadratic", backtransform = FALSE), + summary(fit_nw_1)$par[, c("Lower", "Upper")]) - f_notrans <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE, transform_rates = FALSE) expect_equivalent( - confint(f_notrans, method = "quadratic", transformed = FALSE), - summary(f_notrans)$par[, c("Lower", "Upper")]) + confint(f_1_mkin_notrans, method = "quadratic", transformed = FALSE), + summary(f_1_mkin_notrans)$par[, c("Lower", "Upper")]) expect_equivalent( - confint(f_notrans, method = "quadratic", transformed = FALSE), - summary(f_notrans)$bpar[, c("Lower", "Upper")]) + confint(f_1_mkin_notrans, method = "quadratic", transformed = FALSE), + summary(f_1_mkin_notrans)$bpar[, c("Lower", "Upper")]) }) @@ -46,20 +23,20 @@ test_that("Quadratic confidence intervals for rate constants are comparable to v # Check fitted parameter values expect_equivalent( - (f_1_mkin_OLS$bparms.optim -coef(f_1_nls_notrans))/f_1_mkin_OLS$bparms.optim, + (f_1_mkin_trans$bparms.optim -coef(f_1_nls_notrans))/f_1_mkin_trans$bparms.optim, rep(0, 2), tolerance = 1e-6) expect_equivalent( - (f_1_mkin_OLS$par[1:2] - coef(f_1_nls_trans))/f_1_mkin_OLS$par[1:2], + (f_1_mkin_trans$par[1:2] - coef(f_1_nls_trans))/f_1_mkin_trans$par[1:2], rep(0, 2), tolerance = 1e-6) # Check the standard error for the transformed parameters se_nls <- summary(f_1_nls_trans)$coefficients[, "Std. Error"] # This is of similar magnitude as the standard error obtained with the mkin - se_mkin <- summary(f_1_mkin_OLS)$par[1:2, "Std. Error"] + se_mkin <- summary(f_1_mkin_trans)$par[1:2, "Std. Error"] se_nls_notrans <- summary(f_1_nls_notrans)$coefficients[, "Std. Error"] # This is also of similar magnitude as the standard error obtained with the mkin - se_mkin_notrans <- summary(f_1_mkin_OLS_notrans)$par[1:2, "Std. Error"] + se_mkin_notrans <- summary(f_1_mkin_notrans)$par[1:2, "Std. Error"] # The difference can partly be explained by the ratio between # the maximum likelihood estimate of the standard error sqrt(rss/n) |