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-rw-r--r--R/confint.mkinfit.R26
-rw-r--r--docs/reference/confint.mkinfit.html33
-rw-r--r--man/confint.mkinfit.Rd20
3 files changed, 48 insertions, 31 deletions
diff --git a/R/confint.mkinfit.R b/R/confint.mkinfit.R
index 75813360..fadd14ae 100644
--- a/R/confint.mkinfit.R
+++ b/R/confint.mkinfit.R
@@ -98,15 +98,17 @@
#' rel_diffs_transformed_ff
#' rel_diffs_untransformed_ff
#'
-#' # The profiling for the following fit does not finish in a reasonable time
-#' #m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-#' # M1 = mkinsub("SFO"),
-#' # M2 = mkinsub("SFO"),
-#' # use_of_ff = "max", quiet = TRUE)
-#' #DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-#' #f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
-#' # error_model_algorithm = "direct", quiet = TRUE)
-#' #confint(f_tc_2, "parent_0")
+#' # The profiling for the following fit does not finish in a reasonable time,
+#' # therefore we use the quadratic approximation
+#' m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+#' M1 = mkinsub("SFO"),
+#' M2 = mkinsub("SFO"),
+#' use_of_ff = "max", quiet = TRUE)
+#' DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
+#' f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
+#' error_model_algorithm = "direct", quiet = TRUE)
+#' confint(f_tc_2, method = "quadratic")
+#' confint(f_tc_2, "parent_0", method = "quadratic")
#' }
#' @export
confint.mkinfit <- function(object, parm,
@@ -164,10 +166,12 @@ confint.mkinfit <- function(object, parm,
if (transformed & backtransform) {
lci_back <- backtransform_odeparms(lci,
object$mkinmod, object$transform_rates, object$transform_fractions)
- lci <- c(lci_back, lci[names(object$errparms)])
uci_back <- backtransform_odeparms(uci,
object$mkinmod, object$transform_rates, object$transform_fractions)
- uci <- c(uci_back, uci[names(object$errparms)])
+
+ return_errparm_names <- intersect(names(object$errparms), return_pnames)
+ lci <- c(lci_back, lci[return_errparm_names])
+ uci <- c(uci_back, uci[return_errparm_names])
}
}
ci <- cbind(lower = lci, upper = uci)
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 0053894b..27fdb304 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -236,7 +236,7 @@ machines, cores &gt; 1 is not supported.</p></td>
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>f_d_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 51.063 0.000 51.090 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span>
+#&gt; 50.787 0.000 50.815 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span>
<span class='co'># system.time(ci_profile &lt;- confint(f_d_1, cores = 5))</span>
<span class='co'># system.time(ci_profile &lt;- confint(f_d_1,</span>
<span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))</span>
@@ -322,16 +322,27 @@ machines, cores &gt; 1 is not supported.</p></td>
#&gt; k_m1 0.0146746451 0.0025300990
#&gt; f_parent_to_m1 0.0046997668 0.0023460293
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'>
-# The profiling for the following fit does not finish in a reasonable time
-#m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-# M1 = mkinsub("SFO"),
-# M2 = mkinsub("SFO"),
-# use_of_ff = "max", quiet = TRUE)
-#DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-#f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
-# error_model_algorithm = "direct", quiet = TRUE)
-#confint(f_tc_2, "parent_0")
-# }
+<span class='co'># The profiling for the following fit does not finish in a reasonable time,</span>
+<span class='co'># therefore we use the quadratic approximation</span>
+<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
+ <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
+ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>DFOP_par_c</span> <span class='kw'>&lt;-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>
+<span class='no'>f_tc_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>,
+ <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 94.596183241 106.19937044
+#&gt; k_M1 0.037605436 0.04490758
+#&gt; k_M2 0.008568746 0.01087675
+#&gt; f_parent_to_M1 0.021464277 0.62023879
+#&gt; f_parent_to_M2 0.015166876 0.37975352
+#&gt; k1 0.273897622 0.33388081
+#&gt; k2 0.018614564 0.02250380
+#&gt; g 0.671943572 0.73583247
+#&gt; sigma_low 0.251284138 0.83992136
+#&gt; rsd_high 0.040410998 0.07661999</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 94.59618 106.1994</div><div class='input'># }
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd
index 99f5875c..bad73407 100644
--- a/man/confint.mkinfit.Rd
+++ b/man/confint.mkinfit.Rd
@@ -112,15 +112,17 @@ rel_diffs_untransformed_ff <- abs((ci_quadratic_untransformed_ff - ci_profile_ff
rel_diffs_transformed_ff
rel_diffs_untransformed_ff
-# The profiling for the following fit does not finish in a reasonable time
-#m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-# M1 = mkinsub("SFO"),
-# M2 = mkinsub("SFO"),
-# use_of_ff = "max", quiet = TRUE)
-#DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-#f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
-# error_model_algorithm = "direct", quiet = TRUE)
-#confint(f_tc_2, "parent_0")
+# The profiling for the following fit does not finish in a reasonable time,
+# therefore we use the quadratic approximation
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+ M1 = mkinsub("SFO"),
+ M2 = mkinsub("SFO"),
+ use_of_ff = "max", quiet = TRUE)
+DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
+f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
+ error_model_algorithm = "direct", quiet = TRUE)
+confint(f_tc_2, method = "quadratic")
+confint(f_tc_2, "parent_0", method = "quadratic")
}
}
\references{

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