diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-10-22 13:14:31 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-10-22 13:17:40 +0200 |
| commit | 0af6a61b84cc29cdbfad16a6fc7ee0e6f88c7d0f (patch) | |
| tree | 7cb2715570688cac8c94b58e4ef78ba8afa29cc3 | |
| parent | cb3adccaa4cdebc36c506fcb76c0d7c1d7e4e455 (diff) | |
Really fix check for nlme::varConstProp
And add output for nlme fit translating the mkinfit error model "obs"
into nlme::varIdent().
| -rw-r--r-- | R/nlme.mmkin.R | 3 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/nlme.mmkin.html | 51 | ||||
| -rw-r--r-- | man/nlme.mmkin.Rd | 3 |
4 files changed, 53 insertions, 6 deletions
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index 7f7e34e9..c8a99d59 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -101,7 +101,7 @@ get_deg_func <- function() { #' endpoints(f_nlme_sfo_sfo) #' endpoints(f_nlme_dfop_sfo) #' -#' if (findFunction("varConstProp")) { # tc error model for nlme available +#' if (length(findFunction("varConstProp")) > 0) { # tc error model for nlme available #' # Attempts to fit metabolite kinetics with the tc error model #' #f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo, #' # "SFO-SFO-ff" = m_sfo_sfo_ff, @@ -126,6 +126,7 @@ get_deg_func <- function() { #' "DFOP-SFO" = m_dfop_sfo), #' ds_2, quiet = TRUE, error_model = "obs") #' f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ]) +#' print(f_nlme_sfo_sfo_obs) #' # The same with DFOP-SFO does not converge, apparently the variances of #' # parent and A1 are too similar in this case, so that the model is #' # overparameterised diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index e3f126c0..4bca36e6 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-10-22T11:08Z +last_built: 2020-10-22T11:16Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index d186d785..6e83b700 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -448,7 +448,7 @@ with additional elements</p> #> parent 11.07091 104.6320 31.49738 4.462384 46.20825 #> A1 162.30536 539.1667 NA NA NA #> </div><div class='input'> - <span class='kw'>if</span> <span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> + <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> <span class='co'># Attempts to fit metabolite kinetics with the tc error model</span> <span class='co'>#f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo,</span> <span class='co'># "SFO-SFO-ff" = m_sfo_sfo_ff,</span> @@ -469,11 +469,56 @@ with additional elements</p> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span> <span class='op'>}</span> -</div><div class='output co'>#> <span class='error'>Error in if (findFunction("varConstProp")) { f_tc <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, error_model = "tc") f_nlme_sfo_tc <- nlme(f_tc["SFO", ]) f_nlme_dfop_tc <- nlme(f_tc["DFOP", ]) AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc) print(f_nlme_dfop_tc)}: argument is not interpretable as logical</span></div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, +</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood +#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1, log_k2, g_ilr) +#> Data: "Not shown" +#> Log-likelihood: -238.4298 +#> Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> parent_0 log_k1 log_k2 g_ilr +#> 94.04774463 -1.82339924 -4.16715509 0.04020161 +#> +#> Random effects: +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Level: ds +#> Structure: Diagonal +#> parent_0 log_k1 log_k2 g_ilr Residual +#> StdDev: 2.473883 0.8499901 1.337187 0.3294411 1 +#> +#> Variance function: +#> Structure: Constant plus proportion of variance covariate +#> Formula: ~fitted(.) +#> Parameter estimates: +#> const prop +#> 2.23222625 0.01262414 +#> Number of Observations: 90 +#> Number of Groups: 5 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> - <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span> + <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> +</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood +#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink) +#> Data: "Not shown" +#> Log-likelihood: -472.976 +#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) +#> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink +#> 87.975536 -3.669816 -4.164127 -4.645073 +#> +#> Random effects: +#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) +#> Level: ds +#> Structure: Diagonal +#> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual +#> StdDev: 3.992214 1.77702 1.054733 0.4821383 6.482585 +#> +#> Variance function: +#> Structure: Different standard deviations per stratum +#> Formula: ~1 | name +#> Parameter estimates: +#> parent A1 +#> 1.0000000 0.2050003 +#> Number of Observations: 170 +#> Number of Groups: 5 </div><div class='input'> <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span> <span class='co'># parent and A1 are too similar in this case, so that the model is</span> <span class='co'># overparameterised</span> <span class='co'>#f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span> diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 0af670a0..08ce1ad8 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -131,7 +131,7 @@ endpoints(f_nlme_dfop) endpoints(f_nlme_sfo_sfo) endpoints(f_nlme_dfop_sfo) - if (findFunction("varConstProp")) { # tc error model for nlme available + if (length(findFunction("varConstProp")) > 0) { # tc error model for nlme available # Attempts to fit metabolite kinetics with the tc error model #f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo, # "SFO-SFO-ff" = m_sfo_sfo_ff, @@ -156,6 +156,7 @@ endpoints(f_nlme_dfop) "DFOP-SFO" = m_dfop_sfo), ds_2, quiet = TRUE, error_model = "obs") f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ]) + print(f_nlme_sfo_sfo_obs) # The same with DFOP-SFO does not converge, apparently the variances of # parent and A1 are too similar in this case, so that the model is # overparameterised |