diff options
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/endpoints.R | 39 | ||||
| -rw-r--r-- | R/nlme.mmkin.R | 5 | ||||
| -rw-r--r-- | docs/news/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/endpoints.html | 29 | ||||
| -rw-r--r-- | docs/reference/nlme.mmkin.html | 29 | ||||
| -rw-r--r-- | man/endpoints.Rd | 12 | ||||
| -rw-r--r-- | man/nlme.mmkin.Rd | 5 |
8 files changed, 101 insertions, 22 deletions
@@ -1,6 +1,6 @@ # mkin 0.9.49.10 (unreleased) -- 'nlme.mmkin': An nlme method for mmkin row objects and an associated class with plot method +- 'nlme.mmkin': An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods - 'mean_degparms, nlme_data, nlme_function': Three new functions to facilitate building nlme models from mmkin row objects diff --git a/R/endpoints.R b/R/endpoints.R index f7ee483a..586ef9ff 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -7,9 +7,13 @@ #' are equivalent to the rate constantes of the DFOP model, but with the #' advantage that the SFORB model can also be used for metabolites. #' -#' @param fit An object of class \code{\link{mkinfit}}. +#' @param fit An object of class \code{\link{mkinfit}} or +#' \code{\link{nlme.mmkin}} #' @importFrom stats optimize -#' @return A list with the components mentioned above. +#' @return A list with a matrix of dissipation times named distimes, +#' and, if applicable, a vector of formation fractions named ff +#' and, if the SFORB model was in use, a vector of eigenvalues +#' of these SFORB models, equivalent to DFOP rate constants #' @note The function is used internally by \code{\link{summary.mkinfit}}. #' @author Johannes Ranke #' @keywords manip @@ -17,6 +21,10 @@ #' #' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) #' endpoints(fit) +#' \dontrun{ +#' fit_2 <- mkinfit("SFORB", FOCUS_2006_C, quiet = TRUE) +#' endpoints(fit_2) +#' } #' #' @export endpoints <- function(fit) { @@ -25,8 +33,22 @@ endpoints <- function(fit) { # Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from # HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models ep <- list() - obs_vars <- fit$obs_vars - parms.all <- c(fit$bparms.optim, fit$bparms.fixed) + if (inherits(fit, "mkinfit")) { + mkinmod <- fit$mkinmod + parms.all <- c(fit$bparms.optim, fit$bparms.fixed) + } else { + if (inherits(fit, "nlme.mmkin")) { + mkinmod <- fit$mmkin_orig[[1]]$mkinmod + bparms.optim <- backtransform_odeparms(fit$coefficients$fixed, + mkinmod, + transform_rates = fit$mmkin_orig[[1]]$transform_rates, + transform_fractions = fit$mmkin_orig[[1]]$transform_fractions) + parms.all <- c(bparms.optim, fit$bparms.fixed) + } else { + stop("Only implemented for mkinfit and nlme.mmkin objects") + } + } + obs_vars <- names(mkinmod$spec) ep$ff <- vector() ep$SFORB <- vector() ep$distimes <- data.frame( @@ -34,7 +56,7 @@ endpoints <- function(fit) { DT90 = rep(NA, length(obs_vars)), row.names = obs_vars) for (obs_var in obs_vars) { - type = names(fit$mkinmod$map[[obs_var]])[1] + type = names(mkinmod$map[[obs_var]])[1] # Get formation fractions if directly fitted, and calculate remaining fraction to sink f_names = grep(paste("^f", obs_var, sep = "_"), names(parms.all), value=TRUE) @@ -56,7 +78,7 @@ endpoints <- function(fit) { k_tot = sum(parms.all[k_names]) DT50 = log(2)/k_tot DT90 = log(10)/k_tot - if (fit$mkinmod$use_of_ff == "min") { + if (mkinmod$use_of_ff == "min" && length(obs_vars) > 1) { for (k_name in k_names) { ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot @@ -78,7 +100,7 @@ endpoints <- function(fit) { n = parms.all[paste("N", obs_var, sep = "_")] k = k_tot # Use the initial concentration of the parent compound - source_name = fit$mkinmod$map[[1]][[1]] + source_name = mkinmod$map[[1]][[1]] c0 = parms.all[paste(source_name, "0", sep = "_")] alpha = 1 / (n - 1) beta = (c0^(1 - n))/(k * (n - 1)) @@ -86,7 +108,7 @@ endpoints <- function(fit) { DT90 = beta * (10^(1/alpha) - 1) DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011 ep$distimes[obs_var, c("DT50back")] = DT50_back - if (fit$mkinmod$use_of_ff == "min") { + if (mkinmod$use_of_ff == "min") { for (k_name in k_names) { ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot @@ -196,6 +218,7 @@ endpoints <- function(fit) { } ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90) } + if (length(ep$ff) == 0) ep$ff <- NULL if (length(ep$SFORB) == 0) ep$SFORB <- NULL return(ep) } diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index 6e3467ed..1d6c2e75 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -31,8 +31,10 @@ #' function(x) subset(x$data[c("name", "time", "value")], name == "parent")) #' f <- mmkin("SFO", ds, quiet = TRUE, cores = 1) #' library(nlme) +#' endpoints(f[[1]]) #' f_nlme <- nlme(f) #' print(f_nlme) +#' endpoints(f_nlme) #' f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1)) #' update(f_nlme_2, random = parent_0 ~ 1) #' \dontrun{ @@ -77,6 +79,9 @@ #' #' anova(f_nlme_dfop_sfo, f_nlme_fomc_sfo, f_nlme_sfo_sfo) #' anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC +#' +#' endpoints(f_nlme_sfo_sfo) +#' endpoints(f_nlme_dfop_sfo) #' } # Code inspired by nlme.nlsList nlme.mmkin <- function(model, data = sys.frame(sys.parent()), diff --git a/docs/news/index.html b/docs/news/index.html index 5fd97344..cb18664e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,7 +134,7 @@ <a href="#mkin-0-9-49-10-unreleased" class="anchor"></a>mkin 0.9.49.10 (unreleased)<small> Unreleased </small> </h1> <ul> -<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated class with plot method</p></li> +<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li> <li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li> <li><p>‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation</p></li> <li><p>Article in compiled models: Add some platform specific code and suppress warnings about zero values being removed from the FOCUS D dataset</p></li> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 68af5fcf..ef38c521 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -154,13 +154,17 @@ advantage that the SFORB model can also be used for metabolites.</p> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> <th>fit</th> - <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code> or +<code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td> </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list with the components mentioned above.</p> + <p>A list with a matrix of dissipation times named distimes, + and, if applicable, a vector of formation fractions named ff + and, if the SFORB model was in use, a vector of eigenvalues + of these SFORB models, equivalent to DFOP rate constants</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> @@ -168,13 +172,24 @@ advantage that the SFORB model can also be used for metabolites.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff -#> logical(0) -#> -#> $distimes + <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 -#> </div><div class='input'> +#> </div><div class='input'> <span class='co'># \dontrun{</span> + <span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>endpoints</span>(<span class='no'>fit_2</span>)</div><div class='output co'>#> $ff +#> parent_free_sink +#> 1 +#> +#> $SFORB +#> parent_b1 parent_b2 +#> 0.4595574 0.0178488 +#> +#> $distimes +#> DT50 DT90 DT50_parent_b1 DT50_parent_b2 +#> parent 1.886925 21.25106 1.508293 38.83438 +#> </div><div class='input'> # } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 01287dda..9af9cbf7 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -253,7 +253,10 @@ parameters taken from the mmkin object are used</p></td> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)) <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) -<span class='no'>f_nlme</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>) +<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='fl'>1</span>]])</div><div class='output co'>#> $distimes +#> DT50 DT90 +#> parent 11.96183 39.73634 +#> </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>) <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood #> Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink) #> Data: "Not shown" @@ -270,7 +273,10 @@ parameters taken from the mmkin object are used</p></td> #> StdDev: 1.30857 1.288591 6.304906 #> #> Number of Observations: 90 -#> Number of Groups: 5 </div><div class='input'><span class='no'>f_nlme_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)) +#> Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#> $distimes +#> DT50 DT90 +#> parent 17.51545 58.18505 +#> </div><div class='input'><span class='no'>f_nlme_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)) <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood #> Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink) #> Data: "Not shown" @@ -410,7 +416,24 @@ parameters taken from the mmkin object are used</p></td> #> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33913 <.0001 #> f_nlme_sfo_sfo 3 9 1085.1821 1113.4042 -533.5910 2 vs 3 270.66712 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_dfop_sfo 1 13 843.8541 884.6194 -408.927 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4042 -533.591 1 vs 2 249.328 <.0001</div><div class='input'># } +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4042 -533.591 1 vs 2 249.328 <.0001</div><div class='input'> + <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> $ff +#> parent_sink parent_A1 A1_sink +#> 0.5912435 0.4087565 1.0000000 +#> +#> $distimes +#> DT50 DT90 +#> parent 19.13517 63.56565 +#> A1 66.02149 219.31865 +#> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_dfop_sfo</span>)</div><div class='output co'>#> $ff +#> parent_A1 parent_sink A1_sink +#> 0.2768571 0.7231429 1.0000000 +#> +#> $distimes +#> DT50 DT90 DT50_k1 DT50_k2 +#> parent 11.07092 104.6325 4.462389 46.2085 +#> A1 162.30937 539.1801 NA NA +#> </div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/man/endpoints.Rd b/man/endpoints.Rd index be180737..26b5ee08 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -8,10 +8,14 @@ with mkinfit} endpoints(fit) } \arguments{ -\item{fit}{An object of class \code{\link{mkinfit}}.} +\item{fit}{An object of class \code{\link{mkinfit}} or +\code{\link{nlme.mmkin}}} } \value{ -A list with the components mentioned above. +A list with a matrix of dissipation times named distimes, + and, if applicable, a vector of formation fractions named ff + and, if the SFORB model was in use, a vector of eigenvalues + of these SFORB models, equivalent to DFOP rate constants } \description{ This function calculates DT50 and DT90 values as well as formation fractions @@ -27,6 +31,10 @@ The function is used internally by \code{\link{summary.mkinfit}}. fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) endpoints(fit) + \dontrun{ + fit_2 <- mkinfit("SFORB", FOCUS_2006_C, quiet = TRUE) + endpoints(fit_2) + } } \author{ diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 26dcce66..97d444e4 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -79,8 +79,10 @@ ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c("name", "time", "value")], name == "parent")) f <- mmkin("SFO", ds, quiet = TRUE, cores = 1) library(nlme) +endpoints(f[[1]]) f_nlme <- nlme(f) print(f_nlme) +endpoints(f_nlme) f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1)) update(f_nlme_2, random = parent_0 ~ 1) \dontrun{ @@ -125,6 +127,9 @@ update(f_nlme_2, random = parent_0 ~ 1) anova(f_nlme_dfop_sfo, f_nlme_fomc_sfo, f_nlme_sfo_sfo) anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC + + endpoints(f_nlme_sfo_sfo) + endpoints(f_nlme_dfop_sfo) } } \seealso{ |