Merge pull request #38 from mathesong/add_spline_tacfit

Add spline tacfit

Author: mathesong

.Rbuildignore

@@ -5,3 +5,6 @@
 ^\.github$
 ^README.Rmd
 ^data-raw
+^CLAUDE\.md$
+^LICENSE\.md$
+^docker*

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: kinfitr
 Title: Kinetic Modelling of PET Time Activity Curves
-Date: 2025-10-14
-Version: 0.9.0
+Date: 2025-10-23
+Version: 0.9.1
 Authors@R: person("Granville", "Matheson", email = "[email protected]", role = c("aut", "cre"))
 Description: This package calculates outcome parameters for PET data using time activity curves (TACs). This will allow for more reproducible PET modelling research.
 Depends:

NAMESPACE

@@ -4,6 +4,7 @@ S3method(plot,blooddata)
 S3method(plot,interpblood)
 S3method(plot,kinfit)
 S3method(predict,blmod)
+S3method(predict,spline_tac)
 export("%>%")
 export(Logan_tstar)
 export(Loganplot)
@@ -105,6 +106,7 @@ export(plot_refLoganfit)
 export(plot_refPatlakfit)
 export(plot_refmlLoganfit)
 export(plot_residuals)
+export(plot_spline_tacfit)
 export(plot_srtm2fit)
 export(plot_srtm_vfit)
 export(plot_srtmfit)
@@ -122,6 +124,7 @@ export(refmlLogan)
 export(refmlLogan_tstar)
 export(shift_timings)
 export(shift_timings_df)
+export(spline_tac)
 export(srtm)
 export(srtm2)
 export(srtm2_model)

R/kinfitr_feng_1tc_ref.R

@@ -19,7 +19,13 @@
 #'   accommodate zero values in the TAC before rising. If FALSE, the TAC must
 #'   rise at time = 0.
 #' @param frameStartEnd Optional. This allows one to specify the beginning and
-#'   final frame to use for modelling, e.g. c(1,20).
+#'   final frame to use for modelling, e.g. c(1,20). This can be used to assess
+#'   time stability for example.
+#' @param timeStartEnd Optional. This allows one to specify the beginning and
+#'   end time point instead of defining the frame numbers using frameStartEnd.
+#'   This function will restrict the model to all time frames whose t_tac is
+#'   between the values, i.e. c(0,5) will select all frames with midtimes
+#'   during the first 5 minutes.
 #' @param multstart_iter Number of iterations for starting parameters. Default
 #'   is 500. For more information, see
 #'   \code{\link[nls.multstart]{nls_multstart}}.
@@ -49,8 +55,14 @@
 feng_1tc_tac <- function(t_tac, tac, weights = NULL,
                          fit_t0 = TRUE,
                          frameStartEnd = NULL,
+                         timeStartEnd = NULL,
                          multstart_iter = 500) {
 
+  # Convert timeStartEnd to frameStartEnd if needed
+  if (is.null(frameStartEnd) && !is.null(timeStartEnd)) {
+    frameStartEnd <- c(which(t_tac >= timeStartEnd[1])[1],
+                       tail(which(t_tac <= timeStartEnd[2]), 1))
+  }
 
   # Tidying
 

R/kinfitr_ma1.R

@@ -3,14 +3,14 @@
 #' Function to fit the MA1 of Ichise et al (2002) to data.
 #'
 #' @param t_tac Numeric vector of times for each frame in minutes. We use the time halfway through the frame as well as a
-#' zero. If a time zero frame is not included, it will be added.
+#' zero. If a time zero frame is not included, it  will be added.
 #' @param tac Numeric vector of radioactivity concentrations in the target tissue for each frame. We include zero at time
 #' zero: if not included, it is added.
 #' @param input Data frame containing the blood, plasma, and parent fraction concentrations over time.  This can be generated
 #' using the \code{blood_interp} function.
-#' @param tstar The t* specification for regression. If tstar_type="frames", 
+#' @param tstar The t* specification for regression. If tstar_type="frames",
 #' this is the number of frames from the end to include (e.g., 10 means last 10 frames).
-#' If tstar_type="time", this is the time point (in minutes) after which all frames 
+#' If tstar_type="time", this is the time point (in minutes) after which all frames
 #' with midpoints later than this time are included. This value can be estimated using \code{ma1_tstar}.
 #' @param tstar_type Either "frames" (default) or "time", specifying how to interpret tstar.
 #' @param tstarIncludedFrames Deprecated. Use 'tstar' with 'tstar_type="frames"' instead.
@@ -63,7 +63,7 @@ ma1 <- function(t_tac, tac, input, tstar, weights = NULL,
 
   # Convert timeStartEnd to frameStartEnd if needed
   if (is.null(frameStartEnd) && !is.null(timeStartEnd)) {
-    frameStartEnd <- c(which(t_tac >= timeStartEnd[1])[1], 
+    frameStartEnd <- c(which(t_tac >= timeStartEnd[1])[1],
                        tail(which(t_tac <= timeStartEnd[2]), 1))
   }
 
@@ -317,7 +317,7 @@ plot_ma1fit <- function(ma1out, roiname = NULL) {
 ma1_tstar <- function(t_tac, lowroi, medroi, highroi, input, filename = NULL, inpshift = 0, vB = 0, frameStartEnd = NULL, timeStartEnd = NULL, gridbreaks = 2) {
   # Convert timeStartEnd to frameStartEnd if needed
   if (is.null(frameStartEnd) && !is.null(timeStartEnd)) {
-    frameStartEnd <- c(which(t_tac >= timeStartEnd[1])[1], 
+    frameStartEnd <- c(which(t_tac >= timeStartEnd[1])[1],
                        tail(which(t_tac <= timeStartEnd[2]), 1))
   }