bugfixes

jdtuck · Oct 7, 2023 · 64330e6 · 64330e6
1 parent 328f5ae
commit 64330e6
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/R/geometry.R b/R/geometry.R
@@ -154,7 +154,7 @@ findkarcherinv <- function(warps, times, round = F){
 #' @keywords srvf alignment
 #' @export
 gam_to_v<-function(gam, smooth=TRUE){
-  if (ndims(gam_obs) == 0){
+  if (ndims(gam) == 0){
     TT = length(gam)
     eps = .Machine$double.eps
     time <- seq(0,1,length.out=TT)
@@ -164,7 +164,7 @@ gam_to_v<-function(gam, smooth=TRUE){
     if (smooth) {
       tmp.spline <- stats::smooth.spline(gam)
       g <- stats::predict(tmp.spline, deriv = 1)$y / binsize
-      g[x<0] = 0
+      g[g<0] = 0
       psi = sqrt(g)
     } else {
         psi = sqrt(gradient(gam,binsize))
@@ -186,7 +186,7 @@ gam_to_v<-function(gam, smooth=TRUE){
       for (i in 1:n) {
         tmp.spline <- stats::smooth.spline(gam[,i])
         g[, i] <- stats::predict(tmp.spline, deriv = 1)$y / binsize
-        g[x<0, i] = 0
+        g[g[,i]<0, i] = 0
         psi[,i] = sqrt(g[, i])
       }
     } else {

diff --git a/R/multiple_align_functions.R b/R/multiple_align_functions.R
@@ -143,9 +143,22 @@ multiple_align_functions <- function(f, time, mu, lambda = 0, pen="roughness",
   amp.var = trapz(time,std_fn^2)
   phase.var = trapz(time,var_fgam)
 
-  out <- list(f0=f,time=time,fn=fn,qn=qn,q0=q0,fmean=fmean,mqn=mqn,gam=gam,
-              orig.var=orig.var,amp.var=amp.var,phase.var=phase.var,
-              qun=0,lambda=lambda,method="mean",omethod=omethod,gamI=gamI,rsamps=F)
+  out <- list(f0=f,time=time,fn=fn,qn=qn,q0=q0,fmean=fmean,mqn=mqn,warping_functions=gam,
+              original_variance=orig.var,amplitude_variance=amp.var,phase_variance=phase.var,
+              qun=0,
+              inverse_average_warping_function = gamI,
+              rsamps = FALSE,
+              call = list(
+                lambda = lambda,
+                penalty_method = pen,
+                centroid_type = "mean",
+                center_warpings = FALSE,
+                smooth_data = smooth_data,
+                sparam = sparam,
+                parallel = parallel,
+                optim_method = omethod,
+                max_iter = MaxItr
+              ))
 
   class(out) <- 'fdawarp'