Dd odeint log

DDD.Rproj

@@ -1,5 +1,4 @@
 Version: 1.0
-ProjectId: cbff7951-4a06-4670-bbdf-df0ae63c05bf
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

R/RcppExports.R

@@ -8,6 +8,13 @@ dd_integrate_bw_odeint <- function(ry, times, pars, atol, rtol, stepper) {
 #' @useDynLib DDD
 NULL
 
+dd_integrate_log_odeint <- function(ry, times, pars, atol, rtol, stepper) {
+    .Call('_DDD_dd_integrate_log_odeint', PACKAGE = 'DDD', ry, times, pars, atol, rtol, stepper)
+}
+
+#' @useDynLib DDD
+NULL
+
 dd_integrate_odeint <- function(ry, times, pars, atol, rtol, stepper) {
     .Call('_DDD_dd_integrate_odeint', PACKAGE = 'DDD', ry, times, pars, atol, rtol, stepper)
 }

R/dd_ML.R

@@ -97,6 +97,8 @@ parsfixdefault = function(ddmodel,brts,missnumspec,idparsopt)
 #' tolerance of parameter values in optimization
 #' @param tolint Sets the tolerance of the numerical integration. COnsists of:
 #' \cr absoltint = absolute tolerance and \cr reltolint = relative tolerance.
+#' @param k_threshold Sets the threshold of number of species above which
+#' logarithmic integration must be used. Default is Inf.
 #' @param maxiter Sets the maximum number of iterations in the optimization
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
@@ -148,6 +150,7 @@ dd_ML = function(
   soc = 2,
   tol = c(1E-3, 1E-4, 1E-6),
   tolint = c(1E-10,1E-8),
+  k_threshold = 3,
   maxiter = 1000 * round((1.25)^length(idparsopt)),
   changeloglikifnoconv = FALSE,
   optimmethod = 'simplex',
@@ -186,7 +189,7 @@ dd_ML = function(
       trparsopt[which(initparsopt == Inf)] = 1
       trparsfix = parsfix/(1 + parsfix)
       trparsfix[which(parsfix == Inf)] = 1
-      pars2 = c(res,ddmodel,cond,btorph,verbose,soc,tol,maxiter,abstolint = tolint[1],reltolint = tolint[2])
+      pars2 = c(res,ddmodel,cond,btorph,verbose,soc,tol,maxiter,abstolint = tolint[1],reltolint = tolint[2],k_threshold = k_threshold)
       optimpars = c(tol,maxiter)
       initloglik = dd_loglik_choosepar(trparsopt = trparsopt,trparsfix = trparsfix,idparsopt = idparsopt,idparsfix = idparsfix,pars2 = pars2,brts = brts,missnumspec = missnumspec, methode = methode)
       cat("The loglikelihood for the initial parameter values is",initloglik,"\n")