Merge branch 'develop' of https://github.com/tece-lab/DAISIEutils int…

…o develop

DESCRIPTION

@@ -38,7 +38,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 URL: https://github.com/tece-lab/DAISIEutils
 BugReports: https://github.com/tece-lab/DAISIEutils/issues
-Depends: R (>= 4.0.0)
+Depends: R (>= 4.2.0)
 Suggests: 
     testthat (>= 3.0.0),
     covr,
@@ -47,8 +47,6 @@ Config/testthat/edition: 3
 Imports: 
     sessioninfo,
     testit,
-    DAISIE (>= 4.3.1),
+    DAISIE (>= 4.4.0),
     ggplot2,
     cowplot
-Remotes:
-    rsetienne/DAISIE@v4.3.1

R/run_daisie_ml.R

@@ -76,6 +76,34 @@ run_daisie_ml <- function(daisie_data,
   ddmodel <- model_arguments$ddmodel
   cs_version <- model_arguments$cs_version
 
+  # for relaxed model run initial optimisation for initial parameters
+  if (grepl("rr", model)) {
+
+    # setup diversity-dependent DAISIE model
+    init_model_arguments <- setup_model(
+      model = "cr_dd",
+      low_rates = low_rates,
+      par_upper_bound = Inf
+    )
+    lik_res <- DAISIE::DAISIE_ML(
+      datalist = daisie_data,
+      initparsopt = init_model_arguments$initparsopt,
+      idparsnoshift = init_model_arguments$idparsnoshift,
+      idparsopt = init_model_arguments$idparsopt,
+      parsfix = init_model_arguments$parsfix,
+      idparsfix = init_model_arguments$idparsfix,
+      res = res,
+      ddmodel = init_model_arguments$ddmodel,
+      cond = cond,
+      methode = methode,
+      optimmethod = optimmethod,
+      CS_version = init_model_arguments$cs_version
+    )
+
+    # extract DAISIE parameters for initial parameters
+    initparsopt[1:5] <- unlist(lik_res)[1:5]
+  }
+
   ##### ML Optimization ####
   lik_res <- DAISIE::DAISIE_ML(
     datalist = daisie_data,

README.md

@@ -12,6 +12,8 @@
 The goal of DAISIEutils is to collect useful utility functions that are used recurrently in DAISIE projects. DAISIEutils is a companion package of the R package [DAISIE](https://github.com/rsetienne/DAISIE).
 This includes pipelines for typical analyses using DAISIE's maximum likelihood inference.
 
+**Note**: DAISIEutils depends on the latest CRAN release of DAISIE. It cannot be used with older versions of the DAISIE package.
+
 ## Installation
 
 You can install the released version of DAISIEutils from [GitHub](https://github.com/tece-lab/DAISIEutils) with: