More work on f_time_norm_focus

4 files changed, 22 insertions, 11 deletions

diff --git a/R/saem.R b/R/saem.R
index 408e62e8..3376d3c6 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -1,3 +1,5 @@
+utils::globalVariables(c("predicted", "std"))
+
 #' Fit nonlinear mixed models with SAEM
 #'
 #' This function uses [saemix::saemix()] as a backend for fitting nonlinear mixed
diff --git a/man/f_time_norm_focus.Rd b/man/f_time_norm_focus.Rd
index 9d858312..bc7faa6a 100644
--- a/man/f_time_norm_focus.Rd
+++ b/man/f_time_norm_focus.Rd
@@ -19,7 +19,14 @@ f_time_norm_focus(object, ...)
   ...
 )
 
-\method{f_time_norm_focus}{mkindsg}(object, Q10 = 2.58, walker = 0.7, f_na = NA, ...)
+\method{f_time_norm_focus}{mkindsg}(
+  object,
+  study_moisture_ref_source = c("meta", "focus"),
+  Q10 = 2.58,
+  walker = 0.7,
+  f_na = NA,
+  ...
+)
 }
 \arguments{
 \item{object}{An object containing information used for the calculations}
@@ -39,21 +46,21 @@ f_time_norm_focus(object, ...)
 
 \item{f_na}{The factor to use for NA values. If set to NA, only factors
 for complete cases will be returned.}
+
+\item{study_moisture_ref_source}{Source for the reference value
+used to calculate the study moisture}
 }
 \description{
 Time step normalisation factors for aerobic soil degradation as described
 in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).
 }
 \examples{
-f_time_norm_focus(25, 20, 25) # 1.37, compare p. 184
+f_time_norm_focus(25, 20, 25) # 1.37, compare FOCUS 2014 p. 184
 
 D24_2014$meta
 # No moisture normalisation in the first dataset, so we use f_na = 1 to get
-# Temperature only normalisation as in the EU evaluation
-f_time_norm_focus(D24_2014, f_na = 1)
-# Moisture normalisation for the other four soils is one, as soil moisture
-# is higher than the approximate field capacity derived from the USDA soil
-# type
+# temperature only normalisation as in the EU evaluation
+f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1)
 }
 \references{
 FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
diff --git a/man/focus_soil_moisture.Rd b/man/focus_soil_moisture.Rd
index 015dd261..789e64c0 100644
--- a/man/focus_soil_moisture.Rd
+++ b/man/focus_soil_moisture.Rd
@@ -16,7 +16,8 @@ Version 2.2, May 2014 \url{https://esdac.jrc.ec.europa.eu/projects/ground-water}
 focus_soil_moisture
 }
 \description{
-FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
+The value were transcribed from p. 36. The table assumes field capacity
+corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.
 }
 \examples{
 focus_soil_moisture
diff --git a/man/saem.Rd b/man/saem.Rd
index 3cd9f7f8..ef5480f1 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -109,7 +109,7 @@ fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
 dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
   A1 = mkinsub("SFO"))
 # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,
-# and compiled ODEs for FOMC, both are fast
+# and compiled ODEs for FOMC that are much slower
 f_mmkin <- mmkin(list(
     "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo),
   ds, quiet = TRUE)
@@ -121,11 +121,12 @@ f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
 # We can use print, plot and summary methods to check the results
 print(f_saem_dfop_sfo)
 plot(f_saem_dfop_sfo)
-summary(f_saem_dfop_sfo, data = FALSE)
+summary(f_saem_dfop_sfo, data = TRUE)
 
 # Using a single core, the following takes about 6 minutes as we do not have an
 # analytical solution. Using 10 cores it is slower instead of faster
-#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
+f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
+plot(f_saem_fomc)
 }
 }
 \seealso{