diff options
| -rw-r--r-- | R/saem.R | 2 | ||||
| -rw-r--r-- | man/f_time_norm_focus.Rd | 21 | ||||
| -rw-r--r-- | man/focus_soil_moisture.Rd | 3 | ||||
| -rw-r--r-- | man/saem.Rd | 7 |
4 files changed, 22 insertions, 11 deletions
@@ -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{ |