2. N excretion: N retention used with the wrong units

IPCC 2019 Eq. 10.33 (p. 10.85) gives N retained in milk and weight gain in kg N per animal per day. On the same page, IPCC says cattle excretion then uses Eq. 10.31A: Nex = (N intake − N retention) × 365.

The package divides milk retention by 365 twice (R/ghg_emission.R:226). It then uses the result as a fraction of intake (:233).

For the dairy cow, the package's N retention is about 365× too small, so almost all intake N is counted as excreted. That overstates manure N2O and the nitrogen balance. The last column applies IPCC Eq. 10.31A to the package's own N intake, so it isolates the retention error from the intake error in section 1. With the fix, the package matches it exactly (test 02).

--- a/R/ghg_emission.R	2026-09-29 10:30:51
+++ b/R/ghg_emission.R	2026-09-29 10:30:51
@@ -223,14 +223,17 @@
                                                  ifelse(livetype_desc== "Pigs - growers" & body_weight %gel% c(40,80),0.024,
                                                         ifelse(livetype_desc== "Pigs - growers" & body_weight %gel% c(80,120),0.021,
                                                                ifelse(livetype_desc== "Pigs - dry sows/boars",0.021,0))))))),
-           n_retained = ifelse(!grepl("Pigs",livetype_desc),ifelse(annual_growth == 0,(annual_milk*(protein_milkcontent/100))/6.38/no_days,((annual_milk*(protein_milkcontent/100))/6.38)+(((annual_growth*(268-(7.03*er_growth/annual_growth)))/1000)/6.25))/no_days,#equation 10.33
+           n_retained = ifelse(!grepl("Pigs",livetype_desc),((annual_milk/no_days)*(protein_milkcontent/100))/6.38+ifelse(annual_growth > 0,(((annual_growth/no_days)*(268-(7.03*er_growth/(annual_growth/no_days))))/1000)/6.25,0),#equation 10.33, kg N/head/day
                                ifelse(livetype_desc=="Pigs - lactating/pregnant sows",n_gain+n_weaned, #equation 10.33A
                                       ifelse(livetype_desc== "Pigs - growers" | livetype_desc== "Pigs - dry sows/boars",(annual_growth*n_gain),0)))) #equation 10.33C
 
 
   #Nitrogen excretion rates
   n_excretion <- n_retention1%>%
-    mutate(n_excretion_rate = n_intake*(1-n_retained)*no_days) #equation 10.31
+    # n_intake is a herd total (ge_intake carries herd_composition); n_retained is per head
+    mutate(n_excretion_rate = ifelse(!grepl("Pigs",livetype_desc),
+                                     (n_intake-(n_retained*herd_composition))*no_days, #equation 10.31A
+                                     n_intake*(1-n_retained)*no_days)) #equation 10.31
 
   #################################################################################################################################
   #Direct N2O emissions

Reproduce this (R runtime; section 2)
Rscript reproduce_critical_issues.R 2 using reproduce_critical_issues.R (installs what it needs into its own library and cleaned @ 800d53a). Add CLEANED_FIXES=proposed_fixes.R with proposed_fixes.R for the fixed column.
Test: test-critical-02-n-excretion.R · Proposed change: F02.diff · Open an issue in CIAT/cleaned