Make na.rm = FALSE the default for geomean()

This makes more sense and is in line with mean() from base R. Adapt
tests and update docs.

1 files changed, 23 insertions, 7 deletions

diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index a9e6c49..a198f24 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -4,14 +4,30 @@
 \alias{PEC_soil}
 \title{Calculate predicted environmental concentrations in soil}
 \usage{
-PEC_soil(rate, rate_units = "g/ha", interception = 0,
-  mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L",
-  interval = NA, n_periods = Inf, tillage_depth = 20,
-  leaching_depth = tillage_depth, crop = "annual",
-  cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA,
-  Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL,
+PEC_soil(
+  rate,
+  rate_units = "g/ha",
+  interception = 0,
+  mixing_depth = 5,
+  PEC_units = "mg/kg",
+  PEC_pw_units = "mg/L",
+  interval = NA,
+  n_periods = Inf,
+  tillage_depth = 20,
+  leaching_depth = tillage_depth,
+  crop = "annual",
+  cultivation = FALSE,
+  chent = NA,
+  DT50 = NA,
+  FOMC = NA,
+  Koc = NA,
+  Kom = Koc/1.724,
+  t_avg = 0,
+  t_act = NULL,
   scenarios = c("default", "EFSA_2017", "EFSA_2015"),
-  leaching = scenarios == "EFSA_2017", porewater = FALSE)
+  leaching = scenarios == "EFSA_2017",
+  porewater = FALSE
+)
 }
 \arguments{
 \item{rate}{Application rate in units specified below}