From 650d6969f7d8af70bc6334adf48d408e68676cec Mon Sep 17 00:00:00 2001
From: Gregor Gorjanc <gregor.gorjanc@gmail.com>
Date: Wed, 20 Dec 2023 16:24:02 +0100
Subject: [PATCH] Fixing SP stuff

---
 R/Functions_L0_auxilary.R | 5 ++---
 man/MultiColony-class.Rd  | 8 ++++----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/R/Functions_L0_auxilary.R b/R/Functions_L0_auxilary.R
index 234ebbe9..3981542c 100644
--- a/R/Functions_L0_auxilary.R
+++ b/R/Functions_L0_auxilary.R
@@ -2513,7 +2513,7 @@ getCsdGeno <- function(x, caste = NULL, nInd = NULL, dronesHaploid = TRUE,
                                              simParamBee$csdPosStart:simParamBee$csdPosStop,
                                              sep="_"), simParam = simParamBee)
     if (dronesHaploid && any(x@sex == "M")) {
-      ret <- reduceDroneGeno(geno = ret, pop = x, simParamBee = SP)
+      ret <- reduceDroneGeno(geno = ret, pop = x)
     }
   } else if (isColony(x)) {
     if (is.null(caste)) {
@@ -2539,8 +2539,7 @@ getCsdGeno <- function(x, caste = NULL, nInd = NULL, dronesHaploid = TRUE,
     } else {
       ret <- getCsdGeno(
         x = getCastePop(x, caste, simParamBee = simParamBee), nInd = nInd,
-        dronesHaploid = dronesHaploid,
-        simParamBee = simParamBee
+          dronesHaploid = dronesHaploid, simParamBee = simParamBee
       )
     }
   } else if (isMultiColony(x)) {
diff --git a/man/MultiColony-class.Rd b/man/MultiColony-class.Rd
index b926b1da..26ab987f 100644
--- a/man/MultiColony-class.Rd
+++ b/man/MultiColony-class.Rd
@@ -7,8 +7,8 @@
 \alias{show,MultiColony-method}
 \alias{c,MultiColony-method}
 \alias{c,MultiColonyOrNULL-method}
-\alias{[,MultiColony,integerOrNumericOrLogical-method}
-\alias{[,MultiColony,character-method}
+\alias{[,MultiColony,integerOrNumericOrLogical,ANY,ANY-method}
+\alias{[,MultiColony,character,ANY,ANY-method}
 \alias{[[,MultiColony,integerOrNumericOrLogical-method}
 \alias{[[,MultiColony,character-method}
 \alias{[<-,MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,MultiColony-method}
@@ -23,9 +23,9 @@ isMultiColony(x)
 
 \S4method{c}{MultiColonyOrNULL}(x, ...)
 
-\S4method{[}{MultiColony,integerOrNumericOrLogical}(x, i, j, drop)
+\S4method{[}{MultiColony,integerOrNumericOrLogical,ANY,ANY}(x, i, j, drop)
 
-\S4method{[}{MultiColony,character}(x, i, j, drop)
+\S4method{[}{MultiColony,character,ANY,ANY}(x, i, j, drop)
 
 \S4method{[[}{MultiColony,integerOrNumericOrLogical}(x, i)