Merge branch 'devel' of https://github.com/LStrachan/SIMplyBee_fork i…

…nto devel
HighlanderLab · Dec 21, 2023 · fb126a0 · fb126a0
2 parents 47cca09 + 8ef1cf4
commit fb126a0
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Showing 4 changed files with 38 additions and 38 deletions.
diff --git a/tests/testthat/test-L0_auxiliary_functions.R b/tests/testthat/test-L0_auxiliary_functions.R
@@ -1,7 +1,7 @@
 # ---- nColonies ----
 test_that("nColonies", {
   founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   expect_equal(nColonies(createMultiColony(n = 2, simParamBee = SP)), 2)
@@ -13,7 +13,7 @@ test_that("nColonies", {
 # ---- nCaste ----
 test_that("nCaste", {
   founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
 
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(x = basePop[1], nInd = 45, simParamBee = SP)
@@ -38,7 +38,7 @@ test_that("nCaste", {
 
 test_that("nQueens", {
   founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 1000, simParamBee = SP)
@@ -58,7 +58,7 @@ test_that("nQueens", {
 # ---- nDrones ----
 test_that("nDrones", {
   founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 1000, simParamBee = SP)
@@ -101,7 +101,7 @@ test_that("isGenoHeterozygous", {
 
 test_that("isCaste", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -229,7 +229,7 @@ test_that("nHomBrood", {
 
 test_that("isQueenPresent", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -257,7 +257,7 @@ test_that("isQueenPresent", {
 
 test_that("isVirginQueensPresent", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -287,7 +287,7 @@ test_that("isVirginQueensPresent", {
 
 test_that("isProductive", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -321,7 +321,7 @@ test_that("isProductive", {
 
 test_that("reduceDroneHaplo", {
   founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(x = basePop[1], nInd = 2, simParamBee = SP)
@@ -345,7 +345,7 @@ test_that("reduceDroneHaplo", {
 
 test_that("reduceDroneGeno", {
   founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(x = basePop[1], nInd = 2, simParamBee = SP)
@@ -555,7 +555,7 @@ test_that("nCsdAlleles", {
 
 test_that("calcBeeGRMIbs", {
   founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   SP$setTrackRec(TRUE)
   SP$setTrackPed(isTrackPed = TRUE)
@@ -663,7 +663,7 @@ test_that("emptyNULL", {
 
 test_that("isDronesPresent", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -688,7 +688,7 @@ test_that("isDronesPresent", {
 
 test_that("isFathersPresent", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -716,7 +716,7 @@ test_that("isFathersPresent", {
 
 test_that("isWorkersPresent", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -772,7 +772,7 @@ test_that("isGenoHeterozygous", {
 # ---- getBV ----
 test_that("getBV", {
    founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-   SP <- SimParamBee$new(founderGenomes)
+   SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
    SP$nThreads = 1L
    SP$addTraitA(nQtlPerChr = 10, var = 1)
    SP$addSnpChip(5)
@@ -802,7 +802,7 @@ test_that("getBV", {
 # ---- getDd ----
 test_that("getDd", {
    founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-   SP <- SimParamBee$new(founderGenomes)
+   SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
    SP$nThreads = 1L
    SP$addTraitAD(nQtlPerChr = 10, meanDD = 0.2, varDD = 0.1)
    basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
@@ -831,7 +831,7 @@ test_that("getDd", {
 # ---- getAa ----
 test_that("getAa", {
    founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-   SP <- SimParamBee$new(founderGenomes)
+   SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
    SP$nThreads = 1L
    SP$addTraitADE(nQtlPerChr = 10, meanDD = 0.2, varDD = 0.1, relAA = 0.5)
    basePop <- createVirginQueens(founderGenomes, simParamBee = SP)

diff --git a/tests/testthat/test-L1_pop_functions.R b/tests/testthat/test-L1_pop_functions.R
@@ -2,7 +2,7 @@
 
 test_that("getCastePop", {
   founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 15, simParamBee = SP)
@@ -37,7 +37,7 @@ test_that("getCastePop", {
 
 test_that("createVirginQueens", {
   founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   #check that output is virginqueens ?
   expect_true(all(isVirginQueen(createVirginQueens(founderGenomes, simParamBee = SP), simParamBee = SP)))
@@ -88,7 +88,7 @@ test_that("createVirginQueens", {
 
 test_that("createDrones", {
   founderGenomes <- quickHaplo(nInd = 6, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   # Error: x can't be a MapPop
   expect_error(createDrones(founderGenomes, simParamBee = SP))
@@ -134,7 +134,7 @@ test_that("createDrones", {
 
 test_that("combineBeeGametes", {
   founderGenomes <- quickHaplo(nInd = 6, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 15, simParamBee = SP)
@@ -165,7 +165,7 @@ test_that("combineBeeGametes", {
 
 test_that("pullCastePop", {
   founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 15, simParamBee = SP)
@@ -221,7 +221,7 @@ test_that("pullCastePop", {
 # ---- cross ----
 test_that("cross", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, nInd = 100, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 1000, simParamBee = SP)
@@ -285,7 +285,7 @@ test_that("cross", {
 # ---- setQueensYearOfBirth ----
 test_that("setQueensYearOfBirth", {
   founderGenomes <- quickHaplo(nInd = 7, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, nInd = 100, simParamBee = SP)
   drones <- createDrones(x = basePop[1], nInd = 1000, simParamBee = SP)
@@ -317,7 +317,7 @@ test_that("setQueensYearOfBirth", {
 # ---- createDCA ----
 test_that("createDCA", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -352,7 +352,7 @@ test_that("createDCA", {
 # ---- pullDroneGroupsFromDCA ----
 test_that("pullDroneGroupsFromDCA", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -382,7 +382,7 @@ test_that("pullDroneGroupsFromDCA", {
 
 test_that("combineBeeGametes", {
    founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
-   SP <- SimParamBee$new(founderGenomes)
+   SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
    SP$nThreads = 1L
    basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -398,7 +398,7 @@ test_that("combineBeeGametes", {
 
 test_that("combineBeeGametesHaploidDiploid", {
    founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
-   SP <- SimParamBee$new(founderGenomes)
+   SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
    SP$nThreads = 1L
    basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 

diff --git a/tests/testthat/test-L2_colony_functions.R b/tests/testthat/test-L2_colony_functions.R
@@ -2,7 +2,7 @@
 
 test_that("createColony", {
    founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
-   SP <- SimParamBee$new(founderGenomes)
+   SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
    SP$nThreads = 1L
    basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
    drones <- createDrones(x = basePop[1], nInd = 15, simParamBee = SP)
@@ -22,7 +22,7 @@ test_that("createColony", {
 
 test_that("reQueen", {
   founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(x = basePop[1], nInd = 30, simParamBee = SP)
@@ -279,7 +279,7 @@ test_that("removeFunctions", {
 # ---- SetLocation ----
 test_that("setLocation", {
   founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 50)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 1000, simParamBee = SP)
@@ -319,7 +319,7 @@ test_that("setLocation", {
 
 test_that("supersede", {
   founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 1000, simParamBee = SP)
@@ -396,7 +396,7 @@ test_that("split", {
 
 test_that("resetEvents", {
   founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -511,7 +511,7 @@ test_that("swarm", {
 
 test_that("collapse", {
   founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 1000, simParamBee = SP)

diff --git a/tests/testthat/test-L3_Colonies_functions.R b/tests/testthat/test-L3_Colonies_functions.R
@@ -4,7 +4,7 @@
 
 test_that("createMultiColony", {
   founderGenomes <- quickHaplo(nInd = 6, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   drones <- createDrones(basePop[1], n = 100, simParamBee = SP)
@@ -41,7 +41,7 @@ test_that("createMultiColony", {
 
 test_that("selectColonies", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
 
@@ -85,7 +85,7 @@ test_that("selectColonies", {
 
 test_that("pullColonies", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   # Error if argument multicolony isn't a multicolony class
@@ -126,7 +126,7 @@ test_that("pullColonies", {
 
 test_that("removeColonies", {
   founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
-  SP <- SimParamBee$new(founderGenomes)
+  SP <- SimParamBee$new(founderGenomes, csdChr = NULL)
   SP$nThreads = 1L
   basePop <- createVirginQueens(founderGenomes, simParamBee = SP)
   # Error if argument multicolony isn't a multicolony class