Merge pull request #576 from LStrachan/devel

Changes to cross() to reduce chance of random warning

.Rbuildignore

@@ -6,7 +6,6 @@
 ^_pkgdown\.yml
 ^SIMplyBee\.Rproj
 ^docs
-^vignettes/*F2*
 ^vignettes/*R
 ^vignettes/*RData
 ^vignettes/*pdf
@@ -16,3 +15,5 @@
 ^vignettes/SIMplyBee\_logo\_small\.png
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^doc$
+^Meta$

vignettes/A_Honeybee_biology.Rmd

@@ -52,14 +52,15 @@ honeybee genomes that represent the founder population. You can quickly generate
 random genomes using AlphaSimR's `quickHaplo()`. These founder genomes are
 rapidly simulated by sampling chromosomes as series of 0s and 1s, and do not
 include any species-specific demographic history. This is equivalent to all loci
-having allele frequency 0.5 and being in linkage equilibrium. We use this approach
-only for demonstrations and testing.
+having allele frequency 0.5 and being in linkage equilibrium. We use this
+approach only for demonstrations and testing.
 
 Alternatively, you can more accurately simulate honeybee genomes with
 SIMplyBee's `simulateHoneyBeeGenomes()`. This function simulates the honeybee
-genome using coalescent simulation of whole chromosomes using MaCS (Chen et al., 2009)
-for three subspecies: *A. m. ligustica*, *A. m. carnica*, and *A. m. mellifera*
-according to the demographic model described by Wallberg et al. (2014).
+genome using coalescent simulation of whole chromosomes using MaCS (Chen et al.,
+2009) for three subspecies: *A. m. ligustica*, *A. m. carnica*, and *A. m.
+mellifera* according to the demographic model described by Wallberg et al.
+(2014).
 
 As a demonstration, we will use `quickHaplo()` and simulate genomes of two
 founding individuals. In this example, the genomes will be represented by only
@@ -71,12 +72,12 @@ simulation here.
 founderGenomes <- quickHaplo(nInd = 2, nChr = 3, segSites = 100)
 ```
 
-As mentioned, the `simulateHoneyBeeGenomes()` generates more realistic chromosome
-samples, but also requires much more time. Hence, when you use `simulateHoneyBeeGenomes()`,
-we suggest you save the output to an RData file that you then load in your
-environment and work with it. See the function documentation using 
-`help(simulateHoneyBeeGenomes)` to learn all the parameters involved in the
-function.
+As mentioned, the `simulateHoneyBeeGenomes()` generates more realistic
+chromosome samples, but also requires much more time. Hence, when you use
+`simulateHoneyBeeGenomes()`, we suggest you save the output to an RData file
+that you then load in your environment and work with it. See the function
+documentation using `help(simulateHoneyBeeGenomes)` to learn all the parameters
+involved in the function.
 
 Now we are ready to setup global simulation parameters using `SimParamBee`.
 `SimParamBee` builds upon AlphaSimR's `SimParam`, which includes genome and
@@ -199,7 +200,7 @@ Let's now mate our virgin queen, so that she is promoted to a queen and can
 start laying eggs of her own workers and drones.
 
 ```{r cross colony}
-colony <- cross(colony, drones = baseDrones)
+colony <- cross(colony, drones = baseDrones, checkCross = "warning")
 colony
 ```
 
@@ -222,7 +223,7 @@ buildUp(colony)
 All the functions in SIMplyBee return objects, hence we need to save them as an
 object, otherwise they are lost.
 
-```{r}
+```{r buildup and save}
 colony <- buildUp(colony)
 colony
 ```
@@ -292,13 +293,13 @@ look at `pull*()` functions. These functions return a list of objects: `pulled`
 being the pulled individuals (`Pop` object), and `remnant` being the remaining
 colony without the pulled individuals.
 
-```{r}
+```{r remnant}
 tmp <- pullWorkers(colony, n = 10)
 colony <- tmp$remnant
 colony
 ```
 
-```{r}
+```{r pulled workers}
 pulledWorkers <- tmp$pulled
 pulledWorkers
 ```
@@ -341,7 +342,7 @@ corresponding `pHomBrood()` and `nHombrood()` functions that can be applied
 either on the queen (`Pop` class) or colony (`Colony` class) directly. You can
 obtain the entire `misc` slot with the `getMisc()` function.
 
-```{r}
+```{r misc}
 getMisc(getQueen(colony))
 ```
 
@@ -371,7 +372,7 @@ current colony and mate her with her brothers. Oh, dear.
 ```{r inbred colony}
 inbredColony <- createColony(x = createVirginQueens(x = colony, nInd = 1))
 fathers <- selectInd(drones, nInd = SP$nFathers, use = "rand")
-inbredColony <- cross(inbredColony, drones = fathers)
+inbredColony <- cross(inbredColony, drones = fathers, checkCross = "warning")
 getCsdAlleles(inbredColony)
 getCsdAlleles(inbredColony, unique = TRUE)
 ```

vignettes/B_Multiple_colonies.Rmd

@@ -157,7 +157,7 @@ of drones as we have colonies in our `MultiColony`.
 # Pull 10 groups of drones from the DCA
 droneGroups <- pullDroneGroupsFromDCA(DCA, n = 10, nDrones = nFathersPoisson)
 # Cross all virgin queens in the apiary to the selected drones
-apiary1 <- cross(apiary1, drones = droneGroups)
+apiary1 <- cross(apiary1, drones = droneGroups, checkCross = "warning")
 # Check whether the queens are present (and hence mated)
 isQueenPresent(apiary1)
 ```
@@ -215,7 +215,7 @@ droneGroups <- pullDroneGroupsFromDCA(DCA,
                                       n = nColonies(apiary2), 
                                       nDrones = nFathersPoisson)
 # Cross virgin queens in apiary2 to selected drones
-apiary2 <- cross(apiary2, drones = droneGroups)
+apiary2 <- cross(apiary2, drones = droneGroups, checkCross = "warning")
 ```
 
 To learn more about the `nFathersPoisson()` function and other similar

vignettes/C_Colony_events.Rmd

@@ -44,11 +44,11 @@ fatherGroups <- pullDroneGroupsFromDCA(drones, n = 30, nDrones = 10)
 
 # Create Colony and MultiColony class, cross them and build them up
 colony <- createColony(x = basePop[11])
-colony <- cross(colony, drones = fatherGroups[[1]])
+colony <- cross(colony, drones = fatherGroups[[1]], checkCross = "warning")
 colony <- buildUp(colony, nWorkers = 100, nDrones = 20)
 
 apiary <- createMultiColony(basePop[12:17])
-apiary <- cross(apiary, drones = fatherGroups[2:7])
+apiary <- cross(apiary, drones = fatherGroups[2:7], checkCross = "warning")
 apiary <- buildUp(apiary, nWorkers = 100, nDrones = 20, exact = TRUE)
 ```
 

vignettes/D_Crossing.Rmd

@@ -155,7 +155,7 @@ to 100 drones!
 # Samples some drone for mating from the DCA
 drones <- selectInd(DCA, nInd = 10, use = "rand")
 # Mate the virgin queen with the drones
-queen1 <- cross(x = virginQueen1, drones = drones)
+queen1 <- cross(x = virginQueen1, drones = drones, checkCross = "warning")
 # Check the number of fathers for the queen
 nFathers(queen1)
 ```
@@ -207,13 +207,13 @@ Now, we can cross our virgin queens to drone groups.
 
 ```{r}
 # Pop-class with multiple queens
-queens1 <- cross(x = virginQueens1, drones = droneGroups[1:3])
+queens1 <- cross(x = virginQueens1, drones = droneGroups[1:3], checkCross = "warning")
 nFathers(queens1)
 ```
 
 ```{r}
 # MultiColony-class
-beekeeper1 <- cross(x = beekeeper1, drones = droneGroups[4:9])
+beekeeper1 <- cross(x = beekeeper1, drones = droneGroups[4:9], checkCross = "warning")
 nFathers(beekeeper1)
 ```
 
@@ -275,7 +275,7 @@ we can cross the colonies of each beekeeper by providing the `crossPlan1` to the
 
 ```{r}
 # Cross the colonies of the beekeeper 2
-beekeeper2 <- cross(x = beekeeper2, drones = DCA, crossPlan = crossPlan1)
+beekeeper2 <- cross(x = beekeeper2, drones = DCA, crossPlan = crossPlan1, checkCross = "warning")
 nFathers(beekeeper2)
 ```
 
@@ -343,7 +343,8 @@ unmated. Once we have the spatial cross plan, we can mate our colonies.
 beekeeper3 <- cross(x = beekeeper3, 
                     crossPlan = crossPlan2,
                     droneColonies = c(beekeeper1, beekeeper2),
-                    nDrones = 13)
+                    nDrones = 13,
+                    checkCross = "warning")
 # Inspect the number of fathers
 nFathers(beekeeper3)
 ```
@@ -387,15 +388,17 @@ beekeeper4 <- cross(x = beekeeper4,
                     droneColonies = c(beekeeper1, beekeeper2, beekeeper3),
                     crossPlan = "create",
                     spatial = FALSE,
-                    nDrones = 12)
+                    nDrones = 12,
+                    checkCross = "warning")
 nFathers(beekeeper4)
 
 beekeeper5 <- cross(x = beekeeper5,
                     droneColonies = c(beekeeper1, beekeeper2, beekeeper3),
                     crossPlan = "create",
                     spatial = TRUE,
                     radius = 3,
-                    nDrones = 12)
+                    nDrones = 12,
+                    checkCross = "warning")
 nFathers(beekeeper5)
 ```
 
@@ -440,7 +443,8 @@ beekeeper6 <- cross(beekeeper6,
                     drones = matingStationDCA,
                     spatial = FALSE,
                     crossPlan = "create",
-                    nDrones = 15)
+                    nDrones = 15,
+                    checkCross = "warning")
 nFathers(beekeeper6)
 ```
 
@@ -471,6 +475,7 @@ crossPlanBeekeeper7 <- c(
 
 beekeeper7 <- cross(x = beekeeper7, 
                     crossPlan = crossPlanBeekeeper7, 
-                    drones = c(singleDrone, DCA, matingStationDCA))
+                    drones = c(singleDrone, DCA, matingStationDCA),
+                    checkCross = "warning")
 nFathers(beekeeper7)
 ```

vignettes/E_Genomics.Rmd

@@ -41,7 +41,7 @@ baseQueens <- createVirginQueens(founderGenomes)
 baseDrones <- createDrones(x = baseQueens[1], nInd = 15)
 
 colony <- createColony(x = baseQueens[2])
-colony <- cross(colony, drones = baseDrones)
+colony <- cross(colony, drones = baseDrones, checkCross = "warning")
 colony <- buildUp(colony)
 ```
 

vignettes/F2_Variance_calculations.Rmd

@@ -40,13 +40,13 @@ head(basePop@gv)
 head(basePop@pheno)
 drones <- createDrones(x = basePop[1:5], nInd = 3)
 colony <- createColony(x = basePop[6])
-colony <- cross(x = colony, drones = drones)
+colony <- cross(x = colony, drones = drones, checkCross = "warning")
 colony <- addWorkers(x = colony, nInd = 50)
 colony <- buildUp(colony)
 apiary <- createMultiColony(basePop[7:20])
 drones <- createDrones(basePop[1:5], nInd = 100)
 droneGroups <- pullDroneGroupsFromDCA(drones, n = nColonies(apiary), nDrones = 15)
-apiary <- cross(x = apiary, drones = droneGroups)
+apiary <- cross(x = apiary, drones = droneGroups, checkCross = "warning")
 apiary <- buildUp(apiary)
 colonyGv <- calcColonyGv(apiary)
 colonyPheno <- calcColonyPheno(apiary)

vignettes/F_Quantitative_Genetics.Rmd

@@ -205,7 +205,7 @@ it, and adding some workers.
 
 ```{r create_colony}
 colony <- createColony(x = basePop[6])
-colony <- cross(x = colony, drones = drones)
+colony <- cross(x = colony, drones = drones, checkCross = "warning")
 colony <- addWorkers(x = colony, nInd = 50)
 colony
 ```
@@ -365,7 +365,7 @@ apiary.
 apiary <- createMultiColony(basePop[7:20])
 drones <- createDrones(basePop[1:5], nInd = 100)
 droneGroups <- pullDroneGroupsFromDCA(drones, n = nColonies(apiary), nDrones = 15)
-apiary <- cross(x = apiary, drones = droneGroups)
+apiary <- cross(x = apiary, drones = droneGroups, checkCross = "warning")
 apiary <- buildUp(apiary)
 ```
 
@@ -460,7 +460,7 @@ basePop <- createVirginQueens(founderGenomes)
 drones <- createDrones(x = basePop[1:5], nInd = 100)
 apiary <- createMultiColony(basePop[6:20])
 droneGroups <- pullDroneGroupsFromDCA(drones, nColonies(apiary), nDrones = 15)
-apiary <- cross(x = apiary, drones = droneGroups)
+apiary <- cross(x = apiary, drones = droneGroups, checkCross = "warning")
 apiary <- buildUp(apiary)
 apiary
 ```
@@ -588,7 +588,7 @@ basePop <- createVirginQueens(founderGenomes)
 drones <- createDrones(x = basePop[1:5], nInd = 100)
 apiary <- createMultiColony(basePop[6:20])
 droneGroups <- pullDroneGroupsFromDCA(drones, nColonies(apiary), nDrones = 15)
-apiary <- cross(x = apiary, drones = droneGroups)
+apiary <- cross(x = apiary, drones = droneGroups, checkCross = "warning")
 ```
 
 Let's explore queen's genetic and phenotypic values for fecundity and honey

vignettes/G_Sampling_functions.Rmd

@@ -80,7 +80,7 @@ DCA to mate with each of the 10 virgin queens.
 
 ```{r}
 droneGroups <- pullDroneGroupsFromDCA(DCA = DCA, n = 10, nDrones = nFathersPoisson)
-apiary <- cross(apiary, drones = droneGroups)
+apiary <- cross(apiary, drones = droneGroups, checkCross = "warning")
 ```
 
 And inspect the number of fathers in each of the colony and their mean.

vignettes/Z_FAQ.Rmd

@@ -56,14 +56,14 @@ baseDrones <- createDrones(baseVirginQueen[1])
 
 # A colony
 colony <- createColony(baseVirginQueen[2])
-colony <- cross(x = colony, crossPlan = "create", drones = baseDrones)
+colony <- cross(x = colony, crossPlan = "create", drones = baseDrones, checkCross = "warning")
 colony <- addDrones(colony, nInd = 100)
 colony
 
 # Crossing one of the remaining virgin queens with drones from the 
 DCA <- createDCA(colony, nInd = 50)
 DCA
-queen <- cross(x = baseVirginQueen[3], crossPlan = "create", drones = DCA)
+queen <- cross(x = baseVirginQueen[3], crossPlan = "create", drones = DCA, checkCross = "warning")
 queen
 getFathers(queen)