Merge pull request #587 from HighlanderLab/devel

Changing vignette D

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SIMplyBee
 Type: Package
 Title: 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: c(
   person("Jana", "Obšteter", email = "[email protected]",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1511-3916")),

NEWS.md

@@ -4,6 +4,17 @@ editor_options:
     wrap: 72
 ---
 
+# SIMplyBee version 0.4.1
+
+-   2024-09-19
+
+## Bug fixes
+
+-   locations of the colonies in the D_Crossing vignettes were previously
+sampled by random. This caused that on some runs some queens were left unmated,
+which caused an error. We now read in the locations from a csv file.
+
+
 # SIMplyBee version 0.4.0
 
 -   2024-08-23

vignettes/Colony_locations.csv

@@ -0,0 +1,36 @@
+ColonyID,X,Y
+1,0.662431162288274,5.97033145745812
+2,0.889869211813095,0.882040306233467
+3,3.20406617225118,4.2012594475023
+4,3.37467634975274,1.85276144978548
+5,6.26877271726022,4.12336288238627
+6,1.49762073729787,0.854711175179748
+7,6.27428327657999,5.28537368571472
+8,0.377119552748809,1.26003243402567
+9,0.884600259265786,2.55843304434275
+10,4.85341262281402,4.34423864421118
+11,0.439273950460384,5.78768883580839
+12,4.85267013629791,5.24037990077726
+13,6.27814888107222,1.67684867115787
+14,5.91398658831959,2.21947012261649
+15,2.2845571049277,2.76273156562477
+16,2.15001173188715,5.30559199476844
+17,3.30277055998226,3.88408253149063
+18,1.59318554922445,3.95724726174676
+19,5.14489315015939,3.48380219722517
+20,4.89542592867685,4.87175443368121
+21,4.98504294579104,4.63186113766538
+22,1.96273450676472,2.98552319129881
+23,1.94181870616625,1.04070091389605
+24,3.71355474699821,3.98892629339701
+25,1.76640287495849,1.81689439235
+26,3.49162610986539,2.007127614613
+27,4.70110619836582,1.98065883153337
+28,2.93773502070683,2.79053982429322
+29,1.69897541097397,2.4435374157815
+30,1.54126706057672,0.265964466739025
+31,0.211675140867833,1.58970616827141
+32,4.38863010920245,4.35616019770602
+33,4.3632705003701,0.955920230806015
+34,5.94574863325625,5.50420647366442
+35,2.86914251070775,0.176914088999066

vignettes/D_Crossing.Rmd

@@ -287,19 +287,26 @@ colonies. Although we are not sampling drones directly, you still need to
 provide `nDrones` argument to determine the number of sampled drone producing
 colonies.
 
-For spatial mating, we need to set the location to our apiaries (all the
-colonies within an beekeeper will have the same location). Here, we are setting
-this locations randomly, but these could be actual coordinated of colonies
-within a country.
+For spatial mating, we need to set the location to our apiaries. Here, we are
+reading the locations in from a file with the coordinates of all colonies, then
+selecting the colonies of a specific beekeeper, creating a list of coordinate
+pairs (with the `Map` function). We could also set locations randomly.
 
 ```{r}
+# Read locations from a file
+locations = read.csv("Colony_locations.csv")
 # Set location to apiaries
+beekeeper1_locations <- locations[locations$ColonyID %in% getId(beekeeper1),]
 beekeeper1 <-  setLocation(beekeeper1, 
-                           location = Map(c, runif(nColonies(beekeeper1), 0, 2*pi), runif(nColonies(beekeeper1), 0, 2*pi)))
+                           location = Map(c, beekeeper1_locations$X, beekeeper1_locations$Y))
+
+beekeeper2_locations <- locations[locations$ColonyID %in% getId(beekeeper2),]
 beekeeper2 <-  setLocation(beekeeper2, 
-                           location = Map(c, runif(nColonies(beekeeper2), 0, 2*pi), runif(nColonies(beekeeper2), 0, 2*pi)))
+                           location = Map(c, beekeeper2_locations$X, beekeeper2_locations$Y))
+
+beekeeper3_locations <- locations[locations$ColonyID %in% getId(beekeeper3),]
 beekeeper3 <-  setLocation(beekeeper3, 
-                           location = Map(c, runif(nColonies(beekeeper2), 0, 2*pi), runif(nColonies(beekeeper3), 0, 2*pi)))
+                           location = Map(c, beekeeper3_locations$X, beekeeper3_locations$Y))
 
 ```
 
@@ -372,10 +379,13 @@ beekeepers 1 to 3 as drone producing colonies. Let's first set the locations of
 the beekeepers 4 and 5 colonies.
 
 ```{r}
+beekeeper4_locations <- locations[locations$ColonyID %in% getId(beekeeper4),]
 beekeeper4 <-  setLocation(beekeeper4, 
-                           location = Map(c, runif(nColonies(beekeeper4), 0, 2*pi), runif(nColonies(beekeeper4), 0, 2*pi)))
+                           location = Map(c, beekeeper4_locations$X, beekeeper4_locations$Y))
+
+beekeeper5_locations <- locations[locations$ColonyID %in% getId(beekeeper5),]
 beekeeper5 <-  setLocation(beekeeper5, 
-                           location = Map(c, runif(nColonies(beekeeper5), 0, 2*pi), runif(nColonies(beekeeper5), 0, 2*pi)))
+                           location = Map(c, beekeeper5_locations$X, beekeeper5_locations$Y))
 ```
 
 Now, we will mate the colonies of beekeeper 4 in a random manner and colonies of