Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Honeybee_biology.Rmd’ using rmarkdown
--- finished re-building ‘A_Honeybee_biology.Rmd’

--- re-building ‘B_Multiple_colonies.Rmd’ using rmarkdown
--- finished re-building ‘B_Multiple_colonies.Rmd’

--- re-building ‘C_Colony_events.Rmd’ using rmarkdown
--- finished re-building ‘C_Colony_events.Rmd’

--- re-building ‘D_Crossing.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/D_Crossing_files/figure-html/unnamed-chunk-12-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10598 bytes
Input file size = 10688 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8078
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8078

Output IDAT size = 8078 bytes (2520 bytes decrease)
Output file size = 8156 bytes (2532 bytes = 23.69% decrease)


Quitting from lines 387-403 [unnamed-chunk-16] (D_Crossing.Rmd)
Error: processing vignette 'D_Crossing.Rmd' failed with diagnostics:
Missing queen!
--- failed re-building ‘D_Crossing.Rmd’

--- re-building ‘E_Genomics.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/plot genoQ with poolW-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9395 bytes
Input file size = 10265 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8893
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 8874
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 8874

Output IDAT size = 8874 bytes (521 bytes decrease)
Output file size = 8952 bytes (1313 bytes = 12.79% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view diagonal-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27984 bytes
Input file size = 28098 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16785
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16785

Output IDAT size = 16785 bytes (11199 bytes decrease)
Output file size = 16863 bytes (11235 bytes = 39.99% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view diagonal-2.png
288x288 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4242 bytes
Input file size = 5094 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3742
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3735
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3735

Output IDAT size = 3735 bytes (507 bytes decrease)
Output file size = 3813 bytes (1281 bytes = 25.15% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3890 bytes
Input file size = 4736 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3450
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3437
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3437

Output IDAT size = 3437 bytes (453 bytes decrease)
Output file size = 3515 bytes (1221 bytes = 25.78% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs fathers 1-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5842 bytes
Input file size = 6700 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5436
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5425
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5425

Output IDAT size = 5425 bytes (417 bytes decrease)
Output file size = 5503 bytes (1197 bytes = 17.87% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs workers 1-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6076 bytes
Input file size = 6934 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5628
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5595
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5595

Output IDAT size = 5595 bytes (481 bytes decrease)
Output file size = 5673 bytes (1261 bytes = 18.19% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs drones 1-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6200 bytes
Input file size = 7058 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5731
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5699
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5699

Output IDAT size = 5699 bytes (501 bytes decrease)
Output file size = 5777 bytes (1281 bytes = 18.15% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/alleleFreq-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5632 bytes
Input file size = 6490 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5216
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5216

Output IDAT size = 5216 bytes (416 bytes decrease)
Output file size = 5294 bytes (1196 bytes = 18.43% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view calcGRMIbd-1.png
288x288 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11340 bytes
Input file size = 12204 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10814
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10266
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10266

Output IDAT size = 10266 bytes (1074 bytes decrease)
Output file size = 10344 bytes (1860 bytes = 15.24% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view calcGRMIbd-2.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 13549 bytes
Input file size = 14416 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13136
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 12994
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 12994

Output IDAT size = 12994 bytes (555 bytes decrease)
Output file size = 13072 bytes (1344 bytes = 9.32% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal1-1.png
288x288 pixels, 8 bits/pixel, 251 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3899 bytes
Input file size = 4742 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3470
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3470

Output IDAT size = 3470 bytes (429 bytes decrease)
Output file size = 3548 bytes (1194 bytes = 25.18% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal1-2.png
288x288 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3810 bytes
Input file size = 4659 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3369
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3369

Output IDAT size = 3369 bytes (441 bytes decrease)
Output file size = 3447 bytes (1212 bytes = 26.01% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs fathers-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5336 bytes
Input file size = 6194 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4884
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4884

Output IDAT size = 4884 bytes (452 bytes decrease)
Output file size = 4962 bytes (1232 bytes = 19.89% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs workers-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5470 bytes
Input file size = 6328 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5046
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5033
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5033

Output IDAT size = 5033 bytes (437 bytes decrease)
Output file size = 5111 bytes (1217 bytes = 19.23% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs drones-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5338 bytes
Input file size = 6196 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4921
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 4920
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 4920

Output IDAT size = 4920 bytes (418 bytes decrease)
Output file size = 4998 bytes (1198 bytes = 19.34% decrease)

--- finished re-building ‘E_Genomics.Rmd’

--- re-building ‘F_Quantitative_Genetics.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/basePop_virgin_queens-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11914 bytes
Input file size = 12784 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10870
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10870

Output IDAT size = 10870 bytes (1044 bytes decrease)
Output file size = 10948 bytes (1836 bytes = 14.36% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/basePop_drones-1.png
480x259 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6006 bytes
Input file size = 6864 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5508
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5470
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5470

Output IDAT size = 5470 bytes (536 bytes decrease)
Output file size = 5548 bytes (1316 bytes = 19.17% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/plot_queen_vs_worker_values-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8463 bytes
Input file size = 9333 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7707
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7707

Output IDAT size = 7707 bytes (756 bytes decrease)
Output file size = 7785 bytes (1548 bytes = 16.59% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/distribution_by_patriline-1.png
576x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 89921 bytes
Input file size = 90119 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 74003
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 74003

Output IDAT size = 74003 bytes (15918 bytes decrease)
Output file size = 74081 bytes (16038 bytes = 17.80% decrease)

calcColonyValue           package:SIMplyBee            R Documentation

_C_a_l_c_u_l_a_t_e _c_o_l_o_n_y _v_a_l_u_e(_s)

_D_e_s_c_r_i_p_t_i_o_n:

     Level 0 function that calculate value(s) of a colony.

_U_s_a_g_e:

     calcColonyValue(x, FUN = NULL, simParamBee = NULL, ...)
     
     calcColonyPheno(x, FUN = mapCasteToColonyPheno, simParamBee = NULL, ...)
     
     calcColonyGv(x, FUN = mapCasteToColonyGv, simParamBee = NULL, ...)
     
     calcColonyBv(x, FUN = mapCasteToColonyBv, simParamBee = NULL, ...)
     
     calcColonyDd(x, FUN = mapCasteToColonyDd, simParamBee = NULL, ...)
     
     calcColonyAa(x, FUN = mapCasteToColonyAa, simParamBee = NULL, ...)
     
_A_r_g_u_m_e_n_t_s:

       x: 'Colony-class' or 'MultiColony-class'

     FUN: function, that calculates colony value from values of colony
          members

simParamBee: 'SimParamBee', global simulation parameters

     ...: other arguments of 'FUN'

_V_a_l_u_e:

     a matrix with one value or a row of values when 'x' is
     'Colony-class' and a row-named matrix when 'x' is
     'MultiColony-class', where names are colony IDs

_F_u_n_c_t_i_o_n_s:

        • 'calcColonyPheno()': Calculate colony phenotype value from
          caste individuals' phenotype values

        • 'calcColonyGv()': Calculate colony genetic value from caste
          individuals' genetic values

        • 'calcColonyBv()': Calculate colony breeding value from caste
          individuals' breeding values

        • 'calcColonyDd()': Calculate colony dominance value from caste
          individuals' dominance values

        • 'calcColonyAa()': Calculate colony epistasis value from caste
          individuals' epistasis value

_S_e_e _A_l_s_o:

     'mapCasteToColonyValue' as an example of 'FUN', 'selectColonies'
     for example for to select colonies based on these values, and
     'vignette(topic = "QuantitativeGenetics", package = "SIMplyBee")'

_E_x_a_m_p_l_e_s:

     founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
     SP <- SimParamBee$new(founderGenomes)
     
     
     # Define two traits that collectively affect colony honey yield:
     # 1) queen's effect on colony honey yield, say via pheromone secretion phenotype
     # 2) workers' effect on colony honey yield, say via foraging ability phenotype
     # The traits will have a negative genetic correlation of -0.5 and heritability
     # of 0.25 (on an individual level)
     nWorkers <- 10
     mean <- c(10, 10 / nWorkers)
     varA <- c(1, 1 / nWorkers)
     corA <- matrix(data = c(
       1.0, -0.5,
       -0.5, 1.0
     ), nrow = 2, byrow = TRUE)
     varE <- c(3, 3 / nWorkers)
     varA / (varA + varE)
     SP$addTraitADE(nQtlPerChr = 100,
                    mean = mean,
                    var = varA, corA = corA,
                    meanDD = 0.1, varDD = 0.2, corD = corA,
                    relAA = 0.1, corAA = corA)
     SP$setVarE(varE = varE)
     
     basePop <- createVirginQueens(founderGenomes)
     drones <- createDrones(x = basePop[1], nInd = 200)
     droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
     
     # Create and cross Colony and MultiColony class
     colony <- createColony(x = basePop[2])
     colony <- cross(colony, drones = droneGroups[[1]])
     colony <- buildUp(colony, nWorkers = nWorkers, nDrones = 3)
     apiary <- createMultiColony(basePop[3:5], n = 2)
     apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
     apiary <- buildUp(apiary, nWorkers = nWorkers, nDrones = 3)
     
     # Colony value - shorthand version
     # (using the default mapCasteToColony*() functions - you can provide yours instead!)
     # Phenotype value
     calcColonyPheno(colony)
     calcColonyPheno(apiary)
     # Genetic value
     calcColonyGv(colony)
     calcColonyGv(apiary)
     
     # Colony value - long version
     # (using the default mapCasteToColony*() function - you can provide yours instead!)
     calcColonyValue(colony, FUN = mapCasteToColonyPheno)
     calcColonyValue(apiary, FUN = mapCasteToColonyPheno)
     
     # Colony value - long version - using a function stored in SimParamBee (SP)
     # (using the default mapCasteToColony*() function - you can provide yours instead!)
     SP$colonyValueFUN <- mapCasteToColonyPheno
     calcColonyValue(colony)
     calcColonyValue(apiary)
     

mapCasteToColonyValue        package:SIMplyBee         R Documentation

_M_a_p _c_a_s_t_e _m_e_m_b_e_r (_i_n_d_i_v_i_d_u_a_l) _v_a_l_u_e_s _t_o _a _c_o_l_o_n_y _v_a_l_u_e

_D_e_s_c_r_i_p_t_i_o_n:

     Maps caste member (individual) values to a colony value - for
     phenotype, genetic, breeding, dominance, and epistasis values.
     This function can be used as 'FUN' argument in 'calcColonyValue'
     function(s). It can also be saved in 'SimParamBee$colonyValueFUN'
     as a default function called by 'calcColonyValue' function(s).

     This is just an example - quite a flexible one! You can provide
     your own "caste functions" that satisfy your needs within this
     mapping function (see 'queenFUN', 'workersFUN', and 'dronesFUN'
     below) or provide a complete replacement of this mapping function!
     For example, this mapping function does not cater for indirect
     (social) genetic effects where colony individuals value impacts
     value of other colony individuals.  Note though that you can
     achieve this impact also via multiple correlated traits, such as a
     queen and a workers trait.

_U_s_a_g_e:

     mapCasteToColonyValue(
       colony,
       value = "pheno",
       queenTrait = 1,
       queenFUN = function(x) x,
       workersTrait = 2,
       workersFUN = colSums,
       dronesTrait = NULL,
       dronesFUN = NULL,
       traitName = NULL,
       combineFUN = function(q, w, d) q + w,
       checkProduction = TRUE,
       notProductiveValue = 0,
       simParamBee = NULL
     )
     
     mapCasteToColonyPheno(colony, simParamBee = NULL, ...)
     
     mapCasteToColonyGv(colony, simParamBee = NULL, ...)
     
     mapCasteToColonyBv(colony, simParamBee = NULL, ...)
     
     mapCasteToColonyDd(colony, simParamBee = NULL, ...)
     
     mapCasteToColonyAa(colony, simParamBee = NULL, ...)
     
_A_r_g_u_m_e_n_t_s:

  colony: 'Colony-class'

   value: character, one of 'pheno' or 'gv'

queenTrait: numeric (column position) or character (column name),
          trait(s) that represents queen's contribution to colony
          value(s); if 'NULL' then this contribution is 0; you can pass
          more than one trait here, but make sure that 'combineFUN'
          works with these trait dimensions

queenFUN: function, function that will be applied to queen's value

workersTrait: numeric (column position) or character (column name),
          trait(s) that represents workers' contribution to colony
          value(s); if 'NULL' then this contribution is 0; you can pass
          more than one trait here, but make sure that 'combineFUN'
          works with these trait dimensions

workersFUN: function, function that will be applied to workers values

dronesTrait: numeric (column position) or character (column name),
          trait(s) that represents drones' contribution to colony
          value(s); if 'NULL' then this contribution is 0; you can pass
          more than one trait here, but make sure that 'combineFUN'
          works with these trait dimensions

dronesFUN: function, function that will be applied to drone values

traitName: the name of the colony trait(s), say, honeyYield; you can
          pass more than one trait name here, but make sure to match
          them with 'combineFUN' trait dimensions

combineFUN: function that will combine the queen, worker, and drone
          contributions - this function should be defined as
          'function(q, w, d)' where 'q' represents queen's, 'q'
          represents workers', and 'd' represents drones' contribution.

checkProduction: logical, does the value depend on the production
          status of colony; if yes and production is 'FALSE', the
          return is 'notProductiveValue' - this will often make sense
          for colony phenotype value only; you can pass more than one
          logical value here (one per trait coming out of 'combineFUN')

notProductiveValue: numeric, returned value when colony is not
          productive; you can pass more than one logical value here
          (one per trait coming out of 'combineFUN')

simParamBee: 'SimParamBee', global simulation parameters

     ...: other arguments of 'mapCasteToColonyValue' (for its aliases)

_D_e_t_a_i_l_s:

     This is a utility/mapping function meant to be called by
     'calcColonyValue'. It only works on a single colony - use
     'calcColonyValue' to get Colony or MultiColony values.

_V_a_l_u_e:

     numeric matrix with one value or a row of values

_F_u_n_c_t_i_o_n_s:

        • 'mapCasteToColonyPheno()': Map caste member (individual)
          phenotype values to a colony phenotype value

        • 'mapCasteToColonyGv()': Map caste member (individual) genetic
          values to a colony genetic value

        • 'mapCasteToColonyBv()': Map caste member (individual)
          breeding values to a colony breeding value

        • 'mapCasteToColonyDd()': Map caste member (individual)
          dominance values to a colony dominance value

        • 'mapCasteToColonyAa()': Map caste member (individual)
          epistasis values to a colony epistasis value

_S_e_e _A_l_s_o:

     'SimParamBee' field 'colonyValueFUN' and functions
     'calcColonyValue', 'calcColonyPheno', 'calcColonyGv', 'getEvents',
     'pheno', and 'gv', as well as 'vignette(topic =
     "QuantitativeGenetics", package = "SIMplyBee")'

_E_x_a_m_p_l_e_s:

     founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
     SP <- SimParamBee$new(founderGenomes)
     
     
     # Define two traits that collectively affect colony honey yield:
     # 1) queen's effect on colony honey yield, say via pheromone secretion phenotype
     # 2) workers' effect on colony honey yield, say via foraging ability phenotype
     # The traits will have a negative genetic correlation of -0.5 and heritability
     # of 0.25 (on an individual level)
     nWorkers <- 10
     mean <- c(10, 10 / nWorkers)
     varA <- c(1, 1 / nWorkers)
     corA <- matrix(data = c(
       1.0, -0.5,
       -0.5, 1.0
     ), nrow = 2, byrow = TRUE)
     varE <- c(3, 3 / nWorkers)
     varA / (varA + varE)
     SP$addTraitADE(nQtlPerChr = 100,
                    mean = mean,
                    var = varA, corA = corA,
                    meanDD = 0.1, varDD = 0.2, corD = corA,
                    relAA = 0.1, corAA = corA)
     SP$setVarE(varE = varE)
     
     basePop <- createVirginQueens(founderGenomes)
     drones <- createDrones(x = basePop[1], nInd = 10)
     colony <- createColony(x = basePop[2])
     colony <- cross(colony, drones = drones)
     colony <- buildUp(colony, nWorkers = nWorkers, nDrones = 3)
     
     # Colony value
     mapCasteToColonyPheno(colony)
     mapCasteToColonyGv(colony)
     
     # To understand where the above values come from, study the contents of
     # mapCasteToColonyValue() and the values below:
     
     # Phenotype values
     getQueenPheno(colony)
     getWorkersPheno(colony)
     
     # Genetic values
     getQueenGv(colony)
     getWorkersGv(colony)
     

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/queen_values-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 13362 bytes
Input file size = 14232 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11654
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11654

Output IDAT size = 11654 bytes (1708 bytes decrease)
Output file size = 11732 bytes (2500 bytes = 17.57% decrease)

nWorkersPoisson           package:SIMplyBee            R Documentation

_S_a_m_p_l_e _a _n_u_m_b_e_r _o_f _w_o_r_k_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Sample a number of workers - used when 'nInd = NULL' (see
     'SimParamBee$nWorkers').

     This is just an example. You can provide your own functions that
     satisfy your needs!

_U_s_a_g_e:

     nWorkersPoisson(colony, n = 1, average = 100)
     
     nWorkersTruncPoisson(colony, n = 1, average = 100, lowerLimit = 0)
     
     nWorkersColonyPhenotype(
       colony,
       queenTrait = 1,
       workersTrait = NULL,
       checkProduction = FALSE,
       lowerLimit = 0,
       simParamBee = NULL,
       ...
     )
     
_A_r_g_u_m_e_n_t_s:

  colony: 'Colony-class'

       n: integer, number of samples

 average: numeric, average number of workers

lowerLimit: numeric, returned numbers will be above this value

queenTrait: numeric (column position) or character (column name), trait
          that represents queen's effect on the colony phenotype
          (defined in 'SimParamBee' - see examples); if '0' then this
          effect is 0

workersTrait: numeric (column position) or character (column name),
          trait that represents workers's effect on the colony
          phenotype (defined in 'SimParamBee' - see examples); if '0'
          then this effect is 0

checkProduction: logical, does the phenotype depend on the production
          status of colony; if yes and production is not 'TRUE', the
          result is above 'lowerLimit'

simParamBee: 'SimParamBee', global simulation parameters

     ...: other arguments of 'mapCasteToColonyPheno'

_D_e_t_a_i_l_s:

     'nWorkersPoisson' samples from a Poisson distribution with a given
     average, which can return a value 0. 'nDronesTruncPoisson' samples
     from a zero truncated Poisson distribution.

     'nWorkersColonyPhenotype' returns a number (above 'lowerLimit') as
     a function of colony phenotype, say queen's fecundity. Colony
     phenotype is provided by 'mapCasteToColonyPheno'. You need to set
     up traits influencing the colony phenotype and their parameters
     (mean and variances) via 'SimParamBee' (see examples).

_V_a_l_u_e:

     numeric, number of workers

_F_u_n_c_t_i_o_n_s:

        • 'nWorkersTruncPoisson()': Sample a non-zero number of workers

        • 'nWorkersColonyPhenotype()': Sample a non-zero number of
          workers based on colony phenotype, say queen's fecundity

_S_e_e _A_l_s_o:

     'SimParamBee' field 'nWorkers' and 'vignette(topic =
     "QuantitativeGenetics", package = "SIMplyBee")'

_E_x_a_m_p_l_e_s:

     nWorkersPoisson()
     nWorkersPoisson()
     n <- nWorkersPoisson(n = 1000)
     hist(n, breaks = seq(from = min(n), to = max(n)), xlim = c(0, 200))
     table(n)
     
     nWorkersTruncPoisson()
     nWorkersTruncPoisson()
     n <- nWorkersTruncPoisson(n = 1000)
     hist(n, breaks = seq(from = min(n), to = max(n)), xlim = c(0, 200))
     table(n)
     
     # Example for nWorkersColonyPhenotype()
     founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
     SP <- SimParamBee$new(founderGenomes)
     
     average <- 100
     h2 <- 0.1
     SP$addTraitA(nQtlPerChr = 100, mean = average, var = average * h2)
     SP$setVarE(varE = average * (1 - h2))
     basePop <- createVirginQueens(founderGenomes)
     drones <- createDrones(x = basePop[1], nInd = 50)
     droneGroups <- pullDroneGroupsFromDCA(drones, n = 2, nDrones = 15)
     colony1 <- createColony(x = basePop[2])
     colony2 <- createColony(x = basePop[3])
     colony1 <- cross(colony1, drones = droneGroups[[1]])
     colony2 <- cross(colony2, drones = droneGroups[[2]])
     colony1@queen@pheno
     colony2@queen@pheno
     createWorkers(colony1, nInd = nWorkersColonyPhenotype)
     createWorkers(colony2, nInd = nWorkersColonyPhenotype)
     

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/colony_pheno_3-1.png
624x528 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 24856 bytes
Input file size = 25750 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 22146
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 22127
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 22127

Output IDAT size = 22127 bytes (2729 bytes decrease)
Output file size = 22205 bytes (3545 bytes = 13.77% decrease)

--- finished re-building ‘F_Quantitative_Genetics.Rmd’

--- re-building ‘G_Sampling_functions.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/G_Sampling_functions_files/figure-html/unnamed-chunk-3-1.png
576x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6392 bytes
Input file size = 7250 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5811
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5811

Output IDAT size = 5811 bytes (581 bytes decrease)
Output file size = 5889 bytes (1361 bytes = 18.77% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/G_Sampling_functions_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4114 bytes
Input file size = 4972 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3640
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3635
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3635

Output IDAT size = 3635 bytes (479 bytes decrease)
Output file size = 3713 bytes (1259 bytes = 25.32% decrease)

--- finished re-building ‘G_Sampling_functions.Rmd’

--- re-building ‘Z_FAQ.Rmd’ using rmarkdown
--- finished re-building ‘Z_FAQ.Rmd’

SUMMARY: processing the following file failed:
  ‘D_Crossing.Rmd’

Error: Vignette re-building failed.
Execution halted