multiply 2d kernel by this

gistfile1.txt

# this is what 'test' looks like: 
# > test
#          s.reg year num      nameID     stratum    lon  lat btemp depth        N Nsite                      spp Z      u.a0          a1         a2
#       1:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83 Acantholithodes hispidus 0 -2.807526  0.60290095 -0.1560553
#       2:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83  Acantholumpenus mackayi 0 -4.294548  0.66363085 -0.1244255
#       3:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83       Actinauge verrilli 0 -2.763588  0.67887606 -0.1261046
#       4:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83            Admete regina 0 -3.658542  0.66688800 -0.1661476
#       5:   ebs 1982  12 ebs_1982_12 -158.5 57.5 -158.5 57.5 -0.16  34.4 919.4999    83         Aforia circinata 0 -9.954288  0.67970755 -0.1168343
#      ---
# 1188968:   ebs 2013  43 ebs_2013_43 -178.5 60.5 -178.5 60.5  1.40 161.0 923.0000   135        Yoldia hyperborea 1 -6.106840  0.19587493 -0.1966885
# 1188969:   ebs 2013  43 ebs_2013_43 -178.5 60.5 -178.5 60.5  1.40 161.0 923.0000   135            Yoldia myalis 0 -5.445181  0.24942092 -0.2363827
# 1188970:   ebs 2013  43 ebs_2013_43 -178.5 60.5 -178.5 60.5  1.40 161.0 923.0000   135          Yoldia seminuda 0 -6.355285  0.28516302 -0.1895990
# 1188971:   ebs 2013  43 ebs_2013_43 -178.5 60.5 -178.5 60.5  1.40 161.0 923.0000   135    Yoldia thraciaeformis 0 -6.527462  0.06389702 -0.2263413
# 1188972:   ebs 2013  43 ebs_2013_43 -178.5 60.5 -178.5 60.5  1.40 161.0 923.0000   135          Zaprora silenus 0 -7.043402 -0.12895978 -0.1414058
#                   a3           a4
#       1:  0.06091388 -0.063946828
#       2:  0.05641806 -0.074596645
#       3:  0.07241147 -0.059670283
#       4:  0.03321085 -0.064787647
#       5: -0.15990573  0.002763577
#      ---
# 1188968:  0.07290525  0.015648874
# 1188969:  0.08595705 -0.049931139
# 1188970:  0.07062934 -0.050667106
# 1188971:  0.05769462 -0.044437200
# 1188972:  0.05623803 -0.050197096

pa <- test[,list(stratum, lon, lat, pa=1)]
pa <- pa[!duplicated(stratum)]
setkey(pa, lon, lat)
pa0 <- copy(pa)
pa[,stratum:=NULL]


skeleton <- pa[,expand.grid(lon=seq(min(lon),max(lon),by=0.1), lat=seq(min(lat),max(lat),by=0.1))]
skeleton <- as.data.table(skeleton)
setkey(skeleton, lon, lat)
pa <- pa[skeleton]

pa[is.na(pa), pa:=0]


pa[paste(roundGrid(lon), roundGrid(lat))%in%pa0[,stratum], pa:=1]

reshape2:::acast(pa, lat~lon)

# pa2 <- as.data.frame(pa)
# pa2[is.na(pa2[,"pa"])] <- 0

roundGrid <- function(x, frac=1){
    # if frac is 1, then place in a 1º grid
    # if frac is 0.5, then place in the 0.5º grid
    floor(x/frac)*frac+frac/2
}