monkeyflower: Projection matrices for monkeyflower
In popbio: Construction and Analysis of Matrix Population Models

Description Usage Format Details Source References Examples

Pooled and annual projection matrices of central and marginal populations of monkeyflowers (Mimulus cardinalis and M. lewisii)

1	monkeyflower

A data frame with 32 matrices, arranged with one matrix per row

species: M. cardinalis or M. lewisii
site: Study site
year: Start year of projection interval or pooled for all three years
a11: matrix element a11; seed to seed transition or seed bank survival
a12: matrix element a12; small nr to seed - fertility
a13: matrix element a13; large nr to seed - fertility
a14: matrix element a14; reprod to seed - fertility
a21: matrix element a21; seed to small nr - growth
a22: matrix element a22; small nr to small nr -stasis
a23: matrix element a23; large nr to small nr - regress
a24: matrix element a24; reprod to small nr - regress
a31: matrix element a31; seed to large nr - growth
a32: matrix element a32; small nr to large nr - growth
a33: matrix element a33; large nr to large nr - stasis
a34: matrix element a34; reprod to large nr - regress
a41: matrix element a41; seed to reprod - growth
a42: matrix element a42; small nr to reprod - growth
a43: matrix element a43; large nr to reprod - growth
a44: matrix element a44; reprod to reprod - stasis

Matrix constructed using a post-breeding census with four stage classes: Seeds, small non-reproductive, large non-reproductive, and reproductive.

http://www.esapubs.org/archive/ecol/E087/126/appendix-E.htm

Amy Lauren Angert. 2006. Demography of central and marginal populations of monkeyflowers (Mimulus cardinalis and M. lewisii). Ecology 87:2014-2025.

monkeyflower
## convert M. cardinalis rows to list of 16 matrices
A <- subset(monkeyflower, species == "cardinalis")
# use as.matrix to convert data.frame to numeric matrix
A <- split(as.matrix(A[, 4:19]), paste(A$site, A$year))
stages <- c("seed", "sm.nr", "lg.nr", "repro")
## convert to list of 16 matrices
A <- lapply(A, matrix, nrow = 4, byrow = TRUE, dimnames = list(stages, stages))
A[8]
image2(A[[8]], round = 8, mar = c(1, 3, 4.5, 1))
title(paste("M. cardinalis - ", names(A[8])), line = 2.5)
## plot like figure 1A
x <- matrix(sapply(A, lambda), ncol = 4)
colnames(x) <- c("BU", "CA", "RP", "WA")
rownames(x) <- c(2000:2002, "pooled")
x <- x[, c(1, 3, 4, 2)]
colrs <- gray(0:3 / 3)[c(1, 3, 2, 4)]
barplot(x, beside = TRUE, las = 1, col = colrs, ylim = c(0, 2),
  ylab = "Population growth rate", main = "Mimulus cardinalis")
box()
abline(h = 1, lwd = .5)
legend(1, 1.95, rownames(x), fill = colrs, bty = "n")

      species         site   year    a11  a12   a13    a14      a21    a22
1  cardinalis Buck Meadows   2000 0.2128    0  2038   9624 2.49e-05 0.0000
2  cardinalis Buck Meadows   2001 0.1840  376   720   1340 2.14e-05 0.0345
3  cardinalis Buck Meadows   2002 0.1840    0   144    916 3.93e-06 0.0000
4  cardinalis Buck Meadows pooled 0.1900  441  1262   3636 2.25e-05 0.0139
5  cardinalis Rainbow Pool   2000 0.1858    0    77    668 5.76e-05 0.2606
6  cardinalis Rainbow Pool   2001 0.1859    8   280   1279 2.39e-05 0.1152
7  cardinalis Rainbow Pool   2002 0.1840    0    28   1210 1.82e-04 0.0143
8  cardinalis Rainbow Pool pooled 0.1900    3   125   1003 5.44e-05 0.1345
9  cardinalis       Wawona   2000 0.2315 5612 38931 133773 2.43e-05 0.0559
10 cardinalis       Wawona   2001 0.2056 2778 26853  87287 2.01e-05 0.0702
11 cardinalis       Wawona   2002 0.1840  241  1739  14790 1.10e-05 0.1437
12 cardinalis       Wawona pooled 0.2000 1980 14162  65242 2.05e-05 0.1018
13 cardinalis       Carlon   2000 0.2239  936 14496  41089 3.77e-05 0.0339
14 cardinalis       Carlon   2001 0.1840 1209 20127  67161 3.14e-05 0.0615
15 cardinalis       Carlon   2002 0.2015   99  3396  24261 3.92e-05 0.0062
16 cardinalis       Carlon pooled 0.2100  893 10987  48924 3.98e-05 0.0349
17    lewisii       Wawona   2000 0.0280    0     0  23488 1.39e-05 0.0000
18    lewisii       Wawona   2001 0.0280    0  9754  11379 3.97e-06 0.0000
19    lewisii       Wawona   2002 0.0280    0  1782   9505 6.34e-06 0.2000
20    lewisii       Wawona pooled 0.0300    0   423  19468 8.80e-06 0.0303
21    lewisii       Carlon   2000 0.0353  719  2810  13588 4.32e-05 0.0909
22    lewisii       Carlon   2001 0.0280    0  1350  12680 8.89e-06 0.0476
23    lewisii       Carlon   2002 0.0611  953  3540  21336 4.63e-05 0.0769
24    lewisii       Carlon pooled 0.0400  238  2385  15124 3.12e-05 0.0594
25    lewisii     May Lake   2000 0.0326    0 24199  89430 3.77e-06 0.0467
26    lewisii     May Lake   2001 0.0280  749 17896  65717 7.46e-06 0.0860
27    lewisii     May Lake   2002 0.0302    0  8543  34830 4.88e-06 0.0566
28    lewisii     May Lake pooled 0.0300  124 16586  63041 6.49e-06 0.0569
29    lewisii  Warren Fork   2000 0.0280    0 22612  99899 5.55e-05 0.1250
30    lewisii  Warren Fork   2001 0.0404  990 29380 112532 2.36e-05 0.2358
31    lewisii  Warren Fork   2002 0.0280    0  8286  78268 3.63e-05 0.1149
32    lewisii  Warren Fork pooled 0.0300  528 15064  96077 3.41e-05 0.1840
      a23    a24      a31    a32    a33    a34      a41    a42    a43    a44
1  0.0000 0.0000 3.74e-05 0.0000 0.3529 0.5000 8.31e-07 0.0000 0.0588 0.2778
2  0.0104 0.0000 2.14e-05 0.2759 0.3229 0.2632 0.00e+00 0.1034 0.1979 0.3684
3  0.0000 0.0000 2.23e-05 0.0303 0.3662 0.2069 0.00e+00 0.0000 0.0704 0.4483
4  0.0043 0.0000 3.26e-05 0.1250 0.3447 0.3725 3.46e-07 0.0417 0.1191 0.3431
5  0.0643 0.0076 1.57e-05 0.0904 0.4143 0.3106 1.16e-06 0.0000 0.0500 0.4318
6  0.0051 0.0000 1.66e-05 0.1264 0.3299 0.3205 7.10e-07 0.0028 0.1066 0.4872
7  0.0149 0.0000 1.59e-04 0.0429 0.1940 0.2258 0.00e+00 0.0000 0.0100 0.4355
8  0.0242 0.0037 2.39e-05 0.0994 0.3011 0.2941 1.08e-06 0.0015 0.0558 0.4485
9  0.0125 0.0000 2.94e-06 0.0721 0.3625 0.0805 2.90e-07 0.0342 0.2375 0.8161
10 0.0511 0.0000 3.06e-06 0.1020 0.2482 0.1488 1.82e-07 0.0234 0.2263 0.7355
11 0.0338 0.0000 1.68e-06 0.1106 0.3768 0.2055 0.00e+00 0.0101 0.0725 0.6164
12 0.0354 0.0000 2.90e-06 0.0954 0.3325 0.1554 1.60e-07 0.0214 0.1533 0.7062
13 0.0769 0.0000 3.70e-06 0.0435 0.4231 0.1316 7.41e-07 0.0174 0.2692 0.7632
14 0.0244 0.0000 3.46e-06 0.1154 0.3537 0.0909 0.00e+00 0.0154 0.2561 0.8545
15 0.0000 0.0000 3.94e-05 0.0372 0.2951 0.1343 5.49e-07 0.0031 0.1066 0.7612
16 0.0174 0.0000 1.68e-05 0.0574 0.3304 0.1188 4.72e-07 0.0145 0.1783 0.7938
17 0.0000 0.0000 1.64e-06 0.0000 0.5000 0.0556 0.00e+00 0.0000 0.0000 0.7778
18 0.0000 0.0000 7.95e-07 0.0000 0.2857 0.1429 0.00e+00 0.0000 0.4286 0.5000
19 0.0000 0.0000 1.59e-05 0.0000 0.5500 0.2000 0.00e+00 0.0000 0.1500 0.8000
20 0.0000 0.0000 1.35e-06 0.0000 0.5500 0.1190 0.00e+00 0.0000 0.1500 0.6905
21 0.0263 0.0000 1.05e-05 0.2727 0.5132 0.3248 3.08e-07 0.0303 0.1184 0.5726
22 0.0000 0.0000 2.78e-06 0.1224 0.4528 0.2500 0.00e+00 0.0000 0.0629 0.5909
23 0.0286 0.0000 7.80e-05 0.0256 0.2000 0.1296 8.90e-07 0.0256 0.0952 0.5741
24 0.0168 0.0000 2.92e-05 0.1279 0.4111 0.2587 3.80e-07 0.0091 0.0913 0.5792
25 0.0625 0.0000 1.24e-06 0.0272 0.6094 0.0652 4.77e-08 0.0000 0.2500 0.9239
26 0.0000 0.0000 2.91e-07 0.2366 0.6081 0.0286 0.00e+00 0.0108 0.2568 0.9429
27 0.0260 0.0000 5.90e-07 0.0755 0.5714 0.1017 5.37e-08 0.0000 0.2078 0.8475
28 0.0279 0.0000 7.79e-07 0.0801 0.5953 0.0667 3.46e-08 0.0018 0.2372 0.9016
29 0.0909 0.0000 3.51e-06 0.0000 0.5152 0.1639 0.00e+00 0.0000 0.1818 0.8033
30 0.0345 0.0000 3.88e-06 0.1992 0.5862 0.0755 1.02e-07 0.0081 0.2414 0.9245
31 0.0230 0.0000 9.26e-07 0.0920 0.6609 0.1286 0.00e+00 0.0000 0.0862 0.8143
32 0.0340 0.0000 2.23e-06 0.1505 0.6241 0.1250 2.69e-08 0.0046 0.1321 0.8424
$`Carlon pooled`
          seed    sm.nr      lg.nr      repro
seed  2.10e-01 893.0000 10987.0000 48924.0000
sm.nr 3.98e-05   0.0349     0.0174     0.0000
lg.nr 1.68e-05   0.0574     0.3304     0.1188
repro 4.72e-07   0.0145     0.1783     0.7938