In this vignette, we will import a MPM created elsewhere into
`lefko3`

and analyze it via LTRE and sLTRE analysis. These
are inherently ahistorical MPMs, and so we do not include historical
analyses in this vignette. To reduce output size, we have prevented some
statements from running if they produce long stretches of output.
Examples include most `summary()`

calls. In these cases, we
include hashtagged versions of these calls, and our text assumes that
the user runs these statements without hashtags. This vignette is only a
sample analysis. Detailed information and instructions on using
`lefko3`

are available through a free online e-book called
*lefko3: a gentle introduction*, available on
the projects page
of the Shefferson lab website. This website also includes links to
long-format vignettes and other demonstrations of this package.

Davison et al. (2010) reported stochastic
contributions made by differences in vital rate means and variances
among nine natural populations of the perennial herb *Anthyllis
vulneraria*, also known as kidney vetch, occurring in calcareous
grasslands in the Viroin Valley of southwestern Belgium. *A.
vulneraria* is a grassland specialist and the unique host plant of
the Red-listed blue butterfly (*Cupido minimus*). It is a
short-lived, rosette-forming legume with a complex life cycle including
stasis and retrogression between four stages but no seedbank (seedlings,
juveniles, small adults and large adults; Figure 9.1).

Figure 9.1. Life
history model of *Anthyllis vulneraria*. Solid arrows indicate
survival transitions while dashed arrows indicate fecundity
transitions.

Nine populations (N = 27-50,000) growing in distinct grassland fragments were surveyed between 2003 and 2006, yielding three (4x4) annual transition matrices for each population. The populations occurred within grassland fragments, and were mostly managed as nature reserves through rotational sheep grazing. These surveys coincided with a summer heat wave (2003), followed by a spring drought (2005) and an even more extreme heat wave (2006). These populations have been subject to detailed study for aspects of their genetics and demography, and further details on the sites can be obtained through the resulting publications (Krauss, Steffan-Dewenter, and Tscharntke 2004; Honnay et al. 2006; Piessens et al. 2009).

Our goal in this exercise will be to import the published MPMs available
for these nine populations of *Anthyllis vulneraria*, and to
analyze the demographic differences between populations using
deterministic and stochastic life table response experiments (LTRE and
sLTRE). We will use the matrices analyzed in Davison et al. (2010), and attempt to reproduce
their results. We begin by loading package `lefko3`

.

```
rm(list=ls(all=TRUE))
library(lefko3)
```

We will first need to describe the life history characterizing the
dataset, matching it to our analyses properly with a
`stageframe`

. Since we do not have the original demographic
dataset that produced the published matrices, we do not need to know the
exact sizes of plants and so will use proxy values. These proxy values
need to be unique and non-negative, and they need non-overlapping bins
usable as size classes defining each stage. However, since we are not
analyzing size itself here, they do not need any further basis in
reality. Other characteristics must be exact and realistic to make sure
that the analyses work properly, including all other stage descriptions
such as reproductive status, propagule status, and observation status.

```
<- c(1, 1, 2, 3) # These sizes are not from the original paper
sizevector <- c("Sdl", "Veg", "SmFlo", "LFlo")
stagevector <- c(0, 0, 1, 1)
repvector <- c(1, 1, 1, 1)
obsvector <- c(0, 1, 1, 1)
matvector <- c(1, 0, 0, 0)
immvector <- c(0, 0, 0, 0)
propvector <- c(1, 1, 1, 1)
indataset <- c(0.5, 0.5, 0.5, 0.5)
binvec <- c("Seedling", "Vegetative adult", "Small flowering",
comments "Large flowering")
<- sf_create(sizes = sizevector, stagenames = stagevector,
anthframe repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
immstatus = immvector, indataset = indataset, binhalfwidth = binvec,
propstatus = propvector, comments = comments)
#anthframe
```

Next we will enter the data for this vignette. Our data is in the form
of matrices published in Davison et al.
(2010). We will enter these matrices as standard R
`matrix`

class objects. All matrices are square with 4
columns, and we fill them by row. As an example, let’s load the first
matrix and take a look at it.

```
<- matrix(c(0, 0, 1.74, 1.74, # POPN C 2003-2004
XC3 0.208333333, 0, 0, 0.057142857,
0.041666667, 0.076923077, 0, 0,
0.083333333, 0.076923077, 0.066666667, 0.028571429), 4, 4, byrow = TRUE)
XC3#> [,1] [,2] [,3] [,4]
#> [1,] 0.00000000 0.00000000 1.74000000 1.74000000
#> [2,] 0.20833333 0.00000000 0.00000000 0.05714286
#> [3,] 0.04166667 0.07692308 0.00000000 0.00000000
#> [4,] 0.08333333 0.07692308 0.06666667 0.02857143
```

These are `A`

matrices, meaning that they include all
survival-transitions and fecundity for the population as a whole. The
corresponding `U`

and `F`

matrices were not
provided in that paper, although it is most likely that the elements
valued at 1.74 in the top right-hand corner are only composed of
fecundity values while the rest of the matrix is only composed of
survival transitions (this might not be the case if clonal reproduction
were possible). The order of rows and columns corresponds to the order
of stages in the stageframe `anthframe`

. Let’s now load the
remaining matrices.

```
<- matrix(c(0, 0, 0.3, 0.6, # POPN C 2004-2005
XC4 0.32183908, 0.142857143, 0, 0,
0.16091954, 0.285714286, 0, 0,
0.252873563, 0.285714286, 0.5, 0.6), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.50625, 0.675, # POPN C 2005-2006
XC5 0, 0, 0, 0.035714286,
0.1, 0.068965517, 0.0625, 0.107142857,
0.3, 0.137931034, 0, 0.071428571), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 2.44, 6.569230769, # POPN E 2003-2004
XE3 0.196428571, 0, 0, 0,
0.125, 0.5, 0, 0,
0.160714286, 0.5, 0.133333333, 0.076923077), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.45, 0.646153846, # POPN E 2004-2005
XE4 0.06557377, 0.090909091, 0.125, 0,
0.032786885, 0, 0.125, 0.076923077,
0.049180328, 0, 0.125, 0.230769231), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 2.85, 3.99, # POPN E 2005-2006
XE5 0.083333333, 0, 0, 0,
0, 0, 0, 0,
0.416666667, 0.1, 0, 0.1), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 1.815, 7.058333333, # POPN F 2003-2004
XF3 0.075949367, 0, 0.05, 0.083333333,
0.139240506, 0, 0, 0.25,
0.075949367, 0, 0, 0.083333333), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 1.233333333, 7.4, # POPN F 2004-2005
XF4 0.223880597, 0, 0.111111111, 0.142857143,
0.134328358, 0.272727273, 0.166666667, 0.142857143,
0.119402985, 0.363636364, 0.055555556, 0.142857143), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 1.06, 3.372727273, # POPN F 2005-2006
XF5 0.073170732, 0.025, 0.033333333, 0,
0.036585366, 0.15, 0.1, 0.136363636,
0.06097561, 0.225, 0.166666667, 0.272727273), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.245454545, 2.1, # POPN G 2003-2004
XG3 0, 0, 0.045454545, 0,
0.125, 0, 0.090909091, 0,
0.125, 0, 0.090909091, 0.333333333), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 1.1, 1.54, # POPN G 2004-2005
XG4 0.111111111, 0, 0, 0,
0, 0, 0, 0,
0.111111111, 0, 0, 0), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0, 1.5, # POPN G 2005-2006
XG5 0, 0, 0, 0,
0.090909091, 0, 0, 0,
0.545454545, 0.5, 0, 0.5), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 1.785365854, 1.856521739, # POPN L 2003-2004
XL3 0.128571429, 0, 0, 0.010869565,
0.028571429, 0, 0, 0,
0.014285714, 0, 0, 0.02173913), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 14.25, 16.625, # POPN L 2004-2005
XL4 0.131443299, 0.057142857, 0, 0.25,
0.144329897, 0, 0, 0,
0.092783505, 0.2, 0, 0.25), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.594642857, 1.765909091, # POPN L 2005-2006
XL5 0, 0, 0.017857143, 0,
0.021052632, 0.018518519, 0.035714286, 0.045454545,
0.021052632, 0.018518519, 0.035714286, 0.068181818), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 11.5, 2.775862069, # POPN O 2003-2004
XO3 0.6, 0.285714286, 0.333333333, 0.24137931,
0.04, 0.142857143, 0, 0,
0.16, 0.285714286, 0, 0.172413793), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 3.78, 1.225, # POPN O 2004-2005
XO4 0.28358209, 0.171052632, 0, 0.166666667,
0.084577114, 0.026315789, 0, 0.055555556,
0.139303483, 0.447368421, 0, 0.305555556), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 1.542857143, 1.035616438, # POPN O 2005-2006
XO5 0.126984127, 0.105263158, 0.047619048, 0.054794521,
0.095238095, 0.157894737, 0.19047619, 0.082191781,
0.111111111, 0.223684211, 0, 0.356164384), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.15, 0.175, # POPN Q 2003-2004
XQ3 0, 0, 0, 0,
0, 0, 0, 0,
1, 0, 0, 0), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0, 0.25, # POPN Q 2004-2005
XQ4 0, 0, 0, 0,
0, 0, 0, 0,
1, 0.666666667, 0, 1), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0, 1.428571429, # POPN Q 2005-2006
XQ5 0, 0, 0, 0.142857143,
0.25, 0, 0, 0,
0.25, 0, 0, 0.571428571), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.7, 0.6125, # POPN R 2003-2004
XR3 0.25, 0, 0, 0.125,
0, 0, 0, 0,
0.25, 0.166666667, 0, 0.25), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0, 0.6, # POPN R 2004-2005
XR4 0.285714286, 0, 0, 0,
0.285714286, 0.333333333, 0, 0,
0.285714286, 0.333333333, 0, 1), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0.7, 0.6125, # POPN R 2005-2006
XR5 0, 0, 0, 0,
0, 0, 0, 0,
0.333333333, 0, 0.333333333, 0.625), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 2.1, 0.816666667, # POPN S 2003-2004
XS3 0.166666667, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0.166666667), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0, 7, # POPN S 2004-2005
XS4 0.333333333, 0.5, 0, 0,
0, 0, 0, 0,
0.333333333, 0, 0, 1), 4, 4, byrow = TRUE)
<- matrix(c(0, 0, 0, 1.4, # POPN S 2005-2006
XS5 0, 0, 0, 0,
0, 0, 0, 0.2,
0.111111111, 0.75, 0, 0.2), 4, 4, byrow = TRUE)
```

We will incorporate all of these matrices into a `lefkoMat`

object. To do so, we will first organize the matrices in the proper
order within a list. Then, we will create the `lefkoMat`

object to hold these matrices by calling function
`create_lM()`

with the list object we created. We will also
include metadata describing the order of populations (here treated as
patches), and the order of monitoring occasions.

```
<- list(XC3, XC4, XC5, XE3, XE4, XE5, XF3, XF4, XF5, XG3, XG4, XG5,
mats_list
XL3, XL4, XL5, XO3, XO4, XO5, XQ3, XQ4, XQ5, XR3, XR4, XR5, XS3, XS4, XS5)
<- create_lM(mats_list, anthframe, hstages = NA,
anth_lefkoMat historical = FALSE, poporder = 1,
patchorder = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7,
8, 8, 8, 9, 9, 9),
yearorder = c(2003, 2004, 2005, 2003, 2004, 2005, 2003, 2004, 2005, 2003,
2004, 2005, 2003, 2004, 2005, 2003, 2004, 2005, 2003, 2004, 2005, 2003,
2004, 2005, 2003, 2004, 2005))
#anth_lefkoMat
```

The resulting object has all of the elements of a standard
`lefkoMat`

object except for those elements related to
quality control in the demographic dataset and linear modeling. The
option `UFdecomp`

was left at its default
(`UFdecomp = TRUE`

), and so `create_lM()`

used the
stageframe to infer where fecundity values were located in the matrices
and created `U`

and `F`

matrices separating those
values. The default option for `historical`

is set to
`FALSE`

, yielding an `NA`

in place of the
`hstages`

element, which would typically list the order of
historical stage pairs.

`#summary(anth_lefkoMat)`

The summary of this new `lefkoMat`

object shows us that we
have 27 matrices with 4 rows and columns each. The estimated numbers of
transitions corresponds to the non-zero entries in each matrix. We see
that we are covering 1 population, 9 patches, and 3 time steps. All of
the survival probabilities observed fall within the bounds of 0 to 1, so
everything seems alright.

Now, we will develop arithmetic mean matrices and assess the deterministic and stochastic population growth rates, \(\lambda\) and \(a\).

```
<- lmean(anth_lefkoMat)
anth_lmean
<- lambda3(anth_lefkoMat)
lambda2 <- lambda3(anth_lmean)
lambda2m set.seed(42)
<- slambda3(anth_lefkoMat) #Stochastic growth rate
sl2 $expa <- exp(sl2$a)
sl2
plot(lambda ~ year2, data = subset(lambda2, patch == 1), ylim = c(0, 2.5),xlab = "Year",
ylab = expression(lambda), type = "l", col = "gray", lty= 2, lwd = 2, bty = "n")
lines(lambda ~ year2, data = subset(lambda2, patch == 2), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 3), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 4), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 5), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 6), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 7), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 8), col = "gray", lty= 2, lwd = 2)
lines(lambda ~ year2, data = subset(lambda2, patch == 9), col = "gray", lty= 2, lwd = 2)
abline(a = lambda2m$lambda[1], b = 0, lty = 1, lwd = 4, col = "orangered")
abline(a = sl2$expa[1], b = 0, lty = 1, lwd = 4, col = "darkred")
legend("topleft", c("det annual", "det mean", "stochastic"), lty = c(2, 1, 1),
col = c("gray", "orangered", "darkred"), lwd = c(2, 4, 4), bty = "n")
```

Clearly, these populations exhibit extremely variable growth across the short field study during which they were monitored. Also very clear is that these populations appear to be on the decline, as shown by \(\lambda\) for the overall mean matrix, and \(e\) to the power of the stochastic growth rate \(a = \text{log} \lambda\).

Let’s conduct a life table response experiment (LTRE) next. This will be
a deterministic LTRE, meaning that we will assess the impacts of
differences in matrix elements between the core matrices input via the
`lefkoMat`

object `anth_lefkoMat`

and the overall
arithmetic grand mean matrix on differences in the deterministic growth
rate, \(\lambda\). We could use a
different reference matrix if we wished, but the default is to use the
arithmetic grand mean.

```
<- ltre3(anth_lefkoMat, stochastic = FALSE, steps = 10000,
trialltre_det time_weights = NA, sparse = "auto")
#> Warning: Matrices input as mats will also be used as reference matrices.
#> Using all refmats matrices as reference matrices.
#trialltre_det
```

The resulting `lefkoLTRE`

object gives the LTRE contributions
for each matrix relative to the arithmetic grand mean matrix. While the
differences in LTRE contributions across space are of interest, we
cannot really infer differences across time this way because, across
time, matrices are not related additively. To assess the contributions
across space while accounting for temporal shifts, we should conduct a
stochastic LTRE (sLTRE), as below.

```
<- ltre3(anth_lefkoMat, stochastic = TRUE, steps = 10000,
trialltre_sto time_weights = NA, sparse = "auto")
#> Warning: Matrices input as mats will also be used as reference matrices.
#> Using all refmats matrices as reference matrices.
#trialltre_sto
```

The sLTRE produces output that is a bit different from the deterministic
LTRE output. In the output, we see two lists of matrices prior to the
MPM metadata. The first, `ltre_mean`

, is a list of matrices
showing the impact of differences in mean elements between the
patch-level temporal mean matrices and the reference temporal mean
matrix. The second, `ltre_sd`

, is a list of matrices showing
the impact of differences in the temporal standard deviation of each
element between the patch-level and reference matrix sets. In other
words, while a standard LTRE shows the impact of changes in matrix
elements on \(\lambda\), the sLTRE
shows the impacts of changes in the temporal mean and variability of
matrix elements on \(\text{log}
\lambda\). The `labels`

element shows the order of
matrices with reference to the populations or patches (remember that
here, the populations are referred to as patches).

The output objects are large and can take a great deal of effort to look over and understand. Therefore, we will show three approaches to assessing these objects, using an approach similar to that used to assess elasticities. These methods can be used to assess patterns in all 9 populations, but for brevity we will focus only on the first population here. First, we will identify the elements most strongly impacting the population growth rate in each case.

```
writeLines(paste0("Highest (i.e most positive) deterministic LTRE contribution: ",
max(trialltre_det$ltre_det[[1]])))
#> Highest (i.e most positive) deterministic LTRE contribution: 0.0240394864327486
writeLines(paste0("Highest deterministic LTRE contribution is associated with element: ",
which(trialltre_det$ltre_det[[1]] == max(trialltre_det$ltre_det[[1]]))))
#> Highest deterministic LTRE contribution is associated with element: 2
writeLines(paste0("Lowest (i.e. most negative) deterministic LTRE contribution: ",
min(trialltre_det$ltre_det[[1]])))
#> Lowest (i.e. most negative) deterministic LTRE contribution: -0.219474383631409
writeLines(paste0("Lowest deterministic LTRE contribution is associated with element: ",
which(trialltre_det$ltre_det[[1]] == min(trialltre_det$ltre_det[[1]]))))
#> Lowest deterministic LTRE contribution is associated with element: 4
writeLines(paste0("Highest stochastic mean LTRE contribution: ",
max(trialltre_sto$ltre_mean[[1]])))
#> Highest stochastic mean LTRE contribution: 0.0179472041741181
writeLines(paste0("Highest stochastic mean LTRE contribution is associated with element: ",
which(trialltre_sto$ltre_mean[[1]] == max(trialltre_sto$ltre_mean[[1]]))))
#> Highest stochastic mean LTRE contribution is associated with element: 3
writeLines(paste0("Lowest stochastic mean LTRE contribution: ",
min(trialltre_sto$ltre_mean[[1]])))
#> Lowest stochastic mean LTRE contribution: -0.370937926897558
writeLines(paste0("Lowest stochastic mean LTRE contribution is associated with element: ",
which(trialltre_sto$ltre_mean[[1]] == min(trialltre_sto$ltre_mean[[1]]))))
#> Lowest stochastic mean LTRE contribution is associated with element: 13
writeLines(paste0("Highest stochastic SD LTRE contribution: ",
max(trialltre_sto$ltre_sd[[1]])))
#> Highest stochastic SD LTRE contribution: 0.014441782311314
writeLines(paste0("Highest stochastic SD LTRE contribution is associated with element: ",
which(trialltre_sto$ltre_sd[[1]] == max(trialltre_sto$ltre_sd[[1]]))))
#> Highest stochastic SD LTRE contribution is associated with element: 13
writeLines(paste0("Lowest stochastic SD LTRE contribution: ",
min(trialltre_sto$ltre_sd[[1]])))
#> Lowest stochastic SD LTRE contribution: -0.0103367392514045
writeLines(paste0("Lowest stochastic SD LTRE contribution is associated with element: ",
which(trialltre_sto$ltre_sd[[1]] == min(trialltre_sto$ltre_sd[[1]]))))
#> Lowest stochastic SD LTRE contribution is associated with element: 16
writeLines(paste0("Total positive deterministic LTRE contributions: ",
sum(trialltre_det$ltre_det[[1]][which(trialltre_det$ltre_det[[1]] > 0)])))
#> Total positive deterministic LTRE contributions: 0.0267527462931098
writeLines(paste0("Total negative deterministic LTRE contributions: ",
sum(trialltre_det$ltre_det[[1]][which(trialltre_det$ltre_det[[1]] < 0)])))
#> Total negative deterministic LTRE contributions: -0.558699941273924
writeLines(paste0("Total positive stochastic mean LTRE contributions: ",
sum(trialltre_sto$ltre_mean[[1]][which(trialltre_sto$ltre_mean[[1]] > 0)])))
#> Total positive stochastic mean LTRE contributions: 0.0447245785886143
writeLines(paste0("Total negative stochastic mean LTRE contributions: ",
sum(trialltre_sto$ltre_mean[[1]][which(trialltre_sto$ltre_mean[[1]] < 0)])))
#> Total negative stochastic mean LTRE contributions: -0.509757776771075
writeLines(paste0("Total positive stochastic SD LTRE contributions: ",
sum(trialltre_sto$ltre_sd[[1]][which(trialltre_sto$ltre_sd[[1]] > 0)])))
#> Total positive stochastic SD LTRE contributions: 0.0151419474124082
writeLines(paste0("Total negative stochastic SD LTRE contributions: ",
sum(trialltre_sto$ltre_sd[[1]][which(trialltre_sto$ltre_sd[[1]] < 0)])))
#> Total negative stochastic SD LTRE contributions: -0.018346643772654
```

The output for the deterministic LTRE shows that element 4, which is the growth transition from seedling to large flowering adult (column 1, row 4), has the strongest influence. This contribution is negative, so it reduces \(\lambda\). The most positive contribution to \(\lambda\) is from element 2, which is the growth transition from seedling to vegetative adult (column 1, row 2). We also see the most positive contribution from shifts in mean elements in the sLTRE is element 3 (transition from seedling to small flowering adult), but the overall greatest impact is a negative contribution from element 13, which is the fecundity transition from large flowering adult to seedling (column 4, row 1). Variability in elements also contributes to shifts in \(\text{log} \lambda\), though less so than shifts in mean elements. The strongest positive contribution is from variation in the fecundity transition from large flowering adult to seedling (column 4, row 1), while the most negative contribution is from stasis as a large flowering adult (row and column 4). A comparison of summed LTRE elements shows that negative contributions of mean elements were most influential in the stochastic case, while variability of elements had little overall influence.

Second, we will identify which stages exerted the strongest impact on the population growth rate.

```
<- trialltre_det$ltre_det[[1]]
ltre_pos <- trialltre_det$ltre_det[[1]]
ltre_neg which(ltre_pos < 0)] <- 0
ltre_pos[which(ltre_neg > 0)] <- 0
ltre_neg[
<- trialltre_sto$ltre_mean[[1]]
sltre_meanpos <- trialltre_sto$ltre_mean[[1]]
sltre_meanneg which(sltre_meanpos < 0)] <- 0
sltre_meanpos[which(sltre_meanneg > 0)] <- 0
sltre_meanneg[
<- trialltre_sto$ltre_sd[[1]]
sltre_sdpos <- trialltre_sto$ltre_sd[[1]]
sltre_sdneg which(sltre_sdpos < 0)] <- 0
sltre_sdpos[which(sltre_sdneg > 0)] <- 0
sltre_sdneg[
<- cbind(colSums(ltre_pos), colSums(sltre_meanpos), colSums(sltre_sdpos))
ltresums_pos <- cbind(colSums(ltre_neg), colSums(sltre_meanneg), colSums(sltre_sdneg))
ltresums_neg
<- trialltre_det$ahstages$stage
ltre_as_names
barplot(t(ltresums_pos), beside = T, col = c("black", "grey", "red"),
ylim = c(-0.50, 0.10))
barplot(t(ltresums_neg), beside = T, col = c("black", "grey", "red"), add = TRUE)
abline(0, 0, lty= 3)
text(cex=1, y = -0.57, x = seq(from = 2, to = 3.98*length(ltre_as_names),
by = 4), ltre_as_names, xpd=TRUE, srt=45)
legend("bottomleft", c("deterministic", "stochastic mean", "stochastic SD"),
col = c("black", "grey", "red"), pch = 15, bty = "n")
```

The output above shows that large flowering adults exerted the strongest influence on both \(\lambda\) and \(\text{log} \lambda\), with the latter influence being through the impact of shifts in the mean. This impact is overwhelmingly negative. The next largest impact comes from seedlings in the deterministic case, and from small flowering adults in the stochastic case, in both cases the influence being negative on the whole.

Finally, we will assess what transition types exert the greatest impact on population growth rate.

```
<- summary(trialltre_det)
det_ltre_summary <- summary(trialltre_sto)
sto_ltre_summary
<- cbind(det_ltre_summary$ahist_det$matrix1_pos,
ltresums_tpos $ahist_mean$matrix1_pos,
sto_ltre_summary$ahist_sd$matrix1_pos)
sto_ltre_summary<- cbind(det_ltre_summary$ahist_det$matrix1_neg,
ltresums_tneg $ahist_mean$matrix1_neg,
sto_ltre_summary$ahist_sd$matrix1_neg)
sto_ltre_summary
barplot(t(ltresums_tpos), beside = T, col = c("black", "grey", "red"),
ylim = c(-0.55, 0.10))
barplot(t(ltresums_tneg), beside = T, col = c("black", "grey", "red"),
add = TRUE)
abline(0, 0, lty = 3)
text(cex=0.85, y = -0.64, x = seq(from = 2, to = 3.98*length(det_ltre_summary$ahist_det$category),
by = 4), det_ltre_summary$ahist_det$category, xpd=TRUE, srt=45)
legend("bottomleft", c("deterministic", "stochastic mean", "stochastic SD"),
col = c("black", "grey", "red"), pch = 15, bty = "n")
```

The overall greatest impact on the population growth rate is from growth transitions in the deterministic case, but from fecundity transitions in the stochastic case. In both cases, the influence is negative. Clearly temporal variation has strong effects here that deserve to be assessed properly.

LTREs and sLTREs are powerful tools, and more complex versions of both analyses exist. Please consult Caswell (2001) and Davison et al. (2013) for more information.

Package `lefko3`

also includes functions to conduct
complex analyses, including two general projection functions that can be
used for analyses such as quasi-extinction analysis as well as for
density dependent analysis. Users wishing to conduct these analyses
should see our free e-manual called ** lefko3: a gentle
introduction** and other vignettes, including long-format
and video vignettes, on
the projects page
of the Shefferson lab website.

Caswell, Hal. 2001. *Matrix Population Models: Construction,
Analysis, and Interpretation*. Second edition. Sunderland,
Massachusetts, USA: Sinauer Associates, Inc.

Davison, Raziel, Hans Jacquemyn, Dries Adriaens, Olivier Honnay, Hans de
Kroon, and Shripad Tuljapurkar. 2010. “Demographic Effects of
Extreme Weather Events on a Short-Lived Calcareous Grassland Species:
Stochastic Life Table Response Experiments.” *Journal of
Ecology* 98 (2): 255–67. https://doi.org/10.1111/j.1365-2745.2009.01611.x.

Davison, Raziel, Florence Nicole, Hans Jacquemyn, and Shripad
Tuljapurkar. 2013. “Contributions of Covariance: Decomposing the
Components of Stochastic Population Growth in
*Cypripedium Calceolus*.” *The American
Naturalist* 181 (3): 410–20. https://doi.org/10.1086/669155.

Honnay, Olivier, Els Coart, Jan Butaye, Dries Adriaens, Sabine van
Glabeke, and Isabel Roldan-Ruiz. 2006. “Low Impact of Present and
Historical Landscape Configuration on the Genetics of Fragmented
*Anthyllis Vulneraria* Populations.”
*Biological Conservation* 127 (4): 411–19. https://doi.org/10.1016/j.biocon.2005.09.006.

Krauss, Jochen, Ingolf Steffan-Dewenter, and Tscharntke. 2004.
“Landscape Occupancy and Local Population Size Depends on Host
Plant Distribution in the Butterfly *Cupido
Minimus*.” *Biological Conservation* 120 (3): 355–61.
https://doi.org/10.1016/j.biocon.2004.03.007.

Piessens, Katrien, Dries Adriaens, Hans Jacquemyn, and Olivier Honnay.
2009. “Synergistic Effects of an Extreme Weather Event and Habitat
Fragmentation on a Specialised Insect Herbivore.”
*Oecologia* 159 (1): 117–26. https://doi.org/10.1007/s00442-008-1204-x.