--- title: "mpmaggregate: An Introduction to Aggregating Matrix Population Models" author: - name: "Richard A. Hinrichsen" orcid: "0000-0003-0761-3005" output: rmarkdown::html_vignette: number_sections: false mathjax: default vignette: > %\VignetteEncoding{UTF-8} %\VignetteIndexEntry{mpmaggregate: An Introduction to Aggregating Matrix Population Models} %\VignetteEngine{knitr::rmarkdown} --- **ORCID:** ```{r setup, include=FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ``` ## Overview Matrix population models (MPMs) are widely used to describe population dynamics, and large demographic databases such as COMPADRE and COMADRE now make it possible to study life-history patterns across a wide range of taxa. However, these models often differ substantially in their structure: they may be constructed with different projection intervals, life-cycle stage definitions, and levels of complexity. Such differences can make models difficult to compare directly, even when they describe similar populations. Aggregation methods address this problem by combining stages while preserving key demographic properties of the original model. The `mpmaggregate` package provides tools for reducing the dimensionality of MPMs under different demographic frameworks, allowing finer-scale models to be compared with coarser models. For example, a 12-stage life-cycle model can be reduced to a simpler 3-stage model that still captures the essential demographic behavior of the population. ### Demographic frameworks: \(\lambda\) and \(R_0\) Aggregation methods can be defined by the demographic quantities they are designed to preserve. In matrix population models, two commonly used measures of growth are the population growth rate \(\lambda\) and the net reproductive rate \(R_0\). These quantities describe different aspects of population dynamics, and therefore preserving them leads to different frameworks for aggregation. The quantity \(\lambda\) is the dominant eigenvalue of the population projection matrix and describes stable population growth per time step (Caswell, 2001). The quantity \(R_0\) measures expected lifetime reproductive output and is interpreted from a cohort-based perspective (Caswell, 2011). In MPMs, \(R_0\) is calculated from the next-generation matrix \(F(I-U)^{-1}\) (Diekmann et al., 1990; Caswell, 2001). Although \(\lambda\) and \(R_0\) share the same population growth threshold, with \(\lambda > 1\) if and only if \(R_0 > 1\), they summarize different aspects of demography: \(\lambda\) emphasizes population trajectories through time, whereas \(R_0\) emphasizes lifetime reproductive pathways through the life cycle (Cushing & Yicang, 1994; de-Camino-Beck & Lewis, 2007). The \(\lambda\) framework describes population growth through repeated time-step projection of the entire population, so reproduction is incorporated into future population states and therefore compounds over time. By contrast, the \(R_0\) framework follows a single cohort through the life cycle and counts the offspring produced by that cohort, but those offspring are not themselves projected forward. In this sense, the \(\lambda\) framework includes compounding reproduction, whereas the \(R_0\) framework does not (see Figure 1). This distinction matters for aggregation, because a method that preserves demographic properties in one framework will not generally preserve those same properties in the other. Aggregation in the \(\lambda\) framework is appropriate when the goal is to preserve stable population growth and related population-based demographic quantities, whereas aggregation in the \(R_0\) framework is appropriate when the goal is to preserve lifetime reproductive output and related cohort-based demographic quantities. ```{r projection matrix, echo=FALSE, out.width="50%", fig.cap=" "} knitr::include_graphics("figures/Slide2.PNG") ``` ```{r lambda-r0-figure, echo=FALSE, out.width="90%", fig.cap="Figure 1. Interpretation of λ and R0 frameworks"} knitr::include_graphics("figures/Slide1.PNG") ``` ### Aggregation criteria: standard and elasticity-consistent Within each framework, users may choose between **standard aggregation**, which maintains consistency of the stable population growth rate and stable stage distribution (Hooley, 2000; Salguero-Gómez & Plotkin, 2010), and **elasticity-consistent aggregation**, which additionally maintains consistency in reproductive values and elasticities (Bienvenu et al., 2017). These aggregators are applied in two forms: general-to-general MPM aggregation and Leslie-to-Leslie MPM aggregation (Hinrichsen, 2023; Hinrichsen et al., 2026). When applying general-to-general MPM aggregation, the projection interval of the aggregated matrix does not change. But when applying Leslie-to-Leslie MPM aggregation, the projection interval changes because, in a Leslie MPM, the projection interval is equal to the age-class width, which increases with the level of aggregation (Hinrichsen et al., 2026). ### Package functions Two primary functions are provided. The function `mpm_aggregate()` aggregates general stage-structured MPMs (Caswell, 2001) to coarser stage classifications, whereas leslie_aggregate() is designed specifically for age-structured Leslie matrices (Leslie, 1945) and returns a lower-dimensional Leslie matrix. In both cases, aggregation is accompanied by an effectiveness metric that quantifies the degree of agreement between the aggregated and original models. Values close to 1 indicate minimal aggregation error and strong agreement, whereas smaller values reflect increasing approximation. Together, these tools make it possible to simplify complex matrix models, compare models constructed at different resolutions, and explore how demographic conclusions depend on the level of aggregation. ## Loading packages We begin by loading the `mpmaggregate` package, which provides the functions used throughout this vignette for aggregating matrix population models under the \(\lambda\) and \(R_0\) demographic frameworks. The package `expm` is used to raise a matrix to a power, `knitr` is used for report generation, and `kableExtra` is used for table formatting. ```{r} library(mpmaggregate) library(expm) library(knitr) library(kableExtra) ``` ## Aggregating general-to-general MPM ```{r table-preserved, echo=FALSE, results='asis'} preserved_tbl <- data.frame( Framework = c("lambda", "lambda", "R0", "R0"), Criterion = c("standard", "elasticity-consistent", "standard", "elasticity-consistent"), Preserved = c( "λ (stable growth rate)
Stable stage distribution
Interstage flow matrix", "λ (stable growth rate)
Stable stage distribution
Reproductive values
Elasticities of λ
Generation time (Ta)", "R0 (net reproductive rate)
Cohort stable stage distribution
Cohort interstage flow matrix", "R0 (net reproductive rate)
Cohort stable stage distribution
Cohort reproductive values
Elasticities of R0
Cohort generation time (Tc)" ), check.names = FALSE ) knitr::kable( preserved_tbl, format = "html", escape = FALSE, align = c("l", "l", "l"), col.names = c("Framework", "Criterion", "Consistent Demographic Quantities"), caption = paste0( "Table 1. Demographic quantities that remain consistent under ", "mpm_aggregate() in the λ and R0 frameworks ", "for both the standard and elasticity-consistent aggregation criteria. ", "Under the λ framework, aggregation maintains consistency in stable ", "growth properties, whereas under the R0 framework it maintains ", "consistency in cohort-based reproductive quantities. ", "Interstage flow weights the columns of A by their respective ", "stable stage densities (Yokomizo et al. 2024). ", "Here, “cohort” denotes the R0-framework analogues of the ", "corresponding λ-framework demographic quantities. ", "Notice the symmetry between the λ and R0 frameworks." ) ) |> kable_styling( full_width = FALSE, bootstrap_options = c("striped", "condensed") ) |> column_spec(3, width = "7cm") |> row_spec(0, extra_css = "border-bottom: 2px solid black;") |> footnote( general_title = "", general = paste0( "
", "", "Note. mpm_aggregate() retains the projection ", "interval of the original matrix population model.", "
" ), footnote_as_chunk = TRUE, escape = FALSE ) ``` To illustrate general-to-general MPM aggregation, we begin with a simple 3x3 stage structured \( \mathbf{A} \) COMPADRE MatrixID = 247940 (Salguero‐Gómez et al., 2015), for a Marula (*Sclerocarya birrea*) population, with a seedling, juvenile, and adult stage (Emanuel et al., 2005). Here, the projection interval is 1 year, and is unchanged by general-to-general MPM aggregation. We define a grouping of stages using the object `groups`, which specifies how the original stages are combined into broader classes. In this example, the first stage is left unchanged, while the second and third stages are aggregated into a single group. Internally, this grouping is converted to a partition matrix using `mpm_partition()`, which is then used to construct the aggregated model. ```{r} # Example matrices used in the general-to-general MPM aggregation examples below #population projection matrix for Sclerocarya birrea #MatrixID = 247940 # Not run: requires Rcompadre and internet access #these matrices can be retrieved with: #library(Rcompadre) #compadre <- cdb_fetch("compadre") #mpm <- compadre[compadre$MatrixID == 247940, ] #A <- matA(mpm)[[1]] #U <- matU(mpm)[[1]] #F <- matF(mpm)[[1]] A <- matrix( c(0.0, 0.0000, 12.46, 0.4, 0.9160, 0.00, 0.0, 0.0371, 0.99), nrow = 3, byrow = TRUE ) #survival/transitions matrix U <- matrix( c(0.0, 0.0000, 0.00, 0.4, 0.9160, 0.00, 0.0, 0.0371, 0.99), nrow = 3, byrow = TRUE ) #reproduction matrix F <- matrix( c(0.0, 0.0000, 12.46, 0.0, 0.0000, 0.00, 0.0, 0.0000, 0.00), nrow = 3, byrow = TRUE ) # Stage aggregation used in later examples: # group vegetative + reproductive stages together, # leaving the seedling stage separate groups <- list( c(1), c(2,3) ) ``` The object `groups` defines how stages are aggregated. Internally, this is converted to a partition matrix using `mpm_partition()`. ### Lambda framework: standard aggregation We first aggregate in the \(\lambda\) framework using **standard aggregation** (Hooley, 2000; Salguero-Gomez & Plotkin, 2010). This option is designed to maintain consistency in the dominant eigenvalue (\(\lambda\)) and the corresponding stable stage distribution, while producing a lower-dimensional matrix consistent with the grouping defined in `groups`. Consistency of interstage flows is also maintained, and this condition can be used to derive the standard aggregator (Hinrichsen et al., 2026). The call below returns (i) the aggregated projection matrix and (ii) an effectiveness value \(\rho^2\), which summarizes how closely the aggregated model reproduces the dynamics of the original model. Values of \(\rho^2\) close to 1 indicate near-perfect agreement. ```{r} # General-to-general MPM aggregation # in the lambda framework, standard aggregation res_lambda_std <- mpm_aggregate( matA = A, groups = groups, framework = "lambda", criterion = "standard" ) # Aggregated projection matrix res_lambda_std$matA_agg # Effectiveness of aggregation res_lambda_std$effectiveness # ---- Check: lambda consistency ---- # Expected spectral_radius(A) # Lambda of aggregated model spectral_radius(res_lambda_std$matA_agg) # ---- Check: stable stage distribution consistency ---- # P is the partitioning matrix that groups stages P <- mpm_partition(groups=groups,n=3) # w is the stable stage distribution w <- stable_stage(A=A) # Expected c(P%*%w) # stable stage distribution of aggregated model w_agg <-stable_stage(res_lambda_std$matA_agg) w_agg # ---- Check: interstage flows consistency ---- # Expected P%*%A%*%diag(w)%*%t(P) # Interstage flows of aggregated model res_lambda_std$matA_agg%*%diag(w_agg) ``` ### Lambda framework: elasticity-consistent aggregation Elasticity-consistent aggregation additionally maintains consistency of reproductive values. This approach can produce survival probabilities greater than 1 in the aggregated matrix (Bienvenu et al. 2017), a behavior that does not occur under standard aggregation. Here, consistency of interstage flows is sacrificed in order to maintain consistency of the elasticities of (\(\lambda\)) with respect to matrix entries. ```{r} # General-to-general MPM aggregation # in the lambda framework, elasticity-consistent aggregation res_lambda_el <- mpm_aggregate( matA = A, matF = F, matU = U, groups = groups, framework = "lambda", criterion = "elasticity" ) # Aggregated matrix res_lambda_el$matA_agg # Effectiveness of aggregation res_lambda_el$effectiveness # ---- Check: lambda consistency ---- # Expected spectral_radius(A) # Lambda of aggregated model spectral_radius(res_lambda_el$matA_agg) # ---- Check: stable stage distribution consistency ---- # P is the partitioning matrix P <- mpm_partition(groups=groups,n=3) # w us the stable stage distribution w <- stable_stage(A=A) # Expected c(P%*%w) # Stable stage distribution of aggregated model stable_stage(res_lambda_el$matA_agg) # ---- Check: reproductive values consistency ---- # v is reproductive values (dominant left eigenvector) v = reproductive_values(A) # Expected c(solve(P%*%diag(w)%*%t(P))%*%P%*%(w*v)) # Reproductive values of aggregated model reproductive_values(res_lambda_el$matA_agg) # ---- Check: elasticities consistency ---- # Elasticity matrix EA <- mpm_elasticity(matA=A,framework="lambda")$elasticity # Expected P%*%EA%*%t(P) # Elasticities of aggregated model mpm_elasticity(matA=res_lambda_el$matA_agg,framework="lambda")$elasticity # ---- Check: generation time consistency ---- # Expected generation_time(matF=F,matU=U,framework="lambda")$generation_time # Generation time from aggregated model generation_time(matF=res_lambda_el$matF_agg, matU=res_lambda_el$matU_agg, framework="lambda")$generation_time ``` **Notice** that the [2,1] entry, which is survival probability of the aggregated matrix `res_lambda_el$matA_agg` exceeds 1, which is a known difficulty with the elasticity-consistent aggregator (Bienvenu et al. 2017). ### \(R_0\)framework: decomposition of \( \mathbf{A} \) We now illustrate aggregation under the \(R_0\) framework, which is based on the decomposition of the population projection matrix into survival and reproduction components. Rather than working directly with the full projection matrix \( \mathbf{A} \), aggregation in this framework is performed using the survival matrix \( \mathbf{U} \) and the fertility matrix \( \mathbf{F} \). For this example, we use the same life cycle as above, with \( \mathbf{U} \) describing survival and transitions among stages and \( \mathbf{F} \) describing reproduction. Together, these matrices satisfy \( \mathbf{A} = \mathbf{U} + \mathbf{F} \) . ### \(R_0\) framework: standard aggregation We first apply standard aggregation in the \(R_0\) framework. In this setting, aggregation is carried out using the survival and reproduction components of the model and is designed to ensure consistency of the net reproductive rate (\(R_0\)) and its associated cohort stable stage distribution. Also consistent is the cohort interstage flow matrix which weights the columns of \( \mathbf{A} \) by their associated cohort stable stage densities. As before, the function returns the aggregated projection matrix and an effectiveness value that summarizes how closely the aggregated model reproduces the demographic behavior of the original model. ```{r} # General-to-general MPM aggregation # in the R0 framework, standard aggregation res_R0_std <- mpm_aggregate( matU = U, matF = F, groups = groups, framework = "R0", criterion = "standard" ) # Aggregated projection matrix res_R0_std$matA_agg # Effectiveness of aggregation res_R0_std$effectiveness # ---- Check: R0 consistency ---- # Expected spectral_radius(F%*%solve(diag(3)-U)) # R0 from aggregated matrix spectral_radius(res_R0_std$matF_agg%*%solve(diag(2)-res_R0_std$matU_agg)) # ---- Check: cohort stable stage distribution consistency ---- # w is the cohort stable stage distribution from a next generation matrix w <- stable_stage(solve(diag(3)-U)%*%F) # Expected for consistency c(P%*%stable_stage(solve(diag(3)-U)%*%F)) # Aggregated cohort stable stage distribution w_agg <- stable_stage(solve(diag(2)-res_R0_std$matU_agg)%*%res_R0_std$matF_agg) w_agg # ---- Check: cohort interstage flows consistency ---- # Expected P%*%A%*%diag(w)%*%t(P) # Aggregated interstage flows res_R0_std$matA_agg%*%diag(w_agg) ``` ### \(R_0\) framework: elasticity-consistent aggregation Elasticity-consistent aggregation in the \(R_0\) framework additionally ensures consistent cohort reproductive values and the elasticities of \(R_0\) with respect to matrix entries. As in the \(\lambda\) framework, this approach can produce survival probabilities greater than 1 in the aggregated matrix. This behavior reflects the constraints imposed by elasticity preservation and does not occur under standard aggregation or in Leslie-to-Leslie aggregation. ```{r} # General-to-general MPM aggregation # in the R0 framework, elasticity-consistent aggregation res_R0_el <- mpm_aggregate( matU = U, matF = F, groups = groups, framework = "R0", criterion = "elasticity" ) # Aggregated projection matrix res_R0_el$matA_agg # Effectiveness of aggregation res_R0_el$effectiveness # ---- Check: R0 consistency ---- # Expected R0 R0 <- spectral_radius(F%*%solve(diag(3)-U)) R0 # R0 from the aggregated model spectral_radius(res_R0_el$matF_agg%*%solve(diag(2)-res_R0_el$matU_agg)) # ---- Check: cohort stable stage distribution consistency ---- # Get partitioning matrix P <- mpm_partition(groups=groups,n=3) # Construct cohort projection matrix Aref = F + U*R0 # Cohort stable stage distribution w <- stable_stage(A=Aref) # Expected for consistency c(P%*%w) # Aggregated cohort projection matrix Aref_agg = res_R0_el$matF_agg+ R0*res_R0_el$matU_agg # Aggregated cohort stable stage distribution stable_stage(Aref_agg) # ---- Check: cohort reproductive values consistency ---- v = reproductive_values(Aref) # Expected c(solve(P%*%diag(w)%*%t(P))%*%P%*%(w*v)) # Cohort reproductive values for aggregated matrix reproductive_values(Aref_agg) # ---- Check: elasticities of R0 consistency ---- # Here elasticities are normalized to sum to 1 # Original elasticities EA <- mpm_elasticity(matF=F,matU=U,framework="R0")$elasticity # Expected for consistency P%*%EA%*%t(P) # Elasticities of R0 from aggregated matrix mpm_elasticity(matF=res_R0_el$matF_agg,matU=res_R0_el$matU_agg,framework="R0")$elasticity # ---- Check: cohort generation time consistency ---- # Expected (from original model) generation_time(matF=F,matU=U,framework="R0")$generation_time # Cohort generation time from aggregated model generation_time(matF = res_R0_el$matF_agg, matU = res_R0_el$matU_agg, framework="R0")$generation_time ``` ## Aggregating Leslie-to-Leslie MPM ```{r table-leslie-preserved, echo=FALSE, results='asis'} preserved_leslie_tbl <- data.frame( Framework = c("lambda", "lambda", "R0", "R0"), Criterion = c("standard", "elasticity-consistent", "standard", "elasticity-consistent"), Preserved = c( "λ (stable growth rate)
Stable age distribution
Interstage flow matrix of Ak", "λ (stable growth rate)
Stable age distribution
Reproductive values
Elasticities of λk with respect to the entries of Ak
Generation time (Ta) of Ak", "R0 (net reproductive rate)
Cohort stable age distribution
consistent of Ak", "R0 (net reproductive rate)
Cohort stable age distribution
Cohort reproductive values
Elasticities of R0 with respect to Ak
Cohort generation time (Tc) for Ak" ), check.names = FALSE ) knitr::kable( preserved_leslie_tbl, format = "html", escape = FALSE, align = c("l", "l", "l"), col.names = c("Framework", "Criterion", "Consistent Demographic Quantities"), caption = paste0( "Table 2. Summary of the demographic properties that remain consistent under ", "leslie_aggregate() when reducing a Leslie matrix from dimensionality ", "n to m. The quantities the remain consistent depend on both the demographic framework ", "(long-term growth under λ or lifetime reproductive output under ", "R0) and the aggregation criterion (standard versus ", "elasticity-consistent). The integer k = n/m defines the ", "temporal rescaling by aggregating a Leslie model. Quantities in the ", "λ framework are defined for Ak, ", "while cohort quantities in the R0 framework are defined for ", "Ak†. Notice the structural symmetry ", "between the λ and R0 frameworks." ) ) |> kable_styling( full_width = FALSE, bootstrap_options = c("striped", "condensed") ) |> column_spec(3, width = "7cm") |> row_spec(0, extra_css = "border-bottom: 2px solid black;") |> footnote( general_title = "", general = paste0( "
", "", "Note. Aggregation with leslie_aggregate() ", "changes the projection interval from Δt to kΔt.
", "† Ak denotes the k-step-ahead projection matrix ", "in the R0 framework.
" ), footnote_as_chunk = TRUE, escape = FALSE ) ``` In some applications, it is desirable to aggregate an age-structured Leslie matrix while retaining its Leslie form (Hinrichsen 2023; Hinrichsen et al., 2026). The function `leslie_aggregate()` is designed for this purpose. It aggregates a Leslie matrix with fine-grained age classes into a coarser Leslie matrix of dimensionality `ngroups`. To illustrate Leslie-to-Leslie MPM aggregation, we begin with a simple 4x4 Leslie matrix \( \mathbf{A} \) COMADRE MatrixID = 248187 (Salguero‐Gómez et al., 2016), for a fathead minnow (*Pimephales promelas*) population (Spromberg & Birge, 2005). ```{r} # New example used for Leslie-to-Leslie aggregation # These matrices replace the earlier example matrices (A, U, F) # Leslie population projection matrix for Pimephales promelas (MatrixID = 248187) # Not run: requires Rcompadre and internet access # Matrices can be retrieved with: # library(Rcompadre) # comadre <- cdb_fetch("comadre",version = "4.23.3.1") # mpm <- comadre[comadre$MatrixID == 248187, ] # A <- matA(mpm)[[1]] # U <- matU(mpm)[[1]] # F <- matF(mpm)[[1]] # Leslie population projection matrix A <- rbind( c(0.00, 0.00, 6.00, 62.50), c(0.50, 0.00, 0.00, 0.00), c(0.00, 0.18, 0.00, 0.00), c(0.00, 0.00, 0.12, 0.00) ) # Reproduction matrix F <- rbind( c(0.00, 0.00, 6.00, 62.50), c(0.00, 0.00, 0.00, 0.00), c(0.00, 0.00, 0.00, 0.00), c(0.00, 0.00, 0.00, 0.00) ) # Survival/transition matrix U <- rbind( c(0.00, 0.00, 0.00, 0.00), c(0.50, 0.00, 0.00, 0.00), c(0.00, 0.18, 0.00, 0.00), c(0.00, 0.00, 0.12, 0.00) ) # Partitioning matrix used for the aggregation examples below # (first two age classes combined, last two combined) # In practice this matrix is constructed automatically inside leslie_aggregate() # It is reproduced here only to verify the aggregation results. P <- rbind( c(1,1,0,0), c(0,0,1,1) ) # Dimensions used in the aggregation examples n <- 4 # dimensionality of the original matrix A m <- 2 # dimensionality of the aggregated matrix k <- n / m #(also constructed automatically) ``` ### Lambda framework: standard aggregation We first aggregate the Leslie matrix in the \(\lambda\) framework using standard aggregation (Hinrichsen, 2023). As in the general-to-general case, this approach ensures consistency of the stable population growth rate (\(\lambda\)) and the stable age distribution, while producing a Leslie matrix of reduced dimensionality. The interstage flow of the aggregated matrix is consistent with that of \( \mathbf{A}^{k} \). ```{r} # Leslie-to-Leslie MPM aggregation # in the lambda framework, standard aggregation res_leslie_lambda_std <- leslie_aggregate( matA = A, ngroups = 2, framework = "lambda", criterion = "standard" ) # Aggregated Leslie matrix res_leslie_lambda_std$matAk_agg # Effectiveness of aggregation res_leslie_lambda_std$effectiveness # ---- Check: lambda consistency ---- # Expected lambda spectral_radius(A)^k # Lambda of aggregated model spectral_radius(res_leslie_lambda_std$matAk_agg) # ---- Check: stable age distribution consistency ---- # Stable age distribution w <- leslie_stable_age(A=A) # Expected c(P%*%w) # Aggregated stable age distribution w_agg <-leslie_stable_age(res_leslie_lambda_std$matAk_agg) w_agg # ---- Check: interstage flow consistency ---- # Expected P%*%(A%^%k)%*%diag(w)%*%t(P) # Interstage flows from aggregated model res_leslie_lambda_std$matAk_agg%*%diag(w_agg) ``` **Note.** In this case, the dimensionality of the aggregated matrix (\(m = 2\)) divides the dimensionality of \( \mathbf{A} \) (\(n = 4\)) evenly. More generally, when these dimensionalities are not compatible, a disaggregation step is used internally to expand \( \mathbf{L} \) to a compatible dimensionality prior to aggregation (Hinrichsen, 2023). ### Lambda framework: elasticity-consistent aggregation We next apply elasticity-consistent aggregation to the Leslie matrix in the \(\lambda\) framework (Hinrichsen et al., 2026). In addition to yielding consistent stable population growth rate and stable age distribution, this approach also yields consistent reproductive values and the elasticities of \(\lambda^{k}\) with respect to the entries entries of \( \mathbf{A}^{k} \). Unlike elasticity-consistent aggregation for general stage-structured MPMs, Leslie-to-Leslie elasticity-consistent aggregation does not produce survival probabilities greater than 1. ```{r} # Leslie-to-Leslie MPM aggregation # in the lambda framework, elasticity-consistent aggregation res_leslie_lambda_el <- leslie_aggregate( matA = A, ngroups = 2, framework = "lambda", criterion = "elasticity" ) # Aggregated Leslie matrix res_leslie_lambda_el$matAk_agg # Effectiveness of aggregation res_leslie_lambda_el$effectiveness # get aggregated F and U F_agg <-matrix(0,2,2) F_agg[1,] <- res_leslie_lambda_el$matAk_agg[1,] U_agg <- res_leslie_lambda_el$matAk_agg U_agg[1,] <-0 # ---- Check: lambda consistency ---- # Expected spectral_radius(A)^k # Lambda for aggregated model spectral_radius(res_leslie_lambda_el$matAk_agg) # ---- Check: stable age distribution consistency ---- # Stable age distribution w <- leslie_stable_age(A=A) # Expected c(P%*%w) # Stable age distribution of aggregated odel w_agg <-leslie_stable_age(res_leslie_lambda_el$matAk_agg) w_agg # ---- Check: reproductive values consistency ---- # Get reproductive values v <- leslie_reproductive_values(A=A) # Expected c(solve(P%*%diag(w)%*%t(P))%*%P%*%(v*w)) # Reproductive values of aggregated model leslie_reproductive_values(A=res_leslie_lambda_el$matAk_agg) # ---- Check: elasticities consistency ---- # Get elasticities of lambda^k EA <- mpm_elasticity(A%^%k,framework="lambda")$elasticity # Expected P%*%EA%*%t(P) # Elasticities of lambda^k for aggregated model mpm_elasticity(res_leslie_lambda_el$matAk_agg,framework="lambda")$elasticity # ---- Check: generation time consistency ---- # Survival/transition matrix U_k <- U%^%k # Reproduction matrix F_k <- A%^%k - U_k # Expected generation time generation_time(matF=F_k,matU=U_k,framework="lambda")$generation_time # Generation time of aggregated model generation_time(matF=F_agg,matU=U_agg,framework="lambda")$generation_time ``` --- ### \(R_0\) framework Leslie-to-Leslie aggregation can also be carried out under the **\(R_0\) framework**, emphasizing net reproductive rate rather than stable population growth. As in the general-to-general case, aggregation in this framework is based on the underlying survival and fertility components of the Leslie matrix, but the result again retains Leslie form. ### \(R_0\) framework: standard aggregation We first apply **standard aggregation** in the \(R_0\) framework. This approach yields consistent net reproductive rate (\(R_0\)) and the cohort stable age distribution, while producing a coarser Leslie matrix compatible with the specified number of age groups. ```{r} # Leslie-to-Leslie MPM aggregation # in the R0 framework, standard aggregation res_leslie_R0_std <- leslie_aggregate( matA = A, ngroups = 2, framework = "R0", criterion = "standard" ) # Aggregated Leslie matrix res_leslie_R0_std$matAk_agg # Effectiveness of aggregation res_leslie_R0_std$effectiveness # get F and U for aggregated matrix F_agg <- matrix(0,2,2) F_agg[1,] <- res_leslie_R0_std$matAk_agg[1,] U_agg <- res_leslie_R0_std$matAk_agg U_agg[1,] <- 0 # ---- Check: generation time consistency ---- # Expected R0 <- spectral_radius(F%*%solve(diag(4)-U)) R0 # R0 for aggregated model spectral_radius(F_agg%*%solve(diag(2)-U_agg)) # ---- Check: cohort stable age distribution consistency ---- # Standardized cohort projection matrix A_ref <- (F + U*R0)/R0 # Standardized cohort projection matrix for aggregated model A_ref_agg <- (F_agg + U_agg*R0)/R0 # w is the stable age distribution w <- leslie_stable_age(A=A_ref) # Expected c(P%*%w) # Stable age distribution for aggregated model w_agg <-leslie_stable_age(A_ref_agg) w_agg # ---- Check: cohort interstage flows consistency ---- # Survival/transition matrix (k steps ahead) U_k <- U%^%k # Reproduction matrix (k steps ahead) F_k <- A%^%k - U_k # A projection matrix (k steps ahead) A_k <- F_k + U_k # Expected P%*%A_k%*%diag(w)%*%t(P) # Interstage flows for aggregated model (F_agg + U_agg)%*%diag(w_agg) ``` ### \(R_0\) framework: elasticity-consistent aggregation We now apply **elasticity-consistent aggregation** in the \(R_0\) framework. In addition to providing consistent net reproductive rate (\(R_0\)) and the cohort stable age distribution, this approach provides consistent cohort reproductive values and the elasticities of \(R_0\) with respect to the entries of \( \mathbf{A}_k^{*} \), the \(k\)-step–ahead version of \( \mathbf{A} \), where \(k = n/m\), \(n\) is the dimensionality of the original model, and \(m\) is the dimensionality of the aggregated model. As in the \(\lambda\) framework, the Leslie structure is maintained and survival probabilities cannot exceed 1. ```{r} # Leslie-to-Leslie MPM aggregation # in the R0 framework, elasticity-consistent aggregation res_leslie_R0_el <- leslie_aggregate( matA = A, ngroups = 2, framework = "R0", criterion = "elasticity" ) # Aggregated Leslie matrix res_leslie_R0_el$matAk_agg # Effectiveness of aggregation res_leslie_R0_el$effectiveness # Get F and U for aggregated matrix F_agg <- matrix(0,2,2) F_agg[1,] <- res_leslie_R0_el$matAk_agg[1,] U_agg <- res_leslie_R0_el$matAk_agg U_agg[1,] <- 0 # ---- Check: R0 consistency ---- # Expected R0 <- spectral_radius(F%*%solve(diag(4)-U)) R0 # R0 of aggregated model spectral_radius(F_agg%*%solve(diag(2)-U_agg)) # ---- Check: cohort stage age distribution consistency ---- # Standardized cohort projection matrix A_ref <- (F + U*R0)/R0 # Standardized cohort projection matrix for aggregated model A_ref_agg <- (F_agg + U_agg*R0)/R0 # Cohort stable age distribution w <- leslie_stable_age(A=A_ref) # Expected c(P%*%w) # Cohort stage age distribution for aggregated model w_agg <-leslie_stable_age(A_ref_agg) w_agg # ---- Check: cohort reproductive values consistency ---- # Cohort reproductive values v <- leslie_reproductive_values(A_ref) # Expected c(solve(P%*%diag(w)%*%t(P))%*%P%*%(v*w)) # Cohort reproductive values of aggregated model leslie_reproductive_values(A_ref_agg) # ---- Check: elasticities of R0 consistency ---- # These elasticities are normalized to sum to 1 # Survival/transition matrix (k steps ahead) U_k <- U%^%k # Reproduction matrix (k steps ahead) F_k <- A%^%k - U_k # Cohort projection matrix (k steps ahead) A_k <- F_k + U_k # Elasticity of R0 (normalized to sum to 1) EA <- mpm_elasticity(matF=F_k,matU=U_k,framework="R0")$elasticity # Expected P%*%EA%*%t(P) # Elasticity of R0 for the aggregated model mpm_elasticity(matF=F_agg,matU=U_agg,framework="R0")$elasticity # ---- Check: cohort generation time consistency ---- # Expected generation_time(matF=F_k, matU = U_k, framework="R0")$generation_time # Generation time of aggregated model generation_time(matF=F_agg,matU=U_agg, framework="R0")$generation_time ``` ## Interpretation - The **lambda framework** ensures consistency of stable growth and stable structure. - The **R0 framework** ensures consistency of generation-based reproductive dynamics. - **Standard aggregation** ensures consistency of the core demographic quantity associated with the chosen framework (either \(\lambda\) or \(R_0\)). - **Elasticity-consistent aggregation** additionally ensures consistency of reproductive values, associated elasticities, and generation times within their respective frameworks. ## References Bienvenu, F., Akçay, E., Legendre, S., & McCandlish, D. 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