我一直在试图弄清楚如何正确格式化MARSS模型（使用R中的MARSS包），这样我就可以在多个地点同时对多个物种进行建模，如果可能的话。在我完整的研究设计中，我有30年来9个不同地点的9个物种的年度样本。我已经能够让模型运行一个地点多个物种和多个地点只有一个物种（参见下面的reprex，尽管我不完全确定这些代码是否正确），但还没有能够弄清楚如何把它放在一起，或者如果这甚至是可以做的事情。如果这是一个适当的方法，我也可以只运行每个网站单独的模型。理想情况下，我想得到单独的B-矩阵为我的每一个网站，使我可以比较网站之间的社区稳定性指标。如果任何人有任何想法（或如果我去这个错误），我真的很感激！

library(MARSS)

dat <- data.frame(site = rep(1:2,each = 20),          # two independent sites
                  year = rep(c(1:20),2),              # sample years (1-20)
                  spp1 = sample(50,40, replace = T),  # simulated count data species 1
                  spp2 = sample(20,40, replace = T),  # simulated count data species 2
                  spp3 = sample(30,40, replace = T))  # simulated count data species 3

# Put count data into wide format (rows = species, columns = years)
site1 <- t(dat[1:20,3:5])
site2 <- t(dat[21:40,3:5])

rownames(site1) <- paste0("site1_", rownames(site1))
rownames(site2) <- paste0("site2_", rownames(site2))

y <- rbind(site1,site2)

# RUN THE MODEL FOR ONE SPECIES AND BOTH SITES
y1 <- rbind(y[1,], y[4,])

# Z-matrix formatting
z.model1 <- matrix(c(1,0,0,1),ncol = 2)

# A-matrix formatting
a.model1 <- matrix(list(0),2,1)
a.model1[2,1] <- c("b")

# U-matrix formatting
u.model1 <- matrix(list(0),2,1)
u.model1[1:2,1] <- c("a","b")

# Put together all parts of model
model.1 <- list(Z = z.model1,                
                A = a.model1,                
                Q = "diagonal and unequal", 
                R = "diagonal and equal",                     
                U = u.model1,                
                tinitx = 1) 

# Run the model
m1.out <- MARSS(y1, model = model.1, method = "BFGS")

# NOW RUN THE MODEL WITH ALL THREE SPECIES BUT ONLY ONE SITE
y2 <- y[1:3,]

# Z-matrix formatting
z.model2 <- matrix(0,3,3)
diag(z.model2) <- 1

# U-matrix formatting
u.model2 <- matrix(list(0),3,1)
u.model2[1:3,1] <- c("a","b","c")

# B-matrix formatting
b.model2 <- matrix(c("b11","b12","b13",
                     "b21","b22","b23",
                     "b31","b32","b33"),
                   ncol = 3)

# Put together all parts of model
model.2 <- list(Z = z.model2,                
                B = b.model2,
                Q = "diagonal and unequal",  
                R = "diagonal and equal",                     
                U = u.model2,                
                tinitx = 1) 

# Run the model
m2.out <- MARSS(y2, model = model.2, method = "BFGS")

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