add_stage: Add a New Stage to an Existing lefkoMat or lefkoMatList...

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Add a New Stage to an Existing lefkoMat or lefkoMatList Object

Description

Function add_stage() adds a new stage to an existing lefkoMat or lefkoMatList object. In addition to altering the ahstages object within the MPM, it alters the hstages and agestages objects and adds the appropriate number of new rows and columns depending on the kind of MPM input. Note that, if entering a lefkoMatList object, then a stage will be added to all lefkoMat objects contained therein.

Usage

add_stage(mpm, add_before = 0L, add_after = 0L, stage_name = NULL)

Arguments

mpm	The lefkoMat or lefkoMatList object to add a stage to.
add_before	The index of the stage to insert a new stage before. This index should be derived from the ahstages of the input mpm. Cannot be set if add_after is to be used.
add_after	The index of the stage to insert a new stage after. This index should be derived from the ahstages of the input mpm. Cannot be set if add_before is to be used.
stage_name	The name of the new stage to add. Defaults to new_stage.

Value

A new copy of the original MPM edited to include new rows and columns in the associated matrices, and with ahstages, agestages, and hstages objects edited to include the new stage.

See Also

edit_lM()

Examples

data(cypdata)

cyp_lesl_data <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004, 
  patchidcol = "patch", individcol = "plantid", blocksize = 4, 
  sizeacol = "Inf2.04", sizebcol = "Inf.04", sizeccol = "Veg.04", 
  repstracol = "Inf.04", repstrbcol = "Inf2.04", fecacol = "Pod.04", 
  stagesize = "sizeadded", NAas0 = TRUE, age_offset = 2)

cyp_survival <- glm(alive3 ~ obsage + as.factor(year2), data = cyp_lesl_data,
  family = "binomial")
cyp_fecundity <- glm(feca2 ~ 1 + obsage + as.factor(year2),
  data = cyp_lesl_data, family = "poisson")

mod_params <- create_pm(name_terms = TRUE)
mod_params$modelparams[22] <- "obsage"

germination <- 0.08
protocorm_to_seedling <- 0.10
seeding_to_adult <- 0.20
seeds_per_fruit <- 8000

cyp_lesl_supp <- supplemental(historical = FALSE, stagebased = FALSE,
  agebased = TRUE, age2 = c(1, 2), type = c(1, 1),
  givenrate = c(protocorm_to_seedling, seeding_to_adult))

cyp_lesl_fb_mpm <- fleslie(data = cyp_lesl_data, surv_model = cyp_survival,
  fec_model = cyp_fecundity, paramnames = mod_params, last_age = 7,
  fecage_min = 3, fecmod = (germination * seeds_per_fruit),
  supplement = cyp_lesl_supp)

altered1 <- add_stage(cyp_lesl_fb_mpm, add_before = 1, stage_name = "DS")

lefko3 documentation built on Nov. 5, 2025, 7:20 p.m.