overwrite {lefko3}

Create Overwrite Table for MPM Development

Description

overwrite() returns a data frame describing which particular transitions within an ahistorical or historical projection matrix to overwrite with either given rates and probabilities, or other estimated transitions. This function is now deprecated in favor of function supplemental().

Usage

overwrite(
  stage3,
  stage2,
  stage1 = NA,
  eststage3 = NA,
  eststage2 = NA,
  eststage1 = NA,
  givenrate = NA,
  type = NA,
  type_t12 = NA
)

Arguments

stage3

The name of the stage in occasion t+1 in the transition to be replaced. Abbreviations for groups of stages are also allowed (see Notes).

stage2

The name of the stage in occasion t in the transition to be replaced. Abbreviations for groups of stages are also allowed (see Notes).

stage1

The name of the stage in occasion t-1 in the transition to be replaced. Only needed if a historical matrix is to be produced. Abbreviations for groups of stages are also allowed (see Notes).

eststage3

The name of the stage to replace stage3. Only needed if a transition will be replaced by another estimated transition.

eststage2

The name of the stage to replace stage2. Only needed if a transition will be replaced by another estimated transition.

eststage1

The name of the stage to replace stage1. Only needed if a transition will be replaced by another estimated transition, and the matrix to be estimated is historical.

givenrate

A fixed rate or probability to replace for the transition described by stage3, stage2, and stage1.

type

A vector denoting the kind of transition between occasions t and t+1 to be replaced. This should be entered as 1, S, or s for the replacement of a survival transition; or 2, F, or f for the replacement of a fecundity transition. If empty or not provided, then defaults to 1 for survival transition.

type_t12

An optional vector denoting the kind of transition between occasions t-1 and t. Only necessary if a historical MPM in deVries format is desired. This should be entered as 1, S, or s for a survival transition; or 2, F, or f for a fecundity transitions. Defaults to 1 for survival transition, with impacts only on the construction of deVries-format hMPMs.

Value

A data frame that puts the above vectors together and can be used as input in flefko3(), flefko2(), rlefko3(),rlefko2(), and aflefko2().

Variables in this data frame include the following:

stage3

Stage at occasion t+1 in the transition to be replaced.

stage2

Stage at occasion t in the transition to be replaced.

stage1

Stage at occasion t-1 in the transition to be replaced.

eststage3

Stage at occasion t+1 in the transition to replace the transition designated by stage3, stage2, and stage1.

eststage2

Stage at occasion t in the transition to replace the transition designated by stage3, stage2, and stage1.

eststage1

Stage at occasion t-1 in the transition to replace the transition designated by stage3, stage2, and stage1.

givenrate

A constant to be used as the value of the transition.

convtype

Designates whether the transition from occasion t to occasion t+1 is a survival-transition probability (1) or a fecundity rate (2).

convtype_t12

Designates whether the transition from occasion t-1 to occasion t is a survival transition probability (1), a fecundity rate (2).

Notes

This function is deprecated. Please use supplemental().

Entries in stage3, stage2, and stage1 can include abbreviations for groups of stages. Use rep if all reproductive stages are to be used, nrep if all mature but non-reproductive stages are to be used, mat if all mature stages are to be used, immat if all immature stages are to be used, prop if all propagule stages are to be used, npr if all non-propagule stages are to be used, and leave empty or use all if all stages in stageframe are to be used.

Examples

cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "SL", "D", 
    "XSm", "Sm"),
  stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL"),
  eststage3 = c(NA, NA, NA, NA, NA, "D", "XSm", "Sm"),
  eststage2 = c(NA, NA, NA, NA, NA, "XSm", "XSm", "XSm"),
  givenrate = c(0.1, 0.2, 0.2, 0.2, 0.25, NA, NA, NA),
  type = c("S", "S", "S", "S", "S", "S", "S", "S"))

cypover2r

cypover3r <- overwrite(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL", 
    "D", "XSm", "Sm", "D", "XSm", "Sm"),
  stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL",
    "SL", "SL", "SL"),
  stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
    "SL", "SL", "SL"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm",
    "Sm"),
  eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm",
    "XSm", "XSm"),
  eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm",
    "XSm", "XSm"),
  givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA),
  type = c("S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S"))

cypover3r