overwrite | R Documentation |
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()
.
overwrite(
stage3,
stage2,
stage1 = NA,
eststage3 = NA,
eststage2 = NA,
eststage1 = NA,
givenrate = NA,
type = NA,
type_t12 = NA
)
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 |
eststage2 |
The name of the stage to replace |
eststage1 |
The name of the stage to replace |
givenrate |
A fixed rate or probability to replace for the transition
described by |
type |
A vector denoting the kind of transition between occasions
t and t+1 to be replaced. This should be entered as |
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 |
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 |
eststage2 |
Stage at occasion t in the transition to replace the
transition designated by |
eststage1 |
Stage at occasion t-1 in the transition to replace
the transition designated by |
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). |
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.
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
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