actualstage3 {lefko3} | R Documentation |
Calculate Actual Stage, Age, Stage-Pair, or Age-Stage Distributions
Description
Function actualstage3()
shows the frequencies and proportions of
each stage, stage pair, age-stage, or age in each year.
Usage
actualstage3(
data,
check_stage = TRUE,
check_age = FALSE,
historical = FALSE,
year2 = NULL,
indices = NULL,
stagecol = NULL,
agecol = NULL,
remove_stage = NULL,
t1_allow = NULL
)
Arguments
data |
A demographic dataset in hfv format. |
check_stage |
A logical value indicating whether to assess frequencies
and proportions of stages. Defaults to |
check_age |
A logical value indicating whether to assess frequencies and
proportions of ages. Defaults to |
historical |
A logical value indicating whether the stage structure
should be ahistorical ( |
year2 |
A string value indicating the name of the variable coding for
monitoring occasion at time t. Defaults to |
indices |
A vector of three strings, indicating the stage indices for
times t+1, t, and t-1, respectively, in |
stagecol |
A vector of three strings, indicating the stage name columns
for times t+1, t, and t-1, respectively, in |
agecol |
A single string indicating the age of individuals in time
t. Defaults to |
remove_stage |
A string vector indicating the names of stages to remove
from consideration. Defaults to |
t1_allow |
A string vector indicating which stages to be removed should
be allowed in the stage at time t-1 portion of historical stage
pairs, if |
Value
A data frame with the following variables:
rowid |
A string identifier term, equal to the monitoring occasion in time t and the stage index. |
stageindex |
The stageframe index of the stage. Only output if
|
stage |
The name of each stage, or |
stage2 |
The name of the stage in time t. Only output if
|
stage1 |
The name of the stage in time t-1, or |
age |
The age at time t. Only output if |
year2 |
Monitoring occasion in time t. |
frequency |
The number of individuals in the respective stage and time. |
actual_prop |
The proportion of individuals alive in time t in the respective stage. |
Notes
This function produces frequencies and proportions of stages in hfv formatted data using stage index variables rather than stage name variables, and so requires the former. The latter is only required if the user wants to know the associated stage names.
Frequencies and proportions will be calculated for all times, including the
last time, which is generally found in the stage3
columns of the last
year2
entry in object data
. The default is to treat the
year2
entry for that time as max(year2) + 1
.
If check_stage = TRUE
and check_age = FALSE
, then this function
will assess frequencies and proportions of stages or historical stage-pairs.
If both check_stage = TRUE
and check_age = TRUE
, then this
function will assess frequencies and proportions of age-stages. If
check_stage = FALSE
and check_age = TRUE
, then the frequencies
and proportions of ages only will be assessed.
Note that no stageframe is required for this function to operate. Stage
names and their order are inferred directly from the object data
.
Examples
sizevector <- c(0, 0, 0, 0, 0, 0, 1, 3, 6, 11, 19.5)
stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm", "Sm", "Md", "Lg",
"XLg")
repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 0, 0, 0, 0, 0.5, 0.5, 1.5, 1.5, 3.5, 5)
comments <- c("Dormant seed", "1st yr protocorm", "2nd yr protocorm",
"3rd yr protocorm", "Seedling", "Dormant adult",
"Extra small adult (1 shoot)", "Small adult (2-4 shoots)",
"Medium adult (5-7 shoots)", "Large adult (8-14 shoots)",
"Extra large adult (>14 shoots)")
cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector,
repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
propstatus = propvector, immstatus = immvector, indataset = indataset,
binhalfwidth = binvec, comments = comments)
cypraw_v1 <- 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",
stageassign = cypframe_raw, stagesize = "sizeadded", NAas0 = TRUE,
NRasRep = TRUE, age_offset = 4)
all_stage_props_ah <- actualstage3(cypraw_v1)
all_stage_props_h <- actualstage3(cypraw_v1, historical = TRUE)
all_stage_props_h_NANotAllow <- actualstage3(cypraw_v1, historical = TRUE,
t1_allow = "none")
all_stage_props_as <- actualstage3(cypraw_v1, check_age = TRUE)
all_age_props <- actualstage3(cypraw_v1, check_stage = FALSE,
check_age = TRUE)