merge_design.covariates: Merge time (occasion) and/or group specific covariates into...

In marked: Mark-Recapture Analysis for Survival and Abundance Estimation

Merge time (occasion) and/or group specific covariates into design data

Description

Adds new design data fields from a dataframe into a design data list (ddl) by matching via time and/or group field in the design data.

Usage

merge_design.covariates(ddl, df, bygroup = FALSE, bytime = TRUE)

Arguments

ddl	current design dataframe for a specific parameter and not the entire design data list (ddl)
df	dataframe with time(occasion) and/or group-specific data
bygroup	logical; if TRUE, then a field named group should be in df and the values can then be group specific.
bytime	logical; if TRUE, then a field named time should be in df and the values can then be time specific.

Details

Design data can be added to the parameter specific design dataframes with R commands. This function simplifies the process by enabling the merging of a dataframe with a time and/or group field and one or more time and/or group specific covariates into the design data list for a specific model parameter. This is a replacement for the older function merge.occasion.data. Unlike the older function, it uses the R function merge but before merging it makes sure all of the fields exist and that you are not merging data that already exists in the design data. It also maintains the row names in the case where design data have been deleted prior to merging the design covariate data.

If bytime=TRUE,the dataframe df must have a field named time that matches 1-1 for each value of time in the design data list (ddl). All fields in df (other than time/group) are added to the design data. If you set bygroup=TRUE and have a field named group in df and its values match the group fields in the design data then group-specific values can be assigned for each time if bytime=TRUE. If bygroup=TRUE and bytime=FALSE then it matches by group and not by time.

Value

Design dataframe (for a particular parameter) with new fields added. See make.design.data for a description of the design data list structure. The return value is only one element in the list rather than the entire list as with the older function merge.occasion.data.

Author(s)

Jeff Laake

See Also

make.design.data, process.data

Examples

data(dipper)
dipper.proc=process.data(dipper)
ddl=make.design.data(dipper.proc)
df=data.frame(time=c(1:7),effort=c(10,5,2,8,1,2,3))
# note that the value for time 1 is superfluous for CJS but not for POPAN
# the value 10 will not appear in the summary because there is no p for time 1
summary(ddl$p)
ddl$p=merge_design.covariates(ddl$p,df)
summary(ddl$p)
#Statement below will create an error because a value for time 7 not given
#ddl=merge.occasion.data(dipper.proc,ddl,"p",data.frame(time=c(1:6),effort=c(10,5,2,8,1,2)))
#
# Assign group-specific values
#

data(dipper)
dipper.proc=process.data(dipper)
ddl=make.design.data(dipper.proc)
df=data.frame(time=c(1:7),effort=c(10,5,2,8,1,2,3))
# note that the value for time 1 is superfluous for CJS but not for POPAN
# the value 10 will not appear in the summary because there is no p for time 1
summary(ddl$p)
ddl$p=merge_design.covariates(ddl$p,df)
summary(ddl$p)
#Statement below will create an error because a value for time 7 not given
#ddl=merge.occasion.data(dipper.proc,ddl,"p",data.frame(time=c(1:6),effort=c(10,5,2,8,1,2)))
#
# Assign group-specific values
#
dipper.proc=process.data(dipper,groups="sex")
ddl=make.design.data(dipper.proc)
df=data.frame(group=c(rep("Female",6),rep("Male",6)),time=rep(c(2:7),2),
		effort=c(10,5,2,8,1,2,3,20,10,4,16,2))
merge_design.covariates(ddl$p,df,bygroup=TRUE)

marked documentation built on Oct. 19, 2023, 5:06 p.m.