Usage
change.analysis(sites, repeats=NULL, subpop=NULL, design, data.cat=NULL, data.cont=NULL, revisitwgt=FALSE, popsize_1=NULL, popsize_2=NULL, popcorrect_1=FALSE, popcorrect_2=FALSE, pcfsize_1=NULL, pcfsize_2=NULL, N.cluster_1=NULL, N.cluster_2=NULL, stage1size_1=NULL, stage1size_2=NULL, sizeweight_1=FALSE, sizeweight_2=FALSE, vartype_1="Local", vartype_2="Local", conf=95)
Arguments
sites
a data frame consisting of three variables: the first variable is
site IDs, and the other variables are logical vectors indicating which
sites to use in the analysis. The first logical vector indicates the
complete set of sites for the first survey. The second logical vector
indicates the complete set of sites for the second survey.
repeats
a data frame that identifies site IDs for repeat visit sites
from the two surveys. The first variable is site IDs for survey one. The
second variable is site IDs for survey two. For each row of the data frame,
the two site IDs must correspond to the same site. This argument should equal
NULL when repeat visit sites are not present. The default is NULL.
subpop
a data frame describing sets of populations and subpopulations
for which estimates will be calculated. The first variable is site
IDs. Each subsequent variable identifies a Type of population, where
the variable name is used to identify Type. A Type variable
identifies each site with one of the subpopulations of that Type. The
default is NULL.
design
a data frame consisting of design variables. Variables should
be named as follows:
siteID = site IDs
wgt = final adjusted weights, which are either the weights for a
single-stage sample or the stage two weights for a two-stage sample
xcoord = x-coordinates for location, which are either the x-coordinates
for a single-stage sample or the stage two x-coordinates for a
two-stage sample
ycoord = y-coordinates for location, which are either the y-coordinates
for a single-stage sample or the stage two y-coordinates for a
two-stage sample
stratum = the stratum codes
cluster = the stage one sampling unit (primary sampling unit or cluster)
codes
wgt1 = final adjusted stage one weights
xcoord1 = the stage one x-coordinates for location
ycoord1 = the stage one y-coordinates for location
support = support values - the value one (1) for a site from a
finite resource or the measure of the sampling unit associated
with a site from an extensive resource, which is required for
calculation of finite and continuous population correction
factors
swgt = size-weights, which is the stage two size-weight for a two-
stage sample
swgt1 = stage one size-weights
data.cat
a data frame of categorical response variables. The first
variable is site IDs. Subsequent variables are response variables.
Missing data (NA) is allowed. The default is NULL.
data.cont
a data frame of continuous response variables. The first
variable is site IDs. Subsequent variables are response variables.
Missing data (NA) is allowed. The default is NULL.
revisitwgt
a logical value that indicates whether each repeat visit
site has the same survey design weight in the two surveys, where TRUE = the
weight for each repeat visit site is the same and FALSE = the weight for
each repeat visit site is not the same. When this argument is FALSE, all
of the repeat visit sites are assigned equal weights when calculating the
covariance component of the change estimate standard error. The default
is FALSE.
popsize_1
known size of the resource for survey one, which is used to
perform ratio adjustment to estimators expressed using measurement units for
the resource and to calculate strata proportions for calculating estimates
for a stratified sample. For a finite resource, this argument is either the
total number of sampling units or the known sum of size-weights. For an
extensive resource, this argument is the measure of the resource, i.e.,
either known total length for a linear resource or known total area for an
areal resource. The argument must be in the form of a list containing an
element for each population Type in the subpop data frame, where NULL is a
valid choice for a population Type. The list must be named using the
column names for the population Types in subpop. If a population Type
doesn't contain subpopulations, then each element of the list is either a
single value for an unstratified sample or a vector containing a value for
each stratum for a stratified sample, where elements of the vector are
named using the stratum codes. If a population Type contains
subpopulations, then each element of the list is a list containing an
element for each subpopulation, where the list is named using the
subpopulation names. The element for each subpopulation will be either a
single value for an unstratified sample or a named vector of values for a
stratified sample. The default is NULL.
Example popsize for a stratified sample:
popsize = list("Pop 1"=c("Stratum 1"=750,
"Stratum 2"=500,
"Stratum 3"=250),
"Pop 2"=list("SubPop 1"=c("Stratum 1"=350,
"Stratum 2"=250,
"Stratum 3"=150),
"SubPop 2"=c("Stratum 1"=250,
"Stratum 2"=150,
"Stratum 3"=100),
"SubPop 3"=c("Stratum 1"=150,
"Stratum 2"=150,
"Stratum 3"=75)),
"Pop 3"=NULL)
Example popsize for an unstratified sample:
popsize = list("Pop 1"=1500,
"Pop 2"=list("SubPop 1"=750,
"SubPop 2"=500,
"SubPop 3"=375),
"Pop 3"=NULL)
popsize_2
known size of the resource for survey two. The default is
NULL.
popcorrect_1
a logical value that indicates whether finite or
continuous population correction factors should be employed during variance
estimation for survey one, where TRUE = use the correction factors and FALSE
= do not use the correction factors. The default is FALSE.
popcorrect_2
a logical value that indicates whether finite or
continuous population correction factors should be employed during variance
estimation for survey two. The default is FALSE.
pcfsize_1
size of the resource for survey one, which is required for
calculation of finite and continuous population correction factors for a
single-stage sample. For a stratified sample this argument must be a vector
containing a value for each stratum and must have the names attribute set to
identify the stratum codes. The default is NULL.
pcfsize_2
size of the resource for survey two. The default is NULL.
N.cluster_1
the number of stage one sampling units in the resource for
survey one, which is required for calculation of finite and continuous
population correction factors for a two-stage sample. For a stratified
sample this variable must be a vector containing a value for each stratum
and must have the names attribute set to identify the stratum codes. The
default is NULL.
N.cluster_2
the number of stage one sampling units in the resource for
survey two. The default is NULL.
stage1size_1
size of the stage one sampling units of a two-stage sample
for survey one, which is required for calculation of finite and continuous
population correction factors for a two-stage sample and must have the names
attribute set to identify the stage one sampling unit codes. For a
stratified sample, the names attribute must be set to identify both
stratum codes and stage one sampling unit codes using a convention where
the two codes are separated by the & symbol, e.g., "Stratum 1&Cluster 1".
The default is NULL.
stage1size_2
size of the stage one sampling units of a two-stage sample
for survey two. The default is NULL.
sizeweight_1
a logical value that indicates whether size-weights should
be used in the analysis of survey one, where TRUE = use the size-weights and
FALSE = do not use the size-weights. The default is FALSE.
sizeweight_2
a logical value that indicates whether size-weights should
be used in the analysis of survey two. The default is FALSE.
vartype_1
the choice of variance estimator for survey one, where
"Local" = local mean estimator and "SRS" = SRS estimator. The default is
"Local".
vartype_2
the choice of variance estimator for survey two. The default
is "Local".
conf
the confidence level. The default is 95%.