Introduction
This document illustrates how to use the MoosePopR() and
SightabilityPopR() functions to replace the MoosePop
(Reed, 1989) and AerialSurvey (Unsworth, 1999) programs. The
results from a 2018 survey of moose conducted according to methods
described in RISC (2002) will be used for illustrative purposes.
Survey protocol
The survey area is divided in blocks (which are the primary sampling
units, PSUs). Blocks could be defined using a grid-system, or based on
ecological factors such as elevation, type of vegetation, etc. The
blocks do not have the same area, nor do they have to rectangular. If
blocks are of different size and the area of the block is not used in
the analysis, no biases are introduced into the estimation procedure,
but the survey design could be inefficient, i.e., the uncertainty in the
estimates could be larger compared to the standard error obtained from
methods that account for different block area (see later in this
document).
Blocks are then stratified using a habitat model into categories of
relative moose densities. In this case, the blocks are stratified into
three strata corresponding to low, medium, and
high density depending on past years results, vegetation cover,
and other attributes. There is no limit on the number of strata that can
be defined, but usually three to five blocks would be sufficient. Blocks
within strata should have similar densities and strata should “as
different” as possible. If the stratification is incorrect (e.g., a
block is classified into the high stratum when in fact is
should be in the low stratum), no biases are introduced into
the estimates
A simple random sample of blocks is selected from each stratum, i.e.,
each block is selected with equal probability within each stratum. The
number of block to select from each stratum is determined using
different allocation methods. The analysis of the completed survey does
not depend on how the sample size was determined in each stratum. Some
selected blocks may not be surveyed due to bad weather etc. These missed
blocks are assumed to be missing completely at random (MCAR) within each
stratum, i.e., the missingness is unrelated to the response or any other
covariate. If a missed block is not replaced by another block chosen at
random from the stratum, the sample size in this stratum will be
reduced. The impact of a reduction in sample size in each stratum (with
increased uncertainty in the estimates for each stratum compared to a
survey with no missing blocks), but no biases are introduced.
When a block is surveyed, moose are observed in groups. When a group
is identified, a count of the number of moose is made separated by age
(adult, juvenile, calves) and sex (bull or cow).
Not all groups of moose can be observed due to sightability issues. A
previous sightability study (e.g., Quayle et al. 2001; RISC, 2002) is
used to estimate the probability of detecting a group of moose based on
a categorical vegetation cover variable with five classes. NOTE
that sightability operates at the group level and not at the moose
level. This means that if a group is sighted, then all members
of the group are enumerated. But entire groups could be “invisible” due
to vegetation cover.
This is a stratified random sampling design where the sampling unit
is the block surveyed in each stratum and the observational
unit is a group of moose. The observations on groups are
pseudo-replicates and must be treated as observations within a cluster
(being the block).
This document will illustrate how to estimate the total number and
density of moose (in various classes) and the ratio of types of moose
(e.g., bulls to cow ratio) without and with correcting for sightability.
The estimates are compared to those generated by the MoosePop
program (Reed, 1989; no correction for sightability) and the
AerialSurvey program (Unsworth, 1999; correction for
sightability).
Data input
Data input consists of several datasets placed into an Excel workbook
using different worksheets for the different information.
Moose data
This consists of information on group of moose observed in a selected
blocks. The data should have a header row with the variable names for
each column.
# Get the actual survey data
dir(system.file("extdata", package = "SightabilityModel"))
## [1] "ExampleDomainStratification.xlsx" "SampleMooseSurveyData.xlsx"
survey.data <- readxl::read_excel(system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="BlockData",
skip=1,.name_repair="universal")
# Skip =xx says to skip xx lines at the top of the worksheet. In this case skip=1 implies start reading in line 2 of
# the worksheet.
# .name_repair="universal" changes all variable names to be compatible with R, e.g., no spaces, no special characters, etc
Variable names for the counts are somewhat arbitrary. Notice how
R converts the column names from the Excel workbook to to
proper R variable names (.name_repair=“universal”
controls this conversion. These (modified) variable names will be used
to identify the quantities to be estimated so simpler names are easier
to use than more complicated names.
# Check the variable names in the input data
names(survey.data)
## [1] "Domain" "Block.ID" "Stratum" "Bulls" "Lone.Cows" "Cow.W.1...calf" "Cow.W.2.calves" "Lone...calf" "Unk.Age.Sex" "NMoose" "..Veg.Cover"
Missing values in the count fields are assume to be zeros and a zero
value must be substituted for the missing values.
# convert all NA in moose counts to 0
survey.data$Bulls [ is.na(survey.data$Bulls) ] <- 0
survey.data$Lone.Cows [ is.na(survey.data$Lone.Cows) ] <- 0
survey.data$Cow.W.1...calf [ is.na(survey.data$Cow.W.1...calf)] <- 0
survey.data$Cow.W.2.calves [ is.na(survey.data$Cow.W.2.calves)] <- 0
survey.data$Lone...calf [ is.na(survey.data$Lone...calf) ] <- 0
survey.data$Unk.Age.Sex [ is.na(survey.data$Unk.Age.Sex) ] <- 0
#head(survey.data)
We check that the NMoose is computed properly by comparing
the recorded total number of moose with a computed total number of
moose.
# check the total moose read in vs computed number
survey.data$myNMoose <- survey.data$Bulls +
survey.data$Lone.Cows+
survey.data$Cow.W.1...calf*2+
survey.data$Cow.W.2.calves*3+
survey.data$Lone...calf+
survey.data$Unk.Age.Sex
ggplot(data=survey.data, aes(x=myNMoose, y=NMoose))+
ggtitle("Compare my count vs. count on spreadsheet")+
geom_point(position=position_jitter(h=.1,w=.1))+
geom_abline(intercept=0, slope=1)
We count the number of observations by sub-unit and stratum to ensure
that Stratum has been coded properly. For example ensure
that
- stratum case is consistent (e.g., h vs. H),
- stratum codes are consistent (e.g., H
vs. HIGH).
xtabs(~Stratum, data=survey.data, exclude=NULL, na.action=na.pass)
## Stratum
## H L M
## 236 92 286
We can also add additional computed variables. For example, the
number of cows is found as
survey.data$Cows <- survey.data$Lone.Cows + survey.data$Cow.W.1...calf + survey.data$Cow.W.2.calves
The first few records of the counts of interest are:
## Block.ID Stratum Bulls Lone.Cows Cow.W.1...calf Cow.W.2.calves Cows Lone...calf Unk.Age.Sex NMoose
## 1 9 M 1 0 0 0 0 0 0 1
## 2 9 M 0 0 1 0 1 0 0 2
## 3 9 M 0 0 1 0 1 0 0 2
## 4 9 M 0 0 1 0 1 0 0 2
## 5 9 M 0 0 1 0 1 0 0 2
## 6 9 M 0 1 0 0 1 0 0 1
Block area
The area of each surveyed block is also needed.
# Get the area of each block
survey.block.area <- readxl::read_excel(
system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="BlockArea",
skip=1,.name_repair="universal")
head(survey.block.area)
## # A tibble: 6 × 2
## Block.ID Block.Area
## <dbl> <dbl>
## 1 9 25.7
## 2 12 19
## 3 13 24
## 4 20 30
## 5 27 26.6
## 6 31 30
The name of the variable identifying the block should match the name
used in the raw data from the previous section.
## [1] "Block.ID" "Block.Area"
## [1] "Domain" "Block.ID" "Stratum" "Bulls" "Lone.Cows" "Cow.W.1...calf" "Cow.W.2.calves" "Lone...calf" "Unk.Age.Sex" "NMoose" "..Veg.Cover"
## [12] "myNMoose" "Cows"
Every block that is surveyed should have an area, but the block area
file can have areas for blocks not surveyed (e.g., every block in the
population of blocks). If a area is available for a block that was not
surveyed, it is ignored.
# Check that every surveyed block has an area. The setdiff() should return null.
setdiff(survey.data$Block.ID, survey.block.area$Block.ID)
## numeric(0)
# It is ok if the block area file has areas for blocks not surveyed
setdiff(survey.block.area$Block.ID, survey.data$Block.ID)
## numeric(0)
Sightability
model.
A logistic regression comparing observed groups of moose to known
groups of moose (e.g., based on radio collared moose) was used to
estimate the sightability model (e.g., Quayle, 2001).
Reading
coefficients of the model
The information from the AerialSurvey (Unsworth, 1999)
program was transferred to the Excel workbook containing the survey
information for this study.
The estimated coefficients of the model and the covariance matrix
(sigma matrix) of the estimated coefficients are input
# number of beta coefficients
nbeta <- readxl::read_excel(
system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="SightabilityModel",
range="B2", col_names=FALSE)[1,1,drop=TRUE]
# Here Range="B2" refers to a SINGLE cell (B2) on the spreadsheet
# extract the names of the terms of the model
beta.terms <- unlist(readxl::read_excel(
system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="SightabilityModel",
range=paste0("B3:",letters[1+nbeta],"3"),
col_names=FALSE, col_type="text")[1,,drop=TRUE], use.names=FALSE)
# Here the range is B3: C3 in the case of nbeta=2 etc
cat("Names of the variables used in the sightability model:", beta.terms, "\n")
## Names of the variables used in the sightability model: Intercept VegCoverClass
# extract the beta coefficients
beta <- unlist(readxl::read_excel(
system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="SightabilityModel",
range=paste0("B4:",letters[1+nbeta],"4"),
col_names=FALSE, col_type="numeric")[1,,drop=TRUE], use.names=FALSE)
# Here the range is B4: C4 in the case of nbeta=2 etc
cat("Beta coefficients used in the sightability model:", beta, "\n")
## Beta coefficients used in the sightability model: 4.9604 -1.8437
# extract the beta covariance matrix
beta.cov <- matrix(unlist(readxl::read_excel(
system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="SightabilityModel",
range=paste0("B5:",letters[1+nbeta],4+nbeta),
col_names=FALSE, col_type="numeric"), use.names=FALSE), ncol=nbeta, nrow=nbeta)
cat("Beta covariance matrix used in the sightability model:\n")
## Beta covariance matrix used in the sightability model:
## [,1] [,2]
## [1,] 0.7822 -0.2820
## [2,] -0.2820 0.1115
These values match those in the AerialSurvey (Unsworth,
1999) package.
The estimated sightability and expansion factors at the group level
(inverse of sightability) are:
Estimated sightability of groups and expansion by Vegetation Cover Class
|
Vegetation Cover Class
|
logit(p)
|
SE logit(p)
|
p
|
SE(p)
|
Expansion Factor
|
SE(EF)
|
|
1
|
3.117
|
0.574
|
0.958
|
0.023
|
1.044
|
0.025
|
|
2
|
1.273
|
0.317
|
0.781
|
0.054
|
1.280
|
0.089
|
|
3
|
-0.571
|
0.306
|
0.361
|
0.071
|
2.770
|
0.542
|
|
4
|
-2.414
|
0.557
|
0.082
|
0.042
|
12.183
|
6.228
|
|
5
|
-4.258
|
0.866
|
0.014
|
0.012
|
71.676
|
61.195
|
So a single moose sighted in Vegetation Cover Class 5 is expanded to
almost 72 moose (!).
Creation of
VegCoverClass variable
We need to compute a VegCoverClass variable in the survey
data. The recode() function from the car package is
used.
# convert the Veg Cover to Veg.Cover.Class
xtabs(~..Veg.Cover, data=survey.data, exclude=NULL, na.action=na.pass)
## ..Veg.Cover
## 0 1 5 10 15 20 25 30 35 40 50 55 <NA>
## 39 1 131 152 82 98 21 38 12 26 5 1 8
survey.data$VegCoverClass <- car::recode(survey.data$..Veg.Cover,
" lo:20=1; 20:40=2; 40:60=3; 60:80=4; 80:100=5")
xtabs(~VegCoverClass+..Veg.Cover, data=survey.data, exclude=NULL, na.action=na.pass)
## ..Veg.Cover
## VegCoverClass 0 1 5 10 15 20 25 30 35 40 50 55 <NA>
## 1 39 1 131 152 82 98 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 21 38 12 26 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 5 1 0
## <NA> 0 0 0 0 0 0 0 0 0 0 0 0 8
Notice that there are 8 groups of moose where the Vegetation
Cover was not recorded. This has implications for estimation as
noted later. Generally speaking, you should not simply delete these
observations because this will introduce substantial bias in the
estimates. Rather, impute a vegetation cover class that gives the
highest sightability for these groups to give a lower bound on the
number of moose in this block. This will reduce (but not eliminate) the
bias caused by simply dropping these observations.
Key variables.
There are several key variables used to match records across the raw
data, block area, and stratum data frames. The default variable names
are:
- Block.ID representing the block identification number. The
Block.ID should not be duplicated in different strata. It can
be numeric or characters.
- Block.Area representing the area of each surveyed block.
This should be numeric.
- Stratum representing the stratum identification. It can be
character or numeric does not have to be a single character.
- Stratum.Blocks representing the total number of blocks in
each stratum.
- Stratum.Area representing the total area of each stratum in
the same units as the Block.Area.
The analysis function has arguments that can be changed if the names
of these key variables differ from above.
Dealing with missing
and zero values
Blocks with no
observed groups.
It is possible that a block will be surveyed and NO animals seen in
the entire block. In this case, you should insert a “dummy” observation
for this block with counts of 0 for the number of moose to ensure that
this surveyed block (with no animals seen) is properly accounted for.
You can set the sightability variables to any value, because \(0 \times \textrm{sightability correction}\)
is still 0.
A single block in a
stratum
If a stratum has only a single block surveyed, then no design based
estimate of variance is possible. This is known as the lonely
primarily sampling unit (lonely PSU). Ad hoc adjustments are
possible; refer to http://r-survey.r-forge.r-project.org/survey/exmample-lonely.html
for some suggestions.
The MoosePopR() function has an argument that can be set
using
MoosePopR(..., survey.lonely.psu="remove")
The the variance for this stratum is not considered when estimating
the variance of the grand totals or density. Unfortunately, it is not
possible, at this time, to estimate a ratio with some strata having
lonely PSU.
The SightabilityPopR() function can deal with lonely PSUs by
using within block variability (e.g., among groups) so this will provide
a lower bound to the true uncertainty.
The bottom line is avoid designs where you sample only a single block
in a stratum!
Analysis
Analysis not
adjusting for sightability
Within a
stratum
Density
Suppose a sample of \(n_h\) blocks
were surveyed in stratum \(h\). For
each block, the number of moose \(m_{hi}\) and the area of the block \(a_{hi}\) are obtained for block \(i\) in stratum \(h\). The estimated density of moose per
unit area in stratum \(h\) is obtained
as: \[\widehat{D}_h = \frac{\sum_i
m_{hi}}{\sum_i a_{hi}}\] i.e., as the total number of moose in
the surveyed blocks divided by the total survey area. This is a standard
ratio estimator and the estimated standard error is found as using
equation 6.9 of Cochran (1977). The estimator and its standard error can
be automatically computed using the svyratio() function in the
survey package (Lumley, 2019) of R.
Similar formula are used for estimating the density of other sex/age
categories.
Abundance
The estimated total number of moose in stratum \(h\) (\(\widehat{M}_h\)) is found by multiplying
the density estimate and its standard error by the stratum area \(A_h\)
\[\widehat{M}_h = \widehat{D}_h \times
A_h\] \[se(\widehat{M}_h) =
se(\widehat{D}_h) \times A_h\] Similar formula are used for
estimating the abundance of other sex/age categories.
Bull to Cow and
other ratios
Suppose a sample of \(n_h\) blocks
were surveyed in stratum \(h\). For
each block, the number of bulls \(b_{hi}\) and the number of cows \(c_{hi}\) are obtained for block \(i\) in stratum \(h\). The estimated bull to cow ratio in
stratum \(h\) is obtained as: \[\widehat{BC}_h = \frac{\sum_i b_{hi}}{\sum_i
c_{hi}}\] i.e., as the total number of bulls (\(\sum_i b_{hi}\)) in the surveyed blocks
divided by the total number of cows (\(\sum_i
c_{hi}\)) in the surveyed blocks. This is a standard ratio
estimator and the estimated standard error is found as using equation
6.9 of Cochran (1977). The estimator and its standard error are
automatically computed using the svyratio() function in the
survey package (Lumley, 2019) of R.
If the number of bulls per 100 cows is wanted, simply multiply the
estimate and its standard error by \(100\times\).
Other ratios such as calves:cows are computed in similar ways.
Across all
strata
Density
The overall density for the number of moose is found as a weighted
averaged of the stratum specific densities: \[\widehat{D}= \sum_h \frac{A_h}{\sum_h
A_h}\widehat{D}_h\]
\[se(\widehat{D}) = \sqrt{\sum_h \left(
\frac{A_h}{\sum_h A_h} \right)^2se(\widehat{D}_h)^2}\]
which is equivalent to the estimated total abundance (see below)
divided by the total stratum area. This is known as a
separate-ratio estimator of the total and is possible because
the expansion factor going from density to abundance (the stratum area)
is known for each stratum.
Similar formula are used for estimating the density of other sex/age
categories.
Abundance
The total abundance of moose is found by summing the estimated
abundances across strata:
\[\widehat{M} = \sum_h
\widehat{M}_h\] and the standard error of the overall abundance
is found as: \[se(\widehat{M}) = \sqrt{\sum_h
se(\widehat{M}_h)^2}\] This is known as a separate-ratio
estimator of the total and is possible because the expansion factor
going from density to abundance (the stratum area) is known for each
stratum.
Similar formula are used for estimating the abundance of other
sex/age categories.
Bull to Cow and
other ratios
The estimation of the overall bull to cow ratio is computed using the
double-ratio estimate (Cochran, 1977, Section 6.19) as \[\widehat{BC}_{\textit{double~ratio}}=\frac{\widehat{B}}{\widehat{C}}\]
where \(\widehat{B}\) and \(\widehat{C}\) are the estimated total
number of bull and cows individually computed. This is equivalent to the
ratio of the overall density of bulls and cows. The above formula can be
expanded to give
\[\widehat{BC}_{\textit{double~ratio}}=\frac{\sum_h
\frac{\sum_i b_{hi}}{\sum_i a_{hi}} \times A_h}
{\sum_h \frac{\sum_i c_{hi}}{\sum_i a_{hi}} \times
A_h}\]
Its standard error is NOT directly available in the survey
package but is readily computed by finding the estimates and the
covariance of the estimates of number of bull and cows for each stratum
and then using the delta method to find the overall ratio and standard
error of the overall ratio.
The
MoosePopR() function.
A MoosePopR() function was created in R to
replicate the results from MoosePop (Reed, 1989). The key
arguments to this function are:
- survey.data - information on each group measured in the
survey. This was read from the Excel workbook earlier.
- survey.block.area - information about the area of each
block surveyed. This was read from the Excel workbook earlier.
- stratum.data - information about each stratum. This was
read from the Excel workbook earlier.
- density, abundance, numerator, denominator - variables for
which the density, abundance, ratio are to be formed as right-sided
formula (e.g., density=~Cows to estimate the density of Cows).
- conf.level=0.90 indicates the confidence level for
confidence intervals to compute with the default being a 90% confidence
interval.
Sample
Analyses
Results differ slightly from those reported on an Excel
spreadsheet because of slight differences in areas of blocks between
data provided to me and that used in MoosePop (Reed, 1989).
We are now ready to do the analysis. I’ve gathered all of the
analysis results into a list object for extraction later.
The UC suffix that I have placed on the estimate
name indicates it is not corrected for sightability.
I have only computed abundance and density estimates for all moose,
but similar code can be used for other age/sex categories. Similarly, I
have only considered the bull:cow ratio and other ratio can be computed
in similar fashion.
Density of all
moose
We compute the (uncorrected for sightability) density of all moose
(regardless of sex or age) using the number of moose (NMoose)
variable.
result <- NULL
result$"All.Density.UC" <- MoosePopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,density=~NMoose # which density
)
result$"All.Density.UC"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL
## 1 H NMoose Block.Area 409 448.9 0.9111161 0.12361519 0.9 0.7077872 1.1144450
## 2 L NMoose Block.Area 161 415.5 0.3874850 0.07772304 0.9 0.2596419 0.5153280
## 3 M NMoose Block.Area 499 981.4 0.5084573 0.07429716 0.9 0.3862493 0.6306653
## 4 .OVERALL <NA> <NA> 1069 1845.8 0.5375760 0.05055619 0.9 0.4544185 0.6207336
The estimate and SE column as the estimated
(uncorrected for sightability) density of all moose with a measure of
uncertainty for each stratum. The overall density is found as a weighted
average (by stratum area) of the density in each stratum.
Similar function calls are used for estimating the density of other
sex/age categories by changing the density argument.
Abundance of all
moose
We compute the estimated (uncorrected for sightability) abundance of
all moose (regardless of sex or age) by expanding the density by the
Stratum.Area. The overall abundance is found as the sum of the
expanded estimates.
result$"All.Abund.UC" <- MoosePopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~NMoose # which density
)
result$"All.Abund.UC"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL Stratum.Area
## 1 H NMoose Block.Area 409 448.9 1886.921 256.0071 0.9 1465.8272 2308.016 2071
## 2 L NMoose Block.Area 161 415.5 1470.505 294.9589 0.9 985.3412 1955.670 3795
## 3 M NMoose Block.Area 499 981.4 3562.252 520.5259 0.9 2706.0629 4418.441 7006
## 4 .OVERALL <NA> <NA> 1069 1845.8 6919.679 650.7593 0.9 5849.2749 7990.082 12872
The estimate and SE column as the estimated
(uncorrected for sightability) density of all moose with a measure of
uncertainty for each stratum. The overall abundance is found as the sum
of the estimates in each stratum.
Similar function calls are used for estimating the abundance of other
sex/age categories by changing the density argument.
Number of bulls
and number of cows
We estimate the (uncorrected for sightability) abundance of Bulls and
Cows.
result$"Bulls.Abund.UC" <- MoosePopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~Bulls # which density
)
result$"Bulls.Abund.UC"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL Stratum.Area
## 1 H Bulls Block.Area 65 448.9 299.8775 51.82288 0.9 214.63643 385.1185 2071
## 2 L Bulls Block.Area 27 415.5 246.6065 101.66226 0.9 79.38696 413.8260 3795
## 3 M Bulls Block.Area 70 981.4 499.7147 91.22475 0.9 349.66333 649.7661 7006
## 4 .OVERALL <NA> <NA> 162 1845.8 1046.1987 146.09168 0.9 805.89923 1286.4981 12872
result$"Cows.Abund.UC" <- MoosePopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~Cows # which density
)
result$"Cows.Abund.UC"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL Stratum.Area
## 1 H Cows Block.Area 265 448.9 1222.5774 172.6861 0.9 938.5340 1506.621 2071
## 2 L Cows Block.Area 95 415.5 867.6895 174.7329 0.9 580.2796 1155.099 3795
## 3 M Cows Block.Area 325 981.4 2320.1039 364.3373 0.9 1720.8224 2919.385 7006
## 4 .OVERALL <NA> <NA> 685 1845.8 4410.3709 439.4243 0.9 3687.5822 5133.160 12872
These values are computed similarly as the total abundance.
Bull to Cow and
other ratios
Finally, we estimate the Bulls:Cows ratio:
result$"Bulls/Cow.UC" <- MoosePopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,numerator=~Bulls, denominator=~Cows # which density
)
result$"Bulls/Cow.UC"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL
## 1 H Bulls Cows 65 265 0.2452830 0.02742502 0.9 0.2001729 0.2903932
## 2 L Bulls Cows 27 95 0.2842105 0.09651642 0.9 0.1254551 0.4429659
## 3 M Bulls Cows 70 325 0.2153846 0.02831107 0.9 0.1688170 0.2619522
## 4 .OVERALL <NA> <NA> 162 685 0.2372133 0.02578894 0.9 0.1947943 0.2796323
Other ratios would be estimated in similar ways by changing the
numerator and denominator arguments to the function
call.
Final object
## [1] "All.Density.UC" "All.Abund.UC" "Bulls.Abund.UC" "Cows.Abund.UC" "Bulls/Cow.UC"
Adjusting for
sightability
The above computations are not adjusted for sightability, i.e., not
all moose can be detected due to visibility concerns.
An adjustment for sightability can be done by also performing a study
where a known number of groups of moose (e.g., radio collared) are
surveyed and information about detection/non detection is recorded at
the group level. A logistic regression (see previous sections) is used
to estimate the probability of detection of a group given covariates
(such as Vegetation Class).
Then the sightability model is used to expand the observed number of
groups of moose by the a sightability correction factor (SCF). This is
related to the inverse of the probability of detection, but includes a
correction to account for the uncertainty in the estimates of the
coefficients of the sightability model (see Fieberg, 2012, Equation 1
and later in this document).
For example, consider a model to estimate detectability given in
Quayle et al. (2001):
Estimated sightability correction factor for each vegetation cover class
|
Veg Cover Class
|
Veg Cover %
|
Detection probability
|
Sightability Correction Factor
|
|
1
|
00-20
|
0.933
|
1.06
|
|
2
|
21-40
|
0.740
|
1.33
|
|
3
|
41-60
|
0.368
|
2.64
|
|
4
|
61-80
|
0.107
|
8.17
|
|
5
|
81-100
|
0.024
|
29.08
|
Notice that that, for example, that 1/= is only approximately equal
to 1.3347203.
It is assumed that all animals in a group (e.g., bulls, cows,
calves) are observed if a group is detected.
Let \(\theta_{hjk}\) represent the
expansion factor for group \(k\) in
block \(j\) of stratum \(h\). In the analyses that follow the block
area is NOT used in the analysis. In its place, a simple expansion based
on the number of blocks surveyed within a stratum are used. This will be
less efficient (i.e., have a larger standard error) compared to an
analysis that uses the individual block areas, but unless there is a
high correlation between the number of animals and the block area, the
loss of efficiency is small. If all blocks had the same area, the two
approaches are identical.
We examined the correlation for the existing survey data and it is
typically small. Cochran (1977) shows that unless the correlation is
larger than a specified cutoff that depends on the coefficient of
variation of the numerator and denominator variables, then there is no
gain in using the block area, i.e., unless \[\rho >
\frac{1}{2}\frac{SD(denominator~variable)/mean(denominator~variable)}{SD(numerator~variable)/mean(numerator~variable)} \]
where \(\rho\) is the correlation
between the numerator and denominator variable (i.e., between abundance
of the numerator variable and block area)$, then a ratio estimator using
the area of blocks is not more efficient.
Estimated correlation between animal counts and block area
|
Stratum
|
Type of Animal
|
Corr
|
Cutoff
|
|
H
|
Bulls
|
0.42
|
0.12
|
|
H
|
Lone.cows
|
0.24
|
0.13
|
|
H
|
Cow.W.1…calf
|
0.13
|
0.12
|
|
H
|
Cow.W.2.calves
|
NA
|
NaN
|
|
H
|
Lone…calf
|
NA
|
NaN
|
|
H
|
Unk.Age.Sex
|
-0.37
|
0.04
|
|
H
|
Cows
|
0.25
|
0.15
|
|
H
|
NMoose
|
0.28
|
0.16
|
|
L
|
Bulls
|
0.02
|
0.08
|
|
L
|
Lone.cows
|
0.39
|
0.12
|
|
L
|
Cow.W.1…calf
|
0.55
|
0.15
|
|
L
|
Cow.W.2.calves
|
NA
|
NaN
|
|
L
|
Lone…calf
|
NA
|
NaN
|
|
L
|
Unk.Age.Sex
|
-0.29
|
0.07
|
|
L
|
Cows
|
0.47
|
0.14
|
|
L
|
NMoose
|
0.39
|
0.15
|
|
M
|
Bulls
|
-0.31
|
0.10
|
|
M
|
Lone.cows
|
-0.12
|
0.10
|
|
M
|
Cow.W.1…calf
|
-0.32
|
0.11
|
|
M
|
Cow.W.2.calves
|
-0.19
|
0.04
|
|
M
|
Lone…calf
|
-0.23
|
0.02
|
|
M
|
Unk.Age.Sex
|
0.17
|
0.05
|
|
M
|
Cows
|
-0.21
|
0.12
|
|
M
|
NMoose
|
-0.28
|
0.13
|
|
Note:
|
|
Cutoff is 0.5 ratio of sd/mean of area and abundance of each
type of animal and unless the correlation exceeds the cutoff, there is
no advantage in using the block area in the analysis
|
The correlations are not high. While about half of the response
variables have correlations of abundance with block area that exceed the
cutoff, the variation in the block areas is not that large, so we don’t
think that also adjusting for block area is necessary. Of course, this
also does not account for sightability issues.
A plot of the two variables for each types of animals shows no strong
relationship between the number of observed animals and the block
area:
Consequently, it not expected that ignoring block area in the
analysis will have a material effect.
Within a
stratum
Abundance
Suppose a sample of \(n_h\) blocks
were surveyed in stratum \(h\) out of
\(N_h\) total number of blocks. For
each block, the number of moose \(m_{hjk}\) are obtained for group \(k\) in block \(j\) in stratum \(h\). The estimated correction factor (for
visibility of the group) is \(\widehat{\theta}_{hjk}\) which is computed
give the vector of covariates (x_{hjk}) as (see page 4 of Fieberg,
2012)
\[\widehat{\theta}_{hjk}= 1+\exp{(-x_{hjk}^t
\widehat{\beta}-x_{hjk}^t \Sigma x_{hjk} / 2)}\]
Notice that the sightability correction factor is not simply \(1/\textit{probability of detection}\) or
\(1+\exp{(-x_{hjk}^t \widehat{\beta}\)
because it includes a correction factor to account for the non-linear
transformation from the logit to the probability scale.
The estimated abundance of moose in stratum \(h\) is obtained as: \[\widehat{M}_h = N_h \times \frac{\sum_{jk}
m_{hjk}\widehat{\theta}_{hjk}}{n_h}\] i.e., as the mean number of
(sightability corrected) moose per surveyed block times the total number
of blocks. The standard error of this estimate is complicated because of
the need to account for the estimated sightability but the theory is
covered in Steinhorst and Samuel (1989), Fieberg (2012) and Wong (1996)
and implemented in the AerialSurvey (Unsworth, 1999) and
SightabilityModel packages of R. The latter package
corrects the variance computations used by Steinhorst and Samuel (1989)
and Fieberg (2012).
Similar computations are used for estimating the abundance of other
sex/age categories.
Density
The estimated density of moose in stratum \(h\) (\(\widehat{D}_h\)) is found by dividing the
abundance estimate and its standard error by the stratum area \(A_h\)
\[\widehat{D}_h =
\frac{\widehat{M{_h}}}{A_h} \] \[se(\widehat{M}_h) =
\frac{se(\widehat{M}_h)}{A_h}\]
Similar computations are used for estimating the density of other
sex/age categories.
Bull to Cow and
other ratios
The ratio of bulls to cows within a stratum is computed as the
estimated abundances in each stratum: \[\widehat{BC}_h =
\frac{\widehat{Bulls}_h}{\widehat{Cows}_h}\] i.e., as the
estimated total number of bulls in the stratum divided by the estimated
total number of cows in the stratum. This ratio estimator is not
available in the SightabilityModel package (Fieberg, 2012), but
a new function was written and added to the package to add this
functionality. The standard error is difficult to compute because of the
need to account for the correlation between the number of bulls and
moose in individual groups and the the uncertainty of the correction
factors but is given in Wong (1996).
Note that if the sightability is equal for all groups, then this
common sightability correction factor would cancel everywhere and you
would get the same results as the ratio estimator based on the observed
groups only. In most cases, the impact of sightability will be small on
the ratio estimator and its standard error.
If the number of bulls per 100 cows is wanted, simply multiply the
estimate and its standard error by \(100\times\).
Similar computations occur for other ratios such as calves:cows.
Across all
strata
Abundance
The total abundance of moose is found by summing the estimated
abundances across strata:
\[\widehat{M} = \sum_h
\widehat{M}_h\] The standard error is difficult to compute
because the same sightability model is used across strata. This has been
implemented in the SightabilityModel package (Fieberg, 2012)
and the AerialSurvey (Unsworth, 1999) program.
Similar computations are used for estimating the abundance of other
sex/age categories.
Density
The overall density of moose and its standard error is found as
estimated total abundance and its standard error divided by the total
area over all strata.. \[\widehat{D}= \frac{
\widehat{M}}{\sum_h A_h}\] \[se(\widehat{D}) = \frac{se(\widehat{M})}{{\sum_h
A_h}}\] Because the total area of all strata is known quantity,
this is straightforward.
Similar computations are used for estimating the density of other
sex/age categories.
Bull to Cow and
other ratios
The estimation of the overall bull to cow ratio is computed as the
ratios of their respective estimated abundances \[\widehat{BC}=\frac{\widehat{Bulls}}{\widehat{Cows}}\]
This ratio estimator was not available in the SightabilityModel
package (Fieberg, 2012), but its functionality has been added as part of
this contract. Standard errors are computed as described in Wong
(1996).
Similar computations can be used for other ratios such as
calves:cows.
The
SightabilityPopR() function
I have created a function with the same calling arguments as the
MoosePopR() function to estimate abundance, density, and ratios
using the SightabilityModel package. Notice that additional
functionality was added to the SightabilityModel package
(Fieberg, 2012) to estimate ratios.
A SightabilityPopR() function has a similar calling sequence
as the MoosePopR function with the same key input
variables.
- survey.data - information on each group measured in the
survey. This was read from the Excel workbook earlier.
- survey.block.area - information about the area of each
block surveyed. This was read from the Excel workbook earlier.
- stratum.data - information about each stratum. This was
read from the Excel workbook earlier.
- density, abundance, numerator, denominator - variables for
which the density, abundance, ratio are to be formed as right-sided
formula (e.g., density=~Cows to estimate the density of Cows).
- conf.level=0.90 indicates the confidence level for
confidence intervals to compute with the default being a 90% confidence
interval.
Additionally, the sightability formula, the beta coefficients and the
estimated covariance matrix must also be specified using the
arguments:
- sight.formula - the formula for the sightability model.
This should use the variables in the survey.data frame
- sight.beta - the beta coefficients for the sightability
model
- sight.beta.cov - the covariance matrix for the beta
coefficients
- sight.logCI - should confidence intervals for abundance be
computed using a logarithmic transformation
- sight.var.method - what method (either “Wong” or
“SS”) should be used to estimate the variances . using the
methods of Wong (1996) or Steinhorst and Samuels (2012). The default
(and preferred) method is “Wong” because she corrects the
variance computations used by Steinhorst and Samuel (1989) and Fieberg
(2012).
These additional parameters are passed to the appropriate functions
in the SightabilityModel package (Fieberg, 2012). Refer to the
examples for details.
Sample
Analyses
Dealing with
missing values in the sightability covariates
Because we are correcting for sightability, we need the
VegCoverClass for all groups. However there are some groups of
moose with missing data for this covariate:
select <- is.na(survey.data$VegCoverClass)
survey.data[select,]
## # A tibble: 8 × 14
## Domain Block.ID Stratum Bulls Lone.Cows Cow.W.1...calf Cow.W.2.calves Lone...calf Unk.Age.Sex NMoose ..Veg.Cover myNMoose Cows VegCoverClass
## <chr> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 A 9 M 0 0 1 0 0 0 2 NA 2 1 NA
## 2 A 27 M 0 0 0 0 0 0 0 NA 0 0 NA
## 3 A 86 L 0 0 0 0 0 0 0 NA 0 0 NA
## 4 A 182 L 0 0 0 0 0 0 0 NA 0 0 NA
## 5 B 405 M 0 0 0 0 0 0 0 NA 0 0 NA
## 6 B 408 H 0 1 0 0 0 0 1 NA 1 1 NA
## 7 B 408 H 1 2 1 0 0 0 5 NA 5 3 NA
## 8 B 408 H 0 1 0 0 0 0 1 NA 1 1 NA
If you simply delete these observations, then estimates can be
severely biased because these groups would be excluded from the
expansions when corrected for sightability. About the best that can be
done is to assign an imputed vegetation class to these observations with
the highest sightability to reduce the bias.
# change the missing values to cover class with highest sightability
survey.data$VegCoverClass[select] <- 1
survey.data[select,]
## # A tibble: 8 × 14
## Domain Block.ID Stratum Bulls Lone.Cows Cow.W.1...calf Cow.W.2.calves Lone...calf Unk.Age.Sex NMoose ..Veg.Cover myNMoose Cows VegCoverClass
## <chr> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 A 9 M 0 0 1 0 0 0 2 NA 2 1 1
## 2 A 27 M 0 0 0 0 0 0 0 NA 0 0 1
## 3 A 86 L 0 0 0 0 0 0 0 NA 0 0 1
## 4 A 182 L 0 0 0 0 0 0 0 NA 0 0 1
## 5 B 405 M 0 0 0 0 0 0 0 NA 0 0 1
## 6 B 408 H 0 1 0 0 0 0 1 NA 1 1 1
## 7 B 408 H 1 2 1 0 0 0 5 NA 5 3 1
## 8 B 408 H 0 1 0 0 0 0 1 NA 1 1 1
We are now ready to do the analysis. I’ve gathered all of the
analysis results into a list object for extraction later.
The C suffix that I have placed on the estimate name
indicates it is corrected for sightability.
I have only computed abundance and density estimates for all moose,
but similar code can be used for other age/sex categories. Similarly, I
have only considered the bull:cow ratio and other ratio can be computed
in similar fashion.
Abundance of all
moose
We compute the (corrected for sightability) abundance of all moose
(regardless of sex or age) using the number of moose (NMoose)
variable.
result <- NULL
result$"All.Abund.C" <- SightabilityPopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
temp <- result$"All.Abund.C"
temp[,-c(1:3,8)] <- round(temp[,-c(1:3,8)]+.00001,0) # force to be numeric
temp
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL tau.hat VarTot VarSamp VarSight VarMod
## 1 H NMoose NA 409 NA 1991 290 0.9 1514 2467 1991 83874 80172 1299 2402
## 2 L NMoose NA 161 NA 1645 360 0.9 1053 2237 1645 129500 121646 4794 3059
## 3 M NMoose NA 499 NA 3948 590 0.9 2978 4919 3948 348050 311067 23882 13100
## 4 .OVERALL <NA> NA 1069 NA 7584 768 0.9 6321 8847 7584 589625 512886 29976 46764
The estimate and SE column as the estimated
(corrected for sightability) density of all moose with a measure of
uncertainty for each stratum. The overall abundance is found as the sum
of the estimates in each stratum. The right most columns are information
about the sources of uncertainty (due to sampling, sightability, or the
model for sightability).
Similar function calls are used for estimating the abundance of other
sex/age categories by changing the abundance argument.
We can show the impact of simply deleting those values missing the
VegCoverClass covariate by setting the observed values of moose
to .001 for these groups. This will retain the correct number of blocks
surveyed. If you simply deleted those groups of moose with missing
VegCoverClass values and a block then had no observations, the
block would “disappear” from the analysis which is not correct.
# mimic impact of deleting observations with missing VegCoverClass
survey.data2 <- survey.data
survey.data2$NMoose[select] <- .001
wrong.way <- SightabilityPopR( # show impact of deleting observations but keeping # blocks the same
survey.data = survey.data2 # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
wrong.way
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL tau.hat VarTot VarSamp VarSight VarMod
## 1 H NMoose NA 402.003 NA 1957.543 276.4433 0.9 1502.834 2412.251 1957.543 76420.91 72801.74 1277.509 2341.656
## 2 L NMoose NA 161.002 NA 1645.393 359.8552 0.9 1053.484 2237.303 1645.393 129495.79 121642.25 4794.383 3059.154
## 3 M NMoose NA 497.003 NA 3933.512 588.6957 0.9 2965.193 4901.830 3933.512 346562.62 309641.47 23874.233 13046.925
## 4 .OVERALL <NA> NA 1060.008 NA 7536.448 761.8704 0.9 6283.282 8789.613 7536.448 580446.44 504085.46 29946.124 46414.851
Notice the negative bias in the estimated abundance computed the
incorrect way (7536) vs. the value when the VegCoverClass is
set to the class with highest sightability (7584) computed above.
In the real world, if a group has missing values for covariates using
in the sightability model, do not change the count data, but change the
missing covariates to values that result in the highest possible
sightability for this group. In this way, the number of blocks surveyed
is computed properly and you have partially the bias in dropping these
groups by including them with an imputed high sightability value.
Density of all
moose
We compute the estimated (corrected for sightability) density of all
moose (regardless of sex or age).
result$"All.Density.C" <- SightabilityPopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,density=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
temp<- result$"All.Density.C"
temp[,-(1:3)] <- round(temp[,-(1:3)]+.00001,2) # force to be numeric
temp
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL tau.hat VarTot VarSamp VarSight VarMod Stratum.Area
## 1 H NMoose NA 409 NA 0.96 0.14 0.9 0.73 1.19 1990.67 83873.94 80172.48 1299.20 2402.26 2071
## 2 L NMoose NA 161 NA 0.43 0.09 0.9 0.28 0.59 1645.37 129499.99 121646.49 4794.38 3059.12 3795
## 3 M NMoose NA 499 NA 0.56 0.08 0.9 0.43 0.70 3948.26 348049.57 311067.03 23882.05 13100.49 7006
## 4 .OVERALL <NA> NA 1069 NA 0.59 0.06 0.9 0.49 0.69 7584.30 589625.35 512885.99 29975.63 46763.73 12872
The estimate and SE column as the estimated
(corrected for sightability) density of all moose with a measure of
uncertainty for each stratum. The overall density is found as a
estimated abundance/total area over all strata. The variance components
are the same for the total abundance because these values are used to
derive the density.
Similar function calls are used for estimating the density of other
sex/age categories by changing the density argument.
Number of bulls
and number of cows
We estimate the (corrected for sightability) abundance of Bulls and
cows.
result$"Bulls.Abund.C" <- result$"All.Density.C" <- SightabilityPopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,density=~Bulls # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
result$"Bulls.Abund.C"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL tau.hat VarTot VarSamp VarSight VarMod Stratum.Area
## 1 H Bulls NA 65 NA 0.15160119 0.02898037 0.9 0.10393273 0.1992697 313.9661 3602.201 3421.794 124.9116 55.49554 2071
## 2 L Bulls NA 27 NA 0.07473830 0.03072910 0.9 0.02419343 0.1252832 283.6319 13599.513 12786.485 702.1133 110.91511 3795
## 3 M Bulls NA 70 NA 0.07946567 0.01502809 0.9 0.05474667 0.1041847 556.7365 11085.303 9569.687 1247.2808 268.33503 7006
## 4 .OVERALL <NA> NA 162 NA 0.08967794 0.01322383 0.9 0.06792667 0.1114292 1154.3344 28973.872 25777.966 2074.3057 1121.60046 12872
result$"Cows.Abund.C" <- SightabilityPopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,density=~Cows # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
result$"Cows.Abund.C"
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL tau.hat VarTot VarSamp VarSight VarMod Stratum.Area
## 1 H Cows NA 265 NA 0.6213613 0.09387521 0.9 0.4669503 0.7757722 1286.8392 37797.41 36163.85 601.7188 1031.8369 2071
## 2 L Cows NA 95 NA 0.2526849 0.05723467 0.9 0.1585422 0.3468275 958.9391 47178.26 44630.73 1575.6599 971.8729 3795
## 3 M Cows NA 325 NA 0.3673888 0.06188781 0.9 0.2655925 0.4691852 2573.9262 187996.80 168711.74 13669.7257 5615.3341 7006
## 4 .OVERALL <NA> NA 685 NA 0.3744332 0.04139389 0.9 0.3063463 0.4425201 4819.7044 283899.43 249506.33 15847.1044 18545.9933 12872
These values are computed similarly as the total abundance.
Bull to Cow and
other ratios
Finally we estimates the Bulls/Cow ratio using the corrected for
sightability values.
result$"Bulls/Cow.C" <- SightabilityPopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,numerator=~Bulls, denominator=~Cows # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
## [1] "Dropping records with 0 animals in both numerator and denominator in the observational data set"
## [1] "Dropping records with 0 animals in both numerator and denominator in the observational data set"
## [1] "Dropping records with 0 animals in both numerator and denominator in the observational data set"
## [1] "Dropping records with 0 animals in both numerator and denominator in the observational data set"
temp<- result$"Bulls/Cow.C"
temp[,-(1:3)] <- round(temp[,-(1:3)]+.00001,3) # force to be numeric
temp
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL ratio.hat VarRatio VarSamp VarSight VarMod
## 1 H Bulls Cows 65 265 0.244 0.027 0.9 0.200 0.288 0.244 0.001 NA NA NA
## 2 L Bulls Cows 27 95 0.296 0.102 0.9 0.128 0.464 0.296 0.010 NA NA NA
## 3 M Bulls Cows 70 325 0.216 0.027 0.9 0.171 0.261 0.216 0.001 NA NA NA
## 4 .OVERALL <NA> <NA> 162 685 0.240 0.027 0.9 0.196 0.283 0.240 0.001 NA NA NA
The ratio is computed within each stratum and overall The sources of
variation computations are set to missing as they are not sensible in
this case.
Notice that this ratio estimator is not that different from that
computed from values uncorrected for sightability. This is a consequence
of the approximately equal sightability correction factor for all
groups.
Other ratios can be computed by changing the numerator and
denominator arguments in the function call.
Final object
The result is a list object with one element each of the analyses
done above.
## [1] "All.Abund.C" "All.Density.C" "Bulls.Abund.C" "Cows.Abund.C" "Bulls/Cow.C"
Domain estimation
Domain estimation refer to estimating density, abundance, or ratios
for subsets of the survey area. For example, in British Columbia, a
survey may take place over a combined Buckley Valley and Lake District
(sub units) survey area, but estimates of abundance are also wanted for
Buckley Valley and Lake District individually. In this case, the
sub-units are domains.
There are four cases to consider depending if information about the
primary sampling units (PSU) (i.e., blocks) and stratum areas are known
or unknown at the domain level \(\times\) the domain separation operates at
the PSU (block) or group level.
Domain at PSU (block)
level; domain population information known
This is the simplest case. Here the primary sampling units (PSU) (or
blocks) are classified as belonging to the domain or not. For example,
the study area could be divided into two or more management units and
each PSU (block) belongs to one and only one management units in its
entirety. The total area of the management unit and the total number of
potential PSUs is known for each management unit.
Because PSUs (blocks) were randomly selected within each stratum with
equal probability, they are also randomly selected from each domain
(management unit).
Consequently, just subset the survey data (observed animals) to those
PSUs (blocks) belonging to the domain of interest and change the stratum
information to refer to the total area and total PSUs (block) for that
domain and estimation for density, abundance, and ratios occurs exactly
as before.
Example
For example, the survey data used in the examples was classified in
Domain \(A\) and \(B\), and a separate worksheet in the
workbook has information about stratum information for Domain \(A\). We subset the survey data, read in the
stratum information for Domain \(A\)
and then use the same methods as shown before.
The PSUs (blocks) in the example are split between two domains
(A and B) as shown below:
# PSU's are split between the domains
xtabs(~Domain+Block.ID, data=survey.data, exclude=NULL, na.action=na.pass)
## Block.ID
## Domain 9 12 13 20 27 31 39 56 83 85 86 97 101 117 119 123 128 129 136 142 143 146 150 156 160 168 175 181 182 198 207 216 218 226 232 240 244 246 256 260 269 295 299 308 314 316 317 318 327 342 348
## A 13 14 7 4 1 11 32 12 14 9 1 6 7 29 14 14 18 9 3 10 6 11 5 4 12 6 4 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 9 13 8 4 6 2 4 2 11 1 3 23 8 2 3 2 10 4 1 6 17
## Block.ID
## Domain 351 352 354 360 379 380 398 401 405 408 409 428 436
## A 0 0 0 0 0 0 0 0 0 0 0 0 0
## B 19 8 21 10 15 6 13 14 1 31 3 15 27
The number of groups of moose in each block is shown.
We subset the survey data:
# Subset the survey data
survey.data.A <- survey.data[ survey.data$Domain == "A",]
The block information (block area) is unchanged and does not need to
be subset.
We need information at the stratum level for domain A which
is available on the workbook:
# Domain information for the population for each stratum
stratum.data.A <- readxl::read_excel(
system.file("extdata", "SampleMooseSurveyData.xlsx", package = "SightabilityModel", mustWork=TRUE),
sheet="Stratum-DomainA",
skip=2,.name_repair="universal")
kable(stratum.data.A, row.names=FALSE,
caption="Stratum totals for Domain A",
col.names=c("Stratum","Stratum Area","Stratum # blocks")) %>%
column_spec(column=c(1:3), width="2cm") %>%
kable_styling("bordered",position = "center", full_width=FALSE)
Stratum totals for Domain A
|
Stratum
|
Stratum Area
|
Stratum # blocks
|
|
L
|
2453
|
65
|
|
M
|
4000
|
120
|
|
H
|
950
|
35
|
We can now estimate abundance, density, or ratios for Domain A in the
same way as before with and without corrections for sightability. We
show only the estimated abundance for all moose after correcting for
sightability. Note the use of survey.data.A and
stratum.data.A*
All.Abund.A.corrected <- SightabilityPopR(
survey.data = survey.data.A # raw data for domain A
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data.A # stratum information for domain A
,abundance=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
temp <- All.Abund.A.corrected
temp[,-c(1:3,8)] <- round(temp[,-c(1:3,8)]+.00001,0) # force to be numeric
temp[,1:10]
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL
## 1 H NMoose NA 197 NA 1239 203 0.9 905 1574
## 2 L NMoose NA 106 NA 978 273 0.9 530 1426
## 3 M NMoose NA 198 NA 1712 254 0.9 1295 2129
## 4 .OVERALL <NA> NA 501 NA 3929 434 0.9 3215 4643
Domain at PSU (block)
level; domain population information unknown.
In some cases, only the surveyed PSUs can be classified by domain and
the stratum total area and stratum total blocks is unknown for the
domain. Cochran (1977, Sections 2.13 and 5A.14) discuss this case.
Abundance and ratios can be estimated by setting all survey data to 0
for blocks/groups not part of the domain, and then using the estimating
functions on the complete data after zeroing. This may seem strange, but
consider the following table
PSU
Domain A A A A B B B B B B
Y 2 3 3 4 5 3 2 3 2 4
The total of \(Y\) in Domain \(A\) is \(2+3+3+4=12\). If we consider the modified
data
PSU
Domain A A A A B B B B B B
Y' 2 3 2 3 0 0 0 0 0 0
and find the mean of \(\overline{Y'}=(2+3+3+4+0+0+0+0+0+0)/10=1.2\)
and multiply the mean of Y’ by the population number of PSU
(10) we get the domain total of \(Total(y)=\overline{Y'} \times 10=1.2 \times
10=12\).
Example
We set the survey data to 0 if the domain is not A (notice
that we do NOT delete observations).
# Set number of moose to zero if not part of domain A
survey.data.A.z <- survey.data
survey.data.A.z$NMoose[ survey.data$Domain != "A"] <- 0
We now use the modified survey data (survey.data.A.Z
but the original group and stratum data:
All.Abund.A.corrected.z <- SightabilityPopR(
survey.data = survey.data.A.z # raw data with non-domain counts set to zero
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
temp <- All.Abund.A.corrected.z
temp[,-c(1:3,8)] <- round(temp[,-c(1:3,8)]+.00001,0) # force to be numeric
temp[,1:10]
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL
## 1 H NMoose NA 197 NA 969 321 0.9 442 1497
## 2 L NMoose NA 106 NA 1092 387 0.9 455 1729
## 3 M NMoose NA 198 NA 1523 353 0.9 942 2104
## 4 .OVERALL <NA> NA 501 NA 3584 620 0.9 2565 4604
The estimates will be similar (but not exactly the same) between this
analysis and the previous section.
Estimates of ratios can be found in the same way because these are
based on abundances
However, estimates of density cannot be found using this
method. Refer to Cochran (1977, Section 5A.14, Estimating
Domain Means) for more details.
Domain at group
level; domain population information known
The analysis in this case is similar to the comparable case when the
domain occurs at the PSU (block) level. Now groups are
classified as belonging to the domain or not. For example, interest may
lie in the number of moose in each vegetation class.
All blocks are used, but now in each block, you will subset the
groups that belong to the domain. The hard part is the area in this
domain of EACH PSU (block) must also be known. Presumably, this is a GIS
exercise in the case of vegetation cover, assuming that entire survey
area has been mapped.
Similarly, the total area in the stratum for this domain must be
known. This is presumably a GIS exercise.
The analysis proceeds by subsetting the survey data to groups that
fall within this domain, but you need to ensure that groups
without this domain are still included (with 0 counts for the response
variable). You also need to use the modified block areas and
modified stratum area in this domain. Please contact me if you are
attempting to do this as the programming R is tricky, to say
the least.
Domain at group
level; domain population information unknown.
In some cases, only the surveyed groups can be classified by domain
and the block area, stratum total area and stratum total blocks is
unknown for the domain.
We use the same trick as above by setting the survey data to 0 if the
domain is not A (notice that we do NOT delete
observations).
Example
Suppose we want moose abundance by vegetation cover class. The
estimate of total abundance is
All.Abund <- SightabilityPopR(
survey.data = survey.data # raw data
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
temp <- All.Abund
temp[,-c(1:3,8)] <- round(temp[,-c(1:3,8)]+.00001,0) # force to be numeric
temp[,1:10]
## Stratum Var1 Var2 Var1.obs.total Var2.obs.total estimate SE conf.level LCL UCL
## 1 H NMoose NA 409 NA 1991 290 0.9 1514 2467
## 2 L NMoose NA 161 NA 1645 360 0.9 1053 2237
## 3 M NMoose NA 499 NA 3948 590 0.9 2978 4919
## 4 .OVERALL <NA> NA 1069 NA 7584 768 0.9 6321 8847
We will compute the total abundance for each vegetation cover
class
All.Abund.vc <- plyr::llply(unique(survey.data$VegCoverClass), function(VegCover){
# Set number of moose to zero if not part of domain A
survey.data.z <- survey.data
survey.data.z$NMoose[ survey.data$VegCoverClass != VegCover] <- 0 # set to zero
#browser()
All.Abund.vc <- SightabilityPopR(
survey.data = survey.data.z # raw data that has been zeroed out
,survey.block.area = survey.block.area # area of each block
,stratum.data = stratum.data # stratum information
,abundance=~NMoose # quantifies to estimate
,sight.formula = observed ~ VegCoverClass # sightability mode;
,sight.beta = beta # the beta coefficients for the sightability model
,sight.beta.cov = beta.cov # the covariance matrix for the beta coefficients
,sight.var.method = "Wong" # method used to estimate the variances
)
list(VegCoverClass=VegCover, est=All.Abund.vc)
})
# extract the total abundance
All.Abund.vc.df <- plyr::ldply(All.Abund.vc, function(x){
#browser()
res <- data.frame(VegCoverClass=as.character(x$VegCoverClass), stringsAsFactors=FALSE)
res$estimate <- x$est[x$est$Stratum==".OVERALL", c("estimate")]
res$SE <- x$est[x$est$Stratum==".OVERALL", c("SE" )]
res
})
All.Abund.vc.df <- plyr::rbind.fill( All.Abund.vc.df,
data.frame(VegCoverClass=".OVERALL", estimate=sum(All.Abund.vc.df$estimate, stringAsFactors=FALSE)))
All.Abund.vc.df
## VegCoverClass estimate SE
## 1 1 5862.2862 506.1674
## 2 2 1406.9505 258.7836
## 3 3 315.0633 185.5436
## 4 .OVERALL 7584.3000 NA
The estimates sum to the estimate firstly computed, but the estimates
from the individual vegetation cover classes are not independent and so
the overall standard error cannot be found from the separate estimates
by vegetation cover class.
Estimates of ratios can be found in the same way because they are
based on abundances.
However, estimates of density cannot be found using this
method. Refer to Cochran (1977, Section 5A.14, Estimating
Domain Means) for more details.
References
Cochran, W.G. (1977). Sampling techniques. 3rd Edition. Wiley. New
York.
Fieberg, J. (2012). Estimating Population Abundance Using
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Gasaway, W.C., S.D. Dubois, D.J. Reed and S.J. Harbo. (1986).
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Univ. Alaska, No. 22. Institute of Arctic Biology, U. of Alaska,
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Lumley, T. (2019) “survey: analysis of complex survey samples”. R
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Quayle, J. F., A. G. MacHutchon, and D. N. Jury. (2001). Modeling
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Ministry of Sustainable Resource Management, Victoria, B.C.
Reed, D.J. (1989). MOOSEPOP program documentation and instructions.
Alaska Department of Fish and Game. Unpublished report.
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