# Analysis of Redstart data illustrating basic RMark features
# 2019-05-01 CJS Initial code
# Sherry TW, Wilson S, Hunter S, Holmes RT (2015)
# Impacts of nest predators and weather on reproductive success and
# population limitation in a long-distance migratory songbird.
# Journal of Avian Biology 46(6): 559-569. https://doi.org/10.1111/jav.00536
# Data from
# Sherry TW, Wilson S, Hunter S, Holmes RT (2015)
# Data from: Impacts of nest predators and weather on reproductive success and
# population limitation in a long-distance migratory songbird.
# Dryad Digital Repository. https://doi.org/10.5061/dryad.73870
library(ggplot2)
## Registered S3 methods overwritten by 'ggplot2':
## method from
## [.quosures rlang
## c.quosures rlang
## print.quosures rlang
library(readxl)
library(RMark)
## This is RMark 2.2.6
## Documentation available at http://www.phidot.org/software/mark/rmark/RMarkDocumentation.zip
# The dataframe must contain the following fields with the following names
#
# FirstFound: day the nest was first found
# LastPresent: last day that a chick was present in the nest
# LastChecked: last day the nest was checked
# Fate: fate of the nest; 0=hatch an
# Freq: number of nests with this data
#
# In this example, the multiple visits to a nest have been collapsed
# to a single record for each nest.
# In more complex examples, you may have multple records per nest
# as shown in the mallard example.
#
reddata <- readxl::read_excel(file.path("..","Sherry.xlsx"),
sheet="NestData")
reddata <- as.data.frame(reddata) # Rmark gets upset with tibbles
head(reddata)
## NestId FirstFound LastPresent LastChecked Fate Freq Height
## 1 /*1983-175*/ 11 11 18 1 1 16.9
## 2 /*1983-176*/ 13 22 23 1 1 10.5
## 3 /*1983-178*/ 7 26 26 0 1 4.8
## 4 /*1983-180*/ 12 14 20 1 1 3.7
## 5 /*1983-181*/ 6 20 25 1 1 10.7
## 6 /*1983-182*/ 11 19 20 1 1 17.8
## BaffleStatus DBH AgeDay1 Year
## 1 N 39.0 -8 1983
## 2 N 10.7 -10 1983
## 3 N 8.8 -4 1983
## 4 N 5.1 -9 1983
## 5 N 15.6 -3 1983
## 6 N 46.2 -8 1983
range(reddata$FirstFound)
## [1] 1 56
range(reddata$LastPresent)
## [1] 2 62
range(reddata$LastChecked)
## [1] 3 62
# what are the parameters of the model
# There is only one parameter, the daily survival probality (S)
setup.parameters("Nest", check=TRUE)
## [1] "S"
# Baffled nests only
dim(reddata)
## [1] 537 11
reddata.baf <- reddata[ reddata$BaffleStatus=="Y",]
dim(reddata.baf)
## [1] 71 11
# 1. Process the data.
# The nocc variable is the data at which hatching occurs
red.baf.proc <- process.data(reddata.baf, model="Nest", nocc=max(reddata.baf$LastChecked))
red.baf.proc
## $data
## NestId FirstFound LastPresent LastChecked Fate freq Height
## 80 /*1985-444*/ 10 32 32 0 1 9.30
## 81 /*1985-448*/ 18 31 35 1 1 16.70
## 82 /*1985-449*/ 9 32 32 0 1 5.90
## 83 /*1985-450*/ 10 33 33 0 1 3.30
## 84 /*1985-451*/ 4 25 25 0 1 6.70
## 85 /*1985-457*/ 11 18 21 1 1 1.90
## 86 /*1985-458*/ 15 35 35 0 1 14.60
## 91 /*1985-464*/ 12 26 26 0 1 3.60
## 110 /*1986-538*/ 7 27 27 0 1 14.00
## 111 /*1986-539*/ 4 26 26 0 1 3.90
## 114 /*1986-548*/ 4 25 25 0 1 1.79
## 119 /*1986-569*/ 4 26 26 0 1 5.00
## 129 /*1986-593*/ 17 37 37 0 1 16.31
## 136 /*1986-638*/ 22 30 30 0 1 13.30
## 138 /*1986-645*/ 23 25 25 0 1 14.33
## 140 /*1986-649*/ 23 35 35 0 1 1.21
## 149 /*1986-661*/ 32 53 53 0 1 4.40
## 153 /*1987-680*/ 3 23 23 0 1 15.35
## 177 /*1987-803*/ 21 26 27 1 1 6.09
## 181 /*1987-811*/ 22 38 38 0 1 5.53
## 183 /*1987-819*/ 23 34 34 0 1 4.85
## 197 /*1988-896*/ 9 15 19 1 1 4.70
## 203 /*1988-917*/ 9 30 30 0 1 1.60
## 205 /*1988-922*/ 17 33 37 1 1 20.10
## 207 /*1988-935*/ 16 31 31 0 1 3.20
## 208 /*1988-936*/ 11 32 32 0 1 4.10
## 210 /*1988-942*/ 21 30 30 0 1 2.90
## 213 /*1988-959*/ 15 29 29 0 1 13.00
## 215 /*1988-961*/ 17 39 39 0 1 12.70
## 217 /*1988-963*/ 22 43 43 0 1 4.40
## 219 /*1988-970*/ 23 29 29 0 1 14.00
## 235 /*1989-1071*/ 8 29 29 0 1 9.80
## 237 /*1989-1077*/ 3 25 25 0 1 13.50
## 238 /*1989-1078*/ 8 25 25 0 1 10.90
## 241 /*1989-1104*/ 9 18 21 1 1 9.20
## 250 /*1989-1121*/ 11 26 26 0 1 3.70
## 253 /*1989-1125*/ 24 27 30 1 1 19.90
## 255 /*1989-1129*/ 25 36 36 0 1 3.00
## 259 /*1989-1135*/ 23 41 41 0 1 1.30
## 265 /*1989-1155*/ 9 32 32 0 1 2.50
## 266 /*1989-1156*/ 11 24 27 1 1 17.10
## 267 /*1989-1158*/ 11 18 20 1 1 1.60
## 270 /*1989-1163*/ 16 30 30 0 1 3.70
## 333 /*1991-209*/ 6 27 27 0 1 3.15
## 342 /*1991-223*/ 1 22 22 0 1 3.50
## 353 /*1991-247*/ 14 30 30 0 1 3.40
## 355 /*1991-252*/ 15 27 27 0 1 1.25
## 378 /*1992-216*/ 9 29 29 0 1 3.20
## 380 /*1992-220*/ 8 29 29 0 1 2.00
## 418 /*1992-302*/ 24 42 42 0 1 2.20
## 419 /*1992-303*/ 27 31 32 1 1 5.00
## 422 /*1992-307*/ 23 40 41 1 1 5.90
## 431 /*1992-320*/ 35 44 45 1 1 4.10
## 439 /*1993-211*/ 3 5 8 1 1 3.00
## 440 /*1993-212*/ 2 23 23 0 1 2.50
## 441 /*1993-213*/ 2 13 14 1 1 3.90
## 443 /*1993-218*/ 9 30 30 0 1 4.40
## 447 /*1993-228*/ 17 25 27 1 1 1.50
## 448 /*1993-229*/ 8 28 28 0 1 10.80
## 449 /*1993-230*/ 4 20 23 1 1 2.10
## 459 /*1993-252*/ 20 39 39 0 1 3.40
## 470 /*1993-270*/ 14 27 28 1 1 8.00
## 487 /*1993-303*/ 35 56 56 0 1 3.40
## 489 /*1994-152*/ 4 26 26 0 1 4.32
## 500 /*1994-171*/ 15 31 31 0 1 2.92
## 502 /*1994-173*/ 19 33 33 0 1 1.82
## 503 /*1994-174*/ 17 38 38 0 1 2.93
## 504 /*1994-177*/ 19 27 28 1 1 4.75
## 509 /*1994-182*/ 21 31 31 0 1 2.53
## 517 /*1995-102*/ 4 15 16 1 1 3.67
## 522 /*1995-113*/ 9 28 28 0 1 3.11
## BaffleStatus DBH AgeDay1 Year
## 80 Y 27.90 -7 1985
## 81 Y 22.90 -15 1985
## 82 Y 4.80 -6 1985
## 83 Y 3.00 -6 1985
## 84 Y 5.10 -1 1985
## 85 Y 1.80 -8 1985
## 86 Y 23.30 -12 1985
## 91 Y 5.80 -2 1985
## 110 Y 33.30 -4 1986
## 111 Y 6.60 -1 1986
## 114 Y 8.20 -1 1986
## 119 Y 3.00 -1 1986
## 129 Y 54.40 -14 1986
## 136 Y 12.10 -7 1986
## 138 Y 33.10 -2 1986
## 140 Y 1.40 -12 1986
## 149 Y 8.80 -29 1986
## 153 Y 32.20 0 1987
## 177 Y 6.70 -8 1987
## 181 Y 9.60 0 1987
## 183 Y 14.10 -11 1987
## 197 Y 6.10 -6 1988
## 203 Y 6.60 -6 1988
## 205 Y 49.30 -14 1988
## 207 Y 5.10 -8 1988
## 208 Y 7.50 -7 1988
## 210 Y 4.70 -7 1988
## 213 Y 22.50 -7 1988
## 215 Y 18.00 -6 1988
## 217 Y 36.10 -20 1988
## 219 Y 35.00 -6 1988
## 235 Y 26.80 -4 1989
## 237 Y 13.00 0 1989
## 238 Y 12.60 -5 1989
## 241 Y 12.60 -3 1989
## 250 Y 3.70 -3 1989
## 253 Y 29.90 -11 1989
## 255 Y 4.10 -13 1989
## 259 Y 1.00 -20 1989
## 265 Y 5.50 -6 1989
## 266 Y 27.00 -7 1989
## 267 Y 5.40 -8 1989
## 270 Y 5.20 -7 1989
## 333 Y 5.10 -2 1991
## 342 Y 7.90 2 1991
## 353 Y 9.40 -7 1991
## 355 Y 3.30 -3 1991
## 378 Y 6.70 -6 1992
## 380 Y 2.20 -5 1992
## 418 Y 4.80 -18 1992
## 419 Y 5.50 -18 1992
## 422 Y 5.30 -21 1992
## 431 Y 6.70 -33 1992
## 439 Y 5.50 0 1993
## 440 Y 4.80 1 1993
## 441 Y 3.30 1 1993
## 443 Y 5.70 -6 1993
## 447 Y 3.00 -15 1993
## 448 Y 24.70 -5 1993
## 449 Y 5.05 -1 1993
## 459 Y 6.80 -17 1993
## 470 Y 16.40 -11 1993
## 487 Y 4.15 -33 1993
## 489 Y 5.90 -1 1994
## 500 Y 5.20 -7 1994
## 502 Y 3.90 -9 1994
## 503 Y 7.10 -14 1994
## 504 Y 9.20 -13 1994
## 509 Y 4.90 -9 1994
## 517 Y 6.60 -1 1995
## 522 Y 4.00 -6 1995
##
## $model
## [1] "Nest"
##
## $mixtures
## [1] 1
##
## $freq
## group1
## 1 1
## 2 1
## 3 1
## 4 1
## 5 1
## 6 1
## 7 1
## 8 1
## 9 1
## 10 1
## 11 1
## 12 1
## 13 1
## 14 1
## 15 1
## 16 1
## 17 1
## 18 1
## 19 1
## 20 1
## 21 1
## 22 1
## 23 1
## 24 1
## 25 1
## 26 1
## 27 1
## 28 1
## 29 1
## 30 1
## 31 1
## 32 1
## 33 1
## 34 1
## 35 1
## 36 1
## 37 1
## 38 1
## 39 1
## 40 1
## 41 1
## 42 1
## 43 1
## 44 1
## 45 1
## 46 1
## 47 1
## 48 1
## 49 1
## 50 1
## 51 1
## 52 1
## 53 1
## 54 1
## 55 1
## 56 1
## 57 1
## 58 1
## 59 1
## 60 1
## 61 1
## 62 1
## 63 1
## 64 1
## 65 1
## 66 1
## 67 1
## 68 1
## 69 1
## 70 1
## 71 1
##
## $nocc
## [1] 56
##
## $nocc.secondary
## NULL
##
## $time.intervals
## [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
## [36] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
##
## $begin.time
## [1] 1
##
## $age.unit
## [1] 1
##
## $initial.ages
## [1] 0
##
## $group.covariates
## NULL
##
## $nstrata
## [1] 1
##
## $strata.labels
## [1] ""
##
## $counts
## NULL
##
## $reverse
## [1] FALSE
##
## $areas
## NULL
##
## $events
## NULL
# 2. Examine and/or modify the ddl. (Not done here)
red.baf.ddl <- make.design.data(red.baf.proc)
str(red.baf.ddl)
## List of 2
## $ S :'data.frame': 55 obs. of 7 variables:
## ..$ par.index : int [1:55] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ model.index: num [1:55] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ group : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
## ..$ age : Factor w/ 55 levels "0","1","2","3",..: 1 2 3 4 5 6 7 8 9 10 ...
## ..$ time : Factor w/ 55 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
## ..$ Age : num [1:55] 0 1 2 3 4 5 6 7 8 9 ...
## ..$ Time : num [1:55] 0 1 2 3 4 5 6 7 8 9 ...
## $ pimtypes:List of 1
## ..$ S:List of 1
## .. ..$ pim.type: chr "all"
red.baf.ddl
## $S
## par.index model.index group age time Age Time
## 1 1 1 1 0 1 0 0
## 2 2 2 1 1 2 1 1
## 3 3 3 1 2 3 2 2
## 4 4 4 1 3 4 3 3
## 5 5 5 1 4 5 4 4
## 6 6 6 1 5 6 5 5
## 7 7 7 1 6 7 6 6
## 8 8 8 1 7 8 7 7
## 9 9 9 1 8 9 8 8
## 10 10 10 1 9 10 9 9
## 11 11 11 1 10 11 10 10
## 12 12 12 1 11 12 11 11
## 13 13 13 1 12 13 12 12
## 14 14 14 1 13 14 13 13
## 15 15 15 1 14 15 14 14
## 16 16 16 1 15 16 15 15
## 17 17 17 1 16 17 16 16
## 18 18 18 1 17 18 17 17
## 19 19 19 1 18 19 18 18
## 20 20 20 1 19 20 19 19
## 21 21 21 1 20 21 20 20
## 22 22 22 1 21 22 21 21
## 23 23 23 1 22 23 22 22
## 24 24 24 1 23 24 23 23
## 25 25 25 1 24 25 24 24
## 26 26 26 1 25 26 25 25
## 27 27 27 1 26 27 26 26
## 28 28 28 1 27 28 27 27
## 29 29 29 1 28 29 28 28
## 30 30 30 1 29 30 29 29
## 31 31 31 1 30 31 30 30
## 32 32 32 1 31 32 31 31
## 33 33 33 1 32 33 32 32
## 34 34 34 1 33 34 33 33
## 35 35 35 1 34 35 34 34
## 36 36 36 1 35 36 35 35
## 37 37 37 1 36 37 36 36
## 38 38 38 1 37 38 37 37
## 39 39 39 1 38 39 38 38
## 40 40 40 1 39 40 39 39
## 41 41 41 1 40 41 40 40
## 42 42 42 1 41 42 41 41
## 43 43 43 1 42 43 42 42
## 44 44 44 1 43 44 43 43
## 45 45 45 1 44 45 44 44
## 46 46 46 1 45 46 45 45
## 47 47 47 1 46 47 46 46
## 48 48 48 1 47 48 47 47
## 49 49 49 1 48 49 48 48
## 50 50 50 1 49 50 49 49
## 51 51 51 1 50 51 50 50
## 52 52 52 1 51 52 51 51
## 53 53 53 1 52 53 52 52
## 54 54 54 1 53 54 53 53
## 55 55 55 1 54 55 54 54
##
## $pimtypes
## $pimtypes$S
## $pimtypes$S$pim.type
## [1] "all"
# 3. Fit a particular model
# This is a model with S constant over time (closest to Mayfield method)
mod.baf <- RMark::mark(red.baf.proc, ddl=red.baf.ddl,
model="Nest",
model.parameters=list(
S =list(formula=~1)
)
)
##
## Output summary for Nest model
## Name : S(~1)
##
## Npar : 1
## -2lnL: 168.636
## AICc : 170.6396
##
## Beta
## estimate se lcl ucl
## S:(Intercept) 4.068001 0.2313847 3.614487 4.521515
##
##
## Real Parameter S
## 1 2 3 4 5 6 7
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 8 9 10 11 12 13 14
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 15 16 17 18 19 20 21
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 22 23 24 25 26 27 28
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 29 30 31 32 33 34 35
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 36 37 38 39 40 41 42
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 43 44 45 46 47 48 49
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 50 51 52 53 54 55
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
summary(mod.baf)
## Output summary for Nest model
## Name : S(~1)
##
## Npar : 1
## -2lnL: 168.636
## AICc : 170.6396
##
## Beta
## estimate se lcl ucl
## S:(Intercept) 4.068001 0.2313847 3.614487 4.521515
##
##
## Real Parameter S
## 1 2 3 4 5 6 7
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 8 9 10 11 12 13 14
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 15 16 17 18 19 20 21
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 22 23 24 25 26 27 28
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 29 30 31 32 33 34 35
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 36 37 38 39 40 41 42
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 43 44 45 46 47 48 49
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
## 50 51 52 53 54 55
## 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763 0.9831763
# Look the objects returned in more details
names(mod.baf)
## [1] "data" "model" "title"
## [4] "model.name" "links" "mixtures"
## [7] "call" "parameters" "time.intervals"
## [10] "number.of.groups" "group.labels" "nocc"
## [13] "begin.time" "covariates" "fixed"
## [16] "design.matrix" "pims" "design.data"
## [19] "strata.labels" "mlogit.list" "profile.int"
## [22] "simplify" "model.parameters" "results"
## [25] "output"
names(mod.baf$results)
## [1] "lnl" "deviance" "deviance.df"
## [4] "npar" "n" "AICc"
## [7] "beta" "real" "beta.vcv"
## [10] "derived" "derived.vcv" "covariate.values"
## [13] "singular" "real.vcv"
# look at estimates on beta and original scale
mod.baf$results$beta # on the logit scale
## estimate se lcl ucl
## S:(Intercept) 4.068001 0.2313847 3.614487 4.521515
mod.baf$results$real# on the regular 0-1 scale for each site
## estimate se lcl ucl fixed note
## S g1 a0 t1 0.9831763 0.0038273 0.9737755 0.9892444
# derived variabldes is the nest survival probability over the 40 (nocc) days
names(mod.baf$results$derived)
## [1] "S Overall Survival"
mod.baf$results$derived$"S Overall Survival"
## estimate se lcl ucl
## 1 0.3933031 0.08420636 0.2450622 0.5642001
# alternatively
get.real(mod.baf, "S", se=TRUE)
## all.diff.index par.index estimate se lcl
## S g1 a0 t1 1 1 0.9831763 0.0038273 0.9737755
## S g1 a1 t2 2 1 0.9831763 0.0038273 0.9737755
## S g1 a2 t3 3 1 0.9831763 0.0038273 0.9737755
## S g1 a3 t4 4 1 0.9831763 0.0038273 0.9737755
## S g1 a4 t5 5 1 0.9831763 0.0038273 0.9737755
## S g1 a5 t6 6 1 0.9831763 0.0038273 0.9737755
## S g1 a6 t7 7 1 0.9831763 0.0038273 0.9737755
## S g1 a7 t8 8 1 0.9831763 0.0038273 0.9737755
## S g1 a8 t9 9 1 0.9831763 0.0038273 0.9737755
## S g1 a9 t10 10 1 0.9831763 0.0038273 0.9737755
## S g1 a10 t11 11 1 0.9831763 0.0038273 0.9737755
## S g1 a11 t12 12 1 0.9831763 0.0038273 0.9737755
## S g1 a12 t13 13 1 0.9831763 0.0038273 0.9737755
## S g1 a13 t14 14 1 0.9831763 0.0038273 0.9737755
## S g1 a14 t15 15 1 0.9831763 0.0038273 0.9737755
## S g1 a15 t16 16 1 0.9831763 0.0038273 0.9737755
## S g1 a16 t17 17 1 0.9831763 0.0038273 0.9737755
## S g1 a17 t18 18 1 0.9831763 0.0038273 0.9737755
## S g1 a18 t19 19 1 0.9831763 0.0038273 0.9737755
## S g1 a19 t20 20 1 0.9831763 0.0038273 0.9737755
## S g1 a20 t21 21 1 0.9831763 0.0038273 0.9737755
## S g1 a21 t22 22 1 0.9831763 0.0038273 0.9737755
## S g1 a22 t23 23 1 0.9831763 0.0038273 0.9737755
## S g1 a23 t24 24 1 0.9831763 0.0038273 0.9737755
## S g1 a24 t25 25 1 0.9831763 0.0038273 0.9737755
## S g1 a25 t26 26 1 0.9831763 0.0038273 0.9737755
## S g1 a26 t27 27 1 0.9831763 0.0038273 0.9737755
## S g1 a27 t28 28 1 0.9831763 0.0038273 0.9737755
## S g1 a28 t29 29 1 0.9831763 0.0038273 0.9737755
## S g1 a29 t30 30 1 0.9831763 0.0038273 0.9737755
## S g1 a30 t31 31 1 0.9831763 0.0038273 0.9737755
## S g1 a31 t32 32 1 0.9831763 0.0038273 0.9737755
## S g1 a32 t33 33 1 0.9831763 0.0038273 0.9737755
## S g1 a33 t34 34 1 0.9831763 0.0038273 0.9737755
## S g1 a34 t35 35 1 0.9831763 0.0038273 0.9737755
## S g1 a35 t36 36 1 0.9831763 0.0038273 0.9737755
## S g1 a36 t37 37 1 0.9831763 0.0038273 0.9737755
## S g1 a37 t38 38 1 0.9831763 0.0038273 0.9737755
## S g1 a38 t39 39 1 0.9831763 0.0038273 0.9737755
## S g1 a39 t40 40 1 0.9831763 0.0038273 0.9737755
## S g1 a40 t41 41 1 0.9831763 0.0038273 0.9737755
## S g1 a41 t42 42 1 0.9831763 0.0038273 0.9737755
## S g1 a42 t43 43 1 0.9831763 0.0038273 0.9737755
## S g1 a43 t44 44 1 0.9831763 0.0038273 0.9737755
## S g1 a44 t45 45 1 0.9831763 0.0038273 0.9737755
## S g1 a45 t46 46 1 0.9831763 0.0038273 0.9737755
## S g1 a46 t47 47 1 0.9831763 0.0038273 0.9737755
## S g1 a47 t48 48 1 0.9831763 0.0038273 0.9737755
## S g1 a48 t49 49 1 0.9831763 0.0038273 0.9737755
## S g1 a49 t50 50 1 0.9831763 0.0038273 0.9737755
## S g1 a50 t51 51 1 0.9831763 0.0038273 0.9737755
## S g1 a51 t52 52 1 0.9831763 0.0038273 0.9737755
## S g1 a52 t53 53 1 0.9831763 0.0038273 0.9737755
## S g1 a53 t54 54 1 0.9831763 0.0038273 0.9737755
## S g1 a54 t55 55 1 0.9831763 0.0038273 0.9737755
## ucl fixed note group age time Age Time
## S g1 a0 t1 0.9892444 1 0 1 0 0
## S g1 a1 t2 0.9892444 1 1 2 1 1
## S g1 a2 t3 0.9892444 1 2 3 2 2
## S g1 a3 t4 0.9892444 1 3 4 3 3
## S g1 a4 t5 0.9892444 1 4 5 4 4
## S g1 a5 t6 0.9892444 1 5 6 5 5
## S g1 a6 t7 0.9892444 1 6 7 6 6
## S g1 a7 t8 0.9892444 1 7 8 7 7
## S g1 a8 t9 0.9892444 1 8 9 8 8
## S g1 a9 t10 0.9892444 1 9 10 9 9
## S g1 a10 t11 0.9892444 1 10 11 10 10
## S g1 a11 t12 0.9892444 1 11 12 11 11
## S g1 a12 t13 0.9892444 1 12 13 12 12
## S g1 a13 t14 0.9892444 1 13 14 13 13
## S g1 a14 t15 0.9892444 1 14 15 14 14
## S g1 a15 t16 0.9892444 1 15 16 15 15
## S g1 a16 t17 0.9892444 1 16 17 16 16
## S g1 a17 t18 0.9892444 1 17 18 17 17
## S g1 a18 t19 0.9892444 1 18 19 18 18
## S g1 a19 t20 0.9892444 1 19 20 19 19
## S g1 a20 t21 0.9892444 1 20 21 20 20
## S g1 a21 t22 0.9892444 1 21 22 21 21
## S g1 a22 t23 0.9892444 1 22 23 22 22
## S g1 a23 t24 0.9892444 1 23 24 23 23
## S g1 a24 t25 0.9892444 1 24 25 24 24
## S g1 a25 t26 0.9892444 1 25 26 25 25
## S g1 a26 t27 0.9892444 1 26 27 26 26
## S g1 a27 t28 0.9892444 1 27 28 27 27
## S g1 a28 t29 0.9892444 1 28 29 28 28
## S g1 a29 t30 0.9892444 1 29 30 29 29
## S g1 a30 t31 0.9892444 1 30 31 30 30
## S g1 a31 t32 0.9892444 1 31 32 31 31
## S g1 a32 t33 0.9892444 1 32 33 32 32
## S g1 a33 t34 0.9892444 1 33 34 33 33
## S g1 a34 t35 0.9892444 1 34 35 34 34
## S g1 a35 t36 0.9892444 1 35 36 35 35
## S g1 a36 t37 0.9892444 1 36 37 36 36
## S g1 a37 t38 0.9892444 1 37 38 37 37
## S g1 a38 t39 0.9892444 1 38 39 38 38
## S g1 a39 t40 0.9892444 1 39 40 39 39
## S g1 a40 t41 0.9892444 1 40 41 40 40
## S g1 a41 t42 0.9892444 1 41 42 41 41
## S g1 a42 t43 0.9892444 1 42 43 42 42
## S g1 a43 t44 0.9892444 1 43 44 43 43
## S g1 a44 t45 0.9892444 1 44 45 44 44
## S g1 a45 t46 0.9892444 1 45 46 45 45
## S g1 a46 t47 0.9892444 1 46 47 46 46
## S g1 a47 t48 0.9892444 1 47 48 47 47
## S g1 a48 t49 0.9892444 1 48 49 48 48
## S g1 a49 t50 0.9892444 1 49 50 49 49
## S g1 a50 t51 0.9892444 1 50 51 50 50
## S g1 a51 t52 0.9892444 1 51 52 51 51
## S g1 a52 t53 0.9892444 1 52 53 52 52
## S g1 a53 t54 0.9892444 1 53 54 53 53
## S g1 a54 t55 0.9892444 1 54 55 54 54
# Notice that the nest survival is the product of the individual S
prod(get.real(mod.baf, "S", se=TRUE)$estimate)
## [1] 0.3933028
# problem is that the derived parameter is computed over 61 days (nocc)
# we only want the probability computed over 20 days.
# Use the deltamethod.special function
# for all 61 days
prod(get.real(mod.baf, "S", se=TRUE)$estimate)
## [1] 0.3933028
deltamethod.special("prod",
get.real(mod.baf, "S", se=TRUE)$estimate,
get.real(mod.baf, "S", se=TRUE, vcv=TRUE, expand=TRUE)$vcv.real)
## [1] 0.08420649
# for 20 days
prod(get.real(mod.baf, "S", se=TRUE)$estimate[1:20])
## [1] 0.7122427
deltamethod.special("prod",
get.real(mod.baf, "S", se=TRUE)$estimate[1:20],
get.real(mod.baf, "S", se=TRUE, vcv=TRUE, expand=TRUE)$vcv.real[1:20, 1:20])
## [1] 0.05545157
# control nests only
dim(reddata)
## [1] 537 11
reddata.cntl <- reddata[ reddata$BaffleStatus=="N" & !reddata$Year %in% c(1983, 1984, 1990),]
dim(reddata.cntl)
## [1] 343 11
# 1. Process the data.
# The nocc variable is the data at which hatching occurs
red.cntl.proc <- process.data(reddata.cntl, model="Nest", nocc=max(reddata.cntl$LastChecked))
red.cntl.proc
## $data
## NestId FirstFound LastPresent LastChecked Fate freq Height
## 71 /*1985-434*/ 7 27 27 0 1 2.60
## 72 /*1985-435*/ 8 8 15 1 1 2.40
## 73 /*1985-436*/ 7 8 15 1 1 2.90
## 74 /*1985-437*/ 7 8 12 1 1 8.50
## 75 /*1985-438*/ 6 26 26 0 1 10.00
## 76 /*1985-439*/ 15 25 25 0 1 28.40
## 77 /*1985-441*/ 7 28 28 0 1 3.40
## 78 /*1985-442*/ 6 28 28 0 1 2.00
## 79 /*1985-443*/ 11 33 33 0 1 3.80
## 87 /*1985-459*/ 8 19 22 1 1 4.00
## 88 /*1985-460*/ 12 29 31 1 1 3.50
## 89 /*1985-462*/ 16 32 35 1 1 4.00
## 90 /*1985-463*/ 18 38 38 0 1 13.80
## 92 /*1985-469*/ 10 30 30 0 1 1.95
## 93 /*1985-485*/ 21 28 31 1 1 6.20
## 94 /*1985-490*/ 24 26 26 0 1 3.00
## 95 /*1985-492*/ 24 33 33 0 1 9.70
## 96 /*1985-498*/ 29 35 36 1 1 14.00
## 97 /*1985-499*/ 29 30 31 1 1 15.70
## 98 /*1985-500*/ 29 35 36 1 1 1.50
## 99 /*1985-502*/ 30 30 31 1 1 16.80
## 100 /*1985-506*/ 31 32 33 1 1 21.40
## 101 /*1985-507*/ 31 44 44 0 1 8.00
## 102 /*1985-508*/ 31 33 33 0 1 18.00
## 103 /*1985-527*/ 49 53 53 0 1 16.40
## 104 /*1985-528*/ 55 56 56 0 1 1.80
## 105 /*1986-529*/ 1 23 23 0 1 3.06
## 106 /*1986-530*/ 3 18 19 1 1 3.81
## 107 /*1986-534*/ 3 25 25 0 1 6.13
## 108 /*1986-536*/ 7 19 23 1 1 6.30
## 109 /*1986-537*/ 4 27 27 0 1 11.50
## 112 /*1986-543*/ 1 6 11 1 1 4.93
## 113 /*1986-547*/ 6 29 29 0 1 17.78
## 115 /*1986-559*/ 8 31 31 0 1 5.27
## 116 /*1986-565*/ 7 30 30 0 1 13.74
## 117 /*1986-567*/ 8 30 30 0 1 3.98
## 118 /*1986-568*/ 10 30 30 0 1 15.89
## 120 /*1986-574*/ 6 20 22 1 1 3.28
## 121 /*1986-575*/ 6 28 28 0 1 3.51
## 122 /*1986-576*/ 10 30 30 0 1 13.91
## 123 /*1986-578*/ 4 21 23 1 1 17.79
## 124 /*1986-579*/ 5 9 11 1 1 2.85
## 125 /*1986-588*/ 12 14 15 1 1 3.80
## 126 /*1986-589*/ 7 27 27 0 1 2.57
## 127 /*1986-590*/ 7 21 22 1 1 2.20
## 128 /*1986-592*/ 13 35 35 0 1 20.83
## 130 /*1986-605*/ 19 30 32 1 1 2.44
## 131 /*1986-623*/ 19 19 20 1 1 11.50
## 132 /*1986-625*/ 24 45 45 0 1 14.85
## 133 /*1986-626*/ 24 46 46 0 1 15.50
## 134 /*1986-627*/ 25 38 41 1 1 1.15
## 135 /*1986-637*/ 20 31 31 0 1 12.85
## 137 /*1986-644*/ 23 24 24 0 1 3.75
## 139 /*1986-648*/ 23 26 26 0 1 2.31
## 141 /*1986-650*/ 25 38 38 0 1 4.73
## 142 /*1986-651*/ 25 31 31 0 1 14.43
## 143 /*1986-652*/ 25 30 30 0 1 2.23
## 144 /*1986-653*/ 25 38 38 0 1 16.44
## 145 /*1986-657*/ 27 28 28 0 1 5.56
## 146 /*1986-658*/ 28 35 35 0 1 16.00
## 147 /*1986-659*/ 29 51 51 0 1 21.79
## 148 /*1986-66*/ 41 49 49 0 1 20.00
## 150 /*1986-671*/ 35 38 38 0 1 19.81
## 151 /*1986-674*/ 37 38 38 0 1 21.14
## 152 /*1986-68*/ 2 23 23 0 1 4.22
## 154 /*1987-694*/ 2 23 23 0 1 19.32
## 155 /*1987-695*/ 4 25 25 0 1 15.60
## 156 /*1987-696*/ 4 24 24 0 1 20.76
## 157 /*1987-705*/ 5 5 10 1 1 17.32
## 158 /*1987-706*/ 5 25 25 0 1 17.91
## 159 /*1987-709*/ 9 31 31 0 1 4.80
## 160 /*1987-712*/ 3 24 24 0 1 20.16
## 161 /*1987-713*/ 4 25 25 0 1 2.80
## 162 /*1987-714*/ 1 21 21 0 1 21.33
## 163 /*1987-716*/ 7 24 26 1 1 4.03
## 164 /*1987-723*/ 9 30 30 0 1 1.88
## 165 /*1987-732*/ 8 28 28 0 1 1.51
## 166 /*1987-737*/ 11 33 33 0 1 19.41
## 167 /*1987-738*/ 4 10 11 1 1 7.12
## 168 /*1987-739*/ 5 16 17 1 1 2.47
## 169 /*1987-771*/ 10 17 23 1 1 2.79
## 170 /*1987-775*/ 16 39 39 0 1 27.75
## 171 /*1987-778*/ 10 10 13 1 1 1.44
## 172 /*1987-785*/ 16 22 22 0 1 16.62
## 173 /*1987-787*/ 17 21 21 0 1 3.96
## 174 /*1987-789*/ 18 30 31 1 1 2.60
## 175 /*1987-797*/ 20 29 29 0 1 1.02
## 176 /*1987-802*/ 20 27 27 0 1 4.08
## 178 /*1987-804*/ 21 26 27 1 1 2.67
## 179 /*1987-808*/ 22 26 27 1 1 12.05
## 180 /*1987-809*/ 22 23 23 0 1 5.35
## 182 /*1987-818*/ 23 25 25 0 1 10.27
## 184 /*1987-820*/ 23 27 27 0 1 5.12
## 185 /*1987-828*/ 25 31 31 0 1 1.41
## 186 /*1987-829*/ 25 28 28 0 1 4.00
## 187 /*1987-840*/ 29 31 31 0 1 1.01
## 188 /*1987-841*/ 29 33 33 0 1 3.83
## 189 /*1987-842*/ 29 35 35 0 1 11.40
## 190 /*1987-846*/ 33 38 38 0 1 16.14
## 191 /*1988-1004*/ 34 51 51 0 1 2.50
## 192 /*1988-1006*/ 39 42 42 0 1 11.30
## 193 /*1988-1008*/ 45 48 48 0 1 21.20
## 194 /*1988-1019*/ 47 54 54 0 1 15.50
## 195 /*1988-890*/ 7 29 29 0 1 3.60
## 196 /*1988-893*/ 9 29 29 0 1 17.40
## 198 /*1988-897*/ 11 12 14 1 1 4.70
## 199 /*1988-899*/ 12 33 33 0 1 2.60
## 200 /*1988-900*/ 7 29 29 0 1 2.90
## 201 /*1988-910*/ 8 29 29 0 1 4.50
## 202 /*1988-911*/ 9 29 29 0 1 2.70
## 204 /*1988-921*/ 17 38 38 0 1 9.10
## 206 /*1988-932*/ 10 30 30 0 1 3.80
## 209 /*1988-938*/ 19 39 39 0 1 3.40
## 211 /*1988-944*/ 21 29 29 0 1 1.90
## 212 /*1988-958*/ 15 15 17 1 1 15.30
## 214 /*1988-960*/ 15 29 29 0 1 6.70
## 216 /*1988-962*/ 26 47 47 0 1 22.80
## 218 /*1988-964*/ 16 32 32 0 1 2.10
## 220 /*1988-972*/ 23 32 32 0 1 15.60
## 221 /*1988-973*/ 32 45 49 1 1 19.80
## 222 /*1988-974*/ 25 48 48 0 1 17.10
## 223 /*1988-976*/ 23 36 36 0 1 15.00
## 224 /*1988-977*/ 24 44 44 0 1 1.50
## 225 /*1988-981*/ 27 31 31 0 1 11.50
## 226 /*1988-983*/ 28 31 31 0 1 19.70
## 227 /*1988-984*/ 29 36 36 0 1 16.50
## 228 /*1988-985*/ 38 45 46 1 1 18.40
## 229 /*1988-991*/ 26 26 27 1 1 10.00
## 230 /*1988-992*/ 33 36 36 0 1 17.80
## 231 /*1988-993*/ 33 42 42 0 1 0.90
## 232 /*1988-994*/ 34 43 43 0 1 10.30
## 233 /*1989-1039*/ 5 26 26 0 1 20.60
## 234 /*1989-1040*/ 2 3 5 1 1 1.80
## 236 /*1989-1076*/ 5 20 23 1 1 1.60
## 239 /*1989-1081*/ 10 30 30 0 1 18.70
## 240 /*1989-1092*/ 11 11 12 1 1 17.00
## 242 /*1989-1109*/ 29 51 51 0 1 17.80
## 243 /*1989-1111*/ 12 21 22 1 1 15.50
## 244 /*1989-1112*/ 12 35 35 0 1 17.10
## 245 /*1989-1114*/ 16 17 18 1 1 5.50
## 246 /*1989-1115*/ 23 43 43 0 1 12.60
## 247 /*1989-1116*/ 23 42 42 0 1 9.70
## 248 /*1989-1118*/ 12 33 33 0 1 1.60
## 249 /*1989-1120*/ 11 11 12 1 1 9.30
## 251 /*1989-1123*/ 16 18 20 1 1 20.50
## 252 /*1989-1124*/ 21 42 42 0 1 0.80
## 254 /*1989-1127*/ 32 39 39 0 1 15.90
## 256 /*1989-1131*/ 41 44 44 0 1 19.70
## 257 /*1989-1133*/ 26 41 41 0 1 16.80
## 258 /*1989-1134*/ 26 36 36 0 1 14.90
## 260 /*1989-1137*/ 29 49 49 0 1 24.40
## 261 /*1989-1151*/ 27 35 35 0 1 22.90
## 262 /*1989-1152*/ 28 28 30 1 1 2.20
## 263 /*1989-1153*/ 27 51 51 0 1 2.20
## 264 /*1989-1154*/ 30 37 37 0 1 0.80
## 268 /*1989-1161*/ 19 20 21 1 1 1.30
## 269 /*1989-1162*/ 16 24 24 0 1 1.60
## 271 /*1989-1180*/ 31 40 41 1 1 17.10
## 272 /*1989-1181*/ 33 39 41 1 1 14.50
## 273 /*1989-1182*/ 33 34 34 0 1 11.10
## 327 /*1991-200*/ 1 24 24 0 1 3.50
## 328 /*1991-201*/ 2 15 18 1 1 1.50
## 329 /*1991-204*/ 5 16 17 1 1 14.60
## 330 /*1991-205*/ 2 11 12 1 1 4.10
## 331 /*1991-206*/ 7 27 27 0 1 3.35
## 332 /*1991-208*/ 5 27 27 0 1 3.57
## 334 /*1991-210*/ 5 19 26 1 1 3.70
## 335 /*1991-211*/ 2 21 24 1 1 3.40
## 336 /*1991-212*/ 1 22 22 0 1 2.60
## 337 /*1991-213*/ 1 23 23 0 1 2.55
## 338 /*1991-218*/ 11 13 14 1 1 8.75
## 339 /*1991-220*/ 13 16 18 1 1 21.00
## 340 /*1991-221*/ 5 27 27 0 1 3.90
## 341 /*1991-222*/ 7 27 28 1 1 2.41
## 343 /*1991-224*/ 5 27 27 0 1 1.95
## 344 /*1991-228*/ 11 32 32 0 1 3.90
## 345 /*1991-229*/ 3 24 24 0 1 3.05
## 346 /*1991-231*/ 16 36 36 0 1 4.40
## 347 /*1991-234*/ 16 36 36 0 1 16.70
## 348 /*1991-235*/ 5 13 17 1 1 13.00
## 349 /*1991-240*/ 11 22 22 0 1 8.35
## 350 /*1991-241*/ 18 39 39 0 1 3.45
## 351 /*1991-242*/ 18 40 40 0 1 7.75
## 352 /*1991-245*/ 16 19 19 0 1 7.70
## 354 /*1991-250*/ 13 35 35 0 1 4.66
## 356 /*1991-253*/ 19 19 21 1 1 5.20
## 357 /*1991-254*/ 27 35 36 1 1 13.10
## 358 /*1991-256*/ 19 27 27 0 1 3.44
## 359 /*1991-257*/ 19 23 23 0 1 5.80
## 360 /*1991-258*/ 7 27 27 0 1 1.38
## 361 /*1991-259*/ 22 25 25 0 1 2.65
## 362 /*1991-261*/ 24 28 28 0 1 3.38
## 363 /*1991-263*/ 28 35 39 1 1 4.60
## 364 /*1991-265*/ 24 26 26 0 1 2.70
## 365 /*1991-266*/ 24 25 25 0 1 9.90
## 366 /*1991-267*/ 28 31 31 0 1 17.60
## 367 /*1991-271*/ 29 30 30 0 1 13.60
## 368 /*1991-273*/ 30 41 41 0 1 15.30
## 369 /*1991-276*/ 36 53 56 1 1 3.00
## 370 /*1991-277*/ 32 33 33 0 1 11.20
## 371 /*1992-161*/ 8 13 17 1 1 2.80
## 372 /*1992-204*/ 7 21 24 1 1 4.30
## 373 /*1992-207*/ 6 27 27 0 1 4.40
## 374 /*1992-210*/ 8 28 28 0 1 13.10
## 375 /*1992-213*/ 7 28 28 0 1 1.90
## 376 /*1992-214*/ 10 23 27 1 1 2.90
## 377 /*1992-215*/ 9 26 28 1 1 5.40
## 379 /*1992-219*/ 10 31 31 0 1 4.70
## 381 /*1992-223*/ 7 19 23 1 1 4.70
## 382 /*1992-224*/ 8 13 17 1 1 2.70
## 383 /*1992-226*/ 8 17 18 1 1 12.00
## 384 /*1992-233*/ 22 27 30 1 1 17.00
## 385 /*1992-234*/ 19 25 29 1 1 3.90
## 386 /*1992-236*/ 9 23 26 1 1 18.70
## 387 /*1992-238*/ 6 12 16 1 1 3.70
## 388 /*1992-239*/ 11 12 16 1 1 3.70
## 389 /*1992-240*/ 8 17 18 1 1 5.40
## 390 /*1992-241*/ 14 35 35 0 1 5.50
## 391 /*1992-242*/ 13 16 20 1 1 2.70
## 392 /*1992-246*/ 12 31 31 0 1 10.20
## 393 /*1992-247*/ 12 21 22 1 1 1.10
## 394 /*1992-248*/ 9 31 31 0 1 6.10
## 395 /*1992-250*/ 7 13 16 1 1 5.50
## 396 /*1992-252*/ 8 29 29 0 1 5.40
## 397 /*1992-259*/ 15 33 33 0 1 21.30
## 398 /*1992-263*/ 19 26 28 1 1 2.90
## 399 /*1992-264*/ 7 19 21 1 1 2.90
## 400 /*1992-266*/ 22 42 42 0 1 18.10
## 401 /*1992-267*/ 17 26 27 1 1 12.60
## 402 /*1992-269*/ 19 21 25 1 1 0.90
## 403 /*1992-274*/ 17 28 29 1 1 18.00
## 404 /*1992-275*/ 23 40 42 1 1 3.70
## 405 /*1992-278*/ 22 41 42 1 1 3.50
## 406 /*1992-280*/ 23 25 28 1 1 5.80
## 407 /*1992-281*/ 25 26 32 1 1 21.80
## 408 /*1992-282*/ 18 18 19 1 1 3.30
## 409 /*1992-283*/ 26 32 33 1 1 15.80
## 410 /*1992-285*/ 21 42 42 0 1 13.30
## 411 /*1992-289*/ 28 50 50 0 1 17.40
## 412 /*1992-293*/ 20 20 22 1 1 4.90
## 413 /*1992-294*/ 22 29 30 1 1 4.50
## 414 /*1992-295*/ 22 26 27 1 1 9.70
## 415 /*1992-296*/ 34 56 56 0 1 21.50
## 416 /*1992-297*/ 26 31 33 1 1 2.30
## 417 /*1992-300*/ 36 46 47 1 1 0.90
## 420 /*1992-304*/ 38 55 56 1 1 3.20
## 421 /*1992-305*/ 34 56 56 0 1 3.80
## 423 /*1992-308*/ 34 56 56 0 1 22.80
## 424 /*1992-309*/ 35 44 44 0 1 3.50
## 425 /*1992-310*/ 35 50 52 1 1 1.10
## 426 /*1992-311*/ 38 42 43 1 1 4.60
## 427 /*1992-312*/ 24 30 30 0 1 18.20
## 428 /*1992-313*/ 24 29 30 1 1 5.10
## 429 /*1992-318*/ 27 27 28 1 1 3.60
## 430 /*1992-319*/ 32 33 33 0 1 21.10
## 432 /*1992-322*/ 40 62 62 0 1 18.00
## 433 /*1992-324*/ 40 41 41 0 1 3.15
## 434 /*1992-326*/ 52 59 59 0 1 18.70
## 435 /*1993-205*/ 1 7 10 1 1 8.10
## 436 /*1993-206*/ 1 15 17 1 1 5.30
## 437 /*1993-207*/ 1 2 3 1 1 2.00
## 438 /*1993-209*/ 2 7 10 1 1 3.00
## 442 /*1993-215*/ 5 10 13 1 1 2.60
## 444 /*1993-221*/ 5 23 25 1 1 8.50
## 445 /*1993-222*/ 5 10 13 1 1 2.20
## 446 /*1993-223*/ 7 10 13 1 1 2.40
## 450 /*1993-233*/ 8 8 11 1 1 2.10
## 451 /*1993-235*/ 11 11 16 1 1 15.80
## 452 /*1993-237*/ 18 28 29 1 1 4.80
## 453 /*1993-238*/ 11 15 15 0 1 20.10
## 454 /*1993-239*/ 8 9 12 1 1 2.00
## 455 /*1993-240*/ 6 12 13 1 1 8.10
## 456 /*1993-241*/ 6 9 12 1 1 8.30
## 457 /*1993-242*/ 7 21 21 0 1 5.80
## 458 /*1993-245*/ 18 43 43 0 1 16.80
## 460 /*1993-253*/ 19 23 23 0 1 3.20
## 461 /*1993-254*/ 30 41 41 0 1 0.93
## 462 /*1993-255*/ 36 38 41 1 1 3.40
## 463 /*1993-257*/ 34 44 47 1 1 14.80
## 464 /*1993-259*/ 11 14 16 1 1 11.80
## 465 /*1993-264*/ 14 29 30 1 1 3.00
## 466 /*1993-266*/ 21 32 35 1 1 12.50
## 467 /*1993-267*/ 21 24 27 1 1 2.20
## 468 /*1993-268*/ 19 26 29 1 1 4.20
## 469 /*1993-269*/ 19 19 22 1 1 2.20
## 471 /*1993-273*/ 15 17 19 1 1 8.30
## 472 /*1993-274*/ 19 20 23 1 1 5.70
## 473 /*1993-275*/ 25 42 43 1 1 1.63
## 474 /*1993-277*/ 18 21 24 1 1 3.90
## 475 /*1993-279*/ 21 33 34 1 1 1.87
## 476 /*1993-280*/ 16 27 30 1 1 3.00
## 477 /*1993-281*/ 17 22 27 1 1 24.30
## 478 /*1993-282*/ 24 33 35 1 1 7.30
## 479 /*1993-284*/ 25 45 45 0 1 18.30
## 480 /*1993-287*/ 25 46 46 0 1 1.80
## 481 /*1993-290*/ 38 58 58 0 1 19.80
## 482 /*1993-294*/ 21 43 43 0 1 14.60
## 483 /*1993-295*/ 23 26 29 1 1 2.30
## 484 /*1993-299*/ 20 24 25 1 1 2.60
## 485 /*1993-300*/ 18 19 24 1 1 4.40
## 486 /*1993-302*/ 33 48 48 0 1 11.40
## 488 /*1994-118*/ 24 24 26 1 1 5.72
## 490 /*1994-153*/ 3 24 24 0 1 10.55
## 491 /*1994-155*/ 10 31 31 0 1 2.96
## 492 /*1994-156*/ 10 26 29 1 1 3.06
## 493 /*1994-158*/ 10 12 16 1 1 3.72
## 494 /*1994-159*/ 12 33 33 0 1 17.77
## 495 /*1994-161*/ 12 17 23 1 1 3.67
## 496 /*1994-164*/ 14 30 30 0 1 3.93
## 497 /*1994-167*/ 18 28 28 0 1 14.82
## 498 /*1994-168*/ 10 15 20 1 1 6.38
## 499 /*1994-169*/ 11 23 27 1 1 2.81
## 501 /*1994-172*/ 19 39 39 0 1 4.88
## 505 /*1994-178*/ 20 33 33 0 1 2.94
## 506 /*1994-179*/ 18 24 24 0 1 2.54
## 507 /*1994-180*/ 20 23 23 0 1 7.74
## 508 /*1994-181*/ 20 21 25 1 1 2.55
## 510 /*1994-183*/ 21 23 23 0 1 3.68
## 511 /*1994-184*/ 34 40 44 1 1 22.70
## 512 /*1994-185*/ 21 24 24 0 1 2.31
## 513 /*1994-186*/ 22 27 27 0 1 5.50
## 514 /*1994-189*/ 35 36 36 0 1 16.54
## 515 /*1994-190*/ 27 33 33 0 1 5.07
## 516 /*1995-101*/ 8 20 23 1 1 3.59
## 518 /*1995-104*/ 11 26 28 1 1 2.86
## 519 /*1995-106*/ 10 10 16 1 1 20.39
## 520 /*1995-109*/ 14 35 35 0 1 7.56
## 521 /*1995-112*/ 18 40 40 0 1 19.58
## 523 /*1995-114*/ 17 26 26 0 1 3.71
## 524 /*1995-115*/ 17 18 19 1 1 8.15
## 525 /*1995-117*/ 25 40 43 1 1 12.13
## 526 /*1995-118*/ 20 27 30 1 1 16.18
## 527 /*1995-119*/ 20 26 26 0 1 14.26
## 528 /*1995-120*/ 20 20 26 1 1 3.57
## 529 /*1995-121*/ 24 26 29 1 1 3.90
## 530 /*1995-122*/ 24 29 29 0 1 5.14
## 531 /*1995-123*/ 23 26 26 0 1 12.64
## 532 /*1995-124*/ 25 32 32 0 1 25.02
## 533 /*1995-125*/ 25 33 33 0 1 4.37
## 534 /*1995-126*/ 26 32 33 1 1 2.10
## 535 /*1995-127*/ 26 30 30 0 1 13.35
## 536 /*1995-128*/ 26 31 31 0 1 1.83
## 537 /*1995-129*/ 27 31 31 0 1 16.89
## BaffleStatus DBH AgeDay1 Year
## 71 N 3.30 -4 1985
## 72 N 3.80 -2 1985
## 73 N 5.60 -4 1985
## 74 N 7.90 -4 1985
## 75 N 11.40 -2 1985
## 76 N 54.10 -1 1985
## 77 N 5.60 -4 1985
## 78 N 5.30 -2 1985
## 79 N 6.90 -8 1985
## 87 N 6.10 -4 1985
## 88 N 4.60 -9 1985
## 89 N 4.60 -13 1985
## 90 N 20.00 -15 1985
## 92 N 1.50 -7 1985
## 93 N 8.90 -11 1985
## 94 N 3.80 -2 1985
## 95 N 25.20 -8 1985
## 96 N 32.00 -9 1985
## 97 N 28.20 -8 1985
## 98 N 1.00 -15 1985
## 99 N 20.30 -9 1985
## 100 N 28.20 -9 1985
## 101 N 7.60 -20 1985
## 102 N 23.60 -8 1985
## 103 N 31.00 -30 1985
## 104 N 5.60 -33 1985
## 105 N 6.40 2 1986
## 106 N 14.90 1 1986
## 107 N 10.10 0 1986
## 108 N 9.10 -5 1986
## 109 N 11.30 -1 1986
## 112 N 6.70 2 1986
## 113 N 28.10 -3 1986
## 115 N 4.70 -5 1986
## 116 N 42.70 -4 1986
## 117 N 4.90 -5 1986
## 118 N 39.30 -7 1986
## 120 N 6.30 -3 1986
## 121 N 5.30 -3 1986
## 122 N 32.00 -7 1986
## 123 N 29.90 -1 1986
## 124 N 5.00 -2 1986
## 125 N 4.30 -10 1986
## 126 N 3.40 -4 1986
## 127 N 4.30 -1 1986
## 128 N 39.10 -10 1986
## 130 N 3.50 -17 1986
## 131 N 19.70 -8 1986
## 132 N 37.50 -21 1986
## 133 N 24.30 -21 1986
## 134 N 2.20 -23 1986
## 135 N 22.40 -8 1986
## 137 N 4.20 -1 1986
## 139 N 9.80 -3 1986
## 141 N 7.00 -15 1986
## 142 N 73.50 -8 1986
## 143 N 4.20 -7 1986
## 144 N 33.20 -15 1986
## 145 N 7.10 -5 1986
## 146 N 42.00 -12 1986
## 147 N 44.80 -26 1986
## 148 N 36.20 -26 1986
## 150 N 43.40 -15 1986
## 151 N 68.00 -15 1986
## 152 N 6.10 1 1986
## 154 N 35.60 2 1987
## 155 N 41.70 0 1987
## 156 N 34.60 -1 1987
## 157 N 25.30 -2 1987
## 158 N 28.70 -2 1987
## 159 N 10.30 -6 1987
## 160 N 30.00 0 1987
## 161 N 6.70 -1 1987
## 162 N 38.40 2 1987
## 163 N 13.80 -4 1987
## 164 N 3.30 -6 1987
## 165 N 2.10 -5 1987
## 166 N 24.10 -8 1987
## 167 N 12.90 -1 1987
## 168 N 4.20 0 1987
## 169 N 4.80 -1 1987
## 170 N 40.20 -14 1987
## 171 N 2.70 -1 1987
## 172 N 29.40 1 1987
## 173 N 9.20 2 1987
## 174 N 6.10 -10 1987
## 175 N 2.90 -6 1987
## 176 N 5.10 -4 1987
## 178 N 10.20 -5 1987
## 179 N 15.80 -1 1987
## 180 N 9.92 -31 1987
## 182 N 27.60 -2 1987
## 184 N 9.70 -4 1987
## 185 N 2.20 -8 1987
## 186 N 4.20 -5 1987
## 187 N 1.80 -8 1987
## 188 N 52.00 -10 1987
## 189 N 34.10 -12 1987
## 190 N 26.50 -15 1987
## 191 N 6.20 -28 1988
## 192 N 15.40 -19 1988
## 193 N 32.90 -25 1988
## 194 N 33.90 -28 1988
## 195 N 7.10 -4 1988
## 196 N 38.00 -6 1988
## 198 N 7.10 -7 1988
## 199 N 3.50 -8 1988
## 200 N 5.40 -4 1988
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## 204 N 45.00 -14 1988
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## 216 N 54.30 -23 1988
## 218 N 3.70 -9 1988
## 220 N 25.70 -9 1988
## 221 N 36.10 -29 1988
## 222 N 29.20 -22 1988
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## 226 N 40.20 -8 1988
## 227 N 48.40 -13 1988
## 228 N 29.70 -35 1988
## 229 N 46.20 -13 1988
## 230 N 53.00 -13 1988
## 231 N 1.00 -20 1988
## 232 N 16.30 -20 1988
## 233 N 39.30 -2 1989
## 234 N 5.00 1 1989
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## 239 N 31.70 -7 1989
## 240 N 31.80 -8 1989
## 242 N 35.60 -26 1989
## 243 N 28.20 -9 1989
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## 245 N 6.00 -7 1989
## 246 N 34.30 -20 1989
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## 249 N 8.70 -2 1989
## 251 N 41.70 -7 1989
## 252 N 1.00 -19 1989
## 254 N 49.30 -16 1989
## 256 N 39.40 -20 1989
## 257 N 52.50 -18 1989
## 258 N 24.30 -13 1989
## 260 N 41.00 -26 1989
## 261 N 24.00 -12 1989
## 262 N 3.40 -11 1989
## 263 N 1.70 -25 1989
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## 268 N 2.00 -16 1989
## 269 N 5.30 0 1989
## 271 N 34.00 -21 1989
## 272 N 29.00 -23 1989
## 273 N 25.10 -11 1989
## 327 N 6.00 2 1991
## 328 N 4.80 0 1991
## 329 N 39.30 -3 1991
## 330 N 13.50 1 1991
## 331 N 5.20 -4 1991
## 332 N 15.50 0 1991
## 334 N 6.70 -2 1991
## 335 N 5.70 0 1991
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## 345 N 9.30 0 1991
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## 365 N 27.50 -3 1991
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## 367 N 18.00 -7 1991
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## 370 N 25.90 -10 1991
## 371 N 6.40 -5 1992
## 372 N 6.20 -4 1992
## 373 N 12.20 -2 1992
## 374 N 52.00 -5 1992
## 375 N 4.90 -4 1992
## 376 N 3.60 -8 1992
## 377 N 11.80 -6 1992
## 379 N 5.00 -7 1992
## 381 N 6.70 -4 1992
## 382 N 3.20 -5 1992
## 383 N 13.00 -4 1992
## 384 N 52.00 -19 1992
## 385 N 5.40 -16 1992
## 386 N 23.30 -6 1992
## 387 N 4.30 -3 1992
## 388 N 4.40 -9 1992
## 389 N 6.70 -4 1992
## 390 N 7.60 -11 1992
## 391 N 2.60 -10 1992
## 392 N 20.90 -9 1992
## 393 N 5.90 -9 1992
## 394 N 6.60 -6 1992
## 395 N 11.40 -4 1992
## 396 N 7.00 -5 1992
## 397 N 44.30 -8 1992
## 398 N 2.90 -17 1992
## 399 N 6.30 -4 1992
## 400 N 35.60 -19 1992
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## 435 N 15.70 2 1993
## 436 N 5.95 2 1993
## 437 N 2.45 2 1993
## 438 N 3.70 1 1993
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## 444 N 19.75 -1 1993
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## 450 N 5.80 -5 1993
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## 453 N 34.30 8 1993
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## 498 N 8.20 1 1994
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## 505 N 19.00 -9 1994
## 506 N 5.40 -1 1994
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## 518 N 2.00 -8 1995
## 519 N 52.70 -7 1995
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## 524 N 16.10 -8 1995
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## 526 N 27.40 -10 1995
## 527 N 18.20 -3 1995
## 528 N 4.90 1 1995
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## 530 N 3.90 -6 1995
## 531 N 13.60 -3 1995
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## 533 N 3.80 -10 1995
## 534 N 2.70 -10 1995
## 535 N 24.30 -7 1995
## 536 N 5.40 -8 1995
## 537 N 33.30 -8 1995
##
## $model
## [1] "Nest"
##
## $mixtures
## [1] 1
##
## $freq
## group1
## 1 1
## 2 1
## 3 1
## 4 1
## 5 1
## 6 1
## 7 1
## 8 1
## 9 1
## 10 1
## 11 1
## 12 1
## 13 1
## 14 1
## 15 1
## 16 1
## 17 1
## 18 1
## 19 1
## 20 1
## 21 1
## 22 1
## 23 1
## 24 1
## 25 1
## 26 1
## 27 1
## 28 1
## 29 1
## 30 1
## 31 1
## 32 1
## 33 1
## 34 1
## 35 1
## 36 1
## 37 1
## 38 1
## 39 1
## 40 1
## 41 1
## 42 1
## 43 1
## 44 1
## 45 1
## 46 1
## 47 1
## 48 1
## 49 1
## 50 1
## 51 1
## 52 1
## 53 1
## 54 1
## 55 1
## 56 1
## 57 1
## 58 1
## 59 1
## 60 1
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## 65 1
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## 138 1
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## 140 1
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## 150 1
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## 239 1
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## 243 1
## 244 1
## 245 1
## 246 1
## 247 1
## 248 1
## 249 1
## 250 1
## 251 1
## 252 1
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## 254 1
## 255 1
## 256 1
## 257 1
## 258 1
## 259 1
## 260 1
## 261 1
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## 263 1
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## 285 1
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## 333 1
## 334 1
## 335 1
## 336 1
## 337 1
## 338 1
## 339 1
## 340 1
## 341 1
## 342 1
## 343 1
##
## $nocc
## [1] 62
##
## $nocc.secondary
## NULL
##
## $time.intervals
## [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
## [36] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
##
## $begin.time
## [1] 1
##
## $age.unit
## [1] 1
##
## $initial.ages
## [1] 0
##
## $group.covariates
## NULL
##
## $nstrata
## [1] 1
##
## $strata.labels
## [1] ""
##
## $counts
## NULL
##
## $reverse
## [1] FALSE
##
## $areas
## NULL
##
## $events
## NULL
# 2. Examine and/or modify the ddl. (Not done here)
red.cntl.ddl <- make.design.data(red.cntl.proc)
str(red.cntl.ddl)
## List of 2
## $ S :'data.frame': 61 obs. of 7 variables:
## ..$ par.index : int [1:61] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ model.index: num [1:61] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ group : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
## ..$ age : Factor w/ 61 levels "0","1","2","3",..: 1 2 3 4 5 6 7 8 9 10 ...
## ..$ time : Factor w/ 61 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
## ..$ Age : num [1:61] 0 1 2 3 4 5 6 7 8 9 ...
## ..$ Time : num [1:61] 0 1 2 3 4 5 6 7 8 9 ...
## $ pimtypes:List of 1
## ..$ S:List of 1
## .. ..$ pim.type: chr "all"
red.cntl.ddl
## $S
## par.index model.index group age time Age Time
## 1 1 1 1 0 1 0 0
## 2 2 2 1 1 2 1 1
## 3 3 3 1 2 3 2 2
## 4 4 4 1 3 4 3 3
## 5 5 5 1 4 5 4 4
## 6 6 6 1 5 6 5 5
## 7 7 7 1 6 7 6 6
## 8 8 8 1 7 8 7 7
## 9 9 9 1 8 9 8 8
## 10 10 10 1 9 10 9 9
## 11 11 11 1 10 11 10 10
## 12 12 12 1 11 12 11 11
## 13 13 13 1 12 13 12 12
## 14 14 14 1 13 14 13 13
## 15 15 15 1 14 15 14 14
## 16 16 16 1 15 16 15 15
## 17 17 17 1 16 17 16 16
## 18 18 18 1 17 18 17 17
## 19 19 19 1 18 19 18 18
## 20 20 20 1 19 20 19 19
## 21 21 21 1 20 21 20 20
## 22 22 22 1 21 22 21 21
## 23 23 23 1 22 23 22 22
## 24 24 24 1 23 24 23 23
## 25 25 25 1 24 25 24 24
## 26 26 26 1 25 26 25 25
## 27 27 27 1 26 27 26 26
## 28 28 28 1 27 28 27 27
## 29 29 29 1 28 29 28 28
## 30 30 30 1 29 30 29 29
## 31 31 31 1 30 31 30 30
## 32 32 32 1 31 32 31 31
## 33 33 33 1 32 33 32 32
## 34 34 34 1 33 34 33 33
## 35 35 35 1 34 35 34 34
## 36 36 36 1 35 36 35 35
## 37 37 37 1 36 37 36 36
## 38 38 38 1 37 38 37 37
## 39 39 39 1 38 39 38 38
## 40 40 40 1 39 40 39 39
## 41 41 41 1 40 41 40 40
## 42 42 42 1 41 42 41 41
## 43 43 43 1 42 43 42 42
## 44 44 44 1 43 44 43 43
## 45 45 45 1 44 45 44 44
## 46 46 46 1 45 46 45 45
## 47 47 47 1 46 47 46 46
## 48 48 48 1 47 48 47 47
## 49 49 49 1 48 49 48 48
## 50 50 50 1 49 50 49 49
## 51 51 51 1 50 51 50 50
## 52 52 52 1 51 52 51 51
## 53 53 53 1 52 53 52 52
## 54 54 54 1 53 54 53 53
## 55 55 55 1 54 55 54 54
## 56 56 56 1 55 56 55 55
## 57 57 57 1 56 57 56 56
## 58 58 58 1 57 58 57 57
## 59 59 59 1 58 59 58 58
## 60 60 60 1 59 60 59 59
## 61 61 61 1 60 61 60 60
##
## $pimtypes
## $pimtypes$S
## $pimtypes$S$pim.type
## [1] "all"
# 3. Fit a particular model
# This is a model with S constant over time (closest to Mayfield method)
mod.cntl <- RMark::mark(red.cntl.proc, ddl=red.cntl.ddl,
model="Nest",
model.parameters=list(
S =list(formula=~1)
)
)
##
## Output summary for Nest model
## Name : S(~1)
##
## Npar : 1
## -2lnL: 1045.026
## AICc : 1047.027
##
## Beta
## estimate se lcl ucl
## S:(Intercept) 3.250525 0.083815 3.086248 3.414803
##
##
## Real Parameter S
## 1 2 3 4 5 6 7 8
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 9 10 11 12 13 14 15 16
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 17 18 19 20 21 22 23 24
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 25 26 27 28 29 30 31 32
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 33 34 35 36 37 38 39 40
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 41 42 43 44 45 46 47 48
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 49 50 51 52 53 54 55 56
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 57 58 59 60 61
## 0.962692 0.962692 0.962692 0.962692 0.962692
summary(mod.cntl)
## Output summary for Nest model
## Name : S(~1)
##
## Npar : 1
## -2lnL: 1045.026
## AICc : 1047.027
##
## Beta
## estimate se lcl ucl
## S:(Intercept) 3.250525 0.083815 3.086248 3.414803
##
##
## Real Parameter S
## 1 2 3 4 5 6 7 8
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 9 10 11 12 13 14 15 16
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 17 18 19 20 21 22 23 24
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 25 26 27 28 29 30 31 32
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 33 34 35 36 37 38 39 40
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 41 42 43 44 45 46 47 48
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 49 50 51 52 53 54 55 56
## 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692 0.962692
## 57 58 59 60 61
## 0.962692 0.962692 0.962692 0.962692 0.962692
# Look the objects returned in more details
names(mod.cntl)
## [1] "data" "model" "title"
## [4] "model.name" "links" "mixtures"
## [7] "call" "parameters" "time.intervals"
## [10] "number.of.groups" "group.labels" "nocc"
## [13] "begin.time" "covariates" "fixed"
## [16] "design.matrix" "pims" "design.data"
## [19] "strata.labels" "mlogit.list" "profile.int"
## [22] "simplify" "model.parameters" "results"
## [25] "output"
names(mod.cntl$results)
## [1] "lnl" "deviance" "deviance.df"
## [4] "npar" "n" "AICc"
## [7] "beta" "real" "beta.vcv"
## [10] "derived" "derived.vcv" "covariate.values"
## [13] "singular" "real.vcv"
# look at estimates on beta and original scale
mod.cntl$results$beta # on the logit scale
## estimate se lcl ucl
## S:(Intercept) 3.250525 0.083815 3.086248 3.414803
mod.cntl$results$real# on the regular 0-1 scale for each site
## estimate se lcl ucl fixed note
## S g1 a0 t1 0.962692 0.0030103 0.9563219 0.968164
# derived variabldes is the nest survival probability over the 40 (nocc) days
names(mod.cntl$results$derived)
## [1] "S Overall Survival"
mod.cntl$results$derived$"S Overall Survival"
## estimate se lcl ucl
## 1 0.09833963 0.01875781 0.06720445 0.1417081
# alternatively
get.real(mod.cntl, "S", se=TRUE)
## all.diff.index par.index estimate se lcl
## S g1 a0 t1 1 1 0.962692 0.0030103 0.9563219
## S g1 a1 t2 2 1 0.962692 0.0030103 0.9563219
## S g1 a2 t3 3 1 0.962692 0.0030103 0.9563219
## S g1 a3 t4 4 1 0.962692 0.0030103 0.9563219
## S g1 a4 t5 5 1 0.962692 0.0030103 0.9563219
## S g1 a5 t6 6 1 0.962692 0.0030103 0.9563219
## S g1 a6 t7 7 1 0.962692 0.0030103 0.9563219
## S g1 a7 t8 8 1 0.962692 0.0030103 0.9563219
## S g1 a8 t9 9 1 0.962692 0.0030103 0.9563219
## S g1 a9 t10 10 1 0.962692 0.0030103 0.9563219
## S g1 a10 t11 11 1 0.962692 0.0030103 0.9563219
## S g1 a11 t12 12 1 0.962692 0.0030103 0.9563219
## S g1 a12 t13 13 1 0.962692 0.0030103 0.9563219
## S g1 a13 t14 14 1 0.962692 0.0030103 0.9563219
## S g1 a14 t15 15 1 0.962692 0.0030103 0.9563219
## S g1 a15 t16 16 1 0.962692 0.0030103 0.9563219
## S g1 a16 t17 17 1 0.962692 0.0030103 0.9563219
## S g1 a17 t18 18 1 0.962692 0.0030103 0.9563219
## S g1 a18 t19 19 1 0.962692 0.0030103 0.9563219
## S g1 a19 t20 20 1 0.962692 0.0030103 0.9563219
## S g1 a20 t21 21 1 0.962692 0.0030103 0.9563219
## S g1 a21 t22 22 1 0.962692 0.0030103 0.9563219
## S g1 a22 t23 23 1 0.962692 0.0030103 0.9563219
## S g1 a23 t24 24 1 0.962692 0.0030103 0.9563219
## S g1 a24 t25 25 1 0.962692 0.0030103 0.9563219
## S g1 a25 t26 26 1 0.962692 0.0030103 0.9563219
## S g1 a26 t27 27 1 0.962692 0.0030103 0.9563219
## S g1 a27 t28 28 1 0.962692 0.0030103 0.9563219
## S g1 a28 t29 29 1 0.962692 0.0030103 0.9563219
## S g1 a29 t30 30 1 0.962692 0.0030103 0.9563219
## S g1 a30 t31 31 1 0.962692 0.0030103 0.9563219
## S g1 a31 t32 32 1 0.962692 0.0030103 0.9563219
## S g1 a32 t33 33 1 0.962692 0.0030103 0.9563219
## S g1 a33 t34 34 1 0.962692 0.0030103 0.9563219
## S g1 a34 t35 35 1 0.962692 0.0030103 0.9563219
## S g1 a35 t36 36 1 0.962692 0.0030103 0.9563219
## S g1 a36 t37 37 1 0.962692 0.0030103 0.9563219
## S g1 a37 t38 38 1 0.962692 0.0030103 0.9563219
## S g1 a38 t39 39 1 0.962692 0.0030103 0.9563219
## S g1 a39 t40 40 1 0.962692 0.0030103 0.9563219
## S g1 a40 t41 41 1 0.962692 0.0030103 0.9563219
## S g1 a41 t42 42 1 0.962692 0.0030103 0.9563219
## S g1 a42 t43 43 1 0.962692 0.0030103 0.9563219
## S g1 a43 t44 44 1 0.962692 0.0030103 0.9563219
## S g1 a44 t45 45 1 0.962692 0.0030103 0.9563219
## S g1 a45 t46 46 1 0.962692 0.0030103 0.9563219
## S g1 a46 t47 47 1 0.962692 0.0030103 0.9563219
## S g1 a47 t48 48 1 0.962692 0.0030103 0.9563219
## S g1 a48 t49 49 1 0.962692 0.0030103 0.9563219
## S g1 a49 t50 50 1 0.962692 0.0030103 0.9563219
## S g1 a50 t51 51 1 0.962692 0.0030103 0.9563219
## S g1 a51 t52 52 1 0.962692 0.0030103 0.9563219
## S g1 a52 t53 53 1 0.962692 0.0030103 0.9563219
## S g1 a53 t54 54 1 0.962692 0.0030103 0.9563219
## S g1 a54 t55 55 1 0.962692 0.0030103 0.9563219
## S g1 a55 t56 56 1 0.962692 0.0030103 0.9563219
## S g1 a56 t57 57 1 0.962692 0.0030103 0.9563219
## S g1 a57 t58 58 1 0.962692 0.0030103 0.9563219
## S g1 a58 t59 59 1 0.962692 0.0030103 0.9563219
## S g1 a59 t60 60 1 0.962692 0.0030103 0.9563219
## S g1 a60 t61 61 1 0.962692 0.0030103 0.9563219
## ucl fixed note group age time Age Time
## S g1 a0 t1 0.968164 1 0 1 0 0
## S g1 a1 t2 0.968164 1 1 2 1 1
## S g1 a2 t3 0.968164 1 2 3 2 2
## S g1 a3 t4 0.968164 1 3 4 3 3
## S g1 a4 t5 0.968164 1 4 5 4 4
## S g1 a5 t6 0.968164 1 5 6 5 5
## S g1 a6 t7 0.968164 1 6 7 6 6
## S g1 a7 t8 0.968164 1 7 8 7 7
## S g1 a8 t9 0.968164 1 8 9 8 8
## S g1 a9 t10 0.968164 1 9 10 9 9
## S g1 a10 t11 0.968164 1 10 11 10 10
## S g1 a11 t12 0.968164 1 11 12 11 11
## S g1 a12 t13 0.968164 1 12 13 12 12
## S g1 a13 t14 0.968164 1 13 14 13 13
## S g1 a14 t15 0.968164 1 14 15 14 14
## S g1 a15 t16 0.968164 1 15 16 15 15
## S g1 a16 t17 0.968164 1 16 17 16 16
## S g1 a17 t18 0.968164 1 17 18 17 17
## S g1 a18 t19 0.968164 1 18 19 18 18
## S g1 a19 t20 0.968164 1 19 20 19 19
## S g1 a20 t21 0.968164 1 20 21 20 20
## S g1 a21 t22 0.968164 1 21 22 21 21
## S g1 a22 t23 0.968164 1 22 23 22 22
## S g1 a23 t24 0.968164 1 23 24 23 23
## S g1 a24 t25 0.968164 1 24 25 24 24
## S g1 a25 t26 0.968164 1 25 26 25 25
## S g1 a26 t27 0.968164 1 26 27 26 26
## S g1 a27 t28 0.968164 1 27 28 27 27
## S g1 a28 t29 0.968164 1 28 29 28 28
## S g1 a29 t30 0.968164 1 29 30 29 29
## S g1 a30 t31 0.968164 1 30 31 30 30
## S g1 a31 t32 0.968164 1 31 32 31 31
## S g1 a32 t33 0.968164 1 32 33 32 32
## S g1 a33 t34 0.968164 1 33 34 33 33
## S g1 a34 t35 0.968164 1 34 35 34 34
## S g1 a35 t36 0.968164 1 35 36 35 35
## S g1 a36 t37 0.968164 1 36 37 36 36
## S g1 a37 t38 0.968164 1 37 38 37 37
## S g1 a38 t39 0.968164 1 38 39 38 38
## S g1 a39 t40 0.968164 1 39 40 39 39
## S g1 a40 t41 0.968164 1 40 41 40 40
## S g1 a41 t42 0.968164 1 41 42 41 41
## S g1 a42 t43 0.968164 1 42 43 42 42
## S g1 a43 t44 0.968164 1 43 44 43 43
## S g1 a44 t45 0.968164 1 44 45 44 44
## S g1 a45 t46 0.968164 1 45 46 45 45
## S g1 a46 t47 0.968164 1 46 47 46 46
## S g1 a47 t48 0.968164 1 47 48 47 47
## S g1 a48 t49 0.968164 1 48 49 48 48
## S g1 a49 t50 0.968164 1 49 50 49 49
## S g1 a50 t51 0.968164 1 50 51 50 50
## S g1 a51 t52 0.968164 1 51 52 51 51
## S g1 a52 t53 0.968164 1 52 53 52 52
## S g1 a53 t54 0.968164 1 53 54 53 53
## S g1 a54 t55 0.968164 1 54 55 54 54
## S g1 a55 t56 0.968164 1 55 56 55 55
## S g1 a56 t57 0.968164 1 56 57 56 56
## S g1 a57 t58 0.968164 1 57 58 57 57
## S g1 a58 t59 0.968164 1 58 59 58 58
## S g1 a59 t60 0.968164 1 59 60 59 59
## S g1 a60 t61 0.968164 1 60 61 60 60
# Notice that the nest survival is the product of the individual S
prod(get.real(mod.cntl, "S", se=TRUE)$estimate)
## [1] 0.09833976
# problem is that the derived parameter is computed over 61 days (nocc)
# we only want the probability computed over 20 days.
# Use the deltamethod.special function
# for all 61 days
prod(get.real(mod.cntl, "S", se=TRUE)$estimate)
## [1] 0.09833976
deltamethod.special("prod",
get.real(mod.cntl, "S", se=TRUE)$estimate,
get.real(mod.cntl, "S", se=TRUE, vcv=TRUE, expand=TRUE)$vcv.real)
## [1] 0.01875785
# for 20 days
prod(get.real(mod.cntl, "S", se=TRUE)$estimate[1:20])
## [1] 0.467463
deltamethod.special("prod",
get.real(mod.cntl, "S", se=TRUE)$estimate[1:20],
get.real(mod.cntl, "S", se=TRUE, vcv=TRUE, expand=TRUE)$vcv.real[1:20, 1:20])
## [1] 0.02923489
# linear effect of date (relative to 27 May)
dim(reddata)
## [1] 537 11
# 1. Process the data.
# The nocc variable is the data at which hatching occurs
red.all.proc <- process.data(reddata, model="Nest", nocc=max(reddata$LastChecked))
red.all.proc
## $data
## NestId FirstFound LastPresent LastChecked Fate freq Height
## 1 /*1983-175*/ 11 11 18 1 1 16.90
## 2 /*1983-176*/ 13 22 23 1 1 10.50
## 3 /*1983-178*/ 7 26 26 0 1 4.80
## 4 /*1983-180*/ 12 14 20 1 1 3.70
## 5 /*1983-181*/ 6 20 25 1 1 10.70
## 6 /*1983-182*/ 11 19 20 1 1 17.80
## 7 /*1983-187*/ 17 17 19 1 1 6.40
## 8 /*1983-188*/ 11 30 30 0 1 13.50
## 9 /*1983-191*/ 10 14 19 1 1 15.10
## 10 /*1983-193*/ 12 21 22 1 1 8.30
## 11 /*1983-196*/ 11 11 14 1 1 10.90
## 12 /*1983-204*/ 12 12 17 1 1 7.30
## 13 /*1983-207*/ 11 31 31 0 1 13.70
## 14 /*1983-220*/ 9 9 13 1 1 2.65
## 15 /*1983-221*/ 18 36 36 0 1 5.90
## 16 /*1983-224*/ 13 13 19 1 1 11.80
## 17 /*1983-229*/ 18 20 21 1 1 2.90
## 18 /*1983-233*/ 18 25 26 1 1 11.40
## 19 /*1983-246*/ 19 19 25 1 1 1.71
## 20 /*1983-249*/ 17 20 21 1 1 3.90
## 21 /*1983-252*/ 18 33 33 0 1 8.20
## 22 /*1983-253*/ 20 32 32 0 1 4.20
## 23 /*1983-254*/ 18 31 31 0 1 3.70
## 24 /*1983-255*/ 18 30 30 0 1 13.40
## 25 /*1983-263*/ 21 24 26 1 1 7.30
## 26 /*1983-264*/ 21 21 25 1 1 10.90
## 27 /*1983-265*/ 24 38 39 1 1 15.90
## 28 /*1983-266*/ 24 45 45 0 1 4.50
## 29 /*1983-270*/ 24 34 40 1 1 7.00
## 30 /*1983-273*/ 26 29 30 1 1 2.07
## 31 /*1983-275*/ 26 27 27 0 1 4.70
## 32 /*1983-278*/ 21 42 42 0 1 5.10
## 33 /*1983-280*/ 34 38 39 1 1 4.40
## 34 /*1983-281*/ 37 55 56 1 1 3.10
## 35 /*1983-282*/ 28 30 30 0 1 10.10
## 36 /*1983-290*/ 33 35 35 0 1 5.00
## 37 /*1983-292*/ 33 33 35 1 1 3.40
## 38 /*1983-293*/ 40 46 46 0 1 0.46
## 39 /*1984-298*/ 10 33 33 0 1 14.03
## 40 /*1984-299*/ 8 10 12 1 1 1.35
## 41 /*1984-300*/ 9 30 30 0 1 15.29
## 42 /*1984-302*/ 9 20 21 1 1 4.90
## 43 /*1984-307*/ 16 38 38 0 1 15.33
## 44 /*1984-309*/ 15 18 22 1 1 1.84
## 45 /*1984-310*/ 16 31 33 1 1 5.65
## 46 /*1984-311*/ 15 37 37 0 1 11.02
## 47 /*1984-313*/ 13 35 36 1 1 1.84
## 48 /*1984-314*/ 15 38 38 0 1 8.51
## 49 /*1984-315*/ 9 28 31 1 1 1.84
## 50 /*1984-316*/ 18 27 28 1 1 18.50
## 51 /*1984-317*/ 15 29 31 1 1 4.26
## 52 /*1984-320*/ 18 40 40 0 1 4.39
## 53 /*1984-323*/ 18 41 42 1 1 1.90
## 54 /*1984-324*/ 12 31 31 0 1 3.10
## 55 /*1984-325*/ 19 44 44 0 1 6.90
## 56 /*1984-326*/ 14 33 33 0 1 4.68
## 57 /*1984-328*/ 19 29 32 1 1 12.09
## 58 /*1984-329*/ 19 27 29 1 1 3.60
## 59 /*1984-332*/ 19 34 34 0 1 1.90
## 60 /*1984-336*/ 27 48 54 1 1 10.53
## 61 /*1984-337*/ 24 24 26 1 1 2.80
## 62 /*1984-338*/ 31 53 53 0 1 2.76
## 63 /*1984-340*/ 25 28 29 1 1 5.15
## 64 /*1984-341*/ 25 35 35 0 1 0.68
## 65 /*1984-342*/ 25 30 31 1 1 2.80
## 66 /*1984-343*/ 25 30 31 1 1 2.48
## 67 /*1984-345*/ 25 30 30 0 1 3.50
## 68 /*1984-346*/ 25 43 43 0 1 2.12
## 69 /*1984-347*/ 26 33 33 0 1 3.38
## 70 /*1984-349*/ 34 40 41 1 1 6.21
## 71 /*1985-434*/ 7 27 27 0 1 2.60
## 72 /*1985-435*/ 8 8 15 1 1 2.40
## 73 /*1985-436*/ 7 8 15 1 1 2.90
## 74 /*1985-437*/ 7 8 12 1 1 8.50
## 75 /*1985-438*/ 6 26 26 0 1 10.00
## 76 /*1985-439*/ 15 25 25 0 1 28.40
## 77 /*1985-441*/ 7 28 28 0 1 3.40
## 78 /*1985-442*/ 6 28 28 0 1 2.00
## 79 /*1985-443*/ 11 33 33 0 1 3.80
## 80 /*1985-444*/ 10 32 32 0 1 9.30
## 81 /*1985-448*/ 18 31 35 1 1 16.70
## 82 /*1985-449*/ 9 32 32 0 1 5.90
## 83 /*1985-450*/ 10 33 33 0 1 3.30
## 84 /*1985-451*/ 4 25 25 0 1 6.70
## 85 /*1985-457*/ 11 18 21 1 1 1.90
## 86 /*1985-458*/ 15 35 35 0 1 14.60
## 87 /*1985-459*/ 8 19 22 1 1 4.00
## 88 /*1985-460*/ 12 29 31 1 1 3.50
## 89 /*1985-462*/ 16 32 35 1 1 4.00
## 90 /*1985-463*/ 18 38 38 0 1 13.80
## 91 /*1985-464*/ 12 26 26 0 1 3.60
## 92 /*1985-469*/ 10 30 30 0 1 1.95
## 93 /*1985-485*/ 21 28 31 1 1 6.20
## 94 /*1985-490*/ 24 26 26 0 1 3.00
## 95 /*1985-492*/ 24 33 33 0 1 9.70
## 96 /*1985-498*/ 29 35 36 1 1 14.00
## 97 /*1985-499*/ 29 30 31 1 1 15.70
## 98 /*1985-500*/ 29 35 36 1 1 1.50
## 99 /*1985-502*/ 30 30 31 1 1 16.80
## 100 /*1985-506*/ 31 32 33 1 1 21.40
## 101 /*1985-507*/ 31 44 44 0 1 8.00
## 102 /*1985-508*/ 31 33 33 0 1 18.00
## 103 /*1985-527*/ 49 53 53 0 1 16.40
## 104 /*1985-528*/ 55 56 56 0 1 1.80
## 105 /*1986-529*/ 1 23 23 0 1 3.06
## 106 /*1986-530*/ 3 18 19 1 1 3.81
## 107 /*1986-534*/ 3 25 25 0 1 6.13
## 108 /*1986-536*/ 7 19 23 1 1 6.30
## 109 /*1986-537*/ 4 27 27 0 1 11.50
## 110 /*1986-538*/ 7 27 27 0 1 14.00
## 111 /*1986-539*/ 4 26 26 0 1 3.90
## 112 /*1986-543*/ 1 6 11 1 1 4.93
## 113 /*1986-547*/ 6 29 29 0 1 17.78
## 114 /*1986-548*/ 4 25 25 0 1 1.79
## 115 /*1986-559*/ 8 31 31 0 1 5.27
## 116 /*1986-565*/ 7 30 30 0 1 13.74
## 117 /*1986-567*/ 8 30 30 0 1 3.98
## 118 /*1986-568*/ 10 30 30 0 1 15.89
## 119 /*1986-569*/ 4 26 26 0 1 5.00
## 120 /*1986-574*/ 6 20 22 1 1 3.28
## 121 /*1986-575*/ 6 28 28 0 1 3.51
## 122 /*1986-576*/ 10 30 30 0 1 13.91
## 123 /*1986-578*/ 4 21 23 1 1 17.79
## 124 /*1986-579*/ 5 9 11 1 1 2.85
## 125 /*1986-588*/ 12 14 15 1 1 3.80
## 126 /*1986-589*/ 7 27 27 0 1 2.57
## 127 /*1986-590*/ 7 21 22 1 1 2.20
## 128 /*1986-592*/ 13 35 35 0 1 20.83
## 129 /*1986-593*/ 17 37 37 0 1 16.31
## 130 /*1986-605*/ 19 30 32 1 1 2.44
## 131 /*1986-623*/ 19 19 20 1 1 11.50
## 132 /*1986-625*/ 24 45 45 0 1 14.85
## 133 /*1986-626*/ 24 46 46 0 1 15.50
## 134 /*1986-627*/ 25 38 41 1 1 1.15
## 135 /*1986-637*/ 20 31 31 0 1 12.85
## 136 /*1986-638*/ 22 30 30 0 1 13.30
## 137 /*1986-644*/ 23 24 24 0 1 3.75
## 138 /*1986-645*/ 23 25 25 0 1 14.33
## 139 /*1986-648*/ 23 26 26 0 1 2.31
## 140 /*1986-649*/ 23 35 35 0 1 1.21
## 141 /*1986-650*/ 25 38 38 0 1 4.73
## 142 /*1986-651*/ 25 31 31 0 1 14.43
## 143 /*1986-652*/ 25 30 30 0 1 2.23
## 144 /*1986-653*/ 25 38 38 0 1 16.44
## 145 /*1986-657*/ 27 28 28 0 1 5.56
## 146 /*1986-658*/ 28 35 35 0 1 16.00
## 147 /*1986-659*/ 29 51 51 0 1 21.79
## 148 /*1986-66*/ 41 49 49 0 1 20.00
## 149 /*1986-661*/ 32 53 53 0 1 4.40
## 150 /*1986-671*/ 35 38 38 0 1 19.81
## 151 /*1986-674*/ 37 38 38 0 1 21.14
## 152 /*1986-68*/ 2 23 23 0 1 4.22
## 153 /*1987-680*/ 3 23 23 0 1 15.35
## 154 /*1987-694*/ 2 23 23 0 1 19.32
## 155 /*1987-695*/ 4 25 25 0 1 15.60
## 156 /*1987-696*/ 4 24 24 0 1 20.76
## 157 /*1987-705*/ 5 5 10 1 1 17.32
## 158 /*1987-706*/ 5 25 25 0 1 17.91
## 159 /*1987-709*/ 9 31 31 0 1 4.80
## 160 /*1987-712*/ 3 24 24 0 1 20.16
## 161 /*1987-713*/ 4 25 25 0 1 2.80
## 162 /*1987-714*/ 1 21 21 0 1 21.33
## 163 /*1987-716*/ 7 24 26 1 1 4.03
## 164 /*1987-723*/ 9 30 30 0 1 1.88
## 165 /*1987-732*/ 8 28 28 0 1 1.51
## 166 /*1987-737*/ 11 33 33 0 1 19.41
## 167 /*1987-738*/ 4 10 11 1 1 7.12
## 168 /*1987-739*/ 5 16 17 1 1 2.47
## 169 /*1987-771*/ 10 17 23 1 1 2.79
## 170 /*1987-775*/ 16 39 39 0 1 27.75
## 171 /*1987-778*/ 10 10 13 1 1 1.44
## 172 /*1987-785*/ 16 22 22 0 1 16.62
## 173 /*1987-787*/ 17 21 21 0 1 3.96
## 174 /*1987-789*/ 18 30 31 1 1 2.60
## 175 /*1987-797*/ 20 29 29 0 1 1.02
## 176 /*1987-802*/ 20 27 27 0 1 4.08
## 177 /*1987-803*/ 21 26 27 1 1 6.09
## 178 /*1987-804*/ 21 26 27 1 1 2.67
## 179 /*1987-808*/ 22 26 27 1 1 12.05
## 180 /*1987-809*/ 22 23 23 0 1 5.35
## 181 /*1987-811*/ 22 38 38 0 1 5.53
## 182 /*1987-818*/ 23 25 25 0 1 10.27
## 183 /*1987-819*/ 23 34 34 0 1 4.85
## 184 /*1987-820*/ 23 27 27 0 1 5.12
## 185 /*1987-828*/ 25 31 31 0 1 1.41
## 186 /*1987-829*/ 25 28 28 0 1 4.00
## 187 /*1987-840*/ 29 31 31 0 1 1.01
## 188 /*1987-841*/ 29 33 33 0 1 3.83
## 189 /*1987-842*/ 29 35 35 0 1 11.40
## 190 /*1987-846*/ 33 38 38 0 1 16.14
## 191 /*1988-1004*/ 34 51 51 0 1 2.50
## 192 /*1988-1006*/ 39 42 42 0 1 11.30
## 193 /*1988-1008*/ 45 48 48 0 1 21.20
## 194 /*1988-1019*/ 47 54 54 0 1 15.50
## 195 /*1988-890*/ 7 29 29 0 1 3.60
## 196 /*1988-893*/ 9 29 29 0 1 17.40
## 197 /*1988-896*/ 9 15 19 1 1 4.70
## 198 /*1988-897*/ 11 12 14 1 1 4.70
## 199 /*1988-899*/ 12 33 33 0 1 2.60
## 200 /*1988-900*/ 7 29 29 0 1 2.90
## 201 /*1988-910*/ 8 29 29 0 1 4.50
## 202 /*1988-911*/ 9 29 29 0 1 2.70
## 203 /*1988-917*/ 9 30 30 0 1 1.60
## 204 /*1988-921*/ 17 38 38 0 1 9.10
## 205 /*1988-922*/ 17 33 37 1 1 20.10
## 206 /*1988-932*/ 10 30 30 0 1 3.80
## 207 /*1988-935*/ 16 31 31 0 1 3.20
## 208 /*1988-936*/ 11 32 32 0 1 4.10
## 209 /*1988-938*/ 19 39 39 0 1 3.40
## 210 /*1988-942*/ 21 30 30 0 1 2.90
## 211 /*1988-944*/ 21 29 29 0 1 1.90
## 212 /*1988-958*/ 15 15 17 1 1 15.30
## 213 /*1988-959*/ 15 29 29 0 1 13.00
## 214 /*1988-960*/ 15 29 29 0 1 6.70
## 215 /*1988-961*/ 17 39 39 0 1 12.70
## 216 /*1988-962*/ 26 47 47 0 1 22.80
## 217 /*1988-963*/ 22 43 43 0 1 4.40
## 218 /*1988-964*/ 16 32 32 0 1 2.10
## 219 /*1988-970*/ 23 29 29 0 1 14.00
## 220 /*1988-972*/ 23 32 32 0 1 15.60
## 221 /*1988-973*/ 32 45 49 1 1 19.80
## 222 /*1988-974*/ 25 48 48 0 1 17.10
## 223 /*1988-976*/ 23 36 36 0 1 15.00
## 224 /*1988-977*/ 24 44 44 0 1 1.50
## 225 /*1988-981*/ 27 31 31 0 1 11.50
## 226 /*1988-983*/ 28 31 31 0 1 19.70
## 227 /*1988-984*/ 29 36 36 0 1 16.50
## 228 /*1988-985*/ 38 45 46 1 1 18.40
## 229 /*1988-991*/ 26 26 27 1 1 10.00
## 230 /*1988-992*/ 33 36 36 0 1 17.80
## 231 /*1988-993*/ 33 42 42 0 1 0.90
## 232 /*1988-994*/ 34 43 43 0 1 10.30
## 233 /*1989-1039*/ 5 26 26 0 1 20.60
## 234 /*1989-1040*/ 2 3 5 1 1 1.80
## 235 /*1989-1071*/ 8 29 29 0 1 9.80
## 236 /*1989-1076*/ 5 20 23 1 1 1.60
## 237 /*1989-1077*/ 3 25 25 0 1 13.50
## 238 /*1989-1078*/ 8 25 25 0 1 10.90
## 239 /*1989-1081*/ 10 30 30 0 1 18.70
## 240 /*1989-1092*/ 11 11 12 1 1 17.00
## 241 /*1989-1104*/ 9 18 21 1 1 9.20
## 242 /*1989-1109*/ 29 51 51 0 1 17.80
## 243 /*1989-1111*/ 12 21 22 1 1 15.50
## 244 /*1989-1112*/ 12 35 35 0 1 17.10
## 245 /*1989-1114*/ 16 17 18 1 1 5.50
## 246 /*1989-1115*/ 23 43 43 0 1 12.60
## 247 /*1989-1116*/ 23 42 42 0 1 9.70
## 248 /*1989-1118*/ 12 33 33 0 1 1.60
## 249 /*1989-1120*/ 11 11 12 1 1 9.30
## 250 /*1989-1121*/ 11 26 26 0 1 3.70
## 251 /*1989-1123*/ 16 18 20 1 1 20.50
## 252 /*1989-1124*/ 21 42 42 0 1 0.80
## 253 /*1989-1125*/ 24 27 30 1 1 19.90
## 254 /*1989-1127*/ 32 39 39 0 1 15.90
## 255 /*1989-1129*/ 25 36 36 0 1 3.00
## 256 /*1989-1131*/ 41 44 44 0 1 19.70
## 257 /*1989-1133*/ 26 41 41 0 1 16.80
## 258 /*1989-1134*/ 26 36 36 0 1 14.90
## 259 /*1989-1135*/ 23 41 41 0 1 1.30
## 260 /*1989-1137*/ 29 49 49 0 1 24.40
## 261 /*1989-1151*/ 27 35 35 0 1 22.90
## 262 /*1989-1152*/ 28 28 30 1 1 2.20
## 263 /*1989-1153*/ 27 51 51 0 1 2.20
## 264 /*1989-1154*/ 30 37 37 0 1 0.80
## 265 /*1989-1155*/ 9 32 32 0 1 2.50
## 266 /*1989-1156*/ 11 24 27 1 1 17.10
## 267 /*1989-1158*/ 11 18 20 1 1 1.60
## 268 /*1989-1161*/ 19 20 21 1 1 1.30
## 269 /*1989-1162*/ 16 24 24 0 1 1.60
## 270 /*1989-1163*/ 16 30 30 0 1 3.70
## 271 /*1989-1180*/ 31 40 41 1 1 17.10
## 272 /*1989-1181*/ 33 39 41 1 1 14.50
## 273 /*1989-1182*/ 33 34 34 0 1 11.10
## 274 /*1990-104*/ 18 26 27 1 1 4.60
## 275 /*1990-105*/ 28 29 30 1 1 3.90
## 276 /*1990-12*/ 7 28 28 0 1 2.20
## 277 /*1990-123*/ 11 33 33 0 1 1.00
## 278 /*1990-127*/ 12 35 35 0 1 5.60
## 279 /*1990-128*/ 11 35 35 0 1 10.60
## 280 /*1990-130*/ 18 29 36 1 1 18.40
## 281 /*1990-132*/ 20 43 43 0 1 11.40
## 282 /*1990-133*/ 27 40 46 1 1 14.80
## 283 /*1990-134*/ 18 33 36 1 1 2.00
## 284 /*1990-135*/ 19 32 32 0 1 8.32
## 285 /*1990-136*/ 26 34 34 0 1 1.40
## 286 /*1990-143*/ 30 34 34 0 1 11.10
## 287 /*1990-145*/ 31 43 44 1 1 24.00
## 288 /*1990-146*/ 32 34 34 0 1 16.40
## 289 /*1990-147*/ 33 45 45 0 1 24.30
## 290 /*1990-148*/ 33 35 35 0 1 1.90
## 291 /*1990-150*/ 17 34 34 0 1 3.70
## 292 /*1990-18*/ 8 31 31 0 1 24.00
## 293 /*1990-19*/ 13 33 33 0 1 20.60
## 294 /*1990-20*/ 11 34 34 0 1 10.20
## 295 /*1990-21*/ 8 30 30 0 1 5.90
## 296 /*1990-315*/ 56 57 57 0 1 5.10
## 297 /*1990-316*/ 26 38 39 1 1 3.00
## 298 /*1990-319*/ 34 36 36 0 1 15.10
## 299 /*1990-327*/ 33 35 35 0 1 1.90
## 300 /*1990-328*/ 33 37 37 0 1 1.60
## 301 /*1990-359*/ 38 39 40 1 1 3.40
## 302 /*1990-360*/ 38 40 44 1 1 1.60
## 303 /*1990-40*/ 12 34 34 0 1 2.50
## 304 /*1990-45*/ 12 12 20 1 1 10.70
## 305 /*1990-47*/ 14 14 16 1 1 6.00
## 306 /*1990-51*/ 11 34 34 0 1 8.40
## 307 /*1990-54*/ 14 35 35 0 1 2.10
## 308 /*1990-56*/ 17 28 29 1 1 2.10
## 309 /*1990-57*/ 12 16 21 1 1 5.10
## 310 /*1990-58*/ 9 29 29 0 1 11.20
## 311 /*1990-59*/ 6 13 18 1 1 17.90
## 312 /*1990-60*/ 9 31 31 0 1 15.10
## 313 /*1990-61*/ 7 28 28 0 1 7.10
## 314 /*1990-66*/ 9 29 32 1 1 2.30
## 315 /*1990-68*/ 15 31 34 1 1 5.00
## 316 /*1990-70*/ 27 47 47 0 1 10.80
## 317 /*1990-71*/ 23 28 31 1 1 1.65
## 318 /*1990-72*/ 16 28 34 1 1 2.40
## 319 /*1990-75*/ 17 24 28 1 1 1.60
## 320 /*1990-76*/ 19 41 41 0 1 14.00
## 321 /*1990-92*/ 20 42 42 0 1 18.40
## 322 /*1990-93*/ 18 38 38 0 1 18.80
## 323 /*1990-95*/ 18 36 36 0 1 2.30
## 324 /*1990-97*/ 26 38 38 0 1 12.90
## 325 /*1990-98*/ 18 42 42 0 1 9.90
## 326 /*1990-99*/ 21 44 44 0 1 3.30
## 327 /*1991-200*/ 1 24 24 0 1 3.50
## 328 /*1991-201*/ 2 15 18 1 1 1.50
## 329 /*1991-204*/ 5 16 17 1 1 14.60
## 330 /*1991-205*/ 2 11 12 1 1 4.10
## 331 /*1991-206*/ 7 27 27 0 1 3.35
## 332 /*1991-208*/ 5 27 27 0 1 3.57
## 333 /*1991-209*/ 6 27 27 0 1 3.15
## 334 /*1991-210*/ 5 19 26 1 1 3.70
## 335 /*1991-211*/ 2 21 24 1 1 3.40
## 336 /*1991-212*/ 1 22 22 0 1 2.60
## 337 /*1991-213*/ 1 23 23 0 1 2.55
## 338 /*1991-218*/ 11 13 14 1 1 8.75
## 339 /*1991-220*/ 13 16 18 1 1 21.00
## 340 /*1991-221*/ 5 27 27 0 1 3.90
## 341 /*1991-222*/ 7 27 28 1 1 2.41
## 342 /*1991-223*/ 1 22 22 0 1 3.50
## 343 /*1991-224*/ 5 27 27 0 1 1.95
## 344 /*1991-228*/ 11 32 32 0 1 3.90
## 345 /*1991-229*/ 3 24 24 0 1 3.05
## 346 /*1991-231*/ 16 36 36 0 1 4.40
## 347 /*1991-234*/ 16 36 36 0 1 16.70
## 348 /*1991-235*/ 5 13 17 1 1 13.00
## 349 /*1991-240*/ 11 22 22 0 1 8.35
## 350 /*1991-241*/ 18 39 39 0 1 3.45
## 351 /*1991-242*/ 18 40 40 0 1 7.75
## 352 /*1991-245*/ 16 19 19 0 1 7.70
## 353 /*1991-247*/ 14 30 30 0 1 3.40
## 354 /*1991-250*/ 13 35 35 0 1 4.66
## 355 /*1991-252*/ 15 27 27 0 1 1.25
## 356 /*1991-253*/ 19 19 21 1 1 5.20
## 357 /*1991-254*/ 27 35 36 1 1 13.10
## 358 /*1991-256*/ 19 27 27 0 1 3.44
## 359 /*1991-257*/ 19 23 23 0 1 5.80
## 360 /*1991-258*/ 7 27 27 0 1 1.38
## 361 /*1991-259*/ 22 25 25 0 1 2.65
## 362 /*1991-261*/ 24 28 28 0 1 3.38
## 363 /*1991-263*/ 28 35 39 1 1 4.60
## 364 /*1991-265*/ 24 26 26 0 1 2.70
## 365 /*1991-266*/ 24 25 25 0 1 9.90
## 366 /*1991-267*/ 28 31 31 0 1 17.60
## 367 /*1991-271*/ 29 30 30 0 1 13.60
## 368 /*1991-273*/ 30 41 41 0 1 15.30
## 369 /*1991-276*/ 36 53 56 1 1 3.00
## 370 /*1991-277*/ 32 33 33 0 1 11.20
## 371 /*1992-161*/ 8 13 17 1 1 2.80
## 372 /*1992-204*/ 7 21 24 1 1 4.30
## 373 /*1992-207*/ 6 27 27 0 1 4.40
## 374 /*1992-210*/ 8 28 28 0 1 13.10
## 375 /*1992-213*/ 7 28 28 0 1 1.90
## 376 /*1992-214*/ 10 23 27 1 1 2.90
## 377 /*1992-215*/ 9 26 28 1 1 5.40
## 378 /*1992-216*/ 9 29 29 0 1 3.20
## 379 /*1992-219*/ 10 31 31 0 1 4.70
## 380 /*1992-220*/ 8 29 29 0 1 2.00
## 381 /*1992-223*/ 7 19 23 1 1 4.70
## 382 /*1992-224*/ 8 13 17 1 1 2.70
## 383 /*1992-226*/ 8 17 18 1 1 12.00
## 384 /*1992-233*/ 22 27 30 1 1 17.00
## 385 /*1992-234*/ 19 25 29 1 1 3.90
## 386 /*1992-236*/ 9 23 26 1 1 18.70
## 387 /*1992-238*/ 6 12 16 1 1 3.70
## 388 /*1992-239*/ 11 12 16 1 1 3.70
## 389 /*1992-240*/ 8 17 18 1 1 5.40
## 390 /*1992-241*/ 14 35 35 0 1 5.50
## 391 /*1992-242*/ 13 16 20 1 1 2.70
## 392 /*1992-246*/ 12 31 31 0 1 10.20
## 393 /*1992-247*/ 12 21 22 1 1 1.10
## 394 /*1992-248*/ 9 31 31 0 1 6.10
## 395 /*1992-250*/ 7 13 16 1 1 5.50
## 396 /*1992-252*/ 8 29 29 0 1 5.40
## 397 /*1992-259*/ 15 33 33 0 1 21.30
## 398 /*1992-263*/ 19 26 28 1 1 2.90
## 399 /*1992-264*/ 7 19 21 1 1 2.90
## 400 /*1992-266*/ 22 42 42 0 1 18.10
## 401 /*1992-267*/ 17 26 27 1 1 12.60
## 402 /*1992-269*/ 19 21 25 1 1 0.90
## 403 /*1992-274*/ 17 28 29 1 1 18.00
## 404 /*1992-275*/ 23 40 42 1 1 3.70
## 405 /*1992-278*/ 22 41 42 1 1 3.50
## 406 /*1992-280*/ 23 25 28 1 1 5.80
## 407 /*1992-281*/ 25 26 32 1 1 21.80
## 408 /*1992-282*/ 18 18 19 1 1 3.30
## 409 /*1992-283*/ 26 32 33 1 1 15.80
## 410 /*1992-285*/ 21 42 42 0 1 13.30
## 411 /*1992-289*/ 28 50 50 0 1 17.40
## 412 /*1992-293*/ 20 20 22 1 1 4.90
## 413 /*1992-294*/ 22 29 30 1 1 4.50
## 414 /*1992-295*/ 22 26 27 1 1 9.70
## 415 /*1992-296*/ 34 56 56 0 1 21.50
## 416 /*1992-297*/ 26 31 33 1 1 2.30
## 417 /*1992-300*/ 36 46 47 1 1 0.90
## 418 /*1992-302*/ 24 42 42 0 1 2.20
## 419 /*1992-303*/ 27 31 32 1 1 5.00
## 420 /*1992-304*/ 38 55 56 1 1 3.20
## 421 /*1992-305*/ 34 56 56 0 1 3.80
## 422 /*1992-307*/ 23 40 41 1 1 5.90
## 423 /*1992-308*/ 34 56 56 0 1 22.80
## 424 /*1992-309*/ 35 44 44 0 1 3.50
## 425 /*1992-310*/ 35 50 52 1 1 1.10
## 426 /*1992-311*/ 38 42 43 1 1 4.60
## 427 /*1992-312*/ 24 30 30 0 1 18.20
## 428 /*1992-313*/ 24 29 30 1 1 5.10
## 429 /*1992-318*/ 27 27 28 1 1 3.60
## 430 /*1992-319*/ 32 33 33 0 1 21.10
## 431 /*1992-320*/ 35 44 45 1 1 4.10
## 432 /*1992-322*/ 40 62 62 0 1 18.00
## 433 /*1992-324*/ 40 41 41 0 1 3.15
## 434 /*1992-326*/ 52 59 59 0 1 18.70
## 435 /*1993-205*/ 1 7 10 1 1 8.10
## 436 /*1993-206*/ 1 15 17 1 1 5.30
## 437 /*1993-207*/ 1 2 3 1 1 2.00
## 438 /*1993-209*/ 2 7 10 1 1 3.00
## 439 /*1993-211*/ 3 5 8 1 1 3.00
## 440 /*1993-212*/ 2 23 23 0 1 2.50
## 441 /*1993-213*/ 2 13 14 1 1 3.90
## 442 /*1993-215*/ 5 10 13 1 1 2.60
## 443 /*1993-218*/ 9 30 30 0 1 4.40
## 444 /*1993-221*/ 5 23 25 1 1 8.50
## 445 /*1993-222*/ 5 10 13 1 1 2.20
## 446 /*1993-223*/ 7 10 13 1 1 2.40
## 447 /*1993-228*/ 17 25 27 1 1 1.50
## 448 /*1993-229*/ 8 28 28 0 1 10.80
## 449 /*1993-230*/ 4 20 23 1 1 2.10
## 450 /*1993-233*/ 8 8 11 1 1 2.10
## 451 /*1993-235*/ 11 11 16 1 1 15.80
## 452 /*1993-237*/ 18 28 29 1 1 4.80
## 453 /*1993-238*/ 11 15 15 0 1 20.10
## 454 /*1993-239*/ 8 9 12 1 1 2.00
## 455 /*1993-240*/ 6 12 13 1 1 8.10
## 456 /*1993-241*/ 6 9 12 1 1 8.30
## 457 /*1993-242*/ 7 21 21 0 1 5.80
## 458 /*1993-245*/ 18 43 43 0 1 16.80
## 459 /*1993-252*/ 20 39 39 0 1 3.40
## 460 /*1993-253*/ 19 23 23 0 1 3.20
## 461 /*1993-254*/ 30 41 41 0 1 0.93
## 462 /*1993-255*/ 36 38 41 1 1 3.40
## 463 /*1993-257*/ 34 44 47 1 1 14.80
## 464 /*1993-259*/ 11 14 16 1 1 11.80
## 465 /*1993-264*/ 14 29 30 1 1 3.00
## 466 /*1993-266*/ 21 32 35 1 1 12.50
## 467 /*1993-267*/ 21 24 27 1 1 2.20
## 468 /*1993-268*/ 19 26 29 1 1 4.20
## 469 /*1993-269*/ 19 19 22 1 1 2.20
## 470 /*1993-270*/ 14 27 28 1 1 8.00
## 471 /*1993-273*/ 15 17 19 1 1 8.30
## 472 /*1993-274*/ 19 20 23 1 1 5.70
## 473 /*1993-275*/ 25 42 43 1 1 1.63
## 474 /*1993-277*/ 18 21 24 1 1 3.90
## 475 /*1993-279*/ 21 33 34 1 1 1.87
## 476 /*1993-280*/ 16 27 30 1 1 3.00
## 477 /*1993-281*/ 17 22 27 1 1 24.30
## 478 /*1993-282*/ 24 33 35 1 1 7.30
## 479 /*1993-284*/ 25 45 45 0 1 18.30
## 480 /*1993-287*/ 25 46 46 0 1 1.80
## 481 /*1993-290*/ 38 58 58 0 1 19.80
## 482 /*1993-294*/ 21 43 43 0 1 14.60
## 483 /*1993-295*/ 23 26 29 1 1 2.30
## 484 /*1993-299*/ 20 24 25 1 1 2.60
## 485 /*1993-300*/ 18 19 24 1 1 4.40
## 486 /*1993-302*/ 33 48 48 0 1 11.40
## 487 /*1993-303*/ 35 56 56 0 1 3.40
## 488 /*1994-118*/ 24 24 26 1 1 5.72
## 489 /*1994-152*/ 4 26 26 0 1 4.32
## 490 /*1994-153*/ 3 24 24 0 1 10.55
## 491 /*1994-155*/ 10 31 31 0 1 2.96
## 492 /*1994-156*/ 10 26 29 1 1 3.06
## 493 /*1994-158*/ 10 12 16 1 1 3.72
## 494 /*1994-159*/ 12 33 33 0 1 17.77
## 495 /*1994-161*/ 12 17 23 1 1 3.67
## 496 /*1994-164*/ 14 30 30 0 1 3.93
## 497 /*1994-167*/ 18 28 28 0 1 14.82
## 498 /*1994-168*/ 10 15 20 1 1 6.38
## 499 /*1994-169*/ 11 23 27 1 1 2.81
## 500 /*1994-171*/ 15 31 31 0 1 2.92
## 501 /*1994-172*/ 19 39 39 0 1 4.88
## 502 /*1994-173*/ 19 33 33 0 1 1.82
## 503 /*1994-174*/ 17 38 38 0 1 2.93
## 504 /*1994-177*/ 19 27 28 1 1 4.75
## 505 /*1994-178*/ 20 33 33 0 1 2.94
## 506 /*1994-179*/ 18 24 24 0 1 2.54
## 507 /*1994-180*/ 20 23 23 0 1 7.74
## 508 /*1994-181*/ 20 21 25 1 1 2.55
## 509 /*1994-182*/ 21 31 31 0 1 2.53
## 510 /*1994-183*/ 21 23 23 0 1 3.68
## 511 /*1994-184*/ 34 40 44 1 1 22.70
## 512 /*1994-185*/ 21 24 24 0 1 2.31
## 513 /*1994-186*/ 22 27 27 0 1 5.50
## 514 /*1994-189*/ 35 36 36 0 1 16.54
## 515 /*1994-190*/ 27 33 33 0 1 5.07
## 516 /*1995-101*/ 8 20 23 1 1 3.59
## 517 /*1995-102*/ 4 15 16 1 1 3.67
## 518 /*1995-104*/ 11 26 28 1 1 2.86
## 519 /*1995-106*/ 10 10 16 1 1 20.39
## 520 /*1995-109*/ 14 35 35 0 1 7.56
## 521 /*1995-112*/ 18 40 40 0 1 19.58
## 522 /*1995-113*/ 9 28 28 0 1 3.11
## 523 /*1995-114*/ 17 26 26 0 1 3.71
## 524 /*1995-115*/ 17 18 19 1 1 8.15
## 525 /*1995-117*/ 25 40 43 1 1 12.13
## 526 /*1995-118*/ 20 27 30 1 1 16.18
## 527 /*1995-119*/ 20 26 26 0 1 14.26
## 528 /*1995-120*/ 20 20 26 1 1 3.57
## 529 /*1995-121*/ 24 26 29 1 1 3.90
## 530 /*1995-122*/ 24 29 29 0 1 5.14
## 531 /*1995-123*/ 23 26 26 0 1 12.64
## 532 /*1995-124*/ 25 32 32 0 1 25.02
## 533 /*1995-125*/ 25 33 33 0 1 4.37
## 534 /*1995-126*/ 26 32 33 1 1 2.10
## 535 /*1995-127*/ 26 30 30 0 1 13.35
## 536 /*1995-128*/ 26 31 31 0 1 1.83
## 537 /*1995-129*/ 27 31 31 0 1 16.89
## BaffleStatus DBH AgeDay1 Year
## 1 N 39.00 -8 1983
## 2 N 10.70 -10 1983
## 3 N 8.80 -4 1983
## 4 N 5.10 -9 1983
## 5 N 15.60 -3 1983
## 6 N 46.20 -8 1983
## 7 N 8.90 -14 1983
## 8 N 25.20 -8 1983
## 9 N 24.20 -7 1983
## 10 N 10.20 -9 1983
## 11 N 11.50 -8 1983
## 12 N 9.00 -9 1983
## 13 N 36.50 -8 1983
## 14 N 3.50 -4 1983
## 15 N 4.70 -15 1983
## 16 N 21.30 -10 1983
## 17 N 6.70 -15 1983
## 18 N 55.70 -15 1983
## 19 N 9.50 -16 1983
## 20 N 8.30 -8 1983
## 21 N 10.40 -8 1983
## 22 N 4.40 -18 1983
## 23 N 5.10 -8 1983
## 24 N 26.70 -7 1983
## 25 N 8.20 -10 1983
## 26 N 16.10 -12 1983
## 27 N 17.80 -14 1983
## 28 N 35.20 -22 1983
## 29 N 6.40 -21 1983
## 30 N 3.10 -17 1983
## 31 N 4.70 -4 1983
## 32 N 10.40 -18 1983
## 33 N 7.80 -30 1983
## 34 N 5.30 -35 1983
## 35 N 6.80 -6 1983
## 36 N 9.00 -15 1983
## 37 N 4.10 -24 1983
## 38 N 1.00 -23 1983
## 39 N 29.70 -6 1984
## 40 N 8.00 -5 1984
## 41 N 21.00 -6 1984
## 42 N 8.40 -6 1984
## 43 N 25.60 -13 1984
## 44 N 4.30 -12 1984
## 45 N 7.20 -13 1984
## 46 N 30.90 -12 1984
## 47 N 5.90 -10 1984
## 48 N 13.00 -12 1984
## 49 N 2.20 -6 1984
## 50 N 29.90 -15 1984
## 51 N 6.30 -12 1984
## 52 N 6.10 -15 1984
## 53 N 3.80 -15 1984
## 54 N 3.80 -8 1984
## 55 N 6.30 -16 1984
## 56 N 7.80 -10 1984
## 57 N 37.70 -16 1984
## 58 N 7.90 -15 1984
## 59 N 6.20 -10 1984
## 60 N 9.30 -25 1984
## 61 N 2.60 -13 1984
## 62 N 6.20 -29 1984
## 63 N 9.20 -16 1984
## 64 N 1.00 -12 1984
## 65 N 6.30 -13 1984
## 66 N 3.10 -4 1984
## 67 N 10.60 -7 1984
## 68 N 6.90 -21 1984
## 69 N 3.90 -10 1984
## 70 N 11.00 -21 1984
## 71 N 3.30 -4 1985
## 72 N 3.80 -2 1985
## 73 N 5.60 -4 1985
## 74 N 7.90 -4 1985
## 75 N 11.40 -2 1985
## 76 N 54.10 -1 1985
## 77 N 5.60 -4 1985
## 78 N 5.30 -2 1985
## 79 N 6.90 -8 1985
## 80 Y 27.90 -7 1985
## 81 Y 22.90 -15 1985
## 82 Y 4.80 -6 1985
## 83 Y 3.00 -6 1985
## 84 Y 5.10 -1 1985
## 85 Y 1.80 -8 1985
## 86 Y 23.30 -12 1985
## 87 N 6.10 -4 1985
## 88 N 4.60 -9 1985
## 89 N 4.60 -13 1985
## 90 N 20.00 -15 1985
## 91 Y 5.80 -2 1985
## 92 N 1.50 -7 1985
## 93 N 8.90 -11 1985
## 94 N 3.80 -2 1985
## 95 N 25.20 -8 1985
## 96 N 32.00 -9 1985
## 97 N 28.20 -8 1985
## 98 N 1.00 -15 1985
## 99 N 20.30 -9 1985
## 100 N 28.20 -9 1985
## 101 N 7.60 -20 1985
## 102 N 23.60 -8 1985
## 103 N 31.00 -30 1985
## 104 N 5.60 -33 1985
## 105 N 6.40 2 1986
## 106 N 14.90 1 1986
## 107 N 10.10 0 1986
## 108 N 9.10 -5 1986
## 109 N 11.30 -1 1986
## 110 Y 33.30 -4 1986
## 111 Y 6.60 -1 1986
## 112 N 6.70 2 1986
## 113 N 28.10 -3 1986
## 114 Y 8.20 -1 1986
## 115 N 4.70 -5 1986
## 116 N 42.70 -4 1986
## 117 N 4.90 -5 1986
## 118 N 39.30 -7 1986
## 119 Y 3.00 -1 1986
## 120 N 6.30 -3 1986
## 121 N 5.30 -3 1986
## 122 N 32.00 -7 1986
## 123 N 29.90 -1 1986
## 124 N 5.00 -2 1986
## 125 N 4.30 -10 1986
## 126 N 3.40 -4 1986
## 127 N 4.30 -1 1986
## 128 N 39.10 -10 1986
## 129 Y 54.40 -14 1986
## 130 N 3.50 -17 1986
## 131 N 19.70 -8 1986
## 132 N 37.50 -21 1986
## 133 N 24.30 -21 1986
## 134 N 2.20 -23 1986
## 135 N 22.40 -8 1986
## 136 Y 12.10 -7 1986
## 137 N 4.20 -1 1986
## 138 Y 33.10 -2 1986
## 139 N 9.80 -3 1986
## 140 Y 1.40 -12 1986
## 141 N 7.00 -15 1986
## 142 N 73.50 -8 1986
## 143 N 4.20 -7 1986
## 144 N 33.20 -15 1986
## 145 N 7.10 -5 1986
## 146 N 42.00 -12 1986
## 147 N 44.80 -26 1986
## 148 N 36.20 -26 1986
## 149 Y 8.80 -29 1986
## 150 N 43.40 -15 1986
## 151 N 68.00 -15 1986
## 152 N 6.10 1 1986
## 153 Y 32.20 0 1987
## 154 N 35.60 2 1987
## 155 N 41.70 0 1987
## 156 N 34.60 -1 1987
## 157 N 25.30 -2 1987
## 158 N 28.70 -2 1987
## 159 N 10.30 -6 1987
## 160 N 30.00 0 1987
## 161 N 6.70 -1 1987
## 162 N 38.40 2 1987
## 163 N 13.80 -4 1987
## 164 N 3.30 -6 1987
## 165 N 2.10 -5 1987
## 166 N 24.10 -8 1987
## 167 N 12.90 -1 1987
## 168 N 4.20 0 1987
## 169 N 4.80 -1 1987
## 170 N 40.20 -14 1987
## 171 N 2.70 -1 1987
## 172 N 29.40 1 1987
## 173 N 9.20 2 1987
## 174 N 6.10 -10 1987
## 175 N 2.90 -6 1987
## 176 N 5.10 -4 1987
## 177 Y 6.70 -8 1987
## 178 N 10.20 -5 1987
## 179 N 15.80 -1 1987
## 180 N 9.92 -31 1987
## 181 Y 9.60 0 1987
## 182 N 27.60 -2 1987
## 183 Y 14.10 -11 1987
## 184 N 9.70 -4 1987
## 185 N 2.20 -8 1987
## 186 N 4.20 -5 1987
## 187 N 1.80 -8 1987
## 188 N 52.00 -10 1987
## 189 N 34.10 -12 1987
## 190 N 26.50 -15 1987
## 191 N 6.20 -28 1988
## 192 N 15.40 -19 1988
## 193 N 32.90 -25 1988
## 194 N 33.90 -28 1988
## 195 N 7.10 -4 1988
## 196 N 38.00 -6 1988
## 197 Y 6.10 -6 1988
## 198 N 7.10 -7 1988
## 199 N 3.50 -8 1988
## 200 N 5.40 -4 1988
## 201 N 10.20 -5 1988
## 202 N 7.20 -6 1988
## 203 Y 6.60 -6 1988
## 204 N 45.00 -14 1988
## 205 Y 49.30 -14 1988
## 206 N 7.40 -6 1988
## 207 Y 5.10 -8 1988
## 208 Y 7.50 -7 1988
## 209 N 8.20 -13 1988
## 210 Y 4.70 -7 1988
## 211 N 3.80 -6 1988
## 212 N 34.20 -5 1988
## 213 Y 22.50 -7 1988
## 214 N 7.80 -6 1988
## 215 Y 18.00 -6 1988
## 216 N 54.30 -23 1988
## 217 Y 36.10 -20 1988
## 218 N 3.70 -9 1988
## 219 Y 35.00 -6 1988
## 220 N 25.70 -9 1988
## 221 N 36.10 -29 1988
## 222 N 29.20 -22 1988
## 223 N 40.40 -13 1988
## 224 N 5.70 -21 1988
## 225 N 15.30 -8 1988
## 226 N 40.20 -8 1988
## 227 N 48.40 -13 1988
## 228 N 29.70 -35 1988
## 229 N 46.20 -13 1988
## 230 N 53.00 -13 1988
## 231 N 1.00 -20 1988
## 232 N 16.30 -20 1988
## 233 N 39.30 -2 1989
## 234 N 5.00 1 1989
## 235 Y 26.80 -4 1989
## 236 N 4.80 -2 1989
## 237 Y 13.00 0 1989
## 238 Y 12.60 -5 1989
## 239 N 31.70 -7 1989
## 240 N 31.80 -8 1989
## 241 Y 12.60 -3 1989
## 242 N 35.60 -26 1989
## 243 N 28.20 -9 1989
## 244 N 35.80 -9 1989
## 245 N 6.00 -7 1989
## 246 N 34.30 -20 1989
## 247 N 11.20 -20 1989
## 248 N 1.00 -9 1989
## 249 N 8.70 -2 1989
## 250 Y 3.70 -3 1989
## 251 N 41.70 -7 1989
## 252 N 1.00 -19 1989
## 253 Y 29.90 -11 1989
## 254 N 49.30 -16 1989
## 255 Y 4.10 -13 1989
## 256 N 39.40 -20 1989
## 257 N 52.50 -18 1989
## 258 N 24.30 -13 1989
## 259 Y 1.00 -20 1989
## 260 N 41.00 -26 1989
## 261 N 24.00 -12 1989
## 262 N 3.40 -11 1989
## 263 N 1.70 -25 1989
## 264 N 1.30 -14 1989
## 265 Y 5.50 -6 1989
## 266 Y 27.00 -7 1989
## 267 Y 5.40 -8 1989
## 268 N 2.00 -16 1989
## 269 N 5.30 0 1989
## 270 Y 5.20 -7 1989
## 271 N 34.00 -21 1989
## 272 N 29.00 -23 1989
## 273 N 25.10 -11 1989
## 274 N 6.40 -14 1990
## 275 N 3.90 -26 1990
## 276 N 2.80 -4 1990
## 277 N 1.00 -8 1990
## 278 N 7.50 -9 1990
## 279 N 13.50 -8 1990
## 280 N 50.70 -15 1990
## 281 N 18.30 -18 1990
## 282 N 29.60 -25 1990
## 283 N 3.30 -15 1990
## 284 N 16.10 -9 1990
## 285 N 1.00 -11 1990
## 286 N 28.25 -11 1990
## 287 N 85.50 -24 1990
## 288 N 24.00 -11 1990
## 289 N 42.70 -20 1990
## 290 N 5.20 -22 1990
## 291 N 6.00 -11 1990
## 292 N 39.50 -5 1990
## 293 N 39.00 -11 1990
## 294 N 9.90 -8 1990
## 295 N 5.35 -5 1990
## 296 N 5.30 -34 1990
## 297 N 4.80 -23 1990
## 298 N 18.20 -13 1990
## 299 N 4.10 -12 1990
## 300 N 4.80 -14 1990
## 301 N 6.50 -17 1990
## 302 N 2.20 -17 1990
## 303 N 4.60 -9 1990
## 304 N 11.80 -7 1990
## 305 N 5.60 -10 1990
## 306 N 27.70 -8 1990
## 307 N 2.60 -12 1990
## 308 N 3.80 -14 1990
## 309 N 6.50 -9 1990
## 310 N 35.00 -5 1990
## 311 N 55.20 -3 1990
## 312 N 22.80 -6 1990
## 313 N 10.30 -3 1990
## 314 N 5.60 -6 1990
## 315 N 8.90 -12 1990
## 316 N 22.90 -24 1990
## 317 N 4.10 -19 1990
## 318 N 3.35 -13 1990
## 319 N 6.80 -14 1990
## 320 N 25.10 -16 1990
## 321 N 50.70 -17 1990
## 322 N 39.80 -15 1990
## 323 N 5.10 -15 1990
## 324 N 14.80 -14 1990
## 325 N 12.80 -16 1990
## 326 N 3.50 -19 1990
## 327 N 6.00 2 1991
## 328 N 4.80 0 1991
## 329 N 39.30 -3 1991
## 330 N 13.50 1 1991
## 331 N 5.20 -4 1991
## 332 N 15.50 0 1991
## 333 Y 5.10 -2 1991
## 334 N 6.70 -2 1991
## 335 N 5.70 0 1991
## 336 N 4.70 2 1991
## 337 N 7.00 3 1991
## 338 N 15.30 -2 1991
## 339 N 23.50 -4 1991
## 340 N 8.00 -3 1991
## 341 N 9.50 -4 1991
## 342 Y 7.90 2 1991
## 343 N 3.00 -2 1991
## 344 N 8.70 -8 1991
## 345 N 9.30 0 1991
## 346 N 5.20 -14 1991
## 347 N 43.00 -13 1991
## 348 N 15.30 -3 1991
## 349 N 17.40 1 1991
## 350 N 9.10 -15 1991
## 351 N 15.70 -15 1991
## 352 N 9.80 4 1991
## 353 Y 9.40 -7 1991
## 354 N 10.00 -10 1991
## 355 Y 3.30 -3 1991
## 356 N 6.50 -6 1991
## 357 N 21.60 -17 1991
## 358 N 4.50 -4 1991
## 359 N 20.50 0 1991
## 360 N 3.50 -4 1991
## 361 N 3.10 -2 1991
## 362 N 9.10 -6 1991
## 363 N 8.20 -26 1991
## 364 N 4.10 -4 1991
## 365 N 27.50 -3 1991
## 366 N 49.10 -8 1991
## 367 N 18.00 -7 1991
## 368 N 20.00 -18 1991
## 369 N 3.50 -34 1991
## 370 N 25.90 -10 1991
## 371 N 6.40 -5 1992
## 372 N 6.20 -4 1992
## 373 N 12.20 -2 1992
## 374 N 52.00 -5 1992
## 375 N 4.90 -4 1992
## 376 N 3.60 -8 1992
## 377 N 11.80 -6 1992
## 378 Y 6.70 -6 1992
## 379 N 5.00 -7 1992
## 380 Y 2.20 -5 1992
## 381 N 6.70 -4 1992
## 382 N 3.20 -5 1992
## 383 N 13.00 -4 1992
## 384 N 52.00 -19 1992
## 385 N 5.40 -16 1992
## 386 N 23.30 -6 1992
## 387 N 4.30 -3 1992
## 388 N 4.40 -9 1992
## 389 N 6.70 -4 1992
## 390 N 7.60 -11 1992
## 391 N 2.60 -10 1992
## 392 N 20.90 -9 1992
## 393 N 5.90 -9 1992
## 394 N 6.60 -6 1992
## 395 N 11.40 -4 1992
## 396 N 7.00 -5 1992
## 397 N 44.30 -8 1992
## 398 N 2.90 -17 1992
## 399 N 6.30 -4 1992
## 400 N 35.60 -19 1992
## 401 N 23.30 -15 1992
## 402 N 1.00 -16 1992
## 403 N 16.00 -14 1992
## 404 N 4.80 -21 1992
## 405 N 7.50 -19 1992
## 406 N 6.90 -20 1992
## 407 N 23.00 -22 1992
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## 412 N 6.40 -5 1992
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## 484 N 2.80 1 1993
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## 493 N 3.90 -7 1994
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## 496 N 6.90 -7 1994
## 497 N 35.00 -4 1994
## 498 N 8.20 1 1994
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## 523 N 4.00 -3 1995
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## 526 N 27.40 -10 1995
## 527 N 18.20 -3 1995
## 528 N 4.90 1 1995
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## 530 N 3.90 -6 1995
## 531 N 13.60 -3 1995
## 532 N 44.20 -9 1995
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## 534 N 2.70 -10 1995
## 535 N 24.30 -7 1995
## 536 N 5.40 -8 1995
## 537 N 33.30 -8 1995
##
## $model
## [1] "Nest"
##
## $mixtures
## [1] 1
##
## $freq
## group1
## 1 1
## 2 1
## 3 1
## 4 1
## 5 1
## 6 1
## 7 1
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##
## $nocc
## [1] 62
##
## $nocc.secondary
## NULL
##
## $time.intervals
## [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
## [36] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
##
## $begin.time
## [1] 1
##
## $age.unit
## [1] 1
##
## $initial.ages
## [1] 0
##
## $group.covariates
## NULL
##
## $nstrata
## [1] 1
##
## $strata.labels
## [1] ""
##
## $counts
## NULL
##
## $reverse
## [1] FALSE
##
## $areas
## NULL
##
## $events
## NULL
# 2. Examine and/or modify the ddl. (Not done here)
red.all.ddl <- make.design.data(red.all.proc)
str(red.all.ddl)
## List of 2
## $ S :'data.frame': 61 obs. of 7 variables:
## ..$ par.index : int [1:61] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ model.index: num [1:61] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ group : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
## ..$ age : Factor w/ 61 levels "0","1","2","3",..: 1 2 3 4 5 6 7 8 9 10 ...
## ..$ time : Factor w/ 61 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
## ..$ Age : num [1:61] 0 1 2 3 4 5 6 7 8 9 ...
## ..$ Time : num [1:61] 0 1 2 3 4 5 6 7 8 9 ...
## $ pimtypes:List of 1
## ..$ S:List of 1
## .. ..$ pim.type: chr "all"
red.all.ddl
## $S
## par.index model.index group age time Age Time
## 1 1 1 1 0 1 0 0
## 2 2 2 1 1 2 1 1
## 3 3 3 1 2 3 2 2
## 4 4 4 1 3 4 3 3
## 5 5 5 1 4 5 4 4
## 6 6 6 1 5 6 5 5
## 7 7 7 1 6 7 6 6
## 8 8 8 1 7 8 7 7
## 9 9 9 1 8 9 8 8
## 10 10 10 1 9 10 9 9
## 11 11 11 1 10 11 10 10
## 12 12 12 1 11 12 11 11
## 13 13 13 1 12 13 12 12
## 14 14 14 1 13 14 13 13
## 15 15 15 1 14 15 14 14
## 16 16 16 1 15 16 15 15
## 17 17 17 1 16 17 16 16
## 18 18 18 1 17 18 17 17
## 19 19 19 1 18 19 18 18
## 20 20 20 1 19 20 19 19
## 21 21 21 1 20 21 20 20
## 22 22 22 1 21 22 21 21
## 23 23 23 1 22 23 22 22
## 24 24 24 1 23 24 23 23
## 25 25 25 1 24 25 24 24
## 26 26 26 1 25 26 25 25
## 27 27 27 1 26 27 26 26
## 28 28 28 1 27 28 27 27
## 29 29 29 1 28 29 28 28
## 30 30 30 1 29 30 29 29
## 31 31 31 1 30 31 30 30
## 32 32 32 1 31 32 31 31
## 33 33 33 1 32 33 32 32
## 34 34 34 1 33 34 33 33
## 35 35 35 1 34 35 34 34
## 36 36 36 1 35 36 35 35
## 37 37 37 1 36 37 36 36
## 38 38 38 1 37 38 37 37
## 39 39 39 1 38 39 38 38
## 40 40 40 1 39 40 39 39
## 41 41 41 1 40 41 40 40
## 42 42 42 1 41 42 41 41
## 43 43 43 1 42 43 42 42
## 44 44 44 1 43 44 43 43
## 45 45 45 1 44 45 44 44
## 46 46 46 1 45 46 45 45
## 47 47 47 1 46 47 46 46
## 48 48 48 1 47 48 47 47
## 49 49 49 1 48 49 48 48
## 50 50 50 1 49 50 49 49
## 51 51 51 1 50 51 50 50
## 52 52 52 1 51 52 51 51
## 53 53 53 1 52 53 52 52
## 54 54 54 1 53 54 53 53
## 55 55 55 1 54 55 54 54
## 56 56 56 1 55 56 55 55
## 57 57 57 1 56 57 56 56
## 58 58 58 1 57 58 57 57
## 59 59 59 1 58 59 58 58
## 60 60 60 1 59 60 59 59
## 61 61 61 1 60 61 60 60
##
## $pimtypes
## $pimtypes$S
## $pimtypes$S$pim.type
## [1] "all"
# 3. Fit a particular model
# This is a model with linear effect of date (relative to 27 May)
mod.T <- RMark::mark(red.all.proc, ddl=red.all.ddl,
model="Nest",
model.parameters=list(
S =list(formula=~Time)
)
)
##
## Output summary for Nest model
## Name : S(~Time)
##
## Npar : 2
## -2lnL: 1640.228
## AICc : 1644.229
##
## Beta
## estimate se lcl ucl
## S:(Intercept) 3.5809203 0.1656975 3.256153 3.9056873
## S:Time -0.0102601 0.0064367 -0.022876 0.0023558
##
##
## Real Parameter S
## 1 2 3 4 5 6 7
## 0.9729046 0.9726328 0.9723583 0.9720812 0.9718014 0.9715189 0.9712336
## 8 9 10 11 12 13 14
## 0.9709456 0.9706547 0.9703611 0.9700646 0.9697652 0.9694629 0.9691577
## 15 16 17 18 19 20 21
## 0.9688495 0.9685384 0.9682242 0.967907 0.9675868 0.9672634 0.966937
## 22 23 24 25 26 27 28
## 0.9666074 0.9662746 0.9659387 0.9655995 0.9652571 0.9649113 0.9645623
## 29 30 31 32 33 34 35
## 0.9642099 0.9638541 0.963495 0.9631324 0.9627663 0.9623968 0.9620237
## 36 37 38 39 40 41 42
## 0.9616471 0.9612669 0.960883 0.9604956 0.9601044 0.9597096 0.959311
## 43 44 45 46 47 48 49
## 0.9589086 0.9585024 0.9580924 0.9576785 0.9572607 0.9568389 0.9564132
## 50 51 52 53 54 55 56
## 0.9559835 0.9555497 0.9551119 0.9546699 0.9542239 0.9537736 0.9533191
## 57 58 59 60 61
## 0.9528604 0.9523974 0.9519301 0.9514584 0.9509823
summary(mod.T)
## Output summary for Nest model
## Name : S(~Time)
##
## Npar : 2
## -2lnL: 1640.228
## AICc : 1644.229
##
## Beta
## estimate se lcl ucl
## S:(Intercept) 3.5809203 0.1656975 3.256153 3.9056873
## S:Time -0.0102601 0.0064367 -0.022876 0.0023558
##
##
## Real Parameter S
## 1 2 3 4 5 6 7
## 0.9729046 0.9726328 0.9723583 0.9720812 0.9718014 0.9715189 0.9712336
## 8 9 10 11 12 13 14
## 0.9709456 0.9706547 0.9703611 0.9700646 0.9697652 0.9694629 0.9691577
## 15 16 17 18 19 20 21
## 0.9688495 0.9685384 0.9682242 0.967907 0.9675868 0.9672634 0.966937
## 22 23 24 25 26 27 28
## 0.9666074 0.9662746 0.9659387 0.9655995 0.9652571 0.9649113 0.9645623
## 29 30 31 32 33 34 35
## 0.9642099 0.9638541 0.963495 0.9631324 0.9627663 0.9623968 0.9620237
## 36 37 38 39 40 41 42
## 0.9616471 0.9612669 0.960883 0.9604956 0.9601044 0.9597096 0.959311
## 43 44 45 46 47 48 49
## 0.9589086 0.9585024 0.9580924 0.9576785 0.9572607 0.9568389 0.9564132
## 50 51 52 53 54 55 56
## 0.9559835 0.9555497 0.9551119 0.9546699 0.9542239 0.9537736 0.9533191
## 57 58 59 60 61
## 0.9528604 0.9523974 0.9519301 0.9514584 0.9509823
# Look the objects returned in more details
names(mod.T)
## [1] "data" "model" "title"
## [4] "model.name" "links" "mixtures"
## [7] "call" "parameters" "time.intervals"
## [10] "number.of.groups" "group.labels" "nocc"
## [13] "begin.time" "covariates" "fixed"
## [16] "design.matrix" "pims" "design.data"
## [19] "strata.labels" "mlogit.list" "profile.int"
## [22] "simplify" "model.parameters" "results"
## [25] "output"
names(mod.T$results)
## [1] "lnl" "deviance" "deviance.df"
## [4] "npar" "n" "AICc"
## [7] "beta" "real" "beta.vcv"
## [10] "derived" "derived.vcv" "covariate.values"
## [13] "singular" "real.vcv"
# look at estimates on beta and original scale
mod.T$results$beta # on the logit scale
## estimate se lcl ucl
## S:(Intercept) 3.5809203 0.1656975 3.256153 3.9056873
## S:Time -0.0102601 0.0064367 -0.022876 0.0023558
mod.T$results$real# on the regular 0-1 scale for each site
## estimate se lcl ucl fixed note
## S g1 a0 t1 0.9729046 0.0043680 0.9628936 0.9802700
## S g1 a1 t2 0.9726328 0.0042547 0.9629370 0.9798452
## S g1 a2 t3 0.9723583 0.0041400 0.9629772 0.9794132
## S g1 a3 t4 0.9720812 0.0040241 0.9630137 0.9789743
## S g1 a4 t5 0.9718014 0.0039071 0.9630461 0.9785286
## S g1 a5 t6 0.9715189 0.0037892 0.9630740 0.9780765
## S g1 a6 t7 0.9712336 0.0036707 0.9630966 0.9776181
## S g1 a7 t8 0.9709456 0.0035518 0.9631135 0.9771541
## S g1 a8 t9 0.9706547 0.0034330 0.9631237 0.9766850
## S g1 a9 t10 0.9703611 0.0033147 0.9631264 0.9762114
## S g1 a10 t11 0.9700646 0.0031973 0.9631204 0.9757341
## S g1 a11 t12 0.9697652 0.0030814 0.9631046 0.9752542
## S g1 a12 t13 0.9694629 0.0029678 0.9630774 0.9747729
## S g1 a13 t14 0.9691577 0.0028574 0.9630371 0.9742918
## S g1 a14 t15 0.9688495 0.0027510 0.9629815 0.9738126
## S g1 a15 t16 0.9685384 0.0026500 0.9629084 0.9733374
## S g1 a16 t17 0.9682242 0.0025555 0.9628149 0.9728688
## S g1 a17 t18 0.9679070 0.0024693 0.9626980 0.9724095
## S g1 a18 t19 0.9675868 0.0023929 0.9625541 0.9719628
## S g1 a19 t20 0.9672634 0.0023284 0.9623794 0.9715322
## S g1 a20 t21 0.9669370 0.0022775 0.9621700 0.9711213
## S g1 a21 t22 0.9666074 0.0022423 0.9619220 0.9707338
## S g1 a22 t23 0.9662746 0.0022246 0.9616318 0.9703730
## S g1 a23 t24 0.9659387 0.0022258 0.9612961 0.9700417
## S g1 a24 t25 0.9655995 0.0022471 0.9609128 0.9697420
## S g1 a25 t26 0.9652571 0.0022890 0.9604805 0.9694747
## S g1 a26 t27 0.9649113 0.0023516 0.9599989 0.9692398
## S g1 a27 t28 0.9645623 0.0024344 0.9594688 0.9690364
## S g1 a28 t29 0.9642099 0.0025367 0.9588915 0.9688626
## S g1 a29 t30 0.9638541 0.0026572 0.9582691 0.9687161
## S g1 a30 t31 0.9634950 0.0027948 0.9576038 0.9685944
## S g1 a31 t32 0.9631324 0.0029482 0.9568978 0.9684948
## S g1 a32 t33 0.9627663 0.0031161 0.9561535 0.9684148
## S g1 a33 t34 0.9623968 0.0032973 0.9553727 0.9683519
## S g1 a34 t35 0.9620237 0.0034908 0.9545575 0.9683039
## S g1 a35 t36 0.9616471 0.0036957 0.9537093 0.9682690
## S g1 a36 t37 0.9612669 0.0039112 0.9528294 0.9682454
## S g1 a37 t38 0.9608830 0.0041365 0.9519191 0.9682316
## S g1 a38 t39 0.9604956 0.0043712 0.9509790 0.9682264
## S g1 a39 t40 0.9601044 0.0046146 0.9500100 0.9682287
## S g1 a40 t41 0.9597096 0.0048664 0.9490126 0.9682375
## S g1 a41 t42 0.9593110 0.0051262 0.9479872 0.9682520
## S g1 a42 t43 0.9589086 0.0053938 0.9469341 0.9682715
## S g1 a43 t44 0.9585024 0.0056689 0.9458534 0.9682955
## S g1 a44 t45 0.9580924 0.0059513 0.9447454 0.9683234
## S g1 a45 t46 0.9576785 0.0062408 0.9436100 0.9683548
## S g1 a46 t47 0.9572607 0.0065373 0.9424471 0.9683892
## S g1 a47 t48 0.9568389 0.0068407 0.9412567 0.9684264
## S g1 a48 t49 0.9564132 0.0071509 0.9400387 0.9684661
## S g1 a49 t50 0.9559835 0.0074679 0.9387928 0.9685079
## S g1 a50 t51 0.9555497 0.0077915 0.9375188 0.9685518
## S g1 a51 t52 0.9551119 0.0081219 0.9362166 0.9685974
## S g1 a52 t53 0.9546699 0.0084589 0.9348858 0.9686445
## S g1 a53 t54 0.9542239 0.0088025 0.9335261 0.9686932
## S g1 a54 t55 0.9537736 0.0091527 0.9321372 0.9687431
## S g1 a55 t56 0.9533191 0.0095096 0.9307187 0.9687942
## S g1 a56 t57 0.9528604 0.0098731 0.9292704 0.9688463
## S g1 a57 t58 0.9523974 0.0102433 0.9277918 0.9688995
## S g1 a58 t59 0.9519301 0.0106202 0.9262825 0.9689535
## S g1 a59 t60 0.9514584 0.0110039 0.9247422 0.9690083
## S g1 a60 t61 0.9509823 0.0113943 0.9231704 0.9690638
# derived variabldes is the nest survival probability over the 40 (nocc) days
names(mod.T$results$derived)
## [1] "S Overall Survival"
mod.T$results$derived$"S Overall Survival"
## estimate se lcl ucl
## 1 0.09989742 0.02060703 0.06614019 0.1481507
# alternatively
get.real(mod.T, "S", se=TRUE)
## all.diff.index par.index estimate se lcl
## S g1 a0 t1 1 1 0.9729046 0.0043680 0.9628936
## S g1 a1 t2 2 2 0.9726328 0.0042547 0.9629370
## S g1 a2 t3 3 3 0.9723583 0.0041400 0.9629772
## S g1 a3 t4 4 4 0.9720812 0.0040241 0.9630137
## S g1 a4 t5 5 5 0.9718014 0.0039071 0.9630461
## S g1 a5 t6 6 6 0.9715189 0.0037892 0.9630740
## S g1 a6 t7 7 7 0.9712336 0.0036707 0.9630966
## S g1 a7 t8 8 8 0.9709456 0.0035518 0.9631135
## S g1 a8 t9 9 9 0.9706547 0.0034330 0.9631237
## S g1 a9 t10 10 10 0.9703611 0.0033147 0.9631264
## S g1 a10 t11 11 11 0.9700646 0.0031973 0.9631204
## S g1 a11 t12 12 12 0.9697652 0.0030814 0.9631046
## S g1 a12 t13 13 13 0.9694629 0.0029678 0.9630774
## S g1 a13 t14 14 14 0.9691577 0.0028574 0.9630371
## S g1 a14 t15 15 15 0.9688495 0.0027510 0.9629815
## S g1 a15 t16 16 16 0.9685384 0.0026500 0.9629084
## S g1 a16 t17 17 17 0.9682242 0.0025555 0.9628149
## S g1 a17 t18 18 18 0.9679070 0.0024693 0.9626980
## S g1 a18 t19 19 19 0.9675868 0.0023929 0.9625541
## S g1 a19 t20 20 20 0.9672634 0.0023284 0.9623794
## S g1 a20 t21 21 21 0.9669370 0.0022775 0.9621700
## S g1 a21 t22 22 22 0.9666074 0.0022423 0.9619220
## S g1 a22 t23 23 23 0.9662746 0.0022246 0.9616318
## S g1 a23 t24 24 24 0.9659387 0.0022258 0.9612961
## S g1 a24 t25 25 25 0.9655995 0.0022471 0.9609128
## S g1 a25 t26 26 26 0.9652571 0.0022890 0.9604805
## S g1 a26 t27 27 27 0.9649113 0.0023516 0.9599989
## S g1 a27 t28 28 28 0.9645623 0.0024344 0.9594688
## S g1 a28 t29 29 29 0.9642099 0.0025367 0.9588915
## S g1 a29 t30 30 30 0.9638541 0.0026572 0.9582691
## S g1 a30 t31 31 31 0.9634950 0.0027948 0.9576038
## S g1 a31 t32 32 32 0.9631324 0.0029482 0.9568978
## S g1 a32 t33 33 33 0.9627663 0.0031161 0.9561535
## S g1 a33 t34 34 34 0.9623968 0.0032973 0.9553727
## S g1 a34 t35 35 35 0.9620237 0.0034908 0.9545575
## S g1 a35 t36 36 36 0.9616471 0.0036957 0.9537093
## S g1 a36 t37 37 37 0.9612669 0.0039112 0.9528294
## S g1 a37 t38 38 38 0.9608830 0.0041365 0.9519191
## S g1 a38 t39 39 39 0.9604956 0.0043712 0.9509790
## S g1 a39 t40 40 40 0.9601044 0.0046146 0.9500100
## S g1 a40 t41 41 41 0.9597096 0.0048664 0.9490126
## S g1 a41 t42 42 42 0.9593110 0.0051262 0.9479872
## S g1 a42 t43 43 43 0.9589086 0.0053938 0.9469341
## S g1 a43 t44 44 44 0.9585024 0.0056689 0.9458534
## S g1 a44 t45 45 45 0.9580924 0.0059513 0.9447454
## S g1 a45 t46 46 46 0.9576785 0.0062408 0.9436100
## S g1 a46 t47 47 47 0.9572607 0.0065373 0.9424471
## S g1 a47 t48 48 48 0.9568389 0.0068407 0.9412567
## S g1 a48 t49 49 49 0.9564132 0.0071509 0.9400387
## S g1 a49 t50 50 50 0.9559835 0.0074679 0.9387928
## S g1 a50 t51 51 51 0.9555497 0.0077915 0.9375188
## S g1 a51 t52 52 52 0.9551119 0.0081219 0.9362166
## S g1 a52 t53 53 53 0.9546699 0.0084589 0.9348858
## S g1 a53 t54 54 54 0.9542239 0.0088025 0.9335261
## S g1 a54 t55 55 55 0.9537736 0.0091527 0.9321372
## S g1 a55 t56 56 56 0.9533191 0.0095096 0.9307187
## S g1 a56 t57 57 57 0.9528604 0.0098731 0.9292704
## S g1 a57 t58 58 58 0.9523974 0.0102433 0.9277918
## S g1 a58 t59 59 59 0.9519301 0.0106202 0.9262825
## S g1 a59 t60 60 60 0.9514584 0.0110039 0.9247422
## S g1 a60 t61 61 61 0.9509823 0.0113943 0.9231704
## ucl fixed note group age time Age Time
## S g1 a0 t1 0.9802700 1 0 1 0 0
## S g1 a1 t2 0.9798452 1 1 2 1 1
## S g1 a2 t3 0.9794132 1 2 3 2 2
## S g1 a3 t4 0.9789743 1 3 4 3 3
## S g1 a4 t5 0.9785286 1 4 5 4 4
## S g1 a5 t6 0.9780765 1 5 6 5 5
## S g1 a6 t7 0.9776181 1 6 7 6 6
## S g1 a7 t8 0.9771541 1 7 8 7 7
## S g1 a8 t9 0.9766850 1 8 9 8 8
## S g1 a9 t10 0.9762114 1 9 10 9 9
## S g1 a10 t11 0.9757341 1 10 11 10 10
## S g1 a11 t12 0.9752542 1 11 12 11 11
## S g1 a12 t13 0.9747729 1 12 13 12 12
## S g1 a13 t14 0.9742918 1 13 14 13 13
## S g1 a14 t15 0.9738126 1 14 15 14 14
## S g1 a15 t16 0.9733374 1 15 16 15 15
## S g1 a16 t17 0.9728688 1 16 17 16 16
## S g1 a17 t18 0.9724095 1 17 18 17 17
## S g1 a18 t19 0.9719628 1 18 19 18 18
## S g1 a19 t20 0.9715322 1 19 20 19 19
## S g1 a20 t21 0.9711213 1 20 21 20 20
## S g1 a21 t22 0.9707338 1 21 22 21 21
## S g1 a22 t23 0.9703730 1 22 23 22 22
## S g1 a23 t24 0.9700417 1 23 24 23 23
## S g1 a24 t25 0.9697420 1 24 25 24 24
## S g1 a25 t26 0.9694747 1 25 26 25 25
## S g1 a26 t27 0.9692398 1 26 27 26 26
## S g1 a27 t28 0.9690364 1 27 28 27 27
## S g1 a28 t29 0.9688626 1 28 29 28 28
## S g1 a29 t30 0.9687161 1 29 30 29 29
## S g1 a30 t31 0.9685944 1 30 31 30 30
## S g1 a31 t32 0.9684948 1 31 32 31 31
## S g1 a32 t33 0.9684148 1 32 33 32 32
## S g1 a33 t34 0.9683519 1 33 34 33 33
## S g1 a34 t35 0.9683039 1 34 35 34 34
## S g1 a35 t36 0.9682690 1 35 36 35 35
## S g1 a36 t37 0.9682454 1 36 37 36 36
## S g1 a37 t38 0.9682316 1 37 38 37 37
## S g1 a38 t39 0.9682264 1 38 39 38 38
## S g1 a39 t40 0.9682287 1 39 40 39 39
## S g1 a40 t41 0.9682375 1 40 41 40 40
## S g1 a41 t42 0.9682520 1 41 42 41 41
## S g1 a42 t43 0.9682715 1 42 43 42 42
## S g1 a43 t44 0.9682955 1 43 44 43 43
## S g1 a44 t45 0.9683234 1 44 45 44 44
## S g1 a45 t46 0.9683548 1 45 46 45 45
## S g1 a46 t47 0.9683892 1 46 47 46 46
## S g1 a47 t48 0.9684264 1 47 48 47 47
## S g1 a48 t49 0.9684661 1 48 49 48 48
## S g1 a49 t50 0.9685079 1 49 50 49 49
## S g1 a50 t51 0.9685518 1 50 51 50 50
## S g1 a51 t52 0.9685974 1 51 52 51 51
## S g1 a52 t53 0.9686445 1 52 53 52 52
## S g1 a53 t54 0.9686932 1 53 54 53 53
## S g1 a54 t55 0.9687431 1 54 55 54 54
## S g1 a55 t56 0.9687942 1 55 56 55 55
## S g1 a56 t57 0.9688463 1 56 57 56 56
## S g1 a57 t58 0.9688995 1 57 58 57 57
## S g1 a58 t59 0.9689535 1 58 59 58 58
## S g1 a59 t60 0.9690083 1 59 60 59 59
## S g1 a60 t61 0.9690638 1 60 61 60 60
plotdata <- get.real(mod.T, "S", se=TRUE)
ggplot(data=plotdata, aes(x=time, y=estimate, group=1))+
ggtitle("Linear effect on DSR")+
geom_line()+
geom_ribbon(aes(ymin=lcl, ymax=ucl), alpha=0.2)+
ylim(0.5,1)
# Notice that the nest survival is the product of the individual S
prod(get.real(mod.T, "S", se=TRUE)$estimate)
## [1] 0.09989747
# problem is that the derived parameter is computed over 61 days (nocc)
# we only want the probability computed over 20 days but starting when?.
# Use the deltamethod.special function
# for 20 days at start of experiment/
prod(get.real(mod.T, "S", se=TRUE)$estimate[1:20])
## [1] 0.5456371
deltamethod.special("prod",
get.real(mod.T, "S", se=TRUE)$estimate[1:20],
get.real(mod.T, "S", se=TRUE, vcv=TRUE, expand=TRUE)$vcv.real[1:20, 1:20])
## [1] 0.03612687
# for 20 days at middle of experiment/
prod(get.real(mod.T, "S", se=TRUE)$estimate[21:40])
## [1] 0.4765181
deltamethod.special("prod",
get.real(mod.T, "S", se=TRUE)$estimate[21:40],
get.real(mod.T, "S", se=TRUE, vcv=TRUE, expand=TRUE)$vcv.real[21:40, 21:40])
## [1] 0.0273521
cleanup(ask=FALSE)