# File: LuckiamuteDesign.R
# Purpose: Example linear GRTS survey design for Luckiamute Watershed Council streams
# Programmer: Tony Olsen
# Date: April 17, 2005

#######
# Load psurvey.design library
#######

#######  Read in dbf file to get attributes
# stream network is in Albers projection. See projection file

# Read in dbf file
att <- read.dbf("luck-ash")
names(att) <- tolower(names(att))
head(att)

# look at attributes that will be used to define strata and 
# unequal probability categories
table(att$minor2)  # 610 - intermittent stream, 0 - perennial stream
table(att$strahler)  # Strahler stream order 1=headwater stream

# summarize frame stream length (km) by mdcaty
sum(att$length)/1000
tapply(att$length, list(att$strahler, att$minor2), sum)/1000

###### Four Example GRTS designs are given. Each can be run independently.

##### Equal probability GRTS survey design
Equaldsgn <- list(None=list(panel=c(Panel_1=50),
                          seltype='Equal'))

sample(100000000,1) # run to get random seed
dsgntime <- proc.time()

Equalsites <- grts(design=Equaldsgn,
                   DesignID='EQUAL',
                   type.frame='linear',
                   src.frame='shapefile',
                   in.shape='luck-ash',
                   att.frame=att,
                   prjfilename='luck-ash',
                   out.shape='Equal Sites')

dsgntime <- ( proc.time() - dsgntime )/60  # time in minutes to complete design
dsgntime 
# Note: output dbf file can be read directly into Excel

##### Stratified GRTS survey design with over sample.
# create strata variable
att$PerInt <- as.factor( att$minor2 )
levels(att$PerInt) <- list(Perennial='0', Intermittent='610')

# specify design
Stratdsgn <- list(Perennial=list(panel=c(Panel_1=50),
                                 seltype='Equal',
                                 over=50),
									Intermittent=list(panel=c(Panel_1=50),
                                 seltype='Equal',
                                 over=50))

sample(100000000,1) # run to get random seed
dsgntime <- proc.time()

Stratsites <- grts(design=Stratdsgn,
                   DesignID='STRATIFIED',
                   type.frame='linear',
                   src.frame='shapefile',
                   in.shape='luck-ash',
                   att.frame=att,
                   stratum='PerInt',
                   prjfilename='luck-ash',
                   out.shape='Stratified Sites')

dsgntime <- ( proc.time() - dsgntime )/60  # time in minutes to complete design
dsgntime 

##### Unequal probability GRTS survey design with over sample and stratification.
# create strata variable
att$PerInt <- as.factor( att$minor2 )
levels(att$PerInt) <- list(Perennial='0', Intermittent='610')

# create Strahler categories for unequal probability design
att$strahcat <- as.factor(att$strahler)
levels(att$strahcat) <- list('1st'=c('0','1'), '2nd'='2', '3rd+'=c('3','4','5') )

Unequaldsgn <- list(Perennial=list(panel=c(Panel_1=75),
                            seltype='Unequal',
                            caty.n=c('1st'=25 , '2nd'=25 ,'3rd+'=25 ),
                            over=36),
															Intermittent=list(panel=c(Panel_1=25),							seltype='Unequal',
				caty.n=c('1st'=17 , '2nd'=5 ,'3rd+'=3 ),
				over=0))

sample(100000000,1) # run to get random seed
dsgntime <- proc.time()

Unequalsites <- grts(design=Unequaldsgn,
                   DesignID='UNEQUAL',
                   type.frame='linear',
                   src.frame='shapefile',
                   in.shape='luck-ash',
                   att.frame=att,
                   stratum='PerInt',
                   mdcaty='strahcat',
                   prjfilename='luck-ash',
                   out.shape='Unequal Sites')

dsgntime <- ( proc.time() - dsgntime )/60  # time in minutes to complete design
dsgntime

##### Panels for surveys over time with unequal probability GRTS survey 
#			design with over sample and stratification.
# create strata variable
att$PerInt <- as.factor( att$minor2 )
levels(att$PerInt) <- list(Perennial='0', Intermittent='610')

# create Strahler categories for unequal probability design
att$strahcat <- as.factor(att$strahler)
levels(att$strahcat) <- list('1st'=c('0','1'), '2nd'='2', '3rd+'=c('3','4','5') )

Paneldsgn <- list(Perennial=list(panel=c(Year1=17, Year2=17, YearAll=16),,
                            seltype='Unequal',
                            caty.n=c('1st'=15 , '2nd'=15 ,'3rd+'=20 ),
                            over=50),
															Intermittent=list(panel=c(YearOnce=25),						          seltype='Unequal',										caty.n=c('1st'=17 , '2nd'=5 ,'3rd+'=3 ),						over=0))

sample(100000000,1) # run to get random seed
dsgntime <- proc.time()

Panelsites <- grts(design=Paneldsgn,
                   DesignID='UNEQUAL',
                   type.frame='linear',
                   src.frame='shapefile',
                   in.shape='luck-ash',
                   att.frame=att,
                   stratum='PerInt',
                   mdcaty='strahcat',
                   prjfilename='luck-ash',
                   out.shape='Panel Sites')

dsgntime <- ( proc.time() - dsgntime )/60  # time in minutes to complete design
dsgntime

# summary of sites

addmargins(table( Panelsites$panel,  Panelsites$mdcaty, Panelsites$stratum) )