# File: in98adjwts_arm.txt
# Purpose: 1998 survey design for Upper Wabash Basin adjust weights
#          using DesignFile, frame information, and Site Evaluation file
# Programmer: Tony Olsen
# Date: January 2006
#
#Example updated for R 2.2.1 and psurvey.analysis 2.9
#
# Frame Stream length from RF3. Length includes all Strahler orders and possibly
# both perennial and Non-perennial streams
# The design documentation has 7663.497 km of stream; with 305.347 km in 5th-7th order
framelen <- c('Upper Wabash'=7358.150)


# Read Design File for 1998 Upper Wabash Basin
# file is in sub folder named Original Data
DesignFile <- read.delim('original_data\\inrb98.txt')
head(DesignFile)


# What are the MDcaty and StrahlerOrder present?
table(DesignFile$MDCaty)
table(DesignFile$StrahlerOrder)
table(DesignFile$StrahlerOrder,DesignFile$MDCaty)


# Import 1998 Site Evaluation file from Indiana
SiteEval <- read.delim('original_data\\siteevaluation98.txt')
head(SiteEval)

# Check codes for StatusB - Biological Site Evaluation status
table(SiteEval$StatusB)
# Note on code meanings
# TS - target and sampled site
# NT - site was non-target (dry, non-wadeable,...)
# LD - landowner denied access to site
# PB - physical barrier - unable to reach site
# OT - target site for which a sample was not collected
# UK - Unknown whether site is target or non-target (shouldn't happen)
# SCNB - target site Sampled for Chemistry but Not Biology (sampled fewer biology sites)

# Create designstatus file
designstatus <- merge(SiteEval, DesignFile, by.x='SiteIDF', by.y='SiteID')
head(designstatus)
nrow(designstatus)

# Add equal area x,y coordinates to be used in variance estimation
# Note that longitude must be changed to be negative
tmp <- marinus(designstatus$Lat.dd,-designstatus$Long.dd)
designstatus$xmarinus <- tmp[,'x']
designstatus$ymarinus <- tmp[,'y']

# Adjust weights to match frame length
# Determine which sites to include in weight adjustment.
# All 100 sites were evaluated so all should be used.
# Note that original design weights assumed sample size of 50; 
# now have sample size of 100
sites <- rep(TRUE, nrow(designstatus) )
designstatus$final.wt <- adjwgt(sites,designstatus$Weight ,
			designstatus$Basin, framelen)
			
# Check out weights. sum of final weights must equal framelen.
sum(designstatus$Weight)
sum(designstatus$final.wt)


# Write out Design Status File
write.table(designstatus, file="designstatus.csv",sep=",",row.names=FALSE)