Merge pull request #1 from baktoft/dev

Dev

.gitignore

@@ -35,3 +35,4 @@ vignettes/*.pdf
 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
 *.Rd
+.Rproj.user

README.md

@@ -1,7 +1,12 @@
-# yaps - YAPS (Yet Another Positioning Solver) (R package)
-The yaps package requires [devtools] and [TMB](https://github.com/kaskr/adcomp). 
-Please see https://github.com/kaskr/adcomp/wiki/Download for instructions on TMB installation. Remember to install Rtools needed for TMB to run.
+# YAPS - (Yet Another Positioning Solver) 
+Based on the original [YAPS](https://www.nature.com/articles/s41598-017-14278-z.pdf) presented in Baktoft, Gjelland, Økland & Thygesen (2017): Positioning of aquatic animals based on time-of-arrival and random walk models using YAPS (Yet Another Positioning Solver). DOI:10.1038/s41598-017-14278-z  
 
+A few changes have been made to improve performance and allow track estimation from random burst interval transmitters.  
+
+To use on own data, compile a toa-matrix based on synchronized hydrophone data and replace the hydros dataframe with actual hydrophone positions. 
+
+The yaps package requires [devtools](https://cran.r-project.org/web/packages/devtools/index.html) and [TMB](https://github.com/kaskr/adcomp).  
+Please see for [instructions](https://github.com/kaskr/adcomp/wiki/Download) on TMB installation. Remember to install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) as specified in the TMB documentation.
 
 Installation:
 ```
@@ -10,24 +15,23 @@ devtools::install_github("baktoft/yaps")
 ```
 
 Usage example:
+
 ```
 rm(list=ls())	
 library(yaps)
 set.seed(42)
 
-# Simulate "true" track of animal movement of n seconds
+# Simulate true track of animal movement of n seconds
 trueTrack <- simTrueTrack(model='crw', n = 15000, deltaTime=1, shape=1, scale=0.5, addDielPattern=TRUE)
 
 # Simulate telemetry observations from true track.
 # Format and parameters depend on type of transmitter burst interval (BI) - stable (sbi) or random (rbi).
 pingType <- 'rbi'
 
-if(pingType == 'sbi') {
-	# # # # stable BI
+if(pingType == 'sbi') { # stable BI
 	sbi_mean <- 5; sbi_sd <- 1e-4;
 	teleTrack <- simTelemetryTrack(trueTrack, ss='rw', pingType=pingType, sbi_mean=sbi_mean, sbi_sd=sbi_sd)
-} else if(pingType == 'rbi'){
-	# # # # random BI
+} else if(pingType == 'rbi'){ # random BI
 	pingType <- 'rbi'; rbi_min <- 20; rbi_max <- 40;
 	teleTrack <- simTelemetryTrack(trueTrack, ss='rw', pingType=pingType, rbi_min=rbi_min, rbi_max=rbi_max)
 }
@@ -49,9 +53,10 @@ maxIter <- ifelse(pingType=="sbi", 500, 5000)
 outTmb <- runTmb(inp, maxIter=maxIter, getPlsd=TRUE, getRep=TRUE)
 str(outTmb)
 
-# Estimates 
+# Estimates in pl
 pl <- outTmb$pl
-# Error estimates
+
+# Error estimates in plsd
 plsd <- outTmb$plsd
 
 # plot the resulting estimated track
@@ -60,4 +65,4 @@ lines(y~x, data=teleTrack)
 points(hy~hx, data=hydros, col="green", pch=20, cex=3)
 lines(pl$Y~pl$X, col="red")
 
-```
+```

yaps.Rproj

@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes