From cec414d060d43599c00722d3a8be4f3b1af22aab Mon Sep 17 00:00:00 2001
From: Gabriel Bowen <gabe.bowen@utah.edu>
Date: Fri, 4 Aug 2023 17:27:39 -0600
Subject: [PATCH] Update mixSource add eprior

---
 CRAN-SUBMISSION     |   3 +++
 R/sysdata.rda       | Bin 526 -> 546 bytes
 R/watercomp.R       |   8 ++++----
 data-raw/prepData.R |   2 +-
 man/mixSource.Rd    |   9 ++++++---
 5 files changed, 14 insertions(+), 8 deletions(-)
 create mode 100644 CRAN-SUBMISSION

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
new file mode 100644
index 0000000..f200cba
--- /dev/null
+++ b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 1.1.2
+Date: 2023-08-04 16:49:40 UTC
+SHA: 14b0b7fe83101169593c0a08727218e727b39e5d
diff --git a/R/sysdata.rda b/R/sysdata.rda
index 7ae57f6b33bb8dcb639badb41b4170b3bb68ebe4..91f6a4f705821895d09fa214321a53c2aec1d041 100644
GIT binary patch
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diff --git a/R/watercomp.R b/R/watercomp.R
index 0669a51..c5e8659 100644
--- a/R/watercomp.R
+++ b/R/watercomp.R
@@ -102,8 +102,8 @@ mwlSource = function(obs, MWL = NULL, slope, stype = 1, ngens=1e4, ncores = 1){
 
 #takes values of observed and hypothesized endmember source waters (each type 'iso'),hypothesized EL slope,
 #prior (as relative contribution of each source to mixture), and number of parameter draws
-mixSource = function(obs, sources, slope, prior=rep(1,nrow(sources)), 
-                   shp=1, ngens=1e5, ncores = 1){
+mixSource = function(obs, sources, slope, mixprior=rep(1,nrow(sources)), 
+                   shp=1, eprior = c(0, 15), ngens=1e5, ncores = 1){
 
   if(!inherits(obs, "iso")){
     warning("Expecting iso object for obs, this argument may be
@@ -143,13 +143,13 @@ mixSource = function(obs, sources, slope, prior=rep(1,nrow(sources)),
   }
   
   #dirchlet priors
-  alphas = prior/min(prior) * shp
+  alphas = mixprior/min(mixprior) * shp
   
   #data
   d = list(nsource = nsource, ndat = ndat, 
            obs = obs, obs.vcov = obs.vcov,
            sources = sources, sources.vcov = sources.vcov,
-           alphas = alphas, slope = slope)
+           alphas = alphas, eprior = eprior, slope = slope)
   
   #parameters
   p = c("mixture_d2H", "mixture_d18O", "fracs", "S", "E")
diff --git a/data-raw/prepData.R b/data-raw/prepData.R
index a5200ba..2ea1373 100644
--- a/data-raw/prepData.R
+++ b/data-raw/prepData.R
@@ -35,7 +35,7 @@ mixModel = "model{
   o_pred = mixture_d18O + E
   
   #evap prior
-  E ~ dunif(0, 15)
+  E ~ dunif(eprior[1], eprior[2])
   
   #EL slope prior
   S ~ dnorm(slope[1], 1 / slope[2] ^ 2)
diff --git a/man/mixSource.Rd b/man/mixSource.Rd
index 17cc09b..11b6f4b 100644
--- a/man/mixSource.Rd
+++ b/man/mixSource.Rd
@@ -11,8 +11,8 @@ Given isotopic compositions of two or more potential sources, generate a posteri
 }
 
 \usage{
-mixSource(obs, sources, slope, prior = rep(1,nrow(sources)), shp = 1, 
-            ngens = 1e5, ncores = 1)
+mixSource(obs, sources, slope, mixprior = rep(1,nrow(sources)), shp = 1, 
+            eprior = c(0, 15), ngens = 1e5, ncores = 1)
 }
 
 \arguments{
@@ -25,12 +25,15 @@ mixSource(obs, sources, slope, prior = rep(1,nrow(sources)), shp = 1,
   \item{slope}{
   numeric. Vector of length two specifying prior parameters for the evaporation line slope (mean, standard deviation).
   }
-  \item{prior}{
+  \item{mixprior}{
   numeric. Vector of length equal to the number of sources, giving prior estimates of relative contributions of different sources.
   }
   \item{shp}{
   numeric. Shape parameter constant used in specifying prior estimates of source contributions (see Details). 
   }
+  \item{eprior}{
+  numeric. Vector of length 2 giving prior estimates of maximum and minimum oxygen isotope evaporation effect.
+  }
   \item{ngens}{
   integer. Number of posterior samples to obtain (per chain).
   }