From 9a0e2e73b806e57c1fe54abc4f6f4499d99d61cd Mon Sep 17 00:00:00 2001
From: Andre Chalom <andrechalom@gmail.com>
Date: Fri, 22 May 2015 02:08:41 -0300
Subject: [PATCH 1/3] updatesad now works for models with fixed params

---
 R/updatesad.R | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/updatesad.R b/R/updatesad.R
index eb607cb..1eaad8a 100644
--- a/R/updatesad.R
+++ b/R/updatesad.R
@@ -1,7 +1,7 @@
 ## updates a fitsad/fitrad object by running the optimizer again starting
 ## on better fit returned by profile
 updatesad <- function(object, ...) {
-	dots <- as.list(...)
+	dots <- list(...)
 	prof <- profile(object)
 	if(class(prof) == "profile.mle2") stop("Cannot update, profile did not find a better fit!")
 	newcall <- as.list(object@call)
@@ -9,9 +9,15 @@ updatesad <- function(object, ...) {
 	newcall[["control"]] <- NULL # removes the "control" slot
 	# merges the original call with arguments supplied by ...
 	for (v in names(dots)) newcall[[v]] <- dots[[v]]
-	names(newcall$start) -> name # bugfix? profile returns coefficient "prob" name as "prob.prob"
-	newcall$start <- list(prof@fullcoef) # TODO: might be coef instead? how to deal with fixed?
-	names(newcall$start) <- name
+	# bugfix? profile returns coefficient "prob" name as "prob.prob", sometimes changes parameters
+	# from start to fixed...
+	names(newcall$start) -> name 
+	for (v in name) {
+		if (v %in% names(prof@coef))
+			newcall$start[[v]] <- as.numeric(prof@coef[[v]])
+		else # then it must be in fixed
+			newcall$start[[v]] <- as.numeric(prof@call.orig$fixed[v])
+	}
 	newobj <- do.call("mle2", newcall)
 	if(class(object) == "fitsad") 
 		return (new("fitsad", newobj, sad=object@sad, distr=object@distr, trunc=object@trunc))

From b04f6148229a84e86d43b520984de87d6bd562f8 Mon Sep 17 00:00:00 2001
From: Andre Chalom <andrechalom@gmail.com>
Date: Sat, 23 May 2015 18:28:15 -0300
Subject: [PATCH 2/3] improved values for fitmand

---
 R/fitmand.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/fitmand.R b/R/fitmand.R
index 931e730..0b4b011 100644
--- a/R/fitmand.R
+++ b/R/fitmand.R
@@ -8,7 +8,9 @@ fitmand <- function(x, trunc, start.value, ...){
     if (min(y)<=trunc) stop("truncation point should be lower than the lowest data value")
   }
   if(missing(start.value)){
-    shat <- 2
+	x75 <- rad.tab[(floor(dim(rad.tab)[1]/4)):dim(rad.tab)[1],]
+    x75 <- x75[x75$abund > 1, ]
+	shat <- - coef(lm(log(abund)~log(rank), data=x75))[2]
     vhat <- 30
   }
   else{

From abcd6020480d626bc4aa2ea7373297f73a7a0e1f Mon Sep 17 00:00:00 2001
From: Andre Chalom <andrechalom@gmail.com>
Date: Thu, 28 May 2015 19:06:46 -0300
Subject: [PATCH 3/3] Quickfix for #52

plotprofmle was issuing an error when the entire profile was
lower than "ratio", i.e., no blue line was to be drawn. Fixed adding
an "if" to check for that condition
---
 R/plotprofmle.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/plotprofmle.R b/R/plotprofmle.R
index 6807b2b..40530ce 100644
--- a/R/plotprofmle.R
+++ b/R/plotprofmle.R
@@ -41,6 +41,7 @@ plotprofmle <- function(profobj, nseg=20, ratio=log(8), which=1:length(profobj@p
         change <- (interpol$y - ratio)[2:l] * (interpol$y - ratio)[1:(l-1)]
         endpoints <- which(change < 0)
         corr <- (interpol$x[2]-interpol$x[1])/2
+		if(length(endpoints) > 0)
         for (j in 1:(length(endpoints)/2)) {
           lower <-interpol$x[endpoints[(2*j)-1]]+corr
           upper <- interpol$x[endpoints[2*j]]+corr