Adjustments to utility functions and compatibility with Julia 1.4

6 files changed, 50 insertions, 17 deletions

diff --git a/.travis.yml b/.travis.yml
index ade2244..d8a0029 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,6 +2,6 @@ language: julia
 
 julia:
   - nightly
-  - 1.3
+  - 1.4
 
 codecov: true
diff --git a/src/design.jl b/src/design.jl
index 2d1a309..0b57d20 100644
--- a/src/design.jl
+++ b/src/design.jl
@@ -52,7 +52,7 @@ function add_levels(df::DataFrame)
   nlev = [n_levels(col) for col = eachcol(df)]
   maxlev = max(nlev...)
   ndf = DataFrame([rep_levels(col, maxlev) for col = eachcol(df)]) 
-  names!(ndf, names(df))
+  rename!(ndf, names(df))
   return ndf
 end
 
@@ -84,7 +84,13 @@ function add_idx!(dm::Array{UmDesign})
     x.idx = idx:(idx+np-1)
     idx += np
   end
-  return idx - 1
+  return nothing
+  #return idx - 1
+end
+
+#Get total parameters
+function get_np(dm::Array{UmDesign})
+  sum(map(x -> length(x.coefnames), dm))
 end
 
 #Transform linear predictor back to response scale
diff --git a/src/nmix.jl b/src/nmix.jl
index dd7e54d..8e1c651 100644
--- a/src/nmix.jl
+++ b/src/nmix.jl
@@ -6,7 +6,7 @@ struct Nmix <: UnmarkedModel
 end
 
 """
-    nmix(λ_formula::FormulaTerm, p_formula::FormulaTerm, data::UmData, K::Int)
+    nmix(λ_formula::FormulaTerm, p_formula::FormulaTerm, data::UmData; K::Int)
 
 Fit single-season N-mixture models. Covariates on abundance and detection 
 are specified with `λ_formula` and `p_formula`, respectively. The `UmData`
@@ -17,15 +17,17 @@ enough that the likelihood of true abundance `K` for any site is ≈ 0 (defaults
 to maximum observed count + 20). Larger `K` will increase runtime.
 """
 function nmix(λ_formula::FormulaTerm, p_formula::FormulaTerm, 
-              data::UmData, K::Union{Int,Nothing}=nothing)
+              data::UmData; K::Union{Int,Nothing}=nothing)
   
   abun = UmDesign(:Abundance, λ_formula, LogLink(), data.site_covs)
   det = UmDesign(:Detection, p_formula, LogitLink(), data.obs_covs)
-  np = add_idx!([abun, det])
+  add_idx!([abun, det])
+  np = get_np([abun, det])
 
   y = data.y
   N, J = size(y)
-  K = isnothing(K) ? maximum(skipmissing(y)) + 20 : K
+  K = check_K(K, y)
+  Kmin = get_Kmin(y)
 
   function loglik(β::Array)
   
@@ -43,10 +45,7 @@ function nmix(λ_formula::FormulaTerm, p_formula::FormulaTerm,
       end
       
       fg = zeros(eltype(β),K+1)
-      for k = 0:K       
-        if maximum(skipmissing(y[i,:])) > k
-          continue
-        end
+      for k = Kmin[i]:K 
         fk = pdf(Poisson(λ[i]), k)
         gk = 1.0
         for j = 1:J
@@ -118,7 +117,8 @@ function simulate(::Type{Nmix}, λ_form::FormulaTerm, p_form::FormulaTerm,
 
   abun = UmDesign(:Abun, λ_form, LogLink(), sc)
   det = UmDesign(:Det, p_form, LogitLink(), oc)
-  np = add_idx!([abun, det])
+  add_idx!([abun, det])
+  np = get_np([abun, det])
 
   if np != length(coef) error(string("Coef array must be length ",np)) end
 
@@ -150,7 +150,7 @@ end
 # Update ----------------------------------------------------------------------
 
 function update(fit::Nmix, data::UmData)
-  nmix(abundance(fit).formula, detection(fit).formula, data, fit.K)
+  nmix(abundance(fit).formula, detection(fit).formula, data, K=fit.K)
 end
 
 # Goodness-of-fit -------------------------------------------------------------
diff --git a/src/occupancy.jl b/src/occupancy.jl
index 39fccca..c08a05f 100644
--- a/src/occupancy.jl
+++ b/src/occupancy.jl
@@ -16,7 +16,8 @@ function occu(ψ_form::FormulaTerm, p_form::FormulaTerm, data::UmData)
   
   occ = UmDesign(:Occupancy, ψ_form, LogitLink(), data.site_covs)
   det = UmDesign(:Detection, p_form, LogitLink(), data.obs_covs)
-  np = add_idx!([occ, det])
+  add_idx!([occ, det])
+  np = get_np([occ, det])
 
   y = data.y
   N, J = size(y)
@@ -96,7 +97,8 @@ function simulate(::Type{Occu}, ψ_form::FormulaTerm, p_form::FormulaTerm,
 
   occ = UmDesign(:Occ, ψ_form, LogitLink(), sc)
   det = UmDesign(:Det, p_form, LogitLink(), oc)
-  np = add_idx!([occ, det])
+  add_idx!([occ, det])
+  np = get_np([occ, det])
 
   if np != length(coef) error(string("Coef array must be length ",np)) end
 
diff --git a/src/utils.jl b/src/utils.jl
index d4d719b..946e224 100644
--- a/src/utils.jl
+++ b/src/utils.jl
@@ -6,13 +6,13 @@ function ndetects(y::Array)
   mapslices(sum2, y, dims=2)
 end
 
-#Simulate random covariate frame based on provided formula"
+#Simulate random covariate frame based on provided formula
 function gen_covs(f::FormulaTerm, n::Int)  
   covs = varnames(f).rhs
   if isnothing(covs) return DataFrame(_dummy=ones(n)) end 
   nc = length(covs)
   out = DataFrame(reshape(rand(Normal(0,1), n*nc), n, nc))
-  DataFrames.names!(out, covs)
+  DataFrames.rename!(out, covs)
   out
 end
 
@@ -22,3 +22,27 @@ function rep_missing!(ynew::Array, y::Array)
   if length(na_idx) == 0 return nothing end
   ynew[na_idx] = fill(missing, length(na_idx))
 end
+
+#Get appropriate value of K
+function check_K(K::Int, y::Array{Union{Missing,Int},2})
+  if(K < (maximum(skipmissing(y))))
+    error("K should be larger than the maximum observed abundance")
+  end
+  K
+end
+
+function check_K(K::Nothing, y::Array{Union{Missing,Int},2})
+  maximum(skipmissing(y)) + 20
+end
+
+#Get minimum bound for integrating over possible abundance values K
+#Minimum bound = maximum abundance ever observed at a site
+function get_Kmin(y::Array{Union{Missing,Int64},2})
+  N = size(y, 1)
+  kmin = zeros(Int64, N)
+  for n in 1:N
+    if(all(ismissing.(y[n, :]))) continue end 
+    kmin[n] = maximum(skipmissing(y[n, :]))
+  end
+  kmin
+end
diff --git a/test/test_design.jl b/test/test_design.jl
index c4518c7..9176585 100644
--- a/test/test_design.jl
+++ b/test/test_design.jl
@@ -26,6 +26,7 @@
   Unmarked.add_idx!([umd, umd2])
   @test isequal(umd.idx, 1:3)
   @test isequal(umd2.idx, 4:4)
+  @test isequal(Unmarked.get_np([umd, umd2]), 4)
 
   #Test transform
   tr = logistic.(umd.mat * [0,0.3,0.5])