diff --git a/.Rbuildignore b/.Rbuildignore
index 2227617..305ab98 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,4 +1,6 @@
 ^\.git$
 ^\.travis\.yml$
 ^shiny$
-^examples$
\ No newline at end of file
+^examples$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index ad8f404..f7d30e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,6 @@
 *.so
 shiny/database/
 shiny/testing/
-shiny/global_coverage.png
\ No newline at end of file
+shiny/global_coverage.png
+.Rproj.user
+*.Rproj
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
index 8258d9d..21d4885 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -45,6 +45,43 @@ r_packages:
   - mapdata
   - TMB
 
+cache: packages
+
+sudo: required
+
+dist: trusty
+
+addons:
+  postgresql: "9.6"
+
+before_install:
+  - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes
+  - sudo apt-get --yes --force-yes update -qq
+  - sudo apt-get install --yes libudunits2-dev libproj-dev libgeos-dev libgdal-dev
+  - # install postgis from source:
+  - sudo apt-get --yes install libjson-c-dev postgresql-server-dev-9.6
+  - wget http://download.osgeo.org/postgis/source/postgis-2.3.2.tar.gz
+  - (mv postgis* /tmp; cd /tmp; tar xzf postgis-2.3.2.tar.gz)
+  - (cd /tmp/postgis-2.3.2 ; ./configure; make; sudo make install)
+  - # activate liblwgeom:
+  - sudo ldconfig
+  - # create postgis databases:
+  - sudo service postgresql restart
+  - createdb postgis
+  - psql -d postgis -c "CREATE EXTENSION postgis;"
+  - psql -d postgis -c "GRANT CREATE ON DATABASE postgis TO travis"
+  - createdb empty
+  - psql -d empty -c "CREATE EXTENSION postgis;"
+
+warnings_are_errors: true
+
+after_success:
+  - dropdb postgis
+  - createdb postgis
+  - psql -d postgis -c "CREATE EXTENSION postgis;"
+  - psql -d postgis -c "GRANT CREATE ON DATABASE postgis TO travis"
+  - Rscript -e 'covr::codecov()'
+
 r_github_packages:
   - kaskr/TMB_contrib_R/TMBhelper
 
diff --git a/DESCRIPTION b/DESCRIPTION
index e4c2c98..f91e1f9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,7 +12,7 @@ Description: SpatialDeltaGLMM is an R package for implementing a spatial delta-
     functions and model-comparison tools, and (3) is intended to improve analysis
     speed, replicability, peer-review, and interpretation of index standardization.
     methods
-Imports: 
+Imports:
     graphics,
     utils,
     mapproj,
@@ -31,17 +31,21 @@ Imports:
     maps,
     mapdata,
     TMB,
-    MatrixModels  
-Depends: 
+    MatrixModels  ,
+    dplyr,
+    purrr,
+    sf,
+    rgdal
+Depends:
     R (>= 3.1.0),
-Suggests: 
+Suggests:
     INLA,
     testthat
-Additional_repositories: 
+Additional_repositories:
     https://www.math.ntnu.no/inla/R/stable
 License: GPL-2
 LazyData: yes
 BuildVignettes: yes
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
 URL: http://github.com/nwfsc-assess/geostatistical_delta-GLMM
 BugReports: http://github.com/nwfsc-assess/geostatistical_delta-GLMM/issues
diff --git a/NAMESPACE b/NAMESPACE
index 129773f..412f725 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -36,6 +36,7 @@ export(Spatial_Information_Fn)
 export(Summarize)
 export(Vessel_Fn)
 export(bilinear_interp)
+export(convert_utm_to_ll_fn)
 export(match_strata_fn)
 export(plot_residuals)
 export(summary_nwfsc)
diff --git a/R/Spatial_Information_Fn.R b/R/Spatial_Information_Fn.R
index a1cea41..1382b3c 100644
--- a/R/Spatial_Information_Fn.R
+++ b/R/Spatial_Information_Fn.R
@@ -1,4 +1,6 @@
 
+
+
 #' Build objects related to spatial information
 #'
 #' \code{Spatial_Information_Fn} builds a tagged list with all the spatial information needed for \code{Data_Fn}
@@ -17,78 +19,174 @@
 #'   \item{MeshList}{A tagged list with inputs related to the SPDE mesh}
 #'   \item{GridList}{A tagged list with inputs related to the 2D AR1 grid}
 #'   \item{a_xl}{A data frame with areas for each knot and each strattum}
-#'   \item{loc_UTM}{A data frame with the converted UTM coordinates for each sample}
+#'   \item{loc_x}{The UTM location for each knot}
+#'   \item{loc_x_lat_long}{A data frame with the corrected lat long for each knot}
 #'   \item{Kmeans}{Output from \code{Calc_Kmeans} with knots for a triangulated mesh}
 #'   \item{knot_i}{The knot associated with each sample}
 #'   \item{Method}{The Method input (for archival purposes)}
-#'   \item{loc_x}{The UTM location for each knot}
 #' }
 
 #' @export
-Spatial_Information_Fn = function( n_x, Lon, Lat, Extrapolation_List, Method="Mesh", grid_size_km=50, grid_size_LL=1, ... ){
-
+Spatial_Information_Fn = function(n_x,
+                                  Lon,
+                                  Lat,
+                                  Extrapolation_List,
+                                  Method = "Mesh",
+                                  grid_size_km = 50,
+                                  grid_size_LL = 1,
+                                  ...) {
   # Convert to an Eastings-Northings coordinate system
-  if( Method=="Spherical_mesh" ){
-    loc_i = data.frame( 'Lon'=Lon, 'Lat'=Lat )
+  if (Method == "Spherical_mesh") {
+    loc_i = data.frame('Lon' = Lon, 'Lat' = Lat)
     # Bounds for 2D AR1 grid
-    Grid_bounds = (grid_size_km/110) * apply(Extrapolation_List$Data_Extrap[,c('Lon','Lat')]/(grid_size_km/110), MARGIN=2, FUN=function(vec){trunc(range(vec))+c(0,1)})
+    Grid_bounds = (grid_size_km / 110) * apply(
+      Extrapolation_List$Data_Extrap[, c('Lon', 'Lat')] / (grid_size_km / 110),
+      MARGIN = 2,
+      FUN = function(vec) {
+        trunc(range(vec)) + c(0, 1)
+      }
+    )
 
     # Calculate k-means centroids
-    Kmeans = SpatialDeltaGLMM::Calc_Kmeans(n_x=n_x, loc_orig=loc_i[,c("Lon", "Lat")], ... )
+    Kmeans = SpatialDeltaGLMM::Calc_Kmeans(n_x = n_x, loc_orig = loc_i[, c("Lon", "Lat")], ...)
 
     # Calculate grid for 2D AR1 process
-    loc_grid = expand.grid( 'Lon'=seq(Grid_bounds[1,1],Grid_bounds[2,1],by=grid_size_LL), 'Lat'=seq(Grid_bounds[1,2],Grid_bounds[2,2],by=grid_size_LL) )
-    Which = sort(unique(RANN::nn2(data=loc_grid, query=Extrapolation_List$Data_Extrap[which(Extrapolation_List$Area_km2_x>0),c('Lon','Lat')], k=1)$nn.idx[,1]))
+    loc_grid = expand.grid(
+      'Lon' = seq(Grid_bounds[1, 1], Grid_bounds[2, 1], by = grid_size_LL),
+      'Lat' = seq(Grid_bounds[1, 2], Grid_bounds[2, 2], by = grid_size_LL)
+    )
+    Which = sort(unique(
+      RANN::nn2(
+        data = loc_grid,
+        query = Extrapolation_List$Data_Extrap[which(Extrapolation_List$Area_km2_x >
+                                                       0), c('Lon', 'Lat')],
+        k = 1
+      )$nn.idx[, 1]
+    ))
     loc_grid = loc_grid[Which,]
-    grid_num = RANN::nn2( data=loc_grid, query=loc_i, k=1)$nn.idx[,1]
+    grid_num = RANN::nn2(data = loc_grid,
+                         query = loc_i,
+                         k = 1)$nn.idx[, 1]
   }
-  if( Method %in% c("Mesh","Grid") ){
-    loc_i = SpatialDeltaGLMM::Convert_LL_to_UTM_Fn( Lon=Lon, Lat=Lat, zone=Extrapolation_List$zone, flip_around_dateline=Extrapolation_List$flip_around_dateline )                                                         #$
-    loc_i = cbind( 'E_km'=loc_i[,'X'], 'N_km'=loc_i[,'Y'])
+
+
+  if (Method %in% c("Mesh", "Grid")) {
+    loc_i = SpatialDeltaGLMM::Convert_LL_to_UTM_Fn(
+      Lon = Lon,
+      Lat = Lat,
+      zone = Extrapolation_List$zone,
+      flip_around_dateline = Extrapolation_List$flip_around_dateline
+    )                                                         #$
+    loc_i = cbind('E_km' = loc_i[, 'X'], 'N_km' = loc_i[, 'Y'])
     # Bounds for 2D AR1 grid
-    Grid_bounds = grid_size_km * apply(Extrapolation_List$Data_Extrap[,c('E_km','N_km')]/grid_size_km, MARGIN=2, FUN=function(vec){trunc(range(vec))+c(0,1)})
+    Grid_bounds = grid_size_km * apply(
+      Extrapolation_List$Data_Extrap[, c('E_km', 'N_km')] / grid_size_km,
+      MARGIN = 2,
+      FUN = function(vec) {
+        trunc(range(vec)) + c(0, 1)
+      }
+    )
 
     # Calculate k-means centroids
-    Kmeans = SpatialDeltaGLMM::Calc_Kmeans(n_x=n_x, loc_orig=loc_i[,c("E_km", "N_km")], ... )
+    Kmeans = SpatialDeltaGLMM::Calc_Kmeans(n_x = n_x, loc_orig = loc_i[, c("E_km", "N_km")], ...)
 
     # Calculate grid for 2D AR1 process
-    loc_grid = expand.grid( 'E_km'=seq(Grid_bounds[1,1],Grid_bounds[2,1],by=grid_size_km), 'N_km'=seq(Grid_bounds[1,2],Grid_bounds[2,2],by=grid_size_km) )
-    Which = sort(unique(RANN::nn2(data=loc_grid, query=Extrapolation_List$Data_Extrap[which(Extrapolation_List$Area_km2_x>0),c('E_km','N_km')], k=1)$nn.idx[,1]))
+    loc_grid = expand.grid(
+      'E_km' = seq(Grid_bounds[1, 1], Grid_bounds[2, 1], by = grid_size_km),
+      'N_km' = seq(Grid_bounds[1, 2], Grid_bounds[2, 2], by = grid_size_km)
+    )
+    Which = sort(unique(
+      RANN::nn2(
+        data = loc_grid,
+        query = Extrapolation_List$Data_Extrap[which(Extrapolation_List$Area_km2_x >
+                                                       0), c('E_km', 'N_km')],
+        k = 1
+      )$nn.idx[, 1]
+    ))
     loc_grid = loc_grid[Which,]
-    grid_num = RANN::nn2( data=loc_grid, query=loc_i, k=1)$nn.idx[,1]
+    grid_num = RANN::nn2(data = loc_grid,
+                         query = loc_i,
+                         k = 1)$nn.idx[, 1]
   }
 
   # Calc design matrix and areas
-  if( Method=="Grid" ){
+  if (Method == "Grid") {
     knot_i = grid_num
     loc_x = loc_grid
   }
-  if( Method %in% c("Mesh","Spherical_mesh") ){
+  if (Method %in% c("Mesh", "Spherical_mesh")) {
     knot_i = Kmeans$cluster
     loc_x = Kmeans$centers
   }
-  PolygonList = Calc_Polygon_Areas_and_Polygons_Fn( loc_x=loc_x, Data_Extrap=Extrapolation_List[["Data_Extrap"]], a_el=Extrapolation_List[["a_el"]])
-  a_xl = PolygonList[["a_xl"]]
 
+  eastings <- loc_x[, 'E_km']
+
+  northings <- loc_x[, 'N_km']
+
+  zone <- Extrapolation_List$zone
+
+  flip_around_dateline <- Extrapolation_List$flip_around_dateline
+  loc_x_lat_long <-
+    convert_utm_to_ll_fn(
+      eastings = eastings,
+      northings = northings,
+      zone = zone,
+      flip_around_dateline = flip_around_dateline
+    )
+
+  loc_x_lat_long$knot <- 1:nrow(loc_x_lat_long)
+
+  if (flip_around_dateline == T){
+    warning("knots have been flipped around dateline; eastings locations and UTM zone are transformed - see loc_x_lat_long for corrected locations")
+  }
+
+  PolygonList = Calc_Polygon_Areas_and_Polygons_Fn(loc_x = loc_x,
+                                                   Data_Extrap = Extrapolation_List[["Data_Extrap"]],
+                                                   a_el = Extrapolation_List[["a_el"]])
+  a_xl = PolygonList[["a_xl"]]
   # Convert loc_x back to location in lat-long coordinates loc_x_LL
   # if zone=NA or NULL, then it automatically detects appropriate zone
-  #tmpUTM = cbind('PID'=1,'POS'=1:nrow(loc_x),'X'=loc_x[,'E_km'],'Y'=loc_x[,'N_km'])
-  #attr(tmpUTM,"projection") = "UTM"
-  #attr(tmpUTM,"zone") = Extrapolation_List$zone
-  #loc_x_LL = PBSmapping::convUL(tmpUTM)                                                         #$
+  # tmpUTM = cbind('PID'=1,'POS'=1:nrow(loc_x),'X'=loc_x[,'E_km'],'Y'=loc_x[,'N_km'])
+  # attr(tmpUTM,"projection") = "UTM"
+  # attr(tmpUTM,"zone") = Extrapolation_List$zone
+  # loc_x_LL = PBSmapping::convUL(tmpUTM)                                                         #$
 
   # Make mesh and info for anisotropy  SpatialDeltaGLMM::
-  MeshList = Calc_Anisotropic_Mesh( Method=Method, loc_x=Kmeans$centers )
+  MeshList = Calc_Anisotropic_Mesh(Method = Method, loc_x = Kmeans$centers)
 
   # Make matrices for 2D AR1 process
-  Dist_grid = dist(loc_grid, diag=TRUE, upper=TRUE)
-  M0 = as( ifelse(as.matrix(Dist_grid)==0, 1, 0), "dgTMatrix" )
-  M1 = as( ifelse(as.matrix(Dist_grid)==grid_size_km, 1, 0), "dgTMatrix" )
-  M2 = as( ifelse(as.matrix(Dist_grid)==sqrt(2)*grid_size_km, 1, 0), "dgTMatrix" )
-  if( Method=="Spherical_mesh" ) GridList = list("M0"=M0, "M1"=M1, "M2"=M2, "grid_size_km"=grid_size_LL)
-  if( Method %in% c("Mesh","Grid") ) GridList = list("M0"=M0, "M1"=M1, "M2"=M2, "grid_size_km"=grid_size_km)
+  Dist_grid = dist(loc_grid, diag = TRUE, upper = TRUE)
+  M0 = as(ifelse(as.matrix(Dist_grid) == 0, 1, 0), "dgTMatrix")
+  M1 = as(ifelse(as.matrix(Dist_grid) == grid_size_km, 1, 0), "dgTMatrix")
+  M2 = as(ifelse(as.matrix(Dist_grid) == sqrt(2) * grid_size_km, 1, 0), "dgTMatrix")
+  if (Method == "Spherical_mesh")
+    GridList = list(
+      "M0" = M0,
+      "M1" = M1,
+      "M2" = M2,
+      "grid_size_km" = grid_size_LL
+    )
+  if (Method %in% c("Mesh", "Grid"))
+    GridList = list(
+      "M0" = M0,
+      "M1" = M1,
+      "M2" = M2,
+      "grid_size_km" = grid_size_km
+    )
 
   # Return
-  Return = list("MeshList"=MeshList, "GridList"=GridList, "a_xl"=a_xl, "loc_i"=loc_i, "Kmeans"=Kmeans, "knot_i"=knot_i, "Method"=Method, "loc_x"=loc_x, "PolygonList"=PolygonList, "NN_Extrap"=PolygonList$NN_Extrap)
-  return( Return )
+  Return = list(
+    "MeshList" = MeshList,
+    "GridList" = GridList,
+    "a_xl" = a_xl,
+    "loc_i" = loc_i,
+    "Kmeans" = Kmeans,
+    "knot_i" = knot_i,
+    "Method" = Method,
+    "loc_x" = loc_x,
+    "loc_x_lat_long" = loc_x_lat_long,
+    "PolygonList" = PolygonList,
+    "NN_Extrap" = PolygonList$NN_Extrap
+  )
+  return(Return)
 }
diff --git a/R/convert_utm_to_ll_fn.R b/R/convert_utm_to_ll_fn.R
new file mode 100644
index 0000000..31a5283
--- /dev/null
+++ b/R/convert_utm_to_ll_fn.R
@@ -0,0 +1,75 @@
+#' Convert from UTM to Lat-long
+#'
+#' If eastings and northings have been flipped
+#' around dateline, will convert back and provide estimtes of "original" lat lon
+#' Values should be viewed as estimates for plotting and general pairing
+#'
+#' @param eastings eastings of points, paired to northings
+#' @param northings northings of points,  paired to eastings
+#' @param zone UTM zone of points
+#' @param flip_around_dateline logical stating if points have been flipped around the dateline
+#' @param meters_per_utm_unit meters per easting/northing
+#'
+#' @return a data.frame with
+#' \describe{
+#' \item{approx_long}{the approximate transformed longitude of each UTM point}
+#' \item{approx_lat}{the approximate transformed latitude of each UTM point}
+#' }
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' eastings <- Spatial_List$loc_x[,'E_km']
+#'
+#' northings <- Spatial_List$loc_x[,'N_km']
+#'
+#' zone <- Extrapolation_List$zone
+#'
+#' flip_around_dateline <- Extrapolation_List$flip_around_dateline
+#'
+#' latlongs <- convert_utm_to_ll_fn(eastings = eastings, northings = northings, zone = zone, flip_around_dateline = flip_around_dateline)
+#'
+#' ggmap::qmplot(x = approx_long, y = approx_lat, data = latlongs, color = 'red')
+#' }
+convert_utm_to_ll_fn <-
+  function(eastings,
+           northings,
+           zone,
+           flip_around_dateline = T,
+           meters_per_utm_unit = 1000) {
+    require(dplyr)
+    # on.exit(detach('package:dplyr'))
+
+if (length(eastings) != length(northings)){
+  stop('eastings and northings are not same length, make sure that they represent paired coordinates')
+}
+
+    utm_coords <-
+      data.frame(easting = eastings, northing = northings) %>%
+      dplyr::mutate(geometry = purrr::map2(eastings, northing, ~ sf::st_point(
+        x = c(.x * meters_per_utm_unit, .y * meters_per_utm_unit), dim = 'XY'
+      ))) %>% # assign a spatial geometry to each knot
+      ungroup() %>%
+      mutate(geometry = sf::st_sfc(geometry, crs = paste0(
+        "+proj=utm +zone=", zone
+      ))) %>%
+      sf::st_sf() # convert to a sf object in UTM projection for supplied zone
+
+
+    ll_coords <-
+      sf::st_transform(utm_coords, crs = "+proj=longlat") #convert to long-lat projection
+
+    ll_geometry <- sf::st_geometry(ll_coords)
+
+    extract_ll <- function(x) {
+      data.frame(approx_long = x[1], approx_lat = x[2])
+    }
+    ll_coords <-  purrr::map_df(ll_geometry, extract_ll) # extract transformed long/lat for knots
+
+    if (flip_around_dateline == T) { # if UTM coordinates were flipped around deadline, reverse flip
+      ll_coords <-
+        dplyr::mutate(ll_coords, approx_long = purrr::map_dbl(approx_long, ~ ifelse(.x > 0, .x - 180, .x + 180)))
+    }
+    return(ll_coords)
+
+  }
\ No newline at end of file
diff --git a/man/Build_TMB_Fn.Rd b/man/Build_TMB_Fn.Rd
index 9283058..8ba1e2f 100644
--- a/man/Build_TMB_Fn.Rd
+++ b/man/Build_TMB_Fn.Rd
@@ -61,4 +61,3 @@ Tagged list containing objects for running a VAST model
 \description{
 \code{Build_TMB_Fn} builds a tagged list with everything necessary to run or interpret inputs to a geostatistical delta-GLMM
 }
-
diff --git a/man/Calc_Anisotropic_Mesh.Rd b/man/Calc_Anisotropic_Mesh.Rd
index cc434a7..06278d8 100644
--- a/man/Calc_Anisotropic_Mesh.Rd
+++ b/man/Calc_Anisotropic_Mesh.Rd
@@ -24,4 +24,3 @@ Tagged list containing distance metrics
 \description{
 \code{Calc_Anistropic_Mesh} builds a tagged list representing distances for isotropic or geometric anisotropic triangulated mesh
 }
-
diff --git a/man/Calc_Kmeans.Rd b/man/Calc_Kmeans.Rd
index 9b65031..028a231 100644
--- a/man/Calc_Kmeans.Rd
+++ b/man/Calc_Kmeans.Rd
@@ -32,4 +32,3 @@ Tagged list containing outputs
 \description{
 \code{Calc_Kmeans} determines the location for a set of knots for approximating spatial variation
 }
-
diff --git a/man/Calc_Polygon_Areas_and_Polygons_Fn.Rd b/man/Calc_Polygon_Areas_and_Polygons_Fn.Rd
index 3227591..bc415a9 100644
--- a/man/Calc_Polygon_Areas_and_Polygons_Fn.Rd
+++ b/man/Calc_Polygon_Areas_and_Polygons_Fn.Rd
@@ -25,4 +25,3 @@ Tagged list containing distance metrics
 \description{
 \code{Calc_Polygon_Areas_and_Polygons_Fn} builds outputs for a given triangulated mesh used for approximating spatial variation
 }
-
diff --git a/man/Check_encounter_prob.Rd b/man/Check_encounter_prob.Rd
index 6339b7b..73f0dd4 100644
--- a/man/Check_encounter_prob.Rd
+++ b/man/Check_encounter_prob.Rd
@@ -29,4 +29,3 @@ Return Tagged list of output
 \description{
 \code{Check_encounter_prob} is a diagnostic function for checking validity of the encounter-probability component of a spatio-temporal model
 }
-
diff --git a/man/Convert_LL_to_UTM_Fn.Rd b/man/Convert_LL_to_UTM_Fn.Rd
index 10e40fc..ffaf360 100644
--- a/man/Convert_LL_to_UTM_Fn.Rd
+++ b/man/Convert_LL_to_UTM_Fn.Rd
@@ -25,4 +25,3 @@ A data frame with the following columns
 \description{
 \code{Convert_LL_to_UTM_Fn} converts from Latitude-Longitude to Universal Transverse Mercator projections for a given location
 }
-
diff --git a/man/Data_Fn.Rd b/man/Data_Fn.Rd
index d527f64..6603a6f 100644
--- a/man/Data_Fn.Rd
+++ b/man/Data_Fn.Rd
@@ -71,4 +71,3 @@ Tagged list containing inputs to function Build_TMB_Fn()
 \description{
 \code{Data_Fn} builds a tagged list of data inputs used by TMB for running the model
 }
-
diff --git a/man/Geostat_Sim.Rd b/man/Geostat_Sim.Rd
index 2b69abf..33aa82e 100644
--- a/man/Geostat_Sim.Rd
+++ b/man/Geostat_Sim.Rd
@@ -39,4 +39,3 @@ Return Tagged list of output
 ## SimList = SpatialDeltaGLMM::Geostat_Sim(Sim_Settings=list(), Extrapolation_List, Data_Geostat=Data_Geostat )
 ## Data_Sim = SimList$Data_Geostat
 }
-
diff --git a/man/Param_Fn.Rd b/man/Param_Fn.Rd
index 8ec293a..085bf9a 100644
--- a/man/Param_Fn.Rd
+++ b/man/Param_Fn.Rd
@@ -59,4 +59,3 @@ Tagged list containing starting values for all fixed effects (parameters) and ra
 \description{
 \code{Param_Fn} generates the \code{parameters} input for \code{TMB::MakeADFun}
 }
-
diff --git a/man/PlotIndex_Fn.Rd b/man/PlotIndex_Fn.Rd
index 3eb1b33..8633d5f 100644
--- a/man/PlotIndex_Fn.Rd
+++ b/man/PlotIndex_Fn.Rd
@@ -8,7 +8,8 @@ PlotIndex_Fn(TmbData, Sdreport, Year_Set = NULL, Years2Include = NULL,
   DirName = paste0(getwd(), "/"), PlotName = "Index.png",
   interval_width = 1, strata_names = NULL, category_names = NULL,
   use_biascorr = FALSE, plot_legend = TRUE, total_area_km2 = NULL,
-  plot_log = FALSE, width = 4, height = 4, ...)
+  plot_log = FALSE, width = 4, height = 4, treat_missing_as_zero = TRUE,
+  ...)
 }
 \arguments{
 \item{TmbData}{Formatted data inputs, from `SpatialDeltaGLMM::Data_Fn(...)`}
@@ -41,6 +42,8 @@ PlotIndex_Fn(TmbData, Sdreport, Year_Set = NULL, Years2Include = NULL,
 
 \item{height}{plot height in inches}
 
+\item{treat_missing_as_zero}{Boolean whether to treat years and species with no (or only NA) data as instances where the index should be zero}
+
 \item{...}{Other inputs to `par()`}
 }
 \value{
@@ -52,4 +55,3 @@ Return Tagged list of output
 \description{
 \code{PlotIndex_Fn} plots an index proportion to population abundance
 }
-
diff --git a/man/PlotMap_Fn.Rd b/man/PlotMap_Fn.Rd
index 8303856..ae682d7 100644
--- a/man/PlotMap_Fn.Rd
+++ b/man/PlotMap_Fn.Rd
@@ -47,4 +47,3 @@ truncating the cocuntry boundaries within the plotting region (which \code{mappr
 so that the post-projection is often missing boundaries that are within the plotting rectangle).  I use rectangular projections by default, but Lamberts or Albers conformal
 projections would also be useful for many cases.
 }
-
diff --git a/man/PlotResultsOnMap_Fn.Rd b/man/PlotResultsOnMap_Fn.Rd
index ff82e06..3c33c41 100644
--- a/man/PlotResultsOnMap_Fn.Rd
+++ b/man/PlotResultsOnMap_Fn.Rd
@@ -65,4 +65,3 @@ Mat_xt a matrix (rows: modeled knots; column: modeled year) for plotted output o
 \description{
 \code{PlotResultsOnMap_Fn} plots a standard set of diagnostic maps
 }
-
diff --git a/man/Plot_data_and_knots.Rd b/man/Plot_data_and_knots.Rd
index a8a62f2..ff3e503 100644
--- a/man/Plot_data_and_knots.Rd
+++ b/man/Plot_data_and_knots.Rd
@@ -23,4 +23,3 @@ Plot_data_and_knots(Extrapolation_List, Spatial_List, Data_Geostat,
 \description{
 \code{Plot_data_and_knots} produces diagnostics plots for the spatial distribution of data and knots
 }
-
diff --git a/man/Plot_range_shifts.Rd b/man/Plot_range_shifts.Rd
index ac4f964..c3f64e6 100644
--- a/man/Plot_range_shifts.Rd
+++ b/man/Plot_range_shifts.Rd
@@ -49,4 +49,3 @@ Return Tagged list of output
 \description{
 \code{Plot_range_shifts} plots center-of-gravity, kernel-area occupied, and effective-area occupied
 }
-
diff --git a/man/Prepare_Extrapolation_Data_Fn.Rd b/man/Prepare_Extrapolation_Data_Fn.Rd
index a2737d4..6745574 100644
--- a/man/Prepare_Extrapolation_Data_Fn.Rd
+++ b/man/Prepare_Extrapolation_Data_Fn.Rd
@@ -29,4 +29,3 @@ Tagged list used in other functions
 \description{
 \code{Prepare_Extrapolation_Data_Fn} builds an object used to determine areas to extrapolation densities to when calculating indices
 }
-
diff --git a/man/SpatialDeltaGLMM.Rd b/man/SpatialDeltaGLMM.Rd
index 39b0e37..b9c1680 100644
--- a/man/SpatialDeltaGLMM.Rd
+++ b/man/SpatialDeltaGLMM.Rd
@@ -11,4 +11,3 @@ Spatial delta-generalized linear mixed model (`SpatialDeltaGLMM`) is used for es
 \details{
 Please see examples folder on github \url{http://github.com/nwfsc-assess/geostatistical_delta-GLMM/tree/master/examples} for up-to-date examples
 }
-
diff --git a/man/Spatial_Information_Fn.Rd b/man/Spatial_Information_Fn.Rd
index a64fab1..d035137 100644
--- a/man/Spatial_Information_Fn.Rd
+++ b/man/Spatial_Information_Fn.Rd
@@ -30,14 +30,13 @@ Tagged list containing objects for running a VAST model
   \item{MeshList}{A tagged list with inputs related to the SPDE mesh}
   \item{GridList}{A tagged list with inputs related to the 2D AR1 grid}
   \item{a_xl}{A data frame with areas for each knot and each strattum}
-  \item{loc_UTM}{A data frame with the converted UTM coordinates for each sample}
+  \item{loc_x}{The UTM location for each knot}
+  \item{loc_x_lat_long}{A data frame with the corrected lat long for each knot}
   \item{Kmeans}{Output from \code{Calc_Kmeans} with knots for a triangulated mesh}
   \item{knot_i}{The knot associated with each sample}
   \item{Method}{The Method input (for archival purposes)}
-  \item{loc_x}{The UTM location for each knot}
 }
 }
 \description{
 \code{Spatial_Information_Fn} builds a tagged list with all the spatial information needed for \code{Data_Fn}
 }
-
diff --git a/man/Summarize.Rd b/man/Summarize.Rd
index 14d480c..cbe9915 100644
--- a/man/Summarize.Rd
+++ b/man/Summarize.Rd
@@ -22,4 +22,3 @@ Tagged list of useful output
 \details{
 Please post on the GitHub issue tracker if you'd like for another specific output to be added and documented here
 }
-
diff --git a/man/Vessel_Fn.Rd b/man/Vessel_Fn.Rd
index 2a2f3e3..42640df 100644
--- a/man/Vessel_Fn.Rd
+++ b/man/Vessel_Fn.Rd
@@ -19,4 +19,3 @@ Return Tagged list of output
 \description{
 \code{Vessel_Fn} plots estimated vessel effects for model components
 }
-
diff --git a/man/bilinear_interp.Rd b/man/bilinear_interp.Rd
index 90c1c59..16dbfcc 100644
--- a/man/bilinear_interp.Rd
+++ b/man/bilinear_interp.Rd
@@ -32,4 +32,3 @@ Tagged list of useful output
   # Should equal 1.7
   }
 }
-
diff --git a/man/convert_utm_to_ll_fn.Rd b/man/convert_utm_to_ll_fn.Rd
new file mode 100644
index 0000000..5e7204f
--- /dev/null
+++ b/man/convert_utm_to_ll_fn.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convert_utm_to_ll_fn.R
+\name{convert_utm_to_ll_fn}
+\alias{convert_utm_to_ll_fn}
+\title{Convert from UTM to Lat-long}
+\usage{
+convert_utm_to_ll_fn(eastings, northings, zone, flip_around_dateline = T,
+  meters_per_utm_unit = 1000)
+}
+\arguments{
+\item{eastings}{eastings of points, paired to northings}
+
+\item{northings}{northings of points,  paired to eastings}
+
+\item{zone}{UTM zone of points}
+
+\item{flip_around_dateline}{logical stating if points have been flipped around the dateline}
+
+\item{meters_per_utm_unit}{meters per easting/northing}
+}
+\value{
+a data.frame with
+\describe{
+\item{approx_long}{the approximate transformed longitude of each UTM point}
+\item{approx_lat}{the approximate transformed latitude of each UTM point}
+}
+}
+\description{
+If eastings and northings have been flipped
+around dateline, will convert back and provide estimtes of "original" lat lon
+Values should be viewed as estimates for plotting and general pairing
+}
+\examples{
+\dontrun{
+eastings <- Spatial_List$loc_x[,'E_km']
+
+northings <- Spatial_List$loc_x[,'N_km']
+
+zone <- Extrapolation_List$zone
+
+flip_around_dateline <- Extrapolation_List$flip_around_dateline
+
+latlongs <- convert_utm_to_ll_fn(eastings = eastings, northings = northings, zone = zone, flip_around_dateline = flip_around_dateline)
+
+ggmap::qmplot(x = approx_long, y = approx_lat, data = latlongs, color = 'red')
+}
+}
diff --git a/man/plot_residuals.Rd b/man/plot_residuals.Rd
index 4fdc00e..4ca47e7 100644
--- a/man/plot_residuals.Rd
+++ b/man/plot_residuals.Rd
@@ -58,4 +58,3 @@ A tagged list of Pearson residuals
 \description{
 \code{plot_residuals} shows average Pearson residual for every knot for encounter probability and positive catch rate components
 }
-
diff --git a/man/smallPlot.Rd b/man/smallPlot.Rd
index a691c2b..64bb51d 100644
--- a/man/smallPlot.Rd
+++ b/man/smallPlot.Rd
@@ -14,4 +14,3 @@ parameters of small plot, invisible.
 \description{
 Inset plot with margins, background and border (based on: https://github.com/cran/berryFunctions/blob/master/R/smallPlot.R)
 }
-
diff --git a/man/summary_nwfsc.Rd b/man/summary_nwfsc.Rd
index 4f1cae0..66e86b8 100644
--- a/man/summary_nwfsc.Rd
+++ b/man/summary_nwfsc.Rd
@@ -24,4 +24,3 @@ Tagged list containing objects for running a VAST model
 \description{
 \code{summary_nwfsc} generates output tables requested by the PFMC SSC
 }
-