Merge branch 'joss' into main

.Rbuildignore

@@ -11,4 +11,4 @@
 ^docs$
 ^pkgdown$
 ^CRAN-SUBMISSION$
-^CONTRIBUTING\.md$
+^CONTRIBUTING\.md$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SSN2
 Title: Spatial Modeling on Stream Networks
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
     person(given = "Michael",
            family = "Dumelle",

NAMESPACE

@@ -146,7 +146,7 @@ export(randcov_initial)
 export(randcov_params)
 export(ssn_create_distmat)
 export(ssn_get_data)
-export(ssn_get_netgeometry)
+export(ssn_get_netgeom)
 export(ssn_get_stream_distmat)
 export(ssn_glm)
 export(ssn_import)

NEWS.md

@@ -1,3 +1,11 @@
+# SSN 0.1.1
+
+## Minor Updates
+
+* Changed network geometry name from `netgeometry` to `netgeom` to avoid exceeding the 10 character limit for column/field names while writing to shapefiles [(#2)](https://github.com/USEPA/SSN2/issues/2).
+
+## Bug Fixes
+
 # SSN2 0.1.0
 
 * Initial CRAN submission.

R/SSN_to_SSN2.R

@@ -53,7 +53,7 @@ SSN_to_SSN2 <- function(object, edge_additive = NULL, site_additive = NULL) {
     }
 
     ## ---------------------------------------------------
-    ## Convert edges to sf and add netgeometry column
+    ## Convert edges to sf and add netgeom column
     ## ---------------------------------------------------
 
     sl <- sp::SpatialLines(object@lines, proj4string = object@proj4string)
@@ -62,7 +62,7 @@ SSN_to_SSN2 <- function(object, edge_additive = NULL, site_additive = NULL) {
 
     nl.coords <- object@network.line.coords
 
-    edges$netgeometry <- paste("ENETWORK",
+    edges$netgeom <- paste("ENETWORK",
       paste("(",
         paste(
           nl.coords$NetworkID,
@@ -100,7 +100,7 @@ SSN_to_SSN2 <- function(object, edge_additive = NULL, site_additive = NULL) {
 
 
     ## ------------------------------------------------
-    ## Convert observed sites to sf and add netgeometry
+    ## Convert observed sites to sf and add netgeom
     ## ------------------------------------------------
     ## sites<- st_as_sf(sp::SpatialPointsDataFrame(object@obspoints@SSNPoints[[1]]@point.coords,
     ##       object@obspoints@SSNPoints[[1]]@point.data,
@@ -116,7 +116,7 @@ SSN_to_SSN2 <- function(object, edge_additive = NULL, site_additive = NULL) {
     np.coords <- object@obspoints@SSNPoints[[1]]@network.point.coords
     np.coords <- cbind(np.coords, sites[, c("ratio", "locID")])
     np.coords$pid <- rownames(object@obspoints@SSNPoints[[1]]@network.point.coords)
-    sites$netgeometry <- paste(
+    sites$netgeom <- paste(
       "SNETWORK",
       paste(
         "(",
@@ -161,7 +161,7 @@ SSN_to_SSN2 <- function(object, edge_additive = NULL, site_additive = NULL) {
 
     ## ------------------------------------------------------------- If
     ## prediction sites are present, convert to list of sf data.frames
-    ## and add netgeometry column
+    ## and add netgeom column
     ## -------------------------------------------------------------
 
     if (length(object@predpoints@ID) > 0) {
@@ -184,7 +184,7 @@ SSN_to_SSN2 <- function(object, edge_additive = NULL, site_additive = NULL) {
           tmp.sf[, c("ratio", "locID")]
         )
         np.coords$pid <- rownames(object@predpoints@SSNPoints[[i]]@network.point.coords)
-        tmp.sf$netgeometry <- paste(
+        tmp.sf$netgeom <- paste(
           "SNETWORK",
           paste(
             "(",

R/amongSitesDistMat.R

@@ -13,7 +13,7 @@ amongSitesDistMat <- function(ssn, pids, name = "obs", bin.table) {
   if (name != "obs") {
     ind.pids <- ssn$preds[[name]]$ng.pid %in% as.character(pids)
     locID.pid.data <- ssn$preds[[name]]$locID[ind.pids]
-    pid.data <- ssn_get_netgeometry(ssn$preds[[name]][ind.pids, ], c(
+    pid.data <- ssn_get_netgeom(ssn$preds[[name]][ind.pids, ], c(
       "pid", "SegmentID", "locID",
       "DistanceUpstream"
     ))
@@ -22,7 +22,7 @@ amongSitesDistMat <- function(ssn, pids, name = "obs", bin.table) {
   } else {
     ind.pids <- ssn$obs$ng.pid %in% as.character(pids)
     locID.pid.data <- ssn$obs$locID[ind.pids]
-    pid.data <- ssn_get_netgeometry(ssn$obs[ind.pids, ], c(
+    pid.data <- ssn_get_netgeom(ssn$obs[ind.pids, ], c(
       "pid", "SegmentID", "locID",
       "DistanceUpstream"
       ), reformat = TRUE)

R/augment.R

@@ -111,7 +111,7 @@ augment.ssn_lm <- function(x, drop = TRUE, newdata = NULL, se_fit = FALSE,
       augment_data$.se.fit <- preds_data$se.fit
     }
     tibble_out <- tibble::tibble(cbind(data, augment_data, influence(x)))
-    tibble_out$pid <- ssn_get_netgeometry(x$ssn.object$obs, netvars = "pid")$pid
+    tibble_out$pid <- ssn_get_netgeom(x$ssn.object$obs, netvars = "pid")$pid
     coords <- sf::st_coordinates(x$ssn.object$obs)
     tibble_out$.xcoord <- coords[, 1, drop = TRUE]
     tibble_out$.ycoord <- coords[, 2, drop = TRUE]
@@ -158,7 +158,7 @@ augment.ssn_lm <- function(x, drop = TRUE, newdata = NULL, se_fit = FALSE,
       }
       coords <- sf::st_coordinates(newdata)
       tibble_out <- tibble::tibble(cbind(sf::st_drop_geometry(newdata), augment_newdata))
-      augment_newdata$pid <- ssn_get_netgeometry(newdata, netvars = "pid")$pid
+      augment_newdata$pid <- ssn_get_netgeom(newdata, netvars = "pid")$pid
       tibble_out$.xcoord <- coords[, 1, drop = TRUE]
       tibble_out$.ycoord <- coords[, 2, drop = TRUE]
       tibble_out <- sf::st_as_sf(tibble_out, coords = c(".xcoord", ".ycoord"), crs = x$crs)

R/create_netgeometry.R

@@ -1,12 +1,12 @@
-## Add netgeometry column to sf data.frame sf_data
-create_netgeometry <- function(sf_data, type = NULL) {
+## Add netgeom column to sf data.frame sf_data
+create_netgeom <- function(sf_data, type = NULL) {
   if (type == "point") {
-    sf_data[, "netgeometry"] <- paste0("SNETWORK (", paste(
+    sf_data[, "netgeom"] <- paste0("SNETWORK (", paste(
       sf_data$netID, sf_data$rid, sf_data$upDist,
       sf_data$ratio, sf_data$pid, sf_data$locID
     ), ")", sep = "")
   } else {
-    sf_data[, "netgeometry"] <- paste0("ENETWORK (", paste(
+    sf_data[, "netgeom"] <- paste0("ENETWORK (", paste(
       sf_data$netID,
       sf_data$rid,
       sf_data$upDist
@@ -15,5 +15,5 @@ create_netgeometry <- function(sf_data, type = NULL) {
     sep = ""
     )
   }
-  return(sf_data) ## Return sf data.frame with netgeometry column added
+  return(sf_data) ## Return sf data.frame with netgeom column added
 }

R/get_data_object.R

@@ -184,7 +184,7 @@ get_data_object <- function(formula, ssn.object, additive, anisotropy,
   order <- unlist(split(seq_len(n), local$index), use.names = FALSE)
 
   # store global pid
-  pid <- ssn_get_netgeometry(ssn.object$obs, "pid")$pid
+  pid <- ssn_get_netgeom(ssn.object$obs, "pid")$pid
 
   # restructure ssn
   ssn.object <- restruct_ssn_missing(ssn.object, observed_index, missing_index)

R/get_data_object_glm.R

@@ -212,7 +212,7 @@ get_data_object_glm <- function(formula, ssn.object, family, additive, anisotrop
   order <- unlist(split(seq_len(n), local$index), use.names = FALSE)
 
   # store global pid
-  pid <- ssn_get_netgeometry(ssn.object$obs, "pid")$pid
+  pid <- ssn_get_netgeom(ssn.object$obs, "pid")$pid
 
   # restructure ssn
   ssn.object <- restruct_ssn_missing(ssn.object, observed_index, missing_index)

R/get_dist_object.R

@@ -1,13 +1,13 @@
 # parent function to get the distance object
 get_dist_object <- function(ssn.object, initial_object, additive, anisotropy) {
-  # get netgeometry
-  netgeometry <- ssn_get_netgeometry(ssn.object$obs, reformat = TRUE)
+  # get netgeom
+  netgeom <- ssn_get_netgeom(ssn.object$obs, reformat = TRUE)
 
   # get network index
-  network_index <- netgeometry$NetworkID
+  network_index <- netgeom$NetworkID
 
   # get pid
-  pid <- netgeometry$pid # not needed now but can reorder by it later
+  pid <- netgeom$pid # not needed now but can reorder by it later
 
   # distance order
   dist_order <- order(network_index, pid)

R/get_dist_pred_object.R

@@ -1,28 +1,28 @@
 # parent function to get the distance object
 get_dist_pred_object <- function(object, newdata_name, initial_object) {
-  # get netgeometry
-  netgeometry <- ssn_get_netgeometry(object$ssn.object$obs, reformat = TRUE)
+  # get netgeom
+  netgeom <- ssn_get_netgeom(object$ssn.object$obs, reformat = TRUE)
 
   # get network index
-  network_index <- netgeometry$NetworkID
+  network_index <- netgeom$NetworkID
 
   # get pid
-  pid <- netgeometry$pid
+  pid <- netgeom$pid
 
   # distance order
   dist_order <- order(network_index, pid)
 
   # inverse of distance order
   inv_dist_order <- order(dist_order)
 
-  # get netgeometry
-  netgeometry_pred <- ssn_get_netgeometry(object$ssn.object$preds[[newdata_name]], reformat = TRUE)
+  # get netgeom
+  netgeom_pred <- ssn_get_netgeom(object$ssn.object$preds[[newdata_name]], reformat = TRUE)
 
   # get network pred index
-  network_index_pred <- netgeometry_pred$NetworkID
+  network_index_pred <- netgeom_pred$NetworkID
 
   # get pid
-  pid_pred <- netgeometry_pred$pid
+  pid_pred <- netgeom_pred$pid
 
   # distance order
   dist_order_pred <- order(network_index_pred, pid_pred)

R/get_dist_predbk_object.R

@@ -1,13 +1,13 @@
 # parent function to get the distance object
 get_dist_predbk_object <- function(object, newdata_name, initial_object) {
-  # get netgeometry
-  netgeometry <- ssn_get_netgeometry(object$ssn.object$preds[[newdata_name]], reformat = TRUE)
+  # get netgeom
+  netgeom <- ssn_get_netgeom(object$ssn.object$preds[[newdata_name]], reformat = TRUE)
 
   # get network index
-  network_index <- netgeometry$NetworkID
+  network_index <- netgeom$NetworkID
 
   # get pid
-  pid <- netgeometry$pid
+  pid <- netgeom$pid
 
   # distance order
   dist_order <- order(network_index, pid)

R/ssn_create_distmat.R

@@ -197,9 +197,9 @@ ssn_create_distmat <- function(ssn.object, predpts = NULL, overwrite = FALSE,
     if (!file.exists(file.path(ssn$path, "distance", predpts))) {
       dir.create(file.path(ssn$path, "distance", predpts))
     }
-    ## Extract netgeometry data from predpts and format
+    ## Extract netgeom data from predpts and format
     tmp.df <- ssn_get_data(ssn, predpts)
-    n.geom <- ssn_get_netgeometry(ssn$preds[[predpts]])
+    n.geom <- ssn_get_netgeom(ssn$preds[[predpts]])
     colnames(n.geom)[4:6] <- paste0("ng.", colnames(n.geom[4:6]))
     n.geom$NetworkID <- as.factor(n.geom$NetworkID)
     n.geom$DistanceUpstream <- as.numeric(n.geom$DistanceUpstream)
@@ -208,9 +208,9 @@ ssn_create_distmat <- function(ssn.object, predpts = NULL, overwrite = FALSE,
     rm(tmp.df, n.geom)
   }
 
-  ## Extract netgeometry and format obs data
+  ## Extract netgeom and format obs data
   tmp.df <- ssn_get_data(ssn)
-  n.geom <- ssn_get_netgeometry(ssn$obs)
+  n.geom <- ssn_get_netgeom(ssn$obs)
   colnames(n.geom)[4:6] <- paste0("ng.", colnames(n.geom[4:6]))
   n.geom$NetworkID <- as.factor(n.geom$NetworkID)
   n.geom$DistanceUpstream <- as.numeric(n.geom$DistanceUpstream)
@@ -229,8 +229,8 @@ ssn_create_distmat <- function(ssn.object, predpts = NULL, overwrite = FALSE,
   net.count <- length(site.nets)
   warned.overwrite <- FALSE
 
-  ## Extract netgeometry and format edges data
-  ssn$edges <- cbind(ssn$edges, ssn_get_netgeometry(ssn$edges))
+  ## Extract netgeom and format edges data
+  ssn$edges <- cbind(ssn$edges, ssn_get_netgeom(ssn$edges))
   ssn$edges$NetworkID <- as.factor(ssn$edges$NetworkID)
   ssn$edges$DistanceUpstream <- as.numeric(ssn$edges$DistanceUpstream)
 
@@ -368,7 +368,7 @@ ssn_create_distmat <- function(ssn.object, predpts = NULL, overwrite = FALSE,
       ## locID.obi<- ssn$obs$ng.locID
 
       ## Create data.frame for obs with columns pid, rid, locID
-      ob.i <- ssn_get_netgeometry(ssn$obs[ind.obs, ], c("pid", "SegmentID", "locID"),
+      ob.i <- ssn_get_netgeom(ssn$obs[ind.obs, ], c("pid", "SegmentID", "locID"),
                                   reformat = TRUE)
       ##ob.i <- as.data.frame(sapply(ob.i, as.numeric))
       colnames(ob.i) <- c("pid", "rid", "locID")

R/ssn_get_netgeometry.R

@@ -1,9 +1,9 @@
-#' @title Extract netgeometry column
+#' @title Extract netgeom column
 #'
-#' @description Extract topological information from netgeometry column
+#' @description Extract topological information from netgeom column
 #'
 #' @param x An sf data.frame found in an \code{SSN} object or the
-#'   netgeometry column as a vector
+#'   netgeom column as a vector
 #'
 #' @param netvars Network coordinate variables to return. Default is
 #'   "all". For edges, valid column names include: "NetworkID",
@@ -13,17 +13,17 @@
 #' @param reformat Convert network coordinate variables from character to numeric.
 #'
 #' @details When an \code{SSN} object is generated using the
-#'   \code{importSSN} function, a text column named "netgeometry" is added
+#'   \code{importSSN} function, a text column named "netgeom" is added
 #'   to the edges, observed sites, and prediction sites (if they
-#'   exist) data.frames. The netgeometry column contains data used to
+#'   exist) data.frames. The netgeom column contains data used to
 #'   describe how edge and site features relate to one another in
-#'   topological space. For edges, netgeometry values contain the
+#'   topological space. For edges, netgeom values contain the
 #'   "ENETWORK" prefix, with 3 space delimited values in parentheses:
 #'   "ENETWORK (NetworkID SegmentID DistanceUpstream)". For point
 #'   datasets (observed and prediction sites), the values contain the
 #'   "SNETWORK" prefix, followed by 6 space delimited values in parentheses:
 #'   "SNETWORK (NetworkID SegmentID DistanceUpstream ratio pid locID)". The
-#'   \code{ssn_get_netgeometry} function extracts and converts these
+#'   \code{ssn_get_netgeom} function extracts and converts these
 #'   values from text to numeric, returning either a data.frame
 #'   (default) or vector containing the variables requested via
 #'   \code{netvars}.
@@ -32,7 +32,7 @@
 #'   function returns a data.frame (default). If only one column is
 #'   requested, the result is a vector.
 #'
-#' @name ssn_get_netgeometry
+#' @name ssn_get_netgeom
 #' @export
 #'
 #' @examples
@@ -43,9 +43,9 @@
 #' temp_path <- paste0(tempdir(), "/MiddleFork04.ssn")
 #' mf04p <- ssn_import(temp_path, overwrite = TRUE)
 #'
-#' ssn_get_netgeometry(mf04p$obs)
-#' ssn_get_netgeometry(mf04p$edges, "DistanceUpstream")
-ssn_get_netgeometry <- function(x, netvars = "all", reformat = FALSE) {
+#' ssn_get_netgeom(mf04p$obs)
+#' ssn_get_netgeom(mf04p$edges, "DistanceUpstream")
+ssn_get_netgeom <- function(x, netvars = "all", reformat = FALSE) {
   # I think this should be an SSN obejct and we should have another column
   # for "type" which can be "edges", "obs", or a prediction name
   if (inherits(x, "SSN")) {
@@ -54,7 +54,7 @@ ssn_get_netgeometry <- function(x, netvars = "all", reformat = FALSE) {
 
 
   if (inherits(x, "data.frame")) {
-    x <- x$netgeometry
+    x <- x$netgeom
   }
 
   ## delete "network"