Merge wiDButil

.Rbuildignore

@@ -14,3 +14,4 @@
 >>>>>>> 79146b21e9e5f977d8ddab23bba1f84504844c48
 ^doc$
 ^Meta$
+^Rdev$

.gitignore

@@ -1,4 +1,39 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
-.Ruserdata
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# Downloads
+/downloads/

.travis.yml

@@ -4,7 +4,6 @@ language: R
 cache: packages
 before_install:
  - sudo apt-get install libgdal-dev
- - R -e 'install.packages("rgdal", repos=c("http://R-Forge.R-project.org", "http://cran.rstudio.com"))'
 
 r_packages:
   - covr

DESCRIPTION

@@ -1,11 +1,17 @@
 Package: isoWater
 Type: Package
-Title: Infer source of water using stable isotope data
-Version: 0.2.0.9000
-Author: Gabe Bowen
-Maintainer: Gabe Bowen <gabe.bowen@utah.edu>
-Description: Bayesian inference of the source and source isotope composition of water samples that may have experienced evaporation. Original algorithms presented in Bowen et al. (2018) <doi:10.1007/s00442-018-4192-5>.
-Imports: R2jags, parallel, abind, R2WinBUGS, doParallel, foreach
+Title: Discovery, Retrieval, and Analysis of Water Isotope Data 
+Version: 0.2.1
+Authors@R: person("Gabriel", "Bowen", email = "gabe.bowen@utah.edu",
+                  role = c("aut", "cre"))
+Description: wiDB_ functions provide interface to the public API of 
+    the wiDB: build, check and submit queries, and receive and 
+    unpack responses. Data analysis functions support Bayesian 
+    inference of the source and source isotope composition of water 
+    samples that may have experienced evaporation. Algorithms 
+    adapted from Bowen et al. (2018) <doi:10.1007/s00442-018-4192-5>.
+Imports: R2jags, parallel, abind, R2WinBUGS, doParallel, foreach, 
+    httr, jsonlite
 Depends: R (>= 3.5)
 Suggests: 
     knitr,

NAMESPACE

@@ -2,10 +2,16 @@ export(mwlSource)
 export(mixSource)
 export(mwl)
 export(iso)
+export(wiDB_sites)
+export(wiDB_data)
+export(wiDB_values)
+importFrom(httr, GET, content)
+importFrom(jsonlite, fromJSON)
 importFrom(doParallel, registerDoParallel, stopImplicitCluster)
 importFrom(foreach, foreach, "%dopar%")
 importFrom(R2jags, jags)
 importFrom(R2WinBUGS, monitor)
 importFrom(stats, sd, var)
 importFrom(graphics, abline, lines, par, points)
-importFrom(abind, abind)
+importFrom(abind, abind)
+importFrom(utils, read.csv, unzip)

NEWS.md

@@ -1,7 +1,9 @@
 # isoWater news
 
-## isoWater 0.2.0.9000
-* Updated documentation
+## isoWater 0.2.1
+* Merged functions and documentation from wiDButil package
+* Updated documentation and vignette
+
 
 ## isoWater 0.2.0
 * Reformatted code to create package

R/constructors.R

@@ -25,6 +25,10 @@ mwl = function(HO, plot = TRUE){
     stop("Non-numeric values in HO")
   }
   ns = nrow(HO)
+  HO = HO[!(is.na(HO[,1]) | is.na(HO[,2])),]
+  if(nrow(HO) != ns){
+    warning("Missing values removed from HO")
+  }
   if(ns < 3){
     stop("At least 3 sample values required")
   }

R/watercomp.R

@@ -89,7 +89,7 @@ mwlSource = function(obs, MWL=c(8.01, 9.57, -8.096, 2564532.2, 5.76, 80672),
 #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=2, ngens=1e5, ncores = 1){
+                   shp=1, ngens=1e5, ncores = 1){
 
   if(class(obs)[2] != "iso"){
     warning("Expecting iso object for obs, this argument may be

R/wiDBfunctions.R

@@ -0,0 +1,223 @@
+#####
+#Validate query input
+#####
+wiDB_validate = function(minLat, maxLat, minLong, maxLong, minElev, maxElev,
+                         minDate, maxDate, countries, states, types, projects){
+
+  qStr = ""
+
+  if(!is.null(minLat)){
+    if(class(minLat) != "numeric"){stop("minLat must be numeric")}
+    qStr = paste0(qStr, "&minLat=", minLat)
+  }
+  if(!is.null(maxLat)){
+    if(class(maxLat) != "numeric"){stop("maxLat must be numeric")}
+    qStr = paste0(qStr, "&maxLat=", maxLat)
+  }
+  if(!is.null(minLong)){
+    if(class(minLong) != "numeric"){stop("minLong must be numeric")}
+    qStr = paste0(qStr, "&minLong=", minLong)
+  }
+  if(!is.null(maxLong)){
+    if(class(maxLong) != "numeric"){stop("maxLong must be numeric")}
+    qStr = paste0(qStr, "&maxLong=", maxLong)
+  }
+  if(!is.null(minElev)){
+    if(class(minElev) != "numeric"){stop("minElev must be numeric")}
+    qStr = paste0(qStr, "&minElev=", minElev)
+  } 
+  if(!is.null(maxElev)){
+    if(class(maxElev) != "numeric"){stop("maxElev must be numeric")}
+    qStr = paste0(qStr, "&maxElev=", maxElev)
+  }
+  if(!is.null(minDate)){
+    if(class(minDate) != "character"){stop("minDate must be string")}
+    td = c(as.numeric(substr(minDate, 1, 4)), as.numeric(substr(minDate, 6, 7)),
+           as.numeric(substr(minDate, 9, 10)))
+    if(NA %in% td){stop("minDate format must be YYYY-MM-DD")}
+    qStr = paste0(qStr, "&minDate=", minDate)
+  }
+  if(!is.null(maxDate)){
+    if(class(maxDate) != "character"){stop("maxDate must be string")}
+    td = c(as.numeric(substr(maxDate, 1, 4)), as.numeric(substr(maxDate, 6, 7)),
+           as.numeric(substr(maxDate, 9, 10)))
+    if(NA %in% td){stop("maxDate format must be YYYY-MM-DD")}
+    qStr = paste0(qStr, "&maxDate=", maxDate)
+  }
+  if(!is.null(countries)){
+    if(class(countries) != "character"){stop("countries must be string")}
+    countries = gsub("  ", "", countries)
+    countries = gsub(" ", "", countries)
+    if(length(countries > 1)){
+      countries = paste0(countries, collapse = ",")
+    }
+    qStr = paste0(qStr, "&countries=", countries)
+  }
+  if(!is.null(states)){
+    if(class(states) != "character"){stop("states must be string")}
+    states = gsub("  ", "", states)
+    states = gsub(" ", "", states)
+    if(length(states > 1)){
+      states = paste0(states, collapse = ",")
+    }
+    qStr = paste0(qStr, "&states=", states)
+  }
+  if(!is.null(types)){
+    if(class(types) != "character"){stop("types must be string")}
+    types = gsub("  ", "", types)
+    types = gsub(" ", "", types)
+    if(length(types > 1)){
+      types = paste0(types, collapse = ",")
+    }
+    qStr = paste0(qStr, "&types=", types)
+  }
+  if(!is.null(projects)){
+    if(class(projects) != "character"){stop("projects must be string")}
+    projects = gsub("  ", "", projects)
+    projects = gsub(" ", "", projects)
+    if(length(types > 1)){
+      types = paste0(types, collapse = ",")
+    }
+    qStr = paste0(qStr, "&projects=", projects)
+  }
+
+  if(nchar(qStr) == 0){stop("No query arguments provided")}
+
+  qStr = paste0("?", substr(qStr, 2, nchar(qStr))) 
+
+  return(qStr)
+}
+
+#####
+#Find sites
+#####
+wiDB_sites = function(minLat = NULL, maxLat = NULL, minLong = NULL, maxLong = NULL,
+                      minElev = NULL, maxElev = NULL, minDate = NULL, maxDate = NULL,
+                      countries = NULL, states = NULL, types = NULL, projects = NULL){
+
+  qStr = wiDB_validate(minLat, maxLat, minLong, maxLong, minElev, maxElev,
+                       minDate, maxDate, countries, states, types, projects)
+
+  baseStr = "https://wateriso.utah.edu/api/v1/sites.php"
+  q = paste0(baseStr, qStr)
+  d = GET(q)
+
+  if(d$status_code != 200){stop(paste("Request returned error code", d$status_code))}
+
+  resp = fromJSON(content(d, as = "text", encoding = "UTF-8"))
+
+  if(length(resp$sites) == 0){
+    warning("No sites returned")
+    return(NULL)
+  }
+
+  return(resp$sites)
+}
+
+#####
+#Obtain data
+#####
+wiDB_data = function(minLat = NULL, maxLat = NULL, minLong = NULL, maxLong = NULL,
+                     minElev = NULL, maxElev = NULL, minDate = NULL, maxDate = NULL,
+                     countries = NULL, states = NULL, types = NULL, projects = NULL, 
+                     fields = NULL, tmpdir = tempdir(), clean = TRUE){
+
+  qStr = wiDB_validate(minLat, maxLat, minLong, maxLong, minElev, maxElev,
+                       minDate, maxDate, countries, states, types, projects)
+
+  if(!dir.exists(tmpdir)){
+    warning("Directory doesn't exist, trying to create")
+    dir.create(tmpdir)
+    if(!dir.exists(tmpdir)){stop("Unable to create directory")}
+  }
+
+  if(class(clean) != "logical"){stop("clean must be TRUE/FALSE")}
+
+  flist = c("Site_ID", "Site_Name", "Latitude", "Longitude", "Elevation", 
+            "Sample_ID", "Type", "Start_Date", "Start_Time_Zone", 
+            "Collection_Date", "Collection_Time_Zone", "Phase", 
+            "Depth_meters", "Sample_Comments", "d2H", "d18O", 
+            "d2H_Analytical_SD", "d18O_Analytical_SD", "WI_Analysis_Source", 
+            "Project_ID")
+
+  if(!is.null(fields)){
+    if(class(fields) != "character"){stop("fields must be a string")}
+    fields = gsub("  ", "", fields)
+    fields = gsub(" ", "", fields)
+    fels = strsplit(fields, ",")
+    fels = fels[[1]]
+    for(i in 1:length(fels)){
+      if(!(fels[i] %in% flist)){stop(paste("Value", i, "in fields is not a valid field name"))}
+    }
+    qStr = paste0(qStr, "&return=", fields)
+  }
+
+  baseStr = "https://wateriso.utah.edu/api/v1/download.php"
+  q = paste0(baseStr, qStr)
+  g = GET(q)
+
+  if(g$status_code != 200){stop(paste("Request returned error code", g$status_code))}
+
+  fn = g$headers$`content-disposition`
+  fn = strsplit(fn, "=")[[1]][2]
+  writeBin(g$content, paste0(tmpdir, "/", fn))
+
+  #unzip and output .csv
+  unzip(paste0(tmpdir, "/", fn), exdir = paste0(tmpdir, "/downloads"))  
+
+  #get and order file list
+  froot = strsplit(fn, "-")[[1]][1]
+  df = paste0(tmpdir, "/downloads/", froot, "-data.csv")
+  pf = paste0(tmpdir, "/downloads/", froot, "-project.csv")
+
+  if(file.size(df) == 0){
+    file.remove(c(paste0(tmpdir, "/", fn), df, pf))  
+    warning("No records returned")
+    return(NULL)
+  }
+
+  #read in data
+  d = read.csv(df)
+
+  #read in projects
+  p = read.csv(pf)
+
+  file.remove(paste0(tmpdir, "/", fn))  
+
+  if(clean){
+    file.remove(c(df, pf))
+  }
+
+  return(list("data" = d, "projects" = p))
+}
+
+#####
+#Get field values
+#####
+wiDB_values = function(fields){
+
+  if(!is.character(fields)){
+    stop("fields values must be character strings")
+  }
+  for(i in 1:length(fields)){
+    if(!(fields[i] %in% c("countries", "states", "types", "projects", 
+                          "Site_ID", "Sample_ID", "WI_Analysis_ID", 
+                          "Climate_ID"))){
+      stop("One or more fields values not supported")
+    }
+  }
+
+  baseStr = "https://wateriso.utah.edu/api/v1/values.php?fields="
+  q = baseStr
+  for(i in fields){
+    q = paste0(q, i, ",")
+  }
+  q = substr(q, 1, nchar(q) - 1)
+  d = GET(q)
+
+  if(d$status_code != 200){stop(paste("Request returned error code", d$status_code))}
+
+  resp = fromJSON(content(d, as = "text", encoding = "UTF-8"))
+
+  return(resp)
+}

README.md

@@ -1,13 +1,15 @@
 # isoWater
 
-An R package for inferring the source of waters based on their isotopic composition and allowing for isotope effects associated with partial evaporation. Install from GitHub using the devtools package:
+An R package for obtaining and analyzing water isotope data. Includes interfaces to the Waterisotopes Database and tools for inferring the source of waters based on their isotopic composition accounting for isotope effects associated with partial evaporation. Install the latest release from GitHub using the devtools package:
 
 ```
 library(devtools)
-install_GitHub("SPATIAL-Lab/isoWater")
+install_GitHub("SPATIAL-Lab/isoWater@*release")
 library(isoWater)
 ```
 
 References:
 
-Bowen, G. J., Putman, A., Brooks, J. R., Bowling, D. R., Oerter, E. J., & Good, S. P. (2018). Inferring the source of evaporated waters using stable H and O isotopes. Oecologia, 187(4), 1025-1039.
+Bowen, G. J., Putman, A. L., Brooks, J. R., Bowling, D. R., Oerter, E. J., & Good, S. P. (2018) Inferring the source of evaporated waters using stable H and O isotopes. Oecologia, 187(4), 1025-1039.
+
+Putman, A. L., & Bowen, G. J. (2019) A global database of the stable isotopic ratios of meteoric and terrestrial waters. Hydrology and Earth System Sciences 23(10), 4389-4396.