amoeba

library(EML)
library(dataone)
library(arcticdatautils);

mpath <- '/home/sjclark/ASL/forKNB/asl_yuk_kusk_metadata.xml'
eml <- read_eml(mpath)

cn <- CNode('PROD')
mn <- getMNode(cn,'urn:node:KNB')
csvpid <- 'urn:uuid:6b37b187-f6a4-4fa1-a1d9-330bf71754ab'

amoeba

cgries.16.1
http://purl.dataone.org/odo/ECSO_00002917



Chenlung.18.7
http://purl.dataone.org/odo/ECSO_00002454
http://purl.dataone.org/odo/ECSO_00002458

amoeba

ark:/90135/q13j39xf/6/mrt-eml.xml

amoeba

> mydf <- data.frame(x = c("A", "B", NA), y = c(NA, "B", "C"))
> mydf
     x    y
1    A <NA>
2    B    B
3 <NA>    C
> ifelse(is.na(mydf[1,"x"]), as.character(mydf[1,"y"]), as.character(mydf[1,"x"]))
[1] "A"

amoeba

path <- "plots"
dir.create(path)

# Make and save a plot for each Region and Location combination
regions <- na.omit(unique(df$SASAP.Region))

for (region in regions) {
  locations <- na.omit(unique(subset(df, SASAP.Region == region)$SASAP.Location))
  
  for (location in locations) {

amoeba

proportion_of_reach_traveled <- function(reach,
                                         days_in_river,
                                         reach_travel_time,
                                         days_to_get_to) {

  if (days_in_river < days_to_get_to[reach]) {
    return(0)
  } else if (days_in_river > days_to_get_to[reach+1]) {
    return(1)
  } else {

amoeba

library(dataone)

cn <- CNode("PROD")
mn <- getMNode(cn, "urn:node:ARCTIC")

qr <- query(mn, 'q=formatType:METADATA+-obsoletedBy:*+"carbon flux"&fl=identifier,title,origin')

qr_enhanced <- lapply(qr, function(r) {
  # Collapse multi-valued origin into comma-separated char vector
  r$origin <- paste0(unlist(r$origin), collapse = ", ")

amoeba

> taxon_coverage <- set_taxonomicCoverage(
+     c("Macrocystis pyrifera", "Homo sapiens"),
+     expand = TRUE)

Retrieving data for taxon 'Macrocystis pyrifera'


Retrieving data for taxon 'Homo sapiens'

> taxon_coverage

amoeba

library(EML)
library(taxize)

specieslist <- c("Melanitta perspicillata","Oncorhynchus nerka")
cls <- classification(specieslist, db = 'itis')

tc <- new("taxonomicClassification")
tc <- c(new("taxonomicClassification", taxonRankName = new("taxonRankName", .Data = cls[nrow(cls), "rank"]), taxonRankValue = new("taxonRankValue", .Data = cls[nrow(cls), "name"])))

while (i > 0) {

amoeba

for(i in 1 : length(image_pids)){
  publish_object(mn,
                 image_paths[i],
                 #  format_id = "image/jpeg",
                 public = F,
                 pid = image_pids[i])
  print(c("image", i, "uploaded"))
}

# set rights