I am trying to use the whatNWISdata function to retrieve all available data for specific USGS sites.
I get the following error after trying to execute the function:
siteNo <- "09508300"
dailyDataAvailable <- whatNWISdata(siteNo, service = "dv", parameterCd = "00060",
statCd = "00003")
Yields:
Error: All components of query must be named
Although I am using the function as recommended in rdocumentation.org and cran, I get the same error. My rstudio is updated to the latest version and so is my dataRetrieval package that this function is part of.
This error was a question that was brought up in 2016 on github, and they recommended downgrading the httr package, but the httr package has been updated since this question was asked and it seems this issue was resolved in the update.
Thanks!
Thank you so much for your input #Dragonthoughts!
I emailed the author and apparently they had made some slight edits in the format of the input values, and yes you are correct in that the first argument needed a value as in the other inputs for the function.
For anyone else having this problem, it works when you change the input to be like this: dailyDataAvailable <- whatNWISdata(siteNumber = "09508300", service = "dv", parameterCd = "00060", statCd = "00003")
Related
I want to create a CytoTree CYT object in R to analyse my .FCS files. When I am using the Quick start code in the package description, I will always get an error when running the createCYT() function that says:
Error in createCYT(raw.data = fcs.data, normalization.method = "log") :
2022-09-26 15:46:26 meta.data must be a data.frame
As the function should not rely on any meta data and that object is optional, I do not know how to solve the error.
Here is the description:
https://ytdai.github.io/CytoTree/quick-start.html#quick-start-code
I thank you very much in advance for your help!
BR
I have encountered same problem previously.
In the end it worked only when the data.frame was added (yes, even though it should not depend on it).
Here is how:
meta.data <- data.frame(cell = rownames(fcs.data), stage = gsub(".fcs.+", "", rownames(fcs.data)))
meta.data$stage <- factor(as.character(meta.data$stage))
You may as well have a look at the Cytotree PDF in case of more issues.
I'm trying to use stringdb in R and i'm getting the following error when i try to plot the network:
Error in if (grepl("The document has moved", res)) { : argument is
of length zero
code:
library(STRINGdb)
#(specify organism)
string_db <- STRINGdb$new( version="10", species=9606, score_threshold=0)
filt_mapped = string_db$map(filt, "GeneID", removeUnmappedRows = TRUE)
head(filt_mapped)
(i have columns titled: GeneID, logFC, FDR, STRING_id with 156 rows)
filt_mapped_hits = filt_mapped$STRING_id
head(filt_mapped_hits)
(156 observations)
string_db$plot_network(filt_mapped_hits, add_link = FALSE)
Error in if (grepl("The document has moved", res)) { : argument is
of length zero
You are using quite few years old version of Bioconductor and by extension the STRING package.
If you update to the newest one, it will work. However the updated package only supports only the latest version STRING (currently version 11), so the underlying network may change a bit.
More detailed reason is this:
The STRING's hardware infrastructure underwent recently major changes which forced a different server setup.
Now all the old calls are forwarded to a different URL, however the cURL call, how it was implemented, does not follow our redirects which breaks the STRINGdb package functionality.
We cannot update the old bioconductor package and our server setup can’t be really changed.
That said, the fix for an old version is relatively simple.
In STRINGdb library there is script with all the methods "rstring.r".
In there you’ll find “get_png” method. In it replace this line:
urlStr = paste("http://string-db.org/version_", version, "/api/image/network", sep="" )
With this line:
urlStr = paste("http://version", version, ".string-db.org/api/image/network", sep="" )
Load the library again and it should create the PNG, as before.
I may not be using the terminology correctly here so please forgive me...
I have a case of one package 'overwriting' a function with the same name loaded by another package and thus changing the behavior (breaking) of a function.
The specific case:
X <- data.frame ( y = rnorm(100), x1 = rnorm(100), x2 = rnorm(100) )
library(CausalImpact)
a <- CausalImpact::CausalImpact( X, c(1,75), c(76, 100) ) # works
library(bfast) # imports quantmod which loads crappy version of as.zoo.data.frame
b <- CausalImpact::CausalImpact( X, c(1,75), c(76, 100) ) # Error
I know the error comes from two versions of the function as.zoo.data.frame.
The problematic version is imported by bfast from the package 'quantmod' (see https://github.com/joshuaulrich/quantmod/issues/168). Unfortunately their hotfix did not prevent this error. Super annoying.
I can hack around this specific problem, but I was wondering if there is a general way to like 'de-register' this function variant from the search path. Neither detach nor unloadNamespace remove the offending function (same behavior after). An explanation and similar problem is discussed here and here, but I wasn't able to find a general solution. For instance I'd rather just remove this function than clone and re-write CausalImpact to deal with this behavior.
From R 3.6.0 onwards, there is a new option called "conflicts.policy" to handle this within an established framework. For small issues like this, you can use the new arguments to library(). If you aren't yet to 3.6, the easiest solution might be to explicitly namespace CausalImpact when you need it, i.e. CausalImpact::CausalImpact. That's a mouthful, so you could do causal_impact <- CausalImpact::CausalImpact and use that alias.
# only attach select
library(dplyr, include.only = "select")
# exclude slice/arrange from being attached.
library(dplyr, exclude = c("slice", "arrange"))
library(bfast, exclude = "CausalImpact") should solve your problem.
Attach means that they are available for use without explicit prefixing with their package. In either of these cases, something like dplyr::slice would work just fine.
For more information, you can see ?library. Also, the R-Core member Luke Tierney wrote a blog explaining how the conflicts.policy works. You can find that here
Here's an answer that works, but is less preferable than de-registering a S3 method because it involves replacing the registered version in the S3 Methods table with the desired method:
library(CausalImpact)
library(bfast)
assignInNamespace("as.zoo.data.frame", zoo:::as.zoo.data.frame, ns = asNamespace("zoo"))
based partially on #smingerson's suggestion in the comments
I am trying to use the acs package in R to download Census data for a basic map, but I am unable to download the data and I'm receiving a confusing error message.
My code is as follows:
#Including all packages here in case this is somehow the issue
install.packages(c("choroplethr", "choroplethrMaps", "tidycensus", "tigris", "leaflet", "acs", "sf"))
library(choroplethr)
library(choroplethrMaps)
library(tidycensus)
library(tigris)
library(leaflet)
library(acs)
library(sf)
library(tidyverse)
api.key.install("my_api_key")
SD_geo <- geo.make(state="CA", county = 73, tract = "*", block.group = "*")
median_income <- acs.fetch(endyear = 2015, span = 5, geography = SD_geo, table.number = "B19013", col.names="pretty")
Everything appears to work until the final command, when I receive the following error message:
trying URL 'http://web.mit.edu/eglenn/www/acs/acs-variables/acs_5yr_2015_var.xml.gz'
Content type 'application/xml' length 735879 bytes (718 KB)
downloaded 718 KB
Error in if (url.test["statusMessage"] != "OK") { :
missing value where TRUE/FALSE needed
In addition: Warning message:
In (function (endyear, span = 5, dataset = "acs", keyword, table.name, :
XML variable lookup tables for this request
seem to be missing from ' https://api.census.gov/data/2015/acs5/variables.xml ';
temporarily downloading and using archived copies instead;
since this is *much* slower, recommend running
acs.tables.install()
This is puzzling to me because 1) it appears like something is in fact being downloaded at first? and 2) 'Error in if (url.test["statusMessage"] != "OK") { :
missing value where TRUE/FALSE needed' makes no sense to me. It doesn't align with any of the arguments in the function.
I have tried:
Downloading the tables using acs.tables.install() as recommended in the second half of the error message. Doesn't help.
Changing the endyear and span to be sure that I'm falling within the years of data supported by the API. I seem to be, according to the API documentation. Have also used the package default arguments with no luck.
Using 'variable =' and the code for the variable as found in the official API documentation. This returns only the two lines with the mysterious "Error in if..." message.
Removing colnames = "pretty"
I'm going to just download the datafile as a CSV and read it into R for now, but I'd like to be able to perform this function from the script for future maps. Any information on what's going on here would be appreciated. I am running R version 3.3.2. Also, I'm new to using this package and the API. But I'm following the documentation and can't find evidence that I'm doing anything wrong.
Tutorial I am working off of:
http://zevross.com/blog/2015/10/14/manipulating-and-mapping-us-census-data-in-r-using-the-acs-tigris-and-leaflet-packages-3/#get-the-tabular-data-acs
And documentation of the acs package: http://eglenn.scripts.mit.edu/citystate/wp-content/uploads/2013/02/wpid-working_with_acs_R2.pdf
To follow up on Brandon's comment, version 2.1.1 of the package is now on CRAN, which should resolve this issue.
Your code runs for me. My guess would be that the Census API was temporarily down.
As you loaded tidycensus and you'd like to do some mapping, you might also consider the following code:
library(tidycensus)
census_api_key("your key here") # use `install = TRUE` to install the key
options(tigris_use_cache = TRUE) # optional - to cache the Census shapefile
median_income <- get_acs(geography = "block group",
variables = "B19013_001",
state = "CA", county = "San Diego",
geometry = TRUE)
This will get you the data you need, along with feature geometry for mapping, as a tidy data frame.
I emailed Ezra Haber Glenn, the author of the package, about this as I was having the same issue. I received a response within 30 minutes and it was after midnight, which I thought was amazing. Long story short, the acs package version 2.1.0 is configured to work with the changes the Census Bureau is making to their API later this summer, and it is currently presenting some problems windows users in the mean time. Ezra is going to be releasing an update with a fix, but in the mean time I reverted back to version 2.0 and it works fine. I'm sure there are a few ways to do this, but I installed the devtools package and ran:
require(devtools)
install_version("acs", version = "2.0", repos = "http://cran.us.r-project.org")
Hope this helps anyone else having a similar issue.
This is my first question to the community. I've read through the guidelines and am doing my best to ask an appropriate question and including a minimal, complete, and verifiable example. That being said, please feel free to suggest ways in which I can ask better questions going forward.
I am having trouble with the choroplethrMaps package, which I have never used in the past. I have had issues installing packages on my work computer before, but have gotten around this issue by pasting the package and its dependencies in my library directory. Part of my issues may stem from that, but I'm not sure.
Here is the code that replicates the issue on my machine.
library(choroplethrMaps)
library(choroplethrAdmin1)
library(choroplethr)
data(state.map)
df<-data.frame(region=unique(x = state.map$region),value=rnorm(n = 51,mean = 500,sd = 45))
debug(state_choropleth)
state_choropleth(df = df,title = "", legend = "", num_colors = 1)
After debugging the state_choropleth function, it looks like there is an error with the "render" portion of the code. When I execute the above code, I get the following error message.
Error in withCallingHandlers(tryCatch(evalq((function (..., call. = TRUE, :
object '.rcpp_warning_recorder' not found
Note that I am only using state_choropleth because when running the choroplethr function, I was advised to use state_choropleth instead. It seems as though choroplethr is out of date.