I have created the following function
FilterIndi <- function(infile,name, date){
sub_file <- infile[,c("NUMBER","CREATE_DTTM_NEW", name)]
sub_file <- subset(sub_file, name==1)
library(data.table)
sub_file <- setDT(sub_file)[, .SD[which.max(CREATE_DTTM_NEW)], NUMBER]
sub_file$date <- sub_file$CREATE_DTTM_NEW
sub_file$CREATE_DTTM_NEW <- NULL
library(dplyr) #to do left_join
Unique <- left_join(Unique,sub_file, by =c("NUMBER"="NUMBER"))
Unique$name[is.na(Unique$name)] <-0
return(Unique)
}
FilterIndi(allfile, pde, pde_date )
pde is in data frame allfile but I get the following error:
Error in '[.data.frame'(infile, c("NUMBER", "CREATE_DTTM_NEW", :
object 'pde' not found
I can't figure out how to make it work.
Can someone please help me? Thanks a lot in advance.
EDIT: I have attached an image of allfile:
Related
My R script looks like this
if (!require("timelineS")) install.packages("timelineS")
library('timelineS')
myevents <- read.csv(
text = "MS1.1.1,2021-12-01
MS1.1.2,2022-03-01
MS1.1.3,2022-09-01
MS1.1.4,2022-09-01
MS1.1.5,2022-09-01
MS1.1.6,2022-11-01
MS1.1.7,2023-03-01
MS1.1.8,2023-09-01
MS1.1.9,2023-09-01",
sep=",",header=F)
head(myevents)
class(myevents)
timelineS(myevents)
and I get the error "Fehler in min(event.dates) - buffer.days :
nicht-numerisches Argument für binären Operator".
I cannot figure out where is my mistake.
Thank you for any hint!
?timelineS
myevents$V2 <- as.Date(myevents$V2)
timelineS(myevents)
I had a similar issue. In my case, my data frame had the event date first and the event second. The reverse order is needed. I fixed my data frame this way:
raw_df <- read_tsv("2022_12.tsv") #from readr package
# reverse order of columns
my_df <- data.frame(raw_df$Events, raw_df$Event_Dates)
names(my_df) <- sort(names(raw_df), decreasing = T)
I have some code that loops over a list of study IDs (ids) and turns them into separate polygons/spatial points. On the first execution of the loop it produces the following error:
Error in (function (x) : attempt to apply non-function
This is from the raster::rasterToPoints function. I've looked at the examples in the help section for this function and passing fun=NULL seems to be an acceptable method (filters out all NA values). All the values are equal to 1 anyways so I tried passing a simple function like it suggests such as function(x){x==1}. When this didn't work, I also tried to just suppress the error message but without any luck using try() or tryCatch().
Main questions:
1. Why does this produce an error at all?
2. Why does it only display the error on the first run through the loop?
Reproducible example:
library(ggplot2)
library(raster)
library(sf)
library(dplyr)
pacific <- map_data("world2")
pac_mod <- pacific
coordinates(pac_mod) <- ~long+lat
proj4string(pac_mod) <- CRS("+init=epsg:4326")
pac_mod2 <- spTransform(pac_mod, CRS("+init=epsg:4326"))
pac_rast <- raster(pac_mod2, resolution=0.5)
values(pac_rast) <- 1
all_diet_density_samples <- data.frame(
lat_min = c(35, 35),
lat_max = c(65, 65),
lon_min = c(140, 180),
lon_max = c(180, 235),
sample_replicates = c(38, 278),
id= c(1,2)
)
ids <- all_diet_density_samples$id
for (idnum in ids){
poly1 = all_diet_density_samples[idnum,]
pol = st_sfc(st_polygon(list(cbind(c(poly1$lon_min, poly1$lon_min, poly1$lon_max, poly1$lon_max, poly1$lon_min), c(poly1$lat_min, poly1$lat_max, poly1$lat_max, poly1$lat_min, poly1$lat_min)))))
pol_sf = st_as_sf(pol)
x <- rasterize(pol_sf, pac_rast)
df1 <- raster::rasterToPoints(x, fun=NULL, spatial=FALSE) #ERROR HERE
df2 <- as.data.frame(df1)
density_poly <- all_diet_density_samples %>% filter(id == idnum) %>% pull(sample_replicates)
df2$density <- density_poly
write.csv(df2, paste0("pol_", idnum, ".csv"))
}
Any help would be greatly appreciated!
These are error messages, but not errors in the strict sense as the script continues to run, and the results are not affected. They are related to garbage collection (removal from memory of objects that are no longer in use) and this makes it tricky to pinpoint what causes it (below you can see a slightly modified example that suggests another culprit), and why it does not always happen at the same spot.
Edit (Oct 2022)
These annoying messages
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x) : attempt to apply non-function
Will disappear with the next release of Rcpp, which is planned for Jan 2023. You can also install the development version of Rcpp like this:
install.packages("Rcpp", repos="https://rcppcore.github.io/drat")
I am using the following code. I create a list of first names and then generate links to an API for each name and then try to capture the data from each link.
mydata$NameGenderURL2 <- paste ("https://gender-api.com/get?name=",mydata$firstname, "&key=suZrzhrNJRvrkWFXAG", sep="")
mynamegenderfunction <- function(x){
GET(url= mydata$NameGenderURL2[x])
this.raw.content <- genderdata$content
this.raw.content <- rawToChar(genderdata$content)
this.content <- fromJSON(this.raw.content)
name1[x] <- this.content$name
gender1[x] <- this.content$gender}
namelist <- mydata$firstname[1:100]
genderdata <- lapply(namelist, mynamegenderfunction)
Oddly enough I receive the following message:
>Error in curl::curl_fetch_memory(url, handle = handle) :
>Could not resolve host: NA`
I tried another API and got the same issue. Any suggestions?
Here is a data sample:
namesurl
https://api.genderize.io/?name=kaan
https://api.genderize.io/?name=Joan
https://api.genderize.io/?name=homeblitz
https://api.genderize.io/?name=Flatmax
https://api.genderize.io/?name=BRYAN
https://api.genderize.io/?name=James
https://api.genderize.io/?name=Dion
https://api.genderize.io/?name=Flintu
https://api.genderize.io/?name=Adriana
The output that I need is the gender for each link, which would be :Male/Female, Null
https://filebin.net/3et86d1gh8cer9mu this is example subset of my data
I try to apply a code that was already working on similar data, now I can't tract where its wrong. The code goes like this:
url <- 'https://filebin.net/3et86d1gh8cer9mu/TCA_subset_GnoG_melt.csv'
TCA_subset_GnoG_melt <- read.csv(url)
L <- data.frame()
IDs <- unique(TCA_subset_GnoG_melt$X1)
for (i in 1 : length(IDs)){
temp<-TCA_subset_GnoG_melt[(TCA_subset_GnoG_melt$X1)==IDs[i],]
temp<- na.omit(temp)
t_test_CTROL_ABC.7<- t.test(temp$value[temp$X1.1=="CTROL"], temp$value[temp$X1.1=="ABC.7"])
t_test_CTROL_ABC.8<- t.test(temp$value[temp$X1.1=="CTROL"], temp$value[temp$X1.1=="ABC.8"])
t_test_CTROL_ABC.7.8<- t.test(temp$value[temp$X1.1=="CTROL"], temp$value[temp$X1.1=="ABC7.8"])
t_test_ABC.7_ABC.8<- t.test(temp$value[temp$X1.1=="ABC.7"], temp$value[temp$X1.1=="ABC.8"])
t_test_ABC.7_ABC.7.8<- t.test(temp$value[temp$X1.1=="ABC.7"], temp$value[temp$X1.1=="ABC7.8"])
t_test_ABC.8_ABC.7.8<- t.test(temp$value[temp$X1.1=="ABC.8"], temp$value[temp$X1.1=="ABC7.8"])
LLc <- cbind(as.character(unique(IDs[i])), t_test_CTROL_ABC.7,t_test_CTROL_ABC.8,t_test_CTROL_ABC.7.8, t_test_ABC.7_ABC.8,t_test_ABC.7_ABC.7.8, t_test_ABC.8_ABC.7.8)
L<-rbind(L,LLc)
}
AA<-rownames(L)
L$names <- AA
p_value_TCA <-L[grep("p.value",L$names), ]
df <- apply(p_value_TCA ,2,as.character)
df = as.matrix(df)
the error i get is:
Error in t.test.default(temp$value[temp$X1.1 == "CTROL"], temp$value[temp$X1.1 == :
not enough 'y' observations
I dpm't understand it, when i check the code line by line it goes until the LLc creation and than the df "L" is empty. it makes no sense to me. help!
I'm using the DESeq package to analyze RNA sequencing data. I have only one replicate and two treatments. My code is:
data <- read.csv()
metadata <- data.frame(row.names = colnames(data), condition =c("treated", "untreated"))
cds2 <- newCountDataSet( countData = data, conditions = metadata )
cds2 <- estimateSizeFactors(cds2)
counts( cds2, normalized=TRUE )
cds2 <- estimateDispersions(cds2, method="blind", sharingMode="fit-only")
res <- nbinomTest(cds2, "treated", "untreated" )
Everything works fine until I call "estimateDispersions". However, the function "nbinomTest" gives me this error:
Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
missing value where TRUE/FALSE needed
I found some documentation on this error, but the answers are not helpful for me. I work with R version 3.1.2 (2014-10-31).
Can someone help my with my problem, please?
Cheers!