Iterating through unknown dates in R - r

I'm new to R (having worked in C++ and Python before) so this is probably just a factor of me not knowing some of R's nuances.
The program I'm working on is supposed to construct matrices of data by date. Here's how I might initialize such a matrix:
dates <- seq(as.Date("1980-01-01"), as.Date("2013-12-31"), by="days")
HN3 <- matrix(nrow=length(dates), ncol = 5, dimnames = list(as.character(dates), c("Value1", "Value2", "Value3", "Value4", "Value5")))
Notice that dates includes every day between 1980 and 2013.
So, from there, I have files containing certain dates and measurements of Value1, etc for those dates, and I need to read those files' contents into HN3. But the problem is that most of the files don't contain measurements for every day.
So what I want to do is read a file into a dataframe (say, v1read) with column 1 being dates and column 2 being the desired data. Then I'd match the dates of v1read to that date's row in HN3 and copy all of the relevant v1read values that way. Here is my attempt at doing so:
for (i in 1:nrow(v1read)) {
HN3[as.character(v1read[i,1]),Value1] <- v1read[i,4]
}
This gives me an out of index range error when the value of i is bumped up unexpectedly. I understand that R doesn't like to iterate through dates, but since the iterator itself is a numeric value rather than a date, I was hoping I'd found a loophole.
Any tips on how to accomplish this would be enormously appreciated.

Let's use library(dplyr). Start with
dates = seq(as.Date("1980-01-01"), as.Date("2013-12-31"), by="days")
HN3 = data.frame(Date=dates)
Now, load in your first file, the one that has a date and Value1.
file1 = read.file(value1.file) #I'm assuming this file has a column already named "Date" and one named #Value1
HN3 = left_join(HN3,file1,by="Date")
This will do a left join (SQL style) matching only the rows where a date exists and filling in the rest with NA. Now you have a data frame with two columns, Date and Value1. Load in your other files, do a left_join with each and you'll be done.

Related

How to rename the columns of a large data table to dates

I am working from an nc file and after extracting the data to a matrix the time variable is the column variable for this it just gave it a number 1:2087 for the range of time for the dataset. I would like to rename it to the date that they should be (starting at 1981/12/31 to 2021/12/31 where each column is a week) I tried to change the names by using
colnames(tmp_mat) <- rep(seq(as.Date('1982-01-05'), as.Date('2021-12-28'), by = 'weeks'))
this changed the column names but it changed it to a number (the number of days for that date since 1971/01/01.
Does anyone have any suggestions in how to make this work
Your data is a matrix , you have to change it to data.frame then apply your code
tmp_mat = data.frame(tmp_mat)
colnames(tmp_mat) <- rep(seq(as.Date('1982-01-05'), as.Date('2021-12-28'), by = 'weeks'))

How to filter via a logical expression that filters via a variable [duplicate]

This question already has an answer here:
r - Filter a rows by a date that alters each day
(1 answer)
Closed 1 year ago.
I have a question about the use of a logical expression in combination with a variable.
Imagine that I have a data frame with multiple rows that each contain a date saved as 2021-09-25T06:04:35:689Z.
I also have a variable that contains the date of yesterday as '2021-09-24' - yesterday <- Sys.Date()-1.
How do I filter the rows in my data frame based on the date of yesterday which is stored in the variable 'yesterday'?
To solve my problem, I have looked at multiple posts, for example:
Using grep to help subset a data frame
I am well aware that this question might be a duplicate. However, current questions do not provide me with the help that I need help. I hope that one of you can help me.
As an initial matter, it looks like you have a vector instead of a data frame (only one column). If you really do have a data frame and only ran str() on one column, the very similar technique at the end will work for you.
The first thing to know is that your dates are stored as character strings, while your yesterday object is in the Date format. R will not let you compare objects of different types, so you need to convert at least one of the two objects.
I suggest converting both to the POSIXct format so that you do not lose any information in your dates column but can still compare it to yesterday. Make sure to set the timezone to the same as your system time (mine is "America/New_York").
Dates <- c("2021-09-09T06:04:35.689Z", "2021-09-09T06:04:35.690Z", "2021-09-09T06:04:35.260Z", "2021-09-24T06:04:35.260Z")
Dates <- gsub("T", " ", Dates)
Dates <- gsub("Z", "", Dates)
Dates <- as.POSIXct(Dates, '%Y-%m-%d %H:%M:%OS', tz = "America/New_York")
yesterday <- Sys.time()-86400 #the number of seconds in one day
Now you can tell R to ignore the time any only compare the dates.
trunc(Dates, units = c("days")) == trunc(yesterday, units = c("days"))]
The other part of your question was about filtering. The easiest way to filter is subsetting. You first ask R for the indices of the matching values in your vector (or column) by wrapping your comparison in the which() function.
Indices <- which(trunc(Dates, units = c("days")) == trunc(yesterday, units = c("days"))])
None of the dates in your str() results match yesterday, so I added one at the end that matches. Calling which() returns a 4 to tell you that the fourth item in your vector matches yesterday's date. If more dates matched, it would have more values. I saved the results in "Indices"
We can then use the Indices from which() to subset your vector or dataframe.
Filtered_Dates <- Dates[Indices]
Filtered_Dataframe <- df[Indices,] #note the comma, which indicates that we are filtering rows instead of columns.

Change the class of a cell of a data-frame to Date

everyone!
As part of my clinical study I created a xlsx spreadsheet containing a data set. Only columns 2 to 12 and lines 1 to 307 are useful to me. I now manipulate my spreadsheet under R, after importing it (read_excel, etc.).
In my columns 11 and 12 ('data' and 'raw_data'), some cells correspond to dates (for example the first 2 rows of 'data' and 'raw_data'). Indeed, this corresponds to the patient's visit dates. However, as you can see, these dates are given to me in number of days since the origin "1899-12-30". However, I would like to be able to transform them into a current date format (2019-07-05).
My problem is that in these columns I don't only have dates, I have different numerical results (times, means, scores, etc.) .
I started by transforming the class of my columns from character to factor/numeric so that I could better manipulate the columns later. But I can't change only the format of cells corresponding to a date.
Do you know if it is possible to transform only the cells concerned and if so how?
I attach my code and a preview of my data frame.
Part "Unsuccessful trial": I tried with this kind of thing. Of course the date changes format here but as soon as I try to make this change in the data frame it doesn't work.
Thank you for your help!
# Indicate the id of the patient
id = "01_AA"
# Get protocol data of patient
idlst <- dir("/data/protocolData", full.names = T, pattern = id)
# Convert the xlsx database into dataframe
idData <- data.table::rbindlist(lapply(
idlst,
read_excel,
n_max = 307,
range = cell_cols("B:M"), # just keep the table
), fill = TRUE)
idData <- as.tibble(idData)
idData<- idData %>%
mutate_at(vars(1:10), as.factor)%>%
mutate_at(vars(11:length(idData)), as.numeric)
# Unsuccessful trial
as.Date.character(data[1:2,11:12], origin ='1899-12-30')
Thank you for your comments and indeed this is one of the problems with R.
I solved my problem with the following code where idData is my df.
# Change the data format of the date cells of the column Data and Raw_data:
idData$Data[grepl("date",idData$Measure)] <- as.character(as.Date(
as.numeric(
idData$Data[grepl("date",idData$Measure)]),
origin = "1899-12-30"))

Research panel analysis in R

I am a newbie to Stackoverflow, stats and R, so apologies for the simple nature of my question/request for advice:
I am completing analysis of a large data-set comprising of 2 files: a txt containing internal temperature data and a second SPSS data file.
To kick off, I have exported the SPSS data into CSV format and stripped back to contain just the few columns i think i need - house type and occupant type. I have imported all the temperature data and merged the two using a common identifier.
So now I have a merged data frame, containing all the data i need (to begin with) to start completing some analysis.
First question: I have year, date and time as separate columns. However the time column has imported with an incorrect date before "30/12/1899". How can i delete the date part of all observations from this column, but retain the time?
Second question Similar to above, the date colum shows the correct date, but has the time following, which is not correct (every observation showing 00:00:00), how can I delete all the times from this column?
Third question How can I combine the correct Time with correct date, to end up with DD/MM/YYYY HH:MM:SS
Fourth question Should i create subsets of merged to facilitate the analysis: ie: each house type (seperate subsets) vs temp, time and occupant type?
Dates can be brought in as they are instead of factor via the parameter as.is = TRUE i.e.
data <- read.csv(choose.files(), as.is = T)
I would try reading the csv file again and then working with the date time. It will come in as a chron or some format like that and you'll need to change it to Posixct, well I do anyway. To view help on a function, type question mark followed by function name i.e. ?as.posixct.
Date.Time: chron "2018/08/04 10:10:00", ... # '%Y-%m-%d %H:%M:%S' current format as read in from my system.
# Date format you want is '%d/%m/%Y %H:%M'
# tz='' is an empty time zone can't remember exactly you probably should read up on
# finally on the left side of the assign <- I am creating a new column Date.
# You can over write the old column, Date.Time, but can't hurt to learn how to delete
# a column.
data$Date <- as.POSIXct(date$Date.Time, tz='', '%d/%m/%Y %H:%M:%S')
# Now remove the original column. -Date.Time take out Date.Time, if you leave the
# minus out, the data will contain the subset Date.Time and no other columns.
data <- subset(data, select = -Date.Time)
Try this first, and I will look into removing time with in a date field. I have an idea, but I'd rather see if this helps with the problem first.
Though if you do want to merge the Year, month, day columns, you could try something like this, seem like a logical thing to do, you can always keep the original format and delete it later. It's not hurting anything.
data$YMD <- paste(data$Year," ",
data$Month, " ",
data$Day)
Also while you are at it. Install a library called dplyr, written by the same guy that did ggplot2, Hadley....
install.packages("dplyr")
# The add it to the top of your file like ggplot.
library(dplyr)

How to avoid date formatted values getting converted to numeric when assigned to a matrix or data frame?

I have run into an issue I do not understand, and I have not been able to find an answer to this issue on this website (I keep running into answers about how to convert dates to numeric or vice versa, but that is exactly what I do not want to know).
The issue is that R converts values that are formatted as a date (for instance "20-09-1992") to numeric values when you assign them to a matrix or data frame.
For example, we have "20-09-1992" with a date format, we have checked this using class().
as.Date("20-09-1992", format = "%d-%m-%Y")
class(as.Date("20-09-1992", format = "%d-%m-%Y"))
We now assign this value to a matrix, imaginatively called Matrix:
Matrix <- matrix(NA,1,1)
Matrix[1,1] <- as.Date("20-09-1992", format = "%d-%m-%Y")
Matrix[1,1]
class(Matrix[1,1])
Suddenly the previously date formatted "20-09-1992" has become a numeric with the value 8298. I don't want a numeric with the value 8298, I want a date that looks like "20-09-1992" in date format.
So I was wondering whether this is simply how R works, and we are not allowed to assign dates to matrices and data frames (somehow I have managed to have dates in other matrices/data frames, but it beats me why those other times were different)? Is there a special method to assigning dates to data frames and matrices that I have missed and have failed to deduce from previous (somehow successful) attempts at assigning dates to data frames/matrices?
I don't think you can store dates in a matrix. Use a data frame or data table. If you must store dates in a matrix, you can use a matrix of lists.
Matrix <- matrix(NA,1,1)
Matrix[1,1] <- as.list(as.Date("20-09-1992", format = "%d-%m-%Y"),1)
Matrix
[[1]]
[1] "1992-09-20"
Edited: I also just re-read you had this issue with data frame. I'm not sure why.
mydate<-as.Date("20-09-1992", format = "%d-%m-%Y")
mydf<-data.frame(mydate)
mydf
mydate
1 1992-09-20
Edited: This has been a learning experience for me with R and dates. Apparently the date you supplied was converted to number of days since origin. Origin is defined as Jan 1st,1970. To convert this back to a date format at some point
Matrix
[,1]
[1,] 8298
as.Date(Matrix, origin ="1970-01-01")
[1] "1992-09-20"
try the following: First specify your date vector & then use
rownames(mat) <- as.character(date_vector)
the dates will appear as a text.
This happens mostly when we are loading Excel Workbook
You need to add detectDates = TRUE in the function
DataFrame <- read.xlsx("File_Nmae", sheet = 3, detectDates = TRUE)

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