How to convert the nested for loop in apply function - r

Here I've nested loop i don't know how to convert this into apply can anyone tell me how to convert this in to apply function
plans_achievements <- function(pa_m,pa_q){
if(nrow(pa_m)==0 & nrow(pa_q==0)){
df = data.frame(a = c(""), b = c("No Data Available"))
colnames(df)=""
}else{
pa_m= pa_m%>% select(inc,month_year,Plans,Achievements,quarter_year)
colnames(pa_mon)[2] = "Period"
pa_q= pa_q%>% select(inc,quarter_year,Plans,Achievements)
colnames(pa_qtr)[2] = "Period"
df = data.frame(inc=c(""),Period=c(""),Plans=c(""),Achievements=c(""))
for (q in unique(pa_q$Period)){
df1 = pa_q[pa_q$Period==q,]
df1$Period = paste0("<span style=\"color:#288D55\">",df1$Period,"</span>")
df1$Plans = paste0("<span style=\"color:#288D55\">",df1$Plans,"</span>")
df1$Achievements = paste0("<span style=\"color:#288D55\">",df1$Achievements,"</span>")
df = rbind(df,df1)
for (m in unique(pa_m$quarter_year)){
if(m==q){
df2 = pa_m[pa_m$quarter_year==q,][-5]
df = rbind(df,df2)
}
}
}
df = df[-1,]
}
return(df)
}
DT::datatable(plans_achievements(pa_m[pa_m$inc=="vate",],pa_q[pa_q$inc=="vate",]), rownames = F,escape = FALSE,selection=list(mode="single",target="row"),options = list(pageLength = 50,scrollX = TRUE,dom = 'tp',ordering=F,columnDefs = list(list(visible=FALSE, targets=c(0)),list(className = 'dt-left', targets = '_all'))))

I could not imagine why you would want to do this, what about vectorizing the function instead?
Note a few typing errors (pa_mon instead of pa_m etc.) has been corrected below
plans_achievements2 <- function(pa_m,pa_q){
if(nrow(pa_m)==0 & nrow(pa_q==0)){
df = data.frame(a = c(""), b = c("No Data Available"))
colnames(df)=""
}else{
pa_m= pa_m%>% select(inc,month_year,Plans,Achievements,quarter_year)
colnames(pa_m)[2] = "Period"
pa_q= pa_q%>% select(inc,quarter_year,Plans,Achievements)
colnames(pa_q)[2] = "Period"
df <- pa_q
df$Period <- paste0("<span style=\"color:#288D55\">",df$Period,"</span>")
df$Plans = paste0("<span style=\"color:#288D55\">",df$Plans,"</span>")
df$Achievements = paste0("<span style=\"color:#288D55\">",df$Achievements,"</span>")
return(rbind(df, pa_m[pa_m$quarter_year %in% pa_q$Period,-5])[-1, ])
}
return(df)
}

Related

how to make two networks connected with selected members

I have a data like this
df<- structure(list(Core = c("Bestman", "Tetra"), member1 = c("Tera1",
"Brownie1"), member2 = c("Tera2", "Brownie2"), member3 = c("Tera3",
"Brownie3"), member4 = c("Tera4", "Brownie4"), member5 = c("Tera5",
"Brownie5"), member6 = c("", "Brownie6"), member7 = c("", "Brownie7"
)), class = "data.frame", row.names = c(NA, -2L))
I want to connect all the members to their Core. for example if you look at the first row, you can see there are 5 members , I want to connect them to their Core
The same for the second row
Then I connect both Core together
Here is what I have done
mydf <- crossprod(table(cbind(df[1], stack(df[-1]))[-3]))
graph_from_adjacency_matrix(mydf, diag = F, weighted = T, mode = "undirected") %>%
plot(edge.width = E(.)$weight)
If i understood correctly, what you want is:
library(igraph)
df<- data.frame(Core = c("Bestman", "Tetra"), member1 = c("Tera1",
"Brownie1"), member2 = c("Tera2", "Brownie2"), member3 = c("Tera3",
"Brownie3"), member4 = c("Tera4", "Brownie4"), member5 = c("Tera5",
"Brownie5"), member6 = c("", "Brownie6"), member7 = c("", "Brownie7"))
edges <- t(do.call(rbind, apply(
df, 1, function(x) cbind(x[1], x[x!=""][-1]))))
core_edges <- if(nrow(df)>1) combn(df$Core,2) else c()
g<-graph(c(edges,core_edges), directed=F )
plot(g , edge.width = E(g)$weight)
EDIT
To colorize and resize nodes:
V(g)$color <- apply(df, 1, \(x) names(V(g)) %in% x) |> apply(1,which)
V(g)$size <- 15
V(g)[df$Core]$size <- degree(g, V(g)[df$Core]) + 15
plot(g)

How to loop dataframe in R

I want to get data from IMF.However the API data is limited
Therefor I get the data by continent.
How to loop the dateframe? (The data can get from "Before loop part",load data from api)
The reference cannot work.https://stackoverflow.com/questions/25284539/loop-over-a-string-variable-in-r
Before the loop
library(imfr)
library(countrycode)
data(codelist)
country_set <- codelist
country_set<- country_set %>%
select(country.name.en , iso2c, iso3c, imf, continent, region) %>% filter(!is.na(imf) & !is.na(iso2c))
africa_iso2<- country_set$iso2c[country_set$continent=="Africa"]
asia_iso2<- country_set$iso2c[country_set$continent=="Asia"]
americas_iso2<- country_set$iso2c[country_set$continent=="Americas"]
europe_iso2<- country_set$iso2c[country_set$continent=="Europe"]
oceania_iso2<- country_set$iso2c[country_set$continent=="Oceania"]
loop part
continent <- c("africa", "asia", "americas","europe","oceania")
for(i in 1:length(continent)){
var <- paste0("gdp_nsa_xdc_", continent[i])
var1 <- paste0(continent[i],"_iso2")
[[var]]<- imf_data(database_id = "IFS" , indicator = c("NGDP_NSA_XDC"),country =[[var1]],start = 2010, end = 2022,return_raw = TRUE)
[[var]]<- [[var]]$CompactData$DataSet$Series
}
data sample is
list(CompactData = list(`#xmlns:xsi` = "http://www.w3.org/2001/XMLSchema-instance",
`#xmlns:xsd` = "http://www.w3.org/2001/XMLSchema", `#xsi:schemaLocation` = "http://www.SDMX.org/resources/SDMXML/schemas/v2_0/message https://registry.sdmx.org/schemas/v2_0/SDMXMessage.xsd http://dataservices.imf.org/compact/IFS http://dataservices.imf.org/compact/IFS.xsd",
`#xmlns` = "http://www.SDMX.org/resources/SDMXML/schemas/v2_0/message",
Header = list(ID = "18e0aeae-09ec-4dfe-ab72-60aa16aaea84",
Test = "false", Prepared = "2022-10-19T12:02:28", Sender = list(
`#id` = "1C0", Name = list(`#xml:lang` = "en", `#text` = "IMF"),
Contact = list(URI = "http://www.imf.org", Telephone = "+ 1 (202) 623-6220")),
Receiver = list(`#id` = "ZZZ"), DataSetID = "IFS"), DataSet = list(
`#xmlns` = "http://dataservices.imf.org/compact/IFS",
Series = list(`#FREQ` = "Q", `#REF_AREA` = "US", `#INDICATOR` = "NGDP_NSA_XDC",
`#UNIT_MULT` = "6", `#TIME_FORMAT` = "P3M", Obs = structure(list(
`#TIME_PERIOD` = c("2020-Q1", "2020-Q2", "2020-Q3",
"2020-Q4", "2021-Q1", "2021-Q2", "2021-Q3", "2021-Q4",
"2022-Q1", "2022-Q2"), `#OBS_VALUE` = c("5254152",
"4930197", "5349433", "5539370", "5444406", "5784816",
"5883177", "6203369", "6010733", "6352982")), class = "data.frame", row.names = c(NA,
10L))))))
I suggest you create a list first, to which you will assign the value you want your loop to create. The following code creates a named list, and then at the end of the loop, assigns the value of each iteration to that named list:
continent <-
sapply(c("africa", "asia", "americas","europe","oceania"),
c, simplify = FALSE, USE.NAMES = TRUE)
for(i in seq_len(length(continent))) {
var <- paste0("gdp_nsa_xdc_", continent[i])
var1 <- get(paste0(continent[i],"_iso2"))
var <- imf_data(database_id = "IFS" , indicator = c("NGDP_NSA_XDC"),
country = var1, start = 2010, end = 2022,
return_raw = TRUE)
continent[[i]] <- var$CompactData$DataSet$Series
}
I don't necessarily understand the double brackets around [[var]]. Let me know if my answer does not correspond to what you were looking for!
We could use assign to create objects in the global env
for(i in 1:length(continent)){
var <- paste0("gdp_nsa_xdc_", continent[i])
var1 <- paste0(continent[i],"_iso2")
assign(var, imf_data(database_id = "IFS" , indicator = c("NGDP_NSA_XDC"),country =[[var1]],start = 2010, end = 2022,
return_raw = TRUE))
assign(var, get(var)$CompactData$DataSet$Series)
}

In R--Change name of list of list of lists when lists have differing lengths

I've tried everything I can...I have a large list of lists. They are of varying depths, but they all have a variable name that I need to rename. I tried breaking apart the list into data frames, it just seems unpractical and doesn't even do what I want.
Here's a toy example:
list1 = list(changethis = c("1", "2"))
list2 = list(varname1 = c("1,2,3,4"), changethis = c("5,6,7,8"), varname2 = c("9, 10, 11"))
list3 = list(varname3 = list(varname4 = c("first", "second", "third", list(changethis = c("15, 16, 19"), varname5 = "cat", "dog", "fish"))))
list4 = list(varname6 = list(varname7 = list2, varname8 = list2))
list5a = list(varname13 = c("hat", "key"), changethis = c("5"))
list5 = list(varname9 = list(varname10 = list5a, varname11 = list5a))
list6 = list(varname12 = list5)
list7 = list(first = list1)
listbig = list(sublist1 = list3, sublist2 = list4, sublist3 = list5, sublist4= list6, sublist5=list7, sublist6 = list5a)
Here's a toy code that produces what I want it to look like. The 'changethis' var is renamed to 'change'
sollist1 = list(changed= c("1", "2"))
sollist2 = list(varname1 = c("1,2,3,4"), changed = c("5,6,7,8"), varname2 = c("9, 10, 11"))
sollist3 = list(varname3 = list(varname4 = c("first", "second", "third", list(changed = c("15, 16, 19"), varname5 = "cat", "dog", "fish"))))
sollist4 = list(varname6 = list(varname7 = sollist2, varname8 = sollist2))
sollist5a = list(varname13 = c("hat", "key"), changed = c("5"))
sollist5 = list(varname9 = list(varname10 = sollist7, varname11 = sollist5a))
sollist6 = list(varname12 = sollist5)
sollist7 = list(first = sollist1)
solution_list = list(sublist1 = sollist3, sublist2 = sollist4, sublist3 = sollist5, sublist4= sollist6, sublist5=sollist7, sublist6=sollist7)
Here is one of my many attempts to do this. I extracted sublist1 from the big list and tried to just change the name for it, but nothing gets changed.
extr_sublist1 <- listbig[1]
names(extr_sublist1[[1]][[1]][[1]][4]) <- "changed" #does not do it...
Another failed attempt:
In this I extract a differently hierarchial sublist and create a Var name which I hope to loop over so I can change the name of the 'changethis' var. Also does not work.
extr_sublist4 <- listbig[4]
numvars <- length(extr_sublist4[[1]][[1]][[1]])
for (i in 1: numvars){
varname<-paste("Var",numvar, sep = "")
paste('Var',[i]) <- extr_sublist4[[1]][[1]][[1]][[1]][2]
namespaste('Var',[i])[paste('Var',[i]) == 'changethis'] <- 'changed'
}
I'm sure there's a simple and elegant solution to this...but have no idea what. Thanks in advance for your help.
You can use a recursive method to do the transformation:
changefun <- function(x, change_name, new_name){
idx <- names(x) == change_name
if(any(idx)) names(x)[idx] <- new_name
if (is.list(x)) lapply(x, changefun, change_name, new_name)
else x
}
Now just call
changefun(listbig, 'changethis', 'changed')

Error in m == q : R comparison (1) is possible only for atomic and list types

The whole function which i need to convert the for loop in to apply for optimization
plans_achievements <- function(pa_m,pa_q){
if(nrow(pa_m)==0 & nrow(pa_q==0)){
df = data.frame(a = c(""), b = c("No Data Available"))
colnames(df)=""
}else{
pa_m= pa_m%>% select(inc,month_year,Plans,Achievements,quarter_year)
colnames(pa_mon)[2] = "Period"
pa_q= pa_q%>% select(inc,quarter_year,Plans,Achievements)
colnames(pa_qtr)[2] = "Period"
df = data.frame(inc=c(""),Period=c(""),Plans=c(""),Achievements=c(""))
for (q in unique(pa_q$Period)){
df1 = pa_q[pa_q$Period==q,]
df1$Period = paste0("<span style=\"color:#288D55\">",df1$Period,"</span>")
df1$Plans = paste0("<span style=\"color:#288D55\">",df1$Plans,"</span>")
df1$Achievements = paste0("<span style=\"color:#288D55\">",df1$Achievements,"</span>")
df = rbind(df,df1)
for (m in unique(pa_m$quarter_year)){
if(m==q){
df2 = pa_m[pa_m$quarter_year==q,][-5]
df = rbind(df,df2)
}
}
}
df = df[-1,]
}
return(df)
}
The apply which i tried
my_fun <- function(q){
df1 = pa_qtr[pa_qtr$Period==q,]
df1$Period = paste0("<span style=\"color:#288D55\">",df1$Period,"</span>")
df1$Plans = paste0("<span style=\"color:#288D55\">",df1$Plans,"</span>")
df1$Achievements = paste0("<span style=\"color:#288D55\">",df1$Achievements,"</span>")
df = rbind(df,df1)
}
df = do.call(rbind,lapply(unique(pa_qtr$Period), my_fun))
my_fun2 <- function(m,my_fun){
if (m == q) {
df2 = pa_mon[pa_mon$qtr_yr == q, ][-5]
df = rbind(df,df2)
}
}
df = do.call(cbind,lapply(unique(pa_mon$qtr_yr), my_fun2))
DT::datatable(plans_achievements(pa_m[pa_m$inc=="vate",],pa_q[pa_q$inc=="vate",]), rownames = F,escape = FALSE,selection=list(mode="single",target="row"),options = list(pageLength = 50,scrollX = TRUE,dom = 'tp',ordering=F,columnDefs = list(list(visible=FALSE, targets=c(0)),list(className = 'dt-left', targets = '_all'))))
Why you get the error comparison is possible only for atomic and list types
I will answer your original question first:
You get the error because you haven't defined q as a variable inside the function my_fun2. Since you haven't defined this variable, R will look for it in the global environment. There R will find the function q() (used to quit R). So you get the error message comparison (1) is possible only for atomic and list types because R thinks you are trying to compare a number m with the function q.
Here is a small example to make it easy to see:
# Run this in a clean environment
m <- 1
m == b # Understandable error message - "b" is not found
m == q # Your error - because R thinks you are comparing m to a function
You fix this error by making sure that q is defined inside your function. Either by creating it inside the function, or by supplying it as an input argument.
A possible solution for your problem
As I understand your code, you want to format, merge and sort the values in pa_q and pa_m, to display them in a html table.
Under is a possible solution, using tidyverse and vectorized operations, rather than a loop or apply functions. Vectorized functions are typically your fastest option in R, as I know you want to optimize your code.
library(dplyr)
plans_achievements <- function(pa_m, pa_q) {
# I've modified the logic a bit: there is no need to wrap the full function in
# an else statement, since we can return early if the data has no rows
if (nrow(pa_m) == 0 && nrow(pa_q == 0)) {
df = data.frame(a = c(""), b = c("No Data Available"))
colnames(df) = ""
return(df)
}
pa_q <-
pa_q %>%
# Select and rename the columns vi need
select(inc, Period = quarter_year, Plans, Achievements, date) %>%
# Format the values
mutate(
Period = paste0("<span style=\"color:#288D55\">", Period,"</span>"),
Plans = paste0("<span style=\"color:#288D55\">", Plans,"</span>"),
Achievements = paste0("<span style=\"color:#288D55\">", Achievements,"</span>")
)
pa_m <-
pa_m %>%
# Select and rename the columns we need
select(inc, Period = month_year, Plans, Achievements, date) #%>%
# Combine the datasets
bind_rows(
pa_q,
pa_m
) %>%
# Make sure that R understand date as a date value
mutate(
date = lubridate::dmy(date)
) %>%
# Sort by date
arrange(desc(date)) %>%
# Remove columns we do not need
select(-date, -inc)
}
DT::datatable(
plans_achievements(
pa_m[pa_m$inc=="vate",],
pa_q[pa_q$inc=="vate",]
),
rownames = FALSE,
escape = FALSE,
selection = list(mode = "single", target = "row"),
options = list(
pageLength = 50,
scrollX = TRUE,
dom = 'tp',
ordering = FALSE,
columnDefs = list(
list(className = 'dt-left', targets = '_all')
)
)
)
Hopefully this solves your problem.

Strange R package behaviour: "could not find function"

I have some functionality which works fine outside of a package, but when I put it into a package, devtools::load_all, and try to run one of the functions (DTL_similarity_search_results_fast) , another function (DTL_similarity_search) which should be loaded by the package is not found when it gets run inside of DTL_similarity_search_results_fast.
The code is:
messagef <- function(...) message(sprintf(...))
printf <- function(...) print(sprintf(...))
pattern_to_vec <- function(pattern, as_int = F, keep_list = FALSE) {
ret <- strsplit(pattern, ",")
if(length(pattern) == 1 && !keep_list)
ret <- ret[[1]]
if(as_int){
ret <- lapply(ret, as.integer)
}
ret
}
DTL_similarity_search <- function(search_pattern = "1,2,1,2,1,2,1,2",
transformation = "interval",
database_names = "dtl,wjazzd,omnibook",
metadata_filters = '{"dtl": {}, "wjazzd": {}, "esac": {}, "omnibook": {}}',
filter_category = "0",
minimum_similarity = 1.0,
max_edit_distance = NA,
max_length_difference = 0) {
url <- suppressWarnings(httr::modify_url("https://staging-dtl-pattern-api.hfm-weimar.de/", path = "/patterns/similar"))
if(is.na(max_edit_distance)){
max_edit_distance <- purrr::map_int(pattern_to_vec(search_pattern, keep_list = T), length) %>% min()
}
messagef("[DTL API] Starting search for %s", search_pattern)
resp <- suppressWarnings(httr::POST(url, body = list( n_gram = search_pattern,
transformation = transformation,
database_names = database_names,
metadata_filters = metadata_filters,
filter_category = filter_category,
minimum_similarity = minimum_similarity,
max_edit_distance = max_edit_distance,
max_length_difference = max_length_difference, filter_category = 0),
encode = "form"))
#browser()
#print(httr::content(resp, "text"))
if (httr::http_error(resp)) {
messagef(
"[DTL API] Similarity Search request failed [%s]\n%s\n<%s>",
httr::status_code(resp),
"",#parsed$message,
""#parsed$documentation_url
)
return(NULL)
}
parsed <- jsonlite::fromJSON(httr::content(resp, "text"), simplifyVector = FALSE)
messagef("[DTL API] Retrieved search ID %s of for pattern %s", parsed$search_id, search_pattern)
parsed$search_id
}
DTL_get_results <- function(search_id) {
url <- suppressWarnings(httr::modify_url("http://staging-dtl-pattern-api.hfm-weimar.de/", path = "/patterns/get"))
#messagef("[DTL API] Retrieving results for search_id %s", search_id)
resp <- suppressWarnings(httr::GET(url, query = list(search_id = search_id)))
if (httr::http_error(resp)) {
messagef(
"[DTL API] Similarity Search request failed [%s]\n%s\n<%s>",
httr::status_code(resp),
"",#parsed$message,
""#parsed$documentation_url
)
return(NULL)
}
print(httr::content(resp, "text"))
#browser()
parsed <- jsonlite::fromJSON(httr::content(resp, "text"), simplifyVector = FALSE)
messagef("[DTL API] Retrieved %s lines for search_id %s", length(parsed), search_id)
purrr::map_dfr(parsed, function(x){
if(is.null(x$within_single_phrase)){
x$within_single_phrase <- FALSE
}
#browser()
tibble::as_tibble(x) %>% dplyr::mutate(melid = as.character(melid))
})
}
DTL_similarity_search_results <- function(search_patterns = "1,2,1,2,1,2,1,2",
transformation = "interval",
database_names = "dtl,wjazzd,omnibook",
metadata_filters = '{"dtl": {}, "wjazzd": {}, "esac": {}, "omnibook": {}}',
filter_category = "0",
minimum_similarity = 1.0,
max_edit_distance = NA,
max_length_difference = 0) {
results <- tibble::tibble()
if(is.na(max_edit_distance)){
max_edit_distance <- purrr:::map_int(pattern_to_vec(search_patterns, keep_list = T), length) %>% min()
}
for(pattern in search_patterns){
print('DTL_similarity_search')
print(DTL_similarity_search)
search_id <- DTL_similarity_search(pattern,
transformation,
database_names,
metadata_filters,
filter_category,
minimum_similarity,
max_edit_distance = max_edit_distance,
max_length_difference = max_length_difference)
if(is.null(search_id)){
next
}
ret <- DTL_get_results(search_id)
if(!is.null(ret) && nrow(ret) > 0){
ret$search_pattern <- pattern
}
results <- dplyr::bind_rows(results, ret)
}
#browser()
if(nrow(results))
results %>% dplyr::distinct(melid, start, length, .keep_all = T)
}
DTL_similarity_search_results_fast <- function(search_patterns = "1,2,1,2,1,2,1,2",
transformation = "interval",
database_names = "dtl,wjazzd,omnibook",
metadata_filters = '{"dtl": {}, "wjazzd": {}, "esac": {}, "omnibook": {}}',
filter_category = "0",
minimum_similarity = 1.0,
max_edit_distance = NA,
max_length_difference = 0){
if(is.na(max_edit_distance)){
max_edit_distance <- purrr::map_int(pattern_to_vec(search_patterns, keep_list = T), length) %>% min()
}
future::plan(future::multisession)
results <- furrr:::future_map_dfr(search_patterns, function(pattern){
print('DTL_similarity_search2')
search_id <- DTL_similarity_search(pattern,
transformation,
database_names,
metadata_filters,
filter_category,
minimum_similarity,
max_edit_distance = max_edit_distance,
max_length_difference = max_length_difference)
if(is.null(search_id)){
return(tibble::tibble())
}
ret <- DTL_get_results(search_id)
if(!is.null(ret) && nrow(ret) > 0 )ret$search_pattern <- pattern
ret
})
#browser()
results %>% dplyr::distinct(melid, start, length, .keep_all = TRUE)
}
Then after load_all() when I try to run:
res <- DTL_similarity_search_results_fast()
I get:
Error in DTL_similarity_search(pattern, transformation,
database_names, : could not find function "DTL_similarity_search
but running a similar, different function works using the same procedure:
res <- DTL_similarity_search_results()

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