I recently asked the question "Can I use group_map or group_walk to iteratively export results?", and the code was working perfectly, but as of today, it no longer works. I tried updating my packages and RStudio, and this did not work. The data are:
| MiniType | MiniAssay | StandardAssay | Freq |
|---|---|---|---|
| Assay1 | neg | neg | 19 |
| Assay1 | neg | pos | 5 |
| Assay1 | pos | neg | 8 |
| Assay1 | pos | pos | 141 |
| Assay2 | neg | neg | 25 |
| Assay2 | neg | pos | 6 |
| Assay2 | pos | neg | 17 |
| Assay2 | pos | pos | 33 |
| Assay3 | neg | neg | 99 |
| Assay3 | neg | pos | 20 |
| Assay3 | pos | neg | 5 |
| Assay3 | pos | pos | 105 |
The code is:
check_create_dir <- function(the_dir) {
if (!dir.exists(the_dir)) {
dir.create(the_dir, recursive = TRUE) } #Creates a directory if it doesn't already exist
}
the_dir_ex <- "data_generated/epidata" #Name the new desired directory
check_create_dir(the_dir_ex) #Make the directory if it doesn't already exist
#Make function for the series of analyses
epi_analysis <- function(a_csv, the_dir){
#Clean data
dat2 <- a_csv %>%
select(c(MiniAssay, StandardAssay, Freq)) %>%
pivot_wider(MiniAssay, names_from = StandardAssay, values_from = Freq) %>%
remove_rownames %>%
column_to_rownames(var = "MiniAssay") %>%
as.matrix()
#Run tests
rval <- epi.tests(dat2, conf.level = 0.95)
rkappa <- epi.kappa(dat2)
gwet <- gwet.ac1.table(dat2)
gwet_ci <- gwet$coeff.ci #CI is presented as (###,###); needs to be cleaned to separate lwr and upr vals
gwet_ci <- gsub('[\\(]', '', gwet_ci)#Removes ( from string
gwet_ci <- gsub('[\\)]', '', gwet_ci)#Removes ) from string
gwet_ci <- strsplit(gwet_ci, ",")#Splits string at , so that it becomes a list of 1 with 2 different characters
kappa2 <- kappa2.table(dat2)
kappa_ci <- kappa2$coeff.ci #CI is presented as (###,###); needs to be cleaned to separate lwr and upr vals
kappa_ci <- gsub('[\\(]', '', kappa_ci)#Removes ( from string
kappa_ci <- gsub('[\\)]', '', kappa_ci)#Removes ) from string
kappa_ci <- strsplit(kappa_ci, ",")#Splits string at , so that it becomes a list of 1 with 2 different characters
#Export results
hd <- c('sensitivity', 'specificity','ppv','npv', 'pfp', 'pfn', 'kappa', 'gwet', 'pabak')
ests <- c(round(rval$elements$sensitivity$est, digits = 3),
round(rval$elements$specificity$est, digits = 3),
round(rval$elements$ppv, digits = 3),
round(rval$elements$npv, digits = 3),
round(rval$element$pfp$est, digits = 3),
round(rval$element$pfn$est, digits = 3),
round(kappa2$coeff.val, digits = 3),
round(gwet$coeff.val, digits = 3),
round(rkappa$pabak$est, digits = 3))
ci_lwr <- c(round(rval$elements$sensitivity$lower, digits = 3),
round(rval$elements$specificity$lower, digits = 3),
round(rval$elements$ppv.low , digits = 3),
round(rval$elements$npv.low, digits = 3),
round(rval$element$pfp$lower, digits = 3),
round(rval$element$pfn$lower, digits = 3),
kappa_ci[[1]][1],
gwet_ci[[1]][1],
round(rkappa$pabak$lower, digits = 3))
ci_upr <- c(round(rval$elements$sensitivity$upper, digits = 3),
round(rval$elements$specificity$upper, digits = 3),
round(rval$elements$ppv.up , digits = 3),
round(rval$elements$npv.up, digits = 3),
round(rval$element$pfp$upper, digits = 3),
round(rval$element$pfn$upper, digits = 3),
kappa_ci[[1]][2],
gwet_ci[[1]][2],
round(rkappa$pabak$upper, digits = 3))
write.csv(df,
file = sprintf('%s/%s.csv', the_dir, a_csv$MiniType[1]),
na = "999.99",
row.names = FALSE)
}
When I try to execute the functions:
#Execute functions
data <- read_csv("data_raw/EpiData.csv") %>%
group_by(MiniType)%>%
group_map(~ epi_analysis(., the_dir_ex), .keep = TRUE)
I get:
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class ‘"function"’ to a data.frame
16.
stop(gettextf("cannot coerce class %s to a data.frame", sQuote(deparse(class(x))[1L])),
domain = NA)
15.
as.data.frame.default(x[[i]], optional = TRUE)
14.
as.data.frame(x[[i]], optional = TRUE)
13.
data.frame(x)
12.
write.table(df, file = sprintf("%s/%s.csv", the_dir, a_csv$MiniType[1]),
na = "999.99", row.names = FALSE, col.names = TRUE, sep = ",",
dec = ".", qmethod = "double")
11.
eval(expr, p)
10.
eval(expr, p)
9.
eval.parent(Call)
8.
write.csv(df, file = sprintf("%s/%s.csv", the_dir, a_csv$MiniType[1]),
na = "999.99", row.names = FALSE)
7.
epi_analysis(., the_dir_ex)
6.
(structure(function (..., .x = ..1, .y = ..2, . = ..1)
epi_analysis(., the_dir_ex), class = c("rlang_lambda_function",
"function")))(dots[[1L]][[1L]], dots[[2L]][[1L]])
5.
mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
4.
map2(chunks, group_keys, .f, ...)
3.
group_map.data.frame(., ~epi_analysis(., the_dir_ex), .keep = TRUE)
2.
group_map(., ~epi_analysis(., the_dir_ex), .keep = TRUE)
1.
read_csv("data_raw/EpiData.csv") %>% group_by(MiniType) %>% group_map(~epi_analysis(.,
the_dir_ex), .keep = TRUE)
If I try to execute the functions with:
#ALTERNATE EXECUTE FUNCTION (AS AN EXAMPLE)
read_csv("data_raw/EpiData.csv") %>%
group_split(MiniType) %>%
map(~ epi_analysis(.x, the_dir_ex))
This had also worked previosly just fine, but now I get:
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class ‘"function"’ to a data.frame
13.
stop(gettextf("cannot coerce class %s to a data.frame", sQuote(deparse(class(x))[1L])),
domain = NA)
12.
as.data.frame.default(x[[i]], optional = TRUE)
11.
as.data.frame(x[[i]], optional = TRUE)
10.
data.frame(x)
9.
write.table(df, file = sprintf("%s/%s.csv", the_dir, a_csv$MiniType[1]),
na = "999.99", row.names = FALSE, col.names = TRUE, sep = ",",
dec = ".", qmethod = "double")
8.
eval(expr, p)
7.
eval(expr, p)
6.
eval.parent(Call)
5.
write.csv(df, file = sprintf("%s/%s.csv", the_dir, a_csv$MiniType[1]),
na = "999.99", row.names = FALSE)
4.
epi_analysis(.x, the_dir_ex)
3.
.f(.x[[i]], ...)
2.
map(., ~epi_analysis(.x, the_dir_ex))
1.
read_csv("data_raw/EpiData.csv") %>% group_split(MiniType) %>%
map(~epi_analysis(.x, the_dir_ex))
I am operating a PC with Windows 10, and R v4.0.3 and RStudio v1.4.1717
I need to get this code working again, any help is appreciated.
