Combining results from multiple chi squared tests - r

I have ran 3 chi suqared tests and I have combined them using the code below.
df2 <- data.frame(chisq.test_age, chisq.test_eth, chisq.test_reg, chisq.test_sex)
I have attached a photo below of what happens. Is there a way I can have this so the results are not just in a straight line? i.e where I have the variables on the y axis and the results (e.g p value) on the x axis.

You could use broom's tidy and dplyr's bind_rows:
library(tidyverse)
library(broom)
chit1 <- chisq.test(xtabs(Freq ~ Sex + Class, data = as.data.frame(Titanic)))
chit2 <- chisq.test(xtabs(mpg ~ disp + hp, data = as.data.frame(mtcars)))
bind_rows(
tidy(chit1),
tidy(chit2)
)
#> # A tibble: 2 × 4
#> statistic p.value parameter method
#> <dbl> <dbl> <int> <chr>
#> 1 350. 1.56e-75 3 Pearson's Chi-squared test
#> 2 13222. 0 546 Pearson's Chi-squared test
Created on 2022-05-12 by the reprex package (v2.0.1)

Here is a base R way. The tests' results are put in a list with mget/ls, then a series of lapply loops gets the relevant list members. Finally, do.call bind them together.
The tests are taken from help("chisq.test").
# 1st test
M <- as.table(rbind(c(762, 327, 468), c(484, 239, 477)))
dimnames(M) <- list(gender = c("F", "M"),
party = c("Democrat","Independent", "Republican"))
chisq.test_Xsq1 <- chisq.test(M)
# 2nd test
x <- matrix(c(12, 5, 7, 7), ncol = 2)
chisq.test_Xsq2 <- chisq.test(x)
# 3rd test
x <- c(A = 20, B = 15, C = 25)
chisq.test_Xsq3 <- chisq.test(x)
test_list <- mget(ls(pattern = "^chisq.test_"))
test_list <- lapply(test_list, unclass)
test_list <- lapply(test_list, `[`, 1:3)
do.call(rbind, test_list)
#> statistic parameter p.value
#> chisq.test_Xsq1 30.07015 2 2.953589e-07
#> chisq.test_Xsq2 0.6411203 1 0.4233054
#> chisq.test_Xsq3 2.5 2 0.2865048
Created on 2022-05-12 by the reprex package (v2.0.1)

Related

How can I extract, label and data.frame values from Console in a loop?

I made a nls loop and get values calculated in console. Now I want to extract those values, specify which values are from which group and put everything in a dataframe to continue working.
my loop so far:
for (i in seq_along(trtlist2)) { loopmm.nls <-
nls(rate ~ (Vmax * conc /(Km + conc)),
data=subset(M3, M3$trtlist==trtlist2[i]),
start=list(Km=200, Vmax=2), trace=TRUE )
summary(loopmm.nls)
print(summary(loopmm.nls))
}
the output in console: (this is what I want to extract and put in a dataframe, I have this same "parameters" thing like 20 times)
Parameters:
Estimate Std. Error t value Pr(>|t|)
Km 23.29820 9.72304 2.396 0.0228 *
Vmax 0.10785 0.01165 9.258 1.95e-10 ***
---
different ways of extracting data from the console that work but not in the loop (so far!)
#####extract data in diff ways from nls#####
## extract coefficients as matrix
Kinall <- summary(mm.nls)$parameters
## extract coefficients save as dataframe
Kin <- as.data.frame(Kinall)
colnames(Kin) <- c("values", "SE", "T", "P")
###create Km Vmax df
Kms <- Kin[1, ]
Vmaxs <- Kin[2, ]
#####extract coefficients each manually
Km <- unname(coef(summary(mm.nls))["Km", "Estimate"])
Vmax <- unname(coef(summary(mm.nls))["Vmax", "Estimate"])
KmSE <- unname(coef(summary(mm.nls))["Km", "Std. Error"])
VmaxSE <- unname(coef(summary(mm.nls))["Vmax", "Std. Error"])
KmP <- unname(coef(summary(mm.nls))["Km", "Pr(>|t|)"])
VmaxP <- unname(coef(summary(mm.nls))["Vmax", "Pr(>|t|)"])
KmT <- unname(coef(summary(mm.nls))["Km", "t value"])
VmaxT <- unname(coef(summary(mm.nls))["Vmax", "t value"])
one thing that works if you extract data through append, but somehow that only works for "estimates" not the rest
Kms <- append(Kms, unname(coef(loopmm.nls)["Km"] ))
Vmaxs <- append(Vmaxs, unname(coef(loopmm.nls)["Vmax"] ))
}
Kindf <- data.frame(trt = trtlist2, Vmax = Vmaxs, Km = Kms)
I would just keep everything in the dataframe for ease. You can nest by the group and then run the regression then pull the coefficients out. Just make sure you have tidyverse and broom installed on your computer.
library(tidyverse)
#example
mtcars |>
nest(data = -cyl) |>
mutate(model = map(data, ~nls(mpg~hp^b,
data = .x,
start = list(b = 1))),
clean_mod = map(model, broom::tidy)) |>
unnest(clean_mod) |>
select(-c(data, model))
#> # A tibble: 3 x 6
#> cyl term estimate std.error statistic p.value
#> <dbl> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 6 b 0.618 0.0115 53.6 2.83e- 9
#> 2 4 b 0.731 0.0217 33.7 1.27e-11
#> 3 8 b 0.504 0.0119 42.5 2.46e-15
#what I expect will work for your data
All_M3_models <- M3 |>
nest(data = -trtlist) |>
mutate(model = map(data, ~nls(rate ~ (Vmax * conc /(Km + conc)),
data=.x,
start=list(Km=200, Vmax=2))),
clean_mod = map(model, broom::tidy))|>
unnest(clean_mod) |>
select(-c(data, model))

Problem using function with "as.formula" in a loop in R

I've created a function that returns an ANOVA table, and it uses formula to create the formula of the oneway.testfunction.
A simplified version of the function is:
anova_table <- function(df, dv, group){
dv_t <- deparse(substitute(dv))
group_t <- deparse(substitute(group))
anova <- oneway.test(formula = formula(paste(dv_t, "~", group_t)),
data = df,
var.equal = F)
return(anova)
}
It works fine when I use it outside a loop:
data("mpg")
mpg <- mpg %>% mutate_if(is.character, as.factor)
anova_table(mpg, displ, drv)
However, I'd like it to work also inside a loop.
When I try the following code, I get this error message:
"Error in model.frame.default(formula = formula(paste(dv_t, "~", group_t)), :
object is not a matrix"
I'm not sure what I'm doing wrong.
vars_sel <- mpg %>% select(where(is.numeric)) %>% names()
vars_sel <- dput(vars_sel)
vars_sel <- syms(vars_sel)
for(i in vars_sel){
var <- sym(i)
print(anova_table(mpg, var, drv))
}
Any help would be much appreciated!
Because of how your function works, the var in your loop is being taken literally, so the function is looking for a column called var in mpg which doesn't exist. You can get round this by building and evaluating a call to your function in the loop:
for(i in vars_sel){
a <- eval(as.call(list(anova_table, df = mpg, dv = i, group = quote(drv))))
print(a)
}
#>
#> One-way analysis of means (not assuming equal variances)
#>
#> data: displ and drv
#> F = 143.9, num df = 2.000, denom df = 67.605, p-value < 2.2e-16
#>
#>
#> One-way analysis of means (not assuming equal variances)
#>
#> data: year and drv
#> F = 0.59072, num df = 2.000, denom df = 67.876, p-value = 0.5567
#>
#>
#> One-way analysis of means (not assuming equal variances)
#>
#> data: cyl and drv
#> F = 129.2, num df = 2.000, denom df = 82.862, p-value < 2.2e-16
#>
#>
#> One-way analysis of means (not assuming equal variances)
#>
#> data: cty and drv
#> F = 89.54, num df = 2.000, denom df = 78.879, p-value < 2.2e-16
#>
#>
#> One-way analysis of means (not assuming equal variances)
#>
#> data: hwy and drv
#> F = 127.14, num df = 2.000, denom df = 71.032, p-value < 2.2e-16
Created on 2022-09-25 with reprex v2.0.2

Run all posible combination of linear regression with 2 independent variables

I want to run every combination possible for every 2 independent variables (OLS regression). I have a csv where I have my data (just one dependent variable and 23 independent variables), and I've tried renaming the variables inside my database from a to z, and I called 'y' to my dependent variable (a column with name "y" which is my dependent variable) to be recognized by the following code:
#all the combinations
all_comb <- combn(letters, 2)
#create the formulas from the combinations above and paste
text_form <- apply(all_comb, 2, function(x) paste('Y ~', paste0(x, collapse = '+')))
lapply(text_form, function(i) lm(i, data= KOFS05.12))
but this error is shown:
Error in eval(predvars, data, env) : object 'y' not found
I need to know the R squared
Any idea to make it work and run every possible regression?
As mentioned in the comments under the question check whether you need y or Y. Having addressed that we can use any of these. There is no need to rename the columns. We use the built in mtcars data set as an example since no test data was provided in the question. (Please always provide that in the future.)
1) ExhaustiveSearch This runs quite fast so you might be able to try combinations higher than 2 as well.
library(ExhaustiveSearch)
ExhaustiveSearch(mpg ~., mtcars, combsUpTo = 2)
2) combn Use the lmfun function defined below with combn.
dep <- "mpg" # name of dependent variable
nms <- setdiff(names(mtcars), dep) # names of indep variables
lmfun <- function(x, dep) do.call("lm", list(reformulate(x, dep), quote(mtcars)))
lms <- combn(nms, 2, lmfun, dep = dep, simplify = FALSE)
names(lms) <- lapply(lms, formula)
3) listcompr Using lmfun from above and listcompr we can use the following. Note that we need version 0.1.1 or later of listcompr which is not yet on CRAN so we get it from github.
# install.github("patrickroocks/listcompr")
library(listcompr)
packageVersion("listcompr") # need version 0.1.1 or later
dep <- "mpg" # name of dependent variable
nms <- setdiff(names(mtcars), dep) # names of indep variables
lms2 <- gen.named.list("{nm1}.{nm2}", lmfun(c(nm1, nm2), dep),
nm1 = nms, nm2 = nms, nm1 < nm2)
You should specify your text_form as formulas:
KOFS05.12 <- data.frame(y = rnorm(10),
a = rnorm(10),
b = rnorm(10),
c = rnorm(10))
all_comb <- combn(letters[1:3], 2)
fmla_form <- apply(all_comb, 2, function(x) as.formula(sprintf("y ~ %s", paste(x, collapse = "+"))))
lapply(fmla_form, function(i) lm(i, KOFS05.12))
#> [[1]]
#>
#> Call:
#> lm(formula = i, data = KOFS05.12)
#>
#> Coefficients:
#> (Intercept) a b
#> 0.19763 -0.15873 0.02854
#>
#>
#> [[2]]
#>
#> Call:
#> lm(formula = i, data = KOFS05.12)
#>
#> Coefficients:
#> (Intercept) a c
#> 0.21395 -0.15967 0.05737
#>
#>
#> [[3]]
#>
#> Call:
#> lm(formula = i, data = KOFS05.12)
#>
#> Coefficients:
#> (Intercept) b c
#> 0.157140 0.002523 0.028088
Created on 2021-02-17 by the reprex package (v1.0.0)

can't group by with a tibble

I'm doing cross validation (five fold). Then I want to calculate the mean value for each group in a given data set I used for that cv. Please note that I need to use the following functions.
data(mpg)
library(modelr)
cv <- crossv_kfold(mpg, k = 5)
models1 <- map(cv$train, ~lm(hwy ~ displ, data = .))
get_pred <- function(model, test_data){
data <- as.data.frame(test_data)
pred <- add_predictions(data, model)
return(pred)
}
pred1 <- map2_df(models1, cv$test, get_pred, .id = "Run")
MSE1 <- pred1 %>% group_by(Run) %>%
summarise(MSE = mean( (hwy - pred)^2))
MSE1
My problem lies with the output of 'summarise'. The function should be applied to each group. The result should look something like this:
## # A tibble: 5 x 2
## Run MSE
## <chr> <dbl>
## 1 1 27.889532
## 2 2 8.673054
## 3 3 17.033056
## 4 4 12.552037
## 5 5 9.138741
Unfortunately, I get only one value:
MSE
1 14.77799
How can I get a tibble like that above?
When I run your code, I get the style of output you are expecting (though the numbers are different (as the seed wasn't set in your example)); I do not see a summarise-type problem like you do:
library(ggplot2)
library(modelr)
library(purrr)
library(dplyr)
data(mpg)
cv <- crossv_kfold(mpg, k = 5)
models1 <- map(cv$train, ~lm(hwy ~ displ, data = .))
get_pred <- function(model, test_data){
data <- as.data.frame(test_data)
pred <- add_predictions(data, model)
return(pred)
}
pred1 <- map2_df(models1, cv$test, get_pred, .id = "Run")
MSE1 <- pred1 %>% group_by(Run) %>%
summarise(MSE = mean( (hwy - pred)^2))
MSE1
# A tibble: 5 x 2
Run MSE
<chr> <dbl>
1 1 7.80
2 2 12.5
3 3 9.82
4 4 27.3
5 5 17.5

R: t test over multiple columns using t.test function

I tried to perform independent t-test for many columns of a dataframe. For example, i created a data frame
set seed(333)
a <- rnorm(20, 10, 1)
b <- rnorm(20, 15, 2)
c <- rnorm(20, 20, 3)
grp <- rep(c('m', 'y'),10)
test_data <- data.frame(a, b, c, grp)
To run the test, i used with(df, t.test(y ~ group))
with(test_data, t.test(a ~ grp))
with(test_data, t.test(b ~ grp))
with(test_data, t.test(c ~ grp))
I would like to have the outputs like this
mean in group m mean in group y p-value
9.747412 9.878820 0.6944
15.12936 16.49533 0.07798
20.39531 20.20168 0.9027
I wonder how can I achieve the results using
1. for loop
2. apply()
3. perhaps dplyr
This link R: t-test over all columns is related but it was 6 years old. Perhaps there are better ways to do the same thing.
Use select_if to select only numeric columns then use purrr:map_df to apply t.test against grp. Finally use broom:tidy to get the results in tidy format
library(tidyverse)
res <- test_data %>%
select_if(is.numeric) %>%
map_df(~ broom::tidy(t.test(. ~ grp)), .id = 'var')
res
#> # A tibble: 3 x 11
#> var estimate estimate1 estimate2 statistic p.value parameter conf.low
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 a -0.259 9.78 10.0 -0.587 0.565 16.2 -1.19
#> 2 b 0.154 15.0 14.8 0.169 0.868 15.4 -1.78
#> 3 c -0.359 20.4 20.7 -0.287 0.778 16.5 -3.00
#> # ... with 3 more variables: conf.high <dbl>, method <chr>,
#> # alternative <chr>
Created on 2019-03-15 by the reprex package (v0.2.1.9000)
Simply extract the estimate and p-value results from t.test call while iterating through all needed columns with sapply. Build formulas from a character vector and transpose with t() for output:
formulas <- paste(names(test_data)[1:(ncol(test_data)-1)], "~ grp")
output <- t(sapply(formulas, function(f) {
res <- t.test(as.formula(f))
c(res$estimate, p.value=res$p.value)
}))
Input data (seeded for reproducibility)
set.seed(333)
a <- rnorm(20, 10, 1)
b <- rnorm(20, 15, 2)
c <- rnorm(20, 20, 3)
grp <- rep(c('m', 'y'),10)
test_data <- data.frame(a, b, c, grp)
Output result
# mean in group m mean in group y p.value
# a ~ grp 9.775477 10.03419 0.5654353
# b ~ grp 14.972888 14.81895 0.8678149
# c ~ grp 20.383679 20.74238 0.7776188
As you asked for a for loop:
a <- rnorm(20, 10, 1)
b <- rnorm(20, 15, 2)
c <- rnorm(20, 20, 3)
grp <- rep(c('m', 'y'),10)
test_data <- data.frame(a, b, c, grp)
meanM=NULL
meanY=NULL
p.value=NULL
for (i in 1:(ncol(test_data)-1)){
meanM=as.data.frame(rbind(meanM, t.test(test_data[,i] ~ grp)$estimate[1]))
meanY=as.data.frame(rbind(meanY, t.test(test_data[,i] ~ grp)$estimate[2]))
p.value=as.data.frame(rbind(p.value, t.test(test_data[,i] ~ grp)$p.value))
}
cbind(meanM, meanY, p.value)
It works, but I am a beginner in R. So maybe there is a more efficient solution
Using lapply this is rather easy.
I have tested the code with set.seed(7060) before creating the dataset, in order to make the results reproducible.
tests_list <- lapply(letters[1:3], function(x) t.test(as.formula(paste0(x, "~ grp")), data = test_data))
result <- do.call(rbind, lapply(tests_list, `[[`, "estimate"))
pval <- sapply(tests_list, `[[`, "p.value")
result <- cbind(result, p.value = pval)
result
# mean in group m mean in group y p.value
#[1,] 9.909818 9.658813 0.6167742
#[2,] 14.578926 14.168816 0.6462151
#[3,] 20.682587 19.299133 0.2735725
Note that a real life application would use names(test_data)[1:3], not letters[1:3], in the first lapply instruction.
This should be a comment rather than an answer, but I'll make it an answer. The reason is that the accepted answer is awesome but with one caveat that may cost others hours, which is at least the case for me.
The original data posted by OP
a <- rnorm(20, 10, 1)
b <- rnorm(20, 15, 2)
c <- rnorm(20, 20, 3)
grp <- rep(c('m', 'y'),10)
test_data <- data.frame(a, b, c, grp)
The answer provided by #Tung
library(tidyverse)
res <- test_data %>%
select_if(is.numeric) %>%
map_df(~ broom::tidy(t.test(. ~ grp)), .id = 'var')
res
The problem, or more accurately, the caveat, of this answer is that one has to define the grp variable separately. Having the group variable outside of the dataframe is not a common practice as far as I know. So, even the answer is neat, it may be better to point out this operation (define group variable outside of the dataframe). Therefore, I use this comment like answer in the hope to save some time for those late comers.

Resources