Basic data analysis with palmerpenguins
[This article was first published on R-posts.com, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.
Introduction
In June 17, nice article for introducing new trial dataset were uploaded via R-bloggers.
iris, one of commonly used dataset for simple data analysis. but there is a little issue for using it.
Too good.
Every data has well-structured and most of analysis method works with iris very well.
In reality, most of dataset is not pretty and requires a lot of pre-process to just start. This can be possible works in pre-process
Remove
NA
s.Select meaningful features
Handle
duplicated
or inconsistent
values.or even, just
loading
the dataset. if is not well-structured like Flipkart-productsHowever, in this penguin dataset, you can try for this work. also there’s pre-processed data too.
For more information, see the page of palmerpenguins.
There is a routine for me with brief data analysis. and today, I want to share them with this lovely penguins.
Contents
0. Load dataset and library on workspace.
library(palmerpenguins) # for data library(dplyr) # for data-handling library(corrplot) # for correlation plot library(GGally) # for parallel coordinate plot library(e1071) # for svm data(penguins) # load pre-processed penguins
palmerpenguins
have 2 data penguins
, penguins_raw
, and as you can see from their name, penguins
is pre-processed data. 1. See the
summary
and plot
of Dataset
summary(penguins) plot(penguins)
It seems
species
, island
and sex
is categorical features.and remaining for numerical features.
2. Set the format of feature
penguins$species <- as.factor(penguins$species) penguins$island <- as.factor(penguins$island) penguins$sex <- as.factor(penguins$sex) summary(penguins) plot(penguins)and see
summary
and plot
again. note that result of plot
is same. There’s unwanted
NA
and .
values in some features.3. Remove not necessary datas ( in this tutorial,
NA
)penguins <- penguins %>% filter(sex == 'MALE' | sex == 'FEMALE') summary(penguins)And here, I additionally defined color values for each penguins to see better
plot
result
# Green, Orange, Purple pCol <- c('#057076', '#ff8301', '#bf5ccb') names(pCol) <- c('Gentoo', 'Adelie', 'Chinstrap') plot(penguins, col = pCol[penguins$species], pch = 19)
Now, plot results are much better to give insights.
Note that, other pre-process step may requires for different datasets.
4. See relation of categorical features
My first purpose of analysis this penguin is
species
So, I will try to see relation between
species
and other categorical values4-1.
species
, island
table(penguins$species, penguins$island) chisq.test(table(penguins$species, penguins$island)) # meaningful difference ggplot(penguins, aes(x = island, y = species, color = species)) + geom_jitter(size = 3) + scale_color_manual(values = pCol)
Wow, there’s strong relationship between
species
and island
–
Adelie
lives in every island –
Gentoo
lives in only Biscoe
–
Chinstrap
lives in only Dream
4-2 & 4.3.
However,
species
and sex
or sex
and island
did not show any meaningful relation.You can try following codes.
# species vs sex table(penguins$sex, penguins$species) chisq.test(table(penguins$sex, penguins$species)[-1,]) # not meaningful difference 0.916 # sex vs island table(penguins$sex, penguins$island) # 0.9716 chisq.test(table(penguins$sex, penguins$island)[-1,]) # not meaningful difference 0.97165. See with numerical features
I will select numerical features.
and see correlation plot and parallel coordinate plots.
# Select numericals penNumeric <- penguins %>% select(-species, -island, -sex) # Cor-relation between numerics corrplot(cor(penNumeric), type = 'lower', diag = FALSE) # parallel coordinate plots ggparcoord(penguins, columns = 3:6, groupColumn = 1, order = c(4,3,5,6)) + scale_color_manual(values = pCol) plot(penNumeric, col = pCol[penguins$species], pch = 19)and below are result of them.
lucky, every numeric features (even only 4) have meaningful correlation and there is trend with their combination for
species
(See parallel coordinate plot)6. Give statistical work on dataset.
In this step, I usually do
linear modeling
or svm
to predict6.1
linear modeling
species
is categorical value, so it needs to be change to numeric valueset.seed(1234) idx <- sample(1:nrow(penguins), size = nrow(penguins)/2) # as. numeric speciesN <- as.numeric(penguins$species) penguins$speciesN <- speciesN train <- penguins[idx,] test <- penguins[-idx,] fm <- lm(speciesN ~ flipper_length_mm + culmen_length_mm + culmen_depth_mm + body_mass_g, train) summary(fm)
It shows that,
body_mass_g
is not meaningful feature as seen in plot
above ( it may explain gentoo
, but not other penguins )To predict, I used this code. however, numeric predict generate not complete value (like 2.123 instead of 2) so I added rounding step.
predRes <- round(predict(fm, test)) predRes[which(predRes>3)] <- 3 predRes <- sort(names(pCol))[predRes] test$predRes <- predRes ggplot(test, aes(x = species, y = predRes, color = species))+ geom_jitter(size = 3) + scale_color_manual(values = pCol) table(test$predRes, test$species)
Accuracy of basic
linear modeling
is 94.6%6-2
svm
using
svm
is also easy step.m <- svm(species ~., train) predRes2 <- predict(m, test) test$predRes2 <- predRes2 ggplot(test, aes(x = species, y = predRes2, color = species)) + geom_jitter(size = 3) + scale_color_manual(values = pCol) table(test$species, test$predRes2)and below are result of this code.
Accuracy of
svm
is 100%. wow.Conclusion
Today I introduced simple routine for EDA and statistical analysis with penguins.
That is not difficult that much, and shows good performances.
Of course, I skipped a lot of things like processing raw-dataset.
However I hope this trial gives inspiration for further data analysis.
Thanks.
To leave a comment for the author, please follow the link and comment on their blog: R-posts.com.
R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.