Tag: r

How to Write a Git Commit Message, in 7 Steps

How to Write a Git Commit Message, in 7 Steps

Version control is an essential tool for any software developer. Hence, any respectable data scientist has to make sure his/her analysis programs and machine learning pipelines are reproducible and maintainable through version control.

Often, we use git for version control. If you don’t know what git is yet, I advise you begin here. If you work in R, start here and here. If you work in Python, start here.

This blog is intended for those already familiar working with git, but who want to learn how to write better, more informative git commit messages. Actually, this blog is just a summary fragment of this original blog by Chris Beams, which I thought deserved a wider audience.

Chris’ 7 rules of great Git commit messaging

  1. Separate subject from body with a blank line
  2. Limit the subject line to 50 characters
  3. Capitalize the subject line
  4. Do not end the subject line with a period
  5. Use the imperative mood in the subject line
  6. Wrap the body at 72 characters
  7. Use the body to explain what and why vs. how

For example:

Summarize changes in around 50 characters or less

More detailed explanatory text, if necessary. Wrap it to about 72
characters or so. In some contexts, the first line is treated as the
subject of the commit and the rest of the text as the body. The
blank line separating the summary from the body is critical (unless
you omit the body entirely); various tools like `log`, `shortlog`
and `rebase` can get confused if you run the two together.

Explain the problem that this commit is solving. Focus on why you
are making this change as opposed to how (the code explains that).
Are there side effects or other unintuitive consequences of this
change? Here's the place to explain them.

Further paragraphs come after blank lines.

 - Bullet points are okay, too

 - Typically a hyphen or asterisk is used for the bullet, preceded
   by a single space, with blank lines in between, but conventions
   vary here

If you use an issue tracker, put references to them at the bottom,
like this:

Resolves: #123
See also: #456, #789

If you’re having a hard time summarizing your commits in a single line or message, you might be committing too many changes at once. Instead, you should try to aim for what’s called atomic commits.

Cover image by XKCD#1296

Predictive Power Score: Finding predictive patterns in your dataset

Predictive Power Score: Finding predictive patterns in your dataset

Last week, I shared this Medium blog on PPS — or Predictive Power Score — on my LinkedIn and got so many enthousiastic responses, that I had to share it with here too.

Basically, the predictive power score is a normalized metric (values range from 0 to 1) that shows you to what extent you can use a variable X (say age) to predict a variable Y (say weight in kgs).

A PPS high score of, for instance, 0.85, would show that weight can be predicted pretty good using age.

A low PPS score, of say 0.10, would imply that weight is hard to predict using age.

The PPS acts a bit like a correlation coefficient we’re used too, but it is also different in many ways that are useful to data scientists:

  1. PPS also detects and summarizes non-linear relationships
  2. PPS is assymetric, so that it models Y ~ X, but not necessarily X ~ Y
  3. PPS can summarize predictive value of / among categorical variables and nominal data

However, you may argue that the PPS is harder to interpret than the common correlation coefficent:

  1. PPS can reflect quite complex and very different patterns
  2. Therefore, PPS are hard to compare: a 0.5 may reflect a linear relationship but also many other relationships
  3. PPS are highly dependent on the used algorithm: you can use any algorithm from OLS to CART to full-blown NN or XGBoost. Your algorithm hihgly depends the patterns you’ll detect and thus your scores
  4. PPS are highly dependent on the the evaluation metric (RMSE, MAE, etc).

Here’s an example picture from the original blog, showing a case in which PSS shows the relevant predictive value of Y ~ X, whereas a correlation coefficient would show no relationship whatsoever:

https://towardsdatascience.com/rip-correlation-introducing-the-predictive-power-score-3d90808b9598

Here’s two more pictures from the original blog showing the differences with a standard correlation matrix on the Titanic data:

I highly suggest you read the original blog for more details and information, and that you check out the associated Python package ppscore:

Installing the package:

pip install ppscore

Calculating the PPS for a given pandas dataframe:

import ppscore as pps
pps.score(df, "feature_column", "target_column")

You can also calculate the whole PPS matrix:

pps.matrix(df)

There’s no R package yet, but it should not be hard to implement this general logic.

Florian Wetschoreck — the author — already noted that there may be several use cases where he’d think PPS may add value:

Find patterns in the data [red: data exploration]: The PPS finds every relationship that the correlation finds — and more. Thus, you can use the PPS matrix as an alternative to the correlation matrix to detect and understand linear or nonlinear patterns in your data. This is possible across data types using a single score that always ranges from 0 to 1.

Feature selection: In addition to your usual feature selection mechanism, you can use the predictive power score to find good predictors for your target column. Also, you can eliminate features that just add random noise. Those features sometimes still score high in feature importance metrics. In addition, you can eliminate features that can be predicted by other features because they don’t add new information. Besides, you can identify pairs of mutually predictive features in the PPS matrix — this includes strongly correlated features but will also detect non-linear relationships.

Detect information leakage: Use the PPS matrix to detect information leakage between variables — even if the information leakage is mediated via other variables.

Data Normalization: Find entity structures in the data via interpreting the PPS matrix as a directed graph. This might be surprising when the data contains latent structures that were previously unknown. For example: the TicketID in the Titanic dataset is often an indicator for a family.

https://towardsdatascience.com/rip-correlation-introducing-the-predictive-power-score-3d90808b9598
Generative art: Let your computer design you a painting

Generative art: Let your computer design you a painting

I really like generative art, or so-called algorithmic art. Basically, it means you take a pattern or a complex system of rules, and apply it to create something new following those patterns/rules.

When I finished my PhD, I got a beautiful poster of where the k-nearest neighbors algorithms was used to generate a set of connected points.

Marcus Volz’ nearest neighbors graph, via https://marcusvolz.com/#nearest-neighbour-graph

My first piece of generative art.

As we recently moved into our new house, I decided I wanted to have a brother for the knn-poster. So I did some research in algorithms I wanted to use to generate a painting. I found some very cool ones, of which I unforunately can’t recollect the artists anymore:

However, I preferred to make one myself. So we again turned to the work of the author that made the knn-poster: Marcus Volz.

He has written (in R) many other algorithms. And we found that one specifically nicely matched the knn-poster. His metropolis – or generative city:

Marcus’ generative city, via https://marcusvolz.com/#generative-city

However, I wanted to make one myself, so I download Marcus code, and tweaked it a bit. Most importantly, I made it start in the center, made it fill up the whole space, and I made it run more efficient so I could generate a couple dozen large cities quickly, and pick the one I liked most. Here’s the end result:

And in action, in my living room:

Free Springer Books during COVID19

Free Springer Books during COVID19

Update: Unfortunately, Springer removed the free access to its books.

Book publisher Springer just released over 400 book titles that can be downloaded free of charge following the corona-virus outbreak.

Here’s the full overview: https://link.springer.com/search?facet-content-type=%22Book%22&package=mat-covid19_textbooks&facet-language=%22En%22&sortOrder=newestFirst&showAll=true

Most of these books will normally set you back about $50 to $150, so this is a great deal!

There are many titles on computer science, programming, business, psychology, and here are some specific titles that might interest my readership:

Note that I only got to page 8 of 21, so there are many more free interesting titles out there!

Join 274 other followers

Simulating and visualizing the Monty Hall problem in Python & R

Simulating and visualizing the Monty Hall problem in Python & R

I recently visited a data science meetup where one of the speakers — Harm Bodewes — spoke about playing out the Monty Hall problem with his kids.

The Monty Hall problem is probability puzzle. Based on the American television game show Let’s Make a Deal and its host, named Monty Hall:

You’re given the choice of three doors.

Behind one door sits a prize: a shiny sports car.

Behind the others doors, something shitty, like goats.

You pick a door — say, door 1.

Now, the host, who knows what’s behind the doors, opens one of the other doors — say, door 2 — which reveals a goat.

The host then asks you:
Do you want to stay with door 1,
or
would you like to switch to door 3?

The probability puzzle here is:

Is switching doors the smart thing to do?

Back to my meetup.

Harm — the presenter — had ran the Monty Hall experiment with his kids.

Twenty-five times, he had hidden candy under one of three plastic cups. His kids could then pick a cup, he’d remove one of the non-candy cups they had not picked, and then he’d proposed them to make the switch.

The results he had tracked, and visualized in a simple Excel graph. And here he was presenting these results to us, his Meetup audience.

People (also statisticans) had been arguing whether it is best to stay or switch doors for years. Yet, here, this random guy ran a play-experiment and provided very visual proof removing any doubts you might have yourself.

You really need to switch doors!

At about the same time, I came across this Github repo by Saghir, who had made some vectorised simulations of the problem in R. I thought it was a fun excercise to simulate and visualize matters in two different data science programming languages — Python & R — and see what I’d run in to.

So I’ll cut to the chase.

As we play more and more games against Monty Hall, it becomes very clear that you really, really, really need to switch doors in order to maximize the probability of winning a car.

Actually, the more games we play, the closer the probability of winning in our sample gets to the actual probability.

Even after 1000 games, the probabilities are still not at their actual values. But, ultimately…

If you stick to your door, you end up with the car in only 33% of the cases.

If you switch to the other door, you end up with the car 66% of the time!

Simulation Code

In both Python and R, I wrote two scripts. You can find the most recent version of the code on my Github. However, I pasted the versions of March 4th 2020 below.

The first script contains a function simulating a single game of Monty Hall. A second script runs this function an X amount of times, and visualizes the outcomes as we play more and more games.

Python

simulate_game.py

import random

def simulate_game(make_switch=False, n_doors=3, seed=None):
    ''' 
    Simulate a game of Monty Hall
    For detailed information: https://en.wikipedia.org/wiki/Monty_Hall_problem
    Basically, there are several closed doors and behind only one of them is a prize.
    The player can choose one door at the start. 
    Next, the game master (Monty Hall) opens all the other doors, but one.
    Now, the player can stick to his/her initial choice or switch to the remaining closed door.
    If the prize is behind the player's final choice he/she wins.

    Keyword arguments:
    make_switch -- a boolean value whether the player switches after its initial choice and Monty Hall opening all other non-prize doors but one (default False)
    n_doors -- an integer value > 2, for the number of doors behind which one prize and (n-1) non-prizes (e.g., goats) are hidden (default 3)
    seed -- a seed to set (default None)
    '''

    # check the arguments
    if type(make_switch) is not bool:
        raise TypeError("`make_switch` must be boolean")
    if type(n_doors) is float:
        n_doors = int(n_doors)
        raise Warning("float value provided for `n_doors`: forced to integer value of", n_doors)
    if type(n_doors) is not int:
        raise TypeError("`n_doors` needs to be a positive integer > 2")
    if n_doors < 2:
        raise ValueError("`n_doors` needs to be a positive integer > 2")

    # if a seed was provided, set it
    if seed is not None:
        random.seed(seed)

    # sample one index for the door to hide the car behind
    prize_index = random.randint(0, n_doors - 1)

    # sample one index for the door initially chosen by the player
    choice_index = random.randint(0, n_doors - 1)

    # we can test for the current result
    current_result = prize_index == choice_index

    # now Monty Hall opens all doors the player did not choose, except for one door
    # next, he asks the player if he/she wants to make a switch
    if (make_switch):
        # if we do, we change to the one remaining door, which inverts our current choice
        # if we had already picked the prize door, the one remaining closed door has a nonprize
        # if we had not already picked the prize door, the one remaining closed door has the prize
        return not current_result
    else:
        # the player sticks with his/her original door,
        # which may or may not be the prize door
        return current_result

visualize_game_results.py

from simulate_game import simulate_game
from random import seed
from numpy import mean, cumsum
from matplotlib import pyplot as plt
import os

# set the seed here
# do not set the `seed` parameter in `simulate_game()`,
# as this will make the function retun `n_games` times the same results
seed(1)

# pick number of games you want to simulate
n_games = 1000

# simulate the games and store the boolean results
results_with_switching = [simulate_game(make_switch=True) for _ in range(n_games)]
results_without_switching = [simulate_game(make_switch=False) for _ in range(n_games)]

# make a equal-length list showing, for each element in the results, the game to which it belongs
games = [i + 1 for i in range(n_games)]

# generate a title based on the results of the simulations
title = f'Switching doors wins you {sum(results_with_switching)} of {n_games} games ({mean(results_with_switching) * 100:.1f}%)' + \
    '\n' + \
    f'as opposed to only {sum(results_without_switching)} games ({mean(results_without_switching) * 100:.1f}%) when not switching'

# set some basic plotting parameters
w = 8
h = 5

# make a line plot of the cumulative wins with and without switching
plt.figure(figsize=(w, h))
plt.plot(games, cumsum(results_with_switching), color='blue', label='switching')
plt.plot(games, cumsum(results_without_switching), color='red', label='no switching')
plt.axis([0, n_games, 0, n_games])
plt.title(title)
plt.legend()
plt.xlabel('Number of games played')
plt.ylabel('Cumulative number of games won')
plt.figtext(0.95, 0.03, 'paulvanderlaken.com', wrap=True, horizontalalignment='right', fontsize=6)

# you can uncomment this to see the results directly,
# but then python will not save the result to your directory
# plt.show()
# plt.close()

# create a directory to store the plots in
# if this directory does not yet exist
try:
    os.makedirs('output')
except OSError:
    None
plt.savefig('output/monty-hall_' + str(n_games) + '_python.png')

Visualizations (matplotlib)

R

simulate-game.R

Note that I wrote a second function, simulate_n_games, which just runs simulate_game an N number of times.

#' Simulate a game of Monty Hall
#' For detailed information: https://en.wikipedia.org/wiki/Monty_Hall_problem
#' Basically, there are several closed doors and behind only one of them is a prize.
#' The player can choose one door at the start. 
#' Next, the game master (Monty Hall) opens all the other doors, but one.
#' Now, the player can stick to his/her initial choice or switch to the remaining closed door.
#' If the prize is behind the player's final choice he/she wins.
#' 
#' @param make_switch A boolean value whether the player switches after its initial choice and Monty Hall opening all other non-prize doors but one. Defaults to `FALSE`
#' @param n_doors An integer value > 2, for the number of doors behind which one prize and (n-1) non-prizes (e.g., goats) are hidden. Defaults to `3L`
#' @param seed A seed to set. Defaults to `NULL`
#'
#' @return A boolean value indicating whether the player won the prize
#'
#' @examples 
#' simulate_game()
#' simulate_game(make_switch = TRUE)
#' simulate_game(make_switch = TRUE, n_doors = 5L, seed = 1)
simulate_game = function(make_switch = FALSE, n_doors = 3L, seed = NULL) {
  
  # check the arguments
  if (!is.logical(make_switch) | is.na(make_switch)) stop("`make_switch` needs to be TRUE or FALSE")
  if (is.double(n_doors)) {
    n_doors = as.integer(n_doors)
    warning(paste("double value provided for `n_doors`: forced to integer value of", n_doors))
  }
  if (!is.integer(n_doors) | n_doors < 2) stop("`n_doors` needs to be a positive integer > 2")
  
  # if a seed was provided, set it
  if (!is.null(seed)) set.seed(seed)
  
  # create a integer vector for the door indices
  doors = seq_len(n_doors)
  
  # create a boolean vector showing which doors are opened
  # all doors are closed at the start of the game
  isClosed = rep(TRUE, length = n_doors)
  
  # sample one index for the door to hide the car behind
  prize_index = sample(doors, size = 1)
  
  # sample one index for the door initially chosen by the player
  # this can be the same door as the prize door
  choice_index = sample(doors, size = 1)
  
  # now Monty Hall opens all doors the player did not choose
  # except for one door
  # if we have already picked the prize door, the one remaining closed door has a nonprize
  # if we have not picked the prize door, the one remaining closed door has the prize
  if (prize_index == choice_index) {
    # if we have the prize, Monty Hall can open all but two doors:
    #   ours, which we remove from the options to sample from and open
    #   and one goat-conceiling door, which we do not open
    isClosed[sample(doors[-prize_index], size = n_doors - 2)] = FALSE
  } else {
    # else, Monty Hall can also open all but two doors:
    #   ours
    #   and the prize-conceiling door
    isClosed[-c(prize_index, choice_index)] = FALSE
  }
  
  # now Monty Hall asks us whether we want to make a switch
  if (make_switch) {
    # if we decide to make a switch, we can pick the closed door that is not our door
    choice_index = doors[isClosed][doors[isClosed] != choice_index]
  }
  
  # we return a boolean value showing whether the player choice is the prize door
  return(choice_index == prize_index)
}


#' Simulate N games of Monty Hall
#' Calls the `simulate_game()` function `n` times and returns a boolean vector representing the games won
#' 
#' @param n An integer value for the number of times to call the `simulate_game()` function
#' @param seed A seed to set in the outer loop. Defaults to `NULL`
#' @param ... Any parameters to be passed to the `simulate_game()` function. 
#' No seed can be passed to the simulate_game function as that would result in `n` times the same result 
#'
#' @return A boolean vector indicating for each of the games whether the player won the prize
#'
#' @examples 
#' simulate_n_games(n = 100)
#' simulate_n_games(n = 500, make_switch = TRUE)
#' simulate_n_games(n = 1000, seed = 123, make_switch = TRUE, n_doors = 5L)
simulate_n_games = function(n, seed = NULL, make_switch = FALSE, ...) {
  # round the number of iterations to an integer value
  if (is.double(n)) {
    n = as.integer(n)
  }
  if (!is.integer(n) | n < 1) stop("`n_games` needs to be a positive integer > 1")
  # if a seed was provided, set it
  if (!is.null(seed)) set.seed(seed)
  return(vapply(rep(make_switch, n), simulate_game, logical(1), ...))
}

visualize-game-results.R

Note that we source in the simulate-game.R file to get access to the simulate_game and simulate_n_games functions.

Also note that I make a second plot here, to show the probabilities of winning converging to their real-world probability as we play more and more games.

source('R/simulate-game.R')

# install.packages('ggplot2')
library(ggplot2)

# set the seed here
# do not set the `seed` parameter in `simulate_game()`,
# as this will make the function return `n_games` times the same results
seed = 1

# pick number of games you want to simulate
n_games = 1000

# simulate the games and store the boolean results
results_without_switching = simulate_n_games(n = n_games, seed = seed, make_switch = FALSE)
results_with_switching = simulate_n_games(n = n_games, seed = seed, make_switch = TRUE)

# store the cumulative wins in a dataframe
results = data.frame(
  game = seq_len(n_games),
  cumulative_wins_without_switching = cumsum(results_without_switching),
  cumulative_wins_with_switching = cumsum(results_with_switching)
)

# function that turns values into nice percentages
format_percentage = function(values, digits = 1) {
  return(paste0(formatC(values * 100, digits = digits, format = 'f'), '%'))
}

# generate a title based on the results of the simulations
title = paste(
  paste0('Switching doors wins you ', sum(results_with_switching), ' of ', n_games, ' games (', format_percentage(mean(results_with_switching)), ')'),
  paste0('as opposed to only ', sum(results_without_switching), ' games (', format_percentage(mean(results_without_switching)), ') when not switching)'),
  sep = '\n'
)

# set some basic plotting parameters
linesize = 1 # size of the plotted lines
x_breaks = y_breaks = seq(from = 0, to = n_games, length.out = 10 + 1) # breaks of the axes
y_limits = c(0, n_games) # limits of the y axis - makes y limits match x limits
w = 8 # width for saving plot
h = 5 # height for saving plot
palette = setNames(c('blue', 'red'), nm = c('switching', 'without switching')) # make a named color scheme

# make a line plot of the cumulative wins with and without switching
ggplot(data = results) +
  geom_line(aes(x = game, y = cumulative_wins_with_switching, col = names(palette[1])), size = linesize) +
  geom_line(aes(x = game, y = cumulative_wins_without_switching, col = names(palette[2])), size = linesize) +
  scale_x_continuous(breaks = x_breaks) +
  scale_y_continuous(breaks = y_breaks, limits = y_limits) +
  scale_color_manual(values = palette) +
  theme_minimal() +
  theme(legend.position = c(1, 1), legend.justification = c(1, 1), legend.background = element_rect(fill = 'white', color = 'transparent')) +
  labs(x = 'Number of games played') +
  labs(y = 'Cumulative number of games won') +
  labs(col = NULL) +
  labs(caption = 'paulvanderlaken.com') +
  labs(title = title)

# save the plot in the output folder
# create the output folder if it does not exist yet
if (!file.exists('output')) dir.create('output', showWarnings = FALSE)
ggsave(paste0('output/monty-hall_', n_games, '_r.png'), width = w, height = h)


# make a line plot of the rolling % win chance with and without switching
ggplot(data = results) +
  geom_line(aes(x = game, y = cumulative_wins_with_switching / game, col = names(palette[1])), size = linesize) +
  geom_line(aes(x = game, y = cumulative_wins_without_switching / game, col = names(palette[2])), size = linesize) +
  scale_x_continuous(breaks = x_breaks) +
  scale_y_continuous(labels = function(x) format_percentage(x, digits = 0)) +
  scale_color_manual(values = palette) +
  theme_minimal() +
  theme(legend.position = c(1, 1), legend.justification = c(1, 1), legend.background = element_rect(fill = 'white', color = 'transparent')) +
  labs(x = 'Number of games played') +
  labs(y = '% of games won') +
  labs(col = NULL) +
  labs(caption = 'paulvanderlaken.com') +
  labs(title = title)


# save the plot in the output folder
# create the output folder if it does not exist yet
if (!file.exists('output')) dir.create('output', showWarnings = FALSE)
ggsave(paste0('output/monty-hall_perc_', n_games, '_r.png'), width = w, height = h)

Visualizations (ggplot2)

I specifically picked a seed (the second one I tried) in which not switching looked like it was better during the first few games played.

In R, I made an additional plot that shows the probabilities converging.

As we play more and more games, our results move to the actual probabilities of winning:

After the first four games, you could have erroneously concluded that not switching would result in better chances of you winning a sports car. However, in the long run, that is definitely not true.

I was actually suprised to see that these lines look to be mirroring each other. But actually, that’s quite logical maybe… We already had the car with our initial door guess in those games. If we would have sticked to that initial choice of a door, we would have won, whereas all the cases where we switched, we lost.

Keep me posted!

I hope you enjoyed these simulations and visualizations, and am curious to see what you come up with yourself!

For instance, you could increase the number of doors in the game, or the number of goat-doors Monty Hall opens. When does it become a disadvantage to switch?

Cover image via Medium

Curated Regular Expression Resources

Curated Regular Expression Resources

Regular expression (also abbreviated to regex) really is a powertool any programmer should know. It was and is one of the things I most liked learning, as it provides you with immediate, godlike powers that can speed up your (data science) workflow tenfold.

I’ve covered many regex related topics on this blog already, but thought I’d combine them and others in a nice curated overview — for myself, and for you of course, to use.

If you have any materials you liked, but are missing, please let me know!

Contents


Introduction & Learning

Reading

Tutorials (interactive)

Video

Corey Shafer

The Coding Train

Language-specific

Python

Corey Shafer

R

Roger Peng

Testing & Debugging

debuggex.com

regex101.com

regextester.com | regexpal.com

regexr.com

ExtendsClass.com/regex-tester

rubular.com

pythex.com

Fun