gower | Python package for Gower distance | Machine Learning library
kandi X-RAY | gower Summary
kandi X-RAY | gower Summary
Gower's distance calculation in Python. Gower Distance is a distance measure that can be used to calculate distance between two entity whose attribute has a mixed of categorical and numerical values. Gower (1971) A general coefficient of similarity and some of its properties. Biometrics 27 857–874. More details and examples can be found on my personal website here:(Core functions are wrote by Marcelo Beckmann.
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Top functions reviewed by kandi - BETA
- Compute the top n features
- Compute the Gower matrix
- Calculate the Gower score
- Returns the indices of the smallest n elements in ary
gower Key Features
gower Examples and Code Snippets
gower.gower_matrix(X)
array([[0. , 0.3590238 , 0.6707398 , 0.31787416, 0.16872811,
0.52622986, 0.59697855, 0.47778758, nan],
[0.3590238 , 0. , 0.6964303 , 0.3138769 , 0.523629 ,
0.16720603, 0.45600235, 0.
import numpy as np
import pandas as pd
import gower
Xd=pd.DataFrame({'age':[21,21,19, 30,21,21,19,30,None],
'gender':['M','M','N','M','F','F','F','F',None],
'civil_status':['MARRIED','SINGLE','SINGLE','SINGLE','MARRIED','SINGLE','WIDOW','DIVORCED',N
gower.gower_topn(Xd.iloc[0:2,:], Xd.iloc[:,], n = 5)
{'index': array([4, 3, 1, 7, 5]),
'values': array([0.16872811, 0.31787416, 0.3590238 , 0.47778758, 0.52622986],
dtype=float32)}
a = np.array ( ... , dtype = float )
np.divide ( a , b , out = np.zeros_like ( a ) , where = b != 0)
for /f "usebackq delims=" %%i in (`
powershell -c "[pscredential]::new('unused', (Read-Host 'enter password' -AsSecureString)).GetNetworkCredential().Password"
`) do set "password=%%i"
np.logical_not(xi == xj).astype(int)
array([[0, 0, 0],
[1, 0, 1]])
from pyclustering.cluster.kmedoids import kmedoids
... ...
pam=kmedoids(D, initial_medoids)
source activate [your_environment_name]
conda install -c conda-forge gdal "libgdal<2.0"
# Import data
dta <- read.table(header = TRUE, textConnection("Var1 var2 var3 var4
1 2 1 1
3 2 1 3
1 2 0 1
3 2 2 3"))
dta <- as.data.frame(lapply(dta, as.factor))
# Create distance matrix
Community Discussions
Trending Discussions on gower
QUESTION
I am using the R programming language. I made an earlier post (R: Using "microbenchmark" and ggplot2 to plot runtimes) where I am learning how to use loops and functions to iterate procedures (7 procedures) in R for sample sizes. Once this is done, I want to produce a plot.
Based on the previous answer, I tried to write a few of these loops in R:
...ANSWER
Answered 2020-Dec-27 at 03:37In order to make procedures 4 - 7 work we needed to make the adjustments listed in the conclusions section of Using microbenchmark and ggplot2 to plot runtimes:
- Wrap the original procedure in a function that we can use as the unit of analysis for
microbenchmark()
, and include asize
argument - Modify the procedure to use
size
as a variable where necessary - Modify the procedure to access objects from previous steps, based on the
size
argument - Modify the procedure to write its outputs with
assign()
andsize
if these are needed for subsequent procedure steps
The modified code looks like this:
QUESTION
I am using the R programming language. I want to learn how to measure and plot the run time of difference procedures as the size of the data increases.
I found a previous stackoverflow post that answers a similar question: Plot the run time of three functions
It seems that the "microbenchmark" library in R should be able to accomplish this task.
Suppose I simulate the following data:
...ANSWER
Answered 2020-Dec-26 at 17:59My first answer severely misunderstood your question. I hope this can be of some help.
QUESTION
I am using the R programming language. I incorporated my own code along with a lengthy tutorial over here : https://michael.hahsler.net/SMU/EMIS7332/R/viz_classifier.html . In the end, I produced a visual "plot" (see the end of this code, "final_plot")
...ANSWER
Answered 2020-Dec-24 at 20:33As @mischva11 commented, I think it is easier to create the ggplot from scratch. Your function is actually returning a matrix and not a kind of plot object. the plot
and countour
functions draw the plots directly in the active graphic window. I am not sure if there is a way to convert these base plots to ggplot (maybe there is).
Here is a way to create a similar plot as you have in ggplot and then convert it to plotly.
QUESTION
I am using the R programming language. I am trying to figure out how to "recreate" plots in ggplot2/plotly, once they have been created in base R.
For example, I created some data and made a plot :
...ANSWER
Answered 2020-Dec-23 at 19:49You can vary the point size based on lof. The tooltip in the ggplotly
graph can also be adjusted to show lof and name.
Edit: Added var1, var2 and var3 to the tooltip
QUESTION
I am using the R programming language and following this tutorial over here: https://michael.hahsler.net/SMU/EMIS7332/R/viz_classifier.html .
I simulated some data and plotted the results as per the tutorial:
...ANSWER
Answered 2020-Dec-22 at 17:09as provided in the comments: (remove contour statement)
QUESTION
This may be a usage misunderstanding, but I expect the following toy example to work. I want to have a lagged predictor in my recipe, but once I include it in the recipe, and try to predict on the same data using a workflow with the recipe, it doesn't recognize the column foo
and cannot compute its lag.
Now, I can get this to work if I:
- Pull the fit out of the workflow that has been fit.
- Independently prep and bake the data I want to fit.
Which I code after the failed workflow fit, and it succeeds. According to the documentation, I should be able to put a workflow fit in the predict slot: https://www.tidymodels.org/start/recipes/#predict-workflow
I am probably fundamentally misunderstanding how workflow is supposed to operate. I have what I consider a workaround, but I do not understand why the failed statement isn't working in the way the workaround is. I expected the failed workflow construct to work under the covers like the workaround I have.
In short, if work_df
is a dataframe, the_rec
is a recipe based off work_df
, rf_mod
is a model, and you create the workflow rf_workflow
, then should I expect the predict()
function to work identically in the two predict()
calls below?
ANSWER
Answered 2020-Oct-19 at 19:49The reason you are experiencing an error is that you have created a predictor variable from the outcome. When it comes time to predict on new data, the outcome is not available; we are predicting the outcome for new data, not assuming that it is there already.
This is a fairly strong assumption of the tidymodels framework, for either modeling or preprocessing, to protect against information leakage. You can read about this a bit more here.
It's possible you already know about these resources, but if you are working with time series models, I'd suggest checking out these resources:
QUESTION
I have this dataset:
...ANSWER
Answered 2020-Oct-13 at 00:37I would suggest two approaches. You can use a line as you want but the number of grouping variables is considerable. So as first instance, I would suggest you using a matrix style plot displayig the lines at different levels.
QUESTION
I am attempting to run a clustering algorithm over a list of dissimilarity matrices for different numbers of clusters k
and extract some information for each run.
This first block of code produces the list of dissimilarity matrices
...ANSWER
Answered 2020-Sep-05 at 06:29I was able to come up with a solution by writing a function clus_func
that extracts the cluster information and then using cross2
and map2
from the purrr
package:
QUESTION
I am attempting to apply the gower_matrix
function from the gower
package to the values of a dictionary using this chunk of code:
ANSWER
Answered 2020-Sep-02 at 16:37Based on a web search for ufunc 'true_divide' output
, it appears that the error occurs (not a Numpy bug, but behaviour that changed several years ago) when attempting to divide an array of integer values through by a floating-point value. It appears to be an unspecified requirement of the gower
package that you pass in floating-point values. So convert the cars
data first. My guess is that you have some columns that contain floating-point values and some that contain integers; the test element of combo_dicts
works fine because it happens to have been produced only from floating-point columns.
QUESTION
I've put together a data preprocessing recipe for the recent coffee dataset featured on TidyTuesday. My intention is to generate a workflow, and then from there tune a hyperparameter. I'm specifically interesting in manually declaring predictors and outcomes through the various update_role()
functions, rather than using a formula, since I have some great plans for this style of variable selection (it's a really great idea!).
The example below produces a recipe that works just fine with prep
and bake(coffee_test)
. It even works if I deselect the outcome column, eg. coffee_recipe %>% bake(select(coffee_test, -cupper_points))
. However, when I run the workflow through tune_grid
I get the errors as shown. It looks like tune_grid
can't find the variables that don't have the "predictor" role, even though bake
does just fine.
Now, if I instead do things the normal way with a formula and step_rm
the variables I don't care about, then things mostly work --- I get a few warnings for rows with missing country_of_origin
values, which I find strange since I should be imputing those. It's entirely possible I've misunderstood the purpose of roles and how to use them.
ANSWER
Answered 2020-Jul-22 at 00:14The error here occurs because on step_string2factor()
during tuning, the recipe starts trying to handle variables that don't have any roles, like species
and owner
.
Try setting the role for all of your nominal variables before picking out the outcomes and predictors.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install gower
You can use gower like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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