Issue with using dissimilarity

zlindaz2411 commented 3 years ago

I followed the step that is listed in the tutorial. However, I get the following errors for CombinedCategoricalDissimilarity.

Moreover, when I use PositionalDissimilarity I get a different error.

Does anyone know how to solve these problems. I want to use PositionalDissimilarity to calculate the agreement.

EDIT: added by @hadware for searchability.

The error is TypeError: G must be a 'd' matrix

hadware commented 3 years ago

Hello! First of all, thanks for reporting this issue.

I'm not sure what might be causing this error yet, i'll need more information. Can you provide us with a couple of informations, namely:

the version of your installed packages (you can run pip3 list and copy the output)
a more detailed error stack for each errors (by clicking on the "n frames" button in the dev environment you seem to be using).

hadware commented 3 years ago

ADDENDUM: regarding the PositionalDissimilarity: this dissimilarity doesn't require the list of categories to work. You can intanciate it with no arguments:

dissim = PositionalDissimilarity()
# then use it all the same:
gamma_results = continuum.compute_gamma(dissim)

zlindaz2411 commented 3 years ago

Thank you. I removed the parameters from PositionalDissimilarity but it gives me the following errors:

This is the output of my pip3 list:

Package Version
absl-py 0.10.0
alabaster 0.7.12
albumentations 0.1.12
altair 4.1.0
appdirs 1.4.4
argon2-cffi 20.1.0
asgiref 3.3.1
astor 0.8.1
astropy 4.2
astunparse 1.6.3
async-generator 1.10
atari-py 0.2.6
atomicwrites 1.4.0
attrs 20.3.0
audioread 2.1.9
autograd 1.3
Babel 2.9.0
backcall 0.2.0
beautifulsoup4 4.6.3
bleach 3.3.0
blis 0.4.1
bokeh 2.1.1
Bottleneck 1.3.2
branca 0.4.2
bs4 0.0.1
CacheControl 0.12.6
cachetools 4.2.1
catalogue 1.0.0
certifi 2020.12.5
cffi 1.14.5
chainer 7.4.0
chardet 3.0.4
click 7.1.2
cloudpickle 1.3.0
cmake 3.12.0
cmdstanpy 0.9.5
colorama 0.4.4
colorlover 0.3.0
community 1.0.0b1
contextlib2 0.5.5
convertdate 2.3.1
coverage 3.7.1
coveralls 0.5
crcmod 1.7
cufflinks 0.17.3
cvxopt 1.2.6
cvxpy 1.0.25
cycler 0.10.0
cymem 2.0.5
Cython 0.29.22
daft 0.0.4
dask 2.12.0
datascience 0.10.6
debugpy 1.0.0
decorator 4.4.2
defusedxml 0.7.0
descartes 1.1.0
dill 0.3.3
distributed 1.25.3
Django 3.1.7
dlib 19.18.0
dm-tree 0.1.5
docopt 0.6.2
docutils 0.16
dopamine-rl 1.0.5
earthengine-api 0.1.254
easydict 1.9
ecos 2.0.7.post1
editdistance 0.5.3
en-core-web-sm 2.2.5
entrypoints 0.3
ephem 3.7.7.1
et-xmlfile 1.0.1
fa2 0.3.5
fancyimpute 0.4.3
fastai 1.0.61
fastdtw 0.3.4
fastprogress 1.0.0
fastrlock 0.5
fbprophet 0.7.1
feather-format 0.4.1
filelock 3.0.12
firebase-admin 4.4.0
fix-yahoo-finance 0.0.22
Flask 1.1.2
flatbuffers 1.12
folium 0.8.3
future 0.16.0
gast 0.3.3
GDAL 2.2.2
gdown 3.6.4
gensim 3.6.0
geographiclib 1.50
geopy 1.17.0
gin-config 0.4.0
glob2 0.7
google 2.0.3
google-api-core 1.26.1
google-api-python-client 1.12.8
google-auth 1.27.1
google-auth-httplib2 0.0.4
google-auth-oauthlib 0.4.3
google-cloud-bigquery 1.21.0
google-cloud-bigquery-storage 1.1.0
google-cloud-core 1.0.3
google-cloud-datastore 1.8.0
google-cloud-firestore 1.7.0
google-cloud-language 1.2.0
google-cloud-storage 1.18.1
google-cloud-translate 1.5.0
google-colab 1.0.0
google-pasta 0.2.0
google-resumable-media 0.4.1
googleapis-common-protos 1.53.0
googledrivedownloader 0.4
graphviz 0.10.1
grpcio 1.32.0
gspread 3.0.1
gspread-dataframe 3.0.8
gym 0.17.3
h5py 2.10.0
HeapDict 1.0.1
hijri-converter 2.1.1
holidays 0.10.5.2
holoviews 1.13.5
html5lib 1.0.1
httpimport 0.5.18
httplib2 0.17.4
httplib2shim 0.0.3
humanize 0.5.1
hyperopt 0.1.2
ideep4py 2.0.0.post3
idna 2.10
image 1.5.33
imageio 2.4.1
imagesize 1.2.0
imbalanced-learn 0.4.3
imblearn 0.0
imgaug 0.2.9
importlib-metadata 3.7.0
importlib-resources 5.1.2
imutils 0.5.4
inflect 2.1.0
iniconfig 1.1.1
intel-openmp 2021.1.2
intervaltree 2.1.0
ipykernel 4.10.1
ipython 5.5.0
ipython-genutils 0.2.0
ipython-sql 0.3.9
ipywidgets 7.6.3
itsdangerous 1.1.0
jax 0.2.9
jaxlib 0.1.60+cuda110 jdcal 1.4.1
jedi 0.18.0
jieba 0.42.1
Jinja2 2.11.3
joblib 1.0.1
jpeg4py 0.1.4
jsonschema 2.6.0
jupyter 1.0.0
jupyter-client 5.3.5
jupyter-console 5.2.0
jupyter-core 4.7.1
jupyterlab-pygments 0.1.2
jupyterlab-widgets 1.0.0
kaggle 1.5.10
kapre 0.1.3.1
Keras 2.4.3
Keras-Preprocessing 1.1.2
keras-vis 0.4.1
kiwisolver 1.3.1
knnimpute 0.1.0
korean-lunar-calendar 0.2.1
librosa 0.8.0
lightgbm 2.2.3
llvmlite 0.34.0
lmdb 0.99
lucid 0.3.8
LunarCalendar 0.0.9
lxml 4.2.6
Markdown 3.3.4
MarkupSafe 1.1.1
matplotlib 3.2.2
matplotlib-venn 0.11.6
missingno 0.4.2
mistune 0.8.4
mizani 0.6.0
mkl 2019.0
mlxtend 0.14.0
more-itertools 8.7.0
moviepy 0.2.3.5
mpmath 1.2.1
msgpack 1.0.2
multiprocess 0.70.11.1
multitasking 0.0.9
murmurhash 1.0.5
music21 5.5.0
natsort 5.5.0
nbclient 0.5.3
nbconvert 5.6.1
nbformat 5.1.2
nest-asyncio 1.5.1
networkx 2.5
nibabel 3.0.2
nltk 3.2.5
notebook 5.3.1
np-utils 0.5.12.1
numba 0.51.2
numexpr 2.7.3
numpy 1.19.5
nvidia-ml-py3 7.352.0
oauth2client 4.1.3
oauthlib 3.1.0
okgrade 0.4.3
opencv-contrib-python 4.1.2.30
opencv-python 4.1.2.30
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opt-einsum 3.3.0
osqp 0.6.2.post0
packaging 20.9
palettable 3.3.0
pandas 1.1.5
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pandas-gbq 0.13.3
pandas-profiling 1.4.1
pandocfilters 1.4.3
panel 0.9.7
param 1.10.1
parso 0.8.1
pathlib 1.0.1
patsy 0.5.1
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pickleshare 0.7.5
Pillow 7.0.0
pip 19.3.1
pip-tools 4.5.1
plac 1.1.3
plotly 4.4.1
plotnine 0.6.0
pluggy 0.7.1
pooch 1.3.0
portpicker 1.3.1
prefetch-generator 1.0.1
preshed 3.0.5
prettytable 2.1.0
progressbar2 3.38.0
prometheus-client 0.9.0
promise 2.3
prompt-toolkit 1.0.18
protobuf 3.12.4
psutil 5.4.8
psycopg2 2.7.6.1
ptyprocess 0.7.0
py 1.10.0
pyannote.core 4.1
pyannote.database 4.0.4
pyarrow 3.0.0
pyasn1 0.4.8
pyasn1-modules 0.2.8
pycocotools 2.0.2
pycparser 2.20
pyct 0.4.8
pydata-google-auth 1.1.0
pydot 1.3.0
pydot-ng 2.0.0
pydotplus 2.0.2
PyDrive 1.3.1
pyemd 0.5.1
pyerfa 1.7.2
pygamma-agreement 0.1.6
pyglet 1.5.0
Pygments 2.6.1
pygobject 3.26.1
pymc3 3.7
PyMeeus 0.5.2
pymongo 3.11.3
pympi-ling 1.69
pymystem3 0.2.0
pynndescent 0.5.2
PyOpenGL 3.1.5
pyparsing 2.4.7
pyrsistent 0.17.3
pysndfile 1.3.8
PySocks 1.7.1
pystan 2.19.1.1
pytest 3.6.4
python-apt 0.0.0
python-chess 0.23.11
python-dateutil 2.8.1
python-louvain 0.15
python-slugify 4.0.1
python-utils 2.5.6
pytz 2018.9
pyviz-comms 2.0.1
PyWavelets 1.1.1
PyYAML 3.13
pyzmq 22.0.3
qdldl 0.1.5.post0
qtconsole 5.0.2
QtPy 1.9.0
regex 2019.12.20
requests 2.23.0
requests-oauthlib 1.3.0
resampy 0.2.2
retrying 1.3.3
rpy2 3.4.2
rsa 4.7.2
scikit-image 0.16.2
scikit-learn 0.22.2.post1
scipy 1.4.1
screen-resolution-extra 0.0.0
scs 2.1.2
seaborn 0.11.1
Send2Trash 1.5.0
setuptools 54.0.0
setuptools-git 1.2
Shapely 1.7.1
shellingham 1.4.0
simplegeneric 0.8.1
simplejson 3.17.2
six 1.15.0
sklearn 0.0
sklearn-pandas 1.8.0
smart-open 4.2.0
snowballstemmer 2.1.0
sortedcontainers 2.3.0
SoundFile 0.10.3.post1
spacy 2.2.4
Sphinx 1.8.5
sphinxcontrib-serializinghtml 1.1.4
sphinxcontrib-websupport 1.2.4
SQLAlchemy 1.3.23
sqlparse 0.4.1
srsly 1.0.5
statsmodels 0.10.2
sympy 1.7.1
tables 3.4.4
tabulate 0.8.9
tblib 1.7.0
tensorboard 2.4.1
tensorboard-plugin-wit 1.8.0
tensorflow 2.4.1
tensorflow-datasets 4.0.1
tensorflow-estimator 2.4.0
tensorflow-gcs-config 2.4.0
tensorflow-hub 0.11.0
tensorflow-metadata 0.28.0
tensorflow-probability 0.12.1
termcolor 1.1.0
terminado 0.9.2
testpath 0.4.4
text-unidecode 1.3
textblob 0.15.3
textgenrnn 1.4.1
TextGrid 1.5
Theano 1.0.5
thinc 7.4.0
tifffile 2021.3.4
toml 0.10.2
toolz 0.11.1
torch 1.8.0+cu101
torchsummary 1.5.1
torchtext 0.9.0
torchvision 0.9.0+cu101
tornado 5.1.1
tqdm 4.59.0
traitlets 5.0.5
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typeguard 2.7.1
typer 0.3.2
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tzlocal 1.5.1
umap-learn 0.5.1
uritemplate 3.0.1
urllib3 1.24.3
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wcwidth 0.2.5
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Werkzeug 1.0.1
wheel 0.36.2
widgetsnbextension 3.5.1
wordcloud 1.5.0
wrapt 1.12.1
xarray 0.15.1
xgboost 0.90
xkit 0.0.0
xlrd 1.1.0
xlwt 1.3.0
yellowbrick 0.9.1
zict 2.0.0
zipp 3.4.1

hadware commented 3 years ago

I think it's because you have cvxopt installed. cvxpy (the convex problem solver we're using) is quite janky with MI optim, and doesn't work when this dependency is installed.

Run pip3 uninstall cvxopt and then try to run your code snippet again.

zlindaz2411 commented 3 years ago

Thank you. It works now

bootphon / pygamma-agreement

Issue with using dissimilarity #22