circaPy 0.1.6.dev1__py3-none-any.whl → 0.1.6.dev3__py3-none-any.whl

circaPy/activity.py

@@ -328,7 +328,7 @@ def calculate_IS(data):
 
 
 @prep.validate_input
-def calculate_TV(data, subject_no=0):
+def calculate_TV(data, col=0):
     r"""
     Calculates Timepoint Variability
 
@@ -363,7 +363,7 @@ def calculate_TV(data, subject_no=0):
     The TV value ranges from 0 to 1, lower is more stable.
     """
     # select the data
-    curr_data = data.iloc[:, subject_no]
+    curr_data = data.iloc[:, col]
 
     # calculate mean
     mean_data = calculate_mean_activity(curr_data)

circaPy/episodes.py

@@ -19,7 +19,7 @@ import circaPy.preprocessing as prep
 
 @prep.validate_input
 def find_episodes(
-    data, subject_no=0, min_length="1s", max_interruption="0s", *args, **kwargs
+    data, col=0, min_length="1s", max_interruption="0s", *args, **kwargs
 ):
     """
     Identifies episodes in a time series of activity data for a specific subject,
@@ -31,7 +31,7 @@ def find_episodes(
     data : pd.DataFrame
         The activity data for multiple subjects, where each column represents
         a subject's activity over time, and the index is a time-based index.
-    subject_no : int, optional
+    col : int, optional
         The column index of the subject to analyze. Default is 0.
     min_length : str or pandas.Timedelta, optional
         The minimum duration for an episode to be included in the results.
@@ -62,13 +62,13 @@ def find_episodes(
     ...     "Subject 1": np.random.choice([0, 1], size=100, p=[0.8, 0.2]),
     ...     "Subject 2": np.random.choice([0, 1], size=100, p=[0.7, 0.3]),
     ... }, index=index)
-    >>> find_episodes(data, subject_no=0, min_length="3s", max_interruption="2s")
+    >>> find_episodes(data, col=0, min_length="3s", max_interruption="2s")
     2024-01-01 00:00:15    7.0
     2024-01-01 00:00:45    5.0
     dtype: float64
     """
     # select single column
-    curr_data = data.iloc[:, subject_no]
+    curr_data = data.iloc[:, col]
 
     # Determine the threshold for episode identification
     zero_data = curr_data == 0

circaPy/periodogram.py

@@ -9,7 +9,7 @@ import circaPy.preprocessing as prep
 
 
 @prep.validate_input
-def lomb_scargle_period(data, subject_no=0, low_period=20, high_period=30, **kwargs):
+def lomb_scargle_period(data, col=0, low_period=20, high_period=30, **kwargs):
     """
     Calculates the Lomb-Scargle periodogram for a single column in a DataFrame.
 
@@ -18,7 +18,7 @@ def lomb_scargle_period(data, subject_no=0, low_period=20, high_period=30, **kwa
     data : pd.DataFrame
         Input DataFrame with time-series data. The index represents time, and
         the columns contain observations.
-    subject_no : int, optional
+    col : int, optional
         The positional index of the column to analyze. Default is 0.
     low_period : float, optional
         The shortest period to search for, in hours. Default is 20.
@@ -42,7 +42,7 @@ def lomb_scargle_period(data, subject_no=0, low_period=20, high_period=30, **kwa
     Raises
     ------
     IndexError
-        If `subject_no` is out of the valid range for the DataFrame columns.
+        If `col` is out of the valid range for the DataFrame columns.
     ValueError
         If `low_period` is greater than or equal to `high_period`.
 
@@ -58,9 +58,9 @@ def lomb_scargle_period(data, subject_no=0, low_period=20, high_period=30, **kwa
       contains only NaNs.
     """
     # Ensure the positional index is valid
-    if subject_no < 0 or subject_no >= len(data.columns):
+    if col < 0 or col >= len(data.columns):
         raise IndexError(
-            f"Invalid subject_no {subject_no}. Must be between 0 and"
+            f"Invalid col {col}. Must be between 0 and"
             f"{len(data.columns) - 1}."
         )
 
@@ -80,7 +80,7 @@ def lomb_scargle_period(data, subject_no=0, low_period=20, high_period=30, **kwa
     freq_hours = 1 / (freq * 3600)
 
     # Prepare observations
-    observations = data.iloc[:, subject_no].values
+    observations = data.iloc[:, col].values
     observation_times = np.arange(len(data)) * sample_freq
 
     # Check if all NaN

circaPy/plots.py

@@ -14,7 +14,7 @@ import circaPy.preprocessing as prep
 @prep.plot_kwarg_decorator
 def plot_actogram(
     data,
-    subject_no=0,
+    col=0,
     light_col=-1,
     ylim=[0, 120],
     fig=False,
@@ -37,7 +37,7 @@ def plot_actogram(
         columns for each subject and one column for the light levels.
         WRONG - currently expecting list of dataframes, one for each animal
         and single column for each day
-    subject_no : int
+    col : int
         which column number to plot, defaults to 0
     light_col : int
         which columns contains light information, defaults to -1
@@ -80,7 +80,7 @@ def plot_actogram(
         raise ValueError("Input Dataframe is empty. Cannot plot actogram")
 
     # select the correct data to plot for activity and light
-    col_data = data.columns[subject_no]
+    col_data = data.columns[col]
     ldr_col = data.columns[light_col]
     data_plot = data.loc[:, col_data].copy()
     data_light = data.loc[:, ldr_col].copy()

{circapy-0.1.6.dev1.dist-info → circapy-0.1.6.dev3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: circaPy
-Version: 0.1.6.dev1
+Version: 0.1.6.dev3
 Summary: For analysing circadian activity data
 Project-URL: Homepage, https://github.com/A-Fisk/circaPy
 Project-URL: Issues, https://github.com/A-Fisk/circaPy/issues
@@ -29,6 +29,8 @@ CircaPy is a python module for circadian analysis of activity data.
 It was developed using laboratory
 rodents data but is applicable across species and monitoring devices.
 
+Full documentation is available at [circapy.readthedocs.io](https://circapy.readthedocs.io)
+
 A limited version is available as an [interactive
 website](https://circapywebsite.streamlit.app/)
 

{circapy-0.1.6.dev1.dist-info → circapy-0.1.6.dev3.dist-info}/RECORD

@@ -1,8 +1,8 @@
 circaPy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-circaPy/activity.py,sha256=EGcd0QA0QwCgQQWWvThwnBctSURWTiRkbx2E_qj1T1s,12544
-circaPy/episodes.py,sha256=sqRFTWlclkh-z9RyA-s5rF463xkDbsE7ALkgr-KqKr4,15382
-circaPy/periodogram.py,sha256=kyzTW2HDBIbcLQut5gOevh_zd3sAfa0RnitCBXzaz8I,4364
-circaPy/plots.py,sha256=w5mw0-YI2rDLDaXrnvRQmEadukK5pLw06m-Zf4KpQdM,12709
+circaPy/activity.py,sha256=I1B6zSlz_kpxRaaGv2h-PdjrOym0HNRhzhGlwiMKMf4,12530
+circaPy/episodes.py,sha256=lzvwNv763ECskGZ2VqLiP4EfT8p6yYJKDvnHL5ZGHEA,15354
+circaPy/periodogram.py,sha256=oIWOl30aokq5YZPU2EM7NZNQUvRN8DWCtg_-OmfSyz0,4308
+circaPy/plots.py,sha256=G8YSb9p1bAekvhN0XqEaWsA5gXZyiBVKuLiIgvQ48wA,12688
 circaPy/preprocessing.py,sha256=WNmeNdOU83sdP9qC8Cj4Od42OjRqR48dlaJQd2OZb6E,9696
 circaPy/sleep_process.py,sha256=vMNFNRx__qls_eCaCEM374RWqvo2bAUNocbIjF5gbnk,2521
 circaPy/.idea/actigraphy_analysis.iml,sha256=6GnoPxQ6gF69BtdpKK3mmgHwqmzJglmUa9iI5jVDo6c,398
@@ -10,7 +10,7 @@ circaPy/.idea/misc.xml,sha256=d8VH1GDzWGVVZo58O51-wfPY_Il-rQ9exolep12oV74,219
 circaPy/.idea/modules.xml,sha256=ELB75pyQII1uEhIxCoEuFJWB5wlJfhAAuDpZkYE5xxU,290
 circaPy/.idea/vcs.xml,sha256=JpBk9bpzB9zTGgO1xpBpizRCwPACTBNYNhVC9J9VCa4,183
 circaPy/.idea/workspace.xml,sha256=2Tgp-vpRFqxCebvXxnPuUCfbcshS26qZ-5jMneikRpM,4178
-circapy-0.1.6.dev1.dist-info/METADATA,sha256=Ho_1FYOWOHK3KNRu0MBinMJkXsfOsa72oZzL7OZV9YE,2875
-circapy-0.1.6.dev1.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
-circapy-0.1.6.dev1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-circapy-0.1.6.dev1.dist-info/RECORD,,
+circapy-0.1.6.dev3.dist-info/METADATA,sha256=w8iv9FCQ-tDtFZEX7r2WPuyvL2ifBU6tLBQFLjwTTEI,2968
+circapy-0.1.6.dev3.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+circapy-0.1.6.dev3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+circapy-0.1.6.dev3.dist-info/RECORD,,