Add rcParams (#615)

* add rcparams

* add rcparams

* lint

* add example

docs/examples.rst

@@ -18,3 +18,4 @@ space like in the previous examples. In all these example the prior predictive d
    examples/Direct_elicitation_in_1D
    examples/Direct_elicitation_in_ND
    examples/predictive_elicitation
+   examples/Global_settings

preliz/__init__.py

@@ -5,21 +5,21 @@
 """
 from os import path as os_path
 
-from matplotlib import rcParams
+from matplotlib import rcParams as mpl_rcParams
 from matplotlib import style
 
 from .distributions import *
 from .predictive import *
 from .unidimensional import *
 from .multidimensional import *
+from .internal.rcparams import rc_context, rcParams
 
 
 __version__ = "0.13.0"
 
 
-# Allow legend outside plot in maxent to be included when saving a figure
-# We may want to make this more explicit by having preliz.rcParams
-rcParams["savefig.bbox"] = "tight"
+# Allow legend outside plot in maxent to be included in the saved figure
+mpl_rcParams["savefig.bbox"] = "tight"
 
 
 # add PreliZ's styles to matplotlib's styles
@@ -28,4 +28,4 @@
 style.core.reload_library()
 
 # clean namespace
-del os_path, rcParams, _preliz_style_path
+del os_path, mpl_rcParams, _preliz_style_path

preliz/distributions/continuous_multivariate.py

@@ -94,7 +94,7 @@ def plot_pdf(
         self,
         marginals=True,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         support="full",
         legend="title",
@@ -114,8 +114,9 @@ def plot_pdf(
             Whether to include a plot of the quantiles. Defaults to False. If True the default is to
             plot the median and two interquantile ranges.
         interval : str
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
         equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+        Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -142,7 +143,7 @@ def plot_pdf(
     def plot_cdf(
         self,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         support="full",
         legend="title",
@@ -158,8 +159,9 @@ def plot_cdf(
             Whether to include a plot of the quantiles. Defaults to False. If True the default is to
             plot the median and two interquantile ranges.
         interval : str
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
         equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+        Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -186,7 +188,7 @@ def plot_cdf(
     def plot_ppf(
         self,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         legend="title",
         figsize=None,
@@ -201,8 +203,9 @@ def plot_ppf(
             Whether to include a plot of the quantiles. Defaults to False. If True the default is to
             plot the median and two interquantile ranges.
         interval : str
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
         equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+        Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -228,7 +231,7 @@ def plot_interactive(
         kind="pdf",
         xy_lim="both",
         pointinterval=True,
-        interval="hdi",
+        interval=None,
         levels=None,
         figsize=None,
     ):
@@ -249,7 +252,7 @@ def plot_interactive(
             Whether to include a plot of the quantiles. Defaults to False.
             If `True` the default is to plot the median and two inter-quantiles ranges.
         interval : str
-            Type of interval. Available options are the highest density interval `"hdi"` (default),
+            Type of interval. Available options are the highest density interval `"hdi"`,
             equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
@@ -424,7 +427,7 @@ def plot_pdf(
         self,
         marginals=True,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         support="full",
         legend="title",
@@ -444,8 +447,9 @@ def plot_pdf(
             Whether to include a plot of the quantiles. Defaults to False. If True the default is to
             plot the median and two interquantiles ranges.
         interval : str
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
         equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+        Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -472,7 +476,7 @@ def plot_pdf(
     def plot_cdf(
         self,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         support="full",
         legend="title",
@@ -488,8 +492,9 @@ def plot_cdf(
             Whether to include a plot of the quantiles. Defaults to False. If True the default is to
             plot the median and two interquantiles ranges.
         interval : str
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
         equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+        Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -516,7 +521,7 @@ def plot_cdf(
     def plot_ppf(
         self,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         legend="title",
         figsize=None,
@@ -531,8 +536,9 @@ def plot_ppf(
             Whether to include a plot of the quantiles. Defaults to False. If True the default is to
             plot the median and two interquantiles ranges.
         interval : str
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
         equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+        Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -558,7 +564,7 @@ def plot_interactive(
         kind="pdf",
         xy_lim="both",
         pointinterval=True,
-        interval="hdi",
+        interval=None,
         levels=None,
         figsize=None,
     ):
@@ -579,8 +585,9 @@ def plot_interactive(
             Whether to include a plot of the quantiles. Defaults to False.
             If `True` the default is to plot the median and two inter-quantiles ranges.
         interval : str
-            Type of interval. Available options are the highest density interval `"hdi"` (default),
+            Type of interval. Available options are the highest density interval `"hdi"`,
             equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+            Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0

preliz/distributions/distributions.py

@@ -28,6 +28,7 @@
 )
 
 from ..internal.optimization import optimize_hdi
+from ..internal.rcparams import rcParams
 
 
 class Distribution:
@@ -75,25 +76,29 @@ def params_dict(self):
         else:
             return None
 
-    def summary(self, mass=0.94, interval="hdi", fmt=".2f"):
+    def summary(self, mass=None, interval=None, fmt=".2f"):
         """
         Namedtuple with the mean, median, standard deviation, and lower and upper bounds
         of the equal-tailed interval.
 
         Parameters
         ----------
         mass: float
-            Probability mass for the equal-tailed interval. Defaults to 0.94
+            Probability mass for the equal-tailed interval. Defaults to None,
+        which results in the value of rcParams["stats.ci_prob"] being used.
         interval : str or list-like
-            Type of interval. Available options are highest density interval `"hdi"` (default),
+            Type of interval. Available options are highest density interval `"hdi"`,
             equal tailed interval `"eti"` or arbitrary interval defined by a list-like object
-            with a pair of values.
+            with a pair of values. Defaults to the value in rcParams["stats.ci_kind"].
         fmt : str
             fmt used to represent results using f-string fmt for floats. Default to ".2f"
             i.e. 2 digits after the decimal point.
         """
         valid_distribution(self)
 
+        if interval is None:
+            interval = rcParams["stats.ci_kind"]
+
         if not isinstance(fmt, str):
             raise ValueError("Invalid format string.")
 
@@ -248,19 +253,23 @@ def moments(self, types="mvsk"):
 
         return moments
 
-    def eti(self, mass=0.94, fmt=".2f"):
+    def eti(self, mass=None, fmt=".2f"):
         """Equal-tailed interval containing `mass`.
 
         Parameters
         ----------
         mass: float
-            Probability mass in the interval. Defaults to 0.94
+            Probability mass in the interval. Defaults to None,
+        which results in the value of rcParams["stats.ci_prob"] being used.
         fmt : str
             fmt used to represent results using f-string fmt for floats. Default to ".2f"
             i.e. 2 digits after the decimal point. Use `"none"` for no format.
         """
         valid_distribution(self)
 
+        if mass is None:
+            mass = rcParams["stats.ci_prob"]
+
         if not isinstance(fmt, str):
             raise ValueError("Invalid format string.")
 
@@ -277,19 +286,23 @@ def eti(self, mass=0.94, fmt=".2f"):
         else:
             return None
 
-    def hdi(self, mass=0.94, fmt=".2f"):
+    def hdi(self, mass=None, fmt=".2f"):
         """Highest density interval containing `mass`.
 
         Parameters
         ----------
         mass: float
-            Probability mass in the interval. Defaults to 0.94
+            Probability mass in the interval. Defaults to None,
+        which results in the value of rcParams["stats.ci_prob"] being used.
         fmt : str
             fmt used to represent results using f-string fmt for floats. Default to ".2f"
             i.e. 2 digits after the decimal point. Use `"none"` for no format.
         """
         valid_distribution(self)
 
+        if mass is None:
+            mass = rcParams["stats.ci_prob"]
+
         if not isinstance(fmt, str):
             raise ValueError("Invalid format string.")
 
@@ -491,7 +504,7 @@ def plot_pdf(
         self,
         moments=None,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         support="restricted",
         legend="legend",
@@ -515,6 +528,7 @@ def plot_pdf(
         interval : str
             Type of interval. Available options are highest density interval `"hdi"` (default),
             equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+            Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -556,7 +570,7 @@ def plot_cdf(
         self,
         moments=None,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         support="restricted",
         legend="legend",
@@ -580,6 +594,7 @@ def plot_cdf(
         interval : str
             Type of interval. Available options are highest density interval `"hdi"` (default),
             equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+            Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -620,7 +635,7 @@ def plot_ppf(
         self,
         moments=None,
         pointinterval=False,
-        interval="hdi",
+        interval=None,
         levels=None,
         legend="legend",
         color=None,
@@ -643,6 +658,7 @@ def plot_ppf(
         interval : str
             Type of interval. Available options are highest density interval `"hdi"` (default),
             equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+            Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0
@@ -671,7 +687,7 @@ def plot_interactive(
         kind="pdf",
         xy_lim="both",
         pointinterval=True,
-        interval="hdi",
+        interval=None,
         levels=None,
         figsize=None,
     ):
@@ -694,6 +710,7 @@ def plot_interactive(
         interval : str
             Type of interval. Available options are highest density interval `"hdi"` (default),
             equal tailed interval `"eti"` or intervals defined by arbitrary `"quantiles"`.
+            Defaults to the value in rcParams["stats.ci_kind"].
         levels : list
             Mass of the intervals. For hdi or eti the number of elements should be 2 or 1.
             For quantiles the number of elements should be 5, 3, 1 or 0

preliz/distributions/vonmises.py

@@ -119,14 +119,14 @@ def _fit_mle(self, sample):
         mu = np.mod(mu + np.pi, 2 * np.pi) - np.pi
         self._update(mu, kappa)
 
-    def eti(self, mass=0.94, fmt=".2f"):
+    def eti(self, mass=None, fmt=".2f"):
         mean = self.mu
         self.mu = 0
         hdi_min, hdi_max = super().eti(mass=mass, fmt=fmt)
         self.mu = mean
         return _warp_interval(hdi_min, hdi_max, self.mu, fmt)
 
-    def hdi(self, mass=0.94, fmt=".2f"):
+    def hdi(self, mass=None, fmt=".2f"):
         mean = self.mu
         self.mu = 0
         hdi_min, hdi_max = super().hdi(mass=mass, fmt=fmt)