requirement.txt added

docs/chapter_exp/Programming Experiments in Psychopy.rst

@@ -22,7 +22,7 @@ measured with higher precision.
 
 	    Some of Galton's tools. The pendulum chronograph is more complicated than any of these!
 
-	    Public domain image taken from 'citation missing'.
+	    Public domain image taken from :cite:`@johnson1985galton`.
 
 .. _Pendulum chronograph: http://galton.org/essays/1880-1889/galton-1889-rba-reaction-time.pdf
 
@@ -69,10 +69,10 @@ computer's low-level capacity for displaying and playing stimuli. Why is this
 necessary? Because we need to work with the computer on a low level in order to
 get it to achieve highly precise timings, and smoothly display even complex
 visual stimuli. That is one half of the experimental program; the other will
-consist in translating the experimental design into
+consist in translating the `experimental design`_ into
 computer code, so that, e.g., a study participant is presented with the required
-number of trials resulting from your power calculation for the
-conditions resulting from your latin square design.
+number of trials resulting from your `power calculation`_ for the
+conditions resulting from your `latin square design`_.
 
 Because Psychopy is written in Python, we having already learned Python,
 learning Psychopy reduces to learning the Psychopy-specific modules.

docs/nbuild/html/_sources/chapter_exp/Programming Experiments in Psychopy.rst.txt

@@ -22,7 +22,7 @@ measured with higher precision.
 
 	    Some of Galton's tools. The pendulum chronograph is more complicated than any of these!
 
-	    Public domain image taken from 'citation missing'.
+	    Public domain image taken from :cite:`@johnson1985galton`.
 
 .. _Pendulum chronograph: http://galton.org/essays/1880-1889/galton-1889-rba-reaction-time.pdf
 
@@ -69,10 +69,10 @@ computer's low-level capacity for displaying and playing stimuli. Why is this
 necessary? Because we need to work with the computer on a low level in order to
 get it to achieve highly precise timings, and smoothly display even complex
 visual stimuli. That is one half of the experimental program; the other will
-consist in translating the experimental design into
+consist in translating the `experimental design`_ into
 computer code, so that, e.g., a study participant is presented with the required
-number of trials resulting from your power calculation for the
-conditions resulting from your latin square design.
+number of trials resulting from your `power calculation`_ for the
+conditions resulting from your `latin square design`_.
 
 Because Psychopy is written in Python, we having already learned Python,
 learning Psychopy reduces to learning the Psychopy-specific modules.

docs/nbuild/html/chapter_exp/Programming Experiments in Psychopy.html

@@ -198,11 +198,11 @@ <h1>3.4. Story Time: Galton’s Pendulum<a class="headerlink" href="#story-time-
 used as an estimate of response time, which allowed a state of the art
 resolution of 1/100th of a second. Never before had mental process been
 measured with higher precision.</p>
-<div class="figure" id="id7">
+<div class="figure" id="id8">
 <img alt="galtons instruments" src="../_images/galtons_instruments.png" />
 <p class="caption"><span class="caption-text">Some of Galton’s tools. The pendulum chronograph is more complicated than any of these!</span></p>
 <div class="legend">
-Public domain image taken from ‘citation missing’.</div>
+Public domain image taken from [&#64;johnson1985galton].</div>
 </div>
 <p>Other experimenters around this time were stopping response latencies with
 manual stopwatches. Galton himself conducted human geographic surveys by
@@ -234,7 +234,7 @@ <h1>3.4. Story Time: Galton’s Pendulum<a class="headerlink" href="#story-time-
 exactly retrace what happened in the original experiment, 2. repeat it ad
 libitum. To actually exploit this reproducibility potential, we must use
 software that is open. The biggest open source experimental presentation
-software is Psychopy <a class="reference internal" href="#peirce2007psychopy" id="id1">[Pei07]</a>.</p>
+software is Psychopy <a class="reference internal" href="#peirce2007psychopy" id="id2">[Pei07]</a>.</p>
 </div>
 <div class="section" id="programming-experiments-in-python-with-psychopy">
 <h1>3.5. Programming Experiments in Python with Psychopy<a class="headerlink" href="#programming-experiments-in-python-with-psychopy" title="Permalink to this headline">¶</a></h1>
@@ -243,10 +243,10 @@ <h1>3.5. Programming Experiments in Python with Psychopy<a class="headerlink" hr
 necessary? Because we need to work with the computer on a low level in order to
 get it to achieve highly precise timings, and smoothly display even complex
 visual stimuli. That is one half of the experimental program; the other will
-consist in translating the experimental design into
+consist in translating the <a href="#id9"><span class="problematic" id="id10">`experimental design`_</span></a> into
 computer code, so that, e.g., a study participant is presented with the required
-number of trials resulting from your power calculation for the
-conditions resulting from your latin square design.</p>
+number of trials resulting from your <a href="#id11"><span class="problematic" id="id12">`power calculation`_</span></a> for the
+conditions resulting from your <a href="#id13"><span class="problematic" id="id14">`latin square design`_</span></a>.</p>
 <p>Because Psychopy is written in Python, we having already learned Python,
 learning Psychopy reduces to learning the Psychopy-specific modules.</p>
 <div class="section" id="the-basic-logic-of-experiments-in-psychopy">
@@ -302,10 +302,10 @@ <h3>3.5.1.3. Storing results and experimental logic<a class="headerlink" href="#
 <div class="section" id="a-caveat-on-accuracy-and-precision">
 <h3>3.5.1.4. A Caveat on Accuracy and Precision<a class="headerlink" href="#a-caveat-on-accuracy-and-precision" title="Permalink to this headline">¶</a></h3>
 <p>In principle, Psychopy can be highly accurate. In practice, much depends on
-specifics of the experiment and context <a class="reference internal" href="#garaizar2014accuracy" id="id2">[GV14]</a><a class="reference internal" href="#plant2016" id="id3">[Pla16]</a>.
+specifics of the experiment and context <a class="reference internal" href="#garaizar2014accuracy" id="id3">[GV14]</a><a class="reference internal" href="#plant2016" id="id4">[Pla16]</a>.
 Consider: one study has reported that Galton observed slightly <em>faster</em>
 response times in Victorian times than are observed in contemporary experiments
-<a class="reference internal" href="#woodley2013were" id="id4">[WTNM13]</a>. Could it be that the Victorians were mentally faster than
+<a class="reference internal" href="#woodley2013were" id="id5">[WTNM13]</a>. Could it be that the Victorians were mentally faster than
 us? An alternative suggestion for this has been that timings on digital devices
 are only ever approximations; i.e.,
 <a class="reference external" href="http://deevybee.blogspot.com/2013/05/have-we-become-slower-and-dumber.html">many digital devices could not record increments shorter than 100 ms</a>!
@@ -318,7 +318,7 @@ <h3>3.5.1.4. A Caveat on Accuracy and Precision<a class="headerlink" href="#a-ca
 of stimulus and response time collection will be random jitter. In many cases,
 this will simply show up as noise in the data (and thus, decrease the power of
 the experiment). Systematic distortions are not a necessary consequence
-<a class="reference internal" href="#vadillo2016" id="id5">[VG16]</a>. But other aspects represent an
+<a class="reference internal" href="#vadillo2016" id="id6">[VG16]</a>. But other aspects represent an
 inherent bias. For example, for build-in sound cards, auditory stimulus
 presentation onset is preceded by a delay. Typically, this delay will be
 approximately the same on every trial; but it will lead to a systematic
@@ -348,7 +348,7 @@ <h1>3.6. Alternative software<a class="headerlink" href="#alternative-software"
 javascript-based tool jsPsych allow conducting online experiments.</p>
 <div class="section" id="opensesame">
 <h2>3.6.1. OpenSesame<a class="headerlink" href="#opensesame" title="Permalink to this headline">¶</a></h2>
-<p>Another powerful option is <a class="reference internal" href="#opensesame">OpenSesame</a>  <a class="reference internal" href="#mathot2012opensesame" id="id6">[MathotST12]</a>,
+<p>Another powerful option is <a class="reference internal" href="#opensesame">OpenSesame</a>  <a class="reference internal" href="#mathot2012opensesame" id="id7">[MathotST12]</a>,
 programmed by Sebastiaan Mathôt.
 OpenSesame provides a graphical front-end, but also allows directly injecting
 Python code for fine-tuning. It is recommended for those who prefer a point-
@@ -381,37 +381,37 @@ <h1>3.7. References<a class="headerlink" href="#references" title="Permalink to
 <p id="bibtex-bibliography-chapter_exp/Programming Experiments in Psychopy-0"><table class="docutils citation" frame="void" id="garaizar2014accuracy" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[GV14]</a></td><td>Pablo Garaizar and Miguel&nbsp;A Vadillo. Accuracy and precision of visual stimulus timing in psychopy: no timing errors in standard usage. <em>PloS one</em>, 9(11):e112033, 2014.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id3">[GV14]</a></td><td>Pablo Garaizar and Miguel&nbsp;A Vadillo. Accuracy and precision of visual stimulus timing in psychopy: no timing errors in standard usage. <em>PloS one</em>, 9(11):e112033, 2014.</td></tr>
 </tbody>
 </table>
 <table class="docutils citation" frame="void" id="mathot2012opensesame" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id6">[MathotST12]</a></td><td>Sebastiaan Mathôt, Daniel Schreij, and Jan Theeuwes. Opensesame: an open-source, graphical experiment builder for the social sciences. <em>Behavior research methods</em>, 44(2):314–324, 2012.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id7">[MathotST12]</a></td><td>Sebastiaan Mathôt, Daniel Schreij, and Jan Theeuwes. Opensesame: an open-source, graphical experiment builder for the social sciences. <em>Behavior research methods</em>, 44(2):314–324, 2012.</td></tr>
 </tbody>
 </table>
 <table class="docutils citation" frame="void" id="peirce2007psychopy" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[Pei07]</a></td><td>Jonathan&nbsp;W Peirce. Psychopy—psychophysics software in python. <em>Journal of neuroscience methods</em>, 162(1-2):8–13, 2007.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id2">[Pei07]</a></td><td>Jonathan&nbsp;W Peirce. Psychopy—psychophysics software in python. <em>Journal of neuroscience methods</em>, 162(1-2):8–13, 2007.</td></tr>
 </tbody>
 </table>
 <table class="docutils citation" frame="void" id="plant2016" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id3">[Pla16]</a></td><td>Richard&nbsp;R. Plant. A reminder on millisecond timing accuracy and potential replication failure in computer-based psychology experiments: an open letter. <em>Behavior Research Methods</em>, 48(1):408–411, Mar 2016. URL: <a class="reference external" href="https://doi.org/10.3758/s13428-015-0577-0">https://doi.org/10.3758/s13428-015-0577-0</a>, <a class="reference external" href="https://doi.org/10.3758/s13428-015-0577-0">doi:10.3758/s13428-015-0577-0</a>.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id4">[Pla16]</a></td><td>Richard&nbsp;R. Plant. A reminder on millisecond timing accuracy and potential replication failure in computer-based psychology experiments: an open letter. <em>Behavior Research Methods</em>, 48(1):408–411, Mar 2016. URL: <a class="reference external" href="https://doi.org/10.3758/s13428-015-0577-0">https://doi.org/10.3758/s13428-015-0577-0</a>, <a class="reference external" href="https://doi.org/10.3758/s13428-015-0577-0">doi:10.3758/s13428-015-0577-0</a>.</td></tr>
 </tbody>
 </table>
 <table class="docutils citation" frame="void" id="vadillo2016" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id5">[VG16]</a></td><td>Miguel&nbsp;A. Vadillo and Pablo Garaizar. The effect of noise-induced variance on parameter recovery from reaction times. <em>BMC Bioinformatics</em>, 17(1):147, Mar 2016. URL: <a class="reference external" href="https://doi.org/10.1186/s12859-016-0993-x">https://doi.org/10.1186/s12859-016-0993-x</a>, <a class="reference external" href="https://doi.org/10.1186/s12859-016-0993-x">doi:10.1186/s12859-016-0993-x</a>.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id6">[VG16]</a></td><td>Miguel&nbsp;A. Vadillo and Pablo Garaizar. The effect of noise-induced variance on parameter recovery from reaction times. <em>BMC Bioinformatics</em>, 17(1):147, Mar 2016. URL: <a class="reference external" href="https://doi.org/10.1186/s12859-016-0993-x">https://doi.org/10.1186/s12859-016-0993-x</a>, <a class="reference external" href="https://doi.org/10.1186/s12859-016-0993-x">doi:10.1186/s12859-016-0993-x</a>.</td></tr>
 </tbody>
 </table>
 <table class="docutils citation" frame="void" id="woodley2013were" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id4">[WTNM13]</a></td><td>Michael&nbsp;A Woodley, Jan Te&nbsp;Nijenhuis, and Raegan Murphy. Were the victorians cleverer than us? the decline in general intelligence estimated from a meta-analysis of the slowing of simple reaction time. <em>Intelligence</em>, 41(6):843–850, 2013.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id5">[WTNM13]</a></td><td>Michael&nbsp;A Woodley, Jan Te&nbsp;Nijenhuis, and Raegan Murphy. Were the victorians cleverer than us? the decline in general intelligence estimated from a meta-analysis of the slowing of simple reaction time. <em>Intelligence</em>, 41(6):843–850, 2013.</td></tr>
 </tbody>
 </table>
 </p>