asasd.json

{"paragraphs":[{"text":"%md\n##General description of the study site and sampling strategy\nGeneral description of the study site and sampling strategy These results are part of a ongoing long-term monitoring program that is being carried out on the west coast of Portugal at Parede/Avencas (38º41'08''N, 9º21'20''W). A 0.04 Km2 portion of an intertidal rocky-shore area which is part of a large rocky platform is being sampled since May 2006. The shoreline is oriented in south-southwesterly directions and is located in the northern margin adjacent to the Tagus estuary. Intertidal sampling is performed during low-tide, in each full and new moon period, using hand nets (mesh size<1mm). Non-destructive sampling consists in the counting and capture of non-resident fish specimens that are measured and subsequently released at the same site where they were previously captured\n","dateUpdated":"2016-12-20T01:37:49+0000","config":{"colWidth":12,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/markdown"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1478473017810_1309619883","id":"20161106-225657_249099400","result":{"code":"SUCCESS","type":"HTML","msg":"<h2>General description of the study site and sampling strategy</h2>\n<p>General description of the study site and sampling strategy These results are part of a ongoing long-term monitoring program that is being carried out on the west coast of Portugal at Parede/Avencas (38º41'08''N, 9º21'20''W). A 0.04 Km2 portion of an intertidal rocky-shore area which is part of a large rocky platform is being sampled since May 2006. The shoreline is oriented in south-southwesterly directions and is located in the northern margin adjacent to the Tagus estuary. Intertidal sampling is performed during low-tide, in each full and new moon period, using hand nets (mesh size&lt;1mm). Non-destructive sampling consists in the counting and capture of non-resident fish specimens that are measured and subsequently released at the same site where they were previously captured</p>\n"},"dateCreated":"2016-11-06T10:56:57+0000","dateStarted":"2016-12-20T01:37:49+0000","dateFinished":"2016-12-20T01:37:49+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7587"},{"text":"%python\nyr = z.input(\"Introduce the desired year\",2009)","dateUpdated":"2016-12-20T01:37:49+0000","config":{"colWidth":6,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala","editorHide":false},"settings":{"params":{"Introduce year":"2009","<h3>Introduce year</h3>":2009,"%html <h3>Introduce year</h3>":2009,"Introduce the desired year":"2011"},"forms":{"Introduce the desired year":{"name":"Introduce the desired year","displayName":"Introduce the desired year","type":"input","defaultValue":2009,"hidden":false}}},"jobName":"paragraph_1476010350537_624733343","id":"20161009-105230_1752607414","result":{"code":"SUCCESS","type":"TEXT","msg":""},"dateCreated":"2016-10-09T10:52:30+0000","dateStarted":"2016-12-20T01:37:49+0000","dateFinished":"2016-12-20T01:37:49+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7588"},{"text":"%python\nfrom pymongo import MongoClient\n\nyrs = int(yr)\nclient = MongoClient()                                                                             \ndb = client.mare                                                                                   \ncollection = db.fishdata\ntotal = 0                                                                       \npipe = [\n        {'$match':{'yr':yrs}},\n        {'$group':{'_id':'$yr','Total':{'$sum':'$abundance'}}}                         \n        ]                                                                                          \nfor doc in collection.aggregate(pipeline=pipe):                                                    \n    total = doc['Total']\n    result = \"%html <h3>Total Abundance for Year \"+str(yrs)+\": \"+str(total)+\"</h3>\"\n    print result\n","dateUpdated":"2016-12-20T01:37:49+0000","config":{"colWidth":6,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala","tableHide":false,"editorHide":false},"settings":{"params":{"Introduce year":"2009"},"forms":{}},"jobName":"paragraph_1475016805721_-736471033","id":"20160927-225325_1307458399","result":{"code":"SUCCESS","type":"HTML","msg":"<h3>Total Abundance for Year 2011: 404984</h3>\n"},"dateCreated":"2016-09-27T10:53:25+0000","dateStarted":"2016-12-20T01:37:49+0000","dateFinished":"2016-12-20T01:37:50+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7589"},{"text":"%python\nimport pandas as pd\nlistResult = list(collection.distinct(\"species\",{\"yr\": yrs,\"species\":{\"$ne\":\"\"}}))\ndf =  pd.DataFrame(listResult,columns=['Species sighted and/or captured this year'])\nz.show(df)\n","dateUpdated":"2016-12-20T01:37:50+0000","config":{"colWidth":12,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1476633307259_-602470977","id":"20161016-155507_165549136","result":{"code":"SUCCESS","type":"TEXT","msg":"Traceback (most recent call last):\n  File \"<stdin>\", line 1, in <module>\n  File \"<stdin>\", line 27, in show\n  File \"<stdin>\", line 32, in show_dataframe\nTypeError: 'list' object is not callable\n"},"dateCreated":"2016-10-16T03:55:07+0000","dateStarted":"2016-12-20T01:37:51+0000","dateFinished":"2016-12-20T01:37:51+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7590"},{"text":"%python\nimport matplotlib.pyplot as plt\nimport numpy as np\n\ndata_list = []                                                                           \ncursor = collection.find( { 'yr': yrs }, { 'abundance': 1,  '_id': 0 } )\n                                                                                         \nfor doc in cursor:                                                    \n    value_list = doc['abundance']\n    data_list.append(value_list)\n\n# plot\nfig, ax = plt.subplots(1)\nmu = np.mean(data_list)\nsigma = np.std(data_list)\nmax = np.max(data_list)\nmin = np.min(data_list)\ntextstr = '$\\mu=%.2f$\\n$\\sigma=%.2f$\\n$\\max=%.2f$\\n$\\min=%.2f$'%(mu, sigma, max, min)\n# these are matplotlib.patch.Patch properties\nprops = dict(boxstyle='round', facecolor='wheat', alpha=0.5)\nax.text(0.10, 0.95, textstr, transform=ax.transAxes, fontsize=14,\n        verticalalignment='top', bbox=props)\n        \nplt.boxplot(data_list,showmeans=True)\nplt.ylabel('Abundance')\nplt.xlabel('All species')\nplt.title('Total abundance - All species')\nz.show(plt)\nplt.close()\nlegend = \"<b>Figure 1.</b> Abundances of intertidal non-resident fish species sighted in all field surveys performed in <b>\"+ str(yrs) +\"</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\"\nprint legend","dateUpdated":"2016-12-20T01:37:51+0000","config":{"colWidth":6,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1476048804607_-166445392","id":"20161009-213324_790049608","result":{"code":"SUCCESS","type":"HTML","msg":"<div style=''><?xml version=\"1.0\" encoding=\"utf-8\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n  \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n<!-- Created with matplotlib 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<use transform=\"translate(1115.70292434 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-99\"/>\n     <use transform=\"translate(1165.51612483 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-105\"/>\n     <use transform=\"translate(1187.63290918 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-101\"/>\n     <use transform=\"translate(1243.02458615 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-115\"/>\n    </g>\n   </g>\n  </g>\n </g>\n <defs>\n  <clipPath id=\"p9d2e551cda\">\n   <rect height=\"345.6\" width=\"446.4\" x=\"72.0\" y=\"43.2\"/>\n  </clipPath>\n </defs>\n</svg>\n<div>\n<b>Figure 1.</b> Abundances of intertidal non-resident fish species sighted in all field surveys performed in <b>2011</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\n"},"dateCreated":"2016-10-09T09:33:24+0000","dateStarted":"2016-12-20T01:37:52+0000","dateFinished":"2016-12-20T01:37:54+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7591"},{"text":"%python\nimport matplotlib.pyplot as plt\nimport numpy as np\n\ndata_list = []                                                                           \ncursor = collection.find( { 'yr': yrs,'standard_length':{'$ne':''} }, { 'standard_length': 1,  '_id': 0 } )\n\nfor doc in cursor:                                                    \n    value_list = doc['standard_length']\n    data_list.append(value_list)\n\n# plot\nfig, ax = plt.subplots(1)\nmu = np.mean(data_list)\nsigma = np.std(data_list)\nmax = np.max(data_list)\nmin = np.min(data_list)\ntextstr = '$\\mu=%.2f$\\n$\\sigma=%.2f$\\n$\\max=%.2f$\\n$\\min=%.2f$'%(mu, sigma, max, min)\n# these are matplotlib.patch.Patch properties\nprops = dict(boxstyle='round', facecolor='wheat', alpha=0.5)\nax.text(0.10, 0.95, textstr, transform=ax.transAxes, fontsize=14,\n        verticalalignment='top', bbox=props)\n\nplt.boxplot(data_list,showmeans=True)\nplt.ylabel('Length(cm)')\nplt.xlabel('All Species')\nplt.title('Total length - All species')\nz.show(plt)\nplt.close()\nlegend = \"<b>Figure 2.</b> Total length of intertidal non-resident fish species sampled in all field surveys performed in <b>\"+ str(yrs) +\"</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\"\nprint legend","dateUpdated":"2016-12-20T01:37:52+0000","config":{"colWidth":6,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1476048693536_-1373523641","id":"20161009-213133_758763552","result":{"code":"SUCCESS","type":"HTML","msg":"<div style=''><?xml 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0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-104\"/>\n     <use transform=\"translate(536.281257905 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-45\"/>\n     <use transform=\"translate(597.151657238 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-65\"/>\n     <use transform=\"translate(663.601688371 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-108\"/>\n     <use transform=\"translate(685.718472719 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-108\"/>\n     <use transform=\"translate(735.530426671 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-115\"/>\n     <use transform=\"translate(785.34362717 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-112\"/>\n     <use transform=\"translate(840.735304133 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-101\"/>\n     <use transform=\"translate(896.126981096 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-99\"/>\n     <use transform=\"translate(945.940181594 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-105\"/>\n     <use transform=\"translate(968.056965943 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-101\"/>\n     <use transform=\"translate(1023.44864291 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-115\"/>\n    </g>\n   </g>\n  </g>\n </g>\n</svg>\n<div>\n<b>Figure 2.</b> Total length of intertidal non-resident fish species sampled in all field surveys performed in <b>2011</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\n"},"dateCreated":"2016-10-09T09:31:33+0000","dateStarted":"2016-12-20T01:37:53+0000","dateFinished":"2016-12-20T01:37:56+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7592"},{"text":"%python\nimport matplotlib.pyplot as plt\n\ncolors = ['gold', 'lightskyblue', 'lightcoral']\nexplode = (0, 0, 0)\nlabels = []\nabundances = []\n\nclient = MongoClient()                                                                             \ndb = client.mare                                                                                   \ncollection = db.fishdata\npipe = [\n        {'$project':\n           {\n              'abundance': 1,\n              '_id':0,\n              'yr':1,\n              'specie': {\n                    '$cond': { \n                        'if': { '$eq': [ '$species', 'Atherina presbyter' ] }, \n                        'then': 'Atherina presbyter',\n                        'else': {\n                            '$cond': {\n                                'if': { '$eq': ['$species','Diplodus sargus']}, \n                                'then': 'Diplodus sargus', \n                                'else': 'Others'\n                            }\n                        }\n                    }\n                },              \n           }\n      },\n      {'$match' : { 'yr' : yrs } },\n      {'$group':{'_id':'$specie','total': { '$sum': '$abundance' }}}\n   ]\n   \nfor doc in collection.aggregate(pipeline=pipe):                                                   \n    species_value = doc['_id']\n    labels.append(species_value)    \n    total_value = doc['total']\n    abundances.append(total_value)\n\nplt.pie(abundances, explode=explode, labels=labels, colors=colors,\n        autopct='%.2f%%', startangle=90)\nplt.title('Most abundant species')        \nplt.axis('equal')\nz.show(plt)\nplt.close()\nlegend = \"<b>Figure 3.</b> Most abundant intertidal non-resident fish species at Parede/Avencas in <b>\"+ str(yrs) +\"</b> (west coast of Portugal - 38º41'08''N, 9º21'20'W).\"\nprint 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xlink:href=\"#Nimbus_Sans_L_Regular-100\"/>\n     <use transform=\"translate(518.550020553 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-97\"/>\n     <use transform=\"translate(573.941697516 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-110\"/>\n     <use transform=\"translate(629.333374479 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-116\"/>\n     <use transform=\"translate(684.723713686 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-115\"/>\n     <use transform=\"translate(734.536914184 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-112\"/>\n     <use transform=\"translate(789.928591147 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-101\"/>\n     <use transform=\"translate(845.320268111 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-99\"/>\n     <use transform=\"translate(895.133468609 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-105\"/>\n     <use transform=\"translate(917.250252958 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-101\"/>\n     <use transform=\"translate(972.641929921 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-115\"/>\n    </g>\n   </g>\n  </g>\n </g>\n</svg>\n<div>\n<b>Figure 3.</b> Most abundant intertidal non-resident fish species at Parede/Avencas in <b>2011</b> (west coast of Portugal - 38º41'08''N, 9º21'20'W).\n"},"dateCreated":"2016-10-09T10:48:14+0000","dateStarted":"2016-12-20T01:37:54+0000","dateFinished":"2016-12-20T01:37:58+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7593"},{"text":"%python\nimport numpy as np\nimport matplotlib.pyplot as plt\n\nresult = []\nfor x in range(1, 13):\n    cursor = collection.distinct(\"species\",{\"yr\": yrs,\"mo\":x,\"abundance\": {\"$gt\": 0},\"species\":{\"$ne\":\"\"}})\n    df =  pd.DataFrame(list(cursor),columns=['species'])\n    result.append(df.species.count())\n\n\nN = 12\nmenMeans = (1, 2, 3, 4, 5,6,7,8,9,10,11,12)\n\nind = np.arange(N)  # the x locations for the groups\nwidth = 0.35       # the width of the bars\n\nfig, ax = plt.subplots()\nrects1 = ax.bar(ind, tuple(result), width, color='r')\n\n# add some text for labels, title and axes ticks\nax.set_ylabel('Number of different species per month')\nax.set_xticks(ind + width)\nax.set_xticklabels(('Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec'))\n\nax.spines['top'].set_visible(False)\ndef autolabel(rects):\n    # attach some text labels\n    for rect in rects:\n        height = rect.get_height()\n        ax.text(rect.get_x() + rect.get_width()/2., 1.05*height,\n                '%d' % int(height),\n                ha='center', va='bottom')\n\nautolabel(rects1)\n\nz.show(plt)\nplt.close()\nlegend = \"<b>Figure 4.</b> Intertidal non-resident species richness per month in <b>\"+ str(yrs) +\"</b>.\"\nprint 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transform=\"scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-51\"/>\n    </g>\n   </g>\n  </g>\n </g>\n <defs>\n  <clipPath id=\"pdba1e0c4b2\">\n   <rect height=\"345.6\" width=\"446.4\" x=\"72.0\" y=\"43.2\"/>\n  </clipPath>\n </defs>\n</svg>\n<div>\n<b>Figure 4.</b> Intertidal non-resident species richness per month in <b>2011</b>.\n"},"dateCreated":"2016-10-25T11:16:52+0000","dateStarted":"2016-12-20T01:37:55+0000","dateFinished":"2016-12-20T01:37:58+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7594"},{"text":"","dateUpdated":"2016-12-20T01:37:54+0000","config":{"colWidth":12,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1482193654024_-968134774","id":"20161220-002734_960112669","result":{"code":"SUCCESS","type":"TEXT","msg":""},"dateCreated":"2016-12-20T12:27:34+0000","dateStarted":"2016-12-20T01:37:54+0000","dateFinished":"2016-12-20T01:37:54+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7595"},{"text":"%python\nimport matplotlib.pyplot as plt\nfrom matplotlib import rc\n\n# activate latex text rendering\nrc('text', usetex=True)\nresult = []\nlen = [0]\n\nfor x in range(1, 13):\n    cursor = collection.find({'yr': yrs, 'mo':x,'species':'Atherina presbyter', 'standard_length': {'$gt': 0}}, {'standard_length': 1,'mo': 1})\n    monthList = []\n    for doc in cursor:\n        value = doc['standard_length']\n        monthList.append(value)\n    result.append(monthList)\n    \n    pipe = [\n            {'$match':{'yr':yrs,'mo':x,'species':'Atherina presbyter'}},\n            {'$group':{'_id':'$mo','abundance':{'$avg':'$abundance'}}}                         \n            ]\n    cursorLen = collection.aggregate(pipeline=pipe)\n    if cursorLen.alive:\n        for docLen in cursorLen:\n            len.append(docLen['abundance'])\n    else:\n        len.append(0)\n\nfig, ax1 = plt.subplots()\nax1.boxplot(result,showmeans=True)\nplt.xlabel('Months')\nlabels = ('Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', \n          'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec')\nplt.xticks(range(1,13),labels, rotation=15)\nplt.title(r'Length vs Average Abundance for \\textit{Atherina presbyter}')\nax2 = ax1.twinx()\nax2.plot(len,'--go')\n\nax1.set_ylabel('Total length')\nax2.set_ylabel('Average Abundance', color='g')\n\nz.show(plt)\nplt.close()\nlegend = \"<b>Figure 5.</b> Monthly variation in size (TL-total length) and abundances of <i>Atherina presbyter</i> (number of individuals sighted)  in <b>\"+ str(yrs) +\"</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\"\nprint legend","dateUpdated":"2016-12-20T01:37:54+0000","config":{"colWidth":6,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1476136875213_1107834162","id":"20161010-220115_1432600131","result":{"code":"SUCCESS","type":"HTML","msg":"<div style=''><?xml version=\"1.0\" encoding=\"utf-8\" standalone=\"no\"?>\n<!DOCTYPE svg 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     <use transform=\"translate(621.86254974 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-100\"/>\n      <use transform=\"translate(677.254226704 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-97\"/>\n      <use transform=\"translate(732.645903667 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-110\"/>\n      <use transform=\"translate(788.03758063 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-99\"/>\n      <use transform=\"translate(837.850781128 0.0)scale(0.996264009963)\" xlink:href=\"#Nimbus_Sans_L_Regular-101\"/>\n     </g>\n    </g>\n   </g>\n  </g>\n </g>\n <defs>\n  <clipPath id=\"p9aafa6d3bf\">\n   <rect height=\"345.6\" width=\"446.4\" x=\"72.0\" y=\"43.2\"/>\n  </clipPath>\n </defs>\n</svg>\n<div>\n<b>Figure 5.</b> Monthly variation in size (TL-total length) and abundances of <i>Atherina presbyter</i> (number of individuals sighted)  in <b>2011</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\n"},"dateCreated":"2016-10-10T10:01:15+0000","dateStarted":"2016-12-20T01:37:56+0000","dateFinished":"2016-12-20T01:37:59+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7596"},{"text":"%python\nimport matplotlib.pyplot as plt\nfrom matplotlib import rc\n\n# activate latex text rendering\nrc('text', usetex=True)\n\nresult = []\nlen = [0]\n\nfor x in range(1, 13):\n    cursor = collection.find({'yr': yrs, 'mo':x,'species':'Diplodus sargus', 'standard_length': {'$gt': 0}}, {'standard_length': 1,'mo': 1})\n    monthList = []\n    for doc in cursor:\n        value = doc['standard_length']\n        monthList.append(value)\n    result.append(monthList)\n    \n    pipe = [\n            {'$match':{'yr':yrs,'mo':x,'species':'Diplodus sargus'}},\n            {'$group':{'_id':'$mo','abundance':{'$avg':'$abundance'}}}                         \n            ]\n    cursorLen = collection.aggregate(pipeline=pipe)\n    if cursorLen.alive:\n        for docLen in cursorLen:\n            len.append(docLen['abundance'])\n    else:\n        len.append(0)\n\nfig, ax1 = plt.subplots()\nax1.boxplot(result,showmeans=True)\nplt.xlabel('Months')\nlabels = ('Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', \n          'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec')\nplt.xticks(range(1,13),labels, rotation=15)\nplt.title(r'Length vs Average Abundance for \\textit{Diplodus sargus}')\nax2 = ax1.twinx()\nax2.plot(len,'--go')\n\nax1.set_ylabel('Total length')\nax2.set_ylabel('Average Abundance', color='g')\n\nz.show(plt)\nplt.close()\nlegend = \"<b>Figure 6.</b> Monthly variation in size (TL-total length) and abundances of <i>Diplodus sargus</i> (number of individuals sighted)  in <b>\"+ str(yrs) +\"</b> (mean is represented by a red dot, the box represents the interquartil distance with a red line representing the median and the bars represent the standard deviation).\"\nprint 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deviation).\n"},"dateCreated":"2016-11-06T11:59:20+0000","dateStarted":"2016-12-20T01:37:58+0000","dateFinished":"2016-12-20T01:38:01+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7597"},{"text":"","dateUpdated":"2016-12-20T01:37:57+0000","config":{"colWidth":12,"graph":{"mode":"table","height":300,"optionOpen":false,"keys":[],"values":[],"groups":[],"scatter":{}},"enabled":true,"editorMode":"ace/mode/scala"},"settings":{"params":{},"forms":{}},"jobName":"paragraph_1482194174826_1661974770","id":"20161220-003614_189030690","result":{"code":"SUCCESS","type":"TEXT","msg":""},"dateCreated":"2016-12-20T12:36:14+0000","dateStarted":"2016-12-20T01:37:58+0000","dateFinished":"2016-12-20T01:37:59+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:7598"}],"name":"MARE - Relatório 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