In [1]:
import numpy as np
from matplotlib import pyplot as plt
import matplotlib as mpl
import datetime as dt
import pandas as pd
mpl.rc('xtick', labelsize=14)
mpl.rc('ytick', labelsize=14)
mpl.rc('legend', fontsize=16)
mpl.rc('axes', titlesize=16)
mpl.rc('figure', titlesize=16)
mpl.rc('axes', labelsize=16)
mpl.rc('font', size=16)
mpl.rc('legend', numpoints= 1)
mpl.rc('lines', markersize= 8)
%matplotlib inline
Mesozooplankton¶
REAL(wp), dimension (1:3) :: zz_rate_mesozoo_sumpeakval !uM N magnitude of mesozooplankton summer concentration peaks
REAL(wp), dimension (1:3) :: zz_rate_mesozoo_sumpeakpos ! year-day times of mesozooplankton summer concentration peaks
REAL(wp), dimension (1:3) :: zz_rate_mesozoo_sumpeakwid ! year-days widths of mesozooplankton summer concentration peaks
In [47]:
#&nampismezo ! parameters for microzooplankton
zz_rate_mesozoo_winterconc = 0.369 #uM N mesozooplankton background concentration
zz_rate_mesozoo_summerconc = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_sumpeakval = np.expand_dims(np.array((0.339, 0.0, 0.0)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakpos = np.expand_dims(np.array((217.000, 120.000, 300.000)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid = np.expand_dims(np.array((114.0, 51.600, 40.000)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
#zz_rate_mesozoo_winterconc3 = 0.39 #uM N mesozooplankton background concentration
#zz_rate_mesozoo_summerconc3 = 1.0 # uM N mesozooplankton relative summer concentration
#zz_rate_mesozoo_sumpeakval3 = np.expand_dims(np.array((0.42, 0.0, 0.0)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
#zz_rate_mesozoo_sumpeakpos3 = np.expand_dims(np.array((217.000, 120.000, 300.000)),0) # year-day times of mesozooplankton summer concentration peaks
#zz_rate_mesozoo_sumpeakwid3 = np.expand_dims(np.array((100.0, 155.00, 218.000)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
#zz_rate_mesozoo_summerconc2 = 1.0 # uM N mesozooplankton relative summer concentration
#zz_rate_mesozoo_winterconc2 = 0.41 #uM N mesozooplankton background concentration
#zz_rate_mesozoo_sumpeakval2 = np.expand_dims(np.array((0.14, 0.18, .22)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
##zz_rate_mesozoo_sumpeakwid2 = np.expand_dims(np.array((50.0, 65.00, 80.00)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
#zz_rate_mesozoo_sumpeakwid2 = np.expand_dims(np.array((281.0, 155.00, 218.00)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
#zz_rate_mesozoo_sumpeakpos2 = np.expand_dims(np.array((281.000, 155.000, 218.00)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc2 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc2 = 0.3 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval2 = np.expand_dims(np.array((0.60, 0.63, .42)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
#zz_rate_mesozoo_sumpeakwid2 = np.expand_dims(np.array((50.0, 65.00, 80.00)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakwid2 = np.expand_dims(np.array((40.0, 70.00, 43.00)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos2 = np.expand_dims(np.array((130.000, 206.000, 290.00)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc4 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc4 = 0.41 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval4 = np.expand_dims(np.array((0.18, 0.26, .22)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid4 = np.expand_dims(np.array((40.0, 65.00, 80.00)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos4 = np.expand_dims(np.array((300.000, 185.000, 230.00)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc5 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc5 = 0.42 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval5 = np.expand_dims(np.array((0.3, .4, 0.22)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid5 = np.expand_dims(np.array((55.00, 74.00, 38.0)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos5 = np.expand_dims(np.array((160.000, 230.00, 300.000)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc6 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc6 = 0.42 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval6 = np.expand_dims(np.array((0.42, .56, 0.31)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid6 = np.expand_dims(np.array((50.00, 66.00, 38.0)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos6 = np.expand_dims(np.array((160.000, 230.00, 298.000)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc7 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc7 = 0.38 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval7 = np.expand_dims(np.array((0.55, .56, 0.36)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid7 = np.expand_dims(np.array((40.00, 67.00, 43.0)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos7 = np.expand_dims(np.array((130.000, 206.00, 290.000)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc8 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc8 = 0.41 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval8 = np.expand_dims(np.array((0.53, .57, 0.35)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid8 = np.expand_dims(np.array((40.00, 65.00, 44.0)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos8 = np.expand_dims(np.array((135.000, 208.00, 296.000)),0) # year-day times of mesozooplankton summer concentration peaks
zz_rate_mesozoo_summerconc3 = 1.0 # uM N mesozooplankton relative summer concentration
zz_rate_mesozoo_winterconc3 = 0.38 #uM N mesozooplankton background concentration
zz_rate_mesozoo_sumpeakval3 = np.expand_dims(np.array((0.55, .55, 0.36)) ,0) #uM N magnitude of mesozooplankton summer concentration peaks
zz_rate_mesozoo_sumpeakwid3 = np.expand_dims(np.array((40.00, 70.00, 43.0)),0) # year-days widths of mesozooplankton summer concentration peaks,0)
zz_rate_mesozoo_sumpeakpos3 = np.expand_dims(np.array((130.000, 206.00, 290.000)),0) # year-day times of mesozooplankton summer concentration peaks
In [48]:
zz_day=np.arange(1,366) # in model, nday_year starts at 1 on jan 1
dts=[dt.datetime(2014,12,31)+dt.timedelta(days=float(ii)) for ii in zz_day]
zz_day=np.expand_dims(zz_day,1)
zz_MesZoBar = zz_rate_mesozoo_winterconc + \
zz_rate_mesozoo_summerconc*(np.sum ( zz_rate_mesozoo_sumpeakval * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos)**2/zz_rate_mesozoo_sumpeakwid**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos-365.25)**2/zz_rate_mesozoo_sumpeakwid**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos+365.25)**2/zz_rate_mesozoo_sumpeakwid**2),1) )
zz_MesZoBar2 = zz_rate_mesozoo_winterconc2 + \
zz_rate_mesozoo_summerconc2*(np.sum ( zz_rate_mesozoo_sumpeakval2 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos2)**2/zz_rate_mesozoo_sumpeakwid2**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval2 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos2-365.25)**2/zz_rate_mesozoo_sumpeakwid2**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval2 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos2+365.25)**2/zz_rate_mesozoo_sumpeakwid2**2),1) )
zz_MesZoBar4 = zz_rate_mesozoo_winterconc4 + \
zz_rate_mesozoo_summerconc4*(np.sum ( zz_rate_mesozoo_sumpeakval4 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos4)**2/zz_rate_mesozoo_sumpeakwid4**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval4 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos4-365.25)**2/zz_rate_mesozoo_sumpeakwid4**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval4 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos4+365.25)**2/zz_rate_mesozoo_sumpeakwid4**2),1) )
zz_MesZoBar5 = zz_rate_mesozoo_winterconc5 + \
zz_rate_mesozoo_summerconc5*(np.sum ( zz_rate_mesozoo_sumpeakval5 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos5)**2/zz_rate_mesozoo_sumpeakwid5**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval5 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos5-365.25)**2/zz_rate_mesozoo_sumpeakwid5**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval5 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos5+365.25)**2/zz_rate_mesozoo_sumpeakwid5**2),1) )
zz_MesZoBar6 = zz_rate_mesozoo_winterconc6 + \
zz_rate_mesozoo_summerconc6*(np.sum ( zz_rate_mesozoo_sumpeakval6 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos6)**2/zz_rate_mesozoo_sumpeakwid6**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval6 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos6-365.25)**2/zz_rate_mesozoo_sumpeakwid6**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval6 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos6+365.25)**2/zz_rate_mesozoo_sumpeakwid6**2),1) )
zz_MesZoBar7 = zz_rate_mesozoo_winterconc7 + \
zz_rate_mesozoo_summerconc7*(np.sum ( zz_rate_mesozoo_sumpeakval7 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos7)**2/zz_rate_mesozoo_sumpeakwid7**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval7 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos7-365.25)**2/zz_rate_mesozoo_sumpeakwid7**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval7 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos7+365.25)**2/zz_rate_mesozoo_sumpeakwid7**2),1) )
zz_MesZoBar8 = zz_rate_mesozoo_winterconc8 + \
zz_rate_mesozoo_summerconc8*(np.sum ( zz_rate_mesozoo_sumpeakval8 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos8)**2/zz_rate_mesozoo_sumpeakwid8**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval8 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos8-365.25)**2/zz_rate_mesozoo_sumpeakwid8**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval8 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos8+365.25)**2/zz_rate_mesozoo_sumpeakwid8**2),1) )
zz_MesZoBar3 = zz_rate_mesozoo_winterconc3 + \
zz_rate_mesozoo_summerconc3*(np.sum ( zz_rate_mesozoo_sumpeakval3 * \
np.exp(-(zz_day-zz_rate_mesozoo_sumpeakpos3)**2/zz_rate_mesozoo_sumpeakwid3**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval3 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos3-365.25)**2/zz_rate_mesozoo_sumpeakwid3**2),1) \
+ np.sum ( zz_rate_mesozoo_sumpeakval3 * \
np.exp( -(zz_day-zz_rate_mesozoo_sumpeakpos3+365.25)**2/zz_rate_mesozoo_sumpeakwid3**2),1) )
In [50]:
fig,ax=plt.subplots(1,1,figsize=(20,6))
ax.plot(dts,zz_MesZoBar8,'b-')
#ax.plot(dts,zz_MesZoBar2,'r-')
ax.plot(dts,zz_MesZoBar3,'c--')
ax.plot([ii+dt.timedelta(days=365) for ii in dts],zz_MesZoBar3,'c--')
ax.plot(dts,zz_MesZoBar2,'g--')
ax.plot([ii+dt.timedelta(days=365) for ii in dts],zz_MesZoBar2,'g--')
#ax.plot(dts,zz_MesZoBar4,'r--')
ax.plot(dts,zz_MesZoBar5,'k--')
ax.plot(dts,zz_MesZoBar6,'y--')
ax.plot(dts,zz_MesZoBar7,'--',color='blueviolet')
ax.set_ylim(0,1.3)
ax.set_title('Mesozo')
Out[50]:
Text(0.5, 1.0, 'Mesozo')
In [ ]:
In [5]:
df=pd.read_excel('/ocean/eolson/MEOPAR/obs/MackasZoop/1-s2.0-S007966111300061X-mmc2.xls',skiprows=1)
df=df.dropna(0,how='any', subset=['Year','Month','Day']).dropna(1,how='any',thresh=200)
In [6]:
df.keys()
Out[6]:
Index(['Sample ID', 'Station name', 'Longitude (deg W)', 'Latitude (deg N)',
'Day', 'Month', 'Year', 'Decimal year', 'Local Time (hr)',
'Day or Night', 'Net + Tow Type', 'Tow Depth Range (m)',
'Bottom Depth (m)', 'Volume Filtered (m3)', 'Total Biomass',
'Total Copepods', 'Calanoids<1mm', 'Calanoids 1-3mm', 'Calanoids 3-5mm',
'Calanoids >5mm', 'Total Euphausiids >1 cm', 'E. pacifica > 1cm',
'Thysanoessa >1cm', 'Gammarids', 'Hyperiids', 'Ostracods', 'Shrimps',
'Crab larvae', 'Cladocerans', 'Chaetognaths', 'Pteropods', 'Larvaceans',
'Polychaetes', 'Siphonophores', 'Medusae', 'Ctenophores'],
dtype='object')
In [7]:
yd=[(dt.datetime(int(r.Year),int(r.Month),int(r.Day))-dt.datetime(int(r.Year)-1,12,31)).days for i,r in df.iterrows()]
In [8]:
df=df.assign(yd=yd).sort_values(by='yd')
In [9]:
dtsdf=[dt.datetime(2014,12,31)+dt.timedelta(days=int(ii)) for ii in df['yd'].values]
In [10]:
fig,ax=plt.subplots(1,1,figsize=(18,6))
ax.plot(df['yd'],df['Total Biomass'],'k-')
ax.plot(np.convolve(df['yd'], np.ones((30,))/30, mode='valid'),np.convolve(df['Total Biomass'].values, np.ones((30,))/30, mode='valid'),'k--')
ax.plot(zz_day,zz_MesZoBar3*25,'--',color='blueviolet')
Out[10]:
[<matplotlib.lines.Line2D at 0x7f3c71656940>]
In [11]:
fig,ax=plt.subplots(1,1,figsize=(18,6))
#ax.plot(df['yd'],df['Total Biomass'],'k-')
ii=30
ax.plot(np.convolve(df['yd'], np.ones((ii,))/ii, mode='valid'),np.convolve(df['Total Biomass'].values, np.ones((ii,))/ii, mode='valid'),'k--')
ax.plot(zz_day,zz_MesZoBar3*21,'c--')
Out[11]:
[<matplotlib.lines.Line2D at 0x7f3c716b38d0>]
In [12]:
fig,ax=plt.subplots(1,1,figsize=(18,6))
ax.plot(df['yd'],df['Total Copepods'],'k-')
ii=30
ax.plot(np.convolve(df['yd'], np.ones((ii,))/ii, mode='valid'),np.convolve(df['Total Copepods'].values, np.ones((ii,))/ii, mode='valid'),'k--')
Out[12]:
[<matplotlib.lines.Line2D at 0x7f3c715dad68>]
In [13]:
fig,ax=plt.subplots(1,1,figsize=(18,6))
#ax.plot(df['yd'],df['Total Copepods'],'k-')
ii=30
tdf=df.dropna(axis=0,subset=['Calanoids<1mm'])
ax.plot(np.convolve(tdf['yd'], np.ones((ii,))/ii, mode='valid'),np.convolve(tdf['Total Biomass'].values-tdf['Calanoids<1mm'].values, np.ones((ii,))/ii, mode='valid'),'k--')
ax.plot(zz_day,zz_MesZoBar8*23,'c--')
Out[13]:
[<matplotlib.lines.Line2D at 0x7f3c701eec50>]
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