Error in library(blme): there is no package called blme Jarad Niemi - PowerPoint PPT Presentation

Error in library(blme): there is no package called ’blme’ Jarad Niemi (STAT544@ISU) Hierarchical linear models (cont.) May 2, 2019 1 / 21

Hierarchical linear models (cont.) Random intercept, random slope Dr. Jarad Niemi STAT 544 - Iowa State University May 2, 2019 Jarad Niemi (STAT544@ISU) Hierarchical linear models (cont.) May 2, 2019 1 / 21

ALFL AMCR AMGO AMRE AMRO BAWW BCCH BHCO BHVI 0.010 0.011 0.012 0.014 0.013 0.013 0.013 0.009 0.009 0.014 0.010 0.010 0.013 0.012 0.012 0.012 0.008 0.009 0.008 0.013 0.011 0.011 0.008 0.011 0.007 0.012 0.008 0.007 0.010 0.010 0.010 0.006 0.012 0.006 0.011 0.009 0.007 0.006 0.009 0.009 0.005 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 BLBW BLJA BRBL BRCR BRTH BTBW BTNW CAWA CCSP 0.012 0.005 0.011 0.009 0.006 0.014 0.004 0.003 0.014 0.010 0.004 0.011 0.013 0.008 0.004 0.003 0.009 0.002 0.010 0.013 0.002 0.002 0.012 0.007 0.008 0.001 0.002 0.001 0.009 0.007 0.011 0.006 0.012 0.000 0.000 0.000 0.000 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 CEDW CHSP CMWA CONW COYE CSWA DOWO EABL EAKI 0.013 0.006 0.0125 0.016 0.006 0.0140 0.012 0.008 0.004 0.0075 0.004 0.0100 0.011 0.0135 0.015 0.004 0.006 0.0050 0.0130 0.010 0.002 0.002 0.0075 0.014 0.002 0.009 0.0125 0.004 0.0025 0.013 0.0050 0.008 0.000 0.000 0.000 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 EATO EAWP EVGR GCFL GCKI GRAJ GRCA GWWA HAWO 0.0132 0.010 0.009 0.009 0.010 0.006 0.010 0.0128 0.0075 0.009 0.008 0.008 0.008 0.004 0.0124 0.008 0.008 0.0050 0.007 0.007 0.008 0.006 0.0120 0.002 0.0025 0.006 0.006 0.006 0.006 0.0116 0.007 0.005 0.004 0.000 0.0000 0.005 0.004 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 HETH HOWR INBU LEFL MAWA MOWA MYWA NAWA NOPA 0.0155 0.006 0.010 0.013 0.0110 0.0160 0.0150 0.009 0.0150 0.008 0.012 0.012 0.0105 0.0145 0.004 0.008 0.0155 0.0145 0.011 0.0100 y 0.0140 0.007 0.0150 0.006 0.011 0.0135 0.002 0.0095 0.0140 0.010 0.0145 0.006 0.0130 0.004 0.0090 0.010 0.0140 0.000 0.005 0.0135 0.009 0.0125 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 NOWA OSFL OVEN PIWA PUFI RBGR RBNU RCKI REVI 0.010 0.0185 0.0185 0.008 0.014 0.013 0.0180 0.014 0.006 0.0180 0.009 0.013 0.0075 0.012 0.006 0.0175 0.0175 0.008 0.012 0.004 0.012 0.0170 0.011 0.0170 0.007 0.011 0.0050 0.004 0.0165 0.010 0.002 0.0165 0.010 0.010 0.006 0.0160 0.0025 0.0160 0.002 0.009 0.000 0.008 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 RUGR RWBL SCTA SOSP SWSP SWTH TEWA VEER VESP 0.008 0.012 0.012 0.006 0.006 0.010 0.011 0.006 0.008 0.015 0.004 0.004 0.011 0.004 0.010 0.004 0.008 0.006 0.002 0.002 0.014 0.002 0.010 0.009 0.002 0.006 0.004 0.008 0.000 0.000 0.000 0.000 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 WBNU WIWR WOTH WPWA WTSP YBFL YBSA YSFL YTVI 0.0155 0.013 0.010 0.0075 0.0075 0.010 0.012 0.008 0.008 0.0150 0.0050 0.0050 0.009 0.012 0.008 0.0145 0.006 0.011 0.006 0.0025 0.0025 0.008 0.011 0.006 0.0140 0.004 0.007 0.010 0.0000 0.0000 0.0135 0.010 0.004 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 YWAR 0.0100 0.0075 0.0050 0.0025 0.0000 1995 2000 2005 2010 year Jarad Niemi (STAT544@ISU) Hierarchical linear models (cont.) May 2, 2019 2 / 21

Independent regressions Initially, we could consider the model ind ∼ N ( β s, 0 + x st β s, 1 , σ 2 y st s ) where y st is the mean log count (+1) for species s at time t x st is the year (minus 2005) for species s at time t This model treats each species completely independently. Jarad Niemi (STAT544@ISU) Hierarchical linear models (cont.) May 2, 2019 3 / 21

ALFL AMCR AMGO AMRE AMRO BAWW BCCH BHCO BHVI 0.010 0.014 0.015 0.011 0.012 0.014 0.013 0.009 0.013 0.013 0.009 0.014 0.010 0.010 0.013 0.012 0.012 0.012 0.008 0.009 0.008 0.008 0.013 0.011 0.011 0.007 0.011 0.012 0.008 0.007 0.010 0.010 0.010 0.006 0.012 0.006 0.011 0.009 0.007 0.006 0.009 0.009 0.005 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 BLBW BLJA BRBL BRCR BRTH BTBW BTNW CAWA CCSP 0.011 0.006 0.012 0.003 0.014 0.009 0.004 0.014 0.010 0.004 0.002 0.011 0.013 0.008 0.004 0.002 0.009 0.002 0.001 0.010 0.013 0.012 0.007 0.008 0.002 0.000 0.000 0.000 0.009 0.007 0.011 0.006 −0.001 0.012 0.000 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 CEDW CHSP CMWA CONW COYE CSWA DOWO EABL EAKI 0.013 0.006 0.0100 0.016 0.006 0.012 0.0140 0.012 0.004 0.008 0.0075 0.004 0.010 0.011 0.0135 0.015 0.004 0.002 0.006 0.0130 0.008 0.010 0.0050 0.002 0.014 0.002 0.009 0.000 0.0125 0.004 0.006 0.0025 0.013 0.000 0.008 0.000 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 EATO EAWP EVGR GCFL GCKI GRAJ GRCA GWWA HAWO 0.0132 0.010 0.009 0.009 0.006 0.010 0.010 0.0075 0.0128 0.009 0.008 0.008 0.008 0.004 0.0124 0.0050 0.008 0.008 0.007 0.007 0.0025 0.008 0.006 0.0120 0.002 0.006 0.006 0.006 0.006 0.0116 0.0000 0.007 0.005 0.004 0.000 0.005 0.004 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 HETH HOWR INBU LEFL MAWA MOWA MYWA NAWA NOPA 0.0155 0.006 0.010 0.013 0.0110 0.0150 0.009 0.0150 0.016 0.008 0.012 0.012 0.0105 0.0145 0.004 0.008 0.0145 0.011 0.0100 y 0.0140 0.007 0.015 0.006 0.011 0.0135 0.002 0.0095 0.0140 0.010 0.006 0.0130 0.004 0.014 0.0090 0.010 0.000 0.005 0.0135 0.009 0.0125 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 NOWA OSFL OVEN PIWA PUFI RBGR RBNU RCKI REVI 0.010 0.008 0.014 0.013 0.014 0.006 0.009 0.018 0.013 0.018 0.0075 0.012 0.006 0.008 0.012 0.004 0.012 0.017 0.011 0.017 0.007 0.011 0.0050 0.004 0.002 0.010 0.010 0.010 0.006 0.016 0.0025 0.000 0.016 0.002 0.009 0.008 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 RUGR RWBL SCTA SOSP SWSP SWTH TEWA VEER VESP 0.008 0.010 0.013 0.016 0.012 0.012 0.006 0.006 0.011 0.011 0.006 0.004 0.008 0.004 0.015 0.011 0.004 0.009 0.010 0.004 0.002 0.002 0.006 0.014 0.002 0.010 0.007 0.009 0.002 0.000 0.000 0.004 0.008 0.000 0.005 0.000 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 WBNU WIWR WOTH WPWA WTSP YBFL YBSA YSFL YTVI 0.010 0.0100 0.0155 0.010 0.0075 0.010 0.013 0.012 0.009 0.0075 0.0150 0.008 0.0050 0.009 0.012 0.008 0.0050 0.007 0.0145 0.011 0.0025 0.008 0.011 0.006 0.006 0.0025 0.0140 0.005 0.007 0.010 0.0000 0.0000 0.0135 0.010 0.004 0.003 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 1995 2000 2005 2010 YWAR 0.0100 0.0075 0.0050 0.0025 0.0000 1995 2000 2005 2010 year Jarad Niemi (STAT544@ISU) Hierarchical linear models (cont.) May 2, 2019 4 / 21

Estimated slopes and 95% confidence intervals WOTH CEDW RBNU PUFI RCKI AMGO CMWA BAWW CCSP YSFL WBNU GCKI BRTH HOWR PIWA TEWA YBSA CAWA HAWO WPWA BCCH NOWA BTNW BLBW AMCR NAWA EABL OVEN AMRE VESP MYWA Species abbreviation GRAJ YWAR BLJA EAKI VEER DOWO SWTH RBGR REVI HETH MAWA CSWA AMRO WTSP NOPA MOWA BRCR SWSP GRCA YBFL CHSP ALFL RWBL COYE EATO BHVI EAWP RUGR LEFL OSFL GWWA BRBL WIWR SCTA GCFL YTVI BTBW INBU BHCO SOSP EVGR CONW −4e−04 −2e−04 0e+00 2e−04 4e−04 Slopes Jarad Niemi (STAT544@ISU) Hierarchical linear models (cont.) May 2, 2019 5 / 21