Last updated: 2016-05-06

Observations

Birds <-read_excel("MyEBirdDataRaw.xlsx")
glimpse(Birds)
## Observations: 1,711
## Variables: 13
## $ Order           (dbl) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,...
## $ Common_Name     (chr) "Greater White-fronted Goose", "Greater White-...
## $ Scientific_Name (chr) "Anser albifrons", "Anser albifrons", "Anser a...
## $ Tax_Order       (chr) "Anseriformes", "Anseriformes", "Anseriformes"...
## $ Count           (chr) "14", "X", "X", "2", "X", "X", "X", "X", "X", ...
## $ State           (chr) "US-MO", "US-KS", "US-KS", "US-MO", "US-KS", "...
## $ County          (chr) "Boone", "Stafford", "Stafford", "Boone", "Sta...
## $ Location        (chr) "Eagle Bluffs CA", "Quivira NWR", "Quivira NWR...
## $ Location_Type   (chr) "Wetland", "Wetland", "Wetland", "Wetland", "W...
## $ Latitude        (dbl) 38.86360, 38.17690, 38.17690, 38.86360, 38.176...
## $ Longitude       (dbl) -92.45040, -98.52590, -98.52590, -92.45040, -9...
## $ Date            (time) 2015-03-21, 2013-10-20, 2013-11-02, 2015-03-2...
## $ Time            (time) 1899-12-30 07:30:00, 1899-12-30 09:30:00, 189...

Dropping X from the Counts

Dropping X from the Counts

Locations as Types

  • Wetlands
    Eagle Bluffs, Quivira, 3M, Perry Philips Lake, Cedar Bluff, Cheyenne Bottoms, Little Dixie Lake, Milford Lake, Payne's Prairie, Plainville Lake, Twin Lakes

  • Grasslands
    Bradford Farm, Grassland Trail, Rooks, Ellis, Hinkson Trail, Owl Field, Red Rocks, Hays

  • Urban
    Fort Hays State, My Yard/Home/My Front Yard, Maynard, Gosnell, South Cove

  • Forest
    Albert Oakland, High Ridge Trail, Bear Creek Trail, Weldon Springs, Busch CA, Rock Bridge, Lost Valley

  • Mixture
    Forum Nature Area, Grindstone, CANS, Payne's Prairie, Garth Avenue, NAMC

All Observations

All Observations

All Observations

Counts by Location Type

summary(fm_LocationType)
## Linear mixed-effects model fit by maximum likelihood
##  Data: Birds 
##       AIC      BIC    logLik
##   14186.6 14234.17 -7084.302
## 
## Random effects:
##  Formula: ~Date | State
##  Structure: General positive-definite, Log-Cholesky parametrization
##             StdDev       Corr  
## (Intercept) 4.274939e+00 (Intr)
## Date        2.507203e-09 -0.558
## Residual    3.102721e+01       
## 
## Fixed effects: Count ~ Location_Type 
##                            Value Std.Error   DF  t-value p-value
## (Intercept)             0.796250  3.079795 1450 0.258540  0.7960
## Location_TypeGrassland 12.390021  2.983131 1450 4.153361  0.0000
## Location_TypeMixture    2.180719  3.057208 1450 0.713304  0.4758
## Location_TypeUrban      3.244043  3.070373 1450 1.056563  0.2909
## Location_TypeWetland    7.591083  2.184098 1450 3.475614  0.0005
##  Correlation: 
##                        (Intr) Lct_TG Lct_TM Lct_TU
## Location_TypeGrassland -0.435                     
## Location_TypeMixture   -0.319  0.328              
## Location_TypeUrban     -0.543  0.427  0.319       
## Location_TypeWetland   -0.520  0.510  0.448  0.514
## 
## Standardized Within-Group Residuals:
##          Min           Q1          Med           Q3          Max 
## -0.517809505 -0.266107426 -0.117745226 -0.008805448 16.629034775 
## 
## Number of Observations: 1459
## Number of Groups: 5

Counts by Location Type

Fixed effects: Count ~ Location_Type 
                           Value Std.Error   DF  t-value p-value
(Intercept)             0.796250  3.079795 1450 0.258540  0.7960
Location_TypeGrassland 12.390021  2.983131 1450 4.153361  0.0000
Location_TypeMixture    2.180719  3.057208 1450 0.713304  0.4758
Location_TypeUrban      3.244043  3.070373 1450 1.056563  0.2909
Location_TypeWetland    7.591083  2.184098 1450 3.475614  0.0005
 Correlation: 
                       (Intr) Lct_TG Lct_TM Lct_TU
Location_TypeGrassland -0.435                     
Location_TypeMixture   -0.319  0.328              
Location_TypeUrban     -0.543  0.427  0.319       
Location_TypeWetland   -0.520  0.510  0.448  0.514

Standardized Within-Group Residuals:
         Min           Q1          Med           Q3          Max 
-0.517809505 -0.266107426 -0.117745226 -0.008805448 16.629034775

Counts by State

summary(fm_State)
## Linear mixed-effects model fit by maximum likelihood
##  Data: Birds 
##        AIC      BIC    logLik
##   14191.74 14239.31 -7086.872
## 
## Random effects:
##  Formula: ~Date | Location_Type
##  Structure: General positive-definite, Log-Cholesky parametrization
##             StdDev       Corr  
## (Intercept) 3.713929e+00 (Intr)
## Date        2.958099e-09 -0.487
## Residual    3.104750e+01       
## 
## Fixed effects: Count ~ State 
##                  Value Std.Error   DF    t-value p-value
## (Intercept)   7.121426  6.613848 1450  1.0767448  0.2818
## StateUS-CO  -11.164244 19.178783 1450 -0.5821143  0.5606
## StateUS-FL   -0.723737  7.743446 1450 -0.0934644  0.9255
## StateUS-KS   -6.021985  6.633637 1450 -0.9077954  0.3641
## StateUS-MO    2.841901  6.534044 1450  0.4349376  0.6637
##  Correlation: 
##            (Intr) SUS-CO SUS-FL SUS-KS
## StateUS-CO -0.327                     
## StateUS-FL -0.752  0.261              
## StateUS-KS -0.913  0.325  0.750       
## StateUS-MO -0.949  0.332  0.770  0.935
## 
## Standardized Within-Group Residuals:
##         Min          Q1         Med          Q3         Max 
## -0.47762519 -0.26363501 -0.14298296 -0.01526384 16.65945160 
## 
## Number of Observations: 1459
## Number of Groups: 5

Counts by State

Fixed effects: Count ~ State 
                 Value Std.Error   DF    t-value p-value
(Intercept)   7.121426  6.613848 1450  1.0767448  0.2818
StateUS-CO  -11.164244 19.178783 1450 -0.5821143  0.5606
StateUS-FL   -0.723737  7.743446 1450 -0.0934644  0.9255
StateUS-KS   -6.021985  6.633637 1450 -0.9077954  0.3641
StateUS-MO    2.841901  6.534044 1450  0.4349376  0.6637
 Correlation: 
           (Intr) SUS-CO SUS-FL SUS-KS
StateUS-CO -0.327                     
StateUS-FL -0.752  0.261              
StateUS-KS -0.913  0.325  0.750       
StateUS-MO -0.949  0.332  0.770  0.935

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-0.47762519 -0.26363501 -0.14298296 -0.01526384 16.65945160 

States modeled by Location Types

summary(fm_LTbS)
Call: lm(formula = State ~ Location_Type, data = Birds)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.8564  0.0000  0.1436  0.2151  1.1436 

Coefficients:
                         Estimate Std. Error t value Pr(>|t|)    
(Intercept)             5.000e+00  3.363e-02 148.688  < 2e-16 ***
Location_TypeGrassland -4.278e-01  5.553e-02  -7.704 2.43e-14 ***
Location_TypeMixture    6.257e-15  5.945e-02   0.000        1    
Location_TypeUrban     -1.144e+00  5.421e-02 -21.094  < 2e-16 ***
Location_TypeWetland   -2.151e-01  4.177e-02  -5.150 2.96e-07 ***
---
Residual standard error: 0.6044 on 1454 degrees of freedom
Multiple R-squared:  0.2674,    Adjusted R-squared:  0.2654 
F-statistic: 132.7 on 4 and 1454 DF,  p-value: < 2.2e-16

Counts in each state by location type

States modeled by Location Types w/o AR, CO, FL

States modeled by Location Types w/o AR, CO, FL

anova(fm_FKM)
## Analysis of Variance Table
## 
## Response: State
##                 Df  Sum Sq Mean Sq F value    Pr(>F)    
## Location_Type    4  36.506  9.1265  78.466 < 2.2e-16 ***
## Residuals     1381 160.625  0.1163                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Missouri ANOVA

anova(fm_MO)
## Analysis of Variance Table
## 
## Response: Count
##                 Df  Sum Sq Mean Sq F value    Pr(>F)    
## Location_Type    4   28878  7219.5  5.9542 9.638e-05 ***
## Residuals     1143 1385884  1212.5                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Missouri ANOVA

summary(fm_MO)
Call: lm(formula = Count ~ Location_Type, data = Birds)

Residuals:
   Min     1Q Median     3Q    Max 
-19.09 -10.77  -3.67  -0.74 512.91 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)    
(Intercept)              4.6687     1.9375   2.410  0.01612 *  
Location_TypeGrassland  15.4198     3.8058   4.052 5.43e-05 ***
Location_TypeMixture     2.1734     3.4250   0.635  0.52584    
Location_TypeUrban      -0.9285     4.4159  -0.210  0.83351    
Location_TypeWetland     8.0994     2.5028   3.236  0.00125 ** 
---
Residual standard error: 34.82 on 1143 degrees of freedom
Multiple R-squared:  0.02041,   Adjusted R-squared:  0.01698 
F-statistic: 5.954 on 4 and 1143 DF,  p-value: 9.638e-05

Missouri Counts

Missouri Counts