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::p_load(sf, tidyverse, tmap, spdep, funModeling, janitor, maps) pacman
November 29, 2022
March 6, 2023
The main aim of this project is to use the water point related data from rural areas at the water point or small water scheme level available from the WPdx Data Repository to explore the applicable geospatial analysis tools in water resources management for Nigeria.
To address the issue of providing clean and sustainable water supply to the rural community.
Apply appropriate global and local measures of spatial Association techniques to reveals the spatial patterns of Not Functional water points.
Below are the list of tasks to be completed :
Import the shapefile into R and save it in a simple feature data frame format with appropriate sf method.
note : Nigeria (NGA) has 3 Projected Coordinate Systems, EPSG: 26391, 26392, and 26303.
Derive the proportion of functional and non-functional water point at LGA level with appropriate tidyr and dplyr methods,
Combine the geospatial and aspatial data frame into simple feature data frame.
Performe outliers / clusters analysis by using appropriate local measures of spatial association methods.
Perform hotspot areas analysis by using appropriate local measures of spatial association methods.
Plot 2 main types of maps below :
Thematic Mapping
Plot maps to show the spatial distribution of functional and non-functional water point rate at LGA level by using appropriate thematic mapping technique provided by tmap package.
Analytical Mapping
Plot hotspot areas and outliers / clusters maps of functional and non-functional water point rate at LGA level by using appropriate thematic mapping technique provided by tmap package.
Following are the packages require for this exercise :
pacman package : to install and load the following R packages into R environment.
sf package :
tidyverse package :
readr :
stringr :
tmap package :
qtm( ) - to plot quick thematic map.
tm_shape( ) - specify the shape object.
spdep package :
poly2nb( ) - compute contiguity weight matrices for the study area.
nb2listw( ) - supplements a neighbours list with spatial weights for the chosen coding scheme.
moran.test( ) - for spatial autocorrelation using a spatial weights matrix in weights list form.
moran.mc( ) - for permutation test with Moran’s I statistic.
geary.test( ) - for spatial autocorrelation using a spatial weights matrix in weights list form.
geary.mc( ) - for permutation test with Geary’s C statistic.
sp.correlogram( ) - spatial correlograms for Moran’s I and the autocorrelation coefficient.
localmoran( ) - to calculate local spatial statistics for each zone based on the spatial weights object used.
moran.plot( ) - plot of spatial data against its spatially lagged values.
knearneigh ( ) - return matrix with the indices of points belonging to the set of the k nearest neighbours of each other.
knn2nb( ) - convert knn object to a neighbours list of class nb.
nbdist( ) - return the length of neighbour relationship edges.
dnearneigh( ) - derive distance-based weight matrices.
localG( ) - calculate local spatial statistic G for each zone based on the spatial weights object used.
funModeling package :
janitor package :
Use the code chunk below.
Aspatial Data
Geospatial Data
Use the code chunk below.
Note :
st_read( ) to import geo_export data set.
#| eval: false to display the code chunks without the output.
Use the code chunk below.
Note :
st_geometry( ) to get the geometry summary of a class data.frame or sf object.
Use the code chunk below.
Note :
glimpse( ) to swtich columns to rows, features to columns.
Avoid performing transformation
if going to use st_intersects()
in geoprocessing stage. This is
because st_intersects() only
works correctly if the geospatial
data are in geographic coordinate
system (i.e. wgs84)
Use the code chunk below.
Notes :
The output file is called “wp_nga.rds” and it is saved in geodata sub-folder.”
Use the code chunk below.
Notes :
Use the code chunk below.
Note :
st_geometry( ) to get the geometry summary of a class data.frame or sf object.
Use the code chunk below.
Note :
glimpse( ) to swtich columns to rows, features to columns.
Use the code chunk below.
Note :
glimpse( ) to recode all the NA values in status_cle field into Unknown.
Use the code chunk below.
Note :
get_dupes( ) to review rows that have duplicates. Specify the data.frame and the variable combination to search for duplicates and get back the duplicated rows.
Assumption :
For the same value of clean_adm2, each observation has unique pair of lat_deg and lon_deg.
Before proceed to analysis stage, sense the data with EDA.
Use the code chunk below.
Note :
freq( ) to display the distribution of status_cle field in wp_nga.
Remarks :
During the first round of EDA, noticed there are 2 values of “Non-functional due to dry season”.
Use mutate( ) with str_replace to combine both values, thereafter update the dataset.
Use the code chunk below.
Note :
filter( ) to get the data tables based on values associated with “Non-Functional” under “status_clean” variable.
According to the variables’ definition from the waterpointdata.org :
usage_cap (usage_capacity) = recommended maximum users per water point :
local_popu (local_population_1km) = number of people living within a 1km radius of the water point.
served_pop (water_point_population) = number of people currently or potentially served by a specific water point.
pressure (pressure_score) = the pressure score ( 0 - 100% ) is calculated based on the ratio of the number of people assigned to that water point over the theoretical maximum population which can be served based on the technology.
crucialness (crucialness_score) = the crucialness score ( 0 - 100% ) is the ratio is likely current users to the total local population within a 1km radius of the water point.
Remarks :
Use the code chunk below.
Note :
filter( ) to get water points that associated to the variation of “Non-Functional”.
Use the code chunk below.
Note :
filter( ) to get water points that associated to the variation of “Functional”.
Use the code chunk below.
Note :
filter( ) to get water points that associated to the variation of “Unknown”.
Use the code chunk below.
nga_wp <- nga %>%
mutate(`total_wpt` = lengths(
st_intersects(nga, wp_nga))) %>%
mutate(`wpt_functional` = lengths(
st_intersects(nga, wpt_functional))) %>%
mutate(`wpt_nonFunctional` = lengths(
st_intersects(nga, wpt_nonfunctional))) %>%
mutate(`wpt_unknown` = lengths(
st_intersects(nga, wpt_unknown)))
Use the code chunk below.
Note :
mutate( ) to add “pct_functional” and “pct_non-functional”.
write_rds( ) to save the sf data table into rds format.
total <- qtm(nga_wp, "total_wpt") +
tm_layout(legend.height = 0.3, legend.width = 0.3)
wp_functional <- qtm(nga_wp, "wpt_functional") +
tm_layout(legend.height = 0.3, legend.width = 0.3)
wp_nonfunctional <- qtm(nga_wp, "wpt_nonFunctional") +
tm_layout(legend.height = 0.3, legend.width = 0.3)
unknown <- qtm(nga_wp, "wpt_unknown") + tm_layout(legend.height = 0.3, legend.width = 0.3)
tmap_arrange(total, wp_functional, wp_nonfunctional, unknown, asp=1.5, ncol=2)
Determine autocorrelation for non-functional water points data.
Compute Contiguity Weight Matrices (CWM) first before compute the Global Spatial Autocorrelation statistics.
Determine the adjacency with 2 methods, Queen and Rook methods and derive Wq and Wr from the methods respectively.
Use the code chunk below.
Note :
poly2nb( ) to return a list of first order neighbours based on Queen criteria.
Use the code chunk below.
Note :
poly2nb( ) to return a list of first order neighbours based on Queen criteria.
Wq | Wr | |
---|---|---|
Number of regions without links | 1 link (#86) | 1 link (#86) |
Number of regions with the most links | 14 links (#508) | 14 links (#508) |
Number of regions with 1 link | #138, #560 | #138, #560 |
Average number of links per region | 5.736 | 5.711 |
Both methods have relatively similar performance, only have 1 region without links.
Identify neighbours of region points by Euclidean distance with a distance band.
Use the code chunk below.
Note :
cbind( ) to combine both longitude and latitude
Use the code chunk below.
Note :
knn2nb( ) to convert knn objects that returned by knearneigh( ) into a neighbours list of class nb.
nbdist( ) to return the length of neighbour relationship edges.
unlist( ) to remove the list structure of the returned object.
Min. 1st Qu. Median Mean 3rd Qu. Max.
13.86 34.82 42.98 45.71 56.00 94.18
Remarks :
The largest first nearest neighbour distance is 39.085 km, using this as the upper threshold gives certainty that all units will have at least one neighbour.
Min. 1st Qu. Median Mean 3rd Qu. Max.
13.86 39.06 50.48 54.58 65.14 147.41
Min. 1st Qu. Median Mean 3rd Qu. Max.
13.86 41.11 52.45 59.26 72.44 192.60
Use the code chunk below.
Note :
dnearneigh( ) to derive distance-based weight matrices.
Wd=3 | Wd=5 | Wd=6 | Wd=8 | |
---|---|---|---|---|
Largest first nearest neighbour distance | 39.08489 | 40.08029 | 42.28107 | 44.87575 |
Use the code chunk below.
Note :
nb2listw( ) to assign weights to each neighboring polygon. Each neighboring polygon will be assigned equal weight by explore with different input for style i.e. “W”, “B” and “C”.
Neighbour list object:
Number of regions: 774
Number of nonzero links: 4440
Percentage nonzero weights: 0.7411414
Average number of links: 5.736434
1 region with no links:
86
[1] FALSE
Characteristics of weights list object:
Neighbour list object:
Number of regions: 774
Number of nonzero links: 4440
Percentage nonzero weights: 0.7411414
Average number of links: 5.736434
1 region with no links:
86
Weights style: W
Weights constants summary:
n nn S0 S1 S2
W 773 597529 773 285.0658 3198.414
[1] TRUE
Characteristics of weights list object:
Neighbour list object:
Number of regions: 774
Number of nonzero links: 4440
Percentage nonzero weights: 0.7411414
Average number of links: 5.736434
1 region with no links:
86
Weights style: B
Weights constants summary:
n nn S0 S1 S2
B 773 597529 4440 8880 112368
[1] TRUE
Characteristics of weights list object:
Neighbour list object:
Number of regions: 774
Number of nonzero links: 4440
Percentage nonzero weights: 0.7411414
Average number of links: 5.736434
1 region with no links:
86
Weights style: C
Weights constants summary:
n nn S0 S1 S2
C 773 597529 773 269.1572 3405.93
Regardless of which input for the style, all have the same result of 1 region without links while the average number of links is 5.736434.
Use the code chunk below.
Note :
moran.test( ) to calculates the Moran’s I Index value and both a a z-score and p-value to evaluate the significance of that Index.
moran.mc( ) to do a permutation test to evaluate the rank of the observed statistic in relation to the statistic of simulated values.
Moran I test under randomisation
data: nga_wp$wpt_nonFunctional
weights: ngaWp_rswmQW n reduced by no-neighbour observations
Moran I statistic standard deviate = 20.043, p-value < 2.2e-16
alternative hypothesis: greater
sample estimates:
Moran I statistic Expectation Variance
0.433932927 -0.001295337 0.000471516
Monte-Carlo simulation of Moran I
data: nga_wp$wpt_nonFunctional
weights: ngaWp_rswmQW
number of simulations + 1: 1000
statistic = 0.43393, observed rank = 1000, p-value = 0.001
alternative hypothesis: greater
Remarks :
The value for both actual and random Moran’s I almost the same, i.e. 0.43393, which means the non-functional water points are positively autocorrelated with the data spatially cluster.
There is a statistical significant with p-value (2.2e-16) < 0.001, smaller than the alpha value to support the rejection of null hypothesis for the test i.e. the non-functional water points are not randomly spatial.
Use the code chunk below.
Note :
hist( ) to examine the simulated Moran’s I test statistics by plotting the distribution of the statistical values as a histogram.
Geary C test under randomisation
data: nga_wp$wpt_nonFunctional
weights: ngaWp_rswmQW
Geary C statistic standard deviate = 14.457, p-value < 2.2e-16
alternative hypothesis: Expectation greater than statistic
sample estimates:
Geary C statistic Expectation Variance
0.6170907765 1.0000000000 0.0007014859
Monte-Carlo simulation of Geary C
data: nga_wp$wpt_nonFunctional
weights: ngaWp_rswmQW
number of simulations + 1: 1000
statistic = 0.61709, observed rank = 1, p-value = 0.001
alternative hypothesis: greater
Remarks :
The value for both actual and random Geary’s C almost the same, i.e. 0.61709, which means the non-functional water points are positively autocorrelated with the data spatially cluster.
There is a statistical significant with p-value (2.2e-16) < 0.001, smaller than the alpha value to support the rejection of null hypothesis for the test i.e. the non-functional water points are not randomly spatial.
The Geary’s C value is greater than the Moran’s I value. However, since both values are less than 1, the observations tend to be clustered and similar.
Use Local Indicators for Spatial Association (LISA) method, especially local Moran’s I to detect cluster and / or outlier.
Use the code chunk below.
Ii E.Ii Var.Ii Z.Ii Pr(z != E(Ii))
1 -0.32365786 -9.995243e-04 1.924638e-01 -0.73547576 0.46204980
2 0.07000542 -4.092463e-05 1.053077e-02 0.68258288 0.49487045
3 1.25819985 -1.627684e-03 4.181728e-01 1.94819847 0.05139122
4 -0.03537489 -5.427505e-05 5.954304e-03 -0.45773361 0.64714384
5 0.01201533 -2.590965e-04 3.988998e-02 0.06145673 0.95099547
6 0.00768085 -1.538445e-07 1.687859e-05 1.86960486 0.06153871
Use the code chunk below.
Ii E.Ii Var.Ii Z.Ii Pr.z....E.Ii..
1 -3.2366e-01 -9.9952e-04 1.9246e-01 -7.3548e-01 4.6205e-01
2 7.0005e-02 -4.0925e-05 1.0531e-02 6.8258e-01 4.9487e-01
3 1.2582e+00 -1.6277e-03 4.1817e-01 1.9482e+00 5.1391e-02
4 -3.5375e-02 -5.4275e-05 5.9543e-03 -4.5773e-01 6.4714e-01
5 1.2015e-02 -2.5910e-04 3.9890e-02 6.1457e-02 9.5100e-01
6 7.6808e-03 -1.5384e-07 1.6879e-05 1.8696e+00 6.1539e-02
7 2.3716e-01 -6.6542e-04 8.5226e-02 8.1464e-01 4.1528e-01
8 1.3499e-01 -6.9507e-05 1.3396e-02 1.1669e+00 2.4326e-01
9 5.8469e-01 -3.9167e-04 6.0293e-02 2.3828e+00 1.7183e-02
10 1.9145e-01 -2.2881e-04 2.5098e-02 1.2099e+00 2.2630e-01
11 6.7485e-01 -7.6926e-04 8.4332e-02 2.3265e+00 1.9992e-02
12 1.3484e-01 -9.2780e-04 8.8869e-02 4.5543e-01 6.4880e-01
13 1.6286e-02 -4.0925e-05 6.3021e-03 2.0567e-01 8.3705e-01
14 -3.1655e-02 -2.9456e-05 2.8239e-03 -5.9514e-01 5.5175e-01
15 -3.1637e-01 -1.0254e-02 1.1135e+00 -2.9010e-01 7.7174e-01
16 6.8612e-02 -9.2780e-04 1.4275e-01 1.8406e-01 8.5397e-01
17 2.4270e-02 -1.9868e-05 5.1126e-03 3.3971e-01 7.3408e-01
18 5.8712e-01 -1.1792e-03 1.8138e-01 1.3814e+00 1.6717e-01
19 -8.6368e-03 -8.6620e-05 1.1101e-02 -8.1152e-02 9.3532e-01
20 -2.1125e-02 -1.8249e-05 2.8103e-03 -3.9815e-01 6.9052e-01
21 -6.1300e-02 -1.4475e-04 2.2288e-02 -4.0963e-01 6.8208e-01
22 2.8968e-01 -1.3297e-03 3.4172e-01 4.9782e-01 6.1861e-01
23 8.3857e-01 -1.1920e-03 1.8334e-01 1.9612e+00 4.9856e-02
24 1.5893e-03 -2.7477e-05 5.2960e-03 2.2217e-02 9.8228e-01
25 1.3175e-01 -8.6620e-05 9.5025e-03 1.3525e+00 1.7623e-01
26 8.0063e-01 -9.3914e-04 1.8085e-01 1.8849e+00 5.9446e-02
27 8.4077e-01 -1.6277e-03 2.5025e-01 1.6840e+00 9.2191e-02
28 -1.9940e-03 -1.2099e-02 1.3113e+00 8.8241e-03 9.9296e-01
29 3.0859e-01 -2.2324e-04 2.4486e-02 1.9735e+00 4.8442e-02
30 2.5468e-01 -3.1865e-04 3.0540e-02 1.4592e+00 1.4452e-01
31 9.3035e-03 -6.3380e-06 8.1230e-04 3.2665e-01 7.4393e-01
32 1.0902e+00 -1.5504e-03 3.9834e-01 1.7298e+00 8.3669e-02
33 8.0526e-02 -1.9868e-05 2.5464e-03 1.5962e+00 1.1045e-01
34 2.2617e-01 -2.7477e-05 3.0145e-03 4.1198e+00 3.7925e-05
35 -1.7370e-01 -3.5422e-04 3.8849e-02 -8.7950e-01 3.7913e-01
36 3.6215e+00 -1.7248e-02 1.6251e+00 2.8544e+00 4.3117e-03
37 -9.7994e-02 -6.9507e-05 4.8271e-03 -1.4094e+00 1.5870e-01
38 2.6132e+00 -5.7830e-03 6.3080e-01 3.2975e+00 9.7543e-04
39 1.8731e+00 -1.5753e-02 2.9886e+00 1.0926e+00 2.7457e-01
40 2.9695e+00 -3.9022e-03 7.4920e-01 3.4353e+00 5.9197e-04
41 4.0806e+00 -1.3638e-02 2.0716e+00 2.8446e+00 4.4471e-03
42 7.7463e-01 -8.2075e-03 1.5690e+00 6.2497e-01 5.3199e-01
43 7.5445e-01 -1.3297e-03 3.4172e-01 1.2929e+00 1.9605e-01
44 -9.4511e-02 -2.0041e-04 2.5680e-02 -5.8852e-01 5.5619e-01
45 -4.0892e-01 -1.0618e-03 2.7294e-01 -7.8067e-01 4.3500e-01
46 1.7264e-02 -1.8555e-06 3.5764e-04 9.1300e-01 3.6124e-01
47 -6.0666e-01 -4.4019e-03 6.7490e-01 -7.3309e-01 4.6350e-01
48 3.8136e-02 -1.0903e-05 2.1016e-03 8.3213e-01 4.0533e-01
49 -2.6481e-01 -9.2780e-04 1.0170e-01 -8.2749e-01 4.0796e-01
50 -3.6486e-01 -1.7389e-04 1.6668e-02 -2.8247e+00 4.7319e-03
51 6.4059e-01 -1.0618e-03 1.0169e-01 2.0122e+00 4.4203e-02
52 5.2295e-01 -6.1632e-04 7.8942e-02 1.8634e+00 6.2399e-02
53 5.1817e-01 -5.6910e-04 5.4530e-02 2.2214e+00 2.6324e-02
54 6.8852e-01 -7.1640e-04 7.8541e-02 2.4593e+00 1.3920e-02
55 7.4747e-01 -8.8063e-04 2.2641e-01 1.5727e+00 1.1578e-01
56 5.8669e-01 -1.6277e-03 2.5025e-01 1.1760e+00 2.3958e-01
57 9.1402e-01 -1.2599e-03 2.4254e-01 1.8585e+00 6.3096e-02
58 7.1930e-01 -1.3297e-03 1.4569e-01 1.8880e+00 5.9027e-02
59 -3.0961e-02 -5.2377e-04 8.0617e-02 -1.0720e-01 9.1463e-01
60 3.2899e-03 -3.3373e-07 3.6614e-05 5.4375e-01 5.8662e-01
61 7.1599e-02 -2.9126e-04 4.4841e-02 3.3949e-01 7.3424e-01
62 1.1170e+00 -1.6277e-03 2.0827e-01 2.4512e+00 1.4236e-02
63 5.9556e-01 -6.0715e-04 7.7767e-02 2.1378e+00 3.2531e-02
64 -7.0312e-02 -2.9456e-05 2.8239e-03 -1.3226e+00 1.8597e-01
65 4.0210e-02 -3.1865e-04 4.9056e-02 1.8298e-01 8.5481e-01
66 9.0458e-02 -1.1259e-03 1.4414e-01 2.4123e-01 8.0938e-01
67 6.6358e-02 -1.8555e-06 2.0357e-04 4.6511e+00 3.3019e-06
68 9.9615e-01 -1.1259e-03 4.3469e-01 1.5126e+00 1.3038e-01
69 9.5142e-01 -1.1259e-03 9.5720e-02 3.0788e+00 2.0782e-03
70 1.5763e+00 -2.3901e-03 3.6719e-01 2.6053e+00 9.1806e-03
71 1.3676e+00 -3.5471e-03 3.0082e-01 2.4999e+00 1.2422e-02
72 9.2471e-02 -1.4925e-04 1.4307e-02 7.7435e-01 4.3873e-01
73 -3.7128e-02 -8.3203e-05 1.0663e-02 -3.5875e-01 7.1978e-01
74 -3.1518e-02 -1.2649e-04 1.6210e-02 -2.4656e-01 8.0525e-01
75 -9.2317e-03 -1.9519e-04 2.1411e-02 -6.1757e-02 9.5076e-01
76 -3.8035e-02 -2.3951e-06 2.2963e-04 -2.5098e+00 1.2079e-02
77 7.1490e-01 -1.0618e-03 1.3594e-01 1.9419e+00 5.2155e-02
78 8.4336e-01 -1.6277e-03 1.7829e-01 2.0012e+00 4.5369e-02
79 7.2523e-01 -9.9952e-04 1.5377e-01 1.8520e+00 6.4030e-02
80 5.3888e-01 -4.8031e-04 7.3931e-02 1.9837e+00 4.7294e-02
81 3.4904e+00 -9.4838e-03 1.4466e+00 2.9099e+00 3.6157e-03
82 1.1262e+00 -3.3198e-03 8.5145e-01 1.2241e+00 2.2090e-01
83 -4.1318e-01 -3.9167e-04 7.5464e-02 -1.5026e+00 1.3293e-01
84 -1.6794e-01 -5.4275e-05 8.3578e-03 -1.8364e+00 6.6298e-02
85 -1.0457e-01 -3.8586e-05 4.2332e-03 -1.6066e+00 1.0814e-01
86 0.0000e+00 0.0000e+00 0.0000e+00 NaN NaN
87 9.7051e-02 -1.4925e-04 1.9126e-02 7.0284e-01 4.8215e-01
88 1.3239e-01 -1.1259e-03 1.4414e-01 3.5167e-01 7.2509e-01
89 8.6819e-01 -5.3489e-03 5.8371e-01 1.1434e+00 2.5289e-01
90 2.8316e-01 -1.6128e-03 1.3704e-01 7.6927e-01 4.4173e-01
91 1.2582e+00 -1.6277e-03 3.1322e-01 2.2510e+00 2.4382e-02
92 1.5674e+00 -3.2090e-03 4.0996e-01 2.4530e+00 1.4167e-02
93 1.5345e-02 -2.7477e-05 3.5215e-03 2.5904e-01 7.9560e-01
94 6.5838e-03 -9.8783e-04 9.4613e-02 2.4616e-02 9.8036e-01
95 7.6830e-02 -6.6449e-05 8.5158e-03 8.3329e-01 4.0468e-01
96 1.0339e-01 -8.3203e-05 9.1276e-03 1.0831e+00 2.7876e-01
97 1.3652e-02 -1.0184e-04 1.5681e-02 1.0983e-01 9.1254e-01
98 1.1441e-01 -8.6620e-05 1.3338e-02 9.9137e-01 3.2151e-01
99 1.7511e+00 -5.0690e-03 7.7665e-01 1.9927e+00 4.6290e-02
100 2.3957e-01 -3.9905e-04 6.1428e-02 9.6821e-01 3.3294e-01
101 -3.3289e-02 -9.9952e-04 1.5377e-01 -8.2343e-02 9.3437e-01
102 1.3164e+00 -1.5358e-03 2.3615e-01 2.7122e+00 6.6840e-03
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718 -4.2922e-03 -1.5384e-07 3.9589e-05 -6.8215e-01 4.9515e-01
719 3.2251e-01 -5.2377e-04 4.0046e-02 1.6142e+00 1.0648e-01
720 6.8852e-01 -7.1640e-04 7.8541e-02 2.4593e+00 1.3920e-02
721 8.3329e-02 -1.4475e-04 1.8549e-02 6.1289e-01 5.3995e-01
722 5.3675e-02 -1.7389e-04 2.2283e-02 3.6074e-01 7.1830e-01
723 4.8583e-02 -5.4275e-05 8.3578e-03 5.3201e-01 5.9472e-01
724 7.1148e-01 -9.2780e-04 1.7867e-01 1.6854e+00 9.1907e-02
725 1.1053e-01 -3.5422e-04 3.8849e-02 5.6258e-01 5.7372e-01
726 -3.1866e-01 -6.5588e-04 8.4006e-02 -1.0972e+00 2.7257e-01
727 1.1424e-02 -2.3951e-06 4.6165e-04 5.3181e-01 5.9486e-01
728 5.7671e-01 -7.1640e-04 7.8541e-02 2.0604e+00 3.9362e-02
729 2.7894e-01 -5.6910e-04 6.2402e-02 1.1189e+00 2.6317e-01
730 6.0619e-03 -3.3373e-07 5.1394e-05 8.4562e-01 3.9776e-01
731 3.0813e-01 -7.6926e-04 6.5421e-02 1.2077e+00 2.2716e-01
732 6.7941e-01 -1.4749e-03 1.6158e-01 1.6939e+00 9.0288e-02
733 -1.1686e-02 -2.3951e-06 3.0697e-04 -6.6684e-01 5.0488e-01
734 4.6362e-03 -2.3951e-06 3.6884e-04 2.4153e-01 8.0915e-01
735 9.6682e-01 -2.9930e-03 3.8244e-01 1.5682e+00 1.1683e-01
736 1.0961e+00 -1.2468e-03 3.2043e-01 1.9386e+00 5.2554e-02
737 6.7907e-01 -1.0618e-03 1.6334e-01 1.6828e+00 9.2404e-02
738 -7.6637e-03 -1.0903e-05 8.3406e-04 -2.6499e-01 7.9102e-01
739 7.8882e-01 -1.5504e-03 1.4841e-01 2.0517e+00 4.0203e-02
740 3.4338e-01 -1.2235e-04 1.8840e-02 2.5026e+00 1.2329e-02
741 2.0732e-02 -1.2162e-05 1.0351e-03 6.4477e-01 5.1908e-01
742 4.6167e-02 -5.4386e-06 8.3753e-04 1.5955e+00 1.1061e-01
743 -2.1810e-04 -1.4475e-04 1.5879e-02 -5.8210e-04 9.9954e-01
744 1.3116e-01 -4.0925e-05 7.8878e-03 1.4773e+00 1.3961e-01
745 1.9287e-01 -3.2531e-04 2.7678e-02 1.1612e+00 2.4555e-01
746 3.4420e-01 -2.0041e-04 2.5680e-02 2.1491e+00 3.1624e-02
747 7.0914e-01 -1.1920e-03 1.8334e-01 1.6589e+00 9.7129e-02
748 -7.6487e-02 -5.6029e-04 6.1436e-02 -3.0633e-01 7.5936e-01
749 1.1859e-01 -6.6449e-05 1.0232e-02 1.1731e+00 2.4077e-01
750 -8.0353e-03 -1.9868e-05 2.1798e-03 -1.7168e-01 8.6369e-01
751 8.4291e-01 -2.5835e-03 2.8271e-01 1.5902e+00 1.1180e-01
752 1.2249e-01 -3.6124e-04 6.9603e-02 4.6565e-01 6.4147e-01
753 6.0254e-02 -6.0715e-04 6.6571e-02 2.3588e-01 8.1352e-01
754 -6.1064e-02 -8.3203e-05 1.0663e-02 -5.9055e-01 5.5482e-01
755 5.4543e-03 -1.5384e-07 1.6879e-05 1.3276e+00 1.8430e-01
756 2.2042e+00 -1.2468e-03 1.3661e-01 5.9669e+00 2.4176e-09
757 1.4624e+00 -6.3882e-03 9.7748e-01 1.4856e+00 1.3738e-01
758 1.4254e+00 -4.4019e-03 4.2017e-01 2.2058e+00 2.7401e-02
759 1.7873e+00 -6.7020e-03 7.3036e-01 2.0992e+00 3.5802e-02
760 -1.1477e-01 -2.9456e-05 4.5360e-03 -1.7036e+00 8.8453e-02
761 -3.4257e-01 -7.1640e-04 1.8422e-01 -7.9648e-01 4.2575e-01
762 4.8213e-01 -6.6542e-04 8.5226e-02 1.6538e+00 9.8170e-02
763 1.0412e+00 -1.4014e-03 5.4087e-01 1.4176e+00 1.5631e-01
764 9.9111e-01 -1.1259e-03 1.7320e-01 2.3842e+00 1.7116e-02
765 9.1919e-02 -5.1577e-05 6.6100e-03 1.1312e+00 2.5796e-01
766 1.0843e+00 -1.6277e-03 3.1322e-01 1.9403e+00 5.2346e-02
767 6.9180e-01 -1.2599e-03 1.9378e-01 1.5744e+00 1.1539e-01
768 8.1963e-02 -1.0184e-04 1.1172e-02 7.7642e-01 4.3750e-01
769 -5.1902e-01 -3.9905e-04 7.6885e-02 -1.8704e+00 6.1429e-02
770 -5.5710e-01 -4.8031e-04 6.1529e-02 -2.2440e+00 2.4834e-02
771 1.0395e+01 -1.1260e-02 2.1459e+00 7.1035e+00 1.2159e-12
772 -2.5409e-01 -4.7222e-04 1.8243e-01 -5.9380e-01 5.5265e-01
773 -2.3990e-02 -5.4386e-06 5.2141e-04 -1.0504e+00 2.9354e-01
774 -1.4493e-01 -2.0041e-04 3.8621e-02 -7.3644e-01 4.6146e-01
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Append local Moran’s I dataframe (i.e.localMI) before mapping the local Moran’s I map.
Variable(s) "Ii" contains positive and negative values, so midpoint is set to 0. Set midpoint = NA to show the full spectrum of the color palette.
localMI.map <- tm_shape(nga_wp.localMI) +
tm_fill(col = "Ii",
style = "pretty",
palette = "RdBu",
title = "local moran statistics") +
tm_borders(alpha = 0.5) +
tm_layout(legend.height = 0.3, legend.width = 0.3)
pvalue.map <- tm_shape(nga_wp.localMI) +
tm_fill(col = "Pr.Ii",
breaks=c(-Inf, 0.001, 0.01, 0.05, 0.1, Inf),
palette="-Blues",
title = "local Moran's I p-values") +
tm_borders(alpha = 0.5) +
tm_layout(legend.height = 0.26, legend.width = 0.3)
tmap_arrange(localMI.map, pvalue.map, asp=1.5, ncol=1)
Variable(s) "Ii" contains positive and negative values, so midpoint is set to 0. Set midpoint = NA to show the full spectrum of the color palette.
Plot the Moran scatterplot before generate the LISA cluster map.
Use the code chunk below.
The Moran scatterplot is an illustration of the relationship between the values of the chosen attribute at each location and the average value of the same attribute at neighboring locations.
Use code chunk below.
quadrant <- vector(mode="numeric",length=nrow(localMI))
DV <- nga_wp$wpt_nonFunctional - mean(nga_wp$wpt_nonFunctional)
C_mI <- localMI[,1] - mean(localMI[,1])
signif <- 0.05
quadrant[DV >0 & C_mI>0] <- 4
quadrant[DV <0 & C_mI<0] <- 1
quadrant[DV <0 & C_mI>0] <- 2
quadrant[DV >0 & C_mI<0] <- 3
quadrant[localMI[,5]>signif] <- 0
nga_wp.localMI$quadrant <- quadrant
colors <- c("#ffffff", "#2c7bb6", "#abd9e9", "#fdae61", "#d7191c")
clusters <- c("insignificant", "low-low", "low-high", "high-low", "high-high")
tm_shape(nga_wp.localMI) +
tm_fill(col = "quadrant",
style = "cat",
palette = colors[c(sort(unique(quadrant)))+1],
labels = clusters[c(sort(unique(quadrant)))+1],
popup.vars = c("")) +
tm_view(set.zoom.limits = c(11,17)) +
tm_borders(alpha=0.5)
wpt_nonFunctional <- qtm(nga_wp, "wpt_nonFunctional") +
tm_layout(legend.height = 0.28, legend.width = 0.25)
nga_wp.localMI$quadrant <- quadrant
colors <- c("#ffffff", "#2c7bb6", "#abd9e9", "#fdae61", "#d7191c")
clusters <- c("insignificant", "low-low", "low-high", "high-low", "high-high")
LISAmap <- tm_shape(nga_wp.localMI) +
tm_fill(col = "quadrant",
style = "cat",
palette = colors[c(sort(unique(quadrant)))+1],
labels = clusters[c(sort(unique(quadrant)))+1],
popup.vars = c("")) +
tm_view(set.zoom.limits = c(11,17)) +
tm_borders(alpha=0.5) +
tm_layout(legend.height = 0.35, legend.width = 0.3)
tmap_arrange(wpt_nonFunctional, LISAmap, asp=1.5, ncol=1)
Min. 1st Qu. Median Mean 3rd Qu. Max.
13.86 28.12 34.99 36.19 44.54 67.50
wpt_nonFunctional <- qtm(nga_wp, "wpt_nonFunctional") +
tm_layout(legend.height = 0.28, legend.width = 0.25)
Gimap <-tm_shape(nga_wp.gi) +
tm_fill(col = "gstat_fixed",
style = "pretty",
palette="-RdBu",
title = "local Gi") +
tm_borders(alpha = 0.5) +
tm_layout(legend.height = 0.28, legend.width = 0.25)
tmap_arrange(nga_wp, Gimap, asp=1.5, ncol=1)
wpt_nonFunctional <- qtm(nga_wp, "wpt_nonFunctional") +
tm_layout(legend.height = 0.28, legend.width = 0.25)
Gimap <- tm_shape(nga_wp.gi) +
tm_fill(col = "gstat_adaptive",
style = "pretty",
palette="-RdBu",
title = "local Gi") +
tm_borders(alpha = 0.5) +
tm_layout(legend.height = 0.28, legend.width = 0.25)
tmap_arrange(wpt_nonFunctional,Gimap,asp=1.5,ncol=1)