Geospatial Analysis with R

Class 5

library(sf)
library(dplyr)
f <- system.file("extdata", "farmer_spatial.csv", package = "geospaar")
farmers <- readr::read_csv(f)
farmers <- farmers %>% select(uuid, x, y) %>% distinct() %>% 
  st_as_sf(., coords = c("x", "y"))
f <- system.file("extdata", "districts.shp", package = "geospaar")
dists <- read_sf(f)
st_crs(farmers) <- st_crs(dists)

# join farmers with districts (h/t https://mattherman.info/blog/point-in-poly/)
farmers_in_dists <- st_join(farmers, dists, join = st_within) %>%
  tidyr::drop_na()
farmer_count <- count(as_tibble(farmers_in_dists), distName)
dists_w_farmers <- left_join(dists, farmer_count) %>% 
  mutate(n = ifelse(is.na(n), 0, n))

png("figures/sms-farmers.png", height = 4, width = 5, res = 300,
    units = "in")
plot(dists_w_farmers["n"], breaks = c(0, 5, 10, 15, 20, 50, 500), 
     reset = FALSE, main = "Number of SMS Farmers by District")
plot(farmers %>% filter(uuid %in% unique(farmers_in_dists$uuid)) %>%
       st_geometry(), add = TRUE, pch = "+", col = "cyan", cex = 0.5)
dev.off()

Today

Projects and package set-up
git / GitHub
- syncing, commit, push, pull, branching, merging
data folder and lazy loads
inst folder and how to get at it
If time
- RMarkdown
- The R ecosystem
- Building blocks of R: data types, functions, etc

Git exercises (1)

Open your personal R repo (e.g. mjc346 in RStudio)
Create a new branch, test_merge. You can create this branch in the Git tab, or in Terminal, using git checkout -b test_merge
With the new branch active, create a new file test_function within the R folder. Create a simple function that takes a number x as an input, and prints “x is my favorite number!”. Save and commit this file in the new branch.
Switch back to the main branch. You should see a pop-up message. What happens to the test_function.R file? Can you see it in your file explorer?
merge the new file to the main branch using the command git merge test_merge in Terminal. What happens?
The merge command automatically merges and commits changes to the main branch

Git exercises (2)

In the test_merge branch, open the Description file. Update the version to 0.0.2. Save and commit.
Switch to the main branch. Add a second author in the Author line. Save and commit.
Now test merging the change from test_merge to main using git merge test_merge. Does this work?

Git exercises (3)

In the test_merge branch, add a third fictional author. Save and commit.
Switch to the main branch. Again add a third author, but use a different author than in the test_merge branch.
Now test merging the change from test_merge to main using git merge test_merge. Does this work?
Open the Description file. What does it look like?
After you are done, delete the branch using git branch -D test_merge
Update the Description file in the main branch by pasting the text you saved. Save and commit.

Tips and Tricks

Tab completion and shortcuts
Reusing code
Code syntax
Posting guide

Knowing how to get help as a skillset

Slack posting guide
Getting help via the search engine
(Eventually) posting to listserves

Search Engine Science

Sometimes you just need the error message

Search Engine Science

Sometimes you need to search

fatal: unable to access 'https://github.com/agroimpacts/xyz346.git/': 
error setting certificate verify locations:
 CAfile: C:/Users/xyz/Desktop/ADP/RStudio/xyz346/Git/mingw64/ssl/
 certs/ca-bundle.crt
 CApath: none

How you search matters

Listserves

Package functions

install.packages : installs binary packages from CRAN
devtools::install_github: installs from Github
devtools::install("C:/Users/micha/Documents/geospaar/") to install locally

Data in packages

packages often include example data
Lazy loading data only loads when used
Lazy loaded data in data/ folder
- formats: .R, .rda, .RData, .tab, .txt, .csv
Non lazy loads (raw data) in inst/extdata

ls()

character(0)

data("farmers_env", package = "geospaar")
ls()

[1] "farmers_env"

farmers_env

        uuid        geometry     rain district
1   009a8424 27.256, -16.926 66.93754       11
2   00df166f 26.942, -16.504 72.00297       11
3   02671a00 27.254, -16.914 66.93754       11
4   03f4dcca 27.237, -16.733 69.78009       11
5   042cf7b3 27.138, -16.807 75.14184       11
6   05618404 26.875, -16.611 66.09323       11
7   064beba0 26.752, -16.862 58.36053       20
8   083a46a2 26.977, -16.765 70.38586       11
9   08eb2224 26.912, -16.248 53.95671       59
10  0ab761d6 27.113, -16.950 72.43802       11
11  0bd19b6a 26.772, -16.860 58.36053       20
12  0c0c6ed8 26.794, -16.843 57.79966       11
13  0c18f625 26.862, -16.674 68.36250       11
14  0cbc4225 26.859, -16.176 57.92710       59
15  0eb65faa 27.056, -16.935 69.99150       11
16  0ed7bf8d 27.294, -16.746 80.89200       11
17  12d7333e 27.237, -16.733 69.78009       11
18  130455fd 26.885, -16.589 73.05731       11
19  146fd88d 27.237, -16.922 73.24045       11
20  14e2047a 27.306, -16.742 78.35793       11
21  14eb1bc1 26.913, -16.251 55.04950       11
22  14f4d804 27.336, -16.834 72.22664       11
23  16d25908 26.780, -16.851 58.36053       20
24  186977a2 26.862, -16.674 68.36250       11
25  19c2befd 26.933, -17.041 63.51126       11
26  1a3ed58f 27.276, -16.878 67.82761       11
27  1a4008c2 26.859, -16.178 57.92710       59
28  1ae8ccff 27.094, -16.813 78.34108       11
29  1c7690e0 27.261, -16.921 66.93754       11
30  1cba393a 26.930, -16.508 72.00297       11
31  261e38c9 26.974, -16.748 69.62228       11
32  26b02eaa 27.114, -16.790 69.24673       11
33  26ccd1ca 27.279, -16.926 66.93754       11
34  26d99644 26.917, -16.532 72.00297       11
35  28706e65 26.969, -16.723 69.62228       11
36  28c79d87 26.857, -16.191 57.92710       59
37  2abd46c3 27.294, -16.744 80.89200       11
38  2b60914d 27.275, -16.884 67.82761       11
39  2cf13d38 27.050, -17.003 69.43579       11
40  2d70af82 26.863, -16.590 73.05731       11
41  30c2e51a 27.313, -16.779 78.28657       11
42  3112ec39 27.272, -16.873 67.82761       11
43  32855ee6 26.975, -16.760 70.38586       11
44  33361d1c 26.830, -16.817 63.43196       11
45  36c0532e 26.953, -16.487 67.75720       11
46  373bc918 27.050, -17.003 69.43579       11
47  381e38ea 27.293, -16.744 80.89200       11
48  38c83136 26.933, -16.463 69.48450       11
49  3a042f06 27.076, -16.952 79.16811       11
50  3a0b6560 27.285, -16.748 80.89200       11
51  3a5c6f75 27.050, -17.004 69.43579       11
52  3b3d1539 26.857, -16.193 57.92710       59
53  3b6cbc47 27.059, -17.006 78.89503       11
54  3e3c2a80 26.971, -16.753 70.38586       11
55  3e8b66b7 27.118, -16.919 72.43802       11
56  3fed4ec6 27.239, -16.741 69.78009       11
57  4120e368 26.979, -16.762 70.38586       11
58  4313155f 27.266, -16.921 66.93754       11
59  44c8a2b6 27.063, -17.004 78.89503       11
60  45a89b91 27.109, -16.980 70.20730       11
61  46fa47e5 26.930, -17.054 52.02611       11
62  47939706 27.275, -16.884 67.82761       11
63  48635f6e 27.099, -16.964 79.16811       11
64  48c828d0 27.265, -16.921 66.93754       11
65  4932fac2 26.810, -16.607 59.16776       11
66  496c557b 27.297, -16.935 66.93754       11
67  499a72b8 26.831, -16.817 63.43196       11
68  4a58fbbb 26.877, -16.585 73.05731       11
69  4afc2d3e 27.067, -16.988 79.16811       11
70  4b671e6b 27.294, -16.744 80.89200       11
71  4ca666fd 27.089, -16.951 79.16811       11
72  4cb11854 27.129, -16.790 69.24673       11
73  4d524878 27.032, -16.961 75.39918       11
74  4f75193d 26.961, -16.727 69.62228       11
75  51d50f10 26.983, -16.765 70.38586       11
76  54d0a15c 26.941, -16.485 69.48450       11
77  55772276 26.864, -16.662 68.36250       11
78  561a6a5d 27.080, -16.972 79.16811       11
79  58d39a53 26.791, -16.841 57.79966       11
80  5b732fcd 26.850, -16.216 53.30880       59
81  5c093270 27.255, -16.908 66.93754       11
82  5c13f0ee 27.255, -16.909 66.93754       11
83  5e0473ca 26.821, -16.604 59.16776       11
84  5e37a888 27.128, -16.772 69.24673       11
85  5e65fc11 27.094, -16.890 73.09578       11
86  5e911b62 27.061, -17.004 78.89503       11
87  61228b69 26.802, -16.832 63.43196       11
88  6132a9b3 27.316, -16.782 78.28657       11
89  62642d7c 27.234, -16.733 69.78009       11
90  646d6573 27.256, -16.926 66.93754       11
91  64a63ad8 27.230, -16.717 69.78009       11
92  664bdf41 26.781, -16.870 58.36053       20
93  66e41828 26.804, -16.854 61.28291       11
94  67cbcae6 26.896, -16.704 72.95570       11
95  684d8902 26.966, -16.733 69.62228       11
96  6b38721b 26.788, -16.876 58.36053       20
97  6c223ecd 26.913, -16.519 72.00297       11
98  6d05224a 26.853, -16.210 53.86879       59
99  6d774598 26.913, -16.250 53.95671       59
100 6dfd9cdf 27.301, -16.816 72.22664       11
101 6ff740a4 27.299, -16.935 66.93754       11
102 703825ba 26.788, -16.876 58.36053       20
103 70b5f403 27.037, -16.954 75.39918       11
104 718d866e 26.859, -16.178 57.92710       59
105 730b727a 27.056, -16.934 69.99150       11
106 732af424 26.833, -16.818 63.43196       11
107 74ccfcac 26.899, -16.856 61.73315       11
108 7572e663 27.199, -16.924 71.00794       11
109 770da037 26.833, -16.817 63.43196       11
110 78284b9d 26.995, -16.972 75.29367       11
111 7af5af0a 27.301, -16.758 78.28657       11
112 7d101d28 27.305, -16.803 72.22664       11
113 7da072ff 27.066, -16.944 69.99150       11
114 7eed2695 26.923, -17.049 63.51126       11
115 7f49bc48 27.284, -16.749 80.89200       11
116 7f9ab0f7 27.094, -16.976 79.16811       11
117 814ca378 27.061, -17.004 78.89503       11
118 85867e62 27.111, -16.933 72.43802       11
119 85f03621 26.938, -16.513 72.00297       11
120 88462901 26.881, -16.597 73.05731       11
121 890ca2c8 27.107, -16.940 72.43802       11
122 8b816f5f 27.255, -16.915 66.93754       11
123 8d074cec 26.869, -16.596 73.05731       11
124 8d2db211 26.934, -17.036 63.51126       11
125 8d690816 26.936, -16.744 72.52380       11
126 8da4a6d6 26.858, -16.594 73.05731       11
127 92563785 27.234, -16.923 73.24045       11
128 926caf97 26.869, -16.610 66.09323       11
129 95374d3f 27.039, -16.842 70.56110       11
130 96b6d097 26.995, -16.953 75.29367       11
131 975ffe94 26.831, -16.818 63.43196       11
132 981208ad 27.344, -16.776 78.28657       11
133 991ece73 27.086, -16.967 79.16811       11
134 99dc8db6 27.182, -16.917 71.00794       11
135 9a8786eb 27.258, -16.929 66.93754       11
136 9b42e80a 26.869, -16.614 66.09323       11
137 9c0fe82f 26.974, -16.760 70.38586       11
138 a006eab2 27.335, -16.798 78.28657       11
139 a0f8b4ef 27.039, -16.830 70.56110       11
140 a30b3bde 27.048, -16.926 71.20597       11
141 a5ad178a 27.060, -17.005 78.89503       11
142 a62be645 26.863, -16.595 73.05731       11
143 a67f255e 26.815, -16.585 66.42364       11
144 a84d2d02 26.831, -16.817 63.43196       11
145 a914f6e1 26.788, -16.863 58.36053       20
146 a9a99b3e 26.920, -17.052 52.02611       11
147 a9d39da7 26.928, -16.520 72.00297       11
148 aa5f0d29 26.951, -16.727 69.62228       11
149 aac48cd5 27.050, -17.003 69.43579       11
150 abd530e7 26.981, -16.762 70.38586       11
151 ace80c2e 27.306, -16.931 66.28913       11
152 ad783a0a 27.336, -16.797 78.28657       11
153 afaecd2e 27.305, -16.793 78.28657       11
154 affb013a 26.963, -16.920 70.25295       11
155 b0e82f78 27.339, -16.834 72.22664       11
156 b1e1a3f3 26.789, -16.878 58.36053       20
157 b3d90826 26.922, -16.526 72.00297       11
158 b5a7a1f4 26.935, -16.513 72.00297       11
159 b66a5a55 26.974, -16.766 70.38586       11
160 b825d94e 27.113, -16.773 69.24673       11
161 b9d85ebc 27.234, -16.923 73.24045       11
162 ba5973c2 26.835, -16.815 63.43196       11
163 baea69b4 27.279, -16.877 67.82761       11
164 bb876912 26.936, -16.505 72.00297       11
165 bba2dfd0 27.339, -16.797 78.28657       11
166 bc32b0b4 26.864, -16.599 73.05731       11
167 bc8d8a74 27.275, -16.877 67.82761       11
168 bf8b44c4 26.791, -16.874 58.36053       20
169 c084cfc1 26.795, -16.879 58.36053       20
170 c124742c 27.209, -16.917 73.24045       11
171 c152455a 27.085, -16.934 69.99150       11
172 c2668cdf 27.123, -16.769 69.24673       11
173 c32d45ee 27.068, -16.939 69.99150       11
174 c42827cf 27.096, -16.949 69.99150       11
175 c6f737ea 27.304, -16.793 78.28657       11
176 c784ee02 26.859, -16.194 57.92710       59
177 c7d6f91c 26.831, -16.817 63.43196       11
178 c7e2a514 26.810, -16.606 59.16776       11
179 c946796f 27.004, -16.841 70.56110       11
180 c9ee7136 27.039, -16.842 70.56110       11
181 c9f5f663 27.128, -16.779 69.24673       11
182 cc014f7d 26.778, -16.870 58.36053       20
183 cc230be1 27.286, -16.788 76.04762       11
184 cdcc9666 27.293, -16.747 80.89200       11
185 ce041f38 26.961, -16.743 69.62228       11
186 d027ee45 27.293, -16.747 80.89200       11
187 d16f790f 27.016, -16.932 71.20597       11
188 d1d9637e 27.136, -16.800 69.24673       11
189 d1e20dc3 26.912, -16.254 55.04950       11
190 d263ea45 26.827, -16.820 63.43196       11
191 d362925c 26.859, -16.193 57.92710       59
192 d6313bed 27.301, -16.758 78.28657       11
193 d644ee96 26.867, -16.610 66.09323       11
194 d6e18dd9 27.086, -16.961 79.16811       11
195 d9ce012d 27.325, -16.757 78.28657       11
196 de338705 27.293, -16.747 80.89200       11
197 dea21f52 27.097, -16.899 73.09578       11
198 df1604d4 27.271, -16.784 76.04762       11
199 dfc6f992 26.823, -16.625 59.16776       11
200 e2510e54 27.123, -16.922 72.43802       11
201 e25b2b0f 26.789, -16.877 58.36053       20
202 e27cd268 27.056, -16.935 69.99150       11
203 e3407303 26.781, -16.856 58.36053       20
204 e340de50 26.956, -16.738 69.62228       11
205 e36fdd30 26.947, -16.746 72.52380       11
206 e82a9751 26.790, -16.823 57.79966       11
207 e91d6065 27.135, -16.770 69.24673       11
208 e9f6b304 27.066, -16.944 69.99150       11
209 ebd881fc 27.310, -16.803 72.22664       11
210 ee2f89cf 27.090, -16.971 79.16811       11
211 f0118efa 27.286, -16.932 66.93754       11
212 f08a0aa3 27.032, -16.961 75.39918       11
213 f0bcb418 27.107, -16.772 69.24673       11
214 f6ebaa5b 27.300, -16.934 66.93754       11
215 f752c993 27.300, -16.756 76.04762       11
216 f825b96c 27.060, -16.986 79.16811       11
217 fb3fc0e0 27.086, -16.783 71.25740       11
218 fb666168 26.780, -16.851 58.36053       20
219 fbdacd81 26.999, -16.956 75.29367       11
220 fbef7ba1 27.227, -16.738 69.78009       11
221 fc263f78 27.232, -16.720 69.78009       11
222 fce31f54 26.826, -16.595 66.42364       11
223 fe096545 27.260, -16.922 66.93754       11
224 0649944b 27.336, -16.784 78.28657       11
225 08683ecf 27.284, -16.749 80.89200       11
226 0a2efd25 27.338, -16.794 78.28657       11
227 0f095777 26.815, -16.599 66.42364       11
228 116e1bcc 26.859, -16.595 73.05731       11
229 16128e91 27.100, -16.894 73.09578       11
230 27fb5351 27.094, -16.906 69.99150       11
231 2a840b88 27.338, -16.794 78.28657       11
232 3182c9bb 27.086, -16.961 79.16811       11
233 3210d99e 26.939, -16.490 69.48450       11
234 36883452 27.051, -16.840 78.34108       11
235 36db3c21 26.769, -16.873 58.36053       20
236 3c0a7255 27.280, -16.872 67.82761       11
237 41b213e1 26.900, -16.852 61.73315       11
238 4285ad8d 26.808, -16.835 63.43196       11
239 46498dc8 26.975, -16.826 69.10195       11
240 48b2c57f 26.781, -16.849 57.79966       11
241 4ae722c5 27.298, -16.930 66.93754       11
242 4bc9a120 27.183, -16.915 71.00794       11
243 5769b555 27.336, -16.834 72.22664       11
244 5ad27ec3 26.812, -16.599 66.42364       11
245 60734a06 26.989, -16.830 69.10195       11
246 646ea49f 27.053, -16.927 69.99150       11
247 6be46cee 26.967, -16.821 69.10195       11
248 6df8bb5e 26.977, -16.819 69.10195       11
249 6e1aeb91 27.045, -16.962 75.39918       11
250 73c31707 27.117, -16.920 72.43802       11
251 748a4af0 26.814, -16.612 59.16776       11
252 79afec99 27.326, -16.764 78.28657       11
253 7a2965b2 27.185, -16.917 71.00794       11
254 7c62ae6a 26.940, -16.727 72.52380       11
255 7c6dbe51 26.886, -16.584 73.05731       11
256 7de10584 27.338, -16.799 78.28657       11
257 7e77ffc9 27.086, -16.970 79.16811       11
258 86f14077 27.299, -16.752 76.04762       11
259 897c6236 27.336, -16.834 72.22664       11
260 8bae7654 27.040, -16.842 70.56110       11
261 9c5f30d9 26.863, -16.620 66.09323       11
262 a039fcbf 27.059, -17.005 78.89503       11
263 a3016253 27.299, -16.753 76.04762       11
264 ae3e29b7 26.977, -16.819 69.10195       11
265 b4a51504 26.944, -16.471 69.48450       11
266 b9b6b017 27.086, -16.961 79.16811       11
267 bb4616c2 27.102, -16.906 72.43802       11
268 bd8c8fda 26.955, -16.558 80.94247       11
269 c07fca86 27.084, -16.999 79.16811       11
270 c276acb6 26.906, -16.857 66.99890       11
271 c482ffa7 27.234, -16.923 73.24045       11
272 c56ed10c 26.967, -16.821 69.10195       11
273 c647d0ba 27.111, -16.933 72.43802       11
274 c69577b4 27.313, -16.784 78.28657       11
275 ca6fc5e6 27.105, -16.915 72.43802       11
276 cc984ea8 26.900, -16.197 57.92710       59
277 cca69f84 26.974, -16.752 70.38586       11
278 d410cd79 26.936, -16.479 69.48450       11
279 d9297c58 27.095, -16.891 73.09578       11
280 de20cb83 27.093, -16.937 69.99150       11
281 e0bd44cb 26.820, -16.834 63.43196       11
282 e4899f8b 26.984, -16.944 70.25295       11
283 f08180bf 27.237, -16.733 69.78009       11
284 f27f24df 26.814, -16.601 59.16776       11
285 f58e95e7 26.934, -16.510 72.00297       11
286 f838678c 27.052, -16.933 69.99150       11
287 f89b6638 26.935, -16.500 69.48450       11
288 fd33886d 26.803, -16.857 61.28291       11
289 0216b983 26.967, -16.821 69.10195       11
290 0360d642 26.825, -16.604 59.16776       11
291 0e49e4ef 26.979, -16.762 70.38586       11
292 0ed18f13 26.959, -16.548 74.59067       11
293 107e8347 26.917, -16.250 53.95671       59
294 14e7cec2 26.810, -16.601 59.16776       11
295 158a59a2 27.099, -16.893 73.09578       11
296 1ad68009 27.200, -16.913 71.00794       11
297 2596a920 26.941, -17.042 63.51126       11
298 25ea180f 27.157, -16.790 69.47702       11
299 2cad566c 26.877, -16.567 73.05731       11
300 31d97950 27.052, -16.942 69.99150       11
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376 930b2f35 27.440, -16.291 59.00846       47
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379 b89376a6 27.237, -16.733 69.78009       11
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388 edd0ab45 27.305, -16.793 78.28657       11
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413 6fe09cc3 26.944, -16.743 72.52380       11
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429 a703fca8 27.048, -16.926 71.20597       11
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432 d89e31a7 26.955, -16.913 70.25295       11
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452 411e992e 26.978, -16.757 70.38586       11
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455 4c1f61f8 26.794, -16.827 57.79966       11
456 54f07739 26.967, -16.821 69.10195       11
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458 571fc71b 26.898, -16.708 72.95570       11
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462 86955d62 27.303, -16.794 78.28657       11
463 8cc611ed 26.947, -16.483 69.48450       11
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465 a347ab0f 26.941, -16.500 69.48450       11
466 c74d0381 26.835, -16.815 63.43196       11
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468 cf95d0b8 27.004, -16.841 70.56110       11
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471 e7d7f01e 27.296, -16.756 76.04762       11
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473 f4798847 26.977, -16.819 69.10195       11
474 f8c5930b 26.930, -16.912 67.12045       11
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478 30454c4c 26.823, -16.625 59.16776       11
479 331900d7 26.827, -16.602 59.16776       11
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481 49d34672 26.978, -16.756 70.38586       11
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483 55b721f3 26.868, -16.617 66.09323       11
484 564a4de5 26.794, -16.827 57.79966       11
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486 638ede33 27.051, -16.840 78.34108       11
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507 62666abd 26.854, -16.219 53.86879       59
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512 a28c4697 27.138, -16.799 69.24673       11
513 a2a144a1 26.862, -16.578 73.05731       11
514 ca1e5256 26.954, -16.700 74.20352       11
515 cf911b7b 26.943, -16.503 72.00297       11
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519 e7f584e2 26.877, -16.270 51.30970       11
520 e7f9d2f6 26.949, -16.726 72.52380       11
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523 0a3d83be 27.252, -16.917 66.93754       11
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525 4e84b690 27.061, -16.985 79.16811       11
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528 8b5ae414 26.913, -16.525 72.00297       11
529 9497a637 26.896, -16.707 72.95570       11
530 94c05d4e 26.868, -16.617 66.09323       11
531 9502b174 26.934, -16.510 72.00297       11
532 a5f6bf50 27.000, -16.916 70.25295       11
533 b626ceb6 27.247, -16.734 69.78009       11
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535 fa8283d2 26.748, -16.865 60.54577       20
536 2b5e2dd8 26.975, -16.826 69.10195       11
537 3f603815 26.828, -16.613 59.16776       11
538 45417d5d 26.827, -16.607 59.16776       11
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540 908ad848 26.977, -16.819 69.10195       11
541 98d64487 26.817, -16.608 59.16776       11
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543 1ae8ed91 26.895, -16.708 72.95570       11
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545 22d422e9 27.285, -16.872 67.82761       11
546 368d706a 26.963, -16.708 69.62228       11
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548 3ddf8640 26.789, -16.877 58.36053       20
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551 9d9960f4 26.789, -16.878 58.36053       20
552 a055b28e 26.875, -16.611 66.09323       11
553 d672e664 26.824, -16.595 66.42364       11
554 d7c10ac8 26.936, -16.744 72.52380       11
555 dc5ee37f 26.968, -16.718 69.62228       11
556 f7425695 26.802, -16.612 59.16776       11
557 6b3963ac 27.298, -16.938 66.93754       11
558 8667383e 27.331, -16.797 78.28657       11
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563 1e8cdd0b 26.796, -16.872 58.36053       20
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566 52f393e1 26.915, -16.520 72.00297       11
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569 b01ff38e 26.869, -16.611 66.09323       11
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571 0610312c 26.936, -16.744 72.52380       11
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576 18a7611d 27.291, -16.741 80.89200       11
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579 e1825268 26.942, -16.501 72.00297       11
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581 0d10b051 26.939, -16.510 72.00297       11
582 326c7d48 27.113, -16.782 69.24673       11
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584 897e4909 26.977, -16.819 69.10195       11
585 e9d10913 26.977, -16.819 69.10195       11
586 0db22d41 26.980, -16.748 69.62228       11
587 06feb6e8 32.266, -10.309 36.54598        9
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589 3704808d 32.252, -10.320 36.54598        9
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591 3ac7b239 33.325, -12.402 42.72912       36
592 46a7f978 28.678, -13.256 63.86148       41
593 58e6bdc7 28.375, -13.336 63.78424       41
594 6259ed92 28.652, -13.385 70.04521       41
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596 6dd49f02 28.694, -13.388 70.04521       41
597 725b0836 32.321, -10.076 32.80511        9
598 74635a76 32.183, -10.610 22.30976        9
599 761655ec 32.183, -10.612 22.30976        9
600 78bc25a2 28.657, -13.671 73.82898       41
601 82db8ad2 27.836, -13.633 79.56444       49
602 8bf1c0c2 28.640, -13.512 72.46116       41
603 9385fcbe 28.646, -13.826 75.62058       41
604 9a9761bb 28.649, -13.836 75.62058       41
605 9d53e0b9 28.657, -13.692 73.82898       41
606 a7b10699 28.649, -13.830 75.62058       41
607 ab7b92b3 32.244, -10.320 33.73501        9
608 ad29db5a 27.921, -13.465 77.63628       49
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611 c1208498 28.688, -13.253 63.86148       41
612 c40143eb 28.660, -13.378 70.04521       41
613 c41a5503 32.315, -10.098 32.80511        9
614 d4bfa888 28.677, -18.222       NA       NA
615 d9f7662d 28.678, -13.221 72.40546       41
616 dbc2d431 32.253, -10.318 36.54598        9
617 f65f5cb6 33.332, -12.408 42.72912       36
618 f8ea87a1 31.311, -14.474 62.22379       63
619 f9e85779 31.216, -14.385 72.91299       63
620 ff09d005 28.438, -13.374 69.39651       49
621 06c32bd5 27.180, -16.913 71.00794       11
622 67b89e9a 26.862, -16.674 68.36250       11
623 a857c6cb 27.039, -16.842 70.56110       11
624 e9f45870 27.043, -16.956 75.39918       11
625 57c1c6e9 27.117, -16.892 76.40279       11
626 019d99f9 24.782, -13.199 55.14384       53
627 02be9843 27.085, -15.407 54.18965       54
628 065cf44d 26.974, -16.766 70.38586       11
629 0fae9736 26.776, -16.413 70.70723       11
630 11ca3539  31.236, -9.360 47.74985       43
631 123d71cb 27.283, -16.872 67.82761       11
632 150ec977 24.781, -13.200 55.14384       53
633 15f36ed3 27.336, -15.193 47.47742       54
634 18e7b7a2 29.069, -13.736 53.63661       45
635 1ad34415 27.094, -16.976 79.16811       11
636 221d7cbe 26.808, -16.585 66.42364       11
637 22bf98e8 29.585, -13.582 63.70206       45
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639 28b573be 25.489, -12.106 68.82276       71
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643 2f8a5a25 26.736, -15.060 62.96255       54
644 33d6b30e  31.659, -9.020 31.98688       43
645 36ccf2f8 26.770, -15.083 57.77769       54
646 3730ea50 26.711, -15.713 30.80526       59
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649 3ff30f50 26.867, -16.683 68.36250       11
650 401cf5dc 26.936, -16.744 72.52380       11
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652 4824f655 24.946, -13.169 58.17973       53
653 494a6547 25.369, -13.056 44.26578       53
654 49fcf7a7 26.742, -15.733 30.80526       59
655 4a6c4ac1 25.487, -12.103 68.82276       71
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657 4fba5ee7 27.332, -15.189 47.47742       54
658 52ad3248 25.886, -12.327 72.05606       71
659 5321d9df 27.125, -16.784 69.24673       11
660 5608a7b3 27.095, -17.196 77.24889       11
661 5656fd92 27.060, -17.005 78.89503       11
662 5683c0a3 27.141, -17.153 78.16374       11
663 583b4e09 27.348, -15.213 48.29046       54
664 5b8060f8 26.734, -15.734 30.80526       59
665 5d8b2b30 28.937, -13.524 61.80630       41
666 609b90dc 25.877, -12.322 72.05606       71
667 662391ac 26.743, -15.065 62.96255       54
668 66d66f3c 29.047, -13.728 38.58265       45
669 6d5970de 27.331, -15.186 47.47742       54
670 72526a74  31.216, -9.542 44.36200       43
671 74fb45af 27.142, -17.155 78.16374       11
672 7721c946 26.771, -16.394 62.40511       11
673 788cab52 27.140, -17.154 78.16374       11
674 7dcbf58f 27.283, -16.872 67.82761       11
675 7e5b01c5 33.111, -18.111       NA       NA
676 816acafe 26.713, -15.712 30.80526       59
677 85405673  31.202, -9.556 42.81581       43
678 8cd6bd60 25.494, -12.102 68.82276       71
679 8ec3639d 24.784, -13.202 64.42429       53
680 9101ebb4  31.680, -8.997 36.49800       43
681 91afe119 27.183, -16.915 71.00794       11
682 92a9664f 28.903, -13.574 58.78981       45
683 93474fad 26.761, -16.472 69.18250       11
684 93839142 26.702, -16.256 55.25837       11
685 95d5a7e7 24.786, -13.202 64.42429       53
686 9678853b 26.869, -16.619 66.09323       11
687 97f5bf98 26.772, -16.391 62.40511       11
688 98123b60 28.650, -14.697 62.07531        4
689 9a5a547c 26.779, -16.859 58.36053       20
690 9b0033a8 25.488, -12.108 68.82276       71
691 9c6f813f 27.200, -16.913 71.00794       11
692 9c736315 25.884, -12.325 72.05606       71
693 9e5bd11e 26.753, -12.235 62.38456       71
694 9e88a4f7 26.144, -12.556 71.91343       71
695 a00ebbbb 27.353, -15.211 49.05542       54
696 a5db60b7 27.275, -16.884 67.82761       11
697 a6d1ad26 26.775, -12.197 58.64490       71
698 a700a3a1 29.445, -13.991 45.75317       45
699 a8d3bcd6 26.864, -16.662 68.36250       11
700 ad6a6d59 27.285, -16.900 67.82761       11
701 ae41c6d0 26.762, -16.471 69.18250       11
702 b00aed40 26.775, -12.202 62.38456       71
703 b92fc9c0 26.931, -14.519 44.70253       54
704 b9a107a7 28.659, -13.383 70.04521       41
705 ba913ba0 26.860, -16.598 73.05731       11
706 bace1435 24.948, -13.169 58.17973       53
707 bd4009d4 24.999, -13.466 42.21804       53
708 bd435876 27.271, -16.784 76.04762       11
709 be8276ce 26.773, -16.389 62.40511       11
710 be904a62 26.788, -16.843 57.79966       11
711 c0956226 25.002, -13.470 38.48902       53
712 c0b44f43 26.700, -16.253 56.39547       59
713 c0dd9cac 32.311, -10.098 32.80511        9
714 c5911f9d 31.215, -14.386 72.91299       63
715 c98d6fab 26.928, -14.554 56.31413       54
716 cb68f842 28.899, -13.540 63.73785       41
717 cf26e9a5 33.323, -12.405 42.72912       36
718 d1ef6a21 27.091, -15.400 56.95235       54
719 d3256de1 27.338, -15.194 47.47742       54
720 d344fef6 25.002, -13.465 38.48902       53
721 d3e5073a 26.719, -15.722 30.80526       59
722 d547ed48 26.691, -16.262 56.39547       59
723 d5fe7151 27.275, -16.924 66.93754       11
724 d87b2ba4 27.110, -17.202 72.66420       11
725 de703d8d 25.380, -13.056 44.26578       53
726 e199fd8a 33.029, -12.154 40.36482       36
727 e39eb833 25.834, -12.329 61.66153       71
728 e4b16f8e 32.311, -10.087 32.80511        9
729 e4ce7051 25.493, -12.101 68.82276       71
730 e589c762 27.110, -17.205 72.66420       11
731 e912f704 32.839, -12.676 58.93127       36
732 eeb933eb 26.954, -14.507 47.66192       54
733 f172d121 27.271, -16.784 76.04762       11
734 f3af4eba 28.444, -13.387 69.39651       49
735 f4831cde 26.779, -16.419 70.70723       11
736 f6062450 32.189, -10.611 22.30976        9
737 f6685654 33.327, -12.419 42.72912       36
738 fa4c6e6e 26.771, -16.393 62.40511       11
739 fb088f30  31.672, -9.026 31.98688       43
740 fcfcc16c  31.196, -9.562 43.63295       50
741 fe787454 27.275, -16.892 67.82761       11
742 0e05db59 26.933, -16.058 63.05702       59
743 140e3941 25.000, -13.466 42.21804       53
744 1fae151e 28.650, -13.828 75.62058       41
745 26195598 32.252, -10.319 36.54598        9
746 53d0495e 27.285, -16.872 67.82761       11
747 5d05bfc1 32.291, -10.098 36.06217        9
748 5f0d09cc 32.267, -10.310 36.54598        9
749 67f251fe 32.315, -10.088 32.80511        9
750 75111bb0 27.346, -15.223 48.29046       54
751 7c69cff0 26.912, -16.282 55.04950       11
752 a85004ef 26.940, -16.501 72.00297       11
753 ca04c2b6 26.690, -16.252 56.39547       59
754 dcc27ec3 29.578, -13.587 63.70206       45
755 e6c88812 33.327, -12.402 42.72912       36
756 e715af5a 27.242, -16.775 74.13513       11
757 e7e416f5 28.646, -13.529 72.46116       41
758 f9938fa0 29.064, -13.726 53.63661       45
759 260773a1 32.839, -12.675 58.93127       36
760 32daae1b 28.659, -13.693 73.82898       41
761 bfa90e8f 25.880, -12.324 72.05606       71
762 cb6d3906   31.94, -10.65 30.82363        9
763 d5217eeb 27.013, -16.933 71.20597       11
764 e911f934  31.196, -9.562 43.63295       50
765 04845532  31.235, -9.384 47.74985       43
766 63001bed 26.866, -16.590 73.05731       11
767 72b2e62d 25.367, -13.058 44.26578       53
768 74b3735b 26.405, -16.142 56.13718       59
769 b1cebf22  31.217, -9.542 44.36200       43
770 d02e3b93 27.286, -16.932 66.93754       11
771 d3dddce3 27.231, -16.738 69.78009       11
772 1fcb8ab8 26.527, -15.921 40.09698       59
773 3cb24370 32.307, -10.135 27.33848        9
774 4ac54ab4 25.506, -12.114 68.72966       71
775 53e9d1a5 32.187, -10.611 22.30976        9
776 7268663b  31.234, -9.357 47.74985       43
777 8b06cf36 28.912, -13.536 61.80630       41
778 8b9b82d2 26.929, -16.029 63.79404       59
779 b704d152 27.111, -16.787 69.24673       11
780 cc7a4975 28.668, -13.682 73.82898       41
781 2d497f79 29.572, -13.577 63.70206       45
782 b4df829f 27.626, -17.113 58.47983       70
783 1132da30 24.777, -13.199 55.14384       53
784 523f840d 26.405, -16.142 56.13718       59
785 6a906acb  31.196, -9.562 43.63295       50
786 9cc78ee8 27.273, -16.872 67.82761       11
787 c62e8af5 26.926, -14.554 56.31413       54
788 187ad80f 29.585, -13.585 63.70206       45
789 3f286438 32.877, -12.687 60.75867       36
790 7743fc52 31.215, -14.384 72.91299       63
791 a0dba7aa 26.914, -14.515 44.70253       54
792 c133f2bc 26.917, -16.522 72.00297       11
793 cc8a8538 28.371, -13.332 63.78424       41

rm(list = ls())
ls()

character(0)

library(geospaar)
ls()

character(0)

farmers_env

Simple feature collection with 793 features and 3 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: 24.777 ymin: -18.222 xmax: 33.332 ymax: -8.997
CRS:           NA
# A tibble: 793 × 4
   uuid             geometry  rain district
 * <chr>             <POINT> <dbl>    <dbl>
 1 009a8424 (27.256 -16.926)  66.9       11
 2 00df166f (26.942 -16.504)  72.0       11
 3 02671a00 (27.254 -16.914)  66.9       11
 4 03f4dcca (27.237 -16.733)  69.8       11
 5 042cf7b3 (27.138 -16.807)  75.1       11
 6 05618404 (26.875 -16.611)  66.1       11
 7 064beba0 (26.752 -16.862)  58.4       20
 8 083a46a2 (26.977 -16.765)  70.4       11
 9 08eb2224 (26.912 -16.248)  54.0       59
10 0ab761d6  (27.113 -16.95)  72.4       11
# ℹ 783 more rows

ls()

character(0)

Raw data in inst/extdata

system.file("extdata", package = "geospaar")

[1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/geospaar/extdata"

dir(system.file("extdata", package = "geospaar"))

 [1] "cdf_corn.csv"          "chilanga_farmer"       "chirps.tif"           
 [4] "districts.geojson"     "EJ_POLY.cpg"           "EJ_POLY.dbf"          
 [7] "EJ_POLY.prj"           "EJ_POLY.sbn"           "EJ_POLY.sbx"          
[10] "EJ_POLY.shp"           "EJ_POLY.shp.xml"       "EJ_POLY.shx"          
[13] "FAOSTAT_maize.csv"     "FAOSTAT_sorghum.csv"   "FAOSTAT_wheat.csv"    
[16] "farmer_spatial.csv"    "filt_data.rda"         "roads.geojson"        
[19] "train_reference.csv"   "westluse.rdc"          "westluse.rst"         
[22] "westroad.vct"          "westroad.vdc"          "whittier_down_d_h.rda"
[25] "whittier_mid_d_h.rda"  "whittier_up_d_h.rda"

f <- system.file("extdata", "farmer_spatial.csv", package = "geospaar")
head(read.csv(f))

      uuid      x       y       date season rained planted
1 009a8424 27.256 -16.926 2015-11-15      1      0       0
2 00df166f 26.942 -16.504 2015-11-15      1      0       0
3 02671a00 27.254 -16.914 2015-11-15      1      0       0
4 03f4dcca 27.237 -16.733 2015-11-15      1      0       0
5 042cf7b3 27.138 -16.807 2015-11-15      1      0       0
6 05618404 26.875 -16.611 2015-11-15      1      0       0

Other package folders

See Chap 9 of “R Packages” for more examples of R packages folders.

A look at RMarkdown

Chunk options

Rmarkdown demo by Lei Song RMarkdown gallery

RMarkdown exercises

In your personal R project, Create new RMarkdown file using usethis::use_vignette(name = "example_vignette")
Create chunks for the following:
- Load the geospaar package
- Load the chirps data and print its structure using str(chirps)
- Plot chirps data using raster::plot(chirps). Above this chunk, include a text description for the CHIRPS data using different text formatting (bold, italics, etc). You can see information on the CHIRPS data in the man folder.
- Include a chunk with an obvious error, like 5 + "string"
- Try knitting this RMD using different chunk options

The R Ecosystem

Common objects

Credit: L. Song

The R Ecosystem

Data types

There are 6 atomic data types:

character e.g. 'hello world', 'abc'
double (real or decimal) e.g. 10, 3.14, 1e10
integer e.g. 1L
logical e.g. TRUE, FALSE, T, F
complex e.g. 1 + 3i (not commonly used by us)
raw (rarely used by us)

The R Ecosystem

Special data types

NULL: Does not exist
Missing data: NA. A special logical type that converts into the type it is associated with.
Infinity: Inf (e.g. 1 / 0) and -Inf (e.g. -1 / 0. A special double type.
Undefined value: NaN. Also a special double type. (e.g. 0 / 0)

The R Ecosystem

Special data types

Date: as.Date('1970-1-5')
Time: as.POSIXct('1970-1-5')
Factor: factors are integers with associated labels.

The R Ecosystem

Checking data type

typeof(x)
is.xxx(x):
- e.g. is.double(x), is.integer(x), is.logical(x), is.character(x), is.complex(x), is.raw(x), is.factor
- is.numeric(x)
- e.g. is.na(y), is.nan(y), is.null(y), is.infinite(y), is.finite(y).

The R Ecosystem

Converting data type

as.xxx(x):
- e.g. as.numeric(x), as.double(x), as.character(x), as.integer(x), as.logical(x), as.complex(x), as.raw(x), as.factor(x), as.Date(x), as.POSIXct(x).
logical < integer < double < character

The R Ecosystem

Data structures

Atomic vectors (most commonly thought of kind):
- A sequence of objects of the same class.
- Arrays and matrices are vectors with more than one dimension.
  - Matrices have 2 dimensions.
  - Arrays could have higher dimensions.
Lists
- Lists can contain objects of different classes.
- Lists can be converted list-matrix or list-array by defining dimensions.
- data.frame and tibble are S3 objects that are lists in tabular form

The R Ecosystem

Vectors

Credit: L. Song

Let’s create some data

vector
matrix
data.frame
list

Creating a vector

v1 <- c(1,2,3,4,5)
v2 <- 6:10
print(v1)

[1] 1 2 3 4 5

print(v2)

[1]  6  7  8  9 10

Combining vectors

v1 <- c(1,2,3,4,5)
v2 <- 6:10
v3 <- c(v1, v2)
print(v3)

 [1]  1  2  3  4  5  6  7  8  9 10

print(class(v3))

[1] "numeric"

Combining vectors

What happens when you combine data types in a vector?

v4 <- c(v1, "test")
print(v4)

[1] "1"    "2"    "3"    "4"    "5"    "test"

print(class(v4))

[1] "character"

Vectorized operations

v1 <- 1:9
print(v1)

[1] 1 2 3 4 5 6 7 8 9

print(v1 + 5) ## addition applied to each element in vector

[1]  6  7  8  9 10 11 12 13 14

print(v1 * 3) ## multiplication applied to each element in vector

[1]  3  6  9 12 15 18 21 24 27

Accessing elements in vector

v1 <- (1:9)*3 
print(v1)

[1]  3  6  9 12 15 18 21 24 27

print(v1[4])

[1] 12

v1 <- letters[1:7]
print(paste0("This letter is ", v1)) # paste0 concatenates strings

[1] "This letter is a" "This letter is b" "This letter is c" "This letter is d"
[5] "This letter is e" "This letter is f" "This letter is g"

Question: How would you say “Letter 1 is a”, “Letter 2 is b”, etc.

Creating a matrix

v1 <- 1:9
m1 <- matrix(v1, nrow = 3, byrow = T)
m2 <- cbind(v1 = 1:3, v2 = 1:3, v3 = 0:0)
print(m1)

     [,1] [,2] [,3]
[1,]    1    2    3
[2,]    4    5    6
[3,]    7    8    9

print(m2)

     v1 v2 v3
[1,]  1  1  0
[2,]  2  2  0
[3,]  3  3  0

Accessing elements in a matrix

m2 <- cbind(v1 = 1:3, v2 = 1:3, v3 = 0:0)
print(m2)

     v1 v2 v3
[1,]  1  1  0
[2,]  2  2  0
[3,]  3  3  0

print("first row:")

[1] "first row:"

print(m2[1, ])

v1 v2 v3 
 1  1  0

print("second column")

[1] "second column"

print(m2[, 2])

[1] 1 2 3

print("access by column name")

[1] "access by column name"

print(m2[, "v2"])

[1] 1 2 3

Question: Create a 3 row, 4 column matrix, where the first column is (1, 2, 3), second column is (4, 5, 6 ) etc.

Lists

Lists can mix object of different types.

l <- list("a", 1, 0.5, TRUE)
print(l)

[[1]]
[1] "a"

[[2]]
[1] 1

[[3]]
[1] 0.5

[[4]]
[1] TRUE

print(str(l)) # structure of l

List of 4
 $ : chr "a"
 $ : num 1
 $ : num 0.5
 $ : logi TRUE
NULL

Lists

Lists can also be nested.

l1 <- list("a", 1, 0.5, TRUE)
l2 <- list(l1, "test", matrix(1:9, nrow = 3)) ## first element of l2 is a list.
print(l2)

[[1]]
[[1]][[1]]
[1] "a"

[[1]][[2]]
[1] 1

[[1]][[3]]
[1] 0.5

[[1]][[4]]
[1] TRUE


[[2]]
[1] "test"

[[3]]
     [,1] [,2] [,3]
[1,]    1    4    7
[2,]    2    5    8
[3,]    3    6    9

Question: what is the length of l1? what is the length of each element of l1? (use length function)

Accessing elements in lists

Use double brackets [[ ]] to access elements in lists.

l1 <- list("a", 1, 0.5, TRUE)
l2 <- list(l1, "test", matrix(1:9, nrow = 3)) ## first element of l2 is a list.
print(l2[[1]])

[[1]]
[1] "a"

[[2]]
[1] 1

[[3]]
[1] 0.5

[[4]]
[1] TRUE

print(l2[[2]])

[1] "test"

print(l2[[3]])

     [,1] [,2] [,3]
[1,]    1    4    7
[2,]    2    5    8
[3,]    3    6    9

Question: The first element of l2 is a list. Access this first element from l2, then the 4th element from l1

Data frames

We will use data frames A LOT. Data frames are really tables, but they are stored in R as lists, with the following conditions.

Each element in the list represents a column.
Each element in the list is an atomic vector.
The length of each vector is the same (the number of rows)

m1 <- cbind(1:3, letters[1:3])
print(m1) # a matrix cannot hold multiple data types.

     [,1] [,2]
[1,] "1"  "a" 
[2,] "2"  "b" 
[3,] "3"  "c"

print(class(m1))

[1] "matrix" "array"

df <- data.frame(numbers = 1:3, abc = letters[1:3])
print(df) # a data frame CAN hold multiple data types.

  numbers abc
1       1   a
2       2   b
3       3   c

print(class(df))

[1] "data.frame"

Useful functions

print
You can print just about anything, but as a generic function, print works differently for different types of objects.

a <- "test"
df <- data.frame(numbers = 1:3, abc = letters[1:3])
print(a) # a data frame CAN hold multiple data types.

[1] "test"

print(df)

  numbers abc
1       1   a
2       2   b
3       3   c

methods(print) ## all the different ways to print...

  [1] print.acf*                                          
  [2] print.activeConcordance*                            
  [3] print.AES*                                          
  [4] print.all_vars*                                     
  [5] print.anova*                                        
  [6] print.any_vars*                                     
  [7] print.aov*                                          
  [8] print.aovlist*                                      
  [9] print.ar*                                           
 [10] print.Arima*                                        
 [11] print.arima0*                                       
 [12] print.AsIs                                          
 [13] print.aspell*                                       
 [14] print.aspell_inspect_context*                       
 [15] print.bbox*                                         
 [16] print.bibentry*                                     
 [17] print.Bibtex*                                       
 [18] print.bootstrap.lca*                                
 [19] print.browseVignettes*                              
 [20] print.by                                            
 [21] print.bytes*                                        
 [22] print.changedFiles*                                 
 [23] print.check_bogus_return*                           
 [24] print.check_code_usage_in_package*                  
 [25] print.check_compiled_code*                          
 [26] print.check_demo_index*                             
 [27] print.check_depdef*                                 
 [28] print.check_details*                                
 [29] print.check_details_changes*                        
 [30] print.check_doi_db*                                 
 [31] print.check_dotInternal*                            
 [32] print.check_make_vars*                              
 [33] print.check_nonAPI_calls*                           
 [34] print.check_package_code_assign_to_globalenv*       
 [35] print.check_package_code_attach*                    
 [36] print.check_package_code_data_into_globalenv*       
 [37] print.check_package_code_startup_functions*         
 [38] print.check_package_code_syntax*                    
 [39] print.check_package_code_unload_functions*          
 [40] print.check_package_compact_datasets*               
 [41] print.check_package_CRAN_incoming*                  
 [42] print.check_package_datalist*                       
 [43] print.check_package_datasets*                       
 [44] print.check_package_depends*                        
 [45] print.check_package_description*                    
 [46] print.check_package_description_encoding*           
 [47] print.check_package_license*                        
 [48] print.check_packages_in_dir*                        
 [49] print.check_packages_used*                          
 [50] print.check_po_files*                               
 [51] print.check_pragmas*                                
 [52] print.check_Rd_line_widths*                         
 [53] print.check_Rd_metadata*                            
 [54] print.check_Rd_xrefs*                               
 [55] print.check_RegSym_calls*                           
 [56] print.check_S3_methods_needing_delayed_registration*
 [57] print.check_so_symbols*                             
 [58] print.check_T_and_F*                                
 [59] print.check_url_db*                                 
 [60] print.check_vignette_index*                         
 [61] print.checkDocFiles*                                
 [62] print.checkDocStyle*                                
 [63] print.checkFF*                                      
 [64] print.checkRd*                                      
 [65] print.checkRdContents*                              
 [66] print.checkReplaceFuns*                             
 [67] print.checkS3methods*                               
 [68] print.checkTnF*                                     
 [69] print.checkVignettes*                               
 [70] print.citation*                                     
 [71] print.classIntervals*                               
 [72] print.cli_ansi_html_style*                          
 [73] print.cli_ansi_string*                              
 [74] print.cli_ansi_style*                               
 [75] print.cli_boxx*                                     
 [76] print.cli_diff_chr*                                 
 [77] print.cli_doc*                                      
 [78] print.cli_progress_demo*                            
 [79] print.cli_rule*                                     
 [80] print.cli_sitrep*                                   
 [81] print.cli_spark*                                    
 [82] print.cli_spinner*                                  
 [83] print.cli_tree*                                     
 [84] print.codoc*                                        
 [85] print.codocClasses*                                 
 [86] print.codocData*                                    
 [87] print.col_spec*                                     
 [88] print.collector*                                    
 [89] print.colorConverter*                               
 [90] print.compactPDF*                                   
 [91] print.condition                                     
 [92] print.connection                                    
 [93] print.CRAN_package_reverse_dependencies_and_views*  
 [94] print.crossdist*                                    
 [95] print.crs*                                          
 [96] print.data.frame                                    
 [97] print.Date                                          
 [98] print.date_names*                                   
 [99] print.default                                       
[100] print.dendrogram*                                   
[101] print.density*                                      
[102] print.difftime                                      
[103] print.dist*                                         
[104] print.Dlist                                         
[105] print.DLLInfo                                       
[106] print.DLLInfoList                                   
[107] print.DLLRegisteredRoutines                         
[108] print.document_context*                             
[109] print.document_position*                            
[110] print.document_range*                               
[111] print.document_selection*                           
[112] print.dplyr_join_by*                                
[113] print.dplyr_sel_vars*                               
[114] print.dummy_coef*                                   
[115] print.dummy_coef_list*                              
[116] print.ecdf*                                         
[117] print.eigen                                         
[118] print.element*                                      
[119] print.evaluate_evaluation*                          
[120] print.factanal*                                     
[121] print.factor                                        
[122] print.family*                                       
[123] print.fclust*                                       
[124] print.fileSnapshot*                                 
[125] print.findLineNumResult*                            
[126] print.flatGridListing*                              
[127] print.formula*                                      
[128] print.fseq*                                         
[129] print.ftable*                                       
[130] print.fun_list*                                     
[131] print.function                                      
[132] print.getAnywhere*                                  
[133] print.ggplot*                                       
[134] print.ggplot2_bins*                                 
[135] print.ggproto*                                      
[136] print.ggproto_method*                               
[137] print.gknn*                                         
[138] print.gList*                                        
[139] print.glm*                                          
[140] print.glue*                                         
[141] print.gpar*                                         
[142] print.GridCoords*                                   
[143] print.GridGrobCoords*                               
[144] print.GridGTreeCoords*                              
[145] print.grob*                                         
[146] print.gtable*                                       
[147] print.hashtab*                                      
[148] print.hclust*                                       
[149] print.help_files_with_topic*                        
[150] print.hexmode                                       
[151] print.hms*                                          
[152] print.HoltWinters*                                  
[153] print.hsearch*                                      
[154] print.hsearch_db*                                   
[155] print.htest*                                        
[156] print.html*                                         
[157] print.html_dependency*                              
[158] print.htmltools.selector*                           
[159] print.htmltools.selector.list*                      
[160] print.ica*                                          
[161] print.infl*                                         
[162] print.integrate*                                    
[163] print.isoreg*                                       
[164] print.json*                                         
[165] print.key_missing*                                  
[166] print.kmeans*                                       
[167] print.knitr_kable*                                  
[168] print.last_dplyr_warnings*                          
[169] print.Latex*                                        
[170] print.LaTeX*                                        
[171] print.lca*                                          
[172] print.libraryIQR                                    
[173] print.lifecycle_warnings*                           
[174] print.listof                                        
[175] print.lm*                                           
[176] print.loadings*                                     
[177] print.locale*                                       
[178] print.loess*                                        
[179] print.logLik*                                       
[180] print.ls_str*                                       
[181] print.m_range*                                      
[182] print.medpolish*                                    
[183] print.MethodsFunction*                              
[184] print.mixed_units*                                  
[185] print.mtable*                                       
[186] print.naiveBayes*                                   
[187] print.NativeRoutineList                             
[188] print.news_db*                                      
[189] print.nls*                                          
[190] print.noquote                                       
[191] print.numeric_version                               
[192] print.object_size*                                  
[193] print.octmode                                       
[194] print.packageDescription*                           
[195] print.packageInfo                                   
[196] print.packageIQR*                                   
[197] print.packageStatus*                                
[198] print.paged_df*                                     
[199] print.pairdist*                                     
[200] print.pairwise.htest*                               
[201] print.path*                                         
[202] print.person*                                       
[203] print.pillar*                                       
[204] print.pillar_1e*                                    
[205] print.pillar_colonnade*                             
[206] print.pillar_ornament*                              
[207] print.pillar_shaft*                                 
[208] print.pillar_squeezed_colonnade*                    
[209] print.pillar_tbl_format_setup*                      
[210] print.pillar_vctr*                                  
[211] print.pillar_vctr_attr*                             
[212] print.POSIXct                                       
[213] print.POSIXlt                                       
[214] print.power.htest*                                  
[215] print.ppr*                                          
[216] print.prcomp*                                       
[217] print.princomp*                                     
[218] print.proc_time                                     
[219] print.proj_pipelines*                               
[220] print.proxy_registry*                               
[221] print.purrr_function_compose*                       
[222] print.purrr_function_partial*                       
[223] print.purrr_rate_backoff*                           
[224] print.purrr_rate_delay*                             
[225] print.quosure*                                      
[226] print.quosures*                                     
[227] print.R6*                                           
[228] print.R6ClassGenerator*                             
[229] print.raster*                                       
[230] print.Rconcordance*                                 
[231] print.Rcpp_stack_trace*                             
[232] print.Rd*                                           
[233] print.recordedplot*                                 
[234] print.registry_entry*                               
[235] print.registry_field*                               
[236] print.rel*                                          
[237] print.restart                                       
[238] print.RGBcolorConverter*                            
[239] print.RGlyphFont*                                   
[240] print.rlang_box_done*                               
[241] print.rlang_box_splice*                             
[242] print.rlang_data_pronoun*                           
[243] print.rlang_dict*                                   
[244] print.rlang_dyn_array*                              
[245] print.rlang_envs*                                   
[246] print.rlang_error*                                  
[247] print.rlang_fake_data_pronoun*                      
[248] print.rlang_lambda_function*                        
[249] print.rlang_message*                                
[250] print.rlang_trace*                                  
[251] print.rlang_warning*                                
[252] print.rlang_zap*                                    
[253] print.rlang:::list_of_conditions*                   
[254] print.rle                                           
[255] print.rlib_bytes*                                   
[256] print.rlib_error_3_0*                               
[257] print.rlib_trace_3_0*                               
[258] print.roman*                                        
[259] print.scalar*                                       
[260] print.sessionInfo*                                  
[261] print.sf*                                           
[262] print.sf_layers*                                    
[263] print.sfc*                                          
[264] print.sfg*                                          
[265] print.sgbp*                                         
[266] print.shiny.tag*                                    
[267] print.shiny.tag.env*                                
[268] print.shiny.tag.list*                               
[269] print.shiny.tag.query*                              
[270] print.simil*                                        
[271] print.simple.list                                   
[272] print.smooth.spline*                                
[273] print.socket*                                       
[274] print.src*                                          
[275] print.srcfile                                       
[276] print.srcref                                        
[277] print.stepfun*                                      
[278] print.stl*                                          
[279] print.stringr_view*                                 
[280] print.StructTS*                                     
[281] print.subdir_tests*                                 
[282] print.summarize_CRAN_check_status*                  
[283] print.summary.aov*                                  
[284] print.summary.aovlist*                              
[285] print.summary.ecdf*                                 
[286] print.summary.glm*                                  
[287] print.summary.lca*                                  
[288] print.summary.lm*                                   
[289] print.summary.loess*                                
[290] print.summary.manova*                               
[291] print.summary.nls*                                  
[292] print.summary.packageStatus*                        
[293] print.summary.ppr*                                  
[294] print.summary.pr_DB*                                
[295] print.summary.prcomp*                               
[296] print.summary.princomp*                             
[297] print.summary.svm*                                  
[298] print.summary.table                                 
[299] print.summary.tune*                                 
[300] print.summary.warnings                              
[301] print.summaryDefault                                
[302] print.svm*                                          
[303] print.table                                         
[304] print.tables_aov*                                   
[305] print.tbl*                                          
[306] print.terms*                                        
[307] print.theme*                                        
[308] print.tidyverse_conflicts*                          
[309] print.tidyverse_logo*                               
[310] print.transform*                                    
[311] print.trunc_mat*                                    
[312] print.ts*                                           
[313] print.tskernel*                                     
[314] print.TukeyHSD*                                     
[315] print.tukeyline*                                    
[316] print.tukeysmooth*                                  
[317] print.tune*                                         
[318] print.undoc*                                        
[319] print.uneval*                                       
[320] print.unit*                                         
[321] print.units*                                        
[322] print.vctrs_bytes*                                  
[323] print.vctrs_sclr*                                   
[324] print.vctrs_unspecified*                            
[325] print.vctrs_vctr*                                   
[326] print.viewport*                                     
[327] print.vignette*                                     
[328] print.warnings                                      
[329] print.xfun_md_viewable*                             
[330] print.xfun_raw_string*                              
[331] print.xfun_record_results*                          
[332] print.xfun_rename_seq*                              
[333] print.xfun_strict_list*                             
[334] print.xgettext*                                     
[335] print.xngettext*                                    
[336] print.xtabs*                                        
[337] print.z_range*                                      
see '?methods' for accessing help and source code

Examining objects

ls, class, str

a <- "test"
df <- data.frame(numbers = 1:3, abc = letters[1:3])
ls() ## list objects in global environemtn

 [1] "a"  "df" "f"  "l"  "l1" "l2" "m1" "m2" "v1" "v2" "v3" "v4"

class(df) ## class

[1] "data.frame"

str(df) ## structure

'data.frame':   3 obs. of  2 variables:
 $ numbers: int  1 2 3
 $ abc    : chr  "a" "b" "c"

Sampling

Sample without replacement

set.seed(1234) ## set a random seed
v <- 1:100
s <- sample(v, 50)
print(s)

 [1] 28 80 22  9  5 38 16  4 86 90 70 79 78 14 56 62 93 84 21 40 92 67 96 66 47
[26] 81 48  3 41 32 42 43  2 54 49 99 51  6 77 29 71 85 57  8 26 17 58 91 60 76

print(sort(s))

 [1]  2  3  4  5  6  8  9 14 16 17 21 22 26 28 29 32 38 40 41 42 43 47 48 49 51
[26] 54 56 57 58 60 62 66 67 70 71 76 77 78 79 80 81 84 85 86 90 91 92 93 96 99

Sample with replacement

s2 <- sample(v, 50, replace = T)
print(sort(s2))

 [1]  2  3  3  6  6  9 10 17 17 19 20 22 22 25 27 28 30 32 35 36 41 41 48 50 51
[26] 55 57 58 58 60 61 63 63 65 66 70 70 71 72 76 77 80 83 85 85 86 86 87 90 96

Does S2 have duplicates?

s2_unique <- unique(s2)
print(length(s2))

[1] 50

print(length(s2_unique))

[1] 40

print(length(s2) == length(s2_unique))

[1] FALSE