Dear Friends,
Today we will perform some basic descriptive statistics from the given ecological data.
#set working directory ( go to session,click on set working directory, choose directory in which your csv file is located)
# codes taken and modifed from https://statsandr.com/blog/descriptive-statistics-in-r/#introduction
data =read.csv(file = "water_chemistry.csv", header = TRUE)
head(data)## Site Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L. pH
## 1 S-1 30.1 98 1514.0 989 7.78
## 2 S-2 30.4 96 1416.0 921 6.13
## 3 S-3 30.6 108 142.3 103 8.33
## 4 S-4 30.6 102 1517.0 988 8.10
## 5 S-5 31.6 69 1531.0 996 8.23
## 6 S-6 31.4 92 1529.0 995 8.35
## D.O Total.alkalinity Total.hardness Total.N2 Nitrate Available.Phosphate BOD
## 1 4.21 172 336 0.0636 0.0228 0.1034 3.8
## 2 5.09 172 340 0.0786 0.0330 0.1576 4.0
## 3 7.08 188 388 0.0556 0.0145 0.1084 4.2
## 4 5.26 168 352 0.0729 0.0237 0.0936 3.6
## 5 6.63 200 364 0.0490 0.0096 0.1256 4.0
## 6 7.44 168 344 0.0875 0.0167 0.0714 3.8
## year
## 1 2021
## 2 2021
## 3 2021
## 4 2021
## 5 2021
## 6 2021#Mean of a coloumn/ head can be estimated by the following code, mean is
mean(data$Water.temperature)## [1] 31.585median(data$Water.temperature)## [1] 31.55# Base R does not have a standard inbuilt function to calculate mode, So, a function needs to be created for mode (the codes were taken and modified from tutorials point.com).
mode=function(X){uniqX=unique(X)
uniqX[which.max(tabulate(match(X, uniqX)))]}
#define the character/ coloum head which needs to be calculated for mode
X =data$Water.temperature
mode(X)## [1] 30.6mode(data$Water.temperature)## [1] 30.6sd(data$Water.temperature)## [1] 0.8292514var(data$Water.temperature)## [1] 0.6876579Summary
#if you want to know the summary of the data
summary(data)## Site Water.temperature Transparency.cm. Specific.Conductivity
## Length:20 Min. :30.10 Min. : 56.00 Min. : 142.3
## Class :character 1st Qu.:31.15 1st Qu.: 71.75 1st Qu.: 981.8
## Mode :character Median :31.55 Median : 75.00 Median :1048.5
## Mean :31.59 Mean : 79.12 Mean :1398.4
## 3rd Qu.:32.12 3rd Qu.: 85.25 3rd Qu.:1529.5
## Max. :33.50 Max. :108.00 Max. :2979.0
## TDS.mg.L. pH D.O Total.alkalinity
## Min. : 103.0 Min. :6.130 Min. :4.210 Min. :148.0
## 1st Qu.: 638.2 1st Qu.:8.290 1st Qu.:6.550 1st Qu.:164.5
## Median : 682.0 Median :8.515 Median :7.015 Median :169.0
## Mean : 911.8 Mean :8.317 Mean :7.026 Mean :169.9
## 3rd Qu.: 995.2 3rd Qu.:8.580 3rd Qu.:7.605 3rd Qu.:172.5
## Max. :1939.0 Max. :8.710 Max. :9.700 Max. :200.0
## Total.hardness Total.N2 Nitrate Available.Phosphate
## Min. :232.0 Min. :0.04900 Min. :0.00890 Min. :0.02800
## 1st Qu.:248.0 1st Qu.:0.05897 1st Qu.:0.01285 1st Qu.:0.03560
## Median :300.0 Median :0.07155 Median :0.01560 Median :0.04510
## Mean :304.1 Mean :0.07296 Mean :0.01718 Mean :0.06932
## 3rd Qu.:355.0 3rd Qu.:0.08055 3rd Qu.:0.02250 3rd Qu.:0.10465
## Max. :388.0 Max. :0.12460 Max. :0.03300 Max. :0.15760
## BOD year
## Min. :2.000 Min. :2021
## 1st Qu.:2.400 1st Qu.:2021
## Median :3.300 Median :2022
## Mean :3.075 Mean :2022
## 3rd Qu.:3.800 3rd Qu.:2022
## Max. :4.200 Max. :2022# if you want to know the summary of the data without the 1st coloumn, i.e sit numbers
summary(data[, -1])## Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L.
## Min. :30.10 Min. : 56.00 Min. : 142.3 Min. : 103.0
## 1st Qu.:31.15 1st Qu.: 71.75 1st Qu.: 981.8 1st Qu.: 638.2
## Median :31.55 Median : 75.00 Median :1048.5 Median : 682.0
## Mean :31.59 Mean : 79.12 Mean :1398.4 Mean : 911.8
## 3rd Qu.:32.12 3rd Qu.: 85.25 3rd Qu.:1529.5 3rd Qu.: 995.2
## Max. :33.50 Max. :108.00 Max. :2979.0 Max. :1939.0
## pH D.O Total.alkalinity Total.hardness
## Min. :6.130 Min. :4.210 Min. :148.0 Min. :232.0
## 1st Qu.:8.290 1st Qu.:6.550 1st Qu.:164.5 1st Qu.:248.0
## Median :8.515 Median :7.015 Median :169.0 Median :300.0
## Mean :8.317 Mean :7.026 Mean :169.9 Mean :304.1
## 3rd Qu.:8.580 3rd Qu.:7.605 3rd Qu.:172.5 3rd Qu.:355.0
## Max. :8.710 Max. :9.700 Max. :200.0 Max. :388.0
## Total.N2 Nitrate Available.Phosphate BOD
## Min. :0.04900 Min. :0.00890 Min. :0.02800 Min. :2.000
## 1st Qu.:0.05897 1st Qu.:0.01285 1st Qu.:0.03560 1st Qu.:2.400
## Median :0.07155 Median :0.01560 Median :0.04510 Median :3.300
## Mean :0.07296 Mean :0.01718 Mean :0.06932 Mean :3.075
## 3rd Qu.:0.08055 3rd Qu.:0.02250 3rd Qu.:0.10465 3rd Qu.:3.800
## Max. :0.12460 Max. :0.03300 Max. :0.15760 Max. :4.200
## year
## Min. :2021
## 1st Qu.:2021
## Median :2022
## Mean :2022
## 3rd Qu.:2022
## Max. :2022# in summary you will get ( min, Max, Mean, median, 1st quartile, 3rd quartile, which is all the elements of boxplot including mean, from min and Max we will get the range of the data)
# if you donot want teh 1st coloumn and last coloumn (14th coloumn) in the summary, then
summary(data[, - c(1, 14)])## Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L.
## Min. :30.10 Min. : 56.00 Min. : 142.3 Min. : 103.0
## 1st Qu.:31.15 1st Qu.: 71.75 1st Qu.: 981.8 1st Qu.: 638.2
## Median :31.55 Median : 75.00 Median :1048.5 Median : 682.0
## Mean :31.59 Mean : 79.12 Mean :1398.4 Mean : 911.8
## 3rd Qu.:32.12 3rd Qu.: 85.25 3rd Qu.:1529.5 3rd Qu.: 995.2
## Max. :33.50 Max. :108.00 Max. :2979.0 Max. :1939.0
## pH D.O Total.alkalinity Total.hardness
## Min. :6.130 Min. :4.210 Min. :148.0 Min. :232.0
## 1st Qu.:8.290 1st Qu.:6.550 1st Qu.:164.5 1st Qu.:248.0
## Median :8.515 Median :7.015 Median :169.0 Median :300.0
## Mean :8.317 Mean :7.026 Mean :169.9 Mean :304.1
## 3rd Qu.:8.580 3rd Qu.:7.605 3rd Qu.:172.5 3rd Qu.:355.0
## Max. :8.710 Max. :9.700 Max. :200.0 Max. :388.0
## Total.N2 Nitrate Available.Phosphate BOD
## Min. :0.04900 Min. :0.00890 Min. :0.02800 Min. :2.000
## 1st Qu.:0.05897 1st Qu.:0.01285 1st Qu.:0.03560 1st Qu.:2.400
## Median :0.07155 Median :0.01560 Median :0.04510 Median :3.300
## Mean :0.07296 Mean :0.01718 Mean :0.06932 Mean :3.075
## 3rd Qu.:0.08055 3rd Qu.:0.02250 3rd Qu.:0.10465 3rd Qu.:3.800
## Max. :0.12460 Max. :0.03300 Max. :0.15760 Max. :4.200#if you want the summary by year and without 1st coloumn
by(data[, -1], data$year, summary)## data$year: 2021
## Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L.
## Min. :30.10 Min. : 69.00 Min. : 142.3 Min. : 103.0
## 1st Qu.:30.60 1st Qu.: 78.62 1st Qu.:1514.8 1st Qu.: 988.2
## Median :31.10 Median : 87.50 Median :1530.0 Median : 995.5
## Mean :31.02 Mean : 88.15 Mean :1803.6 Mean :1175.1
## 3rd Qu.:31.48 3rd Qu.: 97.50 3rd Qu.:2500.0 3rd Qu.:1630.5
## Max. :31.80 Max. :108.00 Max. :2979.0 Max. :1939.0
## pH D.O Total.alkalinity Total.hardness
## Min. :6.130 Min. :4.210 Min. :168.0 Min. :332.0
## 1st Qu.:8.133 1st Qu.:5.603 1st Qu.:172.0 1st Qu.:341.0
## Median :8.280 Median :7.090 Median :172.0 Median :358.0
## Mean :8.050 Mean :6.953 Mean :177.6 Mean :358.8
## 3rd Qu.:8.325 3rd Qu.:7.897 3rd Qu.:183.0 3rd Qu.:377.0
## Max. :8.710 Max. :9.700 Max. :200.0 Max. :388.0
## Total.N2 Nitrate Available.Phosphate BOD
## Min. :0.04900 Min. :0.00960 Min. :0.04430 Min. :3.40
## 1st Qu.:0.05672 1st Qu.:0.01505 1st Qu.:0.08063 1st Qu.:3.60
## Median :0.06205 Median :0.02065 Median :0.10590 Median :3.80
## Mean :0.06612 Mean :0.02003 Mean :0.10318 Mean :3.77
## 3rd Qu.:0.07717 3rd Qu.:0.02347 3rd Qu.:0.12190 3rd Qu.:3.95
## Max. :0.08750 Max. :0.03300 Max. :0.15760 Max. :4.20
## year
## Min. :2021
## 1st Qu.:2021
## Median :2021
## Mean :2021
## 3rd Qu.:2021
## Max. :2021
## ------------------------------------------------------------
## data$year: 2022
## Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L.
## Min. :31.30 Min. :56.00 Min. : 936.0 Min. :609.0
## 1st Qu.:31.80 1st Qu.:68.75 1st Qu.: 973.5 1st Qu.:633.0
## Median :32.15 Median :72.00 Median : 994.0 Median :648.0
## Mean :32.15 Mean :70.10 Mean : 993.1 Mean :648.4
## 3rd Qu.:32.45 3rd Qu.:72.00 3rd Qu.:1012.5 3rd Qu.:674.5
## Max. :33.50 Max. :75.00 Max. :1049.0 Max. :682.0
## pH D.O Total.alkalinity Total.hardness
## Min. :8.500 Min. :6.420 Min. :148.0 Min. :232.0
## 1st Qu.:8.530 1st Qu.:6.553 1st Qu.:157.0 1st Qu.:246.5
## Median :8.575 Median :6.885 Median :163.0 Median :248.0
## Mean :8.584 Mean :7.098 Mean :162.2 Mean :249.4
## 3rd Qu.:8.640 3rd Qu.:7.430 3rd Qu.:168.0 3rd Qu.:255.0
## Max. :8.680 Max. :8.390 Max. :174.0 Max. :268.0
## Total.N2 Nitrate Available.Phosphate BOD
## Min. :0.05390 Min. :0.00890 Min. :0.02800 Min. :2.00
## 1st Qu.:0.06525 1st Qu.:0.01022 1st Qu.:0.03370 1st Qu.:2.20
## Median :0.07645 Median :0.01340 Median :0.03550 Median :2.40
## Mean :0.07979 Mean :0.01433 Mean :0.03545 Mean :2.38
## 3rd Qu.:0.08715 3rd Qu.:0.01713 3rd Qu.:0.03750 3rd Qu.:2.40
## Max. :0.12460 Max. :0.02640 Max. :0.04590 Max. :3.20
## year
## Min. :2022
## 1st Qu.:2022
## Median :2022
## Mean :2022
## 3rd Qu.:2022
## Max. :2022#Now, if you want to remove"'year' and 'site'" from the summary and also want to classify by year
by(data[, - c(1, 14)], data$year, summary)## data$year: 2021
## Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L.
## Min. :30.10 Min. : 69.00 Min. : 142.3 Min. : 103.0
## 1st Qu.:30.60 1st Qu.: 78.62 1st Qu.:1514.8 1st Qu.: 988.2
## Median :31.10 Median : 87.50 Median :1530.0 Median : 995.5
## Mean :31.02 Mean : 88.15 Mean :1803.6 Mean :1175.1
## 3rd Qu.:31.48 3rd Qu.: 97.50 3rd Qu.:2500.0 3rd Qu.:1630.5
## Max. :31.80 Max. :108.00 Max. :2979.0 Max. :1939.0
## pH D.O Total.alkalinity Total.hardness
## Min. :6.130 Min. :4.210 Min. :168.0 Min. :332.0
## 1st Qu.:8.133 1st Qu.:5.603 1st Qu.:172.0 1st Qu.:341.0
## Median :8.280 Median :7.090 Median :172.0 Median :358.0
## Mean :8.050 Mean :6.953 Mean :177.6 Mean :358.8
## 3rd Qu.:8.325 3rd Qu.:7.897 3rd Qu.:183.0 3rd Qu.:377.0
## Max. :8.710 Max. :9.700 Max. :200.0 Max. :388.0
## Total.N2 Nitrate Available.Phosphate BOD
## Min. :0.04900 Min. :0.00960 Min. :0.04430 Min. :3.40
## 1st Qu.:0.05672 1st Qu.:0.01505 1st Qu.:0.08063 1st Qu.:3.60
## Median :0.06205 Median :0.02065 Median :0.10590 Median :3.80
## Mean :0.06612 Mean :0.02003 Mean :0.10318 Mean :3.77
## 3rd Qu.:0.07717 3rd Qu.:0.02347 3rd Qu.:0.12190 3rd Qu.:3.95
## Max. :0.08750 Max. :0.03300 Max. :0.15760 Max. :4.20
## ------------------------------------------------------------
## data$year: 2022
## Water.temperature Transparency.cm. Specific.Conductivity TDS.mg.L.
## Min. :31.30 Min. :56.00 Min. : 936.0 Min. :609.0
## 1st Qu.:31.80 1st Qu.:68.75 1st Qu.: 973.5 1st Qu.:633.0
## Median :32.15 Median :72.00 Median : 994.0 Median :648.0
## Mean :32.15 Mean :70.10 Mean : 993.1 Mean :648.4
## 3rd Qu.:32.45 3rd Qu.:72.00 3rd Qu.:1012.5 3rd Qu.:674.5
## Max. :33.50 Max. :75.00 Max. :1049.0 Max. :682.0
## pH D.O Total.alkalinity Total.hardness
## Min. :8.500 Min. :6.420 Min. :148.0 Min. :232.0
## 1st Qu.:8.530 1st Qu.:6.553 1st Qu.:157.0 1st Qu.:246.5
## Median :8.575 Median :6.885 Median :163.0 Median :248.0
## Mean :8.584 Mean :7.098 Mean :162.2 Mean :249.4
## 3rd Qu.:8.640 3rd Qu.:7.430 3rd Qu.:168.0 3rd Qu.:255.0
## Max. :8.680 Max. :8.390 Max. :174.0 Max. :268.0
## Total.N2 Nitrate Available.Phosphate BOD
## Min. :0.05390 Min. :0.00890 Min. :0.02800 Min. :2.00
## 1st Qu.:0.06525 1st Qu.:0.01022 1st Qu.:0.03370 1st Qu.:2.20
## Median :0.07645 Median :0.01340 Median :0.03550 Median :2.40
## Mean :0.07979 Mean :0.01433 Mean :0.03545 Mean :2.38
## 3rd Qu.:0.08715 3rd Qu.:0.01713 3rd Qu.:0.03750 3rd Qu.:2.40
## Max. :0.12460 Max. :0.02640 Max. :0.04590 Max. :3.20length=c(12,15,20, 21,25,31,34,35,37,40, 41,46,51, 72)
breaks= seq(1,61, by=10)
breaks= c(1,11, 21, 31, 41, 51,61, 71, 81)
length.cut=cut(length, breaks, right=FALSE)
length.frequency = table(length.cut)
length.frequency## length.cut
## [1,11) [11,21) [21,31) [31,41) [41,51) [51,61) [61,71) [71,81)
## 0 3 2 5 2 1 0 1sessionInfo()## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 22621)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_India.utf8 LC_CTYPE=English_India.utf8
## [3] LC_MONETARY=English_India.utf8 LC_NUMERIC=C
## [5] LC_TIME=English_India.utf8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.31 R6_2.5.1 jsonlite_1.8.4 evaluate_0.20
## [5] cachem_1.0.7 rlang_1.1.0 cli_3.6.0 rstudioapi_0.14
## [9] jquerylib_0.1.4 bslib_0.4.2 rmarkdown_2.20 tools_4.2.2
## [13] xfun_0.37 yaml_2.3.7 fastmap_1.1.1 compiler_4.2.2
## [17] htmltools_0.5.5 knitr_1.42 sass_0.4.5git remote add origin https://github.com/pranayaparida/descriptive-stistics-.git git branch -M main