Manejo Habil de Datos
y Ciencia Reproducible
Taller Dia 1
2018-03-26
Preambulo
Quien soy?
Gabriel Muñoz
- Biólogo
- Ecólogo Computacional
Consultor en Datos Biodiversidad y Geoespaciales
Coordinador General
Charla introductoria
Material para este taller
Como organizar datos en las hojas de cálculo?
Una Variable, Una Columna!!!!
Control de Calidad
Como asegurar la calidad de nuestros datos?
Errores de tipeo
Discrepancias
Fueras de lugar
Errores de formato
Irregularidades
Datos faltantes
Contradicciones
Duplicaciones
Fueras de rango
Incongruencias
- Multiples valores
Google Open Refine
Exportar datos
Como exportar hojas de cálculo?
Registros similares en un dataset
Seguir standards internacionales en unidades y formatos (e.g. yyyy-mm-dd)
Se consistente (e.g. Mts, (m), metros)
Preserva en formatos estables (.csv, .txt, .tsv)
Análisis y visualización de datos en R
Intro a R
R version 3.4.4 (Someone to Lean On)
RStudio Desktop 1.1.442
Que es R?
Software gratis y abierto para el computación estadÃstica y graficos.
Lenguaje de programación
Crear un proyecto
Un proyecto, una carpeta!
Empezar un script
Buenas prácticas de programación
Estandarización
- nombrar con sentido
- xx11223
datosMediaLab
- nombrar con forma
- datosMediaLab_ene
datosMediaLab_feb
Indentación
Simple
Vectores
# Numericos
num = c(2,4,5,6,7,5)
num## [1] 2 4 5 6 7 5# Logicos
tOf = c(TRUE, FALSE, T,T, F)
tOf## [1] TRUE FALSE TRUE TRUE FALSE# texto (strings)
text = c("a","b","c","d")
text ## [1] "a" "b" "c" "d"# Examinar:
length(text)## [1] 4# Combinar
comb = c(num ,tOf, text)
comb # Numeros a texto ## [1] "2" "4" "5" "6" "7" "5" "TRUE" "FALSE"
## [9] "TRUE" "TRUE" "FALSE" "a" "b" "c" "d"Vectores
Variables
# "<-" asigna un valor a la variable
x <- 3
# "=" tambien asigna un valor a la variable
y = 4
# Operaciones aritmeticas
z = x + y
z## [1] 7w = ((x^2) + (y^2))/z
w## [1] 3.571429Vectores
Indices []
text## [1] "a" "b" "c" "d"text[3]## [1] "c"text[-3]## [1] "a" "b" "d"text[c(1,3)]## [1] "a" "c"text[c(4,3,2,1)]## [1] "d" "c" "b" "a"text[c(1:3)]## [1] "a" "b" "c"tOf## [1] TRUE FALSE TRUE TRUE FALSEtext[tOf]## [1] "a" "c" "d"Vectores
Nombres
nombres = c("Michelle", "Diana", "Gabriel", "Horacio","Pablo")
names(num)## NULLnames(num) = nombres
num## Michelle Diana Gabriel Horacio Pablo <NA>
## 2 4 5 6 7 5names(num) = c(nombres,"Sara")
num## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 5 6 7 5num["Diana"]## Diana
## 4num[c("Diana","Gabriel")]## Diana Gabriel
## 4 5Mas tipos de objetos en R
Matrix
matrix1 = matrix(c(1,2,3,4, 5,6,7,8), nrow = 2,ncol = 4)
matrix1## [,1] [,2] [,3] [,4]
## [1,] 1 3 5 7
## [2,] 2 4 6 8str(matrix1)## num [1:2, 1:4] 1 2 3 4 5 6 7 8matrix2 = matrix(c(11,12,13,14,15,16,17,18), 2 , 4)
matrix2## [,1] [,2] [,3] [,4]
## [1,] 11 13 15 17
## [2,] 12 14 16 18Mas tipos de objetos en R
Unir matrices
# por columna
cbind(matrix1, matrix2)## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
## [1,] 1 3 5 7 11 13 15 17
## [2,] 2 4 6 8 12 14 16 18#por fila
rbind(matrix1, matrix2)## [,1] [,2] [,3] [,4]
## [1,] 1 3 5 7
## [2,] 2 4 6 8
## [3,] 11 13 15 17
## [4,] 12 14 16 18Mas tipos de objetos en R
Lista
lista = list(text, num, tOf)
lista## [[1]]
## [1] "a" "b" "c" "d"
##
## [[2]]
## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 5 6 7 5
##
## [[3]]
## [1] TRUE FALSE TRUE TRUE FALSEMas tipos de objetos en R
Lista
lista[[2]]## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 5 6 7 5lista[[2]][3]## Gabriel
## 5lista[[2]][3] = 4
lista[[2]]## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 4 6 7 5Mas tipos de objetos en R
Lista con nombres (named list)
lista = list("letras" = text, "numeros"= num, "opLogicos" = tOf)
lista## $letras
## [1] "a" "b" "c" "d"
##
## $numeros
## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 5 6 7 5
##
## $opLogicos
## [1] TRUE FALSE TRUE TRUE FALSElista$letras## [1] "a" "b" "c" "d"Mas tipos de objetos en R
Lista con nombres (named list)
lista$letras[2]## [1] "b"lista[c("numeros", "opLogicos")]## $numeros
## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 5 6 7 5
##
## $opLogicos
## [1] TRUE FALSE TRUE TRUE FALSEMas tipos de objetos en R
Data Frame
# Lista de vectores del mismo tamaño
data.frame(text, num, tOf)## Error in data.frame(text, num, tOf): arguments imply differing number of rows: 4, 6, 5# install.packages("datasets")
library(datasets)
str(datasets::beaver1)## 'data.frame': 114 obs. of 4 variables:
## $ day : num 346 346 346 346 346 346 346 346 346 346 ...
## $ time : num 840 850 900 910 920 930 940 950 1000 1010 ...
## $ temp : num 36.3 36.3 36.4 36.4 36.5 ...
## $ activ: num 0 0 0 0 0 0 0 0 0 0 ...data2play = datasets::beaver1
data2play[1]## day
## 1 346
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## 114 347data2play[,1]## [1] 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346
## [18] 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346
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## [86] 346 346 346 346 346 346 347 347 347 347 347 347 347 347 347 347 347
## [103] 347 347 347 347 347 347 347 347 347 347 347 347data2play[1,]## day time temp activ
## 1 346 840 36.33 0data2play$day## [1] 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346
## [18] 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346 346
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## [103] 347 347 347 347 347 347 347 347 347 347 347 347data2play["day"]## day
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## 114 347Importar datos a R
# subir csv file to R.
dataset = read.csv(file = "data/dataset.csv", header = T)
# examinar dataset
head(dataset)
tail(dataset)
str(dataset)Objectos
# Objeto
num## Michelle Diana Gabriel Horacio Pablo Sara
## 2 4 5 6 7 5Funciones
# Funciones
# functionNombre = function(argumentos) {
# codigo operacion ,
# resultado }
sueldoMes = function(lista, sueldo){
saldoFinal = lista + sueldo
return(saldoFinal)
}
sueldoMes(num, 0.14)## Michelle Diana Gabriel Horacio Pablo Sara
## 2.14 4.14 5.14 6.14 7.14 5.14mes1 = c(0.15,0.13,0.16,0.14,0.3,0.23)
sueldoMes(num, mes1)## Michelle Diana Gabriel Horacio Pablo Sara
## 2.15 4.13 5.16 6.14 7.30 5.23loops
mes2 = c()
for ( i in 1:length(num)){
mes2[i] = num[i] + 0.43
names(mes2)[i] = names(num)[i]
}
mes2## Michelle Diana Gabriel Horacio Pablo Sara
## 2.43 4.43 5.43 6.43 7.43 5.43sapply / lapply
# sapply
sapply(num, function(x) x + 0.13)## Michelle Diana Gabriel Horacio Pablo Sara
## 2.13 4.13 5.13 6.13 7.13 5.13# lapply
lapply(num, function(x) x + 0.13)## $Michelle
## [1] 2.13
##
## $Diana
## [1] 4.13
##
## $Gabriel
## [1] 5.13
##
## $Horacio
## [1] 6.13
##
## $Pablo
## [1] 7.13
##
## $Sara
## [1] 5.13Exploración de datos
summary(), dim()
summary(data2play)## day time temp activ
## Min. :346.0 Min. : 0.0 Min. :36.33 Min. :0.00000
## 1st Qu.:346.0 1st Qu.: 932.5 1st Qu.:36.76 1st Qu.:0.00000
## Median :346.0 Median :1415.0 Median :36.87 Median :0.00000
## Mean :346.2 Mean :1312.0 Mean :36.86 Mean :0.05263
## 3rd Qu.:346.0 3rd Qu.:1887.5 3rd Qu.:36.96 3rd Qu.:0.00000
## Max. :347.0 Max. :2350.0 Max. :37.53 Max. :1.00000dim(data2play)## [1] 114 4Exploración de datos
aggregate()
aggregate(time~day, mean, data =data2play)## day time
## 1 346 1601.3187
## 2 347 167.3913aggregate(temp~day, max, data =data2play)## day temp
## 1 346 37.53
## 2 347 37.15aggregate(temp~day, min, data =data2play)## day temp
## 1 346 36.33
## 2 347 36.70Exploración de datos
melt()
meltData =reshape::melt(data2play)## Using as id variablesmeltData## variable value
## 1 day 346.00
## 2 day 346.00
## 3 day 346.00
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## 115 time 840.00
## 116 time 850.00
## 117 time 900.00
## 118 time 910.00
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## 120 time 930.00
## 121 time 940.00
## 122 time 950.00
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## 125 time 1020.00
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## 148 time 1410.00
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## 160 time 1610.00
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## 185 time 2020.00
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## 187 time 2040.00
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## 225 time 310.00
## 226 time 320.00
## 227 time 330.00
## 228 time 340.00
## 229 temp 36.33
## 230 temp 36.34
## 231 temp 36.35
## 232 temp 36.42
## 233 temp 36.55
## 234 temp 36.69
## 235 temp 36.71
## 236 temp 36.75
## 237 temp 36.81
## 238 temp 36.88
## 239 temp 36.89
## 240 temp 36.91
## 241 temp 36.85
## 242 temp 36.89
## 243 temp 36.89
## 244 temp 36.67
## 245 temp 36.50
## 246 temp 36.74
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## 248 temp 36.76
## 249 temp 36.78
## 250 temp 36.82
## 251 temp 36.89
## 252 temp 36.99
## 253 temp 36.92
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## 257 temp 36.92
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## 259 temp 36.91
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## 261 temp 36.77
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## 264 temp 36.54
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## 267 temp 36.69
## 268 temp 36.62
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## 270 temp 36.59
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## 272 temp 36.75
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## 274 temp 36.81
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## 277 temp 36.89
## 278 temp 36.94
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## 280 temp 36.95
## 281 temp 37.00
## 282 temp 37.07
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## 284 temp 37.00
## 285 temp 36.95
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## 287 temp 36.94
## 288 temp 36.88
## 289 temp 36.93
## 290 temp 36.98
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## 295 temp 37.01
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## 299 temp 36.96
## 300 temp 36.84
## 301 temp 36.87
## 302 temp 36.85
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## 304 temp 36.87
## 305 temp 36.89
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## 307 temp 36.91
## 308 temp 37.53
## 309 temp 37.23
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## 311 temp 37.25
## 312 temp 37.20
## 313 temp 37.21
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## 315 temp 37.10
## 316 temp 37.20
## 317 temp 37.18
## 318 temp 36.93
## 319 temp 36.83
## 320 temp 36.93
## 321 temp 36.83
## 322 temp 36.80
## 323 temp 36.75
## 324 temp 36.71
## 325 temp 36.73
## 326 temp 36.75
## 327 temp 36.72
## 328 temp 36.76
## 329 temp 36.70
## 330 temp 36.82
## 331 temp 36.88
## 332 temp 36.94
## 333 temp 36.79
## 334 temp 36.78
## 335 temp 36.80
## 336 temp 36.82
## 337 temp 36.84
## 338 temp 36.86
## 339 temp 36.88
## 340 temp 36.93
## 341 temp 36.97
## 342 temp 37.15
## 343 activ 0.00
## 344 activ 0.00
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## 453 activ 0.00
## 454 activ 0.00
## 455 activ 0.00
## 456 activ 1.00# factores
unique(meltData$variable)## [1] day time temp activ
## Levels: day time temp activVisualización de datos en R
par(mfrow = c(1,2))
plot(activ~temp, data = data2play)
plot(data2play$activ~data2play$time)Visualización de datos en R
Plots base
Histograms
hist(data2play$temp, breaks = 10)
Plots base
Boxplot
data2play2 = datasets::beaver2
boxplot(data2play2$temp, data2play$temp,
xlab = "Castores", ylab = "T (ºc)",
main = "Diferencia de temperatura entre especies de castor")
legend("bottomleft", " T = ªC")Plots base
Boxplot
Plots base
Scatterplot
plot(data2play$temp~data2play$time,
xlab = "Hora del dÃa",
ylab = "Temperatura",
ylim = c(35,39))
points(data2play2$temp~data2play2$time,
pch = 16,
col = "red")
abline(h = mean(data2play$temp))
abline(h = mean(data2play2$temp), col = "red")
legend("bottomleft", c("Species1", "Species2"),
pch = c(1,16), col = c("black", "red"), bty = "n")Plots base
Scatterplot
Colores
Colores
par(las = 1)
col = c("#8da54f", "#bb5542")
plot(data2play$temp~data2play$time,
xlab = "Hora del dÃa",
ylab = "Temperatura",
ylim = c(35,39),
col = col[1],
pch = 16)
points(data2play2$temp~data2play2$time,
pch = 16,
col = col[2])
abline(h = mean(data2play$temp))
abline(h = mean(data2play2$temp), col = "red")
legend("bottomleft", c("Species1", "Species2"),
pch = c(16,16), col = col , bty = "n")
legend("bottomright", c("x_Species1", "x_Species2"),lty = 1,
col = col , bty = "n")Colores
Plots base
- ?plot
- ?legend
- help(abline)
- ?par
Layout
layout(matrix(c(1,2,3,3),2, 2, byrow = T))
par(mar = c(4,4,2,2), las = 1)
boxplot(data2play$temp, data2play2$temp,
xlab = "Castores ",
ylab = "temperatura",
col = col )
hist(data2play2$day, xlim = c(300,360),
xlab = "dia")
hist(data2play$day, add = T)
plot(data2play$temp~data2play$time,
xlab = "Hora del dÃa",
ylab = "Temperatura",
ylim = c(35,39),
col = col[1],
pch = 16)
points(data2play2$temp~data2play2$time,
pch = 16,
col = col[2])
abline(h = mean(data2play$temp))
abline(h = mean(data2play2$temp), col = "red")
legend("bottomleft", c("Species1", "Species2"),
pch = c(16,16), col = col , bty = "n")
legend("bottomright", c("x_Species1", "x_Species2"),lty = 1, col = col , bty = "n")Layout
# Add boxplots to a scatterplot
par(fig=c(0,0.8,0,0.8))
plot(data2play$temp~data2play$time,
xlab = "Hora del dÃa",
ylab = "Temperatura",
ylim = c(35,39),
col = col[1],
pch = 16)
points(data2play2$temp~data2play2$time,
pch = 16,
col = col[2])
abline(h = mean(data2play$temp))
abline(h = mean(data2play2$temp), col = "red")
legend("bottomleft", c("Species1", "Species2"),
pch = c(16,16), col = col , bty = "n")
par(fig=c(0,0.8,0.55,1), new=TRUE)
boxplot(data2play$time, data2play2$time,
col = col ,
yaxt = "n",
axes = F, horizontal = T)
par(fig=c(0.65,1,0,0.8),new=TRUE)
boxplot(data2play$temp, data2play2$temp,
col = col ,
yaxt = "n",
axes = F)
Exportar figuras
res = 200
width = 1500
height = 1200
units = "px"
png(filename = "figs/figura1.png", res = res, width = width, height = height, units = units)
layout(matrix(c(1,2,3,3),2, 2, byrow = T))
par(mar = c(4,4,2,2), las = 1)
boxplot(data2play$temp, data2play2$temp,
xlab = "Castores ",
ylab = "temperatura",
col = col )
hist(data2play2$day, xlim = c(300,360),
xlab = "dia")
hist(data2play$day, add = T)
plot(data2play$temp~data2play$time,
xlab = "Hora del dÃa",
ylab = "Temperatura",
ylim = c(35,39),
col = col[1],
pch = 16)
points(data2play2$temp~data2play2$time,
pch = 16,
col = col[2])
abline(h = mean(data2play$temp))
abline(h = mean(data2play2$temp), col = "red")
legend("bottomleft", c("Species1", "Species2"),
pch = c(16,16), col = col , bty = "n")
legend("bottomright", c("x_Species1", "x_Species2"),lty = 1, col = col , bty = "n")
dev.off()## quartz_off_screen
## 2Exportar figuras
pdf(file = "figs/figure1.pdf",paper = )
# Add boxplots to a scatterplot
par(fig=c(0,0.8,0,0.8))
plot(data2play$temp~data2play$time,
xlab = "Hora del dÃa",
ylab = "Temperatura",
ylim = c(35,39),
col = col[1],
pch = 16)
points(data2play2$temp~data2play2$time,
pch = 16,
col = col[2])
abline(h = mean(data2play$temp))
abline(h = mean(data2play2$temp), col = "red")
legend("bottomleft", c("Species1", "Species2"),
pch = c(16,16), col = col , bty = "n")
par(fig=c(0,0.8,0.55,1), new=TRUE)
boxplot(data2play$time, data2play2$time,
col = col ,
yaxt = "n",
axes = F, horizontal = T)
par(fig=c(0.65,1,0,0.8),new=TRUE)
boxplot(data2play$temp, data2play2$temp,
col = col ,
yaxt = "n",
axes = F)