#agrupamientos -clusters- multivariados
setwd("~/Dropbox/Clases_UPJ/Ecosistemas/2017_1/Alumnos/Salida") # selección directorio de trabajo
campo=read.table("cluster.txt", header=T) # lectura de la base de datos
campo2=transform(campo, temp.amb=scale(temp.amb), luz=scale(luz), ph=scale(ph), humedad.suelo=scale(humedad.suelo), humedad.amb=scale(humedad.amb)) # estandarizar variables
d <- dist(campo2, method = "euclidean") # matriz de distancias
## Warning in dist(campo2, method = "euclidean"): NAs introduced by coercion
fit <- hclust(d, method="ward.D") # genera cluster jerarquico
plot(fit) # dibuja el cluster
#componentes de varianza
campo3=read.table("compilada2.txt", header=T) # lectura de la base de datos
campo4=transform(campo3, temp.amb=scale(temp.amb), luz=scale(luz), ph=scale(ph), humedad.suelo=scale(humedad.suelo), humedad.amb=scale(humedad.amb)) # estandarizar variables
attach(campo4)
library(lme4)
## Loading required package: Matrix
fit4=lmer(temp.amb ~ 1 + (1 | lugar/sitio))
fit7=lmer(luz ~ 1 + (1 | lugar/sitio))
fit8=lmer(ph ~ 1 + (1 | lugar/sitio))
fit9=lmer(humedad.suelo ~ 1 + (1 | lugar/sitio))
fit10=lmer(humedad.amb ~ 1 + (1 | lugar/sitio))
summary(fit4)
## Linear mixed model fit by REML ['lmerMod']
## Formula: temp.amb ~ 1 + (1 | lugar/sitio)
##
## REML criterion at convergence: 292.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.2344 -0.6120 0.0062 0.5538 2.6526
##
## Random effects:
## Groups Name Variance Std.Dev.
## sitio:lugar (Intercept) 0.0000 0.0000
## lugar (Intercept) 0.4821 0.6943
## Residual 0.7606 0.8721
## Number of obs: 112, groups: sitio:lugar, 9; lugar, 2
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) -0.06051 0.49794 -0.122
summary(fit7)
## Linear mixed model fit by REML ['lmerMod']
## Formula: luz ~ 1 + (1 | lugar/sitio)
##
## REML criterion at convergence: 296.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9530 -0.6239 -0.1792 0.5578 3.1629
##
## Random effects:
## Groups Name Variance Std.Dev.
## sitio:lugar (Intercept) 3.180e-01 5.639e-01
## lugar (Intercept) 2.317e-16 1.522e-08
## Residual 7.069e-01 8.408e-01
## Number of obs: 112, groups: sitio:lugar, 9; lugar, 2
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 0.02195 0.20415 0.108
summary(fit8)
## Linear mixed model fit by REML ['lmerMod']
## Formula: ph ~ 1 + (1 | lugar/sitio)
##
## REML criterion at convergence: 306.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.2457 -0.5442 0.0230 0.6291 1.8649
##
## Random effects:
## Groups Name Variance Std.Dev.
## sitio:lugar (Intercept) 2.298e-01 4.793e-01
## lugar (Intercept) 1.154e-14 1.074e-07
## Residual 7.925e-01 8.902e-01
## Number of obs: 112, groups: sitio:lugar, 9; lugar, 2
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) -0.004149 0.180660 -0.023
summary(fit9)
## Linear mixed model fit by REML ['lmerMod']
## Formula: humedad.suelo ~ 1 + (1 | lugar/sitio)
##
## REML criterion at convergence: 247.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.6273 -0.7710 0.1190 0.7197 2.7117
##
## Random effects:
## Groups Name Variance Std.Dev.
## sitio:lugar (Intercept) 0.3851 0.6206
## lugar (Intercept) 0.4562 0.6755
## Residual 0.4281 0.6543
## Number of obs: 112, groups: sitio:lugar, 9; lugar, 2
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 0.04549 0.52464 0.087
summary(fit10)
## Linear mixed model fit by REML ['lmerMod']
## Formula: humedad.amb ~ 1 + (1 | lugar/sitio)
##
## REML criterion at convergence: 315.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -6.8080 -0.4469 0.0283 0.5167 2.4925
##
## Random effects:
## Groups Name Variance Std.Dev.
## sitio:lugar (Intercept) 0.02915 0.1707
## lugar (Intercept) 0.09979 0.3159
## Residual 0.92506 0.9618
## Number of obs: 112, groups: sitio:lugar, 9; lugar, 2
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 0.02285 0.24808 0.092
#diferencias entre lugares
detach(campo4)
attach(campo3)
fit11=t.test(temp.amb~lugar)
fit11
##
## Welch Two Sample t-test
##
## data: temp.amb by lugar
## t = -6.0102, df = 104.27, p-value = 2.757e-08
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -2.811859 -1.416713
## sample estimates:
## mean in group Chingaza mean in group Encenillo
## 16.60000 18.71429
fit14=t.test(luz~lugar)
fit14
##
## Welch Two Sample t-test
##
## data: luz by lugar
## t = 0.95601, df = 92.938, p-value = 0.3415
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -2.104253 6.011147
## sample estimates:
## mean in group Chingaza mean in group Encenillo
## 10.846939 8.893492
fit15=t.test(ph~lugar)
fit15
##
## Welch Two Sample t-test
##
## data: ph by lugar
## t = -1.0126, df = 105.67, p-value = 0.3135
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.26426603 0.08558123
## sample estimates:
## mean in group Chingaza mean in group Encenillo
## 6.383673 6.473016
fit16=t.test(humedad.suelo~lugar)
fit16
##
## Welch Two Sample t-test
##
## data: humedad.suelo by lugar
## t = 6.2518, df = 82.625, p-value = 1.695e-08
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 18.61982 35.99696
## sample estimates:
## mean in group Chingaza mean in group Encenillo
## 69.81633 42.50794
fit17=t.test(humedad.amb~lugar)
fit17
##
## Welch Two Sample t-test
##
## data: humedad.amb by lugar
## t = 2.5046, df = 73.967, p-value = 0.01446
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 0.9891629 8.6870275
## sample estimates:
## mean in group Chingaza mean in group Encenillo
## 73.97143 69.13333