ANÁLISIS DE MALEZAS EN CULTIVO DE CEBADA
Grupo 6, manejos integrados
2023-2S
library(psych)
library(readxl)
library(ggplot2)##
## Attaching package: 'ggplot2'## The following objects are masked from 'package:psych':
##
## %+%, alphalibrary(lattice)
library(tidyverse)## -- Attaching packages --------------------------------------- tidyverse 1.3.1 --## v tibble 3.1.6 v dplyr 1.0.8
## v tidyr 1.2.0 v stringr 1.4.0
## v readr 2.1.2 v forcats 0.5.1
## v purrr 0.3.4## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x ggplot2::%+%() masks psych::%+%()
## x ggplot2::alpha() masks psych::alpha()
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()library(dplyr)
###### Análisis descriptivo numérico ####
######## GRUPO 6 ########
MALEZASDENSI <- read_xlsx("C:\\Users\\andre\\OneDrive\\Escritorio\\MALEZAS PROMG6.xlsx",col_types = c("numeric", "text", "numeric",
"numeric", "numeric"))
attach(MALEZASDENSI)
psych::describe(DENSIDADSUM)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 15.91 22.43 1 12.78 1.48 0 60 60 0.86 -1.06 6.76describe.by(DENSIDADSUM, group = ESPECIES)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 12 NA 12 12 0 12 12 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 14 NA 14 14 0 14 14 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 44 NA 44 44 0 44 44 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 60 NA 60 60 0 60 60 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1 NA 1 1 0 1 1 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 44 NA 44 44 0 44 44 0 NA NA NA(sd22 <- sd(DENSIDADSUM))## [1] 22.42523(mean22 <- mean(DENSIDADSUM))## [1] 15.90909(Coeficientevar <- sd22/mean22)## [1] 1.409586#################
##### MODA #####
library(modeest)## Registered S3 methods overwritten by 'rmutil':
## method from
## plot.residuals psych
## print.response httrmlv(DENSIDADSUM, method = "meanshift") ## [1] 2.62856
## attr(,"iterations")
## [1] 12##### Gráficas de análisis descriptivo densidad ####
ggplot(MALEZASDENSI, aes(x = ESPECIES, y = DENSIDADSUM, fill = ESPECIES)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Densidad de especies grupo 6") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("Número de individuos") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
ggplot(MALEZASDENSI, aes(x = ESPECIES, y = COBERTURAS, fill = ESPECIES)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Cobertura total por especies grupo 6") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("cobertura en 1 m^2") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
DENSIDAD, DOMINANCIA Y FRECUENCIA TOTAL Y POR METRO CUADRADO
DMTOTAL <- read_excel("C:\\Users\\andre\\OneDrive\\Escritorio\\MALEZASGRUPALES.xlsx",
col_types = c("numeric", "text", "numeric",
"numeric", "numeric", "numeric",
"numeric", "numeric", "numeric",
"numeric", "numeric", "numeric"))
attach(DMTOTAL)## The following object is masked from MALEZASDENSI:
##
## MUESTREO# Densidades:
psych::describe(DENSIDADMT)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 151.91 276.71 12 104 14.83 1 734 733 1.29 -0.18 83.43describe.by(DENSIDADMT, group = ESPECIESGL)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1 NA 1 1 0 1 1 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 2 NA 2 2 0 2 2 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 12 NA 12 12 0 12 12 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 5 NA 5 5 0 5 5 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 15 NA 15 15 0 15 15 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 4 NA 4 4 0 4 4 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 14 NA 14 14 0 14 14 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 654 NA 654 654 0 654 654 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 734 NA 734 734 0 734 734 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1 NA 1 1 0 1 1 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 229 NA 229 229 0 229 229 0 NA NA NA# densidad relativa:
psych::describe(DENSIDADRELATIVA)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 9.08 16.56 0.71 6.22 0.89 0.05 43.92 43.87 1.29 -0.18 4.99describe.by(DENSIDADRELATIVA, group = ESPECIESGL)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.05 NA 0.05 0.05 0 0.05 0.05 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.11 NA 0.11 0.11 0 0.11 0.11 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.71 NA 0.71 0.71 0 0.71 0.71 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.29 NA 0.29 0.29 0 0.29 0.29 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.89 NA 0.89 0.89 0 0.89 0.89 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.23 NA 0.23 0.23 0 0.23 0.23 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.83 NA 0.83 0.83 0 0.83 0.83 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 39.13 NA 39.13 39.13 0 39.13 39.13 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 43.92 NA 43.92 43.92 0 43.92 43.92 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.05 NA 0.05 0.05 0 0.05 0.05 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 13.7 NA 13.7 13.7 0 13.7 13.7 0 NA NA NA# frecuencia:
psych::describe(FRECUENCIATOTAL)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 0.22 0.33 0.03 0.15 0 0.03 0.97 0.94 1.29 -0.01 0.1describe.by(FRECUENCIATOTAL, group = ESPECIESGL)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.03 NA 0.03 0.03 0 0.03 0.03 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.06 NA 0.06 0.06 0 0.06 0.06 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.09 NA 0.09 0.09 0 0.09 0.09 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.03 NA 0.03 0.03 0 0.03 0.03 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.03 NA 0.03 0.03 0 0.03 0.03 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.03 NA 0.03 0.03 0 0.03 0.03 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.03 NA 0.03 0.03 0 0.03 0.03 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.72 NA 0.72 0.72 0 0.72 0.72 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.97 NA 0.97 0.97 0 0.97 0.97 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.03 NA 0.03 0.03 0 0.03 0.03 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.37 NA 0.37 0.37 0 0.37 0.37 0 NA NA NA# frecuencia relativa:
psych::describe(FRECUENCIARELATIVA)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 9.08 13.71 1.29 6.49 0 1.29 40.25 38.96 1.28 -0.02 4.13describe.by(FRECUENCIARELATIVA, group = ESPECIESGL)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.29 NA 1.29 1.29 0 1.29 1.29 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 2.59 NA 2.59 2.59 0 2.59 2.59 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 3.89 NA 3.89 3.89 0 3.89 3.89 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.29 NA 1.29 1.29 0 1.29 1.29 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.29 NA 1.29 1.29 0 1.29 1.29 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.29 NA 1.29 1.29 0 1.29 1.29 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.29 NA 1.29 1.29 0 1.29 1.29 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 29.87 NA 29.87 29.87 0 29.87 29.87 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 40.25 NA 40.25 40.25 0 40.25 40.25 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.29 NA 1.29 1.29 0 1.29 1.29 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 15.58 NA 15.58 15.58 0 15.58 15.58 0 NA NA NA# Dominancia:
psych::describe(COBERTURATOTAL)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 89.36 216.1 5 28.78 4.45 0 724 724 2.26 3.78 65.16describe.by(COBERTURATOTAL, group = ESPECIESGL)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 2 NA 2 2 0 2 2 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 11 NA 11 11 0 11 11 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 5 NA 5 5 0 5 5 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 6 NA 6 6 0 6 6 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 5 NA 5 5 0 5 5 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 5 NA 5 5 0 5 5 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 165 NA 165 165 0 165 165 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 724 NA 724 724 0 724 724 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 3.5 NA 3.5 3.5 0 3.5 3.5 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 56.5 NA 56.5 56.5 0 56.5 56.5 0 NA NA NA#Dominancia relativa:
psych::describe(DOMINANCIARELATIVA)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 11 9.09 21.98 0.5 2.93 0.44 0 73.65 73.65 2.26 3.78 6.63describe.by(DOMINANCIARELATIVA, group = ESPECIESGL)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0 NA 0 0 0 0 0 0 NA NA NA
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.2 NA 0.2 0.2 0 0.2 0.2 0 NA NA NA
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 1.12 NA 1.12 1.12 0 1.12 1.12 0 NA NA NA
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.5 NA 0.5 0.5 0 0.5 0.5 0 NA NA NA
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.61 NA 0.61 0.61 0 0.61 0.61 0 NA NA NA
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.5 NA 0.5 0.5 0 0.5 0.5 0 NA NA NA
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.5 NA 0.5 0.5 0 0.5 0.5 0 NA NA NA
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 16.79 NA 16.79 16.79 0 16.79 16.79 0 NA NA NA
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 73.65 NA 73.65 73.65 0 73.65 73.65 0 NA NA NA
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 0.36 NA 0.36 0.36 0 0.36 0.36 0 NA NA NA
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 1 5.75 NA 5.75 5.75 0 5.75 5.75 0 NA NA NA## Resultados gráficos por especie
#Densidad por metro cuadrado de cada especie en los 8 metros cuadrados en total
ggplot(DMTOTAL, aes(x = ESPECIESGL, y = DENSIDADMCUADRADO, fill = ESPECIESGL)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Densidad de especies por metro cuadrado") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("Número de individuos") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
#Densidad relativa de cada especie en los 8 metros cuadrados en total
ggplot(DMTOTAL, aes(x = ESPECIESGL, y = DENSIDADRELATIVA, fill = ESPECIESGL)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Densidad relativa de especies en las 32 muestras") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("Densidad relativa %") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
#Frecuencia relativa de cada especie en los 8 metros cuadrados en total
ggplot(DMTOTAL, aes(x = ESPECIESGL, y = FRECUENCIARELATIVA, fill = ESPECIESGL)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Frecuencia relativa de especies en las 32 muestras") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("frecuencia relativa %") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
#Dominancia relativa de cada especie en los 8 metros cuadrados en total
ggplot(DMTOTAL, aes(x = ESPECIESGL, y = DOMINANCIARELATIVA, fill = ESPECIESGL)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Dominancia relativa de especies en las 32 muestras") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("Dominancia relativa %") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
#Dominancia relativa de cada especie en los 8 metros cuadrados en total
ggplot(DMTOTAL, aes(x = ESPECIESGL, y = IVI, fill = ESPECIESGL)) +
geom_bar(stat = "identity") +
guides(fill = guide_legend(title = "ESPECIES")) +
ggtitle("Indice de valor de importancia") +
theme(panel.border = element_rect(fill = "transparent", color = 4,size = 2)) +
theme(plot.background = element_rect(fill = "gray86")) +
theme(plot.background = element_rect(color = "black", size = 2)) +
xlab("Especies") + ylab("Valor de importancia") +
theme(axis.title.x = element_text(size = 13, color = "black")) + theme(axis.title.y = element_text(size = 13, color = "black")) + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
Análisis por cada especie y muestra de cada grupo
\[Ho={\mu1... =\mu11 }\] \[H1={\mu1... \neq \mu11 }\]
muestras <- read_excel("C:\\Users\\andre\\OneDrive\\Escritorio\\mALEZAS.xlsx",
col_types = c("numeric", "numeric", "numeric",
"text", "numeric", "numeric", "numeric"))
attach(muestras)## The following object is masked from DMTOTAL:
##
## MUESTREO## The following objects are masked from MALEZASDENSI:
##
## FRECUENCIA, MUESTREO# Análisis de densidad de cada grupo
psych::describe(DENSIDAD)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 352 4.74 15.32 0 0.92 0 0 147 147 5.37 36.64 0.82describe.by(DENSIDAD, group = GRUPO)## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: 1
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 3.89 11.52 0 0.83 0 0 64 64 3.81 15.32 1.74
## ------------------------------------------------------------
## group: 2
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 2.27 6.1 0 0.58 0 0 26 26 2.84 7.3 0.92
## ------------------------------------------------------------
## group: 3
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 5.57 14.69 0 2 0 0 78 78 3.48 12.78 2.22
## ------------------------------------------------------------
## group: 4
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 9.02 30.21 0 0.89 0 0 147 147 3.69 12.85 4.55
## ------------------------------------------------------------
## group: 5
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 2.43 7.08 0 0.42 0 0 30 30 3.04 8.13 1.07
## ------------------------------------------------------------
## group: 6
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 3.98 9.16 0 1.56 0 0 35 35 2.24 3.74 1.38
## ------------------------------------------------------------
## group: 7
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 7 18.44 0 1.61 0 0 76 76 2.65 5.76 2.78
## ------------------------------------------------------------
## group: 8
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 44 3.75 10.23 0 1.08 0 0 46 46 2.91 8.01 1.54#Análisis de densidad de cada especie
psych::describe(DENSIDAD)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 352 4.74 15.32 0 0.92 0 0 147 147 5.37 36.64 0.82describe.by(DENSIDAD, group = ESPECIE) ## Warning: describe.by is deprecated. Please use the describeBy function##
## Descriptive statistics by group
## group: Amaranthaceae
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.03 0.18 0 0 0 0 1 1 5.14 25.18 0.03
## ------------------------------------------------------------
## group: Cotula australis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.06 0.25 0 0 0 0 1 1 3.45 10.2 0.04
## ------------------------------------------------------------
## group: fumaria capreolata
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.38 1.36 0 0 0 0 6 6 3.41 10.26 0.24
## ------------------------------------------------------------
## group: Lepidium
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.16 0.88 0 0 0 0 5 5 5.14 25.18 0.16
## ------------------------------------------------------------
## group: Lolium multiflorum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.47 2.65 0 0 0 0 15 15 5.14 25.18 0.47
## ------------------------------------------------------------
## group: Oxalis
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.12 0.71 0 0 0 0 4 4 5.14 25.18 0.12
## ------------------------------------------------------------
## group: Poace sp
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.44 2.47 0 0 0 0 14 14 5.14 25.18 0.44
## ------------------------------------------------------------
## group: Polygonum segetum
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 20.44 35.67 5.5 11.5 8.15 0 147 147 2.4 5.04 6.31
## ------------------------------------------------------------
## group: Raphanus
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 22.84 18.48 16 21.12 17.05 0 64 64 0.76 -0.55 3.27
## ------------------------------------------------------------
## group: Rumex
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 0.03 0.18 0 0 0 0 1 1 5.14 25.18 0.03
## ------------------------------------------------------------
## group: Veronica
## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 32 7.16 16.09 0 2.96 0 0 76 76 2.87 8.4 2.85#análisis de cada especie por grupo
psych::describe(GRUPO)## vars n mean sd median trimmed mad min max range skew kurtosis se
## X1 1 352 4.5 2.29 4.5 4.5 2.97 1 8 7 0 -1.25 0.12#mAnálisis de varianza de la densidad.
mod01 <- aov(DENSIDAD~ESPECIE)
anova(mod01)## Analysis of Variance Table
##
## Response: DENSIDAD
## Df Sum Sq Mean Sq F value Pr(>F)
## ESPECIE 10 23819 2381.88 13.87 < 2.2e-16 ***
## Residuals 341 58559 171.73
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1mod02 <- aov(DENSIDAD~GRUPO+ESPECIE)
anova(mod02)## Analysis of Variance Table
##
## Response: DENSIDAD
## Df Sum Sq Mean Sq F value Pr(>F)
## GRUPO 1 34 33.55 0.1949 0.6591
## ESPECIE 10 23819 2381.88 13.8373 <2e-16 ***
## Residuals 340 58526 172.13
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1ggplot(data = muestras, aes(x = ESPECIE, y = DENSIDAD)) +
geom_jitter(aes(color = ESPECIE), size = 1, alpha = 0.7) +
geom_boxplot(aes(color = ESPECIE), alpha = 0.7) +
xlab('Especie') + stat_summary(fun.y = mean)+
ylab('Densidad') +
ggtitle('Densidad de las especies con la media') +
theme_minimal() + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))## Warning: `fun.y` is deprecated. Use `fun` instead.## Warning: Removed 1 rows containing non-finite values (stat_boxplot).## Warning: Removed 1 rows containing non-finite values (stat_summary).## Warning: Removed 1 rows containing missing values (geom_point).## Warning: Removed 11 rows containing missing values (geom_segment).
class(muestras)## [1] "tbl_df" "tbl" "data.frame"rapha <- filter(muestras, ESPECIE == "Raphanus")
raphan <- muestras %>%
filter(ESPECIE == "Raphanus")
## Indices de diversidad
library(abdiv)##
## Attaching package: 'abdiv'## The following objects are masked from 'package:psych':
##
## manhattan, minkowski, shannonlibrary(vegan)## Loading required package: permute## This is vegan 2.6-4library(codyn)
library(divo)## Loading required package: clusterlibrary(fossil)## Loading required package: sp## Loading required package: maps##
## Attaching package: 'maps'## The following object is masked from 'package:cluster':
##
## votes.repub## The following object is masked from 'package:purrr':
##
## map## Loading required package: shapefiles## Loading required package: foreign##
## Attaching package: 'shapefiles'## The following objects are masked from 'package:foreign':
##
## read.dbf, write.dbf## The following object is masked from 'package:divo':
##
## dp##
## Attaching package: 'fossil'## The following objects are masked from 'package:abdiv':
##
## euclidean, jaccard, manhattan, simpson, sorenson## The following object is masked from 'package:psych':
##
## manhattan#Índice de Shannon
diversity(DMTOTAL$DENSIDADMT, index = "shannon")## [1] 1.16747#Índice de Simpson
diversity(DMTOTAL$DENSIDADRELATIVA, index = "simpson")## [1] 0.6343469#Índice de Pielou
pielou_e(DMTOTAL$DENSIDADRELATIVA)## [1] 0.485396#Índice de Margalef
margalef(DMTOTAL$DENSIDADRELATIVA)## [1] 2.171897soronsen <- li(DMTOTAL, CI = 0.95, resample = 100, graph = FALSE, csv_output = FALSE,
PlugIn = FALSE, size = 1, saveBootstrap = FALSE)## Warning in li(DMTOTAL, CI = 0.95, resample = 100, graph = FALSE, csv_output =
## FALSE, : NAs introducidos por coerciónsoronsen## $Mean
## MUESTREO ESPECIESGL DENSIDADMT DENSIDADRELATIVA
## MUESTREO 1.0000000 0.0000000 0.0000000 0.0000000
## ESPECIESGL 1.0000000 1.0000000 0.0000000 0.0000000
## DENSIDADMT 1.0000000 1.0000000 1.0000000 0.0000000
## DENSIDADRELATIVA 0.4285714 0.4285714 0.4285714 1.0000000
## FRECUENCIATOTAL 0.0000000 0.0000000 0.0000000 0.0000000
## FRECUENCIARELATIVA 1.0000000 1.0000000 1.0000000 0.4285714
## COBERTURATOTAL 0.9523810 0.9523810 0.9523810 0.4615385
## DOMINANCIARELATIVA 0.5333333 0.5333333 0.5333333 0.8571429
## DENSIDADPROMT 0.4285714 0.4285714 0.4285714 1.0000000
## COBERTURAPROMT 0.4285714 0.4285714 0.4285714 1.0000000
## DENSIDADMCUADRADO 0.7058824 0.7058824 0.7058824 0.6666667
## IVI 1.0000000 1.0000000 1.0000000 0.4285714
## FRECUENCIATOTAL FRECUENCIARELATIVA COBERTURATOTAL
## MUESTREO 0 0.0000000 0.0000000
## ESPECIESGL 0 0.0000000 0.0000000
## DENSIDADMT 0 0.0000000 0.0000000
## DENSIDADRELATIVA 0 0.0000000 0.0000000
## FRECUENCIATOTAL 1 0.0000000 0.0000000
## FRECUENCIARELATIVA 0 1.0000000 0.0000000
## COBERTURATOTAL 0 0.9523810 1.0000000
## DOMINANCIARELATIVA 0 0.5333333 0.5714286
## DENSIDADPROMT 0 0.4285714 0.4615385
## COBERTURAPROMT 0 0.4285714 0.4615385
## DENSIDADMCUADRADO 0 0.7058824 0.7500000
## IVI 0 1.0000000 0.9523810
## DOMINANCIARELATIVA DENSIDADPROMT COBERTURAPROMT
## MUESTREO 0.0000000 0.0000000 0.0000000
## ESPECIESGL 0.0000000 0.0000000 0.0000000
## DENSIDADMT 0.0000000 0.0000000 0.0000000
## DENSIDADRELATIVA 0.0000000 0.0000000 0.0000000
## FRECUENCIATOTAL 0.0000000 0.0000000 0.0000000
## FRECUENCIARELATIVA 0.0000000 0.0000000 0.0000000
## COBERTURATOTAL 0.0000000 0.0000000 0.0000000
## DOMINANCIARELATIVA 1.0000000 0.0000000 0.0000000
## DENSIDADPROMT 0.8571429 1.0000000 0.0000000
## COBERTURAPROMT 0.8571429 1.0000000 1.0000000
## DENSIDADMCUADRADO 0.8000000 0.6666667 0.6666667
## IVI 0.5333333 0.4285714 0.4285714
## DENSIDADMCUADRADO IVI
## MUESTREO 0.0000000 0
## ESPECIESGL 0.0000000 0
## DENSIDADMT 0.0000000 0
## DENSIDADRELATIVA 0.0000000 0
## FRECUENCIATOTAL 0.0000000 0
## FRECUENCIARELATIVA 0.0000000 0
## COBERTURATOTAL 0.0000000 0
## DOMINANCIARELATIVA 0.0000000 0
## DENSIDADPROMT 0.0000000 0
## COBERTURAPROMT 0.0000000 0
## DENSIDADMCUADRADO 1.0000000 0
## IVI 0.7058824 1
##
## $Lower.Quantile
## MUESTREO ESPECIESGL DENSIDADMT DENSIDADRELATIVA
## MUESTREO 1.0000000 0.0000000 0.0000000 0.0000000
## ESPECIESGL 1.0000000 1.0000000 0.0000000 0.0000000
## DENSIDADMT 1.0000000 1.0000000 1.0000000 0.0000000
## DENSIDADRELATIVA 0.4285714 0.4285714 0.4285714 1.0000000
## FRECUENCIATOTAL 0.0000000 0.0000000 0.0000000 0.0000000
## FRECUENCIARELATIVA 1.0000000 1.0000000 1.0000000 0.4285714
## COBERTURATOTAL 0.9523810 0.9523810 0.9523810 0.4615385
## DOMINANCIARELATIVA 0.5333333 0.5333333 0.5333333 0.8571429
## DENSIDADPROMT 0.4285714 0.4285714 0.4285714 1.0000000
## COBERTURAPROMT 0.4285714 0.4285714 0.4285714 1.0000000
## DENSIDADMCUADRADO 0.7058824 0.7058824 0.7058824 0.6666667
## IVI 1.0000000 1.0000000 1.0000000 0.4285714
## FRECUENCIATOTAL FRECUENCIARELATIVA COBERTURATOTAL
## MUESTREO 0 0.0000000 0.0000000
## ESPECIESGL 0 0.0000000 0.0000000
## DENSIDADMT 0 0.0000000 0.0000000
## DENSIDADRELATIVA 0 0.0000000 0.0000000
## FRECUENCIATOTAL 1 0.0000000 0.0000000
## FRECUENCIARELATIVA 0 1.0000000 0.0000000
## COBERTURATOTAL 0 0.9523810 1.0000000
## DOMINANCIARELATIVA 0 0.5333333 0.5714286
## DENSIDADPROMT 0 0.4285714 0.4615385
## COBERTURAPROMT 0 0.4285714 0.4615385
## DENSIDADMCUADRADO 0 0.7058824 0.7500000
## IVI 0 1.0000000 0.9523810
## DOMINANCIARELATIVA DENSIDADPROMT COBERTURAPROMT
## MUESTREO 0.0000000 0.0000000 0.0000000
## ESPECIESGL 0.0000000 0.0000000 0.0000000
## DENSIDADMT 0.0000000 0.0000000 0.0000000
## DENSIDADRELATIVA 0.0000000 0.0000000 0.0000000
## FRECUENCIATOTAL 0.0000000 0.0000000 0.0000000
## FRECUENCIARELATIVA 0.0000000 0.0000000 0.0000000
## COBERTURATOTAL 0.0000000 0.0000000 0.0000000
## DOMINANCIARELATIVA 1.0000000 0.0000000 0.0000000
## DENSIDADPROMT 0.8571429 1.0000000 0.0000000
## COBERTURAPROMT 0.8571429 1.0000000 1.0000000
## DENSIDADMCUADRADO 0.8000000 0.6666667 0.6666667
## IVI 0.5333333 0.4285714 0.4285714
## DENSIDADMCUADRADO IVI
## MUESTREO 0.0000000 0
## ESPECIESGL 0.0000000 0
## DENSIDADMT 0.0000000 0
## DENSIDADRELATIVA 0.0000000 0
## FRECUENCIATOTAL 0.0000000 0
## FRECUENCIARELATIVA 0.0000000 0
## COBERTURATOTAL 0.0000000 0
## DOMINANCIARELATIVA 0.0000000 0
## DENSIDADPROMT 0.0000000 0
## COBERTURAPROMT 0.0000000 0
## DENSIDADMCUADRADO 1.0000000 0
## IVI 0.7058824 1
##
## $Upper.Quantile
## MUESTREO ESPECIESGL DENSIDADMT DENSIDADRELATIVA
## MUESTREO 1.0000000 0.0000000 0.0000000 0.0000000
## ESPECIESGL 1.0000000 1.0000000 0.0000000 0.0000000
## DENSIDADMT 1.0000000 1.0000000 1.0000000 0.0000000
## DENSIDADRELATIVA 0.4285714 0.4285714 0.4285714 1.0000000
## FRECUENCIATOTAL 0.0000000 0.0000000 0.0000000 0.0000000
## FRECUENCIARELATIVA 1.0000000 1.0000000 1.0000000 0.4285714
## COBERTURATOTAL 0.9523810 0.9523810 0.9523810 0.4615385
## DOMINANCIARELATIVA 0.5333333 0.5333333 0.5333333 0.8571429
## DENSIDADPROMT 0.4285714 0.4285714 0.4285714 1.0000000
## COBERTURAPROMT 0.4285714 0.4285714 0.4285714 1.0000000
## DENSIDADMCUADRADO 0.7058824 0.7058824 0.7058824 0.6666667
## IVI 1.0000000 1.0000000 1.0000000 0.4285714
## FRECUENCIATOTAL FRECUENCIARELATIVA COBERTURATOTAL
## MUESTREO 0 0.0000000 0.0000000
## ESPECIESGL 0 0.0000000 0.0000000
## DENSIDADMT 0 0.0000000 0.0000000
## DENSIDADRELATIVA 0 0.0000000 0.0000000
## FRECUENCIATOTAL 1 0.0000000 0.0000000
## FRECUENCIARELATIVA 0 1.0000000 0.0000000
## COBERTURATOTAL 0 0.9523810 1.0000000
## DOMINANCIARELATIVA 0 0.5333333 0.5714286
## DENSIDADPROMT 0 0.4285714 0.4615385
## COBERTURAPROMT 0 0.4285714 0.4615385
## DENSIDADMCUADRADO 0 0.7058824 0.7500000
## IVI 0 1.0000000 0.9523810
## DOMINANCIARELATIVA DENSIDADPROMT COBERTURAPROMT
## MUESTREO 0.0000000 0.0000000 0.0000000
## ESPECIESGL 0.0000000 0.0000000 0.0000000
## DENSIDADMT 0.0000000 0.0000000 0.0000000
## DENSIDADRELATIVA 0.0000000 0.0000000 0.0000000
## FRECUENCIATOTAL 0.0000000 0.0000000 0.0000000
## FRECUENCIARELATIVA 0.0000000 0.0000000 0.0000000
## COBERTURATOTAL 0.0000000 0.0000000 0.0000000
## DOMINANCIARELATIVA 1.0000000 0.0000000 0.0000000
## DENSIDADPROMT 0.8571429 1.0000000 0.0000000
## COBERTURAPROMT 0.8571429 1.0000000 1.0000000
## DENSIDADMCUADRADO 0.8000000 0.6666667 0.6666667
## IVI 0.5333333 0.4285714 0.4285714
## DENSIDADMCUADRADO IVI
## MUESTREO 0.0000000 0
## ESPECIESGL 0.0000000 0
## DENSIDADMT 0.0000000 0
## DENSIDADRELATIVA 0.0000000 0
## FRECUENCIATOTAL 0.0000000 0
## FRECUENCIARELATIVA 0.0000000 0
## COBERTURATOTAL 0.0000000 0
## DOMINANCIARELATIVA 0.0000000 0
## DENSIDADPROMT 0.0000000 0
## COBERTURAPROMT 0.0000000 0
## DENSIDADMCUADRADO 1.0000000 0
## IVI 0.7058824 1vegdist(DMTOTAL$DENSIDADRELATIVA, method = "jaccard", diag = F)## 1 2 3 4 5 6 7
## 2 0.10906193
## 3 0.64988500 0.68806922
## 4 0.99258881 0.99339709 0.97883212
## 5 0.97878865 0.98110200 0.93941606 0.65060241
## 6 0.99872221 0.99886157 0.99635036 0.82758621 0.93975904
## 7 0.99718886 0.99749545 0.99197080 0.62068966 0.86746988 0.54545455
## 8 0.97725530 0.97973588 0.93503650 0.67415730 0.06741573 0.94382022 0.87640449
## 9 0.99872221 0.99886157 0.99635036 0.82758621 0.93975904 0.00000000 0.54545455
## 10 0.98185535 0.98383424 0.94817518 0.59154930 0.14457831 0.92957746 0.84507042
## 11 0.99412216 0.99476321 0.98321168 0.20689655 0.72289157 0.78260870 0.52173913
## 8 9 10
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9 0.94382022
## 10 0.20224719 0.92957746
## 11 0.74157303 0.78260870 0.67605634