Data analysis of 5-square - Vietnam 2023

Data Analysis of 5-square - Vietnam 2023

Introduction

The 5-square study from Vietnam-2023 comprises 386 observations collected across 2 provinces: Sơn La and Lao Cai. A total of 193 males and females were both assessed in this study.

Analysis of 5-square for Bananas

Upset diagram of 5-square study for Bananas

Table of varieties for each square and intersections for Bananas

Upset diagram of 5-square study grouped by gender for Bananas

Table of varieties for each square and intersections by gender for Bananas

Varietal uniqueness by village

Table of varietal uniqueness by village

Upset diagram of 5-square study grouped by province for Bananas

Table of varieties for each square and intersections by province for Bananas

Upset diagram of 5-square study grouped by district for Bananas

Table of varieties for each square and intersections by district for Bananas

Varietal richness and eveness of 5-square for Bananas

Shanon index of 5-square

province	shannon_index
Lao Cai	2.343933
Sơn La	2.767535

ggpubr::ggdotchart(tbl_shanon, x = "province", y = "shannon_index", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Shannon index")

Pielou index for evenness

library(plyr)
tbl_pileu_adm3 <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
         data.frame(Pielou=diversity(x[-1], index="simpson")/log(sum(x[-1]>0))) })
flextable(tbl_pileu_adm3)

province	Pielou
Lao Cai	0.3751849
Sơn La	0.3219677

ggpubr::ggdotchart(tbl_pileu_adm3, x = "province", y = "Pielou", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Pielou index of evenness")

Analysis of 5-square for Taro

Varietal richness and eveness of 5-square for Taro

library(plyr)
tbl_shanon <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
                        data.frame(shannon_index=diversity(x[-1], index="shannon"))
 })
flextable(tbl_shanon)

province	shannon_index
Lao Cai	2.985631
Sơn La	2.384226

ggpubr::ggdotchart(tbl_shanon, x = "province", y = "shannon_index", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Shannon index")

library(plyr)
tbl_pileu_adm3 <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
         data.frame(Pielou=diversity(x[-1], index="simpson")/log(sum(x[-1]>0))) })
flextable(tbl_pileu_adm3)

province	Pielou
Lao Cai	0.3108627
Sơn La	0.3486914

ggpubr::ggdotchart(tbl_pileu_adm3, x = "province", y = "Pielou", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Pielou index of evenness")

Upset diagram of 5-square study for Taro

Table of varieties for each square and intersections for Taro

Varietal uniqueness by village

Table of varietal uniqueness by village

Upset diagram of 5-square study grouped by gender for Taro

Table of varieties for each square and intersections by gender for Taro

Upset diagram of 5-square study grouped by province for Taro

Table of varieties for each square and intersections by province for Taro

Upset diagram of 5-square study grouped by district for Taro

Table of varieties for each square and intersections by district for Taro

Varietal richness and eveness of 5-square for Taro

library(plyr)
tbl_shanon <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
                        data.frame(shannon_index=diversity(x[-1], index="shannon"))
 })
flextable(tbl_shanon)

province	shannon_index
Lao Cai	2.985631
Sơn La	2.384226

ggpubr::ggdotchart(tbl_shanon, x = "province", y = "shannon_index", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Shannon index")

library(plyr)
tbl_pileu_adm3 <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
         data.frame(Pielou=diversity(x[-1], index="simpson")/log(sum(x[-1]>0))) })
flextable(tbl_pileu_adm3)

province	Pielou
Lao Cai	0.3108627
Sơn La	0.3486914

ggpubr::ggdotchart(tbl_pileu_adm3, x = "province", y = "Pielou", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Pielou index of evenness")

Analysis of 5-square for Pumpkin

Upset diagram of 5-square study for Pumpkins

Table of varieties for each square and intersections for Pumpkin

Varietal uniqueness by village

Table of varietal uniqueness by village

Upset diagram of 5-square study grouped by gender for Pumpkin

Table of varieties for each square and intersections by gender for Pumpkin

Upset diagram of 5-square study grouped by province for Pumpkin

Table of varieties for each square and intersections by province for Pumpkin

Upset diagram of 5-square study grouped by district for Pumpkin

Table of varieties for each square and intersections by district for Pumpkin

Varietal richness and eveness of 5-square for Pumpkin

province	shannon_index
Lao Cai	2.659323
Sơn La	3.018161

province	Pielou
Lao Cai	0.3419161
Sơn La	0.3017087

ggpubr::ggdotchart(tbl_pileu_adm3, x = "province", y = "Pielou", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Pielou index of evenness")

Analysis of 5-square for Mustard

Upset diagram of 5-square study for Mustard

Table of varieties for each square and intersections for Mustard

Varietal uniqueness by village

Table of varietal uniqueness by province

Upset diagram of 5-square study grouped by gender for Mustard

Table of varieties for each square and intersections by gender for Mustard

Upset diagram of 5-square study grouped by province for Mustard

Table of varieties for each square and intersections by province for Pumpkin

Upset diagram of 5-square study grouped by district for Mustard

Table of varieties for each square and intersections by district for Pumpkin

Varietal richness and eveness of 5-square for Mustard

library(plyr)
tbl_shanon <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
                        data.frame(shannon_index=diversity(x[-1], index="shannon"))
 })
flextable(tbl_shanon)

province	shannon_index
Lao Cai	2.775976
Sơn La	2.687639

ggpubr::ggdotchart(tbl_shanon, x = "province", y = "shannon_index", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Shannon index")

library(plyr)
tbl_pileu_adm3 <-  ddply(tbl_freq_varie_adm3,~province,function(x) {
         data.frame(Pielou=diversity(x[-1], index="simpson")/log(sum(x[-1]>0))) })
flextable(tbl_pileu_adm3)

province	Pielou
Lao Cai	0.3296202
Sơn La	0.3436257

ggpubr::ggdotchart(tbl_pileu_adm3, x = "province", y = "Pielou", color="province", dot.size = 5, y.text.col=TRUE, rotate=TRUE,  ggtheme = theme_pubr(), palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
                   sorting = "descending" ) + theme_cleveland()  + xlab("Pielou index of evenness")