Y_UTM=data.site$Y_UTM,
zone_UTM=data.site$zone_UTM,
sampling_start_month = data.site$sampling_start_month,
sampling_end_month = data.site$sampling_end_month,
sampling_year = data.site$sampling_year,
field_size = data.site$field_size,
yield=data.site$yield,
yield_units=data.site$yield_units,
yield2=data.site$yield2,
yield2_units=data.site$yield2_units,
yield_treatments_no_pollinators=data.site$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site$fruits_per_plant,
fruit_weight= data.site$fruit_weight,
plant_density=data.site$plant_density,
seeds_per_fruit=data.site$seeds_per_fruit,
seeds_per_plant=data.site$seeds_per_plant,
seed_weight=data.site$seed_weight,
observed_pollinator_richness=data.site$observed_pollinator_richness,
other_pollinator_richness=data.site$other_pollinator_richness,
other_richness_estimator_method=data.site$other_richness_estimator_method,
richness_restriction = data.site$richness_restriction,
abundance = data.site$total,
ab_honeybee = data.site$honeybees,
ab_bombus = data.site$bumblebees,
ab_wildbees = data.site$other_wild_bees,
ab_syrphids = data.site$syrphids,
ab_humbleflies= data.site$humbleflies,
ab_other_flies= data.site$other_flies,
ab_beetles=data.site$beetles,
ab_lepidoptera=data.site$lepidoptera,
ab_nonbee_hymenoptera=data.site$non_bee_hymenoptera,
ab_others = data.site$other,
total_sampled_area = data.site$area,
total_sampled_time = data.site$time,
visitation_rate_units = NA,
visitation_rate = NA,
visit_honeybee = NA,
visit_bombus = NA,
visit_wildbees = NA,
visit_syrphids = NA,
visit_humbleflies = NA,
visit_other_flies = NA,
visit_beetles = NA,
visit_lepidoptera = NA,
visit_nonbee_hymenoptera = NA,
visit_others = NA,
Publication = data.site$Publication,
Credit = data.site$Credit,
Email_contact = data.site$Email_contact
)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
# load libraries
library(tidyverse)
library("iNEXT")
library(readxl)
library(openxlsx)
dir_ini <- getwd()
data.transects <- read_excel("05 BW data all OBServ.xls", sheet = "Transects") %>%
filter(is.na(Notes),!is.na(Species))
data.transects <- as_tibble(data.transects)
time.sampling <- data.transects %>%
select(Field,Series,Transect) %>% unique() %>%
group_by(Field,Series) %>% count() %>% mutate(time=30*n) #Each transect takes 30 min.
# Species abundance obtain from transect counts
data.transects_ag <- data.transects %>%
group_by(Field,Series,Species) %>% count(wt=`No ind.`) %>% filter(!is.na(Species))
data.transects$month_of_sampling <- NA
for (i in 1:nrow(data.transects)){
x <- as.character(data.transects$Date[i])
month <- unlist(strsplit(x, ""))[5:6]
data.transects$month_of_sampling[i] <- as.numeric(paste0(month[1],month[2]))
}
data.site_aux <- read_excel("05 BW data all OBServ.xls", sheet = "Resume_crop_yield")
data.site_aux <- as_tibble(data.site_aux)
data.site_aux <- data.site_aux %>% rename(site_id=Field,plant_density=`no. plants/ha`,seeds_per_plant=`No. seeds/plant`,
seeds_ha = `no. seeds`,yield = `yield in kg/ha`) %>%
mutate(plant_density=plant_density/10000,seed_weight=1000*100*yield/seeds_ha)
data.site <- data.site_aux %>% select(site_id,plant_density,seeds_per_plant,yield) %>%
group_by(site_id) %>% summarise_all(mean,rm.na=T)
# Fix yield values for	Kolonia Branewska and Wólka Ratajska
data.site$yield[c(4,6)] <- NA
data.site$study_id <-  "Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005"
data.site$crop <-  "Fagopyrum esculentum"
data.site$variety <-  NA
data.site$management <-  "conventional" #extracted from RADER
data.site$country <-  "Poland"
data.site$latitude <-  NA
data.site$longitude <-  NA
data.site$X_UTM <- NA
data.site$Y_UTM <- NA
data.site$zone_UTM <- NA
data.site$sampling_start_month <-  NA
data.site$sampling_end_month <-  NA
data.site$sampling_year <-  2005
data.site$field_size <-  NA
data.site$yield_units <-  "kg/ha"
data.site$yield2 <-  NA
data.site$yield2_units <-  NA
data.site$yield_treatments_no_pollinators <-  NA
data.site$yield_treatments_pollen_supplement <- NA
data.site$yield_treatments_no_pollinators2 <-  NA
data.site$yield_treatments_pollen_supplement2 <- NA
data.site$fruits_per_plant <-  NA
data.site$fruit_weight <-   NA
data.site$seeds_per_fruit <-  NA
data.site$seed_weight <-  NA
data.site$Publication <- "10.1016/j.agee.2009.05.001"
data.site$Credit  <- "Hajnalka Szentgyorgyi"
data.site$Email_contact <- "hajnalka.szentgyorgyi@gmail.com"
sites <- unique(data.site$site_id)
sites == unique(data.transects$Field)
data.transects$Field[data.transects$Field=="Kolonia Branewka"] <- "Kolonia Branewska"
for (i in sites){
data.site$sampling_start_month[data.site$site_id==i] <-
data.transects %>% filter(Field==i) %>%
select(month_of_sampling) %>% filter(!is.na(month_of_sampling)) %>% min()
data.site$sampling_end_month[data.site$site_id==i] <-
data.transects %>% filter(Field==i) %>%
select(month_of_sampling) %>% filter(!is.na(month_of_sampling)) %>% max()
}
data_raw_obs <- data.transects_ag %>% ungroup %>%  rename(Organism_ID=Species,round=Series)
gild_list_raw <- read_csv("C:/Users/USUARIO/Desktop/OBservData/Thesaurus_Pollinators/Table_organism_guild_META.csv")
gild_list <- gild_list_raw %>% select(-Family) %>% unique()
list_organisms <- select(data_raw_obs,Organism_ID) %>% unique() %>% filter(!is.na(Organism_ID))
list_organisms_guild <- list_organisms %>% left_join(gild_list,by=c("Organism_ID"))
#Check NA's in guild
list_organisms_guild %>% filter(is.na(Guild)) %>% group_by(Organism_ID) %>% count()
list_organisms_guild$Guild[grepl("Andrena",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Anthophora",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Apidae",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Atylotus rusticus",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Dasypoda",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Eristalis",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "syrphids"
list_organisms_guild$Guild[grepl("Evylaeus",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Gymnosoma",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Haemmatopota plurails",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Helophillus",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "syrphids"
list_organisms_guild$Guild[grepl("Hylaeus",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Rhagio",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Scathophaga",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Specodes",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild$Guild[grepl("Systoechus ctenopterus",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "humbleflies"
list_organisms_guild$Guild[grepl("Tabanus bovine",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Talmerus atricapillus",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild$Guild[grepl("Volucella pelluceris",list_organisms_guild$Organism_ID,ignore.case = FALSE)] <- "syrphids"
#Sanity Checks
list_organisms_guild %>% filter(is.na(Guild)) %>% group_by(Organism_ID) %>% count()
#Add guild to observations
data_obs_guild <- data_raw_obs %>% left_join(list_organisms_guild, by = "Organism_ID")
sampling <- time.sampling %>% rename(site_id=Field,round=Series) %>%
mutate(area=n*150*4) %>% select(site_id,round,time,area) %>% unique() %>% ungroup() %>%
select(-round) %>% group_by(site_id) %>% summarise_all(sum)
data_obs_guild  <- data_obs_guild  %>% rename(site_id=Field,abundance=n) %>%
left_join(sampling,by="site_id")
insect_sampling <- tibble(
study_id = "Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005",
site_id = data_obs_guild$site_id,
pollinator = data_obs_guild$Organism_ID,
guild = data_obs_guild$Guild,
sampling_method = "transects",
abundance = data_obs_guild$abundance,
total_sampled_area = data_obs_guild$area,
total_sampled_time =  data_obs_guild$time,
total_sampled_flowers = NA,
Description = "In each site, two sets of pan traps were placed and a 150 m-long (4-m wide) standardized transect line was set (observer walked this line in 30 min). Four rounds of bee sampling using both methods were conducted during the main flowering period for each crop from May to August 2005")
data_raw_obs_pa <- read_excel("05 BW data all OBServ.xls", sheet = "Pantraps") %>%
filter(is.na(Uwagi)) %>% mutate(`hour of collection`=as.numeric(`hour of collection`),
hour=`hour of collection`-`hour of exposure`) %>%
select(Field,series,Species,`No. ind.`,hour) %>%
rename(Organism_ID=Species,round=series,abundance=`No. ind.`) %>%
filter(!is.na(Organism_ID))
# fix hour for Wólka Ratajska
data_raw_obs_pa$hour[data_raw_obs_pa$Field=="Wólka Ratajska" & is.na(data_raw_obs_pa$hour) ] <- 0
gild_list_raw <- read_csv("C:/Users/USUARIO/Desktop/OBservData/Thesaurus_Pollinators/Table_organism_guild_META.csv")
gild_list <- gild_list_raw %>% select(-Family) %>% unique()
list_organisms_pa <- select(data_raw_obs_pa,Organism_ID) %>% unique() %>% filter(!is.na(Organism_ID))
list_organisms_guild_pa <- list_organisms_pa %>% left_join(gild_list,by=c("Organism_ID"))
#Check NA's in guild
list_organisms_guild_pa %>% filter(is.na(Guild)) %>% group_by(Organism_ID) %>% count()
list_organisms_guild_pa$Guild[grepl("Andrena",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Anthophora",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Apidae",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Atylotus rusticus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Dasypoda",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Eristalis",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "syrphids"
list_organisms_guild_pa$Guild[grepl("Evylaeus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Gymnosoma",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Haemmatopota plurails",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Helophillus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "syrphids"
list_organisms_guild_pa$Guild[grepl("Hylaeus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Rhagio",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Scathophaga",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Specodes",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Systoechus ctenopterus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "humbleflies"
list_organisms_guild_pa$Guild[grepl("Tabanus bovine",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Talmerus atricapillus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Volucella pelluceris",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "syrphids"
list_organisms_guild_pa$Guild[grepl("Bombus veteranus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "bumblebees"
list_organisms_guild_pa$Guild[grepl("Chloromyia",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Chrysotus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Haematopora pluralis",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Myiatropa florea",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "syrphids"
list_organisms_guild_pa$Guild[grepl("Psithyrus silvestris",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "bumblebees"
list_organisms_guild_pa$Guild[grepl("Psythirus bohemicus",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "bumblebees"
list_organisms_guild_pa$Guild[grepl("Rhangio tringarius",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_flies"
list_organisms_guild_pa$Guild[grepl("Seladonia tumulorum",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "other_wild_bees"
list_organisms_guild_pa$Guild[grepl("Tabornus bromius",list_organisms_guild_pa$Organism_ID,ignore.case = FALSE)] <- "NA"
#Sanity Checks
list_organisms_guild_pa %>% filter(is.na(Guild)) %>% group_by(Organism_ID) %>% count()
#Add guild to observations
data_obs_guild_pa <- data_raw_obs_pa %>% left_join(list_organisms_guild_pa, by = "Organism_ID")
sampling_pa <- data_raw_obs_pa %>% select(Field,round,hour) %>%
mutate(time=24*60+100*hour) %>% unique() %>% select(-round,-hour) %>%
group_by(Field) %>% summarise_all(sum,rm.na=T) %>% mutate(area=NA) %>% rename(site_id=Field)
data_obs_guild_pa  <- data_obs_guild_pa  %>% rename(site_id=Field) %>%
left_join(sampling_pa,by="site_id")
insect_sampling_pa <- tibble(
study_id = "Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005",
site_id = data_obs_guild_pa$site_id,
pollinator = data_obs_guild_pa$Organism_ID,
guild = data_obs_guild_pa$Guild,
sampling_method = "pantraps",
abundance = data_obs_guild_pa$abundance,
total_sampled_area = data_obs_guild_pa$area,
total_sampled_time =  data_obs_guild_pa$time,
total_sampled_flowers = NA,
Description = "In each site, two sets of pan traps were placed and a 150 m-long (4-m wide) standardized transect line was set (observer walked this line in 30 min). Four rounds of bee sampling using both methods were conducted during the main flowering period for each crop from May to August 2005")
insect_sampling_total <- bind_rows(insect_sampling,insect_sampling_pa)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling_total, "insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
abundance_aux <- data_obs_guild %>% select(site_id,Guild,abundance) %>%
group_by(site_id,Guild) %>% count(wt=abundance) %>%
spread(key=Guild, value=n)
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(lepidoptera=0,beetles=0,
other=0,non_bee_hymenoptera=0,total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
abundance_aux$site_id[abundance_aux$site_id=="Kolonia Branewka"] <- "Kolonia Branewska"
data.site <- data.site %>% left_join(abundance_aux, by = "site_id")
abundace_field <- data_obs_guild %>%
filter(!is.na(Guild)) %>%
select(site_id,Organism_ID,abundance)%>%
group_by(site_id,Organism_ID) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=Organism_ID,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$r_obser <-  0
abundace_field$r_chao <-  0
for (i in 1:nrow(abundace_field)) {
x <- as.numeric(abundace_field[i,2:(ncol(abundace_field)-2)])
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
abundace_field$r_obser[i] <-  chao$Observed
abundace_field$r_chao[i] <-  chao$Estimator
}
# Load our estimation for taxonomic resolution
percentage_species_morphos <- .9
richness_aux <- abundace_field %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction=NA)
if (percentage_species_morphos < 0.8){
richness_aux[,2:ncol(richness_aux)] <- NA
}
richness_aux$site_id[richness_aux$site_id=="Kolonia Branewka"] <- "Kolonia Branewska"
data.site <- data.site %>% left_join(richness_aux,by="site_id")
##################
# SAMPLING
##################
sampling$site_id[sampling$site_id=="Kolonia Branewka"] <- "Kolonia Branewska"
data.site <- data.site %>% left_join(sampling,by="site_id")
field_level_data <- tibble(
study_id = data.site$study_id,
site_id = data.site$site_id,
crop = data.site$crop,
variety = data.site$variety,
management = data.site$management,
country = data.site$country,
latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=data.site$X_UTM,
Y_UTM=data.site$Y_UTM,
zone_UTM=data.site$zone_UTM,
sampling_start_month = data.site$sampling_start_month,
sampling_end_month = data.site$sampling_end_month,
sampling_year = data.site$sampling_year,
field_size = data.site$field_size,
yield=data.site$yield,
yield_units=data.site$yield_units,
yield2=data.site$yield2,
yield2_units=data.site$yield2_units,
yield_treatments_no_pollinators=data.site$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site$fruits_per_plant,
fruit_weight= data.site$fruit_weight,
plant_density=data.site$plant_density,
seeds_per_fruit=data.site$seeds_per_fruit,
seeds_per_plant=data.site$seeds_per_plant,
seed_weight=data.site$seed_weight,
observed_pollinator_richness=data.site$observed_pollinator_richness,
other_pollinator_richness=data.site$other_pollinator_richness,
other_richness_estimator_method=data.site$other_richness_estimator_method,
richness_restriction = data.site$richness_restriction,
abundance = data.site$total,
ab_honeybee = data.site$honeybees,
ab_bombus = data.site$bumblebees,
ab_wildbees = data.site$other_wild_bees,
ab_syrphids = data.site$syrphids,
ab_humbleflies= data.site$humbleflies,
ab_other_flies= data.site$other_flies,
ab_beetles=data.site$beetles,
ab_lepidoptera=data.site$lepidoptera,
ab_nonbee_hymenoptera=data.site$non_bee_hymenoptera,
ab_others = data.site$other,
total_sampled_area = data.site$area,
total_sampled_time = data.site$time,
visitation_rate_units = NA,
visitation_rate = NA,
visit_honeybee = NA,
visit_bombus = NA,
visit_wildbees = NA,
visit_syrphids = NA,
visit_humbleflies = NA,
visit_other_flies = NA,
visit_beetles = NA,
visit_lepidoptera = NA,
visit_nonbee_hymenoptera = NA,
visit_others = NA,
Publication = data.site$Publication,
Credit = data.site$Credit,
Email_contact = data.site$Email_contact
)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
# load libraries
library(tidyverse)
library("iNEXT")
library(readxl)
library(openxlsx)
dir_ini <- getwd()
insect_sampling <- read_excel("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xslx", sheet = "Arkusz2")
library(readxl)
library(openxlsx)
dir_ini <- getwd()
insect_sampling <- read_excel("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xslx", sheet = "Arkusz2")
insect_sampling <- read_excel("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xslx")
insect_sampling <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xslx")
insect_sampling <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xslx")
# load libraries
library(tidyverse)
library("iNEXT")
library(readxl)
library(openxlsx)
dir_ini <- getwd()
field_level_data <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xslx")
list.files()
field_level_data <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
View(field_level_data)
library(parzer)
parse_lat(field_level_data$latitude)
parse_lon(field_level_data$longitude)
field_level_data$latitude <- parse_lat(field_level_data$latitude)
field_level_data$longitude <- parse_lon(field_level_data$longitude)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
#################
# INSECT SAMPLING
#################
insect_sampling_total <- openxlsx::read.xlsx("SzH_insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
View(insect_sampling_total)
#################
# INSECT SAMPLING
#################
field_level_data <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
View(insect_sampling_total)
#################
# INSECT SAMPLING
#################
insect_sampling <- openxlsx::read.xlsx("SzH_insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
write_csv(insect_sampling, "insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
#################
# INSECT SAMPLING
#################
insect_sampling <- openxlsx::read.xlsx("SzH_insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
list.files()
setwd(dir_ini)
list.files()
#################
# INSECT SAMPLING
#################
insect_sampling <- openxlsx::read.xlsx("SzH_insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
View(insect_sampling)
abundance_aux <- insect_sampling %>% filter(sampling_method=="transects") %>% select(site_id,Guild,abundance) %>%
group_by(site_id,Guild) %>% count(wt=abundance) %>%
spread(key=Guild, value=n)
abundance_aux <- insect_sampling %>% filter(sampling_method=="transects") %>% select(site_id,guild,abundance) %>%
group_by(site_id,guild) %>% count(wt=abundance) %>%
spread(key=Guild, value=n)
abundance_aux <- insect_sampling %>% filter(sampling_method=="transects") %>% select(site_id,guild,abundance) %>%
group_by(site_id,guild) %>% count(wt=abundance) %>%
spread(key=guild, value=n)
names(abundance_aux)
View(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(lepidoptera=0,beetles=0,
other=0,non_bee_hymenoptera=0,total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
View(field_level_data)
View(abundance_aux)
View(field_level_data)
View(abundance_aux)
abundace_field <- insect_sampling %>%
filter(!is.na(guild)) %>%
select(site_id,pollinator,abundance)%>%
group_by(site_id,pollinator) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=pollinator,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$r_obser <-  0
abundace_field$r_chao <-  0
for (i in 1:nrow(abundace_field)) {
x <- as.numeric(abundace_field[i,2:(ncol(abundace_field)-2)])
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
abundace_field$r_obser[i] <-  chao$Observed
abundace_field$r_chao[i] <-  chao$Estimator
}
# Load our estimation for taxonomic resolution
percentage_species_morphos <- .9
richness_aux <- abundace_field %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction=NA)
if (percentage_species_morphos < 0.8){
richness_aux[,2:ncol(richness_aux)] <- NA
}
View(richness_aux)
abundace_field <- insect_sampling %>% filter(sampling_method=="transects") %>%
filter(!is.na(guild)) %>%
select(site_id,pollinator,abundance)%>%
group_by(site_id,pollinator) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=pollinator,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$r_obser <-  0
abundace_field$r_chao <-  0
for (i in 1:nrow(abundace_field)) {
x <- as.numeric(abundace_field[i,2:(ncol(abundace_field)-2)])
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
abundace_field$r_obser[i] <-  chao$Observed
abundace_field$r_chao[i] <-  chao$Estimator
}
# Load our estimation for taxonomic resolution
percentage_species_morphos <- .9
richness_aux <- abundace_field %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction=NA)
if (percentage_species_morphos < 0.8){
richness_aux[,2:ncol(richness_aux)] <- NA
}
field_level_data <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
field_level_data$latitude <- parse_lat(field_level_data$latitude)
field_level_data$longitude <- parse_lon(field_level_data$longitude)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
#################
# INSECT SAMPLING
#################
insect_sampling <- openxlsx::read.xlsx("SzH_insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
# load libraries
library(tidyverse)
library("iNEXT")
library(readxl)
library(openxlsx)
library(parzer)
dir_ini <- getwd()
# list of files
list.files()
#################
# INSECT SAMPLING
#################
insect_sampling <- openxlsx::read.xlsx("SzH_insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
field_level_data <- openxlsx::read.xlsx("SzH_field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.xlsx")
View(field_level_data)
field_level_data$latitude <- parse_lat(field_level_data$latitude)
field_level_data$longitude <- parse_lon(field_level_data$longitude)
# Fix richness abundances
field_level_data$X_UTM <- NA
field_level_data$Y_UTM <- NA
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Hajnalka_Szentgyorgyi_Fagopyrum_esculentum_Poland_2005.csv")
setwd(dir_ini)
