library(tidyverse)
library(openxlsx)
library("iNEXT")
dir_ini <- getwd()
data.site <- read.xlsx("Crop_pollination_database_Bloom-Crowder.xlsx",
sheet = "field_level_data", startRow = 1)
View(data.site)
View(data.site)
View(data.site)
data.site <- data.site[,c(1:26,53:55)]
View(data.site)
View(data.site)
data.site <- read.xlsx("Crop_pollination_database_Bloom-Crowder.xlsx",
sheet = "field_level_data", startRow = 1)
data.site <- as_tibble(data.site)
data.site <- data.site[,c(1:26,54:56)]
View(data.site)
data.site %>% group_by(management) %>% count()
View(data.site)
data.site$management[data.site$management=="Cerified Organic"] <- "organic"
data.site$management[data.site$management=="Organic Practices"] <- "organic"
data.site$Credit <- "Elias H. Bloom (bloomel1@msu.edu); Elisabeth C. Oeller (elisabeth.oeller@wsu.edu)"
data.site$email <- "dcrowder@wsu.edu"
# Sanity check names
data.site %>% group_by(site_id) %>% count() %>% filter(n>1) #All site_id (per year) are unique
data.insect <- read.xlsx("Crop_pollination_database_Bloom-Crowder.xlsx",
sheet = "insect_sampling", startRow = 1)
data.insect <- as_tibble(data.insect)
data.insect %>% group_by(guild) %>% count()
View(data.insect)
names(data.insect)[names(data.insect)=="Description_(Fee_text)"] <- "Description"
View(data.insect)
names(data.insect)
# Fix guilds names
data.insect$guild[data.insect$guild=="bumblebee"] <- "bumblebees"
data.insect$guild[data.insect$guild=="honeybee"] <- "honeybees"
data.insect$guild[data.insect$guild=="other_wild_bee"] <- "other_wild_bees"
data.insect$total_sampled_time <- 60*data.insect$total_sampled_time
View(data.insect)
data.insect %>% group_by(sampling_method) %>% count()
abundance_aux <- data.insect %>% filter(sampling_method =="sweep_net") %>%
group_by(site_id,guild) %>% count(wt=abundance) %>%
spread(key=guild, value=n) %>% rename()
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(beetles=0,lepidoptera=0,non_bee_hymenoptera=0,other_flies=0,
syrphids=0,other=0, humbleflies=0,total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
View(abundance_aux)
data.site <- data.site %>% left_join(abundance_aux, by = "site_id")
abundace_field <- data.insect %>% filter(sampling_method=="sweep_net") %>%
select(site_id,pollinator,abundance)%>%
group_by(site_id,pollinator) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=pollinator,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$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$Estimator
}
# Percentage of species+morphos:
percentage_species_morphos <- 1
richness_aux <- abundace_field %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao 1",richness_restriction="Only bees")
if (percentage_species_morphos < 0.8){
richness_aux[,2:ncol(richness_aux)] <- NA
}
View(richness_aux)
data.site <- data.site %>% left_join(richness_aux, by = "site_id")
sampling_aux <- data.insect %>% filter(sampling_method=="sweep_net") %>%
group_by(site_id,sampling_method) %>%
summarize(total_sampled_area=mean(total_sampled_area),
total_sampled_time=mean(total_sampled_time)
) %>%
group_by(site_id) %>%
summarize(total_sampled_area=sum(total_sampled_area),
total_sampled_time=sum(total_sampled_time)
)
View(sampling_aux)
data.site <- data.site %>% left_join(sampling_aux, by = "site_id")
insect_sampling <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
site_id = data.insect$site_id,
pollinator = data.insect$pollinator,
guild = data.insect$guild,
sampling_method = data.insect$sampling_method,
abundance = data.insect$abundance,
total_sampled_area = data.insect$total_sampled_area,
total_sampled_time = data.insect$total_sampled_time,
total_sampled_flowers = data.insect$total_sampled_flowers,
Description = data.insect$Description
)
View(insect_sampling)
data.insect
names(data.insect)[names(data.insect)=="Description_(fee_text)"] <- "Description"
insect_sampling <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
site_id = data.insect$site_id,
pollinator = data.insect$pollinator,
guild = data.insect$guild,
sampling_method = data.insect$sampling_method,
abundance = data.insect$abundance,
total_sampled_area = data.insect$total_sampled_area,
total_sampled_time = data.insect$total_sampled_time,
total_sampled_flowers = data.insect$total_sampled_flowers,
Description = data.insect$Description
)
View(insect_sampling)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_David_Crowder_Fragaria_ananassa_USA_2016.csv")
setwd(dir_ini)
field_level_data <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
site_id = data.site$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=NA,
Y_UTM=NA,
zone_UTM=NA,
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=NA,
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_pollinator_richness,
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$total_sampled_area,
total_sampled_time = data.site$total_sampled_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$email
)
View(field_level_data)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_David_Crowder_Fragaria_ananassa_USA_2016.csv")
setwd(dir_ini)
insect_sampling <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
site_id = data.insect$site_id,
pollinator = data.insect$pollinator,
guild = data.insect$guild,
sampling_method = data.insect$sampling_method,
abundance = data.insect$abundance,
total_sampled_area = data.insect$total_sampled_area,
total_sampled_time = data.insect$total_sampled_time,
total_sampled_flowers = data.insect$total_sampled_flowers,
Description = paste0(data.insect$Description,". Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour.")
)
View(insect_sampling)
insect_sampling$Description[insect_sampling$Description=="NA. Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour."] <-
"Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour."]
insect_sampling$Description[insect_sampling$Description=="NA. Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour."] <-
"Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour."
View(insect_sampling)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_David_Crowder_Fragaria_ananassa_USA_2016.csv")
setwd(dir_ini)
View(insect_sampling)
library(tidyverse)
library(openxlsx)
library("iNEXT")
dir_ini <- getwd()
data.site <- read.xlsx("Crop_pollination_database_Bloom-Crowder.xlsx",
sheet = "field_level_data", startRow = 1)
data.site <- as_tibble(data.site)
data.site <- data.site[,c(1:26,54:56)]
data.site$crop <- "Fragaria x ananassa"
data.site$country <- "USA"
data.site$management[data.site$management=="Cerified Organic"] <- "organic"
data.site$management[data.site$management=="Organic Practices"] <- "organic"
data.site$Credit <- "Elias H. Bloom (bloomel1@msu.edu); Elisabeth C. Oeller (elisabeth.oeller@wsu.edu)"
data.site$email <- "dcrowder@wsu.edu"
# Sanity check names
data.site %>% group_by(site_id) %>% count() %>% filter(n>1) #All site_id (per year) are unique
data.insect <- read.xlsx("Crop_pollination_database_Bloom-Crowder.xlsx",
sheet = "insect_sampling", startRow = 1)
data.insect <- as_tibble(data.insect)
data.insect %>% group_by(guild) %>% count()
names(data.insect)[names(data.insect)=="Description_(fee_text)"] <- "Description"
# Fix guilds names
data.insect$guild[data.insect$guild=="bumblebee"] <- "bumblebees"
data.insect$guild[data.insect$guild=="honeybee"] <- "honeybees"
data.insect$guild[data.insect$guild=="other_wild_bee"] <- "other_wild_bees"
data.insect$total_sampled_time <- 60*data.insect$total_sampled_time
data.insect %>% group_by(sampling_method) %>% count()
abundance_aux <- data.insect %>% filter(sampling_method =="sweep_net") %>%
group_by(site_id,guild) %>% count(wt=abundance) %>%
spread(key=guild, value=n) %>% rename()
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(beetles=0,lepidoptera=0,non_bee_hymenoptera=0,other_flies=0,
syrphids=0,other=0, humbleflies=0,total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
data.site <- data.site %>% left_join(abundance_aux, by = "site_id")
abundace_field <- data.insect %>% filter(sampling_method=="sweep_net") %>%
select(site_id,pollinator,abundance)%>%
group_by(site_id,pollinator) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=pollinator,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$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$Estimator
}
# Percentage of species+morphos:
percentage_species_morphos <- 1
richness_aux <- abundace_field %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao 1",richness_restriction="Only bees")
if (percentage_species_morphos < 0.8){
richness_aux[,2:ncol(richness_aux)] <- NA
}
data.site <- data.site %>% left_join(richness_aux, by = "site_id")
sampling_aux <- data.insect %>% filter(sampling_method=="sweep_net") %>%
group_by(site_id,sampling_method) %>%
summarize(total_sampled_area=mean(total_sampled_area),
total_sampled_time=mean(total_sampled_time)
) %>%
group_by(site_id) %>%
summarize(total_sampled_area=sum(total_sampled_area),
total_sampled_time=sum(total_sampled_time)
)
data.site <- data.site %>% left_join(sampling_aux, by = "site_id")
insect_sampling <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
site_id = data.insect$site_id,
pollinator = data.insect$pollinator,
guild = data.insect$guild,
sampling_method = data.insect$sampling_method,
abundance = data.insect$abundance,
total_sampled_area = data.insect$total_sampled_area,
total_sampled_time = data.insect$total_sampled_time,
total_sampled_flowers = data.insect$total_sampled_flowers,
Description = paste0(data.insect$Description,". Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour.")
)
insect_sampling$Description[insect_sampling$Description=="NA. Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour."] <-
"Both traps and sweep nets were conducted over a 50m transect. Traps were left for 9 hours, sweeping was done for 1 hour."
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_David_Crowder_Fragaria_ananassa_USA_2016.csv")
setwd(dir_ini)
field_level_data <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
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$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = data.site$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$yield_treatments_pollen_supplement2,
fruits_per_plant=NA,
fruit_weight= data.site$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$other_pollinator_richness,
richness_restriction = data.site$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$other,
total_sampled_area = data.site$total_sampled_area,
total_sampled_time = data.site$total_sampled_time,
visitation_rate_units = NA,
visitation_rate = NA,
visit_honeybee = NA,
visit_bombus = NA,
visit_wildbees = NA,
visit_syrphids = NA,
visit_humbleflies = NA,
visit_other_flies = NA,
visit_beetles = NA,
visit_lepidoptera = NA,
visit_nonbee_hymenoptera = NA,
visit_others = NA,
Publication = data.site$Publication,
Credit = data.site$Credit,
Email_contact = data.site$email
)
data.site$other_richness_estimator_method
field_level_data <- tibble(
study_id = "David_Crowder_Fragaria_ananassa_USA_2016",
site_id = data.site$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=NA,
Y_UTM=NA,
zone_UTM=NA,
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=NA,
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$total_sampled_area,
total_sampled_time = data.site$total_sampled_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
)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_David_Crowder_Fragaria_ananassa_USA_2016.csv")
setwd(dir_ini)
