In adamhsparks/ChickpeaAscoDispersal: Research Compendium for the Paper 'The role of conidia in the dispersal of Ascochyta rabiei'

library("tidyverse")
library("knitr")

This vignette documents the raw data import, calculation of mean lesion values and exports the new data to "data/lesion_counts.rda" for further use in visualisation and analysis.

In the first step, the data is imported, the "m" from the distance column is dropped and the column is converted to numeric. A new column, SpEv (Spread Event), is created for each location and replicated event at that location. Another new column, degrees, is added for each transect to indicate the direction in degrees based on J. Fanning's best information. Lastly the mean lesions counted per plant within the pot, m_lesions is calculated for each of the transects at each distance, 0, 10, 25, 50 and 75 metres from the plots.

After the data are updated, a column for precipitation type, ptype, is added and the spread events, SpEv, are renamed for clarity and ordered as factors for data visualisation.

Import and Inspect Lesion Data

lesion_counts <-
   read_csv(
      system.file(
         "extdata",
         "lesion_counts.csv",
         package = "ChickpeaAscoDispersal",
         mustWork = TRUE
      )
   ) %>%
   mutate(site = str_remove(site, " SPA")) %>%
   mutate(distance = as.numeric(str_replace(distance, " m", ""))) %>%
   unite(SpEv, c(site, rep), remove = FALSE) %>%
   mutate(
      degrees = case_when(
         site == "Curyo" & transect == 1 ~ 290,
         site == "Curyo" & transect == 2 ~ 300,
         site == "Curyo" & transect == 3 ~ 310,
         site == "Curyo" & transect == 4 ~ 320,
         site == "Curyo" & transect == 5 ~ 330,
         site == "Curyo" & transect == 6 ~ 340,
         site == "Curyo" & transect == 7 ~ 350,
         site == "Curyo" & transect == 8 ~ 360,
         site == "Curyo" & transect == 9 ~ 10,
         site == "Curyo" & transect == 10 ~ 20,
         site == "Horsham" & transect == 1 ~ 45,
         site == "Horsham" & transect == 2 ~ 55,
         site == "Horsham" & transect == 3 ~ 65,
         site == "Horsham" & transect == 4 ~ 75,
         site == "Horsham" & transect == 5 ~ 85,
         site == "Horsham" & transect == 6 ~ 95,
         site == "Horsham" & transect == 7 ~ 105,
         site == "Horsham" & transect == 8 ~ 115,
         site == "Horsham" & transect == 9 ~ 125,
         site == "Horsham" & transect == 10 ~ 135,
         site == "pbc" & transect == 1 ~ 45,
         site == "pbc" & transect == 2 ~ 55,
         site == "pbc" & transect == 3 ~ 65,
         site == "pbc" & transect == 4 ~ 75,
         site == "pbc" & transect == 5 ~ 85,
         site == "pbc" & transect == 6 ~ 95,
         site == "pbc" & transect == 7 ~ 105,
         site == "pbc" & transect == 8 ~ 115,
         site == "pbc" & transect == 9 ~ 125,
         site == "pbc" & transect == 10 ~ 135
      )
   ) %>%
   mutate(
      ptype = case_when(
         SpEv == "pbc_1" ~ "irrigation",
         SpEv == "pbc_2" ~ "irrigation",
         SpEv == "pbc_3" ~ "mixed",
         SpEv == "Horsham_1" ~ "rainfall",
         SpEv == "Horsham_2" ~ "rainfall",
         SpEv == "Curyo_1" ~ "rainfall"
      )
   ) %>%
   mutate(
      site = case_when(
         site == "pbc" ~ "Horsham irrigated",
         site == "Horsham" ~ "Horsham dryland",
         site == "Curyo" ~ "Curyo"
      )
   ) %>%
   mutate(
      SpEv = case_when(
         SpEv == "pbc_1" ~ "Horsham Irrg 1",
         SpEv == "pbc_2" ~ "Horsham Irrg 2",
         SpEv == "pbc_3" ~ "Horsham Mixd 1",
         SpEv == "Horsham_1" ~ "Horsham Rain 1",
         SpEv == "Horsham_2" ~ "Horsham Rain 2",
         SpEv == "Curyo_1" ~ "Curyo Rain 1"
      )
   ) %>%
   mutate_at(vars(SpEv, site, rep), factor) %>%
   mutate(m_lesions = rowMeans(select(., counts_p1:counts_p5),
                                    na.rm = TRUE)) %>% 
   select(-dist_stat) %>% 
   arrange(SpEv, transect, distance)

kable(lesion_counts)

Save lesion count data for use in visualisation and modelling. This only needs to be done once.

save(lesion_counts, file = "../data/lesion_counts.rda")

adamhsparks/ChickpeaAscoDispersal documentation built on April 29, 2024, 12:32 p.m.