HoneybushTransplantExperiments

Explanation of methods:

1. Plot selection:

• Plots were subjectively chosen so as to be in close proximity to one another (thereby avoiding much variability in environmental conditions), while also being representative of the different types of land.
• Each plot measured approximately 60 x 40 m.
• The old lands and ploughed lands plots were fenced so as to exclude cattle.

2. Treatments:

• A total of five treatments were used, three cleared and two uncleared.
• Ploughed (cleared) - Agricultural land that had been repeated ploughed for pasture. Was ploughed 8 months prior to the start of the experiment and again on the day of planting.
• Old lands cleared (vegetation was brush-cut, removing only the plant parts above the soil and leaving roots) - cleared on the day of planting. Each quadrat was sprayed with 200ml of concentrated smoke water immediately prior to watering.
• Fynbos cleared (vegetation was brush-cut, removing only the plant parts above the soil and leaving roots) - cleared on the day of planting. Each quadrat was sprayed with 200ml of concentrated smoke water immediately prior to watering.
• Old lands uncleared (a small gap in the existing vegetation was made into which the seeds and seedlings were planted).
• Fynbos uncleared (a small gap in the existing vegetation was made into which the seeds and seedlings were planted).

3. Replicates per treatment:

• Subternata survival: 80 reps per treatment (400 in total)
• Subternata germination: 160 reps per treatment (800 in total)
• Intermedia germination: 160 reps per treatment (800 in total)

4. Layout:

• All plants allocated to the cleared treatments were laid out in evenly dispersed 1 x 1 m quadrats within the designated plots. Each plot contained 10 quadrats.
• All plants allocated to the uncleared treatments were laid out at 1 m intervals on transects along the edges of the designated plots.
• The layout of quadrats and transects in each plot are shown in the file: AB_MSC_RHB_layout.png

5. Planting and sowing:

• 6-month-old seedlings of subternata were planted from unigro propagation tubes into the soil.
• Seeds were scarified by pouring boiled and slightly cooled water onto the seeds and allowing them to stand for 3 minutes. The hot water was removed and replaced with cold water before being drained. Any seeds that floated in the water were removed and discarded.
• Seeds were sown two-at-a-time into the ground by making a small hole in the soil and burying them under about 5 mm of soil.

6. Watering:

• All plants and seeds were watered once at the start of the trial. Just enough water was used to soak the soil.
• Cleared quadrats that were treated with concentrated smoke water were done so prior to watering to allow for the smoke water to be diluted and filter down upon watering.

7. Monitoring:

• Seedling heights were measured at the time of planting and every two months thereafter. Survival and mortality were recorded.
• Seeds that were sown were monitored for germination and growth two months after planting and every two months thereafter. Where seeds had germinated the seedling heights were recorded.
• Any seedlings that showed signs of grazing were recorded as such.

setwd("D:/Dropbox/100_PROJECTS/2016.4_PROJECT_Cyclopia.transplants")
read.csv("Data/SamplingDates.csv")%>%tbl_df()%>%
  rename(SamplingEvent=ColumnHeading)->
  sampling_dates

read.csv("Data/AB_MSC_RHB_data VER3-2014-2016.csv")%>%tbl_df()%>%
  mutate(H5a=as.numeric(H5a))%>% # one numeric column was imported as a factor. Can't see why...
  select(-N1,-N2a,-N2b,-N3a,-N3b,-N4a,-N4b,-N5a,-N5b)%>%
  tidyr::gather("SamplingEvent","Height",c(H1,H2a,H2b,H3a,H3b,H4a,H4b,H5a,H5b))->
  tutu
read.csv("Data/AB_MSC_RHB_data VER3-2014-2016.csv")%>%tbl_df()%>%
  mutate(H5a=as.numeric(H5a))%>% # one numeric column was imported as a factor. Can't see why...
  select(-H1,-H2a,-H2b,-H3a,-H3b,-H4a,-H4b,-H5a,-H5b)%>%
  rename(H1=N1,H2a=N2a,H2b=N2b,H3a=N3a,H3b=N3b,H4a=N4a,H4b=N4b,H5a=N5a,H5b=N5b)%>%
  tidyr::gather("SamplingEvent","SamplingNote",c(H1,H2a,H2b,H3a,H3b,H4a,H4b,H5a,H5b))->
  toto

## Warning: attributes are not identical across measure variables;
## they will be dropped

full_join(tutu,toto,by=c("Year","CODE","SPECIES","TYPE","LT","TR","GP","SamplingEvent"))%>%
  filter(!(TYPE=="SEEDLING"&SamplingEvent=="H2b"))%>% # There are no second replicates for seedlings
  filter(!(TYPE=="SEEDLING"&SamplingEvent=="H3b"))%>% # There are no second replicates for seedlings
  filter(!(TYPE=="SEEDLING"&SamplingEvent=="H4b"))%>% # There are no second replicates for seedlings
  filter(!(TYPE=="SEEDLING"&SamplingEvent=="H5b"))%>% # There are no second replicates for seedlings
  left_join(sampling_dates,by=c("Year","SamplingEvent"))%>%
  mutate(Replicate=substr(SamplingEvent,3,3),
         Index=paste(CODE,TYPE,Year,Replicate,sep="-"))%>%
  rename(YEAR=Year)->
  dat.long

## Warning: Column `SamplingEvent` joining character vector and factor,
## coercing into character vector

read.csv("Data/AB_MSC_RHB_data VER3-2014-2016.csv")%>%tbl_df()%>%
  mutate(H5a=as.numeric(H5a))->
  dat.wide

#dat.long%>%group_by(YEAR,SPECIES,TYPE,LT,TR,GP)%>%tally()%>%View

dat.long%>%group_by(YEAR,SPECIES,TYPE,LT,TR,GP)%>%tally()

## # A tibble: 165 x 7
## # Groups:   YEAR, SPECIES, TYPE, LT, TR [?]
##    YEAR  SPECIES TYPE  LT    TR       GP     n
##    <fct> <fct>   <fct> <fct> <fct> <int> <int>
##  1 14/15 INT     SEED  FY    CL        1    72
##  2 14/15 INT     SEED  FY    CL        2    72
##  3 14/15 INT     SEED  FY    CL        3    72
##  4 14/15 INT     SEED  FY    CL        4    72
##  5 14/15 INT     SEED  FY    CL        5    72
##  6 14/15 INT     SEED  FY    CL        6    72
##  7 14/15 INT     SEED  FY    CL        7    72
##  8 14/15 INT     SEED  FY    CL        8    72
##  9 14/15 INT     SEED  FY    CL        9    72
## 10 14/15 INT     SEED  FY    CL       10    72
## # ... with 155 more rows

dat.long%>%group_by(YEAR,SPECIES,TYPE)%>%tally()

## # A tibble: 6 x 4
## # Groups:   YEAR, SPECIES [?]
##   YEAR  SPECIES TYPE         n
##   <fct> <fct>   <fct>    <int>
## 1 14/15 INT     SEED      3609
## 2 14/15 SUB     SEED      3609
## 3 14/15 SUB     SEEDLING  2025
## 4 15/16 INT     SEEDLING  2010
## 5 15/16 SUB     SEED      3609
## 6 15/16 SUB     SEEDLING  2005

• Germination (of seeds)
• Survival versus growth
• Two species
• 5 treatments
• Two different years

2014/15: SUB seeds and seedling, INT seeds 2015/16: SUB seeds and seedlings, INT seedlings

Coding structure

• x: not germinated
• d: dead
• ba: barely alive
• db: dead and b?
• de: dead and eaten
• dm: ???
• e: eaten (but alive)
• resprouting

C. subternata seed germination and survival overall

C. subternata seed germination and seed+seedling survival overall

C. subternata & C. intermedia seed germination and seed+seedling survival overall

C. subternata seedling survival overall

C. intermedia seedling survival overall

Final sizes: All combinations

dat.long%>%
  filter(SamplingEvent%in%c("H5a","H5b"))%>%
  filter(!is.na(Height))%>%
  filter(Height!=1)%>%
  ggplot(aes((Height)))+
  geom_histogram(bins=5)+
  facet_grid(LT+SPECIES+TYPE~Date+TR)+
  coord_flip()

Final sizes: C. subternata

dat.long%>%
  filter(SamplingEvent%in%c("H5a","H5b"))%>%
  filter(!is.na(Height))%>%
  filter(SPECIES=="SUB")%>%
  filter(Height!=1)%>%
  ggplot(aes((Height)))+
  geom_histogram(bins=5,aes(fill=TYPE))+
  facet_grid(LT~Date+TR)+
  coord_flip()+
  theme(legend.position="top",
        legend.title = element_blank())+
  xlab("Height class (mm)")

Final sizes: C. subternata

dat.long%>%
  filter(SamplingEvent%in%c("H5a","H5b"))%>%
  filter(!is.na(Height))%>%
  filter(SPECIES=="INT")%>%
  filter(Height!=1)%>%
  ggplot(aes((Height)))+
  geom_histogram(bins=5,aes(fill=TYPE))+
  facet_grid(LT~Date+TR)+
  coord_flip()+
  theme(legend.position="top",
        legend.title = element_blank())+
  xlab("Height class (cm)")