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R_project_overview.Rmd
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---
title: "Interactive plant identification with R"
author: "Heather Kates"
date: "April 24, 2015"
output: html_document
---
---
title: "Interactive Plant Identification in R"
author: "Heather Kates"
date: "April 24, 2015"
output: slidy_presentation
---
# Project Goal: Create an interactive key for identifying plant families
1. Requiring specific code for each set of characters
2. Reading user input for each set of characters
3. Reading user input for each character
##### Traditional dichotomous key
## Data and input to subset data
**Data**
```{r, echo=FALSE}
plant_families <- read.csv(file="Plant_families_for_R.csv")
head(plant_families)
```
**Input**
herbaceous alternate absent inferior umbel bilateral
**Output**
Family: Apiaceae
## 1. Learn a little about plant family characteristics
#### What proportion of plant families are woody?
```{r}
plant_families <- read.csv(file="Plant_families_for_R.csv")
prop <- nrow(subset(plant_families, habit == "woody"))/(nrow(plant_families))
percent <- ((signif(prop, digits=3))*100)
cat(percent, "% of the families are woody")
```
#### What proportion of plant families have stipules?
```{r, echo=FALSE}
plant_families <- read.csv(file="Plant_families_for_R.csv")
```
```{r}
prop <- nrow(subset(plant_families, stipules == "present"))/nrow(plant_families)
percent <- ((signif(prop, digits=3))*100)
cat(percent, "% of the families have stipules")
```
####What proportion of the plant families are vines?
```{r, echo=FALSE}
plant_families <- read.csv(file="Plant_families_for_R.csv")
```
```{r}
prop <- nrow(subset(plant_families, habit == "vine"))/nrow(plant_families)
percent <- ((signif(prop, digits=3))*100)
cat(percent, "% of the families are vines")
```
## Use the same approach to identify plant families from a set of character
###I have a plant that is a vine with no stipules. What family could it be?
```{r, echo=FALSE}
plant_families <- read.csv(file="Plant_families_for_R.csv")
```
```{r}
Vine_nostipule_families <- subset(plant_families, habit =="vine" & stipules == "absent")
Family <- as.vector(Vine_nostipule_families$Family)
cat("Possible Families:", Family)
```
But this requires the code:
```{r, eval=FALSE}
subset(plant_families, habit =="vine" & stipules == "absent")
```
to be rewritten for each query!
Instead, we can prompt the user to enter these values and update the code
## Prompting user to enter values that will update the code
```{r}
prompt <- "Describe your plant:
habit(woody/herbaceous/vine)\nstipules(present/absent)\nleaf arrangement(opposite/alternate)
ovary position(superior/inferior)\ninflorescence(umbel/head/cyme/terminal)\nfloral symmetry(radial/zygomorphic/actinomorphic)"
Character_list <- as.vector(strsplit(readline(prompt), " ")[[1]])
```
## Prompting user to enter values that will update the code
Describe this plant:
user-input in console
```{r, eval=FALSE}
> herbaceous absent alternate inferior umbel radial
```
Character_list is now a vector with 6 members
```{r, eval=FALSE}
> Character_list
[1] "herbaceous" "absent" "alternate" "inferior" "umbel" "radial"
```
## User-created vector is used subset the data frame
Check to see what families (rows) have all the charaters entered by the user:
```{r, echo=FALSE}
plant_families <- read.csv(file="Plant_families_for_R.csv")
Character_list <- c("herbaceous","absent","alternate","inferior","umbel","bilateral")
```
```{r}
Matching_rows <- subset(plant_families, habit == Character_list[1] & stipules == Character_list[2]
& leaf.arrangement == Character_list[3] & ovary.position== Character_list[4]
& inflorescence == Character_list[5]
& floral.symmetry ==Character_list[6] )
Matching_families <- (Matching_rows[1])
print(Matching_families[1])
```
This works, but it relies on the user following instructions exactly and is awkward
## Creating vector from responses to multiple user prompts
###Function that prompts user for multiple inputs about plant characteristics
```{r}
fun <- function(test)
{
habit <-readline("habit? ")
leaf <-readline("leaf arrangement? ")
stipules <-readline("stipules? ")
ovary <- readline("ovary position? ")
inflorescence <- readline("inflorescence type? ")
symmetry <- readline("floral symmetry? ")
habit <- as.character(habit)
leaf <- as.character(leaf)
stipules <- as.character(stipules)
ovary <- as.character(ovary)
inflorescence <- as.character(inflorescence)
symmetry <- as.character(symmetry)
#assign the six prompt responses to a vector called "input"
input <- c(habit, leaf, stipules, ovary, inflorescence, symmetry)
}
#This only works in an interactive R session
if(interactive()) fun(test)
```
## Creating vector from responses to multiple user prompts
###Once the function is defined, you can run it over and over and assign its returned values (input) to vector "character_suite"
```{r, eval=FALSE}
character_suite <- fun(test)
> character_suite <- fun(test)
habit? herbaceous
leaf arrangement? alternate
stipules? absent
ovary position? inferior
inflorescence type? umbel
floral symmetry? radial
> character_suite
[1] "herbaceous" "absent" "alternate" "inferior" "umbel" "radial"
```
## Subsetting data.frame with the user input character suite
### This works the same way as when user input is read from a single line
```{r}
plant_families <- read.csv(file="Plant_families_for_R.csv")
character_suite <- c("herbaceous","absent","alternate","inferior","umbel","bilateral")
Matching_rows <- subset(plant_families, habit == character_suite[1] & leaf.arrangement == character_suite[3]
& stipules== character_suite[2] & ovary.position== character_suite[4]
& inflorescence == character_suite[5]
& floral.symmetry ==character_suite[6])
Matching_families <- (Matching_rows$Family)
print(Matching_rows[1])
```