OpenMindat.Rmd

---
title: "OpenMindat"
author: "Xiang Que"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{OpenMindat}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Mindat.org is the world's largest open database of minerals, rocks, meteorites and the localities they come from.Mindat.org is run by the not-for-profit.

Learn  Learn more about rocks and minerals, their origins and their uses: [Enter our learning center](https://www.mindat.org/a/learn).

OpenMindat is a package for retrieving and processing data from mindat.org database through its open data API.

Mindat and University of Idaho collaborate on  OpenMindat Project.


### Get started
####  Load libraries
The OpenMindat R package require the following libraries:
```{r setup}
library(httr)
library(jsonlite)
library(OpenMindat)
library("stringr")
library(readxl)
```

####  Initializing API Call
Users can set the `page_size` from 0 to 1500 (default is 800). The Mindat API returns the largest record size per request.

```{r}
test_base_token = "9ce67655d74bcd981e937be80dcea9cb"
#mindat_connection(test_base_token,page_size = 1500)
```

####  1. Qurey Geomaterials
##### by chemical elements:
(1) query geomaterials records that contain any elements in a given list: 
```{r}
#geomaterials_contain_any_elems (c('Fe','S'),fields ="id,name,mindat_formula,elements,sigelements")
```
(2) query geomaterials records that contain all of the elements in a given list: 
```{r}
#geomaterials_contain_all_elems (c('Fe','S'),fields ="id,name,mindat_formula,elements,sigelements")
```
(3) query geomaterials records that only contain the elements in a given list:
```{r}
#geomaterials_contain_only_elems (c('Fe','S'),fields ="id,name,mindat_formula,elements,sigelements")
```
(4) query geomaterials records that not contain any of the elements in a given list:
```{r}
#geomaterials_not_contain_elems (c('Fe','S','O'),fields ="id,name,mindat_formula,elements,sigelements")
```
(5) query geomaterials records that contain all the elements in the first given list,but not contain the elements in the second given list:
```{r}
#geomaterials_contain_all_but_not_elems(c('Fe','S'), c('O'),fields ="id,name,mindat_formula,elements,sigelements")
```
(6) query geomaterials records that contain any of the elements in the first given list,but not the elements in the second given list:
```{r}
#geomaterials_contain_any_but_not_elems(c('Fe','S'), c('O'),fields ="id,name,mindat_formula,elements,sigelements")
```
#### by physical properties:
(7) query geomaterials records that have hardness within a given range: 
```{r}
#geomaterials_hardness_range(3,3.5,fields="id,name,hmin,hmax,hardtype,commenthard")
```
(8) query geomaterials records that have hardness higher than a given value: 
```{r}
#geomaterials_hardness_gt(9,fields="id,name,hmin,hmax,hardtype,commenthard")
```
(9) query geomaterials records that have hardness lower than a given value: 
```{r}
#geomaterials_hardness_lt(9,fields="id,name,hmin,hmax,hardtype,commenthard")
```
(10) query geomaterials records that have density within a given range: 
```{r}
#geomaterials_dens_range(3,3.2,fields="id,name,dmeas,dmeas2,dmeaserror,dcalcerror")
```
(11) query geomaterials records that have birefringence within a given range: 
```{r}
#geomaterials_bi_range(0.6,0.7,fields = "id,name,rimin,rimax,opticalbirefringence,opticalbireflectance")
```
(12) query geomaterials records that have optical2v within a given range:
```{r}
#geomaterials_optical2v_range(9,10,fields = "id,name,optical2vmeasured,optical2vmeasured2,optical2vcalc,optical2vcalc2,optical2vcalcerror,optical2vmeasurederror")
```
(13) query geomaterials records that have a given crystal system
```{r}
#geomaterials_crystal_system(c("Icosahedral"),fields = "id,name,elements,csystem,cleavagetype,commentcrystal")
```
(14) query geomaterials records that have a given fracturetype
```{r}
#geomaterials_fracturetype(c("Step-Like"),fields = "id,name,fracturetype,elements,csystem,crystal_system,cleavagetype")
```
(15) query geomaterials records that have a list of given colours
```{r}
#geomaterials_colour(c("bright blue"),fields = "id,name,elements,csystem,colour,opticalcolour,commentcolor")
```
(16) query the geomaterials records that match an given steak.
```{r}
#geomaterials_streak(c("orange"),fields = "id,name,elements,csystem,colour,opticalcolour,commentcolor,streak")
```
(17) query the geomaterials records that match an given diapheny.
```{r}
#geomaterials_diapheny("Transparent",fields = "id,name,elements,csystem,colour,diapheny")
```
(18) query the geomaterials records that match an given lustretype.
```{r}
#geomaterials_lustretype(c("Sub-Adamantine"),fields = "id,name,elements,csystem,cleavage,cleavagetype,rimin,rimax,lustre,lustretype")
```
(19)query the geomaterials records by names, fields:
```{r}
#geomaterials_meteoritical_code_exists("true",fields ="id,name,meteoritical_code,meteoritical_code_exists")
#geomaterials_search_name("Quartz",fields = "id,name")
#geomaterials_name("qu_rtz",fields = "id,name")
#geomaterials_name("qu*",fields = "id,name")
```

####  2. Qurey Localities
```{r}
#localities_list_country("Norway")
#localities_list_description("volcano")
#localities_list_elems_inc(c("Dy"))
#localities_list_elems_inc_exc(c("Dy"),c("Li"))
#locality_age_list()
```
####  3. Qurey IMA Minerals
```{r}
#minerals_ima_list()
#minerals_ima_list_ima(0)
```
####  4. Save the retrieved R dataframe as a specified format file.
```{r}
#saveMindatDataAs(df,"df_geomaterials.ttl")
#saveMindatDataAs(df,"df_geomaterials.jsonld")
```

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```