API-Docs

Field Design API

AgriOS Field Design API

URL	http://your.server.com/ocpu/library/AgriOS/R/design_exp
Request Method	curl http://your.server.com/ocpu/library/AgriOS/R/design_exp -d”parameters”

Parameters of field design API

Parameters Field Design

Name	Meaning	Description	Required	Default
data	input file path		true	NULL
design	design name		true	NULL
reps	number of reps	Valid and mandatory for “crd”, “contrast”, “interval_contrast”	true/false	NULL
blocks	number of blocks	Valid and mandatory for “rcbd”, “augmented”, “split-plot”	true/false	NULL
block.size	size of incomplete block	Valid and mandatory for “alpha”	true/false	NULL
nrows	number of rows	Maximum number of rows (ranges) of the experiment field	true	NULL
ncols	number of cols	Maximum number of cols (pass) of the experiment field	true	NULL
seed	random seed	Valid for all design except for “contrast” and “interval_contrast”	false	NULL
interval	interval size	Valid and mandatory for “interval_contrast”	true/false	NULL
filler.interval	filling method	Valid and mandatory for “interval_contrast”. Indicate if empty plots at the end of each interval should be filled by “interval_contrast” fillers. If false, the allocation of next rep will continue from the empty plots of the previous interval.	false	true
filler	name of filler	Valid for “interval_contrast”	false	FILLER_No_Name
trt.wp	list of whole-plot treatments	Valid and mandatory for “split-plot”	true	none
trt.sp	list of split-plot treatments	Valid and mandatory for “split-plot”	true	none
loc_id	id of location		false	“”
exp_id	id of experiment		false	“”
as.json	output format	If the output should be written in json or r data.frame	false	false
log.path	a path for saving the log file	If the path is not specified, log messages will be printed in the console	false	NULL

Example input data of field design

[
  {
    "ped_id": "G1",
    "sub_group": 1,
    "design_check": 0
  },
  {
    "ped_id": "G2",
    "sub_group": 1,
    "design_check": 0
  },
  {
    "ped_id": "G3",
    "sub_group": 1,
    "design_check": 0
  },
  {
    "ped_id": "G4",
    "sub_group": 1,
    "design_check": 0
  },
  {
    "ped_id": "G5",
    "sub_group": 1,
    "design_check": 0
  },
  {
    "ped_id": "G6",
    "sub_group": 1,
    "design_check": 0
  },

Showcase of field design usage

Field design of diagonal augmented trials

curl http://your.server.com/ocpu/library/AgriOS/R/design_exp \
-d "data=home/root/Data/entries-diagonal.json&design='diagonal'&nrows=18&ncols=18&as.json=true"

Field design of randomized complete block design

curl http://your.server.com/ocpu/library/AgriOS/R/design_exp \
-d "data=home/root/Data/entries-rcbd.json&design='rcbd'&blocks=3&nrows=7&ncols=10&as.json=true"

Data Analysis API

AgriOS Field Data Analysis API

Variable	Meaning	Description
ped_id	genotype id	identity of the genotypes to be planted;
sub_group	number of subgroup	Divide the field into subgroups; this is only valid for diagonal design for now;
design_check	if a genotype is check	indicate checks for certain designs; the values can be either 0 (not check) or 1 (check);

Parameters of field design API

Parameters Data Analysis

Name	Meaning	Description	Required	Default
file	path to input data	for the format of this file please see the table below	true	NULL
design	name of design	a string to specify the type of design please see field design for more information	true	NULL
log.path	a path for saving the log file	If the path is not specified, log messages will be printed in the console	false	NULL
as.json	output format	If the output should be written in json or r data.frame	false	false

Structure of Input File for Data Analysis

Variable	Meaning	Description	Required
num	data entry number	number of row of the input data entry	true
loc_id	location id	identity of the trial location	true
year	year of trial	year during which the trial was harvested	false
env_id	environment id	identity of the trial environment	false
pass	column of the plot	column coordination of the plot on field	false
ranges	row of field the plot	row coordination of the plot on field	false
block	block of the plot	block number of the plot (only valid for certain designs)	false
rep_num	rep of the plot	replication number of the plot	true
entry_id	entry id	id of the entry	true
plot_id	plot_id	id of the plot	true
treatment	agronomic treatment 1	agronomic treatment 1	false
treatment2	agronomic treatment 2	agronomic treatment 2	false
treatment3	agronomic treatment 3	agronomic treatment 3	false
ped_id	id of the genotype	Id of the genotype of the plot	true
female_ped_name	name of mather line	for GCA analysis	false
male_ped_name	name of father line	for GCA analysis	false
check_type	indicator of check plots	Value can be 1, 2, 3, or 4;	false
value	value of observation	value of the trait observation	true
trait	trait id	Id of the trait	true

Output of analysis of contrast design

Output of Contrast Design Analysis

FUN_TYPE	MAP_FUN_ID	DESRIPTION	指标名称	指标类型	是否常用	数据类型
ConExp	CHECK_MEAN_EXP	The mean of CHECK_VALUE for the experiment	对照平均（对比）	试验总结	是	decimal(18,2)
ConExp	DIFF_CHECK_EXP	The mean of DIFFERENCE_CHECK for the experment	与对照差异（对比）	试验总结	是	decimal(18,2)
ConExp	PCT_CHECK_EXP	The mean of PCT_CHECK for the experiment	与对照差异百分比（对比）	试验总结	是	decimal(18,2)
ConLoc	CHECK_MEAN_LOC	The mean of CHECK_VALUE for the location	对照平均（对比）	试点总结	是	decimal(18,2)
ConLoc	DIFF_CHECK_LOC	The mean of DIFFERENCE_CHECK for the location	与对照差异（对比）	试点总结	是	decimal(18,2)
ConLoc	PCT_CHECK_LOC	The mean of PCT_CHECK for the location	与对照差异百分比（对比）	试点总结	是	decimal(18,2)
ConPlot	CHECK_VALUE	The check value for the plot	对照值（对比）	小区总结	否	decimal(18,2)
ConPlot	DIFFERENCE_CHECK	The difference between genotype plot and check plot	与对照差异（对比）	小区总结	否	decimal(18,2)
ConPlot	PCT_CHECK	The percentage of DIFF_CHECK_EXP	与对照差异百分比（对比）	小区总结	否	decimal(18,2)

Output of analysis of interval contrast design

Output of Interval Contrast Design Analysis

FUN_TYPE	MAP_FUN_ID	DESRIPTION	指标名称	指标类型	是否常用	数据类型
ConPlotSummary	VALUE	Genotype value of the plot	观察值（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	CK_BEFORE	check value before the plot	前侧对照值（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	CK_AFTER	check value before the plot	后侧对照值（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	CK_SUM	Sum of the checks on both sides of the plot	对照加和（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	CK_MEAN	Mean of the checks on both sides of the plot	对照平均（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	PED_DIFF	Difference between VALUE and CK_MEAN	与对照差异（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	PED_PCT	Percentage of PED_DIFF on the CK_MEAN	与对照差异百分比（间比）	小区总结	否	decimal(18,2)
ConPlotSummary	CK_NAME	ped_id of the ck	对照名称（间比）	小区总结	否	varchar(256)
ConSummary	CK_MEAN_LOC	Mean of the CK_MEAN of the location	对照平均（间比）	试点总结	是	decimal(18,2)
ConSummary	PED_DIFF_LOC	Mean of the PED_DIFF of the location	与对照差异（间比）	试点总结	是	decimal(18,2)
ConSummary	PED_PCT_LOC	Mean of the PED_PCT of the location	与对照差异百分比（间比）	试点总结	是	decimal(18,2)
ConSummary	CK_MEAN_EXP	Mean of the CK_MEAN of the experiment	对照平均（间比）	试验总结	是	decimal(18,2)
ConSummary	PED_DIFF_EXP	Mean of the PED_DIFF of the experiment	与对照差异（间比）	试验总结	是	decimal(18,2)
ConSummary	PED_PCT_EXP	Mean of the PED_PCT of the experiment	与对照差异百分比（间比）	试验总结	是	decimal(18,2)
ConSummary	CK_NAME	ped_id of the ck	对照名称（间比）	试验总结、试验总结	是	varchar(256)

Showcase of data analysis usage

# Analysis of randomized design trials
curl http://your.server.com/ocpu/library/AgriOS/R/fd_analysis \
-d "file='home/root/Data/besag.json'&design='rcbd'&log.path='/your/log/path'&as.json=true"

curl http://180.184.76.202:8080/ocpu/library/AgriOS/R/fd_analysis \
-d "file='/home/root/Data/data_contrast.json'&design='contrast'&as.json=true"

curl http://180.184.76.202:8080/ocpu/library/AgriOS/R/fd_analysis \
-d "file='/home/root/Data/data_contrast.json'&design='interval_contrast'&as.json=true"